Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015807.1 Corchorus olitorius cultivar O-4 contig15840, 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: 17805
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.34
Found at i:1396 original size:16 final size:15
Alignment explanation
Indices: 1375--1416 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
1365 TTACTTTGCT
1375 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
*
1391 TTGTTTTATGTTTAA
1 TTGTTTTCTGTTTAA
*
1406 TTGCTTTCTGT
1 TTGTTTTCTGT
1417 CAACCTCTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 15 0.65
16 8 0.35
ACGTcount: A:0.14, C:0.07, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:4869 original size:74 final size:74
Alignment explanation
Indices: 4780--4923 Score: 270
Period size: 74 Copynumber: 1.9 Consensus size: 74
4770 GTATACCTTA
*
4780 ACACATAGTGATAGTACACACTTTTATACGTTTTTCATGTCTTTTCCAATTTAAATCAAGACAAA
1 ACACATAGTGATAGTACACACTTTTATACGTTTTTCATGTCCTTTCCAATTTAAATCAAGACAAA
4845 CGTGATAGT
66 CGTGATAGT
*
4854 ACACATAGTGATAGTACATACTTTTATACGTTTTTCATGTCCTTTCCAATTTAAATCAAGACAAA
1 ACACATAGTGATAGTACACACTTTTATACGTTTTTCATGTCCTTTCCAATTTAAATCAAGACAAA
4919 CGTGA
66 CGTGA
4924 AAACCTCGTT
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
74 68 1.00
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (74 bp):
ACACATAGTGATAGTACACACTTTTATACGTTTTTCATGTCCTTTCCAATTTAAATCAAGACAAA
CGTGATAGT
Found at i:6118 original size:268 final size:272
Alignment explanation
Indices: 5592--6130 Score: 1005
Period size: 268 Copynumber: 2.0 Consensus size: 272
5582 TTCCTTTAAC
5592 CTTGGAAAATACTCAAATCTTTTTCTTTTTGTTCAATATAGGAATGATAAAGTTTAATTAAAAGG
1 CTTGGAAAATACTCAAATCTTTTTCTTTTTGTTCAATAT--GAATGATAAAGTTTAATTAAAAGG
*
5657 CATTCCAAATATTATTGACCTATAATAATGAAGTGTTGCTCACGAGGCACACCTTTATTTAACAC
64 CATTCCAAATATTATTGACCTAAAATAATGAAGTGTTGCTCACGAGGCACACCTTTATTTAACAC
5722 ATGGTACTACACTTTACAATGTTCATGTCTTTTCCAATCAAATCAAGAAAAACATGAAAAGCACA
129 ATGGTACTACACTTTACAATGTTCATGTCTTTTCCAATCAAATCAAGAAAAACATGAAAAGCACA
5787 TAGTGAAGGCTAGAAATGGCTTTGGCTTGGTTCCTACATTTTCTGCAAACCGTTTCAACTTTGAA
194 TAGTGAAGGCTAGAAATGGCTTTGGCTTGGTTCCTACATTTTCTGCAAACCGTTTCAACTTTGAA
5852 TATGTATATGTAAT
259 TATGTATATGTAAT
*
5866 CTTGGAAAATACTCAAATC-TTTTCTTTTTGTTC-A-AT-AATGATGAAGTTTAATTAAAAGGCA
1 CTTGGAAAATACTCAAATCTTTTTCTTTTTGTTCAATATGAATGATAAAGTTTAATTAAAAGGCA
5927 TTCCAAATATTATTGACCTAAAATAATGAAGTGTTGCTCACGAGGCACACCTTTATTTAACACAT
66 TTCCAAATATTATTGACCTAAAATAATGAAGTGTTGCTCACGAGGCACACCTTTATTTAACACAT
*
5992 GGTACTACACTTTACAATGTTCATGTCTTTTCCAATCAAATCAAGATAAACATGAAAAGCACATA
131 GGTACTACACTTTACAATGTTCATGTCTTTTCCAATCAAATCAAGAAAAACATGAAAAGCACATA
6057 GTGAAGGCTAGAAATGGCTTTGGCTTGGTTCCTACATTTTCTGCAAACCGTTTCAACTTTGAATA
196 GTGAAGGCTAGAAATGGCTTTGGCTTGGTTCCTACATTTTCTGCAAACCGTTTCAACTTTGAATA
6122 TGTATATGT
261 TGTATATGT
6131 TGATCATTAT
Statistics
Matches: 262, Mismatches: 3, Indels: 6
0.97 0.01 0.02
Matches are distributed among these distances:
268 226 0.86
271 2 0.01
272 1 0.00
273 14 0.05
274 19 0.07
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35
Consensus pattern (272 bp):
CTTGGAAAATACTCAAATCTTTTTCTTTTTGTTCAATATGAATGATAAAGTTTAATTAAAAGGCA
TTCCAAATATTATTGACCTAAAATAATGAAGTGTTGCTCACGAGGCACACCTTTATTTAACACAT
GGTACTACACTTTACAATGTTCATGTCTTTTCCAATCAAATCAAGAAAAACATGAAAAGCACATA
GTGAAGGCTAGAAATGGCTTTGGCTTGGTTCCTACATTTTCTGCAAACCGTTTCAACTTTGAATA
TGTATATGTAAT
Found at i:8086 original size:27 final size:27
Alignment explanation
Indices: 8056--8107 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
8046 TAGCTGCGAC
*
8056 GTTGTCATTATTATTGTTGTTGTTGAT
1 GTTGTCATTATCATTGTTGTTGTTGAT
* * *
8083 GTTGTCCTTGTCGTTGTTGTTGTTG
1 GTTGTCATTATCATTGTTGTTGTTG
8108 TTTCCATGAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.08, C:0.08, G:0.27, T:0.58
Consensus pattern (27 bp):
GTTGTCATTATCATTGTTGTTGTTGAT
Found at i:8603 original size:27 final size:27
Alignment explanation
Indices: 8569--8630 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 27
8559 ATTTTTTTCC
*
8569 AAAT-ATATTTCTAAATTA-TCATTATT-
1 AAATAATATTT-T-AATTATTCACTATTA
8595 AAATAATATTTTAATTATTTCACTATTA
1 AAATAATATTTTAATTA-TTCACTATTA
8623 AAATAATA
1 AAATAATA
8631 AAAATTTAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
25 5 0.16
26 5 0.16
27 13 0.42
28 8 0.26
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (27 bp):
AAATAATATTTTAATTATTCACTATTA
Found at i:9743 original size:22 final size:22
Alignment explanation
Indices: 9715--9948 Score: 113
Period size: 22 Copynumber: 10.5 Consensus size: 22
9705 TGTCTCTGTG
9715 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * *
9737 TGGTTATTATAATTTCATGAGA
1 TGGTTATCAAAATTTCATAAGA
* *
9759 AGATTATCAAAA-TTC-TATAG-
1 TGGTTATCAAAATTTCATA-AGA
* *
9779 TGTGCTTACCAAAATTTCATATGGA
1 TG-G-TTATCAAAATTTCATA-AGA
* **
9804 -AGTTATCAAAATTTCATGGGA
1 TGGTTATCAAAATTTCATAAGA
* *
9825 AGGTTATCAAAATTTCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
* *
9847 TGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAAGA
* * *
9869 TCAGGTTATTAAAATTTCTTAGGA
1 T--GGTTATCAAAATTTCATAAGA
* * ** *
9893 AGCTTATTGAAATTTCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
*
9915 TGGTTATCATAAATTTTAT-AGAA
1 TGGTTATCA-AAATTTCATAAG-A
*
9938 AGGTTATCAAA
1 TGGTTATCAAA
9949 GAGATTATCA
Statistics
Matches: 160, Mismatches: 39, Indels: 26
0.71 0.17 0.12
Matches are distributed among these distances:
20 2 0.01
21 10 0.06
22 103 0.64
23 23 0.14
24 22 0.14
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.38
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:9818 original size:66 final size:66
Alignment explanation
Indices: 9712--9948 Score: 230
Period size: 66 Copynumber: 3.5 Consensus size: 66
9702 TCTTGTCTCT
* * * *
9712 GTGTGGTTATCAAAATTTCATAAGATGGTTATTATAATTTCATGAGAAGATTATCAAAA-TTCTA
1 GTGTGGTTACCAAAATTTCATAAGATAGTTATCAAAATTTCATGAGAAGATTATCAAAATTTC-A
9776 TA
65 TA
* * * *
9778 GTGTGCTTACCAAAATTTCATATGGA-AGTTATCAAAATTTCATGGGAAGGTTATCAAAATTTCA
1 GTGTGGTTACCAAAATTTCATA-AGATAGTTATCAAAATTTCATGAGAAGATTATCAAAATTTCA
9842 TA
65 TA
* * * * **
9844 GTGTGGTTACCAAAATTTCATAGGATCAGGTTATTAAAATTTC-TTAGGAAGCTTATTGAAATTT
1 GTGTGGTTACCAAAATTTCATAAGAT-A-GTTATCAAAATTTCATGA-GAAGATTATCAAAATTT
9908 CATA
63 CATA
* * *
9912 GTGTGGTTATCATAAATTTTAT-AGAAAGGTTATCAAA
1 GTGTGGTTACCA-AAATTTCATAAGATA-GTTATCAAA
9949 GAGATTATCA
Statistics
Matches: 144, Mismatches: 20, Indels: 13
0.81 0.11 0.07
Matches are distributed among these distances:
65 3 0.02
66 72 0.50
67 17 0.12
68 44 0.31
69 8 0.06
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (66 bp):
GTGTGGTTACCAAAATTTCATAAGATAGTTATCAAAATTTCATGAGAAGATTATCAAAATTTCAT
A
Found at i:9836 original size:44 final size:42
Alignment explanation
Indices: 9717--10679 Score: 226
Period size: 44 Copynumber: 21.9 Consensus size: 42
9707 TCTCTGTGTG
** * *
9717 GTTATCAAAATTTCATAAGATGGTTATTATAATTTCAT-GAGAA
1 GTTATCAAAATTTCATGGGA-GGTTATCAAAATTTCATAG-GAA
* * * *
9760 GATTATCAAAA-TTCTATAGTGTGCTTACCAAAATTTCATATGGAA
1 G-TTATCAAAATTTC-AT-GGGAGGTTATCAAAATTTCATA-GGAA
**
9805 GTTATCAAAATTTCATGGGAAGGTTATCAAAATTTCATAGTGTG
1 GTTATCAAAATTTCATGGG-AGGTTATCAAAATTTCATAG-GAA
* * * *
9849 GTTACCAAAATTTCATAGGATCAGGTTATTAAAATTTCTTAGGAA
1 GTTATCAAAATTTCAT-GG--GAGGTTATCAAAATTTCATAGGAA
** * * * *
9894 GCTTATTGAAATTTCATAGTGTGGTTATCATAAATTTTATAGAAA
1 G-TTATCAAAATTTCAT-GGGAGGTTATCA-AAATTTCATAGGAA
* * *
9939 GGTTATC--AA----A---GAGATTATCAAAATGTCATAGCGAG
1 -GTTATCAAAATTTCATGGGAGGTTATCAAAATTTCATAG-GAA
* * * *
9974 GTTAT-AAGAATTTCATAGTGTGGTTAACAAAATTTCATAAGGAG
1 GTTATCAA-AATTTCAT-GGGAGGTTATCAAAATTTCAT-AGGAA
*
10018 GTTA-CAAATATTTCATGGGGAGGTTATCAAAATTTCATAAGAA
1 GTTATCAAA-ATTTCAT-GGGAGGTTATCAAAATTTCATAGGAA
* ** * * * *
10061 GGTTATAAAAGTCTCAATTTCATAAGATG-TACCAACATTTGATA-GAA
1 -GTTAT-CAA-----AATTTCATGGGAGGTTATCAAAATTTCATAGGAA
* * * *
10108 GGTTATC-AAATCTCAT-AGAGTGATTATCGAAATTTCATAGAGATCG
1 -GTTATCAAAATTTCATGGGAG-G-TTATCAAAATTTCATAG-GA--A
* * **
10154 GATTATCAAAATTT-ATAGGAAGATTATCAAAATTTCATAGTGTT
1 G-TTATCAAAATTTCAT-GGGAGGTTATCAAAATTTCATAG-GAA
* * * *
10198 GTTATCAAAATTCCAAAGCGAGGTTATCAAAATTGCATAATGTG-A
1 GTTATCAAAATTTC-ATGGGAGGTTATCAAAATTTCAT-A-G-GAA
* * * *
10243 -TTATCAAAATTTTCATAGAGG-GGTCCA-CAAAATTTTATATAGAG
1 GTTATCAAAA-TTTCAT-G-GGAGGT-TATCAAAATTTCATA-GGAA
** * * *
10287 GTTATCAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATGTAA
1 GTTATCAAAATTTCAT-GGGAGGTTATCAAAATTTC-ATA-GGAA
* * * *
10332 -TTACCAAAATTTCATAGTGGTATTTCTGGTTATTAAACTTTTATTACGG-A
1 GTTATCAAAATTTCAT-G-GG-A-----GGTTATCAAAATTTCA-TA-GGAA
* * *
10382 GTAATCAAAATTTCA-GGGAGGATATCAAAATTTCATATGAA
1 GTTATCAAAATTTCATGGGAGGTTATCAAAATTTCATAGGAA
** *
10423 GGTTATCAAAATTTCATAGTTTA-GTTTTCAAAATTTCATAAGAGAA
1 -GTTATCAAAATTTCAT-G-GGAGGTTATCAAAATTTCAT-AG-GAA
* * * * *
10469 -TTATCAAAATTTCATAGTATGTAGATCAAAATTTCATAGGGA
1 GTTATCAAAATTTCATGGGAGGT-TATCAAAATTTCATAGGAA
* ** * ** *
10511 GATTAACAAAATTTCATAATGAGGTTATAAAAAAATCATAGGGAG
1 G-TTATCAAAATTTCAT-GGGAGGTTATCAAAATTTCATA-GGAA
* * * * *
10556 GTTAT-AAAAATT--T-GTA-GTTATCAAGATTTTATAAGGAG
1 GTTATCAAAATTTCATGGGAGGTTATCAAAATTTCAT-AGGAA
* * * *
10594 GTTATCAAAATTTTAAAGGGAGGTTTATCAAAATCTAATAGGAA
1 GTTATCAAAA-TTTCATGGGAGG-TTATCAAAATTTCATAGGAA
* * *
10638 GGTTTATCAAAATTTCATAGCGAGATTATCACAATTTCATAG
1 -G-TTATCAAAATTTCAT-GGGAGGTTATCAAAATTTCATAG
10680 TGTGATTATC
Statistics
Matches: 673, Mismatches: 153, Indels: 186
0.67 0.15 0.18
Matches are distributed among these distances:
34 14 0.02
35 9 0.01
36 2 0.00
38 20 0.03
39 10 0.01
40 12 0.02
41 4 0.01
42 41 0.06
43 39 0.06
44 266 0.40
45 103 0.15
46 82 0.12
47 15 0.02
48 16 0.02
49 4 0.01
50 9 0.01
51 27 0.04
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (42 bp):
GTTATCAAAATTTCATGGGAGGTTATCAAAATTTCATAGGAA
Found at i:9978 original size:22 final size:21
Alignment explanation
Indices: 9953--10323 Score: 180
Period size: 22 Copynumber: 16.7 Consensus size: 21
9943 ATCAAAGAGA
*
9953 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAG-GAGG
*
9975 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAG-GAGG
*
9997 TTAACAAAATTTCATAAGGAGG
1 TTATCAAAATTTCAT-AGGAGG
*
10019 TTA-CAAATATTTCATGGGGAGG
1 TTATCAAA-ATTTCAT-AGGAGG
*
10041 TTATCAAAATTTCATAAGAAGG
1 TTATCAAAATTTCAT-AGGAGG
* * *
10063 TTATAAAAGTCTCAATTTCATAAGATG
1 TTAT-CAA-----AATTTCATAGGAGG
* * * *
10090 -TACCAACATTTGATAGAAGG
1 TTATCAAAATTTCATAGGAGG
*
10110 TTATC-AAATCTCATA-GAGTG
1 TTATCAAAATTTCATAGGAG-G
*
10130 ATTATCGAAATTTCATAGAGATCGG
1 -TTATCAAAATTTCATAG-GA--GG
*
10155 ATTATCAAAATTT-ATAGGAAGA
1 -TTATCAAAATTTCATAGG-AGG
**
10177 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAG-GAGG
* *
10199 TTATCAAAATTCCAAAGCGAGG
1 TTATCAAAATTTCATAG-GAGG
* * * *
10221 TTATCAAAATTGCATAATGTGA
1 TTATCAAAATTTCAT-AGGAGG
*
10243 TTATCAAAATTTTCATAGAGGGG
1 TTATCAAAA-TTTCATAG-GAGG
* * *
10266 TCCA-CAAAATTTTATATAGAGG
1 T-TATCAAAATTTCATA-GGAGG
*
10288 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCAT-AGGAGG
*
10310 TTATCAAATTTTCA
1 TTATCAAAATTTCA
10324 AAATGTAATT
Statistics
Matches: 267, Mismatches: 53, Indels: 58
0.71 0.14 0.15
Matches are distributed among these distances:
19 2 0.01
20 17 0.06
21 27 0.10
22 157 0.59
23 27 0.10
24 8 0.03
25 15 0.06
26 3 0.01
27 3 0.01
28 8 0.03
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGAGG
Found at i:10274 original size:89 final size:88
Alignment explanation
Indices: 10181--10348 Score: 205
Period size: 89 Copynumber: 1.9 Consensus size: 88
10171 GGAAGATTAT
** * * *
10181 CAAAATTTCATAGT-GTTGTTATCAAAATTCCA-AAGCGAGGTTATCAAAATTGCATAATGTGAT
1 CAAAATTTCATA-TAGAGGTTATCAAAATTCCATAA-AGAGGTTATCAAAATTGCAAAATGTAAT
*
10244 TATCAAAATTTTCATAGAGGGGTCCA
64 TACCAAAA-TTTCATAGAGGGGTCCA
* * * *
10270 CAAAATTTTATATAGAGGTTATCAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATGTAATTA
1 CAAAATTTCATATAGAGGTTATCAAAATTCCATAAAGAGGTTATCAAAATTGCAAAATGTAATTA
10335 CCAAAATTTCATAG
66 CCAAAATTTCATAG
10349 TGGTATTTCT
Statistics
Matches: 67, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
88 9 0.13
89 56 0.84
90 2 0.03
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.34
Consensus pattern (88 bp):
CAAAATTTCATATAGAGGTTATCAAAATTCCATAAAGAGGTTATCAAAATTGCAAAATGTAATTA
CCAAAATTTCATAGAGGGGTCCA
Found at i:10320 original size:21 final size:22
Alignment explanation
Indices: 10107--10678 Score: 132
Period size: 22 Copynumber: 25.9 Consensus size: 22
10097 ATTTGATAGA
* *
10107 AGGTTATC-AAATCTCATAGAG
1 AGGTTATCAAAATTTCATAAAG
* * * *
10128 TGATTATCGAAATTTCATAGAG
1 AGGTTATCAAAATTTCATAAAG
10150 ATCGGATTATCAAAATTT-ATAGGAAG
1 A--GG-TTATCAAAATTTCATA--AAG
**
10176 A--TTATCAAAATTTCATAGTG
1 AGGTTATCAAAATTTCATAAAG
** * *
10196 TTGTTATCAAAATTCCA-AAGCG
1 AGGTTATCAAAATTTCATAA-AG
* *
10218 AGGTTATCAAAATTGCATAATG
1 AGGTTATCAAAATTTCATAAAG
* * *
10240 TGATTATCAAAATTTTCATAGAG
1 AGGTTATCAAAA-TTTCATAAAG
* * * *
10263 GGGTCCA-CAAAATTTTATATAG
1 AGGT-TATCAAAATTTCATAAAG
10285 AGGTTATCAAAATTTCATAAAG
1 AGGTTATCAAAATTTCATAAAG
*
10307 AGGTTATCAAATTTTCA-AAATG
1 AGGTTATCAAAATTTCATAAA-G
* * **
10329 TA-ATTACCAAAATTTCATAGTGG
1 -AGGTTATCAAAATTTCATA-AAG
* * * * *
10352 TATTTCTGGTTATTAAACTTTTATTACG
1 -A-----GGTTATCAAAATTTCATAAAG
* **
10380 -GAGTAATCAAAATTTC--AGGG
1 AG-GTTATCAAAATTTCATAAAG
* *
10400 AGGATATCAAAATTTCAT-ATG
1 AGGTTATCAAAATTTCATAAAG
***
10421 AAGGTTATCAAAATTTCATAGTTT
1 -AGGTTATCAAAATTTCATA-AAG
*
10445 A-GTTTTCAAAATTTCAT-AAG
1 AGGTTATCAAAATTTCATAAAG
*
10465 AGAATTATCAAAATTTCAT--AG
1 AG-GTTATCAAAATTTCATAAAG
* * **
10486 TATGTAGATCAAAATTTCATAGGG
1 -AGGT-TATCAAAATTTCATAAAG
* * *
10510 AGATTAACAAAATTTCATAATG
1 AGGTTATCAAAATTTCATAAAG
* ** **
10532 AGGTTATAAAAAAATCATAGGG
1 AGGTTATCAAAATTTCATAAAG
* *
10554 AGGTTATAAAAATTT-GT----
1 AGGTTATCAAAATTTCATAAAG
* * *
10571 A-GTTATCAAGATTTTATAAGG
1 AGGTTATCAAAATTTCATAAAG
10592 AGGTTATCAAAATTT--TAAAGGG
1 AGGTTATCAAAATTTCATAAA--G
* *
10614 AGGTTTATCAAAATCTAATAGGAAG
1 AGG-TTATCAAAATTTCATA--AAG
* **
10639 -GTTTATCAAAATTTCATAGCG
1 AGGTTATCAAAATTTCATAAAG
* *
10660 AGATTATCACAATTTCATA
1 AGGTTATCAAAATTTCATA
10679 GTGTGATTAT
Statistics
Matches: 402, Mismatches: 98, Indels: 101
0.67 0.16 0.17
Matches are distributed among these distances:
16 11 0.03
17 2 0.00
20 18 0.04
21 32 0.08
22 251 0.62
23 49 0.12
24 8 0.02
25 14 0.03
26 3 0.01
27 2 0.00
28 1 0.00
29 11 0.03
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.35
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATAAAG
Found at i:10432 original size:22 final size:22
Alignment explanation
Indices: 10385--10779 Score: 195
Period size: 22 Copynumber: 18.2 Consensus size: 22
10375 TTACGGAGTA
*
10385 ATCAAAATTTC--AGGGAGGAT
1 ATCAAAATTTCATAGGGAGGTT
* *
10405 ATCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCATAGGGAGGTT
**
10427 ATCAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATAG-GGAGGTT
* * *
10449 TTCAAAATTTCATA-AGAGAATT
1 ATCAAAATTTCATAGGGAG-GTT
* * *
10471 ATCAAAATTTCATA-GTATGTAG
1 ATCAAAATTTCATAGGGAGGT-T
*
10493 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATAGGGAGGTT
* **
10515 AACAAAATTTCATAATGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* **
10537 ATAAAAAAATCATAGGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* *
10559 AT-AAAAATT--T--GTA-GTT
1 ATCAAAATTTCATAGGGAGGTT
* * *
10575 ATCAAGATTTTATAAGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* *
10597 ATCAAAATTTTAAAGGGAGGTTT
1 ATCAAAATTTCATAGGGAGG-TT
* * *
10620 ATCAAAATCTAATAGGAAGGTTT
1 ATCAAAATTTCATAGGGAGG-TT
* *
10643 ATCAAAATTTCATAGCGAGATT
1 ATCAAAATTTCATAGGGAGGTT
* * * *
10665 ATCACAATTTCATAGTGTGATT
1 ATCAAAATTTCATAGGGAGGTT
* * * * *
10687 ATCAAAACTTCAGAGTGTGATT
1 ATCAAAATTTCATAGGGAGGTT
*
10709 A-CTAACAA-TTCATATGGAGGTT
1 ATC-AA-AATTTCATAGGGAGGTT
* * * ** *
10731 TTTAAATTTTCATAACGTGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * *
10753 ATCAATATATCATATGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
10775 ATCAA
1 ATCAA
10780 CATCTCAAAA
Statistics
Matches: 285, Mismatches: 72, Indels: 34
0.73 0.18 0.09
Matches are distributed among these distances:
16 5 0.02
17 7 0.02
19 2 0.01
20 12 0.04
21 11 0.04
22 206 0.72
23 42 0.15
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (22 bp):
ATCAAAATTTCATAGGGAGGTT
Found at i:10625 original size:23 final size:23
Alignment explanation
Indices: 10573--10652 Score: 94
Period size: 23 Copynumber: 3.5 Consensus size: 23
10563 AAATTTGTAG
*
10573 TTATCAAGATTTTATAA-GGAGG-
1 TTATCAAAATTTTA-AAGGGAGGT
10595 TTATCAAAATTTTAAAGGGAGGT
1 TTATCAAAATTTTAAAGGGAGGT
* *
10618 TTATCAAAA-TCTAATAGGAAGGT
1 TTATCAAAATTTTAA-AGGGAGGT
10641 TTATCAAAATTT
1 TTATCAAAATTT
10653 CATAGCGAGA
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
21 2 0.04
22 22 0.44
23 25 0.50
24 1 0.02
ACGTcount: A:0.40, C:0.06, G:0.17, T:0.36
Consensus pattern (23 bp):
TTATCAAAATTTTAAAGGGAGGT
Found at i:10938 original size:20 final size:20
Alignment explanation
Indices: 10909--10946 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
10899 CCATAGTATC
*
10909 GTTATTAAAATTTCATAAAG
1 GTTATCAAAATTTCATAAAG
10929 GTTATCAAAATTTCATAA
1 GTTATCAAAATTTCATAA
10947 GGAGGTCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (20 bp):
GTTATCAAAATTTCATAAAG
Found at i:15556 original size:20 final size:21
Alignment explanation
Indices: 15528--15566 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
15518 ATTTCCTTCT
15528 TCCTCTTTCTTT-TTTTTTCC
1 TCCTCTTTCTTTCTTTTTTCC
*
15548 TCCTTTTTCTTTCTTTTTT
1 TCCTCTTTCTTTCTTTTTT
15567 TTTTTATTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (21 bp):
TCCTCTTTCTTTCTTTTTTCC
Done.