Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1130
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: 18798
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Found at i:214 original size:14 final size:14
Alignment explanation
Indices: 195--221 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
185 TCTTTCTTTT
195 ATTTTTTAAATTTA
1 ATTTTTTAAATTTA
209 ATTTTTTAAATTT
1 ATTTTTTAAATTT
222 TATATTAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
ATTTTTTAAATTTA
Found at i:445 original size:14 final size:15
Alignment explanation
Indices: 428--456 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
418 TCTAAAAAAA
428 TTAT-TTTAAATTTT
1 TTATATTTAAATTTT
442 TTATATTTAAATTTT
1 TTATATTTAAATTTT
457 CAATATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TTATATTTAAATTTT
Found at i:462 original size:15 final size:15
Alignment explanation
Indices: 432--465 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
422 AAAAAATTAT
**
432 TTTAAATTTTTTATA
1 TTTAAATTTTCAATA
447 TTTAAATTTTCAATA
1 TTTAAATTTTCAATA
462 TTTA
1 TTTA
466 TTTAATTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTAAATTTTCAATA
Found at i:847 original size:29 final size:28
Alignment explanation
Indices: 782--848 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 28
772 TAAAAAATTT
782 AAATATATAATTATTATTTAATAAAATTAA
1 AAAT-TAT-ATTATTATTTAATAAAATTAA
** * *
812 ATTTTATATTATTTTTTATTAATAATTAA
1 AAATTATATTATTATTTAATAA-AATTAA
841 AAATTATA
1 AAATTATA
849 AAAAATTAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
28 13 0.43
29 15 0.50
30 2 0.07
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
AAATTATATTATTATTTAATAAAATTAA
Found at i:2103 original size:19 final size:19
Alignment explanation
Indices: 2079--2129 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 19
2069 TGATAACTTT
2079 AAACATAATTATAATATAA
1 AAACATAATTATAATATAA
*
2098 AAACATAAAAATATAATATAA
1 AAACAT--AATTATAATATAA
2119 ATAA-ATAATTA
1 A-AACATAATTA
2130 ATTAAATCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
19 10 0.37
21 15 0.56
22 2 0.07
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (19 bp):
AAACATAATTATAATATAA
Found at i:3480 original size:21 final size:21
Alignment explanation
Indices: 3456--3516 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
3446 ATAATGTTAT
*
3456 TAACTATTAACATAATTTTGA
1 TAACTATTAATATAATTTTGA
* * *
3477 TAACTTTTGATATGATTTTGA
1 TAACTATTAATATAATTTTGA
3498 TAA-TATTTAATATAATTTT
1 TAACTA-TTAATATAATTTT
3517 ATCATTTTGA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
20 1 0.03
21 31 0.97
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.51
Consensus pattern (21 bp):
TAACTATTAATATAATTTTGA
Found at i:3513 original size:42 final size:42
Alignment explanation
Indices: 3304--3528 Score: 129
Period size: 42 Copynumber: 5.4 Consensus size: 42
3294 TTTGGATTTT
* * * *
3304 TTTTGTTAACATTTGA-ATAA-TTTGAATAATATTTGATACAA
1 TTTTGATAACTTTTGATATAATTTTG-ATAATATTTAATATAA
* * ** * * ** * *
3345 TTTTGACACCAGTTGATATGATTTTCATAACCTTTAGTATGA
1 TTTTGATAACTTTTGATATAATTTTGATAATATTTAATATAA
* * * * *
3387 TTTTAATAGCTTTTGATTTAATTTTGATAATTTTTTATATAA
1 TTTTGATAACTTTTGATATAATTTTGATAATATTTAATATAA
* * * * * * *
3429 GTTTGATGACGTTCGAAATAATGTT-ATTAACTA-TTAACATAA
1 TTTTGATAACTTTTGATATAATTTTGA-TAA-TATTTAATATAA
*
3471 TTTTGATAACTTTTGATATGATTTTGATAATATTTAATATAA
1 TTTTGATAACTTTTGATATAATTTTGATAATATTTAATATAA
*
3513 TTTT-ATCA-TTTTGATA
1 TTTTGATAACTTTTGATA
3529 ACTTTTTATA
Statistics
Matches: 132, Mismatches: 46, Indels: 13
0.69 0.24 0.07
Matches are distributed among these distances:
40 8 0.06
41 18 0.14
42 101 0.77
43 5 0.04
ACGTcount: A:0.34, C:0.07, G:0.11, T:0.49
Consensus pattern (42 bp):
TTTTGATAACTTTTGATATAATTTTGATAATATTTAATATAA
Found at i:3731 original size:21 final size:21
Alignment explanation
Indices: 3662--3733 Score: 69
Period size: 21 Copynumber: 3.4 Consensus size: 21
3652 ATAATATTAT
3662 TATAATTTT-GATAACTTTTGA
1 TATAATTTTAGA-AACTTTTGA
* *
3683 GATTATTTTA-AAACTTTTGA
1 TATAATTTTAGAAACTTTTGA
*
3703 CGTA-AATTTTAGAAACCTTTGA
1 --TATAATTTTAGAAACTTTTGA
3725 TATAATTTT
1 TATAATTTT
3734 TGATATAATT
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
20 11 0.27
21 20 0.49
22 10 0.24
ACGTcount: A:0.35, C:0.07, G:0.10, T:0.49
Consensus pattern (21 bp):
TATAATTTTAGAAACTTTTGA
Found at i:3737 original size:12 final size:12
Alignment explanation
Indices: 3720--3745 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3710 TTTAGAAACC
3720 TTTGATATAATT
1 TTTGATATAATT
3732 TTTGATATAATT
1 TTTGATATAATT
3744 TT
1 TT
3746 AATAACCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (12 bp):
TTTGATATAATT
Found at i:3766 original size:26 final size:26
Alignment explanation
Indices: 3731--3782 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
3721 TTGATATAAT
*
3731 TTTTGATATAATTTTAATAACCTTTA
1 TTTTCATATAATTTTAATAACCTTTA
*
3757 TTTTCATATAATTTTAATAACTTTTA
1 TTTTCATATAATTTTAATAACCTTTA
3783 CATGATTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.35, C:0.08, G:0.02, T:0.56
Consensus pattern (26 bp):
TTTTCATATAATTTTAATAACCTTTA
Found at i:3866 original size:21 final size:21
Alignment explanation
Indices: 3830--4028 Score: 111
Period size: 21 Copynumber: 9.5 Consensus size: 21
3820 GTAATCATTG
*
3830 ATATAATTTTTTATAACCTTTA
1 ATATAA-TTTTGATAACCTTTA
* *
3852 ATATAATTTTGATAACTTTTG
1 ATATAATTTTGATAACCTTTA
** * *
3873 ATAGGATTTTGATATCTTTTA
1 ATATAATTTTGATAACCTTTA
* * *
3894 ATAAAATTTTAATAA-CTGTGA
1 ATATAATTTTGATAACCT-TTA
**
3915 ATATAATTTTGATAATATTTA
1 ATATAATTTTGATAACCTTTA
* * * *
3936 ATATAGTTCTGATAA-ATTTT
1 ATATAATTTTGATAACCTTTA
*
3956 ATATAATTTTGATAA-CTTTT
1 ATATAATTTTGATAACCTTTA
* **
3976 ATA-AATATTTGGATAATCTTGG
1 ATATAAT-TTT-GATAACCTTTA
* * *
3998 ATATGATTTTGATGACATTCTA
1 ATATAATTTTGATAACCTT-TA
4020 A-ATAATTTT
1 ATATAATTTT
4029 AATAGCATTC
Statistics
Matches: 138, Mismatches: 32, Indels: 15
0.75 0.17 0.08
Matches are distributed among these distances:
19 3 0.02
20 28 0.20
21 88 0.64
22 17 0.12
23 2 0.01
ACGTcount: A:0.37, C:0.05, G:0.09, T:0.49
Consensus pattern (21 bp):
ATATAATTTTGATAACCTTTA
Found at i:3949 original size:63 final size:62
Alignment explanation
Indices: 3851--3972 Score: 140
Period size: 63 Copynumber: 2.0 Consensus size: 62
3841 TATAACCTTT
* * * **
3851 AATATAATTTTGATAACTTTTGATAGGATTTTGATATCTTTTAATAAAATTTTAATAACTGTG
1 AATATAATTTTGATAACTTTTAATAAGATTCTGATAAATTTT-ATAAAATTTTAATAACTGTG
* *
3914 AATATAATTTTGATAA-TATTTAATATAG-TTCTGATAAATTTTATATAATTTTGATAACT
1 AATATAATTTTGATAACT-TTTAATA-AGATTCTGATAAATTTTATAAAATTTTAATAACT
3973 TTTATAAATA
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
62 16 0.32
63 33 0.66
64 1 0.02
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.48
Consensus pattern (62 bp):
AATATAATTTTGATAACTTTTAATAAGATTCTGATAAATTTTATAAAATTTTAATAACTGTG
Found at i:4048 original size:21 final size:22
Alignment explanation
Indices: 3998--4049 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
3988 ATAATCTTGG
*
3998 ATATGATTTTGATGACATTCTA
1 ATATGATTTTAATGACATTCTA
*
4020 A-ATAATTTTAAT-AGCATTC-A
1 ATATGATTTTAATGA-CATTCTA
4040 ATATGATTTT
1 ATATGATTTT
4050 GTAATTTTGC
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 3 0.12
21 21 0.84
22 1 0.04
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.46
Consensus pattern (22 bp):
ATATGATTTTAATGACATTCTA
Found at i:4097 original size:21 final size:22
Alignment explanation
Indices: 4073--4119 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
4063 CATTTGACAT
4073 ATTTTTGATAAT-GTTTATAAA
1 ATTTTTGATAATAGTTTATAAA
* *
4094 A-TTTTGATAATATTTTATATA
1 ATTTTTGATAATAGTTTATAAA
4115 ATTTT
1 ATTTT
4120 GGCAACATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 10 0.45
21 9 0.41
22 3 0.14
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.57
Consensus pattern (22 bp):
ATTTTTGATAATAGTTTATAAA
Found at i:4120 original size:21 final size:21
Alignment explanation
Indices: 4051--4159 Score: 78
Period size: 21 Copynumber: 5.2 Consensus size: 21
4041 TATGATTTTG
* * * *
4051 TAATTTTGCTAACATTTGACA
1 TAATTTTGATAATATTTTATA
* *
4072 TATTTTTGATAAT-GTTTATA
1 TAATTTTGATAATATTTTATA
*
4092 AAATTTTGATAATATTTTATA
1 TAATTTTGATAATATTTTATA
** * * *
4113 TAATTTTGGCAACATATAATA
1 TAATTTTGATAATATTTTATA
*
4134 TAATTTTGATAACT-TTTTATG
1 TAATTTTGATAA-TATTTTATA
4155 TAATT
1 TAATT
4160 GATAATCTTT
Statistics
Matches: 65, Mismatches: 21, Indels: 4
0.72 0.23 0.04
Matches are distributed among these distances:
20 15 0.23
21 50 0.77
ACGTcount: A:0.36, C:0.06, G:0.08, T:0.50
Consensus pattern (21 bp):
TAATTTTGATAATATTTTATA
Found at i:4399 original size:21 final size:21
Alignment explanation
Indices: 4375--4588 Score: 61
Period size: 21 Copynumber: 10.3 Consensus size: 21
4365 TTTAACAAAT
4375 TTTTTGTAACTTTTGATATAA
1 TTTTTGTAACTTTTGATATAA
* *
4396 -TTTTGATAATTTTTG-TGATAC
1 TTTTTG-TAACTTTTGAT-ATAA
** * **
4417 TTTTAATAACCTTACATATAA
1 TTTTTGTAACTTTTGATATAA
* *
4438 TTTTAGTAACTTTTTATATAA
1 TTTTTGTAACTTTTGATATAA
***
4459 TTTGCATAACTTTT--TATAA
1 TTTTTGTAACTTTTGATATAA
* *
4478 TTGTGGTAA-TTATT-ATATAA
1 TTTTTGTAACTT-TTGATATAA
** * *
4498 TTTTACATAGCTCTTGATATAA
1 TTTT-TGTAACTTTTGATATAA
*
4520 -TTTTGATAATTTTTG-TA-AGA
1 TTTTTG-TAACTTTTGATATA-A
* * *
4540 ATTTTGATAACATTT-ATAATAG
1 TTTTTG-TAACTTTTGAT-ATAA
* * *
4562 TTTTAGAAATTTTTGATATAA
1 TTTTTGTAACTTTTGATATAA
4583 TTTTTG
1 TTTTTG
4589 ATAAAATTTT
Statistics
Matches: 137, Mismatches: 40, Indels: 32
0.66 0.19 0.15
Matches are distributed among these distances:
18 2 0.01
19 13 0.09
20 17 0.12
21 86 0.63
22 18 0.13
23 1 0.01
ACGTcount: A:0.33, C:0.06, G:0.09, T:0.52
Consensus pattern (21 bp):
TTTTTGTAACTTTTGATATAA
Found at i:4530 original size:42 final size:42
Alignment explanation
Indices: 4381--4533 Score: 138
Period size: 42 Copynumber: 3.7 Consensus size: 42
4371 AAATTTTTTG
* * *
4381 TAACTTTTGATATAATTTTGATAATTTTTGTGATACTTTTA-A
1 TAACTCTTGATATAATTTTGATAATTTTTAT-ATAATTTTACA
* *
4423 TAAC-CTTACATATAATTTT-AGTAACTTTTTATATAA-TTTGCA
1 TAACTCTT-GATATAATTTTGA-TAA-TTTTTATATAATTTTACA
* * * *
4465 TAACT-TT-TTATAATTGTGGTAATTATTATATAATTTTACA
1 TAACTCTTGATATAATTTTGATAATTTTTATATAATTTTACA
*
4505 TAGCTCTTGATATAATTTTGATAATTTTT
1 TAACTCTTGATATAATTTTGATAATTTTT
4534 GTAAGAATTT
Statistics
Matches: 87, Mismatches: 15, Indels: 18
0.73 0.12 0.15
Matches are distributed among these distances:
39 10 0.11
40 20 0.23
41 8 0.09
42 43 0.49
43 6 0.07
ACGTcount: A:0.33, C:0.07, G:0.08, T:0.52
Consensus pattern (42 bp):
TAACTCTTGATATAATTTTGATAATTTTTATATAATTTTACA
Found at i:4586 original size:12 final size:12
Alignment explanation
Indices: 4568--4598 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
4558 ATAGTTTTAG
4568 AAATTTTTGATA
1 AAATTTTTGATA
*
4580 TAATTTTTGATA
1 AAATTTTTGATA
4592 AAATTTT
1 AAATTTT
4599 GTAAAAATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (12 bp):
AAATTTTTGATA
Found at i:4603 original size:10 final size:11
Alignment explanation
Indices: 4511--4646 Score: 61
Period size: 11 Copynumber: 12.5 Consensus size: 11
4501 TACATAGCTC
*
4511 TTGATATAATT
1 TTGATAAAATT
*
4522 TTGAT-AATTT
1 TTGATAAAATT
4532 TTG-TAAGAATT
1 TTGATAA-AATT
*
4543 TTGATAACA-T
1 TTGATAAAATT
*
4553 TT-ATAATAGTT
1 TTGATAA-AATT
* *
4564 TT-AGAAATTT
1 TTGATAAAATT
*
4574 TTGATATAATTT
1 TTGATA-AAATT
4586 TTGATAAAATT
1 TTGATAAAATT
*
4597 TTG-TAAAA-A
1 TTGATAAAATT
* * *
4606 TTCAAACAAACT
1 TTGATA-AAATT
*
4618 TTGTATATAATT
1 TTG-ATAAAATT
*
4630 TTGATAATATT
1 TTGATAAAATT
4641 TTGATA
1 TTGATA
4647 TAAGTTTGAC
Statistics
Matches: 94, Mismatches: 20, Indels: 22
0.69 0.15 0.16
Matches are distributed among these distances:
9 7 0.07
10 21 0.22
11 42 0.45
12 22 0.23
13 2 0.02
ACGTcount: A:0.39, C:0.03, G:0.10, T:0.49
Consensus pattern (11 bp):
TTGATAAAATT
Found at i:4815 original size:12 final size:11
Alignment explanation
Indices: 4790--4837 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 11
4780 GGTGACATCG
4790 TAATTTT-A-A
1 TAATTTTGATA
4799 TAATTGTTGATA
1 TAATT-TTGATA
4811 TAATTTTG--A
1 TAATTTTGATA
*
4820 TAATCTTGATA
1 TAATTTTGATA
4831 TAATTTT
1 TAATTTT
4838 AATAACCTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
9 13 0.41
10 2 0.06
11 11 0.34
12 6 0.19
ACGTcount: A:0.35, C:0.02, G:0.08, T:0.54
Consensus pattern (11 bp):
TAATTTTGATA
Found at i:5872 original size:38 final size:38
Alignment explanation
Indices: 5814--5911 Score: 106
Period size: 38 Copynumber: 2.6 Consensus size: 38
5804 AGTTAACGGT
* * * * *
5814 TAAAAAATTCAATTTAAAATTGATTGACGACTGATGAT
1 TAAAAAATTTAATTTGAAATTGACTGACGACTGACGAC
* * * **
5852 TAGAGAATTTAATTTGAAATTAACTGGTGACTGACGAC
1 TAAAAAATTTAATTTGAAATTGACTGACGACTGACGAC
5890 TAAAAAATTTAATTTGAAATTG
1 TAAAAAATTTAATTTGAAATTG
5912 GCTGGTGATC
Statistics
Matches: 47, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
38 47 1.00
ACGTcount: A:0.43, C:0.07, G:0.15, T:0.35
Consensus pattern (38 bp):
TAAAAAATTTAATTTGAAATTGACTGACGACTGACGAC
Found at i:6417 original size:31 final size:31
Alignment explanation
Indices: 6379--6440 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
6369 GTACCATCAC
6379 AAAGTCCTAATTCTCTCAAGCTCCATGGCCA
1 AAAGTCCTAATTCTCTCAAGCTCCATGGCCA
* *
6410 AAAGTCCTAATTTTCTCGAGCTCCATGGCCA
1 AAAGTCCTAATTCTCTCAAGCTCCATGGCCA
6441 CTTCTTTCGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.27
Consensus pattern (31 bp):
AAAGTCCTAATTCTCTCAAGCTCCATGGCCA
Found at i:9271 original size:34 final size:34
Alignment explanation
Indices: 9214--9432 Score: 271
Period size: 34 Copynumber: 6.5 Consensus size: 34
9204 TGCCCAGCCA
*
9214 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * * *
9247 ATTATTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
9281 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* ** *
9315 ATTGTTGATTAAATGAGAAATTTGATAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
9349 ATTATTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
9383 ATTGTTGACTAAAT-GGTAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGT-GATTTGGTAGCTTACC
9417 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
9433 TGGTTTTTAC
Statistics
Matches: 158, Mismatches: 25, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
33 16 0.10
34 141 0.89
35 1 0.01
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
Found at i:9389 original size:102 final size:101
Alignment explanation
Indices: 9214--9432 Score: 348
Period size: 102 Copynumber: 2.2 Consensus size: 101
9204 TGCCCAGCCA
** * * * *
9214 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTATTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGAAATTTGATAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
9279 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
66 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
9315 ATTGTTGATTAAATGAGAAATTTGATAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
1 ATTGTTGATTAAATG-GAAATTTGATAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
* * *
9380 ACCATTGTTGACTAAATGGTAGATTTGGTAGGTTGCC
65 ACCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
9417 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
9433 TGGTTTTTAC
Statistics
Matches: 108, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
101 16 0.15
102 92 0.85
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.41
Consensus pattern (101 bp):
ATTGTTGATTAAATGGAAATTTGATAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
Found at i:13477 original size:24 final size:24
Alignment explanation
Indices: 13447--13494 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
13437 TTTCCGAGTT
13447 TTTGACGTTCGAAT-TAGGGTTAAG
1 TTTGACGTTCG-ATGTAGGGTTAAG
*
13471 TTTGACGTTTGATGTAGGGTTAAG
1 TTTGACGTTCGATGTAGGGTTAAG
13495 CAAATTTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 2 0.09
24 20 0.91
ACGTcount: A:0.23, C:0.06, G:0.31, T:0.40
Consensus pattern (24 bp):
TTTGACGTTCGATGTAGGGTTAAG
Found at i:14111 original size:21 final size:21
Alignment explanation
Indices: 14073--14137 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
14063 TTCAAAAGAT
14073 TATTAAAAG-TAT-AAAATTA
1 TATTAAAAGTTATCAAAATTA
14092 TATTAAAAGTTATCAAAATTA
1 TATTAAAAGTTATCAAAATTA
* * *
14113 T-TTCAAATGTTAACAAAATCA
1 TATT-AAAAGTTATCAAAATTA
14134 TATT
1 TATT
14138 GGTTAACAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
19 9 0.23
20 5 0.13
21 23 0.59
22 2 0.05
ACGTcount: A:0.51, C:0.06, G:0.05, T:0.38
Consensus pattern (21 bp):
TATTAAAAGTTATCAAAATTA
Found at i:14200 original size:10 final size:10
Alignment explanation
Indices: 14187--14286 Score: 52
Period size: 10 Copynumber: 10.1 Consensus size: 10
14177 AAAGGTTATC
14187 AAAATTATAT
1 AAAATTATAT
14197 AAAA-TAT-T
1 AAAATTATAT
*
14205 AAAAAT-TAT
1 AAAATTATAT
*
14214 AAAATAATAT
1 AAAATTATAT
*
14224 CAAA-TAT-T
1 AAAATTATAT
14232 ACTAAATTATAT
1 A--AAATTATAT
*
14244 CAAA-TACTATT
1 AAAATTA-TA-T
14255 AAAATTATAT
1 AAAATTATAT
*
14265 CAAAAGTTA-CT
1 -AAAA-TTATAT
14276 AAAATTATAT
1 AAAATTATAT
14286 A
1 A
14287 CAAAATTAGC
Statistics
Matches: 68, Mismatches: 9, Indels: 26
0.66 0.09 0.25
Matches are distributed among these distances:
8 7 0.10
9 16 0.24
10 25 0.37
11 14 0.21
12 6 0.09
ACGTcount: A:0.57, C:0.06, G:0.01, T:0.36
Consensus pattern (10 bp):
AAAATTATAT
Found at i:14223 original size:27 final size:28
Alignment explanation
Indices: 14182--14301 Score: 84
Period size: 27 Copynumber: 4.0 Consensus size: 28
14172 TAATCAAAGG
*
14182 TTATCAAAATTATATAAAATATTA-AAAA
1 TTAT-AAAATAATATAAAATATTACAAAA
* *
14210 TTATAAAATAATATCAAATATTACTAAA
1 TTATAAAATAATATAAAATATTACAAAA
*
14238 TTATATCAAATACTATTAAAAT-TATATCAAAA
1 TTATA--AAATAATA-TAAAATAT-TA-CAAAA
*
14270 GTTACTAAAATTATATACAAA-ATTAGCAAAA
1 -TTA-TAAAATAATATA-AAATATTA-CAAAA
14301 T
1 T
14302 CGTTTCAAAG
Statistics
Matches: 73, Mismatches: 9, Indels: 18
0.73 0.09 0.18
Matches are distributed among these distances:
27 17 0.23
28 12 0.16
30 9 0.12
31 16 0.22
32 14 0.19
33 3 0.04
34 2 0.03
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.35
Consensus pattern (28 bp):
TTATAAAATAATATAAAATATTACAAAA
Found at i:14232 original size:20 final size:20
Alignment explanation
Indices: 14183--14421 Score: 114
Period size: 21 Copynumber: 11.6 Consensus size: 20
14173 AATCAAAGGT
*
14183 TATCAAAATTA-TATAAAATA
1 TATCAAAATTACTA-AAATTA
* *
14203 T-TAAAAATTA-TAAAATAA
1 TATCAAAATTACTAAAATTA
14221 TATCAAATATTACT-AAATTA
1 TATCAAA-ATTACTAAAATTA
* *
14241 TATCAAATACTATTAAAATTA
1 TATCAAA-ATTACTAAAATTA
14262 TATCAAAAGTTACTAAAATTA
1 TATCAAAA-TTACTAAAATTA
**
14283 TATACAAAATTAGC-AAAATCG
1 TAT-CAAAATTA-CTAAAATTA
* * *
14304 TTTCAAAGGTTA-TAAAAGAATA
1 TATCAAA-ATTACT-AAA-ATTA
* *
14326 TATCAAATCTTACCAAAATTA
1 TATCAAA-ATTACTAAAATTA
* *
14347 TATAAAAAGTTATTAAAATTA
1 TATCAAAA-TTACTAAAATTA
* * *
14368 TTTAAAAAGTTA-TAAAATTG
1 TATCAAAA-TTACTAAAATTA
* * *
14388 TATTAAAAATTATTTAAATTA
1 TA-TCAAAATTACTAAAATTA
*
14409 CATCAAAAGTTAC
1 TATCAAAA-TTAC
14422 CAATACTATA
Statistics
Matches: 170, Mismatches: 33, Indels: 31
0.73 0.14 0.13
Matches are distributed among these distances:
18 5 0.03
19 14 0.08
20 43 0.25
21 89 0.52
22 19 0.11
ACGTcount: A:0.53, C:0.08, G:0.04, T:0.35
Consensus pattern (20 bp):
TATCAAAATTACTAAAATTA
Found at i:14353 original size:10 final size:11
Alignment explanation
Indices: 14340--14405 Score: 50
Period size: 11 Copynumber: 6.2 Consensus size: 11
14330 AAATCTTACC
14340 AAAATTATATA
1 AAAATTATATA
14351 AAAAGTTAT-T-
1 AAAA-TTATATA
*
14361 AAAATTATTTA
1 AAAATTATATA
*
14372 AAAAGT-TAT-
1 AAAATTATATA
*
14381 AAAATTGTATTA
1 AAAATTATA-TA
*
14393 AAAATTATTTA
1 AAAATTATATA
14404 AA
1 AA
14406 TTACATCAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
9 9 0.20
10 9 0.20
11 15 0.34
12 11 0.25
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (11 bp):
AAAATTATATA
Found at i:14365 original size:64 final size:64
Alignment explanation
Indices: 14260--14384 Score: 153
Period size: 64 Copynumber: 2.0 Consensus size: 64
14250 CTATTAAAAT
* * * * *
14260 TATATCAAAAGTTACTAAAATTATATACAAAATTAGCAAAATCGTTTCAAAGGTTATAAAAGAA
1 TATATCAAAACTTACCAAAATTATATACAAAATTAGCAAAATCATTTAAAAAGTTATAAAAGAA
* ** *
14324 TATATCAAATCTTACCAAAATTATATA-AAAAGTTATTAAAATTATTTAAAAAGTTATAAAA
1 TATATCAAAACTTACCAAAATTATATACAAAA-TTAGCAAAATCATTTAAAAAGTTATAAAA
14385 TTGTATTAAA
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
63 4 0.08
64 47 0.92
ACGTcount: A:0.53, C:0.08, G:0.06, T:0.33
Consensus pattern (64 bp):
TATATCAAAACTTACCAAAATTATATACAAAATTAGCAAAATCATTTAAAAAGTTATAAAAGAA
Found at i:14417 original size:41 final size:41
Alignment explanation
Indices: 14340--14442 Score: 109
Period size: 41 Copynumber: 2.5 Consensus size: 41
14330 AAATCTTACC
**
14340 AAAATTATATAAAAAGTTATTAAAATTATTTAAAAAGTTAT
1 AAAATTATATAAAAAGTTATTAAAATTACATAAAAAGTTAT
* * * *
14381 AAAATTGTATTAAAAA-TTATTTAAATTACATCAAAAGTTACC
1 AAAATTATA-TAAAAAGTTATTAAAATTACATAAAAAGTTA-T
* *
14423 AATACTATATAAAAAGTTAT
1 AAAATTATATAAAAAGTTAT
14443 CAAATATCAT
Statistics
Matches: 50, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
41 34 0.68
42 16 0.32
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (41 bp):
AAAATTATATAAAAAGTTATTAAAATTACATAAAAAGTTAT
Found at i:15657 original size:34 final size:33
Alignment explanation
Indices: 15609--15829 Score: 257
Period size: 34 Copynumber: 6.5 Consensus size: 33
15599 TGGTAAAAAC
*
15609 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
*
15642 CTACCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
15676 CACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** *
15710 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * *
15744 CTCCCATTTAGTCAACAATGGCAAACC-ACCAAAT
1 C-ACCATTTAATCAACAATGG-TAACCTACCAAAT
* *
15778 CACCCATTTAATCAATAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
15812 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
15830 TCTCCCACTT
Statistics
Matches: 160, Mismatches: 19, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
33 22 0.14
34 132 0.82
35 6 0.04
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:15725 original size:68 final size:67
Alignment explanation
Indices: 15611--15829 Score: 287
Period size: 68 Copynumber: 3.2 Consensus size: 67
15601 GTAAAAACCA
* * *
15611 CCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAAT-TACCATTTAATCAACAATGGTAAGCTACCAAAT
15676 CAC
65 CAC
* * * *
15679 CCATTTAATCAATAATGGTAAGCTACCAAATTTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTAC-CATTTAATCAACAATGGTAAGCTACCAAAT
*
15744 CTC
65 CAC
* * * * *
15747 CCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAATAATGGTAAACTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTA-CCATTTAATCAACAATGGTAAGCTACCAAAT
15812 CA-
65 CAC
15814 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
15830 TCTCCCACTT
Statistics
Matches: 131, Mismatches: 18, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
67 17 0.13
68 113 0.86
69 1 0.01
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.26
Consensus pattern (67 bp):
CCATTTAATCAACAATGGCAAACTACCAAATTACCATTTAATCAACAATGGTAAGCTACCAAATC
AC
Found at i:15753 original size:102 final size:101
Alignment explanation
Indices: 15609--15829 Score: 361
Period size: 102 Copynumber: 2.2 Consensus size: 101
15599 TGGTAAAAAC
* *
15609 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
*
15674 ATCACCCATTTAATCAATAATGGTAAGCTACCAAAT
66 ATCACCCATTTAATCAATAATGGTAAACTACCAAAT
** * * *
15710 TTCTCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCA
1 CAC-CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCA
15775 AATCACCCATTTAATCAATAATGGTAAACTACCAAAT
65 AATCACCCATTTAATCAATAATGGTAAACTACCAAAT
15812 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
15830 TCTCCCACTT
Statistics
Matches: 109, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
101 16 0.15
102 93 0.85
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAATAATGGTAAACTACCAAAT
Done.