Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007164.1 Corchorus capsularis cultivar CVL-1 contig07185, 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: 81567
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1670 original size:12 final size:12
Alignment explanation
Indices: 1655--1726 Score: 58
Period size: 12 Copynumber: 6.1 Consensus size: 12
1645 CACAAAACCA
1655 AAAAAAAAAAAC
1 AAAAAAAAAAAC
*
1667 AAAAACAAAAAC
1 AAAAAAAAAAAC
* *
1679 --AACACAAAAC
1 AAAAAAAAAAAC
**
1689 AAAAACGAAAAC
1 AAAAAAAAAAAC
**
1701 AAAAGCAAAAAC
1 AAAAAAAAAAAC
1713 AAAAAAAGAAAAC
1 AAAAAAA-AAAAC
1726 A
1 A
1727 TATGTTTACA
Statistics
Matches: 46, Mismatches: 11, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
10 7 0.15
12 33 0.72
13 6 0.13
ACGTcount: A:0.81, C:0.15, G:0.04, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAC
Found at i:1685 original size:5 final size:5
Alignment explanation
Indices: 1646--1716 Score: 56
Period size: 6 Copynumber: 13.2 Consensus size: 5
1636 AAGTTCAGTC
*
1646 ACAAA ACCAAA A-AAA A-AAA ACAAAA ACAAAA ACAAC ACAAA ACAAAA
1 ACAAA A-CAAA ACAAA ACAAA AC-AAA AC-AAA ACAAA ACAAA AC-AAA
1693 ACGAAA ACAAA AGCAAAA ACAAA A
1 AC-AAA ACAAA A-C-AAA ACAAA A
1717 AAAGAAAACA
Statistics
Matches: 57, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
4 8 0.14
5 17 0.30
6 28 0.49
7 4 0.07
ACGTcount: A:0.79, C:0.18, G:0.03, T:0.00
Consensus pattern (5 bp):
ACAAA
Found at i:1717 original size:6 final size:6
Alignment explanation
Indices: 1655--1717 Score: 76
Period size: 6 Copynumber: 10.8 Consensus size: 6
1645 CACAAAACCA
* * *
1655 AAAAAA AAAAAC AAAAAC AAAAAC -AACAC -AAAAC AAAAAC GAAAAC
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC
*
1701 AAAAGC AAAAAC AAAAA
1 AAAAAC AAAAAC AAAAA
1718 AAGAAAACAT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
5 8 0.16
6 41 0.84
ACGTcount: A:0.81, C:0.16, G:0.03, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:1777 original size:39 final size:40
Alignment explanation
Indices: 1734--1810 Score: 138
Period size: 39 Copynumber: 1.9 Consensus size: 40
1724 ACATATGTTT
1734 ACATATACAACAACAATGGCCTATGTCG-CCATATATACA
1 ACATATACAACAACAATGGCCTATGTCGCCCATATATACA
*
1773 ACATATACAATAACAATGGCCTATGTCGCCCATATATA
1 ACATATACAACAACAATGGCCTATGTCGCCCATATATA
1811 TTAAATGACC
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 27 0.75
40 9 0.25
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.25
Consensus pattern (40 bp):
ACATATACAACAACAATGGCCTATGTCGCCCATATATACA
Found at i:1858 original size:35 final size:35
Alignment explanation
Indices: 1819--1901 Score: 148
Period size: 35 Copynumber: 2.4 Consensus size: 35
1809 TATTAAATGA
*
1819 CCTATGTCGCCACATATCATGTACTATTACCTTGG
1 CCTATGTCGCCACATATCATGAACTATTACCTTGG
1854 CCTATGTCGCCACATATCATGAACTATTACCTTGG
1 CCTATGTCGCCACATATCATGAACTATTACCTTGG
*
1889 CCTATGACGCCAC
1 CCTATGTCGCCAC
1902 TCCATATATA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 46 1.00
ACGTcount: A:0.24, C:0.31, G:0.14, T:0.30
Consensus pattern (35 bp):
CCTATGTCGCCACATATCATGAACTATTACCTTGG
Found at i:1989 original size:29 final size:28
Alignment explanation
Indices: 1886--1983 Score: 115
Period size: 29 Copynumber: 3.3 Consensus size: 28
1876 ACTATTACCT
*
1886 TGGCCTATGACGCCACTCCATATATATAAAA
1 TGGCCTATGATGCCA---CATATATATAAAA
* *
1917 TGGCCTATGATGCCACACATATATAACAT
1 TGGCCTATGATGCCACATATATATAA-AA
1946 TGGCCTATGATGCCACATATATATAATAA
1 TGGCCTATGATGCCACATATATATAA-AA
*
1975 TGGCTTATG
1 TGGCCTATG
1984 TCGCCAAACA
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
28 10 0.17
29 35 0.59
31 14 0.24
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (28 bp):
TGGCCTATGATGCCACATATATATAAAA
Found at i:2177 original size:88 final size:87
Alignment explanation
Indices: 2061--2306 Score: 348
Period size: 88 Copynumber: 2.8 Consensus size: 87
2051 AAATATTTTC
* *
2061 ATTGCCGCTAATCAAAGCGAGCTAAATATCTAAATGCTCCCTCCAAGTAGCAGAATCTTTTCTCC
1 ATTGCCGCTAA-CAAAGCGAGCTCAATATCTAAATGCTCCCTCCAAGTAGTAGAATCTTTTCTCC
*
2126 TTGTAGAGGTCGGAAGCACTCTT
65 TTGTAGAGGTCGAAAGCACTCTT
* * *
2149 ATTGCTGCTAACAAAAGCAAGCTCAATATCTAAATGCTCCCTCTAAGTAGTAGAATCTTTTCTCC
1 ATTGCCGCTAAC-AAAGCGAGCTCAATATCTAAATGCTCCCTCCAAGTAGTAGAATCTTTTCTCC
*
2214 TTGTAGAGGTTGAAAGCACTCTT
65 TTGTAGAGGTCGAAAGCACTCTT
* * * * *
2237 ACTGCCGTTGATCAAAGCGAGCTCAATATCTTAATGCTCCCTCCAAGTAGTAGAATCAATTTCTC
1 ATTGCCGCT-AACAAAGCGAGCTCAATATCTAAATGCTCCCTCCAAGTAGTAGAATC-TTTTCTC
2302 CTTGT
64 CTTGT
2307 TGTAGAGGCC
Statistics
Matches: 140, Mismatches: 15, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
87 1 0.01
88 126 0.90
89 13 0.09
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (87 bp):
ATTGCCGCTAACAAAGCGAGCTCAATATCTAAATGCTCCCTCCAAGTAGTAGAATCTTTTCTCCT
TGTAGAGGTCGAAAGCACTCTT
Found at i:3914 original size:30 final size:31
Alignment explanation
Indices: 3875--3946 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 31
3865 GACACCCTGC
*
3875 TACAGGTAATA-CCCACATGGTTAAACATAT
1 TACAGGTAATACCCCACATGGTTAAACACAT
* * * *
3905 TATAGGTAATACCCCACTTGGTTACACACGT
1 TACAGGTAATACCCCACATGGTTAAACACAT
3936 TACAGGTAATA
1 TACAGGTAATA
3947 TACTCTGTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
30 10 0.29
31 25 0.71
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (31 bp):
TACAGGTAATACCCCACATGGTTAAACACAT
Found at i:3979 original size:16 final size:16
Alignment explanation
Indices: 3958--4008 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
3948 ACTCTGTAAC
3958 TGGTAATACATGTTGT
1 TGGTAATACATGTTGT
* *
3974 TGGTAATACCT-TGTGAC
1 TGGTAATACATGT-TG-T
3991 TGGTAATACATGTTGT
1 TGGTAATACATGTTGT
4007 TG
1 TG
4009 TTGGTAATAC
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
15 1 0.04
16 14 0.50
17 12 0.43
18 1 0.04
ACGTcount: A:0.24, C:0.10, G:0.25, T:0.41
Consensus pattern (16 bp):
TGGTAATACATGTTGT
Found at i:4015 original size:36 final size:34
Alignment explanation
Indices: 3946--4030 Score: 111
Period size: 36 Copynumber: 2.5 Consensus size: 34
3936 TACAGGTAAT
*
3946 ATACTCTGT-AACTGGTAATACATGTTGTTGGTA
1 ATACCCTGTGAACTGGTAATACATGTTGTTGGTA
*
3979 ATACCTTGTG-ACTGGTAATACATGTTGTTGTTGGTA
1 ATACCCTGTGAACTGGTAATACA---TGTTGTTGGTA
4015 ATACCCTGTGAACTGG
1 ATACCCTGTGAACTGG
4031 AAACAGTTCA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
33 19 0.43
36 20 0.45
37 5 0.11
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.38
Consensus pattern (34 bp):
ATACCCTGTGAACTGGTAATACATGTTGTTGGTA
Found at i:4633 original size:46 final size:46
Alignment explanation
Indices: 4541--4636 Score: 138
Period size: 46 Copynumber: 2.1 Consensus size: 46
4531 CCGATGGGAG
* * ** *
4541 TGACGTGGCCTACCCTTACCTCTTCAGGAACATACCACTGTTACCA
1 TGACGTGGCCTACCCTTACCTCTTCAGAAAAATACCACCATCACCA
*
4587 TGACGTGGCTTACCCTTACCTCTTCAGAAAAATACCACCATCACCA
1 TGACGTGGCCTACCCTTACCTCTTCAGAAAAATACCACCATCACCA
4633 TGAC
1 TGAC
4637 ATACACTTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.27, C:0.34, G:0.14, T:0.25
Consensus pattern (46 bp):
TGACGTGGCCTACCCTTACCTCTTCAGAAAAATACCACCATCACCA
Found at i:4763 original size:41 final size:41
Alignment explanation
Indices: 4688--4830 Score: 126
Period size: 50 Copynumber: 3.2 Consensus size: 41
4678 ATATTTAAGG
*
4688 GATAATTATAGTGATTATA-TAATTAGCCATATTATCCATAGA
1 GATAATTAT-G-GATTATATTTATTAGCCATATTATCCATAGA
*
4730 GATAATTATGGATTATATTTATTAACCATATTATCTACATAAATATTAGA
1 GATAATTATGGATTATATTTATTAGCCATATTATC--C------A-TAGA
* ** *
4780 GATAATTATGGATTATATTTATTAGTCATATTATCTTTAAA
1 GATAATTATGGATTATATTTATTAGCCATATTATCCATAGA
4821 GATAATTATG
1 GATAATTATG
4831 ACAATTATCA
Statistics
Matches: 84, Mismatches: 7, Indels: 21
0.75 0.06 0.19
Matches are distributed among these distances:
40 7 0.08
41 29 0.35
42 9 0.11
43 1 0.01
49 1 0.01
50 37 0.44
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (41 bp):
GATAATTATGGATTATATTTATTAGCCATATTATCCATAGA
Found at i:6053 original size:12 final size:11
Alignment explanation
Indices: 6036--6080 Score: 63
Period size: 12 Copynumber: 3.9 Consensus size: 11
6026 TGGCAGTGTG
*
6036 TTTTTTTTATT
1 TTTTTTTTGTT
6047 CTTTTTTTTGTT
1 -TTTTTTTTGTT
6059 TTTTGTTTTGTT
1 TTTT-TTTTGTT
6071 TTTTTTTTGT
1 TTTTTTTTGT
6081 GCTTTCTGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
11 10 0.32
12 21 0.68
ACGTcount: A:0.02, C:0.02, G:0.09, T:0.87
Consensus pattern (11 bp):
TTTTTTTTGTT
Found at i:6060 original size:21 final size:21
Alignment explanation
Indices: 6034--6076 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
6024 GCTGGCAGTG
6034 TGTTTTTT-TTATTCTTTTTTT
1 TGTTTTTTGTT-TTCTTTTTTT
*
6055 TGTTTTTTGTTTTGTTTTTTT
1 TGTTTTTTGTTTTCTTTTTTT
6076 T
1 T
6077 TTGTGCTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.02, C:0.02, G:0.09, T:0.86
Consensus pattern (21 bp):
TGTTTTTTGTTTTCTTTTTTT
Found at i:6067 original size:16 final size:16
Alignment explanation
Indices: 6034--6080 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
6024 GCTGGCAGTG
*
6034 TGTTTTTTTTATTCTTT
1 TGTTTTTTTT-TTGTTT
6051 T-TTTTGTTTTTTGTTT
1 TGTTTT-TTTTTTGTTT
6067 TGTTTTTTTTTTGT
1 TGTTTTTTTTTTGT
6081 GCTTTCTGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 18 0.67
17 9 0.33
ACGTcount: A:0.02, C:0.02, G:0.11, T:0.85
Consensus pattern (16 bp):
TGTTTTTTTTTTGTTT
Found at i:6072 original size:18 final size:20
Alignment explanation
Indices: 6045--6092 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
6035 GTTTTTTTTA
* *
6045 TTCTTTTTTTTGTTTTTTG-T
1 TTCTGTTTTTT-TTTTGTGCT
6065 TT-TGTTTTTTTTTTGTGCT
1 TTCTGTTTTTTTTTTGTGCT
6084 TTCTGTTTT
1 TTCTGTTTT
6093 ATTATAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 6 0.25
19 10 0.42
20 8 0.33
ACGTcount: A:0.00, C:0.06, G:0.12, T:0.81
Consensus pattern (20 bp):
TTCTGTTTTTTTTTTGTGCT
Found at i:10661 original size:18 final size:19
Alignment explanation
Indices: 10638--10675 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
10628 GAAATAGGAT
10638 TTCAAATCCAACAGA-AGA
1 TTCAAATCCAACAGATAGA
*
10656 TTCAAATTCAACAGATAGA
1 TTCAAATCCAACAGATAGA
10675 T
1 T
10676 AGGATAAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.47, C:0.18, G:0.11, T:0.24
Consensus pattern (19 bp):
TTCAAATCCAACAGATAGA
Found at i:15494 original size:31 final size:31
Alignment explanation
Indices: 15459--15524 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
15449 TGGCAATTTA
** *
15459 GAAATATGTTTTTTTAAA-AAGGGTACAATTG
1 GAAATATG-TTTTAAAAATAAGGGTACAATCG
15490 GAAATATGTTTTAAAAATAAGGGTACAATCG
1 GAAATATGTTTTAAAAATAAGGGTACAATCG
15521 GAAA
1 GAAA
15525 ACATAAAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 7 0.23
31 24 0.77
ACGTcount: A:0.44, C:0.05, G:0.20, T:0.32
Consensus pattern (31 bp):
GAAATATGTTTTAAAAATAAGGGTACAATCG
Found at i:18384 original size:22 final size:22
Alignment explanation
Indices: 18359--18434 Score: 64
Period size: 22 Copynumber: 3.5 Consensus size: 22
18349 TTATAGTGTG
18359 GTTACCAAAATTTCATATAGAA
1 GTTACCAAAATTTCATATAGAA
* * *
18381 GTTATCAAAACTTCATAGT-GTA
1 GTTACCAAAATTTCATA-TAGAA
* * ** *
18403 CTTATCAAAATTTCATGCAGAG
1 GTTACCAAAATTTCATATAGAA
18425 GTTACCAAAA
1 GTTACCAAAA
18435 CATAGGGAGG
Statistics
Matches: 41, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
22 40 0.98
23 1 0.02
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.32
Consensus pattern (22 bp):
GTTACCAAAATTTCATATAGAA
Found at i:18399 original size:44 final size:44
Alignment explanation
Indices: 18318--18418 Score: 116
Period size: 44 Copynumber: 2.3 Consensus size: 44
18308 TGACAATCAA
* * **
18318 ACCAAAATTACATAGAAAGATTATCAAACTTTTATAGTGTGGTT
1 ACCAAAATTTCATAGAAAGATTATCAAACTTTCATAGTGTACTT
*
18362 ACCAAAATTTCATATAGAAG-TTATCAAAAC-TTCATAGTGTACTT
1 ACCAAAATTTCATAGA-AAGATTATC-AAACTTTCATAGTGTACTT
*
18406 ATCAAAATTTCAT
1 ACCAAAATTTCAT
18419 GCAGAGGTTA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
44 42 0.86
45 7 0.14
ACGTcount: A:0.42, C:0.14, G:0.10, T:0.35
Consensus pattern (44 bp):
ACCAAAATTTCATAGAAAGATTATCAAACTTTCATAGTGTACTT
Found at i:18449 original size:23 final size:23
Alignment explanation
Indices: 18422--18480 Score: 118
Period size: 23 Copynumber: 2.6 Consensus size: 23
18412 ATTTCATGCA
18422 GAGGTTACCAAAACATAGGGAGG
1 GAGGTTACCAAAACATAGGGAGG
18445 GAGGTTACCAAAACATAGGGAGG
1 GAGGTTACCAAAACATAGGGAGG
18468 GAGGTTACCAAAA
1 GAGGTTACCAAAA
18481 TTTGTGCTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.41, C:0.14, G:0.32, T:0.14
Consensus pattern (23 bp):
GAGGTTACCAAAACATAGGGAGG
Found at i:18540 original size:22 final size:22
Alignment explanation
Indices: 18488--18835 Score: 79
Period size: 22 Copynumber: 15.6 Consensus size: 22
18478 AAATTTGTGC
**
18488 TTATCAAAATTTCCTAGGGAGG
1 TTATCAAAATTTTATAGGGAGG
*
18510 TTAACAAAATTTTATAGGGAGG
1 TTATCAAAATTTTATAGGGAGG
* * *
18532 TTATGAAAATGTTAT-GGACAGG
1 TTATCAAAATTTTATAGG-GAGG
* * ** **
18554 TTATAAAAAAAATACATATAGAGG
1 TTAT--CAAAATTTTATAGGGAGG
* *
18578 ATATCAAAGTTTTATTCTCATAGGGAGG
1 TTATCAAA-----ATT-TTATAGGGAGG
* * **
18606 TTATCGAAATTTCAT-GGTGTTG
1 TTATCAAAATTTTATAGG-GAGG
18628 TTATCAAAATTTTAT---GAGG
1 TTATCAAAATTTTATAGGGAGG
** *
18647 TTATCAAAATTTTCATATTGCGG
1 TTATCAAAATTTT-ATAGGGAGG
* * * *
18670 TTA-C-CAATTTTATTTAGTGTGA
1 TTATCAAAATTTTA--TAGGGAGG
* *
18692 TTATTAAAATTTTATAGGCG-GA
1 TTATCAAAATTTTATAGG-GAGG
* * **
18714 TTATCAAAATTTCACACTGAGG
1 TTATCAAAATTTTATAGGGAGG
* * *
18736 TTATCGAAATTTCATA-GTATGG
1 TTATCAAAATTTTATAGGGA-GG
* * * * *
18758 TTACCAAAATTTCACAGTGTGG
1 TTATCAAAATTTTATAGGGAGG
*
18780 TTATC-AAATTTTCATAGGGAAG
1 TTATCAAAATTTT-ATAGGGAGG
* ** *
18802 TTATCGAAATTTTATAATGATG
1 TTATCAAAATTTTATAGGGAGG
18824 TTATC-AAATTTT
1 TTATCAAAATTTT
18836 CAAAATGTGG
Statistics
Matches: 239, Mismatches: 62, Indels: 51
0.68 0.18 0.14
Matches are distributed among these distances:
19 15 0.06
20 3 0.01
21 25 0.10
22 144 0.60
23 17 0.07
24 19 0.08
27 2 0.01
28 14 0.06
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (22 bp):
TTATCAAAATTTTATAGGGAGG
Found at i:18767 original size:66 final size:65
Alignment explanation
Indices: 18602--18835 Score: 183
Period size: 66 Copynumber: 3.6 Consensus size: 65
18592 TTCTCATAGG
* * *
18602 GAGGTTATCGAAATTTCATGGTGTTGTTATCAAAATTTTAT--GAGGTTATCAAAATTTTCATAT
1 GAGGTTATCGAAATTTCATAGTGTGGTTATCAAAATTTTATAGGAGGTTATCAAAA-TTTCATAC
18665 T
65 T
* * * * * * *
18666 GCGGTTA-C-CAATTTTATTTAGTGTGATTATTAAAATTTTATAGGCGGATTATCAAAATTTCAC
1 GAGGTTATCGAAATTTCA--TAGTGTGGTTATCAAAATTTTATAGGAGG-TTATCAAAATTTCAT
18729 ACT
63 ACT
* * * * * * *
18732 GAGGTTATCGAAATTTCATAGTATGGTTACCAAAATTTCACAGTGTGGTTATCAAATTTTCATAG
1 GAGGTTATCGAAATTTCATAGTGTGGTTATCAAAATTTTATAG-GAGGTTATCAAAATTTCATAC
*
18797 G
65 T
* * *
18798 GAAGTTATCGAAATTTTATAATGAT-GTTATC-AAATTTT
1 GAGGTTATCGAAATTTCATAGTG-TGGTTATCAAAATTTT
18836 CAAAATGTGG
Statistics
Matches: 131, Mismatches: 30, Indels: 17
0.74 0.17 0.10
Matches are distributed among these distances:
62 6 0.05
63 1 0.01
64 25 0.19
65 6 0.05
66 73 0.56
67 14 0.11
68 6 0.05
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.41
Consensus pattern (65 bp):
GAGGTTATCGAAATTTCATAGTGTGGTTATCAAAATTTTATAGGAGGTTATCAAAATTTCATACT
Found at i:18812 original size:44 final size:44
Alignment explanation
Indices: 18698--18837 Score: 119
Period size: 44 Copynumber: 3.2 Consensus size: 44
18688 GTGATTATTA
* * *
18698 AAATTTT-ATAGGCGGA-TTATCAAAATTTCACACTGAGGTTATC
1 AAATTTTCATAGG-GAAGTTATCAAAATTTCACAATGTGGTTATC
* * * *
18741 GAAA-TTTCATA-GTATGGTTACCAAAATTTCACAGTGTGGTTATC
1 -AAATTTTCATAGGGA-AGTTATCAAAATTTCACAATGTGGTTATC
* * *
18785 AAATTTTCATAGGGAAGTTATCGAAATTTTATAATGAT-GTTATC
1 AAATTTTCATAGGGAAGTTATCAAAATTTCACAATG-TGGTTATC
18829 AAATTTTCA
1 AAATTTTCA
18838 AAATGTGGTT
Statistics
Matches: 77, Mismatches: 13, Indels: 12
0.75 0.13 0.12
Matches are distributed among these distances:
43 7 0.09
44 67 0.87
45 3 0.04
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.38
Consensus pattern (44 bp):
AAATTTTCATAGGGAAGTTATCAAAATTTCACAATGTGGTTATC
Found at i:18842 original size:22 final size:22
Alignment explanation
Indices: 18714--18858 Score: 84
Period size: 22 Copynumber: 6.5 Consensus size: 22
18704 TATAGGCGGA
* * * *
18714 TTATCAAAATTTCACACTGAGG
1 TTATCAAATTTTCATAATGATG
*
18736 TTATCGAAA-TTTCATAGT-ATGG
1 TTATC-AAATTTTCATAATGAT-G
* * * *
18758 TTACCAAAATTTCACAGTG-TGG
1 TTATCAAATTTTCATAATGAT-G
** *
18780 TTATCAAATTTTCATAGGGAAG
1 TTATCAAATTTTCATAATGATG
18802 TTATCGAAATTTT-ATAATGATG
1 TTATC-AAATTTTCATAATGATG
*
18824 TTATCAAATTTTCAAAATG-TGG
1 TTATCAAATTTTCATAATGAT-G
18846 TTATCAATATTTT
1 TTATCAA-ATTTT
18859 TACATTGGAG
Statistics
Matches: 100, Mismatches: 14, Indels: 17
0.76 0.11 0.13
Matches are distributed among these distances:
21 12 0.12
22 73 0.73
23 15 0.15
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.40
Consensus pattern (22 bp):
TTATCAAATTTTCATAATGATG
Found at i:20730 original size:28 final size:28
Alignment explanation
Indices: 20673--20731 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
20663 TTAAGGTTGG
* *
20673 TTGAGTTGGTAAACCTTTGAACCTCTGC
1 TTGAGTTGGTAAACCTTTAAACCTCCGC
** *
20701 TTGAGTTGGTAAGGCTTTAAACTTCCGC
1 TTGAGTTGGTAAACCTTTAAACCTCCGC
20729 TTG
1 TTG
20732 TAAGGTTTGG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.37
Consensus pattern (28 bp):
TTGAGTTGGTAAACCTTTAAACCTCCGC
Found at i:20802 original size:29 final size:29
Alignment explanation
Indices: 20756--20812 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
20746 GAGTCGTGCC
**
20756 AACGATTATCATGGTGGGTGATCTGTAAG
1 AACGATTATCATAATGGGTGATCTGTAAG
20785 AACGATTATCATAATGGGTGATCTGTAA
1 AACGATTATCATAATGGGTGATCTGTAA
20813 ATACCAATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.32
Consensus pattern (29 bp):
AACGATTATCATAATGGGTGATCTGTAAG
Found at i:28941 original size:12 final size:12
Alignment explanation
Indices: 28924--28950 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
28914 ACCCACATGG
28924 CTTTTTATATTA
1 CTTTTTATATTA
28936 CTTTTTATATTA
1 CTTTTTATATTA
28948 CTT
1 CTT
28951 CAGGCCAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.11, G:0.00, T:0.67
Consensus pattern (12 bp):
CTTTTTATATTA
Found at i:29094 original size:34 final size:32
Alignment explanation
Indices: 29056--29126 Score: 99
Period size: 31 Copynumber: 2.2 Consensus size: 32
29046 TATTGAAGGC
29056 ATTTGTTCATAAGTGAACAACTATGAAGAGACTT
1 ATTTGTTC-TAA-TGAACAACTATGAAGAGACTT
* *
29090 ATTTG-TCTTATGAACAATTATGAAGAGACTT
1 ATTTGTTCTAATGAACAACTATGAAGAGACTT
29121 ATTTGT
1 ATTTGT
29127 CTATAAAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 25 0.74
32 2 0.06
33 2 0.06
34 5 0.15
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (32 bp):
ATTTGTTCTAATGAACAACTATGAAGAGACTT
Found at i:29105 original size:31 final size:31
Alignment explanation
Indices: 29069--29128 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
29059 TGTTCATAAG
29069 TGAACAACTATGAAGAGACTTATTTGTCTTA
1 TGAACAACTATGAAGAGACTTATTTGTCTTA
*
29100 TGAACAATTATGAAGAGACTTATTTGTCT
1 TGAACAACTATGAAGAGACTTATTTGTCT
29129 ATAAAAGGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.37
Consensus pattern (31 bp):
TGAACAACTATGAAGAGACTTATTTGTCTTA
Found at i:29207 original size:37 final size:38
Alignment explanation
Indices: 29157--29235 Score: 124
Period size: 37 Copynumber: 2.1 Consensus size: 38
29147 ATATAATTAT
* *
29157 TCATAAAGTTATGTCTATTTGGAAAGACATG-TGTTGA
1 TCATAAAGTTATGTCTATATGAAAAGACATGATGTTGA
29194 TCATAAAGTTATGTCTATATGAAAAGACATGTATGTTGA
1 TCATAAAGTTATGTCTATATGAAAAGACATG-ATGTTGA
29233 TCA
1 TCA
29236 AGTATATAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
37 29 0.76
39 9 0.24
ACGTcount: A:0.35, C:0.09, G:0.19, T:0.37
Consensus pattern (38 bp):
TCATAAAGTTATGTCTATATGAAAAGACATGATGTTGA
Found at i:29810 original size:21 final size:21
Alignment explanation
Indices: 29786--29827 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
29776 TTTGACTAAA
29786 TGATTATTATAAAACAAATAT
1 TGATTATTATAAAACAAATAT
*
29807 TGATTATTATAAAAGAAATAT
1 TGATTATTATAAAACAAATAT
29828 GCAGAGACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.38
Consensus pattern (21 bp):
TGATTATTATAAAACAAATAT
Found at i:33990 original size:94 final size:94
Alignment explanation
Indices: 33843--34014 Score: 283
Period size: 94 Copynumber: 1.8 Consensus size: 94
33833 TCTGTCAGCA
* *
33843 GGTACTAGTACATGATCACATTCATTGATGACTATTCAAGGTATGTCATGGTTCATTTTATGAAA
1 GGTACTAGTACATGATCACATTCATTGACGACTATTCAAGGTATGTCATGGTTCATTTCATGAAA
33908 GAAAAATCTAAGGTAACCTTCTGTTAATG
66 GAAAAATCTAAGGTAACCTTCTGTTAATG
* *
33937 GGTACTAGTACATTATCACATTCATTGGCGACTATTCAAGGTATGTC-TGGGTTCATTTCATGAA
1 GGTACTAGTACATGATCACATTCATTGACGACTATTCAAGGTATGTCAT-GGTTCATTTCATGAA
*
34001 AGAATAATCTAAGG
65 AGAAAAATCTAAGG
34015 CACTTGCCAA
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
93 1 0.01
94 71 0.99
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (94 bp):
GGTACTAGTACATGATCACATTCATTGACGACTATTCAAGGTATGTCATGGTTCATTTCATGAAA
GAAAAATCTAAGGTAACCTTCTGTTAATG
Found at i:39727 original size:45 final size:45
Alignment explanation
Indices: 39663--39752 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
39653 GTGAGTCCTC
39663 ATCTCTCCCCCGTGCGGCCCAACCCATCAAGTCTTAAGCCAATTA
1 ATCTCTCCCCCGTGCGGCCCAACCCATCAAGTCTTAAGCCAATTA
*
39708 ATCTCTCCCCCGTGCGGCCCAACCCGTCAAGTCTTAAGCCAATTA
1 ATCTCTCCCCCGTGCGGCCCAACCCATCAAGTCTTAAGCCAATTA
39753 CCGACTATCC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.23, C:0.40, G:0.14, T:0.22
Consensus pattern (45 bp):
ATCTCTCCCCCGTGCGGCCCAACCCATCAAGTCTTAAGCCAATTA
Found at i:42060 original size:52 final size:53
Alignment explanation
Indices: 41975--42076 Score: 152
Period size: 52 Copynumber: 1.9 Consensus size: 53
41965 GACGTGGCAC
** *
41975 GCCACATGTACCAAAAAGTGACATGTGGCACGCCACATGTACCAAAAAGTCGT
1 GCCACATGTACCAAAAAGTGACACATGGCACGCCACATATACCAAAAAGTCGT
* *
42028 GCCACATGTACC-AAAAGTGACACATGTCACGCCACGTATACCAAAAAGT
1 GCCACATGTACCAAAAAGTGACACATGGCACGCCACATATACCAAAAAGT
42077 GACACGTGGC
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
52 32 0.73
53 12 0.27
ACGTcount: A:0.37, C:0.27, G:0.19, T:0.17
Consensus pattern (53 bp):
GCCACATGTACCAAAAAGTGACACATGGCACGCCACATATACCAAAAAGTCGT
Found at i:42093 original size:31 final size:30
Alignment explanation
Indices: 42027--42095 Score: 84
Period size: 31 Copynumber: 2.3 Consensus size: 30
42017 CAAAAAGTCG
* *
42027 TGCCACATGTACCAAAAGTGACACATGTCA
1 TGCCACATATACCAAAAGTGACACATGGCA
* * *
42057 CGCCACGTATACCAAAAAGTGACACGTGGCA
1 TGCCACATATACC-AAAAGTGACACATGGCA
42088 TGCCACAT
1 TGCCACAT
42096 GTTTCAAAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
30 10 0.32
31 21 0.68
ACGTcount: A:0.35, C:0.29, G:0.19, T:0.17
Consensus pattern (30 bp):
TGCCACATATACCAAAAGTGACACATGGCA
Found at i:47270 original size:17 final size:17
Alignment explanation
Indices: 47244--47284 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
47234 CATTTAAGTT
47244 AAAAAA-AAAAGGAAAA
1 AAAAAAGAAAAGGAAAA
*
47260 AAAAAAGAAAATGAAAA
1 AAAAAAGAAAAGGAAAA
*
47277 AAAGAAGA
1 AAAAAAGA
47285 GAACTATTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 6 0.27
17 16 0.73
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (17 bp):
AAAAAAGAAAAGGAAAA
Found at i:49178 original size:1 final size:1
Alignment explanation
Indices: 49172--49213 Score: 84
Period size: 1 Copynumber: 42.0 Consensus size: 1
49162 CACAAAGAGG
49172 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
49214 CTAGAACAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:50944 original size:11 final size:11
Alignment explanation
Indices: 50930--50954 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
50920 TGGATTGGTA
50930 TTGGACATTGG
1 TTGGACATTGG
50941 TTGGACATTGG
1 TTGGACATTGG
50952 TTG
1 TTG
50955 AAGAACCTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.08, G:0.36, T:0.40
Consensus pattern (11 bp):
TTGGACATTGG
Found at i:63169 original size:16 final size:15
Alignment explanation
Indices: 63138--63180 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
63128 TTGTTGTTGC
* *
63138 TTTTTCGTTTTCTGT
1 TTTTTTGTTTTTTGT
63153 TTGTTTTGTTTTTTGT
1 TT-TTTTGTTTTTTGT
63169 TTTTTT-TTTTTT
1 TTTTTTGTTTTTT
63181 CAAACTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 6 0.24
15 6 0.24
16 13 0.52
ACGTcount: A:0.00, C:0.05, G:0.12, T:0.84
Consensus pattern (15 bp):
TTTTTTGTTTTTTGT
Found at i:65004 original size:31 final size:31
Alignment explanation
Indices: 64935--65097 Score: 110
Period size: 31 Copynumber: 5.5 Consensus size: 31
64925 TCCTTTTGTG
* * **
64935 CACGTGGCATGCCACGTGCCATTTTTTGAAA
1 CACGTGGCATGCCACGTGTCACTTTTTGGTA
* *
64966 CATGTGGCATGCCACATGTCACTTTTTGGTA
1 CACGTGGCATGCCACGTGTCACTTTTTGGTA
* * * *
64997 TACGTGGCGTGACATGTGTCACTTTTTGGTA
1 CACGTGGCATGCCACGTGTCACTTTTTGGTA
*
65028 CA--T-G--TGGCAC--G--ACTTTTTGGTA
1 CACGTGGCATGCCACGTGTCACTTTTTGGTA
* * * *
65050 CATGTAGCGTGCCACATGTCACTTTTTGGTA
1 CACGTGGCATGCCACGTGTCACTTTTTGGTA
* *
65081 CACGTGACGTGCCACGT
1 CACGTGGCATGCCACGT
65098 CGGACACCGT
Statistics
Matches: 103, Mismatches: 20, Indels: 18
0.73 0.14 0.13
Matches are distributed among these distances:
22 13 0.13
24 2 0.02
25 1 0.01
26 4 0.04
27 5 0.05
28 1 0.01
29 2 0.02
31 75 0.73
ACGTcount: A:0.19, C:0.23, G:0.25, T:0.33
Consensus pattern (31 bp):
CACGTGGCATGCCACGTGTCACTTTTTGGTA
Found at i:74302 original size:2 final size:2
Alignment explanation
Indices: 74297--74322 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
74287 ATTTGATTGA
74297 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
74323 TTTTAGCAAA
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:80292 original size:22 final size:22
Alignment explanation
Indices: 80267--80324 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
80257 CTAAGGAAGC
**
80267 AACTCGCAAGAAGCAAGGTGAA
1 AACTCGCAAGAAGCAAGAAGAA
80289 AACTCGCAA-ACAGCAAGAAGAA
1 AACTCGCAAGA-AGCAAGAAGAA
* *
80311 AACCCGCACGAAGC
1 AACTCGCAAGAAGC
80325 CAAAGGGGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
21 1 0.03
22 28 0.93
23 1 0.03
ACGTcount: A:0.47, C:0.26, G:0.22, T:0.05
Consensus pattern (22 bp):
AACTCGCAAGAAGCAAGAAGAA
Found at i:80559 original size:31 final size:31
Alignment explanation
Indices: 80494--80554 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
80484 AACTTTATGT
* *
80494 TTTCCGATTGTACCCTTATTTTTAAAACATA
1 TTTCCAATTGTACACTTATTTTTAAAACATA
80525 TTTCCAATTGTACACTT-TTTTTAAAA-ATA
1 TTTCCAATTGTACACTTATTTTTAAAACATA
80554 T
1 T
80555 ATTTCTAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 4 0.14
30 9 0.32
31 15 0.54
ACGTcount: A:0.31, C:0.16, G:0.05, T:0.48
Consensus pattern (31 bp):
TTTCCAATTGTACACTTATTTTTAAAACATA
Done.