Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009579.1 Hibiscus syriacus cultivar Beakdansim tig00116951_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: 6215474
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 29
Found at i:2373190 original size:21 final size:21
Alignment explanation
Indices: 2373137--2373176 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2373127 TTTATGTATG
2373137 ATATAACTTAAACTAACAATA
1 ATATAACTTAAACTAACAATA
*
2373158 ATAAAACTTAAACTAACAA
1 ATATAACTTAAACTAACAA
2373177 ACTAATTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.60, C:0.15, G:0.00, T:0.25
Consensus pattern (21 bp):
ATATAACTTAAACTAACAATA
Found at i:2373208 original size:39 final size:39
Alignment explanation
Indices: 2373164--2373248 Score: 152
Period size: 39 Copynumber: 2.2 Consensus size: 39
2373154 AATAATAAAA
2373164 CTTAAACTAACAAACTAATTAACTAAAATTTTGTTTTAC
1 CTTAAACTAACAAACTAATTAACTAAAATTTTGTTTTAC
* *
2373203 CTTAAACTAACTAACTAATTAATTAAAATTTTGTTTTAC
1 CTTAAACTAACAAACTAATTAACTAAAATTTTGTTTTAC
2373242 CTTAAAC
1 CTTAAAC
2373249 CATAAACTAA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.42, C:0.15, G:0.02, T:0.40
Consensus pattern (39 bp):
CTTAAACTAACAAACTAATTAACTAAAATTTTGTTTTAC
Found at i:2373272 original size:39 final size:37
Alignment explanation
Indices: 2373175--2373272 Score: 110
Period size: 39 Copynumber: 2.6 Consensus size: 37
2373165 TTAAACTAAC
*
2373175 AAACTAATTAACTAA-AATTTTGTTTTACCTTAAACT
1 AAACTAACTAACTAATAATTTTGTTTTACCTTAAACT
*
2373211 -AACTAACTAATTAATTAAAATTTTGTTTTACCTTAAACCAT
1 AAACTAACTAACTAA-T--AATTTTGTTTTACCTTAAA-C-T
*
2373252 AAACTAACAAACTAATAATTT
1 AAACTAACTAACTAATAATTT
2373273 AAAATAATAA
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
35 12 0.24
39 24 0.47
40 1 0.02
41 2 0.04
42 12 0.24
ACGTcount: A:0.45, C:0.14, G:0.02, T:0.39
Consensus pattern (37 bp):
AAACTAACTAACTAATAATTTTGTTTTACCTTAAACT
Found at i:2373504 original size:23 final size:23
Alignment explanation
Indices: 2373473--2373538 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 23
2373463 ACGTGAGTTG
2373473 AAGGACTGCAATAATGCAGCAAT
1 AAGGACTGCAATAATGCAGCAAT
* *
2373496 AAGGGCTGCAATAATGCAGTAAT
1 AAGGACTGCAATAATGCAGCAAT
** *
2373519 AAGTCCTGCAATAATACAGC
1 AAGGACTGCAATAATGCAGC
2373539 TGAATTCACG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.41, C:0.18, G:0.21, T:0.20
Consensus pattern (23 bp):
AAGGACTGCAATAATGCAGCAAT
Found at i:2373746 original size:29 final size:29
Alignment explanation
Indices: 2373677--2373760 Score: 116
Period size: 29 Copynumber: 2.9 Consensus size: 29
2373667 GAGCAACGTT
* *
2373677 GGTCGTCGGGCGTGCATGGCAACCTACAA
1 GGTCGTCGGGAGTGCATGGCGACCTACAA
2373706 GGTCG-CTGGGAGTGCATGGCGACCTACAA
1 GGTCGTC-GGGAGTGCATGGCGACCTACAA
* *
2373735 GGTCGTCCGGAGGGCATGGCGACCTA
1 GGTCGTCGGGAGTGCATGGCGACCTA
2373761 TGTGTTGGGA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
28 1 0.02
29 47 0.96
30 1 0.02
ACGTcount: A:0.19, C:0.26, G:0.38, T:0.17
Consensus pattern (29 bp):
GGTCGTCGGGAGTGCATGGCGACCTACAA
Found at i:2375410 original size:4 final size:4
Alignment explanation
Indices: 2375403--2375432 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
2375393 TACCTGTTTC
2375403 TGTA TGTA TGTA TGTAA TGTA TGTA TGTA T
1 TGTA TGTA TGTA TGT-A TGTA TGTA TGTA T
2375433 AAGAGATGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:2375424 original size:13 final size:13
Alignment explanation
Indices: 2375406--2375431 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2375396 CTGTTTCTGT
2375406 ATGTATGTATGTA
1 ATGTATGTATGTA
2375419 ATGTATGTATGTA
1 ATGTATGTATGTA
2375432 TAAGAGATGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (13 bp):
ATGTATGTATGTA
Found at i:2383600 original size:2 final size:2
Alignment explanation
Indices: 2383593--2383620 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2383583 TACTAAATTG
2383593 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2383621 TATTAATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2385421 original size:43 final size:44
Alignment explanation
Indices: 2385179--2385421 Score: 226
Period size: 44 Copynumber: 5.5 Consensus size: 44
2385169 AAAAATAATG
* ** *
2385179 AAATT-AGGGTCCTAAATTATAAAATTAAAAGGTGAGATTGAAAA
1 AAATTAAGGG-CCTCAATTATAAAGGTAAAAAGTGAGATTGAAAA
** *
2385223 AAATT-AGGAGTTTCAATTATGAAGGTAAAAAGTGAGATTGAAAA
1 AAATTAAGG-GCCTCAATTATAAAGGTAAAAAGTGAGATTGAAAA
* ** *
2385267 AAATTAAGGGCCTCACTTATAAATATAAAAAGTGTGATTGAAAA
1 AAATTAAGGGCCTCAATTATAAAGGTAAAAAGTGAGATTGAAAA
* * *
2385311 AAATTAGGGGCCTCAATTATAAATGTAAAATGTGAGATT-AAAA
1 AAATTAAGGGCCTCAATTATAAAGGTAAAAAGTGAGATTGAAAA
* * * *
2385354 AGAATT-AGATGCCTCTATTATAAAGGTAAAAAATGAGATT-ACAA
1 A-AATTAAG-GGCCTCAATTATAAAGGTAAAAAGTGAGATTGAAAA
* * *
2385398 AAATTAAGGACCTTAATCATAAAG
1 AAATTAAGGGCCTCAATTATAAAG
2385422 AGAAAATAAA
Statistics
Matches: 163, Mismatches: 31, Indels: 11
0.80 0.15 0.05
Matches are distributed among these distances:
43 21 0.13
44 138 0.85
45 4 0.02
ACGTcount: A:0.48, C:0.07, G:0.18, T:0.27
Consensus pattern (44 bp):
AAATTAAGGGCCTCAATTATAAAGGTAAAAAGTGAGATTGAAAA
Found at i:2389530 original size:26 final size:25
Alignment explanation
Indices: 2389501--2389558 Score: 66
Period size: 23 Copynumber: 2.4 Consensus size: 25
2389491 TATTATCAAG
*
2389501 TATAATAACATATTAGGTAGCGCTTA
1 TATAATAA-ATAATAGGTAGCGCTTA
* *
2389527 TATAAT--GTAATAGGTAGCGTTTA
1 TATAATAAATAATAGGTAGCGCTTA
2389550 TATAATAAA
1 TATAATAAA
2389559 ATAAGCATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
23 20 0.77
26 6 0.23
ACGTcount: A:0.41, C:0.07, G:0.16, T:0.36
Consensus pattern (25 bp):
TATAATAAATAATAGGTAGCGCTTA
Found at i:2389561 original size:23 final size:23
Alignment explanation
Indices: 2389514--2389561 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
2389504 AATAACATAT
**
2389514 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATAAAA
*
2389537 TAGGTAGCGTTTATATAATAAAA
1 TAGGTAGCGCTTATATAATAAAA
2389560 TA
1 TA
2389562 AGCATTTAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.06, G:0.19, T:0.35
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATAAAA
Found at i:2389623 original size:87 final size:87
Alignment explanation
Indices: 2389477--2389639 Score: 281
Period size: 87 Copynumber: 1.9 Consensus size: 87
2389467 AATATTATAT
* *
2389477 CATTTAACTAGAAATATTATCAAGTATAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
1 CATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
*
2389542 AGCGTTTATATAATAAAATAAG
66 AGCGCTTATATAATAAAATAAG
* *
2389564 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCTCTTATATAATGTAATAGGT
1 CATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
2389629 AGCGCTTATAT
66 AGCGCTTATAT
2389640 TAATCTATTT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 71 1.00
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.34
Consensus pattern (87 bp):
CATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
AGCGCTTATATAATAAAATAAG
Found at i:2390075 original size:200 final size:195
Alignment explanation
Indices: 2389657--2390365 Score: 732
Period size: 200 Copynumber: 3.5 Consensus size: 195
2389647 TTTTCGAAGT
* * * * * *
2389657 AAACCGATATATTTATACTGGTAACATT-ACAAATTTACATATTACATTATTATTATCGGTTACG
1 AAACCGGTATATTTATACCGGTTACATTGA-AAATTTACCTATTACATTATAATTATCGGTTTCG
** * *
2389721 ATGTTTTTTAGATCGATACAATTT-TAAATGTATCGACACTTTATGCTTGCA-CCTGGTTGGACA
65 ATGTTTTTGGGATCGATAC-TTTTATAAATGTATCGACACTTTATGCTTGCACCCT-TTTGG---
*
2389784 TTCATATTTCATTCTGGA-AAAAAGTATCGACACAAACTAACAACGTGTCGATACATTAT-TTAG
125 --C--A-TTCATTCTGGACAAAAA-TATCGACACAAATTAACAA-GTGTCGATAC-TTATGTT-G
*
2389847 ACCTATTCTCTCATA
181 ACCTATTTTCTCATA
* *
2389862 AAACCGGTATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATACTTATAGGTTTCGA
1 AAACCGGTATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATAATTATCGGTTTCGA
* *
2389927 TGTTTTCGGGATCGATACATTTTATAAATGTATCGACACTTTATGGTTGCACCCTTCTTGGCATT
66 TGTTTTTGGGATCGATAC-TTTTATAAATGTATCGACACTTTATGCTTGCACCCTT-TTGGCATT
* * *
2389992 CATTCTGGACCAAAAATATCGACACAAATTTATCAAGTGTCGATACTTGATGCTGACCTATTTTA
129 CATTCTGGA-CAAAAATATCGACACAAA-TTAACAAGTGTCGATACTT-ATGTTGACCTATTTTC
2390057 TCATA
191 TCATA
* * * *
2390062 AAACCGGTATATTTATATCGGTTACATTGTAAATTTACCTAATACATTATAATTAGCGGTTTCGA
1 AAACCGGTATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATAATTATCGGTTTCGA
* * *
2390127 TGTTTTTGGGATCGATACTTTTAATAAATGTATCGACATTTTATGCATGCACCTCGTTTGTGCAT
66 TGTTTTTGGGATCGATACTTTT-ATAAATGTATCGACACTTTATGCTTGCACC-CTTTTG-GCAT
* * * * * * *
2390192 TCATCCTGGACAATAAGTATTGACACAAATTACACAAGTGTCAATATATTATGTTGATCTGTTTT
128 TCATTCTGGACAA-AAATATCGACACAAATTA-ACAAGTGTCGATA-CTTATGTTGACCTATTTT
*
2390257 CTAAT-
190 CTCATA
* ** * *
2390262 TAACCGGTATATTTATACCGGTTACATTGTTAATTTACCTATTACATTATAATTATTC-TTTTTG
1 AAACCGGTATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATAATTA-TCGGTTTCG
* *
2390326 ATGTTTTTTGGG-TCGATACTTGTATAAAATATATCGACAC
65 ATG-TTTTTGGGATCGATACTTTTAT-AAATGTATCGACAC
2390366 ATATTTGGGT
Statistics
Matches: 435, Mismatches: 51, Indels: 41
0.83 0.10 0.08
Matches are distributed among these distances:
199 19 0.04
200 231 0.53
201 74 0.17
202 3 0.01
205 74 0.17
206 27 0.06
207 7 0.02
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (195 bp):
AAACCGGTATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATAATTATCGGTTTCGA
TGTTTTTGGGATCGATACTTTTATAAATGTATCGACACTTTATGCTTGCACCCTTTTGGCATTCA
TTCTGGACAAAAATATCGACACAAATTAACAAGTGTCGATACTTATGTTGACCTATTTTCTCATA
Found at i:2393236 original size:199 final size:200
Alignment explanation
Indices: 2392896--2393443 Score: 780
Period size: 200 Copynumber: 2.7 Consensus size: 200
2392886 TTTATTTACA
* * * ** *
2392896 AAGTGTCGTTACATGTTGTAGACATATTCTCTCATAAAACAAGTATATTTATACATGTTATATTA
1 AAGTGTCGATACATGTTATAGACCTATTCTCTCATAAAACCGGTATATTTATACAGGTTATATTA
*
2392961 CAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTCGGTATCGACACTTTTAATAAAT
66 CAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGTATCGACACTTTTAATAAAT
* * * *
2393026 GTATCGACACTTTGTGTGTTCATCCTTTTTGGCATCCATTCT-GAAAAAAAGTATCGACACAA-A
131 GTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTATGGAAAAAAAGTATCGACACAATA
2393089 TTTAAC
196 -TTAAC
* * * * *
2393095 AAGTGTCGCTGCATGTTATAGACCTATTCTCTCATAAAACCGGTATATTTATACCGGTTACATTG
1 AAGTGTCGATACATGTTATAGACCTATTCTCTCATAAAACCGGTATATTTATACAGGTTATATTA
* * * *
2393160 TAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGTATCAACATTTTTTAA-AAA
66 CAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGTATCGACA-CTTTTAATAAA
* *
2393224 TGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTATGGACAAAAATTATCGACACAAT
130 TGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTATGGAAAAAAAGTATCGACACAAT
*
2393289 ATTAAG
195 ATTAAC
* * * *
2393295 AAGTGTCGATACATATTATAGACCTATTCTCTCATAAAATCGGTATATGTATACTGGTTATATTA
1 AAGTGTCGATACATGTTATAGACCTATTCTCTCATAAAACCGGTATATTTATACAGGTTATATTA
*
2393360 CAAAATTACCTATTACATTATAATTATGGGTTTTGATGTTTTTGAG-ATCGACACTTTTAATAAA
66 CAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTG-GTATCGACACTTTTAATAAA
*
2393424 TGTATCGAAACTTTATGCGT
130 TGTATCGACACTTTATGCGT
2393444 GCAACCATTT
Statistics
Matches: 308, Mismatches: 36, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
199 152 0.49
200 154 0.50
201 2 0.01
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (200 bp):
AAGTGTCGATACATGTTATAGACCTATTCTCTCATAAAACCGGTATATTTATACAGGTTATATTA
CAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGTATCGACACTTTTAATAAAT
GTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTATGGAAAAAAAGTATCGACACAATA
TTAAC
Found at i:2393384 original size:200 final size:198
Alignment explanation
Indices: 2392896--2393443 Score: 771
Period size: 199 Copynumber: 2.7 Consensus size: 198
2392886 TTTATTTACA
* * * *
2392896 AAGTGTCGTTACATGTTGTAGACATATTCTCTCATAAAACAAGTATATTTATACAT-GTTATATT
1 AAGTGTCGATACATGTTATAGACCTATTCTCTCATAAAAC-GGTATATTTATAC-TGGTTATATT
*
2392960 ACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTCGGTATCGACACTTTTAATAAA
64 ACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGTATCGACACTTTTAATAAA
* * * *
2393025 TGTATCGACACTTTGTGTGTTCATCCTTTTTGGCATCCATTCTGAAAAAAAGTATCGACACAAAT
129 TGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTATGAAAAAAAGTATCGACACAAAT
2393090 TTAAC
194 TTAAC
* * * * *
2393095 AAGTGTCGCTGCATGTTATAGACCTATTCTCTCATAAAACCGGTATATTTATACCGGTTACATTG
1 AAGTGTCGATACATGTTATAGACCTATTCTCTCATAAAA-CGGTATATTTATACTGGTTATATTA
* * * *
2393160 TAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGTATCAACATTTTTTAA-AAA
65 CAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGTATCGACA-CTTTTAATAAA
* *
2393224 TGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTATGGACAAAAATTATCGACAC-AA
129 TGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTAT-GAAAAAAAGTATCGACACAAA
*
2393288 TATTAAG
193 T-TTAAC
* *
2393295 AAGTGTCGATACATATTATAGACCTATTCTCTCATAAAATCGGTATATGTATACTGGTTATATTA
1 AAGTGTCGATACATGTTATAGACCTATTCTCTCATAAAA-CGGTATATTTATACTGGTTATATTA
*
2393360 CAAAATTACCTATTACATTATAATTATGGGTTTTGATGTTTTTGAG-ATCGACACTTTTAATAAA
65 CAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTG-GTATCGACACTTTTAATAAA
*
2393424 TGTATCGAAACTTTATGCGT
129 TGTATCGACACTTTATGCGT
2393444 GCAACCATTT
Statistics
Matches: 308, Mismatches: 34, Indels: 13
0.87 0.10 0.04
Matches are distributed among these distances:
199 154 0.50
200 153 0.50
201 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (198 bp):
AAGTGTCGATACATGTTATAGACCTATTCTCTCATAAAACGGTATATTTATACTGGTTATATTAC
AAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGTATCGACACTTTTAATAAATG
TATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTATGAAAAAAAGTATCGACACAAATTT
AAC
Found at i:2396810 original size:201 final size:201
Alignment explanation
Indices: 2396463--2397010 Score: 934
Period size: 201 Copynumber: 2.7 Consensus size: 201
2396453 TATTTAAATT
* * *
2396463 AGTATCGACACTAAATTAAAAACGTGTCAATACATGTTGTAGACCTATTCTCTCATAAAACCGGT
1 AGTATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGT
*
2396528 ATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATACTTATGGATGCATATGTTTTTG
66 ATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
* *
2396593 GGATCGATAATTTTTATAAATGTATCGACACTTTATGGTTGCACCCTTTTTGATATTCATTCTGG
131 GGATCGATAATTTTTATAAATGTACCGACACTTTATGGTTGCACCCTTTTTGACATTCATTCTGG
2396658 ACCAAA
196 ACCAAA
2396664 AGTATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGT
1 AGTATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGT
*
2396729 ATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATACTTATGGATGCATATATTTCTG
66 ATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
* * *
2396794 GGATCGATACTTTTTATAAATGTACCGACACTTTATGGTTGCATCCTTTTTGGCATTCATTCTGG
131 GGATCGATAATTTTTATAAATGTACCGACACTTTATGGTTGCACCCTTTTTGACATTCATTCTGG
2396859 ACCAAA
196 ACCAAA
* * *
2396865 AGTATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTATACATATTCTCTCATAAAACCGAT
1 AGTATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGT
* * * *
2396930 ATATTTATGCCGGTTACATTGAAAATTTACCTATTGCATTATACTTATAGATGCATATGTTTCTA
66 ATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
*
2396995 GGATCGATAAATTTTA
131 GGATCGATAATTTTTA
2397011 CCTATTACAT
Statistics
Matches: 327, Mismatches: 20, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
201 327 1.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (201 bp):
AGTATCGACACAAAATTAAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGT
ATATTTATACCGGTTACATTGAAAATTTACCTATTACATTATACTTATGGATGCATATGTTTCTG
GGATCGATAATTTTTATAAATGTACCGACACTTTATGGTTGCACCCTTTTTGACATTCATTCTGG
ACCAAA
Found at i:2397290 original size:19 final size:19
Alignment explanation
Indices: 2397266--2397314 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
2397256 TTACATTCAC
*
2397266 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCAT
2397285 ATACAAAATTATAAATCAT
1 ATACAAAATTATAAATCAT
*
2397304 ATAAAAAATTA
1 ATACAAAATTA
2397315 ACCCTACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCAT
Found at i:2398837 original size:33 final size:33
Alignment explanation
Indices: 2398800--2398894 Score: 163
Period size: 33 Copynumber: 2.9 Consensus size: 33
2398790 CATCTTAAGA
2398800 TCACCCCTTAACACCTCAACTTCTTTCACCACT
1 TCACCCCTTAACACCTCAACTTCTTTCACCACT
*
2398833 TCACCCCTTAACATCTCAACTTCTTTCACCACT
1 TCACCCCTTAACACCTCAACTTCTTTCACCACT
* *
2398866 TCACCCCTCAACACCTCTACTTCTTTCAC
1 TCACCCCTTAACACCTCAACTTCTTTCAC
2398895 AACTCCATCT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.23, C:0.45, G:0.00, T:0.32
Consensus pattern (33 bp):
TCACCCCTTAACACCTCAACTTCTTTCACCACT
Found at i:2398957 original size:21 final size:21
Alignment explanation
Indices: 2398932--2398975 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
2398922 CCCCTTATGC
2398932 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
* *
2398953 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
2398974 CT
1 CT
2398976 TGATTATCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.32, G:0.11, T:0.41
Consensus pattern (21 bp):
CTCTCAAGTGTATCTTCGACT
Found at i:2401496 original size:182 final size:182
Alignment explanation
Indices: 2401181--2401647 Score: 609
Period size: 182 Copynumber: 2.6 Consensus size: 182
2401171 GAAAGTATCG
* * *
2401181 ACACTTTCAATATATTCGATAGCGCTTTATCGATTTTATCATTTTGATACCGGTTTTATCATATT
1 ACACTTTAAATATATTCGATAGCGCTTTACCGATTTTATCATTTCGATACCGGTTTTATCATATT
*
2401246 TTTACCTGTTATATCGTTGTGTATCGATACATTTTTATAAAGTATCGACACTTTATAAGCGCTAA
66 TTTACCTGTTATATAGTTGTGTATCGATACATTTTTATAAAGTATCGACACTTTATAAGCGCTAA
2401311 AACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATTAAAGTACTA
131 AACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATTAAAGTACTA
* * * * *
2401363 ACACTTTAAATATATTTGGTAGCTCTTTACCGATTTTATCATTTCGATATCGGTTTTGTCATATT
1 ACACTTTAAATATATTCGATAGCGCTTTACCGATTTTATCATTTCGATACCGGTTTTATCATATT
* * *
2401428 TTTACTTGTTATATAGTTGT-TGATCGATACATTTTTATAAAGTATCGACACTTTATAGGCGTTA
66 TTTACCTGTTATATAGTTGTGT-ATCGATACATTTTTATAAAGTATCGACACTTTATAAGCGCTA
* *
2401492 AAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATTAAAGTA-TCG
130 AAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATTAAAGTACT-A
* * * * * * * * *
2401545 ACACGTTCAATATATCCGGTAAG-GATTTACCGGTATTGTCTTTTCG-TGACCGGTTTTATCGAT
1 ACACTTTAAATATATTCGAT-AGCGCTTTACCGATTTTATCATTTCGAT-ACCGGTTTTATC-AT
* * * * *
2401608 ATTTTTACATGTTATATTGATATGGATCGATACATTTTTA
63 ATTTTTACCTGTTATATAGTTGTGTATCGATACATTTTTA
2401648 ATTTGGATCG
Statistics
Matches: 248, Mismatches: 31, Indels: 11
0.86 0.11 0.04
Matches are distributed among these distances:
181 3 0.01
182 207 0.83
183 38 0.15
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.43
Consensus pattern (182 bp):
ACACTTTAAATATATTCGATAGCGCTTTACCGATTTTATCATTTCGATACCGGTTTTATCATATT
TTTACCTGTTATATAGTTGTGTATCGATACATTTTTATAAAGTATCGACACTTTATAAGCGCTAA
AACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATTAAAGTACTA
Found at i:2402168 original size:2 final size:2
Alignment explanation
Indices: 2402161--2402214 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
2402151 TTAAAATTTA
2402161 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
2402203 AT GT AT AT AT AT
1 AT AT AT AT AT AT
2402215 TTATTAAAAG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2402837 original size:36 final size:35
Alignment explanation
Indices: 2402756--2402894 Score: 206
Period size: 35 Copynumber: 3.9 Consensus size: 35
2402746 AAATGAACAA
** *
2402756 TTGAATCGAAAGTGTTGATGCTTCCTTCCGTTCAC
1 TTGAATCGAAAGTGCCGATGCTTCCTTTCGTTCAC
*
2402791 TTGAATCGAAAGTGCCGATGCTTCCTTTCGTTCTTC
1 TTGAATCGAAAGTGCCGATGCTTCCTTTCGTTC-AC
* *
2402827 TTGAATCGAAAGTGTCGATGCTTCCTTTTGTTCAC
1 TTGAATCGAAAGTGCCGATGCTTCCTTTCGTTCAC
*
2402862 TTGAATCGAAAGTGCCGATGCTTACTTTCGTTC
1 TTGAATCGAAAGTGCCGATGCTTCCTTTCGTTC
2402895 TTCTTATTCA
Statistics
Matches: 93, Mismatches: 10, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
35 61 0.66
36 32 0.34
ACGTcount: A:0.19, C:0.22, G:0.20, T:0.38
Consensus pattern (35 bp):
TTGAATCGAAAGTGCCGATGCTTCCTTTCGTTCAC
Found at i:2402872 original size:71 final size:71
Alignment explanation
Indices: 2402756--2402899 Score: 252
Period size: 71 Copynumber: 2.0 Consensus size: 71
2402746 AAATGAACAA
* *
2402756 TTGAATCGAAAGTGTTGATGCTTCCTTCCGTTCACTTGAATCGAAAGTGCCGATGCTTCCTTTCG
1 TTGAATCGAAAGTGTCGATGCTTCCTTCCGTTCACTTGAATCGAAAGTGCCGATGCTTACTTTCG
2402821 TTCTTC
66 TTCTTC
**
2402827 TTGAATCGAAAGTGTCGATGCTTCCTTTTGTTCACTTGAATCGAAAGTGCCGATGCTTACTTTCG
1 TTGAATCGAAAGTGTCGATGCTTCCTTCCGTTCACTTGAATCGAAAGTGCCGATGCTTACTTTCG
2402892 TTCTTC
66 TTCTTC
2402898 TT
1 TT
2402900 ATTCACCTTC
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
71 69 1.00
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.40
Consensus pattern (71 bp):
TTGAATCGAAAGTGTCGATGCTTCCTTCCGTTCACTTGAATCGAAAGTGCCGATGCTTACTTTCG
TTCTTC
Found at i:2403590 original size:36 final size:35
Alignment explanation
Indices: 2403509--2403647 Score: 206
Period size: 35 Copynumber: 3.9 Consensus size: 35
2403499 AAATGAACAA
** *
2403509 TTGAATCGAAAGTGTTGATGCTTCCTTCCGTTCAC
1 TTGAATCGAAAGTGCCGATGCTTCCTTTCGTTCAC
*
2403544 TTGAATCGAAAGTGCCGATGCTTCCTTTCGTTCTTC
1 TTGAATCGAAAGTGCCGATGCTTCCTTTCGTTC-AC
* *
2403580 TTGAATCGAAAGTGTCGATGCTTCCTTTTGTTCAC
1 TTGAATCGAAAGTGCCGATGCTTCCTTTCGTTCAC
*
2403615 TTGAATCGAAAGTGCCGATGCTTACTTTCGTTC
1 TTGAATCGAAAGTGCCGATGCTTCCTTTCGTTC
2403648 TTCTTATTCA
Statistics
Matches: 93, Mismatches: 10, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
35 61 0.66
36 32 0.34
ACGTcount: A:0.19, C:0.22, G:0.20, T:0.38
Consensus pattern (35 bp):
TTGAATCGAAAGTGCCGATGCTTCCTTTCGTTCAC
Found at i:2403625 original size:71 final size:71
Alignment explanation
Indices: 2403509--2403652 Score: 252
Period size: 71 Copynumber: 2.0 Consensus size: 71
2403499 AAATGAACAA
* *
2403509 TTGAATCGAAAGTGTTGATGCTTCCTTCCGTTCACTTGAATCGAAAGTGCCGATGCTTCCTTTCG
1 TTGAATCGAAAGTGTCGATGCTTCCTTCCGTTCACTTGAATCGAAAGTGCCGATGCTTACTTTCG
2403574 TTCTTC
66 TTCTTC
**
2403580 TTGAATCGAAAGTGTCGATGCTTCCTTTTGTTCACTTGAATCGAAAGTGCCGATGCTTACTTTCG
1 TTGAATCGAAAGTGTCGATGCTTCCTTCCGTTCACTTGAATCGAAAGTGCCGATGCTTACTTTCG
2403645 TTCTTC
66 TTCTTC
2403651 TT
1 TT
2403653 ATTCACCTTC
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
71 69 1.00
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.40
Consensus pattern (71 bp):
TTGAATCGAAAGTGTCGATGCTTCCTTCCGTTCACTTGAATCGAAAGTGCCGATGCTTACTTTCG
TTCTTC
Found at i:2414723 original size:3 final size:3
Alignment explanation
Indices: 2414707--2414740 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
2414697 ATTTCATTCA
*
2414707 TTC TTC TT- TGC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
2414741 TTTGTATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 1 0.04
3 27 0.96
ACGTcount: A:0.00, C:0.29, G:0.03, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:2423754 original size:83 final size:86
Alignment explanation
Indices: 2423633--2423797 Score: 255
Period size: 83 Copynumber: 1.9 Consensus size: 86
2423623 ACAATATTTT
* *
2423633 TTAGTAAGATAAAGATCTCCAAAATCTTAATTGCATAATAAAATATTATTATG-G-TAAACACTA
1 TTAGTAAGATAAAGATCTCCAAAATCCTAATTGCATAATAAAATATTATTAGGAGATAAACACTA
2423696 CACAAATTATTATTATGGTTA
66 CACAAATTATTATTATGGTTA
* *
2423717 TTAGTAAGATAAAGATCT-CAAAATCCTAATTGCATAATATAATATTATTAGGAAGATAATCACT
1 TTAGTAAGATAAAGATCTCCAAAATCCTAATTGCATAATAAAATATTATTAGG-AGATAAACACT
*
2423781 ACACAAATTATTGTTAT
65 ACACAAATTATTATTAT
2423798 AATTATTAAT
Statistics
Matches: 73, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
83 31 0.42
84 18 0.25
85 1 0.01
86 23 0.32
ACGTcount: A:0.44, C:0.11, G:0.10, T:0.35
Consensus pattern (86 bp):
TTAGTAAGATAAAGATCTCCAAAATCCTAATTGCATAATAAAATATTATTAGGAGATAAACACTA
CACAAATTATTATTATGGTTA
Found at i:2430103 original size:21 final size:20
Alignment explanation
Indices: 2429981--2430096 Score: 142
Period size: 20 Copynumber: 5.8 Consensus size: 20
2429971 ATTTTCGCAA
* *
2429981 CGCGTTACGAATTTGAAAAC
1 CGCGTTGCGAATTTGAAAAT
*
2430001 CGCGTTACGAATTTGAAAAT
1 CGCGTTGCGAATTTGAAAAT
*
2430021 CGCGTTGTGAATTTGAAAAT
1 CGCGTTGCGAATTTGAAAAT
* *
2430041 CGCGTTGTGAATTTGAAAAC
1 CGCGTTGCGAATTTGAAAAT
* *
2430061 CGCGTTGCGATTTTGGAGAAT
1 CGCGTTGCGAATTT-GAAAAT
*
2430082 CGCGTTGCGATTTTG
1 CGCGTTGCGAATTTG
2430097 GATAATCTTT
Statistics
Matches: 87, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
20 69 0.79
21 18 0.21
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.32
Consensus pattern (20 bp):
CGCGTTGCGAATTTGAAAAT
Found at i:2436152 original size:9 final size:9
Alignment explanation
Indices: 2436140--2436165 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
2436130 TAAAAATTAA
2436140 AAAAAGAAT
1 AAAAAGAAT
2436149 AAAAAGAAT
1 AAAAAGAAT
2436158 AAAAAGAA
1 AAAAAGAA
2436166 AAGATCATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.12, T:0.08
Consensus pattern (9 bp):
AAAAAGAAT
Found at i:2440140 original size:2 final size:2
Alignment explanation
Indices: 2440133--2440167 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2440123 TGAGTTAAAA
2440133 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2440168 AACTGTGGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2442794 original size:31 final size:30
Alignment explanation
Indices: 2442736--2442819 Score: 87
Period size: 31 Copynumber: 2.7 Consensus size: 30
2442726 TGGGGACCGA
* * *
2442736 GAGCCTACCAAAAAAGGTTACTCGGGGCCAC
1 GAGCCTACCCAAGAAGGAT-CTCGGGGCCAC
2442767 GGAGCCTACCCAAGAAGGATCTCGGGGCCAC
1 -GAGCCTACCCAAGAAGGATCTCGGGGCCAC
* * *
2442798 AAGGCCAACCCAAGAAAGATCT
1 GA-GCCTACCCAAGAAGGATCT
2442820 TGGAGCCTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
30 1 0.02
31 28 0.62
32 16 0.36
ACGTcount: A:0.33, C:0.30, G:0.26, T:0.11
Consensus pattern (30 bp):
GAGCCTACCCAAGAAGGATCTCGGGGCCAC
Found at i:2444563 original size:19 final size:20
Alignment explanation
Indices: 2444508--2444584 Score: 61
Period size: 19 Copynumber: 4.0 Consensus size: 20
2444498 TCGAAATCGG
* *
2444508 TTTGACCGGTTTTCAACCGGT
1 TTTGACCGGATTTGAACC-GT
*
2444529 TTTGACC-GATTCGAACCGT
1 TTTGACCGGATTTGAACCGT
* *
2444548 TTTGACCAG-TTTGAACCGG
1 TTTGACCGGATTTGAACCGT
* *
2444567 TCTGACCGG-TCTGAACCG
1 TTTGACCGGATTTGAACCG
2444585 ACCCGAACCG
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
19 32 0.68
20 8 0.17
21 7 0.15
ACGTcount: A:0.18, C:0.26, G:0.25, T:0.31
Consensus pattern (20 bp):
TTTGACCGGATTTGAACCGT
Found at i:2444608 original size:22 final size:22
Alignment explanation
Indices: 2444582--2444626 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
2444572 CCGGTCTGAA
2444582 CCGACCCGAACCGACCGTTGAC
1 CCGACCCGAACCGACCGTTGAC
**
2444604 CCGACCCGCCCCGACCGTTGAC
1 CCGACCCGAACCGACCGTTGAC
2444626 C
1 C
2444627 GTTGACTTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.51, G:0.22, T:0.09
Consensus pattern (22 bp):
CCGACCCGAACCGACCGTTGAC
Found at i:2451853 original size:19 final size:19
Alignment explanation
Indices: 2451806--2451863 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 19
2451796 CGCTGCTAGA
*
2451806 AACCGGTTTGACCGAT-TCG
1 AACCGGTTTGACCGGTCT-G
* *
2451825 AATCGTTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
2451844 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
2451863 A
1 A
2451864 CCCGACCCGA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
19 32 0.97
20 1 0.03
ACGTcount: A:0.19, C:0.24, G:0.28, T:0.29
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:2453321 original size:17 final size:17
Alignment explanation
Indices: 2453283--2453321 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
2453273 GATAGTATAA
*
2453283 TTTATTTATAATTTCAT
1 TTTATTTATAATGTCAT
* *
2453300 GTTATTTATAATGTGAT
1 TTTATTTATAATGTCAT
2453317 TTTAT
1 TTTAT
2453322 ATTGATAGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.28, C:0.03, G:0.08, T:0.62
Consensus pattern (17 bp):
TTTATTTATAATGTCAT
Found at i:2456498 original size:21 final size:21
Alignment explanation
Indices: 2456474--2456639 Score: 137
Period size: 21 Copynumber: 7.9 Consensus size: 21
2456464 ACTTCGACTA
*
2456474 TCGCATTGCGATAGTCCAAGT
1 TCGCGTTGCGATAGTCCAAGT
*
2456495 TCGCGTTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCCAAGT
** *
2456516 TCGCGTTGCGATTTTTTCCAAAT
1 TCGCGTTGCGA--TAGTCCAAGT
*
2456539 T--CGTTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCCAAGT
* *
2456558 TCGTGTTGCGATTTATTCCAAGT
1 TCGCGTTGCGA--TAGTCCAAGT
*
2456581 T--CGTTGCGATAGTCTAAGT
1 TCGCGTTGCGATAGTCCAAGT
* *
2456600 TCGCGTTGCAATTTATTCCAAGT
1 TCGCGTTGCGA--TAGTCCAAGT
2456623 T--CGTTGCGATAGTCCAA
1 TCGCGTTGCGATAGTCCAA
2456640 AATCGTAACG
Statistics
Matches: 114, Mismatches: 21, Indels: 22
0.73 0.13 0.14
Matches are distributed among these distances:
19 23 0.20
21 66 0.58
23 25 0.22
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCCAAGT
Found at i:2456526 original size:42 final size:41
Alignment explanation
Indices: 2456474--2456636 Score: 211
Period size: 42 Copynumber: 3.9 Consensus size: 41
2456464 ACTTCGACTA
* *
2456474 TCGCATTGCGA-TAGTCCAAGTTCGCGTTGCGATAGTCGAAGT
1 TCGCGTTGCGATTATTCCAAGTT--CGTTGCGATAGTCGAAGT
* *
2456516 TCGCGTTGCGATTTTTTCCAAATTCGTTGCGATAGTCGAAGT
1 TCGCGTTGCGA-TTATTCCAAGTTCGTTGCGATAGTCGAAGT
* *
2456558 TCGTGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCTAAGT
1 TCGCGTTGCGA-TTATTCCAAGTTCGTTGCGATAGTCGAAGT
*
2456600 TCGCGTTGCAATTTATTCCAAGTTCGTTGCGATAGTC
1 TCGCGTTGCGA-TTATTCCAAGTTCGTTGCGATAGTC
2456637 CAAAATCGTA
Statistics
Matches: 109, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
42 101 0.93
44 8 0.07
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.36
Consensus pattern (41 bp):
TCGCGTTGCGATTATTCCAAGTTCGTTGCGATAGTCGAAGT
Found at i:2457463 original size:21 final size:21
Alignment explanation
Indices: 2457439--2457579 Score: 160
Period size: 21 Copynumber: 6.6 Consensus size: 21
2457429 TGCGATTTTG
2457439 GACTATCGCAACGCGAACTTC
1 GACTATCGCAACGCGAACTTC
* *
2457460 GACTATCGCAA--CGAATTTT
1 GACTATCGCAACGCGAACTTC
*
2457479 GAATAAATCGCAACGCGAACTTC
1 GACT--ATCGCAACGCGAACTTC
2457502 GACTATCGCAACGCGAACTTC
1 GACTATCGCAACGCGAACTTC
* * *
2457523 GACTATCACAACGCGAATTTG
1 GACTATCGCAACGCGAACTTC
* *
2457544 GAATAAATCGCAACGCGAACTTG
1 GACT--ATCGCAACGCGAACTTC
2457567 GACTATCGCAACG
1 GACTATCGCAACG
2457580 AATTTGGAAA
Statistics
Matches: 101, Mismatches: 13, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
19 9 0.09
21 65 0.64
23 27 0.27
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.21
Consensus pattern (21 bp):
GACTATCGCAACGCGAACTTC
Found at i:2457558 original size:44 final size:40
Alignment explanation
Indices: 2457506--2457595 Score: 126
Period size: 44 Copynumber: 2.1 Consensus size: 40
2457496 AACTTCGACT
2457506 ATCGCAACGCGAACTTCGACTATCACAACGCGAATTTGGAATAA
1 ATCGCAACGCGAACTTCGACTATCACAA--CGAATTTGG-A-AA
* *
2457550 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAAA
1 ATCGCAACGCGAACTTCGACTATCACAACGAATTTGGAAA
2457590 ATCGCA
1 ATCGCA
2457596 TTGCGATAGT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
40 8 0.18
41 1 0.02
42 9 0.20
44 26 0.59
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (40 bp):
ATCGCAACGCGAACTTCGACTATCACAACGAATTTGGAAA
Found at i:2457571 original size:65 final size:63
Alignment explanation
Indices: 2457436--2457579 Score: 243
Period size: 65 Copynumber: 2.3 Consensus size: 63
2457426 CGTTGCGATT
* *
2457436 TTGGACTATCGCAACGCGAACTTCGACTATCGCAACGAATTTTGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAACTTCGACTATCACAACGAATTTGGAATAAATCGCAACGCGAAC
*
2457499 TTCGACTATCGCAACGCGAACTTCGACTATCACAACGCGAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAACTTCGACTATCACAA--CGAATTTGGAATAAATCGCAACGCGAAC
2457564 TTGGACTATCGCAACG
1 TTGGACTATCGCAACG
2457580 AATTTGGAAA
Statistics
Matches: 75, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
63 33 0.44
65 42 0.56
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (63 bp):
TTGGACTATCGCAACGCGAACTTCGACTATCACAACGAATTTGGAATAAATCGCAACGCGAAC
Found at i:2457593 original size:19 final size:20
Alignment explanation
Indices: 2457464--2457595 Score: 61
Period size: 21 Copynumber: 6.3 Consensus size: 20
2457454 AACTTCGACT
*
2457464 ATCGCAA-CGAATTTTGAATAA
1 ATCGCAACCGAA-TTTGGA-AA
* * **
2457485 ATCGCAACGCGAACTTCGACT
1 ATCGCAAC-CGAATTTGGAAA
* * **
2457506 ATCGCAACGCGAACTTCGACT
1 ATCGCAAC-CGAATTTGGAAA
*
2457527 ATCACAACGCGAATTTGGAATAA
1 ATCGCAAC-CGAATTTGG-A-AA
* **
2457550 ATCGCAACGCGAACTTGGACT
1 ATCGCAAC-CGAATTTGGAAA
2457571 ATCGCAA-CGAATTTGGAAA
1 ATCGCAACCGAATTTGGAAA
2457590 ATCGCA
1 ATCGCA
2457596 TTGCGATAGT
Statistics
Matches: 90, Mismatches: 17, Indels: 10
0.77 0.15 0.09
Matches are distributed among these distances:
19 15 0.17
21 50 0.56
22 5 0.06
23 20 0.22
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (20 bp):
ATCGCAACCGAATTTGGAAA
Found at i:2457642 original size:21 final size:21
Alignment explanation
Indices: 2457591--2457643 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 21
2457581 ATTTGGAAAA
2457591 TCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
*
2457612 TCGCGA-TGCGATAGTCGATGT
1 TCGC-ATTGCGATAGTCGAAGT
2457633 TCGCATTGCGA
1 TCGCATTGCGA
2457644 ATCTGGAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 1 0.03
21 27 0.93
22 1 0.03
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (21 bp):
TCGCATTGCGATAGTCGAAGT
Found at i:2463356 original size:17 final size:18
Alignment explanation
Indices: 2463336--2463369 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2463326 TAATTTTATT
*
2463336 AATAATTTATT-TTTTTA
1 AATAATGTATTATTTTTA
2463353 AATAATGTATTATTTTT
1 AATAATGTATTATTTTT
2463370 TTGAGTTGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (18 bp):
AATAATGTATTATTTTTA
Found at i:2464045 original size:48 final size:48
Alignment explanation
Indices: 2463989--2464085 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
2463979 ACATATGCAG
2463989 ACAAACCGCTTCAATTTGAGACATCTAAGGAAAATAGCATTCCCTTCA
1 ACAAACCGCTTCAATTTGAGACATCTAAGGAAAATAGCATTCCCTTCA
2464037 ACAAACCGCTTCAATTTGAGACATCTAAGGAAAATAGCATTCCCTTCA
1 ACAAACCGCTTCAATTTGAGACATCTAAGGAAAATAGCATTCCCTTCA
2464085 A
1 A
2464086 TCATTAATAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (48 bp):
ACAAACCGCTTCAATTTGAGACATCTAAGGAAAATAGCATTCCCTTCA
Found at i:2465398 original size:17 final size:16
Alignment explanation
Indices: 2465376--2465411 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
2465366 ACTTATAGTA
*
2465376 ATAAATAATATTATAAC
1 ATAAATAATA-AATAAC
2465393 ATAAATAATAAATAAC
1 ATAAATAATAAATAAC
2465409 ATA
1 ATA
2465412 TTAAGTTGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.31
Consensus pattern (16 bp):
ATAAATAATAAATAAC
Found at i:2467305 original size:14 final size:17
Alignment explanation
Indices: 2467286--2467321 Score: 51
Period size: 14 Copynumber: 2.3 Consensus size: 17
2467276 TAGATCCATA
2467286 TATTTTA-AATT-TA-T
1 TATTTTATAATTATATT
2467300 TATTTTATAATTATATT
1 TATTTTATAATTATATT
2467317 TATTT
1 TATTT
2467322 ATTTATTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 7 0.37
15 4 0.21
16 2 0.11
17 6 0.32
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TATTTTATAATTATATT
Found at i:2467990 original size:2 final size:2
Alignment explanation
Indices: 2467983--2468015 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2467973 GATGGAATAT
2467983 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2468016 GTGTATGTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2470688 original size:28 final size:28
Alignment explanation
Indices: 2470635--2470695 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 28
2470625 AATTTTAGAG
2470635 AAAAAAATCATATTATCAATATAAAATAT
1 AAAAAAATCATATTAT-AATATAAAATAT
*
2470664 AAAAAATATTCATATTAT-ATA-AAAATTT
1 AAAAAA-A-TCATATTATAATATAAAATAT
2470692 AAAA
1 AAAA
2470696 CTTTTAAGAG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
28 10 0.34
29 9 0.31
30 1 0.03
31 9 0.31
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (28 bp):
AAAAAAATCATATTATAATATAAAATAT
Found at i:2472720 original size:29 final size:30
Alignment explanation
Indices: 2472688--2472763 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 30
2472678 ATTTTTTATT
* * *
2472688 TAAGTACCTAAAGTGT-TTTTTGGTCAAAG
1 TAAGTACATAAAGTATGTTTTTGGTCAAAA
*
2472717 TAAGTACTTAAAGTTATGTTTTTGGTCAAAA
1 TAAGTACATAAAG-TATGTTTTTGGTCAAAA
*
2472748 TAGGTACATAAAGTAT
1 TAAGTACATAAAGTAT
2472764 TCTATCTATT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
29 12 0.30
30 5 0.12
31 23 0.57
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.38
Consensus pattern (30 bp):
TAAGTACATAAAGTATGTTTTTGGTCAAAA
Found at i:2485495 original size:92 final size:92
Alignment explanation
Indices: 2485362--2485546 Score: 370
Period size: 92 Copynumber: 2.0 Consensus size: 92
2485352 AAAGAAGAAG
2485362 TTTCTCCTCTAACAGATTCCACAGTTTTAGTAGAGAGATGAGGTATGACATTTGATTCTTTACCG
1 TTTCTCCTCTAACAGATTCCACAGTTTTAGTAGAGAGATGAGGTATGACATTTGATTCTTTACCG
2485427 GAATGGATACTTTGGGAAGCAGATGGA
66 GAATGGATACTTTGGGAAGCAGATGGA
2485454 TTTCTCCTCTAACAGATTCCACAGTTTTAGTAGAGAGATGAGGTATGACATTTGATTCTTTACCG
1 TTTCTCCTCTAACAGATTCCACAGTTTTAGTAGAGAGATGAGGTATGACATTTGATTCTTTACCG
2485519 GAATGGATACTTTGGGAAGCAGATGGA
66 GAATGGATACTTTGGGAAGCAGATGGA
2485546 T
1 T
2485547 CACTCTTAGA
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 93 1.00
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (92 bp):
TTTCTCCTCTAACAGATTCCACAGTTTTAGTAGAGAGATGAGGTATGACATTTGATTCTTTACCG
GAATGGATACTTTGGGAAGCAGATGGA
Found at i:2487354 original size:33 final size:31
Alignment explanation
Indices: 2487323--2487384 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
2487313 CTGTTAATAA
* *
2487323 AACTGGCATAATTATACATTTGGTCCCTAAT
1 AACTGGAATAATTATACATTTGCTCCCTAAT
* *
2487354 -ATTGGAATAATTATACATTTGCTCCTTAAT
1 AACTGGAATAATTATACATTTGCTCCCTAAT
2487384 A
1 A
2487385 TTTATATATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (31 bp):
AACTGGAATAATTATACATTTGCTCCCTAAT
Found at i:2487364 original size:30 final size:30
Alignment explanation
Indices: 2487330--2487386 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
2487320 TAAAACTGGC
*
2487330 ATAATTATACATTTGGTCCCTAATATTGGA
1 ATAATTATACATTTGCTCCCTAATATTGGA
*
2487360 ATAATTATACATTTGCTCCTTAATATT
1 ATAATTATACATTTGCTCCCTAATATT
2487387 TATATATTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (30 bp):
ATAATTATACATTTGCTCCCTAATATTGGA
Found at i:2487865 original size:26 final size:27
Alignment explanation
Indices: 2487835--2487886 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 27
2487825 TTTTCTTTAA
2487835 CATTAATCGAACCGAAA-TTATTTGAC
1 CATTAATCGAACCGAAATTTATTTGAC
2487861 CATTAATCGAACCGAAATTTATTTGA
1 CATTAATCGAACCGAAATTTATTTGA
2487887 AAATTATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 17 0.68
27 8 0.32
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (27 bp):
CATTAATCGAACCGAAATTTATTTGAC
Found at i:2487892 original size:27 final size:26
Alignment explanation
Indices: 2487836--2487892 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
2487826 TTTCTTTAAC
**
2487836 ATTAATCGAACCGAAATTATTTGACC
1 ATTAATCGAACCGAAATTATTTGAAA
2487862 ATTAATCGAACCGAAATTTATTTGAAA
1 ATTAATCGAACCGAAA-TTATTTGAAA
2487889 ATTA
1 ATTA
2487893 TTAACCGAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
26 16 0.57
27 12 0.43
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.33
Consensus pattern (26 bp):
ATTAATCGAACCGAAATTATTTGAAA
Found at i:2488090 original size:185 final size:187
Alignment explanation
Indices: 2487777--2488216 Score: 670
Period size: 185 Copynumber: 2.4 Consensus size: 187
2487767 CGTCAAATAA
* * * *
2487777 AACCAAAATTTATTTAAAAATTATTAACCAAACCAAATCCATCGATTTTTTTCTTTAACATTAAT
1 AACCGAAATTTATTTAAAAATTATTAACCGAACCAAATCAACCGATTTTTTTCTTTAACATTAAT
* *
2487842 CGAACCGAAATTATTTGACCATTAATCGAACCGAAATTTATTTGAAAATTATTAACCGAACCAAA
66 CGAACCAAAATTATTTGACCATTAATCAAACCGAAATTTATTTGAAAATTATTAACCGAACCAAA
* *
2487907 TCAACC-A-ATTTTTTCTTTAACATTAATCGAACTGAAATTATTTGATCGTTAATCG
131 TCAACCGATATTTTTTCTTTAACATTAATCGAACCGAAATTATTTGACCGTTAATCG
* **
2487962 AACC-AAATTTTTTTTGGAAATTATTAACCGAACCAAATCAACCGATTTTTTTCTTTAACATTAA
1 AACCGAAA-TTTATTTAAAAATTATTAACCGAACCAAATCAACCGATTTTTTTCTTTAACATTAA
** *
2488026 TCGAACCAAAATTATTTGACTGTTAATCAAACCGAAATTTATTTGAAAATTATTAACTGAACCAA
65 TCGAACCAAAATTATTTGACCATTAATCAAACCGAAATTTATTTGAAAATTATTAACCGAACCAA
* *
2488091 ATCCACCGATTTTTTTTCTTTAACATTAATCGAACCGAAATTATTTGACCGTTAATCG
130 ATCAACCGATATTTTTTCTTTAACATTAATCGAACCGAAATTATTTGACCGTTAATCG
* *
2488149 AACCGAAATTTATTTAAAAATTATTAACCGAACCAAATTAACCGAATTTTTTTTCTTAAACATTA
1 AACCGAAATTTATTTAAAAATTATTAACCGAACCAAATCAACCG-A-TTTTTTTCTTTAACATTA
2488214 ATC
64 ATC
2488217 AAACTGAATT
Statistics
Matches: 229, Mismatches: 20, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
184 3 0.01
185 120 0.52
186 1 0.00
187 81 0.35
188 4 0.02
189 20 0.09
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.36
Consensus pattern (187 bp):
AACCGAAATTTATTTAAAAATTATTAACCGAACCAAATCAACCGATTTTTTTCTTTAACATTAAT
CGAACCAAAATTATTTGACCATTAATCAAACCGAAATTTATTTGAAAATTATTAACCGAACCAAA
TCAACCGATATTTTTTCTTTAACATTAATCGAACCGAAATTATTTGACCGTTAATCG
Found at i:2488132 original size:94 final size:93
Alignment explanation
Indices: 2487777--2488216 Score: 659
Period size: 93 Copynumber: 4.7 Consensus size: 93
2487767 CGTCAAATAA
* * * * *
2487777 AACCAAAATTTATTTAAAAATTATTAACCAAACCAAATCCATCGATTTTTTTCTTTAACATTAAT
1 AACCGAAATTTATTTGAAAATTATTAACCGAACCAAATCAACCGATTTTTTTCTTTAACATTAAT
*
2487842 CGAACCGAAATTATTTGACCATTAATCG
66 CGAACCGAAATTATTTGACCGTTAATCG
*
2487870 AACCGAAATTTATTTGAAAATTATTAACCGAACCAAATCAACC-AATTTTTTCTTTAACATTAAT
1 AACCGAAATTTATTTGAAAATTATTAACCGAACCAAATCAACCGATTTTTTTCTTTAACATTAAT
* *
2487934 CGAACTGAAATTATTTGATCGTTAATCG
66 CGAACCGAAATTATTTGACCGTTAATCG
* *
2487962 AACC-AAATTTTTTTTGGAAATTATTAACCGAACCAAATCAACCGATTTTTTTCTTTAACATTAA
1 AACCGAAA-TTTATTTGAAAATTATTAACCGAACCAAATCAACCGATTTTTTTCTTTAACATTAA
* * *
2488026 TCGAACCAAAATTATTTGACTGTTAATCA
65 TCGAACCGAAATTATTTGACCGTTAATCG
* *
2488055 AACCGAAATTTATTTGAAAATTATTAACTGAACCAAATCCACCGATTTTTTTTCTTTAACATTAA
1 AACCGAAATTTATTTGAAAATTATTAACCGAACCAAATCAACCGA-TTTTTTTCTTTAACATTAA
2488120 TCGAACCGAAATTATTTGACCGTTAATCG
65 TCGAACCGAAATTATTTGACCGTTAATCG
* * *
2488149 AACCGAAATTTATTTAAAAATTATTAACCGAACCAAATTAACCGAATTTTTTTTCTTAAACATTA
1 AACCGAAATTTATTTGAAAATTATTAACCGAACCAAATCAACCG-A-TTTTTTTCTTTAACATTA
2488214 ATC
64 ATC
2488217 AAACTGAATT
Statistics
Matches: 313, Mismatches: 29, Indels: 8
0.89 0.08 0.02
Matches are distributed among these distances:
91 3 0.01
92 82 0.26
93 118 0.38
94 88 0.28
95 22 0.07
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.36
Consensus pattern (93 bp):
AACCGAAATTTATTTGAAAATTATTAACCGAACCAAATCAACCGATTTTTTTCTTTAACATTAAT
CGAACCGAAATTATTTGACCGTTAATCG
Found at i:2488298 original size:26 final size:27
Alignment explanation
Indices: 2488269--2488326 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
2488259 TTTCTTTAAC
*
2488269 ATTAATCGAACCAA-AATTTCGGTTCG
1 ATTAATCGAACAAATAATTTCGGTTCG
**
2488295 ATTAA-CGGTCAAATAATTTCGGTTCG
1 ATTAATCGAACAAATAATTTCGGTTCG
2488321 ATTAAT
1 ATTAAT
2488327 GTTAAAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 5 0.19
26 22 0.81
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (27 bp):
ATTAATCGAACAAATAATTTCGGTTCG
Found at i:2488800 original size:30 final size:30
Alignment explanation
Indices: 2488764--2488820 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
2488754 AGAATATATA
2488764 AATATTAAGGACCAAATGTATAATTATTCT
1 AATATTAAGGACCAAATGTATAATTATTCT
*
2488794 AATATTAAGGTCCAAATGTATAATTAT
1 AATATTAAGGACCAAATGTATAATTAT
2488821 ACCAGTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.37
Consensus pattern (30 bp):
AATATTAAGGACCAAATGTATAATTATTCT
Found at i:2489270 original size:17 final size:17
Alignment explanation
Indices: 2489243--2489275 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2489233 AAACCATTTG
2489243 TGAGAAGAATAAGTAATT
1 TGAGAAGAATAA-TAATT
2489261 TGAG-AGAATAATAAT
1 TGAGAAGAATAATAAT
2489276 GACTAAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 7 0.47
18 4 0.27
ACGTcount: A:0.52, C:0.00, G:0.21, T:0.27
Consensus pattern (17 bp):
TGAGAAGAATAATAATT
Found at i:2489563 original size:29 final size:30
Alignment explanation
Indices: 2489514--2489571 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
2489504 TAAATAATAT
* *
2489514 ATAGTTTTTAGAAGACGGA-TTTTGAAAAC
1 ATAGTTTTTAAAAAACGGATTTTTGAAAAC
2489543 ATAGTTTTTAAAAAATC-GATTTTTGAAAA
1 ATAGTTTTTAAAAAA-CGGATTTTTGAAAA
2489572 TATGTATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.41, C:0.05, G:0.16, T:0.38
Consensus pattern (30 bp):
ATAGTTTTTAAAAAACGGATTTTTGAAAAC
Found at i:2489628 original size:37 final size:37
Alignment explanation
Indices: 2489543--2489871 Score: 200
Period size: 37 Copynumber: 8.6 Consensus size: 37
2489533 TTTTGAAAAC
* *
2489543 ATAGTTTTTAAAAA-ATCGATTTTTGAAAATATGTATATAAT
1 ATAG-TTTTAAAAACAT--ATTTTTGAAAACATATA-AT-AT
* * *
2489584 ATGGTTTTAAAAACATGTTTTTGAAAACGTATAATAT
1 ATAGTTTTAAAAACATATTTTTGAAAACATATAATAT
* ** * *
2489621 ATAGTTTTGAAAACATA-TTTAAAAAAAATATGATAT
1 ATAGTTTTAAAAACATATTTTTGAAAACATATAATAT
* * * ** * *
2489657 ATGGTTTTTTAAATC-GGTTTTGGAATACATATAATATT
1 ATAG-TTTTAAAAACATATTTTTGAAAACATATAATA-T
*
2489695 ATA-TAATTCTAAAAACACATTTTTGAAAACATATAATAT
1 ATAGT--TT-TAAAAACATATTTTTGAAAACATATAATAT
* * ** *
2489734 TTAGTTTTTTAAAATTTCTTTTTGAAAACATATATATAAT
1 ATAG-TTTTAAAAACATATTTTTGAAAACATATA-AT-AT
* * *
2489774 ATAATTTTTGAAAACGTATTTTTGAAAACATATAATAT
1 AT-AGTTTTAAAAACATATTTTTGAAAACATATAATAT
* * * *
2489812 ATAATCTTTTAAAA-ATATTTTTGAAAATATATAACAT
1 ATAGT-TTTAAAAACATATTTTTGAAAACATATAATAT
*
2489849 ATAGTTTTTAAAAACATTTTTTT
1 ATAG-TTTTAAAAACATATTTTT
2489872 TAATATATAC
Statistics
Matches: 222, Mismatches: 50, Indels: 35
0.72 0.16 0.11
Matches are distributed among these distances:
36 18 0.08
37 69 0.31
38 47 0.21
39 27 0.12
40 54 0.24
41 7 0.03
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.44
Consensus pattern (37 bp):
ATAGTTTTAAAAACATATTTTTGAAAACATATAATAT
Found at i:2489763 original size:38 final size:37
Alignment explanation
Indices: 2489601--2489869 Score: 175
Period size: 40 Copynumber: 7.1 Consensus size: 37
2489591 TAAAAACATG
* * *
2489601 TTTTTGAAAACGTATAATATAT-AGTTTTGAAAACATA
1 TTTTTGAAAACATATAATATATAATTTTTTAAAA-ATA
** * * ** ****
2489638 -TTTAAAAAAAATATGATATATGGTTTTTTAAATCGG
1 TTTTTGAAAACATATAATATATAATTTTTTAAAAATA
* * * * * *
2489674 TTTTGGAATACATATAATATTATATAATTCTAAAAACACA
1 TTTTTGAAAACATATAATA-TATA-ATTTTTTAAAA-ATA
* * * *
2489714 TTTTTGAAAACATATAATATTTAGTTTTTTAAAATTTC
1 TTTTTGAAAACATATAATATATAATTTTTTAAAA-ATA
* *
2489752 TTTTTGAAAACATATATATAATATAATTTTTGAAAACGTA
1 TTTTTGAAAACATATA-AT-ATATAATTTTTTAAAA-ATA
*
2489792 TTTTTGAAAACATATAATATATAATCTTTTAAAAATA
1 TTTTTGAAAACATATAATATATAATTTTTTAAAAATA
* * * *
2489829 TTTTTGAAAATATATAACATAT-AGTTTTTAAAAACA
1 TTTTTGAAAACATATAATATATAATTTTTTAAAAATA
2489865 TTTTT
1 TTTTT
2489870 TTTAATATAT
Statistics
Matches: 174, Mismatches: 51, Indels: 15
0.73 0.21 0.06
Matches are distributed among these distances:
36 32 0.18
37 42 0.24
38 40 0.23
39 13 0.07
40 47 0.27
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.44
Consensus pattern (37 bp):
TTTTTGAAAACATATAATATATAATTTTTTAAAAATA
Found at i:2489767 original size:78 final size:78
Alignment explanation
Indices: 2489674--2489845 Score: 204
Period size: 78 Copynumber: 2.2 Consensus size: 78
2489664 TTTAAATCGG
* * * * *
2489674 TTTTGGAATACATATAATATTATATAA-TTCTAAAAACACATTTTTGAAAACATATAATATTTAG
1 TTTTTGAAAACATATAATATAATATAATTTCTAAAAACACATTTTTGAAAACATATAATATATAA
* * *
2489738 TTTTTTAAAATTTC
66 TCTTTTAAAA-ATA
* * **
2489752 TTTTTGAAAACATAT-ATATAATATAATTTTTGAAAACGTATTTTTGAAAACATATAATATATAA
1 TTTTTGAAAACATATAATATAATATAATTTCTAAAAACACATTTTTGAAAACATATAATATATAA
2489816 TCTTTTAAAAATA
66 TCTTTTAAAAATA
*
2489829 TTTTTGAAAATATATAA
1 TTTTTGAAAACATATAA
2489846 CATATAGTTT
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
77 25 0.32
78 54 0.68
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44
Consensus pattern (78 bp):
TTTTTGAAAACATATAATATAATATAATTTCTAAAAACACATTTTTGAAAACATATAATATATAA
TCTTTTAAAAATA
Found at i:2489880 original size:38 final size:36
Alignment explanation
Indices: 2489695--2489880 Score: 140
Period size: 38 Copynumber: 4.9 Consensus size: 36
2489685 ATATAATATT
* * * *
2489695 ATATAATTCTAAAAACACATTTTTGAAAACATATAA
1 ATATAATTTTTAAAACATATTTTTGAAAATATATAA
* * ** *
2489731 TATTTAGTTTTTTAAAATTTCTTTTTGAAAACATATATATA
1 -ATATA-ATTTTTAAAACATATTTTTG-AAA-ATATATA-A
* *
2489772 ATATAATTTTTGAAAACGTATTTTTGAAAACATATAA
1 ATATAATTTTT-AAAACATATTTTTGAAAATATATAA
2489809 TATATAATCTTTTAAAA-ATATTTTTGAAAATATATAA
1 -ATATAAT-TTTTAAAACATATTTTTGAAAATATATAA
* * * *
2489846 CATATAGTTTTTAAAAACATTTTTTTTAATATATA
1 -ATATAATTTTT-AAAACATATTTTTGAAAATATA
2489881 CATATTATTA
Statistics
Matches: 118, Mismatches: 22, Indels: 17
0.75 0.14 0.11
Matches are distributed among these distances:
36 4 0.03
37 33 0.28
38 44 0.37
39 15 0.13
40 21 0.18
41 1 0.01
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (36 bp):
ATATAATTTTTAAAACATATTTTTGAAAATATATAA
Found at i:2491724 original size:17 final size:17
Alignment explanation
Indices: 2491704--2491758 Score: 58
Period size: 18 Copynumber: 3.2 Consensus size: 17
2491694 TTAATTTTCT
2491704 TTTAGTTATTTTA-TTTA
1 TTTA-TTATTTTACTTTA
* *
2491721 TTTAATATTTTATTTTA
1 TTTATTATTTTACTTTA
*
2491738 TTTCATTATTTAACTTTA
1 TTT-ATTATTTTACTTTA
2491756 TTT
1 TTT
2491759 TTGACTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
16 7 0.22
17 11 0.34
18 14 0.44
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.69
Consensus pattern (17 bp):
TTTATTATTTTACTTTA
Found at i:2491731 original size:25 final size:25
Alignment explanation
Indices: 2491703--2491750 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
2491693 TTTAATTTTC
*
2491703 TTTTA-GTTATTTTATTTATTTAATA
1 TTTTATGTTATTTCA-TTATTTAATA
*
2491728 TTTTATTTTATTTCATTATTTAA
1 TTTTATGTTATTTCATTATTTAA
2491751 CTTTATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 13 0.65
26 7 0.35
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (25 bp):
TTTTATGTTATTTCATTATTTAATA
Found at i:2494510 original size:20 final size:20
Alignment explanation
Indices: 2494485--2494536 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
2494475 ACGCGATATC
2494485 AAAATCGCAACGGTCAAAAG
1 AAAATCGCAACGGTCAAAAG
2494505 AAAATCGCAACGGTCAAAAG
1 AAAATCGCAACGGTCAAAAG
2494525 AAAATCGCAACG
1 AAAATCGCAACG
2494537 CGATATTCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.50, C:0.21, G:0.19, T:0.10
Consensus pattern (20 bp):
AAAATCGCAACGGTCAAAAG
Found at i:2494603 original size:49 final size:50
Alignment explanation
Indices: 2494527--2494626 Score: 148
Period size: 49 Copynumber: 2.0 Consensus size: 50
2494517 GTCAAAAGAA
* * *
2494527 AATCGCAACGCGATATTCCAAGAATCGCAATACTATTAAGAGAATCGCAAC
1 AATCGCAACGCGA-ATTCCAAGAATCGCAACACGATTAAGAAAATCGCAAC
*
2494578 AATCGCAACGCG-ATTCCAAGAATCGCAACGCGATTAAGAAAATCGCAAC
1 AATCGCAACGCGAATTCCAAGAATCGCAACACGATTAAGAAAATCGCAAC
2494627 GCGATTCAGA
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
49 33 0.73
51 12 0.27
ACGTcount: A:0.41, C:0.25, G:0.17, T:0.17
Consensus pattern (50 bp):
AATCGCAACGCGAATTCCAAGAATCGCAACACGATTAAGAAAATCGCAAC
Found at i:2494639 original size:20 final size:20
Alignment explanation
Indices: 2494578--2494640 Score: 92
Period size: 20 Copynumber: 3.1 Consensus size: 20
2494568 GAATCGCAAC
*
2494578 AATCGCAACGCGATTCCA-AG
1 AATCGCAACGCGATT-CAGAA
*
2494598 AATCGCAACGCGATTAAGAA
1 AATCGCAACGCGATTCAGAA
2494618 AATCGCAACGCGATTCAGAA
1 AATCGCAACGCGATTCAGAA
2494638 AAT
1 AAT
2494641 GAGTAAATTC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
19 1 0.03
20 38 0.97
ACGTcount: A:0.41, C:0.24, G:0.19, T:0.16
Consensus pattern (20 bp):
AATCGCAACGCGATTCAGAA
Found at i:2494747 original size:6 final size:6
Alignment explanation
Indices: 2494736--2494818 Score: 120
Period size: 6 Copynumber: 14.5 Consensus size: 6
2494726 TACACGTATT
2494736 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
* *
2494783 ACC-CG ACCACG ACCCCG ACCCCG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
2494819 CGAGACGAGA
Statistics
Matches: 74, Mismatches: 1, Indels: 5
0.93 0.01 0.06
Matches are distributed among these distances:
5 20 0.27
6 54 0.73
ACGTcount: A:0.28, C:0.55, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:2494759 original size:18 final size:18
Alignment explanation
Indices: 2494736--2494818 Score: 120
Period size: 17 Copynumber: 4.8 Consensus size: 18
2494726 TACACGTATT
2494736 ACCACGACCACGACCACG
1 ACCACGACCACGACCACG
2494754 ACCACGACCACGACCACG
1 ACCACGACCACGACCACG
2494772 ACC-CGACCACGACC-CG
1 ACCACGACCACGACCACG
* *
2494788 ACCACGACCCCGACCCCG
1 ACCACGACCACGACCACG
2494806 ACC-CGACC-CGACC
1 ACCACGACCACGACC
2494819 CGAGACGAGA
Statistics
Matches: 62, Mismatches: 1, Indels: 6
0.90 0.01 0.09
Matches are distributed among these distances:
16 10 0.16
17 26 0.42
18 26 0.42
ACGTcount: A:0.28, C:0.55, G:0.17, T:0.00
Consensus pattern (18 bp):
ACCACGACCACGACCACG
Found at i:2495341 original size:6 final size:6
Alignment explanation
Indices: 2495315--2495392 Score: 135
Period size: 6 Copynumber: 13.5 Consensus size: 6
2495305 TCTCGTCTCG
2495315 GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
2495360 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
2495393 AATACGTGTC
Statistics
Matches: 72, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 15 0.21
6 57 0.79
ACGTcount: A:0.00, C:0.17, G:0.53, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:2495497 original size:20 final size:20
Alignment explanation
Indices: 2495474--2495611 Score: 140
Period size: 20 Copynumber: 6.8 Consensus size: 20
2495464 AACTTTTTGG
2495474 AATCGCGTTGCGATTTTCTT
1 AATCGCGTTGCGATTTTCTT
2495494 AATCGCGTTGCGA--TTCTT
1 AATCGCGTTGCGATTTTCTT
2495512 GGAATCGCGTTGCGATTTTCTT
1 --AATCGCGTTGCGATTTTCTT
*
2495534 AATCGCGTTGCGATTTT-TGG
1 AATCGCGTTGCGATTTTCT-T
***
2495554 AATCGCGTTGCGATTCTTGGA
1 AATCGCGTTGCGATT-TTCTT
* **
2495575 AGATCGCGTTGCGGTTTTGAT
1 A-ATCGCGTTGCGATTTTCTT
2495596 -ATCGCGTTGCGATTTT
1 AATCGCGTTGCGATTTT
2495612 GTTGGTCATT
Statistics
Matches: 103, Mismatches: 7, Indels: 17
0.81 0.06 0.13
Matches are distributed among these distances:
18 5 0.05
19 16 0.16
20 58 0.56
21 6 0.06
22 18 0.17
ACGTcount: A:0.15, C:0.18, G:0.27, T:0.40
Consensus pattern (20 bp):
AATCGCGTTGCGATTTTCTT
Found at i:2495525 original size:40 final size:39
Alignment explanation
Indices: 2495468--2495611 Score: 200
Period size: 40 Copynumber: 3.6 Consensus size: 39
2495458 AAATGCAACT
2495468 TTTTGGAATCGCGTTGCGATTTTCTTAATCGCGTTGCGA
1 TTTTGGAATCGCGTTGCGATTTTCTTAATCGCGTTGCGA
2495507 TTCTTGGAATCGCGTTGCGATTTTCTTAATCGCGTTGCGA
1 TT-TTGGAATCGCGTTGCGATTTTCTTAATCGCGTTGCGA
*** *
2495547 TTTTTGGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGG
1 -TTTTGGAATCGCGTTGCGATT-TTCTTA-ATCGCGTTGCGA
2495589 TTTT-GATATCGCGTTGCGATTTT
1 TTTTGGA-ATCGCGTTGCGATTTT
2495612 GTTGGTCATT
Statistics
Matches: 96, Mismatches: 4, Indels: 9
0.88 0.04 0.08
Matches are distributed among these distances:
39 2 0.02
40 60 0.62
41 23 0.24
42 11 0.11
ACGTcount: A:0.15, C:0.17, G:0.27, T:0.41
Consensus pattern (39 bp):
TTTTGGAATCGCGTTGCGATTTTCTTAATCGCGTTGCGA
Found at i:2495546 original size:60 final size:62
Alignment explanation
Indices: 2495474--2495611 Score: 203
Period size: 60 Copynumber: 2.3 Consensus size: 62
2495464 AACTTTTTGG
* *
2495474 AATCGCGTTGCGATTTTCT-TAATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCGATTTTCTT
1 AATCGCGTTGCGATTTT-TGGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTCAT
* *
2495534 AATCGCGTTGCGATTTTTGGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGGTTTTGAT
1 AATCGCGTTGCGATTTTTGGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTCAT
2495596 -ATCGCGTTGCGATTTT
1 AATCGCGTTGCGATTTT
2495612 GTTGGTCATT
Statistics
Matches: 71, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
59 1 0.01
60 37 0.52
61 17 0.24
62 16 0.23
ACGTcount: A:0.15, C:0.18, G:0.27, T:0.40
Consensus pattern (62 bp):
AATCGCGTTGCGATTTTTGGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTCAT
Found at i:2498668 original size:21 final size:21
Alignment explanation
Indices: 2498643--2498683 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2498633 CATGAACAGT
* *
2498643 GCTACAGTGTACCAATGCACC
1 GCTACAATATACCAATGCACC
*
2498664 GCTACAATATACCGATGCAC
1 GCTACAATATACCAATGCAC
2498684 AAAAACATTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.32, G:0.17, T:0.20
Consensus pattern (21 bp):
GCTACAATATACCAATGCACC
Found at i:2499313 original size:22 final size:22
Alignment explanation
Indices: 2499285--2499345 Score: 86
Period size: 22 Copynumber: 2.8 Consensus size: 22
2499275 GGCATGTGAA
*
2499285 ATTTGTCCCGAATGACCTATGT
1 ATTTGTCCTGAATGACCTATGT
*
2499307 ATTTGTCCTGAATGACCTCTGT
1 ATTTGTCCTGAATGACCTATGT
**
2499329 AAATGTCCTGAATGACC
1 ATTTGTCCTGAATGACC
2499346 GCGTAGACCC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (22 bp):
ATTTGTCCTGAATGACCTATGT
Found at i:2501623 original size:14 final size:14
Alignment explanation
Indices: 2501604--2501651 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
2501594 AGTCAACGGG
2501604 TTGACTAGGACGAA
1 TTGACTAGGACGAA
* *
2501618 TTGACTCA-TACGAG
1 TTGACT-AGGACGAA
2501632 TTGACTAGGACGAA
1 TTGACTAGGACGAA
2501646 TTGACT
1 TTGACT
2501652 CAGTCTGAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 1 0.04
14 26 0.93
15 1 0.04
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (14 bp):
TTGACTAGGACGAA
Found at i:2510989 original size:61 final size:60
Alignment explanation
Indices: 2510906--2511020 Score: 144
Period size: 60 Copynumber: 1.9 Consensus size: 60
2510896 AAATAGTCCC
** * *
2510906 TTGACTATAGTGTTATTCTTTGTTGAGTTCCCCCGACTATTGAAAGTTACAAAATGATCCA
1 TTGACTATAGTGTTATTCTTTGTTGAG-TAACCCGACTAATAAAAGTTACAAAATGATCCA
*
2510967 TTGACTATAAG-G-TATTGCTTTGTTGAGTAATCCGACTAATAAAAGTTACAAAAT
1 TTGACTAT-AGTGTTATT-CTTTGTTGAGTAACCCGACTAATAAAAGTTACAAAAT
2511021 AGTCATCTGA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
60 26 0.55
61 19 0.40
62 2 0.04
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.37
Consensus pattern (60 bp):
TTGACTATAGTGTTATTCTTTGTTGAGTAACCCGACTAATAAAAGTTACAAAATGATCCA
Found at i:2511207 original size:28 final size:28
Alignment explanation
Indices: 2511175--2511250 Score: 134
Period size: 28 Copynumber: 2.7 Consensus size: 28
2511165 CTCTGTTTAT
*
2511175 ATTATGTCGTCGAGCCAATGCTTAAAAC
1 ATTATATCGTCGAGCCAATGCTTAAAAC
*
2511203 ATTATATCGTTGAGCCAATGCTTAAAAC
1 ATTATATCGTCGAGCCAATGCTTAAAAC
2511231 ATTATATCGTCGAGCCAATG
1 ATTATATCGTCGAGCCAATG
2511251 TTTGAAAGCA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (28 bp):
ATTATATCGTCGAGCCAATGCTTAAAAC
Found at i:2512450 original size:19 final size:19
Alignment explanation
Indices: 2512417--2512453 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2512407 ATGATCAACA
*
2512417 AAATCGCAATACGATCTCT
1 AAATCGCAACACGATCTCT
*
2512436 AAATCGCAACGCGATCTC
1 AAATCGCAACACGATCTC
2512454 CAGTATCGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.30, G:0.14, T:0.22
Consensus pattern (19 bp):
AAATCGCAACACGATCTCT
Found at i:2512636 original size:20 final size:20
Alignment explanation
Indices: 2512564--2512633 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
2512554 GAATATGTAA
2512564 ATCGCAACGCAATTCTGACT
1 ATCGCAACGCAATTCTGACT
2512584 ATCGCAACGCAATTCTGACT
1 ATCGCAACGCAATTCTGACT
*
2512604 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCAATTCTGACT
2512624 ATCGCAACGC
1 ATCGCAACGC
2512634 GATAATACAT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCAATTCTGACT
Found at i:2512686 original size:21 final size:21
Alignment explanation
Indices: 2512624--2512678 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
2512614 GATTCTGACT
*
2512624 ATCGCAACGCGATAATACATA
1 ATCGCAACGCGATAATACAAA
2512645 ATCGCAACGCGATAATACAAA
1 ATCGCAACGCGATAATACAAA
*
2512666 ATCGCAATGCGAT
1 ATCGCAACGCGAT
2512679 TTTCCAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.42, C:0.24, G:0.16, T:0.18
Consensus pattern (21 bp):
ATCGCAACGCGATAATACAAA
Found at i:2513194 original size:22 final size:21
Alignment explanation
Indices: 2513169--2513225 Score: 64
Period size: 19 Copynumber: 2.7 Consensus size: 21
2513159 ACTATCGCAA
*
2513169 CAACACGTTTTTCAAACTCTCG
1 CAACAC-TTTTTCAAACTATCG
*
2513191 CAACACATTTT--AACTATCG
1 CAACACTTTTTCAAACTATCG
2513210 CAACACATTTTTCAAA
1 CAACAC-TTTTTCAAA
2513226 ATCGCGTTGC
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 13 0.45
20 4 0.14
21 4 0.14
22 8 0.28
ACGTcount: A:0.35, C:0.28, G:0.05, T:0.32
Consensus pattern (21 bp):
CAACACTTTTTCAAACTATCG
Found at i:2513210 original size:19 final size:19
Alignment explanation
Indices: 2513183--2513220 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
2513173 ACGTTTTTCA
*
2513183 AACTCTCGCAACACATTTT
1 AACTATCGCAACACATTTT
2513202 AACTATCGCAACACATTTT
1 AACTATCGCAACACATTTT
2513221 TCAAAATCGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.29, G:0.05, T:0.32
Consensus pattern (19 bp):
AACTATCGCAACACATTTT
Found at i:2517073 original size:36 final size:37
Alignment explanation
Indices: 2517012--2517083 Score: 87
Period size: 36 Copynumber: 2.0 Consensus size: 37
2517002 TAATCACCAT
2517012 AGGATTATAATATTAAAAAAATAAAAT-ATAATAAAA
1 AGGATTATAATATTAAAAAAATAAAATCATAATAAAA
* *
2517048 AGGATT-TAATA-TAAAAATATTTAAAATCATTATAAA
1 AGGATTATAATATTAAAAA-A-ATAAAATCATAATAAA
2517084 TATATATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
34 6 0.19
35 6 0.19
36 12 0.39
37 7 0.23
ACGTcount: A:0.61, C:0.01, G:0.06, T:0.32
Consensus pattern (37 bp):
AGGATTATAATATTAAAAAAATAAAATCATAATAAAA
Found at i:2520512 original size:11 final size:11
Alignment explanation
Indices: 2520496--2520534 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
2520486 TTCAGATACT
2520496 TATATATAAAA
1 TATATATAAAA
2520507 TATATATAAAA
1 TATATATAAAA
*
2520518 TATATAT-ATA
1 TATATATAAAA
2520528 TATATAT
1 TATATAT
2520535 GTTGTCACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
10 9 0.33
11 18 0.67
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
TATATATAAAA
Found at i:2520514 original size:13 final size:14
Alignment explanation
Indices: 2520496--2520534 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
2520486 TTCAGATACT
2520496 TATATATAAA-ATA
1 TATATATAAATATA
2520509 TATATA-AAATATA
1 TATATATAAATATA
*
2520522 TATATATATATAT
1 TATATATAAATAT
2520535 GTTGTCACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 3 0.13
13 15 0.65
14 5 0.22
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TATATATAAATATA
Found at i:2527747 original size:39 final size:39
Alignment explanation
Indices: 2527665--2527747 Score: 89
Period size: 39 Copynumber: 2.1 Consensus size: 39
2527655 TTTTAATTAT
* * * * *
2527665 TATTATTATTAAATAAAATATATTTATATATATATATAT
1 TATTATCATTAAATAAAATATAATAATATATATATAAAA
2527704 TATTATCATTAAATAAAATAATAATAATA-ATA-ATAAAAA
1 TATTATCATTAAATAAAAT-ATAATAATATATATAT-AAAA
2527743 TATTA
1 TATTA
2527748 CAAAGCCCAA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
38 2 0.05
39 28 0.76
40 7 0.19
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (39 bp):
TATTATCATTAAATAAAATATAATAATATATATATAAAA
Found at i:2528414 original size:13 final size:13
Alignment explanation
Indices: 2528396--2528421 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2528386 GCCACCGTTT
2528396 ACGGTGGCCGGCG
1 ACGGTGGCCGGCG
2528409 ACGGTGGCCGGCG
1 ACGGTGGCCGGCG
2528422 GCGAAGCACG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.31, G:0.54, T:0.08
Consensus pattern (13 bp):
ACGGTGGCCGGCG
Found at i:2529011 original size:12 final size:12
Alignment explanation
Indices: 2528981--2529022 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
2528971 ATTACTTTTA
2528981 TATTTTAATTAT
1 TATTTTAATTAT
**
2528993 TGCTTTAATTAT
1 TATTTTAATTAT
2529005 TATTTT-ATTAT
1 TATTTTAATTAT
2529016 TATTTTA
1 TATTTTA
2529023 GTCATATAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
11 11 0.44
12 14 0.56
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (12 bp):
TATTTTAATTAT
Found at i:2529897 original size:24 final size:22
Alignment explanation
Indices: 2529849--2529907 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 22
2529839 CATATATTTA
2529849 ATTTATAAT-TT-TTTTTATAT
1 ATTTATAATATTATTTTTATAT
2529869 A--TATACATATTATTTTTATAGT
1 ATTTATA-ATATTATTTTTATA-T
2529891 ATTTATATATATTATTT
1 ATTTATA-ATATTATTT
2529908 ATATTACAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
18 4 0.12
19 2 0.06
20 3 0.09
21 8 0.25
22 2 0.06
24 13 0.41
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (22 bp):
ATTTATAATATTATTTTTATAT
Found at i:2529900 original size:22 final size:21
Alignment explanation
Indices: 2529849--2529911 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
2529839 CATATATTTA
*
2529849 ATTTATA-ATTTTTTTTATAT
1 ATTTATATATTATTTTTATAT
* *
2529869 ATATACATATTATTTTTATAGT
1 ATTTATATATTATTTTTATA-T
2529891 ATTTATATA-TATTATTTATAT
1 ATTTATATATTATT-TTTATAT
2529912 TACAAGTATT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
20 5 0.14
21 16 0.46
22 14 0.40
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (21 bp):
ATTTATATATTATTTTTATAT
Found at i:2534253 original size:2 final size:2
Alignment explanation
Indices: 2534246--2534271 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2534236 TTATCCTTTA
2534246 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2534272 CCTTTGTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2540327 original size:76 final size:76
Alignment explanation
Indices: 2540201--2541370 Score: 2268
Period size: 76 Copynumber: 15.4 Consensus size: 76
2540191 TTATTTCCCA
2540201 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2540266 AGCCTTCGGGT
66 AGCCTTCGGGT
2540277 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2540342 AGCCTTCGGGT
66 AGCCTTCGGGT
2540353 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2540418 AGCCTTCGGGT
66 AGCCTTCGGGT
*
2540429 CATTTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2540494 AGCCTTCGGGT
66 AGCCTTCGGGT
*
2540505 CATCTGTAAGTCCTTCAGTACATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2540570 AGCCTTCGGGT
66 AGCCTTCGGGT
2540581 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2540646 AGCCTTCGGGT
66 AGCCTTCGGGT
*
2540657 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGCGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2540722 AGCCTTCGGGT
66 AGCCTTCGGGT
2540733 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2540798 AGCCTTCGGGT
66 AGCCTTCGGGT
*
2540809 CATCTGTAAGTCCTTCCGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2540874 AGCCTTCGGGT
66 AGCCTTCGGGT
*
2540885 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGAGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2540950 AGCCTTCGGGT
66 AGCCTTCGGGT
* *
2540961 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGACTTCGGTAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2541026 AGCCTTCGGGT
66 AGCCTTCGGGT
*
2541037 CATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2541102 AGCCTTCGGGT
66 AGCCTTCGGGT
2541113 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2541178 AGCCTTCGGGT
66 AGCCTTCGGGT
2541189 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2541254 AGCCTTCGGGT
66 AGCCTTCGGGT
2541265 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
2541330 AGCCTTCGGGT
66 AGCCTTCGGGT
2541341 CATCTGTAAGTCCTTCAGTGCATGATGTTT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTT
2541371 TCAATATTTC
Statistics
Matches: 1078, Mismatches: 16, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 1078 1.00
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGT
Found at i:2542662 original size:12 final size:12
Alignment explanation
Indices: 2542632--2542673 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
2542622 ATTACTTTTA
2542632 TATTTTAATTAT
1 TATTTTAATTAT
**
2542644 TGCTTTAATTAT
1 TATTTTAATTAT
2542656 TATTTT-ATTAT
1 TATTTTAATTAT
2542667 TATTTTA
1 TATTTTA
2542674 GTCATATAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
11 11 0.44
12 14 0.56
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (12 bp):
TATTTTAATTAT
Found at i:2546118 original size:15 final size:15
Alignment explanation
Indices: 2546103--2546155 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
2546093 CCGGTTTCGG
*
2546103 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACC-G-A
*
2546120 TTTTTAAAAAACCGA
1 TTTTAAAAAAACCGA
*
2546135 TTATAAAAAAACCGA
1 TTTTAAAAAAACCGA
2546150 TTTTAA
1 TTTTAA
2546156 TATTCCAGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
15 18 0.58
16 1 0.03
17 12 0.39
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.34
Consensus pattern (15 bp):
TTTTAAAAAAACCGA
Found at i:2546506 original size:13 final size:13
Alignment explanation
Indices: 2546485--2546539 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
2546475 AAGTTCGATA
*
2546485 AATTCAAATACTT
1 AATTGAAATACTT
2546498 AATTGAAATACTT
1 AATTGAAATACTT
* *
2546511 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
2546525 AATTGAAATACTT
1 AATTGAAATACTT
2546538 AA
1 AA
2546540 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:2546621 original size:32 final size:33
Alignment explanation
Indices: 2546525--2546623 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
2546515 AACTCAACAT
* * *
2546525 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
2546558 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
2546591 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
2546623 A
1 A
2546624 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:2546642 original size:21 final size:21
Alignment explanation
Indices: 2546618--2546657 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2546608 ACTTCAAGTT
2546618 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
2546639 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
2546658 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:2554170 original size:76 final size:76
Alignment explanation
Indices: 2553904--2554810 Score: 1606
Period size: 76 Copynumber: 12.0 Consensus size: 76
2553894 AGCTAATGCT
*
2553904 TTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATG
1 TTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATG
2553969 TTTT-AAAGCC
66 TTTTCAAAGCC
*
2553979 TTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATG
1 TTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATG
2554044 TTTT-AAAGCC
66 TTTTCAAAGCC
*
2554054 TTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATG
1 TTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATG
2554119 TTTTCAAAGCC
66 TTTTCAAAGCC
*
2554130 TTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATG
1 TTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATG
2554195 TTTT-AAAGCC
66 TTTTCAAAGCC
* * *
2554205 TTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTTCAAAAAGCCTTCGGGATCTTTTTAATG
1 TTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATG
2554270 TTTT-AAAGCC
66 TTTTCAAAGCC
* * * *
2554280 TTAGGGTCATCTGTAAGTCATGCAGTGCATGATGTTTCTAAAAAGCCTTCGAGATCTTTTTGATG
1 TTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATG
2554345 TTTTCAAAGCC
66 TTTTCAAAGCC
2554356 TTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATG
1 TTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATG
2554421 TTTTCAAAGCC
66 TTTTCAAAGCC
2554432 TTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATG
1 TTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATG
2554497 TTTTCAAAGCC
66 TTTTCAAAGCC
* * *
2554508 TTAGGGTCATATGTAAGTCCTTTAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCCTTTTGATG
1 TTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATG
2554573 TTTTCAAAGCC
66 TTTTCAAAGCC
* *
2554584 TTAGGGTAATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGGTCTTTTTGATG
1 TTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATG
*
2554649 TTTTTAAAGCC
66 TTTTCAAAGCC
*
2554660 TTAGGGTCATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATG
1 TTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATG
2554725 TTTTCAAAGCC
66 TTTTCAAAGCC
*
2554736 TTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGGTCTTTTTGATG
1 TTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATG
*
2554801 TTTTTAAAGC
66 TTTTCAAAGC
2554811 TTCTAGAAGA
Statistics
Matches: 797, Mismatches: 33, Indels: 3
0.96 0.04 0.00
Matches are distributed among these distances:
75 283 0.36
76 514 0.64
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.37
Consensus pattern (76 bp):
TTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATG
TTTTCAAAGCC
Found at i:2555066 original size:14 final size:14
Alignment explanation
Indices: 2555047--2555105 Score: 64
Period size: 14 Copynumber: 4.2 Consensus size: 14
2555037 AAAGAAAAGG
*
2555047 AACCGACGACAGCA
1 AACCGACGACAACA
2555061 AACCGACGACAACA
1 AACCGACGACAACA
* *
2555075 GACGGACGACAACA
1 AACCGACGACAACA
* * *
2555089 GACGGACAACAACA
1 AACCGACGACAACA
2555103 AAC
1 AAC
2555106 AAAAAAAAGA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 40 1.00
ACGTcount: A:0.47, C:0.32, G:0.20, T:0.00
Consensus pattern (14 bp):
AACCGACGACAACA
Found at i:2555398 original size:13 final size:13
Alignment explanation
Indices: 2555380--2555404 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2555370 CACCGTTCAC
2555380 GGTGGCCGGCGGT
1 GGTGGCCGGCGGT
2555393 GGTGGCCGGCGG
1 GGTGGCCGGCGG
2555405 CGGAGTACGG
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:0.24, G:0.64, T:0.12
Consensus pattern (13 bp):
GGTGGCCGGCGGT
Found at i:2561213 original size:2 final size:2
Alignment explanation
Indices: 2561206--2561231 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2561196 TTATCCTTTA
2561206 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2561232 CCTTTGTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2564030 original size:114 final size:114
Alignment explanation
Indices: 2563826--2564032 Score: 324
Period size: 114 Copynumber: 1.8 Consensus size: 114
2563816 TGCCACGTTC
* * * *
2563826 TCATTGTAGAAATAAGGAGCCCCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGG
1 TCATTGTAGAAATAAGGAGACCCAATAGCATATTCTGGAAATATTCTTTGAGTTATCTGATATGG
* *
2563891 TTTAGTATGAACCCCAAAAACAATCATTAGATTTGAAAGATAAATTTGT
66 TTCAGTAGGAACCCCAAAAACAATCATTAGATTTGAAAGATAAATTTGT
*
2563940 TCATTGTAGAAATAAGGAGACCCAATAGCATATTCTGGAAATGTTCTTTGAGTTATCTGATATGG
1 TCATTGTAGAAATAAGGAGACCCAATAGCATATTCTGGAAATATTCTTTGAGTTATCTGATATGG
* * *
2564005 TTCGGTAGGAACCCCAGAAATAATCATT
66 TTCAGTAGGAACCCCAAAAACAATCATT
2564033 GGAATAAGAA
Statistics
Matches: 83, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
114 83 1.00
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (114 bp):
TCATTGTAGAAATAAGGAGACCCAATAGCATATTCTGGAAATATTCTTTGAGTTATCTGATATGG
TTCAGTAGGAACCCCAAAAACAATCATTAGATTTGAAAGATAAATTTGT
Found at i:2566540 original size:22 final size:22
Alignment explanation
Indices: 2566470--2566549 Score: 70
Period size: 22 Copynumber: 3.6 Consensus size: 22
2566460 TACATCTGCA
* *
2566470 CTTTTTAAAGATAATAGATTCT
1 CTTTTCAAAGATGATAGATTCT
** * * * *
2566492 CACTTCAGAGATGACAAATTTT
1 CTTTTCAAAGATGATAGATTCT
* *
2566514 ATTTTTAAAGATGATAGATTCT
1 CTTTTCAAAGATGATAGATTCT
2566536 CTTTTCAAAGATGA
1 CTTTTCAAAGATGA
2566550 AAGCTTTATG
Statistics
Matches: 40, Mismatches: 18, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.40
Consensus pattern (22 bp):
CTTTTCAAAGATGATAGATTCT
Found at i:2567326 original size:76 final size:76
Alignment explanation
Indices: 2567227--2568354 Score: 1894
Period size: 76 Copynumber: 14.9 Consensus size: 76
2567217 CTATTTCTCA
*
2567227 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCGA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
2567292 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
2567303 CATCTGTAAGTCCTTCATTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTT-AA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
2567367 AGCCTTAGGGT
66 AGCCTTAGGGT
*
2567378 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTT-AA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
2567442 AGCCTTAGGGT
66 AGCCTTAGGGT
*
2567453 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTT-AA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
2567517 AGCCTTAGGGT
66 AGCCTTAGGGT
*
2567528 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
2567593 AGCCTTAGGGT
66 AGCCTTAGGGT
*
2567604 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTT-AA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
2567668 AGCCTTAGGGT
66 AGCCTTAGGGT
* * *
2567679 CATCTGTAAGTCCTGCAGTGCATGATGTTTTCAAAAAGCCTTCGGGATCTTTTTAATGTTTT-AA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
2567743 AGCCTTAGGGT
66 AGCCTTAGGGT
* * * *
2567754 CATCTGTAAGTCATGCAGTGCATGATGTTTCTAAAAAGCCTTCGAGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
2567819 AGCCTTAGGGT
66 AGCCTTAGGGT
*
2567830 CATTTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
2567895 AGCCTTAGGGT
66 AGCCTTAGGGT
2567906 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
2567971 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
2567982 CATCTGTAAGTCCTTTAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCCTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
2568047 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
2568058 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGGTCTTTTTGATGTTTTTAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
2568123 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
2568134 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTT-A
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAAGCCTTCGGGATCTTTTTGATGTTTTCA
2568198 AAGCCTTAGGGT
65 AAGCCTTAGGGT
*
2568210 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCC-AAAAAGCCTTCGGGATCTTTTTGATGTTTTCA
* *
2568274 AAGTCTTCGGGT
65 AAGCCTTAGGGT
** * *
2568286 CATCTGTAAGTCCTGT-AGTGCATGATGTTTTTAAAAAAAAGCCTTCGGGAGCTTTTTTATGTTT
1 CATCTGTAAGTCCT-TCAGTGCATGATG--TTT-CCAAAAAGCCTTCGGGATCTTTTTGATGTTT
2568350 TCAAA
62 TCAAA
2568355 ACCCTTCAAT
Statistics
Matches: 1005, Mismatches: 38, Indels: 15
0.95 0.04 0.01
Matches are distributed among these distances:
75 362 0.36
76 579 0.58
77 29 0.03
78 33 0.03
79 2 0.00
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.37
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:2568603 original size:18 final size:19
Alignment explanation
Indices: 2568541--2568610 Score: 74
Period size: 18 Copynumber: 3.6 Consensus size: 19
2568531 TTAAAATTAT
2568541 TATTATTATTATTA-TAAA
1 TATTATTATTATTATTAAA
2568559 TATTATTATTA-TATTATATA
1 TATTATTATTATTATTA-A-A
2568579 TATATATTATATTATTATTAAA
1 TAT-TA-T-TATTATTATTAAA
2568601 TA-TATTATTA
1 TATTATTATTA
2568611 CAAGGCCCAA
Statistics
Matches: 45, Mismatches: 0, Indels: 14
0.76 0.00 0.24
Matches are distributed among these distances:
17 2 0.04
18 18 0.40
19 2 0.04
20 6 0.13
21 2 0.04
22 4 0.09
23 6 0.13
24 5 0.11
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TATTATTATTATTATTAAA
Found at i:2568606 original size:15 final size:16
Alignment explanation
Indices: 2568544--2568610 Score: 81
Period size: 15 Copynumber: 4.5 Consensus size: 16
2568534 AAATTATTAT
2568544 TATTATTATTATAA-A
1 TATTATTATTATAATA
*
2568559 TATTATTATTATATTA
1 TATTATTATTATAATA
*
2568575 TA-TA-TA-TATATTA
1 TATTATTATTATAATA
2568588 TATTATTATTA-AATA
1 TATTATTATTATAATA
2568603 TATTATTA
1 TATTATTA
2568611 CAAGGCCCAA
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
13 9 0.20
14 4 0.09
15 28 0.61
16 5 0.11
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TATTATTATTATAATA
Found at i:2568610 original size:3 final size:3
Alignment explanation
Indices: 2568536--2568598 Score: 69
Period size: 3 Copynumber: 21.3 Consensus size: 3
2568526 TTAAATTAAA
* *
2568536 ATT ATT ATT ATT ATT ATT ATA AAT ATT ATT ATT A-T ATT A-T ATAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T
2568580 ATAT ATT A-T ATT ATT ATT A
1 AT-T ATT ATT ATT ATT ATT A
2568599 AATATATTAT
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
2 6 0.12
3 39 0.75
4 7 0.13
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:2569036 original size:14 final size:14
Alignment explanation
Indices: 2569017--2569075 Score: 64
Period size: 14 Copynumber: 4.2 Consensus size: 14
2569007 AAAGAAAAGG
2569017 AACCGACGACAACA
1 AACCGACGACAACA
2569031 AACCGACGACAACA
1 AACCGACGACAACA
* * *
2569045 GACGGATGACAACA
1 AACCGACGACAACA
* * *
2569059 GACGGACAACAACA
1 AACCGACGACAACA
2569073 AAC
1 AAC
2569076 AGAAAAAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 39 1.00
ACGTcount: A:0.49, C:0.31, G:0.19, T:0.02
Consensus pattern (14 bp):
AACCGACGACAACA
Found at i:2579813 original size:15 final size:16
Alignment explanation
Indices: 2579793--2579822 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2579783 ATTTTTCTTC
2579793 TTCTTTTTCT-TTTAT
1 TTCTTTTTCTATTTAT
2579808 TTCTTTTTCTATTTA
1 TTCTTTTTCTATTTA
2579823 AATCTAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (16 bp):
TTCTTTTTCTATTTAT
Found at i:2582730 original size:25 final size:24
Alignment explanation
Indices: 2582695--2582751 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 24
2582685 AACTTAATAC
2582695 TAAAATAGGTATTTCACAAATCTA
1 TAAAATAGGTATTTCACAAATCTA
*
2582719 TAAAATTAGGTATTTCACCAATC--
1 TAAAA-TAGGTATTTCACAAATCTA
2582742 TAAAATAGGT
1 TAAAATAGGT
2582752 TTTTTTTATA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 5 0.16
23 5 0.16
24 5 0.16
25 16 0.52
ACGTcount: A:0.44, C:0.12, G:0.11, T:0.33
Consensus pattern (24 bp):
TAAAATAGGTATTTCACAAATCTA
Found at i:2582881 original size:27 final size:26
Alignment explanation
Indices: 2582845--2582902 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
2582835 ATTAGGCCCC
*
2582845 ATTTTGATTTATG-AAAATATTCTTTTT
1 ATTTTCATTTATGAAAAATA-T-TTTTT
* *
2582872 ATTTTCATTTCTTAAAAATATTTTTT
1 ATTTTCATTTATGAAAAATATTTTTT
2582898 ATTTT
1 ATTTT
2582903 ATATTTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 10 0.37
27 11 0.41
28 6 0.22
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.62
Consensus pattern (26 bp):
ATTTTCATTTATGAAAAATATTTTTT
Found at i:2582912 original size:26 final size:28
Alignment explanation
Indices: 2582858--2582916 Score: 79
Period size: 26 Copynumber: 2.2 Consensus size: 28
2582848 TTGATTTATG
2582858 AAAATATTCTTTTTATTTTCATTTCTTA
1 AAAATATTCTTTTTATTTTCATTTCTTA
*
2582886 AAAATA-T-TTTTTATTTT-ATATTTTTA
1 AAAATATTCTTTTTATTTTCAT-TTCTTA
2582912 AAAAT
1 AAAAT
2582917 TAAGAAACAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 2 0.07
26 20 0.69
27 1 0.03
28 6 0.21
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (28 bp):
AAAATATTCTTTTTATTTTCATTTCTTA
Found at i:2583163 original size:14 final size:14
Alignment explanation
Indices: 2583144--2583190 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
2583134 ATTTTGTTTT
2583144 AAATTTATTTAATG
1 AAATTTATTTAATG
*
2583158 AAATTTA-TT-ATT
1 AAATTTATTTAATG
*
2583170 AGAAGTTATTTAATG
1 A-AATTTATTTAATG
2583185 AAATTT
1 AAATTT
2583191 TGCAAAACTT
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
12 3 0.12
13 7 0.27
14 13 0.50
15 3 0.12
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.49
Consensus pattern (14 bp):
AAATTTATTTAATG
Found at i:2583687 original size:30 final size:30
Alignment explanation
Indices: 2583636--2583693 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
2583626 TTGATGGCCT
* *
2583636 TAATTGCTTTTTTAGTTAAGTTCGAAGACG
1 TAATTGATTTTTTAGTAAAGTTCGAAGACG
*
2583666 TAATTGATTATTTTAG-AAAGTTTGAAGA
1 TAATTGATT-TTTTAGTAAAGTTCGAAGA
2583694 TTTATTTAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 18 0.75
31 6 0.25
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (30 bp):
TAATTGATTTTTTAGTAAAGTTCGAAGACG
Found at i:2586797 original size:21 final size:20
Alignment explanation
Indices: 2586773--2586829 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 20
2586763 ATTTTAAATT
2586773 TTATTTTTTTAAATAAAATAA
1 TTATTTTTTTAAATAAAA-AA
*
2586794 TTATTATATTTATAA-AAAAAA
1 TTATT-TTTTTA-AATAAAAAA
2586815 TTATTTCTTTTAAAT
1 TTATTT-TTTTAAAT
2586830 TACAAAAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
20 3 0.10
21 16 0.53
22 9 0.30
23 2 0.07
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (20 bp):
TTATTTTTTTAAATAAAAAA
Found at i:2586809 original size:24 final size:23
Alignment explanation
Indices: 2586769--2586820 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
2586759 CGTAATTTTA
* * *
2586769 AATTTTATTTTTTTAAATAAAAT
1 AATTTTATATTTATAAAAAAAAT
2586792 AATTATTATATTTATAAAAAAAAT
1 AATT-TTATATTTATAAAAAAAAT
*
2586816 TATTT
1 AATTT
2586821 CTTTTAAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AATTTTATATTTATAAAAAAAAT
Found at i:2589994 original size:174 final size:174
Alignment explanation
Indices: 2589697--2590045 Score: 644
Period size: 174 Copynumber: 2.0 Consensus size: 174
2589687 GCGAGAGATT
*
2589697 TGCGTTTTGGTTCTCCAGTTTCAAAAACACTTAATTTGGTCCTCTGAATCGATTATTGAACCTGA
1 TGCGTTTTGGTTCTCCAGTTTCAAAAACACTTAATTTGGTCATCTGAATCGATTATTGAACCTGA
* *
2589762 AATTCTTGTAAATTGACCCTTGAGTTTATTTTGTTTTCAATTTAATCCCTACTATTATTATATAC
66 AATCCTTGTAAATTGACCCTTGAGTTTATTTCGTTTTCAATTTAATCCCTACTATTATTATATAC
2589827 TATATTTTCATTATTATTATATTTTACTCCCTTATTTATATATA
131 TATATTTTCATTATTATTATATTTTACTCCCTTATTTATATATA
**
2589871 TGCGTTTTGGTTCTCCAGTTTCAAAAACGTTTAATTTGGTCATCTGAATCGATTATTGAACCTGA
1 TGCGTTTTGGTTCTCCAGTTTCAAAAACACTTAATTTGGTCATCTGAATCGATTATTGAACCTGA
*
2589936 AATCCTTGTAAATTGACCCTTGAGTTTATTTCGTTTTCAATTTAATCCCTATTATTATTATATAC
66 AATCCTTGTAAATTGACCCTTGAGTTTATTTCGTTTTCAATTTAATCCCTACTATTATTATATAC
2590001 TATATTTTCATTATTATTATATTTTACTCCCTTATTTATATATA
131 TATATTTTCATTATTATTATATTTTACTCCCTTATTTATATATA
2590045 T
1 T
2590046 ATATCTTATG
Statistics
Matches: 169, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
174 169 1.00
ACGTcount: A:0.27, C:0.16, G:0.09, T:0.48
Consensus pattern (174 bp):
TGCGTTTTGGTTCTCCAGTTTCAAAAACACTTAATTTGGTCATCTGAATCGATTATTGAACCTGA
AATCCTTGTAAATTGACCCTTGAGTTTATTTCGTTTTCAATTTAATCCCTACTATTATTATATAC
TATATTTTCATTATTATTATATTTTACTCCCTTATTTATATATA
Done.