Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold163
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: 1887244
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.31
Warning! 142876 characters in sequence are not A, C, G, or T
File 2 of 7
Found at i:287785 original size:5 final size:5
Alignment explanation
Indices: 287775--287800 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
287765 TGATTATTCA
287775 TTTTC TTTTC TTTTC TTTTC TTTTC T
1 TTTTC TTTTC TTTTC TTTTC TTTTC T
287801 GATGAATAAA
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:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:289376 original size:32 final size:32
Alignment explanation
Indices: 289334--289394 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
289324 TTTTTTGAAA
289334 AATAATTATAACTATTTAAAT-AAT-ATTATTTG
1 AATAATTATAA-TA-TTAAATGAATAATTATTTG
*
289366 AATAGTTATAATATTAAATGAATAATTAT
1 AATAATTATAATATTAAATGAATAATTAT
289395 GTGTTTATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 6 0.23
31 5 0.19
32 15 0.58
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (32 bp):
AATAATTATAATATTAAATGAATAATTATTTG
Found at i:289387 original size:20 final size:20
Alignment explanation
Indices: 289353--289394 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
289343 AACTATTTAA
** *
289353 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
289373 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
289393 AT
1 AT
289395 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:297853 original size:20 final size:20
Alignment explanation
Indices: 297830--297872 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
297820 AACTATTTAA
** *
297830 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
297850 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
297870 ATA
1 ATA
297873 TTTTTATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:297853 original size:32 final size:32
Alignment explanation
Indices: 297811--297871 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
297801 TTTTTTGAAA
297811 AATAATTATAACTATTTAAAT-AAT-ATTATTTG
1 AATAATTATAA-TA-TTAAATGAATAATTATTTG
*
297843 AATAGTTATAATATTAAATGAATAATTAT
1 AATAATTATAATATTAAATGAATAATTAT
297872 ATTTTTATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 6 0.23
31 5 0.19
32 15 0.58
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (32 bp):
AATAATTATAATATTAAATGAATAATTATTTG
Found at i:302444 original size:411 final size:406
Alignment explanation
Indices: 301616--303222 Score: 2220
Period size: 411 Copynumber: 4.0 Consensus size: 406
301606 TTATTAAGGG
** *
301616 TTTTCTTGACCTTGAAAATGTATTACTTGTACAATGATTGAAAACTAATGTAATAAGCATAAATC
1 TTTTCTTGACCTTGAAAATGTATTACTTGTACAGGGATTGAAAACTAAT-TAATAAGCATAAGTC
* * *
301681 AAGCATGTGACCAAAGACTTAATATGTGATTTAACAAAAATAGTTGTGATGTAATTAATGAAAAA
65 AA-CATATGACCAAAGGCTTAATATGAGATTTAACAAAAATAGTTGTGATGTAATTAATG-AAAA
** * *
301746 AAATT-TTGGAATAAGAAGAGCAAAAACTTTTGATAATTGCTACAAAGTTTTTAATGAAGTTATT
128 AAATTGTTATAATAAGAGGAGCAAAAACTTTTGAAAATTGCTACAAAGTTTTTAATGAAGTTATT
* * *
301810 TTCAATAAAGCTACTATGCAAGATCTAGATGTGTGACATCAAAAGATTGGTGGTGTGAATTATCG
193 TGCAATAAAGCTACTATGCAAGATCTAGAGGTGTGACATCAAAAGATTGGTGATGTGAATTATCG
* * *
301875 AAGCTTACAAAGAATTGATCAATATGATGCAATTAGAAGACTTTTAAAACTCGAAAGTGTTGTGA
258 AAACTTACAAAGACTTGATCAATATGATGCAATTAGAAGACTTTCAAAACTCGAAAGTGTTGTGA
* *
301940 CCAAACGTTGTGGAGATTGTGTTTTGGGGAGACAACACATGGTGACCCATCTAATTTTGCCACAA
323 CCAAACCTTGTGGAGATTGTGTTTTGGGGAAACAACACATGGTGACCCATCTAATTTTGCCACAA
*
302005 GTAGTGACACAATTAAAGG
388 GTAGTGACACAATTAAAGA
* * * *
302024 TTTTCTTGACCTTTAAAATATATTACTTGTA-TGTGGATTGAAAGCTAAGTTAATAAGCATAAGT
1 TTTTCTTGACCTTGAAAATGTATTACTTGTACAG-GGATTGAAAACTAA-TTAATAAGCATAAGT
* *
302088 CAACTATATGACCAAAGGCTTAATATGATATTTAACAAAAATAGTTGGGATGTAATTAATGAAAA
64 CAAC-ATATGACCAAAGGCTTAATATGAGATTTAACAAAAATAGTTGTGATGTAATTAATGAAAA
* * *
302153 GAATTGTTATAATAGGAGGAGCAAAAATTTTTGAAAATTGCTACAAAGTTTTTAATGAAGTTATT
128 AAATTGTTATAATAAGAGGAGCAAAAACTTTTGAAAATTGCTACAAAGTTTTTAATGAAGTTATT
*
302218 TGCAATAAAGCTACTATGCAAGATCTAAAGGTGTGACAATATCAAAAGATTGGTGATGTGAATTA
193 TGCAATAAAGCTACTATGCAAGATCTAGAGGTGTGAC---ATCAAAAGATTGGTGATGTGAATTA
* * * *
302283 TCGAAACTTACAAAGACTTTATCAATATGATGTAATTAGAATACTTTCAAAACTCAAAAGTGTTG
255 TCGAAACTTACAAAGACTTGATCAATATGATGCAATTAGAAGACTTTCAAAACTCGAAAGTGTTG
*
302348 TGACCAAACCTTGTGGAGATTGTGTTTTGGGGAAACAACACATGGTGACCTATCTAATTTTGCCA
320 TGACCAAACCTTGTGGAGATTGTGTTTTGGGGAAACAACACATGGTGACCCATCTAATTTTGCCA
302413 CAAGTAGTGACACAATTAAAGA
385 CAAGTAGTGACACAATTAAAGA
* *
302435 TTTTCTTGACCTTGATAATGTACTACTTGTACAGGGATTGAAAACTAACTTAATAAGCATAAGTC
1 TTTTCTTGACCTTGAAAATGTATTACTTGTACAGGGATTGAAAACTAA-TTAATAAGCATAAGTC
302500 AA-ATATGTGACCAAAGGCTTAATATGAGATTTAACAAAAATAGTTGTGATGTAATTAATGAAAA
65 AACATA--TGACCAAAGGCTTAATATGAGATTTAACAAAAATAGTTGTGATGTAATTAATGAAAA
* ** * *
302564 AAATTCTTATAATAAGAGGAGCAAAAAAATTTGAAACTTGTTACAAAGTTTTTAATGAAGTTATT
128 AAATTGTTATAATAAGAGGAGCAAAAACTTTTGAAAATTGCTACAAAGTTTTTAATGAAGTTATT
* * *
302629 TGCAATAAAGCTACTATGCAAGATCTGGAGGTGTTACATCAAAAGATTGGTGATGTGAACTATCG
193 TGCAATAAAGCTACTATGCAAGATCTAGAGGTGTGACATCAAAAGATTGGTGATGTGAATTATCG
* * * *
302694 AAACTTACAAAGACTTGATCAATATGATGCAATTAGAAGATTTTCAAAAGTTGAATGTGTTGTGA
258 AAACTTACAAAGACTTGATCAATATGATGCAATTAGAAGACTTTCAAAACTCGAAAGTGTTGTGA
* * * * * * * * * *
302759 TCAGACCTTGTAGAGATTGTATTTTGGGTAAACAGCACGTGTTGTCTCATCTAATTTTGCCACAA
323 CCAAACCTTGTGGAGATTGTGTTTTGGGGAAACAACACATGGTGACCCATCTAATTTTGCCACAA
* * *
302824 GTAATAACACAATTAAA-T
388 GTAGTGACACAATTAAAGA
*
302842 TTTTCCTTGACC-TGAAAATGTATTACTTTTACAGGGATTGAAAAC-------TAA-C-T---T-
1 TTTT-CTTGACCTTGAAAATGTATTACTTGTACAGGGATTGAAAACTAATTAATAAGCATAAGTC
*
302893 -A-ATA--ACAAAAGGCTTAATATGAGATTTAACAAAAAATAGTTGTGATGTAATTAATGAAAAA
65 AACATATGACCAAAGGCTTAATATGAGATTTAAC-AAAAATAGTTGTGATGTAATTAATGAAAAA
* * * * *
302954 AA-TGTTATAATAAAAGGAGCAAGAACTTTTGACAATTGCTACAAAGTTTTTAAGGAAATTATTT
129 AATTGTTATAATAAGAGGAGCAAAAACTTTTGAAAATTGCTACAAAGTTTTTAATGAAGTTATTT
* * * *
303018 GCAATAAAGCTACTATGCAAGATCTGGAGGTGTTACATTAAAA-ATT-TTGATGTGAATTATCGA
194 GCAATAAAGCTACTATGCAAGATCTAGAGGTGTGACATCAAAAGATTGGTGATGTGAATTATCGA
* *
303081 AACTTACAAAGACTTGATCAATATGATGCAATTAGAAGACTTTCGAAACCCGAAAGTGTTGTGAC
259 AACTTACAAAGACTTGATCAATATGATGCAATTAGAAGACTTTCAAAACTCGAAAGTGTTGTGAC
* * *
303146 CAGACCTTGTGGAGATTGTGTTTTGGGGAAACAACACATGTTGTCCCATCTAATTTTGCCACAAG
324 CAAACCTTGTGGAGATTGTGTTTTGGGGAAACAACACATGGTGACCCATCTAATTTTGCCACAAG
303211 TAGTGACACAAT
389 TAGTGACACAAT
303223 GGCCATTGGA
Statistics
Matches: 1079, Mismatches: 108, Indels: 46
0.88 0.09 0.04
Matches are distributed among these distances:
386 142 0.13
387 3 0.00
388 119 0.11
389 32 0.03
392 4 0.00
394 1 0.00
397 1 0.00
398 1 0.00
399 3 0.00
407 43 0.04
408 355 0.33
409 4 0.00
411 370 0.34
412 1 0.00
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (406 bp):
TTTTCTTGACCTTGAAAATGTATTACTTGTACAGGGATTGAAAACTAATTAATAAGCATAAGTCA
ACATATGACCAAAGGCTTAATATGAGATTTAACAAAAATAGTTGTGATGTAATTAATGAAAAAAA
TTGTTATAATAAGAGGAGCAAAAACTTTTGAAAATTGCTACAAAGTTTTTAATGAAGTTATTTGC
AATAAAGCTACTATGCAAGATCTAGAGGTGTGACATCAAAAGATTGGTGATGTGAATTATCGAAA
CTTACAAAGACTTGATCAATATGATGCAATTAGAAGACTTTCAAAACTCGAAAGTGTTGTGACCA
AACCTTGTGGAGATTGTGTTTTGGGGAAACAACACATGGTGACCCATCTAATTTTGCCACAAGTA
GTGACACAATTAAAGA
Found at i:309508 original size:5 final size:5
Alignment explanation
Indices: 309498--309529 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
309488 GTAATTTGAT
309498 AATTA AATTA AATTA AATTA AATTA AATTA AA
1 AATTA AATTA AATTA AATTA AATTA AATTA AA
309530 ACCAAAATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
AATTA
Found at i:310924 original size:20 final size:20
Alignment explanation
Indices: 310899--310938 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
310889 ATAAATTATG
310899 AATGTGTTGATTATTTGAAT
1 AATGTGTTGATTATTTGAAT
310919 AATGTGTTGATTATTTGAAT
1 AATGTGTTGATTATTTGAAT
310939 TGAAATGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (20 bp):
AATGTGTTGATTATTTGAAT
Found at i:310984 original size:16 final size:16
Alignment explanation
Indices: 310959--310992 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
310949 ATATACATAT
* *
310959 ATGTGTAAATTTGATA
1 ATGTGCAAATATGATA
310975 ATGTGCAAATATGATA
1 ATGTGCAAATATGATA
310991 AT
1 AT
310993 TGGATATTGG
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:0.41, C:0.03, G:0.18, T:0.38
Consensus pattern (16 bp):
ATGTGCAAATATGATA
Found at i:325040 original size:13 final size:13
Alignment explanation
Indices: 325022--325046 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
325012 CAATCAAATG
325022 CACACAAAATAAA
1 CACACAAAATAAA
325035 CACACAAAATAA
1 CACACAAAATAA
325047 TATTAAAATA
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:0.24, G:0.00, T:0.08
Consensus pattern (13 bp):
CACACAAAATAAA
Found at i:325378 original size:27 final size:27
Alignment explanation
Indices: 325348--325828 Score: 386
Period size: 27 Copynumber: 17.8 Consensus size: 27
325338 ACATTCGAAT
* **
325348 GGTATAATGACTGAAATACCCTTAAAG
1 GGTAAAATGACTGAAATACCCCCAAAG
* *
325375 GGTAAAATAACTGAAATACCCCCATAG
1 GGTAAAATGACTGAAATACCCCCAAAG
* *
325402 GGTAAAATGATTGAAATACCCCCATAG
1 GGTAAAATGACTGAAATACCCCCAAAG
* *
325429 GGTAAAATTACTGAAATACCCCCATAG
1 GGTAAAATGACTGAAATACCCCCAAAG
* *
325456 GATAAAATGACTGAAATACCCCCATAG
1 GGTAAAATGACTGAAATACCCCCAAAG
* * * *
325483 GATAAAATGA-TCAAATTACCCTCGAAG
1 GGTAAAATGACTGAAA-TACCCCCAAAG
* *
325510 GGTAAAATGACCGAATTACCCCCAAAG
1 GGTAAAATGACTGAAATACCCCCAAAG
* *
325537 GGTAAAACGA-TCGAATTACCCCCAAAG
1 GGTAAAATGACT-GAAATACCCCCAAAG
* *
325564 GGTAAAATGACTGAATTACCCTCAAAG
1 GGTAAAATGACTGAAATACCCCCAAAG
* * *
325591 GGTAAAATTA-TCAAAATACCCTCGAAA-
1 GGTAAAATGACT-GAAATACCC-CCAAAG
* * *
325618 GGTAAAATTA-TCGAAATACCCTCGAAG
1 GGTAAAATGACT-GAAATACCCCCAAAG
*
325645 GGTAAAATGATTGAAATACCCCCGAAA-
1 GGTAAAATGACTGAAATACCCCC-AAAG
* *
325672 GGTAAAATGATCT-AAATACTCTCATAA-
1 GGTAAAATGA-CTGAAATACCCCCA-AAG
* * *
325699 GGTAAAATGACCGAAATACTCCCGAAG
1 GGTAAAATGACTGAAATACCCCCAAAG
* * *
325726 GGCAAAATGA-TCGAAATACCCCTATAG
1 GGTAAAATGACT-GAAATACCCCCAAAG
* * ** * *
325753 AGTAAAATAACCAAAATACCCCTATAG
1 GGTAAAATGACTGAAATACCCCCAAAG
* * * *
325780 GATAAAATGACCGAAATACCCTCATAG
1 GGTAAAATGACTGAAATACCCCCAAAG
**
325807 GGTAAAATGACTGTTATACCCC
1 GGTAAAATGACTGAAATACCCC
325829 TAGGAGATAA
Statistics
Matches: 374, Mismatches: 65, Indels: 30
0.80 0.14 0.06
Matches are distributed among these distances:
26 11 0.03
27 353 0.94
28 10 0.03
ACGTcount: A:0.43, C:0.21, G:0.16, T:0.21
Consensus pattern (27 bp):
GGTAAAATGACTGAAATACCCCCAAAG
Found at i:327985 original size:49 final size:48
Alignment explanation
Indices: 327927--328023 Score: 158
Period size: 49 Copynumber: 2.0 Consensus size: 48
327917 TATAGTGATT
* * *
327927 TAAAACCATCGTTGTCGGGCTACTCGAGATGGTAGAATTTGCAAATAG
1 TAAAACCATCGTTGTCGGGCCACCCGAGATGGTAGAATATGCAAATAG
327975 TAAAAGCCATCGTTGTCGGGCCACCCGAGATGGTAGAATATGCAAATAG
1 TAAAA-CCATCGTTGTCGGGCCACCCGAGATGGTAGAATATGCAAATAG
328024 CCACCTGGGA
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
48 5 0.11
49 40 0.89
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.24
Consensus pattern (48 bp):
TAAAACCATCGTTGTCGGGCCACCCGAGATGGTAGAATATGCAAATAG
Found at i:331820 original size:18 final size:18
Alignment explanation
Indices: 331793--331848 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
331783 CGATCCCGGG
*
331793 CCTTTGCTCTCTCCCTGTC
1 CCTTT-CTCTGTCCCTGTC
* *
331812 TCTTTCTCTGTCCCTCTC
1 CCTTTCTCTGTCCCTGTC
*
331830 CCTTTCCCTGTCCCTGTC
1 CCTTTCTCTGTCCCTGTC
331848 C
1 C
331849 TTGCTCTTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
18 27 0.87
19 4 0.13
ACGTcount: A:0.00, C:0.48, G:0.09, T:0.43
Consensus pattern (18 bp):
CCTTTCTCTGTCCCTGTC
Found at i:333460 original size:16 final size:16
Alignment explanation
Indices: 333411--333462 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
333401 AAAAATTATG
* * *
333411 TTTTCCATCCATCTAG
1 TTTTCCATCCTTCCAA
* *
333427 TTTTCTACCCTT-CAA
1 TTTTCCATCCTTCCAA
333442 TTTTCCATCCTTCCAA
1 TTTTCCATCCTTCCAA
333458 TTTTC
1 TTTTC
333463 TTTTCACTCT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
15 11 0.39
16 17 0.61
ACGTcount: A:0.17, C:0.33, G:0.02, T:0.48
Consensus pattern (16 bp):
TTTTCCATCCTTCCAA
Found at i:338331 original size:312 final size:312
Alignment explanation
Indices: 337766--338389 Score: 1239
Period size: 312 Copynumber: 2.0 Consensus size: 312
337756 ATTATCATAT
337766 AGTATATTTAATTTTTCTTATGATATAAATTACATAATATATAAAATAAATAAATAAAAATACTA
1 AGTATATTTAATTTTTCTTATGATATAAATTACATAATATATAAAATAAATAAATAAAAATACTA
337831 TAAACTTGAAATTGGGTTGGGCGGTTGCCCAAGCTCAGTTTTCAAACCTAATATTTGTGTCCAAG
66 TAAACTTGAAATTGGGTTGGGCGGTTGCCCAAGCTCAGTTTTCAAACCTAATATTTGTGTCCAAG
337896 CCCTCCCAAATTTCAAGAGGGCCTTTGAGCTTGAGTGAGTAACCCAACCCTTTAACAGGTCTACA
131 CCCTCCCAAATTTCAAGAGGGCCTTTGAGCTTGAGTGAGTAACCCAACCCTTTAACAGGTCTACA
337961 CATGCCAATCGTCCCACCTACCTAGCACTACCTCGAAAACATCGTTCACATGTTGCTCCAACACA
196 CATGCCAATCGTCCCACCTACCTAGCACTACCTCGAAAACATCGTTCACATGTTGCTCCAACACA
338026 ACCCAGGATTGCCTTGCACAACTCTATTCATTTGTGTGACGCACTGCTTTAG
261 ACCCAGGATTGCCTTGCACAACTCTATTCATTTGTGTGACGCACTGCTTTAG
*
338078 AGTATATTTCATTTTTCTTATGATATAAATTACATAATATATAAAATAAATAAATAAAAATACTA
1 AGTATATTTAATTTTTCTTATGATATAAATTACATAATATATAAAATAAATAAATAAAAATACTA
338143 TAAACTTGAAATTGGGTTGGGCGGTTGCCCAAGCTCAGTTTTCAAACCTAATATTTGTGTCCAAG
66 TAAACTTGAAATTGGGTTGGGCGGTTGCCCAAGCTCAGTTTTCAAACCTAATATTTGTGTCCAAG
338208 CCCTCCCAAATTTCAAGAGGGCCTTTGAGCTTGAGTGAGTAACCCAACCCTTTAACAGGTCTACA
131 CCCTCCCAAATTTCAAGAGGGCCTTTGAGCTTGAGTGAGTAACCCAACCCTTTAACAGGTCTACA
338273 CATGCCAATCGTCCCACCTACCTAGCACTACCTCGAAAACATCGTTCACATGTTGCTCCAACACA
196 CATGCCAATCGTCCCACCTACCTAGCACTACCTCGAAAACATCGTTCACATGTTGCTCCAACACA
338338 ACCCAGGATTGCCTTGCACAACTCTATTCATTTGTGTGACGCACTGCTTTAG
261 ACCCAGGATTGCCTTGCACAACTCTATTCATTTGTGTGACGCACTGCTTTAG
338390 GTTACTACTC
Statistics
Matches: 311, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
312 311 1.00
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.30
Consensus pattern (312 bp):
AGTATATTTAATTTTTCTTATGATATAAATTACATAATATATAAAATAAATAAATAAAAATACTA
TAAACTTGAAATTGGGTTGGGCGGTTGCCCAAGCTCAGTTTTCAAACCTAATATTTGTGTCCAAG
CCCTCCCAAATTTCAAGAGGGCCTTTGAGCTTGAGTGAGTAACCCAACCCTTTAACAGGTCTACA
CATGCCAATCGTCCCACCTACCTAGCACTACCTCGAAAACATCGTTCACATGTTGCTCCAACACA
ACCCAGGATTGCCTTGCACAACTCTATTCATTTGTGTGACGCACTGCTTTAG
Found at i:341873 original size:24 final size:25
Alignment explanation
Indices: 341846--341904 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
341836 CAGCTCGAAA
* *
341846 GAGCGTCCCGAT-ATTAGCTCTCAT
1 GAGCATCCCGATAAATAGCTCTCAT
* *
341870 GAGCATCTCGATAAATGGCTCTCAT
1 GAGCATCCCGATAAATAGCTCTCAT
*
341895 GAGCTTCCCG
1 GAGCATCCCG
341905 CTATATGGTT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
24 10 0.36
25 18 0.64
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27
Consensus pattern (25 bp):
GAGCATCCCGATAAATAGCTCTCAT
Found at i:341912 original size:25 final size:25
Alignment explanation
Indices: 341862--341929 Score: 68
Period size: 25 Copynumber: 2.7 Consensus size: 25
341852 CCCGATATTA
* *
341862 GCTCTCATGAGCATCTCGATAAATG
1 GCTCTCATGAGCTTCCCGATAAATG
* *
341887 GCTCTCATGAGCTTCCCGCTATATG
1 GCTCTCATGAGCTTCCCGATAAATG
341912 G-T-TCATGCAAGCTTCCCG
1 GCTCTCATG--AGCTTCCCG
341930 TTAATAGCTC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
23 5 0.14
24 1 0.03
25 31 0.84
ACGTcount: A:0.21, C:0.29, G:0.21, T:0.29
Consensus pattern (25 bp):
GCTCTCATGAGCTTCCCGATAAATG
Found at i:342031 original size:26 final size:26
Alignment explanation
Indices: 341985--342074 Score: 94
Period size: 26 Copynumber: 3.5 Consensus size: 26
341975 GCAGCTTTTA
* *
341985 TGAGCGTCCCG-TTATATGGCTCTTCG
1 TGAGCTTCCCGATTA-AAGGCTCTTCG
* *
342011 TAAGCTTCCCGATTAAAGGCTCTTTG
1 TGAGCTTCCCGATTAAAGGCTCTTCG
* * *
342037 TGAGCTTCCTGATTAATGGCTCTCCG
1 TGAGCTTCCCGATTAAAGGCTCTTCG
342063 -GAGCTTCCCGAT
1 TGAGCTTCCCGAT
342075 ACGGCTCGCT
Statistics
Matches: 53, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
25 11 0.21
26 39 0.74
27 3 0.06
ACGTcount: A:0.17, C:0.27, G:0.23, T:0.33
Consensus pattern (26 bp):
TGAGCTTCCCGATTAAAGGCTCTTCG
Found at i:345815 original size:13 final size:13
Alignment explanation
Indices: 345797--345821 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
345787 ACCCCATGAA
345797 TTTCTTCTTCTTC
1 TTTCTTCTTCTTC
345810 TTTCTTCTTCTT
1 TTTCTTCTTCTT
345822 TAAATTTATA
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTCTTCTTCTTC
Found at i:349045 original size:6 final size:6
Alignment explanation
Indices: 349034--349066 Score: 57
Period size: 6 Copynumber: 5.3 Consensus size: 6
349024 TTTTGGGGTT
349034 TTAGGG TTAGGG TTAGGG TTAGGG TTTAGGG TT
1 TTAGGG TTAGGG TTAGGG TTAGGG -TTAGGG TT
349067 TTTAGGATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.15, C:0.00, G:0.45, T:0.39
Consensus pattern (6 bp):
TTAGGG
Found at i:349064 original size:7 final size:7
Alignment explanation
Indices: 349019--349067 Score: 50
Period size: 6 Copynumber: 7.3 Consensus size: 7
349009 TCTCCCCACG
*
349019 TTAGGTT
1 TTAGGGT
*
349026 TTGGGGTT
1 TTAGGG-T
349034 TTAGGG-
1 TTAGGGT
349040 TTAGGG-
1 TTAGGGT
349046 TTAGGG-
1 TTAGGGT
349052 TTAGGGT
1 TTAGGGT
349059 TTAGGGT
1 TTAGGGT
349066 TT
1 TT
349068 TTAGGATTTG
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
6 18 0.49
7 13 0.35
8 6 0.16
ACGTcount: A:0.12, C:0.00, G:0.43, T:0.45
Consensus pattern (7 bp):
TTAGGGT
Found at i:351292 original size:6 final size:6
Alignment explanation
Indices: 351281--351313 Score: 57
Period size: 6 Copynumber: 5.3 Consensus size: 6
351271 TTTTGGGGTT
351281 TTAGGG TTAGGG TTAGGG TTAGGG TTTAGGG TT
1 TTAGGG TTAGGG TTAGGG TTAGGG -TTAGGG TT
351314 TTTAGGATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.15, C:0.00, G:0.45, T:0.39
Consensus pattern (6 bp):
TTAGGG
Found at i:351311 original size:7 final size:7
Alignment explanation
Indices: 351266--351314 Score: 50
Period size: 6 Copynumber: 7.3 Consensus size: 7
351256 TCTCCCCACG
*
351266 TTAGGTT
1 TTAGGGT
*
351273 TTGGGGTT
1 TTAGGG-T
351281 TTAGGG-
1 TTAGGGT
351287 TTAGGG-
1 TTAGGGT
351293 TTAGGG-
1 TTAGGGT
351299 TTAGGGT
1 TTAGGGT
351306 TTAGGGT
1 TTAGGGT
351313 TT
1 TT
351315 TTAGGATTTG
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
6 18 0.49
7 13 0.35
8 6 0.16
ACGTcount: A:0.12, C:0.00, G:0.43, T:0.45
Consensus pattern (7 bp):
TTAGGGT
Found at i:351765 original size:124 final size:125
Alignment explanation
Indices: 351500--351786 Score: 486
Period size: 125 Copynumber: 2.3 Consensus size: 125
351490 ATTTATTAAG
* * *
351500 GAAATCGCTCCCACGTGGACGCGCTTTTGCTATATTAGGTCCTAAAAAAATAATTTTGAGTTGAT
1 GAAATCGCTCCCACGTGGACGCGCTTTTGCTATAGTAGGTCCTAAAAAAATAATTTCGAGTTGAA
* *
351565 GTTTCTGAGCAAATAGTATAAAAAATGCTTCAAGCAGGATGCTTTATCAGAAGAATTTCT
66 ATTTCTGAGCAAATAGTATAAAAAACGCTTCAAGCAGGATGCTTTATCAGAAGAATTTCT
* *
351625 GAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCGAGTTGAA
1 GAAATCGCTCCCACGTGGACGCGCTTTTGCTATAGTAGGTCCTAAAAAAATAATTTCGAGTTGAA
351690 ATTTCTGAGCAAATAGTAT-AAAAACGCTTCAAGCAGGATGCTTTATCAGAAGAATTTCT
66 ATTTCTGAGCAAATAGTATAAAAAACGCTTCAAGCAGGATGCTTTATCAGAAGAATTTCT
* *
351749 GAAATCTCTCCCACGTGGACGCGTTTTTGCTATAGTAG
1 GAAATCGCTCCCACGTGGACGCGCTTTTGCTATAGTAG
351787 CATGTTTGGG
Statistics
Matches: 152, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
124 74 0.49
125 78 0.51
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.30
Consensus pattern (125 bp):
GAAATCGCTCCCACGTGGACGCGCTTTTGCTATAGTAGGTCCTAAAAAAATAATTTCGAGTTGAA
ATTTCTGAGCAAATAGTATAAAAAACGCTTCAAGCAGGATGCTTTATCAGAAGAATTTCT
Found at i:352905 original size:29 final size:29
Alignment explanation
Indices: 352863--352921 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
352853 TGAAATAACA
352863 TAGCATCAATAACGGCGTTAACTATCACG
1 TAGCATCAATAACGGCGTTAACTATCACG
352892 TAGCATCAATAACGGCGTTAACTATCACG
1 TAGCATCAATAACGGCGTTAACTATCACG
352921 T
1 T
352922 GGTTAAATCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (29 bp):
TAGCATCAATAACGGCGTTAACTATCACG
Found at i:354991 original size:49 final size:49
Alignment explanation
Indices: 354847--354967 Score: 197
Period size: 49 Copynumber: 2.5 Consensus size: 49
354837 TAAGAATATT
* ** * *
354847 AACTATTTTGTATTTTATTAAATGGAATAATATCAAAATATTCAAAATA
1 AACTATTTTGTATTTTATTACATCAAATAATATCAAAATACTCAAATTA
354896 AACTATTTTGTATTTTATTACATCAAATAATATCAAAATACTCAAATTA
1 AACTATTTTGTATTTTATTACATCAAATAATATCAAAATACTCAAATTA
354945 AACTATTTTGTATTTTATTACAT
1 AACTATTTTGTATTTTATTACAT
354968 TAATATAAAT
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 67 1.00
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.44
Consensus pattern (49 bp):
AACTATTTTGTATTTTATTACATCAAATAATATCAAAATACTCAAATTA
Found at i:355559 original size:18 final size:18
Alignment explanation
Indices: 355532--355569 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
355522 GAAAAATGAA
* *
355532 ACATATAAGGGTTAGGAT
1 ACATAAAAGGGCTAGGAT
355550 ACATAAAAGGGCTAGGAT
1 ACATAAAAGGGCTAGGAT
355568 AC
1 AC
355570 TGCATCATCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.42, C:0.11, G:0.26, T:0.21
Consensus pattern (18 bp):
ACATAAAAGGGCTAGGAT
Found at i:356346 original size:108 final size:108
Alignment explanation
Indices: 356157--356373 Score: 434
Period size: 108 Copynumber: 2.0 Consensus size: 108
356147 TGGATCCTCG
356157 TACGGTGTCCATTCAAACTATATGACCATGATGGAAATATTAGTTATGTACTAAATACTAAATAC
1 TACGGTGTCCATTCAAACTATATGACCATGATGGAAATATTAGTTATGTACTAAATACTAAATAC
356222 CAATCGGCTATCTCATTATGGAAATATCTATTTTATTTAATAC
66 CAATCGGCTATCTCATTATGGAAATATCTATTTTATTTAATAC
356265 TACGGTGTCCATTCAAACTATATGACCATGATGGAAATATTAGTTATGTACTAAATACTAAATAC
1 TACGGTGTCCATTCAAACTATATGACCATGATGGAAATATTAGTTATGTACTAAATACTAAATAC
356330 CAATCGGCTATCTCATTATGGAAATATCTATTTTATTTAATAC
66 CAATCGGCTATCTCATTATGGAAATATCTATTTTATTTAATAC
356373 T
1 T
356374 TGTGCTTCCG
Statistics
Matches: 109, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
108 109 1.00
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (108 bp):
TACGGTGTCCATTCAAACTATATGACCATGATGGAAATATTAGTTATGTACTAAATACTAAATAC
CAATCGGCTATCTCATTATGGAAATATCTATTTTATTTAATAC
Found at i:356356 original size:52 final size:52
Alignment explanation
Indices: 356187--356356 Score: 166
Period size: 52 Copynumber: 3.2 Consensus size: 52
356177 TATGACCATG
356187 ATGGAAATATTAGTTATGTACTAAATACTAAATACCAATCGGCTATCTCATT
1 ATGGAAATATTAGTTATGTACTAAATACTAAATACCAATCGGCTATCTCATT
* * ** * * ** * *
356239 ATGGAAATATCTA-TT-T-TATTTAATACTACGGTGTCCATTCAAACTATATGACCATG
1 ATGGAAATAT-TAGTTATGTACTAAATACTA-AAT-ACCAATC-GGCTATCT---CATT
356295 ATGGAAATATTAGTTATGTACTAAATACTAAATACCAATCGGCTATCTCATT
1 ATGGAAATATTAGTTATGTACTAAATACTAAATACCAATCGGCTATCTCATT
356347 ATGGAAATAT
1 ATGGAAATAT
356357 CTATTTTATT
Statistics
Matches: 88, Mismatches: 20, Indels: 20
0.69 0.16 0.16
Matches are distributed among these distances:
50 10 0.11
51 2 0.02
52 30 0.34
53 7 0.08
55 7 0.08
56 20 0.23
57 2 0.02
58 10 0.11
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (52 bp):
ATGGAAATATTAGTTATGTACTAAATACTAAATACCAATCGGCTATCTCATT
Found at i:357399 original size:24 final size:24
Alignment explanation
Indices: 357372--357418 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
357362 AATTTTTATG
357372 ATTTAAAAAAATTTAAAAAATAAA
1 ATTTAAAAAAATTTAAAAAATAAA
** *
357396 ATTTAAAACTATTTTAAAAATAA
1 ATTTAAAAAAATTTAAAAAATAA
357419 TTAAAAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (24 bp):
ATTTAAAAAAATTTAAAAAATAAA
Found at i:357463 original size:11 final size:11
Alignment explanation
Indices: 357447--357500 Score: 67
Period size: 11 Copynumber: 4.9 Consensus size: 11
357437 TTTAAATAGA
357447 AATTTGAGAGG
1 AATTTGAGAGG
357458 AATTTGAGAGG
1 AATTTGAGAGG
357469 AATTTGAGA-G
1 AATTTGAGAGG
357479 AATATT-AGAGAG
1 AAT-TTGAGAG-G
*
357491 AAATTGAGAG
1 AATTTGAGAG
357501 AAATGATTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
10 7 0.18
11 24 0.63
12 7 0.18
ACGTcount: A:0.43, C:0.00, G:0.31, T:0.26
Consensus pattern (11 bp):
AATTTGAGAGG
Found at i:357491 original size:12 final size:10
Alignment explanation
Indices: 357444--357504 Score: 59
Period size: 11 Copynumber: 5.6 Consensus size: 10
357434 TCTTTTAAAT
357444 AGAAATTTGAG
1 AGAAA-TTGAG
*
357455 AGGAATTTGAG
1 A-GAAATTGAG
*
357466 AGGAATTTGAG
1 A-GAAATTGAG
357477 AGAATATTAGAG
1 AGAA-ATT-GAG
357489 AGAAATTGAG
1 AGAAATTGAG
357499 AGAAAT
1 AGAAAT
357505 GATTTAGTTG
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
10 12 0.27
11 23 0.51
12 10 0.22
ACGTcount: A:0.46, C:0.00, G:0.30, T:0.25
Consensus pattern (10 bp):
AGAAATTGAG
Found at i:373383 original size:17 final size:17
Alignment explanation
Indices: 373361--373398 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
373351 TTGAATGGCA
373361 TACACATACTTTTCTTT
1 TACACATACTTTTCTTT
373378 TACACATACTTTTCTTT
1 TACACATACTTTTCTTT
373395 TACA
1 TACA
373399 TTTAAGGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.26, C:0.24, G:0.00, T:0.50
Consensus pattern (17 bp):
TACACATACTTTTCTTT
Found at i:374222 original size:21 final size:22
Alignment explanation
Indices: 374177--374224 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
374167 ATGTTTCATT
* * *
374177 TTTTGAATTTTTTTATTATTAA
1 TTTTAAATTTTATAATTATTAA
374199 TTTTAAATTTTATAATTATT-A
1 TTTTAAATTTTATAATTATTAA
374220 TTTTA
1 TTTTA
374225 TTTTTGAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (22 bp):
TTTTAAATTTTATAATTATTAA
Found at i:387200 original size:6 final size:6
Alignment explanation
Indices: 387188--387271 Score: 78
Period size: 6 Copynumber: 14.0 Consensus size: 6
387178 TCCCTTCTCT
* * * * * *
387188 TTGCTG CTGCTG CTGCTG GTGTTG TGGCTG TTGCTG TTGCTG TCGCTG
1 TTGCTG TTGCTG TTGCTG TTGCTG TTGCTG TTGCTG TTGCTG TTGCTG
* * * *
387236 TTGCTG TTGTTG TTGCTG CTGATG CTGCTG TTGCTG
1 TTGCTG TTGCTG TTGCTG TTGCTG TTGCTG TTGCTG
387272 AGCATGCCTC
Statistics
Matches: 63, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
6 63 1.00
ACGTcount: A:0.01, C:0.19, G:0.36, T:0.44
Consensus pattern (6 bp):
TTGCTG
Found at i:390725 original size:44 final size:44
Alignment explanation
Indices: 390651--390804 Score: 254
Period size: 44 Copynumber: 3.5 Consensus size: 44
390641 TTTGAGTACT
* * *
390651 TCTGATCAGTAACAAGTGATAAATGGTAGCTTTAGCTACAGTTA
1 TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* * *
390695 TCTGATCAGTGACAAGTGACAAGTGATAGCTTTAACTACACTTA
1 TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
390739 TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
390783 TCTGATCAGTGACAAGTGATAA
1 TCTGATCAGTGACAAGTGATAA
390805 ATGTGATCTG
Statistics
Matches: 101, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 101 1.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.31
Consensus pattern (44 bp):
TCTGATCAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
Found at i:393829 original size:51 final size:50
Alignment explanation
Indices: 393642--393830 Score: 222
Period size: 51 Copynumber: 3.7 Consensus size: 50
393632 CATGAGAACT
* * * *
393642 CATGTGTAGTACTATGTGTAGGCTACTATGAGTA--TAAGATAGTTATGGTCA
1 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCGAAGATA--T-TGGTCA
*
393693 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCGGAAGCT-TTGGTCA
1 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACC-GAAGATATTGGTCA
* * * *
393743 CGTGTGTAGTATTATGTGCAGGCTACTACGTGTACCGAATGATATTGGTCA
1 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCGAA-GATATTGGTCA
*
393794 CATGTGTAGTACTAAGTGTAGGCTACTATGTGTACCG
1 CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCG
393831 GATAACATTG
Statistics
Matches: 118, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
49 3 0.03
50 40 0.34
51 71 0.60
54 4 0.03
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.33
Consensus pattern (50 bp):
CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCGAAGATATTGGTCA
Found at i:393876 original size:101 final size:101
Alignment explanation
Indices: 393687--393877 Score: 217
Period size: 101 Copynumber: 1.9 Consensus size: 101
393677 AAGATAGTTA
* * ** **
393687 TGGTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCGGAAGCTTTGGTCACGTGTGTAG
1 TGGTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCGGAAACATTGACCAAATGTGTAG
* * * *
393752 TATTATGTGCAGGCTACTACGTGTACCGAATGATAT
66 TACTATGTACAGGCAACCACGTGTACCGAATGATAT
*
393788 TGGTCACATGTGTAGTACTAAGTGTAGGCTACTATGTGTACCGGATAACATTGACCATAATG-GT
1 TGGTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCGGA-AACATTGACCA-AATGTGT
* *
393852 GGTGCTATGTAC-GG-AACCACCGTGTA
64 AGTACTATGTACAGGCAACCA-CGTGTA
393878 TCTGTTATTA
Statistics
Matches: 74, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
100 3 0.04
101 52 0.70
102 17 0.23
103 2 0.03
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.30
Consensus pattern (101 bp):
TGGTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCGGAAACATTGACCAAATGTGTAG
TACTATGTACAGGCAACCACGTGTACCGAATGATAT
Found at i:396462 original size:24 final size:24
Alignment explanation
Indices: 396429--396524 Score: 156
Period size: 24 Copynumber: 4.0 Consensus size: 24
396419 TCGTTCTGTG
*
396429 GCAAATGATGAATTGACGGTAAAT
1 GCAAAGGATGAATTGACGGTAAAT
*
396453 GCAAAGGATGAATTGATGGTAAAT
1 GCAAAGGATGAATTGACGGTAAAT
*
396477 GCAAAGGATGAATTGACGGTATAT
1 GCAAAGGATGAATTGACGGTAAAT
*
396501 GCAAAGGATGAATTGACGGCAAAT
1 GCAAAGGATGAATTGACGGTAAAT
396525 TACCCAAGTA
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 66 1.00
ACGTcount: A:0.41, C:0.08, G:0.28, T:0.23
Consensus pattern (24 bp):
GCAAAGGATGAATTGACGGTAAAT
Found at i:396634 original size:21 final size:21
Alignment explanation
Indices: 396610--396682 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
396600 GTTTAACTTA
*
396610 TATGAGTTTCTGTTTAACCCT
1 TATGAGTTTCTGTTCAACCCT
* * *
396631 TATGGGTTTCAGTTCAGCTCC-
1 TATGAGTTTCTGTTCAAC-CCT
**
396652 TATGAGTTTCCATTCAACCCT
1 TATGAGTTTCTGTTCAACCCT
*
396673 TATGGGTTTC
1 TATGAGTTTC
396683 AATTTAGCAC
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
20 2 0.05
21 37 0.90
22 2 0.05
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.42
Consensus pattern (21 bp):
TATGAGTTTCTGTTCAACCCT
Found at i:396695 original size:21 final size:21
Alignment explanation
Indices: 396629--396697 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 21
396619 CTGTTTAACC
* *
396629 CTTATGGGTTTCAGTTCAGCT
1 CTTATGGGTTTCAATTCAGCA
* * * * *
396650 CCTATGAGTTTCCATTCAACC
1 CTTATGGGTTTCAATTCAGCA
*
396671 CTTATGGGTTTCAATTTAGCA
1 CTTATGGGTTTCAATTCAGCA
396692 CTTATG
1 CTTATG
396698 CAGCATTCGG
Statistics
Matches: 36, Mismatches: 12, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.20, C:0.22, G:0.17, T:0.41
Consensus pattern (21 bp):
CTTATGGGTTTCAATTCAGCA
Found at i:405007 original size:13 final size:13
Alignment explanation
Indices: 404991--405069 Score: 88
Period size: 13 Copynumber: 6.1 Consensus size: 13
404981 TTTAAACCAA
404991 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
* *
405004 ACTTATCAAAAGT
1 ACTTTTCAAAAGC
*
405017 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
* *
405030 ACATTTCCACAA-C
1 AC-TTTTCAAAAGC
*
405043 ACTTTTGAAAAGC
1 ACTTTTCAAAAGC
405056 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
405069 A
1 A
405070 TTGCCAAACT
Statistics
Matches: 53, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
12 6 0.11
13 41 0.77
14 6 0.11
ACGTcount: A:0.41, C:0.24, G:0.08, T:0.28
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:415789 original size:20 final size:21
Alignment explanation
Indices: 415756--415795 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
415746 TGCCGAATTA
415756 ATTTGAGCATTGAA-TGATTG
1 ATTTGAGCATTGAATTGATTG
415776 ATTTCGAGCA-TGAATTGATT
1 ATTT-GAGCATTGAATTGATT
415796 TAATCACGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.30, C:0.07, G:0.23, T:0.40
Consensus pattern (21 bp):
ATTTGAGCATTGAATTGATTG
Found at i:425987 original size:74 final size:75
Alignment explanation
Indices: 425884--426033 Score: 284
Period size: 74 Copynumber: 2.0 Consensus size: 75
425874 TAAAGTATAT
425884 TTAATCAAATAAAAATCCAACTTCCTAAAAAATTAAAATTATTTTTAATTAAAATAATTTCATTT
1 TTAATCAAAT-AAAATCCAACTTCCTAAAAAATTAAAATTATTTTTAATTAAAATAATTTCATTT
425949 CTTCGGGAACA
65 CTTCGGGAACA
425960 TTAATCAAAT-AAATCCAACTTCCTAAAAAATTAAAATTATTTTTAATTAAAATAATTTCATTTC
1 TTAATCAAATAAAATCCAACTTCCTAAAAAATTAAAATTATTTTTAATTAAAATAATTTCATTTC
426024 TTCGGGAACA
66 TTCGGGAACA
426034 ATCAAAAATA
Statistics
Matches: 74, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
74 64 0.86
76 10 0.14
ACGTcount: A:0.45, C:0.13, G:0.04, T:0.37
Consensus pattern (75 bp):
TTAATCAAATAAAATCCAACTTCCTAAAAAATTAAAATTATTTTTAATTAAAATAATTTCATTTC
TTCGGGAACA
Found at i:434029 original size:34 final size:34
Alignment explanation
Indices: 433987--434096 Score: 139
Period size: 34 Copynumber: 3.0 Consensus size: 34
433977 GTATTGATAC
433987 AAAGAAAGTAGCTTAATTTCTCAAAAAATTATTA
1 AAAGAAAGTAGCTTAATTTCTCAAAAAATTATTA
*
434021 AAATAAAGTAGCTTAATTTCTCAAAAAATTATTAGAATTA
1 AAAGAAAGTAGCTTAATTTCTC-AAAAA--ATT---ATTA
*
434061 CAAAGAAAGTAGCTTAATTTATCAAAAAATTATTA
1 -AAAGAAAGTAGCTTAATTTCTCAAAAAATTATTA
434096 A
1 A
434097 TGCAATTATA
Statistics
Matches: 66, Mismatches: 3, Indels: 14
0.80 0.04 0.17
Matches are distributed among these distances:
34 22 0.33
35 9 0.14
37 3 0.05
38 3 0.05
40 9 0.14
41 20 0.30
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.33
Consensus pattern (34 bp):
AAAGAAAGTAGCTTAATTTCTCAAAAAATTATTA
Found at i:434072 original size:41 final size:39
Alignment explanation
Indices: 433984--434097 Score: 157
Period size: 41 Copynumber: 3.0 Consensus size: 39
433974 GAAGTATTGA
433984 TACAAAGAAAGTAGCTTAATTTCTC-AAAAA--ATT-AT
1 TACAAAGAAAGTAGCTTAATTTCTCAAAAAATTATTAAT
*
434019 TA-AAATAAAGTAGCTTAATTTCTCAAAAAATTATTAGAAT
1 TACAAAGAAAGTAGCTTAATTTCTCAAAAAATTATT--AAT
*
434059 TACAAAGAAAGTAGCTTAATTTATCAAAAAATTATTAAT
1 TACAAAGAAAGTAGCTTAATTTCTCAAAAAATTATTAAT
434098 GCAATTATAA
Statistics
Matches: 69, Mismatches: 3, Indels: 10
0.84 0.04 0.12
Matches are distributed among these distances:
34 21 0.30
35 7 0.10
37 3 0.04
39 3 0.04
40 4 0.06
41 31 0.45
ACGTcount: A:0.50, C:0.09, G:0.08, T:0.33
Consensus pattern (39 bp):
TACAAAGAAAGTAGCTTAATTTCTCAAAAAATTATTAAT
Found at i:435034 original size:41 final size:41
Alignment explanation
Indices: 434987--435069 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
434977 TATTAGTATT
434987 AATTATGTATTATAAAATTGTAAGTAAATATTATCTTGCTG
1 AATTATGTATTATAAAATTGTAAGTAAATATTATCTTGCTG
* * *
435028 AATTATGTTTTGTAAAATTGTAGGTAAATATTATCTTGCTG
1 AATTATGTATTATAAAATTGTAAGTAAATATTATCTTGCTG
435069 A
1 A
435070 TGCTGGATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.36, C:0.05, G:0.14, T:0.45
Consensus pattern (41 bp):
AATTATGTATTATAAAATTGTAAGTAAATATTATCTTGCTG
Found at i:435565 original size:80 final size:80
Alignment explanation
Indices: 435469--435625 Score: 305
Period size: 80 Copynumber: 2.0 Consensus size: 80
435459 TTGCACAAAC
435469 TATGTGGACTAATTATATGGTTAGAAATATTAGGTAGGTTTAAGGCTTAGGGTTATTGTTTCTAT
1 TATGTGGACTAATTATATGGTTAGAAATATTAGGTAGGTTTAAGGCTTAGGGTTATTGTTTCTAT
435534 GTTATGTATGTTATG
66 GTTATGTATGTTATG
*
435549 TATGTGGACTAATTATATGGTTAGAAATATTAGGTAGGTTTTAGGCTTAGGGTTATTGTTTCTAT
1 TATGTGGACTAATTATATGGTTAGAAATATTAGGTAGGTTTAAGGCTTAGGGTTATTGTTTCTAT
435614 GTTATGTATGTT
66 GTTATGTATGTT
435626 TTAGTTTAAA
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 76 1.00
ACGTcount: A:0.25, C:0.04, G:0.25, T:0.46
Consensus pattern (80 bp):
TATGTGGACTAATTATATGGTTAGAAATATTAGGTAGGTTTAAGGCTTAGGGTTATTGTTTCTAT
GTTATGTATGTTATG
Found at i:435762 original size:59 final size:60
Alignment explanation
Indices: 435689--435828 Score: 176
Period size: 59 Copynumber: 2.3 Consensus size: 60
435679 AAATTTTAGT
* *
435689 TTGTTGGATTTTGAAATTATTATGTCTTGAA-TTTGTTAGATATTG-ATTATGTTTTAAGC
1 TTGTTGGATATTGAAATTATTATGT-TTGAAGCTTGTTAGATATTGTATTATGTTTTAAGC
* * *
435748 TTGTTAGATATTGAATTTATTATGTTTTAAGCTTGTTAGATATTGAATTTATTATGTTTTAAGC
1 TTGTTGGATATTGAAATTATTATGTTTGAAGCTTGTTAGATATTG----TATTATGTTTTAAGC
435812 TTGTTGGATATTGAAAT
1 TTGTTGGATATTGAAAT
435829 GATTGACAAT
Statistics
Matches: 68, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
58 4 0.06
59 35 0.51
64 29 0.43
ACGTcount: A:0.27, C:0.03, G:0.18, T:0.52
Consensus pattern (60 bp):
TTGTTGGATATTGAAATTATTATGTTTGAAGCTTGTTAGATATTGTATTATGTTTTAAGC
Found at i:435773 original size:32 final size:32
Alignment explanation
Indices: 435734--435826 Score: 177
Period size: 32 Copynumber: 2.9 Consensus size: 32
435724 TTAGATATTG
435734 ATTATGTTTTAAGCTTGTTAGATATTGAATTT
1 ATTATGTTTTAAGCTTGTTAGATATTGAATTT
435766 ATTATGTTTTAAGCTTGTTAGATATTGAATTT
1 ATTATGTTTTAAGCTTGTTAGATATTGAATTT
*
435798 ATTATGTTTTAAGCTTGTTGGATATTGAA
1 ATTATGTTTTAAGCTTGTTAGATATTGAA
435827 ATGATTGACA
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 60 1.00
ACGTcount: A:0.28, C:0.03, G:0.17, T:0.52
Consensus pattern (32 bp):
ATTATGTTTTAAGCTTGTTAGATATTGAATTT
Found at i:436353 original size:13 final size:13
Alignment explanation
Indices: 436335--436408 Score: 121
Period size: 13 Copynumber: 5.7 Consensus size: 13
436325 AGTTCTTCAT
436335 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
436348 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
* * *
436361 TGCTGTGGAAAAG
1 TGCTTTTGAGAAG
436374 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
436387 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
436400 TGCTTTTGA
1 TGCTTTTGA
436409 AAAATTTGAG
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 55 1.00
ACGTcount: A:0.23, C:0.08, G:0.31, T:0.38
Consensus pattern (13 bp):
TGCTTTTGAGAAG
Found at i:444341 original size:176 final size:176
Alignment explanation
Indices: 443900--444420 Score: 747
Period size: 176 Copynumber: 2.9 Consensus size: 176
443890 TCTATACTTG
* * *
443900 TCCATTC-TTTTTTCTTTTCTTTTGACATAAAAAAATAGTGGCTAAATTTTAGTTCTAATCCCTC
1 TCCATTCTTTTTTTCTTTTCTTTTGACATAGAAAAATA-TGGCTAAATTTCAGTTCTAATCCATC
* * * * * * * *
443964 TACTTTTTTAAGATTATATAAGTATGGTTAAATTTTAATTTTGATCTCTGTATTTTGCTCAAATT
65 AACTTTTTAAAGATTATATAAGAATGGCTAAATTTTAATTTTGCTCCCTATATTTAGCTCAAATT
* *
444029 TAAGATTTAATCTCTATACTTTAATTTTGACATAATTTAGACACATG
130 TGAGATTTAATCTCTATACTTTAATTTTGACATAATTTAGACACATA
* * *
444076 GCCATTCTTTTTTTTCCTTTTCTTTTGACATAGAAAATTATGGCTAAATTTCAATTCTAATCCAT
1 TCCATTC-TTTTTTT-CTTTTCTTTTGACATAGAAAAATATGGCTAAATTTCAGTTCTAATCCAT
* * * * *
444141 CAAATTTTTAAAGATGATATAAGAATGGCTAAATTTCATTTTTGCTCCCTATATTTAGCTTAAAT
64 CAACTTTTTAAAGATTATATAAGAATGGCTAAATTTTAATTTTGCTCCCTATATTTAGCTCAAAT
444206 TTGAGATTTAATCTCTATACTTTAATTTTGACATAATTTAGACACATA
129 TTGAGATTTAATCTCTATACTTTAATTTTGACATAATTTAGACACATA
* * *
444254 TCCATTCTTTTTTTCTTTTCTATTGTCATAGAAAACTATGGCTAAATTTCAGTTCTAATCCATCA
1 TCCATTCTTTTTTTCTTTTCTTTTGACATAGAAAAATATGGCTAAATTTCAGTTCTAATCCATCA
* * * * *
444319 ACTTTTTAAAGATTATATAAGAATAGCTAAATTTTAGTTTTGCTCCCCATATTTCGCACAAATTT
66 ACTTTTTAAAGATTATATAAGAATGGCTAAATTTTAATTTTGCTCCCTATATTTAGCTCAAATTT
444384 GAGATTTAATCTCTATACTTTAATTTTGACATAATTT
131 GAGATTTAATCTCTATACTTTAATTTTGACATAATTT
444421 GATGCCTCAA
Statistics
Matches: 307, Mismatches: 35, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
176 146 0.48
177 7 0.02
178 132 0.43
179 22 0.07
ACGTcount: A:0.31, C:0.15, G:0.09, T:0.46
Consensus pattern (176 bp):
TCCATTCTTTTTTTCTTTTCTTTTGACATAGAAAAATATGGCTAAATTTCAGTTCTAATCCATCA
ACTTTTTAAAGATTATATAAGAATGGCTAAATTTTAATTTTGCTCCCTATATTTAGCTCAAATTT
GAGATTTAATCTCTATACTTTAATTTTGACATAATTTAGACACATA
Found at i:446641 original size:29 final size:29
Alignment explanation
Indices: 446571--446641 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 29
446561 GTTTTGATCA
*
446571 AGCACTTCGGTGATATTCTATTCTAACAT
1 AGCACTTCGGTGCTATTCTATTCTAACAT
* * * * ***
446600 GGCACTCCAGTGCTATTCTGTTCTGTTAT
1 AGCACTTCGGTGCTATTCTATTCTAACAT
446629 AGCACTTCGGTGC
1 AGCACTTCGGTGC
446642 ATCCATGTAC
Statistics
Matches: 31, Mismatches: 11, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.37
Consensus pattern (29 bp):
AGCACTTCGGTGCTATTCTATTCTAACAT
Found at i:447053 original size:17 final size:17
Alignment explanation
Indices: 447033--447066 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
447023 ATGTTATCTC
*
447033 CACTATTTTGTTTTAAG
1 CACTATTTTATTTTAAG
447050 CACTATTTTATTTTAAG
1 CACTATTTTATTTTAAG
447067 TATATGACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.12, G:0.09, T:0.53
Consensus pattern (17 bp):
CACTATTTTATTTTAAG
Found at i:451453 original size:185 final size:185
Alignment explanation
Indices: 451136--452667 Score: 3010
Period size: 185 Copynumber: 8.3 Consensus size: 185
451126 TTTATTATGA
* * * * * *
451136 ACATGTATTTCTGGTAATTTTATATTTTTTTATAATTTCAAATAATAATATATAATTTATTTTTA
1 ACATATATTTCTAGCAATTATATATATATTTATAATTTCAAATAATAATATATAATTTATTTTTA
451201 AAATAAATTCTAGGTGTTTTAGAAAATTTTTAGTTTTTTGAATTTTTGTTGAATTTTAGCAATTT
66 AAATAAATTCTAGGTGTTTTAGAAAATTTTTAGTTTTTTGAATTTTTGTTGAATTTTAGCAATTT
451266 TTTTATTTCACATGTACAATAAACTTTAGCAAATGGTTATTCAAGTTCATTCTAT
131 TTTTATTTCACATGTACAATAAACTTTAGCAAATGGTTATTCAAGTTCATTCTAT
451321 ACATATATTTCTAGCAATTATATATATATTTATAATTTCAAATAATAATATATAATTTATTTTTA
1 ACATATATTTCTAGCAATTATATATATATTTATAATTTCAAATAATAATATATAATTTATTTTTA
451386 AAATAAATTCTAGGTGTTTTAGAAAATTTTTAGTTTTTTGAATTTTTGTTGAATTTTAGCAATTT
66 AAATAAATTCTAGGTGTTTTAGAAAATTTTTAGTTTTTTGAATTTTTGTTGAATTTTAGCAATTT
451451 TTTTATTTCACATGTACAATAAACTTTAGCAAATGGTTATTCAAGTTCATTCTAT
131 TTTTATTTCACATGTACAATAAACTTTAGCAAATGGTTATTCAAGTTCATTCTAT
451506 ACATATATTTCTAGCAATTATATATATATTTATAATTTCAAATAATAATATATAATTTATTTTTA
1 ACATATATTTCTAGCAATTATATATATATTTATAATTTCAAATAATAATATATAATTTATTTTTA
451571 AAATAAATTCTAGGTGTTTTAGAAAATTTTTAGTTTTTTGAATTTTTGTTGAATTTTAGCAATTT
66 AAATAAATTCTAGGTGTTTTAGAAAATTTTTAGTTTTTTGAATTTTTGTTGAATTTTAGCAATTT
451636 TTTTATTTCACATGTACAATAAACTTTAGCAAATGGTTATTCAAGTTCATTCTAT
131 TTTTATTTCACATGTACAATAAACTTTAGCAAATGGTTATTCAAGTTCATTCTAT
451691 ACATATATTTCTAGCAATTATATATATATTTATAATTTCAAATAATAATATATAATTTATTTTTA
1 ACATATATTTCTAGCAATTATATATATATTTATAATTTCAAATAATAATATATAATTTATTTTTA
451756 AAATAAATTCTAGGTGTTTTAGAAAATTTTTAGTTTTTTGAATTTTTGTTGAATTTTAGCAATTT
66 AAATAAATTCTAGGTGTTTTAGAAAATTTTTAGTTTTTTGAATTTTTGTTGAATTTTAGCAATTT
451821 TTTTATTTCACATGTACAATAAACTTTAGCAAATGGTTATTCAAGTTCATTCTAT
131 TTTTATTTCACATGTACAATAAACTTTAGCAAATGGTTATTCAAGTTCATTCTAT
451876 ACATATATTTCTAGCAATTATATATATATTTATAATTTCAAATAATAATATATAATTTATTTTTA
1 ACATATATTTCTAGCAATTATATATATATTTATAATTTCAAATAATAATATATAATTTATTTTTA
451941 AAATAAATTCTAGGTGTTTTAGAAAATTTTTAGTTTTTTGAATTTTTGTTGAATTTTAGCAATTT
66 AAATAAATTCTAGGTGTTTTAGAAAATTTTTAGTTTTTTGAATTTTTGTTGAATTTTAGCAATTT
452006 TTTTATTTCACATGTACAATAAACTTTAGCAAATGGTTATTCAAGTTCATTCTAT
131 TTTTATTTCACATGTACAATAAACTTTAGCAAATGGTTATTCAAGTTCATTCTAT
452061 ACATATATTTCTAGCAATTATATATATATTTATAATTTCAAATAATAATATATAATTTATTTTTA
1 ACATATATTTCTAGCAATTATATATATATTTATAATTTCAAATAATAATATATAATTTATTTTTA
452126 AAATAAATTCTAGGTGTTTTAGAAAATTTTTAGTTTTTTGAATTTTTGTTGAATTTTAGCAATTT
66 AAATAAATTCTAGGTGTTTTAGAAAATTTTTAGTTTTTTGAATTTTTGTTGAATTTTAGCAATTT
452191 TTTTATTTCACATGTACAATAAACTTTAGCAAATGGTTATTCAAGTTCATTCTAT
131 TTTTATTTCACATGTACAATAAACTTTAGCAAATGGTTATTCAAGTTCATTCTAT
452246 ACATATATTTCTAGCAATTATATATATATTTATAATTTCAAATAATAATATATAATTTATTTTTA
1 ACATATATTTCTAGCAATTATATATATATTTATAATTTCAAATAATAATATATAATTTATTTTTA
452311 AAATAAATTCTAGGTGTTTTAGAAAATTTTTAGTTTTTTGAATTTTTGTTGAATTTTAGCAATTT
66 AAATAAATTCTAGGTGTTTTAGAAAATTTTTAGTTTTTTGAATTTTTGTTGAATTTTAGCAATTT
452376 TTTTATTTCACATGTACAATAAACTTTAGCAAATGGTTATTCAAGTTCATTCTAT
131 TTTTATTTCACATGTACAATAAACTTTAGCAAATGGTTATTCAAGTTCATTCTAT
452431 ACATATATTTCTAGCAATTATATATATATTTATAATTTCAAATAATAATATATAATTTATTTTTA
1 ACATATATTTCTAGCAATTATATATATATTTATAATTTCAAATAATAATATATAATTTATTTTTA
452496 AAATAAATTCTAGGTGTTTTAGAAAATTTTTAGTTTTTTGAATTTTTGTTGAATTTTAGCAATTT
66 AAATAAATTCTAGGTGTTTTAGAAAATTTTTAGTTTTTTGAATTTTTGTTGAATTTTAGCAATTT
452561 TTTTATTTCACATGTACAATAAACTTTAGCAAATGGTTATTCAAGTTCATTCTAT
131 TTTTATTTCACATGTACAATAAACTTTAGCAAATGGTTATTCAAGTTCATTCTAT
452616 ACATATATTTCTAGCAATTATATATATATTTATAATTTCAAATAATAATATA
1 ACATATATTTCTAGCAATTATATATATATTTATAATTTCAAATAATAATATA
452668 AAAAATATTT
Statistics
Matches: 1341, Mismatches: 6, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
185 1341 1.00
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.49
Consensus pattern (185 bp):
ACATATATTTCTAGCAATTATATATATATTTATAATTTCAAATAATAATATATAATTTATTTTTA
AAATAAATTCTAGGTGTTTTAGAAAATTTTTAGTTTTTTGAATTTTTGTTGAATTTTAGCAATTT
TTTTATTTCACATGTACAATAAACTTTAGCAAATGGTTATTCAAGTTCATTCTAT
Found at i:452947 original size:20 final size:22
Alignment explanation
Indices: 452922--452970 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
452912 TCTCCCACTC
452922 GAATTTAT-TTA-AAAAACATG
1 GAATTTATATTATAAAAACATG
*
452942 GAATTTATATTATAAAAACTTG
1 GAATTTATATTATAAAAACATG
452964 GAATTTA
1 GAATTTA
452971 AAAAAAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 8 0.31
21 3 0.12
22 15 0.58
ACGTcount: A:0.47, C:0.04, G:0.10, T:0.39
Consensus pattern (22 bp):
GAATTTATATTATAAAAACATG
Found at i:452997 original size:13 final size:14
Alignment explanation
Indices: 452979--453008 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
452969 TAAAAAAAAT
452979 ATTATT-ATTTTAA
1 ATTATTAATTTTAA
452992 ATTATTAATTTTAA
1 ATTATTAATTTTAA
453006 ATT
1 ATT
453009 TTTTAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
ATTATTAATTTTAA
Found at i:453194 original size:14 final size:14
Alignment explanation
Indices: 453158--453194 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 14
453148 GTTAATGCGC
*
453158 ATATTAAATTTATA
1 ATATTAATTTTATA
453172 ATATT--TTTTATA
1 ATATTAATTTTATA
453184 ATATTAATTTT
1 ATATTAATTTT
453195 TGTTTAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
12 11 0.55
14 9 0.45
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
ATATTAATTTTATA
Found at i:453209 original size:19 final size:18
Alignment explanation
Indices: 453163--453210 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
453153 TGCGCATATT
453163 AAATTTATAATATTTTTTA
1 AAATTT-TAATATTTTTTA
* * *
453182 TAATATTAATTTTTGTTTA
1 AAATTTTAATATTT-TTTA
453201 AAATTTTAAT
1 AAATTTTAAT
453211 GAATTTCTTC
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (18 bp):
AAATTTTAATATTTTTTA
Found at i:457205 original size:24 final size:25
Alignment explanation
Indices: 457152--457204 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 25
457142 TTATTATTCT
*
457152 AAAATTAAAAGTATATAAATTTTAA
1 AAAATTAAAAGTATATAAATTATAA
457177 AAAATTAAAA-TATATAAATTAATAA
1 AAAATTAAAAGTATATAAATT-ATAA
457202 AAA
1 AAA
457205 TATAAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 10 0.38
25 16 0.62
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (25 bp):
AAAATTAAAAGTATATAAATTATAA
Found at i:457210 original size:25 final size:25
Alignment explanation
Indices: 457152--457211 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 25
457142 TTATTATTCT
*
457152 AAAAT-TAAAAGTATATAAATTTTA
1 AAAATATAAAAGTATATAAATTATA
457176 AAAA-ATTAAAA-TATATAAATTAATA
1 AAAATA-TAAAAGTATATAAATT-ATA
457201 AAAATATAAAA
1 AAAATATAAAA
457212 AAATTTACAT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
24 14 0.45
25 16 0.52
26 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (25 bp):
AAAATATAAAAGTATATAAATTATA
Found at i:457497 original size:17 final size:18
Alignment explanation
Indices: 457444--457498 Score: 58
Period size: 19 Copynumber: 3.1 Consensus size: 18
457434 AGAATTATAA
*
457444 TTTTTATTAATTTATATAT
1 TTTTTACTAATTTATAT-T
* * *
457463 TTTTAACTATTTTTTATT
1 TTTTTACTAATTTATATT
457481 TTTTTA-TAATTTATATT
1 TTTTTACTAATTTATATT
457498 T
1 T
457499 GCCACCTGAC
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
17 10 0.34
18 6 0.21
19 13 0.45
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTTACTAATTTATATT
Found at i:457826 original size:18 final size:17
Alignment explanation
Indices: 457796--457831 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
457786 TCATCCGGTC
457796 TCTTTTTCTCTTCTCTT
1 TCTTTTTCTCTTCTCTT
*
457813 TCTTTTTTTGCTTCTCTT
1 TCTTTTTCT-CTTCTCTT
457831 T
1 T
457832 TGGCATAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.00, C:0.25, G:0.03, T:0.72
Consensus pattern (17 bp):
TCTTTTTCTCTTCTCTT
Found at i:462047 original size:17 final size:17
Alignment explanation
Indices: 462025--462058 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
462015 ACAAAAACTG
*
462025 AATTTAATTTTCAATTT
1 AATTTAATTTCCAATTT
462042 AATTTAATTTCCAATTT
1 AATTTAATTTCCAATTT
462059 GTTTAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (17 bp):
AATTTAATTTCCAATTT
Found at i:463418 original size:15 final size:15
Alignment explanation
Indices: 463397--463436 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
463387 AAAATTGAAA
463397 CTTTGTTTTTAACTT
1 CTTTGTTTTTAACTT
*
463412 TTTTGTTTTTAACTT
1 CTTTGTTTTTAACTT
*
463427 CATTGTTTTT
1 CTTTGTTTTT
463437 TTTTTTTGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.12, C:0.10, G:0.07, T:0.70
Consensus pattern (15 bp):
CTTTGTTTTTAACTT
Found at i:469477 original size:16 final size:15
Alignment explanation
Indices: 469451--469480 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
469441 TTATCATCTG
469451 AAAAATAAAAATATA
1 AAAAATAAAAATATA
469466 AAAAATATAAAATAT
1 AAAAATA-AAAATAT
469481 TCTAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
AAAAATAAAAATATA
Found at i:469637 original size:15 final size:14
Alignment explanation
Indices: 469617--469658 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
469607 ATATAAAATA
*
469617 TATTTTTTATGTTTT
1 TATTTTTAAT-TTTT
469632 TATTTTTAATTTTT
1 TATTTTTAATTTTT
469646 T-TTTTATAATTTT
1 TATTTT-TAATTTT
469659 CAGATGATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 4 0.16
14 12 0.48
15 9 0.36
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (14 bp):
TATTTTTAATTTTT
Found at i:475792 original size:28 final size:28
Alignment explanation
Indices: 475761--475832 Score: 110
Period size: 28 Copynumber: 2.6 Consensus size: 28
475751 AAAAATAAAA
* *
475761 ATTTACCAAAATACTA-CAAGTTTTTTTT
1 ATTTACCAAAATA-TATAAACTTTTTTTT
475789 ATTTACCAAAATATATAAACTTTTTTTT
1 ATTTACCAAAATATATAAACTTTTTTTT
475817 ATTTACCAAAATATAT
1 ATTTACCAAAATATAT
475833 CAAAAAAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
27 2 0.05
28 39 0.95
ACGTcount: A:0.40, C:0.12, G:0.01, T:0.46
Consensus pattern (28 bp):
ATTTACCAAAATATATAAACTTTTTTTT
Found at i:475943 original size:27 final size:27
Alignment explanation
Indices: 475913--475979 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 27
475903 CGCCAATGGT
475913 ATTGGCGGCACCAAAGGTGCCAAAACC
1 ATTGGCGGCACCAAAGGTGCCAAAACC
* **
475940 ATTGGCGGCACCAATGGTGCCAATGCC
1 ATTGGCGGCACCAAAGGTGCCAAAACC
475967 ATTGGCGGCACCA
1 ATTGGCGGCACCA
475980 CTCGTATTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.27, C:0.30, G:0.28, T:0.15
Consensus pattern (27 bp):
ATTGGCGGCACCAAAGGTGCCAAAACC
Found at i:476215 original size:3 final size:3
Alignment explanation
Indices: 476197--476237 Score: 64
Period size: 3 Copynumber: 13.3 Consensus size: 3
476187 AAAATAAAAG
*
476197 TAT TAGT TAG TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
476238 GTTGTTGTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:476242 original size:3 final size:3
Alignment explanation
Indices: 476236--476548 Score: 626
Period size: 3 Copynumber: 104.3 Consensus size: 3
476226 ATTATTATTA
476236 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
476284 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
476332 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
476380 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
476428 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
476476 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
476524 TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG T
476549 ATAAATTTTT
Statistics
Matches: 310, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 310 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:477119 original size:21 final size:18
Alignment explanation
Indices: 477088--477141 Score: 90
Period size: 18 Copynumber: 3.0 Consensus size: 18
477078 AATATTACAC
* *
477088 CCGATGAAGAAGAATGTG
1 CCGACGAAGAAGAAGGTG
477106 CCGACGAAGAAGAAGGTG
1 CCGACGAAGAAGAAGGTG
477124 CCGACGAAGAAGAAGGTG
1 CCGACGAAGAAGAAGGTG
477142 GTGGCGATCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.39, C:0.15, G:0.37, T:0.09
Consensus pattern (18 bp):
CCGACGAAGAAGAAGGTG
Found at i:477511 original size:170 final size:171
Alignment explanation
Indices: 477217--477561 Score: 593
Period size: 170 Copynumber: 2.0 Consensus size: 171
477207 GATATTGACG
477217 CTGAAGATGTCAACAACGATGAAGGCATTAACGCTTCTTCGGTCGGGGAGCAGATGCGGCGTATT
1 CTGAAGATGTCAACAACGATGAAGGCATTAACGCTTCTTCGGTCGGGGAGCAGA------GTATT
*
477282 GTGATACACAATAATCCTGGGCCACACATGTCGCTCATAGACCCCGACGCAGCGTATATATCTGA
60 CTGATACACAATAATCCTGGGCCACACATGTCGCTCATAGACCCCGACGCAGCGTATATATCTGA
477347 GTTTCCGGAGTACCCTGAAATAGTTCATTCTCACGGGCTGGCCGTAA
125 GTTTCCGGAGTACCCTGAAATAGTTCATTCTCACGGGCTGGCCGTAA
* *
477394 CTGAAGATGTCAACAATGATGAAGGCATTAACGCTTCTTCGGTCGGGGAGCAGA-TATTCTGATC
1 CTGAAGATGTCAACAACGATGAAGGCATTAACGCTTCTTCGGTCGGGGAGCAGAGTATTCTGATA
477458 CACAATAATCCTGGGCCACACATGTCGCTCATAGACCCCGACGCAGCGTATATATCTGAGTTTCC
66 CACAATAATCCTGGGCCACACATGTCGCTCATAGACCCCGACGCAGCGTATATATCTGAGTTTCC
*
477523 GGAGTACCTTGAAATAGTTCATTCTCACGGGCTGGCCGT
131 GGAGTACCCTGAAATAGTTCATTCTCACGGGCTGGCCGT
477562 GACATCTTCT
Statistics
Matches: 164, Mismatches: 4, Indels: 7
0.94 0.02 0.04
Matches are distributed among these distances:
170 111 0.68
177 53 0.32
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.25
Consensus pattern (171 bp):
CTGAAGATGTCAACAACGATGAAGGCATTAACGCTTCTTCGGTCGGGGAGCAGAGTATTCTGATA
CACAATAATCCTGGGCCACACATGTCGCTCATAGACCCCGACGCAGCGTATATATCTGAGTTTCC
GGAGTACCCTGAAATAGTTCATTCTCACGGGCTGGCCGTAA
Found at i:482823 original size:21 final size:20
Alignment explanation
Indices: 482797--482897 Score: 107
Period size: 21 Copynumber: 4.8 Consensus size: 20
482787 TCTTCCCTCT
*
482797 TCTTCTTCTTCTTCTTTTTTC
1 TCTTCTTCTT-TCCTTTTTTC
*
482818 TCTTCTCCTTTCCCTTTCTTTC
1 TCTTCTTCTTT-CCTTT-TTTC
482840 -CTTCCTTCTTT-CTTTTTTC
1 TCTT-CTTCTTTCCTTTTTTC
482859 TTCTTCTTTCTTTCCTTTTTTC
1 -TCTTC-TTCTTTCCTTTTTTC
*
482881 TCTTCTCCTTTCCTTTT
1 TCTTCTTCTTTCCTTTT
482898 CTTTCTTTCC
Statistics
Matches: 69, Mismatches: 4, Indels: 15
0.78 0.05 0.17
Matches are distributed among these distances:
19 4 0.06
20 17 0.25
21 30 0.43
22 18 0.26
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (20 bp):
TCTTCTTCTTTCCTTTTTTC
Found at i:482850 original size:22 final size:22
Alignment explanation
Indices: 482825--482932 Score: 65
Period size: 21 Copynumber: 5.2 Consensus size: 22
482815 TTCTCTTCTC
482825 CTTTCCCTTTCTTTCCTTCCTT
1 CTTTCCCTTTCTTTCCTTCCTT
*
482847 CTTT--CTTT-TTTCTTCTTCTTT
1 CTTTCCCTTTCTTTC--CTTCCTT
*
482868 CTTT-CCTTT-TTTCTCTT-CTC
1 CTTTCCCTTTCTTTC-CTTCCTT
* *
482888 CTTTCCTTTTCTTTCTTTCC-T
1 CTTTCCCTTTCTTTCCTTCCTT
* *
482909 C---CCCTTTCTTTCTTTCTTT
1 CTTTCCCTTTCTTTCCTTCCTT
482928 CTTTC
1 CTTTC
482933 TTTCCTCTCC
Statistics
Matches: 68, Mismatches: 8, Indels: 20
0.71 0.08 0.21
Matches are distributed among these distances:
18 14 0.21
19 6 0.09
20 9 0.13
21 21 0.31
22 18 0.26
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (22 bp):
CTTTCCCTTTCTTTCCTTCCTT
Found at i:482852 original size:4 final size:4
Alignment explanation
Indices: 482831--482959 Score: 97
Period size: 4 Copynumber: 31.5 Consensus size: 4
482821 TCTCCTTTCC
* *
482831 CTTT CTTT CCTT CCTT CTTT CTTT -TTT C-TT C-TT CTTT CTTT CCTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT -CTTT
* **
482877 -TTT CTCTT C-TC CTTT CCTTTT CTTT CTTT CCTCCC CTTT CTTT CTTT
1 CTTT CT-TT CTTT CTTT -C-TTT CTTT CTTT -CT-TT CTTT CTTT CTTT
*
482924 CTTT CTTT CTTT CCTCTC CTTT CTTT CTTT CTTT CT
1 CTTT CTTT CTTT -CT-TT CTTT CTTT CTTT CTTT CT
482960 CTCCTTCTGC
Statistics
Matches: 103, Mismatches: 10, Indels: 24
0.75 0.07 0.18
Matches are distributed among these distances:
3 14 0.14
4 68 0.66
5 17 0.17
6 4 0.04
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (4 bp):
CTTT
Found at i:482877 original size:63 final size:65
Alignment explanation
Indices: 482794--482938 Score: 201
Period size: 63 Copynumber: 2.3 Consensus size: 65
482784 CTTTCTTCCC
* *
482794 TCTTCTTC-TTCTTCTTCTTTTTTCTCTTCTCCTTTCCCTTTCTTTCCTTCCT-TCTTTCTTT-T
1 TCTTCTTCTTTCTT-TCCTTTTTTCTCTTCTCCTTTCCCTTTCTTTCCTTCCTCCCTTTCTTTCT
482856 T
65 T
* *
482857 TCTTCTTCTTTCTTTCCTTTTTTCTCTTCTCCTTTCCTTTTCTTTCTTTCCTCCCCTTTCTTTCT
1 TCTTCTTCTTTCTTTCCTTTTTTCTCTTCTCCTTTCCCTTTCTTTCCTTCCT-CCCTTTCTTTCT
482922 T
65 T
482923 TC-T-TTCTTTCTTTCCT
1 TCTTCTTCTTTCTTTCCT
482939 CTCCTTTCTT
Statistics
Matches: 74, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
63 43 0.58
64 18 0.24
65 9 0.12
66 4 0.05
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (65 bp):
TCTTCTTCTTTCTTTCCTTTTTTCTCTTCTCCTTTCCCTTTCTTTCCTTCCTCCCTTTCTTTCTT
Found at i:482929 original size:30 final size:30
Alignment explanation
Indices: 482895--482959 Score: 121
Period size: 30 Copynumber: 2.2 Consensus size: 30
482885 CTCCTTTCCT
482895 TTTCTTTCTTTCCTCCCCTTTCTTTCTTTC
1 TTTCTTTCTTTCCTCCCCTTTCTTTCTTTC
*
482925 TTTCTTTCTTTCCTCTCCTTTCTTTCTTTC
1 TTTCTTTCTTTCCTCCCCTTTCTTTCTTTC
482955 TTTCT
1 TTTCT
482960 CTCCTTCTGC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (30 bp):
TTTCTTTCTTTCCTCCCCTTTCTTTCTTTC
Found at i:482945 original size:22 final size:21
Alignment explanation
Indices: 482831--482959 Score: 74
Period size: 22 Copynumber: 6.1 Consensus size: 21
482821 TCTCCTTTCC
* *
482831 CTTTCTTTCCTTC-CTTCTTT
1 CTTTCTTTCTTTCTCTCCTTT
482851 CTTT-TTTC-TTCT-T-CTTT
1 CTTTCTTTCTTTCTCTCCTTT
*
482868 CTTTCCTTTTTTCTCTTCTCCTTT
1 CTTT-CTTTCTT-TC-TCTCCTTT
*
482892 CCTTTTCTTTCTTTCCTCCCCTTT
1 -C-TTTCTTTCTTT-CTCTCCTTT
*
482916 CTTTCTTTCTTTCT-TTCTTT
1 CTTTCTTTCTTTCTCTCCTTT
* *
482936 CCTCTCCTTTCTTTCT-TTCTTT
1 -CT-TTCTTTCTTTCTCTCCTTT
482958 CT
1 CT
482960 CTCCTTCTGC
Statistics
Matches: 90, Mismatches: 6, Indels: 25
0.74 0.05 0.21
Matches are distributed among these distances:
17 8 0.09
18 4 0.04
19 7 0.08
20 9 0.10
21 8 0.09
22 29 0.32
23 2 0.02
24 12 0.13
25 8 0.09
26 3 0.03
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (21 bp):
CTTTCTTTCTTTCTCTCCTTT
Found at i:482964 original size:26 final size:26
Alignment explanation
Indices: 482831--482964 Score: 119
Period size: 26 Copynumber: 5.4 Consensus size: 26
482821 TCTCCTTTCC
*
482831 CTTTCTTTCCT-TCC-TTCTTTCTTT
1 CTTTCTCTCCTCTCCTTTCTTTCTTT
482855 -TTTCT-T-CT-T-CTTTCTTTCCTTT
1 CTTTCTCTCCTCTCCTTTCTTT-CTTT
482877 -TTTCTCT--TCTCCTTTCCTTTTCTTT
1 CTTTCTCTCCTCTCCTTT-C-TTTCTTT
* *
482902 CTTTC-CTCCCCTTTCTTTCTTTCTTT
1 CTTTCTCTCCTC-TCCTTTCTTTCTTT
*
482928 CTTTCTTTCCTCTCCTTTCTTTCTTT
1 CTTTCTCTCCTCTCCTTTCTTTCTTT
482954 CTTTCTCTCCT
1 CTTTCTCTCCT
482965 TCTGCCCCCA
Statistics
Matches: 92, Mismatches: 6, Indels: 22
0.77 0.05 0.18
Matches are distributed among these distances:
20 1 0.01
21 9 0.10
22 11 0.12
23 7 0.08
24 4 0.04
25 7 0.08
26 42 0.46
27 6 0.07
28 5 0.05
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (26 bp):
CTTTCTCTCCTCTCCTTTCTTTCTTT
Found at i:483128 original size:18 final size:17
Alignment explanation
Indices: 483097--483132 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
483087 TTTGTCAGGT
*
483097 TTTTTTTTTAATTTTGG
1 TTTTTTTATAATTTTGG
483114 TTTTTTTATATATTTTGG
1 TTTTTTTATA-ATTTTGG
483132 T
1 T
483133 AAATAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.14, C:0.00, G:0.11, T:0.75
Consensus pattern (17 bp):
TTTTTTTATAATTTTGG
Found at i:483148 original size:27 final size:27
Alignment explanation
Indices: 483118--483191 Score: 121
Period size: 27 Copynumber: 2.7 Consensus size: 27
483108 TTTTGGTTTT
483118 TTTATATATTTTGGTAAATAAAAAAAA
1 TTTATATATTTTGGTAAATAAAAAAAA
483145 TTTATATATTTTGGTAAATAAAAAAAA
1 TTTATATATTTTGGTAAATAAAAAAAA
* *
483172 CTTGTAGTATTTTGGTAAAT
1 TTTATA-TATTTTGGTAAAT
483192 TTTTATTTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
27 31 0.70
28 13 0.30
ACGTcount: A:0.45, C:0.01, G:0.11, T:0.43
Consensus pattern (27 bp):
TTTATATATTTTGGTAAATAAAAAAAA
Found at i:484350 original size:20 final size:21
Alignment explanation
Indices: 484325--484370 Score: 76
Period size: 20 Copynumber: 2.2 Consensus size: 21
484315 TTAAAAATTA
484325 TTTTGATTTTTTTGTTG-AAT
1 TTTTGATTTTTTTGTTGTAAT
*
484345 TTTTGATTTTTTTTTTGTAAT
1 TTTTGATTTTTTTGTTGTAAT
484366 TTTTG
1 TTTTG
484371 TTGAGAGTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.13, C:0.00, G:0.13, T:0.74
Consensus pattern (21 bp):
TTTTGATTTTTTTGTTGTAAT
Found at i:484357 original size:21 final size:20
Alignment explanation
Indices: 484325--484370 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 20
484315 TTAAAAATTA
484325 TTTTGATTTTTTTGTTG-AAT
1 TTTTGATTTTTTT-TTGTAAT
484345 TTTTGATTTTTTTTTTGTAAT
1 TTTTGA-TTTTTTTTTGTAAT
484366 TTTTG
1 TTTTG
484371 TTGAGAGTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.13, C:0.00, G:0.13, T:0.74
Consensus pattern (20 bp):
TTTTGATTTTTTTTTGTAAT
Found at i:488178 original size:346 final size:346
Alignment explanation
Indices: 487545--488237 Score: 1386
Period size: 346 Copynumber: 2.0 Consensus size: 346
487535 TAATTATGAC
487545 TATTTGTTAATAATCAAGTAACATAACTTTTGAATTTAGGAGACATAACTCATCAATATAAATAG
1 TATTTGTTAATAATCAAGTAACATAACTTTTGAATTTAGGAGACATAACTCATCAATATAAATAG
487610 TGACAACTTTTGGTTAATAACCAAGTGGCACAACTTTTGGTTACTTATAACTTTTCATTTGCAAC
66 TGACAACTTTTGGTTAATAACCAAGTGGCACAACTTTTGGTTACTTATAACTTTTCATTTGCAAC
487675 TATTAGAACACTATATATATTTTGAAAATGTTCCAACAAGACATGAGTTTTAAAGGACCTGCATT
131 TATTAGAACACTATATATATTTTGAAAATGTTCCAACAAGACATGAGTTTTAAAGGACCTGCATT
487740 TATTTGTAACCCATGACCACAGTTTTGAGAGATTAGATTGAGCCATTTTTAAAATTGAATGGGAT
196 TATTTGTAACCCATGACCACAGTTTTGAGAGATTAGATTGAGCCATTTTTAAAATTGAATGGGAT
487805 GTGAACATGCCCAAGACAACGATTTATTACCTACCAAAACTCAAATCCAATCATTAGCCTATGAT
261 GTGAACATGCCCAAGACAACGATTTATTACCTACCAAAACTCAAATCCAATCATTAGCCTATGAT
487870 TGTGGAGATAAGGAAGAAAAA
326 TGTGGAGATAAGGAAGAAAAA
487891 TATTTGTTAATAATCAAGTAACATAACTTTTGAATTTAGGAGACATAACTCATCAATATAAATAG
1 TATTTGTTAATAATCAAGTAACATAACTTTTGAATTTAGGAGACATAACTCATCAATATAAATAG
487956 TGACAACTTTTGGTTAATAACCAAGTGGCACAACTTTTGGTTACTTATAACTTTTCATTTGCAAC
66 TGACAACTTTTGGTTAATAACCAAGTGGCACAACTTTTGGTTACTTATAACTTTTCATTTGCAAC
488021 TATTAGAACACTATATATATTTTGAAAATGTTCCAACAAGACATGAGTTTTAAAGGACCTGCATT
131 TATTAGAACACTATATATATTTTGAAAATGTTCCAACAAGACATGAGTTTTAAAGGACCTGCATT
488086 TATTTGTAACCCATGACCACAGTTTTGAGAGATTAGATTGAGCCATTTTTAAAATTGAATGGGAT
196 TATTTGTAACCCATGACCACAGTTTTGAGAGATTAGATTGAGCCATTTTTAAAATTGAATGGGAT
488151 GTGAACATGCCCAAGACAACGATTTATTACCTACCAAAACTCAAATCCAATCATTAGCCTATGAT
261 GTGAACATGCCCAAGACAACGATTTATTACCTACCAAAACTCAAATCCAATCATTAGCCTATGAT
488216 TGTGGAGATAAGGAAGAAAAA
326 TGTGGAGATAAGGAAGAAAAA
488237 T
1 T
488238 TATGGCCAAG
Statistics
Matches: 347, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
346 347 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.32
Consensus pattern (346 bp):
TATTTGTTAATAATCAAGTAACATAACTTTTGAATTTAGGAGACATAACTCATCAATATAAATAG
TGACAACTTTTGGTTAATAACCAAGTGGCACAACTTTTGGTTACTTATAACTTTTCATTTGCAAC
TATTAGAACACTATATATATTTTGAAAATGTTCCAACAAGACATGAGTTTTAAAGGACCTGCATT
TATTTGTAACCCATGACCACAGTTTTGAGAGATTAGATTGAGCCATTTTTAAAATTGAATGGGAT
GTGAACATGCCCAAGACAACGATTTATTACCTACCAAAACTCAAATCCAATCATTAGCCTATGAT
TGTGGAGATAAGGAAGAAAAA
Found at i:499324 original size:12 final size:10
Alignment explanation
Indices: 499301--499344 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
499291 TAAAACAGAA
499301 AAAAATAAAG
1 AAAAATAAAG
499311 AAAAATAAAG
1 AAAAATAAAG
* * *
499321 AGAAAGAAAA
1 AAAAATAAAG
499331 AAAAAT-AAG
1 AAAAATAAAG
499340 AAAAA
1 AAAAA
499345 GAAAAAGGAG
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
9 7 0.25
10 21 0.75
ACGTcount: A:0.82, C:0.00, G:0.11, T:0.07
Consensus pattern (10 bp):
AAAAATAAAG
Found at i:499333 original size:19 final size:19
Alignment explanation
Indices: 499301--499350 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
499291 TAAAACAGAA
* *
499301 AAAAATAAAGAAAAATAAAG
1 AAAAAGAAAAAAAAAT-AAG
*
499321 AGAAAGAAAAAAAAATAAG
1 AAAAAGAAAAAAAAATAAG
499340 AAAAAGAAAAA
1 AAAAAGAAAAA
499351 GGAGAGGCCA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.82, C:0.00, G:0.12, T:0.06
Consensus pattern (19 bp):
AAAAAGAAAAAAAAATAAG
Found at i:499978 original size:108 final size:108
Alignment explanation
Indices: 499685--499979 Score: 386
Period size: 103 Copynumber: 2.8 Consensus size: 108
499675 CGTAATTAGT
*
499685 AAATTTACTATCTTGATTAATTTATTCATTTCGAGCTTTGTTCTCAATAAAATTCCATATTGTCC
1 AAATTTACTATCTTGATTAATTTATTCATTTTGAGCTTTGTTCTCAATAAAATTCCATATTGTCC
* ** *
499750 ATTGTGATAGTCTTTTT-ATCTTATTCAATTTGTATCTTAGCA
66 ATTGTGATAATCTTTTTCATCTTATTCAATTCATACCTTAGCA
* ** * *
499792 AAATGTGTTATCTTG----ATTTATTCATTTTGAGCTTTGTTCTCAATAAAATTCCATCTTATCC
1 AAATTTACTATCTTGATTAATTTATTCATTTTGAGCTTTGTTCTCAATAAAATTCCATATTGTCC
* *
499853 ATTGTCATAATAC-TTTTCATCTTATTCAGTTCATACCTTAGCA
66 ATTGTGATAAT-CTTTTTCATCTTATTCAATTCATACCTTAGCA
* * * *
499896 AAATTTACTATCTTGATTAATTTATTCATTTTGAGCCTTATTCTCAATAAAATTTCATTTTGTCC
1 AAATTTACTATCTTGATTAATTTATTCATTTTGAGCTTTGTTCTCAATAAAATTCCATATTGTCC
*
499961 ATTTTGATAATCTTTTTCA
66 ATTGTGATAATCTTTTTCA
499980 AGCATTTTTC
Statistics
Matches: 159, Mismatches: 22, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
103 56 0.35
104 34 0.21
107 13 0.08
108 56 0.35
ACGTcount: A:0.27, C:0.16, G:0.08, T:0.48
Consensus pattern (108 bp):
AAATTTACTATCTTGATTAATTTATTCATTTTGAGCTTTGTTCTCAATAAAATTCCATATTGTCC
ATTGTGATAATCTTTTTCATCTTATTCAATTCATACCTTAGCA
Found at i:502078 original size:46 final size:46
Alignment explanation
Indices: 500873--502072 Score: 1721
Period size: 46 Copynumber: 26.2 Consensus size: 46
500863 GACTAGAAGC
* *
500873 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGAAGAT
1 AGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
* * *
500919 AGCAGATCTTATCTTCCTGTATTTAGCAGCGGAGTAAATCGAAGAT
1 AGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
*
500965 AGCAGATCTTATCTTCCTATATTTGGCAGCGGAGGAGATCGAAGAT
1 AGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
*
501011 AGCAGATCTTATCTTCCTATATTTGGCAGCGGAGGAGATCGAAGAT
1 AGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
* *
501057 AACAGATCTTATCTTCCTGTATTTGGCAGGGGAGGAGATCGAAGAT
1 AGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
*
501103 AGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATCAAAGAT
1 AGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
*
501149 AGCAGATCTTATCTTCCTGTATTTGACAGCGGAGGAGATCGAAGAT
1 AGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
* *
501195 AGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGAAGATAGAAGAT
1 AGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
* *
501241 AGCAGATTTTATCTTCCTATATTTGGCAGCGGAGGAGATCGAAGAT
1 AGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
* *************
501287 AGCAGATCTTATCTTCCTATATTT----NNNNNNNNNNNNNAAGAT
1 AGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
* *
501329 AGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGAAGATAGAAGAT
1 AGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
* *
501375 AGCAGATTTTATCTTCCTATATTTGGCAGCGGAGGAGATCGAAGAT
1 AGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
* **
501421 AGCAGATCTTGTCTTCCTGTATTTGGCAGTAGAGTG-GATCGAAGAT
1 AGCAGATCTTATCTTCCTGTATTTGGCAGCGGAG-GAGATCGAAGAT
* *
501467 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATTGAAGAT
1 AGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
* * * *
501513 AGCAGATCTTATCTTCTTGTATTTCGCAGTGGAGGAGATCAAAGAT
1 AGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
*
501559 AGCAGATCTTATCTTCCTGTATTTGGTAGCGGAGGAGATCGAAGAT
1 AGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
*
501605 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
1 AGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
* * * * *
501651 AGCATATCTTATCTTCCTGTATTTCGCAGTGGAGGATATCAAAGAT
1 AGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
*
501697 AGCAGATCTTATCTTCCTGTATTTGGCAGTGGAGGAGATCGAAGAT
1 AGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
* * *
501743 AGCAGATCTTGTCTTTCTGTATTTGGTAGCGGAGGAGATCGAAGAT
1 AGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
*
501789 AGCAGATCTTATCTTCCTGTATTTGGTAGCGGAGGAGATCGAAGAT
1 AGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
* *
501835 AGCAGATCTTATCTTCCTGTATTTTGCA-CTGGAGGAGATCAAAGAT
1 AGCAGATCTTATCTTCCTGTATTTGGCAGC-GGAGGAGATCGAAGAT
* *
501881 AGCAGATCTTATCTTCCTATATTTGGCAGTGGAGGAGATCGAAGAT
1 AGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
* *
501927 AGCAGATCTTGTCTTCCTGTATTTGGCAGTGGAGTG-GATCGAAGAT
1 AGCAGATCTTATCTTCCTGTATTTGGCAGCGGAG-GAGATCGAAGAT
*
501973 AGCAGATCTTATCTTCCTGTATTTGGTAGCGGAGGAGATCGAAGAT
1 AGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
* * * * *
502019 AGAAGATCTTGTCTTCCTGTATTTGGCAGTGAAGTAGATCGAAGAT
1 AGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
*
502065 TGCAGATC
1 AGCAGATC
502073 CTGTCTCCCT
Statistics
Matches: 1033, Mismatches: 111, Indels: 20
0.89 0.10 0.02
Matches are distributed among these distances:
42 28 0.03
45 3 0.00
46 1000 0.97
47 2 0.00
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.30
Consensus pattern (46 bp):
AGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
Found at i:502089 original size:41 final size:41
Alignment explanation
Indices: 502043--502133 Score: 96
Period size: 44 Copynumber: 2.1 Consensus size: 41
502033 TCCTGTATTT
*
502043 GGCAGT-GAAGTA-GATCGAAGATTGCAGATCCTGTCTCCCTA
1 GGCAGTGGAA-TAGGAT-GAAGATTGCAGATCCTATCTCCCTA
*
502084 GGCAGTAGTGGAATAGGATGAAGATTGCAGATCTTATCTCCCTA
1 GGC---AGTGGAATAGGATGAAGATTGCAGATCCTATCTCCCTA
*
502128 AGCAGT
1 GGCAGT
502134 AGTTGAGCAA
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
41 6 0.14
44 30 0.71
45 6 0.14
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (41 bp):
GGCAGTGGAATAGGATGAAGATTGCAGATCCTATCTCCCTA
Found at i:502151 original size:44 final size:44
Alignment explanation
Indices: 502059--502173 Score: 117
Period size: 44 Copynumber: 2.6 Consensus size: 44
502049 GAAGTAGATC
* * * * *
502059 GAAGATTGCAGATCCTGTCTCCCTAGGCAGTAGTGGAATAGGAT
1 GAAGATTGCAGATCTTATCTCCCTAAGCAGTAGTGGAACAGAAT
* *
502103 GAAGATTGCAGATCTTATCTCCCTAAGCAGTAGTTGAGCA-AAT
1 GAAGATTGCAGATCTTATCTCCCTAAGCAGTAGTGGAACAGAAT
* *
502146 AGAAGATGGC-GAATCTTATCTTCCTAAG
1 -GAAGATTGCAG-ATCTTATCTCCCTAAG
502174 GTAGTAGGGA
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
43 3 0.05
44 57 0.95
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.27
Consensus pattern (44 bp):
GAAGATTGCAGATCTTATCTCCCTAAGCAGTAGTGGAACAGAAT
Found at i:504036 original size:29 final size:29
Alignment explanation
Indices: 504001--504059 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
503991 TTTATACTTT
504001 AATATATGAATACACATACTTTAT-TTTTATG
1 AATATAT--ATACACATAC-TTATCTTTTATG
*
504032 AATATATATATACATACTTATCTTTTAT
1 AATATATATACACATACTTATCTTTTAT
504060 TATTTTATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 4 0.15
29 15 0.58
31 7 0.27
ACGTcount: A:0.39, C:0.10, G:0.03, T:0.47
Consensus pattern (29 bp):
AATATATATACACATACTTATCTTTTATG
Found at i:508358 original size:23 final size:23
Alignment explanation
Indices: 508328--508372 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
508318 CGTGAAAGGA
508328 AAGACTGAGAGAGAGCACAGAGT
1 AAGACTGAGAGAGAGCACAGAGT
508351 AAGACTGAGAGAGAGCACAGAG
1 AAGACTGAGAGAGAGCACAGAG
508373 CACATAGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.44, C:0.13, G:0.36, T:0.07
Consensus pattern (23 bp):
AAGACTGAGAGAGAGCACAGAGT
Found at i:513211 original size:62 final size:62
Alignment explanation
Indices: 513111--513333 Score: 232
Period size: 62 Copynumber: 3.6 Consensus size: 62
513101 TATAGGAGTT
* * * * * * *
513111 ACACAGGCTGACACACGGGCGTGTATCTAGGCCATGTAACTCACTGACTTTGGATTTGGATT
1 ACACGGGCTAACACACGGGCGTGTGTCCAGGCCGTGTAACTCACTGACTTTGGATATGGATC
* * * *
513173 ACACGGGCTAACACACGGGTGTGTGTCCAGGCCGTGTAAATCACTGACTTTGGATATGAAAC
1 ACACGGGCTAACACACGGGCGTGTGTCCAGGCCGTGTAACTCACTGACTTTGGATATGGATC
* * * * *** *
513235 ACACGGGCTAACACACGAGCGTATGTCCAAGCCGTGTAACTTACTGACTACAGATCTGAGA-C
1 ACACGGGCTAACACACGGGCGTGTGTCCAGGCCGTGTAACTCACTGACTTTGGATATG-GATC
* * *
513297 ACACGGGCTGACACATGGGTGTGTGTCCAGGCCGTGT
1 ACACGGGCTAACACACGGGCGTGTGTCCAGGCCGTGT
513334 GGAGCCACAC
Statistics
Matches: 132, Mismatches: 28, Indels: 2
0.81 0.17 0.01
Matches are distributed among these distances:
62 131 0.99
63 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (62 bp):
ACACGGGCTAACACACGGGCGTGTGTCCAGGCCGTGTAACTCACTGACTTTGGATATGGATC
Found at i:517962 original size:14 final size:14
Alignment explanation
Indices: 517924--517965 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
517914 CTTCTAAAAG
517924 AAAAC-TCAAGAGA
1 AAAACTTCAAGAGA
**
517937 AATTCTTCAAGAGA
1 AAAACTTCAAGAGA
*
517951 AAAACTTGAAGAGA
1 AAAACTTCAAGAGA
517965 A
1 A
517966 TTTTATTAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
13 3 0.13
14 20 0.87
ACGTcount: A:0.55, C:0.12, G:0.17, T:0.17
Consensus pattern (14 bp):
AAAACTTCAAGAGA
Found at i:525967 original size:5 final size:5
Alignment explanation
Indices: 525954--526000 Score: 51
Period size: 5 Copynumber: 9.2 Consensus size: 5
525944 TGAAGTTTTC
* *
525954 TCGAA TCGAG TCGAA T-GAGA TGGAA TTCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGA-A TCGAA -TCGAA TCGAA TCGAA TCGAA T
526001 ATATTTGTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
4 2 0.06
5 28 0.78
6 6 0.17
ACGTcount: A:0.36, C:0.15, G:0.26, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:526323 original size:16 final size:16
Alignment explanation
Indices: 526272--526323 Score: 52
Period size: 16 Copynumber: 3.0 Consensus size: 16
526262 GGGTGAGAAG
526272 TAAAAGTTTAGAGGGAAAA
1 TAAAAGTTT-GAGGG--AA
526291 TAAAAAGTTTTGA-GGAA
1 T-AAAAG-TTTGAGGGAA
526308 TAAAAGTTTGAGGGAA
1 TAAAAGTTTGAGGGAA
526324 AGTAAATAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
15 5 0.17
16 9 0.30
17 3 0.10
19 3 0.10
20 7 0.23
21 3 0.10
ACGTcount: A:0.48, C:0.00, G:0.27, T:0.25
Consensus pattern (16 bp):
TAAAAGTTTGAGGGAA
Found at i:526443 original size:30 final size:29
Alignment explanation
Indices: 526409--526466 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
526399 GGATGTGGGA
*
526409 TGGGAAGAGAATAAAAGTTTTAGGGGAAAG
1 TGGG-AGAGAATAAAAATTTTAGGGGAAAG
* * *
526439 TGGGAGGGAGTAAAAATTTTGGGGGAAA
1 TGGGAGAGAATAAAAATTTTAGGGGAAA
526467 ATAAAAGGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 20 0.83
30 4 0.17
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.21
Consensus pattern (29 bp):
TGGGAGAGAATAAAAATTTTAGGGGAAAG
Found at i:529772 original size:16 final size:16
Alignment explanation
Indices: 529747--529782 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
529737 AAAGAATTTA
*
529747 CTAAATTAACAGTTTC
1 CTAAAATAACAGTTTC
529763 CTAAAATAACAGTTTC
1 CTAAAATAACAGTTTC
529779 CTAA
1 CTAA
529783 CTGATTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.33
Consensus pattern (16 bp):
CTAAAATAACAGTTTC
Found at i:533094 original size:49 final size:49
Alignment explanation
Indices: 533013--533204 Score: 231
Period size: 49 Copynumber: 3.9 Consensus size: 49
533003 ACGGAGGAAG
* * ** * *
533013 AGTCAGCAGTTTATCTGGAACGACTAGTGGTTCATCCACAACGTATTTT
1 AGTCGGCAATTTATCTACAACGACCAGTGGTTCATCCACAACGTATTTC
* * * * *
533062 AGTCGGCACTTTATCTACAATGACTAGTGGTTCATCCATAATGTATTTC
1 AGTCGGCAATTTATCTACAACGACCAGTGGTTCATCCACAACGTATTTC
* *
533111 AGTCGGCAATTTATCTACAACGACCAGTGTTTCATCCACAACATATTTC
1 AGTCGGCAATTTATCTACAACGACCAGTGGTTCATCCACAACGTATTTC
* * * *
533160 AGTTGGCAGTTTATCTACAACAACCAGTGGTTCATCCAAAACGTA
1 AGTCGGCAATTTATCTACAACGACCAGTGGTTCATCCACAACGTA
533205 CTAGCAGCTT
Statistics
Matches: 122, Mismatches: 21, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
49 122 1.00
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (49 bp):
AGTCGGCAATTTATCTACAACGACCAGTGGTTCATCCACAACGTATTTC
Found at i:533290 original size:96 final size:96
Alignment explanation
Indices: 533172--533351 Score: 234
Period size: 96 Copynumber: 1.9 Consensus size: 96
533162 TTGGCAGTTT
** * * * * *
533172 ATCTACAACAACCAGTGGTTCATCCAAAACGTACTAGCAGCTTTTATCTTCACCAATGGATGGTT
1 ATCTACAACAACCAGTAATTCATCCAAAACATACTAACAACTTTTATCTACACCAATAGATGGTT
* *
533237 CATCCACCAGTATTTTTATTGTTAGCAATTC
66 CATCAACCAATATTTTTATTGTTAGCAATTC
** * * *
533268 ATCTACAACAATTAGTAATTCATCCACAATATACTAACAACTTTTATCTACACCGATAGATGGTT
1 ATCTACAACAACCAGTAATTCATCCAAAACATACTAACAACTTTTATCTACACCAATAGATGGTT
533333 CATCAACCAATATTTTTAT
66 CATCAACCAATATTTTTAT
533352 CGTCGATAGT
Statistics
Matches: 70, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
96 70 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.34
Consensus pattern (96 bp):
ATCTACAACAACCAGTAATTCATCCAAAACATACTAACAACTTTTATCTACACCAATAGATGGTT
CATCAACCAATATTTTTATTGTTAGCAATTC
Found at i:535261 original size:19 final size:20
Alignment explanation
Indices: 535222--535267 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
535212 ACAAGAATTT
*
535222 ACTAAAAATAATCCTAAATCA
1 ACTAAAAATAAT-CGAAATCA
535243 ACTAAAAATAAT-GAAATCA
1 ACTAAAAATAATCGAAATCA
535262 A-TAAAA
1 ACTAAAA
535268 CAAAGCTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 5 0.21
19 7 0.29
21 12 0.50
ACGTcount: A:0.63, C:0.13, G:0.02, T:0.22
Consensus pattern (20 bp):
ACTAAAAATAATCGAAATCA
Found at i:536668 original size:24 final size:24
Alignment explanation
Indices: 536632--536689 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
536622 GCGCTTTGTG
*
536632 AAAAGCGCCGCAAAATATATTAACC
1 AAAA-CGCAGCAAAATATATTAACC
*
536657 AAAACGCAGCAAAATATATTAATC
1 AAAACGCAGCAAAATATATTAACC
536681 AAAACGCAG
1 AAAACGCAG
536690 AGTTTGGTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 27 0.87
25 4 0.13
ACGTcount: A:0.52, C:0.21, G:0.12, T:0.16
Consensus pattern (24 bp):
AAAACGCAGCAAAATATATTAACC
Found at i:536893 original size:114 final size:114
Alignment explanation
Indices: 536657--536984 Score: 399
Period size: 114 Copynumber: 2.9 Consensus size: 114
536647 TATATTAACC
* * *
536657 AAAA-CGCAGCAAAATATATTAATCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGAATTAGTG
1 AAAAGCGCCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGAATTAGTG
* * ** ** * * *
536721 GCGTTTATGGGAAAACGTCGCTAACGCATAGTATTAGCGGTGCTTCGTG
66 GCGCTTACGAAAAAACACCGCTAAAGCATACTATTAGCGGCGCTTCGTG
* * * * *
536770 AAAAGCGCCGCAAAATATCTTAACCAAAGCGCAGTGTTTTGGTCTTGATGCATACTAGAATTAGT
1 AAAAGCGCCGCAAAATATCTTAACCAAAACGCAGAG-TTTGGTCTTGAGGTATATTAGAATTAGT
*
536835 GGCGCTTACGAAAAAACACCGCTAAAGCA-ACTATTAGCGGCGCTTTGTG
65 GGCGCTTACGAAAAAACACCGCTAAAGCATACTATTAGCGGCGCTTCGTG
*
536884 AAAAGCGCCGCAAAATATCTCAACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGAATTAGTG
1 AAAAGCGCCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGAATTAGTG
* * ** * * *
536949 GCACTTATGGGAAAACGCCGCTAACGCATAGTATTA
66 GCGCTTACGAAAAAACACCGCTAAAGCATACTATTA
536985 AGTGCCGCAA
Statistics
Matches: 181, Mismatches: 31, Indels: 5
0.83 0.14 0.02
Matches are distributed among these distances:
113 52 0.29
114 82 0.45
115 47 0.26
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.26
Consensus pattern (114 bp):
AAAAGCGCCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGAATTAGTG
GCGCTTACGAAAAAACACCGCTAAAGCATACTATTAGCGGCGCTTCGTG
Found at i:537160 original size:98 final size:97
Alignment explanation
Indices: 536890--537187 Score: 438
Period size: 98 Copynumber: 3.0 Consensus size: 97
536880 TGTGAAAAGC
* * *
536890 GCCGCAAAATATCTCAACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGCACTT
1 GCCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGA-GTGTATTAGAATTAGTGGCGCTT
*
536955 ATGGGAAAACGCCGCTAACGCATAGTATTAAG-T
65 ATGGGAAAACGCCGCTAACGCATAGTATT-AGCG
* *
536988 GCCGCAAAAATATCTTAACCCAAACGCAGCGTTTTGGTCTTGA-TGTATACTAGAATTAGTGGCG
1 GCCGC-AAAATATCTTAACCAAAACGCAGAG-TTTGGTCTTGAGTGTAT--TAGAATTAGTGGCG
* * *
537052 CTTACGGGAAAACGCAGCTAAAGCATAGTATTAGCG
62 CTTATGGGAAAACGCCGCTAACGCATAGTATTAGCG
537088 GCCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGCTGTATTAGAATTAGTGGCGCTT
1 GCCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGAG-TGTATTAGAATTAGTGGCGCTT
537153 ATGGGAAAACGCCGCTAACGCATAGTATTAGCG
65 ATGGGAAAACGCCGCTAACGCATAGTATTAGCG
537186 GC
1 GC
537188 GCTTTGTGAG
Statistics
Matches: 179, Mismatches: 14, Indels: 14
0.86 0.07 0.07
Matches are distributed among these distances:
98 69 0.39
99 47 0.26
100 63 0.35
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.25
Consensus pattern (97 bp):
GCCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGTGTATTAGAATTAGTGGCGCTTA
TGGGAAAACGCCGCTAACGCATAGTATTAGCG
Found at i:537191 original size:312 final size:315
Alignment explanation
Indices: 536776--537416 Score: 907
Period size: 312 Copynumber: 2.0 Consensus size: 315
536766 CGTGAAAAGC
* *
536776 GCCGCAAAATATCTTAACCAAAGCGCAGTGTTTTGGTCTTGATGCATACTAGAATTAGTGGCGCT
1 GCCGCAAAATATCTTAACCAAAACGCAGAGTTTTGGTCTTGATGCATACTAGAATTAGTGGCGCT
536841 TACGAAAAAACACCGCTAAAGCAACTATTAGCGGCGCTTTGTGAAAAGCGCCGCAAAATATCTCA
66 TACGAAAAAACACCGCTAAAGCAACTATTAGCGGCGCTTTGTGAAAAGCGCCGCAAAATATCTCA
*
536906 ACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGCACTTATGGGAAAACGCCGCT
131 ACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGCACTTATGGGAAAACACCGCT
*
536971 AACGCATAG-TA-T-T-AAGTGCCGCAAAAATATCTTAACCCAAACGCAGCGTTTTGGTCTTGAT
196 AACGCATAGTTAGTGTGAAGTGCCGC-AAAATATCTTAACCAAAACGCAGCGTTTTGGTCTTGAT
*
537032 GTATACTAGAATTAGTGGCGCTTACGGGAAAACGCAGCTAAAGCATAGTATTAGCG
260 GTATACTAGAATTAGTGGCGCTTACGGGAAAACGCAGCTAAAGCATAGAATTAGCG
* *
537088 GCCGCAAAATATCTTAACCAAAACGCAGAG-TTTGGTCTTGA-GCTGTATTAGAATTAGTGGCGC
1 GCCGCAAAATATCTTAACCAAAACGCAGAGTTTTGGTCTTGATGC-ATACTAGAATTAGTGGCGC
* ** * * * * *
537151 TTATGGGAAAACGCCGCTAACGCATAGTATTAGCGGCGCTTTGTGAGAAGTGCCGCAAAATATCT
65 TTACGAAAAAACACCGCTAAAGCA-ACTATTAGCGGCGCTTTGTGAAAAGCGCCGCAAAATATCT
* *
537216 TAACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTTATGGGAAAACACCG
129 CAACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGCACTTATGGGAAAACACCG
* * *
537281 CTAATGCATAGTATTAGCGGCGCTTTGTGAGAAGTGCTGCAAAATATCTTAACCAAAATGCAGCG
194 CTAACGCATAG--TTA-----G---TGT--GAAGTGCCGCAAAATATCTTAACCAAAACGCAGCG
* *
537346 TTTTGGTCTTGATGTATACTAGAATTAGTGGCGCTTACTGGAAAACGCCGCTAAAGCATAGAATT
247 TTTTGGTCTTGATGTATACTAGAATTAGTGGCGCTTACGGGAAAACGCAGCTAAAGCATAGAATT
537411 AGCG
312 AGCG
537415 GC
1 GC
537417 ACTTTGTGAG
Statistics
Matches: 289, Mismatches: 22, Indels: 21
0.87 0.07 0.06
Matches are distributed among these distances:
310 2 0.01
311 47 0.16
312 137 0.47
315 2 0.01
324 1 0.00
325 1 0.00
327 91 0.31
328 8 0.03
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.26
Consensus pattern (315 bp):
GCCGCAAAATATCTTAACCAAAACGCAGAGTTTTGGTCTTGATGCATACTAGAATTAGTGGCGCT
TACGAAAAAACACCGCTAAAGCAACTATTAGCGGCGCTTTGTGAAAAGCGCCGCAAAATATCTCA
ACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGCACTTATGGGAAAACACCGCT
AACGCATAGTTAGTGTGAAGTGCCGCAAAATATCTTAACCAAAACGCAGCGTTTTGGTCTTGATG
TATACTAGAATTAGTGGCGCTTACGGGAAAACGCAGCTAAAGCATAGAATTAGCG
Found at i:537290 original size:114 final size:114
Alignment explanation
Indices: 537088--537454 Score: 592
Period size: 114 Copynumber: 3.2 Consensus size: 114
537078 AGTATTAGCG
* *
537088 GCCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGCTGTATTAGAATTAGTGGCGCTT
1 GCCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTT
*
537153 ATGGGAAAACGCCGCTAACGCATAGTATTAGCGGCGCTTTGTGAGAAGT
66 ATGGGAAAACGCCGCTAAAGCATAGTATTAGCGGCGCTTTGTGAGAAGT
537202 GCCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTT
1 GCCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTT
* *
537267 ATGGGAAAACACCGCTAATGCATAGTATTAGCGGCGCTTTGTGAGAAGT
66 ATGGGAAAACGCCGCTAAAGCATAGTATTAGCGGCGCTTTGTGAGAAGT
* * * * *
537316 GCTGCAAAATATCTTAACCAAAATGCAGCGTTTTGGTCTTGATGTATACTAGAATTAGTGGCGCT
1 GCCGCAAAATATCTTAACCAAAACGCAGAG-TTTGGTCTTGAGGTATATTAGAATTAGTGGCGCT
* * *
537381 TACT-GGAAAACGCCGCTAAAGCATAGAATTAGCGGCACTTTGTGAGAAGC
65 TA-TGGGAAAACGCCGCTAAAGCATAGTATTAGCGGCGCTTTGTGAGAAGT
537431 GCCGCAAAATATCTTAACCAAAAC
1 GCCGCAAAATATCTTAACCAAAAC
537455 ACATCGTTTT
Statistics
Matches: 235, Mismatches: 16, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
114 137 0.58
115 97 0.41
116 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (114 bp):
GCCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTT
ATGGGAAAACGCCGCTAAAGCATAGTATTAGCGGCGCTTTGTGAGAAGT
Found at i:537595 original size:14 final size:14
Alignment explanation
Indices: 537578--537650 Score: 51
Period size: 14 Copynumber: 5.2 Consensus size: 14
537568 TTGGATTATA
537578 GTTTAGGGTTTAAG
1 GTTTAGGGTTTAAG
* *
537592 GTTTACGGTGT-AG
1 GTTTAGGGTTTAAG
* **
537605 GTTTAGTGTTTTTG
1 GTTTAGGGTTTAAG
*
537619 ATTTAGGGTTTAAG
1 GTTTAGGGTTTAAG
*
537633 AGTTT-GGTGATTAAG
1 -GTTTAGG-GTTTAAG
537648 GTT
1 GTT
537651 CAGTGATTAT
Statistics
Matches: 44, Mismatches: 12, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
13 10 0.23
14 25 0.57
15 9 0.20
ACGTcount: A:0.19, C:0.01, G:0.33, T:0.47
Consensus pattern (14 bp):
GTTTAGGGTTTAAG
Found at i:537793 original size:7 final size:7
Alignment explanation
Indices: 537750--537833 Score: 64
Period size: 7 Copynumber: 12.0 Consensus size: 7
537740 TAGAGTTTGA
537750 GTTTAGG
1 GTTTAGG
*
537757 GTTTATG
1 GTTTAGG
* *
537764 ATGTA-G
1 GTTTAGG
*
537770 GTTTTGG
1 GTTTAGG
*
537777 TGTTTTGG
1 -GTTTAGG
537785 GTTTAGG
1 GTTTAGG
*
537792 GTTTAAGA
1 GTTT-AGG
537800 GTTTAGG
1 GTTTAGG
*
537807 GTTTAAG
1 GTTTAGG
537814 GTTT-GG
1 GTTTAGG
*
537820 GTTTGGG
1 GTTTAGG
537827 GTTTAGG
1 GTTTAGG
537834 CCGCTTTAGT
Statistics
Matches: 61, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
6 8 0.13
7 40 0.66
8 13 0.21
ACGTcount: A:0.14, C:0.00, G:0.39, T:0.46
Consensus pattern (7 bp):
GTTTAGG
Found at i:537803 original size:15 final size:14
Alignment explanation
Indices: 537784--537833 Score: 66
Period size: 15 Copynumber: 3.6 Consensus size: 14
537774 TGGTGTTTTG
537784 GGTTTAGGGTTTAA
1 GGTTTAGGGTTTAA
537798 GAGTTTAGGGTTTAA
1 G-GTTTAGGGTTTAA
**
537813 GGTTT-GGGTTTGG
1 GGTTTAGGGTTTAA
537826 GGTTTAGG
1 GGTTTAGG
537834 CCGCTTTAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
13 11 0.34
14 7 0.22
15 14 0.44
ACGTcount: A:0.16, C:0.00, G:0.42, T:0.42
Consensus pattern (14 bp):
GGTTTAGGGTTTAA
Found at i:538627 original size:82 final size:82
Alignment explanation
Indices: 538483--538723 Score: 277
Period size: 82 Copynumber: 2.9 Consensus size: 82
538473 TAATAGTAAT
* * * * * * *
538483 AAAAATTTGATAGTGGCGTTTTTAGGGGAAACGCCGCAATGATTGATTAACTTTTCGAATGCGGC
1 AAAAATTTAATAGTGGCGTTTTTAAGGAAAACGCCGCAATGATTAATTAAATTTCCCAATGCGGC
** *
538548 GCCGTTTCAGTGTTGGA
66 GCCGTTTCAGTACTAGA
* *
538565 AAAAATTTTATAGTGGCGTTTTTAAGGAAAACGCCGCAATGATTAATTAAATTTCCCTATGCGGC
1 AAAAATTTAATAGTGGCGTTTTTAAGGAAAACGCCGCAATGATTAATTAAATTTCCCAATGCGGC
*
538630 GCCGTTTCTGTACTAGA
66 GCCGTTTCAGTACTAGA
* *
538647 AAATAATTTAATAGTGGCGTTCTTTAA-GAAAACGCCGCAATTATTTATATATAAACTTCCCCAA
1 AAA-AATTTAATAGTGGCGTT-TTTAAGGAAAACGCCGCAATGA-TTA-AT-TAAA-TTTCCCAA
*
538711 TGCGGCACCGTTT
60 TGCGGCGCCGTTT
538724 GTGAGCTTCA
Statistics
Matches: 136, Mismatches: 17, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
82 73 0.54
83 31 0.23
84 8 0.06
85 2 0.01
86 4 0.03
87 18 0.13
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (82 bp):
AAAAATTTAATAGTGGCGTTTTTAAGGAAAACGCCGCAATGATTAATTAAATTTCCCAATGCGGC
GCCGTTTCAGTACTAGA
Found at i:540977 original size:9 final size:9
Alignment explanation
Indices: 540952--541193 Score: 155
Period size: 9 Copynumber: 27.1 Consensus size: 9
540942 NACTTACATA
540952 ATAACTTAC
1 ATAACTTAC
* *
540961 ATAGCTTAT
1 ATAACTTAC
540970 ATAACTTAC
1 ATAACTTAC
*
540979 ATAACTTAT
1 ATAACTTAC
540988 ATAACTTAC
1 ATAACTTAC
*
540997 AT-AC-TCC
1 ATAACTTAC
541004 ATAACTTAC
1 ATAACTTAC
*
541013 ATAATTTAC
1 ATAACTTAC
*
541022 TTAA--TAC
1 ATAACTTAC
*
541029 ATAA-TCAAC
1 ATAACT-TAC
*
541038 ATATATTATATC
1 ATA-ACT-TA-C
*
541050 TTAACTTAC
1 ATAACTTAC
541059 ATAATAACTTAC
1 ---ATAACTTAC
* *
541071 ATAGCTTAT
1 ATAACTTAC
541080 ATAACTTAC
1 ATAACTTAC
541089 ATAA--TAC
1 ATAACTTAC
*
541096 ATAACCTAC
1 ATAACTTAC
*
541105 ATAACTTAT
1 ATAACTTAC
541114 ATAACTTAC
1 ATAACTTAC
541123 ATAA--TAC
1 ATAACTTAC
541130 ATAACTTAC
1 ATAACTTAC
* **
541139 ATATCTTTT
1 ATAACTTAC
*
541148 ATAATATATAC
1 ATAA-CT-TAC
541159 ATAACTTAC
1 ATAACTTAC
*
541168 ATAATTTAC
1 ATAACTTAC
*
541177 TTAA--TAC
1 ATAACTTAC
541184 ATAACTTAC
1 ATAACTTAC
541193 A
1 A
541194 AGTTGTTCCA
Statistics
Matches: 180, Mismatches: 35, Indels: 36
0.72 0.14 0.14
Matches are distributed among these distances:
7 30 0.17
8 4 0.02
9 121 0.67
10 5 0.03
11 9 0.05
12 11 0.06
ACGTcount: A:0.44, C:0.18, G:0.01, T:0.38
Consensus pattern (9 bp):
ATAACTTAC
Found at i:541031 original size:25 final size:25
Alignment explanation
Indices: 540976--541193 Score: 114
Period size: 25 Copynumber: 8.5 Consensus size: 25
540966 TTATATAACT
* * * *
540976 TACATAACTTATATAACTTACATAC
1 TACATAACTTACATAATTTACTTAA
*
541001 TCCATAACTTACATAATTTACTTAA
1 TACATAACTTACATAATTTACTTAA
*
541026 TACATAA-TCAACATATATTATATCTTAA
1 TACATAACT-TACATA-ATT-TA-CTTAA
* *
541054 CTTACATAA-TAACTTACA--TAGCTT-A
1 --TACATAACTTACATA-ATTTA-CTTAA
*
541079 T--ATAACTTACATAA--TACATAA
1 TACATAACTTACATAATTTACTTAA
* * *
541100 CCTACATAACTTATATAACTTACATAA
1 --TACATAACTTACATAATTTACTTAA
*
541127 TACATAACTTACATATCTTTTA-TAATATA
1 TACATAACTTACATA--ATTTACT--TA-A
541156 TACATAACTTACATAATTTACTTAA
1 TACATAACTTACATAATTTACTTAA
541181 TACATAACTTACA
1 TACATAACTTACA
541194 AGTTGTTCCA
Statistics
Matches: 154, Mismatches: 19, Indels: 40
0.72 0.09 0.19
Matches are distributed among these distances:
20 2 0.01
21 8 0.05
22 5 0.03
23 2 0.01
24 1 0.01
25 72 0.47
26 10 0.06
27 16 0.10
28 8 0.05
29 22 0.14
30 8 0.05
ACGTcount: A:0.44, C:0.18, G:0.00, T:0.38
Consensus pattern (25 bp):
TACATAACTTACATAATTTACTTAA
Found at i:541105 original size:16 final size:16
Alignment explanation
Indices: 541080--541141 Score: 88
Period size: 16 Copynumber: 3.8 Consensus size: 16
541070 CATAGCTTAT
541080 ATAACTTACATAATAC
1 ATAACTTACATAATAC
* *
541096 ATAACCTACATAACTTAT
1 ATAACTTACATAA--TAC
541114 ATAACTTACATAATAC
1 ATAACTTACATAATAC
541130 ATAACTTACATA
1 ATAACTTACATA
541142 TCTTTTATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
16 26 0.65
18 14 0.35
ACGTcount: A:0.48, C:0.19, G:0.00, T:0.32
Consensus pattern (16 bp):
ATAACTTACATAATAC
Found at i:541106 original size:34 final size:34
Alignment explanation
Indices: 540958--541171 Score: 164
Period size: 34 Copynumber: 6.5 Consensus size: 34
540948 CATAATAACT
* * * *
540958 TACATAGCTTATATAACTTACATAACTTATATAA
1 TACATAACTTACATAACTTATATAACTTACATAA
* * * *
540992 CTTACAT-AC-TCCATAACTTACATAATTTACTTAA
1 --TACATAACTTACATAACTTATATAACTTACATAA
* *
541026 TACATAA-TCAACATATA-TTATAT--CTTAACTTACA
1 TACATAACT-TACATA-ACTTATATAACTT-ACATA-A
*
541060 TA-ATAACTTACATAGCTTATATAACTTACATAA
1 TACATAACTTACATAACTTATATAACTTACATAA
*
541093 TACATAACCTACATAACTTATATAACTTACATAA
1 TACATAACTTACATAACTTATATAACTTACATAA
* *
541127 TACATAACTTACATATCTTTTATAA--T--AT-A
1 TACATAACTTACATAACTTATATAACTTACATAA
541156 TACATAACTTACATAA
1 TACATAACTTACATAA
541172 TTTACTTAAT
Statistics
Matches: 148, Mismatches: 19, Indels: 29
0.76 0.10 0.15
Matches are distributed among these distances:
29 16 0.11
30 2 0.01
32 8 0.05
33 24 0.16
34 88 0.59
35 5 0.03
36 5 0.03
ACGTcount: A:0.44, C:0.18, G:0.01, T:0.37
Consensus pattern (34 bp):
TACATAACTTACATAACTTATATAACTTACATAA
Found at i:541107 original size:67 final size:64
Alignment explanation
Indices: 540977--541128 Score: 163
Period size: 67 Copynumber: 2.4 Consensus size: 64
540967 TATATAACTT
* * * *
540977 ACATAACTTATATAACTTAC---AT-AC-TCCATAACTTACATAATTTACTTAATACATAATCA
1 ACATAACTTATATAACTTACATAATAACTTACATAACTTACATAACTTACATAATACATAACCA
* *
541036 ACATATA-TTATATCTTAACTTACATAATAACTTACATAGCTTATATAACTTACATAATACATAA
1 ACATA-ACTTATA---TAACTTACATAATAACTTACATAACTTACATAACTTACATAATACATAA
*
541100 CCT
62 CCA
541103 ACATAACTTATATAACTTACATAATA
1 ACATAACTTATATAACTTACATAATA
541129 CATAACTTAC
Statistics
Matches: 76, Mismatches: 7, Indels: 15
0.78 0.07 0.15
Matches are distributed among these distances:
59 10 0.13
60 1 0.01
62 8 0.11
64 14 0.18
65 2 0.03
66 3 0.04
67 38 0.50
ACGTcount: A:0.45, C:0.18, G:0.01, T:0.36
Consensus pattern (64 bp):
ACATAACTTATATAACTTACATAATAACTTACATAACTTACATAACTTACATAATACATAACCA
Found at i:541179 original size:110 final size:108
Alignment explanation
Indices: 540943--541172 Score: 279
Period size: 110 Copynumber: 2.1 Consensus size: 108
540933 NNNNNNNNNN
* * *
540943 ACTTACATAATAACTTACATAGCTTATATAACTTACATAACTTATATAACTTACATACTCCATAA
1 ACTTACATAATAACTTACATAGCTTATATAACTTACATAAC-TACATAACCTACATACTACATAA
* * *
541008 CTTACATAATTTACTTAATACATAATCAACATATATTATATCTTA
65 CTTACATAA-TTACATAATACATAATCAACATATAATATATCATA
*
541053 ACTTACATAATAACTTACATAGCTTATATAACTTACATAA-TACATAACCTACATAACTTATATA
1 ACTTACATAATAACTTACATAGCTTATATAACTTACATAACTACATAACCTACAT-AC-TACATA
***
541117 ACTTACATAA-TACATAACTTACAT-ATC-TTTTATAATATATACATA
64 ACTTACATAATTACATAA--TACATAATCAACATATAATATAT-CATA
541162 ACTTACATAAT
1 ACTTACATAAT
541173 TTACTTAATA
Statistics
Matches: 105, Mismatches: 10, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
108 27 0.26
109 19 0.18
110 59 0.56
ACGTcount: A:0.44, C:0.18, G:0.01, T:0.37
Consensus pattern (108 bp):
ACTTACATAATAACTTACATAGCTTATATAACTTACATAACTACATAACCTACATACTACATAAC
TTACATAATTACATAATACATAATCAACATATAATATATCATA
Found at i:543804 original size:21 final size:21
Alignment explanation
Indices: 543759--543829 Score: 108
Period size: 21 Copynumber: 3.4 Consensus size: 21
543749 CTACAACTTA
* *
543759 AAGCAGAGGCGGCAGTAAG-G
1 AAGCAGAGGCTGCAGCAAGAG
*
543779 AAGCAGAGGCTGCAGCGAGAG
1 AAGCAGAGGCTGCAGCAAGAG
543800 AAGCAGAGGCTGCAGCAAGAG
1 AAGCAGAGGCTGCAGCAAGAG
543821 AAGCAGAGG
1 AAGCAGAGG
543830 TTCAAAAGAA
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.37, C:0.17, G:0.42, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCAAGAG
Found at i:544353 original size:42 final size:42
Alignment explanation
Indices: 544275--544553 Score: 364
Period size: 42 Copynumber: 6.6 Consensus size: 42
544265 CGTTAAAAGT
* * * *
544275 CATGTTCTATAGCGGCGTTTTTTATC-AAGTGCCGCTAAAGAA
1 CATGATCTTTAGCGGCATTTTTT-TCTAAGCGCCGCTAAAGAA
* * * *
544317 CATGATCTTTTGCGGCGTTTTTCTTC-GAGCGTCGCTAAAGAA
1 CATGATCTTTAGCGGCATTTTT-TTCTAAGCGCCGCTAAAGAA
*
544359 CATGATCTTTAGCGGCATCTTTTTTTTAAGCGCCGCTAAAGAA
1 CATGATCTTTAGCGGCAT-TTTTTTCTAAGCGCCGCTAAAGAA
* * *
544402 CATGATCTTTAGCGGCGTTTTTTTCTAATCGCCGCTAAAGAT
1 CATGATCTTTAGCGGCATTTTTTTCTAAGCGCCGCTAAAGAA
* *
544444 CATGTTCTTTAGCGGCATTTTTTTCTAAGCCCCGCTAAAGAA
1 CATGATCTTTAGCGGCATTTTTTTCTAAGCGCCGCTAAAGAA
*
544486 CATGATCTTTAGCGGCATTTTTTTCTAAACGCCGCTAAAGAA
1 CATGATCTTTAGCGGCATTTTTTTCTAAGCGCCGCTAAAGAA
*
544528 CATGACCTTTAGCGGCATTTATTTTC
1 CATGATCTTTAGCGGCATTT-TTTTC
544554 GTAAACGCTG
Statistics
Matches: 209, Mismatches: 24, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
42 168 0.80
43 41 0.20
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.36
Consensus pattern (42 bp):
CATGATCTTTAGCGGCATTTTTTTCTAAGCGCCGCTAAAGAA
Found at i:544436 original size:127 final size:125
Alignment explanation
Indices: 544275--544553 Score: 373
Period size: 127 Copynumber: 2.2 Consensus size: 125
544265 CGTTAAAAGT
* * * *
544275 CATGTTCTATAGCGGCGTTTTTTATCAAGTGCCGCTAAAGAACATGATCTTTTGCGGCGTTTTTC
1 CATGATCTTTAGCGGCGTTTTTT-TCAAGTGCCGCTAAAGAACATGATCTTTAGCGGCATTTTT-
* ** * *
544340 TTC-GAGCGTCGCTAAAGAACATGATCTTTAGCGGCATCTTTTTTTTAAGCGCCGCTAAAGAA
64 TTCTAAGCCCCGCTAAAGAACATGATCTTTAGCGGCAT-TTTTTTCTAAACGCCGCTAAAGAA
* *
544402 CATGATCTTTAGCGGCGTTTTTTTCTAA-TCGCCGCTAAAGATCATGTTCTTTAGCGGCATTTTT
1 CATGATCTTTAGCGGCGTTTTTTTC-AAGT-GCCGCTAAAGAACATGATCTTTAGCGGCATTTTT
544466 TTCTAAGCCCCGCTAAAGAACATGATCTTTAGCGGCATTTTTTTCTAAACGCCGCTAAAGAA
64 TTCTAAGCCCCGCTAAAGAACATGATCTTTAGCGGCATTTTTTTCTAAACGCCGCTAAAGAA
* *
544528 CATGACCTTTAGCGGCATTTATTTTC
1 CATGATCTTTAGCGGCGTTT-TTTTC
544554 GTAAACGCTG
Statistics
Matches: 135, Mismatches: 13, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
126 46 0.34
127 89 0.66
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.36
Consensus pattern (125 bp):
CATGATCTTTAGCGGCGTTTTTTTCAAGTGCCGCTAAAGAACATGATCTTTAGCGGCATTTTTTT
CTAAGCCCCGCTAAAGAACATGATCTTTAGCGGCATTTTTTTCTAAACGCCGCTAAAGAA
Done.