Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017256.1 Corchorus olitorius cultivar O-4 contig17289, 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: 33168
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3320 original size:104 final size:104
Alignment explanation
Indices: 3207--3462 Score: 379
Period size: 104 Copynumber: 2.4 Consensus size: 104
3197 TTTTTCTAAT
* **
3207 CCTTAAAATAAAATTTTAATTTTAATTTGGGCTAAACTTTAGTGAATTAGTTATATATTTTATTT
1 CCTTAAAATAAAAATAAAATTTTAATTTGGGCTAAAC-TTAGTGAATTAGTTATATATTTTATTT
* *
3272 CTTAAACCCTATAACAAT-ATTATTAATTATGGAATTTAC
65 CTAAAACCCTATAACAATAATTATTAATTATGAAATTTAC
* *
3311 CCTTAAAATAAAAATAAAATTTTAATTTGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTATTT
1 CCTTAAAATAAAAATAAAATTTTAATTTGGGCTAAACTTAGTG-AATTAGTTATATATTTTATTT
* * *
3376 CTAAAATCCTATAACAATAAATTATTAATTTTGAAATTTAT
65 CTAAAACCCTATAACAAT-AATTATTAATTATGAAATTTAC
3417 CCTTAAAATAAAAATAAAATTTTAATTTGGGACTAAACTTAGTGAA
1 CCTTAAAATAAAAATAAAATTTTAATTTGGG-CTAAACTTAGTGAA
3463 ATTAAGGCTA
Statistics
Matches: 138, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
103 6 0.04
104 69 0.50
106 51 0.37
107 12 0.09
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.42
Consensus pattern (104 bp):
CCTTAAAATAAAAATAAAATTTTAATTTGGGCTAAACTTAGTGAATTAGTTATATATTTTATTTC
TAAAACCCTATAACAATAATTATTAATTATGAAATTTAC
Found at i:4506 original size:7 final size:7
Alignment explanation
Indices: 4494--4565 Score: 68
Period size: 7 Copynumber: 11.3 Consensus size: 7
4484 AAATAATATT
4494 TAGTATA
1 TAGTATA
4501 TAGTATA
1 TAGTATA
4508 TA-TATA
1 TAGTATA
4514 TA-TATA
1 TAGTATA
4520 TA-TATA
1 TAGTATA
4526 TA-T-T-
1 TAGTATA
*
4530 TAGTATT
1 TAGTATA
*
4537 TAGTATT
1 TAGTATA
*
4544 TAGTATT
1 TAGTATA
4551 TAGTATA
1 TAGTATA
4558 TA-TATA
1 TAGTATA
4564 TA
1 TA
4566 TAAATAATGG
Statistics
Matches: 61, Mismatches: 1, Indels: 7
0.88 0.01 0.10
Matches are distributed among these distances:
4 2 0.03
5 2 0.03
6 26 0.43
7 31 0.51
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.51
Consensus pattern (7 bp):
TAGTATA
Found at i:4509 original size:2 final size:2
Alignment explanation
Indices: 4497--4567 Score: 61
Period size: 2 Copynumber: 33.0 Consensus size: 2
4487 TAATATTTAG
* *
4497 TA TA TA GTA TA TA TA TA TA TA TA TA TA TA TA TT TA GTA TT TA GTA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA
* *
4542 TT TA GTA TT TA GTA TA TA TA TA TA TA
1 TA TA -TA TA TA -TA TA TA TA TA TA TA
4568 AATAATGGGC
Statistics
Matches: 56, Mismatches: 8, Indels: 10
0.76 0.11 0.14
Matches are distributed among these distances:
2 46 0.82
3 10 0.18
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4523 original size:14 final size:14
Alignment explanation
Indices: 4497--4567 Score: 61
Period size: 15 Copynumber: 4.7 Consensus size: 14
4487 TAATATTTAG
4497 TATATAGTATATATA
1 TATATA-TATATATA
4512 TATATATATATATA
1 TATATATATATATA
* *
4526 TATTTAGTATTTAGTA
1 TATATA-TATATA-TA
* *
4542 TTTAGTATTTAGTATA
1 TATA-TATATA-TATA
4558 TATATATATA
1 TATATATATA
4568 AATAATGGGC
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
14 13 0.30
15 16 0.36
16 11 0.25
17 4 0.09
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (14 bp):
TATATATATATATA
Found at i:5020 original size:33 final size:33
Alignment explanation
Indices: 4973--5042 Score: 106
Period size: 33 Copynumber: 2.1 Consensus size: 33
4963 GCTTTAGCAA
4973 ATAAAAAACTTGTTCTTCTGTCTT-TTTTTCTTT
1 ATAAAAAACTTGTTCTTCTGTCTTATTTTT-TTT
*
5006 ATAACAAACTTGTTCTTCTGTCTTAATTTTTTTT
1 ATAAAAAACTTGTTCTTCTGTCTT-ATTTTTTTT
5040 ATA
1 ATA
5043 TACAGATACA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
33 23 0.68
34 6 0.18
35 5 0.15
ACGTcount: A:0.24, C:0.14, G:0.06, T:0.56
Consensus pattern (33 bp):
ATAAAAAACTTGTTCTTCTGTCTTATTTTTTTT
Found at i:5310 original size:68 final size:68
Alignment explanation
Indices: 5201--5338 Score: 276
Period size: 68 Copynumber: 2.0 Consensus size: 68
5191 AAAAAAAAAG
5201 AACATATATATCCCTATCAATCCCCCAAGTTACTCATTAATTACATATAAAAGGTAATTTTTTCG
1 AACATATATATCCCTATCAATCCCCCAAGTTACTCATTAATTACATATAAAAGGTAATTTTTTCG
5266 TTT
66 TTT
5269 AACATATATATCCCTATCAATCCCCCAAGTTACTCATTAATTACATATAAAAGGTAATTTTTTCG
1 AACATATATATCCCTATCAATCCCCCAAGTTACTCATTAATTACATATAAAAGGTAATTTTTTCG
5334 TTT
66 TTT
5337 AA
1 AA
5339 TTAAAGCATT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 70 1.00
ACGTcount: A:0.36, C:0.20, G:0.06, T:0.38
Consensus pattern (68 bp):
AACATATATATCCCTATCAATCCCCCAAGTTACTCATTAATTACATATAAAAGGTAATTTTTTCG
TTT
Found at i:6747 original size:166 final size:163
Alignment explanation
Indices: 6226--6747 Score: 757
Period size: 163 Copynumber: 3.2 Consensus size: 163
6216 CTGAAATTGA
* * * * * *
6226 ATATAGCGGCG-TCTGACATCAAGACGCCGCCATTTAGTGGCGTTTCG-ATA-GATAGACGCCGC
1 ATATAGCGGCGTTTTGACATC-AGACGCCGCTAATTAGTGGCGTCTAGAAAAGGA-A-ACGCCGC
* * * *
6288 CATATTAATATATGGAGGGAGAGATTTTTTTT-CTTTTTTTTGGATGGAAAAATTCCCTC-CCCC
63 TATTTTAATATATGGAGGGAGAGATTTTTTTTCCTTTTTTTTTGAGGGAAAAATTCCCTCTCCCC
*
6351 TAAAACAAAGAAAGTTTCCAACTCTACGCCTATAAT
128 TAAAACAAAGAAAGTTTCCAACTCTATGCCTATAAT
6387 ATATAGCGGCGTTTTGACATCAGACGCCGCTAATTAGTGGCGTCTAGAAAAGGAAACGCCGCTAT
1 ATATAGCGGCGTTTTGACATCAGACGCCGCTAATTAGTGGCGTCTAGAAAAGGAAACGCCGCTAT
* *
6452 TTTAATATATGAAGGGAGAGATTTTTTTTCCTTTTTTTTTGAGGGAAAAATTCCCTCTCCTCTAA
66 TTTAATATATGGAGGGAGAGATTTTTTTTCCTTTTTTTTTGAGGGAAAAATTCCCTCTCCCCTAA
* *
6517 AACAAAGAAAGTTTTCAACTCTATACCTATAAT
131 AACAAAGAAAGTTTCCAACTCTATGCCTATAAT
* * *
6550 ATATAGCGGCATTTTGACTTCAGATGCCGCTAATTAGTGGCGTCTAGAAAAGGAAACGCCGCTAT
1 ATATAGCGGCGTTTTGACATCAGACGCCGCTAATTAGTGGCGTCTAGAAAAGGAAACGCCGCTAT
* *
6615 TTTAATATATGGAGGGGGAGATTTTTTTTTTCCTTTTTTTTTGAGGGTAAAAATTCCATCTCCCC
66 TTTAATATATGGAGGGAGAGA--TTTTTTTTCCTTTTTTTTTGAGGG-AAAAATTCCCTCTCCCC
6680 TAAAACAAAGAAAGTTTCCAACTCTATGCCTATAAT
128 TAAAACAAAGAAAGTTTCCAACTCTATGCCTATAAT
* *
6716 ATATAGCGGCGTTTTCACATAAGACGCCGCTA
1 ATATAGCGGCGTTTTGACATCAGACGCCGCTA
6748 TGGCGTCTAA
Statistics
Matches: 324, Mismatches: 29, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
161 69 0.21
162 36 0.11
163 119 0.37
165 24 0.07
166 76 0.23
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (163 bp):
ATATAGCGGCGTTTTGACATCAGACGCCGCTAATTAGTGGCGTCTAGAAAAGGAAACGCCGCTAT
TTTAATATATGGAGGGAGAGATTTTTTTTCCTTTTTTTTTGAGGGAAAAATTCCCTCTCCCCTAA
AACAAAGAAAGTTTCCAACTCTATGCCTATAAT
Found at i:6807 original size:32 final size:32
Alignment explanation
Indices: 6748--6830 Score: 105
Period size: 32 Copynumber: 2.6 Consensus size: 32
6738 GACGCCGCTA
* * *
6748 TGGCGTCTAAGAAAGG-AAACTCTGCTAACTAG
1 TGGCGTCT-AGGAAGGAAAACACCGCTAACTAG
*
6780 TGGCGTCTAGGAAGGAAAACACCGCTAATTAG
1 TGGCGTCTAGGAAGGAAAACACCGCTAACTAG
6812 TGGCGTCTAGGAAAGGAAA
1 TGGCGTCTAGG-AAGGAAA
6831 CGCCGCAATT
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
31 6 0.13
32 32 0.71
33 7 0.16
ACGTcount: A:0.35, C:0.17, G:0.29, T:0.19
Consensus pattern (32 bp):
TGGCGTCTAGGAAGGAAAACACCGCTAACTAG
Found at i:7278 original size:21 final size:21
Alignment explanation
Indices: 7235--7312 Score: 97
Period size: 21 Copynumber: 3.8 Consensus size: 21
7225 GTTTGGCAAT
*
7235 TGTACAGATGAGATTA--CAC
1 TGTACAGATGAGATTATGTAC
* *
7254 TGTATAGATTAGATTATGTAC
1 TGTACAGATGAGATTATGTAC
*
7275 TGTACCGATGAGATTATGTAC
1 TGTACAGATGAGATTATGTAC
*
7296 TGTACCGATGAGATTAT
1 TGTACAGATGAGATTAT
7313 TAGAGCAGCA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
19 14 0.27
21 37 0.73
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.35
Consensus pattern (21 bp):
TGTACAGATGAGATTATGTAC
Found at i:7840 original size:14 final size:14
Alignment explanation
Indices: 7821--7854 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
7811 TTTTATAATT
*
7821 ATTTTATTTTTACC
1 ATTTTATTATTACC
*
7835 ATTTTATTATTACT
1 ATTTTATTATTACC
7849 ATTTTA
1 ATTTTA
7855 ATTTAAAAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.65
Consensus pattern (14 bp):
ATTTTATTATTACC
Found at i:7902 original size:15 final size:15
Alignment explanation
Indices: 7882--7912 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
7872 GATTAACCTA
7882 TTTCTATTTGATAGT
1 TTTCTATTTGATAGT
7897 TTTCTATTTGATAGT
1 TTTCTATTTGATAGT
7912 T
1 T
7913 AATGTATTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.13, T:0.61
Consensus pattern (15 bp):
TTTCTATTTGATAGT
Found at i:9535 original size:34 final size:34
Alignment explanation
Indices: 9494--9562 Score: 122
Period size: 34 Copynumber: 2.0 Consensus size: 34
9484 TCAAATTATA
9494 TATAGCGGCG-TTGAAACGCCGCTATATTTAAGGG
1 TATAGCGGCGCTT-AAACGCCGCTATATTTAAGGG
9528 TATAGCGGCGCTTAAACGCCGCTATATTTAAGGG
1 TATAGCGGCGCTTAAACGCCGCTATATTTAAGGG
9562 T
1 T
9563 GTTTTAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
34 32 0.94
35 2 0.06
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.28
Consensus pattern (34 bp):
TATAGCGGCGCTTAAACGCCGCTATATTTAAGGG
Found at i:9603 original size:60 final size:60
Alignment explanation
Indices: 9533--9800 Score: 468
Period size: 59 Copynumber: 4.5 Consensus size: 60
9523 AAGGGTATAG
* *
9533 CGGCGCTTAAACGCCGCTATATTTAAGGGTGTTTTAAAAAAAATCTCAAATTAAACATAA
1 CGGCGTTTAAACGCCGCTATATTTAAGGGTGTTTTTAAAAAAATCTCAAATTAAACATAA
* *
9593 CGGCGTTTAAACGCCGCTATATTTAAGGGTG-TTTTAAAAAAATCTCAAATTAAATATAG
1 CGGCGTTTAAACGCCGCTATATTTAAGGGTGTTTTTAAAAAAATCTCAAATTAAACATAA
* *
9652 CGGCGTTTAAACGCCGCTATATTTAAGGGTGTTTTTAAAAAAATCTCAAACTAAATATAA
1 CGGCGTTTAAACGCCGCTATATTTAAGGGTGTTTTTAAAAAAATCTCAAATTAAACATAA
9712 CGGCGTTTAAACGCCGCTATATTTAAGGGT-TTTTTAAAAAAATCTCAAATTAAACATAA
1 CGGCGTTTAAACGCCGCTATATTTAAGGGTGTTTTTAAAAAAATCTCAAATTAAACATAA
9771 CGGCGTTTAAACGCCGCTATATTTAAGGGT
1 CGGCGTTTAAACGCCGCTATATTTAAGGGT
9801 TTAAACGCCG
Statistics
Matches: 199, Mismatches: 8, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
59 113 0.57
60 86 0.43
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (60 bp):
CGGCGTTTAAACGCCGCTATATTTAAGGGTGTTTTTAAAAAAATCTCAAATTAAACATAA
Found at i:9712 original size:119 final size:119
Alignment explanation
Indices: 9528--9800 Score: 483
Period size: 119 Copynumber: 2.3 Consensus size: 119
9518 TATTTAAGGG
* *
9528 TATAGCGGCGCTTAAACGCCGCTATATTTAAGGGTGTTTTAAAAAAAATCTCAAATTAAACATAA
1 TATAGCGGCGTTTAAACGCCGCTATATTTAAGGGTGTTTTAAAAAAAATCTCAAACTAAACATAA
9593 CGGCGTTTAAACGCCGCTATATTTAAGGGTGTTTTAAAAAAATCTCAAATTAAA
66 CGGCGTTTAAACGCCGCTATATTTAAGGGTGTTTTAAAAAAATCTCAAATTAAA
* *
9647 TATAGCGGCGTTTAAACGCCGCTATATTTAAGGGTGTTTTTAAAAAAATCTCAAACTAAATATAA
1 TATAGCGGCGTTTAAACGCCGCTATATTTAAGGGTGTTTTAAAAAAAATCTCAAACTAAACATAA
*
9712 CGGCGTTTAAACGCCGCTATATTTAAGGGTTTTTTAAAAAAATCTCAAATTAAA
66 CGGCGTTTAAACGCCGCTATATTTAAGGGTGTTTTAAAAAAATCTCAAATTAAA
* *
9766 CATAACGGCGTTTAAACGCCGCTATATTTAAGGGT
1 TATAGCGGCGTTTAAACGCCGCTATATTTAAGGGT
9801 TTAAACGCCG
Statistics
Matches: 147, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
119 147 1.00
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.31
Consensus pattern (119 bp):
TATAGCGGCGTTTAAACGCCGCTATATTTAAGGGTGTTTTAAAAAAAATCTCAAACTAAACATAA
CGGCGTTTAAACGCCGCTATATTTAAGGGTGTTTTAAAAAAATCTCAAATTAAA
Found at i:12029 original size:86 final size:86
Alignment explanation
Indices: 11881--12054 Score: 330
Period size: 86 Copynumber: 2.0 Consensus size: 86
11871 TGTTAAGATG
*
11881 GAGTTTCATATTTCATCTCATTATGCTTACAACCTTTTTTCACAATAACTTTATTTTCAAACAGA
1 GAGTTTCATATTTCATCTCATTATGCTTACAACCCTTTTTCACAATAACTTTATTTTCAAACAGA
11946 ACACATCCAGATTCCTAAACA
66 ACACATCCAGATTCCTAAACA
*
11967 GAGTTTCATATTTCATCTCATTATGCTTACAACCCTTTTTCACAATAACTTTATTTTGAAACAGA
1 GAGTTTCATATTTCATCTCATTATGCTTACAACCCTTTTTCACAATAACTTTATTTTCAAACAGA
12032 ACACATCCAGATTCCTAAACA
66 ACACATCCAGATTCCTAAACA
12053 GA
1 GA
12055 CCTGCACCAG
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
86 86 1.00
ACGTcount: A:0.34, C:0.23, G:0.07, T:0.36
Consensus pattern (86 bp):
GAGTTTCATATTTCATCTCATTATGCTTACAACCCTTTTTCACAATAACTTTATTTTCAAACAGA
ACACATCCAGATTCCTAAACA
Found at i:13913 original size:17 final size:17
Alignment explanation
Indices: 13891--13924 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
13881 TCAAATAGGG
13891 GCGTTTCACAGCAAAAA
1 GCGTTTCACAGCAAAAA
13908 GCGTTTCACAGCAAAAA
1 GCGTTTCACAGCAAAAA
13925 CGCCACTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.24, G:0.18, T:0.18
Consensus pattern (17 bp):
GCGTTTCACAGCAAAAA
Found at i:13960 original size:31 final size:31
Alignment explanation
Indices: 13922--14036 Score: 140
Period size: 31 Copynumber: 3.7 Consensus size: 31
13912 TTCACAGCAA
*
13922 AAACGCCACTATTTAGTGGTGTCTGTAAAGT
1 AAACGCCACTATTTAGTGGCGTCTGTAAAGT
* *
13953 AAACGCCACTATTTAGTGGCGTTTCTAAAGT
1 AAACGCCACTATTTAGTGGCGTCTGTAAAGT
* * **
13984 AAATGCCACCAAATAGTGGCGTCTGTAAAGT
1 AAACGCCACTATTTAGTGGCGTCTGTAAAGT
* **
14015 AAAGGCCACTAAATAGTGGCGT
1 AAACGCCACTATTTAGTGGCGT
14037 TTATAAGACA
Statistics
Matches: 73, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 73 1.00
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (31 bp):
AAACGCCACTATTTAGTGGCGTCTGTAAAGT
Found at i:18355 original size:48 final size:46
Alignment explanation
Indices: 18297--18404 Score: 144
Period size: 48 Copynumber: 2.3 Consensus size: 46
18287 AAGGAACAAT
***
18297 AAAAAGTAAAAGATCAATTTTATCTTAAAAATTGAGAAAAAGTGCAAGG
1 AAAAA-TAAAAGATCAATTTTATAGCAAAAATTGAGAAAAAGTGC-A-G
*
18346 AAAAATAAAAGATCAATTTTGTAGCAAAAATTGAGAAAAAGTGCAG
1 AAAAATAAAAGATCAATTTTATAGCAAAAATTGAGAAAAAGTGCAG
*
18392 AAAAGTAAAAGAT
1 AAAAATAAAAGAT
18405 TGCTTTGAGT
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
46 13 0.24
47 1 0.02
48 35 0.65
49 5 0.09
ACGTcount: A:0.56, C:0.06, G:0.17, T:0.22
Consensus pattern (46 bp):
AAAAATAAAAGATCAATTTTATAGCAAAAATTGAGAAAAAGTGCAG
Found at i:19690 original size:9 final size:9
Alignment explanation
Indices: 19670--19707 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
19660 TTAATTCATT
19670 TAATTTCC-
1 TAATTTCCA
19678 TAATTTCCA
1 TAATTTCCA
*
19687 TAATTTCCC
1 TAATTTCCA
19696 TAATTTCCA
1 TAATTTCCA
19705 TAA
1 TAA
19708 GTAATTTGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
8 8 0.30
9 19 0.70
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.45
Consensus pattern (9 bp):
TAATTTCCA
Found at i:19699 original size:18 final size:17
Alignment explanation
Indices: 19670--19707 Score: 67
Period size: 18 Copynumber: 2.2 Consensus size: 17
19660 TTAATTCATT
19670 TAATTTCCTAATTTCCA
1 TAATTTCCTAATTTCCA
19687 TAATTTCCCTAATTTCCA
1 TAATTT-CCTAATTTCCA
19705 TAA
1 TAA
19708 GTAATTTGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.45
Consensus pattern (17 bp):
TAATTTCCTAATTTCCA
Found at i:27999 original size:15 final size:15
Alignment explanation
Indices: 27954--28003 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
27944 TGCACCATTT
* *
27954 CCATTATTGTTCACA
1 CCATTGTTGTTCGCA
27969 CCATTGTTGTTCGCA
1 CCATTGTTGTTCGCA
*
27984 CCATTGTTGTTTGCA
1 CCATTGTTGTTCGCA
27999 CCATT
1 CCATT
28004 CACCCTAGCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.18, C:0.26, G:0.14, T:0.42
Consensus pattern (15 bp):
CCATTGTTGTTCGCA
Found at i:28941 original size:48 final size:46
Alignment explanation
Indices: 28863--28970 Score: 144
Period size: 48 Copynumber: 2.3 Consensus size: 46
28853 AAGGAACAAT
***
28863 AAAAAGTAAAAGATCAATTTTATCTTAAAAATTGAGAAAAAGTGCAAGG
1 AAAAA-TAAAAGATCAATTTTATAGCAAAAATTGAGAAAAAGTGC-A-G
*
28912 AAAAATAAAAGATCAATTTTGTAGCAAAAATTGAGAAAAAGTGCAG
1 AAAAATAAAAGATCAATTTTATAGCAAAAATTGAGAAAAAGTGCAG
*
28958 AAAAGTAAAAGAT
1 AAAAATAAAAGAT
28971 TGCTTTGAGT
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
46 13 0.24
47 1 0.02
48 35 0.65
49 5 0.09
ACGTcount: A:0.56, C:0.06, G:0.17, T:0.22
Consensus pattern (46 bp):
AAAAATAAAAGATCAATTTTATAGCAAAAATTGAGAAAAAGTGCAG
Found at i:30257 original size:9 final size:9
Alignment explanation
Indices: 30235--30272 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
30225 TGAAATCATT
30235 TAATTTCC-
1 TAATTTCCA
30243 TAATTTCCA
1 TAATTTCCA
*
30252 TAATTTCCC
1 TAATTTCCA
30261 TAATTTCCA
1 TAATTTCCA
30270 TAA
1 TAA
30273 GTAATTTGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
8 8 0.30
9 19 0.70
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.45
Consensus pattern (9 bp):
TAATTTCCA
Found at i:30264 original size:18 final size:17
Alignment explanation
Indices: 30235--30272 Score: 67
Period size: 18 Copynumber: 2.2 Consensus size: 17
30225 TGAAATCATT
30235 TAATTTCCTAATTTCCA
1 TAATTTCCTAATTTCCA
30252 TAATTTCCCTAATTTCCA
1 TAATTT-CCTAATTTCCA
30270 TAA
1 TAA
30273 GTAATTTGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.45
Consensus pattern (17 bp):
TAATTTCCTAATTTCCA
Done.