Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1187
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: 47219
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Found at i:286 original size:19 final size:19
Alignment explanation
Indices: 257--404 Score: 77
Period size: 19 Copynumber: 7.4 Consensus size: 19
247 TTTAAAAAAT
*
257 ATATAACAATAAATTTAATA
1 ATATAA-AATAAAATTAATA
* *
277 ATATAAAATAAAAATAAAA
1 ATATAAAATAAAATTAATA
*
296 ATAGTAATAT-AAATTAATA
1 ATA-TAAAATAAAATTAATA
*
315 ATAATAATATAAAAATATTAATA
1 AT-ATAA-A-ATAAA-ATTAATA
* *
338 TTGTAATAATATAAATT-A-A
1 ATATAA-AATA-AAATTAATA
357 ATATATAAATAAAAATTAATA
1 ATATA-AAAT-AAAATTAATA
* * *
378 ACATTATAATAAATTTAATA
1 ATA-TAAAATAAAATTAATA
*
398 AAATAAA
1 ATATAAA
405 CTTAATATAT
Statistics
Matches: 98, Mismatches: 18, Indels: 25
0.70 0.13 0.18
Matches are distributed among these distances:
19 40 0.41
20 27 0.28
21 12 0.12
22 11 0.11
23 8 0.08
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (19 bp):
ATATAAAATAAAATTAATA
Found at i:292 original size:25 final size:25
Alignment explanation
Indices: 272--332 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
262 ACAATAAATT
272 TAATAATATAAAATAAAAATAAAAA
1 TAATAATATAAAATAAAAATAAAAA
* * *
297 TAGTAATATAAATTAATAATAATAATA
1 TAATAATATAAAATAAAAATAA-AA-A
*
324 TAAAAATAT
1 TAATAATAT
333 TAATATTGTA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
25 19 0.66
26 2 0.07
27 8 0.28
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (25 bp):
TAATAATATAAAATAAAAATAAAAA
Found at i:1331 original size:3 final size:3
Alignment explanation
Indices: 1288--1319 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1278 CTTTAATGCT
*
1288 ATA ATA ATA ATA ACA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1320 GGTTCTAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:3244 original size:2 final size:2
Alignment explanation
Indices: 3232--3267 Score: 63
Period size: 2 Copynumber: 17.5 Consensus size: 2
3222 GCTTTGATAG
3232 AT AT GAT AT AT 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 AT AT AT AT AT A
3268 GTTTCAATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5629 original size:31 final size:31
Alignment explanation
Indices: 5585--5646 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
5575 ATGACCAAAC
* *
5585 TTTTGTTTTTTGATTAAATTTTGACACTCAA
1 TTTTGATTGTTGATTAAATTTTGACACTCAA
** *
5616 TTTTGATTGTTGATTGGATTTTGCCACTCAA
1 TTTTGATTGTTGATTAAATTTTGACACTCAA
5647 CAATGGTTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.23, C:0.11, G:0.15, T:0.52
Consensus pattern (31 bp):
TTTTGATTGTTGATTAAATTTTGACACTCAA
Found at i:6947 original size:23 final size:23
Alignment explanation
Indices: 6921--6964 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
6911 AAACTATAAA
*
6921 TATTAAATTTTAATTTTTAAATT
1 TATTAAATATTAATTTTTAAATT
*
6944 TATTAAATATTATTTTTTAAA
1 TATTAAATATTAATTTTTAAA
6965 ATTAATTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
TATTAAATATTAATTTTTAAATT
Found at i:8141 original size:26 final size:24
Alignment explanation
Indices: 8112--8160 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
8102 CTTAAAAGAT
8112 AATTAAAAATATTTTAAAAATTTTAA
1 AATT-AAAATATTTT-AAAATTTTAA
* *
8138 AATTACAATATTTTTAAATTTTA
1 AATTAAAATATTTTAAAATTTTA
8161 TAATCATTCG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 8 0.38
25 9 0.43
26 4 0.19
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (24 bp):
AATTAAAATATTTTAAAATTTTAA
Found at i:8338 original size:16 final size:16
Alignment explanation
Indices: 8317--8349 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
8307 TGATATTAAA
8317 AATTAATAT-TAATTAT
1 AATTAAT-TGTAATTAT
8333 AATTAATTGTAATTAT
1 AATTAATTGTAATTAT
8349 A
1 A
8350 TTGTTCAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 1 0.06
16 15 0.94
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (16 bp):
AATTAATTGTAATTAT
Found at i:8705 original size:6 final size:6
Alignment explanation
Indices: 8689--8755 Score: 53
Period size: 6 Copynumber: 10.5 Consensus size: 6
8679 TTATTTTGAC
* * * *
8689 AAAGAA GAAGAA AAAGAA AAGAAAA ATAAGAA AAAAAA AGAAAAA AAAGAA
1 AAAGAA AAAGAA AAAGAA AA-AGAA A-AAGAA AAAGAA A-AAGAA AAAGAA
*
8740 AAAGGAA ATAGAA AAA
1 AAA-GAA AAAGAA AAA
8756 AAGATATAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
6 29 0.59
7 19 0.39
8 1 0.02
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (6 bp):
AAAGAA
Found at i:8719 original size:9 final size:9
Alignment explanation
Indices: 8700--8742 Score: 59
Period size: 9 Copynumber: 4.6 Consensus size: 9
8690 AAGAAGAAGA
8700 AAAAGAAAAG
1 AAAA-AAAAG
*
8710 AAAAATAAG
1 AAAAAAAAG
8719 AAAAAAAAAG
1 -AAAAAAAAG
8729 AAAAAAAAG
1 AAAAAAAAG
8738 AAAAA
1 AAAAA
8743 GGAAATAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
9 18 0.60
10 12 0.40
ACGTcount: A:0.86, C:0.00, G:0.12, T:0.02
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:8723 original size:10 final size:10
Alignment explanation
Indices: 8696--8757 Score: 65
Period size: 10 Copynumber: 6.0 Consensus size: 10
8686 GACAAAGAAG
8696 AAGAAAAAGAA
1 AAGAAAAA-AA
*
8707 AAG-AAAAAT
1 AAGAAAAAAA
8716 AAGAAAAAAA
1 AAGAAAAAAA
8726 AAG-AAAAAA
1 AAGAAAAAAA
8735 AAGAAAAAGGAA
1 AAGAAAAA--AA
8747 ATAGAAAAAAA
1 A-AGAAAAAAA
8758 GATATAAATG
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
9 13 0.30
10 16 0.36
11 5 0.11
12 3 0.07
13 7 0.16
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (10 bp):
AAGAAAAAAA
Found at i:8725 original size:23 final size:23
Alignment explanation
Indices: 8690--8736 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 23
8680 TATTTTGACA
8690 AAGAAGAAGAAAAAGAAAAGAAAAAT
1 AAGAA-AA-AAAAAGAAAA-AAAAAT
8716 AAGAAAAAAAAAGAAAAAAAA
1 AAGAAAAAAAAAGAAAAAAAA
8737 GAAAAAGGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 4 0.19
24 10 0.48
25 2 0.10
26 5 0.24
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (23 bp):
AAGAAAAAAAAAGAAAAAAAAAT
Found at i:8727 original size:19 final size:20
Alignment explanation
Indices: 8696--8757 Score: 90
Period size: 19 Copynumber: 3.0 Consensus size: 20
8686 GACAAAGAAG
*
8696 AAGAAAAAGAAAAGAAAAAT
1 AAGAAAAAGAAAAGAAAAAA
8716 AAGAAAAA-AAAAGAAAAAA
1 AAGAAAAAGAAAAGAAAAAA
8735 AAGAAAAAGGAAATAGAAAAAA
1 AAGAAAAA-GAAA-AGAAAAAA
8757 A
1 A
8758 GATATAAATG
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
19 18 0.47
20 8 0.21
21 3 0.08
22 9 0.24
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (20 bp):
AAGAAAAAGAAAAGAAAAAA
Found at i:8736 original size:33 final size:32
Alignment explanation
Indices: 8693--8757 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
8683 TTTGACAAAG
*
8693 AAGAAGAAAAAG-AAAAGAAAAATAAGAAAAAAA
1 AAGAAAAAAAAGAAAAAG-AAAAT-AGAAAAAAA
*
8726 AAGAAAAAAAAGAAAAAGGAAATAGAAAAAAA
1 AAGAAAAAAAAGAAAAAGAAAATAGAAAAAAA
8758 GATATAAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 9 0.31
33 15 0.52
34 5 0.17
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (32 bp):
AAGAAAAAAAAGAAAAAGAAAATAGAAAAAAA
Found at i:9976 original size:6 final size:6
Alignment explanation
Indices: 9967--10008 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
9957 TTATAAAAAT
9967 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
10009 TTTTTTATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
ATATAA
Found at i:10229 original size:15 final size:16
Alignment explanation
Indices: 10194--10224 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
10184 ATGTTATGAG
*
10194 ATCAATTATGAAAAAT
1 ATCAATTAAGAAAAAT
10210 ATCAATTAAGAAAAA
1 ATCAATTAAGAAAAA
10225 CTCAAGATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.26
Consensus pattern (16 bp):
ATCAATTAAGAAAAAT
Found at i:11325 original size:32 final size:32
Alignment explanation
Indices: 11289--11352 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
11279 AGAAAGAAAG
11289 AAAAAAAAGTATTTCACAAATAAAAAATTTGT
1 AAAAAAAAGTATTTCACAAATAAAAAATTTGT
11321 AAAAAAAAGTATTTCACAAATAAAAAATTTGT
1 AAAAAAAAGTATTTCACAAATAAAAAATTTGT
11353 TTGTTGATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.28
Consensus pattern (32 bp):
AAAAAAAAGTATTTCACAAATAAAAAATTTGT
Found at i:11350 original size:16 final size:16
Alignment explanation
Indices: 11299--11350 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
11289 AAAAAAAAGT
11299 ATTTCACAAATAAAAA
1 ATTTCACAAATAAAAA
* *
11315 ATTTGTA-AAA-AAAAGT
1 ATTT-CACAAATAAAA-A
11331 ATTTCACAAATAAAAA
1 ATTTCACAAATAAAAA
11347 ATTT
1 ATTT
11351 GTTTGTTGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 8
0.70 0.10 0.20
Matches are distributed among these distances:
15 5 0.18
16 18 0.64
17 5 0.18
ACGTcount: A:0.58, C:0.08, G:0.04, T:0.31
Consensus pattern (16 bp):
ATTTCACAAATAAAAA
Found at i:12463 original size:15 final size:15
Alignment explanation
Indices: 12437--12483 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
12427 GAAATAAGTA
12437 AAAAATTATAAATATT
1 AAAAATT-TAAATATT
12453 AAAAATTTAAATA-T
1 AAAAATTTAAATATT
*
12467 AAATATATTAAATATT
1 AAAAAT-TTAAATATT
12483 A
1 A
12484 TTTTTTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 6 0.21
15 13 0.46
16 9 0.32
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAAAATTTAAATATT
Found at i:14226 original size:23 final size:22
Alignment explanation
Indices: 14200--14262 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 22
14190 TAAATTATTG
14200 TATAAATATGTCAATATA-TAAAA
1 TATAAATAT-T-AATATATTAAAA
14223 TATAAATTATTAATATATTAAAA
1 TATAAA-TATTAATATATTAAAA
* *
14246 TATATATATAAATATAT
1 TATAAATATTAATATAT
14263 AATATTTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
22 16 0.44
23 17 0.47
24 3 0.08
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (22 bp):
TATAAATATTAATATATTAAAA
Found at i:14240 original size:22 final size:21
Alignment explanation
Indices: 14212--14264 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 21
14202 TAAATATGTC
*
14212 AATATATAAAATATAAATTATT
1 AATATATAAAATATAAA-TATA
*
14234 AATATATTAAAATATATATATA
1 AATATA-TAAAATATAAATATA
14256 AATATATAA
1 AATATATAA
14265 TATTTTAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 3 0.11
22 15 0.54
23 10 0.36
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AATATATAAAATATAAATATA
Found at i:17421 original size:33 final size:33
Alignment explanation
Indices: 17380--17495 Score: 157
Period size: 33 Copynumber: 3.5 Consensus size: 33
17370 TTACTTAGAT
17380 ATATATTGTATAGATATAGAGTAAAGATTATAG
1 ATATATTGTATAGATATAGAGTAAAGATTATAG
17413 ATATATTGTATAGATATAGAGTAAAGATTATAG
1 ATATATTGTATAGATATAGAGTAAAGATTATAG
* * *
17446 ATATA-T-TATAGATATATAGTATAGATCATAG
1 ATATATTGTATAGATATAGAGTAAAGATTATAG
*
17477 AT-TATAGGTTATAGATATA
1 ATATAT-TG-TATAGATATA
17496 TAATATTTAA
Statistics
Matches: 75, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
30 2 0.03
31 24 0.32
32 1 0.01
33 38 0.51
34 10 0.13
ACGTcount: A:0.45, C:0.01, G:0.16, T:0.38
Consensus pattern (33 bp):
ATATATTGTATAGATATAGAGTAAAGATTATAG
Found at i:17468 original size:13 final size:13
Alignment explanation
Indices: 17375--17471 Score: 58
Period size: 13 Copynumber: 7.4 Consensus size: 13
17365 AAATCTTACT
17375 TAGATATATATTGTA
1 TAGATATATA--GTA
*
17390 TAGATATAGAGTA
1 TAGATATATAGTA
*
17403 AAGAT-TATAGATA
1 TAGATATATAG-TA
* *
17416 TA-TTGTATAGATA
1 TAGATATATAG-TA
* * *
17429 TAGAGTAAAGATTA
1 TAGA-TATATAGTA
17443 TAGATATAT--TA
1 TAGATATATAGTA
17454 TAGATATATAGTA
1 TAGATATATAGTA
17467 TAGAT
1 TAGAT
17472 CATAGATTAT
Statistics
Matches: 64, Mismatches: 12, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
11 11 0.17
12 5 0.08
13 30 0.47
14 6 0.09
15 12 0.19
ACGTcount: A:0.45, C:0.00, G:0.16, T:0.38
Consensus pattern (13 bp):
TAGATATATAGTA
Found at i:17478 original size:20 final size:20
Alignment explanation
Indices: 17388--17501 Score: 74
Period size: 20 Copynumber: 5.5 Consensus size: 20
17378 ATATATATTG
* *
17388 TATAGATATAGAGTAAAGAT
1 TATAGATATATAGTATAGAT
*
17408 TATAGATATATTGTATAGA-
1 TATAGATATATAGTATAGAT
*
17427 TATAGAGTAAAGATTATAG-ATATAT
1 TATAGA-T----A-TATAGTATAGAT
17452 TATAGATATATAGTATAGAT
1 TATAGATATATAGTATAGAT
*
17472 CATAGAT-TATAGGTTATAGAT
1 TATAGATATATA-G-TATAGAT
17493 ATATA-ATAT
1 -TATAGATAT
17502 TTAAATTTAA
Statistics
Matches: 74, Mismatches: 8, Indels: 22
0.71 0.08 0.21
Matches are distributed among these distances:
19 15 0.20
20 30 0.41
21 9 0.12
22 4 0.05
24 6 0.08
25 10 0.14
ACGTcount: A:0.46, C:0.01, G:0.16, T:0.38
Consensus pattern (20 bp):
TATAGATATATAGTATAGAT
Found at i:17488 original size:7 final size:7
Alignment explanation
Indices: 17388--17497 Score: 67
Period size: 7 Copynumber: 16.6 Consensus size: 7
17378 ATATATATTG
17388 TATAGA-
1 TATAGAT
*
17394 TATAGAG
1 TATAGAT
*
17401 TAAAGAT
1 TATAGAT
17408 TATAGA-
1 TATAGAT
*
17414 TATA-TT
1 TATAGAT
17420 GTATAGA-
1 -TATAGAT
*
17427 TATAGAG
1 TATAGAT
*
17434 TAAAGAT
1 TATAGAT
17441 TATAGA-
1 TATAGAT
17447 TAT--AT
1 TATAGAT
17452 TATAGAT
1 TATAGAT
17459 ATATAG--
1 -TATAGAT
17465 TATAGAT
1 TATAGAT
*
17472 CATAGAT
1 TATAGAT
*
17479 TATAGGT
1 TATAGAT
17486 TATAGAT
1 TATAGAT
17493 ATATA
1 -TATA
17498 ATATTTAAAT
Statistics
Matches: 80, Mismatches: 12, Indels: 22
0.70 0.11 0.19
Matches are distributed among these distances:
4 1 0.01
5 8 0.10
6 19 0.24
7 43 0.54
8 9 0.11
ACGTcount: A:0.45, C:0.01, G:0.16, T:0.37
Consensus pattern (7 bp):
TATAGAT
Found at i:18904 original size:21 final size:22
Alignment explanation
Indices: 18860--18907 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
18850 TTTTAACTTT
*
18860 TATTTAAATTTAAATTATAAAA
1 TATTTAAATATAAATTATAAAA
18882 TATTTAAATATAAGA-TA-AAAA
1 TATTTAAATATAA-ATTATAAAA
18903 TATTT
1 TATTT
18908 TTTTAATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 9 0.38
22 14 0.58
23 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
TATTTAAATATAAATTATAAAA
Found at i:20638 original size:13 final size:13
Alignment explanation
Indices: 20620--20664 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
20610 TTAACACGTG
20620 ATATAATATAAAA
1 ATATAATATAAAA
20633 ATATAATATAAATA
1 ATATAATATAAA-A
*
20647 A-AT-ATATTAAA
1 ATATAATATAAAA
20658 AT-TAATA
1 ATATAATA
20665 AAACATAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
11 3 0.11
12 9 0.32
13 14 0.50
14 2 0.07
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
ATATAATATAAAA
Found at i:20659 original size:25 final size:25
Alignment explanation
Indices: 20625--20674 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
20615 ACGTGATATA
*
20625 ATATAAAAATATAATATAA-ATAAAT
1 ATATAAAAAT-TAATAAAACATAAAT
*
20650 ATATTAAAATTAATAAAACATAAAT
1 ATATAAAAATTAATAAAACATAAAT
20675 GATTAATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (25 bp):
ATATAAAAATTAATAAAACATAAAT
Found at i:20664 original size:14 final size:15
Alignment explanation
Indices: 20620--20674 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 15
20610 TTAACACGTG
20620 ATATAATAT-AA-AA
1 ATATAATATAAATAA
20633 ATATAATATAAATAA
1 ATATAATATAAATAA
* *
20648 ATATATTA-AAATTA
1 ATATAATATAAATAA
* *
20662 ATAAAACATAAAT
1 ATATAATATAAAT
20675 GATTAATTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
13 9 0.26
14 12 0.35
15 13 0.38
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (15 bp):
ATATAATATAAATAA
Found at i:20679 original size:24 final size:25
Alignment explanation
Indices: 20630--20680 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
20620 ATATAATATA
* *
20630 AAAATATAATATAAATAAATATATT
1 AAAATATAATAAAAATAAATAGATT
20655 AAAAT-TAATAAAACATAAAT-GATT
1 AAAATATAATAAAA-ATAAATAGATT
20679 AA
1 AA
20681 TTAAGATTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 12 0.52
25 11 0.48
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (25 bp):
AAAATATAATAAAAATAAATAGATT
Found at i:21842 original size:23 final size:23
Alignment explanation
Indices: 21816--21860 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
21806 AAATAAAATA
*
21816 ATAATAAT-TTTTATAAAATATAC
1 ATAATAATATTATA-AAAATATAC
*
21839 ATAATTATATTATAAAAATATA
1 ATAATAATATTATAAAAATATA
21861 ATTTTTATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (23 bp):
ATAATAATATTATAAAAATATAC
Found at i:21870 original size:17 final size:19
Alignment explanation
Indices: 21808--21870 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 19
21798 CATTAGTAAA
21808 ATAAAATAATAATAATTTTT
1 ATAAAAT-ATAATAATTTTT
21828 ATAAAATATACATAATTATATT
1 ATAAAATATA-ATAATT-T-TT
21850 ATAAAA-AT-ATAATTTTT
1 ATAAAATATAATAATTTTT
21867 ATAA
1 ATAA
21871 TAAAAGAACT
Statistics
Matches: 40, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
17 6 0.15
18 1 0.03
19 9 0.22
20 13 0.32
21 3 0.08
22 8 0.20
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
ATAAAATATAATAATTTTT
Found at i:21979 original size:19 final size:19
Alignment explanation
Indices: 21948--21986 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
21938 TCTAAATAGA
*
21948 TATTTTTTTATCTAA-ATT
1 TATTTTTTAATCTAATATT
21966 TATTTTTTAAATCTAATATT
1 TATTTTTT-AATCTAATATT
21986 T
1 T
21987 TTATCCATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
19 6 0.33
20 4 0.22
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (19 bp):
TATTTTTTAATCTAATATT
Found at i:23481 original size:17 final size:16
Alignment explanation
Indices: 23455--23496 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
23445 TGAAATCGAT
23455 TAACTCAAACTTCAAAA
1 TAACTCAAACTT-AAAA
*
23472 TAACTTAAACTTAAAA
1 TAACTCAAACTTAAAA
*
23488 TAATTCAAA
1 TAACTCAAA
23497 TCTATATTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 11 0.50
17 11 0.50
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.29
Consensus pattern (16 bp):
TAACTCAAACTTAAAA
Found at i:25505 original size:22 final size:22
Alignment explanation
Indices: 25440--25505 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
25430 CTTGAGTGTC
* *
25440 AAACTCCATTGACTTGAATTGTT
1 AAACTCAATTGACTTGAA-TATT
* * *
25463 AAACTCAATTAATTTGTATATT
1 AAACTCAATTGACTTGAATATT
25485 AAACTCAATTGACTTGAATAT
1 AAACTCAATTGACTTGAATAT
25506 GAATTGATCT
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
22 21 0.60
23 14 0.40
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.39
Consensus pattern (22 bp):
AAACTCAATTGACTTGAATATT
Found at i:25640 original size:29 final size:30
Alignment explanation
Indices: 25602--25672 Score: 81
Period size: 33 Copynumber: 2.3 Consensus size: 30
25592 ATAAATAAAA
* *
25602 TCAACTTGAT-CTGAAACTAACACAATTCGC
1 TCAA-TTGATACTAAAACTAACACAACTCGC
25632 TCAATTGATATGACTAAAACTAACACAACTCGC
1 TCAATTG--AT-ACTAAAACTAACACAACTCGC
25665 TCAATTGA
1 TCAATTGA
25673 CATGATTAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
29 3 0.09
30 4 0.11
31 3 0.09
33 25 0.71
ACGTcount: A:0.39, C:0.24, G:0.10, T:0.27
Consensus pattern (30 bp):
TCAATTGATACTAAAACTAACACAACTCGC
Found at i:25652 original size:33 final size:33
Alignment explanation
Indices: 25615--25677 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
25605 ACTTGATCTG
* *
25615 AAACTAACACAATTCGCTCAATTGATATGACTA
1 AAACTAACACAACTCGCTCAATTGACATGACTA
25648 AAACTAACACAACTCGCTCAATTGACATGA
1 AAACTAACACAACTCGCTCAATTGACATGA
25678 TTAAGAGATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.43, C:0.24, G:0.10, T:0.24
Consensus pattern (33 bp):
AAACTAACACAACTCGCTCAATTGACATGACTA
Found at i:26539 original size:2 final size:2
Alignment explanation
Indices: 26532--26564 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
26522 AAGAGGCTGT
26532 TA TA TA TA 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 TA TA TA TA T
26565 TTGTCTATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:26926 original size:19 final size:19
Alignment explanation
Indices: 26892--26931 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
26882 ATATTAATAT
*
26892 TTATAAAAAAATTTAACCA
1 TTATAAAAAAATTTAAACA
26911 TTAT-AAAAAATATTAAACA
1 TTATAAAAAAAT-TTAAACA
26930 TT
1 TT
26932 TGAGATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.35
Consensus pattern (19 bp):
TTATAAAAAAATTTAAACA
Found at i:32195 original size:15 final size:14
Alignment explanation
Indices: 32161--32198 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
32151 ACATGTATTT
32161 ATTTTTAATTAAAA
1 ATTTTTAATTAAAA
*
32175 A-ATTTAATTGAAAA
1 ATTTTTAATT-AAAA
32189 ATTTTTAATT
1 ATTTTTAATT
32199 TAATTGATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
13 7 0.35
14 6 0.30
15 7 0.35
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (14 bp):
ATTTTTAATTAAAA
Found at i:32213 original size:20 final size:20
Alignment explanation
Indices: 32174--32219 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
32164 TTTAATTAAA
32174 AAATTTAATTGAAAAATTTT
1 AAATTTAATTGAAAAATTTT
* ** *
32194 TAATTTAATTGATTACTTTT
1 AAATTTAATTGAAAAATTTT
32214 AAATTT
1 AAATTT
32220 GTTTAGGATT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.52
Consensus pattern (20 bp):
AAATTTAATTGAAAAATTTT
Found at i:32345 original size:29 final size:30
Alignment explanation
Indices: 32306--32379 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 30
32296 ACCCTTCAAG
* * *
32306 GTTTAATAAAAAATACATTTACCTTTTATA
1 GTTTGATAAAAAATACACTTACCTTTTAAA
*
32336 GTTTGA-AAAATACT-CACTTACCTTTTAAA
1 GTTTGATAAAA-AATACACTTACCTTTTAAA
32365 GTTTGATAAAAAATA
1 GTTTGATAAAAAATA
32380 TATTAATCCC
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
29 25 0.69
30 11 0.31
ACGTcount: A:0.43, C:0.11, G:0.07, T:0.39
Consensus pattern (30 bp):
GTTTGATAAAAAATACACTTACCTTTTAAA
Found at i:34775 original size:29 final size:29
Alignment explanation
Indices: 34742--34885 Score: 108
Period size: 29 Copynumber: 4.8 Consensus size: 29
34732 TTAAATTTTA
**
34742 TTATTTTATTTAAATAATTTTTTATGTTT
1 TTATTTTATTTAAATAATTTTTTAACTTT
* *
34771 TTATTATATTTAAATATTTTTTTAACTTT
1 TTATTTTATTTAAATAATTTTTTAACTTT
* *
34800 TAATTTATACTTAAATAAATTTTTTAATCTTT
1 TTATTT-TATTTAAAT-AATTTTTTAA-CTTT
* * ** * *
34832 TAACTTGTATCAAAATAAGTCTTTTAACGTT
1 TTA-TTTTATTTAAATAA-TTTTTTAACTTT
* *
34863 TAATTTATATTTAAATAAATTTT
1 TTATTT-TATTTAAATAATTTTT
34886 CAAGATAAAT
Statistics
Matches: 90, Mismatches: 19, Indels: 11
0.75 0.16 0.09
Matches are distributed among these distances:
29 29 0.32
30 13 0.14
31 26 0.29
32 20 0.22
33 2 0.02
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.58
Consensus pattern (29 bp):
TTATTTTATTTAAATAATTTTTTAACTTT
Found at i:34826 original size:31 final size:31
Alignment explanation
Indices: 34729--34885 Score: 142
Period size: 31 Copynumber: 5.1 Consensus size: 31
34719 AATTAAAAAG
*
34729 TTTTTAAATTTTATTATTT-TATTTAAAT-AAT
1 TTTTTAACTTTTA--ATTTATATTTAAATAAAT
** * *
34760 TTTTTATGTTTTTA-TTATATTTAAAT-ATT
1 TTTTTAACTTTTAATTTATATTTAAATAAAT
*
34789 TTTTTAACTTTTAATTTATACTTAAATAAAT
1 TTTTTAACTTTTAATTTATATTTAAATAAAT
* * ** *
34820 TTTTTAATCTTTTAACTTGTATCAAAATAAGT
1 TTTTTAA-CTTTTAATTTATATTTAAATAAAT
* *
34852 CTTTTAACGTTTAATTTATATTTAAATAAAT
1 TTTTTAACTTTTAATTTATATTTAAATAAAT
34883 TTT
1 TTT
34886 CAAGATAAAT
Statistics
Matches: 99, Mismatches: 23, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
28 2 0.02
29 23 0.23
30 11 0.11
31 39 0.39
32 24 0.24
ACGTcount: A:0.34, C:0.04, G:0.03, T:0.59
Consensus pattern (31 bp):
TTTTTAACTTTTAATTTATATTTAAATAAAT
Found at i:36555 original size:2 final size:2
Alignment explanation
Indices: 36548--36596 Score: 50
Period size: 2 Copynumber: 26.0 Consensus size: 2
36538 TTTGTTCATA
* *
36548 AT AT AT AT AT AT AT -T AT AT CT GT A- AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
36588 GT AT -T AT AT
1 AT AT AT AT AT
36597 CTGCATGCAT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
1 3 0.08
2 36 0.92
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (2 bp):
AT
Found at i:39428 original size:28 final size:28
Alignment explanation
Indices: 39360--39431 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 28
39350 CCACCCTTTA
39360 TGTTTGTCAAAAATGATGATTTTTTTTG
1 TGTTTGTCAAAAATGATGATTTTTTTTG
** * *
39388 TGTTAATAAAAAAAT-AGTGATTTTTTTTT
1 TGTTTGT-CAAAAATGA-TGATTTTTTTTG
39417 TGTTTGTCAAAAATG
1 TGTTTGTCAAAAATG
39432 GTGGCTTGTT
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
28 12 0.35
29 22 0.65
ACGTcount: A:0.32, C:0.03, G:0.15, T:0.50
Consensus pattern (28 bp):
TGTTTGTCAAAAATGATGATTTTTTTTG
Found at i:41626 original size:40 final size:41
Alignment explanation
Indices: 41552--41643 Score: 109
Period size: 40 Copynumber: 2.3 Consensus size: 41
41542 CTTAATTAAT
41552 TTAATTTAATTAGAAATAAACTCTTTTATTTATC-TCATAA
1 TTAATTTAATTAGAAATAAACTCTTTTATTTATCTTCATAA
* * * *
41592 TTAATTTAGTTAGAGATAAA-T-TTATTTTTATATCTTCTTAA
1 TTAATTTAATTAGAAATAAACTCTT-TTATT-TATCTTCATAA
41633 TTAATTTAATT
1 TTAATTTAATT
41644 TAATTAGAGA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
38 2 0.05
39 5 0.11
40 22 0.50
41 15 0.34
ACGTcount: A:0.37, C:0.07, G:0.04, T:0.52
Consensus pattern (41 bp):
TTAATTTAATTAGAAATAAACTCTTTTATTTATCTTCATAA
Found at i:44252 original size:21 final size:23
Alignment explanation
Indices: 44222--44273 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
44212 TTAATTAAAA
44222 TAATATATTTAAAGTT-AAAAATT
1 TAATA-ATTTAAAGTTAAAAAATT
* *
44245 T-ATAATTTTAATTTAAAAAATT
1 TAATAATTTAAAGTTAAAAAATT
44267 TAATAAT
1 TAATAAT
44274 AAAAATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 8 0.32
22 11 0.44
23 6 0.24
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
TAATAATTTAAAGTTAAAAAATT
Found at i:45811 original size:26 final size:28
Alignment explanation
Indices: 45756--45820 Score: 71
Period size: 26 Copynumber: 2.4 Consensus size: 28
45746 ACTTATCAGG
*
45756 TTAGTAATTTTCATCATTTGAGGGCTATT
1 TTAGTAATTTT-ATCATTTGAGGGCCATT
*
45785 TTAGTAATTTT-T-ATTTTAGGGCCATT
1 TTAGTAATTTTATCATTTGAGGGCCATT
* *
45811 TAAGTTATTT
1 TTAGTAATTT
45821 AACAAGGTCT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 20 0.62
27 1 0.03
29 11 0.34
ACGTcount: A:0.25, C:0.08, G:0.15, T:0.52
Consensus pattern (28 bp):
TTAGTAATTTTATCATTTGAGGGCCATT
Found at i:45916 original size:58 final size:57
Alignment explanation
Indices: 45806--45917 Score: 138
Period size: 57 Copynumber: 1.9 Consensus size: 57
45796 TATTTTAGGG
** *
45806 CCATTTAAGTTATTTAACAAGGTCTAGGTCATTTTAATAATTTTCATCATTTTAACA
1 CCATTTAAGTTATTTAACAAACTCTAGGTCATTTTAACAATTTTCATCATTTTAACA
* *
45863 CCATTTAGGTTATTTAACAAAACT-TAGAGTCATTTTCACAA-TTTCTATCATTTTA
1 CCATTTAAGTTATTTAAC-AAACTCTAG-GTCATTTTAACAATTTTC-ATCATTTTA
45918 GAGTCATGTA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
57 24 0.51
58 23 0.49
ACGTcount: A:0.33, C:0.15, G:0.08, T:0.44
Consensus pattern (57 bp):
CCATTTAAGTTATTTAACAAACTCTAGGTCATTTTAACAATTTTCATCATTTTAACA
Done.