Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014779.1 Corchorus capsularis cultivar CVL-1 contig14800, 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: 23742
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Found at i:2804 original size:20 final size:20
Alignment explanation
Indices: 2779--2822 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
2769 GTTGTTCAAC
2779 TGTTCCATTTTGAAGTTAGT
1 TGTTCCATTTTGAAGTTAGT
2799 TGTTCCATTTTGAAGTTAGT
1 TGTTCCATTTTGAAGTTAGT
2819 TGTT
1 TGTT
2823 TCTATTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.18, C:0.09, G:0.20, T:0.52
Consensus pattern (20 bp):
TGTTCCATTTTGAAGTTAGT
Found at i:7152 original size:15 final size:15
Alignment explanation
Indices: 7129--7169 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
7119 TTTCTTAATA
7129 TATTCTTTTATAATTT
1 TATT-TTTTATAATTT
7145 T-TCTTTTTATAATTT
1 TAT-TTTTTATAATTT
7160 TATTTTTTAT
1 TATTTTTTAT
7170 TAATAATCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 20 0.87
16 3 0.13
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (15 bp):
TATTTTTTATAATTT
Found at i:16289 original size:32 final size:32
Alignment explanation
Indices: 16229--16289 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
16219 TTCGATTATA
* * *
16229 CCTTTATTTTTAAAATATATTTCCAATTGTAC
1 CCTTTATTTTAAAAACATATTTCAAATTGTAC
16261 CCTTT-TTTTAAAAACATATTTCTAAATTG
1 CCTTTATTTTAAAAACATATTTC-AAATTG
16290 CCATTACTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 15 0.60
32 10 0.40
ACGTcount: A:0.33, C:0.15, G:0.03, T:0.49
Consensus pattern (32 bp):
CCTTTATTTTAAAAACATATTTCAAATTGTAC
Found at i:16509 original size:19 final size:20
Alignment explanation
Indices: 16482--16519 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
16472 TACTATTAGT
16482 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
16502 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
16520 AATGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:16713 original size:22 final size:22
Alignment explanation
Indices: 16685--16868 Score: 151
Period size: 22 Copynumber: 8.3 Consensus size: 22
16675 TGTCTCTATG
*
16685 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAGGA
* *
16707 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AGGA
*
16730 -GGTTATCAAAATTCCATAGCG-
1 TGGTTATCAAAATTTCATAG-GA
*
16751 TGGTTACCAAAATTTCATATGGA
1 TGGTTATCAAAATTTCATA-GGA
* *
16774 -AGTTATCAAAATTTTATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
*
16795 TGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAGGA
* * * *
16817 TCAGTTTATTAAAATTTCTTAGGT
1 T--GGTTATCAAAATTTCATAGGA
** *
16841 TGGTTATTGAAATTTCATAGGG
1 TGGTTATCAAAATTTCATAGGA
16863 TGGTTA
1 TGGTTA
16869 ATTTTCACAA
Statistics
Matches: 129, Mismatches: 23, Indels: 20
0.75 0.13 0.12
Matches are distributed among these distances:
21 4 0.03
22 104 0.81
23 4 0.03
24 17 0.13
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.39
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAGGA
Found at i:17037 original size:44 final size:44
Alignment explanation
Indices: 16904--17295 Score: 134
Period size: 44 Copynumber: 8.8 Consensus size: 44
16894 ATCAAAGAGA
* * *
16904 TTATCAAAATGTCATAGCGAGATTAT-AAGAATTTCATAATG-TGG
1 TTATCAAAATTTCATAGCGAGGTTATCAA-AATTTCAT-ATGAAGG
* * *
16948 TTAACAAAATTTCATTAG-GAGGTTA-CTAATATTTCAT-GGAGAGG
1 TTATCAAAATTTCA-TAGCGAGGTTATC-AAAATTTCATATGA-AGG
* *
16992 TTATCAAAATTTTATAGCGTGGTTATCAAAATTTCATATGAAGG
1 TTATCAAAATTTCATAGCGAGGTTATCAAAATTTCATATGAAGG
* * *
17036 TTATAAAAGTCTCAATTTCATAAG-GA-G-TACCAAAATTTGATA-GAAGG
1 TTAT-CAA-----AATTTCAT-AGCGAGGTTATCAAAATTTCATATGAAGG
* * * * * * *
17083 TTGTC-AAATCTCATAGAGTGATTATCGAAATTTCATA-GAGCTCAGA
1 TTATCAAAATTTCATAGCGAGGTTATCAAAATTTCATATGA----AGG
* **
17129 TTATCAAAATTT-ATAG-GAAGATTATCAAAATTTCATAATG-TTG
1 TTATCAAAATTTCATAGCG-AGGTTATCAAAATTTCAT-ATGAAGG
* * * * * *
17172 TTATCAAAATTGCAAAGCGTGGTTATCAAAATTACATAATG-TGA
1 TTATCAAAATTTCATAGCGAGGTTATCAAAATTTCAT-ATGAAGG
* * * * * * *
17216 TTATCAGAATTTTATAGAGGGGTCAACAAAATTT--TATAAAGAG
1 TTATCAAAATTTCATAGCGAGGTTATCAAAATTTCATATGAAG-G
* ** *
17259 ATTATCAAAATTTCAGAAAGAGGTTATCAAATTTTCA
1 -TTATCAAAATTTCATAGCGAGGTTATCAAAATTTCA
17296 GAACGTGATT
Statistics
Matches: 256, Mismatches: 59, Indels: 64
0.68 0.16 0.17
Matches are distributed among these distances:
39 2 0.01
40 8 0.03
41 2 0.01
42 17 0.07
43 14 0.05
44 135 0.53
45 13 0.05
46 26 0.10
47 14 0.05
48 14 0.05
49 1 0.00
50 8 0.03
51 2 0.01
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (44 bp):
TTATCAAAATTTCATAGCGAGGTTATCAAAATTTCATATGAAGG
Found at i:17039 original size:22 final size:22
Alignment explanation
Indices: 16933--17043 Score: 63
Period size: 22 Copynumber: 5.1 Consensus size: 22
16923 AGATTATAAG
* *
16933 AATTTCATAATG-TGGTTAACAA
1 AATTTCAT-ATGAAGGTTATCAA
*
16955 AATTTCAT-TAGGAGGTTA-CTAA
1 AATTTCATAT-GAAGGTTATC-AA
* *
16977 TATTTCAT-GGAGAGGTTATCAA
1 AATTTCATATGA-AGGTTATCAA
* **
16999 AATTTTATA-GCGTGGTTATCAA
1 AATTTCATATG-AAGGTTATCAA
17021 AATTTCATATGAAGGTTAT-AA
1 AATTTCATATGAAGGTTATCAA
17042 AA
1 AA
17044 GTCTCAATTT
Statistics
Matches: 70, Mismatches: 11, Indels: 17
0.71 0.11 0.17
Matches are distributed among these distances:
20 1 0.01
21 7 0.10
22 60 0.86
23 2 0.03
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.37
Consensus pattern (22 bp):
AATTTCATATGAAGGTTATCAA
Found at i:17118 original size:22 final size:23
Alignment explanation
Indices: 17088--17320 Score: 107
Period size: 22 Copynumber: 10.5 Consensus size: 23
17078 GAAGGTTGTC
* *
17088 AAATCTCATAGAG-TGATTATCG
1 AAATTTCATAGAGATGATTATCA
*
17110 AAATTTCATAGAGCTCAGATTATCA
1 AAATTTCATAGAGAT--GATTATCA
*
17135 AAATTT-ATAG-GAAGATTATCA
1 AAATTTCATAGAGATGATTATCA
*
17156 AAATTTCATA-ATGTTG-TTATCA
1 AAATTTCATAGA-GATGATTATCA
* * * *
17178 AAATTGCAAAGCG-TGGTTATCA
1 AAATTTCATAGAGATGATTATCA
*
17200 AAATTACATA-ATG-TGATTATCA
1 AAATTTCATAGA-GATGATTATCA
* * * * * *
17222 GAATTTTATAGAG-GGGTCAACA
1 AAATTTCATAGAGATGATTATCA
* *
17244 AAATTTTATAAAGA-GATTATCA
1 AAATTTCATAGAGATGATTATCA
* * *
17266 AAATTTCAGAAAGA-GGTTATCA
1 AAATTTCATAGAGATGATTATCA
* *
17288 AATTTTCAGA-ACG-TGATTA-CAA
1 AAATTTCATAGA-GATGATTATC-A
17310 AAATTTCATAG
1 AAATTTCATAG
17321 TGGTATTTTT
Statistics
Matches: 164, Mismatches: 32, Indels: 29
0.73 0.14 0.13
Matches are distributed among these distances:
21 18 0.11
22 124 0.76
23 5 0.03
24 4 0.02
25 13 0.08
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (23 bp):
AAATTTCATAGAGATGATTATCA
Found at i:17138 original size:25 final size:22
Alignment explanation
Indices: 17102--17165 Score: 76
Period size: 21 Copynumber: 2.8 Consensus size: 22
17092 CTCATAGAGT
* *
17102 GATTATCGAAATTTCATAGAGCTCA
1 GATTATCAAAATTTCATAG-G--AA
17127 GATTATCAAAATTT-ATAGGAA
1 GATTATCAAAATTTCATAGGAA
17148 GATTATCAAAATTTCATA
1 GATTATCAAAATTTCATA
17166 ATGTTGTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
21 15 0.42
22 3 0.08
23 1 0.03
24 4 0.11
25 13 0.36
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.34
Consensus pattern (22 bp):
GATTATCAAAATTTCATAGGAA
Found at i:17462 original size:22 final size:22
Alignment explanation
Indices: 17437--17847 Score: 124
Period size: 22 Copynumber: 18.5 Consensus size: 22
17427 AGTTTAGTTT
17437 TCAAAATTTCATAAGAGGGTTA
1 TCAAAATTTCATAAGAGGGTTA
* ***
17459 TCAAAATTTCAT-AGTATGCAGA
1 TCAAAATTTCATAAG-AGGGTTA
17481 TCAAAATTTCAT-AG-GGAGATTA
1 TCAAAATTTCATAAGAGG-G-TTA
*
17503 ACAAAATTTCATAATGA-GGTTA
1 TCAAAATTTCATAA-GAGGGTTA
**
17525 TCAAAAAATCAT-AG-GGAAGTTA
1 TCAAAATTTCATAAGAGG--GTTA
* *
17547 TCAAAATTTTAT-AGCGTGGTTA
1 TCAAAATTTCATAAGAG-GGTTA
* *
17569 TCAAAATTTCATATGAAGGTTA
1 TCAAAATTTCATAAGAGGGTTA
* *
17591 TAAAAGTCTCAATTTCATAAG-GAG-TA
1 T-CAA-----AATTTCATAAGAGGGTTA
* * *
17617 CCAAAATTTGAT-AGAAGGTTA
1 TCAAAATTTCATAAGAGGGTTA
* *
17638 TC-AAATCTCAT-AGAGTGATTA
1 TCAAAATTTCATAAGAG-GGTTA
* *
17659 TCGAAATTTCAT-AGAGCTCAGATTA
1 TCAAAATTTCATAAGAG----GGTTA
* * *
17684 TCAAAATTT-ATAGGAAGATTA
1 TCAAAATTTCATAAGAGGGTTA
**
17705 TCAAAATTTCATAATG-TTGTTA
1 TCAAAATTTCATAA-GAGGGTTA
* * *
17727 TCAAAATTCCA-AAGCGATGTTA
1 TCAAAATTTCATAAGAG-GGTTA
* * *
17749 TCAAAATTACATAATG-TGATTA
1 TCAAAATTTCATAA-GAGGGTTA
* *
17771 TCAGAATTTCAT-AGAGGGGTCA
1 TCAAAATTTCATAAGA-GGGTTA
* * *
17793 ACAAAATTTTATAA-AGAGATTA
1 TCAAAATTTCATAAGAG-GGTTA
*
17815 TCAAAATTTCAGAA-AGAGGTTA
1 TCAAAATTTCATAAGAG-GGTTA
*
17837 TCAAATTTTCA
1 TCAAAATTTCA
17848 GAATGTGATT
Statistics
Matches: 290, Mismatches: 63, Indels: 72
0.68 0.15 0.17
Matches are distributed among these distances:
19 2 0.01
20 23 0.08
21 30 0.10
22 189 0.65
23 10 0.03
24 6 0.02
25 17 0.06
26 2 0.01
27 1 0.00
28 10 0.03
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.33
Consensus pattern (22 bp):
TCAAAATTTCATAAGAGGGTTA
Found at i:17550 original size:66 final size:65
Alignment explanation
Indices: 17438--17595 Score: 162
Period size: 66 Copynumber: 2.4 Consensus size: 65
17428 GTTTAGTTTT
** * * *
17438 CAAAATTTCATAA-GAGGGTTATCAAAATTTCATAGTATGCAGATCAAAATTTCATAGGGAGATT
1 CAAAATTTCATAATGA-GGTTATCAAAAAATCATAG-AGGAAGATCAAAATTTCATAGCGAGATT
17502 AA
64 AA
* * *
17504 CAAAATTTCATAATGAGGTTATCAAAAAATCATAG-GGAAGTTATCAAAATTTTATAGCGTGGTT
1 CAAAATTTCATAATGAGGTTATCAAAAAATCATAGAGGAAG--ATCAAAATTTCATAGCGAGATT
*
17568 AT
64 AA
17570 CAAAATTTCAT-ATGAAGGTTAT-AAAA
1 CAAAATTTCATAATG-AGGTTATCAAAA
17596 GTCTCAATTT
Statistics
Matches: 79, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
64 3 0.04
65 7 0.09
66 67 0.85
67 2 0.03
ACGTcount: A:0.43, C:0.09, G:0.16, T:0.32
Consensus pattern (65 bp):
CAAAATTTCATAATGAGGTTATCAAAAAATCATAGAGGAAGATCAAAATTTCATAGCGAGATTAA
Found at i:17591 original size:44 final size:44
Alignment explanation
Indices: 17400--18223 Score: 257
Period size: 44 Copynumber: 19.1 Consensus size: 44
17390 GGAGGATATC
* * * *
17400 ATTTCAT-GG-AGGATATCAAAATTTCATAGTTTAGTTTTCAAA
1 ATTTCATAGGAAGGTTATCAAAATTTCATAGTGTGGTTATCAAA
* * * ***
17442 ATTTCATAAGAGGGTTATCAAAATTTCATAGTATGCAGATCAAA
1 ATTTCATAGGAAGGTTATCAAAATTTCATAGTGTGGTTATCAAA
* * * * *
17486 ATTTCATAGGGAGATTAACAAAATTTCATAATGAGGTTATCAAA
1 ATTTCATAGGAAGGTTATCAAAATTTCATAGTGTGGTTATCAAA
** * *
17530 AAATCATAGGGAA-GTTATCAAAATTTTATAGCGTGGTTATCAAA
1 ATTTCATA-GGAAGGTTATCAAAATTTCATAGTGTGGTTATCAAA
* * * *
17574 ATTTCATATGAAGGTTATAAAAGTCTCAATTTCATAAG-G-AG-TACCAAA
1 ATTTCATAGGAAGGTTAT-CAA-----AATTTCAT-AGTGTGGTTATCAAA
* * * * *
17622 ATTTGATA-GAAGGTTATC-AAATCTCATAGAGTGATTATCGAA
1 ATTTCATAGGAAGGTTATCAAAATTTCATAGTGTGGTTATCAAA
* * * *
17664 ATTTCATAGAGCTCAGATTATCAAAATTT-ATAG-GAAGATTATCAAA
1 ATTTCATAG-G--AAGGTTATCAAAATTTCATAGTG-TGGTTATCAAA
* * * *
17710 ATTTCATA--ATGTTGTTATCAAAATTCCAAAGCGAT-GTTATCAAA
1 ATTTCATAGGAAG--GTTATCAAAATTTCATAGTG-TGGTTATCAAA
* * * * * * *
17754 ATTACATA--ATGTGATTATCAGAATTTCATAGAGGGGTCAACAAA
1 ATTTCATAGGAAG-G-TTATCAAAATTTCATAGTGTGGTTATCAAA
* * ** *
17798 ATTTTATA--AAGAGATTATCAAAATTTCAGAAAGAGGTTATCAAA
1 ATTTCATAGGAAG-G-TTATCAAAATTTCATAGTGTGGTTATCAAA
*
17842 TTTTC--A-GAATGTGATTA-CAAAAATTTCATA--GTGG---T----
1 ATTTCATAGGAA-G-G-TTATC-AAAATTTCATAGTGTGGTTATCAAA
* * *
17877 ATTTC-TGGGAAGGTTATCAAAATTTCATAGTATGGTTA-CCAA
1 ATTTCATAGGAAGGTTATCAAAATTTCATAGTGTGGTTATCAAA
* * * * *
17919 A--T--TAGGAAGGTTATTAAACTTTTATTA-TGGAGGATATCAAA
1 ATTTCATAGGAAGGTTATCAAAATTTCA-TAGT-GTGGTTATCAAA
* * * * *
17960 ATTTC--AGGGAGGATATCAAAATTTCATAGTTTAGTTTTCAAA
1 ATTTCATAGGAAGGTTATCAAAATTTCATAGTGTGGTTATCAAA
* * * * ***
18002 ATTTTATAAGAGGGTTATCAAAATTTCATAGTATGCAGATCAAA
1 ATTTCATAGGAAGGTTATCAAAATTTCATAGTGTGGTTATCAAA
* * *** * *
18046 ATTTCATAGTATGCAGATCAAAATTTCATAATGAGGTTATCAAAA
1 ATTTCATAGGAAGGTTATCAAAATTTCATAGTGTGGTTATC-AAA
* * *
18091 AATT-ATAGGGAGGTTATCAAAATTTGC--A-----GTTATCAAG
1 ATTTCATAGGAAGGTTATCAAAATTT-CATAGTGTGGTTATCAAA
* * * * *
18128 ATTTCATAAGAAAGTTATCAAAATTTTATAGGGAGGTTTATCAAA
1 ATTTCATAGGAAGGTTATCAAAATTTCATAGTGTGG-TTATCAAA
* * * **
18173 ATTTTATTGGAAGATTTATCAAAATTTCATAGTGTAATTATCAAA
1 ATTTCATAGGAAG-GTTATCAAAATTTCATAGTGTGGTTATCAAA
18218 ATTTCA
1 ATTTCA
18224 GAGTATGATT
Statistics
Matches: 571, Mismatches: 149, Indels: 121
0.68 0.18 0.14
Matches are distributed among these distances:
34 14 0.02
35 6 0.01
36 4 0.01
37 8 0.01
38 24 0.04
39 23 0.04
40 15 0.03
41 5 0.01
42 37 0.06
43 39 0.07
44 268 0.47
45 45 0.08
46 45 0.08
47 14 0.02
48 13 0.02
49 1 0.00
50 8 0.01
51 2 0.00
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.35
Consensus pattern (44 bp):
ATTTCATAGGAAGGTTATCAAAATTTCATAGTGTGGTTATCAAA
Found at i:17868 original size:22 final size:22
Alignment explanation
Indices: 17794--17869 Score: 82
Period size: 22 Copynumber: 3.5 Consensus size: 22
17784 GAGGGGTCAA
* *
17794 CAAAATTTTATAAAGAGATTAT
1 CAAAATTTCAGAAAGAGATTAT
*
17816 CAAAATTTCAGAAAGAGGTTAT
1 CAAAATTTCAGAAAGAGATTAT
* * *
17838 CAAATTTTCAGAATGTGATTA-
1 CAAAATTTCAGAAAGAGATTAT
17859 CAAAAATTTCA
1 C-AAAATTTCA
17870 TAGTGGTATT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
21 1 0.02
22 44 0.98
ACGTcount: A:0.46, C:0.09, G:0.12, T:0.33
Consensus pattern (22 bp):
CAAAATTTCAGAAAGAGATTAT
Found at i:17972 original size:20 final size:20
Alignment explanation
Indices: 17947--17985 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
17937 CTTTTATTAT
17947 GGAGGATATCAAAATTTCAG
1 GGAGGATATCAAAATTTCAG
17967 GGAGGATATCAAAATTTCA
1 GGAGGATATCAAAATTTCA
17986 TAGTTTAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.10, G:0.23, T:0.26
Consensus pattern (20 bp):
GGAGGATATCAAAATTTCAG
Found at i:18043 original size:22 final size:22
Alignment explanation
Indices: 18018--18075 Score: 116
Period size: 22 Copynumber: 2.6 Consensus size: 22
18008 TAAGAGGGTT
18018 ATCAAAATTTCATAGTATGCAG
1 ATCAAAATTTCATAGTATGCAG
18040 ATCAAAATTTCATAGTATGCAG
1 ATCAAAATTTCATAGTATGCAG
18062 ATCAAAATTTCATA
1 ATCAAAATTTCATA
18076 ATGAGGTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.33
Consensus pattern (22 bp):
ATCAAAATTTCATAGTATGCAG
Found at i:18087 original size:22 final size:22
Alignment explanation
Indices: 17968--18389 Score: 99
Period size: 22 Copynumber: 19.3 Consensus size: 22
17958 AAATTTCAGG
* *
17968 GAGGATATCAAAATTTCATAGTT
1 GAGGTTATCAAAATTTCATA-AT
* * *
17991 TA-GTTTTCAAAATTTTATAA-
1 GAGGTTATCAAAATTTCATAAT
18011 GAGGGTTATCAAAATTTCATAGTAT
1 GA-GGTTATCAAAATTTCATA--AT
18036 GCA-G--ATCAAAATTTCATAGTAT
1 G-AGGTTATCAAAATTTCATA--AT
18058 GCA-G--ATCAAAATTTCATAAT
1 G-AGGTTATCAAAATTTCATAAT
* **
18078 GAGGTTATCAAAAAATT-ATAGG
1 GAGGTTATC-AAAATTTCATAAT
18100 GAGGTTATCAAAA--T--T--T
1 GAGGTTATCAAAATTTCATAAT
*
18116 GCA-GTTATCAAGATTTCATAA-
1 G-AGGTTATCAAAATTTCATAAT
* * **
18137 GAAAGTTATCAAAATTTTATAGG
1 G-AGGTTATCAAAATTTCATAAT
*
18160 GAGGTTTATCAAAATTT--TATT
1 GAGG-TTATCAAAATTTCATAAT
* *
18181 GGAAGATTTATCAAAATTTCATAGT
1 -G-AG-GTTATCAAAATTTCATAAT
* *
18206 GTA-ATTATCAAAATTTCAGAGTAT
1 G-AGGTTATCAAAATTTCATA--AT
18230 GA--TTA-CTAACAA-TTCAT-AT
1 GAGGTTATC-AA-AATTTCATAAT
* * * *
18249 GGAGGTTTTTAAATTTTCATAAC
1 -GAGGTTATCAAAATTTCATAAT
* * *
18272 GTGGTTATCAATATATCAT-AT
1 GAGGTTATCAAAATTTCATAAT
* * *
18293 GGAGGTTATCAACATCTCATAGT
1 -GAGGTTATCAAAATTTCATAAT
* *
18316 GTTGGTTATCAAAATTTCATACT
1 G-AGGTTATCAAAATTTCATAAT
* * * **
18339 AAGGTCT-TCAAAATTCCTTAGG
1 GAGGT-TATCAAAATTTCATAAT
*
18361 GAGGTTAACAAAATTTCATAA-
1 GAGGTTATCAAAATTTCATAAT
18382 GAAGGTTA
1 G-AGGTTA
18390 AAAAAAATTA
Statistics
Matches: 301, Mismatches: 57, Indels: 83
0.68 0.13 0.19
Matches are distributed among these distances:
16 10 0.03
17 1 0.00
18 2 0.01
19 4 0.01
20 8 0.03
21 13 0.04
22 195 0.65
23 57 0.19
24 6 0.02
25 4 0.01
26 1 0.00
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (22 bp):
GAGGTTATCAAAATTTCATAAT
Found at i:18157 original size:60 final size:61
Alignment explanation
Indices: 18062--18176 Score: 171
Period size: 60 Copynumber: 1.9 Consensus size: 61
18052 TAGTATGCAG
*
18062 ATCAAAATTTCATAATGAGGTTATCAAAAAATTATAGGGAGG-TTATCAAAATTTGCAGTT
1 ATCAAAATTTCATAATGAAGTTATCAAAAAATTATAGGGAGGTTTATCAAAATTTGCAGTT
* **
18122 ATCAAGATTTCATAA-GAAAGTTATCAAAATTTTATAGGGAGGTTTATCAAAATTT
1 ATCAAAATTTCATAATG-AAGTTATCAAAAAATTATAGGGAGGTTTATCAAAATTT
18177 TATTGGAAGA
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
59 1 0.02
60 36 0.73
61 12 0.24
ACGTcount: A:0.42, C:0.08, G:0.16, T:0.35
Consensus pattern (61 bp):
ATCAAAATTTCATAATGAAGTTATCAAAAAATTATAGGGAGGTTTATCAAAATTTGCAGTT
Found at i:18170 original size:23 final size:23
Alignment explanation
Indices: 18120--18221 Score: 93
Period size: 23 Copynumber: 4.5 Consensus size: 23
18110 AAATTTGCAG
* * * *
18120 TTATCAAGATTTCATAAGAA-AG
1 TTATCAAAATTTTATAGGAAGAT
* *
18142 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGGAAGAT
*
18165 TTATCAAAATTTTATTGGAAGAT
1 TTATCAAAATTTTATAGGAAGAT
* *
18188 TTATCAAAATTTCATAGTGTA-A-
1 TTATCAAAATTTTATAG-GAAGAT
18210 TTATCAAAATTT
1 TTATCAAAATTT
18222 CAGAGTATGA
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
22 28 0.42
23 36 0.55
24 2 0.03
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.40
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGAAGAT
Found at i:18282 original size:552 final size:544
Alignment explanation
Indices: 16991--18223 Score: 1811
Period size: 552 Copynumber: 2.2 Consensus size: 544
16981 TCATGGAGAG
* * *
16991 GTTATCAAAATTTTATAGCGTGGTTATCAAAATTTCATATGAAGGTTATAAAAGTCTCAATTTCA
1 GTTATCAAAA-TTTATAGCG-AGTTATCAAAATTTCATAAGAAAGTTATAAAA--CT--ATTTCA
* * *
17056 TAAGGAGTACCAAAATTTGATAGAAGGTTGTCAAATCTCATAGAGTGATTATCGAAATTTCATAG
60 TAAGGAGTACCAAAATTTGATAGAAGGTTATCAAATCTCATAGAGTAATTATCAAAATTTCA-AG
* *
17121 AGCTCAGATTATCAAAATTTATAGGAAGATTATCAAAATTTCATAATGTTGTTATCAAAATTGCA
124 AGCTCAGATTATCAAAATTCATAGGAAGATTATCAAAATTTCATAATGTTGTTATCAAAATTCCA
*
17186 AAGCGTGGTTATCAAAATTACATAATGTGATTATCAGAATTTTATAGAGGGGTCAACAAAATTTT
189 AAGCGTGGTTATCAAAATTACATAATGTGATTATCAGAATTTCATAGAGGGGTCAACAAAATTTT
17251 ATAAAGAGATTATCAAAATTTCAGAAAGAGGTTATCAAATTTTCAGAACGTGATTACAAAAATTT
254 ATAAAGAGATTATCAAAATTTCAGAAAGAGGTTATCAAATTTTCAGAACGTGATTACAAAAATTT
* *
17316 CATAGTGGTATTTTTGGGAAGGTTATCAAAATTTCATAGTATGGTTACCTAATTAGGAAGGTTAA
319 CATAGTGGTATTTCTGGGAAGGTTATCAAAATTTCATAGTATGGTTACCAAATTAGGAAGGTTAA
*
17381 ACTTATTATGGAGGATATCATTTCATGGAGGATATCAAAATTTCATAGTTTAGTTTTCAAAATTT
384 ACTTATTATGGAGGATATCATTTCAGGGAGGATATCAAAATTTCATAGTTTAGTTTTCAAAATTT
*
17446 CATAAGAGGGTTATCAAAATTTCATAGTATGCAGATCAAAATTTCATAGGGAGATTAACAAAATT
449 CATAAGAGGGTTATCAAAATTTCATAGTATGCAGATCAAAATTTCATAGGCAGATT-ACAAAATT
17511 TCATAATGAGGTTATCAAAAAATCATAGGGAA
513 TCATAATGAGGTTATCAAAAAATCATAGGGAA
* * *
17543 GTTATCAAAATTTTATAGCGTGGTTATCAAAATTTCATATGAAGGTTATAAAAGTCTCAATTTCA
1 GTTATCAAAA-TTTATAGCG-AGTTATCAAAATTTCATAAGAAAGTTATAAAA--CT--ATTTCA
* *
17608 TAAGGAGTACCAAAATTTGATAGAAGGTTATCAAATCTCATAGAGTGATTATCGAAATTTCATAG
60 TAAGGAGTACCAAAATTTGATAGAAGGTTATCAAATCTCATAGAGTAATTATCAAAATTTCA-AG
*
17673 AGCTCAGATTATCAAAATTTATAGGAAGATTATCAAAATTTCATAATGTTGTTATCAAAATTCCA
124 AGCTCAGATTATCAAAATTCATAGGAAGATTATCAAAATTTCATAATGTTGTTATCAAAATTCCA
17738 AAGCGAT-GTTATCAAAATTACATAATGTGATTATCAGAATTTCATAGAGGGGTCAACAAAATTT
189 AAGCG-TGGTTATCAAAATTACATAATGTGATTATCAGAATTTCATAGAGGGGTCAACAAAATTT
*
17802 TATAAAGAGATTATCAAAATTTCAGAAAGAGGTTATCAAATTTTCAGAATGTGATTACAAAAATT
253 TATAAAGAGATTATCAAAATTTCAGAAAGAGGTTATCAAATTTTCAGAACGTGATTACAAAAATT
17867 TCATAGTGGTATTTCTGGGAAGGTTATCAAAATTTCATAGTATGGTTACCAAATTAGGAAGGTTA
318 TCATAGTGGTATTTCTGGGAAGGTTATCAAAATTTCATAGTATGGTTACCAAATTAGGAAGG---
17932 TTAAACTTTTATTATGGAGGATATCAAAATTTCAGGGAGGATATCAAAATTTCATAGTTTAGTTT
380 TTAAAC--TTATTATGGAGGATATC---ATTTCAGGGAGGATATCAAAATTTCATAGTTTAGTTT
*
17997 TCAAAATTTTATAAGAGGGTTATCAAAATTTCATAGTATGCAGATCAAAATTTCATAGTATGCAG
440 TCAAAATTTCATAAGAGGGTTATCAAAATTTCATAGTATGCAGATCAAAATTTCATAG---GCAG
* *
18062 A-T-CAAAATTTCATAATGAGGTTATCAAAAAATTATAGGGAG
502 ATTACAAAATTTCATAATGAGGTTATCAAAAAATCATAGGGAA
* *
18103 GTTATCAAAA-TT-T-GC-AGTTATCAAGATTTCATAAGAAAGTTATCAAAA-T-TTT-ATAGGG
1 GTTATCAAAATTTATAGCGAGTTATCAAAATTTCATAAGAAAGTTAT-AAAACTATTTCATAAGG
* * * * * *
18161 AGGTTTATCAAAATTTTATTGGAAGATTTATCAAAATTTCATAGTGTAATTATCAAAATTTCA
65 A-G--TACCAAAATTTGA-TAGAAG-GTTATC-AAATCTCATAGAGTAATTATCAAAATTTCA
18224 GAGTATGATT
Statistics
Matches: 638, Mismatches: 24, Indels: 36
0.91 0.03 0.05
Matches are distributed among these distances:
548 6 0.01
549 4 0.01
551 11 0.02
552 384 0.60
553 6 0.01
554 50 0.08
555 10 0.02
556 2 0.00
557 18 0.03
558 2 0.00
560 140 0.22
562 1 0.00
563 4 0.01
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (544 bp):
GTTATCAAAATTTATAGCGAGTTATCAAAATTTCATAAGAAAGTTATAAAACTATTTCATAAGGA
GTACCAAAATTTGATAGAAGGTTATCAAATCTCATAGAGTAATTATCAAAATTTCAAGAGCTCAG
ATTATCAAAATTCATAGGAAGATTATCAAAATTTCATAATGTTGTTATCAAAATTCCAAAGCGTG
GTTATCAAAATTACATAATGTGATTATCAGAATTTCATAGAGGGGTCAACAAAATTTTATAAAGA
GATTATCAAAATTTCAGAAAGAGGTTATCAAATTTTCAGAACGTGATTACAAAAATTTCATAGTG
GTATTTCTGGGAAGGTTATCAAAATTTCATAGTATGGTTACCAAATTAGGAAGGTTAAACTTATT
ATGGAGGATATCATTTCAGGGAGGATATCAAAATTTCATAGTTTAGTTTTCAAAATTTCATAAGA
GGGTTATCAAAATTTCATAGTATGCAGATCAAAATTTCATAGGCAGATTACAAAATTTCATAATG
AGGTTATCAAAAAATCATAGGGAA
Found at i:18326 original size:23 final size:22
Alignment explanation
Indices: 18272--18336 Score: 67
Period size: 23 Copynumber: 2.9 Consensus size: 22
18262 TTTTCATAAC
*
18272 GTGGTTATCAATATATCATATG
1 GTGGTTATCAAAATATCATATG
* * *
18294 GAGGTTATCAACATCTCATAGTG
1 GTGGTTATCAAAATATCATA-TG
* *
18317 TTGGTTATCAAAATTTCATA
1 GTGGTTATCAAAATATCATA
18337 CTAAGGTCTT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
22 17 0.49
23 18 0.51
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.38
Consensus pattern (22 bp):
GTGGTTATCAAAATATCATATG
Found at i:18402 original size:21 final size:22
Alignment explanation
Indices: 18362--18409 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
18352 TTCCTTAGGG
* * *
18362 AGGTTAACAAAATTTCATAAGA
1 AGGTTAAAAAAAATTCATAAAA
18384 AGGTTAAAAAAAATT-ATAAAA
1 AGGTTAAAAAAAATTCATAAAA
18405 AGGTT
1 AGGTT
18410 CTCGAAATTC
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:20803 original size:48 final size:48
Alignment explanation
Indices: 20747--20847 Score: 193
Period size: 48 Copynumber: 2.1 Consensus size: 48
20737 TTGGCTATCT
*
20747 TGAATAGGCTGTCTACTAAAGATAGGCTTTTGACATGGGGTTTCTCTA
1 TGAATAGGCTGCCTACTAAAGATAGGCTTTTGACATGGGGTTTCTCTA
20795 TGAATAGGCTGCCTACTAAAGATAGGCTTTTGACATGGGGTTTCTCTA
1 TGAATAGGCTGCCTACTAAAGATAGGCTTTTGACATGGGGTTTCTCTA
20843 TGAAT
1 TGAAT
20848 TAAGATAACC
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 52 1.00
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.35
Consensus pattern (48 bp):
TGAATAGGCTGCCTACTAAAGATAGGCTTTTGACATGGGGTTTCTCTA
Found at i:20964 original size:15 final size:15
Alignment explanation
Indices: 20944--20975 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
20934 GAGAAGAGTT
20944 TTGAACTTTTCAGGA
1 TTGAACTTTTCAGGA
20959 TTGAACTTTTCAGGA
1 TTGAACTTTTCAGGA
20974 TT
1 TT
20976 AAGCAGGCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.44
Consensus pattern (15 bp):
TTGAACTTTTCAGGA
Found at i:21274 original size:25 final size:25
Alignment explanation
Indices: 21240--21290 Score: 86
Period size: 25 Copynumber: 2.0 Consensus size: 25
21230 AAAATTGGGG
21240 ATTTTGTCTTGATAT-TTTTGAGCCT
1 ATTTTGTCTTGATATCTTTT-AGCCT
21265 ATTTTGTCTTGATATCTTTTAGCCT
1 ATTTTGTCTTGATATCTTTTAGCCT
21290 A
1 A
21291 ATTCTGATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 21 0.84
26 4 0.16
ACGTcount: A:0.18, C:0.14, G:0.14, T:0.55
Consensus pattern (25 bp):
ATTTTGTCTTGATATCTTTTAGCCT
Found at i:22995 original size:32 final size:32
Alignment explanation
Indices: 22946--23019 Score: 112
Period size: 32 Copynumber: 2.3 Consensus size: 32
22936 GGCTTGAGTT
* *
22946 GGGTTCGGGTTGGATTTGGGCCAGGTTAATTC
1 GGGTTCGGGTCGAATTTGGGCCAGGTTAATTC
* *
22978 GGGTTTGGGTCGAATTTGGGTCAGGTTAATTC
1 GGGTTCGGGTCGAATTTGGGCCAGGTTAATTC
23010 GGGTTCGGGT
1 GGGTTCGGGT
23020 TCTGTTTGGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.12, C:0.11, G:0.42, T:0.35
Consensus pattern (32 bp):
GGGTTCGGGTCGAATTTGGGCCAGGTTAATTC
Found at i:23028 original size:32 final size:32
Alignment explanation
Indices: 22946--23030 Score: 111
Period size: 32 Copynumber: 2.7 Consensus size: 32
22936 GGCTTGAGTT
* *
22946 GGGTTCGGGTTGGATTTGGGCCAGGTTAATTC
1 GGGTTCGGGTTCGATTTGGGTCAGGTTAATTC
*
22978 GGGTTTGGG-TCGAATTTGGGTCAGGTTAATTC
1 GGGTTCGGGTTCG-ATTTGGGTCAGGTTAATTC
23010 GGGTTCGGGTTCTG-TTTGGGT
1 GGGTTCGGGTTC-GATTTGGGT
23031 TTTGGCCAGA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
31 2 0.04
32 41 0.89
33 2 0.04
34 1 0.02
ACGTcount: A:0.11, C:0.11, G:0.41, T:0.38
Consensus pattern (32 bp):
GGGTTCGGGTTCGATTTGGGTCAGGTTAATTC
Found at i:23203 original size:16 final size:15
Alignment explanation
Indices: 23184--23269 Score: 73
Period size: 16 Copynumber: 5.4 Consensus size: 15
23174 GATTCGGGTT
23184 TTTTTCGGTTTTGAGC
1 TTTTTCGG-TTTGAGC
* * *
23200 TTTTTCGGGTTCAGAT
1 TTTTTCGGTTTGAG-C
23216 TTTTTCGGGTTTGAGC
1 TTTTTC-GGTTTGAGC
* **
23232 TTTTTCGGGTTCGAAT
1 TTTTTC-GGTTTGAGC
23248 TTTTTCGAGTTTGAGC
1 TTTTTCG-GTTTGAGC
23264 TTTTTC
1 TTTTTC
23270 AGATTCGGGT
Statistics
Matches: 55, Mismatches: 12, Indels: 6
0.75 0.16 0.08
Matches are distributed among these distances:
15 5 0.09
16 44 0.80
17 6 0.11
ACGTcount: A:0.09, C:0.13, G:0.24, T:0.53
Consensus pattern (15 bp):
TTTTTCGGTTTGAGC
Found at i:23229 original size:32 final size:32
Alignment explanation
Indices: 23183--23269 Score: 140
Period size: 32 Copynumber: 2.7 Consensus size: 32
23173 GGATTCGGGT
*
23183 TTTTTTCGGTTTTGAGCTTTTTCGGGTTC-AGA
1 TTTTTTCGGGTTTGAGCTTTTTCGGGTTCGA-A
23215 TTTTTTCGGGTTTGAGCTTTTTCGGGTTCGAA
1 TTTTTTCGGGTTTGAGCTTTTTCGGGTTCGAA
*
23247 TTTTTTCGAGTTTGAGCTTTTTC
1 TTTTTTCGGGTTTGAGCTTTTTC
23270 AGATTCGGGT
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
32 51 0.98
33 1 0.02
ACGTcount: A:0.09, C:0.13, G:0.24, T:0.54
Consensus pattern (32 bp):
TTTTTTCGGGTTTGAGCTTTTTCGGGTTCGAA
Found at i:23283 original size:32 final size:31
Alignment explanation
Indices: 23168--23290 Score: 138
Period size: 32 Copynumber: 3.8 Consensus size: 31
23158 TTTTCATAAA
*
23168 TTTTCGGATTCGGGTTTTTTTCGGTTTTGAGCT
1 TTTTCGGATTC-GGATTTTTTCGG-TTTGAGCT
* *
23201 TTTTCGGGTTCAGATTTTTTCGGGTTTGAGCT
1 TTTTCGGATTCGGATTTTTTC-GGTTTGAGCT
* *
23233 TTTTCGGGTTCGAATTTTTTCGAGTTTGAGCT
1 TTTTCGGATTCGGATTTTTTCG-GTTTGAGCT
* *
23265 TTTTCAGATTCGGGTTTTTTCAGGTT
1 TTTTCGGATTCGGATTTTTTC-GGTT
23291 CAGATTCAGA
Statistics
Matches: 78, Mismatches: 9, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
31 1 0.01
32 64 0.82
33 13 0.17
ACGTcount: A:0.10, C:0.12, G:0.26, T:0.52
Consensus pattern (31 bp):
TTTTCGGATTCGGATTTTTTCGGTTTGAGCT
Done.