Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003764.1 Hibiscus syriacus cultivar Beakdansim tig00008064_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: 72945
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:7741 original size:46 final size:43
Alignment explanation
Indices: 7668--7754 Score: 102
Period size: 46 Copynumber: 2.0 Consensus size: 43
7658 AATATTACGC
*
7668 TTAGGATGAAAACCCGAAAACGTGCCCTAAGTAGAAAAAAAAACGT
1 TTAGGATGAAAACCCGAAAACGCGCCCT-AG-A-AAAAAAAAACGT
* * **
7714 TTAGGGTGAAAACCTGAAAGGGCGCCCTAGAAAAAAAAAAC
1 TTAGGATGAAAACCCGAAAACGCGCCCTAGAAAAAAAAAAC
7755 AAAAAAGTGG
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
43 10 0.28
44 1 0.03
45 2 0.06
46 23 0.64
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (43 bp):
TTAGGATGAAAACCCGAAAACGCGCCCTAGAAAAAAAAAACGT
Found at i:8551 original size:106 final size:105
Alignment explanation
Indices: 8360--8973 Score: 996
Period size: 106 Copynumber: 5.8 Consensus size: 105
8350 GAAATCTTCA
* *
8360 AACTTACCAATTTCAGAGCCAATTTCAACTTTACAGCGAAGGATATTGGACTCCAGACAACGCAA
1 AACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAA
*
8425 GTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAATAAAC
66 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA-AAAC
* *
8466 AATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAA
1 AACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAA
8531 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAAC
66 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA-AAAC
*
8572 AACTCCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAA
1 AACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAA
* *
8637 GTTCAACTTCACGACGAAGGGACCGCTAGTTGTCAACAAC
66 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAAAAC
* * *
8677 AACTTCCCAATTTCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGGACTCTAAGACAACACA
1 AACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC-CAGACAACGCA
* * *
8742 AGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACAAT
65 AGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAAAAC
*
8783 AACTTCCCAATTTTAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAA
1 AACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAA
*
8848 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAC
66 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAAAAC
** * *
8888 AAAATCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAGCACAA
1 AACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAA
*
8953 GCTCAACTTCAC-AGCGAAGGG
66 GTTCAACTTCACGA-CGAAGGG
8974 GCGGCTGACT
Statistics
Matches: 477, Mismatches: 29, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
104 1 0.00
105 180 0.38
106 296 0.62
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (105 bp):
AACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAA
GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAAAAC
Found at i:8833 original size:211 final size:211
Alignment explanation
Indices: 8360--8973 Score: 1016
Period size: 211 Copynumber: 2.9 Consensus size: 211
8350 GAAATCTTCA
* *
8360 AACTTACCAATTTCAGAGCCAATTTCAACTTTACAGCGAAGGATATTGGACTCCAGACAACGCAA
1 AACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAA
* * *
8425 GTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATT
66 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA-CAACAAATTCCCAATTTCAGAGCCAATT
* *
8490 TCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACC
130 TCAACTTCACAGCGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACC
8555 GCTGGTTGTCAATAAAC
195 GCTGGTTGTCAATAAAC
*
8572 AACTCCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAA
1 AACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAA
* *
8637 GTTCAACTTCACGACGAAGGGACCGCTAGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTT
66 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAAATTCCCAATTTCAGAGCCAATTT
* * *
8702 TAACTTCACAGCGAAGGATATTGGACTCTAAGACAACACAAGTTCAACTTCACGATGAAGGGACC
131 CAACTTCACAGCGAAGGATATTGGACTC-CAGACAACACAAGTTCAACTTCACGACGAAGGGACC
* *
8767 GCTGGTTGTCAA-CAAT
195 GCTGGTTGTCAATAAAC
*
8783 AACTTCCCAATTTTAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAA
1 AACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAA
*
8848 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAAAATCCCAATTTCAGAGCCAATTT
66 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAAATTCCCAATTTCAGAGCCAATTT
* *
8913 CAACTTCACAGCGAAGGATATTGGACTCCAGACAGCACAAGCTCAACTTCAC-AGCGAAGGG
131 CAACTTCACAGCGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGA-CGAAGGG
8974 GCGGCTGACT
Statistics
Matches: 376, Mismatches: 24, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
209 1 0.00
210 27 0.07
211 207 0.55
212 141 0.38
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (211 bp):
AACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAA
GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAAATTCCCAATTTCAGAGCCAATTT
CAACTTCACAGCGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCG
CTGGTTGTCAATAAAC
Found at i:10010 original size:23 final size:23
Alignment explanation
Indices: 9980--10023 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
9970 TGATTTTATT
9980 CTAATTAACAGATAAATTACACA
1 CTAATTAACAGATAAATTACACA
* *
10003 CTAATTAATAGATAATTTACA
1 CTAATTAACAGATAAATTACA
10024 GTCAATGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.50, C:0.14, G:0.05, T:0.32
Consensus pattern (23 bp):
CTAATTAACAGATAAATTACACA
Found at i:12443 original size:28 final size:28
Alignment explanation
Indices: 12411--12469 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
12401 GATCCTATAA
12411 TATGTGTTAAAATTTGTTATCAAAATTT
1 TATGTGTTAAAATTTGTTATCAAAATTT
* * *
12439 TATGTGTTAGAATTTGTTATGAAATTTT
1 TATGTGTTAAAATTTGTTATCAAAATTT
12467 TAT
1 TAT
12470 ATGAACCTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.02, G:0.14, T:0.53
Consensus pattern (28 bp):
TATGTGTTAAAATTTGTTATCAAAATTT
Found at i:16132 original size:14 final size:14
Alignment explanation
Indices: 16113--16142 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
16103 TTGATCTTTT
16113 AAGTTTTATTAAGA
1 AAGTTTTATTAAGA
16127 AAGTTTTATTAAGA
1 AAGTTTTATTAAGA
16141 AA
1 AA
16143 CTCAATGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.40
Consensus pattern (14 bp):
AAGTTTTATTAAGA
Found at i:16797 original size:33 final size:32
Alignment explanation
Indices: 16760--16847 Score: 95
Period size: 33 Copynumber: 2.7 Consensus size: 32
16750 GGGTCGAGTT
16760 AAATTTGGTTCAGTTTTCTTTCAGATCGGGTTA
1 AAATTTGGTTCAG-TTTCTTTCAGATCGGGTTA
* * * *
16793 AAATTTGGTTCGGGTTTCTTTCGGTTCTGGTTA
1 AAATTTGGTTC-AGTTTCTTTCAGATCGGGTTA
* *
16826 AAATCTGATTCGAGTTTCTTTC
1 AAATTTGGTTC-AGTTTCTTTC
16848 GGTTTGGGTT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
33 46 0.98
34 1 0.02
ACGTcount: A:0.18, C:0.14, G:0.22, T:0.47
Consensus pattern (32 bp):
AAATTTGGTTCAGTTTCTTTCAGATCGGGTTA
Found at i:16848 original size:33 final size:33
Alignment explanation
Indices: 16774--16858 Score: 107
Period size: 33 Copynumber: 2.6 Consensus size: 33
16764 TTGGTTCAGT
* * * * *
16774 TTTCTTTCAGATCGGGTTAAAATTTGGTTCGGG
1 TTTCTTTCGGTTCGGGTTAAAATCTGATTCGAG
*
16807 TTTCTTTCGGTTCTGGTTAAAATCTGATTCGAG
1 TTTCTTTCGGTTCGGGTTAAAATCTGATTCGAG
*
16840 TTTCTTTCGGTTTGGGTTA
1 TTTCTTTCGGTTCGGGTTA
16859 TTTTTGGTTC
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.15, C:0.13, G:0.25, T:0.47
Consensus pattern (33 bp):
TTTCTTTCGGTTCGGGTTAAAATCTGATTCGAG
Found at i:16872 original size:16 final size:16
Alignment explanation
Indices: 16843--16888 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
16833 ATTCGAGTTT
*
16843 CTTTCGGTTTGGGTTA
1 CTTTTGGTTTGGGTTA
* * *
16859 TTTTTGGTTCGGGTTG
1 CTTTTGGTTTGGGTTA
16875 CTTTTGGTTTGGGT
1 CTTTTGGTTTGGGT
16889 CAATTTTAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.02, C:0.09, G:0.35, T:0.54
Consensus pattern (16 bp):
CTTTTGGTTTGGGTTA
Found at i:16895 original size:16 final size:16
Alignment explanation
Indices: 16848--16913 Score: 60
Period size: 16 Copynumber: 4.1 Consensus size: 16
16838 AGTTTCTTTC
*
16848 GGTTTGGGTTATTTTT
1 GGTTTGGGTTAATTTT
* **
16864 GGTTCGGGTTGCTTTT
1 GGTTTGGGTTAATTTT
*
16880 GGTTTGGGTCAATTTT
1 GGTTTGGGTTAATTTT
** *
16896 AATTTAGGTTAATTTT
1 GGTTTGGGTTAATTTT
16912 GG
1 GG
16914 ATGGGGTTGT
Statistics
Matches: 37, Mismatches: 13, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.12, C:0.05, G:0.30, T:0.53
Consensus pattern (16 bp):
GGTTTGGGTTAATTTT
Found at i:20662 original size:20 final size:20
Alignment explanation
Indices: 20639--20708 Score: 113
Period size: 20 Copynumber: 3.5 Consensus size: 20
20629 GCAAAAATAG
**
20639 ATTTTGAAAATCAAAATTTA
1 ATTTTGAAAATCAAAATGAA
20659 ATTTTGAAAATCAAAATGAA
1 ATTTTGAAAATCAAAATGAA
*
20679 ATTTTTAAAATCAAAATGAA
1 ATTTTGAAAATCAAAATGAA
20699 ATTTTGAAAA
1 ATTTTGAAAA
20709 ATGATTTAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.53, C:0.04, G:0.07, T:0.36
Consensus pattern (20 bp):
ATTTTGAAAATCAAAATGAA
Found at i:22168 original size:21 final size:20
Alignment explanation
Indices: 22135--22173 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
22125 AAATATTTGA
*
22135 AAAAAGATTGATCCCTTTGGT
1 AAAAAGATCGAT-CCTTTGGT
*
22156 AAAAGGATCGATCCTTTG
1 AAAAAGATCGATCCTTTG
22174 TGCCTTAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (20 bp):
AAAAAGATCGATCCTTTGGT
Found at i:23665 original size:40 final size:39
Alignment explanation
Indices: 23577--23665 Score: 92
Period size: 40 Copynumber: 2.2 Consensus size: 39
23567 TTTATGAATT
*
23577 TAATATTAATAAAATATTTTAATATCATTTTAATCAAAA
1 TAATATTATTAAAATATTTTAATATCATTTTAATCAAAA
* * *
23616 TATTAATTATTAAAATATATTTATTAAT-ATTTCTAAT-AATA
1 TAAT-ATTATTAAAATAT-TTTAAT-ATCATTT-TAATCAAAA
23657 TAATATTAT
1 TAATATTAT
23666 ATTTTTAATA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
39 3 0.07
40 17 0.41
41 15 0.37
42 6 0.15
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (39 bp):
TAATATTATTAAAATATTTTAATATCATTTTAATCAAAA
Found at i:23667 original size:22 final size:23
Alignment explanation
Indices: 23637--23683 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
23627 AAAATATATT
23637 TATTAATATTTCTAATAATATAA
1 TATTAATATTTCTAATAATATAA
* *
23660 TATT-ATATTTTTAATATTATAA
1 TATTAATATTTCTAATAATATAA
23682 TA
1 TA
23684 AAATAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TATTAATATTTCTAATAATATAA
Found at i:23882 original size:23 final size:23
Alignment explanation
Indices: 23863--23907 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
23853 AGTAATATTT
23863 TAATAAATATATTTAAAATATAC
1 TAATAAATATATTTAAAATATAC
* *
23886 TAATTAATATTTTTAAAATATA
1 TAATAAATATATTTAAAATATA
23908 ATATAACACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
TAATAAATATATTTAAAATATAC
Found at i:27096 original size:2 final size:2
Alignment explanation
Indices: 27089--27149 Score: 113
Period size: 2 Copynumber: 30.5 Consensus size: 2
27079 GAATGTACAA
*
27089 AG AG AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
27131 AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG A
27150 AGGAATTAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:33129 original size:52 final size:52
Alignment explanation
Indices: 33051--33153 Score: 197
Period size: 52 Copynumber: 2.0 Consensus size: 52
33041 TTATAATATT
33051 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGC
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGC
*
33103 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTTTCCTATTTCTATG
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATG
33154 TGTCCAATTT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.42
Consensus pattern (52 bp):
CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGC
Found at i:37685 original size:52 final size:52
Alignment explanation
Indices: 37607--37709 Score: 197
Period size: 52 Copynumber: 2.0 Consensus size: 52
37597 TTATAATATT
37607 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGC
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGC
*
37659 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTTTCCTATTTCTATG
1 CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATG
37710 TGTCCAATTT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.42
Consensus pattern (52 bp):
CTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTCTATGC
Found at i:38818 original size:21 final size:21
Alignment explanation
Indices: 38789--38829 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
38779 ATAAATAATT
38789 TATTATTAAATAATTTAAATA
1 TATTATTAAATAATTTAAATA
*
38810 TATTTTTAAATAATTTAAAT
1 TATTATTAAATAATTTAAAT
38830 TAAATATAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TATTATTAAATAATTTAAATA
Found at i:39597 original size:23 final size:23
Alignment explanation
Indices: 39571--39634 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 23
39561 TAAGCTATTA
*
39571 AAAGGCAGAGAAAAATGTGTCAC
1 AAAGGCAGAGAAAAATGTGCCAC
* * * *
39594 AAAGGTAGAGATAAACGTGCCAT
1 AAAGGCAGAGAAAAATGTGCCAC
* *
39617 AAACGCAGAGAAACATGT
1 AAAGGCAGAGAAAAATGT
39635 CACATTAGAC
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.47, C:0.14, G:0.25, T:0.14
Consensus pattern (23 bp):
AAAGGCAGAGAAAAATGTGCCAC
Found at i:43671 original size:104 final size:104
Alignment explanation
Indices: 43546--43753 Score: 380
Period size: 104 Copynumber: 2.0 Consensus size: 104
43536 ATATCTGCAT
43546 GTATTAAAGTATTAACGCGATACTATCACATATAATGAAACGAGGAAATAATTAAGAATAAATTT
1 GTATTAAAGTATTAACGCGATACTATCACATATAATGAAACGAGGAAATAATTAAGAATAAATTT
*
43611 TAATATTATATTTTTAATTATTGTAAAGTTGCTTTGTAA
66 TAATAATATATTTTTAATTATTGTAAAGTTGCTTTGTAA
* *
43650 GTATTAAAGTATTAACGCGATACTATCACATATAATGAAATGAGGAAATAATTGAGAATAAATTT
1 GTATTAAAGTATTAACGCGATACTATCACATATAATGAAACGAGGAAATAATTAAGAATAAATTT
*
43715 TAATAATATATTTTTAATTATTGTAAATTTGCTTTGTAA
66 TAATAATATATTTTTAATTATTGTAAAGTTGCTTTGTAA
43754 CAAGAGTTTA
Statistics
Matches: 100, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
104 100 1.00
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.39
Consensus pattern (104 bp):
GTATTAAAGTATTAACGCGATACTATCACATATAATGAAACGAGGAAATAATTAAGAATAAATTT
TAATAATATATTTTTAATTATTGTAAAGTTGCTTTGTAA
Found at i:51724 original size:17 final size:17
Alignment explanation
Indices: 51702--51745 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
51692 ACACATTTGG
*
51702 TTCTTTTTATTTACAT-A
1 TTCTTTTAATTTA-ATCA
51719 TTCTTTTAATTTAATCA
1 TTCTTTTAATTTAATCA
51736 TTCTTTTAAT
1 TTCTTTTAAT
51746 AAATTAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 2 0.08
17 23 0.92
ACGTcount: A:0.25, C:0.11, G:0.00, T:0.64
Consensus pattern (17 bp):
TTCTTTTAATTTAATCA
Found at i:51848 original size:19 final size:18
Alignment explanation
Indices: 51813--51860 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
51803 GAGGACTAAC
* *
51813 TTTATTTTAATTAATATT
1 TTTATTTTAACTAATATA
51831 TTTATTTTAAGCTAATATA
1 TTTATTTTAA-CTAATATA
51850 TTTATTATTAA
1 TTTATT-TTAA
51861 TTTAATTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 10 0.38
19 12 0.46
20 4 0.15
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (18 bp):
TTTATTTTAACTAATATA
Found at i:51905 original size:21 final size:22
Alignment explanation
Indices: 51861--51914 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
51851 TTATTATTAA
*
51861 TTTA-ATTTAAAAATACTTTAT
1 TTTATATTTAAAAATACTATAT
* *
51882 TTTTTATTTAAACATA-TATAT
1 TTTATATTTAAAAATACTATAT
*
51903 TTTATGTTTAAA
1 TTTATATTTAAA
51915 TATTTTGAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 17 0.63
22 10 0.37
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.56
Consensus pattern (22 bp):
TTTATATTTAAAAATACTATAT
Found at i:52159 original size:31 final size:31
Alignment explanation
Indices: 52121--52184 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
52111 TGATGACCAC
52121 ATCTTAATTAAATAAAAAAGAAAGTGATCAT
1 ATCTTAATTAAATAAAAAAGAAAGTGATCAT
*
52152 ATCTTAATTAAATAAAAATGAAAGTGATCAT
1 ATCTTAATTAAATAAAAAAGAAAGTGATCAT
52183 AT
1 AT
52185 ATTATGGTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.53, C:0.06, G:0.09, T:0.31
Consensus pattern (31 bp):
ATCTTAATTAAATAAAAAAGAAAGTGATCAT
Found at i:55192 original size:31 final size:31
Alignment explanation
Indices: 55157--55247 Score: 72
Period size: 31 Copynumber: 3.1 Consensus size: 31
55147 ATTTTAAATT
55157 TTAAATGAGTGATTGTGATTAAATCGAATAA
1 TTAAATGAGTGATTGTGATTAAATCGAATAA
* *
55188 TTAAA--A-T-ATT-T--TTAAAATTCAAAT-G
1 TTAAATGAGTGATTGTGATT-AAA-TCGAATAA
*
55213 TTAAATGAGTGACTGTGATTAAATCGAAATAA
1 TTAAATGAGTGATTGTGATTAAATCG-AATAA
55245 TTA
1 TTA
55248 TTGTTTCGTA
Statistics
Matches: 44, Mismatches: 5, Indels: 21
0.63 0.07 0.30
Matches are distributed among these distances:
24 2 0.05
25 8 0.18
26 6 0.14
27 4 0.09
28 2 0.05
29 3 0.07
30 3 0.07
31 11 0.25
32 5 0.11
ACGTcount: A:0.44, C:0.04, G:0.14, T:0.37
Consensus pattern (31 bp):
TTAAATGAGTGATTGTGATTAAATCGAATAA
Found at i:55462 original size:21 final size:20
Alignment explanation
Indices: 55416--55463 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 20
55406 TTAGTATAAA
* *
55416 TATAATTTAAATGCTATATT
1 TATAATTTAAATACTATATC
* *
55436 TTTAATTTACAATATTATATC
1 TATAATTTA-AATACTATATC
55457 TATAATT
1 TATAATT
55464 AATATTTTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.52
Consensus pattern (20 bp):
TATAATTTAAATACTATATC
Found at i:59693 original size:14 final size:15
Alignment explanation
Indices: 59674--59702 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
59664 CCAATTAACA
59674 AATTAAAA-ATAAAT
1 AATTAAAATATAAAT
59688 AATTAAAATATAAAT
1 AATTAAAATATAAAT
59703 TATTTATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AATTAAAATATAAAT
Found at i:69450 original size:21 final size:21
Alignment explanation
Indices: 69424--69498 Score: 98
Period size: 21 Copynumber: 3.6 Consensus size: 21
69414 GCGAATAAGT
69424 AATCGCAACGCGAATTGGGAA
1 AATCGCAACGCGAATTGGGAA
* ** *
69445 AATCGCAATGCGAA-TAAGTA
1 AATCGCAACGCGAATTGGGAA
69465 AATCGCAACGCGAATTGGGAA
1 AATCGCAACGCGAATTGGGAA
*
69486 AATCGCAATGCGA
1 AATCGCAACGCGA
69499 TACTGACTAT
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.36
21 28 0.64
ACGTcount: A:0.40, C:0.19, G:0.25, T:0.16
Consensus pattern (21 bp):
AATCGCAACGCGAATTGGGAA
Found at i:69451 original size:40 final size:41
Alignment explanation
Indices: 69407--69498 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
69397 TTTTCCCAAT
69407 TCGCAATGCGAATAAGT-AATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
69447 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
69488 TCGCAATGCGA
1 TCGCAATGCGA
69499 TACTGACTAT
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
40 17 0.33
41 34 0.67
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:69511 original size:41 final size:41
Alignment explanation
Indices: 69425--69621 Score: 143
Period size: 41 Copynumber: 4.8 Consensus size: 41
69415 CGAATAAGTA
* *
69425 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGATATT-GGAAAATCGCAATGCG-ATACTG-ACT
69466 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGATATT-GGAAAATCGCAATGCGATACTGACT
* * ** * * *
69507 ATCGCAATGCGATAATACAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGATATTGGAAAATCGCAATGCGATACTGACT
* * *** *
69548 TTCGCAACGCGATACT-GACTTTCGCAATGCGATTCTGACT
1 ATCGCAACGCGATATTGGAAAATCGCAATGCGATACTGACT
* * ** *
69588 TTCGCAACGCGATAATACATAATCGCAATGCGAT
1 ATCGCAACGCGATATTGGAAAATCGCAATGCGAT
69622 TTTCAAAGCG
Statistics
Matches: 127, Mismatches: 25, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
40 35 0.28
41 90 0.71
42 2 0.02
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.22
Consensus pattern (41 bp):
ATCGCAACGCGATATTGGAAAATCGCAATGCGATACTGACT
Found at i:69512 original size:20 final size:20
Alignment explanation
Indices: 69487--69621 Score: 112
Period size: 20 Copynumber: 6.7 Consensus size: 20
69477 AATTGGGAAA
69487 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
69507 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* * *
69528 ATCGCAACGAGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
69548 TTCGCAACGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
69568 TTCGCAATGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* * *
69588 TTCGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
69608 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
69622 TTTCAAAGCG
Statistics
Matches: 94, Mismatches: 16, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
19 4 0.04
20 64 0.68
21 24 0.26
22 2 0.02
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:69812 original size:22 final size:22
Alignment explanation
Indices: 69784--69827 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
69774 CACTCTCTCA
69784 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
69806 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
69828 TATCTCCATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.45, G:0.14, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:70121 original size:20 final size:20
Alignment explanation
Indices: 70067--70125 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
70057 GCGATTCTCT
**
70067 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
70087 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
70107 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
70126 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:71450 original size:16 final size:17
Alignment explanation
Indices: 71414--71455 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
71404 TCCACTTCGG
*
71414 GAGCCATCACCTCGCCA
1 GAGCCATCACCTCGACA
*
71431 GAGCTATCACCTC-ACA
1 GAGCCATCACCTCGACA
71447 GAGCCATCA
1 GAGCCATCA
71456 TCTGATCGAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 10 0.45
17 12 0.55
ACGTcount: A:0.29, C:0.40, G:0.17, T:0.14
Consensus pattern (17 bp):
GAGCCATCACCTCGACA
Found at i:71857 original size:18 final size:19
Alignment explanation
Indices: 71834--71872 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
71824 TGCTAAACTG
71834 TTTTGTTAGTATTTGT-TT
1 TTTTGTTAGTATTTGTCTT
* *
71852 TTTTGTTTGTTTTTGTCTT
1 TTTTGTTAGTATTTGTCTT
71871 TT
1 TT
71873 GGTTGAAGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.05, C:0.03, G:0.15, T:0.77
Consensus pattern (19 bp):
TTTTGTTAGTATTTGTCTT
Found at i:71984 original size:19 final size:20
Alignment explanation
Indices: 71930--71985 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
71920 TAGTTTACTT
* *
71930 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
71950 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
*
71970 TCGCAATGC-GAAATGA
1 TCGCAACGCGGAAATGA
71986 AAATTGCAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 6 0.19
20 25 0.81
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:72077 original size:14 final size:14
Alignment explanation
Indices: 72058--72114 Score: 60
Period size: 14 Copynumber: 3.8 Consensus size: 14
72048 TTGTGTTTCG
72058 CGTTGCGATTTTAT
1 CGTTGCGATTTTAT
*
72072 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TAT
*
72088 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTAT
72104 CGTTGCGATTT
1 CGTTGCGATTT
72115 CATTTCGTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 22 0.59
16 4 0.11
18 11 0.30
ACGTcount: A:0.11, C:0.18, G:0.25, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTAT
Found at i:72092 original size:32 final size:32
Alignment explanation
Indices: 72053--72130 Score: 129
Period size: 32 Copynumber: 2.4 Consensus size: 32
72043 GCGATTTGTG
72053 TTTCGCGTTGCGATTTTATCGTTGCGATTTCA
1 TTTCGCGTTGCGATTTTATCGTTGCGATTTCA
*
72085 TTTCGCGTTGCGATTTTGTCGTTGCGATTTCA
1 TTTCGCGTTGCGATTTTATCGTTGCGATTTCA
**
72117 TTTCGTATTGCGAT
1 TTTCGCGTTGCGAT
72131 AGCCATTTCC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.12, C:0.18, G:0.23, T:0.47
Consensus pattern (32 bp):
TTTCGCGTTGCGATTTTATCGTTGCGATTTCA
Found at i:72165 original size:19 final size:19
Alignment explanation
Indices: 72104--72168 Score: 71
Period size: 19 Copynumber: 3.5 Consensus size: 19
72094 GCGATTTTGT
*
72104 CGTTGCGAT-TTCATTTCG
1 CGTTGCGATAGTCATTTCG
** *
72122 TATTGCGATAGCCATTTC-
1 CGTTGCGATAGTCATTTCG
72140 CGCTTGCGATAGTCATTTCG
1 CG-TTGCGATAGTCATTTCG
72160 CGTTGCGAT
1 CGTTGCGAT
72169 TTTAAGTTTC
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
18 7 0.19
19 28 0.76
20 2 0.05
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.38
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Done.