Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000756.1 Hibiscus syriacus cultivar Beakdansim tig00001459_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: 47378
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:2625 original size:30 final size:30
Alignment explanation
Indices: 2591--2680 Score: 83
Period size: 30 Copynumber: 3.0 Consensus size: 30
2581 TCTAACCCAT
* *
2591 TGACC-TTGACCCGAACCATTGACTTTGACA
1 TGACCGTTGACACG-ACCATTAACTTTGACA
* * *
2621 TGACCGCTGACATGCCCATTAACTTTGACA
1 TGACCGTTGACACGACCATTAACTTTGACA
* * *
2651 TGACCGTTGACATGGCCATTGACTGTTGAC
1 TGACCGTTGACACGACCATTAACT-TTGAC
2681 CTACCCGTTA
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
30 40 0.80
31 10 0.20
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (30 bp):
TGACCGTTGACACGACCATTAACTTTGACA
Found at i:3586 original size:27 final size:27
Alignment explanation
Indices: 3556--3618 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
3546 TAAATTATTG
*
3556 AAATACCCTTGAACTGTA-AAATAACCA
1 AAATACCCCTGAACTG-AGAAATAACCA
* * *
3583 AAATACCCCTGAAGTGAGAAATGACCT
1 AAATACCCCTGAACTGAGAAATAACCA
3610 AAATACCCC
1 AAATACCCC
3619 AAGCTCTGGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 1 0.03
27 30 0.97
ACGTcount: A:0.44, C:0.25, G:0.11, T:0.19
Consensus pattern (27 bp):
AAATACCCCTGAACTGAGAAATAACCA
Found at i:4756 original size:32 final size:32
Alignment explanation
Indices: 4684--4789 Score: 108
Period size: 32 Copynumber: 3.3 Consensus size: 32
4674 CTTGGGTGGC
* *
4684 TCTAAGGCCCCAAGGCA-TTTCCTTAGGTAGGC
1 TCTAAGGCCCCAAGGTACTTT-CTTAGGTAGGT
* *
4716 TCTAAGGCCCCAAGGTACTTTCTTGGGTATGT
1 TCTAAGGCCCCAAGGTACTTTCTTAGGTAGGT
* * *
4748 TCTTAGGCCCTAAGATACTATT-TTAGGTAGGT
1 TCTAAGGCCCCAAGGTACT-TTCTTAGGTAGGT
*
4780 TCTCAGGCCC
1 TCTAAGGCCC
4790 TAAAATATTC
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
32 57 0.92
33 5 0.08
ACGTcount: A:0.21, C:0.25, G:0.24, T:0.31
Consensus pattern (32 bp):
TCTAAGGCCCCAAGGTACTTTCTTAGGTAGGT
Found at i:9805 original size:21 final size:21
Alignment explanation
Indices: 9762--9854 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
9752 TTTTCCCAAT
** *
9762 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTGGGAAAA
*
9782 TCGCAAAGCGAATTGGGAAAA
1 TCGCAATGCGAATTGGGAAAA
** *
9803 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTGGGAAAA
*
9823 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTGGGAAAA
9844 TCGCAATGCGA
1 TCGCAATGCGA
9855 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.41, C:0.17, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTGGGAAAA
Found at i:9869 original size:41 final size:41
Alignment explanation
Indices: 9762--9854 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
9752 TTTTCCCAAT
9762 TCGCAATGCGAATAAGTAAATCGCAAAGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAAAGCGAATTGGGAAAA
*
9803 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAAAGCGAATTGGGAAAA
9844 TCGCAATGCGA
1 TCGCAATGCGA
9855 TACTGACTAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.41, C:0.17, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAAAGCGAATTGGGAAAA
Found at i:9889 original size:21 final size:20
Alignment explanation
Indices: 9840--9890 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
9830 GCGAATTGGG
* *
9840 AAAATCGCAATGCGATACTG
1 AAAATCGCAATGCGATAATA
**
9860 ACTATCGCAATGCGATAATAA
1 AAAATCGCAATGCGATAAT-A
9881 AAAATCGCAA
1 AAAATCGCAA
9891 CGAGACTTAC
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.45, C:0.20, G:0.16, T:0.20
Consensus pattern (20 bp):
AAAATCGCAATGCGATAATA
Found at i:9908 original size:18 final size:18
Alignment explanation
Indices: 9885--9930 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 18
9875 TAATAAAAAA
*
9885 TCGCAACGAGACTTACTT
1 TCGCAACGAGACTGACTT
*
9903 TCGCAACACGATACTGACTT
1 TCGC-A-ACGAGACTGACTT
9923 TCGCAACG
1 TCGCAACG
9931 CAATTTACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 7 0.29
19 2 0.08
20 15 0.62
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.24
Consensus pattern (18 bp):
TCGCAACGAGACTGACTT
Found at i:10511 original size:18 final size:19
Alignment explanation
Indices: 10446--10501 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
10436 TTCGAGAATG
*
10446 AAAATCGCAACGTGGAAATA
1 AAAATCGCAACG-CGAAATA
**
10466 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
10485 AAAATCGCAACGCGAAA
1 AAAATCGCAACGCGAAA
10502 CCAAATCGCA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 21 0.68
20 10 0.32
ACGTcount: A:0.48, C:0.21, G:0.18, T:0.12
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:10553 original size:20 final size:19
Alignment explanation
Indices: 10507--10672 Score: 127
Period size: 20 Copynumber: 9.1 Consensus size: 19
10497 CGAAACCAAA
*
10507 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
10526 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
10545 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
* *
10565 TCGCGTTGCAATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
10581 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
10598 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
10612 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
10631 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
10651 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
10671 TC
1 TC
10673 AACCAAAAGA
Statistics
Matches: 117, Mismatches: 17, Indels: 26
0.73 0.11 0.16
Matches are distributed among these distances:
14 19 0.16
15 1 0.01
16 3 0.03
17 3 0.03
18 1 0.01
19 40 0.34
20 49 0.42
21 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:10588 original size:39 final size:39
Alignment explanation
Indices: 10512--10588 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 39
10502 CCAAATCGCA
* * **
10512 TTGCGATTTTCATTTCGCGTTGCGATTTTTATTTCGCGG
1 TTGCGATTTTCATTTCGCGTTGCAATTTCTAGGTCGCGG
10551 TTGCGATTTTCATTTCGCGTTGCAATTGTCT-GGTCGCG
1 TTGCGATTTTCATTTCGCGTTGCAATT-TCTAGGTCGCG
10589 ATAGTCATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 31 0.94
40 2 0.06
ACGTcount: A:0.10, C:0.19, G:0.25, T:0.45
Consensus pattern (39 bp):
TTGCGATTTTCATTTCGCGTTGCAATTTCTAGGTCGCGG
Found at i:10597 original size:33 final size:33
Alignment explanation
Indices: 10560--10647 Score: 122
Period size: 33 Copynumber: 2.6 Consensus size: 33
10550 GTTGCGATTT
* *
10560 TCATTTCGCGTTGCAATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCAATTCTCTCGTCGCGATAG
* *
10593 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCAATTCTCTCGTCGCGATAG
*
10626 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCAATTCTC
10648 ATTATCTCGT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 35 0.70
34 15 0.30
ACGTcount: A:0.12, C:0.25, G:0.24, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCAATTCTCTCGTCGCGATAG
Found at i:12730 original size:21 final size:21
Alignment explanation
Indices: 12706--12772 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
12696 TCATTCCTCG
12706 AGAGTCCCCTCCCACCATTCA
1 AGAGTCCCCTCCCACCATTCA
* * ** * * *
12727 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCATTCA
12748 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCATTCA
12769 AGAG
1 AGAG
12773 CCCGATTCAC
Statistics
Matches: 31, Mismatches: 14, Indels: 3
0.65 0.29 0.06
Matches are distributed among these distances:
20 1 0.03
21 29 0.94
22 1 0.03
ACGTcount: A:0.25, C:0.36, G:0.19, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCATTCA
Found at i:12730 original size:42 final size:42
Alignment explanation
Indices: 12650--12772 Score: 115
Period size: 42 Copynumber: 2.9 Consensus size: 42
12640 GCCCGACTCG
* * * * * * *
12650 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCATTCAAGAGGCC
12692 CCTATCATTCCTCGAGAGTCCCCTCCCACCATTCAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCATTCAAGAGGCC
* * * *
12734 ACTGTCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 CCTATCATTCCTCG-AGA-GTCCCCTCCCACCATTCAAGAG
12773 CCCGATTCAC
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
41 4 0.06
42 62 0.91
43 2 0.03
ACGTcount: A:0.24, C:0.37, G:0.17, T:0.23
Consensus pattern (42 bp):
CCTATCATTCCTCGAGAGTCCCCTCCCACCATTCAAGAGGCC
Found at i:15595 original size:19 final size:19
Alignment explanation
Indices: 15571--15636 Score: 89
Period size: 20 Copynumber: 3.5 Consensus size: 19
15561 GAAACTTAAA
15571 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
15590 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCG-AAATGACT
* *
15610 ATCGCAATGCGAAATGA-A
1 ATCGCAACGCGAAATGACT
15628 ATCGCAACG
1 ATCGCAACG
15637 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
18 8 0.20
19 16 0.39
20 17 0.41
ACGTcount: A:0.38, C:0.24, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:15643 original size:19 final size:18
Alignment explanation
Indices: 15569--15687 Score: 101
Period size: 14 Copynumber: 6.9 Consensus size: 18
15559 ACGAAACTTA
15569 AAATCGCAACGCGAAATG
1 AAATCGCAACGCGAAATG
*
15587 ACTATCGCAACGCGAAAATGG
1 A-AATCGCAACGCG-AAAT-G
** *
15608 CTATCGCAATGCGAAATG
1 AAATCGCAACGCGAAATG
*
15626 AAATCGCAA--CGACA--
1 AAATCGCAACGCGAAATG
15640 AAATCGCAACGCGAAATG
1 AAATCGCAACGCGAAATG
*
15658 AAATCGCAA--CGACA--
1 AAATCGCAACGCGAAATG
15672 AAATCGCAACGCGAAA
1 AAATCGCAACGCGAAA
15688 CATAAATCGC
Statistics
Matches: 83, Mismatches: 9, Indels: 20
0.74 0.08 0.18
Matches are distributed among these distances:
14 18 0.22
16 16 0.19
18 18 0.22
19 15 0.18
20 15 0.18
21 1 0.01
ACGTcount: A:0.44, C:0.24, G:0.20, T:0.12
Consensus pattern (18 bp):
AAATCGCAACGCGAAATG
Found at i:15654 original size:32 final size:32
Alignment explanation
Indices: 15610--15687 Score: 147
Period size: 32 Copynumber: 2.4 Consensus size: 32
15600 GAAAATGGCT
*
15610 ATCGCAATGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
15642 ATCGCAACGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
15674 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
15688 CATAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.10
Consensus pattern (32 bp):
ATCGCAACGCGAAATGAAATCGCAACGACAAA
Found at i:15735 original size:14 final size:14
Alignment explanation
Indices: 15716--15773 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
15706 TTTCATTTCG
15716 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
15730 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
15746 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
15762 CGTTGCGATTTT
1 CGTTGCGATTTT
15774 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:15780 original size:33 final size:33
Alignment explanation
Indices: 15699--15789 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
15689 ATAAATCGCA
*
15699 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
15732 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
15764 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
15790 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:15808 original size:20 final size:19
Alignment explanation
Indices: 15774--15828 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
15764 TTGCGATTTT
*
15774 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
15793 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
15813 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
15829 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:16326 original size:18 final size:18
Alignment explanation
Indices: 16300--16344 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
16290 GTCGATCAGA
*
16300 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
16318 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
16336 TGATGGCTC
1 TGATGGCTC
16345 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:17690 original size:20 final size:20
Alignment explanation
Indices: 17665--17702 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
17655 AATAGTTTCT
17665 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
17685 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
17703 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:17991 original size:22 final size:22
Alignment explanation
Indices: 17966--18009 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
17956 GATTTAGATA
17966 GACGGATTTCGCCGAAGATGGG
1 GACGGATTTCGCCGAAGATGGG
* *
17988 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGAAGATGGG
18010 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.16, G:0.43, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGAAGATGGG
Found at i:18222 original size:20 final size:20
Alignment explanation
Indices: 18197--18290 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
18187 GATTATGTAT
18197 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
18217 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
18237 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
18258 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
18278 TATCGCATTGCGA
1 TATCGCGTTGCGA
18291 TTTTTCCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:18291 original size:20 final size:20
Alignment explanation
Indices: 18177--18291 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
18167 CGCTTTGAAA
*
18177 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
18198 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
18218 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
18238 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
18259 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
18279 ATCGCATTGCGAT
1 ATCGCATTGCGAT
18292 TTTTCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:18310 original size:41 final size:41
Alignment explanation
Indices: 18217--18312 Score: 113
Period size: 41 Copynumber: 2.3 Consensus size: 41
18207 CGAAAGTCAG
* * * * *
18217 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTTCAA
* *
18258 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTTCCAA
1 TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTT-CAA
18300 T-TCGCGTTGCGAT
1 TATCGCGTTGCGAT
18313 TTACTTATTC
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
41 44 0.96
42 2 0.04
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.39
Consensus pattern (41 bp):
TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTTCAA
Found at i:19010 original size:30 final size:30
Alignment explanation
Indices: 18976--19035 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
18966 AAATGTCCAA
18976 AACTGTATTTGTTACACATAACTCATATTT
1 AACTGTATTTGTTACACATAACTCATATTT
19006 AACTGTATTTGTTACACATAACTCATATTT
1 AACTGTATTTGTTACACATAACTCATATTT
19036 CATATTTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.33, C:0.17, G:0.07, T:0.43
Consensus pattern (30 bp):
AACTGTATTTGTTACACATAACTCATATTT
Found at i:22792 original size:2 final size:2
Alignment explanation
Indices: 22780--22812 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
22770 GGTTTCGAAG
*
22780 TA TA TA AA 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 TA T
22813 TCACACACAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:28508 original size:14 final size:14
Alignment explanation
Indices: 28475--28508 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
28465 AAATGAATTA
*
28475 TATTTTATAAAAAT
1 TATTTTCTAAAAAT
28489 TA-TTTCTAAAAAT
1 TATTTTCTAAAAAT
28502 TATTTTC
1 TATTTTC
28509 CAGTATCGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (14 bp):
TATTTTCTAAAAAT
Found at i:30919 original size:68 final size:66
Alignment explanation
Indices: 30841--31031 Score: 228
Period size: 68 Copynumber: 2.8 Consensus size: 66
30831 ATAGGACAAT
*
30841 TATTATTTTAAATAATTAAAATTAAAAAGATATTTATTATCTATTTAACTTTGACTATTAAAA-G
1 TATTATTTTAAATAATTAAAATT-AAAAGATA-TTATTAT-TATTTAACTTTGAATATTAAAATG
30905 -ATTA
63 TA-TA
* *
30909 TATTATTTTAAATATTTTAAATTAAAAGATATTATTTATT-TTTAAACTTTGAATATTAAAATGT
1 TATTATTTTAAATAATTAAAATTAAAAGATATTA-TTATTATTT-AACTTTGAATATTAAAATGT
30973 ATA
64 ATA
* *
30976 TATATATTTTGAAT-ATCTAAAATTAAAAGATATTATTATATATTTAAATTTGAATA
1 TAT-TATTTTAAATAAT-TAAAATTAAAAGATATTATTAT-TATTTAACTTTGAATA
31032 AGCAAATCAC
Statistics
Matches: 108, Mismatches: 7, Indels: 16
0.82 0.05 0.12
Matches are distributed among these distances:
65 3 0.03
66 20 0.19
67 23 0.21
68 59 0.55
69 3 0.03
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.48
Consensus pattern (66 bp):
TATTATTTTAAATAATTAAAATTAAAAGATATTATTATTATTTAACTTTGAATATTAAAATGTAT
A
Found at i:30935 original size:32 final size:32
Alignment explanation
Indices: 30839--31014 Score: 126
Period size: 34 Copynumber: 5.2 Consensus size: 32
30829 TAATAGGACA
*
30839 ATTATTATTTTAAATAATTAAAATTAAAAAGAT
1 ATTATTATTTTAAATATTTAAAATT-AAAAGAT
* * **
30872 ATTTATTATCTATTTAACT-TTGACTATTAAAAGAT
1 A-TTATTA--T-TTTAAATATTTAAAATTAAAAGAT
*
30907 -TATATTATTTTAAATATTTTAAATTAAAAGAT
1 AT-TATTATTTTAAATATTTAAAATTAAAAGAT
* *
30939 ATTATTTATTTTTAAACT-TTGAATATTAAAATG-T
1 ATTA-TTA-TTTTAAA-TATTTAAAATTAAAA-GAT
* *
30973 ATATATATATTTTGAATATCTAAAATTAAAAGAT
1 AT-TAT-TATTTTAAATATTTAAAATTAAAAGAT
31007 ATTATTAT
1 ATTATTAT
31015 ATATTTAAAT
Statistics
Matches: 111, Mismatches: 17, Indels: 31
0.70 0.11 0.19
Matches are distributed among these distances:
31 6 0.05
32 18 0.16
33 11 0.10
34 51 0.46
35 13 0.12
36 6 0.05
37 6 0.05
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.48
Consensus pattern (32 bp):
ATTATTATTTTAAATATTTAAAATTAAAAGAT
Found at i:31078 original size:21 final size:21
Alignment explanation
Indices: 31052--31093 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
31042 TTTTGAGAAT
31052 CCCTATAGATAGAGAGCTAAC
1 CCCTATAGATAGAGAGCTAAC
31073 CCCTATAGATAGAGAGCTAAC
1 CCCTATAGATAGAGAGCTAAC
31094 ATTCTTGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (21 bp):
CCCTATAGATAGAGAGCTAAC
Found at i:32380 original size:43 final size:43
Alignment explanation
Indices: 32333--32426 Score: 170
Period size: 43 Copynumber: 2.2 Consensus size: 43
32323 AGCCTAGGGA
*
32333 AACTGTAAGGCTTACCCTTGCACACAACAAAGGGACTTGGGGG
1 AACTGTAAGGCTTACCCTTGCACACAACAAAGGGACCTGGGGG
*
32376 AACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGG
1 AACTGTAAGGCTTACCCTTGCACACAACAAAGGGACCTGGGGG
32419 AACTGTAA
1 AACTGTAA
32427 CGGTAATTAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.31, C:0.23, G:0.28, T:0.18
Consensus pattern (43 bp):
AACTGTAAGGCTTACCCTTGCACACAACAAAGGGACCTGGGGG
Found at i:35857 original size:28 final size:28
Alignment explanation
Indices: 35825--35893 Score: 113
Period size: 28 Copynumber: 2.5 Consensus size: 28
35815 ATGTAGCAAT
35825 TACATCGATTAATTGTTATGATTAACAG
1 TACATCGATTAATTGTTATGATTAACAG
*
35853 TACATCGATTAATTGTTATGATTAACGG
1 TACATCGATTAATTGTTATGATTAACAG
*
35881 TA-ATGGATTAATT
1 TACATCGATTAATT
35894 AGAACACCCC
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 10 0.26
28 29 0.74
ACGTcount: A:0.35, C:0.09, G:0.16, T:0.41
Consensus pattern (28 bp):
TACATCGATTAATTGTTATGATTAACAG
Found at i:42268 original size:25 final size:25
Alignment explanation
Indices: 42240--42290 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
42230 TTTGCTTATG
*
42240 GATTGATAACTACTTGAGCTTCTAT
1 GATTGATAACTACTTGAGATTCTAT
42265 GATTGATAACTACTTGAGATTCTAT
1 GATTGATAACTACTTGAGATTCTAT
42290 G
1 G
42291 GTTAATGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (25 bp):
GATTGATAACTACTTGAGATTCTAT
Done.