Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012785.1 Corchorus olitorius cultivar O-4 contig12818, 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: 69129
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Found at i:9469 original size:15 final size:15
Alignment explanation
Indices: 9449--9489 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
9439 CAAATACTAT
*
9449 CATTTTGAAATGATG
1 CATTTTAAAATGATG
*
9464 CATTTTAAAATGATT
1 CATTTTAAAATGATG
*
9479 CATTTCAAAAT
1 CATTTTAAAAT
9490 TCTTCAAACT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (15 bp):
CATTTTAAAATGATG
Found at i:15612 original size:23 final size:22
Alignment explanation
Indices: 15529--15627 Score: 85
Period size: 21 Copynumber: 4.5 Consensus size: 22
15519 GGGTGATTAA
* * *
15529 CAAAATCTCACAAGGAGGTTAT
1 CAAAATTTCATAAGAAGGTTAT
* *
15551 CAAAA-ATCATAGGAAGGTTA-
1 CAAAATTTCATAAGAAGGTTAT
*
15571 CAAAATTTCATAGGAAGGTTTAT
1 CAAAATTTCATAAGAAGG-TTAT
* **
15594 TAAAATTTCATAATTAGGTTAT
1 CAAAATTTCATAAGAAGGTTAT
*
15616 CAAAGTTTCATA
1 CAAAATTTCATA
15628 TGGAGTTTAT
Statistics
Matches: 63, Mismatches: 11, Indels: 6
0.79 0.14 0.08
Matches are distributed among these distances:
20 5 0.08
21 22 0.35
22 22 0.35
23 14 0.22
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.31
Consensus pattern (22 bp):
CAAAATTTCATAAGAAGGTTAT
Found at i:15673 original size:22 final size:22
Alignment explanation
Indices: 15647--15717 Score: 74
Period size: 22 Copynumber: 3.2 Consensus size: 22
15637 TCATAATTAC
* *
15647 AATTTTATAGGTAAATTATCAA
1 AATTTAATAGGTAAGTTATCAA
* *
15669 AATTTCATAGCGT-GGTTATCAA
1 AATTTAATAG-GTAAGTTATCAA
15691 AATTTAATAGG-ATAGTTATCAA
1 AATTTAATAGGTA-AGTTATCAA
15713 AATTT
1 AATTT
15718 CATAAAAATG
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
21 1 0.02
22 38 0.93
23 2 0.05
ACGTcount: A:0.41, C:0.07, G:0.13, T:0.39
Consensus pattern (22 bp):
AATTTAATAGGTAAGTTATCAA
Found at i:20646 original size:21 final size:23
Alignment explanation
Indices: 20622--20670 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
20612 TAATTTCGGA
*
20622 GGTTATC-AAAA-TTCATTGTGT
1 GGTTATCTAAAATTTCATAGTGT
*
20643 GGTTA-CTAAAATTTTATAGTGT
1 GGTTATCTAAAATTTCATAGTGT
20665 GGTTAT
1 GGTTAT
20671 AGTGAGGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 1 0.04
21 9 0.39
22 13 0.57
ACGTcount: A:0.29, C:0.06, G:0.20, T:0.45
Consensus pattern (23 bp):
GGTTATCTAAAATTTCATAGTGT
Found at i:20769 original size:22 final size:20
Alignment explanation
Indices: 20667--20952 Score: 103
Period size: 22 Copynumber: 13.1 Consensus size: 20
20657 TATAGTGTGG
*
20667 TTATAGTGAGGTTACCAAAATT
1 TTATAG-GA-GTTATCAAAATT
*
20689 TTATAGGA--TATTAAAATT
1 TTATAGGAGTTATCAAAATT
20707 TTATAGTGTAGTTATCAAAATT
1 TTATAG-G-AGTTATCAAAATT
* *
20729 TCATGGGATGTTATCAAAATT
1 TTATAGGA-GTTATCAAAATT
*
20750 TTATAAGGAGGTTATTAAAATAAAAT
1 TTAT-AGGA-GTTATCAAAAT----T
*
20776 TTCATATGGATGTTACCAAAATT
1 TT-ATA-GGA-GTTATCAAAATT
* *
20799 TCATCTGGGAGGTTATC-AAATT
1 T--TATAGGA-GTTATCAAAATT
*
20821 TTCATAAGGAGGTTATCGAAA-T
1 TT-AT-AGGA-GTTATCAAAATT
* *
20843 TCATGAGAAGTTATCAAAATT
1 TTAT-AGGAGTTATCAAAATT
* * * *
20864 TCATATGGAGGCTAACAAACTT
1 TTATA-GGA-GTTATCAAAATT
* * *
20886 TCATAGGGCGATTATCGAAATT
1 TTATA-GGAG-TTATCAAAATT
20908 TTATATGGAGGTTATCAAAATT
1 TTATA-GGA-GTTATCAAAATT
* *
20930 TCATAAGAAGATTATCAAAATT
1 TTAT-AGGAG-TTATCAAAATT
20952 T
1 T
20953 CATAATGTGC
Statistics
Matches: 202, Mismatches: 38, Indels: 48
0.70 0.13 0.17
Matches are distributed among these distances:
18 14 0.07
19 1 0.00
20 13 0.06
21 33 0.16
22 106 0.52
23 15 0.07
24 1 0.00
25 1 0.00
26 4 0.02
27 14 0.07
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (20 bp):
TTATAGGAGTTATCAAAATT
Found at i:20796 original size:70 final size:71
Alignment explanation
Indices: 20700--20836 Score: 190
Period size: 70 Copynumber: 1.9 Consensus size: 71
20690 TATAGGATAT
* * * *
20700 TAAAATTTTATAGTGTAGTTATCAAAATTTCA-TGGGATGTTATCAAAATTTT-ATAAGGAGGTT
1 TAAAATTTCATAGTGGAGTTACCAAAATTTCACTGGGAGGTTATC-AAATTTTCATAAGGAGGTT
20763 ATTAAAA
65 ATTAAAA
20770 TAAAATTTCATA-TGGATGTTACCAAAATTTCATCTGGGAGGTTATCAAATTTTCATAAGGAGGT
1 TAAAATTTCATAGTGGA-GTTACCAAAATTTCA-CTGGGAGGTTATCAAATTTTCATAAGGAGGT
20834 TAT
64 TAT
20837 CGAAATTCAT
Statistics
Matches: 59, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
69 3 0.05
70 25 0.42
71 7 0.12
72 24 0.41
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.39
Consensus pattern (71 bp):
TAAAATTTCATAGTGGAGTTACCAAAATTTCACTGGGAGGTTATCAAATTTTCATAAGGAGGTTA
TTAAAA
Found at i:20889 original size:64 final size:66
Alignment explanation
Indices: 20772--20934 Score: 179
Period size: 64 Copynumber: 2.5 Consensus size: 66
20762 TATTAAAATA
* * * * * * *
20772 AAATTTCATATGGATGTTACCAAAATTTCATCTGGGAGGTTATCAAATTTTCATAAGGAGGTTAT
1 AAATTTCATA-GGAAGTTATCAAAATTTCATATGGGAGGCTAACAAACTTTCATAAGGAGATTAT
20837 CG
65 CG
* *
20839 AAA-TTCAT-GAGAAGTTATCAAAATTTCATAT-GGAGGCTAACAAACTTTCATAGGGCGATTAT
1 AAATTTCATAG-GAAGTTATCAAAATTTCATATGGGAGGCTAACAAACTTTCATAAGGAGATTAT
20901 CG
65 CG
* *
20903 AAATTTTATATGGAGGTTATCAAAATTTCATA
1 AAATTTCATA-GGAAGTTATCAAAATTTCATA
20935 AGAAGATTAT
Statistics
Matches: 81, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
64 31 0.38
65 22 0.27
66 24 0.30
67 4 0.05
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (66 bp):
AAATTTCATAGGAAGTTATCAAAATTTCATATGGGAGGCTAACAAACTTTCATAAGGAGATTATC
G
Found at i:20907 original size:87 final size:88
Alignment explanation
Indices: 20771--20956 Score: 243
Period size: 87 Copynumber: 2.1 Consensus size: 88
20761 TTATTAAAAT
* * * * *
20771 AAAATTTCATATGGATGTTACCAAAATTTCATCTGGGAGGTTATCAAATTTTCATAAGGAGGTTA
1 AAAATTTCATATGGAGGCTAACAAAATTTCATCAGGGAGATTATCAAATTTT-ATAAGGAGGTTA
* *
20836 TCGAAA-TTCATGAGAAG-TTATC
65 TCAAAATTTCATAAGAAGATTATC
* * *
20858 AAAATTTCATATGGAGGCTAACAAACTTTCAT-AGGGCGATTATCGAAATTTTATATGGAGGTTA
1 AAAATTTCATATGGAGGCTAACAAAATTTCATCAGGGAGATTATC-AAATTTTATAAGGAGGTTA
20922 TCAAAATTTCATAAGAAGATTATC
65 TCAAAATTTCATAAGAAGATTATC
20946 AAAATTTCATA
1 AAAATTTCATA
20957 ATGTGCTTAT
Statistics
Matches: 86, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
86 25 0.29
87 45 0.52
88 16 0.19
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (88 bp):
AAAATTTCATATGGAGGCTAACAAAATTTCATCAGGGAGATTATCAAATTTTATAAGGAGGTTAT
CAAAATTTCATAAGAAGATTATC
Found at i:20953 original size:22 final size:22
Alignment explanation
Indices: 20717--20957 Score: 182
Period size: 22 Copynumber: 10.8 Consensus size: 22
20707 TTATAGTGTA
* *
20717 GTTATCAAAATTTCAT-GGGAT
1 GTTATCAAAATTTCATAAGGAG
*
20738 GTTATCAAAATTTTATAAGGAG
1 GTTATCAAAATTTCATAAGGAG
* * *
20760 GTTATTAAAATAAAATTTCATATGGAT
1 GTTA-T----CAAAATTTCATAAGGAG
* **
20787 GTTACCAAAATTTCATCTGGGAG
1 GTTATCAAAATTTCAT-AAGGAG
*
20810 GTTATCAAATTTTCATAAGGAG
1 GTTATCAAAATTTCATAAGGAG
* * *
20832 GTTATCGAAA-TTCATGA-GAA
1 GTTATCAAAATTTCATAAGGAG
*
20852 GTTATCAAAATTTCATATGGAG
1 GTTATCAAAATTTCATAAGGAG
* * * * *
20874 GCTAACAAACTTTCATAGGGCG
1 GTTATCAAAATTTCATAAGGAG
* * * *
20896 ATTATCGAAATTTTATATGGAG
1 GTTATCAAAATTTCATAAGGAG
*
20918 GTTATCAAAATTTCATAAGAAG
1 GTTATCAAAATTTCATAAGGAG
*
20940 ATTATCAAAATTTCATAA
1 GTTATCAAAATTTCATAA
20958 TGTGCTTATA
Statistics
Matches: 168, Mismatches: 43, Indels: 17
0.74 0.19 0.07
Matches are distributed among these distances:
20 11 0.07
21 26 0.15
22 96 0.57
23 18 0.11
27 17 0.10
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.35
Consensus pattern (22 bp):
GTTATCAAAATTTCATAAGGAG
Found at i:21065 original size:22 final size:22
Alignment explanation
Indices: 21040--21115 Score: 82
Period size: 22 Copynumber: 3.5 Consensus size: 22
21030 TGATATAATA
*
21040 ATCACAATTTCATGGGGAGGTT
1 ATCAAAATTTCATGGGGAGGTT
* *
21062 ATCAAAATTTTA-GAGGGAGATT
1 ATCAAAATTTCATG-GGGAGGTT
* * *
21084 ATCAAAATTTCATAGTGTGGTT
1 ATCAAAATTTCATGGGGAGGTT
21106 ATCAAAATTT
1 ATCAAAATTT
21116 TATAATGTGC
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
21 1 0.02
22 43 0.98
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.36
Consensus pattern (22 bp):
ATCAAAATTTCATGGGGAGGTT
Found at i:21124 original size:22 final size:22
Alignment explanation
Indices: 21058--21593 Score: 152
Period size: 22 Copynumber: 24.9 Consensus size: 22
21048 TTCATGGGGA
* * *
21058 GGTTATCAAAATTTTAGAGGGA
1 GGTTATCAAAATTTTATAGTGT
* *
21080 GATTATCAAAATTTCATAGTGT
1 GGTTATCAAAATTTTATAGTGT
*
21102 GGTTATCAAAATTTTATAATGT
1 GGTTATCAAAATTTTATAGTGT
* * * *
21124 -G----C--TATTTTAGAGGGAGA
1 GGTTATCAAAATTTTATA--GTGT
*
21141 GGTTATC-AAATTTTCATTGTGT
1 GGTTATCAAAATTTT-ATAGTGT
* * * * * *
21163 GGTAATTAAAGTTTCATAATGA
1 GGTTATCAAAATTTTATAGTGT
* *
21185 GTTTATCAAAA-TTTATAGTGA
1 GGTTATCAAAATTTTATAGTGT
* * *
21206 GATTAACAAAATTTGATAGTGT
1 GGTTATCAAAATTTTATAGTGT
* * * *
21228 GGTTCTCAAAATTCTATAGAGA
1 GGTTATCAAAATTTTATAGTGT
* * * *
21250 GATTATCAAAATTTCATTG-GG
1 GGTTATCAAAATTTTATAGTGT
21271 GGTTATC-AAA----ATAGTGT
1 GGTTATCAAAATTTTATAGTGT
** ** *
21288 TCTTATCAAAATTTCGTAG-GA
1 GGTTATCAAAATTTTATAGTGT
* * *
21309 GGATAACAAAATTTTATAAG-GA
1 GGTTATCAAAATTTTAT-AGTGT
*
21331 GGTTAT-AGAAAATTTATAG-GT
1 GGTTATCA-AAATTTTATAGTGT
* * *
21352 ATGTTATCAAAATTTCATAAG-AT
1 -GGTTATCAAAATTTTAT-AGTGT
* *
21375 GGTTATCAAAATTTTATAGGGA
1 GGTTATCAAAATTTTATAGTGT
*
21397 GGTTTAT-AAAATTTTCATAGTGA
1 GG-TTATCAAAATTTT-ATAGTGT
* * *
21420 GG-TATCACAATTTCAT-GATAT
1 GGTTATCAAAATTTTATAG-TGT
* *
21441 GGTTATCAAAATTTCATAATGT
1 GGTTATCAAAATTTTATAGTGT
* * * * * *
21463 GATTAACGATATTTTATCG-GAA
1 GGTTATCAAAATTTTATAGTG-T
* *
21485 GGTTATCAAAATTTCATAATGT
1 GGTTATCAAAATTTTATAGTGT
* * * * *
21507 GCGCTTA-CTAACATTTCATTGGGA
1 G-G-TTATC-AAAATTTTATAGTGT
* *
21531 GGTTATCAAAATTTCATAGGGT
1 GGTTATCAAAATTTTATAGTGT
*
21553 GGTTATCAAAATTTCATTAG-GT
1 GGTTATCAAAATTTTA-TAGTGT
*
21575 GGTTATTAAAATTTTATAG
1 GGTTATCAAAATTTTATAG
21594 GCAGTGTAAC
Statistics
Matches: 371, Mismatches: 107, Indels: 73
0.67 0.19 0.13
Matches are distributed among these distances:
15 7 0.02
16 3 0.01
17 8 0.02
18 4 0.01
20 4 0.01
21 55 0.15
22 241 0.65
23 34 0.09
24 15 0.04
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.38
Consensus pattern (22 bp):
GGTTATCAAAATTTTATAGTGT
Found at i:21163 original size:61 final size:59
Alignment explanation
Indices: 21068--21183 Score: 160
Period size: 61 Copynumber: 1.9 Consensus size: 59
21058 GGTTATCAAA
* *
21068 ATTTTAGAGGGAGATTATCAAAATTTCATAGTGTGGTTATCAAAATTTTATAATGTGCT
1 ATTTTAGAGGGAGATTATCAAAATTTCATAGTGTGGTAATCAAAATTTCATAATGTGCT
* * * *
21127 ATTTTAGAGGGAGAGGTTATCAAATTTTCATTGTGTGGTAATTAAAGTTTCATAATG
1 ATTTTAGAGGGAGA--TTATCAAAATTTCATAGTGTGGTAATCAAAATTTCATAATG
21184 AGTTTATCAA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
59 14 0.29
61 35 0.71
ACGTcount: A:0.33, C:0.06, G:0.21, T:0.41
Consensus pattern (59 bp):
ATTTTAGAGGGAGATTATCAAAATTTCATAGTGTGGTAATCAAAATTTCATAATGTGCT
Found at i:21416 original size:23 final size:22
Alignment explanation
Indices: 21187--21652 Score: 174
Period size: 22 Copynumber: 21.5 Consensus size: 22
21177 CATAATGAGT
* *
21187 TTATCAAAA-TTTATAGTGAGA
1 TTATCAAAATTTTATAGGGAGG
* * * *
21208 TTAACAAAATTTGATAGTGTGG
1 TTATCAAAATTTTATAGGGAGG
* * * *
21230 TTCTCAAAATTCTATAGAGAGA
1 TTATCAAAATTTTATAGGGAGG
* *
21252 TTATCAAAATTTCATTGGG-GG
1 TTATCAAAATTTTATAGGGAGG
* ***
21273 TTATC-AAA----ATAGTGTTC
1 TTATCAAAATTTTATAGGGAGG
**
21290 TTATCAAAATTTCGTA-GGAGG
1 TTATCAAAATTTTATAGGGAGG
* * *
21311 ATAACAAAATTTTATAAGGAGG
1 TTATCAAAATTTTATAGGGAGG
* * *
21333 TTAT-AGAAAATTTATAGGTATG
1 TTATCA-AAATTTTATAGGGAGG
* *
21355 TTATCAAAATTTCATA-AGATGG
1 TTATCAAAATTTTATAGGGA-GG
21377 TTATCAAAATTTTATAGGGAGG
1 TTATCAAAATTTTATAGGGAGG
*
21399 TTTAT-AAAATTTTCATAGTGAGG
1 -TTATCAAAATTTT-ATAGGGAGG
* * **
21422 -TATCACAATTTCAT-GATATGG
1 TTATCAAAATTTTATAGGGA-GG
* ** * *
21443 TTATCAAAATTTCATAATGTGA
1 TTATCAAAATTTTATAGGGAGG
* * * * *
21465 TTAACGATATTTTATCGGAAGG
1 TTATCAAAATTTTATAGGGAGG
* * * *
21487 TTATCAAAATTTCATAATGTGCGC
1 TTATCAAAATTTTAT-A-GGGAGG
* * *
21511 TTA-CTAACATTTCATTGGGAGG
1 TTATC-AAAATTTTATAGGGAGG
* *
21533 TTATCAAAATTTCATAGGGTGG
1 TTATCAAAATTTTATAGGGAGG
* *
21555 TTATCAAAATTTCATTA-GGTGG
1 TTATCAAAATTTTA-TAGGGAGG
* *
21577 TTATTAAAATTTTATAGGCA-G
1 TTATCAAAATTTTATAGGGAGG
* *
21598 TGTAACAAAA-TTTATAGGGAAG
1 T-TATCAAAATTTTATAGGGAGG
* * *
21620 TTAACATAATTTTATATGGAGG
1 TTATCAAAATTTTATAGGGAGG
* *
21642 TTCTCGAAATT
1 TTATCAAAATT
21653 CGATAATATT
Statistics
Matches: 323, Mismatches: 95, Indels: 53
0.69 0.20 0.11
Matches are distributed among these distances:
16 4 0.01
17 5 0.02
18 3 0.01
20 5 0.02
21 56 0.17
22 217 0.67
23 19 0.06
24 14 0.04
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.37
Consensus pattern (22 bp):
TTATCAAAATTTTATAGGGAGG
Found at i:21586 original size:44 final size:44
Alignment explanation
Indices: 21290--21588 Score: 195
Period size: 44 Copynumber: 6.8 Consensus size: 44
21280 AATAGTGTTC
* * * * *
21290 TTATCAAAATTTC-GTAGGAGGATAACAAAATTTTATAAGGAGG
1 TTATCAAAATTTCATTAGGAGGTTATCAAAATTTCATAAGGTGG
* * *
21333 TTATAGAAAATTT-A-TAGGTATGTTATCAAAATTTCATAAGATGG
1 TTAT-CAAAATTTCATTAGG-AGGTTATCAAAATTTCATAAGGTGG
*
21377 TTATCAAAATTTTA-TAGGGAGGTTTAT-AAAATTTTCAT-A-GTGAG
1 TTATCAAAATTTCATTA-GGAGG-TTATCAAAA-TTTCATAAGGTG-G
* * * * * *
21421 GTATCACAATTTCATGA-TATGGTTATCAAAATTTCATAATGTGA
1 TTATCAAAATTTCATTAGGA-GGTTATCAAAATTTCATAAGGTGG
* * * * * *
21465 TTAACGATATTTTA-TCGGAAGGTTATCAAAATTTCATAATGTGCG
1 TTATCAAAATTTCATTAGG-AGGTTATCAAAATTTCATAAGGTG-G
* * *
21510 CTTA-CTAACATTTCATTGGGAGGTTATCAAAATTTCATAGGGTGG
1 -TTATC-AAAATTTCATTAGGAGGTTATCAAAATTTCATAAGGTGG
* *
21555 TTATCAAAATTTCATTAGGTGGTTATTAAAATTT
1 TTATCAAAATTTCATTAGGAGGTTATCAAAATTT
21589 TATAGGCAGT
Statistics
Matches: 200, Mismatches: 36, Indels: 39
0.73 0.13 0.14
Matches are distributed among these distances:
43 28 0.14
44 118 0.59
45 20 0.10
46 31 0.16
47 3 0.01
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.38
Consensus pattern (44 bp):
TTATCAAAATTTCATTAGGAGGTTATCAAAATTTCATAAGGTGG
Found at i:21624 original size:21 final size:21
Alignment explanation
Indices: 21582--21631 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
21572 GGTGGTTATT
*
21582 AAAATTTTATAGGCAGTGTAAC
1 AAAA-TTTATAGGAAGTGTAAC
21604 AAAATTTATAGGGAAGT-TAAC
1 AAAATTTATA-GGAAGTGTAAC
*
21625 ATAATTT
1 AAAATTT
21632 TATATGGAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 16 0.64
22 9 0.36
ACGTcount: A:0.44, C:0.06, G:0.16, T:0.34
Consensus pattern (21 bp):
AAAATTTATAGGAAGTGTAAC
Found at i:21731 original size:20 final size:21
Alignment explanation
Indices: 21685--21735 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 21
21675 TTATAATGTA
*
21685 ATTATCAAAATTTGATATGGAG
1 ATTATCAAAATTT-ATATAGAG
*
21707 ATTATCAAAATTT-TATAGTG
1 ATTATCAAAATTTATATAGAG
21727 ATTATCAAA
1 ATTATCAAA
21736 TTTCATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 14 0.52
22 13 0.48
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.39
Consensus pattern (21 bp):
ATTATCAAAATTTATATAGAG
Found at i:23948 original size:42 final size:44
Alignment explanation
Indices: 23897--23990 Score: 131
Period size: 45 Copynumber: 2.2 Consensus size: 44
23887 AGTGTATTAC
* *
23897 CTAA-ATTCTACT-C-CATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACTCCTCATCTCTAGATAATTCATCAAAATAAAA
23938 CTAATATTCTACTCCTTCATCTCTAGATAATTCATCAAAATAAAA
1 CTAATATTCTACTCC-TCATCTCTAGATAATTCATCAAAATAAAA
*
23983 TTAATATT
1 CTAATATT
23991 AATTGTTGTT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 4 0.09
42 8 0.17
43 1 0.02
45 33 0.72
ACGTcount: A:0.39, C:0.20, G:0.04, T:0.36
Consensus pattern (44 bp):
CTAATATTCTACTCCTCATCTCTAGATAATTCATCAAAATAAAA
Found at i:41623 original size:25 final size:25
Alignment explanation
Indices: 41589--41637 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
41579 CCAAACAATC
*
41589 TTGAGTACTCTCGCTCGGTCTCTAT
1 TTGAGCACTCTCGCTCGGTCTCTAT
*
41614 TTGAGCACTCTCGCTTGGTCTCTA
1 TTGAGCACTCTCGCTCGGTCTCTA
41638 CAAACTAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.12, C:0.29, G:0.20, T:0.39
Consensus pattern (25 bp):
TTGAGCACTCTCGCTCGGTCTCTAT
Found at i:42494 original size:24 final size:26
Alignment explanation
Indices: 42452--42503 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 26
42442 TAACTCTCAC
* * *
42452 TCAATCTCTCAACCCAAT-CTAACAA
1 TCAATCTCTAAACCAAATCCAAACAA
42477 TCAAT-TCTAAACCAAATCCAAACAA
1 TCAATCTCTAAACCAAATCCAAACAA
42502 TC
1 TC
42504 TTGAGCAATC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 10 0.43
25 13 0.57
ACGTcount: A:0.44, C:0.33, G:0.00, T:0.23
Consensus pattern (26 bp):
TCAATCTCTAAACCAAATCCAAACAA
Found at i:42546 original size:25 final size:25
Alignment explanation
Indices: 42504--42552 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
42494 CCAAACAATC
*
42504 TTGAGCAATCTCGTTCGGTCTCTAT
1 TTGAGCAATCTCGCTCGGTCTCTAT
* *
42529 TTGAGCACTCTTGCTCGGTCTCTA
1 TTGAGCAATCTCGCTCGGTCTCTA
42553 CAAACTAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.14, C:0.27, G:0.20, T:0.39
Consensus pattern (25 bp):
TTGAGCAATCTCGCTCGGTCTCTAT
Found at i:48057 original size:13 final size:13
Alignment explanation
Indices: 48041--48065 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48031 AATTAAATAA
48041 ATAAATAAAAATT
1 ATAAATAAAAATT
48054 ATAAATAAAAAT
1 ATAAATAAAAAT
48066 ATTTATGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
ATAAATAAAAATT
Found at i:51320 original size:7 final size:7
Alignment explanation
Indices: 51308--51332 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
51298 TAAAGAAATT
51308 AAAAGGG
1 AAAAGGG
51315 AAAAGGG
1 AAAAGGG
51322 AAAAGGG
1 AAAAGGG
51329 AAAA
1 AAAA
51333 ACTTAATTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (7 bp):
AAAAGGG
Found at i:52773 original size:21 final size:21
Alignment explanation
Indices: 52730--52776 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
52720 AGGGATCGAG
*
52730 CTGGGCGCTGAGCCTTGTCGC
1 CTGGGCGCTGAGCATTGTCGC
*
52751 CTGGGCGCTGAGGCATT-TTGC
1 CTGGGCGCTGA-GCATTGTCGC
52772 CTGGG
1 CTGGG
52777 TGCCCAGCGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.06, C:0.28, G:0.40, T:0.26
Consensus pattern (21 bp):
CTGGGCGCTGAGCATTGTCGC
Found at i:53013 original size:13 final size:14
Alignment explanation
Indices: 52995--53044 Score: 52
Period size: 13 Copynumber: 3.7 Consensus size: 14
52985 AGTTAGTAAC
52995 AAAAATTCAAAA-T
1 AAAAATTCAAAATT
*
53008 AAAAA-TGAAAATT
1 AAAAATTCAAAATT
53021 AAAAATT-AAGAATT
1 AAAAATTCAA-AATT
*
53035 AGAAATTCAA
1 AAAAATTCAA
53045 TTGGATTGCC
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
12 5 0.16
13 13 0.42
14 11 0.35
15 2 0.06
ACGTcount: A:0.66, C:0.04, G:0.06, T:0.24
Consensus pattern (14 bp):
AAAAATTCAAAATT
Found at i:63642 original size:22 final size:22
Alignment explanation
Indices: 63617--63661 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
63607 AAAAATTACC
*
63617 AATTCTCTTGCAAACTAAATCA
1 AATTCTCTTGAAAACTAAATCA
*
63639 AATTCTTTTGAAAACTAAATCA
1 AATTCTCTTGAAAACTAAATCA
63661 A
1 A
63662 GAATTCCCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.44, C:0.18, G:0.04, T:0.33
Consensus pattern (22 bp):
AATTCTCTTGAAAACTAAATCA
Found at i:63831 original size:12 final size:12
Alignment explanation
Indices: 63792--63833 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
63782 CAACTAAGAT
63792 AAAAATTGCAGC
1 AAAAATTGCAGC
* *
63804 AAAAGTAG-AG-
1 AAAAATTGCAGC
63814 AAAAATTGCAGC
1 AAAAATTGCAGC
63826 AAAAATTG
1 AAAAATTG
63834 GAGGAGATGA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
10 6 0.25
11 4 0.17
12 14 0.58
ACGTcount: A:0.55, C:0.10, G:0.19, T:0.17
Consensus pattern (12 bp):
AAAAATTGCAGC
Done.