Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2481
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: 56766
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:2435 original size:15 final size:16
Alignment explanation
Indices: 2395--2437 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
2385 TTGTTTTAAA
*
2395 TTTAATGATATTTGTT
1 TTTAATAATATTTGTT
*
2411 TCT-ATAATATTTGTT
1 TTTAATAATATTTGTT
2426 TTTAAT-ATATTT
1 TTTAATAATATTT
2438 TTTAAATTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 19 0.83
16 4 0.17
ACGTcount: A:0.28, C:0.02, G:0.07, T:0.63
Consensus pattern (16 bp):
TTTAATAATATTTGTT
Found at i:2758 original size:24 final size:24
Alignment explanation
Indices: 2731--2776 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
2721 TCATAGTATA
2731 TTAACAAAAT-TTT-AAAACTATATT
1 TTAA-AAAATGTTTCAAAA-TATATT
2755 TTAAAAAATGTTTCAAAATATA
1 TTAAAAAATGTTTCAAAATATA
2777 ATTAATATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 5 0.25
24 11 0.55
25 4 0.20
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (24 bp):
TTAAAAAATGTTTCAAAATATATT
Found at i:3441 original size:16 final size:17
Alignment explanation
Indices: 3403--3442 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
3393 ATTATTAAAA
3403 TAAAAT-ATTGTCATAT
1 TAAAATAATTGTCATAT
*
3419 T-AAATAATTGT-TTAT
1 TAAAATAATTGTCATAT
3434 TAAAATAAT
1 TAAAATAAT
3443 ATAAATATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (17 bp):
TAAAATAATTGTCATAT
Found at i:3558 original size:15 final size:15
Alignment explanation
Indices: 3525--3564 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
3515 AATGCTTAAT
*
3525 AATATTCAAAATAAA
1 AATATTGAAAATAAA
* *
3540 AATATTGAAAATTAC
1 AATATTGAAAATAAA
3555 AATATTGAAA
1 AATATTGAAA
3565 TAATTTATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.30
Consensus pattern (15 bp):
AATATTGAAAATAAA
Found at i:6264 original size:418 final size:425
Alignment explanation
Indices: 5696--6544 Score: 1427
Period size: 418 Copynumber: 2.0 Consensus size: 425
5686 AGTAATATCT
5696 TAAAAAACAGAATTTTGGGTGGGTGGTTTTCTAAAACCAAAGGGTAATTTTTTGAAGGAAGTACT
1 TAAAAAACAGAATTTTGGGTGGGTGGTTTTCTAAAACCAAAGGGTAATTTTTTGAAGGAAGTACT
* *
5761 TAATTTTTAAACTAAATTTGGATGGCTCTTTTAAAATTTTTATTAATGACTTTAAAAATTAGTTT
66 TAATTTTTAAACTAAATTTGGATGGCTCTTTTAAAATTTTTATTAATGACTTTAAAAATGAATTT
*
5826 TATTGAATTATTAAAATATTTTGATAATTATAATCAAAATTATTTTTACAGTAT-ATCTACTTTA
131 TATTGAATTATTAAAATATTTTGATAATTATAATCAAAATTATTTTTACAGTATAAACTAC-TTA
5890 TATATAACATG-TTTTTTGCAAT-AATATTTATCTTTATGTAAAAACAATAAAAAAATTGAAAAA
195 TATATAACATGTTTTTTTGCAATAAATATTTATCTTTATGTAAAAACAATAAAAAAA---AAAAA
* *
5953 AATT-AAAAAATATGAGTTTTTTTAATACTTTGACTTGTATCAATCAAGTCACGTAGATACATGA
257 AATTAAAAAAATATGAGTTTTTTTAATACTTTGACTTGCATCAACCAAGTCACGTAGATACATGA
6017 ATA-TTTTTATTA-TTTTTTAAATTTTTGACTAAAATATG-AAGGAATGGTGAAAATTTTTAAAA
322 ATATTTTTTATTATTTTTTTAAA-TTTTGACTAAAATATGAAAGGAAT-GTGAAAATTTTTAAAA
*
6079 AGTTCTGGATAAT-ATATATTTTTTAAAAATCATGAATAAA
385 AGTTATGGATAATAATATATTTTTTAAAAATCATGAATAAA
*
6119 TAAAAAA-GGAATTTTGGGTGGGT-GTTTTCTAAAA-CAAAGGGTAATTTTTTGAAGGAAGTACT
1 TAAAAAACAGAATTTTGGGTGGGTGGTTTTCTAAAACCAAAGGGTAATTTTTTGAAGGAAGTACT
*
6181 TAATTTTTTAACTAAATTTGGATGGC-CTTTTAAAA-TTTTATTAATGACTTTAAAAATGAATTT
66 TAATTTTTAAACTAAATTTGGATGGCTCTTTTAAAATTTTTATTAATGACTTTAAAAATGAATTT
6244 TATTGAATTATTAAAATATTTTGATAATTATAATCAAAATTATTTTTACAGTATAAACTACTTAT
131 TATTGAATTATTAAAATATTTTGATAATTATAATCAAAATTATTTTTACAGTATAAACTACTTAT
*
6309 ATATAACATGTTTTTTTGCAATAAATTTTTATCTTTATGTAAAAACAATAAAAAAAAAAAAAATT
196 ATATAACATGTTTTTTTGCAATAAATATTTATCTTTATGTAAAAACAATAAAAAAAAAAAAAATT
*
6374 AAAAAAATATGAGTTTTTTTAATACTTTGACTTGCATCAACCAAGTCACGTGGATACATGAATAT
261 AAAAAAATATGAGTTTTTTTAATACTTTGACTTGCATCAACCAAGTCACGTAGATACATGAATAT
*
6439 TTTTTATTATTTTTTTTAAATTTTGACTAAAATATGAAAGGAATGTGAAAATTTTTGAAAAGTTA
326 TTTTTATTA-TTTTTTTAAATTTTGACTAAAATATGAAAGGAATGTGAAAATTTTTAAAAAGTTA
*
6504 TGGATAATACATATATTTTTTTAAAATCATGAATAAA
390 TGGATAATA-ATATATTTTTTAAAAATCATGAATAAA
6541 TAAA
1 TAAA
6545 TGTAATTTTT
Statistics
Matches: 404, Mismatches: 12, Indels: 21
0.92 0.03 0.05
Matches are distributed among these distances:
417 9 0.02
418 154 0.38
419 34 0.08
420 128 0.32
421 27 0.07
422 45 0.11
423 7 0.02
ACGTcount: A:0.41, C:0.06, G:0.11, T:0.41
Consensus pattern (425 bp):
TAAAAAACAGAATTTTGGGTGGGTGGTTTTCTAAAACCAAAGGGTAATTTTTTGAAGGAAGTACT
TAATTTTTAAACTAAATTTGGATGGCTCTTTTAAAATTTTTATTAATGACTTTAAAAATGAATTT
TATTGAATTATTAAAATATTTTGATAATTATAATCAAAATTATTTTTACAGTATAAACTACTTAT
ATATAACATGTTTTTTTGCAATAAATATTTATCTTTATGTAAAAACAATAAAAAAAAAAAAAATT
AAAAAAATATGAGTTTTTTTAATACTTTGACTTGCATCAACCAAGTCACGTAGATACATGAATAT
TTTTTATTATTTTTTTAAATTTTGACTAAAATATGAAAGGAATGTGAAAATTTTTAAAAAGTTAT
GGATAATAATATATTTTTTAAAAATCATGAATAAA
Found at i:7149 original size:21 final size:21
Alignment explanation
Indices: 7123--7165 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
7113 GCATCGATGC
7123 TTGGACAAATAACATAATCTA
1 TTGGACAAATAACATAATCTA
7144 TTGGACAAATAACATAATCTA
1 TTGGACAAATAACATAATCTA
7165 T
1 T
7166 GAACACCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.14, G:0.09, T:0.30
Consensus pattern (21 bp):
TTGGACAAATAACATAATCTA
Found at i:8737 original size:2 final size:2
Alignment explanation
Indices: 8730--8767 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
8720 GAATAATTAG
**
8730 AC AC AC AC TG AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
8768 TTCACTTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.47, G:0.03, T:0.03
Consensus pattern (2 bp):
AC
Found at i:10018 original size:17 final size:18
Alignment explanation
Indices: 9986--10019 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
9976 ATAATTTTAT
*
9986 ATTAATATTTATATAATA
1 ATTAATATTTAAATAATA
10004 ATTAA-ATTTAAATAAT
1 ATTAATATTTAAATAAT
10020 TTTTTTATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTAATATTTAAATAATA
Found at i:10381 original size:20 final size:20
Alignment explanation
Indices: 10351--10403 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
10341 TTTAGAAATT
10351 ATAAA-ATAATTGTATG-AA
1 ATAAATATAATTGTATGAAA
*
10369 ATAAAATATAATT-TATTAAA
1 AT-AAATATAATTGTATGAAA
*
10389 ATAAATATAAGTGTA
1 ATAAATATAATTGTA
10404 AAAATTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
18 2 0.07
19 15 0.52
20 12 0.41
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.36
Consensus pattern (20 bp):
ATAAATATAATTGTATGAAA
Found at i:11811 original size:32 final size:32
Alignment explanation
Indices: 11772--11835 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
11762 AAAAAATTAT
* * *
11772 AATATTAAAT-TTATAATTTTTGATATTAAATA
1 AATATTAAATATAATAAATTTTGA-ATAAAATA
11804 AATATTAAATATAATAAATTTTGAATAAAATA
1 AATATTAAATATAATAAATTTTGAATAAAATA
11836 TGTATTTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (32 bp):
AATATTAAATATAATAAATTTTGAATAAAATA
Found at i:11944 original size:19 final size:20
Alignment explanation
Indices: 11907--11945 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
11897 ATATCTTAAA
11907 ATTGGTTTAATATGTATTTT
1 ATTGGTTTAATATGTATTTT
* *
11927 ATTGTTTTAGTATG-ATTTT
1 ATTGGTTTAATATGTATTTT
11946 TATTAATTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.23, C:0.00, G:0.15, T:0.62
Consensus pattern (20 bp):
ATTGGTTTAATATGTATTTT
Found at i:14359 original size:25 final size:25
Alignment explanation
Indices: 14331--14404 Score: 78
Period size: 25 Copynumber: 2.9 Consensus size: 25
14321 TATAAAAGAA
14331 TAAATTTAAATTTTATATTTATTTT
1 TAAATTTAAATTTTATATTTATTTT
* ** *
14356 TAAATTT-AATTATATAAATATAATT
1 TAAATTTAAATTTTATATTTAT-TTT
*
14381 TAAAATTAAACTTTTATATTTATT
1 TAAATTTAAA-TTTTATATTTATT
14405 ATAAATAAAT
Statistics
Matches: 37, Mismatches: 9, Indels: 5
0.73 0.18 0.10
Matches are distributed among these distances:
24 11 0.30
25 15 0.41
26 2 0.05
27 9 0.24
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.55
Consensus pattern (25 bp):
TAAATTTAAATTTTATATTTATTTT
Found at i:14409 original size:25 final size:24
Alignment explanation
Indices: 14330--14409 Score: 63
Period size: 24 Copynumber: 3.2 Consensus size: 24
14320 TTATAAAAGA
*
14330 ATAAATTTAAATTTTATATTTATT
1 ATAAAATTAAATTTTATATTTATT
* * * * *
14354 TTTAAATTTAATTATATAAATATAATT
1 ATAAAATTAAATT-T-TATAT-TTATT
14381 -TAAAATTAAACTTTTATATTTATT
1 ATAAAATTAAA-TTTTATATTTATT
14405 ATAAA
1 ATAAA
14410 TAAATATTTT
Statistics
Matches: 41, Mismatches: 10, Indels: 9
0.68 0.17 0.15
Matches are distributed among these distances:
24 13 0.32
25 9 0.22
26 13 0.32
27 6 0.15
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (24 bp):
ATAAAATTAAATTTTATATTTATT
Found at i:16263 original size:20 final size:20
Alignment explanation
Indices: 16226--16264 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
16216 TATATGTTGA
* *
16226 TATATTTTATATAATATAAT
1 TATATTTAAAATAATATAAT
*
16246 TATATTTAAAATATTATAA
1 TATATTTAAAATAATATAA
16265 ATTTATATAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TATATTTAAAATAATATAAT
Found at i:16325 original size:6 final size:6
Alignment explanation
Indices: 16314--16351 Score: 58
Period size: 6 Copynumber: 6.2 Consensus size: 6
16304 TATATTTTAA
*
16314 TATATT TATATT TATATT TTTATAT TATATT TATATT T
1 TATATT TATATT TATATT TATAT-T TATATT TATATT T
16352 TTTATTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 24 0.83
7 5 0.17
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TATATT
Found at i:16350 original size:25 final size:24
Alignment explanation
Indices: 16285--16351 Score: 84
Period size: 25 Copynumber: 2.8 Consensus size: 24
16275 ATTTTAAAAC
*
16285 TTTAATA-ATTTATATGATATATAT
1 TTTAATATATTTATAT-TTATATAT
16309 TTTAATATATTTATATTTATAT-T
1 TTTAATATATTTATATTTATATAT
16332 TTTATATTATATTTATATTT
1 TTTA-A-TATATTTATATTT
16352 TTTATTATTT
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
23 5 0.13
24 13 0.33
25 21 0.54
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (24 bp):
TTTAATATATTTATATTTATATAT
Found at i:16365 original size:19 final size:19
Alignment explanation
Indices: 16304--16359 Score: 78
Period size: 19 Copynumber: 2.8 Consensus size: 19
16294 TTATATGATA
16304 TATATTTTAATATATTTATATT
1 TATATTTT--TATA-TTATATT
16326 TATATTTTTATATTATATT
1 TATATTTTTATATTATATT
16345 TATATTTTT-TATTAT
1 TATATTTTTATATTAT
16360 TTTTTAATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.18
19 16 0.47
20 4 0.12
22 8 0.24
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TATATTTTTATATTATATT
Found at i:16383 original size:12 final size:12
Alignment explanation
Indices: 16344--16385 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
16334 TATATTATAT
*
16344 TTATATTTTTTA
1 TTATGTTTTTTA
*
16356 TTAT-TTTTTAA
1 TTATGTTTTTTA
*
16367 TTATGTTTTTTT
1 TTATGTTTTTTA
16379 TTATGTT
1 TTATGTT
16386 CTATATATCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
11 10 0.38
12 16 0.62
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.76
Consensus pattern (12 bp):
TTATGTTTTTTA
Found at i:17777 original size:51 final size:51
Alignment explanation
Indices: 17701--17802 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
17691 GGAAAAAGGA
17701 AAGAGAAATCGCTTTGGATGAGCATATTCTATGAATTAATACTGTATGTAT
1 AAGAGAAATCGCTTTGGATGAGCATATTCTATGAATTAATACTGTATGTAT
17752 AAGAGAAATCGCTTTGGATGAGCATATTCTATGAATTAATACTGTATGTAT
1 AAGAGAAATCGCTTTGGATGAGCATATTCTATGAATTAATACTGTATGTAT
17803 CTTTCACAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (51 bp):
AAGAGAAATCGCTTTGGATGAGCATATTCTATGAATTAATACTGTATGTAT
Found at i:19371 original size:21 final size:22
Alignment explanation
Indices: 19346--19395 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
19336 TTGTTTAGGG
*
19346 TTAATATTTA-TTATAATGTTA
1 TTAATATTTATTTATAATATTA
* *
19367 TTAATTTTTATTTATATTATTA
1 TTAATATTTATTTATAATATTA
19389 -TAATATT
1 TTAATATT
19396 AATATTTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (22 bp):
TTAATATTTATTTATAATATTA
Found at i:19417 original size:27 final size:27
Alignment explanation
Indices: 19365--19417 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
19355 ATTATAATGT
* * *
19365 TATTAATTTTTATTTATATTATTATAA
1 TATTAATTTTTATTTAAAATACTATAA
19392 TATTAATATTTTA-TTAAAATACTATA
1 TATTAAT-TTTTATTTAAAATACTATA
19418 CTTGTTTACT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 17 0.77
28 5 0.23
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (27 bp):
TATTAATTTTTATTTAAAATACTATAA
Found at i:20479 original size:2 final size:2
Alignment explanation
Indices: 20472--20497 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20462 CAAAGAGGTG
20472 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
20498 CACTAGGTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:27809 original size:27 final size:27
Alignment explanation
Indices: 27773--27843 Score: 106
Period size: 27 Copynumber: 2.6 Consensus size: 27
27763 CCATCCTTTG
* *
27773 TTTGTTAAAAATAGTGGTTACTTTGTA
1 TTTGTCAAAAATGGTGGTTACTTTGTA
* *
27800 TTTGTCAAAAATGGTGGTTTCTTTTTA
1 TTTGTCAAAAATGGTGGTTACTTTGTA
27827 TTTGTCAAAAATGGTGG
1 TTTGTCAAAAATGGTGG
27844 CATGTTGTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.27, C:0.06, G:0.21, T:0.46
Consensus pattern (27 bp):
TTTGTCAAAAATGGTGGTTACTTTGTA
Found at i:27854 original size:24 final size:25
Alignment explanation
Indices: 27798--27860 Score: 74
Period size: 27 Copynumber: 2.5 Consensus size: 25
27788 GGTTACTTTG
* *
27798 TATTTGTCAAAAATGGTGGTTTCTTTT
1 TATTTGTCAAAAATGGTGG--TCATGT
27825 TATTTGTCAAAAATGGTGG-CATGT
1 TATTTGTCAAAAATGGTGGTCATGT
*
27849 TGTTTGTCAAAA
1 TATTTGTCAAAA
27861 TTTGTGGCTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
24 14 0.42
27 19 0.58
ACGTcount: A:0.27, C:0.08, G:0.21, T:0.44
Consensus pattern (25 bp):
TATTTGTCAAAAATGGTGGTCATGT
Found at i:32367 original size:27 final size:27
Alignment explanation
Indices: 32336--32407 Score: 99
Period size: 27 Copynumber: 2.7 Consensus size: 27
32326 ACTATCTTTT
*
32336 GTTTGTTAAAAATAGTGGTTTCTTTGC
1 GTTTGTCAAAAATAGTGGTTTCTTTGC
**
32363 GTTTGTCAAAAATAGTGGTTTCTTTTT
1 GTTTGTCAAAAATAGTGGTTTCTTTGC
* *
32390 ATTTGTCAAAAATGGTGG
1 GTTTGTCAAAAATAGTGG
32408 CATGTTGTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.25, C:0.07, G:0.22, T:0.46
Consensus pattern (27 bp):
GTTTGTCAAAAATAGTGGTTTCTTTGC
Found at i:32515 original size:13 final size:13
Alignment explanation
Indices: 32499--32532 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
32489 CCTCTCAAGC
*
32499 ATCCTTCTCTTGT
1 ATCCCTCTCTTGT
32512 ATCCCTCTCTTGT
1 ATCCCTCTCTTGT
*
32525 ATCTCTCT
1 ATCCCTCT
32533 TTAATTCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.09, C:0.35, G:0.06, T:0.50
Consensus pattern (13 bp):
ATCCCTCTCTTGT
Found at i:33266 original size:24 final size:25
Alignment explanation
Indices: 33202--33260 Score: 109
Period size: 25 Copynumber: 2.4 Consensus size: 25
33192 AACAAAAAAT
33202 AAATTTTCTTTATTCTTTTTTTTAA
1 AAATTTTCTTTATTCTTTTTTTTAA
*
33227 AAAATTTCTTTATTCTTTTTTTTAA
1 AAATTTTCTTTATTCTTTTTTTTAA
33252 AAATTTTCT
1 AAATTTTCT
33261 GATTCTCCCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.64
Consensus pattern (25 bp):
AAATTTTCTTTATTCTTTTTTTTAA
Found at i:36584 original size:20 final size:20
Alignment explanation
Indices: 36559--36598 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
36549 TTTTAATAAG
*
36559 GCATTTATTGCTTGAATTTT
1 GCATTTATTACTTGAATTTT
36579 GCATTTATTACTTGAATTTT
1 GCATTTATTACTTGAATTTT
36599 TAATATGTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.23, C:0.10, G:0.12, T:0.55
Consensus pattern (20 bp):
GCATTTATTACTTGAATTTT
Found at i:38247 original size:17 final size:17
Alignment explanation
Indices: 38211--38257 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
38201 TTTTTTGTAT
*
38211 TATTTATTTAAGATATA
1 TATTTATTTAAGATAAA
*
38228 TATTTTATTTGAG-TAAA
1 TA-TTTATTTAAGATAAA
38245 TATTTATTTAAGA
1 TATTTATTTAAGA
38258 CAAAAAAGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
16 9 0.36
17 7 0.28
18 9 0.36
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (17 bp):
TATTTATTTAAGATAAA
Found at i:40865 original size:47 final size:47
Alignment explanation
Indices: 40780--40876 Score: 135
Period size: 47 Copynumber: 2.1 Consensus size: 47
40770 GAAAATCACC
*
40780 TCATTGATTATTTTGAACAAAGAAATACTTTCTCTAAATAAGTAAAA
1 TCATTGATTATTTTAAACAAAGAAATACTTTCTCTAAATAAGTAAAA
* *
40827 TCATTTATTATTTTAAACAAA-AGAATATCTTT-TTTAAATAAGTAAAA
1 TCATTGATTATTTTAAACAAAGA-AATA-CTTTCTCTAAATAAGTAAAA
40874 TCA
1 TCA
40877 AAATTTTTGA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
46 1 0.02
47 40 0.89
48 4 0.09
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.39
Consensus pattern (47 bp):
TCATTGATTATTTTAAACAAAGAAATACTTTCTCTAAATAAGTAAAA
Found at i:45119 original size:153 final size:154
Alignment explanation
Indices: 44940--45231 Score: 358
Period size: 155 Copynumber: 1.9 Consensus size: 154
44930 TGATTACTTT
* * * * * ** *
44940 TGAGTCCTTTAAGGTTACTGATATACTTTTATATCAAATGTAGT-CTTAAGGGTATTTTGGTAAT
1 TGAGTCCTTGAAGGTTACTGAGATACTTTCATATCAAAGGTA-TACTCAAGGACATTTTGATAAT
* * *
45004 TT-TTCTAAAATCAAGTTCGATATAGTCACTAAGATGCTTTTATGCCAAAGGTGTGCATT-TAGG
65 TTCTTCTAAAACCAAGTCCGATATAGTCACTAAGATGATTTTATGCCAAAGGTGTGC-TTGTAGG
*
45067 ATATGTTCACTTCTATGTTTATTTTC
129 ATAGGTTCACTTCTATGTTTATTTTC
* *
45093 TGAGTCCTTGAAGGTTACCT-AGATACTTTCATATCGAAGGTATACCTCATGGACATTTTGATAA
1 TGAGTCCTTGAAGGTTA-CTGAGATACTTTCATATCAAAGGTATA-CTCAAGGACATTTTGATAA
* * * *
45157 TTTCTTTTAGAACCAAGTCCGATATAGTCACTGAGATGATTTTATGCCAAAGGTTTGCTTGTAGG
64 TTTCTTCTAAAACCAAGTCCGATATAGTCACTAAGATGATTTTATGCCAAAGGTGTGCTTGTAGG
45222 ATAGGTTCAC
129 ATAGGTTCAC
45232 CCTTCTACAA
Statistics
Matches: 116, Mismatches: 18, Indels: 8
0.82 0.13 0.06
Matches are distributed among these distances:
152 1 0.01
153 34 0.29
154 21 0.18
155 60 0.52
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.39
Consensus pattern (154 bp):
TGAGTCCTTGAAGGTTACTGAGATACTTTCATATCAAAGGTATACTCAAGGACATTTTGATAATT
TCTTCTAAAACCAAGTCCGATATAGTCACTAAGATGATTTTATGCCAAAGGTGTGCTTGTAGGAT
AGGTTCACTTCTATGTTTATTTTC
Found at i:45681 original size:20 final size:20
Alignment explanation
Indices: 45623--45675 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
45613 TATCGATATA
*
45623 ATAAGAGAATGTATTGATAC
1 ATAAGTGAATGTATTGATAC
45643 ATAAGTGAATGTATTGATAC
1 ATAAGTGAATGTATTGATAC
45663 ATAAGTGAATGTA
1 ATAAGTGAATGTA
45676 ACGATATACC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.43, C:0.04, G:0.21, T:0.32
Consensus pattern (20 bp):
ATAAGTGAATGTATTGATAC
Done.