Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022057.1 Corchorus olitorius cultivar O-4 contig22090, 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: 53553
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:4158 original size:13 final size:13
Alignment explanation
Indices: 4140--4178 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
4130 CTACTTTTAT
4140 ACTAGTAATAATA
1 ACTAGTAATAATA
*
4153 ACTAGTAGTAAT-
1 ACTAGTAATAATA
4165 ACTAGTAATAATA
1 ACTAGTAATAATA
4178 A
1 A
4179 AAATAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 11 0.48
13 12 0.52
ACGTcount: A:0.51, C:0.08, G:0.10, T:0.31
Consensus pattern (13 bp):
ACTAGTAATAATA
Found at i:4170 original size:12 final size:12
Alignment explanation
Indices: 4138--4177 Score: 62
Period size: 12 Copynumber: 3.2 Consensus size: 12
4128 TACTACTTTT
4138 ATACTAGTAATA
1 ATACTAGTAATA
*
4150 ATAACTAGTAGTA
1 AT-ACTAGTAATA
4163 ATACTAGTAATA
1 ATACTAGTAATA
4175 ATA
1 ATA
4178 AAAATAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 14 0.56
13 11 0.44
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (12 bp):
ATACTAGTAATA
Found at i:6872 original size:38 final size:38
Alignment explanation
Indices: 6821--6896 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
6811 GAAGCTTCAA
6821 CTGTTTTTTAGGATGAAGATCACAATCATCATAATCAT
1 CTGTTTTTTAGGATGAAGATCACAATCATCATAATCAT
6859 CTGTTTTTTAGGATGAAGATCACAATCATCATAATCAT
1 CTGTTTTTTAGGATGAAGATCACAATCATCATAATCAT
6897 AAATTCATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (38 bp):
CTGTTTTTTAGGATGAAGATCACAATCATCATAATCAT
Found at i:8735 original size:46 final size:46
Alignment explanation
Indices: 8685--8784 Score: 132
Period size: 46 Copynumber: 2.2 Consensus size: 46
8675 ATTTGTTTAT
* *
8685 GGAATCAATCTTTTG-TGT-GTTGATGGAAAATACCTGATGAAATGAA
1 GGAATCAATCTTTTGAT-TCCTT-ATGGAAAAGACCTGATGAAATGAA
*
8731 GGAATCAATCTTTTGATTCCTTATGGAAAAGACCTGATGAAGTGAA
1 GGAATCAATCTTTTGATTCCTTATGGAAAAGACCTGATGAAATGAA
*
8777 TGAATCAA
1 GGAATCAA
8785 AATATACAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
46 45 0.94
47 3 0.06
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (46 bp):
GGAATCAATCTTTTGATTCCTTATGGAAAAGACCTGATGAAATGAA
Found at i:16682 original size:12 final size:12
Alignment explanation
Indices: 16665--16689 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16655 ACTCCCTCCG
16665 TCCCATTTTGTT
1 TCCCATTTTGTT
16677 TCCCATTTTGTT
1 TCCCATTTTGTT
16689 T
1 T
16690 GTCCACCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.24, G:0.08, T:0.60
Consensus pattern (12 bp):
TCCCATTTTGTT
Found at i:18184 original size:22 final size:21
Alignment explanation
Indices: 18156--18367 Score: 147
Period size: 22 Copynumber: 9.5 Consensus size: 21
18146 CTTGTCTCTG
18156 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCAT-AGA
* *
18178 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-A-GA
* *
18201 -GGTTATCAAAATTCCATAGTG
1 TGGTTATCAAAATTTCATAG-A
* *
18222 TGGTTACCAAAACTTCATATGA
1 TGGTTATCAAAATTTCATA-GA
** *
18244 AAGTTATCAAAATTTTCATGGGA
1 TGGTTATCAAAA-TTTCAT-AGA
* *
18267 AGGTTATCAAAATTTCATAGTG
1 TGGTTATCAAAATTTCATAG-A
*
18289 TGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATA-GA
**
18311 TCAGGTTATTGAAATTTCATAGTA
1 T--GGTTATCAAAATTTCATAG-A
* *
18335 TGGTTATCACAATTTTATAGAA
1 TGGTTATCAAAATTTCATAG-A
*
18357 AGGTTATCAAA
1 TGGTTATCAAA
18368 GAGATTATCA
Statistics
Matches: 147, Mismatches: 32, Indels: 22
0.73 0.16 0.11
Matches are distributed among these distances:
20 1 0.01
21 2 0.01
22 104 0.71
23 23 0.16
24 17 0.12
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.36
Consensus pattern (21 bp):
TGGTTATCAAAATTTCATAGA
Found at i:18289 original size:67 final size:66
Alignment explanation
Indices: 18154--18493 Score: 215
Period size: 66 Copynumber: 5.3 Consensus size: 66
18144 TTCTTGTCTC
* ** * *
18154 TGTGGTTATCAAAATTTCATAAGATGGTTATTATAATTTCATGAGGAGGTTATCAAAATTCCATA
1 TGTGGTTACCAAAATTTCATAAGAAAGTTATCAAAATTTCATGAGGAGGTTATCAAAATTCCATA
18219 G
66 G
* * *
18220 TGTGGTTACCAAAACTTCATATGAAAGTTATCAAAATTTTCATG-GGAAGGTTATCAAAATTTCA
1 TGTGGTTACCAAAATTTCATAAGAAAGTTATCAAAA-TTTCATGAGG-AGGTTATCAAAATTCCA
18284 TAG
64 TAG
* * ** * * **
18287 TGTGGTTACCAAAATTTCATAGGATCAGGTTATTGAAATTTCAT-AGTATGGTTATCACAATTTT
1 TGTGGTTACCAAAATTTCATAAGA--AAGTTATCAAAATTTCATGAGGA-GGTTATCAAAATTCC
18351 ATAG
63 ATAG
*** * * *
18355 AAAGGTT------A--TCA-AAGAGA-TTATCAAAATGTCAT-AGCGAGGTTAT-AAGAATTTCA
1 TGTGGTTACCAAAATTTCATAAGAAAGTTATCAAAATTTCATGAG-GAGGTTATCAA-AATTCCA
18408 TAG
64 TAG
* * * * * * **
18411 TGTGGTTAACAAAATTTTATAAGGAGGTTA-CTAATATTTCATGGGGAGGTTATCAAAATTTTAT
1 TGTGGTTACCAAAATTTCATAAGAAAGTTATC-AAAATTTCATGAGGAGGTTATCAAAATTCCAT
18475 AG
65 AG
* *
18477 TATGGTTATCAAAATTT
1 TGTGGTTACCAAAATTT
18494 TTTAGTGTGG
Statistics
Matches: 212, Mismatches: 41, Indels: 42
0.72 0.14 0.14
Matches are distributed among these distances:
55 1 0.00
56 33 0.16
57 1 0.00
59 3 0.01
60 3 0.01
62 2 0.01
64 2 0.01
65 4 0.02
66 74 0.35
67 52 0.25
68 28 0.13
69 9 0.04
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.36
Consensus pattern (66 bp):
TGTGGTTACCAAAATTTCATAAGAAAGTTATCAAAATTTCATGAGGAGGTTATCAAAATTCCATA
G
Found at i:18328 original size:46 final size:44
Alignment explanation
Indices: 18156--19447 Score: 394
Period size: 44 Copynumber: 29.9 Consensus size: 44
18146 CTTGTCTCTG
* * * * *
18156 TGGTTATCAAAATTTCATAAGATGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCAT-AGTA
* * * *
18201 -GGTTATCAAAATTCCATAGTG-TGGTTACCAAAACTTCATA-TGA
1 TGGTTATCAAAATTTCATAG-GAAGGTTATCAAAATTTCATAGT-A
** * *
18244 AAGTTATCAAAATTTTCATGGGAAGGTTATCAAAATTTCATAGTG
1 TGGTTATCAAAA-TTTCATAGGAAGGTTATCAAAATTTCATAGTA
* **
18289 TGGTTACCAAAATTTCATAGGATCAGGTTATTGAAATTTCATAGTA
1 TGGTTATCAAAATTTCATAGGA--AGGTTATCAAAATTTCATAGTA
* * *
18335 TGGTTATCACAATTTTATAGAAAGGTTATC---A----A-AG-A
1 TGGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTA
* * *
18370 -GATTATCAAAATGTCATAGCG-AGGTTAT-AAGAATTTCATAGTG
1 TGGTTATCAAAATTTCATAG-GAAGGTTATCAA-AATTTCATAGTA
* * * * *
18413 TGGTTAACAAAATTTTATAAGG-AGGTTA-CTAATATTTCATGGGGA
1 TGGTTATCAAAATTTCAT-AGGAAGGTTATC-AAAATTTCAT-AGTA
* * * ** *
18458 -GGTTATCAAAATTTTATAGTATGGTTATCAAAATTTTTTAGTG
1 TGGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTA
* * * *
18501 TGGTTAACAAAATTTCATATGAAGGTTAT-AAAAGTCTCAATTTCA-CA
1 TGGTTATCAAAATTTCATAGGAAGGTTATCAAAA-TTTC-A--T-AGTA
* * * * * * *
18548 AGGAGTACCAACATTTGATA-GAAGGTTATC-AAATCTCATAGAA
1 TGG-TTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTA
* * * * *
18591 TGATTATCGAAATTTCATAGAGATCAGATTATGAAAATTT-ATAGGAA
1 TGGTTATCAAAATTTCATAG-GA--AGGTTATCAAAATTTCATA-GTA
* ** * * *
18638 T-ATTATCAAAATTTCATAGTG-TTGTTATCAAAATTCCAAAGCGA
1 TGGTTATCAAAATTTCATAG-GAAGGTTATCAAAATTTCATAG-TA
* * *
18682 -GGTTATCAAAATTACATAATGTAA--TTATCAAAATTTTATAG-A
1 TGGTTATCAAAATTTCAT-A-GGAAGGTTATCAAAATTTCATAGTA
* * *
18724 GGGGTTAACAAAATTTTATA-GAGAGGTTATCAAAATTTCATAAAG-A
1 -TGGTTATCAAAATTTCATAGGA-AGGTTATCAAAATTTCAT--AGTA
* *
18770 -GGTTATCAAATTTTCA-A--AATGTGATTACCAAAATTTCATAG--
1 TGGTTATCAAAATTTCATAGGAA-G-G-TTATCAAAATTTCATAGTA
* *
18811 TGG---T----ATTTC-TGGGGAGGTTATCAAAATTTCATAGTA
1 TGGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTA
* * * *
18847 TGGTTA-CCAAA--T--TAGGAAGGTTATTAAACTTT--TATTA
1 TGGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTA
* * * *
18884 TGTAGTAATCAAAATTTC--AGGGAGGATATCAAAATTTCATAGTT
1 TG--GTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTA
* * * * * *
18928 TAGTTTTCAAAAGTTCATAAGAGGGTTATCAAAATTGCATAGTA
1 TGGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTA
* * * * * *
18972 T-GTAGATCAAAATTTCATAGGGAGATTAACAAAATTTAATAATGA
1 TGGT-TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGT-A
* **
19017 -GGTTATAAAAAAATCATAGGAAGGTTATCAAAA-TT--T-GTA
1 TGGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTA
* * * *
19056 --GTTATCAAGATTTCATAAGG-AGATTATCAAAATTTTATAGGGA
1 TGGTTATCAAAATTTCAT-AGGAAGGTTATCAAAATTTCATA-GTA
* * *
19099 -GGTTTATCAAAATTTTATAGGAAGGTTTATCGAAATTTCATAGCGA
1 TGG-TTATCAAAATTTCATAGGAAGG-TTATCAAAATTTCATAG-TA
* * * * * * * * *
19145 -GATTATCACAATTTTATAGTATGATTATTAAAATTTCAGAGTG
1 TGGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTA
* ** * * * ***
19188 TGATTA-CTAACAA-TTCATATAAAGGTTTTTAAATTTTCATAACG
1 TGGTTATC-AA-AATTTCATAGGAAGGTTATCAAAATTTCATAGTA
* * * * *
19232 TGGTTATCAATATATCATATGG-AGGTTATCAACATCTCATAGTGT
1 TGGTTATCAAAATTTCATA-GGAAGGTTATCAAAATTTCATAGT-A
* *
19277 TGGTTATTAAAATTTCATTGGGAA-GTTATCAAAATTTCATAGTGA
1 TGGTTATCAAAATTTCA-TAGGAAGGTTATCAAAATTTCATAGT-A
* * *
19322 -GGTCT-TCAAAA-TTCTTTAGGGAGGTTAACAAAATTTCATAAG-A
1 TGGT-TATCAAAATTTC-ATAGGAAGGTTATCAAAATTTCAT-AGTA
* ** * ** * * *
19365 AGGTTAAAAAAAATT-ATAAAAAGGCTCTCAAAA-TCCATAGTA
1 TGGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTA
* * *
19407 TCGTTATTAAAATTTCATAGGAAGGTTATCAAAACTTCATA
1 TGGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATA
19448 AGGAAGTCAT
Statistics
Matches: 911, Mismatches: 223, Indels: 227
0.67 0.16 0.17
Matches are distributed among these distances:
34 38 0.04
35 6 0.01
36 6 0.01
37 9 0.01
38 23 0.03
39 26 0.03
40 6 0.01
41 8 0.01
42 65 0.07
43 68 0.07
44 408 0.45
45 119 0.13
46 92 0.10
47 24 0.03
48 13 0.01
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.35
Consensus pattern (44 bp):
TGGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTA
Found at i:18397 original size:22 final size:21
Alignment explanation
Indices: 18372--18785 Score: 156
Period size: 22 Copynumber: 18.7 Consensus size: 21
18362 ATCAAAGAGA
*
18372 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAG-GAGG
*
18394 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAG-GAGG
* *
18416 TTAACAAAATTTTATAAGGAGG
1 TTATCAAAATTTCAT-AGGAGG
* *
18438 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCAT-AGGAGG
* *
18460 TTATCAAAATTTTATAGTATGG
1 TTATCAAAATTTCATAGGA-GG
** *
18482 TTATCAAAATTTTTTAGTGTGG
1 TTATCAAAATTTCATAG-GAGG
* *
18504 TTAACAAAATTTCATATGAAGG
1 TTATCAAAATTTCATA-GGAGG
* **
18526 TTAT-AAAAGTCTCAATTTCACAAGG
1 TTATCAAAA-TTTC-A--T-AGGAGG
* * * * *
18551 AGTACCAACATTTGATAGAAGG
1 -TTATCAAAATTTCATAGGAGG
* * *
18573 TTATC-AAATCTCATAGAATGA
1 TTATCAAAATTTCATAGGA-GG
* *
18594 TTATCGAAATTTCATAGAGATCAGA
1 TTATCAAAATTTCATAG-G---AGG
* **
18619 TTATGAAAATTT-ATAGGAATA
1 TTATCAAAATTTCATAGG-AGG
**
18640 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAG-GAGG
* *
18662 TTATCAAAATTCCAAAGCGAGG
1 TTATCAAAATTTCATAG-GAGG
* * *
18684 TTATCAAAATTACATAATGTA-A
1 TTATCAAAATTTCAT-A-GGAGG
* *
18706 TTATCAAAATTTTATAGAGGGG
1 TTATCAAAATTTCATAG-GAGG
* *
18728 TTAACAAAATTTTATAGAGAGG
1 TTATCAAAATTTCATAG-GAGG
*
18750 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCAT-AGGAGG
*
18772 TTATCAAATTTTCA
1 TTATCAAAATTTCA
18786 AAATGTGATT
Statistics
Matches: 298, Mismatches: 66, Indels: 56
0.71 0.16 0.13
Matches are distributed among these distances:
20 11 0.04
21 32 0.11
22 210 0.70
23 13 0.04
24 5 0.02
25 18 0.06
26 6 0.02
27 3 0.01
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.35
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGAGG
Found at i:18486 original size:122 final size:122
Alignment explanation
Indices: 18267--18489 Score: 292
Period size: 122 Copynumber: 1.8 Consensus size: 122
18257 TTTCATGGGA
* *
18267 AGGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATAGGATCAGGTTATTGAAATTTCATA
1 AGGTTATCAAAATTTCATAGTGTGGTTAACAAAATTTCATAGGA--AGGTTACTGAAATTTCATA
* *
18332 GTATGGTTATCACAATTTTATAGAAAGGTTATCAAAGAGATTATCAAAATGTCATAGCG
64 GGATGGTTATCAAAATTTTATAGAAAGGTTATCAAAGAGATTATCAAAATGTCATAGCG
*
18391 AGGTTAT-AAGAATTTCATAGTGTGGTTAACAAAATTTTATAAGG-AGGTTACT-AATATTTCAT
1 AGGTTATCAA-AATTTCATAGTGTGGTTAACAAAATTTCAT-AGGAAGGTTACTGAA-ATTTCAT
* * *
18453 GGGGA-GGTTATCAAAATTTTATAGTATGGTTATCAAA
63 -AGGATGGTTATCAAAATTTTATAGAAAGGTTATCAAA
18490 ATTTTTTAGT
Statistics
Matches: 87, Mismatches: 8, Indels: 10
0.83 0.08 0.10
Matches are distributed among these distances:
121 2 0.02
122 43 0.49
123 4 0.05
124 35 0.40
125 3 0.03
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.36
Consensus pattern (122 bp):
AGGTTATCAAAATTTCATAGTGTGGTTAACAAAATTTCATAGGAAGGTTACTGAAATTTCATAGG
ATGGTTATCAAAATTTTATAGAAAGGTTATCAAAGAGATTATCAAAATGTCATAGCG
Found at i:19087 original size:82 final size:84
Alignment explanation
Indices: 18977--19136 Score: 207
Period size: 82 Copynumber: 1.9 Consensus size: 84
18967 TAGTATGTAG
* *
18977 ATCAAAATTTCATAGGGAGATTAACAAAATTTAATAATGAGG-TTATAAAAAAATCATAGGAAGG
1 ATCAAAATTTCATAAGGAGATTAACAAAATTTAATAAGGAGGTTTATAAAAAAATCATAGGAAGG
19041 -TTATCAAAATTTGTAGTT
66 TTTATCAAAATTTGTAGTT
* * * * * ** *
19059 ATCAAGATTTCATAAGGAGATTATCAAAATTTTATAGGGAGGTTTATCAAAATTTTATAGGAAGG
1 ATCAAAATTTCATAAGGAGATTAACAAAATTTAATAAGGAGGTTTATAAAAAAATCATAGGAAGG
*
19124 TTTATCGAAATTT
66 TTTATCAAAATTT
19137 CATAGCGAGA
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
82 36 0.55
83 18 0.28
84 11 0.17
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.34
Consensus pattern (84 bp):
ATCAAAATTTCATAAGGAGATTAACAAAATTTAATAAGGAGGTTTATAAAAAAATCATAGGAAGG
TTTATCAAAATTTGTAGTT
Found at i:19434 original size:22 final size:22
Alignment explanation
Indices: 18825--19453 Score: 175
Period size: 22 Copynumber: 29.1 Consensus size: 22
18815 ATTTCTGGGG
*
18825 AGGTTATCAAAATTTCATAGTA
1 AGGTTATCAAAATTTCATAGGA
* *
18847 TGGTTA-CCAAA--T--TAGGA
1 AGGTTATCAAAATTTCATAGGA
* * * * *
18864 AGGTTATTAAACTTTTATTATGT
1 AGGTTATCAAAATTTCA-TAGGA
* *
18887 A-GTAATCAAAATTTC--AGGG
1 AGGTTATCAAAATTTCATAGGA
* **
18906 AGGATATCAAAATTTCATAGTTT
1 AGGTTATCAAAATTTCATAG-GA
* * *
18929 A-GTTTTCAAAAGTTCATAAGA
1 AGGTTATCAAAATTTCATAGGA
* * *
18950 GGGTTATCAAAATTGCATA-GT
1 AGGTTATCAAAATTTCATAGGA
* * *
18971 ATGTAGATCAAAATTTCATAGGG
1 AGGT-TATCAAAATTTCATAGGA
* * * *
18994 AGATTAACAAAATTTAATAATG-
1 AGGTTATCAAAATTTCAT-AGGA
* **
19016 AGGTTATAAAAAAATCATAGGA
1 AGGTTATCAAAATTTCATAGGA
*
19038 AGGTTATCAAAA-TT--T--GT
1 AGGTTATCAAAATTTCATAGGA
*
19055 A-GTTATCAAGATTTCATAAGG-
1 AGGTTATCAAAATTTCAT-AGGA
* * *
19076 AGATTATCAAAATTTTATAGGG
1 AGGTTATCAAAATTTCATAGGA
*
19098 AGGTTTATCAAAATTTTATAGGA
1 AGG-TTATCAAAATTTCATAGGA
*
19121 AGGTTTATCGAAATTTCATAGCG-
1 AGG-TTATCAAAATTTCATAG-GA
* * * *
19144 AGATTATCACAATTTTATAGTA
1 AGGTTATCAAAATTTCATAGGA
* * * *
19166 TGATTATTAAAATTTCAGAGTG-
1 AGGTTATCAAAATTTCATAG-GA
* * **
19188 TGATTA-CTAACAA-TTCATATAA
1 AGGTTATC-AA-AATTTCATAGGA
* * * *
19210 AGGTTTTTAAATTTTCATAACG-
1 AGGTTATCAAAATTTCAT-AGGA
* * *
19232 TGGTTATCAATATATCATATGG-
1 AGGTTATCAAAATTTCATA-GGA
* * *
19254 AGGTTATCAACATCTCATAGTGT
1 AGGTTATCAAAATTTCATAG-GA
* * *
19277 TGGTTATTAAAATTTCATTGGGA
1 AGGTTATCAAAATTTCA-TAGGA
19300 A-GTTATCAAAATTTCATAGTG-
1 AGGTTATCAAAATTTCATAG-GA
* *
19321 AGGTCT-TCAAAA-TTCTTTAGGG
1 AGGT-TATCAAAATTTC-ATAGGA
* *
19343 AGGTTAACAAAATTTCATAAGA
1 AGGTTATCAAAATTTCATAGGA
** * **
19365 AGGTTAAAAAAAATT-ATAAAA
1 AGGTTATCAAAATTTCATAGGA
* * * *
19386 AGGCTCTCAAAA-TCCATAGTA
1 AGGTTATCAAAATTTCATAGGA
** *
19407 TCGTTATTAAAATTTCATAGGA
1 AGGTTATCAAAATTTCATAGGA
*
19429 AGGTTATCAAAACTTCATAAGGA
1 AGGTTATCAAAATTTCAT-AGGA
19452 AG
1 AG
19454 TCATAAAAAA
Statistics
Matches: 434, Mismatches: 126, Indels: 93
0.66 0.19 0.14
Matches are distributed among these distances:
16 9 0.02
17 13 0.03
18 2 0.00
19 6 0.01
20 14 0.03
21 49 0.11
22 262 0.60
23 76 0.18
24 3 0.01
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.35
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATAGGA
Found at i:19462 original size:22 final size:22
Alignment explanation
Indices: 19415--19462 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
19405 TATCGTTATT
* * *
19415 AAAATTTCATAGGAAGGTTATC
1 AAAACTTCATAGGAAGGTCATA
19437 AAAACTTCATAAGGAA-GTCATA
1 AAAACTTCAT-AGGAAGGTCATA
19459 AAAA
1 AAAA
19463 ATAGTGTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.50, C:0.10, G:0.15, T:0.25
Consensus pattern (22 bp):
AAAACTTCATAGGAAGGTCATA
Found at i:19684 original size:28 final size:29
Alignment explanation
Indices: 19624--19704 Score: 83
Period size: 28 Copynumber: 2.7 Consensus size: 29
19614 GTTAAATACC
* *
19624 CAAAAAAATCTCTTATGTTTTTTCTTTTGGGA
1 CAAAATAATCTCTTATG---TTTCTTTTAGGA
19656 CAAAATAATCTCTTATGTTT-TTTTAGGA
1 CAAAATAATCTCTTATGTTTCTTTTAGGA
* * *
19684 CAAATTAATCTTTTACGTTTC
1 CAAAATAATCTCTTATGTTTC
19705 AAAAGTGAGC
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
28 24 0.56
29 3 0.07
32 16 0.37
ACGTcount: A:0.30, C:0.14, G:0.10, T:0.47
Consensus pattern (29 bp):
CAAAATAATCTCTTATGTTTCTTTTAGGA
Found at i:23468 original size:22 final size:22
Alignment explanation
Indices: 23438--23542 Score: 97
Period size: 22 Copynumber: 4.7 Consensus size: 22
23428 GCCAACGTAG
*
23438 AAATATTGATAACCATACTGTGA
1 AAAT-TTGATAACCATACTATGA
* *
23461 AAATTTGATAACCTTATTATG-
1 AAATTTGATAACCATACTATGA
*
23482 AAATTTCGATAACC-TATCTATAA
1 AAATTT-GATAACCATA-CTATGA
** *
23505 AAATTTGATAACCGCACTGTGA
1 AAATTTGATAACCATACTATGA
*
23527 AATTTTGATAACCATA
1 AAATTTGATAACCATA
23543 ATCTTTTGAT
Statistics
Matches: 67, Mismatches: 11, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
21 8 0.12
22 48 0.72
23 11 0.16
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.34
Consensus pattern (22 bp):
AAATTTGATAACCATACTATGA
Found at i:23667 original size:44 final size:43
Alignment explanation
Indices: 23611--23771 Score: 155
Period size: 44 Copynumber: 3.7 Consensus size: 43
23601 TCTCTATAAT
* *
23611 TTTTGATAACCACTCTATGAAGTTTTGATAACCTTCATATGAAA
1 TTTTGATAACCA-TCTATGAAATTTTGATAACCTCCATATGAAA
* * *
23655 TTTTGGTAACCA-CAGTATGAATTTTTTATAACCTCCATAT-AAA
1 TTTTGATAACCATC--TATGAAATTTTGATAACCTCCATATGAAA
* * * * *
23698 ATTTGGTAACCATACTATGAAATTTTGATAATCTGCTTATGAAA
1 TTTTGATAACCAT-CTATGAAATTTTGATAACCTCCATATGAAA
*
23742 TTTTTGATAACCTATTTATGAAATTTTGAT
1 -TTTTGATAACC-ATCTATGAAATTTTGAT
23772 TACCAAACAA
Statistics
Matches: 97, Mismatches: 13, Indels: 13
0.79 0.11 0.11
Matches are distributed among these distances:
42 1 0.01
43 34 0.35
44 36 0.37
45 24 0.25
46 2 0.02
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.42
Consensus pattern (43 bp):
TTTTGATAACCATCTATGAAATTTTGATAACCTCCATATGAAA
Found at i:23750 original size:23 final size:23
Alignment explanation
Indices: 23567--23768 Score: 115
Period size: 22 Copynumber: 9.0 Consensus size: 23
23557 CAAAAAAAAA
*
23567 TTGATAACCTTCCTT-TGAAA-TT
1 TTGATAACC-TACTTATGAAATTT
*
23589 TTAATAACCTAATCTCTAT--AATTT
1 TTGATAACCT-A-CT-TATGAAATTT
*
23613 TTGATAACC-ACTCTATG-AAGTT
1 TTGATAACCTACT-TATGAAATTT
* *
23635 TTGATAACCTTCATATGAAA-TT
1 TTGATAACCTACTTATGAAATTT
* *
23657 TTGGTAACC-ACAGTATG-AATTT
1 TTGATAACCTAC-TTATGAAATTT
* * * *
23679 TTTATAACCTCCATAT-AAA-AT
1 TTGATAACCTACTTATGAAATTT
*
23700 TTGGTAACCATAC-TATGAAA-TT
1 TTGATAACC-TACTTATGAAATTT
* *
23722 TTGATAATCTGCTTATGAAATTT
1 TTGATAACCTACTTATGAAATTT
*
23745 TTGATAACCTATTTATGAAATTT
1 TTGATAACCTACTTATGAAATTT
23768 T
1 T
23769 GATTACCAAA
Statistics
Matches: 140, Mismatches: 24, Indels: 31
0.72 0.12 0.16
Matches are distributed among these distances:
21 23 0.16
22 74 0.53
23 31 0.22
24 11 0.08
25 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.42
Consensus pattern (23 bp):
TTGATAACCTACTTATGAAATTT
Found at i:23872 original size:22 final size:22
Alignment explanation
Indices: 23846--23895 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
23836 AATTTTCCTC
*
23846 ATGAAAGCTTGATAATCTCACT
1 ATGAAAACTTGATAATCTCACT
*
23868 ATGAAAATTTGATAATCTCACT
1 ATGAAAACTTGATAATCTCACT
23890 AT-AAAA
1 ATGAAAA
23896 TTTTTTGATA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 4 0.15
22 22 0.85
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.32
Consensus pattern (22 bp):
ATGAAAACTTGATAATCTCACT
Found at i:23897 original size:21 final size:22
Alignment explanation
Indices: 23854--23898 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
23844 TCATGAAAGC
23854 TTGATAATCTCACTATGAAAAT
1 TTGATAATCTCACTATGAAAAT
23876 TTGATAATCTCACTAT-AAAAT
1 TTGATAATCTCACTATGAAAAT
23897 TT
1 TT
23899 TTTGATAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.40
Consensus pattern (22 bp):
TTGATAATCTCACTATGAAAAT
Found at i:25602 original size:19 final size:20
Alignment explanation
Indices: 25578--25632 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
25568 TATAAAAAAT
25578 ATAGTGTGATTATCAA-TTG
1 ATAGTGTGATTATCAATTTG
* * * *
25597 ATAGTGCGGTTACCAATTTT
1 ATAGTGTGATTATCAATTTG
*
25617 ATAGTATGATTATCAA
1 ATAGTGTGATTATCAA
25633 AATTTCACAC
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
19 13 0.48
20 14 0.52
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.40
Consensus pattern (20 bp):
ATAGTGTGATTATCAATTTG
Found at i:25653 original size:22 final size:22
Alignment explanation
Indices: 25628--25683 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
25618 TAGTATGATT
25628 ATCAAAATTTCACACTG-AGGTA
1 ATCAAAATTTCACACTGTA-GTA
* *
25650 ATC-AAATTATCACAGTGTAGTT
1 ATCAAAATT-TCACACTGTAGTA
25672 ATCAAAATTTCA
1 ATCAAAATTTCA
25684 TATGGATTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
21 5 0.17
22 18 0.62
23 6 0.21
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32
Consensus pattern (22 bp):
ATCAAAATTTCACACTGTAGTA
Found at i:25768 original size:21 final size:22
Alignment explanation
Indices: 25668--25796 Score: 118
Period size: 22 Copynumber: 5.8 Consensus size: 22
25658 ATCACAGTGT
25668 AGTTATCAAAATTTCATATGGATTA
1 AGTTATCAAAATTTCATA-GGA--A
* *
25693 GGTTATTAAAATTTCATAGGAA
1 AGTTATCAAAATTTCATAGGAA
* *
25715 AGTTATCAAAATTTCATAGTAT
1 AGTTATCAAAATTTCATAGGAA
* * *
25737 GGTTCTCAAAATTT-ATAGGGA
1 AGTTATCAAAATTTCATAGGAA
* * *
25758 AGTTATTAAAATTCCATAGTGAG
1 AGTTATCAAAATTTCATAG-GAA
25781 A-TTATCAAAATTTCAT
1 AGTTATCAAAATTTCAT
25797 GACATCTAAA
Statistics
Matches: 83, Mismatches: 19, Indels: 7
0.76 0.17 0.06
Matches are distributed among these distances:
21 14 0.17
22 48 0.58
23 2 0.02
24 3 0.04
25 16 0.19
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.38
Consensus pattern (22 bp):
AGTTATCAAAATTTCATAGGAA
Found at i:25769 original size:43 final size:46
Alignment explanation
Indices: 25668--25796 Score: 142
Period size: 43 Copynumber: 2.9 Consensus size: 46
25658 ATCACAGTGT
* *
25668 AGTTATCAAAATTTCATATGGATTAGGTTATTAAAATTTCATAGGAA
1 AGTTATCAAAATTTCATA-GTATTAGGTTATCAAAATTTCATAGGAA
* *
25715 AGTTATCAAAATTTCATAGTA-T-GGTTCTCAAAATTT-ATAGGGA
1 AGTTATCAAAATTTCATAGTATTAGGTTATCAAAATTTCATAGGAA
* * * *
25758 AGTTATTAAAATTCCATAG--TGAGATTATCAAAATTTCAT
1 AGTTATCAAAATTTCATAGTATTAGGTTATCAAAATTTCAT
25797 GACATCTAAA
Statistics
Matches: 70, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
43 35 0.50
44 14 0.20
45 1 0.01
46 2 0.03
47 18 0.26
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.38
Consensus pattern (46 bp):
AGTTATCAAAATTTCATAGTATTAGGTTATCAAAATTTCATAGGAA
Found at i:25822 original size:13 final size:13
Alignment explanation
Indices: 25804--25828 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25794 CATGACATCT
25804 AAAAGATTAAAAC
1 AAAAGATTAAAAC
25817 AAAAGATTAAAA
1 AAAAGATTAAAA
25829 GGAATTTTGA
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:0.04, G:0.08, T:0.16
Consensus pattern (13 bp):
AAAAGATTAAAAC
Found at i:27961 original size:8 final size:8
Alignment explanation
Indices: 27948--27972 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
27938 TCAGCAATGC
27948 TTTGGTTG
1 TTTGGTTG
27956 TTTGGTTG
1 TTTGGTTG
27964 TTTGGTTG
1 TTTGGTTG
27972 T
1 T
27973 CATACCATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.36, T:0.64
Consensus pattern (8 bp):
TTTGGTTG
Found at i:35266 original size:104 final size:105
Alignment explanation
Indices: 35075--35280 Score: 378
Period size: 104 Copynumber: 2.0 Consensus size: 105
35065 AATTGTCAGG
*
35075 TATCGGGCCAAATCAAACTATTTAAGATCCAAAAACATTTAAGATATAACCAACTCATCTTGCTA
1 TATCGGGCCAAATCAAACTATTTAAGATCCAAAAACATTTAAGATATAACAAACTCATCTTGCTA
*
35140 TAAGTGGCATGGCATCAGATGCAACAGTACCAGAGCAAAC
66 TAAGTGGCATGGCATCAAATGCAACAGTACCAGAGCAAAC
35180 TATCGGGCCAAATCAAACTATTTAAGATCCAAAAACATTT-AGATATAACAAACTCATCTTGCTA
1 TATCGGGCCAAATCAAACTATTTAAGATCCAAAAACATTTAAGATATAACAAACTCATCTTGCTA
*
35244 TGAGTGGCATGGCATCAAATGCAACAGTACCAGAGCA
66 TAAGTGGCATGGCATCAAATGCAACAGTACCAGAGCA
35281 GAATAGGACA
Statistics
Matches: 98, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
104 58 0.59
105 40 0.41
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.23
Consensus pattern (105 bp):
TATCGGGCCAAATCAAACTATTTAAGATCCAAAAACATTTAAGATATAACAAACTCATCTTGCTA
TAAGTGGCATGGCATCAAATGCAACAGTACCAGAGCAAAC
Found at i:38470 original size:83 final size:83
Alignment explanation
Indices: 38363--38553 Score: 364
Period size: 83 Copynumber: 2.3 Consensus size: 83
38353 ATCAAATCCT
* *
38363 CAATAAGAGAATGATAGCATGCATAGGATTATATAAGCTCAAAATTTCTGACTTTCCCAATCACA
1 CAATTAGAGAATGATAGCATGCATAGGATTATATAAGCTCAAAATTTCTGACTTCCCCAATCACA
38428 TAATCAACTTTTCGTCCC
66 TAATCAACTTTTCGTCCC
38446 CAATTAGAGAATGATAGCATGCATAGGATTATATAAGCTCAAAATTTCTGACTTCCCCAATCACA
1 CAATTAGAGAATGATAGCATGCATAGGATTATATAAGCTCAAAATTTCTGACTTCCCCAATCACA
38511 TAATCAACTTTTCGTCCC
66 TAATCAACTTTTCGTCCC
38529 CAATTAGAGAATGATAGCATGCATA
1 CAATTAGAGAATGATAGCATGCATA
38554 ATCAACTTTT
Statistics
Matches: 106, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 106 1.00
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.29
Consensus pattern (83 bp):
CAATTAGAGAATGATAGCATGCATAGGATTATATAAGCTCAAAATTTCTGACTTCCCCAATCACA
TAATCAACTTTTCGTCCC
Found at i:52479 original size:18 final size:18
Alignment explanation
Indices: 52458--52495 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
52448 TTAACCTCTG
52458 TGTGTTTAAATTT-TTTTC
1 TGTGTTT-AATTTGTTTTC
*
52476 TGTGTTTCATTTGTTTTC
1 TGTGTTTAATTTGTTTTC
52494 TG
1 TG
52496 ATTTCTTTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.11, C:0.08, G:0.16, T:0.66
Consensus pattern (18 bp):
TGTGTTTAATTTGTTTTC
Found at i:52525 original size:14 final size:15
Alignment explanation
Indices: 52506--52535 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
52496 ATTTCTTTGG
52506 TGATTCTA-TTTCTT
1 TGATTCTATTTTCTT
52520 TGATTCTATTTTCTT
1 TGATTCTATTTTCTT
52535 T
1 T
52536 TGCTCTTCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.13, C:0.13, G:0.07, T:0.67
Consensus pattern (15 bp):
TGATTCTATTTTCTT
Done.