Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold786
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: 60707
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:2829 original size:2 final size:2
Alignment explanation
Indices: 2822--2846 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2812 ACAAAAATAG
2822 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 A
2847 ATTTGATTTG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3692 original size:25 final size:25
Alignment explanation
Indices: 3664--3712 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
3654 TTATTTCTTT
*
3664 TAAT-TATTTATAATATTAAAAATAG
1 TAATATATTT-TAATACTAAAAATAG
*
3689 TAATATATTTTATTACTAAAAATA
1 TAATATATTTTAATACTAAAAATA
3713 TGTATGATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (25 bp):
TAATATATTTTAATACTAAAAATAG
Found at i:4028 original size:22 final size:24
Alignment explanation
Indices: 3979--4037 Score: 81
Period size: 23 Copynumber: 2.6 Consensus size: 24
3969 TTATAATATT
3979 TAAAATAAAA-ATTTTTAAAATTA
1 TAAAATAAAATATTTTTAAAATTA
4002 TAAAATAAAATATTTTT-AAATTA
1 TAAAATAAAATATTTTTAAAATTA
4025 -AAAA-ACAAATATT
1 TAAAATA-AAATATT
4038 CATGCCTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
21 1 0.03
22 11 0.32
23 16 0.47
24 6 0.18
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (24 bp):
TAAAATAAAATATTTTTAAAATTA
Found at i:4494 original size:11 final size:12
Alignment explanation
Indices: 4472--4500 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
4462 ATTTTTTAAA
4472 AAATATATAATT
1 AAATATATAATT
4484 AAATA-ATAATT
1 AAATATATAATT
4495 AAATAT
1 AAATAT
4501 TTAAATAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
AAATATATAATT
Found at i:5017 original size:20 final size:20
Alignment explanation
Indices: 4989--5037 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
4979 AGAAAGAATT
4989 GAAGAGGGATACAAGAGAGG
1 GAAGAGGGATACAAGAGAGG
* * **
5009 GATGAGGGATGCTTGAGAGG
1 GAAGAGGGATACAAGAGAGG
5029 GAAGAGGGA
1 GAAGAGGGA
5038 GCCTCTATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.37, C:0.04, G:0.49, T:0.10
Consensus pattern (20 bp):
GAAGAGGGATACAAGAGAGG
Found at i:5160 original size:28 final size:27
Alignment explanation
Indices: 5113--5181 Score: 72
Period size: 28 Copynumber: 2.6 Consensus size: 27
5103 AAACAAGCCT
*
5113 CCATATTTGACAAATCCAAAGGA-AACCA
1 CCATTTTTGACAAATCCAAA--ATAACCA
5141 CCATTTTTGACAAA-CACAAAATAACCA
1 CCATTTTTGACAAATC-CAAAATAACCA
*
5168 TCA-TTTTGACAAAT
1 CCATTTTTGACAAAT
5182 AAATGGGTGG
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
26 11 0.31
27 8 0.22
28 17 0.47
ACGTcount: A:0.45, C:0.23, G:0.07, T:0.25
Consensus pattern (27 bp):
CCATTTTTGACAAATCCAAAATAACCA
Found at i:7103 original size:21 final size:22
Alignment explanation
Indices: 7065--7110 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
7055 ATTTGTTGAA
* **
7065 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
7086 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
7108 ACT
1 ACT
7111 TGTCTGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGCGGAGTACT
Found at i:7325 original size:21 final size:21
Alignment explanation
Indices: 7299--7392 Score: 136
Period size: 21 Copynumber: 4.5 Consensus size: 21
7289 TATCCAAATA
7299 TATCGATACATTTGTAGAATG
1 TATCGATACATTTGTAGAATG
*
7320 TATCGATACATTTGTGGAATG
1 TATCGATACATTTGTAGAATG
*
7341 TATCGATACATTTGTGGAATG
1 TATCGATACATTTGTAGAATG
* *
7362 TATCGATACA-TTCTACAAATG
1 TATCGATACATTTGTA-GAATG
7383 TATCGATACA
1 TATCGATACA
7393 GGGTCCCAAC
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
20 3 0.04
21 65 0.96
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (21 bp):
TATCGATACATTTGTAGAATG
Found at i:7527 original size:33 final size:33
Alignment explanation
Indices: 7485--7549 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
7475 CAAGGAAATG
***
7485 TATCGATACATTTTTCTGTGTATCGATACATTA
1 TATCGATACATGGATCTGTGTATCGATACATTA
*
7518 TATCGATACATGGATCTTTGTATCGATACATT
1 TATCGATACATGGATCTGTGTATCGATACATT
7550 TGGAAATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.43
Consensus pattern (33 bp):
TATCGATACATGGATCTGTGTATCGATACATTA
Found at i:9949 original size:51 final size:53
Alignment explanation
Indices: 9885--10226 Score: 210
Period size: 52 Copynumber: 6.5 Consensus size: 53
9875 AGTTTCTCAA
* * * * *
9885 TTCTCCACAATCGGGGATATTCCAACTCCTATTTTATTTTC-AAAACACTAAT
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
* *
9937 TT-TTTATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAAT
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAAACACCAAT
* * * *** * *
9990 TTCTTCACAATCGGGGATACTCCAAC-CCCA-TTAATCATCGGGGATACTCCAACCCCGT
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTAT-TTC-CAAAAACACCAA-----T
* * * * *
10048 TAT-TTC-CGA--GGGGATACTCCAAC-CCCAGTTTTA-TTGCTAAAACACTAAT
1 T-TCTTCACAATCGGGGATACTCCAACTCCGA-TTTTATTTCCAAAAACACCAAT
* * * *
10097 TT-TTCCACAATCGGGGATACTCCAAC-CCAGGTTTTATTTTC-AAAACGCTAATT
1 TTCTT-CACAATCGGGGATACTCCAACTCC-GATTTTATTTCCAAAAACACCAA-T
** *
10150 TTCTT-TTAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAAT
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
*
10202 TT-TTCACAATCGAGGATACTCCAAC
1 TTCTTCACAATCGGGGATACTCCAAC
10227 CTCGTTATTT
Statistics
Matches: 224, Mismatches: 42, Indels: 48
0.71 0.13 0.15
Matches are distributed among these distances:
48 3 0.01
49 3 0.01
50 2 0.01
51 34 0.15
52 84 0.38
53 39 0.17
54 29 0.13
55 19 0.08
57 5 0.02
58 5 0.02
59 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (53 bp):
TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
Found at i:10029 original size:27 final size:28
Alignment explanation
Indices: 9999--10074 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 28
9989 TTTCTTCACA
9999 ATCGGGGATACTCCAACCCCATTA-ATC
1 ATCGGGGATACTCCAACCCCATTATATC
* *
10026 ATCGGGGATACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCATTATATC
***
10054 CGAGGGGATACTCCAACCCCA
1 ATCGGGGATACTCCAACCCCA
10075 GTTTTATTGC
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 23 0.55
28 19 0.45
ACGTcount: A:0.26, C:0.34, G:0.18, T:0.21
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCATTATATC
Found at i:10246 original size:28 final size:30
Alignment explanation
Indices: 10210--10286 Score: 108
Period size: 28 Copynumber: 2.7 Consensus size: 30
10200 ATTTTTCACA
*
10210 ATCGAGGATACTCCAACCTCGTTA-TTTC-
1 ATCGGGGATACTCCAACCTCGTTACTTTCG
*
10238 ATCGGGGATACTCCAACCCCGTTACTTTCG
1 ATCGGGGATACTCCAACCTCGTTACTTTCG
10268 A--GGGGATACTCCAACCTCG
1 ATCGGGGATACTCCAACCTCG
10287 GCTTTATTCC
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
28 39 0.89
29 4 0.09
30 1 0.02
ACGTcount: A:0.23, C:0.31, G:0.19, T:0.26
Consensus pattern (30 bp):
ATCGGGGATACTCCAACCTCGTTACTTTCG
Found at i:10255 original size:212 final size:212
Alignment explanation
Indices: 9888--10283 Score: 640
Period size: 212 Copynumber: 1.9 Consensus size: 212
9878 TTCTCAATTC
*
9888 TCCACAATCGGGGATATTCCAACTCCTATTTTATTTTCAAAACACTAATTTTTTATAATCGGGGA
1 TCCACAATCGGGGATACTCCAACTCCTATTTTATTTTCAAAACACTAATTTTTTATAATCGGGGA
*
9953 TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCCAACCC
66 TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
10018 CATTAATCATCGGGGATACTCCAACCCCGTTA-TTTCCGAGGGGATACTCCAACCCCAGTTTTAT
131 CATTAATCATCGGGGATACTCCAACCCCGTTACTTT-CGAGGGGATACTCCAACCCCAGTTTTAT
10082 TGCTAAAACACTAATTTT
195 TGCTAAAACACTAATTTT
* *
10100 TCCACAATCGGGGATACTCCAAC-CC-AGGTTTTATTTTCAAAACGCTAATTTTCTTTTAATCGG
1 TCCACAATCGGGGATACTCCAACTCCTA--TTTTATTTTCAAAACACTAATTTT-TTATAATCGG
*
10163 GGATACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATACTCCAA
63 GGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAA
* * *
10226 CCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTTCGAGGGGATACTCCAACC
128 CCCCATTA-ATCATCGGGGATACTCCAACCCCGTTACTTTCGAGGGGATACTCCAACC
10284 TCGGCTTTAT
Statistics
Matches: 171, Mismatches: 8, Indels: 10
0.90 0.04 0.05
Matches are distributed among these distances:
210 1 0.01
211 29 0.17
212 102 0.60
213 39 0.23
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (212 bp):
TCCACAATCGGGGATACTCCAACTCCTATTTTATTTTCAAAACACTAATTTTTTATAATCGGGGA
TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
CATTAATCATCGGGGATACTCCAACCCCGTTACTTTCGAGGGGATACTCCAACCCCAGTTTTATT
GCTAAAACACTAATTTT
Found at i:13874 original size:20 final size:20
Alignment explanation
Indices: 13846--13894 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
13836 AAAAAGAATT
13846 GAAGAGGGATACAAGAGAGG
1 GAAGAGGGATACAAGAGAGG
* * **
13866 GATGAGGGATGCTTGAGAGG
1 GAAGAGGGATACAAGAGAGG
13886 GAAGAGGGA
1 GAAGAGGGA
13895 GCCTCTATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.37, C:0.04, G:0.49, T:0.10
Consensus pattern (20 bp):
GAAGAGGGATACAAGAGAGG
Found at i:15814 original size:4 final size:4
Alignment explanation
Indices: 15805--15835 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
15795 TAATGAAAAG
*
15805 ATAC ATAC ATAA ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
15836 GATATATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.55, C:0.19, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:16906 original size:19 final size:18
Alignment explanation
Indices: 16864--16906 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
16854 GATTTCGAGT
16864 TTTTAGCATCCGATATCC
1 TTTTAGCATCCGATATCC
** *
16882 AATTAGCATCGCTATATCC
1 TTTTAGCATC-CGATATCC
16901 TTTTAG
1 TTTTAG
16907 TACAACCGGA
Statistics
Matches: 19, Mismatches: 5, Indels: 1
0.76 0.20 0.04
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.26, C:0.23, G:0.12, T:0.40
Consensus pattern (18 bp):
TTTTAGCATCCGATATCC
Found at i:21236 original size:12 final size:12
Alignment explanation
Indices: 21219--21243 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
21209 CGAAATGATC
21219 TATATATATAAA
1 TATATATATAAA
21231 TATATATATAAA
1 TATATATATAAA
21243 T
1 T
21244 CTGAACACGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TATATATATAAA
Found at i:22048 original size:17 final size:18
Alignment explanation
Indices: 22012--22050 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
22002 TGGTAATTAG
22012 ACAAGTCAAGCAACATGA
1 ACAAGTCAAGCAACATGA
*
22030 ACAAGTCCAGCAA-ATGA
1 ACAAGTCAAGCAACATGA
22047 ACAA
1 ACAA
22051 TTCAGTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.51, C:0.23, G:0.15, T:0.10
Consensus pattern (18 bp):
ACAAGTCAAGCAACATGA
Found at i:23887 original size:21 final size:21
Alignment explanation
Indices: 23861--23903 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
23851 GTTTATGCCG
23861 ACACAAATCAGCCAGTAGAGA
1 ACACAAATCAGCCAGTAGAGA
23882 ACACAAATCAGCCAGTAGAGA
1 ACACAAATCAGCCAGTAGAGA
23903 A
1 A
23904 AAACTGATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.49, C:0.23, G:0.19, T:0.09
Consensus pattern (21 bp):
ACACAAATCAGCCAGTAGAGA
Found at i:24244 original size:13 final size:13
Alignment explanation
Indices: 24226--24251 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
24216 GTAGCATGGG
24226 ACTTACAATGCAC
1 ACTTACAATGCAC
24239 ACTTACAATGCAC
1 ACTTACAATGCAC
24252 GTATCAAACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.31, G:0.08, T:0.23
Consensus pattern (13 bp):
ACTTACAATGCAC
Found at i:24439 original size:22 final size:22
Alignment explanation
Indices: 24407--24468 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 22
24397 TCATGTCTAA
*
24407 AATATTTATATATTT-TTCTTAT
1 AATATTT-TATATTTATTTTTAT
*
24429 AAT-TTTTATATTTATTTTTTT
1 AATATTTTATATTTATTTTTAT
24450 AATATTTTATATTTATTTT
1 AATATTTTATATTTATTTT
24469 ATTTATATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.19
21 11 0.31
22 18 0.50
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (22 bp):
AATATTTTATATTTATTTTTAT
Found at i:24449 original size:15 final size:16
Alignment explanation
Indices: 24431--24476 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
24421 TTTCTTATAA
24431 TTTTTATATTTAT-TT
1 TTTTTATATTTATATT
*
24446 TTTTAATATTTTATATT
1 TTTTTATA-TTTATATT
*
24463 TATTT-TATTTATAT
1 TTTTTATATTTATAT
24477 ATGATTAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 14 0.54
16 7 0.27
17 5 0.19
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTATATTTATATT
Found at i:24476 original size:22 final size:22
Alignment explanation
Indices: 24408--24476 Score: 74
Period size: 22 Copynumber: 3.2 Consensus size: 22
24398 CATGTCTAAA
*
24408 ATATTTATATATTT-TTCTTA-TA
1 ATATTT-TATATTTATT-TTATTT
24430 AT-TTTTATATTTATTTT-TTT
1 ATATTTTATATTTATTTTATTT
24450 AATATTTTATATTTATTTTATTT
1 -ATATTTTATATTTATTTTATTT
24473 ATAT
1 ATAT
24477 ATGATTAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
20 10 0.24
21 7 0.17
22 21 0.51
23 3 0.07
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.70
Consensus pattern (22 bp):
ATATTTTATATTTATTTTATTT
Found at i:25572 original size:13 final size:14
Alignment explanation
Indices: 25554--25582 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
25544 CAATAAATTG
25554 CTAAAAA-CACTTT
1 CTAAAAAGCACTTT
25567 CTAAAAAGCACTTT
1 CTAAAAAGCACTTT
25581 CT
1 CT
25583 GTCTCAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.41, C:0.24, G:0.03, T:0.31
Consensus pattern (14 bp):
CTAAAAAGCACTTT
Found at i:33284 original size:16 final size:16
Alignment explanation
Indices: 33263--33295 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
33253 GATTGATTAA
33263 TTGTTTCTTTTTTCTT
1 TTGTTTCTTTTTTCTT
*
33279 TTGTTTTTTTTTTCTT
1 TTGTTTCTTTTTTCTT
33295 T
1 T
33296 GGCCGTTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.09, G:0.06, T:0.85
Consensus pattern (16 bp):
TTGTTTCTTTTTTCTT
Found at i:36020 original size:15 final size:14
Alignment explanation
Indices: 35986--36054 Score: 56
Period size: 13 Copynumber: 5.1 Consensus size: 14
35976 TCTTTTTCGT
*
35986 TAATTTTTAATTTA
1 TAATTTTTAATATA
*
36000 TTATTTTTAAATATA
1 TAATTTTT-AATATA
*
36015 TAA--TTTAAT-CA
1 TAATTTTTAATATA
* *
36026 TCATTTATAA-ATA
1 TAATTTTTAATATA
36039 TAATTTTTAATATA
1 TAATTTTTAATATA
36053 TA
1 TA
36055 TATATATATT
Statistics
Matches: 41, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
11 3 0.07
12 3 0.07
13 16 0.39
14 12 0.29
15 7 0.17
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (14 bp):
TAATTTTTAATATA
Found at i:36047 original size:26 final size:26
Alignment explanation
Indices: 35986--36049 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 26
35976 TCTTTTTCGT
* * *
35986 TAATTTTTAATTTATTATTTTTAAATA
1 TAATTTTTAA-TCATCATTTATAAATA
*
36013 T-ATAATTTAATCATCATTTATAAATA
1 TAAT-TTTTAATCATCATTTATAAATA
36039 TAATTTTTAAT
1 TAATTTTTAAT
36050 ATATATATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
26 22 0.73
27 8 0.27
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (26 bp):
TAATTTTTAATCATCATTTATAAATA
Found at i:36103 original size:25 final size:26
Alignment explanation
Indices: 36062--36114 Score: 83
Period size: 25 Copynumber: 2.1 Consensus size: 26
36052 ATATATATAT
36062 ATTAATTATATATAAAAATAAT-AATA
1 ATTAATTATAT-TAAAAATAATAAATA
36088 ATTAA-TATATTAAAAATAATAAATA
1 ATTAATTATATTAAAAATAATAAATA
36113 AT
1 AT
36115 AAATGAAAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
24 10 0.38
25 11 0.42
26 5 0.19
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (26 bp):
ATTAATTATATTAAAAATAATAAATA
Found at i:36105 original size:21 final size:22
Alignment explanation
Indices: 36031--36115 Score: 75
Period size: 22 Copynumber: 3.9 Consensus size: 22
36021 AATCATCATT
* **
36031 TATAAATATAATTTTTAATATA
1 TATAAAAATAATAATTAATATA
* * *
36053 TATATATATATTAATT-ATATA
1 TATAAAAATAATAATTAATATA
*
36074 TAAAAATAATAATAATTAATATA
1 TATAAA-AATAATAATTAATATA
*
36097 T-TAAAAATAATAAATAATA
1 TATAAAAATAATAATTAATA
36116 AATGAAAGCC
Statistics
Matches: 51, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
21 22 0.43
22 23 0.45
23 6 0.12
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TATAAAAATAATAATTAATATA
Found at i:37716 original size:4 final size:4
Alignment explanation
Indices: 37707--37749 Score: 68
Period size: 4 Copynumber: 10.8 Consensus size: 4
37697 TAATGAAAAG
* *
37707 ATAC ATAC ATAC ATAA ATAC ATAA ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
37750 TATATAGTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.56, C:0.19, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:38821 original size:19 final size:18
Alignment explanation
Indices: 38779--38821 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
38769 GATTTCGAGT
38779 TTTTAGCATCCGATATCC
1 TTTTAGCATCCGATATCC
** *
38797 AATTAGCATCGCTATATCC
1 TTTTAGCATC-CGATATCC
38816 TTTTAG
1 TTTTAG
38822 TACAGCCGGA
Statistics
Matches: 19, Mismatches: 5, Indels: 1
0.76 0.20 0.04
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.26, C:0.23, G:0.12, T:0.40
Consensus pattern (18 bp):
TTTTAGCATCCGATATCC
Found at i:43158 original size:12 final size:12
Alignment explanation
Indices: 43141--43165 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43131 CGAAATGATC
43141 TATATATATAAA
1 TATATATATAAA
43153 TATATATATAAA
1 TATATATATAAA
43165 T
1 T
43166 CTGAACACGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TATATATATAAA
Found at i:43969 original size:17 final size:18
Alignment explanation
Indices: 43933--43971 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
43923 TGGTAATTAG
43933 ACAAGTCAAGCAACATGA
1 ACAAGTCAAGCAACATGA
*
43951 ACAAGTCCAGCAA-ATGA
1 ACAAGTCAAGCAACATGA
43968 ACAA
1 ACAA
43972 TTCAGTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.51, C:0.23, G:0.15, T:0.10
Consensus pattern (18 bp):
ACAAGTCAAGCAACATGA
Found at i:44633 original size:42 final size:42
Alignment explanation
Indices: 44574--44657 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
44564 CCAAGCCTAA
*
44574 ACCCAAGCTTAATCCAACTCGACTCGATGGTGGTATTCACAT
1 ACCCAAGCTTAACCCAACTCGACTCGATGGTGGTATTCACAT
*
44616 ACCCAAGCTTAACCCAACTCGGCTCGATGGTGGTATTCACAT
1 ACCCAAGCTTAACCCAACTCGACTCGATGGTGGTATTCACAT
44658 GTGTAGTCCA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (42 bp):
ACCCAAGCTTAACCCAACTCGACTCGATGGTGGTATTCACAT
Found at i:45772 original size:21 final size:21
Alignment explanation
Indices: 45746--45790 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
45736 GTTTATGCCG
45746 ACACAAATCAGCCAGTAGAGA
1 ACACAAATCAGCCAGTAGAGA
45767 ACACAAATCAGCCAGTAGAGA
1 ACACAAATCAGCCAGTAGAGA
45788 ACA
1 ACA
45791 ATTGATTACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.49, C:0.24, G:0.18, T:0.09
Consensus pattern (21 bp):
ACACAAATCAGCCAGTAGAGA
Found at i:48210 original size:22 final size:23
Alignment explanation
Indices: 48182--48237 Score: 96
Period size: 22 Copynumber: 2.5 Consensus size: 23
48172 TGGACATGTT
*
48182 AAAAATGCATGAAGCATAAT-AA
1 AAAAATGCATGAAACATAATAAA
48204 AAAAATGCATGAAACATAATAAA
1 AAAAATGCATGAAACATAATAAA
48227 AAAAATGCATG
1 AAAAATGCATG
48238 GTCAAAGGCT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 19 0.59
23 13 0.41
ACGTcount: A:0.61, C:0.09, G:0.12, T:0.18
Consensus pattern (23 bp):
AAAAATGCATGAAACATAATAAA
Found at i:49164 original size:20 final size:20
Alignment explanation
Indices: 49117--49191 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 20
49107 AAAAAGACAT
*
49117 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
49136 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
49157 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
*
49177 AATGTATTGATACAT
1 AATGTATCGATACAT
49192 CAGGGTATGA
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 42 0.95
21 2 0.05
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:49189 original size:40 final size:39
Alignment explanation
Indices: 49114--49191 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
49104 GGTAAAAAGA
* *
49114 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* * *
49153 CATACATGTATCGATATATTGAAAAATGTATTGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
49192 CAGGGTATGA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.36
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:49830 original size:22 final size:22
Alignment explanation
Indices: 49798--49859 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 22
49788 TCATGTCTAA
*
49798 AATATTTATATATTT-TTCTTAT
1 AATATTT-TATATTTATTTTTAT
*
49820 AAT-TTTTATATTTATTTTTTT
1 AATATTTTATATTTATTTTTAT
49841 AATATTTTATATTTATTTT
1 AATATTTTATATTTATTTT
49860 ATTTATTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.19
21 11 0.31
22 18 0.50
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (22 bp):
AATATTTTATATTTATTTTTAT
Done.