Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold665
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: 38090
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:302 original size:19 final size:19
Alignment explanation
Indices: 269--307 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
259 TTTATTTAAT
269 TTTTTTAAATATTAAATAAA
1 TTTTTTAAATATTAAA-AAA
*
289 TTTTTT-AATTTTAAAAAA
1 TTTTTTAAATATTAAAAAA
307 T
1 T
308 AATCTAACCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 8 0.44
20 6 0.33
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTTTTAAATATTAAAAAA
Found at i:1066 original size:20 final size:21
Alignment explanation
Indices: 1022--1066 Score: 51
Period size: 20 Copynumber: 2.2 Consensus size: 21
1012 TTAATAAAAA
1022 AAAT-TACTAATTATTATATT
1 AAATATACTAATTATTATATT
*
1042 TAATATACT-ATTATTA-ATAT
1 AAATATACTAATTATTATAT-T
1062 AAATA
1 AAATA
1067 ATAAATCAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
19 2 0.10
20 15 0.71
21 4 0.19
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (21 bp):
AAATATACTAATTATTATATT
Found at i:2701 original size:17 final size:17
Alignment explanation
Indices: 2657--2703 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 17
2647 ATTATAAATT
2657 TTTTAAAAT-TATTT--
1 TTTTAAAATATATTTAA
2671 TTTTATAAA-A-ATTTAA
1 TTTTA-AAATATATTTAA
2687 TTTTAAAATATATTTAA
1 TTTTAAAATATATTTAA
2704 AATATTAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
14 9 0.33
15 6 0.22
16 6 0.22
17 6 0.22
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTTAAAATATATTTAA
Found at i:2705 original size:24 final size:24
Alignment explanation
Indices: 2678--2728 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
2668 TTTTTTTATA
* *
2678 AAAAT-TTAATTTTAAAATATATTT
1 AAAATATTAATATAAAAATAT-TTT
2702 AAAATATTAATATAAAAATATTTT
1 AAAATATTAATATAAAAATATTTT
2726 AAA
1 AAA
2729 TGGTACAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 11 0.46
25 13 0.54
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
AAAATATTAATATAAAAATATTTT
Found at i:2788 original size:25 final size:25
Alignment explanation
Indices: 2760--2812 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
2750 TGATAGTATA
2760 AATTAAATTTATTAAATATTAATTT
1 AATTAAATTTATTAAATATTAATTT
* * * *
2785 AATTTAATTTATTTAATTTTATTTT
1 AATTAAATTTATTAAATATTAATTT
2810 AAT
1 AAT
2813 CATTTTTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
AATTAAATTTATTAAATATTAATTT
Found at i:3593 original size:58 final size:57
Alignment explanation
Indices: 3502--3622 Score: 208
Period size: 58 Copynumber: 2.1 Consensus size: 57
3492 TCATAGGCTG
*
3502 TGAGATGTAGATTAAATTTGCTTAGGGATAATTTGGTAATATTCTTTTT-AAAAAAAT
1 TGAGATATAGATTAAATTTGCTTAGGGATAATTTGGTAATATT-TTTTTAAAAAAAAT
3559 TGGAGATATAGATTAAATTTGCTTAGGGATAATTTGGTAATATTTTTTTAAAAAAAAT
1 T-GAGATATAGATTAAATTTGCTTAGGGATAATTTGGTAATATTTTTTTAAAAAAAAT
3617 TGAGAT
1 TGAGAT
3623 GGTAAAATTT
Statistics
Matches: 61, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
57 11 0.18
58 50 0.82
ACGTcount: A:0.38, C:0.02, G:0.18, T:0.41
Consensus pattern (57 bp):
TGAGATATAGATTAAATTTGCTTAGGGATAATTTGGTAATATTTTTTTAAAAAAAAT
Found at i:3859 original size:15 final size:15
Alignment explanation
Indices: 3839--3872 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
3829 TTTTATTTAA
*
3839 ATTTAATTATAAAAT
1 ATTTAAATATAAAAT
3854 ATTTAAATATAAAAT
1 ATTTAAATATAAAAT
3869 -TTTA
1 ATTTA
3873 TTTTTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTTAAATATAAAAT
Found at i:4787 original size:8 final size:8
Alignment explanation
Indices: 4774--4830 Score: 51
Period size: 8 Copynumber: 6.9 Consensus size: 8
4764 ATAAATATTT
4774 TATAAATA
1 TATAAATA
4782 TATAAATTA
1 TATAAA-TA
* *
4791 TTTAATTA
1 TATAAATA
*
4799 TTTAATATA
1 TATAA-ATA
*
4808 TATATATA
1 TATAAATA
*
4816 TATATATA
1 TATAAATA
4824 TATAAAT
1 TATAAAT
4831 TTGGACCTAC
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
8 30 0.73
9 11 0.27
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (8 bp):
TATAAATA
Found at i:4810 original size:2 final size:2
Alignment explanation
Indices: 4803--4827 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4793 TAATTATTTA
4803 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
4828 AATTTGGACC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6519 original size:34 final size:34
Alignment explanation
Indices: 6451--6667 Score: 294
Period size: 34 Copynumber: 6.4 Consensus size: 34
6441 CATATCAGTT
* * *
6451 TTGTTGATTAAAT-GGTGATTTAGTAGTTTACCA
1 TTGTTGATTAAATGGGAGATTTGGTAGCTTACCA
* * * *
6484 TTGTTGATTAAATGGGTGATTTGGTGGTTTGCCA
1 TTGTTGATTAAATGGGAGATTTGGTAGCTTACCA
*
6518 TTGTTGACTAAAT-GGAGATTTGGTAGCTTACCA
1 TTGTTGATTAAATGGGAGATTTGGTAGCTTACCA
*
6551 TTGTTGATTAAATGGGAAATTTGGTAGCTTACCA
1 TTGTTGATTAAATGGGAGATTTGGTAGCTTACCA
* *
6585 TTGTTGATTAAATGGGTGATTTGGTGGCTTACCA
1 TTGTTGATTAAATGGGAGATTTGGTAGCTTACCA
* * *
6619 TTGTTGACTAAATGGGAGATTTGGTAGGTTGCCA
1 TTGTTGATTAAATGGGAGATTTGGTAGCTTACCA
6653 TTGTTGATTAAATGG
1 TTGTTGATTAAATGG
6668 TGGTTTTTAC
Statistics
Matches: 163, Mismatches: 19, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
33 41 0.25
34 122 0.75
ACGTcount: A:0.24, C:0.08, G:0.27, T:0.41
Consensus pattern (34 bp):
TTGTTGATTAAATGGGAGATTTGGTAGCTTACCA
Found at i:6633 original size:68 final size:67
Alignment explanation
Indices: 6451--6669 Score: 321
Period size: 67 Copynumber: 3.3 Consensus size: 67
6441 CATATCAGTT
* * * * *
6451 TTGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTGC
1 TTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGC
6516 CA
66 CA
* * * *
6518 TTGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGAAATTTGGTAGCTTAC
1 TTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGC
6583 CA
66 CA
* * *
6585 TTGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTTG
1 TTGTTGATTAAAT-GGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
6650 CCA
65 CCA
6653 TTGTTGATTAAATGGTG
1 TTGTTGATTAAATGGTG
6670 GTTTTTACCA
Statistics
Matches: 135, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
67 74 0.55
68 61 0.45
ACGTcount: A:0.24, C:0.08, G:0.27, T:0.41
Consensus pattern (67 bp):
TTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGC
CA
Found at i:7028 original size:19 final size:19
Alignment explanation
Indices: 6972--7034 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
6962 TGGTTGTCGA
**
6972 GGTACTATTCACGTATATA
1 GGTACTATTCACGTATACG
6991 GGTACTATTCACGTATACG
1 GGTACTATTCACGTATACG
*
7010 GGTACTATTCAAGTATACG
1 GGTACTATTCACGTATACG
*
7029 GTTACT
1 GGTACT
7035 GTACACGTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (19 bp):
GGTACTATTCACGTATACG
Found at i:11169 original size:34 final size:34
Alignment explanation
Indices: 11100--11317 Score: 296
Period size: 34 Copynumber: 6.5 Consensus size: 34
11090 AAGTGGGAGA
* * *
11100 ATTGTTGATTAAAT-GGTGATTTAGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
11133 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
11167 ATTGTTGACTAAAT-GGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
11200 ATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
11234 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
11268 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
11302 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
11318 TGGTTTTTAC
Statistics
Matches: 164, Mismatches: 19, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
33 42 0.26
34 122 0.74
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:11283 original size:68 final size:67
Alignment explanation
Indices: 11100--11319 Score: 323
Period size: 67 Copynumber: 3.3 Consensus size: 67
11090 AAGTGGGAGA
* * * * *
11100 ATTGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
11165 CC
66 CC
* * * *
11167 ATTGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGAAATTTGGTAGCTTA
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
11232 CC
66 CC
* * *
11234 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTT
1 ATTGTTGATTAAAT-GGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTT
11299 GCC
65 GCC
11302 ATTGTTGATTAAATGGTG
1 ATTGTTGATTAAATGGTG
11320 GTTTTTACCA
Statistics
Matches: 136, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
67 75 0.55
68 61 0.45
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (67 bp):
ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
CC
Found at i:13450 original size:12 final size:12
Alignment explanation
Indices: 13406--13471 Score: 60
Period size: 12 Copynumber: 5.2 Consensus size: 12
13396 AATTAATATT
*
13406 TAAAACTTTCAAA
1 TAAAAATTT-AAA
* *
13419 AAAAAATGTAAA
1 TAAAAATTTAAA
13431 TAAAAATTTAAA
1 TAAAAATTTAAA
13443 TAAAAATTATAAA
1 TAAAAATT-TAAA
*
13456 TTATAAATTATAAA
1 -TAAAAATT-TAAA
13470 TA
1 TA
13472 TTTACTATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
12 21 0.47
13 12 0.27
14 12 0.27
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.32
Consensus pattern (12 bp):
TAAAAATTTAAA
Found at i:13458 original size:7 final size:7
Alignment explanation
Indices: 13434--13470 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
13424 ATGTAAATAA
13434 AAATT-T
1 AAATTAT
*
13440 AAA-TAA
1 AAATTAT
13446 AAATTAT
1 AAATTAT
13453 AAATTAT
1 AAATTAT
13460 AAATTAT
1 AAATTAT
13467 AAAT
1 AAAT
13471 ATTTACTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
5 1 0.04
6 6 0.22
7 20 0.74
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (7 bp):
AAATTAT
Found at i:13465 original size:14 final size:14
Alignment explanation
Indices: 13427--13470 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
13417 AAAAAAAATG
13427 TAAA-TAAAAATT-
1 TAAATTAAAAATTA
13439 TAAA-TAAAAATTA
1 TAAATTAAAAATTA
*
13452 TAAATTATAAATTA
1 TAAATTAAAAATTA
13466 TAAAT
1 TAAAT
13471 ATTTACTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 12 0.41
13 4 0.14
14 13 0.45
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
TAAATTAAAAATTA
Found at i:13996 original size:34 final size:34
Alignment explanation
Indices: 13929--14113 Score: 239
Period size: 34 Copynumber: 5.5 Consensus size: 34
13919 TCCTTTCATT
* *
13929 CATTGTTGATTAAAT-GGTGATTTGGTAGTTTAC
1 CATTGTTGATTAAATGGGAGATTTGGTAGCTTAC
* *
13962 CATTGTTGACTAAATGGGAAATTTGGTAGCTTAC
1 CATTGTTGATTAAATGGGAGATTTGGTAGCTTAC
* *
13996 CATTGTTGATTAAATAGGAGATTTAGTAGCTTAC
1 CATTGTTGATTAAATGGGAGATTTGGTAGCTTAC
* * * *
14030 CATTATTGATTAAATGGGTGATTTGGTGGTTTAC
1 CATTGTTGATTAAATGGGAGATTTGGTAGCTTAC
* * *
14064 CATTGTTGACTAAAT-GGAGATTTGGTAGGTTGC
1 CATTGTTGATTAAATGGGAGATTTGGTAGCTTAC
14097 CATTGTTGATTAAATGG
1 CATTGTTGATTAAATGG
14114 TGGTTTTTAC
Statistics
Matches: 129, Mismatches: 21, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
33 42 0.33
34 87 0.67
ACGTcount: A:0.27, C:0.08, G:0.25, T:0.40
Consensus pattern (34 bp):
CATTGTTGATTAAATGGGAGATTTGGTAGCTTAC
Found at i:14109 original size:101 final size:101
Alignment explanation
Indices: 13929--14111 Score: 305
Period size: 101 Copynumber: 1.8 Consensus size: 101
13919 TCCTTTCATT
*
13929 CATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTT
1 CATTATTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTT
13994 ACCATTGTTGATTAAATAGGAGATTTAGTAGCTTAC
66 ACCATTGTTGATTAAATAGGAGATTTAGTAGCTTAC
* * *
14030 CATTATTGATTAAATGGGTGATTTGGTGGTTTACCATTGTTGACTAAAT-GGAGATTTGGTAGGT
1 CATTATTGATTAAAT-GGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCT
*
14094 TGCCATTGTTGATTAAAT
65 TACCATTGTTGATTAAAT
14112 GGTGGTTTTT
Statistics
Matches: 76, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
101 44 0.58
102 32 0.42
ACGTcount: A:0.27, C:0.08, G:0.24, T:0.40
Consensus pattern (101 bp):
CATTATTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGGGAAATTTGGTAGCTT
ACCATTGTTGATTAAATAGGAGATTTAGTAGCTTAC
Found at i:14474 original size:19 final size:19
Alignment explanation
Indices: 14418--14480 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
14408 TGGTTGTCGA
**
14418 GGTACTATTCACGTATATA
1 GGTACTATTCACGTATACG
14437 GGTACTATTCACGTATACG
1 GGTACTATTCACGTATACG
*
14456 GGTACTATTCAAGTATACG
1 GGTACTATTCACGTATACG
*
14475 GTTACT
1 GGTACT
14481 GTACACGTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (19 bp):
GGTACTATTCACGTATACG
Found at i:18612 original size:34 final size:33
Alignment explanation
Indices: 18546--18730 Score: 235
Period size: 34 Copynumber: 5.5 Consensus size: 33
18536 AAGTGGGAGA
* *
18546 ATTGTTGATTAAATGGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGAGATTTGGTAGCTTACC
* *
18579 ATTGTTGACTAAATGGAAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGG-AGATTTGGTAGCTTACC
18613 ATTGTTGATTAAATAGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAAT-GGAGATTTGGTAGCTTACC
* * * *
18647 ATTATTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAAT-GGAGATTTGGTAGCTTACC
* * *
18681 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAAT-GGAGATTTGGTAGCTTACC
18715 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
18731 TGGTTTTTAC
Statistics
Matches: 132, Mismatches: 18, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
33 17 0.13
34 113 0.86
35 2 0.02
ACGTcount: A:0.27, C:0.08, G:0.25, T:0.40
Consensus pattern (33 bp):
ATTGTTGATTAAATGGAGATTTGGTAGCTTACC
Found at i:19545 original size:28 final size:28
Alignment explanation
Indices: 19492--19546 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
19482 TATTTTATTT
* *
19492 TTAATTATAAAAATTTATATTGTAAATA
1 TTAATTATAAAAATTAATAATGTAAATA
*
19520 TTAATTTTAAAAAATTAATAAT-TAAAT
1 TTAATTAT-AAAAATTAATAATGTAAAT
19547 TTTGATTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 12 0.52
29 11 0.48
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (28 bp):
TTAATTATAAAAATTAATAATGTAAATA
Found at i:20115 original size:15 final size:15
Alignment explanation
Indices: 20074--20116 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
20064 AGGTCTATTA
* *
20074 GAGTTTGAGTTTTTTT
1 GAGTTTGA-ATTTTTC
20090 GAGTTTAGAATTTTTC
1 GAGTTT-GAATTTTTC
20106 GAGTTTGAATT
1 GAGTTTGAATT
20117 CAAATCTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 5 0.21
16 17 0.71
17 2 0.08
ACGTcount: A:0.21, C:0.02, G:0.23, T:0.53
Consensus pattern (15 bp):
GAGTTTGAATTTTTC
Found at i:20326 original size:20 final size:19
Alignment explanation
Indices: 20301--20339 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
20291 GTTATTTTTA
20301 CTATATTTATTTATTAAAAT
1 CTATATTTATTTA-TAAAAT
20321 CTATATTTATTTATAAAAT
1 CTATATTTATTTATAAAAT
20340 TAAGTTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (19 bp):
CTATATTTATTTATAAAAT
Found at i:21449 original size:15 final size:16
Alignment explanation
Indices: 21412--21446 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
21402 GTTCAAATTT
*
21412 TTTTAAGTTTATATTA
1 TTTTAAGTTTATATCA
21428 TTTTAAGTTTATATCA
1 TTTTAAGTTTATATCA
21444 TTT
1 TTT
21447 AAGATTCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.03, G:0.06, T:0.63
Consensus pattern (16 bp):
TTTTAAGTTTATATCA
Found at i:25994 original size:2 final size:2
Alignment explanation
Indices: 25987--26021 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
25977 TCCTTCCTCC
25987 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
26022 AAAAAAGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:29312 original size:17 final size:18
Alignment explanation
Indices: 29287--29320 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
29277 TTTTTTGAAA
*
29287 ATTTATTTTTTATTTATG
1 ATTTATTTTTTACTTATG
29305 ATTT-TTTTTTACTTAT
1 ATTTATTTTTTACTTAT
29321 CTATAAATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (18 bp):
ATTTATTTTTTACTTATG
Found at i:29426 original size:28 final size:25
Alignment explanation
Indices: 29332--29405 Score: 130
Period size: 25 Copynumber: 2.9 Consensus size: 25
29322 TATAAATTGT
29332 ATTTATGAATATTTTTACTTGTCTCAG
1 ATTTATG--TATTTTTACTTGTCTCAG
29359 ATTTATGTATTTTTACTTGTCTCAG
1 ATTTATGTATTTTTACTTGTCTCAG
29384 ATTTATGTATTTTTACTTGTCT
1 ATTTATGTATTTTTACTTGTCT
29406 ACTCAGATTT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
25 40 0.85
27 7 0.15
ACGTcount: A:0.22, C:0.11, G:0.11, T:0.57
Consensus pattern (25 bp):
ATTTATGTATTTTTACTTGTCTCAG
Found at i:29903 original size:2 final size:2
Alignment explanation
Indices: 29896--29932 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
29886 CGATTACTTT
29896 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
29933 GAAGGACTTG
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:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:33615 original size:21 final size:22
Alignment explanation
Indices: 33577--33622 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
33567 ATCTATTGAA
* **
33577 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
33598 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
33620 ACT
1 ACT
33623 TGTCTGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGCGGAGTACT
Found at i:36231 original size:28 final size:27
Alignment explanation
Indices: 36186--36265 Score: 81
Period size: 28 Copynumber: 2.9 Consensus size: 27
36176 TTTGACAAAT
* * *
36186 AATAAGCCTCCATATTTGACAAATACAA
1 AATAA-CCACCATTTTTGACAAACACAA
36214 AGGA-AACCACCATTTTTGACAAACACAA
1 A--ATAACCACCATTTTTGACAAACACAA
* *
36242 AATAACTATCATTTTTGACAAACA
1 AATAACCACCATTTTTGACAAACA
36266 AATGGGTGGC
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
26 1 0.02
27 19 0.43
28 21 0.48
29 2 0.05
30 1 0.02
ACGTcount: A:0.46, C:0.21, G:0.07, T:0.25
Consensus pattern (27 bp):
AATAACCACCATTTTTGACAAACACAA
Done.