Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1267
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: 38754
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Found at i:312 original size:51 final size:50
Alignment explanation
Indices: 239--357 Score: 166
Period size: 51 Copynumber: 2.3 Consensus size: 50
229 TATTTTCAAG
* * *
239 GGGATACTCTAACCCCGGTTTTATTTCTAAAACATCAATTTTCCATAATC
1 GGGATACTCCAACCCCGATTTTATTTCCAAAACATCAATTTTCCATAATC
* * *
289 AGGGATACTCCAACTCTGATTTTATTTCCAAAACATCAATTTTTCATAATC
1 -GGGATACTCCAACCCCGATTTTATTTCCAAAACATCAATTTTCCATAATC
340 GGAGATACTCCAACCCCG
1 GG-GATACTCCAACCCCG
358 TTATTTCTGA
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
50 2 0.03
51 57 0.97
ACGTcount: A:0.31, C:0.25, G:0.11, T:0.33
Consensus pattern (50 bp):
GGGATACTCCAACCCCGATTTTATTTCCAAAACATCAATTTTCCATAATC
Found at i:373 original size:79 final size:79
Alignment explanation
Indices: 290--435 Score: 204
Period size: 79 Copynumber: 1.8 Consensus size: 79
280 TCCATAATCA
* ** * *
290 GGGATACTCCAACTCTGATTTTATTTCCAAAACATCAATTTTTCATAATCG-GAGATACTCCAAC
1 GGGATACTCCAACCCCAATTTTATTTCCAAAACATCAATTTCTCACAATCGAG-GATACTCCAAC
354 CCCGTTATTTCTGAG
65 CCCGTTATTTCTGAG
* **
369 GGGATACTCCAACCCCAATTTTATTTCCAAAATATTGATTTCTCACAATCGAGGATACTCCAACC
1 GGGATACTCCAACCCCAATTTTATTTCCAAAACATCAATTTCTCACAATCGAGGATACTCCAACC
434 CC
66 CC
436 AGCCTTATTT
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
79 57 0.98
80 1 0.02
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.32
Consensus pattern (79 bp):
GGGATACTCCAACCCCAATTTTATTTCCAAAACATCAATTTCTCACAATCGAGGATACTCCAACC
CCGTTATTTCTGAG
Found at i:430 original size:130 final size:129
Alignment explanation
Indices: 197--564 Score: 447
Period size: 130 Copynumber: 2.8 Consensus size: 129
187 GGGTTATCCC
* * *
197 ATTTTTTACAATCGGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCTAACCCCGGTTTTA
1 ATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCTAACCCCGATTTTA
* * ** * * **
262 TTTCTAAAACATCAATTTTCCATAATCAGGGATACTCCAA-CTCTGATTTTATTTCCAAAACATC
66 TTTCCAAAATATTGATTTT-CATAATCAGGGATACTCCAACCCCAG-CCTTATTTCCAAAACATC
326 A
129 A
* * * *
327 ATTTTTCATAATCGGAGATACTCCAACCCCGTTA-TTTCTGAGGGGATACTCCAACCCCAATTTT
1 ATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTC-GAGGGGATACTCTAACCCCGATTTT
* * *
391 ATTTCCAAAATATTGATTTCTCACAATC-GAGGATACTCCAACCCCAGCCTTATTTCTAAAGCAT
65 ATTTCCAAAATATTGATTT-TCATAATCAG-GGATACTCCAACCCCAGCCTTATTTCCAAAACAT
*
455 CG
128 CA
* *
457 ATTTTTCACAATTGGGGATACTCCAACCTCGTTATTTTCGAGGGGATACTCTAACCCCGATTTTA
1 ATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCTAACCCCGATTTTA
*
522 TTTTCAAAAT-TTCGATTTTCTATAATCAGGGATACTCCAACCC
66 TTTCCAAAATATT-GATTTTC-ATAATCAGGGATACTCCAACCC
565 TATTATTTTC
Statistics
Matches: 203, Mismatches: 27, Indels: 16
0.83 0.11 0.07
Matches are distributed among these distances:
129 9 0.04
130 185 0.91
131 9 0.04
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.34
Consensus pattern (129 bp):
ATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCTAACCCCGATTTTA
TTTCCAAAATATTGATTTTCATAATCAGGGATACTCCAACCCCAGCCTTATTTCCAAAACATCA
Found at i:431 original size:51 final size:51
Alignment explanation
Indices: 370--484 Score: 140
Period size: 51 Copynumber: 2.3 Consensus size: 51
360 ATTTCTGAGG
** * *
370 GGATACTCCAACCCCAATTTTATTTCCAAAATATTGATTTCTCACAATCGA
1 GGATACTCCAACCCCAACCTTATTTCCAAAACATCGATTTCTCACAATCGA
* * * * * *
421 GGATACTCCAACCCCAGCCTTATTTCTAAAGCATCGATTTTTCACAATTGG
1 GGATACTCCAACCCCAACCTTATTTCCAAAACATCGATTTCTCACAATCGA
472 GGATACTCCAACC
1 GGATACTCCAACC
485 TCGTTATTTT
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.30, C:0.28, G:0.11, T:0.30
Consensus pattern (51 bp):
GGATACTCCAACCCCAACCTTATTTCCAAAACATCGATTTCTCACAATCGA
Found at i:523 original size:79 final size:78
Alignment explanation
Indices: 443--637 Score: 218
Period size: 79 Copynumber: 2.4 Consensus size: 78
433 CCCAGCCTTA
* * *
443 TTTCTAAAGCATCGATTTTTCACAATTGGGGATACTCCAA-CCTCGTTATTTTCGAGGGGATA-C
1 TTTC-AAA-CATCGATTTTTCATAATCGGGGATACTCCAACCCT-ATTATTTTCGAGGGGATATC
506 TCTAACCCCGATTTTAT
63 TC-AACCCCGATTTTAT
* *
523 TTTCAAA-ATTTCGA-TTTTCTATAATCAGGGATACTCCAACCCTATTATTTTCGAGGGGATATT
1 TTTCAAACA--TCGATTTTTC-ATAATCGGGGATACTCCAACCCTATTATTTTCGAGGGGATATC
*
586 TCAACCCCGGTTTTAT
63 TCAACCCCGATTTTAT
* *
602 TTTCAGAACACCGATTTTCCATAATCGGGGATACTC
1 TTTCA-AACATCGATTTTTCATAATCGGGGATACTC
638 TAGCCCTGTT
Statistics
Matches: 98, Mismatches: 9, Indels: 17
0.79 0.07 0.14
Matches are distributed among these distances:
77 1 0.01
78 5 0.05
79 76 0.78
80 15 0.15
81 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.36
Consensus pattern (78 bp):
TTTCAAACATCGATTTTTCATAATCGGGGATACTCCAACCCTATTATTTTCGAGGGGATATCTCA
ACCCCGATTTTAT
Found at i:4870 original size:79 final size:79
Alignment explanation
Indices: 4754--4900 Score: 213
Period size: 79 Copynumber: 1.9 Consensus size: 79
4744 CCAATTATGA
* * *
4754 AAAATCAATGTTCTGAAAATAAAATCGGGGTTAGAGTATCCCCTCTAAAAAAATAGGGTTGGAGT
1 AAAATCAATGTTCTGAAAATAAAATCAGGGTTAGAGTATCCCCTCGAAAAAAATAGGGCTGGAGT
4819 ATCTTTGATTATAG
66 ATCTTTGATTATAG
* * * * * *
4833 AAAATCGATGTTTTGAAAATAAAATCAGGGTTGGAGTATCCTCTCGAAAATAATGGGGCTGGAGT
1 AAAATCAATGTTCTGAAAATAAAATCAGGGTTAGAGTATCCCCTCGAAAAAAATAGGGCTGGAGT
4898 ATC
66 ATC
4901 CCCGATGAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
79 59 1.00
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (79 bp):
AAAATCAATGTTCTGAAAATAAAATCAGGGTTAGAGTATCCCCTCGAAAAAAATAGGGCTGGAGT
ATCTTTGATTATAG
Found at i:4934 original size:28 final size:30
Alignment explanation
Indices: 4860--4934 Score: 95
Period size: 28 Copynumber: 2.6 Consensus size: 30
4850 AATAAAATCA
*
4860 GGGTTGGAGTATCCTC--TCGAAAATAATG
1 GGGTTGGAGTATCCTCGATCGAAAATAACG
* *
4888 GGGCTGGAGTATCCCCGAT-GAAAA-AACG
1 GGGTTGGAGTATCCTCGATCGAAAATAACG
4916 GGGTTGGAGTATCCTCGAT
1 GGGTTGGAGTATCCTCGAT
4935 TGTGAAAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
28 34 0.85
29 5 0.12
30 1 0.03
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (30 bp):
GGGTTGGAGTATCCTCGATCGAAAATAACG
Found at i:5033 original size:51 final size:51
Alignment explanation
Indices: 4908--5033 Score: 155
Period size: 51 Copynumber: 2.5 Consensus size: 51
4898 ATCCCCGATG
*
4908 AAAAAACGGGGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTGAAAA
1 AAAAAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTGAAAA
* * * * *
4959 AAAAATCGGAGTTGGAATATCCCCGATTGTGGAAAATTGGTGTTTT-AGAAA
1 AAAAAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTGA-AAA
* * *
5010 TAAAACCGGGGTTGGAGTGTCCCC
1 AAAAAACGGGGTTGGAGTATCCCC
5034 TCAGAAATAA
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
50 1 0.02
51 62 0.98
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.28
Consensus pattern (51 bp):
AAAAAACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTGAAAA
Found at i:7503 original size:25 final size:25
Alignment explanation
Indices: 7469--7519 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
7459 GAATGTATTG
* *
7469 ATACAATGAATAATGTATCGATACA
1 ATACAATGAACAATGCATCGATACA
7494 ATACAATGAACAATGCATCGATACA
1 ATACAATGAACAATGCATCGATACA
7519 A
1 A
7520 ATTGTGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.49, C:0.16, G:0.12, T:0.24
Consensus pattern (25 bp):
ATACAATGAACAATGCATCGATACA
Found at i:10069 original size:23 final size:23
Alignment explanation
Indices: 10028--10071 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
10018 GAATTTTTAT
10028 TATTTTATAAATTTTTAAATATA
1 TATTTTATAAATTTTTAAATATA
*
10051 TATTTT-TATATTTTATAAATA
1 TATTTTATAAATTTT-TAAATA
10072 AATACAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
TATTTTATAAATTTTTAAATATA
Found at i:10464 original size:21 final size:21
Alignment explanation
Indices: 10438--10493 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 21
10428 ACACTAATTC
10438 AATTAATAAAATTATAAAAAA
1 AATTAATAAAATTATAAAAAA
*
10459 AATTAA-AATAATGTTATAAAAAT
1 AATTAATAA-AA--TTATAAAAAA
10482 AA--AATAAAATTA
1 AATTAATAAAATTA
10494 CAAATATTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 10
0.73 0.02 0.24
Matches are distributed among these distances:
19 3 0.10
20 2 0.07
21 12 0.40
22 2 0.07
23 11 0.37
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (21 bp):
AATTAATAAAATTATAAAAAA
Found at i:10761 original size:2 final size:2
Alignment explanation
Indices: 10750--10784 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
10740 ATTAGTAGTG
10750 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10785 CAAATCAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:12214 original size:21 final size:19
Alignment explanation
Indices: 12166--12221 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
12156 TGCAGGGTAG
12166 TTTTGTATCGATACAACAC
1 TTTTGTATCGATACAACAC
* **
12185 TTATGTATCGATACATTTAC
1 TTTTGTATCGATACA-ACAC
12205 TGTTTGTATCGATACAA
1 T-TTTGTATCGATACAA
12222 ATTGTTGAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 14 0.47
20 3 0.10
21 13 0.43
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.41
Consensus pattern (19 bp):
TTTTGTATCGATACAACAC
Found at i:14365 original size:25 final size:25
Alignment explanation
Indices: 14332--14379 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
14322 TTAAAGATAT
* * *
14332 ATTTTTTATTATTATTAAATTTAAA
1 ATTTATTATTATAAATAAATTTAAA
14357 ATTTATTATTATAAATAAATTTA
1 ATTTATTATTATAAATAAATTTA
14380 TTAAAATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
ATTTATTATTATAAATAAATTTAAA
Found at i:14467 original size:27 final size:28
Alignment explanation
Indices: 14433--14493 Score: 83
Period size: 27 Copynumber: 2.2 Consensus size: 28
14423 TAATAAATAT
*
14433 ATAATATTTTAA-ATAT-AAATATAAAAA
1 ATAATATTTAAATATATAAAAT-TAAAAA
14460 ATAATA-TTAAATATATAAAATTAAAAA
1 ATAATATTTAAATATATAAAATTAAAAA
14487 ATAATAT
1 ATAATAT
14494 AAAAAAAGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 4 0.13
27 22 0.73
28 4 0.13
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (28 bp):
ATAATATTTAAATATATAAAATTAAAAA
Found at i:14472 original size:19 final size:18
Alignment explanation
Indices: 14444--14499 Score: 58
Period size: 20 Copynumber: 2.9 Consensus size: 18
14434 TAATATTTTA
14444 AATATAAATATAAAAAAT
1 AATATAAATATAAAAAAT
*
14462 AATATTAAATATATAAAATT
1 AATA-TAAATATA-AAAAAT
* *
14482 AAAAAATAATATAAAAAA
1 AATATA-AATATAAAAAA
14500 AGATCTTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
18 4 0.13
19 13 0.42
20 14 0.45
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
AATATAAATATAAAAAAT
Found at i:14757 original size:8 final size:8
Alignment explanation
Indices: 14736--14802 Score: 75
Period size: 8 Copynumber: 8.2 Consensus size: 8
14726 AAAGGAAAGG
*
14736 AAGAAAGA
1 AAGAAAAA
14744 AA-AAAAA
1 AAGAAAAA
14751 AAG-AAAA
1 AAGAAAAA
14758 AAGAAAAA
1 AAGAAAAA
*
14766 AAGGAAAA
1 AAGAAAAA
14774 AAGAAAAA
1 AAGAAAAA
14782 AAGGAAAAAA
1 AA-G-AAAAA
14792 AAGAAAGAA
1 AAGAAA-AA
14801 AA
1 AA
14803 AATTATATGT
Statistics
Matches: 51, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
7 13 0.25
8 25 0.49
9 6 0.12
10 7 0.14
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (8 bp):
AAGAAAAA
Found at i:14759 original size:9 final size:9
Alignment explanation
Indices: 14739--14803 Score: 73
Period size: 9 Copynumber: 7.3 Consensus size: 9
14729 GGAAAGGAAG
14739 AAAGAAAAA
1 AAAGAAAAA
14748 AAA-AAGAAA
1 AAAGAA-AAA
14757 AAAG-AAAA
1 AAAGAAAAA
*
14765 AAAG-GAAA
1 AAAGAAAAA
14773 AAAGAAAAA
1 AAAGAAAAA
*
14782 AAGGAAAAA
1 AAAGAAAAA
14791 AAAGAAAGAA
1 AAAGAAA-AA
14801 AAA
1 AAA
14804 ATTATATGTT
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
8 16 0.33
9 27 0.56
10 5 0.10
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (9 bp):
AAAGAAAAA
Found at i:14769 original size:34 final size:35
Alignment explanation
Indices: 14726--14802 Score: 104
Period size: 34 Copynumber: 2.2 Consensus size: 35
14716 TTCCAGCTGA
* *
14726 AAAGGAAAGGAAGAAAGAAAAAAA-AAAGAAAAAAG
1 AAAGAAAAGGAAAAAAGAAAAAAAGAAA-AAAAAAG
*
14761 AAA-AAAAGGAAAAAAGAAAAAAAGGAAAAAAAAG
1 AAAGAAAAGGAAAAAAGAAAAAAAGAAAAAAAAAG
14795 AAAGAAAA
1 AAAGAAAA
14803 AATTATATGT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
34 28 0.76
35 9 0.24
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (35 bp):
AAAGAAAAGGAAAAAAGAAAAAAAGAAAAAAAAAG
Found at i:15117 original size:20 final size:22
Alignment explanation
Indices: 15077--15117 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
15067 TATTCGTGTC
*
15077 GTGTTTATATTTTTTTCATATT
1 GTGTTTATAATTTTTTCATATT
15099 GTGTTTA-AATTTTTT-ATAT
1 GTGTTTATAATTTTTTCATAT
15118 CTATCTATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 7 0.39
22 7 0.39
ACGTcount: A:0.22, C:0.02, G:0.10, T:0.66
Consensus pattern (22 bp):
GTGTTTATAATTTTTTCATATT
Found at i:18520 original size:16 final size:16
Alignment explanation
Indices: 18489--18530 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
18479 TTTAATATTT
*
18489 ATAAAATTTTTAATTAA
1 ATAAAATTTATAATT-A
18506 ATAAAA-TTATAATTA
1 ATAAAATTTATAATTA
18521 ATAAATATTT
1 ATAAA-ATTT
18531 TTTAAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 6 0.27
16 8 0.36
17 8 0.36
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATAAAATTTATAATTA
Found at i:18851 original size:57 final size:59
Alignment explanation
Indices: 18789--18909 Score: 147
Period size: 58 Copynumber: 2.1 Consensus size: 59
18779 ACACATAAAA
* * * *
18789 AGATATAAT-TTTTTAATTGAATCACTATAATAAATTATG-AAAAAATATCATAAATTG
1 AGATATAATACTTTAAATTAAATCACTATAATAAATTATGTAAAAAATATCATAAATGG
* * * * *
18846 AGATATGATACTTTAAATTAAATTATTATGATAAATTATGTAAAATATATCATAAATGG
1 AGATATAATACTTTAAATTAAATCACTATAATAAATTATGTAAAAAATATCATAAATGG
18905 AGATA
1 AGATA
18910 CGATACGAAT
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
57 8 0.15
58 24 0.45
59 21 0.40
ACGTcount: A:0.49, C:0.04, G:0.09, T:0.38
Consensus pattern (59 bp):
AGATATAATACTTTAAATTAAATCACTATAATAAATTATGTAAAAAATATCATAAATGG
Found at i:18999 original size:18 final size:19
Alignment explanation
Indices: 18967--19002 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
18957 TTTTTTAAAT
*
18967 TTTTTATTTTAATTTTAAC
1 TTTTAATTTTAATTTTAAC
18986 TTTTAATTTT-ATTTTAA
1 TTTTAATTTTAATTTTAA
19003 AATAATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTAATTTTAATTTTAAC
Found at i:19187 original size:17 final size:16
Alignment explanation
Indices: 19147--19188 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
19137 AAAATTGATG
19147 ATAATA-ATA-TTTAA
1 ATAATATATATTTTAA
19161 ATAATATATATTTTAA
1 ATAATATATATTTTAA
*
19177 TATAATTTATAT
1 -ATAATATATAT
19189 AATAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 6 0.25
15 3 0.12
16 5 0.21
17 10 0.42
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATAATATATATTTTAA
Found at i:19298 original size:15 final size:14
Alignment explanation
Indices: 19269--19306 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
19259 ACTAAATTAC
19269 TTAAGTTTTTATTT
1 TTAAGTTTTTATTT
19283 TTAAGTTTTGTATTT
1 TTAAGTTTT-TATTT
19298 TTAA-TTTTT
1 TTAAGTTTTT
19307 TTTAGTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 1 0.04
14 13 0.57
15 9 0.39
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.71
Consensus pattern (14 bp):
TTAAGTTTTTATTT
Found at i:19307 original size:16 final size:15
Alignment explanation
Indices: 19274--19320 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
19264 ATTACTTAAG
*
19274 TTTTTATTTTTAAGT
1 TTTTTATTTTTAATT
*
19289 TTTGTATTTTTAATTT
1 TTTTTATTTTTAA-TT
*
19305 TTTTTAGTTTTAATT
1 TTTTTATTTTTAATT
19320 T
1 T
19321 ATTCCTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 15 0.56
16 12 0.44
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.74
Consensus pattern (15 bp):
TTTTTATTTTTAATT
Found at i:20153 original size:24 final size:23
Alignment explanation
Indices: 20109--20157 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
20099 TAACTCAATA
20109 AATTTTTTTAAAAAAAAATATTT
1 AATTTTTTTAAAAAAAAATATTT
* * *
20132 AATTTATTTTTAAATAATATATTT
1 AATTT-TTTTAAAAAAAAATATTT
20156 AA
1 AA
20158 AAAATTGGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
AATTTTTTTAAAAAAAAATATTT
Found at i:20273 original size:30 final size:30
Alignment explanation
Indices: 20189--20275 Score: 90
Period size: 30 Copynumber: 2.9 Consensus size: 30
20179 TTAAATTAAT
*
20189 TTAAATTTTATATT-TTATTATAAATAAAA
1 TTAAATTTTATATTATTATTATTAATAAAA
* ** *
20218 ATAAA-AATATATAATTATTATTTAATAAAA
1 TTAAATTTTATATTATTATTA-TTAATAAAA
20248 TTAAATTTTATATTACTT-TTATTAATAA
1 TTAAATTTTATATTA-TTATTATTAATAA
20276 TTAAAAATTA
Statistics
Matches: 45, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
28 5 0.11
29 10 0.22
30 19 0.42
31 9 0.20
32 2 0.04
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (30 bp):
TTAAATTTTATATTATTATTATTAATAAAA
Found at i:20286 original size:28 final size:28
Alignment explanation
Indices: 20211--20287 Score: 75
Period size: 28 Copynumber: 2.7 Consensus size: 28
20201 TTTTATTATA
* *
20211 AATAAAAATAAAAATATATAATTATTATTT
1 AATAAAATTAAAAAT-TAT-ATTACTATTT
**
20241 AATAAAATTAAATTTTATATTACT-TTT
1 AATAAAATTAAAAATTATATTACTATTT
*
20268 ATTAATAATTAAAAATTATA
1 AATAA-AATTAAAAATTATA
20288 AAAAAATTAA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
27 7 0.18
28 17 0.44
29 3 0.08
30 12 0.31
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (28 bp):
AATAAAATTAAAAATTATATTACTATTT
Found at i:20737 original size:25 final size:25
Alignment explanation
Indices: 20703--20763 Score: 81
Period size: 25 Copynumber: 2.5 Consensus size: 25
20693 TACTATAATA
20703 ATTTATTATTAAATAATAA-AAAATT
1 ATTTATTATTAAATAATAATAAAA-T
* *
20728 ATTTATTATTATATTATAATAAAAT
1 ATTTATTATTAAATAATAATAAAAT
20753 A-TTATTATTAA
1 ATTTATTATTAA
20764 TGTAACTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 9 0.28
25 19 0.59
26 4 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
ATTTATTATTAAATAATAATAAAAT
Found at i:20775 original size:31 final size:28
Alignment explanation
Indices: 20703--20762 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 28
20693 TACTATAATA
20703 ATTTATTATTA-A--ATAATAAAAAATT
1 ATTTATTATTATATTATAATAAAAAATT
*
20728 ATTTATTATTATATTATAATAAAATATT
1 ATTTATTATTATATTATAATAAAAAATT
20756 A-TTATTA
1 ATTTATTA
20763 ATGTAACTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 11 0.35
26 1 0.03
27 6 0.19
28 13 0.42
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (28 bp):
ATTTATTATTATATTATAATAAAAAATT
Found at i:24414 original size:2 final size:2
Alignment explanation
Indices: 24407--24444 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
24397 TTCTTGTGAG
24407 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24445 GCATCTAAGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26302 original size:19 final size:20
Alignment explanation
Indices: 26278--26319 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
26268 AAGAAAAGAA
26278 AAAGGAAATGTA-A-GTTTTT
1 AAAGGAAA-GTATAGGTTTTT
26297 AAAGGAAAGTATAGGTTTTT
1 AAAGGAAAGTATAGGTTTTT
26317 AAA
1 AAA
26320 AGGGAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 3 0.14
19 9 0.43
20 9 0.43
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.33
Consensus pattern (20 bp):
AAAGGAAAGTATAGGTTTTT
Found at i:26833 original size:51 final size:50
Alignment explanation
Indices: 26760--26878 Score: 166
Period size: 51 Copynumber: 2.3 Consensus size: 50
26750 TATTTTCAAG
* * *
26760 GGGATACTCTAACCCCGGTTTTATTTCTAAAACATCAATTTTCCATAATC
1 GGGATACTCCAACCCCGATTTTATTTCCAAAACATCAATTTTCCATAATC
* * *
26810 AGGGATACTCCAACTCTGATTTTATTTCCAAAACATCAATTTTTCATAATC
1 -GGGATACTCCAACCCCGATTTTATTTCCAAAACATCAATTTTCCATAATC
26861 GGAGATACTCCAACCCCG
1 GG-GATACTCCAACCCCG
26879 TTATTTCTGA
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
50 2 0.03
51 57 0.97
ACGTcount: A:0.31, C:0.25, G:0.11, T:0.33
Consensus pattern (50 bp):
GGGATACTCCAACCCCGATTTTATTTCCAAAACATCAATTTTCCATAATC
Found at i:26894 original size:79 final size:79
Alignment explanation
Indices: 26811--26956 Score: 204
Period size: 79 Copynumber: 1.8 Consensus size: 79
26801 TCCATAATCA
* ** * *
26811 GGGATACTCCAACTCTGATTTTATTTCCAAAACATCAATTTTTCATAATCG-GAGATACTCCAAC
1 GGGATACTCCAACCCCAATTTTATTTCCAAAACATCAATTTCTCACAATCGAG-GATACTCCAAC
26875 CCCGTTATTTCTGAG
65 CCCGTTATTTCTGAG
* **
26890 GGGATACTCCAACCCCAATTTTATTTCCAAAATATTGATTTCTCACAATCGAGGATACTCCAACC
1 GGGATACTCCAACCCCAATTTTATTTCCAAAACATCAATTTCTCACAATCGAGGATACTCCAACC
26955 CC
66 CC
26957 AGCCTTATTT
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
79 57 0.98
80 1 0.02
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.32
Consensus pattern (79 bp):
GGGATACTCCAACCCCAATTTTATTTCCAAAACATCAATTTCTCACAATCGAGGATACTCCAACC
CCGTTATTTCTGAG
Found at i:26951 original size:130 final size:129
Alignment explanation
Indices: 26718--27085 Score: 447
Period size: 130 Copynumber: 2.8 Consensus size: 129
26708 GGGTTATCCC
* * *
26718 ATTTTTTACAATCGGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCTAACCCCGGTTTTA
1 ATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCTAACCCCGATTTTA
* * ** * * **
26783 TTTCTAAAACATCAATTTTCCATAATCAGGGATACTCCAA-CTCTGATTTTATTTCCAAAACATC
66 TTTCCAAAATATTGATTTT-CATAATCAGGGATACTCCAACCCCAG-CCTTATTTCCAAAACATC
26847 A
129 A
* * * *
26848 ATTTTTCATAATCGGAGATACTCCAACCCCGTTA-TTTCTGAGGGGATACTCCAACCCCAATTTT
1 ATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTC-GAGGGGATACTCTAACCCCGATTTT
* * *
26912 ATTTCCAAAATATTGATTTCTCACAATC-GAGGATACTCCAACCCCAGCCTTATTTCTAAAGCAT
65 ATTTCCAAAATATTGATTT-TCATAATCAG-GGATACTCCAACCCCAGCCTTATTTCCAAAACAT
*
26976 CG
128 CA
* *
26978 ATTTTTCACAATTGGGGATACTCCAACCTCGTTATTTTCGAGGGGATACTCTAACCCCGATTTTA
1 ATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCTAACCCCGATTTTA
*
27043 TTTTCAAAAT-TTCGATTTTCTATAATCAGGGATACTCCAACCC
66 TTTCCAAAATATT-GATTTTC-ATAATCAGGGATACTCCAACCC
27086 TATTATTTTC
Statistics
Matches: 203, Mismatches: 27, Indels: 16
0.83 0.11 0.07
Matches are distributed among these distances:
129 9 0.04
130 185 0.91
131 9 0.04
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.34
Consensus pattern (129 bp):
ATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCTAACCCCGATTTTA
TTTCCAAAATATTGATTTTCATAATCAGGGATACTCCAACCCCAGCCTTATTTCCAAAACATCA
Found at i:26952 original size:51 final size:51
Alignment explanation
Indices: 26891--27005 Score: 140
Period size: 51 Copynumber: 2.3 Consensus size: 51
26881 ATTTCTGAGG
** * *
26891 GGATACTCCAACCCCAATTTTATTTCCAAAATATTGATTTCTCACAATCGA
1 GGATACTCCAACCCCAACCTTATTTCCAAAACATCGATTTCTCACAATCGA
* * * * * *
26942 GGATACTCCAACCCCAGCCTTATTTCTAAAGCATCGATTTTTCACAATTGG
1 GGATACTCCAACCCCAACCTTATTTCCAAAACATCGATTTCTCACAATCGA
26993 GGATACTCCAACC
1 GGATACTCCAACC
27006 TCGTTATTTT
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.30, C:0.28, G:0.11, T:0.30
Consensus pattern (51 bp):
GGATACTCCAACCCCAACCTTATTTCCAAAACATCGATTTCTCACAATCGA
Found at i:27044 original size:79 final size:79
Alignment explanation
Indices: 26964--27158 Score: 200
Period size: 79 Copynumber: 2.5 Consensus size: 79
26954 CCCAGCCTTA
* ** *
26964 TTTCTAAAGCATCGATTTT-TCACAATTGGGGATACTCCAA-CCTCGTTATTTTCGAGGGGATA-
1 TTTC-AAAACATCGATTTTCT-ACAATCAGGGATACTCCAACCCT-ATTATTTTCGAGGGGATAT
27026 CTCTAACCCCGATTTTAT
63 CTC-AACCCCGATTTTAT
** * *
27044 TTTCAAAATTTCGATTTTCTATAATCAGGGATACTCCAACCCTATTATTTTCGAGGGGATATTTC
1 TTTCAAAACATCGATTTTCTACAATCAGGGATACTCCAACCCTATTATTTTCGAGGGGATATCTC
*
27109 AACCCCGGTTTTAT
66 AACCCCGATTTTAT
* * * *
27123 TTTCAGAACA-CTGATTTTCCATAATCGGGGATACTC
1 TTTCAAAACATC-GATTTTCTACAATCAGGGATACTC
27159 TAGCCCTGTT
Statistics
Matches: 97, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
78 1 0.01
79 86 0.89
80 10 0.10
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (79 bp):
TTTCAAAACATCGATTTTCTACAATCAGGGATACTCCAACCCTATTATTTTCGAGGGGATATCTC
AACCCCGATTTTAT
Found at i:31389 original size:79 final size:79
Alignment explanation
Indices: 31273--31419 Score: 213
Period size: 79 Copynumber: 1.9 Consensus size: 79
31263 CCAATTATGA
* * *
31273 AAAATCAATGTTCTGAAAATAAAATCGGGGTTAGAGTATCCCCTCTAAAAAAATAGGGTTGGAGT
1 AAAATCAATGTTCTGAAAATAAAATCAGGGTTAGAGTATCCCCTCGAAAAAAATAGGGCTGGAGT
31338 ATCTTTGATTATAG
66 ATCTTTGATTATAG
* * * * * *
31352 AAAATCGATGTTTTGAAAATAAAATCAGGGTTGGAGTATCCTCTCGAAAATAATGGGGCTGGAGT
1 AAAATCAATGTTCTGAAAATAAAATCAGGGTTAGAGTATCCCCTCGAAAAAAATAGGGCTGGAGT
31417 ATC
66 ATC
31420 CCCGATGAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
79 59 1.00
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (79 bp):
AAAATCAATGTTCTGAAAATAAAATCAGGGTTAGAGTATCCCCTCGAAAAAAATAGGGCTGGAGT
ATCTTTGATTATAG
Found at i:31453 original size:28 final size:30
Alignment explanation
Indices: 31379--31453 Score: 95
Period size: 28 Copynumber: 2.6 Consensus size: 30
31369 AATAAAATCA
*
31379 GGGTTGGAGTATCCTC--TCGAAAATAATG
1 GGGTTGGAGTATCCTCGATCGAAAATAACG
* *
31407 GGGCTGGAGTATCCCCGAT-GAAAA-AACG
1 GGGTTGGAGTATCCTCGATCGAAAATAACG
31435 GGGTTGGAGTATCCTCGAT
1 GGGTTGGAGTATCCTCGAT
31454 TGTGAAAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
28 34 0.85
29 5 0.12
30 1 0.03
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (30 bp):
GGGTTGGAGTATCCTCGATCGAAAATAACG
Found at i:31500 original size:52 final size:52
Alignment explanation
Indices: 31427--31534 Score: 146
Period size: 52 Copynumber: 2.1 Consensus size: 52
31417 ATCCCCGATG
* * *
31427 AAAAAACGGGGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTT-GAAAA
1 AAAAAACGGAGTTGGAATATCCCCGATTGTGAAAAATTGGTATTTTAGAAAA
* * *
31478 AAAAAATCGGAGTTGGAATATCCCCGATTGTGGAAAATTGGTGTTTTAGAAAT
1 AAAAAA-CGGAGTTGGAATATCCCCGATTGTGAAAAATTGGTATTTTAGAAAA
31531 AAAA
1 AAAA
31535 CCGGGGTTGG
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
51 6 0.12
52 35 0.71
53 8 0.16
ACGTcount: A:0.39, C:0.08, G:0.24, T:0.29
Consensus pattern (52 bp):
AAAAAACGGAGTTGGAATATCCCCGATTGTGAAAAATTGGTATTTTAGAAAA
Found at i:34023 original size:25 final size:25
Alignment explanation
Indices: 33989--34039 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
33979 GAATGTATTG
* *
33989 ATACAATGAATAATGTATCGATACA
1 ATACAATGAACAATGCATCGATACA
34014 ATACAATGAACAATGCATCGATACA
1 ATACAATGAACAATGCATCGATACA
34039 A
1 A
34040 ATTGTGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.49, C:0.16, G:0.12, T:0.24
Consensus pattern (25 bp):
ATACAATGAACAATGCATCGATACA
Found at i:36587 original size:23 final size:23
Alignment explanation
Indices: 36546--36589 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
36536 GAATTTTTAT
36546 TATTTTATAAATTTTTAAATATA
1 TATTTTATAAATTTTTAAATATA
*
36569 TATTTT-TATATTTTATAAATA
1 TATTTTATAAATTTT-TAAATA
36590 AATACAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
TATTTTATAAATTTTTAAATATA
Found at i:36982 original size:21 final size:21
Alignment explanation
Indices: 36956--37011 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 21
36946 ACACTAATTC
36956 AATTAATAAAATTATAAAAAA
1 AATTAATAAAATTATAAAAAA
*
36977 AATTAA-AATAATGTTATAAAAAT
1 AATTAATAA-AA--TTATAAAAAA
37000 AA--AATAAAATTA
1 AATTAATAAAATTA
37012 CAAATATGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 10
0.73 0.02 0.24
Matches are distributed among these distances:
19 3 0.10
20 2 0.07
21 12 0.40
22 2 0.07
23 11 0.37
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (21 bp):
AATTAATAAAATTATAAAAAA
Found at i:37280 original size:2 final size:2
Alignment explanation
Indices: 37269--37303 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
37259 ATTAGTAGTG
37269 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
37304 CAAATCAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:38735 original size:21 final size:19
Alignment explanation
Indices: 38687--38742 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
38677 TGCAGGGTAG
38687 TTTTGTATCGATACAACAC
1 TTTTGTATCGATACAACAC
* **
38706 TTATGTATCGATACATTTAC
1 TTTTGTATCGATACA-ACAC
38726 TGTTTGTATCGATACAA
1 T-TTTGTATCGATACAA
38743 ATTGTTGAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 14 0.47
20 3 0.10
21 13 0.43
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.41
Consensus pattern (19 bp):
TTTTGTATCGATACAACAC
Done.