Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023376.1 Corchorus olitorius cultivar O-4 contig23409, 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: 44440
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.31
Found at i:2159 original size:21 final size:21
Alignment explanation
Indices: 2135--2268 Score: 182
Period size: 21 Copynumber: 6.4 Consensus size: 21
2125 CTTAGGCAAT
*
2135 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGGAACCTTC
* *
2156 TCCAATGATCATGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
2177 TCCAATGAACTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
2198 TCCAATGAACTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
2219 TCCAATGAGCTTGGAA-CTTGT
1 TCCAATGAGCTTGGAACCTT-C
2240 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
2261 TCCAATGA
1 TCCAATGA
2269 ACTTCTAGCA
Statistics
Matches: 104, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
20 3 0.03
21 101 0.97
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.29
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Found at i:2736 original size:21 final size:21
Alignment explanation
Indices: 2695--2736 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2685 GCACAAAGAA
*
2695 GTTTCAAGCTCATTGGAGTTG
1 GTTTCAAGCTCATCGGAGTTG
*
2716 GTTTCAAGCTCATCGGTGTTG
1 GTTTCAAGCTCATCGGAGTTG
2737 CCTAAGATGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.17, C:0.17, G:0.29, T:0.38
Consensus pattern (21 bp):
GTTTCAAGCTCATCGGAGTTG
Found at i:3620 original size:25 final size:24
Alignment explanation
Indices: 3584--3630 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
3574 TCCTTCTATT
3584 CATCTATCATC-AAGTTTTTCATC
1 CATCTATCATCAAAGTTTTTCATC
3607 CATCTCATCCATCAAAGTTTTTCA
1 CATCT-AT-CATCAAAGTTTTTCA
3631 AAATTTTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 2 0.10
25 4 0.19
26 10 0.48
ACGTcount: A:0.28, C:0.28, G:0.04, T:0.40
Consensus pattern (24 bp):
CATCTATCATCAAAGTTTTTCATC
Found at i:10741 original size:22 final size:22
Alignment explanation
Indices: 10701--10762 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
10691 GTCTCTGTGT
10701 GGTTATCAAAATTTT-ATAAGAA
1 GGTTATC-AAATTTTCATAAGAA
* * *
10723 GGTTATTACATTTTCATAAGGA
1 GGTTATCAAATTTTCATAAGAA
10745 GGTTATCAAATTTTCATA
1 GGTTATCAAATTTTCATA
10763 GTGTGATTAC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 6 0.18
22 28 0.82
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.40
Consensus pattern (22 bp):
GGTTATCAAATTTTCATAAGAA
Found at i:10776 original size:22 final size:22
Alignment explanation
Indices: 10745--10896 Score: 91
Period size: 22 Copynumber: 6.9 Consensus size: 22
10735 TTCATAAGGA
* *
10745 GGTTATCAAATTTTCATAGTGT
1 GGTTACCAAAATTTCATAGTGT
* *
10767 GATTACCAAAACTTCTCAT--TGA
1 GGTTACCAAAA-TT-TCATAGTGT
*
10789 GGTT-TCAAAATTTCATAGTGT
1 GGTTACCAAAATTTCATAGTGT
10810 GGTTACCAAAATTTCATAG-GAAT
1 GGTTACCAAAATTTCATAGTG--T
* *
10833 -GTTATCAAAAATTCATAG-GAT
1 GGTTACCAAAATTTCATAGTG-T
** * *
10854 CAGGTTATTAAAATTTCATAATAT
1 --GGTTACCAAAATTTCATAGTGT
*
10878 GGTTATCAAAATTTCATAG
1 GGTTACCAAAATTTCATAG
10897 GGTTATCAAA
Statistics
Matches: 103, Mismatches: 16, Indels: 22
0.73 0.11 0.16
Matches are distributed among these distances:
19 4 0.04
20 2 0.02
21 14 0.14
22 60 0.58
23 3 0.03
24 20 0.19
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (22 bp):
GGTTACCAAAATTTCATAGTGT
Found at i:11072 original size:22 final size:21
Alignment explanation
Indices: 11047--11122 Score: 77
Period size: 22 Copynumber: 3.6 Consensus size: 21
11037 CACAAGGAGT
11047 TTATCAAAATTTATTAGCGAGG
1 TTATCAAAATTT-TTAGCGAGG
*
11069 TTATCAAAATTTTATA-CTGTGG
1 TTATCAAAATTTT-TAGC-GAGG
*
11091 TTAT-AAAAATTTTAG-GAAGG
1 TTATCAAAATTTTTAGCG-AGG
11111 TTATCAAAATTT
1 TTATCAAAATTT
11123 CATAACTTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
19 1 0.02
20 8 0.18
21 15 0.33
22 21 0.47
ACGTcount: A:0.38, C:0.07, G:0.14, T:0.41
Consensus pattern (21 bp):
TTATCAAAATTTTTAGCGAGG
Found at i:11272 original size:251 final size:252
Alignment explanation
Indices: 10907--11378 Score: 650
Period size: 251 Copynumber: 1.9 Consensus size: 252
10897 GGTTATCAAA
* *
10907 GAGGTTATCAGAATTTCATAGCAAGGTTATCAAGATTTCACAAGGAGGTTACAAAAATTTCTTTG
1 GAGGTTATCAGAATTTCATAGCAAGGTTATCAAAATTTCACAAGGAGGTTACAAAAATTTCTATG
* * *
10972 GGAAGTTATCGAAATTTCAGCTTGGTTATCAAAATTTCATATGAAGGTTATAAAAATCTCAATTA
66 GGAAGTTATCAAAATTTCAGCTTGGTTACCAAAATTTCATAGGAAGGTTATAAAAATCTCAATTA
* * * **
11037 CACAAGGAGTTTATCAAAATTTATTAGCG-AGGTTATCAAAATTTTATACTGTGGTTATAAAAAT
131 CAAAAGGAGTTTATCAAAATTTAATAG-GAAGGTTATCAAAACTTTATACTGAAGTTATAAAAAT
*
11101 TT-T-AGGAAGGTTATCAAAATTTCATAACTTTATCAAGATGTTATCAGAATTTCATAGC
195 TTATAAGG-AGGTT-TCAAAATCTCATAACTTTATCAAGATGTTATCAGAATTTCATAGC
* * * * * **
11159 GAGGTTATCATAATTTCATAGTATGGTTATCAAAATTTCATAAGGAGTTTAC-TGAATTTCATAT
1 GAGGTTATCAGAATTTCATAGCAAGGTTATCAAAATTTCACAAGGAGGTTACAAAAATTTC-TAT
*
11223 -GGAGGTTATCAAAATTTCAG-TGTGGTTACCAAAATTTCATAGGAAGGTTATAAAAATCTCAAT
65 GGGAAGTTATCAAAATTTCAGCT-TGGTTACCAAAATTTCATAGGAAGGTTATAAAAATCTCAAT
* * *
11286 TTCAAAAGGAGTTTATCATAATTTAATAGGAAGGTTATCAAAACTTTATAGTGAAGTTATAAAAA
129 TACAAAAGGAGTTTATCAAAATTTAATAGGAAGGTTATCAAAACTTTATACTGAAGTTATAAAAA
11351 TTTCATAAGGAGGTTTCAAAATCTCATA
194 TTT-ATAAGGAGGTTTCAAAATCTCATA
11379 GAGTGGTTAT
Statistics
Matches: 192, Mismatches: 22, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
250 2 0.01
251 121 0.63
252 60 0.31
253 6 0.03
254 3 0.02
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.35
Consensus pattern (252 bp):
GAGGTTATCAGAATTTCATAGCAAGGTTATCAAAATTTCACAAGGAGGTTACAAAAATTTCTATG
GGAAGTTATCAAAATTTCAGCTTGGTTACCAAAATTTCATAGGAAGGTTATAAAAATCTCAATTA
CAAAAGGAGTTTATCAAAATTTAATAGGAAGGTTATCAAAACTTTATACTGAAGTTATAAAAATT
TATAAGGAGGTTTCAAAATCTCATAACTTTATCAAGATGTTATCAGAATTTCATAGC
Found at i:11446 original size:90 final size:91
Alignment explanation
Indices: 11320--11489 Score: 236
Period size: 90 Copynumber: 1.9 Consensus size: 91
11310 AATAGGAAGG
*
11320 TTATCAAAACTTTATAGTGAAGTTATAAAAATTTCATAAGGAGGTT-TCAAAATCTCATAGAGTG
1 TTATCAAAACTTTATAGTGAAGTTATAAAAACTTCATAAGGAGGTTATCAAAATCTCATAGAGTG
11384 GTTATCAAAATTTCATAAAGATCAGA
66 GTTATCAAAATTTCATAAAGATCAGA
* * * * * * * *
11410 TTATTAAAA-TTTCATAGTGTAGTTATCAAAACTTCATAGGGATGTTATCAAAATTTCATGGTGT
1 TTATCAAAACTTT-ATAGTGAAGTTATAAAAACTTCATAAGGAGGTTATCAAAATCTCATAGAGT
11474 GGTTATCAAAATTTCA
65 GGTTATCAAAATTTCA
11490 ATGTAGTTAT
Statistics
Matches: 69, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
89 3 0.04
90 36 0.52
91 30 0.43
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (91 bp):
TTATCAAAACTTTATAGTGAAGTTATAAAAACTTCATAAGGAGGTTATCAAAATCTCATAGAGTG
GTTATCAAAATTTCATAAAGATCAGA
Found at i:11488 original size:22 final size:22
Alignment explanation
Indices: 11140--11612 Score: 241
Period size: 22 Copynumber: 21.6 Consensus size: 22
11130 TTATCAAGAT
* * *
11140 GTTATCAGAATTTCATAGCGAG
1 GTTATCAAAATTTCATAGTGTG
* *
11162 GTTATCATAATTTCATAGTATG
1 GTTATCAAAATTTCATAGTGTG
*
11184 GTTATCAAAATTTCATAAG-GAG
1 GTTATCAAAATTTCAT-AGTGTG
* ** *
11206 TTTA-CTGAATTTCATA-TGGAG
1 GTTATCAAAATTTCATAGT-GTG
11227 GTTATCAAAATTTC--AGTGTG
1 GTTATCAAAATTTCATAGTGTG
* *
11247 GTTACCAAAATTTCATAG-GAAG
1 GTTATCAAAATTTCATAGTG-TG
* * **
11269 GTTATAAAAATCTCAATTTCAAAAG-G
1 GTTATCAAAATTTC-A--T--AGTGTG
* * *
11295 AGTTTATCATAATTTAATAG-GAAG
1 -G-TTATCAAAATTTCATAGTG-TG
**
11319 GTTATCAAAACTTT-ATAGTGAA
1 GTTATCAAAA-TTTCATAGTGTG
* *
11341 GTTATAAAAATTTCATAAG-GAG
1 GTTATCAAAATTTCAT-AGTGTG
* *
11363 GTT-TCAAAATCTCATAGAGTG
1 GTTATCAAAATTTCATAGTGTG
**
11384 GTTATCAAAATTTCATAAAGATCAG
1 GTTATCAAAATTTCAT--AG-TGTG
* * *
11409 ATTATTAAAATTTCATAGTGTA
1 GTTATCAAAATTTCATAGTGTG
* *
11431 GTTATCAAAACTTCATAGGGAT-
1 GTTATCAAAATTTCATAGTG-TG
*
11453 GTTATCAAAATTTCATGGTGTG
1 GTTATCAAAATTTCATAGTGTG
*
11475 GTTATCAAAATTTCA-A-TGTA
1 GTTATCAAAATTTCATAGTGTG
*
11495 GTTATC-AAATTTCATACG-GAG
1 GTTATCAAAATTTCATA-GTGTG
*
11516 G-T-TCAAAATTTTATAGTGTG
1 GTTATCAAAATTTCATAGTGTG
* *
11536 GTTATCAAATTTTCATAGAGTG
1 GTTATCAAAATTTCATAGTGTG
* *
11558 ATTATC-AAATTTCATTAG-GAG
1 GTTATCAAAATTTCA-TAGTGTG
* *
11579 G-TATCAAAATTTCATGGCGTG
1 GTTATCAAAATTTCATAGTGTG
*
11600 ATTATCAAAATTT
1 GTTATCAAAATTT
11613 TAGAGGTATT
Statistics
Matches: 347, Mismatches: 64, Indels: 80
0.71 0.13 0.16
Matches are distributed among these distances:
19 11 0.03
20 48 0.14
21 58 0.17
22 182 0.52
23 14 0.04
24 3 0.01
25 17 0.05
26 1 0.00
27 3 0.01
28 10 0.03
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (22 bp):
GTTATCAAAATTTCATAGTGTG
Found at i:11584 original size:42 final size:39
Alignment explanation
Indices: 11538--11653 Score: 128
Period size: 42 Copynumber: 2.9 Consensus size: 39
11528 ATAGTGTGGT
*
11538 TATCAAATTTTCATAGAGTGATTATCAAATTTCATTAGGAGG
1 TATCAAATTTTCATAGAGTGATTATCAAAATT--TTA-GAGG
* * *
11580 TATCAAAATTTCATGGCGTGATTATCAAAATTTTAGAGG
1 TATCAAATTTTCATAGAGTGATTATCAAAATTTTAGAGG
*
11619 TATTAAAATTTT-ATA-ATGTGATTATCAAAATTTTA
1 TA-TCAAATTTTCATAGA-GTGATTATCAAAATTTTA
11654 CGAACATGAG
Statistics
Matches: 64, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
39 26 0.41
40 10 0.16
42 28 0.44
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.41
Consensus pattern (39 bp):
TATCAAATTTTCATAGAGTGATTATCAAAATTTTAGAGG
Found at i:11605 original size:105 final size:103
Alignment explanation
Indices: 11415--11652 Score: 231
Period size: 105 Copynumber: 2.3 Consensus size: 103
11405 TCAGATTATT
* * ** * * *
11415 AAAATTTCATAGTGTAGTTATCAAAACTTCATAGGGATGTTATCAAAATTTCATGGTGTGGTTAT
1 AAAATTTTATAGTGTGGTTATCAAATTTTCATAGAGATGTTATCAAAATTTCATAGTGAGGTTAT
11480 CAAAATTTCAATGTAGTTATC-AAATTTCATACGGAGGT-TC
66 CAAAATTTCAATGTAGTTATCAAAATTT--TA--GAGGTATC
11520 AAAATTTTATAGTGTGGTTATCAAATTTTCATAGAG-TGATTATC-AAATTTCATTAG-GAGG-T
1 AAAATTTTATAGTGTGGTTATCAAATTTTCATAGAGATG-TTATCAAAATTTCA-TAGTGAGGTT
*
11581 ATCAAAATTTC-ATGGCGT-GATTATCAAAATTTTAGAGGTATT
64 ATCAAAATTTCAAT---GTAG-TTATCAAAATTTTAGAGGTATC
* *
11623 AAAATTTTATAATGTGATTATCAAAATTTT
1 AAAATTTTATAGTGTGGTTATC-AAATTTT
11653 ACGAACATGA
Statistics
Matches: 114, Mismatches: 10, Indels: 19
0.80 0.07 0.13
Matches are distributed among these distances:
102 7 0.06
103 33 0.29
104 23 0.20
105 45 0.39
106 6 0.05
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.39
Consensus pattern (103 bp):
AAAATTTTATAGTGTGGTTATCAAATTTTCATAGAGATGTTATCAAAATTTCATAGTGAGGTTAT
CAAAATTTCAATGTAGTTATCAAAATTTTAGAGGTATC
Found at i:11640 original size:39 final size:39
Alignment explanation
Indices: 11538--11653 Score: 119
Period size: 39 Copynumber: 2.9 Consensus size: 39
11528 ATAGTGTGGT
*
11538 TATC-AAATTTTCATAGAGTGATTATCAAATTTCATTAGGAGG
1 TATCAAAATTTT-ATA-AGTGATTATCAAAATT--TTAGGAGG
* **
11580 TATCAAAATTTCATGGCGTGATTATCAAAATTTTA-GAGG
1 TATCAAAATTTTAT-AAGTGATTATCAAAATTTTAGGAGG
*
11619 TATTAAAATTTTATAATGTGATTATCAAAATTTTA
1 TATCAAAATTTTATAA-GTGATTATCAAAATTTTA
11654 CGAACATGAG
Statistics
Matches: 63, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
39 34 0.54
40 3 0.05
42 20 0.32
43 6 0.10
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.41
Consensus pattern (39 bp):
TATCAAAATTTTATAAGTGATTATCAAAATTTTAGGAGG
Found at i:11648 original size:22 final size:21
Alignment explanation
Indices: 11518--11653 Score: 79
Period size: 22 Copynumber: 6.5 Consensus size: 21
11508 ATACGGAGGT
* *
11518 TCAAAATTTTATAGTGTGGTTA
1 TCAAAATTTTATA-AGTGATTA
11540 TC-AAATTTTCATAGAGTGATTA
1 TCAAAATTTT-ATA-AGTGATTA
* * *
11562 TC-AAATTTCATTAG-GAGGTA
1 TCAAAATTTTATAAGTGA-TTA
* **
11582 TCAAAATTTCATGGCGTGATTA
1 TCAAAATTTTAT-AAGTGATTA
*
11604 TCAAAATTTTA-GAG-G--TA
1 TCAAAATTTTATAAGTGATTA
*
11621 TTAAAATTTTATAATGTGATTA
1 TCAAAATTTTATAA-GTGATTA
11643 TCAAAATTTTA
1 TCAAAATTTTA
11654 CGAACATGAG
Statistics
Matches: 91, Mismatches: 13, Indels: 20
0.73 0.10 0.16
Matches are distributed among these distances:
17 12 0.13
18 1 0.01
19 4 0.04
20 9 0.10
21 18 0.20
22 45 0.49
23 2 0.02
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (21 bp):
TCAAAATTTTATAAGTGATTA
Found at i:13747 original size:28 final size:28
Alignment explanation
Indices: 13707--13763 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
13697 GTTAAAAGTA
13707 TCTGACATTAGTTAGAGTTTGTTTGTCC
1 TCTGACATTAGTTAGAGTTTGTTTGTCC
13735 TCTGACATTAGTTAGAGTTTGTTTGTCC
1 TCTGACATTAGTTAGAGTTTGTTTGTCC
13763 T
1 T
13764 TTTAGGCATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.18, C:0.14, G:0.21, T:0.47
Consensus pattern (28 bp):
TCTGACATTAGTTAGAGTTTGTTTGTCC
Found at i:29590 original size:2 final size:2
Alignment explanation
Indices: 29585--29621 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
29575 AAAAAGAAAT
* *
29585 AG AG AG AG AG AG AG AA AT AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
29622 TACAGTAGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.54, C:0.00, G:0.43, T:0.03
Consensus pattern (2 bp):
AG
Found at i:29602 original size:18 final size:18
Alignment explanation
Indices: 29579--29617 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
29569 AAAGAAAAAA
29579 AGAAATAGAGAGAGAGAG
1 AGAAATAGAGAGAGAGAG
29597 AGAAATAGAGAGAGAGAG
1 AGAAATAGAGAGAGAGAG
29615 AGA
1 AGA
29618 GAGATACAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.38, T:0.05
Consensus pattern (18 bp):
AGAAATAGAGAGAGAGAG
Found at i:37277 original size:84 final size:83
Alignment explanation
Indices: 37189--37468 Score: 257
Period size: 84 Copynumber: 3.4 Consensus size: 83
37179 CAGGAATATA
* * * * * *
37189 ATTATCGGTTTGTTGAAGTTGAACACCATCACCAAGCTCATTCTCATT-ATCAGTTGAATCCTCT
1 ATTATCGGTTTCTTCAAGTTGAACATCATTACCAAGCT-ATTCTCATTAAT-AGGTGAATCATCT
37253 AACAACTCACCATGAGTACC
64 AACAACTCACCATGAGTACC
** * * * *
37273 ATTATCAATTTCTTTAAGTCGAACATCATTACCAAGCATAATCTCCTTAATAGGTGAATCATCTA
1 ATTATCGGTTTCTTCAAGTTGAACATCATTACCAAGC-TATTCTCATTAATAGGTGAATCATCTA
*
37338 CCAACTCACCATGAGTACC
65 ACAACTCACCATGAGTACC
* * *
37357 ATGATCAGG-TTCTTCAAGTTGAACATCATTACCAAGCTTATTCTCA-TCAT---TTAAGTCATC
1 ATTATC-GGTTTCTTCAAGTTGAACATCATTACCAAGC-TATTCTCATTAATAGGTGAA-TCATC
** * *
37417 TAACAACTGGCCACGAGTACT
63 TAACAACTCACCATGAGTACC
* * *
37438 GTTGTCAGTTTCTTCAAGTTGAACATCATTA
1 ATTATCGGTTTCTTCAAGTTGAACATCATTA
37469 TCAGGTTCCA
Statistics
Matches: 160, Mismatches: 31, Indels: 13
0.78 0.15 0.06
Matches are distributed among these distances:
80 4 0.03
81 46 0.29
83 3 0.02
84 104 0.65
85 3 0.02
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (83 bp):
ATTATCGGTTTCTTCAAGTTGAACATCATTACCAAGCTATTCTCATTAATAGGTGAATCATCTAA
CAACTCACCATGAGTACC
Found at i:37777 original size:4 final size:4
Alignment explanation
Indices: 37758--37790 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
37748 AGGTAATACC
37758 ATAA ATACA A-AA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATA-A ATAA ATAA ATAA ATAA ATAA ATAA A
37791 ATGACAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
3 2 0.07
4 23 0.85
5 2 0.07
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (4 bp):
ATAA
Found at i:40727 original size:146 final size:145
Alignment explanation
Indices: 40455--40739 Score: 545
Period size: 146 Copynumber: 2.0 Consensus size: 145
40445 GCTAAATTAG
40455 AATCTGAATATAGGGCTCAAGAAAAGATAAAAGCATGCTAATTCTAATTCTAATTGCGTTGAAAA
1 AATCTGAATATAGGGCTCAAGAAAAGATAAAAGCATGCTAATTCTAATTCTAATTGCGTTGAAAA
40520 CAAGGCTGTTTTGGTTGATAAGAAAACTAGCTCTAAGAAAGTTGTTAAAGAGTGTATGTTAGCTA
66 CAAGGCTGTTTTGGTTGATAAGAAAACTAGCTCTAAGAAAGTTGTTAAAGAGTGTATGTTAGCTA
40585 CTAAGAGTGAGCCCT
131 CTAAGAGTGAGCCCT
40600 AATCTGAATATATAGGGCTCAAGAAAAGAT-AAAGCATGCTAATTCTAATTCTAATTGCGTTGAA
1 AATCTG-A-ATATAGGGCTCAAGAAAAGATAAAAGCATGCTAATTCTAATTCTAATTGCGTTGAA
40664 AACAAGGCTGTTTTGGTTGATAAGAAAACTAGCTCTAAGAAAGTTGTTAAAGAGTGTATGTTAGC
64 AACAAGGCTGTTTTGGTTGATAAGAAAACTAGCTCTAAGAAAGTTGTTAAAGAGTGTATGTTAGC
40729 TACTAAGAGTG
129 TACTAAGAGTG
40740 GGATTAAGAA
Statistics
Matches: 138, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
145 6 0.04
146 111 0.80
147 21 0.15
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (145 bp):
AATCTGAATATAGGGCTCAAGAAAAGATAAAAGCATGCTAATTCTAATTCTAATTGCGTTGAAAA
CAAGGCTGTTTTGGTTGATAAGAAAACTAGCTCTAAGAAAGTTGTTAAAGAGTGTATGTTAGCTA
CTAAGAGTGAGCCCT
Done.