Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015097.1 Kokia drynarioides strain JFW-HI SEQ_130141, whole genome shotgun sequence
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: 157143
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:626 original size:29 final size:29
Alignment explanation
Indices: 593--683 Score: 73
Period size: 29 Copynumber: 3.2 Consensus size: 29
583 ATAAAACCAA
593 ATATAGAACCTTACTTCCACTAAACTTAT
1 ATATAGAACCTTACTTCCACTAAACTTAT
* * * * * *
622 ATATATAGTCATTAACAT--A-TAAAAC-CAA
1 ATATAGA-ACCTT-ACTTCCACT-AAACTTAT
650 ATATAGAACCTTACTTCCACTAAACTTAT
1 ATATAGAACCTTACTTCCACTAAACTTAT
679 ATATA
1 ATATA
684 TACTATAGTA
Statistics
Matches: 43, Mismatches: 12, Indels: 14
0.62 0.17 0.20
Matches are distributed among these distances:
26 3 0.07
27 3 0.07
28 13 0.30
29 18 0.42
30 3 0.07
31 3 0.07
ACGTcount: A:0.44, C:0.20, G:0.03, T:0.33
Consensus pattern (29 bp):
ATATAGAACCTTACTTCCACTAAACTTAT
Found at i:640 original size:57 final size:57
Alignment explanation
Indices: 571--685 Score: 230
Period size: 57 Copynumber: 2.0 Consensus size: 57
561 ACAAGCATTA
571 AGTCATTAACATATAAAACCAAATATAGAACCTTACTTCCACTAAACTTATATATAT
1 AGTCATTAACATATAAAACCAAATATAGAACCTTACTTCCACTAAACTTATATATAT
628 AGTCATTAACATATAAAACCAAATATAGAACCTTACTTCCACTAAACTTATATATAT
1 AGTCATTAACATATAAAACCAAATATAGAACCTTACTTCCACTAAACTTATATATAT
685 A
1 A
686 CTATAGTAGG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.46, C:0.19, G:0.03, T:0.31
Consensus pattern (57 bp):
AGTCATTAACATATAAAACCAAATATAGAACCTTACTTCCACTAAACTTATATATAT
Found at i:674 original size:28 final size:28
Alignment explanation
Indices: 586--674 Score: 69
Period size: 28 Copynumber: 3.1 Consensus size: 28
576 TTAACATATA
586 AAACCAAATATAGAACCTTACTTCCACT
1 AAACCAAATATAGAACCTTACTTCCACT
* * * *
614 AAACTTATATATATAG-TCATTAACAT--A-T
1 AAAC-CA-A-ATATAGAACCTT-ACTTCCACT
642 AAAACCAAATATAGAACCTTACTTCCACT
1 -AAACCAAATATAGAACCTTACTTCCACT
671 AAAC
1 AAAC
675 TTATATATAT
Statistics
Matches: 44, Mismatches: 8, Indels: 18
0.63 0.11 0.26
Matches are distributed among these distances:
26 9 0.20
27 4 0.09
28 11 0.25
29 7 0.16
30 4 0.09
31 9 0.20
ACGTcount: A:0.46, C:0.22, G:0.03, T:0.28
Consensus pattern (28 bp):
AAACCAAATATAGAACCTTACTTCCACT
Found at i:862 original size:19 final size:18
Alignment explanation
Indices: 830--865 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
820 AATTACCCTA
830 AAAACCCAAACCCAAATT
1 AAAACCCAAACCCAAATT
*
848 AAAACCTAAAGCCCAAAT
1 AAAACCCAAA-CCCAAAT
866 GGGCCGAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.56, C:0.31, G:0.03, T:0.11
Consensus pattern (18 bp):
AAAACCCAAACCCAAATT
Found at i:2465 original size:14 final size:15
Alignment explanation
Indices: 2448--2480 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
2438 CCGCGTTCAT
*
2448 TTTTCATTAAAA-TG
1 TTTTAATTAAAATTG
2462 TTTTAATTAAAATTG
1 TTTTAATTAAAATTG
2477 TTTT
1 TTTT
2481 TCTGATTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.33, C:0.03, G:0.06, T:0.58
Consensus pattern (15 bp):
TTTTAATTAAAATTG
Found at i:5028 original size:2 final size:2
Alignment explanation
Indices: 5021--5048 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5011 AAAGATAATA
5021 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5049 TTCATCTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5217 original size:23 final size:23
Alignment explanation
Indices: 5174--5218 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
5164 TGTAAAACCA
*
5174 AATAATTGTCACATGTTTATTAC
1 AATAATTGTCACATGTATATTAC
*
5197 AATAGTTG-CACATGTAATATTA
1 AATAATTGTCACATGT-ATATTA
5219 TTAACCTTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Consensus pattern (23 bp):
AATAATTGTCACATGTATATTAC
Found at i:8580 original size:34 final size:34
Alignment explanation
Indices: 8539--8606 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
8529 GGTTTTTGAC
8539 ATTGGATTCTCCTAACTCTTTTTTCATTCTCCTT
1 ATTGGATTCTCCTAACTCTTTTTTCATTCTCCTT
*
8573 ATTGGATTCTGCTAACTCTTTTTTCATTCTCCTT
1 ATTGGATTCTCCTAACTCTTTTTTCATTCTCCTT
8607 TTCCCCCTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.15, C:0.25, G:0.07, T:0.53
Consensus pattern (34 bp):
ATTGGATTCTCCTAACTCTTTTTTCATTCTCCTT
Found at i:18809 original size:28 final size:29
Alignment explanation
Indices: 18764--18827 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 29
18754 TGAAAATAAG
* *
18764 ATTTTCGATACTCGGGGGCCAAAATGTTA
1 ATTTTGGATACTCGGGGGCCAAAATGGTA
18793 ATTTTGGATACTCGGGGG-CAAAATGGTA
1 ATTTTGGATACTCGGGGGCCAAAATGGTA
18821 ATTTTGG
1 ATTTTGG
18828 GAAAGTTCAG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
28 16 0.48
29 17 0.52
ACGTcount: A:0.27, C:0.12, G:0.28, T:0.33
Consensus pattern (29 bp):
ATTTTGGATACTCGGGGGCCAAAATGGTA
Found at i:18966 original size:59 final size:58
Alignment explanation
Indices: 18899--19185 Score: 335
Period size: 58 Copynumber: 4.9 Consensus size: 58
18889 GATATTCAAA
** * * *
18899 GGTAAAATGGTAATTTTGGAAAAAATTGGGGTCAAAAATAAAAATTTTGGAAGTTTA-AG
1 GGTAAAATGGTAATTTTGG-AAAAATTAAGGTTAAAAATAGAATTTTTGGAAG-TTAGAG
* * * *
18958 GGTGAAATGGTAATTTTTGG-AAAATTAAGGTTAAAAATGGAATTTTTGGAAGTTTGGG
1 GGTAAAATGGTAA-TTTTGGAAAAATTAAGGTTAAAAATAGAATTTTTGGAAGTTAGAG
*
19016 GGTAAAATGGTAATTTTGGAAAAATTGAGGTTAAAAATAGAATTTTTGGAAGTTAGAG
1 GGTAAAATGGTAATTTTGGAAAAATTAAGGTTAAAAATAGAATTTTTGGAAGTTAGAG
* * *
19074 GGTAAAATGGTAATTTTTGGAGAAATCAAGGTTAAAAATGGAATTTTTGGAAGTTAGAG
1 GGTAAAATGGTAA-TTTTGGAAAAATTAAGGTTAAAAATAGAATTTTTGGAAGTTAGAG
** ** * *
19133 GGTAAAATGGTAATTATTGGGTAAATCGAGGTCAAAAATGGTAATTTTTGGAA
1 GGTAAAATGGTAATT-TTGGAAAAATTAAGGTTAAAAATAG-AATTTTTGGAA
19186 AAATTAAGGT
Statistics
Matches: 200, Mismatches: 22, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
57 8 0.04
58 88 0.44
59 87 0.44
60 17 0.09
ACGTcount: A:0.39, C:0.01, G:0.26, T:0.33
Consensus pattern (58 bp):
GGTAAAATGGTAATTTTGGAAAAATTAAGGTTAAAAATAGAATTTTTGGAAGTTAGAG
Found at i:18975 original size:90 final size:90
Alignment explanation
Indices: 18812--18975 Score: 215
Period size: 90 Copynumber: 1.8 Consensus size: 90
18802 ACTCGGGGGC
* * * * * *
18812 AAAATGGTAATTTTGGGAAAGTTCAGGGTCAAAAATAGAATTTTTGGAAGTTTGAGGTTTAAAAT
1 AAAATGGTAATTTTGGAAAAATTCAGGGTCAAAAATAAAAATTTTGGAAGTTTAAGGTGTAAAAT
*
18877 GGAGTTTTTTGAGATATTCAAAGGT
66 GGAATTTTTTGAGATATTCAAAGGT
* *
18902 AAAATGGTAATTTTGGAAAAAATT-GGGGTCAAAAATAAAAATTTTGGAAGTTTAAGG-GTGAAA
1 AAAATGGTAATTTTGG-AAAAATTCAGGGTCAAAAATAAAAATTTTGGAAGTTTAAGGTGTAAAA
18965 TGGTAATTTTT
65 TGG-AATTTTT
18976 GGAAAATTAA
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
89 7 0.11
90 51 0.81
91 5 0.08
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.35
Consensus pattern (90 bp):
AAAATGGTAATTTTGGAAAAATTCAGGGTCAAAAATAAAAATTTTGGAAGTTTAAGGTGTAAAAT
GGAATTTTTTGAGATATTCAAAGGT
Found at i:18985 original size:29 final size:30
Alignment explanation
Indices: 18812--19470 Score: 274
Period size: 29 Copynumber: 22.5 Consensus size: 30
18802 ACTCGGGGGC
* * *
18812 AAAATGGTAATTTTGGGAAAGTTCAGGGTCA
1 AAAATGGTAATTTTTGGAAAATTAAGGGT-A
* ** * * *
18843 AAAATAG-AATTTTTGGAAGTTTGAGGTTT
1 AAAATGGTAATTTTTGGAAAATTAAGGGTA
* * * *
18872 AAAATGG-AGTTTTTTGAGATATTCAAAGGT-
1 AAAATGGTAATTTTTGGA-AAATT-AAGGGTA
*
18902 AAAATGGTAA-TTTTGGAAAAAATT-GGGGTCA
1 AAAATGGTAATTTTTGG--AAAATTAAGGGT-A
** * **
18933 AAAAT-AAAAATTTTGGAAGTTTAAGGGT-
1 AAAATGGTAATTTTTGGAAAATTAAGGGTA
* *
18961 GAAATGGTAATTTTTGGAAAATTAAGGTTA
1 AAAATGGTAATTTTTGGAAAATTAAGGGTA
** **
18991 AAAATGG-AATTTTTGGAAGTTTGGGGGT-
1 AAAATGGTAATTTTTGGAAAATTAAGGGTA
* *
19019 AAAATGGTAA-TTTTGGAAAAATTGAGGTTA
1 AAAATGGTAATTTTTGG-AAAATTAAGGGTA
* *
19049 AAAATAG-AATTTTTGG-AAGTTAGAGGGT-
1 AAAATGGTAATTTTTGGAAAATTA-AGGGTA
* *
19077 AAAATGGTAATTTTTGGAGAAATCAAGGTTA
1 AAAATGGTAATTTTTGGA-AAATTAAGGGTA
*
19108 AAAATGG-AATTTTTGG-AAGTTAGAGGGT-
1 AAAATGGTAATTTTTGGAAAATTA-AGGGTA
* * **
19136 AAAATGGTAATTATTGGGTAAATCGA-GGTCA
1 AAAATGGTAATT-TTTGGAAAATTAAGGGT-A
19167 AAAATGGTAATTTTTGGAAAAATTAA-GGTAA
1 AAAATGGTAATTTTTGG-AAAATTAAGGGT-A
* * **
19198 AAAAAGG-AATTTTTAGAAGTTTAAGGGT-
1 AAAATGGTAATTTTTGGAAAATTAAGGGTA
* * * *
19226 AAAATTGTAATTTTTAG-AAA-TCAGGGTC
1 AAAATGGTAATTTTTGGAAAATTAAGGGTA
* **
19254 AAAATAG-AATTTTT--AAAAGCTCGAGGGT-
1 AAAATGGTAATTTTTGGAAAA--TTAAGGGTA
** * * *
19282 AAAATAATAATTTTGGGAAAATCAA-GGTC
1 AAAATGGTAATTTTTGGAAAATTAAGGGTA
* * **
19311 AAAATTG-AATTTTTGG-AAGTTCGGGGGT-
1 AAAATGGTAATTTTTGGAAAATT-AAGGGTA
* * *
19339 AAAATGGTAATTTTTTGAAAAATCAA-GTTAA
1 AAAATGGTAA-TTTTTGGAAAATTAAGGGT-A
* ** *
19370 AAAATGG-ATTTTTTGGAAGTTTAGGGGT-
1 AAAATGGTAATTTTTGGAAAATTAAGGGTA
* *
19398 AAAATGGTAATTTTTGGAAAAATAAAGGTTA
1 AAAATGGTAATTTTTGG-AAAATTAAGGGTA
* * *
19429 AAAAT--TGATTTTTGGAAAGTTTAGGGT-
1 AAAATGGTAATTTTTGGAAAATTAAGGGTA
19456 AAAATGGTAATTTTT
1 AAAATGGTAATTTTT
19471 AAATAAATTT
Statistics
Matches: 467, Mismatches: 110, Indels: 104
0.69 0.16 0.15
Matches are distributed among these distances:
26 3 0.01
27 21 0.04
28 88 0.19
29 165 0.35
30 104 0.22
31 85 0.18
32 1 0.00
ACGTcount: A:0.40, C:0.02, G:0.24, T:0.34
Consensus pattern (30 bp):
AAAATGGTAATTTTTGGAAAATTAAGGGTA
Found at i:19005 original size:58 final size:58
Alignment explanation
Indices: 18850--19185 Score: 340
Period size: 59 Copynumber: 5.7 Consensus size: 58
18840 TCAAAAATAG
** * * * *
18850 AATTTTTGGAAGTTTGAGGTTTAAAATGGAGTTTTTTGAGATA-TTCAAAGGTAAAATGGT
1 AATTTTTGGAAAATTGAGGTTAAAAATGGA-ATTTTTG-GA-AGTTTAAGGGTAAAATGGT
* * ** * *
18910 AA-TTTTGGAAAAAATTGGGGTCAAAAATAAAAATTTTGGAAGTTTAAGGGTGAAATGGT
1 AATTTTTGG--AAAATTGAGGTTAAAAATGGAATTTTTGGAAGTTTAAGGGTAAAATGGT
* **
18969 AATTTTTGGAAAATTAAGGTTAAAAATGGAATTTTTGGAAGTTTGGGGGTAAAATGGT
1 AATTTTTGGAAAATTGAGGTTAAAAATGGAATTTTTGGAAGTTTAAGGGTAAAATGGT
*
19027 AA-TTTTGGAAAAATTGAGGTTAAAAATAGAATTTTTGGAAG-TTAGAGGGTAAAATGGT
1 AATTTTTGG-AAAATTGAGGTTAAAAATGGAATTTTTGGAAGTTTA-AGGGTAAAATGGT
**
19085 AATTTTTGGAGAAATCAAGGTTAAAAATGGAATTTTTGGAAG-TTAGAGGGTAAAATGGT
1 AATTTTTGGA-AAATTGAGGTTAAAAATGGAATTTTTGGAAGTTTA-AGGGTAAAATGGT
* * * *
19144 AATTATTGGGTAAATCGAGGTCAAAAATGGTAATTTTTGGAA
1 AATT-TTTGGAAAATTGAGGTTAAAAATGG-AATTTTTGGAA
19186 AAATTAAGGT
Statistics
Matches: 234, Mismatches: 32, Indels: 20
0.82 0.11 0.07
Matches are distributed among these distances:
57 8 0.03
58 88 0.38
59 96 0.41
60 28 0.12
61 14 0.06
ACGTcount: A:0.38, C:0.01, G:0.26, T:0.34
Consensus pattern (58 bp):
AATTTTTGGAAAATTGAGGTTAAAAATGGAATTTTTGGAAGTTTAAGGGTAAAATGGT
Found at i:19324 original size:57 final size:56
Alignment explanation
Indices: 19167--19352 Score: 156
Period size: 57 Copynumber: 3.2 Consensus size: 56
19157 ATCGAGGTCA
* * * * * * * **
19167 AAAATGGTAATTTTTGGAAAAATTAAGGTAAAAAAAGGAATTTTTAGAAGTTTAAGGGT
1 AAAATAGTAA-TTTT-GAGAAATCAAGGTCAAAATA-GAATTTTTAAAAGCTCGAGGGT
* * *
19226 AAAATTGTAATTTTTAGAAATCAGGGTCAAAATAGAATTTTTAAAAGCTCGAGGGT
1 AAAATAGTAATTTTGAGAAATCAAGGTCAAAATAGAATTTTTAAAAGCTCGAGGGT
* * * ** * *
19282 AAAATAATAATTTTGGGAAAATCAAGGTCAAAATTGAATTTTTGGAAGTTCGGGGGT
1 AAAATAGTAATTTTGAG-AAATCAAGGTCAAAATAGAATTTTTAAAAGCTCGAGGGT
*
19339 AAAATGGTAATTTT
1 AAAATAGTAATTTT
19353 TTGAAAAATC
Statistics
Matches: 103, Mismatches: 23, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
56 31 0.30
57 59 0.57
58 4 0.04
59 9 0.09
ACGTcount: A:0.42, C:0.04, G:0.22, T:0.33
Consensus pattern (56 bp):
AAAATAGTAATTTTGAGAAATCAAGGTCAAAATAGAATTTTTAAAAGCTCGAGGGT
Found at i:19412 original size:58 final size:57
Alignment explanation
Indices: 19167--19513 Score: 288
Period size: 59 Copynumber: 6.0 Consensus size: 57
19157 ATCGAGGTCA
* * * *
19167 AAAATGGTAATTTTTGGAAAAATTAAGGTAAAAAAAGGAATTTTTAGAAGTTTAAGGGT
1 AAAATGGTAATTTTT-GAAAAATCAAGGT-AAAAATGGAATTTTTGGAAGTTTAGGGGT
* * * * * ** * *
19226 AAAATTGTAATTTTT-AGAAATCAGGGTCAAAATAGAATTTTTAAAAG-CTCGAGGGT
1 AAAATGGTAATTTTTGAAAAATCAAGGTAAAAATGGAATTTTTGGAAGTTTAG-GGGT
** * * * * **
19282 AAAATAATAATTTTGGGAAAATCAAGGTCAAAATTGAATTTTTGGAAGTTCGGGGGT
1 AAAATGGTAATTTTTGAAAAATCAAGGTAAAAATGGAATTTTTGGAAGTTTAGGGGT
* *
19339 AAAATGGTAATTTTTTGAAAAATCAAGTTAAAAAATGGATTTTTTGGAAGTTTAGGGGT
1 AAAATGGTAA-TTTTTGAAAAATCAAGGT-AAAAATGGAATTTTTGGAAGTTTAGGGGT
* *
19398 AAAATGGTAATTTTTGGAAAAATAAAGGTTAAAAATTG-ATTTTTGGAAAGTTTA-GGGT
1 AAAATGGTAATTTTT-GAAAAATCAAGG-TAAAAATGGAATTTTTGG-AAGTTTAGGGGT
* *** * *
19456 AAAATGGTAATTTTTAAATAAATTTGGGTTAAAAATGAAATTTTTGAATAGTTTAGGG
1 AAAATGGTAATTTTTGAA-AAATCAAGG-TAAAAATGGAATTTTTGGA-AGTTTAGGG
19514 AACTTTAGGG
Statistics
Matches: 232, Mismatches: 44, Indels: 23
0.78 0.15 0.08
Matches are distributed among these distances:
55 1 0.00
56 32 0.14
57 49 0.21
58 62 0.27
59 85 0.37
60 3 0.01
ACGTcount: A:0.41, C:0.02, G:0.22, T:0.35
Consensus pattern (57 bp):
AAAATGGTAATTTTTGAAAAATCAAGGTAAAAATGGAATTTTTGGAAGTTTAGGGGT
Found at i:21030 original size:11 final size:11
Alignment explanation
Indices: 20986--21052 Score: 59
Period size: 11 Copynumber: 6.2 Consensus size: 11
20976 GTAATTGAAC
20986 TTAAATTTATAA
1 TTAAATTTA-AA
*
20998 -TAATTTTAAA
1 TTAAATTTAAA
*
21008 TTAAA--AAAA
1 TTAAATTTAAA
*
21017 TTAAACTTAAA
1 TTAAATTTAAA
21028 TTAAATTTAAAA
1 TTAAATTT-AAA
*
21040 ATAAATTTAAA
1 TTAAATTTAAA
21051 TT
1 TT
21053 TAAAATAAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
9 8 0.18
10 2 0.05
11 24 0.55
12 10 0.23
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:21037 original size:6 final size:6
Alignment explanation
Indices: 21017--21067 Score: 52
Period size: 6 Copynumber: 8.8 Consensus size: 6
21007 ATTAAAAAAA
* * * *
21017 TTAAAC TTAAA- TTAAAT TTAAAA ATAAAT TTAAAT TTAAA- ATAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
21063 TTAAA
1 TTAAA
21068 ATGGGTTTGG
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
5 9 0.24
6 28 0.76
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (6 bp):
TTAAAT
Found at i:21044 original size:23 final size:25
Alignment explanation
Indices: 21003--21068 Score: 69
Period size: 29 Copynumber: 2.5 Consensus size: 25
20993 TATAATAATT
21003 TTAAATTAAAAAAATTAAACTTAAA
1 TTAAATTAAAAAAATTAAACTTAAA
*
21028 TTAAATTTAAAAATAAATTTAAATTTAAA
1 TTAAA-TT-AAAA-AAA-TTAAACTTAAA
* *
21057 ATAAATTTAAAA
1 TTAAATTAAAAA
21069 TGGGTTTGGT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
25 5 0.15
26 3 0.09
27 7 0.21
28 5 0.15
29 14 0.41
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (25 bp):
TTAAATTAAAAAAATTAAACTTAAA
Found at i:21064 original size:17 final size:18
Alignment explanation
Indices: 21024--21067 Score: 74
Period size: 17 Copynumber: 2.6 Consensus size: 18
21014 AAATTAAACT
21024 TAAA-TTAAATTTAAAAA
1 TAAATTTAAATTTAAAAA
21041 TAAATTTAAATTT-AAAA
1 TAAATTTAAATTTAAAAA
21058 TAAATTTAAA
1 TAAATTTAAA
21068 ATGGGTTTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 18 0.69
18 8 0.31
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAATTTAAATTTAAAAA
Found at i:23333 original size:32 final size:32
Alignment explanation
Indices: 23293--23621 Score: 330
Period size: 32 Copynumber: 10.4 Consensus size: 32
23283 TAGTAAACAA
* *
23293 TATGCTTGTAAGAGCTATCAATCTATGAATAG
1 TATGCTCGTAAGAGCTGTCAATCTATGAATAG
* * * * *
23325 TATACTTGTAAGAGCTATCAATCTGTGAATAA
1 TATGCTCGTAAGAGCTGTCAATCTATGAATAG
* * *
23357 TATGCTCTTAAGAGCTGTCAATCTATGAACAA
1 TATGCTCGTAAGAGCTGTCAATCTATGAATAG
* * *
23389 TATGCTCATAAAAGCTATCAATCTAT-AATCAG
1 TATGCTCGTAAGAGCTGTCAATCTATGAAT-AG
* *
23421 TATGCTCGTAAGAGCTGTCAATCTTTGAACAG
1 TATGCTCGTAAGAGCTGTCAATCTATGAATAG
* *
23453 TATACTCGTAAGGGCTGTCAATCTATGAATAG
1 TATGCTCGTAAGAGCTGTCAATCTATGAATAG
* *
23485 TATGCTC-TAAGAGCTTTCAATCTGT-AATCAG
1 TATGCTCGTAAGAGCTGTCAATCTATGAAT-AG
* * *
23516 TATGCTCGTAAGAGTTGTCAATAT-TTAATCAG
1 TATGCTCGTAAGAGCTGTCAATCTATGAAT-AG
* *
23548 TATGCTAGTAAGAGCTGTCAATCTATGAACAG
1 TATGCTCGTAAGAGCTGTCAATCTATGAATAG
* * *
23580 CATGCTCGTAAG-GCTATCAATC-AT-ACATTG
1 TATGCTCGTAAGAGCTGTCAATCTATGA-ATAG
23610 TATGCTCGTAAG
1 TATGCTCGTAAG
23622 TGTTATCCAA
Statistics
Matches: 249, Mismatches: 41, Indels: 16
0.81 0.13 0.05
Matches are distributed among these distances:
29 1 0.00
30 18 0.07
31 36 0.14
32 189 0.76
33 5 0.02
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Consensus pattern (32 bp):
TATGCTCGTAAGAGCTGTCAATCTATGAATAG
Found at i:23535 original size:95 final size:96
Alignment explanation
Indices: 23301--23621 Score: 393
Period size: 95 Copynumber: 3.4 Consensus size: 96
23291 AATATGCTTG
* * * * * * *
23301 TAAGAGCTATCAATCTATGAAT-AGTATACTTGTAAGAGCTATCAATCTGTGAATAATATGCTCT
1 TAAGAGCTATCAATCTAT-AATCAGTATGCTCGTAAGAGCTGTCAATCTTTGAACAGTATGCTCG
*
23365 TAAGAGCTGTCAATCTATGAACAATATGCTCA
65 TAAGAGCTGTCAATCTATGAACAGTATGCTCA
* *
23397 TAAAAGCTATCAATCTATAATCAGTATGCTCGTAAGAGCTGTCAATCTTTGAACAGTATACTCGT
1 TAAGAGCTATCAATCTATAATCAGTATGCTCGTAAGAGCTGTCAATCTTTGAACAGTATGCTCGT
* *
23462 AAGGGCTGTCAATCTATGAATAGTATGCTC-
66 AAGAGCTGTCAATCTATGAACAGTATGCTCA
* * * * *
23492 TAAGAGCTTTCAATCTGTAATCAGTATGCTCGTAAGAGTTGTCAATATTT-AATCAGTATGCTAG
1 TAAGAGCTATCAATCTATAATCAGTATGCTCGTAAGAGCTGTCAATCTTTGAA-CAGTATGCTCG
* *
23556 TAAGAGCTGTCAATCTATGAACAGCATGCTCG
65 TAAGAGCTGTCAATCTATGAACAGTATGCTCA
*
23588 TAAG-GCTATCAATC-ATACAT-TGTATGCTCGTAAG
1 TAAGAGCTATCAATCTATA-ATCAGTATGCTCGTAAG
23622 TGTTATCCAA
Statistics
Matches: 196, Mismatches: 25, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
94 17 0.09
95 96 0.49
96 83 0.42
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (96 bp):
TAAGAGCTATCAATCTATAATCAGTATGCTCGTAAGAGCTGTCAATCTTTGAACAGTATGCTCGT
AAGAGCTGTCAATCTATGAACAGTATGCTCA
Found at i:29451 original size:17 final size:17
Alignment explanation
Indices: 29431--29529 Score: 110
Period size: 17 Copynumber: 5.8 Consensus size: 17
29421 ATTGAACCCA
*
29431 ATTTTAAATTTTAATTT
1 ATTTTAAATTTAAATTT
*
29448 ATTTTAAGTTTAAATTT
1 ATTTTAAATTTAAATTT
* * *
29465 ATTTTAAATTTAGACTA
1 ATTTTAAATTTAAATTT
* *
29482 ATTTTGAGTTTAAATTT
1 ATTTTAAATTTAAATTT
29499 ATTTTAAATTTAAATTT
1 ATTTTAAATTTAAATTT
*
29516 AAATTT-AATTTAAA
1 -ATTTTAAATTTAAA
29530 AAAAAGGTTC
Statistics
Matches: 67, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
17 63 0.94
18 4 0.06
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:29459 original size:6 final size:6
Alignment explanation
Indices: 29433--29529 Score: 69
Period size: 6 Copynumber: 17.0 Consensus size: 6
29423 TGAACCCAAT
* * * * *
29433 TTTAAA TTTTAA TTT-AT TTTAAG TTTAAA TTT-AT TTTAAA TTTAGA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * * *
29479 -CTAAT TTTGAG TTTAAA TTT-AT TTTAAA TTTAAA TTTAAA TTT-AA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
29524 TTTAAA
1 TTTAAA
29530 AAAAAGGTTC
Statistics
Matches: 69, Mismatches: 17, Indels: 10
0.72 0.18 0.10
Matches are distributed among these distances:
5 19 0.28
6 50 0.72
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:29470 original size:11 final size:11
Alignment explanation
Indices: 29433--29529 Score: 81
Period size: 11 Copynumber: 8.5 Consensus size: 11
29423 TGAACCCAAT
29433 TTTAAATTTTAA
1 TTTAAA-TTTAA
*
29445 TTT-ATTTTAA
1 TTTAAATTTAA
*
29455 GTTTAAATTTAT
1 -TTTAAATTTAA
29467 TTTAAATTTAGA
1 TTTAAATTTA-A
* * *
29479 -CTAATTTTGAG
1 TTTAAATTT-AA
*
29490 TTTAAATTTAT
1 TTTAAATTTAA
29501 TTTAAATTTAAA
1 TTTAAATTT-AA
29513 TTTAAATTTAA
1 TTTAAATTTAA
29524 TTTAAA
1 TTTAAA
29530 AAAAAGGTTC
Statistics
Matches: 68, Mismatches: 11, Indels: 13
0.74 0.12 0.14
Matches are distributed among these distances:
10 5 0.07
11 38 0.56
12 25 0.37
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:29476 original size:23 final size:23
Alignment explanation
Indices: 29434--29529 Score: 79
Period size: 23 Copynumber: 4.2 Consensus size: 23
29424 GAACCCAATT
* *
29434 TTAAATTTTAATTT-ATTTTAAGT
1 TTAAATTTAAATTTAAATTT-AGT
* *
29457 TTAAATTT-ATTTTAAATTTAGA
1 TTAAATTTAAATTTAAATTTAGT
* * * * *
29479 CTAATTTTGAGTTTAAATTTATT
1 TTAAATTTAAATTTAAATTTAGT
*
29502 TTAAATTTAAATTTAAATTTAAT
1 TTAAATTTAAATTTAAATTTAGT
29525 TTAAA
1 TTAAA
29530 AAAAAGGTTC
Statistics
Matches: 58, Mismatches: 13, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
22 12 0.21
23 46 0.79
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (23 bp):
TTAAATTTAAATTTAAATTTAGT
Found at i:31117 original size:59 final size:57
Alignment explanation
Indices: 31044--31409 Score: 359
Period size: 59 Copynumber: 6.3 Consensus size: 57
31034 CACTGCTTTG
*
31044 TTTT-AAAATTACATTTTAACCCTAAAACTTTTCCAAAATTACATTTTAA-CCTCAAAC
1 TTTTCAAAATTACATTTTAA-CCTCAAACTTTTCCAAAATTACATTTTAACCCT-AAAC
* * * ** * *
31101 TTATTCAAAATTACATTTTAACCTTAAAC-TTCCCACAATTATGTTTTGACACC-GAAC
1 TT-TTCAAAATTACATTTTAACCTCAAACTTTTCCAAAATTACATTTTAAC-CCTAAAC
** * * *
31158 TTCTTTTAAATTACATTTTTGACCTCAAACTTCTCCAAAATTACATTTTGACCCTCAAAC
1 TT-TTCAAAATTACA-TTTTAACCTCAAACTTTTCCAAAATTACATTTTAACCCT-AAAC
* *
31218 TTCTCTAAAATTACATTTTGACACTCAAACTTTTCCAAAATTACATTTTAACCCCTAAAC
1 TTTTC-AAAATTACATTTTAAC-CTCAAACTTTTCCAAAATTACATTTTAA-CCCTAAAC
* * * *
31278 TTCTCTAAAATTACATTTTGACCTCAAACTTGTCTAAAATTACATTTTAACCCTAAA-
1 TTTTC-AAAATTACATTTTAACCTCAAACTTTTCCAAAATTACATTTTAACCCTAAAC
* * * *
31335 TATT-ATAAATTGCATTTTAACCTCAACCTTTT-CAAAATTACATTTTGACCCTAAAC
1 TTTTCA-AAATTACATTTTAACCTCAAACTTTTCCAAAATTACATTTTAACCCTAAAC
31391 TTTTCCAAAATTACATTTT
1 TTTT-CAAAATTACATTTT
31410 GACACCCAAT
Statistics
Matches: 259, Mismatches: 35, Indels: 30
0.80 0.11 0.09
Matches are distributed among these distances:
55 22 0.08
56 25 0.10
57 45 0.17
58 31 0.12
59 67 0.26
60 65 0.25
61 4 0.02
ACGTcount: A:0.36, C:0.22, G:0.03, T:0.39
Consensus pattern (57 bp):
TTTTCAAAATTACATTTTAACCTCAAACTTTTCCAAAATTACATTTTAACCCTAAAC
Found at i:31410 original size:29 final size:30
Alignment explanation
Indices: 31048--31412 Score: 330
Period size: 30 Copynumber: 12.5 Consensus size: 30
31038 GCTTTGTTTT
* *
31048 AAAATTACATTTTAACCCTAAAACTTTTCC
1 AAAATTACATTTTGACCCTCAAACTTTTCC
*
31078 AAAATTACATTTT-AACCTCAAACTTATT-C
1 AAAATTACATTTTGACCCTCAAACTT-TTCC
* * *
31107 AAAATTACATTTT-AACCTTAAAC-TTCCC
1 AAAATTACATTTTGACCCTCAAACTTTTCC
* ** * * *
31135 ACAATTATGTTTTGACAC-CGAACTTCTT-T
1 AAAATTACATTTTGACCCTCAAACTT-TTCC
* *
31164 TAAATTACATTTTTGA-CCTCAAACTTCTCC
1 AAAATTACA-TTTTGACCCTCAAACTTTTCC
* *
31194 AAAATTACATTTTGACCCTCAAACTTCTCT
1 AAAATTACATTTTGACCCTCAAACTTTTCC
*
31224 AAAATTACATTTTGACACTCAAACTTTTCC
1 AAAATTACATTTTGACCCTCAAACTTTTCC
* * *
31254 AAAATTACATTTTAACCC-CTAAACTTCTCT
1 AAAATTACATTTTGACCCTC-AAACTTTTCC
* *
31284 AAAATTACATTTTGA-CCTCAAACTTGTCT
1 AAAATTACATTTTGACCCTCAAACTTTTCC
* *
31313 AAAATTACATTTTAACCCT-AAA-TATT--
1 AAAATTACATTTTGACCCTCAAACTTTTCC
* * *
31339 ATAAATTGCATTTT-AACCTCAACCTTTT-C
1 A-AAATTACATTTTGACCCTCAAACTTTTCC
31368 AAAATTACATTTTGACCCT-AAACTTTTCC
1 AAAATTACATTTTGACCCTCAAACTTTTCC
31397 AAAATTACATTTTGAC
1 AAAATTACATTTTGAC
31413 ACCCAATTTT
Statistics
Matches: 275, Mismatches: 42, Indels: 37
0.78 0.12 0.10
Matches are distributed among these distances:
26 5 0.02
27 14 0.05
28 38 0.14
29 100 0.36
30 118 0.43
ACGTcount: A:0.36, C:0.23, G:0.03, T:0.38
Consensus pattern (30 bp):
AAAATTACATTTTGACCCTCAAACTTTTCC
Found at i:35354 original size:18 final size:18
Alignment explanation
Indices: 35331--35367 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
35321 ATCTCAAAGG
35331 AGCATTATAAGTGAGCTA
1 AGCATTATAAGTGAGCTA
35349 AGCATTATAAGTGAGCTA
1 AGCATTATAAGTGAGCTA
35367 A
1 A
35368 CACAGCTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.11, G:0.22, T:0.27
Consensus pattern (18 bp):
AGCATTATAAGTGAGCTA
Found at i:40544 original size:3 final size:3
Alignment explanation
Indices: 40536--40568 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
40526 TTATGATATT
*
40536 GAA GAA GAA GAA GAA AAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
40569 AGGGATGATC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:42874 original size:39 final size:39
Alignment explanation
Indices: 42812--43175 Score: 266
Period size: 39 Copynumber: 9.3 Consensus size: 39
42802 TGAAGATTCG
* *
42812 ATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGTCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGTCA
* * * * **** * * *
42851 ATCTCTTACCCCAAGCTTAGGGCAAATTTGTAACCATTCG
1 ATCTCTTACCCCGAGCCTGGGGCAGA-TCACCATCAGTCA
*
42891 ATCTCTTACCCCGAGCCTGAGGCAGATCACCATCAGTCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGTCA
* * * * * * *
42930 ATCTCTTATCCCTAGCCTGGGGCAGATTA-GAGCCATTCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCA-TCAGTCA
* * * * *
42969 ATCTTTTACCCCTAGCTTAGGGCAGATCACCATCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGTCA
* * * * **
43008 ATCTCTTACCTCGAGCCTGGGGCAGATTA-CAGCCATTTG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCA-TCAGTCA
* * * *
43047 ATCTTTTACCCCAAGCTTGGGGCAGATCACCATCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGTCA
* * * * * *
43086 ATCTCTTACCCCGAGCCTAGGACAGATTA-CAGCCATTCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCA-TCAGTCA
* * *
43125 ATCTTTTACCCCGAGCCTGGGGCAGATCACCATAAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGTCA
43164 ATCTCTTACCCC
1 ATCTCTTACCCC
43176 ACGACAAAGG
Statistics
Matches: 236, Mismatches: 82, Indels: 14
0.71 0.25 0.04
Matches are distributed among these distances:
38 5 0.02
39 199 0.84
40 32 0.14
ACGTcount: A:0.24, C:0.32, G:0.18, T:0.25
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGTCA
Found at i:43002 original size:78 final size:78
Alignment explanation
Indices: 42807--43175 Score: 513
Period size: 78 Copynumber: 4.7 Consensus size: 78
42797 CTGATTGAAG
* * *
42807 ATTCGATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGTCAATCTCTTACCCCAAGCTTAGG
1 ATTCGATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTAGG
* ** *
42872 GCAAATTTGTAACC
66 GCAGA-TTACAGCC
* * * * * * *
42886 ATTCGATCTCTTACCCCGAGCCTGAGGCAGATCACCATCAGTCAATCTCTTATCCCTAGCCTGGG
1 ATTCGATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTAGG
*
42951 GCAGATTAGAGCC
66 GCAGATTACAGCC
* * * *
42964 ATTCGATCTTTTACCCCTAGCTTAGGGCAGATCACCATCAGCCAATCTCTTACCTCGAGCCTGGG
1 ATTCGATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTAGG
43029 GCAGATTACAGCC
66 GCAGATTACAGCC
* *
43042 ATTTGATCTTTTACCCCAAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTAGG
1 ATTCGATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTAGG
*
43107 ACAGATTACAGCC
66 GCAGATTACAGCC
* *
43120 ATTCGATCTTTTACCCCGAGCCTGGGGCAGATCACCATAAGCCAATCTCTTACCCC
1 ATTCGATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCC
43176 ACGACAAAGG
Statistics
Matches: 259, Mismatches: 31, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
78 197 0.76
79 62 0.24
ACGTcount: A:0.24, C:0.32, G:0.18, T:0.25
Consensus pattern (78 bp):
ATTCGATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTAGG
GCAGATTACAGCC
Found at i:43095 original size:117 final size:117
Alignment explanation
Indices: 42809--43156 Score: 304
Period size: 117 Copynumber: 3.0 Consensus size: 117
42799 GATTGAAGAT
*
42809 TCGATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGTCAATCTCTTACCCCAAGCTTAGGGC
1 TCGATCTTTTACCCCAAGCTTGGGGCAGATCACCATCAGTCAATCTCTTACCCCAAGCTTAGGGC
* *** ** * *
42874 AAATTTGTAACCATTCGATCTCTTACCCCGAGCCTGAGGCAGATCACCATCAG
66 AGA-TCACAACCAGCCAATCTCTTACCCCGAGCCTGAGGCAGATCACCACCAG
* * * * * * * * * * * *
42927 TCAATCTCTTATCCCTAGCCTGGGGCAGATTA-GAGCCATTCGATCTTTTACCCCTAGCTTAGGG
1 TCGATCTTTTACCCCAAGCTTGGGGCAGATCACCA-TCAGTCAATCTCTTACCCCAAGCTTAGGG
* * * * * *
42991 CAGATCACCATCAGCCAATCTCTTACCTCGAGCCTGGGGCAGATTA-CAGCCAT
65 CAGATCACAACCAGCCAATCTCTTACCCCGAGCCTGAGGCAGATCACCA-CCAG
* * * * *
43044 TTGATCTTTTACCCCAAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTAGGAC
1 TCGATCTTTTACCCCAAGCTTGGGGCAGATCACCATCAGTCAATCTCTTACCCCAAGCTTAGGGC
* * ** * * *
43109 AGATTACAGCCATTCGATCTTTTACCCCGAGCCTGGGGCAGATCACCA
66 AGATCACAACCAGCCAATCTCTTACCCCGAGCCTGAGGCAGATCACCA
43157 TAAGCCAATC
Statistics
Matches: 174, Mismatches: 52, Indels: 8
0.74 0.22 0.03
Matches are distributed among these distances:
116 2 0.01
117 116 0.67
118 56 0.32
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (117 bp):
TCGATCTTTTACCCCAAGCTTGGGGCAGATCACCATCAGTCAATCTCTTACCCCAAGCTTAGGGC
AGATCACAACCAGCCAATCTCTTACCCCGAGCCTGAGGCAGATCACCACCAG
Found at i:43739 original size:17 final size:17
Alignment explanation
Indices: 43719--43785 Score: 89
Period size: 17 Copynumber: 3.9 Consensus size: 17
43709 ATTGAACCCA
*
43719 ATTTTAAATTTTAATTT
1 ATTTTAAATTTAAATTT
*
43736 ATTTTAAATTTAAACTT
1 ATTTTAAATTTAAATTT
* * *
43753 ATTTTGAGTTTAAAATT
1 ATTTTAAATTTAAATTT
43770 ATTTTAAATTTAAATT
1 ATTTTAAATTTAAATT
43786 CAATTTAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 42 1.00
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:45364 original size:29 final size:29
Alignment explanation
Indices: 45332--45724 Score: 367
Period size: 29 Copynumber: 13.5 Consensus size: 29
45322 ACTTTGTTTT
* * * *
45332 AAAATTACATTTTGATCCAAAACTTTTCT
1 AAAATTACATTTTGACCCCAAACTTCTCC
* * *
45361 AAAATTACATTTTGACCTCAAAATTCTCT
1 AAAATTACATTTTGACCCCAAACTTCTCC
*
45390 AAAATTACATTTTGACCTCAAACTTCTCC
1 AAAATTACATTTTGACCCCAAACTTCTCC
* * **
45419 AAAATTGCATTTTGATCTTAAACTTCTCC
1 AAAATTACATTTTGACCCCAAACTTCTCC
* **
45448 AAAATTACATTTTTAACCTTAAACTTCTCC
1 AAAATTACA-TTTTGACCCCAAACTTCTCC
* *
45478 AAAATTACATTTTGACCCTAAACTTCTCT
1 AAAATTACATTTTGACCCCAAACTTCTCC
* ** *
45507 AAAATTACATTTTTAACCTTAAACTTCTTC
1 AAAATTACA-TTTTGACCCCAAACTTCTCC
* *
45537 AAAATTACATTTTTACCTCAAACTTCTCC
1 AAAATTACATTTTGACCCCAAACTTCTCC
* * *
45566 AAAATTATATTTTGACCCTCGAACCTCTCC
1 AAAATTACATTTTGACCC-CAAACTTCTCC
* ** * *
45596 AAAATTACATTTTGATCTTAAGCTTCTCT
1 AAAATTACATTTTGACCCCAAACTTCTCC
* * * *
45625 AAAATTA-AATTTGACCCCAAAATTTTCT
1 AAAATTACATTTTGACCCCAAACTTCTCC
* * * *
45653 AAAATTACATGTTTAACCCTAACCTTC-CA
1 AAAATTACAT-TTTGACCCCAAACTTCTCC
*
45682 AAAATTACATTTTGACCCCAAACTTTTCC
1 AAAATTACATTTTGACCCCAAACTTCTCC
*
45711 AAAATTGCATTTTG
1 AAAATTACATTTTG
45725 TCGAATTTTT
Statistics
Matches: 302, Mismatches: 56, Indels: 12
0.82 0.15 0.03
Matches are distributed among these distances:
28 33 0.11
29 182 0.60
30 87 0.29
ACGTcount: A:0.35, C:0.23, G:0.04, T:0.38
Consensus pattern (29 bp):
AAAATTACATTTTGACCCCAAACTTCTCC
Found at i:45491 original size:59 final size:59
Alignment explanation
Indices: 45331--45724 Score: 386
Period size: 59 Copynumber: 6.8 Consensus size: 59
45321 TACTTTGTTT
* * * * * * *
45331 TAAAATTACATTTTGATCC-AAAACTTTTCTAAAATTACATTTTGACCTCAAAATTCTC
1 TAAAATTACATTTTTAACCTCAAACTTCTCCAAAATTACATTTTGACCTTAAACTTCTC
* * *
45389 TAAAATTACA-TTTTGACCTCAAACTTCTCCAAAATTGCATTTTGATCTTAAACTTCTC
1 TAAAATTACATTTTTAACCTCAAACTTCTCCAAAATTACATTTTGACCTTAAACTTCTC
* * *
45447 CAAAATTACATTTTTAACCTTAAACTTCTCCAAAATTACATTTTGACCCTAAACTTCTC
1 TAAAATTACATTTTTAACCTCAAACTTCTCCAAAATTACATTTTGACCTTAAACTTCTC
* * * *
45506 TAAAATTACATTTTTAACCTTAAACTTCTTCAAAATTACATTTTTACCTCAAACTTCTC
1 TAAAATTACATTTTTAACCTCAAACTTCTCCAAAATTACATTTTGACCTTAAACTTCTC
* * * * * * * *
45565 CAAAATTATATTTTGACCCTCGAACCTCTCCAAAATTACATTTTGATCTTAAGCTTCTC
1 TAAAATTACATTTTTAACCTCAAACTTCTCCAAAATTACATTTTGACCTTAAACTTCTC
* * * * * * * * *
45624 TAAAATTA-A-ATTTGACCCCAAAATTTTCTAAAATTACATGTTTAACCCTAACCTTC-C
1 TAAAATTACATTTTTAACCTCAAACTTCTCCAAAATTACAT-TTTGACCTTAAACTTCTC
* * * * *
45681 AAAAATTACA-TTTTGACCCCAAACTTTTCCAAAATTGCATTTTG
1 TAAAATTACATTTTTAACCTCAAACTTCTCCAAAATTACATTTTG
45725 TCGAATTTTT
Statistics
Matches: 278, Mismatches: 54, Indels: 9
0.82 0.16 0.03
Matches are distributed among these distances:
57 36 0.13
58 91 0.33
59 151 0.54
ACGTcount: A:0.35, C:0.23, G:0.04, T:0.38
Consensus pattern (59 bp):
TAAAATTACATTTTTAACCTCAAACTTCTCCAAAATTACATTTTGACCTTAAACTTCTC
Found at i:45511 original size:88 final size:89
Alignment explanation
Indices: 45332--45723 Score: 431
Period size: 88 Copynumber: 4.5 Consensus size: 89
45322 ACTTTGTTTT
** * * *
45332 AAAATTACATTTTGATCCAAAACTTTTCTAAAATTACA-TTTTGACCTCAAAATTCTCTAAAATT
1 AAAATTACATTTTGATCTTAAACTTCTCCAAAATTACATTTTTGACCTCAAAATTCTCCAAAATT
45396 ACATTTTGA-CCTCAAACTTCTCC
66 ACATTTTGACCCTCAAACTTCTCC
* * * *
45419 AAAATTGCATTTTGATCTTAAACTTCTCCAAAATTACATTTTTAACCTTAAACTTCTCCAAAATT
1 AAAATTACATTTTGATCTTAAACTTCTCCAAAATTACATTTTTGACCTCAAAATTCTCCAAAATT
*
45484 ACATTTTGACCCT-AAACTTCTCT
66 ACATTTTGACCCTCAAACTTCTCC
* * * *
45507 AAAATTACATTTTTAACCTTAAACTTCTTCAAAATTACATTTTT-ACCTCAAACTTCTCCAAAAT
1 AAAATTACA-TTTTGATCTTAAACTTCTCCAAAATTACATTTTTGACCTCAAAATTCTCCAAAAT
* * *
45571 TATATTTTGACCCTCGAACCTCTCC
65 TACATTTTGACCCTCAAACTTCTCC
* * * * * *
45596 AAAATTACATTTTGATCTTAAGCTTCTCTAAAATTA-A-ATTTGACCCCAAAATTTTCTAAAATT
1 AAAATTACATTTTGATCTTAAACTTCTCCAAAATTACATTTTTGACCTCAAAATTCTCCAAAATT
* * *
45659 ACATGTTTAACCCT-AACCTTC-CA
66 ACAT-TTTGACCCTCAAACTTCTCC
* ** * *
45682 AAAATTACATTTTGACCCCAAACTTTTCCAAAATTGCATTTT
1 AAAATTACATTTTGATCTTAAACTTCTCCAAAATTACATTTT
45724 GTCGAATTTT
Statistics
Matches: 254, Mismatches: 43, Indels: 15
0.81 0.14 0.05
Matches are distributed among these distances:
86 33 0.13
87 59 0.23
88 112 0.44
89 50 0.20
ACGTcount: A:0.35, C:0.23, G:0.04, T:0.38
Consensus pattern (89 bp):
AAAATTACATTTTGATCTTAAACTTCTCCAAAATTACATTTTTGACCTCAAAATTCTCCAAAATT
ACATTTTGACCCTCAAACTTCTCC
Found at i:47844 original size:96 final size:96
Alignment explanation
Indices: 47656--47844 Score: 231
Period size: 96 Copynumber: 2.0 Consensus size: 96
47646 ATTTTGGGAA
* * **
47656 AAGGATATTCGATTATCTGGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGTGCAATATTTCA
1 AAGGATATTCGATTATCTCGATTTGAAAAAAGGTTGCACCTAGTAAGTTAAGGCACAATATTTCA
* * *
47721 GAATCGAAGATAAGGAAACATTGCCTCGTTT
66 AAATCGAAGATAAAGAAACATTACCTCGTTT
* * *
47752 AAGGGTATTCGATTATTTCGATTTGAAAAAAGTTTGCACCTAGTAAGTTAAGGCACAA-ACTTTC
1 AAGGATATTCGATTATCTCGATTTGAAAAAAGGTTGCACCTAGTAAGTTAAGGCACAATA-TTTC
*
47816 AAAACTCGAA-ATAAA-AGAATATTACCTCG
65 AAAA-TCGAAGATAAAGA-AACATTACCTCG
47845 ATTTTAAAGT
Statistics
Matches: 79, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
95 2 0.03
96 72 0.91
97 5 0.06
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.30
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTGAAAAAAGGTTGCACCTAGTAAGTTAAGGCACAATATTTCA
AAATCGAAGATAAAGAAACATTACCTCGTTT
Found at i:48300 original size:29 final size:30
Alignment explanation
Indices: 48268--48547 Score: 256
Period size: 30 Copynumber: 9.5 Consensus size: 30
48258 AAATTCGAAA
* *
48268 TTTT-GAAGGTTCGAGAGTAAAAATGGCAT
1 TTTTGGAAGGTTCGAGGGTAAAAATGGAAT
**
48297 TTTTGGAA-GTTTTAGGGTAAAAAATGGAAT
1 TTTTGGAAGGTTCGAGGGT-AAAAATGGAAT
* * *
48327 TTTTGGAAGTTTAG-GGGTAAAAAAGGAAT
1 TTTTGGAAGGTTCGAGGGTAAAAATGGAAT
** *
48356 TTTTGGAA-GTTTTAGGGTCAAAAATGGAAA
1 TTTTGGAAGGTTCGAGGGT-AAAAATGGAAT
*
48386 TTTTGG-AGGTTTG-GGGTTAAAAATGGAAT
1 TTTTGGAAGGTTCGAGGG-TAAAAATGGAAT
* *
48415 TTTTGGAAGCTTCG-GGATAAAAAATGGAATT
1 TTTTGGAAGGTTCGAGGGT-AAAAATGGAA-T
*
48446 TTTTGGAA-GTTCGGGGGTAAAAATGGAAT
1 TTTTGGAAGGTTCGAGGGTAAAAATGGAAT
*** *
48475 TTTTGGAA-GTTTTTGGGTCAAAAATGGGAT
1 TTTTGGAAGGTTCGAGGGT-AAAAATGGAAT
*
48505 TTTTGGAA-GTTCGAGGGTAAAAATGAAAT
1 TTTTGGAAGGTTCGAGGGTAAAAATGGAAT
*
48534 TTTTGGAAGTTTCG
1 TTTTGGAAGGTTCG
48548 GGACCTTCAA
Statistics
Matches: 208, Mismatches: 30, Indels: 25
0.79 0.11 0.10
Matches are distributed among these distances:
28 2 0.01
29 87 0.42
30 105 0.50
31 14 0.07
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.35
Consensus pattern (30 bp):
TTTTGGAAGGTTCGAGGGTAAAAATGGAAT
Found at i:48307 original size:59 final size:59
Alignment explanation
Indices: 48226--48545 Score: 364
Period size: 59 Copynumber: 5.4 Consensus size: 59
48216 CACCCGAGGG
* * * * *
48226 AAAAATGGTAATTTCTT-AAAGTTTTAGGGTCAAAATTCGAAATTTT-GAAGGTTCGAGAGT
1 AAAAATGG-AATTT-TTGGAAGTTTTAGGGTCAAAAATGGAATTTTTGGAAGGTTCG-GGGT
* * * *
48286 AAAAATGGCATTTTTGGAAGTTTTAGGGTAAAAAATGGAATTTTTGGAAGTTTAGGGGT
1 AAAAATGGAATTTTTGGAAGTTTTAGGGTCAAAAATGGAATTTTTGGAAGGTTCGGGGT
* * *
48345 AAAAAAGGAATTTTTGGAAGTTTTAGGGTCAAAAATGGAAATTTTGG-AGGTTTGGGGTT
1 AAAAATGGAATTTTTGGAAGTTTTAGGGTCAAAAATGGAATTTTTGGAAGGTTCGGGG-T
* * *
48404 AAAAATGGAATTTTTGGAAG-CTTCGGGATAAAAAATGGAATTTTTTGGAA-GTTCGGGGGT
1 AAAAATGGAATTTTTGGAAGTTTTAGGG-TCAAAAATGGAA-TTTTTGGAAGGTTC-GGGGT
* *
48464 AAAAATGGAATTTTTGGAAGTTTTTGGGTCAAAAATGGGATTTTTGGAA-GTTCGAGGGT
1 AAAAATGGAATTTTTGGAAGTTTTAGGGTCAAAAATGGAATTTTTGGAAGGTTCG-GGGT
*
48523 AAAAATGAAATTTTTGGAAGTTT
1 AAAAATGGAATTTTTGGAAGTTT
48546 CGGGACCTTC
Statistics
Matches: 225, Mismatches: 26, Indels: 19
0.83 0.10 0.07
Matches are distributed among these distances:
58 16 0.07
59 144 0.64
60 55 0.24
61 10 0.04
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.35
Consensus pattern (59 bp):
AAAAATGGAATTTTTGGAAGTTTTAGGGTCAAAAATGGAATTTTTGGAAGGTTCGGGGT
Found at i:48320 original size:30 final size:30
Alignment explanation
Indices: 48226--48545 Score: 298
Period size: 29 Copynumber: 10.8 Consensus size: 30
48216 CACCCGAGGG
* *
48226 AAAAATGGTAATTTCTT-AAAGTTTTAGGGTC
1 AAAAATGG-AATTT-TTGGAAGTTTTAGGGTA
* * * ** *
48257 AAAATTCGAAATTTT-GAAGGTTCGAGAGT-
1 AAAAATGGAATTTTTGGAA-GTTTTAGGGTA
*
48286 AAAAATGGCATTTTTGGAAGTTTTAGGGTA
1 AAAAATGGAATTTTTGGAAGTTTTAGGGTA
48316 AAAAATGGAATTTTTGGAAG-TTTAGGGGTA
1 AAAAATGGAATTTTTGGAAGTTTTA-GGGTA
*
48346 AAAAA-GGAATTTTTGGAAGTTTTAGGGTC
1 AAAAATGGAATTTTTGGAAGTTTTAGGGTA
* * * *
48375 AAAAATGGAAATTTTGG-AGGTTTGGGGTT
1 AAAAATGGAATTTTTGGAAGTTTTAGGGTA
* *
48404 AAAAATGGAATTTTTGGAAG-CTTCGGGATA
1 AAAAATGGAATTTTTGGAAGTTTTAGGG-TA
***
48434 AAAAATGGAATTTTTTGGAAGTTCGGGGGT-
1 AAAAATGGAA-TTTTTGGAAGTTTTAGGGTA
* *
48464 AAAAATGGAATTTTTGGAAGTTTTTGGGTC
1 AAAAATGGAATTTTTGGAAGTTTTAGGGTA
* **
48494 AAAAATGGGATTTTTGGAAGTTCGAGGGT-
1 AAAAATGGAATTTTTGGAAGTTTTAGGGTA
*
48523 AAAAATGAAATTTTTGGAAGTTT
1 AAAAATGGAATTTTTGGAAGTTT
48546 CGGGACCTTC
Statistics
Matches: 240, Mismatches: 38, Indels: 24
0.79 0.13 0.08
Matches are distributed among these distances:
29 115 0.48
30 105 0.44
31 17 0.07
32 3 0.01
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.35
Consensus pattern (30 bp):
AAAAATGGAATTTTTGGAAGTTTTAGGGTA
Found at i:49665 original size:3 final size:3
Alignment explanation
Indices: 49657--49698 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
49647 TTCGGCTTTT
* *
49657 TTA TTA TTA TTAA TAA CTA TTA TTA TTA TTA TTA -TA TTA TTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
49699 ATAATATTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.88
4 2 0.06
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:50443 original size:6 final size:6
Alignment explanation
Indices: 50432--50513 Score: 71
Period size: 6 Copynumber: 14.2 Consensus size: 6
50422 AATGGGACTT
* * * ** *
50432 TTTAAA TTTAAA -ATAAT TTTAAT TTTAAA AGTAAA TTTAAA CTT-AA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
50478 TTTAAA TTTGAA TTTAAA -ATAAA TTTAAA TTTAAA T
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T
50514 AAATTAAATC
Statistics
Matches: 59, Mismatches: 14, Indels: 6
0.75 0.18 0.08
Matches are distributed among these distances:
5 11 0.19
6 48 0.81
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:50451 original size:17 final size:17
Alignment explanation
Indices: 50432--50539 Score: 121
Period size: 17 Copynumber: 6.4 Consensus size: 17
50422 AATGGGACTT
*
50432 TTTAAATTTAAAATAAT
1 TTTAAATTTAAAATAAA
*
50449 TTTAATTTTAAAAGTAAA
1 TTTAAATTTAAAA-TAAA
* **
50467 TTTAAACTTAATTTAAA
1 TTTAAATTTAAAATAAA
*
50484 TTTGAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
50501 TTTAAATTT-AAATAAA
1 TTTAAATTTAAAATAAA
*
50517 -TTAAATCTTATAATAAA
1 TTTAAAT-TTAAAATAAA
50534 TTTAAA
1 TTTAAA
50540 AAAGATTTTA
Statistics
Matches: 75, Mismatches: 12, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
15 6 0.08
16 9 0.12
17 43 0.57
18 17 0.23
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:50481 original size:23 final size:23
Alignment explanation
Indices: 50450--50506 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
50440 TAAAATAATT
*
50450 TTAATTTTAAAAGTAAATTTAAAC
1 TTAA-TTTAAAAGTAAATTTAAAA
** *
50474 TTAATTTAAATTTGAATTTAAAA
1 TTAATTTAAAAGTAAATTTAAAA
*
50497 TAAATTTAAA
1 TTAATTTAAA
50507 TTTAAATAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 24 0.86
24 4 0.14
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.44
Consensus pattern (23 bp):
TTAATTTAAAAGTAAATTTAAAA
Found at i:50507 original size:23 final size:23
Alignment explanation
Indices: 50465--50509 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
50455 TTTAAAAGTA
* *
50465 AATTTAAACTTAATTTAAATTTG
1 AATTTAAAATAAATTTAAATTTG
50488 AATTTAAAATAAATTTAAATTT
1 AATTTAAAATAAATTTAAATTT
50510 AAATAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
AATTTAAAATAAATTTAAATTTG
Found at i:55616 original size:20 final size:21
Alignment explanation
Indices: 55591--55642 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
55581 AGGAGTCTTT
*
55591 AAATCAATTTGAA-TAGAATC
1 AAATCAATTTGAATTAGAAAC
*
55611 AAATCAATTT-AATTGGAAAC
1 AAATCAATTTGAATTAGAAAC
*
55631 AAATCAAATTGA
1 AAATCAATTTGA
55643 GATATTTGTC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 2 0.07
20 24 0.89
21 1 0.04
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.29
Consensus pattern (21 bp):
AAATCAATTTGAATTAGAAAC
Found at i:56443 original size:3 final size:3
Alignment explanation
Indices: 56435--56490 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
56425 TCTTATTTTA
*
56435 AAT AAT AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
56483 AAT AAT AA
1 AAT AAT AA
56491 AAGAAGCCAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:59489 original size:7 final size:7
Alignment explanation
Indices: 59477--59553 Score: 154
Period size: 7 Copynumber: 11.0 Consensus size: 7
59467 AATATACCAA
59477 TCGATTC
1 TCGATTC
59484 TCGATTC
1 TCGATTC
59491 TCGATTC
1 TCGATTC
59498 TCGATTC
1 TCGATTC
59505 TCGATTC
1 TCGATTC
59512 TCGATTC
1 TCGATTC
59519 TCGATTC
1 TCGATTC
59526 TCGATTC
1 TCGATTC
59533 TCGATTC
1 TCGATTC
59540 TCGATTC
1 TCGATTC
59547 TCGATTC
1 TCGATTC
59554 GATCAATTGA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 70 1.00
ACGTcount: A:0.14, C:0.29, G:0.14, T:0.43
Consensus pattern (7 bp):
TCGATTC
Found at i:65762 original size:20 final size:19
Alignment explanation
Indices: 65734--65778 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
65724 TTGCGTAGTT
* *
65734 AATTATTAAAGAAAATTTAA
1 AATTTTTAAAG-AAAGTTAA
*
65754 AATTTTTAAAGAGAGTTAA
1 AATTTTTAAAGAAAGTTAA
65773 AATTTT
1 AATTTT
65779 AAAATTTTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (19 bp):
AATTTTTAAAGAAAGTTAA
Found at i:69987 original size:22 final size:22
Alignment explanation
Indices: 69962--70050 Score: 65
Period size: 22 Copynumber: 4.0 Consensus size: 22
69952 TTTTCTTGCT
*
69962 TTTTTTTATTATTTAGCTATTA
1 TTTTATTATTATTTAGCTATTA
* * *
69984 TTTTCTTATTATTT-TCTCACTA
1 TTTTATTATTATTTAGCT-ATTA
*
70006 TTTTATTATTATTTCA-TTATTA
1 TTTTATTATTATTT-AGCTATTA
* * * *
70028 TGTTGTTATTATTTGGATATTA
1 TTTTATTATTATTTAGCTATTA
70050 T
1 T
70051 ATAACTCTTG
Statistics
Matches: 53, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
21 2 0.04
22 50 0.94
23 1 0.02
ACGTcount: A:0.22, C:0.07, G:0.06, T:0.65
Consensus pattern (22 bp):
TTTTATTATTATTTAGCTATTA
Found at i:69993 original size:11 final size:11
Alignment explanation
Indices: 69941--70041 Score: 66
Period size: 11 Copynumber: 9.3 Consensus size: 11
69931 AATATATTGT
* *
69941 TTTTTTTATCA
1 TTTTCTTATTA
*
69952 TTTTCTTGCTT-
1 TTTTCTT-ATTA
69963 TTTT-TTATTA
1 TTTTCTTATTA
*
69973 TTTAGC-TATTA
1 TTT-TCTTATTA
69984 TTTTCTTATTA
1 TTTTCTTATTA
* *
69995 TTTTCTCACTA
1 TTTTCTTATTA
*
70006 TTTTATTATTA
1 TTTTCTTATTA
70017 -TTTCATTATTA
1 TTTTC-TTATTA
* *
70028 TGTTGTTATTA
1 TTTTCTTATTA
70039 TTT
1 TTT
70042 GGATATTATA
Statistics
Matches: 68, Mismatches: 15, Indels: 14
0.70 0.15 0.14
Matches are distributed among these distances:
9 2 0.03
10 9 0.13
11 54 0.79
12 3 0.04
ACGTcount: A:0.19, C:0.09, G:0.04, T:0.68
Consensus pattern (11 bp):
TTTTCTTATTA
Found at i:73206 original size:2 final size:2
Alignment explanation
Indices: 73199--73231 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
73189 TTAAAACTCC
73199 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
73232 AAAGATAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:77528 original size:23 final size:23
Alignment explanation
Indices: 77497--77545 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
77487 AATTGAGCCT
*
77497 AAAATTTAAAAT-TTAAAAAGTAA
1 AAAAATTAAAATCTTAAAAA-TAA
*
77520 AAAAATTAAATTCTTAAAAATAA
1 AAAAATTAAAATCTTAAAAATAA
77543 AAA
1 AAA
77546 TATATTAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (23 bp):
AAAAATTAAAATCTTAAAAATAA
Found at i:92006 original size:17 final size:17
Alignment explanation
Indices: 91971--92026 Score: 76
Period size: 17 Copynumber: 3.2 Consensus size: 17
91961 TTGAGTTCAA
*
91971 ATTTTAAAATTTTAATTT
1 ATTTT-AAATTTAAATTT
*
91989 ATTTTAAGTTTAAATTT
1 ATTTTAAATTTAAATTT
*
92006 ATTTTAAATTTAAATTC
1 ATTTTAAATTTAAATTT
92023 ATTT
1 ATTT
92027 AAAAGTCCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 29 0.85
18 5 0.15
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:93920 original size:30 final size:29
Alignment explanation
Indices: 93841--94133 Score: 221
Period size: 29 Copynumber: 10.0 Consensus size: 29
93831 AAGGTCCCTG
* *
93841 AACTATCCAAAAA-TA-TATTTTAACCCTCA
1 AACTTTCCAAAAATTACCATTTT-ACCC-CA
*
93870 AACTTTCTAAAAATTA-CATTTTGACCCCA
1 AACTTTCCAAAAATTACCATTTT-ACCCCA
* *
93899 AACTTTCCAAAAATTACCATTTTGCCCTCG
1 AACTTTCCAAAAATTACCATTTTACCC-CA
* * *
93929 AAC-TTCCAAAAAAATCCCATTTTTGACCTCA
1 AACTTTCC-AAAAATTACCA-TTTT-ACCCCA
* *
93960 AACATTCTAAAAATTACCATTTTACCCCTA
1 AACTTTCCAAAAATTACCATTTTACCCC-A
*
93990 AAC-TT-CATGAAATTTACCATTTTAACCCCA
1 AACTTTCCA--AAAATTACCATTTT-ACCCCA
* *
94020 AA-TTGCCAAAAATT-CCATTTTTAACCCCT
1 AACTTTCCAAAAATTACCA-TTTT-ACCCCA
*
94049 AACTTT-TAAAAATTACCATTTTACCCCA
1 AACTTTCCAAAAATTACCATTTTACCCCA
**
94077 AA-TTTCCAAAAATT-CCATTTTTTACCCTG
1 AACTTTCCAAAAATTACCA--TTTTACCCCA
*
94106 AACTTTCCAAAAATTACTATTTTACCCC
1 AACTTTCCAAAAATTACCATTTTACCCC
94134 TGGGCATCCA
Statistics
Matches: 214, Mismatches: 29, Indels: 42
0.75 0.10 0.15
Matches are distributed among these distances:
27 6 0.03
28 18 0.08
29 87 0.41
30 72 0.34
31 26 0.12
32 5 0.02
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.34
Consensus pattern (29 bp):
AACTTTCCAAAAATTACCATTTTACCCCA
Found at i:94010 original size:61 final size:61
Alignment explanation
Indices: 93864--94097 Score: 156
Period size: 61 Copynumber: 4.0 Consensus size: 61
93854 TATATTTTAA
* * * * *
93864 CCCTCAAACTTTCTAAAAATTA-CA-TTTTGACCCCAAACTTTCCAAAAATTACCATTTTG
1 CCCTCAAACTTCCAAAAAAATACCATTTTTGACCCCAAACATTCCAAAAATTACCATTTTC
* * * *
93923 CCCTCGAACTTCCAAAAAAATCCCATTTTTGACCTCAAACATTCTAAAAATTACCATTTTAC
1 CCCTCAAACTTCCAAAAAAATACCATTTTTGACCCCAAACATTCCAAAAATTACCATTTT-C
* ** *
93985 CCCT-AAACTT-CATGAAATTTACCA-TTTTAACCCC-AA-ATTGCCAAAAATT-CCATTTTTAA
1 CCCTCAAACTTCCA-AAAAAATACCATTTTTGACCCCAAACATT-CCAAAAATTACCA-TTTT--
94044 C
61 C
** * *
94045 CCCT--AACTT-TTAAAAATTACCA-TTTT-ACCCCAAA-TTTCCAAAAATT-CCATTTT
1 CCCTCAAACTTCCAAAAAAATACCATTTTTGACCCCAAACATTCCAAAAATTACCATTTT
94098 TTACCCTGAA
Statistics
Matches: 145, Mismatches: 22, Indels: 19
0.78 0.12 0.10
Matches are distributed among these distances:
56 4 0.03
57 17 0.12
58 23 0.16
59 36 0.25
60 18 0.12
61 43 0.30
62 4 0.03
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.34
Consensus pattern (61 bp):
CCCTCAAACTTCCAAAAAAATACCATTTTTGACCCCAAACATTCCAAAAATTACCATTTTC
Found at i:100631 original size:27 final size:27
Alignment explanation
Indices: 100592--100657 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
100582 TGGTAGGGGT
*
100592 GGTGCCTATCTGACAGGCGGCACCAAA
1 GGTGCCTACCTGACAGGCGGCACCAAA
* * **
100619 GGTGCCTACCTGATAGGCGGCACTAGT
1 GGTGCCTACCTGACAGGCGGCACCAAA
100646 GGTGCCTACCTG
1 GGTGCCTACCTG
100658 TCAGCTTATC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.20, C:0.29, G:0.32, T:0.20
Consensus pattern (27 bp):
GGTGCCTACCTGACAGGCGGCACCAAA
Found at i:100794 original size:32 final size:30
Alignment explanation
Indices: 100727--100797 Score: 81
Period size: 32 Copynumber: 2.3 Consensus size: 30
100717 GATTTTTACA
100727 TAAATAATACAAAAAAAAAAATTATACACC
1 TAAATAATACAAAAAAAAAAATTATACACC
* * *
100757 AAAATATATTACAAAAAATAAAATTAATA-ACT
1 TAAATA-A-TACAAAAAAAAAAATT-ATACACC
100789 TAAATAATA
1 TAAATAATA
100798 TAAATATATA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
30 7 0.21
31 2 0.06
32 22 0.65
33 3 0.09
ACGTcount: A:0.66, C:0.08, G:0.00, T:0.25
Consensus pattern (30 bp):
TAAATAATACAAAAAAAAAAATTATACACC
Found at i:101016 original size:20 final size:21
Alignment explanation
Indices: 100967--101016 Score: 52
Period size: 20 Copynumber: 2.4 Consensus size: 21
100957 TTAAAAAATA
100967 TATTATTATTCAATATTTAATT
1 TATTATT-TTCAATATTTAATT
*
100989 TAGT-TTTTCAAT-TTT-ATAT
1 TATTATTTTCAATATTTAAT-T
101008 TATTATTTT
1 TATTATTTT
101017 TTATAATTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
18 2 0.08
19 7 0.29
20 10 0.42
21 2 0.08
22 3 0.12
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (21 bp):
TATTATTTTCAATATTTAATT
Found at i:101389 original size:16 final size:16
Alignment explanation
Indices: 101343--101383 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
101333 CCCGTATCAA
* *
101343 TATTTTTTAAAAAATT
1 TATTATTTAAATAATT
101359 TATTATTTAAATAATT
1 TATTATTTAAATAATT
*
101375 TTTTATTTA
1 TATTATTTA
101384 TTTAATATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TATTATTTAAATAATT
Found at i:104590 original size:31 final size:30
Alignment explanation
Indices: 104519--104592 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 30
104509 ATATAATATG
* * *
104519 GTAATTAAATTAAATCAAATATTATGTAGT
1 GTAATTAAATTAAATAAAATATTATATACT
* *
104549 GTGATTAAATTAAATTAAAATGTTATATACT
1 GTAATTAAATTAAA-TAAAATATTATATACT
104580 GTAATTAAATTAA
1 GTAATTAAATTAA
104593 GTTGATAGTG
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 13 0.35
31 24 0.65
ACGTcount: A:0.47, C:0.03, G:0.09, T:0.41
Consensus pattern (30 bp):
GTAATTAAATTAAATAAAATATTATATACT
Found at i:114355 original size:26 final size:26
Alignment explanation
Indices: 114326--114375 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
114316 GGGTTTTATT
*
114326 CTTGTAGACCAAGAAACTAAAATTAA
1 CTTGTAGAACAAGAAACTAAAATTAA
* *
114352 CTTGTAGAATAAGAAACTATAATT
1 CTTGTAGAACAAGAAACTAAAATT
114376 TAGGAAACTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.28
Consensus pattern (26 bp):
CTTGTAGAACAAGAAACTAAAATTAA
Found at i:136928 original size:22 final size:22
Alignment explanation
Indices: 136903--136964 Score: 54
Period size: 22 Copynumber: 2.8 Consensus size: 22
136893 AGCATAGTCG
*
136903 AAATTTAATTATAATTTTTTAT
1 AAATTTAATTATAATTTATTAT
* *
136925 AAATTAAAATATATATTTATTAT
1 AAATTTAATTATA-ATTTATTAT
**
136948 GTA-TTAATTTATAATTT
1 AAATTTAA-TTATAATTT
136965 CATCATTTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
22 18 0.58
23 13 0.42
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
AAATTTAATTATAATTTATTAT
Found at i:138673 original size:6 final size:6
Alignment explanation
Indices: 138662--138690 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
138652 ATAAACAGAA
138662 AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
138691 AATGGAAGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Done.