Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold867
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: 107622
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1019 original size:20 final size:19
Alignment explanation
Indices: 996--1060 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
986 AAGCTCAAAC
996 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
1016 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
1036 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
1056 GAGCT
1 GAGCT
1061 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:2875 original size:33 final size:33
Alignment explanation
Indices: 2837--2899 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
2827 GATTACTCAC
2837 TTCACTCG-TTTCTTTT-ATAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
2870 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
2900 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.25, G:0.06, T:0.56
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:2951 original size:26 final size:26
Alignment explanation
Indices: 2896--2950 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 26
2886 TCAAGCTCTC
*
2896 TTTCAATTTCTTTTTTCGCTTTTCTT
1 TTTCAATTTCTTTTTTCGATTTTCTT
2922 TTTCAATTTTCTTTTCTTC-ATTTTCTT
1 TTTCAA-TTTCTTTT-TTCGATTTTCTT
2949 TT
1 TT
2951 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 6 0.23
27 17 0.65
28 3 0.12
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (26 bp):
TTTCAATTTCTTTTTTCGATTTTCTT
Found at i:2952 original size:14 final size:14
Alignment explanation
Indices: 2896--2950 Score: 62
Period size: 14 Copynumber: 4.1 Consensus size: 14
2886 TCAAGCTCTC
2896 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
2909 TTTCGCTTTTC-TT
1 TTTCAATTTTCTTT
2922 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
2936 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
2950 T
1 T
2951 CTCTCACTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
13 15 0.43
14 17 0.49
15 3 0.09
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:2976 original size:16 final size:16
Alignment explanation
Indices: 2957--3038 Score: 78
Period size: 16 Copynumber: 5.1 Consensus size: 16
2947 TTTTCTCTCA
*
2957 CTTTTTCGATTTCTTT
1 CTTTTTCAATTTCTTT
*
2973 CTTTTGCAATTTCTTT
1 CTTTTTCAATTTCTTT
**
2989 CTTTTTCGTTTTCTTT
1 CTTTTTCAATTTCTTT
*
3005 TTTTTTC--TTTCAATTT
1 CTTTTTCAATTTC--TTT
*
3021 CTTTTTCAATCTCTTT
1 CTTTTTCAATTTCTTT
3037 CT
1 CT
3039 CCTTTTCTCG
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
14 4 0.07
16 47 0.87
18 3 0.06
ACGTcount: A:0.09, C:0.20, G:0.04, T:0.68
Consensus pattern (16 bp):
CTTTTTCAATTTCTTT
Found at i:4099 original size:11 final size:11
Alignment explanation
Indices: 4085--4117 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
4075 TTTTTGCTCG
*
4085 TTTTTTTTCAC
1 TTTTTTTTCAA
4096 TTTTTTTT-AA
1 TTTTTTTTCAA
4106 TTTTTTTTCAA
1 TTTTTTTTCAA
4117 T
1 T
4118 CAAATTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTTTTTCAA
Found at i:4099 original size:30 final size:28
Alignment explanation
Indices: 4043--4103 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
4033 TTAAACTTGA
4043 TTTTTTTGCTCACCTTTTTTTTCTTTTCTT
1 TTTTTTTGCT-ACCTTTTTTTTCTTTT-TT
* **
4073 TTTTTTTGCT-CGTTTTTTTTCACTTTT
1 TTTTTTTGCTACCTTTTTTTTCTTTTTT
4100 TTTT
1 TTTT
4104 AATTTTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 6 0.21
28 12 0.43
30 10 0.36
ACGTcount: A:0.03, C:0.16, G:0.05, T:0.75
Consensus pattern (28 bp):
TTTTTTTGCTACCTTTTTTTTCTTTTTT
Found at i:5562 original size:16 final size:16
Alignment explanation
Indices: 5541--5601 Score: 104
Period size: 16 Copynumber: 3.7 Consensus size: 16
5531 GATATCAAGT
5541 TGAAAAAAAAAATTCG
1 TGAAAAAAAAAATTCG
5557 TGAAAAAAAAAATTCG
1 TGAAAAAAAAAATTCG
5573 TGAAAAAAAAAATTTTCG
1 TGAAAAAAAAAA--TTCG
5591 TGAAAAAAAAA
1 TGAAAAAAAAA
5602 GAAGCTAGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
16 28 0.65
18 15 0.35
ACGTcount: A:0.64, C:0.05, G:0.11, T:0.20
Consensus pattern (16 bp):
TGAAAAAAAAAATTCG
Found at i:5566 original size:18 final size:18
Alignment explanation
Indices: 5543--5601 Score: 86
Period size: 18 Copynumber: 3.4 Consensus size: 18
5533 TATCAAGTTG
5543 AAAAAAAAAATTCGTG--
1 AAAAAAAAAATTCGTGAA
5559 AAAAAAAAAATTCGTGAA
1 AAAAAAAAAATTCGTGAA
**
5577 AAAAAAAATTTTCGTGAA
1 AAAAAAAAAATTCGTGAA
5595 AAAAAAA
1 AAAAAAA
5602 GAAGCTAGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
16 16 0.41
18 23 0.59
ACGTcount: A:0.66, C:0.05, G:0.10, T:0.19
Consensus pattern (18 bp):
AAAAAAAAAATTCGTGAA
Found at i:5781 original size:11 final size:12
Alignment explanation
Indices: 5760--5794 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
5750 ATAGTAGTTT
5760 CTCGAAAAAAAA
1 CTCGAAAAAAAA
5772 CTCGAAAAAAAA
1 CTCGAAAAAAAA
*
5784 TTC-AAAAAAAA
1 CTCGAAAAAAAA
5795 AATTTGGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 8 0.36
12 14 0.64
ACGTcount: A:0.69, C:0.14, G:0.06, T:0.11
Consensus pattern (12 bp):
CTCGAAAAAAAA
Found at i:18295 original size:45 final size:45
Alignment explanation
Indices: 18246--18478 Score: 394
Period size: 45 Copynumber: 5.2 Consensus size: 45
18236 TCGGCCATGG
* * * *
18246 TGCTTCCTCAATTTGTTCCATAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
18291 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
18336 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATATTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
18381 TGCTTCCTCAAATTCTTCCATGAATTATGAATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
18426 TGCTTCCTCAAATTCTCCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
18471 TGCTTCCT
1 TGCTTCCT
18479 TAATTTCATG
Statistics
Matches: 177, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 177 1.00
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (45 bp):
TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
Found at i:19972 original size:10 final size:10
Alignment explanation
Indices: 19957--20018 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
19947 TTTGAACCAT
*
19957 TACCAATTCG
1 TACCAATTCA
*
19967 TACCAAATACCA
1 TACC-AAT-TCA
*
19979 TACCATTTCA
1 TACCAATTCA
19989 TACCAATTCCA
1 TACCAATT-CA
* *
20000 TACCATTTCG
1 TACCAATTCA
20010 TACCAATTC
1 TACCAATTC
20019 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:20002 original size:21 final size:21
Alignment explanation
Indices: 19957--20019 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
19947 TTTGAACCAT
* *
19957 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
19979 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
20000 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
20020 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:20367 original size:13 final size:13
Alignment explanation
Indices: 20345--20369 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20335 AAAAAAAAAG
20345 AAAAAAAAATTGA
1 AAAAAAAAATTGA
20358 AAAAAAAAATTG
1 AAAAAAAAATTG
20370 CATACGGTTT
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:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (13 bp):
AAAAAAAAATTGA
Found at i:21171 original size:15 final size:15
Alignment explanation
Indices: 21139--21172 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
21129 GTTCAACGAA
*
21139 GAGGCCAACGCAACC
1 GAGGCCAACGAAACC
*
21154 GAGGCCAACGAAATC
1 GAGGCCAACGAAACC
21169 GAGG
1 GAGG
21173 TGATACAACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.29, G:0.32, T:0.03
Consensus pattern (15 bp):
GAGGCCAACGAAACC
Found at i:21334 original size:20 final size:20
Alignment explanation
Indices: 21288--21334 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
21278 AGCTCGTTTC
21288 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCGAGCTCAAGT
* *
21308 CAACTCACTCGAGCTCAATT
1 CAGCTCACTCGAGCTCAAGT
21328 CAGCTCA
1 CAGCTCA
21335 ATCTTAACCC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.28, C:0.36, G:0.15, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCGAGCTCAAGT
Found at i:22841 original size:14 final size:15
Alignment explanation
Indices: 22809--22848 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
22799 TGGAGTATCA
22809 AAAAAAAAGAAATTC
1 AAAAAAAAGAAATTC
* *
22824 AAAAAAAA-AATTTG
1 AAAAAAAAGAAATTC
22838 AAAAAAAAGAA
1 AAAAAAAAGAA
22849 GTGAGCAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.78, C:0.03, G:0.07, T:0.12
Consensus pattern (15 bp):
AAAAAAAAGAAATTC
Found at i:22866 original size:22 final size:23
Alignment explanation
Indices: 22839--22899 Score: 81
Period size: 22 Copynumber: 2.7 Consensus size: 23
22829 AAAAATTTGA
**
22839 AAAAAAAGAAGTGAGCAAAA-AAG
1 AAAAAAA-AAGTGAAAAAAAGAAG
22862 AAAAAAAAAGT-AAAAAAAGAAG
1 AAAAAAAAAGTGAAAAAAAGAAG
22884 AAAAAAAAAGTGAAAA
1 AAAAAAAAAGTGAAAA
22900 GTCTTGCGAG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 5 0.15
22 18 0.53
23 11 0.32
ACGTcount: A:0.77, C:0.02, G:0.16, T:0.05
Consensus pattern (23 bp):
AAAAAAAAAGTGAAAAAAAGAAG
Found at i:22870 original size:10 final size:10
Alignment explanation
Indices: 22855--22893 Score: 60
Period size: 11 Copynumber: 3.7 Consensus size: 10
22845 AGAAGTGAGC
22855 AAAAAAGAAA
1 AAAAAAGAAA
22865 AAAAAAGTAAA
1 AAAAAAG-AAA
22876 AAAAGAAGAAA
1 AAAA-AAGAAA
22887 AAAAAAG
1 AAAAAAG
22894 TGAAAAGTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 10 0.37
11 14 0.52
12 3 0.11
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.03
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:22877 original size:12 final size:11
Alignment explanation
Indices: 22855--22892 Score: 51
Period size: 12 Copynumber: 3.5 Consensus size: 11
22845 AGAAGTGAGC
22855 AAAAAAG-AAA
1 AAAAAAGAAAA
22865 AAAAAAGTAAAA
1 AAAAAAG-AAAA
*
22877 AAAGAAGAAAA
1 AAAAAAGAAAA
22888 AAAAA
1 AAAAA
22893 GTGAAAAGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 7 0.29
11 8 0.33
12 9 0.38
ACGTcount: A:0.87, C:0.00, G:0.11, T:0.03
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:22898 original size:12 final size:12
Alignment explanation
Indices: 22825--22899 Score: 52
Period size: 11 Copynumber: 6.3 Consensus size: 12
22815 AAGAAATTCA
*
22825 AAAAAAAAATTTG
1 AAAAAAAAA-GTG
22838 AAAAAAAAGAAGTG
1 -AAAAAAA-AAGTG
**
22852 AGCAAAAAA--G
1 AAAAAAAAAGTG
22862 AAAAAAAAAGT-
1 AAAAAAAAAGTG
22873 AAAAAAAGAA--G
1 AAAAAAA-AAGTG
22884 AAAAAAAAAGTG
1 AAAAAAAAAGTG
22896 AAAA
1 AAAA
22900 GTCTTGCGAG
Statistics
Matches: 49, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
10 10 0.20
11 14 0.29
12 9 0.18
13 5 0.10
14 9 0.18
15 2 0.04
ACGTcount: A:0.76, C:0.01, G:0.15, T:0.08
Consensus pattern (12 bp):
AAAAAAAAAGTG
Found at i:23966 original size:48 final size:47
Alignment explanation
Indices: 23887--23992 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
23877 GAGTGTCATG
*
23887 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
23935 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
23983 GAAAAAGAAA
1 GAAAAAGAAA
23993 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:25681 original size:20 final size:20
Alignment explanation
Indices: 25635--25681 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
25625 AGCTCGTTTC
*
25635 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
25655 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
25675 CAGCTCA
1 CAGCTCA
25682 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:30320 original size:21 final size:21
Alignment explanation
Indices: 30275--30337 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
30265 TTTGAACCAT
* *
30275 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
30297 TACCATTTCGTACCCATTCCA
1 TACCATTTCGTACCAATTCCA
* *
30318 TACTATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
30338 CAAATACCAA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
21 22 0.63
22 13 0.37
ACGTcount: A:0.32, C:0.33, G:0.05, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:32732 original size:21 final size:21
Alignment explanation
Indices: 32687--32749 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
32677 TTTGAACCAT
* *
32687 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
32709 TACCATTTCGTACCCATTCCA
1 TACCATTTCGTACCAATTCCA
* *
32730 TACTATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
32750 CAAATACCAA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
21 22 0.63
22 13 0.37
ACGTcount: A:0.32, C:0.33, G:0.05, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:34543 original size:50 final size:50
Alignment explanation
Indices: 34476--34610 Score: 191
Period size: 50 Copynumber: 2.7 Consensus size: 50
34466 TTCTGTACTT
* *
34476 CCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTG
1 CCAATGCCATGTCCCAGATATGGTCTTACATGGGACTTCTCATATCGGTG
* * ** *
34526 CCCATGCCATGTCCCAGACATGGTCTTACGGGGGACTTCTCATCTCGGTG
1 CCAATGCCATGTCCCAGATATGGTCTTACATGGGACTTCTCATATCGGTG
34576 CCAATGCCATGTCCCAGACT-TGGTCTTACATGGGA
1 CCAATGCCATGTCCCAGA-TATGGTCTTACATGGGA
34611 TCTCTTTACC
Statistics
Matches: 73, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
50 73 1.00
ACGTcount: A:0.21, C:0.28, G:0.24, T:0.27
Consensus pattern (50 bp):
CCAATGCCATGTCCCAGATATGGTCTTACATGGGACTTCTCATATCGGTG
Found at i:41393 original size:18 final size:18
Alignment explanation
Indices: 41337--41396 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
41327 AGTACGAGCG
41337 AGAAAAAGAAATCGAAAGAAA
1 AGAAAAAGAAATC--AA-AAA
* **
41358 AGAAAAAGAGATTGAAAA
1 AGAAAAAGAAATCAAAAA
41376 AGAAAAAGAAATCAAAAA
1 AGAAAAAGAAATCAAAAA
41394 AGA
1 AGA
41397 GAGTGAGGTC
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
18 21 0.64
19 1 0.03
21 11 0.33
ACGTcount: A:0.72, C:0.03, G:0.18, T:0.07
Consensus pattern (18 bp):
AGAAAAAGAAATCAAAAA
Found at i:45163 original size:33 final size:34
Alignment explanation
Indices: 45120--45185 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 34
45110 TTAAAGATGT
*
45120 TGTTCTACATGC-ATGGAACGGCAATT-AATGAGA
1 TGTTCCACATGCAATGG-ACGGCAATTAAATGAGA
*
45153 TGTTCCACATGCAATGGACGGCATTTAAATGAG
1 TGTTCCACATGCAATGGACGGCAATTAAATGAG
45186 GGAGAGTGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 19 0.66
34 10 0.34
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (34 bp):
TGTTCCACATGCAATGGACGGCAATTAAATGAGA
Found at i:49543 original size:20 final size:20
Alignment explanation
Indices: 49520--49573 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
49510 AGTTTTTCCC
*
49520 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
49540 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
49560 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
49574 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:49555 original size:30 final size:30
Alignment explanation
Indices: 49520--49593 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
49510 AGTTTTTCCC
49520 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
49550 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
49580 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
49594 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:49583 original size:20 final size:20
Alignment explanation
Indices: 49520--49584 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
49510 AGTTTTTCCC
* * * *
49520 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
49540 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
49559 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
49580 AGCTC
1 AGCTC
49585 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:54417 original size:21 final size:22
Alignment explanation
Indices: 54367--54417 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
54357 TCCACGTCTT
*
54367 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
54389 -TTCATTTTCTCTTC-TTTTC-AA
1 TTTC-TTTTCT-TTCTTTTTCTAA
54410 TTTCTTTT
1 TTTCTTTT
54418 TCACTCTCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 9 0.36
22 13 0.52
23 3 0.12
ACGTcount: A:0.10, C:0.18, G:0.02, T:0.71
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:55729 original size:9 final size:9
Alignment explanation
Indices: 55715--55748 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
55705 GAATTTCGTA
*
55715 TTTTTTGAT
1 TTTTTTGAC
55724 TTTTTTGAC
1 TTTTTTGAC
55733 TTTTTTGAC
1 TTTTTTGAC
55742 TTATTTT
1 TT-TTTT
55749 TTTGCGGGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 19 0.83
10 4 0.17
ACGTcount: A:0.12, C:0.06, G:0.09, T:0.74
Consensus pattern (9 bp):
TTTTTTGAC
Found at i:57804 original size:13 final size:13
Alignment explanation
Indices: 57783--57817 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
57773 ATAAGTTTCT
* *
57783 GTTAGTTAAATTA
1 GTTAATTAAATAA
57796 GTTAATTAAATAA
1 GTTAATTAAATAA
57809 GTTAATTAA
1 GTTAATTAA
57818 TTTGTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (13 bp):
GTTAATTAAATAA
Found at i:58065 original size:23 final size:24
Alignment explanation
Indices: 58035--58097 Score: 94
Period size: 23 Copynumber: 2.7 Consensus size: 24
58025 TTTTCCAGAT
58035 AATTTAATGTATGTCTT-TGGCCG
1 AATTTAATGTATGTCTTCTGGCCG
*
58058 AATTTAATGTATGT-TTCTGGCTG
1 AATTTAATGTATGTCTTCTGGCCG
*
58081 AATTTAATGCATGTCTT
1 AATTTAATGTATGTCTT
58098 AAATGGTGTC
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
22 2 0.06
23 32 0.89
24 2 0.06
ACGTcount: A:0.24, C:0.11, G:0.19, T:0.46
Consensus pattern (24 bp):
AATTTAATGTATGTCTTCTGGCCG
Found at i:61486 original size:21 final size:21
Alignment explanation
Indices: 61437--61503 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
61427 CCTCTTTGAA
* * *
61437 CCATAACCAATTCGTACCAAATA
1 CCAT-ACCATTTCATACC-AATT
*
61460 CCATACTATTTCATACCAATT
1 CCATACCATTTCATACCAATT
*
61481 CCATACCATTTCGTACCAATT
1 CCATACCATTTCATACCAATT
61502 CC
1 CC
61504 CAAATACCAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 24 0.63
22 10 0.26
23 4 0.11
ACGTcount: A:0.34, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
CCATACCATTTCATACCAATT
Found at i:61845 original size:27 final size:26
Alignment explanation
Indices: 61802--61854 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 26
61792 ATAGGTGCGT
* *
61802 AAAAAAAAAGTTCAAAAAAAAAATTG
1 AAAAAAAAAATTAAAAAAAAAAATTG
61828 AAAAAAAAAATTGAAAAAAAAAAATTG
1 AAAAAAAAAATT-AAAAAAAAAAATTG
61855 CATACGGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 11 0.46
27 13 0.54
ACGTcount: A:0.75, C:0.02, G:0.08, T:0.15
Consensus pattern (26 bp):
AAAAAAAAAATTAAAAAAAAAAATTG
Found at i:61854 original size:14 final size:13
Alignment explanation
Indices: 61802--61850 Score: 80
Period size: 13 Copynumber: 3.8 Consensus size: 13
61792 ATAGGTGCGT
* *
61802 AAAAAAAAAGTTC
1 AAAAAAAAAATTG
61815 AAAAAAAAAATTG
1 AAAAAAAAAATTG
61828 AAAAAAAAAATTG
1 AAAAAAAAAATTG
61841 AAAAAAAAAA
1 AAAAAAAAAA
61851 ATTGCATACG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.80, C:0.02, G:0.06, T:0.12
Consensus pattern (13 bp):
AAAAAAAAAATTG
Found at i:64116 original size:17 final size:17
Alignment explanation
Indices: 64069--64124 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
64059 AGAAAAGACC
* *
64069 GAAAATACAAAAGAAAA
1 GAAAATTCAAAAAAAAA
64086 GAAAAATGAT-AAAAAAAAA
1 G-AAAAT--TCAAAAAAAAA
*
64105 GAAAATTCAAAAAAAGA
1 GAAAATTCAAAAAAAAA
64122 GAA
1 GAA
64125 TGAAAAGAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
16 1 0.03
17 12 0.38
18 10 0.31
19 9 0.28
ACGTcount: A:0.75, C:0.04, G:0.12, T:0.09
Consensus pattern (17 bp):
GAAAATTCAAAAAAAAA
Found at i:64117 original size:18 final size:19
Alignment explanation
Indices: 64077--64119 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
64067 CCGAAAATAC
* *
64077 AAAAGAAAAGAAAAATGAT
1 AAAAAAAAAGAAAAATCAT
*
64096 AAAAAAAAAGAAAATTCA-
1 AAAAAAAAAGAAAAATCAT
64114 AAAAAA
1 AAAAAA
64120 GAGAATGAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.79, C:0.02, G:0.09, T:0.09
Consensus pattern (19 bp):
AAAAAAAAAGAAAAATCAT
Found at i:68414 original size:21 final size:21
Alignment explanation
Indices: 68365--68431 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
68355 CCTCTTTGAA
* * *
68365 CCATAACCAATTCGTACCAAATA
1 CCAT-ACCATTTCATACC-AATT
*
68388 CCATACTATTTCATACCAATT
1 CCATACCATTTCATACCAATT
*
68409 CCATACCATTTCGTACCAATT
1 CCATACCATTTCATACCAATT
68430 CC
1 CC
68432 CAAATACCAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 24 0.63
22 10 0.26
23 4 0.11
ACGTcount: A:0.34, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
CCATACCATTTCATACCAATT
Found at i:69498 original size:13 final size:13
Alignment explanation
Indices: 69480--69540 Score: 63
Period size: 14 Copynumber: 4.6 Consensus size: 13
69470 CGTAGCTTCG
69480 AAAAAAAAAGTTA
1 AAAAAAAAAGTTA
69493 AAAAAAAAAGTTTCA
1 AAAAAAAAAG-TT-A
* *
69508 AAAAAAAAAATCTG
1 AAAAAAAAAGT-TA
69522 AAAAAAAAAG--A
1 AAAAAAAAAGTTA
69533 AAAAAAAA
1 AAAAAAAA
69541 TTTGCAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
11 8 0.20
13 10 0.24
14 12 0.29
15 11 0.27
ACGTcount: A:0.79, C:0.03, G:0.07, T:0.11
Consensus pattern (13 bp):
AAAAAAAAAGTTA
Found at i:69499 original size:14 final size:15
Alignment explanation
Indices: 69480--69530 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 15
69470 CGTAGCTTCG
69480 AAAAAAAAAGTT--A
1 AAAAAAAAAGTTCAA
69493 AAAAAAAAAGTTTCAA
1 AAAAAAAAAG-TTCAA
*
69509 AAAAAAAAA-TCTGAA
1 AAAAAAAAAGT-TCAA
69524 AAAAAAA
1 AAAAAAA
69531 GAAAAAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
13 10 0.30
14 3 0.09
15 10 0.30
16 10 0.30
ACGTcount: A:0.76, C:0.04, G:0.06, T:0.14
Consensus pattern (15 bp):
AAAAAAAAAGTTCAA
Found at i:69539 original size:23 final size:24
Alignment explanation
Indices: 69509--69554 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
69499 AAAGTTTCAA
69509 AAAAAAAAATCTG-AAAAAAAAAG
1 AAAAAAAAATCTGCAAAAAAAAAG
*
69532 AAAAAAAAATTTGCAAAAAAAAA
1 AAAAAAAAATCTGCAAAAAAAAA
69555 AATTGCATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.78, C:0.04, G:0.07, T:0.11
Consensus pattern (24 bp):
AAAAAAAAATCTGCAAAAAAAAAG
Found at i:69550 original size:15 final size:15
Alignment explanation
Indices: 69480--69561 Score: 56
Period size: 15 Copynumber: 6.0 Consensus size: 15
69470 CGTAGCTTCG
*
69480 AAAAAAAAAGTT--A
1 AAAAAAAAAATTGCA
* *
69493 AAAAAAAAAGTTTCA
1 AAAAAAAAAATTGCA
69508 AAAAAAAAAATCTG--
1 AAAAAAAAAAT-TGCA
69522 -AAAAAAAAA--G--
1 AAAAAAAAAATTGCA
*
69532 AAAAAAAAATTTGCA
1 AAAAAAAAAATTGCA
69547 AAAAAAAAAATTGCA
1 AAAAAAAAAATTGCA
69562 TACGGTCTAG
Statistics
Matches: 57, Mismatches: 4, Indels: 14
0.76 0.05 0.19
Matches are distributed among these distances:
10 1 0.02
11 8 0.14
13 22 0.39
15 25 0.44
16 1 0.02
ACGTcount: A:0.73, C:0.05, G:0.07, T:0.15
Consensus pattern (15 bp):
AAAAAAAAAATTGCA
Found at i:72931 original size:10 final size:11
Alignment explanation
Indices: 72894--72931 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
72884 AAGAAGTGAC
72894 AAAAAAAACGAG
1 AAAAAAAA-GAG
72906 AAAAAAAAGAG
1 AAAAAAAAGAG
*
72917 AAAAAAAAGTG
1 AAAAAAAAGAG
72928 AAAA
1 AAAA
72932 GTCTTGCGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
11 17 0.68
12 8 0.32
ACGTcount: A:0.79, C:0.03, G:0.16, T:0.03
Consensus pattern (11 bp):
AAAAAAAAGAG
Found at i:85745 original size:21 final size:23
Alignment explanation
Indices: 85700--85746 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
85690 TCACCTGCAA
* *
85700 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
85723 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
85744 TAA
1 TAA
85747 TCATACTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:91088 original size:16 final size:15
Alignment explanation
Indices: 91067--91122 Score: 103
Period size: 15 Copynumber: 3.7 Consensus size: 15
91057 TAGCTTCTTC
91067 TTTTTTTTCACGAAAT
1 TTTTTTTTCACG-AAT
91083 TTTTTTTTCACGAAT
1 TTTTTTTTCACGAAT
91098 TTTTTTTTCACGAAT
1 TTTTTTTTCACGAAT
91113 TTTTTTTTCA
1 TTTTTTTTCA
91123 ACTTGATATC
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
15 28 0.70
16 12 0.30
ACGTcount: A:0.20, C:0.12, G:0.05, T:0.62
Consensus pattern (15 bp):
TTTTTTTTCACGAAT
Found at i:91180 original size:13 final size:12
Alignment explanation
Indices: 91160--91209 Score: 91
Period size: 12 Copynumber: 4.2 Consensus size: 12
91150 ATGGAAACCA
91160 AATTTTTTTTTG
1 AATTTTTTTTTG
91172 AATTTTTTTTTG
1 AATTTTTTTTTG
91184 AATTTTTTTTTG
1 AATTTTTTTTTG
*
91196 AAATTTTTTTTG
1 AATTTTTTTTTG
91208 AA
1 AA
91210 GAAACTACTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.22, C:0.00, G:0.08, T:0.70
Consensus pattern (12 bp):
AATTTTTTTTTG
Found at i:93031 original size:20 final size:19
Alignment explanation
Indices: 93008--93072 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
92998 AAGCTCAAAC
93008 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
93028 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
93048 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
93068 GAGCT
1 GAGCT
93073 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:93292 original size:20 final size:20
Alignment explanation
Indices: 93246--93292 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
93236 AGCTCGTTTC
*
93246 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
93266 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
93286 CAGCTCA
1 CAGCTCA
93293 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:94858 original size:23 final size:22
Alignment explanation
Indices: 94823--94869 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
94813 AGAAGTGAGC
*
94823 AAAAAAAGAAAAAAAAAGTAAA
1 AAAAAAACAAAAAAAAAGTAAA
*
94845 AAAAAGAACAAAAAAAAAGTGAA
1 AAAAA-AACAAAAAAAAAGTAAA
94868 AA
1 AA
94870 GTCTTGTGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.83, C:0.02, G:0.11, T:0.04
Consensus pattern (22 bp):
AAAAAAACAAAAAAAAAGTAAA
Found at i:94869 original size:10 final size:10
Alignment explanation
Indices: 94823--94860 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
94813 AGAAGTGAGC
94823 AAAAAAAGAA
1 AAAAAAAGAA
*
94833 AAAAAAAGTA
1 AAAAAAAGAA
94843 AAAAAAAGAA
1 AAAAAAAGAA
94853 CAAAAAAA
1 -AAAAAAA
94861 AAGTGAAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 18 0.72
11 7 0.28
ACGTcount: A:0.87, C:0.03, G:0.08, T:0.03
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:97727 original size:20 final size:20
Alignment explanation
Indices: 97681--97727 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
97671 AGCTCGTTTC
*
97681 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
97701 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
97721 CAGCTCA
1 CAGCTCA
97728 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:99263 original size:23 final size:21
Alignment explanation
Indices: 99237--99303 Score: 84
Period size: 22 Copynumber: 3.1 Consensus size: 21
99227 ATCAAAATTC
*
99237 AAAAAAA-AAAAAAGAAGTGA
1 AAAAAAAGAAAAAAAAAGTGA
99257 GCAAAAAAAGAAAAAAAAAGT-A
1 --AAAAAAAGAAAAAAAAAGTGA
99279 AAAAAAAGAATAAAAAAAGTGA
1 AAAAAAAGAA-AAAAAAAGTGA
99301 AAA
1 AAA
99304 GTCTTGTGAG
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
20 10 0.24
21 9 0.22
22 12 0.29
23 10 0.24
ACGTcount: A:0.79, C:0.01, G:0.13, T:0.06
Consensus pattern (21 bp):
AAAAAAAGAAAAAAAAAGTGA
Found at i:99275 original size:11 final size:10
Alignment explanation
Indices: 99259--99297 Score: 60
Period size: 10 Copynumber: 3.8 Consensus size: 10
99249 AGAAGTGAGC
99259 AAAAAAAGAA
1 AAAAAAAGAA
*
99269 AAAAAAAGTA
1 AAAAAAAGAA
99279 AAAAAAAGAA
1 AAAAAAAGAA
99289 TAAAAAAAG
1 -AAAAAAAG
99298 TGAAAAGTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
10 18 0.69
11 8 0.31
ACGTcount: A:0.85, C:0.00, G:0.10, T:0.05
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:99303 original size:10 final size:10
Alignment explanation
Indices: 99259--99303 Score: 54
Period size: 10 Copynumber: 4.3 Consensus size: 10
99249 AGAAGTGAGC
*
99259 AAAAAAAGAA
1 AAAAAAAGTA
99269 AAAAAAAGTA
1 AAAAAAAGTA
*
99279 AAAAAAAGAA
1 AAAAAAAGTA
99289 TAAAAAAAGTGA
1 -AAAAAAAGT-A
99301 AAA
1 AAA
99304 GTCTTGTGAG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
10 18 0.60
11 11 0.37
12 1 0.03
ACGTcount: A:0.82, C:0.00, G:0.11, T:0.07
Consensus pattern (10 bp):
AAAAAAAGTA
Found at i:100284 original size:4 final size:4
Alignment explanation
Indices: 100275--100302 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
100265 AAGTTTTATT
100275 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
100303 CTTAGTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:104074 original size:12 final size:13
Alignment explanation
Indices: 104052--104080 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
104042 AAGTTTTATT
104052 TTTATTTTATTTA
1 TTTATTTTATTTA
104065 TTTA-TTTATTTA
1 TTTATTTTATTTA
104077 TTTA
1 TTTA
104081 CTTAGTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTATTTTATTTA
Done.