Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005290.1 Hibiscus syriacus cultivar Beakdansim tig00011966_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: 60019
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:1357 original size:21 final size:21
Alignment explanation
Indices: 1314--1369 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
1304 TGGTGTATGG
* *
1314 CGTGATGAGGTATCCACTTTA
1 CGTGATGAGGTAGCCACTCTA
**
1335 CGTGATGAGGTAGCGGCTCTA
1 CGTGATGAGGTAGCCACTCTA
1356 CGTGA-GATGGTAGC
1 CGTGATGA-GGTAGC
1370 ATCGTTGCAG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 2 0.07
21 28 0.93
ACGTcount: A:0.21, C:0.18, G:0.34, T:0.27
Consensus pattern (21 bp):
CGTGATGAGGTAGCCACTCTA
Found at i:1662 original size:20 final size:20
Alignment explanation
Indices: 1639--1707 Score: 111
Period size: 20 Copynumber: 3.5 Consensus size: 20
1629 GAAACTTAAA
1639 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
1659 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGAAAATGACT
**
1679 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
1699 ATCGCAACG
1 ATCGCAACG
1708 GGATAATCGT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.35, C:0.26, G:0.22, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1736 original size:33 final size:34
Alignment explanation
Indices: 1699--1773 Score: 89
Period size: 33 Copynumber: 2.2 Consensus size: 34
1689 GAATTTGACT
* *
1699 ATCGCAACGGGATAATCGTAATGCG-AAATAAAA
1 ATCGCAACGGGAAAATCGCAATGCGAAAATAAAA
* * *
1732 ATCGCAACGTGAAAATTGCAATGCGAAAATGAAA
1 ATCGCAACGGGAAAATCGCAATGCGAAAATAAAA
*
1766 ATCACAAC
1 ATCGCAAC
1774 ACGAATTTAG
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
33 21 0.60
34 14 0.40
ACGTcount: A:0.47, C:0.17, G:0.19, T:0.17
Consensus pattern (34 bp):
ATCGCAACGGGAAAATCGCAATGCGAAAATAAAA
Found at i:1816 original size:19 final size:20
Alignment explanation
Indices: 1779--1817 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
1769 ACAACACGAA
* *
1779 TTTAGTTTCGCGTTGTGATT
1 TTTAGTTTCGCATTATGATT
1799 TTTA-TTTCGCATTATGATT
1 TTTAGTTTCGCATTATGATT
1818 ATCTTGTTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.15, C:0.10, G:0.18, T:0.56
Consensus pattern (20 bp):
TTTAGTTTCGCATTATGATT
Found at i:1848 original size:20 final size:20
Alignment explanation
Indices: 1823--1870 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
1813 TGATTATCTT
1823 GTTGCGATAGTCATTTCCGC
1 GTTGCGATAGTCATTTCCGC
*
1843 GTTGCGATAGTCATTTTCGC
1 GTTGCGATAGTCATTTCCGC
1863 GTTGCGAT
1 GTTGCGAT
1871 TTTAAGTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.15, C:0.21, G:0.27, T:0.38
Consensus pattern (20 bp):
GTTGCGATAGTCATTTCCGC
Found at i:2426 original size:21 final size:21
Alignment explanation
Indices: 2402--2471 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
2392 CTATCATCCC
2402 TCAAGAGTCCCCTCCCACCGT
1 TCAAGAGTCCCCTCCCACCGT
* ** *
2423 TCAAGAGGCCCCTATCATCGT
1 TCAAGAGTCCCCTCCCACCGT
* *
2444 TGAAGAGGT-CCCTCCCACCAT
1 TCAAGA-GTCCCCTCCCACCGT
2465 TCAAGAG
1 TCAAGAG
2472 CCTGATTCAC
Statistics
Matches: 37, Mismatches: 11, Indels: 3
0.73 0.22 0.06
Matches are distributed among these distances:
20 1 0.03
21 35 0.95
22 1 0.03
ACGTcount: A:0.24, C:0.37, G:0.19, T:0.20
Consensus pattern (21 bp):
TCAAGAGTCCCCTCCCACCGT
Found at i:2437 original size:42 final size:42
Alignment explanation
Indices: 2388--2471 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 42
2378 CATCGTTCAA
*
2388 GCCCCTATCATCCCTCAAGA-GTCCCCTCCCACCGTTCAAGAG
1 GCCCCTATCATCCCTCAAGAGGT-CCCTCCCACCATTCAAGAG
** *
2430 GCCCCTATCATCGTTGAAGAGGTCCCTCCCACCATTCAAGAG
1 GCCCCTATCATCCCTCAAGAGGTCCCTCCCACCATTCAAGAG
2472 CCTGATTCAC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
42 35 0.95
43 2 0.05
ACGTcount: A:0.23, C:0.40, G:0.17, T:0.20
Consensus pattern (42 bp):
GCCCCTATCATCCCTCAAGAGGTCCCTCCCACCATTCAAGAG
Found at i:3698 original size:20 final size:19
Alignment explanation
Indices: 3675--3720 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
3665 GGAAACTAAT
*
3675 TTGCGATACTGGAGATCGCA
1 TTGCGAT-CTAGAGATCGCA
*
3695 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
3714 TTGCGAT
1 TTGCGAT
3721 TTTGTTGGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:3710 original size:19 final size:19
Alignment explanation
Indices: 3686--3722 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
3676 TGCGATACTG
3686 GAGATCGCATTGCGATTTA
1 GAGATCGCATTGCGATTTA
3705 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
3723 TGTTGGTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:5921 original size:20 final size:20
Alignment explanation
Indices: 5896--5935 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
5886 GTTTCAACAC
*
5896 TCGACTACTAATACTCTGAA
1 TCGACTACCAATACTCTGAA
*
5916 TCGACTACCAATCCTCTGAA
1 TCGACTACCAATACTCTGAA
5936 AAGTGTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.30, G:0.10, T:0.28
Consensus pattern (20 bp):
TCGACTACCAATACTCTGAA
Found at i:7063 original size:16 final size:16
Alignment explanation
Indices: 7042--7086 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
7032 AAAAATTAAA
7042 ATTAAAAGTTAAAGTG
1 ATTAAAAGTTAAAGTG
7058 ATTAAAA--TAAGAGTG
1 ATTAAAAGTTAA-AGTG
7073 ATTTAAAAGTTAAA
1 A-TTAAAAGTTAAA
7087 TAATTAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
14 3 0.12
15 5 0.20
16 13 0.52
17 1 0.04
18 3 0.12
ACGTcount: A:0.53, C:0.00, G:0.16, T:0.31
Consensus pattern (16 bp):
ATTAAAAGTTAAAGTG
Found at i:16701 original size:21 final size:20
Alignment explanation
Indices: 16615--16771 Score: 93
Period size: 20 Copynumber: 7.8 Consensus size: 20
16605 AAATGACCAA
**
16615 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
16634 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
16654 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
16674 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * **
16695 GAAAATCGCAATGCGATAGT
1 CAAAATCGCAACGCGATTTT
* **
16715 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
16735 ACAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
16756 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
16772 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 9
0.73 0.20 0.06
Matches are distributed among these distances:
19 16 0.15
20 56 0.54
21 32 0.31
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:16724 original size:41 final size:41
Alignment explanation
Indices: 16674--16771 Score: 110
Period size: 41 Copynumber: 2.4 Consensus size: 41
16664 AATCAGTTTC
* *
16674 CAAAATCGCAACGCGATTCTT-GAAAATCGCAATGCG-ATAGT
1 CAAAATCGCAACGCGATT-TTACAAAATCGCAACGCGAATA-T
* **
16715 CAAATTCGCATTGCGATTTTACAAAATCGCAACGCGAATAT
1 CAAAATCGCAACGCGATTTTACAAAATCGCAACGCGAATAT
*
16756 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
16772 ACACATAAAT
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
40 2 0.04
41 41 0.89
42 3 0.07
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.21
Consensus pattern (41 bp):
CAAAATCGCAACGCGATTTTACAAAATCGCAACGCGAATAT
Found at i:16785 original size:61 final size:61
Alignment explanation
Indices: 16614--16790 Score: 182
Period size: 61 Copynumber: 2.9 Consensus size: 61
16604 AAAATGACCA
* * * *
16614 ACAAAATCGCAACGCGAA-ATAAAAATCGCAACGCGATCCCCAGAATCGCAAAT-C-AGTTT
1 ACAAAATCGCAACGCGAATATGAAAATCGCAACGCGATACACAAAATCGC-AATGCGAGTTT
* * * * ** * * *
16673 CCAAAATCGCAACGCGATTCTTGAAAATCGCAATGCGATAGTCAAATTCGCATTGCGATTTT
1 ACAAAATCGCAACGCGAAT-ATGAAAATCGCAACGCGATACACAAAATCGCAATGCGAGTTT
16735 ACAAAATCGCAACGCGAATATGAAAATCGCAACGCGA-ACACATAAATCGCAATGCG
1 ACAAAATCGCAACGCGAATATGAAAATCGCAACGCGATACACA-AAATCGCAATGCG
16791 TATCCGTAAA
Statistics
Matches: 93, Mismatches: 20, Indels: 8
0.77 0.17 0.07
Matches are distributed among these distances:
59 16 0.17
60 5 0.05
61 51 0.55
62 21 0.23
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.19
Consensus pattern (61 bp):
ACAAAATCGCAACGCGAATATGAAAATCGCAACGCGATACACAAAATCGCAATGCGAGTTT
Found at i:16813 original size:20 final size:20
Alignment explanation
Indices: 16738--16951 Score: 234
Period size: 20 Copynumber: 10.7 Consensus size: 20
16728 CGATTTTACA
* ** *
16738 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
16758 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
*
16778 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
16798 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
16818 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
16838 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
16858 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* *
16878 ATATCGCAACGCGTATCGGT
1 AAATCGCAACGCGTATCCGT
* * *
16898 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
16918 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
16939 AAATCGCAACGCG
1 AAATCGCAACGCG
16952 ATATTTAAAG
Statistics
Matches: 162, Mismatches: 27, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
19 2 0.01
20 142 0.88
21 17 0.10
22 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:17373 original size:33 final size:33
Alignment explanation
Indices: 17334--17401 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
17324 TTCACTTAGA
17334 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
17367 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
17400 TT
1 TT
17402 CAAGTTAGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.10, C:0.24, G:0.18, T:0.49
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:17540 original size:41 final size:41
Alignment explanation
Indices: 17482--17559 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
17472 TTGCAGAAGA
*
17482 GTCGCAACGAGATAAATGAAAATCGCAACGAGAGAATGACT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
17523 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
17560 CGCAAAGCGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.45, C:0.17, G:0.26, T:0.13
Consensus pattern (41 bp):
GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
Found at i:17556 original size:21 final size:21
Alignment explanation
Indices: 17483--17558 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
17473 TGCAGAAGAG
*
17483 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
***
17504 TCGCAACGAGAG-AATGACTG
1 TCGCAACGAGAGAAATGAAAA
17524 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
17545 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
17559 TCGCAAAGCG
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.46, C:0.17, G:0.25, T:0.12
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGAAAA
Found at i:17562 original size:14 final size:14
Alignment explanation
Indices: 17543--17599 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
17533 GAGAAATGAA
17543 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
17557 AATCGCAAAGCGATATGAA
1 AATCGC-AA-CG--A-GAG
17576 AATCGCAACGAGAG
1 AATCGCAACGAGAG
17590 AATCGCAACG
1 AATCGCAACG
17600 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 18 0.50
15 3 0.08
16 2 0.06
17 2 0.06
18 3 0.08
19 8 0.22
ACGTcount: A:0.44, C:0.21, G:0.25, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:17576 original size:33 final size:33
Alignment explanation
Indices: 17538--17602 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
17528 AACGAGAGAA
17538 ATGAAAATCGCAACGAGAGAATCGCAAAGCGAT
1 ATGAAAATCGCAACGAGAGAATCGCAAAGCGAT
*
17571 ATGAAAATCGCAACGAGAGAATCGCAACGCGA
1 ATGAAAATCGCAACGAGAGAATCGCAAAGCGA
17603 AACCAAAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.45, C:0.20, G:0.25, T:0.11
Consensus pattern (33 bp):
ATGAAAATCGCAACGAGAGAATCGCAAAGCGAT
Found at i:17611 original size:33 final size:33
Alignment explanation
Indices: 17541--17615 Score: 114
Period size: 33 Copynumber: 2.3 Consensus size: 33
17531 GAGAGAAATG
* **
17541 AAAATCGCAACGAGAGAATCGCAAAGCGATATG
1 AAAATCGCAACGAGAGAATCGCAAAGCGAAACC
*
17574 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
1 AAAATCGCAACGAGAGAATCGCAAAGCGAAACC
17607 AAAATCGCA
1 AAAATCGCA
17616 TTGCGATTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.09
Consensus pattern (33 bp):
AAAATCGCAACGAGAGAATCGCAAAGCGAAACC
Found at i:17633 original size:19 final size:19
Alignment explanation
Indices: 17611--17675 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
17601 GAAACCAAAA
*
17611 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
17630 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
17644 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
17663 TCGCGTTGCGATT
1 TCGCGTTGCGATT
17676 CTCTCGTTGC
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
14 10 0.26
16 3 0.08
17 3 0.08
19 22 0.58
ACGTcount: A:0.11, C:0.23, G:0.22, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:17652 original size:14 final size:14
Alignment explanation
Indices: 17633--17689 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
17623 TTTCATTTCG
17633 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
17647 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
17666 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
17680 CGTTGCGATT
1 CGTTGCGATT
17690 TTCATTTCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:17658 original size:33 final size:33
Alignment explanation
Indices: 17616--17697 Score: 164
Period size: 33 Copynumber: 2.5 Consensus size: 33
17606 CAAAATCGCA
17616 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
17649 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
17682 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
17698 AACCAAAAGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.10, C:0.23, G:0.20, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:19552 original size:93 final size:93
Alignment explanation
Indices: 19393--19675 Score: 550
Period size: 93 Copynumber: 3.1 Consensus size: 93
19383 TAGATTGCTT
*
19393 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
19458 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
19486 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
19551 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
19579 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
19644 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
19671 AGTAA
1 AGTAA
19676 TGCAATCCAT
Statistics
Matches: 189, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
92 6 0.03
93 183 0.97
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:19763 original size:19 final size:19
Alignment explanation
Indices: 19723--19851 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
19713 TAGTTTACTT
* *
19723 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
19743 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
19762 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
19781 TCGCAA--C--AA-CAGAA
1 TCGCAACGCGAAACCAAAA
19795 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
* *
19814 TCGCAA--CG--A-TAAGA
1 TCGCAACGCGAAACCAAAA
19828 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
19847 TCGCA
1 TCGCA
19852 TTGCGATTTT
Statistics
Matches: 88, Mismatches: 11, Indels: 21
0.73 0.09 0.17
Matches are distributed among these distances:
14 18 0.20
15 3 0.03
16 3 0.03
17 3 0.03
18 3 0.03
19 45 0.51
20 13 0.15
ACGTcount: A:0.47, C:0.28, G:0.16, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:19802 original size:33 final size:34
Alignment explanation
Indices: 19760--19851 Score: 136
Period size: 33 Copynumber: 2.8 Consensus size: 34
19750 GCGAAACCAA
**
19760 AATCGCAACGCGAAATGAAAATCGCAAC-A-ACAG
1 AATCGCAACGCGAAACCAAAATCGCAACGATA-AG
19793 AATCGCAACGCGAAACCAAAATCGCAACGATAAG
1 AATCGCAACGCGAAACCAAAATCGCAACGATAAG
19827 -ATCGCAACGCGAAACCAAAATCGCA
1 AATCGCAACGCGAAACCAAAATCGCA
19852 TTGCGATTTT
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
33 51 0.93
34 3 0.05
35 1 0.02
ACGTcount: A:0.47, C:0.27, G:0.17, T:0.09
Consensus pattern (34 bp):
AATCGCAACGCGAAACCAAAATCGCAACGATAAG
Found at i:19849 original size:52 final size:51
Alignment explanation
Indices: 19723--19851 Score: 136
Period size: 52 Copynumber: 2.5 Consensus size: 51
19713 TAGTTTACTT
* * *
19723 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACGCGAAAC-CAAAATCGCAACGCGAAACCAAAATCGCAACGAGAAA
* * * *
19775 T-GAAAATCGC-AACAACAGAATCGCAACGCGAAACCAAAATCGCAACGATAAGA
1 TCG-CAA-CGCGAA-ACCAAAATCGCAACGCGAAACCAAAATCGCAACGAGAA-A
19828 TCGCAACGCGAAACCAAAATCGCA
1 TCGCAACGCGAAACCAAAATCGCA
19852 TTGCGATTTT
Statistics
Matches: 61, Mismatches: 10, Indels: 12
0.73 0.12 0.14
Matches are distributed among these distances:
51 1 0.02
52 50 0.82
53 9 0.15
54 1 0.02
ACGTcount: A:0.47, C:0.28, G:0.16, T:0.09
Consensus pattern (51 bp):
TCGCAACGCGAAACCAAAATCGCAACGCGAAACCAAAATCGCAACGAGAAA
Found at i:19869 original size:19 final size:18
Alignment explanation
Indices: 19847--19965 Score: 110
Period size: 19 Copynumber: 6.8 Consensus size: 18
19837 GAAACCAAAA
*
19847 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTC-TT
19866 TCGCGTTGCGA--TTCTT
1 TCGCGTTGCGATTTTCTT
*
19882 T--CGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTT-CTT
*
19899 TCGCGTTGCGA--TTCTG
1 TCGCGTTGCGATTTTCTT
19915 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTC-TT
*
19932 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTT-CTT
19951 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
19966 AAGTTTCGTG
Statistics
Matches: 83, Mismatches: 6, Indels: 22
0.75 0.05 0.20
Matches are distributed among these distances:
14 16 0.19
16 10 0.12
17 10 0.12
19 47 0.57
ACGTcount: A:0.08, C:0.19, G:0.25, T:0.47
Consensus pattern (18 bp):
TCGCGTTGCGATTTTCTT
Found at i:19888 original size:14 final size:14
Alignment explanation
Indices: 19869--19925 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
19859 TTTCATTTCG
19869 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
*
19883 CGTTGCGATTTTGGTTT
1 CGTTGCGA--TT-CTTT
*
19900 CGCGTTGCGATTCTGT
1 --CGTTGCGATTCTTT
19916 CGTTGCGATT
1 CGTTGCGATT
19926 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 18 0.51
16 4 0.11
17 5 0.14
19 8 0.23
ACGTcount: A:0.07, C:0.19, G:0.28, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:19894 original size:33 final size:33
Alignment explanation
Indices: 19852--19944 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
19842 CAAAATCGCA
*
19852 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
**
19885 TTGCGATTTTGGTTTCGCGTTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
19918 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
19945 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.09, C:0.19, G:0.25, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:19973 original size:20 final size:19
Alignment explanation
Indices: 19847--19981 Score: 105
Period size: 19 Copynumber: 7.6 Consensus size: 19
19837 GAAACCAAAA
*
19847 TCGCATTGCGATTTTCA-TT
1 TCGCGTTGCGATTTT-AGTT
*
19866 TCGCGTTGCGA--TT-CTT
1 TCGCGTTGCGATTTTAGTT
*
19882 T--CGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTAGTT
*
19899 TCGCGTTGCGATTCT-G--
1 TCGCGTTGCGATTTTAGTT
19915 T--CGTTGCGATTTTCA-TT
1 TCGCGTTGCGATTTT-AGTT
*
19932 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTAGTT
19951 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTT-AGTT
*
19971 TCGTGTTGCGA
1 TCGCGTTGCGA
19982 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 7, Indels: 27
0.74 0.05 0.21
Matches are distributed among these distances:
14 19 0.20
16 6 0.06
17 6 0.06
18 1 0.01
19 50 0.53
20 13 0.14
ACGTcount: A:0.10, C:0.19, G:0.26, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTAGTT
Found at i:21924 original size:14 final size:14
Alignment explanation
Indices: 21905--21940 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
21895 ATTGTTTAAT
21905 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
21919 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
21933 TGATTTGT
1 TGATTTGT
21941 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:22063 original size:19 final size:19
Alignment explanation
Indices: 22047--22144 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
22037 AAAAATGACT
22047 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
22066 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
22085 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
22099 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
22118 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
22138 ATCGCAA
1 ATCGCAA
22145 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:22176 original size:53 final size:53
Alignment explanation
Indices: 22047--22162 Score: 225
Period size: 53 Copynumber: 2.2 Consensus size: 53
22037 AAAAATGACT
22047 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
22099 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
22152 ATCGCAATGCG
1 ATCGCAATGCG
22163 TTTATAATTT
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.46
53 34 0.54
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:22215 original size:19 final size:19
Alignment explanation
Indices: 22191--22425 Score: 269
Period size: 19 Copynumber: 13.4 Consensus size: 19
22181 GATTCTCTCG
22191 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
22210 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
22229 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
22243 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
22262 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
22281 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
22295 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
22314 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
22333 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
22352 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
22366 TTGCGA-TTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
22385 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
22399 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
22418 TTGCGATT
1 TTGCGATT
22426 GTAATTTCCG
Statistics
Matches: 187, Mismatches: 8, Indels: 42
0.79 0.03 0.18
Matches are distributed among these distances:
14 29 0.16
15 3 0.02
16 22 0.12
17 20 0.11
18 1 0.01
19 107 0.57
20 5 0.03
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:22226 original size:52 final size:52
Alignment explanation
Indices: 22169--22425 Score: 362
Period size: 52 Copynumber: 4.9 Consensus size: 52
22159 TGCGTTTATA
22169 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
22221 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
22273 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* * * * *
22325 ATTTCGCATTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCGTTGCGA-TTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
* * *
22376 ATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTCATTTCGCGTTGCGATT
1 ATTT-CGCATTGCGATTCTC-TCGTTGCGATTTTCATTTCGCATTGCGATT
22426 GTAATTTCCG
Statistics
Matches: 186, Mismatches: 10, Indels: 17
0.87 0.05 0.08
Matches are distributed among these distances:
50 9 0.05
51 13 0.07
52 151 0.81
53 6 0.03
54 6 0.03
55 1 0.01
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:22269 original size:71 final size:71
Alignment explanation
Indices: 22169--22425 Score: 299
Period size: 71 Copynumber: 3.8 Consensus size: 71
22159 TGCGTTTATA
* *
22169 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATT-T-TCATTTCG
1 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCATTGCG
22227 CA-TTGC
66 -ATTTGC
* * *
22233 GATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTG
1 -ATT-TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCATTG
*
22298 CGATTTTC
64 CGATTTGC
*
22306 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCG
1 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCATTGCG
22371 ATTT-C
66 ATTTGC
* *
22376 ATTTCCGCATTGCGATTTTCA--T-G--TTGGGATTTTCATTTCGCGTTGCGATT
1 ATTT-CGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATT
22426 GTAATTTCCG
Statistics
Matches: 172, Mismatches: 10, Indels: 19
0.86 0.05 0.09
Matches are distributed among these distances:
65 3 0.02
66 34 0.20
68 4 0.02
69 5 0.03
70 5 0.03
71 107 0.62
72 5 0.03
73 9 0.05
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (71 bp):
ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCATTGCG
ATTTGC
Found at i:24724 original size:12 final size:12
Alignment explanation
Indices: 24707--24731 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
24697 TCTTCGGGGA
24707 CTTTTTCTTCTT
1 CTTTTTCTTCTT
24719 CTTTTTCTTCTT
1 CTTTTTCTTCTT
24731 C
1 C
24732 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:24940 original size:24 final size:24
Alignment explanation
Indices: 24906--24952 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
24896 CTGAAACATC
24906 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
24930 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
24953 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:25662 original size:20 final size:20
Alignment explanation
Indices: 25634--25843 Score: 206
Period size: 20 Copynumber: 10.5 Consensus size: 20
25624 AAATTTCAGT
* * *
25634 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
25654 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
25674 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
25694 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
25714 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* **
25734 GTTGCGATATACGGAAACGC
1 GTTGCGATTTACGGATTCGC
** *
25754 GTTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
* *
25774 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
25794 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
25814 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
25834 GTTGCGATTT
1 GTTGCGATTT
25844 TGGAAACTGA
Statistics
Matches: 162, Mismatches: 26, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
20 161 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:27913 original size:20 final size:20
Alignment explanation
Indices: 27887--27941 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
27877 AGAATGTTAT
* *
27887 CAGGGTATCTATACTATAGG
1 CAGGGTATCTATACCATAGA
*
27907 GAGGGTATCTATACCATAGA
1 CAGGGTATCTATACCATAGA
*
27927 CAAGGTATCTATACC
1 CAGGGTATCTATACC
27942 TCAGTTAGGG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (20 bp):
CAGGGTATCTATACCATAGA
Found at i:34740 original size:20 final size:20
Alignment explanation
Indices: 34714--34768 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
34704 AGAATGTTAT
* *
34714 CAGGGTATCTATACTATAGG
1 CAGGGTATCTATACCATAGA
*
34734 GAGGGTATCTATACCATAGA
1 CAGGGTATCTATACCATAGA
*
34754 CAAGGTATCTATACC
1 CAGGGTATCTATACC
34769 TCAGTTAGGG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (20 bp):
CAGGGTATCTATACCATAGA
Found at i:35338 original size:22 final size:22
Alignment explanation
Indices: 35303--35361 Score: 91
Period size: 22 Copynumber: 2.7 Consensus size: 22
35293 ATGGTTACAG
* *
35303 TGGTCCTTCAGGACATATCCAA
1 TGGTCATTCGGGACATATCCAA
35325 TGGTCATTCGGGACATATCCAA
1 TGGTCATTCGGGACATATCCAA
*
35347 TGGTCATTCGAGACA
1 TGGTCATTCGGGACA
35362 AATATTCAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (22 bp):
TGGTCATTCGGGACATATCCAA
Found at i:42383 original size:13 final size:14
Alignment explanation
Indices: 42363--42390 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
42353 TAGTTCTTTC
42363 CAAAAAAAAGACTA
1 CAAAAAAAAGACTA
42377 CAAAAAAAAGACTA
1 CAAAAAAAAGACTA
42391 ATGAAGGTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.14, G:0.07, T:0.07
Consensus pattern (14 bp):
CAAAAAAAAGACTA
Found at i:49503 original size:21 final size:21
Alignment explanation
Indices: 49477--49517 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
49467 ACTGACACTC
49477 CTATGGGCAATATCGATACTT
1 CTATGGGCAATATCGATACTT
*
49498 CTATGGGCAATATTGATACT
1 CTATGGGCAATATCGATACT
49518 CCCATGAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (21 bp):
CTATGGGCAATATCGATACTT
Found at i:50273 original size:23 final size:23
Alignment explanation
Indices: 50239--50304 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 23
50229 CACCACAGCT
* *
50239 CGTATAAATGCACTGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
50262 CGTAGAATTGCACCGAAGTGTCG
1 CGTAGAAATGCACCGAAGTGCCA
50285 CGTAGAAATGCACCGAAGTG
1 CGTAGAAATGCACCGAAGTG
50305 GCATATAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.32, C:0.21, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:50407 original size:21 final size:21
Alignment explanation
Indices: 50359--50407 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
50349 CATATACATA
50359 TTCCAAATGACCAAATATATG
1 TTCCAAATGACCAAATATATG
**
50380 -TCTCAAATGACCGCATATATG
1 TTC-CAAATGACCAAATATATG
50401 TTCCAAA
1 TTCCAAA
50408 GGATTACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 2 0.08
21 20 0.83
22 2 0.08
ACGTcount: A:0.39, C:0.22, G:0.10, T:0.29
Consensus pattern (21 bp):
TTCCAAATGACCAAATATATG
Found at i:51091 original size:21 final size:21
Alignment explanation
Indices: 51067--51120 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
51057 TAGCCCTGTA
51067 GTATCGATACCCATTCATCTG
1 GTATCGATACCCATTCATCTG
51088 GTATCGATACCCATTCATCTG
1 GTATCGATACCCATTCATCTG
51109 GTATCGATACCC
1 GTATCGATACCC
51121 CTTACCCAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.24, C:0.30, G:0.15, T:0.31
Consensus pattern (21 bp):
GTATCGATACCCATTCATCTG
Found at i:53354 original size:15 final size:17
Alignment explanation
Indices: 53324--53360 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
53314 CACTACCTTC
53324 ATTTTGTAGTATAATTT
1 ATTTTGTAGTATAATTT
*
53341 -TTTTGTATTA-AATTT
1 ATTTTGTAGTATAATTT
53356 ATTTT
1 ATTTT
53361 TTATCTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (17 bp):
ATTTTGTAGTATAATTT
Done.