Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010180.1 Corchorus capsularis cultivar CVL-1 contig10201, 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: 40260
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:13093 original size:17 final size:17
Alignment explanation
Indices: 13071--13107 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
13061 GTTATCCAGC
*
13071 ACCTCATGCTACCTAGT
1 ACCTCATACTACCTAGT
*
13088 ACCTCATACTACCTGGT
1 ACCTCATACTACCTAGT
13105 ACC
1 ACC
13108 ATGAGGGGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.24, C:0.38, G:0.11, T:0.27
Consensus pattern (17 bp):
ACCTCATACTACCTAGT
Found at i:26830 original size:17 final size:17
Alignment explanation
Indices: 26808--26841 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
26798 CTTTAAGCAC
26808 CTTTAATG-ATTGTTACT
1 CTTTAATGCATT-TTACT
26825 CTTTAATGCATTTTACT
1 CTTTAATGCATTTTACT
26842 TTTGAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.24, C:0.15, G:0.09, T:0.53
Consensus pattern (17 bp):
CTTTAATGCATTTTACT
Found at i:31864 original size:27 final size:26
Alignment explanation
Indices: 31834--31933 Score: 105
Period size: 27 Copynumber: 3.8 Consensus size: 26
31824 AGGGTCACCT
*
31834 AGGGGTATTTTGGTCATTCTTACATTC
1 AGGGGCATTTTGGTCATT-TTACATTC
* *
31861 AGGGGCATTTTAGTCATTTT-TATT-
1 AGGGGCATTTTGGTCATTTTACATTC
* *
31885 AAGGGCATTTTGGTCATTTGCACATTC
1 AGGGGCATTTTGGTCATTT-TACATTC
*
31912 AGGGTGCATTTTGGTAATTTTA
1 AGGG-GCATTTTGGTCATTTTA
31934 GTATACTTTT
Statistics
Matches: 59, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
24 17 0.29
25 3 0.05
26 5 0.08
27 20 0.34
28 14 0.24
ACGTcount: A:0.21, C:0.12, G:0.23, T:0.44
Consensus pattern (26 bp):
AGGGGCATTTTGGTCATTTTACATTC
Found at i:31924 original size:28 final size:25
Alignment explanation
Indices: 31834--31931 Score: 90
Period size: 24 Copynumber: 3.8 Consensus size: 25
31824 AGGGTCACCT
*
31834 AGGGGTATTTTGGTCATTCTTACATTC
1 AGGGGCATTTTGGTCA-T-TTACATTC
* **
31861 AGGGGCATTTTAGTCATTTTTATT-
1 AGGGGCATTTTGGTCATTTACATTC
*
31885 AAGGGCATTTTGGTCATTTGCACATTC
1 AGGGGCATTTTGGTCATTT--ACATTC
*
31912 AGGGTGCATTTTGGTAATTT
1 AGGG-GCATTTTGGTCATTT
31932 TAGTATACTT
Statistics
Matches: 57, Mismatches: 10, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
24 17 0.30
25 5 0.09
26 4 0.07
27 17 0.30
28 14 0.25
ACGTcount: A:0.20, C:0.12, G:0.23, T:0.44
Consensus pattern (25 bp):
AGGGGCATTTTGGTCATTTACATTC
Found at i:34936 original size:28 final size:28
Alignment explanation
Indices: 34904--34976 Score: 110
Period size: 28 Copynumber: 2.6 Consensus size: 28
34894 GGGTCATCCA
34904 GGGGCATTTTGGTCATTTTCACATCTAG
1 GGGGCATTTTGGTCATTTTCACATCTAG
** *
34932 GGGGCATTTTGGTCATTTTTGCATTTAG
1 GGGGCATTTTGGTCATTTTCACATCTAG
*
34960 GGGGTATTTTGGTCATT
1 GGGGCATTTTGGTCATT
34977 CTTAATCTAC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.15, C:0.12, G:0.29, T:0.44
Consensus pattern (28 bp):
GGGGCATTTTGGTCATTTTCACATCTAG
Found at i:35663 original size:26 final size:26
Alignment explanation
Indices: 35634--35685 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
35624 AACACTAAAG
35634 GAAACAAGGAACATGCAAGGGGCTGT
1 GAAACAAGGAACATGCAAGGGGCTGT
35660 GAAACAAGGAACATGCAAGGGGCTGT
1 GAAACAAGGAACATGCAAGGGGCTGT
35686 CAAGCAAGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.35, T:0.12
Consensus pattern (26 bp):
GAAACAAGGAACATGCAAGGGGCTGT
Found at i:35693 original size:26 final size:26
Alignment explanation
Indices: 35635--35693 Score: 100
Period size: 26 Copynumber: 2.3 Consensus size: 26
35625 ACACTAAAGG
*
35635 AAACAAGGAACATGCAAGGGGCTGTG
1 AAACAAGGAACATGCAAGGGGCTGTC
35661 AAACAAGGAACATGCAAGGGGCTGTC
1 AAACAAGGAACATGCAAGGGGCTGTC
*
35687 AAGCAAG
1 AAACAAG
35694 CATGCATCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.41, C:0.17, G:0.32, T:0.10
Consensus pattern (26 bp):
AAACAAGGAACATGCAAGGGGCTGTC
Found at i:38402 original size:17 final size:17
Alignment explanation
Indices: 38366--38400 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
38356 GAAGAAGATG
38366 AAGAAGAAAAAAAAGAA
1 AAGAAGAAAAAAAAGAA
*
38383 AAGAA-AAAAAAAGGAA
1 AAGAAGAAAAAAAAGAA
38399 AA
1 AA
38401 AGGCTAAACG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (17 bp):
AAGAAGAAAAAAAAGAA
Found at i:39302 original size:34 final size:36
Alignment explanation
Indices: 39258--39344 Score: 115
Period size: 40 Copynumber: 2.4 Consensus size: 36
39248 AATAAAAGAG
*
39258 GAAGTGATCAGTA-G-AATTAAGAGTAAAAGTAAAA
1 GAAGTAATCAGTAGGTAATTAAGAGTAAAAGTAAAA
39292 GAAGTAATCAGTAAAATGGTAATTAAGAGTAAAAGTAAAA
1 GAAGTAATCAGT---A-GGTAATTAAGAGTAAAAGTAAAA
39332 GAAGTAATCAGTA
1 GAAGTAATCAGTA
39345 AATCGGTAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
34 11 0.24
37 2 0.04
39 1 0.02
40 32 0.70
ACGTcount: A:0.53, C:0.03, G:0.22, T:0.22
Consensus pattern (36 bp):
GAAGTAATCAGTAGGTAATTAAGAGTAAAAGTAAAA
Found at i:39370 original size:40 final size:39
Alignment explanation
Indices: 39276--39407 Score: 127
Period size: 40 Copynumber: 3.5 Consensus size: 39
39266 CAGTAGAATT
39276 AAGAGTAAAA--GTAAAAGAAGTAATCAGTAAAAT-GGTAA
1 AAGAGTAAAATGGTAAAAGAAGTAATCAGT-AAATCGGT-A
39314 TTAAGAGTAAAA--GTAAAAGAAGTAATCAGTAAATCGGTA
1 --AAGAGTAAAATGGTAAAAGAAGTAATCAGTAAATCGGTA
* ** *
39353 AAGAATAAAAATGGT-AAA-AAGTAAAGAGT-AATCAGTA
1 AAGAGT-AAAATGGTAAAAGAAGTAATCAGTAAATCGGTA
39390 AAGAGTAAAATGGTAAAA
1 AAGAGTAAAATGGTAAAA
39408 TGGTAATCAA
Statistics
Matches: 82, Mismatches: 5, Indels: 13
0.82 0.05 0.13
Matches are distributed among these distances:
36 8 0.10
37 20 0.24
38 13 0.16
39 8 0.10
40 33 0.40
ACGTcount: A:0.57, C:0.03, G:0.20, T:0.20
Consensus pattern (39 bp):
AAGAGTAAAATGGTAAAAGAAGTAATCAGTAAATCGGTA
Found at i:39407 original size:36 final size:36
Alignment explanation
Indices: 39345--39690 Score: 125
Period size: 36 Copynumber: 9.3 Consensus size: 36
39335 GTAATCAGTA
* *
39345 AATCGGTAAAGAATAAAAATGGTAAAAAGTAAAGAGT
1 AATCAGTAAAGAGT-AAAATGGTAAAAAGTAAAGAGT
* * *
39382 AATCAGTAAAGAGTAAAATGGTAAAATGGTAATCAAATT
1 AATCAGTAAAGAGTAAAATGGTAAAA-AGTAA--AGAGT
** *
39421 CAAAGAGTAAA-A-TGACAAATGGTAATTAAATTCAAAGAGT
1 -AATCAGTAAAGAGT-A-AAATGGTAA--AAAGT-AAAGAGT
* * *
39461 AA--A--AATAGTAGTTAAAT--TCAAGAGAGTAAAAATAGT
1 AATCAGTAA-AG-AGTAAAATGGT-AA-AAAGTAAAGA--GT
*
39497 AATCAGTAAAGAG-AAAA-GAGTAAAGAGTAAA-ATGGT
1 AATCAGTAAAGAGTAAAATG-GTAAAAAGTAAAGA--GT
**
39533 AAAGAGTAAAGAGTAAAA-GAG-AAAAGAGTAAAGAGT
1 AATCAGTAAAGAGTAAAATG-GTAAAA-AGTAAAGAGT
** *
39569 AAAGAGTAATCAGTAAAGAGTAAAATGGTCAAAAGTAAAGAGT
1 AATCAGTAA--AG---AG--TAAAATGGTAAAAAGTAAAGAGT
39612 AATCAGTAAA-AG-AAGAATGGTAAAAAGTAAAGAGT
1 AATCAGTAAAGAGTAA-AATGGTAAAAAGTAAAGAGT
* *
39647 AATCAGTAAAG-G-AAGAATGGT-AAGAGTAAAGGGT
1 AATCAGTAAAGAGTAA-AATGGTAAAAAGTAAAGAGT
39681 AATCAGTAAA
1 AATCAGTAAA
39691 AAGATAATCA
Statistics
Matches: 245, Mismatches: 27, Indels: 77
0.70 0.08 0.22
Matches are distributed among these distances:
34 27 0.11
35 45 0.18
36 48 0.20
37 47 0.19
38 10 0.04
39 11 0.04
40 22 0.09
41 4 0.02
42 4 0.02
43 23 0.09
44 4 0.02
ACGTcount: A:0.55, C:0.04, G:0.22, T:0.19
Consensus pattern (36 bp):
AATCAGTAAAGAGTAAAATGGTAAAAAGTAAAGAGT
Found at i:39466 original size:33 final size:33
Alignment explanation
Indices: 39389--39464 Score: 120
Period size: 32 Copynumber: 2.3 Consensus size: 33
39379 AGTAATCAGT
39389 AAAGAGTAAAATGGTAAAATGGTAATCAAATTC
1 AAAGAGTAAAATGGTAAAATGGTAATCAAATTC
*
39422 AAAGAGTAAAAT-G-ACAAATGGTAATTAAATTC
1 AAAGAGTAAAATGGTA-AAATGGTAATCAAATTC
39454 AAAGAGTAAAA
1 AAAGAGTAAAA
39465 ATAGTAGTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
31 1 0.02
32 28 0.68
33 12 0.29
ACGTcount: A:0.55, C:0.05, G:0.17, T:0.22
Consensus pattern (33 bp):
AAAGAGTAAAATGGTAAAATGGTAATCAAATTC
Found at i:39494 original size:27 final size:26
Alignment explanation
Indices: 39437--39499 Score: 99
Period size: 26 Copynumber: 2.4 Consensus size: 26
39427 GTAAAATGAC
*
39437 AAATGGTAATTAAATTCAAAGAGTAA
1 AAATAGTAATTAAATTCAAAGAGTAA
*
39463 AAATAGTAGTTAAATTCAAGAGAGTAA
1 AAATAGTAATTAAATTCAA-AGAGTAA
39490 AAATAGTAAT
1 AAATAGTAAT
39500 CAGTAAAGAG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
26 17 0.52
27 16 0.48
ACGTcount: A:0.54, C:0.03, G:0.16, T:0.27
Consensus pattern (26 bp):
AAATAGTAATTAAATTCAAAGAGTAA
Found at i:39514 original size:7 final size:7
Alignment explanation
Indices: 39501--39648 Score: 117
Period size: 7 Copynumber: 20.7 Consensus size: 7
39491 AATAGTAATC
39501 AGTAAAG
1 AGTAAAG
*
39508 AGAAAAG
1 AGTAAAG
39515 AGTAAAG
1 AGTAAAG
39522 AGTAAA-
1 AGTAAAG
39528 ATGGTAAAG
1 A--GTAAAG
39537 AGTAAAG
1 AGTAAAG
39544 AGTAAAAG
1 AGT-AAAG
*
39552 AGAAAAG
1 AGTAAAG
39559 AGTAAAG
1 AGTAAAG
39566 AGTAAAG
1 AGTAAAG
**
39573 AGTAATC
1 AGTAAAG
39580 AGTAAAG
1 AGTAAAG
39587 AGTAAA-
1 AGTAAAG
39593 ATGGTCAAA-
1 A--GT-AAAG
39602 AGTAAAG
1 AGTAAAG
**
39609 AGTAATC
1 AGTAAAG
39616 AGTAAAAG
1 AGT-AAAG
*
39624 AAG-AATG
1 -AGTAAAG
*
39631 -GTAAAA
1 AGTAAAG
39637 AGTAAAG
1 AGTAAAG
39644 AGTAA
1 AGTAA
39649 TCAGTAAAGG
Statistics
Matches: 113, Mismatches: 16, Indels: 24
0.74 0.10 0.16
Matches are distributed among these distances:
5 1 0.01
6 7 0.06
7 83 0.73
8 15 0.13
9 7 0.06
ACGTcount: A:0.57, C:0.02, G:0.25, T:0.16
Consensus pattern (7 bp):
AGTAAAG
Found at i:39538 original size:29 final size:28
Alignment explanation
Indices: 39505--39648 Score: 100
Period size: 29 Copynumber: 5.0 Consensus size: 28
39495 GTAATCAGTA
39505 AAGAGAAAAGAGTAAAGAGTAAA-ATGGTA
1 AAGAGAAAAGAGTAAAGAGTAAAGA--GTA
* *
39534 AAGAGTAAAGAGTAAAAGAGAAAAGAGTA
1 AAGAGAAAAGAGT-AAAGAGTAAAGAGTA
* **
39563 AAGAGTAAAGAGTAATCAGTAAAGAGTA
1 AAGAGAAAAGAGTAAAGAGTAAAGAGTA
* **
39591 AA-ATGGTCAAA-AGTAAAGAGTAATCAGTA
1 AAGA--G-AAAAGAGTAAAGAGTAAAGAGTA
*
39620 AA-AGAAGAATG-GTAAAAAGTAAAGAGTA
1 AAGAGAA-AA-GAGTAAAGAGTAAAGAGTA
39648 A
1 A
39649 TCAGTAAAGG
Statistics
Matches: 93, Mismatches: 14, Indels: 17
0.75 0.11 0.14
Matches are distributed among these distances:
26 1 0.01
27 4 0.04
28 29 0.31
29 46 0.49
30 12 0.13
31 1 0.01
ACGTcount: A:0.58, C:0.02, G:0.25, T:0.15
Consensus pattern (28 bp):
AAGAGAAAAGAGTAAAGAGTAAAGAGTA
Found at i:39539 original size:22 final size:22
Alignment explanation
Indices: 39504--39613 Score: 129
Period size: 22 Copynumber: 5.0 Consensus size: 22
39494 AGTAATCAGT
*
39504 AAAGAGAAAAGAGTAAAGAGTA
1 AAAGAGTAAAGAGTAAAGAGTA
39526 AAATG-GTAAAGAGTAAAGAGTA
1 AAA-GAGTAAAGAGTAAAGAGTA
*
39548 AAAGAGAAAAGAGTAAAGAGT-
1 AAAGAGTAAAGAGTAAAGAGTA
**
39569 AAAGAGTAATCAGTAAAGAGTA
1 AAAGAGTAAAGAGTAAAGAGTA
39591 AAATG-GTCAAA-AGTAAAGAGTA
1 AAA-GAGT-AAAGAGTAAAGAGTA
39613 A
1 A
39614 TCAGTAAAAG
Statistics
Matches: 77, Mismatches: 6, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
21 19 0.25
22 54 0.70
23 4 0.05
ACGTcount: A:0.58, C:0.02, G:0.25, T:0.15
Consensus pattern (22 bp):
AAAGAGTAAAGAGTAAAGAGTA
Found at i:39620 original size:43 final size:43
Alignment explanation
Indices: 39504--39620 Score: 132
Period size: 43 Copynumber: 2.7 Consensus size: 43
39494 AGTAATCAGT
**
39504 AAAGAGAAAAGAGTAAAGAGTAAA-ATGGTAAAGAGTAAAGAGTA
1 AAAGAGAAAAGAGTAAAGAGTAAACA--GTAATCAGTAAAGAGTA
*
39548 AAAGAGAAAAGAGTAAAGAGTAAAGAGTAATCAGTAAAGAGTA
1 AAAGAGAAAAGAGTAAAGAGTAAACAGTAATCAGTAAAGAGTA
* *
39591 AAATG-GTCAAA-AGTAAAGAGTAATCAGTAA
1 AAA-GAG-AAAAGAGTAAAGAGTAAACAGTAA
39621 AAGAAGAATG
Statistics
Matches: 65, Mismatches: 5, Indels: 7
0.84 0.06 0.09
Matches are distributed among these distances:
43 36 0.55
44 28 0.43
45 1 0.02
ACGTcount: A:0.57, C:0.03, G:0.25, T:0.15
Consensus pattern (43 bp):
AAAGAGAAAAGAGTAAAGAGTAAACAGTAATCAGTAAAGAGTA
Found at i:39631 original size:35 final size:34
Alignment explanation
Indices: 39531--39691 Score: 191
Period size: 35 Copynumber: 4.6 Consensus size: 34
39521 GAGTAAAATG
** *
39531 GTAAAGAGTAAAGAGTAAAAG-AGAAAAGAGTAAAGA
1 GTAAAGAGTAATCAGTAAAAGAAG-AATG-GTAAA-A
39567 GTAAAGAGTAATCAGTAAAGAGTAA-AATGGTCAAAA
1 GTAAAGAGTAATCAGTAAA-AG-AAGAATGGT-AAAA
39603 GTAAAGAGTAATCAGTAAAAGAAGAATGGTAAAAA
1 GTAAAGAGTAATCAGTAAAAGAAGAATGGT-AAAA
* *
39638 GTAAAGAGTAATCAGTAAAGGAAGAATGGTAAGA
1 GTAAAGAGTAATCAGTAAAAGAAGAATGGTAAAA
*
39672 GTAAAGGGTAATCAGTAAAA
1 GTAAAGAGTAATCAGTAAAA
39692 AGATAATCAG
Statistics
Matches: 112, Mismatches: 8, Indels: 12
0.85 0.06 0.09
Matches are distributed among these distances:
34 23 0.21
35 41 0.37
36 39 0.35
37 8 0.07
39 1 0.01
ACGTcount: A:0.55, C:0.03, G:0.25, T:0.17
Consensus pattern (34 bp):
GTAAAGAGTAATCAGTAAAAGAAGAATGGTAAAA
Found at i:39700 original size:15 final size:15
Alignment explanation
Indices: 39680--39736 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 15
39670 GAGTAAAGGG
39680 TAATCAGTAAAAAGA
1 TAATCAGTAAAAAGA
*
39695 TAATCAGTAAAGAGTA
1 TAATCAGTAAAAAG-A
* *
39711 AAAT-AGT-AAAAGG
1 TAATCAGTAAAAAGA
39724 TAATCAGTAAAAA
1 TAATCAGTAAAAA
39737 AAAGTAACGA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
13 3 0.09
14 7 0.21
15 20 0.59
16 4 0.12
ACGTcount: A:0.58, C:0.05, G:0.16, T:0.21
Consensus pattern (15 bp):
TAATCAGTAAAAAGA
Found at i:39704 original size:22 final size:21
Alignment explanation
Indices: 39679--39867 Score: 134
Period size: 22 Copynumber: 8.6 Consensus size: 21
39669 AGAGTAAAGG
*
39679 GTAATCAGTAAAAAGATAATCA
1 GTAATCAGTAAAAAGAAAAT-A
** *
39701 GTAAAGAGTAAAATAGTAAAA-G
1 GTAATCAGTAAAA-AG-AAAATA
*
39723 GTAATCAGTAAAAA-AAAGTAA
1 GTAATCAGTAAAAAGAAAAT-A
*
39744 CGATAATCAGTAAAAGGTAAAATA
1 -G-TAATCAGTAAAAAG-AAAATA
* *
39768 GTAATCAGT-AAGAGCAAAATG
1 GTAATCAGTAAAAAG-AAAATA
* *
39789 GAAATCAGTAAAGAGTAAAATA
1 GTAATCAGTAAAAAG-AAAATA
*
39811 GTAATCAGTAAAAAGTAAGAA-G
1 GTAATCAGTAAAAAG-AA-AATA
*
39833 GTAATCAGTAAAGAGTAAAATA
1 GTAATCAGTAAAAAG-AAAATA
39855 GTAATCAGTAAAA
1 GTAATCAGTAAAA
39868 GGTAATCAGT
Statistics
Matches: 133, Mismatches: 23, Indels: 22
0.75 0.13 0.12
Matches are distributed among these distances:
19 3 0.02
21 19 0.14
22 86 0.65
23 17 0.13
24 4 0.03
25 4 0.03
ACGTcount: A:0.56, C:0.06, G:0.19, T:0.20
Consensus pattern (21 bp):
GTAATCAGTAAAAAGAAAATA
Found at i:39704 original size:29 final size:28
Alignment explanation
Indices: 39671--39858 Score: 83
Period size: 29 Copynumber: 6.7 Consensus size: 28
39661 GAATGGTAAG
*
39671 AGTAAAGGGT-AATCAGTAAAAAGATAATC
1 AGTAAAGAGTAAAT-AGT-AAAAGATAATC
*
39700 AGTAAAGAGTAAAATAGTAAAAGGTAATC
1 AGTAAAGAGT-AAATAGTAAAAGATAATC
*
39729 AGTAAA-A--AAA-AGT-AACGATAATC
1 AGTAAAGAGTAAATAGTAAAAGATAATC
* *
39752 AGTAAA-AGGTAAAATAGTAATCAG-TAA-G
1 AGTAAAGA-GT-AAATAGTAA-AAGATAATC
* * *
39780 AGCAAA-ATGGAAATCAGTAAAGAGTAAAAT-
1 AGTAAAGA-GTAAAT-AGTAAA-AG-ATAATC
** * *
39810 AGTAATCAGTAAAAAGTAAGAAGGTAATC
1 AGTAAAGAGTAAATAGTAA-AAGATAATC
39839 AGTAAAGAGTAAAATAGTAA
1 AGTAAAGAGT-AAATAGTAA
39859 TCAGTAAAAG
Statistics
Matches: 120, Mismatches: 21, Indels: 35
0.68 0.12 0.20
Matches are distributed among these distances:
23 15 0.12
24 3 0.03
25 3 0.03
27 7 0.06
28 21 0.17
29 44 0.37
30 23 0.19
31 4 0.03
ACGTcount: A:0.55, C:0.05, G:0.20, T:0.20
Consensus pattern (28 bp):
AGTAAAGAGTAAATAGTAAAAGATAATC
Found at i:39742 original size:24 final size:23
Alignment explanation
Indices: 39690--39758 Score: 66
Period size: 23 Copynumber: 2.7 Consensus size: 23
39680 TAATCAGTAA
39690 AAAGATAATCAGTAAAGAGTAAAATAGT
1 AAAGATAATCAGT-AA-A--AAAA-AGT
*
39718 AAAAGGTAATCAGTAAAAAAAAGT
1 -AAAGATAATCAGTAAAAAAAAGT
*
39742 AACGATAATCAGTAAAA
1 AAAGATAATCAGTAAAA
39759 GGTAAAATAG
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
23 15 0.41
24 3 0.08
25 4 0.11
27 1 0.03
28 2 0.05
29 12 0.32
ACGTcount: A:0.59, C:0.06, G:0.16, T:0.19
Consensus pattern (23 bp):
AAAGATAATCAGTAAAAAAAAGT
Found at i:39859 original size:44 final size:45
Alignment explanation
Indices: 39715--39872 Score: 184
Period size: 44 Copynumber: 3.6 Consensus size: 45
39705 AGAGTAAAAT
* * *
39715 AGTAAAA-GGTAATCAGTAAAAA-AAAGTAACGATAATCAGTAAA-
1 AGTAAAATAGTAATCAGTAAAAAGTAAG-AACGGTAATCAGTAAAG
* * * *
39758 AGGTAAAATAGTAATCAGT-AAGAGCAA-AATGGAAATCAGTAAAG
1 A-GTAAAATAGTAATCAGTAAAAAGTAAGAACGGTAATCAGTAAAG
39802 AGTAAAATAGTAATCAGTAAAAAGTAAGAA-GGTAATCAGTAAAG
1 AGTAAAATAGTAATCAGTAAAAAGTAAGAACGGTAATCAGTAAAG
*
39846 AGTAAAATAGTAATCAGTAAAAGGTAA
1 AGTAAAATAGTAATCAGTAAAAAGTAA
39873 TCAGTAAGAG
Statistics
Matches: 99, Mismatches: 10, Indels: 11
0.82 0.08 0.09
Matches are distributed among these distances:
43 31 0.31
44 55 0.56
45 13 0.13
ACGTcount: A:0.55, C:0.06, G:0.20, T:0.20
Consensus pattern (45 bp):
AGTAAAATAGTAATCAGTAAAAAGTAAGAACGGTAATCAGTAAAG
Found at i:39872 original size:22 final size:22
Alignment explanation
Indices: 39747--39872 Score: 143
Period size: 22 Copynumber: 5.8 Consensus size: 22
39737 AAAGTAACGA
39747 TAATCAGTAAAAGGTAAAATAG
1 TAATCAGTAAAAGGTAAAATAG
* * *
39769 TAATCAGTAAGA-GCAAAATGG
1 TAATCAGTAAAAGGTAAAATAG
*
39790 AAATCAGT-AAAGAGTAAAATAG
1 TAATCAGTAAAAG-GTAAAATAG
* *
39812 TAATCAGTAAAAAGTAAGAA-GG
1 TAATCAGTAAAAGGTAA-AATAG
39834 TAATCAGT-AAAGAGTAAAATAG
1 TAATCAGTAAAAG-GTAAAATAG
39856 TAATCAGTAAAAGGTAA
1 TAATCAGTAAAAGGTAA
39873 TCAGTAAGAG
Statistics
Matches: 85, Mismatches: 12, Indels: 14
0.77 0.11 0.13
Matches are distributed among these distances:
20 2 0.02
21 19 0.22
22 55 0.65
23 9 0.11
ACGTcount: A:0.54, C:0.06, G:0.20, T:0.21
Consensus pattern (22 bp):
TAATCAGTAAAAGGTAAAATAG
Done.