Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold165.1
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: 1724686
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 30232 characters in sequence are not A, C, G, or T
File 3 of 8
Found at i:496480 original size:15 final size:15
Alignment explanation
Indices: 496460--496488 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
496450 GATTTAGTTT
496460 TTTATTTTATTATTG
1 TTTATTTTATTATTG
496475 TTTATTTTATTATT
1 TTTATTTTATTATT
496489 TATCATTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (15 bp):
TTTATTTTATTATTG
Found at i:496513 original size:13 final size:13
Alignment explanation
Indices: 496495--496532 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
496485 TATTTATCAT
496495 TTAAATATATAAA
1 TTAAATATATAAA
*
496508 TTAAATATATTAA
1 TTAAATATATAAA
496521 -T-AATATATAAA
1 TTAAATATATAAA
496532 T
1 T
496533 AATATTAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
11 9 0.41
12 1 0.05
13 12 0.55
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
TTAAATATATAAA
Found at i:496525 original size:11 final size:11
Alignment explanation
Indices: 496511--496553 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
496501 ATATAAATTA
496511 AATATATTAAT
1 AATATATTAAT
*
496522 AATATATAAAT
1 AATATATTAAT
496533 -A-ATATTAAT
1 AATATATTAAT
*
496542 AATATAATAAT
1 AATATATTAAT
496553 A
1 A
496554 TAGAAAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
9 7 0.26
10 2 0.07
11 18 0.67
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
AATATATTAAT
Found at i:496541 original size:17 final size:17
Alignment explanation
Indices: 496514--496554 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 17
496504 TAAATTAAAT
496514 ATATTAATAATATATAAATA
1 ATATTAAT-A-ATAT-AATA
496534 ATATTAATAATATAATA
1 ATATTAATAATATAATA
496551 ATAT
1 ATAT
496555 AGAAAGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.38
18 4 0.19
19 1 0.05
20 8 0.38
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATATTAATAATATAATA
Found at i:496553 original size:20 final size:20
Alignment explanation
Indices: 496509--496547 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
496499 ATATATAAAT
496509 TAAAT-ATATTAATAATATA
1 TAAATAATATTAATAATATA
496528 TAAATAATATTAATAATATA
1 TAAATAATATTAATAATATA
496548 ATAATATAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TAAATAATATTAATAATATA
Found at i:499275 original size:6 final size:6
Alignment explanation
Indices: 499260--499292 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
499250 CTCATTCATT
499260 GAAA-A GAAAGA GAAAGA GAAAGA GAAAGA GAAA
1 GAAAGA GAAAGA GAAAGA GAAAGA GAAAGA GAAA
499293 ATAATAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.15
6 23 0.85
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (6 bp):
GAAAGA
Found at i:501436 original size:30 final size:31
Alignment explanation
Indices: 501400--501458 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
501390 TTAACATTTA
*
501400 TAAAAATAATAATAATTT-AATTTAATTTTT
1 TAAAAATAATAAAAATTTAAATTTAATTTTT
*
501430 TAAAAATTATAAAAATTTAAAATTTAATT
1 TAAAAATAATAAAAATTT-AAATTTAATT
501459 CCGGCCCTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 16 0.64
32 9 0.36
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (31 bp):
TAAAAATAATAAAAATTTAAATTTAATTTTT
Found at i:507796 original size:21 final size:22
Alignment explanation
Indices: 507770--507812 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
507760 TAAAATTGAT
507770 AAAAATT-TAATT-TAATTTTTA
1 AAAAATTATAATTGT-ATTTTTA
507791 AAAAATTATAATTGTATTTTTA
1 AAAAATTATAATTGTATTTTTA
507813 CTATGAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 7 0.35
22 12 0.60
23 1 0.05
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
AAAAATTATAATTGTATTTTTA
Found at i:526110 original size:77 final size:77
Alignment explanation
Indices: 525973--526115 Score: 198
Period size: 77 Copynumber: 1.9 Consensus size: 77
525963 CCAAAATAAC
* * * *
525973 CTGAACCCGATATGACCCGAACAAGTAACCCAAAATTACATGAACCCAAGATACCCGACTTGAAA
1 CTGAACCCAATATGACCCAAACAAGTAACCCAAAATGACATGAACCCAAGACACCCGACTTGAAA
526038 ATCCCAATTAAA
66 ATCCCAATTAAA
* * * *
526050 CTGAGCCCAATATGACCCAAACAAGTAATCCGAAAA-GACATGAACCCAAGCCACCTGACTTGAA
1 CTGAACCCAATATGACCCAAACAAGTAA-CCCAAAATGACATGAACCCAAGACACCCGACTTGAA
526114 AA
65 AA
526116 AACCAATTGA
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
77 51 0.89
78 6 0.11
ACGTcount: A:0.43, C:0.29, G:0.13, T:0.15
Consensus pattern (77 bp):
CTGAACCCAATATGACCCAAACAAGTAACCCAAAATGACATGAACCCAAGACACCCGACTTGAAA
ATCCCAATTAAA
Found at i:526185 original size:16 final size:16
Alignment explanation
Indices: 526166--526203 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
526156 CTCAAATCCA
526166 AAATAACCTGAACTTG
1 AAATAACCTGAACTTG
* *
526182 AAATGACTTGAACTTG
1 AAATAACCTGAACTTG
526198 AAATAA
1 AAATAA
526204 GCCAAAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.26
Consensus pattern (16 bp):
AAATAACCTGAACTTG
Found at i:532512 original size:25 final size:24
Alignment explanation
Indices: 532470--532517 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
532460 CCCATATATT
532470 ATACTTTCAATTCTTTCACATTTA
1 ATACTTTCAATTCTTTCACATTTA
532494 ATACATTTCAATGTC-TTCACATTT
1 ATAC-TTTCAAT-TCTTTCACATTT
532518 TTCCCATGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 4 0.18
25 16 0.73
26 2 0.09
ACGTcount: A:0.29, C:0.21, G:0.02, T:0.48
Consensus pattern (24 bp):
ATACTTTCAATTCTTTCACATTTA
Found at i:543442 original size:45 final size:45
Alignment explanation
Indices: 543378--543469 Score: 175
Period size: 45 Copynumber: 2.0 Consensus size: 45
543368 ATGCCTGTGT
543378 TGAACTTGGTAGGTTAGGTGAGTGTGAAGAGGTCAAAGGTTGAGG
1 TGAACTTGGTAGGTTAGGTGAGTGTGAAGAGGTCAAAGGTTGAGG
*
543423 TGAACTTGGTAGGTTAGGTGAGTGTGAAGATGTCAAAGGTTGAGG
1 TGAACTTGGTAGGTTAGGTGAGTGTGAAGAGGTCAAAGGTTGAGG
543468 TG
1 TG
543470 TGGTGATGGT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.26, C:0.04, G:0.41, T:0.28
Consensus pattern (45 bp):
TGAACTTGGTAGGTTAGGTGAGTGTGAAGAGGTCAAAGGTTGAGG
Found at i:549186 original size:27 final size:28
Alignment explanation
Indices: 549131--549195 Score: 114
Period size: 27 Copynumber: 2.4 Consensus size: 28
549121 ATAAAAAAAA
*
549131 ACCAAAATATTATAACTTTTTTTTATTT
1 ACCAAAATATTATAACATTTTTTTATTT
549159 ACCAAAATATTATAA-ATTTTTTTATTT
1 ACCAAAATATTATAACATTTTTTTATTT
549186 ACCAAAATAT
1 ACCAAAATAT
549196 ACCAAAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 21 0.58
28 15 0.42
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.48
Consensus pattern (28 bp):
ACCAAAATATTATAACATTTTTTTATTT
Found at i:550499 original size:27 final size:27
Alignment explanation
Indices: 550457--550509 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
550447 ACATTTTAGT
550457 TCTTTGGCACCATTGGTGCCGCCAATC
1 TCTTTGGCACCATTGGTGCCGCCAATC
* *
550484 TCTTTGGCACCTTTGGTGCCTCCAAT
1 TCTTTGGCACCATTGGTGCCGCCAAT
550510 GTGATTGGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.13, C:0.32, G:0.21, T:0.34
Consensus pattern (27 bp):
TCTTTGGCACCATTGGTGCCGCCAATC
Found at i:550517 original size:27 final size:27
Alignment explanation
Indices: 550460--550518 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
550450 TTTTAGTTCT
*
550460 TTGGCACCATTGGTGCCGCCAATCTCT
1 TTGGCACCATTGGTGCCGCCAATCTCA
* * * *
550487 TTGGCACCTTTGGTGCCTCCAATGTGA
1 TTGGCACCATTGGTGCCGCCAATCTCA
550514 TTGGC
1 TTGGC
550519 CTGATCAGGC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.14, C:0.29, G:0.25, T:0.32
Consensus pattern (27 bp):
TTGGCACCATTGGTGCCGCCAATCTCA
Found at i:550622 original size:26 final size:28
Alignment explanation
Indices: 550570--550633 Score: 114
Period size: 26 Copynumber: 2.4 Consensus size: 28
550560 TTTTTTTGGT
550570 ATATTTTGGTAAATAAAAAAATTTTATA
1 ATATTTTGGTAAATAAAAAAATTTTATA
550598 ATATTTTGGTAAAT-AAAAAA-TTTATA
1 ATATTTTGGTAAATAAAAAAATTTTATA
550624 ATATTTTGGT
1 ATATTTTGGT
550634 TATTTTTATT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
26 16 0.44
27 6 0.17
28 14 0.39
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAATTTTATA
Found at i:553699 original size:46 final size:46
Alignment explanation
Indices: 553627--553786 Score: 311
Period size: 46 Copynumber: 3.5 Consensus size: 46
553617 TGATCAGTGA
*
553627 CAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
553673 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
553719 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
553765 CAAGTGACAAAGTGATAAGTGG
1 CAAGTGACAAAGTGATAAGTGG
553787 CTACACTTAT
Statistics
Matches: 113, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
46 113 1.00
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (46 bp):
CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
Found at i:553791 original size:37 final size:37
Alignment explanation
Indices: 553749--553894 Score: 233
Period size: 37 Copynumber: 4.0 Consensus size: 37
553739 GGTAGCTTTA
**
553749 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
553786 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
553823 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
553860 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
553895 ATCATACGTA
Statistics
Matches: 103, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 88 0.85
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:554695 original size:115 final size:115
Alignment explanation
Indices: 554493--554714 Score: 381
Period size: 115 Copynumber: 1.9 Consensus size: 115
554483 GACTTCAACA
*
554493 CTTTCGTTTTTTAGTGTTTGAGTAGGGTTTTCATTAACCCTAGACTCAACTTCGTCGCCTGCTTC
1 CTTTCGTTTTCTAGTGTTTGAGTAGGGTTTTCATTAACCCTAGACTCAACTTCGTCGCCTGCTTC
**
554558 TATTTCCGGTGATGGGTTACTCTGAGTCCCTACCACCTCTGAGTCCTACT
66 TATTTCCGGCAATGGGTTACTCTGAGTCCCTACCACCTCTGAGTCCTACT
* *
554608 CTTTCGTTTTCTAGTTTTTGAGTAGGGTTTTCATTAACCCTAGACTCAACTTCGTTGCCTGCTTC
1 CTTTCGTTTTCTAGTGTTTGAGTAGGGTTTTCATTAACCCTAGACTCAACTTCGTCGCCTGCTTC
* *
554673 TATTTCTGGCAATGGGTTACTCTGAGTCTCTACCACCTCTGA
66 TATTTCCGGCAATGGGTTACTCTGAGTCCCTACCACCTCTGA
554715 CTGTTTTTTT
Statistics
Matches: 100, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
115 100 1.00
ACGTcount: A:0.16, C:0.25, G:0.18, T:0.40
Consensus pattern (115 bp):
CTTTCGTTTTCTAGTGTTTGAGTAGGGTTTTCATTAACCCTAGACTCAACTTCGTCGCCTGCTTC
TATTTCCGGCAATGGGTTACTCTGAGTCCCTACCACCTCTGAGTCCTACT
Found at i:555864 original size:12 final size:13
Alignment explanation
Indices: 555843--555871 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
555833 GAAATTAAAT
555843 CTAAATAATAATC
1 CTAAATAATAATC
555856 CTAAA-AATAATC
1 CTAAATAATAATC
555868 CTAA
1 CTAA
555872 TAAAATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (13 bp):
CTAAATAATAATC
Found at i:558699 original size:39 final size:39
Alignment explanation
Indices: 558648--558722 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 39
558638 TGAGAAAGTT
*
558648 TTTTTTATTCATTTCTTTATTACTAATAATTCTTTTAAG
1 TTTTTTATTCATTTCTTTATTACTAATAATTATTTTAAG
*
558687 TTTTTTATTCATTTCTTTATTTCTAATAATTATTTT
1 TTTTTTATTCATTTCTTTATTACTAATAATTATTTT
558723 TCATATATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.24, C:0.09, G:0.01, T:0.65
Consensus pattern (39 bp):
TTTTTTATTCATTTCTTTATTACTAATAATTATTTTAAG
Found at i:567263 original size:21 final size:22
Alignment explanation
Indices: 567239--567279 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
567229 TGTAATTTCA
567239 TCTAAATTATTTA-TTTATTGT
1 TCTAAATTATTTACTTTATTGT
**
567260 TCTATTTTATTTACTTTATT
1 TCTAAATTATTTACTTTATT
567280 ATATAATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.66
Consensus pattern (22 bp):
TCTAAATTATTTACTTTATTGT
Found at i:568882 original size:21 final size:21
Alignment explanation
Indices: 568856--568910 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
568846 AACAGCGGTG
* *
568856 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGGTACTATA
*
568877 GCGGTGAGATTGGGTACTATA
1 GCGGTGAGATTAGGTACTATA
568898 GCGGTGAGATTAG
1 GCGGTGAGATTAG
568911 AAATAATGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.24, C:0.09, G:0.38, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGGTACTATA
Found at i:572799 original size:30 final size:30
Alignment explanation
Indices: 572756--573102 Score: 432
Period size: 30 Copynumber: 11.8 Consensus size: 30
572746 TGACTACTTT
572756 ATATATATTTTTTATTTTTAAAATACACTAC
1 ATATAT-TTTTTTATTTTTAAAATACACTAC
*
572787 ATATATTTTTTTACTTTTAAAATACACTAC
1 ATATATTTTTTTATTTTTAAAATACACTAC
*
572817 ATATA----TATATTTTTAAAATACACTAC
1 ATATATTTTTTTATTTTTAAAATACACTAC
*
572843 ATATATTTTTTTACTTTTAAAATACACTAC
1 ATATATTTTTTTATTTTTAAAATACACTAC
*
572873 ATATA----TATATTTTTAAAATACACTAC
1 ATATATTTTTTTATTTTTAAAATACACTAC
*
572899 ATATATATTTTTTATTTTTAAAATATACTAC
1 ATATAT-TTTTTTATTTTTAAAATACACTAC
*
572930 ATATATTTTTTTTACTTTTAAAATACACTAC
1 ATATA-TTTTTTTATTTTTAAAATACACTAC
*
572961 ATATA----TATA-TTTTAAAATACACTAC
1 ATATATTTTTTTATTTTTAAAATACACTAC
* *
572986 ATATATATATTTTTTATTTTTAAAATATAGTAC
1 --ATATAT-TTTTTTATTTTTAAAATACACTAC
573019 ATATATTTTTTTATTTTTAAAATACACTAC
1 ATATATTTTTTTATTTTTAAAATACACTAC
573049 ATATATATTTTTTATTTTTAAAATACACTAC
1 ATATAT-TTTTTTATTTTTAAAATACACTAC
** *
573080 ACGTATTTTTTAATTTTTAAAAT
1 ATATATTTTTTTATTTTTAAAAT
573103 TTTAAATACA
Statistics
Matches: 277, Mismatches: 20, Indels: 39
0.82 0.06 0.12
Matches are distributed among these distances:
25 16 0.06
26 51 0.18
27 5 0.02
30 96 0.35
31 91 0.33
32 4 0.01
33 14 0.05
ACGTcount: A:0.39, C:0.10, G:0.01, T:0.50
Consensus pattern (30 bp):
ATATATTTTTTTATTTTTAAAATACACTAC
Found at i:572828 original size:56 final size:56
Alignment explanation
Indices: 572768--573102 Score: 374
Period size: 56 Copynumber: 5.8 Consensus size: 56
572758 ATATATTTTT
*
572768 TATTTTTAAAATACACTACATATATTTTTTTACTTTTAAAATACACTACATATATA
1 TATTTTTAAAATACACTACATATATTTTTTTATTTTTAAAATACACTACATATATA
*
572824 TATTTTTAAAATACACTACATATATTTTTTTACTTTTAAAATACACTACATATATA
1 TATTTTTAAAATACACTACATATATTTTTTTATTTTTAAAATACACTACATATATA
* *
572880 TATTTTTAAAATACACTACATATATATTTTTTATTTTTAAAATATACTACATATATTTTTTT
1 TATTTTTAAAATACACTACATATAT-TTTTTTATTTTTAAAATACACTACATATA-----TA
* *
572942 TACTTTTAAAATACACTACATATA----TATA-TTTTAAAATACACTACATATATATA
1 TATTTTTAAAATACACTACATATATTTTTTTATTTTTAAAATACACTAC--ATATATA
* *
572995 TTTTTTATTTTTAAAATATAGTACATATATTTTTTTATTTTTAAAATACACTACATATATA
1 -----TATTTTTAAAATACACTACATATATTTTTTTATTTTTAAAATACACTACATATATA
** *
573056 TTTTTTATTTTTAAAATACACTACACGTATTTTTTAATTTTTAAAAT
1 -----TATTTTTAAAATACACTACATATATTTTTTTATTTTTAAAAT
573103 TTTAAATACA
Statistics
Matches: 245, Mismatches: 16, Indels: 31
0.84 0.05 0.11
Matches are distributed among these distances:
53 1 0.00
56 96 0.39
57 30 0.12
58 26 0.11
61 49 0.20
62 27 0.11
63 16 0.07
ACGTcount: A:0.40, C:0.10, G:0.01, T:0.50
Consensus pattern (56 bp):
TATTTTTAAAATACACTACATATATTTTTTTATTTTTAAAATACACTACATATATA
Found at i:572993 original size:23 final size:24
Alignment explanation
Indices: 572945--572998 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 24
572935 TTTTTTTTAC
572945 TTTTAAAATACACTACATATATATA
1 TTTTAAAATACACTACA-ATATATA
572970 TTTTAAAATACACTACATATATATA
1 TTTTAAAATACACTACA-ATATATA
572995 TTTT
1 TTTT
572999 TTATTTTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (24 bp):
TTTTAAAATACACTACAATATATA
Found at i:573155 original size:15 final size:15
Alignment explanation
Indices: 573137--573171 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
573127 TTCCCATCTC
*
573137 CCCTCTTCCATCATT
1 CCCTCTTCCACCATT
*
573152 CCCTCTTCCACCGTT
1 CCCTCTTCCACCATT
573167 CCCTC
1 CCCTC
573172 CTCCCATTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.09, C:0.54, G:0.03, T:0.34
Consensus pattern (15 bp):
CCCTCTTCCACCATT
Found at i:573242 original size:28 final size:28
Alignment explanation
Indices: 573207--573306 Score: 94
Period size: 28 Copynumber: 3.4 Consensus size: 28
573197 ACCCATTCCA
*
573207 ATTTCCCATTCCACCGTGCCGTCCTCCC
1 ATTTCCCATTCCACCGTGCCCTCCTCCC
* * *
573235 ATTTCCCATTCCCATC-TCCCCTCTTCCATC
1 ATTTCCCATT-CCACCGTGCCCTCCTCC--C
* *
573265 GATTCCCCTCTTCCACCGTGCCCTCCTCCC
1 -ATTTCCC-ATTCCACCGTGCCCTCCTCCC
573295 ATTTCCCATTCC
1 ATTTCCCATTCC
573307 CATGCAATAC
Statistics
Matches: 55, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
28 22 0.40
29 10 0.18
30 2 0.04
31 10 0.18
32 11 0.20
ACGTcount: A:0.11, C:0.51, G:0.06, T:0.32
Consensus pattern (28 bp):
ATTTCCCATTCCACCGTGCCCTCCTCCC
Found at i:573296 original size:118 final size:117
Alignment explanation
Indices: 573118--573336 Score: 386
Period size: 118 Copynumber: 1.9 Consensus size: 117
573108 ATACAATGCA
*
573118 ATTTCTCCATTCCCATCTCCCCTCTTCCATCATTCCCTCTTCCACCGTTCCCTCCTCCCATTTCC
1 ATTTCTCCATTCCCATCTCCCCTCTTCCATCATTCCCTCTTCCACCGTGCCCTCCTCCCATTTCC
*
573183 TATTCCCATGCAATACCCATTCCAATTTCCCATTCCACCGTGCCGTCCTCCC
66 CATTCCCATGCAATACCCATTCCAATTTCCCATTCCACCGTGCCGTCCTCCC
573235 ATTTC-CCATTCCCATCTCCCCTCTTCCATCGATTCCCCTCTTCCACCGTGCCCTCCTCCCATTT
1 ATTTCTCCATTCCCATCTCCCCTCTTCCATC-ATT-CCCTCTTCCACCGTGCCCTCCTCCCATTT
*
573299 CCCATTCCCATGCAATACCCATTCCCATTTCCCATTCC
64 CCCATTCCCATGCAATACCCATTCCAATTTCCCATTCC
573337 CATTCCCATT
Statistics
Matches: 97, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
116 25 0.26
117 8 0.08
118 64 0.66
ACGTcount: A:0.15, C:0.48, G:0.04, T:0.33
Consensus pattern (117 bp):
ATTTCTCCATTCCCATCTCCCCTCTTCCATCATTCCCTCTTCCACCGTGCCCTCCTCCCATTTCC
CATTCCCATGCAATACCCATTCCAATTTCCCATTCCACCGTGCCGTCCTCCC
Found at i:573308 original size:6 final size:6
Alignment explanation
Indices: 573291--573352 Score: 72
Period size: 6 Copynumber: 10.2 Consensus size: 6
573281 CGTGCCCTCC
* * *
573291 TCCCATT TCCCAT TCCCA- TGCAAT ACCCAT TCCCATT TCCCAT TCCCAT
1 TCCCA-T TCCCAT TCCCAT TCCCAT TCCCAT TCCCA-T TCCCAT TCCCAT
573340 TCCCAT TCCCAT T
1 TCCCAT TCCCAT T
573353 ATCAACAATA
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
5 3 0.06
6 33 0.70
7 11 0.23
ACGTcount: A:0.19, C:0.45, G:0.02, T:0.34
Consensus pattern (6 bp):
TCCCAT
Found at i:573309 original size:13 final size:13
Alignment explanation
Indices: 573291--573352 Score: 72
Period size: 13 Copynumber: 4.5 Consensus size: 13
573281 CGTGCCCTCC
573291 TCCCATTTCCCAT
1 TCCCATTTCCCAT
*
573304 TCCCATGCAATACCCAT
1 TCCCAT----TTCCCAT
573321 TCCCATTTCCCAT
1 TCCCATTTCCCAT
573334 TCCCA-TTCCCAT
1 TCCCATTTCCCAT
573346 TCCCATT
1 TCCCATT
573353 ATCAACAATA
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
12 12 0.29
13 18 0.43
17 12 0.29
ACGTcount: A:0.19, C:0.45, G:0.02, T:0.34
Consensus pattern (13 bp):
TCCCATTTCCCAT
Found at i:573331 original size:60 final size:60
Alignment explanation
Indices: 573152--573331 Score: 219
Period size: 60 Copynumber: 3.0 Consensus size: 60
573142 TTCCATCATT
* * *
573152 CCCTCTTCCACCGTTCCCTCCTCCCATTTCCTATTCCCATGCAATACCCATTCCAATTT-
1 CCCTCTTCCACCGTGCCCTCCTCCCATTTCCCATTCCCATGCAATACCCATTCCCATTTC
* * * *
573211 CCC-ATTCCACCGTGCCGTCCTCCCATTTCCCATTCCCAT-C--T-CCCCTCTTCCATCGATTC
1 CCCTCTTCCACCGTGCCCTCCTCCCATTTCCCATTCCCATGCAATACCCAT-TCCCAT---TTC
573270 CCCTCTTCCACCGTGCCCTCCTCCCATTTCCCATTCCCATGCAATACCCATTCCCATTTC
1 CCCTCTTCCACCGTGCCCTCCTCCCATTTCCCATTCCCATGCAATACCCATTCCCATTTC
573330 CC
1 CC
573332 ATTCCCATTC
Statistics
Matches: 100, Mismatches: 11, Indels: 19
0.77 0.08 0.15
Matches are distributed among these distances:
54 4 0.04
55 5 0.05
57 1 0.01
58 34 0.34
59 6 0.06
60 39 0.39
61 1 0.01
63 6 0.06
64 4 0.04
ACGTcount: A:0.14, C:0.49, G:0.05, T:0.31
Consensus pattern (60 bp):
CCCTCTTCCACCGTGCCCTCCTCCCATTTCCCATTCCCATGCAATACCCATTCCCATTTC
Found at i:575885 original size:21 final size:20
Alignment explanation
Indices: 575861--575922 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 20
575851 AACAAAGTAT
*
575861 AAAAGAGGGGAGAAACTAGCA
1 AAAAGA-GGGAGAAACCAGCA
* *
575882 AAAACGAGGGATAAACCAGTA
1 AAAA-GAGGGAGAAACCAGCA
*
575903 AACA-AGGGAGAAACCAGCA
1 AAAAGAGGGAGAAACCAGCA
575922 A
1 A
575923 GAACGAGGGG
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
19 14 0.41
21 18 0.53
22 2 0.06
ACGTcount: A:0.53, C:0.15, G:0.27, T:0.05
Consensus pattern (20 bp):
AAAAGAGGGAGAAACCAGCA
Found at i:575910 original size:19 final size:19
Alignment explanation
Indices: 575883--575919 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
575873 AAACTAGCAA
* *
575883 AAACGAGGGATAAACCAGT
1 AAACAAGGGAGAAACCAGT
575902 AAACAAGGGAGAAACCAG
1 AAACAAGGGAGAAACCAG
575920 CAAGAACGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.16, G:0.27, T:0.05
Consensus pattern (19 bp):
AAACAAGGGAGAAACCAGT
Found at i:583970 original size:33 final size:33
Alignment explanation
Indices: 583932--584049 Score: 227
Period size: 33 Copynumber: 3.6 Consensus size: 33
583922 TGATACGGTA
583932 GAATCAGCACTTAGCAACCACCAATGAATCGGG
1 GAATCAGCACTTAGCAACCACCAATGAATCGGG
583965 GAATCAGCACTTAGCAACCACCAATGAATCGGG
1 GAATCAGCACTTAGCAACCACCAATGAATCGGG
*
583998 GAATCAGCACTTAGCAACCACCAATGAATCAGG
1 GAATCAGCACTTAGCAACCACCAATGAATCGGG
584031 GAATCAGCACTTAGCAACC
1 GAATCAGCACTTAGCAACC
584050 CCCTTCACAT
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
33 84 1.00
ACGTcount: A:0.37, C:0.28, G:0.19, T:0.15
Consensus pattern (33 bp):
GAATCAGCACTTAGCAACCACCAATGAATCGGG
Found at i:586500 original size:19 final size:20
Alignment explanation
Indices: 586468--586505 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
586458 TTTTTAATAT
586468 TTATTTTTTATA-CCTTTTA
1 TTATTTTTTATACCCTTTTA
586487 TTATTTTCTT-TACCCTTTT
1 TTATTTT-TTATACCCTTTT
586506 TTAATGTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (20 bp):
TTATTTTTTATACCCTTTTA
Found at i:588570 original size:481 final size:470
Alignment explanation
Indices: 587893--588749 Score: 1437
Period size: 481 Copynumber: 1.8 Consensus size: 470
587883 CAGTCCCCAG
* * *
587893 TCCAACTACAATCGAGTAAATGAACATACTATCTCATATTTTAAACTGATGTTGTAACATTTAAC
1 TCCAACTACAATCAAGTAAATGAACATACCACCTCATATTTTAAACTGATGTTGTAACATTTAAC
* *
587958 CGAGTTAATCTCATAAAATTAACAATTTTTTTCAACTATTACGAAAAATATAATCTTGTTAATTT
66 CGAGTTAATCTAAAAAAATTAACAATTTTTTTCAACTATTACGAAAAATATAATCTTGTTAATTT
588023 ATCTACCTACAAGGATCTTTATCTTTATTTTAACAAAAATACATTCTTCATTATGGTACAGGGAC
131 ATCTACCTACAAGGATCTTTATCTTTATTTTAACAAAAATACATTCTTCATTATGGTACAGGGAC
*
588088 CGATGTAGTATTTTTACCAATAATTCCCTAATGGAAAATTGGAAATCTGTTTGGTAGTATATTAA
196 CGATGTAGTATTTTTACCAATAATTCCCTAATAGAAAATTGGAAATCTGTTTGGTAGTATATTAA
* *
588153 TAAAATCAAATAAAAGAGGTCATTTGTGAATCCAAGGCTTGGTTCAGAATCGAATCTCAACATTG
261 TAAAATCAAATAAAAAAGGTCATTTGTGAATCCAAGGCTTGGTCCAGAATCGAATCTCAACATTG
*
588218 TATCGTTTACTATCTGCATATTATTTTTTTATAGACCCCAAAGTATTGATTTCTTTGTATCATAA
326 TA-----T-C--TC--CATATTATTTTTTTATAGACCCCAAACTATTGATTTCTTTGTATCATAA
588283 CCAAGAATCTAATCCCTAGCTTGATTTCACAACACTCCCCCGACGGATGCATATTCCCCGATTTC
381 CCAAGAATCTAATCCCTAGCTTGATTTCACAACACTCCCCCGACGGATGCATATTCCCCGATTTC
588348 GTATTTTATTAATCGATTAAATGCA
446 GTATTTTATTAATCGATTAAATGCA
* * * *
588373 TCCAGCTACAATCAAGTAAATGAACATACCACCTCATATTTTAAACTTATGTTGTATCATTTAAT
1 TCCAACTACAATCAAGTAAATGAACATACCACCTCATATTTTAAACTGATGTTGTAACATTTAAC
588438 CGAGTTAATCTAAAAAAATTAACAACTTTTTTTCAACTATTACGAAAAATATAAGT-TTGTTAAT
66 CGAGTTAATCTAAAAAAATTAACAA-TTTTTTTCAACTATTACGAAAAATATAA-TCTTGTTAAT
* * *
588502 TTATCTACCTACAAGGATCTTTATGTTTATTTTAACTAAAATGCATTCTTCATTATGGTACAGGG
129 TTATCTACCTACAAGGATCTTTATCTTTATTTTAACAAAAATACATTCTTCATTATGGTACAGGG
* *
588567 ACCGATGTAGTATTTTTACCAATAATTCCCTAATAGAAAATTGTAAATTTGTTTGGTAGTATATT
194 ACCGATGTAGTATTTTTACCAATAATTCCCTAATAGAAAATTGGAAATCTGTTTGGTAGTATATT
588632 AATAAAATCAAATAAAAAAGGTCATTTGTGAATCCAAGGCTTGGTCCAGAATCGAATCTCAACAT
259 AATAAAATCAAATAAAAAAGGTCATTTGTGAATCCAAGGCTTGGTCCAGAATCGAATCTCAACAT
588697 TGTATCTCCATATTATTTTTTTATAGACCCCAAACTATTGATTTCTTTGTATC
324 TGTATCTCCATATTATTTTTTTATAGACCCCAAACTATTGATTTCTTTGTATC
588750 CCCCCCCCCC
Statistics
Matches: 357, Mismatches: 18, Indels: 13
0.92 0.05 0.03
Matches are distributed among these distances:
471 44 0.12
473 2 0.01
475 1 0.00
476 1 0.00
480 81 0.23
481 227 0.64
482 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.37
Consensus pattern (470 bp):
TCCAACTACAATCAAGTAAATGAACATACCACCTCATATTTTAAACTGATGTTGTAACATTTAAC
CGAGTTAATCTAAAAAAATTAACAATTTTTTTCAACTATTACGAAAAATATAATCTTGTTAATTT
ATCTACCTACAAGGATCTTTATCTTTATTTTAACAAAAATACATTCTTCATTATGGTACAGGGAC
CGATGTAGTATTTTTACCAATAATTCCCTAATAGAAAATTGGAAATCTGTTTGGTAGTATATTAA
TAAAATCAAATAAAAAAGGTCATTTGTGAATCCAAGGCTTGGTCCAGAATCGAATCTCAACATTG
TATCTCCATATTATTTTTTTATAGACCCCAAACTATTGATTTCTTTGTATCATAACCAAGAATCT
AATCCCTAGCTTGATTTCACAACACTCCCCCGACGGATGCATATTCCCCGATTTCGTATTTTATT
AATCGATTAAATGCA
Found at i:591709 original size:61 final size:61
Alignment explanation
Indices: 591614--591837 Score: 322
Period size: 61 Copynumber: 3.7 Consensus size: 61
591604 TTTTATAGGG
* * * * *
591614 GCTGAATTGACTCACTAATATTCTACTGAGAGCCAAATTCAGCTATGTATCTATGGAAGGA
1 GCTGAATTGACTCACTGATATGCTACTGAGAGCCAAATTCAGCTATCTAACTATGAAAGGA
* * *
591675 GCTGAATCGACTCACTGATATTCTACTTAGAGCCAAATTCAGCTATCTAACTATGAAAGGA
1 GCTGAATTGACTCACTGATATGCTACTGAGAGCCAAATTCAGCTATCTAACTATGAAAGGA
* * *
591736 GCTGAATTGGCTCACTGTTGTGCTACTGAGAGCCAAATTCAGCTATCTAACTATGAAAGGA
1 GCTGAATTGACTCACTGATATGCTACTGAGAGCCAAATTCAGCTATCTAACTATGAAAGGA
* * *
591797 GCTGAATTGGCTCACTGATCTGCTACTTAGAGCCAAATTCA
1 GCTGAATTGACTCACTGATATGCTACTGAGAGCCAAATTCA
591838 ACCATGTATC
Statistics
Matches: 148, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
61 148 1.00
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.29
Consensus pattern (61 bp):
GCTGAATTGACTCACTGATATGCTACTGAGAGCCAAATTCAGCTATCTAACTATGAAAGGA
Found at i:609624 original size:18 final size:18
Alignment explanation
Indices: 609589--609623 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
609579 GTTTTGGTAA
609589 AATTGATTTTTTATTTTT
1 AATTGATTTTTTATTTTT
609607 AATT-ATTTTTTATTTTT
1 AATTGATTTTTTATTTTT
609624 TTTTAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (18 bp):
AATTGATTTTTTATTTTT
Found at i:609706 original size:18 final size:18
Alignment explanation
Indices: 609683--609742 Score: 56
Period size: 18 Copynumber: 3.5 Consensus size: 18
609673 TTTTTAAATA
*
609683 TAATTTTTCA-TATTCTTT
1 TAATTTTTAATTATT-TTT
609701 TAATTTTTAATTATTTTT
1 TAATTTTTAATTATTTTT
* *
609719 TAA--TATAATTA-TTAT
1 TAATTTTTAATTATTTTT
609734 TAATTTTTA
1 TAATTTTTA
609743 TGAATATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
15 6 0.17
16 7 0.20
17 3 0.09
18 15 0.43
19 4 0.11
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (18 bp):
TAATTTTTAATTATTTTT
Found at i:613073 original size:6 final size:6
Alignment explanation
Indices: 613062--613097 Score: 56
Period size: 6 Copynumber: 6.0 Consensus size: 6
613052 TTTATCTCTG
613062 TCCCTA TCCCTA TCCCTA TCCCTA TACCC-A TCCCTA
1 TCCCTA TCCCTA TCCCTA TCCCTA T-CCCTA TCCCTA
613098 GCAATCCTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 3 0.11
6 22 0.79
7 3 0.11
ACGTcount: A:0.19, C:0.50, G:0.00, T:0.31
Consensus pattern (6 bp):
TCCCTA
Found at i:613406 original size:17 final size:16
Alignment explanation
Indices: 613375--613416 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
613365 TATGAATTCT
613375 CTTTAAATTTATTTTG
1 CTTTAAATTTATTTTG
613391 CTTTAAATTCTATTTTG
1 CTTTAAATT-TATTTTG
*
613408 -TGTAAATTT
1 CTTTAAATTT
613417 TATCCAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 1 0.04
16 16 0.67
17 7 0.29
ACGTcount: A:0.26, C:0.07, G:0.07, T:0.60
Consensus pattern (16 bp):
CTTTAAATTTATTTTG
Found at i:615366 original size:20 final size:19
Alignment explanation
Indices: 615313--615371 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 19
615303 ATGATTTTTG
*
615313 AAATTTATTATTTATTAAT
1 AAATTTATTATTTTTTAAT
* *
615332 AAATATTATAATTTTGTAAT
1 AAAT-TTATTATTTTTTAAT
*
615352 AAATTTATTGTTTTTATAAT
1 AAATTTATTATTTTT-TAAT
615372 TTTAACAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
19 12 0.38
20 20 0.62
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (19 bp):
AAATTTATTATTTTTTAAT
Found at i:616963 original size:2 final size:2
Alignment explanation
Indices: 616956--616993 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
616946 GTGAAGGAAG
616956 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
616994 TATGTATTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:618661 original size:27 final size:28
Alignment explanation
Indices: 618626--618688 Score: 85
Period size: 27 Copynumber: 2.3 Consensus size: 28
618616 TTTTTAAATT
618626 TTTTAAAAATTAAAAAAT-ATAAAAACTA
1 TTTTAAAAATT-AAAAATCATAAAAACTA
* *
618654 TTTTAAAAATT-AAAATCATTAAAATTA
1 TTTTAAAAATTAAAAATCATAAAAACTA
618681 TTTTAAAA
1 TTTTAAAA
618689 TTATATTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
26 5 0.16
27 16 0.50
28 11 0.34
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (28 bp):
TTTTAAAAATTAAAAATCATAAAAACTA
Found at i:618700 original size:26 final size:27
Alignment explanation
Indices: 618626--618688 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 27
618616 TTTTTAAATT
618626 TTTTAAAAATTAAAA-AATATAAAAACTA
1 TTTTAAAAATTAAAATAAT-T-AAAACTA
* *
618654 TTTTAAAAATTAAAATCATTAAAATTA
1 TTTTAAAAATTAAAATAATTAAAACTA
618681 TTTTAAAA
1 TTTTAAAA
618689 TTATATTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
27 14 0.44
28 16 0.50
29 2 0.06
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (27 bp):
TTTTAAAAATTAAAATAATTAAAACTA
Found at i:618737 original size:19 final size:20
Alignment explanation
Indices: 618685--618737 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
618675 AAATTATTTT
618685 AAAATTATATTAATTATATAA
1 AAAATTA-ATTAATTATATAA
** *
618706 AAATATTTTTTAA-TATTTAA
1 AAA-ATTAATTAATTATATAA
618726 AAAATTAATTAA
1 AAAATTAATTAA
618738 AAGCTAACAT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
19 7 0.27
20 9 0.35
21 7 0.27
22 3 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AAAATTAATTAATTATATAA
Found at i:625063 original size:14 final size:15
Alignment explanation
Indices: 625037--625077 Score: 59
Period size: 14 Copynumber: 2.8 Consensus size: 15
625027 TTATGTACAT
625037 TTTAATAATTTAT-A
1 TTTAATAATTTATGA
625051 TTTAA-AATATTATGA
1 TTTAATAAT-TTATGA
625066 TTTAATAATTTA
1 TTTAATAATTTA
625078 GTTATCTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 3 0.12
14 9 0.38
15 9 0.38
16 3 0.12
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TTTAATAATTTATGA
Found at i:630056 original size:20 final size:20
Alignment explanation
Indices: 630027--630064 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
630017 ATGAAAGAAC
*
630027 ATCCGTCGAGACAAATCGGG
1 ATCCGACGAGACAAATCGGG
*
630047 ATCCGACGAGACTAATCG
1 ATCCGACGAGACAAATCG
630065 AAGAGCTTTC
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:0.32, C:0.26, G:0.26, T:0.16
Consensus pattern (20 bp):
ATCCGACGAGACAAATCGGG
Found at i:631583 original size:29 final size:31
Alignment explanation
Indices: 631537--631594 Score: 75
Period size: 29 Copynumber: 1.9 Consensus size: 31
631527 AAAAGGTAGG
* **
631537 AAGATTAAATTTTTAATTTT-T-AAAGTATA
1 AAGATTAAATCTCAAATTTTGTCAAAGTATA
631566 AAGATTAAATCTCAAATTTTGTCAAAGTA
1 AAGATTAAATCTCAAATTTTGTCAAAGTA
631595 CATAAACTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 17 0.71
30 1 0.04
31 6 0.25
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.41
Consensus pattern (31 bp):
AAGATTAAATCTCAAATTTTGTCAAAGTATA
Found at i:632734 original size:21 final size:21
Alignment explanation
Indices: 632710--632751 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
632700 ATAAGTATAT
*
632710 AAAAATACATAA-ATATTTAA
1 AAAAATACATAATAAATTTAA
*
632730 AAAAATATATAATAAATTTAA
1 AAAAATACATAATAAATTTAA
632751 A
1 A
632752 CTTTATATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (21 bp):
AAAAATACATAATAAATTTAA
Found at i:632789 original size:19 final size:19
Alignment explanation
Indices: 632761--632799 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
632751 ACTTTATATC
*
632761 AATAATTATA-TTAATATTA
1 AATAAATATAGTT-ATATTA
632780 AATAAATATAGTTATATTA
1 AATAAATATAGTTATATTA
632799 A
1 A
632800 TAATAGTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 16 0.89
20 2 0.11
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (19 bp):
AATAAATATAGTTATATTA
Found at i:632812 original size:25 final size:23
Alignment explanation
Indices: 632758--632804 Score: 58
Period size: 25 Copynumber: 2.0 Consensus size: 23
632748 TAAACTTTAT
*
632758 ATCAATAATTATATTAATATTAA
1 ATCAATAATTATATTAATAATAA
*
632781 ATAAATATAGTTATATTAATAATA
1 ATCAATA-A-TTATATTAATAATA
632805 GTTCAATACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 6 0.30
24 1 0.05
25 13 0.65
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (23 bp):
ATCAATAATTATATTAATAATAA
Found at i:633877 original size:14 final size:14
Alignment explanation
Indices: 633860--633886 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
633850 TAGAGTTCGA
633860 GGTTTAAGATTTAG
1 GGTTTAAGATTTAG
633874 GGTTTAAGATTTA
1 GGTTTAAGATTTA
633887 TGGCTTATGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.26, T:0.44
Consensus pattern (14 bp):
GGTTTAAGATTTAG
Found at i:633886 original size:21 final size:21
Alignment explanation
Indices: 633813--633886 Score: 51
Period size: 21 Copynumber: 3.5 Consensus size: 21
633803 ATGTTTGAGA
*
633813 TTTAAGATTTAAGATTTGGGG
1 TTTAAGATTTAAGATTTAGGG
* * * * *
633834 TTTAGGGCTCT-AGGTTTAGAG
1 TTTA-AGATTTAAGATTTAGGG
** *
633855 TTCGAGGTTTAAGATTTAGGG
1 TTTAAGATTTAAGATTTAGGG
633876 TTTAAGATTTA
1 TTTAAGATTTA
633887 TGGCTTATGG
Statistics
Matches: 35, Mismatches: 16, Indels: 4
0.64 0.29 0.07
Matches are distributed among these distances:
20 3 0.09
21 29 0.83
22 3 0.09
ACGTcount: A:0.26, C:0.04, G:0.28, T:0.42
Consensus pattern (21 bp):
TTTAAGATTTAAGATTTAGGG
Found at i:634417 original size:20 final size:19
Alignment explanation
Indices: 634379--634417 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
634369 AATTTTTTAG
**
634379 AAAATTCTTTTAAGTCCTC
1 AAAATTCTTTTAAAACCTC
634398 AAAATTCTTATTAAAACCTC
1 AAAATTCTT-TTAAAACCTC
634418 GAGGAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.38, C:0.21, G:0.03, T:0.38
Consensus pattern (19 bp):
AAAATTCTTTTAAAACCTC
Found at i:641542 original size:11 final size:11
Alignment explanation
Indices: 641526--641550 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
641516 CTCAATTGAA
641526 TTTTTATAAAT
1 TTTTTATAAAT
641537 TTTTTATAAAT
1 TTTTTATAAAT
641548 TTT
1 TTT
641551 ATAATTTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTTTATAAAT
Found at i:650720 original size:20 final size:20
Alignment explanation
Indices: 650683--650722 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
650673 TTACTTTCTT
* *
650683 GCAGCAAAGTTTAGGGAAAG
1 GCAGCAAAGTTCAAGGAAAG
650703 GCAGCAAAGTTCAAGGAAAG
1 GCAGCAAAGTTCAAGGAAAG
650723 ACTTGAACCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.12, G:0.33, T:0.12
Consensus pattern (20 bp):
GCAGCAAAGTTCAAGGAAAG
Found at i:650939 original size:28 final size:28
Alignment explanation
Indices: 650897--650953 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
650887 ACTCCTGCAA
650897 TACATGTTAAGACTTAAATTATGTTAAG
1 TACATGTTAAGACTTAAATTATGTTAAG
*
650925 TACATGTTAATACTTAAATTATGTTAAG
1 TACATGTTAAGACTTAAATTATGTTAAG
650953 T
1 T
650954 CTGATTATGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.42
Consensus pattern (28 bp):
TACATGTTAAGACTTAAATTATGTTAAG
Found at i:660318 original size:19 final size:19
Alignment explanation
Indices: 660276--660310 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
660266 TCTCACAACA
660276 AAAAT-TTTA-AAAAATTC
1 AAAATATTTATAAAAATTC
660293 AAAATATTTATAAAAATT
1 AAAATATTTATAAAAATT
660311 TGAAATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 4 0.25
19 7 0.44
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAATATTTATAAAAATTC
Found at i:661586 original size:12 final size:12
Alignment explanation
Indices: 661571--661595 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
661561 AACAACCTTC
661571 ACAACATGACCG
1 ACAACATGACCG
661583 ACAACATGACCG
1 ACAACATGACCG
661595 A
1 A
661596 TAATGCTTAT
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:0.44, C:0.32, G:0.16, T:0.08
Consensus pattern (12 bp):
ACAACATGACCG
Found at i:663115 original size:3 final size:3
Alignment explanation
Indices: 663096--663140 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
663086 TTGCCTTTAT
* * * *
663096 GCA GGA GCA GGA GCA GCA GCA GCA GGA GCA GCA GCA GCA GGA GCA
1 GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA
663141 ACCACCAATG
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.33, C:0.24, G:0.42, T:0.00
Consensus pattern (3 bp):
GCA
Found at i:663119 original size:15 final size:15
Alignment explanation
Indices: 663096--663140 Score: 81
Period size: 15 Copynumber: 3.0 Consensus size: 15
663086 TTGCCTTTAT
*
663096 GCAGGAGCAGGAGCA
1 GCAGCAGCAGGAGCA
663111 GCAGCAGCAGGAGCA
1 GCAGCAGCAGGAGCA
663126 GCAGCAGCAGGAGCA
1 GCAGCAGCAGGAGCA
663141 ACCACCAATG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.33, C:0.24, G:0.42, T:0.00
Consensus pattern (15 bp):
GCAGCAGCAGGAGCA
Found at i:663910 original size:15 final size:16
Alignment explanation
Indices: 663892--663921 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
663882 AATTTTAGTG
663892 ATAAA-ATTTTTAAAA
1 ATAAATATTTTTAAAA
663907 ATAAATATTTTTAAA
1 ATAAATATTTTTAAA
663922 CTTATTGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
ATAAATATTTTTAAAA
Found at i:666380 original size:20 final size:20
Alignment explanation
Indices: 666347--666386 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
666337 TAATGAAAAA
* *
666347 TATTTCAATTTTATTTTATT
1 TATTTCAATATTATATTATT
*
666367 TATTTTAATATTATATTATT
1 TATTTCAATATTATATTATT
666387 CTATAAAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (20 bp):
TATTTCAATATTATATTATT
Found at i:668074 original size:134 final size:133
Alignment explanation
Indices: 667912--668213 Score: 351
Period size: 133 Copynumber: 2.3 Consensus size: 133
667902 CAGCAACAGT
* * * * *
667912 CACTCAAGTTCCTGCTTAAGTGCATCAAACAATTTTCTTTAGGCTGGGAAGG-TAAGAACATGAA
1 CACTCAAGTTCCTGCCTAAGTGCATCAAACAATTCTCCTCAGGCTGGG-AGGATAA-AAAATGAA
* * *** ** *
667976 AGAAGGACACGAAACCA-TCTAAGCATTTTTGAGC-TTCAGCTATTGAA-ATCAATGAAGGATCA
64 AGAAAGACACGAAA-CAGTCTAAGAAACATCAAGCGTT-AGCTATT-AACAACAATGAAGGATCA
668038 ACAAGACC
126 ACAAGACC
* *
668046 CACTCAAGTTCCCGCCTAAGTGCATCAAAAAATTCTCCTCAGGCTGGGAGGATAAAAAATGAAAG
1 CACTCAAGTTCCTGCCTAAGTGCATCAAACAATTCTCCTCAGGCTGGGAGGATAAAAAATGAAAG
* * * *
668111 AAATACATGAAACAGTCTAAGAAACATCAAGCGTTAGCTGTTAACAACAATGAAGGATCCACAAG
66 AAAGACACGAAACAGTCTAAGAAACATCAAGCGTTAGCTATTAACAACAATGAAGGATCAACAAG
*
668176 ACT
131 ACC
668179 CACTCAAGTTCCTGCCTAAGTGCATCAAACAATTC
1 CACTCAAGTTCCTGCCTAAGTGCATCAAACAATTC
668214 CCTTTTGGTC
Statistics
Matches: 142, Mismatches: 22, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
132 4 0.03
133 91 0.64
134 47 0.33
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.23
Consensus pattern (133 bp):
CACTCAAGTTCCTGCCTAAGTGCATCAAACAATTCTCCTCAGGCTGGGAGGATAAAAAATGAAAG
AAAGACACGAAACAGTCTAAGAAACATCAAGCGTTAGCTATTAACAACAATGAAGGATCAACAAG
ACC
Found at i:673290 original size:22 final size:23
Alignment explanation
Indices: 673250--673292 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
673240 ATTTTTTATA
* *
673250 TTTTTTTAATTTTTTAAAAATAT
1 TTTTTTTAATATTTAAAAAATAT
673273 TTTTTTTAA-ATTTAAAAAAT
1 TTTTTTTAATATTTAAAAAAT
673293 TTAACAACTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
TTTTTTTAATATTTAAAAAATAT
Found at i:677946 original size:16 final size:17
Alignment explanation
Indices: 677922--677959 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
677912 TTTTCAGAAG
*
677922 TATTTTTTAAATAAAAA
1 TATTTTTAAAATAAAAA
*
677939 TATTTTTAAAATAAAAG
1 TATTTTTAAAATAAAAA
677956 TATT
1 TATT
677960 ACTAAATAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
TATTTTTAAAATAAAAA
Found at i:679071 original size:315 final size:315
Alignment explanation
Indices: 678499--679128 Score: 1251
Period size: 315 Copynumber: 2.0 Consensus size: 315
678489 GTTGCAATTT
678499 GTCTCCTAAATACCATGTTTCCAATCTTCATTCACCTCAAGAAAATATTATTTTATACGCAAATG
1 GTCTCCTAAATACCATGTTTCCAATCTTCATTCACCTCAAGAAAATATTATTTTATACGCAAATG
678564 GGAAAATTTGAATGCGATATTAAGTGTAATAGTTGTAAGACCGACGTTTAATTTAACGAAGAATA
66 GGAAAATTTGAATGCGATATTAAGTGTAATAGTTGTAAGACCGACGTTTAATTTAACGAAGAATA
678629 TTTGATGCATTGTTGGTACATAAGTTTCATGCACTATCAATGAATAATAATATGACATCCTCATT
131 TTTGATGCATTGTTGGTACATAAGTTTCATGCACTATCAATGAATAATAATATGACATCCTCATT
678694 GTTAAATGAAATAAATTAGGATACATCAATTACACCCAATTCGGTGAGACCCAACAATTACATTG
196 GTTAAATGAAATAAATTAGGATACATCAATTACACCCAATTCGGTGAGACCCAACAATTACATTG
678759 ATGAGAAATGATTGTATGAAACAGGGATATTATCTCTGTCTAATAGTTTAATGTC
261 ATGAGAAATGATTGTATGAAACAGGGATATTATCTCTGTCTAATAGTTTAATGTC
*
678814 GTCTCCTAAATATCATGTTTCCAATCTTCATTCACCTCAAGAAAATATTATTTTATACGCAAATG
1 GTCTCCTAAATACCATGTTTCCAATCTTCATTCACCTCAAGAAAATATTATTTTATACGCAAATG
678879 GGAAAATTTGAATGCGATATTAAGTGTAATAGTTGTAAGACCGACGTTTAATTTAACGAAGAATA
66 GGAAAATTTGAATGCGATATTAAGTGTAATAGTTGTAAGACCGACGTTTAATTTAACGAAGAATA
678944 TTTGATGCATTGTTGGTACATAAGTTTCATGCACTATCAATGAATAATAATATGACATCCTCATT
131 TTTGATGCATTGTTGGTACATAAGTTTCATGCACTATCAATGAATAATAATATGACATCCTCATT
679009 GTTAAATGAAATAAATTAGGATACATCAATTACACCCAATTCGGTGAGACCCAACAATTACATTG
196 GTTAAATGAAATAAATTAGGATACATCAATTACACCCAATTCGGTGAGACCCAACAATTACATTG
679074 ATGAGAAATGATTGTATGAAACAGGGATATTATCTCTGTCTAATAGTTTAATGTC
261 ATGAGAAATGATTGTATGAAACAGGGATATTATCTCTGTCTAATAGTTTAATGTC
679129 ACATCAACAA
Statistics
Matches: 314, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
315 314 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (315 bp):
GTCTCCTAAATACCATGTTTCCAATCTTCATTCACCTCAAGAAAATATTATTTTATACGCAAATG
GGAAAATTTGAATGCGATATTAAGTGTAATAGTTGTAAGACCGACGTTTAATTTAACGAAGAATA
TTTGATGCATTGTTGGTACATAAGTTTCATGCACTATCAATGAATAATAATATGACATCCTCATT
GTTAAATGAAATAAATTAGGATACATCAATTACACCCAATTCGGTGAGACCCAACAATTACATTG
ATGAGAAATGATTGTATGAAACAGGGATATTATCTCTGTCTAATAGTTTAATGTC
Found at i:679212 original size:20 final size:21
Alignment explanation
Indices: 679183--679221 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
679173 TGTTTTTTCT
*
679183 TTTAGGATGAAAAT-CTGAAA
1 TTTAGAATGAAAATGCTGAAA
679203 TTTAGAATGAAAATGCTGA
1 TTTAGAATGAAAATGCTGA
679222 TATGGCATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.31
Consensus pattern (21 bp):
TTTAGAATGAAAATGCTGAAA
Found at i:680867 original size:28 final size:27
Alignment explanation
Indices: 680790--680867 Score: 68
Period size: 28 Copynumber: 2.8 Consensus size: 27
680780 GCAACTAATT
* * *
680790 AATTTTTTAAAAATTTATAAATTTAAAA
1 AATTTTTTAAAAA-CTATAAAATGAAAA
*
680818 AATTATTTTAAAAAACTA-AAAATGATTAA
1 AATT-TTTT-AAAAACTATAAAATGA-AAA
*
680847 AATTTTTTAAAAAGTATAAAA
1 AATTTTTTAAAAACTATAAAA
680868 CATATATTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
27 7 0.17
28 17 0.41
29 12 0.29
30 5 0.12
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (27 bp):
AATTTTTTAAAAACTATAAAATGAAAA
Found at i:684286 original size:4 final size:4
Alignment explanation
Indices: 684277--684305 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
684267 CAACTATTAT
684277 TATG TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG T
684306 TTGTTTATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:686519 original size:12 final size:12
Alignment explanation
Indices: 686502--686526 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
686492 TTAAAAATCA
686502 TTTTGAAATTTT
1 TTTTGAAATTTT
686514 TTTTGAAATTTT
1 TTTTGAAATTTT
686526 T
1 T
686527 GTTTAGAGAG
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:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (12 bp):
TTTTGAAATTTT
Found at i:690605 original size:34 final size:36
Alignment explanation
Indices: 690532--690608 Score: 113
Period size: 36 Copynumber: 2.2 Consensus size: 36
690522 CCATACGCCT
* *
690532 ACACCTGTAATAATATATCTATCCTCTTAAAACTTG
1 ACACCTGTAACAAGATATCTATCCTCTTAAAACTTG
*
690568 ACACCTGTAACAAGATATCTATCCTC-T-CAACTTG
1 ACACCTGTAACAAGATATCTATCCTCTTAAAACTTG
690602 ACACCTG
1 ACACCTG
690609 ACACCAGTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
34 13 0.34
35 1 0.03
36 24 0.63
ACGTcount: A:0.34, C:0.27, G:0.08, T:0.31
Consensus pattern (36 bp):
ACACCTGTAACAAGATATCTATCCTCTTAAAACTTG
Found at i:693878 original size:3 final size:3
Alignment explanation
Indices: 693862--693911 Score: 82
Period size: 3 Copynumber: 16.3 Consensus size: 3
693852 TTGAAAAAGG
*
693862 TTC TTC TTTA TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC -TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
693908 TTC T
1 TTC T
693912 CCCTTAAGTG
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 42 0.95
4 2 0.05
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:696391 original size:24 final size:24
Alignment explanation
Indices: 696364--696415 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
696354 TTAGTAAGTC
*
696364 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
696388 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
696412 AAAT
1 AAAT
696416 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:698361 original size:24 final size:24
Alignment explanation
Indices: 698334--698385 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
698324 TTAGTAAGTC
*
698334 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
698358 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
698382 AAAT
1 AAAT
698386 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:700331 original size:24 final size:24
Alignment explanation
Indices: 700304--700355 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
700294 TTAGTAAGTC
*
700304 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
700328 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
700352 AAAT
1 AAAT
700356 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:702301 original size:24 final size:24
Alignment explanation
Indices: 702274--702325 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
702264 TTAGTAAGTC
*
702274 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
702298 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
702322 AAAT
1 AAAT
702326 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:706849 original size:3 final size:3
Alignment explanation
Indices: 706841--706873 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
706831 AAGGAAATAG
706841 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
706874 TTTACGTAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:707502 original size:28 final size:28
Alignment explanation
Indices: 707471--707532 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
707461 TATATATTTA
707471 ATATATTAACTTGTAA-ATATAACATAAT
1 ATATATTAACTTG-AATATATAACATAAT
*
707499 ATATATTAACTTGAATATATAATATAAT
1 ATATATTAACTTGAATATATAACATAAT
707527 ATATAT
1 ATATAT
707533 ATCATATATT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 2 0.06
28 30 0.94
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (28 bp):
ATATATTAACTTGAATATATAACATAAT
Found at i:707517 original size:16 final size:16
Alignment explanation
Indices: 707471--707519 Score: 52
Period size: 14 Copynumber: 3.3 Consensus size: 16
707461 TATATATTTA
707471 ATATATTAACTTG--T
1 ATATATTAACTTGAAT
* *
707485 AAATA-TAACAT-AAT
1 ATATATTAACTTGAAT
707499 ATATATTAACTTGAAT
1 ATATATTAACTTGAAT
707515 ATATA
1 ATATA
707520 ATATAATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
13 5 0.19
14 9 0.33
15 5 0.19
16 8 0.30
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (16 bp):
ATATATTAACTTGAAT
Found at i:707532 original size:16 final size:16
Alignment explanation
Indices: 707513--707546 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
707503 ATTAACTTGA
707513 ATATATAATATAATAT
1 ATATATAATATAATAT
* *
707529 ATATATCATATATTAT
1 ATATATAATATAATAT
707545 AT
1 AT
707547 TAACTTGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
ATATATAATATAATAT
Found at i:707533 original size:42 final size:43
Alignment explanation
Indices: 707487--707567 Score: 112
Period size: 42 Copynumber: 1.9 Consensus size: 43
707477 TAACTTGTAA
707487 ATATAACATA-ATATATATTAACTTGAATATATA-ATATAATAT
1 ATATAACATATAT-TATATTAACTTGAATATATATATATAATAT
* * *
707529 ATATATCATATATTATATTAACTTGTATTTATATATATA
1 ATATAACATATATTATATTAACTTGAATATATATATATA
707568 TAAATCTGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
42 27 0.79
43 7 0.21
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.46
Consensus pattern (43 bp):
ATATAACATATATTATATTAACTTGAATATATATATATAATAT
Found at i:709824 original size:69 final size:66
Alignment explanation
Indices: 709676--709844 Score: 176
Period size: 69 Copynumber: 2.5 Consensus size: 66
709666 TTCAAAGGCT
* * * * *
709676 TCTCCGTATTTTTGTTTATAACTACCTGCTCGAGAATTGTTTTCTCATTTGGCTTTTTAATTATC
1 TCTCCGTATTTTCGTTTATAACCACCTGCTCGAGAATTGTCTTCTCATTAGACTTTTTAATTATC
709741 A
66 A
* * * *
709742 TCGTCTCTATATTTTCGTTTATCACCACCTGCTTGAGAATTGTCTTCTCATTCAAAGACTTTTTT
1 TC-TC-C-GTATTTTCGTTTATAACCACCTGCTCGAGAATTGTCTTCTCATT---AGACTTTTTA
*
709807 ATTCTCA
60 ATTATCA
**
709814 TCTCCGTATTTTCGTTTATTGCCACCTGCTC
1 TCTCCGTATTTTCGTTTATAACCACCTGCTC
709845 AAGTAACGGA
Statistics
Matches: 83, Mismatches: 14, Indels: 9
0.78 0.13 0.08
Matches are distributed among these distances:
66 2 0.02
67 2 0.02
68 1 0.01
69 60 0.72
70 1 0.01
71 2 0.02
72 15 0.18
ACGTcount: A:0.18, C:0.23, G:0.11, T:0.47
Consensus pattern (66 bp):
TCTCCGTATTTTCGTTTATAACCACCTGCTCGAGAATTGTCTTCTCATTAGACTTTTTAATTATC
A
Found at i:713935 original size:18 final size:18
Alignment explanation
Indices: 713909--713943 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
713899 CAAATTTTCA
*
713909 AAATGATTTTTAAAAATC
1 AAATGATTTATAAAAATC
*
713927 AAATTATTTATAAAAAT
1 AAATGATTTATAAAAAT
713944 TCCAAAATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (18 bp):
AAATGATTTATAAAAATC
Found at i:713972 original size:28 final size:27
Alignment explanation
Indices: 713933--713990 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
713923 AATCAAATTA
* *
713933 TTTATAAAAATTCCAAAA-TTTATATTTT
1 TTTAAAAAAATT-AAAAATTTTA-ATTTT
713961 TTTAAAAAAATTAAAAATTTTAATTTT
1 TTTAAAAAAATTAAAAATTTTAATTTT
713988 TTT
1 TTT
713991 CTAAAATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 12 0.44
28 15 0.56
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (27 bp):
TTTAAAAAAATTAAAAATTTTAATTTT
Found at i:713996 original size:27 final size:28
Alignment explanation
Indices: 713933--713996 Score: 78
Period size: 27 Copynumber: 2.3 Consensus size: 28
713923 AATCAAATTA
*
713933 TTTATAAAAATTCCAAAATTTATATTTT
1 TTTATAAAAATTCAAAAATTTATATTTT
*
713961 TTTAAAAAAATT-AAAAATTT-TAATTTT
1 TTTATAAAAATTCAAAAATTTAT-ATTTT
*
713988 TTTCTAAAA
1 TTTATAAAA
713997 TAATAATTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
26 1 0.03
27 19 0.61
28 11 0.35
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (28 bp):
TTTATAAAAATTCAAAAATTTATATTTT
Found at i:722349 original size:27 final size:27
Alignment explanation
Indices: 722319--722375 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
722309 TAGTTAATAG
*
722319 GTCTGACTTAAAACATGCATTGATGCT
1 GTCTGAATTAAAACATGCATTGATGCT
722346 GTCTGAATTAAAACATGCATTGATGCT
1 GTCTGAATTAAAACATGCATTGATGCT
722373 GTC
1 GTC
722376 CAAATTATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (27 bp):
GTCTGAATTAAAACATGCATTGATGCT
Found at i:722381 original size:27 final size:27
Alignment explanation
Indices: 722326--722388 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 27
722316 TAGGTCTGAC
**
722326 TTAAAACATGCATTGATGCTGTCTGAA
1 TTAAAACATGCATTGATGCTGTCCAAA
722353 TTAAAACATGCATTGATGCTGTCCAAA
1 TTAAAACATGCATTGATGCTGTCCAAA
*
722380 TTATAACAT
1 TTAAAACAT
722389 TCTTAATAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (27 bp):
TTAAAACATGCATTGATGCTGTCCAAA
Found at i:725713 original size:19 final size:19
Alignment explanation
Indices: 725689--725726 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
725679 ATGAATGTAA
*
725689 ACATGTTAAGCTTTGAAAT
1 ACATGTTAAGCTTCGAAAT
725708 ACATGTTAAGCTTCGAAAT
1 ACATGTTAAGCTTCGAAAT
725727 TTTTAGTTGC
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:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (19 bp):
ACATGTTAAGCTTCGAAAT
Found at i:750714 original size:7 final size:7
Alignment explanation
Indices: 750702--750727 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
750692 TTCAATAAAC
750702 TGCCCAT
1 TGCCCAT
750709 TGCCCAT
1 TGCCCAT
750716 TGCCCAT
1 TGCCCAT
750723 TGCCC
1 TGCCC
750728 CAATAATCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.46, G:0.15, T:0.27
Consensus pattern (7 bp):
TGCCCAT
Found at i:751760 original size:23 final size:23
Alignment explanation
Indices: 751731--751777 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
751721 AACCAGATGT
751731 CACCAAGGGAAACCATCAAGCTG
1 CACCAAGGGAAACCATCAAGCTG
751754 CACCAAGGGAAACCATCAAGCTG
1 CACCAAGGGAAACCATCAAGCTG
751777 C
1 C
751778 TGTGGTGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.32, G:0.21, T:0.09
Consensus pattern (23 bp):
CACCAAGGGAAACCATCAAGCTG
Found at i:758960 original size:22 final size:21
Alignment explanation
Indices: 758935--758976 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
758925 TCATAACATA
*
758935 TTCAATTCTCATCACTTGCTAT
1 TTCAAATCTCAT-ACTTGCTAT
*
758957 TTCAAATCTCATTCTTGCTA
1 TTCAAATCTCATACTTGCTA
758977 GACAAATAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.24, C:0.26, G:0.05, T:0.45
Consensus pattern (21 bp):
TTCAAATCTCATACTTGCTAT
Found at i:759187 original size:40 final size:40
Alignment explanation
Indices: 759143--759265 Score: 126
Period size: 40 Copynumber: 3.1 Consensus size: 40
759133 CCAGTTTGGT
**
759143 ACCCAGTACCTCATCGGATAATTTGAAGTAATAAATTGAC
1 ACCCAGTACCTCATCGGATAATCCGAAGTAATAAATTGAC
* * * * * *
759183 ACCCAGTATCTTATTGGCTAAACCGAAG---TAAATTGGC
1 ACCCAGTACCTCATCGGATAATCCGAAGTAATAAATTGAC
* *
759220 ACCCAGTGCCTCATCGAATTAATCCGAAGTAATAAATTGAC
1 ACCCAGTACCTCATCGGA-TAATCCGAAGTAATAAATTGAC
759261 ACCCA
1 ACCCA
759266 ACGTCTCATC
Statistics
Matches: 63, Mismatches: 16, Indels: 7
0.73 0.19 0.08
Matches are distributed among these distances:
37 20 0.32
38 9 0.14
40 21 0.33
41 13 0.21
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.25
Consensus pattern (40 bp):
ACCCAGTACCTCATCGGATAATCCGAAGTAATAAATTGAC
Found at i:759868 original size:18 final size:19
Alignment explanation
Indices: 759842--759877 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
759832 TAAACTAGAT
*
759842 TTAACTCTCT-AATTTCAC
1 TTAAATCTCTAAATTTCAC
759860 TTAAATCTCTAAATTTCA
1 TTAAATCTCTAAATTTCA
759878 AAATTTTTAC
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:0.33, C:0.22, G:0.00, T:0.44
Consensus pattern (19 bp):
TTAAATCTCTAAATTTCAC
Found at i:760178 original size:21 final size:22
Alignment explanation
Indices: 760154--760207 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
760144 TTTTCTCCTT
*
760154 CTTTCTTTCTCTT-TTTATTTC
1 CTTTCTTTCTCTTCTATATTTC
760175 CTTTCTTTC-CTTCTATATTTC
1 CTTTCTTTCTCTTCTATATTTC
*
760196 GTTTCTTTCTCT
1 CTTTCTTTCTCT
760208 CCTTCTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 3 0.10
21 24 0.83
22 2 0.07
ACGTcount: A:0.06, C:0.26, G:0.02, T:0.67
Consensus pattern (22 bp):
CTTTCTTTCTCTTCTATATTTC
Found at i:760298 original size:39 final size:38
Alignment explanation
Indices: 760254--760339 Score: 104
Period size: 38 Copynumber: 2.3 Consensus size: 38
760244 TTTAATATAA
760254 TATAATAATATA-TATATACACTTAACATTTAAGTTTTAT
1 TATAATAATATATTATATA-ACTTAAC-TTTAAGTTTTAT
* **
760293 TATAATATTATATTATATATTTTAACTTTAAGTTTTAT
1 TATAATAATATATTATATAACTTAACTTTAAGTTTTAT
*
760331 AATAA-AATA
1 TATAATAATA
760340 CACTTATGCC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
37 3 0.07
38 16 0.39
39 16 0.39
40 6 0.15
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (38 bp):
TATAATAATATATTATATAACTTAACTTTAAGTTTTAT
Found at i:761052 original size:175 final size:174
Alignment explanation
Indices: 760729--761056 Score: 388
Period size: 175 Copynumber: 1.9 Consensus size: 174
760719 CTCTTATTTC
* * *
760729 AATTCAGTCACTCAACTTTTAAAAAATAACAAATCAGTCACTAACATTATCGAAAAGTGACAAAT
1 AATTCAGTCACTCAACTTTAAAAAAATAACAAAACAGTCACTAACATTATCAAAAAGTGACAAAT
* *** ** * * *
760794 CAGTCACCCATTAACATTTTCTATTAAAGACCTAAGGGGTCAGGTGACGTGATTAGTTAACTGGC
66 CAGTCACCCATTAACATTTTCTATTAAAGACCTAACGGAAAAGGTGACGTGACCAATAAACTAGC
*
760859 TAACGTGGTCAATTAACTTGCCACATTGGACAAGGTAAAGTTTT
131 TAACGTGGCCAATTAACTTGCCACATTGGACAAGGTAAAGTTTT
* * *
760903 AATTCAGTCACTTAACTTTCAAAAAAATAACAAAACAGTCACTAACGTTATCAAAAAGTTACAAA
1 AATTCAGTCACTCAACTTT-AAAAAAATAACAAAACAGTCACTAACATTATCAAAAAGTGACAAA
* * * * * * *
760968 TTAGTCACTCATTAACATTTT-TCGTTATAGGCGTAACGGAAAAGGTGACGTGACCAATAAATTA
65 TCAGTCACCCATTAACATTTTCT-ATTAAAGACCTAACGGAAAAGGTGACGTGACCAATAAACTA
* * * *
761032 GTTGATGTGGCCAGTTAACTTGCCA
129 GCTAACGTGGCCAATTAACTTGCCA
761057 TGTTAAACGA
Statistics
Matches: 125, Mismatches: 27, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
174 19 0.15
175 106 0.85
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.29
Consensus pattern (174 bp):
AATTCAGTCACTCAACTTTAAAAAAATAACAAAACAGTCACTAACATTATCAAAAAGTGACAAAT
CAGTCACCCATTAACATTTTCTATTAAAGACCTAACGGAAAAGGTGACGTGACCAATAAACTAGC
TAACGTGGCCAATTAACTTGCCACATTGGACAAGGTAAAGTTTT
Found at i:764088 original size:23 final size:23
Alignment explanation
Indices: 764062--764108 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
764052 GTAATTATAA
764062 ATACATGTGTAATAAATATATGT
1 ATACATGTGTAATAAATATATGT
* *
764085 ATACATTTGTAATTAATATATGT
1 ATACATGTGTAATAAATATATGT
764108 A
1 A
764109 CATACTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.43, C:0.04, G:0.11, T:0.43
Consensus pattern (23 bp):
ATACATGTGTAATAAATATATGT
Found at i:764250 original size:13 final size:13
Alignment explanation
Indices: 764219--764258 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
764209 AACGAAACAG
*
764219 AGAAGGAAAG-AA
1 AGAAAGAAAGAAA
*
764231 GGAAAGAAAGAAA
1 AGAAAGAAAGAAA
764244 AGAAAGAAAGAAA
1 AGAAAGAAAGAAA
764257 AG
1 AG
764259 GGAAAATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
12 8 0.33
13 16 0.67
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (13 bp):
AGAAAGAAAGAAA
Found at i:765149 original size:25 final size:25
Alignment explanation
Indices: 765120--765224 Score: 126
Period size: 25 Copynumber: 4.3 Consensus size: 25
765110 ACCTTAGTGC
765120 GCTATCTGATTATTAGCACATCAGT
1 GCTATCTGATTATTAGCACATCAGT
**
765145 GCTATCTGATTATTAGCATGTCAGT
1 GCTATCTGATTATTAGCACATCAGT
* *
765170 GCTATCTGATTACTAGCACGTCAGT
1 GCTATCTGATTATTAGCACATCAGT
* *
765195 GCTCTCTG--T-TTAGCACATCTGT
1 GCTATCTGATTATTAGCACATCAGT
*
765217 GCTCTCTG
1 GCTATCTG
765225 TATAGCACTT
Statistics
Matches: 72, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
22 18 0.25
23 1 0.01
25 53 0.74
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.37
Consensus pattern (25 bp):
GCTATCTGATTATTAGCACATCAGT
Found at i:765218 original size:22 final size:22
Alignment explanation
Indices: 765132--765248 Score: 99
Period size: 22 Copynumber: 5.0 Consensus size: 22
765122 TATCTGATTA
*
765132 TTAGCACATCAGTGCTATCTGATT
1 TTAGCACATCAGTGCTCTCTG--T
** *
765156 ATTAGCATGTCAGTGCTATCTGAT
1 -TTAGCACATCAGTGCTCTCTG-T
*
765180 TACTAGCACGTCAGTGCTCTCTGT
1 T--TAGCACATCAGTGCTCTCTGT
*
765204 TTAGCACATCTGTGCTCTCTGT
1 TTAGCACATCAGTGCTCTCTGT
* * *
765226 ATAGCACTTCAATGCTCTCTGT
1 TTAGCACATCAGTGCTCTCTGT
765248 T
1 T
765249 CATTAGTGCA
Statistics
Matches: 78, Mismatches: 12, Indels: 7
0.80 0.12 0.07
Matches are distributed among these distances:
22 37 0.47
23 1 0.01
24 3 0.04
25 37 0.47
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.38
Consensus pattern (22 bp):
TTAGCACATCAGTGCTCTCTGT
Found at i:767526 original size:7 final size:7
Alignment explanation
Indices: 767514--767543 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
767504 CTGAGAGGAT
767514 TATGGTA
1 TATGGTA
767521 TATGGTA
1 TATGGTA
767528 TATGGTA
1 TATGGTA
767535 TATGGTA
1 TATGGTA
767542 TA
1 TA
767544 ATTGGAATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.27, T:0.43
Consensus pattern (7 bp):
TATGGTA
Found at i:768557 original size:25 final size:25
Alignment explanation
Indices: 768521--768598 Score: 79
Period size: 25 Copynumber: 3.2 Consensus size: 25
768511 ACCGTCTCTC
768521 GAGCCATATAACAGAAAGCTCATGT
1 GAGCCATATAACAGAAAGCTCATGT
* *
768546 GAGCCATGTAACAGGAAGCTCATAG-
1 GAGCCATATAACAGAAAGCTCAT-GT
* * * *
768571 GAGTCATA-ATCGGGAAGCTCATGT
1 GAGCCATATAACAGAAAGCTCATGT
768595 GAGC
1 GAGC
768599 TAATAACGGG
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
23 1 0.02
24 15 0.34
25 27 0.61
26 1 0.02
ACGTcount: A:0.35, C:0.19, G:0.27, T:0.19
Consensus pattern (25 bp):
GAGCCATATAACAGAAAGCTCATGT
Found at i:768608 original size:24 final size:24
Alignment explanation
Indices: 768536--768614 Score: 72
Period size: 24 Copynumber: 3.2 Consensus size: 24
768526 ATATAACAGA
* * *
768536 AAGCTCATGTGAGCCATGTAACAGG
1 AAGCTCATGTGAGCTA-ATAACGGG
*
768561 AAGCTCATAG-GAG-TCATAATCGGG
1 AAGCTCAT-GTGAGCTAATAA-CGGG
768585 AAGCTCATGTGAGCTAATAACGGG
1 AAGCTCATGTGAGCTAATAACGGG
*
768609 TAGCTC
1 AAGCTC
768615 CGAAGGGCCA
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
23 4 0.09
24 23 0.52
25 16 0.36
26 1 0.02
ACGTcount: A:0.32, C:0.19, G:0.28, T:0.22
Consensus pattern (24 bp):
AAGCTCATGTGAGCTAATAACGGG
Found at i:770085 original size:176 final size:176
Alignment explanation
Indices: 769791--770152 Score: 715
Period size: 176 Copynumber: 2.1 Consensus size: 176
769781 CATCTTTTTC
769791 TTTCTAATTTAGTCATTTTCTTTATTTTATTTTCCATGGATGAATCATCATACTTATCTACTAAC
1 TTTCTAATTTAGTCATTTTCTTTATTTTATTTTCCATGGATGAATCATCATACTTATCTACTAAC
769856 TCCTCTTAATGGTCTATTTGCCATATAAGGACCTCAACTTTTGAATTCCATAGCTAGTTAATACT
66 TCCTCTTAATGGTCTATTTGCCATATAAGGACCTCAACTTTTGAATTCCATAGCTAGTTAATACT
769921 TATAGCTACTAGAATTCAACTTTTGCATTTTATGCAATTTGGTCCT
131 TATAGCTACTAGAATTCAACTTTTGCATTTTATGCAATTTGGTCCT
769967 TTTCTAATTTAGTCATTTTCTTTATTTTATTTTCCATGGATGAATCATCATACTTATCTACTAAC
1 TTTCTAATTTAGTCATTTTCTTTATTTTATTTTCCATGGATGAATCATCATACTTATCTACTAAC
770032 TCCTCTTAATGGTCTATTTGCCATATAAGGACCTCAACTTTTGAATTCCATAGCTAGTTAATACT
66 TCCTCTTAATGGTCTATTTGCCATATAAGGACCTCAACTTTTGAATTCCATAGCTAGTTAATACT
770097 TATAGCTACTAGAATTCAACTTTTGCATTTTATGCAATTTGGTCCT
131 TATAGCTACTAGAATTCAACTTTTGCATTTTATGCAATTTGGTCCT
770143 TTTCTCAATT
1 TTTCT-AATT
770153 AATCATATAA
Statistics
Matches: 185, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
176 181 0.98
177 4 0.02
ACGTcount: A:0.27, C:0.19, G:0.10, T:0.45
Consensus pattern (176 bp):
TTTCTAATTTAGTCATTTTCTTTATTTTATTTTCCATGGATGAATCATCATACTTATCTACTAAC
TCCTCTTAATGGTCTATTTGCCATATAAGGACCTCAACTTTTGAATTCCATAGCTAGTTAATACT
TATAGCTACTAGAATTCAACTTTTGCATTTTATGCAATTTGGTCCT
Found at i:779097 original size:5 final size:5
Alignment explanation
Indices: 779087--779113 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
779077 GAGCATTCGG
779087 TCGAA TCGAA TCGAA TCGAA TCGAA TC
1 TCGAA TCGAA TCGAA TCGAA TCGAA TC
779114 AAAAATTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (5 bp):
TCGAA
Found at i:779896 original size:9 final size:9
Alignment explanation
Indices: 779882--779918 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
779872 TATAGTTTGA
779882 TATTCGAAT
1 TATTCGAAT
779891 TATTCGAAT
1 TATTCGAAT
*
779900 TATTCGAGT
1 TATTCGAAT
779909 TATTCGAAT
1 TATTCGAAT
779918 T
1 T
779919 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:793623 original size:22 final size:22
Alignment explanation
Indices: 793582--793623 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
793572 ACTAGTTTAC
* *
793582 TGTTGTTTTTCTACTGTTTTGT
1 TGTTGTTTTTCTAATATTTTGT
793604 TGTTGTTTTTCTAATATTTT
1 TGTTGTTTTTCTAATATTTT
793624 AATGTCATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.10, C:0.07, G:0.14, T:0.69
Consensus pattern (22 bp):
TGTTGTTTTTCTAATATTTTGT
Found at i:794394 original size:8 final size:8
Alignment explanation
Indices: 794367--794397 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
794357 TTTTAATTTT
794367 TTTTAAAA
1 TTTTAAAA
*
794375 TTTAAAAA
1 TTTTAAAA
794383 TTTTAAAA
1 TTTTAAAA
794391 TTTTAAA
1 TTTTAAA
794398 TTAATAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
TTTTAAAA
Found at i:795483 original size:22 final size:22
Alignment explanation
Indices: 795456--795522 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
795446 TTCTAAAATC
795456 TTATAAATATATAAATTAAAAA
1 TTATAAATATATAAATTAAAAA
* *
795478 TTATAAAAAAATAAA-TAAAAA
1 TTATAAATATATAAATTAAAAA
** *
795499 TGCTAAATTATATATATTTAAAAA
1 TTATAAA-TATATA-AATTAAAAA
795523 AATTTCTAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
21 11 0.31
22 17 0.49
23 1 0.03
24 6 0.17
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (22 bp):
TTATAAATATATAAATTAAAAA
Found at i:796007 original size:22 final size:20
Alignment explanation
Indices: 795969--796009 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
795959 ATTATATTTT
*
795969 AAATATATATATTAAAATAA
1 AAATATATATATAAAAATAA
795989 AAATATTATTATATAAAAATA
1 AAATA-TA-TATATAAAAATA
796010 TCTTATTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 2 0.11
22 11 0.61
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AAATATATATATAAAAATAA
Found at i:806107 original size:117 final size:118
Alignment explanation
Indices: 805924--806148 Score: 301
Period size: 117 Copynumber: 1.9 Consensus size: 118
805914 TTGAATGTTA
***
805924 TTCCTCGGGATAGGCACACGTATTTGTTTTCTGCAACCATGACCAAAAAGGTACGTGGGGGAAAA
1 TTCCTCGGGATAGGCACAC-TATTTGTTTTCTGCAACCATGACCAAAAAGGTACAACGGGGAAAA
* * *
805989 CAAACATTTTATTTATTATTTAAGAAATATGTCCATATACTATCTTGAACATTG
65 CAAACATTTTATGTATTATATAAGAAACATGTCCATATACTATCTTGAACATTG
* * * * *
806043 TTCCTCGTGATAGGCACA-TGTTTGTTTTCTGCGACCATGACCAGAAAAGGTATAACTGGG-AAA
1 TTCCTCGGGATAGGCACACTATTTGTTTTCTGCAACCATGACCA-AAAAGGTACAACGGGGAAAA
* *
806106 CAAATATTTTATGTATTCTATAAGAAACATGTCCATATACTAT
65 CAAACATTTTATGTATTATATAAGAAACATGTCCATATACTAT
806149 TTTCTTATGT
Statistics
Matches: 92, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
117 64 0.70
118 11 0.12
119 17 0.18
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (118 bp):
TTCCTCGGGATAGGCACACTATTTGTTTTCTGCAACCATGACCAAAAAGGTACAACGGGGAAAAC
AAACATTTTATGTATTATATAAGAAACATGTCCATATACTATCTTGAACATTG
Found at i:806769 original size:24 final size:24
Alignment explanation
Indices: 806737--806783 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
806727 ACAAGGTTGC
*
806737 TTAATCTTCTTAGCTTTAAAATTT
1 TTAATCTTCTTAGCATTAAAATTT
806761 TTAATCTTCTTAGCATTAAAATT
1 TTAATCTTCTTAGCATTAAAATT
806784 CTTTTTCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.32, C:0.13, G:0.04, T:0.51
Consensus pattern (24 bp):
TTAATCTTCTTAGCATTAAAATTT
Found at i:810306 original size:21 final size:21
Alignment explanation
Indices: 810281--810322 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
810271 GGGTTTCAAT
810281 TTTGCGTTTTCATGCACCTCA
1 TTTGCGTTTTCATGCACCTCA
*
810302 TTTGCGTTTTTATGCACCTCA
1 TTTGCGTTTTCATGCACCTCA
810323 ACGGGTCAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.14, C:0.26, G:0.14, T:0.45
Consensus pattern (21 bp):
TTTGCGTTTTCATGCACCTCA
Found at i:818596 original size:17 final size:17
Alignment explanation
Indices: 818574--818606 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
818564 GAATCGAGAT
818574 AATATTTACTATTTAAA
1 AATATTTACTATTTAAA
*
818591 AATATTTACTGTTTAA
1 AATATTTACTATTTAA
818607 TAGAGTTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.48
Consensus pattern (17 bp):
AATATTTACTATTTAAA
Found at i:824726 original size:29 final size:29
Alignment explanation
Indices: 824694--824756 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
824684 ATTTACTGAA
* *
824694 ATTTTTAAAAA-ATATATATATTTTTCATT
1 ATTTTTAAAAATATATATA-ATTTTTAAAT
* *
824723 ATTTTTGAAAATATTTATAATTTTTAAAT
1 ATTTTTAAAAATATATATAATTTTTAAAT
824752 ATTTT
1 ATTTT
824757 AGGATTTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 23 0.79
30 6 0.21
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (29 bp):
ATTTTTAAAAATATATATAATTTTTAAAT
Found at i:824727 original size:28 final size:29
Alignment explanation
Indices: 824692--824757 Score: 73
Period size: 28 Copynumber: 2.3 Consensus size: 29
824682 TAATTTACTG
824692 AAAT-TTTTAAAAAATATATAT-ATTTTT
1 AAATATTTTAAAAAATATATATAATTTTT
* * ** *
824719 CATTATTTTTGAAAATATTTATAATTTTT
1 AAATATTTTAAAAAATATATATAATTTTT
824748 AAATATTTTA
1 AAATATTTTA
824758 GGATTTTTAT
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
27 2 0.07
28 14 0.48
29 13 0.45
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (29 bp):
AAATATTTTAAAAAATATATATAATTTTT
Found at i:825583 original size:32 final size:32
Alignment explanation
Indices: 825523--825584 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
825513 AATTGTGAGC
* * **
825523 GTTTGGGTAAAAATATTAGGTCTGAAAAATGA
1 GTTTGGGAAAAAATATTAGGCCCAAAAAATGA
825555 GTTTGGGAAAAAATATTAGGCCCAAAAAAT
1 GTTTGGGAAAAAATATTAGGCCCAAAAAAT
825585 ATGGGTTGGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.44, C:0.06, G:0.23, T:0.27
Consensus pattern (32 bp):
GTTTGGGAAAAAATATTAGGCCCAAAAAATGA
Done.