Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014040.1 Corchorus capsularis cultivar CVL-1 contig14061, 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: 123701
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:4383 original size:6 final size:6
Alignment explanation
Indices: 4372--4400 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
4362 TGGCTCTGCC
4372 TGGAAT TGGAAT TGGAAT TGGAAT TGGAA
1 TGGAAT TGGAAT TGGAAT TGGAAT TGGAA
4401 GTCTCCCCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.31
Consensus pattern (6 bp):
TGGAAT
Found at i:6737 original size:14 final size:14
Alignment explanation
Indices: 6720--6746 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6710 TGGTTTAGGG
6720 TATATATATGTTTA
1 TATATATATGTTTA
6734 TATATATATGTTT
1 TATATATATGTTT
6747 CATGTCATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.59
Consensus pattern (14 bp):
TATATATATGTTTA
Found at i:9442 original size:21 final size:20
Alignment explanation
Indices: 9418--9456 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
9408 CGTATATAAG
9418 ATTAGTAAAAAAGCTATACAC
1 ATTA-TAAAAAAGCTATACAC
* *
9439 ATTATGAAAATGCTATAC
1 ATTATAAAAAAGCTATAC
9457 TCTTATTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.49, C:0.13, G:0.10, T:0.28
Consensus pattern (20 bp):
ATTATAAAAAAGCTATACAC
Found at i:12610 original size:14 final size:15
Alignment explanation
Indices: 12591--12623 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
12581 ACATGTTTAT
*
12591 AAATTAAT-TAATTA
1 AAATTAATCTAAATA
12605 AAATTAATCTAAATA
1 AAATTAATCTAAATA
12620 AAAT
1 AAAT
12624 AAAAATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (15 bp):
AAATTAATCTAAATA
Found at i:12747 original size:15 final size:16
Alignment explanation
Indices: 12714--12745 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
12704 TTTGAAATTT
12714 AAGATTATAGAGTATA
1 AAGATTATAGAGTATA
12730 AAGA-TATAG-GTATA
1 AAGATTATAGAGTATA
12744 AA
1 AA
12746 AGTTTTCTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 5 0.31
16 4 0.25
ACGTcount: A:0.53, C:0.00, G:0.19, T:0.28
Consensus pattern (16 bp):
AAGATTATAGAGTATA
Found at i:18503 original size:39 final size:39
Alignment explanation
Indices: 18460--18576 Score: 166
Period size: 39 Copynumber: 3.0 Consensus size: 39
18450 TCTCTAAGTG
* *
18460 TTCTCATCAGTTCATCTTCTTTCAGTTTATCCGTTAGCT
1 TTCTCATCAGTTCATCCTCTTTCAGTTTATCCATTAGCT
* *
18499 TTCTCATCAATTCATCCTCTTTCAGTTTATTCATTAGCT
1 TTCTCATCAGTTCATCCTCTTTCAGTTTATCCATTAGCT
18538 TTCTCATC-GATTCATCCTCTTTCA-TTGTATCCATTAGCT
1 TTCTCATCAG-TTCATCCTCTTTCAGTT-TATCCATTAGCT
18577 CTCTGTATTT
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
38 2 0.03
39 68 0.97
ACGTcount: A:0.18, C:0.26, G:0.08, T:0.48
Consensus pattern (39 bp):
TTCTCATCAGTTCATCCTCTTTCAGTTTATCCATTAGCT
Found at i:18559 original size:20 final size:20
Alignment explanation
Indices: 18497--18560 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
18487 TATCCGTTAG
18497 CTTTCTCATCAATTCATCCT
1 CTTTCTCATCAATTCATCCT
** ***
18517 C-TT-TCAGTTTATTCATTAG
1 CTTTCTCA-TCAATTCATCCT
*
18536 CTTTCTCATCGATTCATCCT
1 CTTTCTCATCAATTCATCCT
18556 CTTTC
1 CTTTC
18561 ATTGTATCCA
Statistics
Matches: 31, Mismatches: 10, Indels: 6
0.66 0.21 0.13
Matches are distributed among these distances:
18 3 0.10
19 10 0.32
20 15 0.48
21 3 0.10
ACGTcount: A:0.17, C:0.30, G:0.05, T:0.48
Consensus pattern (20 bp):
CTTTCTCATCAATTCATCCT
Found at i:22045 original size:2 final size:2
Alignment explanation
Indices: 22038--22065 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
22028 TTGTTATTAG
22038 AT 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 AT
22066 GATAAATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22986 original size:41 final size:41
Alignment explanation
Indices: 22941--23018 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
22931 GTCTCTCCTA
22941 ATAATTAAGGAAACAAATTAAATCCAGGTTTAACCCCCCTG
1 ATAATTAAGGAAACAAATTAAATCCAGGTTTAACCCCCCTG
* * *
22982 ATAATTAAGGTAAGAAATTAAATCCAGGTTTAGCCCC
1 ATAATTAAGGAAACAAATTAAATCCAGGTTTAACCCC
23019 TAGTTATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.26
Consensus pattern (41 bp):
ATAATTAAGGAAACAAATTAAATCCAGGTTTAACCCCCCTG
Found at i:23708 original size:30 final size:30
Alignment explanation
Indices: 23672--23728 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
23662 GGCCCAACTT
*
23672 TTTCTTAAACAATTAAGGCCCAAGGTTCTA
1 TTTCTTAAAAAATTAAGGCCCAAGGTTCTA
23702 TTTCTTAAAAAATTAAGGCCCAAGGTT
1 TTTCTTAAAAAATTAAGGCCCAAGGTT
23729 TTGTAAGAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (30 bp):
TTTCTTAAAAAATTAAGGCCCAAGGTTCTA
Found at i:25030 original size:4 final size:4
Alignment explanation
Indices: 25021--25056 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
25011 ATTTTTGACC
25021 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
25057 CTTCATTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:26703 original size:22 final size:22
Alignment explanation
Indices: 26678--27236 Score: 168
Period size: 22 Copynumber: 25.6 Consensus size: 22
26668 GATCCCATTT
26678 TGAAATTTTGATAACCTTCCTA
1 TGAAATTTTGATAACCTTCCTA
* *** *
26700 TGAAATTTTAATAATGATACTA
1 TGAAATTTTGATAACCTTCCTA
* ** * * **
26722 TGGAATTTCAAGAATCTTTTTA
1 TGAAATTTTGATAACCTTCCTA
* ** * *
26744 T-AATTTTTTTTAACTTTCTTA
1 TGAAATTTTGATAACCTTCCTA
* *
26765 TGAAATTTTGTTAACCTCCCTA
1 TGAAATTTTGATAACCTTCCTA
* * *
26787 AGGAATTTTGA-AGACC-TCAATA
1 TGAAATTTTGATA-ACCTTC-CTA
* *
26809 TGAAATTTTGATAACTTTCCAA
1 TGAAATTTTGATAACCTTCCTA
**
26831 TGAAATTTTGATAACCAACACTA
1 TGAAATTTTGATAACCTTC-CTA
* *
26854 TGAGATGTTGATAACC-TCCATA
1 TGAAATTTTGATAACCTTCC-TA
* *
26876 TGATATATTGATAACTACTT--TA
1 TGAAATTTTGATAAC--CTTCCTA
* * * *
26898 TAAAAATTTAAAAACC-TCCATA
1 TGAAATTTTGATAACCTTCC-TA
** * * *
26920 TG-AATTGCGAGTAATC-ACACTT
1 TGAAATTTTGA-TAACCTTC-CTA
* * * *
26942 TAAAATTTTGATAATC-ACAATA
1 TGAAATTTTGATAACCTTC-CTA
* *
26964 TGAAATTGTGATAACC-TCGTTA
1 TGAAATTTTGATAACCTTC-CTA
*
26986 TGAAATTTTGATAAATCTTCCTA
1 TGAAATTTTGAT-AACCTTCCTA
* * *
27009 TAAAATTTTAATAAACCTCCCTA
1 TGAAATTTTGAT-AACCTTCCTA
* * *
27032 TAAAATTTTGATAACTTTCTTA
1 TGAAATTTTGATAACCTTCCTA
*
27054 TGAAATCTTGATAA-----CTA
1 TGAAATTTTGATAACCTTCCTA
* * *
27071 -CAAATTTTGATAAGCTCCCTA
1 TGAAATTTTGATAACCTTCCTA
** * *
27092 TGATTTTTTGATTACC-TCATTA
1 TGAAATTTTGATAACCTTC-CTA
* * *
27114 TGAAATTTTGTTAATCTTCCGA
1 TGAAATTTTGATAACCTTCCTA
* * *
27136 TGAAATTTTGATCTA-CATACTA
1 TGAAATTTTGAT-AACCTTCCTA
* *
27158 TGAAATTTTGATAACCCTCTTA
1 TGAAATTTTGATAACCTTCCTA
* * **
27180 TGAAAATTTGA-AAACTAAACTA
1 TGAAATTTTGATAACCT-TCCTA
* *
27202 TGAAAATTTGATAACCTTCATA
1 TGAAATTTTGATAACCTTCCTA
27224 TGAAATTTTGATA
1 TGAAATTTTGATA
27237 TCCTCACTGA
Statistics
Matches: 386, Mismatches: 121, Indels: 60
0.68 0.21 0.11
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
19 1 0.00
20 1 0.00
21 27 0.07
22 272 0.70
23 68 0.18
24 3 0.01
25 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.40
Consensus pattern (22 bp):
TGAAATTTTGATAACCTTCCTA
Found at i:27022 original size:23 final size:23
Alignment explanation
Indices: 26966--27045 Score: 90
Period size: 23 Copynumber: 3.5 Consensus size: 23
26956 TCACAATATG
* ** *
26966 AAATTGTGAT-AACCTCGTTATG
1 AAATTTTGATAAACCTCCCTATA
* *
26988 AAATTTTGATAAATCTTCCTATA
1 AAATTTTGATAAACCTCCCTATA
*
27011 AAATTTTAATAAACCTCCCTATA
1 AAATTTTGATAAACCTCCCTATA
27034 AAATTTTGATAA
1 AAATTTTGATAA
27046 CTTTCTTATG
Statistics
Matches: 47, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
22 9 0.19
23 38 0.81
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.39
Consensus pattern (23 bp):
AAATTTTGATAAACCTCCCTATA
Found at i:27291 original size:20 final size:19
Alignment explanation
Indices: 27227--27293 Score: 98
Period size: 19 Copynumber: 3.5 Consensus size: 19
27217 CTTCATATGA
*
27227 AATTTTGATATCCTCACTG
1 AATTTTGATATCCTCCCTG
*
27246 AATTTCGATATCCTCCCTG
1 AATTTTGATATCCTCCCTG
*
27265 AATTTTGGTATCCTCCCTG
1 AATTTTGATATCCTCCCTG
27284 AGATTTTGAT
1 A-ATTTTGAT
27294 TACTCCATCA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
19 35 0.83
20 7 0.17
ACGTcount: A:0.22, C:0.22, G:0.13, T:0.42
Consensus pattern (19 bp):
AATTTTGATATCCTCCCTG
Found at i:27424 original size:22 final size:22
Alignment explanation
Indices: 27399--27623 Score: 133
Period size: 22 Copynumber: 10.3 Consensus size: 22
27389 AATCACATTT
*
27399 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
*
27421 TGAAATTTTGATAACATCTTTA
1 TGAAATTTTGATAACCTCTTTA
* * * * *
27443 TAAAATTTTGCTGACCCCTCTA
1 TGAAATTTTGATAACCTCTTTA
* * * *
27465 TGAAATTTTGATAATCACATAA
1 TGAAATTTTGATAACCTCTTTA
* *
27487 TGTAATTTTGATAACCTCGCTT-
1 TGAAATTTTGATAACCTC-TTTA
27509 TGAAATTTTGATAA--TCTTCATA
1 TGAAATTTTGATAACCTCTT--TA
*
27531 T-AAATTTTGATAATCCTATGTTTA
1 TGAAATTTTGATAA-CC--TCTTTA
* * * *
27555 TGAAATTTCGATAATCACTCTA
1 TGAAATTTTGATAACCTCTTTA
* *
27577 TGAGA-TTTGATAACCT-TCTA
1 TGAAATTTTGATAACCTCTTTA
* * *
27597 TCAAATTTTGGT-ACTTC-TTA
1 TGAAATTTTGATAACCTCTTTA
27617 TGAAATT
1 TGAAATT
27624 GAGACTTTTA
Statistics
Matches: 152, Mismatches: 39, Indels: 26
0.70 0.18 0.12
Matches are distributed among these distances:
19 1 0.01
20 20 0.13
21 26 0.17
22 86 0.57
23 1 0.01
24 4 0.03
25 11 0.07
26 3 0.02
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTTTA
Found at i:27494 original size:44 final size:44
Alignment explanation
Indices: 27374--27991 Score: 192
Period size: 44 Copynumber: 13.5 Consensus size: 44
27364 AGAAATACCA
* *
27374 CTATGAAATTTTTG-TAATCACATTTTGAAAATTTGATAACCTCT
1 CTATGAAA-TTTTGATAATCACATTATGAAATTTTGATAACCTCT
* * * * * *
27418 TTATGAAATTTTGATAA-CATCTTTATAAAATTTTGCTGACCCCT
1 CTATGAAATTTTGATAATCA-CATTATGAAATTTTGATAACCTCT
* * *
27462 CTATGAAATTTTGATAATCACATAATGTAATTTTGATAACCTCG
1 CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCTCT
* * *
27506 CTTTGAAATTTTGATAATCTTCA-TAT-AAATTTTGATAATCCTATGT
1 CTATGAAATTTTGATAATC-ACATTATGAAATTTTGATAA-CC--TCT
* * *
27552 TTATGAAATTTCGATAATCAC-TCTATGAGA-TTTGATAACCT-T
1 CTATGAAATTTTGATAATCACAT-TATGAAATTTTGATAACCTCT
* * * * *
27594 CTATCAAATTTTGGTACT-TC-TTATGAAATTGAGACTTTTATAACCT-T
1 CTATGAAATTTTGATAATCACATTATGAAA-T-----TTTGATAACCTCT
* * * * *
27641 CATAAGAAATTTTGATAA-CTACACTATCAAACTTTGATAACCTCC
1 C-TATGAAATTTTGATAATC-ACATTATGAAATTTTGATAACCTCT
* * * * * *
27686 CGATGAAATATT-AGTAA-C-CTTCTAATGAAATTTTGTTAACCACA
1 CTATGAAATTTTGA-TAATCACAT-T-ATGAAATTTTGATAACCTCT
* *
27730 CTATGAAACTTTTGTATAACCTTGCTATGACATTTTGAAATCTTTTTGATAACCTTT
1 CTATGAAA-TTTTG-ATAA---T-C----ACATTATGAAA---TTTTGATAACCTCT
* * ** ** *
27787 CTATAAAATTGTGATAATTAACCACCCTATGAAATTTCAATAACCAAC-
1 CTATGAAATTTTGATAA-T---CACATTATGAAATTTTGATAACC-TCT
* * * * *
27835 CTAAGAAATTTTAATAA-CATGATCCTATGAAATTTTGGTAACCACT
1 CTATGAAATTTTGATAATCA-CAT--TATGAAATTTTGATAACCTCT
* * * * *
27881 CTATGAAATTTTGGTAA-CGACACTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAATC-ACATTATGAAATTTTGATAACCTCT
* * * * * * * *
27925 CTATGGAATTTTGATAACCTCCTCATGGAATTATAATAACCATCT
1 CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACC-TCT
*
27970 -TATGAAATTTTGATAACCACAT
1 CTATGAAATTTTGATAATCACAT
27992 AGAGACAAGA
Statistics
Matches: 418, Mismatches: 105, Indels: 102
0.67 0.17 0.16
Matches are distributed among these distances:
40 6 0.01
41 2 0.00
42 15 0.04
43 23 0.06
44 193 0.46
45 15 0.04
46 62 0.15
47 16 0.04
48 34 0.08
49 1 0.00
50 6 0.01
51 9 0.02
53 2 0.00
54 5 0.01
55 6 0.01
56 6 0.01
57 17 0.04
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (44 bp):
CTATGAAATTTTGATAATCACATTATGAAATTTTGATAACCTCT
Found at i:27533 original size:88 final size:87
Alignment explanation
Indices: 27374--27539 Score: 214
Period size: 88 Copynumber: 1.9 Consensus size: 87
27364 AGAAATACCA
** *
27374 CTATGAAATTTTTGTAATCACATTTTGAAAATTTGATAACCTCTTTATGAAATTTTGATAACATC
1 CTATGAAATTTTTGTAATCACATAATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACATC
27439 TTTATAAAATTTTGCTGACCCCT
66 TTTAT-AAATTTTGCTGACCCCT
* *
27462 CTATGAAA-TTTTGATAATCACATAATGTAATTTTGATAACCTCGCTT-TGAAATTTTGAT-A-A
1 CTATGAAATTTTTG-TAATCACATAATGAAAATTTGATAACCTC-CTTATGAAATTTTGATAACA
27523 TCTTCATATAAATTTTG
64 TCTT--TATAAATTTTG
27540 ATAATCCTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
86 5 0.07
87 14 0.20
88 48 0.70
89 2 0.03
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (87 bp):
CTATGAAATTTTTGTAATCACATAATGAAAATTTGATAACCTCCTTATGAAATTTTGATAACATC
TTTATAAATTTTGCTGACCCCT
Found at i:27725 original size:22 final size:22
Alignment explanation
Indices: 27700--27766 Score: 64
Period size: 23 Copynumber: 2.9 Consensus size: 22
27690 GAAATATTAG
27700 TAACCTTCTAATGAAATTTTGT-
1 TAACCTTCT-ATGAAATTTTGTA
**
27722 TAACCACACTATGAAACTTTTGTA
1 TAACC-TTCTATGAAA-TTTTGTA
*
27746 TAACCTTGCTATGACATTTTG
1 TAACCTT-CTATGAAATTTTG
27767 AAATCTTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
22 11 0.31
23 13 0.36
24 12 0.33
ACGTcount: A:0.31, C:0.18, G:0.10, T:0.40
Consensus pattern (22 bp):
TAACCTTCTATGAAATTTTGTA
Found at i:27866 original size:24 final size:22
Alignment explanation
Indices: 27805--27988 Score: 108
Period size: 22 Copynumber: 8.3 Consensus size: 22
27795 TTGTGATAAT
* *
27805 TAACCACCCTATGAAATTTCAA
1 TAACCAACCTATGAAATTTTAA
*
27827 TAACCAACCTAAGAAATTTTAA
1 TAACCAACCTATGAAATTTTAA
**
27849 TAA-CATGATCCTATGAAATTTTGG
1 TAACCA--A-CCTATGAAATTTTAA
**
27873 TAACC-ACTCTATGAAATTTTGG
1 TAACCAAC-CTATGAAATTTTAA
* **
27895 TAA-CGACACTATGAAATTTTGG
1 TAACCAAC-CTATGAAATTTTAA
* *
27917 TAACC-ACACTATGGAATTTTGA
1 TAACCAAC-CTATGAAATTTTAA
* * *
27939 TAACC-TCCTCATGGAATTATAA
1 TAACCAACCT-ATGAAATTTTAA
* * *
27961 TAACCATCTTATGAAATTTTGA
1 TAACCAACCTATGAAATTTTAA
27983 TAACCA
1 TAACCA
27989 CATAGAGACA
Statistics
Matches: 137, Mismatches: 16, Indels: 18
0.80 0.09 0.11
Matches are distributed among these distances:
21 6 0.04
22 110 0.80
23 5 0.04
24 15 0.11
25 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (22 bp):
TAACCAACCTATGAAATTTTAA
Found at i:27877 original size:46 final size:44
Alignment explanation
Indices: 27812--27922 Score: 118
Period size: 46 Copynumber: 2.5 Consensus size: 44
27802 AATTAACCAC
***
27812 CCTATGAAATTTCAATAACCAAC-CTAAGAAATTTTAATAACATGA
1 CCTATGAAATTTTGGTAACCAACTCTAAGAAATTTTAATAAC--GA
* **
27857 TCCTATGAAATTTTGGTAACC-ACTCTATGAAATTTTGGTAACGA
1 -CCTATGAAATTTTGGTAACCAACTCTAAGAAATTTTAATAACGA
27901 CACTATGAAATTTTGGTAACCA
1 C-CTATGAAATTTTGGTAACCA
27923 CACTATGGAA
Statistics
Matches: 56, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
43 1 0.02
44 21 0.38
45 2 0.04
46 32 0.57
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (44 bp):
CCTATGAAATTTTGGTAACCAACTCTAAGAAATTTTAATAACGA
Found at i:28131 original size:6 final size:6
Alignment explanation
Indices: 28120--28151 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
28110 AGTATTGTAC
*
28120 GTGTTA GTGTTA GTATTA GTGTTA GTGTTA GT
1 GTGTTA GTGTTA GTGTTA GTGTTA GTGTTA GT
28152 TTAATCTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.19, C:0.00, G:0.31, T:0.50
Consensus pattern (6 bp):
GTGTTA
Found at i:28341 original size:31 final size:31
Alignment explanation
Indices: 28276--28341 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
28266 TGGCAATTAA
* * *
28276 GAAATATGTTTTAATAAAAAGTGTGCAATTG
1 GAAATATGTTTTAATAAAAAGGGTACAATCG
*
28307 GAAATTTGTTTTAA-AAATAAGGGTACAATCG
1 GAAATATGTTTTAATAAA-AAGGGTACAATCG
28338 GAAA
1 GAAA
28342 ACATAAAGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 3 0.10
31 27 0.90
ACGTcount: A:0.44, C:0.05, G:0.20, T:0.32
Consensus pattern (31 bp):
GAAATATGTTTTAATAAAAAGGGTACAATCG
Found at i:29499 original size:11 final size:11
Alignment explanation
Indices: 29462--29499 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
29452 TTCCTATATA
*
29462 AAATAAATTAT
1 AAATTAATTAT
29473 CAAA-TAATTAT
1 -AAATTAATTAT
29484 AAATTAATTAT
1 AAATTAATTAT
29495 AAATT
1 AAATT
29500 TGCTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:30826 original size:2 final size:2
Alignment explanation
Indices: 30787--30815 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
30777 ATGCATGGTC
30787 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
30816 TGGGTATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31464 original size:171 final size:170
Alignment explanation
Indices: 31187--31500 Score: 382
Period size: 171 Copynumber: 1.8 Consensus size: 170
31177 TGAAAGACTT
* **
31187 GAAAACTAAATTTAATGTTCAAGTATCAAAAAAGCTTCCAAATAATTAGTTGTTTCGGTTAACGG
1 GAAAACTAAATTTAATGTTCAAGTATCAAAAAAGCTTCCAAATAATTAATTGTTTCGGTTAACAA
* * * * **
31252 GAATGGACGATCCATTTAATATAACATCACTTTTGCTCCAGATGTCTTATTGAGCTGATTCAAGT
66 GAATGAACGATCCACTAAATATAACATAACTTTTGCTCCAGATGTCCGATTGAGCTGATTCAAGT
31317 GTCTCATAAAAGGTTATTTTATGATCTACAACTTTGACGC
131 GTCTCATAAAAGGTTATTTTATGATCTACAACTTTGACGC
* * * *
31357 GAAAGCTAAATTTAATGTTTCAAGTAT-AAAAAATGCTTTCAAGA-AATTAATTTTTTCGGTTAG
1 GAAAACTAAATTTAATG-TTCAAGTATCAAAAAA-GCTTCCAA-ATAATTAATTGTTTCGGTTAA
* * * * * *
31420 CAAGAATGAACGGTCTACTAAATA-ATATATAATTTTTGCTCCAGATGTCCGATTGAGGTGATTT
63 CAAGAATGAACGATCCACTAAATATA-ACATAACTTTTGCTCCAGATGTCCGATTGAGCTGATTC
**
31484 AAGTGTCTGTTAAAAGG
127 AAGTGTCTCATAAAAGG
31501 CTGTTTCGTG
Statistics
Matches: 119, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
170 23 0.19
171 95 0.80
172 1 0.01
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (170 bp):
GAAAACTAAATTTAATGTTCAAGTATCAAAAAAGCTTCCAAATAATTAATTGTTTCGGTTAACAA
GAATGAACGATCCACTAAATATAACATAACTTTTGCTCCAGATGTCCGATTGAGCTGATTCAAGT
GTCTCATAAAAGGTTATTTTATGATCTACAACTTTGACGC
Found at i:41149 original size:14 final size:14
Alignment explanation
Indices: 41116--41154 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
41106 AAATTTCCTT
*
41116 AACCCGAAACTAACCT
1 AACCC-AAA-TAACCG
41132 AACCCAAATAACCG
1 AACCCAAATAACCG
41146 AACCCAAAT
1 AACCCAAAT
41155 CCAACCCGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 14 0.64
15 3 0.14
16 5 0.23
ACGTcount: A:0.49, C:0.36, G:0.05, T:0.10
Consensus pattern (14 bp):
AACCCAAATAACCG
Found at i:50735 original size:2 final size:2
Alignment explanation
Indices: 50728--50761 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
50718 AATTTGCCCC
50728 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
50762 ACCTTGGTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:62623 original size:1 final size:1
Alignment explanation
Indices: 62619--62644 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
62609 TTTTTTTTTT
62619 GGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGG
62645 TGCTATGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:68082 original size:107 final size:106
Alignment explanation
Indices: 67924--68195 Score: 365
Period size: 107 Copynumber: 2.6 Consensus size: 106
67914 AAGGTTTTTA
* * * *
67924 TTATAGAGTTTTAGAAATAAAAT---ATACTAATTTCACTAAATTTAGCCCCAAATTAAAATTTT
1 TTATAGAGTTTTAAAAATAAAATACAAAACTAATTTCACTAAGTTTAG-CCCAAATTAAAATTCT
* * *
67986 ATCTTTATTTTAAGGGTAAATTTCAAAATTAATAATTTATTG
65 ATCTTTATTTTAAGGGTAAATTCCAAAATTAACAACTTATTG
*
68028 TTATATG-GTTTTAAAAATAAAATACAAAACTAATTTAACTAAGTTTAGCTCCAAATTAAAATTC
1 TTATA-GAGTTTTAAAAATAAAATACAAAACTAATTTCACTAAGTTTAGC-CCAAATTAAAATTC
* *
68092 TATTTTTATTTTAAGGGTAAATTCCATAATTAACAACTTATTG
64 TATCTTTATTTTAAGGGTAAATTCCAAAATTAACAACTTATTG
* * *
68135 TTATAGAGTTTTAGAAATAAAATATATAACTAA-TTCACTAAGTTTAGCCCAAATTAAAATT
1 TTATAGAGTTTTAAAAATAAAATACAAAACTAATTTCACTAAGTTTAGCCCAAATTAAAATT
68196 AAAATTAAAA
Statistics
Matches: 148, Mismatches: 14, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
104 20 0.14
105 14 0.09
106 16 0.11
107 98 0.66
ACGTcount: A:0.43, C:0.10, G:0.08, T:0.40
Consensus pattern (106 bp):
TTATAGAGTTTTAAAAATAAAATACAAAACTAATTTCACTAAGTTTAGCCCAAATTAAAATTCTA
TCTTTATTTTAAGGGTAAATTCCAAAATTAACAACTTATTG
Found at i:70747 original size:20 final size:21
Alignment explanation
Indices: 70708--70747 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
70698 TTAAAACCAA
70708 AAAACTATATTACCATATATT
1 AAAACTATATTACCATATATT
* *
70729 AAAAGTATA-TACTATATAT
1 AAAACTATATTACCATATAT
70748 ATACAAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.50, C:0.10, G:0.03, T:0.38
Consensus pattern (21 bp):
AAAACTATATTACCATATATT
Found at i:81997 original size:12 final size:13
Alignment explanation
Indices: 81973--82001 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
81963 CGGGAATCGT
81973 GATAGATTAGATA
1 GATAGATTAGATA
81986 GATAGA-TAGATA
1 GATAGATTAGATA
81998 GATA
1 GATA
82002 TGAACGAGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.48, C:0.00, G:0.24, T:0.28
Consensus pattern (13 bp):
GATAGATTAGATA
Found at i:86710 original size:14 final size:13
Alignment explanation
Indices: 86688--86726 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
86678 GGAAAAAGAG
86688 TGCTCTGTTTTTCT
1 TGCTCTGTTTTT-T
*
86702 TGTTCTG-TTTTT
1 TGCTCTGTTTTTT
86714 TGCTCTGTTTTTT
1 TGCTCTGTTTTTT
86727 CTTCAAGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 7 0.32
13 9 0.41
14 6 0.27
ACGTcount: A:0.00, C:0.15, G:0.15, T:0.69
Consensus pattern (13 bp):
TGCTCTGTTTTTT
Found at i:86722 original size:12 final size:12
Alignment explanation
Indices: 86688--86726 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
86678 GGAAAAAGAG
86688 TGCTCTGTTTTTCT
1 TGCTCTG-TTTT-T
*
86702 TGTTCTGTTTTT
1 TGCTCTGTTTTT
86714 TGCTCTGTTTTT
1 TGCTCTGTTTTT
86726 T
1 T
86727 CTTCAAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 13 0.57
13 4 0.17
14 6 0.26
ACGTcount: A:0.00, C:0.15, G:0.15, T:0.69
Consensus pattern (12 bp):
TGCTCTGTTTTT
Found at i:93354 original size:23 final size:23
Alignment explanation
Indices: 93303--93356 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
93293 TGGTAACCTT
*
93303 ATAGAAATTTTAGTAATGTTTCA
1 ATAGAGATTTTAGTAATGTTTCA
93326 ATAGAGATTTTAGTAATGTTTCA
1 ATAGAGATTTTAGTAATGTTTCA
93349 ATAGAGAT
1 ATAGAGAT
93357 GAGCTGGTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.39, C:0.04, G:0.17, T:0.41
Consensus pattern (23 bp):
ATAGAGATTTTAGTAATGTTTCA
Found at i:101172 original size:3 final size:3
Alignment explanation
Indices: 101164--101229 Score: 68
Period size: 3 Copynumber: 23.0 Consensus size: 3
101154 GTTTATATAT
* * *
101164 ATC ATC ATC A-G ATC TTC ATC ATC ATC ATTC ATC A-C AT- ATC CTC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC A-TC ATC ATC ATC ATC ATC
101207 ATC A-C ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC
101230 CCATGCAAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
2 7 0.13
3 42 0.81
4 3 0.06
ACGTcount: A:0.32, C:0.33, G:0.02, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:102603 original size:32 final size:33
Alignment explanation
Indices: 102562--102653 Score: 109
Period size: 32 Copynumber: 2.9 Consensus size: 33
102552 ATTTTTGGGA
* *
102562 GGGTTTGGACAAAAATTTGAAG-CCCGTTGGAT
1 GGGTTTGGACAAAAATTTGAAGACCCGCTGGAC
*
102594 GGGTTTGGAC-AAAATTTTAAGACCCGCTGGAC
1 GGGTTTGGACAAAAATTTGAAGACCCGCTGGAC
** *
102626 AAGTTTGGAC-AAAATTTTAAGACCCGCT
1 GGGTTTGGACAAAAATTTGAAGACCCGCT
102654 TACAAAATGG
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
31 10 0.19
32 44 0.81
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.27
Consensus pattern (33 bp):
GGGTTTGGACAAAAATTTGAAGACCCGCTGGAC
Found at i:105967 original size:23 final size:23
Alignment explanation
Indices: 105917--105996 Score: 90
Period size: 23 Copynumber: 3.5 Consensus size: 23
105907 TCACATTATG
* * **
105917 AAATTGTGAT-AACCTCGCTATG
1 AAATTTTGATAAACCTCCCTACA
* *
105939 AAATTTTGATAAATCTTCCTACA
1 AAATTTTGATAAACCTCCCTACA
*
105962 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAACCTCCCTACA
105985 AAATTTTGATAA
1 AAATTTTGATAA
105997 CTTTCTTATG
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
22 9 0.19
23 39 0.81
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.36
Consensus pattern (23 bp):
AAATTTTGATAAACCTCCCTACA
Found at i:106065 original size:21 final size:22
Alignment explanation
Indices: 106026--106066 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
106016 TAACTAAAAA
*
106026 TTTTGATAACCTCCCTATGATT
1 TTTTGATAACCTCACTATGATT
*
106048 TTTTGAT-ACCTCATTATGA
1 TTTTGATAACCTCACTATGA
106067 AATTTTGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.24, C:0.20, G:0.10, T:0.46
Consensus pattern (22 bp):
TTTTGATAACCTCACTATGATT
Found at i:106140 original size:22 final size:21
Alignment explanation
Indices: 105647--106140 Score: 171
Period size: 22 Copynumber: 22.6 Consensus size: 21
105637 ATGATCCCAT
*
105647 TATGAAATTTTAATAACCTTCC
1 TATGAAATTTTGATAACC-TCC
* ** *
105669 TATGAAATTTTAATAATGATAC
1 TATGAAATTTTGATAA-CCTCC
* * **
105691 TATGAAATTTCGAGAACCATTT
1 TATGAAATTTTGATAACC-TCC
** *
105713 TAT-AAATTTTTTTTAACCTTCT
1 TATGAAA-TTTTGATAACC-TCC
*
105735 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCT-CC
* * **
105757 TAAGGAATTTTGA-AGACCTTAA
1 TATGAAATTTTGATA-ACC-TCC
**
105779 TATGAAATTTTGATAAATTCCC
1 TATGAAATTTTGATAACCT-CC
* * *
105801 AATAAAAATTTTGATAACCAACAC
1 TAT-GAAATTTTGATAACC-TC-C
* *
105825 TATGAGATGTTGATAACCTCC
1 TATGAAATTTTGATAACCTCC
* * * *
105846 ATATGATATATTGATAACCACA
1 -TATGAAATTTTGATAACCTCC
* * * *
105868 TCATGAAAATTTAAAAACCACC
1 T-ATGAAATTTTGATAACCTCC
* * * *
105890 -ATGTGAATTGTT-AGTAATCACAT
1 TATG-AAATT-TTGA-TAACCTC-C
*
105913 TATGAAATTGTGATAACCTCGC
1 TATGAAATTTTGATAACCTC-C
*
105935 TATGAAATTTTGATAAATCTTCC
1 TATGAAATTTTGAT-AA-CCTCC
**
105958 TACAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCT-CC
* * *
105981 TATAAAATTTTGATAACTTTCT
1 TATGAAATTTTGATAAC-CTCC
*
106003 TATGAAATCTTGATAA----C
1 TATGAAATTTTGATAACCTCC
*
106020 TA-AAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCT-CC
** *
106041 TATGATTTTTTGAT-ACCTCAT
1 TATGAAATTTTGATAACCTC-C
* *
106062 TATGAAATTTTGTTAATCTTCC
1 TATGAAATTTTGATAA-CCTCC
* * *
106084 TATGAAATTTTGATCTACATAC
1 TATGAAATTTTGAT-AACCTCC
*
106106 TATGAAATTTTGATAACCCTCT
1 TATGAAATTTTGATAA-CCTCC
106128 TATGAAATTTTGA
1 TATGAAATTTTGA
106141 AAACTAAACT
Statistics
Matches: 347, Mismatches: 90, Indels: 70
0.68 0.18 0.14
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
20 4 0.01
21 31 0.09
22 217 0.63
23 73 0.21
24 9 0.03
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.39
Consensus pattern (21 bp):
TATGAAATTTTGATAACCTCC
Found at i:107034 original size:2 final size:2
Alignment explanation
Indices: 107027--107063 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
107017 TCGAGCAATT
107027 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
107064 GAGTTTTATA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:121520 original size:7 final size:7
Alignment explanation
Indices: 121508--121534 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
121498 ATTATGGAGG
121508 TTACAAC
1 TTACAAC
121515 TTACAAC
1 TTACAAC
121522 TTACAAC
1 TTACAAC
121529 TTACAA
1 TTACAA
121535 GGCTTTTGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.26, G:0.00, T:0.30
Consensus pattern (7 bp):
TTACAAC
Done.