Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr9
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: 48574783
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2023350 characters in sequence are not A, C, G, or T
File 111 of 135
Found at i:40826421 original size:16 final size:16
Alignment explanation
Indices: 40826400--40826451 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
40826390 TTTGGTTCGC
40826400 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
40826416 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* *
40826432 TGTAATGGAATAGAGG
1 TGTATTGGATTAGAGG
40826448 TGTA
1 TGTA
40826452 ATAGCAAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.29, C:0.00, G:0.37, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:40826537 original size:39 final size:43
Alignment explanation
Indices: 40826432--40826541 Score: 129
Period size: 45 Copynumber: 2.6 Consensus size: 43
40826422 GGATTAGAGG
40826432 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTT--A
* * ***
40826477 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGG-T-
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
40826517 TG-AATGGAATAGAGGTGTAATAGCA
1 TGTAATGGAATAGAGGTGTAATAGCA
40826542 TAATGGAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
39 20 0.35
40 2 0.04
43 1 0.02
44 11 0.19
45 23 0.40
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (43 bp):
TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
Found at i:40826714 original size:14 final size:15
Alignment explanation
Indices: 40826675--40826716 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
40826665 TTTTAACATA
*
40826675 ATTATTATTAAATAT
1 ATTATAATTAAATAT
40826690 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
40826704 A-TATAATTTAATA
1 ATTATAATTAAATA
40826717 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:40830842 original size:28 final size:28
Alignment explanation
Indices: 40830780--40830850 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 28
40830770 AAAAACTCCC
**
40830780 TATAT-AATATTTTAATATTATTTTTAT
1 TATATAAATATTAAAATATTATTTTTAT
*
40830807 TATTTAAATA-TAAAATATTTATTTTTA-
1 TATATAAATATTAAAATA-TTATTTTTAT
40830834 TATCATAAATATTAAAA
1 TAT-ATAAATATTAAAA
40830851 ATAACAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
27 12 0.33
28 19 0.53
29 5 0.14
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (28 bp):
TATATAAATATTAAAATATTATTTTTAT
Found at i:40830843 original size:21 final size:22
Alignment explanation
Indices: 40830802--40830846 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
40830792 TAATATTATT
40830802 TTTATTATTTAAATATAAAATA
1 TTTATTATTTAAATATAAAATA
*
40830824 TTTATT-TTTATATCAT-AAATA
1 TTTATTATTTAAAT-ATAAAATA
40830845 TT
1 TT
40830847 AAAAATAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTATTATTTAAATATAAAATA
Found at i:40832073 original size:28 final size:28
Alignment explanation
Indices: 40832011--40832081 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 28
40832001 AAAAACTCCC
**
40832011 TATAT-AATATTTTAATATTATTTTTAT
1 TATATAAATATTAAAATATTATTTTTAT
*
40832038 TATTTAAATA-TAAAATATTTATTTTTA-
1 TATATAAATATTAAAATA-TTATTTTTAT
40832065 TATCATAAATATTAAAA
1 TAT-ATAAATATTAAAA
40832082 ATAACAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
27 12 0.33
28 19 0.53
29 5 0.14
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (28 bp):
TATATAAATATTAAAATATTATTTTTAT
Found at i:40832074 original size:21 final size:22
Alignment explanation
Indices: 40832033--40832077 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
40832023 TAATATTATT
40832033 TTTATTATTTAAATATAAAATA
1 TTTATTATTTAAATATAAAATA
*
40832055 TTTATT-TTTATATCAT-AAATA
1 TTTATTATTTAAAT-ATAAAATA
40832076 TT
1 TT
40832078 AAAAATAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTATTATTTAAATATAAAATA
Found at i:40835719 original size:14 final size:14
Alignment explanation
Indices: 40835700--40835729 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
40835690 ATTATTTGTT
40835700 TTATTTATTTTTAA
1 TTATTTATTTTTAA
*
40835714 TTATTTGTTTTTAA
1 TTATTTATTTTTAA
40835728 TT
1 TT
40835730 TTAAATCCAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.73
Consensus pattern (14 bp):
TTATTTATTTTTAA
Found at i:40838167 original size:17 final size:18
Alignment explanation
Indices: 40838141--40838178 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
40838131 TTTTTTATAA
40838141 TTATTAAGGA-TTTTAAG
1 TTATTAAGGAGTTTTAAG
* *
40838158 TTATTTAGGAGTTTTATG
1 TTATTAAGGAGTTTTAAG
40838176 TTA
1 TTA
40838179 GCAAGAAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.29, C:0.00, G:0.18, T:0.53
Consensus pattern (18 bp):
TTATTAAGGAGTTTTAAG
Found at i:40838608 original size:17 final size:18
Alignment explanation
Indices: 40838588--40838624 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
40838578 ATTATTCTAA
*
40838588 TATTTTATTTA-TTATTT
1 TATTTTAGTTATTTATTT
40838605 TATTTTAGTTATTTATTT
1 TATTTTAGTTATTTATTT
40838623 TA
1 TA
40838625 ATTGTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (18 bp):
TATTTTAGTTATTTATTT
Found at i:40838611 original size:13 final size:13
Alignment explanation
Indices: 40838588--40838636 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
40838578 ATTATTCTAA
40838588 TATTTTA-TTTAT
1 TATTTTATTTTAT
40838600 TATTTTATTTTAGT
1 TATTTTATTTTA-T
40838614 TA-TTTATTTTAAT
1 TATTTTATTTT-AT
*
40838627 TGTTTTATTT
1 TATTTTATTT
40838637 GACTTGGATT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
12 7 0.22
13 14 0.44
14 11 0.34
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.73
Consensus pattern (13 bp):
TATTTTATTTTAT
Found at i:40843772 original size:47 final size:46
Alignment explanation
Indices: 40843721--40843809 Score: 115
Period size: 46 Copynumber: 1.9 Consensus size: 46
40843711 TTCTGGAAGT
*
40843721 TTGGCTACAATTATAGTGGCCCGACCACACATATCTGTTCTAGCAAC
1 TTGGCTACAA-TATAGTGGCCCGACCACACATATCTGATCTAGCAAC
* * ** *
40843768 TTGGCTGCAATATGGTGGCTTGACCACATATATCTGATCTAG
1 TTGGCTACAATATAGTGGCCCGACCACACATATCTGATCTAG
40843810 TAGTTTAACT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
46 27 0.75
47 9 0.25
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (46 bp):
TTGGCTACAATATAGTGGCCCGACCACACATATCTGATCTAGCAAC
Found at i:40845392 original size:11 final size:11
Alignment explanation
Indices: 40845376--40845400 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
40845366 TAGTAACTTT
40845376 ATTTAAACATA
1 ATTTAAACATA
40845387 ATTTAAACATA
1 ATTTAAACATA
40845398 ATT
1 ATT
40845401 AATTATAAAT
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:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (11 bp):
ATTTAAACATA
Found at i:40859906 original size:25 final size:25
Alignment explanation
Indices: 40859878--40859927 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
40859868 TTAAACCAAG
*
40859878 TAAAATGAAACTACGAAAGGGCACA
1 TAAAATGAAACTACGAAAGAGCACA
*
40859903 TAAAATGAAACTGCGAAAGAGCACA
1 TAAAATGAAACTACGAAAGAGCACA
40859928 AGTTACCACC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.52, C:0.16, G:0.20, T:0.12
Consensus pattern (25 bp):
TAAAATGAAACTACGAAAGAGCACA
Found at i:40867194 original size:30 final size:32
Alignment explanation
Indices: 40867158--40867219 Score: 101
Period size: 30 Copynumber: 2.0 Consensus size: 32
40867148 ATAAATTATA
*
40867158 AAAAATATTAATTAA-ATTAAAAAA-TGAAAT
1 AAAAATATTAAATAATATTAAAAAAGTGAAAT
40867188 AAAAATATTAAATAATATTAAAAAAGTGAAAT
1 AAAAATATTAAATAATATTAAAAAAGTGAAAT
40867220 TAACCTTTAC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 14 0.48
31 9 0.31
32 6 0.21
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (32 bp):
AAAAATATTAAATAATATTAAAAAAGTGAAAT
Found at i:40868886 original size:13 final size:13
Alignment explanation
Indices: 40868866--40868901 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
40868856 TTTATTAAAA
40868866 CAACGAGTTTGGT
1 CAACGAGTTTGGT
*
40868879 CCACGAGTTTGGT
1 CAACGAGTTTGGT
40868892 CAACGA-TTTG
1 CAACGAGTTTG
40868902 ATTAGCACCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 4 0.19
13 17 0.81
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (13 bp):
CAACGAGTTTGGT
Found at i:40875503 original size:22 final size:22
Alignment explanation
Indices: 40875478--40875720 Score: 299
Period size: 22 Copynumber: 11.0 Consensus size: 22
40875468 CCAACATTCA
* * *
40875478 GACAACATTTAATTAACATTTG
1 GACAGCATTTAATCAACAATTG
40875500 GACAGCATTTAATCAACAATTG
1 GACAGCATTTAATCAACAATTG
* *
40875522 GACAACATTAAATCAAC-ATGTG
1 GACAGCATTTAATCAACAAT-TG
* *
40875544 GACAACATTTAATTAACAATTG
1 GACAGCATTTAATCAACAATTG
* * * *
40875566 GACAACATTCAATCAATATTTG
1 GACAGCATTTAATCAACAATTG
40875588 GACAGCATTTAATCAACAATTG
1 GACAGCATTTAATCAACAATTG
** *
40875610 GACAGCATAAAATCAACATTTG
1 GACAGCATTTAATCAACAATTG
40875632 GACAGCATTTAATCAACAATTG
1 GACAGCATTTAATCAACAATTG
* * *
40875654 GACAGCATTCAATCAATATTTG
1 GACAGCATTTAATCAACAATTG
*
40875676 GACAACATTTAATCAACAATTG
1 GACAGCATTTAATCAACAATTG
*
40875698 GATAGCATTTAATCAACAATTG
1 GACAGCATTTAATCAACAATTG
40875720 G
1 G
40875721 CACTACACCA
Statistics
Matches: 189, Mismatches: 30, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
21 2 0.01
22 185 0.98
23 2 0.01
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.29
Consensus pattern (22 bp):
GACAGCATTTAATCAACAATTG
Found at i:40875526 original size:44 final size:44
Alignment explanation
Indices: 40875478--40875720 Score: 333
Period size: 44 Copynumber: 5.5 Consensus size: 44
40875468 CCAACATTCA
* *
40875478 GACAACATTTAATTAACATTTGGACAGCATTTAATCAACAATTG
1 GACAACATTAAATCAACATTTGGACAGCATTTAATCAACAATTG
* * *
40875522 GACAACATTAAATCAACATGTGGACAACATTTAATTAACAATTG
1 GACAACATTAAATCAACATTTGGACAGCATTTAATCAACAATTG
* *
40875566 GACAACATTCAATCAATATTTGGACAGCATTTAATCAACAATTG
1 GACAACATTAAATCAACATTTGGACAGCATTTAATCAACAATTG
* *
40875610 GACAGCATAAAATCAACATTTGGACAGCATTTAATCAACAATTG
1 GACAACATTAAATCAACATTTGGACAGCATTTAATCAACAATTG
* * * *
40875654 GACAGCATTCAATCAATATTTGGACAACATTTAATCAACAATTG
1 GACAACATTAAATCAACATTTGGACAGCATTTAATCAACAATTG
* * * *
40875698 GATAGCATTTAATCAACAATTGG
1 GACAACATTAAATCAACATTTGG
40875721 CACTACACCA
Statistics
Matches: 177, Mismatches: 22, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 177 1.00
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.29
Consensus pattern (44 bp):
GACAACATTAAATCAACATTTGGACAGCATTTAATCAACAATTG
Found at i:40875587 original size:88 final size:88
Alignment explanation
Indices: 40875478--40875715 Score: 368
Period size: 88 Copynumber: 2.7 Consensus size: 88
40875468 CCAACATTCA
* * * *
40875478 GACAACATTTAATTAACATTTGGACAGCATTTAATCAACAATTGGACAACATTAAATCAACATGT
1 GACAACATTCAATCAATATTTGGACAGCATTTAATCAACAATTGGACAGCATTAAATCAACATGT
*
40875543 GGACAACATTTAATTAACAATTG
66 GGACAACATTTAATCAACAATTG
* *
40875566 GACAACATTCAATCAATATTTGGACAGCATTTAATCAACAATTGGACAGCATAAAATCAACATTT
1 GACAACATTCAATCAATATTTGGACAGCATTTAATCAACAATTGGACAGCATTAAATCAACATGT
*
40875631 GGACAGCATTTAATCAACAATTG
66 GGACAACATTTAATCAACAATTG
* * * *
40875654 GACAGCATTCAATCAATATTTGGACAACATTTAATCAACAATTGGATAGCATTTAATCAACA
1 GACAACATTCAATCAATATTTGGACAGCATTTAATCAACAATTGGACAGCATTAAATCAACA
40875716 ATTGGCACTA
Statistics
Matches: 137, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
88 137 1.00
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.29
Consensus pattern (88 bp):
GACAACATTCAATCAATATTTGGACAGCATTTAATCAACAATTGGACAGCATTAAATCAACATGT
GGACAACATTTAATCAACAATTG
Found at i:40875917 original size:42 final size:43
Alignment explanation
Indices: 40875856--40876080 Score: 233
Period size: 43 Copynumber: 5.3 Consensus size: 43
40875846 TTATTTTTAT
* * * * *** *
40875856 AAACGCTGCTAAAGGTCATGTTCTTTAGCGGTGC-TATGAAAA
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTTCCAC
*
40875898 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCACTTTTTCCAC
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTTCCAC
* * *
40875941 AAACGTCGCTAAAGATCATGTTCCTTAGCGACGCTTTTTCCAC
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTTCCAC
* *
40875984 AAACGCCGCTAAAGATAATGTTCTTTAGCGGCG-TTTCTTCCGC
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTT-TTCCAC
* * *
40876027 AAACGCCACTAAATG-TCATGTTCTTTTAGCGGAG-TTTTTACAC
1 AAACGCCGCTAAA-GATCATGTTC-TTTAGCGGCGCTTTTTCCAC
*
40876070 AAATGCCGCTA
1 AAACGCCGCTA
40876081 TTTCTTTGGT
Statistics
Matches: 154, Mismatches: 25, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
42 33 0.21
43 108 0.70
44 13 0.08
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (43 bp):
AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTTTCCAC
Found at i:40876493 original size:21 final size:21
Alignment explanation
Indices: 40876469--40876519 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
40876459 TTCTTTTGAA
* *
40876469 CCTCTGCTTCTCTCGTTGCAG
1 CCTCTGCTTCCCTCGCTGCAG
*
40876490 CCTCTGCTTCCCTCGCTGCCG
1 CCTCTGCTTCCCTCGCTGCAG
40876511 CCTCTGCTT
1 CCTCTGCTT
40876520 TAAGTTGTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.02, C:0.45, G:0.18, T:0.35
Consensus pattern (21 bp):
CCTCTGCTTCCCTCGCTGCAG
Found at i:40876544 original size:87 final size:87
Alignment explanation
Indices: 40876385--40876619 Score: 409
Period size: 87 Copynumber: 2.7 Consensus size: 87
40876375 CATTTTCTGT
* ** * * *
40876385 TCTGCTTC-CTCGCTGCAGTGTCTGCTTCTCTCGATGCCGCATCTGCTTTAAGTTGTAGCTGGAG
1 TCTGCTTCTCTCGTTGCAGCCTCTGCTTCCCTCGCTGCCGCCTCTGCTTTAAGTTGTAGCTGGAG
40876449 TTCTTCATATTTCTTTTGAACC
66 TTCTTCATATTTCTTTTGAACC
40876471 TCTGCTTCTCTCGTTGCAGCCTCTGCTTCCCTCGCTGCCGCCTCTGCTTTAAGTTGTAGCTGGAG
1 TCTGCTTCTCTCGTTGCAGCCTCTGCTTCCCTCGCTGCCGCCTCTGCTTTAAGTTGTAGCTGGAG
40876536 TTCTTCATATTTCTTTTGAACC
66 TTCTTCATATTTCTTTTGAACC
40876558 TCTGCTTCTCTCGTTGCAGCCTCTGCTTCCCTCGCTGCCGCCTCTGCTTTAAGTTGTAGCTG
1 TCTGCTTCTCTCGTTGCAGCCTCTGCTTCCCTCGCTGCCGCCTCTGCTTTAAGTTGTAGCTG
40876620 TCGAAGCCAT
Statistics
Matches: 142, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
86 8 0.06
87 134 0.94
ACGTcount: A:0.10, C:0.31, G:0.20, T:0.40
Consensus pattern (87 bp):
TCTGCTTCTCTCGTTGCAGCCTCTGCTTCCCTCGCTGCCGCCTCTGCTTTAAGTTGTAGCTGGAG
TTCTTCATATTTCTTTTGAACC
Found at i:40876580 original size:21 final size:21
Alignment explanation
Indices: 40876556--40876606 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
40876546 TTCTTTTGAA
* *
40876556 CCTCTGCTTCTCTCGTTGCAG
1 CCTCTGCTTCCCTCGCTGCAG
*
40876577 CCTCTGCTTCCCTCGCTGCCG
1 CCTCTGCTTCCCTCGCTGCAG
40876598 CCTCTGCTT
1 CCTCTGCTT
40876607 TAAGTTGTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.02, C:0.45, G:0.18, T:0.35
Consensus pattern (21 bp):
CCTCTGCTTCCCTCGCTGCAG
Found at i:40879229 original size:500 final size:491
Alignment explanation
Indices: 40878287--40879277 Score: 1858
Period size: 500 Copynumber: 2.0 Consensus size: 491
40878277 TGATCTGTCG
*
40878287 TCGATGTTATCTCTACTTCTACTGCCCATGTCAAACAAGTCTCTAGGGATGTTACGGAGTACAAC
1 TCGATGTTATCTCTACTTCCACTGCCCATGTCAAACAAGTCTCTAGGGATGTTACGGAGTACAAC
*
40878352 GTACCAACCCTCATCGGTTGGATCTTTTGAGTAAAAAACTTGTTTGACTTGAGATGAGAATACAT
66 ATACCAACCCTCATCGGTTGGATCTTTTGAGTAAAAAACTTGTTTGACTTGAGATGAGAATACAT
*
40878417 ACGGCTCATCTATCAGTTGTTGTCCTGTGTGAATCAATCGAGCGAAGTTTACTATTGTAAAACCA
131 AAGGCTCATCTATCAGTTGTTGTCCTGTGTGAATCAATCGAGCGAAGTTTACTATTGTAAAACCA
40878482 AATTGATCTTGCTTAATTCCACAAGCAGTATTAACATCGGCCCAATCACCTTGAAATAAGACAAC
196 AATTGATCTTGCTTAATTCCACAAGCAGTATTAACATCGGCCCAATCACCTTGAAATAAGACAAC
40878547 TTTCCATTTGCCGTAGTAATCTTAACTCAATTATGTCAGTAAGAAGTCCGAAATATTACACATTT
261 TTTCCATTTGCCGTAGTAATCTTAACTCAATTATGTCAGTAAGAAGTCCGAAATATTACACATTT
40878612 CCCTCGACAGAATTATTGTCCCTAGAACTAACATAACTTGTAATTGAGGAATTAACAACTATTCC
326 CCCTCGACAGAATTATTGTCCCTAGAACTAACATAACTTGTAATTGAGGAATTAACAACTATTCC
40878677 ACAATTTTGCGTTCTTCTCAATCTCTCGCAATATTTTGTCTGAAATCTGAATATGTTGATGAGGA
391 ACAATTTTGCGTTCTTCTCAATCTCTCGCAATATTTTGTCTGAAATCTGAATATGTTGATGAGGA
40878742 ACGCACTATATCTTTTAACCACTCGATTTGGACCTT
456 ACGCACTATATCTTTTAACCACTCGATTTGGACCTT
40878778 NNNNNNNNNNTCGATGTTATCTCTACTTCCACTGCCCATGTCAAACAAGTCTCTAGGGATGTTAC
1 ----------TCGATGTTATCTCTACTTCCACTGCCCATGTCAAACAAGTCTCTAGGGATGTTAC
40878843 GGAGTACAACATACCAACCCTCATCGGTTGGATCTTTTGAG-AAAAAACTTGTTTGACTTGAGAT
56 GGAGTACAACATACCAACCCTCATCGGTTGGATCTTTTGAGTAAAAAACTTGTTTGACTTGAGAT
40878907 GAGAATACATAAGGCTCATCTATCAGTTGTTGTCCTGTGTGAATCAATCGAGCGAAGTTTACTAT
121 GAGAATACATAAGGCTCATCTATCAGTTGTTGTCCTGTGTGAATCAATCGAGCGAAGTTTACTAT
40878972 TGTAAAACCAAATTGATCTTGCTTAATTCCACAAGCAGTATTAACATCGGCCCAATCACCTTGAA
186 TGTAAAACCAAATTGATCTTGCTTAATTCCACAAGCAGTATTAACATCGGCCCAATCACCTTGAA
40879037 ATAAGACAACTTTCCATTTGCCGTAGTAATCTTAACTCAATTATGTCAGTAAGAAGTCCGAAATA
251 ATAAGACAACTTTCCATTTGCCGTAGTAATCTTAACTCAATTATGTCAGTAAGAAGTCCGAAATA
40879102 TTACACATTTCCCTCGACAGAATTATTGTCCCTAGAACTAACATAACTTGTAATTGAGGAATTAA
316 TTACACATTTCCCTCGACAGAATTATTGTCCCTAGAACTAACATAACTTGTAATTGAGGAATTAA
40879167 CAACTATTCCACAATTTTGCGTTCTTCTCAATCTCTCGCAATATTTTGTCTGAAATCTGAATATG
381 CAACTATTCCACAATTTTGCGTTCTTCTCAATCTCTCGCAATATTTTGTCTGAAATCTGAATATG
40879232 TTGATGAGGAACGCACTATATCTTTTAACCACTCGATTTGGACCTT
446 TTGATGAGGAACGCACTATATCTTTTAACCACTCGATTTGGACCTT
40879278 GGGAAAGCCA
Statistics
Matches: 487, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
500 393 0.81
501 94 0.19
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.32
Consensus pattern (491 bp):
TCGATGTTATCTCTACTTCCACTGCCCATGTCAAACAAGTCTCTAGGGATGTTACGGAGTACAAC
ATACCAACCCTCATCGGTTGGATCTTTTGAGTAAAAAACTTGTTTGACTTGAGATGAGAATACAT
AAGGCTCATCTATCAGTTGTTGTCCTGTGTGAATCAATCGAGCGAAGTTTACTATTGTAAAACCA
AATTGATCTTGCTTAATTCCACAAGCAGTATTAACATCGGCCCAATCACCTTGAAATAAGACAAC
TTTCCATTTGCCGTAGTAATCTTAACTCAATTATGTCAGTAAGAAGTCCGAAATATTACACATTT
CCCTCGACAGAATTATTGTCCCTAGAACTAACATAACTTGTAATTGAGGAATTAACAACTATTCC
ACAATTTTGCGTTCTTCTCAATCTCTCGCAATATTTTGTCTGAAATCTGAATATGTTGATGAGGA
ACGCACTATATCTTTTAACCACTCGATTTGGACCTT
Found at i:40882485 original size:9 final size:9
Alignment explanation
Indices: 40882471--40882625 Score: 110
Period size: 9 Copynumber: 17.8 Consensus size: 9
40882461 TTTTTATGTA
40882471 TTATGTAAG
1 TTATGTAAG
*
40882480 TTATGTAAC
1 TTATGTAAG
*
40882489 TTACGTAAG
1 TTATGTAAG
** *
40882498 TTA-CCAAA
1 TTATGTAAG
*
40882506 TTAATGTATG
1 TT-ATGTAAG
40882516 TTATGTAAG
1 TTATGTAAG
40882525 -T-TGTAAG
1 TTATGTAAG
*
40882532 TTAT-TATG
1 TTATGTAAG
40882540 TATTATGTAAG
1 --TTATGTAAG
40882551 TTATGT-A-
1 TTATGTAAG
*
40882558 TTATGTAGG
1 TTATGTAAG
40882567 TTATGTAAG
1 TTATGTAAG
*
40882576 TTGTGTAAG
1 TTATGTAAG
* *
40882585 ATATTTAAG
1 TTATGTAAG
40882594 TTATGTAAG
1 TTATGTAAG
* *
40882603 TTTTG-CA-
1 TTATGTAAG
40882610 TTATGTAAG
1 TTATGTAAG
40882619 TTATGTA
1 TTATGTA
40882626 TGCTATGTAT
Statistics
Matches: 110, Mismatches: 25, Indels: 22
0.70 0.16 0.14
Matches are distributed among these distances:
7 16 0.15
8 12 0.11
9 72 0.65
10 7 0.06
11 3 0.03
ACGTcount: A:0.32, C:0.03, G:0.19, T:0.46
Consensus pattern (9 bp):
TTATGTAAG
Found at i:40882485 original size:16 final size:16
Alignment explanation
Indices: 40882464--40882821 Score: 125
Period size: 16 Copynumber: 21.4 Consensus size: 16
40882454 TGATATATTT
40882464 TTATGTATTATGTAAG
1 TTATGTATTATGTAAG
*
40882480 TTATGTAACTTACGTAAG
1 TTATGT-A-TTATGTAAG
*** *
40882498 TTACCAAATTAATGTATG
1 TTA-TGTATT-ATGTAAG
*
40882516 TTATGTAAGT-TGTAAG
1 TTATGT-ATTATGTAAG
40882532 TTATTATGTATTATGTAAG
1 ---TTATGTATTATGTAAG
*
40882551 TTATGTATTATGTAGG
1 TTATGTATTATGTAAG
*
40882567 TTATGTAAGTTGTGTAAG
1 TTATGT-A-TTATGTAAG
* *
40882585 ATATTTAAGTTATGTAAG
1 TTATGT-A-TTATGTAAG
* *
40882603 TTTTGCATTATGTAAG
1 TTATGTATTATGTAAG
40882619 TTATGTATGCTATGT-A-
1 TTATGTAT--TATGTAAG
* *
40882635 TAATGTA--A-GT-TG
1 TTATGTATTATGTAAG
*
40882647 TTATGTATAATGTAAG
1 TTATGTATTATGTAAG
40882663 TTA---A-TATGTAAG
1 TTATGTATTATGTAAG
* *
40882675 TAACGTATTATGTAAG
1 TTATGTATTATGTAAG
* *
40882691 TTTATATAAAAATTTTATATAAG
1 -TTATGT----A--TTATGTAAG
40882714 TTATGTATTATGTAAGG
1 TTATGTATTATGTAA-G
40882731 TAACATATAAGT-TTATGTAAG
1 T----TAT--GTATTATGTAAG
40882752 TTATG-A--ATGTAAG
1 TTATGTATTATGTAAG
40882765 TTATGTATTATGTAAG
1 TTATGTATTATGTAAG
* *
40882781 TTATTTAAATTATTTAAG
1 TTATGT--ATTATGTAAG
* *
40882799 TTGTGTATTATATAAG
1 TTATGTATTATGTAAG
*
40882815 TCATGTA
1 TTATGTA
40882822 GGCTATGCGT
Statistics
Matches: 257, Mismatches: 43, Indels: 84
0.67 0.11 0.22
Matches are distributed among these distances:
11 2 0.01
12 16 0.06
13 13 0.05
14 2 0.01
15 4 0.02
16 98 0.38
17 14 0.05
18 67 0.26
19 12 0.05
21 6 0.02
22 13 0.05
23 10 0.04
ACGTcount: A:0.34, C:0.03, G:0.18, T:0.46
Consensus pattern (16 bp):
TTATGTATTATGTAAG
Found at i:40882540 original size:19 final size:19
Alignment explanation
Indices: 40882516--40882554 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
40882506 TTAATGTATG
40882516 TTATGTAAGT-TGTAAGTTA
1 TTATGT-AGTATGTAAGTTA
*
40882535 TTATGTATTATGTAAGTTA
1 TTATGTAGTATGTAAGTTA
40882554 T
1 T
40882555 GTATTATGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.31, C:0.00, G:0.18, T:0.51
Consensus pattern (19 bp):
TTATGTAGTATGTAAGTTA
Found at i:40882576 original size:25 final size:24
Alignment explanation
Indices: 40882536--40882641 Score: 88
Period size: 25 Copynumber: 4.2 Consensus size: 24
40882526 TGTAAGTTAT
40882536 TATGTA-TTATGTAAGTTATGTAT
1 TATGTAGTTATGTAAGTTATGTAT
* *
40882559 TATGTAGGTTATGTAAGTTGTGTAAGA
1 TATGTA-GTTATGTAAGTTATGT-A-T
* * *
40882586 TATTTAAGTTATGTAAGTTTTGCAT
1 TATGT-AGTTATGTAAGTTATGTAT
* *
40882611 TATGTAAGTTATGTATGCTATGTAT
1 TATGT-AGTTATGTAAGTTATGTAT
*
40882636 AATGTA
1 TATGTA
40882642 AGTTGTTATG
Statistics
Matches: 66, Mismatches: 12, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
23 6 0.09
24 1 0.02
25 38 0.58
26 2 0.03
27 18 0.27
28 1 0.02
ACGTcount: A:0.30, C:0.02, G:0.21, T:0.47
Consensus pattern (24 bp):
TATGTAGTTATGTAAGTTATGTAT
Found at i:40882615 original size:52 final size:50
Alignment explanation
Indices: 40882509--40882625 Score: 137
Period size: 52 Copynumber: 2.3 Consensus size: 50
40882499 TACCAAATTA
* * * *
40882509 ATGTATGTTATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTATGTATT
1 ATGTAAGTTATGTAAGTTGTAAGATATTAAG-ATTATGTAAGTTATGCATT
* *
40882560 ATGTAGGTTATGTAAGTTGTGTAAGATATTTAAG-TTATGTAAGTTTTGCATT
1 ATGTAAGTTATGTAAG-T-TGTAAGATA-TTAAGATTATGTAAGTTATGCATT
40882612 ATGTAAGTTATGTA
1 ATGTAAGTTATGTA
40882626 TGCTATGTAT
Statistics
Matches: 57, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
51 15 0.26
52 30 0.53
53 8 0.14
54 4 0.07
ACGTcount: A:0.30, C:0.01, G:0.21, T:0.48
Consensus pattern (50 bp):
ATGTAAGTTATGTAAGTTGTAAGATATTAAGATTATGTAAGTTATGCATT
Found at i:40882670 original size:19 final size:19
Alignment explanation
Indices: 40882629--40882672 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
40882619 TTATGTATGC
**
40882629 TATGTATAATGTAAGTTGT
1 TATGTATAATGTAAGTTAA
40882648 TATGTATAATGTAAGTTAA
1 TATGTATAATGTAAGTTAA
40882667 TATGTA
1 TATGTA
40882673 AGTAACGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.45
Consensus pattern (19 bp):
TATGTATAATGTAAGTTAA
Found at i:40882763 original size:13 final size:15
Alignment explanation
Indices: 40882744--40882784 Score: 59
Period size: 13 Copynumber: 2.8 Consensus size: 15
40882734 CATATAAGTT
40882744 TATGTAAGTTATG-A
1 TATGTAAGTTATGTA
40882758 -ATGTAAGTTATGTA
1 TATGTAAGTTATGTA
40882772 TTATGTAAGTTAT
1 -TATGTAAGTTAT
40882785 TTAAATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 12 0.50
14 1 0.04
16 11 0.46
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (15 bp):
TATGTAAGTTATGTA
Found at i:40887445 original size:114 final size:114
Alignment explanation
Indices: 40887194--40888026 Score: 1085
Period size: 114 Copynumber: 7.3 Consensus size: 114
40887184 AGACAAATAA
* * * * * * *
40887194 TTTTTTTGCAGCGCTTTCCCACAAACGCCGCTAAATCCCAGAGCATTAGCGGCG-TTGTATTAAA
1 TTTTTTTGCGGCACTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTT-TCTTAAA
* * * * * * *
40887258 AATGCCACTAAAGCCCCCGAAAGGTCAGAAAATGGCATCGTTGGGCTTATG
65 AACGCCGCTAAA-TCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGG
** * *
40887309 TTTTTTTGCGGTGCTTTATCAAAAACGTCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAA
1 TTTTTTTGCGGCACTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAA
* *
40887374 ACGCCGCTAAATCCCCGAAAGGTCAGAAAACGACGTCGTTGGGCTTAGG
66 ACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGG
* * * *
40887423 TTTTTTTGCGGCACTTTGTCAAAAACACCGCTAAAGCCCTAAGCATTAGCGGCGCTTTATTAAAA
1 TTTTTTTGCGGCACTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAA
* *
40887488 ACGCCGCTAAATCCCCGAAAGGTCAGAAAACGACGTCGTTGGGCTTAGG
66 ACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGG
* * * *
40887537 TTTTTTTGCGGCACTTTGTCAAAAACACCGCTAAAGCCCTAAGCATTAGCGGCGCTTTATTAAAA
1 TTTTTTTGCGGCACTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAA
* * *
40887602 ACGCCGCTAAATCCCCGAAAAGATTAGAAAACGGCGTCGTTGGGATTAGG
66 ACGCCGCTAAATCCCCG-AAAGCTCAGAAAACGGCGTCGTTGGGCTTAGG
* * * * * * *
40887652 ATTTTTTGCAGCGCTTTCTCAAAAACGCCGCTAAATCCCTAAGCATTAGCGGCGCTTCCTGAAAA
1 TTTTTTTGCGGCACTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAA
*
40887717 ACGCCGCTAAATCCCCGAATGCTCAGAAAACGGCGTCGTTGGGCTTAGG
66 ACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGG
* * * * *
40887766 TTTTTTTGTGGCGCTTTCTCAAAAACGCCGCTAAAACCCTGAGCATTAGCGGCGCTTCCTCAAAA
1 TTTTTTTGCGGCACTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAA
* * *
40887831 ATGCCGCTAAATCCCCGAATGCTCAGAAAATGGCGTCGTTGGGCTTAGG
66 ACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGG
* * * *
40887880 TTTTTTTACGGCACTTTCTCAAAAACACCGCTAAAGCCCTGAGCATTAGCGGCGCTTCCTCAAAA
1 TTTTTTTGCGGCACTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAA
* * *
40887945 ACGGCGCTAAATCCCCGAATGCTCAAAAAACGGCGTCGTTGGGCTTAGG
66 ACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGG
* * * *
40887994 -TTTTTTGAGGCGCTTTCTGAAAAACGCTGCTAA
1 TTTTTTTGCGGCACTTTCTCAAAAACGCCGCTAA
40888027 TACTTATTTT
Statistics
Matches: 653, Mismatches: 63, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
113 27 0.04
114 461 0.71
115 163 0.25
116 2 0.00
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.25
Consensus pattern (114 bp):
TTTTTTTGCGGCACTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAA
ACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGG
Found at i:40887685 original size:229 final size:228
Alignment explanation
Indices: 40887194--40888026 Score: 1096
Period size: 229 Copynumber: 3.6 Consensus size: 228
40887184 AGACAAATAA
* * * * * *
40887194 TTTTTTTGCAGCGCTTTCCCACAAACGCCGCTAAATCCC-AGAGCATTAGCGGCG-TTGTATTAA
1 TTTTTTTGCAGCACTTTCTCAAAAACACCGCTAAAGCCCTA-AGCATTAGCGGCGCTT-CATTAA
* * * * * * * *
40887257 AAATGCCACTAAAGCCCCCGAAAGGTCAGAAAATGGCATCGTTGGGCTTATGTTTTTTTGCGGTG
64 AAACGCCGCTAAA-TCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCG
*
40887322 CTTTATCAAAAACGTCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATC
128 CTTTATCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATC
* *
40887387 CCCGAAAGGTCAGAAAACGACGTCGTTGGGCTTAGG
193 CCCGAAAGATCAGAAAACGGCGTCGTTGGGCTTAGG
* * *
40887423 TTTTTTTGCGGCACTTTGTCAAAAACACCGCTAAAGCCCTAAGCATTAGCGGCGCTTTATTAAAA
1 TTTTTTTGCAGCACTTTCTCAAAAACACCGCTAAAGCCCTAAGCATTAGCGGCGCTTCATTAAAA
* * *
40887488 ACGCCGCTAAATCCCCGAAAGGTCAGAAAACGACGTCGTTGGGCTTAGGTTTTTTTGCGGCACTT
66 ACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTT
* * * *
40887553 TGTCAAAAACACCGCTAAAGCCCTAAGCATTAGCGGCGCTTTATTAAAAACGCCGCTAAATCCCC
131 TATCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCC
* *
40887618 GAAAAGATTAGAAAACGGCGTCGTTGGGATTAGG
196 G-AAAGATCAGAAAACGGCGTCGTTGGGCTTAGG
* * * * * *
40887652 ATTTTTTGCAGCGCTTTCTCAAAAACGCCGCTAAATCCCTAAGCATTAGCGGCGCTTCCTGAAAA
1 TTTTTTTGCAGCACTTTCTCAAAAACACCGCTAAAGCCCTAAGCATTAGCGGCGCTTCATTAAAA
* *
40887717 ACGCCGCTAAATCCCCGAATGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGTGGCGCTT
66 ACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTT
* * * * *
40887782 TCTCAAAAACGCCGCTAAAACCCTGAGCATTAGCGGCGCTTCCTCAAAAATGCCGCTAAATCCCC
131 TATCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCC
* * *
40887847 GAATGCTCAGAAAATGGCGTCGTTGGGCTTAGG
196 GAAAGATCAGAAAACGGCGTCGTTGGGCTTAGG
* * * * *
40887880 TTTTTTTACGGCACTTTCTCAAAAACACCGCTAAAGCCCTGAGCATTAGCGGCGCTTCCTCAAAA
1 TTTTTTTGCAGCACTTTCTCAAAAACACCGCTAAAGCCCTAAGCATTAGCGGCGCTTCATTAAAA
* * * *
40887945 ACGGCGCTAAATCCCCGAATGCTCAAAAAACGGCGTCGTTGGGCTTAGG-TTTTTTGAGGCGCTT
66 ACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTT
* * *
40888009 TCTGAAAAACGCTGCTAA
131 TATCAAAAACGCCGCTAA
40888027 TACTTATTTT
Statistics
Matches: 536, Mismatches: 65, Indels: 8
0.88 0.11 0.01
Matches are distributed among these distances:
227 30 0.06
228 239 0.45
229 264 0.49
230 3 0.01
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.25
Consensus pattern (228 bp):
TTTTTTTGCAGCACTTTCTCAAAAACACCGCTAAAGCCCTAAGCATTAGCGGCGCTTCATTAAAA
ACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTGCGGCGCTT
TATCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCC
GAAAGATCAGAAAACGGCGTCGTTGGGCTTAGG
Found at i:40887820 original size:343 final size:341
Alignment explanation
Indices: 40887207--40888026 Score: 1106
Period size: 343 Copynumber: 2.4 Consensus size: 341
40887197 TTTTGCAGCG
* * * * * *
40887207 CTTTCCCACAAACGCCGCTAAATCCC-AGAGCATTAGCGGCG-TTGTATTAAAAATGCCACTAAA
1 CTTTCTCAAAAACACCGCTAAAGCCCTA-AGCATTAGCGGCGCTT-TATTAAAAACGCCGCTAAA
* * * * * * * *
40887270 GCCCCCGAAAGGTCAGAAAATGGCATCGTTGGGCTTATGTTTTTTTGCGGTGCTTTATCAAAAAC
64 -TCCCCGAAAGATCAGAAAACGGCGTCGTTGGGCTTA-GGTTTTTTGCAGCGCTTTCTCAAAAAC
* * * * *
40887335 GTCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGGTCAG
127 GCCGCTAAAGCCCTAAGCATTAGCGGCGCTTCCTGAAAAACGCCGCTAAATCCCCGAAAGCTCAG
* *
40887400 AAAACGACGTCGTTGGGCTTAGGTTTTTTTGCGGCACTTTGTCAAAAACACCGCTAAAGCCCTAA
192 AAAACGACGTCGTTGGGCTTAGGTTTTTTTGCGGCACTTTCTCAAAAACACCGCTAAAACCCTAA
* * *
40887465 GCATTAGCGGCGCTTTATTAAAAACGCCGCTAAATCCCCGAAAGGTCAGAAAACGACGTCGTTGG
257 GCATTAGCGGCGCTTCATCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGACGTCGTTGG
*
40887530 GCTTAGGTTTTTTTGCGGCA
322 GCTTAGGTTTTTTTACGGCA
*
40887550 CTTTGTCAAAAACACCGCTAAAGCCCTAAGCATTAGCGGCGCTTTATTAAAAACGCCGCTAAATC
1 CTTTCTCAAAAACACCGCTAAAGCCCTAAGCATTAGCGGCGCTTTATTAAAAACGCCGCTAAATC
* *
40887615 CCCGAAAAGATTAGAAAACGGCGTCGTTGGGATTAGGATTTTTTGCAGCGCTTTCTCAAAAACGC
66 CCCG-AAAGATCAGAAAACGGCGTCGTTGGGCTTAGG-TTTTTTGCAGCGCTTTCTCAAAAACGC
* *
40887680 CGCTAAATCCCTAAGCATTAGCGGCGCTTCCTGAAAAACGCCGCTAAATCCCCGAATGCTCAGAA
129 CGCTAAAGCCCTAAGCATTAGCGGCGCTTCCTGAAAAACGCCGCTAAATCCCCGAAAGCTCAGAA
* * * * *
40887745 AACGGCGTCGTTGGGCTTAGGTTTTTTTGTGGCGCTTTCTCAAAAACGCCGCTAAAACCCTGAGC
194 AACGACGTCGTTGGGCTTAGGTTTTTTTGCGGCACTTTCTCAAAAACACCGCTAAAACCCTAAGC
* * * * *
40887810 ATTAGCGGCGCTTCCTCAAAAATGCCGCTAAATCCCCGAATGCTCAGAAAATGGCGTCGTTGGGC
259 ATTAGCGGCGCTTCATCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGACGTCGTTGGGC
40887875 TTAGGTTTTTTTACGGCA
324 TTAGGTTTTTTTACGGCA
* ** * *
40887893 CTTTCTCAAAAACACCGCTAAAGCCCTGAGCATTAGCGGCGCTTCCTCAAAAACGGCGCTAAATC
1 CTTTCTCAAAAACACCGCTAAAGCCCTAAGCATTAGCGGCGCTTTATTAAAAACGCCGCTAAATC
* * * * *
40887958 CCCGAATGCTCAAAAAACGGCGTCGTTGGGCTTAGGTTTTTTG-AGGCGCTTTCTGAAAAACGCT
66 CCCGAAAGATCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTGCA-GCGCTTTCTCAAAAACGCC
40888022 GCTAA
130 GCTAA
40888027 TACTTATTTT
Statistics
Matches: 419, Mismatches: 53, Indels: 12
0.87 0.11 0.02
Matches are distributed among these distances:
340 1 0.00
341 29 0.07
342 33 0.08
343 353 0.84
344 3 0.01
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (341 bp):
CTTTCTCAAAAACACCGCTAAAGCCCTAAGCATTAGCGGCGCTTTATTAAAAACGCCGCTAAATC
CCCGAAAGATCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTGCAGCGCTTTCTCAAAAACGCCG
CTAAAGCCCTAAGCATTAGCGGCGCTTCCTGAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAA
CGACGTCGTTGGGCTTAGGTTTTTTTGCGGCACTTTCTCAAAAACACCGCTAAAACCCTAAGCAT
TAGCGGCGCTTCATCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGACGTCGTTGGGCTT
AGGTTTTTTTACGGCA
Found at i:40888157 original size:22 final size:23
Alignment explanation
Indices: 40888129--40888194 Score: 91
Period size: 22 Copynumber: 3.0 Consensus size: 23
40888119 GTGTAGTGTG
40888129 GACAACATTTAATCAACAATTT-
1 GACAACATTTAATCAACAATTTA
* *
40888151 GACAACATTCAATCAA-TATTTA
1 GACAACATTTAATCAACAATTTA
*
40888173 GACAGCATTTAATCAACAATTT
1 GACAACATTTAATCAACAATTT
40888195 TTTACTTCAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
21 4 0.11
22 29 0.78
23 4 0.11
ACGTcount: A:0.44, C:0.18, G:0.06, T:0.32
Consensus pattern (23 bp):
GACAACATTTAATCAACAATTTA
Found at i:40889045 original size:43 final size:42
Alignment explanation
Indices: 40888998--40889095 Score: 117
Period size: 42 Copynumber: 2.3 Consensus size: 42
40888988 CCCAGACGTG
* * *
40888998 GTCTTTCATGTAATCAAACAACGATGCCACTGTCCCAGATAGA
1 GTCTTACACGTAATCAAA-AACGATGCCAATGTCCCAGATAGA
* * *
40889041 GTCTTACACGTAATCATATACGATGCCAATGTCCCAGACATG-
1 GTCTTACACGTAATCAAAAACGATGCCAATGTCCCAGATA-GA
40889083 GTCTTACACGTAA
1 GTCTTACACGTAA
40889096 ATCTCAAATC
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
42 32 0.67
43 16 0.33
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.27
Consensus pattern (42 bp):
GTCTTACACGTAATCAAAAACGATGCCAATGTCCCAGATAGA
Found at i:40890777 original size:16 final size:16
Alignment explanation
Indices: 40890756--40890821 Score: 52
Period size: 16 Copynumber: 4.3 Consensus size: 16
40890746 CCTCTCCTTG
*
40890756 TATTTATTTTATTTAT
1 TATTTATTTTACTTAT
40890772 TATTTA-TTTAGCTTA-
1 TATTTATTTTA-CTTAT
* *
40890787 T-TTAATTTTATTTGAT
1 TATTTATTTTACTT-AT
40890803 T-TTTATTTTACTT-T
1 TATTTATTTTACTTAT
40890817 TATTT
1 TATTT
40890822 TAGTTCTAGA
Statistics
Matches: 40, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
14 7 0.17
15 13 0.32
16 20 0.50
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.71
Consensus pattern (16 bp):
TATTTATTTTACTTAT
Found at i:40890779 original size:11 final size:10
Alignment explanation
Indices: 40890756--40890821 Score: 55
Period size: 11 Copynumber: 6.5 Consensus size: 10
40890746 CCTCTCCTTG
40890756 TATTTA-TTT
1 TATTTATTTT
40890765 TATTTATTATT
1 TATTTATT-TT
**
40890776 TATTTA-GCT
1 TATTTATTTT
*
40890785 TATTTAATTT
1 TATTTATTTT
40890795 TATTTGATTTT
1 TATTT-ATTTT
*
40890806 TATTTTACTTT
1 TA-TTTATTTT
40890817 TATTT
1 TATTT
40890822 TAGTTCTAGA
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
9 13 0.28
10 10 0.22
11 20 0.43
12 3 0.07
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.71
Consensus pattern (10 bp):
TATTTATTTT
Found at i:40891014 original size:24 final size:23
Alignment explanation
Indices: 40890984--40891030 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
40890974 ATTCGTAGGT
* *
40890984 TCTATTTTTATTATCTTTTCATCA
1 TCTATTTTCATCATC-TTTCATCA
40891008 TCTATTTTCATCATCTTTCATCA
1 TCTATTTTCATCATCTTTCATCA
40891031 AAAAACATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.57
Consensus pattern (23 bp):
TCTATTTTCATCATCTTTCATCA
Found at i:40891017 original size:13 final size:13
Alignment explanation
Indices: 40890999--40891023 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40890989 TTTTATTATC
40890999 TTTTCATCATCTA
1 TTTTCATCATCTA
40891012 TTTTCATCATCT
1 TTTTCATCATCT
40891024 TTCATCAAAA
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:0.20, C:0.24, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTTCATCATCTA
Found at i:40891892 original size:25 final size:24
Alignment explanation
Indices: 40891864--40891974 Score: 87
Period size: 25 Copynumber: 4.5 Consensus size: 24
40891854 ACAGCTCTCT
*
40891864 TGAGCTTCCCGATACTTGGCTCTTA
1 TGAGCTTCCCGATA-TTGGCTCATA
* * *
40891889 TGAGTTTCTCGATATTTGGCTCACA
1 TGAGCTTCCCGATA-TTGGCTCATA
* ** *
40891914 AGAGCTTCCCGATATACAGCTCGTA
1 TGAGCTTCCCGATAT-TGGCTCATA
* *
40891939 TGAGCTTCCCGTTATATGGCTCAGA
1 TGAGCTTCCCGATAT-TGGCTCATA
*
40891964 AGAGCTTCCCG
1 TGAGCTTCCCG
40891975 TTTACATGCT
Statistics
Matches: 66, Mismatches: 19, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
24 1 0.02
25 65 0.98
ACGTcount: A:0.21, C:0.26, G:0.22, T:0.32
Consensus pattern (24 bp):
TGAGCTTCCCGATATTGGCTCATA
Found at i:40891941 original size:50 final size:50
Alignment explanation
Indices: 40891865--40891974 Score: 132
Period size: 50 Copynumber: 2.2 Consensus size: 50
40891855 CAGCTCTCTT
** * * * *
40891865 GAGCTTCCCGATACTTGGCTCTTATGAGTTTCTCGATATTTGGCTCACAA
1 GAGCTTCCCGATACTCAGCTCGTATGAGCTTCCCGATATATGGCTCACAA
* *
40891915 GAGCTTCCCGATA-TACAGCTCGTATGAGCTTCCCGTTATATGGCTCAGAA
1 GAGCTTCCCGATACT-CAGCTCGTATGAGCTTCCCGATATATGGCTCACAA
40891965 GAGCTTCCCG
1 GAGCTTCCCG
40891975 TTTACATGCT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
49 1 0.02
50 50 0.98
ACGTcount: A:0.21, C:0.26, G:0.22, T:0.31
Consensus pattern (50 bp):
GAGCTTCCCGATACTCAGCTCGTATGAGCTTCCCGATATATGGCTCACAA
Found at i:40892730 original size:28 final size:28
Alignment explanation
Indices: 40892691--40892804 Score: 142
Period size: 28 Copynumber: 4.1 Consensus size: 28
40892681 CTATACAGTA
*
40892691 ACAGT-ACAGTGTGGGCCTTAGCCTAGA-
1 ACAGTAACAGTGTGGGCCTTAGCCCA-AT
*
40892718 ACAGTAACAGTGTGGGCTTTAGCCCAAT
1 ACAGTAACAGTGTGGGCCTTAGCCCAAT
* *
40892746 ATAGTAATAGTGTGGGCCTTAGCCCAAT
1 ACAGTAACAGTGTGGGCCTTAGCCCAAT
* * *
40892774 ATAGTAACAGTTTAGGCCTTAGCCCAAT
1 ACAGTAACAGTGTGGGCCTTAGCCCAAT
40892802 ACA
1 ACA
40892805 ATAATAGTAC
Statistics
Matches: 76, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
27 6 0.08
28 70 0.92
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (28 bp):
ACAGTAACAGTGTGGGCCTTAGCCCAAT
Found at i:40893208 original size:27 final size:27
Alignment explanation
Indices: 40893162--40893329 Score: 164
Period size: 27 Copynumber: 6.3 Consensus size: 27
40893152 GGTATCACAA
*
40893162 TCATTTTACCCTAT-GAGGGTGTTTCAG
1 TCATTTTACCCT-TCGAGGGTATTTCAG
* **
40893189 TCATTTTACCCTTCGGGGGTATTTTGG
1 TCATTTTACCCTTCGAGGGTATTTCAG
*
40893216 TCATTTTACCCTTC-AGGGGTATTTCCG
1 TCATTTTACCCTTCGA-GGGTATTTCAG
* * *
40893243 TTA-TTT-CCCTTTCGGGGGTATTTTAG
1 TCATTTTACCC-TTCGAGGGTATTTCAG
* *
40893269 TCATTTTACCCTTCTAAGGTATTTCAG
1 TCATTTTACCCTTCGAGGGTATTTCAG
* *
40893296 TCATTTTATCCTTCGAGGGTATTTCGG
1 TCATTTTACCCTTCGAGGGTATTTCAG
*
40893323 TTATTTT
1 TCATTTT
40893330 CCTACGAATT
Statistics
Matches: 114, Mismatches: 21, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
25 3 0.03
26 18 0.16
27 90 0.79
28 3 0.03
ACGTcount: A:0.15, C:0.19, G:0.20, T:0.46
Consensus pattern (27 bp):
TCATTTTACCCTTCGAGGGTATTTCAG
Found at i:40893290 original size:80 final size:80
Alignment explanation
Indices: 40893178--40893328 Score: 205
Period size: 80 Copynumber: 1.9 Consensus size: 80
40893168 TACCCTATGA
* ** **
40893178 GGGTGTTTCAGTCATTTTACCCTTCGGGGGTATTTTGGTCATTTTACCCTTC-AGGGGTATTTCC
1 GGGTATTTCAGTCATTTTACCCTTCGAAGGTATTTCAGTCATTTTACCCTTCGA-GGGTATTTCC
40893242 GTTATTTCCCTTTCGG
65 GTTATTTCCCTTTCGG
* * * *
40893258 GGGTATTTTAGTCATTTTACCCTTCTAAGGTATTTCAGTCATTTTATCCTTCGAGGGTATTTCGG
1 GGGTATTTCAGTCATTTTACCCTTCGAAGGTATTTCAGTCATTTTACCCTTCGAGGGTATTTCCG
40893323 TTATTT
66 TTATTT
40893329 TCCTACGAAT
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
80 60 0.98
81 1 0.02
ACGTcount: A:0.15, C:0.19, G:0.21, T:0.46
Consensus pattern (80 bp):
GGGTATTTCAGTCATTTTACCCTTCGAAGGTATTTCAGTCATTTTACCCTTCGAGGGTATTTCCG
TTATTTCCCTTTCGG
Found at i:40893726 original size:27 final size:27
Alignment explanation
Indices: 40893558--40893725 Score: 214
Period size: 27 Copynumber: 6.3 Consensus size: 27
40893548 TCCTTTTCGC
*
40893558 GGTATTTCGGTCATTTTACCCTTCG-G
1 GGTATTTCGATCATTTTACCCTTCGAG
*
40893584 AGGTATTTCGATCATTTTACCC-TCGTG
1 -GGTATTTCGATCATTTTACCCTTCGAG
* * *
40893611 GGTATTTCGGTCATTTTACCCTCCGGG
1 GGTATTTCGATCATTTTACCCTTCGAG
40893638 GGTATTTCGATCATTTTACCCTTCGAG
1 GGTATTTCGATCATTTTACCCTTCGAG
* * *
40893665 GGTGTTTAGATTATTTTACCCTTCGAG
1 GGTATTTCGATCATTTTACCCTTCGAG
* * *
40893692 GGTATTTTGGTCATTTTACCCTTCAAG
1 GGTATTTCGATCATTTTACCCTTCGAG
40893719 GGTATTT
1 GGTATTT
40893726 TAGTTATTTG
Statistics
Matches: 124, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
26 23 0.19
27 101 0.81
ACGTcount: A:0.16, C:0.20, G:0.21, T:0.42
Consensus pattern (27 bp):
GGTATTTCGATCATTTTACCCTTCGAG
Found at i:40899639 original size:21 final size:21
Alignment explanation
Indices: 40899613--40899652 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
40899603 AGATCATTAA
40899613 TTTTATCTATTTT-ATTTTTAG
1 TTTTAT-TATTTTCATTTTTAG
*
40899634 TTTTATTTTTTTCATTTTT
1 TTTTATTATTTTCATTTTT
40899653 TTTGTTTCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.15, C:0.05, G:0.03, T:0.78
Consensus pattern (21 bp):
TTTTATTATTTTCATTTTTAG
Found at i:40904742 original size:63 final size:63
Alignment explanation
Indices: 40904643--40904773 Score: 244
Period size: 63 Copynumber: 2.1 Consensus size: 63
40904633 AGGAGCTAGC
*
40904643 TTACTGATATCATTAAGAATAAGAGAGGCCTAATTCTAACCAATAAACACACACAAGCGGGTT
1 TTACTGATATCATTAAGAATAAGAGAGGCCTAATTCTAACAAATAAACACACACAAGCGGGTT
*
40904706 TTACTGATATCATTAAGAATGAGAGAGGCCTAATTCTAACAAATAAACACACACAAGCGGGTT
1 TTACTGATATCATTAAGAATAAGAGAGGCCTAATTCTAACAAATAAACACACACAAGCGGGTT
40904769 TTACT
1 TTACT
40904774 TAGATGAGAT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 66 1.00
ACGTcount: A:0.40, C:0.18, G:0.16, T:0.25
Consensus pattern (63 bp):
TTACTGATATCATTAAGAATAAGAGAGGCCTAATTCTAACAAATAAACACACACAAGCGGGTT
Found at i:40914540 original size:1 final size:1
Alignment explanation
Indices: 40914536--40914629 Score: 170
Period size: 1 Copynumber: 94.0 Consensus size: 1
40914526 TTTTTCCTCA
* *
40914536 TTTTTCTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
40914601 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
40914630 GTGCGTGTGT
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
1 89 1.00
ACGTcount: A:0.00, C:0.02, G:0.00, T:0.98
Consensus pattern (1 bp):
T
Found at i:40915547 original size:21 final size:22
Alignment explanation
Indices: 40915508--40915548 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
40915498 TCAAAAAAAA
*
40915508 TAATACAAATGGATGAATTTTT
1 TAATACAAATGGATCAATTTTT
*
40915530 TAATAGAAA-GGATCAATTT
1 TAATACAAATGGATCAATTT
40915549 ACTATTTGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.44, C:0.05, G:0.15, T:0.37
Consensus pattern (22 bp):
TAATACAAATGGATCAATTTTT
Found at i:40918664 original size:20 final size:20
Alignment explanation
Indices: 40918639--40918676 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
40918629 GCAGTGGAAA
40918639 TTTATTTTCTTA-GAATAAAT
1 TTTATTTT-TTAGGAATAAAT
40918659 TTTATTTTTTAGGAATAA
1 TTTATTTTTTAGGAATAA
40918677 TAATTTTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.34, C:0.03, G:0.08, T:0.55
Consensus pattern (20 bp):
TTTATTTTTTAGGAATAAAT
Found at i:40922620 original size:29 final size:27
Alignment explanation
Indices: 40922588--40922665 Score: 95
Period size: 26 Copynumber: 2.9 Consensus size: 27
40922578 AGTGCATTAA
*
40922588 CAGAACAGAGGTGCACCGAAGTGCAATGC
1 CAGAACAGAGG-ACACCGAAGTGCAAT-C
* *
40922617 CAGAACGGAGGACACCGTAGTGCAATC
1 CAGAACAGAGGACACCGAAGTGCAATC
*
40922644 C-GAATAGAGGACACCGAAGTGC
1 CAGAACAGAGGACACCGAAGTGC
40922666 TAATAGAATA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
26 18 0.42
27 2 0.05
28 13 0.30
29 10 0.23
ACGTcount: A:0.35, C:0.24, G:0.31, T:0.10
Consensus pattern (27 bp):
CAGAACAGAGGACACCGAAGTGCAATC
Found at i:40922664 original size:26 final size:26
Alignment explanation
Indices: 40922601--40922679 Score: 88
Period size: 26 Copynumber: 3.0 Consensus size: 26
40922591 AACAGAGGTG
**
40922601 CACCGAAGTGCAATGCCAGAACGGAGGA
1 CACCGAAGTGCAAT-CC-GAATAGAGGA
*
40922629 CACCGTAGTGCAATCCGAATAGAGGA
1 CACCGAAGTGCAATCCGAATAGAGGA
*
40922655 CACCGAAGTGCTAAT-AGAATAGAGG
1 CACCGAAGTGC-AATCCGAATAGAGG
40922680 GCGCACTAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
26 27 0.60
27 5 0.11
28 13 0.29
ACGTcount: A:0.37, C:0.22, G:0.29, T:0.13
Consensus pattern (26 bp):
CACCGAAGTGCAATCCGAATAGAGGA
Found at i:40925768 original size:6 final size:6
Alignment explanation
Indices: 40925759--40925783 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
40925749 TTATATTTGT
40925759 TTAATA TTAATA TTAATA TTAATA T
1 TTAATA TTAATA TTAATA TTAATA T
40925784 ATTTTTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTAATA
Found at i:40925798 original size:31 final size:31
Alignment explanation
Indices: 40925722--40925798 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 31
40925712 TTGTAGAAGA
40925722 ATTTTTAATTTT-TTAATATTAATATAATTAT
1 ATTTTT-ATTTTATTAATATTAATATAATTAT
**
40925753 ATTTGTT-TAATATTAATATTAATATTAA-TAT
1 ATTT-TTATTTTATTAATATTAATA-TAATTAT
40925784 ATTTTTATTTTATTA
1 ATTTTTATTTTATTA
40925799 TTATACTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
30 4 0.11
31 29 0.76
32 5 0.13
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (31 bp):
ATTTTTATTTTATTAATATTAATATAATTAT
Found at i:40938510 original size:203 final size:200
Alignment explanation
Indices: 40938161--40938563 Score: 754
Period size: 203 Copynumber: 2.0 Consensus size: 200
40938151 AATGCGTACT
40938161 ACAGGGCGTTTTTACTGATGTGGCAGTGAAAAGGCGCCCTGTAGGACGCGTTTTCCTTTCTCTAT
1 ACAGGGCGTTTTTACTGATGTGGCAGTGAAAAGGCGCCCTGTAGGACGCGTTTTCCTTTCTCTAT
*
40938226 AAAAAACAACGTAGATTAGTAAATTTTTAGAAAATCAGCATAGTTTATCAAAAAAAAAAGAAATT
66 AAAAAACAACATAGATTAGTAAATTTTTAGAAAATCAGCATAGTTTATCAAAAAAAAAAGAAATT
40938291 TCAACATATTTAGATAAATCCGCCGCCATATTCGCTTATTATTATTATTATTATTATTTGGCATA
131 TCAACATATTTAGATAAATCCGCCGCCATATTCGC---TTATTATTATTATTATTATTTGGCATA
40938356 ACCACTTA
193 ACCACTTA
40938364 ACAGGGCGTTTTTACTGATGTGGCAGTGAAAAGGCGCCCTGTAGGACGCGTTTTCCTTTCTCTAT
1 ACAGGGCGTTTTTACTGATGTGGCAGTGAAAAGGCGCCCTGTAGGACGCGTTTTCCTTTCTCTAT
40938429 AAAAAAACAACATAGATTAGTAAATTTTTAGAAAATCAGCATAGTTTATC-AAAAAAAAAGAAAT
66 -AAAAAACAACATAGATTAGTAAATTTTTAGAAAATCAGCATAGTTTATCAAAAAAAAAAGAAAT
40938493 TTCAACATATTTAGATAAATCCGCCGCCATATTCGCTTATTATTATTATTATTATTTGGCATAAC
130 TTCAACATATTTAGATAAATCCGCCGCCATATTCGCTTATTATTATTATTATTATTTGGCATAAC
40938558 CACTTA
195 CACTTA
40938564 TTTGGCCCTC
Statistics
Matches: 198, Mismatches: 1, Indels: 5
0.97 0.00 0.02
Matches are distributed among these distances:
200 35 0.18
203 115 0.58
204 48 0.24
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Consensus pattern (200 bp):
ACAGGGCGTTTTTACTGATGTGGCAGTGAAAAGGCGCCCTGTAGGACGCGTTTTCCTTTCTCTAT
AAAAAACAACATAGATTAGTAAATTTTTAGAAAATCAGCATAGTTTATCAAAAAAAAAAGAAATT
TCAACATATTTAGATAAATCCGCCGCCATATTCGCTTATTATTATTATTATTATTTGGCATAACC
ACTTA
Found at i:40944227 original size:21 final size:21
Alignment explanation
Indices: 40944201--40944241 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
40944191 CCACCGCCAG
40944201 CCTTTTTCTGCTCCCCTCCAC
1 CCTTTTTCTGCTCCCCTCCAC
40944222 CCTTTTTCTGCTCCCCTCCA
1 CCTTTTTCTGCTCCCCTCCA
40944242 GCCATATGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.05, C:0.51, G:0.05, T:0.39
Consensus pattern (21 bp):
CCTTTTTCTGCTCCCCTCCAC
Found at i:40952328 original size:21 final size:21
Alignment explanation
Indices: 40952304--40952343 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
40952294 TTACAATTTT
*
40952304 TAAAGTTAAAAGTTAAAACCA
1 TAAAGTTAAAAGATAAAACCA
40952325 TAAAGTTAAAAGATAAAAC
1 TAAAGTTAAAAGATAAAAC
40952344 TACGTCACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.60, C:0.07, G:0.10, T:0.23
Consensus pattern (21 bp):
TAAAGTTAAAAGATAAAACCA
Found at i:40959956 original size:1 final size:1
Alignment explanation
Indices: 40959950--40959978 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
40959940 TCGAAGCTGC
40959950 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
40959979 GAGACAAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:40961457 original size:20 final size:18
Alignment explanation
Indices: 40961405--40961463 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 18
40961395 TGTATAAAAT
40961405 GAACATTTTAATTTCTCAA
1 GAACATTTTAATTT-TCAA
*
40961424 GACAAATATTTAATTTTCATTA
1 GA-ACAT-TTTAATTTTCA--A
40961446 GAACATTTTAATTTTCAA
1 GAACATTTTAATTTTCAA
40961464 TATCATGTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
18 1 0.03
19 2 0.06
20 17 0.50
21 11 0.32
22 3 0.09
ACGTcount: A:0.39, C:0.12, G:0.05, T:0.44
Consensus pattern (18 bp):
GAACATTTTAATTTTCAA
Found at i:40962090 original size:16 final size:16
Alignment explanation
Indices: 40962069--40962106 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
40962059 TTTGGTTCGC
40962069 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
40962085 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
*
40962101 CGTAAT
1 TGTAAT
40962107 AGTAATTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.37, C:0.03, G:0.34, T:0.26
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:40964009 original size:30 final size:29
Alignment explanation
Indices: 40963970--40964030 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
40963960 ATACATGTAT
40963970 ATCTTTTTATATGTTCA-TAATT-TTTATTC
1 ATCTTTTTAT-TGTT-ATTAATTATTTATTC
*
40963999 ATCTTCTTTATTGTTATTATTTATTTATTC
1 ATCTT-TTTATTGTTATTAATTATTTATTC
40964029 AT
1 AT
40964031 GTGTTCATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
28 1 0.04
29 13 0.46
30 14 0.50
ACGTcount: A:0.23, C:0.10, G:0.03, T:0.64
Consensus pattern (29 bp):
ATCTTTTTATTGTTATTAATTATTTATTC
Found at i:40964213 original size:64 final size:65
Alignment explanation
Indices: 40964133--40964264 Score: 257
Period size: 64 Copynumber: 2.0 Consensus size: 65
40964123 TATTTATTTC
40964133 ATTTTGTTGATTGTTTGCATTATTTATGCTTAACTTGTCGTATTCATTATCGTTTTGTTATGCAT
1 ATTTTGTTGATTGTTTGCATTATTTATGCTTAACTTGTCGTATTCATTATCGTTTTGTTATGCAT
40964198 ATTTTGTTGA-TGTTTGCATTATTTATGCTTAACTTGTCGTATTCATTATCGTTTTGTTATGCAT
1 ATTTTGTTGATTGTTTGCATTATTTATGCTTAACTTGTCGTATTCATTATCGTTTTGTTATGCAT
40964262 ATT
1 ATT
40964265 AACACCGTAC
Statistics
Matches: 67, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
64 57 0.85
65 10 0.15
ACGTcount: A:0.19, C:0.11, G:0.15, T:0.55
Consensus pattern (65 bp):
ATTTTGTTGATTGTTTGCATTATTTATGCTTAACTTGTCGTATTCATTATCGTTTTGTTATGCAT
Found at i:40964500 original size:104 final size:105
Alignment explanation
Indices: 40964307--40964503 Score: 229
Period size: 104 Copynumber: 1.9 Consensus size: 105
40964297 TAAGGTAATA
* * * **
40964307 TTTTGTGTTTAGAAAATCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTACTGTTTGGCCAA
1 TTTTGCGTTTAGAAAATCGAGAAAACGTGCCCCAAGGTGCTGGGTTTCGATTACTGTTTAACCAA
* * *
40964372 ATAGTCGAATATCTTTTCGAAATTTTAAAACGAGGCAATG
66 ATAGCCAAATATCTCTTCGAAATTTTAAAACGAGGCAATG
* * * * *
40964412 TTTTGCGTTTAGAAATTTGAG-GAACGTGCCCCAAGGTGCTGGGTTTCGATTTCTCGTTTAATCA
1 TTTTGCGTTTAGAAAATCGAGAAAACGTGCCCCAAGGTGCTGGGTTTCGATTACT-GTTTAACCA
*
40964476 AATTGCCAAATATCCTCTT-G-AATTTTAA
65 AATAGCCAAATAT-CTCTTCGAAATTTTAA
40964504 TCTATGCTAT
Statistics
Matches: 76, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
104 37 0.49
105 35 0.46
106 4 0.05
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36
Consensus pattern (105 bp):
TTTTGCGTTTAGAAAATCGAGAAAACGTGCCCCAAGGTGCTGGGTTTCGATTACTGTTTAACCAA
ATAGCCAAATATCTCTTCGAAATTTTAAAACGAGGCAATG
Found at i:40968747 original size:48 final size:48
Alignment explanation
Indices: 40968693--40968789 Score: 131
Period size: 48 Copynumber: 2.0 Consensus size: 48
40968683 ATCCGATTCG
* *
40968693 AAAAAAAGGAAAAGAAAAAGAGAAAAAAATCAAAATCAAAATCAAAAT
1 AAAAAAAGAAAAAGAAAAAGAGAAAAAAATCAAAATCAAAATAAAAAT
* * ** *
40968741 AAAAAAATAAAAAGAAAAATAGAAATCAATCAAAGTCAAAATAAAAAT
1 AAAAAAAGAAAAAGAAAAAGAGAAAAAAATCAAAATCAAAATAAAAAT
40968789 A
1 A
40968790 TGAAAAGCAA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.74, C:0.06, G:0.08, T:0.11
Consensus pattern (48 bp):
AAAAAAAGAAAAAGAAAAAGAGAAAAAAATCAAAATCAAAATAAAAAT
Found at i:40969379 original size:346 final size:346
Alignment explanation
Indices: 40968746--40969438 Score: 1377
Period size: 346 Copynumber: 2.0 Consensus size: 346
40968736 AAAATAAAAA
40968746 AATAAAAAGAAAAATAGAAATCAATCAAAGTCAAAATAAAAATATGAAAAGCAAAGAAAAGAAAA
1 AATAAAAAGAAAAATAGAAATCAATCAAAGTCAAAATAAAAATATGAAAAGCAAAGAAAAGAAAA
*
40968811 GAAGAGGCCAAGGTGAAAACCCAAAAAGGGCGCTTTGTGACCAAAGGTGGTTTTGAGTTGAAAAC
66 GAAGAGGCCAAGGTAAAAACCCAAAAAGGGCGCTTTGTGACCAAAGGTGGTTTTGAGTTGAAAAC
40968876 CCGAAAAGGGCGACTCAAATTTCGAGCAAAATGGGGCATGGACATCACCATTATCGAAGACTTCT
131 CCGAAAAGGGCGACTCAAATTTCGAGCAAAATGGGGCATGGACATCACCATTATCGAAGACTTCT
40968941 AATGGGCATTGCTTCACAATTGAGATCATTAATTACTTCATCAAAGGGATAGAGGCTATTGCACG
196 AATGGGCATTGCTTCACAATTGAGATCATTAATTACTTCATCAAAGGGATAGAGGCTATTGCACG
40969006 CGTCAATGTCATCATATGCTGATATAGAATTCTATAGAGGATGGTATTGGAAAATGCATTGAACT
261 CGTCAATGTCATCATATGCTGATATAGAATTCTATAGAGGATGGTATTGGAAAATGCATTGAACT
40969071 GGAATGACAACACGATAGCTG
326 GGAATGACAACACGATAGCTG
40969092 AATAAAAAGAAAAATAGAAATCAATCAAAGTCAAAATAAAAATATGAAAAGCAAAGAAAAGAAAA
1 AATAAAAAGAAAAATAGAAATCAATCAAAGTCAAAATAAAAATATGAAAAGCAAAGAAAAGAAAA
40969157 GAAGAGGCCAAGGTAAAAACCCAAAAAGGGCGCTTTGTGACCAAAGGTGGTTTTGAGTTGAAAAC
66 GAAGAGGCCAAGGTAAAAACCCAAAAAGGGCGCTTTGTGACCAAAGGTGGTTTTGAGTTGAAAAC
40969222 CCGAAAAGGGCGACTCAAATTTCGAGCAAAATGGGGCATGGACATCACCATTATCGAAGACTTCT
131 CCGAAAAGGGCGACTCAAATTTCGAGCAAAATGGGGCATGGACATCACCATTATCGAAGACTTCT
40969287 AATGGGCATTGCTTCACAATTGAGATCATTAATTACTTCATCAAAGGGATAGAGGCTATTGCACG
196 AATGGGCATTGCTTCACAATTGAGATCATTAATTACTTCATCAAAGGGATAGAGGCTATTGCACG
40969352 CGTCAATGTCATCATATGCTGATATAGAATTCTATAGAGGATGGTATTGGAAAATGCATTGAACT
261 CGTCAATGTCATCATATGCTGATATAGAATTCTATAGAGGATGGTATTGGAAAATGCATTGAACT
40969417 GGAATGACAACACGATAGCTG
326 GGAATGACAACACGATAGCTG
40969438 A
1 A
40969439 GGGCTGTAAT
Statistics
Matches: 346, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
346 346 1.00
ACGTcount: A:0.41, C:0.15, G:0.22, T:0.22
Consensus pattern (346 bp):
AATAAAAAGAAAAATAGAAATCAATCAAAGTCAAAATAAAAATATGAAAAGCAAAGAAAAGAAAA
GAAGAGGCCAAGGTAAAAACCCAAAAAGGGCGCTTTGTGACCAAAGGTGGTTTTGAGTTGAAAAC
CCGAAAAGGGCGACTCAAATTTCGAGCAAAATGGGGCATGGACATCACCATTATCGAAGACTTCT
AATGGGCATTGCTTCACAATTGAGATCATTAATTACTTCATCAAAGGGATAGAGGCTATTGCACG
CGTCAATGTCATCATATGCTGATATAGAATTCTATAGAGGATGGTATTGGAAAATGCATTGAACT
GGAATGACAACACGATAGCTG
Found at i:40972217 original size:17 final size:17
Alignment explanation
Indices: 40972195--40972228 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
40972185 AACGATAGAG
40972195 ATAAAAAATCTTAACTC
1 ATAAAAAATCTTAACTC
*
40972212 ATAAAAAATCTTGACTC
1 ATAAAAAATCTTAACTC
40972229 CAAGTTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.18, G:0.03, T:0.29
Consensus pattern (17 bp):
ATAAAAAATCTTAACTC
Found at i:40975010 original size:27 final size:27
Alignment explanation
Indices: 40974980--40975040 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
40974970 TATCTCGGTT
40974980 GACTATCCCATATTTAA-TGTCTCGTCA
1 GACTATCCCATATTTAACTGTCT-GTCA
* * * *
40975007 GACTATCTCGTGTTTAACTTTCTGTCA
1 GACTATCCCATATTTAACTGTCTGTCA
40975034 GACTATC
1 GACTATC
40975041 TATGATACCG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 25 0.86
28 4 0.14
ACGTcount: A:0.23, C:0.25, G:0.13, T:0.39
Consensus pattern (27 bp):
GACTATCCCATATTTAACTGTCTGTCA
Found at i:40979444 original size:20 final size:20
Alignment explanation
Indices: 40979419--40979458 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
40979409 AATATTTTCC
*
40979419 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
40979439 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
40979459 TCATTTTACG
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:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:40979464 original size:34 final size:35
Alignment explanation
Indices: 40979407--40979473 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
40979397 CAAACACTAG
*
40979407 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
40979442 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
40979474 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:40980706 original size:29 final size:29
Alignment explanation
Indices: 40980656--40980711 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
40980646 ATAAGAACTT
*
40980656 GATCAATTTAGTCCATGCACTATTAAATG
1 GATCAAATTAGTCCATGCACTATTAAATG
** *
40980685 GATCAAATTAGTCTTTGTACTATTAAA
1 GATCAAATTAGTCCATGCACTATTAAA
40980712 AAGAATTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (29 bp):
GATCAAATTAGTCCATGCACTATTAAATG
Found at i:40998705 original size:13 final size:13
Alignment explanation
Indices: 40998687--40998717 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
40998677 GTCATGTGTC
*
40998687 ACACACGGCTGAA
1 ACACACGCCTGAA
40998700 ACACACGCCTGAA
1 ACACACGCCTGAA
40998713 ACACA
1 ACACA
40998718 TGCCCGTGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.42, C:0.35, G:0.16, T:0.06
Consensus pattern (13 bp):
ACACACGCCTGAA
Found at i:41003426 original size:15 final size:15
Alignment explanation
Indices: 41003395--41003447 Score: 65
Period size: 15 Copynumber: 3.6 Consensus size: 15
41003385 TCCTTTTGCT
*
41003395 TTTCTTTTCCTTTTTC
1 TTTCTTTTTC-TTTTC
41003411 TTTCTTTTTCTTTTC
1 TTTCTTTTTCTTTTC
*
41003426 TTTCTTTCTCTTTT-
1 TTTCTTTTTCTTTTC
41003440 TTT-TTTTT
1 TTTCTTTTT
41003448 AAAAATTTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
13 4 0.12
14 3 0.09
15 18 0.53
16 9 0.26
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTCTTTTTCTTTTC
Found at i:41003431 original size:19 final size:19
Alignment explanation
Indices: 41003407--41003443 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
41003397 TCTTTTCCTT
41003407 TTTCTTTCT-TTTTCTTTTC
1 TTTCTTTCTCTTTT-TTTTC
41003426 TTTCTTTCTCTTTTTTTT
1 TTTCTTTCTCTTTTTTTT
41003444 TTTTAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTCTTTCTCTTTTTTTTC
Found at i:41007982 original size:19 final size:21
Alignment explanation
Indices: 41007944--41007982 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
41007934 CCTTTTTTAA
*
41007944 AATCGTAAATAAGTAAAAAAT
1 AATCGTAAATAAGAAAAAAAT
41007965 AATCG-AAA-AAGAAAAAAA
1 AATCGTAAATAAGAAAAAAA
41007983 AAAGAAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.69, C:0.05, G:0.10, T:0.15
Consensus pattern (21 bp):
AATCGTAAATAAGAAAAAAAT
Found at i:41008210 original size:21 final size:21
Alignment explanation
Indices: 41008177--41008256 Score: 105
Period size: 21 Copynumber: 4.0 Consensus size: 21
41008167 ATTACAAAAT
41008177 CATATC-T-TCTAAGATTGTA
1 CATATCATATCTAAGATTGTA
* *
41008196 TATATCATATCTAAGATTGCA
1 CATATCATATCTAAGATTGTA
*
41008217 CATATCATATTTAAGATTG--
1 CATATCATATCTAAGATTGTA
41008236 CATATCATATCTAAGATTGTA
1 CATATCATATCTAAGATTGTA
41008257 TATCCTCGAA
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
19 23 0.44
20 1 0.02
21 28 0.54
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (21 bp):
CATATCATATCTAAGATTGTA
Found at i:41008241 original size:19 final size:19
Alignment explanation
Indices: 41008197--41008260 Score: 92
Period size: 19 Copynumber: 3.3 Consensus size: 19
41008187 AAGATTGTAT
41008197 ATATCATATCTAAGATTGCAC
1 ATATCATATCTAAGATTG--C
*
41008218 ATATCATATTTAAGATTGC
1 ATATCATATCTAAGATTGC
*
41008237 ATATCATATCTAAGATTGT
1 ATATCATATCTAAGATTGC
41008256 ATATC
1 ATATC
41008261 CTCGAAAATT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
19 23 0.57
21 17 0.43
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.39
Consensus pattern (19 bp):
ATATCATATCTAAGATTGC
Found at i:41009077 original size:42 final size:42
Alignment explanation
Indices: 41009030--41009124 Score: 131
Period size: 42 Copynumber: 2.3 Consensus size: 42
41009020 ACCCACAAGA
*
41009030 GTTAAACGGAAGCTCATAAGAGCTGAAC-GAAAACCC-GTAGAG
1 GTTAAACGGAAGCTCAAAAGAGCTGAACTG-AAACCCAGTAG-G
* *
41009072 GTTAAACTGAAGCTCAAAAGAGCTGAACTGAAACCCATTAGG
1 GTTAAACGGAAGCTCAAAAGAGCTGAACTGAAACCCAGTAGG
41009114 GTTAAACGGAA
1 GTTAAACGGAA
41009125 ACTCGTATGA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
42 43 0.91
43 4 0.09
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.17
Consensus pattern (42 bp):
GTTAAACGGAAGCTCAAAAGAGCTGAACTGAAACCCAGTAGG
Found at i:41019961 original size:107 final size:106
Alignment explanation
Indices: 41019586--41020316 Score: 1050
Period size: 106 Copynumber: 6.9 Consensus size: 106
41019576 AAAAAATTCT
* *
41019586 TTTGGGTGCTGGCCTATCAATGCCCGGCACCCAGTACAATTTTAAAAAAAAAATTCTTTTTTTTT
1 TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAA-TTT--AAAAAAAATTCTTTTTTTTT
* * *
41019651 -GTGTCAGAGTCAAATATCAGTATACGAAAAAATTTAAAAAAAAA
63 CGTGTCAGAATCAGATATCAGTATACGAAAAAA-ATAAAAAAAAA
*
41019695 TTTGGGTG-TTGCTCTGTCAATGGCCGGCACCCAGTACAATTT-AAAAAAATTC-TTTTTTTTCG
1 TTTGGGTGCTGGC-CTGTCAATGGCCGGCACCCAGTACAATTTAAAAAAAATTCTTTTTTTTTCG
41019757 TGTCAGAATCAGATATCAGTATACGAAAAAAATATAAAAAAAAA
65 TGTCAGAATCAGATATCAGTATACG-AAAAAA-ATAAAAAAAAA
* **
41019801 TTTAGGTGCTGGCCTGTCAATGGCCAACACCCAGTACAATTTAAAAAAAATTCTTTTTTTTTCGT
1 TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTTAAAAAAAATTCTTTTTTTTTCGT
41019866 GTCAGAATCAGATATCAGTATACGAAAAAAAT-AAAAAAAA
66 GTCAGAATCAGATATCAGTATACGAAAAAAATAAAAAAAAA
41019906 TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTTTAAAAAAATATTCTTTTTTTTTC
1 TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAA-TTTAAAAAAA-ATTCTTTTTTTTTC
*
41019971 GTGTCAGAATTAGATATCAGTATACGAAAAAAAT-AAAAAAAA
64 GTGTCAGAATCAGATATCAGTATACGAAAAAAATAAAAAAAAA
*
41020013 TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTTAAAAAAAGATT-TCTTTTTTTCG
1 TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTTAAAAAAA-ATTCTTTTTTTTTCG
41020077 TGTCAGAATCAGATATCAGTATACGAAAAAAATAAAAAAAAA
65 TGTCAGAATCAGATATCAGTATACGAAAAAAATAAAAAAAAA
*
41020119 TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTTAAAAAAAGATT-TCTTTTTTTCG
1 TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTTAAAAAAA-ATTCTTTTTTTTTCG
*
41020183 TGTCAGAATCAGATATCAGTAT-CATAAAAAAATAAAAAAAAA
65 TGTCAGAATCAGATATCAGTATAC-GAAAAAAATAAAAAAAAA
* * *
41020225 TTTTGGGTGTTGGGTCTGTCAATGGCTGGCACCCAGTAC-ATTTAAAAAAAA---------TTTC
1 -TTTGGGTGCT-GGCCTGTCAATGGCCGGCACCCAGTACAATTTAAAAAAAATTCTTTTTTTTTC
*
41020280 GTGTCAGAATCAGATATCAATATACGAAAAAAATAAA
64 GTGTCAGAATCAGATATCAGTATACGAAAAAAATAAA
41020317 CATAATTATA
Statistics
Matches: 586, Mismatches: 23, Indels: 37
0.91 0.04 0.06
Matches are distributed among these distances:
98 37 0.06
99 1 0.00
104 8 0.01
105 121 0.21
106 188 0.32
107 133 0.23
108 66 0.11
109 32 0.05
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (106 bp):
TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTTAAAAAAAATTCTTTTTTTTTCGT
GTCAGAATCAGATATCAGTATACGAAAAAAATAAAAAAAAA
Found at i:41020818 original size:28 final size:28
Alignment explanation
Indices: 41020744--41020818 Score: 82
Period size: 28 Copynumber: 2.6 Consensus size: 28
41020734 CTATATATTT
41020744 TTTTGTAAATTTAGAATTTAGTTTGTATA
1 TTTT-TAAATTTAGAATTTAGTTTGTATA
**
41020773 TTTTTATTTTTAAGAATTTAG-TT-TATA
1 TTTTTAAATTT-AGAATTTAGTTTGTATA
41020800 TTTTTAAATATTACGAATT
1 TTTTTAAAT-TTA-GAATT
41020819 CATATATTCA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
27 12 0.31
28 14 0.36
29 13 0.33
ACGTcount: A:0.32, C:0.01, G:0.09, T:0.57
Consensus pattern (28 bp):
TTTTTAAATTTAGAATTTAGTTTGTATA
Found at i:41021202 original size:12 final size:12
Alignment explanation
Indices: 41021185--41021214 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
41021175 ACGTGCTTCA
41021185 GGGTGGAAGTCC
1 GGGTGGAAGTCC
41021197 GGGTGGAAGTCC
1 GGGTGGAAGTCC
41021209 GGGTGG
1 GGGTGG
41021215 TATGAGGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.13, C:0.13, G:0.57, T:0.17
Consensus pattern (12 bp):
GGGTGGAAGTCC
Found at i:41021519 original size:95 final size:97
Alignment explanation
Indices: 41021408--41021602 Score: 313
Period size: 97 Copynumber: 2.0 Consensus size: 97
41021398 AATAAAAAAA
* *
41021408 TTATTTTTTTCATATACTGATATCTGATTCTG-ACAAAAAAAATTTAAAATTGTACTGGGTGCCG
1 TTATTTTTTTCATATACTGAAATCTGACTCTGAACAAAAAAAATTTAAAATTGTACTGGGTGCCG
*
41021472 GCCATTGACAGGCCAACACCC-AAAATTTTTT
66 ACCATTGACAGGCCAACACCCAAAAATTTTTT
* *
41021503 TTATTTTTTTCCTATACTGAAATCTGACTCTGACACAAAAAAAATTTTAAATTGTACTGGGTGCC
1 TTATTTTTTTCATATACTGAAATCTGACTCTGA-ACAAAAAAAATTTAAAATTGTACTGGGTGCC
*
41021568 GACCATTGACAGGCCAGCACCCAAAAATTTTTT
65 GACCATTGACAGGCCAACACCCAAAAATTTTTT
41021601 TT
1 TT
41021603 TTTCGTTTTT
Statistics
Matches: 91, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
95 29 0.32
97 50 0.55
98 12 0.13
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.35
Consensus pattern (97 bp):
TTATTTTTTTCATATACTGAAATCTGACTCTGAACAAAAAAAATTTAAAATTGTACTGGGTGCCG
ACCATTGACAGGCCAACACCCAAAAATTTTTT
Found at i:41022943 original size:89 final size:90
Alignment explanation
Indices: 41022848--41023013 Score: 248
Period size: 90 Copynumber: 1.9 Consensus size: 90
41022838 ATAATATTAT
* *
41022848 TTTAATAAATTTAATA-TAATA-TTAAATTTAATACTTATCTTGAT-AGTATTTTATTAATTTAA
1 TTTAATAAATTTAATATTAA-ACTT-AATCTAATACTTATCTTGATAAGTATTATATTAATTTAA
*
41022910 TATTAAAGTTATTATTTTAGTATTAAA
64 TATTAAAGTGATTATTTTAGTATTAAA
* *
41022937 TTTAATAGATTTAATATTAAACTTAATCTAATATTTATCTTGATAAGTATTATATTAATTTAATA
1 TTTAATAAATTTAATATTAAACTTAATCTAATACTTATCTTGATAAGTATTATATTAATTTAATA
41023002 TTAAAGTGATTA
66 TTAAAGTGATTA
41023014 AATTTAATCA
Statistics
Matches: 69, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
89 34 0.49
90 35 0.51
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (90 bp):
TTTAATAAATTTAATATTAAACTTAATCTAATACTTATCTTGATAAGTATTATATTAATTTAATA
TTAAAGTGATTATTTTAGTATTAAA
Found at i:41022954 original size:21 final size:20
Alignment explanation
Indices: 41022902--41022963 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
41022892 AGTATTTTAT
* *
41022902 TAATTTAATATTAAAGTTAT
1 TAATTTAATATTAAACTTAA
* * *
41022922 TATTTTAGTATTAAATTTAA
1 TAATTTAATATTAAACTTAA
41022942 TAGATTTAATATTAAACTTAA
1 TA-ATTTAATATTAAACTTAA
41022963 T
1 T
41022964 CTAATATTTA
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
20 18 0.53
21 16 0.47
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.50
Consensus pattern (20 bp):
TAATTTAATATTAAACTTAA
Found at i:41023579 original size:27 final size:27
Alignment explanation
Indices: 41023543--41023596 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
41023533 ACTCAGAACT
41023543 GAGTTAGAGAGTATTTTAGACCTTGAG
1 GAGTTAGAGAGTATTTTAGACCTTGAG
*
41023570 GAGTTGGAGAGTATTTTAGACCTTGAG
1 GAGTTAGAGAGTATTTTAGACCTTGAG
41023597 CCTAAACAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.28, C:0.07, G:0.31, T:0.33
Consensus pattern (27 bp):
GAGTTAGAGAGTATTTTAGACCTTGAG
Found at i:41026751 original size:26 final size:26
Alignment explanation
Indices: 41026722--41026774 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
41026712 ATTGTTTTTA
* *
41026722 ATCTCA-CTGCTACATTATCTAATCTC
1 ATCTCATC-GCTACAGTAACTAATCTC
41026748 ATCTCATCGCTACAGTAACTAATCTC
1 ATCTCATCGCTACAGTAACTAATCTC
41026774 A
1 A
41026775 CCATCACCAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 23 0.96
27 1 0.04
ACGTcount: A:0.30, C:0.30, G:0.06, T:0.34
Consensus pattern (26 bp):
ATCTCATCGCTACAGTAACTAATCTC
Found at i:41030854 original size:78 final size:79
Alignment explanation
Indices: 41030720--41030871 Score: 236
Period size: 78 Copynumber: 1.9 Consensus size: 79
41030710 TATTTATCCC
* * *
41030720 AATTTAAATCATTAATTAATTTTTTCAAATATAGATTGAAAATAATTAAATAATTATATGCTAAG
1 AATTTAAATCATTAATTAATTTTTTCAAAAATAGATCGAAAATAAATAAATAATTATATGCTAAG
*
41030785 TGAATTTTAATTAT
66 TGAAGTTTAATTAT
*
41030799 AATTTAAATCATTAATT-ATTTTTTCAAAAATAGATCGACAAA-AAATAAATTATTATATGCTAA
1 AATTTAAATCATTAATTAATTTTTTCAAAAATAGATCGA-AAATAAATAAATAATTATATGCTAA
41030862 GTGAAGTTTA
65 GTGAAGTTTA
41030872 CGTCAGTTTG
Statistics
Matches: 67, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
78 47 0.70
79 20 0.30
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.41
Consensus pattern (79 bp):
AATTTAAATCATTAATTAATTTTTTCAAAAATAGATCGAAAATAAATAAATAATTATATGCTAAG
TGAAGTTTAATTAT
Found at i:41031542 original size:29 final size:30
Alignment explanation
Indices: 41031480--41031549 Score: 90
Period size: 29 Copynumber: 2.3 Consensus size: 30
41031470 ACTGCAAAAA
* *
41031480 TAGTCACTTTTGTTTGCCACATATTACATTT
1 TAGTCACTTATGTTTG-CAAATATTACATTT
41031511 TAGTCACTTATGTTTG-AAATATTATC-TTT
1 TAGTCACTTATGTTTGCAAATATTA-CATTT
41031540 TAGTCACTTA
1 TAGTCACTTA
41031550 CGTAGTAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
29 20 0.56
30 1 0.03
31 15 0.42
ACGTcount: A:0.26, C:0.16, G:0.10, T:0.49
Consensus pattern (30 bp):
TAGTCACTTATGTTTGCAAATATTACATTT
Found at i:41037076 original size:29 final size:30
Alignment explanation
Indices: 41037014--41037083 Score: 90
Period size: 29 Copynumber: 2.3 Consensus size: 30
41037004 ACTGCAAAAA
* *
41037014 TAGTCACTTTTGTTTGCCACATATTACATTT
1 TAGTCACTTATGTTTG-CAAATATTACATTT
41037045 TAGTCACTTATGTTTG-AAATATTATC-TTT
1 TAGTCACTTATGTTTGCAAATATTA-CATTT
41037074 TAGTCACTTA
1 TAGTCACTTA
41037084 CGTAGTAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
29 20 0.56
30 1 0.03
31 15 0.42
ACGTcount: A:0.26, C:0.16, G:0.10, T:0.49
Consensus pattern (30 bp):
TAGTCACTTATGTTTGCAAATATTACATTT
Found at i:41042905 original size:91 final size:90
Alignment explanation
Indices: 41042756--41042924 Score: 230
Period size: 91 Copynumber: 1.9 Consensus size: 90
41042746 TACCCACAAA
* * * * *
41042756 TTACTTGCAACTTTTATCTGCAAACTTGTTGTGTATTCACAACCACTGGCAGCGTATTAACCTAC
1 TTACTGGCAACTTTTATCTGCAAACTCGTTGTGTATTCAAAACCACCGACAGCGTATTAACCTAC
41042821 AAACACTAGTGGTTTATCCATAATTT
66 -AACACTAGTGGTTTATCCATAATTT
* * * * *
41042847 TTACTGGCAACTTTTATTTGCAAACTCGTTGTGTATTCAAAACTACCGATAGCTTATTAACCTGC
1 TTACTGGCAACTTTTATCTGCAAACTCGTTGTGTATTCAAAACCACCGACAGCGTATTAACCTAC
*
41042912 AATACTAGTGGTT
66 AACACTAGTGGTT
41042925 CATCAATGAC
Statistics
Matches: 67, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
90 12 0.18
91 55 0.82
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (90 bp):
TTACTGGCAACTTTTATCTGCAAACTCGTTGTGTATTCAAAACCACCGACAGCGTATTAACCTAC
AACACTAGTGGTTTATCCATAATTT
Found at i:41046107 original size:39 final size:40
Alignment explanation
Indices: 41046026--41046181 Score: 174
Period size: 39 Copynumber: 3.9 Consensus size: 40
41046016 CCGGCTTACT
* * * * *
41046026 GATTAGGCAC-TTATGTGCCGACTACTGTTACTGTTA-CT
1 GATTCGGCACTTTGTGTGTCGAATACTGTTACTGTTATCA
41046064 GATTCGGCACTTTGTGTGTCGAATACTGTTACTGTTATC-
1 GATTCGGCACTTTGTGTGTCGAATACTGTTACTGTTATCA
*
41046103 GATTCGGCACTTTGTGTGTCGAATACTGTTACCGTTACTGTTACA
1 GATTCGGCACTTTGTGTGTCGAATACTGTTACTGTTA----T-CA
* *
41046148 GATTCAGCACTTTGTGTGTTGAATACTGTTACTG
1 GATTCGGCACTTTGTGTGTCGAATACTGTTACTG
41046182 CTACCGTTAC
Statistics
Matches: 102, Mismatches: 8, Indels: 9
0.86 0.07 0.08
Matches are distributed among these distances:
38 9 0.09
39 59 0.58
40 1 0.01
43 1 0.01
44 1 0.01
45 31 0.30
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.39
Consensus pattern (40 bp):
GATTCGGCACTTTGTGTGTCGAATACTGTTACTGTTATCA
Found at i:41046191 original size:45 final size:45
Alignment explanation
Indices: 41046048--41046196 Score: 202
Period size: 45 Copynumber: 3.4 Consensus size: 45
41046038 ATGTGCCGAC
41046048 TACTGTTACTGTTACTGATTCGGCACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACTGATTCGGCACTTTGTGTGTCGAATACTGT
41046093 TACTGTTA----T-C-GATTCGGCACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACTGATTCGGCACTTTGTGTGTCGAATACTGT
* * * *
41046132 TACCGTTACTGTTACAGATTCAGCACTTTGTGTGTTGAATACTGT
1 TACTGTTACTGTTACTGATTCGGCACTTTGTGTGTCGAATACTGT
* *
41046177 TACTGCTACCGTTACTGATT
1 TACTGTTACTGTTACTGATT
41046197 ACTGTATACT
Statistics
Matches: 91, Mismatches: 7, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
39 36 0.40
40 1 0.01
41 1 0.01
43 1 0.01
44 1 0.01
45 51 0.56
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.41
Consensus pattern (45 bp):
TACTGTTACTGTTACTGATTCGGCACTTTGTGTGTCGAATACTGT
Found at i:41051143 original size:20 final size:20
Alignment explanation
Indices: 41051126--41051168 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
41051116 TATGACAATG
41051126 TTTAAAAATTTTATACAAAA
1 TTTAAAAATTTTATACAAAA
**
41051146 TTTTTAAATTTTATACAAAA
1 TTTAAAAATTTTATACAAAA
41051166 TTT
1 TTT
41051169 TGAAAACAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (20 bp):
TTTAAAAATTTTATACAAAA
Found at i:41051147 original size:12 final size:12
Alignment explanation
Indices: 41051130--41051169 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
41051120 ACAATGTTTA
41051130 AAAATTTTATAC
1 AAAATTTTATAC
41051142 AAAATTTT-T--
1 AAAATTTTATAC
41051151 -AAATTTTATAC
1 AAAATTTTATAC
41051162 AAAATTTT
1 AAAATTTT
41051170 GAAAACAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
8 7 0.29
9 1 0.04
11 1 0.04
12 15 0.62
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (12 bp):
AAAATTTTATAC
Found at i:41051169 original size:20 final size:20
Alignment explanation
Indices: 41051131--41051169 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
41051121 CAATGTTTAA
41051131 AAATTTTATACAAAATTTTT
1 AAATTTTATACAAAATTTTT
41051151 AAATTTTATACAAAATTTT
1 AAATTTTATACAAAATTTT
41051170 GAAAACAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (20 bp):
AAATTTTATACAAAATTTTT
Found at i:41058606 original size:81 final size:82
Alignment explanation
Indices: 41058514--41058664 Score: 207
Period size: 81 Copynumber: 1.8 Consensus size: 82
41058504 CCTAAAAAGG
*** * *
41058514 AAAAAAATTTCAATTTTGTCCTCTTATATATAAAGAA-ACTATAAATTAATATA-GTGAAATTAC
1 AAAAAAATTTCAATTCAATCCTCTTATAAATAAAGAATA-TATAAATTAATATATGTAAAATTAC
41058577 ACTTTGACTCCCCAAAAT
65 ACTTTGACTCCCCAAAAT
* *
41058595 AAAAAATTTTCAATTCAATCCTCTTATAAATAAAGAATATATATATTAATATATTGTAAAATTAC
1 AAAAAAATTTCAATTCAATCCTCTTATAAATAAAGAATATATAAATTAATATA-TGTAAAATTAC
41058660 ACTTT
65 ACTTT
41058665 AACCCTCTAA
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
81 45 0.75
82 1 0.02
83 14 0.23
ACGTcount: A:0.46, C:0.13, G:0.05, T:0.37
Consensus pattern (82 bp):
AAAAAAATTTCAATTCAATCCTCTTATAAATAAAGAATATATAAATTAATATATGTAAAATTACA
CTTTGACTCCCCAAAAT
Found at i:41059649 original size:20 final size:21
Alignment explanation
Indices: 41059608--41059649 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
41059598 ATATGGTAGG
*
41059608 TATATACTGTTTACAATTTGA
1 TATATACTGTTTACAATATGA
41059629 TATATA-TGTTTTA-AATATGA
1 TATATACTG-TTTACAATATGA
41059649 T
1 T
41059650 TTACGTTAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.36, C:0.05, G:0.10, T:0.50
Consensus pattern (21 bp):
TATATACTGTTTACAATATGA
Found at i:41065018 original size:31 final size:32
Alignment explanation
Indices: 41064980--41065050 Score: 94
Period size: 31 Copynumber: 2.3 Consensus size: 32
41064970 AAGCATGCCC
*
41064980 ATATTATTTTTAAT-TTTTAA-ATATTTATATT
1 ATATTATTTTTAATATTTTAATAT-TTTATAAT
41065011 ATATTA-TTTTAATATTTTAATATTTTATAAT
1 ATATTATTTTTAATATTTTAATATTTTATAAT
*
41065042 ATTTTATTT
1 ATATTATTT
41065051 ATTGAACTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
30 7 0.20
31 24 0.69
32 4 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (32 bp):
ATATTATTTTTAATATTTTAATATTTTATAAT
Found at i:41065043 original size:10 final size:10
Alignment explanation
Indices: 41064984--41065048 Score: 59
Period size: 10 Copynumber: 6.8 Consensus size: 10
41064974 ATGCCCATAT
41064984 TATTTT-TAA
1 TATTTTATAA
41064993 T-TTTTA-AA
1 TATTTTATAA
*
41065001 TATTTATATTA
1 TATTT-TATAA
*
41065012 TATTATTTTAA
1 TATT-TTATAA
41065023 TA-TTT-TAA
1 TATTTTATAA
41065031 TATTTTATAA
1 TATTTTATAA
41065041 TATTTTAT
1 TATTTTAT
41065049 TTATTGAACT
Statistics
Matches: 46, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
8 12 0.26
9 9 0.20
10 14 0.30
11 10 0.22
12 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
TATTTTATAA
Found at i:41074681 original size:21 final size:19
Alignment explanation
Indices: 41074643--41074686 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
41074633 GAGTGAGAAG
*
41074643 TAAAAATTTAGGGGAAAAA
1 TAAAAATTTAGGGAAAAAA
*
41074662 TAAAAAGTTTGAGGGAAAAAG
1 TAAAAA-TTT-AGGGAAAAAA
41074683 TAAA
1 TAAA
41074687 TAGGGGAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 6 0.29
20 3 0.14
21 12 0.57
ACGTcount: A:0.57, C:0.00, G:0.23, T:0.20
Consensus pattern (19 bp):
TAAAAATTTAGGGAAAAAA
Found at i:41087414 original size:31 final size:31
Alignment explanation
Indices: 41087346--41087407 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
41087336 GATTTAATTA
* *
41087346 AAAACTTTCAAATAATTTAATAACTTAAATG
1 AAAACTTTCAAATAATTTAATAACTGAAACG
* *
41087377 AAAACTTTCTAATAATTTAATGACTGAAACG
1 AAAACTTTCAAATAATTTAATAACTGAAACG
41087408 TGAACTTACT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.48, C:0.11, G:0.06, T:0.34
Consensus pattern (31 bp):
AAAACTTTCAAATAATTTAATAACTGAAACG
Found at i:41088798 original size:269 final size:270
Alignment explanation
Indices: 41088498--41089036 Score: 1071
Period size: 269 Copynumber: 2.0 Consensus size: 270
41088488 TTAGATAGTT
41088498 TTGAATAAAAGATACATATGGTAACTTGAATATTTCATTTAAAAAAAGATAATTTATTCAACATT
1 TTGAATAAAAGATACATATGGTAACTTGAATATTTCATTTAAAAAAAGATAATTTATTCAACATT
41088563 TTTTTAAAAAAAAATTATATTAAATAAAAAAATTAAAATAATTATCAAATGCATTTAAAATATTA
66 TTTTTAAAAAAAAATTATATTAAATAAAAAAATTAAAATAATTATCAAATGCATTTAAAATATTA
41088628 AATGTTGAAATTTTTTATTTTCAATGGGTTATCAAGCACACCATAAATTTGGTGATTAACCTTTC
131 AATGTTGAAATTTTTTATTTTCAATGGGTTATCAAGCACACCATAAATTTGGTGATTAACCTTTC
41088693 AAAAAGAGTCAAATTGTTTTTTTTATTGAAAATGTTGACTAAAACGTTAATTTCTTTAATGATGT
196 AAAAAGAGTCAAATTGTTTTTTTTATTGAAAATGTTGACTAAAACGTTAATTTCTTTAATGATGT
41088758 TGGTGTGATA
261 TGGTGTGATA
41088768 TTGAATAAAA-ATACATATGGTAACTTGAATATTTCATTTAAAAAAAGATAATTTATTCAACATT
1 TTGAATAAAAGATACATATGGTAACTTGAATATTTCATTTAAAAAAAGATAATTTATTCAACATT
41088832 TTTTTAAAAAAAAATTATATTAAATAAAAAAATTAAAATAATTATCAAATGCATTTAAAATATTA
66 TTTTTAAAAAAAAATTATATTAAATAAAAAAATTAAAATAATTATCAAATGCATTTAAAATATTA
41088897 AATGTTGAAATTTTTTATTTTCAATGGGTTATCAAGCACACCATAAATTTGGTGATTAACCTTTC
131 AATGTTGAAATTTTTTATTTTCAATGGGTTATCAAGCACACCATAAATTTGGTGATTAACCTTTC
41088962 AAAAAGAGTCAAATTGTTTTTTTTATTGAAAATGTTGACTAAAACGTTAATTTCTTTAATGATGT
196 AAAAAGAGTCAAATTGTTTTTTTTATTGAAAATGTTGACTAAAACGTTAATTTCTTTAATGATGT
41089027 TGGTGTGATA
261 TGGTGTGATA
41089037 AACTCACATA
Statistics
Matches: 269, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
269 259 0.96
270 10 0.04
ACGTcount: A:0.42, C:0.07, G:0.11, T:0.40
Consensus pattern (270 bp):
TTGAATAAAAGATACATATGGTAACTTGAATATTTCATTTAAAAAAAGATAATTTATTCAACATT
TTTTTAAAAAAAAATTATATTAAATAAAAAAATTAAAATAATTATCAAATGCATTTAAAATATTA
AATGTTGAAATTTTTTATTTTCAATGGGTTATCAAGCACACCATAAATTTGGTGATTAACCTTTC
AAAAAGAGTCAAATTGTTTTTTTTATTGAAAATGTTGACTAAAACGTTAATTTCTTTAATGATGT
TGGTGTGATA
Found at i:41098194 original size:23 final size:22
Alignment explanation
Indices: 41098160--41098236 Score: 70
Period size: 23 Copynumber: 3.5 Consensus size: 22
41098150 TTTTTTTGTA
* *
41098160 AATTTCAAAATTTTGTATTTTT
1 AATTTTAAAATTTAGTATTTTT
*
41098182 AATTTTAAGAATTTAGTTTTTTT
1 AATTTTAA-AATTTAGTATTTTT
* *
41098205 AATTTTCAGATTTA--A-TTTT
1 AATTTTAAAATTTAGTATTTTT
41098224 AATTATTAAAATT
1 AATT-TTAAAATT
41098237 ATTAAAATTA
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
19 8 0.18
20 6 0.13
22 12 0.27
23 19 0.42
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (22 bp):
AATTTTAAAATTTAGTATTTTT
Found at i:41098238 original size:9 final size:9
Alignment explanation
Indices: 41098224--41098250 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
41098214 ATTTAATTTT
41098224 AATTATTAA
1 AATTATTAA
41098233 AATTATTAA
1 AATTATTAA
41098242 AATTATTAA
1 AATTATTAA
41098251 TATGATATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
AATTATTAA
Found at i:41098600 original size:7 final size:7
Alignment explanation
Indices: 41098584--41098646 Score: 80
Period size: 7 Copynumber: 9.4 Consensus size: 7
41098574 CAATATTATT
41098584 AAAA-AA
1 AAAATAA
41098590 AAAATAA
1 AAAATAA
41098597 AAAATAA
1 AAAATAA
41098604 AAAATAA
1 AAAATAA
41098611 AAAATAA
1 AAAATAA
41098618 AAAAT--
1 AAAATAA
41098623 -AAATAA
1 AAAATAA
*
41098629 AAAATTTA
1 AAAA-TAA
41098637 AAAATAA
1 AAAATAA
41098644 AAA
1 AAA
41098647 TACATGAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
4 4 0.08
6 4 0.08
7 36 0.72
8 6 0.12
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (7 bp):
AAAATAA
Found at i:41098619 original size:32 final size:33
Alignment explanation
Indices: 41098583--41098646 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
41098573 GCAATATTAT
41098583 TAAAAAAAAAATAAAAAA-TAAAAAATAAAAAA
1 TAAAAAAAAAATAAAAAATTAAAAAATAAAAAA
* *
41098615 TAAAAAATAAATAAAAAATTTAAAAATAAAAA
1 TAAAAAAAAAATAAAAAATTAAAAAATAAAAA
41098647 TACATGAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (33 bp):
TAAAAAAAAAATAAAAAATTAAAAAATAAAAAA
Found at i:41098647 original size:14 final size:13
Alignment explanation
Indices: 41098581--41098647 Score: 66
Period size: 13 Copynumber: 5.2 Consensus size: 13
41098571 TAGCAATATT
41098581 ATTAAAAA-AAAA
1 ATTAAAAATAAAA
*
41098593 ATAAAAAATAAAAA
1 ATTAAAAAT-AAAA
*
41098607 ATAAAAAATAAAA
1 ATTAAAAATAAAA
*
41098620 AATAAATAA-AAAA
1 ATTAAA-AATAAAA
*
41098633 TTTAAAAATAAAA
1 ATTAAAAATAAAA
41098646 AT
1 AT
41098648 ACATGAAAAG
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
12 9 0.20
13 21 0.47
14 15 0.33
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (13 bp):
ATTAAAAATAAAA
Found at i:41098656 original size:26 final size:25
Alignment explanation
Indices: 41098583--41098646 Score: 85
Period size: 25 Copynumber: 2.5 Consensus size: 25
41098573 GCAATATTAT
*
41098583 TAAAAAA-AAAATAAAAAATAAAAAA
1 TAAAAAATAAAA-AATAAATAAAAAA
41098608 TAAAAAATAAAAAATAAATAAAAAA
1 TAAAAAATAAAAAATAAATAAAAAA
*
41098633 TTTAAAAATAAAAA
1 -TAAAAAATAAAAA
41098647 TACATGAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
25 19 0.54
26 16 0.46
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (25 bp):
TAAAAAATAAAAAATAAATAAAAAA
Found at i:41104467 original size:86 final size:86
Alignment explanation
Indices: 41104320--41104492 Score: 310
Period size: 86 Copynumber: 2.0 Consensus size: 86
41104310 ATCTTATTTT
* *
41104320 GGGGTTTTGGTTGTTGGGGGGGGGGGTTTGGGGGGGGGAAGAGAAAAAGAGAATGGGATTAGGAT
1 GGGGTTTTGGTTGTTGGGGGGGGGGGTTTGAGGGAGGGAAGAGAAAAAGAGAATGGGATTAGGAT
41104385 GTTTAGTATTTGATATAAATG
66 GTTTAGTATTTGATATAAATG
* *
41104406 GGGGTTTTGGTTGTTGGGGGGGGGGGTTTGAGGGAGGGAAGAGAAATAGAGAATGGTATTAGGAT
1 GGGGTTTTGGTTGTTGGGGGGGGGGGTTTGAGGGAGGGAAGAGAAAAAGAGAATGGGATTAGGAT
41104471 GTTTAGTATTTGATATAAATG
66 GTTTAGTATTTGATATAAATG
41104492 G
1 G
41104493 TGTCATTGTG
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
86 83 1.00
ACGTcount: A:0.25, C:0.00, G:0.45, T:0.30
Consensus pattern (86 bp):
GGGGTTTTGGTTGTTGGGGGGGGGGGTTTGAGGGAGGGAAGAGAAAAAGAGAATGGGATTAGGAT
GTTTAGTATTTGATATAAATG
Found at i:41106965 original size:98 final size:99
Alignment explanation
Indices: 41106795--41106992 Score: 274
Period size: 98 Copynumber: 2.0 Consensus size: 99
41106785 TTTCTGCCAA
* * *
41106795 TGACAAGTTCTCAATGGCTAAGGAAAAAGTATCATGGATATCTTGTGTTAAGAGTAATATTATAT
1 TGACAAGTTCTCAATGGCTAAGGAAAAAGTATCATGGATACCTTGTGTTAAGAGTAAGATTACAT
*
41106860 TTTGATCCTATTTAAAAAATAGATAAATTAGTCC
66 TTTGATCCTATTTAAAAAATAGACAAATTAGTCC
* * * *
41106894 TGACAAGTTCTCGATGGC-CAGGTAAAAA-TATCATGGATGCCTTGTGTTAAGAGTAAGATTGCA
1 TGACAAGTTCTCAATGGCTAAGG-AAAAAGTATCATGGATACCTTGTGTTAAGAGTAAGATTACA
* * *
41106957 TTTTGATCCTATTTAAGAAATGGGCAAATTAGTCC
65 TTTTGATCCTATTTAAAAAATAGACAAATTAGTCC
41106992 T
1 T
41106993 TGTACGTTAG
Statistics
Matches: 87, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
98 65 0.75
99 22 0.25
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.34
Consensus pattern (99 bp):
TGACAAGTTCTCAATGGCTAAGGAAAAAGTATCATGGATACCTTGTGTTAAGAGTAAGATTACAT
TTTGATCCTATTTAAAAAATAGACAAATTAGTCC
Found at i:41118901 original size:107 final size:107
Alignment explanation
Indices: 41118688--41118890 Score: 243
Period size: 107 Copynumber: 1.9 Consensus size: 107
41118678 ACGTGACTGA
41118688 CTGAGTAACCGGGGTGGGGTGCTTGGGTTGTTATTCCACTTTGCGTCAAAAAATCCAAAACATTC
1 CTGAGTAACCGGGGTGGGGTGCTTGGGTTGTTATTCCACTTTGCGTCAAAAAATCCAAAACATTC
* * * ** *
41118753 TTAACAAAATATATATAATAAAAAAATTAAGAGTGTGTTGGG
66 TTAACAAAATAGATAAAAGAAAAAAAAAAAAAGTGTGTTGGG
** ** *
41118795 CTGAGTAACCGGGGTGGGGTGCTTGGGTTGTTA-TCTTTCTTTGCGTCAAAAGGGT-CAATACAT
1 CTGAGTAACCGGGGTGGGGTGCTTGGGTTGTTATTC-CACTTTGCGTCAAAA-AATCCAAAACAT
*
41118858 TCTTAAGAAAA-AGA-AAAAGAAAACAAAAAAAAA
64 TCTTAACAAAATAGATAAAAGAAAA-AAAAAAAAA
41118891 TTGCATTTGG
Statistics
Matches: 81, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
105 7 0.09
106 10 0.12
107 63 0.78
108 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.28
Consensus pattern (107 bp):
CTGAGTAACCGGGGTGGGGTGCTTGGGTTGTTATTCCACTTTGCGTCAAAAAATCCAAAACATTC
TTAACAAAATAGATAAAAGAAAAAAAAAAAAAGTGTGTTGGG
Found at i:41118962 original size:16 final size:16
Alignment explanation
Indices: 41118941--41118972 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
41118931 TGTAGGTTTA
41118941 GTAAATTACCTAATTT
1 GTAAATTACCTAATTT
41118957 GTAAATTACCTAATTT
1 GTAAATTACCTAATTT
41118973 TCATGAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (16 bp):
GTAAATTACCTAATTT
Found at i:41119512 original size:12 final size:12
Alignment explanation
Indices: 41119492--41119524 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
41119482 TAAGATATTA
*
41119492 TTTAGATTTAAT
1 TTTATATTTAAT
41119504 TTTATATTTAAT
1 TTTATATTTAAT
41119516 TTT-TATTTA
1 TTTATATTTA
41119525 TCTTTTAGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (12 bp):
TTTATATTTAAT
Found at i:41122847 original size:67 final size:67
Alignment explanation
Indices: 41122730--41122862 Score: 178
Period size: 67 Copynumber: 2.0 Consensus size: 67
41122720 TTTTAATTGT
* * * *
41122730 TTAATATTAAATTAAATTTAATACTTATCTTAATAGTATTTTATTAATTTAATATTAAAGTGATT
1 TTAATATTAAATTAAATCTAATAC-TATCTTAATAATATTATATTAATTTAATATTAAAGCGATT
41122795 ATC
65 ATC
* **
41122798 TTAATATTAAATTTAATCTAATA-TATCTTGGTAAATATTATATTAATTTAATATTAAAGCGATT
1 TTAATATTAAATTAAATCTAATACTATCTTAAT-AATATTATATTAATTTAATATTAAAGCGATT
41122862 A
65 A
41122863 AGTTTAATCA
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
66 7 0.12
67 29 0.51
68 21 0.37
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.48
Consensus pattern (67 bp):
TTAATATTAAATTAAATCTAATACTATCTTAATAATATTATATTAATTTAATATTAAAGCGATTA
TC
Found at i:41125438 original size:26 final size:26
Alignment explanation
Indices: 41125404--41125455 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
41125394 CAATTAAGTG
41125404 ATCAAATTGCTTCTTGTGCAATCCTT
1 ATCAAATTGCTTCTTGTGCAATCCTT
41125430 ATCAAATTGCTTCTTGTGCAATCCTT
1 ATCAAATTGCTTCTTGTGCAATCCTT
41125456 TTGAAAGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.42
Consensus pattern (26 bp):
ATCAAATTGCTTCTTGTGCAATCCTT
Found at i:41136474 original size:114 final size:115
Alignment explanation
Indices: 41136330--41136558 Score: 451
Period size: 114 Copynumber: 2.0 Consensus size: 115
41136320 TTTTTTTTAA
41136330 ATATAAAATTTGAATATTATTAATAAAAATATAGGTAAAAAACATTTATAATTTTTTTTATGTTT
1 ATATAAAATTTGAATATTATTAATAAAAATATAGGTAAAAAACATTTATAATTTTTTTTATGTTT
41136395 TTCAAAAATAAAAGATCTCTTTTTTAAAATTTCACCAACTAAATGGATGT
66 TTCAAAAATAAAAGATCTCTTTTTTAAAATTTCACCAACTAAATGGATGT
41136445 ATATAAAA-TTGAATATTATTAATAAAAATATAGGTAAAAAACATTTATAATTTTTTTTATGTTT
1 ATATAAAATTTGAATATTATTAATAAAAATATAGGTAAAAAACATTTATAATTTTTTTTATGTTT
41136509 TTCAAAAATAAAAGATCTCTTTTTTAAAATTTCACCAACTAAATGGATGT
66 TTCAAAAATAAAAGATCTCTTTTTTAAAATTTCACCAACTAAATGGATGT
41136559 TTTTTTTAAC
Statistics
Matches: 114, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
114 106 0.93
115 8 0.07
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (115 bp):
ATATAAAATTTGAATATTATTAATAAAAATATAGGTAAAAAACATTTATAATTTTTTTTATGTTT
TTCAAAAATAAAAGATCTCTTTTTTAAAATTTCACCAACTAAATGGATGT
Found at i:41139930 original size:10 final size:10
Alignment explanation
Indices: 41139917--41139952 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
41139907 CTTTTCTTTC
41139917 ATTTTTATGA
1 ATTTTTATGA
*
41139927 ATTTTTATAA
1 ATTTTTATGA
41139937 ATTTTT-TGA
1 ATTTTTATGA
41139946 ATTTTTA
1 ATTTTTA
41139953 ATTTTGTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.64
Consensus pattern (10 bp):
ATTTTTATGA
Found at i:41141582 original size:18 final size:17
Alignment explanation
Indices: 41141539--41141582 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
41141529 TTTTTAAGCT
41141539 TGTAATGTTTTATATTTA
1 TGTAAT-TTTTATATTTA
* *
41141557 TATTATTTTTATATATTA
1 TGTAATTTTTATAT-TTA
41141575 TGTAATTT
1 TGTAATTT
41141583 ATAACACAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.64
Consensus pattern (17 bp):
TGTAATTTTTATATTTA
Found at i:41144937 original size:25 final size:25
Alignment explanation
Indices: 41144903--41145011 Score: 155
Period size: 25 Copynumber: 4.4 Consensus size: 25
41144893 CGGACACACC
***
41144903 ACAGCTCGTATGAGCTTTTTGATTT
1 ACAGCTCGTATGAGCTTCCCGATTT
41144928 ACAGCTCGTATGAGCTTCCCGATTT
1 ACAGCTCGTATGAGCTTCCCGATTT
* *
41144953 GCAGCTCGTATGAGCTTCCCAATTT
1 ACAGCTCGTATGAGCTTCCCGATTT
* *
41144978 GCAGCTCGTATGAGCTTCCCGATTC
1 ACAGCTCGTATGAGCTTCCCGATTT
41145003 ACAGCTCGT
1 ACAGCTCGT
41145012 GAGAGTATAC
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 76 1.00
ACGTcount: A:0.19, C:0.27, G:0.21, T:0.33
Consensus pattern (25 bp):
ACAGCTCGTATGAGCTTCCCGATTT
Found at i:41145046 original size:25 final size:25
Alignment explanation
Indices: 41144902--41145046 Score: 103
Period size: 25 Copynumber: 5.8 Consensus size: 25
41144892 GCGGACACAC
* ***
41144902 CACAGCTCGTATGAGCTTTTTGATT
1 CACAGCTCGTATGAGCATACCGATT
* * *
41144927 TACAGCTCGTATGAGCTTCCCGATT
1 CACAGCTCGTATGAGCATACCGATT
** * * *
41144952 TGCAGCTCGTATGAGCTTCCCAATT
1 CACAGCTCGTATGAGCATACCGATT
** * *
41144977 TGCAGCTCGTATGAGCTTCCCGATT
1 CACAGCTCGTATGAGCATACCGATT
* *
41145002 CACAGCTCGTGA-GAGTATACTGATT
1 CACAGCTCGT-ATGAGCATACCGATT
*
41145027 CATAGCTCGTATGAGCATAC
1 CACAGCTCGTATGAGCATAC
41145047 ATGAATATAA
Statistics
Matches: 103, Mismatches: 15, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
24 1 0.01
25 101 0.98
26 1 0.01
ACGTcount: A:0.22, C:0.25, G:0.21, T:0.32
Consensus pattern (25 bp):
CACAGCTCGTATGAGCATACCGATT
Done.