Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006886.1 Corchorus capsularis cultivar CVL-1 contig06907, 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: 20397
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Found at i:3286 original size:26 final size:26
Alignment explanation
Indices: 3247--3398 Score: 143
Period size: 26 Copynumber: 5.8 Consensus size: 26
3237 AAATTAGTAG
*
3247 TCAGTAAAAAAGAGTAGGAAACAATAT
1 TCAGT-AAAAAGAGTAAGAAACAATAT
* *
3274 TCAATAAAAAGAGTAAGAAA-AGAGCCA-
1 TCAGTAAAAAGAGTAAGAAACA-A--TAT
*
3301 TCAGTAAAAAGAGTAAGAAACAGTAT
1 TCAGTAAAAAGAGTAAGAAACAATAT
* *
3327 TTAGTAAGAAGAGT-AGAAA-AGAGTCA-
1 TCAGTAAAAAGAGTAAGAAACA-A-T-AT
*
3353 TCAGTAAAAAGAGTAGGAAACAATAT
1 TCAGTAAAAAGAGTAAGAAACAATAT
3379 TCAGTAAAAAGAGTAAGAAA
1 TCAGTAAAAAGAGTAAGAAA
3399 AGCGCAATAG
Statistics
Matches: 101, Mismatches: 13, Indels: 23
0.74 0.09 0.17
Matches are distributed among these distances:
24 1 0.01
25 8 0.08
26 60 0.59
27 29 0.29
28 3 0.03
ACGTcount: A:0.55, C:0.07, G:0.20, T:0.17
Consensus pattern (26 bp):
TCAGTAAAAAGAGTAAGAAACAATAT
Found at i:3364 original size:52 final size:53
Alignment explanation
Indices: 3247--3400 Score: 238
Period size: 52 Copynumber: 2.9 Consensus size: 53
3237 AAATTAGTAG
*
3247 TCAGTAAAAAAGAGTAGGAAACAATATTCAATAAAAAGAGTAAGAAAAGAGCCA
1 TCAGT-AAAAAGAGTAGGAAACAATATTCAGTAAAAAGAGTAAGAAAAGAGCCA
* * * * *
3301 TCAGTAAAAAGAGTAAGAAACAGTATTTAGTAAGAAGAGT-AGAAAAGAGTCA
1 TCAGTAAAAAGAGTAGGAAACAATATTCAGTAAAAAGAGTAAGAAAAGAGCCA
3353 TCAGTAAAAAGAGTAGGAAACAATATTCAGTAAAAAGAGTAAGAAAAG
1 TCAGTAAAAAGAGTAGGAAACAATATTCAGTAAAAAGAGTAAGAAAAG
3401 CGCAATAGTA
Statistics
Matches: 89, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
52 47 0.53
53 37 0.42
54 5 0.06
ACGTcount: A:0.55, C:0.07, G:0.21, T:0.17
Consensus pattern (53 bp):
TCAGTAAAAAGAGTAGGAAACAATATTCAGTAAAAAGAGTAAGAAAAGAGCCA
Found at i:3582 original size:40 final size:40
Alignment explanation
Indices: 3513--3605 Score: 100
Period size: 40 Copynumber: 2.3 Consensus size: 40
3503 ATGGTAAAGA
* *
3513 GTAAAGAGTAAAGTAAAGAGAGATAAGTAAA-AAGAAAATT
1 GTAAAGAGTAAAGTAAAAAGAGATAAGTAAAGAA-AAAATG
* *
3553 GTAAAGAGTGAAGTAAAAAGTA-ATCAGTAAAGAAAAAATG
1 GTAAAGAGTAAAGTAAAAAG-AGATAAGTAAAGAAAAAATG
**
3593 GTAATCAGTAAAG
1 GTAAAGAGTAAAG
3606 AGTAATAGTA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
40 41 0.93
41 3 0.07
ACGTcount: A:0.57, C:0.02, G:0.23, T:0.18
Consensus pattern (40 bp):
GTAAAGAGTAAAGTAAAAAGAGATAAGTAAAGAAAAAATG
Found at i:3651 original size:55 final size:56
Alignment explanation
Indices: 3564--3687 Score: 153
Period size: 55 Copynumber: 2.2 Consensus size: 56
3554 TAAAGAGTGA
* * *
3564 AGTAAAAAGTAATCAGTAAAGAAAAAATGGTAATCAGTAAAGAGT-AATAGTAATC
1 AGTAAAAAGTAATCAGTAAAGAAAAAAAGGTAATCACTAAAAAGTAAATAGTAATC
* ** *
3619 AGTAAGAAGTAATC-GTAATTAATAAAAAGGTAATCACTAAAAAGTACAATGGTAATC
1 AGTAAAAAGTAATCAGTAAAGAA-AAAAAGGTAATCACTAAAAAGTA-AATAGTAATC
3676 AGTAAAAAGTAA
1 AGTAAAAAGTAA
3688 AGGTAATCAG
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
54 6 0.10
55 32 0.55
57 20 0.34
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (56 bp):
AGTAAAAAGTAATCAGTAAAGAAAAAAAGGTAATCACTAAAAAGTAAATAGTAATC
Found at i:3675 original size:22 final size:22
Alignment explanation
Indices: 3641--3788 Score: 180
Period size: 22 Copynumber: 6.9 Consensus size: 22
3631 TCGTAATTAA
* *
3641 TAAAAAGGTAATCACTAAAAAG
1 TAAAATGGTAATCAGTAAAAAG
*
3663 TACAATGGTAATCAGTAAAAAG
1 TAAAATGGTAATCAGTAAAAAG
*
3685 T-AAA-GGTAATCAGTGAAAAG
1 TAAAATGGTAATCAGTAAAAAG
*
3705 TAAAATGGTAATTAG-AAAAGAG
1 TAAAATGGTAATCAGTAAAA-AG
*
3727 TAAAAGGGTAATCAGTAAAAAG
1 TAAAATGGTAATCAGTAAAAAG
*
3749 TAAAATGGTAATTAGTAAAAAG
1 TAAAATGGTAATCAGTAAAAAG
3771 T-AAA-GAGTAATCAGTAAA
1 TAAAATG-GTAATCAGTAAA
3789 GAAAAAAAAT
Statistics
Matches: 109, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
20 17 0.16
21 22 0.20
22 66 0.61
23 4 0.04
ACGTcount: A:0.54, C:0.05, G:0.20, T:0.22
Consensus pattern (22 bp):
TAAAATGGTAATCAGTAAAAAG
Found at i:3687 original size:64 final size:64
Alignment explanation
Indices: 3641--3790 Score: 169
Period size: 64 Copynumber: 2.3 Consensus size: 64
3631 TCGTAATTAA
* * * *
3641 TAAAAAGGTAATCACTAAAA-AGTACAATGGTAATCAGTAAAAAGTAAAGGTAATCAGTGAAAAG
1 TAAAAAGGTAATCA-GAAAAGAGTAAAAGGGTAATCAGTAAAAAGTAAAAGTAATCAGTGAAAAG
* * * *
3705 TAAAATGGTAATTAGAAAAGAGTAAAAGGGTAATCAGTAAAAAGTAAAATGGTAATTAGTAAAAA
1 TAAAAAGGTAATCAGAAAAGAGTAAAAGGGTAATCAGTAAAAAGTAAAA--GTAATCAGTGAAAA
3770 G
64 G
* *
3771 TAAAGA-GTAATCAGTAAAGA
1 TAAAAAGGTAATCAGAAAAGA
3791 AAAAAAATAG
Statistics
Matches: 71, Mismatches: 12, Indels: 5
0.81 0.14 0.06
Matches are distributed among these distances:
63 4 0.06
64 38 0.54
65 12 0.17
66 17 0.24
ACGTcount: A:0.54, C:0.05, G:0.20, T:0.21
Consensus pattern (64 bp):
TAAAAAGGTAATCAGAAAAGAGTAAAAGGGTAATCAGTAAAAAGTAAAAGTAATCAGTGAAAAG
Found at i:3779 original size:14 final size:14
Alignment explanation
Indices: 3762--3831 Score: 68
Period size: 14 Copynumber: 4.9 Consensus size: 14
3752 AATGGTAATT
3762 AGTAAAAAGTAAAG
1 AGTAAAAAGTAAAG
**
3776 AGTAATCAGTAAAG
1 AGTAAAAAGTAAAG
**
3790 AAAAAAAATAGTAAAG
1 -AGTAAAA-AGTAAAG
**
3806 AGTAATCAGTAAAG
1 AGTAAAAAGTAAAG
3820 AGTAAAAAGTAA
1 AGTAAAAAGTAA
3832 TCAGTAAAGA
Statistics
Matches: 42, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
14 29 0.69
15 6 0.14
16 7 0.17
ACGTcount: A:0.61, C:0.03, G:0.19, T:0.17
Consensus pattern (14 bp):
AGTAAAAAGTAAAG
Found at i:3798 original size:44 final size:43
Alignment explanation
Indices: 3644--3824 Score: 206
Period size: 44 Copynumber: 4.2 Consensus size: 43
3634 TAATTAATAA
* * *
3644 AAAG-GTAATCACTAAAAAGTACAATGGTAATCAGTAAAAAGT
1 AAAGAGTAATCAGTAAAAAGTAAAATGGTAATTAGTAAAAAGT
*
3686 AAAG-GTAATCAGTGAAAAGTAAAATGGTAATTAG-AAAAGAGT
1 AAAGAGTAATCAGTAAAAAGTAAAATGGTAATTAGTAAAA-AGT
*
3728 AAAAGGGTAATCAGTAAAAAGTAAAATGGTAATTAGTAAAAAGT
1 -AAAGAGTAATCAGTAAAAAGTAAAATGGTAATTAGTAAAAAGT
** * ** **
3772 AAAGAGTAATCAGTAAAGAAAAAAAATAGTAAAGAGTAATCAGT
1 AAAGAGTAATCAGTAAA-AAGTAAAATGGTAATTAGTAAAAAGT
3816 AAAGAGTAA
1 AAAGAGTAA
3825 AAAGTAATCA
Statistics
Matches: 121, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
41 4 0.03
42 33 0.27
43 20 0.17
44 60 0.50
45 4 0.03
ACGTcount: A:0.55, C:0.04, G:0.20, T:0.20
Consensus pattern (43 bp):
AAAGAGTAATCAGTAAAAAGTAAAATGGTAATTAGTAAAAAGT
Found at i:3825 original size:21 final size:21
Alignment explanation
Indices: 3799--3841 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
3789 GAAAAAAAAT
*
3799 AGTAAAGAGTAATCAGTAAAG
1 AGTAAAAAGTAATCAGTAAAG
3820 AGTAAAAAGTAATCAGTAAAG
1 AGTAAAAAGTAATCAGTAAAG
3841 A
1 A
3842 AAAAATAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.56, C:0.05, G:0.21, T:0.19
Consensus pattern (21 bp):
AGTAAAAAGTAATCAGTAAAG
Found at i:3851 original size:21 final size:21
Alignment explanation
Indices: 3806--3852 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
3796 AATAGTAAAG
*
3806 AGTAATCAGTAAAGAGTAAAA
1 AGTAATCAGTAAAGAGAAAAA
3827 AGTAATCAGTAAAGA-AAAAA
1 AGTAATCAGTAAAGAGAAAAA
3847 TAGTAA
1 -AGTAA
3853 GGAGTGAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 4 0.17
21 20 0.83
ACGTcount: A:0.60, C:0.04, G:0.17, T:0.19
Consensus pattern (21 bp):
AGTAATCAGTAAAGAGAAAAA
Found at i:3852 original size:35 final size:34
Alignment explanation
Indices: 3799--3938 Score: 94
Period size: 35 Copynumber: 4.2 Consensus size: 34
3789 GAAAAAAAAT
**
3799 AGTAAAGAGTAATCAGTAAAGAGTAAAAAGTAATC
1 AGTAAAGAAAAAT-AGTAAAGAGTAAAAAGTAATC
* * * *
3834 AGTAAAGAAAAAATAGTAAGGAGTGAGAAGAAATC
1 AGTAAAG-AAAAATAGTAAAGAGTAAAAAGTAATC
* *
3869 AGT-----AAAATGGTAAAG-GATAAAGAGTAATC
1 AGTAAAGAAAAATAGTAAAGAG-TAAAAAGTAATC
* * **
3898 AGTAGAGAAAAATGGTAAAGAGTAAAATCTTAATC
1 AGTAAAGAAAAATAGTAAAGAGTAAAA-AGTAATC
3933 AGTAAA
1 AGTAAA
3939 AAGTAATGGC
Statistics
Matches: 80, Mismatches: 16, Indels: 18
0.70 0.14 0.16
Matches are distributed among these distances:
28 1 0.01
29 21 0.26
34 16 0.20
35 38 0.47
36 4 0.05
ACGTcount: A:0.54, C:0.04, G:0.22, T:0.19
Consensus pattern (34 bp):
AGTAAAGAAAAATAGTAAAGAGTAAAAAGTAATC
Found at i:7575 original size:55 final size:55
Alignment explanation
Indices: 7486--7628 Score: 234
Period size: 55 Copynumber: 2.6 Consensus size: 55
7476 ATTGGGGGTT
* * *
7486 ACTTGAGTTGAAAACCCAAAAAGGGCGGCACAAGTGAATGATGGAAAAGGAGAAA
1 ACTTGAGTTGAAAACCCGAAAAGGGCGGCTCAAGTGAAGGATGGAAAAGGAGAAA
7541 ACTTGAGTTGAAAACCCGAAAAGGGCGGCTCAAGTGAAGGATGGAAAAGGAGAAA
1 ACTTGAGTTGAAAACCCGAAAAGGGCGGCTCAAGTGAAGGATGGAAAAGGAGAAA
*
7596 ACTTGAGTTGAAAACCCGCAAAA-GGCAGCTCAA
1 ACTTGAGTTGAAAACCCG-AAAAGGGCGGCTCAA
7629 AGTGGAACAG
Statistics
Matches: 83, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
55 79 0.95
56 4 0.05
ACGTcount: A:0.43, C:0.15, G:0.29, T:0.13
Consensus pattern (55 bp):
ACTTGAGTTGAAAACCCGAAAAGGGCGGCTCAAGTGAAGGATGGAAAAGGAGAAA
Found at i:9276 original size:10 final size:10
Alignment explanation
Indices: 9261--9289 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
9251 GTCCTTTCAG
9261 TAATGGGTCA
1 TAATGGGTCA
9271 TAATGGGTCA
1 TAATGGGTCA
9281 TAATGGGTC
1 TAATGGGTC
9290 TAGTTTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.28, C:0.10, G:0.31, T:0.31
Consensus pattern (10 bp):
TAATGGGTCA
Found at i:12371 original size:26 final size:26
Alignment explanation
Indices: 12325--12476 Score: 143
Period size: 26 Copynumber: 5.8 Consensus size: 26
12315 AAATTAGTAG
*
12325 TCAGTAAAAACGAGTAGGAAACAATAT
1 TCAGTAAAAA-GAGTAAGAAACAATAT
*
12352 TCAGTAAAAAGAGTAAGAAA-AGAGCCA-
1 TCAGTAAAAAGAGTAAGAAACA-A--TAT
*
12379 TCAGTAAAAAGAGTAAGAAACAGTAT
1 TCAGTAAAAAGAGTAAGAAACAATAT
* *
12405 TCAGTAAGAATAGT-AGAAA-AGAGTCA-
1 TCAGTAAAAAGAGTAAGAAACA-A-T-AT
*
12431 TCAGTAAAAAGAGTAGGAAACAATAT
1 TCAGTAAAAAGAGTAAGAAACAATAT
*
12457 TCAGTAAAGAGAGTAAGAAA
1 TCAGTAAAAAGAGTAAGAAA
12477 AGCGCAATAG
Statistics
Matches: 102, Mismatches: 12, Indels: 23
0.74 0.09 0.17
Matches are distributed among these distances:
24 1 0.01
25 8 0.08
26 54 0.53
27 36 0.35
28 3 0.03
ACGTcount: A:0.53, C:0.09, G:0.21, T:0.17
Consensus pattern (26 bp):
TCAGTAAAAAGAGTAAGAAACAATAT
Found at i:12440 original size:52 final size:53
Alignment explanation
Indices: 12325--12478 Score: 238
Period size: 52 Copynumber: 2.9 Consensus size: 53
12315 AAATTAGTAG
12325 TCAGTAAAAACGAGTAGGAAACAATATTCAGTAAAAAGAGTAAGAAAAGAGCCA
1 TCAGTAAAAA-GAGTAGGAAACAATATTCAGTAAAAAGAGTAAGAAAAGAGCCA
* * * * *
12379 TCAGTAAAAAGAGTAAGAAACAGTATTCAGTAAGAATAGT-AGAAAAGAGTCA
1 TCAGTAAAAAGAGTAGGAAACAATATTCAGTAAAAAGAGTAAGAAAAGAGCCA
*
12431 TCAGTAAAAAGAGTAGGAAACAATATTCAGTAAAGAGAGTAAGAAAAG
1 TCAGTAAAAAGAGTAGGAAACAATATTCAGTAAAAAGAGTAAGAAAAG
12479 CGCAATAGTA
Statistics
Matches: 89, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
52 46 0.52
53 33 0.37
54 10 0.11
ACGTcount: A:0.53, C:0.08, G:0.21, T:0.17
Consensus pattern (53 bp):
TCAGTAAAAAGAGTAGGAAACAATATTCAGTAAAAAGAGTAAGAAAAGAGCCA
Found at i:12633 original size:35 final size:34
Alignment explanation
Indices: 12558--12645 Score: 122
Period size: 35 Copynumber: 2.6 Consensus size: 34
12548 AGGCAATCAG
* *
12558 TAAAGAGTAATCAGTGAAAAAAAATGGTAAAGAG
1 TAAAGAGTAATCAGTAAAAAAAAATGGTAAAGAA
*
12592 TAAAGAGTAATCAGTAAAGAAAAAATGGTGAAGAA
1 TAAAGAGTAATCAGTAAA-AAAAAATGGTAAAGAA
* *
12627 TGAAGAGTAATTAGTAAAA
1 TAAAGAGTAATCAGTAAAA
12646 TGGTAAAGAG
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
34 18 0.38
35 30 0.62
ACGTcount: A:0.56, C:0.02, G:0.23, T:0.19
Consensus pattern (34 bp):
TAAAGAGTAATCAGTAAAAAAAAATGGTAAAGAA
Found at i:12701 original size:40 final size:38
Alignment explanation
Indices: 12534--12908 Score: 192
Period size: 40 Copynumber: 9.7 Consensus size: 38
12524 AGTGGTGATT
*
12534 AGTAAAAATTGAAAA-GGCAATCAGTAAAG---AGTAATC
1 AGTAAAAA--GAAAATGGTAATCAGTAAAGTAAAGTAATC
* **
12570 AGTGAAAA-AAAATGGTAAAGAGTAAAG---AGTAATC
1 AGTAAAAAGAAAATGGTAATCAGTAAAGTAAAGTAATC
* * *
12604 AGTAAAGAA-AAAATGGTGA--AG-AATG-AAGAGTAATT
1 AGTAAA-AAGAAAATGGTAATCAGTAAAGTAA-AGTAATC
* * **
12639 AGTAAAATGGTAAA-GAGTAAAGAGTAAAGTAAAGTGAGATC
1 AGTAAAA-AGAAAATG-GTAATCAGTAAAGTAAAGT-A-ATC
** *
12680 AGTAAAAAGAAAATGGTAAAGAGTGAAGTAAAAAGTAATC
1 AGTAAAAAGAAAATGGTAATCAGTAAAGT--AAAGTAATC
12720 AGTAAAGAA-AAAATGGTAATCAGTAAAGATTAATAGTAATC
1 AGTAAA-AAGAAAATGGTAATCAGTAAAG--TAA-AGTAATC
* * *
12761 AGTAAGAAG-TAATGGTAATCAGTAAA--AAGGTAATC
1 AGTAAAAAGAAAATGGTAATCAGTAAAGTAAAGTAATC
* *
12796 ACTAAAAAGTAAAATGGTAATCAGTAAAAAGTAAGGTAATC
1 AGTAAAAAG-AAAATGGTAATCAGT--AAAGTAAAGTAATC
* * *
12837 AGTGAAAAGTAAAATGGTAATTAGAAAAGAGTAAAAGGGTAATC
1 AGTAAAAAG-AAAATGGTAATCAG-TAA-AGT-AAA--GTAATC
* *
12881 AGTAAAAAGTAAAATTGTAATTAGTAAA
1 AGTAAAAAG-AAAATGGTAATCAGTAAA
12909 AAGTAAAGAG
Statistics
Matches: 273, Mismatches: 33, Indels: 60
0.75 0.09 0.16
Matches are distributed among these distances:
32 3 0.01
33 6 0.02
34 24 0.09
35 37 0.14
36 15 0.05
37 13 0.05
38 2 0.01
39 9 0.03
40 67 0.25
41 58 0.21
42 9 0.03
43 2 0.01
44 28 0.10
ACGTcount: A:0.54, C:0.04, G:0.22, T:0.21
Consensus pattern (38 bp):
AGTAAAAAGAAAATGGTAATCAGTAAAGTAAAGTAATC
Found at i:12760 original size:20 final size:21
Alignment explanation
Indices: 12713--12786 Score: 89
Period size: 20 Copynumber: 3.6 Consensus size: 21
12703 TGAAGTAAAA
*
12713 AGTAATCAGTAAAGAAAAAAT
1 AGTAATCAGTAAAGAAATAAT
* *
12734 GGTAATCAGTAAAG-ATTAAT
1 AGTAATCAGTAAAGAAATAAT
*
12754 AGTAATCAGT-AAGAAGTAAT
1 AGTAATCAGTAAAGAAATAAT
*
12774 GGTAATCAGTAAA
1 AGTAATCAGTAAA
12787 AAGGTAATCA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
19 3 0.07
20 27 0.60
21 15 0.33
ACGTcount: A:0.51, C:0.05, G:0.19, T:0.24
Consensus pattern (21 bp):
AGTAATCAGTAAAGAAATAAT
Found at i:12807 original size:22 final size:22
Alignment explanation
Indices: 12781--12956 Score: 175
Period size: 22 Copynumber: 8.2 Consensus size: 22
12771 AATGGTAATC
*
12781 AGTAAAAAGGTAATCACTAAAA
1 AGTAAAAAGGTAATCAGTAAAA
*
12803 AGTAAAATGGTAATCAGTAAAA
1 AGTAAAAAGGTAATCAGTAAAA
*
12825 AGT---AAGGTAATCAGTGAAA
1 AGTAAAAAGGTAATCAGTAAAA
* *
12844 AGTAAAATGGTAATTAG-AAAA
1 AGTAAAAAGGTAATCAGTAAAA
*
12865 GAGTAAAAGGGTAATCAGTAAAA
1 -AGTAAAAAGGTAATCAGTAAAA
** *
12888 AGTAAAATTGTAATTAGTAAAA
1 AGTAAAAAGGTAATCAGTAAAA
* * *
12910 AGTAAAGA-GTAATTAGTAAAG
1 AGTAAAAAGGTAATCAGTAAAA
**
12931 AGTAAAAA-GTAAAGAGTAAAA
1 AGTAAAAAGGTAATCAGTAAAA
12952 AGTAA
1 AGTAA
12957 TCAGTAAAGA
Statistics
Matches: 130, Mismatches: 19, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
19 17 0.13
21 37 0.28
22 72 0.55
23 4 0.03
ACGTcount: A:0.56, C:0.03, G:0.20, T:0.22
Consensus pattern (22 bp):
AGTAAAAAGGTAATCAGTAAAA
Found at i:12822 original size:15 final size:15
Alignment explanation
Indices: 12774--12804 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
12764 AAGAAGTAAT
*
12774 GGTAATCAGTAAAAA
1 GGTAATCACTAAAAA
12789 GGTAATCACTAAAAA
1 GGTAATCACTAAAAA
12804 G
1 G
12805 TAAAATGGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.10, G:0.19, T:0.19
Consensus pattern (15 bp):
GGTAATCACTAAAAA
Found at i:12891 original size:7 final size:7
Alignment explanation
Indices: 12881--12956 Score: 71
Period size: 7 Copynumber: 10.7 Consensus size: 7
12871 AAGGGTAATC
12881 AGTAAAA
1 AGTAAAA
12888 AGTAAAA
1 AGTAAAA
* **
12895 TTGTAATT
1 -AGTAAAA
12903 AGTAAAA
1 AGTAAAA
*
12910 AGTAAAG
1 AGTAAAA
**
12917 AGTAATT
1 AGTAAAA
*
12924 AGTAAAG
1 AGTAAAA
12931 AGTAAAA
1 AGTAAAA
*
12938 AGTAAAG
1 AGTAAAA
12945 AGTAAAA
1 AGTAAAA
12952 AGTAA
1 AGTAA
12957 TCAGTAAAGA
Statistics
Matches: 54, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
7 50 0.93
8 4 0.07
ACGTcount: A:0.59, C:0.00, G:0.18, T:0.22
Consensus pattern (7 bp):
AGTAAAA
Found at i:12964 original size:14 final size:14
Alignment explanation
Indices: 12903--12956 Score: 90
Period size: 14 Copynumber: 3.9 Consensus size: 14
12893 AATTGTAATT
12903 AGTAAAAAGTAAAG
1 AGTAAAAAGTAAAG
**
12917 AGTAATTAGTAAAG
1 AGTAAAAAGTAAAG
12931 AGTAAAAAGTAAAG
1 AGTAAAAAGTAAAG
12945 AGTAAAAAGTAA
1 AGTAAAAAGTAA
12957 TCAGTAAAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 36 1.00
ACGTcount: A:0.61, C:0.00, G:0.20, T:0.19
Consensus pattern (14 bp):
AGTAAAAAGTAAAG
Found at i:12976 original size:21 final size:21
Alignment explanation
Indices: 12938--12977 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
12928 AAGAGTAAAA
*
12938 AGTAAAGAGTAAAAAGTAATC
1 AGTAAAGAGAAAAAAGTAATC
12959 AGTAAAGA-AAAAATAGTAA
1 AGTAAAGAGAAAAA-AGTAA
12978 GGAGTGAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.62, C:0.03, G:0.17, T:0.17
Consensus pattern (21 bp):
AGTAAAGAGAAAAAAGTAATC
Found at i:12977 original size:35 final size:34
Alignment explanation
Indices: 12902--13063 Score: 113
Period size: 35 Copynumber: 4.8 Consensus size: 34
12892 AAATTGTAAT
* * *
12902 TAGTAAAAAGTAAAGAGTAATTAGTAAAGAGTAAAA
1 TAGTAAAGAGTAAAAAGTAATCAGTAAAGA--AAAA
12938 -AGTAAAGAGTAAAAAGTAATCAGTAAAGAAAAAA
1 TAGTAAAGAGTAAAAAGTAATCAGTAAAG-AAAAA
* * * *
12972 TAGTAAGGAGTGAGAAGAAATCAGT-----AAAA
1 TAGTAAAGAGTAAAAAGTAATCAGTAAAGAAAAA
* * *
13001 TGGTAAAG-GATAAACAGTAATCAGTAGAGAAAAA
1 TAGTAAAGAG-TAAAAAGTAATCAGTAAAGAAAAA
* **
13035 TGGTAAAGAGTAAAATCTTAATCAGTAAA
1 TAGTAAAGAGTAAAA-AGTAATCAGTAAA
13064 AAGTAATGGC
Statistics
Matches: 99, Mismatches: 17, Indels: 21
0.72 0.12 0.15
Matches are distributed among these distances:
28 1 0.01
29 21 0.21
34 20 0.20
35 56 0.57
36 1 0.01
ACGTcount: A:0.56, C:0.04, G:0.21, T:0.20
Consensus pattern (34 bp):
TAGTAAAGAGTAAAAAGTAATCAGTAAAGAAAAA
Found at i:17561 original size:33 final size:33
Alignment explanation
Indices: 17524--17644 Score: 154
Period size: 33 Copynumber: 3.7 Consensus size: 33
17514 AGCTAAAGGA
* *
17524 TCATGTGCCCGGTTGTGGCCAGGCATGGTCGAG
1 TCATGTGGCCGGTTGTGGCCGGGCATGGTCGAG
* *
17557 TCATGTGGCTGGTTGTGGCCGGGCATGGCCGAG
1 TCATGTGGCCGGTTGTGGCCGGGCATGGTCGAG
* *
17590 TCATGTGGCCGGTGGTGGCCGGGCAT-CTCCGAG
1 TCATGTGGCCGGTTGTGGCCGGGCATGGT-CGAG
* *
17623 TTATGTGGCTGGTTGTGGCCGG
1 TCATGTGGCCGGTTGTGGCCGG
17645 TGGTGGCCGG
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
33 76 1.00
ACGTcount: A:0.09, C:0.22, G:0.43, T:0.26
Consensus pattern (33 bp):
TCATGTGGCCGGTTGTGGCCGGGCATGGTCGAG
Found at i:17641 original size:43 final size:43
Alignment explanation
Indices: 17593--17674 Score: 155
Period size: 43 Copynumber: 1.9 Consensus size: 43
17583 GGCCGAGTCA
*
17593 TGTGGCCGGTGGTGGCCGGGCATCTCCGAGTTATGTGGCTGGT
1 TGTGGCCGGTGGTGGCCGGGCATCTCCGAGTCATGTGGCTGGT
17636 TGTGGCCGGTGGTGGCCGGGCATCTCCGAGTCATGTGGC
1 TGTGGCCGGTGGTGGCCGGGCATCTCCGAGTCATGTGGC
17675 CGGTCACAAG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.07, C:0.23, G:0.44, T:0.26
Consensus pattern (43 bp):
TGTGGCCGGTGGTGGCCGGGCATCTCCGAGTCATGTGGCTGGT
Done.