Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005990.1 Hibiscus syriacus cultivar Beakdansim tig00014086_pilon, 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: 106411
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:3906 original size:13 final size:13
Alignment explanation
Indices: 3888--3926 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
3878 ATCACTAACC
3888 CTTTCTTTGATTA
1 CTTTCTTTGATTA
*
3901 CTTTCTTTGA-GA
1 CTTTCTTTGATTA
3913 -TTTCTTTGATTA
1 CTTTCTTTGATTA
3925 CT
1 CT
3927 ATTGAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 9 0.41
12 2 0.09
13 11 0.50
ACGTcount: A:0.15, C:0.15, G:0.10, T:0.59
Consensus pattern (13 bp):
CTTTCTTTGATTA
Found at i:4893 original size:20 final size:20
Alignment explanation
Indices: 4868--5008 Score: 151
Period size: 20 Copynumber: 7.1 Consensus size: 20
4858 TGATTTTTCT
4868 GAATACGTAAATCGCAACGC
1 GAATACGTAAATCGCAACGC
*
4888 GAATACGTAAATCGCAACTC
1 GAATACGTAAATCGCAACGC
**
4908 GAATACGTAAATCGGTACGC
1 GAATACGTAAATCGCAACGC
* *
4928 GATTACGTAAATCACAACGC
1 GAATACGTAAATCGCAACGC
* *
4948 GTAT-CTGTAAAT-GCAATGC
1 GAATAC-GTAAATCGCAACGC
* **
4967 GTATTTGTAAATCGCAACGC
1 GAATACGTAAATCGCAACGC
* *
4987 GTATCCGTAAATCGCAACGC
1 GAATACGTAAATCGCAACGC
5007 GA
1 GA
5009 TTTTTTAAGC
Statistics
Matches: 101, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
19 16 0.16
20 85 0.84
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (20 bp):
GAATACGTAAATCGCAACGC
Found at i:5626 original size:21 final size:21
Alignment explanation
Indices: 5565--5643 Score: 94
Period size: 20 Copynumber: 3.9 Consensus size: 21
5555 TTCTAAACTT
5565 AAAATCGCAAC-ATGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
5585 AAAATCGCAAC-ACGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
**
5605 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAACGAGAGAAATG
5626 AAAATCGCAACGAGAGAA
1 AAAATCGCAACGAGAGAA
5644 TCGCAACGCG
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
20 30 0.58
21 22 0.42
ACGTcount: A:0.52, C:0.18, G:0.19, T:0.11
Consensus pattern (21 bp):
AAAATCGCAACGAGAGAAATG
Found at i:5710 original size:33 final size:33
Alignment explanation
Indices: 5668--5758 Score: 164
Period size: 33 Copynumber: 2.8 Consensus size: 33
5658 CAAAATCGCA
5668 TGCGATTTTAATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTAATTTCGCGTTGCGATTCTCTCGT
5701 TGCGATTTTAATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTAATTTCGCGTTGCGATTCTCTCGT
* *
5734 TACGATTTTCATTTCGCGTTGCGAT
1 TGCGATTTTAATTTCGCGTTGCGAT
5759 AGTCATTTTC
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.45
Consensus pattern (33 bp):
TGCGATTTTAATTTCGCGTTGCGATTCTCTCGT
Found at i:5758 original size:19 final size:19
Alignment explanation
Indices: 5668--5807 Score: 84
Period size: 19 Copynumber: 7.8 Consensus size: 19
5658 CAAAATCGCA
*
5668 TGCGATTTTAATTTCGCGT
1 TGCGATTTTCATTTCGCGT
*
5687 TGCGA--TTC---TCTCGT
1 TGCGATTTTCATTTCGCGT
*
5701 TGCGATTTTAATTTCGCGT
1 TGCGATTTTCATTTCGCGT
*
5720 TGCGA--TTC---TCTCGT
1 TGCGATTTTCATTTCGCGT
*
5734 TACGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
** *
5753 TGCGATAGTCATTTTCGTGT
1 TGCGATTTTCA-TTTCGCGT
** * *
5773 TGCGATAGTCATTCTCTCAT
1 TGCGATTTTCATT-TCGCGT
5793 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
5808 AACCAAAAGA
Statistics
Matches: 92, Mismatches: 17, Indels: 24
0.69 0.13 0.18
Matches are distributed among these distances:
14 19 0.21
16 5 0.05
17 4 0.04
19 32 0.35
20 32 0.35
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.46
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:5805 original size:20 final size:20
Alignment explanation
Indices: 5724--5798 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
5714 TCGCGTTGCG
* **
5724 ATTCTCTCGTTACGATTTTC
1 ATTCTCTCGTTGCGATAGTC
*
5744 ATT-TCGCGTTGCGATAGTC
1 ATTCTCTCGTTGCGATAGTC
*
5763 ATTTTCGT-GTTGCGATAGTC
1 ATTCTC-TCGTTGCGATAGTC
*
5783 ATTCTCTCATTGCGAT
1 ATTCTCTCGTTGCGAT
5799 TTTCATTTCA
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
19 16 0.36
20 29 0.64
ACGTcount: A:0.16, C:0.21, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATAGTC
Found at i:7490 original size:33 final size:33
Alignment explanation
Indices: 7445--7612 Score: 192
Period size: 33 Copynumber: 4.9 Consensus size: 33
7435 GTTGAAGGCA
* *
7445 ATTTCGCGTTGCGATTTTGTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTCTCGTTGCGATTTTC
*
7478 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTCTCGTTGCGATTTTC
*
7511 ATTTCGCATTGCGATAGTCATTTCCGCGTTGCGATTTTC
1 ATTTCGCATTGCG--A-T--TTT-CTCGTTGCGATTTTC
* * * *
7550 ATATTCGCGTTACAATTTTCACGTTGCGATTTTC
1 AT-TTCGCATTGCGATTTTCTCGTTGCGATTTTC
*
7584 ATTTCGCATTGCGATTCTCTCGTTGCGAT
1 ATTTCGCATTGCGATTTTCTCGTTGCGAT
7613 AGTAATTTTC
Statistics
Matches: 114, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
33 65 0.57
34 16 0.14
35 4 0.04
36 1 0.01
37 1 0.01
38 3 0.03
39 16 0.14
40 8 0.07
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.44
Consensus pattern (33 bp):
ATTTCGCATTGCGATTTTCTCGTTGCGATTTTC
Found at i:7491 original size:19 final size:19
Alignment explanation
Indices: 7467--7599 Score: 115
Period size: 20 Copynumber: 7.4 Consensus size: 19
7457 GATTTTGTCG
7467 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
7486 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
7500 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
** *
7519 TTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTT-CGCA
*
7539 TTGCGATTTTCATATTCGCG
1 TTGCGATTTTCAT-TTCGCA
* *
7559 TTACAATTTTCA---CG--
1 TTGCGATTTTCATTTCGCA
7573 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
7592 TTGCGATT
1 TTGCGATT
7600 CTCTCGTTGC
Statistics
Matches: 91, Mismatches: 11, Indels: 24
0.72 0.09 0.19
Matches are distributed among these distances:
14 16 0.18
16 9 0.10
17 9 0.10
19 27 0.30
20 28 0.31
21 2 0.02
ACGTcount: A:0.16, C:0.22, G:0.18, T:0.44
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:7544 original size:20 final size:19
Alignment explanation
Indices: 7498--7632 Score: 65
Period size: 20 Copynumber: 7.5 Consensus size: 19
7488 GCGATTCTCT
**
7498 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
7517 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTT-CG
**
7537 CGTTGCGATTTTCATATTCG
1 CGTTGCGATAGTCAT-TTCG
* *
7557 CGTTAC-A-A-T--TTTCA
1 CGTTGCGATAGTCATTTCG
**
7571 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* *
7590 CATTGCGAT--TC---TCT
1 CGTTGCGATAGTCATTTCG
*
7604 CGTTGCGATAGTAATTTTCG
1 CGTTGCGATAGTCA-TTTCG
7624 CGTTGCGAT
1 CGTTGCGAT
7633 TGACATTAAG
Statistics
Matches: 86, Mismatches: 17, Indels: 25
0.67 0.13 0.20
Matches are distributed among these distances:
14 18 0.21
15 2 0.02
16 1 0.01
17 4 0.05
19 27 0.31
20 32 0.37
21 2 0.02
ACGTcount: A:0.16, C:0.21, G:0.20, T:0.42
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:10171 original size:24 final size:24
Alignment explanation
Indices: 10137--10190 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
10127 CTGAAAAATC
10137 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
10161 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
10185 ATCAAA
1 ATCAAA
10191 TTTTGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:11554 original size:19 final size:19
Alignment explanation
Indices: 11527--11565 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
11517 ATTAGGTAAC
*
11527 AAAATTAATATTTTAAATA
1 AAAAATAATATTTTAAATA
11546 AAAAATAATATTTTAAATA
1 AAAAATAATATTTTAAATA
11565 A
1 A
11566 TATTTTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAAATAATATTTTAAATA
Found at i:11565 original size:12 final size:12
Alignment explanation
Indices: 11548--11572 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
11538 TTTAAATAAA
11548 AAATAATATTTT
1 AAATAATATTTT
11560 AAATAATATTTT
1 AAATAATATTTT
11572 A
1 A
11573 TTAAAAATAT
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:0.00, T:0.48
Consensus pattern (12 bp):
AAATAATATTTT
Found at i:11603 original size:32 final size:29
Alignment explanation
Indices: 11544--11607 Score: 76
Period size: 32 Copynumber: 2.1 Consensus size: 29
11534 ATATTTTAAA
11544 TAAAAAATAATATTTTAAATAATATTTTAT
1 TAAAAAATAATATTTTAAATAATATTTT-T
*
11574 TAAAAATATTAATATTTTCAAT-ATGATTTTT
1 TAAAAA-A-TAATATTTTAAATAAT-ATTTTT
11605 TAA
1 TAA
11608 TTGTATATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
30 6 0.20
31 7 0.23
32 17 0.57
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (29 bp):
TAAAAAATAATATTTTAAATAATATTTTT
Found at i:11781 original size:12 final size:13
Alignment explanation
Indices: 11745--11778 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
11735 TTAAGAGAAT
11745 AATATATATTTAAA
1 AATA-ATATTTAAA
11759 AATAATATTTAAA
1 AATAATATTTAAA
11772 AAGTAAT
1 AA-TAAT
11779 TTATATTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (13 bp):
AATAATATTTAAA
Found at i:13261 original size:20 final size:21
Alignment explanation
Indices: 13188--13264 Score: 81
Period size: 20 Copynumber: 3.9 Consensus size: 21
13178 GGTCCTAGTT
13188 AACTCGAACCAGA-CTGAGTC
1 AACTCGAACCAGATCTGAGTC
* *
13208 AACTCAAACCAAATC-GAGTC
1 AACTCGAACCAGATCTGAGTC
* *
13228 AACTTGAATC-GATCTGAGTC
1 AACTCGAACCAGATCTGAGTC
*
13248 AACTCGAA-CTGATCTGA
1 AACTCGAACCAGATCTGA
13265 CCCGTTGACT
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
19 4 0.09
20 42 0.89
21 1 0.02
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (21 bp):
AACTCGAACCAGATCTGAGTC
Found at i:19022 original size:28 final size:29
Alignment explanation
Indices: 18991--19045 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
18981 AATAAAGAAA
*
18991 TTTAAAATATATATTAAAAAA-CAAAATT
1 TTTAAAATATATAATAAAAAACCAAAATT
* *
19019 TTTAAAATTTTTAATAAAAAACCAAAA
1 TTTAAAATATATAATAAAAAACCAAAA
19046 AACTTTGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 18 0.78
29 5 0.22
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (29 bp):
TTTAAAATATATAATAAAAAACCAAAATT
Found at i:20424 original size:17 final size:19
Alignment explanation
Indices: 20389--20426 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
20379 GCGTGGGCAC
*
20389 ATATATATTCATAATAAAA
1 ATATATAATCATAATAAAA
20408 ATATATAAT-ATAA-AAAA
1 ATATATAATCATAATAAAA
20425 AT
1 AT
20427 GAGATTTCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 4 0.22
19 8 0.44
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (19 bp):
ATATATAATCATAATAAAA
Found at i:24104 original size:14 final size:15
Alignment explanation
Indices: 24076--24111 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
24066 GTCGTAACTT
24076 TTGCAACATCCACAA
1 TTGCAACATCCACAA
24091 TTGCAACA-CCACAA
1 TTGCAACATCCACAA
*
24105 TCGCAAC
1 TTGCAAC
24112 CGCAATTTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.39, C:0.36, G:0.08, T:0.17
Consensus pattern (15 bp):
TTGCAACATCCACAA
Found at i:28882 original size:2 final size:2
Alignment explanation
Indices: 28875--28947 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
28865 ATACCTTCAT
28875 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28917 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28948 GTAGTATTTC
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:29105 original size:17 final size:17
Alignment explanation
Indices: 29083--29115 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
29073 TAAAACCATG
29083 TCTATTTTTTATTTAGA
1 TCTATTTTTTATTTAGA
29100 TCTATTTTTTATTTAG
1 TCTATTTTTTATTTAG
29116 TAAACAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.06, G:0.06, T:0.67
Consensus pattern (17 bp):
TCTATTTTTTATTTAGA
Found at i:31427 original size:19 final size:19
Alignment explanation
Indices: 31400--31438 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
31390 TAAATATATT
*
31400 TAAACATATAGTATTGTAA
1 TAAAAATATAGTATTGTAA
* *
31419 TAAAAATATATTATTTTAA
1 TAAAAATATAGTATTGTAA
31438 T
1 T
31439 TAACATTAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.44
Consensus pattern (19 bp):
TAAAAATATAGTATTGTAA
Found at i:32692 original size:18 final size:20
Alignment explanation
Indices: 32648--32689 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
32638 TTTGATTCAC
* *
32648 GAAATATAAGATTACCAGTG
1 GAAATAAAAGATTACCAGAG
32668 GAAATAAAAGATTACCA-AG
1 GAAATAAAAGATTACCAGAG
32687 GAA
1 GAA
32690 TAAGATTACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.52, C:0.10, G:0.19, T:0.19
Consensus pattern (20 bp):
GAAATAAAAGATTACCAGAG
Found at i:32940 original size:22 final size:22
Alignment explanation
Indices: 32899--32940 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
32889 TACAAAATTA
* * *
32899 AAAATATAAAAAAGATTTAATG
1 AAAAGATAAAAAAAAATTAATG
32921 AAAAGATAAAAAAAAATTAA
1 AAAAGATAAAAAAAAATTAA
32941 CCCCTAAACT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.21
Consensus pattern (22 bp):
AAAAGATAAAAAAAAATTAATG
Found at i:53521 original size:24 final size:24
Alignment explanation
Indices: 53494--53627 Score: 135
Period size: 24 Copynumber: 5.6 Consensus size: 24
53484 CATAATTCAT
* *
53494 GTCAAATATCATATCAAAATCCAG
1 GTCAAATATCATATCAGAATCCAA
*
53518 GTCAAGTATCATATCAGAATCCAA
1 GTCAAATATCATATCAGAATCCAA
* * *
53542 GTCAAATATCAGATCAGAATCTAT
1 GTCAAATATCATATCAGAATCCAA
* * * *
53566 GTCAGATATCAAATTAGAATCCAT
1 GTCAAATATCATATCAGAATCCAA
* * *
53590 GTCAAGTATCACATCAGAATTCAA
1 GTCAAATATCATATCAGAATCCAA
53614 GTCGAAA-ATCATAT
1 GTC-AAATATCATAT
53628 AAAATATTCA
Statistics
Matches: 90, Mismatches: 19, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
24 88 0.98
25 2 0.02
ACGTcount: A:0.43, C:0.19, G:0.12, T:0.27
Consensus pattern (24 bp):
GTCAAATATCATATCAGAATCCAA
Found at i:56095 original size:13 final size:13
Alignment explanation
Indices: 56077--56107 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
56067 GGTCAACACC
56077 GGTCAACGGATCG
1 GGTCAACGGATCG
*
56090 GGTCAACGGGTCG
1 GGTCAACGGATCG
56103 GGTCA
1 GGTCA
56108 GGTTATAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.19, C:0.23, G:0.42, T:0.16
Consensus pattern (13 bp):
GGTCAACGGATCG
Found at i:63196 original size:25 final size:25
Alignment explanation
Indices: 63168--63218 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
63158 AATCATCTTC
63168 AACATTCCTACATCTCTGTTCTTTA
1 AACATTCCTACATCTCTGTTCTTTA
63193 AACATTCCTACATCTCTGTTCTTTA
1 AACATTCCTACATCTCTGTTCTTTA
63218 A
1 A
63219 GAACTTAGGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.25, C:0.27, G:0.04, T:0.43
Consensus pattern (25 bp):
AACATTCCTACATCTCTGTTCTTTA
Found at i:67052 original size:14 final size:13
Alignment explanation
Indices: 67032--67081 Score: 61
Period size: 14 Copynumber: 3.9 Consensus size: 13
67022 TCGTGAACGT
67032 TCGGTTATGTTCG
1 TCGGTTATGTTCG
67045 TACGGTTATGTTCG
1 T-CGGTTATGTTCG
67059 T---TTATGTTCG
1 TCGGTTATGTTCG
67069 TTCGGTTATGTTC
1 -TCGGTTATGTTC
67082 ATTTATGTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
10 9 0.28
11 1 0.03
13 1 0.03
14 21 0.66
ACGTcount: A:0.10, C:0.14, G:0.26, T:0.50
Consensus pattern (13 bp):
TCGGTTATGTTCG
Found at i:67057 original size:24 final size:24
Alignment explanation
Indices: 67030--67091 Score: 97
Period size: 24 Copynumber: 2.6 Consensus size: 24
67020 GTTCGTGAAC
*
67030 GTTCGGTTATGTTCGTACGGTTAT
1 GTTCGTTTATGTTCGTACGGTTAT
*
67054 GTTCGTTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTACGGTTAT
*
67078 GTTCATTTATGTTC
1 GTTCGTTTATGTTC
67092 ATTCATTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.11, C:0.13, G:0.24, T:0.52
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTACGGTTAT
Found at i:67101 original size:24 final size:24
Alignment explanation
Indices: 67049--67104 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
67039 TGTTCGTACG
* * *
67049 GTTATGTTCGTTTATGTTCGTTCG
1 GTTATGTTCATTTATGTTCATTCA
67073 GTTATGTTCATTTATGTTCATTCA
1 GTTATGTTCATTTATGTTCATTCA
*
67097 TTTATGTT
1 GTTATGTT
67105 TAACCCAATC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.14, C:0.11, G:0.18, T:0.57
Consensus pattern (24 bp):
GTTATGTTCATTTATGTTCATTCA
Found at i:68228 original size:16 final size:16
Alignment explanation
Indices: 68179--68237 Score: 77
Period size: 16 Copynumber: 3.8 Consensus size: 16
68169 GGGTATTCAA
68179 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
* * *
68195 CATTTATATTC--ATT
1 CGTTTATGTTCGTGTT
68209 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
68225 CGTTTATGTTCGT
1 CGTTTATGTTCGT
68238 TTATTTATTA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
14 11 0.31
16 24 0.69
ACGTcount: A:0.12, C:0.14, G:0.19, T:0.56
Consensus pattern (16 bp):
CGTTTATGTTCGTGTT
Found at i:68245 original size:30 final size:30
Alignment explanation
Indices: 68181--68245 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
68171 GTATTCAACG
*
68181 TTTATGTTCGTGTTCATTTATATTCATTCG
1 TTTATGTTCGTGTTCATTTATATTCATTCA
* * * *
68211 TTTATGTTCGTGTTCGTTTATGTTCGTTTA
1 TTTATGTTCGTGTTCATTTATATTCATTCA
68241 TTTAT
1 TTTAT
68246 TAAATGAACG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.14, C:0.11, G:0.15, T:0.60
Consensus pattern (30 bp):
TTTATGTTCGTGTTCATTTATATTCATTCA
Found at i:68327 original size:16 final size:16
Alignment explanation
Indices: 68306--68338 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
68296 AAAAAAAAAT
68306 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
68322 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
68338 T
1 T
68339 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:71833 original size:29 final size:29
Alignment explanation
Indices: 71779--71851 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 29
71769 ACAGTGGCCG
* * **
71779 TAGGTCGCCATGCACTCCCAGTGACCTCC
1 TAGGTCGCCATGCACGCCCAGCGACCAAC
* *
71808 TAGGTCGCCATGCACGCCCGGCGACCAAG
1 TAGGTCGCCATGCACGCCCAGCGACCAAC
*
71837 GAGGTCGCCATGCAC
1 TAGGTCGCCATGCAC
71852 TCGCGGCAAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.19, C:0.38, G:0.27, T:0.15
Consensus pattern (29 bp):
TAGGTCGCCATGCACGCCCAGCGACCAAC
Found at i:72657 original size:47 final size:46
Alignment explanation
Indices: 72561--72658 Score: 108
Period size: 47 Copynumber: 2.1 Consensus size: 46
72551 CACGTAGGGG
* ** * * *
72561 TATAGCGCGGGACAGGGGCCGCGTCTTACCTTTAATTCTGATTTATA
1 TATAGCGCGGGACAGGGGACGCACCATACCTTTAA-TCGGATTAATA
72608 TATAGCGCGGGACAGGGGACGCACCATACCTTTAA-CGGATATAATTA
1 TATAGCGCGGGACAGGGGACGCACCATACCTTTAATCGGAT-TAA-TA
72655 TATA
1 TATA
72659 AGGCGCGATG
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
45 4 0.09
46 2 0.05
47 37 0.86
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (46 bp):
TATAGCGCGGGACAGGGGACGCACCATACCTTTAATCGGATTAATA
Found at i:78513 original size:9 final size:9
Alignment explanation
Indices: 78483--78531 Score: 50
Period size: 8 Copynumber: 5.8 Consensus size: 9
78473 ATCTGCAAAA
78483 AAATTAAAT
1 AAATTAAAT
*
78492 -AAGTAAA-
1 AAATTAAAT
*
78499 ATATTAAAT
1 AAATTAAAT
78508 AAATTAAAT
1 AAATTAAAT
*
78517 -ACTTAAAT
1 AAATTAAAT
78525 AAATTAA
1 AAATTAA
78532 GTACAAAATA
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
8 18 0.58
9 13 0.42
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (9 bp):
AAATTAAAT
Found at i:78515 original size:17 final size:17
Alignment explanation
Indices: 78480--78531 Score: 63
Period size: 16 Copynumber: 3.1 Consensus size: 17
78470 TATATCTGCA
* *
78480 AAAAAATTAAAT-AAGT
1 AAAATATTAAATAAATT
78496 AAAATATTAAATAAATT
1 AAAATATTAAATAAATT
78513 -AAATACTTAAATAAATT
1 AAAATA-TTAAATAAATT
78530 AA
1 AA
78532 GTACAAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 16 0.52
17 14 0.45
18 1 0.03
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (17 bp):
AAAATATTAAATAAATT
Found at i:83340 original size:2 final size:2
Alignment explanation
Indices: 83333--83399 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
83323 TGTATTGTAG
83333 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
83375 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
83400 GATTTCAAGT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:84014 original size:21 final size:21
Alignment explanation
Indices: 83967--84015 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
83957 TTATAACTTG
*
83967 ACTCGAATTTAAAAAAATTCA
1 ACTCGAATTTAAAAAAATACA
* *
83988 AGTCGAGTTT-AAAAAATCACA
1 ACTCGAATTTAAAAAAAT-ACA
84009 ACTCGAA
1 ACTCGAA
84016 ATAAATTTGA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.49, C:0.16, G:0.10, T:0.24
Consensus pattern (21 bp):
ACTCGAATTTAAAAAAATACA
Found at i:88113 original size:28 final size:26
Alignment explanation
Indices: 88039--88101 Score: 126
Period size: 26 Copynumber: 2.4 Consensus size: 26
88029 ACTTAAACTA
88039 AAAAAAATTAATTTAACCATTTGACC
1 AAAAAAATTAATTTAACCATTTGACC
88065 AAAAAAATTAATTTAACCATTTGACC
1 AAAAAAATTAATTTAACCATTTGACC
88091 AAAAAAATTAA
1 AAAAAAATTAA
88102 ACGTTAACCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.56, C:0.13, G:0.03, T:0.29
Consensus pattern (26 bp):
AAAAAAATTAATTTAACCATTTGACC
Found at i:90888 original size:21 final size:23
Alignment explanation
Indices: 90863--90913 Score: 79
Period size: 22 Copynumber: 2.3 Consensus size: 23
90853 CCACTATAAA
90863 TTTTAGTGA-CTAAATTGATA-T
1 TTTTAGTGATCTAAATTGATACT
*
90884 TTTTAGTGATCTAATTTGATACT
1 TTTTAGTGATCTAAATTGATACT
90907 TTTTAGT
1 TTTTAGT
90914 ATATTTGCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 9 0.33
22 10 0.37
23 8 0.30
ACGTcount: A:0.27, C:0.06, G:0.14, T:0.53
Consensus pattern (23 bp):
TTTTAGTGATCTAAATTGATACT
Found at i:94660 original size:22 final size:22
Alignment explanation
Indices: 94635--94681 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
94625 AGTAAAAAAA
* *
94635 TTACTTAAAACATTATTATTTT
1 TTACCTAAAACATTAATATTTT
94657 TTACCTAAAACATTAATATTTT
1 TTACCTAAAACATTAATATTTT
94679 TTA
1 TTA
94682 ATATTTCCTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.51
Consensus pattern (22 bp):
TTACCTAAAACATTAATATTTT
Found at i:103119 original size:61 final size:61
Alignment explanation
Indices: 103002--103120 Score: 161
Period size: 61 Copynumber: 2.0 Consensus size: 61
102992 TCACCAGTTC
* * *
103002 AAAAAGAGCGATTTTGGTCCCTTACGTTATCGATCCGTTCGGTTCACGTGTCTTCTTCAAA
1 AAAAAGAGCGATTTTGGTCCCTTACGTTATCGATCCGTTCGATTCACGTATATTCTTCAAA
* *
103063 AAAAAG-GACGATTTTGGTCTCTTACGTTA-CTGATCCGTTCGATTCATGTATATTCTTC
1 AAAAAGAG-CGATTTTGGTCCCTTACGTTATC-GATCCGTTCGATTCACGTATATTCTTC
103121 TTCTTCTTCC
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
60 2 0.04
61 49 0.96
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.37
Consensus pattern (61 bp):
AAAAAGAGCGATTTTGGTCCCTTACGTTATCGATCCGTTCGATTCACGTATATTCTTCAAA
Done.