Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008789.1 Corchorus capsularis cultivar CVL-1 contig08810, 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: 100898
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:188 original size:26 final size:25
Alignment explanation
Indices: 131--203 Score: 82
Period size: 26 Copynumber: 3.0 Consensus size: 25
121 CACAATGTGG
*
131 TTATCAAAATTTCATA-AT-G-TGA
1 TTATCAAAATTTCATAGATAGTTAA
153 TTA-CAAAAATTTCATAGGATAGTTAA
1 TTATC-AAAATTTCATA-GATAGTTAA
179 TTATCAAAATTTCATAGTATAGTTA
1 TTATCAAAATTTCATAG-ATAGTTA
204 CCAAAATTCA
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
21 1 0.02
22 14 0.33
24 2 0.05
25 2 0.05
26 23 0.53
27 1 0.02
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.40
Consensus pattern (25 bp):
TTATCAAAATTTCATAGATAGTTAA
Found at i:266 original size:41 final size:39
Alignment explanation
Indices: 221--341 Score: 118
Period size: 41 Copynumber: 2.9 Consensus size: 39
211 TCATTAGGAG
*
221 GTTATTAAATTTCAGTGTGGTTATAAAAATTTCATTGAGAC
1 GTTATTAAATTTCAGTGTGGTTATCAAAATTTCA-TGA-AC
* * *
262 GTTATTTGAATTTCATGTTGTGATTATCAAAATTTCA-GAAG
1 GTTA-TTAAATTTCA-G-TGTGGTTATCAAAATTTCATGAAC
*
303 GTTATTAAAATTTCATAATGTGGTTATCAAAATTTCATG
1 GTTATT-AAATTTC--AGTGTGGTTATCAAAATTTCATG
342 TGAAGATTAC
Statistics
Matches: 66, Mismatches: 7, Indels: 13
0.77 0.08 0.15
Matches are distributed among these distances:
40 2 0.03
41 33 0.50
42 12 0.18
43 2 0.03
44 17 0.26
ACGTcount: A:0.34, C:0.07, G:0.16, T:0.43
Consensus pattern (39 bp):
GTTATTAAATTTCAGTGTGGTTATCAAAATTTCATGAAC
Found at i:489 original size:21 final size:21
Alignment explanation
Indices: 463--520 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
453 GTGGTTATTA
463 AAATTTCATAGAGAGGCAATC
1 AAATTTCATAGAGAGGCAATC
484 AAATTTCATA-AGGAGGCAATC
1 AAATTTCATAGA-GAGGCAATC
*
505 AAATTTCGTAGAGAGG
1 AAATTTCATAGAGAGG
521 TTATCAAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
20 1 0.03
21 32 0.94
22 1 0.03
ACGTcount: A:0.41, C:0.12, G:0.22, T:0.24
Consensus pattern (21 bp):
AAATTTCATAGAGAGGCAATC
Found at i:599 original size:43 final size:43
Alignment explanation
Indices: 534--687 Score: 125
Period size: 43 Copynumber: 3.6 Consensus size: 43
524 TCAAAATTGC
* * ** * *
534 ATAGGGAGTTTATCAAGTTTTCATAGTGCGGTTTCTGAAATTT
1 ATAGAGAGGTTATCAAAATTTCATAGTGTGGTTTCTAAAATTT
* * *
577 ATAGAGAGGTTATCAAAATTTCAAAGTGTGGTTAC-CAAATTT
1 ATAGAGAGGTTATCAAAATTTCATAGTGTGGTTTCTAAAATTT
*
619 CATA-ATGATGTTATCAAAATTTCATAGTGTGGTTAT-TAAAATTTT
1 -ATAGA-GAGGTTATCAAAATTTCATAGTGTGGTT-TCTAAAA-TTT
* ** *
664 ATAGGGATATTATCGAAATTTCAT
1 ATAGAGAGGTTATCAAAATTTCAT
688 GAGGAAATAA
Statistics
Matches: 90, Mismatches: 15, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
42 7 0.08
43 57 0.63
44 23 0.26
45 3 0.03
ACGTcount: A:0.34, C:0.08, G:0.18, T:0.40
Consensus pattern (43 bp):
ATAGAGAGGTTATCAAAATTTCATAGTGTGGTTTCTAAAATTT
Found at i:667 original size:22 final size:22
Alignment explanation
Indices: 110--667 Score: 171
Period size: 22 Copynumber: 25.7 Consensus size: 22
100 ATAAGAAAAA
* * *
110 TATCACAATTTCACAATGTGGT
1 TATCAAAATTTCATAGTGTGGT
* *
132 TATCAAAATTTCATAATGTGAT
1 TATCAAAATTTCATAGTGTGGT
**
154 TA-CAAAAATTTCATAGGATAGTTAAT
1 TATC-AAAATTTCATA-G-T-G-TGGT
* *
180 TATCAAAATTTCATAGTATAGT
1 TATCAAAATTTCATAGTGTGGT
* *
202 TACCAAAA-TTCATTAG-GAGGT
1 TATCAAAATTTCA-TAGTGTGGT
*
223 TAT-TAAATTTC--AGTGTGGT
1 TATCAAAATTTCATAGTGTGGT
* * * **
242 TATAAAAATTTCATTGAGACGT
1 TATCAAAATTTCATAGTGTGGT
*** *
264 TATTTGAATTTCAT-GTTGTGAT
1 TATCAAAATTTCATAG-TGTGGT
**
286 TATCAAAATTTC--AG-AAGGT
1 TATCAAAATTTCATAGTGTGGT
* *
305 TATTAAAATTTCATAATGTGGT
1 TATCAAAATTTCATAGTGTGGT
* *
327 TATCAAAATTTCAT-GTGAAGAT
1 TATCAAAATTTCATAGTG-TGGT
* * *
349 TACCAAAATTTCATAG-GTAAGA
1 TATCAAAATTTCATAGTGT-GGT
* **
371 TAGCAAAATTTACAT--TGTGCA
1 TATCAAAATTT-CATAGTGTGGT
** *
392 TATTTAAATTTCATAGAGAT--T
1 TATCAAAATTTCATAGTG-TGGT
* *
413 CA-CAAATTTTCATAAG-GAT-GT
1 TATCAAAATTTCAT-AGTG-TGGT
*
434 TA-CTAAAATTTGATAGTGTGTGGT
1 TATC-AAAATTTCATA--GTGTGGT
* * * *
458 TATTAAAATTTCATAGAGAGGC
1 TATCAAAATTTCATAGTGTGGT
* * *
480 AATC-AAATTTCATAAG-GAGGC
1 TATCAAAATTTCAT-AGTGTGGT
* * * *
501 AATC-AAATTTCGTAGAGAGGT
1 TATCAAAATTTCATAGTGTGGT
* * * *
522 TATCAAAATTGCATAGGGAGTT
1 TATCAAAATTTCATAGTGTGGT
** *
544 TATCAAGTTTTCATAGTGCGGT
1 TATCAAAATTTCATAGTGTGGT
* * *
566 T-TCTGAAATTT-ATAGAGAGGT
1 TATC-AAAATTTCATAGTGTGGT
*
587 TATCAAAATTTCAAAGTGTGGT
1 TATCAAAATTTCATAGTGTGGT
* *
609 TA-CCAAATTTCATAATGAT-GT
1 TATCAAAATTTCATAGTG-TGGT
630 TATCAAAATTTCATAGTGTGGT
1 TATCAAAATTTCATAGTGTGGT
* *
652 TATTAAAATTTTATAG
1 TATCAAAATTTCATAG
668 GGATATTATC
Statistics
Matches: 398, Mismatches: 96, Indels: 84
0.69 0.17 0.15
Matches are distributed among these distances:
18 2 0.01
19 20 0.05
20 26 0.07
21 100 0.25
22 207 0.52
23 7 0.02
24 17 0.04
25 2 0.01
26 16 0.04
27 1 0.00
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.37
Consensus pattern (22 bp):
TATCAAAATTTCATAGTGTGGT
Found at i:914 original size:22 final size:22
Alignment explanation
Indices: 865--914 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
855 TCGTTGTGTG
* *
865 GTTATCAAAATTTTGTAAGAAT
1 GTTATTAAAATTTTATAAGAAT
887 GTTATTAAAATTTTATAAGAAT
1 GTTATTAAAATTTTATAAGAAT
909 GTTATT
1 GTTATT
915 GAAGTGTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.46
Consensus pattern (22 bp):
GTTATTAAAATTTTATAAGAAT
Found at i:18676 original size:15 final size:14
Alignment explanation
Indices: 18641--18696 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 14
18631 AATTAAATTC
18641 TAACGTTATATA-T
1 TAACGTTATATATT
18654 TAACGTTATATATT
1 TAACGTTATATATT
* *
18668 TAATTGTTATTTATTTT
1 TAA-CGTTA--TATATT
18685 TAACGTTATATA
1 TAACGTTATATA
18697 AATTAAATTC
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
13 12 0.34
14 7 0.20
15 4 0.11
16 4 0.11
17 8 0.23
ACGTcount: A:0.34, C:0.05, G:0.07, T:0.54
Consensus pattern (14 bp):
TAACGTTATATATT
Found at i:18717 original size:22 final size:23
Alignment explanation
Indices: 18684--18742 Score: 93
Period size: 22 Copynumber: 2.6 Consensus size: 23
18674 TTATTTATTT
*
18684 TTAACGTTATATAAATTAAATTC
1 TTAATGTTATATAAATTAAATTC
*
18707 -TAATGTTATATATATTAAATTC
1 TTAATGTTATATAAATTAAATTC
18729 TTAATGTTATATAA
1 TTAATGTTATATAA
18743 CGTTATATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
22 20 0.62
23 12 0.38
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (23 bp):
TTAATGTTATATAAATTAAATTC
Found at i:18737 original size:23 final size:23
Alignment explanation
Indices: 18684--18790 Score: 99
Period size: 23 Copynumber: 4.4 Consensus size: 23
18674 TTATTTATTT
*
18684 TTAACGTTATATAAATTAAATTC
1 TTAACGTTATATATATTAAATTC
*
18707 -TAATGTTATATATATTAAATTC
1 TTAACGTTATATATATTAAATTC
* * *
18729 TTAATGTTATATAACGTTATATTTAATTT
1 TTAACG-T-TAT-A---TATATTAAATTC
*
18758 TTAAGGTTATATATATTAAATTC
1 TTAACGTTATATATATTAAATTC
18781 TTAACGTTAT
1 TTAACGTTAT
18791 GTTTAGGGTT
Statistics
Matches: 69, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
22 20 0.29
23 24 0.35
24 1 0.01
25 3 0.04
26 2 0.03
27 3 0.04
28 1 0.01
29 15 0.22
ACGTcount: A:0.38, C:0.06, G:0.07, T:0.50
Consensus pattern (23 bp):
TTAACGTTATATATATTAAATTC
Found at i:20057 original size:2 final size:2
Alignment explanation
Indices: 20052--20104 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
20042 TGTGTGTGTG
20052 TA TA TA TA TA TA TA TA TA TA 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 TA TA TA
20094 TA TA TA TA TA T
1 TA TA TA TA TA T
20105 TGGAAAATGG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:20855 original size:19 final size:19
Alignment explanation
Indices: 20823--20885 Score: 53
Period size: 18 Copynumber: 3.5 Consensus size: 19
20813 ATAAAAAATA
* *
20823 TATATATTTCATATATAAT
1 TATATATATAATATATAAT
* *
20842 TATATATCTGATATCAT-A-
1 TATATATATAATAT-ATAAT
20860 TATATATATAATAT-TAAT
1 TATATATATAATATATAAT
20878 T-TATATAT
1 TATATATAT
20886 GTTTTTTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
16 1 0.03
17 8 0.22
18 13 0.35
19 13 0.35
20 2 0.05
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.51
Consensus pattern (19 bp):
TATATATATAATATATAAT
Found at i:21434 original size:19 final size:19
Alignment explanation
Indices: 21410--21460 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
21400 AGTTTAAAAC
*
21410 TTTAAACGATGAAGTTCAG
1 TTTAAATGATGAAGTTCAG
*
21429 TTTAAATGATGAAGTTCGG
1 TTTAAATGATGAAGTTCAG
21448 TTTAAATGATGAA
1 TTTAAATGATGAA
21461 AGATGAATGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.37, C:0.06, G:0.22, T:0.35
Consensus pattern (19 bp):
TTTAAATGATGAAGTTCAG
Found at i:21848 original size:2 final size:2
Alignment explanation
Indices: 21843--21867 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
21833 TATATATATA
21843 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
21868 ATGTAAGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:22060 original size:23 final size:23
Alignment explanation
Indices: 22034--22099 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 23
22024 GGGTCCCTAG
* *
22034 TTGAGCTGTAATTGGACTCCCAA
1 TTGAGATGTAATCGGACTCCCAA
* *
22057 TTGAGATGTAATCGGGCTCCCAG
1 TTGAGATGTAATCGGACTCCCAA
*
22080 TTGAGATGTAATCGGGCTCC
1 TTGAGATGTAATCGGACTCC
22100 TACTTGGACT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (23 bp):
TTGAGATGTAATCGGACTCCCAA
Found at i:23327 original size:19 final size:18
Alignment explanation
Indices: 23303--23340 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
23293 GAAGTTCGTG
23303 ATTGAAGATAATTTGAAGA
1 ATTGAAGATAA-TTGAAGA
*
23322 ATTGAAGATCATTGAAGA
1 ATTGAAGATAATTGAAGA
23340 A
1 A
23341 ATATTTCAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.47, C:0.03, G:0.21, T:0.29
Consensus pattern (18 bp):
ATTGAAGATAATTGAAGA
Found at i:25489 original size:19 final size:19
Alignment explanation
Indices: 25465--25511 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
25455 ATAAATTCTA
25465 TTTCGTGTATAGGTACATC
1 TTTCGTGTATAGGTACATC
25484 TTTCGTGTATAGGTACATC
1 TTTCGTGTATAGGTACATC
25503 TTTCGTGTA
1 TTTCGTGTA
25512 AGATATATGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.19, C:0.15, G:0.21, T:0.45
Consensus pattern (19 bp):
TTTCGTGTATAGGTACATC
Found at i:28819 original size:2 final size:2
Alignment explanation
Indices: 28812--28837 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28802 CATAGATTAA
28812 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
28838 GAAGAATTTT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29352 original size:23 final size:22
Alignment explanation
Indices: 29326--29372 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 22
29316 GGCCCAAGAA
29326 TATTATAAACTAAAATCATGTT-T
1 TATT-TAAA-TAAAATCATGTTGT
*
29349 TA-TTCAATAAAATCATGTTGT
1 TATTTAAATAAAATCATGTTGT
29370 TAT
1 TAT
29373 AATTTTAACC
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
20 12 0.57
21 6 0.29
22 1 0.05
23 2 0.10
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.45
Consensus pattern (22 bp):
TATTTAAATAAAATCATGTTGT
Found at i:29485 original size:10 final size:10
Alignment explanation
Indices: 29470--29498 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
29460 GGGATGATGC
29470 AAAGCCCACA
1 AAAGCCCACA
29480 AAAGCCCACA
1 AAAGCCCACA
29490 AAAGCCCAC
1 AAAGCCCAC
29499 CAAGCGTACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.48, C:0.41, G:0.10, T:0.00
Consensus pattern (10 bp):
AAAGCCCACA
Found at i:29617 original size:39 final size:40
Alignment explanation
Indices: 29574--29684 Score: 145
Period size: 39 Copynumber: 2.8 Consensus size: 40
29564 TCTCTCTCCC
29574 CAAAGTCCCCAAACACATATAACACAGGGGCAACT-CACT
1 CAAAGTCCCCAAACACATATAACACAGGGGCAACTACACT
* * * * *
29613 CAAAGTCCTCAAACACATATAACACAGAGACATCTATACT
1 CAAAGTCCCCAAACACATATAACACAGGGGCAACTACACT
* *
29653 -AAAGTCCCTAAACACATATAACACAAGGGCAA
1 CAAAGTCCCCAAACACATATAACACAGGGGCAA
29685 TTTTTTTCTC
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
39 57 0.95
40 3 0.05
ACGTcount: A:0.45, C:0.29, G:0.11, T:0.15
Consensus pattern (40 bp):
CAAAGTCCCCAAACACATATAACACAGGGGCAACTACACT
Found at i:32201 original size:122 final size:122
Alignment explanation
Indices: 32059--32279 Score: 361
Period size: 122 Copynumber: 1.8 Consensus size: 122
32049 ATTTAAGAAA
* * *
32059 TATATTTTAAAAATTCTAATATATCTAAGTTTTTTAATTAAATTAGTAAAATGATAAAAATAAAA
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGATAAAAATAAAA
*
32124 TTGGAATAAGGATATTAGATTTAATTAAATAAAATTAGTTGAGTAAAACTATAAAAG
66 TAGGAATAAGGATATTAGATTTAATTAAATAAAATTAGTTGAGTAAAACTATAAAAG
* * *
32181 TATATTTAAAAAATTGTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGGTAAAAATTAAA
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGATAAAAATAAAA
**
32246 TAGTTATAAGGATATTAGATTTAATTAAATAAAA
66 TAGGAATAAGGATATTAGATTTAATTAAATAAAA
32280 ATATAGTATT
Statistics
Matches: 90, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
122 90 1.00
ACGTcount: A:0.51, C:0.01, G:0.10, T:0.38
Consensus pattern (122 bp):
TATATTTAAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGATAAAAATAAAA
TAGGAATAAGGATATTAGATTTAATTAAATAAAATTAGTTGAGTAAAACTATAAAAG
Found at i:36458 original size:6 final size:6
Alignment explanation
Indices: 36447--36474 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
36437 TTTGCTTCTT
36447 TTTTTC TTTTTC TTTTTC TTTTTC TTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTT
36475 CAGAATTGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTC
Found at i:38705 original size:3 final size:3
Alignment explanation
Indices: 38697--38738 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
38687 TAAGTGAAAA
38697 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
38739 CACTCCACAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:47664 original size:2 final size:2
Alignment explanation
Indices: 47657--47687 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
47647 TGCTTATTAT
47657 TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
47688 ACTATAGTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:47841 original size:22 final size:22
Alignment explanation
Indices: 47813--47856 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
47803 AACAATATCT
47813 ATCTTAATATATTCTTATAGAA
1 ATCTTAATATATTCTTATAGAA
*
47835 ATCTTAATATATTTTTATAGAA
1 ATCTTAATATATTCTTATAGAA
47857 TCGATCCGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.48
Consensus pattern (22 bp):
ATCTTAATATATTCTTATAGAA
Found at i:48291 original size:39 final size:40
Alignment explanation
Indices: 48201--48284 Score: 111
Period size: 40 Copynumber: 2.1 Consensus size: 40
48191 TGTGTCAAAG
* *
48201 TTAAACTTATACAATAAAAAAACTAGTTTATTATATTTTA
1 TTAAACTTATATAATAAAAAAACTAGTTTATTATATATTA
48241 TTAAACTTATATAATAAAAAATAC-A-TTTA-TATATAATTA
1 TTAAACTTATATAATAAAAAA-ACTAGTTTATTATAT-ATTA
48280 TTAAA
1 TTAAA
48285 TATATATTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
38 5 0.12
39 12 0.30
40 21 0.52
41 2 0.05
ACGTcount: A:0.51, C:0.06, G:0.01, T:0.42
Consensus pattern (40 bp):
TTAAACTTATATAATAAAAAAACTAGTTTATTATATATTA
Found at i:52728 original size:2 final size:2
Alignment explanation
Indices: 52721--52758 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
52711 ATGACATACA
52721 AT AT AT AT AT AT AT AT AT AT AT AT A- AT -T AT -T AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
52759 ACTGTCGGGC
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.09
2 30 0.91
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53871 original size:13 final size:13
Alignment explanation
Indices: 53853--53877 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53843 TATAGATGTT
53853 TGTATAGATATAA
1 TGTATAGATATAA
53866 TGTATAGATATA
1 TGTATAGATATA
53878 GATATAGATA
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:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (13 bp):
TGTATAGATATAA
Found at i:54117 original size:30 final size:31
Alignment explanation
Indices: 54071--54129 Score: 102
Period size: 30 Copynumber: 1.9 Consensus size: 31
54061 GCTCGGCCCA
54071 TATAGGCGCCATGGCCCTACGCGTTGTTCTTT
1 TATAGGCG-CATGGCCCTACGCGTTGTTCTTT
54103 TATAGGCG-ATGGCCCTACGCGTTGTTC
1 TATAGGCGCATGGCCCTACGCGTTGTTC
54130 ACACAACAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 19 0.70
32 8 0.30
ACGTcount: A:0.14, C:0.27, G:0.27, T:0.32
Consensus pattern (31 bp):
TATAGGCGCATGGCCCTACGCGTTGTTCTTT
Found at i:55334 original size:18 final size:18
Alignment explanation
Indices: 55311--55349 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
55301 AGTTTCCAGT
*
55311 TTCTTTATCGTGGATATA
1 TTCTTTATCATGGATATA
55329 TTCTTTATCATGGATATA
1 TTCTTTATCATGGATATA
55347 TTC
1 TTC
55350 ATCTGAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.23, C:0.13, G:0.13, T:0.51
Consensus pattern (18 bp):
TTCTTTATCATGGATATA
Found at i:62105 original size:29 final size:29
Alignment explanation
Indices: 62072--62129 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
62062 TAACTATCCA
* *
62072 TTTTGGGATAAATTGGTCCCTTAACTTTT
1 TTTTGGGACAAATTGGCCCCTTAACTTTT
62101 TTTTGGGACAAATTGGCCCCTTAACTTTT
1 TTTTGGGACAAATTGGCCCCTTAACTTTT
62130 AAAAACGAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.21, C:0.17, G:0.17, T:0.45
Consensus pattern (29 bp):
TTTTGGGACAAATTGGCCCCTTAACTTTT
Found at i:84703 original size:1 final size:1
Alignment explanation
Indices: 84697--84724 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
84687 AGCGGAGTAG
84697 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
84725 AAAAGGACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:94207 original size:22 final size:22
Alignment explanation
Indices: 94179--94224 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
94169 GCTATGATGA
94179 TTGTCCATCAATAACACAAAAG
1 TTGTCCATCAATAACACAAAAG
94201 TTGTCCATCAATAACACAAAAG
1 TTGTCCATCAATAACACAAAAG
94223 TT
1 TT
94225 TGGCTTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.43, C:0.22, G:0.09, T:0.26
Consensus pattern (22 bp):
TTGTCCATCAATAACACAAAAG
Done.