Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018419.1 Corchorus olitorius cultivar O-4 contig18452, 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: 71507
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:3066 original size:14 final size:14
Alignment explanation
Indices: 3043--3085 Score: 68
Period size: 14 Copynumber: 3.1 Consensus size: 14
3033 CTATTCGAAA
3043 TTATAAAAATTATT
1 TTATAAAAATTATT
* *
3057 TTATAGAAATTCTT
1 TTATAAAAATTATT
3071 TTATAAAAATTATT
1 TTATAAAAATTATT
3085 T
1 T
3086 GGCAAAAATG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (14 bp):
TTATAAAAATTATT
Found at i:5469 original size:50 final size:50
Alignment explanation
Indices: 5366--5474 Score: 118
Period size: 50 Copynumber: 2.2 Consensus size: 50
5356 GTTTATCAAC
**
5366 TTTTC-CTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCTTTAGTGT
1 TTTTCTCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCTACAGTGT
*
5415 TTTTCTCTTGTTTCA-ATCTTGTCTCCA-GAC-ATACAAACACTGTACACGTGT
1 TTTTCTCTTGTTT-AGATCTTGTCT-CAGGACAAT-CAAACACTCTACA-GTGT
5466 TTTCTCTCT
1 TTT-TCTCT
5475 CAGAAATAAC
Statistics
Matches: 51, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
49 7 0.14
50 29 0.57
51 10 0.20
52 5 0.10
ACGTcount: A:0.21, C:0.24, G:0.12, T:0.43
Consensus pattern (50 bp):
TTTTCTCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCTACAGTGT
Found at i:6159 original size:22 final size:22
Alignment explanation
Indices: 6100--6160 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
6090 GTCTCTGTGT
6100 AATTATTAAAATTTCATAATGA
1 AATTATTAAAATTTCATAATGA
*
6122 AATTATCAAAATTTCATAA-GA
1 AATTATTAAAATTTCATAATGA
* *
6143 ATATTATTATAACTTCAT
1 A-ATTATTAAAATTTCAT
6161 GAGGAGGTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 3 0.09
22 31 0.91
ACGTcount: A:0.48, C:0.08, G:0.03, T:0.41
Consensus pattern (22 bp):
AATTATTAAAATTTCATAATGA
Found at i:6181 original size:22 final size:22
Alignment explanation
Indices: 6124--6290 Score: 69
Period size: 22 Copynumber: 7.6 Consensus size: 22
6114 CATAATGAAA
* * **
6124 TTATCAAAATTTCATAAGAATA
1 TTATCAAAATTTCATGAGGAGG
* * *
6146 TTATTATAACTTCATGAGGAGG
1 TTATCAAAATTTCATGAGGAGG
*
6168 TTATCAGAATTTCATTGTA--AGG
1 TTATCAAAATTTCA-TG-AGGAGG
* * *
6190 TTATTAGAATTT-AT-AGTGGGG
1 TTATCAAAATTTCATGAG-GAGG
* * * *
6211 TTAGCAAAATTTTATAAGGAGA
1 TTATCAAAATTTCATGAGGAGG
6233 TTA-CTAAAATTTCAT-AGGGAGG
1 TTATC-AAAATTTCATGA-GGAGG
* *
6255 TTATCAAATTTTCATG-GTGTGG
1 TTATCAAAATTTCATGAG-GAGG
*
6277 TCATCAAAATTTCA
1 TTATCAAAATTTCA
6291 CAGTTTGGTT
Statistics
Matches: 110, Mismatches: 23, Indels: 24
0.70 0.15 0.15
Matches are distributed among these distances:
18 1 0.01
20 1 0.01
21 15 0.14
22 87 0.79
23 5 0.05
24 1 0.01
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.38
Consensus pattern (22 bp):
TTATCAAAATTTCATGAGGAGG
Found at i:7179 original size:22 final size:22
Alignment explanation
Indices: 7112--7214 Score: 79
Period size: 22 Copynumber: 4.7 Consensus size: 22
7102 AATAAAGAAA
* * *
7112 TTATCGAAATTTCATAGTTTAG
1 TTATCAAAATTTTATAGTGTAG
* * * *
7134 TTTTCAGAATTTCATAG-GAGAG
1 TTATCAAAATTTTATAGTG-TAG
7156 TTATCAAAATTTTATAGTGTAG
1 TTATCAAAATTTTATAGTGTAG
7178 -T-TCAAAATTTTCATAGTGT-G
1 TTATCAAAATTTT-ATAGTGTAG
*
7198 TAGATCAAAATTTTATA
1 T-TATCAAAATTTTATA
7215 ATGAGGTTAG
Statistics
Matches: 65, Mismatches: 10, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
20 11 0.17
21 8 0.12
22 35 0.54
23 11 0.17
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.43
Consensus pattern (22 bp):
TTATCAAAATTTTATAGTGTAG
Found at i:7195 original size:21 final size:21
Alignment explanation
Indices: 7158--7214 Score: 80
Period size: 23 Copynumber: 2.7 Consensus size: 21
7148 TAGGAGAGTT
7158 ATCAAAATTTTATA-GTGTAG
1 ATCAAAATTTTATAGGTGTAG
*
7178 TTCAAAATTTTCATAGTGTGTAG
1 ATCAAAATTTT-ATAG-GTGTAG
7201 ATCAAAATTTTATA
1 ATCAAAATTTTATA
7215 ATGAGGTTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 10 0.31
21 3 0.09
22 3 0.09
23 16 0.50
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.42
Consensus pattern (21 bp):
ATCAAAATTTTATAGGTGTAG
Found at i:7258 original size:22 final size:22
Alignment explanation
Indices: 7231--7286 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
7221 TTAGTTTTCA
7231 AAAATTTCATAGGAGGATTATC
1 AAAATTTCATAGGAGGATTATC
* * *
7253 AAAATTTCATAAGAGGGTTATT
1 AAAATTTCATAGGAGGATTATC
7275 AAAATTTCATAG
1 AAAATTTCATAG
7287 TGTGGTTTCC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.43, C:0.07, G:0.16, T:0.34
Consensus pattern (22 bp):
AAAATTTCATAGGAGGATTATC
Found at i:7382 original size:22 final size:22
Alignment explanation
Indices: 7311--7401 Score: 76
Period size: 22 Copynumber: 3.9 Consensus size: 22
7301 GGTGTAGATC
*
7311 AAATTTTCATACGGAGA-TTAACA
1 AAATTTT-ATA-GGAGAGTTATCA
* *
7334 AAATTTTATAACGATGTTAGTTTTCA
1 AAATTTTAT-AGGA-G--AGTTATCA
7360 AAATTTTATAGGAGAGTTATCA
1 AAATTTTATAGGAGAGTTATCA
* *
7382 AAATTTCATAGGAGGGTTAT
1 AAATTTTATAGGAGAGTTAT
7402 TTCATGGTGT
Statistics
Matches: 56, Mismatches: 7, Indels: 11
0.76 0.09 0.15
Matches are distributed among these distances:
22 29 0.52
23 9 0.16
24 1 0.02
25 4 0.07
26 13 0.23
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.37
Consensus pattern (22 bp):
AAATTTTATAGGAGAGTTATCA
Found at i:7429 original size:129 final size:125
Alignment explanation
Indices: 7203--7468 Score: 299
Period size: 129 Copynumber: 2.1 Consensus size: 125
7193 GTGTGTAGAT
*
7203 CAAAATTTTATAATGAGGTTAGTTTTCAAAAATTTCATAGGAGGATTATCAAAATTTCATAAGAG
1 CAAAATTTTATAACGAGGTTAGTTTTCAAAAATTTCATAGGAGGATTATCAAAATTTCATAAGAG
*
7268 GGTTATTAAAATTTCATAGTGTGGTTTCCATAGGGTGTAGATCAAATTTTCAT-ACGGAGATTAA
66 GG-T-TT--AATTTCATAGTGTGGTTTCCATAGGGTGTAGATCAAAATTTCATAAC-GAGATTAA
* * *
7332 CAAAATTTTATAACGATGTTAGTTTTC-AAAATTTTATAGGA-GAGTTATCAAAATTTCATAGGA
1 CAAAATTTTATAACGAGGTTAGTTTTCAAAAATTTCATAGGAGGA-TTATCAAAATTTCATAAGA
* * * *
7395 GGG-TT-ATTTCATGGTGTGGTTCAAAATTTTCATAGTGTGTAGATCAAAATTTCATAACGAGGT
65 GGGTTTAATTTCATAGTGTGG-------TTTCCATAGGGTGTAGATCAAAATTTCATAACGAGAT
7458 TAA
123 TAA
7461 CAAAATTT
1 CAAAATTT
7469 CATATTGAGA
Statistics
Matches: 119, Mismatches: 9, Indels: 18
0.82 0.06 0.12
Matches are distributed among these distances:
122 13 0.11
125 2 0.02
127 2 0.02
128 34 0.29
129 66 0.55
130 2 0.02
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.37
Consensus pattern (125 bp):
CAAAATTTTATAACGAGGTTAGTTTTCAAAAATTTCATAGGAGGATTATCAAAATTTCATAAGAG
GGTTTAATTTCATAGTGTGGTTTCCATAGGGTGTAGATCAAAATTTCATAACGAGATTAA
Found at i:7570 original size:23 final size:23
Alignment explanation
Indices: 7517--7596 Score: 74
Period size: 23 Copynumber: 3.5 Consensus size: 23
7507 AAATTTGTGG
* * **
7517 TTATCAAAATTTCATA-AGAAGG
1 TTATCAAAATTTTATAGGGAAAT
7539 TTATCAAAATTTT-TCAGGGAAAT
1 TTATCAAAATTTTAT-AGGGAAAT
* **
7562 TTATTAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGGAAAT
7585 TTATCAAAATTT
1 TTATCAAAATTT
7597 CATAACGAGG
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
21 1 0.02
22 13 0.28
23 32 0.68
24 1 0.02
ACGTcount: A:0.40, C:0.06, G:0.14, T:0.40
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAAAT
Found at i:7769 original size:22 final size:22
Alignment explanation
Indices: 7437--7951 Score: 196
Period size: 22 Copynumber: 23.4 Consensus size: 22
7427 TAGTGTGTAG
**
7437 ATCAAAATTTCATAACGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* ** *
7459 AACAAAATTTCATATTGAGATT
1 ATCAAAATTTCATAGGGAGGTT
*
7481 ATCAAAATATCATAGGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* *
7503 ATCTAAA-TT--T---GTGGTT
1 ATCAAAATTTCATAGGGAGGTT
* *
7519 ATCAAAATTTCATAAGAAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* **
7541 ATCAAAATTT-TTCAGGGAAATTT
1 ATCAAAATTTCAT-AGGG-AGGTT
* *
7564 ATTAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATAGGGAGG-TT
**
7587 ATCAAAATTTCATAACGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * *** *
7609 ATCACAATTTCGTAGTTTGATT
1 ATCAAAATTTCATAGGGAGGTT
* * * **
7631 ATCAAAATTTCACAGTG-TGAA
1 ATCAAAATTTCATAGGGAGGTT
* *
7652 AACTAACATTTCAT-GCAGG-GGTT
1 ATC-AAAATTTCATAG--GGAGGTT
* * * *
7675 TTCAAATTTTCATTATGTGCTA-ATT
1 ATCAAAATTTCA-TA-G-G-GAGGTT
*
7700 ATCAACATTTCATAGGG-GGTT
1 ATCAAAATTTCATAGGGAGGTT
**
7721 ATCAAAATTTCATAGTGTTGGTT
1 ATCAAAATTTCATAG-GGAGGTT
* *
7744 ATCAAAATTTCATTGGGAAGTT
1 ATCAAAATTTCATAGGGAGGTT
* *
7766 ATCAAAATTTCATTGGGAAGTT
1 ATCAAAATTTCATAGGGAGGTT
* *
7788 ATCAAAATTCCATAGTGAGGTCT
1 ATCAAAATTTCATAGGGAGGT-T
**
7811 -TCAAAATTTCATATTGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
** *
7832 AAAAAAATTTCATAGGAAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * ***
7854 AACTAAAATTCCA-ACAAAAGGTT
1 ATC-AAAATTTCATA-GGGAGGTT
* * * * **
7877 CTCGAAATTCCATAGTGTCGTT
1 ATCAAAATTTCATAGGGAGGTT
* * ***
7899 ATCAAAATTTTC-TCGGAAAAAT
1 ATCAAAA-TTTCATAGGGAGGTT
*
7921 ATCAAAATTTCATAGGGAGGTC
1 ATCAAAATTTCATAGGGAGGTT
7943 ATCAAAATT
1 ATCAAAATT
7952 GTAATAGTGT
Statistics
Matches: 358, Mismatches: 107, Indels: 56
0.69 0.21 0.11
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
19 2 0.01
21 26 0.07
22 224 0.63
23 77 0.22
24 4 0.01
25 12 0.03
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (22 bp):
ATCAAAATTTCATAGGGAGGTT
Found at i:7789 original size:44 final size:45
Alignment explanation
Indices: 7516--8001 Score: 182
Period size: 44 Copynumber: 10.9 Consensus size: 45
7506 TAAATTTGTG
* * *
7516 GTTATCAAAATTTCATAAGAAGGTTATCAAAATTT-TTCAG-GGAAA
1 GTTATCAAAATTTCATAGGGAGGTTATCAAAATTTCAT-AGTGG-AA
* * * ** *
7561 TTTATTAAAATTTTATAGGGAGGTTTATCAAAATTTCATA-ACGAG
1 GTTATCAAAATTTCATAGGGAGG-TTATCAAAATTTCATAGTGGAA
* * *** * *
7606 GTTATCACAATTTCGTAGTTTGATTATCAAAATTTCACAGTGTGAA
1 GTTATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAGTG-GAA
* * * * *
7652 ---AACTAACATTTCAT-GCAGG-GGTTTTCAAATTTTCATTATGTGCTAA
1 GTTATC-AAAATTTCATAG--GGAGGTTATCAAAATTTCA-TA-GTG-GAA
* ***
7698 -TTATCAACATTTCATAGGG-GGTTATCAAAATTTCATAGTGTTG
1 GTTATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAGTGGAA
* * *
7741 GTTATCAAAATTTCATTGGGAAGTTATCAAAATTTCATTG-GGAA
1 GTTATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAGTGGAA
* * * *
7785 GTTATCAAAATTCCATAGTGAGGTCT-TCAAAATTTCATA-TTGAG
1 GTTATCAAAATTTCATAGGGAGGT-TATCAAAATTTCATAGTGGAA
** * * * ***
7829 GTTAAAAAAATTTCATAGGAAGGTTAACTAAAATTCCA-A-CAAAA
1 GTTATCAAAATTTCATAGGGAGGTTATC-AAAATTTCATAGTGGAA
* * * * ** * *
7873 GGTTCTCGAAATTCCATAGTGTCGTTATCAAAATTTTC-TCG-GAAA
1 -GTTATCAAAATTTCATAGGGAGGTTATCAAAA-TTTCATAGTGGAA
** * * *
7918 AATATCAAAATTTCATAGGGAGGTCATCAAAATTGTAATAGTGTAA
1 GTTATCAAAATTTCATAGGGAGGTTATCAAAATT-TCATAGTGGAA
* * * *
7964 -TTATCATAATCTT-ATAGGTAGGTAATCACAATTTCATA
1 GTTATCAAAAT-TTCATAGGGAGGTTATCAAAATTTCATA
8002 TAATATTTAA
Statistics
Matches: 320, Mismatches: 94, Indels: 55
0.68 0.20 0.12
Matches are distributed among these distances:
43 7 0.02
44 144 0.45
45 113 0.35
46 42 0.13
47 11 0.03
48 3 0.01
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.36
Consensus pattern (45 bp):
GTTATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAGTGGAA
Found at i:11007 original size:14 final size:14
Alignment explanation
Indices: 10988--11018 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
10978 TGTTAGCTCT
10988 TCAATACAGGAAAA
1 TCAATACAGGAAAA
*
11002 TCAATACATGAAAA
1 TCAATACAGGAAAA
11016 TCA
1 TCA
11019 CAAAAACCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.55, C:0.16, G:0.10, T:0.19
Consensus pattern (14 bp):
TCAATACAGGAAAA
Found at i:11782 original size:29 final size:29
Alignment explanation
Indices: 11738--11835 Score: 187
Period size: 29 Copynumber: 3.4 Consensus size: 29
11728 CTGTTAACTC
*
11738 CACTTGAGGGACCAAATTACATATTTTTT
1 CACTTGAGGGATCAAATTACATATTTTTT
11767 CACTTGAGGGATCAAATTACATATTTTTT
1 CACTTGAGGGATCAAATTACATATTTTTT
11796 CACTTGAGGGATCAAATTACATATTTTTT
1 CACTTGAGGGATCAAATTACATATTTTTT
11825 CACTTGAGGGA
1 CACTTGAGGGA
11836 CCAATTTGCT
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
29 68 1.00
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (29 bp):
CACTTGAGGGATCAAATTACATATTTTTT
Found at i:13312 original size:116 final size:116
Alignment explanation
Indices: 13108--13334 Score: 445
Period size: 116 Copynumber: 2.0 Consensus size: 116
13098 ATATTTAGCT
13108 TTTGGGTTTCATTGTGGGCTTGAAAAGAAAAACAAATTATGGCATTTGTTTTTGGGTTTCAGCCC
1 TTTGGGTTTCATTGTGGGCTTGAAAAGAAAAACAAATTATGGCATTTGTTTTTGGGTTTCAGCCC
*
13173 ATTTATAGAAAAACCAGATAAAATGGGTTCACATGATGGAGAAAAACCAGA
66 ATTTATAGAAAAACCAGATAAAATGGGTTCACACGATGGAGAAAAACCAGA
13224 TTTGGGTTTCATTGTGGGCTTGAAAAGAAAAACAAATTATGGCATTTGTTTTTGGGTTTCAGCCC
1 TTTGGGTTTCATTGTGGGCTTGAAAAGAAAAACAAATTATGGCATTTGTTTTTGGGTTTCAGCCC
13289 ATTTATAGAAAAACCAGATAAAATGGGTTCACACGATGGAGAAAAA
66 ATTTATAGAAAAACCAGATAAAATGGGTTCACACGATGGAGAAAAA
13335 TGAAAGCCTA
Statistics
Matches: 110, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
116 110 1.00
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.30
Consensus pattern (116 bp):
TTTGGGTTTCATTGTGGGCTTGAAAAGAAAAACAAATTATGGCATTTGTTTTTGGGTTTCAGCCC
ATTTATAGAAAAACCAGATAAAATGGGTTCACACGATGGAGAAAAACCAGA
Found at i:24189 original size:29 final size:28
Alignment explanation
Indices: 24145--24200 Score: 85
Period size: 29 Copynumber: 2.0 Consensus size: 28
24135 TTCTTCAAAC
* *
24145 TTTCTAATTTCAAGAACGTTCAAGAACA
1 TTTCTAATTTCAAGAACGCTAAAGAACA
24173 TTTCTAATCTTCAAGAACGCTAAAGAAC
1 TTTCTAAT-TTCAAGAACGCTAAAGAAC
24201 GTGGAATAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 8 0.32
29 17 0.68
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (28 bp):
TTTCTAATTTCAAGAACGCTAAAGAACA
Found at i:24756 original size:25 final size:24
Alignment explanation
Indices: 24711--24757 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
24701 GGTAATTGGG
*
24711 CGGGTCAGGTTAGGTTCGGGTTAT
1 CGGGTCAGGTCAGGTTCGGGTTAT
* *
24735 CGGGTTCAGGTCAGTTTTGGGTT
1 CGGG-TCAGGTCAGGTTCGGGTT
24758 CGGGTTTGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 4 0.21
25 15 0.79
ACGTcount: A:0.11, C:0.13, G:0.40, T:0.36
Consensus pattern (24 bp):
CGGGTCAGGTCAGGTTCGGGTTAT
Found at i:24865 original size:32 final size:32
Alignment explanation
Indices: 24780--24874 Score: 77
Period size: 32 Copynumber: 3.0 Consensus size: 32
24770 AGGTTGTGTT
* * *
24780 AAATTTGGTTCAGATTGATTCG-GATTCAGG-TC
1 AAATTTGGGTCAGGTTAATTCGAGA-TC-GGATC
* * * *
24812 AAATTTGGGTTATGTTGATTCGAGTTCGGATC
1 AAATTTGGGTCAGGTTAATTCGAGATCGGATC
* *
24844 AATTTTGGGTCAGGTTAATTCGGGATCGGAT
1 AAATTTGGGTCAGGTTAATTCGAGATCGGAT
24875 TAGGACTGGG
Statistics
Matches: 50, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
31 2 0.04
32 47 0.94
33 1 0.02
ACGTcount: A:0.23, C:0.11, G:0.28, T:0.38
Consensus pattern (32 bp):
AAATTTGGGTCAGGTTAATTCGAGATCGGATC
Found at i:25048 original size:20 final size:20
Alignment explanation
Indices: 25015--25053 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
25005 CATAAATGAA
*
25015 ATTTTCAGAAATTATTATTT
1 ATTTTCAGAAATTAGTATTT
25035 ATTTTCA-AATATTAGTATT
1 ATTTTCAGAA-ATTAGTATT
25054 GAATTCGGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (20 bp):
ATTTTCAGAAATTAGTATTT
Found at i:25115 original size:16 final size:17
Alignment explanation
Indices: 25096--25155 Score: 54
Period size: 16 Copynumber: 3.7 Consensus size: 17
25086 GGGTAAAAGA
25096 TTTTTCGGATTCTG-GT
1 TTTTTCGGATTCTGAGT
* * *
25112 TTTTTTGGGTT-TGAGA
1 TTTTTCGGATTCTGAGT
*
25128 TTTTTCGGGTTC-GAGT
1 TTTTTCGGATTCTGAGT
*
25144 TTTTTTGGATTC
1 TTTTTCGGATTC
25156 GGATTCGGAC
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
15 2 0.06
16 33 0.94
ACGTcount: A:0.08, C:0.08, G:0.27, T:0.57
Consensus pattern (17 bp):
TTTTTCGGATTCTGAGT
Found at i:40832 original size:117 final size:117
Alignment explanation
Indices: 40607--40845 Score: 419
Period size: 117 Copynumber: 2.1 Consensus size: 117
40597 GACTCCATGG
*
40607 GCTCTAAGTCCCCCGTTCCCTCTTAAACACCGGTGATTCCATGGCGAGGGGCAGACCTGCGGGCA
1 GCTCTAAGTCCCCCGCTCCCTCTTAAACACCGGTGATTCCATGGCGAGGGGCAGACCTGCGGGCA
* *
40672 GTAGTGGGGCGTGCCAAGAGTGGATCTTACGACATGGTGGAAACAAGCAAGA
66 GTAGTGGGGCGTGCCAAGAGTGGATCTTACCACATGGTGGAAACAAACAAGA
40724 GCTCTAAGTCCCCCGCTCCCTCTTAAACACCGGTGATTCCATGGCGAGGGGCAGACCTGCGGGCA
1 GCTCTAAGTCCCCCGCTCCCTCTTAAACACCGGTGATTCCATGGCGAGGGGCAGACCTGCGGGCA
*
40789 GTAGT-GGGCGTGTCAAGAGTGGATCTTACCACATGGTGTGAAACAAACAAGA
66 GTAGTGGGGCGTGCCAAGAGTGGATCTTACCACATGGTG-GAAACAAACAAGA
40841 G-TCTA
1 GCTCTA
40846 TCTAAGAAAA
Statistics
Matches: 117, Mismatches: 4, Indels: 3
0.94 0.03 0.02
Matches are distributed among these distances:
116 35 0.30
117 82 0.70
ACGTcount: A:0.24, C:0.26, G:0.30, T:0.20
Consensus pattern (117 bp):
GCTCTAAGTCCCCCGCTCCCTCTTAAACACCGGTGATTCCATGGCGAGGGGCAGACCTGCGGGCA
GTAGTGGGGCGTGCCAAGAGTGGATCTTACCACATGGTGGAAACAAACAAGA
Found at i:46254 original size:22 final size:21
Alignment explanation
Indices: 46202--46255 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
46192 TGCTTCTCAA
46202 AATAATTCTTC-AATGATCTTC
1 AATAA-TCTTCAAATGATCTTC
*
46223 -A-AATCTTCAAATTATCTTC
1 AATAATCTTCAAATGATCTTC
46242 AATAAGTCTTCAAA
1 AATAA-TCTTCAAA
46256 CACGAACTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.18
19 11 0.39
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.39
Consensus pattern (21 bp):
AATAATCTTCAAATGATCTTC
Found at i:52456 original size:20 final size:22
Alignment explanation
Indices: 52433--52482 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
52423 AAAGGTCTTG
52433 ATATTTTT-AAAAAAGAA-TAT
1 ATATTTTTCAAAAAAGAATTAT
*
52453 ATATTTTTCATAAAAGAATTAT
1 ATATTTTTCAAAAAAGAATTAT
52475 ATATTTTT
1 ATATTTTT
52483 TAGTTTTTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 8 0.30
21 8 0.30
22 11 0.41
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (22 bp):
ATATTTTTCAAAAAAGAATTAT
Found at i:52460 original size:21 final size:22
Alignment explanation
Indices: 52436--52484 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 22
52426 GGTCTTGATA
52436 TTTTTAAAAAAGAA-TATATAT
1 TTTTTAAAAAAGAATTATATAT
* *
52457 TTTTCATAAAAGAATTATATAT
1 TTTTTAAAAAAGAATTATATAT
52479 TTTTTA
1 TTTTTA
52485 GTTTTTACCC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (22 bp):
TTTTTAAAAAAGAATTATATAT
Found at i:56494 original size:5 final size:5
Alignment explanation
Indices: 56484--56510 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
56474 CTAATATATT
56484 AATTA AATTA AATTA AATTA AATTA AA
1 AATTA AATTA AATTA AATTA AATTA AA
56511 AGAAGTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
AATTA
Found at i:57766 original size:16 final size:16
Alignment explanation
Indices: 57745--57776 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
57735 TTGAATCTTA
57745 TTAAATTAATTAAACT
1 TTAAATTAATTAAACT
*
57761 TTAAATTAATTTAACT
1 TTAAATTAATTAAACT
57777 AGATTGCTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (16 bp):
TTAAATTAATTAAACT
Found at i:60695 original size:164 final size:164
Alignment explanation
Indices: 60424--60737 Score: 522
Period size: 164 Copynumber: 1.9 Consensus size: 164
60414 GCCCAAAATC
* *
60424 GGGTGTTGACTGAGTTTTGACCGGGTCAAACTTTCCGGGTTTTACCTCCTCCTCCGGGCCGGATA
1 GGGTGTTGACTGAGTTTTGACCGGGCCAAACTTTCCGGGTTTTACCTCCTCCTCCGGACCGGATA
* * *
60489 GGTCATTTGGTCCCAATTAAACTGATCCGACCAGCCGGTCTGGTCCGGATTCGGAAACATTGGAT
66 GGTCATCTGGTCCCAATTAAACTGATCCGACCAACCGGTCTGGTCCGGATTCGGAAACACTGGAT
60554 TTAGCTAGGTCTAGAAGCTATATGCAAAAAAACT
131 TTAGCTAGGTCTAGAAGCTATATGCAAAAAAACT
*
60588 GGGTGTTGGCTGAGTTTTGACCGGGCCAAACTTTCCGGGTTTTA-CTCCCTCCTCCGGACCGGAT
1 GGGTGTTGACTGAGTTTTGACCGGGCCAAACTTTCCGGGTTTTACCT-CCTCCTCCGGACCGGAT
* * *
60652 AGGTCATCTGGTCCCAATTGAACTGGTCCGACCAACCGGTCTGGTCCGGATTTGGAAACACTGGA
65 AGGTCATCTGGTCCCAATTAAACTGATCCGACCAACCGGTCTGGTCCGGATTCGGAAACACTGGA
*
60717 TTTAGCTAGGTCTCGAAGCTA
130 TTTAGCTAGGTCTAGAAGCTA
60738 GGAATTTGAA
Statistics
Matches: 139, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
163 2 0.01
164 137 0.99
ACGTcount: A:0.21, C:0.25, G:0.27, T:0.28
Consensus pattern (164 bp):
GGGTGTTGACTGAGTTTTGACCGGGCCAAACTTTCCGGGTTTTACCTCCTCCTCCGGACCGGATA
GGTCATCTGGTCCCAATTAAACTGATCCGACCAACCGGTCTGGTCCGGATTCGGAAACACTGGAT
TTAGCTAGGTCTAGAAGCTATATGCAAAAAAACT
Found at i:63223 original size:10 final size:10
Alignment explanation
Indices: 63208--63262 Score: 83
Period size: 10 Copynumber: 5.5 Consensus size: 10
63198 TACCTCGATG
63208 TATCCGTAAA
1 TATCCGTAAA
63218 TATCCGTAAA
1 TATCCGTAAA
*
63228 TATCTGTAAA
1 TATCCGTAAA
*
63238 TATCTGTAAA
1 TATCCGTAAA
*
63248 TATCTGTAAA
1 TATCCGTAAA
63258 TATCC
1 TATCC
63263 ATATTTAATT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 43 1.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.36
Consensus pattern (10 bp):
TATCCGTAAA
Found at i:63236 original size:20 final size:20
Alignment explanation
Indices: 63208--63262 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
63198 TACCTCGATG
*
63208 TATCCGTAAATATCCGTAAA
1 TATCTGTAAATATCCGTAAA
*
63228 TATCTGTAAATATCTGTAAA
1 TATCTGTAAATATCCGTAAA
63248 TATCTGTAAATATCC
1 TATCTGTAAATATCC
63263 ATATTTAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.36
Consensus pattern (20 bp):
TATCTGTAAATATCCGTAAA
Found at i:64987 original size:25 final size:24
Alignment explanation
Indices: 64957--65029 Score: 76
Period size: 25 Copynumber: 3.0 Consensus size: 24
64947 TCCGTGCTTA
64957 TTCTTTCTCCAGGCCCTGCGCCAC
1 TTCTTTCTCCAGGCCCTGCGCCAC
* * *
64981 TTCCTTTATTCATGCCCTGCGCCAC
1 TT-CTTTCTCCAGGCCCTGCGCCAC
*
65006 TT-TTCTCTCATAGGCCCTGCGCCA
1 TTCTT-TCTC-CAGGCCCTGCGCCA
65030 TCCTCTGCAG
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
23 2 0.05
24 4 0.10
25 33 0.85
ACGTcount: A:0.11, C:0.41, G:0.15, T:0.33
Consensus pattern (24 bp):
TTCTTTCTCCAGGCCCTGCGCCAC
Done.