Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009443.1 Corchorus capsularis cultivar CVL-1 contig09464, 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: 46912
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:9023 original size:71 final size:71
Alignment explanation
Indices: 8945--9113 Score: 268
Period size: 71 Copynumber: 2.4 Consensus size: 71
8935 ATTAAGAACA
* *
8945 AATTAAGAAGAGTGAAATCTTAATTCAGGGTAATTAAGAAAAGAAAGTGCAGTCAGGGTCCTAAT
1 AATTAAGAAGAGTGAAATCTTAATTCAGGGTAATTAAGAAAAGAAAGTACAGTCAAGGTCCTAAT
9010 TTGGAT
66 TTGGAT
* *
9016 AATTAAGAAGAGT-AAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACAGTCAATGTCTTAA
1 AATTAAGAAGAGTGAAA-TCTTAATTCAGGGTAATTAAGAAAAGAAAGTACAGTCAAGGTCCTAA
9080 TTTGGAT
65 TTTGGAT
* *
9087 AATCAAGAAGAGTGAAGTCTTAATTCA
1 AATTAAGAAGAGTGAAATCTTAATTCA
9114 TAGAAATTAA
Statistics
Matches: 90, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
70 3 0.03
71 85 0.94
72 2 0.02
ACGTcount: A:0.43, C:0.08, G:0.21, T:0.28
Consensus pattern (71 bp):
AATTAAGAAGAGTGAAATCTTAATTCAGGGTAATTAAGAAAAGAAAGTACAGTCAAGGTCCTAAT
TTGGAT
Found at i:9277 original size:40 final size:40
Alignment explanation
Indices: 9231--9634 Score: 521
Period size: 40 Copynumber: 10.6 Consensus size: 40
9221 TTAGAGCGCA
9231 GACTTAATTTCAAGAAAGGAAATTAGGTAAAGAAAAGACT
1 GACTTAATTTCAAGAAAGGAAATTAGGTAAAGAAAAGACT
9271 -AGCTTAATTTCAAGAAAGGAAATTAGGTAAAGAAAAGACT
1 GA-CTTAATTTCAAGAAAGGAAATTAGGTAAAGAAAAGACT
*
9311 GACTTAATTTC----AAGGAAATTAGGTAAAG-ATAGACT
1 GACTTAATTTCAAGAAAGGAAATTAGGTAAAGAAAAGACT
* * *
9346 GGCTTAATTTC----AAGGAAATTAAGT-AA-AACAGACT
1 GACTTAATTTCAAGAAAGGAAATTAGGTAAAGAAAAGACT
*
9380 GACTTAATTTCAAGGAAGGAAATTAGGT-AA-AAAA-ACT
1 GACTTAATTTCAAGAAAGGAAATTAGGTAAAGAAAAGACT
* *
9417 GGCTTAATTTCAAGAAAGGAAATTAGGTAAAGAAGAGACT
1 GACTTAATTTCAAGAAAGGAAATTAGGTAAAGAAAAGACT
* *
9457 GACTTAATTTCAAGGAAGGAAATTAAGT--AGAAAAGACT
1 GACTTAATTTCAAGAAAGGAAATTAGGTAAAGAAAAGACT
*
9495 GGCTTAATTTCAAGAAAGGAAATTAGGTAAAGAAAAGACT
1 GACTTAATTTCAAGAAAGGAAATTAGGTAAAGAAAAGACT
9535 GACTTAATTTC----AAGGAAATTAGGTAAAG-AAAGACT
1 GACTTAATTTCAAGAAAGGAAATTAGGTAAAGAAAAGACT
*
9570 GACTTAATTTCAAGGAAGGAAATTAGGTAAA-AGAAAGACT
1 GACTTAATTTCAAGAAAGGAAATTAGGTAAAGA-AAAGACT
*
9610 GACTTAATTTCAAGGAAGGAAATTA
1 GACTTAATTTCAAGAAAGGAAATTA
9635 AGTAGAATAA
Statistics
Matches: 328, Mismatches: 18, Indels: 36
0.86 0.05 0.09
Matches are distributed among these distances:
34 18 0.05
35 46 0.14
36 34 0.10
37 29 0.09
38 53 0.16
39 20 0.06
40 127 0.39
41 1 0.00
ACGTcount: A:0.47, C:0.08, G:0.21, T:0.24
Consensus pattern (40 bp):
GACTTAATTTCAAGAAAGGAAATTAGGTAAAGAAAAGACT
Found at i:9502 original size:115 final size:114
Alignment explanation
Indices: 9231--9634 Score: 567
Period size: 115 Copynumber: 3.6 Consensus size: 114
9221 TTAGAGCGCA
* *
9231 GACTTAATTTCAAGAAAGGAAATTAGGTAAAGAAAAGACT-AGCTTAATTTCAAGAAAGGAAATT
1 GACTTAATTTCAAGGAAGGAAATTAAGT-AAGAAAAGACTGA-CTTAATTTCAAGAAAGGAAATT
*
9295 AGGTAAAGAAAAGACTGACTTAATTTCAAGGAAATTAGGTAAAGATAGACT
64 AGGTAAAGAAAAGACTGACTTAATTTCAAGGAAATTAGGTAAAGAAAGACT
* * *
9346 GGCTTAATTTC----AAGGAAATTAAGTAA-AACAGACTGACTTAATTTCAAGGAAGGAAATTAG
1 GACTTAATTTCAAGGAAGGAAATTAAGTAAGAAAAGACTGACTTAATTTCAAGAAAGGAAATTAG
*
9406 GT-AA-AAAA-ACTGGCTTAATTTCAAGAAAGGAAATTAGGTAAAGAAGAGACT
66 GTAAAGAAAAGACTGACTTAATTTC----AAGGAAATTAGGTAAAGAA-AGACT
*
9457 GACTTAATTTCAAGGAAGGAAATTAAGT-AGAAAAGACTGGCTTAATTTCAAGAAAGGAAATTAG
1 GACTTAATTTCAAGGAAGGAAATTAAGTAAGAAAAGACTGACTTAATTTCAAGAAAGGAAATTAG
9521 GTAAAGAAAAGACTGACTTAATTTCAAGGAAATTAGGTAAAGAAAGACT
66 GTAAAGAAAAGACTGACTTAATTTCAAGGAAATTAGGTAAAGAAAGACT
* * *
9570 GACTTAATTTCAAGGAAGGAAATTAGGTAAAAGAAAGACTGACTTAATTTCAAGGAAGGAAATTA
1 GACTTAATTTCAAGGAAGGAAATTAAGTAAGA-AAAGACTGACTTAATTTCAAGAAAGGAAATTA
9635 AGTAGAATAA
Statistics
Matches: 258, Mismatches: 15, Indels: 32
0.85 0.05 0.10
Matches are distributed among these distances:
106 13 0.05
107 4 0.02
108 2 0.01
109 32 0.12
110 21 0.08
111 27 0.10
113 32 0.12
114 22 0.09
115 86 0.33
116 2 0.01
117 4 0.02
118 13 0.05
ACGTcount: A:0.47, C:0.08, G:0.21, T:0.24
Consensus pattern (114 bp):
GACTTAATTTCAAGGAAGGAAATTAAGTAAGAAAAGACTGACTTAATTTCAAGAAAGGAAATTAG
GTAAAGAAAAGACTGACTTAATTTCAAGGAAATTAGGTAAAGAAAGACT
Found at i:9607 original size:75 final size:74
Alignment explanation
Indices: 9246--9626 Score: 517
Period size: 75 Copynumber: 5.1 Consensus size: 74
9236 AATTTCAAGA
*
9246 AAGGAAATTAGGTAAAGAAAAGACTAGCTTAATTTCAAGAAAGGAAATTAGGTAAAGAAAAGACT
1 AAGGAAATTAGGTAAAG-AAAGACTGGCTTAATTTCAAGAAAGGAAATTAGGTAAAG-AAAGACT
9311 GACTTAATTTC
64 GACTTAATTTC
* * *
9322 AAGGAAATTAGGTAAAGATAGACTGGCTTAATTTC----AAGGAAATTAAGTAAA-ACAGACTGA
1 AAGGAAATTAGGTAAAGAAAGACTGGCTTAATTTCAAGAAAGGAAATTAGGTAAAGAAAGACTGA
9382 CTTAATTTC
66 CTTAATTTC
9391 AAGGAAGGAAATTAGGTAAA-AAA-ACTGGCTTAATTTCAAGAAAGGAAATTAGGTAAAGAAGAG
1 ----AAGGAAATTAGGTAAAGAAAGACTGGCTTAATTTCAAGAAAGGAAATTAGGTAAAGAA-AG
9454 ACTGACTTAATTTC
61 ACTGACTTAATTTC
* *
9468 AAGGAAGGAAATTAAGTAGA-AAAGACTGGCTTAATTTCAAGAAAGGAAATTAGGTAAAGAAAAG
1 ----AAGGAAATTAGGTAAAGAAAGACTGGCTTAATTTCAAGAAAGGAAATTAGGTAAAG-AAAG
9532 ACTGACTTAATTTC
61 ACTGACTTAATTTC
* *
9546 AAGGAAATTAGGTAAAGAAAGACTGACTTAATTTCAAGGAAGGAAATTAGGTAAAAGAAAGACTG
1 AAGGAAATTAGGTAAAGAAAGACTGGCTTAATTTCAAGAAAGGAAATTAGGT-AAAGAAAGACTG
9611 ACTTAATTTC
65 ACTTAATTTC
9621 AAGGAA
1 AAGGAA
9627 GGAAATTAAG
Statistics
Matches: 278, Mismatches: 13, Indels: 29
0.87 0.04 0.09
Matches are distributed among these distances:
69 17 0.06
71 29 0.10
72 2 0.01
73 16 0.06
74 14 0.05
75 88 0.32
76 22 0.08
77 37 0.13
78 51 0.18
79 2 0.01
ACGTcount: A:0.47, C:0.08, G:0.21, T:0.24
Consensus pattern (74 bp):
AAGGAAATTAGGTAAAGAAAGACTGGCTTAATTTCAAGAAAGGAAATTAGGTAAAGAAAGACTGA
CTTAATTTC
Found at i:9740 original size:35 final size:35
Alignment explanation
Indices: 9700--9777 Score: 138
Period size: 35 Copynumber: 2.2 Consensus size: 35
9690 ATTCAGGGTA
* *
9700 ATTAAGTGGAATAAAAGAACTTAATCTAAAAAGAG
1 ATTAAGTAGAATAAAAGAACTTAATCTAAAAAAAG
9735 ATTAAGTAGAATAAAAGAACTTAATCTAAAAAAAG
1 ATTAAGTAGAATAAAAGAACTTAATCTAAAAAAAG
9770 ATTAAGTA
1 ATTAAGTA
9778 AAACAATAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.56, C:0.05, G:0.14, T:0.24
Consensus pattern (35 bp):
ATTAAGTAGAATAAAAGAACTTAATCTAAAAAAAG
Found at i:9758 original size:19 final size:18
Alignment explanation
Indices: 9701--9758 Score: 50
Period size: 19 Copynumber: 3.2 Consensus size: 18
9691 TTCAGGGTAA
9701 TTAAGTGGAATAAAAGAAC
1 TTAAGT-GAATAAAAGAAC
**
9720 TTAA-TCTA-AAAAGAGA-
1 TTAAGTGAATAAAAGA-AC
9736 TTAAGTAGAATAAAAGAAC
1 TTAAGT-GAATAAAAGAAC
9755 TTAA
1 TTAA
9759 TCTAAAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 10
0.68 0.09 0.23
Matches are distributed among these distances:
16 10 0.33
17 3 0.10
18 3 0.10
19 14 0.47
ACGTcount: A:0.55, C:0.05, G:0.16, T:0.24
Consensus pattern (18 bp):
TTAAGTGAATAAAAGAAC
Found at i:11157 original size:26 final size:27
Alignment explanation
Indices: 11128--11199 Score: 119
Period size: 27 Copynumber: 2.7 Consensus size: 27
11118 AAGTAGACTT
11128 AAAATGACCAAAATGCCCCTA-GTGCA
1 AAAATGACCAAAATGCCCCTATGTGCA
*
11154 AAAATGACCAAAATGCCCCTATGTGTA
1 AAAATGACCAAAATGCCCCTATGTGCA
*
11181 AAGATGACCAAAATGCCCC
1 AAAATGACCAAAATGCCCC
11200 CAAGGTGACC
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
26 21 0.49
27 22 0.51
ACGTcount: A:0.42, C:0.26, G:0.15, T:0.17
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTATGTGCA
Found at i:11195 original size:27 final size:25
Alignment explanation
Indices: 11127--11199 Score: 110
Period size: 26 Copynumber: 2.8 Consensus size: 25
11117 AAAGTAGACT
11127 TAAAATGACCAAAATGCCCCTAGTG
1 TAAAATGACCAAAATGCCCCTAGTG
*
11152 CAAAAATGACCAAAATGCCCCTATGTG
1 -TAAAATGACCAAAATGCCCCTA-GTG
11179 TAAAGATGACCAAAATGCCCC
1 TAAA-ATGACCAAAATGCCCC
11200 CAAGGTGACC
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
26 24 0.56
27 19 0.44
ACGTcount: A:0.41, C:0.26, G:0.15, T:0.18
Consensus pattern (25 bp):
TAAAATGACCAAAATGCCCCTAGTG
Found at i:14644 original size:13 final size:13
Alignment explanation
Indices: 14626--14652 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
14616 AATTATAAAT
14626 TAAATTAAAGTTA
1 TAAATTAAAGTTA
14639 TAAATTAAAGTTA
1 TAAATTAAAGTTA
14652 T
1 T
14653 GGTGTCATCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (13 bp):
TAAATTAAAGTTA
Found at i:14758 original size:20 final size:21
Alignment explanation
Indices: 14733--14774 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
14723 TCTTGGGTTC
14733 TACTCTCACGGAA-TGTGAGT
1 TACTCTCACGGAATTGTGAGT
*
14753 TACTCTCGCGGAATTGTGAGT
1 TACTCTCACGGAATTGTGAGT
14774 T
1 T
14775 TTCTTTGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.33
Consensus pattern (21 bp):
TACTCTCACGGAATTGTGAGT
Found at i:20254 original size:30 final size:30
Alignment explanation
Indices: 20180--20255 Score: 118
Period size: 29 Copynumber: 2.5 Consensus size: 30
20170 GAGTATGACG
*
20180 AGGAGGAAGATTCTGATCTCTTTGTTTGTGT
1 AGGA-GAAGATTCTGATCTCTTTGTTTGTGA
20211 AGGAG-AGATTCTGATCTCTTTGTTTGTGA
1 AGGAGAAGATTCTGATCTCTTTGTTTGTGA
*
20240 AGGAGAAAATTCTGAT
1 AGGAGAAGATTCTGAT
20256 TTTGTTTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
29 28 0.67
30 10 0.24
31 4 0.10
ACGTcount: A:0.25, C:0.09, G:0.28, T:0.38
Consensus pattern (30 bp):
AGGAGAAGATTCTGATCTCTTTGTTTGTGA
Found at i:23100 original size:24 final size:24
Alignment explanation
Indices: 23064--23110 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
23054 GTTTATGTTA
* *
23064 TTTCCTAGAAGGAGTAGGTTTTAC
1 TTTCCTAGAAGGAATAGGATTTAC
23088 TTTCCTA-ACAGGAATAGGATTTA
1 TTTCCTAGA-AGGAATAGGATTTA
23111 GATTAAGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (24 bp):
TTTCCTAGAAGGAATAGGATTTAC
Found at i:23210 original size:18 final size:18
Alignment explanation
Indices: 23187--23223 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
23177 CAGAAATTAT
23187 TCAGAGGTTATTCAACCC
1 TCAGAGGTTATTCAACCC
23205 TCAGAGGTTATTCAACCC
1 TCAGAGGTTATTCAACCC
23223 T
1 T
23224 AATTATCTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (18 bp):
TCAGAGGTTATTCAACCC
Found at i:25635 original size:74 final size:72
Alignment explanation
Indices: 25498--25635 Score: 188
Period size: 74 Copynumber: 1.9 Consensus size: 72
25488 ACATTGCTCC
* * * *
25498 TAGGGCTACTTGATTGCATCACACGAACAGGAAGAGAGCAAAAATGGTAGGCTTCACTCTTGGGA
1 TAGGGCTACTTGATTGCATCACACGAACAAGAAGAGAGCAAAAATCGCAGGCTTCACACTTGGGA
25563 TCGCTTT
66 TCGCTTT
* *
25570 TAGGGCTACTTGATTGTGCATCACAC-AAGCAAGAAGAGAGCGAAAATCGCAGGCTTCACAGTTG
1 TAGGGCTACTTGA-T-TGCATCACACGAA-CAAGAAGAGAGCAAAAATCGCAGGCTTCACACTTG
25634 GG
63 GG
25636 TTTCTCCTAA
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
72 13 0.23
73 3 0.05
74 41 0.72
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.22
Consensus pattern (72 bp):
TAGGGCTACTTGATTGCATCACACGAACAAGAAGAGAGCAAAAATCGCAGGCTTCACACTTGGGA
TCGCTTT
Found at i:34532 original size:22 final size:22
Alignment explanation
Indices: 34507--34589 Score: 71
Period size: 22 Copynumber: 3.8 Consensus size: 22
34497 TTCAAGAACT
*
34507 TCCCTATGAAATTTTGTTGACC
1 TCCCTATGAAATTTTGATGACC
** *
34529 TCCCTAT-AGAATTTTGAAAACA
1 TCCCTATGA-AATTTTGATGACC
** *
34551 TTACTATAAAATTTTGATGACC
1 TCCCTATGAAATTTTGATGACC
34573 T-CCTAATGAAATTTTGA
1 TCCCT-ATGAAATTTTGA
34590 CCATCCACTT
Statistics
Matches: 47, Mismatches: 11, Indels: 6
0.73 0.17 0.09
Matches are distributed among these distances:
21 3 0.06
22 43 0.91
23 1 0.02
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.39
Consensus pattern (22 bp):
TCCCTATGAAATTTTGATGACC
Found at i:34629 original size:22 final size:22
Alignment explanation
Indices: 34510--34633 Score: 62
Period size: 22 Copynumber: 5.8 Consensus size: 22
34500 AAGAACTTCC
* * * *
34510 CTATGAAATTTTGTTGACCTCC
1 CTATGAAATTTTGATAACCACA
* *
34532 CTAT-AGAATTTTGA-AAACATTA
1 CTATGA-AATTTTGATAACCA-CA
* * *
34554 CTATAAAATTTTGATGACCTC-
1 CTATGAAATTTTGATAACCACA
** *
34575 CTAATGAAATTTTGACCATC-CA
1 CT-ATGAAATTTTGATAACCACA
*
34597 CT-T-AAAGTTTGATAACCACA
1 CTATGAAATTTTGATAACCACA
34617 CTATGAAATTTTGATAA
1 CTATGAAATTTTGATAA
34634 TCTCCATGTG
Statistics
Matches: 74, Mismatches: 19, Indels: 18
0.67 0.17 0.16
Matches are distributed among these distances:
19 10 0.14
20 5 0.07
21 7 0.09
22 49 0.66
23 3 0.04
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.36
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCACA
Found at i:34789 original size:23 final size:23
Alignment explanation
Indices: 34756--34835 Score: 83
Period size: 23 Copynumber: 3.5 Consensus size: 23
34746 ACTCGGTATG
*
34756 AAATTTTGATAAA-CATTCATATA
1 AAATTTTGATAAAGC-TCCATATA
* *
34779 AAGTTTTGATAAAGCTCCCTATA
1 AAATTTTGATAAAGCTCCATATA
* * *
34802 AAATTTTGAT-AACCTCCTTATG
1 AAATTTTGATAAAGCTCCATATA
34824 AAATTTTGATAA
1 AAATTTTGATAA
34836 TCACAAATTT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
22 19 0.40
23 28 0.58
24 1 0.02
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.39
Consensus pattern (23 bp):
AAATTTTGATAAAGCTCCATATA
Found at i:34827 original size:22 final size:21
Alignment explanation
Indices: 34752--35622 Score: 232
Period size: 22 Copynumber: 39.8 Consensus size: 21
34742 ATGCACTCGG
* *
34752 TATGAAATTTTGATAAACATTCA
1 TATGAAATTTTGAT-AAC-CTCC
*
34775 TAT-AAAGTTTTGATAAAGCTCCC
1 TATGAAA-TTTTGAT-AACCT-CC
*
34798 TATAAAATTTTGATAACCTCC
1 TATGAAATTTTGATAACCTCC
34819 TTATGAAATTTTGATAA--T-C
1 -TATGAAATTTTGATAACCTCC
*
34838 -A-CAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCT-CC
* * * *
34858 TATG-ATTTTTCGATCACTTCAT
1 TATGAAATTTT-GATAACCTC-C
* * * *
34880 TGTGAAA-TTTGTTAACTTCTA
1 TATGAAATTTTGATAACCTC-C
34901 TATGAAATTTTGATAACC-CC
1 TATGAAATTTTGATAACCTCC
* * *
34921 TATAAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT--CC
*
34943 TATGAAATTTTGATAATCCCCC
1 TATGAAATTTTGATAA-CCTCC
* * *
34965 TTTGAAATTTTAATAACCTTCA
1 TATGAAATTTTGATAACC-TCC
* * *
34987 TACGAAATTTTGGTAACCACAC
1 TATGAAATTTTGATAACCTC-C
* * *
35009 AAATGTAATTTTGAAAACCTCCC
1 -TATGAAATTTTGATAACCT-CC
* **
35032 TTTG-AA--TT-ACCACACT-C
1 TATGAAATTTTGATAAC-CTCC
* *** *
35049 TA--AATTTTTGATAATAACAT
1 TATGAAATTTTGATAACCTC-C
*
35069 TATGAAATTTCGATAACCTCCC
1 TATGAAATTTTGATAACCT-CC
**
35091 TATGAAATTTCAATAACCTTCC
1 TATGAAATTTTGATAACC-TCC
* * *
35113 AATGAAATTTCGCTAACCTCTC
1 TATGAAATTTTGATAACCTC-C
* *
35135 TATGAAATTTTGATAATCATAC
1 TATGAAATTTTGATAA-CCTCC
35157 TATGAAA-TTTGA-AACCTCC
1 TATGAAATTTTGATAACCTCC
* **
35176 -ATGTAAAATTTTAATAA-C-AA
1 TATG--AAATTTTGATAACCTCC
*
35196 TATGAAAAATTTTCATAACCTCAC
1 TATG--AAATTTTGATAACCTC-C
** *
35220 TGGGAAATTTCGATAACCTCGC
1 TATGAAATTTTGATAACCTC-C
* * *
35242 TTTAAAATTTTGATAACATTCC
1 TATGAAATTTTGATAAC-CTCC
* *
35264 TATGAAATTTTGGTAATCTGATCTC
1 TATGAAATTTTGATAA-C--CTC-C
* * *
35289 TATGAATTTTTGACCAA-CTACTT
1 TATGAAATTTTGA-TAACCT-C-C
* ** *
35312 TATGAGATTTTGATTGCTTCC
1 TATGAAATTTTGATAACCTCC
* *
35333 TGATGAAATTTTGATAACTATAC
1 T-ATGAAATTTTGATAAC-CTCC
* **
35356 TAT-AAAGTTTTAATAACCTTTG
1 TATGAAA-TTTTGATAACC-TCC
* * *
35378 TATGAAATTTAGATTTTTCTAACATTAC
1 TATGAAATTTTGA------TAAC-CTCC
* *
35406 TATGAAATTTTGGTAACCACAC
1 TATGAAATTTTGATAACCTC-C
*
35428 TATGACATCTTTGATAACCTCC
1 TATGAAAT-TTTGATAACCTCC
* *
35450 TTATAAAATTTTGATAACCACAC
1 -TATGAAATTTTGATAACCTC-C
35473 TATGAAATTTTGATAACCTCGC
1 TATGAAATTTTGATAACCTC-C
*
35495 TATGGAATTTTGATAACCTCCCTAGC
1 TATGAAATTTTGATAACCT--C---C
35521 TATGAAATTTTGATAA----C
1 TATGAAATTTTGATAACCTCC
* *
35538 TATAAAATTTTAATAACCTAATCC
1 TATGAAATTTTGATAACC---TCC
* *
35562 ATATGAAATTTTGAGAACCACAC
1 -TATGAAATTTTGATAACCTC-C
* *
35585 TGTGAAATTTTGATAATCTTCC
1 TATGAAATTTTGATAA-CCTCC
*
35607 TATGAAATTTCGATAA
1 TATGAAATTTTGATAA
35623 TCACACAATA
Statistics
Matches: 618, Mismatches: 149, Indels: 163
0.66 0.16 0.18
Matches are distributed among these distances:
16 13 0.02
17 18 0.03
18 9 0.01
19 13 0.02
20 21 0.03
21 59 0.10
22 324 0.52
23 88 0.14
24 11 0.02
25 27 0.04
26 19 0.03
28 16 0.03
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.38
Consensus pattern (21 bp):
TATGAAATTTTGATAACCTCC
Found at i:35474 original size:45 final size:44
Alignment explanation
Indices: 35405--35537 Score: 151
Period size: 45 Copynumber: 2.9 Consensus size: 44
35395 TCTAACATTA
* * *
35405 CTATGAAATTTTGGTAACCACACTATGACATCTTTGATAACCTC-
1 CTATAAAATTTTGATAACCACACTATGAAAT-TTTGATAACCTCG
35449 CTTATAAAATTTTGATAACCACACTATGAAATTTTGATAACCTCG
1 C-TATAAAATTTTGATAACCACACTATGAAATTTTGATAACCTCG
** *
35494 CTATGGAATTTTGATAACCTCCCTAGCTATGAAATTTTGATAAC
1 CTATAAAATTTTGATAA-C-CAC-A-CTATGAAATTTTGATAAC
35538 TATAAAATTT
Statistics
Matches: 77, Mismatches: 6, Indels: 8
0.85 0.07 0.09
Matches are distributed among these distances:
44 27 0.35
45 29 0.38
46 2 0.03
47 1 0.01
48 18 0.23
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.35
Consensus pattern (44 bp):
CTATAAAATTTTGATAACCACACTATGAAATTTTGATAACCTCG
Found at i:35545 original size:17 final size:17
Alignment explanation
Indices: 35520--35554 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
35510 ACCTCCCTAG
* *
35520 CTATGAAATTTTGATAA
1 CTATAAAATTTTAATAA
35537 CTATAAAATTTTAATAA
1 CTATAAAATTTTAATAA
35554 C
1 C
35555 CTAATCCATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.40
Consensus pattern (17 bp):
CTATAAAATTTTAATAA
Done.