Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2110
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: 54245
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Found at i:306 original size:15 final size:15
Alignment explanation
Indices: 288--321 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
278 TTTAAAAATT
288 AATAAAATAAATTA-A
1 AATAAAAT-AATTATA
303 AATAAAATAATTATA
1 AATAAAATAATTATA
318 AATA
1 AATA
322 TACTAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AATAAAATAATTATA
Found at i:645 original size:2 final size:2
Alignment explanation
Indices: 638--667 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
628 TTAGTGTAAA
638 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
668 TTGATAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:908 original size:22 final size:21
Alignment explanation
Indices: 864--905 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
854 TTATTTATTT
864 TATTTAAATTTAATTATAAAA
1 TATTTAAATTTAATTATAAAA
885 TATTTAAATATTAA-TATAAAA
1 TATTTAAAT-TTAATTATAAAA
906 ATAATATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TATTTAAATTTAATTATAAAA
Found at i:1140 original size:13 final size:13
Alignment explanation
Indices: 1118--1172 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
1108 ACTACTTAAT
1118 TTTTTAAATATTTA
1 TTTTT-AATATTTA
1132 TTTTTAATATTTA
1 TTTTTAATATTTA
* *
1145 TATTTGATATTTA
1 TTTTTAATATTTA
* * *
1158 TATTTGATATATA
1 TTTTTAATATTTA
1171 TT
1 TT
1173 CAAACATAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
13 32 0.86
14 5 0.14
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
TTTTTAATATTTA
Found at i:2269 original size:14 final size:15
Alignment explanation
Indices: 2247--2292 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
2237 TATTTGATTT
*
2247 ATTAAAATATAAA-A
1 ATTATAATATAAATA
2261 ATTATAATA-AAATA
1 ATTATAATATAAATA
2275 ATTATTTAATATAAATA
1 ATTA--TAATATAAATA
2292 A
1 A
2293 ATAAAAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 3 0.11
14 13 0.48
16 5 0.19
17 6 0.22
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
ATTATAATATAAATA
Found at i:2380 original size:21 final size:22
Alignment explanation
Indices: 2356--2398 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
2346 TATTATAAAA
*
2356 TTTAAATTTTTAATA-AATTTT
1 TTTAAATTTTTAAAATAATTTT
*
2377 TTTAATTTTTTAAAATAATTTT
1 TTTAAATTTTTAAAATAATTTT
2399 ATGAATCATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TTTAAATTTTTAAAATAATTTT
Found at i:3446 original size:2 final size:2
Alignment explanation
Indices: 3427--3468 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
3417 CTCACTTCCC
* **
3427 AT AT AC AT AT AT GC AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3468 A
1 A
3469 GCAAAGAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:5371 original size:2 final size:2
Alignment explanation
Indices: 5364--5404 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
5354 GTTTCCCCTT
5364 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
5405 TATCAACAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:7393 original size:12 final size:13
Alignment explanation
Indices: 7374--7418 Score: 58
Period size: 12 Copynumber: 3.5 Consensus size: 13
7364 TAAATTATAA
7374 AAAATTTAAGTTT
1 AAAATTTAAGTTT
*
7387 -GAATTTAA-TTT
1 AAAATTTAAGTTT
7398 AAAATTTAAGATTT
1 AAAATTTAAG-TTT
7412 AAAATTT
1 AAAATTT
7419 GATTTAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 3 0.11
12 14 0.52
14 10 0.37
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (13 bp):
AAAATTTAAGTTT
Found at i:8994 original size:15 final size:15
Alignment explanation
Indices: 8942--9012 Score: 51
Period size: 16 Copynumber: 4.8 Consensus size: 15
8932 ATACTTTTTC
* *
8942 TAAT-TATATATATA
1 TAATATATAAATATT
8956 TAA-ATATAAA-ATT
1 TAATATATAAATATT
*
8969 TAAAAATTATAAATATT
1 T-AATA-TATAAATATT
*
8986 TAATATATAAAATTTT
1 TAATATAT-AAATATT
9002 TAATA-ATAAAT
1 TAATATATAAAT
9013 TAATAAAATA
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
13 3 0.06
14 14 0.30
15 6 0.13
16 20 0.43
17 4 0.09
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TAATATATAAATATT
Found at i:9700 original size:12 final size:12
Alignment explanation
Indices: 9663--9726 Score: 69
Period size: 12 Copynumber: 5.5 Consensus size: 12
9653 ATATGTATCG
9663 TATT-TATTTTA
1 TATTATATTTTA
* * * *
9674 TTTTTTATGTCA
1 TATTATATTTTA
9686 TATTATATTTTA
1 TATTATATTTTA
9698 TATTATATTTTA
1 TATTATATTTTA
*
9710 -ATTATTTTTTA
1 TATTATATTTTA
9721 TATTAT
1 TATTAT
9727 GTAATCGTAT
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
11 13 0.30
12 30 0.70
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.69
Consensus pattern (12 bp):
TATTATATTTTA
Found at i:9988 original size:22 final size:23
Alignment explanation
Indices: 9963--10047 Score: 93
Period size: 25 Copynumber: 3.6 Consensus size: 23
9953 ATTATTCGTA
9963 TATATAAAATT-TATTTATAAAT
1 TATATAAAATTATATTTATAAAT
9985 TATA-AAAATTATATTTATAAAT
1 TATATAAAATTATATTTATAAAT
* * *
10007 AATAATTAAAATTATATTAAAAAAT
1 TAT-A-TAAAATTATATTTATAAAT
10032 TAATTATAAAATTATA
1 T-A-TATAAAATTATA
10048 ATAAAAGAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
21 6 0.11
22 17 0.32
23 1 0.02
25 26 0.49
26 2 0.04
27 1 0.02
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
TATATAAAATTATATTTATAAAT
Found at i:9990 original size:20 final size:21
Alignment explanation
Indices: 9965--10011 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 21
9955 TATTCGTATA
9965 TATAAAATT-TATTTATAAAT
1 TATAAAATTATATTTATAAAT
9985 TATAAAAATTATATTTATAAAT
1 TAT-AAAATTATATTTATAAAT
*
10007 AATAA
1 TATAA
10012 TTAAAATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 3 0.12
21 8 0.33
22 13 0.54
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TATAAAATTATATTTATAAAT
Found at i:10232 original size:8 final size:8
Alignment explanation
Indices: 10221--10322 Score: 67
Period size: 8 Copynumber: 13.1 Consensus size: 8
10211 ATAATATGAT
10221 TATATAAA
1 TATATAAA
10229 TATATTAAA
1 TATA-TAAA
*
10238 -ATTTAAA
1 TATATAAA
10245 TAAATATATAA
1 T--ATATA-AA
* *
10256 TATTTTAA
1 TATATAAA
10264 T-TAT-AA
1 TATATAAA
10270 T-TATAATA
1 TATATAA-A
*
10278 TATAAAAA
1 TATATAAA
10286 TATATAAA
1 TATATAAA
10294 T-TAT---
1 TATATAAA
10298 TATATAAA
1 TATATAAA
10306 TATATAAA
1 TATATAAA
10314 TATATAAA
1 TATATAAA
10322 T
1 T
10323 TTATTTAAAA
Statistics
Matches: 75, Mismatches: 7, Indels: 24
0.71 0.07 0.23
Matches are distributed among these distances:
4 1 0.01
5 3 0.04
6 6 0.08
7 10 0.13
8 37 0.49
9 11 0.15
10 4 0.05
11 3 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (8 bp):
TATATAAA
Found at i:10296 original size:30 final size:28
Alignment explanation
Indices: 10210--10323 Score: 99
Period size: 28 Copynumber: 4.0 Consensus size: 28
10200 TGATTATGAA
* * *
10210 TATAATATGATTATATAAATATATTAAAAT
1 TATAATATAAATATAAAAATATA-T-AAAT
* * *
10240 T-TAA-ATAAATAT-ATAATATTTTAAT
1 TATAATATAAATATAAAAATATATAAAT
10265 TATAATTATAATATATAAAAATATATAAAT
1 TATAA-TATAA-ATATAAAAATATATAAAT
* *
10295 TATTATATAAATATATAAATATATAAAT
1 TATAATATAAATATAAAAATATATAAAT
10323 T
1 T
10324 TATTTAAAAC
Statistics
Matches: 68, Mismatches: 11, Indels: 12
0.75 0.12 0.13
Matches are distributed among these distances:
25 4 0.06
26 4 0.06
27 5 0.07
28 28 0.41
29 12 0.18
30 15 0.22
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (28 bp):
TATAATATAAATATAAAAATATATAAAT
Found at i:10313 original size:20 final size:20
Alignment explanation
Indices: 10209--10314 Score: 82
Period size: 20 Copynumber: 5.4 Consensus size: 20
10199 ATGATTATGA
*
10209 ATATAATATGATTATATAAAT
1 ATATAA-ATTATTATATAAAT
* *
10230 ATATTAAAAT-TTAAATAAAT
1 ATA-TAAATTATTATATAAAT
10250 ATATAATATT-TTA-ATTATAAT
1 ATATAA-ATTATTATA-TA-AAT
*
10271 -TAT-AA-TA-TATAAAAAT
1 ATATAAATTATTATATAAAT
10287 ATATAAATTATTATATAAAT
1 ATATAAATTATTATATAAAT
10307 ATATAAAT
1 ATATAAAT
10315 ATATAAATTT
Statistics
Matches: 69, Mismatches: 6, Indels: 21
0.72 0.06 0.22
Matches are distributed among these distances:
16 3 0.04
17 7 0.10
18 4 0.06
19 7 0.10
20 38 0.55
21 7 0.10
22 3 0.04
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (20 bp):
ATATAAATTATTATATAAAT
Found at i:10554 original size:17 final size:17
Alignment explanation
Indices: 10534--10569 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
10524 ATTAAAAAAA
10534 ATATTAAATATAAATAT
1 ATATTAAATATAAATAT
**
10551 ATATTTGATATAAATAT
1 ATATTAAATATAAATAT
10568 AT
1 AT
10570 TTATTTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
ATATTAAATATAAATAT
Found at i:16784 original size:35 final size:35
Alignment explanation
Indices: 16744--16828 Score: 95
Period size: 35 Copynumber: 2.5 Consensus size: 35
16734 TTATATTATA
16744 TAAAAATAAATATTATAA-TA-TTATAATATAAAATT
1 TAAAAA-AAATATTA-AATTATTTATAATATAAAATT
* * *
16779 TAAAAAATATATTAAATTATTTATATTTTAAAATT
1 TAAAAAAAATATTAAATTATTTATAATATAAAATT
*
16814 TAATAAAAA-ATTAAA
1 TAAAAAAAATATTAAA
16829 ATTTATCACA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
33 2 0.05
34 15 0.35
35 26 0.60
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (35 bp):
TAAAAAAAATATTAAATTATTTATAATATAAAATT
Found at i:29813 original size:10 final size:10
Alignment explanation
Indices: 29798--29831 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
29788 TAGGTGTAAA
29798 TAAATATTTT
1 TAAATATTTT
* *
29808 TAAATATATG
1 TAAATATTTT
29818 TAAATATTTT
1 TAAATATTTT
29828 TAAA
1 TAAA
29832 AAAATTTAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (10 bp):
TAAATATTTT
Found at i:29841 original size:20 final size:20
Alignment explanation
Indices: 29798--29843 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
29788 TAGGTGTAAA
* *
29798 TAAATATTTTTAAATATATG
1 TAAATATTTTTAAAAAAATG
*
29818 TAAATATTTTTAAAAAAATT
1 TAAATATTTTTAAAAAAATG
29838 TAAATA
1 TAAATA
29844 GAATAATGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (20 bp):
TAAATATTTTTAAAAAAATG
Found at i:30853 original size:13 final size:14
Alignment explanation
Indices: 30824--30856 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
30814 ATTTGAATTT
*
30824 AAATTTAAGTATAA
1 AAATTTAAATATAA
30838 AAATTTAAAT-TAA
1 AAATTTAAATATAA
30851 AAATTT
1 AAATTT
30857 TATATGCCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (14 bp):
AAATTTAAATATAA
Found at i:31306 original size:9 final size:9
Alignment explanation
Indices: 31294--31325 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
31284 CAAAATAATT
31294 AAAAATTAA
1 AAAAATTAA
31303 AAAAATTAA
1 AAAAATTAA
31312 AAAAA-TAA
1 AAAAATTAA
31320 AAAAAT
1 AAAAAT
31326 ATTTTTAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAAAATTAA
Found at i:31309 original size:16 final size:17
Alignment explanation
Indices: 31285--31325 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
31275 AAAATTATTC
* *
31285 AAAATAATT-AAAAATT
1 AAAAAAATTAAAAAAAT
31301 AAAAAAATTAAAAAAAT
1 AAAAAAATTAAAAAAAT
31318 AAAAAAAT
1 AAAAAAAT
31326 ATTTTTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (17 bp):
AAAAAAATTAAAAAAAT
Found at i:34851 original size:2 final size:2
Alignment explanation
Indices: 34846--34882 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
34836 TGGCTAGAAA
34846 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34883 GATGAATTGG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:35646 original size:18 final size:18
Alignment explanation
Indices: 35601--35652 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
35591 TTAGATTAAT
35601 TTTTAATTATATTTA-AAA
1 TTTTAA-TATATTTATAAA
* *
35619 TATTATATATTTTTATAAA
1 TTTTA-ATATATTTATAAA
35638 TTTTAATATATTTAT
1 TTTTAATATATTTAT
35653 GATATATTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 20 0.71
19 8 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTTAATATATTTATAAA
Found at i:36239 original size:11 final size:12
Alignment explanation
Indices: 36219--36251 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
36209 TATTTTTAAA
*
36219 AAATTTAATATT
1 AAATATAATATT
36231 AAATA-AATATT
1 AAATATAATATT
36242 AAATATAATA
1 AAATATAATA
36252 AATAATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 11 0.58
12 8 0.42
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
AAATATAATATT
Found at i:38368 original size:2 final size:2
Alignment explanation
Indices: 38363--38391 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
38353 TTCTGTTTGT
38363 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 T
38392 GTATGAATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39092 original size:16 final size:16
Alignment explanation
Indices: 39065--39115 Score: 63
Period size: 16 Copynumber: 3.2 Consensus size: 16
39055 TTCGAAAATC
39065 ATATTGAAAATTTATAA
1 ATATT-AAAATTTATAA
39082 ATATTAAAA-TT-TAA
1 ATATTAAAATTTATAA
39096 AT-TTAAAATTTATTAA
1 ATATTAAAATTTA-TAA
39112 ATAT
1 ATAT
39116 GCCTTTTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
13 6 0.20
14 7 0.23
15 2 0.07
16 9 0.30
17 6 0.20
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (16 bp):
ATATTAAAATTTATAA
Found at i:39103 original size:13 final size:14
Alignment explanation
Indices: 39065--39107 Score: 52
Period size: 13 Copynumber: 2.9 Consensus size: 14
39055 TTCGAAAATC
39065 ATATTGAAAATTTATAA
1 ATATT-AAAA-TT-TAA
39082 ATATTAAAATTTAA
1 ATATTAAAATTTAA
39096 AT-TTAAAATTTA
1 ATATTAAAATTTA
39108 TTAAATATGC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 10 0.38
14 5 0.19
15 2 0.08
16 4 0.15
17 5 0.19
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (14 bp):
ATATTAAAATTTAA
Found at i:40944 original size:25 final size:23
Alignment explanation
Indices: 40900--40946 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
40890 TTTTTTTATG
*
40900 TAAAAAAAATCATAATTTAAAAA
1 TAAAAAAAATCATAAATTAAAAA
*
40923 TAAAAAAAATTATACAAATTAAAA
1 TAAAAAAAATCAT--AAATTAAAA
40947 TTTAAATCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
25 8 0.40
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (23 bp):
TAAAAAAAATCATAAATTAAAAA
Found at i:41975 original size:18 final size:19
Alignment explanation
Indices: 41952--41991 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
41942 GTAAAAAATA
*
41952 TAATCTATGAC-ATAAACT
1 TAATCTACGACTATAAACT
41970 TAATCTACGACTTATAAACT
1 TAATCTACGAC-TATAAACT
41990 TA
1 TA
41992 GATCAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 10 0.53
20 9 0.47
ACGTcount: A:0.42, C:0.17, G:0.05, T:0.35
Consensus pattern (19 bp):
TAATCTACGACTATAAACT
Found at i:43217 original size:25 final size:25
Alignment explanation
Indices: 43183--43232 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
43173 AGTGCAATGG
43183 AAAATTCACATAATAATCAGTCTTT
1 AAAATTCACATAATAATCAGTCTTT
43208 AAAATTCACATAATAATCAGTCTTT
1 AAAATTCACATAATAATCAGTCTTT
43233 CTTGCTGGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.44, C:0.16, G:0.04, T:0.36
Consensus pattern (25 bp):
AAAATTCACATAATAATCAGTCTTT
Found at i:43746 original size:20 final size:18
Alignment explanation
Indices: 43723--43774 Score: 61
Period size: 20 Copynumber: 2.8 Consensus size: 18
43713 TATAATAATA
43723 AAATCATTTAAATAATTTTT
1 AAAT-ATTTAAAT-ATTTTT
43743 AAATATTTTAAAT-TTTTT
1 AAATA-TTTAAATATTTTT
*
43761 AAAAATTTAAATAT
1 AAATATTTAAATAT
43775 ATTCCTATCG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
17 7 0.24
18 10 0.34
19 1 0.03
20 11 0.38
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (18 bp):
AAATATTTAAATATTTTT
Found at i:43761 original size:18 final size:17
Alignment explanation
Indices: 43728--43772 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
43718 TAATAAAATC
43728 ATTTAAATAATTTTTAAATA
1 ATTTAAAT--TTTTTAAA-A
*
43748 TTTTAAATTTTTTAAAA
1 ATTTAAATTTTTTAAAA
43765 ATTTAAAT
1 ATTTAAAT
43773 ATATTCCTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 8 0.35
18 8 0.35
20 7 0.30
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTAAATTTTTTAAAA
Found at i:45957 original size:2 final size:2
Alignment explanation
Indices: 45946--45978 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
45936 ATTTTTCTAC
*
45946 AT AT -T AT AT AT AT AT AT AT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
45979 TCTTTTGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
AT
Found at i:47797 original size:13 final size:13
Alignment explanation
Indices: 47779--47806 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
47769 TATTTTTTAA
47779 AATATTTATATTT
1 AATATTTATATTT
47792 AATATTTATATTT
1 AATATTTATATTT
47805 AA
1 AA
47807 AATATATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
AATATTTATATTT
Found at i:47822 original size:9 final size:11
Alignment explanation
Indices: 47798--47823 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
47788 ATTTAATATT
47798 TATATTTAAAA
1 TATATTTAAAA
47809 TATATTTAAAA
1 TATATTTAAAA
47820 TATA
1 TATA
47824 AATATTACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
TATATTTAAAA
Found at i:49495 original size:17 final size:17
Alignment explanation
Indices: 49469--49502 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
49459 GAAATACCAA
*
49469 TAATTGTTGTATCAAAG
1 TAATTCTTGTATCAAAG
*
49486 TAATTCTTGTTTCAAAG
1 TAATTCTTGTATCAAAG
49503 GAAAAACAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.09, G:0.15, T:0.44
Consensus pattern (17 bp):
TAATTCTTGTATCAAAG
Found at i:51143 original size:19 final size:19
Alignment explanation
Indices: 51116--51158 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
51106 TATTTTAACT
* *
51116 TAATTTTTTTATAAATATA
1 TAATATTTTAATAAATATA
*
51135 TAATATTTTAATAATTATA
1 TAATATTTTAATAAATATA
*
51154 AAATA
1 TAATA
51159 AAAATAATAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TAATATTTTAATAAATATA
Found at i:51327 original size:28 final size:27
Alignment explanation
Indices: 51286--51412 Score: 98
Period size: 28 Copynumber: 4.6 Consensus size: 27
51276 ATTAAATACG
* * *
51286 TTATATAAATTTTAATATTTTAATAAT
1 TTATATTATTTTTTATATTTTAATAAT
51313 TTATATTATTTTTTATATTATATAAT-AT
1 TTATATTATTTTTTATATT-T-TAATAAT
* *
51341 TTATATTATTTTTTATATTATATATATTT
1 TTATATTATTTTTTATATTTTA-ATA-AT
* * * *
51370 TTATTTTATATTTTA-A-TTAAATATT
1 TTATATTATTTTTTATATTTTAATAAT
*
51395 TTATATTATATTTATATA
1 TTATATTAT-TTTTTATA
51413 ATAATATAAA
Statistics
Matches: 81, Mismatches: 12, Indels: 14
0.76 0.11 0.13
Matches are distributed among these distances:
25 10 0.12
26 9 0.11
27 21 0.26
28 23 0.28
29 18 0.22
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (27 bp):
TTATATTATTTTTTATATTTTAATAAT
Found at i:51329 original size:12 final size:12
Alignment explanation
Indices: 51312--51361 Score: 64
Period size: 12 Copynumber: 3.8 Consensus size: 12
51302 ATTTTAATAA
51312 TTTATATTATTT
1 TTTATATTATTT
51324 TTTATATTATATAAT
1 TTTATATTAT-T--T
51339 ATTTATATTATTT
1 -TTTATATTATTT
51352 TTTATATTAT
1 TTTATATTAT
51362 ATATATTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
12 20 0.59
13 2 0.06
15 2 0.06
16 10 0.29
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTATATTATTT
Found at i:51333 original size:5 final size:5
Alignment explanation
Indices: 51313--51411 Score: 56
Period size: 5 Copynumber: 21.2 Consensus size: 5
51303 TTTTAATAAT
*
51313 TTATA TTAT- TT-T- TTATA TTATA TAATA TTTATA TTAT- TT-T- TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA -TTATA TTATA TTATA TTATA
* * * *
51358 TTATA -TATA TT-T- TTATT TTATA TTTTAA TTA-A ATATT TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTAT-A TTATA TTATA TTATA TTATA
51405 TTTATA T
1 -TTATA T
51412 AATAATATAA
Statistics
Matches: 74, Mismatches: 9, Indels: 22
0.70 0.09 0.21
Matches are distributed among these distances:
3 8 0.11
4 15 0.20
5 39 0.53
6 12 0.16
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (5 bp):
TTATA
Found at i:51376 original size:6 final size:7
Alignment explanation
Indices: 51294--51401 Score: 66
Period size: 7 Copynumber: 15.4 Consensus size: 7
51284 CGTTATATAA
51294 ATTTTAAT
1 ATTTT-AT
51302 ATTTTAAT
1 ATTTT-AT
*
51310 AATTTAT
1 ATTTTAT
51317 A--TTAT
1 ATTTTAT
*
51322 TTTTTAT
1 ATTTTAT
*
51329 ATTATAT
1 ATTTTAT
51336 AATATTTAT
1 -AT-TTTAT
51345 A--TTAT
1 ATTTTAT
*
51350 TTTTTAT
1 ATTTTAT
51357 ATTATATAT
1 ATT-T-TAT
51366 ATTTT-T
1 ATTTTAT
51372 ATTTTAT
1 ATTTTAT
51379 ATTTTA-
1 ATTTTAT
**
51385 ATTAAAT
1 ATTTTAT
51392 ATTTTAT
1 ATTTTAT
51399 ATT
1 ATT
51402 ATATTTATAT
Statistics
Matches: 79, Mismatches: 11, Indels: 21
0.71 0.10 0.19
Matches are distributed among these distances:
5 8 0.10
6 10 0.13
7 34 0.43
8 17 0.22
9 10 0.13
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (7 bp):
ATTTTAT
Found at i:51512 original size:27 final size:29
Alignment explanation
Indices: 51482--51560 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 29
51472 GGTAATTGTA
51482 TTTAAAATATTTTATATTTA-TATA-AAT
1 TTTAAAATATTTTATATTTATTATATAAT
*
51509 TTTAAAATA-TTAATAATTAATATTATATAAT
1 TTTAAAATATTTTAT-ATT--TATTATATAAT
51540 TTTAAAATTATATTTATATTT
1 TTTAAAA-TAT-TTTATATTT
51561 TATCTTTATT
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
26 4 0.10
27 12 0.29
29 2 0.05
30 4 0.10
31 11 0.26
32 2 0.05
33 3 0.07
34 4 0.10
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (29 bp):
TTTAAAATATTTTATATTTATTATATAAT
Found at i:51548 original size:22 final size:20
Alignment explanation
Indices: 51518--51562 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 20
51508 TTTTAAAATA
51518 TTAATAATTAATATTATATAATT
1 TTAATAATT-ATATT-TAT-ATT
51541 TTAA-AATTATATTTATATT
1 TTAATAATTATATTTATATT
51560 TTA
1 TTA
51563 TCTTTATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.27
20 3 0.14
21 5 0.23
22 4 0.18
23 4 0.18
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTAATAATTATATTTATATT
Found at i:51549 original size:16 final size:16
Alignment explanation
Indices: 51499--51552 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
51489 TATTTTATAT
51499 TTATATAAATTTTAAAA
1 TTATAT-AATTTTAAAA
* *
51516 -TAT-TAATAATTAATA
1 TTATATAAT-TTTAAAA
51531 TTATATAATTTTAAAA
1 TTATATAATTTTAAAA
51547 TTATAT
1 TTATAT
51553 TTATATTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
14 3 0.10
15 6 0.20
16 17 0.57
17 4 0.13
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTATATAATTTTAAAA
Found at i:51961 original size:16 final size:17
Alignment explanation
Indices: 51937--52001 Score: 53
Period size: 18 Copynumber: 3.8 Consensus size: 17
51927 GAAAATTTTA
*
51937 TTTA-ATTTTTAATAAT
1 TTTATATTTTTAAAAAT
*
51953 TTTATTTTTTTAAAAATT
1 TTTATATTTTTAAAAA-T
* *
51971 TTTAAATTTTGAATAAA-
1 TTTATATTTTTAA-AAAT
51988 TTTATACTTTTTAA
1 TTTATA-TTTTTAA
52002 TATTTATATT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
16 4 0.11
17 14 0.37
18 17 0.45
19 3 0.08
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (17 bp):
TTTATATTTTTAAAAAT
Found at i:52153 original size:17 final size:16
Alignment explanation
Indices: 52122--52152 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
52112 AAATTTTGAT
52122 TTAAATTTATTTTTTA
1 TTAAATTTATTTTTTA
52138 TTAAATTTATTTTTT
1 TTAAATTTATTTTTT
52153 TGATTTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTAAATTTATTTTTTA
Done.