Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007294.1 Corchorus capsularis cultivar CVL-1 contig07315, 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: 17514
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Found at i:555 original size:2 final size:2
Alignment explanation
Indices: 548--574 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
538 AGAAATGGAG
548 AT AT AT 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 A
575 ATAATGAGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:922 original size:64 final size:64
Alignment explanation
Indices: 821--946 Score: 252
Period size: 64 Copynumber: 2.0 Consensus size: 64
811 TATATATATA
821 TAAAATAATGAGAGACAAATGAAGGTAAACCCTCTTGGTGGTGGGGCCGGGTGAAGTAGGGGAT
1 TAAAATAATGAGAGACAAATGAAGGTAAACCCTCTTGGTGGTGGGGCCGGGTGAAGTAGGGGAT
885 TAAAATAATGAGAGACAAATGAAGGTAAACCCTCTTGGTGGTGGGGCCGGGTGAAGTAGGGG
1 TAAAATAATGAGAGACAAATGAAGGTAAACCCTCTTGGTGGTGGGGCCGGGTGAAGTAGGGG
947 GATTGGGTTA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.33, C:0.11, G:0.37, T:0.20
Consensus pattern (64 bp):
TAAAATAATGAGAGACAAATGAAGGTAAACCCTCTTGGTGGTGGGGCCGGGTGAAGTAGGGGAT
Found at i:12352 original size:36 final size:34
Alignment explanation
Indices: 12304--12408 Score: 96
Period size: 30 Copynumber: 3.1 Consensus size: 34
12294 AATGGGATCA
12304 TTCAGAAAAGTAAAAAGGGTAATCAGAGTAATTAAG
1 TTCA-AAAAGTAAAAA-GGTAATCAGAGTAATTAAG
**
12340 TTCCAAAAAGTAAAAAAGACAATC--AGTAATTAAG
1 TT-CAAAAAGT-AAAAAGGTAATCAGAGTAATTAAG
* *
12374 TTCAATAAG-AAAAA-GTAATC--AGTGATTAAG
1 TTCAAAAAGTAAAAAGGTAATCAGAGTAATTAAG
12404 TTCAA
1 TTCAA
12409 TAAGAAAGAT
Statistics
Matches: 61, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
30 18 0.30
31 5 0.08
33 6 0.10
34 12 0.20
36 13 0.21
37 7 0.11
ACGTcount: A:0.51, C:0.09, G:0.16, T:0.24
Consensus pattern (34 bp):
TTCAAAAAGTAAAAAGGTAATCAGAGTAATTAAG
Found at i:12395 original size:30 final size:30
Alignment explanation
Indices: 12330--12429 Score: 112
Period size: 30 Copynumber: 3.2 Consensus size: 30
12320 GGGTAATCAG
* *
12330 AGTAATTAAGTTCCAAAAAGTAAAAAAGACAATC
1 AGTAATTAAGTT-CAATAAG--AAAAAG-TAATC
12364 AGTAATTAAGTTCAATAAGAAAAAGTAATC
1 AGTAATTAAGTTCAATAAGAAAAAGTAATC
*
12394 AGTGATTAAGTTCAATAAGAAAGATA-TAATC
1 AGTAATTAAGTTCAATAAGAAA-A-AGTAATC
12425 AGTAA
1 AGTAA
12430 AAGGTAAAAT
Statistics
Matches: 60, Mismatches: 4, Indels: 7
0.85 0.06 0.10
Matches are distributed among these distances:
30 25 0.42
31 16 0.27
32 1 0.02
33 6 0.10
34 12 0.20
ACGTcount: A:0.53, C:0.08, G:0.14, T:0.25
Consensus pattern (30 bp):
AGTAATTAAGTTCAATAAGAAAAAGTAATC
Found at i:12490 original size:20 final size:22
Alignment explanation
Indices: 12449--12529 Score: 77
Period size: 20 Copynumber: 3.8 Consensus size: 22
12439 TGGCAATTAA
12449 TAAAGAA-TAA-AGTGATAATCAG
1 TAAAGAAGTAATAGT-A-AATCAG
12471 TAAAG-AGTAATAG-AAATCAG
1 TAAAGAAGTAATAGTAAATCAG
12491 T-AAGAAGTAATAGTAAA-CAG
1 TAAAGAAGTAATAGTAAATCAG
12511 TAAA-AAGGTAATCAGTAAA
1 TAAAGAA-GTAAT-AGTAAA
12530 AAAGTAAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 14
0.79 0.00 0.21
Matches are distributed among these distances:
19 3 0.06
20 21 0.40
21 12 0.23
22 14 0.27
23 2 0.04
ACGTcount: A:0.56, C:0.05, G:0.19, T:0.21
Consensus pattern (22 bp):
TAAAGAAGTAATAGTAAATCAG
Found at i:12526 original size:15 final size:15
Alignment explanation
Indices: 12502--12537 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
12492 AAGAAGTAAT
12502 AGTAAACAGTAAAAA
1 AGTAAACAGTAAAAA
* *
12517 GGTAATCAGTAAAAA
1 AGTAAACAGTAAAAA
12532 AGTAAA
1 AGTAAA
12538 AAGGTATCTG
Statistics
Matches: 17, Mismatches: 4, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.61, C:0.06, G:0.17, T:0.17
Consensus pattern (15 bp):
AGTAAACAGTAAAAA
Found at i:12630 original size:8 final size:8
Alignment explanation
Indices: 12617--12657 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
12607 TCAGTAAGAA
12617 GTAAAAAG
1 GTAAAAAG
12625 GTAAAAAG
1 GTAAAAAG
**
12633 GTAATCA-
1 GTAAAAAG
12640 GTAAAAA-
1 GTAAAAAG
12647 GTAAAAAG
1 GTAAAAAG
12655 GTA
1 GTA
12658 TCTGAAAGGG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 12 0.43
8 16 0.57
ACGTcount: A:0.59, C:0.02, G:0.22, T:0.17
Consensus pattern (8 bp):
GTAAAAAG
Found at i:12650 original size:22 final size:22
Alignment explanation
Indices: 12489--12779 Score: 159
Period size: 22 Copynumber: 13.0 Consensus size: 22
12479 AATAGAAATC
* *
12489 AGTAAGAA-GTAAT-AGTAAAC
1 AGTAAAAAGGTAATCAGTAAAA
12509 AGTAAAAAGGTAATCAGTAAAAA
1 AGTAAAAAGGTAATCAGT-AAAA
* *
12532 AGTAAAAAGGT-ATCTG-AAAG
1 AGTAAAAAGGTAATCAGTAAAA
* * * *
12552 GGTAAAATGGTAATTAGTAAAG
1 AGTAAAAAGGTAATCAGTAAAA
** * *
12574 AGTAAAGTGATAATCAGTAAAG
1 AGTAAAAAGGTAATCAGTAAAA
* * *
12596 AGT-AATA-GAAATCAGTAAGA
1 AGTAAAAAGGTAATCAGTAAAA
12616 AGTAAAAAGGTAAAAAGGTAATCAGTAAAA
1 AGTAAAAAGGT---AA--T---CAGTAAAA
* *
12646 AGTAAAAAGGT-ATCTG-AAAG
1 AGTAAAAAGGTAATCAGTAAAA
* * * *
12666 GGTAAAATGGTAATTAGTAAAG
1 AGTAAAAAGGTAATCAGTAAAA
* * *
12688 AGTAAAATGGTAATCCGTAACA
1 AGTAAAAAGGTAATCAGTAAAA
12710 AGT-AAAAGAGTAATCAGTAAAAA
1 AGTAAAAAG-GTAATCAGT-AAAA
* *
12733 AGGTAAAAATGGTAATTAGTAAAG
1 A-GTAAAAA-GGTAATCAGTAAAA
*
12757 AGTAAAATGGTAATCAGTAAAA
1 AGTAAAAAGGTAATCAGTAAAA
12779 A
1 A
12780 AATAATAAAA
Statistics
Matches: 209, Mismatches: 40, Indels: 42
0.72 0.14 0.14
Matches are distributed among these distances:
20 43 0.21
21 22 0.11
22 78 0.37
23 24 0.11
24 7 0.03
25 14 0.07
26 2 0.01
27 1 0.00
30 18 0.09
ACGTcount: A:0.53, C:0.04, G:0.22, T:0.21
Consensus pattern (22 bp):
AGTAAAAAGGTAATCAGTAAAA
Found at i:12687 original size:114 final size:114
Alignment explanation
Indices: 12432--12768 Score: 436
Period size: 114 Copynumber: 2.9 Consensus size: 114
12422 ATCAGTAAAA
* * *
12432 GGTAAAATGGCAATTAATAAAGAATAAAGTGATAATCAGTAAAGAGTAATAGAAATCAGTAAGAA
1 GGTAAAATGGTAATTAGTAAAGAGTAAAGTGATAATCAGTAAAGAGTAATAGAAATCAGTAAGAA
*
12497 GTAATAGTAAACAGTAAAAAGGTAATCAGTAAAAAAGTAAAAAGGTATCTGAAAG
66 GT-A-A--AAA-GGTAAAAAGGTAATCAGT-AAAAAGTAAAAAGGTATCTGAAAG
12552 GGTAAAATGGTAATTAGTAAAGAGTAAAGTGATAATCAGTAAAGAGTAATAGAAATCAGTAAGAA
1 GGTAAAATGGTAATTAGTAAAGAGTAAAGTGATAATCAGTAAAGAGTAATAGAAATCAGTAAGAA
12617 GTAAAAAGGTAAAAAGGTAATCAGTAAAAAGTAAAAAGGTATCTGAAAG
66 GTAAAAAGGTAAAAAGGTAATCAGTAAAAAGTAAAAAGGTATCTGAAAG
* * * *
12666 GGTAAAATGGTAATTAGTAAAGAGTAAAATGGTAATCCGTAACA-AGTAAAAGAGTAATCAGT--
1 GGTAAAATGGTAATTAGTAAAGAGTAAAGTGATAATCAGTAA-AGAGTAATAGA--AATCAGTAA
* * *
12728 --A--AAAAAGGTAAAAATGGTAATTAGTAAAGAGTAAAATGGTA
63 GAAGTAAAAAGGTAAAAA-GGTAATCAGTAAAAAGTAAAAAGGTA
12769 ATCAGTAAAA
Statistics
Matches: 202, Mismatches: 11, Indels: 17
0.88 0.05 0.07
Matches are distributed among these distances:
110 13 0.06
111 23 0.11
112 1 0.00
114 71 0.35
115 18 0.09
116 10 0.05
118 1 0.00
119 1 0.00
120 64 0.32
ACGTcount: A:0.53, C:0.04, G:0.22, T:0.22
Consensus pattern (114 bp):
GGTAAAATGGTAATTAGTAAAGAGTAAAGTGATAATCAGTAAAGAGTAATAGAAATCAGTAAGAA
GTAAAAAGGTAAAAAGGTAATCAGTAAAAAGTAAAAAGGTATCTGAAAG
Found at i:12803 original size:15 final size:15
Alignment explanation
Indices: 12785--12824 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
12775 AAAAAAATAA
12785 TAAAAGAGTAAAAAG
1 TAAAAGAGTAAAAAG
**
12800 TAAAAGAGTAATCAG
1 TAAAAGAGTAAAAAG
12815 T-AAAGAGTAA
1 TAAAAGAGTAA
12825 CCAGTAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 9 0.39
15 14 0.61
ACGTcount: A:0.60, C:0.03, G:0.20, T:0.17
Consensus pattern (15 bp):
TAAAAGAGTAAAAAG
Found at i:12818 original size:22 final size:22
Alignment explanation
Indices: 12616--12824 Score: 118
Period size: 22 Copynumber: 9.5 Consensus size: 22
12606 ATCAGTAAGA
12616 AGTAAAAAGGTAAAA-AGGTAATC
1 AGTAAAAA-GTAAAAGA-GTAATC
12639 AGTAAAAAGTAAAA-AGGT-ATC
1 AGTAAAAAGTAAAAGA-GTAATC
* ** *
12660 TG-AAAGGGTAAAATG-GTAATT
1 AGTAAAAAGTAAAA-GAGTAATC
*
12681 AGTAAAGAGTAAAATG-GTAATC
1 AGTAAAAAGTAAAA-GAGTAATC
* *
12703 CGTAACAAGTAAAAGAGTAATC
1 AGTAAAAAGTAAAAGAGTAATC
*
12725 AGTAAAAAAGGTAAAA-ATGGTAATT
1 AGT-AAAAA-GTAAAAGA--GTAATC
*
12750 AGTAAAGAGTAAAATG-GTAATC
1 AGTAAAAAGTAAAA-GAGTAATC
* **
12772 AGTAAAAA--AATA-A-TAAAAG
1 AGTAAAAAGTAAAAGAGT-AATC
12791 AGTAAAAAGTAAAAGAGTAATC
1 AGTAAAAAGTAAAAGAGTAATC
*
12813 AGTAAAGAGTAA
1 AGTAAAAAGTAA
12825 CCAGTAAAGA
Statistics
Matches: 146, Mismatches: 23, Indels: 35
0.72 0.11 0.17
Matches are distributed among these distances:
18 1 0.01
19 10 0.07
20 14 0.10
21 11 0.08
22 72 0.49
23 20 0.14
24 10 0.07
25 8 0.05
ACGTcount: A:0.55, C:0.04, G:0.21, T:0.21
Consensus pattern (22 bp):
AGTAAAAAGTAAAAGAGTAATC
Found at i:12821 original size:14 final size:14
Alignment explanation
Indices: 12787--12932 Score: 86
Period size: 14 Copynumber: 10.3 Consensus size: 14
12777 AAAAATAATA
**
12787 AAAGAGTAAAAAGT
1 AAAGAGTAATCAGT
12801 AAAAGAGTAATCAGT
1 -AAAGAGTAATCAGT
*
12816 AAAGAGTAACCAGT
1 AAAGAGTAATCAGT
12830 AAAGAAAAATGGTAATCAGT
1 AAAG----A--GTAATCAGT
12850 AAAGAGTAATCAGT
1 AAAGAGTAATCAGT
** *
12864 AAAGAAAAAT-GGT
1 AAAGAGTAATCAGT
**
12877 AAAGAGTAAAGAGT
1 AAAGAGTAATCAGT
**
12891 AAAGA--AAAGAGT
1 AAAGAGTAATCAGT
12903 AAAGAGTAA--AGT
1 AAAGAGTAATCAGT
* *
12915 TAAGAGTAATCAGC
1 AAAGAGTAATCAGT
12929 AAAG
1 AAAG
12933 TAAAATGGCA
Statistics
Matches: 106, Mismatches: 14, Indels: 23
0.74 0.10 0.16
Matches are distributed among these distances:
12 23 0.22
13 9 0.08
14 48 0.45
15 12 0.11
16 1 0.01
18 1 0.01
20 12 0.11
ACGTcount: A:0.56, C:0.05, G:0.23, T:0.16
Consensus pattern (14 bp):
AAAGAGTAATCAGT
Found at i:12846 original size:34 final size:34
Alignment explanation
Indices: 12807--12991 Score: 173
Period size: 34 Copynumber: 5.5 Consensus size: 34
12797 AAGTAAAAGA
* *
12807 GTAATCAGTAAAGAGTAACCAGTAAAGAAAAATG
1 GTAAACAGTAAAGAGTAATCAGTAAAGAAAAATG
*
12841 GTAATCAGTAAAGAGTAATCAGTAAAGAAAAATG
1 GTAAACAGTAAAGAGTAATCAGTAAAGAAAAATG
* * *
12875 GTAAAGAGTAAAGAGTAA--AGAAAAGAGTAAA-G
1 GTAAACAGTAAAGAGTAATCAGTAAAGA-AAAATG
* * *
12907 AGT-AA-AGTTAAGAGTAATCAGCAAAGTAAAATG
1 -GTAAACAGTAAAGAGTAATCAGTAAAGAAAAATG
* * **
12940 GCAAAAAGTAAAAGAGTAATCAGTAAAGTGAAATG
1 GTAAACAGT-AAAGAGTAATCAGTAAAGAAAAATG
* *
12975 ATAAAGAGTAAAGAGTA
1 GTAAACAGTAAAGAGTA
12992 GAGTAAAGAG
Statistics
Matches: 127, Mismatches: 16, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
31 11 0.09
32 14 0.11
33 14 0.11
34 60 0.47
35 28 0.22
ACGTcount: A:0.55, C:0.05, G:0.23, T:0.18
Consensus pattern (34 bp):
GTAAACAGTAAAGAGTAATCAGTAAAGAAAAATG
Found at i:12849 original size:20 final size:20
Alignment explanation
Indices: 12821--12888 Score: 67
Period size: 20 Copynumber: 3.7 Consensus size: 20
12811 TCAGTAAAGA
*
12821 GTAACCAGTAAAGAAAAATG
1 GTAATCAGTAAAGAAAAATG
12841 GTAATCAGTAAAG----A--
1 GTAATCAGTAAAGAAAAATG
12855 GTAATCAGTAAAGAAAAATG
1 GTAATCAGTAAAGAAAAATG
**
12875 GTAAAGAGTAAAGA
1 GTAATCAGTAAAGA
12889 GTAAAGAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
14 13 0.33
16 1 0.03
18 1 0.03
20 24 0.62
ACGTcount: A:0.54, C:0.06, G:0.22, T:0.18
Consensus pattern (20 bp):
GTAATCAGTAAAGAAAAATG
Found at i:12857 original size:7 final size:7
Alignment explanation
Indices: 12847--13004 Score: 72
Period size: 7 Copynumber: 23.7 Consensus size: 7
12837 AATGGTAATC
12847 AGTAAAG
1 AGTAAAG
**
12854 AGTAATC
1 AGTAAAG
12861 AGTAAAG
1 AGTAAAG
*
12868 A-AAAATG
1 AGTAAA-G
12875 -GTAAAG
1 AGTAAAG
12881 AGTAAAG
1 AGTAAAG
12888 AGTAAAG
1 AGTAAAG
12895 A--AAAG
1 AGTAAAG
12900 AGTAAAG
1 AGTAAAG
12907 AGT-AA-
1 AGTAAAG
*
12912 AGTTAAG
1 AGTAAAG
**
12919 AGTAATC
1 AGTAAAG
*
12926 AG-CAA-
1 AGTAAAG
12931 AGTAAA-
1 AGTAAAG
* *
12937 ATGGCAAAA
1 A--GTAAAG
12946 AGTAAAAG
1 AGT-AAAG
**
12954 AGTAATC
1 AGTAAAG
12961 AGTAAAG
1 AGTAAAG
*
12968 TG-AAATG
1 AGTAAA-G
12975 A-TAAAG
1 AGTAAAG
12981 AGTAAAG
1 AGTAAAG
12988 AGT--AG
1 AGTAAAG
12993 AGTAAAG
1 AGTAAAG
13000 AGTAA
1 AGTAA
13005 TCAACAAAGG
Statistics
Matches: 113, Mismatches: 21, Indels: 34
0.67 0.12 0.20
Matches are distributed among these distances:
5 15 0.13
6 17 0.15
7 70 0.62
8 10 0.09
9 1 0.01
ACGTcount: A:0.56, C:0.03, G:0.24, T:0.17
Consensus pattern (7 bp):
AGTAAAG
Found at i:12878 original size:27 final size:26
Alignment explanation
Indices: 12847--12912 Score: 89
Period size: 27 Copynumber: 2.5 Consensus size: 26
12837 AATGGTAATC
*
12847 AGTAAAGAGTAATCAGTAAAGAAAA-
1 AGTAAAGAGTAAACAGTAAAGAAAAG
*
12872 ATGGTAAAGAGTAAAGAGTAAAGAAAAG
1 A--GTAAAGAGTAAACAGTAAAGAAAAG
12900 AGTAAAGAGTAAA
1 AGTAAAGAGTAAA
12913 GTTAAGAGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
25 1 0.03
26 12 0.33
27 22 0.61
28 1 0.03
ACGTcount: A:0.59, C:0.02, G:0.24, T:0.15
Consensus pattern (26 bp):
AGTAAAGAGTAAACAGTAAAGAAAAG
Found at i:12901 original size:19 final size:19
Alignment explanation
Indices: 12877--12923 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
12867 GAAAAATGGT
12877 AAAGAGTAAAGAGTAAAGA
1 AAAGAGTAAAGAGTAAAGA
*
12896 AAAGAGTAAAGAGTAAAGT
1 AAAGAGTAAAGAGTAAAGA
*
12915 TAAGAGTAA
1 AAAGAGTAA
12924 TCAGCAAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.60, C:0.00, G:0.26, T:0.15
Consensus pattern (19 bp):
AAAGAGTAAAGAGTAAAGA
Found at i:12965 original size:100 final size:100
Alignment explanation
Indices: 12794--13004 Score: 273
Period size: 100 Copynumber: 2.1 Consensus size: 100
12784 ATAAAAGAGT
* * **
12794 AAAA-AGTAAAAGAGTAATCAGTAAAGAGTAACCAGTAAAGAAAAATGGTAATCAGTAAAGAGTA
1 AAAAGAGT-AAAGAGTAA-CAGTAAAGAGTAACCAGCAAAGAAAAATGGCAAAAAGTAAAGAGTA
*
12858 ATCAGTAAAGAAAAATGGTAAAGAGTAAAGAGTAAAG
64 ATCAGTAAAGAAAAATGATAAAGAGTAAAGAGTAAAG
* * *
12895 AAAAGAGTAAAGAGTAA-AGTTAAGAGTAATCAGCAAAGTAAAATGGCAAAAAGTAAAAGAGTAA
1 AAAAGAGTAAAGAGTAACAGTAAAGAGTAACCAGCAAAGAAAAATGGCAAAAAGT-AAAGAGTAA
** *
12959 TCAGTAAAGTGAAATGATAAAGAGTAAAGAGTAGAG
65 TCAGTAAAGAAAAATGATAAAGAGTAAAGAGTAAAG
*
12995 TAAAGAGTAA
1 AAAAGAGTAA
13005 TCAACAAAGG
Statistics
Matches: 96, Mismatches: 12, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
99 30 0.31
100 50 0.52
101 13 0.14
102 3 0.03
ACGTcount: A:0.56, C:0.04, G:0.23, T:0.17
Consensus pattern (100 bp):
AAAAGAGTAAAGAGTAACAGTAAAGAGTAACCAGCAAAGAAAAATGGCAAAAAGTAAAGAGTAAT
CAGTAAAGAAAAATGATAAAGAGTAAAGAGTAAAG
Found at i:12996 original size:12 final size:12
Alignment explanation
Indices: 12979--13003 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12969 GAAATGATAA
12979 AGAGTAAAGAGT
1 AGAGTAAAGAGT
12991 AGAGTAAAGAGT
1 AGAGTAAAGAGT
13003 A
1 A
13004 ATCAACAAAG
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:0.52, C:0.00, G:0.32, T:0.16
Consensus pattern (12 bp):
AGAGTAAAGAGT
Found at i:13001 original size:81 final size:80
Alignment explanation
Indices: 12896--13081 Score: 216
Period size: 81 Copynumber: 2.3 Consensus size: 80
12886 AGAGTAAAGA
* * *
12896 AAAGAGTAAAGAGTAAAGTTAAGAGTAATCAGCAAAGTAAAATGGCAAAAAGTAAAAGAGTAA-T
1 AAAGAGTAAAGAGTAAAGTAAAGAGTAATCAACAAAGGAAAATGGCAAAAAGT-AAAGAG-AAGT
12960 CAGTAAAGTGAAATGAT
64 CAGTAAAGTGAAATGAT
* * * *
12977 AAAGAGTAAAGAGTAGAGTAAAGAGTAATCAACAAAGGAAAATGGTAAAGAGTGAAGAGAAGTCA
1 AAAGAGTAAAGAGTAAAGTAAAGAGTAATCAACAAAGGAAAATGGCAAAAAGTAAAGAGAAGTCA
*
13042 GTAAA--GAAATTGGT
66 GTAAAGTGAAA-TGAT
* *
13056 GAAGAGTAAAAAGTAATCAGTAAAGA
1 AAAGAGTAAAGAGTAA--AGTAAAGA
13082 AAAATGGTAA
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
78 4 0.04
79 18 0.20
80 13 0.14
81 55 0.61
ACGTcount: A:0.54, C:0.04, G:0.25, T:0.17
Consensus pattern (80 bp):
AAAGAGTAAAGAGTAAAGTAAAGAGTAATCAACAAAGGAAAATGGCAAAAAGTAAAGAGAAGTCA
GTAAAGTGAAATGAT
Found at i:13035 original size:34 final size:34
Alignment explanation
Indices: 12991--13114 Score: 135
Period size: 34 Copynumber: 3.6 Consensus size: 34
12981 AGTAAAGAGT
**
12991 AGAGTAAAGAGTAATCAACAAAGGAAAATGGTAA
1 AGAGTAAAGAGTAATCAGTAAAGGAAAATGGTAA
* * *
13025 AGAGTGAAGAG-AAGTCAGTAAA-GAAATTGGTGA
1 AGAGTAAAGAGTAA-TCAGTAAAGGAAAATGGTAA
* *
13058 AGAGTAAAAAGTAATCAGTAAAGAAAAATGGTAA
1 AGAGTAAAGAGTAATCAGTAAAGGAAAATGGTAA
* *
13092 AGAGTAAAATATTAATCAGTAAA
1 AGAGT-AAAGAGTAATCAGTAAA
13115 AAGTAAATGG
Statistics
Matches: 74, Mismatches: 12, Indels: 7
0.80 0.13 0.08
Matches are distributed among these distances:
33 28 0.38
34 31 0.42
35 15 0.20
ACGTcount: A:0.54, C:0.04, G:0.23, T:0.19
Consensus pattern (34 bp):
AGAGTAAAGAGTAATCAGTAAAGGAAAATGGTAA
Found at i:13048 original size:148 final size:148
Alignment explanation
Indices: 12794--13114 Score: 334
Period size: 148 Copynumber: 2.2 Consensus size: 148
12784 ATAAAAGAGT
*
12794 AAAAAGTAAAAGAGTAATCAGTAAAGAGTAACCAGTAAAGAAAAATGGTAATCAGTAAAGAGTAA
1 AAAAAGTAAAAGAGTAATCAGTAAAGAGAAACCAGTAAAGAAAAATGGTAATCAGTAAAGAGTAA
** * *
12859 TCAGTAAAGAAAAATGGTAAAGAGTAAAGAGTAAAGAAAAGAGTAA-AGAGT-AA-AGTTAAGAG
66 TCAACAAAGAAAAATGGTAAAGAGTAAAGAGTAAAGAAAAGA--AATAG-GTGAAGAGTAAAAAG
*
12921 TAATCAGCAAAGTAAAATGGC
128 TAATCAGCAAAGAAAAATGGC
* ** * *
12942 AAAAAGTAAAAGAGTAATCAGTAAAGTGAAATGA-TAAAGAGTAAA-GAGT-A-GAGTAAAGAGT
1 AAAAAGTAAAAGAGTAATCAGTAAAGAGAAACCAGTAAAGA-AAAATG-GTAATCAGTAAAGAGT
* * * *
13003 AATCAACAAAGGAAAATGGTAAAGAGTGAAGAGAAGT-CAGTAAAGAAATTGGTGAAGAGTAAAA
64 AATCAACAAAGAAAAATGGTAAAGAGT-AA-AG-AGTAAAGAAAAGAAATAGGTGAAGAGTAAAA
* *
13067 AGTAATCAGTAAAGAAAAATGGT
126 AGTAATCAGCAAAGAAAAATGGC
* * *
13090 AAAGAGTAAAATATTAATCAGTAAA
1 AAAAAGTAAAAGAGTAATCAGTAAA
13115 AAGTAAATGG
Statistics
Matches: 145, Mismatches: 20, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
146 38 0.26
147 13 0.09
148 91 0.63
149 3 0.02
ACGTcount: A:0.55, C:0.04, G:0.23, T:0.18
Consensus pattern (148 bp):
AAAAAGTAAAAGAGTAATCAGTAAAGAGAAACCAGTAAAGAAAAATGGTAATCAGTAAAGAGTAA
TCAACAAAGAAAAATGGTAAAGAGTAAAGAGTAAAGAAAAGAAATAGGTGAAGAGTAAAAAGTAA
TCAGCAAAGAAAAATGGC
Found at i:13119 original size:22 final size:22
Alignment explanation
Indices: 13088--13156 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 22
13078 AAGAAAAATG
* *
13088 GTAAAGAGTAAAATATTAATCA
1 GTAAAAAGTAAAATAGTAATCA
* *
13110 GTAAAAAGT-AAATGGCAATCA
1 GTAAAAAGTAAAATAGTAATCA
*
13131 GTAAAGAA-TAAAATAGTAATTA
1 GTAAA-AAGTAAAATAGTAATCA
13153 GTAA
1 GTAA
13157 TCAGTACAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
21 15 0.39
22 23 0.61
ACGTcount: A:0.55, C:0.04, G:0.16, T:0.25
Consensus pattern (22 bp):
GTAAAAAGTAAAATAGTAATCA
Found at i:13170 original size:21 final size:21
Alignment explanation
Indices: 13139--13205 Score: 75
Period size: 21 Copynumber: 3.1 Consensus size: 21
13129 CAGTAAAGAA
13139 TAAAATAGTAATTAGTAATCAG
1 TAAAATAGTAA-TAGTAATCAG
*
13161 TACAA-AGTAA-AGAATAATCAG
1 TAAAATAGTAATAG--TAATCAG
*
13182 TAAAATAGTAATAGTAATCCG
1 TAAAATAGTAATAGTAATCAG
13203 TAA
1 TAA
13206 TTCAGTAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
19 2 0.05
21 25 0.66
22 9 0.24
23 2 0.05
ACGTcount: A:0.52, C:0.07, G:0.13, T:0.27
Consensus pattern (21 bp):
TAAAATAGTAATAGTAATCAG
Found at i:13171 original size:29 final size:28
Alignment explanation
Indices: 13109--13171 Score: 65
Period size: 29 Copynumber: 2.2 Consensus size: 28
13099 AATATTAATC
*
13109 AGTAAAAAGTAAATGGCAATCAGTAAAG
1 AGTAAAAAGTAAATAGCAATCAGTAAAG
* * *
13137 AATAAAATAGTAATTAGTAATCAGTACAA-
1 AGTAAAA-AGTAAATAGCAATCAGTA-AAG
13166 AGTAAA
1 AGTAAA
13172 GAATAATCAG
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
28 6 0.21
29 20 0.71
30 2 0.07
ACGTcount: A:0.56, C:0.06, G:0.16, T:0.22
Consensus pattern (28 bp):
AGTAAAAAGTAAATAGCAATCAGTAAAG
Found at i:13191 original size:36 final size:34
Alignment explanation
Indices: 13130--13197 Score: 84
Period size: 36 Copynumber: 1.9 Consensus size: 34
13120 AATGGCAATC
*
13130 AGTAAAGAATAAAATAGTAATTAGTAATCAGTACAA
1 AGTAAAGAAT-AAATAGTAAATAGTAAT-AGTACAA
13166 AGTAAAGAAT-AATCAGTAAAATAGTAATAGTA
1 AGTAAAGAATAAAT-AGT-AAATAGTAATAGTA
13198 ATCCGTAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 3 0.10
35 7 0.24
36 19 0.66
ACGTcount: A:0.56, C:0.04, G:0.15, T:0.25
Consensus pattern (34 bp):
AGTAAAGAATAAATAGTAAATAGTAATAGTACAA
Done.