Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008032.1 Hibiscus syriacus cultivar Beakdansim tig00110514_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: 1200719
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:330523 original size:20 final size:20
Alignment explanation
Indices: 330461--330523 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
330451 AAAATCTGCA
*
330461 CTGAAGGGCTTACAGATGAC
1 CTGAAGGACTTACAGATGAC
** * *
330481 C-GAAGGTTTTCCACATG-C
1 CTGAAGGACTTACAGATGAC
330499 ACTGAAGGACTTACAGATGAC
1 -CTGAAGGACTTACAGATGAC
330520 CTGA
1 CTGA
330524 GGTTTTGAAA
Statistics
Matches: 32, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
18 1 0.03
19 13 0.41
20 17 0.53
21 1 0.03
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.22
Consensus pattern (20 bp):
CTGAAGGACTTACAGATGAC
Found at i:338943 original size:20 final size:20
Alignment explanation
Indices: 338907--338944 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
338897 TACAGAACTC
*
338907 TTTATGAATTATTTATATGT
1 TTTATGAATTATGTATATGT
338927 TTTAT-AATTAATGTATAT
1 TTTATGAATT-ATGTATAT
338945 ACCAATACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (20 bp):
TTTATGAATTATGTATATGT
Found at i:341526 original size:26 final size:28
Alignment explanation
Indices: 341492--341549 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
341482 TGAAAATAAA
*
341492 AAAATAAT-A-TACATATAAATATTATG
1 AAAATAATAAGTACATATAAAAATTATG
*
341518 AAAATAATAAGTATATATAAAAATTATG
1 AAAATAATAAGTACATATAAAAATTATG
341546 AAAA
1 AAAA
341550 GAAAGAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 8 0.29
27 1 0.04
28 19 0.68
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (28 bp):
AAAATAATAAGTACATATAAAAATTATG
Found at i:343910 original size:3 final size:3
Alignment explanation
Indices: 343904--343945 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
343894 TTTTTTTATT
* *
343904 TAA TAA TAA TAA TAAA GAA TAA TAA TAA TAA TAA AAA TAA TA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TA
343946 GAAAAAATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 32 0.94
4 2 0.06
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:344276 original size:23 final size:23
Alignment explanation
Indices: 344236--344285 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
344226 GTTGTTAAAA
* * *
344236 ATTAAAAGATATATTGATGTGAT
1 ATTAAAAAAAATAATGATGTGAT
344259 ATTAAAAAAAATAATGATGTGAT
1 ATTAAAAAAAATAATGATGTGAT
344282 ATTA
1 ATTA
344286 TCTTTTGATG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (23 bp):
ATTAAAAAAAATAATGATGTGAT
Found at i:347792 original size:21 final size:19
Alignment explanation
Indices: 347742--347798 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 19
347732 GGCAAACTTG
347742 GACTATCGCAATGCGAATAT
1 GACTATCGCAATGCG-ATAT
*
347762 GTA-AATCGCAATGCGATAGT
1 G-ACTATCGCAATGCGATA-T
347782 CGACTATCGCAATGCGA
1 -GACTATCGCAATGCGA
347799 ACTTGGACTA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
19 3 0.10
20 14 0.45
21 14 0.45
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (19 bp):
GACTATCGCAATGCGATAT
Found at i:347807 original size:21 final size:21
Alignment explanation
Indices: 347736--347821 Score: 88
Period size: 21 Copynumber: 4.1 Consensus size: 21
347726 AACTATGGCA
347736 AACTTGGACTATCGCAATGCG
1 AACTTGGACTATCGCAATGCG
* *
347757 AA-TATGTA-AATCGCAATGCG
1 AACT-TGGACTATCGCAATGCG
* *
347777 ATA-GTCGACTATCGCAATGCG
1 A-ACTTGGACTATCGCAATGCG
*
347798 AACTTGGACTATCGCAACGCG
1 AACTTGGACTATCGCAATGCG
347819 AAC
1 AAC
347822 GTGGTATTGC
Statistics
Matches: 52, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
20 16 0.31
21 36 0.69
ACGTcount: A:0.33, C:0.23, G:0.22, T:0.22
Consensus pattern (21 bp):
AACTTGGACTATCGCAATGCG
Found at i:348580 original size:21 final size:21
Alignment explanation
Indices: 348556--348718 Score: 97
Period size: 21 Copynumber: 7.6 Consensus size: 21
348546 TTTGGAATAA
*
348556 ATCGCAACGCGAACTTCGACT
1 ATCGCAATGCGAACTTCGACT
* *
348577 ATCGCAATGTGAACTTGGACT
1 ATCGCAATGCGAACTTCGACT
*
348598 ATCGCAATGCGAA-TATCGCAATGCGAA
1 ATCGCAATGCGAACT-TCG--A--C--T
*
348625 ATCGCAATGCGAA-TAT-GTA-A
1 ATCGCAATGCGAACT-TCG-ACT
*
348645 ATCGCAATGCGAA-TAT-GTA-A
1 ATCGCAATGCGAACT-TCG-ACT
*
348665 ATCGCAATGCGAACTTGGACT
1 ATCGCAATGCGAACTTCGACT
*
348686 ATCGCAACGCGAACTTCGACT
1 ATCGCAATGCGAACTTCGACT
*
348707 ATCGCATTGCGA
1 ATCGCAATGCGA
348719 TTTACATATT
Statistics
Matches: 120, Mismatches: 12, Indels: 20
0.79 0.08 0.13
Matches are distributed among these distances:
20 37 0.31
21 63 0.52
23 1 0.01
25 2 0.02
26 1 0.01
27 16 0.13
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (21 bp):
ATCGCAATGCGAACTTCGACT
Found at i:348630 original size:13 final size:14
Alignment explanation
Indices: 348597--348640 Score: 81
Period size: 14 Copynumber: 3.2 Consensus size: 14
348587 GAACTTGGAC
348597 TATCGCAATGCGAA
1 TATCGCAATGCGAA
348611 TATCGCAATGCGAA
1 TATCGCAATGCGAA
348625 -ATCGCAATGCGAA
1 TATCGCAATGCGAA
348638 TAT
1 TAT
348641 GTAAATCGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
13 13 0.45
14 16 0.55
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.23
Consensus pattern (14 bp):
TATCGCAATGCGAA
Found at i:348648 original size:20 final size:20
Alignment explanation
Indices: 348623--348677 Score: 110
Period size: 20 Copynumber: 2.8 Consensus size: 20
348613 TCGCAATGCG
348623 AAATCGCAATGCGAATATGT
1 AAATCGCAATGCGAATATGT
348643 AAATCGCAATGCGAATATGT
1 AAATCGCAATGCGAATATGT
348663 AAATCGCAATGCGAA
1 AAATCGCAATGCGAA
348678 CTTGGACTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.42, C:0.16, G:0.20, T:0.22
Consensus pattern (20 bp):
AAATCGCAATGCGAATATGT
Found at i:348781 original size:42 final size:42
Alignment explanation
Indices: 348727--348820 Score: 170
Period size: 42 Copynumber: 2.2 Consensus size: 42
348717 GATTTACATA
*
348727 TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAGTTCGCATTGCGATAGTCGAAG
348769 TTCGCGTTGCGATAGTCCAAGTTCGCATTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAGTTCGCATTGCGATAGTCGAAG
*
348811 TTCGTGTTGC
1 TTCGCGTTGC
348821 AAATCTGGAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.20, C:0.21, G:0.28, T:0.31
Consensus pattern (42 bp):
TTCGCGTTGCGATAGTCCAAGTTCGCATTGCGATAGTCGAAG
Found at i:348820 original size:21 final size:21
Alignment explanation
Indices: 348727--348814 Score: 149
Period size: 21 Copynumber: 4.2 Consensus size: 21
348717 GATTTACATA
348727 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
348748 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
*
348769 TTCGCGTTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
348790 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
348811 TTCG
1 TTCG
348815 TGTTGCAAAT
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 62 1.00
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.30
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:357324 original size:14 final size:13
Alignment explanation
Indices: 357274--357324 Score: 57
Period size: 14 Copynumber: 3.7 Consensus size: 13
357264 AAAGTCAACG
357274 GGTTGACTCAGAT
1 GGTTGACTCAGAT
*
357287 GAGTTGACTCAGAC
1 G-GTTGACTCAGAT
*
357301 GGTTTAACTCAGAT
1 GG-TTGACTCAGAT
357315 AGGTTGACTC
1 -GGTTGACTC
357325 GGACCGAGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
13 2 0.06
14 27 0.87
15 2 0.06
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.29
Consensus pattern (13 bp):
GGTTGACTCAGAT
Found at i:358788 original size:16 final size:16
Alignment explanation
Indices: 358767--358807 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
358757 ATCTTTCCCC
358767 TTTCAATTTTCTAAAA
1 TTTCAATTTTCTAAAA
358783 TTTCAATTTTCTAAAA
1 TTTCAATTTTCTAAAA
358799 TTTCAATTT
1 TTTCAATTT
358808 AGTTACTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.34, C:0.12, G:0.00, T:0.54
Consensus pattern (16 bp):
TTTCAATTTTCTAAAA
Found at i:359695 original size:804 final size:792
Alignment explanation
Indices: 358094--360131 Score: 2379
Period size: 798 Copynumber: 2.5 Consensus size: 792
358084 AAATATCAGG
* * * *
358094 ATAATATTTCTC-ACCTCCTACTACCATACTTCAAATTTTTGTAAACTTCTGATTCAATCTAGTT
1 ATAATATTT-TCAACCTCATACTACCAT-CTTCAAATTTTTGTAAACTT-TAATTCGATCTGGTT
* * * * * *
358158 ATCCGAATATTTTACTGAACTTTATCTCTTAATAGCATTTTATATAAATTCCGGAT-AGAAATCT
63 ATCCGAATATTTTACCGAACTTTATCACTTAATA-AATTTTAAACAAATTCCGAATCAG-AATCT
* ** *
358222 AAATTCCATAAAAACTCCATTCTTAAAAATGAACTATTCATTTTCGAA-ACAA--T-TTTTTGGG
126 AAATTCCATAAAAACTCAATTCTTAAAAATGAACTATTCATTTAAGAATAAAATTTCTTTTTGGG
** * * * * *
358283 AAAATTGTCACTTTGTTCCTTGAATTTTTCCC-ATGTTTATACTTTTGTCACAAAATTTTCAAAA
191 AAAATTACCACTTTGGTCCTTGAACTTTTCCCAAGGTCT-TACTTTGGTCACAAAATTTTCAAAA
* * * * **
358347 TTTACGTTTTGGTCACTTGTCAAAATTTAGGAAAATATTTACCATCACTAGAGAGATTTGAACTC
255 TTTACATTTTGGTCACTTGTCAAAATTTTGGAAAATAATTACCGTCACTA-AGAGATTAAAACTC
** * *
358412 TTGTGGGTGAAATACTAACACCAAATGAAAGAGAATTTAATGGGGAATATTTTTCTATTTCACAA
319 TCATGGGTGAAATACTAACACCAAATGAAAGAGTATTTAATGGGGAATATTTTTCTATTTCTCAA
* * *
358477 CTTAGTCCAAAAATCCTAATTAAATGGATCAAAATTG-AAGAAATAAAGCTCACTAACCTTGGCT
384 CTTAGTCC-AAAATCCTAATAAAATGGATCAAAAATGAAAAAAATAAAGCTCACTAACCTTGGCT
* * *
358541 ATGGAGACCCACCACAATGAAGAGGAAGATGAGAGATTTCTTCTTGAATTTTCTCCAAAAATATC
448 ATGGAGACCCACAACAATGAAAAGGAAGATGAGAGAATTCTTCTTGAATTTTCTCCAAAAATATC
*
358606 TAGGACACTTGTATATATTCTAATTAAAATTCATTTTAATCCAAAAGTCCAATTTACCCTTAATG
513 TAGGACACCTGTATATATTCTAATTAAAATTCATTTTAATCCAAAAGTCCAATTTACCCTTAATG
* *
358671 AATCTTGATAATTACCTCATGCCATCCTTTCATCACTAATTTAATAACATTAAATAAATATAAAA
578 AATCTTGATAATTACCCCATGCCATCCTTTCATCACCAATTTAATAACATTAAATAAATAT-AAA
* *
358736 AAAACATATTTATTGGTTTCCATCTTTCCCCTTTCAATTTTCTAAAATTTCAATTTTCTAAAATT
642 AAAACATATTTATTGATTTCCATCTTT-CCC--TC----TTC----ATTTCAATTTTCCAAAATT
* *
358801 TCAATTTAGTTACTTAAATTCCATTATTCCACTTTAACATGGAAAATTCATCTAATTCCACTGAT
696 TCAATTTAGTCACTTAAATTCCACTATTCCACTTTAACATGGAAAATTCATCTAATTCCACTGAT
* *
358866 CCATATTAAATTCTAATGATAAAAATACCAAA
761 CCATATTAAATTATAATAATAAAAATACCAAA
* * * *
358898 ATAATATTTTCAACCTCATAATACCATCGTTCAAAATTTTGTAAACTTTTTATTCGATCCGGTTA
1 ATAATATTTTCAACCTCATACTACCATC-TTCAAATTTTTGTAAAC-TTTAATTCGATCTGGTTA
* * *
358963 TCCGAATATTTTACCAAACTTTATCGCTTTATAAATTTTTAAACAAATTCCGAATCAGAATCTAA
64 TCCGAATATTTTACCGAACTTTATCACTTAATAAA-TTTTAAACAAATTCCGAATCAGAATCTAA
* * * *
359028 ATTCCATAAAAACTCAATTCTTAAAAATAAACTATTTATTCAAGAAGTAAAATTTCTTTTTGGAA
128 ATTCCATAAAAACTCAATTCTTAAAAATGAACTATTCATTTAAGAA-TAAAATTTCTTTTTGGGA
* *
359093 AAATTACCAC-TGGGTCCTTAAACTTTTCCCAAGGTCTTACTTTGGTCACAAAATTTTCAAAATT
192 AAATTACCACTTTGGTCCTTGAACTTTTCCCAAGGTCTTACTTTGGTCACAAAATTTTCAAAATT
* * * *** *
359157 TACATTTTGGTTACTTATCAAAATTTTTGGGAAATAATTGTTGTCGCATAAGAGATTAAAACTCT
257 TACATTTTGGTCACTTGTCAAAA-TTTTGGAAAATAATTACCGTCAC-TAAGAGATTAAAACTCT
* * * *
359222 CACGGATGAAATACTAACACCAAATGAAAGAGTATTTAATAGGGAATATTTTTCTATTTCTCAAT
320 CATGGGTGAAATACTAACACCAAATGAAAGAGTATTTAATGGGGAATATTTTTCTATTTCTCAAC
** * *
359287 TTAGTCCAAAATCCTAATAAAATATATCAAAAATGAAAAAAAATAAAGCTCACTCACCTTGGGTA
385 TTAGTCCAAAATCCTAATAAAATGGATCAAAAATG-AAAAAAATAAAGCTCACTAACCTTGGCTA
*
359352 TGGAGACCCACAACAATGAAAAGGAATATGAGAGAATTCTTCTTGAATTTTCTCCAAAAATATCT
449 TGGAGACCCACAACAATGAAAAGGAAGATGAGAGAATTCTTCTTGAATTTTCTCCAAAAATATCT
* *
359417 AGGACACCTGTATATATTCTAGTTAAAAATGAATTTAAAATTCATTTTTAA-CTAGAAGTCCAAT
514 AGGACACCTGTATATATTC----------T-AA-TTAAAATTCA-TTTTAATCCAAAAGTCCAAT
* * *
359481 TTGCCC-TAATGAATCTTGATAATTACCCCATGCCATCCTTTCATCACCATTTTAATAATATTAA
566 TTACCCTTAATGAATCTTGATAATTACCCCATGCCATCCTTTCATCACCAATTTAATAACATTAA
**
359545 ATAAATAT-AAAAGTCATATTTATTGATTTCCATC-TT-CC-C-TC-TTTCAATTTTCCAAAATT
631 ATAAATATAAAAAAACATATTTATTGATTTCCATCTTTCCCTCTTCATTTCAATTTTCCAAAATT
* *
359604 TCAATTTAGTCACTTAAATTCTACTATTCCACTTTATCATGGAAAATTCATCTAATTCCA-TCGA
696 TCAATTTAGTCACTTAAATTCCACTATTCCACTTTAACATGGAAAATTCATCTAATTCCACT-GA
* * ** *
359668 TCCATGTTAAATTATACTAATTAAAAATATTAAC
760 TCCATATTAAATTATAATAA-TAAAAATACCAAA
* * * * *
359702 ATAATATTTCCAACAT-TTGCTACCATCCTTCAAATTTTTGTAAA----AATTCGATATGGTTAT
1 ATAATATTTTCAACCTCATACTACCAT-CTTCAAATTTTTGTAAACTTTAATTCGATCTGGTTAT
** ** * * *
359762 ATGAATATTTTACCGAACTTTATCACTTAATAGCCTTTTACACAAATT-CAAGATCAAAATCTAA
65 CCGAATATTTTACCGAACTTTATCACTTAATA-AATTTTAAACAAATTCCGA-ATCAGAATCTAA
* *
359826 ATTCCATAAAAACT-ACATTCTTAAAAATGAACTATTCATTTATGAAATAAAATTTCTTTTCGGG
128 ATTCCATAAAAACTCA-ATTCTTAAAAATGAACTATTCATTTAAG-AATAAAATTTCTTTTTGGG
* ** * * *
359890 AAAATTACCACTTTGGTCTTTGAACTTTTCTTAAGTTC-TACTTTGGTCATAAAATTTTCAAGAT
191 AAAATTACCACTTTGGTCCTTGAACTTTTCCCAAGGTCTTACTTTGGTCACAAAATTTTCAAAAT
* * * *
359954 CTACATTTTGGTCACTTGTCAAAATTTTGGATAAATAATTACCGTCTCTTGAGAGATTCAAACTC
256 TTACATTTTGGTCACTTGTCAAAATTTTGGA-AAATAATTACCGTCAC-TAAGAGATTAAAACTC
* * *
360019 TCATGGGTGCAATACTAACATC-AATGAAAGA-TAATTTAATGGGGAATATTTTTTTATTTCTCA
319 TCATGGGTGAAATACTAACACCAAATGAAAGAGT-ATTTAATGGGGAATATTTTTCTATTTCTCA
360082 ACTTAGTCCAAAATCCTAATAAAATGGATCAAAAAT-AAAAAAATAAAGCT
383 ACTTAGTCCAAAATCCTAATAAAATGGATCAAAAATGAAAAAAATAAAGCT
360132 GGCTCCCCTT
Statistics
Matches: 1056, Mismatches: 140, Indels: 85
0.82 0.11 0.07
Matches are distributed among these distances:
795 14 0.01
796 1 0.00
797 79 0.07
798 216 0.20
799 22 0.02
802 1 0.00
803 117 0.11
804 167 0.16
805 4 0.00
806 3 0.00
808 89 0.08
809 112 0.11
810 106 0.10
813 1 0.00
816 2 0.00
818 2 0.00
819 23 0.02
820 1 0.00
821 64 0.06
822 26 0.02
823 6 0.01
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (792 bp):
ATAATATTTTCAACCTCATACTACCATCTTCAAATTTTTGTAAACTTTAATTCGATCTGGTTATC
CGAATATTTTACCGAACTTTATCACTTAATAAATTTTAAACAAATTCCGAATCAGAATCTAAATT
CCATAAAAACTCAATTCTTAAAAATGAACTATTCATTTAAGAATAAAATTTCTTTTTGGGAAAAT
TACCACTTTGGTCCTTGAACTTTTCCCAAGGTCTTACTTTGGTCACAAAATTTTCAAAATTTACA
TTTTGGTCACTTGTCAAAATTTTGGAAAATAATTACCGTCACTAAGAGATTAAAACTCTCATGGG
TGAAATACTAACACCAAATGAAAGAGTATTTAATGGGGAATATTTTTCTATTTCTCAACTTAGTC
CAAAATCCTAATAAAATGGATCAAAAATGAAAAAAATAAAGCTCACTAACCTTGGCTATGGAGAC
CCACAACAATGAAAAGGAAGATGAGAGAATTCTTCTTGAATTTTCTCCAAAAATATCTAGGACAC
CTGTATATATTCTAATTAAAATTCATTTTAATCCAAAAGTCCAATTTACCCTTAATGAATCTTGA
TAATTACCCCATGCCATCCTTTCATCACCAATTTAATAACATTAAATAAATATAAAAAAACATAT
TTATTGATTTCCATCTTTCCCTCTTCATTTCAATTTTCCAAAATTTCAATTTAGTCACTTAAATT
CCACTATTCCACTTTAACATGGAAAATTCATCTAATTCCACTGATCCATATTAAATTATAATAAT
AAAAATACCAAA
Found at i:360907 original size:105 final size:104
Alignment explanation
Indices: 360706--360913 Score: 242
Period size: 105 Copynumber: 2.0 Consensus size: 104
360696 GGCATTGCAC
** *
360706 ACTTAGTGTGACAACATTGGTGGTCATAAAATATACTTTTAGCTTAAAGCAAATTTGTCACAATT
1 ACTTAGTGTGACAACATTAATGGTCATAAAATATACTTTTAGCTTAAAGCAAATTCGTCACAATT
* * **
360771 TTTATTGATAATAGTATCGAACATTTAATCACTAAAAAAT
66 TATATTGATAATAGTATCAAACAGATAATCAC-AAAAAAT
* *
360811 ACTTAGTGTGACAATATTAATGGTCACT-AAATATATTTTTAG-TGTCAAA-CAAATTCGTCACA
1 ACTTAGTGTGACAACATTAATGGTCA-TAAAATATACTTTTAGCT-T-AAAGCAAATTCGTCACA
* * * *
360873 ATTTATATTGATAATTGTGTCAAATAGATGATCACAAAAAA
63 ATTTATATTGATAATAGTATCAAACAGATAATCACAAAAAA
360914 CGAAAAATTG
Statistics
Matches: 87, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
104 7 0.08
105 76 0.87
106 4 0.05
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (104 bp):
ACTTAGTGTGACAACATTAATGGTCATAAAATATACTTTTAGCTTAAAGCAAATTCGTCACAATT
TATATTGATAATAGTATCAAACAGATAATCACAAAAAAT
Found at i:361097 original size:23 final size:24
Alignment explanation
Indices: 361052--361097 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
361042 ACAACAATTC
** *
361052 AAAAAACTAATCATTTTTTAAAGA
1 AAAAAACTAATCATCATTAAAAGA
361076 AAAAAACTAATCA-CATTAAAAG
1 AAAAAACTAATCATCATTAAAAG
361098 TTTTATAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.59, C:0.11, G:0.04, T:0.26
Consensus pattern (24 bp):
AAAAAACTAATCATCATTAAAAGA
Found at i:362901 original size:12 final size:12
Alignment explanation
Indices: 362886--362910 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
362876 GACGAAGAGG
362886 CTGCTTGTGATA
1 CTGCTTGTGATA
362898 CTGCTTGTGATA
1 CTGCTTGTGATA
362910 C
1 C
362911 CCAAAAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.20, G:0.24, T:0.40
Consensus pattern (12 bp):
CTGCTTGTGATA
Found at i:367405 original size:128 final size:128
Alignment explanation
Indices: 367086--367456 Score: 422
Period size: 128 Copynumber: 2.9 Consensus size: 128
367076 AAATAATTTT
* * * *
367086 AAGAGAAAAAAATAATAATCTAATTATTTACAATCGAGAATAAATGACCTTTCATGCCTTAAAAT
1 AAGAGAAAACAATAAT-ATCTAATTATTTTCAATCGAGAATAAATGACCTCTCATGCCTTAAAAC
* * * * * * * *
367151 AATCATTTATTACTCCAATTGAAATGAAGAAATGTCATTATCATGTCTTAAAATTCAATATCGAT
65 AATCATTTATTGCTCCAATCGAAATGAAGAGATATCACTAT--T-TCTCAAAAATCAATATCAAT
367216 TC
127 TC
* * * * * * *
367218 GAGTGAAAACAATAATATCTAA-CAATTTCTAATCAATAATAAATGACCTCTCATACCTTAAAAC
1 AAGAGAAAACAATAATATCTAATTATTTTC-AATCGAGAATAAATGACCTCTCATGCCTTAAAAC
*
367282 AATCATTTATTGCTCCAATCGAAATGAAGAGATATCACTATTTCTCAAAAATCAATATTAATTC
65 AATCATTTATTGCTCCAATCGAAATGAAGAGATATCACTATTTCTCAAAAATCAATATCAATTC
** * *
367346 AAGAGAAAACGGTAATATCAAATTATTTTCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
1 AAGAGAAAACAATAATATCTAATTATTTTCAATCGAGAATAAATGACCTCTCATGCCTTAAAACA
* * * * *
367411 GTCATTTATTGCTCCAACCAAAATGAAAAGATATTACTA-TTCTCAA
66 ATCATTTATTGCTCCAATCGAAATGAAGAGATATCACTATTTCTCAA
367457 TACATATTCA
Statistics
Matches: 201, Mismatches: 36, Indels: 9
0.82 0.15 0.04
Matches are distributed among these distances:
127 7 0.03
128 100 0.50
129 6 0.03
130 4 0.02
131 71 0.35
132 13 0.06
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.31
Consensus pattern (128 bp):
AAGAGAAAACAATAATATCTAATTATTTTCAATCGAGAATAAATGACCTCTCATGCCTTAAAACA
ATCATTTATTGCTCCAATCGAAATGAAGAGATATCACTATTTCTCAAAAATCAATATCAATTC
Found at i:369435 original size:3 final size:3
Alignment explanation
Indices: 369427--369463 Score: 65
Period size: 3 Copynumber: 12.0 Consensus size: 3
369417 AAAAATAAAG
369427 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
369464 CCGAAACACA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:369611 original size:20 final size:20
Alignment explanation
Indices: 369578--369617 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
369568 CTTACTTATG
*
369578 TTTATTTACTTGATTGGTGT
1 TTTATTTACTTGATTAGTGT
369598 TTTATTTA-TGTGATTAGTGT
1 TTTATTTACT-TGATTAGTGT
369618 GGGCTTGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.17, C:0.03, G:0.20, T:0.60
Consensus pattern (20 bp):
TTTATTTACTTGATTAGTGT
Found at i:377039 original size:32 final size:32
Alignment explanation
Indices: 377003--377099 Score: 106
Period size: 32 Copynumber: 3.0 Consensus size: 32
376993 TTGACCAAAA
* *
377003 CCAAAAATCAACCGATCCAATATTGACCCGAC
1 CCAAAAATCAACAGATCCGATATTGACCCGAC
* * *
377035 CC-AAAATCTAACATATCCGATATTAACCCGGC
1 CCAAAAATC-AACAGATCCGATATTGACCCGAC
* * *
377067 CCAAAAATCAACTGATTCGATATTGATCCGAC
1 CCAAAAATCAACAGATCCGATATTGACCCGAC
377099 C
1 C
377100 TGATATTAAC
Statistics
Matches: 52, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
31 6 0.12
32 40 0.77
33 6 0.12
ACGTcount: A:0.38, C:0.31, G:0.10, T:0.21
Consensus pattern (32 bp):
CCAAAAATCAACAGATCCGATATTGACCCGAC
Found at i:377185 original size:16 final size:16
Alignment explanation
Indices: 377160--377193 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
377150 AAAAACAATC
*
377160 GATCTGATAATCACCT
1 GATCTAATAATCACCT
377176 GATCTAATAATCACCT
1 GATCTAATAATCACCT
377192 GA
1 GA
377194 CCCGATACCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.35, C:0.24, G:0.12, T:0.29
Consensus pattern (16 bp):
GATCTAATAATCACCT
Found at i:379146 original size:21 final size:23
Alignment explanation
Indices: 379113--379154 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
379103 TTTCTTTTCT
379113 TTTATTTTCAAGTTTT-TTTTAC
1 TTTATTTTCAAGTTTTATTTTAC
379135 TTTATTTT-AAGTTTTATTTT
1 TTTATTTTCAAGTTTTATTTT
379155 TAAACATGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.19, C:0.05, G:0.05, T:0.71
Consensus pattern (23 bp):
TTTATTTTCAAGTTTTATTTTAC
Found at i:383383 original size:20 final size:21
Alignment explanation
Indices: 383343--383384 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
383333 ATGTATGAGA
383343 ATGTTGTGGCAAAATGAAATGG
1 ATGTTGTGG-AAAATGAAATGG
*
383365 ATGTTGTGG-AAATGGAATGG
1 ATGTTGTGGAAAATGAAATGG
383385 TGGTATAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
22 9 0.47
ACGTcount: A:0.33, C:0.02, G:0.36, T:0.29
Consensus pattern (21 bp):
ATGTTGTGGAAAATGAAATGG
Found at i:388761 original size:12 final size:12
Alignment explanation
Indices: 388746--388795 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 12
388736 TCTAAAAAAG
*
388746 ACAAGGAAAATA
1 ACAAGTAAAATA
388758 ACAAGTAAAACTA
1 ACAAGTAAAA-TA
388771 TACAA--AAAATGA
1 -ACAAGTAAAAT-A
388783 ACAAGTAAAATA
1 ACAAGTAAAATA
388795 A
1 A
388796 AAATGCTTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
11 5 0.16
12 16 0.50
13 7 0.22
14 4 0.12
ACGTcount: A:0.66, C:0.10, G:0.10, T:0.14
Consensus pattern (12 bp):
ACAAGTAAAATA
Found at i:389067 original size:20 final size:21
Alignment explanation
Indices: 389027--389068 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
389017 ACAAATGAGA
389027 ATGTTGTGGCAAAATGAAATGG
1 ATGTTGTGG-AAAATGAAATGG
*
389049 ATGTTGTGG-AAATGGAATGG
1 ATGTTGTGGAAAATGAAATGG
389069 TGGTAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
22 9 0.47
ACGTcount: A:0.33, C:0.02, G:0.36, T:0.29
Consensus pattern (21 bp):
ATGTTGTGGAAAATGAAATGG
Found at i:390264 original size:36 final size:37
Alignment explanation
Indices: 390207--390282 Score: 120
Period size: 36 Copynumber: 2.1 Consensus size: 37
390197 TTTCGTCCTA
390207 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
1 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
*
390244 CTAGGATTC-AACTC-CTAAAAATAGGATAGAATTTTG
1 CTAGGATTCAAACTCTC-AAAAATAGGATAGAATTCTG
390280 CTA
1 CTA
390283 TGTTTTAAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
35 1 0.03
36 27 0.73
37 9 0.24
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (37 bp):
CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
Found at i:390306 original size:37 final size:36
Alignment explanation
Indices: 390207--390307 Score: 114
Period size: 37 Copynumber: 2.8 Consensus size: 36
390197 TTTCGTCCTA
390207 CTAGGATTCAAACT-CTCAAAAATAGGATAGAATTCTG
1 CTAGGATT-AAACTCCT-AAAAATAGGATAGAATTCTG
* *
390244 CTAGGATTCAACTCCTAAAAATAGGATAGAATTTTG
1 CTAGGATTAAACTCCTAAAAATAGGATAGAATTCTG
** * *
390280 CTATGTTTTAAATTCCTAAAGATAGGAT
1 CTA-GGATTAAACTCCTAAAAATAGGAT
390308 CCACAAGCAC
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
36 26 0.47
37 29 0.53
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (36 bp):
CTAGGATTAAACTCCTAAAAATAGGATAGAATTCTG
Found at i:390803 original size:27 final size:25
Alignment explanation
Indices: 390786--390835 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
390776 AAAGTTATTA
390786 TATATATA-TATATATTTATAACTAT
1 TATATATATTAT-TATTTATAACTAT
*
390811 TATATTTATTATTATTT-T-ACTAT
1 TATATATATTATTATTTATAACTAT
390834 TA
1 TA
390836 ACGTATATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 7 0.30
24 1 0.04
25 12 0.52
26 3 0.13
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (25 bp):
TATATATATTATTATTTATAACTAT
Found at i:394373 original size:22 final size:21
Alignment explanation
Indices: 394348--394396 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 21
394338 CAAAAAGGGT
394348 AAAAATAAAAAAGAAAAGAAGCA
1 AAAAATAAAAAA-AAAAGAA-CA
* *
394371 AAAAATGAAAAAACAAGAACA
1 AAAAATAAAAAAAAAAGAACA
394392 AAAAA
1 AAAAA
394397 GAAAGAACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 7 0.29
22 6 0.25
23 11 0.46
ACGTcount: A:0.80, C:0.06, G:0.10, T:0.04
Consensus pattern (21 bp):
AAAAATAAAAAAAAAAGAACA
Found at i:394400 original size:20 final size:20
Alignment explanation
Indices: 394363--394417 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
394353 TAAAAAAGAA
394363 AAGAAGCAAAAAATGAAAAAAC
1 AAGAA-CAAAAAA-GAAAAAAC
*
394385 AAGAACAAAAAAGAAAGAAC
1 AAGAACAAAAAAGAAAAAAC
* *
394405 AAAAATAAAAAAG
1 AAGAACAAAAAAG
394418 GGAACAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 18 0.60
21 7 0.23
22 5 0.17
ACGTcount: A:0.76, C:0.07, G:0.13, T:0.04
Consensus pattern (20 bp):
AAGAACAAAAAAGAAAAAAC
Found at i:395053 original size:22 final size:22
Alignment explanation
Indices: 395025--395075 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
395015 CCCCATCAAT
395025 CCTTTGAGCATCAAATACCAAA
1 CCTTTGAGCATCAAATACCAAA
* *
395047 CCTTTGAGCATCAAATGCGAAA
1 CCTTTGAGCATCAAATACCAAA
395069 CCTTTGA
1 CCTTTGA
395076 CCAAACACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.25
Consensus pattern (22 bp):
CCTTTGAGCATCAAATACCAAA
Found at i:395984 original size:36 final size:37
Alignment explanation
Indices: 395937--396040 Score: 131
Period size: 39 Copynumber: 2.8 Consensus size: 37
395927 CTCACCATTT
395937 TCTCTCTTGAGACAGTTTCCCTTGAAACAAA-CTTTG
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAATCTTTG
* *
395973 TCTCTCTTGAGACAGTTTCCCTTGAAA-AAATTTTTTTTT
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAA---TCTTTG
* *
396012 TCTCCCTTGAGACAGTTTCTCTTGAAACA
1 TCTCTCTTGAGACAGTTTCCCTTGAAACA
396041 TAAACATTGA
Statistics
Matches: 59, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
35 3 0.05
36 27 0.46
39 28 0.47
40 1 0.02
ACGTcount: A:0.24, C:0.23, G:0.12, T:0.40
Consensus pattern (37 bp):
TCTCTCTTGAGACAGTTTCCCTTGAAACAAATCTTTG
Found at i:396036 original size:39 final size:36
Alignment explanation
Indices: 395934--396244 Score: 160
Period size: 36 Copynumber: 8.9 Consensus size: 36
395924 GTGCTCACCA
395934 TTTTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
1 TTTTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
* *
395970 TTGTCTCTCTTGAGACAGTTTCCCTTGAAA-AAATTTTTT
1 TTTTCTCTCTTGAGACAGTTTCCCTTGAAACAAA----CT
* *
396009 TTTTCTCCCTTGAGACAGTTTCTCTTGAAACATAA--
1 TTTTCTCTCTTGAGACAGTTTCCCTTGAAACA-AACT
* * * * *
396044 -----AC-ATTGAAAACA-TTTCCCTTGAAA-TAAGT
1 TTTTCTCTCTTG-AGACAGTTTCCCTTGAAACAAACT
* *
396073 TTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATT
1 TTT-TCTCTCTTGAGACAGTTTCCCTTGAAAC-AAACT
* * *
396111 TTTTCTCCCTTGAGATAGTTTCTCTTGAAACATAA--
1 TTTTCTCTCTTGAGACAGTTTCCCTTGAAACA-AACT
* * * * **
396146 ----ATAT-TGGAAACA-TTTCCCTTGAAATGAA-T
1 TTTTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
* *
396175 TTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAAT
1 TTT-TCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
*
396212 TTTGTCTCCCTTGAGACAGTTTCTCC-TGAAACA
1 TTT-TCTCTCTTGAGACAGTTTC-CCTTGAAACA
396245 TAAACATTGA
Statistics
Matches: 209, Mismatches: 36, Indels: 59
0.69 0.12 0.19
Matches are distributed among these distances:
27 2 0.01
28 2 0.01
29 25 0.12
30 10 0.05
31 1 0.00
34 2 0.01
35 12 0.06
36 59 0.28
37 57 0.27
38 8 0.04
39 28 0.13
40 1 0.00
41 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.40
Consensus pattern (36 bp):
TTTTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
Found at i:396130 original size:37 final size:37
Alignment explanation
Indices: 396056--396147 Score: 123
Period size: 37 Copynumber: 2.5 Consensus size: 37
396046 ATTGAAAACA
* * *
396056 TTTCCCTTGAAA-TAAGTTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGATAG
*
396092 TTTCCCTTGAAACAAAATTTTTTCTCCCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGATAG
*
396129 TTTCTCTTGAAACATAAAT
1 TTTCCCTTGAAACA-AAAT
396148 ATTGGAAACA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
36 12 0.24
37 33 0.67
38 4 0.08
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.42
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGATAG
Found at i:396157 original size:102 final size:101
Alignment explanation
Indices: 395952--396412 Score: 611
Period size: 102 Copynumber: 4.5 Consensus size: 101
395942 CTTGAGACAG
* * * * *
395952 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAA-AAATTTTTTTTTTCTC
1 TTTCCCTTGAAA-TAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAA---ATTTTGTCTC
396016 CCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
62 CCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
*
396056 TTTCCCTTGAAATAAGTTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTTTCTCCCT
1 TTTCCCTTGAAATAA-TTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
* * *
396121 TGAGATAGTTTCTCTTGAAACATAAATATTGGAAACA
65 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
396158 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
1 TTTCCCTTGAAAT-AATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
*
396223 TGAGACAGTTTCTCCTGAAACATAAACATTGAAAACA
65 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* *
396260 TTTCCCTTGAAATGAATTTCGTCTCTCTTGAGATAATTTCCCTTGAAAC-AAATTTTGTCTCCCT
1 TTTCCCTTGAAAT-AATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
* * * **
396324 TGAGACAGTTTCTCTTGAAACACAAAACCTTTGAGATTA
65 TGAGACAGTTTCTCTTGAAACA-TAAA-CATTGAAAACA
* * * * * *
396363 TTTCCCTCGAAACAAATTTTGTCTCCCATGAGAAAGTTTCTCTTGAAACA
1 TTTCCCTTGAAA-TAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA
396413 TAAAATCTTT
Statistics
Matches: 322, Mismatches: 28, Indels: 14
0.88 0.08 0.04
Matches are distributed among these distances:
101 36 0.11
102 190 0.59
103 51 0.16
104 42 0.13
105 3 0.01
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.38
Consensus pattern (101 bp):
TTTCCCTTGAAATAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTT
GAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
Found at i:396225 original size:37 final size:37
Alignment explanation
Indices: 396158--396244 Score: 115
Period size: 37 Copynumber: 2.4 Consensus size: 37
396148 ATTGGAAACA
** * *
396158 TTTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
396194 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
396231 TTTCTCC-TGAAACA
1 TTTC-CCTTGAAACA
396245 TAAACATTGA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
36 12 0.27
37 31 0.69
38 2 0.04
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
Found at i:396306 original size:36 final size:36
Alignment explanation
Indices: 396259--396345 Score: 111
Period size: 36 Copynumber: 2.4 Consensus size: 36
396249 CATTGAAAAC
** * *
396259 ATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGATA
1 ATTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACA
*
396295 ATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
1 ATTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACA
* *
396331 GTTTCTCTTGAAACA
1 ATTTCCCTTGAAACA
396346 CAAAACCTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.26, C:0.22, G:0.13, T:0.39
Consensus pattern (36 bp):
ATTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACA
Found at i:396395 original size:67 final size:67
Alignment explanation
Indices: 396287--396424 Score: 222
Period size: 67 Copynumber: 2.1 Consensus size: 67
396277 TTCGTCTCTC
* * *
396287 TTGAGATAATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAAC
1 TTGAGATAATTTCCCTCGAAACAAATTTTGTCTCCCATGAGAAAGTTTCTCTTGAAACACAAAAC
396352 CT
66 CT
* * *
396354 TTGAGATTATTTCCCTCGAAACAAATTTTGTCTCCCATGAGAAAGTTTCTCTTGAAACATAAAAT
1 TTGAGATAATTTCCCTCGAAACAAATTTTGTCTCCCATGAGAAAGTTTCTCTTGAAACACAAAAC
396419 CT
66 CT
396421 TTGA
1 TTGA
396425 ATTTATCTCC
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
67 65 1.00
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (67 bp):
TTGAGATAATTTCCCTCGAAACAAATTTTGTCTCCCATGAGAAAGTTTCTCTTGAAACACAAAAC
CT
Found at i:396436 original size:67 final size:67
Alignment explanation
Indices: 396287--396445 Score: 221
Period size: 67 Copynumber: 2.4 Consensus size: 67
396277 TTCGTCTCTC
* * * *
396287 TTGAGATAATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAAC
1 TTGAGATTATCTCCCTTGAAACAAATTTTGTCTCCCATGAGAAAGTTTCTCTTGAAACACAAAAC
396352 CT
66 CT
* * * *
396354 TTGAGATTATTTCCCTCGAAACAAATTTTGTCTCCCATGAGAAAGTTTCTCTTGAAACATAAAAT
1 TTGAGATTATCTCCCTTGAAACAAATTTTGTCTCCCATGAGAAAGTTTCTCTTGAAACACAAAAC
396419 CT
66 CT
*
396421 TTGA-ATTTATCTCCCTTAAAACAAA
1 TTGAGA-TTATCTCCCTTGAAACAAA
396446 ATTTCGTTTC
Statistics
Matches: 82, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
66 1 0.01
67 81 0.99
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.35
Consensus pattern (67 bp):
TTGAGATTATCTCCCTTGAAACAAATTTTGTCTCCCATGAGAAAGTTTCTCTTGAAACACAAAAC
CT
Found at i:397229 original size:106 final size:104
Alignment explanation
Indices: 397026--397435 Score: 431
Period size: 106 Copynumber: 3.9 Consensus size: 104
397016 TAGCTAGAGT
* * ** *
397026 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGCCAACAACAATTTT-AGTTTCA-TCCGCGA
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAACAATTTTCAGTTTCAGAGC-CAA
* *
397089 TTTCAACTCCAC-GACGGAGGATATTGTGCCACTCGAGACAACA
65 TTTCAACTTCACAG-CGAAGGATATTG-G--ACTCGAGACAACA
* * * * *
397132 CAAGTTCAACTTCACAATGAAGGGACAGCTGGTTGTCAACAAACATTTTTCAAATTTCAGAGCCA
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAAC-AACAATTTTC-AGTTTCAGAGCCA
*
397197 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAAACAACA
64 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACA
* *
397238 CAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAA-GA-TTTC-G-TTCAGAGTCAAT
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAACAATTTTCAGTTTCAGAGCCAAT
* *
397299 TTCAACTTCACAGCGAAGGATATTAGACTCGAGACAGCA
66 TTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACA
* * ** * * * * *
397338 CAAGCTCAACTTCACAGCGAAGGGGTGGCTGACTGTCAACAAACAATTTCCCGGTTCCAGAACCA
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAAC-AACAATTT-TCAGTTTCAGAGCCA
*
397403 ATTTCAACTTCACAGC-AGATGATATTGGACTCG
64 ATTTCAACTTCACAGCGA-AGGATATTGGACTCG
397436 GAACAATATT
Statistics
Matches: 259, Mismatches: 33, Indels: 24
0.82 0.10 0.08
Matches are distributed among these distances:
100 82 0.32
101 2 0.01
102 1 0.00
103 6 0.02
104 1 0.00
105 4 0.02
106 122 0.47
107 8 0.03
108 1 0.00
109 30 0.12
110 2 0.01
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (104 bp):
CAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAACAATTTTCAGTTTCAGAGCCAAT
TTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACA
Found at i:397406 original size:206 final size:211
Alignment explanation
Indices: 397026--397441 Score: 488
Period size: 206 Copynumber: 2.0 Consensus size: 211
397016 TAGCTAGAGT
* * *
397026 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGCCAACAACAATTTTAGTTTCATCCGCGATT
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGATTGCCAACAACAATTTTAGTTTCATCAGCAATT
* * * *
397091 TCAACTCCACGACGGAGGATATTGTGCCACTCGAGACAACACAAGTTCAACTTCACAATGAAGGG
66 TCAACTCCACGACGAAGGATATTGAG-CACTCGAGACAACACAAGCTCAACTTCACAACGAAGGG
** * * * *
397156 ACAGCTGGTTGTCAACAAACATTTTTCAAATTTCAGAGCCAATTTCAACTTCACAGC-GAAGGAT
130 ACAGCTGACTGTCAACAAACAATTTCCAAATTCCAGAACCAATTTCAACTTCACAGCAG-AGGAT
397220 ATTGGACTCGAAACAACA
194 ATTGGACTCGAAACAACA
* * * *
397238 CAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAA-GA-TTTCG-TTCA-GAGTCAAT
1 CAAGTTCAACTTCACAACGAAGGGACGGCTGATTGCCAACAACAATTTTAGTTTCATCAG-CAAT
* * *
397299 TTCAACTTCAC-AGCGAAGGATATT-AG-ACTCGAGACAGCACAAGCTCAACTTCACAGCGAAGG
65 TTCAACTCCACGA-CGAAGGATATTGAGCACTCGAGACAACACAAGCTCAACTTCACAACGAAGG
*** *** *
397361 GGTGGCTGACTGTCAACAAACAATTTCCCGGTTCCAGAACCAATTTCAACTTCACAGCAGATGAT
129 GACAGCTGACTGTCAACAAACAATTTCCAAATTCCAGAACCAATTTCAACTTCACAGCAGAGGAT
*
397426 ATTGGACTCGGAACAA
194 ATTGGACTCGAAACAA
397442 TATTTGGATT
Statistics
Matches: 173, Mismatches: 28, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
206 97 0.56
207 1 0.01
208 3 0.02
209 27 0.16
210 4 0.02
211 1 0.01
212 40 0.23
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (211 bp):
CAAGTTCAACTTCACAACGAAGGGACGGCTGATTGCCAACAACAATTTTAGTTTCATCAGCAATT
TCAACTCCACGACGAAGGATATTGAGCACTCGAGACAACACAAGCTCAACTTCACAACGAAGGGA
CAGCTGACTGTCAACAAACAATTTCCAAATTCCAGAACCAATTTCAACTTCACAGCAGAGGATAT
TGGACTCGAAACAACA
Found at i:397897 original size:36 final size:37
Alignment explanation
Indices: 397840--397915 Score: 111
Period size: 36 Copynumber: 2.1 Consensus size: 37
397830 TTTCGTCCTA
397840 CTAGGATTCAAACTCTAAAAAATAGGATAAAATTCTG
1 CTAGGATTCAAACTCTAAAAAATAGGATAAAATTCTG
* *
397877 CTAGGATTC-AACTCCT-AAAAATAGGATAGAATTTTG
1 CTAGGATTCAAACT-CTAAAAAATAGGATAAAATTCTG
397913 CTA
1 CTA
397916 TGTTTTAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
36 25 0.69
37 11 0.31
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.29
Consensus pattern (37 bp):
CTAGGATTCAAACTCTAAAAAATAGGATAAAATTCTG
Found at i:397930 original size:37 final size:36
Alignment explanation
Indices: 397840--397940 Score: 105
Period size: 37 Copynumber: 2.8 Consensus size: 36
397830 TTTCGTCCTA
397840 CTAGGATTCAAACT-CTAAAAAATAGGATAAAATTCTG
1 CTAGGATT-AAACTCCT-AAAAATAGGATAAAATTCTG
* * *
397877 CTAGGATTCAACTCCTAAAAATAGGATAGAATTTTG
1 CTAGGATTAAACTCCTAAAAATAGGATAAAATTCTG
** * *
397913 CTATGTTTTAAATTCCTAAAGATAGGAT
1 CTA-GGATTAAACTCCTAAAAATAGGAT
397941 CCACAAGCAC
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
36 25 0.46
37 29 0.54
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.32
Consensus pattern (36 bp):
CTAGGATTAAACTCCTAAAAATAGGATAAAATTCTG
Found at i:398647 original size:16 final size:16
Alignment explanation
Indices: 398626--398659 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
398616 CATGAATTTA
398626 TATTATATTACATTAT
1 TATTATATTACATTAT
* *
398642 TATTATTTTACTTTAT
1 TATTATATTACATTAT
398658 TA
1 TA
398660 AATTTTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTATATTACATTAT
Found at i:404316 original size:20 final size:19
Alignment explanation
Indices: 404291--404329 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
404281 CACAGACAAG
*
404291 GAGTATAGGTACTGACCCTT
1 GAGTATAGATACT-ACCCTT
*
404311 GAGTATCGATACTACCCTT
1 GAGTATAGATACTACCCTT
404330 TACATTTTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.31
Consensus pattern (19 bp):
GAGTATAGATACTACCCTT
Found at i:404432 original size:22 final size:23
Alignment explanation
Indices: 404375--404432 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 23
404365 TACCCAGAGG
* *
404375 TTAGTATCGATACTCAAGGGTCA
1 TTAGTATCGATACTAAAGGGGCA
* * *
404398 GTAGTACCTATACTAAAGGGGC-
1 TTAGTATCGATACTAAAGGGGCA
404420 TTAGTATCGATAC
1 TTAGTATCGATAC
404433 CCACGAAAAG
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
22 10 0.37
23 17 0.63
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.29
Consensus pattern (23 bp):
TTAGTATCGATACTAAAGGGGCA
Found at i:408662 original size:3 final size:3
Alignment explanation
Indices: 408654--408700 Score: 62
Period size: 3 Copynumber: 16.0 Consensus size: 3
408644 TTACCAAATG
*
408654 ATA ATA AT- ATG A-A ATA ATA ATA ATA ATA ATA ATA TATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA
408698 ATA
1 ATA
408701 TATGCATATT
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
2 3 0.08
3 34 0.85
4 3 0.08
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:408671 original size:10 final size:11
Alignment explanation
Indices: 408651--408697 Score: 51
Period size: 10 Copynumber: 4.1 Consensus size: 11
408641 ATTTTACCAA
408651 ATGATAATAAT
1 ATGATAATAAT
408662 ATGAAATAATAAT
1 ATG--ATAATAAT
*
408675 AATAATAATAAT
1 -ATGATAATAAT
408687 AT-ATAATAAT
1 ATGATAATAAT
408697 A
1 A
408698 ATATATGCAT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
10 9 0.28
11 5 0.16
12 8 0.25
13 8 0.25
14 2 0.06
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (11 bp):
ATGATAATAAT
Found at i:408673 original size:16 final size:16
Alignment explanation
Indices: 408649--408697 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
408639 GCATTTTACC
* *
408649 AAATGATAATAATATG
1 AAATAATAATAATATA
408665 AAATAATAATAATAATA
1 AAATAATAATAAT-ATA
408682 ATAATATATAATAATA
1 A-AATA-ATAATAATA
408698 ATATATGCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 12 0.43
17 3 0.11
18 5 0.18
19 8 0.29
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (16 bp):
AAATAATAATAATATA
Found at i:408678 original size:19 final size:20
Alignment explanation
Indices: 408654--408703 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
408644 TTACCAAATG
408654 ATAATAATATGA-AATA-ATA
1 ATAATAATAT-ATAATATATA
408673 ATAATAATA-ATAATATATA
1 ATAATAATATATAATATATA
408692 ATAATAATATAT
1 ATAATAATATAT
408704 GCATATTTGC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
17 1 0.04
18 4 0.14
19 21 0.75
20 2 0.07
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (20 bp):
ATAATAATATATAATATATA
Found at i:408682 original size:22 final size:22
Alignment explanation
Indices: 408654--408700 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
408644 TTACCAAATG
408654 ATAATAAT-ATGAAATAATAATA
1 ATAATAATAAT-AAATAATAATA
*
408676 ATAATAATAATATATAATAATA
1 ATAATAATAATAAATAATAATA
408698 ATA
1 ATA
408701 TATGCATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 21 0.91
23 2 0.09
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (22 bp):
ATAATAATAATAAATAATAATA
Found at i:408702 original size:13 final size:13
Alignment explanation
Indices: 408654--408703 Score: 77
Period size: 13 Copynumber: 3.9 Consensus size: 13
408644 TTACCAAATG
408654 ATAATAATATGA-A
1 ATAATAATAT-ATA
408667 ATAATAATA-ATA
1 ATAATAATATATA
408679 ATAATAATATATA
1 ATAATAATATATA
408692 ATAATAATATAT
1 ATAATAATATAT
408704 GCATATTTGC
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
11 1 0.03
12 10 0.29
13 24 0.69
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (13 bp):
ATAATAATATATA
Found at i:409590 original size:28 final size:28
Alignment explanation
Indices: 409559--409618 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 28
409549 GAAGGAAAAA
409559 TAAATACTGA-AAATT-AAGGACTGAAAT
1 TAAATACT-ATAAATTAAAGGACTGAAAT
*
409586 GTAAATACTATAAATTAAAGGATTGAAAT
1 -TAAATACTATAAATTAAAGGACTGAAAT
409615 TAAA
1 TAAA
409619 ATAATAGAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 1 0.03
28 17 0.59
29 11 0.38
ACGTcount: A:0.53, C:0.05, G:0.13, T:0.28
Consensus pattern (28 bp):
TAAATACTATAAATTAAAGGACTGAAAT
Found at i:416361 original size:11 final size:11
Alignment explanation
Indices: 416345--416407 Score: 60
Period size: 11 Copynumber: 5.9 Consensus size: 11
416335 AAAATTACAT
416345 TATTAAAAATA
1 TATTAAAAATA
416356 TATTAAAAATA
1 TATTAAAAATA
* ***
416367 TACTATTTATA
1 TATTAAAAATA
416378 -ATTATAAAAT-
1 TATTA-AAAATA
416388 T-TTAAAAATA
1 TATTAAAAATA
416398 TATTAAAAAT
1 TATTAAAAAT
416408 TCTATAATAC
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
9 5 0.12
10 7 0.17
11 28 0.70
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:416722 original size:25 final size:26
Alignment explanation
Indices: 416694--416748 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
416684 TTAATAAAAA
416694 AATAT-TTATCTAATGACAA-ATATTT
1 AATATATT-TCTAATGACAATATATTT
* *
416719 AATATATTTCTAATGATAATATTTTT
1 AATATATTTCTAATGACAATATATTT
416745 AATA
1 AATA
416749 ACTTTTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 15 0.58
26 11 0.42
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (26 bp):
AATATATTTCTAATGACAATATATTT
Found at i:416902 original size:7 final size:7
Alignment explanation
Indices: 416890--416919 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
416880 ATTTGCAATG
416890 AACCCTA
1 AACCCTA
416897 AACCCTA
1 AACCCTA
*
416904 AACTCTA
1 AACCCTA
416911 AACCCTA
1 AACCCTA
416918 AA
1 AA
416920 TCATAAACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.47, C:0.37, G:0.00, T:0.17
Consensus pattern (7 bp):
AACCCTA
Found at i:416913 original size:14 final size:14
Alignment explanation
Indices: 416894--416937 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
416884 GCAATGAACC
416894 CTAAACCCTAAACT
1 CTAAACCCTAAACT
416908 CTAAACCCTAAA-T
1 CTAAACCCTAAACT
**
416921 CATAAACTATAAACT
1 C-TAAACCCTAAACT
416936 CT
1 CT
416938 TAATCCGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
13 2 0.08
14 22 0.85
15 2 0.08
ACGTcount: A:0.45, C:0.30, G:0.00, T:0.25
Consensus pattern (14 bp):
CTAAACCCTAAACT
Found at i:416942 original size:21 final size:21
Alignment explanation
Indices: 416890--416934 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
416880 ATTTGCAATG
* * *
416890 AACCCTAAACCCTAAACTCTA
1 AACCCTAAATCATAAACTATA
416911 AACCCTAAATCATAAACTATA
1 AACCCTAAATCATAAACTATA
416932 AAC
1 AAC
416935 TCTTAATCCG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.49, C:0.31, G:0.00, T:0.20
Consensus pattern (21 bp):
AACCCTAAATCATAAACTATA
Found at i:418337 original size:12 final size:12
Alignment explanation
Indices: 418320--418364 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
418310 TTCAATCTTG
418320 AATCGAGCTTAA
1 AATCGAGCTTAA
*
418332 AATCGAGCTT-G
1 AATCGAGCTTAA
*
418343 AATCGAGCTAAA
1 AATCGAGCTTAA
*
418355 AATTGAGCTT
1 AATCGAGCTT
418365 CAATCGAGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 9 0.33
12 18 0.67
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.27
Consensus pattern (12 bp):
AATCGAGCTTAA
Found at i:418342 original size:23 final size:23
Alignment explanation
Indices: 418316--418372 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
418306 AGGCTTCAAT
*
418316 CTTGAATCGAGCTTAAAATCGAG
1 CTTGAATCGAGCTAAAAATCGAG
*
418339 CTTGAATCGAGCTAAAAATTGAG
1 CTTGAATCGAGCTAAAAATCGAG
*
418362 CTTCAATCGAG
1 CTTGAATCGAG
418373 TTCGAGTCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (23 bp):
CTTGAATCGAGCTAAAAATCGAG
Found at i:418348 original size:11 final size:11
Alignment explanation
Indices: 418316--418351 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
418306 AGGCTTCAAT
418316 CTTGAATCGAG
1 CTTGAATCGAG
*
418327 CTTAAAATCGAG
1 CTT-GAATCGAG
418339 CTTGAATCGAG
1 CTTGAATCGAG
418350 CT
1 CT
418352 AAAAATTGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (11 bp):
CTTGAATCGAG
Found at i:422999 original size:37 final size:37
Alignment explanation
Indices: 422919--423002 Score: 91
Period size: 37 Copynumber: 2.3 Consensus size: 37
422909 GGGAAACTAC
* * * *
422919 CTCAATTGAGACTAAATTTATTTTAAGAGAAACATTA
1 CTCAAGTGAGACAAAATTTATTTTAAGAAAAACATAA
* *
422956 -TTAAGTGAGACAAAACTTTATTTTAATAAAAACA-AA
1 CTCAAGTGAGACAAAA-TTTATTTTAAGAAAAACATAA
422992 CTCAAGTGAGA
1 CTCAAGTGAGA
423003 TAAGATTTCT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
36 13 0.34
37 25 0.66
ACGTcount: A:0.46, C:0.11, G:0.12, T:0.31
Consensus pattern (37 bp):
CTCAAGTGAGACAAAATTTATTTTAAGAAAAACATAA
Found at i:428523 original size:20 final size:21
Alignment explanation
Indices: 428489--428530 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
428479 TGTAGATATT
*
428489 TCATCCCCAAACGACTAGAAA
1 TCATCCCCAAACGACAAGAAA
428510 TCATCCCC-AACGACAAGAAA
1 TCATCCCCAAACGACAAGAAA
428530 T
1 T
428531 GACCACAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.43, C:0.33, G:0.10, T:0.14
Consensus pattern (21 bp):
TCATCCCCAAACGACAAGAAA
Found at i:429696 original size:12 final size:12
Alignment explanation
Indices: 429666--429711 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
429656 AAAGATTCAA
**
429666 ATAAAGAAGTGG
1 ATAAAGAAGACG
*
429678 ATGAAGAAGACG
1 ATAAAGAAGACG
429690 ATAAAGAAGACG
1 ATAAAGAAGACG
429702 ATAAAGAAGA
1 ATAAAGAAGA
429712 AGAGATGTAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.57, C:0.04, G:0.28, T:0.11
Consensus pattern (12 bp):
ATAAAGAAGACG
Found at i:431865 original size:20 final size:20
Alignment explanation
Indices: 431840--431879 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
431830 TGTAGAGATT
431840 TCATCCCAAACGACTAGAAA
1 TCATCCCAAACGACTAGAAA
*
431860 TCATCCCCAACGACTAGAAA
1 TCATCCCAAACGACTAGAAA
431880 CGACCACAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.42, C:0.33, G:0.10, T:0.15
Consensus pattern (20 bp):
TCATCCCAAACGACTAGAAA
Found at i:435205 original size:20 final size:21
Alignment explanation
Indices: 435180--435219 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
435170 CTTTACATAG
435180 TAGTATCGATACCAT-AGGCA
1 TAGTATCGATACCATCAGGCA
435200 TAGTATCGATACCATCAGGC
1 TAGTATCGATACCATCAGGC
435220 CCCAATGACT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.25
Consensus pattern (21 bp):
TAGTATCGATACCATCAGGCA
Found at i:435354 original size:20 final size:21
Alignment explanation
Indices: 435323--435361 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
435313 AGAGATTCCA
435323 TCCCCAAACGGCTAGAAATCC
1 TCCCCAAACGGCTAGAAATCC
435344 TCCCC-AACGGCTAGAAAT
1 TCCCCAAACGGCTAGAAAT
435362 GGCCACAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.33, C:0.36, G:0.15, T:0.15
Consensus pattern (21 bp):
TCCCCAAACGGCTAGAAATCC
Found at i:437133 original size:20 final size:19
Alignment explanation
Indices: 437099--437146 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
437089 AATAATTTGG
*
437099 TTTTG-AAAGCAAAATTTAA
1 TTTTGAAAAGCAAAA-TGAA
*
437118 TTTTGAAAATCAAAATGAA
1 TTTTGAAAAGCAAAATGAA
437137 TCTTTGAAAA
1 T-TTTGAAAA
437147 ATGATTTAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.48, C:0.06, G:0.10, T:0.35
Consensus pattern (19 bp):
TTTTGAAAAGCAAAATGAA
Found at i:438663 original size:20 final size:21
Alignment explanation
Indices: 438638--438677 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
438628 CTTTACATAG
438638 TAGTATCGATACCAT-AGGCA
1 TAGTATCGATACCATCAGGCA
438658 TAGTATCGATACCATCAGGC
1 TAGTATCGATACCATCAGGC
438678 CCCAATGACT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.25
Consensus pattern (21 bp):
TAGTATCGATACCATCAGGCA
Found at i:438812 original size:20 final size:21
Alignment explanation
Indices: 438781--438819 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
438771 AGAGATTCCA
438781 TCCCCAAACGGCTAGAAATCC
1 TCCCCAAACGGCTAGAAATCC
438802 TCCCC-AACGGCTAGAAAT
1 TCCCCAAACGGCTAGAAAT
438820 GGCCACAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.33, C:0.36, G:0.15, T:0.15
Consensus pattern (21 bp):
TCCCCAAACGGCTAGAAATCC
Found at i:441068 original size:21 final size:21
Alignment explanation
Indices: 441010--441075 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
441000 ACCTAAAACA
*
441010 TTATTTTTTCTACCGGAAATG
1 TTATTTTTTCTACCGAAAATG
* * *
441031 TTAATATTGGATGCTACCTAAAATG
1 TT-AT-TT--TTTCTACCGAAAATG
441056 TTATTTTTTCTACCGAAAAT
1 TTATTTTTTCTACCGAAAAT
441076 TAGGTAGCGA
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
21 13 0.38
22 2 0.06
23 4 0.12
24 2 0.06
25 13 0.38
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44
Consensus pattern (21 bp):
TTATTTTTTCTACCGAAAATG
Found at i:441663 original size:17 final size:17
Alignment explanation
Indices: 441643--441690 Score: 71
Period size: 17 Copynumber: 2.8 Consensus size: 17
441633 ATTTATTTAT
441643 ATAAAATATAATATAAA
1 ATAAAATATAATATAAA
*
441660 ATAAAGTATAATATAAA
1 ATAAAATATAATATAAA
441677 ATAAAGA-ATAATAT
1 ATAAA-ATATAATAT
441691 TATGATCTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (17 bp):
ATAAAATATAATATAAA
Found at i:441854 original size:20 final size:19
Alignment explanation
Indices: 441831--441872 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
441821 TAATTAATAT
441831 AATAATTATAAAAAATATAA
1 AATAATTATAAAAAAT-TAA
* *
441851 AATAATTTTAAATAATTAA
1 AATAATTATAAAAAATTAA
441870 AAT
1 AAT
441873 TTTAAAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AATAATTATAAAAAATTAA
Found at i:441890 original size:18 final size:17
Alignment explanation
Indices: 441854--441895 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
441844 AATATAAAAT
*
441854 AATTTT-AAATAATTAA
1 AATTTTAAAATAAATAA
441870 AATTTTAAAATAAAATAA
1 AATTTTAAAAT-AAATAA
441888 AATCTTTA
1 AAT-TTTA
441896 TATATTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 6 0.27
17 4 0.18
18 8 0.36
19 4 0.18
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (17 bp):
AATTTTAAAATAAATAA
Found at i:442517 original size:2 final size:2
Alignment explanation
Indices: 442512--442539 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
442502 ACACACACAC
442512 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
442540 TTTATGATCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:449817 original size:21 final size:20
Alignment explanation
Indices: 449779--449817 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
449769 GTCTAAATTA
* *
449779 TTTTTCAAAATTTCATTTTG
1 TTTTTCAAAATATAATTTTG
449799 TTTTTCAAAATAATAATTT
1 TTTTTCAAAAT-ATAATTT
449818 GCTTTCAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.33, C:0.08, G:0.03, T:0.56
Consensus pattern (20 bp):
TTTTTCAAAATATAATTTTG
Found at i:451843 original size:23 final size:23
Alignment explanation
Indices: 451813--452013 Score: 312
Period size: 23 Copynumber: 8.7 Consensus size: 23
451803 TCAAGGGTTC
* *
451813 TATGTGGTCCTTCTGGACAAAAT
1 TATGTGGTCCTTCGGGACAAACT
451836 TATGTGGTCCTTCGGGACAAACT
1 TATGTGGTCCTTCGGGACAAACT
*
451859 TATGTGGTCCTTCGGGATAAACT
1 TATGTGGTCCTTCGGGACAAACT
451882 TATGTGGTCCTTCGGGACAAACT
1 TATGTGGTCCTTCGGGACAAACT
*
451905 TATGTGGTCCTTCGGGATAAACT
1 TATGTGGTCCTTCGGGACAAACT
451928 TATGTGGTCCTTCGGGACAAACT
1 TATGTGGTCCTTCGGGACAAACT
* *
451951 TATGTGGTCCTTCGAGACAAACC
1 TATGTGGTCCTTCGGGACAAACT
* * *
451974 TATGTTGTCCTTCGAGACAAACC
1 TATGTGGTCCTTCGGGACAAACT
*
451997 TATGTGGTCATTCGGGA
1 TATGTGGTCCTTCGGGA
452014 TAAATATGTG
Statistics
Matches: 166, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 166 1.00
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (23 bp):
TATGTGGTCCTTCGGGACAAACT
Found at i:457064 original size:54 final size:54
Alignment explanation
Indices: 457000--457475 Score: 774
Period size: 54 Copynumber: 8.8 Consensus size: 54
456990 TTACAAATAG
457000 GCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCA
1 GCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCA
* * *
457054 ACACTAAGTGTGCAATTCACAGAATTCATCATATGTTGATGAATAACCGTTTCG
1 GCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCA
*
457108 GCACTAAGTGTGCAATTCACAGAATTCATCATATGTTGATGAATAACCGTTTCA
1 GCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCA
* *
457162 GCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAATCGTTTCG
1 GCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCA
* *
457216 GCACTAAATGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCG
1 GCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCA
* * *
457270 GCACTAAATGTGCACTTCACAGAATTCATCATATGTTGATGAATAACCGTTTC-
1 GCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCA
*
457323 GACACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAACCGTTTCA
1 G-CACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCA
*
457378 GCACTAAATGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCA
1 GCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCA
* * * * *
457432 ACACTATGTGTGCAAATCACGGAATTCATAATATGTTTATGAAT
1 GCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAAT
457476 GAACGTATGG
Statistics
Matches: 396, Mismatches: 24, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
53 1 0.00
54 394 0.99
55 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (54 bp):
GCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCA
Found at i:457431 original size:26 final size:27
Alignment explanation
Indices: 457294--457440 Score: 69
Period size: 26 Copynumber: 5.5 Consensus size: 27
457284 CTTCACAGAA
457294 TTCATCA-TATGTTGATGAATAACCGT
1 TTCATCACTATGTTGATGAATAACCGT
* * *
457320 TTCGA-CACTAAG-TG-TGCAAT-TCACGAAA
1 TTC-ATCACTATGTTGATG-AATAAC-CG--T
457348 TTCATCA-TATGTTGATGAATAACCGT
1 TTCATCACTATGTTGATGAATAACCGT
* ** * * *
457374 TTCAGCACTA-AATG-TGCAATTCACGGAA
1 TTCATCACTATGTTGATG-AA-TAACCG-T
457402 TTCATCA-TATGTTGATGAATAACCGT
1 TTCATCACTATGTTGATGAATAACCGT
*
457428 TTCAACACTATGT
1 TTCATCACTATGT
457441 GTGCAAATCA
Statistics
Matches: 85, Mismatches: 19, Indels: 33
0.62 0.14 0.24
Matches are distributed among these distances:
25 5 0.06
26 28 0.33
27 25 0.29
28 22 0.26
29 5 0.06
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (27 bp):
TTCATCACTATGTTGATGAATAACCGT
Found at i:462927 original size:10 final size:10
Alignment explanation
Indices: 462912--462948 Score: 74
Period size: 10 Copynumber: 3.7 Consensus size: 10
462902 CATGACTTCA
462912 TTCATTTATT
1 TTCATTTATT
462922 TTCATTTATT
1 TTCATTTATT
462932 TTCATTTATT
1 TTCATTTATT
462942 TTCATTT
1 TTCATTT
462949 TCATCATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.19, C:0.11, G:0.00, T:0.70
Consensus pattern (10 bp):
TTCATTTATT
Found at i:470928 original size:20 final size:21
Alignment explanation
Indices: 470883--470931 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
470873 ATTGCATCAA
470883 TATCGATA-TTGAGAGAAGGG
1 TATCGATACTTGAGAGAAGGG
*
470903 TGTCGATACTATGAG-GAA-GG
1 TATCGATACT-TGAGAGAAGGG
470923 TATCGATAC
1 TATCGATAC
470932 CATTGATCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 17 0.68
21 4 0.16
22 4 0.16
ACGTcount: A:0.33, C:0.10, G:0.31, T:0.27
Consensus pattern (21 bp):
TATCGATACTTGAGAGAAGGG
Found at i:470996 original size:19 final size:19
Alignment explanation
Indices: 470958--470996 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
470948 CAAAAATCGA
* * *
470958 ATCGGTACCGTATTAGAGT
1 ATCGGTACCATAGTACAGT
470977 ATCGGTACCATAGTACAGT
1 ATCGGTACCATAGTACAGT
470996 A
1 A
470997 GTATCGATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (19 bp):
ATCGGTACCATAGTACAGT
Found at i:471728 original size:215 final size:217
Alignment explanation
Indices: 471350--471755 Score: 663
Period size: 215 Copynumber: 1.9 Consensus size: 217
471340 TTACCAAATA
* *
471350 GGCACTAAGTGTGCAATTCAAGGAATTTATCATATGTTGATGAATAACAGTTTCGACATTAAGTG
1 GGCACTAAGTGTGCAATTCAAGGAATTCATCATATGTTGATGAATAACAGTTTCGACACTAAGTG
*
471415 TGCAATTCACGGAATTCATCATATGTTGATGAATAACCATTTCGGAACTAAGTGTGCAATTCACA
66 TGCAATTCACAGAATTCATCATATGTTGATGAATAACCATTTCGGAACTAAGTGTGCAATTCACA
*
471480 AAATTCATCATATGTTGATGAATAATCGTTTCGGCACTAAGTGTGCAATTCACGGAATTCAACAT
131 AAATTCATCATATGTTGATGAATAATCGTTTCGGCACTAAGTGTGCAAATCACGGAATTCAACAT
471545 ATGTTGATTAATAACTATTTTC
196 ATGTTGATTAATAACTATTTTC
* * *
471567 GGCACTAAGTGTGCACTTCACGGAATTCATCATATG-TGATGAATAAC-GTTTCGGCACTAAGTG
1 GGCACTAAGTGTGCAATTCAAGGAATTCATCATATGTTGATGAATAACAGTTTCGACACTAAGTG
* * * * * *
471630 TGTAATTTACAGAATTCATCATATGTTGATGAATAATCGTTTTGGCACTAAGTGTGCAATTCACA
66 TGCAATTCACAGAATTCATCATATGTTGATGAATAACCATTTCGGAACTAAGTGTGCAATTCACA
* *
471695 AAATTCATCATATGTTGATGAATAATTGTTTCGGCACTATGTGTGCAAATCACGGAATTCA
131 AAATTCATCATATGTTGATGAATAATCGTTTCGGCACTAAGTGTGCAAATCACGGAATTCA
471756 TAATATATTT
Statistics
Matches: 174, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
215 130 0.75
216 11 0.06
217 33 0.19
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (217 bp):
GGCACTAAGTGTGCAATTCAAGGAATTCATCATATGTTGATGAATAACAGTTTCGACACTAAGTG
TGCAATTCACAGAATTCATCATATGTTGATGAATAACCATTTCGGAACTAAGTGTGCAATTCACA
AAATTCATCATATGTTGATGAATAATCGTTTCGGCACTAAGTGTGCAAATCACGGAATTCAACAT
ATGTTGATTAATAACTATTTTC
Found at i:471785 original size:54 final size:54
Alignment explanation
Indices: 471350--471787 Score: 567
Period size: 54 Copynumber: 8.1 Consensus size: 54
471340 TTACCAAATA
* * *
471350 GGCACTAAGTGTGCAATTCAAGGAATTTATCATATGTTGATGAATAACAGTTTC
1 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTC
* * *
471404 GACATTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCATTTC
1 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTC
* ** *
471458 GGAACTAAGTGTGCAATTCACAAAATTCATCATATGTTGATGAATAATCGTTTC
1 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTC
* * **
471512 GGCACTAAGTGTGCAATTCACGGAATTCAACATATGTTGATTAATAACTATTTTC
1 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAAC-CGTTTC
*
471567 GGCACTAAGTGTGCACTTCACGGAATTCATCATATG-TGATGAATAA-CGTTTC
1 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTC
* * * * *
471619 GGCACTAAGTGTGTAATTTACAGAATTCATCATATGTTGATGAATAATCGTTTT
1 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTC
** **
471673 GGCACTAAGTGTGCAATTCACAAAATTCATCATATGTTGATGAATAATTGTTTC
1 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTC
* * * * * *
471727 GGCACTATGTGTGCAAATCACGGAATTCATAATATATTTATGAATGACCGTATT-
1 GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGT-TTC
471781 GGCACTA
1 GGCACTA
471788 CGGGTTCATT
Statistics
Matches: 334, Mismatches: 46, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
52 36 0.11
53 10 0.03
54 248 0.74
55 40 0.12
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (54 bp):
GGCACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTC
Found at i:477406 original size:6 final size:6
Alignment explanation
Indices: 477395--477420 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
477385 GCCATGAGGT
477395 GGTAGA GGTAGA GGTAGA GGTAGA GG
1 GGTAGA GGTAGA GGTAGA GGTAGA GG
477421 GAGGGGATAT
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:0.31, C:0.00, G:0.54, T:0.15
Consensus pattern (6 bp):
GGTAGA
Found at i:479781 original size:29 final size:30
Alignment explanation
Indices: 479748--479808 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
479738 AAATTTTGTC
**
479748 TAGTGACTAAAATATAAGTTTTG-AAAGTT
1 TAGTGACTAAAATATAAACTTTGAAAAGTT
*
479777 TAGTGACTAAAGTATAAACTTTGAAAAGTT
1 TAGTGACTAAAATATAAACTTTGAAAAGTT
479807 TA
1 TA
479809 AGGACCAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 20 0.71
30 8 0.29
ACGTcount: A:0.43, C:0.05, G:0.16, T:0.36
Consensus pattern (30 bp):
TAGTGACTAAAATATAAACTTTGAAAAGTT
Found at i:481730 original size:12 final size:12
Alignment explanation
Indices: 481713--481737 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
481703 GATCGAGGAC
481713 GACTTGCGATAA
1 GACTTGCGATAA
481725 GACTTGCGATAA
1 GACTTGCGATAA
481737 G
1 G
481738 TCAACTTCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.16, G:0.28, T:0.24
Consensus pattern (12 bp):
GACTTGCGATAA
Found at i:483007 original size:23 final size:23
Alignment explanation
Indices: 482981--483077 Score: 101
Period size: 23 Copynumber: 4.3 Consensus size: 23
482971 GGGTGTTACA
*
482981 TATGTGGTCATTCGGGACAAAAT
1 TATGTGGTCCTTCGGGACAAAAT
*
483004 TATGTGGTCCTTCAGGA-AAAACT
1 TATGTGGTCCTTCGGGACAAAA-T
* **
483027 TATATGGTCCTTCGGGACAAACC
1 TATGTGGTCCTTCGGGACAAAAT
* *
483050 TATGTGGTTCTTTGGGAC-AAA-
1 TATGTGGTCCTTCGGGACAAAAT
483071 TATGTGG
1 TATGTGG
483078 CACTTTGGTG
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
21 7 0.11
22 6 0.10
23 46 0.74
24 3 0.05
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.32
Consensus pattern (23 bp):
TATGTGGTCCTTCGGGACAAAAT
Found at i:483083 original size:21 final size:22
Alignment explanation
Indices: 483040--483098 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 22
483030 ATGGTCCTTC
**
483040 GGGACAAACCTATGTGGTTCTTT
1 GGGACAAA-CTATGTGGCACTTT
483063 GGGACAAA-TATGTGGCACTTT
1 GGGACAAACTATGTGGCACTTT
*
483084 GGTG-CAAATTATGTG
1 GG-GACAAACTATGTG
483099 AGCTGTGGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 17 0.53
22 7 0.22
23 8 0.25
ACGTcount: A:0.25, C:0.14, G:0.29, T:0.32
Consensus pattern (22 bp):
GGGACAAACTATGTGGCACTTT
Found at i:488371 original size:28 final size:26
Alignment explanation
Indices: 488330--488395 Score: 78
Period size: 28 Copynumber: 2.5 Consensus size: 26
488320 TTAATTGCTT
488330 AATTATAAAATTTTTCATAAATAAAAA
1 AATTATAAAATTTTTCATAAA-AAAAA
* * **
488357 ACATTATTAATTTTTTTTTAAAAAAAA
1 A-ATTATAAAATTTTTCATAAAAAAAA
488384 AATTATAAAATT
1 AATTATAAAATT
488396 CAAAAAATAT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
26 9 0.28
27 7 0.22
28 16 0.50
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (26 bp):
AATTATAAAATTTTTCATAAAAAAAA
Found at i:489519 original size:28 final size:28
Alignment explanation
Indices: 489467--489521 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
489457 AAACCCCTAA
*
489467 AAGCTCTTAACTATAAATTCGGGATGTC
1 AAGCTCTTAACTATAAATTCAGGATGTC
489495 AAGCTCTTAACTATAAAATT-AGGATGT
1 AAGCTCTTAACTAT-AAATTCAGGATGT
489522 GACATGCTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 20 0.80
29 5 0.20
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (28 bp):
AAGCTCTTAACTATAAATTCAGGATGTC
Found at i:492498 original size:29 final size:29
Alignment explanation
Indices: 492456--492545 Score: 108
Period size: 29 Copynumber: 3.1 Consensus size: 29
492446 AGTTCATTAT
* ** *
492456 TCTTTTGCTTAACAGTGTTTAATTGTTCC
1 TCTTTTACTTAACAGTGTTTAACCGTTCA
* *
492485 TCTTTTACTCAACAGTTTTTAACCGTTCA
1 TCTTTTACTTAACAGTGTTTAACCGTTCA
* *
492514 TCTTTTACTTAACAGTGTTTAACTGGTCA
1 TCTTTTACTTAACAGTGTTTAACCGTTCA
492543 TCT
1 TCT
492546 AACTGGCATA
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.21, C:0.20, G:0.11, T:0.48
Consensus pattern (29 bp):
TCTTTTACTTAACAGTGTTTAACCGTTCA
Found at i:492625 original size:81 final size:80
Alignment explanation
Indices: 492514--492926 Score: 529
Period size: 81 Copynumber: 5.1 Consensus size: 80
492504 TAACCGTTCA
* * * * * * *
492514 TCTTTTACTTAACAGTGTTTAACTGGTCATCTAACTGGCATAATTGACACCTTTTTGCCAAATGC
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAAATGACA-CTTTTTGTCAAATGC
*
492579 ATAACTAGGCCATTAT
65 ACAACTAGGCCATTAT
* * *
492595 TCTTTTACTCAACGGTATTTAATCGTTCATCTAACTGGCATAATTGACACTTTTCTGCCAAATGC
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAAATGACACTTTT-TGTCAAATGC
* * *
492660 ACAGCTAAGCCATTTT
65 ACAACTAGGCCATTAT
*
492676 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAAGTGACACTTTTCTGTCAAATGC
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAAATGACACTTTT-TGTCAAATGC
*
492741 CCAACTAGGCCATTAT
65 ACAACTAGGCCATTAT
* * * * *
492757 TCTTTTACTCAAAGGTATTTAATCGTTCATCTAGCTGCCATAAATGACATCTTTCTGTCAAATGC
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAAATGACA-CTTTTTGTCAAATGC
*
492822 ACAACTAGGTCATTAT
65 ACAACTAGGCCATTAT
* *
492838 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTAGAATAAATGACACCTTTTTGTCAAATGC
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAAATGACA-CTTTTTGTCAAATGC
* * *
492903 ATAGCTAGGCCTATTAC
65 ACAACTAGGCC-ATTAT
492920 TCTTTTA
1 TCTTTTA
492927 TTTTAGATCA
Statistics
Matches: 292, Mismatches: 37, Indels: 5
0.87 0.11 0.01
Matches are distributed among these distances:
80 5 0.02
81 272 0.93
82 15 0.05
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.37
Consensus pattern (80 bp):
TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAAATGACACTTTTTGTCAAATGCA
CAACTAGGCCATTAT
Found at i:496661 original size:2 final size:2
Alignment explanation
Indices: 496654--496686 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
496644 TGTAATACAT
496654 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
496687 CCTTTCATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:496863 original size:29 final size:28
Alignment explanation
Indices: 496821--496910 Score: 85
Period size: 29 Copynumber: 3.1 Consensus size: 28
496811 AGTCCATTAT
*
496821 TCTTTTAC-CTAACAGTGTTTAATTGTT-
1 TCTTTTACTC-AACAGTGTTTAAATGTTA
**
496848 TCTAATTTACTCAACAGTGTTTAACCGTTCA
1 TCT--TTTACTCAACAGTGTTTAAATGTT-A
*
496879 TCTTTTACTTAACAGTGTTTAAATGTTCA
1 TCTTTTACTCAACAGTGTTTAAATGTT-A
496908 TCT
1 TCT
496911 AACTAGCATA
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
27 3 0.06
29 46 0.87
30 1 0.02
31 3 0.06
ACGTcount: A:0.26, C:0.18, G:0.10, T:0.47
Consensus pattern (28 bp):
TCTTTTACTCAACAGTGTTTAAATGTTA
Found at i:497021 original size:81 final size:81
Alignment explanation
Indices: 496879--497289 Score: 465
Period size: 81 Copynumber: 5.1 Consensus size: 81
496869 TAACCGTTCA
* * * ** * *
496879 TCTTTTACTTAACAGTGTTTAAATGTTCATCTAACTAGCATAAATGACACATTTTTGCCAAATGC
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTAGCATAAATGACACATTTCTGTCAAATGC
*
496944 ACAGCTAGGCTATTAT
66 ACAACTAGGCTATTAT
* * * * * * **
496960 TCTTTTACTAAATGGTATTTAATCGTTTATCTAACATA-CATAATTAACACATTTCTACCAAATG
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAAC-TAGCATAAATGACACATTTCTGTCAAATG
497024 CACAACTAGG-TCATTAT
65 CACAACTAGGCT-ATTAT
* * *
497041 TCTTTTACTCAACGGTATTTAACTGTTCATCTAACTGGCATAAATGACACCTTTCTGTCAAATGC
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTAGCATAAATGACACATTTCTGTCAAATGC
* * *
497106 ATAGA-TAGACCATTAT
66 ACA-ACTAGGCTATTAT
* * *
497122 TCTTTTGCTCAACGGTATTTAACCATTCATCTAACTAGCTTAAATGACATC-TTT-TGTTCAAAT
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTAGCATAAATGACA-CATTTCTG-TCAAAT
*
497185 GCACAACTAGG-TCACTAT
64 GCACAACTAGGCT-ATTAT
*
497203 TCTTTTACTCAACGGTATTTAACCGTTCATCTAATTAGCATAAATGACACATTTCTGTCAAATGC
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTAGCATAAATGACACATTTCTGTCAAATGC
*
497268 ACAACTAGGCCTATTAC
66 ACAACTAGG-CTATTAT
497285 TCTTT
1 TCTTT
497290 ATTTTAGATC
Statistics
Matches: 276, Mismatches: 41, Indels: 25
0.81 0.12 0.07
Matches are distributed among these distances:
80 6 0.02
81 255 0.92
82 14 0.05
83 1 0.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.37
Consensus pattern (81 bp):
TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTAGCATAAATGACACATTTCTGTCAAATGC
ACAACTAGGCTATTAT
Found at i:497990 original size:54 final size:54
Alignment explanation
Indices: 497926--498044 Score: 202
Period size: 54 Copynumber: 2.2 Consensus size: 54
497916 ACTATACTAG
497926 GGTATCGATACTCTATTACAGTACATATACCATTTTTGTATTATGTGATCAAAT
1 GGTATCGATACTCTATTACAGTACATATACCATTTTTGTATTATGTGATCAAAT
* * *
497980 GGTATCGATACTCTATTACGGTACCTATACCATTTTTGTATTCTGTGATCAAAT
1 GGTATCGATACTCTATTACAGTACATATACCATTTTTGTATTATGTGATCAAAT
*
498034 GGTATCAATAC
1 GGTATCGATAC
498045 CATCATTACG
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 61 1.00
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.39
Consensus pattern (54 bp):
GGTATCGATACTCTATTACAGTACATATACCATTTTTGTATTATGTGATCAAAT
Found at i:506097 original size:27 final size:26
Alignment explanation
Indices: 506067--506125 Score: 93
Period size: 26 Copynumber: 2.2 Consensus size: 26
506057 TAATTTTTTT
506067 AAAATATTTTAAATATAA-AAATATTCA
1 AAAATA-TTTAAATATAATAAATATT-A
506094 AAAATATTTAAATATAATAAATATTA
1 AAAATATTTAAATATAATAAATATTA
506120 AAAATA
1 AAAATA
506126 AATATTAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
26 18 0.58
27 13 0.42
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.36
Consensus pattern (26 bp):
AAAATATTTAAATATAATAAATATTA
Found at i:506124 original size:18 final size:18
Alignment explanation
Indices: 506076--506129 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
506066 TAAAATATTT
506076 TAAATA-TAAAAATATTCAA
1 TAAATATTAAAAATA-T-AA
*
506095 -AAATATT-TAAATATAA
1 TAAATATTAAAAATATAA
506111 TAAATATTAAAAATA-AA
1 TAAATATTAAAAATATAA
506128 TA
1 TA
506130 TTAATTTACT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
16 2 0.07
17 12 0.40
18 15 0.50
19 1 0.03
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAATATTAAAAATATAA
Found at i:506125 original size:13 final size:13
Alignment explanation
Indices: 506109--506133 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
506099 ATTTAAATAT
506109 AATAAATATTAAA
1 AATAAATATTAAA
506122 AATAAATATTAA
1 AATAAATATTAA
506134 TTTACTAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AATAAATATTAAA
Found at i:506182 original size:25 final size:26
Alignment explanation
Indices: 506139--506197 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 26
506129 ATTAATTTAC
** *
506139 TAAAAATGTAAATTTATATTAAAAAT
1 TAAAAATGTAAATACATATCAAAAAT
*
506165 TAAAAAT-TAAATACATATCATAAAT
1 TAAAAATGTAAATACATATCAAAAAT
506190 TATAAAAT
1 TA-AAAAT
506198 AATAACTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 16 0.57
26 12 0.43
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (26 bp):
TAAAAATGTAAATACATATCAAAAAT
Found at i:513561 original size:121 final size:117
Alignment explanation
Indices: 513409--513819 Score: 426
Period size: 121 Copynumber: 3.5 Consensus size: 117
513399 TAATTTGGCG
* * * *
513409 TCATATGTGATGAATTAAGGCAAGGTTGAACAAATTCTTCTCATTATGAACTTCTCCTCCTTCTT
1 TCATTTGTGATGAATTAAAGAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTCCTCCTTCTT
* * *
513474 CAGATGAGTTATTCTCATTATGAACACTTCTGAAAATGTTGATGTCGATATATC
66 CAGATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATGTCG-T-TATC
* * *
513528 TCATTCTGTGATAGAATTAAAGAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCATC
1 TCATT-TGTGAT-GAATTAAAGAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTCCTCCTTC
* * * *
513593 TTCAGATGAGTTCTTCTCATTATGAATTTCCTATGGAAATGTTGA--TC--CATC
64 TTCAGATGAGTTCTTCTCATTATGAA-CTCTTCTGGAAATGTTGATGTCGTTATC
* * * * *
513644 -GA---GTGATGAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCGTT
1 TCATTTGTGATGAATTAAAG--AAAGGTTGAACAAGTTCTTCTCATTATGAACTTC-TCCTCCTT
* *
513705 CTTCAGATGAGTTCTTCTCATTATTAACTCTTCTGGAAAT-TCTGATGTTGTTCTATC
63 CTTCAGATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGT-TGATGTCG-T-TATC
* * *
513762 TCCTTATGTGATAGAATCAAACAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTC
1 TCATT-TGTGAT-GAATTAAAGAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTC
513820 TGGAAAAGTT
Statistics
Matches: 239, Mismatches: 34, Indels: 36
0.77 0.11 0.12
Matches are distributed among these distances:
110 8 0.03
111 6 0.03
112 46 0.19
113 29 0.12
114 1 0.00
115 1 0.00
116 3 0.01
118 3 0.01
119 4 0.02
120 8 0.03
121 73 0.31
122 46 0.19
123 5 0.02
124 6 0.03
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.39
Consensus pattern (117 bp):
TCATTTGTGATGAATTAAAGAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTCCTCCTTCTT
CAGATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATGTCGTTATC
Found at i:514162 original size:113 final size:112
Alignment explanation
Indices: 513958--514401 Score: 712
Period size: 112 Copynumber: 4.0 Consensus size: 112
513948 AGAATCAAAC
* *
513958 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTT-CATCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * *
514022 ATGAACT-TCCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAGCA
66 ATGAACTCTAC-CTGG-CATGTTGATCCATCGAGTGATGAATTCAAGCA
* *
514070 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
514135 ATGAACTCTACCTGGCAATGCTGATCCATCAAGTGATGAATTCAAGCA
66 ATGAACTCTACCTGGC-ATGTTGATCCATCGAGTGATGAATTCAAGCA
514183 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
514248 ATGAACTCTACCTGGCATGTTGATCCATTGAGTGATGGATTCAAGCA
66 ATGAACTCTACCTGGCATGTTGATCCATCGAGTGATGAATTCAAGCA
*
514295 AAAGGTTGAACAAGTTCTTCTCATTATGAACTGCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * *
514360 ATGAACTCTACATGGCATGTTGATCCATTGAGTGATGGATTC
66 ATGAACTCTACCTGGCATGTTGATCCATCGAGTGATGAATTC
514402 GAATCTTTAT
Statistics
Matches: 312, Mismatches: 17, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
112 168 0.54
113 142 0.46
114 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37
Consensus pattern (112 bp):
AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTCTACCTGGCATGTTGATCCATCGAGTGATGAATTCAAGCA
Found at i:514283 original size:225 final size:224
Alignment explanation
Indices: 513958--514401 Score: 712
Period size: 225 Copynumber: 2.0 Consensus size: 224
513948 AGAATCAAAC
513958 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCATCTTCAGATGAGTTCTTCTCATTA
1 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCATCTTCAGATGAGTTCTTCTCATTA
*
514023 TGAACTTCCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAGCAAAAGGTTGAACAAATTCT
66 TGAACTTACTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAGCAAAAGGTTGAACAAATTCT
* * *
514088 TCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGCAA
131 TCTCATTATGAACTGCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACATGGC-A
514153 TGCTGATCCATCAAGTGATGAATTCAAGCA
195 TGCTGATCCATCAAGTGATGAATTCAAGCA
* *
514183 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTT-CATCTTCAGATGAGTTCTTCTCATT
* * * * *
514248 ATGAACTCTAC-CTGG-CATGTTGATCCATTGAGTGATGGATTCAAGCAAAAGGTTGAACAAGTT
65 ATGAACT-TACTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAGCAAAAGGTTGAACAAATT
514311 CTTCTCATTATGAACTGCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACATGGC
129 CTTCTCATTATGAACTGCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACATGGC
* ** *
514376 ATGTTGATCCATTGAGTGATGGATTC
194 ATGCTGATCCATCAAGTGATGAATTC
514402 GAATCTTTAT
Statistics
Matches: 202, Mismatches: 15, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
224 22 0.11
225 143 0.71
226 35 0.17
227 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37
Consensus pattern (224 bp):
AAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCATCTTCAGATGAGTTCTTCTCATTA
TGAACTTACTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAGCAAAAGGTTGAACAAATTCT
TCTCATTATGAACTGCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACATGGCAT
GCTGATCCATCAAGTGATGAATTCAAGCA
Found at i:516351 original size:24 final size:24
Alignment explanation
Indices: 516306--516351 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
516296 CTGTTATTTC
* *
516306 AAATTTATTAATATAATTTTTAAA
1 AAATATATTAATATAATATTTAAA
516330 AAATATATTAATA-AGATATTTA
1 AAATATATTAATATA-ATATTTA
516352 TTACTTAGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 1 0.05
24 18 0.95
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (24 bp):
AAATATATTAATATAATATTTAAA
Found at i:519623 original size:13 final size:13
Alignment explanation
Indices: 519605--519639 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
519595 ACCAGAATAC
*
519605 ACCACCGTGCACA
1 ACCACCATGCACA
519618 ACCACCATGCACA
1 ACCACCATGCACA
519631 ACCACCATG
1 ACCACCATG
519640 TATAAGGCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.34, C:0.46, G:0.11, T:0.09
Consensus pattern (13 bp):
ACCACCATGCACA
Found at i:520992 original size:168 final size:168
Alignment explanation
Indices: 520714--521049 Score: 672
Period size: 168 Copynumber: 2.0 Consensus size: 168
520704 GCCTTTGAAG
520714 TTCAAATGACCAGCACCACTGCCCATTAGTGTTTGATATAGATGCGCCAACGGATGAATAAATGT
1 TTCAAATGACCAGCACCACTGCCCATTAGTGTTTGATATAGATGCGCCAACGGATGAATAAATGT
520779 TGCTATTGTTATCAAACCTAGAAAGTTCTAGACTCGATTAAAGAACGAGAGGGAATGACTAGATG
66 TGCTATTGTTATCAAACCTAGAAAGTTCTAGACTCGATTAAAGAACGAGAGGGAATGACTAGATG
520844 AGAGCGGCGACAAATATGGATAATGTAGGGATTAGGTT
131 AGAGCGGCGACAAATATGGATAATGTAGGGATTAGGTT
520882 TTCAAATGACCAGCACCACTGCCCATTAGTGTTTGATATAGATGCGCCAACGGATGAATAAATGT
1 TTCAAATGACCAGCACCACTGCCCATTAGTGTTTGATATAGATGCGCCAACGGATGAATAAATGT
520947 TGCTATTGTTATCAAACCTAGAAAGTTCTAGACTCGATTAAAGAACGAGAGGGAATGACTAGATG
66 TGCTATTGTTATCAAACCTAGAAAGTTCTAGACTCGATTAAAGAACGAGAGGGAATGACTAGATG
521012 AGAGCGGCGACAAATATGGATAATGTAGGGATTAGGTT
131 AGAGCGGCGACAAATATGGATAATGTAGGGATTAGGTT
521050 GCTAGAAATC
Statistics
Matches: 168, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
168 168 1.00
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (168 bp):
TTCAAATGACCAGCACCACTGCCCATTAGTGTTTGATATAGATGCGCCAACGGATGAATAAATGT
TGCTATTGTTATCAAACCTAGAAAGTTCTAGACTCGATTAAAGAACGAGAGGGAATGACTAGATG
AGAGCGGCGACAAATATGGATAATGTAGGGATTAGGTT
Found at i:521470 original size:21 final size:21
Alignment explanation
Indices: 521444--521486 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
521434 AGTAATGAAT
*
521444 ATTGCTACAGTATACTGATGC
1 ATTGCTACAGTATACCGATGC
*
521465 ATTGCTACAGTGTACCGATGC
1 ATTGCTACAGTATACCGATGC
521486 A
1 A
521487 CAAAAACATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (21 bp):
ATTGCTACAGTATACCGATGC
Found at i:521539 original size:21 final size:21
Alignment explanation
Indices: 521509--521573 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
521499 ATATAAAATT
*
521509 GTGTATCGATGCACTGCTACA
1 GTGTACCGATGCACTGCTACA
521530 GTGTACCGATGCACTGCTACA
1 GTGTACCGATGCACTGCTACA
*
521551 GTGTACCGATGTACTGCTACA
1 GTGTACCGATGCACTGCTACA
521572 GT
1 GT
521574 AACTTCAGCT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.28
Consensus pattern (21 bp):
GTGTACCGATGCACTGCTACA
Found at i:525046 original size:2 final size:2
Alignment explanation
Indices: 525039--525087 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
525029 ATAAATTTCT
525039 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
525081 TA TA TA T
1 TA TA TA T
525088 GGTTGCACTC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:525608 original size:18 final size:17
Alignment explanation
Indices: 525569--525620 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
525559 TTTTCTTCCG
*
525569 GTATTGTTTCTTTTTGT
1 GTATTGTTTCTTTTTCT
*
525586 ATATTGTTTCTATTTTCT
1 GTATTGTTTCT-TTTTCT
* *
525604 GTATTGCTCCTTTTTCT
1 GTATTGTTTCTTTTTCT
525621 TATACGATTA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
17 16 0.55
18 13 0.45
ACGTcount: A:0.10, C:0.13, G:0.12, T:0.65
Consensus pattern (17 bp):
GTATTGTTTCTTTTTCT
Found at i:525668 original size:17 final size:17
Alignment explanation
Indices: 525648--525696 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
525638 TGTATCGTTC
*
525648 ATTGTATAATATCTTTT
1 ATTGTATTATATCTTTT
* *
525665 ATTGTATTATTTCATTT
1 ATTGTATTATATCTTTT
*
525682 ACTGTATTATATCTT
1 ATTGTATTATATCTT
525697 AAATTTCATT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.27, C:0.08, G:0.06, T:0.59
Consensus pattern (17 bp):
ATTGTATTATATCTTTT
Found at i:527314 original size:30 final size:31
Alignment explanation
Indices: 527264--527326 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 31
527254 CCATCATTTC
* * * *
527264 TAAAATTATTGATTTGGTCCCCTAACTTTTT
1 TAAAATTATCGATATGGTCCCCCAAATTTTT
527295 TAAAATTATCGA-ATGGTCCCCCAAATTTTT
1 TAAAATTATCGATATGGTCCCCCAAATTTTT
527325 TA
1 TA
527327 TAAGGCTTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 17 0.61
31 11 0.39
ACGTcount: A:0.30, C:0.17, G:0.10, T:0.43
Consensus pattern (31 bp):
TAAAATTATCGATATGGTCCCCCAAATTTTT
Found at i:535684 original size:66 final size:66
Alignment explanation
Indices: 535471--535673 Score: 298
Period size: 66 Copynumber: 3.1 Consensus size: 66
535461 GGTCTGTATG
*
535471 TATTCAATTATCACTCCACCTAATGCACCACAAAGGTACACGAGTCACATCGAGTGATCTTATAC
1 TATTCAATTATCACTCCACCTCATGCACCACAAAGGTACACGAGTCACATCGAGTGATC-TATAC
535536 AA
65 AA
* * * * * * *
535538 CATTCAATTATCACTCCACCTCATGCACCACAGAGGTACATGAGTTACATCGATTAATCTGTACA
1 TATTCAATTATCACTCCACCTCATGCACCACAAAGGTACACGAGTCACATCGAGTGATCTATACA
535603 A
66 A
* * *
535604 TATTCAATTATCACTACACCTCATGCACCACAAAGGTATACGAGTCACATCGAGTGATCAATACA
1 TATTCAATTATCACTCCACCTCATGCACCACAAAGGTACACGAGTCACATCGAGTGATCTATACA
535669 A
66 A
535670 TATT
1 TATT
535674 TAGTAATCAC
Statistics
Matches: 118, Mismatches: 18, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
66 66 0.56
67 52 0.44
ACGTcount: A:0.35, C:0.26, G:0.12, T:0.27
Consensus pattern (66 bp):
TATTCAATTATCACTCCACCTCATGCACCACAAAGGTACACGAGTCACATCGAGTGATCTATACA
A
Found at i:535805 original size:15 final size:16
Alignment explanation
Indices: 535775--535809 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
535765 TCATCGGAAA
535775 ATTATTAAACTCATAT
1 ATTATTAAACTCATAT
*
535791 ATTATTTAA-TCATAT
1 ATTATTAAACTCATAT
535806 ATTA
1 ATTA
535810 ATACTTTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.49
Consensus pattern (16 bp):
ATTATTAAACTCATAT
Found at i:541730 original size:14 final size:14
Alignment explanation
Indices: 541711--541741 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
541701 TTGACTTTTT
*
541711 GGTCAAAGTCAATG
1 GGTCAAAGTCAACG
541725 GGTCAAAGTCAACG
1 GGTCAAAGTCAACG
541739 GGT
1 GGT
541742 TGATTCGGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.16, G:0.32, T:0.19
Consensus pattern (14 bp):
GGTCAAAGTCAACG
Found at i:541757 original size:14 final size:15
Alignment explanation
Indices: 541740--541778 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
541730 AAGTCAACGG
*
541740 GTTGATTCGGAC-GA
1 GTTGACTCGGACAGA
*
541754 GTTGACTCAGACAGA
1 GTTGACTCGGACAGA
541769 GTTGACTCGG
1 GTTGACTCGG
541779 TGACTGGACC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 10 0.48
15 11 0.52
ACGTcount: A:0.23, C:0.18, G:0.33, T:0.26
Consensus pattern (15 bp):
GTTGACTCGGACAGA
Found at i:548253 original size:13 final size:13
Alignment explanation
Indices: 548235--548292 Score: 53
Period size: 13 Copynumber: 4.2 Consensus size: 13
548225 CGTGTCAAGC
548235 TGAGTCAACTCAT
1 TGAGTCAACTCAT
*
548248 TGAGTCAACCCAGT
1 TGAGTCAACTCA-T
* *
548262 TGAGACAACTTTAAT
1 TGAGTCAAC--TCAT
*
548277 AGAGTCAACTCAT
1 TGAGTCAACTCAT
548290 TGA
1 TGA
548293 ATTTGACTAG
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
13 16 0.47
14 9 0.26
15 8 0.24
16 1 0.03
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (13 bp):
TGAGTCAACTCAT
Done.