Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021015.1 Corchorus olitorius cultivar O-4 contig21048, 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: 25458
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:881 original size:12 final size:12
Alignment explanation
Indices: 864--888 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
854 GCGCATGCCT
864 TTTTTATTGTAA
1 TTTTTATTGTAA
876 TTTTTATTGTAA
1 TTTTTATTGTAA
888 T
1 T
889 CTTATGTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (12 bp):
TTTTTATTGTAA
Found at i:2144 original size:37 final size:37
Alignment explanation
Indices: 2094--2165 Score: 135
Period size: 37 Copynumber: 1.9 Consensus size: 37
2084 TGCACTAACA
2094 TTCTTCACCATCATAGTTATCATAGCTAAAGCGAACC
1 TTCTTCACCATCATAGTTATCATAGCTAAAGCGAACC
*
2131 TTCTTCATCATCATAGTTATCATAGCTAAAGCGAA
1 TTCTTCACCATCATAGTTATCATAGCTAAAGCGAA
2166 TGGAAGGGTC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.33, C:0.24, G:0.11, T:0.32
Consensus pattern (37 bp):
TTCTTCACCATCATAGTTATCATAGCTAAAGCGAACC
Found at i:5398 original size:47 final size:47
Alignment explanation
Indices: 5327--5752 Score: 306
Period size: 47 Copynumber: 9.7 Consensus size: 47
5317 TTGTCTAATT
* * *
5327 CCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTCTAAGTCTACTTTA
1 CCCAATTTGCCCTTCCCCACCGGAAGGTGTTGTCTAAGTCTACTTTA
* ** *
5374 CCTAATTTATCCTTCCCCACCGGAAGGTGTTGTTTAA----A--TT-
1 CCCAATTTGCCCTTCCCCACCGGAAGGTGTTGTCTAAGTCTACTTTA
* * * *
5414 CCCAATTTGCCCTTCCTCATCGGAATGTGTTG-CTTAAGTCTATTTTA
1 CCCAATTTGCCCTTCCCCACCGGAAGGTGTTGTC-TAAGTCTACTTTA
*
5461 CCCAATTTGCCC-TCCCCTACCGGAAGGTGTTGTTTAA----A--TT-
1 CCCAATTTGCCCTTCCCC-ACCGGAAGGTGTTGTCTAAGTCTACTTTA
* ** * *
5501 CCCAGTTTGCCCTTCCTTATCGGAAGGTGTTGTTTAAGTCTACTTTA
1 CCCAATTTGCCCTTCCCCACCGGAAGGTGTTGTCTAAGTCTACTTTA
** * *
5548 CCCAATTCACCCTTCCCCACCGGAA-G-G-TGT-T-A-TGTA-ATT-
1 CCCAATTTGCCCTTCCCCACCGGAAGGTGTTGTCTAAGTCTACTTTA
* * * *
5587 CCCAGTTTGCCCTTCCTCATCAGAAGGTGTTGTCTAAGTCTACTTTA
1 CCCAATTTGCCCTTCCCCACCGGAAGGTGTTGTCTAAGTCTACTTTA
* * *
5634 CCTAATTTGCCCTTCCCCACTGGAAGGTG-TG-----GTCTA-ATT-
1 CCCAATTTGCCCTTCCCCACCGGAAGGTGTTGTCTAAGTCTACTTTA
* * *
5673 CCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGAT-TAAGTCTACTTTA
1 CCCAATTTGCCCTTCCCCACCGGAAGGTGTTG-TCTAAGTCTACTTTA
*
5720 ACCAATTTGCCCTTCCCCACCGGAAGGTGTTGT
1 CCCAATTTGCCCTTCCCCACCGGAAGGTGTTGT
5753 TTAAATCCCT
Statistics
Matches: 290, Mismatches: 55, Indels: 69
0.70 0.13 0.17
Matches are distributed among these distances:
39 43 0.15
40 65 0.22
41 16 0.06
42 4 0.01
43 4 0.01
44 6 0.02
45 9 0.03
46 16 0.06
47 127 0.44
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (47 bp):
CCCAATTTGCCCTTCCCCACCGGAAGGTGTTGTCTAAGTCTACTTTA
Found at i:5483 original size:87 final size:86
Alignment explanation
Indices: 5323--5793 Score: 664
Period size: 87 Copynumber: 5.4 Consensus size: 86
5313 TGCTTTGTCT
* **
5323 AATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTCTAAGTCTACTTTACCTAATTTATCCTT
1 AATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGT-TAAGTCTACTTTACCCAATTTGCCCTT
5388 CCCCACCGGAAGGTGTTGTTTA
65 CCCCACCGGAAGGTGTTGTTTA
* * *
5410 AATTCCCAATTTGCCCTTCCTCATCGGAATGTGTTGCTTAAGTCTATTTTACCCAATTTGCCC-T
1 AATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTG-TTAAGTCTACTTTACCCAATTTGCCCTT
5474 CCCCTACCGGAAGGTGTTGTTTA
65 CCCC-ACCGGAAGGTGTTGTTTA
* **
5497 AATTCCCAGTTTGCCCTTCCTTATCGGAAGGTGTTGTTTAAGTCTACTTTACCCAATTCACCCTT
1 AATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTG-TTAAGTCTACTTTACCCAATTTGCCCTT
* *
5562 CCCCACCGGAAGGTGTTATGT-
65 CCCCACCGGAAGGTGTTGTTTA
* *
5583 AATTCCCAGTTTGCCCTTCCTCATCAGAAGGTGTTGTCTAAGTCTACTTTACCTAATTTGCCCTT
1 AATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGT-TAAGTCTACTTTACCCAATTTGCCCTT
* * *
5648 CCCCACTGGAAGGTGTGGTCT-
65 CCCCACCGGAAGGTGTTGTTTA
*
5669 AATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGATTAAGTCTACTTTAACCAATTTGCCCTT
1 AATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTG-TTAAGTCTACTTTACCCAATTTGCCCTT
5734 CCCCACCGGAAGGTGTTGTTTA
65 CCCCACCGGAAGGTGTTGTTTA
* *
5756 AA-TCCCTAGTTTG-CCTGTCCTCACCAGAAGGTGTTGTT
1 AATTCCC-AGTTTGCCCT-TCCTCATCGGAAGGTGTTGTT
5794 TAAGCTTACC
Statistics
Matches: 344, Mismatches: 32, Indels: 17
0.88 0.08 0.04
Matches are distributed among these distances:
85 1 0.00
86 167 0.49
87 170 0.49
88 6 0.02
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.35
Consensus pattern (86 bp):
AATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTAAGTCTACTTTACCCAATTTGCCCTTC
CCCACCGGAAGGTGTTGTTTA
Found at i:5625 original size:86 final size:86
Alignment explanation
Indices: 5317--5879 Score: 664
Period size: 86 Copynumber: 6.6 Consensus size: 86
5307 CAGTCTTGCT
* *
5317 TTGTCTAATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTCTAAGTCTACTTTACCTAATTT
1 TTGTTTAATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTCTAAGTCTACTTTACCCAATTT
**
5382 ATCCTTCCCCACCGGAAGGTG
66 GCCCTTCCCCACCGGAAGGTG
* * *
5403 TTGTTTAAATTCCCAATTTGCCCTTCCTCATCGGAATGTGTTG-CTTAAGTCTATTTTACCCAAT
1 TTGTTT-AATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTC-TAAGTCTACTTTACCCAAT
5467 TTGCCC-TCCCCTACCGGAAGGTG
64 TTGCCCTTCCCC-ACCGGAAGGTG
* *
5490 TTGTTTAAATTCCCAGTTTGCCCTTCCTTATCGGAAGGTGTTGTTTAAGTCTACTTTACCCAATT
1 TTGTTT-AATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTCTAAGTCTACTTTACCCAATT
**
5555 CACCCTTCCCCACCGGAAGGTG
65 TGCCCTTCCCCACCGGAAGGTG
* * * *
5577 TTATGTAATTCCCAGTTTGCCCTTCCTCATCAGAAGGTGTTGTCTAAGTCTACTTTACCTAATTT
1 TTGTTTAATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTCTAAGTCTACTTTACCCAATTT
*
5642 GCCCTTCCCCACTGGAAGGTG
66 GCCCTTCCCCACCGGAAGGTG
* * *
5663 TGGTCTAATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGAT-TAAGTCTACTTTAACCAATT
1 TTGTTTAATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTG-TCTAAGTCTACTTTACCCAATT
5727 TGCCCTTCCCCACCGGAAGGTG
65 TGCCCTTCCCCACCGGAAGGTG
* * * * *
5749 TTGTTTAAATCCCTAGTTTG-CCTGTCCTCACCAGAAGGTGTTGTTTAAG----C-TTA-CCAGT
1 TTGTTTAATTCCC-AGTTTGCCCT-TCCTCATCGGAAGGTGTTGTCTAAGTCTACTTTACCCAAT
* * *
5807 TTGACCC-TCCTCATCGAAAGGTG
64 TTG-CCCTTCCCCACCGGAAGGTG
* * * * *
5830 TTG-TTAAGTTTACTAGTTTGTCCTTCCTCATCGGAAGGTGTCGTTTAAGT
1 TTGTTTAA--TTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTCTAAGT
5880 TCACCAGTTT
Statistics
Matches: 418, Mismatches: 45, Indels: 32
0.84 0.09 0.06
Matches are distributed among these distances:
80 4 0.01
81 51 0.12
82 11 0.03
83 1 0.00
86 175 0.42
87 171 0.41
88 5 0.01
ACGTcount: A:0.20, C:0.26, G:0.18, T:0.36
Consensus pattern (86 bp):
TTGTTTAATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTCTAAGTCTACTTTACCCAATTT
GCCCTTCCCCACCGGAAGGTG
Found at i:5828 original size:41 final size:39
Alignment explanation
Indices: 5720--5914 Score: 196
Period size: 40 Copynumber: 4.8 Consensus size: 39
5710 GTCTACTTTA
* * * *
5720 ACCAATTTGCCCTTCCCCACCGGAAGGTGTTGTTTAA-AT
1 ACCAGTTTG-CCTTCCTCATCGGAAGGTGTTGTTTAAGTT
* * *
5759 CCCTAGTTTGCCTGTCCTCACCAGAAGGTGTTGTTTAAGCTT
1 ACC-AGTTTGCCT-TCCTCATCGGAAGGTGTTGTTTAAG-TT
* *
5801 ACCAGTTTGACCCTCCTCATCGAAAGGTGTTG-TTAAGTTT
1 ACCAGTTTG-CCTTCCTCATCGGAAGGTGTTGTTTAAG-TT
* *
5841 ACTAGTTTGTCCTTCCTCATCGGAAGGTGTCGTTTAAGTT
1 ACCAGTTTG-CCTTCCTCATCGGAAGGTGTTGTTTAAGTT
5881 CACCAGTTTGCCTTTCCTCATCGGAAGGTGTTGT
1 -ACCAGTTTGCC-TTCCTCATCGGAAGGTGTTGT
5915 CTACATTTCT
Statistics
Matches: 130, Mismatches: 18, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
39 5 0.04
40 65 0.50
41 55 0.42
42 5 0.04
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.35
Consensus pattern (39 bp):
ACCAGTTTGCCTTCCTCATCGGAAGGTGTTGTTTAAGTT
Found at i:5858 original size:81 final size:81
Alignment explanation
Indices: 5761--5914 Score: 215
Period size: 81 Copynumber: 1.9 Consensus size: 81
5751 GTTTAAATCC
*
5761 CTAGTTTGCCTGTCCTCACCAGAAGGTGTTGTTTAAGCTT-ACCAGTTTGACC-CTCCTCATCGA
1 CTAGTTTGCCTGTCCTCACCAGAAGGTGTCGTTTAAG-TTCACCAGTTTG-CCTCTCCTCATCGA
5824 AAGGTGTTGTTAAGTTTA
64 AAGGTGTTGTTAAGTTTA
* * * *
5842 CTAGTTTGTCCT-TCCTCATCGGAAGGTGTCGTTTAAGTTCACCAGTTTGCCTTTCCTCATCGGA
1 CTAGTTTG-CCTGTCCTCACCAGAAGGTGTCGTTTAAGTTCACCAGTTTGCCTCTCCTCATCGAA
5906 AGGTGTTGT
65 AGGTGTTGT
5915 CTACATTTCT
Statistics
Matches: 65, Mismatches: 5, Indels: 6
0.86 0.07 0.08
Matches are distributed among these distances:
80 4 0.06
81 58 0.89
82 3 0.05
ACGTcount: A:0.18, C:0.23, G:0.22, T:0.37
Consensus pattern (81 bp):
CTAGTTTGCCTGTCCTCACCAGAAGGTGTCGTTTAAGTTCACCAGTTTGCCTCTCCTCATCGAAA
GGTGTTGTTAAGTTTA
Found at i:5929 original size:41 final size:39
Alignment explanation
Indices: 5317--5935 Score: 276
Period size: 47 Copynumber: 14.6 Consensus size: 39
5307 CAGTCTTGCT
*
5317 TTGTCTAATTCCCAGTTTGCCCTTCCTCATCGGAAGGTG
1 TTGTCTAATTTCCAGTTTGCCCTTCCTCATCGGAAGGTG
* ** * *
5356 TTGTCTAAGTCTACTTTACCTAATTTATCCTTCCCCACCGGAAGGTG
1 TTGTCT-A----A-TTT-CC-AGTTTGCCCTTCCTCATCGGAAGGTG
* * *
5403 TTGTTTAAATTCCCAATTTGCCCTTCCTCATCGGAATGTGTTG
1 TTGTCT-AATTTCCAGTTTGCCCTTCCTCATCGGAA-G-G-TG
* * * *
5446 CTTAAGTCTATTTTACCCAATTTGCCC-TCCCCTACCGGAAGGTG
1 -TT--GTCTAATTT--CCAGTTTGCCCTTCCTC-ATCGGAAGGTG
* * *
5490 TTGTTTAAATTCCCAGTTTGCCCTTCCTTATCGGAAGGTGTTG
1 TTGTCT-AATTTCCAGTTTGCCCTTCCTCATCGGAA-G-G-TG
* * ** * *
5533 TTTAAGTCTACTTTACCCAATTCACCCTTCCCCACCGGAAGGTG
1 -TT--GTCTAATTT--CCAGTTTGCCCTTCCTCATCGGAAGGTG
* * * *
5577 TTATGTAATTCCCAGTTTGCCCTTCCTCATCAGAAGGTG
1 TTGTCTAATTTCCAGTTTGCCCTTCCTCATCGGAAGGTG
* *
5616 TTGTCTAAGTCTACTTTACCTAATTTGCCCTTCCCCA-CTGGAAGGTG
1 TTGTCT-A----A-TTT-CC-AGTTTGCCCTTCCTCATC-GGAAGGTG
* *
5663 TGGTCTAATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTG
1 TTGTCTAATTTCCAGTTTGCCCTTCCTCATCGGAA-G-G-TG
* * * *
5705 ATTAAGTCTACTTTAACCAATTTGCCCTTCCCCACCGGAAGGTG
1 -TT--GTCTAATTT--CCAGTTTGCCCTTCCTCATCGGAAGGTG
* * * * *
5749 TTGTTTAAATCCCTAGTTTG-CCTGTCCTCACCAGAAGGTG
1 TTGTCTAATTTCC-AGTTTGCCCT-TCCTCATCGGAAGGTG
* * *
5789 TTGTTTAAGCTTACCAGTTTGACCC-TCCTCATCGAAAGGTG
1 TTGTCTAA--TTTCCAGTTTG-CCCTTCCTCATCGGAAGGTG
* *
5830 TTGT-TAAGTTTACTAGTTTGTCCTTCCTCATCGGAAGGTG
1 TTGTCTAA-TTT-CCAGTTTGCCCTTCCTCATCGGAAGGTG
* * * *
5870 TCGTTTAAGTTCACCAGTTTGCCTTTCCTCATCGGAAGGTG
1 TTGTCTAA-TT-TCCAGTTTGCCCTTCCTCATCGGAAGGTG
5911 TTGTCTACATTTCTCAGTTTGCCCT
1 TTGTCTA-ATTTC-CAGTTTGCCCT
5936 CCCTGTAGAC
Statistics
Matches: 438, Mismatches: 85, Indels: 112
0.69 0.13 0.18
Matches are distributed among these distances:
39 59 0.13
40 96 0.22
41 94 0.21
42 14 0.03
43 14 0.03
44 12 0.03
45 20 0.05
46 19 0.04
47 110 0.25
ACGTcount: A:0.19, C:0.26, G:0.18, T:0.36
Consensus pattern (39 bp):
TTGTCTAATTTCCAGTTTGCCCTTCCTCATCGGAAGGTG
Found at i:8338 original size:14 final size:15
Alignment explanation
Indices: 8319--8349 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
8309 TAAAAGAAAA
8319 TTCAAGTTTTT-ATT
1 TTCAAGTTTTTGATT
8333 TTCAAGTTTTTGATT
1 TTCAAGTTTTTGATT
8348 TT
1 TT
8350 TAAACGTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.19, C:0.06, G:0.10, T:0.65
Consensus pattern (15 bp):
TTCAAGTTTTTGATT
Found at i:13449 original size:2 final size:2
Alignment explanation
Indices: 13442--13478 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
13432 TTCCATTATG
13442 TA TA TA TA 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 TA TA TA TA T
13479 TCTACTGTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:13928 original size:13 final size:14
Alignment explanation
Indices: 13903--13933 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
13893 TTTTTTCAAA
13903 AAAAATGGTTTTTC
1 AAAAATGGTTTTTC
13917 AAAAATGG-TTTTC
1 AAAAATGGTTTTTC
13930 AAAA
1 AAAA
13934 TTTATTTCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.35
Consensus pattern (14 bp):
AAAAATGGTTTTTC
Found at i:15647 original size:37 final size:36
Alignment explanation
Indices: 15454--15793 Score: 257
Period size: 35 Copynumber: 9.5 Consensus size: 36
15444 ATTTCAGACG
* * *
15454 CTTCAGTTCATTTCAGTTGACCCAGGGCGGTC-TTT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
* * * * *
15489 ATTCAGTTTATTTTAGCTGACCCAGGGCGGTC-TTT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
* * * * *
15524 CTTCAATTCACTTCAATTGATCCAGGGCGATC-CTT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
* * * * * * * *
15559 ATTCAATTCATTTTAGTTGA-CCTAGGGTGGTCCTAT
1 CTTCAGTTTATTTCAGTTGATCC-AGGGCGATCTTTT
*
15595 -TTCAGTTTATTTCAGTTTGATCCAGGGTGATCTTTT
1 CTTCAGTTTATTTCAG-TTGATCCAGGGCGATCTTTT
* *
15631 CTTCATTTTACTTCAGTTGATCCAGGGCGATTCTTTTAT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGA-TC-TTT-T
*
15670 CTT-A-TTTATTTCAGTCGATCCAGGGCGATCTTTTTT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATC--TTTT
* * * *
15706 TTTCAATTTATTTCAATGGATCCAGGGCGATC-TTT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
*
15741 CTTCAGTTTATTTCAGTTGATCCAGGGTGATCTCTTT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCT-TTT
* *
15778 -TTAAGTTTGTTTCAGT
1 CTTCAGTTTATTTCAGT
15794 AGACCACAAA
Statistics
Matches: 249, Mismatches: 43, Indels: 25
0.79 0.14 0.08
Matches are distributed among these distances:
34 2 0.01
35 121 0.49
36 47 0.19
37 47 0.19
38 28 0.11
39 4 0.02
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.44
Consensus pattern (36 bp):
CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTT
Found at i:15779 original size:73 final size:73
Alignment explanation
Indices: 15594--15779 Score: 227
Period size: 73 Copynumber: 2.5 Consensus size: 73
15584 GGTGGTCCTA
* * * *
15594 TTTCAGTTTATTTCAGTTTGATCCAGGGTGA--TCTTTTCTTCATTTTACTTCAGTTGATCCAGG
1 TTTCAGTTTATTTCAG-TTGATCCAGGGTGATCTCTTTTTTTCAATTTACTTCAATGGATCCAGG
15657 GCGATTCTT
65 GCGATTCTT
* * * *
15666 TTATCTTA-TTTATTTCAGTCGATCCAGGGCGATCTTTTTTTTTCAATTTATTTCAATGGATCCA
1 TT-TC--AGTTTATTTCAGTTGATCCAGGGTGATCTCTTTTTTTCAATTTACTTCAATGGATCCA
15730 GGGCGA-TCTT
63 GGGCGATTCTT
15740 TCTTCAGTTTATTTCAGTTGATCCAGGGTGATCTCTTTTT
1 T-TTCAGTTTATTTCAGTTGATCCAGGGTGATCTCTTTTT
15780 AAGTTTGTTT
Statistics
Matches: 96, Mismatches: 11, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
72 3 0.03
73 44 0.46
74 17 0.18
75 32 0.33
ACGTcount: A:0.18, C:0.18, G:0.17, T:0.47
Consensus pattern (73 bp):
TTTCAGTTTATTTCAGTTGATCCAGGGTGATCTCTTTTTTTCAATTTACTTCAATGGATCCAGGG
CGATTCTT
Found at i:16082 original size:30 final size:30
Alignment explanation
Indices: 16048--16725 Score: 989
Period size: 30 Copynumber: 22.9 Consensus size: 30
16038 TTTTTGGTTG
*
16048 TTGCTTTATTTTAATCCTGTTTGAGGATCA
1 TTGCTTTATTTTAATCCTGGTTGAGGATCA
* * * *
16078 TTGCTTCATTTCAATCCTGGTTGAGGACCG
1 TTGCTTTATTTTAATCCTGGTTGAGGATCA
*
16108 TTGCTTTATTTTAATCCTGGTTGAGGATCG
1 TTGCTTTATTTTAATCCTGGTTGAGGATCA
* * *
16138 TTGCTTCATTTTAATCCTGTTTGAGGATCG
1 TTGCTTTATTTTAATCCTGGTTGAGGATCA
* *
16168 TTGCTTTA-TGTAATCCTGTTTGAGGATCA
1 TTGCTTTATTTTAATCCTGGTTGAGGATCA
16197 TTGCTTTATTTTAATCCTGGTTGAGGATCA
1 TTGCTTTATTTTAATCCTGGTTGAGGATCA
16227 TTGC-TTA-TTTAATCCTGGTTGAGGATCA
1 TTGCTTTATTTTAATCCTGGTTGAGGATCA
*
16255 TTGCTTTATTTTAATCCTGTTTGAGGATCA
1 TTGCTTTATTTTAATCCTGGTTGAGGATCA
*
16285 TTGCTATATTTTAATCCTGGTTGAGGATCA
1 TTGCTTTATTTTAATCCTGGTTGAGGATCA
16315 TTGCTTTATTTTAATCCTGGTTGAGGATCA
1 TTGCTTTATTTTAATCCTGGTTGAGGATCA
*
16345 TTGCTTTATTTTAATCCTGGTAGAGGATCA
1 TTGCTTTATTTTAATCCTGGTTGAGGATCA
*
16375 TCGCTTTATTTTAATCCTGGTTGAGGATCA
1 TTGCTTTATTTTAATCCTGGTTGAGGATCA
16405 TTGCTTTATTTTAATCCTGGTTGAGGATCA
1 TTGCTTTATTTTAATCCTGGTTGAGGATCA
16435 TTGCTTTATTTTAATCCTGGTTGAGGATCA
1 TTGCTTTATTTTAATCCTGGTTGAGGATCA
*
16465 TTGCTTTATTTTAATCCTGGTAGAGGATCA
1 TTGCTTTATTTTAATCCTGGTTGAGGATCA
*
16495 TCGCTTTATTTTAATCCTGGTTGAGGATCA
1 TTGCTTTATTTTAATCCTGGTTGAGGATCA
*
16525 TTGCTTTGTTTTAATCCTGGTTGAGGATCA
1 TTGCTTTATTTTAATCCTGGTTGAGGATCA
* **
16555 TTGCTTTATTTTAATCTTGGTTGAATATCA
1 TTGCTTTATTTTAATCCTGGTTGAGGATCA
* *
16585 TTGATTTATTTTAATCCTGGTTTAGGATCA
1 TTGCTTTATTTTAATCCTGGTTGAGGATCA
16615 TTG-TTTATTTTAATCCTGGTT----A--A
1 TTGCTTTATTTTAATCCTGGTTGAGGATCA
* * * *
16638 TTGCTTCATTCTAATCCTGGATGAAGATCA
1 TTGCTTTATTTTAATCCTGGTTGAGGATCA
* *
16668 ATGCTTTATTTTAATCCTGGTTGACGATCA
1 TTGCTTTATTTTAATCCTGGTTGAGGATCA
* * * *
16698 GTGCTTTATTTCAATCCTGATTTAGGAT
1 TTGCTTTATTTTAATCCTGGTTGAGGAT
16726 TATCACTCTA
Statistics
Matches: 588, Mismatches: 50, Indels: 20
0.89 0.08 0.03
Matches are distributed among these distances:
23 4 0.01
24 15 0.03
25 1 0.00
28 26 0.04
29 51 0.09
30 491 0.84
ACGTcount: A:0.21, C:0.14, G:0.19, T:0.46
Consensus pattern (30 bp):
TTGCTTTATTTTAATCCTGGTTGAGGATCA
Done.