Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023407.1 Corchorus olitorius cultivar O-4 contig23440, whole genome shotgun sequence
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: 50755
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Found at i:9174 original size:38 final size:39
Alignment explanation
Indices: 9085--9187 Score: 140
Period size: 39 Copynumber: 2.7 Consensus size: 39
9075 AATCAATTAA
* *
9085 TTTCCAAAATATTCTTTT-GAGA-TATCTTAAACTTTTATT
1 TTTCCAAAATCTTCTTTTGGA-ATTA-CCTAAACTTTTATT
*
9124 TTTCTAAAATCTTCTTTTGGAATTACCTAAACTTTTA-T
1 TTTCCAAAATCTTCTTTTGGAATTACCTAAACTTTTATT
9162 TTTCCAAAATCTTCTTTTGGAATTAC
1 TTTCCAAAATCTTCTTTTGGAATTAC
9188 TTAATTAAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
38 26 0.45
39 28 0.48
40 4 0.07
ACGTcount: A:0.29, C:0.16, G:0.06, T:0.50
Consensus pattern (39 bp):
TTTCCAAAATCTTCTTTTGGAATTACCTAAACTTTTATT
Found at i:18347 original size:39 final size:39
Alignment explanation
Indices: 18304--18847 Score: 386
Period size: 39 Copynumber: 14.6 Consensus size: 39
18294 CGCTGTAGAA
* **
18304 AAACTTGCTTAGGTCTTTGTTTAGAAGTTTCGTTTAAAC
1 AAACCTGCTTAGGTCTTTGTTTAGAAGTTTCGTTTAAGT
* *
18343 AAA-CTCACTTAGGTCCTTGTTTAGAA-TTTCCGTTTAAGT
1 AAACCT-GCTTAGGTCTTTGTTTAGAAGTTT-CGTTTAAGT
*
18382 AAACCTGCTTAGGTC----TCT----GTTTCGTTTAAGT
1 AAACCTGCTTAGGTCTTTGTTTAGAAGTTTCGTTTAAGT
** * * *
18413 AAACCTGCTTAGGATCTCCGCTTAG-AGTTTCATTCAAGT
1 AAACCTGCTTAGG-TCTTTGTTTAGAAGTTTCGTTTAAGT
* **
18452 AAACATGCTTAGGTCTTTGTTTAGAAGTTTCGTTTAAAC
1 AAACCTGCTTAGGTCTTTGTTTAGAAGTTTCGTTTAAGT
*
18491 AAACCTGCTTAGGT-TCTTGTGTAGAA-TTTCAGTTTAAGT
1 AAACCTGCTTAGGTCT-TTGTTTAGAAGTTTC-GTTTAAGT
* * * *
18530 AAACCTACTTAGGTC----TCT---A-TTTTGTCTAAGT
1 AAACCTGCTTAGGTCTTTGTTTAGAAGTTTCGTTTAAGT
* * * *
18561 AAACCTGCTTAGGAT-TTCCGCTTAG-AGTTTCATTCAAGT
1 AAACCTGCTTAGG-TCTT-TGTTTAGAAGTTTCGTTTAAGT
* * *
18600 AAACCTGCTTAGGTTTTTGTTTAAAAATTTCGTTTAA-T
1 AAACCTGCTTAGGTCTTTGTTTAGAAGTTTCGTTTAAGT
* *
18638 CAAACCTGCTTAGGTCCTTGTTTAGAA-TTTCTATTTAAGT
1 -AAACCTGCTTAGGTCTTTGTTTAGAAGTTTC-GTTTAAGT
* * *
18678 AAACTTGCTTAGGTC----TCT----GTTTCATTTAAGT
1 AAACCTGCTTAGGTCTTTGTTTAGAAGTTTCGTTTAAGT
* * * *
18709 AAACCTGCTTAGGATCTTCGCTTAG-AGTTTCATTCAAGT
1 AAACCTGCTTAGG-TCTTTGTTTAGAAGTTTCGTTTAAGT
*
18748 AAACCTGCTTAGGTCTTTGTTTAGAAGTTTCGTTTAAAT
1 AAACCTGCTTAGGTCTTTGTTTAGAAGTTTCGTTTAAGT
*
18787 AAACCTGCTTAGGTCCTTGTTTAGAA-TTTCCGTTTAAGT
1 AAACCTGCTTAGGTCTTTGTTTAGAAGTTT-CGTTTAAGT
* *
18826 AAAACTGCTTAGGT-TTCGTTTA
1 AAACCTGCTTAGGTCTTTGTTTA
18848 AGTAAACCTG
Statistics
Matches: 404, Mismatches: 60, Indels: 83
0.74 0.11 0.15
Matches are distributed among these distances:
31 61 0.15
32 16 0.04
35 6 0.01
36 3 0.01
38 46 0.11
39 269 0.67
40 3 0.01
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.41
Consensus pattern (39 bp):
AAACCTGCTTAGGTCTTTGTTTAGAAGTTTCGTTTAAGT
Found at i:18403 original size:26 final size:29
Alignment explanation
Indices: 18373--18430 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 29
18363 TTAGAATTTC
18373 CGTTTAAGTAAACCTGCTTAGG-TCTCTGTTT
1 CGTTTAAGTAAACCTGCTTAGGATCTC---TT
18404 CGTTTAAGTAAACCTGCTTAGGATCTC
1 CGTTTAAGTAAACCTGCTTAGGATCTC
18431 CGCTTAGAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
31 22 0.85
32 4 0.15
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (29 bp):
CGTTTAAGTAAACCTGCTTAGGATCTCTT
Found at i:18480 original size:148 final size:148
Alignment explanation
Indices: 18304--18981 Score: 1019
Period size: 148 Copynumber: 4.6 Consensus size: 148
18294 CGCTGTAGAA
* *
18304 AAACTTGCTTAGGTCTTTGTTTAGAAGTTTCGTTTAAACAAA-CTCACTTAGGTCCTTGTTTAGA
1 AAACCTGCTTAGGTCTTTGTTTAGAAGTTTCGTTTAAACAAACCT-GCTTAGGTCCTTGTTTAGA
18368 ATTTCCGTTTAAGTAAACCTGCTTAGGTCTCTGTTTCGTTTAAGTAAACCTGCTTAGGATCTCCG
65 ATTTCCGTTTAAGTAAACCTGCTTAGGTCTCTGTTTCGTTTAAGTAAACCTGCTTAGGATCTCCG
18433 CTTAGAGTTTCATTCAAGT
130 CTTAGAGTTTCATTCAAGT
* * *
18452 AAACATGCTTAGGTCTTTGTTTAGAAGTTTCGTTTAAACAAACCTGCTTAGGTTCTTGTGTAGAA
1 AAACCTGCTTAGGTCTTTGTTTAGAAGTTTCGTTTAAACAAACCTGCTTAGGTCCTTGTTTAGAA
* * * * * *
18517 TTTCAGTTTAAGTAAACCTACTTAGGTCTCTATTTTGTCTAAGTAAACCTGCTTAGGATTTCCGC
66 TTTCCGTTTAAGTAAACCTGCTTAGGTCTCTGTTTCGTTTAAGTAAACCTGCTTAGGATCTCCGC
18582 TTAGAGTTTCATTCAAGT
131 TTAGAGTTTCATTCAAGT
* * * *
18600 AAACCTGCTTAGGTTTTTGTTTAAAAATTTCGTTTAATCAAACCTGCTTAGGTCCTTGTTTAGAA
1 AAACCTGCTTAGGTCTTTGTTTAGAAGTTTCGTTTAAACAAACCTGCTTAGGTCCTTGTTTAGAA
** * * *
18665 TTTCTATTTAAGTAAACTTGCTTAGGTCTCTGTTTCATTTAAGTAAACCTGCTTAGGATCTTCGC
66 TTTCCGTTTAAGTAAACCTGCTTAGGTCTCTGTTTCGTTTAAGTAAACCTGCTTAGGATCTCCGC
18730 TTAGAGTTTCATTCAAGT
131 TTAGAGTTTCATTCAAGT
*
18748 AAACCTGCTTAGGTCTTTGTTTAGAAGTTTCGTTTAAATAAACCTGCTTAGGTCCTTGTTTAGAA
1 AAACCTGCTTAGGTCTTTGTTTAGAAGTTTCGTTTAAACAAACCTGCTTAGGTCCTTGTTTAGAA
* * *
18813 TTTCCGTTTAAGTAAAACTGCTTA-G-----GTTTCGTTTAAGTAAACCTGCCTAGGATTTCCGC
66 TTTCCGTTTAAGTAAACCTGCTTAGGTCTCTGTTTCGTTTAAGTAAACCTGCTTAGGATCTCCGC
*
18872 TTAAAGTTTCATTCAAGT
131 TTAGAGTTTCATTCAAGT
* * **
18890 AAACCTGCTTAGGTCTTTGTTTAGAAATTTCGTTTAATCAAACCTGCTTAGGTCCTCATTTAGAA
1 AAACCTGCTTAGGTCTTTGTTTAGAAGTTTCGTTTAAACAAACCTGCTTAGGTCCTTGTTTAGAA
* *
18955 TTCCCGTTTAAGTGAACCTGCTTAGGT
66 TTTCCGTTTAAGTAAACCTGCTTAGGT
18982 TTATGCTTAG
Statistics
Matches: 478, Mismatches: 49, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
142 128 0.27
143 1 0.00
147 1 0.00
148 346 0.72
149 2 0.00
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (148 bp):
AAACCTGCTTAGGTCTTTGTTTAGAAGTTTCGTTTAAACAAACCTGCTTAGGTCCTTGTTTAGAA
TTTCCGTTTAAGTAAACCTGCTTAGGTCTCTGTTTCGTTTAAGTAAACCTGCTTAGGATCTCCGC
TTAGAGTTTCATTCAAGT
Found at i:18845 original size:25 final size:26
Alignment explanation
Indices: 18812--18868 Score: 80
Period size: 25 Copynumber: 2.2 Consensus size: 26
18802 CTTGTTTAGA
*
18812 ATTTCCGTTTAAGTAAAACTGCTTAGG
1 ATTT-CGTTTAAGTAAAACTGCCTAGG
*
18839 -TTTCGTTTAAGTAAACCTGCCTAGG
1 ATTTCGTTTAAGTAAAACTGCCTAGG
18864 ATTTC
1 ATTTC
18869 CGCTTAAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 20 0.74
26 7 0.26
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.39
Consensus pattern (26 bp):
ATTTCGTTTAAGTAAAACTGCCTAGG
Found at i:18893 original size:103 final size:103
Alignment explanation
Indices: 18728--18942 Score: 267
Period size: 103 Copynumber: 2.1 Consensus size: 103
18718 TAGGATCTTC
* * * * *
18728 GCTTAGAGTTTCATTCAAGTAAACCTGCTTAGGTCTTTGTTTAGAAGTTTCGTTTAAATAAACCT
1 GCTTAG-GTTTCATTCAAGTAAACCTGCCTAGGTCTTCGCTTAGAAGTTTCATTCAAATAAACCT
18793 GCTTAGGTCCTTGTTTAG-AATTTCCGTTTAAGT-AAAACT
65 GCTTAGGTCCTTGTTTAGAAATTT-CGTTTAA-TCAAAACT
* * *
18832 GCTTAGGTTTCGTTTAAGTAAACCTGCCTAGGAT-TTCCGCTTA-AAGTTTCATTCAAGTAAACC
1 GCTTAGGTTTCATTCAAGTAAACCTGCCTAGG-TCTT-CGCTTAGAAGTTTCATTCAAATAAACC
* *
18895 TGCTTAGGTCTTTGTTTAGAAATTTCGTTTAATCAAACCT
64 TGCTTAGGTCCTTGTTTAGAAATTTCGTTTAATCAAAACT
18935 GCTTAGGT
1 GCTTAGGT
18943 CCTCATTTAG
Statistics
Matches: 97, Mismatches: 10, Indels: 9
0.84 0.09 0.08
Matches are distributed among these distances:
102 1 0.01
103 80 0.82
104 16 0.16
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.40
Consensus pattern (103 bp):
GCTTAGGTTTCATTCAAGTAAACCTGCCTAGGTCTTCGCTTAGAAGTTTCATTCAAATAAACCTG
CTTAGGTCCTTGTTTAGAAATTTCGTTTAATCAAAACT
Found at i:18933 original size:39 final size:38
Alignment explanation
Indices: 18890--19017 Score: 143
Period size: 39 Copynumber: 3.3 Consensus size: 38
18880 TCATTCAAGT
18890 AAACCTGCTTAGGTCTTTGTTTAGAAATTTCGTTTAATC
1 AAACCTGCTTAGGTCTTTGTTTAG-AATTTCGTTTAATC
* ** *
18929 AAACCTGCTTAGGTCCTCATTTAGAATTCCCGTTTAAGT-
1 AAACCTGCTTAGGTCTTTGTTTAGAATT-TCGTTTAA-TC
* * *
18968 GAACCTGCTTAGGT-TTATGCTTAGAGTTTCGTTTAATC
1 AAACCTGCTTAGGTCTT-TGTTTAGAATTTCGTTTAATC
19006 AAACCTGCTTAG
1 AAACCTGCTTAG
19018 TTCCCTCTTT
Statistics
Matches: 73, Mismatches: 12, Indels: 9
0.78 0.13 0.10
Matches are distributed among these distances:
37 1 0.01
38 23 0.32
39 48 0.66
40 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.39
Consensus pattern (38 bp):
AAACCTGCTTAGGTCTTTGTTTAGAATTTCGTTTAATC
Found at i:19029 original size:77 final size:78
Alignment explanation
Indices: 18886--19032 Score: 219
Period size: 77 Copynumber: 1.9 Consensus size: 78
18876 AGTTTCATTC
*
18886 AAGTAAACCTGCTTAGGTCTTTGTTTAGAAATTTCGTTTAATCAAACCTGCTTAGGTCCTCATTT
1 AAGTAAACCTGCTTAGGTCTTTGCTTAGAAATTTCGTTTAATCAAACCTGCTTAGGTCCTCATTT
18951 AGAATTCCCGTTT
66 AGAATTCCCGTTT
* * *
18964 AAGTGAACCTGCTTAGGT-TTATGCTTAG-AGTTTCGTTTAATCAAACCTGCTTAGTTCCCTC-T
1 AAGTAAACCTGCTTAGGTCTT-TGCTTAGAAATTTCGTTTAATCAAACCTGCTTAGGT-CCTCAT
19026 TTAGAAT
64 TTAGAAT
19033 CTCGCCTTAG
Statistics
Matches: 63, Mismatches: 4, Indels: 5
0.88 0.06 0.07
Matches are distributed among these distances:
77 36 0.57
78 27 0.43
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.39
Consensus pattern (78 bp):
AAGTAAACCTGCTTAGGTCTTTGCTTAGAAATTTCGTTTAATCAAACCTGCTTAGGTCCTCATTT
AGAATTCCCGTTT
Found at i:19128 original size:30 final size:30
Alignment explanation
Indices: 19089--19154 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
19079 AAGAAAGTCT
19089 GCTCAAGTACCTTTCGTTTTGTCAACTTTC
1 GCTCAAGTACCTTTCGTTTTGTCAACTTTC
* * *
19119 GCTCGAGTACTTTTCGTTTTGTCAATTTTC
1 GCTCAAGTACCTTTCGTTTTGTCAACTTTC
*
19149 GTTCAA
1 GCTCAA
19155 ACCCTGCTTC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.17, C:0.23, G:0.15, T:0.45
Consensus pattern (30 bp):
GCTCAAGTACCTTTCGTTTTGTCAACTTTC
Found at i:19513 original size:13 final size:13
Alignment explanation
Indices: 19491--19552 Score: 61
Period size: 13 Copynumber: 4.8 Consensus size: 13
19481 TTTTGCATTG
*
19491 CATTAACATATCA
1 CATTAGCATATCA
*
19504 TATTAGCATATCA
1 CATTAGCATATCA
* **
19517 CGTTAAAATATCA
1 CATTAGCATATCA
*
19530 GATTAGCATATCA
1 CATTAGCATATCA
*
19543 CATTTGCATA
1 CATTAGCATA
19553 GTATGTTTGC
Statistics
Matches: 37, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
13 37 1.00
ACGTcount: A:0.40, C:0.18, G:0.08, T:0.34
Consensus pattern (13 bp):
CATTAGCATATCA
Found at i:19522 original size:26 final size:26
Alignment explanation
Indices: 19493--19543 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
19483 TTGCATTGCA
* *
19493 TTAACATATCATATTAGCATATCACG
1 TTAAAATATCAGATTAGCATATCACG
19519 TTAAAATATCAGATTAGCATATCAC
1 TTAAAATATCAGATTAGCATATCAC
19544 ATTTGCATAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.33
Consensus pattern (26 bp):
TTAAAATATCAGATTAGCATATCACG
Found at i:23674 original size:8 final size:7
Alignment explanation
Indices: 23643--23673 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
23633 TCTCTGTAAG
23643 AATTCCAA
1 AATT-CAA
23651 AATTCAA
1 AATTCAA
23658 AATTCAA
1 AATTCAA
23665 AATTCAA
1 AATTCAA
23672 AA
1 AA
23674 AAAAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 19 0.83
8 4 0.17
ACGTcount: A:0.58, C:0.16, G:0.00, T:0.26
Consensus pattern (7 bp):
AATTCAA
Found at i:25846 original size:91 final size:91
Alignment explanation
Indices: 25688--25865 Score: 320
Period size: 91 Copynumber: 2.0 Consensus size: 91
25678 TTCATGCAAA
* * *
25688 TATGTTATATATCAAGGACTCCTACTGAAGTGGCTAGTCGTGCTCAGATATACTAAATTAGGTAG
1 TATGTTATATATCAAGGACTCCTACTAAAGTGGCTAGCCGTGCTCAGATATACTAAATTAGGCAG
25753 TCCAATGTATCAAGGAGAAAAAGACT
66 TCCAATGTATCAAGGAGAAAAAGACT
*
25779 TATGTTATATATCAAGGACTCCTACTAAAGTGGCTAGCCGTGCTCAGATATTCTAAATTAGGCAG
1 TATGTTATATATCAAGGACTCCTACTAAAGTGGCTAGCCGTGCTCAGATATACTAAATTAGGCAG
25844 TCCAATGTATCAAGGAGAAAAA
66 TCCAATGTATCAAGGAGAAAAA
25866 AACGTTCTCA
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
91 83 1.00
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.28
Consensus pattern (91 bp):
TATGTTATATATCAAGGACTCCTACTAAAGTGGCTAGCCGTGCTCAGATATACTAAATTAGGCAG
TCCAATGTATCAAGGAGAAAAAGACT
Found at i:28165 original size:19 final size:18
Alignment explanation
Indices: 28141--28176 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
28131 TGAAGACTTA
28141 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
28160 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
28177 ATTATCTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:31691 original size:13 final size:13
Alignment explanation
Indices: 31673--31698 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31663 CAAGGTACAA
31673 CAAAAATCATCAC
1 CAAAAATCATCAC
31686 CAAAAATCATCAC
1 CAAAAATCATCAC
31699 TCATGCCAAG
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:0.54, C:0.31, G:0.00, T:0.15
Consensus pattern (13 bp):
CAAAAATCATCAC
Found at i:35610 original size:15 final size:16
Alignment explanation
Indices: 35586--35625 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
35576 AGCGGTTGAA
*
35586 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
35601 AGAAAACAATTAAACT
1 AGAAAACAATTAAACT
35617 AGAAAACAA
1 AGAAAACAA
35626 AGCAAAGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.65, C:0.12, G:0.10, T:0.12
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:41238 original size:26 final size:27
Alignment explanation
Indices: 41195--41248 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 27
41185 AGAAAAGAAA
*
41195 TTTTTTTTTTAAATAAAAACACAAAAAC
1 TTTTTTTTTT-AAGAAAAACACAAAAAC
41223 TTTTTTTTTT-AGAAAAACACAAAAAC
1 TTTTTTTTTTAAGAAAAACACAAAAAC
41249 ACAAAACAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 15 0.60
28 10 0.40
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (27 bp):
TTTTTTTTTTAAGAAAAACACAAAAAC
Found at i:41719 original size:16 final size:15
Alignment explanation
Indices: 41681--41720 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
41671 AGAGGTTGAA
*
41681 AGAAAGCAATTAAAC
1 AGAAAACAATTAAAC
*
41696 AAAAAACAATTAAAC
1 AGAAAACAATTAAAC
41711 TAGAAAACAA
1 -AGAAAACAA
41721 AGCAAAGTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.68, C:0.12, G:0.07, T:0.12
Consensus pattern (15 bp):
AGAAAACAATTAAAC
Found at i:46111 original size:8 final size:8
Alignment explanation
Indices: 46100--46289 Score: 70
Period size: 8 Copynumber: 23.8 Consensus size: 8
46090 ATAGGTATAG
46100 AGATAAAT
1 AGATAAAT
46108 AGATAAAT
1 AGATAAAT
* *
46116 AGATACAG
1 AGATAAAT
46124 AGA-ATAAT
1 AGATA-AAT
46132 AGATAAAT
1 AGATAAAT
* **
46140 AGGTAGCT
1 AGATAAAT
* *
46148 AAAAAAAT
1 AGATAAAT
*
46156 ATATAAAT
1 AGATAAAT
**
46164 A-ATAGCT
1 AGATAAAT
* *
46171 AAATTAAT
1 AGATAAAT
* *
46179 AAATAAAA
1 AGATAAAT
46187 AGATAAAT
1 AGATAAAT
46195 AGTAAGTAAAT
1 AG--A-TAAAT
46206 AGAT-AAT
1 AGATAAAT
*
46213 AGCTAAATT
1 AGATAAA-T
46222 A-ATAAAT
1 AGATAAAT
* *
46229 AAAT-AGT
1 AGATAAAT
*
46236 AAATAAAT
1 AGATAAAT
46244 AGAT-AAT
1 AGATAAAT
*
46251 AGTTAAAAAT
1 AG--ATAAAT
* *
46261 AAATAAAA
1 AGATAAAT
46269 AGATAAAT
1 AGATAAAT
46277 AG-TAAAT
1 AGATAAAT
*
46284 AAATAA
1 AGATAA
46290 TAAAAAATAT
Statistics
Matches: 133, Mismatches: 35, Indels: 28
0.68 0.18 0.14
Matches are distributed among these distances:
7 31 0.23
8 85 0.64
9 5 0.04
10 5 0.04
11 7 0.05
ACGTcount: A:0.62, C:0.02, G:0.11, T:0.25
Consensus pattern (8 bp):
AGATAAAT
Found at i:46115 original size:24 final size:24
Alignment explanation
Indices: 46078--46144 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
46068 AAAATAAAAT
* * *
46078 AATAATAAAAAAATAGGTATAGAG
1 AATAATAGATAAATAGGTACAGAG
*
46102 -ATAAATAGATAAATAGATACAGAG
1 AAT-AATAGATAAATAGGTACAGAG
46126 AATAATAGATAAATAGGTA
1 AATAATAGATAAATAGGTA
46145 GCTAAAAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
23 2 0.06
24 32 0.89
25 2 0.06
ACGTcount: A:0.60, C:0.01, G:0.16, T:0.22
Consensus pattern (24 bp):
AATAATAGATAAATAGGTACAGAG
Found at i:46180 original size:19 final size:19
Alignment explanation
Indices: 46158--46266 Score: 71
Period size: 19 Copynumber: 5.4 Consensus size: 19
46148 AAAAAAATAT
46158 ATAAATAATAGCTAAATTA
1 ATAAATAATAGCTAAATTA
* *
46177 ATAAATAAAAAGATAAATAGTA
1 ATAAAT-AATAGCTAAAT--TA
46199 AGTAAATAGATAATAGCTAAATTA
1 A-T--A-A-ATAATAGCTAAATTA
*
46223 ATAAATAAATAG-TAAATAA
1 ATAAAT-AATAGCTAAATTA
* *
46242 ATAGATAATAGTTAAA--A
1 ATAAATAATAGCTAAATTA
46259 ATAAATAA
1 ATAAATAA
46267 AAAGATAAAT
Statistics
Matches: 73, Mismatches: 7, Indels: 22
0.72 0.07 0.22
Matches are distributed among these distances:
17 8 0.11
18 5 0.07
19 23 0.32
20 15 0.21
21 1 0.01
22 3 0.04
23 2 0.03
24 3 0.04
25 1 0.01
26 10 0.14
27 2 0.03
ACGTcount: A:0.62, C:0.02, G:0.08, T:0.28
Consensus pattern (19 bp):
ATAAATAATAGCTAAATTA
Found at i:46183 original size:4 final size:4
Alignment explanation
Indices: 46147--46298 Score: 63
Period size: 4 Copynumber: 39.5 Consensus size: 4
46137 AATAGGTAGC
* * ** *
46147 TAAA AAAA TATA TAAA T-AA TAGC TAAA TTAA TAAA TAAA -AAGA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAA-A TAAA
* * * ** * *
46194 T-AG TAAG TAAA TAGA T-AA TAGC TAAA TTAA TAAA TAAA T-AG TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
* * *
46239 TAAA TAGA TAATA GTTAA -AAA TAAA TAAA -AAGA TAAA T-AG TAAA TAAA
1 TAAA TAAA TAA-A -TAAA TAAA TAAA TAAA TAA-A TAAA TAAA TAAA TAAA
46287 T-AA TAAA -AAA TA
1 TAAA TAAA TAAA TA
46299 TTTTTGGTCT
Statistics
Matches: 106, Mismatches: 28, Indels: 28
0.65 0.17 0.17
Matches are distributed among these distances:
3 23 0.22
4 75 0.71
5 6 0.06
6 2 0.02
ACGTcount: A:0.65, C:0.01, G:0.07, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:46206 original size:11 final size:11
Alignment explanation
Indices: 46189--46298 Score: 64
Period size: 11 Copynumber: 9.6 Consensus size: 11
46179 AAATAAAAAG
46189 ATAAATAGTAA
1 ATAAATAGTAA
*
46200 GTAAATAGATAA
1 ATAAATAG-TAA
*
46212 TAGCTAAATTAATAA
1 -A--TAAA-TAGTAA
46227 ATAAATAGTAA
1 ATAAATAGTAA
46238 ATAAATAG-ATA
1 ATAAATAGTA-A
** *
46249 ATAGTTA-AAA
1 ATAAATAGTAA
**
46259 ATAAATAAAAA
1 ATAAATAGTAA
46270 GATAAATAGTAA
1 -ATAAATAGTAA
*
46282 ATAAATAATAA
1 ATAAATAGTAA
46293 A-AAATA
1 ATAAATA
46299 TTTTTGGTCT
Statistics
Matches: 79, Mismatches: 11, Indels: 19
0.72 0.10 0.17
Matches are distributed among these distances:
10 12 0.15
11 41 0.52
12 16 0.20
14 1 0.01
15 7 0.09
16 2 0.03
ACGTcount: A:0.65, C:0.01, G:0.08, T:0.26
Consensus pattern (11 bp):
ATAAATAGTAA
Found at i:46231 original size:38 final size:36
Alignment explanation
Indices: 46189--46277 Score: 124
Period size: 38 Copynumber: 2.4 Consensus size: 36
46179 AAATAAAAAG
*
46189 ATAAATAGTAAGTAAATAGATAATAGCTAAATTAATAA
1 ATAAATAGTAAATAAATAGATAATAGCTAAA--AATAA
*
46227 ATAAATAGTAAATAAATAGATAATAGTTAAAAATAA
1 ATAAATAGTAAATAAATAGATAATAGCTAAAAATAA
*
46263 ATAAAAAGATAAATA
1 ATAAATAG-TAAATA
46278 GTAAATAAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
36 12 0.26
37 6 0.13
38 29 0.62
ACGTcount: A:0.63, C:0.01, G:0.09, T:0.27
Consensus pattern (36 bp):
ATAAATAGTAAATAAATAGATAATAGCTAAAAATAA
Found at i:46272 original size:25 final size:27
Alignment explanation
Indices: 46164--46295 Score: 119
Period size: 26 Copynumber: 4.9 Consensus size: 27
46154 ATATATAAAT
*
46164 AATAGCTAAATTAATAAATAAAAAGATA
1 AATAG-TAAATAAATAAATAAAAAGATA
* * * *
46192 AATAGTAAGTAAATAGAT-AATAGCTA
1 AATAGTAAATAAATAAATAAAAAGATA
* *
46218 AATTAATAAATAAATAGTAAATAAATAGAT-
1 AA-TAGTAAAT-AA-A-TAAATAAAAAGATA
*
46248 AATAGTTAA-AAATAAATAAAAAGATA
1 AATAGTAAATAAATAAATAAAAAGATA
46274 AATAGTAAATAAAT-AATAAAAA
1 AATAGTAAATAAATAAATAAAAA
46296 ATATTTTTGG
Statistics
Matches: 84, Mismatches: 13, Indels: 16
0.74 0.12 0.14
Matches are distributed among these distances:
25 12 0.14
26 25 0.30
27 22 0.26
28 7 0.08
29 6 0.07
30 6 0.07
31 6 0.07
ACGTcount: A:0.64, C:0.02, G:0.08, T:0.26
Consensus pattern (27 bp):
AATAGTAAATAAATAAATAAAAAGATA
Found at i:46284 original size:19 final size:19
Alignment explanation
Indices: 46178--46286 Score: 87
Period size: 19 Copynumber: 5.4 Consensus size: 19
46168 GCTAAATTAA
46178 TAAATAAAAAGATAAATAG
1 TAAATAAAAAGATAAATAG
* *
46197 TAAGTAAATAGAT-AATAG
1 TAAATAAAAAGATAAATAG
*
46215 CTAAATTAATAA-ATAAATAG
1 -TAAA-TAAAAAGATAAATAG
* *
46235 TAAATAAATAGATAATAGTTAAAAA
1 TAAATAAAAAGATAA-A--T---AG
46260 TAAATAAAAAGATAAATAG
1 TAAATAAAAAGATAAATAG
46279 TAAATAAA
1 TAAATAAA
46287 TAATAAAAAA
Statistics
Matches: 70, Mismatches: 10, Indels: 20
0.70 0.10 0.20
Matches are distributed among these distances:
18 9 0.13
19 33 0.47
20 10 0.14
22 2 0.03
24 1 0.01
25 15 0.21
ACGTcount: A:0.64, C:0.01, G:0.09, T:0.26
Consensus pattern (19 bp):
TAAATAAAAAGATAAATAG
Found at i:47881 original size:16 final size:15
Alignment explanation
Indices: 47843--47884 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
47833 ACAGAGATTG
*
47843 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
47858 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
47873 ACTAGAAAACAA
1 AC-AGAAAACAA
47885 AGCAAAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Done.