Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001705.1 Hibiscus syriacus cultivar Beakdansim tig00003420_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: 31129
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:471 original size:75 final size:76
Alignment explanation
Indices: 329--477 Score: 230
Period size: 75 Copynumber: 2.0 Consensus size: 76
319 ATACCCATAA
* * *
329 TATCATATACAATAAAGCTTGAGTTGTCCCTCTAAGCAATTGGTTAAATGCCCCGGCCTTATGGA
1 TATCATATACAATAAAGCTTAAGTTGTCCCTCTAAGCAATTGGTTAAACGCCCCGGCCTTATAGA
394 TAAGATTCATC
66 TAAGATTCATC
* *
405 TATC-TATACAATAAAGCTTAAGTTGTCCCTCTAAGGC-ATTGGTTAAACGCCCTGGCTTTATAG
1 TATCATATACAATAAAGCTTAAGTTGTCCCTCTAA-GCAATTGGTTAAACGCCCCGGCCTTATAG
468 ATAAGATTCA
65 ATAAGATTCA
478 ACTAATCTGA
Statistics
Matches: 67, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
75 61 0.91
76 6 0.09
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (76 bp):
TATCATATACAATAAAGCTTAAGTTGTCCCTCTAAGCAATTGGTTAAACGCCCCGGCCTTATAGA
TAAGATTCATC
Found at i:1647 original size:64 final size:64
Alignment explanation
Indices: 1424--1635 Score: 279
Period size: 63 Copynumber: 3.4 Consensus size: 64
1414 TTTTGTAGCT
* * *
1424 TTCAGAG-CTAATTTCAACTTCACAACAAAGG--ATTGGACTCAACAAACAACTTTCCAATTTCA
1 TTCAGAGTC-AATTTCAACTTCACAGCAAAGGATATTGGACTCAACAAAAAACTTTCCAGTTTCA
* ** * *
1486 TTTAGAGTCAATTTCAACTTCACAGTGAAGGATATTGGACTCAAC-AAATACTTTTCAGTTTCA
1 TTCAGAGTCAATTTCAACTTCACAGCAAAGGATATTGGACTCAACAAAAAACTTTCCAGTTTCA
* * *
1549 TTCAGGGTCAATTTTAACTTCACAGCAAAGGATATTGAACTCAACAAAAAACTTTCCAGTTTCA
1 TTCAGAGTCAATTTCAACTTCACAGCAAAGGATATTGGACTCAACAAAAAACTTTCCAGTTTCA
*
1613 TTCAGAGTCAATTTAAACTTCAC
1 TTCAGAGTCAATTTCAACTTCAC
1636 GACGAAGGAT
Statistics
Matches: 128, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
62 25 0.20
63 54 0.42
64 49 0.38
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.31
Consensus pattern (64 bp):
TTCAGAGTCAATTTCAACTTCACAGCAAAGGATATTGGACTCAACAAAAAACTTTCCAGTTTCA
Found at i:1658 original size:63 final size:63
Alignment explanation
Indices: 1424--1647 Score: 242
Period size: 64 Copynumber: 3.6 Consensus size: 63
1414 TTTTGTAGCT
* * * * *
1424 TTCAGAG-CTAATTTCAACTTCACAACAAAGG--ATTGGACTCAACAAACAACTTTCCAATTTCA
1 TTCAGAGTC-AATTTAAACTTCACAGCGAAGGATATTGG-CTCAACAAAAAACTTTCCAGTTTCA
* * * * *
1486 TTTAGAGTCAATTTCAACTTCACAGTGAAGGATATTGGACTCAAC-AAATACTTTTCAGTTTCA
1 TTCAGAGTCAATTTAAACTTCACAGCGAAGGATATTGG-CTCAACAAAAAACTTTCCAGTTTCA
* * * *
1549 TTCAGGGTCAATTTTAACTTCACAGCAAAGGATATTGAACTCAACAAAAAACTTTCCAGTTTCA
1 TTCAGAGTCAATTTAAACTTCACAGCGAAGGATATTG-GCTCAACAAAAAACTTTCCAGTTTCA
1613 TTCAGAGTCAATTTAAACTTCAC-GACGAAGGATAT
1 TTCAGAGTCAATTTAAACTTCACAG-CGAAGGATAT
1648 CGTGCCAACA
Statistics
Matches: 137, Mismatches: 19, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
62 25 0.18
63 54 0.39
64 58 0.42
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.30
Consensus pattern (63 bp):
TTCAGAGTCAATTTAAACTTCACAGCGAAGGATATTGGCTCAACAAAAAACTTTCCAGTTTCA
Found at i:1760 original size:109 final size:109
Alignment explanation
Indices: 1623--1922 Score: 437
Period size: 109 Copynumber: 2.8 Consensus size: 109
1613 TTCAGAGTCA
*
1623 ATTTAAACTTCACGACGAAGGATATCGTGCCAACAATACTTGGATTTCAACTTCACAACGAAGGA
1 ATTTCAACTTCACGACGAAGGATATCGTGCCAACAATACTTGGATTTCAACTTCACAACGAAGGA
* * * * *
1688 TATTCAATTCAAAGCTCAACTTCATAACGAATGGGTCATCCACG
66 TATCCAATTCAAAGCTCAACTTCACAACAAAAGAGTCATCCACG
* * *
1732 ATTTCAACTTCACGACGATGGATATCGTGCCAACAATACTTGGATTTCAACTTCACAATGAATGA
1 ATTTCAACTTCACGACGAAGGATATCGTGCCAACAATACTTGGATTTCAACTTCACAACGAAGGA
1797 TATCCAATTC-AAGCTCAACTTCACAACAAAAGAGTCATCCACG
66 TATCCAATTCAAAGCTCAACTTCACAACAAAAGAGTCATCCACG
* **
1840 ATTTCAACTTCACGACTAAGG--ATCGTGCCAACAAT-CTTTGGATTTCAACTTCATGACGAAGG
1 ATTTCAACTTCACGACGAAGGATATCGTGCCAACAATAC-TTGGATTTCAACTTCACAACGAAGG
* *
1902 ATATCCAATTTAATGCTCAAC
65 ATATCCAATTCAAAGCTCAAC
1923 GAATGAGCCA
Statistics
Matches: 172, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
105 1 0.01
106 45 0.26
107 8 0.05
108 48 0.28
109 70 0.41
ACGTcount: A:0.35, C:0.24, G:0.14, T:0.27
Consensus pattern (109 bp):
ATTTCAACTTCACGACGAAGGATATCGTGCCAACAATACTTGGATTTCAACTTCACAACGAAGGA
TATCCAATTCAAAGCTCAACTTCACAACAAAAGAGTCATCCACG
Found at i:2437 original size:84 final size:84
Alignment explanation
Indices: 2285--2527 Score: 319
Period size: 84 Copynumber: 2.9 Consensus size: 84
2275 CATCCCAGTG
* * * * * * *
2285 CAACATAACTCAAGGCGAGAATGGTTATATGTCATCAAAGGCCTTCGAGTTCGATTATATTCACT
1 CAACATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCACT
*
2350 CAAAGGCATATCCAATTTA
66 CAAAGGCACATCCAATTTA
* *
2369 CAACATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAA-ACCTTTGAGTTCGATTACACTCAGT
1 CAACATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCA-C
2433 TCAAAGGCACATCCAATTTA
65 TCAAAGGCACATCCAATTTA
* *
2453 CAACATAACTCAAGG-TGAGAAGGGTTATCTGTCAACAAAAGACCTTCGAGTTCGATTTCATTCA
1 CAACATAACTCAAGGCT-AGAAGGGTTATCTGTCAAC-AAAGACCTTCGAGTTCGATTACACTC-
*
2517 ACTCAAGGGCA
63 ACTCAAAGGCA
2528 TGTCAAATTT
Statistics
Matches: 139, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
83 20 0.14
84 88 0.63
85 3 0.02
86 27 0.19
87 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.26
Consensus pattern (84 bp):
CAACATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCACT
CAAAGGCACATCCAATTTA
Found at i:4550 original size:22 final size:21
Alignment explanation
Indices: 4512--4784 Score: 93
Period size: 21 Copynumber: 13.2 Consensus size: 21
4502 TTTCTCTTTC
*
4512 TTTAT-TATTATTATTATTAT
1 TTTATATATTTTTATTATTAT
4532 TTTATATATTTTTCATTATTAT
1 TTTATATATTTTT-ATTATTAT
4554 TTTATATA-TTTTA-TA-TA-
1 TTTATATATTTTTATTATTAT
* *
4571 TGTATATTTTTTTATTATT-T
1 TTTATATATTTTTATTATTAT
* *
4591 TTCTAT-T-TTTTTATTTTTGGTT
1 TT-TATATATTTTTATTATT--AT
* **
4613 TTTATTTATTACTATTATGGTAT
1 TTTATATATTTTTATTAT--TAT
* *
4636 TTTAT-T-TTTTTATTTTTTTAC
1 TTTATATATTTTTA--TTATTAT
*
4657 TTTATTATATTGTTTCA-CATTAT
1 TTTA-TATATT-TTT-ATTATTAT
* * * *
4680 TCTCT-TGTCTTTATTATTAT
1 TTTATATATTTTTATTATTAT
*
4700 TATTAT-TATTGTTA-TATATAT
1 T-TTATATATTTTTATTAT-TAT
*
4721 TTTAT-TATTATTATTGCA-TAT
1 TTTATATATTTTTATT--ATTAT
*
4742 TTTACATA-TTTTATT-TTAT
1 TTTATATATTTTTATTATTAT
4761 TTTAT-T-TTTTGT-TTATTAT
1 TTTATATATTTT-TATTATTAT
4780 TTTAT
1 TTTAT
4785 TTTATTCTAT
Statistics
Matches: 191, Mismatches: 30, Indels: 65
0.67 0.10 0.23
Matches are distributed among these distances:
17 6 0.03
18 13 0.07
19 32 0.17
20 32 0.17
21 53 0.28
22 25 0.13
23 23 0.12
24 2 0.01
25 4 0.02
26 1 0.01
ACGTcount: A:0.23, C:0.04, G:0.04, T:0.69
Consensus pattern (21 bp):
TTTATATATTTTTATTATTAT
Found at i:4698 original size:3 final size:3
Alignment explanation
Indices: 4690--4735 Score: 60
Period size: 3 Copynumber: 15.7 Consensus size: 3
4680 TCTCTTGTCT
*
4690 TTA TTA TTA TTA TTA TTA TTG TTA -TA TATA TT- TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
4734 TT
1 TT
4736 GCATATTTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
2 4 0.11
3 31 0.82
4 3 0.08
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:4758 original size:5 final size:5
Alignment explanation
Indices: 4748--4860 Score: 64
Period size: 5 Copynumber: 24.2 Consensus size: 5
4738 ATATTTTACA
* *
4748 TATTT TATTT TATTT TATTT T-TTGT T-TAT TATTT TATTT TATTC TATTT
1 TATTT TATTT TATTT TATTT TATT-T TATTT TATTT TATTT TATTT TATTT
* * * * * * *
4797 T-TTC T-TTT TATTT TCTCT T-CTT TATTG TA-TT TGTTT T-TTT TACTT
1 TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATTT
*
4842 T-CTT TATTT TA-TT TATTT T
1 TATTT TATTT TATTT TATTT T
4861 TGCTACTTTT
Statistics
Matches: 84, Mismatches: 16, Indels: 16
0.72 0.14 0.14
Matches are distributed among these distances:
4 26 0.31
5 58 0.69
ACGTcount: A:0.14, C:0.06, G:0.03, T:0.77
Consensus pattern (5 bp):
TATTT
Found at i:4766 original size:24 final size:24
Alignment explanation
Indices: 4721--4790 Score: 61
Period size: 24 Copynumber: 2.8 Consensus size: 24
4711 TTATATATAT
*
4721 TTTATTATTATTATTGCATATTTTACA
1 TTTATTATT-TTATT--TTATTTTACA
***
4748 TATT-TTATTTTATTTTATTTTTTG
1 T-TTATTATTTTATTTTATTTTACA
4772 TTTATTATTTTATTTTATT
1 TTTATTATTTTATTTTATT
4791 CTATTTTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
23 2 0.05
24 22 0.59
26 5 0.14
27 6 0.16
28 2 0.05
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.71
Consensus pattern (24 bp):
TTTATTATTTTATTTTATTTTACA
Found at i:4780 original size:29 final size:28
Alignment explanation
Indices: 4748--4810 Score: 99
Period size: 29 Copynumber: 2.2 Consensus size: 28
4738 ATATTTTACA
* *
4748 TATTTTATTTTATTTTATTTTTTGTTTAT
1 TATTTTATTTTATTCTATTTTTTCTTT-T
4777 TATTTTATTTTATTCTATTTTTTCTTTT
1 TATTTTATTTTATTCTATTTTTTCTTTT
4805 TATTTT
1 TATTTT
4811 CTCTTCTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 7 0.22
29 25 0.78
ACGTcount: A:0.16, C:0.03, G:0.02, T:0.79
Consensus pattern (28 bp):
TATTTTATTTTATTCTATTTTTTCTTTT
Found at i:4808 original size:13 final size:13
Alignment explanation
Indices: 4760--4822 Score: 56
Period size: 14 Copynumber: 4.5 Consensus size: 13
4750 TTTTATTTTA
*
4760 TTTTATTTTTTGT
1 TTTTATTTTTTCT
4773 TTATTATTTTATT-T
1 TT-TTATTTT-TTCT
4787 TATTCTATTTTTTCT
1 T-TT-TATTTTTTCT
*
4802 TTTTATTTTCTCT
1 TTTTATTTTTTCT
4815 TCTTTATT
1 T-TTTATT
4823 GTATTTGTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
13 12 0.28
14 20 0.47
15 11 0.26
ACGTcount: A:0.13, C:0.08, G:0.02, T:0.78
Consensus pattern (13 bp):
TTTTATTTTTTCT
Found at i:4828 original size:32 final size:30
Alignment explanation
Indices: 4751--4861 Score: 86
Period size: 32 Copynumber: 3.6 Consensus size: 30
4741 TTTTACATAT
* *
4751 TTTATTTTATTT-TATTTTTTGTTTA-TTAT-
1 TTTACTTTATTTAT-TTTTTTTTTTACTT-TC
* *
4780 TTTATTTTATTCTATTTTTTCTTTTTATTTTC
1 TTTACTTTATT-TATTTTTT-TTTTTACTTTC
4812 TCTT-CTTTATTGTATTTGTTTTTTTTACTTTC
1 T-TTACTTTATT-TATTT-TTTTTTTTACTTTC
*
4844 TTTATTTTATTTATTTTT
1 TTTACTTTATTTATTTTT
4862 GCTACTTTTT
Statistics
Matches: 69, Mismatches: 5, Indels: 15
0.78 0.06 0.17
Matches are distributed among these distances:
29 11 0.16
30 8 0.12
31 14 0.20
32 31 0.45
33 5 0.07
ACGTcount: A:0.14, C:0.06, G:0.03, T:0.77
Consensus pattern (30 bp):
TTTACTTTATTTATTTTTTTTTTTACTTTC
Found at i:4856 original size:9 final size:9
Alignment explanation
Indices: 4519--4860 Score: 76
Period size: 9 Copynumber: 37.8 Consensus size: 9
4509 TTCTTTATTA
4519 TTATTATTA-
1 TTATT-TTAT
4528 TTATTTTAT
1 TTATTTTAT
*
4537 ATATTTTTCATT
1 TTA-TTTT-A-T
4549 ATTATTTTAT
1 -TTATTTTAT
*
4559 ATATTTTAT
1 TTATTTTAT
* *
4568 ATATGTATAT
1 TTAT-TTTAT
4578 TT-TTTTA-
1 TTATTTTAT
4585 TTATTTT-T
1 TTATTTTAT
*
4593 CTATTTT-T
1 TTATTTTAT
4601 TTATTTT-T
1 TTATTTTAT
*
4609 GGT-TTTTAT
1 -TTATTTTAT
*
4618 TTATTACTA-
1 TTATT-TTAT
**
4627 TTATGGTATT
1 TTATTTTA-T
4637 TTATTTT-T
1 TTATTTTAT
4645 TTATTTT-T
1 TTATTTTAT
*
4653 TTACTTTAT
1 TTATTTTAT
*
4662 TATATTGT-T
1 T-TATTTTAT
* **
4671 TCACATTAT
1 TTATTTTAT
* * *
4680 TCTCTTGTCT
1 T-TATTTTAT
4690 TTATTATTA-
1 TTATT-TTAT
4699 TTATTATTA-
1 TTATT-TTAT
* *
4708 TTGTTATAT
1 TTATTTTAT
*
4717 ATATTTTA-
1 TTATTTTAT
4725 TTATTATTAT
1 TTATT-TTAT
*
4735 TGCATATTTTAC
1 T---TATTTTAT
*
4747 ATATTTTATT
1 TTATTTTA-T
4757 TTATTTTA-
1 TTATTTTAT
*
4765 TT-TTTTGT
1 TTATTTTAT
*
4773 TTATTAT-T
1 TTATTTTAT
4781 TTATTTTAT
1 TTATTTTAT
4790 TCTATTTT-T
1 T-TATTTTAT
4799 TCT-TTTTAT
1 T-TATTTTAT
*
4808 TT-TCTCTTCT
1 TTAT-T-TTAT
*
4818 TTATTGTAT
1 TTATTTTAT
* *
4827 TTGTTTTTT
1 TTATTTTAT
* *
4836 TTACTTTCT
1 TTATTTTAT
4845 TTATTTTAT
1 TTATTTTAT
4854 TTATTTT
1 TTATTTT
4861 TGCTACTTTT
Statistics
Matches: 244, Mismatches: 55, Indels: 68
0.66 0.15 0.19
Matches are distributed among these distances:
7 6 0.02
8 71 0.29
9 105 0.43
10 45 0.18
11 3 0.01
12 8 0.03
13 6 0.02
ACGTcount: A:0.21, C:0.05, G:0.04, T:0.70
Consensus pattern (9 bp):
TTATTTTAT
Found at i:4867 original size:27 final size:27
Alignment explanation
Indices: 4814--4869 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
4804 TTATTTTCTC
* **
4814 TTCTTTATTGTATTTGTTTTTTTTACT
1 TTCTTTATTGTATTTATTTTTGCTACT
*
4841 TTCTTTATTTTATTTATTTTTGCTACT
1 TTCTTTATTGTATTTATTTTTGCTACT
4868 TT
1 TT
4870 TTATCTAACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.12, C:0.09, G:0.05, T:0.73
Consensus pattern (27 bp):
TTCTTTATTGTATTTATTTTTGCTACT
Found at i:5705 original size:8 final size:8
Alignment explanation
Indices: 5686--5730 Score: 72
Period size: 8 Copynumber: 5.5 Consensus size: 8
5676 CAATAGAATT
5686 AAAAATGAA
1 AAAAATG-A
5695 AAAAATGA
1 AAAAATGA
5703 AAAAATGA
1 AAAAATGA
5711 AAAAATGA
1 AAAAATGA
*
5719 AAAAAAGA
1 AAAAATGA
5727 AAAA
1 AAAA
5731 GAAAATAAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
8 28 0.80
9 7 0.20
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (8 bp):
AAAAATGA
Found at i:5740 original size:15 final size:15
Alignment explanation
Indices: 5695--5741 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
5685 TAAAAATGAA
*
5695 AAAAATGAAAAAATG
1 AAAAATGAAAAAAAG
5710 AAAAAATGAAAAAAAG
1 -AAAAATGAAAAAAAG
5726 AAAAA-GAAAATAAAG
1 AAAAATGAAAA-AAAG
5741 A
1 A
5742 CATGTACAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 5 0.17
15 10 0.34
16 14 0.48
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.09
Consensus pattern (15 bp):
AAAAATGAAAAAAAG
Found at i:6540 original size:32 final size:31
Alignment explanation
Indices: 6494--6596 Score: 118
Period size: 32 Copynumber: 3.2 Consensus size: 31
6484 GTAAAATCAT
* *
6494 TTTATAACATTTTAATAAAATTTAATAATTA
1 TTTATAATAATTTAATAAAATTTAATAATTA
* **
6525 CTTTATAATAGTTTAATAAAATCCAATAAATTA
1 -TTTATAATAATTTAATAAAATTTAAT-AATTA
6558 TTTTATAATAATTTAAT-AAATTTAATAATTA
1 -TTTATAATAATTTAATAAAATTTAATAATTA
6589 TATTATAA
1 T-TTATAA
6597 ATCTAAAAAT
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
30 1 0.02
31 11 0.18
32 29 0.48
33 20 0.33
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.47
Consensus pattern (31 bp):
TTTATAATAATTTAATAAAATTTAATAATTA
Found at i:8913 original size:25 final size:25
Alignment explanation
Indices: 8885--8932 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
8875 TAAATTATAT
8885 GAAGGCTTAATACAAAAATAAGTAC
1 GAAGGCTTAATACAAAAATAAGTAC
* *
8910 GAAGGCTTAATAGAAAATTAAGT
1 GAAGGCTTAATACAAAAATAAGT
8933 GTCTAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.50, C:0.08, G:0.19, T:0.23
Consensus pattern (25 bp):
GAAGGCTTAATACAAAAATAAGTAC
Found at i:14239 original size:2 final size:2
Alignment explanation
Indices: 14232--14271 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
14222 TTTCGTTTCG
14232 AT AT AT AT 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 AT AT AT AT
14272 GAACTGTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15506 original size:20 final size:20
Alignment explanation
Indices: 15483--15536 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
15473 AACGCGATTT
*
15483 AGAAAATCGCAACGTTAAAA
1 AGAAAATCGCAACGGTAAAA
*
15503 AGAAAATCGCAACGGTCAAA
1 AGAAAATCGCAACGGTAAAA
15523 AGAAAATCGCAACG
1 AGAAAATCGCAACG
15537 CGAGCTTACA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.52, C:0.19, G:0.19, T:0.11
Consensus pattern (20 bp):
AGAAAATCGCAACGGTAAAA
Found at i:15803 original size:20 final size:20
Alignment explanation
Indices: 15571--15801 Score: 300
Period size: 20 Copynumber: 11.4 Consensus size: 20
15561 TTTAGAAGAA
**
15571 AATCGCAATGCGATTGATTG
1 AATCGCAATGCGATTGAGAG
* *
15591 AATCGCAATGCGATTTATAG
1 AATCGCAATGCGATTGAGAG
15611 AATCGCAATGCGATTGAGAG
1 AATCGCAATGCGATTGAGAG
* * *
15631 AGTCGCAACGCGATTTAGAAGAA
1 AATCGCAATGCGA-TT-G-AGAG
*
15654 AATCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTGAGAG
*
15674 AATCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTGAGAG
*
15694 AATCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTGAGAG
* *
15714 AATCGCAATGCGATTTATAG
1 AATCGCAATGCGATTGAGAG
15734 AATCGCAATGCGATTGAGAG
1 AATCGCAATGCGATTGAGAG
15754 AATCGCAATGCGATTGAGAG
1 AATCGCAATGCGATTGAGAG
* * *
15774 AATCGCAACGCGATTTAGAA
1 AATCGCAATGCGATTGAGAG
15794 AATCGCAA
1 AATCGCAA
15802 CGTTAAAAAG
Statistics
Matches: 189, Mismatches: 19, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
20 170 0.90
21 3 0.02
22 2 0.01
23 14 0.07
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.21
Consensus pattern (20 bp):
AATCGCAATGCGATTGAGAG
Found at i:15813 original size:20 final size:20
Alignment explanation
Indices: 15790--15833 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
15780 AACGCGATTT
*
15790 AGAAAATCGCAACGTTAAAA
1 AGAAAATCGCAACGGTAAAA
*
15810 AGAAAATCGCAACGGTCAAA
1 AGAAAATCGCAACGGTAAAA
15830 AGAA
1 AGAA
15834 TAGTTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.55, C:0.16, G:0.18, T:0.11
Consensus pattern (20 bp):
AGAAAATCGCAACGGTAAAA
Found at i:15818 original size:60 final size:60
Alignment explanation
Indices: 15467--15821 Score: 228
Period size: 60 Copynumber: 5.8 Consensus size: 60
15457 TGACCAATAA
** * * ** *
15467 AATCGCAACGCGATTTAGAAAATCGCAACGTTAAAAAGAAAATCGCAA--CGGTCAAAAGAA
1 AATCGCAACGCGATTTAGAAAATCGCAACGCGAATAAGAAAATCGCAATGCGAT--TGAGAG
* * ** * **
15527 AATCGCAACGCGAGCTTACAAGTTCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATTG
1 AATCGCAACGCGA-TTTAGAAAATCGCAACGCGA---ATAAGAAAATCGCAATGCGATTGAGAG
* * * * * * * * * *
15591 AATCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAGAGTCGCAACGCGATTTAGAAGAA
1 AATCGCAACGCGATTTAGAAAATCGCAACGCGAATAAGAAAATCGCAATGCGA-TT-G-AGAG
* * * * * * * * *
15654 AATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAG
1 AATCGCAACGCGATTTAGAAAATCGCAACGCGAATAAGAAAATCGCAATGCGATTGAGAG
* * * * * * *
15714 AATCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAGAATCGCAATGCGATTGAGAG
1 AATCGCAACGCGATTTAGAAAATCGCAACGCGAATAAGAAAATCGCAATGCGATTGAGAG
** *
15774 AATCGCAACGCGATTTAGAAAATCGCAACGTTAAAAAGAAAATCGCAA
1 AATCGCAACGCGATTTAGAAAATCGCAACGCGAATAAGAAAATCGCAA
15822 CGGTCAAAAG
Statistics
Matches: 234, Mismatches: 52, Indels: 18
0.77 0.17 0.06
Matches are distributed among these distances:
60 123 0.53
61 17 0.07
62 2 0.01
63 62 0.26
64 27 0.12
66 3 0.01
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGATTTAGAAAATCGCAACGCGAATAAGAAAATCGCAATGCGATTGAGAG
Found at i:16464 original size:6 final size:6
Alignment explanation
Indices: 16453--16527 Score: 150
Period size: 6 Copynumber: 12.5 Consensus size: 6
16443 TCTCGTCTCG
16453 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
16501 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
16528 AATACGTGTC
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 69 1.00
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:16626 original size:20 final size:20
Alignment explanation
Indices: 16601--16898 Score: 179
Period size: 20 Copynumber: 14.6 Consensus size: 20
16591 AATTTTTTAA
16601 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
16621 CGTTGCGATTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* *
16641 CATTGCGATTCTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
16661 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
*
16681 CATTGCGATTCTCTTCTAAATCG
1 CGTTGCGA-T-T-TTCTAAATCG
* * *
16704 CGTTGCGACTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
16724 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* *** *
16744 CATTGCGATTCAATCAATCG
1 CGTTGCGATTTTCTAAATCG
*
16764 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
** ** *
16787 CGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
* *
16808 CGTTGCGATTTTCT--TTTG
1 CGTTGCGATTTTCTAAATCG
*** **
16826 ACCGTTGCGATTTTCTTTTTAA
1 --CGTTGCGATTTTCTAAATCG
16848 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
16868 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCTAAATCG
16887 CGTTGCGATTTT
1 CGTTGCGATTTT
16899 ATTGGTCATT
Statistics
Matches: 223, Mismatches: 44, Indels: 23
0.77 0.15 0.08
Matches are distributed among these distances:
18 2 0.01
19 17 0.08
20 157 0.70
21 15 0.07
22 5 0.02
23 27 0.12
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:16658 original size:40 final size:40
Alignment explanation
Indices: 16603--16794 Score: 258
Period size: 40 Copynumber: 4.7 Consensus size: 40
16593 TTTTTTAACG
*
16603 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
1 TTGCGATTCTCTAAATCGCGTTGCGATTCTCTCAATCGCA
* *
16643 TTGCGATTCTCTAAATCGCATTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTAAATCGCGTTGCGATTCTCTCAATCGCA
*
16683 TTGCGATTCTCTTCTAAATCGCGTTGCGACTCTCTCAATCGCA
1 TTGCGA-T-TC-TCTAAATCGCGTTGCGATTCTCTCAATCGCA
* * **
16726 TTGCGATTCTATAAATCGCATTGCGATTCAATCAATCGCA
1 TTGCGATTCTCTAAATCGCGTTGCGATTCTCTCAATCGCA
16766 TTGCGATTTTCTTCTAAATCGCGTTGCGA
1 TTGCGA--TTC-TCTAAATCGCGTTGCGA
16795 ACTTGGAAGC
Statistics
Matches: 133, Mismatches: 13, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
40 75 0.56
41 3 0.02
42 6 0.05
43 49 0.37
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.36
Consensus pattern (40 bp):
TTGCGATTCTCTAAATCGCGTTGCGATTCTCTCAATCGCA
Found at i:16750 original size:83 final size:83
Alignment explanation
Indices: 16611--16794 Score: 314
Period size: 83 Copynumber: 2.2 Consensus size: 83
16601 CGTTGCGATT
* * **
16611 TTCTAAATCGCGTTGCGATTCTCTCAATCGCATTGCGATTCTCTAAATCGCATTGCGATTCTCTC
1 TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCAATC
*
16676 AGTCGCATTGCGATTCTC
66 AATCGCATTGCGATTCTC
16694 TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCAATC
1 TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCAATC
*
16759 AATCGCATTGCGATTTTC
66 AATCGCATTGCGATTCTC
16777 TTCTAAATCGCGTTGCGA
1 TTCTAAATCGCGTTGCGA
16795 ACTTGGAAGC
Statistics
Matches: 95, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
83 95 1.00
ACGTcount: A:0.22, C:0.26, G:0.17, T:0.35
Consensus pattern (83 bp):
TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCAATC
AATCGCATTGCGATTCTC
Found at i:16888 original size:19 final size:20
Alignment explanation
Indices: 16848--16898 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
16838 TTCTTTTTAA
*
16848 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
16868 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
16887 CGTTGCGATTTT
1 CGTTGCGATTTT
16899 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:18312 original size:60 final size:60
Alignment explanation
Indices: 18235--18361 Score: 159
Period size: 60 Copynumber: 2.1 Consensus size: 60
18225 TCTCATTCTT
* * *
18235 AAACCATGACTATCATTCTAAATTAGT-CCTCAAA-ATTTTGAGCATTTCAATTTCATCCCC
1 AAACTATGACTATCATTCTAAATTAGTCCCT-AAACATTTTGAACATTCCAATTTCAT-CCC
* * * *
18295 AAACTATGACTTTCATTCTAAATTGGTCCCTAAACTTTTTGAACATTCCAATTTTATCCC
1 AAACTATGACTATCATTCTAAATTAGTCCCTAAACATTTTGAACATTCCAATTTCATCCC
18355 AAACTAT
1 AAACTAT
18362 ACATATATAC
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
60 37 0.64
61 21 0.36
ACGTcount: A:0.33, C:0.24, G:0.06, T:0.37
Consensus pattern (60 bp):
AAACTATGACTATCATTCTAAATTAGTCCCTAAACATTTTGAACATTCCAATTTCATCCC
Found at i:18587 original size:60 final size:60
Alignment explanation
Indices: 18488--18605 Score: 150
Period size: 60 Copynumber: 2.0 Consensus size: 60
18478 GATGAATTTG
* * * *
18488 GGGATGAAATTGGAAGATTTAAAAGTTTTGGAACCAATTTAGAATGAGGGTCATAGTTCA
1 GGGATGAAATTAGAAGATTTAAAAGTTTAGGAACCAATTTAAAATGAGAGTCATAGTTCA
**
18548 GGGATGAAATTAGAATG-TTTAAAAGTTTAAGG-ATTAATTTAAAATGAGAGTCATAGTT
1 GGGATGAAATTAGAA-GATTTAAAAGTTT-AGGAACCAATTTAAAATGAGAGTCATAGTT
18606 TGAGGATAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
60 47 0.94
61 3 0.06
ACGTcount: A:0.39, C:0.04, G:0.25, T:0.32
Consensus pattern (60 bp):
GGGATGAAATTAGAAGATTTAAAAGTTTAGGAACCAATTTAAAATGAGAGTCATAGTTCA
Done.