Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007430.1 Hibiscus syriacus cultivar Beakdansim tig00020144_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: 75525
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Found at i:10818 original size:3 final size:3
Alignment explanation
Indices: 10795--10849 Score: 74
Period size: 3 Copynumber: 17.7 Consensus size: 3
10785 GTATTATAAA
*
10795 TAT TAAT TAT ATAT AAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT T-AT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
10842 TAA TAT TA
1 TAT TAT TA
10850 CATATTAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
3 40 0.87
4 6 0.13
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:11349 original size:21 final size:21
Alignment explanation
Indices: 11325--11364 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
11315 ATGTAAATCA
11325 CATTGCAATTTTCCAAATTTG
1 CATTGCAATTTTCCAAATTTG
*
11346 CATTGCGATTTTCCAAATT
1 CATTGCAATTTTCCAAATT
11365 CACAACACAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.20, G:0.10, T:0.42
Consensus pattern (21 bp):
CATTGCAATTTTCCAAATTTG
Found at i:11570 original size:22 final size:22
Alignment explanation
Indices: 11544--11594 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
11534 CTAGGGCAAC
*
11544 ATCCGTCCCCATCTCTGACGAA
1 ATCCGTCCCCATCTCAGACGAA
*
11566 ATCCGTCCCCATCTCAGGCGAA
1 ATCCGTCCCCATCTCAGACGAA
11588 ATCCGTC
1 ATCCGTC
11595 TATCTCCATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.22, C:0.41, G:0.16, T:0.22
Consensus pattern (22 bp):
ATCCGTCCCCATCTCAGACGAA
Found at i:11983 original size:19 final size:20
Alignment explanation
Indices: 11961--12013 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
11951 AAATCGCAAC
11961 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTAAGTTTCGCGTT
*
11980 GCGATTTTCA-TTTCGCGTT
1 GCGATTTTAAGTTTCGCGTT
*
11999 GCAATTTTAAGTTTC
1 GCGATTTTAAGTTTC
12014 ATAAACTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 25 0.83
20 5 0.17
ACGTcount: A:0.15, C:0.17, G:0.21, T:0.47
Consensus pattern (20 bp):
GCGATTTTAAGTTTCGCGTT
Found at i:13960 original size:12 final size:12
Alignment explanation
Indices: 13934--13975 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
13924 TTTTTAGGCA
13934 TTATTTATTTG-T
1 TTATTTA-TTGAT
13946 TTATTTATTGAT
1 TTATTTATTGAT
* *
13958 TTATGTATTAAT
1 TTATTTATTGAT
13970 TTATTT
1 TTATTT
13976 TTAGCGGCCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
11 3 0.12
12 23 0.88
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (12 bp):
TTATTTATTGAT
Found at i:14210 original size:21 final size:21
Alignment explanation
Indices: 14123--14216 Score: 98
Period size: 21 Copynumber: 4.5 Consensus size: 21
14113 CACCTGTCAT
* * *
14123 CGTTCAAGAGGCCTCTCCTAT
1 CGTTCAAGAGGCCCCTCCCAC
14144 CGTTCAAGAGGCCCCTCCCAC
1 CGTTCAAGAGGCCCCTCCCAC
* * ** *
14165 CATTCAAGAGACCCCTGTCAT
1 CGTTCAAGAGGCCCCTCCCAC
*
14186 CGTTCAAGAGGTCCCTCCCAC
1 CGTTCAAGAGGCCCCTCCCAC
*
14207 CGTTCGAGAG
1 CGTTCAAGAG
14217 CCCGATTCAC
Statistics
Matches: 58, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 58 1.00
ACGTcount: A:0.21, C:0.37, G:0.20, T:0.21
Consensus pattern (21 bp):
CGTTCAAGAGGCCCCTCCCAC
Found at i:15577 original size:13 final size:14
Alignment explanation
Indices: 15552--15584 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
15542 TGCGTGATGT
15552 ATTTGTAAAAGTTG
1 ATTTGTAAAAGTTG
15566 ATTTGT-AAAGTTG
1 ATTTGTAAAAGTTG
15579 ATTTGT
1 ATTTGT
15585 TTAATTGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.30, C:0.00, G:0.21, T:0.48
Consensus pattern (14 bp):
ATTTGTAAAAGTTG
Found at i:15666 original size:64 final size:64
Alignment explanation
Indices: 15563--15709 Score: 219
Period size: 64 Copynumber: 2.3 Consensus size: 64
15553 TTTGTAAAAG
15563 TTGATTTGT-AAAGTTGATTTGTTTAATTGATGAGGAAATACA-AATTATTTTTTACTTGTTTAA
1 TTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATA-ATAATTATTTTTTACTTGTTTAA
* * ** *
15626 TTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTTTTGCTTGTTTAA
1 TTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAATAATTATTTTTTACTTGTTTAA
15690 TTGATTTGTAAAAG-TGATTT
1 TTGATTTGTAAAAGTTGATTT
15710 TTTGTTTTAA
Statistics
Matches: 77, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
63 16 0.21
64 61 0.79
ACGTcount: A:0.29, C:0.03, G:0.16, T:0.52
Consensus pattern (64 bp):
TTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAATAATTATTTTTTACTTGTTTAA
Found at i:15889 original size:54 final size:54
Alignment explanation
Indices: 15782--15915 Score: 145
Period size: 54 Copynumber: 2.6 Consensus size: 54
15772 TCGCAGCGCG
* * *
15782 AAAGTCAAATTCGCGTTGCGA---T--GGTTGCGAAAGTCAAATTTACAACGCG
1 AAAGTCAAATTCGCGTTGCGAGTTTCACGTTGCGAAAGTCAAATTGACAACGCA
* * *
15831 AAAGTCAAATTCGTGTTGCGAGTTTCACGTTGCGATAGTCAAATTCGA-AATGCA
1 AAAGTCAAATTCGCGTTGCGAGTTTCACGTTGCGAAAGTCAAATT-GACAACGCA
* *
15885 AAAGTCAAATTCGCGTTGCGATTTTCGCGTT
1 AAAGTCAAATTCGCGTTGCGAGTTTCACGTT
15916 TTGAATTTGA
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
49 20 0.29
52 1 0.01
54 48 0.69
55 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (54 bp):
AAAGTCAAATTCGCGTTGCGAGTTTCACGTTGCGAAAGTCAAATTGACAACGCA
Found at i:15951 original size:29 final size:29
Alignment explanation
Indices: 15918--15973 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
15908 TTCGCGTTTT
15918 GAATTTGACTTTCGCAACAATCGCAACGC
1 GAATTTGACTTTCGCAACAATCGCAACGC
*
15947 GAATTTGACTTTTGCAACAATCGCAAC
1 GAATTTGACTTTCGCAACAATCGCAAC
15974 AAAAAATCTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (29 bp):
GAATTTGACTTTCGCAACAATCGCAACGC
Found at i:18646 original size:12 final size:12
Alignment explanation
Indices: 18625--18658 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
18615 GGTTGTGGGT
*
18625 TTTGAGATTGTG
1 TTTGATATTGTG
18637 TTTGATATTGTG
1 TTTGATATTGTG
*
18649 TTTGGTATTG
1 TTTGATATTG
18659 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:19470 original size:20 final size:19
Alignment explanation
Indices: 19424--19494 Score: 65
Period size: 20 Copynumber: 3.7 Consensus size: 19
19414 CCCAAAACAT
*
19424 TTGTGTTGCGAAACTAAAA
1 TTGTGTTGCGAAATTAAAA
**
19443 -CCTGTTGCGAAATTAAAA
1 TTGTGTTGCGAAATTAAAA
19461 TTTGTGTTGCG-AATTCGAAAA
1 -TTGTGTTGCGAAATT--AAAA
*
19482 TTGAGTTGCGAAA
1 TTGTGTTGCGAAA
19495 AAAAAATTCA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
18 15 0.37
19 4 0.10
20 16 0.39
21 6 0.15
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (19 bp):
TTGTGTTGCGAAATTAAAA
Found at i:19529 original size:20 final size:20
Alignment explanation
Indices: 19506--19598 Score: 100
Period size: 20 Copynumber: 4.6 Consensus size: 20
19496 AAAAATTCAC
**
19506 GTTGCGAATTCAGAAATCAA
1 GTTGCGAATTTGGAAATCAA
*
19526 GTTGCGAATTT-GAAATTCATT
1 GTTGCGAATTTGGAAA-TCA-A
*
19547 GTTGCGAATTTGGAAATCGCA
1 GTTGCGAATTTGGAAATC-AA
*
19568 -TTGCGAATTTGGAAATCGA
1 GTTGCGAATTTGGAAATCAA
19587 GTTGCGAATTTG
1 GTTGCGAATTTG
19599 ACTTCTATGT
Statistics
Matches: 63, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
19 5 0.08
20 41 0.65
21 13 0.21
22 4 0.06
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (20 bp):
GTTGCGAATTTGGAAATCAA
Found at i:19563 original size:41 final size:40
Alignment explanation
Indices: 19498--19598 Score: 109
Period size: 41 Copynumber: 2.5 Consensus size: 40
19488 TGCGAAAAAA
**
19498 AAATTCACGTTGCGAATTCAGAAATC-AAGTTGCGAATTT-G
1 AAATTCA-GTTGCGAATTTGGAAATCGAA-TTGCGAATTTGG
*
19538 AAATTCATTGTTGCGAATTTGGAAATCGCATTGCGAATTTGG
1 AAATTCA--GTTGCGAATTTGGAAATCGAATTGCGAATTTGG
19580 AAA-TCGAGTTGCGAATTTG
1 AAATTC-AGTTGCGAATTTG
19599 ACTTCTATGT
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
40 19 0.36
41 28 0.53
42 6 0.11
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.33
Consensus pattern (40 bp):
AAATTCAGTTGCGAATTTGGAAATCGAATTGCGAATTTGG
Found at i:19644 original size:20 final size:20
Alignment explanation
Indices: 19615--19653 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
19605 ATGTTATGAA
*
19615 TTACAAATTCGCGTTGTGAT
1 TTACAAATTCGCATTGTGAT
*
19635 TTACATATTCGCATTGTGA
1 TTACAAATTCGCATTGTGA
19654 ATTTGGAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.41
Consensus pattern (20 bp):
TTACAAATTCGCATTGTGAT
Found at i:21189 original size:6 final size:6
Alignment explanation
Indices: 20482--21188 Score: 1377
Period size: 6 Copynumber: 118.5 Consensus size: 6
20472 CCGTTTGAAG
20482 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
1 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
20530 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
1 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
20578 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
1 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
20626 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
1 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
20674 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
1 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
20722 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
1 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
20770 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
1 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
20818 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
1 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
20866 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
1 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
20914 TATG-- TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
1 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
20960 TATGTA TATGTA TATGTA TATGTA TATGTA TA--TA TATGTA TATGTA
1 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
21006 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
1 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
21054 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
1 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
21102 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
1 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
*
21150 TATGTA TATGTA TATGTA TATGTA TATGTA TATATA TAT
1 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TAT
21189 AAGTAGGACA
Statistics
Matches: 696, Mismatches: 1, Indels: 8
0.99 0.00 0.01
Matches are distributed among these distances:
4 8 0.01
6 688 0.99
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (6 bp):
TATGTA
Found at i:21641 original size:55 final size:54
Alignment explanation
Indices: 21570--22080 Score: 593
Period size: 55 Copynumber: 9.3 Consensus size: 54
21560 AGGGAATATA
* *
21570 AGACTCGAACGATCTTCTAC-ATACGTGTCTGCTCCATATTTCTTCAGAGAGTATG
1 AGACTCGAACAATCTTC-ACAAT-CGTGTCTGCTCCCTATTTCTTCAGAGAGTATG
* * * * *
21625 AGAATCAAACAATCTTCAAAAATCGTCTCTGCACCCTATTTCTTCAGAGAG--TG
1 AGACTCGAACAATCTTC-ACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATG
*
21678 AGACTCGAACAATATTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATG
1 AGACTCGAACAATCTTC-ACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATG
* * * *
21733 AGACTCAAACAATCCTCAACAATCGTGTCTTCTCCCTATTTCTTCGGAGAGTATG
1 AGACTCGAACAATCTTC-ACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATG
21788 AGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATG
1 AGACTCGAACAATCTTC-ACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATG
** * * * *
21843 AGACTCGAACAATCTTCA-ATGATTTTGTCTTCTCTCTATTTCTTCAAAGAGTATA
1 AGACTCGAACAATCTTCACA--ATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATG
* * * *
21898 AGACTCGAACAATCTTCAATAATTGTGTCTGCTCCCTATTCCTTCAGAGAGTATA
1 AGACTCGAACAATCTTC-ACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATG
* * *
21953 AGACTCGAACAATCTTCAACAATCTTGTCTGCTCCCTATTTCTTTAGAGAGTATA
1 AGACTCGAACAATCTTC-ACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATG
* * *
22008 AGACTCGAACAATCTGCAATAATCGTATCTGCTCCCTATTTCTTTCAG-GCAGTAT-
1 AGACTCGAACAATCTTC-ACAATCGTGTCTGCTCCCTATTTC-TTCAGAG-AGTATG
*
22063 AGAACTCGAATAATCTTC
1 AG-ACTCGAACAATCTTC
22081 TGGGGACGAG
Statistics
Matches: 400, Mismatches: 46, Indels: 19
0.86 0.10 0.04
Matches are distributed among these distances:
53 48 0.12
54 1 0.00
55 325 0.81
56 25 0.06
57 1 0.00
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.32
Consensus pattern (54 bp):
AGACTCGAACAATCTTCACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATG
Found at i:21842 original size:110 final size:110
Alignment explanation
Indices: 21566--22051 Score: 663
Period size: 110 Copynumber: 4.4 Consensus size: 110
21556 CTTTAGGGAA
* * * *
21566 TATAAGACTCGAACGATCTTCTAC-ATACGTGTCTGCTCCATATTTCTTCAGAGAGTATGAGAAT
1 TATAAGACTCGAACAATCTTCAACAAT-CGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACT
* * *
21630 CAAACAATCTTCAAAAATCGTCTCTGCACCCTATTTCTTCAGAGAG
65 CAAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAG
* *
21676 --TGAGACTCGAACAATATTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTC
1 TATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTC
* * *
21739 AAACAATCCTCAACAATCGTGTCTTCTCCCTATTTCTTCGGAGAG
66 AAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAG
*
21784 TATGAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTC
1 TATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTC
* ** ** * * *
21849 GAACAATCTTCAATGATTTTGTCTTCTCTCTATTTCTTCAAAGAG
66 AAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAG
* * * *
21894 TATAAGACTCGAACAATCTTCAATAATTGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTC
1 TATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTC
* * *
21959 GAACAATCTTCAACAATCTTGTCTGCTCCCTATTTCTTTAGAGAG
66 AAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAG
* * *
22004 TATAAGACTCGAACAATCTGCAATAATCGTATCTGCTCCCTATTTCTT
1 TATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTT
22052 TCAGGCAGTA
Statistics
Matches: 335, Mismatches: 38, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
108 93 0.28
109 2 0.01
110 240 0.72
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (110 bp):
TATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTC
AAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAG
Found at i:21950 original size:165 final size:165
Alignment explanation
Indices: 21566--22051 Score: 665
Period size: 165 Copynumber: 3.0 Consensus size: 165
21556 CTTTAGGGAA
* * *
21566 TATAAGACTCGAACGATCTTC--TACATACGTGTCTGCTCCATATTTCTTCAGAGAGTATGAGAA
1 TATAAGACTCGAACAATCTTCAATA-AT-CGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGAC
* * * * *
21629 TCAAACAATCTTCAAAAATCGTCTCTGCACCCTATTTCTTCAGAGAG--TGAGACTCGAACAATA
64 TCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATC
* *
21692 TTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAG
129 TTCAATAATCGTGTCTGCTCCCTATTTCTTCAAAGAG
* * * * * *
21729 TATGAGACTCAAACAATCCTCAACAATCGTGTCTTCTCCCTATTTCTTCGGAGAGTATGAGACTC
1 TATAAGACTCGAACAATCTTCAATAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTC
21794 GAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTT
66 GAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTT
* ** * *
21859 CAATGATTTTGTCTTCTCTCTATTTCTTCAAAGAG
131 CAATAATCGTGTCTGCTCCCTATTTCTTCAAAGAG
* * *
21894 TATAAGACTCGAACAATCTTCAATAATTGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTC
1 TATAAGACTCGAACAATCTTCAATAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTC
* * * *
21959 GAACAATCTTCAACAATCTTGTCTGCTCCCTATTTCTTTAGAGAGTATAAGACTCGAACAATCTG
66 GAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTT
*
22024 CAATAATCGTATCTGCTCCCTATTTCTT
131 CAATAATCGTGTCTGCTCCCTATTTCTT
22052 TCAGGCAGTA
Statistics
Matches: 279, Mismatches: 40, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
163 92 0.33
164 2 0.01
165 185 0.66
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (165 bp):
TATAAGACTCGAACAATCTTCAATAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTC
GAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTT
CAATAATCGTGTCTGCTCCCTATTTCTTCAAAGAG
Found at i:22266 original size:54 final size:54
Alignment explanation
Indices: 22038--22573 Score: 505
Period size: 54 Copynumber: 9.8 Consensus size: 54
22028 AATCGTATCT
* * * * **** *
22038 GCTCCCTATTTCTTTCAGGCAGTATAGAACTCGAATAATCTTCTGGGGACGAGTTC
1 GCTCCCTCTTTCTCT-AGGGAGTATAGAACTCGGA-AATCTTCTTCAAACGGGTTC
* * * * * ****
22094 GATCCCTATTTCTTTCAGGAAGTATAGAACTCGAATAATCTTCTAGGGACGGGTTC
1 GCTCCCTCTTTCTCT-AGGGAGTATAGAACTCGGA-AATCTTCTTCAAACGGGTTC
* * * *
22150 GCTCCCTATTTCTTTCAGGAAGTATAGAACTCGAATAATCTTCTGT-AAACGGGTTC
1 GCTCCCTCTTTCTCT-AGGGAGTATAGAACTCGGA-AATCTTCT-TCAAACGGGTTC
* *
22206 GCTCCCTTTTTCTCTAGGGAGTATAGAACTCGGAAATCTTCTTCTTAA-GGGTTC
1 GCTCCCTCTTTCTCTAGGGAGTATAGAACTCGGAAATCTTCTTC-AAACGGGTTC
* * *
22260 ACTCCCTCTTTCT-TCAGGGAGTATAGAACTCGGATATCTTCTTCAAATGGGTTC
1 GCTCCCTCTTTCTCT-AGGGAGTATAGAACTCGGAAATCTTCTTCAAACGGGTTC
*
22314 GCTCCCTCTTTCTCTAGGGAGTATAGAACTC-GATCATCTTCTTCAAACGGGTTC
1 GCTCCCTCTTTCTCTAGGGAGTATAGAACTCGGA-AATCTTCTTCAAACGGGTTC
* * *
22368 ACTACCTCTTTCT-TCAGGGAGTATATAACTC-GAATATCTTCTTCAAACGGGTTC
1 GCTCCCTCTTTCTCT-AGGGAGTATAGAACTCGGAA-ATCTTCTTCAAACGGGTTC
** * * ** *
22422 ATTCCCTCTTTCTCTAGGGAATATAGAACTCGAAAATCTTCTTCTTAGGGGTTC
1 GCTCCCTCTTTCTCTAGGGAGTATAGAACTCGGAAATCTTCTTCAAACGGGTTC
* *
22476 GCTCCCTCTTTCTATAGGGAGTAT-GAAACTCGGATA-CTTTCTTCAAACGGGTTC
1 GCTCCCTCTTTCTCTAGGGAGTATAG-AACTCGGAAATC-TTCTTCAAACGGGTTC
*
22530 GCTCCCTCTTTCTCTAGGGAGTATGGAACTC-GAACATCTTCTTC
1 GCTCCCTCTTTCTCTAGGGAGTATAGAACTCGGAA-ATCTTCTTC
22574 TGCTTCACTA
Statistics
Matches: 421, Mismatches: 43, Indels: 34
0.85 0.09 0.07
Matches are distributed among these distances:
53 11 0.03
54 269 0.64
55 25 0.06
56 116 0.28
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.34
Consensus pattern (54 bp):
GCTCCCTCTTTCTCTAGGGAGTATAGAACTCGGAAATCTTCTTCAAACGGGTTC
Found at i:22327 original size:108 final size:108
Alignment explanation
Indices: 22039--22574 Score: 591
Period size: 108 Copynumber: 4.9 Consensus size: 108
22029 ATCGTATCTG
* * **** * * *
22039 CTCCCTATTTCTTTCAGGCAGTATAGAACTCGAATAATCTTCTGGGGACGAGTTCGATCCCTATT
1 CTCCCTCTTTC-TTCAGGGAGTATAGAACTCGAAT-ATCTTCTTCAAACGGGTTCGCTCCCTCTT
* * * **** * *
22104 TCTTTCAGGAAGTATAGAACTCGAATAATCTTCTAGGGACGGGTTCG
64 TCTCT-AGGGAGTATAGAACTCGGA-AATCTTCTTCTTAAGGGTTCA
* * *
22151 CTCCCTATTTCTTTCAGGAAGTATAGAACTCGAATAATCTTCTGT-AAACGGGTTCGCTCCCTTT
1 CTCCCTCTTTC-TTCAGGGAGTATAGAACTCGAAT-ATCTTCT-TCAAACGGGTTCGCTCCCTCT
22215 TTCTCTAGGGAGTATAGAACTCGGAAATCTTCTTCTTAAGGGTTCA
63 TTCTCTAGGGAGTATAGAACTCGGAAATCTTCTTCTTAAGGGTTCA
* *
22261 CTCCCTCTTTCTTCAGGGAGTATAGAACTCGGATATCTTCTTCAAATGGGTTCGCTCCCTCTTTC
1 CTCCCTCTTTCTTCAGGGAGTATAGAACTCGAATATCTTCTTCAAACGGGTTCGCTCCCTCTTTC
* *
22326 TCTAGGGAGTATAGAACTC-GATCATCTTCTTC-AAACGGGTTCA
66 TCTAGGGAGTATAGAACTCGGA-AATCTTCTTCTTAA-GGGTTCA
* * **
22369 CTACCTCTTTCTTCAGGGAGTATATAACTCGAATATCTTCTTCAAACGGGTTCATTCCCTCTTTC
1 CTCCCTCTTTCTTCAGGGAGTATAGAACTCGAATATCTTCTTCAAACGGGTTCGCTCCCTCTTTC
* * * *
22434 TCTAGGGAATATAGAACTCGAAAATCTTCTTCTTAGGGGTTCG
66 TCTAGGGAGTATAGAACTCGGAAATCTTCTTCTTAAGGGTTCA
*
22477 CTCCCTCTTTCTAT-AGGGAGTAT-GAAACTCGGATA-CTTTCTTCAAACGGGTTCGCTCCCTCT
1 CTCCCTCTTTCT-TCAGGGAGTATAG-AACTCGAATATC-TTCTTCAAACGGGTTCGCTCCCTCT
*
22539 TTCTCTAGGGAGTATGGAACTC-GAACATCTTCTTCT
63 TTCTCTAGGGAGTATAGAACTCGGAA-ATCTTCTTCT
22575 GCTTCACTAC
Statistics
Matches: 371, Mismatches: 43, Indels: 24
0.85 0.10 0.05
Matches are distributed among these distances:
107 8 0.02
108 236 0.64
109 24 0.06
110 25 0.07
111 17 0.05
112 61 0.16
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.35
Consensus pattern (108 bp):
CTCCCTCTTTCTTCAGGGAGTATAGAACTCGAATATCTTCTTCAAACGGGTTCGCTCCCTCTTTC
TCTAGGGAGTATAGAACTCGGAAATCTTCTTCTTAAGGGTTCA
Found at i:22389 original size:162 final size:162
Alignment explanation
Indices: 22096--22574 Score: 560
Period size: 162 Copynumber: 2.9 Consensus size: 162
22086 ACGAGTTCGA
* * **** *
22096 TCCCTATTTCTTTCAGGAAGTATAGAACTCGAATAATCTTCTAGGGACGGGTTCGCTCCCTATTT
1 TCCCTCTTTC-TTCAGGGAGTATAGAACTCGAAT-ATCTTCTTCAAACGGGTTCGCTCCCTCTTT
* * *
22161 CTTTCAGGAAGTATAGAACTCGAATAATCTTCTGT-AAACGGGTTCGCTCCCTTTTTCTCTAGGG
64 CTAT-AGGGAGTATAGAACTCG-AT-ATCTTCT-TCAAACGGGTTCGCTCCCTCTTTCTCTAGGG
*
22225 AGTATAGAACTCGGAA-ATCTTCTTCTTAA-GGGTTCAC
125 AGTATAGAACTC-GAACATCTTCTTCTAAACGGGTTCAC
* *
22262 TCCCTCTTTCTTCAGGGAGTATAGAACTCGGATATCTTCTTCAAATGGGTTCGCTCCCTCTTTCT
1 TCCCTCTTTCTTCAGGGAGTATAGAACTCGAATATCTTCTTCAAACGGGTTCGCTCCCTCTTTCT
* * *
22327 CTAGGGAGTATAGAACTCGATCATCTTCTTCAAACGGGTTCACTACCTCTTTCT-TCAGGGAGTA
66 ATAGGGAGTATAGAACTCGAT-ATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTA
* * *
22391 TATAACTCGAATATCTTCTTC-AAACGGGTTCAT
129 TAGAACTCGAACATCTTCTTCTAAACGGGTTCAC
* * ** *
22424 TCCCTCTTTC-TCTAGGGAATATAGAACTCGAAAATCTTCTTCTTAGGGGTTCGCTCCCTCTTTC
1 TCCCTCTTTCTTC-AGGGAGTATAGAACTCGAATATCTTCTTCAAACGGGTTCGCTCCCTCTTTC
22488 TATAGGGAGTAT-GAAACTCGGATA-CTTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAG
65 TATAGGGAGTATAG-AACTC-GATATC-TTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAG
*
22551 TATGGAACTCGAACATCTTCTTCT
127 TATAGAACTCGAACATCTTCTTCT
22575 GCTTCACTAC
Statistics
Matches: 273, Mismatches: 30, Indels: 23
0.84 0.09 0.07
Matches are distributed among these distances:
161 11 0.04
162 185 0.68
163 20 0.07
164 27 0.10
165 21 0.08
166 9 0.03
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.35
Consensus pattern (162 bp):
TCCCTCTTTCTTCAGGGAGTATAGAACTCGAATATCTTCTTCAAACGGGTTCGCTCCCTCTTTCT
ATAGGGAGTATAGAACTCGATATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATA
GAACTCGAACATCTTCTTCTAAACGGGTTCAC
Found at i:23835 original size:16 final size:14
Alignment explanation
Indices: 23805--23859 Score: 60
Period size: 12 Copynumber: 3.9 Consensus size: 14
23795 TTCTTCTTTT
*
23805 TTTTAATTTTTT--
1 TTTTCATTTTTTCA
23817 TTTTCATTTTTTCA
1 TTTTCATTTTTTCA
23831 GTTTTCAATTTTTTTCA
1 -TTTTC-A-TTTTTTCA
23848 TTTTCATTTTTT
1 TTTTCATTTTTT
23860 TCTTCTCTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
12 11 0.30
14 6 0.16
15 6 0.16
16 6 0.16
17 8 0.22
ACGTcount: A:0.15, C:0.09, G:0.02, T:0.75
Consensus pattern (14 bp):
TTTTCATTTTTTCA
Found at i:23835 original size:21 final size:21
Alignment explanation
Indices: 23792--23835 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
23782 CCTCCTTTTC
* *
23792 TTTTTCTTCTTTTTTTTAATT
1 TTTTTCTTCATTTTTTCAATT
* *
23813 TTTTTTTTCATTTTTTCAGTT
1 TTTTTCTTCATTTTTTCAATT
23834 TT
1 TT
23836 CAATTTTTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.09, G:0.02, T:0.80
Consensus pattern (21 bp):
TTTTTCTTCATTTTTTCAATT
Found at i:23860 original size:15 final size:16
Alignment explanation
Indices: 23817--23861 Score: 67
Period size: 15 Copynumber: 2.9 Consensus size: 16
23807 TTAATTTTTT
23817 TTTTCA-TTTTTTCAG
1 TTTTCATTTTTTTCAG
23832 TTTTCAATTTTTTTCA-
1 TTTTC-ATTTTTTTCAG
23848 TTTTCATTTTTTTC
1 TTTTCATTTTTTTC
23862 TTCTCTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
15 14 0.50
16 6 0.21
17 8 0.29
ACGTcount: A:0.13, C:0.13, G:0.02, T:0.71
Consensus pattern (16 bp):
TTTTCATTTTTTTCAG
Found at i:23871 original size:14 final size:15
Alignment explanation
Indices: 23823--23872 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
23813 TTTTTTTTCA
*
23823 TTTTTTCAGTTTTCAAT
1 TTTTTTCA-TTCTC-AT
*
23840 TTTTTTCATTTTCAT
1 TTTTTTCATTCTCAT
23855 TTTTTTC-TTCTC-T
1 TTTTTTCATTCTCAT
23868 TTTTT
1 TTTTT
23873 CTATCTTTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
13 6 0.19
14 4 0.12
15 9 0.28
16 5 0.16
17 8 0.25
ACGTcount: A:0.10, C:0.14, G:0.02, T:0.74
Consensus pattern (15 bp):
TTTTTTCATTCTCAT
Found at i:27393 original size:2 final size:2
Alignment explanation
Indices: 27388--27415 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
27378 TATATATATA
27388 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
27416 CATATGGGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:32270 original size:25 final size:25
Alignment explanation
Indices: 32228--32301 Score: 103
Period size: 25 Copynumber: 3.0 Consensus size: 25
32218 ACATTAAAAC
32228 CCTAACCACATGATATCTAGTTCAA
1 CCTAACCACATGATATCTAGTTCAA
* * * *
32253 CTTAATCGCATGATATCTAATTCAA
1 CCTAACCACATGATATCTAGTTCAA
*
32278 CCTAACCACATGATCTCTAGTTCA
1 CCTAACCACATGATATCTAGTTCA
32302 CATGCATTTA
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.34, C:0.27, G:0.08, T:0.31
Consensus pattern (25 bp):
CCTAACCACATGATATCTAGTTCAA
Found at i:35643 original size:2 final size:2
Alignment explanation
Indices: 35636--35693 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
35626 TTTATTTACT
35636 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35678 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
35694 AGTAGGACAC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:38178 original size:6 final size:6
Alignment explanation
Indices: 38162--38304 Score: 65
Period size: 6 Copynumber: 24.5 Consensus size: 6
38152 GAACCCCCCC
* *
38162 TTTTC- TTTTCT TTTTC- -TCTCT TTTTC- TTTTCT TCTTCT TTTTC-
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
* * * *
38205 -TTCCAT TTTTCTT TTTTCT TATTCT TATTCT TATTC- -TTT-T TTTTCT
1 TTTTC-T TTTTC-T TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
* * *
38251 TATTCTT TTTTCT TTTT-T TCTCTCTCT CTTT-T ATTTCT TTTTCTT TTTTCT
1 TTTTC-T TTTTCT TTTTCT T-T-T-TCT TTTTCT TTTTCT TTTTC-T TTTTCT
38302 TTT
1 TTT
38305 CTCATCTTCA
Statistics
Matches: 107, Mismatches: 14, Indels: 33
0.69 0.09 0.21
Matches are distributed among these distances:
4 8 0.07
5 19 0.18
6 55 0.51
7 22 0.21
8 2 0.02
9 1 0.01
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.76
Consensus pattern (6 bp):
TTTTCT
Found at i:38185 original size:15 final size:14
Alignment explanation
Indices: 38164--38304 Score: 73
Period size: 15 Copynumber: 9.9 Consensus size: 14
38154 ACCCCCCCTT
38164 TTCTTTTCTTTTTC
1 TTCTTTTCTTTTTC
38178 TCTCTTTT-TCTTTTC
1 T-TCTTTTCT-TTTTC
38193 TTC--TTCTTTTTC
1 TTCTTTTCTTTTTC
38205 TTCCATTTT-TCTTTT-
1 TT-C-TTTTCT-TTTTC
*
38220 TTCTTATTCTTATTC
1 TTCTT-TTCTTTTTC
* *
38235 -T-TATTCTTTTTT
1 TTCTTTTCTTTTTC
38247 TTCTTATTCTTTTTTC
1 TTCTT-TTC-TTTTTC
* *
38263 TTTTTTTCTCTCTCTC
1 TTCTTTTCT-T-TTTC
*
38279 TTTTATTTCTTTTTC
1 TTCT-TTTCTTTTTC
38294 TT-TTTTCTTTT
1 TTCTTTTCTTTT
38305 CTCATCTTCA
Statistics
Matches: 100, Mismatches: 9, Indels: 37
0.68 0.06 0.25
Matches are distributed among these distances:
12 16 0.16
13 14 0.14
14 14 0.14
15 28 0.28
16 23 0.23
17 5 0.05
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.76
Consensus pattern (14 bp):
TTCTTTTCTTTTTC
Found at i:38187 original size:21 final size:20
Alignment explanation
Indices: 38162--38297 Score: 93
Period size: 21 Copynumber: 6.5 Consensus size: 20
38152 GAACCCCCCC
38162 TTTTCTTTTCTTTTTCTCTCT
1 TTTTCTTTTCTTTTTCT-TCT
*
38183 TTTTCTTTTCTTCTTCTT-T
1 TTTTCTTTTCTTTTTCTTCT
38202 TTCTTCCATTTT-TCTTTT-TTCT
1 TT-TT-C-TTTTCT-TTTTCTTCT
* * *
38224 TATTCTTATTCTTATTCTTTT
1 TTTTCTT-TTCTTTTTCTTCT
38245 TTTTCTTATTCTTTTTTCTT-T
1 TTTTCTT-TTC-TTTTTCTTCT
38266 TTTTCTCTCTCTCTTTTAT-TTCT
1 TTTTCT-T-T-TCTTTT-TCTTCT
38289 TTTTCTTTT
1 TTTTCTTTT
38298 TTCTTTTCTC
Statistics
Matches: 94, Mismatches: 8, Indels: 27
0.73 0.06 0.21
Matches are distributed among these distances:
19 5 0.05
20 10 0.11
21 44 0.47
22 25 0.27
23 10 0.11
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTTCTTTTCTTTTTCTTCT
Found at i:38213 original size:27 final size:28
Alignment explanation
Indices: 38161--38260 Score: 93
Period size: 27 Copynumber: 3.6 Consensus size: 28
38151 TGAACCCCCC
38161 CTTTTCTT-TTCTTTTTCTCTC-TTTTT
1 CTTTTCTTCTTCTTTTTCTCTCATTTTT
38187 CTTTTCTTCTTCTTTTTCT-TCCATTTTT
1 CTTTTCTTCTTCTTTTTCTCT-CATTTTT
* *
38215 CTTTT-TTCTTATTCTTAT-TCTTATTCTTT
1 CTTTTCTTCTTCTT-TT-TCTCTCATT-TTT
* *
38244 TTTTTCTTATTCTTTTT
1 CTTTTCTTCTTCTTTTT
38261 TCTTTTTTTC
Statistics
Matches: 61, Mismatches: 5, Indels: 14
0.76 0.06 0.17
Matches are distributed among these distances:
26 9 0.15
27 18 0.30
28 17 0.28
29 11 0.18
30 6 0.10
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.75
Consensus pattern (28 bp):
CTTTTCTTCTTCTTTTTCTCTCATTTTT
Found at i:38242 original size:36 final size:37
Alignment explanation
Indices: 38173--38242 Score: 99
Period size: 36 Copynumber: 1.9 Consensus size: 37
38163 TTTCTTTTCT
* *
38173 TTTTCTCTCTTTTTCTTTTCTTCTTCTTTTTCTTCCA
1 TTTTCTCTCTTTTTCTTTTCTTATTCTTATTCTTCCA
38210 TTTT-TCT-TTTTTCTTATTCTTATTCTTATTCTT
1 TTTTCTCTCTTTTTCTT-TTCTTATTCTTATTCTT
38243 TTTTTTCTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
35 8 0.27
36 18 0.60
37 4 0.13
ACGTcount: A:0.06, C:0.21, G:0.00, T:0.73
Consensus pattern (37 bp):
TTTTCTCTCTTTTTCTTTTCTTATTCTTATTCTTCCA
Found at i:38280 original size:23 final size:23
Alignment explanation
Indices: 38212--38304 Score: 70
Period size: 25 Copynumber: 4.0 Consensus size: 23
38202 TTCTTCCATT
*
38212 TTTC-TTTTTTCTTATTCTTATTCT
1 TTTCTTTTTTTCTTATTCTT-TT-A
38236 TATTCTTTTTTTTCTTATTC-TTT-
1 T-TTC-TTTTTTTCTTATTCTTTTA
*
38259 TTTCTTTTTTTCTCTCTCTCTTTTA
1 TTTCTTTTTTTCT-TAT-TCTTTTA
38284 TTTCTTTTTCTT-TT-TTCTTTT
1 TTTCTTTTT-TTCTTATTCTTTT
38305 CTCATCTTCA
Statistics
Matches: 60, Mismatches: 1, Indels: 18
0.76 0.01 0.23
Matches are distributed among these distances:
21 9 0.15
22 11 0.18
23 4 0.07
24 5 0.08
25 15 0.25
26 3 0.05
27 13 0.22
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.77
Consensus pattern (23 bp):
TTTCTTTTTTTCTTATTCTTTTA
Found at i:44529 original size:21 final size:22
Alignment explanation
Indices: 44503--44546 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
44493 AAATTTTAAA
*
44503 TTTTAAATT-TTAATAAAGATT
1 TTTTAAATTATCAATAAAGATT
44524 TTTTAAATTATCAATAAAGATT
1 TTTTAAATTATCAATAAAGATT
44546 T
1 T
44547 AAATTTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (22 bp):
TTTTAAATTATCAATAAAGATT
Found at i:47585 original size:60 final size:60
Alignment explanation
Indices: 47511--47635 Score: 196
Period size: 60 Copynumber: 2.1 Consensus size: 60
47501 CAGCCTTTGA
* * ** *
47511 TTGGTGATTGGGGTGGCTGCTATCATAGAGTTTAGGTTTATACCCGGGTCGGGTTTAATT
1 TTGGTGATTAGGGTGGCTGCTATCATAGAGTTTAGGTTTAGACCCAAGTCGGGTCTAATT
*
47571 TTGGTGATTAGGGTGGCTGCTATCGTAGAGTTTAGGTTTAGACCCAAGTCGGGTCTAATT
1 TTGGTGATTAGGGTGGCTGCTATCATAGAGTTTAGGTTTAGACCCAAGTCGGGTCTAATT
47631 TTGGT
1 TTGGT
47636 TTTGGGTCGG
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.18, C:0.12, G:0.33, T:0.38
Consensus pattern (60 bp):
TTGGTGATTAGGGTGGCTGCTATCATAGAGTTTAGGTTTAGACCCAAGTCGGGTCTAATT
Found at i:58097 original size:21 final size:20
Alignment explanation
Indices: 58053--58114 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
58043 TTAACAATTA
* *
58053 TTTCGAAACTAGAGAC-ATAG
1 TTTCGAAACTCGA-ACTAAAG
*
58073 TTTCGAAACTCTAACTTAAAG
1 TTTCGAAACTCGAAC-TAAAG
*
58094 TTTCGAAATTCGAACTAAAG
1 TTTCGAAACTCGAACTAAAG
58114 T
1 T
58115 ATCAAAATCA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 2 0.06
20 17 0.49
21 16 0.46
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.31
Consensus pattern (20 bp):
TTTCGAAACTCGAACTAAAG
Found at i:58114 original size:20 final size:21
Alignment explanation
Indices: 58071--58114 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
58061 CTAGAGACAT
*
58071 AGTTTCGAAACTCTAACTTAA
1 AGTTTCGAAACTCGAACTTAA
*
58092 AGTTTCGAAATTCGAAC-TAA
1 AGTTTCGAAACTCGAACTTAA
58112 AGT
1 AGT
58115 ATCAAAATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.32
Consensus pattern (21 bp):
AGTTTCGAAACTCGAACTTAA
Found at i:74014 original size:18 final size:17
Alignment explanation
Indices: 73960--74008 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
73950 GTTGGACCTT
* *
73960 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
73978 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
73996 AGTGCATTCGATG
1 AGTGCA-TCGATG
74009 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:74494 original size:16 final size:16
Alignment explanation
Indices: 74473--74512 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
74463 CCCCTTACTA
74473 TAACACTTCTCCCCTT
1 TAACACTTCTCCCCTT
74489 TAACACTTCTCCCCTT
1 TAACACTTCTCCCCTT
74505 TAACACTT
1 TAACACTT
74513 AATATTCTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.23, C:0.40, G:0.00, T:0.38
Consensus pattern (16 bp):
TAACACTTCTCCCCTT
Done.