Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold88
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: 1260485
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
File 8 of 8
Found at i:1103348 original size:6 final size:6
Alignment explanation
Indices: 1103329--1103376 Score: 75
Period size: 6 Copynumber: 8.5 Consensus size: 6
1103319 TTGACCAAAC
1103329 CAAAA- CAAAA- CAAAAG CAAAAG CAAAAG CAAAAG CAAAAG C-AAAG
1 CAAAAG CAAAAG CAAAAG CAAAAG CAAAAG CAAAAG CAAAAG CAAAAG
1103374 CAA
1 CAA
1103377 GATTATTCCA
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
5 15 0.37
6 26 0.63
ACGTcount: A:0.69, C:0.19, G:0.12, T:0.00
Consensus pattern (6 bp):
CAAAAG
Found at i:1104306 original size:3 final size:3
Alignment explanation
Indices: 1104298--1104323 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1104288 TTATTAATAT
1104298 ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC AT
1104324 TATTATCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.31, G:0.00, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:1108484 original size:12 final size:12
Alignment explanation
Indices: 1108467--1108491 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1108457 CCCCCCCCCC
1108467 CAAAAAAAAAAA
1 CAAAAAAAAAAA
1108479 CAAAAAAAAAAA
1 CAAAAAAAAAAA
1108491 C
1 C
1108492 TTTCATTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (12 bp):
CAAAAAAAAAAA
Found at i:1110300 original size:1 final size:1
Alignment explanation
Indices: 1110294--1110319 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
1110284 TGTTGAATTC
1110294 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
1110320 GAACCAAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1110514 original size:3 final size:3
Alignment explanation
Indices: 1110506--1110542 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
1110496 AGAATCCAAG
1110506 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1110543 TGAAAAATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:1110776 original size:52 final size:53
Alignment explanation
Indices: 1110714--1110926 Score: 168
Period size: 52 Copynumber: 4.1 Consensus size: 53
1110704 ATCATTCTGA
* * * *
1110714 GTTCGGGTCATTTC-GGATTTGGGTCAATCAGG-TTAACATTCGAGTTAATCGG
1 GTTCGAGTCATTTCTGGATTCGGATCAATCAGGTTTAACACTCG-GTTAATCGG
* *
1110766 GTTCGAGTCA-TTCTGGATTCGGATCAATTAGGTTTAACACTCGGTTAATTGG
1 GTTCGAGTCATTTCTGGATTCGGATCAATCAGGTTTAACACTCGGTTAATCGG
* * * * * * *
1110818 GTTTGAGTCA-TTCTAGATTC-AAGTCAATTAGATTTAACACTTGGTTAATCGA
1 GTTCGAGTCATTTCTGGATTCGGA-TCAATCAGGTTTAACACTCGGTTAATCGG
* * * * ** *
1110870 GCTCGAATCATTT-TGAATTCGGGTCAATTGGGTTTAACATTCAGGTTAAATCGG
1 GTTCGAGTCATTTCTGGATTCGGATCAATCAGGTTTAACACTC-GGTT-AATCGG
1110924 GTT
1 GTT
1110927 TAAATCATTT
Statistics
Matches: 128, Mismatches: 26, Indels: 12
0.77 0.16 0.07
Matches are distributed among these distances:
51 4 0.03
52 102 0.80
53 15 0.12
54 7 0.05
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.37
Consensus pattern (53 bp):
GTTCGAGTCATTTCTGGATTCGGATCAATCAGGTTTAACACTCGGTTAATCGG
Found at i:1111757 original size:22 final size:24
Alignment explanation
Indices: 1111714--1111761 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
1111704 TATCAATTCA
1111714 AATTAAATTAAATTTAAATTTAAATT
1 AATTAAATTAAATTT--ATTTAAATT
1111740 AATT-AATTAAATTT-TTTAAATT
1 AATTAAATTAAATTTATTTAAATT
1111762 CGAACAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 8 0.36
25 10 0.45
26 4 0.18
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
AATTAAATTAAATTTATTTAAATT
Found at i:1113281 original size:2 final size:2
Alignment explanation
Indices: 1113276--1113306 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1113266 ACACACACAC
1113276 AT AT 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 AT AT A
1113307 ATTCATTGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1114536 original size:28 final size:28
Alignment explanation
Indices: 1114504--1114561 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
1114494 AGACTATATA
1114504 ATAGCTAGGTTTCGTTGGGTTGAGAAGC
1 ATAGCTAGGTTTCGTTGGGTTGAGAAGC
1114532 ATAGCTAGGTTTCGTTGGGTTGAGAAGC
1 ATAGCTAGGTTTCGTTGGGTTGAGAAGC
1114560 AT
1 AT
1114562 GCATGCATGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.22, C:0.10, G:0.34, T:0.33
Consensus pattern (28 bp):
ATAGCTAGGTTTCGTTGGGTTGAGAAGC
Found at i:1120618 original size:31 final size:31
Alignment explanation
Indices: 1120580--1120735 Score: 177
Period size: 31 Copynumber: 5.0 Consensus size: 31
1120570 GATTTCAAAC
* *
1120580 CGTGCCACCAGTTAAGAATAATGGTTTTTGT
1 CGTGCCACCAGATAAGAATAGTGGTTTTTGT
* **
1120611 CGTGCCACCGGATAAGAATAGTGGTTTTTAC
1 CGTGCCACCAGATAAGAATAGTGGTTTTTGT
1120642 CGTGCCACCAGATAAGAATAGTGGTTTTTGT
1 CGTGCCACCAGATAAGAATAGTGGTTTTTGT
** * * *
1120673 CGTGCCACTGGATAAAAATAGTAGTTTTTTGC
1 CGTGCCACCAGATAAGAATAGT-GGTTTTTGT
*** *
1120705 CGTGCCATTGGATAAGAATAGTGATTTTTGT
1 CGTGCCACCAGATAAGAATAGTGGTTTTTGT
1120736 TCTGAACCGT
Statistics
Matches: 107, Mismatches: 17, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
31 80 0.75
32 27 0.25
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.34
Consensus pattern (31 bp):
CGTGCCACCAGATAAGAATAGTGGTTTTTGT
Found at i:1120675 original size:62 final size:63
Alignment explanation
Indices: 1120578--1120735 Score: 219
Period size: 62 Copynumber: 2.5 Consensus size: 63
1120568 TCGATTTCAA
* * *
1120578 ACCGTGCCACCAGTTAAGAATAATGGTTTTTGTCGTGCCACCGGATAAGAATAGT-GGTTTTT
1 ACCGTGCCACCAGATAAGAATAGTGGTTTTTGTCGTGCCACCGGATAAAAATAGTAGGTTTTT
* *
1120640 ACCGTGCCACCAGATAAGAATAGTGGTTTTTGTCGTGCCACTGGATAAAAATAGTAGTTTTTT
1 ACCGTGCCACCAGATAAGAATAGTGGTTTTTGTCGTGCCACCGGATAAAAATAGTAGGTTTTT
* *** *
1120703 GCCGTGCCATTGGATAAGAATAGTGATTTTTGT
1 ACCGTGCCACCAGATAAGAATAGTGGTTTTTGT
1120736 TCTGAACCGT
Statistics
Matches: 85, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
62 51 0.60
63 34 0.40
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.34
Consensus pattern (63 bp):
ACCGTGCCACCAGATAAGAATAGTGGTTTTTGTCGTGCCACCGGATAAAAATAGTAGGTTTTT
Found at i:1122342 original size:72 final size:72
Alignment explanation
Indices: 1122223--1122518 Score: 429
Period size: 72 Copynumber: 4.1 Consensus size: 72
1122213 ACGATAATTC
* * * *
1122223 GAGATAATCTGCATGATAAATACAATCAACAACTATTT-TCGCTTATTTAAAACTAATATCAATA
1 GAGATAATCTGCACGATAAATACAATCAACAACTATTTCT-GCATATTTAAAACTACTATCAACA
1122287 ACTAATCT
65 ACTAATCT
* * *
1122295 GAGATAATCTGTACGATAAATACAATCAATAAC-ATTTTTTGCATATTTAAAACTACTATCAACA
1 GAGATAATCTGCACGATAAATACAATCAACAACTA-TTTCTGCATATTTAAAACTACTATCAACA
*
1122359 ACTAATCC
65 ACTAATCT
*
1122367 GAGATAATCTGCACGATAAATACAATCAACAACTATTTCTGCATATTT-AAACTACTATCATCAA
1 GAGATAATCTGCACGATAAATACAATCAACAACTATTTCTGCATATTTAAAACTACTATCAACAA
*
1122431 ATAAT-T
66 CTAATCT
* *
1122437 CGAGATAATCTGTACGATAAATACAATCAAAAACTATTTCTGCATATTTAAAACTACTATCAACA
1 -GAGATAATCTGCACGATAAATACAATCAACAACTATTTCTGCATATTTAAAACTACTATCAACA
1122502 ACTAATCT
65 ACTAATCT
1122510 GAGATAATC
1 GAGATAATC
1122519 AACAACTTTC
Statistics
Matches: 201, Mismatches: 17, Indels: 12
0.87 0.07 0.05
Matches are distributed among these distances:
71 66 0.33
72 132 0.66
73 3 0.01
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.31
Consensus pattern (72 bp):
GAGATAATCTGCACGATAAATACAATCAACAACTATTTCTGCATATTTAAAACTACTATCAACAA
CTAATCT
Found at i:1122482 original size:143 final size:144
Alignment explanation
Indices: 1122217--1122518 Score: 461
Period size: 143 Copynumber: 2.1 Consensus size: 144
1122207 GATGAAACGA
* * *
1122217 TAATTCGAGATAATCTGCATGATAAATACAATCAACAACTATTTTCGCTTATTTAAAACTAATAT
1 TAATCCGAGATAATCTGCACGATAAATACAATCAACAACTATTTTCGCATATTTAAAACTAATAT
* * *
1122282 CAATAACTAATCTGAGATAATCTGTACGATAAATACAATCAATAACATTTTTTGCATATTTAAAA
66 CAATAAATAATCTGAGATAATCTGTACGATAAATACAATCAAAAACATTTTCTGCATATTTAAAA
1122347 CTACTATCAACAAC
131 CTACTATCAACAAC
*
1122361 TAATCCGAGATAATCTGCACGATAAATACAATCAACAACTA-TTTCTGCATATTT-AAACTACTA
1 TAATCCGAGATAATCTGCACGATAAATACAATCAACAACTATTTTC-GCATATTTAAAACTAATA
1122424 TC-ATCAAATAAT-TCGAGATAATCTGTACGATAAATACAATCAAAAAC-TATTTCTGCATATTT
65 TCAAT-AAATAATCT-GAGATAATCTGTACGATAAATACAATCAAAAACAT-TTTCTGCATATTT
1122486 AAAACTACTATCAACAAC
127 AAAACTACTATCAACAAC
*
1122504 TAATCTGAGATAATC
1 TAATCCGAGATAATC
1122519 AACAACTTTC
Statistics
Matches: 146, Mismatches: 8, Indels: 9
0.90 0.05 0.06
Matches are distributed among these distances:
142 4 0.03
143 96 0.66
144 46 0.32
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.32
Consensus pattern (144 bp):
TAATCCGAGATAATCTGCACGATAAATACAATCAACAACTATTTTCGCATATTTAAAACTAATAT
CAATAAATAATCTGAGATAATCTGTACGATAAATACAATCAAAAACATTTTCTGCATATTTAAAA
CTACTATCAACAAC
Found at i:1122812 original size:27 final size:27
Alignment explanation
Indices: 1122782--1122841 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 27
1122772 TTGGGTCATG
1122782 GTAGGATATGATAG-GCATGGAGGTTGA
1 GTAGGATATGA-AGAGCATGGAGGTTGA
* *
1122809 GTAGGATATGACGAGTATGGAGGTTGA
1 GTAGGATATGAAGAGCATGGAGGTTGA
1122836 GTAGGA
1 GTAGGA
1122842 AAATATGGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 1 0.03
27 29 0.97
ACGTcount: A:0.30, C:0.03, G:0.42, T:0.25
Consensus pattern (27 bp):
GTAGGATATGAAGAGCATGGAGGTTGA
Found at i:1127369 original size:14 final size:14
Alignment explanation
Indices: 1127293--1127370 Score: 59
Period size: 15 Copynumber: 5.2 Consensus size: 14
1127283 AAATTTTTTA
1127293 TACTATAAACTAAT
1 TACTATAAACTAAT
**
1127307 TACCCCTAAACTAAT
1 TA-CTATAAACTAAT
* *
1127322 TATTTTAAACCTAAT
1 TACTATAAA-CTAAT
1127337 TCAACATAATAAA-TAAT
1 T--AC-T-ATAAACTAAT
1127354 TACTATAAACTAAT
1 TACTATAAACTAAT
1127368 TAC
1 TAC
1127371 ACAAAAATAA
Statistics
Matches: 50, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
13 5 0.10
14 14 0.28
15 20 0.40
17 6 0.12
18 1 0.02
19 4 0.08
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.35
Consensus pattern (14 bp):
TACTATAAACTAAT
Found at i:1127477 original size:15 final size:15
Alignment explanation
Indices: 1127457--1127511 Score: 53
Period size: 15 Copynumber: 3.8 Consensus size: 15
1127447 GAATTTACTG
1127457 TTAAAAAAATAATAA
1 TTAAAAAAATAATAA
***
1127472 TTAAAATTTTAATATA
1 TTAAAAAAATAATA-A
1127488 TT-AAAAAATAA-AA
1 TTAAAAAAATAATAA
1127501 -TAAAAAAATAA
1 TTAAAAAAATAA
1127512 AAAAAATAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
12 1 0.03
13 10 0.31
14 1 0.03
15 17 0.53
16 3 0.09
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
TTAAAAAAATAATAA
Found at i:1127612 original size:28 final size:26
Alignment explanation
Indices: 1127579--1127635 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 26
1127569 GATAAAATTT
1127579 TAAAGAAAA-GTTAAAGAATTTTAAAAAA
1 TAAAGAAAATG-TAAA-AA-TTTAAAAAA
*
1127607 TAAAGAGAATGTAAAAATTTAAAAAA
1 TAAAGAAAATGTAAAAATTTAAAAAA
1127633 TAA
1 TAA
1127636 TAAAAGTGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 12 0.44
27 2 0.07
28 12 0.44
29 1 0.04
ACGTcount: A:0.65, C:0.00, G:0.11, T:0.25
Consensus pattern (26 bp):
TAAAGAAAATGTAAAAATTTAAAAAA
Found at i:1132139 original size:2 final size:2
Alignment explanation
Indices: 1132134--1132169 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1132124 AAAAAGAAAT
*
1132134 TA TA TA TA TG 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
1132170 GTTAGTTGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1133264 original size:19 final size:21
Alignment explanation
Indices: 1133237--1133278 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1133227 TTAATAATTA
1133237 TTAAAAATA-A-TTTTTATTT
1 TTAAAAATATATTTTTTATTT
*
1133256 TTAATAATATATTTTTTATTT
1 TTAAAAATATATTTTTTATTT
1133277 TT
1 TT
1133279 TATTTTAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 8 0.40
20 1 0.05
21 11 0.55
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TTAAAAATATATTTTTTATTT
Found at i:1133491 original size:14 final size:15
Alignment explanation
Indices: 1133467--1133495 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1133457 GTTACTAAGT
1133467 TATATATATTAATAA
1 TATATATATTAATAA
1133482 TATA-ATATTAATAA
1 TATATATATTAATAA
1133496 AAAATATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATATATATTAATAA
Found at i:1133512 original size:20 final size:20
Alignment explanation
Indices: 1133487--1133524 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1133477 AATAATATAA
1133487 TATTAATAAAAAATATTTTT
1 TATTAATAAAAAATATTTTT
**
1133507 TATTAATATTAAATATTT
1 TATTAATAAAAAATATTT
1133525 AGTACATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TATTAATAAAAAATATTTTT
Found at i:1134150 original size:18 final size:19
Alignment explanation
Indices: 1134123--1134159 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
1134113 TCAACTATCA
*
1134123 TTTTATATTATTTTAATTT
1 TTTTATATTATTTAAATTT
1134142 TTTTA-ATTATTTAAATTT
1 TTTTATATTATTTAAATTT
1134160 AAAATGATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTTATATTATTTAAATTT
Found at i:1136723 original size:27 final size:27
Alignment explanation
Indices: 1136681--1136748 Score: 100
Period size: 27 Copynumber: 2.5 Consensus size: 27
1136671 TTTCATCTAA
*
1136681 ATGCATATTTTCATAAAAATTGTGATT
1 ATGCATCTTTTCATAAAAATTGTGATT
* *
1136708 ATGCATCTTTTTATAAAGATTGTGATT
1 ATGCATCTTTTCATAAAAATTGTGATT
*
1136735 ATACATCTTTTCAT
1 ATGCATCTTTTCAT
1136749 CCAAGATGAT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.32, C:0.10, G:0.10, T:0.47
Consensus pattern (27 bp):
ATGCATCTTTTCATAAAAATTGTGATT
Found at i:1138416 original size:3 final size:3
Alignment explanation
Indices: 1138408--1138444 Score: 65
Period size: 3 Copynumber: 12.0 Consensus size: 3
1138398 TATAAATAAA
1138408 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT
1138445 GTAAGAATAC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1146461 original size:4 final size:4
Alignment explanation
Indices: 1146434--1146490 Score: 78
Period size: 4 Copynumber: 14.2 Consensus size: 4
1146424 TGGATCATTA
* * * *
1146434 ATAT ATAC ATAC ATAC ATAC ATAT ATAT ATAT ATAT ATAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
1146482 ATAT ATAT A
1 ATAT ATAT A
1146491 GGATTCACAC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 51 1.00
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (4 bp):
ATAT
Found at i:1147246 original size:2 final size:2
Alignment explanation
Indices: 1147239--1147274 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1147229 CTGCAGTTAA
1147239 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
1147275 TTGCTGCACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1149110 original size:3 final size:3
Alignment explanation
Indices: 1149102--1149128 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1149092 ATTTTATATT
1149102 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1149129 TACTTTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1149661 original size:2 final size:2
Alignment explanation
Indices: 1149654--1149695 Score: 50
Period size: 2 Copynumber: 21.0 Consensus size: 2
1149644 AAAATGATTC
* *
1149654 AT AT AT AT AT AT AT AT AT AC AT AT AT AC AT -T AT AT CAT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT
1149696 TGCACACTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
1 1 0.03
2 31 0.91
3 2 0.06
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1151142 original size:8 final size:8
Alignment explanation
Indices: 1151129--1151164 Score: 56
Period size: 8 Copynumber: 4.5 Consensus size: 8
1151119 GTCACAATAC
1151129 AAAATAAA
1 AAAATAAA
1151137 AAAATAAAA
1 AAAAT-AAA
1151146 AAAATAAA
1 AAAATAAA
1151154 AAAA-AAA
1 AAAATAAA
1151161 AAAA
1 AAAA
1151165 CAACAACAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 7 0.26
8 12 0.44
9 8 0.30
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (8 bp):
AAAATAAA
Found at i:1151148 original size:9 final size:9
Alignment explanation
Indices: 1151129--1151164 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
1151119 GTCACAATAC
1151129 AAAAT-AAA
1 AAAATAAAA
1151137 AAAATAAAA
1 AAAATAAAA
1151146 AAAATAAAA
1 AAAATAAAA
1151155 AAAA-AAAA
1 AAAATAAAA
1151163 AA
1 AA
1151165 CAACAACAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 11 0.41
9 16 0.59
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (9 bp):
AAAATAAAA
Found at i:1151151 original size:17 final size:16
Alignment explanation
Indices: 1151129--1151164 Score: 63
Period size: 17 Copynumber: 2.2 Consensus size: 16
1151119 GTCACAATAC
1151129 AAAATAAAAAAATAAAA
1 AAAATAAAAAAA-AAAA
1151146 AAAATAAAAAAAAAAA
1 AAAATAAAAAAAAAAA
1151162 AAA
1 AAA
1151165 CAACAACAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (16 bp):
AAAATAAAAAAAAAAA
Found at i:1155314 original size:27 final size:27
Alignment explanation
Indices: 1155284--1155340 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
1155274 AATTAATAAG
*
1155284 AATGTTTTTCTATTATAAAACAAAATT
1 AATGTTTTTCTACTATAAAACAAAATT
* * *
1155311 AATGTTTTTCTACTGTAGAACAACATT
1 AATGTTTTTCTACTATAAAACAAAATT
1155338 AAT
1 AAT
1155341 TCTTATCGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.42
Consensus pattern (27 bp):
AATGTTTTTCTACTATAAAACAAAATT
Found at i:1156327 original size:1 final size:1
Alignment explanation
Indices: 1156321--1156436 Score: 232
Period size: 1 Copynumber: 116.0 Consensus size: 1
1156311 GAAGAAGAGA
1156321 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1156386 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1156437 AGAGGGGAGG
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 115 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:1156668 original size:17 final size:17
Alignment explanation
Indices: 1156646--1156680 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1156636 TTTAATGTTC
1156646 TTTAATACAAATTTTAT
1 TTTAATACAAATTTTAT
* *
1156663 TTTAATATATATTTTAT
1 TTTAATACAAATTTTAT
1156680 T
1 T
1156681 ATTTAATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTAATACAAATTTTAT
Found at i:1156687 original size:19 final size:18
Alignment explanation
Indices: 1156646--1156708 Score: 74
Period size: 19 Copynumber: 3.5 Consensus size: 18
1156636 TTTAATGTTC
* *
1156646 TTTAATACAAATTTTA-T
1 TTTAATATATATTTTATT
1156663 TTTAATATATATTTTATT
1 TTTAATATATATTTTATT
* *
1156681 ATTTAATATATATATAATT
1 -TTTAATATATATTTTATT
1156700 TTTAATATA
1 TTTAATATA
1156709 AAAATAATTC
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
17 14 0.35
18 10 0.25
19 16 0.40
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTAATATATATTTTATT
Found at i:1156715 original size:18 final size:18
Alignment explanation
Indices: 1156682--1156717 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1156672 TATTTTATTA
* *
1156682 TTTAATATATATATAATT
1 TTTAATATAAAAATAATT
1156700 TTTAATATAAAAATAATT
1 TTTAATATAAAAATAATT
1156718 CTAATTTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTAATATAAAAATAATT
Found at i:1156807 original size:35 final size:35
Alignment explanation
Indices: 1156696--1156813 Score: 111
Period size: 35 Copynumber: 3.4 Consensus size: 35
1156686 ATATATATAT
* *
1156696 AATT-TTTAATATAAAAATAATTCTAAT--TTTTA
1 AATTATTTAATATAAATATAATTTTAATAATTTTA
* * *
1156728 ATTATTATTCAACATAAATATAATTTTATTTATATTTT-
1 A--ATTATTTAATATAAATATAATTTTA-ATA-ATTTTA
1156766 -ATTATTTAATATAAATATAATTTTAATAATTTTA
1 AATTATTTAATATAAATATAATTTTAATAATTTTA
*
1156800 AATTATTTATTATA
1 AATTATTTAATATA
1156814 TATTTTTTAA
Statistics
Matches: 68, Mismatches: 9, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
32 1 0.01
33 5 0.07
34 5 0.07
35 52 0.76
36 1 0.01
39 4 0.06
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (35 bp):
AATTATTTAATATAAATATAATTTTAATAATTTTA
Found at i:1157872 original size:14 final size:15
Alignment explanation
Indices: 1157849--1157885 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
1157839 TAAGTAAATT
*
1157849 TTTA-TTATAATGTA
1 TTTATTTATAATATA
1157863 -TTATTTATAATATA
1 TTTATTTATAATATA
1157877 TTTATTTAT
1 TTTATTTAT
1157886 TGAAATCTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 3 0.15
14 9 0.45
15 8 0.40
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (15 bp):
TTTATTTATAATATA
Found at i:1159188 original size:16 final size:16
Alignment explanation
Indices: 1159167--1159197 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1159157 ATTTTTTATT
1159167 TGTGTGTATATATATG
1 TGTGTGTATATATATG
*
1159183 TGTGTGTTTATATAT
1 TGTGTGTATATATAT
1159198 ATATATATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.55
Consensus pattern (16 bp):
TGTGTGTATATATATG
Found at i:1161037 original size:18 final size:19
Alignment explanation
Indices: 1161006--1161041 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1160996 TAATATTTAG
1161006 TTATTTTAAAATTTTTATT
1 TTATTTTAAAATTTTTATT
*
1161025 TTATTTT-ACATTTTTAT
1 TTATTTTAAAATTTTTAT
1161042 CACAATATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (19 bp):
TTATTTTAAAATTTTTATT
Found at i:1165069 original size:2 final size:2
Alignment explanation
Indices: 1165062--1165087 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1165052 TGTTACAGTG
1165062 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
1165088 ACACACACAC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1165943 original size:5 final size:5
Alignment explanation
Indices: 1165933--1165962 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
1165923 TAATGATAAT
*
1165933 AGAAG AGAAG AGAAG AGAAG AGAAG TGAAG
1 AGAAG AGAAG AGAAG AGAAG AGAAG AGAAG
1165963 CAGTCCAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.57, C:0.00, G:0.40, T:0.03
Consensus pattern (5 bp):
AGAAG
Found at i:1166442 original size:6 final size:6
Alignment explanation
Indices: 1166433--1166468 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
1166423 TTTCTTTGCA
* *
1166433 TTTGCC TTTGGC TCTGGC TTTGGC TTTGGC TTTGGC
1 TTTGGC TTTGGC TTTGGC TTTGGC TTTGGC TTTGGC
1166469 AGGCCGGATC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.22, G:0.31, T:0.47
Consensus pattern (6 bp):
TTTGGC
Found at i:1171857 original size:14 final size:14
Alignment explanation
Indices: 1171838--1171870 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1171828 CAGAATAACC
1171838 AAAAATCAAAAAAA
1 AAAAATCAAAAAAA
*
1171852 AAAAATTAAAAAAA
1 AAAAATCAAAAAAA
1171866 AAAAA
1 AAAAA
1171871 AGAGACAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.88, C:0.03, G:0.00, T:0.09
Consensus pattern (14 bp):
AAAAATCAAAAAAA
Found at i:1171951 original size:15 final size:15
Alignment explanation
Indices: 1171928--1171966 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1171918 ACGGACACAC
* *
1171928 AGAAGAGAAAAGGGA
1 AGAAAAGAAAAGAGA
1171943 AGAAAAGAAAAGAGA
1 AGAAAAGAAAAGAGA
1171958 AGAGAAAGA
1 AGA-AAAGA
1171967 CAGAGGGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 16 0.76
16 5 0.24
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (15 bp):
AGAAAAGAAAAGAGA
Found at i:1172527 original size:27 final size:28
Alignment explanation
Indices: 1172482--1172567 Score: 83
Period size: 27 Copynumber: 3.1 Consensus size: 28
1172472 AATTTTATAA
* *
1172482 TTTAAATATTCATACTATATTTATAATAT
1 TTTATATATTAATA-TATATTTATAATAT
*
1172511 TTTATAGTA-TAAT-TATATTCA-AA-AT
1 TTTATA-TATTAATATATATTTATAATAT
1172536 TTTATATATTAATATAATATTT-TAATAT
1 TTTATATATTAATAT-ATATTTATAATAT
1172564 TTTA
1 TTTA
1172568 AAAATTTATT
Statistics
Matches: 47, Mismatches: 4, Indels: 13
0.73 0.06 0.20
Matches are distributed among these distances:
24 2 0.04
25 12 0.26
26 3 0.06
27 14 0.30
28 6 0.13
29 8 0.17
30 2 0.04
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.53
Consensus pattern (28 bp):
TTTATATATTAATATATATTTATAATAT
Found at i:1175212 original size:2 final size:2
Alignment explanation
Indices: 1175205--1175236 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1175195 AGTAATAATC
1175205 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1175237 ATATATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1175276 original size:2 final size:2
Alignment explanation
Indices: 1175271--1175301 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1175261 AGAGAGAAAG
1175271 AT AT 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 AT AT A
1175302 CACACATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1180847 original size:21 final size:21
Alignment explanation
Indices: 1180821--1180860 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1180811 CACGTTAATC
1180821 TTTTTATTATT-AAATTAAATA
1 TTTTTATT-TTAAAATTAAATA
1180842 TTTTTATTTTAAAATTAAA
1 TTTTTATTTTAAAATTAAA
1180861 ACACATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTTTATTTTAAAATTAAATA
Found at i:1183964 original size:37 final size:36
Alignment explanation
Indices: 1183876--1183988 Score: 113
Period size: 38 Copynumber: 3.0 Consensus size: 36
1183866 TTGTGGCATA
*
1183876 GGTT-AGAACAAAAACCACTATTCTAATCAGGTGGCAC
1 GGTTCAGAACAAAAA-CACTATTCTTATC-GGTGGCAC
*
1183913 GGTTCAGAATAAAAATCACTATTCTTATCGGTGGCAC
1 GGTTCAGAACAAAAA-CACTATTCTTATCGGTGGCAC
* * *
1183950 TTGTTGA-AACAAAAACTATTATTCTTATCCGGTGGCAC
1 -GGTTCAGAACAAAAAC-ACTATTCTTAT-CGGTGGCAC
1183988 G
1 G
1183989 ACAAAACTAC
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
36 1 0.02
37 29 0.45
38 34 0.53
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (36 bp):
GGTTCAGAACAAAAACACTATTCTTATCGGTGGCAC
Found at i:1183994 original size:31 final size:31
Alignment explanation
Indices: 1183958--1184162 Score: 211
Period size: 31 Copynumber: 6.6 Consensus size: 31
1183948 ACTTGTTGAA
*
1183958 ACAAAAACTATTATTCTTATCCGGTGGCACG
1 ACAAAAACTACTATTCTTATCCGGTGGCACG
*
1183989 AC-AAAACTACTATTCTTATCCGGTGGCATG
1 ACAAAAACTACTATTCTTATCCGGTGGCACG
* *
1184019 ATAAAAACTACTATTCTTATCCGTGTGGCA-T
1 ACAAAAACTACTATTCTTATCCG-GTGGCACG
* *
1184050 AGCAAAAA-TCACTATTTTTATCCAGTGGCACG
1 A-CAAAAACT-ACTATTCTTATCCGGTGGCACG
* * * *
1184082 A-TAAAATTACTATTCTTAACCAGTGGCACG
1 ACAAAAACTACTATTCTTATCCGGTGGCACG
* *
1184112 GCAAAAACTACTATTCTTATCCTGTGGCACG
1 ACAAAAACTACTATTCTTATCCGGTGGCACG
** *
1184143 GTAAAAGCCTACTATTCTTA
1 ACAAAA-ACTACTATTCTTA
1184163 ACCGATTGCA
Statistics
Matches: 148, Mismatches: 18, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
30 51 0.34
31 61 0.41
32 36 0.24
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.31
Consensus pattern (31 bp):
ACAAAAACTACTATTCTTATCCGGTGGCACG
Found at i:1184093 original size:93 final size:92
Alignment explanation
Indices: 1183969--1184140 Score: 254
Period size: 93 Copynumber: 1.9 Consensus size: 92
1183959 CAAAAACTAT
* * * * *
1183969 TATTCTTATCCGGTGGCACGACAAAACTACTATTCTTATCCGGTGGCATGATAAAAACTACTATT
1 TATTCTTATCCAGTGGCACGACAAAACTACTATTCTTAACCAGTGGCACGACAAAAACTACTATT
1184034 CTTATCCGTGTGGCATAGCAAAAATCAC
66 CTTATCC-TGTGGCATAGCAAAAATCAC
* * * *
1184062 TATTTTTATCCAGTGGCACGATAAAATTACTATTCTTAACCAGTGGCACGGCAAAAACTACTATT
1 TATTCTTATCCAGTGGCACGACAAAACTACTATTCTTAACCAGTGGCACGACAAAAACTACTATT
1184127 CTTATCCTGTGGCA
66 CTTATCCTGTGGCA
1184141 CGGTAAAAGC
Statistics
Matches: 70, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
92 7 0.10
93 63 0.90
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (92 bp):
TATTCTTATCCAGTGGCACGACAAAACTACTATTCTTAACCAGTGGCACGACAAAAACTACTATT
CTTATCCTGTGGCATAGCAAAAATCAC
Found at i:1184157 original size:93 final size:93
Alignment explanation
Indices: 1183959--1184162 Score: 248
Period size: 93 Copynumber: 2.2 Consensus size: 93
1183949 CTTGTTGAAA
* * * * * * *
1183959 CAAAAACTATTATTCTTATCCGGTGGCACGACAAAACTACTATTCTTATCCGGTGGCATGATAAA
1 CAAAAACCACTATTCTTATCCAGTGGCACGACAAAACTACTATTCTTAACCAGTGGCACGACAAA
*
1184024 AACTACTATTCTTATCCGTGTGGCATAG
66 AACTACTATTCTTATCCGTGTGGCACAG
* * * * *
1184052 CAAAAATCACTATTTTTATCCAGTGGCACGATAAAATTACTATTCTTAACCAGTGGCACGGCAAA
1 CAAAAACCACTATTCTTATCCAGTGGCACGACAAAACTACTATTCTTAACCAGTGGCACGACAAA
*
1184117 AACTACTATTCTTATCC-TGTGGCACGG
66 AACTACTATTCTTATCCGTGTGGCACAG
* *
1184144 TAAAAGCCTACTATTCTTA
1 CAAAAACC-ACTATTCTTA
1184163 ACCGATTGCA
Statistics
Matches: 92, Mismatches: 18, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
92 13 0.14
93 79 0.86
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Consensus pattern (93 bp):
CAAAAACCACTATTCTTATCCAGTGGCACGACAAAACTACTATTCTTAACCAGTGGCACGACAAA
AACTACTATTCTTATCCGTGTGGCACAG
Found at i:1185949 original size:87 final size:88
Alignment explanation
Indices: 1185746--1185984 Score: 354
Period size: 87 Copynumber: 2.7 Consensus size: 88
1185736 AGATTCCTTT
* * *
1185746 GACAGAAAATATTTGACTAATACTTAATCAATTTCTTGAAACTCGAAAGATGTAACAGATATATG
1 GACAGAAAATATTTGACTAATACCTAATAAATTTCTTGAAACTCGAAAGATGTAACAGATACATG
*
1185811 GACTATCAGATTCCTTTTAACAC
66 GACTATCAGATTCCTTTCAACAC
* * * *
1185834 GATAGAAAATATTTGACTAATACCTAATAAATTTTTTGAAACTCGAAAGATGTGACAGATGCATG
1 GACAGAAAATATTTGACTAATACCTAATAAATTTCTTGAAACTCGAAAGATGTAACAGATACATG
* * * *
1185899 GA-TATTATATTCCTTTCGACAT
66 GACTATCAGATTCCTTTCAACAC
*
1185921 TACAGAAAATATTTGACTAATACCTAATAAATTTCTTGAAACTCGAAAGATGTAACAGATACAT
1 GACAGAAAATATTTGACTAATACCTAATAAATTTCTTGAAACTCGAAAGATGTAACAGATACAT
1185985 AGGTTTCTGA
Statistics
Matches: 134, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
87 74 0.55
88 60 0.45
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.32
Consensus pattern (88 bp):
GACAGAAAATATTTGACTAATACCTAATAAATTTCTTGAAACTCGAAAGATGTAACAGATACATG
GACTATCAGATTCCTTTCAACAC
Found at i:1189090 original size:28 final size:29
Alignment explanation
Indices: 1189055--1189141 Score: 115
Period size: 28 Copynumber: 3.1 Consensus size: 29
1189045 AAGGGGCAAG
1189055 TTCTCATCTTGCCCATCGAGAGGGTGAGT
1 TTCTCATCTTGCCCATCGAGAGGGTGAGT
* * *
1189084 TTC-CATCTCGCCCATCGAGAAGATGAG-
1 TTCTCATCTTGCCCATCGAGAGGGTGAGT
* *
1189111 TTCTCATCTTGCCCACCGAGAGGGCGAGT
1 TTCTCATCTTGCCCATCGAGAGGGTGAGT
1189140 TT
1 TT
1189142 TGAACGATAA
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
27 3 0.06
28 40 0.83
29 5 0.10
ACGTcount: A:0.20, C:0.28, G:0.25, T:0.28
Consensus pattern (29 bp):
TTCTCATCTTGCCCATCGAGAGGGTGAGT
Found at i:1189602 original size:2 final size:2
Alignment explanation
Indices: 1189595--1189621 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1189585 CAAGGTGTCA
1189595 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1189622 ATATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1198399 original size:1 final size:1
Alignment explanation
Indices: 1198395--1198434 Score: 62
Period size: 1 Copynumber: 40.0 Consensus size: 1
1198385 TTTTTTTTTT
* *
1198395 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGCGGGGAGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1198435 ATAAATTGGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.03, C:0.03, G:0.95, T:0.00
Consensus pattern (1 bp):
G
Found at i:1205577 original size:2 final size:2
Alignment explanation
Indices: 1205570--1205610 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1205560 CAACAGGAAA
1205570 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1205611 ATATTAATCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1205683 original size:2 final size:2
Alignment explanation
Indices: 1205676--1205705 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1205666 AACAACAGAA
*
1205676 TC TC TC TC TC CC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1205706 AGAAAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
TC
Found at i:1207759 original size:2 final size:2
Alignment explanation
Indices: 1207752--1207781 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1207742 ATTAATTTCC
1207752 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1207782 CATAATACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1212158 original size:2 final size:2
Alignment explanation
Indices: 1212151--1212195 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
1212141 GCTTTTATAG
*
1212151 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1212193 TC T
1 TC T
1212196 GCTTCAGATG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:1212433 original size:2 final size:2
Alignment explanation
Indices: 1212426--1212455 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1212416 TTTAGAAACA
1212426 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
1212456 TTATTATTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1220761 original size:2 final size:2
Alignment explanation
Indices: 1220754--1220778 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1220744 ATCATGGTTG
1220754 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1220779 TCCCAATCAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1229686 original size:28 final size:28
Alignment explanation
Indices: 1229655--1229708 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
1229645 TTTTATTTTT
1229655 AATTATATTT-TATATATAATATAAATAA
1 AATTATATTTATATA-ATAATATAAATAA
*
1229683 AATTATATTTATATAATAATTTAAAT
1 AATTATATTTATATAATAATATAAAT
1229709 TCTATAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 20 0.83
29 4 0.17
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (28 bp):
AATTATATTTATATAATAATATAAATAA
Found at i:1230049 original size:35 final size:35
Alignment explanation
Indices: 1230010--1230076 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
1230000 GAGATTTAAG
1230010 GTTTTAAGGTTACGAG-TTAAGATTTAAAGTTTTGA
1 GTTTTAAGGTTA-GAGTTTAAGATTTAAAGTTTTGA
* *
1230045 GTTTTAAGGTTAGAGTTTAGGGTTTAAAGTTT
1 GTTTTAAGGTTAGAGTTTAAGATTTAAAGTTT
1230077 AATGTTAAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 3 0.10
35 26 0.90
ACGTcount: A:0.28, C:0.01, G:0.25, T:0.45
Consensus pattern (35 bp):
GTTTTAAGGTTAGAGTTTAAGATTTAAAGTTTTGA
Found at i:1230230 original size:22 final size:22
Alignment explanation
Indices: 1230199--1230246 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
1230189 TTAGGGTTGA
1230199 GGTTTAAGGTTTAAAGTTGTAG
1 GGTTTAAGGTTTAAAGTTGTAG
* *
1230221 GGTTTTAGGTTTAAGGTTGTAG
1 GGTTTAAGGTTTAAAGTTGTAG
1230243 GGTT
1 GGTT
1230247 ATGATTTAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.35, T:0.44
Consensus pattern (22 bp):
GGTTTAAGGTTTAAAGTTGTAG
Found at i:1230326 original size:13 final size:13
Alignment explanation
Indices: 1230308--1230349 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
1230298 GGTTTAAAGT
1230308 TTTAAGGGTCGAG
1 TTTAAGGGTCGAG
* *
1230321 TTTAAGGTTTGAG
1 TTTAAGGGTCGAG
1230334 TTT-AGGGTTCGAG
1 TTTAAGGG-TCGAG
1230347 TTT
1 TTT
1230350 TTGTTTAGGG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
12 3 0.12
13 21 0.88
ACGTcount: A:0.19, C:0.05, G:0.33, T:0.43
Consensus pattern (13 bp):
TTTAAGGGTCGAG
Found at i:1230377 original size:7 final size:7
Alignment explanation
Indices: 1230358--1230408 Score: 54
Period size: 7 Copynumber: 7.6 Consensus size: 7
1230348 TTTTGTTTAG
1230358 GGTTCAA
1 GGTTCAA
1230365 -GTTCAA
1 GGTTCAA
1230371 GGTTCAA
1 GGTTCAA
*
1230378 GGTTCGA
1 GGTTCAA
1230385 GGTTCGAA
1 GGTTC-AA
1230393 -GTTCAA
1 GGTTCAA
*
1230399 -GTTTAA
1 GGTTCAA
1230405 GGTT
1 GGTT
1230409 TAGAGTTTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
6 13 0.34
7 24 0.63
8 1 0.03
ACGTcount: A:0.25, C:0.12, G:0.29, T:0.33
Consensus pattern (7 bp):
GGTTCAA
Found at i:1230456 original size:14 final size:13
Alignment explanation
Indices: 1230427--1230478 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 13
1230417 TAAGCTACGG
*
1230427 TTTAGG-TTAGGA
1 TTTAGGTTTAAGA
1230439 TTTAGGATTTAAGA
1 TTTAGG-TTTAAGA
*
1230453 TTTATGGTTTAAGG
1 TTTA-GGTTTAAGA
1230467 TCTTAGGTTTAA
1 T-TTAGGTTTAA
1230479 AGTTTAAAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
12 6 0.18
14 23 0.68
15 5 0.15
ACGTcount: A:0.27, C:0.02, G:0.25, T:0.46
Consensus pattern (13 bp):
TTTAGGTTTAAGA
Found at i:1230738 original size:21 final size:21
Alignment explanation
Indices: 1230645--1230751 Score: 85
Period size: 21 Copynumber: 5.1 Consensus size: 21
1230635 GGTTTGAGAC
1230645 TTAAAGTTTTA-GATTT-AGGAT
1 TTAAAG-TTTAGGATTTAAGG-T
* * * * *
1230666 TTAAGGTTTGGGGTTTGAGAT
1 TTAAAGTTTAGGATTTAAGGT
* * *
1230687 TTGAAGTTTAAGATTTAAGGA
1 TTAAAGTTTAGGATTTAAGGT
*
1230708 TTAGAGTTTAGGATTTAAGGT
1 TTAAAGTTTAGGATTTAAGGT
1230729 TTAAAGTTTAAGGA-TTAAGGT
1 TTAAAGTTT-AGGATTTAAGGT
1230750 TT
1 TT
1230752 GGGGATAAAG
Statistics
Matches: 66, Mismatches: 17, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
20 3 0.05
21 57 0.86
22 6 0.09
ACGTcount: A:0.31, C:0.00, G:0.26, T:0.43
Consensus pattern (21 bp):
TTAAAGTTTAGGATTTAAGGT
Found at i:1230746 original size:7 final size:7
Alignment explanation
Indices: 1230665--1231015 Score: 132
Period size: 7 Copynumber: 50.4 Consensus size: 7
1230655 AGATTTAGGA
1230665 TTTAAGG
1 TTTAAGG
**
1230672 TTTGGGG
1 TTTAAGG
* *
1230679 TTTGAGA
1 TTTAAGG
1230686 TTTGAA-G
1 TTT-AAGG
*
1230693 TTTAAGA
1 TTTAAGG
1230700 TTTAAGG
1 TTTAAGG
*
1230707 ATT-AGAG
1 TTTAAG-G
1230714 TTT-AGG
1 TTTAAGG
1230720 ATTTAAGG
1 -TTTAAGG
*
1230728 TTTAAAG
1 TTTAAGG
1230735 TTTAAGG
1 TTTAAGG
*
1230742 ATTAAGG
1 TTTAAGG
**
1230749 TTTGGGG
1 TTTAAGG
* *
1230756 ATAAAGG
1 TTTAAGG
*
1230763 ATT-AGAG
1 TTTAAG-G
1230770 TTTAAGG
1 TTTAAGG
*
1230777 -TTAGGG
1 TTTAAGG
*
1230783 TTTTAGGG
1 -TTTAAGG
*
1230791 TATAAGG
1 TTTAAGG
1230798 TTTAAGGG
1 TTTAA-GG
1230806 TTTAAGG
1 TTTAAGG
*
1230813 TTTAGGG
1 TTTAAGG
* *
1230820 ATTAAAG
1 TTTAAGG
*
1230827 ATTAAGG
1 TTTAAGG
1230834 TTTAAGG
1 TTTAAGG
1230841 -TTAAGG
1 TTTAAGG
**
1230847 TTTGGGG
1 TTTAAGG
1230854 TTTAAGG
1 TTTAAGG
*
1230861 TTTAGGG
1 TTTAAGG
*
1230868 TTTAAGA
1 TTTAAGG
1230875 TTT-AGG
1 TTTAAGG
*
1230881 -TTAAGT
1 TTTAAGG
*
1230887 TATGTTAGG
1 T-T-TAAGG
*
1230896 ATTTAGGG
1 -TTTAAGG
1230904 TTTAAGG
1 TTTAAGG
*
1230911 GTT-AGG
1 TTTAAGG
*
1230917 GTT-AGG
1 TTTAAGG
*
1230923 GTT-AGG
1 TTTAAGG
*
1230929 GTT-AGG
1 TTTAAGG
* *
1230935 GTTAGGG
1 TTTAAGG
* *
1230942 GTTAGGG
1 TTTAAGG
*
1230949 TTTAGGG
1 TTTAAGG
*
1230956 TTTTAGG
1 TTTAAGG
* *
1230963 TTCAGGG
1 TTTAAGG
**
1230970 TTCGAGG
1 TTTAAGG
* *
1230977 ATTGAGG
1 TTTAAGG
1230984 TTTAAGG
1 TTTAAGG
1230991 TTTAAGG
1 TTTAAGG
*
1230998 TTTAGAGT
1 TTTA-AGG
1231006 TTTAAGG
1 TTTAAGG
1231013 TTT
1 TTT
1231016 TAGGGTTTAG
Statistics
Matches: 264, Mismatches: 62, Indels: 36
0.73 0.17 0.10
Matches are distributed among these distances:
5 2 0.01
6 46 0.17
7 182 0.69
8 29 0.11
9 4 0.02
10 1 0.00
ACGTcount: A:0.26, C:0.01, G:0.34, T:0.39
Consensus pattern (7 bp):
TTTAAGG
Found at i:1230919 original size:6 final size:6
Alignment explanation
Indices: 1230898--1230957 Score: 84
Period size: 6 Copynumber: 9.3 Consensus size: 6
1230888 ATGTTAGGAT
1230898 TTAGGG TTTAAGGG TTAGGG TTAGGG TTAGGG TTAGGG TTAGGGG TTAGGG
1 TTAGGG -TT-AGGG TTAGGG TTAGGG TTAGGG TTAGGG TTA-GGG TTAGGG
1230949 TTTAGGG TT
1 -TTAGGG TT
1230958 TTAGGTTCAG
Statistics
Matches: 50, Mismatches: 0, Indels: 7
0.88 0.00 0.12
Matches are distributed among these distances:
6 30 0.60
7 16 0.32
8 4 0.08
ACGTcount: A:0.17, C:0.00, G:0.47, T:0.37
Consensus pattern (6 bp):
TTAGGG
Found at i:1231012 original size:22 final size:22
Alignment explanation
Indices: 1230984--1231048 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 22
1230974 AGGATTGAGG
1230984 TTTAAGGTTTAAGGTTTA-GAGT
1 TTTAAGGTTTAAGGTTTAGGA-T
*
1231006 TTTAAGGTTTTAGGGTTTAGGAT
1 TTTAAGG-TTTAAGGTTTAGGAT
* * *
1231029 TTTACGATTTAAGATTTAGG
1 TTTAAGGTTTAAGGTTTAGG
1231049 TTACCTTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
22 18 0.50
23 16 0.44
24 2 0.06
ACGTcount: A:0.26, C:0.02, G:0.26, T:0.46
Consensus pattern (22 bp):
TTTAAGGTTTAAGGTTTAGGAT
Found at i:1233894 original size:19 final size:19
Alignment explanation
Indices: 1233870--1233912 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
1233860 TATTTTACCC
*
1233870 AATAATCATATAATTTATT
1 AATAATCATATAATCTATT
1233889 AATAATCATATAATCTATT
1 AATAATCATATAATCTATT
1233908 AATAA
1 AATAA
1233913 AGTATTCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (19 bp):
AATAATCATATAATCTATT
Found at i:1241709 original size:141 final size:139
Alignment explanation
Indices: 1241476--1241738 Score: 427
Period size: 141 Copynumber: 1.9 Consensus size: 139
1241466 TACAAGCTTG
*
1241476 TTTTTTTTTTTTTGGATAATTGAATTTGCATTTCAACATCCAAGACAAGCAGAATGTCTGCTACA
1 TTTTTTTTTTTTTGGATAATTGAATTTGCATTTCAACATCCAAAACAAGCAGAATGTCTGCTACA
* *
1241541 AGTGTACGAGTAAAGCCTCACAAGCTTACCGGCTTATACCCCATTGTATACATAAGCTTGCTTTT
66 AGTATACGAGTAAAGCCTCACAAGCTTACCAGCTTATA-CCCATTGTATACATAAGCTTGCTTTT
1241606 TAAATTTTTT
130 TAAATTTTTT
* * *
1241616 TTTTTTTTTTTTTGGGATAATTGAATTTGCATTTCAACATCCAAAAGACGCAGAATGTTTGCTAC
1 TTTTTTTTTTTTT-GGATAATTGAATTTGCATTTCAACATCCAAAACAAGCAGAATGTCTGCTAC
* * *
1241681 AAGTATACGAGTAAAGCCTCACAAGCTTACCAGCTTCTACCCATTGTGTATATAAGCT
65 AAGTATACGAGTAAAGCCTCACAAGCTTACCAGCTTATACCCATTGTATACATAAGCT
1241739 AGCTGTTTCT
Statistics
Matches: 113, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
140 30 0.27
141 83 0.73
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (139 bp):
TTTTTTTTTTTTTGGATAATTGAATTTGCATTTCAACATCCAAAACAAGCAGAATGTCTGCTACA
AGTATACGAGTAAAGCCTCACAAGCTTACCAGCTTATACCCATTGTATACATAAGCTTGCTTTTT
AAATTTTTT
Found at i:1243859 original size:14 final size:14
Alignment explanation
Indices: 1243840--1243871 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
1243830 CATGATTCCA
1243840 ATGGAATATGATTG
1 ATGGAATATGATTG
1243854 ATGGAATATGATTG
1 ATGGAATATGATTG
1243868 ATGG
1 ATGG
1243872 GAATGTGCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (14 bp):
ATGGAATATGATTG
Found at i:1245426 original size:538 final size:543
Alignment explanation
Indices: 1244738--1245791 Score: 1380
Period size: 538 Copynumber: 1.9 Consensus size: 543
1244728 ATTTTTTTCC
* * *
1244738 CAAAATTCAATTAATAAAATATTTTAAAATAAAAAAATTTAATCAATAAAGTATGTGTAATTACA
1 CAAAATTCAATTAATAAAATATTTTAAAATAAAAAAAATTAAACAATAAAATATGTGTAATTACA
* *** *
1244803 TTGAAATATTTTAAAAAATAATGTTTACGTAATTAATTTAAAAATAAAAATTAATTTTGTTGGAA
66 TTGAAATA-TATAAAAAATAATGTTTAAAAAATTAATTTAAAAATAAAAATTAA--TTCTTGGAA
1244868 TTTTTTTTCCTTTTGATATTCAAAAATTTTTAATAAA-TTTCAAATTAATAAAACTTATCATTCT
128 TTTTTTTTCCTTTTGATATTCAAAAATTTTTAA-AAATTTTCAAATTAATAAAACTTATCATTCT
*
1244932 CTTGAAACATTACG-AGTACAATTTTGTCTCACAATTTTATTTTAACTTCCCTAAAGCATGGGAA
192 CTTGAAACATT-CGAAGGACAATTTTGTCTCACAATTTTATTTTAACTTCCC-AAAGCATGGGAA
* * ** *
1244996 AGTAACTTTACCAACCTTTTT-AGAAAGGAAGACATTCCCATGATTCATGATAATGAGATTCACA
255 AATAACTTTACCAACCTTTTTGAAAAAAAAAGACATTCACATGATTCATGATAATGAGATTCACA
* * * *
1245060 TGGGAAAGCTACATTCCCAAAAATGTACCTTACCAAACATGGGAATCGACTT-CTACCAATTAAA
320 TGCGAAAGCTACATACCCAAAAATGTACCATACCAAACATGGGAATCGACTTCCCACCAATTAAA
* * * * **
1245124 TTCCTAGGAATGTGAGCACATTCCATCATACCAAATGCACCCTAACGGGGCATTTGGTTGAG-AA
385 TTCCTAAGAATGTGAGCAAAATCCATCATACCAAACGCACCCTAACAAGGCATTTGGTTG-GCAA
* * * * * * *
1245188 AATATTTCATTA-TG-GGGTCATATAATATTTTGTCATGACATTATCATATTTGTTTTAAAAAAT
449 AATATTTCATTACCGAGGGTAACATAATATTCTATCATGACATTACCATATTTGTTTCAAAAAAT
1245251 ATTCCTCAAGTTTCATAATGTATTATTTTT
514 ATTCCTCAAGTTTCATAATGTATTATTTTT
* *
1245281 CAAAATTTAATTAATAAAATATTTTAAAAAATAAAAAAAATTAAACAATAAAATTTGTGTAATTA
1 CAAAATTCAATTAATAAAATATTTT--AAAATAAAAAAAATTAAACAATAAAATATGTGTAATTA
*
1245346 CATTTAAA-A-ATAAAACAA-AATGTTTAAAAAATATTAATTTAAAAATAAAAATTAA-TCTT-G
64 CATTGAAATATATAAAA-AATAATGTTT-AAAAA-ATTAATTTAAAAATAAAAATTAATTCTTGG
* ** *
1245406 -A-TTTTTTTCTTTTTGATATTCAAAAATTTTTAAAAATTTTTTAATTAATAAGACTTATCATTC
126 AATTTTTTTTCCTTTTGATATTCAAAAATTTTTAAAAATTTTCAAATTAATAAAACTTATCATTC
* * * * * * *
1245469 TTTTGTAAGATTGGAAGGAGAATTTTGTCTCACAATTTTATTTTAGCTTCCCAGAGCATGGGAAA
191 TCTTGAAACATTCGAAGGACAATTTTGTCTCACAATTTTATTTTAACTTCCCAAAGCATGGGAAA
* * * *
1245534 ATAACTTTACGAATCTTTTTGGAAAAAAAAAAGACATTCACATGATTCATGATAATTAGATTCCC
256 ATAACTTTACCAACCTTTTT-G-AAAAAAAAAGACATTCACATGATTCATGATAATGAGATTCAC
* * *
1245599 ATGCGAAAGCTACATACCCAAAAATGTACCATACCGAACATGGGAATCTACTTCCCACTAATTAA
319 ATGCGAAAGCTACATACCCAAAAATGTACCATACCAAACATGGGAATCGACTTCCCACCAATTAA
* *
1245664 ATTCCTAAGAATGTGAGCAAAATCCATCATACCAAACGCACGCTAACAAGGCATTTGGTTGGCAT
384 ATTCCTAAGAATGTGAGCAAAATCCATCATACCAAACGCACCCTAACAAGGCATTTGGTTGGCAA
* *
1245729 AATATTTCATTACCGAGGGTAACATAATATTCTATCATGACATTGCCATGTTTGTTTCAAAAA
449 AATATTTCATTACCGAGGGTAACATAATATTCTATCATGACATTACCATATTTGTTTCAAAAA
1245792 CATTCCCCAA
Statistics
Matches: 441, Mismatches: 56, Indels: 28
0.84 0.11 0.05
Matches are distributed among these distances:
537 33 0.07
538 97 0.22
539 1 0.00
540 86 0.20
541 79 0.18
542 13 0.03
543 67 0.15
544 24 0.05
545 41 0.09
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.35
Consensus pattern (543 bp):
CAAAATTCAATTAATAAAATATTTTAAAATAAAAAAAATTAAACAATAAAATATGTGTAATTACA
TTGAAATATATAAAAAATAATGTTTAAAAAATTAATTTAAAAATAAAAATTAATTCTTGGAATTT
TTTTTCCTTTTGATATTCAAAAATTTTTAAAAATTTTCAAATTAATAAAACTTATCATTCTCTTG
AAACATTCGAAGGACAATTTTGTCTCACAATTTTATTTTAACTTCCCAAAGCATGGGAAAATAAC
TTTACCAACCTTTTTGAAAAAAAAAGACATTCACATGATTCATGATAATGAGATTCACATGCGAA
AGCTACATACCCAAAAATGTACCATACCAAACATGGGAATCGACTTCCCACCAATTAAATTCCTA
AGAATGTGAGCAAAATCCATCATACCAAACGCACCCTAACAAGGCATTTGGTTGGCAAAATATTT
CATTACCGAGGGTAACATAATATTCTATCATGACATTACCATATTTGTTTCAAAAAATATTCCTC
AAGTTTCATAATGTATTATTTTT
Found at i:1247833 original size:20 final size:19
Alignment explanation
Indices: 1247808--1247846 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
1247798 ATGCTTTATT
1247808 TATTATTGTTATTTATTAAA
1 TATTATTGTTA-TTATTAAA
*
1247828 TATTATTTTTATTATTAAA
1 TATTATTGTTATTATTAAA
1247847 AAATAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (19 bp):
TATTATTGTTATTATTAAA
Found at i:1254361 original size:26 final size:26
Alignment explanation
Indices: 1254331--1254380 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
1254321 CAGTGCATAG
* *
1254331 TGCATCAAAGAGCGAAACGGATAGGC
1 TGCATCAAAGAGCAAAAAGGATAGGC
1254357 TGCATCAAAGAGCAAAAAGGATAG
1 TGCATCAAAGAGCAAAAAGGATAG
1254381 ACTTCTTCAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.44, C:0.16, G:0.28, T:0.12
Consensus pattern (26 bp):
TGCATCAAAGAGCAAAAAGGATAGGC
Found at i:1255874 original size:31 final size:31
Alignment explanation
Indices: 1255836--1255929 Score: 170
Period size: 31 Copynumber: 3.0 Consensus size: 31
1255826 TAAAAGAGTA
1255836 AGATCACTCCTTAAAAGCTGTGAAAAACATG
1 AGATCACTCCTTAAAAGCTGTGAAAAACATG
1255867 AGATCACTCCTTAAAAGCTGTGAAAAACATG
1 AGATCACTCCTTAAAAGCTGTGAAAAACATG
* *
1255898 AGATTACTCCTTAAAAGTTGTGAAAAACATG
1 AGATCACTCCTTAAAAGCTGTGAAAAACATG
1255929 A
1 A
1255930 TGGACCTCCA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 61 1.00
ACGTcount: A:0.43, C:0.17, G:0.16, T:0.24
Consensus pattern (31 bp):
AGATCACTCCTTAAAAGCTGTGAAAAACATG
Done.