Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008016.1 Corchorus capsularis cultivar CVL-1 contig08037, 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: 56561
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:7137 original size:21 final size:21
Alignment explanation
Indices: 7083--7137 Score: 51
Period size: 22 Copynumber: 2.5 Consensus size: 21
7073 TGGTCAGATG
*
7083 AATTTAGACGAAAGGAAGAAGA
1 AATTTAGAC-AAAGCAAGAAGA
7105 AA-TTAGGTACAAAGCAA-AAGAA
1 AATTTA-G-ACAAAGCAAGAAG-A
7127 AATTTAGACAA
1 AATTTAGACAA
7138 TAAAGAAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 9
0.74 0.03 0.24
Matches are distributed among these distances:
21 10 0.36
22 13 0.46
23 5 0.18
ACGTcount: A:0.56, C:0.07, G:0.20, T:0.16
Consensus pattern (21 bp):
AATTTAGACAAAGCAAGAAGA
Found at i:8825 original size:89 final size:89
Alignment explanation
Indices: 8611--8881 Score: 298
Period size: 89 Copynumber: 3.0 Consensus size: 89
8601 GTCATTTAAC
* * * * *
8611 ATAGATTTTGAAAACCAACAAAAACTCAGCAGAAACATAGATCTATTACCAAGAAAATAACTAAA
1 ATAGATATTGAGAACCAACAAAGACTCAGCAGAAACATAGATCTATTACCAGGAAAATAACCAAA
* **
8676 CAAAACCAGAACTTCCAGAGCCAA
66 CAAAACCACAACAGCCAGAGCCAA
*
8700 ATAG-TAAGTGAGAACCAACAAAGACTCAGCAGAAACATAGATCTATTACCAGGAAAATAACCAA
1 ATAGAT-ATTGAGAACCAACAAAGACTCAGCAGAAACATAGATCTATTACCAGGAAAATAACCAA
* *
8764 ACAAAACTTACAA-AGCCAAATAG-CAA
65 ACAAAAC-CACAACAGCC--AGAGCCAA
* * * * *
8790 ATAGATATTGAGAACCAACAAAGACT-GGCAAAAACATTGATTTATTACCAGGAAATTAACCAAA
1 ATAGATATTGAGAACCAACAAAGACTCAGCAGAAACATAGATCTATTACCAGGAAAATAACCAAA
* ***
8854 CAAAACCAAAACCTACAGAGCCAA
66 CAAAACCACAACAGCCAGAGCCAA
8878 ATAG
1 ATAG
8882 CAAGTAATGC
Statistics
Matches: 152, Mismatches: 23, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
87 3 0.02
88 11 0.07
89 105 0.69
90 29 0.19
91 4 0.03
ACGTcount: A:0.51, C:0.20, G:0.12, T:0.16
Consensus pattern (89 bp):
ATAGATATTGAGAACCAACAAAGACTCAGCAGAAACATAGATCTATTACCAGGAAAATAACCAAA
CAAAACCACAACAGCCAGAGCCAA
Found at i:9275 original size:5 final size:5
Alignment explanation
Indices: 9265--9304 Score: 57
Period size: 5 Copynumber: 8.2 Consensus size: 5
9255 AAAGGAATTA
9265 AATAT AATAT AATAT AATAT AATAT AA-AGT AATAT -ATAT A
1 AATAT AATAT AATAT AATAT AATAT AATA-T AATAT AATAT A
9305 GTCATAAAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
4 5 0.16
5 26 0.81
6 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (5 bp):
AATAT
Found at i:11395 original size:30 final size:30
Alignment explanation
Indices: 11361--11422 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
11351 TATATTAAGA
11361 ATGTTTAATATTTGAACAAATATATACTAT
1 ATGTTTAATATTTGAACAAATATATACTAT
11391 ATGTTTAATATTTGAACAAATATATACTAT
1 ATGTTTAATATTTGAACAAATATATACTAT
11421 AT
1 AT
11423 ATTATTTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (30 bp):
ATGTTTAATATTTGAACAAATATATACTAT
Found at i:14944 original size:17 final size:17
Alignment explanation
Indices: 14922--14955 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
14912 TCAATCCAGT
14922 CGGTTC-GACCAGTAATC
1 CGGTTCAGACCAG-AATC
14939 CGGTTCAGACCAGAATC
1 CGGTTCAGACCAGAATC
14956 TTCTCTTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.26, C:0.29, G:0.24, T:0.21
Consensus pattern (17 bp):
CGGTTCAGACCAGAATC
Found at i:15477 original size:30 final size:30
Alignment explanation
Indices: 15334--15780 Score: 529
Period size: 30 Copynumber: 14.6 Consensus size: 30
15324 AGTCTCCAAA
* *
15334 TGACACCAGAAGTTGTCATGATAAATCT-CCAT
1 TGACACCAGAAGTTGTCATGAT---TTTGCAAT
* * *
15366 TGACACCAGAAGTTGTCAATGGTGTTACAAT
1 TGACACCAGAAGTTGTC-ATGATTTTGCAAT
* * * *
15397 TGACACCAGAAGTTGTCAATAATCTTACAAA
1 TGACACCAGAAGTTGTC-ATGATTTTGCAAT
* * * *
15428 TGACACCAGAAAGTTGTCATGGTCTTACAAA
1 TGACACCAG-AAGTTGTCATGATTTTGCAAT
*
15459 TGACACCAGAAATTGTCATGATTTTGCAAT
1 TGACACCAGAAGTTGTCATGATTTTGCAAT
* * * *
15489 TGGCACTAGAATTTGTCATGATTTTGTAAT
1 TGACACCAGAAGTTGTCATGATTTTGCAAT
*
15519 TGACACCAGGAA-TTGTCATCATTTTGCAAT
1 TGACACCA-GAAGTTGTCATGATTTTGCAAT
* * *
15549 TGACACTATAAGTTGTCATAATTTTGCAAT
1 TGACACCAGAAGTTGTCATGATTTTGCAAT
15579 TGACACCAGAAGTTGTCATGATTTTGCAAT
1 TGACACCAGAAGTTGTCATGATTTTGCAAT
15609 TGACACCAGAAGTTGTCATGATTTTGCAAT
1 TGACACCAGAAGTTGTCATGATTTTGCAAT
15639 TGACACCAGAAGTTGTCATGATTTTGCAAT
1 TGACACCAGAAGTTGTCATGATTTTGCAAT
* * *
15669 GGACACCAAAAGTTGTCATAATTTTTGCAAT
1 TGACACCAGAAGTTGTCATGA-TTTTGCAAT
15700 TGACACCAGAAGTTGTCATGATTTTGCAAT
1 TGACACCAGAAGTTGTCATGATTTTGCAAT
** * *
15730 TGACACTTGAAGATGTCATGATTTTATTCAAT
1 TGACACCAGAAGTTGTCATGA-TTT-TGCAAT
15762 TGACACCAGAAGTTGTCAT
1 TGACACCAGAAGTTGTCAT
15781 ATACACAATG
Statistics
Matches: 365, Mismatches: 42, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
29 2 0.01
30 221 0.61
31 92 0.25
32 46 0.13
33 4 0.01
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (30 bp):
TGACACCAGAAGTTGTCATGATTTTGCAAT
Found at i:24607 original size:31 final size:32
Alignment explanation
Indices: 24572--24655 Score: 116
Period size: 32 Copynumber: 2.6 Consensus size: 32
24562 ATTTTCTATA
* *
24572 ACAAACACCA-TAAATAGTGGCGCTTTATTCT
1 ACAAACACCACAAAATAGTGGCGCTTTATACT
*
24603 ACAAACGCCACAAAATAGTGGCGCTTTATACT
1 ACAAACACCACAAAATAGTGGCGCTTTATACT
*
24635 ACAAACGCCACAAAAATAGTG
1 ACAAACACCAC-AAAATAGTG
24656 ACGTTTTTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
31 9 0.19
32 30 0.62
33 9 0.19
ACGTcount: A:0.40, C:0.24, G:0.14, T:0.21
Consensus pattern (32 bp):
ACAAACACCACAAAATAGTGGCGCTTTATACT
Found at i:24620 original size:32 final size:33
Alignment explanation
Indices: 24583--24655 Score: 130
Period size: 32 Copynumber: 2.2 Consensus size: 33
24573 CAAACACCAT
*
24583 AAATAGTGGCGCTTTATTCTACAAACGCCAC-A
1 AAATAGTGGCGCTTTATACTACAAACGCCACAA
24615 AAATAGTGGCGCTTTATACTACAAACGCCACAA
1 AAATAGTGGCGCTTTATACTACAAACGCCACAA
24648 AAATAGTG
1 AAATAGTG
24656 ACGTTTTTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
32 30 0.77
33 9 0.23
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.23
Consensus pattern (33 bp):
AAATAGTGGCGCTTTATACTACAAACGCCACAA
Found at i:29125 original size:30 final size:30
Alignment explanation
Indices: 29089--29148 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
29079 AAGGATCAAA
*
29089 TGGCATCTCCATGAGGCTTTGCGATTCCAT
1 TGGCATCTCCATGAGACTTTGCGATTCCAT
*
29119 TGGCATCTTCATGAGACTTTGCGATTCCAT
1 TGGCATCTCCATGAGACTTTGCGATTCCAT
29149 CCTCTCCTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.18, C:0.25, G:0.22, T:0.35
Consensus pattern (30 bp):
TGGCATCTCCATGAGACTTTGCGATTCCAT
Found at i:41141 original size:55 final size:55
Alignment explanation
Indices: 41069--41197 Score: 165
Period size: 55 Copynumber: 2.3 Consensus size: 55
41059 CAAGACAATT
*
41069 AAGT-AAAGAGAAG-GTAATCAGTAATTAGTTTAACTCAGAATAATTAAGCTAAAG
1 AAGTAAAAG-GAAGAGTAATCAGTAAGTAGTTTAACTCAGAATAATTAAGCTAAAG
* * *
41123 AAGTAAAAGGAAGAGTAATCAGTAGGTAGTTTAATTCAGAGTAATTAAGCTAAAG
1 AAGTAAAAGGAAGAGTAATCAGTAAGTAGTTTAACTCAGAATAATTAAGCTAAAG
*
41178 AAG-AAACAGTAAGCAGTAAT
1 AAGTAAA-AGGAAG-AGTAAT
41198 TAATTTAATC
Statistics
Matches: 66, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
54 11 0.17
55 49 0.74
56 6 0.09
ACGTcount: A:0.48, C:0.07, G:0.21, T:0.24
Consensus pattern (55 bp):
AAGTAAAAGGAAGAGTAATCAGTAAGTAGTTTAACTCAGAATAATTAAGCTAAAG
Found at i:41478 original size:16 final size:16
Alignment explanation
Indices: 41452--41872 Score: 195
Period size: 16 Copynumber: 26.4 Consensus size: 16
41442 AAAATGGTAA
41452 TAAAGAGAAGTAATCAG
1 TAAA-AGAAGTAATCAG
* *
41469 TAGAAGAAGTAGTCAG
1 TAAAAGAAGTAATCAG
* *
41485 TAAAAGGAGTAA-AAG
1 TAAAAGAAGTAATCAG
41500 TAAAAG-AGATAATCAG
1 TAAAAGAAG-TAATCAG
**
41516 TAAAAGTAAAAG-AGCAAAAG
1 TAAAAG---AAGTA--ATCAG
*
41536 TAAAAAAAAGTAATCAG
1 T-AAAAGAAGTAATCAG
*
41553 -AAAA-ATGGTAATC--
1 TAAAAGA-AGTAATCAG
*
41566 -AAGAGAAGTAATCAG
1 TAAAAGAAGTAATCAG
*
41581 TAGAAGAAGTAATCAG
1 TAAAAGAAGTAATCAG
* *
41597 TAAAAGGAGTAAAC-G
1 TAAAAGAAGTAATCAG
*
41612 TAAAAGAGGTAATCAG
1 TAAAAGAAGTAATCAG
**
41628 TAAAAGTAAAAG-AGCAAAAG
1 TAAAAG---AAGTA--ATCAG
41648 TAAAAGAAGTAATCAG
1 TAAAAGAAGTAATCAG
*
41664 -AAAA-ATGGTAATC--
1 TAAAAGA-AGTAATCAG
*
41677 -AAGAGAAGTAATCAG
1 TAAAAGAAGTAATCAG
*
41692 TAGAAGAAGTAATCAG
1 TAAAAGAAGTAATCAG
* *
41708 TAAAAGGAGTAA-AAG
1 TAAAAGAAGTAATCAG
*
41723 TAAAAGAGGTAATCAG
1 TAAAAGAAGTAATCAG
**
41739 TAAAAGTAAAAG-AGCAAAAG
1 TAAAAG---AAGTA--ATCAG
*
41759 TAAAACAAAGTAATCAG
1 TAAAA-GAAGTAATCAG
*
41776 -AAAA-ATGGTAATC--
1 TAAAAGA-AGTAATCAG
*
41789 -AAGAGAAGTAATCAG
1 TAAAAGAAGTAATCAG
* *
41804 TAGAGGAAGTAATCAG
1 TAAAAGAAGTAATCAG
*
41820 TAGAAGAAGTAATCAG
1 TAAAAGAAGTAATCAG
* *
41836 TAAAAGGAGTAA-AAG
1 TAAAAGAAGTAATCAG
*
41851 TAAAAGAGGTAATCAG
1 TAAAAGAAGTAATCAG
41867 TAAAAG
1 TAAAAG
41873 TAAAAGAAGT
Statistics
Matches: 305, Mismatches: 58, Indels: 83
0.68 0.13 0.19
Matches are distributed among these distances:
13 27 0.09
14 8 0.03
15 73 0.24
16 142 0.47
17 12 0.04
18 10 0.03
19 6 0.02
20 23 0.08
21 4 0.01
ACGTcount: A:0.55, C:0.06, G:0.23, T:0.16
Consensus pattern (16 bp):
TAAAAGAAGTAATCAG
Found at i:41569 original size:223 final size:223
Alignment explanation
Indices: 41287--41901 Score: 934
Period size: 223 Copynumber: 2.7 Consensus size: 223
41277 ATAGAAGAAG
** * * * *
41287 TAATCAGTAAAAGCCAAAGACCAAAAGT-AAGAGAAGTAATCAGAAAAATGGTTATCAAGAGAAG
1 TAATCAGTAAAAGTAAAAGAGCAAAAGTAAAAAAAAGTAATCAGAAAAATGGTAATCAAGAGAAG
* *
41351 TAATCAGTAGAAAAAGTAGTCAGTAAAAGGAGTAAAAGTAAAAGAGATAATCAGTAAAAGTAAAA
66 TAATCAGTAGAAGAAGTAATCAGTAAAAGGAGTAAAAGTAAAAGAGATAATCAGTAAAAGTAAAA
41416 GAGCAAAAGTAAAA-ACAGTAATCAGAAAAATGGTAATAAAGAGAAGTAATCAGTAGAAGAAGTA
131 GAGCAAAAGTAAAAGA-AGTAATCAGAAAAATGGTAATAAAGAGAAGTAATCAGTAGAAGAAGTA
*
41480 GTCAGTAAAAGGAGTAAAAGTAAAAGAGA
195 ATCAGTAAAAGGAGTAAAAGTAAAAGAGA
41509 TAATCAGTAAAAGTAAAAGAGCAAAAGTAAAAAAAAGTAATCAGAAAAATGGTAATCAAGAGAAG
1 TAATCAGTAAAAGTAAAAGAGCAAAAGTAAAAAAAAGTAATCAGAAAAATGGTAATCAAGAGAAG
* *
41574 TAATCAGTAGAAGAAGTAATCAGTAAAAGGAGTAAACGTAAAAGAGGTAATCAGTAAAAGTAAAA
66 TAATCAGTAGAAGAAGTAATCAGTAAAAGGAGTAAAAGTAAAAGAGATAATCAGTAAAAGTAAAA
*
41639 GAGCAAAAGTAAAAGAAGTAATCAGAAAAATGGTAATCAAGAGAAGTAATCAGTAGAAGAAGTAA
131 GAGCAAAAGTAAAAGAAGTAATCAGAAAAATGGTAATAAAGAGAAGTAATCAGTAGAAGAAGTAA
*
41704 TCAGTAAAAGGAGTAAAAGTAAAAGAGG
196 TCAGTAAAAGGAGTAAAAGTAAAAGAGA
*
41732 TAATCAGTAAAAGTAAAAGAGCAAAAGTAAAACAAAGTAATCAGAAAAATGGTAATCAAGAGAAG
1 TAATCAGTAAAAGTAAAAGAGCAAAAGTAAAAAAAAGTAATCAGAAAAATGGTAATCAAGAGAAG
* * * * *
41797 TAATCAGTAGAGGAAGTAATCAGTAGAAGAAGTAATCAGTAAAAG-GAGTAA-AAGTAAAAG-AG
66 TAATCAGTAGAAGAAGTAATCAGTAAAAGGAGTAA-AAGTAAAAGAGA-TAATCAGTAAAAGTA-
** *
41859 GTAATCAGTAAAAGTAAAAGAAGTAATCAGAAAAAATGGTAAT
128 --AAAGAGCAAAAGTAAAAGAAGTAATCAG-AAAAATGGTAAT
41902 CAGTAAAGAG
Statistics
Matches: 361, Mismatches: 24, Indels: 12
0.91 0.06 0.03
Matches are distributed among these distances:
222 26 0.07
223 287 0.80
224 11 0.03
225 25 0.07
226 12 0.03
ACGTcount: A:0.56, C:0.06, G:0.22, T:0.17
Consensus pattern (223 bp):
TAATCAGTAAAAGTAAAAGAGCAAAAGTAAAAAAAAGTAATCAGAAAAATGGTAATCAAGAGAAG
TAATCAGTAGAAGAAGTAATCAGTAAAAGGAGTAAAAGTAAAAGAGATAATCAGTAAAAGTAAAA
GAGCAAAAGTAAAAGAAGTAATCAGAAAAATGGTAATAAAGAGAAGTAATCAGTAGAAGAAGTAA
TCAGTAAAAGGAGTAAAAGTAAAAGAGA
Found at i:41607 original size:112 final size:111
Alignment explanation
Indices: 41287--41903 Score: 925
Period size: 111 Copynumber: 5.5 Consensus size: 111
41277 ATAGAAGAAG
** * * * *
41287 TAATCAGTAAAAGCCAAAGACCAAAAGTAAGAGAAGTAATCAGAAAAATGGTTATCAAGAGAAGT
1 TAATCAGTAAAAGTAAAAGAGCAAAAGTAAAAAAAGTAATCAGAAAAATGGTAATCAAGAGAAGT
* *
41352 AATCAGTAGAAAAAGTAGTCAGTAAAAGGAGTAAAAGTAAAAGAGA
66 AATCAGTAGAAGAAGTAATCAGTAAAAGGAGTAAAAGTAAAAGAGA
* *
41398 TAATCAGTAAAAGTAAAAGAGCAAAAGTAAAAACAGTAATCAGAAAAATGGTAATAAAGAGAAGT
1 TAATCAGTAAAAGTAAAAGAGCAAAAGTAAAAAAAGTAATCAGAAAAATGGTAATCAAGAGAAGT
*
41463 AATCAGTAGAAGAAGTAGTCAGTAAAAGGAGTAAAAGTAAAAGAGA
66 AATCAGTAGAAGAAGTAATCAGTAAAAGGAGTAAAAGTAAAAGAGA
41509 TAATCAGTAAAAGTAAAAGAGCAAAAGTAAAAAAAAGTAATCAGAAAAATGGTAATCAAGAGAAG
1 TAATCAGTAAAAGTAAAAGAGCAAAAGT-AAAAAAAGTAATCAGAAAAATGGTAATCAAGAGAAG
* *
41574 TAATCAGTAGAAGAAGTAATCAGTAAAAGGAGTAAACGTAAAAGAGG
65 TAATCAGTAGAAGAAGTAATCAGTAAAAGGAGTAAAAGTAAAAGAGA
*
41621 TAATCAGTAAAAGTAAAAGAGCAAAAGTAAAAGAAGTAATCAGAAAAATGGTAATCAAGAGAAGT
1 TAATCAGTAAAAGTAAAAGAGCAAAAGTAAAAAAAGTAATCAGAAAAATGGTAATCAAGAGAAGT
*
41686 AATCAGTAGAAGAAGTAATCAGTAAAAGGAGTAAAAGTAAAAGAGG
66 AATCAGTAGAAGAAGTAATCAGTAAAAGGAGTAAAAGTAAAAGAGA
41732 TAATCAGTAAAAGTAAAAGAGCAAAAGTAAAACAAAGTAATCAGAAAAATGGTAATCAAGAGAAG
1 TAATCAGTAAAAGTAAAAGAGCAAAAGTAAAA-AAAGTAATCAGAAAAATGGTAATCAAGAGAAG
* * * *
41797 TAATCAGTAGAGGAAGTAATCAGTAGAAGAAGTAATCAGTAAAAG-GA
65 TAATCAGTAGAAGAAGTAATCAGTAAAAGGAGTAA-AAGTAAAAGAGA
* ** * *
41844 GTAA-AAGTAAAAG-AGGTAATCAGTAAAAGTAAAAGAAGTAATCAGAAAAAATGGTAATCA
1 -TAATCAGTAAAAGTA---AAAGAGCAAAAGTAAAAAAAGTAATCAG-AAAAATGGTAATCA
41904 GTAAAGAGTA
Statistics
Matches: 471, Mismatches: 27, Indels: 13
0.92 0.05 0.03
Matches are distributed among these distances:
111 244 0.52
112 178 0.38
113 21 0.04
114 28 0.06
ACGTcount: A:0.56, C:0.06, G:0.22, T:0.17
Consensus pattern (111 bp):
TAATCAGTAAAAGTAAAAGAGCAAAAGTAAAAAAAGTAATCAGAAAAATGGTAATCAAGAGAAGT
AATCAGTAGAAGAAGTAATCAGTAAAAGGAGTAAAAGTAAAAGAGA
Found at i:41735 original size:31 final size:31
Alignment explanation
Indices: 41690--41872 Score: 151
Period size: 31 Copynumber: 5.8 Consensus size: 31
41680 AGAAGTAATC
*
41690 AGTAGAAGAAGTAATCAGTAAAAGGAGTAAA
1 AGTAAAAGAAGTAATCAGTAAAAGGAGTAAA
* *
41721 AGTAAAAGAGGTAATCAGTAAAAGTAAAAGAGCAAA
1 AGTAAAAGAAGTAATCAGTAAAAG-----GAGTAAA
* * *
41757 AGTAAAACAAAGTAATCAGAAAAATG-GT--A
1 AGTAAAA-GAAGTAATCAGTAAAAGGAGTAAA
* * *
41786 A-TCAAGAGAAGTAATCAGT-AGAGGAAGTAATC
1 AGT-AAAAGAAGTAATCAGTAAAAGG-AGTAA-A
*
41818 AGTAGAAGAAGTAATCAGTAAAAGGAGTAAA
1 AGTAAAAGAAGTAATCAGTAAAAGGAGTAAA
*
41849 AGTAAAAGAGGTAATCAGTAAAAG
1 AGTAAAAGAAGTAATCAGTAAAAG
41873 TAAAAGAAGT
Statistics
Matches: 118, Mismatches: 20, Indels: 28
0.71 0.12 0.17
Matches are distributed among these distances:
27 3 0.03
28 11 0.09
29 7 0.06
31 45 0.38
32 21 0.18
33 5 0.04
36 13 0.11
37 13 0.11
ACGTcount: A:0.55, C:0.05, G:0.23, T:0.16
Consensus pattern (31 bp):
AGTAAAAGAAGTAATCAGTAAAAGGAGTAAA
Found at i:41868 original size:22 final size:22
Alignment explanation
Indices: 41843--41893 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
41833 CAGTAAAAGG
*
41843 AGTAAAAGTAAAAGAGGTAATC
1 AGTAAAAGTAAAAGAAGTAATC
41865 AGTAAAAGTAAAAGAAGTAATC
1 AGTAAAAGTAAAAGAAGTAATC
*
41887 AGAAAAA
1 AGTAAAA
41894 ATGGTAATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.61, C:0.04, G:0.20, T:0.16
Consensus pattern (22 bp):
AGTAAAAGTAAAAGAAGTAATC
Found at i:42033 original size:14 final size:15
Alignment explanation
Indices: 41995--42031 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
41985 ATCAATAAAA
41995 AGTAAAAAGGTAATC
1 AGTAAAAAGGTAATC
42010 AGTAAAAAGGTAATC
1 AGTAAAAAGGTAATC
42025 AGTAAAA
1 AGTAAAA
42032 GGGAAAGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.57, C:0.05, G:0.19, T:0.19
Consensus pattern (15 bp):
AGTAAAAAGGTAATC
Found at i:44297 original size:21 final size:21
Alignment explanation
Indices: 44271--44319 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
44261 GCACTGGAGG
* * *
44271 ACATGGGTCGCGAGGCAAACC
1 ACATGGGGCGCCAAGCAAACC
*
44292 ACATGGGGCGCCAAGCATACC
1 ACATGGGGCGCCAAGCAAACC
44313 ACATGGG
1 ACATGGG
44320 CCCCCAGCTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.29, C:0.29, G:0.33, T:0.10
Consensus pattern (21 bp):
ACATGGGGCGCCAAGCAAACC
Found at i:46605 original size:11 final size:11
Alignment explanation
Indices: 46589--46620 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
46579 GAAGTTCGTG
46589 TTTGAAGATTA
1 TTTGAAGATTA
*
46600 TTTGAAGATAA
1 TTTGAAGATTA
46611 TTTGAAGATT
1 TTTGAAGATT
46621 TGAAGACAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.44
Consensus pattern (11 bp):
TTTGAAGATTA
Found at i:46623 original size:19 final size:18
Alignment explanation
Indices: 46599--46636 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
46589 TTTGAAGATT
*
46599 ATTTGAAGATAATTTGAAG
1 ATTTGAAGACAA-TTGAAG
46618 ATTTGAAGACAATTGAAG
1 ATTTGAAGACAATTGAAG
46636 A
1 A
46637 ATTATCAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.45, C:0.03, G:0.21, T:0.32
Consensus pattern (18 bp):
ATTTGAAGACAATTGAAG
Found at i:47993 original size:6 final size:6
Alignment explanation
Indices: 47982--48012 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
47972 ATAATTGCTA
47982 TAGATT TAGATT TAGATT TAGATT TA-ATT TA
1 TAGATT TAGATT TAGATT TAGATT TAGATT TA
48013 TTTTGCTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (6 bp):
TAGATT
Found at i:48367 original size:17 final size:18
Alignment explanation
Indices: 48347--48383 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
48337 TAAAAAATTT
*
48347 TTGCGTCGAAAAAA-AAA
1 TTGCGTCAAAAAAATAAA
48364 TTGCGTCAAAAAAATAAA
1 TTGCGTCAAAAAAATAAA
48382 TT
1 TT
48384 TAGGGTTTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.51, C:0.11, G:0.14, T:0.24
Consensus pattern (18 bp):
TTGCGTCAAAAAAATAAA
Done.