Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001711.1 Hibiscus syriacus cultivar Beakdansim tig00003454_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4148933
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 13
Found at i:340198 original size:23 final size:23
Alignment explanation
Indices: 340170--340222 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
340160 AAAATCAGCA
*
340170 AAGAAAATAAAAGCACTCAAAAG
1 AAGAAAATAAAAGCACTAAAAAG
* *
340193 AAGAAATTGAAAGCACTAAAAAG
1 AAGAAAATAAAAGCACTAAAAAG
340216 AAGAAAA
1 AAGAAAA
340223 AGAAAGAAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.66, C:0.09, G:0.15, T:0.09
Consensus pattern (23 bp):
AAGAAAATAAAAGCACTAAAAAG
Found at i:340227 original size:23 final size:23
Alignment explanation
Indices: 340170--340228 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
340160 AAAATCAGCA
*
340170 AAGAAAATA-AAAGCACTCAAAAG
1 AAGAAAA-AGAAAGCACTAAAAAG
**
340193 AAGAAATTGAAAGCACTAAAAAG
1 AAGAAAAAGAAAGCACTAAAAAG
340216 AAGAAAAAGAAAG
1 AAGAAAAAGAAAG
340229 AAAGAAAAGT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.66, C:0.08, G:0.17, T:0.08
Consensus pattern (23 bp):
AAGAAAAAGAAAGCACTAAAAAG
Found at i:342796 original size:28 final size:28
Alignment explanation
Indices: 342763--342846 Score: 141
Period size: 28 Copynumber: 3.0 Consensus size: 28
342753 TCATGGGGTT
*
342763 CATAACAGCATGTTCATCATTTTTTTTG
1 CATAACAGCATGTTCATCATTTGTTTTG
342791 CATAACAGCATGTTCATCATTTGTTTTG
1 CATAACAGCATGTTCATCATTTGTTTTG
* *
342819 CATAACAGCATATTTATCATTTGTTTTG
1 CATAACAGCATGTTCATCATTTGTTTTG
342847 TTAAATTTAC
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 53 1.00
ACGTcount: A:0.26, C:0.17, G:0.12, T:0.45
Consensus pattern (28 bp):
CATAACAGCATGTTCATCATTTGTTTTG
Found at i:344444 original size:22 final size:23
Alignment explanation
Indices: 344413--344467 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
344403 GAAATTCATC
*
344413 TTAAAAAAAAAGAATTCCGAAAA
1 TTAAAAAAAATGAATTCCGAAAA
*
344436 TTAAAAAAAATGAATTCTGAAAA
1 TTAAAAAAAATGAATTCCGAAAA
344459 TTAAAAAAA
1 TTAAAAAAA
344468 GAAAAGTTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.65, C:0.05, G:0.07, T:0.22
Consensus pattern (23 bp):
TTAAAAAAAATGAATTCCGAAAA
Found at i:344477 original size:24 final size:22
Alignment explanation
Indices: 344413--344478 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 22
344403 GAAATTCATC
*
344413 TTAAAAAAAAAGAATTCCGAAAA
1 TTAAAAAAAAA-AATTCTGAAAA
*
344436 TTAAAAAAAATGAATTCTGAAAA
1 TTAAAAAAAA-AAATTCTGAAAA
344459 TTAAAAAAAGAAAAGTTCTG
1 TTAAAAAAA-AAAA-TTCTG
344479 GTCTTGAGAC
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
23 31 0.84
24 6 0.16
ACGTcount: A:0.61, C:0.06, G:0.11, T:0.23
Consensus pattern (22 bp):
TTAAAAAAAAAAATTCTGAAAA
Found at i:348655 original size:19 final size:21
Alignment explanation
Indices: 348617--348665 Score: 75
Period size: 19 Copynumber: 2.4 Consensus size: 21
348607 ACAAGTCAAG
348617 GACAATATTGAAAGAAGAACTA
1 GACAATATT-AAAGAAGAACTA
348639 GACAATATT-AA-AAGAACTA
1 GACAATATTAAAGAAGAACTA
348658 GACAATAT
1 GACAATAT
348666 GAGCAGCAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 16 0.59
20 2 0.07
22 9 0.33
ACGTcount: A:0.55, C:0.10, G:0.14, T:0.20
Consensus pattern (21 bp):
GACAATATTAAAGAAGAACTA
Found at i:349231 original size:28 final size:28
Alignment explanation
Indices: 349198--349281 Score: 132
Period size: 28 Copynumber: 3.0 Consensus size: 28
349188 TCGTGGGGTT
349198 CATAACAGCATGTTCATCATTTGTTTTG
1 CATAACAGCATGTTCATCATTTGTTTTG
* *
349226 CATAACATCAGGTTCATCATTTGTTTTG
1 CATAACAGCATGTTCATCATTTGTTTTG
* *
349254 CATAACAGCATATTTATCATTTGTTTTG
1 CATAACAGCATGTTCATCATTTGTTTTG
349282 TTAAATTTAC
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 50 1.00
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.44
Consensus pattern (28 bp):
CATAACAGCATGTTCATCATTTGTTTTG
Found at i:364275 original size:286 final size:286
Alignment explanation
Indices: 363763--364336 Score: 1112
Period size: 286 Copynumber: 2.0 Consensus size: 286
363753 CCAAGGGTTA
363763 TTTCCCTCCATCTAGGGCTGAAACATTATGTCATTTAGCATTAAAATTATTTCATTTTATAGAGA
1 TTTCCCTCCATCTAGGGCTGAAACATTATGTCATTTAGCATTAAAATTATTTCATTTTATAGAGA
363828 CACAAGGGCTGGACGAATCCTTTTATAACCATTCGGTCATGTCTCCCCATTTCCTATAAATAGCA
66 CACAAGGGCTGGACGAATCCTTTTATAACCATTCGGTCATGTCTCCCCATTTCCTATAAATAGCA
363893 AAGCAATCATCATTTGTAATCAGACCATTATTTTTAATTGAAGTGAGATTATTCTCTTTCTTAAG
131 AAGCAATCATCATTTGTAATCAGACCATTATTTTTAATTGAAGTGAGATTATTCTCTTTCTTAAG
363958 TCCTGGTGACTTTTTATCGACTTATCAAGTATTTTATACTTGTGGCGTCAACCCCTTCCTTTTCA
196 TCCTGGTGACTTTTTATCGACTTATCAAGTATTTTATACTTGTGGCGTCAACCCCTTCCTTTTCA
*
364023 CCTTGATACTAGTGGTTCCTAGTCCT
261 CCTTGATACTACTGGTTCCTAGTCCT
364049 TTTCCCTCCATCTAGGGCTGAAACATTATGTCATTTAGCATTAAAATTATTTCATTTTATAGAGA
1 TTTCCCTCCATCTAGGGCTGAAACATTATGTCATTTAGCATTAAAATTATTTCATTTTATAGAGA
*
364114 CACAAGGGCTGGCCGAATCCTTTTATAACCATTCGGTCATGTCTCCCCATTTCCTATAAATAGCA
66 CACAAGGGCTGGACGAATCCTTTTATAACCATTCGGTCATGTCTCCCCATTTCCTATAAATAGCA
364179 AAGCAATCATCATTTGTAATCAGACCATTATTTTTAATTGAAGTGAGATTATTCTCTTTCTTAAG
131 AAGCAATCATCATTTGTAATCAGACCATTATTTTTAATTGAAGTGAGATTATTCTCTTTCTTAAG
364244 TCCTGGTGACTTTTTATCGACTTATCAAGTATTTTATACTTGTGGCGTCAACCCCTTCCTTTTCA
196 TCCTGGTGACTTTTTATCGACTTATCAAGTATTTTATACTTGTGGCGTCAACCCCTTCCTTTTCA
* *
364309 CCTTGATACTTCTGGTTCCTAGTTCT
261 CCTTGATACTACTGGTTCCTAGTCCT
364335 TT
1 TT
364337 ATAACTAGTG
Statistics
Matches: 284, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
286 284 1.00
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (286 bp):
TTTCCCTCCATCTAGGGCTGAAACATTATGTCATTTAGCATTAAAATTATTTCATTTTATAGAGA
CACAAGGGCTGGACGAATCCTTTTATAACCATTCGGTCATGTCTCCCCATTTCCTATAAATAGCA
AAGCAATCATCATTTGTAATCAGACCATTATTTTTAATTGAAGTGAGATTATTCTCTTTCTTAAG
TCCTGGTGACTTTTTATCGACTTATCAAGTATTTTATACTTGTGGCGTCAACCCCTTCCTTTTCA
CCTTGATACTACTGGTTCCTAGTCCT
Found at i:366744 original size:23 final size:22
Alignment explanation
Indices: 366710--366752 Score: 52
Period size: 23 Copynumber: 1.9 Consensus size: 22
366700 GCAAAGCAAA
366710 AGAAAAATAGAAGAAAAAAAATC
1 AGAAAAATAGAA-AAAAAAAATC
*
366733 AGAAAAGA-AGAAAAGAAAAA
1 AGAAAA-ATAGAAAAAAAAAA
366753 GAAGTTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 7 0.39
23 10 0.56
24 1 0.06
ACGTcount: A:0.77, C:0.02, G:0.16, T:0.05
Consensus pattern (22 bp):
AGAAAAATAGAAAAAAAAAATC
Found at i:373475 original size:11 final size:13
Alignment explanation
Indices: 373441--373472 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
373431 TTTGGCCAAA
373441 GTTGAAAAGGTAT
1 GTTGAAAAGGTAT
373454 GTTGAAAAGGTAT
1 GTTGAAAAGGTAT
373467 G-TGAAA
1 GTTGAAA
373473 GGTGTTTAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.41, C:0.00, G:0.31, T:0.28
Consensus pattern (13 bp):
GTTGAAAAGGTAT
Found at i:374272 original size:117 final size:118
Alignment explanation
Indices: 374096--374329 Score: 332
Period size: 117 Copynumber: 2.0 Consensus size: 118
374086 TAAGGTAGAA
* * *
374096 TGATGTAGGCTGAATCTATACGCTTTGGGAGAAGAGAGTAGATAGCCTTTTTATGTCCCGATCTA
1 TGATGTAGGCTGAATCTACAAGCTTTGGGAGAAGAGAGTAGATAGCCTTATTATGTCCCGATCTA
* * *
374161 GGATTGACAAGTACTGATATCCTTGAATTTATAAG-TTCGGGCTGCAAAATAAG
66 GGATTGACAAGTACTAATATCCTTGAATTAATAAGCTT-GGGCCGCAAAATAAG
*
374214 TGATGTAAGG-TGAATCTACAAGCTTTGGTGA-AA-AGAGTAGATAGCCTTATTGTGTCCCGATC
1 TGATGT-AGGCTGAATCTACAAGCTTTGG-GAGAAGAGAGTAGATAGCCTTATTATGTCCCGATC
* *
374276 TAGGATTGACAAGTACTAATGTCCTTGAATTAATAAGCTTGTGCCGCAAAATAA
64 TAGGATTGACAAGTACTAATATCCTTGAATTAATAAGCTTGGGCCGCAAAATAA
374330 TAAGAAAAAA
Statistics
Matches: 104, Mismatches: 9, Indels: 7
0.87 0.08 0.06
Matches are distributed among these distances:
117 73 0.70
118 26 0.25
119 5 0.05
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.31
Consensus pattern (118 bp):
TGATGTAGGCTGAATCTACAAGCTTTGGGAGAAGAGAGTAGATAGCCTTATTATGTCCCGATCTA
GGATTGACAAGTACTAATATCCTTGAATTAATAAGCTTGGGCCGCAAAATAAG
Found at i:382010 original size:567 final size:568
Alignment explanation
Indices: 380935--382067 Score: 2142
Period size: 567 Copynumber: 2.0 Consensus size: 568
380925 CGTACAAATG
*
380935 AAGGCAAGCCACTCTATTTATAGGAAATGAGAGGGCTTGGCCGAATGGTTACATGATGTTTCGGC
1 AAGGCAAGCCACTCTATTTATAGGAAATGAGAGGGCTTGGCCGAATAGTTACATGATGTTTCGGC
381000 TAGATACATGACTTTAGGAAGATACATAATGTTTTAAAATGAAAGATCAAGTCATTTGGGCTTGT
66 TAGATACATGACTTTAGGAAGATACATAATGTTTTAAAATGAAAGATCAAGTCATTTGGGCTTGT
*
381065 GATGGTTTGGCTAACCCTTCATAAAGGGACTTGATGATTCAGCTAAGGATGGGAAGACATCTCCC
131 GATGGTTCGGCTAACCCTTCATAAAGGGACTTGATGATTCAGCTAAGGATGGGAAGACATCTCCC
* *
381130 TTGGCCGAATGGTGATGCTGGTTCATCTTGGCACCATTTCTCTTCTCTTTAGCCGAATGGGTTTG
196 TTGGCCGAATGGTGATGCTGGTTCATCTTGGCACCATTTCTATTCTCTTTAGCCCAATGGGTTTG
381195 TATCTCCTCAAGTTGGCGCCAAATGTTCTCATGTGCATGGCATGTGATGTGGTCGAATAGGCATA
261 TATCTCCTCAAGTTGGCGCCAAATGTTCTCATGTGCATGGCATGTGATGTGGTCGAATAGGCATA
381260 GAGCTCTATCTCATGTCTCTTGGTGATTTAAGCCTCCAATGCTAGCAAACTCTTCACCAACGTGC
326 GAGCTCTATCTCATGTCTCTTGGTGATTTAAGCCTCCAATGCTAGCAAACTCTTCACCAACGTGC
381325 TCCTAGATGAAAAGGCATCTTCATGGGCAGCATCATTCATGAAAGGTCACAATGTTTGATAATGG
391 TCCTAGATGAAAAGGCATCTTCATGGGCAGCATCATTCATGAAAGGTCACAATGTTTGATAATGG
*
381390 TGTCCCTTCATGTTTGAGCTATTTATGGTGTGAATGAGCTGGTGGTGAGCTGGCCTTAGATGACT
456 TGTCCCTTCATGTTTGAGCTATTTATGCTGTGAATGAGCTGGTGGTGAGCTGGCCTTAGATGACT
381455 TGTAACATGATGAACGTTTGGGCAGCTCCTTGTGGAAAGGTACCTCCC
521 TGTAACATGATGAACGTTTGGGCAGCTCCTTGTGGAAAGGTACCTCCC
*
381503 AAGGCAAGCCACTCTATTTATATGAAATGAGAGGGCTTGGCCGAATAGTTACATGATGTTTCGGC
1 AAGGCAAGCCACTCTATTTATAGGAAATGAGAGGGCTTGGCCGAATAGTTACATGATGTTTCGGC
381568 TAGATACATGACTTTAGGAAGATACATAATGTTTTAAAATGAAAGATCAAGTCATTTGGGCTTGT
66 TAGATACATGACTTTAGGAAGATACATAATGTTTTAAAATGAAAGATCAAGTCATTTGGGCTTGT
* *
381633 GATGGTTCGGTTAACCCTTCA-AAAGGGACTTGATGATTCGGCTAAGGATGGGAAGACATCTCCC
131 GATGGTTCGGCTAACCCTTCATAAAGGGACTTGATGATTCAGCTAAGGATGGGAAGACATCTCCC
**
381697 TTGGCCGAATGGTGATGCTGGTTCATCTTGGTGCCATTTCTATTCTCTTTAGCCCAATGGGTTTG
196 TTGGCCGAATGGTGATGCTGGTTCATCTTGGCACCATTTCTATTCTCTTTAGCCCAATGGGTTTG
* *
381762 TATCTCCTCAAGTTGGTGCCAAATGTTCTCATGTGCATGGCATGTGATGTGGTCGAATAGGCATG
261 TATCTCCTCAAGTTGGCGCCAAATGTTCTCATGTGCATGGCATGTGATGTGGTCGAATAGGCATA
381827 GAGCTCTATCTCATGTCTCTTGGTGATTTAAGCCTCCAATGCTAGCAAACTCTTCACCAACGTGC
326 GAGCTCTATCTCATGTCTCTTGGTGATTTAAGCCTCCAATGCTAGCAAACTCTTCACCAACGTGC
*
381892 TCCTAGATGAAAAGGCATCTTCATGGGTAGCATCATTCATGAAAGGTCACAATGTTTGATAATGG
391 TCCTAGATGAAAAGGCATCTTCATGGGCAGCATCATTCATGAAAGGTCACAATGTTTGATAATGG
381957 TGTCCCTTCATGTTTGAGCTATTTATGCTGTGAATGAGCTGGTGGTGAGCTGGCCTTAGATGACT
456 TGTCCCTTCATGTTTGAGCTATTTATGCTGTGAATGAGCTGGTGGTGAGCTGGCCTTAGATGACT
382022 TGTAACATGATGAACGTTTGGGCAGCTCCTTGTGGAAAGGTACCTC
521 TGTAACATGATGAACGTTTGGGCAGCTCCTTGTGGAAAGGTACCTC
382068 TCGAGGTGGC
Statistics
Matches: 552, Mismatches: 13, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
567 405 0.73
568 147 0.27
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (568 bp):
AAGGCAAGCCACTCTATTTATAGGAAATGAGAGGGCTTGGCCGAATAGTTACATGATGTTTCGGC
TAGATACATGACTTTAGGAAGATACATAATGTTTTAAAATGAAAGATCAAGTCATTTGGGCTTGT
GATGGTTCGGCTAACCCTTCATAAAGGGACTTGATGATTCAGCTAAGGATGGGAAGACATCTCCC
TTGGCCGAATGGTGATGCTGGTTCATCTTGGCACCATTTCTATTCTCTTTAGCCCAATGGGTTTG
TATCTCCTCAAGTTGGCGCCAAATGTTCTCATGTGCATGGCATGTGATGTGGTCGAATAGGCATA
GAGCTCTATCTCATGTCTCTTGGTGATTTAAGCCTCCAATGCTAGCAAACTCTTCACCAACGTGC
TCCTAGATGAAAAGGCATCTTCATGGGCAGCATCATTCATGAAAGGTCACAATGTTTGATAATGG
TGTCCCTTCATGTTTGAGCTATTTATGCTGTGAATGAGCTGGTGGTGAGCTGGCCTTAGATGACT
TGTAACATGATGAACGTTTGGGCAGCTCCTTGTGGAAAGGTACCTCCC
Found at i:390467 original size:13 final size:12
Alignment explanation
Indices: 390448--390533 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
390438 AAATAGGCGT
390448 GATATGGTGATG
1 GATATGGTGATG
390460 GAATATGGTGAT-
1 G-ATATGGTGATG
*
390472 GATATAGGCG-T-
1 GATAT-GGTGATG
390483 GATAATGGTGATG
1 GAT-ATGGTGATG
390496 GACTATGGTGAT-
1 GA-TATGGTGATG
*
390508 GATATAGGCG-T-
1 GATAT-GGTGATG
390519 GATAATGGTGATG
1 GAT-ATGGTGATG
390532 GA
1 GA
390534 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:390503 original size:36 final size:36
Alignment explanation
Indices: 390430--390534 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
390420 ATTTATAAGT
* * *
390430 TGGTGATAAAATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
390465 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
390501 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
390535 AGATTGTATC
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 19 0.29
36 47 0.71
ACGTcount: A:0.30, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:394024 original size:14 final size:14
Alignment explanation
Indices: 394007--394045 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
393997 TTGCTTTTGA
394007 TTTTCTTCTTTTTC
1 TTTTCTTCTTTTTC
*
394021 TTTTCTT-TCTTTTG
1 TTTTCTTCT-TTTTC
394035 TTTTCTTCTTT
1 TTTTCTTCTTT
394046 CTTGTTGCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 1 0.05
14 20 0.91
15 1 0.05
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (14 bp):
TTTTCTTCTTTTTC
Found at i:394061 original size:28 final size:28
Alignment explanation
Indices: 393989--394045 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
393979 ACTTGCTTCA
393989 CTTTTCTTTTGCTTTTGATTTTCTTCTTTTT
1 CTTTTC-TTT-CTTTTGATTTTCTTC-TTTT
394020 CTTTTCTTTCTTTTG-TTTTCTTCTTT
1 CTTTTCTTTCTTTTGATTTTCTTCTTT
394046 CTTGTTGCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 3 0.12
28 8 0.31
29 6 0.23
30 3 0.12
31 6 0.23
ACGTcount: A:0.02, C:0.18, G:0.05, T:0.75
Consensus pattern (28 bp):
CTTTTCTTTCTTTTGATTTTCTTCTTTT
Found at i:394519 original size:34 final size:34
Alignment explanation
Indices: 394460--394542 Score: 123
Period size: 34 Copynumber: 2.4 Consensus size: 34
394450 GTGATAAAAT
394460 AGGCGTGAT-ATGGTGATGGAATATGGTGATGATAC
1 AGGCGTGATAAT-G-GATGGAATATGGTGATGATAC
* *
394495 AGGCGTGATAATGGATGGACTATGGTGATGATAT
1 AGGCGTGATAATGGATGGAATATGGTGATGATAC
394529 AGGCGTGATAATGG
1 AGGCGTGATAATGG
394543 TGATGGACAA
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
34 33 0.73
35 10 0.22
36 2 0.04
ACGTcount: A:0.29, C:0.06, G:0.37, T:0.28
Consensus pattern (34 bp):
AGGCGTGATAATGGATGGAATATGGTGATGATAC
Found at i:398039 original size:28 final size:28
Alignment explanation
Indices: 398008--398063 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
397998 CTTGCTTCAC
398008 TTTTCTT-TTGCTTTTGATTTTCTTCTTT
1 TTTTCTTCTTGCTTTTG-TTTTCTTCTTT
*
398036 TTTTCTTCTTTCTTTTGTTTTCTTCTTT
1 TTTTCTTCTTGCTTTTGTTTTCTTCTTT
398064 CTTGTTGCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 18 0.69
29 8 0.31
ACGTcount: A:0.02, C:0.16, G:0.05, T:0.77
Consensus pattern (28 bp):
TTTTCTTCTTGCTTTTGTTTTCTTCTTT
Found at i:398056 original size:17 final size:18
Alignment explanation
Indices: 398026--398066 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
398016 TGCTTTTGAT
*
398026 TTTCTTCTTTTTTTCTTC
1 TTTCTTCTTGTTTTCTTC
398044 TTTCTT-TTGTTTTCTTC
1 TTTCTTCTTGTTTTCTTC
398061 TTTCTT
1 TTTCTT
398067 GTTGCTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 16 0.73
18 6 0.27
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (18 bp):
TTTCTTCTTGTTTTCTTC
Found at i:398074 original size:28 final size:29
Alignment explanation
Indices: 398018--398079 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 29
398008 TTTTCTTTTG
* *
398018 CTTTTGATTTTCTTCTTTTTTTCTTCTTT
1 CTTTTGATTTTCTTCTTTTTGTCTGCTTT
398047 CTTTTG-TTTTCTTCTTTCTTGT-TGCTTT
1 CTTTTGATTTTCTTCTTT-TTGTCTGCTTT
*
398075 TTTTT
1 CTTTT
398080 TGTAGCACTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 20 0.69
29 9 0.31
ACGTcount: A:0.02, C:0.16, G:0.06, T:0.76
Consensus pattern (29 bp):
CTTTTGATTTTCTTCTTTTTGTCTGCTTT
Found at i:398528 original size:34 final size:34
Alignment explanation
Indices: 398476--398558 Score: 123
Period size: 34 Copynumber: 2.4 Consensus size: 34
398466 GGTGATAAAT
398476 AGGCGTGAT-ATGGTGATGGAATATGGTGATGATAC
1 AGGCGTGATAAT-G-GATGGAATATGGTGATGATAC
* *
398511 AGGCGTGATAATGGATGGACTATGGTGATGATAT
1 AGGCGTGATAATGGATGGAATATGGTGATGATAC
398545 AGGCGTGATAATGG
1 AGGCGTGATAATGG
398559 TGATGGACAA
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
34 33 0.73
35 10 0.22
36 2 0.04
ACGTcount: A:0.29, C:0.06, G:0.37, T:0.28
Consensus pattern (34 bp):
AGGCGTGATAATGGATGGAATATGGTGATGATAC
Found at i:402059 original size:14 final size:14
Alignment explanation
Indices: 402042--402080 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
402032 TTGCTTTTGA
402042 TTTTCTTCTTTTTC
1 TTTTCTTCTTTTTC
*
402056 TTTTCTT-TCTTTTG
1 TTTTCTTCT-TTTTC
402070 TTTTCTTCTTT
1 TTTTCTTCTTT
402081 CTTGTTGCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 1 0.05
14 20 0.91
15 1 0.05
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (14 bp):
TTTTCTTCTTTTTC
Found at i:402091 original size:28 final size:27
Alignment explanation
Indices: 402024--402098 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 27
402014 ACTTGCTTCA
402024 CTTTTCTTTTGCTTTTGATTTTCTTCTTTTT
1 CTTTTC-TTT-CTTTTG-TTTTCTTC-TTTT
402055 CTTTTCTTTCTTTTGTTTTCTTC-TTT
1 CTTTTCTTTCTTTTGTTTTCTTCTTTT
*
402081 CTTGTTGCTTTTTTTTGT
1 CTT-TT-CTTTCTTTTGT
402099 AGCACTTTGA
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
26 6 0.15
27 2 0.05
28 18 0.44
29 6 0.15
30 3 0.07
31 6 0.15
ACGTcount: A:0.01, C:0.16, G:0.08, T:0.75
Consensus pattern (27 bp):
CTTTTCTTTCTTTTGTTTTCTTCTTTT
Found at i:402552 original size:34 final size:34
Alignment explanation
Indices: 402493--402575 Score: 123
Period size: 34 Copynumber: 2.4 Consensus size: 34
402483 GTGATAAAAT
402493 AGGCGTGAT-ATGGTGATGGAATATGGTGATGATAC
1 AGGCGTGATAAT-G-GATGGAATATGGTGATGATAC
* *
402528 AGGCGTGATAATGGATGGACTATGGTGATGATAT
1 AGGCGTGATAATGGATGGAATATGGTGATGATAC
402562 AGGCGTGATAATGG
1 AGGCGTGATAATGG
402576 TGATGGACAA
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
34 33 0.73
35 10 0.22
36 2 0.04
ACGTcount: A:0.29, C:0.06, G:0.37, T:0.28
Consensus pattern (34 bp):
AGGCGTGATAATGGATGGAATATGGTGATGATAC
Found at i:405148 original size:19 final size:18
Alignment explanation
Indices: 405126--405174 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
405116 TTGAAATTTC
405126 TTTTTCTTTTCTGAT-TTTT
1 TTTTTCTTTT-TG-TCTTTT
405145 TTTTTCTTTTTGTCTTTT
1 TTTTTCTTTTTGTCTTTT
*
405163 TCTTTCTTTTTG
1 TTTTTCTTTTTG
405175 CACTCCAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 1 0.04
18 17 0.61
19 10 0.36
ACGTcount: A:0.02, C:0.12, G:0.06, T:0.80
Consensus pattern (18 bp):
TTTTTCTTTTTGTCTTTT
Found at i:407922 original size:10 final size:10
Alignment explanation
Indices: 407907--407934 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
407897 ATGTCAATGG
407907 TAGCTGAATA
1 TAGCTGAATA
407917 TAGCTGAATA
1 TAGCTGAATA
407927 TAGCTGAA
1 TAGCTGAA
407935 CGTGCTGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (10 bp):
TAGCTGAATA
Found at i:410497 original size:16 final size:16
Alignment explanation
Indices: 410476--410514 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
410466 AGATGAGTAC
*
410476 AAATGAAAGAATAAGG
1 AAATGAAAGAATAAGA
* *
410492 AAATGAAATAGTAAGA
1 AAATGAAAGAATAAGA
410508 AAATGAA
1 AAATGAA
410515 GATACTTTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.21, T:0.15
Consensus pattern (16 bp):
AAATGAAAGAATAAGA
Found at i:411657 original size:10 final size:10
Alignment explanation
Indices: 411644--411700 Score: 69
Period size: 10 Copynumber: 5.6 Consensus size: 10
411634 ATTTTTTTCA
411644 AAAAAAAAAC
1 AAAAAAAAAC
411654 AAAAAAAAAC
1 AAAAAAAAAC
* *
411664 AAAAACAAAG
1 AAAAAAAAAC
**
411674 AGGCAAAAAAC
1 A-AAAAAAAAC
411685 AAAAAAAAAC
1 AAAAAAAAAC
411695 AAAAAA
1 AAAAAA
411701 GCCAAAATTT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
10 32 0.84
11 6 0.16
ACGTcount: A:0.84, C:0.11, G:0.05, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:411707 original size:25 final size:25
Alignment explanation
Indices: 411653--411707 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
411643 AAAAAAAAAA
* *
411653 CAAAAAAAAACAAAAAC-AAAGAGG
1 CAAAAAAAAACAAAAACAAAAAAGC
*
411677 CAAAAAACAAAAAAAAACAAAAAAGC
1 CAAAAAA-AAACAAAAACAAAAAAGC
411703 CAAAA
1 CAAAA
411708 TTTCAAAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 7 0.27
25 9 0.35
26 10 0.38
ACGTcount: A:0.78, C:0.15, G:0.07, T:0.00
Consensus pattern (25 bp):
CAAAAAAAAACAAAAACAAAAAAGC
Found at i:422949 original size:35 final size:37
Alignment explanation
Indices: 422903--422973 Score: 119
Period size: 35 Copynumber: 2.0 Consensus size: 37
422893 TTAGAAGTTG
422903 GTGATAATATAGGCGTGAT-ATGGTGATGGA-ATATA
1 GTGATAATATAGGCGTGATAATGGTGATGGACATATA
*
422938 GTGATGATATAGGCGTGATAATGGTGATGGACATAT
1 GTGATAATATAGGCGTGATAATGGTGATGGACATAT
422974 TGTATCTTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
35 18 0.55
36 11 0.33
37 4 0.12
ACGTcount: A:0.32, C:0.04, G:0.32, T:0.31
Consensus pattern (37 bp):
GTGATAATATAGGCGTGATAATGGTGATGGACATATA
Found at i:424679 original size:16 final size:16
Alignment explanation
Indices: 424658--424695 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
424648 GATTAGAATA
424658 AAATAAACAAAAGATG
1 AAATAAACAAAAGATG
**
424674 AAATAAACGGAAGATG
1 AAATAAACAAAAGATG
424690 AAATAA
1 AAATAA
424696 GATAATAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.66, C:0.05, G:0.16, T:0.13
Consensus pattern (16 bp):
AAATAAACAAAAGATG
Found at i:438229 original size:21 final size:21
Alignment explanation
Indices: 438205--438259 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
438195 TTTTTTGAAA
* *
438205 TTTTGGCTTTTTTGGCTTTTG
1 TTTTTGCTTTTTTGCCTTTTG
* *
438226 TTTTTGTTTTTTTGCCTTTTT
1 TTTTTGCTTTTTTGCCTTTTG
438247 TTTTTGCTTTTTT
1 TTTTTGCTTTTTT
438260 TTGAAAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.00, C:0.09, G:0.15, T:0.76
Consensus pattern (21 bp):
TTTTTGCTTTTTTGCCTTTTG
Found at i:438248 original size:13 final size:12
Alignment explanation
Indices: 438232--438261 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
438222 TTTGTTTTTG
438232 TTTTTTTGCCTTT
1 TTTTTTTG-CTTT
438245 TTTTTTTGCTTT
1 TTTTTTTGCTTT
438257 TTTTT
1 TTTTT
438262 GAAAAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.53
13 8 0.47
ACGTcount: A:0.00, C:0.10, G:0.07, T:0.83
Consensus pattern (12 bp):
TTTTTTTGCTTT
Found at i:452608 original size:18 final size:19
Alignment explanation
Indices: 452576--452612 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
452566 TGTAGGAGTC
*
452576 TTTTTCTTTTCTTTTTGTT
1 TTTTTCTTCTCTTTTTGTT
452595 TTTTTCTTCT-TTTTTGTT
1 TTTTTCTTCTCTTTTTGTT
452613 GCTTTTGTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.00, C:0.11, G:0.05, T:0.84
Consensus pattern (19 bp):
TTTTTCTTCTCTTTTTGTT
Found at i:454575 original size:13 final size:11
Alignment explanation
Indices: 454534--454618 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
454524 ACAATCTGTC
454534 CATCACCATTAT
1 CATCACCA-TAT
*
454546 CA-CGCCTATAT
1 CATCACC-ATAT
454557 CATCACCATAGT
1 CATCACCATA-T
454569 CCATCACCATTAT
1 -CATCACCA-TAT
*
454582 CA-CGCCTATAT
1 CATCACC-ATAT
454593 CATCACCATATT
1 CATCACCATA-T
454605 CCATCACCATAT
1 -CATCACCATAT
454617 CA
1 CA
454619 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:454578 original size:36 final size:36
Alignment explanation
Indices: 454531--454635 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
454521 GATACAATCT
454531 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
454567 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
454603 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
454636 ACTTATAAAT
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 21 0.31
36 46 0.69
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:455116 original size:14 final size:15
Alignment explanation
Indices: 455082--455128 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
455072 AATTTGGAGT
455082 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
455097 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
455111 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
455128 G
1 G
455129 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:459022 original size:13 final size:11
Alignment explanation
Indices: 458981--459065 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
458971 ACAATCTGTC
458981 CATCACCATTAT
1 CATCACCA-TAT
*
458993 CA-CGCCTATAT
1 CATCACC-ATAT
459004 CATCACCATAGT
1 CATCACCATA-T
459016 CCATCACCATTAT
1 -CATCACCA-TAT
*
459029 CA-CGCCTATAT
1 CATCACC-ATAT
459040 CATCACCATATT
1 CATCACCATA-T
459052 CCATCACCATAT
1 -CATCACCATAT
459064 CA
1 CA
459066 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:459025 original size:36 final size:36
Alignment explanation
Indices: 458978--459082 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
458968 GATACAATCT
458978 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
459014 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
459050 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
459083 ACTTATAAAT
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 21 0.31
36 46 0.69
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:463648 original size:23 final size:24
Alignment explanation
Indices: 463606--463658 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
463596 TTTCTTTCTT
463606 TTTCTTCTTTTCGAGTGCTTTCAA
1 TTTCTTCTTTTCGAGTGCTTTCAA
* *
463630 TTTCTTCTTTT-GAGTGCTTTTAT
1 TTTCTTCTTTTCGAGTGCTTTCAA
463653 TTTCTT
1 TTTCTT
463659 TGCTGATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.09, C:0.17, G:0.11, T:0.62
Consensus pattern (24 bp):
TTTCTTCTTTTCGAGTGCTTTCAA
Found at i:468989 original size:11 final size:11
Alignment explanation
Indices: 468975--469012 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
468965 TTTTTTTTTC
468975 AAAAAAACAAA
1 AAAAAAACAAA
468986 AAAAAAACAAA
1 AAAAAAACAAA
* *
468997 AAAAAAGCCAA
1 AAAAAAACAAA
469008 AAAAA
1 AAAAA
469013 CAAAATAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.87, C:0.11, G:0.03, T:0.00
Consensus pattern (11 bp):
AAAAAAACAAA
Found at i:469000 original size:20 final size:19
Alignment explanation
Indices: 468974--469030 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 19
468964 ATTTTTTTTT
*
468974 CAAAAAAACAAAAAAAAAA
1 CAAAAAAAAAAAAAAAAAA
**
468993 CAAAAAAAAAGCCAAAAAAA
1 CAAAAAAAAA-AAAAAAAAA
469013 CAAAATAAATAAAAAAAA
1 CAAAA-AAA-AAAAAAAA
469031 GCCAAAAAGC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
19 9 0.30
20 12 0.40
21 7 0.23
22 2 0.07
ACGTcount: A:0.84, C:0.11, G:0.02, T:0.04
Consensus pattern (19 bp):
CAAAAAAAAAAAAAAAAAA
Found at i:469038 original size:11 final size:10
Alignment explanation
Indices: 468975--469030 Score: 53
Period size: 10 Copynumber: 5.5 Consensus size: 10
468965 TTTTTTTTTC
468975 AAAAAAACAAA
1 AAAAAAAC-AA
468986 AAAAAAACAA
1 AAAAAAACAA
*
468996 AAAAAAAGC-C
1 AAAAAAA-CAA
469006 AAAAAAACAA
1 AAAAAAACAA
*
469016 AATAAATA-AA
1 AA-AAAAACAA
469026 AAAAA
1 AAAAA
469031 GCCAAAAAGC
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
9 4 0.10
10 22 0.56
11 13 0.33
ACGTcount: A:0.86, C:0.09, G:0.02, T:0.04
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:469054 original size:28 final size:27
Alignment explanation
Indices: 468983--469056 Score: 80
Period size: 28 Copynumber: 2.7 Consensus size: 27
468973 TCAAAAAAAC
468983 AAAAA-AAAA-ACAAAAAAAAAGCCAA
1 AAAAACAAAATACAAAAAAAAAGCCAA
*
469008 AAAAACAAAATAAATAAAAAAAAGCCAA
1 AAAAACAAAATACA-AAAAAAAAGCCAA
** *
469036 AAAGCCAAAATTTCAAAAAAA
1 AAAAACAAAA-TACAAAAAAA
469057 TTGCAAACGA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
25 5 0.12
26 4 0.10
27 2 0.05
28 27 0.68
29 2 0.05
ACGTcount: A:0.77, C:0.12, G:0.04, T:0.07
Consensus pattern (27 bp):
AAAAACAAAATACAAAAAAAAAGCCAA
Found at i:479863 original size:15 final size:17
Alignment explanation
Indices: 479827--479860 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
479817 TTTGATAACA
479827 TTTC-TATCTATTTCCT
1 TTTCTTATCTATTTCCT
479843 TTTCTTATC-ATTTCCT
1 TTTCTTATCTATTTCCT
479859 TT
1 TT
479861 CTTCTTTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.12, C:0.24, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTCTTATCTATTTCCT
Found at i:480434 original size:36 final size:36
Alignment explanation
Indices: 480333--480481 Score: 178
Period size: 36 Copynumber: 4.2 Consensus size: 36
480323 ATTGGTGGTT
* *
480333 ATATAGGCGTG-AAATGGTTATATAAGATGGTAATG
1 ATATAGGCGTGAAAATGGTAATAGAAGATGGTAATG
* * *
480368 ATATAGGCGT-ACAATGGTAATGGAAGATGGTGATG
1 ATATAGGCGTGAAAATGGTAATAGAAGATGGTAATG
* * *
480403 TTATAGGCGTGAAAATGGTGATAGAATATGGTAATG
1 ATATAGGCGTGAAAATGGTAATAGAAGATGGTAATG
*
480439 ATATAGGCGTGAAAATGGTAAT-GAAAGATGGTGATG
1 ATATAGGCGTGAAAATGGTAATAG-AAGATGGTAATG
*
480475 TTATAGG
1 ATATAGG
480482 TAGTTTCTTA
Statistics
Matches: 95, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
35 39 0.41
36 56 0.59
ACGTcount: A:0.36, C:0.03, G:0.32, T:0.29
Consensus pattern (36 bp):
ATATAGGCGTGAAAATGGTAATAGAAGATGGTAATG
Found at i:480435 original size:71 final size:71
Alignment explanation
Indices: 480334--480481 Score: 235
Period size: 71 Copynumber: 2.1 Consensus size: 71
480324 TTGGTGGTTA
* * * *
480334 TATAGGCGTGAAATGGTTATATAAGATGGTAATGATATAGGCGT-ACAATGGTAATGGAAGATGG
1 TATAGGCGTGAAATGGTGATAGAAGATGGTAATGATATAGGCGTGAAAATGGTAATGAAAGATGG
480398 TGATGT
66 TGATGT
*
480404 TATAGGCGTGAAAATGGTGATAGAATATGGTAATGATATAGGCGTGAAAATGGTAATGAAAGATG
1 TATAGGCGTG-AAATGGTGATAGAAGATGGTAATGATATAGGCGTGAAAATGGTAATGAAAGATG
480469 GTGATGT
65 GTGATGT
480476 TATAGG
1 TATAGG
480482 TAGTTTCTTA
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
70 10 0.14
71 31 0.44
72 30 0.42
ACGTcount: A:0.36, C:0.03, G:0.32, T:0.29
Consensus pattern (71 bp):
TATAGGCGTGAAATGGTGATAGAAGATGGTAATGATATAGGCGTGAAAATGGTAATGAAAGATGG
TGATGT
Found at i:485460 original size:13 final size:11
Alignment explanation
Indices: 485419--485503 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
485409 ACAATCTGTC
485419 CATCACCATTAT
1 CATCACCA-TAT
*
485431 CA-CGCCTATAT
1 CATCACC-ATAT
485442 CATCACCATAGT
1 CATCACCATA-T
485454 CCATCACCATTAT
1 -CATCACCA-TAT
*
485467 CA-CGCCTATAT
1 CATCACC-ATAT
485478 CATCACCATATT
1 CATCACCATA-T
485490 CCATCACCATAT
1 -CATCACCATAT
485502 CA
1 CA
485504 CGCCTATTTT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:485463 original size:36 final size:36
Alignment explanation
Indices: 485416--485520 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
485406 GATACAATCT
485416 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
485452 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
485488 TTCCATCACCA-TATCACGCCTATTTTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
485521 ACTTATAAAT
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 20 0.30
36 46 0.70
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.30
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:491742 original size:7 final size:6
Alignment explanation
Indices: 491713--491753 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
491703 TGTAGGAGTC
* *
491713 TTTTCT TTCTCT TTTTGT TTTTCT TCTTTCT TTTTCT TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT T-TTTCT TTTTCT TTTT
491754 GTTGCTTTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
6 24 0.80
7 6 0.20
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.80
Consensus pattern (6 bp):
TTTTCT
Found at i:491746 original size:19 final size:18
Alignment explanation
Indices: 491713--491753 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
491703 TGTAGGAGTC
*
491713 TTTTCTTTCTCTTTTTGT
1 TTTTCTTTCTCTTTTTCT
*
491731 TTTTCTTCTTTCTTTTTCT
1 TTTTCTT-TCTCTTTTTCT
491750 TTTT
1 TTTT
491754 GTTGCTTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.80
Consensus pattern (18 bp):
TTTTCTTTCTCTTTTTCT
Found at i:491972 original size:33 final size:32
Alignment explanation
Indices: 491910--491973 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 32
491900 AAAATTAAAA
*
491910 GAAAGAAATGATTAAAAAGGAATATGAAAGAG
1 GAAAGAAATGATTAAAAAGGAAAATGAAAGAG
491942 GAAAGGAAATGA-TAAGAAA-GAAAATGGAAAGA
1 GAAA-GAAATGATTAA-AAAGGAAAAT-GAAAGA
491974 AATGTTATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
32 12 0.43
33 16 0.57
ACGTcount: A:0.61, C:0.00, G:0.27, T:0.12
Consensus pattern (32 bp):
GAAAGAAATGATTAAAAAGGAAAATGAAAGAG
Found at i:492153 original size:35 final size:35
Alignment explanation
Indices: 492122--492249 Score: 166
Period size: 36 Copynumber: 3.6 Consensus size: 35
492112 ATTGGTAGTT
* *
492122 ATATAGGCATGAAATGGTGATATAAGATGGTAATG
1 ATATAGGCGTGAAATGGTGATAGAAGATGGTAATG
* * * *
492157 ATATAGGCGTGCAATGGTAATGGAAGATGGTGATG
1 ATATAGGCGTGAAATGGTGATAGAAGATGGTAATG
* *
492192 TTATAGGCGTAAAAATGGTGATAGAAGATGGTAATG
1 ATATAGGCGT-GAAATGGTGATAGAAGATGGTAATG
492228 ATATAGGCGTGAAAATGGTGAT
1 ATATAGGCGTG-AAATGGTGAT
492250 GTTATAGGTA
Statistics
Matches: 77, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
35 38 0.49
36 39 0.51
ACGTcount: A:0.37, C:0.04, G:0.32, T:0.27
Consensus pattern (35 bp):
ATATAGGCGTGAAATGGTGATAGAAGATGGTAATG
Found at i:495084 original size:19 final size:21
Alignment explanation
Indices: 495060--495099 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
495050 TTCTACCTTA
495060 ATTTAT-ATTATAT-TTACTC
1 ATTTATCATTATATATTACTC
495079 ATTTATGCATTATATATTACT
1 ATTTAT-CATTATATATTACT
495100 ATGAGCATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
21 7 0.39
22 5 0.28
ACGTcount: A:0.33, C:0.10, G:0.03, T:0.55
Consensus pattern (21 bp):
ATTTATCATTATATATTACTC
Found at i:496162 original size:19 final size:21
Alignment explanation
Indices: 496138--496189 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
496128 TGGCCACGAG
*
496138 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
496157 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
496178 CATGTATTTTCA
1 CATGTATTTTCA
496190 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:496960 original size:18 final size:18
Alignment explanation
Indices: 496895--496960 Score: 53
Period size: 18 Copynumber: 3.6 Consensus size: 18
496885 ATTGGTGTGC
**
496895 AAAAAGAAAAGAAAAGAC-
1 AAAAAG-AAAGAAAATTCA
* *
496913 AAAAAGAAAAAAAATCTGA
1 AAAAAGAAAGAAAAT-TCA
*
496932 AAAAGAAAAAGAAAATTCA
1 AAAA-AGAAAGAAAATTCA
496951 AAAAAGAAAG
1 AAAAAGAAAG
496961 CAAGCCAAGG
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
17 7 0.19
18 11 0.30
19 10 0.27
20 9 0.24
ACGTcount: A:0.76, C:0.05, G:0.14, T:0.06
Consensus pattern (18 bp):
AAAAAGAAAGAAAATTCA
Found at i:506058 original size:25 final size:25
Alignment explanation
Indices: 506026--506083 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
506016 TTTTCTCGTT
506026 CATGCATATCTTCATTAATTCCTCC
1 CATGCATATCTTCATTAATTCCTCC
*
506051 CATTCATATCTTCATTAATTCCTCC
1 CATGCATATCTTCATTAATTCCTCC
506076 CATGCATA
1 CATGCATA
506084 AGTCCTTTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.26, C:0.31, G:0.03, T:0.40
Consensus pattern (25 bp):
CATGCATATCTTCATTAATTCCTCC
Found at i:506345 original size:22 final size:22
Alignment explanation
Indices: 506320--506365 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
506310 ACCAACTCTT
506320 CAATTACCTTTAGTCTTCTTAG
1 CAATTACCTTTAGTCTTCTTAG
506342 CAATTACCTTTAGTCTTCTTAG
1 CAATTACCTTTAGTCTTCTTAG
506364 CA
1 CA
506366 TCCAATGACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.24, C:0.24, G:0.09, T:0.43
Consensus pattern (22 bp):
CAATTACCTTTAGTCTTCTTAG
Found at i:507293 original size:15 final size:15
Alignment explanation
Indices: 507270--507311 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
507260 AACACACTCA
507270 TCTTCACTCTCAATGC
1 TCTT-ACTCTCAATGC
*
507286 TCTTACTCTTAATGC
1 TCTTACTCTCAATGC
507301 TCTTACTCTCA
1 TCTTACTCTCA
507312 TTTTCAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 20 0.83
16 4 0.17
ACGTcount: A:0.19, C:0.33, G:0.05, T:0.43
Consensus pattern (15 bp):
TCTTACTCTCAATGC
Found at i:516679 original size:19 final size:21
Alignment explanation
Indices: 516655--516694 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
516645 TTCTACCTTA
516655 ATTTAT-ATTATAT-TTACTC
1 ATTTATCATTATATATTACTC
516674 ATTTATGCATTATATATTACT
1 ATTTAT-CATTATATATTACT
516695 ATTAGCATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
21 7 0.39
22 5 0.28
ACGTcount: A:0.33, C:0.10, G:0.03, T:0.55
Consensus pattern (21 bp):
ATTTATCATTATATATTACTC
Found at i:517820 original size:36 final size:36
Alignment explanation
Indices: 517746--517851 Score: 169
Period size: 36 Copynumber: 3.0 Consensus size: 36
517736 ATTTATAAGT
* * *
517746 TGGTGATAATATAGGAGTGAT-ATGGTGATGGAAAA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACAA
*
517781 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACAA
517817 TGGTGATGATATAGGCGTGATAATGGTGATGGACA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACA
517852 GATTGTATCT
Statistics
Matches: 65, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
35 19 0.29
36 46 0.71
ACGTcount: A:0.31, C:0.04, G:0.36, T:0.29
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACAA
Found at i:521779 original size:14 final size:14
Alignment explanation
Indices: 521762--521800 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
521752 TTGCTTTTGA
521762 TTTTCTTCTTTTTC
1 TTTTCTTCTTTTTC
*
521776 TTTTCTT-TCTTTTG
1 TTTTCTTCT-TTTTC
521790 TTTTCTTCTTT
1 TTTTCTTCTTT
521801 CTTGTTGCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 1 0.05
14 20 0.91
15 1 0.05
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (14 bp):
TTTTCTTCTTTTTC
Found at i:521816 original size:28 final size:28
Alignment explanation
Indices: 521744--521800 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
521734 ACTTGCTTCA
521744 CTTTTCTTTTGCTTTTGATTTTCTTCTTTTT
1 CTTTTC-TTT-CTTTTGATTTTCTTC-TTTT
521775 CTTTTCTTTCTTTTG-TTTTCTTCTTT
1 CTTTTCTTTCTTTTGATTTTCTTCTTT
521801 CTTGTTGCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 3 0.12
28 8 0.31
29 6 0.23
30 3 0.12
31 6 0.23
ACGTcount: A:0.02, C:0.18, G:0.05, T:0.75
Consensus pattern (28 bp):
CTTTTCTTTCTTTTGATTTTCTTCTTTT
Found at i:522047 original size:15 final size:15
Alignment explanation
Indices: 522027--522057 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
522017 AAAGTAAATG
522027 GAAATGGAAAGAATA
1 GAAATGGAAAGAATA
*
522042 GAAATGGATAGAATA
1 GAAATGGAAAGAATA
522057 G
1 G
522058 TTATCAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.29, T:0.16
Consensus pattern (15 bp):
GAAATGGAAAGAATA
Found at i:522244 original size:35 final size:36
Alignment explanation
Indices: 522197--522264 Score: 120
Period size: 35 Copynumber: 1.9 Consensus size: 36
522187 ATTTATAAGT
522197 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
*
522232 TGGTGATGATATAGGCGTGATAATGGTGATGGA
1 TGGTGATAATATAGGCGTGATAATGGTGATGGA
522265 CAGATTGTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 20 0.65
36 11 0.35
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (36 bp):
TGGTGATAATATAGGCGTGATAATGGTGATGGAATA
Found at i:531071 original size:19 final size:20
Alignment explanation
Indices: 531035--531083 Score: 82
Period size: 19 Copynumber: 2.5 Consensus size: 20
531025 AACCCATTTT
531035 AAAATACATGATTTTTAATG
1 AAAATACATGATTTTTAATG
531055 AAAATACATGA-TTTTAATG
1 AAAATACATGATTTTTAATG
*
531074 AAGATACATG
1 AAAATACATG
531084 CTCTTGGCTG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (20 bp):
AAAATACATGATTTTTAATG
Found at i:544215 original size:16 final size:16
Alignment explanation
Indices: 544194--544232 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
544184 AGATGAGTAC
*
544194 AAATGAAAGAATAAGG
1 AAATGAAAGAATAAGA
* *
544210 AAATGAAATAGTAAGA
1 AAATGAAAGAATAAGA
544226 AAATGAA
1 AAATGAA
544233 GATACTTACA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.21, T:0.15
Consensus pattern (16 bp):
AAATGAAAGAATAAGA
Found at i:544451 original size:16 final size:15
Alignment explanation
Indices: 544432--544477 Score: 58
Period size: 16 Copynumber: 3.0 Consensus size: 15
544422 ATGTAGGAGA
544432 CTTTTCTTTTCTTTTT
1 CTTTT-TTTTCTTTTT
544448 C-TTTTTTTCTTATTT
1 CTTTTTTTTCTT-TTT
*
544463 ATTTTTTTTCTTTTT
1 CTTTTTTTTCTTTTT
544478 GTTGCAGTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 7 0.26
15 9 0.33
16 11 0.41
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.83
Consensus pattern (15 bp):
CTTTTTTTTCTTTTT
Found at i:545226 original size:22 final size:22
Alignment explanation
Indices: 545201--545261 Score: 104
Period size: 22 Copynumber: 2.8 Consensus size: 22
545191 GAAACCCTTT
*
545201 TGAAAATACATGATTTTTTTAA
1 TGAAAATACATGATTTTTTAAA
545223 TGAAAATACATGATTTTTTAAA
1 TGAAAATACATGATTTTTTAAA
*
545245 TAAAAATACATGATTTT
1 TGAAAATACATGATTTT
545262 AATGAAGATA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.43
Consensus pattern (22 bp):
TGAAAATACATGATTTTTTAAA
Found at i:548674 original size:16 final size:16
Alignment explanation
Indices: 548653--548691 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
548643 AGATGAGTAC
*
548653 AAATGAAAGAATAAGG
1 AAATGAAAGAATAAGA
* *
548669 AAATGAAATAGTAAGA
1 AAATGAAAGAATAAGA
548685 AAATGAA
1 AAATGAA
548692 GATACTTACA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.21, T:0.15
Consensus pattern (16 bp):
AAATGAAAGAATAAGA
Found at i:548903 original size:5 final size:5
Alignment explanation
Indices: 548893--548943 Score: 52
Period size: 5 Copynumber: 10.0 Consensus size: 5
548883 ATGTAGGAGA
*
548893 CTTTT CTTTT CTTTT CTTTT -TTCTT TTTTT CTTATTT CTTTT -TTTT
1 CTTTT CTTTT CTTTT CTTTT CTT-TT CTTTT C-T-TTT CTTTT CTTTT
548939 CTTTT
1 CTTTT
548944 TGTTGCAGTA
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
4 6 0.15
5 26 0.65
6 4 0.10
7 4 0.10
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (5 bp):
CTTTT
Found at i:548918 original size:22 final size:24
Alignment explanation
Indices: 548893--548943 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
548883 ATGTAGGAGA
*
548893 CTTTTCTT-TTCTTT-TCTTTTTT
1 CTTTTCTTCTTATTTCTCTTTTTT
* *
548915 CTTTTTTTCTTATTTCTTTTTTTT
1 CTTTTCTTCTTATTTCTCTTTTTT
548939 CTTTT
1 CTTTT
548944 TGTTGCAGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 7 0.29
23 5 0.21
24 12 0.50
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (24 bp):
CTTTTCTTCTTATTTCTCTTTTTT
Found at i:548922 original size:15 final size:16
Alignment explanation
Indices: 548894--548944 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
548884 TGTAGGAGAC
548894 TTTTCTTTTCTTTTCTT
1 TTTTCTTTT-TTTTCTT
548911 TTTTC-TTTTTTTCTT
1 TTTTCTTTTTTTTCTT
*
548926 ATTTCTTTTTTTTCTT
1 TTTTCTTTTTTTTCTT
548942 TTT
1 TTT
548945 GTTGCAGTAC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
15 11 0.35
16 15 0.48
17 5 0.16
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTCTTTTTTTTCTT
Found at i:549707 original size:19 final size:20
Alignment explanation
Indices: 549669--549721 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 20
549659 GAAACCCTTT
549669 TGAAAATACATGATTTTTTTAA
1 TGAAAATACATGA--TTTTTAA
549691 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
549710 TGAAGATACATG
1 TGAAAATACATG
549722 CTCTTGGCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 17 0.57
22 13 0.43
ACGTcount: A:0.43, C:0.06, G:0.13, T:0.38
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:550259 original size:30 final size:31
Alignment explanation
Indices: 550223--550282 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
550213 CTTAGCTTTA
**
550223 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
*
550253 TATTATGTTTGCATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
550283 GGCAGCATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.53
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:552953 original size:15 final size:15
Alignment explanation
Indices: 552933--552961 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
552923 ATGACGCCAT
552933 AAGTATATGAATTAG
1 AAGTATATGAATTAG
552948 AAGTATATGAATTA
1 AAGTATATGAATTA
552962 TACTTGCTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.17, T:0.34
Consensus pattern (15 bp):
AAGTATATGAATTAG
Found at i:569868 original size:23 final size:22
Alignment explanation
Indices: 569841--569898 Score: 55
Period size: 24 Copynumber: 2.5 Consensus size: 22
569831 ACTTTTCTTT
569841 CTTTTTTTCTTCTTCTTTTGAGTG
1 CTTTTTTTCTTC-T-TTTTGAGTG
569865 -TTTTCAATTTCTTCTTTTTGAGTG
1 CTTTT---TTTCTTCTTTTTGAGTG
*
569889 CTTCTTTTCT
1 CTTTTTTTCT
569899 GATTTTTTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 10
0.73 0.03 0.25
Matches are distributed among these distances:
22 5 0.17
23 4 0.14
24 9 0.31
25 4 0.14
26 7 0.24
ACGTcount: A:0.07, C:0.17, G:0.10, T:0.66
Consensus pattern (22 bp):
CTTTTTTTCTTCTTTTTGAGTG
Found at i:581866 original size:23 final size:24
Alignment explanation
Indices: 581824--581876 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
581814 TTTCTTTCTT
581824 TTTCTTCTTTTCGAGTGCTTTCAA
1 TTTCTTCTTTTCGAGTGCTTTCAA
* *
581848 TTTCTTCTTTT-GAGTGCTTTTAT
1 TTTCTTCTTTTCGAGTGCTTTCAA
581871 TTTCTT
1 TTTCTT
581877 TGCTGATTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.09, C:0.17, G:0.11, T:0.62
Consensus pattern (24 bp):
TTTCTTCTTTTCGAGTGCTTTCAA
Found at i:583699 original size:19 final size:21
Alignment explanation
Indices: 583656--583707 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
583646 GAAACCCCTT
*
583656 TGAAAATACATTATTTTTAAA
1 TGAAAATACATGATTTTTAAA
583677 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
583696 TGAAGATACATG
1 TGAAAATACATG
583708 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 13 0.45
20 4 0.14
21 12 0.41
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.37
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:584775 original size:35 final size:37
Alignment explanation
Indices: 584729--584808 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
584719 TTTGAGAATT
*
584729 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
584764 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
584801 TGGGGATG
1 TGGTGATG
584809 GAAATAGTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 21 0.52
36 4 0.10
37 15 0.38
ACGTcount: A:0.28, C:0.04, G:0.39, T:0.30
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:588362 original size:13 final size:11
Alignment explanation
Indices: 588322--588405 Score: 64
Period size: 11 Copynumber: 7.1 Consensus size: 11
588312 CAATCTGTCA
588322 ATCACCATTATC
1 ATCACCA-TATC
*
588334 A-CGCCTATATC
1 ATCACC-ATATC
588345 ATCACCATAGTCC
1 ATCACCATA-T-C
588358 ATCACCATTATC
1 ATCACCA-TATC
*
588370 A-CGCCTATATC
1 ATCACC-ATATC
588381 ATCACCATATTCC
1 ATCACCATA-T-C
588394 ATCACCATATC
1 ATCACCATATC
588405 A
1 A
588406 CGCCTATTTT
Statistics
Matches: 59, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.41
12 14 0.24
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.29
Consensus pattern (11 bp):
ATCACCATATC
Found at i:588369 original size:36 final size:36
Alignment explanation
Indices: 588322--588422 Score: 168
Period size: 36 Copynumber: 2.8 Consensus size: 36
588312 CAATCTGTCA
588322 ATCACCATTATCACGCCTATATCATCACCATAGTCC
1 ATCACCATTATCACGCCTATATCATCACCATAGTCC
*
588358 ATCACCATTATCACGCCTATATCATCACCATATTCC
1 ATCACCATTATCACGCCTATATCATCACCATAGTCC
* *
588394 ATCACCA-TATCACGCCTATTTTATCACCA
1 ATCACCATTATCACGCCTATATCATCACCA
588423 ACTTATAAAT
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
35 20 0.32
36 42 0.68
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.30
Consensus pattern (36 bp):
ATCACCATTATCACGCCTATATCATCACCATAGTCC
Found at i:588831 original size:28 final size:27
Alignment explanation
Indices: 588799--588873 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 27
588789 TCAAAGTGCT
588799 ACAAAAAAAAGCAACAAG-AAAGAAGAAA
1 ACAAAAAAAAG-AA-AAGAAAAGAAGAAA
*
588827 ACAAAAGAAAGAAAAGAAAAAGAAGAAA
1 ACAAAAAAAAGAAAAG-AAAAGAAGAAA
588855 ATCAAAAGCAAAAGAAAAG
1 A-CAAAA--AAAAGAAAAG
588874 TGAAGCAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
26 3 0.08
27 2 0.05
28 21 0.52
29 5 0.12
31 9 0.22
ACGTcount: A:0.75, C:0.08, G:0.16, T:0.01
Consensus pattern (27 bp):
ACAAAAAAAAGAAAAGAAAAGAAGAAA
Found at i:588840 original size:14 final size:14
Alignment explanation
Indices: 588817--588872 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
588807 AAGCAACAAG
588817 AAAG-AAGAAAACA
1 AAAGAAAGAAAACA
*
588830 AAAGAAAGAAAAGA
1 AAAGAAAGAAAACA
588844 AAA-AGAAGAAAATCA
1 AAAGA-AAGAAAA-CA
588859 AAAGCAAAAGAAAA
1 AAAG--AAAGAAAA
588873 GTGAAGCAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
13 5 0.14
14 18 0.51
15 4 0.11
17 7 0.20
18 1 0.03
ACGTcount: A:0.77, C:0.05, G:0.16, T:0.02
Consensus pattern (14 bp):
AAAGAAAGAAAACA
Found at i:590969 original size:19 final size:21
Alignment explanation
Indices: 590945--590996 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
590935 CGGCCAAGAG
* *
590945 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAA
590964 CATGTATTTTCATTTAAAAAA
1 CATGTATTTTCATTTAAAAAA
590985 CATGTATTTTCA
1 CATGTATTTTCA
590997 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 11 0.38
20 2 0.07
21 16 0.55
ACGTcount: A:0.37, C:0.13, G:0.06, T:0.44
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAA
Found at i:591453 original size:23 final size:23
Alignment explanation
Indices: 591406--591456 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
591396 CTCTATCTTT
*
591406 TTATTTATTTCATTTCATTCTTA
1 TTATTTATTTCATTTCATTCATA
591429 TTATTTATTTTCATTT-ACTT-ATA
1 TTATTTA-TTTCATTTCA-TTCATA
591452 TTATT
1 TTATT
591457 ATCCTTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 15 0.60
24 10 0.40
ACGTcount: A:0.24, C:0.10, G:0.00, T:0.67
Consensus pattern (23 bp):
TTATTTATTTCATTTCATTCATA
Found at i:591736 original size:17 final size:17
Alignment explanation
Indices: 591714--591761 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
591704 AATAAGAGTG
591714 CAAAAAGAAAGAAAAGT
1 CAAAAAGAAAGAAAAGT
*
591731 CAAAAA-AAAGAAAATT
1 CAAAAAGAAAGAAAAGT
591747 CAGAAAAG-AAGAAAA
1 CA-AAAAGAAAGAAAA
591762 AGAAAAAGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 11 0.39
17 17 0.61
ACGTcount: A:0.73, C:0.06, G:0.15, T:0.06
Consensus pattern (17 bp):
CAAAAAGAAAGAAAAGT
Found at i:592019 original size:24 final size:24
Alignment explanation
Indices: 591987--592041 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
591977 GAATCCTTTC
*
591987 TTCTTCCTTTCCATTTCTATTCCT
1 TTCTACCTTTCCATTTCTATTCCT
592011 TTCTACCTTTCCATTTCTATTCCT
1 TTCTACCTTTCCATTTCTATTCCT
592035 TTCTACC
1 TTCTACC
592042 CTAACCTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.11, C:0.35, G:0.00, T:0.55
Consensus pattern (24 bp):
TTCTACCTTTCCATTTCTATTCCT
Found at i:595143 original size:19 final size:21
Alignment explanation
Indices: 595119--595170 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
595109 CGGCCAAGAG
*
595119 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
595138 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
595159 CATGTATTTTCA
1 CATGTATTTTCA
595171 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:598827 original size:13 final size:11
Alignment explanation
Indices: 598786--598870 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
598776 ACAATCTGTC
598786 CATCACCATTAT
1 CATCACCA-TAT
*
598798 CA-CGCCTATAT
1 CATCACC-ATAT
598809 CATCACCATAGT
1 CATCACCATA-T
598821 CCATCACCATTAT
1 -CATCACCA-TAT
*
598834 CA-CGCCTATAT
1 CATCACC-ATAT
598845 CATCACCATATT
1 CATCACCATA-T
598857 CCATCACCATAT
1 -CATCACCATAT
598869 CA
1 CA
598871 CGCCTATTTT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:598830 original size:36 final size:36
Alignment explanation
Indices: 598783--598886 Score: 174
Period size: 36 Copynumber: 2.9 Consensus size: 36
598773 GATACAATCT
598783 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
598819 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
598855 TTCCATCACCA-TATCACGCCTATTTTATCACC
1 GTCCATCACCATTATCACGCCTATATCATCACC
598887 GACTTATAAA
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 19 0.29
36 46 0.71
ACGTcount: A:0.29, C:0.37, G:0.05, T:0.30
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:608258 original size:568 final size:568
Alignment explanation
Indices: 607182--608315 Score: 2151
Period size: 568 Copynumber: 2.0 Consensus size: 568
607172 GCCACCTCGA
607182 GAGGTACCTTTCCACAAGGAGCTGCCCAAACGTTCATCATGTTACAAGTCATCTAAGGCCAGCTC
1 GAGGTACCTTTCCACAAGGAGCTGCCCAAACGTTCATCATGTTACAAGTCATCTAAGGCCAGCTC
*
607247 ACCACCAGCTCATTCACACCATAAATAACTCAAATATGAAGGGACACCATTATCAAACATTGTGA
66 ACCACCAGCTCATTCACACCATAAATAACTCAAACATGAAGGGACACCATTATCAAACATTGTGA
607312 CCTTTCATGAATGATGCTACCCATGAAGATGCCTTTTCATCTAGGAGCACGTTGGTGAAGAGTTT
131 CCTTTCATGAATGATGCTACCCATGAAGATGCCTTTTCATCTAGGAGCACGTTGGTGAAGAGTTT
607377 GCTAGCATTGGAGGCTTAAATCACCAAGAGACATGAGATAGAGCTCCATGCCTATTCGGCCACAT
196 GCTAGCATTGGAGGCTTAAATCACCAAGAGACATGAGATAGAGCTCCATGCCTATTCGGCCACAT
* *
607442 CACATGCCATGCACATGAGAACATTTGGTGCCAACTTGAGGAGATACAAACCCATTGGGCTAAAG
261 CACATGCCATGCACATGAGAACATTTGGCGCCAACTTGAGGAGATACAAACCCATTCGGCTAAAG
* *
607507 AGAAGAGAAATGGCGCCAAGATGAACCAGCATCACCATTCGGCCAAGGGAGATGTCTTCCCATCC
326 AGAAGAGAAATAGCGCCAAGATGAACCAACATCACCATTCGGCCAAGGGAGATGTCTTCCCATCC
*
607572 TTAGCCGAATCATCAAGTCCCTTTATGAAGGGTTAGCCGAACCATCACAAGCCCAAATGACTTGA
391 TTAGCCGAATCATCAAGTCCCTTTATGAAGGGTTAACCGAACCATCACAAGCCCAAATGACTTGA
607637 TCTTTCATTTTAAAACATTATGTATATTCCTAAAGTCATGTATCTAGCCGAAACATCATGTAACC
456 TCTTTCATTTTAAAACATTATGTATATTCCTAAAGTCATGTATCTAGCCGAAACATCATGTAACC
607702 ATTCGACCAAGCCCTCTCATTTCCTATAAATAAAGTGGCTTGCCTTGG
521 ATTCGACCAAGCCCTCTCATTTCCTATAAATAAAGTGGCTTGCCTTGG
607750 GAGGTACCTTTCCACAAGGAGCTGCCCAAACGTTCATCATGTTACAAGTCATCTAAGGCCAGCTC
1 GAGGTACCTTTCCACAAGGAGCTGCCCAAACGTTCATCATGTTACAAGTCATCTAAGGCCAGCTC
* *
607815 ACCACCAGCTCATTCACACCATAAATAGCTCAAACATGAAGGGACACCATTATGAAACATTGTGA
66 ACCACCAGCTCATTCACACCATAAATAACTCAAACATGAAGGGACACCATTATCAAACATTGTGA
*
607880 CCTTTCATGAATGATGCTGCCCATGAAGATGCCTTTTCATCTAGGAGCACGTTGGTGAAGAGTTT
131 CCTTTCATGAATGATGCTACCCATGAAGATGCCTTTTCATCTAGGAGCACGTTGGTGAAGAGTTT
607945 GCTAGCATTGGAGGCTTAAATCACCAAGAGACATGAGATAGAGCTCCATGCCTATTCGGCCACAT
196 GCTAGCATTGGAGGCTTAAATCACCAAGAGACATGAGATAGAGCTCCATGCCTATTCGGCCACAT
608010 CACATGCCATGCACATGAGAACATTTGGCGCCAACTTGAGGAGATACAAACCCATTCGGCTAAAG
261 CACATGCCATGCACATGAGAACATTTGGCGCCAACTTGAGGAGATACAAACCCATTCGGCTAAAG
608075 AGAAGAGAAATAGCGCCAAGATGAACCAACATCACCATTCGGCCAAGGGAGATGTCTTCCCATCC
326 AGAAGAGAAATAGCGCCAAGATGAACCAACATCACCATTCGGCCAAGGGAGATGTCTTCCCATCC
*
608140 TTAGCTGAATCATCAAGTCCCTTTATGAAGGGTTAACCGAACCATCACAAGCCCAAATGACTTGA
391 TTAGCCGAATCATCAAGTCCCTTTATGAAGGGTTAACCGAACCATCACAAGCCCAAATGACTTGA
*
608205 TCTTTCATTTTAAAACATTATGTATCTTCCTAAAGTCATGTATCTAGCCGAAACATCATGTAACC
456 TCTTTCATTTTAAAACATTATGTATATTCCTAAAGTCATGTATCTAGCCGAAACATCATGTAACC
* *
608270 ATTCGGCCAAGCCCTCTCATTTCCTATAAATAGAGTGGCTTGCCTT
521 ATTCGACCAAGCCCTCTCATTTCCTATAAATAAAGTGGCTTGCCTT
608316 CATTTATACG
Statistics
Matches: 553, Mismatches: 13, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
568 553 1.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (568 bp):
GAGGTACCTTTCCACAAGGAGCTGCCCAAACGTTCATCATGTTACAAGTCATCTAAGGCCAGCTC
ACCACCAGCTCATTCACACCATAAATAACTCAAACATGAAGGGACACCATTATCAAACATTGTGA
CCTTTCATGAATGATGCTACCCATGAAGATGCCTTTTCATCTAGGAGCACGTTGGTGAAGAGTTT
GCTAGCATTGGAGGCTTAAATCACCAAGAGACATGAGATAGAGCTCCATGCCTATTCGGCCACAT
CACATGCCATGCACATGAGAACATTTGGCGCCAACTTGAGGAGATACAAACCCATTCGGCTAAAG
AGAAGAGAAATAGCGCCAAGATGAACCAACATCACCATTCGGCCAAGGGAGATGTCTTCCCATCC
TTAGCCGAATCATCAAGTCCCTTTATGAAGGGTTAACCGAACCATCACAAGCCCAAATGACTTGA
TCTTTCATTTTAAAACATTATGTATATTCCTAAAGTCATGTATCTAGCCGAAACATCATGTAACC
ATTCGACCAAGCCCTCTCATTTCCTATAAATAAAGTGGCTTGCCTTGG
Found at i:615062 original size:24 final size:24
Alignment explanation
Indices: 614996--615060 Score: 64
Period size: 24 Copynumber: 2.7 Consensus size: 24
614986 TTGTGAATCA
* *
614996 CCAAAAGTCATGACTATTGGTTCTT
1 CCAAAAGCCATGA-TTTTGGTTCTT
615021 -CAAAAGTCACAT-ATTTTGGTT-TT
1 CCAAAAG-C-CATGATTTTGGTTCTT
615044 CCAAAAGCCATGATTTT
1 CCAAAAGCCATGATTTT
615061 TGAATCATCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
22 3 0.09
23 8 0.24
24 19 0.56
25 1 0.03
26 3 0.09
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (24 bp):
CCAAAAGCCATGATTTTGGTTCTT
Found at i:616253 original size:23 final size:22
Alignment explanation
Indices: 616219--616261 Score: 52
Period size: 23 Copynumber: 1.9 Consensus size: 22
616209 TTTGAACTTC
616219 TTTTTCTTTTCT-TCTTTTCTGA
1 TTTTTCTTTTCTAT-TTTTCTGA
*
616241 TTTTTTTTCTTCTATTTTTCT
1 TTTTTCTT-TTCTATTTTTCT
616262 TTTGCTTTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 7 0.39
23 10 0.56
24 1 0.06
ACGTcount: A:0.05, C:0.16, G:0.02, T:0.77
Consensus pattern (22 bp):
TTTTTCTTTTCTATTTTTCTGA
Found at i:624552 original size:36 final size:36
Alignment explanation
Indices: 624500--624612 Score: 167
Period size: 36 Copynumber: 3.2 Consensus size: 36
624490 GATACTATTT
624500 TCATCACCATAATCCAT-ATCCATTATCACGCCTATA
1 TCATCACCATAATCCATCA-CCATTATCACGCCTATA
*
624536 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
624572 TCATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
624607 ACATCA
1 TCATCA
624613 TCCTTCCATT
Statistics
Matches: 72, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
35 17 0.24
36 54 0.75
37 1 0.01
ACGTcount: A:0.34, C:0.35, G:0.04, T:0.27
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:624555 original size:13 final size:11
Alignment explanation
Indices: 624533--624598 Score: 62
Period size: 13 Copynumber: 5.5 Consensus size: 11
624523 TATCACGCCT
624533 ATATCATCACC
1 ATATCATCACC
624544 ATAGTCCATCACC
1 ATA-T-CATCACC
*
624557 ATTATCA-CGCC
1 A-TATCATCACC
624568 TATATCATCACC
1 -ATATCATCACC
624580 ATATTCCATCACC
1 ATA-T-CATCACC
624593 ATATCA
1 ATATCA
624599 CGCCAATAAC
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
11 16 0.35
12 9 0.20
13 19 0.41
14 2 0.04
ACGTcount: A:0.33, C:0.35, G:0.03, T:0.29
Consensus pattern (11 bp):
ATATCATCACC
Found at i:624627 original size:33 final size:33
Alignment explanation
Indices: 624501--624627 Score: 105
Period size: 36 Copynumber: 3.6 Consensus size: 33
624491 ATACTATTTT
* *
624501 CATCACCATAATCCAT-ATCCATTATCACGCCTATAT
1 CATCACCAT--TCCATCA-CCA-TATCACGCCAATAA
* *
624537 CATCACCATAGTCCATCACCATTATCACGCCTATAT
1 CATCACCAT--TCCATCACCA-TATCACGCCAATAA
624573 CATCACCATATTCCATCACCATATCACGCCAATAA
1 CATCACC--ATTCCATCACCATATCACGCCAATAA
*
624608 CATCATCC-TTCCATTACCAT
1 CATCA-CCATTCCATCACCAT
624628 TTCATCACCA
Statistics
Matches: 83, Mismatches: 4, Indels: 11
0.85 0.04 0.11
Matches are distributed among these distances:
33 11 0.13
35 17 0.20
36 52 0.63
37 1 0.01
38 2 0.02
ACGTcount: A:0.32, C:0.36, G:0.03, T:0.28
Consensus pattern (33 bp):
CATCACCATTCCATCACCATATCACGCCAATAA
Found at i:628938 original size:36 final size:36
Alignment explanation
Indices: 628886--628998 Score: 167
Period size: 36 Copynumber: 3.2 Consensus size: 36
628876 GATACTATTT
628886 TCATCACCATAATCCAT-ATCCATTATCACGCCTATA
1 TCATCACCATAATCCATCA-CCATTATCACGCCTATA
*
628922 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
628958 TCATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
628993 ACATCA
1 TCATCA
628999 TCCTTCCATT
Statistics
Matches: 72, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
35 17 0.24
36 54 0.75
37 1 0.01
ACGTcount: A:0.34, C:0.35, G:0.04, T:0.27
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:628941 original size:13 final size:11
Alignment explanation
Indices: 628919--628984 Score: 62
Period size: 13 Copynumber: 5.5 Consensus size: 11
628909 TATCACGCCT
628919 ATATCATCACC
1 ATATCATCACC
628930 ATAGTCCATCACC
1 ATA-T-CATCACC
*
628943 ATTATCA-CGCC
1 A-TATCATCACC
628954 TATATCATCACC
1 -ATATCATCACC
628966 ATATTCCATCACC
1 ATA-T-CATCACC
628979 ATATCA
1 ATATCA
628985 CGCCAATAAC
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
11 16 0.35
12 9 0.20
13 19 0.41
14 2 0.04
ACGTcount: A:0.33, C:0.35, G:0.03, T:0.29
Consensus pattern (11 bp):
ATATCATCACC
Found at i:629013 original size:33 final size:33
Alignment explanation
Indices: 628887--629013 Score: 105
Period size: 36 Copynumber: 3.6 Consensus size: 33
628877 ATACTATTTT
* *
628887 CATCACCATAATCCAT-ATCCATTATCACGCCTATAT
1 CATCACCAT--TCCATCA-CCA-TATCACGCCAATAA
* *
628923 CATCACCATAGTCCATCACCATTATCACGCCTATAT
1 CATCACCAT--TCCATCACCA-TATCACGCCAATAA
628959 CATCACCATATTCCATCACCATATCACGCCAATAA
1 CATCACC--ATTCCATCACCATATCACGCCAATAA
*
628994 CATCATCC-TTCCATTACCAT
1 CATCA-CCATTCCATCACCAT
629014 TTCATCACCA
Statistics
Matches: 83, Mismatches: 4, Indels: 11
0.85 0.04 0.11
Matches are distributed among these distances:
33 11 0.13
35 17 0.20
36 52 0.63
37 1 0.01
38 2 0.02
ACGTcount: A:0.32, C:0.36, G:0.03, T:0.28
Consensus pattern (33 bp):
CATCACCATTCCATCACCATATCACGCCAATAA
Found at i:634763 original size:24 final size:21
Alignment explanation
Indices: 634729--634771 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
634719 TCCACAAGAT
*
634729 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
634751 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
634772 AGATTGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:639659 original size:27 final size:28
Alignment explanation
Indices: 639587--639669 Score: 141
Period size: 28 Copynumber: 3.0 Consensus size: 28
639577 GTAAATTTAA
* *
639587 CAAAACAAATGATAAATATGCTGTTATG
1 CAAAACAAATGATGAACATGCTGTTATG
639615 CAAAACAAATGATGAACATGCTGTTATG
1 CAAAACAAATGATGAACATGCTGTTATG
639643 CAAAA-AAATGATGAACATGCTGTTATG
1 CAAAACAAATGATGAACATGCTGTTATG
639670 AACCCCATGA
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
27 22 0.42
28 31 0.58
ACGTcount: A:0.45, C:0.12, G:0.17, T:0.27
Consensus pattern (28 bp):
CAAAACAAATGATGAACATGCTGTTATG
Found at i:642254 original size:23 final size:24
Alignment explanation
Indices: 642212--642264 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
642202 TTTCTTTCTT
642212 TTTCTTCTTTTCGAGTGCTTTCAA
1 TTTCTTCTTTTCGAGTGCTTTCAA
* *
642236 TTTCTTCTTTT-GAGTGCTTTTAT
1 TTTCTTCTTTTCGAGTGCTTTCAA
642259 TTTCTT
1 TTTCTT
642265 TGCTGATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.09, C:0.17, G:0.11, T:0.62
Consensus pattern (24 bp):
TTTCTTCTTTTCGAGTGCTTTCAA
Found at i:650566 original size:11 final size:11
Alignment explanation
Indices: 650550--650605 Score: 64
Period size: 11 Copynumber: 5.3 Consensus size: 11
650540 TTTTTTGAAA
650550 TTTTGGCTTTT
1 TTTTGGCTTTT
650561 TTTTGGCTCTTT
1 TTTTGGCT-TTT
650573 TTTTGG--TTT
1 TTTTGGCTTTT
*
650582 TTTTGCCTTTT
1 TTTTGGCTTTT
*
650593 TTTTTG-TTTT
1 TTTTGGCTTTT
650603 TTT
1 TTT
650606 GAAAAAAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
9 8 0.21
10 7 0.18
11 15 0.38
12 9 0.23
ACGTcount: A:0.00, C:0.09, G:0.14, T:0.77
Consensus pattern (11 bp):
TTTTGGCTTTT
Found at i:650582 original size:20 final size:21
Alignment explanation
Indices: 650558--650606 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 21
650548 AATTTTGGCT
*
650558 TTTTTTTGGCTCTTTTTTTGG
1 TTTTTTTGCCTCTTTTTTTGG
*
650579 TTTTTTTGCCT-TTTTTTTTG
1 TTTTTTTGCCTCTTTTTTTGG
650599 TTTTTTTG
1 TTTTTTTG
650607 AAAAAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.00, C:0.08, G:0.14, T:0.78
Consensus pattern (21 bp):
TTTTTTTGCCTCTTTTTTTGG
Found at i:659816 original size:19 final size:20
Alignment explanation
Indices: 659794--659857 Score: 73
Period size: 19 Copynumber: 3.4 Consensus size: 20
659784 TTTGAACTTC
659794 TCTTTTTCTT-TTCTTT-TCT
1 TCTTTTTCTTATT-TTTCTCT
659813 TC-TTTTCTTATTTTTCTCT
1 TCTTTTTCTTATTTTTCTCT
* *
659832 TC-TTTTCTGATTTTTGTCT
1 TCTTTTTCTTATTTTTCTCT
659851 TCTTTTT
1 TCTTTTT
659858 GTACTCCAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
18 10 0.25
19 26 0.65
20 4 0.10
ACGTcount: A:0.03, C:0.19, G:0.03, T:0.75
Consensus pattern (20 bp):
TCTTTTTCTTATTTTTCTCT
Found at i:668058 original size:19 final size:19
Alignment explanation
Indices: 667996--668055 Score: 79
Period size: 19 Copynumber: 3.2 Consensus size: 19
667986 TTGGAGTACA
* *
667996 AAAAGAAGACAAAAATCAG
1 AAAAGAAGAGAAAAATAAG
668015 AAAAGAAGAGAAAAATAAG
1 AAAAGAAGAGAAAAATAAG
668034 AAAAGAAGA-AAAGAA-AAG
1 AAAAGAAGAGAAA-AATAAG
668052 AAAA
1 AAAA
668056 AGAGAAGTTC
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
18 10 0.26
19 28 0.74
ACGTcount: A:0.75, C:0.03, G:0.18, T:0.03
Consensus pattern (19 bp):
AAAAGAAGAGAAAAATAAG
Found at i:679827 original size:23 final size:25
Alignment explanation
Indices: 679799--679852 Score: 87
Period size: 23 Copynumber: 2.3 Consensus size: 25
679789 AAAATCAGCA
679799 AAGAAAATT-AAAGCACTC-AAAAG
1 AAGAAAATTGAAAGCACTCGAAAAG
679822 AAG-AAATTGAAAGCACTCGAAAAG
1 AAGAAAATTGAAAGCACTCGAAAAG
679846 AAGAAAA
1 AAGAAAA
679853 AGAAAGAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
22 5 0.18
23 12 0.43
24 8 0.29
25 3 0.11
ACGTcount: A:0.61, C:0.11, G:0.17, T:0.11
Consensus pattern (25 bp):
AAGAAAATTGAAAGCACTCGAAAAG
Found at i:679849 original size:24 final size:22
Alignment explanation
Indices: 679803--679851 Score: 80
Period size: 24 Copynumber: 2.1 Consensus size: 22
679793 TCAGCAAAGA
679803 AAATTAAAGCACTCAAAAGAAG
1 AAATTAAAGCACTCAAAAGAAG
679825 AAATTGAAAGCACTCGAAAAGAAG
1 AAATT-AAAGCACTC-AAAAGAAG
679849 AAA
1 AAA
679852 AAGAAAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 5 0.20
23 9 0.36
24 11 0.44
ACGTcount: A:0.59, C:0.12, G:0.16, T:0.12
Consensus pattern (22 bp):
AAATTAAAGCACTCAAAAGAAG
Found at i:682426 original size:29 final size:28
Alignment explanation
Indices: 682394--682455 Score: 106
Period size: 29 Copynumber: 2.2 Consensus size: 28
682384 TCATGGGGTT
*
682394 CATAACAGCATGTTCATCATTTTTTTTTG
1 CATAACAGCATGTTCATCA-TTTGTTTTG
682423 CATAACAGCATGTTCATCATTTGTTTTG
1 CATAACAGCATGTTCATCATTTGTTTTG
682451 CATAA
1 CATAA
682456 GATAACTAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 13 0.41
29 19 0.59
ACGTcount: A:0.27, C:0.18, G:0.11, T:0.44
Consensus pattern (28 bp):
CATAACAGCATGTTCATCATTTGTTTTG
Found at i:682662 original size:13 final size:11
Alignment explanation
Indices: 682621--682705 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
682611 ACAATCTGTC
682621 CATCACCATTAT
1 CATCACCA-TAT
*
682633 CA-CGCCTATAT
1 CATCACC-ATAT
682644 CATCACCATACT
1 CATCACCATA-T
682656 CCATCACCATTAT
1 -CATCACCA-TAT
*
682669 CA-CGCCTATAT
1 CATCACC-ATAT
682680 CATCACCATATT
1 CATCACCATA-T
682692 CCATCACCATAT
1 -CATCACCATAT
682704 CA
1 CA
682706 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.38, G:0.02, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:682666 original size:36 final size:36
Alignment explanation
Indices: 682619--682722 Score: 183
Period size: 36 Copynumber: 2.9 Consensus size: 36
682609 ATACAATCTG
682619 TCCATCACCATTATCACGCCTATATCATCACCATAC
1 TCCATCACCATTATCACGCCTATATCATCACCATAC
*
682655 TCCATCACCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAC
*
682691 TCCATCACCA-TATCACGCCTATATTATCACCA
1 TCCATCACCATTATCACGCCTATATCATCACCA
682723 ACTTATAAAT
Statistics
Matches: 66, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 21 0.32
36 45 0.68
ACGTcount: A:0.31, C:0.38, G:0.03, T:0.29
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAC
Found at i:683356 original size:16 final size:15
Alignment explanation
Indices: 683330--683381 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
683320 GAGTTGTAAG
683330 TTATC-TTCATTTTT
1 TTATCTTTCATTTTT
*
683344 TTATCATTTCATTTCT
1 TTATC-TTTCATTTTT
683360 TTATTCTTTCATCTTTT
1 TTA-TCTTTCAT-TTTT
683377 CTTAT
1 -TTAT
683382 TTCATTACCA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
14 5 0.16
16 17 0.55
17 6 0.19
18 3 0.10
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.67
Consensus pattern (15 bp):
TTATCTTTCATTTTT
Found at i:686750 original size:22 final size:23
Alignment explanation
Indices: 686708--686761 Score: 74
Period size: 22 Copynumber: 2.4 Consensus size: 23
686698 TCACTATAGT
*
686708 CCATCACCATTATCACGCCTATA
1 CCATCACCATTATAACGCCTATA
686731 CCATCACCA-TATAACGCCTATA
1 CCATCACCATTATAACGCCTATA
**
686753 TTATCACCA
1 CCATCACCA
686762 ACTTATAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 19 0.68
23 9 0.32
ACGTcount: A:0.33, C:0.37, G:0.04, T:0.26
Consensus pattern (23 bp):
CCATCACCATTATAACGCCTATA
Found at i:695490 original size:36 final size:36
Alignment explanation
Indices: 695443--695547 Score: 158
Period size: 36 Copynumber: 2.9 Consensus size: 36
695433 GATACAATCT
695443 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
695479 GTCCATCACCATTATCACGCCTATATCACCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * * *
695515 TTCCATCACCA-TATCACACCTATTTTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
695548 ACTTATAAAT
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
35 18 0.29
36 45 0.71
ACGTcount: A:0.30, C:0.37, G:0.04, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:695544 original size:22 final size:24
Alignment explanation
Indices: 695501--695547 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 24
695491 TATCACGCCT
695501 ATATCACCACCATATTCCATCACC
1 ATATCACCACCATATTCCATCACC
**
695525 ATATCA-CACC-TATTTTATCACC
1 ATATCACCACCATATTCCATCACC
695547 A
1 A
695548 ACTTATAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 11 0.52
23 4 0.19
24 6 0.29
ACGTcount: A:0.34, C:0.36, G:0.00, T:0.30
Consensus pattern (24 bp):
ATATCACCACCATATTCCATCACC
Found at i:703700 original size:23 final size:22
Alignment explanation
Indices: 703649--703702 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
703639 ATTTATAAGT
** *
703649 TGGTGATAATATAGGCGTTATA
1 TGGTGATGGTATAGGCGTGATA
703671 TGGTGATGGTATAGGCGTGATAA
1 TGGTGATGGTATAGGCGTGAT-A
703694 TGGTGATGG
1 TGGTGATGG
703703 ACTATGGTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 18 0.64
23 10 0.36
ACGTcount: A:0.26, C:0.04, G:0.37, T:0.33
Consensus pattern (22 bp):
TGGTGATGGTATAGGCGTGATA
Found at i:703709 original size:36 final size:36
Alignment explanation
Indices: 703669--703739 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
703659 ATAGGCGTTA
*
703669 TATGGTGATGGTATAGGCGTGATAATGGTGATGGAC
1 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
703705 TATGGTGATGATATAGGCGTGATAATGGTGATGGA
1 TATGGTGATGATATAGGCGTGATAATGGTGATGGA
703740 AAGATTGTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.27, C:0.04, G:0.38, T:0.31
Consensus pattern (36 bp):
TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
Found at i:709533 original size:13 final size:12
Alignment explanation
Indices: 709514--709601 Score: 62
Period size: 13 Copynumber: 7.3 Consensus size: 12
709504 ATATAGGCGT
709514 GATATGGTGATG
1 GATATGGTGATG
709526 GAATATGGTGAT-
1 G-ATATGGTGATG
*
709538 GATATAGGCG-T-
1 GATAT-GGTGATG
709549 GATAATGGTGATG
1 GAT-ATGGTGATG
709562 GACTATGGTGAT-
1 GA-TATGGTGATG
*
709574 GATATAGGCG-T-
1 GATAT-GGTGATG
709585 GATAATGGTGATG
1 GAT-ATGGTGATG
709598 GATA
1 GATA
709602 GATTGTATCT
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.34
12 17 0.27
13 23 0.37
14 1 0.02
ACGTcount: A:0.30, C:0.03, G:0.36, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:709569 original size:36 final size:36
Alignment explanation
Indices: 709496--709599 Score: 183
Period size: 36 Copynumber: 2.9 Consensus size: 36
709486 ATTTATAAGT
*
709496 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
*
709531 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
709567 TGGTGATGATATAGGCGTGATAATGGTGATGGA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGA
709600 TAGATTGTAT
Statistics
Matches: 66, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 20 0.30
36 46 0.70
ACGTcount: A:0.29, C:0.04, G:0.37, T:0.31
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
Done.