Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007741.1 Corchorus capsularis cultivar CVL-1 contig07762, 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: 46778
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:5703 original size:20 final size:19
Alignment explanation
Indices: 5665--5703 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
5655 AAATAAAATA
*
5665 AAAACTACCCATTTTAGAT
1 AAAACTACCCATTTAAGAT
5684 AAAACTACCCATTATAAGAT
1 AAAACTACCCATT-TAAGAT
5704 TAATTTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.46, C:0.21, G:0.05, T:0.28
Consensus pattern (19 bp):
AAAACTACCCATTTAAGAT
Found at i:10106 original size:22 final size:22
Alignment explanation
Indices: 10068--10127 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
10058 CAAACCTCCA
*
10068 TATG-AATTGTTAGTAATCACAC
1 TATGAAATTGTGA-TAATCACAC
* *
10090 TCTGAAATTTTGATAATCACAC
1 TATGAAATTGTGATAATCACAC
10112 TATGAAATTGTGATAA
1 TATGAAATTGTGATAA
10128 CCTCGCTATA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 26 0.81
23 6 0.19
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (22 bp):
TATGAAATTGTGATAATCACAC
Found at i:10136 original size:22 final size:22
Alignment explanation
Indices: 10085--10341 Score: 93
Period size: 22 Copynumber: 11.9 Consensus size: 22
10075 TGTTAGTAAT
* *
10085 CACACTCTGAAATTTTGATAAT
1 CACACTATGAAATTTTGATAAC
*
10107 CACACTATGAAATTGTGATAAC
1 CACACTATGAAATTTTGATAAC
* *
10129 CTCGCTAT-AAATTTTGATAAATC
1 CACACTATGAAATTTTGAT-AA-C
** *
10152 TTC-CTATAAAATTTTGATAAAC
1 CACACTATGAAATTTTGAT-AAC
* * * * *
10174 CTCCCTATAAAAATTTGATATC
1 CACACTATGAAATTTTGATAAC
** * *
10196 TTTC-TTATGAAATCTTGAT---
1 -CACACTATGAAATTTTGATAAC
* **
10215 -A-ACTA-AAAATTTTGATATG
1 CACACTATGAAATTTTGATAAC
* * **
10234 CTCCCTATGATTTTTTGATAAC
1 CACACTATGAAATTTTGATAAC
* * * *
10256 CTCATTATGAAATTTTGTTAAT
1 CACACTATGAAATTTTGATAAC
* *
10278 CTCCCTATGAAATTTTGATAAC
1 CACACTATGAAATTTTGATAAC
* *
10300 C-CTCTTATGAAATTTTGAAAAC
1 CACAC-TATGAAATTTTGATAAC
* *
10322 TAAACTATGAAATTTTGATA
1 CACACTATGAAATTTTGATA
10342 TCCTCCCTGA
Statistics
Matches: 179, Mismatches: 42, Indels: 28
0.72 0.17 0.11
Matches are distributed among these distances:
16 9 0.05
17 2 0.01
21 14 0.08
22 121 0.68
23 33 0.18
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.40
Consensus pattern (22 bp):
CACACTATGAAATTTTGATAAC
Found at i:10166 original size:23 final size:23
Alignment explanation
Indices: 10094--10193 Score: 98
Period size: 23 Copynumber: 4.5 Consensus size: 23
10084 TCACACTCTG
* * * *
10094 AAATTTTGAT-AATCACACTATG
1 AAATTTTGATAAACCTCCCTATA
* *
10116 AAATTGTGAT-AACCTCGCTAT-
1 AAATTTTGATAAACCTCCCTATA
* *
10137 AAATTTTGATAAATCTTCCTATA
1 AAATTTTGATAAACCTCCCTATA
10160 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAACCTCCCTATA
*
10183 AAAATTTGATA
1 AAATTTTGATA
10194 TCTTTCTTAT
Statistics
Matches: 65, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
21 9 0.14
22 25 0.38
23 31 0.48
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.37
Consensus pattern (23 bp):
AAATTTTGATAAACCTCCCTATA
Found at i:10214 original size:45 final size:43
Alignment explanation
Indices: 10098--10216 Score: 109
Period size: 45 Copynumber: 2.7 Consensus size: 43
10088 ACTCTGAAAT
* * *
10098 TTTGATAATC-ACACTATGAAATTGTGAT-AACCTCGCTATAAAT
1 TTTGATAATCTTC-CTATGAAATT-TGATAAACCTCCCTATAAAA
*
10141 TTTGATAAATCTTCCTATAAAATTTTGATAAACCTCCCTATAAAAA
1 TTTGAT-AATCTTCCTATGAAA-TTTGATAAACCTCCCTAT-AAAA
*
10187 TTTGAT-ATCTTTCTTATGAAATCTTGATAA
1 TTTGATAATC-TTCCTATGAAAT-TTGATAA
10217 CTAAAAATTT
Statistics
Matches: 63, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
43 6 0.10
44 19 0.30
45 29 0.46
46 9 0.14
ACGTcount: A:0.37, C:0.15, G:0.08, T:0.39
Consensus pattern (43 bp):
TTTGATAATCTTCCTATGAAATTTGATAAACCTCCCTATAAAA
Found at i:10284 original size:44 final size:44
Alignment explanation
Indices: 10092--10317 Score: 136
Period size: 44 Copynumber: 5.2 Consensus size: 44
10082 AATCACACTC
* * * *
10092 TGAAATTTTGATAAT-CACACTATGAAATTGTGATAA-CCTCGCTA
1 TGAAATTTTGAT-ATGCTCCCTATGAAATTTTGATAACCCTC-TTA
* * * *
10136 T-AAATTTTGATAAAT-CTTCCTATAAAATTTTGATAAACCTCCCTA
1 TGAAATTTTGAT--ATGCTCCCTATGAAATTTTGATAACCCT-CTTA
* * * * *
10181 TAAAAATTTGATAT-CTTTCTTATGAAATCTTGATAA----C-TA
1 TGAAATTTTGATATGC-TCCCTATGAAATTTTGATAACCCTCTTA
* **
10220 -AAAATTTTGATATGCTCCCTATGATTTTTTGATAA-CCTCATTA
1 TGAAATTTTGATATGCTCCCTATGAAATTTTGATAACCCTC-TTA
*
10263 TGAAATTTTGTTAAT-CTCCCTATGAAATTTTGATAACCCTCTTA
1 TGAAATTTTGAT-ATGCTCCCTATGAAATTTTGATAACCCTCTTA
10307 TGAAATTTTGA
1 TGAAATTTTGA
10318 AAACTAAACT
Statistics
Matches: 148, Mismatches: 20, Indels: 28
0.76 0.10 0.14
Matches are distributed among these distances:
38 27 0.18
39 3 0.02
40 1 0.01
41 1 0.01
43 12 0.08
44 64 0.43
45 30 0.20
46 10 0.07
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (44 bp):
TGAAATTTTGATATGCTCCCTATGAAATTTTGATAACCCTCTTA
Found at i:10330 original size:44 final size:44
Alignment explanation
Indices: 10246--10346 Score: 125
Period size: 44 Copynumber: 2.3 Consensus size: 44
10236 CCCTATGATT
* * **
10246 TTTTGATAACCTCATTATGAAATTTTGTTAATCTCCCTATGAAA
1 TTTTGATAACCTCATTATGAAATTTTGTAAAACTAACTATGAAA
10290 TTTTGATAACCCTC-TTATGAAATTTTG-AAAACTAAACTATGAAA
1 TTTTGATAA-CCTCATTATGAAATTTTGTAAAACT-AACTATGAAA
*
10334 TTTTGATATCCTC
1 TTTTGATAACCTC
10347 CCTGAAATTT
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
43 8 0.16
44 38 0.76
45 4 0.08
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.42
Consensus pattern (44 bp):
TTTTGATAACCTCATTATGAAATTTTGTAAAACTAACTATGAAA
Found at i:10561 original size:44 final size:44
Alignment explanation
Indices: 10441--10672 Score: 175
Period size: 44 Copynumber: 5.2 Consensus size: 44
10431 AAAAATACCA
* * * *
10441 CTATGAAATTTTTG-TAATCACATTTTGAAAATTTGATAACCTCT
1 CTATGAAA-TTTCGATAATCACACTATGAAATTTTGATAACCTCT
* * * * ** ** * * *
10485 TTATGAAATTTTGATAACCTCTTTACAAAATTTTGTTGACCCCT
1 CTATGAAATTTCGATAATCACACTATGAAATTTTGATAACCTCT
* * *
10529 CTATGAAATTTCGATAATCACATTATGCAATTTTGATAACCTCA
1 CTATGAAATTTCGATAATCACACTATGAAATTTTGATAACCTCT
* * *
10573 CTTTGAAATTTTGTTAA-CAACACTATGAAATTTTGATAATCCGATCT
1 CTATGAAATTTCGATAATC-ACACTATGAAATTTTGATAA-CC--TCT
* *
10620 CTATGAAATTTCGATAATCACTCTATGAGA-TTTGATAACCT-T
1 CTATGAAATTTCGATAATCACACTATGAAATTTTGATAACCTCT
*
10662 CTATCAAATTT
1 CTATGAAATTT
10673 TGGTACTCCT
Statistics
Matches: 147, Mismatches: 35, Indels: 14
0.75 0.18 0.07
Matches are distributed among these distances:
42 11 0.07
43 7 0.05
44 91 0.62
45 4 0.03
46 8 0.05
47 25 0.17
48 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (44 bp):
CTATGAAATTTCGATAATCACACTATGAAATTTTGATAACCTCT
Found at i:10582 original size:66 final size:65
Alignment explanation
Indices: 10485--10613 Score: 161
Period size: 66 Copynumber: 2.0 Consensus size: 65
10475 GATAACCTCT
* ** *
10485 TTATGAAATTTTGATAACCTCTTTACAAAATTTTGTTGACCCCTCTATGAAATTTCGATAATCAC
1 TTATGAAATTTTGATAACCTCTTTA-AAAATTTTGTTAACAACACTATGAAATTTCGATAATCAC
10550 A
65 A
* * *
10551 TTATGCAATTTTGATAACCTCACTTT-GAAATTTTGTTAACAACACTATGAAATTTTGATAATC
1 TTATGAAATTTTGATAACCT--CTTTAAAAATTTTGTTAACAACACTATGAAATTTCGATAATC
10614 CGATCTCTAT
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
66 50 0.93
68 4 0.07
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.40
Consensus pattern (65 bp):
TTATGAAATTTTGATAACCTCTTTAAAAATTTTGTTAACAACACTATGAAATTTCGATAATCACA
Found at i:10646 original size:22 final size:22
Alignment explanation
Indices: 10441--10674 Score: 126
Period size: 22 Copynumber: 10.6 Consensus size: 22
10431 AAAAATACCA
10441 CTATGAAATTTTTG-TAATCACAT
1 CTATGAAA-TTTTGATAATCAC-T
* * * *
10464 -TTTGAAAATTTGATAACCTCT
1 CTATGAAATTTTGATAATCACT
* * *
10485 TTATGAAATTTTGATAACCTCT
1 CTATGAAATTTTGATAATCACT
* ** * * * *
10507 TTACAAAATTTTGTTGACCCCT
1 CTATGAAATTTTGATAATCACT
*
10529 CTATGAAATTTCGATAATCACAT
1 CTATGAAATTTTGATAATCAC-T
*
10552 -TATGCAATTTTGATAACCTCACT
1 CTATGAAATTTTGATAA--TCACT
* *
10575 -T-TGAAATTTTGTTAA-CAACA
1 CTATGAAATTTTGATAATC-ACT
10595 CTATGAAATTTTGATAATCCGATCT
1 CTATGAAATTTTGATAAT-C-A-CT
*
10620 CTATGAAATTTCGATAATCACT
1 CTATGAAATTTTGATAATCACT
*
10642 CTATGAGA-TTTGATAA-C-CTT
1 CTATGAAATTTTGATAATCAC-T
*
10662 CTATCAAATTTTG
1 CTATGAAATTTTG
10675 GTACTCCTTA
Statistics
Matches: 166, Mismatches: 32, Indels: 28
0.73 0.14 0.12
Matches are distributed among these distances:
19 2 0.01
20 10 0.06
21 17 0.10
22 108 0.65
23 4 0.02
24 7 0.04
25 18 0.11
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (22 bp):
CTATGAAATTTTGATAATCACT
Found at i:10726 original size:22 final size:21
Alignment explanation
Indices: 10697--10834 Score: 84
Period size: 22 Copynumber: 6.3 Consensus size: 21
10687 AAATTGAGAC
10697 TTTT-ATAACCTTCATATGAAA
1 TTTTGATAACC-TCATATGAAA
* *
10718 TTTTGATAACCACATTATAAAA
1 TTTTGATAACCTCA-TATGAAA
* **
10740 TTTTGATAACCCCCCCATGAAA
1 TTTTGATAA-CCTCATATGAAA
* *
10762 TATT-AGTAACCTCCTAATGAAA
1 TTTTGA-TAACCTCAT-ATGAAA
* *
10784 TTTTGTTAACCGCACTATGAAA
1 TTTTGATAACCTCA-TATGAAA
* *
10806 TTCTT-ATAACCTCGCTATGACA
1 TT-TTGATAACCTC-ATATGAAA
10828 TTTTGAT
1 TTTTGAT
10835 GGCTAAATGC
Statistics
Matches: 90, Mismatches: 17, Indels: 19
0.71 0.13 0.15
Matches are distributed among these distances:
21 13 0.14
22 71 0.79
23 6 0.07
ACGTcount: A:0.35, C:0.20, G:0.09, T:0.37
Consensus pattern (21 bp):
TTTTGATAACCTCATATGAAA
Found at i:10785 original size:44 final size:44
Alignment explanation
Indices: 10737--10834 Score: 110
Period size: 44 Copynumber: 2.2 Consensus size: 44
10727 CCACATTATA
*
10737 AAATTTTGATAACCCCCCCATGAAA-TATTAGTAACCTC-CTAATG
1 AAATTTTGATAACCCCACCATGAAATTATTA-TAACCTCGCT-ATG
* * * *
10781 AAATTTTGTTAACCGCACTATGAAATTCTTATAACCTCGCTATG
1 AAATTTTGATAACCCCACCATGAAATTATTATAACCTCGCTATG
*
10825 ACATTTTGAT
1 AAATTTTGAT
10835 GGCTAAATGC
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
44 39 0.87
45 6 0.13
ACGTcount: A:0.34, C:0.21, G:0.10, T:0.35
Consensus pattern (44 bp):
AAATTTTGATAACCCCACCATGAAATTATTATAACCTCGCTATG
Found at i:11039 original size:12 final size:12
Alignment explanation
Indices: 11012--11085 Score: 62
Period size: 12 Copynumber: 6.2 Consensus size: 12
11002 CCTGACGTGG
11012 CTTTT-TTTTTC
1 CTTTTCTTTTTC
* *
11023 ATTTTCATTTTC
1 CTTTTCTTTTTC
*
11035 CTTTTCTTCTTTT
1 CTTTTCTT-TTTC
*
11048 CTATTTCTTTTCC
1 CT-TTTCTTTTTC
*
11061 CTTTTCTTTTTT
1 CTTTTCTTTTTC
*
11073 C-TTTCTATTTC
1 CTTTTCTTTTTC
11084 CT
1 CT
11086 ACCCAAAACC
Statistics
Matches: 48, Mismatches: 11, Indels: 7
0.73 0.17 0.11
Matches are distributed among these distances:
11 13 0.27
12 20 0.42
13 9 0.19
14 6 0.12
ACGTcount: A:0.05, C:0.23, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTCTTTTTC
Found at i:11072 original size:25 final size:26
Alignment explanation
Indices: 11016--11074 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
11006 ACGTGGCTTT
11016 TTTTTTC-ATTTTCATTTTCCTTTTC
1 TTTTTTCTATTTTCATTTTCCTTTTC
11041 TTCTTTTCTA-TTTC-TTTTCCCTTTTC
1 TT-TTTTCTATTTTCATTTT-CCTTTTC
11067 TTTTTTCT
1 TTTTTTCT
11075 TTCTATTTCC
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
25 12 0.39
26 18 0.58
27 1 0.03
ACGTcount: A:0.05, C:0.22, G:0.00, T:0.73
Consensus pattern (26 bp):
TTTTTTCTATTTTCATTTTCCTTTTC
Found at i:12635 original size:21 final size:22
Alignment explanation
Indices: 12609--12655 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
12599 GCTATATCAA
*
12609 GTCTATGTGGC-TAAAAAAATG
1 GTCTATGTGGCAAAAAAAAATG
12630 GTCTATGTGGCAAAAAAAAATG
1 GTCTATGTGGCAAAAAAAAATG
12652 GTCT
1 GTCT
12656 CTGACTCGCG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.28
Consensus pattern (22 bp):
GTCTATGTGGCAAAAAAAAATG
Found at i:13700 original size:37 final size:37
Alignment explanation
Indices: 13652--13728 Score: 120
Period size: 37 Copynumber: 2.1 Consensus size: 37
13642 CGTTGAAGAT
13652 AAAGACAAAAAGCAAAATTAAATACAACGATTGGAAAC
1 AAAGACAAAAAGCAAAATTAAATACAACG-TTGGAAAC
**
13690 AAAGAC-AAAAGCAAAATTAAATAGGACGTTGGAAAC
1 AAAGACAAAAAGCAAAATTAAATACAACGTTGGAAAC
13726 AAA
1 AAA
13729 AAGTCAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 11 0.30
37 20 0.54
38 6 0.16
ACGTcount: A:0.60, C:0.12, G:0.16, T:0.13
Consensus pattern (37 bp):
AAAGACAAAAAGCAAAATTAAATACAACGTTGGAAAC
Found at i:19578 original size:27 final size:26
Alignment explanation
Indices: 19534--19591 Score: 89
Period size: 27 Copynumber: 2.2 Consensus size: 26
19524 CAAACCCTCC
* *
19534 CAATCTCACTCTTTCAATCTCGTAGT
1 CAATCTCACTCTCTCAATCTCGTACT
19560 CAATCTCACCTCTCTCAATCTCGTACT
1 CAATCTCA-CTCTCTCAATCTCGTACT
19587 CAATC
1 CAATC
19592 AACGTAGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.24, C:0.36, G:0.05, T:0.34
Consensus pattern (26 bp):
CAATCTCACTCTCTCAATCTCGTACT
Found at i:22754 original size:6 final size:6
Alignment explanation
Indices: 22743--22772 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
22733 AAAGTGAGGA
22743 CGCCTC CGCCTC CGCCTC CGCCTC CGCCTC
1 CGCCTC CGCCTC CGCCTC CGCCTC CGCCTC
22773 AGGTTATGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.67, G:0.17, T:0.17
Consensus pattern (6 bp):
CGCCTC
Found at i:26835 original size:67 final size:67
Alignment explanation
Indices: 26727--26860 Score: 259
Period size: 67 Copynumber: 2.0 Consensus size: 67
26717 CAAAAGACTA
*
26727 TACAACTGTCTCCAAGATGCCCCCCTAAGGATTACTTTATGCACTTCTATCCAATTACTCATCAA
1 TACAACTATCTCCAAGATGCCCCCCTAAGGATTACTTTATGCACTTCTATCCAATTACTCATCAA
26792 GG
66 GG
26794 TACAACTATCTCCAAGATGCCCCCCTAAGGATTACTTTATGCACTTCTATCCAATTACTCATCAA
1 TACAACTATCTCCAAGATGCCCCCCTAAGGATTACTTTATGCACTTCTATCCAATTACTCATCAA
26859 GG
66 GG
26861 ATGTTAAAAG
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.29, C:0.30, G:0.11, T:0.30
Consensus pattern (67 bp):
TACAACTATCTCCAAGATGCCCCCCTAAGGATTACTTTATGCACTTCTATCCAATTACTCATCAA
GG
Found at i:30781 original size:21 final size:21
Alignment explanation
Indices: 30757--30820 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
30747 GCTGTTCTAA
30757 TAATCTCATCTGTACAGTACC
1 TAATCTCATCTGTACAGTACC
* * *
30778 TAATTTGATCTATACAGTA--
1 TAATCTCATCTGTACAGTACC
* *
30797 TAATCTCATCTGTAAACTACC
1 TAATCTCATCTGTACAGTACC
30818 TAA
1 TAA
30821 ACAGTGTCAA
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
19 14 0.42
21 19 0.58
ACGTcount: A:0.34, C:0.22, G:0.08, T:0.36
Consensus pattern (21 bp):
TAATCTCATCTGTACAGTACC
Found at i:35873 original size:16 final size:16
Alignment explanation
Indices: 35852--35938 Score: 131
Period size: 16 Copynumber: 5.5 Consensus size: 16
35842 GGCAATTGGG
35852 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
** *
35868 CGGGTTCGAATAATTT
1 CGGGTTCGGGTATTTT
*
35884 CGGGTTCGGATATTTT
1 CGGGTTCGGGTATTTT
35900 CGGGTTCGGGTA-TTT
1 CGGGTTCGGGTATTTT
35915 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
35931 CGGGTTCG
1 CGGGTTCG
35939 TGCTCGAGTC
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
15 15 0.23
16 49 0.77
ACGTcount: A:0.10, C:0.14, G:0.36, T:0.40
Consensus pattern (16 bp):
CGGGTTCGGGTATTTT
Found at i:35907 original size:6 final size:6
Alignment explanation
Indices: 35898--35983 Score: 50
Period size: 6 Copynumber: 13.5 Consensus size: 6
35888 TTCGGATATT
* * *
35898 TTCGGG TTCGGG TATTTCGGG TTCGGG TATTTTCGGG TTCGTG CTCGAG
1 TTCGGG TTCGGG ---TTCGGG TTCGGG ---T-TCGGG TTCGGG TTCGGG
**
35947 -TCGGG TTCGGG TTCGGG CCCGGG -TCGGG TTCGGG TTC
1 TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTC
35984 ATTTTCGATA
Statistics
Matches: 64, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
5 8 0.12
6 43 0.67
7 1 0.02
9 7 0.11
10 5 0.08
ACGTcount: A:0.03, C:0.20, G:0.43, T:0.34
Consensus pattern (6 bp):
TTCGGG
Found at i:35918 original size:31 final size:32
Alignment explanation
Indices: 35852--35938 Score: 140
Period size: 31 Copynumber: 2.8 Consensus size: 32
35842 GGCAATTGGG
35852 CGGGTTCGGGTATTTTCGGGTTCGAATAATTT
1 CGGGTTCGGGTATTTTCGGGTTCGAATAATTT
* **
35884 CGGGTTCGGATATTTTCGGGTTCGGGT-ATTT
1 CGGGTTCGGGTATTTTCGGGTTCGAATAATTT
35915 CGGGTTCGGGTATTTTCGGGTTCG
1 CGGGTTCGGGTATTTTCGGGTTCG
35939 TGCTCGAGTC
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
31 27 0.53
32 24 0.47
ACGTcount: A:0.10, C:0.14, G:0.36, T:0.40
Consensus pattern (32 bp):
CGGGTTCGGGTATTTTCGGGTTCGAATAATTT
Found at i:35951 original size:48 final size:48
Alignment explanation
Indices: 35852--35958 Score: 126
Period size: 48 Copynumber: 2.2 Consensus size: 48
35842 GGCAATTGGG
***
35852 CGGGTTCGGGTATTTTCGGGTTCGAATAATTTCGGGTTCGGATATTTT
1 CGGGTTCGGGTATTTTCGGGTTCGAATAATTTCGGGTTCGGATAGAGT
** * * *
35900 CGGGTTCGGGTA-TTTCGGGTTCGGGTATTTTCGGGTTCGTGCTCGAGT
1 CGGGTTCGGGTATTTTCGGGTTCGAATAATTTCGGGTTCG-GATAGAGT
35948 CGGGTTCGGGT
1 CGGGTTCGGGT
35959 TCGGGCCCGG
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
47 24 0.48
48 26 0.52
ACGTcount: A:0.09, C:0.15, G:0.37, T:0.38
Consensus pattern (48 bp):
CGGGTTCGGGTATTTTCGGGTTCGAATAATTTCGGGTTCGGATAGAGT
Found at i:35958 original size:23 final size:23
Alignment explanation
Indices: 35929--35983 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
35919 TTCGGGTATT
* *
35929 TTCGGGTTCGTGCTCGAGTCGGG
1 TTCGGGTTCGGGCCCGAGTCGGG
*
35952 TTCGGGTTCGGGCCCGGGTCGGG
1 TTCGGGTTCGGGCCCGAGTCGGG
35975 TTCGGGTTC
1 TTCGGGTTC
35984 ATTTTCGATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.02, C:0.24, G:0.45, T:0.29
Consensus pattern (23 bp):
TTCGGGTTCGGGCCCGAGTCGGG
Found at i:36730 original size:5 final size:6
Alignment explanation
Indices: 36714--36789 Score: 50
Period size: 6 Copynumber: 11.8 Consensus size: 6
36704 TATTTTGATC
36714 TCGGGT TCGGG- TCGGGT TCGGGT TCGAGTTGT CTCGGGT TCGGGTATTT
1 TCGGGT TCGGGT TCGGGT TCGGGT TCG-G--GT -TCGGGT TCGGG----T
*
36763 TCGGGT TCGGGT ACGGG- -CGGGT TCGGG
1 TCGGGT TCGGGT TCGGGT TCGGGT TCGGG
36790 ACGTTGACTT
Statistics
Matches: 58, Mismatches: 1, Indels: 22
0.72 0.01 0.27
Matches are distributed among these distances:
4 4 0.07
5 5 0.09
6 34 0.59
7 3 0.05
9 3 0.05
10 9 0.16
ACGTcount: A:0.04, C:0.17, G:0.47, T:0.32
Consensus pattern (6 bp):
TCGGGT
Found at i:46223 original size:18 final size:20
Alignment explanation
Indices: 46187--46224 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
46177 TGTACAGACT
46187 AATTAGTAGGGATTTGACAA
1 AATTAGTAGGGATTTGACAA
46207 AATTAG-AGGGA-TTGACAA
1 AATTAGTAGGGATTTGACAA
46225 CCTAATTGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
19 5 0.28
20 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.26, T:0.26
Consensus pattern (20 bp):
AATTAGTAGGGATTTGACAA
Done.