Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008814.1 Corchorus capsularis cultivar CVL-1 contig08835, 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: 49009
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Found at i:2454 original size:8 final size:8
Alignment explanation
Indices: 2441--2474 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
2431 CACCTTCTTG
2441 AAAAATTC
1 AAAAATTC
2449 AAAAATTC
1 AAAAATTC
*
2457 AGAAACTTC
1 A-AAAATTC
2466 AAAAATTC
1 AAAAATTC
2474 A
1 A
2475 TAACCGATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.59, C:0.15, G:0.03, T:0.24
Consensus pattern (8 bp):
AAAAATTC
Found at i:2565 original size:5 final size:5
Alignment explanation
Indices: 2548--2577 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
2538 GTTATATCGA
2548 AAAAT ATAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT A-AAAT AAAAT AAAAT AAAAT AAAA
2578 AAATTTTCGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:4048 original size:33 final size:32
Alignment explanation
Indices: 3951--4055 Score: 129
Period size: 33 Copynumber: 3.2 Consensus size: 32
3941 TTGCAAAGAG
*
3951 TGTTTTAGATGTTGTTTGCGATGATACTAAACC
1 TGTTTTAG-TGTTGTTTGCGATGATACTAAATC
* * * *
3984 TAATTTGAGTGTTGTTTGCAATGACACTAAATC
1 T-GTTTTAGTGTTGTTTGCGATGATACTAAATC
*
4017 TGTTTTAAGTGTTGTTTGTGATGATACTAAATC
1 TGTTTT-AGTGTTGTTTGCGATGATACTAAATC
4050 TGTTTT
1 TGTTTT
4056 GGATGCTAAT
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
32 3 0.05
33 52 0.87
34 5 0.08
ACGTcount: A:0.25, C:0.10, G:0.20, T:0.46
Consensus pattern (32 bp):
TGTTTTAGTGTTGTTTGCGATGATACTAAATC
Found at i:4115 original size:33 final size:33
Alignment explanation
Indices: 4078--4189 Score: 188
Period size: 33 Copynumber: 3.4 Consensus size: 33
4068 TGATGAAAAC
*
4078 AATTCTGTTTTGGTTGATCAGAGCATTGCAAAT
1 AATTCTGTTTTGGTTGATCATAGCATTGCAAAT
4111 AATTCTGTTTTGGTTGATCATAGCATTGCAAAT
1 AATTCTGTTTTGGTTGATCATAGCATTGCAAAT
** *
4144 AATTCTGTTTTGGTTGATCATAATATTGAAAAT
1 AATTCTGTTTTGGTTGATCATAGCATTGCAAAT
4177 AATTCTGTTTTGG
1 AATTCTGTTTTGG
4190 GTGAAAAGAA
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 75 1.00
ACGTcount: A:0.28, C:0.10, G:0.19, T:0.44
Consensus pattern (33 bp):
AATTCTGTTTTGGTTGATCATAGCATTGCAAAT
Found at i:4731 original size:21 final size:21
Alignment explanation
Indices: 4687--4731 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
4677 AATTCACCAA
* **
4687 GAAGATGCCATTTGGTCCTTT
1 GAAGATGCCATTAGGTCCGAT
4708 GAAGATGCCATTAGGTCCGAT
1 GAAGATGCCATTAGGTCCGAT
4729 GAA
1 GAA
4732 AAGAGCAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.29
Consensus pattern (21 bp):
GAAGATGCCATTAGGTCCGAT
Found at i:6273 original size:30 final size:31
Alignment explanation
Indices: 6239--6308 Score: 99
Period size: 30 Copynumber: 2.3 Consensus size: 31
6229 TAAAAAGGGC
*
6239 AATCAGTAATTAAGTTCAATAAGGAAA-A-GT
1 AATCAGTAATTAAGTTCAATAA-GAAAGATGA
*
6269 AATCAGTGATTAAGTTCAATAAGAAAGATGA
1 AATCAGTAATTAAGTTCAATAAGAAAGATGA
6300 AATCAGTAA
1 AATCAGTAA
6309 AAGGTAAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
29 4 0.11
30 22 0.63
31 9 0.26
ACGTcount: A:0.50, C:0.07, G:0.17, T:0.26
Consensus pattern (31 bp):
AATCAGTAATTAAGTTCAATAAGAAAGATGA
Found at i:6328 original size:22 final size:22
Alignment explanation
Indices: 6300--6499 Score: 116
Period size: 22 Copynumber: 9.5 Consensus size: 22
6290 AGAAAGATGA
6300 AATCAGTAAAAGGTAAAATGGT
1 AATCAGTAAAAGGTAAAATGGT
* **
6322 AATCAGT-AAAGAGTAAAGTAAT
1 AATCAGTAAAAG-GTAAAATGGT
* *
6344 AATCAGT-AAAGAGT--AATAGA
1 AATCAGTAAAAG-GTAAAATGGT
*
6364 AATCAGTAAGAA-GT--AATAGT
1 AATCAGTAA-AAGGTAAAATGGT
* * *
6384 AAACAGTAAAAAGTAAAAAGGT
1 AATCAGTAAAAGGTAAAATGGT
* * *
6406 AATCAATAAAAAGTAAAAAGGT
1 AATCAGTAAAAGGTAAAATGGT
* * *
6428 -ATC-GGAAAGGGTAAAATAGT
1 AATCAGTAAAAGGTAAAATGGT
* *
6448 AATCAGTAAAAAGT--AATGAT
1 AATCAGTAAAAGGTAAAATGGT
* *
6468 GATCAGTAAAAGGAAAAATGGT
1 AATCAGTAAAAGGTAAAATGGT
*
6490 AATTAGTAAA
1 AATCAGTAAA
6500 GAGTAATAGT
Statistics
Matches: 139, Mismatches: 29, Indels: 20
0.74 0.15 0.11
Matches are distributed among these distances:
19 2 0.01
20 53 0.38
21 11 0.08
22 73 0.53
ACGTcount: A:0.55, C:0.04, G:0.20, T:0.21
Consensus pattern (22 bp):
AATCAGTAAAAGGTAAAATGGT
Found at i:6369 original size:20 final size:21
Alignment explanation
Indices: 6322--6593 Score: 92
Period size: 20 Copynumber: 13.1 Consensus size: 21
6312 GTAAAATGGT
6322 AATCAGTAAAGAGTAA-AGTAA
1 AATCAGTAAAGAGTAATAGT-A
6343 TAATCAGTAAAGAGTAATAG-A
1 -AATCAGTAAAGAGTAATAGTA
6364 AATCAGT-AAGAAGTAATAGTA
1 AATCAGTAAAG-AGTAATAGTA
* *
6385 AA-CAGTAAAAAGTAAAAAGGT-
1 AATCAGTAAAGAGT-AATA-GTA
* * *
6406 AATCAATAAAAAGTAAAAAGGT-
1 AATCAGTAAAGAGT-AATA-GTA
* *
6428 -ATC-GGAAAGGGTAAAATAGT-
1 AATCAGTAAAGAGT--AATAGTA
*
6448 AATCAGTAAAAAGTAAT-G-A
1 AATCAGTAAAGAGTAATAGTA
* ** *
6467 TGATCAGTAAAAGGAAAAATGGT-
1 -AATCAGT-AAA-GAGTAATAGTA
*
6490 AATTAGTAAAGAGTAATAGT-
1 AATCAGTAAAGAGTAATAGTA
*
6510 AATTAGT-AAGAGTAATAGT-
1 AATCAGTAAAGAGTAATAGTA
* ** *
6529 AATCAGTGATCAGTAAAGAGT-
1 AATCAGTAAAGAGT-AATAGTA
* ** *
6550 AATCAGTGAAGAAAAATGGTA
1 AATCAGTAAAGAGTAATAGTA
*
6571 AA-GAGTAAAGAGTAATCAGTA
1 AATCAGTAAAGAGTAAT-AGTA
6592 AA
1 AA
6594 GAAAAAATGG
Statistics
Matches: 195, Mismatches: 35, Indels: 41
0.72 0.13 0.15
Matches are distributed among these distances:
19 22 0.11
20 70 0.36
21 49 0.25
22 51 0.26
23 3 0.02
ACGTcount: A:0.53, C:0.04, G:0.21, T:0.22
Consensus pattern (21 bp):
AATCAGTAAAGAGTAATAGTA
Found at i:6410 original size:42 final size:42
Alignment explanation
Indices: 6300--6925 Score: 244
Period size: 42 Copynumber: 15.0 Consensus size: 42
6290 AGAAAGATGA
* * *
6300 AATCAGTAAAAGGTAAAATGGTAATCAGTAA-AGAGTAAAGTAAT
1 AATCAGTAAAAAGTAAAAAGGTAATCAGTAAGA-AGT-AA-TAGT
* * *
6344 AATCAGTAAAGAGT-AATA-GAAATCAGTAAGAAGTAATAGT
1 AATCAGTAAAAAGTAAAAAGGTAATCAGTAAGAAGTAATAGT
* * * *
6384 AAACAGTAAAAAGTAAAAAGGTAATCAATAAAAAGTAAAAAGGT
1 AATCAGTAAAAAGTAAAAAGGTAATCAGTAAGAAGT-AATA-GT
* ** *
6428 -ATC-GGAAAGGGTAAAATA-GTAATCAGTAAAAAGTAAT-GAT
1 AATCAGTAAAAAGTAAAA-AGGTAATCAGTAAGAAGTAATAG-T
* * *
6468 GATCAGT-AAAAGGAAAAATGGTAATTAGTAA-AGAGTAATAGT
1 AATCAGTAAAAAGTAAAAA-GGTAATCAGTAAGA-AGTAATAGT
* * * * ** *
6510 AATTAGT-AAGAGT-AATA-GTAATCAGTGATCAGTAAAGAGT
1 AATCAGTAAAAAGTAAAAAGGTAATCAGTAAGAAGT-AATAGT
* * *
6550 AATCAGT--GAAG-AAAAATGGTAA--AG--AGTA--AAGAGT
1 AATCAGTAAAAAGTAAAAA-GGTAATCAGTAAGAAGTAATAGT
* ** *
6584 AATCAGTAAAGAA--AAAATGGTAAAGAATGAAG-AGTAATTAGT
1 AATCAGTAAA-AAGTAAAAAGGTAATCAGT-AAGAAGTAA-TAGT
* * * * *
6626 AAAAT-GGTAAAGAGTAGAGTAAAGAG-AGATCAGTAAAAAGAAAATGGT
1 --AATCAGTAAAAAGTA-A--AAAG-GTA-ATCAGTAAGAAG-TAATAGT
** * ** *
6674 AAAGAGT--AAAGT-AAAAGGTGATCAGTAAAGAAAAAATGGT
1 AATCAGTAAAAAGTAAAAAGGTAATCAGT-AAGAAGTAATAGT
* * *
6714 AATCAGTAAAGAGT-AATA-GTAATCAGTAAGAAGTAATGGT
1 AATCAGTAAAAAGTAAAAAGGTAATCAGTAAGAAGTAATAGT
*
6754 AATCAGTAAAAAGTAAAAAAGGTAATCAGTAAGAAGTAATGGT
1 AATCAGTAAAAAGT-AAAAAGGTAATCAGTAAGAAGTAATAGT
* *
6797 AATCAGTAAAAAGTAAAAAGGTAATCAGTAAAAAGTAAAATGGT
1 AATCAGTAAAAAGTAAAAAGGTAATCAGTAAGAAGT--AATAGT
* * *
6841 AAACAGTAAAAAGT--AAAGGTAATTAGTGAA-AAGTAAAATGGT
1 AATCAGTAAAAAGTAAAAAGGTAATCAGT-AAGAAGT--AATAGT
* * *
6883 AATTAGTAAAAAGTAAAGA-GTAATCAGTAAAGAA-AAATAGT
1 AATCAGTAAAAAGTAAAAAGGTAATCAGT-AAGAAGTAATAGT
6924 AA
1 AA
6926 AGAGTAATCA
Statistics
Matches: 451, Mismatches: 77, Indels: 111
0.71 0.12 0.17
Matches are distributed among these distances:
34 13 0.03
35 5 0.01
36 4 0.01
37 5 0.01
39 21 0.05
40 73 0.16
41 50 0.11
42 149 0.33
43 64 0.14
44 41 0.09
45 5 0.01
46 2 0.00
47 8 0.02
48 9 0.02
49 2 0.00
ACGTcount: A:0.54, C:0.04, G:0.22, T:0.21
Consensus pattern (42 bp):
AATCAGTAAAAAGTAAAAAGGTAATCAGTAAGAAGTAATAGT
Found at i:6522 original size:19 final size:20
Alignment explanation
Indices: 6488--6531 Score: 81
Period size: 19 Copynumber: 2.2 Consensus size: 20
6478 AGGAAAAATG
6488 GTAATTAGTAAAGAGTAATA
1 GTAATTAGTAAAGAGTAATA
6508 GTAATTAGT-AAGAGTAATA
1 GTAATTAGTAAAGAGTAATA
6527 GTAAT
1 GTAAT
6532 CAGTGATCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (20 bp):
GTAATTAGTAAAGAGTAATA
Found at i:6554 original size:14 final size:14
Alignment explanation
Indices: 6507--6561 Score: 51
Period size: 14 Copynumber: 4.1 Consensus size: 14
6497 AAAGAGTAAT
*
6507 AGTAATTAGT-AAG
1 AGTAATCAGTAAAG
**
6520 AGTAAT-AGTAATC
1 AGTAATCAGTAAAG
*
6533 AGTGATCAGTAAAG
1 AGTAATCAGTAAAG
*
6547 AGTAATCAGTGAAG
1 AGTAATCAGTAAAG
6561 A
1 A
6562 AAAATGGTAA
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
12 3 0.09
13 12 0.36
14 18 0.55
ACGTcount: A:0.45, C:0.05, G:0.24, T:0.25
Consensus pattern (14 bp):
AGTAATCAGTAAAG
Found at i:6677 original size:40 final size:40
Alignment explanation
Indices: 6626--6724 Score: 130
Period size: 40 Copynumber: 2.5 Consensus size: 40
6616 AGTAATTAGT
*
6626 AAAATGGTAAAGAGTAGAGT-AAAGAGAGATCAGTAAA-AA
1 AAAATGGTAAAGAGTAAAGTAAAAG-GAGATCAGTAAAGAA
*
6665 GAAAATGGTAAAGAGTAAAGTAAAAGGTGATCAGTAAAGAA
1 -AAAATGGTAAAGAGTAAAGTAAAAGGAGATCAGTAAAGAA
**
6706 AAAATGGTAATCAGTAAAG
1 AAAATGGTAAAGAGTAAAG
6725 AGTAATAGTA
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
40 47 0.89
41 6 0.11
ACGTcount: A:0.55, C:0.03, G:0.25, T:0.17
Consensus pattern (40 bp):
AAAATGGTAAAGAGTAAAGTAAAAGGAGATCAGTAAAGAA
Found at i:6700 original size:19 final size:21
Alignment explanation
Indices: 6654--6919 Score: 155
Period size: 20 Copynumber: 12.7 Consensus size: 21
6644 GTAAAGAGAG
6654 ATCAGTAAA-AAGAAAATGGTA
1 ATCAGTAAAGAA-AAAATGGTA
** * *
6675 AAGAGTAAAG-TAAAA-GGTG
1 ATCAGTAAAGAAAAAATGGTA
6694 ATCAGTAAAGAAAAAATGGTA
1 ATCAGTAAAGAAAAAATGGTA
** *
6715 ATCAGTAAAG-AGTAATAGTA
1 ATCAGTAAAGAAAAAATGGTA
**
6735 ATCAGT-AAGAAGTAATGGTA
1 ATCAGTAAAGAAAAAATGGTA
6755 ATCAGTAAAAAGTAAAAAA-GGTA
1 ATCAGT--AAAG-AAAAAATGGTA
**
6778 ATCAGT-AAGAAGTAATGGTA
1 ATCAGTAAAGAAAAAATGGTA
*
6798 ATCAGTAAA-AAGTAAAAAGGTA
1 ATCAGTAAAGAA--AAAATGGTA
6820 ATCAGTAAA-AAGTAAAATGGTA
1 ATCAGTAAAGAA--AAAATGGTA
* *
6842 AACAGTAAA-AAGTAAA-GGTA
1 ATCAGTAAAGAA-AAAATGGTA
* *
6862 ATTAGTGAAA-AGTAAAATGGTA
1 ATCAGT-AAAGA-AAAAATGGTA
* *
6884 ATTAGTAAA-AAGTAAA-GAGTA
1 ATCAGTAAAGAA-AAAATG-GTA
6905 ATCAGTAAAGAAAAA
1 ATCAGTAAAGAAAAA
6920 TAGTAAAGAG
Statistics
Matches: 196, Mismatches: 31, Indels: 36
0.75 0.12 0.14
Matches are distributed among these distances:
19 18 0.09
20 60 0.31
21 52 0.27
22 49 0.25
23 13 0.07
24 4 0.02
ACGTcount: A:0.55, C:0.04, G:0.21, T:0.21
Consensus pattern (21 bp):
ATCAGTAAAGAAAAAATGGTA
Found at i:6729 original size:14 final size:13
Alignment explanation
Indices: 6712--6960 Score: 82
Period size: 14 Copynumber: 18.3 Consensus size: 13
6702 AGAAAAAATG
6712 GTAATCAGTAAAGA
1 GTAAT-AGTAAAGA
**
6726 GTAATAGTAATCA
1 GTAATAGTAAAGA
* *
6739 GTAAGAAGTAATG-
1 GTAA-TAGTAAAGA
*
6752 GTAATCAGTAAAAA
1 GTAAT-AGTAAAGA
6766 GTAA-A--AAAG-
1 GTAATAGTAAAGA
6775 GTAATCAGT-AAGAA
1 GTAAT-AGTAAAG-A
* **
6789 GTAATGGTAATCA
1 GTAATAGTAAAGA
* *
6802 GTAAAAAGTAAAAA
1 GT-AATAGTAAAGA
*
6816 GGTAATCAGTAAAAA
1 -GTAAT-AGTAAAGA
* *
6831 GTAAAATGGTAAACA
1 GT--AATAGTAAAGA
*
6846 GTAAAAAGTAAAG-
1 GT-AATAGTAAAGA
6859 GTAATTAGTGAAA-A
1 GTAA-TAGT-AAAGA
* **
6873 GTAAAATGGTAATTA
1 GT--AATAGTAAAGA
*
6888 GTAAAAAGTAAAGA
1 GT-AATAGTAAAGA
6902 GTAATCAGTAAAGA
1 GTAAT-AGTAAAGA
**
6916 AAAATAGTAAAGA
1 GTAATAGTAAAGA
6929 GTAATCAGTAAAGA
1 GTAAT-AGTAAAGA
*
6943 GTAAAGAGTAAAGA
1 GT-AATAGTAAAGA
6957 GTAA
1 GTAA
6961 AAAGTAATTA
Statistics
Matches: 177, Mismatches: 34, Indels: 49
0.68 0.13 0.19
Matches are distributed among these distances:
9 4 0.02
10 3 0.02
11 1 0.01
12 6 0.03
13 44 0.25
14 88 0.50
15 26 0.15
16 5 0.03
ACGTcount: A:0.54, C:0.04, G:0.21, T:0.21
Consensus pattern (13 bp):
GTAATAGTAAAGA
Found at i:6811 original size:7 final size:7
Alignment explanation
Indices: 6801--6967 Score: 88
Period size: 7 Copynumber: 23.7 Consensus size: 7
6791 AATGGTAATC
6801 AGTAAAA
1 AGTAAAA
6808 AGTAAAA
1 AGTAAAA
**
6815 AGGTAATC
1 A-GTAAAA
6823 AGTAAAA
1 AGTAAAA
6830 AGTAAAA
1 AGTAAAA
* *
6837 TGGTAAAC
1 -AGTAAAA
6845 AGTAAAA
1 AGTAAAA
6852 AGT-AAA
1 AGTAAAA
* **
6858 GGTAATT
1 AGTAAAA
*
6865 AGTGAAA
1 AGTAAAA
6872 AGTAAAA
1 AGTAAAA
* **
6879 TGGTAATT
1 -AGTAAAA
6887 AGTAAAA
1 AGTAAAA
*
6894 AGTAAAG
1 AGTAAAA
**
6901 AGTAATC
1 AGTAAAA
6908 AGTAAAGA
1 AGTAAA-A
*
6916 A--AAAT
1 AGTAAAA
*
6921 AGTAAAG
1 AGTAAAA
**
6928 AGTAATC
1 AGTAAAA
*
6935 AGTAAAG
1 AGTAAAA
*
6942 AGTAAAG
1 AGTAAAA
*
6949 AGTAAAG
1 AGTAAAA
6956 AGTAAAA
1 AGTAAAA
6963 AGTAA
1 AGTAA
6968 TTAGTAAAGA
Statistics
Matches: 119, Mismatches: 34, Indels: 14
0.71 0.20 0.08
Matches are distributed among these distances:
5 1 0.01
6 8 0.07
7 95 0.80
8 15 0.13
ACGTcount: A:0.57, C:0.02, G:0.20, T:0.20
Consensus pattern (7 bp):
AGTAAAA
Found at i:6924 original size:27 final size:27
Alignment explanation
Indices: 6890--6960 Score: 108
Period size: 27 Copynumber: 2.6 Consensus size: 27
6880 GGTAATTAGT
6890 AAAAAGTAAAGAGTAATCAGTAAAGA-
1 AAAAAGTAAAGAGTAATCAGTAAAGAG
6916 AAAATAGTAAAGAGTAATCAGTAAAGAG
1 AAAA-AGTAAAGAGTAATCAGTAAAGAG
*
6944 TAAAGAGTAAAGAGTAA
1 -AAAAAGTAAAGAGTAA
6961 AAAGTAATTA
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
26 4 0.10
27 22 0.54
28 12 0.29
29 3 0.07
ACGTcount: A:0.59, C:0.03, G:0.21, T:0.17
Consensus pattern (27 bp):
AAAAAGTAAAGAGTAATCAGTAAAGAG
Found at i:6959 original size:21 final size:21
Alignment explanation
Indices: 6887--6977 Score: 85
Period size: 21 Copynumber: 4.4 Consensus size: 21
6877 AATGGTAATT
* **
6887 AGTAAAAAGTAAAGAGTAATC
1 AGTAAAGAGTAAAGAGTAAAG
* *
6908 AGTAAAGA-AAAATAGTAAAG
1 AGTAAAGAGTAAAGAGTAAAG
**
6928 AGTAATCAGTAAAGAGTAAAG
1 AGTAAAGAGTAAAGAGTAAAG
* **
6949 AGTAAAGAGTAAAAAGTAATT
1 AGTAAAGAGTAAAGAGTAAAG
6970 AGTAAAGA
1 AGTAAAGA
6978 AAAAATAGTA
Statistics
Matches: 55, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 14 0.25
21 41 0.75
ACGTcount: A:0.58, C:0.02, G:0.21, T:0.19
Consensus pattern (21 bp):
AGTAAAGAGTAAAGAGTAAAG
Found at i:6961 original size:14 final size:14
Alignment explanation
Indices: 6801--6967 Score: 117
Period size: 14 Copynumber: 11.9 Consensus size: 14
6791 AATGGTAATC
*
6801 AGTAAAAAGTAAAA
1 AGTAAAAAGTAAAG
** *
6815 AGGTAATCAGTAAAA
1 A-GTAAAAAGTAAAG
* *
6830 AGTAAAATGGTAAAC
1 AGTAAAA-AGTAAAG
6845 AGTAAAAAGTAAAG
1 AGTAAAAAGTAAAG
**
6859 -GTAATTAGTGAAA-
1 AGTAAAAAGT-AAAG
* **
6872 AGTAAAATGGTAATT
1 AGTAAAA-AGTAAAG
6887 AGTAAAAAGTAAAG
1 AGTAAAAAGTAAAG
**
6901 AGTAATCAGTAAAG
1 AGTAAAAAGTAAAG
6915 A--AAAATAGTAAAG
1 AGTAAAA-AGTAAAG
**
6928 AGTAATCAGTAAAG
1 AGTAAAAAGTAAAG
*
6942 AGTAAAGAGTAAAG
1 AGTAAAAAGTAAAG
6956 AGTAAAAAGTAA
1 AGTAAAAAGTAA
6968 TTAGTAAAGA
Statistics
Matches: 118, Mismatches: 26, Indels: 18
0.73 0.16 0.11
Matches are distributed among these distances:
12 2 0.02
13 15 0.13
14 66 0.56
15 35 0.30
ACGTcount: A:0.57, C:0.02, G:0.20, T:0.20
Consensus pattern (14 bp):
AGTAAAAAGTAAAG
Found at i:6973 original size:14 final size:14
Alignment explanation
Indices: 6801--6988 Score: 80
Period size: 14 Copynumber: 13.4 Consensus size: 14
6791 AATGGTAATC
*
6801 AGTAAAAAGTAAAA
1 AGTAAAAAGTAAAT
** *
6815 AGGTAATCAGTAAAA
1 A-GTAAAAAGTAAAT
* *
6830 AGTAAAATGGTAAAC
1 AGTAAAA-AGTAAAT
6845 AGTAAAAAGTAAA-
1 AGTAAAAAGTAAAT
* **
6858 GGTAATTAGTGAAA-
1 AGTAAAAAGT-AAAT
* *
6872 AGTAAAATGGTAATT
1 AGTAAAA-AGTAAAT
*
6887 AGTAAAAAGTAAAG
1 AGTAAAAAGTAAAT
**
6901 AGTAATCAGT-AA-
1 AGTAAAAAGTAAAT
* *
6913 AGAAAAATAGTAAAG
1 AGTAAAA-AGTAAAT
** *
6928 AGTAATCAGTAAAG
1 AGTAAAAAGTAAAT
* *
6942 AGTAAAGAGTAAAG
1 AGTAAAAAGTAAAT
*
6956 AGTAAAAAGTAATT
1 AGTAAAAAGTAAAT
*
6970 AGTAAAGAA-AAAAT
1 AGTAAA-AAGTAAAT
6984 AGTAA
1 AGTAA
6989 GGAGTGAGAA
Statistics
Matches: 132, Mismatches: 33, Indels: 18
0.72 0.18 0.10
Matches are distributed among these distances:
12 4 0.03
13 12 0.09
14 77 0.58
15 39 0.30
ACGTcount: A:0.58, C:0.02, G:0.20, T:0.20
Consensus pattern (14 bp):
AGTAAAAAGTAAAT
Found at i:6987 original size:21 final size:21
Alignment explanation
Indices: 6875--7059 Score: 76
Period size: 21 Copynumber: 8.9 Consensus size: 21
6865 AGTGAAAAGT
* *
6875 AAAATGGTAATTAGTAAA-AA
1 AAAATAGTAATGAGTAAAGAA
* * *
6895 GTAAAGAGTAATCAGTAAAG-A
1 -AAAATAGTAATGAGTAAAGAA
* ** *
6916 AAAATAGTAAAGAGTAATCAG
1 AAAATAGTAATGAGTAAAGAA
* * * *
6937 TAAAGAGTAAAGAGTAAAGAGT
1 AAAATAGTAATGAGTAAAGA-A
*
6959 AAAA-AGTAATTAGTAAAGAA
1 AAAATAGTAATGAGTAAAGAA
* *
6979 AAAATAGTAAGGAGT-GAGAA
1 AAAATAGTAATGAGTAAAGAA
* *
6999 GAAATCAGTAAAATG-GTAAAGGA
1 AAAAT-AGT--AATGAGTAAAGAA
* * *
7022 TAAAGAGTAATCAGTAAAG-A
1 AAAATAGTAATGAGTAAAGAA
* *
7042 AAAATGGTAAAGAGTAAA
1 AAAATAGTAATGAGTAAA
7060 ATCTTAATCA
Statistics
Matches: 120, Mismatches: 35, Indels: 19
0.69 0.20 0.11
Matches are distributed among these distances:
20 42 0.35
21 61 0.51
22 8 0.07
23 9 0.08
ACGTcount: A:0.57, C:0.02, G:0.22, T:0.19
Consensus pattern (21 bp):
AAAATAGTAATGAGTAAAGAA
Found at i:7130 original size:14 final size:14
Alignment explanation
Indices: 7111--7137 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
7101 AATATTAACT
7111 AGTAATCAGTAAAG
1 AGTAATCAGTAAAG
7125 AGTAATCAGTAAA
1 AGTAATCAGTAAA
7138 AGTGAATAAA
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:0.52, C:0.07, G:0.19, T:0.22
Consensus pattern (14 bp):
AGTAATCAGTAAAG
Found at i:19575 original size:22 final size:24
Alignment explanation
Indices: 19524--19576 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 24
19514 CAAATTATGC
19524 ATGTTTTTATAGCTATTTCTATAT
1 ATGTTTTTATAGCTATTTCTATAT
* *
19548 A--CTTTT-T-GCTATTTTTATAT
1 ATGTTTTTATAGCTATTTCTATAT
19568 ATGTTTTTA
1 ATGTTTTTA
19577 CCCTATTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 7
0.70 0.09 0.21
Matches are distributed among these distances:
20 13 0.57
21 1 0.04
22 8 0.35
24 1 0.04
ACGTcount: A:0.23, C:0.08, G:0.08, T:0.62
Consensus pattern (24 bp):
ATGTTTTTATAGCTATTTCTATAT
Found at i:26229 original size:10 final size:10
Alignment explanation
Indices: 26214--26265 Score: 50
Period size: 10 Copynumber: 4.9 Consensus size: 10
26204 TAAAGGATCA
26214 TGTGGCCGGT
1 TGTGGCCGGT
*
26224 TGTGGCCGGG
1 TGTGGCCGGT
**
26234 CATGGCCGAGT
1 TGTGGCCG-GT
26245 CATGTGGCCGGT
1 --TGTGGCCGGT
26257 TGTGGCCGG
1 TGTGGCCGG
26266 GCATGGCCAT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
10 24 0.73
11 1 0.03
12 2 0.06
13 6 0.18
ACGTcount: A:0.06, C:0.23, G:0.48, T:0.23
Consensus pattern (10 bp):
TGTGGCCGGT
Found at i:26313 original size:33 final size:32
Alignment explanation
Indices: 26215--26355 Score: 147
Period size: 33 Copynumber: 4.3 Consensus size: 32
26205 AAAGGATCAT
** * **
26215 GTGGCCGGTTGTGGCCGGGCATGGCCGAGTCAT
1 GTGGCCGG-TGTGGCCGGGCATCTCCAAGTCGC
** *
26248 GTGGCCGGTTGTGGCCGGGCATGGCCATGTCGC
1 GTGGCCGG-TGTGGCCGGGCATCTCCAAGTCGC
*
26281 GTGGCCGGTGATGGCCGGGTATCTCCAAGTCGC
1 GTGGCCGGTG-TGGCCGGGCATCTCCAAGTCGC
* *
26314 ATGGCCGGTGTTGCGCGGGCATCTCCAAGTCGC
1 GTGGCCGGTGTGGC-CGGGCATCTCCAAGTCGC
26347 GTGGCCGGT
1 GTGGCCGGT
26356 CACAAGTGCT
Statistics
Matches: 94, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
32 5 0.05
33 89 0.95
ACGTcount: A:0.09, C:0.27, G:0.43, T:0.21
Consensus pattern (32 bp):
GTGGCCGGTGTGGCCGGGCATCTCCAAGTCGC
Found at i:32104 original size:10 final size:10
Alignment explanation
Indices: 32089--32140 Score: 50
Period size: 10 Copynumber: 4.9 Consensus size: 10
32079 TAAAGGATCA
32089 TGTGGCCGGT
1 TGTGGCCGGT
*
32099 TGTGGCCGGG
1 TGTGGCCGGT
**
32109 CATGGCCGAGT
1 TGTGGCCG-GT
32120 CATGTGGCCGGT
1 --TGTGGCCGGT
32132 TGTGGCCGG
1 TGTGGCCGG
32141 GCATGGCCAT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
10 24 0.73
11 1 0.03
12 2 0.06
13 6 0.18
ACGTcount: A:0.06, C:0.23, G:0.48, T:0.23
Consensus pattern (10 bp):
TGTGGCCGGT
Found at i:32188 original size:33 final size:32
Alignment explanation
Indices: 32090--32230 Score: 174
Period size: 33 Copynumber: 4.3 Consensus size: 32
32080 AAAGGATCAT
* **
32090 GTGGCCGGTTGTGGCCGGGCATGGCCGAGTCAT
1 GTGGCCGG-TGTGGCCGGGCATGGCCAAGTCGC
*
32123 GTGGCCGGTTGTGGCCGGGCATGGCCATGTCGC
1 GTGGCCGG-TGTGGCCGGGCATGGCCAAGTCGC
32156 GTGGCCGGTGATGGCCGGGCATGGCCAAGTCGC
1 GTGGCCGGTG-TGGCCGGGCATGGCCAAGTCGC
* * **
32189 ATGGCCGGTGTTGCGCGGGCATCTCCAAGTCGC
1 GTGGCCGGTGTGGC-CGGGCATGGCCAAGTCGC
32222 GTGGCCGGT
1 GTGGCCGGT
32231 CACAAGTGCT
Statistics
Matches: 96, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
32 5 0.05
33 91 0.95
ACGTcount: A:0.09, C:0.27, G:0.44, T:0.20
Consensus pattern (32 bp):
GTGGCCGGTGTGGCCGGGCATGGCCAAGTCGC
Found at i:38264 original size:37 final size:36
Alignment explanation
Indices: 38183--38310 Score: 125
Period size: 37 Copynumber: 3.4 Consensus size: 36
38173 TTAATTCATA
*
38183 GAAATTAAGTAAAAACAGTAGTCAAAAGACTTAATTCATA-
1 GAAATTAAGTAAAAGCAGT--T-AAAAGACTTAA-TC-TAG
*
38223 GAAATTAAGTAAAAGCAGTTAAAAGACTCAATCTAGG
1 GAAATTAAGTAAAAGCAGTTAAAAGACTTAATCTA-G
* * *
38260 GAAATTAAGTAACAGCAG-TCAAAGTACTTAATTCAAG
1 GAAATTAAGTAAAAGCAGTTAAAAG-ACTTAA-TCTAG
38297 GAAATTAAGTAAAA
1 GAAATTAAGTAAAA
38311 ATAGACTGAC
Statistics
Matches: 77, Mismatches: 7, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
35 2 0.03
36 7 0.09
37 46 0.60
38 4 0.05
40 18 0.23
ACGTcount: A:0.51, C:0.10, G:0.16, T:0.23
Consensus pattern (36 bp):
GAAATTAAGTAAAAGCAGTTAAAAGACTTAATCTAG
Found at i:38400 original size:35 final size:35
Alignment explanation
Indices: 38285--38476 Score: 178
Period size: 36 Copynumber: 5.5 Consensus size: 35
38275 CAGTCAAAGT
38285 ACTTAA-TTCAAGGAAATTAAGTAAA-AATAGACTG
1 ACTTAATTTCAAGGAAATTAAGTAAAGAA-AGACTG
** ** * *
38319 ACTTAATGGCAA-TTAAGTAAG-AACATTAGAAGACTG
1 ACTTAATTTCAAGGAAATTAAGTAA-A-GA-AAGACTG
* *
38355 ATTTAATTTCAAGGAAATTAAGTAAAGATAGACTG
1 ACTTAATTTCAAGGAAATTAAGTAAAGAAAGACTG
* * *
38390 ACTTAGTTTCAAGGAAACTAGGTAAAGAAAAGACTG
1 ACTTAATTTCAAGGAAATTAAGTAAAG-AAAGACTG
*
38426 GCTTAATTTCAAGGAAATTAAGTAAA-AAAGACTG
1 ACTTAATTTCAAGGAAATTAAGTAAAGAAAGACTG
* *
38460 GCTTAGTTTCAAGGAAA
1 ACTTAATTTCAAGGAAA
38477 CTAGGTAGAG
Statistics
Matches: 127, Mismatches: 23, Indels: 16
0.77 0.14 0.10
Matches are distributed among these distances:
33 2 0.02
34 37 0.29
35 32 0.25
36 46 0.36
37 8 0.06
38 2 0.02
ACGTcount: A:0.45, C:0.09, G:0.19, T:0.27
Consensus pattern (35 bp):
ACTTAATTTCAAGGAAATTAAGTAAAGAAAGACTG
Found at i:38436 original size:36 final size:36
Alignment explanation
Indices: 38348--38498 Score: 173
Period size: 36 Copynumber: 4.3 Consensus size: 36
38338 AGAACATTAG
** *
38348 AAGACTGATTTAATTTCAAGGAAATTAAGTAAAG-A
1 AAGACTGGCTTAATTTCAAGGAAACTAAGTAAAGAA
* * * *
38383 TAGACTGACTTAGTTTCAAGGAAACTAGGTAAAGAA
1 AAGACTGGCTTAATTTCAAGGAAACTAAGTAAAGAA
*
38419 AAGACTGGCTTAATTTCAAGGAAATTAAGT-AA-AA
1 AAGACTGGCTTAATTTCAAGGAAACTAAGTAAAGAA
* * *
38453 AAGACTGGCTTAGTTTCAAGGAAACTAGGTAGAGAA
1 AAGACTGGCTTAATTTCAAGGAAACTAAGTAAAGAA
*
38489 AAGATTGGCT
1 AAGACTGGCT
38499 CAGTTTTAAG
Statistics
Matches: 98, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
34 29 0.30
35 32 0.33
36 37 0.38
ACGTcount: A:0.43, C:0.09, G:0.22, T:0.26
Consensus pattern (36 bp):
AAGACTGGCTTAATTTCAAGGAAACTAAGTAAAGAA
Found at i:38489 original size:70 final size:71
Alignment explanation
Indices: 38348--38498 Score: 241
Period size: 70 Copynumber: 2.1 Consensus size: 71
38338 AGAACATTAG
** *
38348 AAGACTGATTTAATTTCAAGGAAATTAAGTAAAGATAGACTGACTTAGTTTCAAGGAAACTAGGT
1 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAAAGACTGACTTAGTTTCAAGGAAACTAGGT
38413 AAAGAA
66 AAAGAA
*
38419 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAA-AAAGACTGGCTTAGTTTCAAGGAAACTAGGT
1 AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAAAGACTGACTTAGTTTCAAGGAAACTAGGT
*
38483 AGAGAA
66 AAAGAA
*
38489 AAGATTGGCT
1 AAGACTGGCT
38499 CAGTTTTAAG
Statistics
Matches: 74, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
70 43 0.58
71 31 0.42
ACGTcount: A:0.43, C:0.09, G:0.22, T:0.26
Consensus pattern (71 bp):
AAGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAAAGACTGACTTAGTTTCAAGGAAACTAGGT
AAAGAA
Found at i:38676 original size:71 final size:71
Alignment explanation
Indices: 38592--38832 Score: 439
Period size: 71 Copynumber: 3.4 Consensus size: 71
38582 AATTTAGGGT
38592 AATTAAGTAAATTAGCAAAGACTTAATTTCACAAGAATTAAGT-AAATTAGCAAAGACTTAATTT
1 AATTAAGTAAATTAGCAAAGACTTAATTTCACAAGAATTAAGTAAAATTAGCAAAGACTTAATTT
38656 CACAAG
66 CACAAG
38662 AATTAAGTAAAATTAGCAAAGACTTAATTTCACAAGAATTAAGTAAAATTAGCAAAGACTTAATT
1 AATTAAGT-AAATTAGCAAAGACTTAATTTCACAAGAATTAAGTAAAATTAGCAAAGACTTAATT
38727 TCACAAG
65 TCACAAG
38734 AATTAAGTAAATTAGCAAAGACTTAATTTCACAAGAATTAAGTAAAATTAGCAAAGACTTAATTT
1 AATTAAGTAAATTAGCAAAGACTTAATTTCACAAGAATTAAGTAAAATTAGCAAAGACTTAATTT
38799 CACAAG
66 CACAAG
* *
38805 AATTAAGTAAAGTCAGCAAAGATTTAAT
1 AATTAAGTAAA-TTAGCAAAGACTTAAT
38833 CCAGAGATGA
Statistics
Matches: 166, Mismatches: 2, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
70 8 0.05
71 109 0.66
72 49 0.30
ACGTcount: A:0.49, C:0.11, G:0.12, T:0.28
Consensus pattern (71 bp):
AATTAAGTAAATTAGCAAAGACTTAATTTCACAAGAATTAAGTAAAATTAGCAAAGACTTAATTT
CACAAG
Found at i:38682 original size:36 final size:36
Alignment explanation
Indices: 38592--38832 Score: 434
Period size: 36 Copynumber: 6.8 Consensus size: 36
38582 AATTTAGGGT
38592 AATTAAGT-AAATTAGCAAAGACTTAATTTCACAAG
1 AATTAAGTAAAATTAGCAAAGACTTAATTTCACAAG
38627 AATTAAGT-AAATTAGCAAAGACTTAATTTCACAAG
1 AATTAAGTAAAATTAGCAAAGACTTAATTTCACAAG
38662 AATTAAGTAAAATTAGCAAAGACTTAATTTCACAAG
1 AATTAAGTAAAATTAGCAAAGACTTAATTTCACAAG
38698 AATTAAGTAAAATTAGCAAAGACTTAATTTCACAAG
1 AATTAAGTAAAATTAGCAAAGACTTAATTTCACAAG
38734 AATTAAGT-AAATTAGCAAAGACTTAATTTCACAAG
1 AATTAAGTAAAATTAGCAAAGACTTAATTTCACAAG
38769 AATTAAGTAAAATTAGCAAAGACTTAATTTCACAAG
1 AATTAAGTAAAATTAGCAAAGACTTAATTTCACAAG
* * *
38805 AATTAAGTAAAGTCAGCAAAGATTTAAT
1 AATTAAGTAAAATTAGCAAAGACTTAAT
38833 CCAGAGATGA
Statistics
Matches: 201, Mismatches: 3, Indels: 3
0.97 0.01 0.01
Matches are distributed among these distances:
35 78 0.39
36 123 0.61
ACGTcount: A:0.49, C:0.11, G:0.12, T:0.28
Consensus pattern (36 bp):
AATTAAGTAAAATTAGCAAAGACTTAATTTCACAAG
Found at i:38717 original size:107 final size:107
Alignment explanation
Indices: 38592--38832 Score: 448
Period size: 107 Copynumber: 2.3 Consensus size: 107
38582 AATTTAGGGT
38592 AATTAAGT-AAATTAGCAAAGACTTAATTTCACAAGAATTAAGTAAATTAGCAAAGACTTAATTT
1 AATTAAGTAAAATTAGCAAAGACTTAATTTCACAAGAATTAAGTAAATTAGCAAAGACTTAATTT
38656 CACAAGAATTAAGTAAAATTAGCAAAGACTTAATTTCACAAG
66 CACAAGAATTAAGTAAAATTAGCAAAGACTTAATTTCACAAG
38698 AATTAAGTAAAATTAGCAAAGACTTAATTTCACAAGAATTAAGTAAATTAGCAAAGACTTAATTT
1 AATTAAGTAAAATTAGCAAAGACTTAATTTCACAAGAATTAAGTAAATTAGCAAAGACTTAATTT
38763 CACAAGAATTAAGTAAAATTAGCAAAGACTTAATTTCACAAG
66 CACAAGAATTAAGTAAAATTAGCAAAGACTTAATTTCACAAG
* * *
38805 AATTAAGTAAAGTCAGCAAAGATTTAAT
1 AATTAAGTAAAATTAGCAAAGACTTAAT
38833 CCAGAGATGA
Statistics
Matches: 131, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
106 8 0.06
107 123 0.94
ACGTcount: A:0.49, C:0.11, G:0.12, T:0.28
Consensus pattern (107 bp):
AATTAAGTAAAATTAGCAAAGACTTAATTTCACAAGAATTAAGTAAATTAGCAAAGACTTAATTT
CACAAGAATTAAGTAAAATTAGCAAAGACTTAATTTCACAAG
Found at i:38917 original size:11 final size:11
Alignment explanation
Indices: 38891--38947 Score: 71
Period size: 11 Copynumber: 5.2 Consensus size: 11
38881 TTAGGCAAAA
*
38891 GAAAGAAGACT
1 GAAAAAAGACT
38902 G-AAAAAGACT
1 GAAAAAAGACT
*
38912 GAAAAAAGGCCT
1 GAAAAAA-GACT
*
38924 GAAAGAAGACT
1 GAAAAAAGACT
38935 GAAAAAAGACT
1 GAAAAAAGACT
38946 GA
1 GA
38948 CTTAATTTCA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
10 9 0.23
11 21 0.54
12 9 0.23
ACGTcount: A:0.56, C:0.11, G:0.25, T:0.09
Consensus pattern (11 bp):
GAAAAAAGACT
Found at i:38934 original size:23 final size:22
Alignment explanation
Indices: 38900--38942 Score: 77
Period size: 23 Copynumber: 1.9 Consensus size: 22
38890 AGAAAGAAGA
38900 CTGAAAAAGACTGAAAAAAGGC
1 CTGAAAAAGACTGAAAAAAGGC
38922 CTGAAAGAAGACTGAAAAAAG
1 CTGAAA-AAGACTGAAAAAAG
38943 ACTGACTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.56, C:0.12, G:0.23, T:0.09
Consensus pattern (22 bp):
CTGAAAAAGACTGAAAAAAGGC
Found at i:39027 original size:36 final size:36
Alignment explanation
Indices: 38938--39237 Score: 376
Period size: 36 Copynumber: 8.3 Consensus size: 36
38928 GAAGACTGAA
38938 AAAAGACTGACTTAATTTCAAGGAAATTAGGTAAA-
1 AAAAGACTGACTTAATTTCAAGGAAATTAGGTAAAG
* *
38973 AGAAA-ACTGACTTAATTTCGAGAAAATTAGGTAAAG
1 A-AAAGACTGACTTAATTTCAAGGAAATTAGGTAAAG
*
39009 AAAAGATTGACTTAATTTCAAGGAAATTAGGTAAA-
1 AAAAGACTGACTTAATTTCAAGGAAATTAGGTAAAG
39044 AGAAA-ACTGACTTAATTTCAAGGAAATTAGGTAAAG
1 A-AAAGACTGACTTAATTTCAAGGAAATTAGGTAAAG
* * * *
39080 GAAATATTGACTTAATTTCAAGGAAATTAGGTAAGG
1 AAAAGACTGACTTAATTTCAAGGAAATTAGGTAAAG
* * * *
39116 AAAAGCCTGGCTTAATTTCGAGGAAATTAAGTAAAG
1 AAAAGACTGACTTAATTTCAAGGAAATTAGGTAAAG
* *
39152 AAAAGACTGGCTTAGTTTCAAGGAAATTAGGTAAAG
1 AAAAGACTGACTTAATTTCAAGGAAATTAGGTAAAG
*
39188 AAAAGACTGGCTTAATTTCAATTCAAGGAAATTAGGTAAAG
1 AAAAGACTGACTTAA--T---TTCAAGGAAATTAGGTAAAG
39229 -AAAGACTGA
1 AAAAGACTGA
39238 GACATAGGCT
Statistics
Matches: 231, Mismatches: 23, Indels: 17
0.85 0.08 0.06
Matches are distributed among these distances:
35 65 0.28
36 137 0.59
38 1 0.00
40 8 0.03
41 20 0.09
ACGTcount: A:0.45, C:0.08, G:0.20, T:0.26
Consensus pattern (36 bp):
AAAAGACTGACTTAATTTCAAGGAAATTAGGTAAAG
Found at i:39171 original size:72 final size:71
Alignment explanation
Indices: 38938--39237 Score: 381
Period size: 71 Copynumber: 4.1 Consensus size: 71
38928 GAAGACTGAA
*
38938 AAAAGACTGACTTAATTTCAAGGAAATTAGGTAAAAGAAAACTGACTTAATTTCGAGAAAATTAG
1 AAAAGACTGACTTAATTTCAAGGAAATTAGGTAAAAGAAAACTGACTTAATTTCGAGGAAATTAG
39003 GTAAAG
66 GTAAAG
* *
39009 AAAAGATTGACTTAATTTCAAGGAAATTAGGTAAAAGAAAACTGACTTAATTTCAAGGAAATTAG
1 AAAAGACTGACTTAATTTCAAGGAAATTAGGTAAAAGAAAACTGACTTAATTTCGAGGAAATTAG
39074 GTAAAG
66 GTAAAG
* * * * *
39080 GAAATATTGACTTAATTTCAAGGAAATTAGGT-AAGGAAAAGCCTGGCTTAATTTCGAGGAAATT
1 AAAAGACTGACTTAATTTCAAGGAAATTAGGTAAAAGAAAA--CTGACTTAATTTCGAGGAAATT
*
39144 AAGTAAAG
64 AGGTAAAG
* * * *
39152 AAAAGACTGGCTTAGTTTCAAGGAAATTAGGT-AAAGAAAAGACTGGCTTAATTTCAATTCAAGG
1 AAAAGACTGACTTAATTTCAAGGAAATTAGGTAAAAG-AAA-ACTGACTTAA--T---TTCGAGG
39216 AAATTAGGTAAAG
59 AAATTAGGTAAAG
39229 -AAAGACTGA
1 AAAAGACTGA
39238 GACATAGGCT
Statistics
Matches: 202, Mismatches: 18, Indels: 13
0.87 0.08 0.06
Matches are distributed among these distances:
70 7 0.03
71 98 0.49
72 66 0.33
73 3 0.01
74 2 0.01
76 8 0.04
77 18 0.09
ACGTcount: A:0.45, C:0.08, G:0.20, T:0.26
Consensus pattern (71 bp):
AAAAGACTGACTTAATTTCAAGGAAATTAGGTAAAAGAAAACTGACTTAATTTCGAGGAAATTAG
GTAAAG
Found at i:39359 original size:36 final size:36
Alignment explanation
Indices: 39310--39397 Score: 108
Period size: 36 Copynumber: 2.4 Consensus size: 36
39300 TTAAGTAAAA
*
39310 CAATAAA-AGACTTAATTCAGGG-TAATTAAGTCAAGT
1 CAATAAAGA-ACTTAATTC-GGGATAATTAAGTCAACT
**
39346 CAATAAAGAACTTAATTCGGGATAATTAAGTGGACT
1 CAATAAAGAACTTAATTCGGGATAATTAAGTCAACT
*
39382 CAATAAAGAAGTTAAT
1 CAATAAAGAACTTAAT
39398 CTAAAAAGAG
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
35 3 0.07
36 42 0.91
37 1 0.02
ACGTcount: A:0.45, C:0.10, G:0.17, T:0.27
Consensus pattern (36 bp):
CAATAAAGAACTTAATTCGGGATAATTAAGTCAACT
Found at i:41251 original size:129 final size:129
Alignment explanation
Indices: 41021--41280 Score: 466
Period size: 129 Copynumber: 2.0 Consensus size: 129
41011 AAGGATAGCT
41021 CATGTTATAACTCGTCATAACATTCATTCGCATCAATTACATAAAAGCAAGAACCCTGATTATTC
1 CATGTTATAACTCGTCATAACATTCATTCGCATCAATTACATAAAAGCAAGAACCCTGATTATTC
41086 ACAGAATTGTAAATGGTCACGACTTTTGGCTTGTGGAAGTTCCTACCAAATTGTGGAGGGACTC
66 ACAGAATTGTAAATGGTCACGACTTTTGGCTTGTGGAAGTTCCTACCAAATTGTGGAGGGACTC
* ** * *
41150 CATGTTATAACTGGTCATAGTATTCATTCGCATCAATTGCATAAAGGCAAGAACCCTGATTATTC
1 CATGTTATAACTCGTCATAACATTCATTCGCATCAATTACATAAAAGCAAGAACCCTGATTATTC
*
41215 ACAGAATTGTAAATGGTCACGGCTTTTGGCTTGTGGAAGTTCCTACCAAATTGTGGAGGGACTC
66 ACAGAATTGTAAATGGTCACGACTTTTGGCTTGTGGAAGTTCCTACCAAATTGTGGAGGGACTC
41279 CA
1 CA
41281 CACCTTTAAA
Statistics
Matches: 125, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
129 125 1.00
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (129 bp):
CATGTTATAACTCGTCATAACATTCATTCGCATCAATTACATAAAAGCAAGAACCCTGATTATTC
ACAGAATTGTAAATGGTCACGACTTTTGGCTTGTGGAAGTTCCTACCAAATTGTGGAGGGACTC
Found at i:44455 original size:33 final size:32
Alignment explanation
Indices: 44381--44497 Score: 103
Period size: 33 Copynumber: 3.6 Consensus size: 32
44371 AAAGGATCAT
* **
44381 GTGGCCGGTTG-TGGCCGGGCATGGCCGAGTCAT
1 GTGGCCGG-TGATGGCCGGGCATGACC-AGTCGC
*
44414 GTGCCCGGTTG-TGGCCGGGCATGACCATGTCGC
1 GTGGCCGG-TGATGGCCGGGCATGACCA-GTCGC
**
44447 GTGGCCGGTGATGGCCGGGCATCTCCAAGTCGC
1 GTGGCCGGTGATGGCCGGGCATGACC-AGTCGC
* *
44480 ATGGCCGGTGTTGGCCGG
1 GTGGCCGGTGATGGCCGG
44498 ACATCTCCCA
Statistics
Matches: 72, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
32 3 0.04
33 68 0.94
34 1 0.01
ACGTcount: A:0.09, C:0.27, G:0.43, T:0.21
Consensus pattern (32 bp):
GTGGCCGGTGATGGCCGGGCATGACCAGTCGC
Found at i:44503 original size:33 final size:33
Alignment explanation
Indices: 44442--44525 Score: 114
Period size: 33 Copynumber: 2.5 Consensus size: 33
44432 GCATGACCAT
* * *
44442 GTCGCGTGGCCGGTGATGGCCGGGCATCTCCAA
1 GTCGCATGGCCGGTGTTGGCCGGACATCTCCAA
*
44475 GTCGCATGGCCGGTGTTGGCCGGACATCTCCCA
1 GTCGCATGGCCGGTGTTGGCCGGACATCTCCAA
* *
44508 GTCACATGACCGGTGTTG
1 GTCGCATGGCCGGTGTTG
44526 CGCGGCTTCT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.13, C:0.30, G:0.36, T:0.21
Consensus pattern (33 bp):
GTCGCATGGCCGGTGTTGGCCGGACATCTCCAA
Found at i:44889 original size:20 final size:20
Alignment explanation
Indices: 44864--44904 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
44854 AATCCCACGT
44864 TACGTGCCTAATAAAGTCCA
1 TACGTGCCTAATAAAGTCCA
44884 TACGTGCCTAATAAAGTCCA
1 TACGTGCCTAATAAAGTCCA
44904 T
1 T
44905 CTTTGGTCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (20 bp):
TACGTGCCTAATAAAGTCCA
Found at i:45068 original size:11 final size:11
Alignment explanation
Indices: 45052--45093 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
45042 TGAAGCAAAG
45052 AAAAAAAAGAA
1 AAAAAAAAGAA
*
45063 AAAAAAACGAA
1 AAAAAAAAGAA
*
45074 AAAACAAAGAA
1 AAAAAAAAGAA
45085 AAAAGAAAA
1 AAAA-AAAA
45094 AAGATAGAGC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
11 23 0.88
12 3 0.12
ACGTcount: A:0.86, C:0.05, G:0.10, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:45077 original size:18 final size:18
Alignment explanation
Indices: 45054--45097 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
45044 AAGCAAAGAA
45054 AAAAAAGAAA-AAAAAACG
1 AAAAAAGAAAGAAAAAA-G
*
45072 AAAAAACAAAGAAAAAAG
1 AAAAAAGAAAGAAAAAAG
45090 AAAAAAGA
1 AAAAAAGA
45098 TAGAGCTCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 17 0.74
19 6 0.26
ACGTcount: A:0.84, C:0.05, G:0.11, T:0.00
Consensus pattern (18 bp):
AAAAAAGAAAGAAAAAAG
Done.