Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1890
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: 56573
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.35
Found at i:123 original size:17 final size:18
Alignment explanation
Indices: 87--132 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
77 TTTTTCTTAC
*
87 AAAGAAAGAAAAATAAAT
1 AAAGAAGGAAAAATAAAT
*
105 AAAGAAGGAGAAA-AAAT
1 AAAGAAGGAAAAATAAAT
*
122 AAAAAAGGAAA
1 AAAGAAGGAAA
133 TATATAAAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 13 0.54
18 11 0.46
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (18 bp):
AAAGAAGGAAAAATAAAT
Found at i:205 original size:2 final size:2
Alignment explanation
Indices: 198--227 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
188 ATACTAAGTG
*
198 AT AT AT AT AT AT AT AT AT AG AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
228 GTAAAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1962 original size:18 final size:18
Alignment explanation
Indices: 1936--1970 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1926 TATTTTCATG
1936 ATTTAAAGACCATTTAGC
1 ATTTAAAGACCATTTAGC
* *
1954 ATTTTAAGATCATTTAG
1 ATTTAAAGACCATTTAG
1971 AATAGTTTGC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.40
Consensus pattern (18 bp):
ATTTAAAGACCATTTAGC
Found at i:4189 original size:2 final size:2
Alignment explanation
Indices: 4184--4247 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
4174 CGTATGAGTG
4184 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
4226 TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
4248 AACTAATAGA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4409 original size:16 final size:17
Alignment explanation
Indices: 4385--4417 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
4375 TACAATCTAT
4385 TTTACATTA-AAAATAA
1 TTTACATTATAAAATAA
*
4401 TTTATATTATAAAATAA
1 TTTACATTATAAAATAA
4418 AAATTTTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
TTTACATTATAAAATAA
Found at i:5336 original size:15 final size:15
Alignment explanation
Indices: 5318--5423 Score: 66
Period size: 15 Copynumber: 7.3 Consensus size: 15
5308 TGAATTTGAT
5318 TTAAATAATTTAATA
1 TTAAATAATTTAATA
*
5333 TTAAAAAATTT--TA
1 TTAAATAATTTAATA
*
5346 TTAGAGAT-ATCTAA-A
1 TTA-A-ATAATTTAATA
5361 TTTAAATAATTTAAT-
1 -TTAAATAATTTAATA
**
5376 TTCGATAATTTAAT-
1 TTAAATAATTTAATA
*
5390 TCAAAATAATTTAA-A
1 T-TAAATAATTTAATA
5405 TTAATATAATTTAA-A
1 TTAA-ATAATTTAATA
5420 TTAA
1 TTAA
5424 TTTTTAAATT
Statistics
Matches: 71, Mismatches: 10, Indels: 20
0.70 0.10 0.20
Matches are distributed among these distances:
13 5 0.07
14 21 0.30
15 42 0.59
16 3 0.04
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (15 bp):
TTAAATAATTTAATA
Found at i:5424 original size:15 final size:15
Alignment explanation
Indices: 5380--5435 Score: 66
Period size: 15 Copynumber: 3.9 Consensus size: 15
5370 TTTAATTTCG
*
5380 ATAATTT-AATTCAAA
1 ATAATTTAAATT-AAT
5395 ATAATTTAAATTAAT
1 ATAATTTAAATTAAT
5410 ATAATTTAAATTAAT
1 ATAATTTAAATTAAT
5425 -T--TTTAAATTAA
1 ATAATTTAAATTAA
5436 AAAATAACTT
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
12 10 0.26
14 1 0.03
15 24 0.62
16 4 0.10
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (15 bp):
ATAATTTAAATTAAT
Found at i:9211 original size:16 final size:16
Alignment explanation
Indices: 9192--9229 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
9182 TATATTAATG
9192 TTATGTTATAGTCATA
1 TTATGTTATAGTCATA
*
9208 TTATGTTATAGTTATA
1 TTATGTTATAGTCATA
9224 TTATGT
1 TTATGT
9230 CTAAGGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.29, C:0.03, G:0.13, T:0.55
Consensus pattern (16 bp):
TTATGTTATAGTCATA
Found at i:10933 original size:15 final size:15
Alignment explanation
Indices: 10915--10944 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
10905 AAAAAGGAGA
10915 AAATAAAAAGAATTT
1 AAATAAAAAGAATTT
*
10930 AAATAAAGAGAATTT
1 AAATAAAAAGAATTT
10945 TAACTTTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.10, T:0.27
Consensus pattern (15 bp):
AAATAAAAAGAATTT
Found at i:15404 original size:19 final size:18
Alignment explanation
Indices: 15382--15426 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 18
15372 TTTATTATAT
15382 TATTAAAATATTATTTTTA
1 TATTAAAATA-TATTTTTA
*
15401 TATTAATATATATTTTTA
1 TATTAAAATATATTTTTA
15419 TAATTAAA
1 T-ATTAAA
15427 TTTTAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TATTAAAATATATTTTTA
Found at i:15460 original size:19 final size:20
Alignment explanation
Indices: 15379--15427 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 20
15369 TTTTTTATTA
15379 TATTATTAAA-ATATTATTTT
1 TATTATTAAATATA-TATTTT
15399 TA-TATT-AATATATATTTT
1 TATTATTAAATATATATTTT
*
15417 TATAATTAAAT
1 TATTATTAAAT
15428 TTTAAATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 10 0.40
19 10 0.40
20 5 0.20
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TATTATTAAATATATATTTT
Found at i:15492 original size:10 final size:10
Alignment explanation
Indices: 15462--15495 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
15452 TATTAAATAA
15462 TAATTTAAAT
1 TAATTTAAAT
* *
15472 AAAATTAAAT
1 TAATTTAAAT
15482 TAATTTAAAT
1 TAATTTAAAT
15492 TAAT
1 TAAT
15496 AAAAATCTTA
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
TAATTTAAAT
Found at i:18427 original size:22 final size:22
Alignment explanation
Indices: 18401--18449 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
18391 AAAAAAATAG
*
18401 AAATTAATATT-AAATAATTAAA
1 AAATTAA-ATTAAAAAAATTAAA
*
18423 TAATTAAATTAAAAAAATTAAA
1 AAATTAAATTAAAAAAATTAAA
18445 AAATT
1 AAATT
18450 TGTAGCAACG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 3 0.13
22 20 0.87
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
AAATTAAATTAAAAAAATTAAA
Found at i:19343 original size:21 final size:22
Alignment explanation
Indices: 19319--19361 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
19309 TATTTGTTTA
* *
19319 ATTAAATAAAT-AATTTTAAAT
1 ATTAAACAAATCAAATTTAAAT
19340 ATTAAACAAATCAAATTTAAAT
1 ATTAAACAAATCAAATTTAAAT
19362 TTTTTTCATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (22 bp):
ATTAAACAAATCAAATTTAAAT
Found at i:19439 original size:27 final size:26
Alignment explanation
Indices: 19412--19475 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 26
19402 TGTCTGATTA
*
19412 TAATTTAGTAATATTATTTTATATTTAT
1 TAATTTA-TAATAATATTTT-TATTTAT
*
19440 TTATTTATAATAATATTTTTATTTTAT
1 TAATTTATAATAATATTTTTA-TTTAT
*
19467 TATTTTATA
1 TAATTTATA
19476 TTTAAAATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
26 2 0.06
27 23 0.74
28 6 0.19
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (26 bp):
TAATTTATAATAATATTTTTATTTAT
Found at i:19440 original size:14 final size:14
Alignment explanation
Indices: 19423--19479 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
19413 AATTTAGTAA
19423 TATTATTTTATATT
1 TATTATTTTATATT
*
19437 TATT-TATTTATA-A
1 TATTAT-TTTATATT
*
19450 TAATATTTT-TATTT
1 TATTATTTTATA-TT
19464 TATTATTTTATATT
1 TATTATTTTATATT
19478 TA
1 TA
19480 AAATTAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
12 2 0.06
13 7 0.21
14 23 0.68
15 2 0.06
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TATTATTTTATATT
Found at i:22780 original size:38 final size:38
Alignment explanation
Indices: 22729--22805 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
22719 GTTAGTACGG
22729 TAGCAAATCAGTCAATCCACATTTTCAGCAAAACTTTA
1 TAGCAAATCAGTCAATCCACATTTTCAGCAAAACTTTA
22767 TAGCAAATCAGTCAATCCACATTTTCAGCAAAACTTTA
1 TAGCAAATCAGTCAATCCACATTTTCAGCAAAACTTTA
22805 T
1 T
22806 TATTGCTAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.39, C:0.23, G:0.08, T:0.30
Consensus pattern (38 bp):
TAGCAAATCAGTCAATCCACATTTTCAGCAAAACTTTA
Found at i:24247 original size:5 final size:5
Alignment explanation
Indices: 24237--24278 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
24227 AATAAAAAAT
* *
24237 ATATA ATATA ATATA ATATA ATA-A AAATA ATAAAA ATATA AT
1 ATATA ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA AT
24279 TTTATTAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
4 3 0.10
5 24 0.77
6 4 0.13
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (5 bp):
ATATA
Found at i:24325 original size:15 final size:16
Alignment explanation
Indices: 24281--24341 Score: 54
Period size: 16 Copynumber: 3.7 Consensus size: 16
24271 AATATAATTT
*
24281 TATTAAAATTTATATAA
1 TATTAAATTTTA-ATAA
24298 TATT-AATTATTAAT-A
1 TATTAAATT-TTAATAA
24313 TATTAAATTTTAAATAAA
1 TATTAAATTTT-AAT-AA
*
24331 TATTTAATTTT
1 TATTAAATTTT
24342 TAAATATAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
15 7 0.19
16 12 0.32
17 7 0.19
18 11 0.30
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TATTAAATTTTAATAA
Found at i:24342 original size:19 final size:20
Alignment explanation
Indices: 24309--24347 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
24299 ATTAATTATT
24309 AATATATTAAATTTTAAATA
1 AATATATTAAATTTTAAATA
*
24329 AATAT-TTAATTTTTAAATA
1 AATATATTAAATTTTAAATA
24348 TAAATATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AATATATTAAATTTTAAATA
Found at i:24357 original size:19 final size:19
Alignment explanation
Indices: 24309--24357 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
24299 ATTAATTATT
*
24309 AATATATTAAATTTTAAATA
1 AATATA-TAATTTTTAAATA
*
24329 AATATTTAATTTTTAAATA
1 AATATATAATTTTTAAATA
24348 TAA-ATATAAT
1 -AATATATAAT
24358 ATAAAAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AATATATAATTTTTAAATA
Found at i:24360 original size:11 final size:11
Alignment explanation
Indices: 24344--24376 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
24334 TTAATTTTTA
24344 AATATAAATAT
1 AATATAAATAT
*
24355 AATATAAAAAT
1 AATATAAATAT
24366 AATATAAATAT
1 AATATAAATAT
24377 GTCTCATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
AATATAAATAT
Found at i:25054 original size:25 final size:25
Alignment explanation
Indices: 25008--25058 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
24998 ATTAAATTTA
25008 TTTAGTTTAAATATATATTTTATAT
1 TTTAGTTTAAATATATATTTTATAT
25033 TTTA-TTTAATATAATATATTTATATA
1 TTTAGTTTAA-AT-ATATATTT-TATA
25059 ATTATAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 5 0.22
25 6 0.26
26 8 0.35
27 4 0.17
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (25 bp):
TTTAGTTTAAATATATATTTTATAT
Found at i:25063 original size:26 final size:23
Alignment explanation
Indices: 25017--25063 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 23
25007 ATTTAGTTTA
*
25017 AATATATATTTTATATTTTATTT
1 AATATATATTTTATATATTATTT
25040 AATATAATATATTTATATAATTAT
1 AATAT-ATAT-TTTATAT-ATTAT
25064 AAAATAATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 5 0.25
24 4 0.20
25 7 0.35
26 4 0.20
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
AATATATATTTTATATATTATTT
Found at i:25064 original size:19 final size:19
Alignment explanation
Indices: 25028--25065 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
25018 ATATATATTT
*
25028 TATATTTTATTTAATATAA
1 TATATTTTATATAATATAA
25047 TATA-TTTATATAATTATAA
1 TATATTTTATATAA-TATAA
25066 AATAATTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TATATTTTATATAATATAA
Found at i:25069 original size:26 final size:23
Alignment explanation
Indices: 25016--25069 Score: 54
Period size: 26 Copynumber: 2.2 Consensus size: 23
25006 TATTTAGTTT
* *
25016 AAATATATATTTTATATTTTATT
1 AAATATATATTTTATATATTATA
*
25039 TAATATAATATATTTATATAATTATA
1 AAATAT-ATAT-TTTATAT-ATTATA
25065 AAATA
1 AAATA
25070 ATTGATTAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
23 5 0.21
24 4 0.17
25 7 0.29
26 8 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AAATATATATTTTATATATTATA
Found at i:26468 original size:92 final size:93
Alignment explanation
Indices: 26305--26491 Score: 358
Period size: 92 Copynumber: 2.0 Consensus size: 93
26295 TGCAAAACCA
26305 AAGCTTGTAGGTCATTGGAATTCCACATTTTTGGTTTAAAAGCAACTTAAATTTGATGTGGCATT
1 AAGCTTGTAGGTCATTGGAATTCCACATTTTTGGTTTAAAAGCAACTTAAATTTGATGTGGCATT
26370 GCATCGAGTTGCAAATTCATTTTCTCCG
66 GCATCGAGTTGCAAATTCATTTTCTCCG
26398 AAGCTTGTAGGTCATTGGAATTCCACA-TTTTGGTTTAAAAGCAACTTAAATTTGATGTGGCATT
1 AAGCTTGTAGGTCATTGGAATTCCACATTTTTGGTTTAAAAGCAACTTAAATTTGATGTGGCATT
*
26462 GTATCGAGTTGCAAATTCATTTTCTCCG
66 GCATCGAGTTGCAAATTCATTTTCTCCG
26490 AA
1 AA
26492 ACGATGGCAG
Statistics
Matches: 93, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
92 66 0.71
93 27 0.29
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (93 bp):
AAGCTTGTAGGTCATTGGAATTCCACATTTTTGGTTTAAAAGCAACTTAAATTTGATGTGGCATT
GCATCGAGTTGCAAATTCATTTTCTCCG
Found at i:34264 original size:2 final size:2
Alignment explanation
Indices: 34257--34281 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
34247 AAAGAGCATT
34257 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 T
34282 TCCGCCATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:38190 original size:17 final size:17
Alignment explanation
Indices: 38165--38204 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
38155 TGAGTACGTG
38165 ATAAAAAAATAATATAAA
1 ATAAAAAAA-AATATAAA
*
38183 ATAAAAAAAAATATAAT
1 ATAAAAAAAAATATAAA
38200 ATAAA
1 ATAAA
38205 TATATAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.23
Consensus pattern (17 bp):
ATAAAAAAAAATATAAA
Found at i:38267 original size:33 final size:34
Alignment explanation
Indices: 38191--38268 Score: 81
Period size: 33 Copynumber: 2.3 Consensus size: 34
38181 AAATAAAAAA
*
38191 AAATATAATATAAATATATAAATATATCAATATTT
1 AAATA-AATATAAATATATAAATATATAAATATTT
* * *
38226 ATAT-AATATAAAT-TATTAATATGTTAAAT-TTT
1 AAATAAATATAAATATATAAATAT-ATAAATATTT
38258 AAATAAATATA
1 AAATAAATATA
38269 TCTTATTTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
32 14 0.39
33 19 0.53
35 3 0.08
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (34 bp):
AAATAAATATAAATATATAAATATATAAATATTT
Found at i:39414 original size:20 final size:21
Alignment explanation
Indices: 39375--39415 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
39365 TTATTTAAAT
*
39375 ATTTTAATTAATTATTTTATA
1 ATTTTAATTAATTATATTATA
*
39396 ATTTT-ATTTATTATATTATA
1 ATTTTAATTAATTATATTATA
39416 TTAAATAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
ATTTTAATTAATTATATTATA
Found at i:42078 original size:2 final size:2
Alignment explanation
Indices: 42073--42100 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
42063 AAAAAAGGTA
42073 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
42101 TAATTATATC
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:46307 original size:19 final size:21
Alignment explanation
Indices: 46285--46332 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
46275 AAAAAAATAA
*
46285 AATATTATTAA-TTTAT-ATT
1 AATATTATAAATTTTATAATT
46304 AATATTTATAAATTTTATAATT
1 AATA-TTATAAATTTTATAATT
*
46326 AAAATTA
1 AATATTA
46333 AATAAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 4 0.17
20 6 0.25
21 8 0.33
22 6 0.25
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
AATATTATAAATTTTATAATT
Found at i:46369 original size:20 final size:22
Alignment explanation
Indices: 46332--46380 Score: 77
Period size: 20 Copynumber: 2.4 Consensus size: 22
46322 AATTAAAATT
46332 AAATAAA-AATATTATTTAATA
1 AAATAAATAATATTATTTAATA
46353 AAATAAATAATA-T-TTTAATA
1 AAATAAATAATATTATTTAATA
46373 AAATAAAT
1 AAATAAAT
46381 TATTTAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 15 0.56
21 8 0.30
22 4 0.15
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
AAATAAATAATATTATTTAATA
Found at i:46643 original size:4 final size:4
Alignment explanation
Indices: 46627--46674 Score: 53
Period size: 4 Copynumber: 11.8 Consensus size: 4
46617 TGCCCAATAT
* *
46627 ATTA ATTA TTTA ATTA ATT- AGTA GTATTA ATTA ATTA ATTA ATTA ATT
1 ATTA ATTA ATTA ATTA ATTA ATTA --ATTA ATTA ATTA ATTA ATTA ATT
46675 TGTAGTACCA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
3 2 0.05
4 32 0.86
6 3 0.08
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (4 bp):
ATTA
Found at i:52341 original size:22 final size:22
Alignment explanation
Indices: 52315--52375 Score: 95
Period size: 22 Copynumber: 2.8 Consensus size: 22
52305 TTAATATCTT
*
52315 TATTAGGTATGTTAGGTAAATA
1 TATTAGGTGTGTTAGGTAAATA
*
52337 TATTAGGTGTGTTACGTAAATA
1 TATTAGGTGTGTTAGGTAAATA
*
52359 TATTATGTGTGTTAGGT
1 TATTAGGTGTGTTAGGT
52376 GAACTTATCT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.30, C:0.02, G:0.25, T:0.44
Consensus pattern (22 bp):
TATTAGGTGTGTTAGGTAAATA
Done.