Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1129
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: 12979
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.35
Found at i:1242 original size:39 final size:37
Alignment explanation
Indices: 1175--1267 Score: 98
Period size: 39 Copynumber: 2.5 Consensus size: 37
1165 ACCAGAATGG
* *
1175 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAG-AA-AGTTGA
* *
1214 CACCCAGTGTCTCATCGGCAAAG-CCGAAGAAAGTTGG
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGAAAGTTGA
* *
1251 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
1268 AATCTATCCG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 19 0.41
38 2 0.04
39 22 0.48
40 3 0.07
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGAAAGTCCGAAGAAAGTTGA
Found at i:1445 original size:25 final size:25
Alignment explanation
Indices: 1411--1469 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
1401 ACATATATTC
*
1411 TCAATTCAATACAATTTT-CACATTT
1 TCAATTCAATACAATTTTCCAC-CTT
*
1436 TCAATTCAAT-CATTTTTCCACCTT
1 TCAATTCAATACAATTTTCCACCTT
1460 TCAA-TCAATA
1 TCAATTCAATA
1470 ATTATTTCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
23 5 0.17
24 12 0.40
25 13 0.43
ACGTcount: A:0.34, C:0.24, G:0.00, T:0.42
Consensus pattern (25 bp):
TCAATTCAATACAATTTTCCACCTT
Found at i:1461 original size:24 final size:25
Alignment explanation
Indices: 1411--1477 Score: 68
Period size: 24 Copynumber: 2.7 Consensus size: 25
1401 ACATATATTC
* *
1411 TCAATTCAATACAATTTT-CACATTT
1 TCAATTCAAT-CATTTTTCCACACTT
1436 TCAATTCAATCATTTTTCCAC-CTT
1 TCAATTCAATCATTTTTCCACACTT
*
1460 TCAA-TCAATAATTATTTC
1 TCAATTCAATCATT-TTTC
1478 ACAACTTCAC
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
23 8 0.22
24 16 0.43
25 13 0.35
ACGTcount: A:0.33, C:0.22, G:0.00, T:0.45
Consensus pattern (25 bp):
TCAATTCAATCATTTTTCCACACTT
Found at i:1629 original size:3 final size:3
Alignment explanation
Indices: 1621--1665 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
1611 ATTCCCACTC
* * * *
1621 ATA ATA ATA ATA ATA CTA ATA ATA ATA CTA ATA CTA ATA TTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1666 CTTACCTCAC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:1666 original size:18 final size:18
Alignment explanation
Indices: 1621--1667 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
1611 ATTCCCACTC
*
1621 ATAATAATAATAATACTA
1 ATAATAATACTAATACTA
1639 ATAATAATACTAATACTA
1 ATAATAATACTAATACTA
*
1657 ATATTAATACT
1 ATAATAATACT
1668 TACCTCACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (18 bp):
ATAATAATACTAATACTA
Found at i:1667 original size:12 final size:12
Alignment explanation
Indices: 1625--1665 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
1615 CCACTCATAA
1625 TAATAATAATAC
1 TAATAATAATAC
1637 TAATAATAATAC
1 TAATAATAATAC
* *
1649 TAATACTAATAT
1 TAATAATAATAC
1661 TAATA
1 TAATA
1666 CTTACCTCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (12 bp):
TAATAATAATAC
Found at i:1765 original size:18 final size:19
Alignment explanation
Indices: 1742--1779 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
1732 ATATAGTAAT
1742 ACAAACCGTAA-TTTCTCG
1 ACAAACCGTAATTTTCTCG
1760 ACAAACCGTAATTTTCTCG
1 ACAAACCGTAATTTTCTCG
1779 A
1 A
1780 GTTTACTCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.29
Consensus pattern (19 bp):
ACAAACCGTAATTTTCTCG
Found at i:2475 original size:11 final size:11
Alignment explanation
Indices: 2437--2475 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
2427 ATATTTATAA
2437 TATAATTAATT
1 TATAATTAATT
*
2448 TAATAATATACTT
1 T-ATAAT-TAATT
2461 TATAATTAATT
1 TATAATTAATT
2472 TATA
1 TATA
2476 TATTTATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 9 0.38
12 10 0.42
13 5 0.21
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (11 bp):
TATAATTAATT
Found at i:2494 original size:24 final size:24
Alignment explanation
Indices: 2409--2491 Score: 86
Period size: 24 Copynumber: 3.6 Consensus size: 24
2399 TGTTTTTTCT
2409 TTTATATATATAA-TAA--TAATA
1 TTTATATATATAATTAATTTAATA
2430 TTTATA-ATATAATTAATTTAATA
1 TTTATATATATAATTAATTTAATA
* *
2453 -ATATACTTTATAATTAATTTATATA
1 TTTATA-TATATAATTAATTTA-ATA
*
2478 TTTATATAAATAAT
1 TTTATATATATAAT
2492 AATATAAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
20 6 0.12
21 9 0.18
22 4 0.08
23 5 0.10
24 13 0.26
25 9 0.18
26 4 0.08
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (24 bp):
TTTATATATATAATTAATTTAATA
Found at i:3395 original size:16 final size:16
Alignment explanation
Indices: 3376--3410 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3366 TTCTTTGTTC
3376 TTTCTATTCTGTTTCT
1 TTTCTATTCTGTTTCT
* *
3392 TTTCTGTTTTGTTTCT
1 TTTCTATTCTGTTTCT
3408 TTT
1 TTT
3411 ATATATAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.03, C:0.14, G:0.09, T:0.74
Consensus pattern (16 bp):
TTTCTATTCTGTTTCT
Found at i:3437 original size:14 final size:14
Alignment explanation
Indices: 3418--3468 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
3408 TTTATATATA
3418 ATAATATAATATTT
1 ATAATATAATATTT
*
3432 ATAATATAATTAATT
1 ATAATATAA-TATTT
3447 -TAATAT-ATACTTT
1 ATAATATAATA-TTT
3460 ATAAT-TAAT
1 ATAATATAAT
3469 TTATATATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
12 2 0.06
13 4 0.13
14 21 0.68
15 4 0.13
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (14 bp):
ATAATATAATATTT
Found at i:3450 original size:23 final size:22
Alignment explanation
Indices: 3408--3485 Score: 88
Period size: 23 Copynumber: 3.5 Consensus size: 22
3398 TTTTGTTTCT
*
3408 TTTATATATAA-TAATATAATA
1 TTTATATATAATTAATTTAATA
3429 TTTATAATATAATTAATTTAATA
1 TTTAT-ATATAATTAATTTAATA
* *
3452 TATACTTTATAATTAATTT-ATA
1 TTTA-TATATAATTAATTTAATA
3474 TATTATATATAA
1 T-TTATATATAA
3486 AAATAATATA
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
21 5 0.10
22 16 0.33
23 26 0.54
24 1 0.02
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (22 bp):
TTTATATATAATTAATTTAATA
Found at i:3480 original size:27 final size:28
Alignment explanation
Indices: 3418--3482 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 28
3408 TTTATATATA
3418 ATAATATAATA-TTTATAATATAATTAAT
1 ATAATAT-ATACTTTATAATATAATTAAT
* *
3446 TTAATATATACTTTATAAT-TAATTTAT
1 ATAATATATACTTTATAATATAATTAAT
*
3473 ATATTATATA
1 ATAATATATA
3483 TAAAAATAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
27 18 0.56
28 14 0.44
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (28 bp):
ATAATATATACTTTATAATATAATTAAT
Found at i:4393 original size:16 final size:16
Alignment explanation
Indices: 4374--4407 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4364 TTCTTTGTTC
4374 TTTCTATTCTGTTTCT
1 TTTCTATTCTGTTTCT
* *
4390 TTTCTGTTTTGTTTCT
1 TTTCTATTCTGTTTCT
4406 TT
1 TT
4408 ATATATAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.03, C:0.15, G:0.09, T:0.74
Consensus pattern (16 bp):
TTTCTATTCTGTTTCT
Found at i:4450 original size:19 final size:20
Alignment explanation
Indices: 4428--4482 Score: 51
Period size: 21 Copynumber: 2.8 Consensus size: 20
4418 ATATAATATT
4428 TATAATATAATTAATTTA-A
1 TATAATATAATTAATTTATA
*
4447 TATACTTTATAATTAA-TTATA
1 TATA--ATATAATTAATTTATA
* *
4468 TATTATATAAATAAT
1 TATAATATAATTAAT
4483 AATATAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
19 12 0.43
20 3 0.11
21 13 0.46
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
TATAATATAATTAATTTATA
Found at i:4473 original size:17 final size:17
Alignment explanation
Indices: 4406--4474 Score: 57
Period size: 19 Copynumber: 3.7 Consensus size: 17
4396 TTTTGTTTCT
*
4406 TTATATATAATAATATAA
1 TTATATATTATAAT-TAA
* *
4424 TATTTATAATATAATTAA
1 T-TATATATTATAATTAA
4442 TTTAATATACTTTATAATTAA
1 -TT-ATATA--TTATAATTAA
4463 TTATATATTATA
1 TTATATATTATA
4475 TAAATAATAA
Statistics
Matches: 41, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
17 5 0.12
18 5 0.12
19 20 0.49
20 2 0.05
21 9 0.22
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (17 bp):
TTATATATTATAATTAA
Found at i:4487 original size:19 final size:19
Alignment explanation
Indices: 4444--4488 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
4434 ATAATTAATT
*
4444 TAATATACTTTATAATTAA
1 TAATATACTTTATAAATAA
*
4463 TTATATA-TTATATAAATAA
1 TAATATACTT-TATAAATAA
4482 TAATATA
1 TAATATA
4489 AAAATCTAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 2 0.09
19 20 0.91
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
TAATATACTTTATAAATAA
Found at i:5432 original size:17 final size:17
Alignment explanation
Indices: 5410--5485 Score: 53
Period size: 16 Copynumber: 4.9 Consensus size: 17
5400 TTCTTTTATA
5410 TATAATAATATAATATT
1 TATAATAATATAATATT
*
5427 TATAAT-ATAT--TAAT
1 TATAATAATATAATATT
*
5441 T-TAATAATAT-A-CTT
1 TATAATAATATAATATT
5455 TATAATTAAT-TATATATT
1 TATAA-TAATATA-ATATT
5473 TAT-ATAA-ATAATA
1 TATAATAATATAATA
5486 ATATAAAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 18
0.68 0.06 0.26
Matches are distributed among these distances:
13 4 0.09
14 10 0.21
15 7 0.15
16 13 0.28
17 8 0.17
18 5 0.11
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (17 bp):
TATAATAATATAATATT
Found at i:5433 original size:14 final size:16
Alignment explanation
Indices: 5412--5451 Score: 57
Period size: 14 Copynumber: 2.6 Consensus size: 16
5402 CTTTTATATA
5412 TAATAATATAAT-ATT
1 TAATAATATAATAATT
*
5427 T-ATAATATATTAATT
1 TAATAATATAATAATT
5442 TAATAATATA
1 TAATAATATA
5452 CTTTATAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 9 0.41
15 5 0.23
16 8 0.36
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TAATAATATAATAATT
Found at i:5440 original size:22 final size:21
Alignment explanation
Indices: 5404--5491 Score: 70
Period size: 23 Copynumber: 3.9 Consensus size: 21
5394 GTTTGTTTCT
5404 TTTATATATAATAATATAATA
1 TTTATATATAATAATATAATA
* *
5425 TTTATAATATATTAATTTAATAA
1 TTTAT-ATATAATAATATAAT-A
* *
5448 TATACTTTATAATTAAT-TATATA
1 TTTA-TATATAA-TAATATA-ATA
5471 TTTATATAAATAATAATATAA
1 TTTATAT--ATAATAATATAA
5492 AAATCTAAGA
Statistics
Matches: 52, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
21 5 0.10
22 15 0.29
23 19 0.37
24 13 0.25
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (21 bp):
TTTATATATAATAATATAATA
Found at i:5469 original size:19 final size:18
Alignment explanation
Indices: 5428--5485 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
5418 TATAATATTT
*
5428 ATAATATA-TTA-ATTTA
1 ATAATATATTTATAATTA
5444 ATAATATACTTTATAATTA
1 ATAATATA-TTTATAATTA
* *
5463 ATTATATATTTAT-ATAA
1 ATAATATATTTATAATTA
5480 ATAATA
1 ATAATA
5486 ATATAAAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
16 8 0.23
17 8 0.23
18 8 0.23
19 11 0.31
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (18 bp):
ATAATATATTTATAATTA
Found at i:5478 original size:20 final size:19
Alignment explanation
Indices: 5441--5490 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 19
5431 ATATATTAAT
5441 TTAATAATATACTTTATAA
1 TTAATAATATACTTTATAA
* *
5460 TTAATTATATATTTATATAA
1 TTAATAATATACTT-TATAA
*
5480 ATAATAATATA
1 TTAATAATATA
5491 AAAATCTAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (19 bp):
TTAATAATATACTTTATAA
Found at i:10424 original size:21 final size:21
Alignment explanation
Indices: 10382--10424 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
10372 TTCACTATAC
*
10382 ATTCTTTCATCAGTATCATTT
1 ATTCTTTCATCAGCATCATTT
*
10403 ATTCTTTCTTCAGACATC-TTT
1 ATTCTTTCATCAG-CATCATTT
10424 A
1 A
10425 ATCTATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.23, C:0.21, G:0.05, T:0.51
Consensus pattern (21 bp):
ATTCTTTCATCAGCATCATTT
Found at i:11504 original size:39 final size:38
Alignment explanation
Indices: 11461--11593 Score: 112
Period size: 39 Copynumber: 3.4 Consensus size: 38
11451 ACCAGAATGG
*
11461 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGATAGTCCGAAG-AATAGTTGA
* * *
11500 CACCCAGTGTCTCATCGGCAAAG-CCGAAGAA-AGTTGG
1 CACCCAGTGCCTCATCGG-ATAGTCCGAAGAATAGTTGA
* * *
11537 TACCCAGTACCTCATCGAATCTA-TCCGAAGAATA-TAGTGA
1 CACCCAGTGCCTCATCGGA--TAGTCCGAAGAATAGT--TGA
*
11577 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
11594 ACTCGAGGTC
Statistics
Matches: 74, Mismatches: 13, Indels: 13
0.74 0.13 0.13
Matches are distributed among these distances:
36 1 0.01
37 19 0.26
38 12 0.16
39 23 0.31
40 19 0.26
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGATAGTCCGAAGAATAGTTGA
Found at i:11730 original size:25 final size:25
Alignment explanation
Indices: 11696--11754 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
11686 ACATATATTC
*
11696 TCAATTCAATACAATTTT-CACATTT
1 TCAATTCAATACAATTTTCCAC-CTT
*
11721 TCAATTCAAT-CATTTTTCCACCTT
1 TCAATTCAATACAATTTTCCACCTT
11745 TCAA-TCAATA
1 TCAATTCAATA
11755 ATTATTTCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
23 5 0.17
24 12 0.40
25 13 0.43
ACGTcount: A:0.34, C:0.24, G:0.00, T:0.42
Consensus pattern (25 bp):
TCAATTCAATACAATTTTCCACCTT
Found at i:11746 original size:24 final size:25
Alignment explanation
Indices: 11696--11762 Score: 68
Period size: 24 Copynumber: 2.7 Consensus size: 25
11686 ACATATATTC
* *
11696 TCAATTCAATACAATTTT-CACATTT
1 TCAATTCAAT-CATTTTTCCACACTT
11721 TCAATTCAATCATTTTTCCAC-CTT
1 TCAATTCAATCATTTTTCCACACTT
*
11745 TCAA-TCAATAATTATTTC
1 TCAATTCAATCATT-TTTC
11763 ACAACTTCAC
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
23 8 0.22
24 16 0.43
25 13 0.35
ACGTcount: A:0.33, C:0.22, G:0.00, T:0.45
Consensus pattern (25 bp):
TCAATTCAATCATTTTTCCACACTT
Found at i:11913 original size:3 final size:3
Alignment explanation
Indices: 11905--11949 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
11895 ATTCCCACTC
* * * *
11905 ATA ATA ATA ATA ATA CTA ATA ATA ATA CTA ATA CTA ATA TTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
11950 CTTACCTCAC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:11950 original size:18 final size:18
Alignment explanation
Indices: 11905--11951 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
11895 ATTCCCACTC
*
11905 ATAATAATAATAATACTA
1 ATAATAATACTAATACTA
11923 ATAATAATACTAATACTA
1 ATAATAATACTAATACTA
*
11941 ATATTAATACT
1 ATAATAATACT
11952 TACCTCACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (18 bp):
ATAATAATACTAATACTA
Found at i:11951 original size:12 final size:12
Alignment explanation
Indices: 11909--11949 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
11899 CCACTCATAA
11909 TAATAATAATAC
1 TAATAATAATAC
11921 TAATAATAATAC
1 TAATAATAATAC
* *
11933 TAATACTAATAT
1 TAATAATAATAC
11945 TAATA
1 TAATA
11950 CTTACCTCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (12 bp):
TAATAATAATAC
Found at i:12688 original size:12 final size:12
Alignment explanation
Indices: 12671--12705 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
12661 TATTTATAAT
12671 ATAATTAATTTA
1 ATAATTAATTTA
*
12683 ATAATTACTTTA
1 ATAATTAATTTA
12695 AT-ATTAATTTA
1 ATAATTAATTTA
12706 TTATATTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 8 0.38
12 13 0.62
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (12 bp):
ATAATTAATTTA
Done.