Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold4281.1
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: 70555
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.32
Warning! 1278 characters in sequence are not A, C, G, or T
Found at i:5865 original size:104 final size:104
Alignment explanation
Indices: 5685--5951 Score: 473
Period size: 104 Copynumber: 2.6 Consensus size: 104
5675 TAGCCGTTAT
* * *
5685 TGGTGGATCCCGCACTTAGCACCA-CCACTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGG
1 TGGTGGATCACGCACATAGCACCACCCA-TAAATCGGGGAATCAGCACTTAGCAACCCCTCGGGG
5749 GAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
65 GAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
5789 TGGTGGATCACGCACATAGCACCACCCATAAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATCACGCACATAGCACCACCCATAAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
5854 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
**
5893 TGGTGGATCACGCACATAGCACCACCCATAAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGATCACGCACATAGCACCACCCATAAATCGGGGAATCAGCACTTAGCAACCCCT
5952 TTTATATACA
Statistics
Matches: 157, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
104 154 0.98
105 3 0.02
ACGTcount: A:0.31, C:0.32, G:0.20, T:0.18
Consensus pattern (104 bp):
TGGTGGATCACGCACATAGCACCACCCATAAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATA
Found at i:6313 original size:29 final size:29
Alignment explanation
Indices: 6280--6343 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
6270 TAATCCACCA
6280 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
6309 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
6339 CCCAA
1 CCCAA
6344 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:6317 original size:30 final size:30
Alignment explanation
Indices: 6287--6343 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
6277 CCACCCAACT
6287 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
6316 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
6344 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:18107 original size:27 final size:27
Alignment explanation
Indices: 18066--18165 Score: 137
Period size: 27 Copynumber: 3.7 Consensus size: 27
18056 CTCTAATCGA
*
18066 TAAAATGACTATTTTTCCCTTATGTGG
1 TAAAATGACTATTTTGCCCTTATGTGG
* *
18093 TAAAATGATTGTTTTGCCCTTATGTGG
1 TAAAATGACTATTTTGCCCTTATGTGG
*
18120 TAAAATGACTATTTTGCCCTTATATGG
1 TAAAATGACTATTTTGCCCTTATGTGG
* * *
18147 TAAGATGGCTGTTTTGCCC
1 TAAAATGACTATTTTGCCC
18166 CTGCGTGATG
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 64 1.00
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.42
Consensus pattern (27 bp):
TAAAATGACTATTTTGCCCTTATGTGG
Found at i:18548 original size:18 final size:18
Alignment explanation
Indices: 18508--18548 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
18498 TAGACTGTTG
*
18508 CTGCACTGATTACTATTG
1 CTGCACTGATTACTATTA
* *
18526 TTGCACTGATTACTTTTA
1 CTGCACTGATTACTATTA
18544 CTGCA
1 CTGCA
18549 ATAGGCCAAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.22, C:0.22, G:0.15, T:0.41
Consensus pattern (18 bp):
CTGCACTGATTACTATTA
Found at i:22008 original size:20 final size:21
Alignment explanation
Indices: 21983--22026 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
21973 GCACGACCTA
21983 GCACACAGCCT-GGCACACGG
1 GCACACAGCCTAGGCACACGG
* *
22003 GCACACAGGCTAGTCACACGG
1 GCACACAGCCTAGGCACACGG
22024 GCA
1 GCA
22027 TGTGTGTTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.27, C:0.36, G:0.30, T:0.07
Consensus pattern (21 bp):
GCACACAGCCTAGGCACACGG
Found at i:29996 original size:37 final size:37
Alignment explanation
Indices: 29946--30058 Score: 172
Period size: 37 Copynumber: 3.1 Consensus size: 37
29936 CTTTAGCTCA
* * * *
29946 GACAAAATCTCCACATGAAGTTATCAGGTCTTACCCG
1 GACAAAATCTCCACACGTAGTCATCGGGTCTTACCCG
*
29983 GACAAAATCTCCACACGTAGTCATTGGGTCTTACCCG
1 GACAAAATCTCCACACGTAGTCATCGGGTCTTACCCG
*
30020 GACATAATCTCCACACGTAGTCATCGGGTCTTACCCG
1 GACAAAATCTCCACACGTAGTCATCGGGTCTTACCCG
30057 GA
1 GA
30059 ATATATTTCC
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 69 1.00
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.24
Consensus pattern (37 bp):
GACAAAATCTCCACACGTAGTCATCGGGTCTTACCCG
Found at i:30329 original size:47 final size:47
Alignment explanation
Indices: 30267--30410 Score: 225
Period size: 47 Copynumber: 3.1 Consensus size: 47
30257 ACACGTTTCG
* * *
30267 CATTAGCCATTCGGCCTTACCACATATATTCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
*
30314 CATTGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
* * *
30361 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
30408 CAT
1 CAT
30411 AAAATCCTAA
Statistics
Matches: 89, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 89 1.00
ACGTcount: A:0.26, C:0.31, G:0.11, T:0.33
Consensus pattern (47 bp):
CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
Found at i:34437 original size:27 final size:27
Alignment explanation
Indices: 34407--34584 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
34397 ATATCGAGTC
* * * *
34407 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
34434 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
34461 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
34489 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
34516 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
34543 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
34570 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
34585 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:34546 original size:82 final size:81
Alignment explanation
Indices: 34428--34583 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
34418 TGCTATATAA
* *
34428 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
34493 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
34510 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
34574 CACTTAGTGC
65 CACTTAGTGC
34584 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:36725 original size:24 final size:24
Alignment explanation
Indices: 36698--36747 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
36688 ACTTCCCGAC
*
36698 TAGGGTCA-ATTTTGGGCTGTCACA
1 TAGGGTCACA-TTAGGGCTGTCACA
*
36722 TAGGGTCACATTAGGGGTGTCACA
1 TAGGGTCACATTAGGGCTGTCACA
36746 TA
1 TA
36748 TGGCTTTGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 22 0.96
25 1 0.04
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.30
Consensus pattern (24 bp):
TAGGGTCACATTAGGGCTGTCACA
Found at i:39014 original size:20 final size:20
Alignment explanation
Indices: 38978--39020 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
38968 CAACAATGTT
*
38978 TTGTGAAAGAGTATGGTATG
1 TTGTGAAAGAGTATGGTAAG
* *
38998 TTGTGAAAGATTTTGGTAAG
1 TTGTGAAAGAGTATGGTAAG
39018 TTG
1 TTG
39021 AAAGTTGGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.28, C:0.00, G:0.33, T:0.40
Consensus pattern (20 bp):
TTGTGAAAGAGTATGGTAAG
Found at i:40034 original size:21 final size:21
Alignment explanation
Indices: 40010--40062 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
40000 CGACCTGCCA
40010 ATACGGGCGTGTCCCAAAGCC
1 ATACGGGCGTGTCCCAAAGCC
40031 ATACGGGCGTGTCCCAAAGCC
1 ATACGGGCGTGTCCCAAAGCC
40052 ATACGGGCGTG
1 ATACGGGCGTG
40063 GGACCCCTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.23, C:0.30, G:0.32, T:0.15
Consensus pattern (21 bp):
ATACGGGCGTGTCCCAAAGCC
Found at i:42309 original size:21 final size:21
Alignment explanation
Indices: 42276--42329 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
42266 ATGTGAAAGG
42276 TTTGTGGTT-ATGTGATTTTGA
1 TTTG-GGTTAATGTGATTTTGA
42297 TTTGGGTTAATGTGATTTTGA
1 TTTGGGTTAATGTGATTTTGA
42318 TTT-GG-TAATGTG
1 TTTGGGTTAATGTG
42330 TAAATGGTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
19 7 0.22
20 6 0.19
21 19 0.59
ACGTcount: A:0.17, C:0.00, G:0.30, T:0.54
Consensus pattern (21 bp):
TTTGGGTTAATGTGATTTTGA
Found at i:43783 original size:26 final size:24
Alignment explanation
Indices: 43753--43809 Score: 78
Period size: 26 Copynumber: 2.3 Consensus size: 24
43743 GACTTACCAT
*
43753 AGCTCATATGAGCATACTGATATATC
1 AGCTCATAAGAGCATACTG-T-TATC
*
43779 AGCTCATAAGAGCTTACTGTTATC
1 AGCTCATAAGAGCATACTGTTATC
43803 AGCTCAT
1 AGCTCAT
43810 TGAAGCTTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 11 0.38
25 1 0.03
26 17 0.59
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.32
Consensus pattern (24 bp):
AGCTCATAAGAGCATACTGTTATC
Found at i:43839 original size:23 final size:24
Alignment explanation
Indices: 43775--43865 Score: 77
Period size: 24 Copynumber: 3.9 Consensus size: 24
43765 CATACTGATA
* **
43775 TATCAGCTCATAAGAGCTTACTGT
1 TATCAGCTCATATGAGCTTACCCT
43799 TATCAGCTCAT-TGAAGCTTACCCT
1 TATCAGCTCATATG-AGCTTACCCT
*
43823 T-TCAGCTCGTATGAGCTTA--C-
1 TATCAGCTCATATGAGCTTACCCT
43843 TATTCAGCTCA-ATAGAGCTTACC
1 TA-TCAGCTCATAT-GAGCTTACC
43866 GGTTCAGCTT
Statistics
Matches: 55, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
20 1 0.02
21 3 0.05
22 14 0.25
23 15 0.27
24 22 0.40
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.33
Consensus pattern (24 bp):
TATCAGCTCATATGAGCTTACCCT
Found at i:43865 original size:45 final size:47
Alignment explanation
Indices: 43777--43889 Score: 117
Period size: 45 Copynumber: 2.4 Consensus size: 47
43767 TACTGATATA
* * *
43777 TCAGCTCATAAGAGCTTACTGTTATCAGCTCATTGAAGCTTACCCTT
1 TCAGCTCATAAGAGCTTACTGATATCAGCTCATAGAAGCTTACCCGT
* * *
43824 TCAGCTCGTATGAGCTTACT-AT-TCAGCTCAATAG-AGCTTACCGGT
1 TCAGCTCATAAGAGCTTACTGATATCAGCTC-ATAGAAGCTTACCCGT
*
43869 TCAGCTTAATAA-AGCTTACTG
1 TCAGC-TCATAAGAGCTTACTG
43890 TTTATTAGTT
Statistics
Matches: 54, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
45 29 0.54
46 7 0.13
47 18 0.33
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.33
Consensus pattern (47 bp):
TCAGCTCATAAGAGCTTACTGATATCAGCTCATAGAAGCTTACCCGT
Found at i:48536 original size:41 final size:41
Alignment explanation
Indices: 48474--48631 Score: 192
Period size: 41 Copynumber: 3.9 Consensus size: 41
48464 TCGGAGTTTA
*
48474 AATCCGAGCTTGGTCTTGAAGGGCTTTTGAGCCAGTGTCAT
1 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
48515 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
1 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
* * * * * * * * * *
48556 AA-CTGAACCTAGTTTCAAAGGGCCTTCGGGCCAATGTCAT
1 AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
*
48596 AATTCGAGCTTGGTCTCGAAGGGCTTTTTGAGCCAG
1 AATCCGAGCTTGGTCTCGAAGGGC-TTTTGAGCCAG
48632 CGCTAAGAAT
Statistics
Matches: 93, Mismatches: 22, Indels: 3
0.79 0.19 0.03
Matches are distributed among these distances:
40 30 0.32
41 56 0.60
42 7 0.08
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.29
Consensus pattern (41 bp):
AATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCAT
Found at i:52359 original size:27 final size:27
Alignment explanation
Indices: 52329--52467 Score: 179
Period size: 27 Copynumber: 5.1 Consensus size: 27
52319 TACTGAAATG
* * *
52329 CCCTCAATTTGTAAAATTACCATTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
* *
52356 CCCTCAATTTATAGAATTACCGTTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
* *
52383 TCCTCGATTTATAGAATTACCGTTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
*
52410 CCCTTGATTTATAGAATTACCATTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
* **
52437 CCCTCGATTTACAGAATTACTGTTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
52464 CCCT
1 CCCT
52468 TGATCAGTAA
Statistics
Matches: 100, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 100 1.00
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (27 bp):
CCCTCGATTTATAGAATTACCATTTTA
Found at i:52482 original size:54 final size:54
Alignment explanation
Indices: 52343--52485 Score: 171
Period size: 54 Copynumber: 2.6 Consensus size: 54
52333 CAATTTGTAA
* ** * * * * *
52343 AATTACCATTTTACCCTCAATTTATAGAATTACCGTTTTATCCTCGATTTATAG
1 AATTACCGTTTTACCCTTGATTCATAAAATTACCATTTTACCCTCGATTTACAG
* *
52397 AATTACCGTTTTACCCTTGATTTATAGAATTACCATTTTACCCTCGATTTACAG
1 AATTACCGTTTTACCCTTGATTCATAAAATTACCATTTTACCCTCGATTTACAG
*
52451 AATTACTGTTTTACCCTTGA-TCAGTAAAATTACCA
1 AATTACCGTTTTACCCTTGATTCA-TAAAATTACCA
52486 AAATACCCCT
Statistics
Matches: 79, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
53 2 0.03
54 77 0.97
ACGTcount: A:0.30, C:0.21, G:0.08, T:0.41
Consensus pattern (54 bp):
AATTACCGTTTTACCCTTGATTCATAAAATTACCATTTTACCCTCGATTTACAG
Found at i:52492 original size:27 final size:27
Alignment explanation
Indices: 52462--52680 Score: 241
Period size: 27 Copynumber: 8.2 Consensus size: 27
52452 ATTACTGTTT
**
52462 TACCCTTGATCAGTAAAATTACCAAAA
1 TACCCTTGATTTGTAAAATTACCAAAA
* *
52489 TACCCCTGGTTTGTAAAATTACCAAAA
1 TACCCTTGATTTGTAAAATTACCAAAA
*
52516 TACCCCT-AGTTTGTAAAATTACCAAAA
1 TACCCTTGA-TTTGTAAAATTACCAAAA
*
52543 TACCCTTGGTTTGTAAAATTACCAAAA
1 TACCCTTGATTTGTAAAATTACCAAAA
* *
52570 TACCCTTGGTTTGTAAAATTACTAAAA
1 TACCCTTGATTTGTAAAATTACCAAAA
* * *
52597 TACACTTGATTTGTGAAATTACC--GA
1 TACCCTTGATTTGTAAAATTACCAAAA
* **
52622 TACCCTTTGATTTGCAAAATTACTGAAA
1 TACCC-TTGATTTGTAAAATTACCAAAA
*
52650 TAACCC--GATTTGTAAAATTACTAAAA
1 T-ACCCTTGATTTGTAAAATTACCAAAA
52676 TACCC
1 TACCC
52681 CTGTAGGGTA
Statistics
Matches: 166, Mismatches: 20, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
25 9 0.05
26 34 0.20
27 117 0.70
28 2 0.01
29 4 0.02
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.32
Consensus pattern (27 bp):
TACCCTTGATTTGTAAAATTACCAAAA
Found at i:52493 original size:81 final size:81
Alignment explanation
Indices: 52335--52512 Score: 196
Period size: 81 Copynumber: 2.2 Consensus size: 81
52325 AATGCCCTCA
* * * * *
52335 ATTTGTAAAATTACCATTTTACCCTCAATTTATAGAATTACCGTTTTATCCTCGATTTATAGAAT
1 ATTTATAAAATTACCATTTTACCCTCAATTTACAGAATTACCGTTTTACCCTCGATTCATAAAAT
**** *
52400 TACCGTTTTACCCTTG
66 TACCAAAATACCCCTG
* * * *
52416 ATTTATAGAATTACCATTTTACCCTCGATTTACAGAATTACTGTTTTACCCTTGA-TCAGTAAAA
1 ATTTATAAAATTACCATTTTACCCTCAATTTACAGAATTACCGTTTTACCCTCGATTCA-TAAAA
52480 TTACCAAAATACCCCTG
65 TTACCAAAATACCCCTG
* *
52497 GTTTGTAAAATTACCA
1 ATTTATAAAATTACCA
52513 AAATACCCCT
Statistics
Matches: 79, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
80 2 0.03
81 77 0.97
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.39
Consensus pattern (81 bp):
ATTTATAAAATTACCATTTTACCCTCAATTTACAGAATTACCGTTTTACCCTCGATTCATAAAAT
TACCAAAATACCCCTG
Found at i:52703 original size:27 final size:27
Alignment explanation
Indices: 52673--52842 Score: 207
Period size: 27 Copynumber: 6.3 Consensus size: 27
52663 AAAATTACTA
*
52673 AAATACCCCTGTAGGGTAGAAATATCG
1 AAATACCCCTGTAGGGTAGAAATACCG
** *
52700 AAATACCCCTGTAATGTA-AAATTACTG
1 AAATACCCCTGTAGGGTAGAAA-TACCG
* * * *
52727 AAATACCCTTATAAGGTAGAAATACTG
1 AAATACCCCTGTAGGGTAGAAATACCG
* *
52754 AAATACCCCTGTAGGGTAGAATTACCT
1 AAATACCCCTGTAGGGTAGAAATACCG
*
52781 AAATACCCTTGTAGGGTAGAAATACCG
1 AAATACCCCTGTAGGGTAGAAATACCG
*
52808 AAATACCCCTGTAGGGTAGAATTACCG
1 AAATACCCCTGTAGGGTAGAAATACCG
*
52835 AGATACCC
1 AAATACCC
52843 TTGGGTAAAA
Statistics
Matches: 122, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
26 3 0.02
27 116 0.95
28 3 0.02
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (27 bp):
AAATACCCCTGTAGGGTAGAAATACCG
Found at i:52841 original size:54 final size:54
Alignment explanation
Indices: 52673--52845 Score: 247
Period size: 54 Copynumber: 3.2 Consensus size: 54
52663 AAAATTACTA
* * ** * *
52673 AAATACCCCTGTAGGGTAGAAATATCGAAATACCCCTGTAATGTAAAATTACTG
1 AAATACCCTTGTAGGGTAGAAATACCGAAATACCCCTGTAGGGTAGAATTACCG
* * * *
52727 AAATACCCTTATAAGGTAGAAATACTGAAATACCCCTGTAGGGTAGAATTACCT
1 AAATACCCTTGTAGGGTAGAAATACCGAAATACCCCTGTAGGGTAGAATTACCG
52781 AAATACCCTTGTAGGGTAGAAATACCGAAATACCCCTGTAGGGTAGAATTACCG
1 AAATACCCTTGTAGGGTAGAAATACCGAAATACCCCTGTAGGGTAGAATTACCG
*
52835 AGATACCCTTG
1 AAATACCCTTG
52846 GGTAAAATTA
Statistics
Matches: 104, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 104 1.00
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (54 bp):
AAATACCCTTGTAGGGTAGAAATACCGAAATACCCCTGTAGGGTAGAATTACCG
Found at i:52994 original size:21 final size:21
Alignment explanation
Indices: 52969--53018 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
52959 ATATTGTTAT
52969 ACATGATAGGACATGATATGC
1 ACATGATAGGACATGATATGC
* **
52990 ACATGATATGTTATGATATGC
1 ACATGATAGGACATGATATGC
53011 ACATGATA
1 ACATGATA
53019 TGCTATGATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (21 bp):
ACATGATAGGACATGATATGC
Found at i:52995 original size:11 final size:11
Alignment explanation
Indices: 52969--53021 Score: 65
Period size: 11 Copynumber: 5.0 Consensus size: 11
52959 ATATTGTTAT
*
52969 ACATGATA-GG
1 ACATGATATGC
52979 ACATGATATGC
1 ACATGATATGC
52990 ACATGATATG-
1 ACATGATATGC
**
53000 TTATGATATGC
1 ACATGATATGC
53011 ACATGATATGC
1 ACATGATATGC
53022 TATGATATAC
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
10 16 0.44
11 20 0.56
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (11 bp):
ACATGATATGC
Found at i:53019 original size:21 final size:21
Alignment explanation
Indices: 52981--53029 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
52971 ATGATAGGAC
*
52981 ATGATATGCACATGATATGTT
1 ATGATATGCACATGATATGCT
53002 ATGATATGCACATGATATGCT
1 ATGATATGCACATGATATGCT
53023 ATGATAT
1 ATGATAT
53030 ACTCACTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (21 bp):
ATGATATGCACATGATATGCT
Found at i:53111 original size:25 final size:25
Alignment explanation
Indices: 53077--53146 Score: 122
Period size: 25 Copynumber: 2.8 Consensus size: 25
53067 AGGAAGTGTT
*
53077 AAAAGGGCTTTGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCA
*
53102 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTACCA
53127 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
53147 ATTAAAAGAG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.26
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCA
Found at i:53159 original size:24 final size:24
Alignment explanation
Indices: 53075--53159 Score: 109
Period size: 25 Copynumber: 3.5 Consensus size: 24
53065 GGAGGAAGTG
53075 TTAAAAGGGCTTTGCCCCAGTTTA
1 TTAAAAGGGCTTTGCCCCAGTTTA
**
53099 CCGAAAAGGGCTTTGCCCCAGTTTA
1 -TTAAAAGGGCTTTGCCCCAGTTTA
*
53124 TCAAAAAGGGCTTTGCCCCAG-TTA
1 T-TAAAAGGGCTTTGCCCCAGTTTA
53148 TTAAAAGAGGCT
1 TTAAAAG-GGCT
53160 AGGCCTCCAG
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
23 5 0.09
24 8 0.15
25 40 0.75
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.27
Consensus pattern (24 bp):
TTAAAAGGGCTTTGCCCCAGTTTA
Found at i:53170 original size:50 final size:50
Alignment explanation
Indices: 53077--53171 Score: 122
Period size: 50 Copynumber: 1.9 Consensus size: 50
53067 AGGAAGTGTT
**
53077 AAAAGGGCTTTGCCCCAGTTTACCGAAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTACCGAAAAGGGCTAGGCCCCAGTTTATCA
**
53127 AAAAGGGCTTTGCCCCAG-TTA-TTAAAAGAGGCTAGGCCTCCAGTT
1 AAAAGGGCTTTGCCCCAGTTTACCGAAAAG-GGCTAGGCC-CCAGTT
53172 ATATGATAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
48 5 0.13
49 10 0.26
50 24 0.62
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.25
Consensus pattern (50 bp):
AAAAGGGCTTTGCCCCAGTTTACCGAAAAGGGCTAGGCCCCAGTTTATCA
Found at i:54322 original size:41 final size:41
Alignment explanation
Indices: 54252--54391 Score: 131
Period size: 41 Copynumber: 3.4 Consensus size: 41
54242 TCGAATTCTC
* * * *
54252 GCACACTAGGTGCCCAAACATAGCCGAAGCTATTTTAATCTT
1 GCACACTAAGTG-CCATACATAGCTGAAGCTATTTCAATCTT
* * * **
54294 GCATACTAAGTGCCTTACATAGCTGAAGCTATCTCGGTCTT
1 GCACACTAAGTGCCATACATAGCTGAAGCTATTTCAATCTT
* * *
54335 GCACACTAAGTGCCATATATAGCTAAAGCTATTCTGAATC--
1 GCACACTAAGTGCCATACATAGCTGAAGCTATT-TCAATCTT
*
54375 ACACACTAAGTGCCATA
1 GCACACTAAGTGCCATA
54392 TATATATTCA
Statistics
Matches: 79, Mismatches: 18, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
40 16 0.20
41 50 0.63
42 13 0.16
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.27
Consensus pattern (41 bp):
GCACACTAAGTGCCATACATAGCTGAAGCTATTTCAATCTT
Found at i:56480 original size:40 final size:39
Alignment explanation
Indices: 56396--56580 Score: 203
Period size: 40 Copynumber: 4.6 Consensus size: 39
56386 TTGAATGATG
* * * *
56396 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
56436 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
* *
56476 TCCGGGCTAAGCCCGAAGGCATTTGTGCTAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
*
56515 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AA
*
56556 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
56581 AACGAGGAGC
Statistics
Matches: 124, Mismatches: 17, Indels: 8
0.83 0.11 0.05
Matches are distributed among these distances:
39 34 0.27
40 80 0.65
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:56532 original size:79 final size:81
Alignment explanation
Indices: 56396--56580 Score: 245
Period size: 79 Copynumber: 2.3 Consensus size: 81
56386 TTGAATGATG
*
56396 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
56460 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * **
56475 TTCCGGGCTAAG-CCCGAAGGCATTTGTGCT-AGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
56537 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
56555 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
56581 AACGAGGAGC
Statistics
Matches: 93, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.62
80 34 0.37
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:56602 original size:79 final size:79
Alignment explanation
Indices: 56397--56613 Score: 192
Period size: 79 Copynumber: 2.7 Consensus size: 79
56387 TGAATGATGT
** * * * **
56397 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAG-CCCGAAGGCATTTGAAC-GAGTGACTAAATCCGGGTTAA-ATCCCGAAGGCATT
*
56460 TGTGCGAGATACTAATT
63 TGTGCGAGATACTAATA
** * * *
56477 CCGGGCTAAGCCCGAAGGCATTTGTGCTAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGT
1 CCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAATCCCGAAGGCATTTGT
*
56542 GCGAGTTACT-ATAA
66 GCGAGATACTAAT-A
* * *
56556 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATTCCGAAGG
1 CCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-CTAAATCCGGGTTAAATCCCGAAGG
56614 TACGTGATTT
Statistics
Matches: 115, Mismatches: 17, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
78 3 0.03
79 71 0.62
80 41 0.36
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAAATCCGGGTTAAATCCCGAAGGCATTTGT
GCGAGATACTAATA
Found at i:61916 original size:40 final size:39
Alignment explanation
Indices: 61832--62016 Score: 180
Period size: 40 Copynumber: 4.6 Consensus size: 39
61822 TCGAATGATG
* * * * *
61832 TCCGGGCTTAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
61872 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
*
61912 TCCGGGCTAAG-CTCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTC-CGAAGGCATTTGTGCGAGTTACTAAA
*
61951 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AA
61992 -CCGGGC-AATGTCCCGAAGGCATTTG
1 TCCGGGCTAA-GT-CCGAAGGCATTTG
62017 AATGAGTAGC
Statistics
Matches: 123, Mismatches: 15, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
38 1 0.01
39 35 0.28
40 76 0.62
41 11 0.09
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:70147 original size:29 final size:27
Alignment explanation
Indices: 70129--70198 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
70119 ATATTAAGTC
70129 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
*
70156 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
*
70184 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
70199 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:70192 original size:28 final size:28
Alignment explanation
Indices: 70129--70226 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
70119 ATATTAAGTC
*
70129 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
70156 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
70184 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
70213 CGCACACTTAGTGC
1 CGCACACTTAGTGC
70227 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Done.