Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010595.1 Corchorus capsularis cultivar CVL-1 contig10616, 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: 26804
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Found at i:10569 original size:32 final size:32
Alignment explanation
Indices: 10531--10611 Score: 126
Period size: 32 Copynumber: 2.5 Consensus size: 32
10521 CAGGTTTAAG
10531 TCGGGTTGAATTTGGGTCAGGTCAATTCGGGT
1 TCGGGTTGAATTTGGGTCAGGTCAATTCGGGT
* *
10563 TCGGGTTGAATTTGGATCAGGTTAATTCGGGT
1 TCGGGTTGAATTTGGGTCAGGTCAATTCGGGT
* *
10595 TCGGGTTCAGTTTGGGT
1 TCGGGTTGAATTTGGGT
10612 TTTAGCCAGA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.15, C:0.11, G:0.37, T:0.37
Consensus pattern (32 bp):
TCGGGTTGAATTTGGGTCAGGTCAATTCGGGT
Found at i:10776 original size:16 final size:16
Alignment explanation
Indices: 10755--10800 Score: 92
Period size: 16 Copynumber: 2.9 Consensus size: 16
10745 AACTTTTGGA
10755 TTCGGGTTCGGGTTTT
1 TTCGGGTTCGGGTTTT
10771 TTCGGGTTCGGGTTTT
1 TTCGGGTTCGGGTTTT
10787 TTCGGGTTCGGGTT
1 TTCGGGTTCGGGTT
10801 CAGACAGGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.00, C:0.13, G:0.39, T:0.48
Consensus pattern (16 bp):
TTCGGGTTCGGGTTTT
Found at i:11456 original size:119 final size:118
Alignment explanation
Indices: 11284--11520 Score: 431
Period size: 119 Copynumber: 2.0 Consensus size: 118
11274 TCCGTGCTAT
*
11284 GCACAATGAGCATAAAACAAACCGAGTCCATCTTAATAATTTAGCTCCCAAAATATTTACTTTCA
1 GCACAATGAGCATAAAACAAACAGAGTCCATCTTAATAATTTAGCTCCCAAAATATTTACTTTCA
11349 AAGATGCTCTCTGACTATGAAAAAAGAAACACTGAATTAGTAAGATAGAAAAG
66 AAGATGCTCTCTGACTATGAAAAAAGAAACACTGAATTAGTAAGATAGAAAAG
*
11402 GCACAATCG-GCATAAAACAAACTAGAGTCCATCTTAATAATTTAGCTTCCAAAATATTTACTTT
1 GCACAAT-GAGCATAAAACAAAC-AGAGTCCATCTTAATAATTTAGCTCCCAAAATATTTACTTT
11466 CAAAGATGCTCTCTGACTATGAAAAAAGAAACACTGAATTAGTAAGATAGAAAAG
64 CAAAGATGCTCTCTGACTATGAAAAAAGAAACACTGAATTAGTAAGATAGAAAAG
11521 ATTCTCTCTA
Statistics
Matches: 115, Mismatches: 2, Indels: 3
0.96 0.02 0.03
Matches are distributed among these distances:
118 20 0.17
119 95 0.83
ACGTcount: A:0.44, C:0.17, G:0.14, T:0.25
Consensus pattern (118 bp):
GCACAATGAGCATAAAACAAACAGAGTCCATCTTAATAATTTAGCTCCCAAAATATTTACTTTCA
AAGATGCTCTCTGACTATGAAAAAAGAAACACTGAATTAGTAAGATAGAAAAG
Found at i:11965 original size:6 final size:6
Alignment explanation
Indices: 11942--12012 Score: 65
Period size: 6 Copynumber: 11.8 Consensus size: 6
11932 ATATATCATA
* * * * *
11942 TATATC TATATC TATATC TATATC TTTTTT TGGTGAT- TATATA TATATC
1 TATATC TATATC TATATC TATATC TATATC T-AT-ATC TATATC TATATC
11991 TATATC TATATC TATA-C TATAT
1 TATATC TATATC TATATC TATAT
12013 ATAAAAGCAC
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
5 7 0.13
6 44 0.81
7 2 0.04
8 1 0.02
ACGTcount: A:0.31, C:0.11, G:0.04, T:0.54
Consensus pattern (6 bp):
TATATC
Found at i:14074 original size:2 final size:2
Alignment explanation
Indices: 14067--14096 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
14057 CAATTTAGAA
14067 AT AT AT AT AT AT AT AT AT AT ACT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT A
14097 AAAGTACGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:14194 original size:27 final size:26
Alignment explanation
Indices: 14138--14213 Score: 71
Period size: 27 Copynumber: 2.8 Consensus size: 26
14128 TCGATTGTAC
*
14138 CCTTATATTCAAATATATTTCTAAATTG
1 CCTT-TATTAAAATATATTT-TAAATTG
* *
14166 CCTTTATTAAAAAATATTTTAATTATG
1 CCTTTATTAAAATATATTTTAAAT-TG
**
14193 CCACTATTAAAATATAATTTT
1 CCTTTATTAAAATAT-ATTTT
14214 GTGTTTTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
26 4 0.10
27 27 0.68
28 9 0.22
ACGTcount: A:0.39, C:0.12, G:0.03, T:0.46
Consensus pattern (26 bp):
CCTTTATTAAAATATATTTTAAATTG
Found at i:18789 original size:62 final size:62
Alignment explanation
Indices: 18706--18860 Score: 231
Period size: 62 Copynumber: 2.5 Consensus size: 62
18696 GAAATATTCA
* * *
18706 TATGAAATTATGATAATCTTCCTATTAAATTAT-AGTAATTACACTATTTTTAATAACGTACT
1 TATGAAATTTTGATAACCTTCCTATGAAATTATGA-TAATTACACTATTTTTAATAACGTACT
* * * *
18768 TATGATATTTTGATAACCTTCCTATGAAATTATGATAATTACACTATTTTTTATGACGTCCT
1 TATGAAATTTTGATAACCTTCCTATGAAATTATGATAATTACACTATTTTTAATAACGTACT
18830 TATGAAATTTTGATAACCTTCCTATGAAATT
1 TATGAAATTTTGATAACCTTCCTATGAAATT
18861 TCAATAACGA
Statistics
Matches: 84, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
62 83 0.99
63 1 0.01
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.44
Consensus pattern (62 bp):
TATGAAATTTTGATAACCTTCCTATGAAATTATGATAATTACACTATTTTTAATAACGTACT
Found at i:18793 original size:22 final size:21
Alignment explanation
Indices: 18768--19381 Score: 128
Period size: 22 Copynumber: 28.7 Consensus size: 21
18758 ATAACGTACT
*
18768 TATGATATTTTGATAACCTTCC
1 TATGAAATTTTGATAA-CTTCC
*
18790 TATGAAATTATGATAA-TTACAC
1 TATGAAATTTTGATAACTT-C-C
* * *
18812 TAT----TTTTTATGACGTCC
1 TATGAAATTTTGATAACTTCC
18829 TTATGAAATTTTGATAACCTTCC
1 -TATGAAATTTTGATAA-CTTCC
** * *
18852 TATGAAATTTCAATAACGATAC
1 TATGAAATTTTGATAAC-TTCC
* * * * **
18874 TGTGGAATTTCGAGAACTTTTT
1 TATGAAATTTTGATAAC-TTCC
** *
18896 TAT-AAATTTGTTTTAACCTTCT
1 TATGAAATTT-TGATAA-CTTCC
*
18918 TATGAAATTTTGTTAACTTCCC
1 TATGAAATTTTGATAACTT-CC
* * *
18940 TAAGGAATTTTGA-AGACCTCAC
1 TATGAAATTTTGATA-ACTTC-C
*
18962 TATGAAATTTTGATAACTTTCA
1 TATGAAATTTTGATAAC-TTCC
* *
18984 AATGAAATTTTGATAACTTTCA
1 TATGAAATTTTGATAAC-TTCC
* **
19006 AATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAA-CTTC-C
* *
19029 TAT-AAGATGTTGATAACCTCC
1 TATGAA-ATTTTGATAACTTCC
* *
19050 ATATGATATATTGATAA--TCAC
1 -TATGAAATTTTGATAACTTC-C
* * * *
19071 GTTATGAAAATTTAAAAACCTCC
1 --TATGAAATTTTGATAACTTCC
* * *
19094 ATATG-AATTGTCAGTAA-TCACAC
1 -TATGAAATTTTGA-TAACT-TC-C
* *
19117 TCTGAAATTTTGATAA-TCACAC
1 TATGAAATTTTGATAACT-TC-C
* * *
19139 TATGAAACTGTGATAACCTCGC
1 TATGAAATTTTGATAACTTC-C
19161 TATGAAATTTTGATAAATCTTCC
1 TATGAAATTTTGAT-AA-CTTCC
*
19184 TAT-ATAA-----AT--CTCCC
1 TATGA-AATTTTGATAACTTCC
* * *
19198 TATAAAATTTTAATAACCTCC
1 TATGAAATTTTGATAACTTCC
*
19219 TTATGAAATCTTGATAA----C
1 -TATGAAATTTTGATAACTTCC
* *
19237 TA-CAAATTTTGATAATCTCCC
1 TATGAAATTTTGATAA-CTTCC
** * *
19258 TATGATTTTTTGATAACCTCAT
1 TATGAAATTTTGATAACTTC-C
* *
19280 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAA-CTTCC
* *
19302 TATGAAATTTTGATAACCCTCT
1 TATGAAATTTTGATAA-CTTCC
* **
19324 TATGAAATTTTGAAAACTAAAC
1 TATGAAATTTTGATAACT-TCC
* *
19346 TATGAAATTTTGATAACCATCA
1 TATGAAATTTTGATAA-CTTCC
19368 TATGAAATTTTGAT
1 TATGAAATTTTGAT
19382 TACTCCATAA
Statistics
Matches: 430, Mismatches: 108, Indels: 108
0.67 0.17 0.17
Matches are distributed among these distances:
14 9 0.02
15 1 0.00
16 11 0.03
17 3 0.01
18 13 0.03
19 3 0.01
20 4 0.01
21 28 0.07
22 307 0.71
23 46 0.11
24 5 0.01
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (21 bp):
TATGAAATTTTGATAACTTCC
Found at i:19192 original size:14 final size:14
Alignment explanation
Indices: 19173--19205 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
19163 TGAAATTTTG
*
19173 ATAAATCTTCCTAT
1 ATAAATCTCCCTAT
19187 ATAAATCTCCCTAT
1 ATAAATCTCCCTAT
19201 A-AAAT
1 ATAAAT
19206 TTTAATAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.42, C:0.21, G:0.00, T:0.36
Consensus pattern (14 bp):
ATAAATCTCCCTAT
Found at i:19303 original size:44 final size:43
Alignment explanation
Indices: 19240--19379 Score: 167
Period size: 44 Copynumber: 3.2 Consensus size: 43
19230 TGATAACTAC
**
19240 AAATTTTGATAATCTCCCTATGATTTTTTGATAACCTCATTATG
1 AAATTTTG-TAATCTCCCTATGAAATTTTGATAACCTCATTATG
19284 AAATTTTGTTAATCTCCCTATGAAATTTTGATAACCCTC-TTATG
1 AAATTTTG-TAATCTCCCTATGAAATTTTGATAA-CCTCATTATG
* * **
19328 AAATTTTGAAAACTAAACTATGAAATTTTGATAACCATCA-TATG
1 AAATTTTGTAATCT-CCCTATGAAATTTTGATAACC-TCATTATG
19372 AAATTTTG
1 AAATTTTG
19380 ATTACTCCAT
Statistics
Matches: 85, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
43 6 0.07
44 75 0.88
45 4 0.05
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.41
Consensus pattern (43 bp):
AAATTTTGTAATCTCCCTATGAAATTTTGATAACCTCATTATG
Found at i:19511 original size:22 final size:22
Alignment explanation
Indices: 19486--19591 Score: 115
Period size: 22 Copynumber: 4.8 Consensus size: 22
19476 AATCACATTT
* *
19486 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTCTA
19508 TGAAATTTTGATAACCTCTCTA
1 TGAAATTTTGATAACCTCTCTA
* * * *
19530 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTCTCTA
* *
19552 TGAAATTTTGATAATCACAT-TA
1 TGAAATTTTGATAACCTC-TCTA
*
19574 TGTAATTTTGATAACCTC
1 TGAAATTTTGATAACCTC
19592 GCGCTTTGAA
Statistics
Matches: 69, Mismatches: 14, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
22 68 0.99
23 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.42
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTCTA
Found at i:19512 original size:44 final size:44
Alignment explanation
Indices: 19461--19591 Score: 140
Period size: 44 Copynumber: 3.0 Consensus size: 44
19451 AGAAGTACCA
* *
19461 CTATGAAATTTTGGTAATCACATTTTGAAAATTTGATAACCTCT
1 CTATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTCT
* * * * * *
19505 TTATGAAATTTTGATAACCTC-TCTAT-AAAATTTTGTTGACCCCT
1 CTATGAAATTTTGATAATCACAT-TATGAAAA-TTTGATAACCTCT
* *
19549 CTATGAAATTTTGATAATCACATTATGTAATTTTGATAACCTC
1 CTATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTC
19592 GCGCTTTGAA
Statistics
Matches: 67, Mismatches: 16, Indels: 8
0.74 0.18 0.09
Matches are distributed among these distances:
43 5 0.07
44 59 0.88
45 3 0.04
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (44 bp):
CTATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTCT
Found at i:19911 original size:30 final size:31
Alignment explanation
Indices: 19876--19940 Score: 96
Period size: 30 Copynumber: 2.1 Consensus size: 31
19866 TGACAATTTA
* *
19876 GAAATATGTTTTAAAAA-AAGGATACAATTG
1 GAAATATATTTTAAAAATAAGGATACAATCG
*
19906 GAAATATATTTTAAAAATAAGGGTACAATCG
1 GAAATATATTTTAAAAATAAGGATACAATCG
19937 GAAA
1 GAAA
19941 ACATAAAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
30 16 0.52
31 15 0.48
ACGTcount: A:0.51, C:0.05, G:0.17, T:0.28
Consensus pattern (31 bp):
GAAATATATTTTAAAAATAAGGATACAATCG
Found at i:20298 original size:16 final size:15
Alignment explanation
Indices: 20244--20303 Score: 66
Period size: 16 Copynumber: 3.8 Consensus size: 15
20234 AATAATAATA
20244 ATATGTCATTATTATT
1 ATATGTCATTATTA-T
* *
20260 AATTTGTTATTATTAT
1 -ATATGTCATTATTAT
20276 ATATGTCATTATATAT
1 ATATGTCATTAT-TAT
*
20292 ATGTGTCATTAT
1 ATATGTCATTAT
20304 CAATTAATTG
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
15 10 0.27
16 15 0.41
17 12 0.32
ACGTcount: A:0.32, C:0.05, G:0.08, T:0.55
Consensus pattern (15 bp):
ATATGTCATTATTAT
Found at i:22301 original size:22 final size:22
Alignment explanation
Indices: 22221--22460 Score: 129
Period size: 22 Copynumber: 10.8 Consensus size: 22
22211 GAAGATCTCA
*
22221 ATATGAAATTTTGATAACTTCTC
1 ATATGAAATTTTGATAACCTC-C
**
22244 A-ATGAAATTTTGATAACCAAC
1 ATATGAAATTTTGATAACCTCC
* *
22265 ACTATGAGATGTTGATAACCTCC
1 A-TATGAAATTTTGATAACCTCC
* * * *
22288 ATATGATATATTGATAACCACG
1 ATATGAAATTTTGATAACCTCC
* * * *
22310 TTATGAAAATTTAAAAACCTCC
1 ATATGAAATTTTGATAACCTCC
22332 ATATG-AATTGTT-AGTAA--TCAC
1 ATATGAAATT-TTGA-TAACCTC-C
*
22353 ACTCTGAAATTTTGATAA--TCAC
1 A-TATGAAATTTTGATAACCTC-C
*
22375 ACTATGAAATTGTGATAACCTCGC
1 A-TATGAAATTTTGATAACCTC-C
*
22399 -TATGAAATTTTGATAAATCTTCC
1 ATATGAAATTTTGAT-AA-CCTCC
* *
22422 -TATAAAATTTTGATAAACGTCC
1 ATATGAAATTTTGAT-AACCTCC
* *
22444 CTATAAAATTTTGATAA
1 ATATGAAATTTTGATAA
22461 ATTTCTTATG
Statistics
Matches: 174, Mismatches: 30, Indels: 27
0.75 0.13 0.12
Matches are distributed among these distances:
20 2 0.01
21 8 0.05
22 102 0.59
23 56 0.32
24 6 0.03
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (22 bp):
ATATGAAATTTTGATAACCTCC
Found at i:22429 original size:23 final size:24
Alignment explanation
Indices: 22398--22462 Score: 98
Period size: 23 Copynumber: 2.8 Consensus size: 24
22388 GATAACCTCG
* *
22398 CTATGAAATTTTGATAAATC-TTC
1 CTATAAAATTTTGATAAATCGTCC
22421 CTATAAAATTTTGATAAA-CGTCC
1 CTATAAAATTTTGATAAATCGTCC
22444 CTATAAAATTTTGATAAAT
1 CTATAAAATTTTGATAAAT
22463 TTCTTATGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
22 1 0.03
23 37 0.97
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (24 bp):
CTATAAAATTTTGATAAATCGTCC
Found at i:22531 original size:22 final size:21
Alignment explanation
Indices: 22481--22625 Score: 94
Period size: 22 Copynumber: 6.6 Consensus size: 21
22471 AAATCTTTAC
**
22481 AAATTTTGATAATCTCCCTATG
1 AAATTTTGATAA-CTTACTATG
** *
22503 ATTTTTTGATAACTTAATTATG
1 AAATTTTGATAACTT-ACTATG
* **
22525 AAATTTTGTTAATCTCCCTATG
1 AAATTTTGATAA-CTTACTATG
* *
22547 AAATTTTGATCTACATACTATG
1 AAATTTTGAT-AACTTACTATG
* *
22569 AAATTTTGATAACCCT-CTTGTG
1 AAATTTTGATAA-CTTAC-TATG
* *
22591 AAATTTTGAAAACTAAACTATG
1 AAATTTTGATAACT-TACTATG
22613 AAATTTTGATAAC
1 AAATTTTGATAAC
22626 CTTCAAATGA
Statistics
Matches: 92, Mismatches: 24, Indels: 14
0.71 0.18 0.11
Matches are distributed among these distances:
21 5 0.05
22 83 0.90
23 4 0.04
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (21 bp):
AAATTTTGATAACTTACTATG
Found at i:22569 original size:44 final size:44
Alignment explanation
Indices: 22481--22624 Score: 152
Period size: 44 Copynumber: 3.3 Consensus size: 44
22471 AAATCTTTAC
** * *
22481 AAATTTTGATAATCTCCCTATGATTTTTTGATAACTTAATTATG
1 AAATTTTGATAATCTCCCTATGAAATTTTGATAACATAACTATG
* *
22525 AAATTTTGTTAATCTCCCTATGAAATTTTGATCTACAT-ACTATG
1 AAATTTTGATAATCTCCCTATGAAATTTTGAT-AACATAACTATG
* *
22569 AAATTTTGATAA-C-CCTCTTGTGAAATTTTGAAAAC-TAAACTATG
1 AAATTTTGATAATCTCC-C-TATGAAATTTTGATAACAT-AACTATG
22613 AAATTTTGATAA
1 AAATTTTGATAA
22625 CCTTCAAATG
Statistics
Matches: 85, Mismatches: 10, Indels: 10
0.81 0.10 0.10
Matches are distributed among these distances:
42 3 0.04
43 4 0.05
44 75 0.88
45 3 0.04
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.42
Consensus pattern (44 bp):
AAATTTTGATAATCTCCCTATGAAATTTTGATAACATAACTATG
Found at i:22635 original size:22 final size:21
Alignment explanation
Indices: 22566--22664 Score: 67
Period size: 22 Copynumber: 4.6 Consensus size: 21
22556 TCTACATACT
**
22566 ATGAAATTTTGATAACCCTCTT
1 ATGAAATTTTGATAA-CCTCAA
* * *
22588 GTGAAATTTTGA-AAACTAAA
1 ATGAAATTTTGATAACCTCAA
22608 CTATGAAATTTTGATAACCTTCAA
1 --ATGAAATTTTGATAACC-TCAA
* * *
22632 ATGAAATTTCGATATCCTC-C
1 ATGAAATTTTGATAACCTCAA
*
22652 CTGAAATTTTGAT
1 ATGAAATTTTGAT
22665 TACTCCATAA
Statistics
Matches: 60, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
20 13 0.22
21 4 0.07
22 37 0.62
23 3 0.05
24 3 0.05
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.37
Consensus pattern (21 bp):
ATGAAATTTTGATAACCTCAA
Found at i:22944 original size:22 final size:21
Alignment explanation
Indices: 22915--23054 Score: 97
Period size: 22 Copynumber: 6.4 Consensus size: 21
22905 AAATTGAGAC
22915 TTTT-ATAACCTTCATATGAAA
1 TTTTGATAACC-TCATATGAAA
* *
22936 TTTTGATAACCACACTATAAAA
1 TTTTGATAACCTCA-TATGAAA
**
22958 TTTTGATAACCTCCCCATGAAA
1 TTTTGATAACCT-CATATGAAA
* *
22980 TATT-AGTAACCTCCTAATGAAA
1 TTTTGA-TAACCTCAT-ATGAAA
* *
23002 TTTTGTTAACCACACTATGAAA
1 TTTTGATAACCTCA-TATGAAA
* *
23024 TTCTT-ATAACCTCGCTATGACA
1 TT-TTGATAACCTC-ATATGAAA
23046 TTTTGATAA
1 TTTTGATAA
23055 TCTCTTTGAT
Statistics
Matches: 93, Mismatches: 16, Indels: 19
0.73 0.12 0.15
Matches are distributed among these distances:
21 11 0.12
22 78 0.84
23 4 0.04
ACGTcount: A:0.36, C:0.19, G:0.08, T:0.36
Consensus pattern (21 bp):
TTTTGATAACCTCATATGAAA
Found at i:22978 original size:44 final size:42
Alignment explanation
Indices: 22930--23054 Score: 124
Period size: 44 Copynumber: 2.8 Consensus size: 42
22920 TAACCTTCAT
* * * *
22930 ATGAAATTTTGATAACCACACTATAAAATTTTGATAACCTCCCC
1 ATGAAATTTT-ATAACCTC-CTATGAAATTTTGATAACCACACC
* * *
22974 ATGAAATATTAGTAACCTCCTAATGAAATTTTGTTAACCACACT
1 ATGAAATTTTA-TAACCTCCT-ATGAAATTTTGATAACCACACC
*
23018 ATGAAATTCTTATAACCTCGCTATGACATTTTGATAA
1 ATGAAATT-TTATAACCTC-CTATGAAATTTTGATAA
23055 TCTCTTTGAT
Statistics
Matches: 67, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
43 3 0.04
44 59 0.88
45 5 0.07
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.34
Consensus pattern (42 bp):
ATGAAATTTTATAACCTCCTATGAAATTTTGATAACCACACC
Found at i:23154 original size:24 final size:22
Alignment explanation
Indices: 23090--23155 Score: 60
Period size: 22 Copynumber: 2.9 Consensus size: 22
23080 TTGTGATAAT
* * *
23090 TAACCACCCTTTGAAATTTCAA
1 TAACCAACCTATGAAATTTTAA
* *
23112 TAACCAACCTAAGAGATTTTAA
1 TAACCAACCTATGAAATTTTAA
*
23134 TAACCCGATCCTATGAAATTTT
1 TAA-CC-AACCTATGAAATTTT
23156 GAACAAAGTG
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
22 20 0.59
23 2 0.06
24 12 0.35
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.32
Consensus pattern (22 bp):
TAACCAACCTATGAAATTTTAA
Found at i:23289 original size:19 final size:20
Alignment explanation
Indices: 23258--23295 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
23248 TATTGACATT
23258 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
23277 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
23296 AATAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:23637 original size:31 final size:31
Alignment explanation
Indices: 23602--23660 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
23592 GGCAATTTAG
* *
23602 AAATATGTTTTAAAGAA-AATGGTACAATTGA
1 AAATATATTTTAAA-AATAAGGGTACAATTGA
23633 AAATATATTTTAAAAATAAGGGTACAAT
1 AAATATATTTTAAAAATAAGGGTACAAT
23661 CAGAAAACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 2 0.08
31 23 0.92
ACGTcount: A:0.51, C:0.03, G:0.14, T:0.32
Consensus pattern (31 bp):
AAATATATTTTAAAAATAAGGGTACAATTGA
Found at i:23702 original size:2 final size:2
Alignment explanation
Indices: 23695--23770 Score: 55
Period size: 2 Copynumber: 36.5 Consensus size: 2
23685 TTCGTACTTT
* * * * *
23695 TA TA TA TA GTA TA GA TA GA TA T- TT TA TA TA TA GTA TA GA TA GA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
*
23738 TA GTA TA GTA TA GA 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 T
23771 CTCGTTATTA
Statistics
Matches: 58, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
1 1 0.02
2 49 0.84
3 8 0.14
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.43
Consensus pattern (2 bp):
TA
Found at i:23724 original size:24 final size:24
Alignment explanation
Indices: 23692--23739 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
23682 TTATTCGTAC
23692 TTTTATATATAGTATAGATAGATA
1 TTTTATATATAGTATAGATAGATA
23716 TTTTATATATAGTATAGATAGATA
1 TTTTATATATAGTATAGATAGATA
23740 GTATAGTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (24 bp):
TTTTATATATAGTATAGATAGATA
Found at i:23746 original size:18 final size:17
Alignment explanation
Indices: 23720--23765 Score: 67
Period size: 18 Copynumber: 2.7 Consensus size: 17
23710 TAGATATTTT
23720 ATATATAGTATAGATAG
1 ATATATAGTATAGATAG
*
23737 ATAGTATAGTATAGATAT
1 ATA-TATAGTATAGATAG
23755 ATATATA-TATA
1 ATATATAGTATA
23766 TATATCTCGT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 4 0.15
17 7 0.26
18 16 0.59
ACGTcount: A:0.48, C:0.00, G:0.13, T:0.39
Consensus pattern (17 bp):
ATATATAGTATAGATAG
Found at i:23755 original size:24 final size:23
Alignment explanation
Indices: 23695--23770 Score: 84
Period size: 24 Copynumber: 3.3 Consensus size: 23
23685 TTCGTACTTT
*
23695 TATATATAGTATAGATAGATATTT
1 TATATATAGTATAGATAGATA-TG
23719 TATATATAGTATAGATAGATA-G
1 TATATATAGTATAGATAGATATG
* * *
23741 TATAGTATAG-ATATATATATATA
1 TATA-TATAGTATAGATAGATATG
23764 TATATAT
1 TATATAT
23771 CTCGTTATTA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
22 16 0.35
23 9 0.20
24 21 0.46
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.43
Consensus pattern (23 bp):
TATATATAGTATAGATAGATATG
Found at i:26070 original size:6 final size:6
Alignment explanation
Indices: 26061--26112 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
26051 TTTTTAATTC
* * *
26061 TCTATA TCTATA TCTATA TCTATC TATCTA TCTATA TC--TA TCTATA
1 TCTATA TCTATA TCTATA TCTATA TCTATA TCTATA TCTATA TCTATA
26107 -CTATA T
1 TCTATA T
26113 ATAAAAGTAC
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
4 4 0.11
5 5 0.14
6 28 0.76
ACGTcount: A:0.31, C:0.19, G:0.00, T:0.50
Consensus pattern (6 bp):
TCTATA
Found at i:26092 original size:18 final size:19
Alignment explanation
Indices: 26071--26115 Score: 74
Period size: 18 Copynumber: 2.4 Consensus size: 19
26061 TCTATATCTA
26071 TATCTATATCTATCTAT-C
1 TATCTATATCTATCTATAC
26089 TATCTATATCTATCTATAC
1 TATCTATATCTATCTATAC
*
26108 TATATATA
1 TATCTATA
26116 AAAGTACGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 17 0.68
19 8 0.32
ACGTcount: A:0.33, C:0.18, G:0.00, T:0.49
Consensus pattern (19 bp):
TATCTATATCTATCTATAC
Done.