Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold48
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: 4619657
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 18863 characters in sequence are not A, C, G, or T
File 8 of 27
Found at i:1022004 original size:19 final size:20
Alignment explanation
Indices: 1021982--1022027 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
1021972 ATTTTTTAAT
*
1021982 ATAAATATAAAATA-TAAAA
1 ATAAATATAAAATAGGAAAA
*
1022001 ATAAATACAAAATAGGAAAA
1 ATAAATATAAAATAGGAAAA
1022021 A-AAATAT
1 ATAAATAT
1022028 GAATTTGCTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.72, C:0.02, G:0.04, T:0.22
Consensus pattern (20 bp):
ATAAATATAAAATAGGAAAA
Found at i:1023459 original size:15 final size:16
Alignment explanation
Indices: 1023420--1023460 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
1023410 TGATCCTGTT
1023420 TAAA-TTATTTTTTAA
1 TAAATTTATTTTTTAA
* *
1023435 TTAATATATTTTTTAA
1 TAAATTTATTTTTTAA
1023451 -AAATTTATTT
1 TAAATTTATTT
1023461 ATAAAAATAT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TAAATTTATTTTTTAA
Found at i:1023959 original size:16 final size:16
Alignment explanation
Indices: 1023938--1023984 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
1023928 GATATATTTA
1023938 TAATTTTTTATTAATT
1 TAATTTTTTATTAATT
*
1023954 TAATTTATTTA-AAATT
1 TAATTT-TTTATTAATT
1023970 TAAATTATTTTATTA
1 T-AATT-TTTTATTA
1023985 TCTGTTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
16 11 0.44
17 12 0.48
18 2 0.08
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TAATTTTTTATTAATT
Found at i:1024788 original size:17 final size:17
Alignment explanation
Indices: 1024751--1024802 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
1024741 TTTTTTTAAA
*
1024751 TATTTAAATATATTTAATT
1 TATTTAAA-AT-TTAAATT
1024770 TATTTAAAATTTAAATT
1 TATTTAAAATTTAAATT
**
1024787 TATTTATTATTTAAAT
1 TATTTAAAATTTAAAT
1024803 AGTTCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
17 20 0.67
18 2 0.07
19 8 0.27
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TATTTAAAATTTAAATT
Found at i:1024790 original size:26 final size:27
Alignment explanation
Indices: 1024739--1024803 Score: 91
Period size: 26 Copynumber: 2.5 Consensus size: 27
1024729 AATATTTATA
*
1024739 AATTTTTTTAAATATTTAAATATATTT
1 AATTTATTTAAATATTTAAATATATTT
*
1024766 AATTTATTTAAA-ATTTAAATTTATTT
1 AATTTATTTAAATATTTAAATATATTT
1024792 -A-TTATTTAAATA
1 AATTTATTTAAATA
1024804 GTTCTATTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 9 0.26
25 2 0.06
26 13 0.37
27 11 0.31
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (27 bp):
AATTTATTTAAATATTTAAATATATTT
Found at i:1024860 original size:17 final size:17
Alignment explanation
Indices: 1024849--1024889 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1024839 TATTTGTCAT
*
1024849 ATATTTAAATTTATTAA
1 ATATTTAAATTTATCAA
*
1024866 ATATTTAAATTTATTAA
1 ATATTTAAATTTATCAA
1024883 ATTATTT
1 A-TATTT
1024890 TTAAAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 18 0.78
18 5 0.22
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATATTTAAATTTATCAA
Found at i:1024865 original size:9 final size:9
Alignment explanation
Indices: 1024853--1024885 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
1024843 TGTCATATAT
1024853 TTAAATTTA
1 TTAAATTTA
*
1024862 TTAAATAT-
1 TTAAATTTA
1024870 TTAAATTTA
1 TTAAATTTA
1024879 TTAAATT
1 TTAAATT
1024886 ATTTTTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (9 bp):
TTAAATTTA
Found at i:1024908 original size:12 final size:12
Alignment explanation
Indices: 1024893--1024928 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
1024883 ATTATTTTTA
1024893 AAAATAAAATAT
1 AAAATAAAATAT
1024905 AAAATAAAATA-
1 AAAATAAAATAT
*
1024916 AAAATTAAATAT
1 AAAATAAAATAT
1024928 A
1 A
1024929 TAAACAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.45
12 12 0.55
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (12 bp):
AAAATAAAATAT
Found at i:1026797 original size:19 final size:19
Alignment explanation
Indices: 1026770--1026807 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1026760 ATAAAGGAAT
*
1026770 AATTAAATATTTTTACTATA
1 AATTAAATAATTTTA-TATA
1026790 AATT-AATAATTTTATATA
1 AATTAAATAATTTTATATA
1026808 TCTCTTTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 9 0.53
20 4 0.24
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (19 bp):
AATTAAATAATTTTATATA
Found at i:1027624 original size:19 final size:17
Alignment explanation
Indices: 1027600--1027667 Score: 84
Period size: 19 Copynumber: 3.8 Consensus size: 17
1027590 TATATATATA
1027600 TATATTAATTGTTTTAATT
1 TATATTAATT-TTTTAA-T
1027619 TATATTAATTTATTT-AT
1 TATATTAATTT-TTTAAT
1027636 TATATTAATTTATTTTAAT
1 TATATTAA-TT-TTTTAAT
1027655 TATATTAATTTTT
1 TATATTAATTTTT
1027668 ATCAGTTAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
17 12 0.27
18 9 0.20
19 24 0.53
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (17 bp):
TATATTAATTTTTTAAT
Found at i:1027632 original size:27 final size:28
Alignment explanation
Indices: 1027600--1027664 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 28
1027590 TATATATATA
* *
1027600 TATATTAATTGTTTTAATTTATATTAAT
1 TATATTAATTATATTAATTTATATTAAT
* *
1027628 T-TATTTATTATATTAATTTATTTTAAT
1 TATATTAATTATATTAATTTATATTAAT
1027655 TATATTAATT
1 TATATTAATT
1027665 TTTATCAGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 23 0.74
28 8 0.26
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (28 bp):
TATATTAATTATATTAATTTATATTAAT
Found at i:1027780 original size:27 final size:28
Alignment explanation
Indices: 1027712--1027780 Score: 72
Period size: 27 Copynumber: 2.5 Consensus size: 28
1027702 TTTAATAAAT
*
1027712 AATTAAATATAAATTTTAATATATTTTA
1 AATTATATATAAATTTTAATATATTTTA
* *
1027740 AATAATA-ATAAAATTTCTCA-A-ATTTTA
1 AATTATATAT-AAATTT-TAATATATTTTA
1027767 AATTATATATAAAT
1 AATTATATATAAAT
1027781 AAAATTTCTT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
27 18 0.53
28 14 0.41
29 2 0.06
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (28 bp):
AATTATATATAAATTTTAATATATTTTA
Found at i:1033759 original size:22 final size:21
Alignment explanation
Indices: 1033729--1033783 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
1033719 AATTAAAATA
*
1033729 TAATTTAATTAAAATTTAATT
1 TAATTTAATTAAAAATTAATT
*
1033750 TAATTGTAATTAAAAATTATTT
1 TAATT-TAATTAAAAATTAATT
*
1033772 TAAGATTAATTA
1 TAA-TTTAATTA
1033784 TATTTTTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 5 0.17
22 23 0.79
23 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (21 bp):
TAATTTAATTAAAAATTAATT
Found at i:1033760 original size:16 final size:16
Alignment explanation
Indices: 1033719--1033754 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
1033709 TATGTACTTG
*
1033719 AATTAAAATATAATTT
1 AATTAAAATTTAATTT
1033735 AATTAAAATTTAATTT
1 AATTAAAATTTAATTT
1033751 AATT
1 AATT
1033755 GTAATTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AATTAAAATTTAATTT
Found at i:1036326 original size:2 final size:2
Alignment explanation
Indices: 1036321--1036348 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1036311 TATATATATA
1036321 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1036349 ATTTATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:1038831 original size:2 final size:2
Alignment explanation
Indices: 1038826--1038854 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1038816 AAGAATATAT
1038826 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1038855 TAGATTGCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1045857 original size:27 final size:27
Alignment explanation
Indices: 1045822--1045875 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
1045812 ATTATGCTGC
**
1045822 TTTTAAAAATTTTATGTATTTAAATTT
1 TTTTAAAAAAATTATGTATTTAAATTT
*
1045849 TTTTAAAAAAATTATGTATTTATATTT
1 TTTTAAAAAAATTATGTATTTAAATTT
1045876 AAATATATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (27 bp):
TTTTAAAAAAATTATGTATTTAAATTT
Found at i:1047755 original size:11 final size:11
Alignment explanation
Indices: 1047731--1047765 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
1047721 GAGGACACGT
*
1047731 AAAAGAAAAAA
1 AAAAGAAATAA
1047742 AAAACGAAATAA
1 AAAA-GAAATAA
1047754 AAAAGAAATAA
1 AAAAGAAATAA
1047765 A
1 A
1047766 TGGCCGTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.83, C:0.03, G:0.09, T:0.06
Consensus pattern (11 bp):
AAAAGAAATAA
Found at i:1048993 original size:31 final size:33
Alignment explanation
Indices: 1048957--1049028 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 33
1048947 TATTGTATTA
* *
1048957 AAATTTTATT-TA-AAATATTTTATATTTATAT
1 AAATTTAATTATATAAATAATTTATATTTATAT
* *
1048988 AAATTTAATTATATTAATAATTTATTTTTATAT
1 AAATTTAATTATATAAATAATTTATATTTATAT
1049021 AAATTTAA
1 AAATTTAA
1049029 AATATTTATA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 9 0.26
32 2 0.06
33 24 0.69
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (33 bp):
AAATTTAATTATATAAATAATTTATATTTATAT
Found at i:1049048 original size:33 final size:33
Alignment explanation
Indices: 1048981--1049048 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
1048971 ATATTTTATA
* *
1048981 TTTATATAAATTTAATTATATTAATAATTTATT
1 TTTATATAAATTTAATAATATTAATAATTAATT
*
1049014 TTTATATAAATTTAA-AATATTTATATATTAATT
1 TTTATATAAATTTAATAATATTAATA-ATTAATT
1049047 TT
1 TT
1049049 ATAATTATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
32 8 0.26
33 23 0.74
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (33 bp):
TTTATATAAATTTAATAATATTAATAATTAATT
Found at i:1049049 original size:32 final size:33
Alignment explanation
Indices: 1048981--1049051 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 33
1048971 ATATTTTATA
* *
1048981 TTTATATAAATTTAATTATATTAATAATTTATT
1 TTTATATAAATTTAATAATATTAATAATTTAAT
*
1049014 TTTATATAAATTTAA-AATATTTAT-ATATTAAT
1 TTTATATAAATTTAATAATATTAATAAT-TTAAT
1049046 TTTATA
1 TTTATA
1049052 ATTATATTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
31 2 0.06
32 17 0.50
33 15 0.44
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (33 bp):
TTTATATAAATTTAATAATATTAATAATTTAAT
Found at i:1049073 original size:21 final size:21
Alignment explanation
Indices: 1049047--1049087 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
1049037 TATATTAATT
1049047 TTAT-AATTATATTAACTTATA
1 TTATAAATTATATTAA-TTATA
*
1049068 TTATAAATTATTTTAATTAT
1 TTATAAATTATATTAATTAT
1049088 TTTTCGTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
TTATAAATTATATTAATTATA
Found at i:1054780 original size:114 final size:114
Alignment explanation
Indices: 1054590--1054929 Score: 590
Period size: 114 Copynumber: 2.9 Consensus size: 114
1054580 ATGGCTCTTG
*
1054590 TTCTCCTCTCCGTTTCTGATTATGAAGTTTTGTTTCTGCATTTTCTCTTTGGCTACCAGTAGCAA
1 TTCTCTTCTCCGTTTCTGATTATGAAGTTTTGTTTCTGCATTTTCTCTTTGGCTACCAGTAGCAA
1054655 GCAATCAAAACTACTCCAATTGGGATCAAAGTTTGTATTATGGCATTTC
66 GCAATCAAAACTACTCCAATTGGGATCAAAGTTTGTATTATGGCATTTC
1054704 TTCTCTTCTCCGTTTCTGATTATGAAGTTTTGTTTCTGCATTTTCTCTTTGGCTACCAGTAGCAA
1 TTCTCTTCTCCGTTTCTGATTATGAAGTTTTGTTTCTGCATTTTCTCTTTGGCTACCAGTAGCAA
1054769 GCAATCAAAACTACTCCAATTGGGATCAAAGTTTGTATTATGGCATTTC
66 GCAATCAAAACTACTCCAATTGGGATCAAAGTTTGTATTATGGCATTTC
1054818 TTCTCTTCTCCGTTTCTGATTATGAAGTTTTGTTTCTGCATTTTCTCTTTGGCAACTTTGGCTAC
1 TTCTCTTCTCCGTTTCTGATTATGAAGTTTTGTTTCTGCA-TTT-TC--T-----CTTTGGCTAC
1054883 CAGTAGCAAGCAATCAAAACTACTCCAATTGGGATCAAAGTTTGTAT
57 CAGTAGCAAGCAATCAAAACTACTCCAATTGGGATCAAAGTTTGTAT
1054930 CCCTAAAATC
Statistics
Matches: 216, Mismatches: 1, Indels: 9
0.96 0.00 0.04
Matches are distributed among these distances:
114 153 0.71
115 3 0.01
116 2 0.01
118 1 0.00
123 57 0.26
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.41
Consensus pattern (114 bp):
TTCTCTTCTCCGTTTCTGATTATGAAGTTTTGTTTCTGCATTTTCTCTTTGGCTACCAGTAGCAA
GCAATCAAAACTACTCCAATTGGGATCAAAGTTTGTATTATGGCATTTC
Found at i:1062381 original size:23 final size:24
Alignment explanation
Indices: 1062355--1062399 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
1062345 TAATTAAATT
1062355 TTATATCTAAATATAT-ATATTAC
1 TTATATCTAAATATATAATATTAC
*
1062378 TTATATTTAAATATATAATATT
1 TTATATCTAAATATATAATATT
1062400 TTATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.51
Consensus pattern (24 bp):
TTATATCTAAATATATAATATTAC
Found at i:1062410 original size:23 final size:22
Alignment explanation
Indices: 1062337--1062410 Score: 57
Period size: 23 Copynumber: 3.2 Consensus size: 22
1062327 AATATAAATG
1062337 ATTAAATATAATTAA-ATTTTA-T
1 ATTAAATAT-A-TAATATTTTATT
1062359 ATCTAAATATAT-ATATTACTTA-T
1 AT-TAAATATATAATATT--TTATT
1062382 ATTTAAATATATAATATTTTATTT
1 A-TTAAATATATAATATTTTA-TT
1062406 ATTAA
1 ATTAA
1062411 TTATTTTCAT
Statistics
Matches: 44, Mismatches: 0, Indels: 15
0.75 0.00 0.25
Matches are distributed among these distances:
20 1 0.02
21 4 0.09
22 6 0.14
23 25 0.57
24 8 0.18
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (22 bp):
ATTAAATATATAATATTTTATT
Found at i:1068644 original size:38 final size:38
Alignment explanation
Indices: 1068592--1068696 Score: 147
Period size: 38 Copynumber: 2.8 Consensus size: 38
1068582 GAATTAGTTG
* ** *
1068592 ACGATTAGAAAATTCAATTTGAAATTGGTTGGCGGCTA
1 ACGATTAGAGAATTCAATTTGAAATTGACTAGCGGCTA
* *
1068630 ACGGTTAGAGAATTCAATTTGAAATTGACTAGCGGCTG
1 ACGATTAGAGAATTCAATTTGAAATTGACTAGCGGCTA
*
1068668 ACGACTAGAGAATTCAATTTGAAATTGAC
1 ACGATTAGAGAATTCAATTTGAAATTGAC
1068697 CGGTGACTGG
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 59 1.00
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.30
Consensus pattern (38 bp):
ACGATTAGAGAATTCAATTTGAAATTGACTAGCGGCTA
Found at i:1073314 original size:38 final size:38
Alignment explanation
Indices: 1073271--1073375 Score: 174
Period size: 38 Copynumber: 2.8 Consensus size: 38
1073261 TTGAATTAGT
* * *
1073271 TGACGGTTAGAGAATTCAATTTGAAATTGGCTGGTGGC
1 TGACGGCTAGAGAATTCAATTTGAAATTGGCTAGCGGC
1073309 TGACGGCTAGAGAATTCAATTTGAAATTGGCTAGCGGC
1 TGACGGCTAGAGAATTCAATTTGAAATTGGCTAGCGGC
*
1073347 TGACGGCTAGAGAATTCAATTTGGAATTG
1 TGACGGCTAGAGAATTCAATTTGAAATTG
1073376 ACCGGTGACT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 63 1.00
ACGTcount: A:0.29, C:0.12, G:0.30, T:0.30
Consensus pattern (38 bp):
TGACGGCTAGAGAATTCAATTTGAAATTGGCTAGCGGC
Found at i:1074846 original size:15 final size:16
Alignment explanation
Indices: 1074828--1074863 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
1074818 TTTTTATTTT
1074828 ATTATTAAATTAA-AA
1 ATTATTAAATTAATAA
*
1074843 ATTATTATATTAATAA
1 ATTATTAAATTAATAA
1074859 ATTAT
1 ATTAT
1074864 CGATAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATTATTAAATTAATAA
Found at i:1075415 original size:2 final size:2
Alignment explanation
Indices: 1075410--1075460 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
1075400 AGACCAACCA
**
1075410 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GG AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1075452 AT AT AT AT A
1 AT AT AT AT A
1075461 CACATTAACA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1075803 original size:26 final size:27
Alignment explanation
Indices: 1075761--1075819 Score: 79
Period size: 26 Copynumber: 2.2 Consensus size: 27
1075751 TATTTATTTT
1075761 TAAATACATAATTATATATTTCAA-ATA
1 TAAATACATAATTATATATTT-AATATA
1075788 TAAATA-A-AATTAATATATTTAATATA
1 TAAATACATAATT-ATATATTTAATATA
1075814 TAAATA
1 TAAATA
1075820 TATCATATTC
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
25 6 0.20
26 18 0.60
27 6 0.20
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (27 bp):
TAAATACATAATTATATATTTAATATA
Found at i:1076432 original size:3 final size:3
Alignment explanation
Indices: 1076424--1076449 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1076414 ACATGAAATT
1076424 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
1076450 TTGATTAGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:1078142 original size:2 final size:2
Alignment explanation
Indices: 1078135--1078183 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
1078125 CTTAAGATGA
*
1078135 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1078177 TC TC TC T
1 TC TC TC T
1078184 ATATATATAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:1079212 original size:14 final size:14
Alignment explanation
Indices: 1079195--1079242 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
1079185 CATAATTTTC
1079195 AAAATATAAAAATT
1 AAAATATAAAAATT
* *
1079209 AAAATATTAAATTT
1 AAAATATAAAAATT
*
1079223 AATAATA-CAAAATT
1 AA-AATATAAAAATT
1079237 AAAATA
1 AAAATA
1079243 ATTTTTTTAC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 4 0.14
14 21 0.72
15 4 0.14
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (14 bp):
AAAATATAAAAATT
Found at i:1079684 original size:405 final size:402
Alignment explanation
Indices: 1078927--1079744 Score: 1453
Period size: 405 Copynumber: 2.0 Consensus size: 402
1078917 TCTATTTTTT
* * *
1078927 ATAA-AAGTCTACTAAAAGTTCATGTATTACTACAAAATAAAGCATTTTAATCTCTGTATTACTG
1 ATAATAAGTGTACTAAAAATACATGTATTACTACAAAATAAAGCATTTTAATCTCTGTATTACTG
*
1078991 AAATTAATATTTTAATCTTTATACTTTAAAAAATATAATAAAAAAAAAATTAATTATGTTAGAAA
66 AAATTAATATTTTAATCTTTATACTTTAAAAAATATAAAAAAAAAAAAATTAATTATGTTAGAAA
*
1079056 ATGTGTTTAAATGTTAAGAAAATTTTGATGTATCATATAATATAAAATTTTAAATTTTATACAGA
131 ATGTGTTTAAATGTTAAGAAAATTTTGATGTATCATATAATATAAAATTTTAAATTTTATACAAA
*
1079121 AAAATAATCTAAATTTGACATGTCTGTATTTTTTTAATATCATTAACTATTTTTTCTTAAATATC
196 AAAATAATCTAAATTTGACACGTCTGTATTTTTTTAATATCATTAACTATTTTTTCTTAAATATC
1079186 ATAATTTTCAAAATATAAAAATTAAAATATTAAATTTAATAATACAAAATTAAAATAATTTTTTT
261 ATAATTTTCAAAATATAAAAATTAAAATATTAAATTTAATAATACAAAATTAAAATAATTTTTTT
1079251 ACTATAATATAAAAGTTTTCGGTAAACTTTTATTTTTTTTCTAGTTTAATTATATCTAGCATTTG
326 ACTATAATATAAAAGTTTTCGGTAAACTTTTATTTTTTTTCTAGTTTAATTATATCTAGCATTTG
*
1079316 CTCCATCCGTTG
391 CTCCATCCGCTG
1079328 ATAATAAGTGTACTAAAAATACATGTATTACTACAAAATAAAGCATTTTAATCTCTGTATTACTG
1 ATAATAAGTGTACTAAAAATACATGTATTACTACAAAATAAAGCATTTTAATCTCTGTATTACTG
*
1079393 AAATTAATATTTTAATCTTTATACTTTGAAAAATATAACAAATAAAAAAAATTTAATTATGTTA-
66 AAATTAATATTTTAATCTTTATACTTTAAAAAATATAA-AAA-AAAAAAAA-TTAATTATGTTAG
*
1079457 AGAAAT-TCGTTTAAATGTTAAGAAAATTTTGATGTATTATATAATATAAAATTTTAAATTTTAT
128 A-AAATGT-GTTTAAATGTTAAGAAAATTTTGATGTATCATATAATATAAAATTTTAAATTTTAT
* * *
1079521 ATAAAAAAATGATCTAAATTTGACACGTCTGTATTTTTTTAATATCATTAACTATTTTTTCTTAT
191 ACAAAAAAATAATCTAAATTTGACACGTCTGTATTTTTTTAATATCATTAACTATTTTTTCTTAA
*
1079586 ATATCATAATTTTCAAAGTATAAAAATTAAAATATTAAATTTAATAATACAAAATTAAAATAATT
256 ATATCATAATTTTCAAAATATAAAAATTAAAATATTAAATTTAATAATACAAAATTAAAATAATT
1079651 TTTTTACTATAATATAAAAGTTTTCGGTAAACTTTTATTTTTTTTCTAGTTTAATTATATCTAGC
321 TTTTTACTATAATATAAAAGTTTTCGGTAAACTTTTATTTTTTTTCTAGTTTAATTATATCTAGC
1079716 ATTTGCTCCATCCGCTG
386 ATTTGCTCCATCCGCTG
1079733 ATAATAAGTGTA
1 ATAATAAGTGTA
1079745 AGCTGTAAAA
Statistics
Matches: 398, Mismatches: 13, Indels: 8
0.95 0.03 0.02
Matches are distributed among these distances:
401 4 0.01
402 94 0.24
403 2 0.01
404 10 0.03
405 288 0.72
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.43
Consensus pattern (402 bp):
ATAATAAGTGTACTAAAAATACATGTATTACTACAAAATAAAGCATTTTAATCTCTGTATTACTG
AAATTAATATTTTAATCTTTATACTTTAAAAAATATAAAAAAAAAAAAATTAATTATGTTAGAAA
ATGTGTTTAAATGTTAAGAAAATTTTGATGTATCATATAATATAAAATTTTAAATTTTATACAAA
AAAATAATCTAAATTTGACACGTCTGTATTTTTTTAATATCATTAACTATTTTTTCTTAAATATC
ATAATTTTCAAAATATAAAAATTAAAATATTAAATTTAATAATACAAAATTAAAATAATTTTTTT
ACTATAATATAAAAGTTTTCGGTAAACTTTTATTTTTTTTCTAGTTTAATTATATCTAGCATTTG
CTCCATCCGCTG
Found at i:1087543 original size:17 final size:17
Alignment explanation
Indices: 1087523--1087557 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1087513 TAAATTGAAT
* *
1087523 TTTAATTTTTTTATATA
1 TTTAATTTATATATATA
1087540 TTTAATTTATATATATA
1 TTTAATTTATATATATA
1087557 T
1 T
1087558 ATATATATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTAATTTATATATATA
Found at i:1099502 original size:19 final size:19
Alignment explanation
Indices: 1099478--1099518 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
1099468 TATTAAGAGC
1099478 CTTTGTCATGTTTTCTTCT
1 CTTTGTCATGTTTTCTTCT
* *
1099497 CTTTGTTATGTTTTCTTTT
1 CTTTGTCATGTTTTCTTCT
1099516 CTT
1 CTT
1099519 AATTTTATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.05, C:0.17, G:0.10, T:0.68
Consensus pattern (19 bp):
CTTTGTCATGTTTTCTTCT
Found at i:1099622 original size:2 final size:2
Alignment explanation
Indices: 1099597--1099650 Score: 74
Period size: 2 Copynumber: 27.5 Consensus size: 2
1099587 ACTTGAGCAT
* * *
1099597 TA TA T- TA TA CA TA TA TG TA CA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1099638 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
1099651 TAATATTGCC
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1100124 original size:22 final size:22
Alignment explanation
Indices: 1100065--1100124 Score: 56
Period size: 22 Copynumber: 2.8 Consensus size: 22
1100055 AGATTAAATT
*
1100065 TATATTA-A-ATTCATA-TTAT
1 TATATTATATATTCATATTTAA
*
1100084 TATTATTTTATGATT-ATATTTAA
1 TA-TATTATAT-ATTCATATTTAA
1100107 TATATTATATATTCATAT
1 TATATTATATATTCATAT
1100125 ATACATTTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
19 2 0.06
20 4 0.12
21 4 0.12
22 14 0.44
23 8 0.25
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (22 bp):
TATATTATATATTCATATTTAA
Found at i:1100235 original size:43 final size:40
Alignment explanation
Indices: 1100178--1100265 Score: 106
Period size: 43 Copynumber: 2.1 Consensus size: 40
1100168 CATGTTCATA
*
1100178 TATTTGTATAATATTTATGTTATTTTTTATATTTAGTTT-TAAC
1 TATTTGTATAATA-TTATGTT-TTTTTT-T-TTAAGTTTATAAC
* *
1100221 TATTTGTCTTATATTATGTTTTTTTTTTTAAGTTTATAAC
1 TATTTGTATAATATTATGTTTTTTTTTTTAAGTTTATAAC
1100261 TATTT
1 TATTT
1100266 TCGAGTGGAC
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
39 7 0.17
40 10 0.24
41 6 0.15
42 7 0.17
43 11 0.27
ACGTcount: A:0.25, C:0.03, G:0.07, T:0.65
Consensus pattern (40 bp):
TATTTGTATAATATTATGTTTTTTTTTTTAAGTTTATAAC
Found at i:1104161 original size:19 final size:21
Alignment explanation
Indices: 1104117--1104166 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 21
1104107 TAATAATGAA
1104117 AATATA-ATAAATATTATATG
1 AATATATATAAATATTATATG
*
1104137 ATATATATATAAATA-TAT-TT
1 A-ATATATATAAATATTATATG
1104157 AATATATATA
1 AATATATATA
1104167 TTTTTATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 9 0.33
20 3 0.11
21 8 0.30
22 7 0.26
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
AATATATATAAATATTATATG
Found at i:1104161 original size:21 final size:21
Alignment explanation
Indices: 1104118--1104181 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
1104108 AATAATGAAA
* *
1104118 ATATA-ATAAATATTATATGAT
1 ATATATATAAATA-TATTTAAT
1104139 ATATATATAAATATATTTAAT
1 ATATATATAAATATATTTAAT
***
1104160 ATATATATTTTTATATTTAAT
1 ATATATATAAATATATTTAAT
1104181 A
1 A
1104182 ATTTATATTA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 30 0.81
22 7 0.19
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (21 bp):
ATATATATAAATATATTTAAT
Found at i:1104167 original size:15 final size:14
Alignment explanation
Indices: 1104131--1104206 Score: 64
Period size: 16 Copynumber: 5.1 Consensus size: 14
1104121 TAATAAATAT
*
1104131 TATATGATATATATA
1 TATAT-ATATTTATA
*
1104146 TAAATATATTTA-A
1 TATATATATTTATA
*
1104159 TATATATATTTTTA
1 TATATATATTTATA
*
1104173 TATTTAATAATTTATA
1 TATAT-AT-ATTTATA
1104189 TTATATTATATTTATA
1 -TATA-TATATTTATA
1104205 TA
1 TA
1104207 ATTAATTTTA
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
13 11 0.22
14 11 0.22
15 8 0.16
16 13 0.27
17 5 0.10
18 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (14 bp):
TATATATATTTATA
Found at i:1104186 original size:14 final size:16
Alignment explanation
Indices: 1104127--1104205 Score: 64
Period size: 15 Copynumber: 5.2 Consensus size: 16
1104117 AATATAATAA
*
1104127 ATATTAT-ATGATATAT
1 ATATTATAAT-ATATTT
1104143 ATA-TA-AATATATTT
1 ATATTATAATATATTT
*
1104157 A-A-TATATATATTTTT
1 ATATTATA-ATATATTT
1104172 ATATT-TAATA-ATTT
1 ATATTATAATATATTT
*
1104186 ATATTATATTATATTT
1 ATATTATAATATATTT
1104202 ATAT
1 ATAT
1104206 AATTAATTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
13 3 0.06
14 15 0.29
15 19 0.37
16 14 0.27
17 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (16 bp):
ATATTATAATATATTT
Found at i:1104188 original size:24 final size:25
Alignment explanation
Indices: 1104150--1104209 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 25
1104140 TATATATAAA
*
1104150 TATATTTA-AT-ATATATATT-T-T
1 TATATTTATATAATTTATATTATAT
1104171 TATATTTA-ATAATTTATATTATAT
1 TATATTTATATAATTTATATTATAT
1104195 TATATTTATATAATT
1 TATATTTATATAATT
1104210 AATTTTAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
21 10 0.29
22 8 0.24
23 1 0.03
24 9 0.26
25 6 0.18
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (25 bp):
TATATTTATATAATTTATATTATAT
Found at i:1104898 original size:29 final size:28
Alignment explanation
Indices: 1104862--1104924 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 28
1104852 ATGTAATGTA
1104862 AAAAAT-AAATTAAATGATA-TTATTTTATT
1 AAAAATAAAATT--ATGATATTTATTTT-TT
*
1104891 AAAAATAAAATTATTATATTTATTTTTT
1 AAAAATAAAATTATGATATTTATTTTTT
1104919 AAAAAT
1 AAAAAT
1104925 TTTTTAATGA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
28 13 0.42
29 13 0.42
30 5 0.16
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (28 bp):
AAAAATAAAATTATGATATTTATTTTTT
Found at i:1105418 original size:15 final size:15
Alignment explanation
Indices: 1105383--1105422 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 15
1105373 TGTATAAAAA
*
1105383 ATATAATA-AAAATT
1 ATATAATATAAATTT
1105397 -TAT-ATATAAATTT
1 ATATAATATAAATTT
1105410 ATATAATATAAAT
1 ATATAATATAAAT
1105423 AATTAATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
12 3 0.14
13 8 0.36
14 3 0.14
15 8 0.36
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
ATATAATATAAATTT
Found at i:1105831 original size:18 final size:19
Alignment explanation
Indices: 1105796--1105838 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
1105786 TTGTATTAAC
*
1105796 TAAAATTTATATTAATATG
1 TAAATTTTATATTAATATG
*
1105815 TAAATTTTAT-TTTATATG
1 TAAATTTTATATTAATATG
*
1105833 CAAATT
1 TAAATT
1105839 AAATAAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (19 bp):
TAAATTTTATATTAATATG
Found at i:1106049 original size:20 final size:19
Alignment explanation
Indices: 1106024--1106072 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
1106014 AGATAAATTT
1106024 TAATAATAAAAAAATTATAA
1 TAATAATAAAAAAA-TATAA
*
1106044 TAATAACT-TAAAAATATAA
1 TAATAA-TAAAAAAATATAA
1106063 TAAATAATAA
1 T-AATAATAA
1106073 TTATCATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
19 7 0.29
20 16 0.67
21 1 0.04
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (19 bp):
TAATAATAAAAAAATATAA
Found at i:1106158 original size:2 final size:2
Alignment explanation
Indices: 1106147--1106194 Score: 57
Period size: 2 Copynumber: 25.5 Consensus size: 2
1106137 TTTCACATTC
* *
1106147 AT AT -T AT AT AT AT AT AT AT AT AT AT AT -T AT AG AT -T AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1106186 AT AT AT AT A
1 AT AT AT AT A
1106195 ATGAAATTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
1 3 0.08
2 36 0.92
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1108046 original size:16 final size:16
Alignment explanation
Indices: 1108025--1108066 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
1108015 TGTCTCTTAT
1108025 TAATAATTATTTATTA
1 TAATAATTATTTATTA
*
1108041 TAATAACTATTT-TTA
1 TAATAATTATTTATTA
1108056 -AATAATT-TTTA
1 TAATAATTATTTA
1108067 AATAATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 3 0.13
14 6 0.26
15 3 0.13
16 11 0.48
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (16 bp):
TAATAATTATTTATTA
Found at i:1108075 original size:10 final size:11
Alignment explanation
Indices: 1108049--1108076 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
1108039 TATAATAACT
1108049 ATTTTTAAATA
1 ATTTTTAAATA
1108060 ATTTTTAAATA
1 ATTTTTAAATA
1108071 ATTTTT
1 ATTTTT
1108077 CTATTTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
ATTTTTAAATA
Found at i:1108375 original size:12 final size:12
Alignment explanation
Indices: 1108345--1108374 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
1108335 TTGTCTCTAC
1108345 TATTTTTAATTT
1 TATTTTTAATTT
1108357 TATTTTTAA-TT
1 TATTTTTAATTT
1108368 TATTTTT
1 TATTTTT
1108375 TTACTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.50
12 9 0.50
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (12 bp):
TATTTTTAATTT
Found at i:1110378 original size:30 final size:30
Alignment explanation
Indices: 1110320--1110423 Score: 131
Period size: 29 Copynumber: 3.5 Consensus size: 30
1110310 TTTTGGTATT
* *
1110320 TAAATAAATTATTAATATTTAA-TTATATC
1 TAAATAAATTTTTAATTTTTAATTTATATC
*
1110349 TAAATTAATTTTTAATTTTTAATTTATATC
1 TAAATAAATTTTTAATTTTTAATTTATATC
* *
1110379 -AAATAAATCTTTAAATTTTAATTTATATC
1 TAAATAAATTTTTAATTTTTAATTTATATC
* *
1110408 AAAATAAACTTTTAAT
1 TAAATAAATTTTTAAT
1110424 ATAATTAAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
29 45 0.70
30 19 0.30
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (30 bp):
TAAATAAATTTTTAATTTTTAATTTATATC
Found at i:1110433 original size:22 final size:22
Alignment explanation
Indices: 1110390--1110434 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
1110380 AATAAATCTT
*
1110390 TAAATTTTAATTTATATCAAAA
1 TAAATTTTAATATATATCAAAA
*
1110412 TAAACTTTTAATATA-ATTAAAA
1 TAAA-TTTTAATATATATCAAAA
1110434 T
1 T
1110435 TTTTATTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (22 bp):
TAAATTTTAATATATATCAAAA
Found at i:1111416 original size:2 final size:2
Alignment explanation
Indices: 1111409--1111437 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1111399 TTTTCATTTA
1111409 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1111438 CTATTGAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1112663 original size:22 final size:22
Alignment explanation
Indices: 1112632--1112690 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
1112622 AATTATCATT
*
1112632 TATATAATTTTTTTACATTTAA
1 TATATAATTTTATTACATTTAA
* *
1112654 TATATTATTTTATTATATTTAA
1 TATATAATTTTATTACATTTAA
* *
1112676 AAAATAATTTATATT
1 TATATAATTT-TATT
1112691 TTTATAAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 26 0.87
23 4 0.13
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
TATATAATTTTATTACATTTAA
Found at i:1112664 original size:19 final size:19
Alignment explanation
Indices: 1112628--1112665 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1112618 ATTTAATTAT
*
1112628 CATTTATATAATTTTTTTA
1 CATTTATATAATTATTTTA
1112647 CATTTA-ATATATTATTTTA
1 CATTTATATA-ATTATTTTA
1112666 TTATATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (19 bp):
CATTTATATAATTATTTTA
Found at i:1116564 original size:20 final size:20
Alignment explanation
Indices: 1116536--1116575 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1116526 AATAGGTTTA
1116536 ACTTAATGTGGTATCCGAGT
1 ACTTAATGTGGTATCCGAGT
*
1116556 ACTTTATGTGGTATCCGAGT
1 ACTTAATGTGGTATCCGAGT
1116576 CAAAGTCTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.23, C:0.15, G:0.25, T:0.38
Consensus pattern (20 bp):
ACTTAATGTGGTATCCGAGT
Found at i:1125127 original size:28 final size:30
Alignment explanation
Indices: 1125051--1125131 Score: 80
Period size: 28 Copynumber: 2.8 Consensus size: 30
1125041 TCTCCTTTAA
*
1125051 AAACATTTCT-CCTAGAAACATCTTGACAG
1 AAACATTTTTCCCTAGAAACATCTTGACAG
*** *
1125080 AAACATTTTGT-TGAAAAAACATCTTGAC-G
1 AAACATTTT-TCCCTAGAAACATCTTGACAG
1125109 AAA-ATTTTTCCCTAGAAACATCT
1 AAACATTTTTCCCTAGAAACATCT
1125132 CATAGAAAAA
Statistics
Matches: 41, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
27 1 0.02
28 14 0.34
29 12 0.29
30 14 0.34
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.31
Consensus pattern (30 bp):
AAACATTTTTCCCTAGAAACATCTTGACAG
Found at i:1125187 original size:45 final size:44
Alignment explanation
Indices: 1125095--1125235 Score: 155
Period size: 45 Copynumber: 3.2 Consensus size: 44
1125085 TTTTGTTGAA
* *
1125095 AAAACATCTTGACGAAAAT--TTTTCCCTAGAAACATCTCATAGA
1 AAAACATCTTGACGAAAATCATCTTCCCTAGAAACATCTCAT-GG
*
1125138 AAAACATCTTGACGAAAATCATCTTCCCTAGAAACATCTTGATGG
1 AAAACATCTTGACGAAAATCATCTTCCCTAGAAACATC-TCATGG
* * *
1125183 AAAACATC-TCATCAAAAATCATC-TCCCTAAAAAACATCTCAGTGG
1 AAAACATCTTGA-CGAAAATCATCTTCCCT-AGAAACATCTCA-TGG
1125228 AAAACATC
1 AAAACATC
1125236 CCCATTAAAA
Statistics
Matches: 85, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
43 19 0.22
44 9 0.11
45 54 0.64
46 3 0.04
ACGTcount: A:0.43, C:0.23, G:0.09, T:0.25
Consensus pattern (44 bp):
AAAACATCTTGACGAAAATCATCTTCCCTAGAAACATCTCATGG
Found at i:1125323 original size:30 final size:29
Alignment explanation
Indices: 1125288--1125388 Score: 78
Period size: 30 Copynumber: 3.4 Consensus size: 29
1125278 TCATTTTGAT
1125288 GAAAATAATCT-CCTTAAAAACATCTTAAC
1 GAAAAT-ATCTCCCTTAAAAACATCTTAAC
* ** * **
1125317 GAAAAATATCCTGCCGAAAAAACATTTTGTC
1 G-AAAATAT-CTCCCTTAAAAACATCTTAAC
*
1125348 GAAAATCATCTCCCTTAAAAACATCTTGAC
1 GAAAAT-ATCTCCCTTAAAAACATCTTAAC
**
1125378 TTAAATATCTC
1 GAAAATATCTC
1125389 GATGGTAAAA
Statistics
Matches: 56, Mismatches: 12, Indels: 8
0.74 0.16 0.11
Matches are distributed among these distances:
29 8 0.14
30 32 0.57
31 16 0.29
ACGTcount: A:0.43, C:0.22, G:0.07, T:0.29
Consensus pattern (29 bp):
GAAAATATCTCCCTTAAAAACATCTTAAC
Found at i:1128142 original size:22 final size:21
Alignment explanation
Indices: 1128116--1128156 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1128106 AGAAGATAGA
*
1128116 AGAAACAGTAAAGAGTAAAAGG
1 AGAAACAG-AAAAAGTAAAAGG
*
1128138 AGAAACTGAAAAAGTAAAA
1 AGAAACAGAAAAAGTAAAA
1128157 AGAAAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.63, C:0.05, G:0.22, T:0.10
Consensus pattern (21 bp):
AGAAACAGAAAAAGTAAAAGG
Found at i:1129223 original size:19 final size:20
Alignment explanation
Indices: 1129186--1129224 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1129176 ATTACATAAC
*
1129186 TAAAATTCATAAATATTAAA
1 TAAAATTCAAAAATATTAAA
*
1129206 TAAATTTCAAAAAT-TTAAA
1 TAAAATTCAAAAATATTAAA
1129225 AATTTAAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (20 bp):
TAAAATTCAAAAATATTAAA
Found at i:1129533 original size:2 final size:2
Alignment explanation
Indices: 1129526--1129553 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1129516 TTTCAAAATA
1129526 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1129554 TTCGCTAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1129676 original size:15 final size:15
Alignment explanation
Indices: 1129658--1129687 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1129648 AATTTGATGT
1129658 TATTAAATTAAATAA
1 TATTAAATTAAATAA
*
1129673 TATTAATTTAAATAA
1 TATTAAATTAAATAA
1129688 AAAATTGATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TATTAAATTAAATAA
Found at i:1130092 original size:16 final size:15
Alignment explanation
Indices: 1130073--1130117 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 15
1130063 TTTTAATTAA
1130073 AAAATAATTATTTATT
1 AAAA-AATTATTTATT
*
1130089 AAAAAAATTACTCTATT
1 -AAAAAATTA-TTTATT
1130106 AAAAAATTATTT
1 AAAAAATTATTT
1130118 TTATTATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
15 2 0.08
16 14 0.56
17 9 0.36
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.42
Consensus pattern (15 bp):
AAAAAATTATTTATT
Found at i:1130122 original size:17 final size:17
Alignment explanation
Indices: 1130063--1130123 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
1130053 TATTTAAATC
* *
1130063 TTTTAATTAAAAAATAA
1 TTTTTATTAAAAAATTA
1130080 TTATTTATTAAAAAAATTA
1 TT-TTTATT-AAAAAATTA
* *
1130099 -CTCTATTAAAAAATTA
1 TTTTTATTAAAAAATTA
1130115 TTTTTATTA
1 TTTTTATTA
1130124 TTTAATTTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
16 9 0.26
17 13 0.37
18 5 0.14
19 8 0.23
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTTTATTAAAAAATTA
Found at i:1131513 original size:30 final size:29
Alignment explanation
Indices: 1131463--1131525 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 29
1131453 AACATATTCT
* *
1131463 TAATTTAAATATTTATATATAGTATATTA
1 TAATTTAAATATTTAAATATAGTAAATTA
*
1131492 TAATTT-AATATTTAAAAATATATTAAATTA
1 TAATTTAAATATTT--AAATATAGTAAATTA
1131522 TAAT
1 TAAT
1131526 ATATTAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 7 0.24
29 6 0.21
30 16 0.55
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (29 bp):
TAATTTAAATATTTAAATATAGTAAATTA
Found at i:1131525 original size:25 final size:26
Alignment explanation
Indices: 1131485--1131533 Score: 75
Period size: 25 Copynumber: 1.9 Consensus size: 26
1131475 TTATATATAG
1131485 TATATTATAATTTAATAT-TTAAAAA
1 TATATTATAATTTAATATATTAAAAA
1131510 TATATTA-AATTATAATATATTAAA
1 TATATTATAATT-TAATATATTAAA
1131534 TTATTAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 4 0.18
25 13 0.59
26 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
TATATTATAATTTAATATATTAAAAA
Found at i:1131528 original size:15 final size:15
Alignment explanation
Indices: 1131508--1131537 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1131498 AATATTTAAA
1131508 AATATATTAAATTAT
1 AATATATTAAATTAT
1131523 AATATATTAAATTAT
1 AATATATTAAATTAT
1131538 TAAAAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AATATATTAAATTAT
Found at i:1131776 original size:21 final size:22
Alignment explanation
Indices: 1131736--1131776 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1131726 TATATAACAT
**
1131736 TTATTTTATTTTTATTAAATAA
1 TTATTTTATTTTTAACAAATAA
1131758 TTATTTTA-TTTTAACAAAT
1 TTATTTTATTTTTAACAAAT
1131777 CAATCATAAA
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:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (22 bp):
TTATTTTATTTTTAACAAATAA
Found at i:1132058 original size:17 final size:17
Alignment explanation
Indices: 1132008--1132064 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
1131998 TTTATATTTT
*
1132008 TATATT-ATAATTATATT
1 TATATTAATAATT-TATA
* * *
1132025 TTTATTAATTATATATA
1 TATATTAATAATTTATA
1132042 TATATTAATAATTTATA
1 TATATTAATAATTTATA
1132059 TTATAT
1 -TATAT
1132065 AAATTTTTTA
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
17 22 0.71
18 9 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TATATTAATAATTTATA
Found at i:1135785 original size:25 final size:25
Alignment explanation
Indices: 1135739--1135787 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
1135729 GTCCATGATA
* *
1135739 ATATAAAATTTAAATATTATATATG
1 ATATAAAATTTAAAGATAATATATG
* *
1135764 ATATTAAATTTATAGATAATATAT
1 ATATAAAATTTAAAGATAATATAT
1135788 AAATTTTTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (25 bp):
ATATAAAATTTAAAGATAATATATG
Found at i:1135792 original size:19 final size:18
Alignment explanation
Indices: 1135748--1135793 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
1135738 AATATAAAAT
* *
1135748 TTAAATATTATATATGATA
1 TTAAAT-TTATAGATAATA
1135767 TTAAATTTATAGATAATA
1 TTAAATTTATAGATAATA
1135785 TATAAATTT
1 T-TAAATTT
1135794 TTATAATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 11 0.46
19 13 0.54
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (18 bp):
TTAAATTTATAGATAATA
Found at i:1136469 original size:17 final size:18
Alignment explanation
Indices: 1136448--1136491 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
1136438 ATATATAATA
1136448 AAAATAATAAAATTTATT
1 AAAATAATAAAATTTATT
* *
1136466 -AAATATTTAAATTTATT
1 AAAATAATAAAATTTATT
1136483 AAAATAATA
1 AAAATAATA
1136492 TTTTGAAGTT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AAAATAATAAAATTTATT
Found at i:1137077 original size:17 final size:17
Alignment explanation
Indices: 1137052--1137089 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1137042 AAATTAGATA
*
1137052 TATTTATATTAAATATT
1 TATTAATATTAAATATT
*
1137069 TATTAATATTTAATATT
1 TATTAATATTAAATATT
1137086 TATT
1 TATT
1137090 TAAAAATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TATTAATATTAAATATT
Found at i:1137160 original size:13 final size:12
Alignment explanation
Indices: 1137142--1137206 Score: 69
Period size: 13 Copynumber: 5.2 Consensus size: 12
1137132 TTAAAAATTT
1137142 TAAAAAATAAATA
1 TAAAAAAT-AATA
*
1137155 TAAAAAAT-TTA
1 TAAAAAATAATA
1137166 TAAAAAATAATA
1 TAAAAAATAATA
*
1137178 TTATAAATATAATAA
1 -TA-AAAAATAAT-A
1137193 TAAAAAATAATA
1 TAAAAAATAATA
1137205 TA
1 TA
1137207 CACTTGTAGA
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
11 10 0.23
12 5 0.11
13 18 0.41
14 10 0.23
15 1 0.02
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
TAAAAAATAATA
Found at i:1137169 original size:24 final size:24
Alignment explanation
Indices: 1137123--1137206 Score: 84
Period size: 24 Copynumber: 3.4 Consensus size: 24
1137113 GAATATAATT
1137123 ATAAATATATTAAAAATTT-TAAAAA
1 ATAAATATA--AAAAATTTATAAAAA
1137148 ATAAATATAAAAAATTTATAAAAA
1 ATAAATATAAAAAATTTATAAAAA
*
1137172 ATAATATTATAAATATAA-TAATAAAAA
1 ATAA-A-TATAAA-A-AATTTATAAAAA
1137199 AT-AATATA
1 ATAAATATA
1137207 CACTTGTAGA
Statistics
Matches: 53, Mismatches: 1, Indels: 11
0.82 0.02 0.17
Matches are distributed among these distances:
23 8 0.15
24 14 0.26
25 11 0.21
26 7 0.13
27 11 0.21
28 2 0.04
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (24 bp):
ATAAATATAAAAAATTTATAAAAA
Found at i:1137193 original size:17 final size:18
Alignment explanation
Indices: 1137148--1137194 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
1137138 ATTTTAAAAA
*
1137148 ATAAATATAA-AAAATTT
1 ATAAATATAATAATATTT
1137165 ATAAA-A-AATAATA-TT
1 ATAAATATAATAATATTT
1137180 ATAAATATAATAATA
1 ATAAATATAATAATA
1137195 AAAAATAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
15 9 0.35
16 5 0.19
17 12 0.46
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
ATAAATATAATAATATTT
Found at i:1137857 original size:22 final size:24
Alignment explanation
Indices: 1137820--1137875 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 24
1137810 ATTAAAAAAT
*
1137820 TAAT-TTTTTTATAAAATA-TAAA
1 TAATATTTTTTATAAAAAAGTAAA
1137842 TAATATTTTTTA-AAAAAAGTAAA
1 TAATATTTTTTATAAAAAAGTAAA
1137865 T-ATAATTTTTT
1 TAAT-ATTTTTT
1137876 TATATGAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 11 0.37
23 19 0.63
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (24 bp):
TAATATTTTTTATAAAAAAGTAAA
Found at i:1137887 original size:23 final size:22
Alignment explanation
Indices: 1137816--1137888 Score: 69
Period size: 24 Copynumber: 3.2 Consensus size: 22
1137806 AGTAATTAAA
1137816 AAAT-TAATTTTTTTATAAAAT
1 AAATATAATTTTTTTATAAAAT
*
1137837 ATAA-ATAATATTTTTTAAAAAAAGT
1 A-AATATAAT-TTTTTT-ATAAAA-T
*
1137862 AAATATAATTTTTTTATATGAAT
1 AAATATAATTTTTTTATA-AAAT
1137885 AAAT
1 AAAT
1137889 TATTTAAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
21 1 0.02
22 6 0.14
23 13 0.31
24 15 0.36
25 7 0.17
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.47
Consensus pattern (22 bp):
AAATATAATTTTTTTATAAAAT
Found at i:1138446 original size:21 final size:21
Alignment explanation
Indices: 1138420--1138464 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
1138410 TAATTCATTC
1138420 ATAA-TTATAATAAATATAA-AT
1 ATAATTTA-AATAAA-ATAAGAT
1138441 ATAATTTAAATAAAATAAGAT
1 ATAATTTAAATAAAATAAGAT
1138462 ATA
1 ATA
1138465 TTCTAACCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.18
21 15 0.68
22 3 0.14
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (21 bp):
ATAATTTAAATAAAATAAGAT
Found at i:1138951 original size:29 final size:29
Alignment explanation
Indices: 1138894--1138952 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
1138884 ATATAATAAG
* *
1138894 TTCCCAAAGTTTATACGAACAAAAGAAAA
1 TTCCCAAAGTTTATACGAAAAAAAAAAAA
*
1138923 TTCCCAAAGTTTA-AGCAAAAACAAAAAAAA
1 TTCCCAAAGTTTATA-CGAAAA-AAAAAAAA
1138953 AAAAGATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
28 1 0.04
29 17 0.68
30 7 0.28
ACGTcount: A:0.56, C:0.17, G:0.08, T:0.19
Consensus pattern (29 bp):
TTCCCAAAGTTTATACGAAAAAAAAAAAA
Found at i:1139116 original size:19 final size:20
Alignment explanation
Indices: 1139089--1139127 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
1139079 TGTATATATG
*
1139089 ATATAATTATATA-AAATAA
1 ATATAATTAAATATAAATAA
*
1139108 ATATGATTAAATATAAATAA
1 ATATAATTAAATATAAATAA
1139128 TTAAAACTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (20 bp):
ATATAATTAAATATAAATAA
Found at i:1139170 original size:30 final size:30
Alignment explanation
Indices: 1139136--1139193 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
1139126 AATTAAAACT
1139136 TAATATAAACATCACATG-ATAAGATAAAAA
1 TAATATAAACATCACATGAATAA-ATAAAAA
* *
1139166 TAATATAAATATTACATGAATAAATAAA
1 TAATATAAACATCACATGAATAAATAAA
1139194 TATATTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.60, C:0.07, G:0.05, T:0.28
Consensus pattern (30 bp):
TAATATAAACATCACATGAATAAATAAAAA
Found at i:1139234 original size:32 final size:33
Alignment explanation
Indices: 1139174--1139244 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 33
1139164 AATAATATAA
*
1139174 ATATTACATGAATAAATAAATATATTAAAATTT
1 ATATAACATGAATAAATAAATATATTAAAATTT
* * * *
1139207 ATATAACATGAAT-TATTAATATGTTAAATTTT
1 ATATAACATGAATAAATAAATATATTAAAATTT
1139239 ATATAA
1 ATATAA
1139245 TATTTTAAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
32 21 0.64
33 12 0.36
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.42
Consensus pattern (33 bp):
ATATAACATGAATAAATAAATATATTAAAATTT
Found at i:1140009 original size:2 final size:2
Alignment explanation
Indices: 1140004--1140037 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1139994 TATGGTTACA
1140004 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1140038 TCAGTTAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1140785 original size:2 final size:2
Alignment explanation
Indices: 1140780--1140811 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1140770 ATATCAAAAC
1140780 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1140812 CAAACAAACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1140895 original size:2 final size:2
Alignment explanation
Indices: 1140888--1140916 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1140878 GAGTAGTAGG
1140888 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1140917 AATAAATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1142892 original size:3 final size:3
Alignment explanation
Indices: 1142880--1142915 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
1142870 TAAAACTATG
1142880 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1142916 TGAGACAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:1144039 original size:2 final size:2
Alignment explanation
Indices: 1144032--1144060 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1144022 ACAGATCAGC
1144032 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1144061 GTACACACAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1144325 original size:20 final size:19
Alignment explanation
Indices: 1144292--1144397 Score: 60
Period size: 18 Copynumber: 5.5 Consensus size: 19
1144282 AGATCCAACG
*
1144292 ATTATTTGTGATATATTTAT
1 ATTATTT-TTATATATTTAT
1144312 ATTATTTTTA-ATATTT-T
1 ATTATTTTTATATATTTAT
* * * **
1144329 AATTATATCTAAATATAAAT
1 -ATTATTTTTATATATTTAT
1144349 ATTAATATATTTATATATTT-T
1 ATT-AT-T-TTTATATATTTAT
1144370 A-TATTTTTATCATATATTA-
1 ATTATTTTTAT-ATAT-TTAT
1144389 ATTATTTTT
1 ATTATTTTT
1144398 TATTATTATA
Statistics
Matches: 66, Mismatches: 10, Indels: 20
0.69 0.10 0.21
Matches are distributed among these distances:
17 6 0.09
18 19 0.29
19 14 0.21
20 18 0.27
21 2 0.03
22 7 0.11
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (19 bp):
ATTATTTTTATATATTTAT
Found at i:1144333 original size:18 final size:20
Alignment explanation
Indices: 1144292--1144334 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1144282 AGATCCAACG
*
1144292 ATTATTTGTGATATATTTAT
1 ATTATTTGTAATATATTTAT
*
1144312 ATTATTTTTAATAT-TTTA-
1 ATTATTTGTAATATATTTAT
1144330 ATTAT
1 ATTAT
1144335 ATCTAAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 4 0.19
20 12 0.57
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.63
Consensus pattern (20 bp):
ATTATTTGTAATATATTTAT
Found at i:1144394 original size:27 final size:28
Alignment explanation
Indices: 1144302--1144412 Score: 82
Period size: 27 Copynumber: 3.9 Consensus size: 28
1144292 ATTATTTGTG
* *
1144302 ATATA-TTTATATTATTTTTAATATTTTA
1 ATATATTTTATATTA-TTATAATATATTA
** * * *
1144330 ATTATATCTAAATATAAATATTAATATATTT
1 A-TATAT-TTTATATTATTA-TAATATATTA
* *
1144361 ATATATTTTATATTTTTATCATATATTA
1 ATATATTTTATATTATTATAATATATTA
*
1144389 AT-TATTTTTTATTATTATAATATA
1 ATATATTTTATATTATTATAATATA
1144413 AAATTATCAA
Statistics
Matches: 62, Mismatches: 17, Indels: 9
0.70 0.19 0.10
Matches are distributed among these distances:
27 19 0.31
28 11 0.18
29 11 0.18
30 6 0.10
31 15 0.24
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (28 bp):
ATATATTTTATATTATTATAATATATTA
Found at i:1145525 original size:13 final size:13
Alignment explanation
Indices: 1145502--1145536 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
1145492 TTATGGTGAT
1145502 ATTATTAAATATTA
1 ATTA-TAAATATTA
1145516 ATTATAAATATTA
1 ATTATAAATATTA
*
1145529 ATAATAAA
1 ATTATAAA
1145537 AAATTAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 16 0.80
14 4 0.20
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
ATTATAAATATTA
Found at i:1145933 original size:30 final size:29
Alignment explanation
Indices: 1145898--1145974 Score: 95
Period size: 30 Copynumber: 2.7 Consensus size: 29
1145888 TAAATAATAA
*
1145898 ATTTTTAATTTTATTAAATTATATTATTT
1 ATTTTTAATTTTATTAAATTAAATTATTT
*
1145927 GATTTTT-ATTATTAATAAATTAAATTATTT
1 -ATTTTTAATT-TTATTAAATTAAATTATTT
*
1145957 A-TATTAATTTTATTAAAT
1 ATTTTTAATTTTATTAAAT
1145975 AATTTTTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
28 11 0.27
29 7 0.17
30 23 0.56
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (29 bp):
ATTTTTAATTTTATTAAATTAAATTATTT
Found at i:1146091 original size:23 final size:23
Alignment explanation
Indices: 1146059--1146131 Score: 82
Period size: 23 Copynumber: 3.3 Consensus size: 23
1146049 TATTAATTTT
* *
1146059 TAAATTATTTAATAAAATTAATA
1 TAAATAATTTAATAATATTAATA
*
1146082 TAAATAATTTAAT-TTATTAATAA
1 TAAATAATTTAATAATATTAAT-A
1146105 TAAA-AATTTAATAATA-TAAT-
1 TAAATAATTTAATAATATTAATA
1146125 TAAATAA
1 TAAATAA
1146132 AATTAAAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
20 4 0.09
21 2 0.05
22 18 0.42
23 19 0.44
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
TAAATAATTTAATAATATTAATA
Found at i:1146103 original size:22 final size:22
Alignment explanation
Indices: 1146075--1146116 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1146065 ATTTAATAAA
1146075 ATTAAT-ATAAATAATTTAATTT
1 ATTAATAATAAA-AATTTAATTT
1146097 ATTAATAATAAAAATTTAAT
1 ATTAATAATAAAAATTTAAT
1146117 AATATAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATTAATAATAAAAATTTAATTT
Found at i:1146486 original size:19 final size:21
Alignment explanation
Indices: 1146449--1146489 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1146439 TCATATTTTT
*
1146449 AATTTTATTTATAATATATAA
1 AATTTTATATATAATATATAA
1146470 AATTTTATATATAATATATA
1 AATTTTATATATAATATATA
1146490 TGTAAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
AATTTTATATATAATATATAA
Found at i:1149191 original size:18 final size:17
Alignment explanation
Indices: 1149170--1149208 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
1149160 TGTTTTTTTA
1149170 ATTAATTATTAAAATAAT
1 ATTAATTATTAAAA-AAT
* *
1149188 ATTATTTTTTAAAAAAT
1 ATTAATTATTAAAAAAT
1149205 ATTA
1 ATTA
1149209 TTAAAATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATTAATTATTAAAAAAT
Found at i:1151561 original size:2 final size:2
Alignment explanation
Indices: 1151554--1151578 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1151544 TCTATCTCAA
1151554 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1151579 AAATACGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1152263 original size:2 final size:2
Alignment explanation
Indices: 1152250--1152291 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
1152240 GCCCACTATG
*
1152250 TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1152292 CATACACTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1156024 original size:17 final size:17
Alignment explanation
Indices: 1156002--1156036 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1155992 AATTAAATGA
1156002 ATTTAACATTA-ATTTTT
1 ATTTAA-ATTATATTTTT
1156019 ATTTAAATTATATTTTT
1 ATTTAAATTATATTTTT
1156036 A
1 A
1156037 ATTTTATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTTAAATTATATTTTT
Found at i:1156049 original size:22 final size:24
Alignment explanation
Indices: 1156010--1156069 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
1156000 GAATTTAACA
*
1156010 TTAATTTTTATTTAAATTATATT-T
1 TTAATTTTTA-TTAAATTAAATTAT
1156034 TTAA-TTTTATTAAATTAAATTAT
1 TTAATTTTTATTAAATTAAATTAT
*
1156057 TAAATTTTTATTA
1 TTAATTTTTATTA
1156070 TTAATAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 11 0.34
23 9 0.28
24 12 0.38
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
TTAATTTTTATTAAATTAAATTAT
Found at i:1156064 original size:30 final size:30
Alignment explanation
Indices: 1156025--1156083 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
1156015 TTTTATTTAA
* *
1156025 ATTATATTTTTAATT-TTATTAAATTAAATT
1 ATTAAATTTTT-ATTATTAATAAATTAAATT
1156055 ATTAAATTTTTATTATTAATAAATTAAAT
1 ATTAAATTTTTATTATTAATAAATTAAAT
1156084 CATATATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 23 0.88
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (30 bp):
ATTAAATTTTTATTATTAATAAATTAAATT
Found at i:1156283 original size:15 final size:16
Alignment explanation
Indices: 1156248--1156289 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
1156238 TAAATGATGT
*
1156248 AATTTAATAAAATTAA
1 AATTTAATAATATTAA
*
1156264 AATTTTATAATATT-A
1 AATTTAATAATATTAA
1156279 AATTTAATAAT
1 AATTTAATAAT
1156290 TCAAAATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATTTAATAATATTAA
Found at i:1159667 original size:29 final size:29
Alignment explanation
Indices: 1159635--1159697 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
1159625 TACATATAAA
*
1159635 TATATAGTATATAT-TAAATTTATTTTTAT
1 TATATAGTATATATATAAATATA-TTTTAT
* * *
1159664 TATACATTATATATATGAATATATTTTAT
1 TATATAGTATATATATAAATATATTTTAT
1159693 TATAT
1 TATAT
1159698 TATTTTTATG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
29 22 0.79
30 6 0.21
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.56
Consensus pattern (29 bp):
TATATAGTATATATATAAATATATTTTAT
Found at i:1159996 original size:4 final size:4
Alignment explanation
Indices: 1159987--1160022 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
1159977 ACTAACAACG
1159987 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
1160023 TTATAATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAA
Found at i:1161151 original size:24 final size:23
Alignment explanation
Indices: 1161122--1161167 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 23
1161112 CAAAGCTTAC
1161122 AAATTTATAAATTT-TATTTTTCAT
1 AAATTT-T-AATTTATATTTTTCAT
1161146 AAATTTTAATTTAATATTTTTC
1 AAATTTTAATTT-ATATTTTTC
1161168 GTAATAAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 5 0.25
23 1 0.05
24 14 0.70
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (23 bp):
AAATTTTAATTTATATTTTTCAT
Found at i:1161358 original size:18 final size:18
Alignment explanation
Indices: 1161327--1161361 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1161317 ATCATTCAAA
*
1161327 TAAATTTACGAATTTATT
1 TAAATTTAAGAATTTATT
*
1161345 TAAATTTAATAATTTAT
1 TAAATTTAAGAATTTAT
1161362 ATATTTATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (18 bp):
TAAATTTAAGAATTTATT
Found at i:1168876 original size:2 final size:2
Alignment explanation
Indices: 1168869--1168906 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1168859 AGTGAACAGG
1168869 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1168907 ACACACACAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1175694 original size:31 final size:31
Alignment explanation
Indices: 1175656--1175714 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
1175646 AAGTTTAGAC
1175656 TTAAATTTAATTGATTTTAATTTTTTTATAT
1 TTAAATTTAATTGATTTTAATTTTTTTATAT
* *
1175687 TTAAATTTAATTGTTTTTACTTTTTTTA
1 TTAAATTTAATTGATTTTAATTTTTTTA
1175715 CATTCGAGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.66
Consensus pattern (31 bp):
TTAAATTTAATTGATTTTAATTTTTTTATAT
Found at i:1176154 original size:27 final size:28
Alignment explanation
Indices: 1176105--1176161 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
1176095 AATTTAAAAT
1176105 ATTTAAATTTAATAAAAAATAAA-TTAA
1 ATTTAAATTTAATAAAAAATAAATTTAA
* *
1176132 ATTTAAATATTTAT-AAAATTAAATTTAA
1 ATTTAAAT-TTAATAAAAAATAAATTTAA
1176160 AT
1 AT
1176162 AACTTACGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 16 0.62
28 10 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (28 bp):
ATTTAAATTTAATAAAAAATAAATTTAA
Found at i:1176496 original size:13 final size:14
Alignment explanation
Indices: 1176474--1176502 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1176464 ATAATTTAAA
1176474 AAAAAGATAAAAAT
1 AAAAAGATAAAAAT
1176488 AAAAA-ATAAAAAT
1 AAAAAGATAAAAAT
1176501 AA
1 AA
1176503 TATCAAACAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (14 bp):
AAAAAGATAAAAAT
Found at i:1177004 original size:2 final size:2
Alignment explanation
Indices: 1176997--1177021 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1176987 AAAGTGAGTG
1176997 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
1177022 CTACCTTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1177385 original size:21 final size:22
Alignment explanation
Indices: 1177359--1177399 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1177349 TGAATATAAC
*
1177359 AATAAAAT-ATTTTTTTAAAAA
1 AATAAAATAATTATTTTAAAAA
1177380 AATAAAATAATTATTTTAAA
1 AATAAAATAATTATTTTAAA
1177400 GATAATATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
AATAAAATAATTATTTTAAAAA
Found at i:1178109 original size:21 final size:21
Alignment explanation
Indices: 1178058--1178111 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
1178048 TTTATATATT
*
1178058 TTATAATTAAAATTAAATAAAA
1 TTATAATT-TAATTAAATAAAA
* *
1178080 ATATTATTTAATTAAA-ATAAA
1 TTATAATTTAATTAAATA-AAA
1178101 TTATAATTTAA
1 TTATAATTTAA
1178112 ATCATAAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 1 0.04
21 19 0.73
22 6 0.23
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TTATAATTTAATTAAATAAAA
Found at i:1178455 original size:13 final size:13
Alignment explanation
Indices: 1178429--1178468 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
1178419 TCATTATCTA
1178429 TAAAAATTA-A-T
1 TAAAAATTATATT
*
1178440 TAAAAATTATTTT
1 TAAAAATTATATT
1178453 TAAAAATTATATT
1 TAAAAATTATATT
1178466 TAA
1 TAA
1178469 TGTATTAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 9 0.36
13 16 0.64
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TAAAAATTATATT
Found at i:1179276 original size:2 final size:2
Alignment explanation
Indices: 1179263--1179298 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1179253 ACGTAAGCTA
*
1179263 TC TC TC TT TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1179299 GTAGTTGCTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:1180183 original size:18 final size:19
Alignment explanation
Indices: 1180150--1180197 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
1180140 TATAATAAAA
*
1180150 TTTAAATAAAATATATTAT
1 TTTAATTAAAATATATTAT
1180169 TTTAATTAAAA-ATATTAT
1 TTTAATTAAAATATATTAT
1180187 TTTAAATTAAA
1 TTT-AATTAAA
1180198 TCAATTCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 10 0.37
19 17 0.63
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TTTAATTAAAATATATTAT
Done.