Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2461
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: 61190
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Found at i:255 original size:14 final size:14
Alignment explanation
Indices: 228--273 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
218 AGATACATCA
228 ATAA-TTTA-AAAT
1 ATAATTTTATAAAT
240 ATAATTTTATAAAT
1 ATAATTTTATAAAT
*
254 ATAATATATATAAA-
1 ATAAT-TTTATAAAT
268 ATAATT
1 ATAATT
274 AAAATATAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
12 4 0.13
13 5 0.17
14 14 0.47
15 7 0.23
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
ATAATTTTATAAAT
Found at i:295 original size:25 final size:26
Alignment explanation
Indices: 250--406 Score: 89
Period size: 25 Copynumber: 6.0 Consensus size: 26
240 ATAATTTTAT
250 AAATATAATATATATAAAATA-ATTA
1 AAATATAATATATATAAAATATATTA
* *
275 AAATATAATATAGTAT-TAATATTTTA
1 AAATATAATATA-TATAAAATATATTA
* *
301 AAATTTTATAATATAAATTATTAATATATT-
1 AAA---TATAATATATA-TA-AAATATATTA
*
331 AAATATTAATATAT-TAAAATTTTATTTA
1 AAATA-TAATATATATAAAA-TATA-TTA
*
359 TAATTATAATATA-AT-AAATATA-TA
1 -AAATATAATATATATAAAATATATTA
* *
383 AAA-ATAATATA-ATTATATATATTA
1 AAATATAATATATATAAAATATATTA
407 CGATATCTAT
Statistics
Matches: 105, Mismatches: 11, Indels: 33
0.70 0.07 0.22
Matches are distributed among these distances:
22 10 0.10
23 8 0.08
24 4 0.04
25 18 0.17
26 17 0.16
27 7 0.07
28 16 0.15
29 14 0.13
30 3 0.03
31 8 0.08
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.45
Consensus pattern (26 bp):
AAATATAATATATATAAAATATATTA
Found at i:332 original size:8 final size:8
Alignment explanation
Indices: 255--347 Score: 57
Period size: 8 Copynumber: 11.4 Consensus size: 8
245 TTTATAAATA
255 TAATATAT
1 TAATATAT
*
263 ATAAAATAAT
1 -TAATAT-AT
*
273 TAAAATAT
1 TAATATAT
*
281 AATATAGTAT
1 TA-ATA-TAT
*
291 TAATATTT
1 TAATATAT
*
299 TAAAAT-T
1 TAATATAT
*
306 TTATAATAT
1 TAAT-ATAT
*
315 AAAT-TAT
1 TAATATAT
322 TAATATAT
1 TAATATAT
330 TAA-ATAT
1 TAATATAT
337 TAATATAT
1 TAATATAT
345 TAA
1 TAA
348 AATTTTATTT
Statistics
Matches: 66, Mismatches: 11, Indels: 15
0.72 0.12 0.16
Matches are distributed among these distances:
7 16 0.24
8 25 0.38
9 19 0.29
10 6 0.09
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (8 bp):
TAATATAT
Found at i:338 original size:46 final size:43
Alignment explanation
Indices: 268--379 Score: 143
Period size: 46 Copynumber: 2.5 Consensus size: 43
258 TATATATAAA
* * *
268 ATAATTAAAATATAATATAGTATTAATATTTTAAAATTTTATAAT
1 ATAATTATAATATAATA-AATATTAATATATTAAAATTTTAT-AT
* *
313 ATAAATTATTAATATATTAAATATTAATATATTAAAATTTTATTT
1 AT-AATTA-TAATATAATAAATATTAATATATTAAAATTTTATAT
358 ATAATTATAATATAATAAATAT
1 ATAATTATAATATAATAAATAT
380 ATAAAAATAA
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
43 14 0.24
44 5 0.08
45 5 0.08
46 27 0.46
47 8 0.14
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (43 bp):
ATAATTATAATATAATAAATATTAATATATTAAAATTTTATAT
Found at i:775 original size:12 final size:12
Alignment explanation
Indices: 761--802 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
751 TAATTTAAAT
761 ATAATT-TTTAA
1 ATAATTATTTAA
772 TATAACTTATTTAA
1 -ATAA-TTATTTAA
*
786 ATTATTATTTAA
1 ATAATTATTTAA
798 ATAAT
1 ATAAT
803 ATAAATAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 16 0.62
13 5 0.19
14 5 0.19
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (12 bp):
ATAATTATTTAA
Found at i:936 original size:18 final size:19
Alignment explanation
Indices: 908--945 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
898 CGCAGTCCAT
908 ACTGAAAAATTCTAGCTCA
1 ACTGAAAAATTCTAGCTCA
927 ACTG-AAAATTCTAGCTCA
1 ACTGAAAAATTCTAGCTCA
945 A
1 A
946 GAAATGGCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.42, C:0.21, G:0.11, T:0.26
Consensus pattern (19 bp):
ACTGAAAAATTCTAGCTCA
Found at i:2347 original size:10 final size:10
Alignment explanation
Indices: 2332--2396 Score: 57
Period size: 10 Copynumber: 6.8 Consensus size: 10
2322 TGATTATTCG
2332 ATATAAAATA
1 ATATAAAATA
2342 ATATAAAA-A
1 ATATAAAATA
*
2351 A-AT-ATATA
1 ATATAAAATA
* *
2359 ATATGATATA
1 ATATAAAATA
*
2369 TTATAAAA-A
1 ATATAAAATA
2378 ATATAAATATA
1 ATATAAA-ATA
2389 ATATAAAA
1 ATATAAAA
2397 ATATTAATAT
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
7 2 0.04
8 4 0.09
9 11 0.24
10 20 0.44
11 8 0.18
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (10 bp):
ATATAAAATA
Found at i:2355 original size:20 final size:21
Alignment explanation
Indices: 2332--2397 Score: 80
Period size: 26 Copynumber: 3.0 Consensus size: 21
2322 TGATTATTCG
2332 ATATAAA-ATAATATAAAAAA
1 ATATAAATATAATATAAAAAA
2352 ATATATAATATGATATATTATAAAAA
1 ATATA-AATAT-A-ATA-TA-AAAAA
2378 ATATAAATATAATATAAAAA
1 ATATAAATATAATATAAAAA
2398 TATTAATATG
Statistics
Matches: 40, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
20 5 0.12
21 6 0.15
22 4 0.10
23 4 0.10
24 4 0.10
25 7 0.17
26 10 0.25
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (21 bp):
ATATAAATATAATATAAAAAA
Found at i:2396 original size:19 final size:20
Alignment explanation
Indices: 2332--2406 Score: 64
Period size: 19 Copynumber: 3.5 Consensus size: 20
2322 TGATTATTCG
2332 ATATAAA-ATAATATAAAAAAA
1 ATATAAATATAATAT--AAAAA
2353 TATATAATATGATATATTATAAAAA
1 -ATATAA-AT-ATA-A-TATAAAAA
2378 ATATAAATATAATAT-AAAA
1 ATATAAATATAATATAAAAA
*
2397 ATATTAATAT
1 ATATAAATAT
2407 GTAAAATTTT
Statistics
Matches: 47, Mismatches: 1, Indels: 13
0.77 0.02 0.21
Matches are distributed among these distances:
19 13 0.28
20 3 0.06
21 1 0.02
22 9 0.19
23 3 0.06
24 6 0.13
25 8 0.17
26 1 0.02
27 3 0.06
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (20 bp):
ATATAAATATAATATAAAAA
Found at i:3014 original size:24 final size:26
Alignment explanation
Indices: 2987--3050 Score: 80
Period size: 24 Copynumber: 2.5 Consensus size: 26
2977 CATGAGTATT
*
2987 ATTTAATAAATAAAA-ATTATTT-AA
1 ATTTAATATATAAAATATTATTTAAA
*
3011 ATTTAAT-TATAAAATATTTTTTAAA
1 ATTTAATATATAAAATATTATTTAAA
3036 ATTGTAATATATAAA
1 ATT-TAATATATAAA
3051 TTAAATAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
23 6 0.18
24 13 0.38
25 5 0.15
26 4 0.12
27 6 0.18
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (26 bp):
ATTTAATATATAAAATATTATTTAAA
Found at i:5998 original size:2 final size:2
Alignment explanation
Indices: 5993--6039 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
5983 GAGCCCCCCT
*
5993 TC TC TC TC TC TC TC TG TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
6035 TC TC T
1 TC TC T
6040 AAATGACCTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.47, G:0.02, T:0.51
Consensus pattern (2 bp):
TC
Found at i:7247 original size:5 final size:5
Alignment explanation
Indices: 7237--7264 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
7227 TACAGATATA
7237 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
7265 TTGAGGGTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:7511 original size:2 final size:2
Alignment explanation
Indices: 7504--7539 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
7494 GTAATTTTTA
7504 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
7540 GTCCGTTACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:8549 original size:17 final size:18
Alignment explanation
Indices: 8496--8542 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
8486 AATATGTTTC
* *
8496 AATATTAAATTCAAGTAAA
1 AATATTTAA-TCAATTAAA
*
8515 AATATTTTATCAATTAAA
1 AATATTTAATCAATTAAA
8533 AATATTTAAT
1 AATATTTAAT
8543 ACTTAAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 17 0.71
19 7 0.29
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (18 bp):
AATATTTAATCAATTAAA
Found at i:8772 original size:16 final size:15
Alignment explanation
Indices: 8745--8776 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
8735 GTTAATAATA
8745 AATATAACATTATAT
1 AATATAACATTATAT
8760 AATATAACTATTATAT
1 AATATAAC-ATTATAT
8776 A
1 A
8777 TTAAAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (15 bp):
AATATAACATTATAT
Found at i:9117 original size:2 final size:2
Alignment explanation
Indices: 9110--9137 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
9100 TTGAACCCTA
9110 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
9138 GGATCTTCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10480 original size:2 final size:2
Alignment explanation
Indices: 10473--10509 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
10463 ACACAAACAC
10473 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
10510 AAGAACAAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:18449 original size:17 final size:18
Alignment explanation
Indices: 18417--18472 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 18
18407 ACCAAAAAAG
18417 AAATAAAATCGGAAAAAT-A
1 AAATAAAATC--AAAAATGA
*
18436 ATATAAAATC-AAAATGA
1 AAATAAAATCAAAAATGA
*
18453 AAATAAAATTAAAAA-GA
1 AAATAAAATCAAAAATGA
18470 AAA
1 AAA
18473 GGAAAAAGGA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
16 5 0.16
17 14 0.44
18 4 0.12
19 9 0.28
ACGTcount: A:0.71, C:0.04, G:0.07, T:0.18
Consensus pattern (18 bp):
AAATAAAATCAAAAATGA
Found at i:20698 original size:51 final size:51
Alignment explanation
Indices: 20611--20708 Score: 133
Period size: 51 Copynumber: 1.9 Consensus size: 51
20601 ATAGTCGAGC
* **
20611 TCTATGTTACTTGGATTAGGTGTGAGTGCCAAAAATAAGTAAATGTCTGAT
1 TCTATGTTACTTGGACTAGGTGTGAGCACCAAAAATAAGTAAATGTCTGAT
* * * *
20662 TCTATGTTACTTGGACTATGTGTGAGCACCAGAAATAGGTACATGTC
1 TCTATGTTACTTGGACTAGGTGTGAGCACCAAAAATAAGTAAATGTC
20709 CAATACATGT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 40 1.00
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.34
Consensus pattern (51 bp):
TCTATGTTACTTGGACTAGGTGTGAGCACCAAAAATAAGTAAATGTCTGAT
Found at i:22434 original size:215 final size:212
Alignment explanation
Indices: 22063--22493 Score: 544
Period size: 215 Copynumber: 2.0 Consensus size: 212
22053 AGTTTGGTAG
* ** ** * *
22063 GATAACCAGGAATGGAATTCAATGCAACCATTCCAGTGATGTCTTCACTGTTAAAGAATTTTAGC
1 GATAACCAGGAATGGAATCCAACCCAACCATTCCAGTGATGTCTTCACCATGAAAGAACTTTAGC
* * * * *
22128 AAGGAGCAAACTCCACAAGCGTTTTCTGAATATATGTTTAAAAACACGAACTCCCCTCTTGCACG
66 AAGGAGAAAACTCAACAAGCATTTTCTAAATATATGTTTAAAAACACGAACTCCCCTCTAGCACG
* * * *
22193 ACTTTTTAGATGCATGGAACAAACAACATTGATCTAAGTTTAATGGCTTCCA-TTTGTAGATTTT
131 ACTTTTTAGATGCATGGAACAAACAAC----ATCAAAGTGTAAGGGCTGCCATTTTGTAGATTTT
*
22257 GGTGGTGAAGACCCGAATGAT
192 GGTGGTGAAGACCCAAATGAT
* ** * *
22278 GATAACCAGGAATGGAATCCAACCCAACTATTGTAGTGATGTCTTCACCATGACATAACTTTAGC
1 GATAACCAGGAATGGAATCCAACCCAACCATTCCAGTGATGTCTTCACCATGAAAGAACTTTAGC
** *
22343 GTGGAGAAAACTGCAAC-AGCATTTTCTAAATATATGTTTAAAAACAGGAACTCCCCTCTAGCAA
66 AAGGAGAAAACT-CAACAAGCATTTTCTAAATATATGTTTAAAAACACGAACTCCCCTCTAGC-A
* *
22407 TG-CTTTTTAGATGCATGGAACAAACAACATCAAAGTGTAAGGGCTGCCATTTTGTATATTTTGG
129 CGACTTTTTAGATGCATGGAACAAACAACATCAAAGTGTAAGGGCTGCCATTTTGTAGATTTTGG
22471 TGGTGAAGACCCAAATGAT
194 TGGTGAAGACCCAAATGAT
22490 GATA
1 GATA
22494 TCAGCAGTAT
Statistics
Matches: 186, Mismatches: 27, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
211 17 0.09
212 35 0.19
215 129 0.69
216 5 0.03
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.29
Consensus pattern (212 bp):
GATAACCAGGAATGGAATCCAACCCAACCATTCCAGTGATGTCTTCACCATGAAAGAACTTTAGC
AAGGAGAAAACTCAACAAGCATTTTCTAAATATATGTTTAAAAACACGAACTCCCCTCTAGCACG
ACTTTTTAGATGCATGGAACAAACAACATCAAAGTGTAAGGGCTGCCATTTTGTAGATTTTGGTG
GTGAAGACCCAAATGAT
Found at i:39388 original size:8 final size:8
Alignment explanation
Indices: 39375--39468 Score: 59
Period size: 8 Copynumber: 11.2 Consensus size: 8
39365 ACATTCATAT
39375 TTTTTATA
1 TTTTTATA
*
39383 TTTTTAAA
1 TTTTTATA
39391 TTATTTAT-
1 TT-TTTATA
39399 TTTTATATA
1 TTTT-TATA
*
39408 TTTTAATA
1 TTTTTATA
* *
39416 TATTAATA
1 TTTTTATA
39424 -TTTTATA
1 TTTTTATA
*
39431 -ATTTATA
1 TTTTTATA
39438 TTTTTTAATA
1 -TTTTT-ATA
39448 TATTTTATTA
1 T-TTTTA-TA
39458 TTTTTAATA
1 TTTTT-ATA
39467 TT
1 TT
39469 ATATATAATT
Statistics
Matches: 69, Mismatches: 8, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
7 13 0.19
8 24 0.35
9 21 0.30
10 11 0.16
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (8 bp):
TTTTTATA
Found at i:39404 original size:23 final size:24
Alignment explanation
Indices: 39375--39434 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 24
39365 ACATTCATAT
*
39375 TTTTTATAT-TTTTAA-ATTATTTA
1 TTTTTATATATTTTAATA-TATTAA
39398 TTTTTATATATTTTAATATATTAA
1 TTTTTATATATTTTAATATATTAA
39422 TATTTTATA-ATTT
1 T-TTTTATATATTT
39435 ATATTTTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
23 9 0.27
24 16 0.48
25 8 0.24
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (24 bp):
TTTTTATATATTTTAATATATTAA
Found at i:39412 original size:15 final size:16
Alignment explanation
Indices: 39376--39491 Score: 57
Period size: 16 Copynumber: 7.3 Consensus size: 16
39366 CATTCATATT
*
39376 TTTTATAT-TTTTAAA
1 TTTTATATATTTTATA
*
39391 TTATT-TATTTTTATATA
1 TT-TTATATATTT-TATA
*
39408 TTTTA-ATATATTAATA
1 TTTTATATAT-TTTATA
*
39424 TTTTATA-ATTTATATT
1 TTTTATATATTT-TATA
39440 TTTTAATATATTTTATTA
1 TTTT-ATATATTTTA-TA
*
39458 TTTT-TA-ATATTATA
1 TTTTATATATTTTATA
* * *
39472 TATAAT-TATTTTTTA
1 TTTTATATATTTTATA
39487 TTTTA
1 TTTTA
39492 AAAAATTTTA
Statistics
Matches: 76, Mismatches: 13, Indels: 24
0.67 0.12 0.21
Matches are distributed among these distances:
14 4 0.05
15 22 0.29
16 28 0.37
17 13 0.17
18 9 0.12
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTTATATATTTTATA
Found at i:39443 original size:41 final size:41
Alignment explanation
Indices: 39384--39485 Score: 118
Period size: 42 Copynumber: 2.4 Consensus size: 41
39374 TTTTTTATAT
*
39384 TTTTA-AATTATTTATTTTTATATATTTTAATA-TATTAATA
1 TTTTATAATTATTT-TTTTAATATATTTTAATATTATTAATA
* *
39424 TTTTATAATTTATATTTTTTAATATATTTTATTATTTTTAATA
1 TTTTATAA-TTAT-TTTTTTAATATATTTTAATATTATTAATA
39467 TTATATATAATTATTTTTT
1 TT-T-TATAATTATTTTTT
39486 ATTTTAAAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
40 5 0.09
41 2 0.04
42 20 0.38
43 16 0.30
44 5 0.09
45 5 0.09
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (41 bp):
TTTTATAATTATTTTTTTAATATATTTTAATATTATTAATA
Found at i:39471 original size:22 final size:22
Alignment explanation
Indices: 39404--39484 Score: 62
Period size: 22 Copynumber: 3.8 Consensus size: 22
39394 TTTATTTTTA
* *
39404 TATATTTTAATA-TATTAATATTT
1 TATATTTTATTATTTTTAATA--T
* *
39427 TATAATTTA-TATTTTT--TAA
1 TATATTTTATTATTTTTAATAT
39446 TATATTTTATTATTTTTAATAT
1 TATATTTTATTATTTTTAATAT
* *
39468 TATATATAATTATTTTT
1 TATATTTTATTATTTTT
39485 TATTTTAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
19 8 0.17
20 7 0.15
21 2 0.04
22 19 0.40
23 11 0.23
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TATATTTTATTATTTTTAATAT
Found at i:39471 original size:34 final size:32
Alignment explanation
Indices: 39400--39474 Score: 98
Period size: 32 Copynumber: 2.3 Consensus size: 32
39390 ATTATTTATT
39400 TTTATATATTTTAATATATTAATATTTTATAA
1 TTTATATATTTTAATATATTAATATTTTATAA
* *
39432 TTTATATTTTTTAATATATTTTATTATTTT-TAA
1 TTTATATATTTTAATATA--TTAATATTTTATAA
39465 TATTATATAT
1 T-TTATATAT
39475 AATTATTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
32 17 0.46
33 4 0.11
34 16 0.43
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (32 bp):
TTTATATATTTTAATATATTAATATTTTATAA
Found at i:39482 original size:42 final size:40
Alignment explanation
Indices: 39371--39486 Score: 108
Period size: 42 Copynumber: 2.8 Consensus size: 40
39361 TTATACATTC
* * *
39371 ATATTTTTTATATTTTTAAATTATTTATTTTTATATATTTTA
1 ATATTTTTAATATTTATAAATTA-TT-TTTTAATATATTTTA
* *
39413 ATA-TATTAATATTTTATAATTTATATTTTTTAATATATTTTA
1 ATATTTTTAATA-TTTATAA-AT-TATTTTTTAATATATTTTA
*
39455 TTATTTTTAATATTATATATAATTATTTTTTA
1 ATATTTTTAATATT-TATA-AATTATTTTTTA
39487 TTTTAAAAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
41 6 0.10
42 36 0.60
43 15 0.25
44 3 0.05
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (40 bp):
ATATTTTTAATATTTATAAATTATTTTTTAATATATTTTA
Found at i:39708 original size:28 final size:30
Alignment explanation
Indices: 39676--39733 Score: 77
Period size: 28 Copynumber: 2.0 Consensus size: 30
39666 TAAGTGTAAA
39676 TATATTAAAATATT-AA-AAA-AATTATTTT
1 TATATTAAAAT-TTAAATAAATAATTATTTT
*
39704 TATATTTAAATTTAAATAAATAATTATTTT
1 TATATTAAAATTTAAATAAATAATTATTTT
39734 AATAAATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 2 0.08
28 12 0.46
29 3 0.12
30 9 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (30 bp):
TATATTAAAATTTAAATAAATAATTATTTT
Found at i:39737 original size:16 final size:17
Alignment explanation
Indices: 39713--39747 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
39703 TTATATTTAA
39713 ATTTAAATAAA-TAATT
1 ATTTAAATAAATTAATT
*
39729 ATTTTAATAAATTAATT
1 ATTTAAATAAATTAATT
39746 AT
1 AT
39748 GATCAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATTTAAATAAATTAATT
Found at i:41486 original size:10 final size:9
Alignment explanation
Indices: 41461--41501 Score: 57
Period size: 10 Copynumber: 4.4 Consensus size: 9
41451 TTATGGACTT
41461 TTATTTATA
1 TTATTTATA
41470 TTATTTATA
1 TTATTTATA
41479 TCTATTTATA
1 T-TATTTATA
41489 -TATTTATA
1 TTATTTATA
41497 CTTAT
1 -TTAT
41502 ATAAAAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
8 8 0.28
9 10 0.34
10 11 0.38
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (9 bp):
TTATTTATA
Found at i:42486 original size:20 final size:21
Alignment explanation
Indices: 42463--42508 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
42453 TCATATAATT
42463 TTTTTAAAAAT-TCAAAAATA
1 TTTTTAAAAATATCAAAAATA
* *
42483 TTTTT-GAAATATGAAAAATA
1 TTTTTAAAAATATCAAAAATA
42503 TTTTTA
1 TTTTTA
42509 TGATTATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (21 bp):
TTTTTAAAAATATCAAAAATA
Found at i:42920 original size:30 final size:32
Alignment explanation
Indices: 42884--42958 Score: 86
Period size: 30 Copynumber: 2.5 Consensus size: 32
42874 ATTATAAAAT
* *
42884 TTTTTAAAAAGTTATTG-GTGAT-AAATATAA
1 TTTTTAAAAAGTTATCGAGTAATAAAATATAA
*
42914 TTTTTAAAAA-TTATCGATTAATAAAATATAA
1 TTTTTAAAAAGTTATCGAGTAATAAAATATAA
*
42945 CTTTT-AAAAGTTAT
1 TTTTTAAAAAGTTAT
42959 AAATAAAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
29 5 0.13
30 17 0.45
31 16 0.42
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (32 bp):
TTTTTAAAAAGTTATCGAGTAATAAAATATAA
Found at i:42922 original size:29 final size:31
Alignment explanation
Indices: 42884--42958 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
42874 ATTATAAAAT
* *
42884 TTTTTAAAAAGTTATTG-GTGAT-AAATATAA
1 TTTTT-AAAAGTTATCGAGTAATAAAATATAA
* *
42914 TTTTTAAAAATTATCGATTAATAAAATATAA
1 TTTTTAAAAGTTATCGAGTAATAAAATATAA
*
42945 CTTTTAAAAGTTAT
1 TTTTTAAAAGTTAT
42959 AAATAAAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
29 9 0.24
30 8 0.22
31 20 0.54
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (31 bp):
TTTTTAAAAGTTATCGAGTAATAAAATATAA
Found at i:43391 original size:22 final size:22
Alignment explanation
Indices: 43366--43413 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
43356 AGATCGATAA
43366 AATAATTT-AATAAATTAAATTT
1 AATAATTTAAAT-AATTAAATTT
* *
43388 AATATTTTAAATTATTAAATTT
1 AATAATTTAAATAATTAAATTT
43410 AATA
1 AATA
43414 TTAAATTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AATAATTTAAATAATTAAATTT
Found at i:43424 original size:22 final size:21
Alignment explanation
Indices: 43379--43420 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
43369 AATTTAATAA
43379 ATTAAATTTAATATTTTAAATT
1 ATTAAATTTAATA-TTTAAATT
43401 ATTAAATTTAATA-TTAAATT
1 ATTAAATTTAATATTTAAATT
43421 TTATAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 7 0.35
22 13 0.65
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
ATTAAATTTAATATTTAAATT
Found at i:43429 original size:22 final size:21
Alignment explanation
Indices: 43382--43432 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 21
43372 TTAATAAATT
*
43382 AAATTTAATATTTTAAATTATT
1 AAATTTAATA-TTTAAATTATA
43404 AAATTTAATA-TTAAATTTTATA
1 AAATTTAATATTTAAA--TTATA
43426 AAATTTA
1 AAATTTA
43433 TAAAATTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 5 0.19
22 21 0.81
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
AAATTTAATATTTAAATTATA
Found at i:43473 original size:24 final size:22
Alignment explanation
Indices: 43399--43489 Score: 73
Period size: 23 Copynumber: 4.0 Consensus size: 22
43389 ATATTTTAAA
43399 TTATTAAATT-TAATATTAAATT
1 TTATTAAATTATAA-ATTAAATT
* *
43421 TTATAAAATTTATAAAATT-TATT
1 TTATTAAA-TTAT-AAATTAAATT
43444 TGTATTAAATTATATAATTAAAATT
1 T-TATTAAATTATA-AATT-AAATT
43469 TTATT--ATTAATAAATTAAATT
1 TTATTAAATT-ATAAATTAAATT
43490 ATTTATTTGA
Statistics
Matches: 57, Mismatches: 4, Indels: 17
0.73 0.05 0.22
Matches are distributed among these distances:
21 5 0.09
22 15 0.26
23 17 0.30
24 14 0.25
25 6 0.11
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (22 bp):
TTATTAAATTATAAATTAAATT
Found at i:43490 original size:16 final size:18
Alignment explanation
Indices: 43447--43492 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 18
43437 ATTTATTTGT
43447 ATTAAATTATATAATTAAA
1 ATTAAATTAT-TAATTAAA
**
43466 ATTTTATTATTAA-T-AA
1 ATTAAATTATTAATTAAA
43482 ATTAAATTATT
1 ATTAAATTATT
43493 TATTTGAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 11 0.48
17 1 0.04
18 3 0.13
19 8 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTAAATTATTAATTAAA
Found at i:43689 original size:29 final size:27
Alignment explanation
Indices: 43623--43689 Score: 66
Period size: 29 Copynumber: 2.4 Consensus size: 27
43613 AATTATTTAA
*
43623 TAAAATTAATATAATTAATTTAATTTAT
1 TAAAATTAA-ATAATTAATTTAATATAT
43651 TAATAA-TAAA-AATTTAATATGTAATATAT
1 TAA-AATTAAATAA-TTAAT-T-TAATATAT
43680 TAAAATTAAA
1 TAAAATTAAA
43690 GTTTTAAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
26 2 0.06
27 6 0.18
28 9 0.27
29 16 0.48
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (27 bp):
TAAAATTAAATAATTAATTTAATATAT
Found at i:43819 original size:20 final size:20
Alignment explanation
Indices: 43796--43846 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
43786 TGTGTATTCA
43796 TATTATA-TTTATATTATTTT
1 TATTATATTTTA-ATTATTTT
*
43816 TATTAAATTTTAATTATTTT
1 TATTATATTTTAATTATTTT
43836 T-TTATATTTTA
1 TATTATATTTTA
43847 TAATTATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 9 0.32
20 15 0.54
21 4 0.14
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
TATTATATTTTAATTATTTT
Found at i:43827 original size:21 final size:20
Alignment explanation
Indices: 43803--43853 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 20
43793 TCATATTATA
43803 TTTATATTATTTTTATTAAAT
1 TTTATATTATTTTT-TTAAAT
*
43824 TTTA-ATTATTTTTTTATAT
1 TTTATATTATTTTTTTAAAT
43843 TTTATAATTAT
1 TTTAT-ATTAT
43854 AATCATCTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 9 0.33
20 9 0.33
21 9 0.33
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTATATTATTTTTTTAAAT
Found at i:44443 original size:36 final size:37
Alignment explanation
Indices: 44403--44479 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
44393 TTTATTTAAA
* **
44403 TTTAATTATAAAAATAT-ATAAATATTATTATAAAAT
1 TTTAATTATAAAAATATAATAAATAATAAAATAAAAT
* *
44439 TTTAATTTTAATAATATAATAAATAATAAAATAAAAT
1 TTTAATTATAAAAATATAATAAATAATAAAATAAAAT
44476 TTTA
1 TTTA
44480 TGTTGAATCT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
36 15 0.43
37 20 0.57
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (37 bp):
TTTAATTATAAAAATATAATAAATAATAAAATAAAAT
Found at i:44858 original size:119 final size:117
Alignment explanation
Indices: 44635--44867 Score: 394
Period size: 119 Copynumber: 2.0 Consensus size: 117
44625 AAATTCACTA
* * *
44635 ATCCACAATGTTAACATTTGCTCGAGATGGTGAAACGTGCCCGAGAAATATCGAGAGCCTTCTTG
1 ATCCACAATGTTAACATTTGCTCGAGACGGTGAAACGTGCCCGAGAAATACCGAGAGCCTTATTG
*
44700 GCGGCAACTGGGGTTTGAAGATGGCGAAGTTAGCAGTAAGCGTCGAGACTGT
66 GCGGCAACTGGGGTTTGAAGATGGCGAAGGTAGCAGTAAGCGTCGAGACTGT
*
44752 ATCCACAATGTTTAACATTTGCTCGAGACGGTGAAATGTGCCCGAGAAAATACCGAGAGCCTTAT
1 ATCCACAATG-TTAACATTTGCTCGAGACGGTGAAACGTGCCCGAG-AAATACCGAGAGCCTTAT
*
44817 TGGCGGCAACTGGGGTTTGAAGATGGCGAAGGTAGCGGTAAGCGTCGAGAC
64 TGGCGGCAACTGGGGTTTGAAGATGGCGAAGGTAGCAGTAAGCGTCGAGAC
44868 GGGAAGAAGT
Statistics
Matches: 108, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
117 10 0.09
118 33 0.31
119 65 0.60
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (117 bp):
ATCCACAATGTTAACATTTGCTCGAGACGGTGAAACGTGCCCGAGAAATACCGAGAGCCTTATTG
GCGGCAACTGGGGTTTGAAGATGGCGAAGGTAGCAGTAAGCGTCGAGACTGT
Found at i:45212 original size:6 final size:6
Alignment explanation
Indices: 45171--45209 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
45161 TTGCTCATGT
45171 TATTTA TATTTA TATTTA TATTTA TA-TTA TATTT- TATTT
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTT
45210 TTAAATTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 10 0.31
6 22 0.69
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TATTTA
Found at i:45212 original size:18 final size:18
Alignment explanation
Indices: 45171--45209 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
45161 TTGCTCATGT
45171 TATTTATATTTATATTTA
1 TATTTATATTTATATTTA
45189 TATTTATA-TTATATTT-
1 TATTTATATTTATATTTA
45205 TATTT
1 TATTT
45210 TTAAATTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 5 0.24
17 8 0.38
18 8 0.38
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TATTTATATTTATATTTA
Found at i:45350 original size:3 final size:3
Alignment explanation
Indices: 45335--45380 Score: 65
Period size: 3 Copynumber: 14.7 Consensus size: 3
45325 TGTTTAAATT
*
45335 TAA TAA TAT TAA TAA TAA TAA TAA TAA TAA TTAA TAA TTAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA -TAA TAA TA
45381 TTAAATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
3 33 0.85
4 6 0.15
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:45429 original size:20 final size:20
Alignment explanation
Indices: 45383--45445 Score: 67
Period size: 19 Copynumber: 3.1 Consensus size: 20
45373 TAATAATATT
45383 AAATTAA-AATTTATATATAATA
1 AAATTAATAATTTAT-T-TAA-A
*
45405 AAATTTATAATTTATTTAAA
1 AAATTAATAATTTATTTAAA
*
45425 AAATTAATAA-ATATTTAAA
1 AAATTAATAATTTATTTAAA
45444 AA
1 AA
45446 CTATTAAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
19 10 0.27
20 10 0.27
21 3 0.08
22 7 0.19
23 7 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AAATTAATAATTTATTTAAA
Found at i:45475 original size:19 final size:19
Alignment explanation
Indices: 45453--45510 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 19
45443 AAACTATTAA
45453 AATAAAAATAAAATAAAAT
1 AATAAAAATAAAATAAAAT
* * * *
45472 AATATATATACATTAAAA-
1 AATAAAAATAAAATAAAAT
* *
45490 AATAAAAATAACATTAAAT
1 AATAAAAATAAAATAAAAT
45509 AA
1 AA
45511 ATATATGAAT
Statistics
Matches: 28, Mismatches: 10, Indels: 2
0.70 0.25 0.05
Matches are distributed among these distances:
18 12 0.43
19 16 0.57
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (19 bp):
AATAAAAATAAAATAAAAT
Found at i:45715 original size:15 final size:16
Alignment explanation
Indices: 45690--45739 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 16
45680 CAATACAAAA
45690 ATATAATATATATTTT
1 ATATAATATATATTTT
*
45706 A-ATTATATATAAATTTT
1 ATA-TA-ATATATATTTT
45723 ATATAAT-TATATTTT
1 ATATAATATATATTTT
45738 AT
1 AT
45740 GTCATAATCG
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
15 10 0.34
16 5 0.17
17 13 0.45
18 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
ATATAATATATATTTT
Found at i:47139 original size:14 final size:12
Alignment explanation
Indices: 47066--47133 Score: 67
Period size: 12 Copynumber: 5.9 Consensus size: 12
47056 AATAAAATAG
47066 TTTAAATTTA--
1 TTTAAATTTATT
47076 TTTAAATTTATT
1 TTTAAATTTATT
47088 TTT--A-TTATT
1 TTTAAATTTATT
47097 TTTAAATTTATT
1 TTTAAATTTATT
47109 TTTAAAAATATT-TT
1 TTT--AAAT-TTATT
47123 TTTAAATTTAT
1 TTTAAATTTAT
47134 AATTTTTTAT
Statistics
Matches: 49, Mismatches: 0, Indels: 16
0.75 0.00 0.25
Matches are distributed among these distances:
9 8 0.16
10 11 0.22
11 3 0.06
12 16 0.33
14 9 0.18
15 2 0.04
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
TTTAAATTTATT
Found at i:50757 original size:4 final size:4
Alignment explanation
Indices: 50748--50779 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
50738 ACATATATTC
50748 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
50780 AATGTTATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:51422 original size:2 final size:2
Alignment explanation
Indices: 51415--51442 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
51405 ATCCATTATT
51415 TA 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 TA
51443 GAGAGAGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:51749 original size:2 final size:2
Alignment explanation
Indices: 51737--51767 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
51727 ACTTGATACC
*
51737 AT AT AT CT 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 A
51768 GTTATTACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:55831 original size:20 final size:20
Alignment explanation
Indices: 55792--55834 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
55782 TACAAACTTC
*
55792 AATAATTTTTTTTTACTTTT
1 AATAATTTATTTTTACTTTT
*
55812 AATATATTTATTTTTATTTTT
1 AATA-ATTTATTTTTACTTTT
55833 AA
1 AA
55835 AATAGTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (20 bp):
AATAATTTATTTTTACTTTT
Found at i:55843 original size:20 final size:21
Alignment explanation
Indices: 55801--55843 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
55791 CAATAATTTT
* *
55801 TTTTTACTTTTAATATATTTA
1 TTTTTACTTTTAAAATATGTA
*
55822 TTTTTATTTTTAAAATA-GTA
1 TTTTTACTTTTAAAATATGTA
55842 TT
1 TT
55844 AAAAATTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (21 bp):
TTTTTACTTTTAAAATATGTA
Found at i:59504 original size:20 final size:19
Alignment explanation
Indices: 59468--59525 Score: 57
Period size: 18 Copynumber: 3.1 Consensus size: 19
59458 ATATAGTAAT
**
59468 AGTAATTTTTTTTAAGAGA
1 AGTAATTTTTTAAAAGAGA
59487 ATGATAA-TTTTTAAAAGA-A
1 A-G-TAATTTTTTAAAAGAGA
*
59506 AGTAATTTTTTACAAGAGA
1 AGTAATTTTTTAAAAGAGA
59525 A
1 A
59526 AAAAGTGTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
17 3 0.09
18 11 0.34
19 5 0.16
20 10 0.31
21 3 0.09
ACGTcount: A:0.45, C:0.02, G:0.14, T:0.40
Consensus pattern (19 bp):
AGTAATTTTTTAAAAGAGA
Found at i:59981 original size:16 final size:18
Alignment explanation
Indices: 59956--59997 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
59946 ATTTTATAAA
*
59956 TTTTATAAAT-ATTTT-T
1 TTTTAAAAATAATTTTAT
59972 TTTTAAAAATAATTTTAT
1 TTTTAAAAATAATTTTAT
59990 TATTTAAA
1 T-TTTAAA
59998 TAGTGATTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 9 0.41
17 5 0.23
18 2 0.09
19 6 0.27
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTTAAAAATAATTTTAT
Done.