Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold59
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: 3999109
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.32
Warning! 268233 characters in sequence are not A, C, G, or T
File 23 of 25
Found at i:3595987 original size:3 final size:3
Alignment explanation
Indices: 3595979--3596014 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
3595969 TAAATACACT
3595979 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3596015 GATGTTGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3599132 original size:6 final size:6
Alignment explanation
Indices: 3599121--3599154 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
3599111 AAACAAAGCA
*
3599121 TTTCTT TTTCTT TTTCTT TTCCTT CTTTCTT TTT
1 TTTCTT TTTCTT TTTCTT TTTCTT -TTTCTT TTT
3599155 TACGATGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 20 0.80
7 5 0.20
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTCTT
Found at i:3599477 original size:2 final size:2
Alignment explanation
Indices: 3599470--3599502 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3599460 TGATTTTGAC
3599470 AT 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 AT A
3599503 ATCATTTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3600352 original size:23 final size:24
Alignment explanation
Indices: 3600322--3600372 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
3600312 TTAAATTATC
** *
3600322 AATTATTAATTATTTTTCATCT-A
1 AATTATTAAAAATATTTCATCTCA
3600345 AATTATTAAAAATATTTCATCTCA
1 AATTATTAAAAATATTTCATCTCA
3600369 AATT
1 AATT
3600373 TTCCTTTCCC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 19 0.79
24 5 0.21
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (24 bp):
AATTATTAAAAATATTTCATCTCA
Found at i:3600638 original size:13 final size:13
Alignment explanation
Indices: 3600620--3600645 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3600610 TCCTAATTTG
3600620 ATAAAAAATAAAA
1 ATAAAAAATAAAA
3600633 ATAAAAAATAAAA
1 ATAAAAAATAAAA
3600646 CTTGAAATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
ATAAAAAATAAAA
Found at i:3602379 original size:16 final size:16
Alignment explanation
Indices: 3602310--3602382 Score: 51
Period size: 16 Copynumber: 4.6 Consensus size: 16
3602300 TATTTAAAAT
*
3602310 AATTTAAAATTTATTTG
1 AATTTAAAA-TAATTTG
* *
3602327 AATTCATAATAA-TTG
1 AATTTAAAATAATTTG
* ***
3602342 ACATATAAAAT-ATCAA
1 A-ATTTAAAATAATTTG
3602358 AATTTAAAATAATTTG
1 AATTTAAAATAATTTG
3602374 AATTTAAAA
1 AATTTAAAA
3602383 AAACTTAAAT
Statistics
Matches: 40, Mismatches: 13, Indels: 7
0.67 0.22 0.12
Matches are distributed among these distances:
15 13 0.32
16 20 0.50
17 7 0.17
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (16 bp):
AATTTAAAATAATTTG
Found at i:3603000 original size:12 final size:12
Alignment explanation
Indices: 3602979--3603012 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
3602969 ATTCTTCATT
*
3602979 TTTCTATTTTTC
1 TTTCTTTTTTTC
3602991 TTTCTTTTTTTC
1 TTTCTTTTTTTC
3603003 TTT-TTTTTTT
1 TTTCTTTTTTT
3603013 AATTTCCTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 7 0.33
12 14 0.67
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTCTTTTTTTC
Found at i:3603617 original size:16 final size:16
Alignment explanation
Indices: 3603572--3603621 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
3603562 TATTTTATAT
3603572 TTATATAAAATTTAATAAA
1 TTATAT-AAATTT--TAAA
3603591 TTA-AT-AA-TTTAAA
1 TTATATAAATTTTAAA
3603604 TTATATAAATTTTAAA
1 TTATATAAATTTTAAA
3603620 TT
1 TT
3603622 TTTATTTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
13 7 0.25
14 2 0.07
15 4 0.14
16 10 0.36
18 2 0.07
19 3 0.11
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTATATAAATTTTAAA
Found at i:3603810 original size:2 final size:2
Alignment explanation
Indices: 3603803--3603830 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3603793 GCCATGCACT
3603803 TC 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 TC
3603831 CTGTTTGTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3604903 original size:19 final size:20
Alignment explanation
Indices: 3604867--3604910 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
3604857 AAATATCTTA
*
3604867 ATTTTATTTTACTATTATG-
1 ATTTTATTTTAATATTATGT
3604886 ATTTTATTTTGAAT-TTATGT
1 ATTTTATTTT-AATATTATGT
3604906 ATTTT
1 ATTTT
3604911 TTACTTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.25, C:0.02, G:0.07, T:0.66
Consensus pattern (20 bp):
ATTTTATTTTAATATTATGT
Found at i:3605180 original size:3 final size:3
Alignment explanation
Indices: 3605172--3605214 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
3605162 AACGGTGATG
3605172 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
3605215 CATAGTGAGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3606163 original size:24 final size:23
Alignment explanation
Indices: 3606136--3606188 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 23
3606126 AAAAATGATT
3606136 AATAATTATATTTAAAAAA-TAAAA
1 AATAATT-T-TTTAAAAAATTAAAA
*
3606160 AATATATTTTTTAAAAAATTTAAA
1 AATA-ATTTTTTAAAAAATTAAAA
3606184 AATAA
1 AATAA
3606189 AAAATTATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
23 10 0.38
24 13 0.50
25 3 0.12
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
AATAATTTTTTAAAAAATTAAAA
Found at i:3606338 original size:20 final size:21
Alignment explanation
Indices: 3606302--3606341 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
3606292 GAAAAAATAT
*
3606302 TTTTAAAATATTTTTATTTTA
1 TTTTAAAATAATTTTATTTTA
3606323 TTTTAAAA-AATTTTATTTT
1 TTTTAAAATAATTTTATTTT
3606342 GTAATGAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTTAAAATAATTTTATTTTA
Found at i:3607430 original size:23 final size:21
Alignment explanation
Indices: 3607380--3607430 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 21
3607370 ATATATCATA
3607380 AAAATATATATTTTAAAATTT
1 AAAATATATATTTTAAAATTT
*
3607401 ATTAAATATATATTATTAATATATT
1 A--AAATATATATT-TTAAAAT-TT
3607426 AAAAT
1 AAAAT
3607431 TAATATAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
21 1 0.04
23 15 0.60
24 6 0.24
25 3 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
AAAATATATATTTTAAAATTT
Found at i:3607436 original size:25 final size:26
Alignment explanation
Indices: 3607417--3607473 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 26
3607407 TATATATTAT
*
3607417 TAATATA-TTAAAATTAATATAAATA
1 TAATATATTTAAAAATAATATAAATA
3607442 TAATATATTTTAAAAATAATAT-AATA
1 TAATATA-TTTAAAAATAATATAAATA
3607468 -AATATA
1 TAATATA
3607474 AAAACAATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 13 0.45
26 4 0.14
27 12 0.41
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (26 bp):
TAATATATTTAAAAATAATATAAATA
Found at i:3607462 original size:21 final size:20
Alignment explanation
Indices: 3607438--3607485 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
3607428 AATTAATATA
* * *
3607438 AATATAATATATTTTAAAAAT
1 AATATAATA-AATATAAAAAC
3607459 AATATAATAAATATAAAAAC
1 AATATAATAAATATAAAAAC
3607479 AATATAA
1 AATATAA
3607486 ATACTTATGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 15 0.62
21 9 0.38
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
AATATAATAAATATAAAAAC
Found at i:3612383 original size:2 final size:2
Alignment explanation
Indices: 3612371--3612401 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3612361 TAGGGTTACC
3612371 AT AT A- 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
3612402 GTGTGTGTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3612764 original size:2 final size:2
Alignment explanation
Indices: 3612757--3612809 Score: 97
Period size: 2 Copynumber: 26.0 Consensus size: 2
3612747 GTTACTTCGC
3612757 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
3612799 AT AT AT GAT AT
1 AT AT AT -AT AT
3612810 TTATGACATC
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 48 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3612814 original size:9 final size:9
Alignment explanation
Indices: 3612757--3612815 Score: 74
Period size: 8 Copynumber: 7.1 Consensus size: 9
3612747 GTTACTTCGC
3612757 ATATATAT-
1 ATATATATG
3612765 ATATATAT-
1 ATATATATG
3612773 ATATATAT-
1 ATATATATG
3612781 ATATATAT-
1 ATATATATG
3612789 ATATATAT-
1 ATATATATG
3612797 ATATATATG
1 ATATATATG
*
3612806 ATATTTATG
1 ATATATATG
3612815 A
1 A
3612816 CATCCTCGAC
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
8 40 0.82
9 9 0.18
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.49
Consensus pattern (9 bp):
ATATATATG
Found at i:3614293 original size:14 final size:14
Alignment explanation
Indices: 3614243--3614293 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
3614233 GCATGCAGCA
*
3614243 TTATATTAATATTT
1 TTATAATAATATTT
3614257 TTAT-AT-ATATTT
1 TTATAATAATATTT
*
3614269 TTAATTAATAATATAT
1 TT-A-TAATAATATTT
3614285 TTATAATAA
1 TTATAATAA
3614294 AATGGAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
12 8 0.26
13 2 0.06
14 11 0.35
15 3 0.10
16 7 0.23
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTATAATAATATTT
Found at i:3615569 original size:24 final size:24
Alignment explanation
Indices: 3615537--3615582 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
3615527 TACGTCAACG
3615537 TTTCATAATAATAATAATAATACT
1 TTTCATAATAATAATAATAATACT
* *
3615561 TTTCCTAATAATGATAATAATA
1 TTTCATAATAATAATAATAATA
3615583 ATACTGTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.48, C:0.09, G:0.02, T:0.41
Consensus pattern (24 bp):
TTTCATAATAATAATAATAATACT
Found at i:3617130 original size:18 final size:18
Alignment explanation
Indices: 3617109--3617148 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
3617099 ATTAGAAGAA
3617109 AAAAT-AAAGAAGAAACAC
1 AAAATAAAAGAA-AAACAC
3617127 AAAATAAAAGAAAAACAC
1 AAAATAAAAGAAAAACAC
3617145 AAAA
1 AAAA
3617149 GAAATTACGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.78, C:0.10, G:0.07, T:0.05
Consensus pattern (18 bp):
AAAATAAAAGAAAAACAC
Found at i:3617387 original size:34 final size:34
Alignment explanation
Indices: 3617341--3617559 Score: 309
Period size: 34 Copynumber: 6.5 Consensus size: 34
3617331 GTAAAGACCA
3617341 CCATTTAATCAACAATGGTAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
3617375 CCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCTC
* *
3617409 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
3617443 CCATTTAATCAACAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
3617477 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* * *
3617511 CCATTTAATCAACAATGGTAAACTACTAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
3617544 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
3617560 TCTCCCACTT
Statistics
Matches: 167, Mismatches: 14, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
33 20 0.12
34 142 0.85
35 5 0.03
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:3617517 original size:102 final size:101
Alignment explanation
Indices: 3617339--3617559 Score: 381
Period size: 102 Copynumber: 2.2 Consensus size: 101
3617329 TGGTAAAGAC
*
3617339 CACCATTTAATCAACAATGGTAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGTAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAA
*
3617404 ATCACCCATTTAATCAACAATGGTAAGCTACCAAATTT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAA--T
*
3617442 C-CCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAA
1 CACCATTTAATCAACAATGGTAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAA
*
3617506 ATCACCCATTTAATCAACAATGGTAAACTACTAAAT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
3617542 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
3617560 TCTCCCACTT
Statistics
Matches: 113, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
100 2 0.02
101 16 0.14
102 94 0.83
103 1 0.01
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGTAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAA
ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:3621649 original size:19 final size:19
Alignment explanation
Indices: 3621622--3621684 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
3621612 TTACGTGTAC
* *
3621622 AGTAACCGTATACTTGAAT
1 AGTACCCGTATACGTGAAT
3621641 AGTACCCGTATACGTGAAT
1 AGTACCCGTATACGTGAAT
**
3621660 AGTACCTATATACGTGAAT
1 AGTACCCGTATACGTGAAT
3621679 AGTACC
1 AGTACC
3621685 TCGACAACCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (19 bp):
AGTACCCGTATACGTGAAT
Found at i:3622038 original size:34 final size:34
Alignment explanation
Indices: 3621992--3622208 Score: 260
Period size: 34 Copynumber: 6.4 Consensus size: 34
3621982 GTAAAAACTA
* *
3621992 CCATTTAATCAACAATGGCAACCTATCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
3622026 TCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCTC
* *
3622060 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
3622094 CCATTTAATCAACAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
3622128 CCATTTAGTCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCTC
* * * *
3622162 CCATTTAATCAACAATGATAAACTACTAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
3622195 CCATTTAATCAACA
1 CCATTTAATCAACA
3622209 GTCTCCAATT
Statistics
Matches: 158, Mismatches: 21, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
33 18 0.11
34 135 0.85
35 5 0.03
ACGTcount: A:0.41, C:0.27, G:0.07, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:3622106 original size:68 final size:68
Alignment explanation
Indices: 3621992--3622208 Score: 292
Period size: 68 Copynumber: 3.2 Consensus size: 68
3621982 GTAAAAACTA
* * * * *
3621992 CCATTTAATCAACAATGGCAACCTATCAAATCTCTCATTTAGTCAACAATGGTAAGCCACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAAAT
3622057 CAC
66 CAC
* * *
3622060 CCATTTAATCAACAATGGTAAGCTACCAAATTTCCCATTTAATCAACAATGGTAAGCTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAAAT
*
3622125 CTC
66 CAC
* * * * * *
3622128 CCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGATAAACTACTAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAAAT
3622193 CA-
66 CAC
3622195 CCATTTAATCAACA
1 CCATTTAATCAACA
3622209 GTCTCCAATT
Statistics
Matches: 130, Mismatches: 19, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
67 13 0.10
68 117 0.90
ACGTcount: A:0.41, C:0.27, G:0.07, T:0.25
Consensus pattern (68 bp):
CCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAAAT
CAC
Found at i:3622134 original size:102 final size:101
Alignment explanation
Indices: 3621991--3622208 Score: 330
Period size: 102 Copynumber: 2.1 Consensus size: 101
3621981 GGTAAAAACT
* * * *
3621991 ACCATTTAATCAACAATGGCAACCTATCAAATCTCTCATTTAGTCAACAATGGTAAGCCACCAAA
1 ACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCAAA
* *
3622056 TCACCCATTTAATCAACAATGGTAAGCTACCAAATTTC
66 TCACCCATTTAATCAACAATGATAAACTACCAAA--TC
* *
3622094 -CCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCAAA
1 ACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCAAA
*
3622158 TCACCCATTTAATCAACAATGATAAACTACTAAATC
66 TCACCCATTTAATCAACAATGATAAACTACCAAATC
3622194 ACCATTTAATCAACA
1 ACCATTTAATCAACA
3622209 GTCTCCAATT
Statistics
Matches: 105, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
100 2 0.02
101 14 0.13
102 89 0.85
ACGTcount: A:0.41, C:0.27, G:0.07, T:0.25
Consensus pattern (101 bp):
ACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCAAA
TCACCCATTTAATCAACAATGATAAACTACCAAATC
Found at i:3627332 original size:19 final size:19
Alignment explanation
Indices: 3627308--3627345 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
3627298 AATATCATGG
3627308 TGCAATTCAATCTTTGAGC
1 TGCAATTCAATCTTTGAGC
3627327 TGCAATTCAATCTTTGAGC
1 TGCAATTCAATCTTTGAGC
3627346 CGATCTTGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (19 bp):
TGCAATTCAATCTTTGAGC
Found at i:3631701 original size:18 final size:18
Alignment explanation
Indices: 3631647--3631748 Score: 75
Period size: 19 Copynumber: 5.6 Consensus size: 18
3631637 AACTTAGATC
*
3631647 TATATTAAAAATTATATAATT
1 TATATTAAATATT-TAT--TT
* *
3631668 TA-ATTAAATGTATATTT
1 TATATTAAATATTTATTT
* *
3631685 TTTATTAAATATTTATTA
1 TATATTAAATATTTATTT
3631703 TAT-TTAAA-ATTTATTT
1 TATATTAAATATTTATTT
*
3631719 TATAATAAATTATTTATTT
1 TATATTAAA-TATTTATTT
*
3631738 AATATTTAAAT
1 TATA-TTAAAT
3631749 TTTTTAATCA
Statistics
Matches: 64, Mismatches: 12, Indels: 12
0.73 0.14 0.14
Matches are distributed among these distances:
16 10 0.16
17 12 0.19
18 14 0.22
19 15 0.23
20 11 0.17
21 2 0.03
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (18 bp):
TATATTAAATATTTATTT
Found at i:3632850 original size:13 final size:13
Alignment explanation
Indices: 3632832--3632856 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3632822 TCTCTCTCTG
3632832 TCTCTCTATATAC
1 TCTCTCTATATAC
3632845 TCTCTCTATATA
1 TCTCTCTATATA
3632857 TATATATATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.28, G:0.00, T:0.48
Consensus pattern (13 bp):
TCTCTCTATATAC
Found at i:3635340 original size:17 final size:17
Alignment explanation
Indices: 3635318--3635356 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
3635308 AATAGTTAAA
*
3635318 AAAAAAGTT-TACGAAAT
1 AAAAAAGTTATA-AAAAT
3635335 AAAAAAGTTATAAAAAT
1 AAAAAAGTTATAAAAAT
3635352 AAAAA
1 AAAAA
3635357 TATAATAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 18 0.90
18 2 0.10
ACGTcount: A:0.69, C:0.03, G:0.08, T:0.21
Consensus pattern (17 bp):
AAAAAAGTTATAAAAAT
Found at i:3635388 original size:18 final size:21
Alignment explanation
Indices: 3635351--3635390 Score: 59
Period size: 18 Copynumber: 2.0 Consensus size: 21
3635341 GTTATAAAAA
3635351 TAAAAATATAATAGTAATTTT
1 TAAAAATATAATAGTAATTTT
3635372 TAAAAAT-TAA-A-TAATTTT
1 TAAAAATATAATAGTAATTTT
3635390 T
1 T
3635391 TTAAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.42
19 1 0.05
20 3 0.16
21 7 0.37
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (21 bp):
TAAAAATATAATAGTAATTTT
Found at i:3638955 original size:3 final size:3
Alignment explanation
Indices: 3638942--3638980 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
3638932 TTCATAAAAT
*
3638942 ATA AAA ATA ATA ATA ATA ATA ATA ATA A-A ATA A-A ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
3638981 TAATTAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 4 0.12
3 28 0.88
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:3638984 original size:20 final size:20
Alignment explanation
Indices: 3638950--3639004 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
3638940 ATATAAAAAT
3638950 AATAATAATAA-TAATAATAA
1 AATAA-AATAATTAATAATAA
*
3638970 AATAAAATAATTAATTAATTA
1 AATAAAATAATTAA-TAATAA
*
3638991 AA-AAATTAATTAAT
1 AATAAAATAATTAAT
3639005 TTTGTACCTG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 6 0.19
20 18 0.58
21 7 0.23
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
AATAAAATAATTAATAATAA
Found at i:3638997 original size:16 final size:17
Alignment explanation
Indices: 3638959--3639005 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 17
3638949 TAATAATAAT
* *
3638959 AATAA-TAATAAAATAA
1 AATAATTAATTAATTAA
3638975 AATAATTAATTAATTAA
1 AATAATTAATTAATTAA
3638992 AA-AATTAATTAATT
1 AATAATTAATTAATT
3639006 TTGTACCTGC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 17 0.61
17 11 0.39
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AATAATTAATTAATTAA
Found at i:3646645 original size:14 final size:14
Alignment explanation
Indices: 3646626--3646701 Score: 59
Period size: 14 Copynumber: 5.6 Consensus size: 14
3646616 TAATTTATCA
*
3646626 AATTAATTAAATTT
1 AATTAATTTAATTT
*
3646640 AATTAATTTTATTT
1 AATTAATTTAATTT
*
3646654 AATTTATTTAATTT
1 AATTAATTTAATTT
* * *
3646668 --TTAAATTGA-TC
1 AATTAATTTAATTT
3646679 AATTAAGTTTAATTT
1 AATTAA-TTTAATTT
*
3646694 ATTTAATT
1 AATTAATT
3646702 AGATCAATCA
Statistics
Matches: 46, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
11 1 0.02
12 6 0.13
13 4 0.09
14 29 0.63
15 6 0.13
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (14 bp):
AATTAATTTAATTT
Found at i:3647015 original size:56 final size:58
Alignment explanation
Indices: 3646948--3647113 Score: 172
Period size: 56 Copynumber: 3.0 Consensus size: 58
3646938 TTTTTAGTTT
3646948 ATTAATTTAATTCAACCACTAATCAACTCTTC-AAATCTATTTGA-TT-TGCAATTTTA
1 ATTAATTTAATTCAACCACTAATCAACTCTTCAAAAT-TATTTGAGTTATGCAATTTTA
* * * * *
3647004 ATTAGTTTAATTCAATCACTGATCAATTCTTCAAAATTATTTGAGTTATTCAATTTT-
1 ATTAATTTAATTCAACCACTAATCAACTCTTCAAAATTATTTGAGTTATGCAATTTTA
* * *
3647061 ATAAATTTTAA---AATCA--AATCAA-TCTTCAAAATTATTTGAGTTATTCAATTTTA
1 ATTAA-TTTAATTCAACCACTAATCAACTCTTCAAAATTATTTGAGTTATGCAATTTTA
3647114 TAAATTTTAA
Statistics
Matches: 97, Mismatches: 8, Indels: 13
0.82 0.07 0.11
Matches are distributed among these distances:
52 30 0.31
53 5 0.05
55 5 0.05
56 35 0.36
57 9 0.09
58 13 0.13
ACGTcount: A:0.37, C:0.13, G:0.05, T:0.45
Consensus pattern (58 bp):
ATTAATTTAATTCAACCACTAATCAACTCTTCAAAATTATTTGAGTTATGCAATTTTA
Found at i:3647066 original size:26 final size:26
Alignment explanation
Indices: 3647037--3647119 Score: 80
Period size: 26 Copynumber: 3.2 Consensus size: 26
3647027 CAATTCTTCA
3647037 AAATTATTTGAGTTATTCAATTTTAT
1 AAATTATTTGAGTTATTCAATTTTAT
** * * * *
3647063 AAATT-TTAAAATCAAATCAATCTTCA-
1 AAATTATTTGAGT-TATTCAAT-TTTAT
3647089 AAATTATTTGAGTTATTCAATTTTAT
1 AAATTATTTGAGTTATTCAATTTTAT
3647115 AAATT
1 AAATT
3647120 TTAAAATCAA
Statistics
Matches: 41, Mismatches: 12, Indels: 8
0.67 0.20 0.13
Matches are distributed among these distances:
25 7 0.17
26 27 0.66
27 7 0.17
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.47
Consensus pattern (26 bp):
AAATTATTTGAGTTATTCAATTTTAT
Found at i:3647094 original size:52 final size:53
Alignment explanation
Indices: 3647025--3647134 Score: 213
Period size: 52 Copynumber: 2.1 Consensus size: 53
3647015 TCAATCACTG
3647025 ATCAATTCTTCAAAATTATTTGAGTTATTCAATTTTATAAATTTTAAAATCAA
1 ATCAATTCTTCAAAATTATTTGAGTTATTCAATTTTATAAATTTTAAAATCAA
3647078 ATCAA-TCTTCAAAATTATTTGAGTTATTCAATTTTATAAATTTTAAAATCAA
1 ATCAATTCTTCAAAATTATTTGAGTTATTCAATTTTATAAATTTTAAAATCAA
3647130 ATCAA
1 ATCAA
3647135 CCCCATGCTA
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 52 0.91
53 5 0.09
ACGTcount: A:0.43, C:0.10, G:0.04, T:0.44
Consensus pattern (53 bp):
ATCAATTCTTCAAAATTATTTGAGTTATTCAATTTTATAAATTTTAAAATCAA
Found at i:3647134 original size:26 final size:26
Alignment explanation
Indices: 3647053--3647134 Score: 78
Period size: 26 Copynumber: 3.2 Consensus size: 26
3647043 TTTGAGTTAT
3647053 TCAATTTTATAAATTTTAAAATCAAA
1 TCAATTTTATAAATTTTAAAATCAAA
* ** * * *
3647079 TCAATCTTCA-AAATTATTTGAGT-TAT
1 TCAAT-TTTATAAATT-TTAAAATCAAA
3647105 TCAATTTTATAAATTTTAAAATCAAA
1 TCAATTTTATAAATTTTAAAATCAAA
3647131 TCAA
1 TCAA
3647135 CCCCATGCTA
Statistics
Matches: 40, Mismatches: 12, Indels: 8
0.67 0.20 0.13
Matches are distributed among these distances:
25 7 0.17
26 26 0.65
27 7 0.17
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.43
Consensus pattern (26 bp):
TCAATTTTATAAATTTTAAAATCAAA
Found at i:3651427 original size:2 final size:2
Alignment explanation
Indices: 3651420--3651452 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3651410 TAACACATGC
3651420 AT 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 AT A
3651453 AACACGCACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3651779 original size:31 final size:28
Alignment explanation
Indices: 3651728--3651807 Score: 99
Period size: 31 Copynumber: 2.8 Consensus size: 28
3651718 TAAAATTTTA
3651728 TTTAATATATT-ATATATTTATATAAAT
1 TTTAATATATTAATATATTTATATAAAT
*
3651755 TTTAATATATTAATAATTATTTTATATAGAT
1 TTTAATATATTAAT-A-TA-TTTATATAAAT
*
3651786 TTTAATATGTTAATGATATTTA
1 TTTAATATATTAAT-ATATTTA
3651808 AATCTTATTA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
27 11 0.24
28 2 0.04
29 5 0.11
30 4 0.09
31 24 0.52
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (28 bp):
TTTAATATATTAATATATTTATATAAAT
Found at i:3653309 original size:23 final size:23
Alignment explanation
Indices: 3653279--3653327 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
3653269 AATTTGTAAA
*
3653279 ATAACATATGTTTAAAATAATCT
1 ATAACATATGTTTAAAAAAATCT
*
3653302 ATAACATATGTTTAAAAAAATTT
1 ATAACATATGTTTAAAAAAATCT
3653325 ATA
1 ATA
3653328 TTCAAAACAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.39
Consensus pattern (23 bp):
ATAACATATGTTTAAAAAAATCT
Found at i:3656916 original size:28 final size:29
Alignment explanation
Indices: 3656883--3656938 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
3656873 ATTAATCAAA
3656883 TCAATTAAACTGAATTTAATC-AATTTTT
1 TCAATTAAACTGAATTTAATCGAATTTTT
* *
3656911 TCAATTAAATTGATTTTAATCGAATTTT
1 TCAATTAAACTGAATTTAATCGAATTTT
3656939 GCACCCTTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 19 0.76
29 6 0.24
ACGTcount: A:0.38, C:0.09, G:0.05, T:0.48
Consensus pattern (29 bp):
TCAATTAAACTGAATTTAATCGAATTTTT
Found at i:3658302 original size:28 final size:29
Alignment explanation
Indices: 3658270--3658339 Score: 99
Period size: 30 Copynumber: 2.4 Consensus size: 29
3658260 AAAACACACA
*
3658270 TAAAATTTAAAATCTAAT-T-GATATATTT
1 TAAAATTTAAAAT-TAATATAAATATATTT
3658298 TAAAATTTAAAATTAATATAAAATATATTT
1 TAAAATTTAAAATTAATAT-AAATATATTT
3658328 TAAAATTTAAAA
1 TAAAATTTAAAA
3658340 ATTACGTATA
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
27 4 0.11
28 14 0.37
30 20 0.53
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (29 bp):
TAAAATTTAAAATTAATATAAATATATTT
Found at i:3660782 original size:158 final size:158
Alignment explanation
Indices: 3660527--3661000 Score: 939
Period size: 158 Copynumber: 3.0 Consensus size: 158
3660517 GAGATGTTAT
3660527 CTTGTGGTTTTTGGTGATAATGAAAGTAAGATTTATGAAAAGAAATATGAATCTAATTTATTCAG
1 CTTGTGGTTTTTGGTGATAATGAAAGTAAGATTTATGAAAAGAAATATGAATCTAATTTATTCAG
3660592 TTAGAATGACTGTAAATTAAATGTTTCTTCTTGCATTTTAGAAAGTTACTCTTAATGCTTTTAAG
66 TTAGAATGACTGTAAATTAAATGTTTCTTCTTGCATTTTAGAAAGTTACTCTTAATGCTTTTAAG
3660657 GTTTCAACCGATGATTCTGAACTTTGGC
131 GTTTCAACCGATGATTCTGAACTTTGGC
3660685 CTTGTGGTTTTTGGTGATAATGAAAGTAAGATTTATGAAAAGAAATATGAATCTAATTTATTCAG
1 CTTGTGGTTTTTGGTGATAATGAAAGTAAGATTTATGAAAAGAAATATGAATCTAATTTATTCAG
3660750 TTAGAATGACTGTAAATTAAATGTTTCTTCTTGCATTTTAGAAAGTTACTCTTAATGCTTTTAAG
66 TTAGAATGACTGTAAATTAAATGTTTCTTCTTGCATTTTAGAAAGTTACTCTTAATGCTTTTAAG
3660815 GTTTCAACCGATGATTCTGAACTTTGGC
131 GTTTCAACCGATGATTCTGAACTTTGGC
3660843 CTTGTGGTTTTTGGTGATAATGAAAGTAAGATTTATGAAAAGAAATATGAATCTAATTTATTCAG
1 CTTGTGGTTTTTGGTGATAATGAAAGTAAGATTTATGAAAAGAAATATGAATCTAATTTATTCAG
*
3660908 TTAGAATGACTGTAAATAAAATGTTTCTTCTTGCATTTTAGAAAGTTACTCTTAATGCTTTTAAG
66 TTAGAATGACTGTAAATTAAATGTTTCTTCTTGCATTTTAGAAAGTTACTCTTAATGCTTTTAAG
3660973 GTTTCAACCGATGATTCTGAACTTTGGC
131 GTTTCAACCGATGATTCTGAACTTTGGC
3661001 ATAAGAGATT
Statistics
Matches: 315, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
158 315 1.00
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.40
Consensus pattern (158 bp):
CTTGTGGTTTTTGGTGATAATGAAAGTAAGATTTATGAAAAGAAATATGAATCTAATTTATTCAG
TTAGAATGACTGTAAATTAAATGTTTCTTCTTGCATTTTAGAAAGTTACTCTTAATGCTTTTAAG
GTTTCAACCGATGATTCTGAACTTTGGC
Found at i:3664683 original size:3 final size:3
Alignment explanation
Indices: 3664675--3664703 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3664665 AAGAATGTTT
3664675 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3664704 CAATTAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3667265 original size:14 final size:14
Alignment explanation
Indices: 3667246--3667274 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3667236 TAATAATTGG
3667246 TTTTTTTATTTTTA
1 TTTTTTTATTTTTA
3667260 TTTTTTTATTTTTA
1 TTTTTTTATTTTTA
3667274 T
1 T
3667275 ATTATTGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTTTTTATTTTTA
Found at i:3670718 original size:24 final size:25
Alignment explanation
Indices: 3670671--3670718 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
3670661 TGTTATTTTA
* *
3670671 TTAAATAAATAATTTAATAATCATT
1 TTAAATAAATAAATAAATAATCATT
3670696 TTAAATAAA-AAATAAATAATCAT
1 TTAAATAAATAAATAAATAATCAT
3670719 CATCTTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (25 bp):
TTAAATAAATAAATAAATAATCATT
Found at i:3670743 original size:16 final size:17
Alignment explanation
Indices: 3670727--3670760 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
3670717 ATCATCTTTT
3670727 ATAAAAAAATATATTTA
1 ATAAAAAAATATATTTA
*
3670744 GATAAAATAATATATTT
1 -ATAAAAAAATATATTT
3670761 GTTAGAAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
ATAAAAAAATATATTTA
Found at i:3674629 original size:16 final size:16
Alignment explanation
Indices: 3674610--3674665 Score: 76
Period size: 16 Copynumber: 3.5 Consensus size: 16
3674600 ATTAGGCGGG
3674610 TTCGGGTTCAGGCTCA
1 TTCGGGTTCAGGCTCA
* *
3674626 TTCGGGTTCGGGCTCG
1 TTCGGGTTCAGGCTCA
* *
3674642 TTCGAGTTCAGGCTCT
1 TTCGGGTTCAGGCTCA
3674658 TTCGGGTT
1 TTCGGGTT
3674666 TGAGCTTTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.07, C:0.23, G:0.34, T:0.36
Consensus pattern (16 bp):
TTCGGGTTCAGGCTCA
Found at i:3674676 original size:16 final size:16
Alignment explanation
Indices: 3674626--3674761 Score: 71
Period size: 16 Copynumber: 8.5 Consensus size: 16
3674616 TTCAGGCTCA
* **
3674626 TTCGGGTTCGGGCTCG
1 TTCGGGTTCGAGCTTT
* *
3674642 TTCGAGTTC-AGGCTCT
1 TTCGGGTTCGA-GCTTT
*
3674658 TTCGGGTTTGAGCTTT
1 TTCGGGTTCGAGCTTT
*
3674674 TTCAGGTTCGAGCTTT
1 TTCGGGTTCGAGCTTT
** * *
3674690 TTCAAGTTTG-GGTTT
1 TTCGGGTTCGAGCTTT
* * *
3674705 TTTGGAGTTTGGGCTTT
1 TTCGG-GTTCGAGCTTT
*
3674722 TTCAGGTTCGAGCTTT
1 TTCGGGTTCGAGCTTT
* *
3674738 TT-GAGGTTCGAACTTA
1 TTCG-GGTTCGAGCTTT
3674754 TTCGGGTT
1 TTCGGGTT
3674762 GGGTTTATTC
Statistics
Matches: 92, Mismatches: 22, Indels: 12
0.73 0.17 0.10
Matches are distributed among these distances:
15 6 0.07
16 77 0.84
17 9 0.10
ACGTcount: A:0.10, C:0.15, G:0.30, T:0.44
Consensus pattern (16 bp):
TTCGGGTTCGAGCTTT
Found at i:3674996 original size:18 final size:18
Alignment explanation
Indices: 3674957--3674996 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
3674947 ATATTTATAT
*
3674957 ATAAAATTAATTTGTTAT
1 ATAAAATTAATTTGTTAA
3674975 ATAAAATTAATTT-TTCAA
1 ATAAAATTAATTTGTT-AA
3674993 ATAA
1 ATAA
3674997 TTTATTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (18 bp):
ATAAAATTAATTTGTTAA
Found at i:3678659 original size:52 final size:52
Alignment explanation
Indices: 3678589--3678709 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
3678579 GAAAATTTAT
*
3678589 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
3678641 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
3678693 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
3678710 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:3678722 original size:52 final size:51
Alignment explanation
Indices: 3678589--3678729 Score: 212
Period size: 52 Copynumber: 2.7 Consensus size: 51
3678579 GAAAATTTAT
3678589 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
3678641 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
3678693 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
3678730 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:3678736 original size:13 final size:13
Alignment explanation
Indices: 3678718--3678742 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3678708 CAAAGATCAG
3678718 TGTATCGATACAA
1 TGTATCGATACAA
3678731 TGTATCGATACA
1 TGTATCGATACA
3678743 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3678826 original size:13 final size:13
Alignment explanation
Indices: 3678808--3678832 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3678798 CAAAAAAATA
3678808 TGTATCGATACAT
1 TGTATCGATACAT
3678821 TGTATCGATACA
1 TGTATCGATACA
3678833 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3678828 original size:33 final size:33
Alignment explanation
Indices: 3678786--3678852 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3678776 AGTAGCTTAA
3678786 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
3678819 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
3678852 A
1 A
3678853 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:3679837 original size:16 final size:17
Alignment explanation
Indices: 3679798--3679843 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
3679788 AAATTTAAGT
3679798 TCGGGTTTAGG-TCAGTC
1 TCGGGTTTAGGTTCA-TC
*
3679815 TCAGGTTTAGGTTC-TC
1 TCGGGTTTAGGTTCATC
*
3679831 TCGGGTTCAGGTT
1 TCGGGTTTAGGTT
3679844 TTTTTAGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 13 0.52
17 10 0.40
18 2 0.08
ACGTcount: A:0.11, C:0.17, G:0.33, T:0.39
Consensus pattern (17 bp):
TCGGGTTTAGGTTCATC
Found at i:3682932 original size:25 final size:26
Alignment explanation
Indices: 3682883--3682932 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
3682873 ATATTATTAT
* *
3682883 TATTATATCATTTATTTAATTAAAGG
1 TATTATATAATTTATTTAATGAAAGG
*
3682909 TATTA-ATAATTTATTTGATGAAAG
1 TATTATATAATTTATTTAATGAAAG
3682933 TAAAATAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.48
Consensus pattern (26 bp):
TATTATATAATTTATTTAATGAAAGG
Found at i:3691376 original size:16 final size:16
Alignment explanation
Indices: 3691337--3691379 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
3691327 TAGCATTATC
*
3691337 ATTGGATAAAGCTTAG
1 ATTGGAAAAAGCTTAG
* *
3691353 ATTAGAAAAAGCTTGG
1 ATTGGAAAAAGCTTAG
*
3691369 GTTGGAAAAAG
1 ATTGGAAAAAG
3691380 TATGTTTAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.42, C:0.05, G:0.28, T:0.26
Consensus pattern (16 bp):
ATTGGAAAAAGCTTAG
Found at i:3694205 original size:2 final size:2
Alignment explanation
Indices: 3694198--3694230 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3694188 GAAATATGCA
3694198 AT 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 AT A
3694231 ATTCCAAAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3696542 original size:9 final size:9
Alignment explanation
Indices: 3696502--3696547 Score: 53
Period size: 9 Copynumber: 5.3 Consensus size: 9
3696492 GTACTAGGTC
3696502 AAATAA-TA
1 AAATAATTA
3696510 AAA-AATT-
1 AAATAATTA
3696517 AAATAATATA
1 AAATAAT-TA
*
3696527 TAATAATTA
1 AAATAATTA
3696536 AAATAATTA
1 AAATAATTA
3696545 AAA
1 AAA
3696548 AGAGAAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
7 5 0.16
8 7 0.22
9 14 0.44
10 6 0.19
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (9 bp):
AAATAATTA
Found at i:3696966 original size:3 final size:3
Alignment explanation
Indices: 3696958--3696984 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3696948 CAGATTATAA
3696958 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
3696985 TATTTAAACT
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3702777 original size:12 final size:12
Alignment explanation
Indices: 3702760--3702789 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3702750 TCAAAGCAGT
3702760 AATAATTTAATA
1 AATAATTTAATA
*
3702772 AATAATTTGATA
1 AATAATTTAATA
3702784 AATAAT
1 AATAAT
3702790 ATATTTTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (12 bp):
AATAATTTAATA
Found at i:3702799 original size:17 final size:16
Alignment explanation
Indices: 3702768--3702801 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
3702758 GTAATAATTT
3702768 AATAAATAATTTGATA
1 AATAAATAATTTGATA
*
3702784 AATAATATATTTTGATA
1 AATAA-ATAATTTGATA
3702801 A
1 A
3702802 TTTATTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (16 bp):
AATAAATAATTTGATA
Found at i:3703289 original size:3 final size:3
Alignment explanation
Indices: 3703281--3703323 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
3703271 TGTTGTCTCT
* * *
3703281 TTC TTC TTC TTT TTC TTC TTC TTC TTC TAC TTC TAC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
3703324 AGTAGTAGAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.05, C:0.30, G:0.00, T:0.65
Consensus pattern (3 bp):
TTC
Found at i:3711264 original size:27 final size:27
Alignment explanation
Indices: 3711207--3711264 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
3711197 GGGACGCTCT
*
3711207 AACCTTATTTCTCAGAAGGGACAATCT
1 AACCTTATTTCTCAGAAGGGACAATCC
* * *
3711234 AACCTTATTTCTCAGAATGGATACTCC
1 AACCTTATTTCTCAGAAGGGACAATCC
3711261 AACC
1 AACC
3711265 CCGTTTTTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.29
Consensus pattern (27 bp):
AACCTTATTTCTCAGAAGGGACAATCC
Found at i:3714347 original size:2 final size:2
Alignment explanation
Indices: 3714340--3714383 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
3714330 GTCTCTAAGA
3714340 CT CT CT CT CT 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 CT CT CT CT CT
3714382 CT
1 CT
3714384 ATATATATAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3716151 original size:47 final size:48
Alignment explanation
Indices: 3716060--3716198 Score: 129
Period size: 47 Copynumber: 2.9 Consensus size: 48
3716050 TTCTAAATTG
* * * * * * *
3716060 AGTTATTTTGAATATTAATTATTTTAAATATGAGCTGTTTTAAACATAA
1 AGTTACTTTGAACATAAACTATTTTAAATATAAGTTATTTTAAACA-AA
*
3716109 A-TTACTTTGAAC-TAAACTATTTTAAATATAAGTTATTCTAAACAAA
1 AGTTACTTTGAACATAAACTATTTTAAATATAAGTTATTTTAAACAAA
* * * * * *
3716155 AGTTATTTTTAACATAGACTGTTTTTAATAAAAGTTATTTTAAA
1 AGTTACTTTGAACATAAACTATTTTAAATATAAGTTATTTTAAA
3716199 TGTAAGCTTT
Statistics
Matches: 73, Mismatches: 15, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
46 3 0.04
47 35 0.48
48 34 0.47
49 1 0.01
ACGTcount: A:0.41, C:0.06, G:0.08, T:0.45
Consensus pattern (48 bp):
AGTTACTTTGAACATAAACTATTTTAAATATAAGTTATTTTAAACAAA
Found at i:3716894 original size:20 final size:20
Alignment explanation
Indices: 3716873--3716933 Score: 61
Period size: 23 Copynumber: 2.9 Consensus size: 20
3716863 ATGATTTTAT
3716873 TTTATTAAAAATAA-AATTA
1 TTTATTAAAAATAATAATTA
*
3716892 TTTATATAAAATGATAATATTTAA
1 TTTAT-TAAAA--ATAATAATT-A
3716916 TTTATTAAAAATATATAA
1 TTTATTAAAAATA-ATAA
3716934 ATATATATAC
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
19 5 0.15
20 5 0.15
21 3 0.09
22 7 0.21
23 8 0.24
24 6 0.18
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
TTTATTAAAAATAATAATTA
Found at i:3716926 original size:24 final size:21
Alignment explanation
Indices: 3716868--3716928 Score: 63
Period size: 20 Copynumber: 2.9 Consensus size: 21
3716858 TTTTGATGAT
*
3716868 TTTATTTTATTAAAAATAAAA
1 TTTAATTTATTAAAAATAAAA
*
3716889 -TT-ATTTATATAAAATGATAATA
1 TTTAATTTAT-TAAAA--ATAAAA
3716911 TTTAATTTATTAAAAATA
1 TTTAATTTATTAAAAATA
3716929 TATAAATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
19 5 0.15
20 7 0.21
21 3 0.09
22 5 0.15
23 7 0.21
24 6 0.18
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
TTTAATTTATTAAAAATAAAA
Found at i:3717705 original size:40 final size:41
Alignment explanation
Indices: 3717655--3717732 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
3717645 AAAAAAATTA
* *
3717655 ATTTTAAGGTTT-TCTCTATAAATTTAAA-AAAATAAGATTG
1 ATTTTAAGGTTTAT-TCTAAAAAATTAAAGAAAATAAGATTG
* *
3717695 ATTTTGAGGTTTATTTTAAAAAATTAAAGAAAATAAGA
1 ATTTTAAGGTTTATTCTAAAAAATTAAAGAAAATAAGA
3717733 CGAATTCAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
40 22 0.69
41 10 0.31
ACGTcount: A:0.46, C:0.03, G:0.12, T:0.40
Consensus pattern (41 bp):
ATTTTAAGGTTTATTCTAAAAAATTAAAGAAAATAAGATTG
Found at i:3724628 original size:2 final size:2
Alignment explanation
Indices: 3724618--3724656 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
3724608 CAAAAAACAA
*
3724618 AG AG GG 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 A
3724657 AGCAAAAAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3728596 original size:2 final size:2
Alignment explanation
Indices: 3728589--3728635 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
3728579 AAAAATCCCC
*
3728589 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT GT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3728631 CT CT C
1 CT CT C
3728636 GTTCTCGTTC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.49, G:0.02, T:0.49
Consensus pattern (2 bp):
CT
Found at i:3729858 original size:3 final size:3
Alignment explanation
Indices: 3729852--3729897 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
3729842 TGAGACAGAG
3729852 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3729898 CTAGTGTTTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3729970 original size:13 final size:13
Alignment explanation
Indices: 3729954--3729978 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3729944 AATTAAAATA
3729954 AAATTATTATAAT
1 AAATTATTATAAT
3729967 AAATTATTATAA
1 AAATTATTATAA
3729979 AATATTTGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATTATTATAAT
Found at i:3732209 original size:2 final size:2
Alignment explanation
Indices: 3732202--3732227 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3732192 AGAAGACTAT
3732202 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
3732228 TGGAGAAATT
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3732768 original size:2 final size:2
Alignment explanation
Indices: 3732761--3732785 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3732751 CACATCTATG
3732761 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
3732786 GTTTTTTTAT
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:3737443 original size:15 final size:15
Alignment explanation
Indices: 3737423--3737455 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
3737413 ATATCATGGG
3737423 AAAAATAAAAAAACC
1 AAAAATAAAAAAACC
3737438 AAAAATAAAAAAACC
1 AAAAATAAAAAAACC
3737453 AAA
1 AAA
3737456 TACGGACGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.82, C:0.12, G:0.00, T:0.06
Consensus pattern (15 bp):
AAAAATAAAAAAACC
Found at i:3746245 original size:9 final size:9
Alignment explanation
Indices: 3746231--3746278 Score: 50
Period size: 9 Copynumber: 5.7 Consensus size: 9
3746221 GTTGATATAA
3746231 ATATAATTT
1 ATATAATTT
3746240 ATATAATTT
1 ATATAATTT
*
3746249 -TAATTATTT
1 AT-ATAATTT
3746258 AT-TAATTT
1 ATATAATTT
3746266 ATA-AA-TT
1 ATATAATTT
3746273 ATATAA
1 ATATAA
3746279 ATTAAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
7 5 0.15
8 12 0.36
9 15 0.45
10 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (9 bp):
ATATAATTT
Found at i:3749306 original size:147 final size:147
Alignment explanation
Indices: 3749117--3749418 Score: 595
Period size: 147 Copynumber: 2.1 Consensus size: 147
3749107 GAAGGAGACT
3749117 AAGAAAACACATCACTACTTCCCTTCTCTTTCTTTTTGCTCTACTTTTAATTACACCTATCTCTA
1 AAGAAAACACATCACTACTTCCCTTCTCTTTCTTTTTGCTCTACTTTTAATTACACCTATCTCTA
*
3749182 TTTGAAGTACACAATAACACAGGCTCCTATGACATAGAATATGACATAACTATATCAGTAAAAGA
66 TTGGAAGTACACAATAACACAGGCTCCTATGACATAGAATATGACATAACTATATCAGTAAAAGA
3749247 TATCAAGCAAAAACAAA
131 TATCAAGCAAAAACAAA
3749264 AAGAAAACACATCACTACTTCCCTTCTCTTTCTTTTTGCTCTACTTTTAATTACACCTATCTCTA
1 AAGAAAACACATCACTACTTCCCTTCTCTTTCTTTTTGCTCTACTTTTAATTACACCTATCTCTA
3749329 TTGGAAGTACACAATAACACAGGCTCCTATGACATAGAATATGACATAACTATATCAGTAAAAGA
66 TTGGAAGTACACAATAACACAGGCTCCTATGACATAGAATATGACATAACTATATCAGTAAAAGA
3749394 TATCAAGCAAAAACAAA
131 TATCAAGCAAAAACAAA
3749411 AAGAAAAC
1 AAGAAAAC
3749419 TACTGAAGTA
Statistics
Matches: 154, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
147 154 1.00
ACGTcount: A:0.40, C:0.22, G:0.09, T:0.29
Consensus pattern (147 bp):
AAGAAAACACATCACTACTTCCCTTCTCTTTCTTTTTGCTCTACTTTTAATTACACCTATCTCTA
TTGGAAGTACACAATAACACAGGCTCCTATGACATAGAATATGACATAACTATATCAGTAAAAGA
TATCAAGCAAAAACAAA
Found at i:3749710 original size:22 final size:20
Alignment explanation
Indices: 3749697--3749736 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
3749687 TTCTTATATC
3749697 TATTATAAAATATTATTAATA
1 TATT-TAAAATATTATTAATA
*
3749718 TATTTAAAAATAATATTAA
1 TATTT-AAAATATTATTAA
3749737 AAAAATATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TATTTAAAATATTATTAATA
Found at i:3749811 original size:20 final size:20
Alignment explanation
Indices: 3749786--3749827 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
3749776 AATAAGACTT
*
3749786 TAATATATTGTATTTAATAA
1 TAATATATTATATTTAATAA
*
3749806 TAATATTTTATATTTAATAA
1 TAATATATTATATTTAATAA
3749826 TA
1 TA
3749828 TATTTAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
TAATATATTATATTTAATAA
Found at i:3753725 original size:21 final size:22
Alignment explanation
Indices: 3753700--3753745 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
3753690 AAATATTAAT
3753700 AATTTAAATT-TATTTAATTTA
1 AATTTAAATTATATTTAATTTA
*
3753721 AATTTAAATTAATTTTTAATTTA
1 AATTTAAATT-ATATTTAATTTA
3753744 AA
1 AA
3753746 ACTTTTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 10 0.45
23 12 0.55
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
AATTTAAATTATATTTAATTTA
Found at i:3753743 original size:17 final size:17
Alignment explanation
Indices: 3753721--3753784 Score: 55
Period size: 16 Copynumber: 3.9 Consensus size: 17
3753711 ATTTAATTTA
3753721 AATTTAAATTAATTTTT
1 AATTTAAATTAATTTTT
*
3753738 AATTT-AA--AACTTTT
1 AATTTAAATTAATTTTT
* *
3753752 AATTCAAAATAA-TTTT
1 AATTTAAATTAATTTTT
*
3753768 AAATTAAACTTAATTTT
1 AATTTAAA-TTAATTTT
3753785 AAAATTTAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
14 10 0.27
15 2 0.05
16 12 0.32
17 10 0.27
18 3 0.08
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (17 bp):
AATTTAAATTAATTTTT
Found at i:3754589 original size:14 final size:13
Alignment explanation
Indices: 3754566--3754600 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
3754556 TAATTTTAAA
3754566 TTAAAATTTATTAT
1 TTAAAATTTA-TAT
*
3754580 TTAAATTTTATAT
1 TTAAAATTTATAT
3754593 TTAAAATT
1 TTAAAATT
3754601 AAGTATAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TTAAAATTTATAT
Found at i:3755579 original size:25 final size:24
Alignment explanation
Indices: 3755545--3755607 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 24
3755535 TAATTTAATT
3755545 TTAAAT-AAAGATAACATA-ATATA
1 TTAAATCAAAGATAACATATATA-A
* *
3755568 TTAATATCAAAGTTAATATATATAA
1 TTAA-ATCAAAGATAACATATATAA
*
3755593 TTAAATTAAAGATAA
1 TTAAATCAAAGATAA
3755608 GTTTAAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
23 4 0.12
24 11 0.33
25 15 0.45
26 3 0.09
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (24 bp):
TTAAATCAAAGATAACATATATAA
Found at i:3756284 original size:23 final size:22
Alignment explanation
Indices: 3756242--3756284 Score: 52
Period size: 23 Copynumber: 1.9 Consensus size: 22
3756232 TTTAAAAAAT
*
3756242 AAAAATAAAAAACTTGAATATA
1 AAAAATAAAAAAATTGAATATA
3756264 AAAAACTAAAAATAATT-AATA
1 AAAAA-TAAAAA-AATTGAATA
3756285 AAATGATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 5 0.28
23 10 0.56
24 3 0.17
ACGTcount: A:0.70, C:0.05, G:0.02, T:0.23
Consensus pattern (22 bp):
AAAAATAAAAAAATTGAATATA
Found at i:3759302 original size:16 final size:16
Alignment explanation
Indices: 3759279--3759314 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
3759269 TCTCGTTAAA
*
3759279 TCTTTTTTTT-TATTT
1 TCTTTTTTTTCGATTT
3759294 TCTTTTTTTTCGATTT
1 TCTTTTTTTTCGATTT
3759310 TCTTT
1 TCTTT
3759315 GTGAATGGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.06, C:0.11, G:0.03, T:0.81
Consensus pattern (16 bp):
TCTTTTTTTTCGATTT
Found at i:3760562 original size:10 final size:9
Alignment explanation
Indices: 3760511--3760559 Score: 71
Period size: 9 Copynumber: 5.2 Consensus size: 9
3760501 CCATTGAGTT
3760511 AAAAAGAAA
1 AAAAAGAAA
*
3760520 AAAAGGAAA
1 AAAAAGAAA
3760529 AAAAAGAAA
1 AAAAAGAAA
3760538 AAAATAGAAA
1 AAAA-AGAAA
3760548 AATAAAGAAA
1 AA-AAAGAAA
3760558 AA
1 AA
3760560 TAATTAAGGA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
9 20 0.56
10 14 0.39
11 2 0.06
ACGTcount: A:0.84, C:0.00, G:0.12, T:0.04
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:3765658 original size:23 final size:24
Alignment explanation
Indices: 3765631--3765679 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
3765621 TTTACCAAAT
* *
3765631 ATCATAGGCATTCACTAAAA-AAA
1 ATCATAAGCATTCACCAAAATAAA
3765654 ATCATAAGCATTCACCAAAATAAA
1 ATCATAAGCATTCACCAAAATAAA
3765678 AT
1 AT
3765680 GCAAACTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.53, C:0.18, G:0.06, T:0.22
Consensus pattern (24 bp):
ATCATAAGCATTCACCAAAATAAA
Found at i:3765845 original size:28 final size:29
Alignment explanation
Indices: 3765795--3765853 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 29
3765785 ATTTTTCTTG
3765795 ACCATATCAAATGCAGAAAAATTCA-TAA
1 ACCATATCAAATGCAGAAAAATTCATTAA
*
3765823 ACCATATCAAATGCA-ACATAATTCATTAA
1 ACCATATCAAATGCAGA-AAAATTCATTAA
3765852 AC
1 AC
3765854 ATACTTATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 1 0.04
28 22 0.79
29 5 0.18
ACGTcount: A:0.51, C:0.20, G:0.05, T:0.24
Consensus pattern (29 bp):
ACCATATCAAATGCAGAAAAATTCATTAA
Found at i:3767773 original size:33 final size:32
Alignment explanation
Indices: 3767736--3767800 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
3767726 ATGAAACAAC
*
3767736 ATGAA-TAGAAAAGCATGTCAAAATTTATATAAA
1 ATGAATTAG-AAA-CATATCAAAATTTATATAAA
* *
3767769 ATGAATTAGTAATATATCAAAATTTATATAAA
1 ATGAATTAGAAACATATCAAAATTTATATAAA
3767801 TATATAACAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 18 0.64
33 7 0.25
34 3 0.11
ACGTcount: A:0.54, C:0.05, G:0.09, T:0.32
Consensus pattern (32 bp):
ATGAATTAGAAACATATCAAAATTTATATAAA
Found at i:3770989 original size:16 final size:16
Alignment explanation
Indices: 3770965--3771071 Score: 97
Period size: 16 Copynumber: 6.7 Consensus size: 16
3770955 GTTTGAGCAG
*
3770965 GTTCGGGTTCGGGCTT
1 GTTCGGGTTCGGGCTC
* *
3770981 GTTCAGGTTCGGTCTC
1 GTTCGGGTTCGGGCTC
* *
3770997 ATTCGGGTTCGAGCTC
1 GTTCGGGTTCGGGCTC
* * *
3771013 GTTTGGGTTAGGGCTT
1 GTTCGGGTTCGGGCTC
3771029 GTTCGGGTTCGGGCTC
1 GTTCGGGTTCGGGCTC
* * * *
3771045 GTTCCGATTCAGACTC
1 GTTCGGGTTCGGGCTC
*
3771061 TTTCGGGTTCG
1 GTTCGGGTTCG
3771072 AGCTTTTTCA
Statistics
Matches: 68, Mismatches: 23, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
16 68 1.00
ACGTcount: A:0.07, C:0.21, G:0.36, T:0.36
Consensus pattern (16 bp):
GTTCGGGTTCGGGCTC
Found at i:3771007 original size:32 final size:32
Alignment explanation
Indices: 3770966--3771121 Score: 107
Period size: 32 Copynumber: 4.8 Consensus size: 32
3770956 TTTGAGCAGG
*
3770966 TTCGGGTTCGGGCTTGTTCAGGTTCGGTCTCA
1 TTCGGGTTCGGGCTTGTTCAGGTTCGGTCTCT
* * ** * *
3770998 TTCGGGTTCGAGCTCGTTTGGGTTAGGGCT-T
1 TTCGGGTTCGGGCTTGTTCAGGTTCGGTCTCT
* * * * *
3771029 GTTCGGGTTCGGGCTCGTTCCGATTCAGACTCT
1 -TTCGGGTTCGGGCTTGTTCAGGTTCGGTCTCT
* * * * *
3771062 TTCGGGTTCGAGCTTTTTCAAGTTCGGGTTTTT
1 TTCGGGTTCGGGCTTGTTCAGGTTC-GGTCTCT
* * *
3771095 TTTGGGTTCAGGCTTATTCAGGTTCGG
1 TTCGGGTTCGGGCTTGTTCAGGTTCGG
3771122 GTTCAGGTTC
Statistics
Matches: 92, Mismatches: 29, Indels: 6
0.72 0.23 0.05
Matches are distributed among these distances:
32 68 0.74
33 24 0.26
ACGTcount: A:0.08, C:0.19, G:0.33, T:0.40
Consensus pattern (32 bp):
TTCGGGTTCGGGCTTGTTCAGGTTCGGTCTCT
Found at i:3771069 original size:48 final size:49
Alignment explanation
Indices: 3770966--3771089 Score: 128
Period size: 48 Copynumber: 2.6 Consensus size: 49
3770956 TTTGAGCAGG
* * * *
3770966 TTCGGGTTCGGGCTTGTTCAGGTTCGGTCTCATTCGGGTTCGAGCTCGT
1 TTCGGGTTAGGGCTTGTTCAGGTTCGGGCTCATTCCGATTCGAGCTCGT
* *
3771015 TT-GGGTTAGGGCTTGTTCGGGTTCGGGCTCGTTCCGATTC-AGACTC-T
1 TTCGGGTTAGGGCTTGTTCAGGTTCGGGCTCATTCCGATTCGAG-CTCGT
* * * *
3771062 TTCGGGTTCGAGCTTTTTCAAGTTCGGG
1 TTCGGGTTAGGGCTTGTTCAGGTTCGGG
3771090 TTTTTTTTGG
Statistics
Matches: 62, Mismatches: 11, Indels: 5
0.79 0.14 0.06
Matches are distributed among these distances:
47 5 0.08
48 55 0.89
49 2 0.03
ACGTcount: A:0.08, C:0.21, G:0.34, T:0.37
Consensus pattern (49 bp):
TTCGGGTTAGGGCTTGTTCAGGTTCGGGCTCATTCCGATTCGAGCTCGT
Found at i:3771128 original size:12 final size:12
Alignment explanation
Indices: 3771111--3771135 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3771101 TTCAGGCTTA
3771111 TTCAGGTTCGGG
1 TTCAGGTTCGGG
3771123 TTCAGGTTCGGG
1 TTCAGGTTCGGG
3771135 T
1 T
3771136 CGATTTCGGG
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:0.08, C:0.16, G:0.40, T:0.36
Consensus pattern (12 bp):
TTCAGGTTCGGG
Found at i:3771361 original size:18 final size:18
Alignment explanation
Indices: 3771312--3771361 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
3771302 ATTGAAATCG
*
3771312 ATTTTTATATATATAATTA
1 ATTTTT-TATATAAAATTA
*
3771331 ATTTGTTATATAAAATTA
1 ATTTTTTATATAAAATTA
*
3771349 ATTTTTTAAATAA
1 ATTTTTTATATAA
3771362 TTTATTATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
18 22 0.81
19 5 0.19
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
ATTTTTTATATAAAATTA
Found at i:3772508 original size:12 final size:12
Alignment explanation
Indices: 3772491--3772532 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
3772481 TAGTATTAAA
3772491 TTTGGGTTCGAG
1 TTTGGGTTCGAG
3772503 TTTGGG-TC-AG
1 TTTGGGTTCGAG
*
3772513 TCTCGGGTTCGAG
1 T-TTGGGTTCGAG
3772526 TTTGGGT
1 TTTGGGT
3772533 CAGTCTAGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
10 3 0.12
11 6 0.24
12 13 0.52
13 3 0.12
ACGTcount: A:0.07, C:0.12, G:0.40, T:0.40
Consensus pattern (12 bp):
TTTGGGTTCGAG
Found at i:3772524 original size:23 final size:23
Alignment explanation
Indices: 3772494--3772544 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
3772484 TATTAAATTT
*
3772494 GGGTTCGAGTTTGGGTCAGTCTC
1 GGGTTCGAGTTTGGGTCAGTCTA
3772517 GGGTTCGAGTTTGGGTCAGTCTA
1 GGGTTCGAGTTTGGGTCAGTCTA
3772540 GGGTT
1 GGGTT
3772545 GGGGTTCTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.10, C:0.14, G:0.41, T:0.35
Consensus pattern (23 bp):
GGGTTCGAGTTTGGGTCAGTCTA
Found at i:3772608 original size:16 final size:16
Alignment explanation
Indices: 3772588--3772641 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
3772578 AGATTTTTTT
* *
3772588 AGGTTCAGGCTTTCTT
1 AGGTTCAGGCTATCTC
* *
3772604 GGGTTTAGGCTATCTC
1 AGGTTCAGGCTATCTC
*
3772620 AGGTTCAGGCTATTTC
1 AGGTTCAGGCTATCTC
3772636 AGGTTC
1 AGGTTC
3772642 GGGTAATTTC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.15, C:0.19, G:0.28, T:0.39
Consensus pattern (16 bp):
AGGTTCAGGCTATCTC
Found at i:3779467 original size:2 final size:2
Alignment explanation
Indices: 3779460--3779486 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3779450 TTAGAAACAT
3779460 TA 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 TA T
3779487 CTTCTAAAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3781803 original size:20 final size:21
Alignment explanation
Indices: 3781780--3781833 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
3781770 CATTTCAGGC
3781780 ATGTATCAATACATTCACT-T
1 ATGTATCAATACATTCACTAT
*
3781800 ATGTATCGAA-ACATTTACTAT
1 ATGTATC-AATACATTCACTAT
* *
3781821 TTGTATCGATACA
1 ATGTATCAATACA
3781834 AATTATAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (21 bp):
ATGTATCAATACATTCACTAT
Found at i:3783000 original size:79 final size:79
Alignment explanation
Indices: 3782813--3783255 Score: 410
Period size: 79 Copynumber: 5.6 Consensus size: 79
3782803 AGAAAAAACA
* * * * * * *
3782813 GGGTTAGAGAATCCCCGATGGTGAAAAGTTGATATTTTGGAAACAAAA-TCGGGGTTGGAGTATC
1 GGGTTGGAGTATCCCCGATGGTGAAAAATCGATGTTTTAGAAATAAAACT-GGGGTTGGAGTATC
*
3782877 CCCTCGAAAAATAACG
65 CCCTCG-AAAATAATG
** * * * * *
3782893 GGGTTAAAGTATCCACGATGGTGAAAAATTGGTGTTTTAAAAATAAAACTGGGGTTGAAGTATCC
1 GGGTTGGAGTATCCCCGATGGTGAAAAATCGATGTTTTAGAAATAAAACTGGGGTTGGAGTATCC
* *
3782958 CTTTGAAAATAATG
66 CCTCGAAAATAATG
* * * * * *
3782972 GGGTTGGAGTATCCCCGATTGTGGAAAATCAATGTTTTAGAAATAAAGCCGGAGTTGGAGTATCC
1 GGGTTGGAGTATCCCCGATGGTGAAAAATCGATGTTTTAGAAATAAAACTGGGGTTGGAGTATCC
3783037 CCTCGAAAATAATG
66 CCTCGAAAATAATG
* * ** * * *
3783051 GGATTGGAATATCCCTAATAGTGAAAAATCAATGTTTTAGAAATAAAAC-GAAGGTTGGAGTATC
1 GGGTTGGAGTATCCCCGATGGTGAAAAATCGATGTTTTAGAAATAAAACTG-GGGTTGGAGTATC
* * * *
3783115 TCTTTGAAAATAATA
65 CCCTCGAAAATAATG
* * *
3783130 GGGTTGGAGTATCCCC-ACTTGTGAAAAATCGATGTTTTAAAAATAAAA-TAGGAGTTGGAGTAT
1 GGGTTGGAGTATCCCCGA-TGGTGAAAAATCGATGTTTTAGAAATAAAACT-GGGGTTGGAGTAT
* * *
3783193 -CCATCGAAAACAACG
64 CCCCTCGAAAATAATG
* * * *
3783208 GGGTTGGAGTATCCCCGATGGTGAAAATTTGGTATTTTAGAAATAAAA
1 GGGTTGGAGTATCCCCGATGGTGAAAAATCGATGTTTTAGAAATAAAA
3783256 ACATGAATGA
Statistics
Matches: 296, Mismatches: 61, Indels: 14
0.80 0.16 0.04
Matches are distributed among these distances:
78 51 0.17
79 187 0.63
80 57 0.19
81 1 0.00
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (79 bp):
GGGTTGGAGTATCCCCGATGGTGAAAAATCGATGTTTTAGAAATAAAACTGGGGTTGGAGTATCC
CCTCGAAAATAATG
Found at i:3783257 original size:158 final size:158
Alignment explanation
Indices: 3782804--3783255 Score: 498
Period size: 158 Copynumber: 2.9 Consensus size: 158
3782794 ATATTTTGGA
* * * * * ** * ** * *
3782804 GAAAA-AACAGGGTTAGAGAATCCCCGATGGTGAAAAGTTGATATTTTGGAAACAAAATCGGGGT
1 GAAAATAATAGGGTTGGAGTATCCCCGATTGTGAAAAATCAATGTTTTAAAAATAAAATCGGAGT
** * *
3782868 TGGAGTATCCCCTCGAAAAATAACGGGGTTAAAGTATCCACGATGGTGAAAAATTGGTGTTTTAA
66 TGGAGTATCCCCTCG-AAAATAACGGGGTTGGAGTATCCCCGATGGTGAAAAATTGGTGTTTTAG
*
3782933 AAATAAAACTGGGGTTGAAGTATCCCTTT
130 AAATAAAACTGAGGTTGAAGTATCCCTTT
* * * **
3782962 GAAAATAATGGGGTTGGAGTATCCCCGATTGTGGAAAATCAATGTTTTAGAAATAAAGCCGGAGT
1 GAAAATAATAGGGTTGGAGTATCCCCGATTGTGAAAAATCAATGTTTTAAAAATAAAATCGGAGT
* * * ** * ***
3783027 TGGAGTATCCCCTCGAAAATAATGGGATTGGAATATCCCTAATAGTGAAAAATCAATGTTTTAGA
66 TGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATGGTGAAAAATTGGTGTTTTAGA
* *
3783092 AATAAAAC-GAAGGTTGGAGTATCTCTTT
131 AATAAAACTG-AGGTTGAAGTATCCCTTT
* *
3783120 GAAAATAATAGGGTTGGAGTATCCCC-ACTTGTGAAAAATCGATGTTTTAAAAATAAAATAGGAG
1 GAAAATAATAGGGTTGGAGTATCCCCGA-TTGTGAAAAATCAATGTTTTAAAAATAAAATCGGAG
* * * *
3783184 TTGGAGTAT-CCATCGAAAACAACGGGGTTGGAGTATCCCCGATGGTGAAAATTTGGTATTTTAG
65 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATGGTGAAAAATTGGTGTTTTAG
3783248 AAATAAAA
130 AAATAAAA
3783256 ACATGAATGA
Statistics
Matches: 240, Mismatches: 51, Indels: 7
0.81 0.17 0.02
Matches are distributed among these distances:
157 52 0.22
158 129 0.54
159 59 0.25
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (158 bp):
GAAAATAATAGGGTTGGAGTATCCCCGATTGTGAAAAATCAATGTTTTAAAAATAAAATCGGAGT
TGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATGGTGAAAAATTGGTGTTTTAGA
AATAAAACTGAGGTTGAAGTATCCCTTT
Found at i:3788666 original size:19 final size:19
Alignment explanation
Indices: 3788642--3788679 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
3788632 GATCGTCTTA
3788642 CTTTTGCAAGAGTTGCTAT
1 CTTTTGCAAGAGTTGCTAT
*
3788661 CTTTTGCAGGAGTTGCTAT
1 CTTTTGCAAGAGTTGCTAT
3788680 ATGATAGCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.18, C:0.16, G:0.24, T:0.42
Consensus pattern (19 bp):
CTTTTGCAAGAGTTGCTAT
Found at i:3790421 original size:3 final size:3
Alignment explanation
Indices: 3790413--3790465 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
3790403 ATTATTTAAT
3790413 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3790461 TAA TA
1 TAA TA
3790466 CAAACGGTGG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:3791117 original size:17 final size:18
Alignment explanation
Indices: 3791089--3791122 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3791079 CATAATTAAT
3791089 TATCATTTAATTATATTA
1 TATCATTTAATTATATTA
*
3791107 TATCA-TTAATTTTATT
1 TATCATTTAATTATATT
3791123 TTTTATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (18 bp):
TATCATTTAATTATATTA
Found at i:3791267 original size:22 final size:20
Alignment explanation
Indices: 3791222--3791261 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3791212 TATATAATAG
*
3791222 AAAAATAATATAAATATGGT
1 AAAAATAATAAAAATATGGT
3791242 AAAAATAGATAAATAATATG
1 AAAAATA-ATAAA-AATATG
3791262 TCAAAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 4 0.24
22 6 0.35
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.28
Consensus pattern (20 bp):
AAAAATAATAAAAATATGGT
Found at i:3791542 original size:19 final size:18
Alignment explanation
Indices: 3791489--3791552 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 18
3791479 GCATCTATAT
*
3791489 AATAAAAA-AATAACACA
1 AATAAAAATAAAAACACA
* * *
3791506 AATATAATATGAATACACTA
1 AATA-AAAATAAAAACAC-A
3791526 AATAAAAATAAAAACACAA
1 AATAAAAATAAAAACAC-A
3791545 AATAAAAA
1 AATAAAAA
3791553 AAATTAAAAT
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
17 4 0.11
18 3 0.08
19 24 0.67
20 5 0.14
ACGTcount: A:0.72, C:0.09, G:0.02, T:0.17
Consensus pattern (18 bp):
AATAAAAATAAAAACACA
Found at i:3792002 original size:14 final size:14
Alignment explanation
Indices: 3791978--3792024 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 14
3791968 AATTTTATTA
3791978 AAAAATCAAAAAAAT
1 AAAAAT-AAAAAAAT
3791993 AAAAATAAAAAAAT
1 AAAAATAAAAAAAT
* *
3792007 AAAATTTAATAAAAT
1 AAAA-ATAAAAAAAT
3792022 AAA
1 AAA
3792025 GTACAATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 12 0.41
15 17 0.59
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (14 bp):
AAAAATAAAAAAAT
Found at i:3794388 original size:21 final size:22
Alignment explanation
Indices: 3794359--3794420 Score: 76
Period size: 21 Copynumber: 2.9 Consensus size: 22
3794349 TTTAAAAATA
* *
3794359 AATATAATAAATTTTATTT-TT
1 AATAAAATAAATATTATTTATT
3794380 AATAAAAT-AATATTATTTATT
1 AATAAAATAAATATTATTTATT
3794401 AATAAAAT-AATATATATTTA
1 AATAAAATAAATAT-TATTTA
3794421 ACACATCAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 9 0.24
21 22 0.59
22 6 0.16
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AATAAAATAAATATTATTTATT
Found at i:3794889 original size:11 final size:11
Alignment explanation
Indices: 3794869--3794929 Score: 60
Period size: 11 Copynumber: 5.8 Consensus size: 11
3794859 GACATAACTA
*
3794869 ATAATTAAAAT
1 ATAATAAAAAT
3794880 ATAATAAAAAT
1 ATAATAAAAAT
3794891 AT-AT-AAAAT
1 ATAATAAAAAT
3794900 A-AA-AAATAAT
1 ATAATAAA-AAT
3794910 ATAA-ATAAAAT
1 ATAATA-AAAAT
3794921 ATAATAAAA
1 ATAATAAAA
3794930 TTTTAAATTT
Statistics
Matches: 43, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
9 9 0.21
10 6 0.14
11 25 0.58
12 3 0.07
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
ATAATAAAAAT
Found at i:3794906 original size:16 final size:15
Alignment explanation
Indices: 3794885--3794930 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 15
3794875 AAAATATAAT
3794885 AAAAATATATAAAATA
1 AAAAATA-ATAAAATA
3794901 AAAAATAATATAAATA
1 AAAAATAATA-AAATA
*
3794917 AAATATAATAAAAT
1 AAAAATAATAAAAT
3794931 TTTAAATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 7 0.25
16 21 0.75
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAAATAATAAAATA
Found at i:3794964 original size:22 final size:21
Alignment explanation
Indices: 3794923--3794965 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
3794913 AATAAAATAT
*
3794923 AATAAAATTTTAAATTTTAAA
1 AATAAAATTTTAAATATTAAA
3794944 AATATAAATTATT-AATATTAAA
1 AATA-AAATT-TTAAATATTAAA
3794966 TATTTTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 4 0.21
22 13 0.68
23 2 0.11
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
AATAAAATTTTAAATATTAAA
Found at i:3797810 original size:28 final size:25
Alignment explanation
Indices: 3797748--3797846 Score: 76
Period size: 24 Copynumber: 3.8 Consensus size: 25
3797738 TTTTACTCTT
*
3797748 AATAATTATAAAATTTTATATTTTAAA
1 AATAAATAT-AAA-TTTATATTTTAAA
3797775 AATAAATATTTAAATTTATTATTTATAAA
1 AATAAATA--TAAATTTA-TATTT-TAAA
* **
3797804 AAT-AATATAAATTTAAATAATAAA
1 AATAAATATAAATTTATATTTTAAA
**
3797828 AATTTATA-AAATTTATATT
1 AATAAATATAAATTTATATT
3797847 CACATCCATT
Statistics
Matches: 60, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
24 16 0.27
25 5 0.08
26 8 0.13
27 11 0.18
28 12 0.20
29 8 0.13
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
AATAAATATAAATTTATATTTTAAA
Found at i:3806565 original size:16 final size:16
Alignment explanation
Indices: 3806546--3806585 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
3806536 TGTGTCGTTT
*
3806546 TAAATTTTTGTTTATA
1 TAAATTTTTGTATATA
* *
3806562 TAAATATATGTATATA
1 TAAATTTTTGTATATA
3806578 TAAATTTT
1 TAAATTTT
3806586 ATTAGTTAAT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (16 bp):
TAAATTTTTGTATATA
Found at i:3817967 original size:305 final size:304
Alignment explanation
Indices: 3817371--3818249 Score: 1126
Period size: 305 Copynumber: 2.9 Consensus size: 304
3817361 TTTTATTTTA
* * * * * *
3817371 TTTAAAATTACAATTATAAATATTCTATTATTAATAATATTTATTTAATATCTAAGTAAGAGGTT
1 TTTAAAA-TACCATTATAAATATTTTATTATTAATAATATTTATCTAATTTATAAGTAAGAAGTT
* * * * *
3817436 TAATTTGAA-TGAAATACTTTTATTAAATAATAATATCAATTATTGTTTATTGTATTGTTTAATA
65 TAATTT-AATTAAAATACTTTTATTAAATGATAATATCAATTATTATTTATTATATTATTTAATA
* * * *
3817500 ACTATTG-AAATAATTTTTTATTATTACATTATATATTATAAGATTAA-ATTATATTTTTGATAT
129 ACTATTGAAAATAATATTTTATTATTATATTATATATTATAAGATTAAGATTATATTTTTAAAAT
** * * *
3817563 TTTTATTTAAATATTTAATCAAAATAA-AGTAATGATAATTTTATTTATTTAAATTTAATTATTA
194 TTTTATCCAAATA-TTAATCAAAATAAGA-TAATAATAATTTTATTTATTTAAATTTAATCATGA
* *
3817627 TTTAATATATTTTGAATTGACAAAAATAATCATTATTATTTACTTTATT
257 -TTAATATATTTTGAATTGACAAAAATAATCATTATTATTTACTCTAAT
* *
3817676 TTTAAAATGCCATTATAAATATTTTATTATTAATAATATTTATCTAATTTATAAGTATGAAGTTT
1 TTTAAAATACCATTATAAATATTTTATTATTAATAATATTTATCTAATTTATAAGTAAGAAGTTT
* *
3817741 AATTTAATTTAAAATA-TTTT-TTAAATGATAATCTCACTTATTATTTATTATATTATTTAATAA
66 AATTTAA-TTAAAATACTTTTATTAAATGATAATATCAATTATTATTTATTATATTATTTAATAA
*
3817804 CTATTGAAAATAATATTTTATTATTATATTATATATTATAAGATTAAGATTGTATTTTTAAAATT
130 CTATTGAAAATAATATTTTATTATTATATTATATATTATAAGATTAAGATTATATTTTTAAAATT
3817869 TTTATCCAAATATATAATCAAAATAAGATAATAATAATTTTATTTATTTAAATTTAATCAGTGAT
195 TTTATCCAAATAT-TAATCAAAATAAGATAATAATAATTTTATTTATTTAAATTTAATCA-TGAT
* ** * *
3817934 TAATTTATTTTGAATTGATGAAAATATTCATTATTGTTTACTCTAAT
258 TAATATATTTTGAATTGACAAAAATAATCATTATTATTTACTCTAAT
* * ** * * *
3817981 TTTAAATTATCATTATTTATATTTTTATTATTAGTAATATTGATCTAATTTAT-AGATAACAAGT
1 TTTAAAATACCATTATAAATA-TTTTATTATTAATAATATTTATCTAATTTATAAG-TAAGAAGT
* * *
3818045 TTAATTTGATTAAAATATTTTTATTAAATGGTAATATCAATTATTATTTATTATATTATTTAATA
64 TTAATTTAATTAAAATACTTTTATTAAATGATAATATCAATTATTATTTATTATATTATTTAATA
* * * * * * *
3818110 ACCATTTAAATTAATATTTTATTTTTTTATTATATATTACAAGATTAGGATTATA-TTTTAAAAT
129 ACTATTGAAAATAATATTTTATTATTATATTATATATTATAAGATTAAGATTATATTTTTAAAAT
* * *
3818174 TTTTATCCAAATATTCAATCAAAATTAGATAATAATAATTTTATTTGTTTAAATCTAATCATTGA
194 TTTTATCCAAATATT-AATCAAAATAAGATAATAATAATTTTATTTATTTAAATTTAATCA-TGA
3818239 TTAATATATTT
257 TTAATATATTT
3818250 ATATTTTAAG
Statistics
Matches: 504, Mismatches: 58, Indels: 23
0.86 0.10 0.04
Matches are distributed among these distances:
303 45 0.09
304 98 0.19
305 147 0.29
306 128 0.25
307 86 0.17
ACGTcount: A:0.41, C:0.04, G:0.05, T:0.50
Consensus pattern (304 bp):
TTTAAAATACCATTATAAATATTTTATTATTAATAATATTTATCTAATTTATAAGTAAGAAGTTT
AATTTAATTAAAATACTTTTATTAAATGATAATATCAATTATTATTTATTATATTATTTAATAAC
TATTGAAAATAATATTTTATTATTATATTATATATTATAAGATTAAGATTATATTTTTAAAATTT
TTATCCAAATATTAATCAAAATAAGATAATAATAATTTTATTTATTTAAATTTAATCATGATTAA
TATATTTTGAATTGACAAAAATAATCATTATTATTTACTCTAAT
Done.