Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1544
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: 34733
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Found at i:886 original size:14 final size:15
Alignment explanation
Indices: 867--897 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
857 CAAGAAATGG
867 GAAGAAAAAT-TGTT
1 GAAGAAAAATGTGTT
881 GAAGAAAAATGTGTT
1 GAAGAAAAATGTGTT
896 GA
1 GA
898 TGAACCCGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.48, C:0.00, G:0.26, T:0.26
Consensus pattern (15 bp):
GAAGAAAAATGTGTT
Found at i:3129 original size:140 final size:140
Alignment explanation
Indices: 2877--3134 Score: 317
Period size: 140 Copynumber: 1.8 Consensus size: 140
2867 TATTCCACGT
* *
2877 GATATTTCTGGTCTATCCTCTTTGATACATCTTGATCTTAGTGGTAACAATTTCATCAGCATACC
1 GATATTTCTGGTCTATCCTCTTTGATACATCTTGATCTTAGGGGTAACAATTTCATCACCATACC
* * * ** *
2942 TGCATCTCTTACTCAGCTCTCGAAGCTTTCGTTTCTTGATTGTCAAATTGCAACATGTGCACACT
66 TGCAGCTCTTACTCAACTCTAGAAGCTTTAATTTCTTGATTATCAAATTGCAACATGTGCACACT
3007 TGGTGAAGCA
131 TGGTGAAGCA
* * *
3017 GATA-TTCATGGTCTATCCTCTTTGAGT-TATCTTTATCTTAGGGGTAACAATTTCATCACCATT
1 GATATTTC-TGGTCTATCCTCTTTGA-TACATCTTGATCTTAGGGGTAACAATTTCATCACCATA
*** *
3080 CCTTTGGCTCTTACTCAACT-TAGCAGGC-TTAATTTCTTCGATTATCAAATTGCAA
64 CCTGCAGCTCTTACTCAACTCTAG-AAGCTTTAATTTCTT-GATTATCAAATTGCAA
3135 GATGCTTAAA
Statistics
Matches: 99, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
139 13 0.13
140 85 0.86
141 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.39
Consensus pattern (140 bp):
GATATTTCTGGTCTATCCTCTTTGATACATCTTGATCTTAGGGGTAACAATTTCATCACCATACC
TGCAGCTCTTACTCAACTCTAGAAGCTTTAATTTCTTGATTATCAAATTGCAACATGTGCACACT
TGGTGAAGCA
Found at i:5979 original size:52 final size:53
Alignment explanation
Indices: 5922--6027 Score: 135
Period size: 52 Copynumber: 2.0 Consensus size: 53
5912 GGAATGCATA
* * * *
5922 AAAGTCTATTCGAATCAATTTA-TCTGACCGAAACTGATGTAATCCCTTT-TAT
1 AAAGTCTATTCAAATAAACTTATTCAG-CCGAAACTGATGTAATCCCTTTATAT
* *
5974 AAAGTCTGTTCAAATAAACTTATTCAGTCGAAACTGATGTAATCCCTTTATAT
1 AAAGTCTATTCAAATAAACTTATTCAGCCGAAACTGATGTAATCCCTTTATAT
6027 A
1 A
6028 CATATCTAGA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
52 39 0.85
53 7 0.15
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.36
Consensus pattern (53 bp):
AAAGTCTATTCAAATAAACTTATTCAGCCGAAACTGATGTAATCCCTTTATAT
Found at i:6999 original size:16 final size:16
Alignment explanation
Indices: 6966--6999 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
6956 CTATACTGTT
* *
6966 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
6982 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
6998 AA
1 AA
7000 TACAAAGTGG
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:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:9814 original size:21 final size:21
Alignment explanation
Indices: 9788--9828 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
9778 AGACGAGCAA
* *
9788 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
9809 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
9829 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:11763 original size:16 final size:16
Alignment explanation
Indices: 11730--11763 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
11720 GGAGATTGTT
* *
11730 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
11746 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
11762 AA
1 AA
11764 TACAAAGTGG
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:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:14684 original size:20 final size:18
Alignment explanation
Indices: 14659--14702 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
14649 TTAAATACAC
14659 TAATTAATAAAATAAATATA
1 TAATTAATAAAATAAA-A-A
*
14679 TAATTAATGAAATAAAAA
1 TAATTAATAAAATAAAAA
14697 TAATTA
1 TAATTA
14703 GACGCATGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.30
19 1 0.04
20 15 0.65
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (18 bp):
TAATTAATAAAATAAAAA
Found at i:17448 original size:28 final size:27
Alignment explanation
Indices: 17391--17542 Score: 241
Period size: 27 Copynumber: 5.6 Consensus size: 27
17381 TAAATTGTGC
*
17391 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
17418 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
17446 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
17473 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
* *
17501 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
17528 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
17543 GACTTAATAT
Statistics
Matches: 119, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
27 66 0.55
28 53 0.45
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGACTATGT
Found at i:17455 original size:55 final size:55
Alignment explanation
Indices: 17391--17542 Score: 259
Period size: 55 Copynumber: 2.8 Consensus size: 55
17381 TAAATTGTGC
*
17391 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
*
17446 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
* * *
17501 AGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCG
17543 GACTTAATAT
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 92 1.00
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
Found at i:23240 original size:16 final size:16
Alignment explanation
Indices: 23212--23258 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
23202 CTTTTTTTGA
23212 AAACACGAAAATTTTA-
1 AAACAC-AAAATTTTAG
*
23228 AAATACAAGAATTTTAG
1 AAACACAA-AATTTTAG
23245 AAACACAAAATTTT
1 AAACACAAAATTTT
23259 TTTTTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 2 0.07
16 18 0.67
17 7 0.26
ACGTcount: A:0.55, C:0.11, G:0.06, T:0.28
Consensus pattern (16 bp):
AAACACAAAATTTTAG
Found at i:23300 original size:40 final size:42
Alignment explanation
Indices: 23223--23306 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 42
23213 AACACGAAAA
*
23223 TTTTAAAATACAAGAATTTTAGAAACACAAAATTTTTTTTTT
1 TTTTAAAATACAAGAATTTTAGAAACACAAAATTTTTTATTT
* *
23265 TTTTAAAA-ACGAAGAA-TTTA-AAACACGAGATTTTTTATTT
1 TTTTAAAATAC-AAGAATTTTAGAAACACAAAATTTTTTATTT
23305 TT
1 TT
23307 ATTTTTGAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
40 19 0.50
41 6 0.16
42 13 0.34
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.44
Consensus pattern (42 bp):
TTTTAAAATACAAGAATTTTAGAAACACAAAATTTTTTATTT
Found at i:23360 original size:16 final size:17
Alignment explanation
Indices: 23329--23364 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
23319 ACGAATCTTC
*
23329 TTTTTGAAACACGAAAA
1 TTTTTAAAACACGAAAA
23346 TTTTTAAAACA-GAAAA
1 TTTTTAAAACACGAAAA
23362 TTT
1 TTT
23365 GTTTTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.36
Consensus pattern (17 bp):
TTTTTAAAACACGAAAA
Found at i:23628 original size:16 final size:17
Alignment explanation
Indices: 23607--23653 Score: 69
Period size: 16 Copynumber: 2.8 Consensus size: 17
23597 AATTTTTTTG
23607 ACACGAAAAATTTTGAA
1 ACACGAAAAATTTTGAA
*
23624 A-ACGAAAATTTTTGAA
1 ACACGAAAAATTTTGAA
*
23640 ACACGAGAAATTTT
1 ACACGAAAAATTTT
23654 TTTTAAAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
16 15 0.58
17 11 0.42
ACGTcount: A:0.49, C:0.11, G:0.13, T:0.28
Consensus pattern (17 bp):
ACACGAAAAATTTTGAA
Found at i:23672 original size:16 final size:16
Alignment explanation
Indices: 23651--23681 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
23641 CACGAGAAAT
23651 TTTTTTTAAAACACGA
1 TTTTTTTAAAACACGA
23667 TTTTTTTAAAACACG
1 TTTTTTTAAAACACG
23682 GGAATTTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.45
Consensus pattern (16 bp):
TTTTTTTAAAACACGA
Found at i:23700 original size:32 final size:32
Alignment explanation
Indices: 23653--23737 Score: 93
Period size: 31 Copynumber: 2.7 Consensus size: 32
23643 CGAGAAATTT
* *
23653 TTTTTAAAACACGATTTTTTTAAAACACGGGAA
1 TTTTTGAAACACGATTTTTTT-AAACACGAGAA
* **
23686 -TTTTGAAACACGA-TTTTATATTCACGAGAA
1 TTTTTGAAACACGATTTTTTTAAACACGAGAA
23716 TTTTTGAAACACGGATTTTTTT
1 TTTTTGAAACAC-GATTTTTTT
23738 TTAAAGAAAG
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
30 8 0.19
31 16 0.37
32 14 0.33
33 5 0.12
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.41
Consensus pattern (32 bp):
TTTTTGAAACACGATTTTTTTAAACACGAGAA
Found at i:23728 original size:17 final size:17
Alignment explanation
Indices: 23412--23728 Score: 67
Period size: 17 Copynumber: 18.8 Consensus size: 17
23402 CGAGGATTTT
*
23412 TTTTTGAAACATGA-AA
1 TTTTTGAAACACGAGAA
* *
23428 -TTTAGAAACATCGA-AG
1 TTTTTGAAACA-CGAGAA
23444 TTTTTGAAAGCACGA-AGA
1 TTTTTGAAA-CACGAGA-A
* *
23462 TTTTTTAAATCATC-TGAA
1 TTTTTGAAA-CA-CGAGAA
*
23480 TTTTTAGAAACGCG-GAA
1 TTTTT-GAAACACGAGAA
* *
23497 ATTTTGAAACACCA-AA
1 TTTTTGAAACACGAGAA
* *
23513 TTTTTAAAAACAC-AAAGA
1 TTTTT-GAAACACGAGA-A
* * * *
23531 TTTTCGAAACACAATATT
1 TTTTTGAAACACGAGA-A
23549 TTTTTGAAACACGA-AA
1 TTTTTGAAACACGAGAA
* **
23565 -ATTTGAAA-ATAAGGAAA
1 TTTTTGAAACACGA-G-AA
* * *
23582 TTTTCGATACAGGAGAA
1 TTTTTGAAACACGAGAA
*** *
23599 TTTTTTTGACACGAAAA
1 TTTTTGAAACACGAGAA
* *
23616 ATTTTGAAA-ACGAAAA
1 TTTTTGAAACACGAGAA
23632 TTTTTGAAACACGAGAAA
1 TTTTTGAAACACGAG-AA
* **
23650 TTTTTTTTAAAACACGA-TT
1 ---TTTTTGAAACACGAGAA
* *
23669 TTTTTAAAACACGGGAA
1 TTTTTGAAACACGAGAA
23686 -TTTTGAAACAC--G-A
1 TTTTTGAAACACGAGAA
**
23699 TTTTAT-ATTCACGAGAA
1 TTTT-TGAAACACGAGAA
23716 TTTTTGAAACACG
1 TTTTTGAAACACG
23729 GATTTTTTTT
Statistics
Matches: 217, Mismatches: 54, Indels: 59
0.66 0.16 0.18
Matches are distributed among these distances:
13 1 0.00
14 10 0.05
15 17 0.08
16 56 0.26
17 67 0.31
18 46 0.21
19 7 0.03
21 13 0.06
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (17 bp):
TTTTTGAAACACGAGAA
Found at i:24274 original size:14 final size:14
Alignment explanation
Indices: 24251--24281 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
24241 CTGCTGCTTC
*
24251 TTTCTTCTTCTTTT
1 TTTCTGCTTCTTTT
24265 TTTCTGCTTCTTTT
1 TTTCTGCTTCTTTT
24279 TTT
1 TTT
24282 GCTTTGTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.00, C:0.19, G:0.03, T:0.77
Consensus pattern (14 bp):
TTTCTGCTTCTTTT
Found at i:24419 original size:10 final size:10
Alignment explanation
Indices: 24406--24497 Score: 50
Period size: 10 Copynumber: 9.0 Consensus size: 10
24396 TTTTTATTTT
24406 CTTTTCTTTC
1 CTTTTCTTTC
24416 CTTTTCTATT-
1 CTTTTCT-TTC
* *
24426 TTTTTCTCTC
1 CTTTTCTTTC
24436 CTTTTTTTCTTTC
1 C---TTTTCTTTC
*
24449 TTTTTCTTTC
1 CTTTTCTTTC
24459 TCTTTTCTTCTC
1 -CTTTTCTT-TC
*
24471 TTTTTC-TT-
1 CTTTTCTTTC
24479 CTCTTT-TTTC
1 CT-TTTCTTTC
24489 CTTTT-TTTC
1 CTTTTCTTTC
24498 TTCCTCTTCT
Statistics
Matches: 64, Mismatches: 8, Indels: 21
0.69 0.09 0.23
Matches are distributed among these distances:
8 1 0.02
9 14 0.22
10 25 0.39
11 14 0.22
12 2 0.03
13 8 0.12
ACGTcount: A:0.01, C:0.25, G:0.00, T:0.74
Consensus pattern (10 bp):
CTTTTCTTTC
Found at i:24448 original size:27 final size:28
Alignment explanation
Indices: 24386--24473 Score: 76
Period size: 30 Copynumber: 3.2 Consensus size: 28
24376 TTTTTGTTTA
* * * *
24386 TCTTTTTATTTTTTTATTTTCTTTTCTT
1 TCTTTCTATTTTTTTCTCTCCTTTTCTT
24414 TCCTTTTCTATTTTTTTCTCTCCTTTT-TT
1 T-C-TTTCTATTTTTTTCTCTCCTTTTCTT
*
24443 TCTTTCT-TTTTCTT-TCT-CTTTTCTT
1 TCTTTCTATTTTTTTCTCTCCTTTTCTT
24468 CTCTTT
1 -TCTTT
24474 TTCTTCTCTT
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
24 5 0.10
25 5 0.10
26 11 0.22
27 5 0.10
28 2 0.04
29 4 0.08
30 19 0.37
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.76
Consensus pattern (28 bp):
TCTTTCTATTTTTTTCTCTCCTTTTCTT
Found at i:24449 original size:37 final size:35
Alignment explanation
Indices: 24397--24493 Score: 90
Period size: 37 Copynumber: 2.6 Consensus size: 35
24387 CTTTTTATTT
*
24397 TTTTATTTTCTTTTCTTTCCTTTTCTATTTTTTTCTC
1 TTTT-TTTTC-TTTCTTTCCTTTTCTATTTTCTTCTC
* *
24434 TCCTTTTTTTCTTTCTTT-TTCTTTCTCTTTTCTTCTC
1 T--TTTTTTTCTTTCTTTCCT-TTTCTATTTTCTTCTC
24471 TTTTTCTTCTCTTT-TTTCCTTTT
1 TTTTT-TT-TCTTTCTTTCCTTTT
24494 TTTCTTCCTC
Statistics
Matches: 50, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
35 4 0.08
36 9 0.18
37 29 0.58
38 5 0.10
39 3 0.06
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.75
Consensus pattern (35 bp):
TTTTTTTTCTTTCTTTCCTTTTCTATTTTCTTCTC
Found at i:24452 original size:11 final size:11
Alignment explanation
Indices: 24407--24488 Score: 64
Period size: 10 Copynumber: 7.5 Consensus size: 11
24397 TTTTATTTTC
*
24407 TTTTCTTTC-C
1 TTTTCTTTCTT
*
24417 TTTTCTAT-TT
1 TTTTCTTTCTT
*
24427 TTTTCTCTCCTTT
1 TTTTCT-TTC-TT
24440 TTTTCTTTC-T
1 TTTTCTTTCTT
*
24450 TTTTCTTTCTC
1 TTTTCTTTCTT
24461 TTTTC-TTCTCT
1 TTTTCTTTCT-T
24472 TTTTCTTCTCTT
1 TTTTCTT-TCTT
24484 TTTTC
1 TTTTC
24489 CTTTTTTTCT
Statistics
Matches: 57, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
10 27 0.47
11 10 0.18
12 9 0.16
13 11 0.19
ACGTcount: A:0.01, C:0.24, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTTCTTTCTT
Found at i:24455 original size:43 final size:44
Alignment explanation
Indices: 24394--24505 Score: 126
Period size: 43 Copynumber: 2.6 Consensus size: 44
24384 TATCTTTTTA
*
24394 TTTTTTTATTTTCTTTTCTTTC-CTTTTCTAT-T-TTTTTC-TCTCC
1 TTTTTTTCTTTT-TTTTCTTTCTCTTTTCT-TCTCTTTTTCTTCT-C
24437 TTTTTTTCTTTCTTTTTCTTTCTCTTTTCTTCTCTTTTTCTTCTC
1 TTTTTTTCTTT-TTTTTCTTTCTCTTTTCTTCTCTTTTTCTTCTC
* *
24482 -TTTTTTCCTTTTTTTCTTCCTCTT
1 TTTTTTTCTTTTTTTTCTTTCTCTT
24506 CTTCGGCCGA
Statistics
Matches: 61, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
43 33 0.54
44 18 0.30
45 7 0.11
46 3 0.05
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.75
Consensus pattern (44 bp):
TTTTTTTCTTTTTTTTCTTTCTCTTTTCTTCTCTTTTTCTTCTC
Found at i:24466 original size:21 final size:21
Alignment explanation
Indices: 24403--24505 Score: 88
Period size: 23 Copynumber: 4.9 Consensus size: 21
24393 ATTTTTTTAT
24403 TTTC-TTTTCTTTC-CTTTTC
1 TTTCTTTTTCTTTCTCTTTTC
* *
24422 TATT-TTTTTCTCTCCTTTTTTTC
1 T-TTCTTTTTCT-TTC-TCTTTTC
24445 TTTCTTTTTCTTTCTCTTTTC
1 TTTCTTTTTCTTTCTCTTTTC
*
24466 TTCTCTTTTTCTTCTCTTTTTTC
1 TT-TCTTTTTCTT-TCTCTTTTC
* *
24489 CTT-TTTTTCTTCCTCTT
1 TTTCTTTTTCTTTCTCTT
24506 CTTCGGCCGA
Statistics
Matches: 68, Mismatches: 8, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
19 1 0.01
20 12 0.18
21 18 0.26
22 15 0.22
23 22 0.32
ACGTcount: A:0.01, C:0.25, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTCTTTTTCTTTCTCTTTTC
Found at i:25082 original size:30 final size:30
Alignment explanation
Indices: 25042--25143 Score: 125
Period size: 30 Copynumber: 3.4 Consensus size: 30
25032 ATTTAGGATT
*
25042 AAAATGAAATTTAATGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAAGGGTC
* * *
25072 TAAGTGAAATTTAAAGAAAGTTTAAAGGTC
1 AAAATGAAATTTAAAGAAAGTTTAAGGGTC
* *
25102 AAAATGAAATTT-AGGAAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAG-AAAGTTTAAGGGTC
*
25132 AAAATGCAATTT
1 AAAATGAAATTT
25144 TTATTTTTTA
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
29 2 0.03
30 59 0.97
ACGTcount: A:0.46, C:0.04, G:0.21, T:0.29
Consensus pattern (30 bp):
AAAATGAAATTTAAAGAAAGTTTAAGGGTC
Found at i:25588 original size:54 final size:55
Alignment explanation
Indices: 25416--25637 Score: 360
Period size: 54 Copynumber: 4.0 Consensus size: 55
25406 CACGTGAACC
* *
25416 AAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTG-AAAACAGAATTTGCAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTG-AA
* *
25471 AAGGCTCAACTCACCTCTCGCAATATGAGTTGTTTTTTTTGAAAAATAGAAATT-AA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTG--ATTTTTGAAAAACAGAAATTGAA
25527 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATT-AA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
25581 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
25636 AA
1 AA
25638 TACCTCAACG
Statistics
Matches: 157, Mismatches: 6, Indels: 8
0.92 0.04 0.05
Matches are distributed among these distances:
54 72 0.46
55 35 0.22
56 34 0.22
57 6 0.04
58 10 0.06
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Consensus pattern (55 bp):
AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
Found at i:25618 original size:111 final size:110
Alignment explanation
Indices: 25416--25637 Score: 360
Period size: 111 Copynumber: 2.0 Consensus size: 110
25406 CACGTGAACC
* *
25416 AAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTGAAAACAGAATTTGCAAAAGGCTCAAC
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATT-CAAAAGGCTCAAC
25481 TCACCTCTCGCAATATGAGTTGTTTTTTTTGAAAAATAGAAATTAA
65 TCACCTCTCGCAATATGAGTTGTTTTTTTTGAAAAATAGAAATTAA
25527 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATT-AAAAGGCTCAAC
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAACAGAAATTCAAAAGGCTCAAC
* *
25591 TCACCTCTCGCAATATGAGTTG--ATTTTTGAAAAACAGAAATTGAA
65 TCACCTCTCGCAATATGAGTTGTTTTTTTTGAAAAATAGAAATT-AA
25636 AA
1 AA
25638 TACCTCAACG
Statistics
Matches: 105, Mismatches: 4, Indels: 6
0.91 0.03 0.05
Matches are distributed among these distances:
108 18 0.17
109 4 0.04
110 34 0.32
111 38 0.36
112 11 0.10
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Consensus pattern (110 bp):
AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTCAAAAGGCTCAACT
CACCTCTCGCAATATGAGTTGTTTTTTTTGAAAAATAGAAATTAA
Found at i:26029 original size:71 final size:72
Alignment explanation
Indices: 25582--26322 Score: 1051
Period size: 72 Copynumber: 10.4 Consensus size: 72
25572 AGAAATTAAA
** *
25582 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAAC
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTG-AAAACAGAAATTGAAAATACCTCAAC
25647 GTGTCTTG
65 GTGTCTTG
* *
25655 AGGCTCAACTCATTTCTCGCAATATGAGTTAAATTTTGAAAACAGAAATTGAAATTACCTCAACG
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAACG
25720 TGTCTTG
66 TGTCTTG
* *
25727 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAGCAAAAATTGAAAATACCTCAAT
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAA-CAGAAATTGAAAATACCTCAAC
25792 GTGTCTTG
65 GTGTCTTG
* * *
25800 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTA-CTCAGCA
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAACG
*
25864 TGTCCTG
66 TGTCTTG
* *
25871 AGGCTCAACTCATTTCTCGCAGTATGAGTTGAA-TTTGAAAAGCA-AAATTGAAAATACCTTAA-
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAA-CAGAAATTGAAAATACCTCAAC
25933 -TGTCTTG
65 GTGTCTTG
*
25940 A-GCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAACG
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAACG
26004 TGTCTTG
66 TGTCTTG
* *
26011 AGGCTC-ACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAAAAATTG-AATTACCTCAACG
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAACG
26074 TGTCTTG
66 TGTCTTG
* * *
26081 AGGCTC-ACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAGCA
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAACG
*
26145 TGTCCTG
66 TGTCTTG
* * * *
26152 AGGCTCAACTCATTTCTCGCAATATGAGTTGAA-ATTAAAACACAAAAATTGAAAATACCTCAGC
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAA-ACAGAAATTGAAAATACCTCAAC
* * **
26216 ATGCCCCG
65 GTGTCTTG
* *
26224 AGGCTCAACTCACTTCTCGCAATATGAGTTG-ATTTTGAAAACA-ACAATTAAAAATACCTCAAC
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGA-AATTGAAAATACCTCAAC
26287 GTGTCTTG
65 GTGTCTTG
* *
26295 A-GCTCAACTCATCTCTCAC-ATATGAGTT
1 AGGCTCAACTCATTTCTCGCAATATGAGTT
26323 TATTTCCCTT
Statistics
Matches: 609, Mismatches: 46, Indels: 30
0.89 0.07 0.04
Matches are distributed among these distances:
68 32 0.05
69 40 0.07
70 104 0.17
71 151 0.25
72 179 0.29
73 103 0.17
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.30
Consensus pattern (72 bp):
AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAAATACCTCAACG
TGTCTTG
Found at i:26286 original size:284 final size:286
Alignment explanation
Indices: 25582--26322 Score: 1153
Period size: 284 Copynumber: 2.6 Consensus size: 286
25572 AGAAATTAAA
** * *
25582 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAATACCTCAAC
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGA-ATTTGAAAAACAAAAATTGAAAATACCTC-AC
* *
25647 GTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTAAATTTTGAAAACAGAAATTGAAATTA
64 ATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTT-GATTTTGAAAACAGAAATTGAAATTA
25712 CCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAGCAAAAAT
128 CCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAGCAAAAAT
*
25777 TGAAAATACCTCAATGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAA
193 TGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAA
25842 CAGAAATTGAAATTACTCAGCATGTCCTG
258 CAGAAATTGAAATTACTCAGCATGTCCTG
* * *
25871 AGGCTCAACTCATTTCTCGCAGTATGAGTTGAATTTGAAAAGC-AAAATTGAAAATACCTTA-AT
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTGAAAAACAAAAATTGAAAATACCTCACAT
25934 GTCTTGA-GCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAATTACC
66 GTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTG-ATTTTGAAAACAGAAATTGAAATTACC
25998 TCAACGTGTCTTGAGGCTC-ACTCATTTCTCGCAATATGAGTTGAATTTTGAAAA-CAAAAATTG
130 TCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAGCAAAAATTG
*
26061 -AATTACCTCAACGTGTCTTGAGGCTC-ACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACA
195 AAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACA
26124 GAAATTGAAATTACCTCAGCATGTCCTG
260 GAAATTGAAATTA-CTCAGCATGTCCTG
*
26152 AGGCTCAACTCATTTCTCGCAATATGAGTTGAAATT-AAAACACAAAAATTGAAAATACCTCAGC
1 AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTGAAAA-ACAAAAATTGAAAATACCTCA-C
* ** * * *
26216 ATGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAACA-ACAATTAAAAATA
64 ATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAACAGA-AATTGAAATTA
* *
26280 CCTCAACGTGTCTTGA-GCTCAACTCATCTCTCAC-ATATGAGTT
128 CCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTT
26323 TATTTCCCTT
Statistics
Matches: 420, Mismatches: 23, Indels: 24
0.90 0.05 0.05
Matches are distributed among these distances:
280 54 0.13
281 73 0.17
282 26 0.06
283 49 0.12
284 128 0.30
285 36 0.09
286 1 0.00
287 15 0.04
288 9 0.02
289 29 0.07
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.30
Consensus pattern (286 bp):
AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTGAAAAACAAAAATTGAAAATACCTCACAT
GTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAACAGAAATTGAAATTACCT
CAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAGCAAAAATTGA
AAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAG
AAATTGAAATTACTCAGCATGTCCTG
Done.