Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007746.1 Hibiscus syriacus cultivar Beakdansim tig00110009_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3674400
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 15
Found at i:1015006 original size:384 final size:386
Alignment explanation
Indices: 1014294--1015067 Score: 1329
Period size: 384 Copynumber: 2.0 Consensus size: 386
1014284 ATTAGGGAGA
1014294 CAAAGTGAGTACATGATATTATGTATAAGTTATTCTATGGAATTAAGACTTGCGATGAGTCTAAT
1 CAAAGTGAGTACATGATATTATGTATAAGTTATTCTATGGAATTAAGACTTGCGATGAGTCTAAT
* *
1014359 TCCGATATTTGATTATATGAGTACATGAATACAAGTATATAGTACTATGATGCTTATCTGTGCAT
66 ACCGATATTTGATTATATGAGTACATGAATACAAG-ATATAGTACTATGATGCTTATCTGTACAT
* *
1014424 GAGTATATGCATATGTCTAGATATTAAGTGCATCTCTATACATGATCTATGTGAATGCATGTATG
130 GAGTATATGCATATGTCTAGATATTAAGTGCATCTATATACATGATCTATGTGAATGAATGTATG
1014489 AGTGATAAACTATGGACTTATGTAATTAAAGGGAGAAAAGAGATAAGCCATGTGACTATAAGCTA
195 AGTGATAAACTATGGACTTATGTAATTAAAGGGAGAAAAGAGATAAGCCATGTGACTATAAGCTA
*
1014554 TGTGATAATAAATTTTATGATTACATGATCACAAGATATAAAACATGTGACAAGAGATATGTGAT
260 TGTGATAATAAATTATATGATTACATGATCACAAGATATAAAACATGTGACAAGAGATATGTGAT
**
1014619 TACATGAAAGTATGATATAAGCTATGTGAAAGTGATCTATGTGACTATATGTCTATGTGATG
325 TACATGAAAGTATGATATAAGCTATGTGAAAGTGATCTATGTGACTATATACCTATGTGATG
*
1014681 CAAAGTGAGTACATGATATTATGTATAAGTTATTTTATGGAATTAAGACTTGCGATGAGTCTAAT
1 CAAAGTGAGTACATGATATTATGTATAAGTTATTCTATGGAATTAAGACTTGCGATGAGTCTAAT
*
1014746 ACCGATATTTGATTATATGAGTACATGAATACAAG-TATAGTACTATGATGCTTATGTGTACATG
66 ACCGATATTTGATTATATGAGTACATGAATACAAGATATAGTACTATGATGCTTATCTGTACATG
* * * *
1014810 AGTATATGCATATGTCTATATTTTAAGTGCATCTATATACGTGATCTATGTGAATGAATGTATGT
131 AGTATATGCATATGTCTAGATATTAAGTGCATCTATATACATGATCTATGTGAATGAATGTATGA
* * *
1014875 GTGAT-AA-TATGTGATTTATGTAATTAAAGGGAGAAAAGAGATAAGCTATGTGACTATGAGCTA
196 GTGATAAACTATG-GACTTATGTAATTAAAGGGAGAAAAGAGATAAGCCATGTGACTATAAGCTA
* **
1014938 TGTGATAATAAATTATATGATTACATGATCATAAGATATATGACATGTGACAAGAGATATGTGAT
260 TGTGATAATAAATTATATGATTACATGATCACAAGATATAAAACATGTGACAAGAGATATGTGAT
*
1015003 TACATGAAAGTATGATATAAGCTATGTTAAAGTGATCTATGTGACTATATACCTATGTGATG
325 TACATGAAAGTATGATATAAGCTATGTGAAAGTGATCTATGTGACTATATACCTATGTGATG
1015065 CAA
1 CAA
1015068 GTTATGTGAC
Statistics
Matches: 366, Mismatches: 20, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
383 4 0.01
384 173 0.47
385 91 0.25
387 98 0.27
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.35
Consensus pattern (386 bp):
CAAAGTGAGTACATGATATTATGTATAAGTTATTCTATGGAATTAAGACTTGCGATGAGTCTAAT
ACCGATATTTGATTATATGAGTACATGAATACAAGATATAGTACTATGATGCTTATCTGTACATG
AGTATATGCATATGTCTAGATATTAAGTGCATCTATATACATGATCTATGTGAATGAATGTATGA
GTGATAAACTATGGACTTATGTAATTAAAGGGAGAAAAGAGATAAGCCATGTGACTATAAGCTAT
GTGATAATAAATTATATGATTACATGATCACAAGATATAAAACATGTGACAAGAGATATGTGATT
ACATGAAAGTATGATATAAGCTATGTGAAAGTGATCTATGTGACTATATACCTATGTGATG
Found at i:1015284 original size:23 final size:23
Alignment explanation
Indices: 1015258--1015304 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
1015248 TAAGGAAAAA
* *
1015258 TCTATGTGGTCCTTCGGGACATT
1 TCTATGCGGTCCTTCGAGACATT
1015281 TCTATGCGGTCCTTCGAGACATT
1 TCTATGCGGTCCTTCGAGACATT
1015304 T
1 T
1015305 TATATGCCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.38
Consensus pattern (23 bp):
TCTATGCGGTCCTTCGAGACATT
Found at i:1017681 original size:17 final size:18
Alignment explanation
Indices: 1017659--1017692 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1017649 AATCAAATGA
1017659 AATTTTTGAA-AAATATT
1 AATTTTTGAATAAATATT
*
1017676 AATTTTTTAATAAATAT
1 AATTTTTGAATAAATAT
1017693 GAAATAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
AATTTTTGAATAAATATT
Found at i:1021936 original size:481 final size:482
Alignment explanation
Indices: 1020670--1022078 Score: 1799
Period size: 481 Copynumber: 2.9 Consensus size: 482
1020660 GGTGACATCC
*
1020670 GATAAGGTGCCATGGACACTAGTA-C-GTACCTAGATACAATTCAATTTCGAACTCTACTTCCCT
1 GATAAGGTGCCATGGACACCAGTAGCGGTACCTAGATACAATTCAATTTCGAACTCTACTT-CCT
* * * * * * * *
1020733 ATTAGGTGGTAAATCAAGCAACTCTTTTAGAAAAACTTTCAGAAAGTCTCTCACAGTATGAATTT
65 CTTAGGTGGTACACCATGCAACTCTTCTAGAAAAACTTT-AGAAAGTCTCTCCCAATAAGAATTT
* * *
1020798 TTTCAATTCTAGAAATAAACTTCCTATAATCCAAAATATAAGCAAGGTATGCTAGGGCACCTTTC
129 GTTCAATTCCAGAAATAGACTTCCTATAATCCAAAATATAAGCAAGGTATGCTAGGGCACCTTTC
* * * * * *
1020863 TGAATAATTTTGTCAGCTACTAAGGCCGATATCATATTTGACAGATAACCCCATCGGTAACAAAT
194 TGAATCATTTTGTCAGCTACCAAGGCTGATATCACATTTGACAGATAACCCCATCGCTAACAGAT
* * *
1020928 TAGAACAATTTCCTTATTATCATAAGTCTTTATAACTGCTCTTTTACGTTCATAATTCAAGTTAA
259 TAGAACAATTTCCTTATTATAAAAAGTCTTTAGAACTGCTCTTTTACGTTCATAATTCAAGTTAA
* *
1020993 CCTGATGTTCTTTCAACCAATCAATACCAAGAATAAGATTAAACTCATATAGTGAGAGTTCCATA
324 CCTGATGTTCTTTCAACCAATCAATACCAAGAATAAGATCAAACTCATCTAGTGAGAGTTCCATA
* * * * * *
1021058 AGGTTTGTCAG-AAGTCTATACACAAAGCTCT-AGAGAAAAATTTT-GGTAGAATTTGTCAACCA
389 AGGTTTGTTAGAAAATCTCTCCACAAAGCT-TAAGAG-GAAATTTTCGGTAGATTTTGTCAACCA
1021120 CTACAGATCGAACGACTTCAAACTAAAATGT
452 CTACAGATCGAACGACTTCAAACTAAAATGT
* * * *
1021151 GATAAAGTTCCATGGACACCAGT-GCGGTACCTAGATACAATTCAATTTCAAACTCTAATTCCCT
1 GATAAGGTGCCATGGACACCAGTAGCGGTACCTAGATACAATTCAATTTCGAACTCTACTT-CCT
* * * *
1021215 CTTAGGTGGTACACCGTGCAACTCTTCTA-AAGAATACTTCCAGAAAGTCTAT-CAAAGTACA-A
65 CTTAGGTGGTACACCATGCAACTCTTCTAGAA-AA-ACTT-TAGAAAGTCTCTCCCAA-TA-AGA
* * *
1021277 ATTTGTTCAATTCCACAAATAGACTTACTATAATCCAAAATATAAGCAAGGTACGCTAGGGCACC
125 ATTTGTTCAATTCCAGAAATAGACTTCCTATAATCCAAAATATAAGCAAGGTATGCTAGGGCACC
* * * * *
1021342 TTTTTGAATCATTTTTGTCAGCTACCTAGGATGATATCACATTTGACAGATAACCCCA-CACTCA
190 TTTCTGAATCA-TTTTGTCAGCTACCAAGGCTGATATCACATTTGACAGATAACCCCATCGCTAA
* * *
1021406 CAGATTAGAACAATTTCCTTATTATCAGAAA-TCTATAGAATTGCTCTTTTACGTTCATAATTCA
254 CAGATTAGAACAATTTCCTTATTAT-AAAAAGTCTTTAGAACTGCTCTTTTACGTTCATAATTCA
* * * * *
1021470 AGTGAACCTGATGTTCTTTCAACCAATCAACACAAAGAATAAGATCGAACTCATCTAGTGAGACT
318 AGTTAACCTGATGTTCTTTCAACCAATCAATACCAAGAATAAGATCAAACTCATCTAGTGAGAGT
** * ** *
1021535 TTGATAAGGTTTGTTAGAAAATATCTCCACAAATATTAAGAGGAAATTTTCTGTAGATTTTGTCA
383 TCCATAAGGTTTGTTAGAAAATCTCTCCACAAAGCTTAAGAGGAAATTTTCGGTAGATTTTGTCA
* * * * *
1021600 ACGACTAC-GAAT-TAACCGA-TATGAGACTGAAATGT
448 ACCACTACAG-ATCGAA-CGACT-TCAAACTAAAATGT
*
1021635 GATAAGGTGCCTTGGACACCA-TAGCGGTACCTAGATACAATTCAATTTCGAACTCTACTT-CTC
1 GATAAGGTGCCATGGACACCAGTAGCGGTACCTAGATACAATTCAATTTCGAACTCTACTTCCTC
** *
1021698 TTAGGTGACACACCATGCAACTCTTCTAGAAAAACTTATGGAAAGTCTCTCCCAATAAGAATTTG
66 TTAGGTGGTACACCATGCAACTCTTCTAGAAAAACTT-TAGAAAGTCTCTCCCAATAAGAATTTG
* * * *
1021763 TTCAATTCCAGAAGTAGACTTCCTAGAATCCAAAACATAAGCAAGGTATGCTAGGGAACCTTTCT
130 TTCAATTCCAGAAATAGACTTCCTATAATCCAAAATATAAGCAAGGTATGCTAGGGCACCTTTCT
* *
1021828 GAATCATTTTGT-ATGCTACCAAGGCTGATATAACATTTGATAGATAACCCCATCGCTAACAGAT
195 GAATCATTTTGTCA-GCTACCAAGGCTGATATCACATTTGACAGATAACCCCATCGCTAACAGAT
* *
1021892 TAGAACAATTTCCTTAATATAAAAAGTCTTTAGAACTACTCTTTTACGTTCATAATTCAAGTTAA
259 TAGAACAATTTCCTTATTATAAAAAGTCTTTAGAACTGCTCTTTTACGTTCATAATTCAAGTTAA
* *
1021957 CCCGATGTTCTTTCAACCAATCAATACCAAGAATAAGATCAAACTCATCTATTGAGAGTTCCATA
324 CCTGATGTTCTTTCAACCAATCAATACCAAGAATAAGATCAAACTCATCTAGTGAGAGTTCCATA
* * * *
1022022 AGGTTTGTTGGAAAAGTCTCTCCATAGAGCTCAAGAGGAAATTTTCGGTAGATTTTG
389 AGGTTTGTTAGAAAA-TCTCTCCACAAAGCTTAAGAGGAAATTTTCGGTAGATTTTG
1022079 AATACCACTA
Statistics
Matches: 792, Mismatches: 113, Indels: 45
0.83 0.12 0.05
Matches are distributed among these distances:
479 1 0.00
480 45 0.06
481 241 0.30
482 129 0.16
483 229 0.29
484 147 0.19
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.31
Consensus pattern (482 bp):
GATAAGGTGCCATGGACACCAGTAGCGGTACCTAGATACAATTCAATTTCGAACTCTACTTCCTC
TTAGGTGGTACACCATGCAACTCTTCTAGAAAAACTTTAGAAAGTCTCTCCCAATAAGAATTTGT
TCAATTCCAGAAATAGACTTCCTATAATCCAAAATATAAGCAAGGTATGCTAGGGCACCTTTCTG
AATCATTTTGTCAGCTACCAAGGCTGATATCACATTTGACAGATAACCCCATCGCTAACAGATTA
GAACAATTTCCTTATTATAAAAAGTCTTTAGAACTGCTCTTTTACGTTCATAATTCAAGTTAACC
TGATGTTCTTTCAACCAATCAATACCAAGAATAAGATCAAACTCATCTAGTGAGAGTTCCATAAG
GTTTGTTAGAAAATCTCTCCACAAAGCTTAAGAGGAAATTTTCGGTAGATTTTGTCAACCACTAC
AGATCGAACGACTTCAAACTAAAATGT
Found at i:1022530 original size:31 final size:31
Alignment explanation
Indices: 1022492--1022554 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
1022482 AAAGTACAAG
*
1022492 TAGGAACAACCCACTGTGTAGAAGAAATACC
1 TAGGAACAACCCACTGTGTAGAAGAAACACC
1022523 TAGGAACAACCCACTGTGTAGAAGAAACACC
1 TAGGAACAACCCACTGTGTAGAAGAAACACC
1022554 T
1 T
1022555 CAACTCTCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.41, C:0.24, G:0.19, T:0.16
Consensus pattern (31 bp):
TAGGAACAACCCACTGTGTAGAAGAAACACC
Found at i:1024319 original size:29 final size:29
Alignment explanation
Indices: 1024285--1024343 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
1024275 ATAGAAATAG
* *
1024285 GATGGGGATAT-AACCCTATGCAGAAACAT
1 GATGGGAATATGAACCC-ATACAGAAACAT
*
1024314 GATGGGAATATGATCCCATACAGAAACAT
1 GATGGGAATATGAACCCATACAGAAACAT
1024343 G
1 G
1024344 TATGTATGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.39, C:0.17, G:0.24, T:0.20
Consensus pattern (29 bp):
GATGGGAATATGAACCCATACAGAAACAT
Found at i:1027243 original size:936 final size:936
Alignment explanation
Indices: 1025575--1027302 Score: 2764
Period size: 936 Copynumber: 1.8 Consensus size: 936
1025565 GCATAAACAA
*
1025575 TATCGATACCATAAGGCAAAAGTTGGTAAAATATTCATGGAGTATCGATATTAAAGTGATAGTAT
1 TATCGATACCATAAGGCAAAAGTTGGTAAAATATTCATGGAGTATCGATACTAAAGTGATAGTAT
* * ** * *
1025640 TGGTACCATGGGTATCGATACCAAGATGGACGTATAGGTACCATTTATGCAATAAAAATTTAGAA
66 CGATACCATGGGTATCGATACCAAGATAAAAGTATAGGTACCATCTATGCAATAAAAATTTAGAA
* * ** *
1025705 TCAAGAATAGGTATCAGTACCGTGTAAGGGTATCAATACTACACGCATAGAGGTATCGGTACCGT
131 TCAAGAATAGGTATCAGTACCGTGGAAAGGTATCAATACTACAAACATAGAGGCATCGGTACCGT
** * * *
1025770 ATTTGTAATATCGATACTACTTAAGTTGGAATTTAGAAATTAGTGCTTTGTTAGTTTGCATTTGT
196 ACATGTAATACCGATACTACTTAAGTTGGAATTTAGAAATTAGTGCTTTCTTAGTTTGCATTAGT
*
1025835 AAGAATCTTTGAGAGTAAATCAAATTTCGATATTTATTGGATTGTATATTCGTGTAGATATAGAT
261 AAAAATCTTTGAGAGTAAATCAAATTTCGATATTTATTGGATTGTATATTCGTGTAGATATAGAT
1025900 TAAAAACAAAGTCCGGACAAGTCGACAAAGTAAGATTACCAAGAGAGAGATAAGAGATTGGTATT
326 TAAAAACAAAGTCCGGACAAGTCGACAAAGTAAGATTACCAAGAGAGAGATAAGAGATTGGTATT
* *
1025965 GACTAATGAGACAAGGTGAGTACATGATATTATGTATGAGTTATTCTATGGAATTAAGACTTGCG
391 GACTAATGAGACAAAGTGAGTACATGATATTATGTATAAGTTATTCTATGGAATTAAGACTTGCG
*
1026030 ATGAGTCTAATTCCGATATTAAATTATAAGAGTACATGAATACAAGTATGTAGTACTATGATGCT
456 ATGAGTCTAATTCCGATATTAAATTATAAGAGTACATGAATACAAGTATATAGTACTATGATGCT
* * * *
1026095 TATATGTACATGAGTATATGCATATGTCTATATGTTAAGTGCATCTATATTCGTGATCTATATGA
521 TATATGTACATGAGTATATGCATATGTCTAGATATTAAGTGCATCTATATACATGATCTATATGA
* * * *
1026160 ATGCATGTATGTGTGATAAACTATTTGATTTATGTAATTAAAGGGAGAAAAGAGATAAGCTATGT
586 ATGCATGTATGAGTGATAAACTATGTGACTTATGTAATTAAAGGGAGAAAAGAGATAAGCCATGT
* * * * *
1026225 GACTATGAGCTATGTGATAATAAATTATATTATTACATGATCATAAGATATAAGACATGTGACAA
651 GACCATAAGCTATGTGATAATAAATTATATGATTACATGATCACAAGATATAAAACATGTGACAA
* *
1026290 GAGATATGTGATTACATGAAAGTATGATATAAGCTATGTGAATGTGATCTATGTGACTATATGTC
716 GAGATATGTGATTACATGAAAGTATGATATAAGCTATGTGAAAGTGATCTATGTGACTATATATC
1026355 TATGTGATGCAAGTTATGTGACAAACATACATGACAATGCCATGTTATGTGATACGAGAGTTAGG
781 TATGTGATGCAAGTTATGTGACAAACATACATGACAATGCCATGTTATGTGATACGAGAGTTAGG
1026420 GGTATAGTTGGCATGCCAAGAGTCGAGGGTTCTTTGTTGTCCTTCGGGACATATATGTAATCCTT
846 GGTATAGTTGGCATGCCAAGAGTCGAGGGTTCTTTGTTGTCCTTCGGGACATATATGTAATCCTT
1026485 TGGAACATATATATGGTACTTTGGGG
911 TGGAACATATATATGGTACTTTGGGG
* * * *
1026511 TATCGATACCATATGG-AAAAGTTGGTAAAATATTTATTGGGGTATCGATACTGAAGTGATAGTA
1 TATCGATACCATAAGGCAAAAGTTGGTAAAATATTCA-TGGAGTATCGATACTAAAGTGATAGTA
* * *
1026575 TCGATACCATGGGTATC-ATATCAAGATAAAAGTATTGGTACCATGCT-TGCAAT-GAAATTTCA
65 TCGATACCATGGGTATCGATACCAAGATAAAAGTATAGGTACCAT-CTATGCAATAAAAATTT-A
* * *
1026637 GAATCAAGAATAGGTATC-GATATCGTGGAAAGGTATCAATACTATAAACATATAGGCATCGGTA
128 GAATCAAGAATAGGTATCAG-TACCGTGGAAAGGTATCAATACTACAAACATAGAGGCATCGGTA
*
1026701 CCGTACATGTAGTACCGATACTACTTAAGTTGGAATTTAGAAATTAGTGCTTTACTTAGTTTGCA
192 CCGTACATGTAATACCGATACTACTTAAGTTGGAATTTAGAAATTAGTGCTTT-CTTAGTTTGCA
* *
1026766 TTAGTAAAAATCTTTGAGAGTAATTCAAATTTTGATATTTATTGGATTGTATATTCGTGTAGATA
256 TTAGTAAAAATCTTTGAGAGTAAATCAAATTTCGATATTTATTGGATTGTATATTCGTGTAGATA
* * * * * *
1026831 TTGCTTGAAAGCAAAGTTCGGACAAGTCGACAAAGTAAGATTACCTAGAGAGAGATAAGAGATTG
321 TAGATTAAAAACAAAGTCCGGACAAGTCGACAAAGTAAGATTACCAAGAGAGAGATAAGAGATTG
* * *
1026896 GTATTGATTAGTGAGACAAAGTGAGTACATGATATTATGTATAAGTTATTCTATTGAATTAAGAC
386 GTATTGACTAATGAGACAAAGTGAGTACATGATATTATGTATAAGTTATTCTATGGAATTAAGAC
* ** *
1026961 TTGCGATGAGTCTAATTTCGATATTTGATTATATGAGTACATGAATACAAGTATATAGTACTATG
451 TTGCGATGAGTCTAATTCCGATATTAAATTATAAGAGTACATGAATACAAGTATATAGTACTATG
* * *
1027026 ATGCTTATCTGTGCATGAGTATATGCATATGTCTAGATATTAAGTGCATCTCTATACATGATCTA
516 ATGCTTATATGTACATGAGTATATGCATATGTCTAGATATTAAGTGCATCTATATACATGATCTA
*
1027091 TGTGAATGCATGTATGAGTGATAAACTATGTGACTTATGTAATTAAAGGGAGAAAAGAGATAAGC
581 TATGAATGCATGTATGAGTGATAAACTATGTGACTTATGTAATTAAAGGGAGAAAAGAGATAAGC
*
1027156 CATGTGACCATAAGCTATGTGATAATAAATTTTATGATTACATGATCACAAGATATAAAACATGT
646 CATGTGACCATAAGCTATGTGATAATAAATTATATGATTACATGATCACAAGATATAAAACATGT
*
1027221 GAGAAGAGATATGTGATTACATGAAAGTATGATATAAGCTATGTGAAAGTGATCTATGTGACTAT
711 GACAAGAGATATGTGATTACATGAAAGTATGATATAAGCTATGTGAAAGTGATCTATGTGACTAT
1027286 ATATCTATGTGATGCAA
776 ATATCTATGTGATGCAA
1027303 AGTGAGTACA
Statistics
Matches: 719, Mismatches: 68, Indels: 10
0.90 0.09 0.01
Matches are distributed among these distances:
934 7 0.01
935 151 0.21
936 561 0.78
ACGTcount: A:0.35, C:0.10, G:0.21, T:0.33
Consensus pattern (936 bp):
TATCGATACCATAAGGCAAAAGTTGGTAAAATATTCATGGAGTATCGATACTAAAGTGATAGTAT
CGATACCATGGGTATCGATACCAAGATAAAAGTATAGGTACCATCTATGCAATAAAAATTTAGAA
TCAAGAATAGGTATCAGTACCGTGGAAAGGTATCAATACTACAAACATAGAGGCATCGGTACCGT
ACATGTAATACCGATACTACTTAAGTTGGAATTTAGAAATTAGTGCTTTCTTAGTTTGCATTAGT
AAAAATCTTTGAGAGTAAATCAAATTTCGATATTTATTGGATTGTATATTCGTGTAGATATAGAT
TAAAAACAAAGTCCGGACAAGTCGACAAAGTAAGATTACCAAGAGAGAGATAAGAGATTGGTATT
GACTAATGAGACAAAGTGAGTACATGATATTATGTATAAGTTATTCTATGGAATTAAGACTTGCG
ATGAGTCTAATTCCGATATTAAATTATAAGAGTACATGAATACAAGTATATAGTACTATGATGCT
TATATGTACATGAGTATATGCATATGTCTAGATATTAAGTGCATCTATATACATGATCTATATGA
ATGCATGTATGAGTGATAAACTATGTGACTTATGTAATTAAAGGGAGAAAAGAGATAAGCCATGT
GACCATAAGCTATGTGATAATAAATTATATGATTACATGATCACAAGATATAAAACATGTGACAA
GAGATATGTGATTACATGAAAGTATGATATAAGCTATGTGAAAGTGATCTATGTGACTATATATC
TATGTGATGCAAGTTATGTGACAAACATACATGACAATGCCATGTTATGTGATACGAGAGTTAGG
GGTATAGTTGGCATGCCAAGAGTCGAGGGTTCTTTGTTGTCCTTCGGGACATATATGTAATCCTT
TGGAACATATATATGGTACTTTGGGG
Found at i:1027886 original size:23 final size:23
Alignment explanation
Indices: 1027859--1027916 Score: 116
Period size: 23 Copynumber: 2.5 Consensus size: 23
1027849 TTGGAATATA
1027859 TATGTGGTCCTTAAGGAAAAATC
1 TATGTGGTCCTTAAGGAAAAATC
1027882 TATGTGGTCCTTAAGGAAAAATC
1 TATGTGGTCCTTAAGGAAAAATC
1027905 TATGTGGTCCTT
1 TATGTGGTCCTT
1027917 CGGGACATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.34
Consensus pattern (23 bp):
TATGTGGTCCTTAAGGAAAAATC
Found at i:1027929 original size:23 final size:23
Alignment explanation
Indices: 1027880--1027949 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
1027870 TAAGGAAAAA
** * **
1027880 TCTATGTGGTCCTTAAGGAAAAA
1 TCTATGTGGTCCTTCGGGACATT
1027903 TCTATGTGGTCCTTCGGGACATT
1 TCTATGTGGTCCTTCGGGACATT
* *
1027926 TCTATGCGGTCCTTCGAGACATT
1 TCTATGTGGTCCTTCGGGACATT
1027949 T
1 T
1027950 TATATGCCAC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (23 bp):
TCTATGTGGTCCTTCGGGACATT
Found at i:1032882 original size:18 final size:18
Alignment explanation
Indices: 1032859--1032894 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1032849 AAACTTTTTG
1032859 ATTTAATGTATGTAAATT
1 ATTTAATGTATGTAAATT
* *
1032877 ATTTAATTTATTTAAATT
1 ATTTAATGTATGTAAATT
1032895 GAGTCTGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.56
Consensus pattern (18 bp):
ATTTAATGTATGTAAATT
Found at i:1038708 original size:27 final size:32
Alignment explanation
Indices: 1038677--1038742 Score: 97
Period size: 27 Copynumber: 2.2 Consensus size: 32
1038667 TGTGAAAAGA
1038677 ATAATAAAAAAT-AATA-ATATA-ATA-ATAT
1 ATAATAAAAAATGAATATATATATATATATAT
1038705 -TAATAAAAAATGAATATATATATATATATAT
1 ATAATAAAAAATGAATATATATATATATATAT
1038736 ATAATAA
1 ATAATAA
1038743 TGTAAAAAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
27 11 0.33
28 4 0.12
29 5 0.15
30 3 0.09
31 4 0.12
32 6 0.18
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (32 bp):
ATAATAAAAAATGAATATATATATATATATAT
Found at i:1039151 original size:33 final size:33
Alignment explanation
Indices: 1039110--1039180 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1039100 AAAATGATTC
**
1039110 GGTTTTAGTGTTTCAATAGGACTCAAATACGTT
1 GGTTTTAGTGTTTCAATAAAACTCAAATACGTT
1039143 GGTTTTAGTGTTTCAATAAAACTCAAATACGTT
1 GGTTTTAGTGTTTCAATAAAACTCAAATACGTT
1039176 GGTTT
1 GGTTT
1039181 ATTTTTTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.28, C:0.11, G:0.20, T:0.41
Consensus pattern (33 bp):
GGTTTTAGTGTTTCAATAAAACTCAAATACGTT
Found at i:1039253 original size:3 final size:3
Alignment explanation
Indices: 1039230--1039291 Score: 67
Period size: 3 Copynumber: 20.7 Consensus size: 3
1039220 GGCCTACAAA
*
1039230 AAT AAT AA- AAT AAA AAT -AT AAT AAT AAT AAT AAT AAT AAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
1039274 AAAT ATAT AAT -AT AAT AA
1 -AAT A-AT AAT AAT AAT AA
1039292 AACGTTTTTG
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
2 6 0.12
3 36 0.69
4 10 0.19
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1039768 original size:84 final size:82
Alignment explanation
Indices: 1039637--1040394 Score: 584
Period size: 84 Copynumber: 9.1 Consensus size: 82
1039627 CTGAATGGAA
* * ** * * * *
1039637 TCGAACTCGAAGG-C-CTTTGGTAGATAGTCCTTCTTGCCATGAGTTATGCTGCAAATGATGGTG
1 TCGAACTCGAAGGTCTTTTTGGCAGATAACCCTTCTAGCCTTAAGTTATGCTGTAAATGAT-GTG
* *
1039700 CCTTTGAGCTGAGTGCAG
65 CCTTGGAGCTGAGTGTAG
* ** * **
1039718 TCGAACTCGAAGGTATTTATTGAAAGATAACCCTTCTAGCCTTGAGTTATGCCATAAATGATGTG
1 TCGAACTCGAAGGTCTTT-TTGGCAGATAACCCTTCTAGCCTTAAGTTATGCTGTAAATGATGTG
* * *
1039783 CCCTCGAAGCTGAGTGTAA
65 -CCTTGGAGCTGAGTGTAG
** * * * * *
1039802 TCGAACTCG-AGGT-TCATTGGAAGATAGCCCTTCT-CCACTTAAGCTATGCTGCAAATGATGTG
1 TCGAACTCGAAGGTCTTTTTGGCAGATAACCCTTCTAGC-CTTAAGTTATGCTGTAAATGATGTG
* **
1039864 CCTTAGAGCTGAGCATAG
65 CCTTGGAGCTGAGTGTAG
* * * * *
1039882 TCGAACTCGAAGGTCTTTGGTTGGAAGATAACCCTTCTCGACTTAAGTTATGCTATAAATGATAT
1 TCGAACTCGAAGGTCTTT--TTGGCAGATAACCCTTCTAGCCTTAAGTTATGCTGTAAATGATGT
*
1039947 GCCTTGGAGCTGAGCGTAG
64 GCCTTGGAGCTGAGTGTAG
* * * *
1039966 TCGAACTCGAATGTC-TTTTGGTCACATATAACCCTTCTAGCCTTGAGTTATGCTATAAATGATG
1 TCGAACTCGAAGGTCTTTTTGG---CAGATAACCCTTCTAGCCTTAAGTTATGCTGTAAATGATG
* * * *
1040030 TGCCCTCGAAGCTGAGTCTAA
63 TG-CCTTGGAGCTGAGTGTAG
* * * *
1040051 TCGAACTC-AAGGGTC--TTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGTAAATGATGTG
1 TCGAACTCGAA-GGTCTTTTTGGCAGATAACCCTTCTAGCCTTAAGTTATGCTGTAAATGATGTG
**
1040113 CCTTGGAGCTGAGCATAG
65 CCTTGGAGCTGAGTGTAG
* * * ** * * * *
1040131 TCAAACTCGAAGGACTTTGATTGGCAGATAACCCCTCCCGACTTAAGTTATACTGCAAATGATAT
1 TCGAACTCGAAGGTCTTT--TTGGCAGATAACCCTTCTAGCCTTAAGTTATGCTGTAAATGATGT
*
1040196 GCCCTGGAGCTGAGCT-TAG
64 GCCTTGGAGCTGAG-TGTAG
* * * * * *
1040215 TCGAACTTGAATGTC-TTTTGGTCAGAGATAACCCTTATAGCTTTGAGTTATGCTGTAAATGATA
1 TCGAACTCGAAGGTCTTTTTGG-C--AGATAACCCTTCTAGCCTTAAGTTATGCTGTAAATGATG
* *
1040279 TGCCCTTGAAGCTGAGTGTAA
63 TG-CCTTGGAGCTGAGTGTAG
* * * * * *
1040300 TCAAACTCGATGGTCTTCGGTTGGCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGATGT
1 TCGAACTCGAAGGTCTT--TTTGGCAGATAACCCTTCTAGCCTTAAGTTATGCTGTAAATGATGT
* *
1040365 GCCTTAGAGCTGAGCGTAG
64 GCCTTGGAGCTGAGTGTAG
1040384 TCGAACTCGAA
1 TCGAACTCGAA
1040395 TGCCTTTGGT
Statistics
Matches: 535, Mismatches: 113, Indels: 55
0.76 0.16 0.08
Matches are distributed among these distances:
80 45 0.08
81 98 0.18
82 4 0.01
83 12 0.02
84 288 0.54
85 82 0.15
86 1 0.00
87 1 0.00
88 4 0.01
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.30
Consensus pattern (82 bp):
TCGAACTCGAAGGTCTTTTTGGCAGATAACCCTTCTAGCCTTAAGTTATGCTGTAAATGATGTGC
CTTGGAGCTGAGTGTAG
Found at i:1040058 original size:249 final size:249
Alignment explanation
Indices: 1039678--1040404 Score: 990
Period size: 249 Copynumber: 2.9 Consensus size: 249
1039668 TCTTGCCATG
* * * * * * *
1039678 AGTTATGCTGCAAATGATGGTGCCTTTGAGCTGAGTGCAGTCGAACTCGAAGGTATTTAT--TGA
1 AGTTATGCTGCAAATGAT-ATGCCTTGGAGCTGAGCGTAGTCGAACTCGAATGTCTTT-TGGTCA
*
1039741 AAGATAACCCTTCTAGCCTTGAGTTATGCCATAAATGATGTGCCCTCGAAGCTGAGTGTAATCGA
64 AAGATAACCCTTCTAGCCTTGAGTTATGCTATAAATGATGTGCCCTCGAAGCTGAGTGTAATCGA
* *
1039806 ACTCGAGGTTCATTGGAAGATAGCCCTTCTCCACTTAAGCTATGCTGCAAATGATGTGCCTTAGA
129 ACTCGAGGTTCATTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTAGA
* * *
1039871 GCTGAGCATAGTCGAACTCGAAGGTCTTTGGTTGGAAGATAACCCTTCTCGACTTA
194 GCTGAGCATAGTCGAACTCGAAGGACTTTGGTTGGAAGATAACCCCTCCCGACTTA
** *
1039927 AGTTATGCTATAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAATGTCTTTTGGTCACA
1 AGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAATGTCTTTTGGTCAAA
* *
1039992 TATAACCCTTCTAGCCTTGAGTTATGCTATAAATGATGTGCCCTCGAAGCTGAGTCTAATCGAAC
66 GATAACCCTTCTAGCCTTGAGTTATGCTATAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAAC
* * * * *
1040057 TCAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGTAAATGATGTGCCTTGGAGC
131 TCGAGGTTCATTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTAGAGC
* * *
1040122 TGAGCATAGTCAAACTCGAAGGACTTTGATTGGCAGATAACCCCTCCCGACTTA
196 TGAGCATAGTCGAACTCGAAGGACTTTGGTTGGAAGATAACCCCTCCCGACTTA
* * * * *
1040176 AGTTATACTGCAAATGATATGCCCTGGAGCTGAGCTTAGTCGAACTTGAATGTCTTTTGGTCAGA
1 AGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAATGTCTTTTGGTCAAA
* * * * * *
1040241 GATAACCCTTATAGCTTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCAAAC
66 GATAACCCTTCTAGCCTTGAGTTATGCTATAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAAC
* * * *
1040306 TCGATGGTCTTCGGTTGGCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGATGTGCCTTA
131 TCGA-GG--TTC-ATTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTA
* * *
1040371 GAGCTGAGCGTAGTCGAACTCGAATGCCTTTGGT
192 GAGCTGAGCATAGTCGAACTCGAAGGACTTTGGT
1040405 GGGCACGATT
Statistics
Matches: 418, Mismatches: 54, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
247 1 0.00
248 33 0.08
249 305 0.73
250 2 0.00
252 2 0.00
253 75 0.18
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (249 bp):
AGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAATGTCTTTTGGTCAAA
GATAACCCTTCTAGCCTTGAGTTATGCTATAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAAC
TCGAGGTTCATTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTAGAGC
TGAGCATAGTCGAACTCGAAGGACTTTGGTTGGAAGATAACCCCTCCCGACTTA
Found at i:1040846 original size:110 final size:110
Alignment explanation
Indices: 1040521--1041168 Score: 908
Period size: 110 Copynumber: 5.9 Consensus size: 110
1040511 TTGTGCTATT
* * * *
1040521 TCGAGGCCAATATCCTTCGCCGTGAAGTTAAAATTGACTC----TGAAACTGGAAAGTTGTTTGT
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
* *
1040582 TGACAGCCAGTCGCACCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
66 TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
* * * * *
1040627 TCGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTATAAAATAAAACTGAAAAGTTTTTTG
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCT-GAATGAAACTGAAAAGTTGTTTG
* * ** * *
1040692 TTGACAGTCAGCCGTCCCTTTACTATGAAGTTTAGCTTGTGTTGTC
65 TTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
* * * *
1040738 TCGAGTCCAATATCTTTCGCAGTGAAATTGAAATCGACTCTGAATGAAACTGAAAAGTTGTTTGT
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
* *
1040803 TGACAGTTAGTCGCCTCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
66 TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
* **
1040848 TCTAGTCCAATATCCTTCATTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
*
1040913 TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGATTGTGTTGTC
66 TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
* * *
1040958 TCGAGTTCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTAAAAAGTTATTTGT
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
*
1041023 TGACAGTCAGTCGCCCCTTTGCTGTGAAGTTGAGCTTGTGTTGTC
66 TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
** * * *
1041068 TCGAGTCCAATATCCTTCATTATGAAGTTGAAATTGACTCTAAATGAAACTGAAAAGTTTATTTG
1 TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAG-TTGTTTG
* *
1041133 TTGACCGTCAGTCGCCCCTTCGTTGTGAAGTTGAGC
65 TTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGC
1041169 AACCACCATC
Statistics
Matches: 477, Mismatches: 59, Indels: 7
0.88 0.11 0.01
Matches are distributed among these distances:
106 35 0.07
110 311 0.65
111 131 0.27
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.34
Consensus pattern (110 bp):
TCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGT
TGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTC
Found at i:1041163 original size:331 final size:327
Alignment explanation
Indices: 1040527--1041168 Score: 937
Period size: 331 Copynumber: 2.0 Consensus size: 327
1040517 TATTTCGAGG
* *
1040527 CCAATATCCTTCGCCGTGAAGTTAAAATTGACTCTGAAACTGGAAAGTTGTTTGTTGACAGCCAG
1 CCAATATCCTTCACCGTGAAGTTAAAATTGACTCTGAAACTGAAAAGTTGTTTGTTGACAGCCAG
*
1040592 TCGCACCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCATTCGCTGTGAAGTTG
66 TCGCACCTTCGCTGTGAAGTTGAGATTGTGTTGTCTCGAGTCCAATATCATTCGCTGTGAAGTTG
* * *
1040657 AAATTGACTATAAAATAAAACTGAAAAGTTTTTTGTTGACAGTCAGCCGTCCCTTTACTATGAAG
131 AAATTGACTATAAAATAAAACTAAAAAGTTATTTGTTGACAGTCAGCCGCCCCTTTACTATGAAG
* * *
1040722 TTTAGCTTGTGTTGTCTCGAGTCCAATATCTTTCGCAGTGAAATTGAAATCGACTCTGAATGAAA
196 TTGAGCTTGTGTTGTCTCGAGTCCAATATCCTTCGCAGTGAAATTGAAATCGACTCTAAATGAAA
* * *
1040787 CTGAAAAGTTGTTTGTTGACAGTTAGTCGCCTCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCTA
261 CTGAAAAGTTATTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCTA
1040852 GT
326 GT
** *
1040854 CCAATATCCTTCATTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGACAG
1 CCAATATCCTTCACCGTGAAGTTAAAATTGACTC----TGAAACTGAAAAGTTGTTTGTTGACAG
* * * *
1040919 TCAGTCGCCCCTTCGCTGTGAAGTTGAGATTGTGTTGTCTCGAGTTCAATATCCTTCGCTGTGAA
62 CCAGTCGCACCTTCGCTGTGAAGTTGAGATTGTGTTGTCTCGAGTCCAATATCATTCGCTGTGAA
* * * * * *
1040984 GTTGAAATTGACTCT-GAATGAAACTAAAAAGTTATTTGTTGACAGTCAGTCGCCCCTTTGCTGT
127 GTTGAAATTGACTATAAAATAAAACTAAAAAGTTATTTGTTGACAGTCAGCCGCCCCTTTACTAT
** * *
1041048 GAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCCTTCATTA-TGAAGTTGAAATTGACTCTAAA
192 GAAGTTGAGCTTGTGTTGTCTCGAGTCCAATATCCTTC-GCAGTGAAATTGAAATCGACTCTAAA
* *
1041112 TGAAACTGAAAAGTTTATTTGTTGACCGTCAGTCGCCCCTTCGTTGTGAAGTTGAGC
256 TGAAACTGAAAAG-TTATTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGC
1041169 AACCACCATC
Statistics
Matches: 278, Mismatches: 31, Indels: 8
0.88 0.10 0.03
Matches are distributed among these distances:
327 30 0.11
330 109 0.39
331 139 0.50
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.35
Consensus pattern (327 bp):
CCAATATCCTTCACCGTGAAGTTAAAATTGACTCTGAAACTGAAAAGTTGTTTGTTGACAGCCAG
TCGCACCTTCGCTGTGAAGTTGAGATTGTGTTGTCTCGAGTCCAATATCATTCGCTGTGAAGTTG
AAATTGACTATAAAATAAAACTAAAAAGTTATTTGTTGACAGTCAGCCGCCCCTTTACTATGAAG
TTGAGCTTGTGTTGTCTCGAGTCCAATATCCTTCGCAGTGAAATTGAAATCGACTCTAAATGAAA
CTGAAAAGTTATTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCTA
GT
Found at i:1052606 original size:6 final size:6
Alignment explanation
Indices: 1052595--1052619 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1052585 GAGGTACCTC
1052595 TTTGCA TTTGCA TTTGCA TTTGCA T
1 TTTGCA TTTGCA TTTGCA TTTGCA T
1052620 AGTATTTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.52
Consensus pattern (6 bp):
TTTGCA
Found at i:1055587 original size:15 final size:16
Alignment explanation
Indices: 1055560--1055596 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
1055550 CTTTATTATC
1055560 TTATTTCATCTTTCGT
1 TTATTTCATCTTTCGT
*
1055576 TTATTT-ATCTTTTGT
1 TTATTTCATCTTTCGT
1055591 TTATTT
1 TTATTT
1055597 TATTCTAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.14, C:0.11, G:0.05, T:0.70
Consensus pattern (16 bp):
TTATTTCATCTTTCGT
Found at i:1055964 original size:10 final size:10
Alignment explanation
Indices: 1055949--1055996 Score: 69
Period size: 10 Copynumber: 4.5 Consensus size: 10
1055939 ATTTTTTTTC
1055949 AAAAAAACAA
1 AAAAAAACAA
1055959 AAAAAAACAA
1 AAAAAAACAA
1055969 AAAAAAAGGCAAA
1 AAAAAAA--C-AA
1055982 AAAAAAACAA
1 AAAAAAACAA
1055992 AAAAA
1 AAAAA
1055997 CCCAAAAAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
10 24 0.69
11 1 0.03
12 1 0.03
13 9 0.26
ACGTcount: A:0.88, C:0.08, G:0.04, T:0.00
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:1056002 original size:10 final size:10
Alignment explanation
Indices: 1055948--1056005 Score: 55
Period size: 10 Copynumber: 5.7 Consensus size: 10
1055938 TATTTTTTTT
1055948 CAAAAAAACA
1 CAAAAAAACA
*
1055958 AAAAAAAACA
1 CAAAAAAACA
*
1055968 AAAAAAAAGGCA
1 CAAAAAAA--CA
*
1055980 -AAAAAAAAA
1 CAAAAAAACA
*
1055989 CAAAAAAACC
1 CAAAAAAACA
1055999 CAAAAAA
1 CAAAAAA
1056006 CCCAAAATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
9 1 0.02
10 31 0.76
11 7 0.17
12 2 0.05
ACGTcount: A:0.83, C:0.14, G:0.03, T:0.00
Consensus pattern (10 bp):
CAAAAAAACA
Found at i:1061313 original size:43 final size:43
Alignment explanation
Indices: 1061195--1061391 Score: 191
Period size: 43 Copynumber: 4.5 Consensus size: 43
1061185 GTGATAGAGA
* * * *
1061195 ATATTCATGGTAAGGTTGGTACGTTCAGCTAAGCTCTGA-AAA
1 ATATTCATGGTAAGGTTGGTACGTTGAGCTTAGCTCCGAGAAG
* *
1061237 ATATTCATATATGTGGTAAGGTTGGTGCTTTGAGCTTAGCTCCGAGAAG
1 ATATTC----A--TGGTAAGGTTGGTACGTTGAGCTTAGCTCCGAGAAG
* *
1061286 ATATTCATGGTAAGTTTGGTACGTTGAGCTTAGCAT-CGAGAAT
1 ATATTCATGGTAAGGTTGGTACGTTGAGCTTAGC-TCCGAGAAG
* * **
1061329 ATATTCGTGGCAAGGTTGGTACGTTGAGCTTAGCTCTTAGAAG
1 ATATTCATGGTAAGGTTGGTACGTTGAGCTTAGCTCCGAGAAG
* *
1061372 ATAGTCTTGGTAAGGTTGGT
1 ATATTCATGGTAAGGTTGGT
1061392 GTGTTGAGAA
Statistics
Matches: 127, Mismatches: 19, Indels: 17
0.78 0.12 0.10
Matches are distributed among these distances:
42 7 0.06
43 82 0.65
44 1 0.01
45 1 0.01
46 1 0.01
48 27 0.21
49 8 0.06
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.34
Consensus pattern (43 bp):
ATATTCATGGTAAGGTTGGTACGTTGAGCTTAGCTCCGAGAAG
Found at i:1061985 original size:12 final size:12
Alignment explanation
Indices: 1061940--1061987 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
1061930 TCCTTAAACA
1061940 GATATGTATGTT
1 GATATGTATGTT
* *
1061952 GAAATGTATCTT
1 GATATGTATGTT
*
1061964 CACTTATGTATGTT
1 GA--TATGTATGTT
1061978 GATATGTATG
1 GATATGTATG
1061988 ATAAGGAAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
12 19 0.68
14 9 0.32
ACGTcount: A:0.27, C:0.06, G:0.21, T:0.46
Consensus pattern (12 bp):
GATATGTATGTT
Found at i:1062096 original size:43 final size:43
Alignment explanation
Indices: 1062035--1062226 Score: 208
Period size: 43 Copynumber: 4.5 Consensus size: 43
1062025 GTGATAGAGA
* * *
1062035 ATATTCATGGTAAGGTTGGTACGTTTAGCTAAGCTCTGAAAAG
1 ATATTCGTGGTAAGGTTGGTGCGTTTAGCTAAGCTCCGAAAAG
*
1062078 ATATTCGTGGTAAGGTTGGTGCGTTGAGCTAAGCTCC-AATAAG
1 ATATTCGTGGTAAGGTTGGTGCGTTTAGCTAAGCTCCGAA-AAG
* * * *
1062121 ATATTTGTGGTAAGGTTGGTGC-TTTGACCTTAGCTCCGAGAAG
1 ATATTCGTGGTAAGGTTGGTGCGTTT-AGCTAAGCTCCGAAAAG
* ** * * * * *
1062164 ATATTCATGGTAATTTTGGTGCGTTGAGCTTAGCACCGAGAAT
1 ATATTCGTGGTAAGGTTGGTGCGTTTAGCTAAGCTCCGAAAAG
1062207 ATATTCGTGGTAAGGTTGGT
1 ATATTCGTGGTAAGGTTGGT
1062227 AGCTTAGCTC
Statistics
Matches: 125, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
42 4 0.03
43 118 0.94
44 3 0.02
ACGTcount: A:0.25, C:0.12, G:0.29, T:0.34
Consensus pattern (43 bp):
ATATTCGTGGTAAGGTTGGTGCGTTTAGCTAAGCTCCGAAAAG
Found at i:1062183 original size:86 final size:85
Alignment explanation
Indices: 1062035--1062231 Score: 232
Period size: 86 Copynumber: 2.3 Consensus size: 85
1062025 GTGATAGAGA
* * * * *
1062035 ATATTCATGGTAAGGTTGGTACGTTTAGCTAAGCTCTGAAAAGATATTCGTGGTAAGGTTGGTGC
1 ATATTCGTGGTAAGGTTGGTGC-TTTACCTAAGCTCCGAAAAGATATTCATGGTAAGGTTGGTGC
* *
1062100 GTTGAGCTAAGCTCCAATAAG
65 GTTGAGCTAAGCACCAAGAAG
* * * **
1062121 ATATTTGTGGTAAGGTTGGTGCTTTGACCTTAGCTCCGAGAAGATATTCATGGTAATTTTGGTGC
1 ATATTCGTGGTAAGGTTGGTGCTTT-ACCTAAGCTCCGAAAAGATATTCATGGTAAGGTTGGTGC
* * *
1062186 GTTGAGCTTAGCACCGAGAAT
65 GTTGAGCTAAGCACCAAGAAG
1062207 ATATTCGTGGTAAGGTTGGTAGCTT
1 ATATTCGTGGTAAGGTTGGT-GCTT
1062232 AGCTCCTAGA
Statistics
Matches: 93, Mismatches: 16, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
85 3 0.03
86 86 0.92
87 4 0.04
ACGTcount: A:0.25, C:0.13, G:0.28, T:0.34
Consensus pattern (85 bp):
ATATTCGTGGTAAGGTTGGTGCTTTACCTAAGCTCCGAAAAGATATTCATGGTAAGGTTGGTGCG
TTGAGCTAAGCACCAAGAAG
Found at i:1062255 original size:37 final size:37
Alignment explanation
Indices: 1062190--1062263 Score: 103
Period size: 37 Copynumber: 2.0 Consensus size: 37
1062180 TGGTGCGTTG
* *
1062190 AGCTTAGCACCGAGAATATATTCGTGGTAAGGTTGGT
1 AGCTTAGCACCGAGAAGATAGTCGTGGTAAGGTTGGT
* * *
1062227 AGCTTAGCTCCTAGAAGATAGTCTTGGTAAGGTTGGT
1 AGCTTAGCACCGAGAAGATAGTCGTGGTAAGGTTGGT
1062264 GTGTTGTGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.26, C:0.14, G:0.30, T:0.31
Consensus pattern (37 bp):
AGCTTAGCACCGAGAAGATAGTCGTGGTAAGGTTGGT
Found at i:1087893 original size:44 final size:45
Alignment explanation
Indices: 1087774--1087986 Score: 346
Period size: 45 Copynumber: 4.8 Consensus size: 45
1087764 TATAAAATTT
*
1087774 CTTATCATTTA-TCCTATAAGCTCGTAAGCTTATTTTACC-A-ATA
1 CTTACCATTTATTCC-ATAAGCTCGTAAGCTTATTTTACCAATATA
1087817 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAA-ATTA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATA-TA
*
1087862 CTTACCA-TTATTCCATAAGCTCGTAAACTTATTTTACCAATATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
1087906 CTTACCATTTATTACATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
1087951 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTT
1087987 CATGGTTACC
Statistics
Matches: 160, Mismatches: 5, Indels: 8
0.92 0.03 0.05
Matches are distributed among these distances:
43 34 0.21
44 46 0.29
45 80 0.50
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.41
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:1087938 original size:89 final size:88
Alignment explanation
Indices: 1087774--1087986 Score: 342
Period size: 89 Copynumber: 2.4 Consensus size: 88
1087764 TATAAAATTT
* *
1087774 CTTATCATTTA-TCCTATAAGCTCGTAAGCTTATTTTACCAATACTTACCATTTATTCCATAAGC
1 CTTACCATTTATTCC-ATAAGCTCGTAAGCTTATTTTACCAATACTTACCATTTATTACATAAGC
1087838 TCGTAAGCTTATTTTACCAA-ATTA
65 TCGTAAGCTTATTTTACCAATA-TA
*
1087862 CTTACCA-TTATTCCATAAGCTCGTAAACTTATTTTACCAATATACTTACCATTTATTACATAAG
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACC-A-ATACTTACCATTTATTACATAAG
1087926 CTCGTAAGCTTATTTTACCAATATA
64 CTCGTAAGCTTATTTTACCAATATA
1087951 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTT
1087987 CATGGTTACC
Statistics
Matches: 116, Mismatches: 4, Indels: 8
0.91 0.03 0.06
Matches are distributed among these distances:
87 26 0.22
88 10 0.09
89 52 0.45
90 28 0.24
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.41
Consensus pattern (88 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATACTTACCATTTATTACATAAGCT
CGTAAGCTTATTTTACCAATATA
Found at i:1088021 original size:7 final size:7
Alignment explanation
Indices: 1088004--1088035 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
1087994 ACCATTTATT
1088004 AACCAATA
1 AACC-ATA
1088012 AACCATA
1 AACCATA
1088019 AACCATA
1 AACCATA
1088026 AACCATA
1 AACCATA
1088033 AAC
1 AAC
1088036 AATAGCCCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 20 0.83
8 4 0.17
ACGTcount: A:0.59, C:0.28, G:0.00, T:0.12
Consensus pattern (7 bp):
AACCATA
Found at i:1088028 original size:14 final size:15
Alignment explanation
Indices: 1088004--1088039 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
1087994 ACCATTTATT
1088004 AACCAATAAACCATA
1 AACCAATAAACCATA
1088019 AACC-ATAAACCATA
1 AACCAATAAACCATA
1088033 AA-CAATA
1 AACCAATA
1088040 GCCCATAGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 1 0.05
14 15 0.75
15 4 0.20
ACGTcount: A:0.61, C:0.25, G:0.00, T:0.14
Consensus pattern (15 bp):
AACCAATAAACCATA
Found at i:1088045 original size:14 final size:14
Alignment explanation
Indices: 1088007--1088056 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
1087997 ATTTATTAAC
*
1088007 CAATAAACCATAAA
1 CAATAGACCATAAA
* *
1088021 CCATAAACCATAAA
1 CAATAGACCATAAA
* *
1088035 CAATAGCCCATAGA
1 CAATAGACCATAAA
1088049 CAATAGAC
1 CAATAGAC
1088057 AATAGCCATA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.54, C:0.26, G:0.06, T:0.14
Consensus pattern (14 bp):
CAATAGACCATAAA
Found at i:1088045 original size:21 final size:21
Alignment explanation
Indices: 1088007--1088063 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
1087997 ATTTATTAAC
* **
1088007 CAATAAACCATAAACCATAAA
1 CAATAAACAATAGCCCATAAA
* *
1088028 CCATAAACAATAGCCCATAGA
1 CAATAAACAATAGCCCATAAA
*
1088049 CAATAGACAATAGCC
1 CAATAAACAATAGCC
1088064 ATAGCCCAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.53, C:0.26, G:0.07, T:0.14
Consensus pattern (21 bp):
CAATAAACAATAGCCCATAAA
Found at i:1088168 original size:40 final size:40
Alignment explanation
Indices: 1088124--1088325 Score: 359
Period size: 40 Copynumber: 5.0 Consensus size: 40
1088114 ACCGTAGTAC
1088124 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* *
1088164 TACACATAAGGTCATACCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* *
1088204 TACACATAAGTTTGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1088244 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
1088284 TACACATAAGATCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1088324 TA
1 TA
1088326 TAAACCTGCA
Statistics
Matches: 153, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 153 1.00
ACGTcount: A:0.34, C:0.27, G:0.15, T:0.24
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:1089174 original size:30 final size:31
Alignment explanation
Indices: 1089127--1089186 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
1089117 CAACCATTCC
* *
1089127 CAACTTTTTCCAAAATTACGAATTGGTCCCT
1 CAACTTTTTCCAAAATTACAAAATGGTCCCT
*
1089158 CAACTTTTT-GAAAATTACAAAATGGTCCC
1 CAACTTTTTCCAAAATTACAAAATGGTCCC
1089187 AAAATTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 17 0.65
31 9 0.35
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (31 bp):
CAACTTTTTCCAAAATTACAAAATGGTCCCT
Found at i:1095603 original size:4 final size:5
Alignment explanation
Indices: 1095575--1095600 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1095565 ACTAAAAAAG
1095575 AAGAA AAGAA AAGAA AAGAA AAGAA A
1 AAGAA AAGAA AAGAA AAGAA AAGAA A
1095601 GAAGTTGAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:1105827 original size:45 final size:46
Alignment explanation
Indices: 1105653--1106179 Score: 628
Period size: 46 Copynumber: 11.6 Consensus size: 46
1105643 ATCGTTATGT
* *
1105653 ATTTTCATTTGTGGCATCCTTTCATGCCAATTATGCACTATTATAC
1 ATTTTCATTTATGGCATCCTTTCATGCCAATTATGCACTGTTATAC
* * *
1105699 ATTTTCATTTATGGTATCCTTTCATGCCAATTATGCATTATTATAC
1 ATTTTCATTTATGGCATCCTTTCATGCCAATTATGCACTGTTATAC
* *
1105745 ATTTTCATTTATGGCATTCTTTCATGCCAATTATGCATTGTTATAC
1 ATTTTCATTTATGGCATCCTTTCATGCCAATTATGCACTGTTATAC
*
1105791 ATTTTCATTTAT-GCATCCTTTCATGCCAATTATGCATTGTTATAC
1 ATTTTCATTTATGGCATCCTTTCATGCCAATTATGCACTGTTATAC
* *
1105836 ATTTTCATTTATGGCATCCTTTTATGCCAATTATGCATTGTTATAC
1 ATTTTCATTTATGGCATCCTTTCATGCCAATTATGCACTGTTATAC
*
1105882 ATTTTCATTTATGGCATCCTTTCATGCCAATTATGCATTGTTATAC
1 ATTTTCATTTATGGCATCCTTTCATGCCAATTATGCACTGTTATAC
* *
1105928 ATTTTCATTTATGGCATCCTTTCATGCC-TTTAATGCACTGTTATGC
1 ATTTTCATTTATGGCATCCTTTCATGCCAATT-ATGCACTGTTATAC
* * ** *
1105974 A-TTTCATTTATGGCATCCTTTCATGCC-TTTAATGCGCCATTATGC
1 ATTTTCATTTATGGCATCCTTTCATGCCAATT-ATGCACTGTTATAC
* * **
1106019 A-TTTCATTTATGGCATCC-TTCATGCC-TTTAATGCACCGTTATGT
1 ATTTTCATTTATGGCATCCTTTCATGCCAATT-ATGCACTGTTATAC
* * ** **
1106063 A-TTTCATTTATGGAATCCTTTCATGCC-TTTAATGCACCATTATGT
1 ATTTTCATTTATGGCATCCTTTCATGCCAATT-ATGCACTGTTATAC
* * * *
1106108 A-TTTCATTTATGGCATCCTTTCACGCC-TTTAATGCACCGTTATGC
1 ATTTTCATTTATGGCATCCTTTCATGCCAATT-ATGCACTGTTATAC
*
1106153 A-TTTCATTTATGACATCCTTTCATGCC
1 ATTTTCATTTATGGCATCCTTTCATGCC
1106180 TTTAATACAC
Statistics
Matches: 452, Mismatches: 26, Indels: 7
0.93 0.05 0.01
Matches are distributed among these distances:
44 40 0.09
45 196 0.43
46 216 0.48
ACGTcount: A:0.23, C:0.21, G:0.11, T:0.45
Consensus pattern (46 bp):
ATTTTCATTTATGGCATCCTTTCATGCCAATTATGCACTGTTATAC
Found at i:1105865 original size:137 final size:137
Alignment explanation
Indices: 1105653--1106179 Score: 615
Period size: 137 Copynumber: 3.9 Consensus size: 137
1105643 ATCGTTATGT
* *
1105653 ATTTTCATTTGTGGCATCCTTTCATGCCAATT-ATGCACTATTATACATTTTCATTTATGGTATC
1 ATTTTCATTTATGGCATCCTTTCATGCC-ATTAATGCACTATTATACA-TTTCATTTATGGCATC
1105717 CTTTCATGCCAATTATGCATTATTATACATTTTCATTTATGGCATTCTTTCATGCCAATTATGCA
64 CTTTCATGCCAATTATGCATTATTATACATTTTCATTTATGGCATTCTTTCATGCCAATTATGCA
1105782 TTGTTATAC
129 TTGTTATAC
* *
1105791 ATTTTCATTTAT-GCATCCTTTCATGCCAATT-ATGCATTGTTATACATTTTCATTTATGGCATC
1 ATTTTCATTTATGGCATCCTTTCATGCC-ATTAATGCACTATTATACA-TTTCATTTATGGCATC
* * *
1105854 CTTTTATGCCAATTATGCATTGTTATACATTTTCATTTATGGCATCCTTTCATGCCAATTATGCA
64 CTTTCATGCCAATTATGCATTATTATACATTTTCATTTATGGCATTCTTTCATGCCAATTATGCA
1105919 TTGTTATAC
129 TTGTTATAC
* * *
1105928 ATTTTCATTTATGGCATCCTTTCATGCCTTTAATGCACTGTTATGCATTTCATTTATGGCATCCT
1 ATTTTCATTTATGGCATCCTTTCATGCCATTAATGCACTATTATACATTTCATTTATGGCATCCT
* *** * * *
1105993 TTCATGCC-TTTAATGCGCCATTATGCA-TTTCATTTATGGCA-TCCTTCATGCC-TTTAATGCA
66 TTCATGCCAATT-ATGCATTATTATACATTTTCATTTATGGCATTCTTTCATGCCAATT-ATGCA
** **
1106054 CCGTTATGT
129 TTGTTATAC
* * * **
1106063 A-TTTCATTTATGGAATCCTTTCATGCCTTTAATGCACCATTATGTATTTCATTTATGGCATCCT
1 ATTTTCATTTATGGCATCCTTTCATGCCATTAATGCACTATTATACATTTCATTTATGGCATCCT
* * *** * * *
1106127 TTCACGCC-TTTAATGCACCGTTATGCA-TTTCATTTATGACATCCTTTCATGCC
66 TTCATGCCAATT-ATGCATTATTATACATTTTCATTTATGGCATTCTTTCATGCC
1106180 TTTAATACAC
Statistics
Matches: 350, Mismatches: 34, Indels: 13
0.88 0.09 0.03
Matches are distributed among these distances:
134 98 0.28
135 29 0.08
136 16 0.05
137 168 0.48
138 39 0.11
ACGTcount: A:0.23, C:0.21, G:0.11, T:0.45
Consensus pattern (137 bp):
ATTTTCATTTATGGCATCCTTTCATGCCATTAATGCACTATTATACATTTCATTTATGGCATCCT
TTCATGCCAATTATGCATTATTATACATTTTCATTTATGGCATTCTTTCATGCCAATTATGCATT
GTTATAC
Found at i:1106181 original size:45 final size:47
Alignment explanation
Indices: 1105646--1106209 Score: 639
Period size: 45 Copynumber: 12.4 Consensus size: 47
1105636 TTAATACATC
* *
1105646 GTTATGTATTTTCATTTGTGGCATCCTTTCATGCCAATT-ATGCACT
1 GTTATGCATTTTCATTTATGGCATCCTTTCATGCCAATTAATGCACT
* * * *
1105692 ATTATACATTTTCATTTATGGTATCCTTTCATGCCAATT-ATGCATT
1 GTTATGCATTTTCATTTATGGCATCCTTTCATGCCAATTAATGCACT
* * * *
1105738 ATTATACATTTTCATTTATGGCATTCTTTCATGCCAATT-ATGCATT
1 GTTATGCATTTTCATTTATGGCATCCTTTCATGCCAATTAATGCACT
* *
1105784 GTTATACATTTTCATTTAT-GCATCCTTTCATGCCAATT-ATGCATT
1 GTTATGCATTTTCATTTATGGCATCCTTTCATGCCAATTAATGCACT
* * *
1105829 GTTATACATTTTCATTTATGGCATCCTTTTATGCCAATT-ATGCATT
1 GTTATGCATTTTCATTTATGGCATCCTTTCATGCCAATTAATGCACT
* *
1105875 GTTATACATTTTCATTTATGGCATCCTTTCATGCCAATT-ATGCATT
1 GTTATGCATTTTCATTTATGGCATCCTTTCATGCCAATTAATGCACT
* *
1105921 GTTATACATTTTCATTTATGGCATCCTTTCATGCC-TTTAATGCACT
1 GTTATGCATTTTCATTTATGGCATCCTTTCATGCCAATTAATGCACT
* * *
1105967 GTTATGCA-TTTCATTTATGGCATCCTTTCATGCC-TTTAATGCGCC
1 GTTATGCATTTTCATTTATGGCATCCTTTCATGCCAATTAATGCACT
* * *
1106012 ATTATGCA-TTTCATTTATGGCATCC-TTCATGCC-TTTAATGCACC
1 GTTATGCATTTTCATTTATGGCATCCTTTCATGCCAATTAATGCACT
* * * *
1106056 GTTATGTA-TTTCATTTATGGAATCCTTTCATGCC-TTTAATGCACC
1 GTTATGCATTTTCATTTATGGCATCCTTTCATGCCAATTAATGCACT
* * * * *
1106101 ATTATGTA-TTTCATTTATGGCATCCTTTCACGCC-TTTAATGCACC
1 GTTATGCATTTTCATTTATGGCATCCTTTCATGCCAATTAATGCACT
* * *
1106146 GTTATGCA-TTTCATTTATGACATCCTTTCATGCC-TTTAATACACCT
1 GTTATGCATTTTCATTTATGGCATCCTTTCATGCCAATTAATGCA-CT
1106192 -TTATGCA-TTTCATTTATG
1 GTTATGCATTTTCATTTATG
1106210 TAATGAAAAC
Statistics
Matches: 483, Mismatches: 31, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
44 40 0.08
45 222 0.46
46 221 0.46
ACGTcount: A:0.23, C:0.21, G:0.11, T:0.45
Consensus pattern (47 bp):
GTTATGCATTTTCATTTATGGCATCCTTTCATGCCAATTAATGCACT
Found at i:1106709 original size:95 final size:95
Alignment explanation
Indices: 1106513--1106693 Score: 217
Period size: 95 Copynumber: 1.9 Consensus size: 95
1106503 ACCCCTACCA
* *
1106513 TAGTATCGATACTTCTATACTATGGTACTGATACCCCGTTTTAGTATCGATACCATTTCTAAATT
1 TAGTATCGATACTACTATACTATGGTACTGATACCCCGTTTCAGTATCGATACCATTTCTAAATT
* *
1106578 CTGTAATTCATGGTATCGATACCTTTATCT
66 CTGAAATCCATGGTATCGATACCTTTATCT
** * *
1106608 CGGTATCGATTA-TACTATACTATGGTA-TCGATACTCCC-TTTCAGTATTGATACCATTT-TGG
1 TAGTATCGA-TACTACTATACTATGGTACT-GATAC-CCCGTTTCAGTATCGATACCATTTCT-A
*
1106669 CATTCTGAAATCCATGGTATCGATA
62 AATTCTGAAATCCATGGTATCGATA
1106694 TTTTCTTTTT
Statistics
Matches: 73, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
94 2 0.03
95 66 0.90
96 5 0.07
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (95 bp):
TAGTATCGATACTACTATACTATGGTACTGATACCCCGTTTCAGTATCGATACCATTTCTAAATT
CTGAAATCCATGGTATCGATACCTTTATCT
Found at i:1112571 original size:46 final size:46
Alignment explanation
Indices: 1112504--1112937 Score: 415
Period size: 46 Copynumber: 9.6 Consensus size: 46
1112494 TACACCAAAG
*
1112504 TGCATTATTATACATTTTCATTTATGGCATCCTTTCATGCCAATTA
1 TGCATTGTTATACATTTTCATTTATGGCATCCTTTCATGCCAATTA
* * *
1112550 TGCATTATTATACATTTTCATTTATGGTATCCTTTTATGCCAATTA
1 TGCATTGTTATACATTTTCATTTATGGCATCCTTTCATGCCAATTA
*
1112596 TGCATTGTTATACATTTTCATTTATGGCATCCTTTTATGCCAATTA
1 TGCATTGTTATACATTTTCATTTATGGCATCCTTTCATGCCAATTA
* *
1112642 CGTATTGTTATACATTTTCATTTATGGCATCCTTTCATGCCAATTA
1 TGCATTGTTATACATTTTCATTTATGGCATCCTTTCATGCCAATTA
* *
1112688 TGCATTGTTATACATTTTCATTTATGGCATCCTATCATGCC-TTTAA
1 TGCATTGTTATACATTTTCATTTATGGCATCCTTTCATGCCAATT-A
* * *
1112734 TTCACTT-TTATGCA-TTTCATTTATGGCATCCTTTCATGCC-TTTAA
1 TGCA-TTGTTATACATTTTCATTTATGGCATCCTTTCATGCCAATT-A
**** * * *
1112779 TGCGCCATTATGCA-TTTCATTTACGGCATCC-TTCATGCC-TTTAA
1 TGCATTGTTATACATTTTCATTTATGGCATCCTTTCATGCCAATT-A
* ** ** *
1112823 TACACCGTTATGTA-TTTCATTTATGGCATCCTTTCATGCC-TTTAA
1 TGCATTGTTATACATTTTCATTTATGGCATCCTTTCATGCCAATT-A
** ** ** *
1112868 TGCACCGTTATGTA-TTTCATTTATCACATCCTTTCATGCC-TTTAA
1 TGCATTGTTATACATTTTCATTTATGGCATCCTTTCATGCCAATT-A
** *
1112913 TGCACCGTTATGCA-TTTCATTTATG
1 TGCATTGTTATACATTTTCATTTATG
1112938 TAATGAAAAC
Statistics
Matches: 355, Mismatches: 29, Indels: 9
0.90 0.07 0.02
Matches are distributed among these distances:
44 39 0.11
45 135 0.38
46 179 0.50
47 2 0.01
ACGTcount: A:0.23, C:0.21, G:0.11, T:0.46
Consensus pattern (46 bp):
TGCATTGTTATACATTTTCATTTATGGCATCCTTTCATGCCAATTA
Found at i:1112848 original size:89 final size:89
Alignment explanation
Indices: 1112648--1112937 Score: 377
Period size: 89 Copynumber: 3.2 Consensus size: 89
1112638 ATTACGTATT
* * ** *
1112648 GTTATACATTTTCATTTATGGCATCCTTTCATGCCAATT-ATGCATTGTTATACATTTTCATTTA
1 GTTATGCA-TTTCATTTATGGCATCCTTTCATGCC-TTTAATGCACCGTTATGCA-TTTCATTTA
* * *
1112712 TGGCATCCTATCATGCCTTTAATTCACT
63 CGGCATCCT-TCATGCCTTTAATACACC
* * *
1112740 TTTATGCATTTCATTTATGGCATCCTTTCATGCCTTTAATGCGCCATTATGCATTTCATTTACGG
1 GTTATGCATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTACGG
1112805 CATCCTTCATGCCTTTAATACACC
66 CATCCTTCATGCCTTTAATACACC
* *
1112829 GTTATGTATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGTATTTCATTTATC-
1 GTTATGCATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTA-CG
* *
1112893 ACATCCTTTCATGCCTTTAATGCACC
65 GCATCC-TTCATGCCTTTAATACACC
1112919 GTTATGCATTTCATTTATG
1 GTTATGCATTTCATTTATG
1112938 TAATGAAAAC
Statistics
Matches: 176, Mismatches: 19, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
89 78 0.44
90 56 0.32
91 36 0.20
92 6 0.03
ACGTcount: A:0.22, C:0.22, G:0.11, T:0.44
Consensus pattern (89 bp):
GTTATGCATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTACGG
CATCCTTCATGCCTTTAATACACC
Found at i:1113394 original size:20 final size:20
Alignment explanation
Indices: 1113369--1113423 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
1113359 ATTCTGTAAT
1113369 TCATGGTATCGATACCTTTA
1 TCATGGTATCGATACCTTTA
1113389 TCATGGTATCGATACCTTTA
1 TCATGGTATCGATACCTTTA
*
1113409 TC-TCGGTATTGATAC
1 TCAT-GGTATCGATAC
1113424 TACTATACTA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 32 0.97
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (20 bp):
TCATGGTATCGATACCTTTA
Found at i:1119726 original size:45 final size:45
Alignment explanation
Indices: 1119377--1119940 Score: 575
Period size: 46 Copynumber: 12.4 Consensus size: 45
1119367 TTAATATGTC
* * * *
1119377 GTTATGTATTTTCATTTGTGGCATCCTTTCATGCCAATTATACACT
1 GTTATGCATTTTCATTTATGGCATCCTTTCATGCC-ATTATGCATT
* * *
1119423 ATTATACATTTTCATTTATGGCATTCTTTCATGCCAATTATGCATT
1 GTTATGCATTTTCATTTATGGCATCCTTTCATGCC-ATTATGCATT
* * * *
1119469 ATTATACATTTTTATTTATGGCATCCTTTCATGTCAATTATGCATT
1 GTTATGCATTTTCATTTATGGCATCCTTTCATG-CCATTATGCATT
* *
1119515 TTTATACATTTTCATTTATGGCATCCTTTCATGCCAATTATGCATT
1 GTTATGCATTTTCATTTATGGCATCCTTTCATGCC-ATTATGCATT
* * *
1119561 GTTATACATTTTCATTTATGGCATCCTTTTATGCCAATTACGCATT
1 GTTATGCATTTTCATTTATGGCATCCTTTCATGCC-ATTATGCATT
*
1119607 GTTATACATTTTCATTTATGGCATCCTTTCATGCCAATTATGCATT
1 GTTATGCATTTTCATTTATGGCATCCTTTCATGCC-ATTATGCATT
* * *
1119653 ATTATACATTTTCATTTATGGCATCCTTTCATGCCTTTAATGCATT
1 GTTATGCATTTTCATTTATGGCATCCTTTCATGCCATT-ATGCATT
* * *
1119699 GTTATGCA-TTTCATTTATGGCATCCTTTCATGCCTTTAATGCGTC
1 GTTATGCATTTTCATTTATGGCATCCTTTCATGCCATT-ATGCATT
* * * * **
1119744 ATTATGCA-ATTCATTTATGGAATCC-TTCATGCCTTTAATGCACC
1 GTTATGCATTTTCATTTATGGCATCCTTTCATGCCATT-ATGCATT
* * * * * **
1119788 GTTATGTA-TTTCATTTATAGCATCATTTCATGCCTTTAATGAACC
1 GTTATGCATTTTCATTTATGGCATCCTTTCATGCCATT-ATGCATT
* * **
1119833 GTTATGTA-TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACC
1 GTTATGCATTTTCATTTATGGCATCCTTTCATGCCATT-ATGCATT
* **
1119878 GTTATGCA-TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACC
1 GTTATGCATTTTCATTTATGGCATCCTTTCATGCCATT-ATGCATT
*
1119923 ATTATGCA-TTTCATTTAT
1 GTTATGCATTTTCATTTAT
1119941 TTAATGAAAA
Statistics
Matches: 473, Mismatches: 41, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
44 36 0.08
45 181 0.38
46 255 0.54
47 1 0.00
ACGTcount: A:0.24, C:0.20, G:0.11, T:0.46
Consensus pattern (45 bp):
GTTATGCATTTTCATTTATGGCATCCTTTCATGCCATTATGCATT
Found at i:1125216 original size:34 final size:34
Alignment explanation
Indices: 1125159--1125322 Score: 149
Period size: 34 Copynumber: 4.9 Consensus size: 34
1125149 GCTATATCTA
* * * *
1125159 AAAGGTT-CTTCAAAAGGATATGTTGTTTCGTCC
1 AAAGGTTGCTTCCAAAGGACATGATGTTTCATCC
*
1125192 AAAGGTTGCTTCCAAAGGAC---ATGTTTCATCT
1 AAAGGTTGCTTCCAAAGGACATGATGTTTCATCC
** *
1125223 AAAGGTTGCTTCC-AAGAGACACAATGTTTCATCT
1 AAAGGTTGCTTCCAAAG-GACATGATGTTTCATCC
* * *
1125257 AAAGGGTGGTTCCAAAGGACATGATTTTTCATCC
1 AAAGGTTGCTTCCAAAGGACATGATGTTTCATCC
** * *
1125291 ATTGGGTGCTTCCAAAGGAGATGATGTTTCAT
1 AAAGGTTGCTTCCAAAGGACATGATGTTTCAT
1125323 TCACACCTCT
Statistics
Matches: 109, Mismatches: 16, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
30 3 0.03
31 24 0.22
33 7 0.06
34 72 0.66
35 3 0.03
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (34 bp):
AAAGGTTGCTTCCAAAGGACATGATGTTTCATCC
Found at i:1125227 original size:31 final size:31
Alignment explanation
Indices: 1125182--1125279 Score: 124
Period size: 31 Copynumber: 3.1 Consensus size: 31
1125172 AAGGATATGT
* *
1125182 TGTTTCGTCCAAAGGTTGCTTCCAAAGGACA
1 TGTTTCATCTAAAGGTTGCTTCCAAAGGACA
*
1125213 TGTTTCATCTAAAGGTTGCTTCCAAGAGACACAA
1 TGTTTCATCTAAAGGTTGCTTCCAA-AG-GAC-A
* *
1125247 TGTTTCATCTAAAGGGTGGTTCCAAAGGACA
1 TGTTTCATCTAAAGGTTGCTTCCAAAGGACA
1125278 TG
1 TG
1125280 ATTTTTCATC
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
31 26 0.45
32 4 0.07
33 4 0.07
34 24 0.41
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (31 bp):
TGTTTCATCTAAAGGTTGCTTCCAAAGGACA
Found at i:1126215 original size:13 final size:14
Alignment explanation
Indices: 1126187--1126215 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1126177 ATCATTTTAA
1126187 TTTTATAATATCAT
1 TTTTATAATATCAT
1126201 TTTTATAATAT-AT
1 TTTTATAATATCAT
1126214 TT
1 TT
1126216 ATTTACTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (14 bp):
TTTTATAATATCAT
Found at i:1127118 original size:78 final size:79
Alignment explanation
Indices: 1126987--1127210 Score: 259
Period size: 75 Copynumber: 2.9 Consensus size: 79
1126977 TAATGAAAGA
* * *
1126987 TGTCATAGCTTTTAGTTTAATGAATTCACTTTAATTTACAAGCACTAATGTATTTCTTTTTATAA
1 TGTCATAGCTTTTAGTTTATTGAATTCACTTTAAATTACAAGCAGTAATGTATTTCTTTTTATAA
1127052 TATTTATACT-TGG
66 TATTTATACTATGG
* * * * *
1127065 TGTCATAGCTTATAGTTTATTGAATTCAATTTAAATTGCAAGCAGTAAAGTATTTC---TTGTAA
1 TGTCATAGCTTTTAGTTTATTGAATTCACTTTAAATTACAAGCAGTAATGTATTTCTTTTTATAA
1127127 TATTTATA-TATGG
66 TATTTATACTATGG
* * * * *
1127140 TATCATAGTTTTTAGTTTATTGAAATCACTATAAATTACAA-AAGCTAATGTA---CTTTTTATA
1 TGTCATAGCTTTTAGTTTATTGAATTCACTTTAAATTACAAGCAG-TAATGTATTTCTTTTTATA
1127201 ATATTTATAC
65 ATATTTATAC
1127211 AATTATGTTC
Statistics
Matches: 122, Mismatches: 18, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
72 1 0.01
74 3 0.02
75 69 0.57
78 49 0.40
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.46
Consensus pattern (79 bp):
TGTCATAGCTTTTAGTTTATTGAATTCACTTTAAATTACAAGCAGTAATGTATTTCTTTTTATAA
TATTTATACTATGG
Found at i:1130264 original size:47 final size:45
Alignment explanation
Indices: 1130190--1130315 Score: 155
Period size: 47 Copynumber: 2.8 Consensus size: 45
1130180 TATAAAATCT
*
1130190 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * * *
1130235 CTTACCATTTAAATTCCATAAGCTTGTAAGCTTATTTTTCCTATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
1130282 CTTGCCA-TTATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
1130316 GCATGGTTAC
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
44 22 0.31
45 10 0.14
46 2 0.03
47 36 0.51
ACGTcount: A:0.29, C:0.22, G:0.08, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:1137255 original size:47 final size:44
Alignment explanation
Indices: 1137155--1137280 Score: 117
Period size: 47 Copynumber: 2.8 Consensus size: 44
1137145 TATAAAATCT
* *
1137155 CTTACCATTTATCCCATAAGCTCGTAAGCTTGTTTTACCAAAATA
1 CTTACCA-TTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * * * **
1137200 TTTACCATTTAAATTCCATAAGCTTGTAAGCTTATTTTTCCTATGTA
1 CTTACCA-TT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
1137247 CTTGCCATTATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTATTCCATAAGCTCGTAAGCTTATTT
1137281 GCATGGTTGC
Statistics
Matches: 66, Mismatches: 13, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
44 22 0.33
45 9 0.14
46 2 0.03
47 33 0.50
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.41
Consensus pattern (44 bp):
CTTACCATTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:1146101 original size:6 final size:6
Alignment explanation
Indices: 1146067--1146092 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1146057 AAAGAATTTG
1146067 TTTTTA TTTTTA TTTTTA TTTTTA TT
1 TTTTTA TTTTTA TTTTTA TTTTTA TT
1146093 ATTTTTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:1155141 original size:184 final size:184
Alignment explanation
Indices: 1154770--1155141 Score: 421
Period size: 184 Copynumber: 2.0 Consensus size: 184
1154760 GTTATCAATG
* * *
1154770 TATAAACATTGTATTCATTTGATCATGATTCTAAAATATTTTAAGTTAATGTTTATATATTGTAC
1 TATAAACAGTGTATTCATTTGATCATGATTCTAAAATATTTCAAGTTAATATTTATATATTGTAC
* ***
1154835 CAATTTGATATTAATTCTAAATTTTTTAGCATTCAGTTCGGTTCTGAAAAAATATAATTACTTTT
66 CAATGTGATATTAATTCTAAAAAATTTAGCATTCAGTTCGGTTCTGAAAAAATATAATTACTTTT
* ** * * * *
1154900 TATAATTTTTTTCTATTGAGTTGGCGTTATAGATTAACCGAACTAAGAATTTAT
131 AATAAAGTTTTTCGATTGAATTGGAGTTATAGATTAACCGAACTAAGAATGTAT
* * * * *
1154954 TATAGACAGTGTATTCATTTGATCTTGATTCTAAAATATTTCAA-TTAATATTTGTGTATTGTAT
1 TATAAACAGTGTATTCATTTGATCATGATTCTAAAATATTTCAAGTTAATATTTATATATTGTAC
* * * * *
1155018 CAATGTGATATTAATTTTAAAAAATTTAGCATTCAGTTTGGTTGTGGATAAATATAATTGTA-TT
66 CAATGTGATATTAATTCTAAAAAATTTAGCATTCAGTTCGGTTCTGAAAAAATATAA-T-TACTT
* * *
1155082 TATAATAAAGTTTTT-GATTGAATTGGAGTTGCAT-G-TTAACCGAATTGAGGATGTAT
129 T-TAATAAAGTTTTTCGATTGAATTGGAGTT--ATAGATTAACCGAACTAAGAATGTAT
1155138 TATA
1 TATA
1155142 TAAAAATTAC
Statistics
Matches: 156, Mismatches: 27, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
183 64 0.41
184 77 0.49
185 13 0.08
186 2 0.01
ACGTcount: A:0.34, C:0.08, G:0.14, T:0.45
Consensus pattern (184 bp):
TATAAACAGTGTATTCATTTGATCATGATTCTAAAATATTTCAAGTTAATATTTATATATTGTAC
CAATGTGATATTAATTCTAAAAAATTTAGCATTCAGTTCGGTTCTGAAAAAATATAATTACTTTT
AATAAAGTTTTTCGATTGAATTGGAGTTATAGATTAACCGAACTAAGAATGTAT
Found at i:1155564 original size:19 final size:19
Alignment explanation
Indices: 1155542--1155583 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
1155532 TTAAAATCAA
1155542 AATGATAA-AATTTATAAGT
1 AATGATAACAATTTATAA-T
1155561 AATGATAATCAATTTATAAT
1 AATGATAA-CAATTTATAAT
1155581 AAT
1 AAT
1155584 ACAAAAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 8 0.38
20 4 0.19
21 9 0.43
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.38
Consensus pattern (19 bp):
AATGATAACAATTTATAAT
Found at i:1162303 original size:21 final size:21
Alignment explanation
Indices: 1162279--1162324 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1162269 CCGGTCAAAT
*
1162279 GGTTCAACTCGAATCAGGTCG
1 GGTTCAACTCAAATCAGGTCG
** *
1162300 GGTTCAGGTCAAATCAGTTCG
1 GGTTCAACTCAAATCAGGTCG
1162321 GGTT
1 GGTT
1162325 ATTTTCAGGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (21 bp):
GGTTCAACTCAAATCAGGTCG
Found at i:1163223 original size:2 final size:2
Alignment explanation
Indices: 1163218--1163277 Score: 102
Period size: 2 Copynumber: 30.0 Consensus size: 2
1163208 AGTATATACT
1163218 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
1163260 TA TA TA CA TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA
1163278 CATAGATAGC
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1164446 original size:25 final size:25
Alignment explanation
Indices: 1164418--1164468 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
1164408 TTAAATAGAA
1164418 TGTTGTTCTCCCTAAAGGTCTTGAG
1 TGTTGTTCTCCCTAAAGGTCTTGAG
*
1164443 TGTTGTTTTCCCTAAAGGTCTTGAG
1 TGTTGTTCTCCCTAAAGGTCTTGAG
1164468 T
1 T
1164469 TCAAGCAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (25 bp):
TGTTGTTCTCCCTAAAGGTCTTGAG
Found at i:1165140 original size:17 final size:18
Alignment explanation
Indices: 1165118--1165155 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1165108 TAAGGTAAAA
* *
1165118 TTTTTTGTTTTAATT-AT
1 TTTTTTGCTTAAATTAAT
1165135 TTTTTTGCTTAAATTAAT
1 TTTTTTGCTTAAATTAAT
1165153 TTT
1 TTT
1165156 GTTTAAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.21, C:0.03, G:0.05, T:0.71
Consensus pattern (18 bp):
TTTTTTGCTTAAATTAAT
Found at i:1165155 original size:15 final size:15
Alignment explanation
Indices: 1165137--1165169 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1165127 TTAATTATTT
1165137 TTTTGCTTAAATTAA
1 TTTTGCTTAAATTAA
*
1165152 TTTTGTTTAAATTAA
1 TTTTGCTTAAATTAA
1165167 TTT
1 TTT
1165170 GTATTTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.30, C:0.03, G:0.06, T:0.61
Consensus pattern (15 bp):
TTTTGCTTAAATTAA
Found at i:1167317 original size:22 final size:22
Alignment explanation
Indices: 1167286--1167327 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1167276 TATTTACGTT
* *
1167286 TTATATTTTGGTAACTATTTAA
1 TTATAATTTGATAACTATTTAA
*
1167308 TTATAATTTGATTACTATTT
1 TTATAATTTGATAACTATTT
1167328 TTTTTATCCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.31, C:0.05, G:0.07, T:0.57
Consensus pattern (22 bp):
TTATAATTTGATAACTATTTAA
Found at i:1169666 original size:14 final size:14
Alignment explanation
Indices: 1169630--1169666 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1169620 TCATTTTCAT
* *
1169630 TTTGCATTCGCACC
1 TTTGCATTTGCAAC
1169644 TTTGCATTTGCAAC
1 TTTGCATTTGCAAC
1169658 TTTGCATTT
1 TTTGCATTT
1169667 TTATATTTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.14, T:0.46
Consensus pattern (14 bp):
TTTGCATTTGCAAC
Found at i:1169683 original size:20 final size:20
Alignment explanation
Indices: 1169612--1169708 Score: 74
Period size: 20 Copynumber: 4.8 Consensus size: 20
1169602 AACACCTTCA
*
1169612 TTGCATTTTCA-TTTT-CATT
1 TTGCATTTGCATTTTTACA-T
* ** *
1169631 TTGCATTCGCACCTTTGCAT
1 TTGCATTTGCATTTTTACAT
*
1169651 TTGCAACTTTGCATTTTTATAT
1 TTGC-A-TTTGCATTTTTACAT
1169673 TTGCATTTGCATTTTTTACAT
1 TTGCATTTGCA-TTTTTACAT
*
1169694 TT-CATTTGTATTTTT
1 TTGCATTTGCATTTTT
1169709 GTTTGTTTCA
Statistics
Matches: 63, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
19 14 0.22
20 21 0.33
21 14 0.22
22 14 0.22
ACGTcount: A:0.18, C:0.16, G:0.09, T:0.57
Consensus pattern (20 bp):
TTGCATTTGCATTTTTACAT
Found at i:1172374 original size:7 final size:8
Alignment explanation
Indices: 1172361--1172411 Score: 54
Period size: 7 Copynumber: 6.5 Consensus size: 8
1172351 CTCTTTTAAG
1172361 GAAATAAA
1 GAAATAAA
1172369 -AAATAAA
1 GAAATAAA
1172376 GAAA-AAA
1 GAAATAAA
1172383 GAAA-AAA
1 GAAATAAA
1172390 GAAATAAAAA
1 GAAAT--AAA
*
1172400 GAAAAAAA
1 GAAATAAA
1172408 GAAA
1 GAAA
1172412 GAAAAAGGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
7 21 0.55
8 10 0.26
10 7 0.18
ACGTcount: A:0.82, C:0.00, G:0.12, T:0.06
Consensus pattern (8 bp):
GAAATAAA
Found at i:1172389 original size:18 final size:18
Alignment explanation
Indices: 1172366--1172423 Score: 73
Period size: 18 Copynumber: 3.2 Consensus size: 18
1172356 TTAAGGAAAT
*
1172366 AAAAAATAAAGAAAAAAG
1 AAAAAAGAAAGAAAAAAG
*
1172384 AAAAAAGAAA-TAAAAAG
1 AAAAAAGAAAGAAAAAAG
*
1172401 AAAAAAAGAAAGAAAAAGG
1 -AAAAAAGAAAGAAAAAAG
1172420 AAAA
1 AAAA
1172424 GGGAAAAGGG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
17 6 0.18
18 23 0.68
19 5 0.15
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (18 bp):
AAAAAAGAAAGAAAAAAG
Found at i:1172412 original size:29 final size:29
Alignment explanation
Indices: 1172361--1172422 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 29
1172351 CTCTTTTAAG
1172361 GAAATAAAAAATAAAGAAAAAAGAAAAAA
1 GAAATAAAAAATAAAGAAAAAAGAAAAAA
*
1172390 GAAATAAAAAGA-AAA-AAAGAAAGAAAAAG
1 GAAATAAAAA-ATAAAGAAA-AAAGAAAAAA
1172419 GAAA
1 GAAA
1172423 AGGGAAAAGG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 3 0.10
29 26 0.87
30 1 0.03
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.05
Consensus pattern (29 bp):
GAAATAAAAAATAAAGAAAAAAGAAAAAA
Found at i:1172430 original size:25 final size:25
Alignment explanation
Indices: 1172376--1172430 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 25
1172366 AAAAAATAAA
*
1172376 GAAAAAAGAAAAAAGAAATAAAAAG
1 GAAAAAAGAAAAAAGAAAGAAAAAG
* * *
1172401 AAAAAAAGAAAGAA-AAAGGAAAAG
1 GAAAAAAGAAAAAAGAAAGAAAAAG
*
1172425 GGAAAA
1 GAAAAA
1172431 GGGAAAAGGG
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
24 12 0.50
25 12 0.50
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (25 bp):
GAAAAAAGAAAAAAGAAAGAAAAAG
Found at i:1172460 original size:7 final size:7
Alignment explanation
Indices: 1172412--1172450 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
1172402 AAAAAAGAAA
*
1172412 GAAAAAG
1 GAAAAGG
1172419 GAAAAGG
1 GAAAAGG
1172426 GAAAAGG
1 GAAAAGG
1172433 GAAAAGG
1 GAAAAGG
1172440 GAAAA-G
1 GAAAAGG
1172446 GAAAA
1 GAAAA
1172451 AAAGGAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
6 6 0.19
7 25 0.81
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (7 bp):
GAAAAGG
Found at i:1175140 original size:137 final size:138
Alignment explanation
Indices: 1174875--1175239 Score: 462
Period size: 137 Copynumber: 2.6 Consensus size: 138
1174865 AGAATGAGAT
* * *
1174875 GGATCAACATTTCTAGTGGAGAGTTCATAATGAGAAGAACTTATCTGATGAGGGAGAAGAAGTTC
1 GGATCAACATTTTTA-TGGAGAGTTCATAATGAGAAGAACTCATCTGATGAGGGAGAAAAAGTTC
* * *
1174940 ATAATGAGACGAACTTGTTCAACCTTAGCTCGATTCATCGCATATAGAGTTGAATCAGTGACCCC
65 ATAATGAGAAGAACTTGTTCAACCTTAGCTCAATTCATCGCATATAGAGTTGAATCAGCGACCCC
*
1175005 TCACTCGAG
130 TCAATCGAG
*
1175014 GGATCAACATTTTTAT-GAGAGTTCATAATGAGAAGAACTCGTCTGATGAGGGAGAAAAAGTTCA
1 GGATCAACATTTTTATGGAGAGTTCATAATGAGAAGAACTCATCTGATGAGGGAGAAAAAGTTCA
* * * * ** * *
1175078 TAATAAGAAGAACTTGTTCAACCTTGGTTCAATTCATTGTTTATGGAGTTGAATTAGCGACCCCT
66 TAATGAGAAGAACTTGTTCAACCTTAGCTCAATTCATCGCATATAGAGTTGAATCAGCGACCCCT
1175143 CAATCGAG
131 CAATCGAG
* * * * * * * * * *
1175151 TGATCAATATTTTCAATGGAATAGTTCATAATGAGAATAACTCATCCGAAGAGGAAGAATAACTT
1 GGATCAACATTTT-TATGG-AGAGTTCATAATGAGAAGAACTCATCTGATGAGGGAGAAAAAGTT
1175216 CATAATGAGAAGAACTTGTTCAAC
64 CATAATGAGAAGAACTTGTTCAAC
1175240 TTTTTGCTCG
Statistics
Matches: 195, Mismatches: 28, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
137 117 0.60
138 3 0.02
139 15 0.08
140 60 0.31
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (138 bp):
GGATCAACATTTTTATGGAGAGTTCATAATGAGAAGAACTCATCTGATGAGGGAGAAAAAGTTCA
TAATGAGAAGAACTTGTTCAACCTTAGCTCAATTCATCGCATATAGAGTTGAATCAGCGACCCCT
CAATCGAG
Found at i:1175308 original size:124 final size:124
Alignment explanation
Indices: 1175153--1175529 Score: 522
Period size: 124 Copynumber: 3.0 Consensus size: 124
1175143 CAATCGAGTG
* * * * * *
1175153 ATCAATATTTTCAATGGAATAGTTCATAATGAGAATAACTCATCCGAAGAGGAAGAATAACTTCA
1 ATCAACATTTCCAATGG-AGAGTTCATAATGAGAAGAACTCATCCGAAGAGGAAGAAGAAGTTCA
1175218 TAATGAGAAGAACTTGTTCAACTTTTTGCTCGACTCTATCGCAGAAGGAGATAGATCAAC
65 TAATGAGAAGAACTTGTTCAACTTTTTGCTCGACTCTATCGCAGAAGGAGATAGATCAAC
* * *
1175278 ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAATTCATCCGATGAGGGAGAAGAAGTTCAT
1 ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAGAGGAAGAAGAAGTTCAT
* * * *
1175343 AATGAGAAGAACTTGTTCAACCTTTTGCTCAACTCTATCGTAGAAGGATATAGATCAAC
66 AATGAGAAGAACTTGTTCAACTTTTTGCTCGACTCTATCGCAGAAGGAGATAGATCAAC
* * *
1175402 ATCAACATTTCCAATAGAGAGTTCATAATGAAAAGAACTCGTCC-AAGGAGGAAGAAGAAGTTCA
1 ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAA-GAGGAAGAAGAAGTTCA
* * * * * *
1175466 TAATAAGAAGAACTTGCTCAACATTTTTGTTTGATTCTATCACAGAAGGAGATAGATCAAC
65 TAATGAGAAGAACTTGTTCAAC-TTTTTGCTCGACTCTATCGCAGAAGGAGATAGATCAAC
1175527 ATC
1 ATC
1175530 GAAATTTTGC
Statistics
Matches: 221, Mismatches: 29, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
123 1 0.00
124 172 0.78
125 48 0.22
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.27
Consensus pattern (124 bp):
ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAGAGGAAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCAACTTTTTGCTCGACTCTATCGCAGAAGGAGATAGATCAAC
Found at i:1181560 original size:152 final size:155
Alignment explanation
Indices: 1181355--1181648 Score: 567
Period size: 152 Copynumber: 1.9 Consensus size: 155
1181345 ATTGGAATGG
1181355 TGTATCCTTTAATGATTGAGTTCCAAGCTCCTAGATCGTTGGCTTGAATGAAGAGCATCATCCTA
1 TGTATCCTTTAATGATTGAGTTCCAAGCTCCTAGATCGTTGGCTTGAATGAAGAGCATCATCCTA
1181420 TTCCTCCAATAGGCATAGTTTTC-CCATTGAAGTA-GGTGGCTTGTTGACTGGTTGTGAATC-TC
66 TTCCTCCAATAGGCATAGTTTTCTCCATTGAAGTAGGGTGGCTTGTTGACTGGTTGTGAATCTTC
1181482 AATGAAATAGGCGATGTGCATAGCC
131 AATGAAATAGGCGATGTGCATAGCC
1181507 TGTATCCTTTAATGATTGAGTTCCAAGCTCCTAGATCGTTGGCTTGAATGAAGAGCATCATCCTA
1 TGTATCCTTTAATGATTGAGTTCCAAGCTCCTAGATCGTTGGCTTGAATGAAGAGCATCATCCTA
1181572 TTCCTCCAATAGGCATAGTTTTCTCCATTGAAGTAGGGTGGCTTGTTGACTGGTTGTGAATCTTC
66 TTCCTCCAATAGGCATAGTTTTCTCCATTGAAGTAGGGTGGCTTGTTGACTGGTTGTGAATCTTC
1181637 AATGAAATAGGC
131 AATGAAATAGGC
1181649 ACCGGAGGTT
Statistics
Matches: 139, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
152 88 0.63
153 11 0.08
154 26 0.19
155 14 0.10
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.34
Consensus pattern (155 bp):
TGTATCCTTTAATGATTGAGTTCCAAGCTCCTAGATCGTTGGCTTGAATGAAGAGCATCATCCTA
TTCCTCCAATAGGCATAGTTTTCTCCATTGAAGTAGGGTGGCTTGTTGACTGGTTGTGAATCTTC
AATGAAATAGGCGATGTGCATAGCC
Found at i:1189463 original size:29 final size:29
Alignment explanation
Indices: 1189421--1189477 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
1189411 GCTAAAAAAT
* *
1189421 TTACATACATAACACACTCCTTTCATCTC
1 TTACACACACAACACACTCCTTTCATCTC
1189450 TTACACACACAACACACTCCTTTCATCT
1 TTACACACACAACACACTCCTTTCATCT
1189478 TCAATCTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.32, C:0.37, G:0.00, T:0.32
Consensus pattern (29 bp):
TTACACACACAACACACTCCTTTCATCTC
Found at i:1191607 original size:16 final size:18
Alignment explanation
Indices: 1191578--1191615 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
1191568 AATTAAAGAT
*
1191578 TTTTCATTTTTTTA-ATA
1 TTTTCATTTGTTTACATA
1191595 TTTT-ATTTGTTTACATA
1 TTTTCATTTGTTTACATA
1191612 TTTT
1 TTTT
1191616 TCAAAGTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.71
Consensus pattern (18 bp):
TTTTCATTTGTTTACATA
Found at i:1195638 original size:34 final size:34
Alignment explanation
Indices: 1195586--1195672 Score: 149
Period size: 34 Copynumber: 2.6 Consensus size: 34
1195576 TATATGTAAT
1195586 TAAAAATTATAAAAAGAAAAATAAAATATTATTA
1 TAAAAATTATAAAAAGAAAAATAAAATATTATTA
1195620 TGAAAAATTA-AAAAAGAAAAATAAAATATTATTA
1 T-AAAAATTATAAAAAGAAAAATAAAATATTATTA
*
1195654 TAAAAATTATAAAGAGAAA
1 TAAAAATTATAAAAAGAAA
1195673 GTATAAGGTT
Statistics
Matches: 50, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
33 8 0.16
34 34 0.68
35 8 0.16
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (34 bp):
TAAAAATTATAAAAAGAAAAATAAAATATTATTA
Found at i:1196117 original size:20 final size:19
Alignment explanation
Indices: 1196092--1196144 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
1196082 TGATTCAATC
*
1196092 AGTATCGATACCGAAGGGA
1 AGTATCGATACCAAAGGGA
*
1196111 GAGTATCGATAACAAAGGGA
1 -AGTATCGATACCAAAGGGA
*
1196131 AGGTGTCGATACCA
1 A-GTATCGATACCA
1196145 TTTCGAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.38, C:0.15, G:0.30, T:0.17
Consensus pattern (19 bp):
AGTATCGATACCAAAGGGA
Found at i:1196647 original size:55 final size:55
Alignment explanation
Indices: 1196558--1197640 Score: 995
Period size: 55 Copynumber: 19.9 Consensus size: 55
1196548 CTAAGTGTAC
* * *
1196558 TACAGGCACTATGTGTGCAAATCCATGGAATTCATCACGAGTTGATGACTAGCCG
1 TACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAGCCG
* * * *
1196613 TACATGCACTATGTTTGTAAATTCACGGAATTCATCATGAGTTGATGAATAGCCG
1 TACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAGCCG
* * * **
1196668 TACATGCACTATGTGTGCAATTCAACAAAATTCATCATGAGTTGATGAATAGCCG
1 TACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAGCCG
* *
1196723 TACAGGCACTATGTGTGCAAA-CTCACGAAATTCATCATGAGTTAATGAATAGCCG
1 TACAGGCACTATGTGTGCAAATC-CACGGAATTCATCATGAGTTGATGAATAGCCG
* * * * *
1196778 TACAGGCACTATATATGCAAATTCACGAAATTCATCATGAGTTGATGAATAGTCG
1 TACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAGCCG
* ** ** ***
1196833 TACATGCACTATGTGTATAAATCCACAAAATTCATCATGAGTTGATGAATAATTG
1 TACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAGCCG
* * *
1196888 TACCGGAACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAGTCG
1 TACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAGCCG
* * * ** *
1196943 TACCA-TCACTATGTATGCAAAACCATAGAATTCATCATGCA-TTGA--ATTA-CCG
1 TA-CAGGCACTATGTGTGCAAATCCACGGAATTCATCATG-AGTTGATGAATAGCCG
* * * ** * * * *
1196995 TATAGGTACTACT-TGTGCATTATAAT-AAATGAA-T-ATGAATAGAAAGTTGTTAAATTA-CCA
1 TACAGGCACTA-TGTGTGC---A-AATCCACGGAATTCAT-CAT-G--AGTTGATGAA-TAGCCG
* * * * * *
1197055 TATTA-GCACTAATG-ATGC--A---ACGG---T-AT-ATCAG-TAAT-AATTGTAC-
1 TA-CAGGCACT-ATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAG-CCG
* * *
1197098 TACAGACACTATGTGTGCAAATCCACGAAATTCATCATGAGTTAATGAATAGCCG
1 TACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAGCCG
* * * ** * *
1197153 TACAGACACTATGTGTGTAAATTCATAGAATTCGTCATGAGTTGATAAATAGCCG
1 TACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAGCCG
*
1197208 TACATGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAGCCG
1 TACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAGCCG
* * *
1197263 TATAGGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAGCCA
1 TACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAGCCG
* * * ** * *
1197318 TACAGGCATTATGTATGCAAATTCACAAAATTCATCATGAGTTGATGAATAGTCA
1 TACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAGCCG
* * * *
1197373 TACATGCACTATGTGTGCAAATTCACAGAATTCATCATGA---CATGAATAGCCCG
1 TACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAG-CCG
1197426 TACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAGCCG
1 TACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAGCCG
** *
1197481 TATTGGCACTATGTATGCAAATCCACGGAATTCATCATGAGTTGATGAATAGCCG
1 TACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAGCCG
* *
1197536 TACCA-ACACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAGCCG
1 TA-CAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAGCCG
* * * * * *
1197591 TACCGACACTATGTGTACAAAACCA-GAGTATTCATCATGAGGTGATGAAT
1 TACAGGCACTATGTGTGCAAATCCACG-GAATTCATCATGAGTTGATGAAT
1197641 TATCGTATAG
Statistics
Matches: 853, Mismatches: 131, Indels: 88
0.80 0.12 0.08
Matches are distributed among these distances:
42 5 0.01
43 11 0.01
44 3 0.00
45 3 0.00
48 5 0.01
50 3 0.00
51 2 0.00
52 24 0.03
53 48 0.06
54 11 0.01
55 704 0.83
56 13 0.02
57 3 0.00
59 1 0.00
60 14 0.02
61 3 0.00
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.29
Consensus pattern (55 bp):
TACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAGCCG
Found at i:1203660 original size:20 final size:19
Alignment explanation
Indices: 1203635--1203686 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
1203625 TGATTCAATC
*
1203635 AGTATCGATACCGTAGGGA
1 AGTATCGATACCGAAGGGA
*
1203654 GAGTATCGATGCCGAAGGGA
1 -AGTATCGATACCGAAGGGA
1203674 AGGTATCGATACC
1 A-GTATCGATACC
1203687 ATTTCGAAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.31, C:0.17, G:0.33, T:0.19
Consensus pattern (19 bp):
AGTATCGATACCGAAGGGA
Found at i:1204200 original size:55 final size:55
Alignment explanation
Indices: 1204114--1205202 Score: 998
Period size: 55 Copynumber: 20.0 Consensus size: 55
1204104 AGACACTCTA
* * *
1204114 TGTGCAAATCCACGGAATTCATCATGAGTTGATGACTAGCCGTACATGCACTATA
1 TGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAGCCGTACAGGCACTATG
* * *
1204169 TTTGCAAATTCACGGAATTCATCATGAGTTGATGAATAGCCGTACAGGAACTATG
1 TGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAGCCGTACAGGCACTATG
* * * *
1204224 TGTGCAAATCAACGAAATTCATCATGAGTTGTTGAATAGCCGTACAGACACTATG
1 TGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAGCCGTACAGGCACTATG
* * *
1204279 TGTGCAAA-CTCACGGAATTCATCATGAGTTAATGAATAGCTGTACAGGCACTATA
1 TGTGCAAATC-CACGGAATTCATCATGAGTTGATGAATAGCCGTACAGGCACTATG
* * * * *
1204334 TTTACAAATTCACGGAATTCATCATGAGTTGATGAATAGTCGTATAGGCACTATG
1 TGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAGCCGTACAGGCACTATG
* ** * * **
1204389 TGTGTAAATCCACAAAATTCATCATGAGTTTATTAATAGTTGTACCA-GCACTATG
1 TGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAGCCGTA-CAGGCACTATG
* * * *
1204444 TGTGCAAATTCACAGAATTTATCATGAGTTGATGAATAGTCGTACCA-GCACTATG
1 TGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAGCCGTA-CAGGCACTATG
* * *** *
1204499 TATGCAAAACCATATAATTCATCATGAGTT-A--AATTA-CCGTATAGGCACTACT-
1 TGTGCAAATCCACGGAATTCATCATGAGTTGATGAA-TAGCCGTACAGGCACTA-TG
* ** * ** * * *
1204551 TGTGCATTCTAAT-AAATGAA-T-ATGAATAGAAAGTTTTTAAATTA-CCATATTA-GCACTAAT
1 TGTGCA----AATCCACGGAATTCAT-CAT-G--AGTTGATGAA-TAGCCGTA-CAGGCACT-AT
1204611 G
55 G
* * * *** *
1204612 -GTGC-AAT----GGTA-T-ATCA-GTA-CTAAGTG--TA--C-TACAGATGCTCTG
1 TGTGCAAATCCACGGAATTCATCATG-AGTTGA-TGAATAGCCGTACAGGCACTATG
*
1204654 TGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAGCCGTACAGACACTATG
1 TGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAGCCGTACAGGCACTATG
* * *
1204709 TGTGCAAATTCACAGAATTCATCATGAGTTGATGAATAGTCGTACAGGCACTATG
1 TGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAGCCGTACAGGCACTATG
* * * *
1204764 TGTGCAAATCCACAGAATTCATCATTAGTTGATGAATAGTCGTATAGGCACTATG
1 TGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAGCCGTACAGGCACTATG
* * *
1204819 TGTGCATATCCACGGAATTCATCATGAGTTGATGAATAGCCGTGCATGCACTATG
1 TGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAGCCGTACAGGCACTATG
** ** * *
1204874 TGTGCAAATTAACAAAATTTATCATGAGTTGATGAATAGCCGTACAGGAACTATG
1 TGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAGCCGTACAGGCACTATG
*
1204929 TGTGCAAA-CTCACGGAATTCATCATGAGTTGATGAATAGCCCGTACATGCACTATG
1 TGTGCAAATC-CACGGAATTCATCATGAGTTGATGAATAG-CCGTACAGGCACTATG
* *
1204985 TGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAGACGTACCA-ACACTATG
1 TGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAGCCGTA-CAGGCACTATG
** * *
1205040 TGTGCAAATCCACATAATTCATCATGAGTTGATGAATAGCCGTACCGACACTATG
1 TGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAGCCGTACAGGCACTATG
* * * *
1205095 TGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACCGACACTATA
1 TGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAGCCGTACAGGCACTATG
* * * ** *
1205150 TATGTAAAACCACATAATTCATCATGAGTTGATGAATTA-CCGTATAGGCACTA
1 TGTGCAAATCCACGGAATTCATCATGAGTTGATGAA-TAGCCGTACAGGCACTA
1205203 CTTGTACATT
Statistics
Matches: 862, Mismatches: 129, Indels: 86
0.80 0.12 0.08
Matches are distributed among these distances:
42 3 0.00
43 8 0.01
44 4 0.00
45 2 0.00
47 1 0.00
48 5 0.01
49 2 0.00
50 7 0.01
51 5 0.01
52 24 0.03
53 5 0.01
54 7 0.01
55 704 0.82
56 58 0.07
57 5 0.01
60 19 0.02
61 3 0.00
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (55 bp):
TGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAGCCGTACAGGCACTATG
Found at i:1205176 original size:276 final size:275
Alignment explanation
Indices: 1204114--1205186 Score: 963
Period size: 276 Copynumber: 3.9 Consensus size: 275
1204104 AGACACTCTA
* * *
1204114 TGTGCAAATCCACGGAATTCATCATGAGTTGATGACTAGCCGTACATG-CACTATATTTGCAAAT
1 TGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAGCCGTACA-GACACTATGTGTGCAAAT
* * * *
1204178 TCACGGAATTCATCATGAGTTGATGAATAGCCGTACAGGA-ACTATGTGTGCAAATCAAC-GAAA
65 CCACAGAATTCATCATGAGTTGATGAATAGACGTACA-GACACTATGTGTGCAAATCCACAG-AA
*
1204241 TTCATCATGAGTTGTTGAATAGCCGTACAGACACTATGTGTGCAAA-CTCACGGAATTCATCATG
128 TTCATCATGAGTTGATGAATAGCCGTACAGACACTATGTGTGCAAATC-CACGGAATTCATCATG
* * * * * * * **
1204305 AGTTAATGAATAGCTGTACAGGCACTATATTTACAAATTC-ACGGAATTCATCATGAGTTGATGA
192 AGTTGATGAATAACCGTACACGCACTATATATGCAAA-ACAACAAAATTCATCATGAGTTGATGA
* * *
1204369 ATAGTCGTATAGGCACTATG
256 ATAGCCGTACAGGAACTATG
* ** * * **
1204389 TGTGTAAATCCACAAAATTCATCATGAGTTTATTAATAGTTGTACCAG-CACTATGTGTGCAAAT
1 TGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAGCCGTA-CAGACACTATGTGTGCAAAT
* * * * * * *
1204453 TCACAGAATTTATCATGAGTTGATGAATAGTCGTACCAG-CACTATGTATGCAAAACCATATAAT
65 CCACAGAATTCATCATGAGTTGATGAATAGACGTA-CAGACACTATGTGTGCAAATCCACAGAAT
* * * **
1204517 TCATCATGAGTT-A--AATTA-CCGTATAGGCACTACT-TGTGCATTCTAAT-AAATGAA-T-AT
129 TCATCATGAGTTGATGAA-TAGCCGTACAGACACTA-TGTGTGCA----AATCCACGGAATTCAT
* ** * * * * * **** * ** *
1204574 GAATAGAAAGTTTTTAAATTACCATATTA-GCACTA-ATGGTGCAATGGTATATCAGT-A-C-T-
188 -CAT-G--AGTTGATGAATAACCGTA-CACGCACTATAT-ATGCAAAACAACAAAATTCATCATG
* * *
1204633 A--AG-TG--TA--C-TACA-GATGCTCTG
247 AGTTGATGAATAGCCGTACAGGA-ACTATG
*
1204654 TGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAGCCGTACAGACACTATGTGTGCAAATT
1 TGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAGCCGTACAGACACTATGTGTGCAAATC
* *
1204719 CACAGAATTCATCATGAGTTGATGAATAGTCGTACAGGCACTATGTGTGCAAATCCACAGAATTC
66 CACAGAATTCATCATGAGTTGATGAATAGACGTACAGACACTATGTGTGCAAATCCACAGAATTC
* * * * *
1204784 ATCATTAGTTGATGAATAGTCGTATAGGCACTATGTGTGCATATCCACGGAATTCATCATGAGTT
131 ATCATGAGTTGATGAATAGCCGTACAGACACTATGTGTGCAAATCCACGGAATTCATCATGAGTT
* * * * * ** *
1204849 GATGAATAGCCGTGCATGCACTATGTGTGCAAATTAACAAAATTTATCATGAGTTGATGAATAGC
196 GATGAATAACCGTACACGCACTATATATGCAAAACAACAAAATTCATCATGAGTTGATGAATAGC
1204914 CGTACAGGAACTATG
261 CGTACAGGAACTATG
1204929 TGTGCAAA-CTCACGGAATTCATCATGAGTTGATGAATAGCCCGTACATG-CACTATGTGTGCAA
1 TGTGCAAATC-CACGGAATTCATCATGAGTTGATGAATAG-CCGTACA-GACACTATGTGTGCAA
* *
1204992 ATCCACGGAATTCATCATGAGTTGATGAATAGACGTACCA-ACACTATGTGTGCAAATCCACATA
63 ATCCACAGAATTCATCATGAGTTGATGAATAGACGTA-CAGACACTATGTGTGCAAATCCACAGA
*
1205056 ATTCATCATGAGTTGATGAATAGCCGTACCGACACTATGTGTGCAAATCCACGGAATTCATCATG
127 ATTCATCATGAGTTGATGAATAGCCGTACAGACACTATGTGTGCAAATCCACGGAATTCATCATG
* * *
1205121 AGTTGATGAATAACCGTAC-CGACACTATATATGTAAAACCACATAATTCATCATGAGTTGATGA
192 AGTTGATGAATAACCGTACACG-CACTATATATGCAAAACAACAAAATTCATCATGAGTTGATGA
1205185 AT
256 AT
1205187 TACCGTATAG
Statistics
Matches: 640, Mismatches: 109, Indels: 97
0.76 0.13 0.11
Matches are distributed among these distances:
262 1 0.00
263 27 0.04
264 11 0.02
265 132 0.21
266 6 0.01
267 6 0.01
268 23 0.04
269 1 0.00
270 4 0.01
271 1 0.00
272 22 0.03
273 6 0.01
274 6 0.01
275 166 0.26
276 200 0.31
277 27 0.04
278 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (275 bp):
TGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAGCCGTACAGACACTATGTGTGCAAATC
CACAGAATTCATCATGAGTTGATGAATAGACGTACAGACACTATGTGTGCAAATCCACAGAATTC
ATCATGAGTTGATGAATAGCCGTACAGACACTATGTGTGCAAATCCACGGAATTCATCATGAGTT
GATGAATAACCGTACACGCACTATATATGCAAAACAACAAAATTCATCATGAGTTGATGAATAGC
CGTACAGGAACTATG
Found at i:1208095 original size:44 final size:44
Alignment explanation
Indices: 1208047--1208139 Score: 134
Period size: 44 Copynumber: 2.1 Consensus size: 44
1208037 GTAACCATGC
* * *
1208047 AAATAAGCTTACGAGCTTATGGAAT-AATAGTAAGTATATTGGTA
1 AAATAAGCTTACAAGCTTATGAAATAAATAGCAAGTATA-TGGTA
*
1208091 AAATAAGCTTACAAGCTTATGAAATAAATGGCAAGTATATGGTA
1 AAATAAGCTTACAAGCTTATGAAATAAATAGCAAGTATATGGTA
1208135 AAATA
1 AAATA
1208140 TTGGATATGC
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 33 0.75
45 11 0.25
ACGTcount: A:0.45, C:0.08, G:0.18, T:0.29
Consensus pattern (44 bp):
AAATAAGCTTACAAGCTTATGAAATAAATAGCAAGTATATGGTA
Found at i:1210128 original size:12 final size:12
Alignment explanation
Indices: 1210113--1210141 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
1210103 TTAATTTAAA
1210113 TTTTAGTGTAAT
1 TTTTAGTGTAAT
1210125 TTTTAGTGTAAT
1 TTTTAGTGTAAT
1210137 TTTTA
1 TTTTA
1210142 TTTTTATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.14, T:0.62
Consensus pattern (12 bp):
TTTTAGTGTAAT
Found at i:1210388 original size:111 final size:105
Alignment explanation
Indices: 1210253--1210727 Score: 358
Period size: 111 Copynumber: 4.3 Consensus size: 105
1210243 TTTTATTGAG
* * *
1210253 ATAAATTATTAAACTAATTATTTTTATTTTACAGATTAAATCGTATTTGAGTGGTTTGGTAAGTT
1 ATAAATTATT-AACTATTTATTTTTATTTTACATATTAAATCGTATTTGAGTGGTTTGATAAGTT
* *
1210318 TAGTTTAAAATTAATTATTTAGGGTTTAGGGTTTTCATTTAAAT
65 TAGTTTAAAATTAATTATTTA--GTTTA-GTTTTTAATTTAAAT
* * *
1210362 AATAAATTAATTACACTATTTATTTTTATTTTAAATATTAAACCGTATTCGAGTGGTTTGATAAG
1 -ATAAATT-ATTA-ACTATTTATTTTTATTTTACATATTAAATCGTATTTGAGTGGTTTGATAAG
* * *
1210427 TTTAATTTAAATTTTCGTGTAATT-TTTAGTATAATTTTTGTTTTTAATTTAAAT
63 TTTAGTTTAAA-----AT-TAATTATTTAG------TTTAGTTTTTAATTTAAAT
* * * *
1210481 -TATAATTATTAGACTATTTATTTTTGATTTTACATATTAAGTTGTATTTGAGTAGTTTCATAAG
1 ATA-AATTATTA-ACTATTTATTTTT-ATTTTACATATTAAATCGTATTTGAGTGGTTTGATAAG
* * *
1210545 TTTAGTTT-AAACT-A-TATTT--TTTA-TTTTTTATTGAGTAAT
63 TTTAGTTTAAAATTAATTATTTAGTTTAGTTTTTAATTTA--AAT
* * *
1210584 ATAAATTATTGATCTATTTATTTTGATTTTACATATTAAATCGTATTTGAGTGGTTTGGTAAGTT
1 ATAAATTATT-AACTATTTATTTTTATTTTACATATTAAATCGTATTTGAGTGGTTTGATAAGTT
* * * * *
1210649 TAGTTTAAATTTTATTGCTTT-TTTTTGTTTTT-ATTGTAAAT
65 TAGTTTAAAATTAATT-ATTTAGTTTAGTTTTTAATT-TAAAT
* * *
1210690 ATAATTTAATTAGACTATTTATTTTGATTTAACATATT
1 ATAAATT-ATTA-ACTATTTATTTTTATTTTACATATT
1210728 TTTTGTTTAA
Statistics
Matches: 295, Mismatches: 40, Indels: 63
0.74 0.10 0.16
Matches are distributed among these distances:
101 9 0.03
102 44 0.15
103 24 0.08
104 4 0.01
105 1 0.00
106 13 0.04
107 32 0.11
108 6 0.02
109 1 0.00
110 12 0.04
111 59 0.20
114 1 0.00
116 5 0.02
117 26 0.09
118 42 0.14
119 13 0.04
120 3 0.01
ACGTcount: A:0.31, C:0.04, G:0.11, T:0.53
Consensus pattern (105 bp):
ATAAATTATTAACTATTTATTTTTATTTTACATATTAAATCGTATTTGAGTGGTTTGATAAGTTT
AGTTTAAAATTAATTATTTAGTTTAGTTTTTAATTTAAAT
Found at i:1210725 original size:107 final size:101
Alignment explanation
Indices: 1210461--1210727 Score: 308
Period size: 102 Copynumber: 2.6 Consensus size: 101
1210451 TTTAGTATAA
* *
1210461 TTTTTGTTTTTAATT-TAAATTATAATTATTAGACTATTTATTTTTGATTTTACATATTAAGTTG
1 TTTTTGTTTTT-ATTGTAAA-TATAATTATTAGACTATTTA-TTTTGATTTTACATATTAAATCG
1210525 TATTTGAGTAGTTTCATAAGTTTAGTTTAAACTATATTT
63 TATTTGAGTAGTTTCATAAGTTTAGTTTAAACTATATTT
*
1210564 TTTAT-TTTTTATTG-AGTAATATAAATTATT-GATCTATTTATTTTGATTTTACATATTAAATC
1 TTTTTGTTTTTATTGTA--AATAT-AATTATTAGA-CTATTTATTTTGATTTTACATATTAAATC
* ** * *
1210626 GTATTTGAGTGGTTTGGTAAGTTTAGTTTAAATTTTATTGCTTT
62 GTATTTGAGTAGTTTCATAAGTTTAGTTTAAA--CTA-T-ATTT
*
1210670 TTTTTGTTTTTATTGTAAATATAATTTAATTAGACTATTTATTTTGATTTAACATATT
1 TTTTTGTTTTTATTGTAAATATAA-TT-ATTAGACTATTTATTTTGATTTTACATATT
1210728 TTTTGTTTAA
Statistics
Matches: 140, Mismatches: 10, Indels: 24
0.80 0.06 0.14
Matches are distributed among these distances:
101 4 0.03
102 59 0.42
103 20 0.14
104 2 0.01
105 3 0.02
106 14 0.10
107 35 0.25
108 3 0.02
ACGTcount: A:0.29, C:0.04, G:0.10, T:0.57
Consensus pattern (101 bp):
TTTTTGTTTTTATTGTAAATATAATTATTAGACTATTTATTTTGATTTTACATATTAAATCGTAT
TTGAGTAGTTTCATAAGTTTAGTTTAAACTATATTT
Found at i:1212816 original size:27 final size:27
Alignment explanation
Indices: 1212766--1212848 Score: 94
Period size: 27 Copynumber: 3.1 Consensus size: 27
1212756 TGAAACTAAG
** *
1212766 ATTAATATCCATCACATTCCTTCAAAT
1 ATTAATATTAATCACATTCATTCAAAT
* *
1212793 ATTAATATTAATCACATTAATTCAACT
1 ATTAATATTAATCACATTCATTCAAAT
* * *
1212820 ATTGATATTAATTACATTCATTAAAAT
1 ATTAATATTAATCACATTCATTCAAAT
1212847 AT
1 AT
1212849 AGCGTCAACA
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.42, C:0.16, G:0.01, T:0.41
Consensus pattern (27 bp):
ATTAATATTAATCACATTCATTCAAAT
Found at i:1213859 original size:22 final size:23
Alignment explanation
Indices: 1213816--1213867 Score: 54
Period size: 22 Copynumber: 2.3 Consensus size: 23
1213806 TAATGGTGCC
*
1213816 ATTATTTTCATCGTTATAATAAAT
1 ATTATTTT-ATCGTCATAATAAAT
* *
1213840 ATTATTTT-TCGTCATTATAATT
1 ATTATTTTATCGTCATAATAAAT
1213862 A-TATTT
1 ATTATTT
1213868 CTTAACATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 5 0.20
22 12 0.48
24 8 0.32
ACGTcount: A:0.33, C:0.08, G:0.04, T:0.56
Consensus pattern (23 bp):
ATTATTTTATCGTCATAATAAAT
Found at i:1215564 original size:17 final size:17
Alignment explanation
Indices: 1215542--1215576 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1215532 AAGATATAGG
1215542 TCCGCTACAACAGGACC
1 TCCGCTACAACAGGACC
1215559 TCCGCTACAACAGGACC
1 TCCGCTACAACAGGACC
1215576 T
1 T
1215577 TCTCGGCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.40, G:0.17, T:0.14
Consensus pattern (17 bp):
TCCGCTACAACAGGACC
Found at i:1227147 original size:14 final size:14
Alignment explanation
Indices: 1227129--1227158 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1227119 AATATACTTA
1227129 ATTTTTA-ATTATG
1 ATTTTTATATTATG
1227142 ATTTTTATATTATG
1 ATTTTTATATTATG
1227156 ATT
1 ATT
1227159 CTTGTGTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (14 bp):
ATTTTTATATTATG
Found at i:1227336 original size:18 final size:18
Alignment explanation
Indices: 1227313--1227453 Score: 112
Period size: 18 Copynumber: 7.9 Consensus size: 18
1227303 ATTAAAGAAC
*
1227313 TATATAATATATAGTTTA
1 TATATACTATATAGTTTA
*
1227331 TATATACTA-ATGAATTATA
1 TATATACTATAT-AGTT-TA
* *
1227350 TAATATACCATATAATTTA
1 T-ATATACTATATAGTTTA
*
1227369 TATATATTATATAGTTTA
1 TATATACTATATAGTTTA
* *
1227387 CATATACTA-AT-G--AA
1 TATATACTATATAGTTTA
* *
1227401 CTATATAATATATACTTTA
1 -TATATACTATATAGTTTA
*
1227420 TATATACTATACAGTTTA
1 TATATACTATATAGTTTA
*
1227438 TATATATTATATAGTT
1 TATATACTATATAGTT
1227454 AGAATAAATT
Statistics
Matches: 96, Mismatches: 18, Indels: 18
0.73 0.14 0.14
Matches are distributed among these distances:
14 1 0.01
15 7 0.07
16 3 0.03
17 4 0.04
18 61 0.64
19 7 0.07
20 11 0.11
21 2 0.02
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.46
Consensus pattern (18 bp):
TATATACTATATAGTTTA
Found at i:1227380 original size:56 final size:51
Alignment explanation
Indices: 1227313--1227443 Score: 163
Period size: 56 Copynumber: 2.5 Consensus size: 51
1227303 ATTAAAGAAC
*
1227313 TATATAATATATAGTTTATATATACTAATGAATTATATAATATACCATATAATTTA
1 TATATAATATATAGTTTATATATACTAATGAACTATAT-A-AT---ATATAATTTA
* * *
1227369 TATATATTATATAGTTTACATATACTAATGAACTATATAATATATACTTTA
1 TATATAATATATAGTTTATATATACTAATGAACTATATAATATATAATTTA
* *
1227420 TATATACTATACAGTTTATATATA
1 TATATAATATATAGTTTATATATA
1227444 TTATATAGTT
Statistics
Matches: 68, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
51 30 0.44
54 2 0.03
55 1 0.01
56 35 0.51
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (51 bp):
TATATAATATATAGTTTATATATACTAATGAACTATATAATATATAATTTA
Found at i:1228328 original size:112 final size:112
Alignment explanation
Indices: 1228172--1228858 Score: 1115
Period size: 112 Copynumber: 6.1 Consensus size: 112
1228162 TTGTCGGTTT
* ** ** *
1228172 GTGTCGATATTTTATAAAAAAAATATTAATCCATAACAATATAACAGGTAAAAAAATGATAAAAC
1 GTGTCGATACTTTAT-AAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAAC
* * *
1228237 CGGTCTATAAATGAAAAAATAGGTAAAGCGCTATCGGATATATTGAAA
65 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
1228285 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* *
1228350 GGTCTATAAATGACAAAACAGATAAAGCGCTATCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* * *
1228397 GTGTCTATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTCAAAAAATGATAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
*
1228462 GGTCTATAAATGACAAAACATGTAAAGCGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
1228509 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGT-TAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
*
1228573 GGTCTATAAATGAAAAAACAGGTAAAGCGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
1228620 GTGTCGATACTTTATAAAAATGTGTCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* *
1228685 GGTCTATAAATGACAAAACAAGTAAAGTGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* *
1228732 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAAAATGACAAAATC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* * * * *
1228797 GGTCTATAAATGACAAAACATGTAAAGCGCTATCGGATGTGTTGATA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
1228844 GTGTCGATACTTTAT
1 GTGTCGATACTTTAT
1228859 TATAAGTATC
Statistics
Matches: 539, Mismatches: 34, Indels: 3
0.94 0.06 0.01
Matches are distributed among these distances:
111 106 0.20
112 419 0.78
113 14 0.03
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.26
Consensus pattern (112 bp):
GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
Found at i:1228675 original size:223 final size:224
Alignment explanation
Indices: 1228172--1228858 Score: 1133
Period size: 223 Copynumber: 3.1 Consensus size: 224
1228162 TTGTCGGTTT
* ** **
1228172 GTGTCGATATTTTATAAAAAAAATATTAATCCATAACAATATAACAGGTAAAAAAATGATAAAAC
1 GTGTCGATACTTTAT-AAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGATAAAAC
* * * *
1228237 CGGTCTATAAATGAAAAAATAGGTAAAGCGCTATCGGATATATTGAAAGTGTCGATACTTTATAA
65 CGGTCTATAAATGACAAAACAAGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAA
1228302 AAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGTCTATAAATGACAAA
130 AAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGTCTATAAATGACAAA
*
1228367 ACAGATAAAGCGCTATCGGATATATTGAAA
195 ACAGGTAAAGCGCTATCGGATATATTGAAA
* *
1228397 GTGTCTATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTCAAAAAATGATAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGATAAAACC
*
1228462 GGTCTATAAATGACAAAACATGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAA
66 GGTCTATAAATGACAAAACAAGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAA
* *
1228527 AATGTATCGATCCATAACAATATAACAGGT-TAAAAATGACAAAACCGGTCTATAAATGAAAAAA
131 AATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGTCTATAAATGACAAAA
*
1228591 CAGGTAAAGCGCTACCGGATATATTGAAA
196 CAGGTAAAGCGCTATCGGATATATTGAAA
* *
1228620 GTGTCGATACTTTATAAAAATGTGTCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGATAAAACC
*
1228685 GGTCTATAAATGACAAAACAAGTAAAGTGCTACCGGATATATTGAAAGTGTCGATACTTTATAAA
66 GGTCTATAAATGACAAAACAAGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAA
* *
1228750 AATGTATCGATCCATAACAATATAACATGTAAAAAAATGACAAAATCGGTCTATAAATGACAAAA
131 AATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGTCTATAAATGACAAAA
* * * *
1228815 CATGTAAAGCGCTATCGGATGTGTTGATA
196 CAGGTAAAGCGCTATCGGATATATTGAAA
1228844 GTGTCGATACTTTAT
1 GTGTCGATACTTTAT
1228859 TATAAGTATC
Statistics
Matches: 431, Mismatches: 30, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
223 212 0.49
224 206 0.48
225 13 0.03
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.26
Consensus pattern (224 bp):
GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGATAAAACC
GGTCTATAAATGACAAAACAAGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAA
AATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGTCTATAAATGACAAAA
CAGGTAAAGCGCTATCGGATATATTGAAA
Found at i:1228849 original size:335 final size:337
Alignment explanation
Indices: 1228172--1228858 Score: 1155
Period size: 335 Copynumber: 2.0 Consensus size: 337
1228162 TTGTCGGTTT
* * *
1228172 GTGTCGATATTTTATAAAAAAAATATTAATCCATAACAATATAACAGGTAAAAAAATGATAAAAC
1 GTGTCGATACTTTATAAAAAAAATATCAATCCATAACAATATAACAGGTAAAAAAATGACAAAAC
* *
1228237 CGGTCTATAAATGAAAAAATAGGTAAAGCGCTATCGGATATATTGAAAGTGTCGATACTTTATAA
66 CGGTCTATAAATGAAAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAA
1228302 AAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGTCTATAAATGACAAA
131 AAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGTCTATAAATGACAAA
* *
1228367 ACAGATAAAGCGCTATCGGATATATTGAAAGTGTCTATACTTTATAAAAATGTATCGATCCATAA
196 ACAGATAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAA
* *
1228432 CAATATAACAGGTCAAAAAATGATAAAACCGGTCTATAAATGACAAAACATGTAAAGCGCTACCG
261 CAATATAACAGGTAAAAAAATGACAAAACCGGTCTATAAATGACAAAACATGTAAAGCGCTACCG
1228497 GATATATTGAAA
326 GATATATTGAAA
** * *
1228509 GTGTCGATACTTTAT-AAAAATGTATCGATCCATAACAATATAACAGGT-TAAAAATGACAAAAC
1 GTGTCGATACTTTATAAAAAAAATATCAATCCATAACAATATAACAGGTAAAAAAATGACAAAAC
1228572 CGGTCTATAAATGAAAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAA
66 CGGTCTATAAATGAAAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAA
*
1228637 AAATGTGTCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGTCTATAAATGACAAA
131 AAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGTCTATAAATGACAAA
*
1228702 ACA-AGTAAAGTGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAAATGTATCGATCCATA
196 ACAGA-TAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAAATGTATCGATCCATA
* * *
1228766 ACAATATAACATGTAAAAAAATGACAAAATCGGTCTATAAATGACAAAACATGTAAAGCGCTATC
260 ACAATATAACAGGTAAAAAAATGACAAAACCGGTCTATAAATGACAAAACATGTAAAGCGCTACC
* * *
1228831 GGATGTGTTGATA
325 GGATATATTGAAA
1228844 GTGTCGATACTTTAT
1 GTGTCGATACTTTAT
1228859 TATAAGTATC
Statistics
Matches: 328, Mismatches: 21, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
334 1 0.00
335 284 0.87
336 29 0.09
337 14 0.04
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.26
Consensus pattern (337 bp):
GTGTCGATACTTTATAAAAAAAATATCAATCCATAACAATATAACAGGTAAAAAAATGACAAAAC
CGGTCTATAAATGAAAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAA
AAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGTCTATAAATGACAAA
ACAGATAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAA
CAATATAACAGGTAAAAAAATGACAAAACCGGTCTATAAATGACAAAACATGTAAAGCGCTACCG
GATATATTGAAA
Found at i:1229615 original size:35 final size:35
Alignment explanation
Indices: 1229544--1229616 Score: 85
Period size: 35 Copynumber: 2.1 Consensus size: 35
1229534 ACACATCATA
* **
1229544 TAAGGCTCTGAGCACAAAGCCGAGAGACCGGTAAG
1 TAAGGCCCTGAGCACAAAGCCGAGAGACCGCCAAG
* *
1229579 TAAGGCCCTGAGCACACAGCCGAG-GAACCTCCAAG
1 TAAGGCCCTGAGCACAAAGCCGAGAG-ACCGCCAAG
1229614 TAA
1 TAA
1229617 TCTTCCTCCA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
34 1 0.03
35 31 0.97
ACGTcount: A:0.34, C:0.27, G:0.27, T:0.11
Consensus pattern (35 bp):
TAAGGCCCTGAGCACAAAGCCGAGAGACCGCCAAG
Found at i:1229725 original size:23 final size:23
Alignment explanation
Indices: 1229691--1229774 Score: 98
Period size: 23 Copynumber: 3.6 Consensus size: 23
1229681 AAACATAATT
*
1229691 CAAGTCAAGTATCATATCA-AATC
1 CAAGTC-AGTATCAGATCAGAATC
1229714 CAAGTCATGTATCAGATCAGAATC
1 CAAGTCA-GTATCAGATCAGAATC
* *
1229738 CATGTCAATATCAGATCAGAATC
1 CAAGTCAGTATCAGATCAGAATC
*
1229761 CAGGTCAGGTATCA
1 CAAGTCA-GTATCA
1229775 TAACAAAATT
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
22 1 0.02
23 37 0.70
24 15 0.28
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.25
Consensus pattern (23 bp):
CAAGTCAGTATCAGATCAGAATC
Found at i:1232277 original size:27 final size:28
Alignment explanation
Indices: 1232230--1232283 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
1232220 TCAAAGTTTT
1232230 GGTCAACAGTGGTCAATGTC-GGTCAAC
1 GGTCAACAGTGGTCAATGTCGGGTCAAC
1232257 GGTCAAC-G-GGTCAATGGGTCGGGTCAA
1 GGTCAACAGTGGTCAAT--GTCGGGTCAA
1232284 GTAAACGGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
25 7 0.29
26 1 0.04
27 10 0.42
28 6 0.25
ACGTcount: A:0.24, C:0.20, G:0.35, T:0.20
Consensus pattern (28 bp):
GGTCAACAGTGGTCAATGTCGGGTCAAC
Found at i:1234034 original size:15 final size:15
Alignment explanation
Indices: 1234014--1234042 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1234004 TGGCCGACCG
1234014 AACCGAATTAACCAT
1 AACCGAATTAACCAT
1234029 AACCGAATTAACCA
1 AACCGAATTAACCA
1234043 AACTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.28, G:0.07, T:0.17
Consensus pattern (15 bp):
AACCGAATTAACCAT
Found at i:1234387 original size:175 final size:173
Alignment explanation
Indices: 1234159--1234476 Score: 464
Period size: 175 Copynumber: 1.8 Consensus size: 173
1234149 ATTTTCTAAT
* *
1234159 TTATATAAAATTAAATATTTTTAATTCAAAAAAGTTTATAATTAATTTAAATAATAAATAATTAT
1 TTATATAAAATTAAATATTTTTAATTCAAAAAAATTTACAATTAATTTAAATAATAAATAATTAT
*
1234224 AAA-ATAAAATTTTAGATAAATTTTTTAATTAA-T-TATTGATTTAAGTTTAAAAGTTATTGGAT
66 AAATA-AAAAATTTAGAT-AATTTTTTAATTAATTATATTGATTTAAGTTTAAAA-TTATTGGAT
* *
1234286 TTTAAATTATTAATTGGTTTTAAATGGTTTGGGCTTAGCCCATATG
128 CTTAAAGTATTAATTGGTTTTAAATGGTTTGGGCTTAGCCCATATG
* * *
1234332 TTATATATATATTTAATATTTTTTAATT-AAAAACAATTTACAATTAATTTAAATAATATATAAT
1 TTATATA-AAATTAAATA-TTTTTAATTCAAAAA-AATTTACAATTAATTTAAATAATAAATAAT
*
1234396 TATAAATAAAAAATTTATATAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAATTATTGGA
63 TATAAATAAAAAATTTAGATAATTTTTTAATTAATT-ATATTGATTTAAGTTTAAAATTATTGGA
1234461 TCTTAAAGTATTAATT
127 TCTTAAAGTATTAATT
1234477 AGATTTTTAT
Statistics
Matches: 129, Mismatches: 9, Indels: 11
0.87 0.06 0.07
Matches are distributed among these distances:
173 7 0.05
174 27 0.21
175 53 0.41
176 23 0.18
177 19 0.15
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.47
Consensus pattern (173 bp):
TTATATAAAATTAAATATTTTTAATTCAAAAAAATTTACAATTAATTTAAATAATAAATAATTAT
AAATAAAAAATTTAGATAATTTTTTAATTAATTATATTGATTTAAGTTTAAAATTATTGGATCTT
AAAGTATTAATTGGTTTTAAATGGTTTGGGCTTAGCCCATATG
Found at i:1234977 original size:17 final size:18
Alignment explanation
Indices: 1234955--1234997 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
1234945 TTTTACTGAA
1234955 AATATTTTCTAAAAA-AC
1 AATATTTTCTAAAAATAC
* *
1234972 AATATTTTTTAAAAATAT
1 AATATTTTCTAAAAATAC
1234990 AATATTTT
1 AATATTTT
1234998 ATTATATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (18 bp):
AATATTTTCTAAAAATAC
Found at i:1240276 original size:2 final size:2
Alignment explanation
Indices: 1240269--1240306 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1240259 TGATTTTCTT
1240269 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1240307 AAACTATTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1240932 original size:29 final size:29
Alignment explanation
Indices: 1240863--1240923 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
1240853 ATTTCTAACG
* * *
1240863 TTTGATCAAGTAGTCATTTTGGCTCATGT
1 TTTGATTAAGTAATCATTTTGGCTCATAT
1240892 TTTGATTAAGTAATCATTTTGGCTCATAT
1 TTTGATTAAGTAATCATTTTGGCTCATAT
1240921 TTT
1 TTT
1240924 TTTAAAGTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.23, C:0.11, G:0.16, T:0.49
Consensus pattern (29 bp):
TTTGATTAAGTAATCATTTTGGCTCATAT
Found at i:1242685 original size:11 final size:11
Alignment explanation
Indices: 1242671--1242713 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
1242661 GAAAAGCATT
1242671 AAAAAAAGAAG
1 AAAAAAAGAAG
* *
1242682 AAAAAATGAAC
1 AAAAAAAGAAG
1242693 AAAAAAAGAGAGG
1 AAAAAAAGA-A-G
1242706 AAAAAAAG
1 AAAAAAAG
1242714 TGCATCTCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
11 17 0.65
12 1 0.04
13 8 0.31
ACGTcount: A:0.77, C:0.02, G:0.19, T:0.02
Consensus pattern (11 bp):
AAAAAAAGAAG
Found at i:1243477 original size:3 final size:3
Alignment explanation
Indices: 1243465--1243493 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1243455 TTTTAGTTTG
1243465 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1243494 TATTTATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1244182 original size:17 final size:17
Alignment explanation
Indices: 1244162--1244196 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1244152 TTTCATTATA
*
1244162 TTTTATTCGTTATTTAC
1 TTTTATTAGTTATTTAC
*
1244179 TTTTATTATTTATTTAC
1 TTTTATTAGTTATTTAC
1244196 T
1 T
1244197 ATCATTATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.20, C:0.09, G:0.03, T:0.69
Consensus pattern (17 bp):
TTTTATTAGTTATTTAC
Found at i:1244203 original size:17 final size:17
Alignment explanation
Indices: 1244171--1244206 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1244161 ATTTTATTCG
* *
1244171 TTATTTACTTTTATTAT
1 TTATTTACTATCATTAT
1244188 TTATTTACTATCATTAT
1 TTATTTACTATCATTAT
1244205 TT
1 TT
1244207 CTAAATCTCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.25, C:0.08, G:0.00, T:0.67
Consensus pattern (17 bp):
TTATTTACTATCATTAT
Found at i:1244745 original size:22 final size:22
Alignment explanation
Indices: 1244702--1244769 Score: 59
Period size: 22 Copynumber: 3.0 Consensus size: 22
1244692 CAAAATATTA
* *
1244702 ATTATTAAAATATTTAAAAATAT
1 ATTATTAATAT-TTTAATAATAT
1244725 -TTATTAATATTTCTAATAATAT
1 ATTATTAATATTT-TAATAATAT
* *
1244747 AATATT-ATATTTTTAATATTAT
1 ATTATTAATA-TTTTAATAATAT
1244769 A
1 A
1244770 ATAAAATAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
21 2 0.05
22 29 0.76
23 7 0.18
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (22 bp):
ATTATTAATATTTTAATAATAT
Found at i:1244770 original size:22 final size:23
Alignment explanation
Indices: 1244726--1244772 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
1244716 TAAAAATATT
1244726 TATTAATATTTCTAATAATATAA
1 TATTAATATTTCTAATAATATAA
* *
1244749 TATT-ATATTTTTAATATTATAA
1 TATTAATATTTCTAATAATATAA
1244771 TA
1 TA
1244773 AAATAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TATTAATATTTCTAATAATATAA
Found at i:1244811 original size:23 final size:23
Alignment explanation
Indices: 1244762--1244815 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
1244752 TATATTTTTA
**
1244762 ATATTATAATAAAATAATCAATT
1 ATATTATAATAAAATAATCAAAG
*
1244785 ATATTATAATAATATAAT-ATAAG
1 ATATTATAATAAAATAATCA-AAG
1244808 ATATTATA
1 ATATTATA
1244816 TTATATTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 1 0.04
23 26 0.96
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (23 bp):
ATATTATAATAAAATAATCAAAG
Found at i:1244936 original size:27 final size:27
Alignment explanation
Indices: 1244858--1244936 Score: 74
Period size: 27 Copynumber: 2.9 Consensus size: 27
1244848 TAAAATTTAA
* *
1244858 ATTATTTAT-TAATTTCATAGAAATAAT
1 ATTATTTATAT-ATTTAATAGTAATAAT
* *
1244885 ATTA-TTAAAT-TATTAATAATGAATAAT
1 ATTATTTATATAT-TTAATAGT-AATAAT
1244912 ATTATTTATATATTTAATAGTAATA
1 ATTATTTATATATTTAATAGTAATA
1244937 TAATAATATA
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
25 1 0.02
26 8 0.20
27 19 0.46
28 12 0.29
29 1 0.02
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (27 bp):
ATTATTTATATATTTAATAGTAATAAT
Found at i:1244983 original size:39 final size:42
Alignment explanation
Indices: 1244896--1244984 Score: 98
Period size: 39 Copynumber: 2.2 Consensus size: 42
1244886 TTATTAAATT
* * *
1244896 ATTAATAATGAATAATATTATTTATATATTTAATAGTAATATA
1 ATTAAT-ATGAATAATATTATTAAGATATTTAATAATAATATA
1244939 A-TAATAT-AATAATATT-TTAAGATATTTAA-AAT-ATACTA
1 ATTAATATGAATAATATTATTAAGATATTTAATAATAATA-TA
1244977 ATTAATAT
1 ATTAATAT
1244985 TTTTAAAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
37 3 0.07
38 5 0.12
39 17 0.41
40 9 0.22
41 2 0.05
42 4 0.10
43 1 0.02
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (42 bp):
ATTAATATGAATAATATTATTAAGATATTTAATAATAATATA
Found at i:1245074 original size:33 final size:29
Alignment explanation
Indices: 1245035--1245115 Score: 92
Period size: 28 Copynumber: 2.7 Consensus size: 29
1245025 AATATAATTT
*
1245035 ATAATATTTTTATTTCAATAAAATATATCAATA
1 ATAATATTTTTA-TT-AATAAAAT-TAT-AAAA
*
1245068 TTAATATTTTTATTAATAAAATTATAAAA
1 ATAATATTTTTATTAATAAAATTATAAAA
*
1245097 ATAATA-TTTTAATAATAAA
1 ATAATATTTTTATTAATAAA
1245116 TAAATTATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
28 12 0.27
29 8 0.18
30 3 0.07
31 8 0.18
32 2 0.05
33 11 0.25
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (29 bp):
ATAATATTTTTATTAATAAAATTATAAAA
Found at i:1245113 original size:14 final size:14
Alignment explanation
Indices: 1245045--1245114 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 14
1245035 ATAATATTTT
*
1245045 TATTTCAATAA-AA
1 TATTTTAATAATAA
* * *
1245058 TATATCAATATTAA
1 TATTTTAATAATAA
*
1245072 TATTTTTATTAATAA
1 TA-TTTTAATAATAA
* * *
1245087 AATTATAAAAATAA
1 TATTTTAATAATAA
1245101 TATTTTAATAATAA
1 TATTTTAATAATAA
1245115 ATAAATTATT
Statistics
Matches: 42, Mismatches: 13, Indels: 3
0.72 0.22 0.05
Matches are distributed among these distances:
13 9 0.21
14 24 0.57
15 9 0.21
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (14 bp):
TATTTTAATAATAA
Found at i:1245282 original size:19 final size:21
Alignment explanation
Indices: 1245260--1245298 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
1245250 TCTAAATATC
1245260 ATAATTC-TTTT-TAAAAAAT
1 ATAATTCATTTTATAAAAAAT
1245279 ATAATTCATTTTATAAAAAA
1 ATAATTCATTTTATAAAAAA
1245299 AATTAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
20 4 0.22
21 7 0.39
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (21 bp):
ATAATTCATTTTATAAAAAAT
Found at i:1249518 original size:27 final size:27
Alignment explanation
Indices: 1249455--1249512 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
1249445 AAAAATAAAA
* * *
1249455 AAAATATTAAAAAACCTTAAAAATTTT
1 AAAATCTTAAAAAAACTCAAAAATTTT
* *
1249482 CAAATCTTAAAAAAACTCAAAACTTTT
1 AAAATCTTAAAAAAACTCAAAAATTTT
1249509 AAAA
1 AAAA
1249513 CTTTAATTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (27 bp):
AAAATCTTAAAAAAACTCAAAAATTTT
Found at i:1256917 original size:19 final size:19
Alignment explanation
Indices: 1256885--1256941 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 19
1256875 CCATAATGCA
*
1256885 AAAATGGTACCGATACCATG
1 AAAA-GGTATCGATACCATG
*
1256905 AAAGGGTATCGATACCATG
1 AAAAGGTATCGATACCATG
1256924 AAAAGGTATCGATACCAT
1 AAAAGGTATCGATACCAT
1256942 AGTGCAAAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 31 0.91
20 3 0.09
ACGTcount: A:0.40, C:0.18, G:0.21, T:0.21
Consensus pattern (19 bp):
AAAAGGTATCGATACCATG
Found at i:1257785 original size:15 final size:15
Alignment explanation
Indices: 1257761--1257791 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1257751 GGTGCCTATT
*
1257761 ACATTGAAGATTCAC
1 ACATTCAAGATTCAC
1257776 ACATTCAAGATTCAC
1 ACATTCAAGATTCAC
1257791 A
1 A
1257792 ACCGGTCAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.23, G:0.10, T:0.26
Consensus pattern (15 bp):
ACATTCAAGATTCAC
Found at i:1258390 original size:6 final size:6
Alignment explanation
Indices: 1258379--1258403 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1258369 TTGATGGTGA
1258379 AGGAAG AGGAAG AGGAAG AGGAAG A
1 AGGAAG AGGAAG AGGAAG AGGAAG A
1258404 AGATGAAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (6 bp):
AGGAAG
Found at i:1260392 original size:24 final size:22
Alignment explanation
Indices: 1260365--1260434 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 22
1260355 TGTGATATCA
1260365 ATACCATAGGCAAAGGTAGTACCG
1 ATACCAT--GCAAAGGTAGTACCG
*
1260389 ATACCAT-C-ATGGTAGTACCG
1 ATACCATGCAAAGGTAGTACCG
*
1260409 ATACCATG-AAAGG--GTATCG
1 ATACCATGCAAAGGTAGTACCG
1260428 ATACCAT
1 ATACCAT
1260435 AGTGCAAAGT
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
19 12 0.29
20 18 0.44
21 4 0.10
24 7 0.17
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.21
Consensus pattern (22 bp):
ATACCATGCAAAGGTAGTACCG
Found at i:1269780 original size:23 final size:23
Alignment explanation
Indices: 1269750--1269793 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
1269740 ATATATTCAG
1269750 TGCAATAGAAATCTTAAAATGAT
1 TGCAATAGAAATCTTAAAATGAT
1269773 TGCAATAGAAATCTTAAAATG
1 TGCAATAGAAATCTTAAAATG
1269794 TCCCCAATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.48, C:0.09, G:0.14, T:0.30
Consensus pattern (23 bp):
TGCAATAGAAATCTTAAAATGAT
Found at i:1271218 original size:101 final size:101
Alignment explanation
Indices: 1271094--1271300 Score: 414
Period size: 101 Copynumber: 2.0 Consensus size: 101
1271084 AAACCAACAA
1271094 AATTTATTAGAGTAACTGGAAGCAGCTCCGTTTTGTTTGAGTTTAAAAAAATCTATAAATAATTA
1 AATTTATTAGAGTAACTGGAAGCAGCTCCGTTTTGTTTGAGTTTAAAAAAATCTATAAATAATTA
1271159 CTTGAACACCCATGACATGATGATGGTCTAACTTAT
66 CTTGAACACCCATGACATGATGATGGTCTAACTTAT
1271195 AATTTATTAGAGTAACTGGAAGCAGCTCCGTTTTGTTTGAGTTTAAAAAAATCTATAAATAATTA
1 AATTTATTAGAGTAACTGGAAGCAGCTCCGTTTTGTTTGAGTTTAAAAAAATCTATAAATAATTA
1271260 CTTGAACACCCATGACATGATGATGGTCTAACTTAT
66 CTTGAACACCCATGACATGATGATGGTCTAACTTAT
1271296 AATTT
1 AATTT
1271301 TCCCAGTTCT
Statistics
Matches: 106, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
101 106 1.00
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (101 bp):
AATTTATTAGAGTAACTGGAAGCAGCTCCGTTTTGTTTGAGTTTAAAAAAATCTATAAATAATTA
CTTGAACACCCATGACATGATGATGGTCTAACTTAT
Found at i:1279450 original size:14 final size:15
Alignment explanation
Indices: 1279428--1279474 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
1279418 TATAAGGTAA
*
1279428 TTTTGTTATAATT-T
1 TTTTATTATAATTAT
*
1279442 TTTTATTATACTTAT
1 TTTTATTATAATTAT
*
1279457 TGTTTATTATGATTAT
1 T-TTTATTATAATTAT
1279473 TT
1 TT
1279475 GAAAAAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 11 0.41
15 3 0.11
16 13 0.48
ACGTcount: A:0.23, C:0.02, G:0.06, T:0.68
Consensus pattern (15 bp):
TTTTATTATAATTAT
Found at i:1282647 original size:20 final size:20
Alignment explanation
Indices: 1282622--1282673 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
1282612 CACTTAGGGA
1282622 ACCGATTCCCCATGAGGGGT
1 ACCGATTCCCCATGAGGGGT
1282642 ACCGATTCCCCATGAGGGGT
1 ACCGATTCCCCATGAGGGGT
1282662 ACCGATTCCCCA
1 ACCGATTCCCCA
1282674 CATGCTCCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.21, C:0.35, G:0.25, T:0.19
Consensus pattern (20 bp):
ACCGATTCCCCATGAGGGGT
Found at i:1285279 original size:22 final size:23
Alignment explanation
Indices: 1285249--1285331 Score: 78
Period size: 23 Copynumber: 3.7 Consensus size: 23
1285239 TAAGGTAGAG
*
1285249 GGAATCGATACCCCC-TTGAAGA
1 GGAACCGATACCCCCTTTGAAGA
* *
1285271 GGAACCGATTCCCCCTTTGAAGG
1 GGAACCGATACCCCCTTTGAAGA
* ** * *
1285294 GGAACCGCTTTCCCTTTTGAAGG
1 GGAACCGATACCCCCTTTGAAGA
*
1285317 GGAACCGATTCCCCC
1 GGAACCGATACCCCC
1285332 CAGGGGAATC
Statistics
Matches: 51, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
22 13 0.25
23 38 0.75
ACGTcount: A:0.23, C:0.31, G:0.24, T:0.22
Consensus pattern (23 bp):
GGAACCGATACCCCCTTTGAAGA
Found at i:1285285 original size:23 final size:23
Alignment explanation
Indices: 1285259--1285332 Score: 94
Period size: 23 Copynumber: 3.2 Consensus size: 23
1285249 GGAATCGATA
*
1285259 CCCCCTTGAAGAGGAACCGATTC
1 CCCCCTTGAAGGGGAACCGATTC
* * *
1285282 CCCCTTTGAAGGGGAACCGCTTT
1 CCCCCTTGAAGGGGAACCGATTC
**
1285305 CCCTTTTGAAGGGGAACCGATTC
1 CCCCCTTGAAGGGGAACCGATTC
1285328 CCCCC
1 CCCCC
1285333 AGGGGAATCG
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.20, C:0.35, G:0.23, T:0.22
Consensus pattern (23 bp):
CCCCCTTGAAGGGGAACCGATTC
Done.