Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2415
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: 48809
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Found at i:2475 original size:19 final size:20
Alignment explanation
Indices: 2420--2476 Score: 82
Period size: 19 Copynumber: 3.0 Consensus size: 20
2410 ACAGTAACCG
* *
2420 TATACTTGAATAGTA-CTCG
1 TATACGTGAATAGTACCTCA
2439 TATACGTGAATAGTACCT-A
1 TATACGTGAATAGTACCTCA
2458 TATACGTGAATAGTACCTC
1 TATACGTGAATAGTACCTC
2477 GACAACCAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 32 0.94
20 2 0.06
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (20 bp):
TATACGTGAATAGTACCTCA
Found at i:2827 original size:34 final size:34
Alignment explanation
Indices: 2781--2998 Score: 273
Period size: 34 Copynumber: 6.5 Consensus size: 34
2771 GTAAAAACCA
*
2781 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
2815 CCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCTC
* *
2849 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
2883 CCATTTAATCAACAATGGTAAGCTACCAAATCT-
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
2916 CCATTTAGTCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCTC
* * *
2950 CCATTTAATCAACAATGGTAAACTACTAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
2983 CCATTTAATTAACAAT
1 CCATTTAATCAACAAT
2999 TTATAGATAT
Statistics
Matches: 161, Mismatches: 18, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
33 44 0.27
34 115 0.71
35 2 0.01
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:2895 original size:68 final size:67
Alignment explanation
Indices: 2779--2998 Score: 314
Period size: 67 Copynumber: 3.3 Consensus size: 67
2769 TGGTAAAAAC
* * *
2779 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
2844 AT
66 AT
* * *
2846 CACCCATTTAATCAACAATGGTAAGCTACCAAATTTCCCATTTAATCAACAATGGTAAGCTACCA
1 CA-CCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCA
2911 AAT
65 AAT
* * * * * *
2914 CTCCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACTAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
2979 AT
66 AT
*
2981 CACCATTTAATTAACAAT
1 CACCATTTAATCAACAAT
2999 TTATAGATAT
Statistics
Matches: 135, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
67 74 0.55
68 61 0.45
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (67 bp):
CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
AT
Found at i:5896 original size:28 final size:28
Alignment explanation
Indices: 5819--5896 Score: 86
Period size: 28 Copynumber: 2.8 Consensus size: 28
5809 AGTTAAGTGT
* * * *
5819 TAAATA-AATTTATTATAATAATTTGATA
1 TAAATATAATTT-TAATAATTATTTAACA
*
5847 TAAATATAAATTTTAATTATTATTTAACA
1 TAAATAT-AATTTTAATAATTATTTAACA
5876 TAAATATAATTTTAATAATTA
1 TAAATATAATTTTAATAATTA
5897 AATTTTTTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
28 19 0.45
29 18 0.43
30 5 0.12
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (28 bp):
TAAATATAATTTTAATAATTATTTAACA
Found at i:9897 original size:2 final size:2
Alignment explanation
Indices: 9890--9920 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
9880 CGTGATTGTT
9890 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
9921 ATATATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:11396 original size:2 final size:2
Alignment explanation
Indices: 11389--11425 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
11379 CCCGATTATT
11389 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
11426 ATATATATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:14898 original size:16 final size:17
Alignment explanation
Indices: 14877--14908 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
14867 AAGTTAACTT
14877 ACTATTTATAT-TTATC
1 ACTATTTATATATTATC
14893 ACTATTTATATATTAT
1 ACTATTTATATATTAT
14909 TTTTTTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.56
Consensus pattern (17 bp):
ACTATTTATATATTATC
Found at i:15587 original size:13 final size:14
Alignment explanation
Indices: 15562--15591 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
15552 AGATAAAAAC
15562 AATATCTTATAAAT
1 AATATCTTATAAAT
15576 AATATC-TATAAAT
1 AATATCTTATAAAT
15589 AAT
1 AAT
15592 TAATGTCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (14 bp):
AATATCTTATAAAT
Found at i:17468 original size:31 final size:31
Alignment explanation
Indices: 17430--17548 Score: 195
Period size: 31 Copynumber: 3.8 Consensus size: 31
17420 AAATCCCGAC
17430 CAGCTTTGGCAATCGGGAAAAGT-CAGCCAAA
1 CAGCTTTGGCAATCGGGAAAAGTCCA-CCAAA
*
17461 CAGCTTTGGCAATCGGGAAAAATCCACCAAA
1 CAGCTTTGGCAATCGGGAAAAGTCCACCAAA
17492 CAGCTTTGGCAATCGGGAAAAGTCCACCAAA
1 CAGCTTTGGCAATCGGGAAAAGTCCACCAAA
* *
17523 CAGCGTTGGCAAGCGGGAAAAGTCCA
1 CAGCTTTGGCAATCGGGAAAAGTCCA
17549 AGCCACAAGT
Statistics
Matches: 83, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
31 81 0.98
32 2 0.02
ACGTcount: A:0.35, C:0.24, G:0.25, T:0.15
Consensus pattern (31 bp):
CAGCTTTGGCAATCGGGAAAAGTCCACCAAA
Found at i:18435 original size:3 final size:3
Alignment explanation
Indices: 18427--18452 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
18417 AAATATAAAA
18427 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
18453 ATTATGAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:23261 original size:2 final size:2
Alignment explanation
Indices: 23249--23287 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
23239 CGCGATTGTT
*
23249 TC TC TC CC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
23288 ATATATATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:23553 original size:16 final size:16
Alignment explanation
Indices: 23524--23557 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
23514 ATGATTGCAG
*
23524 AATAAATTTTGAAAAA
1 AATAAATTTAGAAAAA
*
23540 AATAAGTTTAGAAAAA
1 AATAAATTTAGAAAAA
23556 AA
1 AA
23558 AGGAAAAAAT
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:0.65, C:0.00, G:0.09, T:0.26
Consensus pattern (16 bp):
AATAAATTTAGAAAAA
Found at i:24577 original size:19 final size:21
Alignment explanation
Indices: 24553--24591 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
24543 TTAATTTGAT
24553 TTAATT-AAT-AAAAATTAAA
1 TTAATTGAATAAAAAATTAAA
*
24572 TTAATTGAGTAAAAAATTAA
1 TTAATTGAATAAAAAATTAA
24592 TTATATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 2 0.12
21 9 0.53
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (21 bp):
TTAATTGAATAAAAAATTAAA
Found at i:24614 original size:22 final size:22
Alignment explanation
Indices: 24588--24650 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
24578 GAGTAAAAAA
**
24588 TTAATTATATATATTTTTATTT
1 TTAATTATATATATTTAAATTT
*
24610 TTAATTA-ATAAAATTTAAATTT
1 TTAATTATAT-ATATTTAAATTT
24632 TTAATTATAT-TA-TTAAATT
1 TTAATTATATATATTTAAATT
24651 AAATATATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
20 7 0.20
21 3 0.09
22 23 0.66
23 2 0.06
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TTAATTATATATATTTAAATTT
Found at i:24688 original size:40 final size:37
Alignment explanation
Indices: 24587--24689 Score: 86
Period size: 40 Copynumber: 2.7 Consensus size: 37
24577 TGAGTAAAAA
24587 ATTAATTATATATATTTTTATTTTT-AATTAATAAAATTT
1 ATTAATTAT-TA-ATTTTT-TTTTTAAATTAATAAAATTT
* * * * *
24626 A--AATTTTTAATTATATTATTAAATTAAATATATATTTT
1 ATTAATTATTAATTTTTTTTTTAAATT-AATA-A-AATTT
24664 ATTAATTATTAATTTTTTTTTTAAAT
1 ATTAATTATTAATTTTTTTTTTAAAT
24690 GGTTTTGTTA
Statistics
Matches: 49, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
34 4 0.08
35 8 0.16
36 6 0.12
37 6 0.12
38 5 0.10
39 1 0.02
40 19 0.39
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (37 bp):
ATTAATTATTAATTTTTTTTTTAAATTAATAAAATTT
Found at i:25483 original size:21 final size:21
Alignment explanation
Indices: 25442--25485 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
25432 TTACATTTTT
* *
25442 ATAAAGAATAAAATAACATTA
1 ATAAAGAATAAAAAAAAATTA
25463 ATAAA-AATAAATAAAAAATTA
1 ATAAAGAATAAA-AAAAAATTA
25484 AT
1 AT
25486 TAATAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.25
Consensus pattern (21 bp):
ATAAAGAATAAAAAAAAATTA
Found at i:25581 original size:19 final size:19
Alignment explanation
Indices: 25558--25606 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
25548 AAAATCAATT
*
25558 TAATTATAAAAATTACTTAA
1 TAATTATAAAAAATA-TTAA
*
25578 -AATTTTTAAAAAATATTAA
1 TAA-TTATAAAAAATATTAA
25597 TAATTATAAA
1 TAATTATAAA
25607 TTAAGAGATA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (19 bp):
TAATTATAAAAAATATTAA
Found at i:25601 original size:20 final size:20
Alignment explanation
Indices: 25564--25601 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
25554 AATTTAATTA
*
25564 TAAAAATTACTTAAAATTTT
1 TAAAAAATACTTAAAATTTT
25584 TAAAAAATA-TTAATAATT
1 TAAAAAATACTTAA-AATT
25602 ATAAATTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (20 bp):
TAAAAAATACTTAAAATTTT
Found at i:26101 original size:25 final size:25
Alignment explanation
Indices: 26055--26103 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
26045 TACAATGATG
* *
26055 TTTAATATTTTATATTTATATATTT
1 TTTAATATTTAATAATTATATATTT
26080 TTTAATATATTAATAATT-TATATT
1 TTTAATAT-TTAATAATTATATATT
26104 ATATAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (25 bp):
TTTAATATTTAATAATTATATATTT
Found at i:26106 original size:18 final size:18
Alignment explanation
Indices: 26056--26115 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 18
26046 ACAATGATGT
26056 TTAATATTTTATATT-TA
1 TTAATATTTTATATTATA
* *
26073 -T-ATATTTTTTAATATA
1 TTAATATTTTATATTATA
*
26089 TTAATAATTTATATTATA
1 TTAATATTTTATATTATA
26107 -TAA-ATTTTA
1 TTAATATTTTA
26116 AAATATTTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
15 10 0.29
16 8 0.24
17 4 0.12
18 12 0.35
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTAATATTTTATATTATA
Found at i:26115 original size:32 final size:33
Alignment explanation
Indices: 26056--26122 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 33
26046 ACAATGATGT
* ** *
26056 TTAATATTTTATATTTATATATTTTTTAATATA
1 TTAATAATTTATATTTATATAAATTTTAAAATA
26089 TTAATAATTTATA-TTATATAAATTTTAAAATA
1 TTAATAATTTATATTTATATAAATTTTAAAATA
26121 TT
1 TT
26123 TATATAATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 18 0.60
33 12 0.40
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (33 bp):
TTAATAATTTATATTTATATAAATTTTAAAATA
Found at i:27212 original size:147 final size:147
Alignment explanation
Indices: 26945--27238 Score: 579
Period size: 147 Copynumber: 2.0 Consensus size: 147
26935 ATAAGTTTGG
26945 GGTTTTCTTTACAATGAAATTATTGACTACCTAATGTTGGGTATATCATATATGCAATTTGATGA
1 GGTTTTCTTTACAATGAAATTATTGACTACCTAATGTTGGGTATATCATATATGCAATTTGATGA
27010 AATTCTGGTAGTATGGTTGGTGCTTACTTTGGACCAAAATTGCGGATGGAAGAATACTGCTAATT
66 AATTCTGGTAGTATGGTTGGTGCTTACTTTGGACCAAAATTGCGGATGGAAGAATACTGCTAATT
27075 GTTTTCCAAATTTGCAC
131 GTTTTCCAAATTTGCAC
27092 GGTTTTCTTTACAATGAAATTATTGACTACCTAATGTTGGGTATATCATATATGCAATTTGATGA
1 GGTTTTCTTTACAATGAAATTATTGACTACCTAATGTTGGGTATATCATATATGCAATTTGATGA
*
27157 AATTCTGGTCGTATGGTTGGTGCTTACTTTGGACCAAAATTGCGGATGGAAGAATACTGCTAATT
66 AATTCTGGTAGTATGGTTGGTGCTTACTTTGGACCAAAATTGCGGATGGAAGAATACTGCTAATT
27222 GTTTTCCAAATTTGCAC
131 GTTTTCCAAATTTGCAC
27239 CTTGTTTATG
Statistics
Matches: 146, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
147 146 1.00
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.38
Consensus pattern (147 bp):
GGTTTTCTTTACAATGAAATTATTGACTACCTAATGTTGGGTATATCATATATGCAATTTGATGA
AATTCTGGTAGTATGGTTGGTGCTTACTTTGGACCAAAATTGCGGATGGAAGAATACTGCTAATT
GTTTTCCAAATTTGCAC
Found at i:27300 original size:61 final size:61
Alignment explanation
Indices: 27205--27329 Score: 216
Period size: 61 Copynumber: 2.0 Consensus size: 61
27195 ATTGCGGATG
*
27205 GAAGAATACTGCTAATTGTTTTCCAAATTTGCACCTTGTTT-ATGTATGTTTATGCTAAGTT
1 GAAGAACACTGCTAATTGTTTTCCAAATTTGCACCTT-TTTCATGTATGTTTATGCTAAGTT
*
27266 GAAGAACACTGCTAATTGTTTTCCAAATTTGCACCTTTTTCGTGTATGTTTATGCTAAGTT
1 GAAGAACACTGCTAATTGTTTTCCAAATTTGCACCTTTTTCATGTATGTTTATGCTAAGTT
27327 GAA
1 GAA
27330 TTTGGTCTCC
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
60 3 0.05
61 58 0.95
ACGTcount: A:0.26, C:0.14, G:0.17, T:0.42
Consensus pattern (61 bp):
GAAGAACACTGCTAATTGTTTTCCAAATTTGCACCTTTTTCATGTATGTTTATGCTAAGTT
Found at i:35434 original size:16 final size:16
Alignment explanation
Indices: 35413--35448 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
35403 AAATTAATAC
*
35413 TTAATTATAAAATAAA
1 TTAATTATAAAACAAA
*
35429 TTAATTATAATACAAA
1 TTAATTATAAAACAAA
35445 TTAA
1 TTAA
35449 ATTGACATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (16 bp):
TTAATTATAAAACAAA
Found at i:38170 original size:2 final size:2
Alignment explanation
Indices: 38163--38192 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
38153 ATAATTTTTC
38163 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
38193 TGTAAAGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38416 original size:17 final size:17
Alignment explanation
Indices: 38394--38426 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
38384 TACATTAAGC
38394 AAATTA-TTAAACATTTT
1 AAATTACTTAAA-ATTTT
38411 AAATTACTTAAAATTT
1 AAATTACTTAAAATTT
38427 AAAGTGCATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (17 bp):
AAATTACTTAAAATTTT
Found at i:47759 original size:20 final size:20
Alignment explanation
Indices: 47734--47797 Score: 78
Period size: 20 Copynumber: 3.3 Consensus size: 20
47724 TATTTATTTA
*
47734 TTATTTATCTTTTAAAATAT
1 TTATTTATTTTTTAAAATAT
*
47754 TTATTTATTTTTTAAAAAAT
1 TTATTTATTTTTTAAAATAT
* *
47774 ATATTT-TTTTTTAAATTA-
1 TTATTTATTTTTTAAAATAT
47792 TTATTT
1 TTATTT
47798 TAAATTAATT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
18 5 0.13
19 10 0.26
20 23 0.61
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (20 bp):
TTATTTATTTTTTAAAATAT
Found at i:47815 original size:13 final size:12
Alignment explanation
Indices: 47780--47813 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
47770 AAATATATTT
47780 TTTTTTAAATTA
1 TTTTTTAAATTA
47792 TTATTTTAAATTA
1 TT-TTTTAAATTA
*
47805 ATTTTTAAA
1 TTTTTTAAA
47814 ATAAATATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTTTTAAATTA
Done.