Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold838
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: 48534
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Found at i:2939 original size:55 final size:54
Alignment explanation
Indices: 2855--2967 Score: 167
Period size: 55 Copynumber: 2.1 Consensus size: 54
2845 TCACAATTTT
*
2855 CAACCCCTTCGACCTTTTCTAATTAAGATGC-CTCATTTTTTATGGATGAAATGTC
1 CAACCCCTTCGACCTTTTCTAATTAAGATGCGC-CATTTTAT-TGGATGAAATGTC
*
2910 CAACCCCTTTC-ACCTTTTCTAATTAAGATGCGCCATTTTATTGGATGAAATGTT
1 CAACCCC-TTCGACCTTTTCTAATTAAGATGCGCCATTTTATTGGATGAAATGTC
2964 CAAC
1 CAAC
2968 ATTTAGAACA
Statistics
Matches: 54, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
54 16 0.30
55 34 0.63
56 4 0.07
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.37
Consensus pattern (54 bp):
CAACCCCTTCGACCTTTTCTAATTAAGATGCGCCATTTTATTGGATGAAATGTC
Found at i:5531 original size:3 final size:3
Alignment explanation
Indices: 5523--5566 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
5513 AAAGAATGAG
5523 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
5567 TTTTATAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:6849 original size:170 final size:170
Alignment explanation
Indices: 6543--6979 Score: 480
Period size: 170 Copynumber: 2.6 Consensus size: 170
6533 GTATACGTGG
* * * * * * ** * *
6543 TTATCAGTTAACTTGCTCGTGGCATTTCTGAATTCCATTATCAGTGTATAGAGGATACTTATATT
1 TTATCAGTTAACTTCCTTGTAGCACTTCTAAACTCCGCTATCAGTGTATATAGGATAATTATATT
* * * * * *
6608 ATAGTTATTCAGCACGTGGCAAATGCATAAAGTCGCTAGCAGAGTTTTTAGCTTCATCGGTGGTG
66 ATAGTTAATCAGCATGTGGCAAATGTATAAAGTCGCTAGCAGAGCTTTTAGCTTCACCGGTAGTG
* *
6673 TATCGTGTAATAGTCCTTTTCTTTGTGATAATAGATTCTT
131 TATCGTGTAATAGTCCTTTTCTTCGTAATAATAGATTCTT
* * * * *
6713 TTATCAGTTGACTTGCTTGTAGCGCTTCTAAACTCCGCTATCAGTGTATCTAAGATAATTATATT
1 TTATCAGTTAACTTCCTTGTAGCACTTCTAAACTCCGCTATCAGTGTATATAGGATAATTATATT
* * ** * *
6778 TTAGTTAATCAGCATGTGGCAAATGTATAAAGTCGCTTGTGGAGCTTTTGGCTTCACCGGTAGTT
66 ATAGTTAATCAGCATGTGGCAAATGTATAAAGTCGCTAGCAGAGCTTTTAGCTTCACCGGTAGTG
* * * *
6843 TATCGTGTAATTGTCTTTTTCTTCGTAATTATTGATTCTT
131 TATCGTGTAATAGTCCTTTTCTTCGTAATAATAGATTCTT
* * * * * * * *
6883 TTATCAGTTAACTTCCTTGTGGCATTTCTGAATTCCTCTATCATTCTATATAGGATAATTATCTT
1 TTATCAGTTAACTTCCTTGTAGCACTTCTAAACTCCGCTATCAGTGTATATAGGATAATTATATT
*
6948 ATAGTTGATCAGCACT-TGGCAAATGTATAAAG
66 ATAGTTAATCAGCA-TGTGGCAAATGTATAAAG
6980 CGTTTATTTT
Statistics
Matches: 220, Mismatches: 46, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
170 219 1.00
171 1 0.00
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.41
Consensus pattern (170 bp):
TTATCAGTTAACTTCCTTGTAGCACTTCTAAACTCCGCTATCAGTGTATATAGGATAATTATATT
ATAGTTAATCAGCATGTGGCAAATGTATAAAGTCGCTAGCAGAGCTTTTAGCTTCACCGGTAGTG
TATCGTGTAATAGTCCTTTTCTTCGTAATAATAGATTCTT
Found at i:8908 original size:66 final size:67
Alignment explanation
Indices: 8779--8909 Score: 169
Period size: 68 Copynumber: 2.0 Consensus size: 67
8769 TGTTTGTGTG
*
8779 TGTGTATGTGTGTTTTAATTGCAATCTACTAATGCCATTTGTGGTAGTCTGAAATCACTGCTAAT
1 TGTGTATGTGTGTTTTAATTGCAATCTACTAATG-CATTAGTGGTAGTCTGAAATCACTGCTAAT
8844 GAT
65 GAT
* * * *
8847 TGTGTGTGTGTGTTTT-ATTCGCAGTCTACTAATG-ATTAGCT-TTAGTTTGAAATCACTGCTAA
1 TGTGTATGTGTGTTTTAATT-GCAATCTACTAATGCATTAG-TGGTAGTCTGAAATCACTGCTAA
8909 T
64 T
8910 TATATTATTT
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
66 24 0.43
67 4 0.07
68 28 0.50
ACGTcount: A:0.24, C:0.13, G:0.21, T:0.43
Consensus pattern (67 bp):
TGTGTATGTGTGTTTTAATTGCAATCTACTAATGCATTAGTGGTAGTCTGAAATCACTGCTAATG
AT
Found at i:20040 original size:26 final size:26
Alignment explanation
Indices: 20011--20061 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
20001 TTAATAATCA
20011 CAGAT-AAAGTTGAACTTTATCAATTT
1 CAGATGAAA-TTGAACTTTATCAATTT
* *
20037 CAGATGAAATTGAATTTTATTAATT
1 CAGATGAAATTGAACTTTATCAATT
20062 CTATTTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 19 0.86
27 3 0.14
ACGTcount: A:0.39, C:0.08, G:0.12, T:0.41
Consensus pattern (26 bp):
CAGATGAAATTGAACTTTATCAATTT
Found at i:20699 original size:14 final size:14
Alignment explanation
Indices: 20661--20699 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
20651 ATCTTAGTTA
* *
20661 ATTTATAAAATCAT
1 ATTTAAAAAATAAT
20675 ATTTAAAAAATAAT
1 ATTTAAAAAATAAT
*
20689 ATTTAATAAAT
1 ATTTAAAAAAT
20700 TTACATTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (14 bp):
ATTTAAAAAATAAT
Found at i:21697 original size:13 final size:13
Alignment explanation
Indices: 21681--21713 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
21671 TAAATACATA
21681 TTATTTATTAATT
1 TTATTTATTAATT
21694 TTATTTA-TAATT
1 TTATTTATTAATT
21706 TT-TTTATT
1 TTATTTATT
21714 TTATCATTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 4 0.21
12 8 0.42
13 7 0.37
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (13 bp):
TTATTTATTAATT
Found at i:22015 original size:37 final size:36
Alignment explanation
Indices: 21963--22033 Score: 90
Period size: 36 Copynumber: 1.9 Consensus size: 36
21953 TAATATTTTA
*
21963 TTAATAAAAAAATATTTATATTTATTT-TTAAAAATTT
1 TTAATAAAAAAATA-TTAT-TTAATTTATTAAAAATTT
**
22000 TTAATAAAATTATATTATTTAATTTATTAAAAAT
1 TTAATAAAAAAATATTATTTAATTTATTAAAAAT
22034 ATATAAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
35 6 0.20
36 12 0.40
37 12 0.40
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (36 bp):
TTAATAAAAAAATATTATTTAATTTATTAAAAATTT
Found at i:27616 original size:20 final size:18
Alignment explanation
Indices: 27553--27628 Score: 58
Period size: 18 Copynumber: 4.5 Consensus size: 18
27543 TAGTTAATAA
27553 TAATTAT-TTATAATAATAT
1 TAATTATATT-TAAT-ATAT
*
27572 T-ATTATATTAAATATA-
1 TAATTATATTTAATATAT
* *
27588 AAATTA-A--TAAT-TTT
1 TAATTATATTTAATATAT
27602 TAATTATATTTAATATAT
1 TAATTATATTTAATATAT
27620 TAATTATAT
1 TAATTATAT
27629 ATAAATTTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 15
0.68 0.09 0.23
Matches are distributed among these distances:
13 1 0.02
14 8 0.18
15 1 0.02
16 1 0.02
17 11 0.25
18 19 0.43
19 3 0.07
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTATATTTAATATAT
Found at i:27666 original size:21 final size:20
Alignment explanation
Indices: 27601--27667 Score: 61
Period size: 20 Copynumber: 3.4 Consensus size: 20
27591 TTAATAATTT
*
27601 TTAATTATAT-TTAA-TATA
1 TTAATTATATATAAATTATA
27619 TTAATTATATATAAATT-TA
1 TTAATTATATATAAATTATA
*
27638 TTTTATTATCA-ATAAATTATA
1 -TTAATTAT-ATATAAATTATA
27659 TTACATTAT
1 TTA-ATTAT
27668 TTTATTAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
18 10 0.25
19 5 0.12
20 17 0.43
21 8 0.20
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (20 bp):
TTAATTATATATAAATTATA
Found at i:27947 original size:18 final size:17
Alignment explanation
Indices: 27924--27972 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
27914 AATAATTTAT
27924 TAATTATTTTATAATAAA
1 TAATTATTTTATAA-AAA
*
27942 TAATTATTTTTTAAAAA
1 TAATTATTTTATAAAAA
*
27959 TGAATTATATTATA
1 T-AATTATTTTATA
27973 TAATTTAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 4 0.15
18 23 0.85
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
TAATTATTTTATAAAAA
Found at i:28001 original size:25 final size:25
Alignment explanation
Indices: 27951--27997 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
27941 ATAATTATTT
**
27951 TTTAAAAATGAATTATATTATATAA
1 TTTAAAAATGAAAAATATTATATAA
27976 TTTAAAAATGAAAAATA-TATAT
1 TTTAAAAATGAAAAATATTATAT
27998 TAATATGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.40
Consensus pattern (25 bp):
TTTAAAAATGAAAAATATTATATAA
Found at i:30087 original size:15 final size:14
Alignment explanation
Indices: 30069--30116 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 14
30059 AAAAAATAAT
*
30069 AAATATTAAAATTTA
1 AAAT-TTAAATTTTA
*
30084 AAATTTTAATTTATA
1 AAATTTAAATTT-TA
30099 AAATTTTAAATTTTA
1 AAA-TTTAAATTTTA
30114 AAA
1 AAA
30117 ATAAAGATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
14 6 0.21
15 14 0.50
16 8 0.29
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
AAATTTAAATTTTA
Found at i:30280 original size:2 final size:2
Alignment explanation
Indices: 30273--30297 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
30263 TTCATTACTT
30273 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
30298 TAATTTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30476 original size:26 final size:30
Alignment explanation
Indices: 30459--30525 Score: 75
Period size: 32 Copynumber: 2.2 Consensus size: 30
30449 AATAAATTAG
*
30459 TTATATTAT-TATATAAAACTAATTGTATA
1 TTATATTATATATATAAAACTAAATGTATA
*
30488 TTATATTATATATATATATTA-TAAATGATATA
1 TTATATTATATATATA-A-AACTAAATG-TATA
30520 TTATAT
1 TTATAT
30526 AATTTTAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
29 9 0.28
30 6 0.19
31 6 0.19
32 11 0.34
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (30 bp):
TTATATTATATATATAAAACTAAATGTATA
Found at i:30510 original size:7 final size:7
Alignment explanation
Indices: 30489--30526 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
30479 AATTGTATAT
30489 TATATTA
1 TATATTA
30496 TATA-TA
1 TATATTA
30502 TATATTA
1 TATATTA
* *
30509 TAAATGA
1 TATATTA
30516 TATATTA
1 TATATTA
30523 TATA
1 TATA
30527 ATTTTAAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
6 6 0.23
7 20 0.77
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (7 bp):
TATATTA
Found at i:30518 original size:18 final size:19
Alignment explanation
Indices: 30484--30525 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
30474 AAACTAATTG
*
30484 TATATTATATTATATATA-
1 TATATTATATAATATATAT
30502 TATATTATA-AATGATATAT
1 TATATTATATAAT-ATATAT
30521 TATAT
1 TATAT
30526 AATTTTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 2 0.10
18 14 0.67
19 5 0.24
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
TATATTATATAATATATAT
Found at i:30534 original size:22 final size:22
Alignment explanation
Indices: 30494--30535 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
30484 TATATTATAT
30494 TATATATATATATTATAAATGA
1 TATATATATATATTATAAATGA
*
30516 TATAT-TATATAATTTTAAAT
1 TATATATATAT-ATTATAAAT
30536 TATTTTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
TATATATATATATTATAAATGA
Found at i:31326 original size:23 final size:23
Alignment explanation
Indices: 31297--31348 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
31287 TTTATGTTAT
*
31297 AAAAATAAGAAATGTAAAAAATA
1 AAAAATAAAAAATGTAAAAAATA
* *
31320 AAAAATAAAAAATTTAAATAATA
1 AAAAATAAAAAATGTAAAAAATA
31343 AGAAAA
1 A-AAAA
31349 ACAATAATCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 21 0.84
24 4 0.16
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (23 bp):
AAAAATAAAAAATGTAAAAAATA
Found at i:35769 original size:4 final size:4
Alignment explanation
Indices: 35746--35797 Score: 77
Period size: 4 Copynumber: 13.0 Consensus size: 4
35736 AAATCAATGT
* * *
35746 CATA CATG CATG CATG CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
35794 CATA
1 CATA
35798 TATATATATA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 46 1.00
ACGTcount: A:0.44, C:0.25, G:0.06, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:40285 original size:24 final size:22
Alignment explanation
Indices: 40240--40285 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
40230 TTGAAATATT
*
40240 CAAATAAATAAATATTATTTTA
1 CAAATAAATAAATATTACTTTA
*
40262 CAAATAACATATAATATTCCTTTA
1 CAAATAA-ATA-AATATTACTTTA
40286 TTTTACATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 7 0.35
23 3 0.15
24 10 0.50
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (22 bp):
CAAATAAATAAATATTACTTTA
Found at i:40680 original size:6 final size:6
Alignment explanation
Indices: 40649--40704 Score: 60
Period size: 6 Copynumber: 9.2 Consensus size: 6
40639 TTTAAAAGCC
**
40649 AAATATT AAACTTT AAATTT GTATTT AAATTT AAATTT AAATTT -AATTT
1 AAAT-TT AAA-TTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
*
40698 TAATTT A
1 AAATTT A
40705 TTCAAATAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
5 5 0.12
6 28 0.67
7 8 0.19
8 1 0.02
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (6 bp):
AAATTT
Found at i:41803 original size:29 final size:30
Alignment explanation
Indices: 41770--41839 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
41760 GATAATTTTA
*
41770 AATATAATATGATT-ATATA-AAATAAATAT
1 AATATAATATGATTAAAATATAAA-AAATAT
* *
41799 AATATAAAAT-TTTAAAATATAAAAAATAT
1 AATATAATATGATTAAAATATAAAAAATAT
41828 AATATAATATGA
1 AATATAATATGA
41840 AAAATAATAT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
28 2 0.06
29 28 0.85
30 3 0.09
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (30 bp):
AATATAATATGATTAAAATATAAAAAATAT
Found at i:41981 original size:19 final size:19
Alignment explanation
Indices: 41822--41988 Score: 80
Period size: 19 Copynumber: 8.7 Consensus size: 19
41812 AAAATATAAA
41822 AAATATAATATAATATGA-A-
1 AAATAT-ATA-AATATGATAT
* *
41841 AAATAATATAAACATGACAT
1 AAAT-ATATAAATATGATAT
*
41861 AGATATATAAATAT-ATAT
1 AAATATATAAATATGATAT
* *
41879 AATTTTATATAATATGAATAAT
1 AAATATATA-AATATG-AT-AT
* *
41901 TAATATATAAA-ATTTATAT
1 AAATATATAAATA-TGATAT
*
41920 AAATATA-AAATAT--TTT
1 AAATATATAAATATGATAT
* * *
41936 AAATACTGTTATAATA-CATAA
1 AAATA-T-ATA-AATATGATAT
41957 AAATATATAAATATGATAT
1 AAATATATAAATATGATAT
*
41976 AAATATATTAATA
1 AAATATATAAATA
41989 ATCATATTTA
Statistics
Matches: 112, Mismatches: 20, Indels: 32
0.68 0.12 0.20
Matches are distributed among these distances:
16 7 0.06
17 1 0.01
18 23 0.21
19 49 0.44
20 13 0.12
21 11 0.10
22 8 0.07
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (19 bp):
AAATATATAAATATGATAT
Found at i:43485 original size:20 final size:20
Alignment explanation
Indices: 43433--43486 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
43423 ATTTAAAAAT
* * *
43433 TAAATTTAATTTATTTTGAA
1 TAAATTTTATTTAATTTAAA
*
43453 TATGATTTT-TTTAATTTAAA
1 TA-AATTTTATTTAATTTAAA
43473 TAAATTTTATTTAA
1 TAAATTTTATTTAA
43487 ATTATTATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
19 5 0.19
20 18 0.67
21 4 0.15
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (20 bp):
TAAATTTTATTTAATTTAAA
Found at i:43851 original size:38 final size:38
Alignment explanation
Indices: 43803--43880 Score: 104
Period size: 38 Copynumber: 2.1 Consensus size: 38
43793 TAATATTTTT
*
43803 AATTTGATATTTATTTTTTA-TAATTAAAAAATTAAAAA
1 AATTTGATATTTATTTTATATTAATT-AAAAATTAAAAA
* * *
43841 AATTTTATATTTATTTTATATTAATTTAAACTTAAAAA
1 AATTTGATATTTATTTTATATTAATTAAAAATTAAAAA
43879 AA
1 AA
43881 AATTAAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 30 0.86
39 5 0.14
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (38 bp):
AATTTGATATTTATTTTATATTAATTAAAAATTAAAAA
Found at i:45340 original size:13 final size:13
Alignment explanation
Indices: 45324--45372 Score: 62
Period size: 13 Copynumber: 3.5 Consensus size: 13
45314 TTTGATTTTC
45324 TATTTTTTTAAAA
1 TATTTTTTTAAAA
45337 TATTTTTTTAAAAA
1 TATTTTTTT-AAAA
45351 TATTTATTTTTAAATA
1 TA-TT-TTTTTAAA-A
45367 TATTTT
1 TATTTT
45373 GAATATGAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
13 9 0.28
14 8 0.25
15 7 0.22
16 8 0.25
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TATTTTTTTAAAA
Found at i:45343 original size:14 final size:14
Alignment explanation
Indices: 45326--45372 Score: 67
Period size: 14 Copynumber: 3.2 Consensus size: 14
45316 TGATTTTCTA
45326 TTTTTTTAAAATAT
1 TTTTTTTAAAATAT
*
45340 TTTTTTAAAAATAT
1 TTTTTTTAAAATAT
45354 TTATTTTTAAATATAT
1 TT-TTTTTAAA-ATAT
45370 TTT
1 TTT
45373 GAATATGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 15 0.52
15 8 0.28
16 6 0.21
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTTTTAAAATAT
Found at i:45826 original size:16 final size:17
Alignment explanation
Indices: 45801--45833 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
45791 TTTATATTTA
45801 AATATATAAAAAATATT
1 AATATATAAAAAATATT
*
45818 AATAT-TAAATAATATT
1 AATATATAAAAAATATT
45834 TTAAAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AATATATAAAAAATATT
Found at i:48032 original size:15 final size:15
Alignment explanation
Indices: 48012--48040 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
48002 ATCCATGCGT
48012 TACGTCAATATCCAA
1 TACGTCAATATCCAA
48027 TACGTCAATATCCA
1 TACGTCAATATCCA
48041 GTACCCATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.28, G:0.07, T:0.28
Consensus pattern (15 bp):
TACGTCAATATCCAA
Done.