Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold331
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: 1033222
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.30
Warning! 83795 characters in sequence are not A, C, G, or T
File 1 of 4
Found at i:4433 original size:14 final size:14
Alignment explanation
Indices: 4414--4445 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
4404 GATGATTGTT
*
4414 CTAATCTAAATTTA
1 CTAATCTAAATTAA
4428 CTAATCTAAATTAA
1 CTAATCTAAATTAA
4442 CTAA
1 CTAA
4446 GAACGCGACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.38
Consensus pattern (14 bp):
CTAATCTAAATTAA
Found at i:7160 original size:6 final size:6
Alignment explanation
Indices: 7151--7212 Score: 99
Period size: 6 Copynumber: 10.5 Consensus size: 6
7141 TAAGTCTAAG
* *
7151 AAAATA AAAATA AAAATA AACATA AACATA AAAATA AAAATA AAAATA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
7199 AAAAT- AAAATA AAA
1 AAAATA AAAATA AAA
7213 CAAATGGACT
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
5 5 0.09
6 48 0.91
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:8749 original size:7 final size:8
Alignment explanation
Indices: 8732--8756 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
8722 CTGCTTAATG
8732 AAAAATAA
1 AAAAATAA
8740 AAAAATAA
1 AAAAATAA
8748 AAAAATAA
1 AAAAATAA
8756 A
1 A
8757 TCAAATCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAATAA
Found at i:8851 original size:4 final size:4
Alignment explanation
Indices: 8842--8912 Score: 52
Period size: 4 Copynumber: 16.2 Consensus size: 4
8832 AATAAACAAT
* * *
8842 AATA AATA AAGA AATA AATAA AATA AGTAA AACTA ATAAA AATAA AATA
1 AATA AATA AATA AATA AAT-A AATA AAT-A AA-TA A-ATA AAT-A AATA
*
8891 ATTA GAATA AATA AATA AATA A
1 AATA -AATA AATA AATA AATA A
8913 TAATCTAATA
Statistics
Matches: 53, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
4 34 0.64
5 17 0.32
6 2 0.04
ACGTcount: A:0.72, C:0.01, G:0.04, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:8914 original size:24 final size:24
Alignment explanation
Indices: 8832--8916 Score: 61
Period size: 24 Copynumber: 3.5 Consensus size: 24
8822 AAAGAAATTG
* *
8832 AATAAACAATAA-TA-AATAAAGA
1 AATAAATAATAATTAGAATAAATA
* *
8854 AATAAATAA-AATAAGTAAAACTAATA
1 AATAAATAATAATTAG-AATA--AATA
*
8880 AA-AATAAAATAATTAGAATAAATA
1 AATAA-ATAATAATTAGAATAAATA
8904 AATAAATAATAAT
1 AATAAATAATAAT
8917 CTAATAATAG
Statistics
Matches: 47, Mismatches: 8, Indels: 14
0.68 0.12 0.20
Matches are distributed among these distances:
21 2 0.04
22 9 0.19
24 16 0.34
25 4 0.09
26 11 0.23
27 5 0.11
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.24
Consensus pattern (24 bp):
AATAAATAATAATTAGAATAAATA
Found at i:13805 original size:22 final size:21
Alignment explanation
Indices: 13779--13830 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
13769 AACCTACCAG
* *
13779 AAACAAATAAAATAAAATTAGA
1 AAACAAAAAAAATAAAACTA-A
*
13801 AAACAAAAAAAATTAAACTAA
1 AAACAAAAAAAATAAAACTAA
13822 AAACAAAAA
1 AAACAAAAA
13831 TAAAATGCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 10 0.37
22 17 0.63
ACGTcount: A:0.77, C:0.08, G:0.02, T:0.13
Consensus pattern (21 bp):
AAACAAAAAAAATAAAACTAA
Found at i:21901 original size:13 final size:12
Alignment explanation
Indices: 21883--21927 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 12
21873 AACCCGACTG
21883 TTCTTTTTTATTT
1 TTCTTTTTT-TTT
21896 TTCTTTTTTCTTT
1 TTCTTTTTT-TTT
21909 TTCTTTGTTTTCTT
1 TTCTTT-TTTT-TT
21923 TTCTT
1 TTCTT
21928 CTTCTTTCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 19 0.66
14 10 0.34
ACGTcount: A:0.02, C:0.13, G:0.02, T:0.82
Consensus pattern (12 bp):
TTCTTTTTTTTT
Found at i:21902 original size:6 final size:6
Alignment explanation
Indices: 21887--21970 Score: 60
Period size: 6 Copynumber: 12.8 Consensus size: 6
21877 CGACTGTTCT
* * *
21887 TTTTTA TTTTTC TTTTTTC TTTTTC TTTGTTT TCTTTTC TTCTTC TTTCTTC
1 TTTTTC TTTTTC -TTTTTC TTTTTC TTT-TTC T-TTTTC TTTTTC TTT-TTC
* *
21939 TTCTTC TTTCTTC TTCTTC TTCTTCTC TTTTT
1 TTTTTC TTT-TTC TTTTTC TT-TT-TC TTTTT
21971 TTCTCTAGCC
Statistics
Matches: 62, Mismatches: 9, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
6 31 0.50
7 25 0.40
8 6 0.10
ACGTcount: A:0.01, C:0.21, G:0.01, T:0.76
Consensus pattern (6 bp):
TTTTTC
Found at i:21908 original size:20 final size:20
Alignment explanation
Indices: 21883--21950 Score: 64
Period size: 20 Copynumber: 3.2 Consensus size: 20
21873 AACCCGACTG
21883 TTCTTTTTTATTTTTCTTTT
1 TTCTTTTTTATTTTTCTTTT
*
21903 TTCTTTTTCTTTGTTTTCTTTT
1 TTCTTTTT-TAT-TTTTCTTTT
* * * *
21925 CTTCTTCTTTCTTCTTCTTCT
1 -TTCTTTTTTATTTTTCTTTT
21946 TTCTT
1 TTCTT
21951 CTTCTTCTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
20 13 0.32
21 9 0.22
22 11 0.28
23 7 0.17
ACGTcount: A:0.01, C:0.19, G:0.01, T:0.78
Consensus pattern (20 bp):
TTCTTTTTTATTTTTCTTTT
Found at i:21931 original size:3 final size:3
Alignment explanation
Indices: 21918--21964 Score: 69
Period size: 3 Copynumber: 15.3 Consensus size: 3
21908 TTTCTTTGTT
21918 TTC TT- TTC TTC TTC TTTC TTC TTC TTC TTTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC -TTC TTC TTC TTC -TTC TTC TTC TTC TTC TTC
21964 T
1 T
21965 CTTTTTTTCT
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 2 0.05
3 33 0.80
4 6 0.15
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
TTC
Found at i:21941 original size:13 final size:13
Alignment explanation
Indices: 21923--21964 Score: 77
Period size: 13 Copynumber: 3.3 Consensus size: 13
21913 TTGTTTTCTT
21923 TTCTTCTTCTTTC
1 TTCTTCTTCTTTC
21936 TTCTTCTTCTTTC
1 TTCTTCTTCTTTC
21949 TTCTTCTTC-TTC
1 TTCTTCTTCTTTC
21961 TTCT
1 TTCT
21965 CTTTTTTTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
12 7 0.24
13 22 0.76
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (13 bp):
TTCTTCTTCTTTC
Found at i:22697 original size:28 final size:28
Alignment explanation
Indices: 22635--22741 Score: 135
Period size: 28 Copynumber: 3.8 Consensus size: 28
22625 CAAAAATCTC
*
22635 GGGGCTAAAATGTAATTTTAG-AAAAAGTTA
1 GGGGCCAAAATGTAA--TTAGTAAAAAG-TA
* *
22665 GGGGCTAAAATGTAAATAGTAAAAAGTA
1 GGGGCCAAAATGTAATTAGTAAAAAGTA
*
22693 GGGGCCAAAATGTAATTAGTAAAAAATA
1 GGGGCCAAAATGTAATTAGTAAAAAGTA
*
22721 GGGGCCAAAATATAATTAGTA
1 GGGGCCAAAATGTAATTAGTA
22742 TATTTTTGTA
Statistics
Matches: 71, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
28 50 0.70
29 6 0.08
30 15 0.21
ACGTcount: A:0.47, C:0.06, G:0.23, T:0.24
Consensus pattern (28 bp):
GGGGCCAAAATGTAATTAGTAAAAAGTA
Found at i:23434 original size:76 final size:76
Alignment explanation
Indices: 23308--23835 Score: 725
Period size: 76 Copynumber: 6.9 Consensus size: 76
23298 ACTGAAATTT
* * ** * * * *
23308 AAAATACCTCGGTGTGCGGCCTAAAGCTCAAATCACCTCTCAGATTATGAGTTAATCTTTGAAAA
1 AAAATACCTCGGCGTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATCTTTGAAAA
*
23373 ATAGAAATTGA
66 ACAGAAATTGA
* * * *
23384 AAAATATCTCGGCGTGCCACTCGAGGCTCAACTCACTTCTCGGATTATGAGTTGATCTTTGAAAA
1 AAAATACCTCGGCGTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATCTTTGAAAA
*
23449 ACAAAAATTGA
66 ACAGAAATTGA
* * * * *
23460 AAAATACCTCAGTGTGCGAGCCGAGGCTCAACTCACCTTTCGGATTATGAGTTGATCTTTAAAAA
1 AAAATACCTCGGCGTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATCTTTGAAAA
*
23525 ATAGAAATTGA
66 ACAGAAATTGA
*
23536 AAAATACCTCGACGTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATCTTTGAAAA
1 AAAATACCTCGGCGTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATCTTTGAAAA
23601 ACAGAAATTGA
66 ACAGAAATTGA
* * * *
23612 AAAATACATCGGCGTGCGACCCGAGGCTCCACTCACCTCTCGGATTATGATTTGATCTTTTAAAA
1 AAAATACCTCGGCGTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATCTTTGAAAA
23677 ACAGAAATTGA
66 ACAGAAATTGA
* * * * * *
23688 AAAACACATCAGCGTGCGACTCGAGGCTCAACTCGCCTCTCGGATTATGAGGTGATCTTTGAAAA
1 AAAATACCTCGGCGTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATCTTTGAAAA
23753 ACAGAAATTG-
66 ACAGAAATTGA
* * * *
23763 AAAATACCTCGGCGTGCGACCCGAGGCTCCACTCACCTATCGGATTATGAGTTGATTTTTTAAAA
1 AAAATACCTCGGCGTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGA-TCTTTGAAA
23828 AACAGAAA
65 AACAGAAA
23836 AAGAAATGAT
Statistics
Matches: 396, Mismatches: 55, Indels: 2
0.87 0.12 0.00
Matches are distributed among these distances:
75 47 0.12
76 349 0.88
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (76 bp):
AAAATACCTCGGCGTGCGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATCTTTGAAAA
ACAGAAATTGA
Found at i:24857 original size:41 final size:42
Alignment explanation
Indices: 24811--24900 Score: 146
Period size: 41 Copynumber: 2.1 Consensus size: 42
24801 TAAAGGTTCG
*
24811 TTTTTGTTCGGTTTTTAAAAATTTTTATGTTTTTGAGATC-T
1 TTTTTGTTCGATTTTTAAAAATTTTTATGTTTTTGAGATCGT
*
24852 TTTTTGTTCGATTTTTGAAAATTTTTATGTTTTTGAGATCGT
1 TTTTTGTTCGATTTTTAAAAATTTTTATGTTTTTGAGATCGT
24894 TGTTTTG
1 T-TTTTG
24901 GGTACTACAA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
41 38 0.84
42 2 0.04
43 5 0.11
ACGTcount: A:0.18, C:0.04, G:0.17, T:0.61
Consensus pattern (42 bp):
TTTTTGTTCGATTTTTAAAAATTTTTATGTTTTTGAGATCGT
Found at i:26248 original size:41 final size:41
Alignment explanation
Indices: 26049--26236 Score: 313
Period size: 41 Copynumber: 4.6 Consensus size: 41
26039 AGTGAAGTAA
*
26049 ACCAGACATTACGTCTAGCAGGCTTGATGCCGGTGAAACAT
1 ACCAGACATTATGTCTAGCAGGCTTGATGCCGGTGAAACAT
* *
26090 ACCAGACATTATGTCTAGCAGGCTTGATGCTGTTGAAACAT
1 ACCAGACATTATGTCTAGCAGGCTTGATGCCGGTGAAACAT
*
26131 ACCAGACATTACGTCTAGCAGGCTTGATGCCGGTGAAACAT
1 ACCAGACATTATGTCTAGCAGGCTTGATGCCGGTGAAACAT
*
26172 ACCAGACTTTATGTCTAGCAGGCTTGATGCCGGTGAAACAT
1 ACCAGACATTATGTCTAGCAGGCTTGATGCCGGTGAAACAT
* *
26213 ATCAGACTTTATGTCTAGCAGGCT
1 ACCAGACATTATGTCTAGCAGGCT
26237 AACTGCCGGT
Statistics
Matches: 138, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 138 1.00
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.26
Consensus pattern (41 bp):
ACCAGACATTATGTCTAGCAGGCTTGATGCCGGTGAAACAT
Found at i:26926 original size:13 final size:13
Alignment explanation
Indices: 26908--26932 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
26898 AATTATATGA
26908 TATTTATGTGTTT
1 TATTTATGTGTTT
26921 TATTTATGTGTT
1 TATTTATGTGTT
26933 GTTTTAGTTA
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:0.16, C:0.00, G:0.16, T:0.68
Consensus pattern (13 bp):
TATTTATGTGTTT
Found at i:34174 original size:292 final size:292
Alignment explanation
Indices: 33650--34233 Score: 1015
Period size: 292 Copynumber: 2.0 Consensus size: 292
33640 GTTATCGATG
*
33650 AGCACATTCGGTACTATGTAACCCTTGTAACTGGTTGTGATGTGTAATGTTTTTACAGAGCCCCT
1 AGCACATTCGGTACTATGTAACCCTTGCAACTGGTTGTGATGTGTAATGTTTTTACAGAGCCCCT
* *
33715 ACCATTCGGTGGCATTTCGTCATCACTAAAAAAGATGAAATTATCTGCATTCAGGTTATTTACCC
66 ACCATTCGGTGGCATTTCCTCATCACTAAAAAAGATGAAATTATCCGCATTCAGGTTATTTACCC
*
33780 ACCTATCGAGCTTTTCTACAGATACATTGCTCGCCACATAAGCTTGATTTAACACTTTTAGCAAT
131 ACCTATCGAGCTTTTCTACAGATACATTGCTCACCACATAAGCTTGATTTAACACTTTTAGCAAT
33845 ACGTTTTGATGTAGCGCTAAGTTCAACAATAGAGATAATACCGAGATTCGCGCCGACTGCTTGTT
196 ACGTTTTGATGTAGCGCTAAGTTCAACAATAGAGATAATACCGAGATTCGCGCCGACTGCTTGTT
* *
33910 TAATTACTCCACAATGCTATATTCACTGTGCT
261 TAATTACTCAACAACGCTATATTCACTGTGCT
33942 AGCACATTCGGTACTATGTAACCCTTGCAACTGGTTGTGATGTGTAATGTTTTTACAGAGCCCCT
1 AGCACATTCGGTACTATGTAACCCTTGCAACTGGTTGTGATGTGTAATGTTTTTACAGAGCCCCT
* * *
34007 ACCATTCGGTGGTATTTCCTCATCACTAAAACAGATGAAATTATCCGCATTCAGGTTATTTATCC
66 ACCATTCGGTGGCATTTCCTCATCACTAAAAAAGATGAAATTATCCGCATTCAGGTTATTTACCC
34072 ACCTATCGAGCTTTTCTACAGATACATTGCTCACCACATAAGCTTGATTTAACACTTTTAGCAAT
131 ACCTATCGAGCTTTTCTACAGATACATTGCTCACCACATAAGCTTGATTTAACACTTTTAGCAAT
* * * * *
34137 ACGTTTTGATGTGGCTCTAAGTTCAGCAATAGAGATAATATCGAGATTTGCGCCGACTGCTTGTT
196 ACGTTTTGATGTAGCGCTAAGTTCAACAATAGAGATAATACCGAGATTCGCGCCGACTGCTTGTT
* * *
34202 TAATTACTCAACAACGTTATATTTATTGTGCT
261 TAATTACTCAACAACGCTATATTCACTGTGCT
34234 TAATAAACTT
Statistics
Matches: 275, Mismatches: 17, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
292 275 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (292 bp):
AGCACATTCGGTACTATGTAACCCTTGCAACTGGTTGTGATGTGTAATGTTTTTACAGAGCCCCT
ACCATTCGGTGGCATTTCCTCATCACTAAAAAAGATGAAATTATCCGCATTCAGGTTATTTACCC
ACCTATCGAGCTTTTCTACAGATACATTGCTCACCACATAAGCTTGATTTAACACTTTTAGCAAT
ACGTTTTGATGTAGCGCTAAGTTCAACAATAGAGATAATACCGAGATTCGCGCCGACTGCTTGTT
TAATTACTCAACAACGCTATATTCACTGTGCT
Found at i:39371 original size:24 final size:24
Alignment explanation
Indices: 39344--39389 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
39334 TACTGTCACA
39344 TACTAAGGCTAGTACGGAGCCTCG
1 TACTAAGGCTAGTACGGAGCCTCG
*
39368 TACTAAGGCTAGTATGGAGCCT
1 TACTAAGGCTAGTACGGAGCCT
39390 TGGTCATCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (24 bp):
TACTAAGGCTAGTACGGAGCCTCG
Found at i:40009 original size:13 final size:13
Alignment explanation
Indices: 39991--40027 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
39981 TTTTGAAAAG
39991 AAAATTCATTTTT
1 AAAATTCATTTTT
40004 AAAATTCATTTTT
1 AAAATTCATTTTT
40017 AAAATTC-TTTT
1 AAAATTCATTTT
40028 ACAAAGAGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 4 0.17
13 20 0.83
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (13 bp):
AAAATTCATTTTT
Found at i:40782 original size:17 final size:17
Alignment explanation
Indices: 40762--40803 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
40752 CTGTTCTAGT
40762 TTTTTTTTTTTTCTTGC
1 TTTTTTTTTTTTCTTGC
* *
40779 TTTTTCTTTTTTCTTTC
1 TTTTTTTTTTTTCTTGC
40796 TTTTTTTT
1 TTTTTTTT
40804 CTCTAGCCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.00, C:0.12, G:0.02, T:0.86
Consensus pattern (17 bp):
TTTTTTTTTTTTCTTGC
Found at i:40790 original size:21 final size:20
Alignment explanation
Indices: 40761--40805 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
40751 GCTGTTCTAG
40761 TTTT-TTTTTT-TTTCTTGCT
1 TTTTCTTTTTTCTTTCTT-CT
*
40780 TTTTCTTTTTTCTTTCTTTT
1 TTTTCTTTTTTCTTTCTTCT
40800 TTTTCT
1 TTTTCT
40806 CTAGCCTTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 4 0.17
20 13 0.57
21 6 0.26
ACGTcount: A:0.00, C:0.13, G:0.02, T:0.84
Consensus pattern (20 bp):
TTTTCTTTTTTCTTTCTTCT
Found at i:41558 original size:13 final size:13
Alignment explanation
Indices: 41540--41572 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
41530 CTGATTTTCC
41540 TTTTTTATTATTA
1 TTTTTTATTATTA
*
41553 TTTTTTATTATTC
1 TTTTTTATTATTA
41566 TTTTTTA
1 TTTTTTA
41573 AAATTAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTTTATTATTA
Found at i:50486 original size:17 final size:18
Alignment explanation
Indices: 50439--50478 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
50429 AAAAGTAAAA
50439 AAGAACGAAAAATTAATT
1 AAGAACGAAAAATTAATT
50457 AAGAACGAAAAATTAATT
1 AAGAACGAAAAATTAATT
50475 AAGA
1 AAGA
50479 GCTAAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.62, C:0.05, G:0.12, T:0.20
Consensus pattern (18 bp):
AAGAACGAAAAATTAATT
Found at i:51216 original size:14 final size:14
Alignment explanation
Indices: 51182--51218 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
51172 AAAGGGTCCA
*
51182 GTTGAACCGCATTG
1 GTTGAATCGCATTG
51196 GTTGAATCGCATTG
1 GTTGAATCGCATTG
51210 GTTGAATCG
1 GTTGAATCG
51219 AATCTAGTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (14 bp):
GTTGAATCGCATTG
Found at i:53998 original size:19 final size:17
Alignment explanation
Indices: 53968--54003 Score: 54
Period size: 19 Copynumber: 2.0 Consensus size: 17
53958 AAACCCACAC
53968 ATATAATAATATATATA
1 ATATAATAATATATATA
53985 ATATATATATATATATATA
1 ATATA-ATA-ATATATATA
54004 TAGCCCCACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 3 0.18
19 9 0.53
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATATAATAATATATATA
Found at i:54023 original size:2 final size:2
Alignment explanation
Indices: 53968--54005 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
53958 AAACCCACAC
53968 AT AT A- AT A- AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
54006 GCCCCACTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.09
2 30 0.91
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:62132 original size:14 final size:14
Alignment explanation
Indices: 62113--62152 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
62103 TGATCAATGT
* *
62113 TAAAATTTTAAGGG
1 TAAAATTTGAAGGC
62127 TAAAATTTGAAGGC
1 TAAAATTTGAAGGC
62141 TAAAATTTGAAG
1 TAAAATTTGAAG
62153 ACACTATCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.45, C:0.03, G:0.20, T:0.33
Consensus pattern (14 bp):
TAAAATTTGAAGGC
Found at i:68554 original size:14 final size:14
Alignment explanation
Indices: 68535--68563 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
68525 AAGGTCTCAT
68535 AGAGTAGAATATGA
1 AGAGTAGAATATGA
68549 AGAGTAGAATATGA
1 AGAGTAGAATATGA
68563 A
1 A
68564 ACCATAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.28, T:0.21
Consensus pattern (14 bp):
AGAGTAGAATATGA
Found at i:74928 original size:20 final size:20
Alignment explanation
Indices: 74891--74930 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
74881 TTGTACGGGA
* * *
74891 TTGCACTTTGGTGTCTCTGT
1 TTGCACTTCGATGCCTCTGT
74911 TTGCACTTCGATGCCTCTGT
1 TTGCACTTCGATGCCTCTGT
74931 AACATCCTGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.07, C:0.25, G:0.23, T:0.45
Consensus pattern (20 bp):
TTGCACTTCGATGCCTCTGT
Found at i:93507 original size:20 final size:19
Alignment explanation
Indices: 93445--93512 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 19
93435 TGGTGTCTTG
*
93445 GTTTGCGCTTCGGTGCCTCT
1 GTTTGCACTTC-GTGCCTCT
* * *
93465 GATCGCACATTCGTGCCTTT
1 GTTTGCAC-TTCGTGCCTCT
93485 GTTTGCACTTCAGTGCCTCT
1 GTTTGCACTTC-GTGCCTCT
93505 GTTATGCA
1 GTT-TGCA
93513 TCTATGATGC
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
19 3 0.08
20 28 0.74
21 7 0.18
ACGTcount: A:0.10, C:0.28, G:0.24, T:0.38
Consensus pattern (19 bp):
GTTTGCACTTCGTGCCTCT
Found at i:96782 original size:20 final size:18
Alignment explanation
Indices: 96735--96783 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
96725 AATAGAATAC
96735 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
96752 ATTAACA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
96772 ATTAAATTAATA
1 ATTAAATTAATA
96784 AAATACTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:98918 original size:14 final size:14
Alignment explanation
Indices: 98901--98936 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
98891 ATGATTGAAA
98901 ACTCTTTATTGTAT
1 ACTCTTTATTGTAT
98915 ACTCTTTATTGTAT
1 ACTCTTTATTGTAT
98929 ACTCTTTA
1 ACTCTTTA
98937 CGAAAGCAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.22, C:0.17, G:0.06, T:0.56
Consensus pattern (14 bp):
ACTCTTTATTGTAT
Found at i:105797 original size:8 final size:8
Alignment explanation
Indices: 105786--105813 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
105776 CTTTTAAAAA
105786 TTTAAATT
1 TTTAAATT
105794 TTTAAATT
1 TTTAAATT
105802 TTTAAATT
1 TTTAAATT
105810 TTTA
1 TTTA
105814 TAAAAATGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TTTAAATT
Found at i:105798 original size:16 final size:16
Alignment explanation
Indices: 105777--105818 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
105767 ATTTAATTTC
105777 TTTTAAAAATTTAAAT
1 TTTTAAAAATTTAAAT
**
105793 TTTTAAATTTTTAAAT
1 TTTTAAAAATTTAAAT
105809 TTTTATAAAA
1 TTTTA-AAAA
105819 ATGTTATAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 19 0.90
17 2 0.10
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTTTAAAAATTTAAAT
Found at i:105830 original size:21 final size:21
Alignment explanation
Indices: 105804--105860 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
105794 TTTAAATTTT
*
105804 TAAATTTTTATAAAAATGTTA
1 TAAATTTTTATAAAAATATTA
* *
105825 TAAATTTGTAAAAAAATATTA
1 TAAATTTTTATAAAAATATTA
105846 -AAA--TTTATAAAAATA
1 TAAATTTTTATAAAAATA
105861 ATAAATAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 10 0.32
20 3 0.10
21 18 0.58
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (21 bp):
TAAATTTTTATAAAAATATTA
Found at i:105847 original size:19 final size:21
Alignment explanation
Indices: 105810--105863 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
105800 TTTTTAAATT
**
105810 TTTATAAAAATGTTA-T-AAA
1 TTTATAAAAATAATATTAAAA
*
105829 TTTGTAAAAA-AATATTAAAA
1 TTTATAAAAATAATATTAAAA
105849 TTTATAAAAATAATA
1 TTTATAAAAATAATA
105864 AATAAATTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 2 0.07
19 10 0.36
20 12 0.43
21 4 0.14
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (21 bp):
TTTATAAAAATAATATTAAAA
Found at i:105859 original size:18 final size:19
Alignment explanation
Indices: 105803--105865 Score: 65
Period size: 18 Copynumber: 3.3 Consensus size: 19
105793 TTTTAAATTT
* *
105803 TTAAATTTTTATAAAAATG
1 TTAAAATTTTATAAAAATA
*
105822 TTATAAATTTGTAAAAAAATA
1 TTA-AAATTT-TATAAAAATA
105843 TTAAAA-TTTATAAAAATA
1 TTAAAATTTTATAAAAATA
*
105861 ATAAA
1 TTAAA
105866 TAAATTTAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
18 13 0.35
19 5 0.14
20 8 0.22
21 11 0.30
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (19 bp):
TTAAAATTTTATAAAAATA
Found at i:105863 original size:21 final size:19
Alignment explanation
Indices: 105810--105877 Score: 59
Period size: 20 Copynumber: 3.5 Consensus size: 19
105800 TTTTTAAATT
**
105810 TTTATAAAAATGTTATAAA
1 TTTATAAAAATAATATAAA
*
105829 TTTGTAAAAA-AATATTAAAA
1 TTTATAAAAATAATA-T-AAA
105849 TTTATAAAAATAATAAATAAA
1 TTTATAAAAATAAT--ATAAA
105870 TTTA-AAAA
1 TTTATAAAA
105878 TAAAAAAAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
18 2 0.05
19 10 0.25
20 16 0.40
21 10 0.25
22 1 0.03
23 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (19 bp):
TTTATAAAAATAATATAAA
Found at i:109401 original size:12 final size:13
Alignment explanation
Indices: 109378--109413 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
109368 ATAGGTATAA
*
109378 TAATATTAATATT
1 TAATACTAATATT
109391 TAATA-TAATATT
1 TAATACTAATATT
109403 TAATACTAATA
1 TAATACTAATA
109414 ATATTACAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 12 0.55
13 10 0.45
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (13 bp):
TAATACTAATATT
Found at i:111035 original size:126 final size:126
Alignment explanation
Indices: 110736--111036 Score: 487
Period size: 126 Copynumber: 2.4 Consensus size: 126
110726 AAGATCTGTG
* * *
110736 ATTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTGA-TTTCTCCTGTCTGCTCTACTGC
1 ATTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATT-ACTTTCTTCTGTCTACTCCACTGC
* *
110800 AACTTCAGGGAGATAAGACTGGATGCGATATGCTCTCTGCAACTTCAGAGAGGTGAGATCTG
65 AACTTCAGGGAGATAAGACTGGATGCGACATGCTCTCTGCAACTTCAGAGAGGTGAGATCTA
* * * * *
110862 ATTTTAATCCGCTCCACTACAACTTTAGGGGGATAAGATTACTTTCTTCTGTCTACTCCGCTGCA
1 ATTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTACTTTCTTCTGTCTACTCCACTGCA
*
110927 TCTTCAGGGAGATAAGACTGGATGCGACATGCTCTCTGCAACTTCAGAGAGGTGAGATCTA
66 ACTTCAGGGAGATAAGACTGGATGCGACATGCTCTCTGCAACTTCAGAGAGGTGAGATCTA
110988 ATTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTACTTTCTTC
1 ATTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTACTTTCTTC
111037 GATCTGTTCT
Statistics
Matches: 159, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
125 1 0.01
126 158 0.99
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.31
Consensus pattern (126 bp):
ATTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTACTTTCTTCTGTCTACTCCACTGCA
ACTTCAGGGAGATAAGACTGGATGCGACATGCTCTCTGCAACTTCAGAGAGGTGAGATCTA
Found at i:115772 original size:23 final size:24
Alignment explanation
Indices: 115738--115812 Score: 82
Period size: 24 Copynumber: 3.1 Consensus size: 24
115728 TGAACAAAAT
*
115738 ATGATTATG-AAATGAATAAAAGA
1 ATGATTATGAAAAAGAATAAAAGA
115761 ATGATGTA-GAAAAAGAATAAAAGA
1 ATGAT-TATGAAAAAGAATAAAAGA
* *
115785 ATAATTACTCGAAAAAGAATGAAAGA
1 ATGATTA-T-GAAAAAGAATAAAAGA
115811 AT
1 AT
115813 ACTGGCTCAA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
23 8 0.18
24 19 0.43
26 17 0.39
ACGTcount: A:0.59, C:0.03, G:0.17, T:0.21
Consensus pattern (24 bp):
ATGATTATGAAAAAGAATAAAAGA
Found at i:115783 original size:24 final size:24
Alignment explanation
Indices: 115751--115813 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 24
115741 ATTATGAAAT
*
115751 GAATAAAAGAATGATGTA-GAAAAA
1 GAATAAAAGAATAAT-TACGAAAAA
115775 GAATAAAAGAATAATTACTCGAAAAA
1 GAATAAAAGAATAATTA--CGAAAAA
*
115801 GAATGAAAGAATA
1 GAATAAAAGAATA
115814 CTGGCTCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 2 0.06
24 14 0.41
26 18 0.53
ACGTcount: A:0.62, C:0.03, G:0.17, T:0.17
Consensus pattern (24 bp):
GAATAAAAGAATAATTACGAAAAA
Found at i:115825 original size:26 final size:26
Alignment explanation
Indices: 115770--115826 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
115760 AATGATGTAG
* *
115770 AAAAAGAATAAAAGAATAATTACTCG
1 AAAAAGAATAAAAGAATAATGACTCA
* * *
115796 AAAAAGAATGAAAGAATACTGGCTCA
1 AAAAAGAATAAAAGAATAATGACTCA
115822 AAAAA
1 AAAAA
115827 TGCATATGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.61, C:0.09, G:0.14, T:0.16
Consensus pattern (26 bp):
AAAAAGAATAAAAGAATAATGACTCA
Found at i:123460 original size:12 final size:13
Alignment explanation
Indices: 123437--123472 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
123427 ATAGGTATAA
*
123437 TAATATTAATATT
1 TAATACTAATATT
123450 TAATA-TAATATT
1 TAATACTAATATT
123462 TAATACTAATA
1 TAATACTAATA
123473 ATATTACAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 12 0.55
13 10 0.45
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (13 bp):
TAATACTAATATT
Found at i:129352 original size:39 final size:40
Alignment explanation
Indices: 129246--129364 Score: 132
Period size: 40 Copynumber: 3.0 Consensus size: 40
129236 GCGTTTGGAC
* * * *
129246 AAAAAACGCCACTAAAAATCAAACAGTAGCGGCGCTTTTG
1 AAAAAACGCCGCTAAAAATCAAACATTAGCGGCGATTTTT
* * * *
129286 GAAAAACGCCGCTAAAGATCGATCATTAGCGGCGATTTTT
1 AAAAAACGCCGCTAAAAATCAAACATTAGCGGCGATTTTT
* * *
129326 AAAAAACGCTGCTAAAAAT-AAGCATTAGCGGCGTTTTTT
1 AAAAAACGCCGCTAAAAATCAAACATTAGCGGCGATTTTT
129365 GGAAAGCACC
Statistics
Matches: 65, Mismatches: 14, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
39 17 0.26
40 48 0.74
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (40 bp):
AAAAAACGCCGCTAAAAATCAAACATTAGCGGCGATTTTT
Found at i:129486 original size:41 final size:41
Alignment explanation
Indices: 129418--130592 Score: 1731
Period size: 41 Copynumber: 28.7 Consensus size: 41
129408 GAGTTTTTGG
* * *
129418 GGTCTTTAGCGGCATTTTCTGAA-AAGCGCCGCTAAAGCTCA
1 GGTCTTTAGCGGCGTTTT-TTAATAAGCGCCGCTAATGCTCA
*
129459 GGTCTTTAGCGGTGTTTTTTAATAAGCGCCGCTAATGCTCA
1 GGTCTTTAGCGGCGTTTTTTAATAAGCGCCGCTAATGCTCA
* * *
129500 GGTCTTTAGCGGCGTTTTTTAATAATCGCCGCTAATTCGCA
1 GGTCTTTAGCGGCGTTTTTTAATAAGCGCCGCTAATGCTCA
129541 GGTCTTTAGCGGCGTTTTTTAATAAGCGCCGCTAATGCTCA
1 GGTCTTTAGCGGCGTTTTTTAATAAGCGCCGCTAATGCTCA
* *
129582 GGTCTTTAGCGGCGTTTTTGAATAAGCACCGCTAATGCTCA
1 GGTCTTTAGCGGCGTTTTTTAATAAGCGCCGCTAATGCTCA
* * *
129623 GGTCTTTAGCGGCGTTTTTGAATAAGCGCCACTAATTCTCA
1 GGTCTTTAGCGGCGTTTTTTAATAAGCGCCGCTAATGCTCA
* * * *
129664 GGTCTTTAGCGGCATTTATTAATAAGCACCGCGAATGCTCA
1 GGTCTTTAGCGGCGTTTTTTAATAAGCGCCGCTAATGCTCA
129705 GGTCTTTAGCGGCGTTTTTTAATAAGCGCCGCTAATGCTCA
1 GGTCTTTAGCGGCGTTTTTTAATAAGCGCCGCTAATGCTCA
* *
129746 GGTCTTTAGCGGCGTTTTTGAATAAGCACCGCTAATGCTCA
1 GGTCTTTAGCGGCGTTTTTTAATAAGCGCCGCTAATGCTCA
* * * *
129787 GGTCTTCAGCGGCGTTTTCTAATAAGCGCCACTAATTCTCA
1 GGTCTTTAGCGGCGTTTTTTAATAAGCGCCGCTAATGCTCA
* * * *
129828 GGTCTTTAGCGGCATTTATTAATAAGCACCGCGAATGCTCA
1 GGTCTTTAGCGGCGTTTTTTAATAAGCGCCGCTAATGCTCA
129869 GGTCTTTAGCGGCGTTTTTTAATAAGCGCCGCTAATGCTCA
1 GGTCTTTAGCGGCGTTTTTTAATAAGCGCCGCTAATGCTCA
* *
129910 GGTCTTTAGCGGCGTTTTTGAATAAGCACCGCTAATGCTCA
1 GGTCTTTAGCGGCGTTTTTTAATAAGCGCCGCTAATGCTCA
* * * *
129951 GGTCTTCAGCGGCGTTTTCTAATAAGCGCCACTAATTCTCA
1 GGTCTTTAGCGGCGTTTTTTAATAAGCGCCGCTAATGCTCA
* * * *
129992 GGTCTTTAGCGGCATTTATTAATAAGCACCGCGAATGCTCA
1 GGTCTTTAGCGGCGTTTTTTAATAAGCGCCGCTAATGCTCA
130033 GGTCTTTAGCGGCGTTTTTTAATAAGCGCCGCTAATGCTCA
1 GGTCTTTAGCGGCGTTTTTTAATAAGCGCCGCTAATGCTCA
* *
130074 GGTCTTTAGCGGCGTTTTTGAATAAGCACCGCTAATGCTCA
1 GGTCTTTAGCGGCGTTTTTTAATAAGCGCCGCTAATGCTCA
* * * *
130115 GGTCTTCAGCGGCGTTTTCTAATAAGCGCCACTAATTCTCA
1 GGTCTTTAGCGGCGTTTTTTAATAAGCGCCGCTAATGCTCA
* * * *
130156 GGTCTTTAGCGGCATTTATTAATAAGCACCGCGAATGCTCA
1 GGTCTTTAGCGGCGTTTTTTAATAAGCGCCGCTAATGCTCA
130197 GGTCTTTAGCGGCGTTTTTTAATAAGCGCCGCTAATGCTCA
1 GGTCTTTAGCGGCGTTTTTTAATAAGCGCCGCTAATGCTCA
* *
130238 GGTCTTTAGCGGCGTTTTTGAATAAGCACCGCTAATGCTCA
1 GGTCTTTAGCGGCGTTTTTTAATAAGCGCCGCTAATGCTCA
* * * *
130279 GGTCTTCAGCGGCGTTTTCTAATAAGCGCCACTAATTCTCA
1 GGTCTTTAGCGGCGTTTTTTAATAAGCGCCGCTAATGCTCA
* * * *
130320 GGTCTTTAGCGGCATTTATTAATAAGCACCGCGAATGCTCA
1 GGTCTTTAGCGGCGTTTTTTAATAAGCGCCGCTAATGCTCA
130361 GGTCTTTAGCGGCGTTTTTTAATAAGCGCCGCTAATGCTCA
1 GGTCTTTAGCGGCGTTTTTTAATAAGCGCCGCTAATGCTCA
* *
130402 GGTCTTTAGCGGCGTTTTTGAATAAGCACCGCTAATGCTCA
1 GGTCTTTAGCGGCGTTTTTTAATAAGCGCCGCTAATGCTCA
* * * *
130443 GGTCTTCAGCGGCGTTTTCTAATAAGCGCCACTAATTCTCA
1 GGTCTTTAGCGGCGTTTTTTAATAAGCGCCGCTAATGCTCA
* * * *
130484 GGTCTTTAGCGGCATTTATTAATAAGCACCGCGAATGCTCA
1 GGTCTTTAGCGGCGTTTTTTAATAAGCGCCGCTAATGCTCA
130525 GGTCTTTAGCGGCGTTTTTTAATAAGCGCCGCTAATGCTCA
1 GGTCTTTAGCGGCGTTTTTTAATAAGCGCCGCTAATGCTCA
*
130566 GGTCTTTAGCGGCGTTTTTGAATAAGC
1 GGTCTTTAGCGGCGTTTTTTAATAAGC
130593 ACATTAGTTT
Statistics
Matches: 1005, Mismatches: 128, Indels: 2
0.89 0.11 0.00
Matches are distributed among these distances:
40 3 0.00
41 1002 1.00
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.32
Consensus pattern (41 bp):
GGTCTTTAGCGGCGTTTTTTAATAAGCGCCGCTAATGCTCA
Found at i:129624 original size:164 final size:164
Alignment explanation
Indices: 129418--130594 Score: 2178
Period size: 164 Copynumber: 7.2 Consensus size: 164
129408 GAGTTTTTGG
* * * * * *
129418 GGTCTTTAGCGGCATTTTCTGAA-AAGCGCCGCTAAAGCTCAGGTCTTTAGCGGTGTTTTTTAAT
1 GGTCTTTAGCGGCGTTTT-TGAATAAGCACCGCTAATGCTCAGGTCTTCAGCGGCGTTTTCTAAT
* * * * * * * * *
129482 AAGCGCCGCTAATGCTCAGGTCTTTAGCGGCGTTTTTTAATAATCGCCGCTAATTCGCAGGTCTT
65 AAGCGCCACTAATTCTCAGGTCTTTAGCGGCATTTATTAATAAGCACCGCGAATGCTCAGGTCTT
129547 TAGCGGCGTTTTTTAATAAGCGCCGCTAATGCTCA
130 TAGCGGCGTTTTTTAATAAGCGCCGCTAATGCTCA
*
129582 GGTCTTTAGCGGCGTTTTTGAATAAGCACCGCTAATGCTCAGGTCTTTAGCGGCGTTTT-TGAAT
1 GGTCTTTAGCGGCGTTTTTGAATAAGCACCGCTAATGCTCAGGTCTTCAGCGGCGTTTTCT-AAT
129646 AAGCGCCACTAATTCTCAGGTCTTTAGCGGCATTTATTAATAAGCACCGCGAATGCTCAGGTCTT
65 AAGCGCCACTAATTCTCAGGTCTTTAGCGGCATTTATTAATAAGCACCGCGAATGCTCAGGTCTT
129711 TAGCGGCGTTTTTTAATAAGCGCCGCTAATGCTCA
130 TAGCGGCGTTTTTTAATAAGCGCCGCTAATGCTCA
129746 GGTCTTTAGCGGCGTTTTTGAATAAGCACCGCTAATGCTCAGGTCTTCAGCGGCGTTTTCTAATA
1 GGTCTTTAGCGGCGTTTTTGAATAAGCACCGCTAATGCTCAGGTCTTCAGCGGCGTTTTCTAATA
129811 AGCGCCACTAATTCTCAGGTCTTTAGCGGCATTTATTAATAAGCACCGCGAATGCTCAGGTCTTT
66 AGCGCCACTAATTCTCAGGTCTTTAGCGGCATTTATTAATAAGCACCGCGAATGCTCAGGTCTTT
129876 AGCGGCGTTTTTTAATAAGCGCCGCTAATGCTCA
131 AGCGGCGTTTTTTAATAAGCGCCGCTAATGCTCA
129910 GGTCTTTAGCGGCGTTTTTGAATAAGCACCGCTAATGCTCAGGTCTTCAGCGGCGTTTTCTAATA
1 GGTCTTTAGCGGCGTTTTTGAATAAGCACCGCTAATGCTCAGGTCTTCAGCGGCGTTTTCTAATA
129975 AGCGCCACTAATTCTCAGGTCTTTAGCGGCATTTATTAATAAGCACCGCGAATGCTCAGGTCTTT
66 AGCGCCACTAATTCTCAGGTCTTTAGCGGCATTTATTAATAAGCACCGCGAATGCTCAGGTCTTT
130040 AGCGGCGTTTTTTAATAAGCGCCGCTAATGCTCA
131 AGCGGCGTTTTTTAATAAGCGCCGCTAATGCTCA
130074 GGTCTTTAGCGGCGTTTTTGAATAAGCACCGCTAATGCTCAGGTCTTCAGCGGCGTTTTCTAATA
1 GGTCTTTAGCGGCGTTTTTGAATAAGCACCGCTAATGCTCAGGTCTTCAGCGGCGTTTTCTAATA
130139 AGCGCCACTAATTCTCAGGTCTTTAGCGGCATTTATTAATAAGCACCGCGAATGCTCAGGTCTTT
66 AGCGCCACTAATTCTCAGGTCTTTAGCGGCATTTATTAATAAGCACCGCGAATGCTCAGGTCTTT
130204 AGCGGCGTTTTTTAATAAGCGCCGCTAATGCTCA
131 AGCGGCGTTTTTTAATAAGCGCCGCTAATGCTCA
130238 GGTCTTTAGCGGCGTTTTTGAATAAGCACCGCTAATGCTCAGGTCTTCAGCGGCGTTTTCTAATA
1 GGTCTTTAGCGGCGTTTTTGAATAAGCACCGCTAATGCTCAGGTCTTCAGCGGCGTTTTCTAATA
130303 AGCGCCACTAATTCTCAGGTCTTTAGCGGCATTTATTAATAAGCACCGCGAATGCTCAGGTCTTT
66 AGCGCCACTAATTCTCAGGTCTTTAGCGGCATTTATTAATAAGCACCGCGAATGCTCAGGTCTTT
130368 AGCGGCGTTTTTTAATAAGCGCCGCTAATGCTCA
131 AGCGGCGTTTTTTAATAAGCGCCGCTAATGCTCA
130402 GGTCTTTAGCGGCGTTTTTGAATAAGCACCGCTAATGCTCAGGTCTTCAGCGGCGTTTTCTAATA
1 GGTCTTTAGCGGCGTTTTTGAATAAGCACCGCTAATGCTCAGGTCTTCAGCGGCGTTTTCTAATA
130467 AGCGCCACTAATTCTCAGGTCTTTAGCGGCATTTATTAATAAGCACCGCGAATGCTCAGGTCTTT
66 AGCGCCACTAATTCTCAGGTCTTTAGCGGCATTTATTAATAAGCACCGCGAATGCTCAGGTCTTT
130532 AGCGGCGTTTTTTAATAAGCGCCGCTAATGCTCA
131 AGCGGCGTTTTTTAATAAGCGCCGCTAATGCTCA
130566 GGTCTTTAGCGGCGTTTTTGAATAAGCAC
1 GGTCTTTAGCGGCGTTTTTGAATAAGCAC
130595 ATTAGTTTTG
Statistics
Matches: 996, Mismatches: 14, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
163 5 0.01
164 990 0.99
165 1 0.00
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.32
Consensus pattern (164 bp):
GGTCTTTAGCGGCGTTTTTGAATAAGCACCGCTAATGCTCAGGTCTTCAGCGGCGTTTTCTAATA
AGCGCCACTAATTCTCAGGTCTTTAGCGGCATTTATTAATAAGCACCGCGAATGCTCAGGTCTTT
AGCGGCGTTTTTTAATAAGCGCCGCTAATGCTCA
Found at i:130878 original size:4 final size:4
Alignment explanation
Indices: 130871--130896 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
130861 ATATATATAT
130871 ATAG ATAG ATAG ATAG ATAG ATAG AT
1 ATAG ATAG ATAG ATAG ATAG ATAG AT
130897 CACTTTATGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.23, T:0.27
Consensus pattern (4 bp):
ATAG
Found at i:131096 original size:12 final size:11
Alignment explanation
Indices: 131079--131125 Score: 53
Period size: 12 Copynumber: 4.2 Consensus size: 11
131069 GGACAGGACC
131079 AAAATATAAGAA
1 AAAATATAA-AA
131091 AAAATAT-AAA
1 AAAATATAAAA
131101 AAAATATAAAA
1 AAAATATAAAA
131112 AGGAAATA-AAAA
1 A--AAATATAAAA
131124 AA
1 AA
131126 CTAAAATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
10 10 0.31
11 5 0.16
12 12 0.38
13 5 0.16
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (11 bp):
AAAATATAAAA
Found at i:131102 original size:10 final size:10
Alignment explanation
Indices: 131079--131125 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
131069 GGACAGGACC
131079 AAAATATAAGAA
1 AAAATAT-A-AA
131091 AAAATATAAA
1 AAAATATAAA
131101 AAAATATAAA
1 AAAATATAAA
131111 AAGGAA-ATAAA
1 AA--AATATAAA
131122 AAAA
1 AAAA
131126 CTAAAATTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
9 2 0.06
10 14 0.42
11 8 0.24
12 9 0.27
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (10 bp):
AAAATATAAA
Found at i:131104 original size:22 final size:21
Alignment explanation
Indices: 131079--131125 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
131069 GGACAGGACC
131079 AAAATATAAGAAA-AAATATAAA
1 AAAATATAA-AAAGAAA-ATAAA
*
131101 AAAATATAAAAAGGAAATAAA
1 AAAATATAAAAAGAAAATAAA
131122 AAAA
1 AAAA
131126 CTAAAATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 12 0.52
22 11 0.48
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (21 bp):
AAAATATAAAAAGAAAATAAA
Found at i:131193 original size:23 final size:22
Alignment explanation
Indices: 131146--131200 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
131136 TAATTTTATC
131146 AAAAACTTT--TAAATATTACT
1 AAAAACTTTAATAAATATTACT
* *
131166 TAAAACTTTAATAATTATTTACT
1 AAAAACTTTAATAAATA-TTACT
*
131189 AAAAATTTTAAT
1 AAAAACTTTAAT
131201 GAAAATACAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 8 0.29
22 5 0.18
23 15 0.54
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (22 bp):
AAAAACTTTAATAAATATTACT
Found at i:131225 original size:4 final size:4
Alignment explanation
Indices: 131203--131244 Score: 50
Period size: 4 Copynumber: 10.5 Consensus size: 4
131193 ATTTTAATGA
* *
131203 AAAT ACAAT AAAA AAAT AAAT AAAT -ACT AAAT AAAT AAAT AA
1 AAAT A-AAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
131245 TGTGAAATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
3 2 0.06
4 26 0.81
5 4 0.12
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:131698 original size:169 final size:170
Alignment explanation
Indices: 131338--131703 Score: 512
Period size: 169 Copynumber: 2.2 Consensus size: 170
131328 TTTAAATTCC
* *
131338 TTAGTGGCGTTTTTGCCAAAAACGCCGC--TAAAGGTAGACATTACCGGCGTTTTTATAAAAAAC
1 TTAGTGGCGTTTTTGTCAAAAACGCCGCAAGAAAGGTAGACATTACCGGCGTTTTTATAAAAAAC
* *
131401 GCCAAAAAAATTTTCCAAGCTTTTTTGGTACGACGTCGTTTCAGTTTATGGATAAAATTTAAAAT
66 GCCAAAAAAATTTTCCAAGCTGTTTTGATACGACGTCGTTTCAGTTTATGGATAAAATTTAAAAT
* * *
131466 TTGGAAAAACGGCGCCGTTTCAGTGGAAGAATAGAATCTG
131 TTGGAAAAACGGCGCCGTTTCAGTCGAAGAATAGAATATA
* *
131506 TTACTGGCGTTTTAT-T-GAAAACGCCGCAAGAAAGGTAGACATTACCGGCGTTTTTATAAAAAA
1 TTAGTGGCGTTTT-TGTCAAAAACGCCGCAAGAAAGGTAGACATTACCGGCGTTTTTATAAAAAA
*
131569 CGCCACAAAAATTTTCCAAGCTGTTTTGATACGACGTCGTTTCAGTTTATGGATAAAATTTAAAA
65 CGCCAAAAAAATTTTCCAAGCTGTTTTGATACGACGTCGTTTCAGTTTATGGATAAAATTTAAAA
** * **
131634 TTTGGAAAAACGGCGCCGTTTCTTTACG-TGCTTTA-AA-ATA
130 TTTGGAAAAACGGCGCCGTTTCAGT-CGAAG-AATAGAATATA
*
131674 TTAGTGGCGTTTTTGTCTAAAACGCCGCAA
1 TTAGTGGCGTTTTTGTCAAAAACGCCGCAA
131704 ATGTGAATAC
Statistics
Matches: 174, Mismatches: 17, Indels: 13
0.85 0.08 0.06
Matches are distributed among these distances:
167 11 0.06
168 26 0.15
169 134 0.77
170 3 0.02
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (170 bp):
TTAGTGGCGTTTTTGTCAAAAACGCCGCAAGAAAGGTAGACATTACCGGCGTTTTTATAAAAAAC
GCCAAAAAAATTTTCCAAGCTGTTTTGATACGACGTCGTTTCAGTTTATGGATAAAATTTAAAAT
TTGGAAAAACGGCGCCGTTTCAGTCGAAGAATAGAATATA
Found at i:144254 original size:43 final size:43
Alignment explanation
Indices: 144174--144469 Score: 152
Period size: 43 Copynumber: 6.9 Consensus size: 43
144164 NNNNNNNNNN
* * ** * *
144174 AAAAAAACGCCACTAAAGGTGTTGGCCTTTAGTGGCGTTTTCG
1 AAAAAAGCGCCACTAAAGATCATGGTCTTTAGCGGCGTTTTCG
*
144217 AAAAAAGCGCCACTAAAGATCATGGTCTTTCGCGGCGTTTGT-G
1 AAAAAAGCGCCACTAAAGATCATGGTCTTTAGCGGCGTTT-TCG
*** * * * * * *
144260 GGGACAGCGCCGCTATAGATCAGGGTCTTTTGCGGCGTTTTAG
1 AAAAAAGCGCCACTAAAGATCATGGTCTTTAGCGGCGTTTTCG
** * * * *
144303 GGAAAAGCGCCACTAAAGACCCTGATCTTTAGCGGCGCTTGTCG
1 AAAAAAGCGCCACTAAAGATCATGGTCTTTAGCGGCG-TTTTCG
* * * * *
144347 CAAAAAA--GCCACTAAAGACCCTGATCTTTAGCGACG-TTTCC
1 -AAAAAAGCGCCACTAAAGATCATGGTCTTTAGCGGCGTTTTCG
** * * ** * *
144388 ACTAAAGCGCCGCTAAAGACCATTATCTTTAGCGGCG-CTTCC
1 AAAAAAGCGCCACTAAAGATCATGGTCTTTAGCGGCGTTTTCG
** * * * * *
144430 ACTAAAGCGCCGCTAAAGGTCTTAGTCTTCAGCGGCGTTT
1 AAAAAAGCGCCACTAAAGATCATGGTCTTTAGCGGCGTTT
144470 GTGCTAGAAG
Statistics
Matches: 201, Mismatches: 45, Indels: 14
0.77 0.17 0.05
Matches are distributed among these distances:
40 4 0.02
41 3 0.01
42 61 0.30
43 124 0.62
44 5 0.02
45 4 0.02
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.25
Consensus pattern (43 bp):
AAAAAAGCGCCACTAAAGATCATGGTCTTTAGCGGCGTTTTCG
Found at i:144417 original size:42 final size:42
Alignment explanation
Indices: 144306--144447 Score: 171
Period size: 42 Copynumber: 3.4 Consensus size: 42
144296 GTTTTAGGGA
144306 AAAGCGCCACTAAAGACCCTGATCTTTAGCGGCGCTTGTCGCA--
1 AAAGCGCCACTAAAGACCCTGATCTTTAGCGGCG-TT-TC-CACT
** *
144349 AAAAAGCCACTAAAGACCCTGATCTTTAGCGACGTTTCCACT
1 AAAGCGCCACTAAAGACCCTGATCTTTAGCGGCGTTTCCACT
* * * *
144391 AAAGCGCCGCTAAAGACCATTATCTTTAGCGGCGCTTCCACT
1 AAAGCGCCACTAAAGACCCTGATCTTTAGCGGCGTTTCCACT
*
144433 AAAGCGCCGCTAAAG
1 AAAGCGCCACTAAAG
144448 GTCTTAGTCT
Statistics
Matches: 87, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
40 2 0.02
41 2 0.02
42 52 0.60
43 31 0.36
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.21
Consensus pattern (42 bp):
AAAGCGCCACTAAAGACCCTGATCTTTAGCGGCGTTTCCACT
Found at i:144464 original size:42 final size:42
Alignment explanation
Indices: 144306--144466 Score: 135
Period size: 42 Copynumber: 3.8 Consensus size: 42
144296 GTTTTAGGGA
* * * * * * *
144306 AAAGCGCCACTAAAGACCCTGATCTTTAGCGGCGCTTGTCGCA
1 AAAGCGCCGCTAAAGACCATTATCTTCAGCGGCGCTT-CCACT
** * * * * * *
144349 AAAAAGCCACTAAAGACCCTGATCTTTAGCGACGTTTCCACT
1 AAAGCGCCGCTAAAGACCATTATCTTCAGCGGCGCTTCCACT
*
144391 AAAGCGCCGCTAAAGACCATTATCTTTAGCGGCGCTTCCACT
1 AAAGCGCCGCTAAAGACCATTATCTTCAGCGGCGCTTCCACT
**
144433 AAAGCGCCGCTAAAGGTC-TTAGTCTTCAGCGGCG
1 AAAGCGCCGCTAAAGACCATTA-TCTTCAGCGGCG
144467 TTTGTGCTAG
Statistics
Matches: 100, Mismatches: 17, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
41 3 0.03
42 64 0.64
43 33 0.33
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.22
Consensus pattern (42 bp):
AAAGCGCCGCTAAAGACCATTATCTTCAGCGGCGCTTCCACT
Found at i:144633 original size:22 final size:22
Alignment explanation
Indices: 144606--144648 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
144596 TTGCGGCGTT
*
144606 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
144628 AAAAAGCGCCGCTAAAAGCCT
1 AAAAAGCGCCGCTAAAAGCCT
144649 GTTTTGGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.42, C:0.28, G:0.21, T:0.09
Consensus pattern (22 bp):
AAAAAGCGCCGCTAAAAGCCTA
Found at i:145208 original size:43 final size:42
Alignment explanation
Indices: 145154--145339 Score: 232
Period size: 43 Copynumber: 4.4 Consensus size: 42
145144 ATCGTCGCAA
* * *
145154 ACTTTTGCGGCGCTTTTAC-CACAAACGCCGCTATAGATCAGG
1 ACTTTAGCGGCGCTTTT-CTAACAAACGCCGCTATAGATCAAG
*
145196 ATCTTTAGCGGCGCTTTTCTAACAAACGCCGCTATAGCTCAAG
1 A-CTTTAGCGGCGCTTTTCTAACAAACGCCGCTATAGATCAAG
*
145239 ACCTTTAGCGGCGCTTTTCTAACAAACGCCGCTATAGCTCAAG
1 A-CTTTAGCGGCGCTTTTCTAACAAACGCCGCTATAGATCAAG
** *
145282 ACTTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGAACAA-
1 AC-TTTAGCGGCGCTTTTCTAACAAACGCCGCTATAGATCAAG
*
145324 ACCTTTAGCGACGCTT
1 A-CTTTAGCGGCGCTT
145340 CTCGCAAAAA
Statistics
Matches: 130, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
42 16 0.12
43 114 0.88
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (42 bp):
ACTTTAGCGGCGCTTTTCTAACAAACGCCGCTATAGATCAAG
Found at i:151088 original size:124 final size:124
Alignment explanation
Indices: 150934--151183 Score: 482
Period size: 124 Copynumber: 2.0 Consensus size: 124
150924 CTTAAAATAT
* *
150934 AAACTCTTAAACCGACCTTAAATCTTAAATAAAATTATATACCCTAAACTGAAAATCCTAAACTA
1 AAACTCTTAAACCGACCTTAAATCTTAAATAAAATCATATACCCTAAACTGAAAACCCTAAACTA
150999 TAGTGATAATTAATTCAATATTTTAAAATTAATAATATCTCTTTTACGATTATATAAGA
66 TAGTGATAATTAATTCAATATTTTAAAATTAATAATATCTCTTTTACGATTATATAAGA
151058 AAACTCTTAAACCGACCTTAAATCTTAAATAAAATCATATACCCTAAACTGAAAACCCTAAACTA
1 AAACTCTTAAACCGACCTTAAATCTTAAATAAAATCATATACCCTAAACTGAAAACCCTAAACTA
151123 TAGTGATAATTAATTCAATATTTTAAAATTAATAATATCTCTTTTACGATTATATAAGA
66 TAGTGATAATTAATTCAATATTTTAAAATTAATAATATCTCTTTTACGATTATATAAGA
151182 AA
1 AA
151184 TTTTTTATTA
Statistics
Matches: 124, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
124 124 1.00
ACGTcount: A:0.46, C:0.15, G:0.05, T:0.34
Consensus pattern (124 bp):
AAACTCTTAAACCGACCTTAAATCTTAAATAAAATCATATACCCTAAACTGAAAACCCTAAACTA
TAGTGATAATTAATTCAATATTTTAAAATTAATAATATCTCTTTTACGATTATATAAGA
Found at i:151545 original size:73 final size:73
Alignment explanation
Indices: 151392--151610 Score: 285
Period size: 73 Copynumber: 3.0 Consensus size: 73
151382 AAACATCGCT
* * * * * * *
151392 AAATCCCTGAAAGCGCAAAAAAAGGTGTAGTTTTGGCTTAGGTTTTTTTGCGGCGCTTCCTTAAA
1 AAATCCCCGAAAGCGCACAAAACGGAGTCGTTTTGGCTTAGG-TTTTTTGCGGCGCTTTCTAAAA
*
151457 AACGCCGCT
65 AACGCCGCA
* *
151466 AAATCCCCGAAAGCGCACAAAACGGAGTCGTTTTGCCTTATGTTTTTTGCGGCGCTTTCTAAAAA
1 AAATCCCCGAAAGCGCACAAAACGGAGTCGTTTTGGCTTAGGTTTTTTGCGGCGCTTTCTAAAAA
151531 ACGCCGCA
66 ACGCCGCA
* * * * **
151539 AAATCCCCGAAAGCTCACAAAACGGCGTCGTTTTGGATTAGGTTTTTTGCAGCGCTTTCCCAAAA
1 AAATCCCCGAAAGCGCACAAAACGGAGTCGTTTTGGCTTAGGTTTTTTGCGGCGCTTTCTAAAAA
151604 ACGCCGC
66 ACGCCGC
151611 TAAAGCCCTG
Statistics
Matches: 127, Mismatches: 18, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
73 92 0.72
74 35 0.28
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (73 bp):
AAATCCCCGAAAGCGCACAAAACGGAGTCGTTTTGGCTTAGGTTTTTTGCGGCGCTTTCTAAAAA
ACGCCGCA
Found at i:151846 original size:113 final size:114
Alignment explanation
Indices: 151514--151949 Score: 678
Period size: 113 Copynumber: 3.8 Consensus size: 114
151504 TATGTTTTTT
* * * * * *
151514 GCGGCGCTTTCTAAAAAACGCCGCAAAATCCCCGAAAGCTCACAAAACGGCGTCGTTTTGGATTA
1 GCGGCGCTTCCTTAAAAACGCCGCTAAATCCACGAAAGCTCGCAAAACTGCGTCGTTTTGGATTA
* * *
151579 GGTTTTTTGCAGCGCTTTCCCAAAAACGCCGCTAAAGCCCTGAGCATTA
66 GGTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCGTGAGCATTA
* * * ** * **
151628 GCGGCGCTTTCTTAAAAACGCCGCTAAACCCCCGAAAGCTCATAAAAATTGCGTCGTTTTACATT
1 GCGGCGCTTCCTTAAAAACGCCGCTAAATCCACGAAAGCTC-GCAAAACTGCGTCGTTTTGGATT
151693 AGGTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCGTGAGCATTA
65 AGGTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCGTGAGCATTA
151743 GCGGCGCTTCCTTAAAAACGCCGCTAAATCCAC-AAAGCTCGCAAAACTGCGTCGTTTTGGATTA
1 GCGGCGCTTCCTTAAAAACGCCGCTAAATCCACGAAAGCTCGCAAAACTGCGTCGTTTTGGATTA
151807 GGTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCGTGAGCATTA
66 GGTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCGTGAGCATTA
151856 GCGGCGCTTCCTTAAAAACGCCGCTAAATCCAC-AAAGCTCGCAAAACTGCGTCGTTTTGGATTA
1 GCGGCGCTTCCTTAAAAACGCCGCTAAATCCACGAAAGCTCGCAAAACTGCGTCGTTTTGGATTA
* *
151920 GGTTTTTTGCGGCGCTTTTTAAAAAACGCC
66 GGTTTTTTGCGGCGCTTTCTCAAAAACGCC
151950 ACTATTGCTT
Statistics
Matches: 299, Mismatches: 22, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
113 160 0.54
114 45 0.15
115 94 0.31
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.26
Consensus pattern (114 bp):
GCGGCGCTTCCTTAAAAACGCCGCTAAATCCACGAAAGCTCGCAAAACTGCGTCGTTTTGGATTA
GGTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCGTGAGCATTA
Found at i:152048 original size:11 final size:12
Alignment explanation
Indices: 152021--152048 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
152011 CGTTTGAATA
152021 AAAAACGCCGCT
1 AAAAACGCCGCT
152033 AAAAACGCCGCT
1 AAAAACGCCGCT
152045 AAAA
1 AAAA
152049 GCCCGTTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.29, G:0.14, T:0.07
Consensus pattern (12 bp):
AAAAACGCCGCT
Found at i:153553 original size:24 final size:25
Alignment explanation
Indices: 153500--153553 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 25
153490 AGAAATTTAA
**
153500 AATAATACATAAAATAGTTAAAAAG
1 AATAATACATAAAATAGCAAAAAAG
*
153525 GATAATA-ATAAAATA-CAAAACAAG
1 AATAATACATAAAATAGCAAAA-AAG
153549 AATAA
1 AATAA
153554 AACGCACCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
23 3 0.12
24 15 0.62
25 6 0.25
ACGTcount: A:0.67, C:0.06, G:0.07, T:0.20
Consensus pattern (25 bp):
AATAATACATAAAATAGCAAAAAAG
Found at i:153651 original size:12 final size:12
Alignment explanation
Indices: 153634--153675 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
153624 TTAAAAAAAG
153634 TAATAATAATGA
1 TAATAATAATGA
* *
153646 TAATAATATTAA
1 TAATAATAATGA
*
153658 TAATAACAATGA
1 TAATAATAATGA
153670 TAATAA
1 TAATAA
153676 AAAAATCTGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (12 bp):
TAATAATAATGA
Found at i:154434 original size:5 final size:5
Alignment explanation
Indices: 154424--154451 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
154414 TTTTCGTTTT
154424 AAAAG AAAAG AAAAG AAAAG AAAAG AAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAA
154452 TAATAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:171294 original size:19 final size:18
Alignment explanation
Indices: 171253--171291 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
171243 AGTACAAAAT
171253 AATTCAAAATAAATTTTAA
1 AATTCAAAAT-AATTTTAA
171272 AATTCAAAAT-ATTTATAA
1 AATTCAAAATAATTT-TAA
171290 AA
1 AA
171292 ATTTCAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.21
18 5 0.26
19 10 0.53
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (18 bp):
AATTCAAAATAATTTTAA
Found at i:177865 original size:26 final size:26
Alignment explanation
Indices: 177830--177895 Score: 82
Period size: 25 Copynumber: 2.6 Consensus size: 26
177820 TACCGAGCTA
177830 CTAACACTAGCTTCAAATC-AGGGTTG
1 CTAACACTAGCTTCAAATCGA-GGTTG
** *
177856 CTAACACTAGCTT-AGTTCGATGTTG
1 CTAACACTAGCTTCAAATCGAGGTTG
177881 CTAACACTAGCTTCA
1 CTAACACTAGCTTCA
177896 GAGAATCCAC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
25 20 0.57
26 15 0.43
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (26 bp):
CTAACACTAGCTTCAAATCGAGGTTG
Found at i:179238 original size:24 final size:23
Alignment explanation
Indices: 179190--179238 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 23
179180 AATAGTATAG
*
179190 TTGCTATTTTAACCTTGAATTAA
1 TTGCTATTTTAACCTTGAATCAA
*
179213 TTGCTAATTTTAATCCTTTAA-CAA
1 TTGCT-ATTTTAA-CCTTGAATCAA
179237 TT
1 TT
179239 ATAATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 5 0.23
24 11 0.50
25 6 0.27
ACGTcount: A:0.31, C:0.14, G:0.06, T:0.49
Consensus pattern (23 bp):
TTGCTATTTTAACCTTGAATCAA
Found at i:181917 original size:18 final size:18
Alignment explanation
Indices: 181896--181938 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
181886 ATAAATTATT
*
181896 AAAAAACCA-TAAAAATA
1 AAAAAAACATTAAAAATA
*
181913 AAAAAAATATTTAAAAATA
1 AAAAAAACA-TTAAAAATA
181932 AAAAAAA
1 AAAAAAA
181939 TCGTTCAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
19 15 0.68
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.16
Consensus pattern (18 bp):
AAAAAAACATTAAAAATA
Found at i:182270 original size:17 final size:18
Alignment explanation
Indices: 182233--182267 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
182223 ATGAAAAAGA
182233 AAAAAAGTATTAATTTTT
1 AAAAAAGTATTAATTTTT
182251 AAAAAA-TATATAATTTT
1 AAAAAAGTAT-TAATTTT
182268 AAAGTTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (18 bp):
AAAAAAGTATTAATTTTT
Found at i:190518 original size:44 final size:45
Alignment explanation
Indices: 190453--190543 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
190443 ACCTCTATTC
* * *
190453 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
190497 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
190542 CA
1 CA
190544 ACTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:190558 original size:17 final size:16
Alignment explanation
Indices: 190524--190576 Score: 88
Period size: 16 Copynumber: 3.2 Consensus size: 16
190514 GATTAGCTAT
190524 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
190540 TACAACTCTAATCCCAA
1 TACACCTCTAAT-CCAA
190557 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
190573 TACA
1 TACA
190577 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
16 19 0.56
17 15 0.44
ACGTcount: A:0.40, C:0.36, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:202222 original size:13 final size:13
Alignment explanation
Indices: 202204--202228 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
202194 CAAATGGGTA
202204 GTTTTCTGCAAAT
1 GTTTTCTGCAAAT
202217 GTTTTCTGCAAA
1 GTTTTCTGCAAA
202229 CCAGTTTCCG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.44
Consensus pattern (13 bp):
GTTTTCTGCAAAT
Found at i:206066 original size:14 final size:14
Alignment explanation
Indices: 206043--206082 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
206033 ACAGAGAAGT
*
206043 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
206057 AAATCATTTTACGG
1 AAAACATTTTACAG
206071 AAAACATTTTAC
1 AAAACATTTTAC
206083 TGCCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:207830 original size:26 final size:26
Alignment explanation
Indices: 207794--207847 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
207784 CTTGTACATA
207794 TCTCTATGCCAATTCAAACAATTAAT
1 TCTCTATGCCAATTCAAACAATTAAT
207820 TCTCTATGCCAATTCAAACAATTAAT
1 TCTCTATGCCAATTCAAACAATTAAT
207846 TC
1 TC
207848 AATCTCATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.35
Consensus pattern (26 bp):
TCTCTATGCCAATTCAAACAATTAAT
Found at i:210983 original size:11 final size:11
Alignment explanation
Indices: 210969--210993 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
210959 ACCCAAATCC
210969 AAATAAATAAA
1 AAATAAATAAA
210980 AAATAAATAAA
1 AAATAAATAAA
210991 AAA
1 AAA
210994 CCAAATACAA
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAATAAATAAA
Found at i:216353 original size:25 final size:25
Alignment explanation
Indices: 216325--216378 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
216315 CTTGTGATGA
216325 TTTTTGAACCAA-TATTCTTTCAGTC
1 TTTTTGAA-CAATTATTCTTTCAGTC
* *
216350 TTTTTGAATAATTATTCTTTCATTC
1 TTTTTGAACAATTATTCTTTCAGTC
216375 TTTT
1 TTTT
216379 GGATTTCCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 2 0.08
25 24 0.92
ACGTcount: A:0.22, C:0.15, G:0.06, T:0.57
Consensus pattern (25 bp):
TTTTTGAACAATTATTCTTTCAGTC
Found at i:217093 original size:6 final size:6
Alignment explanation
Indices: 217082--217109 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
217072 TTCAATCAAA
217082 AAAATC AAAATC AAAATC AAAATC AAAA
1 AAAATC AAAATC AAAATC AAAATC AAAA
217110 AAGAAGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.71, C:0.14, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAATC
Found at i:217126 original size:29 final size:28
Alignment explanation
Indices: 217094--217184 Score: 105
Period size: 29 Copynumber: 3.1 Consensus size: 28
217084 AATCAAAATC
217094 AAAATCAAAATCAAAAAAGAAGAA-AAAGA
1 AAAATCAAAATCAAAAAA-AA-AATAAAGA
*
217123 AAAATCAAAGTCAAAAGCAAAAAATAAA-A
1 AAAATCAAAATCAAAA--AAAAAATAAAGA
*
217152 AAAATCAAAATAAAAAATAAAAATAAAGA
1 AAAATCAAAATCAAAAA-AAAAATAAAGA
217181 AAAA
1 AAAA
217185 AGAAAAAAGA
Statistics
Matches: 54, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
27 1 0.02
28 9 0.17
29 37 0.69
30 5 0.09
31 2 0.04
ACGTcount: A:0.77, C:0.07, G:0.07, T:0.10
Consensus pattern (28 bp):
AAAATCAAAATCAAAAAAAAAATAAAGA
Found at i:217166 original size:13 final size:13
Alignment explanation
Indices: 217150--217204 Score: 51
Period size: 13 Copynumber: 4.4 Consensus size: 13
217140 CAAAAAATAA
*
217150 AAAAAATCAAAAT
1 AAAAAATAAAAAT
217163 AAAAAATAAAAAT
1 AAAAAATAAAAAT
* *
217176 -AAAGA-AAAAAG
1 AAAAAATAAAAAT
* *
217187 AAAAAAGAAAAAG
1 AAAAAATAAAAAT
217200 AAAAA
1 AAAAA
217205 GGAGAGGCTA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
11 5 0.14
12 8 0.22
13 23 0.64
ACGTcount: A:0.84, C:0.02, G:0.07, T:0.07
Consensus pattern (13 bp):
AAAAAATAAAAAT
Found at i:217167 original size:41 final size:41
Alignment explanation
Indices: 217081--217204 Score: 109
Period size: 41 Copynumber: 3.1 Consensus size: 41
217071 ATTCAATCAA
* * *
217081 AAAAATCAAAATCAAAATCAAAATCAAAAAAGAAGAAAAAG
1 AAAAATCAAAATCAAAAGCAAAATAAAAAAAAAAGAAAAAG
* *
217122 AAAAATCAAAGTCAAAAGCAAAA-AATAAAAAAAATCAAAATA-
1 AAAAATCAAAATCAAAAGCAAAATAA-AAAAAAAA-GAAAA-AG
* *
217164 AAAAATAAAAAT--AAAG--AAA-AAAGAAAAAAGAAAAAG
1 AAAAATCAAAATCAAAAGCAAAATAAAAAAAAAAGAAAAAG
217200 AAAAA
1 AAAAA
217205 GGAGAGGCTA
Statistics
Matches: 70, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
35 1 0.01
36 9 0.13
37 7 0.10
38 5 0.07
40 5 0.07
41 28 0.40
42 14 0.20
43 1 0.01
ACGTcount: A:0.77, C:0.06, G:0.07, T:0.09
Consensus pattern (41 bp):
AAAAATCAAAATCAAAAGCAAAATAAAAAAAAAAGAAAAAG
Found at i:217205 original size:6 final size:7
Alignment explanation
Indices: 217176--217204 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
217166 AAATAAAAAT
217176 AAAGAAA
1 AAAGAAA
217183 AAAGAAA
1 AAAGAAA
217190 AAAG-AA
1 AAAGAAA
217196 AAAGAAA
1 AAAGAAA
217203 AA
1 AA
217205 GGAGAGGCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (7 bp):
AAAGAAA
Found at i:218086 original size:21 final size:21
Alignment explanation
Indices: 218061--218103 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
218051 CAGAAAAAAT
218061 ATGAAAAAGGAAAAAATGAAA
1 ATGAAAAAGGAAAAAATGAAA
*
218082 ATGAAAAATGAAAAAATGAAA
1 ATGAAAAAGGAAAAAATGAAA
218103 A
1 A
218104 AGTAAAAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.72, C:0.00, G:0.16, T:0.12
Consensus pattern (21 bp):
ATGAAAAAGGAAAAAATGAAA
Found at i:218096 original size:8 final size:8
Alignment explanation
Indices: 218055--218104 Score: 54
Period size: 8 Copynumber: 6.6 Consensus size: 8
218045 TTAAGTCAGA
218055 AAAAATATG
1 AAAAA-ATG
*
218064 -AAAAAGG
1 AAAAAATG
218071 AAAAAATG
1 AAAAAATG
218079 --AAAATG
1 AAAAAATG
218085 -AAAAATG
1 AAAAAATG
218092 AAAAAATG
1 AAAAAATG
218100 AAAAA
1 AAAAA
218105 GTAAAAATGG
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
6 6 0.17
7 8 0.22
8 22 0.61
ACGTcount: A:0.74, C:0.00, G:0.14, T:0.12
Consensus pattern (8 bp):
AAAAAATG
Found at i:218097 original size:15 final size:15
Alignment explanation
Indices: 218055--218113 Score: 61
Period size: 14 Copynumber: 4.0 Consensus size: 15
218045 TTAAGTCAGA
*
218055 AAAAATATGAAAAAGG
1 AAAAA-ATGAAAAATG
218071 AAAAAATG-AAAATG
1 AAAAAATGAAAAATG
218085 -AAAAATGAAAAAATG
1 AAAAAATG-AAAAATG
*
218100 AAAAAGT-AAAAATG
1 AAAAAATGAAAAATG
218114 GAGAGGCTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
13 7 0.18
14 12 0.32
15 9 0.24
16 10 0.26
ACGTcount: A:0.71, C:0.00, G:0.15, T:0.14
Consensus pattern (15 bp):
AAAAAATGAAAAATG
Found at i:218110 original size:21 final size:21
Alignment explanation
Indices: 218063--218111 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
218053 GAAAAAATAT
*
218063 GAAAAAGGAAAAAATGAAAAT
1 GAAAAAGGAAAAAATGAAAAA
*
218084 GAAAAATGAAAAAATGAAAAA
1 GAAAAAGGAAAAAATGAAAAA
218105 GTAAAAA
1 G-AAAAA
218112 TGGAGAGGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 20 0.80
22 5 0.20
ACGTcount: A:0.73, C:0.00, G:0.16, T:0.10
Consensus pattern (21 bp):
GAAAAAGGAAAAAATGAAAAA
Found at i:219560 original size:44 final size:44
Alignment explanation
Indices: 219512--219988 Score: 184
Period size: 44 Copynumber: 10.8 Consensus size: 44
219502 CCTGGGCAGC
* *
219512 AGTGGAATAGATTGAAGATTTCAGATCTTACCTCCCTAAGTAGT
1 AGTGGAGTAGATTGAAGATGTCAGATCTTACCTCCCTAAGTAGT
* * * *
219556 AGTGGAGTAGATCGAAGATGGCAGATTTTACCTCCCT--GTGATT
1 AGTGGAGTAGATTGAAGATGTCAGATCTTACCTCCCTAAGT-AGT
* * ** * *
219599 ACAGTGGAGTACATTGAAGCCA-GT-A-AT-TCTACTTCCCTGGGCAGC
1 --AGTGGAGTAGATTGAAG--ATGTCAGATCT-TACCTCCCTAAGTAGT
* * * *
219644 AGTGGAATAGATTGAAGATTTTAGATCTTACCTCTCTAAGTAGT
1 AGTGGAGTAGATTGAAGATGTCAGATCTTACCTCCCTAAGTAGT
* ** * *
219688 AGTGGAGTAGATCGAAGATGGAAGATTTTACCTCCCT--GTGGTT
1 AGTGGAGTAGATTGAAGATGTCAGATCTTACCTCCCTAAGTAG-T
* * ** * * * *
219731 ACAGTGGAGTACATTAAAGCCGGT-A-AT-TCTACTTCCCTGAGCAGC
1 --AGTGGAGTAGATTGAAG-ATGTCAGATCT-TACCTCCCTAAGTAGT
* * *
219776 AGTGGAATATATTGAAGATTTCAGATCTTACCTCCCTAAGTAGT
1 AGTGGAGTAGATTGAAGATGTCAGATCTTACCTCCCTAAGTAGT
* * * * *
219820 AGTGGAGTAGATCGAAGATGGTGA-ATTTTTCCTCCCT--GTGGTT
1 AGTGGAGTAGATTGAAGAT-GTCAGATCTTACCTCCCTAAGTAG-T
* * * * *
219863 ACAGTGGAGTACATTGAAGCCA-GT-A-AT-TCTATCTCTCT-GGACAGT
1 --AGTGGAGTAGATTGAAG--ATGTCAGATCT-TACCTCCCTAAG-TAGT
* * * *
219908 AGTGGAATAGATTGAAGAT-TATAGATCTTATCTCCCTAAGCAGT
1 AGTGGAGTAGATTGAAGATGT-CAGATCTTACCTCCCTAAGTAGT
* * * *
219952 AGTGGAGCAGATTGAAGATGGCGGATTTTACCTCCCT
1 AGTGGAGTAGATTGAAGATGTCAGATCTTACCTCCCT
219989 GAGGTTACAG
Statistics
Matches: 319, Mismatches: 76, Indels: 76
0.68 0.16 0.16
Matches are distributed among these distances:
41 3 0.01
42 10 0.03
43 54 0.17
44 187 0.59
45 57 0.18
46 6 0.02
47 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.30
Consensus pattern (44 bp):
AGTGGAGTAGATTGAAGATGTCAGATCTTACCTCCCTAAGTAGT
Found at i:219670 original size:132 final size:132
Alignment explanation
Indices: 219429--220021 Score: 895
Period size: 132 Copynumber: 4.5 Consensus size: 132
219419 TTGACAGCGA
** * * **
219429 AGTAGATCGAAGATGGTGGATTTTACCTCCCTGTGGTTATAGTGGAGTAAATTGAAGATAGTAAT
1 AGTAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
*
219494 TCTGCTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTACCTCCCTAAGTAGTAGT
66 TCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTACCTCCCTAAGTAGTAGT
219559 GG
131 GG
*
219561 AGTAGATCGAAGATGGCAGATTTTACCTCCCTGTGATTACAGTGGAGTACATTGAAGCCAGTAAT
1 AGTAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* *
219626 TCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTTAGATCTTACCTCTCTAAGTAGTAGT
66 TCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTACCTCCCTAAGTAGTAGT
219691 GG
131 GG
* * *
219693 AGTAGATCGAAGATGGAAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTAAAGCCGGTAAT
1 AGTAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* *
219758 TCTACTTCCCTGAGCAGCAGTGGAATATATTGAAGATTTCAGATCTTACCTCCCTAAGTAGTAGT
66 TCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTACCTCCCTAAGTAGTAGT
219823 GG
131 GG
* *
219825 AGTAGATCGAAGATGG-TGAATTTTTCCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAA
1 AGTAGATCGAAGATGGCAG-ATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAA
* * * * *
219889 TTCTA-TCTCTCTGGACAGTAGTGGAATAGATTGAAGATTAT-AGATCTTATCTCCCTAAGCAGT
65 TTCTACT-TCCCTGGGCAGCAGTGGAATAGATTGAAGATT-TCAGATCTTACCTCCCTAAGTAGT
219952 AGTGG
128 AGTGG
* * * * *
219957 AGCAGATTGAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCACTAAT
1 AGTAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
220022 CCTATCTCCC
Statistics
Matches: 422, Mismatches: 35, Indels: 8
0.91 0.08 0.02
Matches are distributed among these distances:
131 2 0.00
132 418 0.99
133 2 0.00
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (132 bp):
AGTAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
TCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTACCTCCCTAAGTAGTAGT
GG
Found at i:223071 original size:228 final size:229
Alignment explanation
Indices: 222674--223130 Score: 898
Period size: 228 Copynumber: 2.0 Consensus size: 229
222664 GTGTTCTAAA
222674 ATCTTTTCAAGTCTTCGATACTAATACATTAAACAATCAATTCGGTACCAATTTTGGGCGCCACG
1 ATCTTTTCAAGTCTTCGATACTAATACATTAAACAATCAATTCGGTACCAATTTTGGGCGCCACG
222739 AGGGTGCTAACCCTTCCTCGTACGTAACCGACTCCCAAAGCTGTTTTCTCAAAATTCGTAGACCT
66 AGGGTGCTAACCCTTCCTCGTACGTAACCGACTCCCAAAGCTGTTTTCTCAAAATTCGTAGACCT
*
222804 AAAATTATTTTCAAGGTGATCCAGTCACACCTCAATAAAAGATCGGTGGCGACTCCCAATTTTTC
131 AAAATTAATTTCAAGGTGATCCAGTCACACCTCAATAAAAGATCGGTGGCGACTCCCAATTTTTC
222869 ATATTAATAAGTCGACAAACAA-TTTTTGTTTTT
196 ATATTAATAAGTCGACAAACAATTTTTTGTTTTT
222902 ATCTTTTCAAGTCTTCGATACTAATACATTAAACAATCAATTCGGTACCAATTTTGGGCGCCACG
1 ATCTTTTCAAGTCTTCGATACTAATACATTAAACAATCAATTCGGTACCAATTTTGGGCGCCACG
222967 AGGGTGCTAACCCTTCCTCGTACGTAACCGACTCCCAAAGCTGTTTTCTCAAAATTCGTAGACCT
66 AGGGTGCTAACCCTTCCTCGTACGTAACCGACTCCCAAAGCTGTTTTCTCAAAATTCGTAGACCT
223032 AAAATTAATTTCAAGGTGATCCAGTCACACCTCAATAAAAGATCGGTGGCGACTCCCAATTTTTC
131 AAAATTAATTTCAAGGTGATCCAGTCACACCTCAATAAAAGATCGGTGGCGACTCCCAATTTTTC
223097 ATATTAATAAGTCGACAAACAATTTTTTGTTTTT
196 ATATTAATAAGTCGACAAACAATTTTTTGTTTTT
223131 TCAATAAAAT
Statistics
Matches: 227, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
228 216 0.95
229 11 0.05
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.32
Consensus pattern (229 bp):
ATCTTTTCAAGTCTTCGATACTAATACATTAAACAATCAATTCGGTACCAATTTTGGGCGCCACG
AGGGTGCTAACCCTTCCTCGTACGTAACCGACTCCCAAAGCTGTTTTCTCAAAATTCGTAGACCT
AAAATTAATTTCAAGGTGATCCAGTCACACCTCAATAAAAGATCGGTGGCGACTCCCAATTTTTC
ATATTAATAAGTCGACAAACAATTTTTTGTTTTT
Found at i:228717 original size:55 final size:55
Alignment explanation
Indices: 228658--228765 Score: 130
Period size: 55 Copynumber: 2.0 Consensus size: 55
228648 GCCCGTGTAG
* *
228658 ATATTCGAAATA-GAGCCACAC-GGCTGTGTCGCAGGCCGTGTGCCAAACCATGTGT
1 ATATTCGAAATATG-GACACACAGTC-GTGTCGCAGGCCGTGTGCCAAACCATGTGT
* * * *
228713 ATATTCGAATTATGGACACACAGTCGTGTCGTAGGCCGTGTGCTAGACCATGT
1 ATATTCGAAATATGGACACACAGTCGTGTCGCAGGCCGTGTGCCAAACCATGT
228766 TACATATTGA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
55 42 0.93
56 3 0.07
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (55 bp):
ATATTCGAAATATGGACACACAGTCGTGTCGCAGGCCGTGTGCCAAACCATGTGT
Found at i:233086 original size:21 final size:21
Alignment explanation
Indices: 233062--233126 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
233052 GTTGAAATTC
233062 TAACTACTTAATGCAATCCAA
1 TAACTACTTAATGCAATCCAA
* *
233083 TAACAACATTAAT-CAATTC--
1 TAACTAC-TTAATGCAATCCAA
233102 TAACTACTTAATGCAATCCAA
1 TAACTACTTAATGCAATCCAA
233123 TAAC
1 TAAC
233127 ACCATTAATC
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
18 5 0.14
19 11 0.31
21 15 0.42
22 5 0.14
ACGTcount: A:0.45, C:0.23, G:0.03, T:0.29
Consensus pattern (21 bp):
TAACTACTTAATGCAATCCAA
Found at i:233094 original size:22 final size:21
Alignment explanation
Indices: 233069--233139 Score: 76
Period size: 21 Copynumber: 3.4 Consensus size: 21
233059 TTCTAACTAC
233069 TTAATGCAATCCAATAACAACA
1 TTAAT-CAATCCAATAACAACA
* *
233091 TTAATCAATTC--TAACTAC-
1 TTAATCAATCCAATAACAACA
*
233109 TTAATGCAATCCAATAACACCA
1 TTAAT-CAATCCAATAACAACA
233131 TTAATCAAT
1 TTAATCAAT
233140 TCTTTAATCT
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
18 5 0.12
19 11 0.28
21 14 0.35
22 10 0.25
ACGTcount: A:0.45, C:0.23, G:0.03, T:0.30
Consensus pattern (21 bp):
TTAATCAATCCAATAACAACA
Found at i:233112 original size:40 final size:40
Alignment explanation
Indices: 233057--233142 Score: 163
Period size: 40 Copynumber: 2.1 Consensus size: 40
233047 TTTAAGTTGA
233057 AATTCTAACTACTTAATGCAATCCAATAACAACATTAATC
1 AATTCTAACTACTTAATGCAATCCAATAACAACATTAATC
*
233097 AATTCTAACTACTTAATGCAATCCAATAACACCATTAATC
1 AATTCTAACTACTTAATGCAATCCAATAACAACATTAATC
233137 AATTCT
1 AATTCT
233143 TTAATCTGTA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.43, C:0.23, G:0.02, T:0.31
Consensus pattern (40 bp):
AATTCTAACTACTTAATGCAATCCAATAACAACATTAATC
Found at i:233118 original size:19 final size:19
Alignment explanation
Indices: 233057--233118 Score: 72
Period size: 19 Copynumber: 3.2 Consensus size: 19
233047 TTTAAGTTGA
233057 AATTCTAACTACTTAATGC
1 AATTCTAACTACTTAATGC
* *
233076 AATCCAATAACAACATTAAT-C
1 AATTC--TAACTAC-TTAATGC
233097 AATTCTAACTACTTAATGC
1 AATTCTAACTACTTAATGC
233116 AAT
1 AAT
233119 CCAATAACAC
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
18 5 0.14
19 14 0.40
21 11 0.31
22 5 0.14
ACGTcount: A:0.44, C:0.21, G:0.03, T:0.32
Consensus pattern (19 bp):
AATTCTAACTACTTAATGC
Found at i:240710 original size:55 final size:55
Alignment explanation
Indices: 240651--240758 Score: 130
Period size: 55 Copynumber: 2.0 Consensus size: 55
240641 GCCCGTGTAG
* *
240651 ATATTCGAAATA-GAGCCACAC-GGCTGTGTCGCAGGCCGTGTGCCAAACCATGTGT
1 ATATTCGAAATATG-GACACACAGTC-GTGTCGCAGGCCGTGTGCCAAACCATGTGT
* * * *
240706 ATATTCGAATTATGGACACACAGTCGTGTCGTAGGCCGTGTGCTAGACCATGT
1 ATATTCGAAATATGGACACACAGTCGTGTCGCAGGCCGTGTGCCAAACCATGT
240759 TACATATTGA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
55 42 0.93
56 3 0.07
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (55 bp):
ATATTCGAAATATGGACACACAGTCGTGTCGCAGGCCGTGTGCCAAACCATGTGT
Found at i:245079 original size:21 final size:21
Alignment explanation
Indices: 245055--245119 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
245045 GTTGAAATTC
245055 TAACTACTTAATGCAATCCAA
1 TAACTACTTAATGCAATCCAA
* *
245076 TAACAACATTAAT-CAATTC--
1 TAACTAC-TTAATGCAATCCAA
245095 TAACTACTTAATGCAATCCAA
1 TAACTACTTAATGCAATCCAA
245116 TAAC
1 TAAC
245120 ACCATTAATC
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
18 5 0.14
19 11 0.31
21 15 0.42
22 5 0.14
ACGTcount: A:0.45, C:0.23, G:0.03, T:0.29
Consensus pattern (21 bp):
TAACTACTTAATGCAATCCAA
Found at i:245087 original size:22 final size:21
Alignment explanation
Indices: 245062--245132 Score: 76
Period size: 21 Copynumber: 3.4 Consensus size: 21
245052 TTCTAACTAC
245062 TTAATGCAATCCAATAACAACA
1 TTAAT-CAATCCAATAACAACA
* *
245084 TTAATCAATTC--TAACTAC-
1 TTAATCAATCCAATAACAACA
*
245102 TTAATGCAATCCAATAACACCA
1 TTAAT-CAATCCAATAACAACA
245124 TTAATCAAT
1 TTAATCAAT
245133 TCTTTAATCT
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
18 5 0.12
19 11 0.28
21 14 0.35
22 10 0.25
ACGTcount: A:0.45, C:0.23, G:0.03, T:0.30
Consensus pattern (21 bp):
TTAATCAATCCAATAACAACA
Found at i:245105 original size:40 final size:40
Alignment explanation
Indices: 245050--245135 Score: 163
Period size: 40 Copynumber: 2.1 Consensus size: 40
245040 TTTAAGTTGA
245050 AATTCTAACTACTTAATGCAATCCAATAACAACATTAATC
1 AATTCTAACTACTTAATGCAATCCAATAACAACATTAATC
*
245090 AATTCTAACTACTTAATGCAATCCAATAACACCATTAATC
1 AATTCTAACTACTTAATGCAATCCAATAACAACATTAATC
245130 AATTCT
1 AATTCT
245136 TTAATCTGTA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.43, C:0.23, G:0.02, T:0.31
Consensus pattern (40 bp):
AATTCTAACTACTTAATGCAATCCAATAACAACATTAATC
Found at i:245111 original size:19 final size:19
Alignment explanation
Indices: 245050--245111 Score: 72
Period size: 19 Copynumber: 3.2 Consensus size: 19
245040 TTTAAGTTGA
245050 AATTCTAACTACTTAATGC
1 AATTCTAACTACTTAATGC
* *
245069 AATCCAATAACAACATTAAT-C
1 AATTC--TAACTAC-TTAATGC
245090 AATTCTAACTACTTAATGC
1 AATTCTAACTACTTAATGC
245109 AAT
1 AAT
245112 CCAATAACAC
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
18 5 0.14
19 14 0.40
21 11 0.31
22 5 0.14
ACGTcount: A:0.44, C:0.21, G:0.03, T:0.32
Consensus pattern (19 bp):
AATTCTAACTACTTAATGC
Found at i:246252 original size:21 final size:21
Alignment explanation
Indices: 246221--246268 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 21
246211 TATGAGCTTG
*
246221 TTACACAACATTGTAGCACCCC
1 TTAC-CAACATTGTAACACCCC
246243 TTACCAACATTGTAACACCCC
1 TTACCAACATTGTAACACCCC
246264 TTACC
1 TTACC
246269 CGACCCAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.31, C:0.38, G:0.06, T:0.25
Consensus pattern (21 bp):
TTACCAACATTGTAACACCCC
Found at i:255249 original size:15 final size:16
Alignment explanation
Indices: 255224--255264 Score: 59
Period size: 15 Copynumber: 2.6 Consensus size: 16
255214 TATTAAATTC
255224 TATATTTTAATAATAA
1 TATATTTTAATAATAA
255240 TATA-TTTAATAATAA
1 TATATTTTAATAATAA
255255 T-TATGTTTAA
1 TATAT-TTTAA
255265 ATATGATGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 2 0.09
15 12 0.52
16 9 0.39
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
TATATTTTAATAATAA
Found at i:255514 original size:16 final size:16
Alignment explanation
Indices: 255489--255553 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
255479 TTGATTTGCT
255489 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
*
255505 ATTACACCTCTATTCC
1 ATTACGCCTCTATTCC
255521 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
255537 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
255553 A
1 A
255554 ATACAGCGAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.22, C:0.37, G:0.05, T:0.37
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:255517 original size:56 final size:55
Alignment explanation
Indices: 255394--255523 Score: 172
Period size: 56 Copynumber: 2.3 Consensus size: 55
255384 CCATTATGCT
* *
255394 ATTACACATCTATTCCATTCAACCAAACACAAGAATACTATCACGTCTCTATTCC
1 ATTACACCTCTATTCCATTCAACCAAACACAAGAATACTATCACGCCTCTATTCC
* * * * *
255449 ATTACGCCTCTATTCCATTCAACCAAACA-ATTGATTTGCTATTACGCCTCTATTCC
1 ATTACACCTCTATTCCATTCAACCAAACACA-AGA-ATACTATCACGCCTCTATTCC
255505 ATTACACCTCTATTCCATT
1 ATTACACCTCTATTCCATT
255524 ACGCCTCTAT
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
54 1 0.02
55 29 0.45
56 35 0.54
ACGTcount: A:0.31, C:0.31, G:0.05, T:0.34
Consensus pattern (55 bp):
ATTACACCTCTATTCCATTCAACCAAACACAAGAATACTATCACGCCTCTATTCC
Found at i:256756 original size:28 final size:28
Alignment explanation
Indices: 256716--256771 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
256706 AAGTCCTACA
256716 ATAAAATTTATCATCATTATCTTAATCT
1 ATAAAATTTATCATCATTATCTTAATCT
*
256744 ATAAAATTTATCATCCTTATCTTAATCT
1 ATAAAATTTATCATCATTATCTTAATCT
256772 TACTCAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.38, C:0.16, G:0.00, T:0.46
Consensus pattern (28 bp):
ATAAAATTTATCATCATTATCTTAATCT
Found at i:271500 original size:23 final size:24
Alignment explanation
Indices: 271456--271503 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 24
271446 TACTTTTATT
271456 CTAAGAGTCCTACCTAACAACTTCTC
1 CTAAGAGTCCTACCT-A-AACTTCTC
*
271482 CTAAGAGTTCTACCT-AACTTCT
1 CTAAGAGTCCTACCTAAACTTCT
271504 AAGTGTCCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 7 0.33
26 14 0.67
ACGTcount: A:0.29, C:0.31, G:0.08, T:0.31
Consensus pattern (24 bp):
CTAAGAGTCCTACCTAAACTTCTC
Found at i:278008 original size:19 final size:19
Alignment explanation
Indices: 277962--278017 Score: 94
Period size: 21 Copynumber: 2.8 Consensus size: 19
277952 AATCTTCAAG
277962 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
277981 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
278002 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
278018 AGATATGATT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
19 16 0.46
21 19 0.54
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:278039 original size:23 final size:22
Alignment explanation
Indices: 277962--278040 Score: 78
Period size: 19 Copynumber: 3.7 Consensus size: 22
277952 AATCTTCAAG
*
277962 GATATGCAATCTTAG-ATATGAT
1 GATATGCAATCTTAGAAGAT-AT
277984 -ATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
278002 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
* *
278024 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
278041 GATTTAATTT
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
18 2 0.04
19 15 0.31
21 12 0.24
22 8 0.16
23 12 0.24
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.38
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:278288 original size:23 final size:23
Alignment explanation
Indices: 278244--278288 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
278234 TCTTATTTTG
*
278244 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTGTATAATTGATTTA
**
278267 TTGATTTGTGTATTGTTGATTT
1 TTGATTTGTGTATAATTGATTT
278289 CAAATCTCTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.00, G:0.18, T:0.62
Consensus pattern (23 bp):
TTGATTTGTGTATAATTGATTTA
Found at i:283770 original size:15 final size:14
Alignment explanation
Indices: 283730--283783 Score: 72
Period size: 14 Copynumber: 3.8 Consensus size: 14
283720 AAAAAACCAA
283730 AAAAAGAAAAAAAT
1 AAAAAGAAAAAAAT
283744 AAAAAGAAAAAAAT
1 AAAAAGAAAAAAAT
* *
283758 AAAAATGACAAAAAG
1 AAAAA-GAAAAAAAT
*
283773 AAAAGGAAAAA
1 AAAAAGAAAAA
283784 GGAGAGGCCA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
14 24 0.69
15 11 0.31
ACGTcount: A:0.81, C:0.02, G:0.11, T:0.06
Consensus pattern (14 bp):
AAAAAGAAAAAAAT
Found at i:285097 original size:44 final size:44
Alignment explanation
Indices: 285042--285182 Score: 205
Period size: 44 Copynumber: 3.2 Consensus size: 44
285032 CACAAAGCTT
*
285042 TATCTCCCTGGTCAGCAATGGAATAGGTTGAAGATTATGAATCC
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTATGAATCC
* * *
285086 TATCTCTCTGGTCAGCAGTGGAATAGGTTGAAGATTCTGAGTCC
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTATGAATCC
*
285130 TATCTCCCTGGTCAGCAGTGAAATAGGTTGAAGATTGTATG--TCC
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGA-T-TATGAATCC
285174 TATCTCCCT
1 TATCTCCCT
285183 TGAAGATTGT
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
44 84 0.95
45 1 0.01
46 3 0.03
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (44 bp):
TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTATGAATCC
Found at i:285191 original size:25 final size:25
Alignment explanation
Indices: 285157--285207 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
285147 GTGAAATAGG
*
285157 TTGAAGATTGT-ATGTCCTATCTCCC
1 TTGAAGATTGTGA-GTCATATCTCCC
285182 TTGAAGATTGTGAGTCATATCTCCC
1 TTGAAGATTGTGAGTCATATCTCCC
285207 T
1 T
285208 GGTCAGCAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 23 0.96
26 1 0.04
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.39
Consensus pattern (25 bp):
TTGAAGATTGTGAGTCATATCTCCC
Found at i:285224 original size:69 final size:69
Alignment explanation
Indices: 285113--285251 Score: 217
Period size: 69 Copynumber: 2.0 Consensus size: 69
285103 GTGGAATAGG
* * *
285113 TTGAAGATTCTGAGTCCTATCTCCCTGGTCAGCAGTGAAATAGGTTGAAGATTGT-ATGTCCTAT
1 TTGAAGATTCTGAGTCATATCTCCCTGGTCAGCAATGAAATAGGTTGAAGATTGTGA-ATCCTAT
285177 CTCCC
65 CTCCC
* *
285182 TTGAAGATTGTGAGTCATATCTCCCTGGTCAGCAATGGAATAGGTTGAAGATTGTGAATCCTATC
1 TTGAAGATTCTGAGTCATATCTCCCTGGTCAGCAATGAAATAGGTTGAAGATTGTGAATCCTATC
285247 TCCC
66 TCCC
285251 T
1 T
285252 GGTCAGTAGT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
69 63 0.98
70 1 0.02
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.33
Consensus pattern (69 bp):
TTGAAGATTCTGAGTCATATCTCCCTGGTCAGCAATGAAATAGGTTGAAGATTGTGAATCCTATC
TCCC
Found at i:285247 original size:44 final size:44
Alignment explanation
Indices: 285182--285484 Score: 405
Period size: 44 Copynumber: 7.1 Consensus size: 44
285172 CCTATCTCCC
* * *
285182 TTGAAGATTGTGAGTCATATCTCCCTGGTCAGCAATGGAATAGG
1 TTGAAGATTGTGAATCCTATCTCCCTGGTCAGCAGTGGAATAGG
*
285226 TTGAAGATTGTGAATCCTATCTCCCTGGTCAGTAGTGGAATAGG
1 TTGAAGATTGTGAATCCTATCTCCCTGGTCAGCAGTGGAATAGG
285270 TTGAAGATTGT-AAGTCCTATCTCCCTGGTCAGCAGTGG-A-A--
1 TTGAAGATTGTGAA-TCCTATCTCCCTGGTCAGCAGTGGAATAGG
* * *
285310 -T--AG---GTGAATCCTATCTCCTTAGTCAGTAGTGGAATAGG
1 TTGAAGATTGTGAATCCTATCTCCCTGGTCAGCAGTGGAATAGG
* * *
285348 TTGAAGATTGTGAGTCCTATCTCCCAGGTCAACAGTGGAATAGG
1 TTGAAGATTGTGAATCCTATCTCCCTGGTCAGCAGTGGAATAGG
*
285392 TTGAAGATTGTGAATCCTATCTTCCTGGTCAGCAGTGGAATAGG
1 TTGAAGATTGTGAATCCTATCTCCCTGGTCAGCAGTGGAATAGG
285436 TTGAAGATTGTGAATCCTATCTCCCTGAG-CAGCAGTGGAATAGG
1 TTGAAGATTGTGAATCCTATCTCCCTG-GTCAGCAGTGGAATAGG
285480 TTGAA
1 TTGAA
285485 AATTACAGAT
Statistics
Matches: 227, Mismatches: 19, Indels: 26
0.83 0.07 0.10
Matches are distributed among these distances:
34 23 0.10
35 3 0.01
36 1 0.00
37 2 0.01
39 2 0.01
41 2 0.01
42 1 0.00
43 3 0.01
44 189 0.83
45 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (44 bp):
TTGAAGATTGTGAATCCTATCTCCCTGGTCAGCAGTGGAATAGG
Found at i:285268 original size:113 final size:113
Alignment explanation
Indices: 285069--285413 Score: 440
Period size: 113 Copynumber: 3.0 Consensus size: 113
285059 ATGGAATAGG
* * *
285069 TTGAAGATTATGAATCCTATCTCTCTGGTCAGCAGTGGAATAGGTTGAAGATTCTGAGTCCTATC
1 TTGAAGATTGTGAATCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAGTCCTATC
* *
285134 TCCCTGGTCAGCAGTGAAATAGGTTGAAGATTGTATGTCCTATCTCCC
66 TCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAGTCCTATCTCCC
* * * *
285182 TTGAAGATTGTGAGTCATATCTCCCTGGTCAGCAATGGAATAGGTTGAAGATTGTGAATCCTATC
1 TTGAAGATTGTGAATCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAGTCCTATC
*
285247 TCCCTGGTCAGTAGTGGAATAGGTTGAAGATTGTAAGTCCTATCTCCC
66 TCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAGTCCTATCTCCC
* * * * *
285295 TGGTCAGCAGTGGAATAGGTGAATCCTATCTCCTTAGTCAGTAGTGGAATAGGTTGAAGATTGTG
1 T--T--G-A--AG-AT-TGTGAATCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTG
* *
285360 AGTCCTATCTCCCAGGTCAACAGTGGAATAGGTTGAAGATTGTGAA-TCCTATCT
57 AGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGT-AAGTCCTATCT
285414 TCCTGGTCAG
Statistics
Matches: 200, Mismatches: 22, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
113 104 0.52
115 1 0.00
117 1 0.00
118 1 0.00
120 1 0.00
121 2 0.01
122 88 0.44
123 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.32
Consensus pattern (113 bp):
TTGAAGATTGTGAATCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAGTCCTATC
TCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAGTCCTATCTCCC
Found at i:285327 original size:34 final size:34
Alignment explanation
Indices: 285284--285348 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
285274 AGATTGTAAG
*
285284 TCCTATCTCCCTGGTCAGCAGTGGAATAGGTGAA
1 TCCTATCTCCCTAGTCAGCAGTGGAATAGGTGAA
* *
285318 TCCTATCTCCTTAGTCAGTAGTGGAATAGGT
1 TCCTATCTCCCTAGTCAGCAGTGGAATAGGT
285349 TGAAGATTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.31
Consensus pattern (34 bp):
TCCTATCTCCCTAGTCAGCAGTGGAATAGGTGAA
Found at i:285364 original size:78 final size:77
Alignment explanation
Indices: 285235--285480 Score: 305
Period size: 78 Copynumber: 3.0 Consensus size: 77
285225 GTTGAAGATT
*
285235 GTGAATCCTATCTCCCTGGTCAGTAGTGGAATAGGTTGAAGATTGTAAGTCCTATCTCCCTGGTC
1 GTGAATCCTATCT-CCTGGTCAGTAGTGGAATAGGTTGAAGATTGTGAGTCCTATCTCCCTGGTC
285300 AGCAGTGGAATAG
65 AGCAGTGGAATAG
* *
285313 GTGAATCCTATCTCCTTAGTCAGTAGTGGAATAGGTTGAAGATTGTGAGTCCTATCTCCCAGGTC
1 GTGAATCCTATCTCC-TGGTCAGTAGTGGAATAGGTTGAAGATTGTGAGTCCTATCTCCCTGGTC
*
285378 AACAGTGGAATAGGTTGAAG
65 AGCAGTGG-A-A---T--AG
* *
285398 ATTGTGAATCCTATCTTCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAATCCTATCTCCCTG
1 ---GTGAATCCTATC-TCCTGGTCAGTAGTGGAATAGGTTGAAGATTGTGAGTCCTATCTCCCTG
285463 AG-CAGCAGTGGAATAG
62 -GTCAGCAGTGGAATAG
285479 GT
1 GT
285481 TGAAAATTAC
Statistics
Matches: 146, Mismatches: 9, Indels: 26
0.81 0.05 0.14
Matches are distributed among these distances:
77 2 0.01
78 68 0.47
79 1 0.01
80 1 0.01
81 2 0.01
83 2 0.01
85 2 0.01
86 1 0.01
87 1 0.01
88 62 0.42
89 4 0.03
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.30
Consensus pattern (77 bp):
GTGAATCCTATCTCCTGGTCAGTAGTGGAATAGGTTGAAGATTGTGAGTCCTATCTCCCTGGTCA
GCAGTGGAATAG
Found at i:285419 original size:122 final size:121
Alignment explanation
Indices: 285079--285436 Score: 466
Period size: 122 Copynumber: 3.0 Consensus size: 121
285069 TTGAAGATTA
*
285079 TGAATCCTATCT-CTCTGGTCAGCAGTGGAATAGGTTGAAGATTCTGAGTCCTATCTCCCTGGTC
1 TGAATCCTATCTCCT-TGGTCAGCAGTGGAATAGGTTGAAGATTGTGAGTCCTATCTCCCTGGTC
* * * *
285143 AGCAGTGAAATAGGTTGAAGATTGTATGTCCTATCTCCCT--T--G-A--AG-AT-TG
65 AGCAGTGGAATAGGTTGAAGATTGTA-ATCCTATCTCCCTGGTCAGCAGTGGAATAGG
* * * * *
285192 TGAGTCATATCTCCCTGGTCAGCAATGGAATAGGTTGAAGATTGTGAATCCTATCTCCCTGGTCA
1 TGAATCCTATCTCCTTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAGTCCTATCTCCCTGGTCA
*
285257 GTAGTGGAATAGGTTGAAGATTGTAAGTCCTATCTCCCTGGTCAGCAGTGGAATAGG
66 GCAGTGGAATAGGTTGAAGATTGTAA-TCCTATCTCCCTGGTCAGCAGTGGAATAGG
* * *
285314 TGAATCCTATCTCCTTAGTCAGTAGTGGAATAGGTTGAAGATTGTGAGTCCTATCTCCCAGGTCA
1 TGAATCCTATCTCCTTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAGTCCTATCTCCCTGGTCA
* *
285379 ACAGTGGAATAGGTTGAAGATTGTGAATCCTATCTTCCTGGTCAGCAGTGGAATAGG
66 GCAGTGGAATAGGTTGAAGATTGT-AATCCTATCTCCCTGGTCAGCAGTGGAATAGG
285436 T
1 T
285437 TGAAGATTGT
Statistics
Matches: 211, Mismatches: 22, Indels: 15
0.85 0.09 0.06
Matches are distributed among these distances:
113 92 0.44
114 1 0.00
115 1 0.00
117 1 0.00
118 1 0.00
120 1 0.00
121 2 0.01
122 110 0.52
123 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (121 bp):
TGAATCCTATCTCCTTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAGTCCTATCTCCCTGGTCA
GCAGTGGAATAGGTTGAAGATTGTAATCCTATCTCCCTGGTCAGCAGTGGAATAGG
Found at i:285517 original size:44 final size:44
Alignment explanation
Indices: 285315--285518 Score: 151
Period size: 44 Copynumber: 4.6 Consensus size: 44
285305 TGGAATAGGT
* ** * * **
285315 GAATCCTATCTCCTTAGTCAGTAGTGGAATAGGTTGAAGATTGT
1 GAATCCTATCTCCCTAACCAGCAGTGGAATAGGTTGAAAATTCA
* ** * * **
285359 GAGTCCTATCTCCC-AGGTCAACAGTGGAATAGGTTGAAGATTGT
1 GAATCCTATCTCCCTA-ACCAGCAGTGGAATAGGTTGAAAATTCA
* *** * **
285403 GAATCCTATCTTCCTGGTCAGCAGTGGAATAGGTTGAAGATTGT
1 GAATCCTATCTCCCTAACCAGCAGTGGAATAGGTTGAAAATTCA
* *
285447 GAATCCTATCTCCCTGAGCAGCAGTGGAATAGGTTGAAAATTACA
1 GAATCCTATCTCCCTAACCAGCAGTGGAATAGGTTGAAAATT-CA
* *
285492 G-ATCTTATCTCCCTAACCAGTAGTGGA
1 GAATCCTATCTCCCTAACCAGCAGTGGA
285519 GCAGATCGAA
Statistics
Matches: 139, Mismatches: 18, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
43 1 0.01
44 137 0.99
45 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (44 bp):
GAATCCTATCTCCCTAACCAGCAGTGGAATAGGTTGAAAATTCA
Found at i:285517 original size:88 final size:88
Alignment explanation
Indices: 285315--285518 Score: 241
Period size: 88 Copynumber: 2.3 Consensus size: 88
285305 TGGAATAGGT
* ** *
285315 GAATCCTATCTCCTTAGTCAGTAGTGGAATAGGTTGAAGATTGTGAGTCCTATCTCCCAGGTCAA
1 GAATCCTATCTCCCTAACCAGTAGTGGAATAGGTTGAAGATTGTGAATCCTATCTCCCAGGTCAA
* **
285380 CAGTGGAATAGGTTGAAGATTGT
66 CAGTGGAATAGGTTGAAAATTCA
* *** * *
285403 GAATCCTATCTTCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAATCCTATCTCCCTGAG-CA
1 GAATCCTATCTCCCTAACCAGTAGTGGAATAGGTTGAAGATTGTGAATCCTATCTCCCAG-GTCA
*
285467 GCAGTGGAATAGGTTGAAAATTACA
65 ACAGTGGAATAGGTTGAAAATT-CA
*
285492 G-ATCTTATCTCCCTAACCAGTAGTGGA
1 GAATCCTATCTCCCTAACCAGTAGTGGA
285519 GCAGATCGAA
Statistics
Matches: 98, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
88 96 0.98
89 2 0.02
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (88 bp):
GAATCCTATCTCCCTAACCAGTAGTGGAATAGGTTGAAGATTGTGAATCCTATCTCCCAGGTCAA
CAGTGGAATAGGTTGAAAATTCA
Done.