Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006995.1 Corchorus capsularis cultivar CVL-1 contig07016, 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: 50235
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.33
Found at i:5304 original size:13 final size:13
Alignment explanation
Indices: 5281--5321 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
5271 TGCTTTATAA
5281 TTATT-GTTTGCT
1 TTATTAGTTTGCT
5293 TTATTAGTTTGCT
1 TTATTAGTTTGCT
* *
5306 TTATTAATCTGCT
1 TTATTAGTTTGCT
5319 TTA
1 TTA
5322 GATTTAGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
12 5 0.19
13 21 0.81
ACGTcount: A:0.17, C:0.10, G:0.12, T:0.61
Consensus pattern (13 bp):
TTATTAGTTTGCT
Found at i:5868 original size:59 final size:59
Alignment explanation
Indices: 5805--5926 Score: 244
Period size: 59 Copynumber: 2.1 Consensus size: 59
5795 GCTTGGGATA
5805 TGATTTTGAAATGCAGTATCATGTAGTCAAAAGGCTTCCCCTCTGTTTTGCTTGATACT
1 TGATTTTGAAATGCAGTATCATGTAGTCAAAAGGCTTCCCCTCTGTTTTGCTTGATACT
5864 TGATTTTGAAATGCAGTATCATGTAGTCAAAAGGCTTCCCCTCTGTTTTGCTTGATACT
1 TGATTTTGAAATGCAGTATCATGTAGTCAAAAGGCTTCCCCTCTGTTTTGCTTGATACT
5923 TGAT
1 TGAT
5927 GCTATTTACT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 63 1.00
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.39
Consensus pattern (59 bp):
TGATTTTGAAATGCAGTATCATGTAGTCAAAAGGCTTCCCCTCTGTTTTGCTTGATACT
Found at i:7246 original size:36 final size:36
Alignment explanation
Indices: 7197--7275 Score: 115
Period size: 36 Copynumber: 2.2 Consensus size: 36
7187 TAAAATAGAT
* *
7197 TGAAGAACGACCGCCCTCGATCGTTCCAGACT-AAAC
1 TGAAGAACAACCGCCCTCGATCATTCC-GACTCAAAC
*
7233 TGAAGAACAACCGCCCTCGATCATTTCGACTCAAAC
1 TGAAGAACAACCGCCCTCGATCATTCCGACTCAAAC
7269 TGAAGAA
1 TGAAGAA
7276 AGACCACCCT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
35 4 0.10
36 35 0.90
ACGTcount: A:0.34, C:0.30, G:0.18, T:0.18
Consensus pattern (36 bp):
TGAAGAACAACCGCCCTCGATCATTCCGACTCAAAC
Found at i:7292 original size:107 final size:107
Alignment explanation
Indices: 7083--7357 Score: 342
Period size: 107 Copynumber: 2.6 Consensus size: 107
7073 ACTCAAAAAT
* * * * *
7083 AAATAA-CTGAAGAAAGACCCCCTTGATCATTCCGAACTGAACTGAAGAACGACCACTCTCGATC
1 AAATAAGCTGAAGAACGACCCCCTCGATCATTCCGAACTAAACTGAAGAACAACCACCCTCGATC
* * *
7147 ATTTCGACGCAATGCTGAAGGAAGATCACCCTGGGTCAACTA
66 ATTTCGACGCAATACTGAAGAAAGACCACCCTGGGTCAACTA
* * *
7189 AAAT-AGATTGAAGAACGACCGCCCTCGATCGTTCC-AGACTAAACTGAAGAACAACCGCCCTCG
1 AAATAAG-CTGAAGAACGACC-CCCTCGATCATTCCGA-ACTAAACTGAAGAACAACCACCCTCG
*
7252 ATCATTTCGACTCAA-ACTGAAGAAAGACCACCCTGGGTCAACTA
63 ATCATTTCGACGCAATACTGAAGAAAGACCACCCTGGGTCAACTA
* * *
7296 AAATAAGCTGAAGAACGACCACCCTCGATCATTCTGAACTGAACTGAAGAATAGACCACCCT
1 AAATAAGCTGAAGAACGACC-CCCTCGATCATTCCGAACTAAACTGAAGAACA-ACCACCCT
7358 GGGTCATTGA
Statistics
Matches: 143, Mismatches: 19, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
105 1 0.01
106 4 0.03
107 80 0.56
108 58 0.41
ACGTcount: A:0.36, C:0.28, G:0.18, T:0.19
Consensus pattern (107 bp):
AAATAAGCTGAAGAACGACCCCCTCGATCATTCCGAACTAAACTGAAGAACAACCACCCTCGATC
ATTTCGACGCAATACTGAAGAAAGACCACCCTGGGTCAACTA
Found at i:7365 original size:37 final size:35
Alignment explanation
Indices: 7266--7365 Score: 112
Period size: 35 Copynumber: 2.8 Consensus size: 35
7256 TTTCGACTCA
*
7266 AACTGAAGAAAGACCACCCTGGGTCA-ACTAAAAT
1 AACTGAAGAAAGACCACCCTGGGTCATTCTAAAAT
* * * * *
7300 AAGCTGAAGAACGACCACCCTCGATCATTCTGAACT
1 AA-CTGAAGAAAGACCACCCTGGGTCATTCTAAAAT
7336 GAACTGAAGAATAGACCACCCTGGGTCATT
1 -AACTGAAGAA-AGACCACCCTGGGTCATT
7366 GAAGCATTGA
Statistics
Matches: 53, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
34 2 0.04
35 21 0.40
36 13 0.25
37 17 0.32
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.18
Consensus pattern (35 bp):
AACTGAAGAAAGACCACCCTGGGTCATTCTAAAAT
Found at i:7459 original size:35 final size:35
Alignment explanation
Indices: 7386--7477 Score: 114
Period size: 35 Copynumber: 2.7 Consensus size: 35
7376 ATAATTGGAG
* * * * *
7386 AATTGAAGAAAGACCACACTGGA-TCATTGAAGTA
1 AATTGAAGAAAGATCGCCCTGGACTAATTGAAATA
* *
7420 AATTGAAGAATGATCGCCCTGGACTAATTGAAATT
1 AATTGAAGAAAGATCGCCCTGGACTAATTGAAATA
7455 AATTGAAGAAAGATCGCCCTGGA
1 AATTGAAGAAAGATCGCCCTGGA
7478 TCGATCAACT
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
34 19 0.39
35 30 0.61
ACGTcount: A:0.40, C:0.15, G:0.22, T:0.23
Consensus pattern (35 bp):
AATTGAAGAAAGATCGCCCTGGACTAATTGAAATA
Found at i:7607 original size:34 final size:35
Alignment explanation
Indices: 7568--7654 Score: 131
Period size: 35 Copynumber: 2.5 Consensus size: 35
7558 AACTGAAGAA
*
7568 AGACCGCCCTGGGTTAATTGAAA-TTATTGAAAAG
1 AGACCGCCCTGGGTCAATTGAAATTTATTGAAAAG
* **
7602 AGACCGCCCTGGATCAATTGAAATTTATTGAATGG
1 AGACCGCCCTGGGTCAATTGAAATTTATTGAAAAG
7637 AGACCGCCCTGGGTCAAT
1 AGACCGCCCTGGGTCAAT
7655 CAACTGAATG
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
34 21 0.45
35 26 0.55
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (35 bp):
AGACCGCCCTGGGTCAATTGAAATTTATTGAAAAG
Found at i:8621 original size:14 final size:14
Alignment explanation
Indices: 8602--8631 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
8592 ACCCTAGAGC
8602 TTCTTTTTTCTTCT
1 TTCTTTTTTCTTCT
*
8616 TTCTTTTTTTTTCT
1 TTCTTTTTTCTTCT
8630 TT
1 TT
8632 TTCTCTCTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TTCTTTTTTCTTCT
Found at i:12110 original size:22 final size:23
Alignment explanation
Indices: 12048--12111 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
12038 TAAACATGAC
* *
12048 TGATAGATGAAATGGAATGGAATA
1 TGATACATG-AATGAAATGGAATA
*
12072 TGATGCATGAATGAAATGGAATA
1 TGATACATGAATGAAATGGAATA
12095 TG-TACAT-AGATGAAATG
1 TGATACATGA-ATGAAATG
12112 TCTAGACATT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
21 1 0.03
22 12 0.34
23 15 0.43
24 7 0.20
ACGTcount: A:0.44, C:0.03, G:0.27, T:0.27
Consensus pattern (23 bp):
TGATACATGAATGAAATGGAATA
Found at i:14000 original size:35 final size:35
Alignment explanation
Indices: 13954--14210 Score: 313
Period size: 35 Copynumber: 7.7 Consensus size: 35
13944 TTCTTACCAA
* * * *
13954 ACTTAATTACCCTGAATTAAGTCGATCAATGATTT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
*
13989 ACTTAATTACCCTGAATTAAGTT-ACTTA-T---TG
1 ACTTAATTACCCTGAATTAAGTTGA-TTACTGACTT
* * *
14020 AC-T-A--A--CTCAATTAAGTTTATTACTTACTT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
*
14049 ACTTAATTACCCTGAATTAAGTTGTTTACTGACTT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
*
14084 ACTTAATTACCCTGAATTAAGTTTATTACTGACTT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
*
14119 GCTTAATTACCCTGAATTAAGTTGATTAC-GACTT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
*
14153 ACTTAATTACCCTGAATTAAGTTAATTACTGACTT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
14188 ACTTAATTACCCTGAATTAAGTT
1 ACTTAATTACCCTGAATTAAGTT
14211 TCTTATTACT
Statistics
Matches: 194, Mismatches: 15, Indels: 26
0.83 0.06 0.11
Matches are distributed among these distances:
25 14 0.07
26 2 0.01
27 1 0.01
29 4 0.02
30 2 0.01
31 4 0.02
33 1 0.01
34 34 0.18
35 132 0.68
ACGTcount: A:0.32, C:0.17, G:0.10, T:0.41
Consensus pattern (35 bp):
ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
Found at i:14183 original size:69 final size:70
Alignment explanation
Indices: 14028--14210 Score: 323
Period size: 69 Copynumber: 2.6 Consensus size: 70
14018 TGACTAACTC
* *
14028 AATTAAGTTTATTACTTACTTACTTAATTACCCTGAATTAAGTTGTTTACTGACTTACTTAATTA
1 AATTAAGTTTATTACTGACTTACTTAATTACCCTGAATTAAGTTGATTACTGACTTACTTAATTA
14093 CCCTG
66 CCCTG
*
14098 AATTAAGTTTATTACTGACTTGCTTAATTACCCTGAATTAAGTTGATTAC-GACTTACTTAATTA
1 AATTAAGTTTATTACTGACTTACTTAATTACCCTGAATTAAGTTGATTACTGACTTACTTAATTA
14162 CCCTG
66 CCCTG
*
14167 AATTAAGTTAATTACTGACTTACTTAATTACCCTGAATTAAGTT
1 AATTAAGTTTATTACTGACTTACTTAATTACCCTGAATTAAGTT
14211 TCTTATTACT
Statistics
Matches: 108, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
69 61 0.56
70 47 0.44
ACGTcount: A:0.32, C:0.16, G:0.10, T:0.42
Consensus pattern (70 bp):
AATTAAGTTTATTACTGACTTACTTAATTACCCTGAATTAAGTTGATTACTGACTTACTTAATTA
CCCTG
Found at i:14793 original size:33 final size:33
Alignment explanation
Indices: 14728--14795 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
14718 GTTTCATCTT
* ** *
14728 TTACTTAAAAGATTTAATCTTTATTTACAAAAA
1 TTACTTAAAAGATTCAATCTTTAACTAAAAAAA
14761 TTACTTAAAAG-TTCAATCTTTTAACTAAAAAAA
1 TTACTTAAAAGATTCAATC-TTTAACTAAAAAAA
14794 TT
1 TT
14796 CGATCTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 6 0.20
33 24 0.80
ACGTcount: A:0.46, C:0.10, G:0.03, T:0.41
Consensus pattern (33 bp):
TTACTTAAAAGATTCAATCTTTAACTAAAAAAA
Found at i:14832 original size:53 final size:53
Alignment explanation
Indices: 14713--14833 Score: 120
Period size: 53 Copynumber: 2.3 Consensus size: 53
14703 TCACATTATT
* * * * *
14713 CAAAGGTTTCATCTTTTACTTAAAAGATTTAATCTTTATTTACAAAAATTACTT
1 CAAA-GTTTAATCTTTTACTAAAAAAATTCAATCTTTATTTACAAAAATTACTC
* * * *
14767 AAAAGTTCAATCTTTTAACTAAAAAAATTCGATCTTTA-TT-CACAAATTACTC
1 CAAAGTTTAATCTTTT-ACTAAAAAAATTCAATCTTTATTTACAAAAATTACTC
14819 CAAAGATTTAATCTT
1 CAAAG-TTTAATCTT
14834 CCAACACAAA
Statistics
Matches: 54, Mismatches: 11, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
52 14 0.26
53 20 0.37
54 20 0.37
ACGTcount: A:0.40, C:0.15, G:0.05, T:0.40
Consensus pattern (53 bp):
CAAAGTTTAATCTTTTACTAAAAAAATTCAATCTTTATTTACAAAAATTACTC
Found at i:15001 original size:31 final size:31
Alignment explanation
Indices: 14960--15020 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
14950 GAAATTCCAA
* *
14960 AGGGCTTAATCGAATCAATC-AACAATTTTTG
1 AGGGCATAATC-AAACAATCTAACAATTTTTG
*
14991 AGGGCATAATCAAACACTCTAACAATTTTT
1 AGGGCATAATCAAACAATCTAACAATTTTT
15021 AGTCTTTATG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 6 0.23
31 20 0.77
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (31 bp):
AGGGCATAATCAAACAATCTAACAATTTTTG
Found at i:16758 original size:59 final size:59
Alignment explanation
Indices: 16692--16825 Score: 225
Period size: 59 Copynumber: 2.3 Consensus size: 59
16682 AATGGGGTGC
16692 TTGCTTGGGA-TATGATTTTGAAATGCAGTATCATGTAGTCAAAAGGCTTCCCCTCTGTT
1 TTGCTTGGGACT-TGATTTTGAAATGCAGTATCATGTAGTCAAAAGGCTTCCCCTCTGTT
*
16751 TTGCTTGGTACTTGATTTTGAAATGCAGTATCATGTAGTCAAAAGGCTTCCCCTCTGTT
1 TTGCTTGGGACTTGATTTTGAAATGCAGTATCATGTAGTCAAAAGGCTTCCCCTCTGTT
**
16810 TTGCTTGATACTTGAT
1 TTGCTTGGGACTTGAT
16826 GCCATTTACT
Statistics
Matches: 72, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
59 71 0.99
60 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.21, T:0.40
Consensus pattern (59 bp):
TTGCTTGGGACTTGATTTTGAAATGCAGTATCATGTAGTCAAAAGGCTTCCCCTCTGTT
Found at i:19681 original size:156 final size:157
Alignment explanation
Indices: 19426--19859 Score: 719
Period size: 157 Copynumber: 2.8 Consensus size: 157
19416 TCATAAGACT
* * * *
19426 AAAAATTTC-AAGTGAAACCGAGCTCTCCTTGATAGTGAACTTGGTTTCTCACCCCCAAACTGTC
1 AAAAAATTCTAAGTAAAACCGAGCTCTCCTTCATGGTGAACTTGGTTTCTCA-CCCCAAACTGTC
* * *
19490 CTTAACTGAAAAACGTGCAGAAGTTTTTCATTCTAAGTCTGGTTGAGCTTAGATTTTTCCAAGAG
65 CTTAACTGAAAAACGTGCATAAGTTTTTCATTCTAAGTCTGGTTGAGCTGAAATTTTTCCAAGAG
19555 GCTTAGATTATCTCCATAAGTGTATGG-
130 GCTTAGATTATCTCCATAAGTGTATGGA
19582 AAAAAATTCTAAGTAAAACCGAGCTCTCCTTCATGGTGAACTTGGTTTCTCACCCCAAACTGTCC
1 AAAAAATTCTAAGTAAAACCGAGCTCTCCTTCATGGTGAACTTGGTTTCTCACCCCAAACTGTCC
*
19647 TTAACTAAAAAACGTGCATAAGTTTTTCATTCTAAGTCTGGTTGAGCTGAAATTTTTCCAAGAGG
66 TTAACTGAAAAACGTGCATAAGTTTTTCATTCTAAGTCTGGTTGAGCTGAAATTTTTCCAAGAGG
19712 CTTAGATTATCTCCATAAGTGTATGGA
131 CTTAGATTATCTCCATAAGTGTATGGA
* *
19739 AAAAAATTCTAAGTAAAACCGAGCTCTCCTTCATGGTGAACTTGGTTTCTCACCCCTAATTGTCC
1 AAAAAATTCTAAGTAAAACCGAGCTCTCCTTCATGGTGAACTTGGTTTCTCACCCCAAACTGTCC
*** *
19804 TTAACTGAAAAACGTGCATAAGTTTTTCATTCTAAGTCCAATTGAGATGAAATTTT
66 TTAACTGAAAAACGTGCATAAGTTTTTCATTCTAAGTCTGGTTGAGCTGAAATTTT
19860 GGCCAAAATG
Statistics
Matches: 261, Mismatches: 15, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
156 108 0.41
157 153 0.59
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.33
Consensus pattern (157 bp):
AAAAAATTCTAAGTAAAACCGAGCTCTCCTTCATGGTGAACTTGGTTTCTCACCCCAAACTGTCC
TTAACTGAAAAACGTGCATAAGTTTTTCATTCTAAGTCTGGTTGAGCTGAAATTTTTCCAAGAGG
CTTAGATTATCTCCATAAGTGTATGGA
Found at i:20760 original size:11 final size:10
Alignment explanation
Indices: 20742--20775 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
20732 GAAGTTCGTG
20742 TTTTGAAGAT
1 TTTTGAAGAT
20752 TTCTTGAAGAT
1 TT-TTGAAGAT
20763 ATTTTGAAGAT
1 -TTTTGAAGAT
20774 TT
1 TT
20776 GAAGCCAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.29, C:0.03, G:0.18, T:0.50
Consensus pattern (10 bp):
TTTTGAAGAT
Found at i:27886 original size:156 final size:155
Alignment explanation
Indices: 27695--28117 Score: 613
Period size: 156 Copynumber: 2.7 Consensus size: 155
27685 TCATAATACT
* * * * *
27695 AAAAATTTC-AAGTGAAACCGAGCTCTCCTTGATGGTGAACTTGGTTTCTCACCCAAAATTGTCC
1 AAAAAATTCTAAGTAAAACCGAG-GCTCCTTCATGGTGAACTTGGTTTCTCACCCCAAATTGTCC
*
27759 TTAACTGAAAAACGTGCATAAGTTTTTCATTCTAAGTCTAGTTGAGCTGAAACTTTTCCAAGAGG
65 TTAACTGAAAAACGTGCATAAGTTTTTCATTCTAAGTCTAGTTGAGCTGAAACTTTTCCAACAGG
*
27824 TTTAGATTATCTCCATAAGTGTATGG
130 CTTAGATTATCTCCATAAGTGTATGG
27850 AAAAAATTCTAAGTAAAACCGAGGACTCCTTCATGGTGAACTTGGTTTCTCACCCCAAATTGTCC
1 AAAAAATTCTAAGTAAAACCGAGG-CTCCTTCATGGTGAACTTGGTTTCTCACCCCAAATTGTCC
* * * * *
27915 TTAACTAAAAAACGTGCATAAGTTTTCCACTCTAAGTCTGGTTGAGCT-AAATTTTTCCAACAGG
65 TTAACTGAAAAACGTGCATAAGTTTTTCATTCTAAGTCTAGTTGAGCTGAAACTTTTCCAACAGG
27979 CTTAGATTATCTCCATAAGTGTATGG
130 CTTAGATTATCTCCATAAGTGTATGG
* * * *
28005 -AAAAATTCTAAGTAAAACCGA-GCT-CTCCTTGGTGGACTTGGTTTCTCACCCCTAATTGTCCT
1 AAAAAATTCTAAGTAAAACCGAGGCTCCTTCATGGTGAACTTGGTTTCTCACCCCAAATTGTCCT
* * * *
28067 TAACTGAAAAACGTGTATAAGTTTTTCATTCTAAGTCCAATTGAGATGAAA
66 TAACTGAAAAACGTGCATAAGTTTTTCATTCTAAGTCTAGTTGAGCTGAAA
28118 TTTGGCCATG
Statistics
Matches: 241, Mismatches: 24, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
151 73 0.30
152 5 0.02
153 1 0.00
154 21 0.09
155 47 0.20
156 94 0.39
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (155 bp):
AAAAAATTCTAAGTAAAACCGAGGCTCCTTCATGGTGAACTTGGTTTCTCACCCCAAATTGTCCT
TAACTGAAAAACGTGCATAAGTTTTTCATTCTAAGTCTAGTTGAGCTGAAACTTTTCCAACAGGC
TTAGATTATCTCCATAAGTGTATGG
Found at i:40723 original size:13 final size:13
Alignment explanation
Indices: 40700--40730 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
40690 TTAATACAGG
40700 TATCG-ACGGATA
1 TATCGAACGGATA
40712 TATCGAACGGATA
1 TATCGAACGGATA
40725 TATCGA
1 TATCGA
40731 GGTATCGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.28
13 13 0.72
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (13 bp):
TATCGAACGGATA
Found at i:42271 original size:13 final size:13
Alignment explanation
Indices: 42236--42277 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
42226 AATATTTTTT
42236 AATTAT-TAAAAA
1 AATTATATAAAAA
*
42248 AGTATTTTATAAAAA
1 A--ATTATATAAAAA
42263 AATTATATAAAAA
1 AATTATATAAAAA
42276 AA
1 AA
42278 AGCTAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
12 1 0.04
13 13 0.52
14 4 0.16
15 7 0.28
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (13 bp):
AATTATATAAAAA
Found at i:43437 original size:21 final size:22
Alignment explanation
Indices: 43400--43442 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
43390 TTTTTTCTTT
43400 TTAATTTCTGCTTAAA-TGACA
1 TTAATTTCTGCTTAAATTGACA
43421 TTAATTTC-GCTTAAAATTGACA
1 TTAATTTCTGCTT-AAATTGACA
43443 ATTTTCAAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 11 0.55
22 5 0.25
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (22 bp):
TTAATTTCTGCTTAAATTGACA
Found at i:44231 original size:29 final size:29
Alignment explanation
Indices: 44153--44237 Score: 109
Period size: 29 Copynumber: 2.9 Consensus size: 29
44143 ACGGCTAAAT
44153 GCTCGATTTGGTCCTAAACCTTTCACGGTCC
1 GCTCGATTTGGTCCTAAACCTTTCAC-G-CC
* *
44184 ACTCGATTTGGTCCTAAACCTTCTGAC-CC
1 GCTCGATTTGGTCCTAAACCTT-TCACGCC
*
44213 GCTCAATTTGGTCCTAAACCTTTCA
1 GCTCGATTTGGTCCTAAACCTTTCA
44238 ATTTCTTAAC
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
28 2 0.04
29 22 0.46
31 21 0.44
32 3 0.06
ACGTcount: A:0.20, C:0.32, G:0.15, T:0.33
Consensus pattern (29 bp):
GCTCGATTTGGTCCTAAACCTTTCACGCC
Found at i:45600 original size:17 final size:17
Alignment explanation
Indices: 45574--45610 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
45564 TAAAAAATAT
*
45574 CATAACATACAGTCTTC
1 CATAAAATACAGTCTTC
45591 CATAAAATACAGTCTTC
1 CATAAAATACAGTCTTC
45608 CAT
1 CAT
45611 TAGTAGCAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.38, C:0.27, G:0.05, T:0.30
Consensus pattern (17 bp):
CATAAAATACAGTCTTC
Done.