Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1222
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: 48731
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Found at i:4411 original size:16 final size:16
Alignment explanation
Indices: 4376--4420 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
4366 TCTTTTCAGA
* *
4376 TTTAGATTACTTCTAT
1 TTTAGATTATTTCTAG
*
4392 TTTAGATTATTTTTAG
1 TTTAGATTATTTCTAG
*
4408 TTTAAATTATTTC
1 TTTAGATTATTTC
4421 GGTTTTAAGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.27, C:0.07, G:0.07, T:0.60
Consensus pattern (16 bp):
TTTAGATTATTTCTAG
Found at i:14529 original size:11 final size:11
Alignment explanation
Indices: 14513--14540 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
14503 CATGTATTTG
14513 GAGGGTCTTTA
1 GAGGGTCTTTA
14524 GAGGGTCTTTA
1 GAGGGTCTTTA
14535 GAGGGT
1 GAGGGT
14541 TATACTTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.18, C:0.07, G:0.43, T:0.32
Consensus pattern (11 bp):
GAGGGTCTTTA
Found at i:15140 original size:2 final size:2
Alignment explanation
Indices: 15133--15168 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
15123 CAGGTACAAC
15133 AT AT AT 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 AT AT AT
15169 GGAGGAATTT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16039 original size:14 final size:14
Alignment explanation
Indices: 16011--16041 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
16001 TAATAATAAA
*
16011 AATATAAAAATATT
1 AATATAAAAAAATT
16025 AATATAAAAAAATT
1 AATATAAAAAAATT
16039 AAT
1 AAT
16042 TTTTTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
AATATAAAAAAATT
Found at i:16466 original size:2 final size:2
Alignment explanation
Indices: 16459--16491 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
16449 TTTATCATTC
16459 AT AT 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 A
16492 ATCCCAACTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16809 original size:2 final size:2
Alignment explanation
Indices: 16802--16832 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
16792 TCTTATATGC
16802 AT 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 A
16833 AAGATTAATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18863 original size:2 final size:2
Alignment explanation
Indices: 18856--18898 Score: 52
Period size: 2 Copynumber: 21.0 Consensus size: 2
18846 ATAACAATAC
*
18856 TA TA TA TA TA TA TA TCA TA T- TA TA TCA TT TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA T-A TA TA TA TA T-A TA TA TA TA TA TA TA TA
18899 CTCGCAATTC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
1 1 0.03
2 31 0.86
3 4 0.11
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:19316 original size:27 final size:26
Alignment explanation
Indices: 19259--19317 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
19249 TTATAATTAT
*
19259 TTTTATTTATTTTTAAAGATTTTTAA
1 TTTTATTTATTTTTAAAGATTTATAA
* * *
19285 ATTTATTTATTTATTAATGATTTATCA
1 TTTTATTTATTT-TTAAAGATTTATAA
19312 TTTTAT
1 TTTTAT
19318 AATTTGCAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 11 0.41
27 16 0.59
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (26 bp):
TTTTATTTATTTTTAAAGATTTATAA
Found at i:21114 original size:2 final size:2
Alignment explanation
Indices: 21107--21151 Score: 56
Period size: 2 Copynumber: 22.5 Consensus size: 2
21097 TTATCATCGT
* *
21107 TA TA TA TA TA TA TA TA TA TA TG TA TA -A GTA TA TA TA TA GA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
21149 TA T
1 TA T
21152 CATGTAGTTG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
1 1 0.03
2 35 0.95
3 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (2 bp):
TA
Found at i:21868 original size:152 final size:153
Alignment explanation
Indices: 21680--21989 Score: 527
Period size: 153 Copynumber: 2.0 Consensus size: 153
21670 AATAAAAATG
* **
21680 TCAAAATTGTTTGATTTATTAATAAAATATTAAATTTTTAATTTTC-ATGATTAAAAATGTTAAT
1 TCAAAATTGTATGATTTATTAATAAAATATTAAATTTTTAA-TTTCAATGATTAAAAAAATTAAT
*
21744 TTTTAATAATTTTAAAT-AAAAAATTATATATTTATATATACAAGATCACCATCTACTTTAATTA
65 TTTTAATAATTTTAAATAAAAAAACTATATATTTATATATACAAGATCACCATCTACTTTAATTA
21808 TTTCTTCAAAATGGGTTTCATGAA
130 TTTCTTCAAAATGGGTTTCATGAA
21832 -CAAAAGTTGTATGATTTATTAATAAAATATTAAATTTTTAATTTCAATGATTAAAAAAATTAAT
1 TCAAAA-TTGTATGATTTATTAATAAAATATTAAATTTTTAATTTCAATGATTAAAAAAATTAAT
*
21896 TTTTAATAATTTTAAATAAAAAAACTATATATTTATATATATAAGATCACCATCTACTTTAATTA
65 TTTTAATAATTTTAAATAAAAAAACTATATATTTATATATACAAGATCACCATCTACTTTAATTA
*
21961 TTTCTTCAAAGTGGGTTTCATGAA
130 TTTCTTCAAAATGGGTTTCATGAA
21985 TCAAA
1 TCAAA
21990 CCCTAAATTT
Statistics
Matches: 148, Mismatches: 6, Indels: 6
0.93 0.04 0.04
Matches are distributed among these distances:
151 9 0.06
152 67 0.45
153 68 0.46
154 4 0.03
ACGTcount: A:0.43, C:0.07, G:0.06, T:0.44
Consensus pattern (153 bp):
TCAAAATTGTATGATTTATTAATAAAATATTAAATTTTTAATTTCAATGATTAAAAAAATTAATT
TTTAATAATTTTAAATAAAAAAACTATATATTTATATATACAAGATCACCATCTACTTTAATTAT
TTCTTCAAAATGGGTTTCATGAA
Found at i:22616 original size:23 final size:23
Alignment explanation
Indices: 22572--22617 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
22562 AAAAATATTT
* *
22572 TTAATTTAAATTTAATTATAATA
1 TTAATATAAATATAATTATAATA
* *
22595 TTAATATAAATATATTTTTAATA
1 TTAATATAAATATAATTATAATA
22618 GTATTTTGAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TTAATATAAATATAATTATAATA
Found at i:25655 original size:18 final size:18
Alignment explanation
Indices: 25632--25669 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
25622 TTTCAAATAA
*
25632 ATGTAAAACACAATAAAT
1 ATGTAAAACAAAATAAAT
*
25650 ATGTAAAAGAAAATAAAT
1 ATGTAAAACAAAATAAAT
25668 AT
1 AT
25670 AATTTATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.63, C:0.05, G:0.08, T:0.24
Consensus pattern (18 bp):
ATGTAAAACAAAATAAAT
Found at i:29094 original size:18 final size:18
Alignment explanation
Indices: 29071--29106 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
29061 CTGTAATTTC
29071 AAATAATTTAGAACATAA
1 AAATAATTTAGAACATAA
29089 AAATAATTTAGAACATAA
1 AAATAATTTAGAACATAA
29107 TGGATTTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.28
Consensus pattern (18 bp):
AAATAATTTAGAACATAA
Found at i:32692 original size:2 final size:2
Alignment explanation
Indices: 32685--32716 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
32675 TTATCATCGT
32685 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
32717 AATCATGTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:33917 original size:2 final size:2
Alignment explanation
Indices: 33905--33934 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
33895 TATCATCTCT
*
33905 TA TA TA CA 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
33935 AGCTTAATCA
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:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:34394 original size:24 final size:24
Alignment explanation
Indices: 34350--34436 Score: 90
Period size: 24 Copynumber: 3.7 Consensus size: 24
34340 ACCCTAAGTT
*
34350 TGGAAACTACAAGGAGAAGAGGAG
1 TGGAAACTACAAGGAAAAGAGGAG
* **
34374 TGGAAATTA-AAGGAAATAGA-GTT
1 TGGAAACTACAAGGAAA-AGAGGAG
*
34397 TGGAAACTACAAGGAGAAGAGGAG
1 TGGAAACTACAAGGAAAAGAGGAG
*
34421 TGGAAATTA-AAGGAAA
1 TGGAAACTACAAGGAAA
34437 TAGTGAGGAA
Statistics
Matches: 50, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
23 24 0.48
24 26 0.52
ACGTcount: A:0.48, C:0.05, G:0.32, T:0.15
Consensus pattern (24 bp):
TGGAAACTACAAGGAAAAGAGGAG
Found at i:34400 original size:23 final size:21
Alignment explanation
Indices: 34371--34439 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 21
34361 AGGAGAAGAG
34371 GAGTGGAAATTAAAGGAAATA
1 GAGTGGAAATTAAAGGAAATA
* *
34392 GAGTTTGGAAACTACAAGGAGAAGA
1 GAG--TGGAAATTA-AAGGA-AATA
34417 GGAGTGGAAATTAAAGGAAATA
1 -GAGTGGAAATTAAAGGAAATA
34439 G
1 G
34440 TGAGGAATGG
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
21 4 0.10
22 3 0.08
23 13 0.33
24 13 0.33
25 3 0.08
26 3 0.08
ACGTcount: A:0.48, C:0.03, G:0.32, T:0.17
Consensus pattern (21 bp):
GAGTGGAAATTAAAGGAAATA
Found at i:34415 original size:47 final size:47
Alignment explanation
Indices: 34346--34439 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
34336 TGAAACCCTA
34346 AGTTTGGAAACTACAAGGAGAAGAGGAGTGGAAATTAAAGGAAATAG
1 AGTTTGGAAACTACAAGGAGAAGAGGAGTGGAAATTAAAGGAAATAG
34393 AGTTTGGAAACTACAAGGAGAAGAGGAGTGGAAATTAAAGGAAATAG
1 AGTTTGGAAACTACAAGGAGAAGAGGAGTGGAAATTAAAGGAAATAG
34440 TGAGGAATGG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.47, C:0.04, G:0.32, T:0.17
Consensus pattern (47 bp):
AGTTTGGAAACTACAAGGAGAAGAGGAGTGGAAATTAAAGGAAATAG
Found at i:35890 original size:2 final size:2
Alignment explanation
Indices: 35883--35916 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
35873 ATAAACCTTT
*
35883 TA TA TA TA TA TA TA TA TA TA TA T- TA TA CA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
35917 CACTTAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:36464 original size:22 final size:22
Alignment explanation
Indices: 36412--36465 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
36402 CTGTCGATTT
36412 TTTTATAAAATTAATCTTTAATA
1 TTTT-TAAAATTAATCTTTAATA
* *
36435 TTTGTAAAATTAAT-TTTAAATC
1 TTTTTAAAATTAATCTTT-AATA
36457 TTTTTAAAA
1 TTTTTAAAA
36466 AATAATAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.11
22 21 0.78
23 3 0.11
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.52
Consensus pattern (22 bp):
TTTTTAAAATTAATCTTTAATA
Found at i:36819 original size:16 final size:18
Alignment explanation
Indices: 36798--36832 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
36788 AGTCTTTATA
36798 ATAAAAAA-TA-AAAATT
1 ATAAAAAATTATAAAATT
36814 ATAAAAAATTATAAAATT
1 ATAAAAAATTATAAAATT
36832 A
1 A
36833 GAATATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 2 0.12
18 7 0.41
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
ATAAAAAATTATAAAATT
Found at i:36916 original size:11 final size:11
Alignment explanation
Indices: 36900--36929 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
36890 ATATAAAAAC
36900 GCACAAATAAT
1 GCACAAATAAT
36911 GCACAAATAAT
1 GCACAAATAAT
*
36922 GAACAAAT
1 GCACAAAT
36930 TATTTAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.57, C:0.17, G:0.10, T:0.17
Consensus pattern (11 bp):
GCACAAATAAT
Found at i:37992 original size:4 final size:4
Alignment explanation
Indices: 37985--38020 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
37975 TTTGAATGAA
37985 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
38021 AAAAAAGTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTAT
Found at i:38727 original size:19 final size:18
Alignment explanation
Indices: 38695--38733 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
38685 TACGATTATC
*
38695 ATATAATAAAATATATAA
1 ATATAATAAAATATACAA
38713 ATATAATATAAATATACAA
1 ATATAATA-AAATATACAA
38732 AT
1 AT
38734 TATCTTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (18 bp):
ATATAATAAAATATACAA
Found at i:39778 original size:23 final size:23
Alignment explanation
Indices: 39746--39794 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
39736 AAAAATATTT
* *
39746 TTAATTTAAATTTAATTATAATA
1 TTAATATAAATATAATTATAATA
* *
39769 TTAATATAAATATATTTTTAATA
1 TTAATATAAATATAATTATAATA
39792 TTA
1 TTA
39795 TTTTGAATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
TTAATATAAATATAATTATAATA
Found at i:42559 original size:7 final size:7
Alignment explanation
Indices: 42547--42574 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
42537 TATAGACATA
42547 ATTAAAT
1 ATTAAAT
42554 ATTAAAT
1 ATTAAAT
42561 ATTAAAT
1 ATTAAAT
42568 ATTAAAT
1 ATTAAAT
42575 TTATCGACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
ATTAAAT
Found at i:42666 original size:13 final size:13
Alignment explanation
Indices: 42650--42680 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
42640 ATTTTTTAAA
*
42650 AATATTTTTATTT
1 AATATTTATATTT
42663 AATATTTATATTT
1 AATATTTATATTT
42676 AATAT
1 AATAT
42681 ATATGAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
AATATTTATATTT
Found at i:43204 original size:28 final size:29
Alignment explanation
Indices: 43165--43247 Score: 84
Period size: 28 Copynumber: 2.9 Consensus size: 29
43155 TAAATTAAAA
*
43165 AATTAAAAATTAATAATAAT-TATATTTAT
1 AATTAAATATTAATAATAATATAT-TTTAT
* *
43194 -ATTAAATATTAATAGTTATATATTTTAT
1 AATTAAATATTAATAATAATATATTTTAT
*
43222 AATTAAAT-TTAA-ATATAAAATATTTT
1 AATTAAATATTAATA-ATAATATATTTT
43248 TATTCTTAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
27 1 0.02
28 34 0.76
29 10 0.22
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (29 bp):
AATTAAATATTAATAATAATATATTTTAT
Found at i:46615 original size:16 final size:16
Alignment explanation
Indices: 46560--46680 Score: 70
Period size: 16 Copynumber: 7.2 Consensus size: 16
46550 AACGACTAAG
*
46560 TTGAATTTGAAAATTAT
1 TTGAATTT-AAAATAAT
* *
46577 TTAAATTTAAAATGAT
1 TTGAATTTAAAATAAT
*
46593 TTAAATTTAAAATAAT
1 TTGAATTTAAAATAAT
* *
46609 ATGAATTCAAAATGAA-
1 TTGAATTTAAAAT-AAT
46625 TTGAATAATTAATTAAAATTAAT
1 TTG---AA-T--TTAAAA-TAAT
46648 TTGAATTTAAAATAA-
1 TTGAATTTAAAATAAT
*
46663 TT-AATTTAATA-AAT
1 TTGAATTTAAAATAAT
46677 TTGA
1 TTGA
46681 GTGTTAAATA
Statistics
Matches: 84, Mismatches: 9, Indels: 24
0.72 0.08 0.21
Matches are distributed among these distances:
13 2 0.02
14 10 0.12
15 3 0.04
16 37 0.44
17 15 0.18
19 3 0.04
20 3 0.04
22 7 0.08
23 4 0.05
ACGTcount: A:0.50, C:0.01, G:0.07, T:0.42
Consensus pattern (16 bp):
TTGAATTTAAAATAAT
Found at i:46638 original size:23 final size:25
Alignment explanation
Indices: 46603--46653 Score: 63
Period size: 23 Copynumber: 2.1 Consensus size: 25
46593 TTAAATTTAA
46603 AATAATATGAATTCAAAATGAA-TTG
1 AATAATATGAATT-AAAATGAATTTG
*
46628 AATAAT-T-AATTAAAATTAATTTG
1 AATAATATGAATTAAAATGAATTTG
46651 AAT
1 AAT
46654 TTAAAATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 7 0.29
23 10 0.42
24 1 0.04
25 6 0.25
ACGTcount: A:0.53, C:0.02, G:0.08, T:0.37
Consensus pattern (25 bp):
AATAATATGAATTAAAATGAATTTG
Found at i:46689 original size:29 final size:30
Alignment explanation
Indices: 46628--46698 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 30
46618 AAATGAATTG
*
46628 AATAATTAATTAAAATTAATTTGAATTTAA
1 AATAATTAATTAAAATAAATTTGAATTTAA
* *
46658 AATAATTAATT-TAATAAATTTGAGTGTTAA
1 AATAATTAATTAAAATAAATTTGAAT-TTAA
*
46688 ATATGATTAAT
1 A-ATAATTAAT
46699 ATGAATGATA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 11 0.31
30 16 0.46
31 8 0.23
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (30 bp):
AATAATTAATTAAAATAAATTTGAATTTAA
Found at i:46799 original size:17 final size:16
Alignment explanation
Indices: 46732--46802 Score: 65
Period size: 16 Copynumber: 4.3 Consensus size: 16
46722 TAAATTTGAT
46732 TGATTTAAATTTAAAA
1 TGATTTAAATTTAAAA
* *
46748 TAATTATTAAATTT--GA
1 TGA-T-TTAAATTTAAAA
46764 TCGATTTAAATTTAAAA
1 T-GATTTAAATTTAAAA
*
46781 TGATTTGAATTTGAAAA
1 TGATTTAAATTT-AAAA
46798 TGATT
1 TGATT
46803 GAAAAATTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
15 8 0.18
16 15 0.34
17 13 0.30
18 8 0.18
ACGTcount: A:0.44, C:0.01, G:0.10, T:0.45
Consensus pattern (16 bp):
TGATTTAAATTTAAAA
Found at i:48174 original size:16 final size:15
Alignment explanation
Indices: 48155--48185 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
48145 TTTTAAAAAG
48155 TTTAAATTTAAATTTA
1 TTTAAATTT-AATTTA
48171 TTTAAATTTAATTTA
1 TTTAAATTTAATTTA
48186 ATAAAAACGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTAAATTTAATTTA
Done.