Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1950
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: 25841
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:66 original size:21 final size:21
Alignment explanation
Indices: 34--73 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
24 AATACTTAAT
*
34 TTAAGTTCGGGTTATTTCGGG
1 TTAAGTTCGGGTCATTTCGGG
55 TTAATGTT-GGGTCATTTCG
1 TTAA-GTTCGGGTCATTTCG
74 AGTTCGAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.15, C:0.10, G:0.30, T:0.45
Consensus pattern (21 bp):
TTAAGTTCGGGTCATTTCGGG
Found at i:111 original size:32 final size:33
Alignment explanation
Indices: 75--148 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 33
65 GTCATTTCGA
*
75 GTTCGAATCATTTTTGAGTTT-AGGTA-TTTCAG
1 GTTCGAATCA-TTTCGAGTTTGAGGTATTTTCAG
* * *
107 GTTCGAGTCATTTCGAGTTTGAGTTATTTTTAG
1 GTTCGAATCATTTCGAGTTTGAGGTATTTTCAG
140 GTTCGAATC
1 GTTCGAATC
149 GATCGGTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
31 9 0.26
32 13 0.37
33 13 0.37
ACGTcount: A:0.20, C:0.11, G:0.23, T:0.46
Consensus pattern (33 bp):
GTTCGAATCATTTCGAGTTTGAGGTATTTTCAG
Found at i:657 original size:15 final size:15
Alignment explanation
Indices: 632--669 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
622 TAAACTCAAG
*
632 AAAAGTTTACAAAAA
1 AAAACTTTACAAAAA
*
647 AAGACTTTACAAAAA
1 AAAACTTTACAAAAA
662 AAAACTTT
1 AAAACTTT
670 GTATTTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.61, C:0.11, G:0.05, T:0.24
Consensus pattern (15 bp):
AAAACTTTACAAAAA
Found at i:986 original size:11 final size:10
Alignment explanation
Indices: 967--992 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
957 AAATTTTACA
967 AAAAATTTTT
1 AAAAATTTTT
977 AAAAATTTTT
1 AAAAATTTTT
987 AAAAAT
1 AAAAAT
993 AAAAAATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
AAAAATTTTT
Found at i:1062 original size:13 final size:14
Alignment explanation
Indices: 1039--1069 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
1029 TTTTAAATTT
1039 TTTTAAAAAAAATA
1 TTTTAAAAAAAATA
1053 TTTT-AAAAAAATA
1 TTTTAAAAAAAATA
1066 TTTT
1 TTTT
1070 TTTCAATGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 13 0.76
14 4 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TTTTAAAAAAAATA
Found at i:1070 original size:14 final size:14
Alignment explanation
Indices: 1033--1070 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
1023 ATTAAATTTT
*
1033 AAATTTTTTTAAAA
1 AAATATTTTTAAAA
1047 AAA-ATATTTTAAAA
1 AAATAT-TTTTAAAA
1061 AAATATTTTT
1 AAATATTTTT
1071 TTCAATGTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 1 0.05
14 18 0.86
15 2 0.10
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
AAATATTTTTAAAA
Found at i:1519 original size:3 final size:3
Alignment explanation
Indices: 1511--1551 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1501 ATAAATGCAA
1511 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1552 AGTTTGAGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3432 original size:1 final size:1
Alignment explanation
Indices: 3426--3451 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
3416 GAACTCTTCC
3426 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
3452 CAAAGAACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:3897 original size:23 final size:23
Alignment explanation
Indices: 3866--3911 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
3856 ATACTTATTT
*
3866 ATTTGATATTTAAAAATTTAAAA
1 ATTTAATATTTAAAAATTTAAAA
* *
3889 ATTTAATATTTATAATTTTAAAA
1 ATTTAATATTTAAAAATTTAAAA
3912 TTTTTATGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
ATTTAATATTTAAAAATTTAAAA
Found at i:6372 original size:15 final size:16
Alignment explanation
Indices: 6349--6379 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
6339 AGGAAATCTC
6349 ATTCTAACTCTATCAT
1 ATTCTAACTCTATCAT
6365 ATTC-AACTCTATCAT
1 ATTCTAACTCTATCAT
6380 TGATTTCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.32, C:0.26, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTCTAACTCTATCAT
Found at i:7455 original size:58 final size:58
Alignment explanation
Indices: 7256--7459 Score: 182
Period size: 58 Copynumber: 3.5 Consensus size: 58
7246 TAATTATCTC
* * * * * * * *
7256 TAAAATACATTAAATCGCATAAAAGTCTTCAGATCATAG-AAATGACCTAAATGATAT
1 TAAAATTCATAAAATTGCATAAAAGTCTTTAGACCATGGAAAATGATCTAAATGACAT
* * * * *
7313 TAACATTCATAAAATTGTATCAAAA-TCCTTAG-CTCATGAAAAATGATCTACATGACAT
1 TAAAATTCATAAAATTGCAT-AAAAGTCTTTAGAC-CATGGAAAATGATCTAAATGACAT
** * ***
7371 CGATATTCATAAAATTGCACCCAAGTCTTTAGACCATGGAAAATGATCTAAATGACAT
1 TAAAATTCATAAAATTGCATAAAAGTCTTTAGACCATGGAAAATGATCTAAATGACAT
7429 TAAAATTCATAAAA-TGACATAAAAGTCTTTA
1 TAAAATTCATAAAATTG-CATAAAAGTCTTTA
7460 AGTCATGAAA
Statistics
Matches: 112, Mismatches: 29, Indels: 11
0.74 0.19 0.07
Matches are distributed among these distances:
57 27 0.24
58 84 0.75
59 1 0.01
ACGTcount: A:0.45, C:0.16, G:0.10, T:0.29
Consensus pattern (58 bp):
TAAAATTCATAAAATTGCATAAAAGTCTTTAGACCATGGAAAATGATCTAAATGACAT
Found at i:9946 original size:617 final size:617
Alignment explanation
Indices: 8764--10002 Score: 1865
Period size: 617 Copynumber: 2.0 Consensus size: 617
8754 TATGTTTTAA
* **
8764 TGTAAAAATGTTTGTTAAGGACCTCTTGTATGGTTATAAAGTAATCCAAGGTCATTAGGAAGGTG
1 TGTAAAAATGTTTGTTAAGGACCTCTTGTATGATTATAAAGTAATCCAAGGTCATTAAAAAGGTG
* * *
8829 AAATTGAGAAAACTTGGGTAAAAAGCTTAATTCTTGGTGAAAAATTCTATGTAGTATCAATATAT
66 AAATTGAGAAAACTTGGGTAAAAAGCTTAATTCATGGTGAAAAATTCTATGCAATATCAATATAT
* * * * * * * * *
8894 TGGTATTTGTGTCGATATAAGTTATTCCTAGAACCAAATAATCTAGAAATTTTGAATTTGCGAGT
131 TGGTATTTATGTCAATAGAAGTGATTCCTAGAACAAAAAAATATAGAAATTTTGAATTTACGACT
* *
8959 TTCGAGAATATCCCTATTCATAGGTTTGAGATCCATATCTATGAATTAAAAGGTCTGAATGATCA
196 TTCAAAAATATCCCTATTCATAGGTTTGAGATCCATATCTATGAATTAAAAGGTCTGAATGATCA
* * *
9024 ACTTTGTAATTAGTTGTTAGAATTAATAGGTTTTTAAATCATTCATTTGAAAAAATTCAAACCTT
261 ACTTTGCAATTAGTTGTTAAAATTAATAGGTCTTTAAATCATTCATTTGAAAAAATTCAAACCTT
* * ** *
9089 CTTACTATATTATCATAATACTTCTCAAAAATAAAAAATTTTGATCTATGGAGGAAGAATAACAT
326 CTTACTAGATTATCATAATACTTCTCAAAAATAAAAAATTTTGATCAATAAAGGAAGAATAACAC
* * * *
9154 TATTTTTTTTCAATAAAATACCAAAGTGGATGATTAACTCATTCCATACTAGAAATAATCATAGG
391 TATTTTTGTTCAATAAAATACCAAAATGGATGATTAACTCATTCCATACTAGAAATAATCACAAG
* * *
9219 ATATCTTTTGATAACACAGATCCCTGTTTCTCAATGATATCCCACGATTAAGACAATTGCCTGAA
456 ATATCTTTTGATAACACAGATCCCTATTTATCAATGATATCCCACGATTAAGACAATTGCCTAAA
9284 TCCCGTGAAACCATTTCATAGAAGTTCATTGATAACTTCTTTTTATAAAGCAAATTGATTTTGAT
521 TCCCGTGAAACCATTTCATAGAAGTTCATTGATAACTTCTTTTTATAAAGCAAATTGATTTTGAT
*
9349 TCTTGAATAATCCATATCACTTCTACTTCTAT
586 TCTTGAATAATCCACATCACTTCTACTTCTAT
9381 TGTAAAAATGTTTGTTAAGGACCTCTTGTATGATTATAAAAGTAATCCAAGGTCATTAAAAAGGT
1 TGTAAAAATGTTTGTTAAGGACCTCTTGTATGATTAT-AAAGTAATCCAAGGTCATTAAAAAGGT
* * *
9446 GAAATGTGAGAAAATTTGGGTGAAAAAG-TTTATTCATGGTGAAAAATTCTATGCAATATCGATA
65 GAAAT-TGAGAAAACTTGGGT-AAAAAGCTTAATTCATGGTGAAAAATTCTATGCAATATCAATA
* * * *
9510 TATTGGTATTTATGTCAATAGCAGTGCTTCTTAGAACAAAAAAATATAGAAATTTTGAATTTATG
128 TATTGGTATTTATGTCAATAGAAGTGATTCCTAGAACAAAAAAATATAGAAATTTTGAATTTACG
* * *
9575 ACTTTCAAAAATATCCTTATTCATATGTTTGAGATCCATATCTATGAATTGAAAGGTCTGAATGA
193 ACTTTCAAAAATATCCCTATTCATAGGTTTGAGATCCATATCTATGAATTAAAAGGTCTGAATGA
* *
9640 TCAACTTTGCAATTAGTTGTTAAAATTAATAGGTCTTTAAGTCATTCATTTGAAAAAATTGAAAC
258 TCAACTTTGCAATTAGTTGTTAAAATTAATAGGTCTTTAAATCATTCATTTGAAAAAATTCAAAC
* * * * *
9705 CTTCTTATTGGATTATCATATTACTT-TTAAAAAT-AAAAATTTTGATCAATAAAGGAAGAATAT
323 CTTCTTACTAGATTATCATAATACTTCTCAAAAATAAAAAATTTTGATCAATAAAGGAAGAATAA
* * *
9768 CACTATTTTTGTTCAATAAGATACCAAAATGGATGATTGACTTATTCCATGA-TAGAAATAATCA
388 CACTATTTTTGTTCAATAAAATACCAAAATGGATGATTAACTCATTCCAT-ACTAGAAATAATCA
* * * *
9832 CAAGATATCTTTTGATAACACAGATTCCTATTTATTAATGATATCCCATGATTAAGACAATTGTC
452 CAAGATATCTTTTGATAACACAGATCCCTATTTATCAATGATATCCCACGATTAAGACAATTGCC
* * *
9897 TAAATCCTGTGAAACCATTTCATAGAAGTTCATTGATAATTTTTTTTTATAAAGCAAATTGATTT
517 TAAATCCCGTGAAACCATTTCATAGAAGTTCATTGATAACTTCTTTTTATAAAGCAAATTGATTT
*
9962 TGATTCTTGAATAATCCACATCACTTCTATTTCTAT
582 TGATTCTTGAATAATCCACATCACTTCTACTTCTAT
9998 TGTAA
1 TGTAA
10003 CGAAAGATTC
Statistics
Matches: 557, Mismatches: 61, Indels: 8
0.89 0.10 0.01
Matches are distributed among these distances:
617 274 0.49
618 38 0.07
619 239 0.43
620 6 0.01
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.37
Consensus pattern (617 bp):
TGTAAAAATGTTTGTTAAGGACCTCTTGTATGATTATAAAGTAATCCAAGGTCATTAAAAAGGTG
AAATTGAGAAAACTTGGGTAAAAAGCTTAATTCATGGTGAAAAATTCTATGCAATATCAATATAT
TGGTATTTATGTCAATAGAAGTGATTCCTAGAACAAAAAAATATAGAAATTTTGAATTTACGACT
TTCAAAAATATCCCTATTCATAGGTTTGAGATCCATATCTATGAATTAAAAGGTCTGAATGATCA
ACTTTGCAATTAGTTGTTAAAATTAATAGGTCTTTAAATCATTCATTTGAAAAAATTCAAACCTT
CTTACTAGATTATCATAATACTTCTCAAAAATAAAAAATTTTGATCAATAAAGGAAGAATAACAC
TATTTTTGTTCAATAAAATACCAAAATGGATGATTAACTCATTCCATACTAGAAATAATCACAAG
ATATCTTTTGATAACACAGATCCCTATTTATCAATGATATCCCACGATTAAGACAATTGCCTAAA
TCCCGTGAAACCATTTCATAGAAGTTCATTGATAACTTCTTTTTATAAAGCAAATTGATTTTGAT
TCTTGAATAATCCACATCACTTCTACTTCTAT
Found at i:10583 original size:19 final size:20
Alignment explanation
Indices: 10559--10611 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
10549 TGCTTTGTAA
*
10559 TGTATCGATACATGTTC-AT
1 TGTATCGATACATGCTCAAT
* *
10578 TGTATCGATGCATACTCAAT
1 TGTATCGATACATGCTCAAT
10598 TGTATCGATACATG
1 TGTATCGATACATG
10612 AAACTGGCAG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (20 bp):
TGTATCGATACATGCTCAAT
Found at i:12297 original size:3 final size:3
Alignment explanation
Indices: 12276--12316 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
12266 AACCATCAAA
* * *
12276 GAT GAT GAA GAT GAA GAT GAT GAT GAT GAT GAT AAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
12317 AGTTGACTCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.41, C:0.00, G:0.32, T:0.27
Consensus pattern (3 bp):
GAT
Found at i:15372 original size:13 final size:13
Alignment explanation
Indices: 15354--15383 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
15344 ACAATTCTTC
15354 ATGTATCGATACA
1 ATGTATCGATACA
15367 ATGTATCGATACA
1 ATGTATCGATACA
15380 ATGT
1 ATGT
15384 CTTACGTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:15471 original size:19 final size:19
Alignment explanation
Indices: 15428--15483 Score: 94
Period size: 19 Copynumber: 2.9 Consensus size: 19
15418 CTGCCAGTTT
15428 CATGTATCGATACAATTGAG
1 CATGTATCGATACAA-TGAG
*
15448 TATGTATCGATACAATGAG
1 CATGTATCGATACAATGAG
15467 CATGTATCGATACAATG
1 CATGTATCGATACAATG
15484 TATCGATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 20 0.59
20 14 0.41
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAG
Found at i:15486 original size:13 final size:13
Alignment explanation
Indices: 15468--15494 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
15458 TACAATGAGC
15468 ATGTATCGATACA
1 ATGTATCGATACA
15481 ATGTATCGATACA
1 ATGTATCGATACA
15494 A
1 A
15495 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:22501 original size:15 final size:15
Alignment explanation
Indices: 22483--22513 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
22473 CAAGTCAATC
22483 TCATCATTATCATCA
1 TCATCATTATCATCA
*
22498 TCATCATTTTCATCA
1 TCATCATTATCATCA
22513 T
1 T
22514 ATTTAACGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.26, G:0.00, T:0.45
Consensus pattern (15 bp):
TCATCATTATCATCA
Found at i:24223 original size:19 final size:20
Alignment explanation
Indices: 24180--24311 Score: 216
Period size: 19 Copynumber: 6.8 Consensus size: 20
24170 CTGCCAGTTT
24180 CATGTATCGATACAATTGAG
1 CATGTATCGATACAATTGAG
*
24200 TATGTATCGATACAA-TGAG
1 CATGTATCGATACAATTGAG
24219 CATGTATCGATACAATTGAG
1 CATGTATCGATACAATTGAG
*
24239 TATGTATCGATACAA-TGAG
1 CATGTATCGATACAATTGAG
24258 CATGTATCGATACAATTGAG
1 CATGTATCGATACAATTGAG
*
24278 TATGTATCGATACAA-TGAG
1 CATGTATCGATACAATTGAG
24297 CATGTATCGATACAA
1 CATGTATCGATACAA
24312 AGCATAATGT
Statistics
Matches: 104, Mismatches: 6, Indels: 5
0.90 0.05 0.04
Matches are distributed among these distances:
19 54 0.52
20 50 0.48
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACAATTGAG
Found at i:24322 original size:78 final size:78
Alignment explanation
Indices: 24180--24330 Score: 252
Period size: 78 Copynumber: 1.9 Consensus size: 78
24170 CTGCCAGTTT
*
24180 CATGTATCGATACAATTGAGTATGTATCGATACAATGAGCATGTATCGATACAATTGAGTATGTA
1 CATGTATCGATACAATTGAGTATGTATCGATACAATGAGCATGTATCGATACAATAGAGTATGTA
*
24245 TCGATACAATGAG
66 TCAATACAATGAG
24258 CATGTATCGATACAATTGAGTATGTATCGATACAATGAGCATGTATCGATACAA-AGCA-TAATG
1 CATGTATCGATACAATTGAGTATGTATCGATACAATGAGCATGTATCGATACAATAG-AGT-ATG
24321 TATCAATACA
64 TATCAATACA
24331 CCTAGGTGTA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
77 2 0.03
78 67 0.97
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.30
Consensus pattern (78 bp):
CATGTATCGATACAATTGAGTATGTATCGATACAATGAGCATGTATCGATACAATAGAGTATGTA
TCAATACAATGAG
Found at i:24330 original size:39 final size:39
Alignment explanation
Indices: 24180--24311 Score: 264
Period size: 39 Copynumber: 3.4 Consensus size: 39
24170 CTGCCAGTTT
24180 CATGTATCGATACAATTGAGTATGTATCGATACAATGAG
1 CATGTATCGATACAATTGAGTATGTATCGATACAATGAG
24219 CATGTATCGATACAATTGAGTATGTATCGATACAATGAG
1 CATGTATCGATACAATTGAGTATGTATCGATACAATGAG
24258 CATGTATCGATACAATTGAGTATGTATCGATACAATGAG
1 CATGTATCGATACAATTGAGTATGTATCGATACAATGAG
24297 CATGTATCGATACAA
1 CATGTATCGATACAA
24312 AGCATAATGT
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 93 1.00
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (39 bp):
CATGTATCGATACAATTGAGTATGTATCGATACAATGAG
Found at i:24345 original size:59 final size:59
Alignment explanation
Indices: 24180--24349 Score: 166
Period size: 59 Copynumber: 2.9 Consensus size: 59
24170 CTGCCAGTTT
* * * * *
24180 CATGTATCGATACAATTGAGTATGTATCGATACAAT-GAGCATGTATCGATACAATTGAG
1 CATGTATCGATACAA-AGAGAATGTATCAATACAATAGAGTATATATCGATACAATTGAG
* * * * * *
24239 TATGTATCGATACAATGAGCATGTATCGATACAATTGAGTATGTATCGATACAA-TGAG
1 CATGTATCGATACAAAGAGAATGTATCAATACAATAGAGTATATATCGATACAATTGAG
* * *
24297 CATGTATCGATACAAAGCATAATGTATCAATACACCTAG-GTGTATATCGATAC
1 CATGTATCGATACAAAG-AGAATGTATCAATACA-ATAGAGTATATATCGATAC
24350 TTTCTAGGGT
Statistics
Matches: 96, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
58 38 0.40
59 56 0.58
60 2 0.02
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (59 bp):
CATGTATCGATACAAAGAGAATGTATCAATACAATAGAGTATATATCGATACAATTGAG
Found at i:25719 original size:52 final size:48
Alignment explanation
Indices: 25641--25751 Score: 152
Period size: 52 Copynumber: 2.2 Consensus size: 48
25631 CAAAATAACA
*
25641 TTGGAGTATCCCCGATTGTGAAAATTAATATTTTTTAAAAATAAAACCGGGG
1 TTGGAGTATCCCCGATTGTGAAAATTAATA--TTTTAAAAAT--AACCCGGG
*
25693 TTGGAGTATCCCC-ATTGTGAAAAATTAATATTTTAGAAATAACCCGGG
1 TTGGAGTATCCCCGATTGTG-AAAATTAATATTTTAAAAATAACCCGGG
25741 TTGGAGTATCC
1 TTGGAGTATCC
25752 TCTCGAAAAT
Statistics
Matches: 56, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
48 18 0.32
50 9 0.16
51 6 0.11
52 23 0.41
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (48 bp):
TTGGAGTATCCCCGATTGTGAAAATTAATATTTTAAAAATAACCCGGG
Done.