Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2295
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: 53872
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Found at i:6348 original size:35 final size:34
Alignment explanation
Indices: 6308--6373 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
6298 AAAATAGTCT
* *
6308 AAATATGGTAGATTAAAAATGCTTTTAAAGTTAGA
1 AAATATGGTAGATT-AAAATACCTTTAAAGTTAGA
**
6343 AAATATTTTAGATTAAAATACCTTTAAAGTT
1 AAATATGGTAGATTAAAATACCTTTAAAGTT
6374 TGTTGGAGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
34 15 0.56
35 12 0.44
ACGTcount: A:0.45, C:0.05, G:0.12, T:0.38
Consensus pattern (34 bp):
AAATATGGTAGATTAAAATACCTTTAAAGTTAGA
Found at i:6420 original size:29 final size:29
Alignment explanation
Indices: 6387--6493 Score: 114
Period size: 29 Copynumber: 3.7 Consensus size: 29
6377 TGGAGTTATG
*
6387 TTAAAGTTAGAAAATATTTTTAAATGCTT
1 TTAAAGTTAGAAAATATTTTTAAATACTT
6416 TTAAAGTTAGAAAATATTTTAGATTAAAATAC--
1 TTAAAGTTAGAAAATA-TTT---TT-AAATACTT
* *
6448 TGAAA-TTAGAAAATATTTTAAAATACTT
1 TTAAAGTTAGAAAATATTTTTAAATACTT
6476 TTAAAGTTA-AAAATATTT
1 TTAAAGTTAGAAAATATTT
6494 AGATTAAAAA
Statistics
Matches: 66, Mismatches: 4, Indels: 17
0.76 0.05 0.20
Matches are distributed among these distances:
26 6 0.09
27 1 0.02
28 13 0.20
29 19 0.29
30 6 0.09
31 10 0.15
32 4 0.06
33 2 0.03
34 5 0.08
ACGTcount: A:0.48, C:0.03, G:0.08, T:0.41
Consensus pattern (29 bp):
TTAAAGTTAGAAAATATTTTTAAATACTT
Found at i:7225 original size:113 final size:111
Alignment explanation
Indices: 7019--7291 Score: 307
Period size: 113 Copynumber: 2.4 Consensus size: 111
7009 ATTTTCTTAA
* * * * * * *
7019 AAAAATATGAATTTGTTATATTCCAAATAACATGGTGCTATAAGGCATG-TGTTTTCTTAAGCAG
1 AAAAATATTAATTTCTTCTATTCCAAATAACATTGTGCCATAA-G-ACGCT-CTTTC--AAGCAG
*
7083 TATTAAAATTATTTTCTTAAAAATATTAATTTATTATATTTTAATTTACTT
61 TATTAAAATTATTTTCCTAAAAATATTAATTTATTATATTTTAATTTACTT
*
7134 AAAAAAATATTAATTTCTTCTGTTCCAAATAAC-TTAGTGCCATAAGACGCTCTTTCAAGCAGTA
1 --AAAAATATTAATTTCTTCTATTCCAAATAACATT-GTGCCATAAGACGCTCTTTCAAGCAGTA
* * * *
7198 TTGAAATTATTTTCCTAAAAATATTAATTTGTTGTATTTTAATTTCCTT
63 TTAAAATTATTTTCCTAAAAATATTAATTTATTATATTTTAATTTACTT
* * * *
7247 AAAAATATTAATTTTTTGTATTTCAAATAACATTGTGCTATAAGA
1 AAAAATATTAATTTCTTCTATTCCAAATAACATTGTGCCATAAGA
7292 TTTTTTTAAG
Statistics
Matches: 135, Mismatches: 18, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
111 37 0.27
112 2 0.01
113 52 0.39
115 6 0.04
116 3 0.02
117 35 0.26
ACGTcount: A:0.37, C:0.10, G:0.09, T:0.44
Consensus pattern (111 bp):
AAAAATATTAATTTCTTCTATTCCAAATAACATTGTGCCATAAGACGCTCTTTCAAGCAGTATTA
AAATTATTTTCCTAAAAATATTAATTTATTATATTTTAATTTACTT
Found at i:7244 original size:32 final size:33
Alignment explanation
Indices: 7208--7269 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
7198 TTGAAATTAT
7208 TTTCC-TAAAAATATTAATTTGTTGTATTTTAA
1 TTTCCTTAAAAATATTAATTTGTTGTATTTTAA
*
7240 TTTCCTTAAAAATATTAATTTTTTGTATTT
1 TTTCCTTAAAAATATTAATTTGTTGTATTT
7270 CAAATAACAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
32 5 0.18
33 23 0.82
ACGTcount: A:0.32, C:0.06, G:0.05, T:0.56
Consensus pattern (33 bp):
TTTCCTTAAAAATATTAATTTGTTGTATTTTAA
Found at i:9049 original size:19 final size:20
Alignment explanation
Indices: 9005--9060 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 20
8995 TAAAATTAAT
* * *
9005 AATTAAATTTTTTATTTTAT
1 AATTAAATTATTTATATTAC
9025 AA-TAAATTATTTA-ATTAC
1 AATTAAATTATTTATATTAC
*
9043 AATTAAATTATTTTTATT
1 AATTAAATTATTTATATT
9061 TTTACTATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
18 5 0.17
19 20 0.67
20 5 0.17
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (20 bp):
AATTAAATTATTTATATTAC
Found at i:10035 original size:20 final size:20
Alignment explanation
Indices: 10010--10055 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
10000 AAGAATTGAA
*
10010 GAGGGATACAAGAGAGGGAT
1 GAGGGATACAAGAGAGGGAG
* **
10030 GAGGGATGCTTGAGAGGGAG
1 GAGGGATACAAGAGAGGGAG
10050 GAGGGA
1 GAGGGA
10056 GCCTCTATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.04, G:0.52, T:0.11
Consensus pattern (20 bp):
GAGGGATACAAGAGAGGGAG
Found at i:12118 original size:21 final size:22
Alignment explanation
Indices: 12080--12125 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
12070 ATCTGTTGAA
* **
12080 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
12101 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
12123 ACT
1 ACT
12126 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:14603 original size:20 final size:20
Alignment explanation
Indices: 14578--14623 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
14568 AAGAATTGAA
*
14578 GAGGGATACAAGAGAGGGAT
1 GAGGGATACAAGAGAGGGAG
* **
14598 GAGGGATGCTTGAGAGGGAG
1 GAGGGATACAAGAGAGGGAG
14618 GAGGGA
1 GAGGGA
14624 GCCTCTATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.04, G:0.52, T:0.11
Consensus pattern (20 bp):
GAGGGATACAAGAGAGGGAG
Found at i:15184 original size:2 final size:2
Alignment explanation
Indices: 15177--15220 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
15167 CTATTTAACC
* * *
15177 AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT AA AT AT AT CT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15219 AT
1 AT
15221 TACACTAACA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:15829 original size:2 final size:2
Alignment explanation
Indices: 15822--15866 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
15812 CGGACAAGTG
* *
15822 TA TA TA TA TA TA TA TA TA GA CA 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
15864 TA T
1 TA T
15867 GCTTCAAATC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:17673 original size:2 final size:2
Alignment explanation
Indices: 17661--17703 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
17651 CTAATTCAAT
* *
17661 TA TA GA TA TA TA TA TA TA TA TA TA GA 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
17703 T
1 T
17704 TAACTTTGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (2 bp):
TA
Found at i:18932 original size:11 final size:11
Alignment explanation
Indices: 18916--18966 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 11
18906 GAATGGCCAG
18916 AAGAAAAAAAA
1 AAGAAAAAAAA
*
18927 AAGAAAAAGAA
1 AAGAAAAAAAA
* *
18938 AGGAAAAAAAG
1 AAGAAAAAAAA
*
18949 AA-AAAAAGAA
1 AAGAAAAAAAA
*
18959 ATGAAAAA
1 AAGAAAAA
18967 CCATTAAACT
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
10 7 0.23
11 24 0.77
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (11 bp):
AAGAAAAAAAA
Found at i:18946 original size:21 final size:21
Alignment explanation
Indices: 18918--18966 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
18908 ATGGCCAGAA
*
18918 GAAAAAAAAAAGAAAAAGAAAG
1 GAAAAAAAGAA-AAAAAGAAAG
*
18940 GAAAAAAAGAAAAAAAGAAAT
1 GAAAAAAAGAAAAAAAGAAAG
18961 GAAAAA
1 GAAAAA
18967 CCATTAAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 15 0.60
22 10 0.40
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (21 bp):
GAAAAAAAGAAAAAAAGAAAG
Found at i:19214 original size:20 final size:20
Alignment explanation
Indices: 19186--19260 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 20
19176 TTTTACCCAG
19186 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
19206 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* *
19226 ATGTATCGATATATTCTTCA
1 ATGTATCGATACATTTTTCA
19246 ATGTATCGATACATT
1 ATGTATCGATACATT
19261 ATGTCTTTTT
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:19246 original size:40 final size:39
Alignment explanation
Indices: 19186--19263 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
19176 TTTTACCCAG
*
19186 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTTCAATATATCGATACAT-TATGA
* *
19226 ATGTATCGATATATTCTTCAATGTATCGATACATTATG
1 ATGTATCGATACATTCTTCAATATATCGATACATTATG
19264 TCTTTTTACC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (39 bp):
ATGTATCGATACATTCTTCAATATATCGATACATTATGA
Found at i:26220 original size:20 final size:20
Alignment explanation
Indices: 26191--26266 Score: 73
Period size: 20 Copynumber: 3.7 Consensus size: 20
26181 TTTGAAACAT
*
26191 GTATCTATACATTTATTAAA
1 GTATCGATACATTTATTAAA
*
26211 GTATCGATACATTT-TGAAGCA
1 GTATCGATACATTTATTAA--A
* * *
26232 TGTATCTATGCATTTATTAAT
1 -GTATCGATACATTTATTAAA
26253 GTATCGATACATTT
1 GTATCGATACATTT
26267 TCTTGGTAGT
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
19 3 0.07
20 25 0.57
21 1 0.02
22 12 0.27
23 3 0.07
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (20 bp):
GTATCGATACATTTATTAAA
Found at i:26245 original size:22 final size:21
Alignment explanation
Indices: 26167--26267 Score: 68
Period size: 22 Copynumber: 4.8 Consensus size: 21
26157 ATAATGAGAA
*
26167 ATGTAT-TGATACAATTTGAAAC
1 ATGTATCT-ATACATTTTG-AAC
*
26189 ATGTATCTATACATTTATTAA-
1 ATGTATCTATACATTT-TGAAC
*
26210 A-GTATCGATACATTTTGAAGC
1 ATGTATCTATACATTTTGAA-C
* *
26231 ATGTATCTATGCATTTAT-TA-
1 ATGTATCTATACATTT-TGAAC
*
26251 ATGTATCGATACATTTT
1 ATGTATCTATACATTTT
26268 CTTGGTAGTA
Statistics
Matches: 64, Mismatches: 9, Indels: 15
0.73 0.10 0.17
Matches are distributed among these distances:
19 4 0.06
20 27 0.42
21 2 0.03
22 28 0.44
23 3 0.05
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.43
Consensus pattern (21 bp):
ATGTATCTATACATTTTGAAC
Found at i:26264 original size:42 final size:42
Alignment explanation
Indices: 26166--26267 Score: 159
Period size: 42 Copynumber: 2.4 Consensus size: 42
26156 TATAATGAGA
* *
26166 AATGTATTGATACAATTTGAAACATGTATCTATACATTTATT
1 AATGTATCGATACATTTTGAAACATGTATCTATACATTTATT
* * *
26208 AAAGTATCGATACATTTTGAAGCATGTATCTATGCATTTATT
1 AATGTATCGATACATTTTGAAACATGTATCTATACATTTATT
26250 AATGTATCGATACATTTT
1 AATGTATCGATACATTTT
26268 CTTGGTAGTA
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.42
Consensus pattern (42 bp):
AATGTATCGATACATTTTGAAACATGTATCTATACATTTATT
Found at i:26921 original size:58 final size:58
Alignment explanation
Indices: 26768--27181 Score: 407
Period size: 58 Copynumber: 7.1 Consensus size: 58
26758 TGCATATTAG
* *
26768 GGACCATGTAGCAATTTCCATACATTTTAAAGTCATTTAGGTTATTTTTCATAAT-TTA
1 GGACCATGTAGCAATTTCCATGCATTTTAAAGTCATTTA-GTTATTTTTCATAATCTAA
* * **
26826 GGAGCCATGTAGCAATTTCCATGCATCTTAAGGTCATTTAGTTCCTTTTCTATAATCTAA
1 GGA-CCATGTAGCAATTTCCATGCATTTTAAAGTCATTTAGTTATTTTTC-ATAATCTAA
* * * * * *
26886 GGACCATTTAGTAGTTT-CATGCATTTTAAAATCATTTA-TATCATTTTTCATAATCCAC
1 GGACCATGTAGCAATTTCCATGCATTTTAAAGTCATTTAGT-T-ATTTTTCATAATCTAA
* **
26944 GGACCATGTAGCAATTTCCATG-ATTTTAAGGTCATAAAAGTTATTTTTCATAATCTAA
1 GGACCATGTAGCAATTTCCATGCATTTTAAAGTCAT-TTAGTTATTTTTCATAATCTAA
*
27002 GGACCATGTAGCAATTT-CATGCATTTTAAAGTCATTTATATTATTTTTCATAATCT-A
1 GGACCATGTAGCAATTTCCATGCATTTTAAAGTCATTTA-GTTATTTTTCATAATCTAA
* * * *
27059 GTGACTATGTTGCAATTTTCC-TGCATTTTGAAGTCATTTAGATTATTTTTCGTAATCTAAA
1 G-GACCATGTAGCAA-TTTCCATGCATTTTAAAGTCATTTAG-TTATTTTTCATAATCT-AA
* *** *
27120 GG-CCTTGTAGCAA-TTCTCATGCATTTTTGGGTCA-TTATGTTATTTTTTCATAATCTAT
1 GGACCATGTAGCAATTTC-CATGCATTTTAAAGTCATTTA-GTTA-TTTTTCATAATCTAA
27178 GGAC
1 GGAC
27182 TATATAACAA
Statistics
Matches: 293, Mismatches: 42, Indels: 41
0.78 0.11 0.11
Matches are distributed among these distances:
57 11 0.04
58 142 0.48
59 130 0.44
60 8 0.03
61 2 0.01
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.43
Consensus pattern (58 bp):
GGACCATGTAGCAATTTCCATGCATTTTAAAGTCATTTAGTTATTTTTCATAATCTAA
Found at i:27154 original size:59 final size:57
Alignment explanation
Indices: 26774--27176 Score: 259
Period size: 59 Copynumber: 6.9 Consensus size: 57
26764 TTAGGGACCA
* ** * * * *
26774 TGTAGCAATTTCCATACATTTTAAAGTCATTTAGGTTATTTTTCATAATTTAGGAGCCA
1 TGTAGCAATTT-CATGCATTTTTGAGTCATTTAGATTATTTTTCATAATCTAAG-GCCT
* * **
26833 TGTAGCAATTTCCATGCA-TCTTAAGGTCATTTAG-TTCCTTTTCTATAATCTAAGGACCAT
1 TGTAGCAATTT-CATGCATTTTTGA-GTCATTTAGATTATTTTTC-ATAATCTAAGG-CC-T
* * ** * * * * * *
26893 T-TAGTAGTTTCATGCATTTTAAAATCATTTATATCATTTTTCATAATCCACGGACCA
1 TGTAGCAATTTCATGCATTTTTGAGTCATTTAGATTATTTTTCATAATCTAAGG-CCT
* * * *
26950 TGTAGCAATTTCCATG-A-TTTTAAGGTCA-TAAAAGTTATTTTTCATAATCTAAGGACCA
1 TGTAGCAATTT-CATGCATTTTTGA-GTCATTTAGA-TTATTTTTCATAATCTAAGG-CCT
** * *
27008 TGTAGCAATTTCATGCATTTTAAAGTCATTTATATTATTTTTCATAATCT-AGTGACT
1 TGTAGCAATTTCATGCATTTTTGAGTCATTTAGATTATTTTTCATAATCTAAG-GCCT
* * *
27065 ATGTTGCAATTTTCCTGCA-TTTTGAAGTCATTTAGATTATTTTTCGTAATCTAAAGGCCT
1 -TGTAGCAA-TTTCATGCATTTTTG-AGTCATTTAGATTATTTTTCATAATCT-AAGGCCT
*
27125 TGTAGCAATTCTCATGCATTTTTGGGTCA-TTATG-TTATTTTTTCATAATCTA
1 TGTAGCAATT-TCATGCATTTTTGAGTCATTTA-GATTA-TTTTTCATAATCTA
27177 TGGACTATAT
Statistics
Matches: 276, Mismatches: 45, Indels: 47
0.75 0.12 0.13
Matches are distributed among these distances:
57 16 0.06
58 121 0.44
59 128 0.46
60 9 0.03
61 2 0.01
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.43
Consensus pattern (57 bp):
TGTAGCAATTTCATGCATTTTTGAGTCATTTAGATTATTTTTCATAATCTAAGGCCT
Found at i:27219 original size:117 final size:117
Alignment explanation
Indices: 26768--27225 Score: 362
Period size: 117 Copynumber: 3.9 Consensus size: 117
26758 TGCATATTAG
* ** * *
26768 GGACCATGTAGCAATTTCCATACATTTTAAAGTCATTTAGGTTATTTTTCATAATTTAG-GAGCC
1 GGACCATGTAGCAATTT-CATGCATTTTAAAGTCATTTATATTATTTTTCATAATCTAGTGA-CT
* * * * * * **
26832 ATGTAGCAATTTCCATGCATCTTA-AGGTCATTTAG-TTCCTTTTCTATAATCTAA
64 ATATAACAATTTTCATACAT-TTAGAAGTCATTCAGATTATTTTTC-ATAATCTAA
* * * * * * *
26886 GGACCATTTAGTAGTTTCATGCATTTTAAAATCATTTATATCATTTTTCATAATCCACG-GACCA
1 GGACCATGTAGCAATTTCATGCATTTTAAAGTCATTTATATTATTTTTCATAATCTA-GTGACTA
* * * * * * *
26950 TGTAGCAATTTCCATGA-TTTTA-AGGTCA-TAAAAGTTATTTTTCATAATCTAA
65 TATAACAATTTTCAT-ACATTTAGAAGTCATTCAGA-TTATTTTTCATAATCTAA
27002 GGACCATGTAGCAATTTCATGCATTTTAAAGTCATTTATATTATTTTTCATAATCTAGTGACTAT
1 GGACCATGTAGCAATTTCATGCATTTTAAAGTCATTTATATTATTTTTCATAATCTAGTGACTAT
* ** * * * * *
27067 GTTGCAATTTTCCTGCATTTTGAAGTCATTTAGATTATTTTTCGTAATCTAAA
66 ATAACAATTTTCATACATTTAGAAGTCATTCAGATTATTTTTCATAATCT-AA
* *** *
27120 GG-CCTTGTAGCAATTCTCATGCATTTTTGGGTCA-TTATGTTATTTTTTCATAATCTA-TGGAC
1 GGACCATGTAGCAATT-TCATGCATTTTAAAGTCATTTATATTA-TTTTTCATAATCTAGT-GAC
* *
27182 TATATAACAATTTTTATACATTTAG-AGTCATTCAGATTAGTTTT
63 TATATAACAATTTTCATACATTTAGAAGTCATTCAGATTATTTTT
27226 GCATTTTGCA
Statistics
Matches: 281, Mismatches: 47, Indels: 25
0.80 0.13 0.07
Matches are distributed among these distances:
115 3 0.01
116 88 0.31
117 116 0.41
118 74 0.26
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.43
Consensus pattern (117 bp):
GGACCATGTAGCAATTTCATGCATTTTAAAGTCATTTATATTATTTTTCATAATCTAGTGACTAT
ATAACAATTTTCATACATTTAGAAGTCATTCAGATTATTTTTCATAATCTAA
Found at i:29545 original size:24 final size:24
Alignment explanation
Indices: 29508--29554 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
29498 TCCTAAATGA
* *
29508 TTTTAGAAAGATTGTTGTTTTAAT
1 TTTTAAAAAAATTGTTGTTTTAAT
29532 TTTTAAAAAAATTGTTGTTTTAA
1 TTTTAAAAAAATTGTTGTTTTAA
29555 AAAGATTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (24 bp):
TTTTAAAAAAATTGTTGTTTTAAT
Found at i:31733 original size:18 final size:20
Alignment explanation
Indices: 31712--31758 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
31702 TATTTTATTT
*
31712 TAAATTATTA-TTTAATA-A
1 TAAATTAATATTTTAATATA
*
31730 TAAAATAATATTTTAATATA
1 TAAATTAATATTTTAATATA
31750 TAAA-TAATA
1 TAAATTAATA
31759 AAATAAACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 8 0.32
19 12 0.48
20 5 0.20
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TAAATTAATATTTTAATATA
Found at i:31744 original size:19 final size:19
Alignment explanation
Indices: 31722--31758 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
31712 TAAATTATTA
31722 TTTAATA-ATAAAATAATAT
1 TTTAATATAT-AAATAATAT
31741 TTTAATATATAAATAATA
1 TTTAATATATAAATAATA
31759 AAATAAACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TTTAATATATAAATAATAT
Found at i:32015 original size:2 final size:2
Alignment explanation
Indices: 32008--32047 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
31998 CTATTTAACC
* *
32008 AT AT AT AT AT AT AT AT AT AT AA AT AT AT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
32048 CATACTAAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 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:34199 original size:21 final size:23
Alignment explanation
Indices: 34151--34207 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 23
34141 TATGTTACAA
*
34151 AATAGGTTTTTTAATTATAATAAT
1 AATAAGTTTTTTAATTAT-ATAAT
* *
34175 AATAATTTTTTTAATTCT-TAA-
1 AATAAGTTTTTTAATTATATAAT
34196 AATAAGTTTTTT
1 AATAAGTTTTTT
34208 GAGAAACATT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 11 0.38
22 3 0.10
24 15 0.52
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (23 bp):
AATAAGTTTTTTAATTATATAAT
Found at i:36386 original size:76 final size:72
Alignment explanation
Indices: 36143--36461 Score: 301
Period size: 74 Copynumber: 4.4 Consensus size: 72
36133 TTAAATAAAA
** * * *** *
36143 ATTTAAACTTCTACAAATAAAAATAATTAATAC-CCTAAAAATTAAAACTCACGTAATTA-ACCT
1 ATTTAAACTTCTACAAATAAAAATAATT-ATACTATTAAAATTTTAAACTCGTATAATCATACC-
*
36206 AAAAAATAA
64 AAAAAATAC
* * * ** *
36215 ATTTAAATTTCTACAAATAAAAATGAATTATA-TGATTAAAAATATAAACTTATATGATCATACC
1 ATTTAAACTTCTACAAATAAAAAT-AATTATACT-ATTAAAATTTTAAACTCGTATAATCATA-C
36279 CAAAAAATAC
63 CAAAAAATAC
*
36289 ATTTAAACTTCTACAAATAAAAATAATTTATACTATTAAAATTTTAAACTCGTATAAGCATATCC
1 ATTTAAACTTCTACAAATAAAAATAA-TTATACTATTAAAATTTTAAACTCGTATAATCATA-CC
*
36354 AAAAAAAACAC
64 --AAAAAATAC
* *
36365 ATTTAAACTTCTATAAATAAAAATAAATTATACCT-TAAAAATTTT-AACTCGTATAATCATAAC
1 ATTTAAACTTCTACAAATAAAAAT-AATTATA-CTATTAAAATTTTAAACTCGTATAATCAT-AC
36428 C-AAAAATA-
63 CAAAAAATAC
*
36436 ATTTAAACTTCTACAAATAAAGATAA
1 ATTTAAACTTCTACAAATAAAAATAA
36462 ATAATACCCT
Statistics
Matches: 209, Mismatches: 26, Indels: 26
0.80 0.10 0.10
Matches are distributed among these distances:
70 2 0.01
71 22 0.11
72 32 0.15
73 23 0.11
74 61 0.29
75 19 0.09
76 46 0.22
77 4 0.02
ACGTcount: A:0.53, C:0.13, G:0.03, T:0.31
Consensus pattern (72 bp):
ATTTAAACTTCTACAAATAAAAATAATTATACTATTAAAATTTTAAACTCGTATAATCATACCAA
AAAATAC
Found at i:36482 original size:147 final size:145
Alignment explanation
Indices: 36142--36482 Score: 382
Period size: 147 Copynumber: 2.3 Consensus size: 145
36132 TTTAAATAAA
* * *
36142 AATTTAAACTTCTACAAATAAAAATAATTAATACCCTAAAAATTAAAACTCACGTAATTAACCTA
1 AATTTAAACTTCTACAAATAAAAATAATTAATACCCTAAAAATTTAAACTCACATAAATAACCTA
* * * * * *
36207 AAAAATAAATTTAAATTTCTACAAATAAAAATGAATTATATGATTAAAAATATAAACTTATATGA
66 AAAAAAAAATTTAAACTTCTACAAATAAAAATAAATTATATCATTAAAAATATAAACTCATATAA
*
36272 TCATACCCAAAAAAT
131 TCATAACCAAAAAAT
* ** * ** *
36287 ACATTTAAACTTCTACAAATAAAAATAATTTATACTATTAAAATTTTAAACTCGTATAAGCATAT
1 A-ATTTAAACTTCTACAAATAAAAATAATTAATAC-CCTAAAAATTTAAACTCACATAA--ATAA
* * * *
36352 CC-AAAAAAAACACATTTAAACTTCTATAAATAAAAATAAATTATA-CCTTAAAAATTTTAACTC
62 CCTAAAAAAAA-A-ATTTAAACTTCTACAAATAAAAATAAATTATATCATTAAAAATATAAACTC
*
36415 GTATAATCATAACC-AAAAAT
125 ATATAATCATAACCAAAAAAT
* *
36435 AATTTAAACTTCTACAAATAAAGATAAATAATACCCTAAAGAATTTAA
1 AATTTAAACTTCTACAAATAAAAATAATTAATACCCTAAA-AATTTAA
36483 TACAAATTTA
Statistics
Matches: 161, Mismatches: 28, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
145 1 0.01
146 36 0.22
147 52 0.32
148 14 0.09
149 29 0.18
150 29 0.18
ACGTcount: A:0.53, C:0.13, G:0.03, T:0.31
Consensus pattern (145 bp):
AATTTAAACTTCTACAAATAAAAATAATTAATACCCTAAAAATTTAAACTCACATAAATAACCTA
AAAAAAAAATTTAAACTTCTACAAATAAAAATAAATTATATCATTAAAAATATAAACTCATATAA
TCATAACCAAAAAAT
Found at i:36792 original size:23 final size:23
Alignment explanation
Indices: 36766--36811 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
36756 ATTATTATTA
36766 TAATAAAAAAA-CTTACAAAATAC
1 TAATAAAAAAATC-TACAAAATAC
36789 TAATAAAAAAATCTACAAAATAC
1 TAATAAAAAAATCTACAAAATAC
36812 ACTTACACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 21 0.95
24 1 0.05
ACGTcount: A:0.65, C:0.13, G:0.00, T:0.22
Consensus pattern (23 bp):
TAATAAAAAAATCTACAAAATAC
Found at i:43898 original size:20 final size:20
Alignment explanation
Indices: 43873--43912 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
43863 TGAACATCCT
43873 TAATTCTATTAAATTTTGCA
1 TAATTCTATTAAATTTTGCA
43893 TAATTCTATTAAATTTTGCA
1 TAATTCTATTAAATTTTGCA
43913 GTAGTACAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.10, G:0.05, T:0.50
Consensus pattern (20 bp):
TAATTCTATTAAATTTTGCA
Found at i:44503 original size:29 final size:29
Alignment explanation
Indices: 44441--44508 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
44431 ATTAAAATTT
*
44441 ATATAAAT-ATAAAATATTTTAAATATGA
1 ATATAAATAATAAAATATTATAAATATGA
* *
44469 TTATAACATAATAAAATA-TATAGATATGA
1 ATATAA-ATAATAAAATATTATAAATATGA
44498 ATATAATATAA
1 ATATAA-ATAA
44509 ATTATCAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
28 5 0.15
29 20 0.61
30 8 0.24
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.37
Consensus pattern (29 bp):
ATATAAATAATAAAATATTATAAATATGA
Found at i:45695 original size:2 final size:2
Alignment explanation
Indices: 45688--45720 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
45678 TGCAATTATT
45688 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
45721 GTGGGCAGGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:46272 original size:9 final size:9
Alignment explanation
Indices: 46258--46288 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
46248 AAAATGTAAA
46258 TTTTATTAT
1 TTTTATTAT
46267 TTTTATTAT
1 TTTTATTAT
46276 TTTTATTAT
1 TTTTATTAT
46285 TTTT
1 TTTT
46289 CAAAAATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTATTAT
Found at i:48163 original size:2 final size:2
Alignment explanation
Indices: 48156--48190 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
48146 AAAAGAATTT
48156 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
48191 GCTTTTGATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:52951 original size:19 final size:18
Alignment explanation
Indices: 52903--52959 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 18
52893 ATTACATAAA
*
52903 TAAAAAATAATACAAATAT
1 TAAAAAAT-ATAAAAATAT
*
52922 CAAACAAATATAAAATATAT
1 TAAA-AAATATAAAA-ATAT
52942 TAAAAAATATATAAAATA
1 TAAAAAATATA-AAAATA
52960 AAATATTAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.26
Consensus pattern (18 bp):
TAAAAAATATAAAAATAT
Found at i:53098 original size:27 final size:26
Alignment explanation
Indices: 53076--53124 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
53066 CCTTTTCCCT
53076 TCCCTTTCT-TTTTCTTTTTTTTTCC
1 TCCCTTTCTGTTTTCTTTTTTTTTCC
* *
53101 TCTCTTTTTGTTTTCTTTTTTTTT
1 TCCCTTTCTGTTTTCTTTTTTTTT
53125 TTTTTTTGGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (26 bp):
TCCCTTTCTGTTTTCTTTTTTTTTCC
Found at i:53685 original size:17 final size:17
Alignment explanation
Indices: 53665--53705 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
53655 CTTGAAAATG
53665 TTACTTTACCTTAGG-AA
1 TTACTTTA-CTTAGGAAA
*
53682 TTACTTTACTTTGGAAA
1 TTACTTTACTTAGGAAA
53699 TTACTTT
1 TTACTTT
53706 CCTACAATCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.27, C:0.15, G:0.10, T:0.49
Consensus pattern (17 bp):
TTACTTTACTTAGGAAA
Done.