Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019002.1 Corchorus olitorius cultivar O-4 contig19035, 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: 46117
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:1609 original size:123 final size:126
Alignment explanation
Indices: 1385--1630 Score: 392
Period size: 131 Copynumber: 1.9 Consensus size: 126
1375 ATTTAAGAAA
*
1385 TATATTTAAAAGTTATAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAAT
1 TATATTTAAAAATTATAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT---AT
*
1450 AGGTATAAGGATATTAGATTTAATTAAATAAAAATAGATTTTTTAGTTGAGTAAAACTGTAAAAG
63 A-GTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAAG
*
1515 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT-TA-
1 TATATTT-AAAAATTATAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATATAG
1578 TA-AA-GATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACT
65 TATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACT
1631 ATCAAAGTTT
Statistics
Matches: 112, Mismatches: 3, Indels: 9
0.90 0.02 0.07
Matches are distributed among these distances:
123 48 0.43
124 2 0.02
125 2 0.02
127 2 0.02
130 7 0.06
131 51 0.46
ACGTcount: A:0.49, C:0.01, G:0.11, T:0.39
Consensus pattern (126 bp):
TATATTTAAAAATTATAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATATAGT
ATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAAG
Found at i:1638 original size:123 final size:126
Alignment explanation
Indices: 1385--1638 Score: 390
Period size: 123 Copynumber: 2.0 Consensus size: 126
1375 ATTTAAGAAA
*
1385 TATATTTAAAAGTTATAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAAT
1 TATATTTAAAAATTATAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT---AT
* *
1450 AGGTATAAGGATATTAGATTTAATTAAATAAAAATAGATTTTTTAGTTGAGTAAAACTGTAAAAG
63 A-GTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
*
1515 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT-TA-
1 TATATTT-AAAAATTATAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATATAG
*
1578 TA-AA-GATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATCAAAG
65 TATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
1638 T
1 T
1639 TTAAACAATG
Statistics
Matches: 118, Mismatches: 5, Indels: 9
0.89 0.04 0.07
Matches are distributed among these distances:
123 54 0.46
124 2 0.02
125 2 0.02
127 2 0.02
130 7 0.06
131 51 0.43
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.38
Consensus pattern (126 bp):
TATATTTAAAAATTATAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATATAGT
ATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
Found at i:1664 original size:123 final size:127
Alignment explanation
Indices: 1406--1664 Score: 339
Period size: 123 Copynumber: 2.0 Consensus size: 127
1396 GTTATAATAT
1406 ATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAAATAGGTATAAGGATATTAGATTT
1 ATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT---ATA-GTATAAGGATATTAGATTT
* * *** *
1471 AATTAAATAAAAATAGATTTTTTAGTTGAGTAAAACTGTAAAAGTATATTTAAAAAATTCTAATA
62 AATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATAAACAAAAAATTCTAAGA
*
1536 T
127 A
1537 ATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAAT-TA-TA-AA-GATATTAGATTTAATT
1 ATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATATAGTATAAGGATATTAGATTTAATT
* * * *
1598 AAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATCAAAGTTTAAACAATGACATT-TAAGAA
66 AAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATAAACAA-AAAATTCTAAGAA
1660 ATATA
1 ATATA
1665 TTCGAAAAAT
Statistics
Matches: 116, Mismatches: 11, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
123 67 0.58
124 6 0.05
125 2 0.02
127 2 0.02
131 39 0.34
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.37
Consensus pattern (127 bp):
ATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATATAGTATAAGGATATTAGATTTAATT
AAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATAAACAAAAAATTCTAAGAA
Found at i:18384 original size:27 final size:23
Alignment explanation
Indices: 18329--18375 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
18319 CTTGCTTTGA
18329 ACATATATTACATTAACTAATGC
1 ACATATATTACATTAACTAATGC
*
18352 ACATATATTACATTTACTAATGC
1 ACATATATTACATTAACTAATGC
18375 A
1 A
18376 GGCACATATG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.17, G:0.04, T:0.36
Consensus pattern (23 bp):
ACATATATTACATTAACTAATGC
Found at i:22567 original size:22 final size:22
Alignment explanation
Indices: 22539--22754 Score: 134
Period size: 22 Copynumber: 9.7 Consensus size: 22
22529 TGTCTCTGTG
22539 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * *
22561 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AAGA
* *
22584 -GGTTATCAAAATTCCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
* *
22605 TGGTTACCAAAATTTCATATGA
1 TGGTTATCAAAATTTCATAAGA
** **
22627 AAGTTATCAAAATTTCATGGGA
1 TGGTTATCAAAATTTCATAAGA
**
22649 AAGTTATCAAAATTTCATAATG-
1 TGGTTATCAAAATTTCATAA-GA
* *
22671 TGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAAGA
** * *
22693 TCGGGTTTATTGAAATTTCTTAGGA
1 T--GG-TTATCAAAATTTCATAAGA
* * *
22718 AGGTTATTAAAATTTCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
*
22740 TGGTTATCACAATTT
1 TGGTTATCAAAATTT
22755 TATTGAAAGG
Statistics
Matches: 149, Mismatches: 35, Indels: 20
0.73 0.17 0.10
Matches are distributed among these distances:
20 1 0.01
21 2 0.01
22 122 0.82
23 7 0.05
24 2 0.01
25 15 0.10
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:22642 original size:66 final size:67
Alignment explanation
Indices: 22536--22935 Score: 261
Period size: 66 Copynumber: 5.9 Consensus size: 67
22526 TCTTGTCTCT
* * ** * * *
22536 GTGTGGTTATCAAAATTTCATAAGATGGTTATTATAATTTCATGAGG-AGGTTATCAAAATTCCA
1 GTGTGGTTACCAAAATTTCATATGAAAGTTATCAAAATTTCATGAGGAAGGTTATCAAAATTTCA
22600 TA
66 TA
*
22602 GTGTGGTTACCAAAATTTCATATGAAAGTTATCAAAATTTCATG-GGAAAGTTATCAAAATTTCA
1 GTGTGGTTACCAAAATTTCATATGAAAGTTATCAAAATTTCATGAGGAAGGTTATCAAAATTTCA
22666 TA
66 TA
* * ** ** * *
22668 ATGTGGTTACCAAAATTTCATAGGATCGGGTTTATTGAAATTTC-TTAGGAAGGTTATTAAAATT
1 GTGTGGTTACCAAAATTTCATATGA--AAG-TTATCAAAATTTCATGAGGAAGGTTATCAAAATT
22732 TCATA
63 TCATA
* * * *
22737 GTGTGGTTATCACAATTTTAT-TGAAAGGTTATCAAAGAGATTATCAAAATGTCATAGCAAGGTT
1 GTGTGGTTACCAAAATTTCATATGAAA-GTTATC-AA-A-ATT-TC---ATG----AGGAAGGTT
22801 AT-AAGAATTTCATA
54 ATCAA-AATTTCATA
* * * * *
22815 GTGTGGTTAACAAAATTT--TATG-AGGTTA-CTAATATTTCATG-GGGAGGTTATTAAAATTTC
1 GTGTGGTTACCAAAATTTCATATGAAAGTTATC-AAAATTTCATGAGGAAGGTTATCAAAATTTC
22875 ATA
65 ATA
* * ** *
22878 GTGTGGTTATCAAAAATTT-TTAGTG-TGGTTATCAAAATTTCAT-ATGAAGGTTAT-AAAA
1 GTGTGGTTA-CCAAAATTTCATA-TGAAAGTTATCAAAATTTCATGAGGAAGGTTATCAAAA
22936 GTCTCAATTT
Statistics
Matches: 267, Mismatches: 41, Indels: 53
0.74 0.11 0.15
Matches are distributed among these distances:
63 26 0.10
64 9 0.03
65 8 0.03
66 106 0.40
67 3 0.01
68 8 0.03
69 51 0.19
70 2 0.01
71 2 0.01
72 3 0.01
74 4 0.01
75 4 0.01
76 2 0.01
77 4 0.01
78 35 0.13
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.38
Consensus pattern (67 bp):
GTGTGGTTACCAAAATTTCATATGAAAGTTATCAAAATTTCATGAGGAAGGTTATCAAAATTTCA
TA
Found at i:22822 original size:22 final size:21
Alignment explanation
Indices: 22797--22935 Score: 99
Period size: 22 Copynumber: 6.5 Consensus size: 21
22787 GTCATAGCAA
22797 GGTTATAAGAATTTCATAGTGT
1 GGTTATAA-AATTTCATAGTGT
* *
22819 GGTTAACAAAATTT--TA-TGA
1 GGTT-ATAAAATTTCATAGTGT
* * * *
22838 GGTTACTAATATTTCATGGGGA
1 GGTTA-TAAAATTTCATAGTGT
22860 GGTTATTAAAATTTCATAGTGT
1 GGTTA-TAAAATTTCATAGTGT
*
22882 GGTTATCAAAAATTT-TTAGTGT
1 GGTTAT--AAAATTTCATAGTGT
*
22904 GGTTATCAAAATTTCATA-TGAA
1 GGTTAT-AAAATTTCATAGTG-T
22926 GGTTATAAAA
1 GGTTATAAAA
22936 GTCTCAATTT
Statistics
Matches: 93, Mismatches: 15, Indels: 19
0.73 0.12 0.15
Matches are distributed among these distances:
18 1 0.01
19 12 0.13
20 2 0.02
21 15 0.16
22 53 0.57
23 10 0.11
ACGTcount: A:0.35, C:0.06, G:0.19, T:0.40
Consensus pattern (21 bp):
GGTTATAAAATTTCATAGTGT
Found at i:22930 original size:44 final size:43
Alignment explanation
Indices: 22777--22935 Score: 139
Period size: 44 Copynumber: 3.7 Consensus size: 43
22767 ATCAAAGAGA
* *
22777 TTATCAAAATGTCATA-GCAAGGTTATAAGAATTTCATAGTGTGG
1 TTATCAAAATTTCATATG--AGGTTATAAAAATTTCATAGTGTGG
* * * * *
22821 TTAACAAAATTT--TATGAGGTTACT-AATATTTCATGGGGAGG
1 TTATCAAAATTTCATATGAGGTTA-TAAAAATTTCATAGTGTGG
* * *
22862 TTATTAAAATTTCATAGTGTGGTTATCAAAAATTT-TTAGTGTGG
1 TTATCAAAATTTCATA-TGAGGTTAT-AAAAATTTCATAGTGTGG
22906 TTATCAAAATTTCATATGAAGGTTATAAAA
1 TTATCAAAATTTCATATG-AGGTTATAAAA
22936 GTCTCAATTT
Statistics
Matches: 90, Mismatches: 17, Indels: 17
0.73 0.14 0.14
Matches are distributed among these distances:
41 28 0.31
42 3 0.03
43 10 0.11
44 43 0.48
45 6 0.07
ACGTcount: A:0.36, C:0.07, G:0.18, T:0.38
Consensus pattern (43 bp):
TTATCAAAATTTCATATGAGGTTATAAAAATTTCATAGTGTGG
Found at i:23005 original size:22 final size:20
Alignment explanation
Indices: 22980--23019 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
22970 GAAGGTTATC
22980 AAATCTCATACAGTGATTATTG
1 AAATCTCAT--AGTGATTATTG
*
23002 AAATTTCATAGTGATTAT
1 AAATCTCATAGTGATTAT
23020 CAAAATATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
22 8 0.47
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (20 bp):
AAATCTCATAGTGATTATTG
Found at i:23025 original size:20 final size:20
Alignment explanation
Indices: 22991--23031 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
22981 AATCTCATAC
** *
22991 AGTGATTATTGAAATTTCAT
1 AGTGATTATCAAAATATCAT
23011 AGTGATTATCAAAATATCAT
1 AGTGATTATCAAAATATCAT
23031 A
1 A
23032 AAGAAGTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.39
Consensus pattern (20 bp):
AGTGATTATCAAAATATCAT
Found at i:23202 original size:22 final size:21
Alignment explanation
Indices: 23169--23635 Score: 184
Period size: 22 Copynumber: 21.3 Consensus size: 21
23159 AAATTTCAGG
*
23169 GAGGATATCAAAATTTCATAT
1 GAGGTTATCAAAATTTCATAT
23190 GAAGGTTATCAAAATTTCATAGTT
1 G-AGGTTATCAAAATTTCATA--T
* * *
23214 TA-GTTTTCAAAATTTCATAA
1 GAGGTTATCAAAATTTCATAT
*
23234 GAGGATTATCAAAATTTCATAGG
1 GAGG-TTATCAAAATTTCATA-T
* *
23257 GAGATTAACAAAATTTCATAAT
1 GAGGTTATCAAAATTTCAT-AT
** *
23279 GAGGTTATCAAAACATCATAGG
1 GAGGTTATCAAAATTTCATA-T
* *
23301 GTGGTTATCAAAA-TT--TGT
1 GAGGTTATCAAAATTTCATAT
* *
23319 -A-GTTATCAAGATTTCATAAG
1 GAGGTTATCAAAATTTCAT-AT
* * *
23339 GAGGCTATCAAAATTTTATAGG
1 GAGGTTATCAAAATTTCATA-T
* *
23361 GACGTTTATCAAAATTTTATA-
1 GA-GGTTATCAAAATTTCATAT
* *
23382 GAAAGATTTATCAAAATTTCATAGC
1 G--AG-GTTATCAAAATTTCATA-T
*
23407 GAGGTTATCACAATTTCATAGT
1 GAGGTTATCAAAATTTCATA-T
* * *
23429 GTGATTATCAAAATTTCAGATT
1 GAGGTTATCAAAATTTCATA-T
* *
23451 GTGATTA-CTAACAA-TTCATTAT
1 GAGGTTATC-AA-AATTTCA-TAT
* * * *
23473 GGAGAATT-TTAAATTTTCATAAC
1 -GAG-GTTATCAAAATTTCAT-AT
* * * *
23496 GTGGTTATCAATATATCAGAT
1 GAGGTTATCAAAATTTCATAT
* *
23517 GGAGGTTATCAACATCTCATAGT
1 -GAGGTTATCAAAATTTCATA-T
*
23540 GTTGGTTATCAAAATTTCAT-T
1 G-AGGTTATCAAAATTTCATAT
*
23561 GGGAAGTTATCAAAATTTCATAGT
1 --GAGGTTATCAAAATTTCATA-T
* *
23585 GAGGTCT-CCAAAATTTCTTAGT
1 GAGGT-TATCAAAATTTCATA-T
* *
23607 GAGGTTAACAAAATTTCATAA
1 GAGGTTATCAAAATTTCATAT
23628 GAAGGTTA
1 G-AGGTTA
23636 AAAAAAATTA
Statistics
Matches: 341, Mismatches: 65, Indels: 79
0.70 0.13 0.16
Matches are distributed among these distances:
16 9 0.03
17 2 0.01
19 2 0.01
20 1 0.00
21 14 0.04
22 237 0.70
23 70 0.21
24 5 0.01
25 1 0.00
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.36
Consensus pattern (21 bp):
GAGGTTATCAAAATTTCATAT
Found at i:23227 original size:44 final size:43
Alignment explanation
Indices: 23159--23635 Score: 244
Period size: 44 Copynumber: 10.9 Consensus size: 43
23149 GGAGTAATCG
23159 AAATTTC--AGGGAGGA-TATCAAAATTTCATATGAAGGTTATCA
1 AAATTTCATAGGGA-GATTATCAAAATTTCATATG-AGGTTATCA
** * *
23201 AAATTTCATAGTTTAG-TTTTCAAAATTTCATAAGAGGATTATCA
1 AAATTTCATAG-GGAGATTATCAAAATTTCATATGAGG-TTATCA
*
23245 AAATTTCATAGGGAGATTAACAAAATTTCATAATGAGGTTATCA
1 AAATTTCATAGGGAGATTATCAAAATTTCAT-ATGAGGTTATCA
** * * *
23289 AAACATCATAGGGTGGTTATCAAAA-TT--TGT-A-GTTATCA
1 AAATTTCATAGGGAGATTATCAAAATTTCATATGAGGTTATCA
* * ** * * *
23327 AGATTTCATAAGGAGGCTATCAAAATTTTATAGGGACGTTTATCA
1 AAATTTCATAGGGAGATTATCAAAATTTCATA-TGA-GGTTATCA
* ** *
23372 AAATTTTATAGAAAGATTTATCAAAATTTCATAGCGAGGTTATCA
1 AAATTTCATAGGGAGA-TTATCAAAATTTCATA-TGAGGTTATCA
* * * * * *
23417 CAATTTCATAGTGTGATTATCAAAATTTCAGATTGTGATTA-CTA
1 AAATTTCATAGGGAGATTATCAAAATTTCATA-TGAGGTTATC-A
* * * * *
23461 ACAA-TTCATTATGGAGAATT-TTAAATTTTCATAACGTGGTTATCA
1 A-AATTTCA-TAGGGAG-ATTATCAAAATTTCAT-ATGAGGTTATCA
* * * * * * * *
23506 ATATATCAGATGGAGGTTATCAACATCTCATAGTGTTGGTTATCA
1 AAATTTCATAGGGAGATTATCAAAATTTCATA-TG-AGGTTATCA
* *
23551 AAATTTCATTGGGA-AGTTATCAAAATTTCATAGTGAGGTCT-CCA
1 AAATTTCATAGGGAGA-TTATCAAAATTTCATA-TGAGGT-TATCA
* * * * *
23595 AAATTTCTTAGTGAGGTTAACAAAATTTCATAAGAAGGTTA
1 AAATTTCATAGGGAGATTATCAAAATTTCATATG-AGGTTA
23636 AAAAAAATTA
Statistics
Matches: 327, Mismatches: 78, Indels: 58
0.71 0.17 0.13
Matches are distributed among these distances:
38 26 0.08
39 3 0.01
40 1 0.00
41 2 0.01
42 7 0.02
43 14 0.04
44 150 0.46
45 102 0.31
46 22 0.07
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (43 bp):
AAATTTCATAGGGAGATTATCAAAATTTCATATGAGGTTATCA
Found at i:23415 original size:45 final size:45
Alignment explanation
Indices: 23344--23446 Score: 118
Period size: 45 Copynumber: 2.3 Consensus size: 45
23334 ATAAGGAGGC
* * * *
23344 TATCAAAATTTTATAGGGACGTTTATCAAAATTTTATAGAAAGATT
1 TATCAAAATTTCATAGCGACGGTTATCAAAATTTCATAGAAAGA-T
* ***
23390 TATCAAAATTTCATAGCGA-GGTTATCACAATTTCATAGTGTGAT
1 TATCAAAATTTCATAGCGACGGTTATCAAAATTTCATAGAAAGAT
23434 TATCAAAATTTCA
1 TATCAAAATTTCA
23447 GATTGTGATT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
44 14 0.29
45 18 0.37
46 17 0.35
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.38
Consensus pattern (45 bp):
TATCAAAATTTCATAGCGACGGTTATCAAAATTTCATAGAAAGAT
Found at i:23648 original size:21 final size:22
Alignment explanation
Indices: 23608--23655 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
23598 TTTCTTAGTG
* * *
23608 AGGTTAACAAAATTTCATAAGA
1 AGGTTAAAAAAAATTCATAAAA
23630 AGGTTAAAAAAAATT-ATAAAA
1 AGGTTAAAAAAAATTCATAAAA
23651 AGGTT
1 AGGTT
23656 CTCGATATTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.54, C:0.04, G:0.15, T:0.27
Consensus pattern (22 bp):
AGGTTAAAAAAAATTCATAAAA
Found at i:23943 original size:22 final size:22
Alignment explanation
Indices: 23895--23950 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
23885 TATTTTTATT
*
23895 AAATTTTGATAACCACACTATG
1 AAATTTTGATAACCACACTATA
* ** *
23917 GAATTTTGATAATTACCCTATA
1 AAATTTTGATAACCACACTATA
*
23939 AAATTCTGATAA
1 AAATTTTGATAA
23951 ACTCCCAATG
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (22 bp):
AAATTTTGATAACCACACTATA
Found at i:24306 original size:22 final size:22
Alignment explanation
Indices: 24154--24340 Score: 96
Period size: 22 Copynumber: 8.5 Consensus size: 22
24144 ACATAGTTTT
* *
24154 ACTATGAAATTTTGATAATCTC
1 ACTATGAAATTTTGATAACCAC
* * *
24176 GCTAT-ATTATTTTGATAACCTC
1 ACTATGA-AATTTTGATAACCAC
* * *
24198 -CTTAAGAAATTGTGATAACCTC
1 AC-TATGAAATTTTGATAACCAC
* * * * * *
24220 CCTGTGGAACTTTAATAACTAC
1 ACTATGAAATTTTGATAACCAC
* *
24242 ACTATGAAATTCTCATAACCATC
1 ACTATGAAATTTTGATAACCA-C
* *
24265 -CTATGAAATTTTGGTCACCAC
1 ACTATGAAATTTTGATAACCAC
*
24286 ACTCTGAAATTTTGATAACCAC
1 ACTATGAAATTTTGATAACCAC
* * *
24308 AGTAT-TAATTTGTGATAACCTC
1 ACTATGAAATTT-TGATAACCAC
24330 TA-TATGAAATT
1 -ACTATGAAATT
24341 AATTTTGATG
Statistics
Matches: 123, Mismatches: 33, Indels: 17
0.71 0.19 0.10
Matches are distributed among these distances:
21 8 0.07
22 107 0.87
23 8 0.07
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (22 bp):
ACTATGAAATTTTGATAACCAC
Found at i:24360 original size:26 final size:27
Alignment explanation
Indices: 24311--24366 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
24301 TAACCACAGT
*
24311 ATTAATTTGTGATAACCTCTATATGAA
1 ATTAATTTGTGATAACCTCTATATAAA
*
24338 ATTAATTT-TGATGACCT-TAATATAAA
1 ATTAATTTGTGATAACCTCT-ATATAAA
24364 ATT
1 ATT
24367 TTGAATACCA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 1 0.04
26 17 0.65
27 8 0.31
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.43
Consensus pattern (27 bp):
ATTAATTTGTGATAACCTCTATATAAA
Found at i:24457 original size:22 final size:21
Alignment explanation
Indices: 24409--24597 Score: 107
Period size: 22 Copynumber: 8.6 Consensus size: 21
24399 GATTTGGTAG
* *
24409 ACTATGAAATTTGGATAATCAA
1 ACTATGAAATTTTGATAA-CAC
24431 ACTATGAAATTTTGATAACATC
1 ACTATGAAATTTTGATAACA-C
* * * *
24453 CCTATGGAATGTTGATAACTTC
1 ACTATGAAATTTTGATAAC-AC
* *
24475 -CATAT-ATAATTTAGTGTTAATCTC
1 AC-TATGA-AATTT--TGATAA-CAC
24499 ACTATGAAATTTTGATAAACAC
1 ACTATGAAATTTTGAT-AACAC
* * *
24521 AATATGAAACTTTGATTAC-C
1 ACTATGAAATTTTGATAACAC
*
24541 TTCTATGAAATTTTTG-TAACCAC
1 -ACTATGAAA-TTTTGATAA-CAC
* *
24564 ATTATGAAATTTTGATAGCCAC
1 ACTATGAAATTTTGATA-ACAC
24586 ACTATGAAATTT
1 ACTATGAAATTT
24598 CAATAATCTA
Statistics
Matches: 129, Mismatches: 22, Indels: 32
0.70 0.12 0.17
Matches are distributed among these distances:
20 1 0.01
21 19 0.15
22 88 0.68
23 3 0.02
24 15 0.12
25 3 0.02
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.38
Consensus pattern (21 bp):
ACTATGAAATTTTGATAACAC
Found at i:29929 original size:21 final size:22
Alignment explanation
Indices: 29903--29943 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
29893 CCAGGTTACA
29903 TAAACCCT-AATTAGTTTAAAC
1 TAAACCCTAAATTAGTTTAAAC
29924 TAAACCCTAAATTAGTTTAA
1 TAAACCCTAAATTAGTTTAA
29944 TACCCATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.44, C:0.17, G:0.05, T:0.34
Consensus pattern (22 bp):
TAAACCCTAAATTAGTTTAAAC
Found at i:30683 original size:20 final size:21
Alignment explanation
Indices: 30658--30724 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 21
30648 TTGTATGAAA
30658 TTTGATAA-TCACTATAAAAT
1 TTTGATAACTCACTATAAAAT
30678 TTTGATAACCTC-CATATAAAAT
1 TTTGATAA-CTCAC-TATAAAAT
* *
30700 TTTGATAATTACACTATAAAGT
1 TTTGATAACT-CACTATAAAAT
30722 TTT
1 TTT
30725 TATGATGATA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
20 8 0.20
21 2 0.05
22 29 0.73
23 1 0.03
ACGTcount: A:0.40, C:0.12, G:0.06, T:0.42
Consensus pattern (21 bp):
TTTGATAACTCACTATAAAAT
Found at i:30698 original size:22 final size:22
Alignment explanation
Indices: 30651--30707 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
30641 TAAATATTTG
30651 TATGAAA-TTTGATAA--T-CA
1 TATGAAATTTTGATAACCTCCA
*
30669 CTATAAAATTTTGATAACCTCCA
1 -TATGAAATTTTGATAACCTCCA
*
30692 TATAAAATTTTGATAA
1 TATGAAATTTTGATAA
30708 TTACACTATA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
19 6 0.18
20 8 0.24
22 17 0.52
23 2 0.06
ACGTcount: A:0.44, C:0.11, G:0.07, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCCA
Found at i:31123 original size:21 final size:22
Alignment explanation
Indices: 30817--31552 Score: 238
Period size: 22 Copynumber: 33.5 Consensus size: 22
30807 CTATAAAAAT
*
30817 TTTTAATAACCA-CCTAATGAAA
1 TTTTGATAACCATCCT-ATGAAA
* *
30839 TTTTGATAACTA-CCCATGAAA
1 TTTTGATAACCATCCTATGAAA
* *
30860 TTTTGATAGCC-TCCCAATGAAA
1 TTTTGATAACCAT-CCTATGAAA
* * * *
30882 TGTTGTTAAGCGCA-CATTATGATA
1 TTTTGATAA-C-CATC-CTATGAAA
* * *
30906 TTTTGATAACCTTCCGATAAAA
1 TTTTGATAACCATCCTATGAAA
* *
30928 TATTGGTAATCACAT--TATGAAA
1 TTTTGATAA-C-CATCCTATGAAA
*
30950 TTTTGATAACCATACC-ATAAAA
1 TTTTGATAACCAT-CCTATGAAA
*
30972 TTGTGAT-ACC-TCACTATGAAA
1 TTTTGATAACCATC-CTATGAAA
* *
30993 TTTTTATAAACC-TCCCTATAAAA
1 TTTTGAT-AACCAT-CCTATGAAA
* *
31016 TTTTGACAAACC-TCCATTTGAAA
1 TTTTGA-TAACCATCC-TATGAAA
31039 TTTTGATAACC-T-C-ATGAAA
1 TTTTGATAACCATCCTATGAAA
*
31058 TTTTGAAAACCA-CCTCATGAAA
1 TTTTGATAACCATCCT-ATGAAA
*
31080 TTTTGATAACCATCTTATGAAA
1 TTTTGATAACCATCCTATGAAA
*
31102 TTTTGGTAA-CATCCCTAT-AAA
1 TTTTGATAACCAT-CCTATGAAA
* * *
31123 TTTTTTATAA-TATCCTTATAAAA
1 -TTTTGATAACCATCC-TATGAAA
* * * **
31146 TTTCGTTAACC-TACTACAAAA
1 TTTTGATAACCATCCTATGAAA
* * *
31167 TTTTTGATAA-GAACACTATTAAA
1 -TTTTGATAACCATC-CTATGAAA
* *
31190 TTTTGATAACC-CCCAATGAAA
1 TTTTGATAACCATCCTATGAAA
* * * **
31211 TTTCGTTAACC-TACTACAAAA
1 TTTTGATAACCATCCTATGAAA
* * *
31232 TTTTTGATAA-GAACACTATTAAA
1 -TTTTGATAACCATC-CTATGAAA
***
31255 TTTTGATAACCAGAGTATGAAA
1 TTTTGATAACCATCCTATGAAA
*
31277 TTTT-AGTAACC-TCCTTGTGAAA
1 TTTTGA-TAACCATCC-TATGAAA
* *
31299 TTTTGACAACC-TTCTCATG-AA
1 TTTTGATAACCATCCT-ATGAAA
* * *
31320 TTTCGATAACCTTCTTATGAAA
1 TTTTGATAACCATCCTATGAAA
31342 TTTTGATAACC-TCCATATGAAAA
1 TTTTGATAACCATCC-TATG-AAA
31365 TTTTGATAA-CATCCTTATGAAATTTTA
1 TTTTGATAACCATCC-TATG-AA----A
*
31392 TTTTAATAACC-TCCTTATGAAA
1 TTTTGATAACCATCC-TATGAAA
* *
31414 TTTTGATAA-CATCCCATGGAA
1 TTTTGATAACCATCCTATGAAA
* * *
31435 TTGTGATAACTA-CACTATAAAA
1 TTTTGATAACCATC-CTATGAAA
* * *
31457 TTTTAACATCC-TACCTATGAAA
1 TTTTGATAACCAT-CCTATGAAA
*
31479 TTTTGGTAACCA-CACTAT-AGAA
1 TTTTGATAACCATC-CTATGA-AA
* *
31501 TTTTGAGAACCA-CACTAT-AAC
1 TTTTGATAACCATC-CTATGAAA
*
31522 TTTT-AGTAACCA-CACAATG-AA
1 TTTTGA-TAACCATC-CTATGAAA
31543 TTTTGATAAC
1 TTTTGATAAC
31553 TTCCAAAATT
Statistics
Matches: 531, Mismatches: 121, Indels: 125
0.68 0.16 0.16
Matches are distributed among these distances:
19 16 0.03
20 7 0.01
21 123 0.23
22 270 0.51
23 79 0.15
24 16 0.03
26 2 0.00
27 17 0.03
28 1 0.00
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.36
Consensus pattern (22 bp):
TTTTGATAACCATCCTATGAAA
Found at i:31264 original size:65 final size:65
Alignment explanation
Indices: 31143--31265 Score: 246
Period size: 65 Copynumber: 1.9 Consensus size: 65
31133 TATCCTTATA
31143 AAATTTCGTTAACCTACTACAAAATTTTTGATAAGAACACTATTAAATTTTGATAACCCCCAATG
1 AAATTTCGTTAACCTACTACAAAATTTTTGATAAGAACACTATTAAATTTTGATAACCCCCAATG
31208 AAATTTCGTTAACCTACTACAAAATTTTTGATAAGAACACTATTAAATTTTGATAACC
1 AAATTTCGTTAACCTACTACAAAATTTTTGATAAGAACACTATTAAATTTTGATAACC
31266 AGAGTATGAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 58 1.00
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.35
Consensus pattern (65 bp):
AAATTTCGTTAACCTACTACAAAATTTTTGATAAGAACACTATTAAATTTTGATAACCCCCAATG
Found at i:31341 original size:43 final size:44
Alignment explanation
Indices: 31270--31390 Score: 131
Period size: 43 Copynumber: 2.8 Consensus size: 44
31260 ATAACCAGAG
* * *
31270 TATGAAATTT-TAGTAACCTCCTTGTGAAATTTTGACAACCTTC-
1 TATGAAATTTCGA-TAACCTCCTTATGAAATTTTGACAACCTCCA
* *
31313 TCATG-AATTTCGATAACCTTCTTATGAAATTTTGATAACCTCCA
1 T-ATGAAATTTCGATAACCTCCTTATGAAATTTTGACAACCTCCA
* *
31357 TATGAAAATTTTGATAACATCCTTATGAAATTTT
1 TATG-AAATTTCGATAACCTCCTTATGAAATTTT
31391 ATTTTAATAA
Statistics
Matches: 65, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
43 35 0.54
44 5 0.08
45 25 0.38
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (44 bp):
TATGAAATTTCGATAACCTCCTTATGAAATTTTGACAACCTCCA
Found at i:31406 original size:27 final size:27
Alignment explanation
Indices: 31341--31417 Score: 99
Period size: 27 Copynumber: 3.0 Consensus size: 27
31331 TTCTTATGAA
*
31341 ATTTTGATAACCTCCATATGAAA----
1 ATTTTGATAACCTCCTTATGAAATTTT
*
31364 ATTTTGATAACATCCTTATGAAATTTT
1 ATTTTGATAACCTCCTTATGAAATTTT
*
31391 ATTTTAATAACCTCCTTATGAAATTTT
1 ATTTTGATAACCTCCTTATGAAATTTT
31418 GATAACATCC
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
23 21 0.46
27 25 0.54
ACGTcount: A:0.35, C:0.14, G:0.06, T:0.44
Consensus pattern (27 bp):
ATTTTGATAACCTCCTTATGAAATTTT
Found at i:32642 original size:26 final size:25
Alignment explanation
Indices: 32594--32644 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
32584 TTTCCATTAA
32594 TTTAATAATGGAATAATTAAAATATT
1 TTTAATAATGGAAT-ATTAAAATATT
32620 TTTAATAATGGCAAT-TTAGAAATAT
1 TTTAATAATGG-AATATTA-AAATAT
32645 ATTTGAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 3 0.13
26 17 0.74
27 3 0.13
ACGTcount: A:0.47, C:0.02, G:0.10, T:0.41
Consensus pattern (25 bp):
TTTAATAATGGAATATTAAAATATT
Found at i:32749 original size:2 final size:2
Alignment explanation
Indices: 32700--32736 Score: 56
Period size: 2 Copynumber: 18.0 Consensus size: 2
32690 TTCGTACTTT
*
32700 TA TA TA TA GTA TA GA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
32737 ATGTGTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (2 bp):
TA
Found at i:33924 original size:21 final size:21
Alignment explanation
Indices: 33882--33924 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
33872 GGTGGTGGTC
* *
33882 GAGGTGGAGGAAGAGGGCGTG
1 GAGGAGGAGGAAGAAGGCGTG
33903 GAGGAGGAGGAATGAAGG-GTG
1 GAGGAGGAGGAA-GAAGGCGTG
33924 G
1 G
33925 GAGCAAGGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.28, C:0.02, G:0.60, T:0.09
Consensus pattern (21 bp):
GAGGAGGAGGAAGAAGGCGTG
Found at i:35737 original size:30 final size:30
Alignment explanation
Indices: 35701--35762 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
35691 GTTAATAAGC
35701 CATTAAAATTTGAGGGTATAAGAGAAAAGT
1 CATTAAAATTTGAGGGTATAAGAGAAAAGT
*
35731 CATTAAAATTTGAGGGTATAAGAGGAAAGT
1 CATTAAAATTTGAGGGTATAAGAGAAAAGT
35761 CA
1 CA
35763 AGATAAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.45, C:0.05, G:0.24, T:0.26
Consensus pattern (30 bp):
CATTAAAATTTGAGGGTATAAGAGAAAAGT
Found at i:36075 original size:24 final size:24
Alignment explanation
Indices: 36048--36096 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
36038 TCCAAACATT
36048 AACAAAATC-TTCAAATCTCAACTA
1 AACAAAATCATTCAAAT-TCAACTA
* *
36072 AACAACATCATTGAAATTCAACTA
1 AACAAAATCATTCAAATTCAACTA
36096 A
1 A
36097 GTTCCAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 16 0.73
25 6 0.27
ACGTcount: A:0.51, C:0.22, G:0.02, T:0.24
Consensus pattern (24 bp):
AACAAAATCATTCAAATTCAACTA
Found at i:36406 original size:6 final size:6
Alignment explanation
Indices: 36395--36420 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
36385 CAGGCTGCAC
36395 CACAAT CACAAT CACAAT CACAAT CA
1 CACAAT CACAAT CACAAT CACAAT CA
36421 TCCGTTAACG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.35, G:0.00, T:0.15
Consensus pattern (6 bp):
CACAAT
Found at i:36576 original size:39 final size:38
Alignment explanation
Indices: 36450--36597 Score: 226
Period size: 38 Copynumber: 3.9 Consensus size: 38
36440 TCGAGTCTAG
*
36450 CCAACAG-TTAACCCCCTGAGGCACGGATCCACTCTTA
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
36487 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
* * *
36525 CCAACAGTTTAACCCCCTGTGGTATGGGTCCACTCTTTA
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTC-TTA
* *
36564 CCATCAGTTTAACCCCCTGAGGTACGGGTCCACT
1 CCAACAGTTTAACCCCCTGAGGCACGGGTCCACT
36598 ATGCACAGCT
Statistics
Matches: 102, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
37 7 0.07
38 61 0.60
39 34 0.33
ACGTcount: A:0.23, C:0.35, G:0.18, T:0.24
Consensus pattern (38 bp):
CCAACAGTTTAACCCCCTGAGGCACGGGTCCACTCTTA
Found at i:36581 original size:77 final size:75
Alignment explanation
Indices: 36450--36597 Score: 224
Period size: 77 Copynumber: 1.9 Consensus size: 75
36440 TCGAGTCTAG
36450 CCAACAGTTAACCCCCTGAGGCACGGATCCACTCTTACCAACAGTTTAACCCCCTGAGGCACGGG
1 CCAACAGTTAACCCCCTGAGGCACGGATCCACTCTTACCAACAGTTTAACCCCCTGAGGCACGGG
36515 TCCACTCTTA
66 TCCACTCTTA
* * * * * *
36525 CCAACAGTTTAACCCCCTGTGGTATGGGTCCACTCTTTACCATCAGTTTAACCCCCTGAGGTACG
1 CCAACAG-TTAACCCCCTGAGGCACGGATCCACTC-TTACCAACAGTTTAACCCCCTGAGGCACG
36590 GGTCCACT
64 GGTCCACT
36598 ATGCACAGCT
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
75 7 0.11
76 23 0.35
77 35 0.54
ACGTcount: A:0.23, C:0.35, G:0.18, T:0.24
Consensus pattern (75 bp):
CCAACAGTTAACCCCCTGAGGCACGGATCCACTCTTACCAACAGTTTAACCCCCTGAGGCACGGG
TCCACTCTTA
Found at i:42208 original size:2 final size:2
Alignment explanation
Indices: 42201--42226 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
42191 GAGCTCAAGG
42201 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
42227 AGCATATACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Done.