Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3406
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: 40709
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:125 original size:14 final size:13
Alignment explanation
Indices: 83--126 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
73 CCCATAATCT
83 TTCTCATCTTCTTC
1 TTCTC-TCTTCTTC
*
97 TTCTCTCTATATTC
1 TTCTCTCT-TCTTC
111 TTCTCTTCTTCTTC
1 TTCTC-TCTTCTTC
125 TT
1 TT
127 TCCTCATATC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
13 3 0.12
14 20 0.77
15 3 0.12
ACGTcount: A:0.07, C:0.32, G:0.00, T:0.61
Consensus pattern (13 bp):
TTCTCTCTTCTTC
Found at i:143 original size:28 final size:26
Alignment explanation
Indices: 84--146 Score: 74
Period size: 25 Copynumber: 2.3 Consensus size: 26
74 CCATAATCTT
*
84 TCTCATCTTCTTCTTCTCTCTATATTC
1 TCTC-TCTTCTTCTTCTCTCTATATCC
*
111 T-TCTCTTCTTCTTCTTTCCTCATATCC
1 TCTCTCTTCTTCTTCTCT-CT-ATATCC
138 TCTCTCTTC
1 TCTCTCTTC
147 AACTTCCATT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
25 13 0.42
26 4 0.13
27 7 0.23
28 7 0.23
ACGTcount: A:0.08, C:0.37, G:0.00, T:0.56
Consensus pattern (26 bp):
TCTCTCTTCTTCTTCTCTCTATATCC
Found at i:145 original size:25 final size:28
Alignment explanation
Indices: 84--146 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 28
74 CCATAATCTT
*
84 TCTCATCTTCTTCTTCTCTCTATATTCT
1 TCTCATCTTCTTCTTCTCTCTATATTCC
*
112 TCTCTTCTTCTTCTT-TC-CTCATA-TCC
1 TCTCATCTTCTTCTTCTCTCT-ATATTCC
138 TCTC-TCTTC
1 TCTCATCTTC
147 AACTTCCATT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
25 5 0.16
26 8 0.25
27 5 0.16
28 14 0.44
ACGTcount: A:0.08, C:0.37, G:0.00, T:0.56
Consensus pattern (28 bp):
TCTCATCTTCTTCTTCTCTCTATATTCC
Found at i:7176 original size:27 final size:27
Alignment explanation
Indices: 7145--7251 Score: 117
Period size: 27 Copynumber: 4.0 Consensus size: 27
7135 AATCTCATAT
* * *
7145 CTGTAGGCTAGTATTATTGAAATACCC
1 CTGTAGGGTAGAATTACTGAAATACCC
* * * *
7172 TTGTAGGGTA-AGTTACTAAAATGCCC
1 CTGTAGGGTAGAATTACTGAAATACCC
* * *
7198 CTGTAGGATTGAATTACTGAAATGCCC
1 CTGTAGGGTAGAATTACTGAAATACCC
7225 CTGTAGGGTAGAATTACTGAAATACCC
1 CTGTAGGGTAGAATTACTGAAATACCC
7252 TTAGTTTACA
Statistics
Matches: 64, Mismatches: 15, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
26 18 0.28
27 46 0.72
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (27 bp):
CTGTAGGGTAGAATTACTGAAATACCC
Found at i:7274 original size:26 final size:27
Alignment explanation
Indices: 7236--7556 Score: 117
Period size: 27 Copynumber: 11.9 Consensus size: 27
7226 TGTAGGGTAG
7236 AATTACTGAAATACCCTTAGTTTACAA
1 AATTACTGAAATACCCTTAGTTTACAA
* *
7263 AATTGCTG-AATACCCTTTGTTTACAA
1 AATTACTGAAATACCCTTAGTTTACAA
** * * *
7289 AATTACCAAAATACCC-TCGATTAGTAA
1 AATTACTGAAATACCCTTAGTTTA-CAA
** * ***
7316 AATTACCAAAATACCCCT-GATTTGTGA
1 AATTACTGAAATACCCTTAG-TTTACAA
* * *
7343 AATTATTGAAATACCTTTGACTTGT--AA
1 AATTACTGAAATACCCTT-AGTT-TACAA
* * *
7370 AATTACTGAAATA-CCTTCGAATTATAA
1 AATTACTGAAATACCCTTAG-TTTACAA
** * * **
7397 AATTTTTGAAATATCCTTAATTTGTAA
1 AATTACTGAAATACCCTTAGTTTACAA
** * **
7424 AATTACCAAAATACCCCCT-GATTTGGAA
1 AATTACTGAAATA-CCCTTAG-TTTACAA
* *
7452 AATTACAGAAATACCATT-GATTTACAA
1 AATTACTGAAATACCCTTAG-TTTACAA
*
7479 AATTA-TAGAAATACCCTTGACTTT-CAAA
1 AATTACT-GAAATACCCTT-AGTTTAC-AA
* *
7507 AATTA-TAGAAATACCCTTGGTTTGCAA
1 AATTACT-GAAATACCCTTAGTTTACAA
*
7534 AATTA-TCGAAATACCCTTGGTTT
1 AATTACT-GAAATACCCTTAGTTT
7557 GTAGATTTTC
Statistics
Matches: 227, Mismatches: 49, Indels: 36
0.73 0.16 0.12
Matches are distributed among these distances:
25 1 0.00
26 31 0.14
27 141 0.62
28 53 0.23
29 1 0.00
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.34
Consensus pattern (27 bp):
AATTACTGAAATACCCTTAGTTTACAA
Found at i:7481 original size:55 final size:55
Alignment explanation
Indices: 7422--7549 Score: 134
Period size: 55 Copynumber: 2.3 Consensus size: 55
7412 CTTAATTTGT
**
7422 AAAATTACCAAAATACCCCCTGA-TTTGGAAAATTACAGAAATACCATTGATTTAC
1 AAAATTA-CAAAATACCCCCTGACTTTCAAAAATTACAGAAATACCATTGATTTAC
* * * * * *
7477 AAAATTATAGAAATA-CCCTTGACTTTCAAAAATTATAGAAATACCCTTGGTTTGC
1 AAAATTACA-AAATACCCCCTGACTTTCAAAAATTACAGAAATACCATTGATTTAC
*
7532 AAAATTATCGAAATACCC
1 AAAATTA-CAAAATACCC
7550 TTGGTTTGTA
Statistics
Matches: 59, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
54 7 0.12
55 50 0.85
56 2 0.03
ACGTcount: A:0.43, C:0.19, G:0.09, T:0.29
Consensus pattern (55 bp):
AAAATTACAAAATACCCCCTGACTTTCAAAAATTACAGAAATACCATTGATTTAC
Found at i:7536 original size:82 final size:80
Alignment explanation
Indices: 7342--7548 Score: 193
Period size: 82 Copynumber: 2.5 Consensus size: 80
7332 CTGATTTGTG
* * * * * * *
7342 AAATTATTGAAATACCTTTGACTTGTAAAATTACTGAAATACCTTCGAATTATAAAATTTTTGAA
1 AAATTATAGAAATACCCTTGATTTGCAAAATTAC-GAAATACCTTCGAATTACAAAATTATAGAA
* **
7407 ATATCCTTAATTTGTA
65 ATACCCTTAATTTCAA
* * * *
7423 AAATTACCA-AAATACCCCCTGATTTGGAAAATTACAGAAATACCATT-GATTTACAAAATTATA
1 AAATTA-TAGAAATA-CCCTTGATTTGCAAAATTAC-GAAATACC-TTCGAATTACAAAATTATA
*
7486 GAAATACCCTTGACTTTCAA
62 GAAATACCCTT-AATTTCAA
*
7506 AAATTATAGAAATACCCTTGGTTTGCAAAATTATCGAAATACC
1 AAATTATAGAAATACCCTTGATTTGCAAAATTA-CGAAATACC
7549 CTTGGTTTGT
Statistics
Matches: 101, Mismatches: 19, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
81 11 0.11
82 71 0.70
83 19 0.19
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.34
Consensus pattern (80 bp):
AAATTATAGAAATACCCTTGATTTGCAAAATTACGAAATACCTTCGAATTACAAAATTATAGAAA
TACCCTTAATTTCAA
Found at i:7557 original size:27 final size:27
Alignment explanation
Indices: 7271--7557 Score: 179
Period size: 27 Copynumber: 10.6 Consensus size: 27
7261 AAAATTGCTG
* * *
7271 AATACCCTTTG-TTTACAAAATTACCAA
1 AATACCC-TTGATTTGCAAAATTATCGA
* * * * *
7298 AATACCCTCGATTAGTAAAATTACCAA
1 AATACCCTTGATTTGCAAAATTATCGA
* ** *
7325 AATACCCCTGATTTGTGAAATTATTGA
1 AATACCCTTGATTTGCAAAATTATCGA
* * *
7352 AATACCTTTGACTTGTAAAATTA-CTGA
1 AATACCCTTGATTTGCAAAATTATC-GA
* ** * *
7379 AATA-CCTTCGAATTATAAAATTTTTGA
1 AATACCCTT-GATTTGCAAAATTATCGA
* * * * *
7406 AATATCCTTAATTTGTAAAATTACCAA
1 AATACCCTTGATTTGCAAAATTATCGA
* *
7433 AATACCCCCTGATTTGGAAAATTA-CAGA
1 AATA-CCCTTGATTTGCAAAATTATC-GA
* * *
7461 AATACCATTGATTTACAAAATTATAGA
1 AATACCCTTGATTTGCAAAATTATCGA
*
7488 AATACCCTTGACTTT-CAAAAATTATAGA
1 AATACCCTTGA-TTTGC-AAAATTATCGA
*
7516 AATACCCTTGGTTTGCAAAATTATCGA
1 AATACCCTTGATTTGCAAAATTATCGA
*
7543 AATACCCTTGGTTTG
1 AATACCCTTGATTTG
7558 TAGATTTTCG
Statistics
Matches: 208, Mismatches: 41, Indels: 22
0.77 0.15 0.08
Matches are distributed among these distances:
26 5 0.02
27 154 0.74
28 49 0.24
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.34
Consensus pattern (27 bp):
AATACCCTTGATTTGCAAAATTATCGA
Found at i:7576 original size:27 final size:27
Alignment explanation
Indices: 7445--7579 Score: 87
Period size: 27 Copynumber: 5.0 Consensus size: 27
7435 TACCCCCTGA
* * * *
7445 TTTGGAAAATTA-CAGAAATACCATTGA
1 TTTGCAAAATTATC-GAAACACCCTTGG
* * * *
7472 TTTACAAAATTATAGAAATACCCTTGAC
1 TTTGCAAAATTATCGAAACACCCTTG-G
* *
7500 TTT-CAAAAATTATAGAAATACCCTTGG
1 TTTGC-AAAATTATCGAAACACCCTTGG
*
7527 TTTGCAAAATTATCGAAATACCCTTGG
1 TTTGCAAAATTATCGAAACACCCTTGG
* * *
7554 TTTG-TAGATTTTCGAAAACACCCTTG
1 TTTGCAAAATTATCG-AAACACCCTTG
7580 TAGGGTGAAA
Statistics
Matches: 92, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
26 7 0.08
27 60 0.65
28 25 0.27
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (27 bp):
TTTGCAAAATTATCGAAACACCCTTGG
Found at i:7864 original size:41 final size:41
Alignment explanation
Indices: 7817--7937 Score: 197
Period size: 41 Copynumber: 3.0 Consensus size: 41
7807 GGAGGAAGAA
7817 ATTGAGGATCACATGGTTGCTTGACGACCGTGGATCCACCG
1 ATTGAGGATCACATGGTTGCTTGACGACCGTGGATCCACCG
** * *
7858 ATTGAGGATTGCATGGTTTCTTGACGACCGTGGATCCATCG
1 ATTGAGGATCACATGGTTGCTTGACGACCGTGGATCCACCG
*
7899 ATTAAGGATCACATGGTTGCTTGACGACCGTGGATCCAC
1 ATTGAGGATCACATGGTTGCTTGACGACCGTGGATCCAC
7938 TGATGGCTTT
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 71 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.27
Consensus pattern (41 bp):
ATTGAGGATCACATGGTTGCTTGACGACCGTGGATCCACCG
Found at i:10065 original size:15 final size:16
Alignment explanation
Indices: 10045--10075 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
10035 TTTAACTAAG
10045 TAAAAT-AAAATAAAA
1 TAAAATAAAAATAAAA
10060 TAAAATAAAAATAAAA
1 TAAAATAAAAATAAAA
10076 GTTCCAATGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (16 bp):
TAAAATAAAAATAAAA
Found at i:10072 original size:6 final size:5
Alignment explanation
Indices: 10045--10075 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
10035 TTTAACTAAG
10045 TAAAA TAAAA TAAAA TAAAA TAAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA T-AAAA TAAAA
10076 GTTCCAATGC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
TAAAA
Found at i:12428 original size:39 final size:39
Alignment explanation
Indices: 12374--12452 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
12364 TTTATGACAA
12374 CTTAAAGATAATTAAGAGAAAAGTGATGGCTAAAAATTG
1 CTTAAAGATAATTAAGAGAAAAGTGATGGCTAAAAATTG
12413 CTTAAAGATAATTAAGAGAAAAGTGATGGCTAAAAATTG
1 CTTAAAGATAATTAAGAGAAAAGTGATGGCTAAAAATTG
12452 C
1 C
12453 AAAGGTTCAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.48, C:0.06, G:0.20, T:0.25
Consensus pattern (39 bp):
CTTAAAGATAATTAAGAGAAAAGTGATGGCTAAAAATTG
Found at i:16057 original size:40 final size:40
Alignment explanation
Indices: 16002--16176 Score: 287
Period size: 40 Copynumber: 4.4 Consensus size: 40
15992 TATGTGCATA
*
16002 GCATTCGTGCAGGTTATTATAACCGGGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
*
16042 GCATTCGTGCGGGTTATTATAACTGGGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
* * * *
16082 GCATCCGTGTGGGTTATTATAACCGGGTTAAGTTCCAAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
16122 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
*
16162 GCATTCGTGCTGGTT
1 GCATTCGTGCGGGTT
16177 GTTACATCCG
Statistics
Matches: 123, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 123 1.00
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.30
Consensus pattern (40 bp):
GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
Found at i:24573 original size:40 final size:40
Alignment explanation
Indices: 24513--24727 Score: 376
Period size: 40 Copynumber: 5.4 Consensus size: 40
24503 TATGTGCATA
*
24513 GCATTCGTGCGGGTTTTTATAACCGGGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
* *
24553 GCATTCGTGCGGGTTATTATAATCGAGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
*
24593 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCAAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
24633 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
*
24673 GCATTCGTGCTGGTTATTATAACCGGGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
*
24713 GCATTCGTGCTGGTT
1 GCATTCGTGCGGGTT
24728 GTTACATCCG
Statistics
Matches: 167, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 167 1.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.30
Consensus pattern (40 bp):
GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
Found at i:25495 original size:21 final size:21
Alignment explanation
Indices: 25439--25496 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
25429 ATATTGTTAT
* *
25439 ACATGATATGAC-ATAATATGC
1 ACATGATATG-CTATGAGATGC
*
25460 ACATGATACT-TTATGAGATGC
1 ACATGATA-TGCTATGAGATGC
25481 ACATGATATGCTATGA
1 ACATGATATGCTATGA
25497 TATACTCATT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
20 1 0.03
21 28 0.93
22 1 0.03
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (21 bp):
ACATGATATGCTATGAGATGC
Found at i:25579 original size:25 final size:25
Alignment explanation
Indices: 25545--25616 Score: 117
Period size: 25 Copynumber: 2.9 Consensus size: 25
25535 GGAGGAAGTG
*
25545 CGAAAAGGGCATTGCCTCAGTTTAC
1 CGAAAAGGGCATTGCCCCAGTTTAC
25570 CGAAAAGGGCATTGCCCCAGTTTAC
1 CGAAAAGGGCATTGCCCCAGTTTAC
* *
25595 CAAAAAGGGCTTTGCCCCAGTT
1 CGAAAAGGGCATTGCCCCAGTT
25617 ATTAAAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 44 1.00
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (25 bp):
CGAAAAGGGCATTGCCCCAGTTTAC
Found at i:28267 original size:62 final size:62
Alignment explanation
Indices: 28166--28290 Score: 196
Period size: 62 Copynumber: 2.0 Consensus size: 62
28156 CAGGTTCATC
* * * * *
28166 TTTTACATGCCTGTTGAACCATTTTGAATAATATTATATACACGGAAAGCTTACACTTAGTG
1 TTTTACATGCCCGTTGAACCATTTAGAATAATATCATATACACGGAAAGCTCACACCTAGTG
*
28228 TTTTACATGCCCGTTGAACCATTTAGAATAATATCATATACACGGGAAGCTCACACCTAGTG
1 TTTTACATGCCCGTTGAACCATTTAGAATAATATCATATACACGGAAAGCTCACACCTAGTG
28290 T
1 T
28291 GCTAACATAT
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
62 57 1.00
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (62 bp):
TTTTACATGCCCGTTGAACCATTTAGAATAATATCATATACACGGAAAGCTCACACCTAGTG
Found at i:32493 original size:29 final size:29
Alignment explanation
Indices: 32461--32519 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 29
32451 TAAAAGCTAC
32461 ATGAATG-CATG-AAATAGATAAAAATCAAA
1 ATGAATGACATGAAAATAG--AAAAATCAAA
32490 ATGAATGATCATGAAAATAGAAAAATCAAA
1 ATGAATGA-CATGAAAATAGAAAAATCAAA
32520 GCTTGTAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
29 7 0.26
30 10 0.37
31 4 0.15
32 6 0.22
ACGTcount: A:0.59, C:0.07, G:0.14, T:0.20
Consensus pattern (29 bp):
ATGAATGACATGAAAATAGAAAAATCAAA
Found at i:33426 original size:38 final size:38
Alignment explanation
Indices: 33384--33461 Score: 120
Period size: 38 Copynumber: 2.1 Consensus size: 38
33374 TATGTTTGGA
*
33384 TCATTTCTAATTCTCTCCATTTCCCTTAACAATTTTCT
1 TCATTTCTAATCCTCTCCATTTCCCTTAACAATTTTCT
* **
33422 TCATTTCTAATCCTCTCCATTTCCTTTAACTCTTTTCT
1 TCATTTCTAATCCTCTCCATTTCCCTTAACAATTTTCT
33460 TC
1 TC
33462 TCTGCATTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.18, C:0.31, G:0.00, T:0.51
Consensus pattern (38 bp):
TCATTTCTAATCCTCTCCATTTCCCTTAACAATTTTCT
Found at i:34766 original size:19 final size:19
Alignment explanation
Indices: 34721--34767 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
34711 TAAATATTAA
*
34721 AATAAAAATAAAAATATAG
1 AATAAAAATAAAAATAAAG
* *
34740 AATCAAAACT-AAAATAAAT
1 AAT-AAAAATAAAAATAAAG
34759 AATAAAAAT
1 AATAAAAAT
34768 TAGATTAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 5 0.22
19 13 0.57
20 5 0.22
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.21
Consensus pattern (19 bp):
AATAAAAATAAAAATAAAG
Found at i:35981 original size:28 final size:28
Alignment explanation
Indices: 35941--35997 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
35931 ATTGTTCAAG
35941 ATTGTTCAAGATTGGAGACAGATGTCTT
1 ATTGTTCAAGATTGGAGACAGATGTCTT
35969 ATTGTTCAAGATTGGAGACAGATGTCTT
1 ATTGTTCAAGATTGGAGACAGATGTCTT
35997 A
1 A
35998 ATTCTGAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.30, C:0.11, G:0.25, T:0.35
Consensus pattern (28 bp):
ATTGTTCAAGATTGGAGACAGATGTCTT
Found at i:40171 original size:27 final size:26
Alignment explanation
Indices: 40141--40223 Score: 82
Period size: 27 Copynumber: 3.2 Consensus size: 26
40131 TTTTTATTAG
40141 TTATTTTATTTATTTATATATATTTCA
1 TTATTTTATTTATTT-TATATATTTCA
*
40168 TTATATTATTTATTTGTATAT-TTT-A
1 TTATTTTATTTATTT-TATATATTTCA
**
40193 TCTA-TAAATTATATTTTATATATTTCA
1 T-TATTTTATT-TATTTTATATATTTCA
40220 TTAT
1 TTAT
40224 ATATTTCCTT
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
25 10 0.22
26 15 0.33
27 21 0.46
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64
Consensus pattern (26 bp):
TTATTTTATTTATTTTATATATTTCA
Found at i:40225 original size:12 final size:12
Alignment explanation
Indices: 40157--40242 Score: 59
Period size: 12 Copynumber: 6.8 Consensus size: 12
40147 TATTTATTTA
40157 TATATATTTCAT
1 TATATATTTCAT
40169 TATATTATTT-ATT
1 TATA-TATTTCA-T
* *
40182 TGTATATTTTAT
1 TATATATTTCAT
*
40194 CTATAAATTAT-ATTT
1 -TATATATT-TCA--T
40209 TATATATTTCAT
1 TATATATTTCAT
*
40221 TATATATTTCCT
1 TATATATTTCAT
40233 TATATTATTT
1 TATA-TATTT
40243 TTGTGTATCA
Statistics
Matches: 60, Mismatches: 5, Indels: 17
0.73 0.06 0.21
Matches are distributed among these distances:
12 27 0.45
13 23 0.38
14 9 0.15
15 1 0.02
ACGTcount: A:0.31, C:0.06, G:0.01, T:0.62
Consensus pattern (12 bp):
TATATATTTCAT
Found at i:40537 original size:19 final size:20
Alignment explanation
Indices: 40473--40538 Score: 64
Period size: 22 Copynumber: 3.2 Consensus size: 20
40463 ATAATAAAAT
*
40473 TTATATTATTA-TATATTACA
1 TTATTTTATTATTA-ATTACA
*
40493 TCTATTTTATTATAAAATATACA
1 T-TATTTTATTAT-TAAT-TACA
40516 TTATTTTATTATTAATTA-A
1 TTATTTTATTATTAATTACA
40535 TTAT
1 TTAT
40539 GTACATTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
19 5 0.13
20 3 0.08
21 12 0.31
22 13 0.33
23 6 0.15
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (20 bp):
TTATTTTATTATTAATTACA
Done.