Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014873.1 Corchorus capsularis cultivar CVL-1 contig14894, 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: 16912
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:3749 original size:8 final size:8
Alignment explanation
Indices: 3736--3774 Score: 60
Period size: 8 Copynumber: 4.9 Consensus size: 8
3726 TTTTGTTCGT
3736 CGGTTTGG
1 CGGTTTGG
*
3744 CGGTTTGA
1 CGGTTTGG
*
3752 CGGTTTAG
1 CGGTTTGG
3760 CGGTTTGG
1 CGGTTTGG
3768 CGGTTTG
1 CGGTTTG
3775 AACCGCCAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.05, C:0.13, G:0.44, T:0.38
Consensus pattern (8 bp):
CGGTTTGG
Found at i:3902 original size:19 final size:20
Alignment explanation
Indices: 3875--3934 Score: 61
Period size: 19 Copynumber: 3.1 Consensus size: 20
3865 TATATAATTA
* *
3875 AATATATATGTTATATATAT
1 AATATATATCTAATATATAT
3895 AATA-ATATCTAATATATAT
1 AATATATATCTAATATATAT
* * *
3914 AAT-TATCTATACTATATAT
1 AATATATATCTAATATATAT
3933 AA
1 AA
3935 AAGTACGAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
19 30 0.88
20 4 0.12
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (20 bp):
AATATATATCTAATATATAT
Found at i:3911 original size:17 final size:17
Alignment explanation
Indices: 3860--3934 Score: 65
Period size: 14 Copynumber: 4.7 Consensus size: 17
3850 AACCGTTTAG
3860 TAATATATATAATTA--
1 TAATATATATAATTATC
* *
3875 -AATATATAT-GTTATA
1 TAATATATATAATTATC
3890 T-ATATA-ATAA-TATC
1 TAATATATATAATTATC
3904 TAATATATATAATTATC
1 TAATATATATAATTATC
3921 TATACTATATATAA
1 TA-A-TATATATAA
3935 AAGTACGAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 14
0.74 0.05 0.22
Matches are distributed among these distances:
13 3 0.06
14 15 0.31
15 10 0.21
16 4 0.08
17 6 0.12
18 1 0.02
19 9 0.19
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (17 bp):
TAATATATATAATTATC
Found at i:4014 original size:30 final size:30
Alignment explanation
Indices: 3958--4019 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 30
3948 GGGAAATTTT
*
3958 ATGTTTTCCGATTGTACCCTTTTTTTTAAA
1 ATGTTTTCCAATTGTACCCTTTTTTTTAAA
3988 ATGTATTTCCAATTGTACCCTTTTTTTTAAA
1 ATGT-TTTCCAATTGTACCCTTTTTTTTAAA
4019 A
1 A
4020 CATATTTCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 4 0.13
31 26 0.87
ACGTcount: A:0.24, C:0.16, G:0.08, T:0.52
Consensus pattern (30 bp):
ATGTTTTCCAATTGTACCCTTTTTTTTAAA
Found at i:4026 original size:31 final size:31
Alignment explanation
Indices: 3962--4027 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
3952 AATTTTATGT
* **
3962 TTTCCGATTGTACCCTTTTTTTTAAAATGTA
1 TTTCCAATTGTACCCTTTTTTTTAAAACATA
3993 TTTCCAATTGTACCCTTTTTTTTAAAACATA
1 TTTCCAATTGTACCCTTTTTTTTAAAACATA
4024 TTTC
1 TTTC
4028 TAAATTACCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.24, C:0.18, G:0.06, T:0.52
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTTTTTTTAAAACATA
Found at i:4087 original size:19 final size:20
Alignment explanation
Indices: 4051--4090 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
4041 CTTAATAATA
**
4051 TTTTTAATTATTCCATTATT
1 TTTTTAATTATTAAATTATT
4071 TTTTTAATTA-TAAATTATT
1 TTTTTAATTATTAAATTATT
4090 T
1 T
4091 CATTATATCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTTTAATTATTAAATTATT
Found at i:4165 original size:22 final size:22
Alignment explanation
Indices: 4140--4224 Score: 143
Period size: 22 Copynumber: 3.9 Consensus size: 22
4130 TCCATGAAGA
*
4140 GGTTATCAAAATTTCATAGTGT
1 GGTTACCAAAATTTCATAGTGT
*
4162 GGTTACCAAAATTTCATAGTCT
1 GGTTACCAAAATTTCATAGTGT
*
4184 GGTTACCAAAATTTCATAGAGT
1 GGTTACCAAAATTTCATAGTGT
4206 GGTTACCAAAATTTCATAG
1 GGTTACCAAAATTTCATAG
4225 GATCAGGTTA
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 59 1.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.35
Consensus pattern (22 bp):
GGTTACCAAAATTTCATAGTGT
Found at i:4188 original size:44 final size:46
Alignment explanation
Indices: 4139--4244 Score: 162
Period size: 44 Copynumber: 2.3 Consensus size: 46
4129 TTCCATGAAG
*
4139 AGGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATA-G-TC
1 AGGTTATCAAAATTTCATAGAGTGGTTACCAAAATTTCATAGGATC
* *
4183 TGGTTACCAAAATTTCATAGAGTGGTTACCAAAATTTCATAGGATC
1 AGGTTATCAAAATTTCATAGAGTGGTTACCAAAATTTCATAGGATC
*
4229 AGGTTATTAAAATTTC
1 AGGTTATCAAAATTTC
4245 TTAGGTTGGT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
44 38 0.70
45 1 0.02
46 15 0.28
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (46 bp):
AGGTTATCAAAATTTCATAGAGTGGTTACCAAAATTTCATAGGATC
Found at i:4255 original size:46 final size:44
Alignment explanation
Indices: 4139--4256 Score: 150
Period size: 44 Copynumber: 2.6 Consensus size: 44
4129 TTCCATGAAG
4139 AGGTTATCAAAATTTCATA-GTGTGGTTACCAAAATTTCATAGTC
1 AGGTTATCAAAATTTCATAGGT-TGGTTACCAAAATTTCATAGTC
* *
4183 TGGTTACCAAAATTTCATAGAG-TGGTTACCAAAATTTCATAGGATC
1 AGGTTATCAAAATTTCATAG-GTTGGTTACCAAAATTTCATA-G-TC
* *
4229 AGGTTATTAAAATTTCTTAGGTTGGTTA
1 AGGTTATCAAAATTTCATAGGTTGGTTA
4257 TTGAAATTTC
Statistics
Matches: 63, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
44 36 0.57
45 2 0.03
46 25 0.40
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (44 bp):
AGGTTATCAAAATTTCATAGGTTGGTTACCAAAATTTCATAGTC
Found at i:4258 original size:22 final size:23
Alignment explanation
Indices: 4140--4256 Score: 127
Period size: 22 Copynumber: 5.2 Consensus size: 23
4130 TCCATGAAGA
* *
4140 GGTTATCAAAATTTCATA-GTGT
1 GGTTACCAAAATTTCATAGGTCT
4162 GGTTACCAAAATTTCATA-GTCT
1 GGTTACCAAAATTTCATAGGTCT
4184 GGTTACCAAAATTTCATAGAG--T
1 GGTTACCAAAATTTCATAG-GTCT
*
4206 GGTTACCAAAATTTCATAGGATCA
1 GGTTACCAAAATTTCATAGG-TCT
** *
4230 GGTTATTAAAATTTCTTAGGT-T
1 GGTTACCAAAATTTCATAGGTCT
4252 GGTTA
1 GGTTA
4257 TTGAAATTTC
Statistics
Matches: 83, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.01
22 63 0.76
23 1 0.01
24 18 0.22
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (23 bp):
GGTTACCAAAATTTCATAGGTCT
Found at i:4276 original size:22 final size:22
Alignment explanation
Indices: 4140--4278 Score: 106
Period size: 22 Copynumber: 6.2 Consensus size: 22
4130 TCCATGAAGA
*
4140 GGTTATCAAAATTTCATA-GTGT
1 GGTTATTAAAATTTCATAGGT-T
**
4162 GGTTACCAAAATTTCATA-GTCT
1 GGTTATTAAAATTTCATAGGT-T
**
4184 GGTTACCAAAATTTCATAGAG-T
1 GGTTATTAAAATTTCATAG-GTT
** *
4206 GGTTACCAAAATTTCATAGGATCA
1 GGTTATTAAAATTTCATAGG-T-T
*
4230 GGTTATTAAAATTTCTTAGGTT
1 GGTTATTAAAATTTCATAGGTT
*
4252 GGTTATTGAAATTTCATATGG-T
1 GGTTATTAAAATTTCATA-GGTT
4274 GGTTA
1 GGTTA
4279 ATTATCACAA
Statistics
Matches: 102, Mismatches: 9, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.01
22 80 0.78
23 3 0.03
24 18 0.18
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.39
Consensus pattern (22 bp):
GGTTATTAAAATTTCATAGGTT
Found at i:4524 original size:22 final size:22
Alignment explanation
Indices: 4494--4699 Score: 129
Period size: 22 Copynumber: 9.4 Consensus size: 22
4484 GAAGGTTGTC
* *
4494 AAATCTCATAGAGTGATTATCG
1 AAATTTCATAGAGTGATTATCA
*
4516 AAATTTCATAAAGATATGATTATCA
1 AAATTTCAT--AGA-GTGATTATCA
*
4541 AAATTT-ATATGA-AGATTATCA
1 AAATTTCATA-GAGTGATTATCA
*
4562 AAATTTCATAGTGTTG-TTATCA
1 AAATTTCATAGAG-TGATTATCA
* * * *
4584 AAATTTCAAAGCGAGGTTATCA
1 AAATTTCATAGAGTGATTATCA
*
4606 AAATTACATA-ATGTGATTATCA
1 AAATTTCATAGA-GTGATTATCA
* * *
4628 AAATTTCATAG-G-GGTCAACA
1 AAATTTCATAGAGTGATTATCA
* *
4648 AAATTTTATAAAGATG-TTATCA
1 AAATTTCATAGAG-TGATTATCA
* * *
4670 AAATTTCATAAAGAGGTTATCA
1 AAATTTCATAGAGTGATTATCA
*
4692 AATTTTCA
1 AAATTTCA
4700 AACTCTGATT
Statistics
Matches: 145, Mismatches: 25, Indels: 28
0.73 0.13 0.14
Matches are distributed among these distances:
20 14 0.10
21 19 0.13
22 89 0.61
23 4 0.03
24 5 0.03
25 14 0.10
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (22 bp):
AAATTTCATAGAGTGATTATCA
Found at i:4552 original size:18 final size:19
Alignment explanation
Indices: 4529--4567 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
4519 TTTCATAAAG
4529 ATAT-GATTATCAAAATTT
1 ATATAGATTATCAAAATTT
4547 ATATGAAGATTATCAAAATTT
1 ATAT--AGATTATCAAAATTT
4568 CATAGTGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
21 14 0.78
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (19 bp):
ATATAGATTATCAAAATTT
Found at i:4626 original size:44 final size:43
Alignment explanation
Indices: 4510--4699 Score: 161
Period size: 44 Copynumber: 4.3 Consensus size: 43
4500 CATAGAGTGA
* * * * *
4510 TTATCGAAATTTCATAAAGATATGATTATCAAAATTT-ATATGAAGA
1 TTATCAAAATTTCATAATG--ATG-TTATCAAAATTTCA-AAGGAGG
* *
4556 TTATCAAAATTTCATAGTGTTGTTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAATGATGTTATCAAAATTTCAAAG-GAGG
* *
4600 TTATCAAAATTACATAATG-TGATTATCAAAATTTCATAGG-GG
1 TTATCAAAATTTCATAATGATG-TTATCAAAATTTCAAAGGAGG
* * * * *
4642 TCAACAAAATTTTATAAAGATGTTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAATGATGTTATCAAAATTTCA-AAGGAGG
*
4686 TTATCAAATTTTCA
1 TTATCAAAATTTCA
4700 AACTCTGATT
Statistics
Matches: 117, Mismatches: 21, Indels: 14
0.77 0.14 0.09
Matches are distributed among these distances:
42 30 0.26
43 21 0.18
44 50 0.43
46 16 0.14
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.36
Consensus pattern (43 bp):
TTATCAAAATTTCATAATGATGTTATCAAAATTTCAAAGGAGG
Found at i:4668 original size:42 final size:43
Alignment explanation
Indices: 4576--4679 Score: 122
Period size: 42 Copynumber: 2.4 Consensus size: 43
4566 TTCATAGTGT
* * * *
4576 TGTTATCAAAATTTCAAAGCGAGGTTATCAAAATTACATAATG
1 TGTTATCAAAATTTCATAGCGAGGTCAACAAAATTACATAAAG
**
4619 TGATTATCAAAATTTCATAG-G-GGTCAACAAAATTTTATAAAG
1 TG-TTATCAAAATTTCATAGCGAGGTCAACAAAATTACATAAAG
4661 ATGTTATCAAAATTTCATA
1 -TGTTATCAAAATTTCATA
4680 AAGAGGTTAT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
42 32 0.60
43 5 0.09
44 16 0.30
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.35
Consensus pattern (43 bp):
TGTTATCAAAATTTCATAGCGAGGTCAACAAAATTACATAAAG
Found at i:4843 original size:19 final size:19
Alignment explanation
Indices: 4813--4879 Score: 107
Period size: 19 Copynumber: 3.5 Consensus size: 19
4803 TGATGGAGTA
4813 ATCAAAATTTCAGGGAGGAT
1 ATCAAAA-TTCAGGGAGGAT
*
4833 ACCAAAATTCAGGGAGGAT
1 ATCAAAATTCAGGGAGGAT
*
4852 ATCAAAATTCAGTGAGGAT
1 ATCAAAATTCAGGGAGGAT
4871 ATCAAAATT
1 ATCAAAATT
4880 TCATATGAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
19 38 0.86
20 6 0.14
ACGTcount: A:0.43, C:0.12, G:0.21, T:0.24
Consensus pattern (19 bp):
ATCAAAATTCAGGGAGGAT
Found at i:4898 original size:22 final size:22
Alignment explanation
Indices: 4870--5122 Score: 114
Period size: 22 Copynumber: 11.7 Consensus size: 22
4860 TCAGTGAGGA
4870 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
* **
4892 TATCAAATTTTCATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* * *
4914 TTTCAAAATTTCATAAGAGGGT
1 TATCAAAATTTCATATGAAGGT
* *
4936 TATCAAAATTTCATA-GTATGT
1 TATCAAAATTTCATATGAAGGT
* ** * *
4957 AGATCAAAATTTCATGGGGAGAT
1 -TATCAAAATTTCATATGAAGGT
*
4980 TAACAAAATTTCATAATG-AGGT
1 TATCAAAATTTCAT-ATGAAGGT
* ** * *
5002 TATAAAAAAATCAT-TGGGAGCT
1 TATCAAAATTTCATAT-GAAGGT
5024 TATCAAAA-TT--TAT--A-GT
1 TATCAAAATTTCATATGAAGGT
* * *
5040 TATCAAGATTTCATCTGAAAGT
1 TATCAAAATTTCATATGAAGGT
* * *
5062 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATATGAAGG-T
* * *
5085 TATTAAAATTTTATA-GAAAGATT
1 TATCAAAATTTCATATG-AAG-GT
5108 TATCAAAATTTCATA
1 TATCAAAATTTCATA
5123 GCGAGATTAT
Statistics
Matches: 170, Mismatches: 44, Indels: 33
0.69 0.18 0.13
Matches are distributed among these distances:
16 8 0.05
17 3 0.02
19 3 0.02
20 2 0.01
21 6 0.04
22 111 0.65
23 37 0.22
ACGTcount: A:0.40, C:0.08, G:0.14, T:0.38
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:4964 original size:44 final size:43
Alignment explanation
Indices: 4870--4994 Score: 135
Period size: 44 Copynumber: 2.9 Consensus size: 43
4860 TCAGTGAGGA
* *
4870 TATCAAAATTTCATATGAAGGTTATCAAATTTTCATAGTTTAG
1 TATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAGTTTAG
* *
4913 TTTTCAAAATTTCATAAGAGGGTTATCAAAATTTCATAGTATGTAG
1 -TATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAGT-T-TAG
** * * *
4959 -ATCAAAATTTCATGGGGAGATTAACAAAATTTCATA
1 TATCAAAATTTCATAAGAAGGTTATCAAAATTTCATA
4995 ATGAGGTTAT
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 64 0.94
45 1 0.01
46 3 0.04
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.38
Consensus pattern (43 bp):
TATCAAAATTTCATAAGAAGGTTATCAAAATTTCATAGTTTAG
Found at i:5139 original size:22 final size:22
Alignment explanation
Indices: 4870--5162 Score: 99
Period size: 22 Copynumber: 13.5 Consensus size: 22
4860 TCAGTGAGGA
* *
4870 TATCAAAATTTCATATG-AAGGT
1 TATCAAAATTTCATA-GCGAGAT
* **
4892 TATCAAATTTTCATAGTTTAG-T
1 TATCAAAATTTCATAG-CGAGAT
* * *
4914 TTTCAAAATTTCATA-AGAGGGT
1 TATCAAAATTTCATAGCGA-GAT
*
4936 TATCAAAATTTCATAG-TATG-T
1 TATCAAAATTTCATAGCGA-GAT
* * *
4957 AGATCAAAATTTCATGGGGAGAT
1 -TATCAAAATTTCATAGCGAGAT
* ** *
4980 TAACAAAATTTCATAATGAGGT
1 TATCAAAATTTCATAGCGAGAT
* ** * * *
5002 TATAAAAAAATCATTGGGAGCT
1 TATCAAAATTTCATAGCGAGAT
5024 TATCAAAATTT-AT----AG-T
1 TATCAAAATTTCATAGCGAGAT
* *
5040 TATCAAGATTTCAT--CTGAAAGT
1 TATCAAAATTTCATAGC-GAGA-T
* * *
5062 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATAGCGA-GAT
* * **
5085 TATTAAAATTTTATAGAAAGATT
1 TATCAAAATTTCATAGCGAGA-T
5108 TATCAAAATTTCATAGCGAGAT
1 TATCAAAATTTCATAGCGAGAT
* * * *
5130 TATCACAATTTTATAGTGTGAT
1 TATCAAAATTTCATAGCGAGAT
5152 TATCAAAATTT
1 TATCAAAATTT
5163 TGAAGTGTTA
Statistics
Matches: 204, Mismatches: 49, Indels: 36
0.71 0.17 0.12
Matches are distributed among these distances:
16 11 0.05
17 4 0.02
20 2 0.01
21 5 0.02
22 141 0.69
23 41 0.20
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.38
Consensus pattern (22 bp):
TATCAAAATTTCATAGCGAGAT
Found at i:5163 original size:22 final size:22
Alignment explanation
Indices: 5061--5163 Score: 107
Period size: 23 Copynumber: 4.6 Consensus size: 22
5051 CATCTGAAAG
* *
5061 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGAGA-GA
* *
5084 TTATTAAAATTTTATAGAAAGA
1 TTATCAAAATTTTATAGAGAGA
* *
5106 TTTATCAAAATTTCATAGCGAGA
1 -TTATCAAAATTTTATAGAGAGA
* * *
5129 TTATCACAATTTTATAGTGTGA
1 TTATCAAAATTTTATAGAGAGA
5151 TTATCAAAATTTT
1 TTATCAAAATTTT
5164 GAAGTGTTAT
Statistics
Matches: 66, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
22 31 0.47
23 35 0.53
ACGTcount: A:0.39, C:0.07, G:0.13, T:0.42
Consensus pattern (22 bp):
TTATCAAAATTTTATAGAGAGA
Found at i:5288 original size:45 final size:45
Alignment explanation
Indices: 5214--5299 Score: 104
Period size: 45 Copynumber: 1.9 Consensus size: 45
5204 TTTTATAAAG
* *
5214 TGGTTATCAATATATCATATGGAGCTTATCAACATCTCATAGTGT
1 TGGTTATCAAAATATCATATGGAGCTTATCAAAATCTCATAGTGT
* *
5259 TGGTTATCAAAATTTCAT-TGGGAAG-TTATCAAAATTTCATA
1 TGGTTATCAAAATATCATAT-GG-AGCTTATCAAAATCTCATA
5300 TTGAGGTCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
44 1 0.03
45 32 0.91
46 2 0.06
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (45 bp):
TGGTTATCAAAATATCATATGGAGCTTATCAAAATCTCATAGTGT
Found at i:10014 original size:3 final size:3
Alignment explanation
Indices: 10001--10042 Score: 75
Period size: 3 Copynumber: 13.7 Consensus size: 3
9991 AATTTAAATA
10001 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
10043 ACACAAGTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:10536 original size:39 final size:40
Alignment explanation
Indices: 10491--10571 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 40
10481 ACAATAATGC
10491 TATC-ATATTATCAA-ATTCATTTAACATACAGAAATAGTT
1 TATCAATATTAT-AATATTCATTTAACATACAGAAATAGTT
* *
10530 TATCATATATTATAATATTCATTTTACATAGAGAAATAGTT
1 TATCA-ATATTATAATATTCATTTAACATACAGAAATAGTT
10571 T
1 T
10572 TTTTGAATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
39 4 0.11
40 2 0.05
41 31 0.84
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.42
Consensus pattern (40 bp):
TATCAATATTATAATATTCATTTAACATACAGAAATAGTT
Found at i:10815 original size:9 final size:9
Alignment explanation
Indices: 10803--10834 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
10793 GTGTCGGGCG
10803 TTTTTTTAT
1 TTTTTTTAT
10812 TTTTTTTA-
1 TTTTTTTAT
10820 -TTTTTTAT
1 TTTTTTTAT
10828 TTTTTTT
1 TTTTTTT
10835 TGCTTTCCGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
7 7 0.33
9 14 0.67
ACGTcount: A:0.09, C:0.00, G:0.00, T:0.91
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:10825 original size:16 final size:16
Alignment explanation
Indices: 10804--10834 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
10794 TGTCGGGCGT
10804 TTTTTTATTTTTTTTA
1 TTTTTTATTTTTTTTA
10820 TTTTTTATTTTTTTT
1 TTTTTTATTTTTTTT
10835 TGCTTTCCGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (16 bp):
TTTTTTATTTTTTTTA
Found at i:11614 original size:11 final size:11
Alignment explanation
Indices: 11598--11630 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
11588 TGAAGGGGAA
11598 TAATTAGATAT
1 TAATTAGATAT
*
11609 TAATTAGCTAT
1 TAATTAGATAT
11620 TAATTAGATAT
1 TAATTAGATAT
11631 AGTATAATGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.45
Consensus pattern (11 bp):
TAATTAGATAT
Found at i:11778 original size:2 final size:2
Alignment explanation
Indices: 11765--11805 Score: 73
Period size: 2 Copynumber: 20.0 Consensus size: 2
11755 GACAAAAATA
11765 AT AT AT AGT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11806 GCTAGAAAGG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 36 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Done.