Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008275.1 Hibiscus syriacus cultivar Beakdansim tig00110933_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: 1991061
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 8
Found at i:283505 original size:3 final size:3
Alignment explanation
Indices: 283497--283590 Score: 66
Period size: 3 Copynumber: 31.7 Consensus size: 3
283487 CTGTAATATG
* * * *
283497 TAA TAA TAA TATT TAT TAA TAA AAA T-A TAA TAA TAA TAG TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * * *
283542 TTA TAA TAA TTA TAA CAA TTA TAA AAA TTA TAA TAA TAA AAA TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
283589 TA
1 TA
283591 GACAAAAATT
Statistics
Matches: 68, Mismatches: 20, Indels: 6
0.72 0.21 0.06
Matches are distributed among these distances:
2 4 0.06
3 62 0.91
4 2 0.03
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:291203 original size:4 final size:4
Alignment explanation
Indices: 291179--291217 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
291169 TTCTGGTATG
* * *
291179 ATAC ATGC ATAC ATAT GTAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
291218 TCGGGATAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.46, C:0.21, G:0.05, T:0.28
Consensus pattern (4 bp):
ATAC
Found at i:291205 original size:16 final size:17
Alignment explanation
Indices: 291175--291209 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
291165 AACTTTCTGG
*
291175 TATGATACATGCATACA
1 TATGATACATACATACA
291192 TATG-TACATACATACA
1 TATGATACATACATACA
291208 TA
1 TA
291210 CATACATATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.31
Consensus pattern (17 bp):
TATGATACATACATACA
Found at i:297261 original size:147 final size:147
Alignment explanation
Indices: 296994--297287 Score: 588
Period size: 147 Copynumber: 2.0 Consensus size: 147
296984 AAATTGAAAC
296994 ATAAACTAAATGTTAAATATGATTTTGAAATAAACTTAGGTGCCAAAAAATAATAATAGTAATAG
1 ATAAACTAAATGTTAAATATGATTTTGAAATAAACTTAGGTGCCAAAAAATAATAATAGTAATAG
297059 TTTAAATACTAAACATGTAGTTTATCCATAATTATACATCATGAATCAAAATAATAACACTTTAT
66 TTTAAATACTAAACATGTAGTTTATCCATAATTATACATCATGAATCAAAATAATAACACTTTAT
297124 GTAAGTGGATTTTCTTG
131 GTAAGTGGATTTTCTTG
297141 ATAAACTAAATGTTAAATATGATTTTGAAATAAACTTAGGTGCCAAAAAATAATAATAGTAATAG
1 ATAAACTAAATGTTAAATATGATTTTGAAATAAACTTAGGTGCCAAAAAATAATAATAGTAATAG
297206 TTTAAATACTAAACATGTAGTTTATCCATAATTATACATCATGAATCAAAATAATAACACTTTAT
66 TTTAAATACTAAACATGTAGTTTATCCATAATTATACATCATGAATCAAAATAATAACACTTTAT
297271 GTAAGTGGATTTTCTTG
131 GTAAGTGGATTTTCTTG
297288 TGATAGGGTT
Statistics
Matches: 147, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
147 147 1.00
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.35
Consensus pattern (147 bp):
ATAAACTAAATGTTAAATATGATTTTGAAATAAACTTAGGTGCCAAAAAATAATAATAGTAATAG
TTTAAATACTAAACATGTAGTTTATCCATAATTATACATCATGAATCAAAATAATAACACTTTAT
GTAAGTGGATTTTCTTG
Found at i:298371 original size:21 final size:20
Alignment explanation
Indices: 298285--298442 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
298275 AAATGACCAA
**
298285 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
298304 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
298324 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
298344 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
298365 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
298386 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
298406 CAAGAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
298427 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
298443 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 42 0.40
21 46 0.44
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:298452 original size:20 final size:20
Alignment explanation
Indices: 298405--298458 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
298395 ATTGCGATTT
*
298405 TCAAGAATCGCAACGCGAATA
1 TCAA-AATCGCAACGCGAACA
*
298426 TGAAAATCGCAACGCGAACA
1 TCAAAATCGCAACGCGAACA
298446 -CATAAATCGCAAC
1 TCA-AAATCGCAAC
298459 ACGTATCCGT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 1 0.03
20 25 0.86
21 3 0.10
ACGTcount: A:0.44, C:0.26, G:0.17, T:0.13
Consensus pattern (20 bp):
TCAAAATCGCAACGCGAACA
Found at i:298471 original size:20 final size:20
Alignment explanation
Indices: 298448--298600 Score: 141
Period size: 20 Copynumber: 7.7 Consensus size: 20
298438 CGCGAACACA
298448 TAAATCGCAACACGTATCCG
1 TAAATCGCAACACGTATCCG
* **
298468 TAAACCGCAACGTGTATCCG
1 TAAATCGCAACACGTATCCG
* *
298488 TAAATAGCAACGCGTATCCG
1 TAAATCGCAACACGTATCCG
** *
298508 TAAATCGCAATGCGTATCCA
1 TAAATCGCAACACGTATCCG
* *
298528 TATATCGCAACGCGTATCCG
1 TAAATCGCAACACGTATCCG
298548 TAAATCGC-A-ACGATAATCCG
1 TAAATCGCAACACG-T-ATCCG
* *
298568 TAAATCGCAACGA-GAATCTG
1 TAAATCGCAAC-ACGTATCCG
*
298588 TAAATCACAACAC
1 TAAATCGCAACAC
298601 TGAAATTTTG
Statistics
Matches: 110, Mismatches: 17, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
18 2 0.02
19 3 0.03
20 102 0.93
21 1 0.01
22 1 0.01
23 1 0.01
ACGTcount: A:0.36, C:0.27, G:0.16, T:0.21
Consensus pattern (20 bp):
TAAATCGCAACACGTATCCG
Found at i:298477 original size:40 final size:40
Alignment explanation
Indices: 298410--298598 Score: 184
Period size: 40 Copynumber: 4.7 Consensus size: 40
298400 GATTTTCAAG
* ** * *
298410 AATCGCAACGCGAATATGAAAATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGTATC-CATA
* * * *
298450 AATCGCAACACGTATCCGTAAACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCATA
* *
298490 AATAGCAACGCGTATCCGTAAATCGCAATGCGTATCCATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCATA
* * *
298530 TATCGCAACGCGTATCCGTAAATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGT-ATCCATA
* * * *
298570 AATCGCAACGAGAATCTGTAAATCACAAC
1 AATCGCAACGCGTATCCGTAAATCGCAAC
298599 ACTGAAATTT
Statistics
Matches: 122, Mismatches: 25, Indels: 4
0.81 0.17 0.03
Matches are distributed among these distances:
39 1 0.01
40 119 0.98
41 2 0.02
ACGTcount: A:0.38, C:0.26, G:0.17, T:0.19
Consensus pattern (40 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCATA
Found at i:298498 original size:60 final size:60
Alignment explanation
Indices: 298429--298578 Score: 169
Period size: 60 Copynumber: 2.5 Consensus size: 60
298419 GCGAATATGA
* *
298429 AAATCGCAACGCG-AACACATAAATCGCAACACGTATCCGTAAACCGCAACGTGTATCCGT
1 AAATCGCAACGCGTAAC-CATAAATCGCAACACGTATCCATAAACCGCAACGCGTATCCGT
* * * ** * *
298489 AAATAGCAACGCGTATCCGTAAATCGCAATGCGTATCCATATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTAACCATAAATCGCAACACGTATCCATAAACCGCAACGCGTATCCGT
* *
298549 AAATCGCAACG-ATAATCCGTAAATCGCAAC
1 AAATCGCAACGCGTAA-CCATAAATCGCAAC
298579 GAGAATCTGT
Statistics
Matches: 75, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
59 2 0.03
60 71 0.95
61 2 0.03
ACGTcount: A:0.36, C:0.28, G:0.17, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTAACCATAAATCGCAACACGTATCCATAAACCGCAACGCGTATCCGT
Found at i:299442 original size:20 final size:20
Alignment explanation
Indices: 299414--299642 Score: 228
Period size: 20 Copynumber: 11.4 Consensus size: 20
299404 AAATTTCAGT
* * *
299414 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
299434 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
299454 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
299474 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
299494 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
299514 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
299534 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
299554 GTTGCTATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
299574 GTTGC-AGTTTACGGATACGC
1 GTTGCGA-TTTACGGATTCGC
*
299594 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
299614 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
299634 GTTGCGATT
1 GTTGCGATT
299643 CTTGAAAATC
Statistics
Matches: 182, Mismatches: 23, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
19 1 0.01
20 179 0.98
21 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:299695 original size:21 final size:20
Alignment explanation
Indices: 299610--299707 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
299600 ATTTATGTGT
* *
299610 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCAAAA
*
299630 TCGCGTTGCGATTCTTGAAAA
1 TCGCGTTGCGATT-TTCAAAA
** **
299651 TCGCAATGCGAATTTGT-ACTA
1 TCGCGTTGCG-ATTT-TCAAAA
*
299672 TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTTCAA-AA
299693 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
299708 GGAAACTGAT
Statistics
Matches: 62, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
19 1 0.02
20 18 0.29
21 39 0.63
22 4 0.06
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCAAAA
Found at i:299703 original size:42 final size:43
Alignment explanation
Indices: 299610--299708 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
299600 ATTTATGTGT
* *
299610 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTCTTGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTTCAAAA
**
299651 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATT-TTCAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTCTTCAA-AA
*
299693 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
299709 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 12 0.26
42 32 0.68
43 3 0.06
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTTCAAAA
Found at i:299959 original size:2 final size:2
Alignment explanation
Indices: 299954--299979 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
299944 GAATTTCAAG
299954 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
299980 TCGCAATTTC
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:301566 original size:44 final size:42
Alignment explanation
Indices: 301507--301594 Score: 140
Period size: 44 Copynumber: 2.0 Consensus size: 42
301497 TTGGGCCGGG
301507 TATATATATTTAAATTAAATATATAAATATTATATATATATA
1 TATATATATTTAAATTAAATATATAAATATTATATATATATA
* *
301549 TATATATTAATTTAAATTAAATTTATTAATATTATATATATATA
1 TATATA-T-ATTTAAATTAAATATATAAATATTATATATATATA
301593 TA
1 TA
301595 ATAATTATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
42 6 0.14
43 1 0.02
44 35 0.83
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (42 bp):
TATATATATTTAAATTAAATATATAAATATTATATATATATA
Found at i:304198 original size:60 final size:61
Alignment explanation
Indices: 304096--304235 Score: 185
Period size: 60 Copynumber: 2.3 Consensus size: 61
304086 CATATAGTAT
* * *
304096 AGGATGAAATTGACATGTTCAAAAAGTTTGAGAACTAATTTAGAATGA-ATGTCATAGTTTC
1 AGGATGAAATTGAAATGTTCAAAAAGATTGAGAACTAATTTAGAATGACA-GTCATAGTTTA
* * * *
304157 AGGGTGGAATTGAAATGTTC-AAAAGATTGAGGACTAGTTTAGAATGACAGTCATAGTTTA
1 AGGATGAAATTGAAATGTTCAAAAAGATTGAGAACTAATTTAGAATGACAGTCATAGTTTA
*
304217 AGGATGAAATTTAAATGTT
1 AGGATGAAATTGAAATGTT
304236 TAAGGATGAA
Statistics
Matches: 68, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
60 50 0.74
61 18 0.26
ACGTcount: A:0.39, C:0.06, G:0.23, T:0.32
Consensus pattern (61 bp):
AGGATGAAATTGAAATGTTCAAAAAGATTGAGAACTAATTTAGAATGACAGTCATAGTTTA
Found at i:304236 original size:21 final size:21
Alignment explanation
Indices: 304212--304259 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
304202 GACAGTCATA
304212 GTTTAAGGATGAAATTTAAAT
1 GTTTAAGGATGAAATTTAAAT
304233 GTTTAAGGATGAAATTTAAAT
1 GTTTAAGGATGAAATTTAAAT
304254 GTTTAA
1 GTTTAA
304260 AAATTTATAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.40
Consensus pattern (21 bp):
GTTTAAGGATGAAATTTAAAT
Found at i:313355 original size:14 final size:13
Alignment explanation
Indices: 313333--313373 Score: 55
Period size: 14 Copynumber: 3.0 Consensus size: 13
313323 AGTGGAAGCA
*
313333 TTATTTATTATTAT
1 TTATATATT-TTAT
313347 TTATATATTTCTAT
1 TTATATATTT-TAT
313361 TTATATATTTTAT
1 TTATATATTTTAT
313374 ATTTCTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 4 0.16
14 21 0.84
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.68
Consensus pattern (13 bp):
TTATATATTTTAT
Found at i:313374 original size:21 final size:21
Alignment explanation
Indices: 313334--313393 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 21
313324 GTGGAAGCAT
313334 TATTTATTATTATTTATATATTTC
1 TATTTA-TA-TATTT-TATATTTC
313358 TATTTATATATTTTATATTTC
1 TATTTATATATTTTATATTTC
*
313379 TATTTCATTTATTTT
1 TATTT-ATATATTTT
313394 CATTTATTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
21 13 0.38
22 13 0.38
23 2 0.06
24 6 0.18
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (21 bp):
TATTTATATATTTTATATTTC
Found at i:320808 original size:2 final size:2
Alignment explanation
Indices: 320801--320848 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
320791 CAATCACTTA
320801 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
320843 AT AT AT
1 AT AT AT
320849 TTAAAAGACT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:321682 original size:6 final size:6
Alignment explanation
Indices: 321671--321697 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
321661 TGTATTTATT
321671 ATTAAA ATTAAA ATTAAA ATTAAA ATT
1 ATTAAA ATTAAA ATTAAA ATTAAA ATT
321698 GAACTGAACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (6 bp):
ATTAAA
Found at i:329034 original size:21 final size:21
Alignment explanation
Indices: 329008--329052 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
328998 CTGAATTTCG
329008 CTTTTTAACTTAATCCTTGAA
1 CTTTTTAACTTAATCCTTGAA
*** *
329029 CTTTTTTGGTTAGTCCTTGAA
1 CTTTTTAACTTAATCCTTGAA
329050 CTT
1 CTT
329053 GGATTTTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.20, C:0.18, G:0.11, T:0.51
Consensus pattern (21 bp):
CTTTTTAACTTAATCCTTGAA
Found at i:334357 original size:2 final size:2
Alignment explanation
Indices: 334350--334374 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
334340 AATAAGGTAA
334350 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 T
334375 AGAGGATGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:335943 original size:24 final size:25
Alignment explanation
Indices: 335915--335963 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
335905 TTTTATTTTA
*
335915 TGAATTTAATATTAAT-AAAATATT
1 TGAATATAATATTAATCAAAATATT
* *
335939 TGAATATCATTTTAATCAAAATATT
1 TGAATATAATATTAATCAAAATATT
335964 AATTATTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (25 bp):
TGAATATAATATTAATCAAAATATT
Found at i:336027 original size:18 final size:18
Alignment explanation
Indices: 336004--336038 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
335994 AATATTTAAT
336004 ATTATAATAAAATAATAA
1 ATTATAATAAAATAATAA
* *
336022 ATTATATTATAATAATA
1 ATTATAATAAAATAATA
336039 TAAGATATTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATTATAATAAAATAATAA
Found at i:336028 original size:23 final size:23
Alignment explanation
Indices: 336002--336052 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
335992 TTAATATTTA
*
336002 ATATTATAATAAAATAATAAATT
1 ATATTATAATAAAATAAGAAATT
* *
336025 ATATTATAATAATATAAGATATT
1 ATATTATAATAAAATAAGAAATT
336048 ATATT
1 ATATT
336053 TTTATTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (23 bp):
ATATTATAATAAAATAAGAAATT
Found at i:336171 original size:27 final size:27
Alignment explanation
Indices: 336091--336176 Score: 70
Period size: 27 Copynumber: 3.1 Consensus size: 27
336081 TAATAAATTT
*
336091 ATATTATTTAT-TAATTTAATAGAAATA
1 ATATTATTTATAT-ATTTAATATAAATA
* * *
336118 GTATTA-TTAAAT-TATTAATAATGAATA
1 ATATTATTTATATAT-TTAAT-ATAAATA
336145 ATATTATTTATATATTTAATATTAATATA
1 ATATTATTTATATATTTAATA-TAA-ATA
336174 ATA
1 ATA
336177 ATCCAATAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
25 1 0.02
26 8 0.18
27 17 0.38
28 12 0.27
29 7 0.16
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTATTTATATATTTAATATAAATA
Found at i:336295 original size:37 final size:37
Alignment explanation
Indices: 336230--336308 Score: 92
Period size: 37 Copynumber: 2.1 Consensus size: 37
336220 ATATTTTTAA
336230 AATATAATATAATACTATTACTTTAAT-AAATA-ATT
1 AATATAATATAATACTATTACTTTAATAAAATATATT
* *
336265 AATATAATTTATAATATTTTTA-TTTCAATAAAATATATT
1 AATATAA--TATAATACTATTACTTT-AATAAAATATATT
336304 AATAT
1 AATAT
336309 TTTTATTAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
35 7 0.19
36 3 0.08
37 14 0.38
38 5 0.14
39 8 0.22
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (37 bp):
AATATAATATAATACTATTACTTTAATAAAATATATT
Found at i:347328 original size:26 final size:26
Alignment explanation
Indices: 347280--347331 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
347270 GTTTTCAAAC
* *
347280 AATGTGTGTATATGTTTGAGATAAAA
1 AATGTGTGTATATATATGAGATAAAA
* *
347306 AATGTTTGTATATATATGTGATAAAA
1 AATGTGTGTATATATATGAGATAAAA
347332 GTGTACGACA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.19, T:0.40
Consensus pattern (26 bp):
AATGTGTGTATATATATGAGATAAAA
Found at i:354748 original size:24 final size:24
Alignment explanation
Indices: 354721--354770 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
354711 TGGTGGTTGA
*
354721 TTTAATGGT-TGTTTGAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
354745 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
354769 TT
1 TT
354771 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.24, C:0.02, G:0.14, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:355266 original size:16 final size:16
Alignment explanation
Indices: 355245--355277 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
355235 CACGTGAGGA
*
355245 TTATTTTCTTTTTATT
1 TTATTTTCATTTTATT
355261 TTATTTTCATTTTATT
1 TTATTTTCATTTTATT
355277 T
1 T
355278 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (16 bp):
TTATTTTCATTTTATT
Found at i:367705 original size:32 final size:32
Alignment explanation
Indices: 367638--367698 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
367628 TAGCTAATTA
* *
367638 TTTTTTCTTTGGTGTAATCAGATACTTAAGCT
1 TTTTTTCTTTGATGCAATCAGATACTTAAGCT
* *
367670 TTTTTTCTTTGATGCAATTAGGTACTTAA
1 TTTTTTCTTTGATGCAATCAGATACTTAA
367699 CATTTTTAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.23, C:0.11, G:0.15, T:0.51
Consensus pattern (32 bp):
TTTTTTCTTTGATGCAATCAGATACTTAAGCT
Found at i:371525 original size:86 final size:87
Alignment explanation
Indices: 371422--371598 Score: 331
Period size: 86 Copynumber: 2.1 Consensus size: 87
371412 TCTGATTTCC
371422 GACTTCTTTTTTCTCACATGCCAAGCATAAATTCAGCTTAAACCGTGACCATTGACATTGACCAA
1 GACTTCTTTTTTCTCACATGCCAAGCATAAATTCAGCTTAAACCGTGACCATTGACATTGACCAA
*
371487 CCCCCTCCCATTCAAAAAGAAA
66 CCCCCTCCAATTCAAAAAGAAA
371509 GACTTC-TTTTTCTCACATGCCAAGCATAAATTCAGCTTAAACCGTGACCATTGACATTGACCAA
1 GACTTCTTTTTTCTCACATGCCAAGCATAAATTCAGCTTAAACCGTGACCATTGACATTGACCAA
371573 CCCCCTCCAATTCAAAAAGAAA
66 CCCCCTCCAATTCAAAAAGAAA
371595 -ACTT
1 GACTT
371599 TCGACTCCCG
Statistics
Matches: 89, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
85 4 0.04
86 79 0.89
87 6 0.07
ACGTcount: A:0.34, C:0.29, G:0.10, T:0.27
Consensus pattern (87 bp):
GACTTCTTTTTTCTCACATGCCAAGCATAAATTCAGCTTAAACCGTGACCATTGACATTGACCAA
CCCCCTCCAATTCAAAAAGAAA
Found at i:386391 original size:2 final size:2
Alignment explanation
Indices: 386384--386410 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
386374 AACGAAATCG
386384 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
386411 CTAAATAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:390824 original size:144 final size:145
Alignment explanation
Indices: 390570--391499 Score: 350
Period size: 147 Copynumber: 6.4 Consensus size: 145
390560 CGAGTCTACA
* * *
390570 TATATCTCAATTAAGAAGAGAAACTATACTCATAATCCAACAAAGTCAAAATTATATGACTCTTT
1 TATATCTCAATCAAGAAGAGAAACTAGACTC--AATCCAACAAAATCAAAATTATATGACTCTTT
* * * * * * *
390635 AACTAATTAAATTAAATCTCACAACTATATGGAATATAAGGTCGAAAGTTAAAATAATATCGATT
64 AACTAACTAAATTAAATCTCACAAATATATAGAACAAAAGATCGAAAGTCAAAATAATATCGATT
390700 ATGTTAGACTATAAGTT
129 ATGTTAGACTATAAGTT
* * * *
390717 TATATCTCAATCAAGGAGAGAAACTAGACTC-ATCCAGCAAAATCGAAATTATATGGCTCTTTAA
1 TATATCTCAATCAAGAAGAGAAACTAGACTCAATCCAACAAAATCAAAATTATATGACTCTTTAA
* * ** * * * *
390781 TTGACTAAATTAAATCTCGTAAATTTTTAGAACAAAATATCGAAAGTCAAGATAATATCGACTTA
66 CTAACTAAATTAAATCTCACAAATATATAGAACAAAAGATCGAAAGTCAAAATAATATCGA-TTA
390846 -G-T---C--T-A---
130 TGTTAGACTATAAGTT
* * * ** * *
390851 TATA--TCAATTAAGAAGAGAAATTAGACTCATAATCCAACAAAGTTGATATTATATGATTCTTT
1 TATATCTCAATCAAGAAGAGAAACTAGACTC--AATCCAACAAAATCAAAATTATATGACTCTTT
* * * * * * * ** * * * * *
390914 AATTAATTGAATTAAA-CATCATAAATATTTGGAACATAAGAAAGAAAATTAAGATAATATAGAC
64 AACTAACTAAATTAAATC-TCACAAATATATAGAACAAAAGATCGAAAGTCAAAATAATATCGAT
* * * ** *
390978 TCTGCTAGATTACGAGTC
128 TATGTTAGACTATAAGTT
* * * * * * *
390996 TATATCTTAA-CTAAAAAGAGGAACTAAACTCATAAT-CAAGCAAAGTCGAAATCATATG-CTTC
1 TATATCTCAATC-AAGAAGAGAAACTAGACTC--AATCCAA-CAAAATCAAAATTATATGAC-TC
* * * * ** * * * * * ** * * *
391058 TTTAATTAATTGAATTGAATCTCGTAAATATTTGGAATATAAGATCCAAAACCAAGATGATATTG
61 TTTAACTAACTAAATTAAATCTCACAAATATATAGAACAAAAGATCGAAAGTCAAAATAATATCG
* ** *
391123 ACTT-TGTTAGATTAGGAGTC
126 A-TTATGTTAGACTATAAGTT
* * ** ** **
391143 TATATCTCAATTAA-AGGGAGAAACTAGACTCATAATTTAACAAAATTGAAATTATACAACTCTT
1 TATATCTCAATCAAGA-AGAGAAACTAGACTC--AATCCAACAAAATCAAAATTATATGACTCTT
* * * * * * * *
391207 TAATTAATTAAATTAAATCTAATAAATATTTAGAATATAAGATCGAAAGTCAAGATAATATCGAC
63 TAACTAACTAAATTAAATCTCACAAATATATAGAACAAAAGATCGAAAGTCAAAATAATATCGA-
*
391272 TT-TGTTAGA-T-TATGTGT
127 TTATGTTAGACTATAAGT-T
* * ** * *
391289 T-TATCTCAAT-TA-AAGAGAAAAGTTAGACTCATAATCCAACAAGGTCGAAATTATATGATTCT
1 TATATCTCAATCAAGAAGAG-AAA-CTAGACTC--AATCCAACAAAATCAAAATTATATGACTCT
* * * * * * * * *
391351 TTAA-TCAATTGAACTGAATCTCATAAATATTTAGAATATAAGATTGAAAGTCAAAATAATATCG
62 TTAACT-AACTAAATTAAATCTCACAAATATATAGAACAAAAGATCGAAAGTCAAAATAATATCG
* * * *
391415 ACTT-TGCTAGATTATGAGTC
126 A-TTATGTTAGACTATAAGTT
* * * * * * * **
391435 TATATCTCAATTACGGAGATAAACCAGACTCATAATCCAGCAAAGTCGGAATTATATGACTCTTT
1 TATATCTCAATCAAGAAGAGAAACTAGACTC--AATCCAACAAAATCAAAATTATATGACTCTTT
391500 GATTAATCGA
Statistics
Matches: 620, Mismatches: 127, Indels: 72
0.76 0.16 0.09
Matches are distributed among these distances:
132 22 0.04
134 6 0.01
135 74 0.12
136 1 0.00
137 1 0.00
138 1 0.00
140 1 0.00
142 1 0.00
143 4 0.01
144 82 0.13
145 115 0.19
146 8 0.01
147 293 0.47
148 8 0.01
149 3 0.00
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.32
Consensus pattern (145 bp):
TATATCTCAATCAAGAAGAGAAACTAGACTCAATCCAACAAAATCAAAATTATATGACTCTTTAA
CTAACTAAATTAAATCTCACAAATATATAGAACAAAAGATCGAAAGTCAAAATAATATCGATTAT
GTTAGACTATAAGTT
Found at i:391115 original size:147 final size:147
Alignment explanation
Indices: 390845--391506 Score: 733
Period size: 147 Copynumber: 4.5 Consensus size: 147
390835 ATATCGACTT
* * * *
390845 AGTCTATATATCAATT-AAGAAGAGAAATTAGACTCATAATCCAACAAAGTTGATATTATATGAT
1 AGTCTATATCTCAATTAAAG-AGAGAAACTAGACTCATAATCCAACAAAGTCGAAATTATATGAT
* * * ** *
390909 TCTTTAATTAATTGAATT-AAACATCATAAATATTTGGAACATAAGAAAGAAAATTAAGATAATA
65 TCTTTAATTAATTGAATTGAATC-TCATAAATATTTAGAATATAAGATCGAAAATCAAGATAATA
* * *
390973 TAGACTCTGCTAGATTACG
129 TCGACTTTGCTAGATTATG
* * * * * * *
390992 AGTCTATATCTTAACTAAAAAGAGGAACTAAACTCATAAT-CAAGCAAAGTCGAAATCATATGCT
1 AGTCTATATCTCAATTAAAGAGAGAAACTAGACTCATAATCCAA-CAAAGTCGAAATTATATGAT
* * * * *
391056 TCTTTAATTAATTGAATTGAATCTCGTAAATATTTGGAATATAAGATCCAAAACCAAGATGATAT
65 TCTTTAATTAATTGAATTGAATCTCATAAATATTTAGAATATAAGATCGAAAATCAAGATAATAT
* * *
391121 TGACTTTGTTAGATTAGG
130 CGACTTTGCTAGATTATG
* ** * * ** *
391139 AGTCTATATCTCAATTAAAGGGAGAAACTAGACTCATAATTTAACAAAATTGAAATTATACAACT
1 AGTCTATATCTCAATTAAAGAGAGAAACTAGACTCATAATCCAACAAAGTCGAAATTATATGATT
* * * *
391204 CTTTAATTAATTAAATTAAATCTAATAAATATTTAGAATATAAGATCGAAAGTCAAGATAATATC
66 CTTTAATTAATTGAATTGAATCTCATAAATATTTAGAATATAAGATCGAAAATCAAGATAATATC
*
391269 GACTTTGTTAGATTATG
131 GACTTTGCTAGATTATG
* * *
391286 TGT-T-TATCTCAATTAAAGAGA-AAAGTTAGACTCATAATCCAACAAGGTCGAAATTATATGAT
1 AGTCTATATCTCAATTAAAGAGAGAAA-CTAGACTCATAATCCAACAAAGTCGAAATTATATGAT
* * * * *
391348 TCTTTAATCAATTGAACTGAATCTCATAAATATTTAGAATATAAGATTGAAAGTCAAAATAATAT
65 TCTTTAATTAATTGAATTGAATCTCATAAATATTTAGAATATAAGATCGAAAATCAAGATAATAT
391413 CGACTTTGCTAGATTATG
130 CGACTTTGCTAGATTATG
** * * * * *
391431 AGTCTATATCTCAATTACGGAGATAAACCAGACTCATAATCCAGCAAAGTCGGAATTATATGACT
1 AGTCTATATCTCAATTAAAGAGAGAAACTAGACTCATAATCCAACAAAGTCGAAATTATATGATT
*
391496 CTTTGATTAAT
66 CTTTAATTAAT
391507 CGAGCATAAT
Statistics
Matches: 428, Mismatches: 79, Indels: 16
0.82 0.15 0.03
Matches are distributed among these distances:
144 3 0.01
145 121 0.28
146 5 0.01
147 289 0.68
148 10 0.02
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (147 bp):
AGTCTATATCTCAATTAAAGAGAGAAACTAGACTCATAATCCAACAAAGTCGAAATTATATGATT
CTTTAATTAATTGAATTGAATCTCATAAATATTTAGAATATAAGATCGAAAATCAAGATAATATC
GACTTTGCTAGATTATG
Found at i:391428 original size:292 final size:292
Alignment explanation
Indices: 390498--391506 Score: 971
Period size: 292 Copynumber: 3.5 Consensus size: 292
390488 GAAAATTTTA
* * * * ** *
390498 AATCTCATAAATATTTAAAATATAAAATCAAAAATTAAGATAATATTAACTTTGTTAGATTACGA
1 AATCTCATAAATATTTAGAATATAAGATCGAAAATCAAGATAATATCGACTTTGCTAGATTA-GA
* **
390563 GTCTACATATATCTCAATTAAGAAGAGAAACTATACTCATAATCCAACAAAGTCAAAATTATATG
65 G--T-C-TATATCTCAATTAAGAAGAGAAACTAGACTCATAATCCAACAAAGTTGAAATTATATG
* * * * * *
390628 ACTCTTTAACTAATTAAATTAAATCTCACAACTATATGGAATATAAGGTCGAAAGTTAAAATAAT
126 ACTCTTTAATTAATTAAATTAAATCTCATAAATATTTGGAATATAAGATCGAAAGTTAAGATAAT
* *
390693 ATCGA-TTATGTTAGACTATAAGT-TTATATCTCAATCAAGGAGAGAAACTAGACTC---ATCCA
191 ATCGACTT-TGTTAGA-T-TAAGTGTTATATCTCAATTAAAGAGAGAAACTAGACTCATAATCCA
* * ** * * * *
390753 GCAAAATCGAAATTATATGGCTCTTTAATTGACTAAATTA
253 ACAAAGTCGAAATTATATGATTCTTTAATTAATTGAATTG
* * * * * *
390793 AATCTCGTAAATTTTTAGAACAAAATATCGAAAGTCAAGATAATATCGA-----C----TT--AG
1 AATCTCATAAATATTTAGAATATAAGATCGAAAATCAAGATAATATCGACTTTGCTAGATTAGAG
* * * *
390847 TCTATATATCAATTAAGAAGAGAAATTAGACTCATAATCCAACAAAGTTGATATTATATGATTCT
66 TCTATATCTCAATTAAGAAGAGAAACTAGACTCATAATCCAACAAAGTTGAAATTATATGACTCT
* * ** * *
390912 TTAATTAATTGAATTAAA-CATCATAAATATTTGGAACATAAGAAAGAAAATTAAGATAATATAG
131 TTAATTAATTAAATTAAATC-TCATAAATATTTGGAATATAAGATCGAAAGTTAAGATAATATCG
* * * * * * * * *
390976 ACTCTGCTAGATTACGAGTCTATATCTTAACTAAAAAGAGGAACTAAACTCATAAT-CAAGCAAA
195 ACTTTGTTAGATTAAGTGT-TATATCTCAATTAAAGAGAGAAACTAGACTCATAATCCAA-CAAA
* *
391040 GTCGAAATCATATGCTTCTTTAATTAATTGAATTG
258 GTCGAAATTATATGATTCTTTAATTAATTGAATTG
* * * * * * *
391075 AATCTCGTAAATATTTGGAATATAAGATCCAAAACCAAGATGATATTGACTTTGTTAGATTAGGA
1 AATCTCATAAATATTTAGAATATAAGATCGAAAATCAAGATAATATCGACTTTGCTAGATTA-GA
* ** * **
391140 GTCTATATCTCAATTAA-AGGGAGAAACTAGACTCATAATTTAACAAAATTGAAATTATACAACT
65 GTCTATATCTCAATTAAGA-AGAGAAACTAGACTCATAATCCAACAAAGTTGAAATTATATGACT
* * *
391204 CTTTAATTAATTAAATTAAATCTAATAAATATTTAGAATATAAGATCGAAAGTCAAGATAATATC
129 CTTTAATTAATTAAATTAAATCTCATAAATATTTGGAATATAAGATCGAAAGTTAAGATAATATC
* * *
391269 GACTTTGTTAGATTATGTGTT-TATCTCAATTAAAGAGA-AAAGTTAGACTCATAATCCAACAAG
194 GACTTTGTTAGATTAAGTGTTATATCTCAATTAAAGAGAGAAA-CTAGACTCATAATCCAACAAA
* *
391332 GTCGAAATTATATGATTCTTTAATCAATTGAACTG
258 GTCGAAATTATATGATTCTTTAATTAATTGAATTG
* * *
391367 AATCTCATAAATATTTAGAATATAAGATTGAAAGTCAAAATAATATCGACTTTGCTAGATTATGA
1 AATCTCATAAATATTTAGAATATAAGATCGAAAATCAAGATAATATCGACTTTGCTAGATTA-GA
* * * * * * *
391432 GTCTATATCTCAATTACGGAGATAAACCAGACTCATAATCCAGCAAAGTCGGAATTATATGACTC
65 GTCTATATCTCAATTAAGAAGAGAAACTAGACTCATAATCCAACAAAGTTGAAATTATATGACTC
*
391497 TTTGATTAAT
130 TTTAATTAAT
391507 CGAGCATAAT
Statistics
Matches: 568, Mismatches: 121, Indels: 53
0.77 0.16 0.07
Matches are distributed among these distances:
277 3 0.01
278 3 0.01
279 137 0.24
280 2 0.00
281 3 0.01
282 72 0.13
283 2 0.00
286 2 0.00
291 4 0.01
292 173 0.30
293 5 0.01
294 123 0.22
295 39 0.07
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.32
Consensus pattern (292 bp):
AATCTCATAAATATTTAGAATATAAGATCGAAAATCAAGATAATATCGACTTTGCTAGATTAGAG
TCTATATCTCAATTAAGAAGAGAAACTAGACTCATAATCCAACAAAGTTGAAATTATATGACTCT
TTAATTAATTAAATTAAATCTCATAAATATTTGGAATATAAGATCGAAAGTTAAGATAATATCGA
CTTTGTTAGATTAAGTGTTATATCTCAATTAAAGAGAGAAACTAGACTCATAATCCAACAAAGTC
GAAATTATATGATTCTTTAATTAATTGAATTG
Found at i:391468 original size:439 final size:425
Alignment explanation
Indices: 390498--391506 Score: 1073
Period size: 439 Copynumber: 2.3 Consensus size: 425
390488 GAAAATTTTA
* * *
390498 AATCTCATAAATATTTAAAATATAAAATCA-AAAATTAAGATAATATTA-ACTTTGTTAGATTAC
1 AATCTCATAAATATTTAGAATATAAGAT-AGAAAATTAAGATAATA-TAGACTTTGCTAGATTAC
* *
390561 GAGTCTACATATATCTCAATTAAGAAGAGAAACTATACTCATAATCCAA-CAAAGTCAAAATTAT
64 GAG--T-C-TATATCTCAATTAAGAAGAGAAACTAAACTCATAAT-CAAGCAAAGTCGAAATTAT
* * * * ***
390625 ATGACTCTTTAACTAATTAAATTAAATCTCACAACTATATGGAATATAAGGTCGAAAGTTAAAAT
124 ATGACTCTTTAATTAATTAAATTAAATCTCACAAATATATGGAATATAAGATCCAAAACCAAAAT
* * * *
390690 AATATCGATTATGTTAGACTATAAGTTTATATCTCAATCAAGGAGAGAAACTAGACTCATCCAGC
189 AATATCGATTATGTTAGACTAGAAGTCTATATCTCAATAAAGGAGAGAAACTAGACTCATCCAAC
*** * ** * *
390755 AAAATCGAAATTATATGGCTCTTTAATTGACTAAATTAAATCTCGTAAATTTTTAGAACAAAATA
254 AAAATCGAAATTATACAACTCTTTAATTAACTAAATTAAATCTAATAAATATTTAGAACAAAAGA
390820 TCGAAAGTCAAGATAATATCGACTTAGTCTATATATCAATTAAGAAGAGAAATTAGACTCATAAT
319 TCGAAAGTCAAGATAATATCGACTTAGTCTATATATCAATTAAGAAGAGAAATTAGACTCATAAT
* * * *
390885 CCAACAAAGTTGATATTATATGATTCTTTAATTAATTGAATT
384 CCAACAAAGTCGAAATTATATGATTCTTTAATCAATTGAATG
* * * * *
390927 AAACATCATAAATATTTGGAACATAAGAAAGAAAATTAAGATAATATAGACTCTGCTAGATTACG
1 AATC-TCATAAATATTTAGAATATAAGATAGAAAATTAAGATAATATAGACTTTGCTAGATTACG
* * * * *
390992 AGTCTATATCTTAACTAAAAAGAGGAACTAAACTCATAATCAAGCAAAGTCGAAATCATATG-CT
65 AGTCTATATCTCAATTAAGAAGAGAAACTAAACTCATAATCAAGCAAAGTCGAAATTATATGAC-
* * ** * * *
391056 TCTTTAATTAATTGAATTGAATCTCGTAAATATTTGGAATATAAGATCCAAAACCAAGATGATAT
129 TCTTTAATTAATTAAATTAAATCTCACAAATATATGGAATATAAGATCCAAAACCAAAATAATAT
* * * **
391121 TGACTT-TGTTAGATTAGGAGTCTATATCTCAATTAAAGG-GAGAAACTAGACTCATAATTTAAC
194 CGA-TTATGTTAGACTAGAAGTCTATATCTCAA-TAAAGGAGAGAAACTAGACTC---ATCCAAC
* * * *
391184 AAAATTGAAATTATACAACTCTTTAATTAATTAAATTAAATCTAATAAATATTTAGAATATAAGA
254 AAAATCGAAATTATACAACTCTTTAATTAACTAAATTAAATCTAATAAATATTTAGAACAAAAGA
*
391249 TCGAAAGTCAAGATAATATCGACTTTGTTAGAT-TATGTGTTTATCTCAATT-A-AAGAGAAAAG
319 TCGAAAGTCAAGATAATATCGAC----TTAG-TCTA------TATATCAATTAAGAAGAG-AAA-
*
391311 TTAGACTCATAATCCAACAAGGTCGAAATTATATGATTCTTTAATCAATTGAACTG
371 TTAGACTCATAATCCAACAAAGTCGAAATTATATGATTCTTTAATCAATTGAA-TG
* * * * * *
391367 AATCTCATAAATATTTAGAATATAAGATTGAAAGTCAAAATAATATCGACTTTGCTAGATTATGA
1 AATCTCATAAATATTTAGAATATAAGATAGAAAATTAAGATAATATAGACTTTGCTAGATTACGA
* * * * * * *
391432 GTCTATATCTCAATTACGGAGATAAACCAGACTCATAATCCAGCAAAGTCGGAATTATATGACTC
66 GTCTATATCTCAATTAAGAAGAGAAACTAAACTCATAATCAAGCAAAGTCGAAATTATATGACTC
*
391497 TTTGATTAAT
131 TTTAATTAAT
391507 CGAGCATAAT
Statistics
Matches: 475, Mismatches: 80, Indels: 40
0.80 0.13 0.07
Matches are distributed among these distances:
425 4 0.01
426 136 0.29
427 8 0.02
428 1 0.00
429 86 0.18
430 50 0.11
433 6 0.01
434 1 0.00
437 5 0.01
438 4 0.01
439 169 0.36
440 5 0.01
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.32
Consensus pattern (425 bp):
AATCTCATAAATATTTAGAATATAAGATAGAAAATTAAGATAATATAGACTTTGCTAGATTACGA
GTCTATATCTCAATTAAGAAGAGAAACTAAACTCATAATCAAGCAAAGTCGAAATTATATGACTC
TTTAATTAATTAAATTAAATCTCACAAATATATGGAATATAAGATCCAAAACCAAAATAATATCG
ATTATGTTAGACTAGAAGTCTATATCTCAATAAAGGAGAGAAACTAGACTCATCCAACAAAATCG
AAATTATACAACTCTTTAATTAACTAAATTAAATCTAATAAATATTTAGAACAAAAGATCGAAAG
TCAAGATAATATCGACTTAGTCTATATATCAATTAAGAAGAGAAATTAGACTCATAATCCAACAA
AGTCGAAATTATATGATTCTTTAATCAATTGAATG
Found at i:393126 original size:23 final size:23
Alignment explanation
Indices: 393100--393145 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
393090 ATCAAGTACA
* * *
393100 ATAATATATTAGGTAGCGCTTAT
1 ATAATATAATAGATAACGCTTAT
*
393123 ATAATGTAATAGATAACGCTTAT
1 ATAATATAATAGATAACGCTTAT
393146 TTTAACCTAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.37
Consensus pattern (23 bp):
ATAATATAATAGATAACGCTTAT
Found at i:394109 original size:182 final size:181
Alignment explanation
Indices: 393768--394218 Score: 708
Period size: 182 Copynumber: 2.5 Consensus size: 181
393758 ACTTTTTTAC
* * *
393768 TACCGGTTTTGTCATTTCGAGATCGATTTTGTCATATTTTTACTTGTTATATTGTTATGGATCGA
1 TACCGGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGA
* *
393833 TACATTTTTATAAA--TCGATACTTTATTAGCGCTATAACTTCTTTTCTTTTAAATTCCAAAAGT
66 TACATTTTTATAAAGTTCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGT
* *
393896 GTCGATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCTCTT
131 GTCGATACTTATAATAAAGTATCGACACTATCAACATATCCGATAGCGCTT
*
393947 TACCGGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTTTTATGGATCGA
1 TACCGGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGA
*
394012 TACATTTTTATAAAGTGTCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCTAAAAG
66 TACATTTTTATAAAGT-TCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAG
*
394077 TGTCGATACTTATAATAAAGTATTGACACTATCAACATATCCGATAGCGCTT
130 TGTCGATACTTATAATAAAGTATCGACACTATCAACATATCCGATAGCGCTT
** ** * * *
394129 TACATGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACCTGTTTTATTGTTATGGATCGA
1 TACCGGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGA
*
394194 TGCATTTTTATAAAGTATCGACACT
66 TACATTTTTATAAAGT-TCGACACT
394219 ATCAATATAT
Statistics
Matches: 249, Mismatches: 20, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
179 75 0.30
182 174 0.70
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.44
Consensus pattern (181 bp):
TACCGGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGA
TACATTTTTATAAAGTTCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGT
GTCGATACTTATAATAAAGTATCGACACTATCAACATATCCGATAGCGCTT
Found at i:394177 original size:20 final size:20
Alignment explanation
Indices: 394127--394178 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
394117 CCGATAGCGC
*
394127 TTTACATGTTTTGTCATTTA
1 TTTACCTGTTTTGTCATTTA
** * *
394147 TAGACCGGTTTTGTCATTTT
1 TTTACCTGTTTTGTCATTTA
394167 TTTACCTGTTTT
1 TTTACCTGTTTT
394179 ATTGTTATGG
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.15, C:0.13, G:0.13, T:0.58
Consensus pattern (20 bp):
TTTACCTGTTTTGTCATTTA
Found at i:394288 original size:112 final size:112
Alignment explanation
Indices: 394091--394667 Score: 884
Period size: 112 Copynumber: 5.1 Consensus size: 112
394081 GATACTTATA
* * * * *
394091 ATAAAGTATTGACACTATCAACATATCCGATAGCGCTTTACATGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
394156 TTTGTCATTTTTTTACCTGTTTTATTGTTATGGATCGATGCATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* * * *
394203 ATAAAGTATCGACACTATCAATATATCTGGTAGCGCTTTACCTGTTTTGTCATTTATATACCGAT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
394268 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCTATATATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
394315 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
394380 TTTGTCATTTTTTTTATCTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCA-TTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* *
394428 ATAAAGTATCAACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* * *
394493 TTTGTCATTTTTTTACCTATTATATTATTATGGATAGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* ** * *
394540 ATAAAGTATCGACACTTTTAATATATTTGGTATCGCTTTACCTGTTTTGTCATTTATAGATCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* * * *
394605 TTTGTCATTTTTTTTACTTGTTATATTGTTATGAATCAATATATTTTT
66 TTTGTCA-TTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
394653 ATAAAGTATCGACAC
1 ATAAAGTATCGACAC
394668 AAACCGACAA
Statistics
Matches: 425, Mismatches: 38, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
112 270 0.64
113 155 0.36
ACGTcount: A:0.25, C:0.14, G:0.13, T:0.47
Consensus pattern (112 bp):
ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
Found at i:394481 original size:225 final size:224
Alignment explanation
Indices: 394091--394667 Score: 904
Period size: 225 Copynumber: 2.6 Consensus size: 224
394081 GATACTTATA
* * * * *
394091 ATAAAGTATTGACACTATCAACATATCCGATAGCGCTTTACATGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
394156 TTTGTCA-TTTTTTTACCTGTTTTATTGTTATGGATCGATGCATTTTTATAAAGTATCGACACTA
66 TTTGTCATTTTTTTTA-CTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTA
* *
394220 TCAATATATCTGGTAGCGCTTTACCTGTTTTGTCATTTATATACCGATTTTGTCATTTTTTTACC
130 TCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGATTTTGTCATTTTTTTACC
* * ** *
394285 TGTTATATTGTTATGGATCTATATATTTTT
195 TATTATATTATTATGGATAGATACATTTTT
394315 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
394380 TTTGTCATTTTTTTTATCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCAACACTT
66 TTTGTCATTTTTTTTA-CTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTA
394445 TCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGATTTTGTCATTTTTTTACC
130 TCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGATTTTGTCATTTTTTTACC
394510 TATTATATTATTATGGATAGATACATTTTT
195 TATTATATTATTATGGATAGATACATTTTT
* ** * *
394540 ATAAAGTATCGACACTTTTAATATATTTGGTATCGCTTTACCTGTTTTGTCATTTATAGATCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* * *
394605 TTTGTCATTTTTTTTACTTGTTATATTGTTATGAATCAATATATTTTTATAAAGTATCGACAC
66 TTTGTCATTTTTTTTAC-TGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACAC
394668 AAACCGACAA
Statistics
Matches: 325, Mismatches: 26, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
224 68 0.21
225 257 0.79
ACGTcount: A:0.25, C:0.14, G:0.13, T:0.47
Consensus pattern (224 bp):
ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTTTACTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTAT
CAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGATTTTGTCATTTTTTTACCT
ATTATATTATTATGGATAGATACATTTTT
Found at i:395144 original size:35 final size:35
Alignment explanation
Indices: 395098--395209 Score: 161
Period size: 35 Copynumber: 3.2 Consensus size: 35
395088 AATAGTCCTT
* *
395098 AATTTTATTCTAAACCCCAAATTCCAAAGTAATTC
1 AATTTAATTCTAAACCCCAAATTCCAAAATAATTC
* *
395133 AATTTCATTCTAAACCCTAAATTCCAAAATAATTC
1 AATTTAATTCTAAACCCCAAATTCCAAAATAATTC
* * *
395168 AATTAAATTCTAAACCCCAAATTCTAAAATACTTC
1 AATTTAATTCTAAACCCCAAATTCCAAAATAATTC
395203 AATTTAA
1 AATTTAA
395210 GGTTTAGAAT
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 68 1.00
ACGTcount: A:0.44, C:0.21, G:0.01, T:0.34
Consensus pattern (35 bp):
AATTTAATTCTAAACCCCAAATTCCAAAATAATTC
Found at i:395271 original size:35 final size:35
Alignment explanation
Indices: 395203--395277 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 35
395193 AAAATACTTC
* * *
395203 AATTTAAGGTTTAGAATGTAATTGAATTATTTTGG
1 AATTTAAGGTTTAGAATGAAATTGAAGTATTTTGA
* *
395238 AATTTAGGGTTTAGAATGAAATT-AAGGTGTTTTGA
1 AATTTAAGGTTTAGAATGAAATTGAA-GTATTTTGA
395273 AATTT
1 AATTT
395278 TGAACATGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
34 2 0.06
35 32 0.94
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (35 bp):
AATTTAAGGTTTAGAATGAAATTGAAGTATTTTGA
Found at i:397316 original size:35 final size:35
Alignment explanation
Indices: 397268--397379 Score: 134
Period size: 35 Copynumber: 3.2 Consensus size: 35
397258 TCTAAACCTT
* *
397268 AAATTGAAGTATTTTAGAATTTGGGGTTTAGAATT
1 AAATTGAACTATTTTAGAATTTGGGGTTTAGAATA
* * *
397303 TAATTGAACTATTTTAGAATTTAGGGTTTAGAGTA
1 AAATTGAACTATTTTAGAATTTGGGGTTTAGAATA
* * * * *
397338 AAATTGAATTACTTTGGAATTTGGAGTTTAGAATG
1 AAATTGAACTATTTTAGAATTTGGGGTTTAGAATA
397373 AAATTGA
1 AAATTGA
397380 GGATTGTTCT
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 64 1.00
ACGTcount: A:0.36, C:0.02, G:0.21, T:0.41
Consensus pattern (35 bp):
AAATTGAACTATTTTAGAATTTGGGGTTTAGAATA
Found at i:398161 original size:18 final size:19
Alignment explanation
Indices: 398138--398175 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
398128 TAATTCCACA
398138 TTATTTGTTTGATTT-TTT
1 TTATTTGTTTGATTTATTT
* *
398156 TTATTTTTTTTATTTATTT
1 TTATTTGTTTGATTTATTT
398175 T
1 T
398176 CTCTAATAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.13, C:0.00, G:0.05, T:0.82
Consensus pattern (19 bp):
TTATTTGTTTGATTTATTT
Found at i:399990 original size:14 final size:15
Alignment explanation
Indices: 399932--399994 Score: 83
Period size: 15 Copynumber: 4.3 Consensus size: 15
399922 AAACAGACCC
**
399932 TTACTGGAATTTGAA
1 TTACTGGAAAATGAA
399947 TTACTGGAAAATGAA
1 TTACTGGAAAATGAA
**
399962 TTACTGGAATTTGAA
1 TTACTGGAAAATGAA
399977 TT-CTGGAAAATGAA
1 TTACTGGAAAATGAA
399991 TTAC
1 TTAC
399995 ATTTCTGTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
14 12 0.29
15 29 0.71
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.35
Consensus pattern (15 bp):
TTACTGGAAAATGAA
Found at i:399992 original size:29 final size:30
Alignment explanation
Indices: 399932--399994 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 30
399922 AAACAGACCC
399932 TTACTGGAATTTGAATTACTGGAAAATGAA
1 TTACTGGAATTTGAATTACTGGAAAATGAA
399962 TTACTGGAATTTGAATT-CTGGAAAATGAA
1 TTACTGGAATTTGAATTACTGGAAAATGAA
399991 TTAC
1 TTAC
399995 ATTTCTGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.35
Consensus pattern (30 bp):
TTACTGGAATTTGAATTACTGGAAAATGAA
Found at i:400000 original size:20 final size:20
Alignment explanation
Indices: 399977--400046 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
399967 GGAATTTGAA
399977 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
*
399997 TTCTGTAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
400017 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
400037 TTCTGGAAAA
1 TTCTGGAAAA
400047 CGTTTTATGA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:400166 original size:21 final size:23
Alignment explanation
Indices: 400142--400184 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
400132 TTATTAAAGT
400142 AATAGT-ACTA-TATATTTTAAA
1 AATAGTAACTAGTATATTTTAAA
* *
400163 AATATTAATTAGTATATTTTAA
1 AATAGTAACTAGTATATTTTAA
400185 TATCTTTACT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 5 0.28
22 3 0.17
23 10 0.56
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (23 bp):
AATAGTAACTAGTATATTTTAAA
Found at i:400232 original size:28 final size:25
Alignment explanation
Indices: 400200--400259 Score: 77
Period size: 25 Copynumber: 2.3 Consensus size: 25
400190 TTACTAAAAT
400200 ATTATTGAAATATATAAAAATATTATTC
1 ATTATT-AAATATA-AAAAAT-TTATTC
400228 ATTATTAAATATAAAAAATTTATT-
1 ATTATTAAATATAAAAAATTTATTC
400252 ATATATTA
1 AT-TATTA
400260 TTAAATAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
24 2 0.06
25 10 0.32
26 6 0.19
27 7 0.23
28 6 0.19
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (25 bp):
ATTATTAAATATAAAAAATTTATTC
Found at i:400260 original size:28 final size:27
Alignment explanation
Indices: 400198--400298 Score: 93
Period size: 28 Copynumber: 3.6 Consensus size: 27
400188 CTTTACTAAA
400198 ATATTATTGAAATATATAAAAA-TATTAT
1 ATATTATT-AAATATA-AAAAATTATTAT
400226 -TCATTATTAAATATAAAAAATTTATTAT
1 AT-ATTATTAAATATAAAAAA-TTATTAT
*
400254 ATATTATTAAATA-AAAATATAATATCT-T
1 ATATTATTAAATATAAAA-A-ATTAT-TAT
400282 ATATTATTATAATATAA
1 ATATTATTA-AATATAA
400299 TTGATTATTT
Statistics
Matches: 63, Mismatches: 1, Indels: 16
0.79 0.01 0.20
Matches are distributed among these distances:
26 5 0.08
27 12 0.19
28 37 0.59
29 7 0.11
30 2 0.03
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (27 bp):
ATATTATTAAATATAAAAAATTATTAT
Found at i:400328 original size:31 final size:31
Alignment explanation
Indices: 400247--400358 Score: 101
Period size: 30 Copynumber: 3.7 Consensus size: 31
400237 TATAAAAAAT
* * *
400247 TTATTAT-ATATTATTAAATAAAAATATAATA
1 TTATTATAATATTAATAAAT-ATAATATTATA
* * *
400278 -TCTTATATTATT-AT-AATATAATTGATTATT
1 TTATTATAATATTAATAAATATAA-T-ATTATA
400308 TTA-TATAATATTAA-AAATATAATATTATA
1 TTATTATAATATTAATAAATATAATATTATA
400337 TTATTATAATATTAATAAATAT
1 TTATTATAATATTAATAAATAT
400359 TTTTAAATAT
Statistics
Matches: 64, Mismatches: 9, Indels: 16
0.72 0.10 0.18
Matches are distributed among these distances:
28 3 0.05
29 12 0.19
30 30 0.47
31 19 0.30
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (31 bp):
TTATTATAATATTAATAAATATAATATTATA
Found at i:400360 original size:52 final size:51
Alignment explanation
Indices: 400265--400369 Score: 142
Period size: 52 Copynumber: 2.0 Consensus size: 51
400255 TATTATTAAA
* *
400265 TAAAAATATAATATCTTATATTATTATAATATAATTGATTATTTTATATAATAT
1 TAAAAATATAATA-CTTATATTATTATAATATAATTAAATATTTT-TA-AATAT
400319 TAAAAATATAATA-TTATATTATTATAATATTAA-TAAATATTTTTAAATAT
1 TAAAAATATAATACTTATATTATTATAATA-TAATTAAATATTTTTAAATAT
400369 T
1 T
400370 TTAATAATTA
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
50 6 0.12
51 2 0.04
52 24 0.50
53 3 0.06
54 13 0.27
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.50
Consensus pattern (51 bp):
TAAAAATATAATACTTATATTATTATAATATAATTAAATATTTTTAAATAT
Found at i:400617 original size:42 final size:42
Alignment explanation
Indices: 400558--400677 Score: 222
Period size: 42 Copynumber: 2.9 Consensus size: 42
400548 ATGAATTACA
*
400558 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACGTT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
400600 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
*
400642 TTCCGAAAAACGAATTACGTGAAACAAACACGGGAA
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAA
400678 TTCGGGGAAA
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 76 1.00
ACGTcount: A:0.45, C:0.19, G:0.20, T:0.16
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:404026 original size:50 final size:50
Alignment explanation
Indices: 403969--404069 Score: 193
Period size: 50 Copynumber: 2.0 Consensus size: 50
403959 GTTATTGTGC
*
403969 AGATTGATAATTGCTGGATATTCACTCCTCAATTATTAGATATTCTTCGT
1 AGATTGATAATTGCTAGATATTCACTCCTCAATTATTAGATATTCTTCGT
404019 AGATTGATAATTGCTAGATATTCACTCCTCAATTATTAGATATTCTTCGT
1 AGATTGATAATTGCTAGATATTCACTCCTCAATTATTAGATATTCTTCGT
404069 A
1 A
404070 AATATATCTA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.42
Consensus pattern (50 bp):
AGATTGATAATTGCTAGATATTCACTCCTCAATTATTAGATATTCTTCGT
Found at i:404586 original size:29 final size:27
Alignment explanation
Indices: 404553--404617 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 27
404543 AGTAAATTAC
*
404553 AAAAAAA-AATATTCATGGATCAAATTTG
1 AAAAAAATAA-ATTCATGGA-CAAAATTG
*
404581 TAAAAAATATAAATTTATGGACAAAATTG
1 -AAAAAA-ATAAATTCATGGACAAAATTG
404610 AAAAAAAT
1 AAAAAAAT
404618 GTAAAATTAC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
27 2 0.06
28 6 0.19
29 13 0.41
30 9 0.28
31 2 0.06
ACGTcount: A:0.58, C:0.05, G:0.09, T:0.28
Consensus pattern (27 bp):
AAAAAAATAAATTCATGGACAAAATTG
Found at i:404601 original size:30 final size:30
Alignment explanation
Indices: 404567--404653 Score: 88
Period size: 29 Copynumber: 3.0 Consensus size: 30
404557 AAAAATATTC
* *
404567 ATGGATCAAATTTGTAAAAAATATAAATTT
1 ATGGATCAAAATTGAAAAAAATATAAATTT
* *
404597 ATGGA-CAAAATTGAAAAAAATGTAAAATT
1 ATGGATCAAAATTGAAAAAAATATAAATTT
*** *
404626 ACAAAT-AAAATTGGAAAAAATATAAATT
1 ATGGATCAAAATTGAAAAAAATATAAATT
404654 AAACAACACA
Statistics
Matches: 46, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
29 41 0.89
30 5 0.11
ACGTcount: A:0.57, C:0.03, G:0.10, T:0.29
Consensus pattern (30 bp):
ATGGATCAAAATTGAAAAAAATATAAATTT
Found at i:412525 original size:52 final size:52
Alignment explanation
Indices: 412463--412621 Score: 138
Period size: 52 Copynumber: 3.2 Consensus size: 52
412453 ATCAAGTGGG
412463 AGCACATCTCAAAATCAAACTCTAAAACAAGTTAATCTTAAAATAAGATTTA
1 AGCACATCTCAAAATCAAACTCTAAAACAAGTTAATCTTAAAATAAGATTTA
* ** * * ** ***
412515 AGCACATCTC--AAT---A-T-TGACTCGAGTTAGT-TTGTGAATCAAG-TGGG
1 AGCACATCTCAAAATCAAACTCTAAAACAAGTTAATCTT-AAAAT-AAGATTTA
*
412560 AGCACATCACAAAATCAAACTCTAAAACAAGTTAATCTTAAAATAAGATTTA
1 AGCACATCTCAAAATCAAACTCTAAAACAAGTTAATCTTAAAATAAGATTTA
412612 AGCACATCTC
1 AGCACATCTC
412622 GATATTGACA
Statistics
Matches: 74, Mismatches: 22, Indels: 22
0.63 0.19 0.19
Matches are distributed among these distances:
44 2 0.03
45 22 0.30
46 4 0.05
47 4 0.05
50 4 0.05
51 4 0.05
52 32 0.43
53 2 0.03
ACGTcount: A:0.43, C:0.18, G:0.11, T:0.27
Consensus pattern (52 bp):
AGCACATCTCAAAATCAAACTCTAAAACAAGTTAATCTTAAAATAAGATTTA
Found at i:412547 original size:97 final size:97
Alignment explanation
Indices: 412427--412630 Score: 374
Period size: 97 Copynumber: 2.1 Consensus size: 97
412417 ACTCGGTTAA
*
412427 CAAT-TTGAACTCGAGTTAGTTTGTGAATCAAGTGGGAGCACATCTCAAAATCAAACTCTAAAAC
1 CAATATTG-ACTCGAGTTAGTTTGTGAATCAAGTGGGAGCACATCACAAAATCAAACTCTAAAAC
412491 AAGTTAATCTTAAAATAAGATTTAAGCACATCT
65 AAGTTAATCTTAAAATAAGATTTAAGCACATCT
412524 CAATATTGACTCGAGTTAGTTTGTGAATCAAGTGGGAGCACATCACAAAATCAAACTCTAAAACA
1 CAATATTGACTCGAGTTAGTTTGTGAATCAAGTGGGAGCACATCACAAAATCAAACTCTAAAACA
412589 AGTTAATCTTAAAATAAGATTTAAGCACATCT
66 AGTTAATCTTAAAATAAGATTTAAGCACATCT
*
412621 CGATATTGAC
1 CAATATTGAC
412631 AAAGTATCAA
Statistics
Matches: 104, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
97 101 0.97
98 3 0.03
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (97 bp):
CAATATTGACTCGAGTTAGTTTGTGAATCAAGTGGGAGCACATCACAAAATCAAACTCTAAAACA
AGTTAATCTTAAAATAAGATTTAAGCACATCT
Found at i:412778 original size:15 final size:15
Alignment explanation
Indices: 412758--412786 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
412748 ATCTTCGTCT
412758 TCGTCGTCATCTTCC
1 TCGTCGTCATCTTCC
412773 TCGTCGTCATCTTC
1 TCGTCGTCATCTTC
412787 AACAGTAGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.38, G:0.14, T:0.41
Consensus pattern (15 bp):
TCGTCGTCATCTTCC
Found at i:417655 original size:16 final size:18
Alignment explanation
Indices: 417634--417670 Score: 60
Period size: 16 Copynumber: 2.2 Consensus size: 18
417624 TGAATTTCTA
417634 AATATTTT-AAAATT-TT
1 AATATTTTCAAAATTATT
417650 AATATTTTCAAAATTATT
1 AATATTTTCAAAATTATT
417668 AAT
1 AAT
417671 TATGTGACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (18 bp):
AATATTTTCAAAATTATT
Found at i:421549 original size:161 final size:171
Alignment explanation
Indices: 421373--421743 Score: 546
Period size: 161 Copynumber: 2.2 Consensus size: 171
421363 TGTCGTGTAT
*
421373 TCGTATTAAAGCTTAAGTTTTTACCTATGGTGACATTGTTATTAGCTAGCAAGT-G-G-A-G-TA
1 TCGTATTAAAGCTTAAGCTTTTACCTATGGTGACATTGTTATTAGCTAGCAAGTGGAGTATGTTA
* *
421433 TT-GTTACTGTTTTTGATTACCGGTTT-AATACGGCTTCTTGATTTATGTTTCATATGCTTGTAC
66 TTCGTTACTGTTTTTGATTACCGGTTTAAATACGGCATCTTGATTTATGTTTCATATGCTTGCAC
* * *
421496 CGTGTGCTCATT-TGGT-GA-GGTTAGATGTTGGCACATAC
131 CGTGTACTCATTCAGGTAGATGGTTAGATGTAGGCACATAC
421534 TCGTATTAAAGCTTAAGCTTTTACCTATGGTGACATTGTTATTAGCTAGCAAGTGGAGTATTGTT
1 TCGTATTAAAGCTTAAGCTTTTACCTATGGTGACATTGTTATTAGCTAGCAAGTGGAGTA-TGTT
421599 ATTCGTTACTGTTTTTGATTACCGGTTTAAATACGGCATCTTGATTTATGTTTCATATGCTTGCA
65 ATTCGTTACTGTTTTTGATTACCGGTTTAAATACGGCATCTTGATTTATGTTTCATATGCTTGCA
* * *
421664 CTGTGTATTCATTCAGGTAAGGATGGTTATATGTAGGCACATAC
130 CCGTGTACTCATTCAGGT-A-GATGGTTAGATGTAGGCACATAC
* *
421708 TCATATTAAAGCTTAAGCTTTTACATATGGTGACAT
1 TCGTATTAAAGCTTAAGCTTTTACCTATGGTGACAT
421744 ATTTTTGATT
Statistics
Matches: 186, Mismatches: 11, Indels: 13
0.89 0.05 0.06
Matches are distributed among these distances:
161 53 0.28
162 1 0.01
163 1 0.01
164 1 0.01
166 1 0.01
167 4 0.02
168 24 0.13
169 44 0.24
170 3 0.02
173 2 0.01
174 52 0.28
ACGTcount: A:0.24, C:0.14, G:0.21, T:0.41
Consensus pattern (171 bp):
TCGTATTAAAGCTTAAGCTTTTACCTATGGTGACATTGTTATTAGCTAGCAAGTGGAGTATGTTA
TTCGTTACTGTTTTTGATTACCGGTTTAAATACGGCATCTTGATTTATGTTTCATATGCTTGCAC
CGTGTACTCATTCAGGTAGATGGTTAGATGTAGGCACATAC
Found at i:421739 original size:174 final size:161
Alignment explanation
Indices: 421376--421743 Score: 520
Period size: 174 Copynumber: 2.2 Consensus size: 161
421366 CGTGTATTCG
*
421376 TATTAAAGCTTAAGTTTTTACCTATGGTGACATTGTTATTAGCTAGCAAGTGGAGTATTGTTACT
1 TATTAAAGCTTAAGCTTTTACCTATGGTGACATTGTTATTAGCTAGCAAGTGGAGTATTGTTACT
* * *
421441 GTTTTTGATTACCGGTTTAATACGGCTTCTTGATTTATGTTTCATATGCTTGTACCGTGTGCTCA
66 GTTTTTGATTACCGGTTTAATACGGCATCTTGATTTATGTTTCATATGCTTGCACCGTGTACTCA
* * *
421506 TTTGGTGAGGTTAGATGTTGGCACATACTCG
131 TTAGGTGAGGTTAGATGTAGGCACATACTCA
421537 TATTAAAGCTTAAGCTTTTACCTATGGTGACATTGTTATTAGCTAGCAAGTGGAGTATTGTTATT
1 TATTAAAGCTTAAGCTTTTACCTATGGTGACATTGTTATTAGCTAGCAAGT-G-G-A--G-TATT
*
421602 CGTTACTGTTTTTGATTACCGGTTTAAATACGGCATCTTGATTTATGTTTCATATGCTTGCACTG
60 -GTTACTGTTTTTGATTACCGGTTT-AATACGGCATCTTGATTTATGTTTCATATGCTTGCACCG
* *
421667 TGTATTCATTCAGGTAAGGATGGTTATATGTAGGCACATACTCA
123 TGTACTCATT-AGGT---GA-GGTTAGATGTAGGCACATACTCA
*
421711 TATTAAAGCTTAAGCTTTTACATATGGTGACAT
1 TATTAAAGCTTAAGCTTTTACCTATGGTGACAT
421744 ATTTTTGATT
Statistics
Matches: 183, Mismatches: 11, Indels: 13
0.88 0.05 0.06
Matches are distributed among these distances:
161 50 0.27
162 1 0.01
163 1 0.01
164 1 0.01
166 1 0.01
167 4 0.02
168 24 0.13
169 44 0.24
170 3 0.02
173 2 0.01
174 52 0.28
ACGTcount: A:0.24, C:0.14, G:0.21, T:0.41
Consensus pattern (161 bp):
TATTAAAGCTTAAGCTTTTACCTATGGTGACATTGTTATTAGCTAGCAAGTGGAGTATTGTTACT
GTTTTTGATTACCGGTTTAATACGGCATCTTGATTTATGTTTCATATGCTTGCACCGTGTACTCA
TTAGGTGAGGTTAGATGTAGGCACATACTCA
Found at i:431693 original size:2 final size:2
Alignment explanation
Indices: 431686--431728 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
431676 ATACTATCCC
431686 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
431728 T
1 T
431729 TAATTCATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:435402 original size:42 final size:44
Alignment explanation
Indices: 435328--435417 Score: 130
Period size: 42 Copynumber: 2.1 Consensus size: 44
435318 GAACCGACCT
* * *
435328 GATCCAATCCGAAAATATATATACCATACACCTTACCTGAATCC
1 GATCAAATCCGAAAATATATATACCATACACCTGACCCGAATCC
*
435372 GATCAAATCCG-AAA-ATATATACCATCCACCTGACCCGAATCC
1 GATCAAATCCGAAAATATATATACCATACACCTGACCCGAATCC
435414 GATC
1 GATC
435418 CGAATTTTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
42 29 0.69
43 3 0.07
44 10 0.24
ACGTcount: A:0.38, C:0.31, G:0.09, T:0.22
Consensus pattern (44 bp):
GATCAAATCCGAAAATATATATACCATACACCTGACCCGAATCC
Found at i:439628 original size:34 final size:34
Alignment explanation
Indices: 439580--439666 Score: 165
Period size: 34 Copynumber: 2.6 Consensus size: 34
439570 AAACGAGCTT
*
439580 ATAAACGAGTCAATAAACGGGTTTCTTTTTTAAC
1 ATAAACGAGCCAATAAACGGGTTTCTTTTTTAAC
439614 ATAAACGAGCCAATAAACGGGTTTCTTTTTTAAC
1 ATAAACGAGCCAATAAACGGGTTTCTTTTTTAAC
439648 ATAAACGAGCCAATAAACG
1 ATAAACGAGCCAATAAACG
439667 AGCTCATGGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 52 1.00
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (34 bp):
ATAAACGAGCCAATAAACGGGTTTCTTTTTTAAC
Found at i:441299 original size:24 final size:24
Alignment explanation
Indices: 441272--441333 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 24
441262 CAGAAATTAT
441272 AACAGAATTCAGATCAAATATCAG
1 AACAGAATTCAGATCAAATATCAG
* * * *
441296 AACATAATCCATATCATATATCAG
1 AACAGAATTCAGATCAAATATCAG
* *
441320 AATAGAAATCAGAT
1 AACAGAATTCAGAT
441334 AAAACGTTCA
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.50, C:0.16, G:0.10, T:0.24
Consensus pattern (24 bp):
AACAGAATTCAGATCAAATATCAG
Found at i:442195 original size:27 final size:28
Alignment explanation
Indices: 442141--442199 Score: 102
Period size: 27 Copynumber: 2.1 Consensus size: 28
442131 AATTCCAGGG
442141 TTTAGAGGTACTTTAGGTCATTTTACAC
1 TTTAGAGGTACTTTAGGTCATTTTACAC
*
442169 TTTAGAGGTATTTTA-GTCATTTTACAC
1 TTTAGAGGTACTTTAGGTCATTTTACAC
442196 TTTA
1 TTTA
442200 TGGGCATTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 16 0.53
28 14 0.47
ACGTcount: A:0.25, C:0.12, G:0.15, T:0.47
Consensus pattern (28 bp):
TTTAGAGGTACTTTAGGTCATTTTACAC
Found at i:442217 original size:27 final size:27
Alignment explanation
Indices: 442160--442217 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
442150 ACTTTAGGTC
* * *
442160 ATTTTACACTTTAGAGGTATTTTAGTC
1 ATTTTACACTTTAGAGGCATTATAGTA
*
442187 ATTTTACACTTTATG-GGCATTATCGTA
1 ATTTTACACTTTA-GAGGCATTATAGTA
442214 ATTT
1 ATTT
442218 ATCCATGACA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 25 0.96
28 1 0.04
ACGTcount: A:0.26, C:0.12, G:0.14, T:0.48
Consensus pattern (27 bp):
ATTTTACACTTTAGAGGCATTATAGTA
Found at i:444096 original size:183 final size:183
Alignment explanation
Indices: 443710--444096 Score: 627
Period size: 183 Copynumber: 2.1 Consensus size: 183
443700 ATTAAATTTT
* * *
443710 AAATATTAAATATATTATATATAACATATGGGCTCAACCCAAATCATTTAAAACTCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGAGCTCAACCCAAACCATTTAAAACCCAATTAATAA
*
443775 TTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTATATAAATTTTT
66 TTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTATATAAAATTTT
* *
443840 TATTTTATAATTATATATTATTTAAATTATTTGTAAACTGTTTTTTAATTAAA
131 TATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTAATTAAA
* *
443893 AAATATTAAATATATTATATATAACATATGAG-TTAAGCCTAAACCATTTAAAACCCAATTAATA
1 AAATATTAAATATATTATATATAACATATGAGCTCAA-CCCAAACCATTTAAAACCCAATTAATA
*
443957 ATTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTTATCTAAAATT
65 ATTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAA-TTATATAAAATT
444022 TTTATTTTATAATTATATATTATTTAAATTAATTATAAACT-TTTTTTGAATTAAA
129 TTTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTT-AATTAAA
* *
444077 AAATATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
444097 AATTAGAAAA
Statistics
Matches: 190, Mismatches: 11, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
182 3 0.02
183 121 0.64
184 66 0.35
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (183 bp):
AAATATTAAATATATTATATATAACATATGAGCTCAACCCAAACCATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTATATAAAATTTT
TATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTAATTAAA
Found at i:450584 original size:103 final size:103
Alignment explanation
Indices: 450400--450617 Score: 375
Period size: 103 Copynumber: 2.1 Consensus size: 103
450390 GTCGAGGGTC
450400 TATGTGG-TCTTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATA
1 TATGTGGTTC-TTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATA
* **
450464 CTTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
65 CTTGATCCCTAACATATGTATATGATTCTTAAGGAATGA
450503 TATGTGGTTCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTTCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
450568 TTGATCCCTAATATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAACATATGTATATGATTCTTAAGGAATGA
*
450606 TATATGGTTCTT
1 TATGTGGTTCTT
450618 ATGGACATTA
Statistics
Matches: 109, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
103 107 0.98
104 2 0.02
ACGTcount: A:0.27, C:0.12, G:0.23, T:0.38
Consensus pattern (103 bp):
TATGTGGTTCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAACATATGTATATGATTCTTAAGGAATGA
Found at i:450671 original size:23 final size:23
Alignment explanation
Indices: 450634--450701 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
450624 ATTATTATAT
*
450634 GGCACTACGGTGCAATTCTACGC
1 GGCACTCCGGTGCAATTCTACGC
* *
450657 GGTACTCCGGTGCAATTCTACGT
1 GGCACTCCGGTGCAATTCTACGC
* * *
450680 GGCACTTCGATGCAATTATACG
1 GGCACTCCGGTGCAATTCTACG
450702 AGCTGTGGTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.22, C:0.26, G:0.25, T:0.26
Consensus pattern (23 bp):
GGCACTCCGGTGCAATTCTACGC
Found at i:453454 original size:41 final size:39
Alignment explanation
Indices: 453409--453486 Score: 120
Period size: 39 Copynumber: 1.9 Consensus size: 39
453399 GAAGAAAAAG
*
453409 AAGTACATATTTTTTTTTATATTTTTTAATTGACACGTAGT
1 AAGTACATA-TATTTTTTATA-TTTTTAATTGACACGTAGT
*
453450 AAGTATATATATTTTTTATATTTTTAATTGACACGTA
1 AAGTACATATATTTTTTATATTTTTAATTGACACGTA
453487 AACACATGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
39 17 0.49
40 10 0.29
41 8 0.23
ACGTcount: A:0.32, C:0.06, G:0.09, T:0.53
Consensus pattern (39 bp):
AAGTACATATATTTTTTATATTTTTAATTGACACGTAGT
Found at i:458890 original size:11 final size:11
Alignment explanation
Indices: 458853--458947 Score: 65
Period size: 11 Copynumber: 8.9 Consensus size: 11
458843 AAATATGACA
*
458853 AAATGATCATT
1 AAATTATCATT
458864 AAATT-T-A-T
1 AAATTATCATT
*
458872 AGAATTATAATT
1 A-AATTATCATT
* *
458884 AAATTATTATA
1 AAATTATCATT
*
458895 AAATAATCATT
1 AAATTATCATT
*
458906 AAATTCT-ATT
1 AAATTATCATT
*
458916 AAATTATTA-T
1 AAATTATCATT
*
458926 AAATAATCATT
1 AAATTATCATT
458937 AAATTTATCAT
1 AAA-TTATCAT
458948 AATTTTGTAT
Statistics
Matches: 65, Mismatches: 12, Indels: 13
0.72 0.13 0.14
Matches are distributed among these distances:
8 2 0.03
9 5 0.08
10 19 0.29
11 31 0.48
12 8 0.12
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.43
Consensus pattern (11 bp):
AAATTATCATT
Found at i:458933 original size:31 final size:32
Alignment explanation
Indices: 458881--458941 Score: 115
Period size: 31 Copynumber: 1.9 Consensus size: 32
458871 TAGAATTATA
458881 ATTAAATTATTATAAAATAATCATTAAATTCT
1 ATTAAATTATTATAAAATAATCATTAAATTCT
458913 ATTAAATTATTAT-AAATAATCATTAAATT
1 ATTAAATTATTATAAAATAATCATTAAATT
458942 TATCATAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 16 0.55
32 13 0.45
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (32 bp):
ATTAAATTATTATAAAATAATCATTAAATTCT
Found at i:465370 original size:23 final size:23
Alignment explanation
Indices: 465309--465370 Score: 54
Period size: 24 Copynumber: 2.6 Consensus size: 23
465299 ATGTTTAGTA
* *
465309 TTTAAATTATTAATTTTTATCTAT
1 TTTAAATCA-TAACTTTTATCTAT
* *
465333 TTTAATATC-TAAACTTTTATTTTT
1 TTTAA-ATCAT-AACTTTTATCTAT
465357 TTTAAATCATAACT
1 TTTAAATCATAACT
465371 AATGTTTAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
23 8 0.26
24 21 0.68
25 2 0.06
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.58
Consensus pattern (23 bp):
TTTAAATCATAACTTTTATCTAT
Found at i:468001 original size:57 final size:57
Alignment explanation
Indices: 467913--468030 Score: 236
Period size: 57 Copynumber: 2.1 Consensus size: 57
467903 CGGTACATGC
467913 TTCTTGTCCATGAAAAAAAGAACCTTGAGGTACTTCGTATGCACCGGCGAAACTTTA
1 TTCTTGTCCATGAAAAAAAGAACCTTGAGGTACTTCGTATGCACCGGCGAAACTTTA
467970 TTCTTGTCCATGAAAAAAAGAACCTTGAGGTACTTCGTATGCACCGGCGAAACTTTA
1 TTCTTGTCCATGAAAAAAAGAACCTTGAGGTACTTCGTATGCACCGGCGAAACTTTA
468027 TTCT
1 TTCT
468031 GCAAAGGCTC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 61 1.00
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.30
Consensus pattern (57 bp):
TTCTTGTCCATGAAAAAAAGAACCTTGAGGTACTTCGTATGCACCGGCGAAACTTTA
Found at i:472997 original size:10 final size:11
Alignment explanation
Indices: 472977--473064 Score: 55
Period size: 9 Copynumber: 8.5 Consensus size: 11
472967 ATGGTAAAAT
472977 AAAAATAATAA
1 AAAAATAATAA
472988 AAAAAT-ATAA
1 AAAAATAATAA
* **
472998 AAAAGT--TTT
1 AAAAATAATAA
473007 AAAAATAAT--
1 AAAAATAATAA
*
473016 AATAATAATAA
1 AAAAATAATAA
*
473027 AATAAGTAAT-A
1 AA-AAATAATAA
473038 AAAAAT-ATAA
1 AAAAATAATAA
*
473048 AAATTATAATAA
1 AAA-AATAATAA
473060 AAAAA
1 AAAAA
473065 ACATAAACGA
Statistics
Matches: 59, Mismatches: 10, Indels: 16
0.69 0.12 0.19
Matches are distributed among these distances:
9 16 0.27
10 16 0.27
11 15 0.25
12 12 0.20
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (11 bp):
AAAAATAATAA
Found at i:473028 original size:39 final size:39
Alignment explanation
Indices: 472974--473059 Score: 104
Period size: 39 Copynumber: 2.2 Consensus size: 39
472964 TCCATGGTAA
* *
472974 AATAAAAATAATAAAA-AAAT-ATAAAAAAGTTTTAAAAAT
1 AATAATAATAATAAAATAAATAATAAAAAA--TATAAAAAT
*
473013 AATAATAATAATAAAATAAGTAATAAAAAATATAAAAAT
1 AATAATAATAATAAAATAAATAATAAAAAATATAAAAAT
*
473052 TATAATAA
1 AATAATAA
473060 AAAAAACATA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
39 30 0.73
40 3 0.07
41 8 0.20
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (39 bp):
AATAATAATAATAAAATAAATAATAAAAAATATAAAAAT
Found at i:473040 original size:30 final size:30
Alignment explanation
Indices: 472974--473050 Score: 86
Period size: 30 Copynumber: 2.6 Consensus size: 30
472964 TCCATGGTAA
472974 AATAAAAATAATAAAAAAATATAAAAAAGT
1 AATAAAAATAATAAAAAAATATAAAAAAGT
** * *
473004 TTTAAAAATAATAATAATAATA-AAATAAGT
1 AATAAAAATAATAA-AAAAATATAAAAAAGT
473034 AATAAAAA-ATATAAAAA
1 AATAAAAATA-ATAAAAA
473051 TTATAATAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
29 3 0.08
30 29 0.76
31 6 0.16
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.25
Consensus pattern (30 bp):
AATAAAAATAATAAAAAAATATAAAAAAGT
Found at i:473042 original size:14 final size:13
Alignment explanation
Indices: 472972--473065 Score: 54
Period size: 12 Copynumber: 7.3 Consensus size: 13
472962 ATTCCATGGT
*
472972 AAAATAAAAATAA
1 AAAATAATAATAA
*
472985 TAAAAAAAT-ATAA
1 -AAAATAATAATAA
**
472998 AAAAGTTTTAA-AA
1 AAAA-TAATAATAA
*
473011 ATAATAATAATAA
1 AAAATAATAATAA
473024 TAAAATAAGTAATAA
1 -AAAATAA-TAATAA
473039 AAAAT-ATAA-AA
1 AAAATAATAATAA
**
473050 ATTATAATAA-AA
1 AAAATAATAATAA
473062 AAAA
1 AAAA
473066 CATAAACGAA
Statistics
Matches: 61, Mismatches: 13, Indels: 14
0.69 0.15 0.16
Matches are distributed among these distances:
11 5 0.08
12 19 0.31
13 13 0.21
14 18 0.30
15 6 0.10
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (13 bp):
AAAATAATAATAA
Found at i:475998 original size:18 final size:18
Alignment explanation
Indices: 475975--476010 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
475965 TTACAGACGA
475975 TGAAACCAAAGAATGACT
1 TGAAACCAAAGAATGACT
475993 TGAAACCAAAGAATGACT
1 TGAAACCAAAGAATGACT
476011 AGTATCAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.17, G:0.17, T:0.17
Consensus pattern (18 bp):
TGAAACCAAAGAATGACT
Found at i:478150 original size:42 final size:42
Alignment explanation
Indices: 478044--478151 Score: 128
Period size: 42 Copynumber: 2.6 Consensus size: 42
478034 CAAAATTTAT
* *
478044 CACCAATGAATGCACACGGTAATCAAGGACACAAACCGGCTA
1 CACCACTGGATGCACACGGTAATCAAGGACACAAACCGGCTA
* * * * *
478086 CACCAGC-AGCTGCACGCAGTAATCAAGGACCCAAACCGGCTA
1 CACCA-CTGGATGCACACGGTAATCAAGGACACAAACCGGCTA
*
478128 CACCACTGGATGCACATGGTAATC
1 CACCACTGGATGCACACGGTAATC
478152 CTATCAAGAA
Statistics
Matches: 52, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
41 1 0.02
42 51 0.98
ACGTcount: A:0.35, C:0.31, G:0.20, T:0.13
Consensus pattern (42 bp):
CACCACTGGATGCACACGGTAATCAAGGACACAAACCGGCTA
Found at i:478957 original size:42 final size:42
Alignment explanation
Indices: 478898--479012 Score: 212
Period size: 42 Copynumber: 2.7 Consensus size: 42
478888 TTTTTATTAC
**
478898 GACTAACAACGAATAAACGATTGTAAAGTAATAAGTAAGAAT
1 GACTAACGGCGAATAAACGATTGTAAAGTAATAAGTAAGAAT
478940 GACTAACGGCGAATAAACGATTGTAAAGTAATAAGTAAGAAT
1 GACTAACGGCGAATAAACGATTGTAAAGTAATAAGTAAGAAT
478982 GACTAACGGCGAATAAACGATTGTAAAGTAA
1 GACTAACGGCGAATAAACGATTGTAAAGTAA
479013 GAATGACTAA
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.49, C:0.10, G:0.20, T:0.21
Consensus pattern (42 bp):
GACTAACGGCGAATAAACGATTGTAAAGTAATAAGTAAGAAT
Found at i:481998 original size:39 final size:38
Alignment explanation
Indices: 481942--482073 Score: 119
Period size: 39 Copynumber: 3.4 Consensus size: 38
481932 GTCCTAACTG
481942 ACCTAGAATAATT-ATCCCTCTTTCGATCATCTCTCTCCC
1 ACCTAGAAT-ATTCATCCCTCTTTCGATCATCT-TCTCCC
* *
481981 ACCTAGAATATTCATCCCTCTTCCGATCCA-CTTTTCCCC
1 ACCTAGAATATTCATCCCTCTTTCGAT-CATCTTCT-CCC
* * * *
482020 ATCTAGAGTATTCAT-CCT-TATTCTGGTCATCTTCCCCCC
1 ACCTAGAATATTCATCCCTCT-TTC-GATCATCTT-CTCCC
482059 ACCTAGAATATTCAT
1 ACCTAGAATATTCAT
482074 AGCTATTCAA
Statistics
Matches: 76, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
37 1 0.01
38 12 0.16
39 61 0.80
40 2 0.03
ACGTcount: A:0.23, C:0.35, G:0.07, T:0.36
Consensus pattern (38 bp):
ACCTAGAATATTCATCCCTCTTTCGATCATCTTCTCCC
Found at i:483415 original size:194 final size:195
Alignment explanation
Indices: 482858--483464 Score: 610
Period size: 192 Copynumber: 3.1 Consensus size: 195
482848 TCTCTCCCTC
* * *
482858 TGTCTGCATCAGAATCAGATTCACTACCCATGTTGTCCCTCTCTCTCCTTTGACTCCCAATTAAT
1 TGTCTGCATCAGAATCAGATTCACTACCCATGTTGTCCCTCTCTCTCCTCTGACTCCCAATCAAA
* * * ** *
482923 TCATTCTTTCGTTTATGAATTTCACCTCT-T-TTCTTTTCCCTCTCGTCATCAGAATCAGAGCCA
66 TCAATCTTTCGTTTTTGAATTTCACCTCTCTCTTCTTTT-CCTCACACCATCAGAATCAGAGTCA
* * * * *
482986 TCCACAATGGAGTCATGCCTATTACGACCTTTT-TTAGCTGTTT-CTTTTTTTCGGCCTCTTTGT
130 TCCTCACTCGAGTCATGCCTATTACGA-CTTTTCTTAGCTGTTTCCTTTTTGTCAGCCTCTTTGT
483049 CT
194 CT
* ** * * * * * * * **
483051 T-TCAGCATCAGAATCAGATTCGTTACCCATATTGCCCCGCTCTCTCCTCAGCCTACCAAACAGC
1 TGTCTGCATCAGAATCAGATTCACTACCCATGTTGTCCCTCTCTCTCCTCTGACTCCCAATCAAA
* *
483115 TCAATCTTTTGTTTTTGAACTTCA-C-CTCTCTTCTTTTCCTTCACACCATCAGAATCAGAGTCA
66 TCAATCTTTCGTTTTTGAATTTCACCTCTCTCTTCTTTTCC-TCACACCATCAGAATCAGAGTCA
* * * *
483178 TCCTCAC-CGGAGTCGTGTCTATTACGACCTTTCTTAGCTGTTTCCTTTTTGT-AGTCTC-TTGT
130 TCCTCACTC-GAGTCATGCCTATTACGACTTTTCTTAGCTGTTTCCTTTTTGTCAGCCTCTTTGT
*
483240 TT
194 CT
* *** * * *
483242 TGTCTGCATCAGAATCAGATCCACTACTTGTGTTTTCCCTCTCTCTCCTCTGGCTCCCAGTCAAA
1 TGTCTGCATCAGAATCAGATTCACTACCCATGTTGTCCCTCTCTCTCCTCTGACTCCCAATCAAA
* * *
483307 TCAGTCTTCCGTTTTTGAATTTCACCTCTCTCTTCTTTTCTCTCCCACCATCAGAATCAGAGTCA
66 TCAATCTTTCGTTTTTGAATTTCACCTCTCTCTTCTTTTC-CTCACACCATCAGAATCAGAGTCA
* * * *
483372 TCCTCACTCGAGTCATGCCTATGACGACTTTTCCTAACTGTTTCCTTTTT-T-AGACCTC-TTGC
130 TCCTCACTCGAGTCATGCCTATTACGACTTTTCTTAGCTGTTTCCTTTTTGTCAG-CCTCTTTGT
*
483434 CC
194 CT
* * *
483436 TATCTGAATCAGAATCTGATTCACTACCC
1 TGTCTGCATCAGAATCAGATTCACTACCC
483465 TGCAATATTA
Statistics
Matches: 331, Mismatches: 71, Indels: 23
0.78 0.17 0.05
Matches are distributed among these distances:
190 2 0.01
191 14 0.04
192 195 0.59
193 12 0.04
194 106 0.32
195 2 0.01
ACGTcount: A:0.19, C:0.30, G:0.12, T:0.39
Consensus pattern (195 bp):
TGTCTGCATCAGAATCAGATTCACTACCCATGTTGTCCCTCTCTCTCCTCTGACTCCCAATCAAA
TCAATCTTTCGTTTTTGAATTTCACCTCTCTCTTCTTTTCCTCACACCATCAGAATCAGAGTCAT
CCTCACTCGAGTCATGCCTATTACGACTTTTCTTAGCTGTTTCCTTTTTGTCAGCCTCTTTGTCT
Found at i:492101 original size:37 final size:39
Alignment explanation
Indices: 492032--492110 Score: 108
Period size: 38 Copynumber: 2.1 Consensus size: 39
492022 TATTTTGTGT
* *
492032 ATAATTTTGTAAGGACTTTAAACAACTTGAA-GGAGTGG
1 ATAATTTTGTAAGGACTTAAAACAACTGGAAGGGAGTGG
* *
492070 ATAATTTTGTGAGTACTTAAAACAAC-GGAAGGGAGTGG
1 ATAATTTTGTAAGGACTTAAAACAACTGGAAGGGAGTGG
492108 ATA
1 ATA
492111 TCTTTGCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
37 3 0.08
38 33 0.92
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.29
Consensus pattern (39 bp):
ATAATTTTGTAAGGACTTAAAACAACTGGAAGGGAGTGG
Found at i:496011 original size:18 final size:16
Alignment explanation
Indices: 495988--496034 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 16
495978 CACAAAGCAC
495988 AAAACAACAGAACACATA
1 AAAACAACAGAACAC--A
496006 AAAACAACA-AA-ACA
1 AAAACAACAGAACACA
496020 AAAACAACAGCAACA
1 AAAACAACAG-AACA
496035 ACGACAACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
14 10 0.38
16 4 0.15
17 3 0.12
18 9 0.35
ACGTcount: A:0.70, C:0.23, G:0.04, T:0.02
Consensus pattern (16 bp):
AAAACAACAGAACACA
Found at i:499346 original size:12 final size:12
Alignment explanation
Indices: 499326--499356 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
499316 TATGTCCTTC
*
499326 TTCCACCTTTCA
1 TTCCTCCTTTCA
499338 TTCCTCCTTTCA
1 TTCCTCCTTTCA
499350 TTCCTCC
1 TTCCTCC
499357 AAATGTCAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.10, C:0.45, G:0.00, T:0.45
Consensus pattern (12 bp):
TTCCTCCTTTCA
Found at i:509616 original size:72 final size:72
Alignment explanation
Indices: 509531--509743 Score: 363
Period size: 72 Copynumber: 2.9 Consensus size: 72
509521 GCAAATTGTA
* *
509531 ACACAAACACGGATAACAAAAGCCAAAAGAGAGTAGAAATCATAGTATTAAATTGTGATCGTCAT
1 ACAC-AACACGGATAACAAAAGCCAAAAGAGAGTAGAAATCATAGTACTAAATTGCGATCGTCAT
509596 TACGGACG
65 TACGGACG
*
509604 ACACAACACGGATAACAAAAGCCAAAAGAAAGTAGAAATCATAGTACTAAATTGCGATCGTCATT
1 ACACAACACGGATAACAAAAGCCAAAAGAGAGTAGAAATCATAGTACTAAATTGCGATCGTCATT
509669 ACGGACG
66 ACGGACG
* * *
509676 ACACATCACGGATAACAAAAGTCAAAAGAGAGTAGAAATCATAGTACTAAATTGCAATCGTCATT
1 ACACAACACGGATAACAAAAGCCAAAAGAGAGTAGAAATCATAGTACTAAATTGCGATCGTCATT
509741 ACG
66 ACG
509744 AACATGATTT
Statistics
Matches: 133, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
72 129 0.97
73 4 0.03
ACGTcount: A:0.46, C:0.18, G:0.18, T:0.19
Consensus pattern (72 bp):
ACACAACACGGATAACAAAAGCCAAAAGAGAGTAGAAATCATAGTACTAAATTGCGATCGTCATT
ACGGACG
Found at i:517912 original size:20 final size:18
Alignment explanation
Indices: 517874--517912 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
517864 ATTTTTTATA
*
517874 TTTTTTAAAAATAACAAT
1 TTTTTTAAAAATAAAAAT
517892 TTTTATTAAAATATAAAAAT
1 TTTT-TTAAAA-ATAAAAAT
517912 T
1 T
517913 AAATTTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 6 0.33
20 8 0.44
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (18 bp):
TTTTTTAAAAATAAAAAT
Found at i:522240 original size:23 final size:22
Alignment explanation
Indices: 522214--522262 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
522204 GCATATCAAG
522214 TAAATTATATGATATATTT-TTAT
1 TAAATT-TAT-ATATATTTGTTAT
*
522237 TAAATTTATTTATATTTGTTAT
1 TAAATTTATATATATTTGTTAT
522259 TAAA
1 TAAA
522263 AATCATCTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 7 0.29
22 11 0.46
23 6 0.25
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (22 bp):
TAAATTTATATATATTTGTTAT
Found at i:526403 original size:18 final size:20
Alignment explanation
Indices: 526367--526406 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
526357 TGCTTCCCAA
526367 TTCTATTGGCTTGCATTTTT
1 TTCTATTGGCTTGCATTTTT
526387 TTCTATTGGC-T-CATTTTT
1 TTCTATTGGCTTGCATTTTT
526405 TT
1 TT
526407 TTTGATAGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 9 0.45
19 1 0.05
20 10 0.50
ACGTcount: A:0.10, C:0.15, G:0.12, T:0.62
Consensus pattern (20 bp):
TTCTATTGGCTTGCATTTTT
Found at i:536776 original size:23 final size:23
Alignment explanation
Indices: 536753--536801 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
536743 TAAATTATTA
*
536753 ATAAAGT-ATTAAATAAACTTTT
1 ATAAAGTAATGAAATAAACTTTT
*
536775 A-AAAGTAATGAAATATACTTTT
1 ATAAAGTAATGAAATAAACTTTT
536797 ATAAA
1 ATAAA
536802 TAAAAGGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 5 0.22
22 15 0.65
23 3 0.13
ACGTcount: A:0.53, C:0.04, G:0.06, T:0.37
Consensus pattern (23 bp):
ATAAAGTAATGAAATAAACTTTT
Found at i:542711 original size:20 final size:18
Alignment explanation
Indices: 542686--542776 Score: 66
Period size: 18 Copynumber: 5.1 Consensus size: 18
542676 TCATATTGTT
*
542686 CAGGGGGTACAGCTTCCCCC
1 CAGGGGGTACAGATT--CCC
*
542706 CAGGGGGAACAGATTCCC
1 CAGGGGGTACAGATTCCC
542724 CAGGGGGTATC-GATTCCC
1 CAGGGGGTA-CAGATTCCC
*
542742 C---GGGAACAGATTCTCC
1 CAGGGGGTACAGATTC-CC
*
542758 CAAGGGGTATC-GATTCCC
1 CAGGGGGTA-CAGATTCCC
542776 C
1 C
542777 GGTACAGATT
Statistics
Matches: 59, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
14 1 0.02
15 9 0.15
16 3 0.05
18 22 0.37
19 10 0.17
20 14 0.24
ACGTcount: A:0.21, C:0.32, G:0.30, T:0.18
Consensus pattern (18 bp):
CAGGGGGTACAGATTCCC
Found at i:542770 original size:34 final size:33
Alignment explanation
Indices: 542710--542790 Score: 128
Period size: 33 Copynumber: 2.5 Consensus size: 33
542700 TCCCCCCAGG
*
542710 GGGAACAGATTCCCCAGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCAAGGGGTATCGATTCCCC
542743 GGGAACAGATTCTCCCAAGGGGTATCGATTCCCC
1 GGGAACAGATTC-CCCAAGGGGTATCGATTCCCC
*
542777 -GGTACAGATTCCCC
1 GGGAACAGATTCCCC
542791 CTGCATGGTT
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
32 3 0.07
33 22 0.49
34 20 0.44
ACGTcount: A:0.22, C:0.31, G:0.27, T:0.20
Consensus pattern (33 bp):
GGGAACAGATTCCCCAAGGGGTATCGATTCCCC
Found at i:542927 original size:21 final size:21
Alignment explanation
Indices: 542903--542944 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
542893 ATTTTAATAT
**
542903 TATGAAGGGGTATTGATTCCC
1 TATGAAGGGGTACCGATTCCC
542924 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
542945 CCCATTCTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.29
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:543006 original size:21 final size:21
Alignment explanation
Indices: 542973--543012 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
542963 TTTTTGTAGA
*
542973 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
542995 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
543013 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:549646 original size:174 final size:169
Alignment explanation
Indices: 549307--549650 Score: 643
Period size: 174 Copynumber: 2.0 Consensus size: 169
549297 TGATGCCTTT
549307 GTACTAGGCAATATAGTTACCTTGTTGTGCTAGCATTGTCAAGAAGCCGTTTTCGTAATGCAATA
1 GTACTAGGCAATATAGTTACCTTGTTGTGCTAGCATTGTCAAGAAGCCGTTTTCGTAATGCAATA
549372 GGCACAAAGAAGATAGATCATTTGATTGTAGCTCTCTTTCATTTTTTTCTCCTTTTTTATGCCAT
66 GGCACAAAGAAGATAGATCATTTGATTGTAGCTCTCTTTCATTTTTTTCTCCTTTTTTATGCCAT
549437 TTTTTGGGGGAAAAATAATATCAAATAGAAAAGTAGTCA
131 TTTTTGGGGGAAAAATAATATCAAATAGAAAAGTAGTCA
549476 GTACTAGGCAATATAGTTACCTTGTTGTGCTAGCATTGTCAAGAAGCCGTTTTCTGTAATGCAAT
1 GTACTAGGCAATATAGTTACCTTGTTGTGCTAGCATTGTCAAGAAGCCGTTTTC-GTAATGCAAT
549541 AGGCACAAAGAAGATAGATCATTTGATTGTAGCTCTCTTTCATTTATTTTCTTCTCCTTTTTTAT
65 AGGCACAAAGAAGATAGATCATTTGATTGTAGCTCTCTTTCA--T-TTTT-TTCTCCTTTTTTAT
549606 GCCATTTTTTGGGGGAAAAATAATATCAAATAGAAAAGTAGTCA
126 GCCATTTTTTGGGGGAAAAATAATATCAAATAGAAAAGTAGTCA
549650 G
1 G
549651 AAAGGAGTGG
Statistics
Matches: 170, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
169 54 0.32
170 52 0.31
172 1 0.01
173 4 0.02
174 59 0.35
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (169 bp):
GTACTAGGCAATATAGTTACCTTGTTGTGCTAGCATTGTCAAGAAGCCGTTTTCGTAATGCAATA
GGCACAAAGAAGATAGATCATTTGATTGTAGCTCTCTTTCATTTTTTTCTCCTTTTTTATGCCAT
TTTTTGGGGGAAAAATAATATCAAATAGAAAAGTAGTCA
Found at i:549840 original size:28 final size:30
Alignment explanation
Indices: 549789--549847 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
549779 GCCTCTTCTT
*
549789 TGTCCTCCCTGCTTTCTCATTTTAGCATTG
1 TGTCCTCCCTGCCTTCTCATTTTAGCATTG
*
549819 TGTCCTTCCTGCCTT-TC-TTTTAGCATTG
1 TGTCCTCCCTGCCTTCTCATTTTAGCATTG
549847 T
1 T
549848 TTTTTATGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 12 0.44
29 2 0.07
30 13 0.48
ACGTcount: A:0.08, C:0.29, G:0.14, T:0.49
Consensus pattern (30 bp):
TGTCCTCCCTGCCTTCTCATTTTAGCATTG
Found at i:550701 original size:22 final size:23
Alignment explanation
Indices: 550673--550716 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
550663 TTTCCCTTTT
550673 TTGATGTCTC-AAACTATGCCCC
1 TTGATGTCTCAAAACTATGCCCC
550695 TTGATGTCTCAAAACTATGCCC
1 TTGATGTCTCAAAACTATGCCC
550717 TCTCTTTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.25, C:0.30, G:0.14, T:0.32
Consensus pattern (23 bp):
TTGATGTCTCAAAACTATGCCCC
Found at i:558591 original size:14 final size:14
Alignment explanation
Indices: 558572--558599 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
558562 TATTTTATCA
558572 TTTAATCATATTTT
1 TTTAATCATATTTT
558586 TTTAATCATATTTT
1 TTTAATCATATTTT
558600 GTACACGCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTAATCATATTTT
Found at i:559488 original size:165 final size:165
Alignment explanation
Indices: 559215--559619 Score: 648
Period size: 165 Copynumber: 2.5 Consensus size: 165
559205 GATTTGGATT
* *
559215 ATGATAAGAATGAGGGGTCAAAGGAAGATAATTGTTTGGGGATTAATGGAGTTGATTCGGTTAAG
1 ATGATAAGAATGAGGGGTCAAAGGAAGATCATTGTTTGGGGATTAATGGGGTTGATTCGGTTAAG
* * * *
559280 AGGATACGAGAAGATCATATTGGTGTCGTAGTGGCCGGATCAGATGAGAGGTTGGAAGAAAGAGT
66 AGGATACAAGAAGAACATATTGGTGTCGAAGTGGCCAGATCAGATGAGAGGTTGGAAGAAAGAGT
* **
559345 GGATAGTGGAAGTGAGGACAATGCGGTTGTAAAAC
131 GGATAGTGGAAGTGAAGACAATGAAGTTGTAAAAC
559380 ATGATAAGAATGAGGGGTCAAAGGAAGATCATTGTTTGGGGATTAATGGGGTTGATTCGGTTAAG
1 ATGATAAGAATGAGGGGTCAAAGGAAGATCATTGTTTGGGGATTAATGGGGTTGATTCGGTTAAG
* * * * *
559445 AGGAAACAAGAGGAACATATTGGTGTTGAAGTGGCCAGATCAGATGAGAGGTTGGAAGTAAGATT
66 AGGATACAAGAAGAACATATTGGTGTCGAAGTGGCCAGATCAGATGAGAGGTTGGAAGAAAGAGT
*
559510 GGATAGTGGAAGTGAAGACAATGAAGTTGTAGAAC
131 GGATAGTGGAAGTGAAGACAATGAAGTTGTAAAAC
* *
559545 ATGCTAAGAATGAGGGGTCAAAGGAAGATCATTGTTTGGGGATTAATGGGGTTGATTCTGTTAAG
1 ATGATAAGAATGAGGGGTCAAAGGAAGATCATTGTTTGGGGATTAATGGGGTTGATTCGGTTAAG
*
559610 AAGATACAAG
66 AGGATACAAG
559620 TTTCCGGAGA
Statistics
Matches: 221, Mismatches: 19, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
165 221 1.00
ACGTcount: A:0.34, C:0.06, G:0.35, T:0.25
Consensus pattern (165 bp):
ATGATAAGAATGAGGGGTCAAAGGAAGATCATTGTTTGGGGATTAATGGGGTTGATTCGGTTAAG
AGGATACAAGAAGAACATATTGGTGTCGAAGTGGCCAGATCAGATGAGAGGTTGGAAGAAAGAGT
GGATAGTGGAAGTGAAGACAATGAAGTTGTAAAAC
Found at i:565861 original size:22 final size:21
Alignment explanation
Indices: 565822--565863 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
565812 AATTATAACT
565822 AATAATATATAAATTATATTA
1 AATAATATATAAATTATATTA
565843 AATAATTATATTAAA-TATATT
1 AATAA-TATA-TAAATTATATT
565864 TATATTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 10 0.53
23 4 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AATAATATATAAATTATATTA
Found at i:565868 original size:15 final size:13
Alignment explanation
Indices: 565833--565869 Score: 56
Period size: 13 Copynumber: 2.7 Consensus size: 13
565823 ATAATATATA
565833 AATTATATTAAAT
1 AATTATATTAAAT
565846 AATTATATTAAAT
1 AATTATATTAAAT
565859 ATATTTATATT
1 A-A-TTATATT
565870 TTAAAAGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 14 0.64
14 1 0.05
15 7 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
AATTATATTAAAT
Found at i:567598 original size:14 final size:16
Alignment explanation
Indices: 567579--567613 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
567569 CGTTCATTTA
567579 ATAAAT-AA-ACGAAC
1 ATAAATAAATACGAAC
567593 ATAAATAAATACGAAC
1 ATAAATAAATACGAAC
567609 ATAAA
1 ATAAA
567614 CGAACAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.32
15 2 0.11
16 11 0.58
ACGTcount: A:0.66, C:0.11, G:0.06, T:0.17
Consensus pattern (16 bp):
ATAAATAAATACGAAC
Found at i:567718 original size:16 final size:16
Alignment explanation
Indices: 567693--567731 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
567683 ATAAACGAAC
567693 ATAAACGAACACAAAT
1 ATAAACGAACACAAAT
* *
567709 ATAAATGAACACGAAT
1 ATAAACGAACACAAAT
567725 ATAAACG
1 ATAAACG
567732 TTAGAGACTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.59, C:0.15, G:0.10, T:0.15
Consensus pattern (16 bp):
ATAAACGAACACAAAT
Found at i:568842 original size:34 final size:35
Alignment explanation
Indices: 568804--568940 Score: 138
Period size: 34 Copynumber: 3.9 Consensus size: 35
568794 GATTGGATTA
* *
568804 AACATAAAT-GAATGAACATAAACAAACATAAACG
1 AACATAAATCGAACGAACATAAACAAAAATAAACG
**
568838 AACAT-AATCGAACGAACATAAACAAAAATAATTG
1 AACATAAATCGAACGAACATAAACAAAAATAAACG
* *
568872 AACAT-AACCGAACGAATATAAACATTCACAAACGTAAACG
1 AACATAAATCGAACGAACATAAACA---A-AAA--TAAACG
568912 AACAT-AATCGAACGAACATAAACAAAAAT
1 AACATAAATCGAACGAACATAAACAAAAAT
568941 CTTGTTCATG
Statistics
Matches: 86, Mismatches: 10, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
33 3 0.03
34 49 0.57
36 3 0.03
37 2 0.02
38 3 0.03
40 26 0.30
ACGTcount: A:0.58, C:0.18, G:0.09, T:0.15
Consensus pattern (35 bp):
AACATAAATCGAACGAACATAAACAAAAATAAACG
Found at i:568849 original size:10 final size:10
Alignment explanation
Indices: 568817--568850 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
568807 ATAAATGAAT
568817 GAACATAAAC
1 GAACATAAAC
*
568827 AAACATAAAC
1 GAACATAAAC
*
568837 GAACATAATC
1 GAACATAAAC
568847 GAAC
1 GAAC
568851 GAACATAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.59, C:0.21, G:0.09, T:0.12
Consensus pattern (10 bp):
GAACATAAAC
Found at i:568855 original size:24 final size:24
Alignment explanation
Indices: 568828--568934 Score: 74
Period size: 24 Copynumber: 4.4 Consensus size: 24
568818 AACATAAACA
568828 AACATAAACGAACATAATCGAACG
1 AACATAAACGAACATAATCGAACG
* * * *
568852 AACATAAACAAAAATAATTGAACAT
1 AACATAAACGAACATAATCGAAC-G
** * * *
568877 AAC-CGAACGAATATAAAC-ATTCACA
1 AACATAAACGAACATAATCGA---ACG
*
568902 AACGTAAACGAACATAATCGAACG
1 AACATAAACGAACATAATCGAACG
568926 AACATAAAC
1 AACATAAAC
568935 AAAAATCTTG
Statistics
Matches: 60, Mismatches: 17, Indels: 12
0.67 0.19 0.13
Matches are distributed among these distances:
23 1 0.02
24 39 0.65
25 6 0.10
26 13 0.22
27 1 0.02
ACGTcount: A:0.56, C:0.20, G:0.09, T:0.15
Consensus pattern (24 bp):
AACATAAACGAACATAATCGAACG
Found at i:571887 original size:27 final size:27
Alignment explanation
Indices: 571856--571939 Score: 97
Period size: 27 Copynumber: 3.3 Consensus size: 27
571846 TAATTATTTA
571856 AATATTTTAATCAAGTCATATATCATT
1 AATATTTTAATCAAGTCATATATCATT
* * *
571883 AATATTTGAA--AATTAAT-TAT--TT
1 AATATTTTAATCAAGTCATATATCATT
571905 AAATATTTTAATCAAGTCATATATCATT
1 -AATATTTTAATCAAGTCATATATCATT
571933 AATATTT
1 AATATTT
571940 GATGGTATAA
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
22 2 0.04
23 9 0.20
24 3 0.07
25 10 0.22
26 3 0.07
27 16 0.36
28 2 0.04
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (27 bp):
AATATTTTAATCAAGTCATATATCATT
Found at i:571895 original size:50 final size:50
Alignment explanation
Indices: 571841--571941 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
571831 GATTAATTAA
571841 AAAATTAATTATTTAAATATTTTAATCAAGTCATATATCATTAATATTTG
1 AAAATTAATTATTTAAATATTTTAATCAAGTCATATATCATTAATATTTG
571891 AAAATTAATTATTTAAATATTTTAATCAAGTCATATATCATTAATATTTG
1 AAAATTAATTATTTAAATATTTTAATCAAGTCATATATCATTAATATTTG
571941 A
1 A
571942 TGGTATAAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.46
Consensus pattern (50 bp):
AAAATTAATTATTTAAATATTTTAATCAAGTCATATATCATTAATATTTG
Found at i:572287 original size:29 final size:29
Alignment explanation
Indices: 572255--572473 Score: 171
Period size: 29 Copynumber: 7.6 Consensus size: 29
572245 TTATTTTTGT
* * *
572255 TTAACTTATAAATCTATTTTATTCTAATT
1 TTAACTTATAAATATATTTTATTCTTATC
*
572284 TTAA--TATAAAAAATATTTTATTAC-TATC
1 TTAACTTAT-AAATATATTTTATT-CTTATC
* * *
572312 TTCACTTA-AAACTATATTTTATTTTTGTC
1 TTAACTTATAAA-TATATTTTATTCTTATC
* * *
572341 TTAACTTAGAAATCTATTTTATTCTTATT
1 TTAACTTATAAATATATTTTATTCTTATC
* *
572370 TTAA--TATAAAAGATATTTTATTATTATC
1 TTAACTTAT-AAATATATTTTATTCTTATC
* * *
572398 TTCACTTAAAATATATATTTTATTCTTATT
1 TTAACTTATAA-ATATATTTTATTCTTATC
* * *
572428 TTAAATTAAAAATATATTTTATTATTATC
1 TTAACTTATAAATATATTTTATTCTTATC
* *
572457 TTAACTTTTAAAAATAT
1 TTAACTTATAAATATAT
572474 AATTTTTAAA
Statistics
Matches: 148, Mismatches: 31, Indels: 22
0.74 0.15 0.11
Matches are distributed among these distances:
27 5 0.03
28 39 0.26
29 73 0.49
30 31 0.21
ACGTcount: A:0.38, C:0.08, G:0.01, T:0.53
Consensus pattern (29 bp):
TTAACTTATAAATATATTTTATTCTTATC
Found at i:572357 original size:86 final size:86
Alignment explanation
Indices: 572233--572450 Score: 305
Period size: 86 Copynumber: 2.5 Consensus size: 86
572223 TTAACTTTTA
* * *
572233 AAAATATTTTTTTTATTTTTGTTTAACTTATAAATCTATTTTATTCTAATTTTAATATAAAAAAT
1 AAAATATATATTTTATTTTTGTTTAACTTAAAAATCTATTTTATTCTAATTTTAATATAAAAAAT
572298 ATTTTATTACTATCTTCACTT
66 ATTTTATTACTATCTTCACTT
* * * *
572319 AAAA-CTATATTTTATTTTTGTCTTAACTTAGAAATCTATTTTATTCTTATTTTAATATAAAAGA
1 AAAATATATATTTTATTTTTGT-TTAACTTAAAAATCTATTTTATTCTAATTTTAATATAAAAAA
*
572383 TATTTTATTATTATCTTCACTT
65 TATTTTATTACTATCTTCACTT
* *
572405 AAAATATATATTTTATTCTTAT-TTTAAATTAAAAATATATTTTATT
1 AAAATATATATTTTATT-TT-TGTTTAACTTAAAAATCTATTTTATT
572451 ATTATCTTAA
Statistics
Matches: 117, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
85 14 0.12
86 68 0.58
87 31 0.26
88 3 0.03
89 1 0.01
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (86 bp):
AAAATATATATTTTATTTTTGTTTAACTTAAAAATCTATTTTATTCTAATTTTAATATAAAAAAT
ATTTTATTACTATCTTCACTT
Found at i:572482 original size:15 final size:17
Alignment explanation
Indices: 572457--572495 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
572447 TATTATTATC
*
572457 TTAACTTTTAAAA-ATA
1 TTAATTTTTAAAACATA
572473 -TAATTTTTAAAACATA
1 TTAATTTTTAAAACATA
572489 TTAATTT
1 TTAATTT
572496 CAAAATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 11 0.55
16 3 0.15
17 6 0.30
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (17 bp):
TTAATTTTTAAAACATA
Found at i:574276 original size:16 final size:15
Alignment explanation
Indices: 574229--574277 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
574219 CTGAACCTAG
574229 AATAACTCAAACTAAA
1 AATAACTCAAA-TAAA
574245 AATAAC-CAAATAAAA
1 AATAACTCAAAT-AAA
* *
574260 AATAACTCGAATGAA
1 AATAACTCAAATAAA
574275 AAT
1 AAT
574278 GAACCCTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
14 1 0.03
15 18 0.62
16 10 0.34
ACGTcount: A:0.63, C:0.14, G:0.04, T:0.18
Consensus pattern (15 bp):
AATAACTCAAATAAA
Found at i:578034 original size:34 final size:34
Alignment explanation
Indices: 577995--578078 Score: 93
Period size: 32 Copynumber: 2.5 Consensus size: 34
577985 TTAAAAATAC
577995 ATATATAATATAGTTTAAAACA-TTTTGAAAA-T
1 ATATATAATATAGTTTAAAACATTTTTGAAAATT
* * *
578027 ATGTATATTATAGTTTTTAAAATATTTTTGAAAATT
1 ATATATAATATAG--TTTAAAACATTTTTGAAAATT
578063 ATATA-ATATATAGTTT
1 ATATATA-ATATAGTTT
578079 TTGAAAACGT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
32 11 0.26
34 11 0.26
35 10 0.24
36 10 0.24
ACGTcount: A:0.44, C:0.01, G:0.07, T:0.48
Consensus pattern (34 bp):
ATATATAATATAGTTTAAAACATTTTTGAAAATT
Found at i:578097 original size:36 final size:36
Alignment explanation
Indices: 577982--578105 Score: 118
Period size: 35 Copynumber: 3.6 Consensus size: 36
577972 TTGCAAATTG
* *
577982 TTTTTAAAAATACATATATAATATAG--TTTAAAACA
1 TTTTTAAAATTATATATAT-ATATAGTTTTTAAAACA
* * *
578017 TTTTGAAAA-TATGTATAT-TATAGTTTTTAAAATA
1 TTTTTAAAATTATATATATATATAGTTTTTAAAACA
*
578051 TTTTTGAAAATTATATA-ATATATAGTTTTTGAAAACG
1 TTTTT-AAAATTATATATATATATAGTTTTT-AAAACA
578088 TTTTTAAAA-TATA-ATATA
1 TTTTTAAAATTATATATATA
578106 CTTTTGAAAA
Statistics
Matches: 74, Mismatches: 8, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
32 5 0.07
34 20 0.27
35 21 0.28
36 19 0.26
37 9 0.12
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.46
Consensus pattern (36 bp):
TTTTTAAAATTATATATATATATAGTTTTTAAAACA
Found at i:578177 original size:25 final size:24
Alignment explanation
Indices: 578149--578217 Score: 68
Period size: 25 Copynumber: 2.8 Consensus size: 24
578139 TAATTTTAAA
578149 AAAATATTTGAAAATATATTTTTTG
1 AAAATATTT-AAAATATATTTTTTG
* * *
578174 AAAATTATATAATATATAGTTTTTG
1 AAAA-TATTTAAAATATATTTTTTG
578199 AAAACGT-TTTAAAATATAT
1 AAAA--TATTTAAAATATAT
578218 ATAATATATA
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
25 30 0.86
26 5 0.14
ACGTcount: A:0.46, C:0.01, G:0.07, T:0.45
Consensus pattern (24 bp):
AAAATATTTAAAATATATTTTTTG
Done.