Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013977.1 Corchorus capsularis cultivar CVL-1 contig13998, 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: 65530
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Found at i:3639 original size:10 final size:10
Alignment explanation
Indices: 3621--3682 Score: 72
Period size: 10 Copynumber: 6.1 Consensus size: 10
3611 ACAATTTCCC
*
3621 AGAAAAAAAA
1 AGAAGAAAAA
3631 AGAAGAAAAA
1 AGAAGAAAAA
3641 AGAAGAGAAAA
1 AGAAGA-AAAA
*
3652 AG-AGAAAGA
1 AGAAGAAAAA
3661 AGAAGAATAAA
1 AGAAGAA-AAA
*
3672 AGAGGAAAAA
1 AGAAGAAAAA
3682 A
1 A
3683 AGAAAAAGAG
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
9 5 0.11
10 26 0.58
11 14 0.31
ACGTcount: A:0.76, C:0.00, G:0.23, T:0.02
Consensus pattern (10 bp):
AGAAGAAAAA
Found at i:3651 original size:20 final size:21
Alignment explanation
Indices: 3628--3691 Score: 60
Period size: 20 Copynumber: 3.0 Consensus size: 21
3618 CCCAGAAAAA
3628 AAAAGAAGAAAAAAGAAG-AG
1 AAAAGAAGAAAAAAGAAGAAG
* *
3648 AAAA-AGAGAAAGAAGAAGAAT
1 AAAAGA-AGAAAAAAGAAGAAG
* *
3669 AAAAGAGGAAAAAAAGAAAAAG
1 AAAAGAAG-AAAAAAGAAGAAG
3691 A
1 A
3692 GCAGAAGCAA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
19 1 0.03
20 15 0.44
21 6 0.18
22 12 0.35
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (21 bp):
AAAAGAAGAAAAAAGAAGAAG
Found at i:3661 original size:17 final size:17
Alignment explanation
Indices: 3639--3692 Score: 56
Period size: 17 Copynumber: 3.0 Consensus size: 17
3629 AAAGAAGAAA
3639 AAAGAAGAGAAAAAGAG
1 AAAGAAGAGAAAAAGAG
3656 AAAGAAGAAGAATAAAAGAGG
1 AAAGAAG-AG-A-AAAAGA-G
*
3677 AAA-AAAAGAAAAAGAG
1 AAAGAAGAGAAAAAGAG
3693 CAGAAGCAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
16 1 0.03
17 13 0.41
18 3 0.09
19 3 0.09
20 8 0.25
21 4 0.12
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (17 bp):
AAAGAAGAGAAAAAGAG
Found at i:3666 original size:30 final size:31
Alignment explanation
Indices: 3624--3691 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
3614 ATTTCCCAGA
* *
3624 AAAAAAAAGAAGAA-AAAAGAAGAGAAAAAG
1 AAAAAGAAGAAGAATAAAAGAAGAAAAAAAG
* *
3654 AGAAAGAAGAAGAATAAAAGAGGAAAAAAAG
1 AAAAAGAAGAAGAATAAAAGAAGAAAAAAAG
3685 AAAAAGA
1 AAAAAGA
3692 GCAGAAGCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 12 0.38
31 20 0.62
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.01
Consensus pattern (31 bp):
AAAAAGAAGAAGAATAAAAGAAGAAAAAAAG
Found at i:3757 original size:45 final size:44
Alignment explanation
Indices: 3704--3850 Score: 177
Period size: 45 Copynumber: 3.2 Consensus size: 44
3694 AGAAGCAATG
*
3704 ATGGTTTTCAAAAAGAGTCATGGATTTCAAAAGGTGTTAATAAA
1 ATGGTTTTCAAAAAGAGTCATGGTTTTCAAAAGGTGTTAATAAA
*
3748 ATGGATTTTCAAAAAGAGTCACGGTTTTCAAAAGGTGTTAATAAA
1 ATGG-TTTTCAAAAAGAGTCATGGTTTTCAAAAGGTGTTAATAAA
* * * *
3793 ATGGTTTTTTTAAAAAAAATAGTTATGGTTTTCAAAAGGTTTTAATAAA
1 ATGG---TTTT--CAAAAAGAGTCATGGTTTTCAAAAGGTGTTAATAAA
*
3842 AGGGTTTTC
1 ATGGTTTTC
3851 TAAAGTTGCA
Statistics
Matches: 88, Mismatches: 10, Indels: 10
0.81 0.09 0.09
Matches are distributed among these distances:
44 4 0.05
45 42 0.48
46 4 0.05
47 4 0.05
49 34 0.39
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.36
Consensus pattern (44 bp):
ATGGTTTTCAAAAAGAGTCATGGTTTTCAAAAGGTGTTAATAAA
Found at i:4247 original size:21 final size:21
Alignment explanation
Indices: 4223--4274 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 21
4213 AAAAGAGGAG
*
4223 GAAAAAGTGAAAATTGAAAGT
1 GAAAAAGTGAAAATTGAAAAT
* **
4244 GAAAAGGAAAAAATTGAAAAT
1 GAAAAAGTGAAAATTGAAAAT
4265 --AAAAGTGAAA
1 GAAAAAGTGAAA
4275 GGAAGAGTGA
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
19 7 0.29
21 17 0.71
ACGTcount: A:0.63, C:0.00, G:0.21, T:0.15
Consensus pattern (21 bp):
GAAAAAGTGAAAATTGAAAAT
Found at i:4251 original size:27 final size:25
Alignment explanation
Indices: 4221--4278 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 25
4211 GAAAAAGAGG
*
4221 AGGAAAAAGTGAAAATTGAAAGTGAAA
1 AGGAAAAAGTGAAAA-TAAAAGTG-AA
*
4248 AGGAAAAAATTGAAAATAAAAGTGAA
1 AGG-AAAAAGTGAAAATAAAAGTGAA
4274 AGGAA
1 AGGAA
4279 GAGTGAAGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 2 0.07
26 5 0.18
27 10 0.36
28 11 0.39
ACGTcount: A:0.62, C:0.00, G:0.24, T:0.14
Consensus pattern (25 bp):
AGGAAAAAGTGAAAATAAAAGTGAA
Found at i:4584 original size:6 final size:6
Alignment explanation
Indices: 4573--4634 Score: 76
Period size: 6 Copynumber: 10.7 Consensus size: 6
4563 AAAAAAAATG
*
4573 AAAGAA AAAGAA AAAGAA AAAG-A AAA-TA AAAGAA AAAGAA AAA-AA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
*
4618 AAAGAA TGAAGAA AAAG
1 AAAGAA -AAAGAA AAAG
4635 GCTCTAGGGT
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
5 13 0.27
6 31 0.63
7 5 0.10
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (6 bp):
AAAGAA
Found at i:4592 original size:22 final size:22
Alignment explanation
Indices: 4578--4634 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 22
4568 AAATGAAAGA
4578 AAAAGAAAAAGAAAAAGAAAAT
1 AAAAGAAAAAGAAAAAGAAAAT
* *
4600 AAAAGAAAAAGAAAAAAAAAAG
1 AAAAGAAAAAGAAAAAGAAAAT
4622 AATGAAGAAAAAG
1 AA--AAGAAAAAG
4635 GCTCTAGGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
22 22 0.71
24 9 0.29
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.04
Consensus pattern (22 bp):
AAAAGAAAAAGAAAAAGAAAAT
Found at i:4619 original size:16 final size:16
Alignment explanation
Indices: 4562--4633 Score: 74
Period size: 17 Copynumber: 4.3 Consensus size: 16
4552 GAGTTTGTGT
4562 AAAAAAAAATGAAAGAA-
1 AAAAAAAAA-GAAA-AAG
*
4579 AAAGAAAAAGAAAAAG
1 AAAAAAAAAGAAAAAG
*
4595 AAAATAAAAGAAAAAG
1 AAAAAAAAAGAAAAAG
*
4611 AAAAAAAAAAGAATGAAG
1 -AAAAAAAAAGAA-AAAG
4629 AAAAA
1 AAAAA
4634 GGCTCTAGGG
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
15 2 0.04
16 18 0.38
17 24 0.51
18 3 0.06
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.04
Consensus pattern (16 bp):
AAAAAAAAAGAAAAAG
Found at i:5608 original size:69 final size:70
Alignment explanation
Indices: 5519--5949 Score: 448
Period size: 69 Copynumber: 6.2 Consensus size: 70
5509 AATGCTCCGA
* * * * *
5519 CTTTTCCACAAGCTAAACTCGTTTCCACACGAGTCTGATCCAGCTTCGGTTCCATCCAAGCA-AG
1 CTTTTCCATAAGCCAAACTCGCTTCCACACGAGTCAGATCCAGCTTTGGTTCCATCCAAGCATAG
5583 AGAGG
66 AGAGG
* ** * *
5588 CTTTTCCATAAGCCAAACTCGCTTCCACGCGAGAT-AG-TTTAGCCTTGGTTCCATCCAAGCATC
1 CTTTTCCATAAGCCAAACTCGCTTCCACACGAG-TCAGATCCAGCTTTGGTTCCATCCAAGCATA
* *
5651 CAGGGG
65 GAGAGG
* *
5657 CTTTTCCACAA-CCAAACTCGCTTCCACACGAGTCAGATCCAGCTTTGGTTCCATCCAGGCA-AG
1 CTTTTCCATAAGCCAAACTCGCTTCCACACGAGTCAGATCCAGCTTTGGTTCCATCCAAGCATAG
*
5720 AGAGT
66 AGAGG
* * * * *
5725 CTTTTCCATAAGCCAAACTCGCTTCCACGCGAGAT-AGTTTCAGATTTGGTTCCATCCAAGCATT
1 CTTTTCCATAAGCCAAACTCGCTTCCACACGAG-TCAGATCCAGCTTTGGTTCCATCCAAGCATA
* *
5789 CAGGGG
65 GAGAGG
* * * * * *
5795 CTTTTCCACAAGCCAAACTCGTTTCCACACGGGTCATATCCAGCTTCGGTTCCATCCAGGCA-AG
1 CTTTTCCATAAGCCAAACTCGCTTCCACACGAGTCAGATCCAGCTTTGGTTCCATCCAAGCATAG
5859 AGAGG
66 AGAGG
* * * ** *
5864 CTTTTCCATAAGCCAAACTCGTTTCCACGCGAGAT-AGTTTAAGATTTGGTTCCATCCAAGCATT
1 CTTTTCCATAAGCCAAACTCGCTTCCACACGAG-TCAGATCCAGCTTTGGTTCCATCCAAGCA-T
*
5928 AAAG-GG
64 AGAGAGG
5934 CTTTTCCATAAGCCAA
1 CTTTTCCATAAGCCAA
5950 GTTCAGTGAG
Statistics
Matches: 295, Mismatches: 56, Indels: 21
0.79 0.15 0.06
Matches are distributed among these distances:
67 1 0.00
68 55 0.19
69 162 0.55
70 74 0.25
71 3 0.01
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (70 bp):
CTTTTCCATAAGCCAAACTCGCTTCCACACGAGTCAGATCCAGCTTTGGTTCCATCCAAGCATAG
AGAGG
Found at i:5860 original size:139 final size:138
Alignment explanation
Indices: 5519--5949 Score: 695
Period size: 139 Copynumber: 3.1 Consensus size: 138
5509 AATGCTCCGA
* *
5519 CTTTTCCACAAGCTAAACTCGTTTCCACACGAGTC-TGATCCAGCTTCGGTTCCATCCAAGCAAG
1 CTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCAT-ATCCAGCTTCGGTTCCATCCAGGCAAG
**
5583 AGAGGCTTTTCCATAAGCCAAACTCGCTTCCACGCGAGATAGTTTAGCCTTGGTTCCATCCAAGC
65 AGAGGCTTTTCCATAAGCCAAACTCGCTTCCACGCGAGATAGTTTAGATTTGGTTCCATCCAAGC
*
5648 ATCCAGGGG
130 ATTCAGGGG
* * *
5657 CTTTTCCACAA-CCAAACTCGCTTCCACACGAGTCAGATCCAGCTTTGGTTCCATCCAGGCAAGA
1 CTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCATATCCAGCTTCGGTTCCATCCAGGCAAGA
*
5721 GAGTCTTTTCCATAAGCCAAACTCGCTTCCACGCGAGATAGTTTCAGATTTGGTTCCATCCAAGC
66 GAGGCTTTTCCATAAGCCAAACTCGCTTCCACGCGAGATAGTTT-AGATTTGGTTCCATCCAAGC
5786 ATTCAGGGG
130 ATTCAGGGG
*
5795 CTTTTCCACAAGCCAAACTCGTTTCCACACGGGTCATATCCAGCTTCGGTTCCATCCAGGCAAGA
1 CTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCATATCCAGCTTCGGTTCCATCCAGGCAAGA
*
5860 GAGGCTTTTCCATAAGCCAAACTCGTTTCCACGCGAGATAGTTTAAGATTTGGTTCCATCCAAGC
66 GAGGCTTTTCCATAAGCCAAACTCGCTTCCACGCGAGATAGTTT-AGATTTGGTTCCATCCAAGC
* *
5925 ATTAAAGGG
130 ATTCAGGGG
*
5934 CTTTTCCATAAGCCAA
1 CTTTTCCACAAGCCAA
5950 GTTCAGTGAG
Statistics
Matches: 271, Mismatches: 19, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
137 90 0.33
138 48 0.18
139 133 0.49
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (138 bp):
CTTTTCCACAAGCCAAACTCGTTTCCACACGAGTCATATCCAGCTTCGGTTCCATCCAGGCAAGA
GAGGCTTTTCCATAAGCCAAACTCGCTTCCACGCGAGATAGTTTAGATTTGGTTCCATCCAAGCA
TTCAGGGG
Found at i:6250 original size:48 final size:47
Alignment explanation
Indices: 6059--6239 Score: 236
Period size: 48 Copynumber: 3.8 Consensus size: 47
6049 ATCCAGGCAA
* * * *
6059 TCTTCTCTCGCTTCCATGCGAATTTTCAATTTAGTGACCAAAGTTGG
1 TCTTTTCTCGCTTCCACGCGAGTTTTCAATTTAGTGACCAAAGATGG
* *
6106 TCTTTTCTCGCTTCCACGCGAGTTTTCAAATCTAGTGACTAAAGATGG
1 TCTTTTCTCGCTTCCACGCGAGTTTTC-AATTTAGTGACCAAAGATGG
* * *
6154 TCTTTTCTCGCTTCCACGCGGGTTTTCAATTTATTTACCAAAGATGG
1 TCTTTTCTCGCTTCCACGCGAGTTTTCAATTTAGTGACCAAAGATGG
* * *
6201 TCTTTCTCTCGCTTCCATGCGAGTCTACAATTTAGTGAC
1 TCTTT-TCTCGCTTCCACGCGAGTTTTCAATTTAGTGAC
6240 AAGAGTTGGT
Statistics
Matches: 115, Mismatches: 17, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
47 45 0.39
48 70 0.61
ACGTcount: A:0.20, C:0.24, G:0.17, T:0.38
Consensus pattern (47 bp):
TCTTTTCTCGCTTCCACGCGAGTTTTCAATTTAGTGACCAAAGATGG
Found at i:6250 original size:95 final size:95
Alignment explanation
Indices: 6059--6239 Score: 247
Period size: 95 Copynumber: 1.9 Consensus size: 95
6049 ATCCAGGCAA
* *
6059 TCTTCTCTCGCTTCCATGCGAATTTTCAATTTAGTGACCAAAGTTGGTCTTTTCTCGCTTCCACG
1 TCTTCTCTCGCTTCCACGCGAATTTTCAATTTAGTGACCAAAGATGGTCTTTTCTCGCTTCCACG
* *
6124 CGAGTTTTCAAATCTAGTGACTAAAGATGG
66 CGAGTCTACAAATCTAGTGACTAAAGATGG
* ** * * *
6154 TCTTTTCTCGCTTCCACGCGGGTTTTCAATTTATTTACCAAAGATGGTCTTTCTCTCGCTTCCAT
1 TCTTCTCTCGCTTCCACGCGAATTTTCAATTTAGTGACCAAAGATGGTCTTT-TCTCGCTTCCAC
*
6219 GCGAGTCTAC-AATTTAGTGAC
65 GCGAGTCTACAAATCTAGTGAC
6240 AAGAGTTGGT
Statistics
Matches: 74, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
95 55 0.74
96 19 0.26
ACGTcount: A:0.20, C:0.24, G:0.17, T:0.38
Consensus pattern (95 bp):
TCTTCTCTCGCTTCCACGCGAATTTTCAATTTAGTGACCAAAGATGGTCTTTTCTCGCTTCCACG
CGAGTCTACAAATCTAGTGACTAAAGATGG
Found at i:6908 original size:14 final size:14
Alignment explanation
Indices: 6889--6915 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6879 GTATATTAAC
6889 TTTAGTCCATTTAT
1 TTTAGTCCATTTAT
6903 TTTAGTCCATTTA
1 TTTAGTCCATTTA
6916 GATTACTATC
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:0.22, C:0.15, G:0.07, T:0.56
Consensus pattern (14 bp):
TTTAGTCCATTTAT
Found at i:7127 original size:20 final size:20
Alignment explanation
Indices: 7102--7140 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
7092 AAATACAACG
7102 CATTTGATTTACAAATTGGA
1 CATTTGATTTACAAATTGGA
*
7122 CATTTGATTTGCAAATTGG
1 CATTTGATTTACAAATTGG
7141 TGCTCTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.41
Consensus pattern (20 bp):
CATTTGATTTACAAATTGGA
Found at i:10611 original size:13 final size:14
Alignment explanation
Indices: 10593--10621 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
10583 ATAATTGGAC
10593 TTTGCATCCAT-CA
1 TTTGCATCCATGCA
10606 TTTGCATCCATGCA
1 TTTGCATCCATGCA
10620 TT
1 TT
10622 AAATAGAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.21, C:0.28, G:0.10, T:0.41
Consensus pattern (14 bp):
TTTGCATCCATGCA
Found at i:13069 original size:15 final size:16
Alignment explanation
Indices: 13037--13070 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
13027 AAAGAAGAAT
*
13037 TAAAATTAAATCTAAC
1 TAAAAGTAAATCTAAC
13053 TAAAAGTAAAT-TAAC
1 TAAAAGTAAATCTAAC
13068 TAA
1 TAA
13071 GAGAGCAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.59, C:0.09, G:0.03, T:0.29
Consensus pattern (16 bp):
TAAAAGTAAATCTAAC
Found at i:16054 original size:33 final size:34
Alignment explanation
Indices: 15993--16061 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 34
15983 TCTAAGATGC
15993 TTAAAAATAAAATCCTAAATCTAGAAAACATAAA
1 TTAAAAATAAAATCCTAAATCTAGAAAACATAAA
* * * *
16027 TTAAAATTAAAATCCTAATTTTA-AAAACCTAAA
1 TTAAAAATAAAATCCTAAATCTAGAAAACATAAA
16060 TT
1 TT
16062 GGTTTAGGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
33 11 0.35
34 20 0.65
ACGTcount: A:0.57, C:0.12, G:0.01, T:0.30
Consensus pattern (34 bp):
TTAAAAATAAAATCCTAAATCTAGAAAACATAAA
Found at i:23062 original size:15 final size:16
Alignment explanation
Indices: 23030--23063 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
23020 AAAGAAGAAT
*
23030 TAAAATTAAATCTAAC
1 TAAAAGTAAATCTAAC
23046 TAAAAGTAAAT-TAAC
1 TAAAAGTAAATCTAAC
23061 TAA
1 TAA
23064 GAGAGCAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.59, C:0.09, G:0.03, T:0.29
Consensus pattern (16 bp):
TAAAAGTAAATCTAAC
Found at i:25513 original size:12 final size:12
Alignment explanation
Indices: 25483--25516 Score: 54
Period size: 10 Copynumber: 3.0 Consensus size: 12
25473 TGCATGGGAC
25483 CATGACCGGCCA
1 CATGACCGGCCA
25495 -A-GACCGGCCA
1 CATGACCGGCCA
25505 CATGACCGGCCA
1 CATGACCGGCCA
25517 TCACATGGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.45
11 2 0.10
12 9 0.45
ACGTcount: A:0.26, C:0.41, G:0.26, T:0.06
Consensus pattern (12 bp):
CATGACCGGCCA
Found at i:27021 original size:2 final size:2
Alignment explanation
Indices: 27014--27044 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
27004 TCCACCCGAG
27014 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27045 TAGAAAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:38868 original size:39 final size:39
Alignment explanation
Indices: 38824--38903 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
38814 ATTTCAACAT
38824 AAAAATTAAGAAAACTAAGATCTTCAAATCAACACAATC
1 AAAAATTAAGAAAACTAAGATCTTCAAATCAACACAATC
38863 AAAAATTAAGAAAACTAAGATCTTCAAATCAACACAATC
1 AAAAATTAAGAAAACTAAGATCTTCAAATCAACACAATC
38902 AA
1 AA
38904 CCATGAAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.57, C:0.17, G:0.05, T:0.20
Consensus pattern (39 bp):
AAAAATTAAGAAAACTAAGATCTTCAAATCAACACAATC
Found at i:39121 original size:26 final size:29
Alignment explanation
Indices: 39092--39154 Score: 89
Period size: 26 Copynumber: 2.3 Consensus size: 29
39082 GTGAACTCAA
39092 AATGACCAAAATG-CCCCT-GGTG-CCAT
1 AATGACCAAAATGTCCCCTAGGTGACCAT
*
39118 AATGACCAAAATGTCCCCTAGGTGACCCT
1 AATGACCAAAATGTCCCCTAGGTGACCAT
39147 AATG-CCAA
1 AATGACCAA
39155 TTAACAAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
26 13 0.39
27 5 0.15
28 8 0.24
29 7 0.21
ACGTcount: A:0.33, C:0.30, G:0.17, T:0.19
Consensus pattern (29 bp):
AATGACCAAAATGTCCCCTAGGTGACCAT
Found at i:39590 original size:87 final size:87
Alignment explanation
Indices: 39473--39794 Score: 439
Period size: 87 Copynumber: 3.7 Consensus size: 87
39463 GACTTCCTTT
* *
39473 CTTTGAAGAAATGCACCGCCTTAACTTGATTCACCGAATCACCATGATCTATTTGAAAATATGTT
1 CTTTGAAGAAATGCACCGCATTAACTTGATTCACCGAATGACCATGATCTATTTGAAAATATGTT
39538 GCACCGAGCTCACCGAATTCAA
66 GCACCGAGCTCACCGAATTCAA
* *
39560 CTTTGAAGAAATGCACTGCATTAACCTGATTCACCGAATGACCATGATCTATTTGAAAATATGTT
1 CTTTGAAGAAATGCACCGCATTAACTTGATTCACCGAATGACCATGATCTATTTGAAAATATGTT
* * *
39625 GCACCGAGCTCACTGAATCCGA
66 GCACCGAGCTCACCGAATTCAA
* * *** * **
39647 CTTTGAAGAAGTAAGGCACTGCCCCAACTTGATTCACCGAATGATCATGATCTATTTGAAAACCT
1 CTTTGAAG-A--AATGCACCGCATTAACTTGATTCACCGAATGACCATGATCTATTTGAAAATAT
* * *
39712 GCTACACCGAGCTCACCAAATTCAA
63 GTTGCACCGAGCTCACCGAATTCAA
*
39737 -TTTGAAGAAATGCACCGTATTAACTTGATTCACCGAATGACCATGATCTATTTGAAAA
1 CTTTGAAGAAATGCACCGCATTAACTTGATTCACCGAATGACCATGATCTATTTGAAAA
39795 CCGAATCCAA
Statistics
Matches: 204, Mismatches: 28, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
86 43 0.21
87 88 0.43
88 2 0.01
89 7 0.03
90 64 0.31
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (87 bp):
CTTTGAAGAAATGCACCGCATTAACTTGATTCACCGAATGACCATGATCTATTTGAAAATATGTT
GCACCGAGCTCACCGAATTCAA
Found at i:39843 original size:73 final size:73
Alignment explanation
Indices: 39758--39922 Score: 321
Period size: 73 Copynumber: 2.3 Consensus size: 73
39748 GCACCGTATT
39758 AACTTGATTCACCGAATGACCATGATCTATTTGAAAACCGAATCCAAATTTAGTAGAAATAAGTC
1 AACTTGATTCACCGAATGACCATGATCTATTTGAAAACCGAATCCAAATTTAGTAGAAATAAGTC
39823 ATCGCCTG
66 ATCGCCTG
39831 AACTTGATTCACCGAATGACCATGATCTATTTGAAAACCGAATCCAAATTTAGTAGAAATAAGTC
1 AACTTGATTCACCGAATGACCATGATCTATTTGAAAACCGAATCCAAATTTAGTAGAAATAAGTC
39896 ATCGCCTG
66 ATCGCCTG
*
39904 AACTGGATTCACCGAATGA
1 AACTTGATTCACCGAATGA
39923 TCCTGAATTG
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 91 1.00
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.27
Consensus pattern (73 bp):
AACTTGATTCACCGAATGACCATGATCTATTTGAAAACCGAATCCAAATTTAGTAGAAATAAGTC
ATCGCCTG
Found at i:44471 original size:2 final size:2
Alignment explanation
Indices: 44418--44454 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
44408 GTGCAGCAAG
*
44418 AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
44455 CCAAGGAAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:51114 original size:9 final size:9
Alignment explanation
Indices: 51100--51133 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
51090 CCTCATTAAT
51100 ATTTCTCCA
1 ATTTCTCCA
51109 ATTTCTCCA
1 ATTTCTCCA
*
51118 ATTTCTCCC
1 ATTTCTCCA
51127 ATTTCTC
1 ATTTCTC
51134 TTCTTCAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.18, C:0.35, G:0.00, T:0.47
Consensus pattern (9 bp):
ATTTCTCCA
Done.