Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008402.1 Corchorus capsularis cultivar CVL-1 contig08423, 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: 63595
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:2196 original size:75 final size:75
Alignment explanation
Indices: 2073--2221 Score: 253
Period size: 75 Copynumber: 2.0 Consensus size: 75
2063 CTCCGTCTAA
* *
2073 CCTTCCCAAAGAGAGTAGAAGAAAATGAGGAAAATGTCTACTCCACTGCAAAAGAGAATGCCCAA
1 CCTTCCCAAAGAGAGTAGAAGAAAATAAGGAAAATGTCTACGCCACTGCAAAAGAGAATGCCCAA
2138 GAAGAACTAT
66 GAAGAACTAT
* * *
2148 CCTTCCCAAAGAGAGTAGGAGAAAATAAGGAACATGTCTACGCCACTGCAAAAGAGAATGTCCAA
1 CCTTCCCAAAGAGAGTAGAAGAAAATAAGGAAAATGTCTACGCCACTGCAAAAGAGAATGCCCAA
2213 GAAGAACTA
66 GAAGAACTA
2222 AGTAATGATG
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 69 1.00
ACGTcount: A:0.44, C:0.20, G:0.21, T:0.15
Consensus pattern (75 bp):
CCTTCCCAAAGAGAGTAGAAGAAAATAAGGAAAATGTCTACGCCACTGCAAAAGAGAATGCCCAA
GAAGAACTAT
Found at i:3414 original size:16 final size:16
Alignment explanation
Indices: 3395--3450 Score: 78
Period size: 16 Copynumber: 3.5 Consensus size: 16
3385 AAATCTGAAT
3395 CCGAAAAAGCTCAAAC
1 CCGAAAAAGCTCAAAC
* *
3411 CCGAAAAA-ATCCGAAC
1 CCGAAAAAGCT-CAAAC
3427 CCGAAAAAGCTCAAAC
1 CCGAAAAAGCTCAAAC
3443 CCGAAAAA
1 CCGAAAAA
3451 ACCCGAATCC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
15 1 0.03
16 32 0.94
17 1 0.03
ACGTcount: A:0.52, C:0.30, G:0.12, T:0.05
Consensus pattern (16 bp):
CCGAAAAAGCTCAAAC
Found at i:3419 original size:32 final size:32
Alignment explanation
Indices: 3383--3465 Score: 139
Period size: 32 Copynumber: 2.6 Consensus size: 32
3373 CTTCAAGTTC
*
3383 AAAAATCTGAATCCGAAAAAGCTCAAACCCGA
1 AAAAATCCGAATCCGAAAAAGCTCAAACCCGA
*
3415 AAAAATCCGAACCCGAAAAAGCTCAAACCCGA
1 AAAAATCCGAATCCGAAAAAGCTCAAACCCGA
*
3447 AAAAACCCGAATCCGAAAA
1 AAAAATCCGAATCCGAAAA
3466 TTTATGAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.52, C:0.28, G:0.12, T:0.08
Consensus pattern (32 bp):
AAAAATCCGAATCCGAAAAAGCTCAAACCCGA
Found at i:3462 original size:16 final size:16
Alignment explanation
Indices: 3408--3465 Score: 71
Period size: 16 Copynumber: 3.6 Consensus size: 16
3398 AAAAAGCTCA
*
3408 AACCCGAAAAAATCCG
1 AACCCGAAAAAACCCG
* * *
3424 AACCCGAAAAAGCTCA
1 AACCCGAAAAAACCCG
3440 AACCCGAAAAAACCCG
1 AACCCGAAAAAACCCG
*
3456 AATCCGAAAA
1 AACCCGAAAA
3466 TTTATGAAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.52, C:0.31, G:0.12, T:0.05
Consensus pattern (16 bp):
AACCCGAAAAAACCCG
Found at i:3656 original size:32 final size:32
Alignment explanation
Indices: 3602--3689 Score: 113
Period size: 32 Copynumber: 2.8 Consensus size: 32
3592 ATCTGGCCAA
* * *
3602 AACCCAAACTGAACTCGAACCCGAATTAACCT
1 AACCCAAATTCAACCCGAACCCGAATTAACCT
*
3634 AACCCAAATTCAACCCGTACCCGAATTAACCT
1 AACCCAAATTCAACCCGAACCCGAATTAACCT
* * *
3666 GATCCAAATTCAACCCGAATCCGA
1 AACCCAAATTCAACCCGAACCCGA
3690 TTCAAATCCG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.39, C:0.35, G:0.09, T:0.17
Consensus pattern (32 bp):
AACCCAAATTCAACCCGAACCCGAATTAACCT
Found at i:3664 original size:16 final size:16
Alignment explanation
Indices: 3619--3664 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
3609 ACTGAACTCG
3619 AACCCGAATTAA-CCT
1 AACCCGAATTAACCCT
*
3634 AACCCAAATTCAACCCGT
1 AACCCGAATT-AACCC-T
3652 -ACCCGAATTAACC
1 AACCCGAATTAACC
3665 TGATCCAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 9 0.35
16 6 0.23
17 10 0.38
18 1 0.04
ACGTcount: A:0.39, C:0.37, G:0.07, T:0.17
Consensus pattern (16 bp):
AACCCGAATTAACCCT
Found at i:3680 original size:16 final size:17
Alignment explanation
Indices: 3635--3682 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
3625 AATTAACCTA
3635 ACCCAAATTCAACCCGT
1 ACCCAAATTCAACCCGT
* *
3652 ACCCGAATT-AACCTG-
1 ACCCAAATTCAACCCGT
*
3667 ATCCAAATTCAACCCG
1 ACCCAAATTCAACCCG
3683 AATCCGATTC
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
15 7 0.28
16 10 0.40
17 8 0.32
ACGTcount: A:0.35, C:0.38, G:0.08, T:0.19
Consensus pattern (17 bp):
ACCCAAATTCAACCCGT
Found at i:3717 original size:17 final size:18
Alignment explanation
Indices: 3697--3738 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
3687 CGATTCAAAT
3697 CCGAACCCA-AAAATAAC
1 CCGAACCCAGAAAATAAC
*
3714 CCGAA-CCAGAAAATGAC
1 CCGAACCCAGAAAATAAC
*
3731 CCAAACCC
1 CCGAACCC
3739 GATGACCCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 3 0.14
17 16 0.76
18 2 0.10
ACGTcount: A:0.48, C:0.38, G:0.10, T:0.05
Consensus pattern (18 bp):
CCGAACCCAGAAAATAAC
Found at i:5697 original size:30 final size:30
Alignment explanation
Indices: 5657--5737 Score: 99
Period size: 30 Copynumber: 2.7 Consensus size: 30
5647 TAAAAAAAAA
*
5657 AAAAATATATATATATATATATATTACCGC
1 AAAAATATATATATATATATATAATACCGC
** * * *
5687 AATTATATATAAATATATATATAATCCCGT
1 AAAAATATATATATATATATATAATACCGC
*
5717 AAAAAAATATATATATATATA
1 AAAAATATATATATATATATA
5738 ATCTAATAAA
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.37
Consensus pattern (30 bp):
AAAAATATATATATATATATATAATACCGC
Found at i:11917 original size:24 final size:22
Alignment explanation
Indices: 11866--11919 Score: 65
Period size: 21 Copynumber: 2.4 Consensus size: 22
11856 GACACATGAC
*
11866 GATCATAAGGAAGAGGAGGAGA
1 GATCATAAGAAAGAGGAGGAGA
*
11888 -AGCATAAGAAAGAGGAGGGAGA
1 GATCATAAGAAAGAGGA-GGAGA
11910 GGATCATAAG
1 -GATCATAAG
11920 GAGGACAAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 14 0.54
22 5 0.19
24 7 0.27
ACGTcount: A:0.46, C:0.06, G:0.39, T:0.09
Consensus pattern (22 bp):
GATCATAAGAAAGAGGAGGAGA
Found at i:18979 original size:32 final size:32
Alignment explanation
Indices: 18932--19045 Score: 131
Period size: 32 Copynumber: 3.6 Consensus size: 32
18922 GAGTTCGGAT
* * *
18932 TTAAGTCGGGTTCGGGTTATATTTGGGTCGGA
1 TTAATTCGGGTTCGGGTTAAATTTGGGTCAGA
* *
18964 TTGATTCGTGTTCGGGTTAAATTTGGGTCAGA
1 TTAATTCGGGTTCGGGTTAAATTTGGGTCAGA
* * *
18996 TTAATTCGGGTTC-GGATAAATTTTGTGTCAGG
1 TTAATTCGGGTTCGGGTTAAA-TTTGGGTCAGA
*
19028 TTAATTCGGATTCGGGTT
1 TTAATTCGGGTTCGGGTT
19046 GGGTTTTGAC
Statistics
Matches: 68, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
31 6 0.09
32 59 0.87
33 3 0.04
ACGTcount: A:0.18, C:0.10, G:0.32, T:0.40
Consensus pattern (32 bp):
TTAATTCGGGTTCGGGTTAAATTTGGGTCAGA
Found at i:19211 original size:20 final size:20
Alignment explanation
Indices: 19178--19216 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
19168 CATAGATGAA
*
19178 ATTTTCAGAAATTATTATTT
1 ATTTTCAGAAATTAGTATTT
19198 ATTTTCA-AATATTAGTATT
1 ATTTTCAGAA-ATTAGTATT
19217 GAATTCAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (20 bp):
ATTTTCAGAAATTAGTATTT
Found at i:19297 original size:15 final size:15
Alignment explanation
Indices: 19266--19322 Score: 53
Period size: 16 Copynumber: 3.7 Consensus size: 15
19256 GGTTTCAGAC
*
19266 TTTTCGGATTCTGA-T
1 TTTTCGGGTT-TGATT
19281 TTTTCGGGTTTGAATT
1 TTTTCGGGTTTG-ATT
*
19297 TTTTCGGGTTTAGGTT
1 TTTTCGGGTTT-GATT
*
19313 TTTTTGGGTT
1 TTTTCGGGTT
19323 CGGGTTCTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
14 2 0.06
15 10 0.28
16 23 0.64
17 1 0.03
ACGTcount: A:0.09, C:0.07, G:0.26, T:0.58
Consensus pattern (15 bp):
TTTTCGGGTTTGATT
Found at i:19718 original size:14 final size:14
Alignment explanation
Indices: 19699--19725 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
19689 CATTTTCCTT
19699 TTTTTTTCTTCTTC
1 TTTTTTTCTTCTTC
19713 TTTTTTTCTTCTT
1 TTTTTTTCTTCTT
19726 ACTTAAACTT
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:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTTTTCTTCTTC
Found at i:20459 original size:21 final size:21
Alignment explanation
Indices: 20421--20461 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
20411 CTTTGGCTTA
*
20421 TGATCTTCAATACTCTTCAAT
1 TGATCTTCAATACACTTCAAT
**
20442 TGATCTTCAATGGACTTCAA
1 TGATCTTCAATACACTTCAA
20462 GCCTTCAAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.39
Consensus pattern (21 bp):
TGATCTTCAATACACTTCAAT
Found at i:25982 original size:9 final size:9
Alignment explanation
Indices: 25968--26001 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
25958 TCTGGTCGAT
*
25968 TTTTTTTTA
1 TTTTTTTGA
25977 TTTTTTTGA
1 TTTTTTTGA
25986 TTTTTTTGA
1 TTTTTTTGA
*
25995 TATTTTT
1 TTTTTTT
26002 CGATATAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.82
Consensus pattern (9 bp):
TTTTTTTGA
Found at i:31966 original size:20 final size:19
Alignment explanation
Indices: 31935--31973 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
31925 ATTTATTTTT
*
31935 TATATATATAATTATATAA
1 TATATATATAATTAAATAA
31954 TATATATTATAATTAAATAA
1 TATATA-TATAATTAAATAA
31974 AACTCTAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TATATATATAATTAAATAA
Found at i:35774 original size:33 final size:32
Alignment explanation
Indices: 35701--35805 Score: 104
Period size: 33 Copynumber: 3.2 Consensus size: 32
35691 TCTATGATCA
** *
35701 ACCAAAACAGA-TTTGTTTTCATCACAATTAGC
1 ACCAAAACAGATTTTG-TTTCATCACAAACAAC
35733 ATCCAAAACAGATTTTGTTTCATCACAAACAAC
1 A-CCAAAACAGATTTTGTTTCATCACAAACAAC
* * **
35766 ACCTAAAACAGATTTAGTGTCATCGGAAACAAC
1 ACC-AAAACAGATTTTGTTTCATCACAAACAAC
35799 ACTCAAA
1 AC-CAAA
35806 TTAGGTTCAG
Statistics
Matches: 62, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
32 3 0.05
33 54 0.87
34 5 0.08
ACGTcount: A:0.42, C:0.23, G:0.10, T:0.26
Consensus pattern (32 bp):
ACCAAAACAGATTTTGTTTCATCACAAACAAC
Found at i:37324 original size:22 final size:22
Alignment explanation
Indices: 37274--37325 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
37264 CTTGTCGCAC
*
37274 GTCGTCGCAATTGATTTATTTG
1 GTCGTCGCAATTGATTTATATG
*
37296 GTAGTCGCAATTG-TTTATAATG
1 GTCGTCGCAATTGATTTAT-ATG
*
37318 TTCGTCGC
1 GTCGTCGC
37326 TGTTTGTCGC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 5 0.20
22 20 0.80
ACGTcount: A:0.19, C:0.15, G:0.23, T:0.42
Consensus pattern (22 bp):
GTCGTCGCAATTGATTTATATG
Found at i:37739 original size:11 final size:11
Alignment explanation
Indices: 37718--37747 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
37708 AGTTCATTCC
37718 TATAT-ATATA
1 TATATAATATA
37728 TATATAATATA
1 TATATAATATA
37739 TATATAATA
1 TATATAATA
37748 AATCTAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.26
11 14 0.74
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
TATATAATATA
Found at i:40040 original size:54 final size:53
Alignment explanation
Indices: 39960--40274 Score: 291
Period size: 54 Copynumber: 5.9 Consensus size: 53
39950 TTTCTTGGAG
* * * *
39960 CAACTCCATTAGTTGATTGAGA-CCTTCCTCCTTGAATTTCAGCATTTACGGCAC
1 CAACTCCATTAGTTGATTCA-ACCCTT-CTCCTTGAATTTCAGAATTTCCAGCAC
* * * *
40014 CATCTCCATTAGTTGAATCAACCCTTCT--TTGAATTTCAGAATTTCCATCAA
1 CAACTCCATTAGTTGATTCAACCCTTCTCCTTGAATTTCAGAATTTCCAGCAC
* * * * * *
40065 GAACTTCATTAGTTGATTCAGCCCTTCCTCTTTGAATTACA-ACATTTCTAGCAC
1 CAACTCCATTAGTTGATTCAACCCTT-CTCCTTGAATTTCAGA-ATTTCCAGCAC
* * * * *
40119 CAACTCCATTAATAGTTTCAACCCTTCT--TTGAATTTTAGAATTTCCAGCAT
1 CAACTCCATTAGTTGATTCAACCCTTCTCCTTGAATTTCAGAATTTCCAGCAC
* * * *
40170 CAACTCCAATAGTTGATTCAACCATTCTTCTTCGAATTTCAGAATTTCCAGCAT
1 CAACTCCATTAGTTGATTCAACCCTTCTCCTT-GAATTTCAGAATTTCCAGCAC
* * * *
40224 CAATTCCATTAGTTGATTCCACCCTTACTCCATGATTTTCAGAATTTCCAG
1 CAACTCCATTAGTTGATTCAACCCTT-CTCCTTGAATTTCAGAATTTCCAG
40275 TAGCTGTTTA
Statistics
Matches: 211, Mismatches: 40, Indels: 20
0.78 0.15 0.07
Matches are distributed among these distances:
51 79 0.37
52 3 0.01
53 8 0.04
54 117 0.55
55 4 0.02
ACGTcount: A:0.27, C:0.26, G:0.10, T:0.37
Consensus pattern (53 bp):
CAACTCCATTAGTTGATTCAACCCTTCTCCTTGAATTTCAGAATTTCCAGCAC
Found at i:40119 original size:105 final size:104
Alignment explanation
Indices: 39960--40274 Score: 319
Period size: 105 Copynumber: 3.0 Consensus size: 104
39950 TTTCTTGGAG
* * * * *
39960 CAACTCCATTAGTTGATTGAGACCTTCCTCCTTGAATTTCAGCATTTACGGCACCATCTCCATTA
1 CAACTCCATTAGTTGATTCAGCCCTTCCTCTTTGAATTTCAACATTT-CAGCACCATCTCCATTA
* *
40025 GTTGAATCAACCCTTCTTTGAATTTCAGAATTTCCATCAA
65 GTTGATTCAACCCTTCTTTGAATTTCAGAATTTCCAGCAA
* * * *
40065 GAACTTCATTAGTTGATTCAGCCCTTCCTCTTTGAATTACAACATTTCTAGCACCAACTCCATTA
1 CAACTCCATTAGTTGATTCAGCCCTTCCTCTTTGAATTTCAACATTTC-AGCACCATCTCCATTA
* * * * *
40130 ATAGTTTCAACCCTTCTTTGAATTTTAGAATTTCCAGCAT
65 GTTGATTCAACCCTTCTTTGAATTTCAGAATTTCCAGCAA
* * * * * *
40170 CAACTCCAATAGTTGATTCAACCATTCTTCTTCGAATTTCAGA-ATTTCCAGCATCAAT-TCCAT
1 CAACTCCATTAGTTGATTCAGCCCTTCCTCTTTGAATTTCA-ACATTT-CAGCA-CCATCTCCAT
* * *
40233 TAGTTGATTCCACCCTTACTCCATGATTTTCAGAATTTCCAG
63 TAGTTGATTCAACCCTT-CT--TTGAATTTCAGAATTTCCAG
40275 TAGCTGTTTA
Statistics
Matches: 170, Mismatches: 33, Indels: 11
0.79 0.15 0.05
Matches are distributed among these distances:
104 1 0.01
105 146 0.86
106 6 0.04
108 17 0.10
ACGTcount: A:0.27, C:0.26, G:0.10, T:0.37
Consensus pattern (104 bp):
CAACTCCATTAGTTGATTCAGCCCTTCCTCTTTGAATTTCAACATTTCAGCACCATCTCCATTAG
TTGATTCAACCCTTCTTTGAATTTCAGAATTTCCAGCAA
Found at i:40303 original size:42 final size:42
Alignment explanation
Indices: 40256--40357 Score: 204
Period size: 42 Copynumber: 2.4 Consensus size: 42
40246 CCTTACTCCA
40256 TGATTTTCAGAATTTCCAGTAGCTGTTTAAACTCTTCCTTTT
1 TGATTTTCAGAATTTCCAGTAGCTGTTTAAACTCTTCCTTTT
40298 TGATTTTCAGAATTTCCAGTAGCTGTTTAAACTCTTCCTTTT
1 TGATTTTCAGAATTTCCAGTAGCTGTTTAAACTCTTCCTTTT
40340 TGATTTTCAGAATTTCCA
1 TGATTTTCAGAATTTCCA
40358 ACAGCAAATC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 60 1.00
ACGTcount: A:0.23, C:0.19, G:0.12, T:0.47
Consensus pattern (42 bp):
TGATTTTCAGAATTTCCAGTAGCTGTTTAAACTCTTCCTTTT
Found at i:43600 original size:33 final size:32
Alignment explanation
Indices: 43563--43670 Score: 101
Period size: 33 Copynumber: 3.3 Consensus size: 32
43553 CGCCAAGCGA
*
43563 TGGCCGGTTCTGGCCGGACATGTCC-ATGTCGCG
1 TGGCCGGTT-TGGCCGGACATCTCCGA-GTCGCG
* *
43596 TGGCCGGTGATGGCCGGGCATCTCCGAGTCGCG
1 TGGCCGGT-TTGGCCGGACATCTCCGAGTCGCG
* * * * *
43629 TGGCCGGTGTTGGCCGGTCTTCTCCAAATCGCA
1 TGGCCGGT-TTGGCCGGACATCTCCGAGTCGCG
43662 TGGCCGGTT
1 TGGCCGGTT
43671 ACTCGCACCT
Statistics
Matches: 64, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
32 1 0.02
33 62 0.97
34 1 0.02
ACGTcount: A:0.09, C:0.30, G:0.37, T:0.24
Consensus pattern (32 bp):
TGGCCGGTTTGGCCGGACATCTCCGAGTCGCG
Found at i:49000 original size:5 final size:5
Alignment explanation
Indices: 48990--49018 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
48980 TGGTCGAAAA
48990 TTTAT TTTAT TTTAT TTTAT TTT-T TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
49019 ATTTTTCGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTAT
Found at i:49119 original size:17 final size:17
Alignment explanation
Indices: 49097--49130 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
49087 GAATCGGCTA
49097 TGAATTTTTGAAGTTTC
1 TGAATTTTTGAAGTTTC
*
49114 TGAATTTTTGAATTTTC
1 TGAATTTTTGAAGTTTC
49131 AAGAAGGGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.06, G:0.15, T:0.56
Consensus pattern (17 bp):
TGAATTTTTGAAGTTTC
Found at i:50127 original size:33 final size:34
Alignment explanation
Indices: 50089--50197 Score: 109
Period size: 33 Copynumber: 3.3 Consensus size: 34
50079 GCGCCAAGCG
*
50089 ATGGCCGGTTG-TGGCCGGACATGTCC-ATGTCGC
1 ATGGCCGGTTGATGGCCGGACATCTCCGA-GTCGC
* *
50122 GTGGCCGG-TGATGGCCGGGCATCTCCGAGTCGC
1 ATGGCCGGTTGATGGCCGGACATCTCCGAGTCGC
* * * * *
50155 ATGGCCGG-TGTTGGTCGGTCTTCTCCAAGTCGC
1 ATGGCCGGTTGATGGCCGGACATCTCCGAGTCGC
50188 ATGGCCGGTT
1 ATGGCCGGTT
50198 ACTCGCACCT
Statistics
Matches: 64, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
32 2 0.03
33 60 0.94
34 2 0.03
ACGTcount: A:0.10, C:0.28, G:0.38, T:0.25
Consensus pattern (34 bp):
ATGGCCGGTTGATGGCCGGACATCTCCGAGTCGC
Found at i:51940 original size:12 final size:12
Alignment explanation
Indices: 51923--51956 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
51913 CCGACTCAGA
51923 TTCGTCGCAAAG
1 TTCGTCGCAAAG
51935 TTCGTCGCAAAG
1 TTCGTCGCAAAG
51947 -TCAGTCGCAA
1 TTC-GTCGCAA
51957 CAGGTAAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 2 0.10
12 19 0.90
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.24
Consensus pattern (12 bp):
TTCGTCGCAAAG
Found at i:54615 original size:28 final size:28
Alignment explanation
Indices: 54578--54636 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
54568 TGAGTGAGGT
54578 TGTTCAAATGTCGGTTAAAAGGTTATTG
1 TGTTCAAATGTCGGTTAAAAGGTTATTG
54606 TGTTCAAATGTCGGTTAAAAGGTTATTG
1 TGTTCAAATGTCGGTTAAAAGGTTATTG
54634 TGT
1 TGT
54637 GATCTACGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.27, C:0.07, G:0.25, T:0.41
Consensus pattern (28 bp):
TGTTCAAATGTCGGTTAAAAGGTTATTG
Found at i:62073 original size:33 final size:33
Alignment explanation
Indices: 62031--62098 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
62021 AGTCAGGAGC
62031 AGCCTCTTCTTTAAGAAGATCTGGATCTGGTCT
1 AGCCTCTTCTTTAAGAAGATCTGGATCTGGTCT
*
62064 AGCCTCTTCTTTAAGAAGATCTGGATTTGGTCT
1 AGCCTCTTCTTTAAGAAGATCTGGATCTGGTCT
62097 AG
1 AG
62099 TTCAATCCTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (33 bp):
AGCCTCTTCTTTAAGAAGATCTGGATCTGGTCT
Found at i:62836 original size:32 final size:31
Alignment explanation
Indices: 62792--62854 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 31
62782 TACCGGATAA
* *
62792 TCTAAATTTTAATAGGGTAGGGTTCGCGGTAG
1 TCTAAATATTAATAGGATAGGGTTCG-GGTAG
62824 TCTAAATATTAATAGGATAGGGTTCGGGTAG
1 TCTAAATATTAATAGGATAGGGTTCGGGTAG
62855 AGGCATTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 5 0.17
32 24 0.83
ACGTcount: A:0.29, C:0.08, G:0.30, T:0.33
Consensus pattern (31 bp):
TCTAAATATTAATAGGATAGGGTTCGGGTAG
Done.