Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004223.1 Hibiscus syriacus cultivar Beakdansim tig00009245_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: 81785
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:347 original size:28 final size:29
Alignment explanation
Indices: 283--386 Score: 156
Period size: 29 Copynumber: 3.6 Consensus size: 29
273 GTTTCCATGG
283 CCGGCGACATGGTAGGTCGCCATGGAGTC
1 CCGGCGACATGGTAGGTCGCCATGGAGTC
* * *
312 CCGACGACATGGTAGGTCTCGA-GGAGTC
1 CCGGCGACATGGTAGGTCGCCATGGAGTC
340 CCGGCGACATGGTAGGTCGCCATGGAGTC
1 CCGGCGACATGGTAGGTCGCCATGGAGTC
* *
369 CTGTCGACATGGTAGGTC
1 CCGGCGACATGGTAGGTC
387 TAACATCATC
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
28 25 0.38
29 41 0.62
ACGTcount: A:0.18, C:0.26, G:0.37, T:0.19
Consensus pattern (29 bp):
CCGGCGACATGGTAGGTCGCCATGGAGTC
Found at i:1699 original size:26 final size:25
Alignment explanation
Indices: 1666--1734 Score: 63
Period size: 26 Copynumber: 2.8 Consensus size: 25
1656 AATCATGACT
*
1666 AAAT-ATTATTAAATCATTAAATATC
1 AAATCATTATTAAAT-AATAAATATC
* *
1691 AAATCATTAGATT-AATAATAATTATT
1 AAATCATT--ATTAAATAATAAATATC
1717 AAATCATTATT-AATAATA
1 AAATCATTATTAAATAATA
1735 TTAGTAATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
24 10 0.26
25 4 0.11
26 18 0.47
27 3 0.08
28 3 0.08
ACGTcount: A:0.52, C:0.06, G:0.01, T:0.41
Consensus pattern (25 bp):
AAATCATTATTAAATAATAAATATC
Found at i:2548 original size:49 final size:49
Alignment explanation
Indices: 2490--2666 Score: 241
Period size: 49 Copynumber: 3.4 Consensus size: 49
2480 ATTAATGATT
2490 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
2539 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTT-A--A--TGAT--T--TGA
*
2597 TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
1 -TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
2647 TAGTAATGATT--TAATAATGA
1 TAGTAATGATTAGTAATAATGA
2667 TTAGTAATAA
Statistics
Matches: 117, Mismatches: 1, Indels: 22
0.84 0.01 0.16
Matches are distributed among these distances:
47 9 0.08
49 50 0.43
50 4 0.03
52 2 0.02
54 8 0.07
56 2 0.02
58 4 0.03
59 38 0.32
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45
Consensus pattern (49 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
Found at i:2601 original size:10 final size:10
Alignment explanation
Indices: 2588--2614 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
2578 AATGATTTGA
2588 TAGTAATGAT
1 TAGTAATGAT
2598 TAGTAATGAT
1 TAGTAATGAT
2608 TAGTAAT
1 TAGTAAT
2615 AATGAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41
Consensus pattern (10 bp):
TAGTAATGAT
Found at i:2658 original size:168 final size:174
Alignment explanation
Indices: 2398--2865 Score: 712
Period size: 168 Copynumber: 2.8 Consensus size: 174
2388 TAATGATGAA
*
2398 ATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATAATTAGT-A-AATGAAATTATTAT
1 ATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATGAAATTATTAT
* *
2461 TAATATTTAATGATTTGAAATTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATT
66 TAATATTTAATGATTTGATATTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATA
*
2526 TTTAATGATTTGATAGTAATGA-T-T-A-G-TAATAATGAAATT
131 TTTAATGATTTAATAGTAATGATTATAATGATAATAATGAAATT
*
2565 ATTATTAATTTTTAATGATTTGATAGTAATGA-TTAGTAATGATTAGTAATAATGAAATTATTAT
1 ATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATGAAATTATTAT
* * *
2629 TAATATTTAATGATTTGATAGTAATGATTTAATAATGATTAGTAATAATGAAATTGTTATTAATA
66 TAATATTTAATGATTTGATATTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATA
2694 TTTAATGATTTAATAGTAATGATTAGTAATGATTAATAATGAAATT
131 TTTAATGATTTAATAGTAATGATTA-TAATGA-TAATAATGAAATT
2740 ATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATG--A--ATTAT
1 ATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATGAAATTATTAT
* * *
2801 TAATATTTAATGATTTGATATTAATGATTTAGTAATGATTTGATAGTAATG--ATTATTATAAAT
66 TAATATTTAATGATTTGATATTAATGATTTAGTAATGATTAG-TAATAATGAAATTATTATTAAT
2864 AT
130 AT
2866 GTCGAATTGT
Statistics
Matches: 275, Mismatches: 15, Indels: 18
0.89 0.05 0.06
Matches are distributed among these distances:
166 14 0.05
167 32 0.12
168 95 0.35
169 1 0.00
171 13 0.05
172 45 0.16
173 8 0.03
174 1 0.00
175 44 0.16
176 22 0.08
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (174 bp):
ATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATGAAATTATTAT
TAATATTTAATGATTTGATATTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATA
TTTAATGATTTAATAGTAATGATTATAATGATAATAATGAAATT
Found at i:2667 original size:25 final size:25
Alignment explanation
Indices: 2636--2854 Score: 99
Period size: 25 Copynumber: 8.9 Consensus size: 25
2626 TATTAATATT
2636 TAATGATTTGATAGTAATGATTTAA
1 TAATGATTTGATAGTAATGATTTAA
* *
2661 TAATGATTAG-TAATAATGA---AA
1 TAATGATTTGATAGTAATGATTTAA
* * *
2682 T--TGTTATTAATATTTAATGATTTAA
1 TAATGAT-TTGATA-GTAATGATTTAA
* *
2707 TAGT-A-ATGATTAGTAATGA-TTAA
1 TAATGATTTGA-TAGTAATGATTTAA
* *
2730 TAATGAAATT-ATTATTAAT-A-TT--
1 TAATG-ATTTGA-TAGTAATGATTTAA
*
2752 TAATGATTTGATAGTAATGATTTAG
1 TAATGATTTGATAGTAATGATTTAA
* *
2777 TAATGATTAG-TAATAATGAATTATTAATA
1 TAATGATTTGATAGTAATG-A-T-TT-A-A
* *
2806 TTTAATGATTTGATATTAATGATTTAG
1 --TAATGATTTGATAGTAATGATTTAA
2833 TAATGATTTGATAGTAATGATT
1 TAATGATTTGATAGTAATGATT
2855 ATTATAAATA
Statistics
Matches: 147, Mismatches: 22, Indels: 50
0.67 0.10 0.23
Matches are distributed among these distances:
19 3 0.02
20 1 0.01
21 14 0.10
22 13 0.09
23 9 0.06
24 26 0.18
25 54 0.37
26 2 0.01
27 3 0.02
28 2 0.01
29 2 0.01
30 1 0.01
31 10 0.07
32 7 0.05
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (25 bp):
TAATGATTTGATAGTAATGATTTAA
Found at i:2667 original size:119 final size:118
Alignment explanation
Indices: 2528--2865 Score: 494
Period size: 116 Copynumber: 2.9 Consensus size: 118
2518 TATTAATTTT
*
2528 TAATGATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTA
1 TAATGATTT-A-A-TAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTA
2593 ATGATTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAG
63 ATGATTAGTAATGATT-GTAATAATGAAATTATTATTAATATTTAATGATTTGATAG
* *
2650 TAATGATTTAATAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTAATAGTAATG
1 TAATGATTTAATAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATG
2715 ATTAGTAATGA-T-TAATAATGAAATTATTATTAATATTTAATGATTTGATAG
66 ATTAGTAATGATTGTAATAATGAAATTATTATTAATATTTAATGATTTGATAG
* *
2766 TAATGATTTAGTAATGATTAGTAATAATG--A--ATTATTAATATTTAATGATTTGATATTAATG
1 TAATGATTTAATAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATG
* *
2827 ATTTAGTAATGATTTGATAGTAATG--ATTATTATAAATAT
66 A-TTAGTAATGA-TTG-TAATAATGAAATTATTATTAATAT
2866 GTCGAATTGT
Statistics
Matches: 202, Mismatches: 9, Indels: 17
0.89 0.04 0.07
Matches are distributed among these distances:
112 29 0.14
113 10 0.05
114 1 0.00
115 14 0.07
116 67 0.33
117 7 0.03
118 1 0.00
119 62 0.31
120 1 0.00
121 1 0.00
122 9 0.04
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45
Consensus pattern (118 bp):
TAATGATTTAATAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATG
ATTAGTAATGATTGTAATAATGAAATTATTATTAATATTTAATGATTTGATAG
Found at i:2706 original size:46 final size:50
Alignment explanation
Indices: 2650--2836 Score: 193
Period size: 56 Copynumber: 3.6 Consensus size: 50
2640 GATTTGATAG
2650 TAATGATTT-A-A-TAATGA-TTAGTAATAATGAAATTGTTATTAATATT
1 TAATGATTTGATAGTAATGATTTAGTAATAATGAAATTGTTATTAATATT
* *
2696 TAATGATTTAATAGTAATGATTAGTAATGATTAATAATGAAATTATTATTAATATT
1 TAATGATTTGATAGTAATGATT--T-A-G--TAATAATGAAATTGTTATTAATATT
* *
2752 TAATGATTTGATAGTAATGATTTAGTAATGATTAGTAATAATGAATTATTAATATT
1 TAATGATTTGATAGTAATGATTTAGTAAT-AAT-G-AA-ATTG--TTATTAATATT
*
2808 TAATGATTTGATATTAATGATTTAGTAAT
1 TAATGATTTGATAGTAATGATTTAGTAAT
2837 GATTTGATAG
Statistics
Matches: 119, Mismatches: 6, Indels: 22
0.81 0.04 0.15
Matches are distributed among these distances:
46 9 0.08
47 1 0.01
48 1 0.01
49 6 0.05
50 5 0.04
51 2 0.02
52 3 0.03
53 4 0.03
54 4 0.03
56 84 0.71
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.45
Consensus pattern (50 bp):
TAATGATTTGATAGTAATGATTTAGTAATAATGAAATTGTTATTAATATT
Found at i:2715 original size:14 final size:14
Alignment explanation
Indices: 2696--2854 Score: 63
Period size: 14 Copynumber: 11.6 Consensus size: 14
2686 TATTAATATT
2696 TAATGATTTAATAG
1 TAATGATTTAATAG
2710 TAATGA--T--TAG
1 TAATGATTTAATAG
2720 TAATGA-TTAATAATG
1 TAATGATTTAAT-A-G
* * *
2735 AAATTATTATTAATATT
1 TAATGA-T-TTAATA-G
*
2752 TAATGATTTGATAG
1 TAATGATTTAATAG
2766 TAATGA-TT--TAG
1 TAATGATTTAATAG
* *
2777 TAATGA-TTAGTAA
1 TAATGATTTAATAG
*
2790 TAATGAATTATTAATATT
1 TAATG-A-T-TTAATA-G
* *
2808 TAATGATTTGATAT
1 TAATGATTTAATAG
2822 TAATGA-TT--TAG
1 TAATGATTTAATAG
*
2833 TAATGATTTGATAG
1 TAATGATTTAATAG
2847 TAATGATT
1 TAATGATT
2855 ATTATAAATA
Statistics
Matches: 115, Mismatches: 12, Indels: 36
0.71 0.07 0.22
Matches are distributed among these distances:
10 9 0.08
11 20 0.17
12 3 0.03
13 12 0.10
14 32 0.28
15 15 0.13
16 2 0.02
17 12 0.10
18 10 0.09
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (14 bp):
TAATGATTTAATAG
Found at i:4967 original size:15 final size:16
Alignment explanation
Indices: 4947--4980 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
4937 CAAAAAAATT
4947 TAATATAAT-AACTTA
1 TAATATAATAAACTTA
4962 TAATATAATAAACTTA
1 TAATATAATAAACTTA
4978 TAA
1 TAA
4981 AGTAACAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (16 bp):
TAATATAATAAACTTA
Found at i:5067 original size:30 final size:30
Alignment explanation
Indices: 5033--5132 Score: 132
Period size: 30 Copynumber: 3.4 Consensus size: 30
5023 TTTCTTTAAA
*
5033 CAACTAATAAACTATTCTTTAATATATCTT
1 CAACTAATAAACTATTCTTTAATATAACTT
5063 CAACTAATAAACTATTCTTTAATATAACTT
1 CAACTAATAAACTATTCTTTAATATAACTT
* * *
5093 AAACTAATAAAATATTTTTTAATTATAA-TT
1 CAACTAATAAACTATTCTTTAA-TATAACTT
*
5123 C-ACTACTAAA
1 CAACTAATAAA
5133 AAAACTAATT
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
29 8 0.13
30 50 0.79
31 5 0.08
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (30 bp):
CAACTAATAAACTATTCTTTAATATAACTT
Found at i:5540 original size:27 final size:27
Alignment explanation
Indices: 5502--5555 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
5492 AGGGTCGGCT
5502 GCCATGCACCAATAATTGAAGAATCAC
1 GCCATGCACCAATAATTGAAGAATCAC
5529 GCCATGCACCAATAATTGAAGAATCAC
1 GCCATGCACCAATAATTGAAGAATCAC
5556 TAGCCGTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.41, C:0.26, G:0.15, T:0.19
Consensus pattern (27 bp):
GCCATGCACCAATAATTGAAGAATCAC
Found at i:5751 original size:28 final size:28
Alignment explanation
Indices: 5715--5810 Score: 75
Period size: 29 Copynumber: 3.4 Consensus size: 28
5705 GTCGCGAGCA
* * * *
5715 GGCGAGCATGCAGCAGGGGATGTCGCCG
1 GGCGTGCATGCAACAGAGGAGGTCGCCG
**
5743 GGCGTGCATGGCAACCTAGGAGGTCGCCG
1 GGCGTGCAT-GCAACAGAGGAGGTCGCCG
* ** *
5772 GGCGTGCATGGCGACCTAGGAGGTCGCTG
1 GGCGTGCAT-GCAACAGAGGAGGTCGCCG
*
5801 GGAGTGCATG
1 GGCGTGCATG
5811 GCGACCTATG
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
28 9 0.16
29 49 0.84
ACGTcount: A:0.17, C:0.24, G:0.45, T:0.15
Consensus pattern (28 bp):
GGCGTGCATGCAACAGAGGAGGTCGCCG
Found at i:5773 original size:29 final size:29
Alignment explanation
Indices: 5736--5818 Score: 139
Period size: 29 Copynumber: 2.9 Consensus size: 29
5726 AGCAGGGGAT
*
5736 GTCGCCGGGCGTGCATGGCAACCTAGGAG
1 GTCGCCGGGCGTGCATGGCGACCTAGGAG
5765 GTCGCCGGGCGTGCATGGCGACCTAGGAG
1 GTCGCCGGGCGTGCATGGCGACCTAGGAG
* *
5794 GTCGCTGGGAGTGCATGGCGACCTA
1 GTCGCCGGGCGTGCATGGCGACCTA
5819 TGGTTGGGTT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.16, C:0.27, G:0.42, T:0.16
Consensus pattern (29 bp):
GTCGCCGGGCGTGCATGGCGACCTAGGAG
Found at i:9974 original size:83 final size:83
Alignment explanation
Indices: 9722--9988 Score: 318
Period size: 85 Copynumber: 3.2 Consensus size: 83
9712 TACCATGCGG
* * * * * * *** *
9722 TTGATATGTCATCGAGCTGAATGGAATCAAACTCGATAGTTTTGTTAACAGATAGATTTTCTCGA
1 TTGATATGTCCTTGAGCTGAATGTAATCGAACTCGA-AGGTTTGTTGACAGATAGCCCTTCTCGC
* *
9787 CTTAAGTTATGCTGTAAAT
65 CTTAAGCTATGATGTAAAT
* * * *
9806 TTGATATGCCCTTAAGATGAATGTAATCGAACTCGAAGGTTTTGGTTGACAAATAGCCCTTCTCG
1 TTGATATGTCCTTGAGCTGAATGTAATCGAACTCGAAGG-TTT-GTTGACAGATAGCCCTTCTCG
* *
9871 CCTTGAGCTATGTTGTAAAT
64 CCTTAAGCTATGATGTAAAT
*
9891 TTGATATGTCCTTGAGCTGAATGTAATTGAACTCGAAGGTTTGTTGACAGATAGCCCTTCTCGCC
1 TTGATATGTCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTGTTGACAGATAGCCCTTCTCGCC
*
9956 TTTAGCTATGATGTAAAT
66 TTAAGCTATGATGTAAAT
*
9974 TTGATATGTCTTTGA
1 TTGATATGTCCTTGA
9989 ACTCGAAGGT
Statistics
Matches: 156, Mismatches: 25, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
83 54 0.35
84 35 0.22
85 67 0.43
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.37
Consensus pattern (83 bp):
TTGATATGTCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTGTTGACAGATAGCCCTTCTCGCC
TTAAGCTATGATGTAAAT
Found at i:10640 original size:83 final size:83
Alignment explanation
Indices: 10379--10646 Score: 338
Period size: 85 Copynumber: 3.2 Consensus size: 83
10369 TACCATGCGG
* * * * ***
10379 TTGATATGTCATCGAGCTGAATGGAATCAAACTCGATAGTTTTTGTTGACAGATAGATTTTCTCG
1 TTGATATGTCATTGAGCTGAATGTAATCGAACTCGA-AG-GTTTGTTGACAGATAGCCCTTCTCG
* *
10444 ACTTAAGCTATGCTGTAAAT
64 CCTTGAGCTATGCTGTAAAT
* * * * *
10464 TTGATATGCCCTTAAGATGAATGTAATCGAACTCGAAGGTTTTGGTTGACAAATAGCCCTTCTCG
1 TTGATATGTCATTGAGCTGAATGTAATCGAACTCGAAGG-TTT-GTTGACAGATAGCCCTTCTCG
10529 CCTTGAGCTATGCTGTAAAT
64 CCTTGAGCTATGCTGTAAAT
* *
10549 TTGATATGTCATTGAGCTGAATGTAATTGAACTCGAAGGTTTGTTGACAGATAGCCCTTCTTGCC
1 TTGATATGTCATTGAGCTGAATGTAATCGAACTCGAAGGTTTGTTGACAGATAGCCCTTCTCGCC
*
10614 TTGAGCTATGATGTAAAT
66 TTGAGCTATGCTGTAAAT
*
10632 TTGATATGTCCTTGA
1 TTGATATGTCATTGA
10647 ACTCGAAGGT
Statistics
Matches: 158, Mismatches: 23, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
83 52 0.33
84 8 0.05
85 98 0.62
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36
Consensus pattern (83 bp):
TTGATATGTCATTGAGCTGAATGTAATCGAACTCGAAGGTTTGTTGACAGATAGCCCTTCTCGCC
TTGAGCTATGCTGTAAAT
Found at i:11654 original size:32 final size:32
Alignment explanation
Indices: 11613--11692 Score: 115
Period size: 32 Copynumber: 2.5 Consensus size: 32
11603 TAGGATGTAA
* * * *
11613 AATCCCCAAATATTCCCCAATATTTGATGTTG
1 AATCTCCAAAGATGCCCCAACATTTGATGTTG
11645 AATCTCCAAAGATGCCCCAACATTTGATGTTG
1 AATCTCCAAAGATGCCCCAACATTTGATGTTG
*
11677 AATCTTCAAAGATGCC
1 AATCTCCAAAGATGCC
11693 ACTATTGTTC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.30
Consensus pattern (32 bp):
AATCTCCAAAGATGCCCCAACATTTGATGTTG
Found at i:13653 original size:16 final size:17
Alignment explanation
Indices: 13632--13666 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
13622 CGGTTTCGAC
13632 CCGACCCGTTGA-CCGA
1 CCGACCCGTTGACCCGA
13648 CCGACCCGTTGACCCGA
1 CCGACCCGTTGACCCGA
13665 CC
1 CC
13667 TGTTGACTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.17, C:0.49, G:0.23, T:0.11
Consensus pattern (17 bp):
CCGACCCGTTGACCCGA
Found at i:13664 original size:13 final size:13
Alignment explanation
Indices: 13629--13673 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 13
13619 GATCGGTTTC
13629 GACCCGACCCGTT
1 GACCCGACCCGTT
13642 GACCGACCGACCCGTT
1 GA-C--CCGACCCGTT
*
13658 GACCCGACCTGTT
1 GACCCGACCCGTT
13671 GAC
1 GAC
13674 TGTTGATAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
13 14 0.50
14 1 0.04
15 1 0.04
16 12 0.43
ACGTcount: A:0.18, C:0.42, G:0.24, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:13735 original size:30 final size:30
Alignment explanation
Indices: 13689--13811 Score: 148
Period size: 30 Copynumber: 4.2 Consensus size: 30
13679 ATAGGGTGAC
13689 ATTTTGGGAA-TTAATTC-AAAATGGGTGCT
1 ATTTTGGGAATTTAATTCGAAAAT-GGTGCT
* *
13718 ATTTTGGGATTTTAATTCAAAAAAT-GTGCT
1 ATTTTGGGAATTTAATTC-GAAAATGGTGCT
* *
13748 ATATTGGGAATTTAATTCGAAAAAT-GTGTT
1 ATTTTGGGAATTTAATTCG-AAAATGGTGCT
13778 ATTTTGGGAATTTAATTCGAAAA-GGTGCT
1 ATTTTGGGAATTTAATTCGAAAATGGTGCT
13807 ATTTT
1 ATTTT
13812 AGTAATTATT
Statistics
Matches: 82, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
29 22 0.27
30 55 0.67
32 5 0.06
ACGTcount: A:0.33, C:0.06, G:0.20, T:0.41
Consensus pattern (30 bp):
ATTTTGGGAATTTAATTCGAAAATGGTGCT
Found at i:13887 original size:10 final size:10
Alignment explanation
Indices: 13864--13903 Score: 62
Period size: 10 Copynumber: 3.8 Consensus size: 10
13854 ATTGACCTCA
13864 TTTGACCAGAAC
1 TTTGACC-G-AC
13876 TTTGACCGAC
1 TTTGACCGAC
13886 TTTGACCGAC
1 TTTGACCGAC
13896 TTTGACCG
1 TTTGACCG
13904 GCCATTAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 20 0.71
11 1 0.04
12 7 0.25
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.30
Consensus pattern (10 bp):
TTTGACCGAC
Found at i:20944 original size:29 final size:29
Alignment explanation
Indices: 20789--20937 Score: 162
Period size: 29 Copynumber: 5.2 Consensus size: 29
20779 ACCGGGTGAC
* * *
20789 ATTTTGGGGA-TTAATTCGAAATGATTGCT
1 ATTTTGGGAATTTAATTCGAAAAG-GTGCT
* * *
20818 ATTTTAGGAA-TTAATTCAAAATAGGTGTT
1 ATTTTGGGAATTTAATTCGAAA-AGGTGCT
20847 ATTTTGGGAATTTAATTC-AAAA-GTGCT
1 ATTTTGGGAATTTAATTCGAAAAGGTGCT
* *
20874 ATATTGGGAATTTAATTCGAAAAATGTGCT
1 ATTTTGGGAATTTAATTCG-AAAAGGTGCT
*
20904 ATTTTGGGAATTTAATTCGAAAAGGTGTT
1 ATTTTGGGAATTTAATTCGAAAAGGTGCT
20933 ATTTT
1 ATTTT
20938 AGTAATTATT
Statistics
Matches: 103, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
27 21 0.20
28 1 0.01
29 50 0.49
30 31 0.30
ACGTcount: A:0.33, C:0.05, G:0.20, T:0.42
Consensus pattern (29 bp):
ATTTTGGGAATTTAATTCGAAAAGGTGCT
Found at i:20954 original size:57 final size:57
Alignment explanation
Indices: 20789--20965 Score: 171
Period size: 57 Copynumber: 3.1 Consensus size: 57
20779 ACCGGGTGAC
* * * * *
20789 ATTTTGGGGA-TTAATTCGAAATGATTGCTATTTTAGGAATTAATTCAAAATAGGTGTT
1 ATTTTGGGAATTTAATTCGAAAAG-GTGCTATTTTAGGAATTATTTCAAAA-AGGTGCT
* * * *
20847 ATTTTGGGAATTTAATTC-AAAA-GTGCTATATTGGGAATTTAATTCGAAAAATGTGCT
1 ATTTTGGGAATTTAATTCGAAAAGGTGCTATTTTAGGAA-TTATTTC-AAAAAGGTGCT
* * * *
20904 ATTTTGGGAATTTAATTCGAAAAGGTGTTATTTTAGTAATTATTTTAAAAAGGATGCC
1 ATTTTGGGAATTTAATTCGAAAAGGTGCTATTTTAGGAATTATTTCAAAAAGG-TGCT
20962 ATTT
1 ATTT
20966 CTGTAAAATA
Statistics
Matches: 98, Mismatches: 15, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
56 12 0.12
57 36 0.37
58 32 0.33
59 18 0.18
ACGTcount: A:0.34, C:0.06, G:0.19, T:0.41
Consensus pattern (57 bp):
ATTTTGGGAATTTAATTCGAAAAGGTGCTATTTTAGGAATTATTTCAAAAAGGTGCT
Found at i:21724 original size:15 final size:15
Alignment explanation
Indices: 21704--21736 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
21694 TGATACGTGA
21704 TTCCTGA-ATATTGAT
1 TTCCTGATAT-TTGAT
21719 TTCCTGATATTTGAT
1 TTCCTGATATTTGAT
21734 TTC
1 TTC
21737 TGTATTTCGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 15 0.88
16 2 0.12
ACGTcount: A:0.21, C:0.15, G:0.12, T:0.52
Consensus pattern (15 bp):
TTCCTGATATTTGAT
Found at i:22461 original size:16 final size:19
Alignment explanation
Indices: 22418--22455 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
22408 CGTTTCAAAG
22418 ATGGTATCGATACCGTCCTT
1 ATGGTATCGATACCG-CCTT
22438 ATGGTATCGATACC-CCTT
1 ATGGTATCGATACCGCCTT
22456 GGTATCAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.22
20 14 0.78
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.34
Consensus pattern (19 bp):
ATGGTATCGATACCGCCTT
Found at i:24333 original size:17 final size:19
Alignment explanation
Indices: 24308--24345 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
24298 TTATTTTCTC
24308 TTTGATTCTTT-TTTTATT
1 TTTGATTCTTTCTTTTATT
24326 TTTG-TTCTTTGCTTTTATT
1 TTTGATTCTTT-CTTTTATT
24345 T
1 T
24346 ATGCTTTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.33
18 4 0.22
19 8 0.44
ACGTcount: A:0.08, C:0.08, G:0.08, T:0.76
Consensus pattern (19 bp):
TTTGATTCTTTCTTTTATT
Found at i:25204 original size:16 final size:18
Alignment explanation
Indices: 25172--25205 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
25162 CAGTCGTTTA
25172 AAAGATTAAACAAACATG
1 AAAGATTAAACAAACATG
25190 AAAGA-TAAA-AAACATG
1 AAAGATTAAACAAACATG
25206 TTCAAACAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.09, G:0.12, T:0.15
Consensus pattern (18 bp):
AAAGATTAAACAAACATG
Found at i:26357 original size:15 final size:15
Alignment explanation
Indices: 26333--26362 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
26323 TGTAAATGAT
*
26333 GAAAATAAAATGAAA
1 GAAAACAAAATGAAA
26348 GAAAACAAAATGAAA
1 GAAAACAAAATGAAA
26363 AGAGTTAGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.73, C:0.03, G:0.13, T:0.10
Consensus pattern (15 bp):
GAAAACAAAATGAAA
Found at i:28386 original size:17 final size:17
Alignment explanation
Indices: 28364--28409 Score: 83
Period size: 17 Copynumber: 2.7 Consensus size: 17
28354 ATTAGGTTAT
28364 GATAGTGGGTAGTAGTG
1 GATAGTGGGTAGTAGTG
*
28381 GATAGTGGGTAGTGGTG
1 GATAGTGGGTAGTAGTG
28398 GATAGTGGGTAG
1 GATAGTGGGTAG
28410 GTTAGGTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.22, C:0.00, G:0.50, T:0.28
Consensus pattern (17 bp):
GATAGTGGGTAGTAGTG
Found at i:28429 original size:3 final size:3
Alignment explanation
Indices: 28416--28452 Score: 65
Period size: 3 Copynumber: 12.0 Consensus size: 3
28406 GTAGGTTAGG
28416 TAA TAA TTAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
28453 CAAAAAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:32178 original size:2 final size:2
Alignment explanation
Indices: 32171--32202 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
32161 TATTAATCGA
32171 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
32203 GTCGTTATAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40211 original size:13 final size:14
Alignment explanation
Indices: 40183--40215 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
40173 CAGAGTGTGG
*
40183 CGGCGGACGGCTGA
1 CGGCGGACGGCAGA
40197 CGGCGG-CGGCAGA
1 CGGCGGACGGCAGA
40210 CGGCGG
1 CGGCGG
40216 GCGGTGGCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.12, C:0.30, G:0.55, T:0.03
Consensus pattern (14 bp):
CGGCGGACGGCAGA
Found at i:63460 original size:59 final size:58
Alignment explanation
Indices: 63347--63487 Score: 194
Period size: 59 Copynumber: 2.4 Consensus size: 58
63337 TAATTCAGTT
* * * *
63347 CATAATTTGAAATTAGTTAATGAATTTGGCTAAGTTTCTTAATTACTTTAATTTACTC
1 CATAATTTGAAATTAGTTAATAAAGTTGGCTAAATTTCTTAATTACTTTAATTTAATC
* * *
63405 CATAATTTAAAATTAATTAGTAAAGTTGGCCTAAATTTCTTAATTGA-TTTAATTTAATC
1 CATAATTTGAAATTAGTTAATAAAGTTGG-CTAAATTTCTTAATT-ACTTTAATTTAATC
63464 CATAATTTGAAATTAGTTAATAAA
1 CATAATTTGAAATTAGTTAATAAA
63488 TGTAACCTTA
Statistics
Matches: 71, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
58 24 0.34
59 46 0.65
60 1 0.01
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (58 bp):
CATAATTTGAAATTAGTTAATAAAGTTGGCTAAATTTCTTAATTACTTTAATTTAATC
Found at i:68310 original size:18 final size:19
Alignment explanation
Indices: 68287--68323 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
68277 CCAGTAATCA
68287 TATTCT-CTGATAATCTTT
1 TATTCTACTGATAATCTTT
68305 TATTCTCACTGATAATCTT
1 TATTCT-ACTGATAATCTT
68324 ATCTTCCGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.24, C:0.19, G:0.05, T:0.51
Consensus pattern (19 bp):
TATTCTACTGATAATCTTT
Found at i:71714 original size:31 final size:31
Alignment explanation
Indices: 71637--71714 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
71627 TTTTAAACAT
* *
71637 AATACTAATTTAATC-TTAAACTTTAGATAA
1 AATATTAATTTAACCTTTAAACTTTAGATAA
* * * *
71667 AATATCATTTTGACCTTTAAAGTTTAGATAA
1 AATATTAATTTAACCTTTAAACTTTAGATAA
71698 AATATTAATTTAACCTT
1 AATATTAATTTAACCTT
71715 CAATAATGTT
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
30 10 0.26
31 28 0.74
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.42
Consensus pattern (31 bp):
AATATTAATTTAACCTTTAAACTTTAGATAA
Found at i:73066 original size:10 final size:10
Alignment explanation
Indices: 73051--73107 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
73041 ACCTTCCAGG
73051 CATCCGAGGC
1 CATCCGAGGC
*
73061 CATCCGAAAG-
1 CATCCG-AGGC
*
73071 CATCCAAGGC
1 CATCCGAGGC
73081 CATCCGAGAG-
1 CATCCGAG-GC
73091 CATCCGAGGC
1 CATCCGAGGC
73101 CATCCGA
1 CATCCGA
73108 ACGAGCTATG
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
9 3 0.08
10 33 0.85
11 3 0.08
ACGTcount: A:0.28, C:0.37, G:0.25, T:0.11
Consensus pattern (10 bp):
CATCCGAGGC
Found at i:73073 original size:20 final size:20
Alignment explanation
Indices: 73050--73108 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
73040 GACCTTCCAG
73050 GCATCCGAGGCCATCCGAAA
1 GCATCCGAGGCCATCCGAAA
* *
73070 GCATCCAAGGCCATCCGAGA
1 GCATCCGAGGCCATCCGAAA
73090 GCATCCGAGGCCATCCGAA
1 GCATCCGAGGCCATCCGAA
73109 CGAGCTATGC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.29, C:0.36, G:0.25, T:0.10
Consensus pattern (20 bp):
GCATCCGAGGCCATCCGAAA
Found at i:73132 original size:33 final size:33
Alignment explanation
Indices: 73085--73178 Score: 116
Period size: 33 Copynumber: 2.8 Consensus size: 33
73075 CAAGGCCATC
* *
73085 CGAGAGCATCCGAGGCCATCCGAACGAGCTATG
1 CGAGGGCATCCGAGGCCAACCGAACGAGCTATG
* * *
73118 CGAGGGCATTCGAGGGCAACCGAGCGAGCTATG
1 CGAGGGCATCCGAGGCCAACCGAACGAGCTATG
* * *
73151 CGAGGGAATCCGAGGGCAACCGAGCGAG
1 CGAGGGCATCCGAGGCCAACCGAACGAG
73179 GGTAGGTCGG
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.27, C:0.27, G:0.37, T:0.10
Consensus pattern (33 bp):
CGAGGGCATCCGAGGCCAACCGAACGAGCTATG
Found at i:73259 original size:10 final size:11
Alignment explanation
Indices: 73231--73287 Score: 50
Period size: 10 Copynumber: 5.4 Consensus size: 11
73221 CATAGCTCGT
73231 TCGGATGGCTC
1 TCGGATGGCTC
73242 GGTCGGATGGCT-
1 --TCGGATGGCTC
73254 TCGGAT-GCTC
1 TCGGATGGCTC
*
73264 TCGGAT-GCTT
1 TCGGATGGCTC
*
73274 TTGGATGGC-C
1 TCGGATGGCTC
73284 TCGG
1 TCGG
73288 TCGGATAAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
9 3 0.08
10 23 0.61
11 2 0.05
13 10 0.26
ACGTcount: A:0.09, C:0.23, G:0.39, T:0.30
Consensus pattern (11 bp):
TCGGATGGCTC
Done.