Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012990.1 Corchorus capsularis cultivar CVL-1 contig13011, 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: 8263
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Found at i:4619 original size:37 final size:36
Alignment explanation
Indices: 4564--5088 Score: 174
Period size: 38 Copynumber: 15.6 Consensus size: 36
4554 ATCAAAAGTT
4564 GACTGGAAACAGGTCATCTTTCAACACTTATCAAGATC
1 GACT-GAAACAGGTCATCTTTCAACA-TTATCAAGATC
*
4602 GACT-AAATCAGGTCATCTTTCAGCAGTTATCAAGATC
1 GACTGAAA-CAGGTCATCTTTCAACA-TTATCAAGATC
*
4639 GACTGGAAACAGGTCATGTTTCAA-ATTATC-AGA--
1 GACT-GAAACAGGTCATCTTTCAACATTATCAAGATC
** **
4672 G---G--TTA--TC-T-TTCAACA-ATTATCAAGATC
1 GACTGAAACAGGTCATCTTTCA-ACATTATCAAGATC
** * *
4699 GAGGGGAACAGGTCATCTTTCAGCAGTTATCAAGATC
1 GACTGAAACAGGTCATCTTTCAACA-TTATCAAGATC
4736 GACTGGAAACAGGTCATCTTTCAA-ATTATC-AGA--
1 GACT-GAAACAGGTCATCTTTCAACATTATCAAGATC
* **
4769 G-GTG----A--TC-T-TTCAACA-ATTATCAAGATC
1 GACTGAAACAGGTCATCTTTCA-ACATTATCAAGATC
* * *
4796 GATTGGAAACAGGTCATCTTTTAGCAGTTATCAAGATC
1 GACT-GAAACAGGTCATCTTTCAACA-TTATCAAGATC
4834 GACTGGAAACAGGTCATCTTTCAA-ATTATCAA-A--
1 GACT-GAAACAGGTCATCTTTCAACATTATCAAGATC
** ** *
4867 G---G--TTA--TC-T-TTCAACA-ATTCTCAAGATC
1 GACTGAAACAGGTCATCTTTCA-ACATTATCAAGATC
4894 GACTGGAAACAGGTCATCTTTCAACAGTTATCAAGATC
1 GACT-GAAACAGGTCATCTTTCAACA-TTATCAAGATC
4932 GACTGGAAACAGGTCATCTTTCAA-ATTATC-AGA--
1 GACT-GAAACAGGTCATCTTTCAACATTATCAAGATC
** ** *
4965 G---G--TTA--TC-T-TTCAACA-ATTATCAAGATT
1 GACTGAAACAGGTCATCTTTCA-ACATTATCAAGATC
* * * *
4992 GACTGGAAACAAGTCATCTTTCAGCACTTGTCAAGTTC
1 GACT-GAAACAGGTCATCTTTCAACA-TTATCAAGATC
5030 GACTGGAAACAGGTCATCTTTCAACAGTTATCAAGATC
1 GACT-GAAACAGGTCATCTTTCAACA-TTATCAAGATC
*
5068 GACTGGAAATAGGTCATCTTT
1 GACT-GAAACAGGTCATCTTT
5089 TAGCAGTTTT
Statistics
Matches: 365, Mismatches: 55, Indels: 134
0.66 0.10 0.24
Matches are distributed among these distances:
23 12 0.03
24 33 0.09
25 18 0.05
27 8 0.02
28 1 0.00
29 4 0.01
30 1 0.00
31 3 0.01
32 2 0.01
33 7 0.02
34 2 0.01
35 17 0.05
36 33 0.09
37 60 0.16
38 161 0.44
39 3 0.01
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (36 bp):
GACTGAAACAGGTCATCTTTCAACATTATCAAGATC
Found at i:4661 original size:38 final size:38
Alignment explanation
Indices: 4564--4669 Score: 148
Period size: 37 Copynumber: 2.9 Consensus size: 38
4554 ATCAAAAGTT
4564 GACTGGAAACAGGTCATCTTTCAACACTTATCAAGATC
1 GACTGGAAACAGGTCATCTTTCAACACTTATCAAGATC
* *
4602 GACT--AAATCAGGTCATCTTTCAGCAGTTATCAAGATC
1 GACTGGAAA-CAGGTCATCTTTCAACACTTATCAAGATC
*
4639 GACTGGAAACAGGTCATGTTTCAA-A-TTATCA
1 GACTGGAAACAGGTCATCTTTCAACACTTATCA
4670 GAGGTTATCT
Statistics
Matches: 61, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
36 9 0.15
37 32 0.52
38 17 0.28
39 3 0.05
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (38 bp):
GACTGGAAACAGGTCATCTTTCAACACTTATCAAGATC
Found at i:4756 original size:38 final size:37
Alignment explanation
Indices: 4671--4766 Score: 124
Period size: 37 Copynumber: 2.6 Consensus size: 37
4661 AAATTATCAG
* *
4671 AGGTTATCTTTCAACAATTATCAAGATCGAGGGGAAC
1 AGGTCATCTTTCAACAATTATCAAGATCGAGGGAAAC
* * *
4708 AGGTCATCTTTCAGCAGTTATCAAGATCGACTGGAAAC
1 AGGTCATCTTTCAACAATTATCAAGATCGA-GGGAAAC
4746 AGGTCATCTTTC-A-AATTATCA
1 AGGTCATCTTTCAACAATTATCA
4767 GAGGTGATCT
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
36 7 0.14
37 27 0.53
38 17 0.33
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (37 bp):
AGGTCATCTTTCAACAATTATCAAGATCGAGGGAAAC
Found at i:4776 original size:22 final size:24
Alignment explanation
Indices: 4746--4790 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
4736 GACTGGAAAC
4746 AGGTCATCTTTC-A-AATTATCAG
1 AGGTCATCTTTCAACAATTATCAG
*
4768 AGGTGATCTTTCAACAATTATCA
1 AGGTCATCTTTCAACAATTATCA
4791 AGATCGATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 11 0.55
23 1 0.05
24 8 0.40
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (24 bp):
AGGTCATCTTTCAACAATTATCAG
Found at i:4849 original size:98 final size:98
Alignment explanation
Indices: 4574--5062 Score: 786
Period size: 98 Copynumber: 5.0 Consensus size: 98
4564 GACTGGAAAC
* *
4574 AGGTCATCTTTCAACACTTATCAAGATCGACT--AAATCAGGTCATCTTTCAGCAGTTATCAAGA
1 AGGTTATCTTTCAACAATTATCAAGATCGACTGGAAA-CAGGTCATCTTTCAGCAGTTATCAAGA
*
4637 TCGACTGGAAACAGGTCATGTTTCAAATTATCAG
65 TCGACTGGAAACAGGTCATCTTTCAAATTATCAG
* *
4671 AGGTTATCTTTCAACAATTATCAAGATCGA-GGGGAACAGGTCATCTTTCAGCAGTTATCAAGAT
1 AGGTTATCTTTCAACAATTATCAAGATCGACTGGAAACAGGTCATCTTTCAGCAGTTATCAAGAT
4735 CGACTGGAAACAGGTCATCTTTCAAATTATCAG
66 CGACTGGAAACAGGTCATCTTTCAAATTATCAG
* * *
4768 AGGTGATCTTTCAACAATTATCAAGATCGATTGGAAACAGGTCATCTTTTAGCAGTTATCAAGAT
1 AGGTTATCTTTCAACAATTATCAAGATCGACTGGAAACAGGTCATCTTTCAGCAGTTATCAAGAT
*
4833 CGACTGGAAACAGGTCATCTTTCAAATTATCAA
66 CGACTGGAAACAGGTCATCTTTCAAATTATCAG
* *
4866 AGGTTATCTTTCAACAATTCTCAAGATCGACTGGAAACAGGTCATCTTTCAACAGTTATCAAGAT
1 AGGTTATCTTTCAACAATTATCAAGATCGACTGGAAACAGGTCATCTTTCAGCAGTTATCAAGAT
4931 CGACTGGAAACAGGTCATCTTTCAAATTATCAG
66 CGACTGGAAACAGGTCATCTTTCAAATTATCAG
* * * * *
4964 AGGTTATCTTTCAACAATTATCAAGATTGACTGGAAACAAGTCATCTTTCAGCACTTGTCAAGTT
1 AGGTTATCTTTCAACAATTATCAAGATCGACTGGAAACAGGTCATCTTTCAGCAGTTATCAAGAT
5029 CGACTGGAAACAGGTCATCTTTCAACAGTTATCA
66 CGACTGGAAACAGGTCATCTTTCAA-A-TTATCA
5063 AGATCGACTG
Statistics
Matches: 364, Mismatches: 23, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
97 117 0.32
98 240 0.66
99 1 0.00
100 6 0.02
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30
Consensus pattern (98 bp):
AGGTTATCTTTCAACAATTATCAAGATCGACTGGAAACAGGTCATCTTTCAGCAGTTATCAAGAT
CGACTGGAAACAGGTCATCTTTCAAATTATCAG
Found at i:4875 original size:60 final size:62
Alignment explanation
Indices: 4806--4927 Score: 185
Period size: 60 Copynumber: 2.0 Consensus size: 62
4796 GATTGGAAAC
* * *
4806 AGGTCATCTTTTAGCAGTTATCAAGATCGACTGGAAACAGGTCATCTTTCAA-A-TTATCAA
1 AGGTCATCTTTCAACAATTATCAAGATCGACTGGAAACAGGTCATCTTTCAACAGTTATCAA
* *
4866 AGGTTATCTTTCAACAATTCTCAAGATCGACTGGAAACAGGTCATCTTTCAACAGTTATCAA
1 AGGTCATCTTTCAACAATTATCAAGATCGACTGGAAACAGGTCATCTTTCAACAGTTATCAA
4928 GATCGACTGG
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
60 47 0.85
61 1 0.02
62 7 0.13
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.31
Consensus pattern (62 bp):
AGGTCATCTTTCAACAATTATCAAGATCGACTGGAAACAGGTCATCTTTCAACAGTTATCAA
Found at i:4925 original size:136 final size:137
Alignment explanation
Indices: 4768--5096 Score: 361
Period size: 136 Copynumber: 2.4 Consensus size: 137
4758 AAATTATCAG
* * *
4768 AGGTGATCTTTCAACAATTATCAAGATCGATTGGAAACAGGTCATCTTTTAGCAGTTATCA-AGA
1 AGGTCATCTTTCAACAGTTATCAAGATCGACTGGAAACAGGTCATCTTTTAGCAGTTATCAGAGA
* * * *
4832 TCGA-CTGGAAACAGGTCATCTTTCAA-ATT-A-T-CAA-AGGTTATCTTTCAACAATTCTCAAG
66 T-GATCTGGAAACA----AT-TATCAAGATTGACTGAAACAAGTCATCTTTCAACAATTCTCAAG
4891 ATCGACTGGAAAC
125 ATCGACTGGAAAC
* * *
4904 AGGTCATCTTTCAACAGTTATCAAGATCGACTGGAAACAGGTCATCTTTCA--AATTATCAGAGG
1 AGGTCATCTTTCAACAGTTATCAAGATCGACTGGAAACAGGTCATCTTTTAGCAGTTATCAGAGA
* *** * * * *
4967 TTATCTTTCAACAATTATCAAGATTGACTGGAAACAAGTCATCTTTCAGCACTTGTCAAGTTCGA
66 TGATCTGGAAACAATTATCAAGATTGACT-GAAACAAGTCATCTTTCAACAATTCTCAAGATCGA
5032 CTGGAAAC
130 CTGGAAAC
*
5040 AGGTCATCTTTCAACAGTTATCAAGATCGACTGGAAATAGGTCATCTTTTAGCAGTT
1 AGGTCATCTTTCAACAGTTATCAAGATCGACTGGAAACAGGTCATCTTTTAGCAGTT
5097 TTCGGTTGCT
Statistics
Matches: 162, Mismatches: 21, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
130 5 0.03
131 5 0.03
132 1 0.01
133 1 0.01
134 8 0.05
135 11 0.07
136 128 0.79
138 3 0.02
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (137 bp):
AGGTCATCTTTCAACAGTTATCAAGATCGACTGGAAACAGGTCATCTTTTAGCAGTTATCAGAGA
TGATCTGGAAACAATTATCAAGATTGACTGAAACAAGTCATCTTTCAACAATTCTCAAGATCGAC
TGGAAAC
Found at i:4972 original size:22 final size:24
Alignment explanation
Indices: 4942--4986 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
4932 GACTGGAAAC
4942 AGGTCATCTTTC-A-AATTATCAG
1 AGGTCATCTTTCAACAATTATCAG
*
4964 AGGTTATCTTTCAACAATTATCA
1 AGGTCATCTTTCAACAATTATCA
4987 AGATTGACTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 11 0.55
23 1 0.05
24 8 0.40
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (24 bp):
AGGTCATCTTTCAACAATTATCAG
Found at i:5148 original size:17 final size:17
Alignment explanation
Indices: 5126--5174 Score: 66
Period size: 16 Copynumber: 2.9 Consensus size: 17
5116 GGCACTTCAG
*
5126 CAACTTTTCAGCTTTTA
1 CAACTTTTCAGCATTTA
5143 CAACTTTTTCA--ATTTA
1 CAAC-TTTTCAGCATTTA
5159 CAACTTTTCAGCATTT
1 CAACTTTTCAGCATTT
5175 CAATTTACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
15 6 0.21
16 8 0.29
17 8 0.29
18 6 0.21
ACGTcount: A:0.27, C:0.22, G:0.04, T:0.47
Consensus pattern (17 bp):
CAACTTTTCAGCATTTA
Found at i:5455 original size:143 final size:142
Alignment explanation
Indices: 5185--5487 Score: 405
Period size: 143 Copynumber: 2.1 Consensus size: 142
5175 CAATTTACAA
* * *
5185 CTTTCCTCACATCCATGTGAGTCAGAAATCCTTCGACCCAAGTTGGTCCTTCCTCACTTCCATGT
1 CTTTCCTCACTTCCATGCGAGCCAGAAATCCTTCGACCCAAGTTGGTCCTTCCTCACTTCCATGT
* * * *
5250 GAGTCAGAAATCGTTTCGACCCAAGTTGGTCTTTCCTCAGTTCCATGTGAGTCAGAAATCCTTCG
66 GAGTCAGAAATCCTTCCCACCCAAGTTGGTCTTTCCTCACTTCCATGTGAGTCAGAAATCCTTCG
5315 ACCCA-AGTTGGT
131 A-CCATAGTTGGT
* * * *
5327 GTTTCCTCACTTCCATGCGAGCCAGTAATCCTTCCGACCCAAGTTGGTCTTTCGTCACTTCCATG
1 CTTTCCTCACTTCCATGCGAGCCAGAAATCCTT-CGACCCAAGTTGGTCCTTCCTCACTTCCATG
* * **
5392 TGAGTCAGGAATCCTTCCCACCCAAGTTGGTGTTTCCTCACTTCCATGTGAGTCA-ACGGTCCTT
65 TGAGTCAGAAATCCTTCCCACCCAAGTTGGTCTTTCCTCACTTCCATGTGAGTCAGA-AATCCTT
5456 CGACCATAGTTGGT
129 CGACCATAGTTGGT
*
5470 CTTAT-CTCACTTCTATGC
1 CTT-TCCTCACTTCCATGC
5488 AAAGTTACAA
Statistics
Matches: 140, Mismatches: 17, Indels: 7
0.85 0.10 0.04
Matches are distributed among these distances:
142 32 0.23
143 107 0.76
144 1 0.01
ACGTcount: A:0.20, C:0.30, G:0.18, T:0.32
Consensus pattern (142 bp):
CTTTCCTCACTTCCATGCGAGCCAGAAATCCTTCGACCCAAGTTGGTCCTTCCTCACTTCCATGT
GAGTCAGAAATCCTTCCCACCCAAGTTGGTCTTTCCTCACTTCCATGTGAGTCAGAAATCCTTCG
ACCATAGTTGGT
Found at i:5456 original size:48 final size:48
Alignment explanation
Indices: 5185--5446 Score: 393
Period size: 48 Copynumber: 5.5 Consensus size: 48
5175 CAATTTACAA
*
5185 CTTTCCTCACATCCATGTGAGTCAGAAATCCTT-CGACCCAAGTTGGT
1 CTTTCCTCACTTCCATGTGAGTCAGAAATCCTTCCGACCCAAGTTGGT
* * *
5232 CCTTCCTCACTTCCATGTGAGTCAGAAATCGTTTCGACCCAAGTTGGT
1 CTTTCCTCACTTCCATGTGAGTCAGAAATCCTTCCGACCCAAGTTGGT
*
5280 CTTTCCTCAGTTCCATGTGAGTCAGAAATCCTT-CGACCCAAGTTGGT
1 CTTTCCTCACTTCCATGTGAGTCAGAAATCCTTCCGACCCAAGTTGGT
* * * *
5327 GTTTCCTCACTTCCATGCGAGCCAGTAATCCTTCCGACCCAAGTTGGT
1 CTTTCCTCACTTCCATGTGAGTCAGAAATCCTTCCGACCCAAGTTGGT
* * *
5375 CTTTCGTCACTTCCATGTGAGTCAGGAATCCTTCCCACCCAAGTTGGT
1 CTTTCCTCACTTCCATGTGAGTCAGAAATCCTTCCGACCCAAGTTGGT
*
5423 GTTTCCTCACTTCCATGTGAGTCA
1 CTTTCCTCACTTCCATGTGAGTCA
5447 ACGGTCCTTC
Statistics
Matches: 194, Mismatches: 19, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
47 72 0.37
48 122 0.63
ACGTcount: A:0.20, C:0.30, G:0.18, T:0.31
Consensus pattern (48 bp):
CTTTCCTCACTTCCATGTGAGTCAGAAATCCTTCCGACCCAAGTTGGT
Found at i:5460 original size:95 final size:93
Alignment explanation
Indices: 5185--5482 Score: 393
Period size: 95 Copynumber: 3.1 Consensus size: 93
5175 CAATTTACAA
* **
5185 CTTTCCTCACATCCATGTGAGTCAGAAATCCTTCGACCCAAGTTGGTCCTTCCTCACTTCCATGT
1 CTTTCCTCACTTCCATGTGAGTCAGAAATCCTTCGACCCAAGTTGGTGTTTCCTCACTTCCATGT
*
5250 GAGTCAGAAATCGTTTCGACCCAAGTTGGT
66 GAGTCA-AAATC-CTTCGACCCAAGTTGGT
* *
5280 CTTTCCTCAGTTCCATGTGAGTCAGAAATCCTTCGACCCAAGTTGGTGTTTCCTCACTTCCATGC
1 CTTTCCTCACTTCCATGTGAGTCAGAAATCCTTCGACCCAAGTTGGTGTTTCCTCACTTCCATGT
* *
5345 GAGCCAGTAATCCTTCCGACCCAAGTTGGT
66 GAGTCA-AAATCCTT-CGACCCAAGTTGGT
* * *
5375 CTTTCGTCACTTCCATGTGAGTCAGGAATCCTTCCCACCCAAGTTGGTGTTTCCTCACTTCCATG
1 CTTTCCTCACTTCCATGTGAGTCAGAAATCCTT-CGACCCAAGTTGGTGTTTCCTCACTTCCATG
**
5440 TGAGTCAACGGTCCTTCGA-CCATAGTTGGT
65 TGAGTCAA-AATCCTTCGACCCA-AGTTGGT
5470 CTTAT-CTCACTTC
1 CTT-TCCTCACTTC
5483 TATGCAAAGT
Statistics
Matches: 180, Mismatches: 18, Indels: 10
0.87 0.09 0.05
Matches are distributed among these distances:
94 5 0.03
95 134 0.74
96 41 0.23
ACGTcount: A:0.20, C:0.30, G:0.18, T:0.32
Consensus pattern (93 bp):
CTTTCCTCACTTCCATGTGAGTCAGAAATCCTTCGACCCAAGTTGGTGTTTCCTCACTTCCATGT
GAGTCAAAATCCTTCGACCCAAGTTGGT
Found at i:5508 original size:47 final size:47
Alignment explanation
Indices: 5457--5563 Score: 144
Period size: 47 Copynumber: 2.3 Consensus size: 47
5447 ACGGTCCTTC
* *
5457 GACCATAGTTGGTCTTATCTCACTTCTATGCAAAGT-TACAATTTGGT
1 GACCACAGTTGGTCTTATCTCACTTCCATGC-AAGTCTACAATTTGGT
* * * *
5504 GACCACAGTCGGTCTTTTCTCGCTTCCATGCGAGTCTACAATTTGGT
1 GACCACAGTTGGTCTTATCTCACTTCCATGCAAGTCTACAATTTGGT
5551 GACCACAGTTGGT
1 GACCACAGTTGGT
5564 TTCCTTCAGC
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
46 3 0.06
47 49 0.94
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.35
Consensus pattern (47 bp):
GACCACAGTTGGTCTTATCTCACTTCCATGCAAGTCTACAATTTGGT
Found at i:5626 original size:33 final size:32
Alignment explanation
Indices: 5588--6010 Score: 161
Period size: 33 Copynumber: 13.2 Consensus size: 32
5578 TCAGTTTCTC
*
5588 TTCAAAGTTGACCTCAGACAGGTCTTTCTCAAT
1 TTCAAA-TCGACCTCAGACAGGTCTTTCTCAAT
* * *
5621 TTCAAAAGCGACCACAGACTGGTCTCTTTCTCAGAT
1 TTC-AAATCGACCTCAGACAGG--TCTTTCTCA-AT
* *
5657 ATTCAATTTCAGAGCTCAGACAGGTCTTTCTCAAT
1 -TTCAA-ATC-GACCTCAGACAGGTCTTTCTCAAT
* * * *
5692 TTCAATATCGACCACGGACTGGTCTTTTTCAAT
1 TTCAA-ATCGACCTCAGACAGGTCTTTCTCAAT
*
5725 TTC--A--GACCTCAGACAGGTCTTTCTCAGT
1 TTCAAATCGACCTCAGACAGGTCTTTCTCAAT
* * * *
5753 TTCTAGAGTCGATCACAGACTGGTC-TTCTTCAAT
1 TTC-A-AATCGACCTCAGACAGGTCTTTC-TCAAT
* * * *
5787 TT----TAGACTTCCGACAGGTCTTTCCCAAT
1 TTCAAATCGACCTCAGACAGGTCTTTCTCAAT
* *
5815 TTCAATATCGACCACAGACTGGTC-TTCTTCAACT
1 TTCAA-ATCGACCTCAGACAGGTCTTTC-TCAA-T
* * *
5849 TT---A--GACTTCAGACAGGTCTTTCTTAGTT
1 TTCAAATCGACCTCAGACAGGTCTTTCTCA-AT
** * * *
5877 TTCTATTTCATACCTTAGACAGGTCTTTCCCAAT
1 TTC-AAATC-GACCTCAGACAGGTCTTTCTCAAT
* *
5911 TTCAATATCGACCACAGACTGGTC-TTCTTCAACT
1 TTCAA-ATCGACCTCAGACAGGTCTTTC-TCAA-T
* *
5945 TT---A--GACCTCAGACAGGTCTTTCTTAGTT
1 TTCAAATCGACCTCAGACAGGTCTTTCTCA-AT
* *
5973 TTCAAAGTTGACC-CTAGACGGGTCTTTCTCAAT
1 TTCAAA-TCGACCTC-AGACAGGTCTTTCTCAAT
6006 TTCAA
1 TTCAA
6011 TGTCGACCAT
Statistics
Matches: 283, Mismatches: 64, Indels: 86
0.65 0.15 0.20
Matches are distributed among these distances:
28 74 0.26
29 9 0.03
30 3 0.01
31 1 0.00
32 6 0.02
33 76 0.27
34 59 0.21
35 28 0.10
36 13 0.05
37 4 0.01
38 10 0.04
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (32 bp):
TTCAAATCGACCTCAGACAGGTCTTTCTCAAT
Found at i:5743 original size:28 final size:28
Alignment explanation
Indices: 5658--5869 Score: 93
Period size: 28 Copynumber: 7.0 Consensus size: 28
5648 TTCTCAGATA
*
5658 TTCAATTTCAGAGCTCAGACAGGTCTTT
1 TTCAATTTCAGACCTCAGACAGGTCTTT
* * * *
5686 CTCAATTTCAATATCGACCACGGACTGGTCTTT
1 TTCAATTTC---A--GACCTCAGACAGGTCTTT
5719 TTCAATTTCAGACCTCAGACAGGTCTTT
1 TTCAATTTCAGACCTCAGACAGGTCTTT
* * * * *
5747 CTCAGTTTCTAGAGTCGATCACAGACTGGTCTTC
1 TTCAATTTC-AGA--C---CTCAGACAGGTCTTT
* * *
5781 TTCAATTTTAGACTTCCGACAGGTCTTT
1 TTCAATTTCAGACCTCAGACAGGTCTTT
** * * *
5809 CCCAATTTCAATATCGACCACAGACTGGTCTTC
1 TTCAATTTC---A--GACCTCAGACAGGTCTTT
*
5842 TTCAACTTT-AGACTTCAGACAGGTCTTT
1 TTCAA-TTTCAGACCTCAGACAGGTCTTT
5870 CTTAGTTTTC
Statistics
Matches: 131, Mismatches: 36, Indels: 34
0.65 0.18 0.17
Matches are distributed among these distances:
28 60 0.46
29 3 0.02
30 2 0.02
31 4 0.03
33 41 0.31
34 21 0.16
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.35
Consensus pattern (28 bp):
TTCAATTTCAGACCTCAGACAGGTCTTT
Found at i:5846 original size:61 final size:61
Alignment explanation
Indices: 5658--5871 Score: 297
Period size: 61 Copynumber: 3.5 Consensus size: 61
5648 TTCTCAGATA
* *
5658 TTCAATTTCAGAGC-TCAGACAGGTCTTTCTCAATTTCAATATCGACCACGGACTGGTCTTT
1 TTCAATTTCAGA-CTTCAGACAGGTCTTTCTCAATTTCAATATCGACCACAGACTGGTCTTC
* * * * *
5719 TTCAATTTCAGACCTCAGACAGGTCTTTCTCAGTTTCTAGAGTCGATCACAGACTGGTCTTC
1 TTCAATTTCAGACTTCAGACAGGTCTTTCTCAATTTCAATA-TCGACCACAGACTGGTCTTC
* * *
5781 TTCAATTTTAGACTTCCGACAGGTCTTTCCCAATTTCAATATCGACCACAGACTGGTCTTC
1 TTCAATTTCAGACTTCAGACAGGTCTTTCTCAATTTCAATATCGACCACAGACTGGTCTTC
5842 TTCAACTTT-AGACTTCAGACAGGTCTTTCT
1 TTCAA-TTTCAGACTTCAGACAGGTCTTTCT
5872 TAGTTTTCTA
Statistics
Matches: 134, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
60 1 0.01
61 79 0.59
62 54 0.40
ACGTcount: A:0.24, C:0.26, G:0.15, T:0.35
Consensus pattern (61 bp):
TTCAATTTCAGACTTCAGACAGGTCTTTCTCAATTTCAATATCGACCACAGACTGGTCTTC
Found at i:5899 original size:96 final size:95
Alignment explanation
Indices: 5798--6041 Score: 359
Period size: 96 Copynumber: 2.6 Consensus size: 95
5788 TTAGACTTCC
*
5798 GACAGGTCTTTCCCAATTTCAATATCGACCACAGACTGGTCTTCTTCAACTTTAGACTTCAGACA
1 GACAGGTCTTTCCCAATTTCAATATCGACCACAGACTGGTCTTCTTCAACTTTAGACCTCAGACA
* * * *
5863 GGTCTTTCTTAGTTTTC-TATTTCATACCTTA
66 GGTCTTTCTTAGTTTTCAAAGTT--GACCCTA
5894 GACAGGTCTTTCCCAATTTCAATATCGACCACAGACTGGTCTTCTTCAACTTTAGACCTCAGACA
1 GACAGGTCTTTCCCAATTTCAATATCGACCACAGACTGGTCTTCTTCAACTTTAGACCTCAGACA
5959 GGTCTTTCTTAGTTTTCAAAGTTGACCCTA
66 GGTCTTTCTTAGTTTTCAAAGTTGACCCTA
* * * * *
5989 GACGGGTCTTTCTCAATTTCAATGTCGACCATAGACTGGTC--CTTCAATTTTAG
1 GACAGGTCTTTCCCAATTTCAATATCGACCACAGACTGGTCTTCTTCAACTTTAG
6042 CATCAGTAAT
Statistics
Matches: 137, Mismatches: 10, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
93 11 0.08
95 42 0.31
96 81 0.59
97 3 0.02
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.36
Consensus pattern (95 bp):
GACAGGTCTTTCCCAATTTCAATATCGACCACAGACTGGTCTTCTTCAACTTTAGACCTCAGACA
GGTCTTTCTTAGTTTTCAAAGTTGACCCTA
Found at i:6024 original size:33 final size:34
Alignment explanation
Indices: 5954--6029 Score: 82
Period size: 33 Copynumber: 2.3 Consensus size: 34
5944 TTTAGACCTC
* * * *
5954 AGACAGGTCTTTCTTAGTTTTCAAAGTTGACCCT
1 AGACAGGTCTTTCTCAGATTTCAAAGTCGACCAT
* *
5988 AGACGGGTCTTTCTCA-ATTTCAATGTCGACCAT
1 AGACAGGTCTTTCTCAGATTTCAAAGTCGACCAT
*
6021 AGACTGGTC
1 AGACAGGTC
6030 CTTCAATTTT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
33 21 0.60
34 14 0.40
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (34 bp):
AGACAGGTCTTTCTCAGATTTCAAAGTCGACCAT
Found at i:7116 original size:21 final size:21
Alignment explanation
Indices: 7092--7133 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
7082 AAAGTTCTAG
* *
7092 CAAAATTGAACTTGTCACCAA
1 CAAAATTGAACCTATCACCAA
7113 CAAAATTGAACCTATCACCAA
1 CAAAATTGAACCTATCACCAA
7134 TATATATTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.45, C:0.26, G:0.07, T:0.21
Consensus pattern (21 bp):
CAAAATTGAACCTATCACCAA
Found at i:7728 original size:19 final size:19
Alignment explanation
Indices: 7704--7742 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
7694 CATTCATCAC
7704 ACAAGCATTTCACATTAGT
1 ACAAGCATTTCACATTAGT
*
7723 ACAAGCATTTTACATTAGT
1 ACAAGCATTTCACATTAGT
7742 A
1 A
7743 TTAGGTTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.33
Consensus pattern (19 bp):
ACAAGCATTTCACATTAGT
Done.