Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011434.1 Corchorus capsularis cultivar CVL-1 contig11455, 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: 25827
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Found at i:2518 original size:10 final size:10
Alignment explanation
Indices: 2503--2537 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
2493 CTGGTCGAAA
2503 TTTTTTTTA-
1 TTTTTTTTAT
2512 TTTTTTTTAT
1 TTTTTTTTAT
2522 TTTTTTTTAT
1 TTTTTTTTAT
2532 ATTTTT
1 -TTTTT
2538 CGATATAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 9 0.38
10 10 0.42
11 5 0.21
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (10 bp):
TTTTTTTTAT
Found at i:2537 original size:9 final size:9
Alignment explanation
Indices: 2502--2528 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
2492 TCTGGTCGAA
2502 ATTTTTTTT
1 ATTTTTTTT
2511 ATTTTTTTT
1 ATTTTTTTT
2520 ATTTTTTTT
1 ATTTTTTTT
2529 TATATTTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (9 bp):
ATTTTTTTT
Found at i:3642 original size:42 final size:42
Alignment explanation
Indices: 3559--3643 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 42
3549 AATGGATCGA
* **
3559 ATGGCCGGTTGTGGCCGGATGGCCCGTGCGATGGCTTGTGCG
1 ATGGCCGGTTGTGGCCGAATGGCCCGTGCGATGGCCCGTGCG
** *
3601 ATGGCCGGTTGTGGCCGAATGGCTTGTGCGATGTCCCGTGCG
1 ATGGCCGGTTGTGGCCGAATGGCCCGTGCGATGGCCCGTGCG
3643 A
1 A
3644 CGTCCCATGC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.09, C:0.24, G:0.42, T:0.25
Consensus pattern (42 bp):
ATGGCCGGTTGTGGCCGAATGGCCCGTGCGATGGCCCGTGCG
Found at i:5145 original size:29 final size:30
Alignment explanation
Indices: 5084--5151 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 30
5074 GACACCTTGG
5084 AATAAAAATTGAGATTTCAAGTAACTTGTA
1 AATAAAAATTGAGATTTCAAGTAACTTGTA
*
5114 AATAAAAGATTGAAGCTTT-AAGTAAC-T-TA
1 AATAAAA-ATTG-AGATTTCAAGTAACTTGTA
5143 AATAAAAAT
1 AATAAAAAT
5152 GTCATCTTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
28 2 0.06
29 9 0.26
30 8 0.23
31 11 0.31
32 5 0.14
ACGTcount: A:0.51, C:0.06, G:0.12, T:0.31
Consensus pattern (30 bp):
AATAAAAATTGAGATTTCAAGTAACTTGTA
Found at i:5207 original size:51 final size:51
Alignment explanation
Indices: 5145--5518 Score: 506
Period size: 50 Copynumber: 7.3 Consensus size: 51
5135 GTAACTTAAA
*
5145 TAAAAATGTCATCTTTGGGTAAAAGATTGAATTTTTTTAGTAATTAGTAAG
1 TAAAAATGTCACCTTTGGGTAAAAGATTGAATTTTTTTAGTAATTAGTAAG
*
5196 TAAAAATGTCATCTTTGGGTAAAAGATTGAA-TTTTTTAGTAATTAGTAAG
1 TAAAAATGTCACCTTTGGGTAAAAGATTGAATTTTTTTAGTAATTAGTAAG
* * *
5246 TAAAAATGTCATCTTTGGGTAAAAGATTGAA-TTTTTTAGAAATTACTAAG
1 TAAAAATGTCACCTTTGGGTAAAAGATTGAATTTTTTTAGTAATTAGTAAG
* *
5296 TAAAAGTGTCATCTTTGGGTAAAAGATTGAATTTCTTTTAGTAATTAGTAAG
1 TAAAAATGTCACCTTTGGGTAAAAGATTGAATTT-TTTTAGTAATTAGTAAG
*
5348 TAAAAATGTCACCTTTGGGTAAAAGTTTGAATTTTTTTAGTAATTAGTAAG
1 TAAAAATGTCACCTTTGGGTAAAAGATTGAATTTTTTTAGTAATTAGTAAG
* * ** *
5399 TAAAAATGTCACCTTTGAGCAAAAGATTG-ATTTTTAGAGTAATTAGTAAA
1 TAAAAATGTCACCTTTGGGTAAAAGATTGAATTTTTTTAGTAATTAGTAAG
* * ** *
5449 TAAAGATGTAACCTTTGAATAAAAGATTGAATCTTTTTTTAAGTAATTTGTGAA-
1 TAAAAATGTCACCTTTGGGTAAAAGATTGAA--TTTTTTT-AGTAATTAGT-AAG
5503 T-AAAATGTCACCTTTG
1 TAAAAATGTCACCTTTG
5519 AATTAAAGTT
Statistics
Matches: 293, Mismatches: 23, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
50 140 0.48
51 77 0.26
52 46 0.16
53 18 0.06
54 10 0.03
55 2 0.01
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.39
Consensus pattern (51 bp):
TAAAAATGTCACCTTTGGGTAAAAGATTGAATTTTTTTAGTAATTAGTAAG
Found at i:5539 original size:203 final size:202
Alignment explanation
Indices: 5145--5555 Score: 517
Period size: 203 Copynumber: 2.0 Consensus size: 202
5135 GTAACTTAAA
* *
5145 TAAAAATGTCATCTTTGGGTAAAAGATTGAATTTTTTTAGTAATTAGTAAGTAAAAATGTCATCT
1 TAAAAATGTCACCTTTGGGTAAAAGATTGAATTTTTTTAGTAATTAGTAAGTAAAAATGTCACCT
* * * * * * **
5210 TTGGGTAAAAGATTGAATTTTTTAGTAATTAGTAAGTAAAAATGTCATCTTTGGGTAAAAGATTG
66 TTGAGCAAAAGATTGAATTTTTGAGTAATTAGTAAATAAAAATGTAACCTTTGAATAAAAGATTG
* ** *
5275 AATTTTTTAGAAATTACTAAGTAAAAGTGTCATCTTTGGGTAAAAGATTGAATTTCTTTTA-GTA
131 AATTTTTTAGAAATTACTAAGTAAAAGTGTCACCTTTGAATAAAAGATTGAA--TCTTTTAGGCA
5339 ATTAGTAAG
194 ATTAGTAAG
*
5348 TAAAAATGTCACCTTTGGGTAAAAGTTTGAATTTTTTTAGTAATTAGTAAGTAAAAATGTCACCT
1 TAAAAATGTCACCTTTGGGTAAAAGATTGAATTTTTTTAGTAATTAGTAAGTAAAAATGTCACCT
*
5413 TTGAGCAAAAGATTG-ATTTTTAGAGTAATTAGTAAATAAAGATGTAACCTTTGAATAAAAGATT
66 TTGAGCAAAAGATTGAATTTTT-GAGTAATTAGTAAATAAAAATGTAACCTTTGAATAAAAGATT
* ** * *
5477 GAATCTTTTTTTAAGTAATTTGTGAA-TAAAA-TGTCACCTTTGAATTAAAGTTTGAA-CTTTTA
130 GAA---TTTTTT-AGAAATTACT-AAGTAAAAGTGTCACCTTTGAATAAAAGATTGAATCTTTTA
*
5539 GGCCATTAGTAAG
190 GGCAATTAGTAAG
5552 TAAA
1 TAAA
5556 TTGATTAGCT
Statistics
Matches: 179, Mismatches: 22, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
202 6 0.03
203 119 0.66
204 14 0.08
206 26 0.15
207 12 0.07
208 2 0.01
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.39
Consensus pattern (202 bp):
TAAAAATGTCACCTTTGGGTAAAAGATTGAATTTTTTTAGTAATTAGTAAGTAAAAATGTCACCT
TTGAGCAAAAGATTGAATTTTTGAGTAATTAGTAAATAAAAATGTAACCTTTGAATAAAAGATTG
AATTTTTTAGAAATTACTAAGTAAAAGTGTCACCTTTGAATAAAAGATTGAATCTTTTAGGCAAT
TAGTAAG
Found at i:5548 original size:103 final size:101
Alignment explanation
Indices: 5145--5555 Score: 362
Period size: 103 Copynumber: 4.0 Consensus size: 101
5135 GTAACTTAAA
* * ** *
5145 TAAAAATGTCATCTTTGGGTAAAAGATTGAATTTTTTTAGTAATTAGTAAGTAAAAATGTCATCT
1 TAAAAATGTAACCTTTGAATAAAAGATTGAATTTTTTTAGTAATTAGTAAGTAAAAATGTCACCT
*** * ** *
5210 TTGGGTAAAAGATTGAATTTTTTAGTAATTAGTAAG
66 TTGAACAAAAGATTGACTTTTAGAGCAATTAGTAAG
* * ** * * * *
5246 TAAAAATGTCATCTTTGGGTAAAAGATTGAA-TTTTTTAGAAATTACTAAGTAAAAGTGTCATCT
1 TAAAAATGTAACCTTTGAATAAAAGATTGAATTTTTTTAGTAATTAGTAAGTAAAAATGTCACCT
*** * ** *
5310 TTGGGTAAAAGATTGAATTTCTTTTAGTAATTAGTAAG
66 TTGAACAAAAGATTG-ACTT-TTAGAGCAATTAGTAAG
* ** *
5348 TAAAAATGTCACCTTTGGGTAAAAGTTTGAATTTTTTTAGTAATTAGTAAGTAAAAATGTCACCT
1 TAAAAATGTAACCTTTGAATAAAAGATTGAATTTTTTTAGTAATTAGTAAGTAAAAATGTCACCT
* * * *
5413 TTGAGCAAAAGATTGATTTTTAGAGTAATTAGTAAA
66 TTGAACAAAAGATTGACTTTTAGAGCAATTAGTAAG
* *
5449 TAAAGATGTAACCTTTGAATAAAAGATTGAATCTTTTTTTAAGTAATTTGTGAA-T-AAAATGTC
1 TAAAAATGTAACCTTTGAATAAAAGATTGAA--TTTTTTT-AGTAATTAGT-AAGTAAAAATGTC
** * *
5512 ACCTTTGAATTAAAGTTTGAACTTTTAG-GCCATTAGTAAG
62 ACCTTTGAACAAAAGATTG-ACTTTTAGAGCAATTAGTAAG
5552 TAAA
1 TAAA
5556 TTGATTAGCT
Statistics
Matches: 273, Mismatches: 29, Indels: 14
0.86 0.09 0.04
Matches are distributed among these distances:
100 45 0.16
101 74 0.27
102 50 0.18
103 85 0.31
104 17 0.06
105 2 0.01
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.39
Consensus pattern (101 bp):
TAAAAATGTAACCTTTGAATAAAAGATTGAATTTTTTTAGTAATTAGTAAGTAAAAATGTCACCT
TTGAACAAAAGATTGACTTTTAGAGCAATTAGTAAG
Found at i:6446 original size:71 final size:70
Alignment explanation
Indices: 6365--6572 Score: 249
Period size: 71 Copynumber: 2.9 Consensus size: 70
6355 AATTAAGTTC
* *
6365 AATAGTAATCAGTAAATCAGCAATCAGGTAAAAAGATAGTAATCAGTAAATTGATAATTAAGGGT
1 AATAGTAATCAGTAAATAAG-AATCAGGTAAAAAGATAGTAATCAGTAAATTGATAATTAAGAGT
*
6430 CCAGAT
65 CAAGAT
* * *
6436 AATAGTAATCAGTAAATTAGTAATTAAGTAAAAAGATAGTAATCAGTAAATTGATAATTAAGAGT
1 AATAGTAATCAGTAAATAAG-AATCAGGTAAAAAGATAGTAATCAGTAAATTGATAATTAAGAGT
*
6501 CAAGGT
65 CAAGAT
* * * *
6507 AAGAGATTAATCAGTAATTAAAGAGTCTAGGT-AAAA-ATAGTAATCAGTAAATCGATAATTAAG
1 AATAG--TAATCAGTAAAT-AAGAATC-AGGTAAAAAGATAGTAATCAGTAAATTGATAATTAAG
6570 AGT
62 AGT
6573 TAAAGTGATC
Statistics
Matches: 119, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
71 68 0.57
72 29 0.24
73 17 0.14
74 5 0.04
ACGTcount: A:0.48, C:0.07, G:0.18, T:0.27
Consensus pattern (70 bp):
AATAGTAATCAGTAAATAAGAATCAGGTAAAAAGATAGTAATCAGTAAATTGATAATTAAGAGTC
AAGAT
Found at i:6449 original size:37 final size:35
Alignment explanation
Indices: 6390--6569 Score: 142
Period size: 34 Copynumber: 5.1 Consensus size: 35
6380 ATCAGCAATC
6390 AGGTAAAAAGATAGTAATCAGTAAATTGATAATTA
1 AGGTAAAAAGATAGTAATCAGTAAATTGATAATTA
* *
6425 AGGGTCCAGATA-ATAGTAATCAGTAAATT-AGTAATTA
1 A-GGT--AAAAAGATAGTAATCAGTAAATTGA-TAATTA
6462 A-GTAAAAAGATAGTAATCAGTAAATTGATAATTA
1 AGGTAAAAAGATAGTAATCAGTAAATTGATAATTA
* * * *
6496 AGAGTCAAGGTAAGAGATTAATCAGT-AATT-AAAGAGTCT-
1 AG-GT-AA--AAAGATAGTAATCAGTAAATTGATA-A-T-TA
*
6535 AGGT-AAAA-ATAGTAATCAGTAAATCGATAATTA
1 AGGTAAAAAGATAGTAATCAGTAAATTGATAATTA
6568 AG
1 AG
6570 AGTTAAAGTG
Statistics
Matches: 115, Mismatches: 13, Indels: 36
0.70 0.08 0.22
Matches are distributed among these distances:
32 1 0.01
33 16 0.14
34 30 0.26
35 6 0.05
36 7 0.06
37 28 0.24
38 10 0.09
39 16 0.14
40 1 0.01
ACGTcount: A:0.48, C:0.06, G:0.18, T:0.28
Consensus pattern (35 bp):
AGGTAAAAAGATAGTAATCAGTAAATTGATAATTA
Found at i:6487 original size:34 final size:34
Alignment explanation
Indices: 6366--6497 Score: 135
Period size: 34 Copynumber: 3.8 Consensus size: 34
6356 ATTAAGTTCA
* * * *
6366 ATAGTAATCAGTAAA-TCAGCAATCAGGTAAAAAG
1 ATAGTAATCAGTAAATTGA-TAATTAAGTAAAAAG
* *
6400 ATAGTAATCAGTAAATTGATAATTAAGGGTCCAGATA-
1 ATAGTAATCAGTAAATTGATAATTAA--GT--AAAAAG
6437 ATAGTAATCAGTAAATT-AGTAATTAAGTAAAAAG
1 ATAGTAATCAGTAAATTGA-TAATTAAGTAAAAAG
6471 ATAGTAATCAGTAAATTGATAATTAAG
1 ATAGTAATCAGTAAATTGATAATTAAG
6498 AGTCAAGGTA
Statistics
Matches: 82, Mismatches: 8, Indels: 16
0.77 0.08 0.15
Matches are distributed among these distances:
33 3 0.04
34 44 0.54
35 5 0.06
36 3 0.04
37 24 0.29
38 3 0.04
ACGTcount: A:0.48, C:0.07, G:0.17, T:0.28
Consensus pattern (34 bp):
ATAGTAATCAGTAAATTGATAATTAAGTAAAAAG
Found at i:6556 original size:33 final size:31
Alignment explanation
Indices: 6490--6556 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 31
6480 AGTAAATTGA
*
6490 TAATTAAGAGTCAAGGTAAGAGATTAATCAG
1 TAATTAAGAGTCAAGGTAAGAAATTAATCAG
*
6521 TAATTAAAGAGTCTAGGTAA-AAATAGTAATCAG
1 TAATT-AAGAGTCAAGGTAAGAAAT--TAATCAG
6554 TAA
1 TAA
6557 ATCGATAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 8 0.26
32 13 0.42
33 10 0.32
ACGTcount: A:0.48, C:0.06, G:0.19, T:0.27
Consensus pattern (31 bp):
TAATTAAGAGTCAAGGTAAGAAATTAATCAG
Found at i:6970 original size:30 final size:28
Alignment explanation
Indices: 6934--7096 Score: 108
Period size: 30 Copynumber: 5.8 Consensus size: 28
6924 AATAGTGATC
6934 AGTAAAAAGTGGTATTCAGTAAAAAAGGA
1 AGTAAAAAGTGGTATTCAGTAAAAAA-GA
* *
6963 GAGTAAAAAATGGTAATTAAGT-AAAAA-A
1 -AGTAAAAAGTGGT-ATTCAGTAAAAAAGA
*
6991 AGTAAAAAGTGGTATTCAGTACAAACAGTA
1 AGTAAAAAGTGGTATTCAGTA-AAAAAG-A
* * *
7021 AG--AAAAGGGGTAATCAGTAAAAAAAAA
1 AGTAAAAAGTGGTATTCAGT-AAAAAAGA
* *
7048 GAGTAAAATA-TGGTAATCAGT-ACAAAG-
1 -AGTAAAA-AGTGGTATTCAGTAAAAAAGA
*
7075 AGTAAAAAATGGTAATT-AGTAA
1 AGTAAAAAGTGGT-ATTCAGTAA
7097 TCAAGAAATA
Statistics
Matches: 107, Mismatches: 13, Indels: 29
0.72 0.09 0.19
Matches are distributed among these distances:
25 1 0.01
26 20 0.19
27 16 0.15
28 29 0.27
29 1 0.01
30 33 0.31
31 7 0.07
ACGTcount: A:0.54, C:0.04, G:0.21, T:0.21
Consensus pattern (28 bp):
AGTAAAAAGTGGTATTCAGTAAAAAAGA
Found at i:7068 original size:58 final size:55
Alignment explanation
Indices: 6985--7096 Score: 145
Period size: 58 Copynumber: 2.0 Consensus size: 55
6975 GTAATTAAGT
*
6985 AAAAAAAGTAAAAAGTGGTATTCAGTACAAACAGTAAGAAAAGGGGTAATCAGTAAA
1 AAAAAAAGTAAAAAGTGGTAATCAGTACAAACAGTAA-AAAA-GGGTAATCAGTAAA
* * *
7042 AAAAAAGAGTAAAATA-TGGTAATCAGTACAAAGAGTAAAAAATGGTAATTAGTAA
1 AAAAAA-AGTAAAA-AGTGGTAATCAGTACAAACAGTAAAAAAGGGTAATCAGTAA
7097 TCAAGAAATA
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
56 11 0.22
57 10 0.20
58 27 0.55
59 1 0.02
ACGTcount: A:0.55, C:0.05, G:0.20, T:0.20
Consensus pattern (55 bp):
AAAAAAAGTAAAAAGTGGTAATCAGTACAAACAGTAAAAAAGGGTAATCAGTAAA
Found at i:7074 original size:26 final size:26
Alignment explanation
Indices: 6934--7096 Score: 119
Period size: 26 Copynumber: 5.8 Consensus size: 26
6924 AATAGTGATC
* *
6934 AGTAAAAAGTGGTATTCAGTAAAAAAGGAG
1 AGTAAAAAATGGTAATCAGT--AAAA--AG
* *
6964 AGTAAAAAATGGTAATTAAGTAAAAAA
1 AGTAAAAAATGGTAA-TCAGTAAAAAG
* * * *
6991 AGTAAAAAGTGGTATTCAGTACAAAC
1 AGTAAAAAATGGTAATCAGTAAAAAG
*
7017 AGTAAGAAAAGGGGTAATCAGTAAAAAAAAAG
1 AGTAA-AAAA-TGGTAATCAGT----AAAAAG
* *
7049 AGTAAAATATGGTAATCAGTACAAAG
1 AGTAAAAAATGGTAATCAGTAAAAAG
*
7075 AGTAAAAAATGGTAATTAGTAA
1 AGTAAAAAATGGTAATCAGTAA
7097 TCAAGAAATA
Statistics
Matches: 106, Mismatches: 20, Indels: 18
0.74 0.14 0.12
Matches are distributed among these distances:
26 37 0.35
27 17 0.16
28 9 0.08
29 4 0.04
30 23 0.22
31 7 0.07
32 9 0.08
ACGTcount: A:0.54, C:0.04, G:0.21, T:0.21
Consensus pattern (26 bp):
AGTAAAAAATGGTAATCAGTAAAAAG
Found at i:12745 original size:18 final size:18
Alignment explanation
Indices: 12722--12848 Score: 121
Period size: 18 Copynumber: 7.1 Consensus size: 18
12712 GCACCAGGCG
*
12722 CCACACCCAGTGGTCGCA
1 CCACACCCAGTGGCCGCA
**
12740 CCACACCCAGTGATCGCA
1 CCACACCCAGTGGCCGCA
12758 CCAC-CCCAAGTGGCCGCA
1 CCACACCC-AGTGGCCGCA
** * *
12776 CCTTATCAAGTGGCCGCA
1 CCACACCCAGTGGCCGCA
*
12794 CCACACCAAGTGGCCGCA
1 CCACACCCAGTGGCCGCA
*
12812 CCACACCTAGTGGCCGCA
1 CCACACCCAGTGGCCGCA
* * * *
12830 TCGCACCAATTGGCCGCA
1 CCACACCCAGTGGCCGCA
12848 C
1 C
12849 TTGTTCAACG
Statistics
Matches: 91, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
17 3 0.03
18 87 0.96
19 1 0.01
ACGTcount: A:0.24, C:0.43, G:0.21, T:0.12
Consensus pattern (18 bp):
CCACACCCAGTGGCCGCA
Found at i:12844 original size:54 final size:54
Alignment explanation
Indices: 12725--12848 Score: 140
Period size: 54 Copynumber: 2.3 Consensus size: 54
12715 CCAGGCGCCA
* * * * * *
12725 CACCCAGTGGTCGCACCACACCCAGTGATCGCACCACCCCAAGTGGCCGCACCT
1 CACCAAGTGGCCGCACCACACCAAGTGACCGCACCACACCAAGTGGCCGCACCG
* * * * *
12779 TATCAAGTGGCCGCACCACACCAAGTGGCCGCACCACACCTAGTGGCCGCATCG
1 CACCAAGTGGCCGCACCACACCAAGTGACCGCACCACACCAAGTGGCCGCACCG
*
12833 CACCAATTGGCCGCAC
1 CACCAAGTGGCCGCAC
12849 TTGTTCAACG
Statistics
Matches: 56, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.23, C:0.43, G:0.22, T:0.12
Consensus pattern (54 bp):
CACCAAGTGGCCGCACCACACCAAGTGACCGCACCACACCAAGTGGCCGCACCG
Found at i:14146 original size:30 final size:30
Alignment explanation
Indices: 14052--14150 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 30
14042 TAGAGGAAGG
*
14052 TGACGGCACTCTAAATGATGGCACCAAAAT
1 TGACGGCACTCTAGATGATGGCACCAAAAT
** * * * ** **
14082 CAACTGCACCCAAGATGATGGCACCTCAGG
1 TGACGGCACTCTAGATGATGGCACCAAAAT
* *
14112 TGACGGCACTCTAGGTGATGGCACCGAAAT
1 TGACGGCACTCTAGATGATGGCACCAAAAT
14142 TGACGGCAC
1 TGACGGCAC
14151 CAAAGATGAT
Statistics
Matches: 49, Mismatches: 20, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.30, C:0.27, G:0.25, T:0.17
Consensus pattern (30 bp):
TGACGGCACTCTAGATGATGGCACCAAAAT
Found at i:14151 original size:60 final size:60
Alignment explanation
Indices: 14049--14166 Score: 164
Period size: 60 Copynumber: 2.0 Consensus size: 60
14039 CCATAGAGGA
* * *
14049 AGGTGACGGCACTCTAAATGATGGCACCAAAATCAACTGCACCCAAGATGATGGCACCTC
1 AGGTGACGGCACTCTAAATGATGGCACCAAAATCAACGGCACCAAAGATGATAGCACCTC
** * **
14109 AGGTGACGGCACTCTAGGTGATGGCACCGAAATTGACGGCACCAAAGATGATAGCACC
1 AGGTGACGGCACTCTAAATGATGGCACCAAAATCAACGGCACCAAAGATGATAGCACC
14167 GAAAGTGTTT
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 50 1.00
ACGTcount: A:0.32, C:0.26, G:0.25, T:0.16
Consensus pattern (60 bp):
AGGTGACGGCACTCTAAATGATGGCACCAAAATCAACGGCACCAAAGATGATAGCACCTC
Found at i:18913 original size:17 final size:17
Alignment explanation
Indices: 18864--18913 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
18854 TTGGTAGAGA
*
18864 GGAAA-GAAATAGGAA-
1 GGAAAGGAAATAAGAAG
*
18879 GGAAAGGAAGT-AGCAAG
1 GGAAAGGAAATAAG-AAG
18896 GGAAAGGAAATAAGAAG
1 GGAAAGGAAATAAGAAG
18913 G
1 G
18914 AAGAGAAAGG
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
15 6 0.21
16 6 0.21
17 14 0.50
18 2 0.07
ACGTcount: A:0.54, C:0.02, G:0.38, T:0.06
Consensus pattern (17 bp):
GGAAAGGAAATAAGAAG
Found at i:19751 original size:17 final size:18
Alignment explanation
Indices: 19723--19759 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
19713 CCTTCCCATA
19723 GTACCTAGGTAGCATGAG
1 GTACCTAGGTAGCATGAG
*
19741 GTACC-AGGTAGTATGAG
1 GTACCTAGGTAGCATGAG
19758 GT
1 GT
19760 GATAGGTTGC
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:0.27, C:0.14, G:0.35, T:0.24
Consensus pattern (18 bp):
GTACCTAGGTAGCATGAG
Found at i:22344 original size:183 final size:182
Alignment explanation
Indices: 22155--22569 Score: 478
Period size: 183 Copynumber: 2.3 Consensus size: 182
22145 ATTAGGTCCC
*
22155 TAGGGTTTTGTAATTTTCGGCCTAATTGGTTAAATCAGCCAAAAATCAGTAGG-TAAACCCTCCA
1 TAGGGTTTTGTGA-TTTCGGCCTAATTGGTTAAATCAGCCAAAAATCAGTAGGTTAAACCCT-CA
* * * * * *
22219 AAATTAGGTCATATCAAATGAACATAATC-CTAATTTGATGAAATCAAGCAAACCCTAATAGGCC
64 AAACTAGGTCATATCAAATAAACATAAGCAC-AATTTAATG-AACCAAGCAAACCCTAATAAGCC
* *
22283 GAACCCCTTTTTGCAAAAATTGCAACTTGGGCGGCAAATTA-CTAGCTTGATAAAT
127 GAACCCCTTTTTGCAAAAATTGCAACATAGGCGGCAAATTAGCTAGCTTGATAAAT
* * **
22338 TAGGGTTCTTGTGATTTCGGCCTAATTGATT-AATCAAGCCCAAAATCAGTAGGTTAAACCCTTT
1 TAGGGTT-TTGTGATTTCGGCCTAATTGGTTAAATC-AGCCAAAAATCAGTAGGTTAAACCCTCA
* * * * * *
22402 AAACTAGGTTATATCACATAAATATAAGCACAATTTAATGAACCAAGCTATCTCTAATAAGCCGA
64 AAACTAGGTCATATCAAATAAACATAAGCACAATTTAATGAACCAAGCAAACCCTAATAAGCCGA
* * * *
22467 GCCCTTTTTTGCAAAAATTGCAACATAGGCGGCAAATTAGCTTGCTTGGTAAAT
129 ACCCCTTTTTGCAAAAATTGCAACATAGGCGGCAAATTAGCTAGCTTGATAAAT
* ** * * *
22521 TAGGGTTTTTGTGATTTAGGCAAAATTAGTTAATTAAGCCAAAAATCAG
1 TAGGG-TTTTGTGATTTCGGCCTAATTGGTTAAATCAGCCAAAAATCAG
22570 AGGGTTTAGT
Statistics
Matches: 194, Mismatches: 31, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
182 59 0.30
183 117 0.60
184 18 0.09
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (182 bp):
TAGGGTTTTGTGATTTCGGCCTAATTGGTTAAATCAGCCAAAAATCAGTAGGTTAAACCCTCAAA
ACTAGGTCATATCAAATAAACATAAGCACAATTTAATGAACCAAGCAAACCCTAATAAGCCGAAC
CCCTTTTTGCAAAAATTGCAACATAGGCGGCAAATTAGCTAGCTTGATAAAT
Done.