Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005282.1 Hibiscus syriacus cultivar Beakdansim tig00011945_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: 98047
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:3524 original size:62 final size:63
Alignment explanation
Indices: 3330--3558 Score: 372
Period size: 63 Copynumber: 3.7 Consensus size: 63
3320 AGAGTCGAGG
* *
3330 GTATATCTATGTTCTAACGGAACATATGGACAGAATTACCTATGTCTTTCGAGAGATATGGACA
1 GTATACCTATGTTCT-ACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
*
3394 GTATACCTATGTTCTACGGAACATATGAACAGAATTACCTATGTCTTTCGAGACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
* *
3457 GTATACCTATGTTCTACGGAACATATGGACA-TATTACCTATGTCTTTCGAGACATATAGACA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
* *
3519 GTATACCTATGTTCTAAGGAACATATGGACAG-TTTACCTA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTA
3559 GGTTCTTCGG
Statistics
Matches: 156, Mismatches: 8, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
62 66 0.42
63 76 0.49
64 14 0.09
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (63 bp):
GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGAGACATATGGACA
Found at i:3564 original size:31 final size:31
Alignment explanation
Indices: 3336--3583 Score: 213
Period size: 31 Copynumber: 7.9 Consensus size: 31
3326 GAGGGTATAT
*
3336 CTATGTTCTAACGGAACATATGGACAGAATTAC
1 CTATGTTCT-ACGGAACATATGGACAG-TTTAC
* * *
3369 CTATG-TCTTTC-GAGAGATATGGACAGTATAC
1 CTATGTTC-TACGGA-ACATATGGACAGTTTAC
* *
3400 CTATGTTCTACGGAACATATGAACAGAATTAC
1 CTATGTTCTACGGAACATATGGACAG-TTTAC
* *
3432 CTATG-TCTTTC-GAGACATATGGACAGTATAC
1 CTATGTTC-TACGGA-ACATATGGACAGTTTAC
3463 CTATGTTCTACGGAACATATGGACA-TATTAC
1 CTATGTTCTACGGAACATATGGACAGT-TTAC
* * *
3494 CTATG-TCTTTC-GAGACATATAGACAGTATAC
1 CTATGTTC-TACGGA-ACATATGGACAGTTTAC
*
3525 CTATGTTCTAAGGAACATATGGACAGTTTAC
1 CTATGTTCTACGGAACATATGGACAGTTTAC
* * * *
3556 CTAGGTTCTTCGGAACCTATAGACAGTT
1 CTATGTTCTACGGAACATATGGACAGTT
3584 ACCGAGGATC
Statistics
Matches: 173, Mismatches: 27, Indels: 32
0.75 0.12 0.14
Matches are distributed among these distances:
30 5 0.03
31 114 0.66
32 48 0.28
33 6 0.03
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Consensus pattern (31 bp):
CTATGTTCTACGGAACATATGGACAGTTTAC
Found at i:5835 original size:18 final size:18
Alignment explanation
Indices: 5812--5904 Score: 87
Period size: 18 Copynumber: 4.9 Consensus size: 18
5802 ACTGAATATT
5812 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
5830 TGTCCCGAAGGACCACTGA
1 TGTCCCGAAGGACCACT-A
* * *
5849 TTGTTCCAAAGAACCACTA
1 -TGTCCCGAAGGACCACTA
* * *
5868 TGTCCCAAAAGACCACTGTT
1 TGTCCCGAAGGACCAC--TA
*
5888 TGTCTCGAAGGACCACT
1 TGTCCCGAAGGACCACT
5905 GATAATCCCT
Statistics
Matches: 61, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
18 31 0.51
19 2 0.03
20 28 0.46
ACGTcount: A:0.29, C:0.30, G:0.19, T:0.22
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:5903 original size:38 final size:38
Alignment explanation
Indices: 5810--5904 Score: 120
Period size: 38 Copynumber: 2.5 Consensus size: 38
5800 GCACTGAATA
* * *
5810 TTTGTCCCGAAGGACCACTATGTCCCGAAGGACCACTG
1 TTTGTCTCGAAGGACCACTATGTCCCAAAAGACCACTG
* * *
5848 ATTGT-TCCAAAGAACCACTATGTCCCAAAAGACCACTG
1 TTTGTCT-CGAAGGACCACTATGTCCCAAAAGACCACTG
5886 TTTGTCTCGAAGGACCACT
1 TTTGTCTCGAAGGACCACT
5905 GATAATCCCT
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
38 45 0.98
39 1 0.02
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.23
Consensus pattern (38 bp):
TTTGTCTCGAAGGACCACTATGTCCCAAAAGACCACTG
Found at i:6519 original size:21 final size:23
Alignment explanation
Indices: 6482--6537 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 23
6472 CTTAATTCAA
*
6482 TTTCATAT-ATTCTTATA-ACCT
1 TTTCATATAACTCTTATAGACCT
*
6503 TTTCATATAACTC-TATAGATCT
1 TTTCATATAACTCTTATAGACCT
*
6525 TTAGCATATAACT
1 TT-TCATATAACT
6538 TATCTTATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 12 0.41
22 8 0.28
23 9 0.31
ACGTcount: A:0.32, C:0.18, G:0.04, T:0.46
Consensus pattern (23 bp):
TTTCATATAACTCTTATAGACCT
Found at i:8408 original size:42 final size:42
Alignment explanation
Indices: 8310--8408 Score: 153
Period size: 42 Copynumber: 2.4 Consensus size: 42
8300 GTGATGGAAT
* * * *
8310 AGGTGATGGCTCTCAGTGTGAAGATGTATAATCGGCTCGATT
1 AGGTGATGGCTCTCGGTGTCAAGATGTAGAATCGGCTCGATC
*
8352 AGGTGATGGCTCTCGGTGTCAAGCTGTAGAATCGGCTCGATC
1 AGGTGATGGCTCTCGGTGTCAAGATGTAGAATCGGCTCGATC
8394 AGGTGATGGCTCTCG
1 AGGTGATGGCTCTCG
8409 AAGTGGGGGG
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.28
Consensus pattern (42 bp):
AGGTGATGGCTCTCGGTGTCAAGATGTAGAATCGGCTCGATC
Found at i:9915 original size:19 final size:20
Alignment explanation
Indices: 9867--9949 Score: 105
Period size: 20 Copynumber: 4.2 Consensus size: 20
9857 TTTGAAACTT
**
9867 AAATTCGCAACATGAAAATA
1 AAATTCGCAACGCGAAAATA
*
9887 AAATTCGCAACGCGAAAATC
1 AAATTCGCAACGCGAAAATA
*
9907 AAA-TCGCAACGCGAAAATG
1 AAATTCGCAACGCGAAAATA
* *
9926 AAATTCGCAACGTGAAACTA
1 AAATTCGCAACGCGAAAATA
9946 AAAT
1 AAAT
9950 CGCTTCGCGA
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
19 18 0.33
20 37 0.67
ACGTcount: A:0.49, C:0.19, G:0.14, T:0.17
Consensus pattern (20 bp):
AAATTCGCAACGCGAAAATA
Found at i:9959 original size:39 final size:39
Alignment explanation
Indices: 9866--9952 Score: 111
Period size: 39 Copynumber: 2.2 Consensus size: 39
9856 TTTTGAAACT
* **
9866 TAAATTCGCAACATGAAAATAAAATTCGCAACGCGAAAA
1 TAAAATCGCAACGCGAAAATAAAATTCGCAACGCGAAAA
* * * *
9905 TCAAATCGCAACGCGAAAATGAAATTCGCAACGTGAAAC
1 TAAAATCGCAACGCGAAAATAAAATTCGCAACGCGAAAA
9944 TAAAATCGC
1 TAAAATCGC
9953 TTCGCGATTT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.47, C:0.21, G:0.15, T:0.17
Consensus pattern (39 bp):
TAAAATCGCAACGCGAAAATAAAATTCGCAACGCGAAAA
Found at i:15579 original size:29 final size:29
Alignment explanation
Indices: 15501--15582 Score: 101
Period size: 29 Copynumber: 2.8 Consensus size: 29
15491 CAGTGGTCGT
* ** *
15501 AGGTCGCCATGCACTCCCAGCGACCTCCT
1 AGGTCGCCATGCACTCCCGGCGACCAACG
* *
15530 AGGTCGCCATGCACGCCCGGCGACCAAGG
1 AGGTCGCCATGCACTCCCGGCGACCAACG
*
15559 AGGTCGCCATGCACTCGCGGCGAC
1 AGGTCGCCATGCACTCCCGGCGAC
15583 ATCCCCTGCT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.18, C:0.40, G:0.29, T:0.12
Consensus pattern (29 bp):
AGGTCGCCATGCACTCCCGGCGACCAACG
Found at i:15852 original size:29 final size:29
Alignment explanation
Indices: 15797--15883 Score: 104
Period size: 29 Copynumber: 3.0 Consensus size: 29
15787 CATGCATGAA
*
15797 TCCTTGGTCGCC-CGAGTGCATGGCGACC
1 TCCTTGGTCGCCGGGAGTGCATGGCGACC
*
15825 TCCTTGGTCGCCGGGCGTGCATGGCGACC
1 TCCTTGGTCGCCGGGAGTGCATGGCGACC
**** *
15854 TAGGAGGTCGCTGGGAGTGCATGGCGACC
1 TCCTTGGTCGCCGGGAGTGCATGGCGACC
15883 T
1 T
15884 ATGTTGGGTT
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
28 12 0.24
29 38 0.76
ACGTcount: A:0.11, C:0.30, G:0.38, T:0.21
Consensus pattern (29 bp):
TCCTTGGTCGCCGGGAGTGCATGGCGACC
Found at i:17168 original size:23 final size:23
Alignment explanation
Indices: 17142--17201 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
17132 CGTGAATTCA
*
17142 GCTGTATTATTGCAACACTTATT
1 GCTGCATTATTGCAACACTTATT
* * *
17165 GCTGCATTATTACAGCCCTTATT
1 GCTGCATTATTGCAACACTTATT
17188 GCTGCATTATTGCA
1 GCTGCATTATTGCA
17202 CTCCTTCAAC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.23, C:0.22, G:0.15, T:0.40
Consensus pattern (23 bp):
GCTGCATTATTGCAACACTTATT
Found at i:17659 original size:27 final size:29
Alignment explanation
Indices: 17595--17659 Score: 73
Period size: 27 Copynumber: 2.3 Consensus size: 29
17585 TATATTAAAA
17595 AAATAATTAATTAGTGTGTTAGTTAGTCT
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
** *
17624 -AATTTTTAATTAGTTTG-TAGTTAGT-T
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
*
17650 AAATAGTTAA
1 AAATAATTAA
17660 GTTATATTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
26 1 0.03
27 15 0.50
28 14 0.47
ACGTcount: A:0.35, C:0.02, G:0.15, T:0.48
Consensus pattern (29 bp):
AAATAATTAATTAGTGTGTTAGTTAGTCT
Found at i:17844 original size:22 final size:23
Alignment explanation
Indices: 17809--17860 Score: 81
Period size: 22 Copynumber: 2.3 Consensus size: 23
17799 ACAAAAAATT
17809 AGTTA-ATTAGTTTGGTAGTTTA
1 AGTTATATTAGTTTGGTAGTTTA
*
17831 AGTTATATTA-TTTGTTAGTTTA
1 AGTTATATTAGTTTGGTAGTTTA
17853 AGTTATAT
1 AGTTATAT
17861 CATATAGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
22 24 0.86
23 4 0.14
ACGTcount: A:0.29, C:0.00, G:0.17, T:0.54
Consensus pattern (23 bp):
AGTTATATTAGTTTGGTAGTTTA
Found at i:18086 original size:29 final size:29
Alignment explanation
Indices: 18049--18126 Score: 97
Period size: 30 Copynumber: 2.6 Consensus size: 29
18039 TAGTAATAAA
18049 TTATAATTAAAAATCA-TTTATTAGTTTAA-G
1 TTAT-ATTAAAAAT-AGTTTATTAG-TTAACG
18079 TTATATTAAAAAATAGTTTATTAGTTAACG
1 TTATATT-AAAAATAGTTTATTAGTTAACG
18109 TTATATTAAAGAATAGTT
1 TTATATTAAA-AATAGTT
18127 AAAGTTATAT
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
29 11 0.25
30 33 0.75
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.45
Consensus pattern (29 bp):
TTATATTAAAAATAGTTTATTAGTTAACG
Found at i:18095 original size:22 final size:22
Alignment explanation
Indices: 18070--18150 Score: 72
Period size: 22 Copynumber: 3.3 Consensus size: 22
18060 AATCATTTAT
*
18070 TAGTTTAAGTTATATTAAAAAA
1 TAGTTTAAGTTATATTAAAGAA
18092 TAGTTTATTAGTTAACGTTATATTAAAGAA
1 TAGTTTA--AG-T----T-ATATTAAAGAA
*
18122 TAGTTAAAGTTATATTAAAGAA
1 TAGTTTAAGTTATATTAAAGAA
18144 TAGTTTA
1 TAGTTTA
18151 TTAGTTGTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
22 24 0.50
23 1 0.02
24 2 0.04
25 1 0.02
27 1 0.02
28 2 0.04
29 1 0.02
30 16 0.33
ACGTcount: A:0.44, C:0.01, G:0.12, T:0.42
Consensus pattern (22 bp):
TAGTTTAAGTTATATTAAAGAA
Found at i:18098 original size:320 final size:318
Alignment explanation
Indices: 17513--18101 Score: 775
Period size: 320 Copynumber: 1.8 Consensus size: 318
17503 TTGCTTGATG
* * * *
17513 GTTATATTATTGTTAGTTTAAGTTATATCATACATAAATATAAAATTATTTAATTAGTTTGTTTG
1 GTTATATTATTGTTAGTTTAAGTTATATCATACAGAAATAAAAAATTATTTAATTAGTATGTTTA
* * * * * * *
17578 ATGGTTATATATTAAAAAAATAATTAATTAGTGTGTTAGTTAGTCTAATTTTTAATTAGTTTGTA
66 ATAGTTACATATTAAAAAAATAATTAATTAGTGCGTTAGTTAATATAATATGTAATTAGTTTGTA
17643 GTTAGTTAAATAGTTAAGTTATATTTTGGTTGTTGAATTTATATTATATAAAAAAAGTAGTTAAT
131 GTTAGTTAAATAGTTAAGTTATATTTTGGTTGTTGAATTTATATTATATAAAAAAAGTAGTTAAT
* * ** *
17708 TAGTTTAAGTTATATAAAAGAATAATTATTTAAATTAGTTTATTGTTATAAATTATTAGCTAATT
196 TAGTTTAAGTTATATAAAAGAATAATTA-TAAAATCAGTTTATTGTTATAAATTATTAGAAAAAT
17773 AGTTTATTATTATAAATTAGGGTAAAACAAAAAATTAGTTAATTAGTTTGGTAGTTTAA
260 AGTTTATTATTATAAATTAGGGTAAAACAAAAAATTAGTTAATTAGTTTGGTAGTTTAA
*
17832 GTTATATTATTTGTTAGTTTAAGTTATATCATATAGAAATAAAAAATTATTTAATTAGTATGTTT
1 GTTATATTA-TTGTTAGTTTAAGTTATATCATACAGAAATAAAAAATTATTTAATTAGTATGTTT
*
17897 AATAGTTACATATTAATAAAAATAATTAGTTAGT-CGTTAGTTATATATAAAAAATATGTAATTA
65 AATAGTTACATATTAA-AAAAATAATTAATTAGTGCGTTAGTTA-ATAT----AATATGTAATTA
* *
17961 GTTTGT-GTTAGTTAAATAGTTAAGTTATA-TTTGTTTGTTGAATTTATATTATATAAAAAAATT
124 GTTTGTAGTTAGTTAAATAGTTAAGTTATATTTTGGTTGTTGAATTTATATTATATAAAAAAAGT
* ** *
18024 AGTTAATTAGTTT--TTTAGTA-ATAAATTATAATTA-AAAATCA-TTTATTAGTT-TAAGTTAT
189 AGTTAATTAGTTTAAGTTA-TATA-AAAGAATAATTATAAAATCAGTTTATT-GTTATAA-AT-T
18083 ATTA-AAAAATAGTTTATTA
249 ATTAGAAAAATAGTTTATTA
18102 GTTAACGTTA
Statistics
Matches: 234, Mismatches: 24, Indels: 23
0.83 0.09 0.08
Matches are distributed among these distances:
319 18 0.08
320 93 0.40
321 27 0.12
322 12 0.05
323 45 0.19
324 23 0.10
325 16 0.07
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.47
Consensus pattern (318 bp):
GTTATATTATTGTTAGTTTAAGTTATATCATACAGAAATAAAAAATTATTTAATTAGTATGTTTA
ATAGTTACATATTAAAAAAATAATTAATTAGTGCGTTAGTTAATATAATATGTAATTAGTTTGTA
GTTAGTTAAATAGTTAAGTTATATTTTGGTTGTTGAATTTATATTATATAAAAAAAGTAGTTAAT
TAGTTTAAGTTATATAAAAGAATAATTATAAAATCAGTTTATTGTTATAAATTATTAGAAAAATA
GTTTATTATTATAAATTAGGGTAAAACAAAAAATTAGTTAATTAGTTTGGTAGTTTAA
Found at i:20601 original size:59 final size:59
Alignment explanation
Indices: 20466--20601 Score: 147
Period size: 59 Copynumber: 2.3 Consensus size: 59
20456 AATATTTAGT
* * *
20466 AATTCGACTATTTTAAATCATTAGTATCAAATAATTAAATATTAATAATAAATCATTATT
1 AATTTGACTATTATAAATCATTAGTATCAAATAATTAAATATT-ATAATAAATCATTATA
* *
20526 AA--T-AATAATTAGTAAATCATTAGTATCAAATCATTAAATATT-TAA-AAATCATTAATA
1 AATTTGACT-ATTA-TAAATCATTAGTATCAAATAATTAAATATTATAATAAATCATT-ATA
20583 AATTTGACTATGTATAAAT
1 AATTTGACTAT-TATAAAT
20602 TTAAACTCGA
Statistics
Matches: 63, Mismatches: 6, Indels: 15
0.75 0.07 0.18
Matches are distributed among these distances:
56 8 0.13
57 9 0.14
58 3 0.05
59 37 0.59
60 6 0.10
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.40
Consensus pattern (59 bp):
AATTTGACTATTATAAATCATTAGTATCAAATAATTAAATATTATAATAAATCATTATA
Found at i:20743 original size:3 final size:3
Alignment explanation
Indices: 20728--20822 Score: 70
Period size: 3 Copynumber: 32.7 Consensus size: 3
20718 CTATTAAATC
* * * *
20728 ATT ATT ATC ATT ATT ATT ATT A-A ATT ATT ATT ATC ATC ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * * * *
20775 A-A ATC ATT ATT ATC ATT ATT ATT A-A ATC ATT ATT ATA ATG ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
20821 AT
1 AT
20823 CAAATCATTA
Statistics
Matches: 72, Mismatches: 17, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
2 3 0.04
3 69 0.96
ACGTcount: A:0.39, C:0.06, G:0.01, T:0.54
Consensus pattern (3 bp):
ATT
Found at i:20743 original size:26 final size:26
Alignment explanation
Indices: 20664--20930 Score: 225
Period size: 26 Copynumber: 10.6 Consensus size: 26
20654 ATTAGTAATA
*
20664 ATTATTAAATCATTAATATTAAATTATT
1 ATTATTAAATCATTATTA-T-AATTATT
* * *
20692 ATTATAAAATCATTACTA-AATAATT
1 ATTATTAAATCATTATTATAATTATT
* *
20717 ACTATTAAATCATTATTATCATTATT
1 ATTATTAAATCATTATTATAATTATT
* * *
20743 ATTATTAAATTATTATTATCATCATT
1 ATTATTAAATCATTATTATAATTATT
*
20769 ATTATTAAATCATTA-T-T-ATCATT
1 ATTATTAAATCATTATTATAATTATT
*
20792 ATTATTAAATCATTATTATAATGATT
1 ATTATTAAATCATTATTATAATTATT
* * * *
20818 ATTATCAAATCATTACTA-AATCATCAA
1 ATTATTAAATCATTATTATAATTAT--T
* *
20845 ATCATT-AA--A-TATT-TAA--ATC
1 ATTATTAAATCATTATTATAATTATT
*
20864 ATTATTAAATCATTATTATAATGATT
1 ATTATTAAATCATTATTATAATTATT
* *
20890 ATTACTAAATCATTATTATAATGATT
1 ATTATTAAATCATTATTATAATTATT
*
20916 ATTATCAAATCATTA
1 ATTATTAAATCATTA
20931 CTAAATCATC
Statistics
Matches: 199, Mismatches: 26, Indels: 30
0.78 0.10 0.12
Matches are distributed among these distances:
19 5 0.03
20 2 0.01
21 2 0.01
22 1 0.01
23 30 0.15
24 6 0.03
25 28 0.14
26 105 0.53
27 4 0.02
28 16 0.08
ACGTcount: A:0.44, C:0.09, G:0.01, T:0.46
Consensus pattern (26 bp):
ATTATTAAATCATTATTATAATTATT
Found at i:20745 original size:23 final size:23
Alignment explanation
Indices: 20689--20821 Score: 131
Period size: 23 Copynumber: 5.4 Consensus size: 23
20679 ATATTAAATT
* * *
20689 ATTATTATAAAATCATTACTAAATA
1 ATTATTATTAAATCATTA-T-TATC
*
20714 ATTACTATTAAATCATTATTATC
1 ATTATTATTAAATCATTATTATC
*
20737 ATTATTATTATTAAATTATTATTATCATC
1 ---ATTATTATTAAATCATTA-T-T-ATC
20766 ATTATTATTAAATCATTATTATC
1 ATTATTATTAAATCATTATTATC
*
20789 ATTATTATTAAATCATTATTATA
1 ATTATTATTAAATCATTATTATC
*
20812 ATGATTATTA
1 ATTATTATTA
20822 TCAAATCATT
Statistics
Matches: 93, Mismatches: 9, Indels: 14
0.80 0.08 0.12
Matches are distributed among these distances:
23 36 0.39
24 2 0.02
25 17 0.18
26 33 0.35
27 1 0.01
28 1 0.01
29 3 0.03
ACGTcount: A:0.42, C:0.08, G:0.01, T:0.50
Consensus pattern (23 bp):
ATTATTATTAAATCATTATTATC
Found at i:20832 original size:23 final size:23
Alignment explanation
Indices: 20681--21015 Score: 134
Period size: 26 Copynumber: 13.7 Consensus size: 23
20671 AATCATTAAT
* *
20681 ATTA-AATTATTATTATAAAATC
1 ATTATAATCATTATTATTAAATC
* *
20703 ATTACTAAATAATTACTATTAAATC
1 ATTA-T-AATCATTATTATTAAATC
* *
20728 ATTATTATCATTATTATTATTAAATT
1 ATTA-TA--ATCATTATTATTAAATC
20754 ATTATTATCATCATTATTATTAAATC
1 ATTA-TA--ATCATTATTATTAAATC
*
20780 ATTATTATCATTATTATTAAATC
1 ATTATAATCATTATTATTAAATC
* *
20803 ATTATTATAATGATTATTATCAAATC
1 ---ATTATAATCATTATTATTAAATC
* *
20829 ATTACTAAATCATCAAATCATTAAAT-
1 ATTA-T-AATCAT--TATTATTAAATC
*
20855 ATT-TAAATCATTATTA--AATCATT
1 ATTAT-AATCATTATTATTAA--ATC
* *
20878 ATTATAATGATTATTACTAAATC
1 ATTATAATCATTATTATTAAATC
* *
20901 ATTATTATAATGATTATTATCAAATC
1 ---ATTATAATCATTATTATTAAATC
* *
20927 ATTACTAAATCATCAAATAATTAAAT-
1 ATTA-T-AATCAT--TATTATTAAATC
*
20953 ATTA-AAT--TTATTATTAAATTT
1 ATTATAATCATTATTATTAAA-TC
*
20974 ATTATTAAATCATTA-T-TTAAATT
1 ATTA-T-AATCATTATTATTAAATC
*
20997 ATTATTAAATCATTTTTAT
1 ATTA-T-AATCATTATTAT
21016 GGTTAATTGA
Statistics
Matches: 249, Mismatches: 30, Indels: 65
0.72 0.09 0.19
Matches are distributed among these distances:
19 8 0.03
20 3 0.01
21 5 0.02
22 9 0.04
23 59 0.24
24 21 0.08
25 35 0.14
26 93 0.37
27 16 0.06
ACGTcount: A:0.44, C:0.08, G:0.01, T:0.47
Consensus pattern (23 bp):
ATTATAATCATTATTATTAAATC
Found at i:20869 original size:98 final size:97
Alignment explanation
Indices: 20767--21003 Score: 342
Period size: 98 Copynumber: 2.5 Consensus size: 97
20757 ATTATCATCA
20767 TTATTATTAAATCATTATT-ATCATTATTATTAAATCATTATTATAATGATTATTATCAAATCAT
1 TTATTATTAAATCATTATTAATCATTATTATTAAATCATTATTATAATGATTATTATCAAATCAT
*
20831 TACTAAATCATCAAATCATTAAATATTTAAATC
66 TACTAAATCATCAAATAATTAAATA-TTAAATC
* *
20864 --ATTATTAAATCATTATTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATC
1 TTATTATTAAATCATTA-T-TAATCATTATTATTAAATCATTATTATAATGATTATTATCAAATC
20927 ATTACTAAATCATCAAATAATTAAATATTAAAT-
64 ATTACTAAATCATCAAATAATTAAATATTAAATC
* *
20960 TTATTATTAAATTTATTATTAAATCATTA-T-TTAAATTATTATTA
1 TTATTATTAAA-TCATTATT-AATCATTATTATTAAATCATTATTA
21004 AATCATTTTT
Statistics
Matches: 126, Mismatches: 7, Indels: 15
0.85 0.05 0.10
Matches are distributed among these distances:
95 15 0.12
96 13 0.10
97 9 0.07
98 84 0.67
99 5 0.04
ACGTcount: A:0.44, C:0.08, G:0.01, T:0.46
Consensus pattern (97 bp):
TTATTATTAAATCATTATTAATCATTATTATTAAATCATTATTATAATGATTATTATCAAATCAT
TACTAAATCATCAAATAATTAAATATTAAATC
Found at i:20967 original size:12 final size:12
Alignment explanation
Indices: 20952--21006 Score: 78
Period size: 12 Copynumber: 4.7 Consensus size: 12
20942 AATAATTAAA
20952 TATTAAATTTAT
1 TATTAAATTTAT
20964 TATTAAATTTAT
1 TATTAAATTTAT
*
20976 TATTAAA-TCAT
1 TATTAAATTTAT
20987 TATTTAAA-TTAT
1 TA-TTAAATTTAT
20999 TATTAAAT
1 TATTAAAT
21007 CATTTTTATG
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.26
12 29 0.74
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (12 bp):
TATTAAATTTAT
Found at i:21205 original size:17 final size:18
Alignment explanation
Indices: 21185--21219 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
21175 TATTAGTAAA
21185 TCATTATTATT-ATAATT
1 TCATTATTATTAATAATT
21202 TCATTATTATTAATAATT
1 TCATTATTATTAATAATT
21220 ACTAATCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (18 bp):
TCATTATTATTAATAATT
Found at i:21294 original size:49 final size:49
Alignment explanation
Indices: 21217--21453 Score: 438
Period size: 49 Copynumber: 4.8 Consensus size: 49
21207 ATTATTAATA
*
21217 ATTACTAATCATTACTATCAAATAATTAAATATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
21266 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
*
21315 ATTACTAATCATTACTATCAAATCTTTAAATATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
* *
21364 ATTAGTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATC
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
21413 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATA
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATA
21454 GATGGGTGCC
Statistics
Matches: 182, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
49 182 1.00
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (49 bp):
ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
Found at i:24877 original size:22 final size:21
Alignment explanation
Indices: 24843--24883 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
24833 CGTATTTATG
24843 CCTTCTTCATTTCCTTTCTTTT
1 CCTTCTTCATTT-CTTTCTTTT
**
24865 CCTTCTTTGTTTCTTTCTT
1 CCTTCTTCATTTCTTTCTT
24884 CGAATCAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.02, C:0.29, G:0.02, T:0.66
Consensus pattern (21 bp):
CCTTCTTCATTTCTTTCTTTT
Found at i:25196 original size:43 final size:49
Alignment explanation
Indices: 25139--25253 Score: 136
Period size: 50 Copynumber: 2.4 Consensus size: 49
25129 GTTTAAAGAC
*
25139 ACTAACAAATTAATTAATATA-TTTTT-TAT-AT-T-TA-ATAACTTAA
1 ACTAACAAACTAATTAATATATTTTTTATATAATATATATATAACTTAA
*
25182 ACTAATAAACTAATTAACTA-ATTTTTTATATAATATAATATATAACTTAA
1 ACTAACAAACTAATTAA-TATATTTTTTATATAATAT-ATATATAACTTAA
25232 ACTAACAAACTAATATAATATA
1 ACTAACAAACTAAT-TAATATA
25254 ACTTAAACTA
Statistics
Matches: 59, Mismatches: 3, Indels: 12
0.80 0.04 0.16
Matches are distributed among these distances:
43 16 0.27
44 7 0.12
45 3 0.05
46 2 0.03
47 1 0.02
49 2 0.03
50 24 0.41
51 4 0.07
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (49 bp):
ACTAACAAACTAATTAATATATTTTTTATATAATATATATATAACTTAA
Found at i:25252 original size:28 final size:30
Alignment explanation
Indices: 25212--25274 Score: 112
Period size: 28 Copynumber: 2.2 Consensus size: 30
25202 ATTTTTTATA
25212 TAATATAATATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
25242 TAATAT-A-ATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
25270 TAATA
1 TAATA
25275 ATTTATACTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 26 0.79
29 1 0.03
30 6 0.18
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAACAAAC
Found at i:25281 original size:28 final size:28
Alignment explanation
Indices: 25216--25281 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
25206 TTTATATAAT
25216 ATAATATATAACTTAAACTAACAAACTA
1 ATAATATATAACTTAAACTAACAAACTA
25244 AT-ATAATATAACTTAAACTAACAAACTA
1 ATAAT-ATATAACTTAAACTAACAAACTA
*
25272 ATAATTTATA
1 ATAATATATA
25282 CTAACAAACT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
27 2 0.06
28 31 0.89
29 2 0.06
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (28 bp):
ATAATATATAACTTAAACTAACAAACTA
Found at i:25284 original size:21 final size:21
Alignment explanation
Indices: 25251--25299 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
25241 CTAATATAAT
25251 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
25272 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
25293 ATTAACT
1 A-TAACT
25300 AGATTTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:25894 original size:29 final size:29
Alignment explanation
Indices: 25852--25907 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
25842 CGAGAACGTT
25852 GGACGCCGGGCGTGCATGGCGACCTATAA
1 GGACGCCGGGCGTGCATGGCGACCTATAA
25881 GGACGCCGGGCGTGCATGGCGACCTAT
1 GGACGCCGGGCGTGCATGGCGACCTAT
25908 GCTGGTTCGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.18, C:0.29, G:0.39, T:0.14
Consensus pattern (29 bp):
GGACGCCGGGCGTGCATGGCGACCTATAA
Found at i:34704 original size:15 final size:13
Alignment explanation
Indices: 34684--34721 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 13
34674 CTTTCTTAGC
34684 ATTATCATATATATT
1 ATTATCAT-TAT-TT
34699 ATTATCATTATTT
1 ATTATCATTATTT
34712 A-TATCATTAT
1 ATTATCATTAT
34722 CATCAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 9 0.39
13 3 0.13
14 3 0.13
15 8 0.35
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (13 bp):
ATTATCATTATTT
Found at i:35018 original size:23 final size:23
Alignment explanation
Indices: 34992--35073 Score: 103
Period size: 23 Copynumber: 3.6 Consensus size: 23
34982 CGTATACATG
*
34992 CACCAAAGTG-CAGCGTAGAATTA
1 CACCATAGTGCCA-CGTAGAATTA
* *
35015 CACCGTAGTGCCACGTAGAATTG
1 CACCATAGTGCCACGTAGAATTA
35038 CACCATAGTGCCACGTAGAATTA
1 CACCATAGTGCCACGTAGAATTA
* *
35061 CAACGTAGTGCCA
1 CACCATAGTGCCA
35074 TATAATAATG
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
23 49 0.96
24 2 0.04
ACGTcount: A:0.33, C:0.26, G:0.22, T:0.20
Consensus pattern (23 bp):
CACCATAGTGCCACGTAGAATTA
Found at i:39359 original size:21 final size:22
Alignment explanation
Indices: 39326--39366 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
39316 GTTAAAATAA
39326 AAAAATAAGAATTAAATAAAAG
1 AAAAATAAGAATTAAATAAAAG
*
39348 AAAAA-AATAATTAAATAAA
1 AAAAATAAGAATTAAATAAA
39367 CAAATTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.20
Consensus pattern (22 bp):
AAAAATAAGAATTAAATAAAAG
Found at i:40049 original size:19 final size:19
Alignment explanation
Indices: 39993--40055 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
39983 TTATTTAAAC
**
39993 TAAAATACCTAAAAAATAAT
1 TAAAATA-CTAAAACCTAAT
* * *
40013 ATAATATTCTAAATCCTAAT
1 -TAAAATACTAAAACCTAAT
*
40033 TAAAATACTAAAACCTATT
1 TAAAATACTAAAACCTAAT
40052 TAAA
1 TAAA
40056 CTAAAATACA
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
19 19 0.58
20 9 0.27
21 5 0.15
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAATACTAAAACCTAAT
Found at i:40143 original size:77 final size:75
Alignment explanation
Indices: 40013--40177 Score: 233
Period size: 77 Copynumber: 2.2 Consensus size: 75
40003 AAAAAATAAT
* *
40013 ATAATATTCTAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAGATA
1 ATAATATCCTAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAA-ATA
40078 AAAT-ATAAAA
65 AAATGATAAAA
*
40088 ATAATATCCTAAAACTTAATTAAAAATACTAAAAGCCTATTTAAACTAAAATACAAAGATAAAAT
1 ATAATATCCTAAAACCTAATT-AAAATACTAAAA-CCTATTTAAACTAAAATACAAAGATAAAAT
* * *
40153 ATAATGTTTAAA
64 AAAATGATAAAA
*
40165 ATATTATCCTAAA
1 ATAATATCCTAAA
40178 TTTGAGTTTA
Statistics
Matches: 80, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
75 18 0.22
76 18 0.22
77 44 0.55
ACGTcount: A:0.56, C:0.11, G:0.03, T:0.30
Consensus pattern (75 bp):
ATAATATCCTAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAATAA
AATGATAAAA
Found at i:41909 original size:10 final size:10
Alignment explanation
Indices: 41896--41934 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
41886 AAAGTTCGCT
41896 AAAAAAATAA
1 AAAAAAATAA
41906 AAAAAAATAA
1 AAAAAAATAA
*
41916 AACGAAAATAA
1 AA-AAAAATAA
41927 AAACAAAA
1 AAA-AAAA
41935 ATATAACGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 12 0.48
11 13 0.52
ACGTcount: A:0.85, C:0.05, G:0.03, T:0.08
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:41923 original size:12 final size:11
Alignment explanation
Indices: 41898--41937 Score: 55
Period size: 10 Copynumber: 3.6 Consensus size: 11
41888 AGTTCGCTAA
41898 AAAAATAAAA-
1 AAAAATAAAAC
41908 AAAAATAAAAC
1 AAAAATAAAAC
*
41919 GAAAATAAAAAC
1 AAAAAT-AAAAC
41931 AAAAATA
1 AAAAATA
41938 TAACGAAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
10 10 0.38
11 6 0.23
12 10 0.38
ACGTcount: A:0.82, C:0.05, G:0.03, T:0.10
Consensus pattern (11 bp):
AAAAATAAAAC
Found at i:41934 original size:23 final size:21
Alignment explanation
Indices: 41899--41945 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 21
41889 GTTCGCTAAA
41899 AAAATAAAAAAAAATAAAACG
1 AAAATAAAAAAAAATAAAACG
*
41920 AAAATAAAAACAAAAATATAACG
1 AAAAT-AAAA-AAAAATAAAACG
41943 AAA
1 AAA
41946 TGGATTGCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.22
22 4 0.17
23 14 0.61
ACGTcount: A:0.79, C:0.06, G:0.04, T:0.11
Consensus pattern (21 bp):
AAAATAAAAAAAAATAAAACG
Found at i:45855 original size:15 final size:15
Alignment explanation
Indices: 45835--45868 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
45825 TTCCTCTTGT
45835 TCTTCCTGATGTGCG
1 TCTTCCTGATGTGCG
45850 TCTTCCTGATGTGCG
1 TCTTCCTGATGTGCG
45865 TCTT
1 TCTT
45869 TTTCTGCTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.06, C:0.26, G:0.24, T:0.44
Consensus pattern (15 bp):
TCTTCCTGATGTGCG
Found at i:47655 original size:21 final size:22
Alignment explanation
Indices: 47616--47662 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
47606 AAGTTGTGGT
*
47616 TAAAATAAAAATAAGAATTAAA
1 TAAAAGAAAAATAAGAATTAAA
*
47638 TAAAAGAAAAA-AATAATTAAA
1 TAAAAGAAAAATAAGAATTAAA
47659 TAAA
1 TAAA
47663 CAAATTAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.21
Consensus pattern (22 bp):
TAAAAGAAAAATAAGAATTAAA
Found at i:48327 original size:66 final size:68
Alignment explanation
Indices: 48252--48451 Score: 230
Period size: 66 Copynumber: 2.9 Consensus size: 68
48242 TAAAACATCT
* *
48252 TAAATCCTAATTAAAACACTAAAAACTATTTAAACTAAAATACCTAAAAATAATAATATAAT-AT
1 TAAATCCTAATTAAAATACTAAAAACTATTTAAACTAAAATACCTAAAGATAA-AATATAATAAT
48316 -T-C
65 ATCC
* * *
48318 TAAATCCTAATTAATATACTAAAACCTATTTAAACTAAAATACAAAGATAAAGATAAAATATAAA
1 TAAATCCTAATTAAAATACTAAAAACTATTTAAACTAAAATAC----CTAAAGATAAAATAT--A
48383 ATAATATCC
60 ATAATATCC
* *
48392 TAAAACTTAATTAAAATACTAAAAACCTATTTAAACTAAAATA-C-AAAGATAAAATATAAT
1 TAAATCCTAATTAAAATACTAAAAA-CTATTTAAACTAAAATACCTAAAGATAAAATATAAT
48452 GTTTAAAATA
Statistics
Matches: 114, Mismatches: 10, Indels: 19
0.80 0.07 0.13
Matches are distributed among these distances:
66 40 0.35
67 3 0.03
69 18 0.16
70 8 0.07
71 3 0.03
72 2 0.02
73 1 0.01
74 22 0.19
75 17 0.15
ACGTcount: A:0.57, C:0.12, G:0.01, T:0.29
Consensus pattern (68 bp):
TAAATCCTAATTAAAATACTAAAAACTATTTAAACTAAAATACCTAAAGATAAAATATAATAATA
TCC
Found at i:48334 original size:19 final size:19
Alignment explanation
Indices: 48305--48350 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
48295 CTAAAAATAA
* *
48305 TAATATAATATTCTAAATCC
1 TAAT-TAATATACTAAAACC
48325 TAATTAATATACTAAAACC
1 TAATTAATATACTAAAACC
*
48344 TATTTAA
1 TAATTAA
48351 ACTAAAATAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (19 bp):
TAATTAATATACTAAAACC
Found at i:48388 original size:74 final size:76
Alignment explanation
Indices: 48298--48471 Score: 237
Period size: 75 Copynumber: 2.3 Consensus size: 76
48288 AAAATACCTA
* * * *
48298 AAAATAATAATATAATATTCTAAATCCTAATTAATATACT-AAAACCTATTTAAACTAAAATACA
1 AAAATAATAAAATAATATCCTAAAACCTAATTAAAATACTAAAAACCTATTTAAACTAAAATACA
48362 AAGATAAAGAT
66 AAGATAAAGAT
*
48373 AAAAT-ATAAAATAATATCCTAAAACTTAATTAAAATACTAAAAACCTATTTAAACTAAAATACA
1 AAAATAATAAAATAATATCCTAAAACCTAATTAAAATACTAAAAACCTATTTAAACTAAAATACA
48437 AAGATAAA-AT
66 AAGATAAAGAT
* ** *
48447 ATAATGTTTAAAATATTATCCTAAA
1 AAAAT-AATAAAATAATATCCTAAA
48472 TTTGAGTTTA
Statistics
Matches: 88, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
74 35 0.40
75 37 0.42
76 16 0.18
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.30
Consensus pattern (76 bp):
AAAATAATAAAATAATATCCTAAAACCTAATTAAAATACTAAAAACCTATTTAAACTAAAATACA
AAGATAAAGAT
Found at i:50525 original size:56 final size:56
Alignment explanation
Indices: 50458--50569 Score: 224
Period size: 56 Copynumber: 2.0 Consensus size: 56
50448 GCATGTGTGT
50458 TAAAGGGTGAATTATTGTCAATATCTATAAGATTCTCATCTAGAAGCTTGATTAGG
1 TAAAGGGTGAATTATTGTCAATATCTATAAGATTCTCATCTAGAAGCTTGATTAGG
50514 TAAAGGGTGAATTATTGTCAATATCTATAAGATTCTCATCTAGAAGCTTGATTAGG
1 TAAAGGGTGAATTATTGTCAATATCTATAAGATTCTCATCTAGAAGCTTGATTAGG
50570 AAGATGGTAC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.36
Consensus pattern (56 bp):
TAAAGGGTGAATTATTGTCAATATCTATAAGATTCTCATCTAGAAGCTTGATTAGG
Found at i:51739 original size:51 final size:51
Alignment explanation
Indices: 51679--51895 Score: 226
Period size: 51 Copynumber: 4.3 Consensus size: 51
51669 AAATTATAAT
* *
51679 TTAACACATACTTACACCGGTGTAAGTGAATAAAATAAAAAAAATGTAACAA
1 TTAACACATACTTACACCGGTGTAAGTAAATAAAAT-AAAAAAATGTAACAC
* ** * *
51731 TT-ACACATAATTACACTAGTG-CAGTAAAT-AAA-AGAAAAATGTAGAACAC
1 TTAACACATACTTACACCGGTGTAAGTAAATAAAATAAAAAAATGT--AACAC
* * * * * *
51780 TTAACACATACTTACATCGGTATAAGTAAATAAAATTAAAAAGTATAATAC
1 TTAACACATACTTACACCGGTGTAAGTAAATAAAATAAAAAAATGTAACAC
* * * *
51831 TTAAGACATACTTACACTGGTGTAAGTAAATAAAATAACAAATTGTAACAC
1 TTAACACATACTTACACCGGTGTAAGTAAATAAAATAAAAAAATGTAACAC
51882 TTAACACATACTTA
1 TTAACACATACTTA
51896 TATTGGTATA
Statistics
Matches: 131, Mismatches: 28, Indels: 13
0.76 0.16 0.08
Matches are distributed among these distances:
47 9 0.07
49 9 0.07
50 20 0.15
51 82 0.63
52 5 0.04
53 6 0.05
ACGTcount: A:0.50, C:0.14, G:0.10, T:0.26
Consensus pattern (51 bp):
TTAACACATACTTACACCGGTGTAAGTAAATAAAATAAAAAAATGTAACAC
Found at i:51806 original size:101 final size:102
Alignment explanation
Indices: 51679--51909 Score: 272
Period size: 101 Copynumber: 2.3 Consensus size: 102
51669 AAATTATAAT
* * * *
51679 TTAACACATACTTACACCGGTGTAAGTGAATAAAATAAAAAAAATGTAACAATT-ACACATAATT
1 TTAACACATACTTACATCGGTATAAGTAAATAAAAT-AAAAAAATATAACAATTAACACATAATT
*
51743 ACACTAGTG-CAGTAAATAAAAGAA-AAA-TGTAGAACAC
65 ACACTAGTGTAAGTAAATAAAAGAACAAATTGT--AACAC
* * * * * *
51780 TTAACACATACTTACATCGGTATAAGTAAATAAAATTAAAAAGTATAATACTTAAGACATACTTA
1 TTAACACATACTTACATCGGTATAAGTAAATAAAATAAAAAAATATAACAATTAACACATAATTA
* *
51845 CACTGGTGTAAGTAAATAAAATAACAAATTGTAACAC
66 CACTAGTGTAAGTAAATAAAAGAACAAATTGTAACAC
* *
51882 TTAACACATACTTATATTGGTATAAGTA
1 TTAACACATACTTACATCGGTATAAGTA
51910 CGTGCATCTC
Statistics
Matches: 111, Mismatches: 15, Indels: 7
0.83 0.11 0.05
Matches are distributed among these distances:
100 12 0.11
101 49 0.44
102 44 0.40
103 3 0.03
104 3 0.03
ACGTcount: A:0.49, C:0.13, G:0.11, T:0.27
Consensus pattern (102 bp):
TTAACACATACTTACATCGGTATAAGTAAATAAAATAAAAAAATATAACAATTAACACATAATTA
CACTAGTGTAAGTAAATAAAAGAACAAATTGTAACAC
Found at i:52262 original size:16 final size:18
Alignment explanation
Indices: 52241--52277 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
52231 ATCATTTAGT
*
52241 ATTAAC-TATTTAAT-TA
1 ATTAACTTATTAAATGTA
52257 ATTAACTTATTAAATGTA
1 ATTAACTTATTAAATGTA
52275 ATT
1 ATT
52278 GTTAAAACGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 6 0.33
17 7 0.39
18 5 0.28
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (18 bp):
ATTAACTTATTAAATGTA
Found at i:56865 original size:30 final size:31
Alignment explanation
Indices: 56808--56879 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
56798 TTAATGGCAG
*
56808 AGTGAGCAAAATGATTAAATCTGAAAGTTTC
1 AGTGAGCAAAATGATCAAATCTGAAAGTTTC
* *
56839 AGTGAGCAAATTGATCAAAT-TGAAAG-TTG
1 AGTGAGCAAAATGATCAAATCTGAAAGTTTC
*
56868 AGTGAGGAAAAT
1 AGTGAGCAAAAT
56880 AAGAGAGAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
29 12 0.33
30 6 0.17
31 18 0.50
ACGTcount: A:0.43, C:0.07, G:0.24, T:0.26
Consensus pattern (31 bp):
AGTGAGCAAAATGATCAAATCTGAAAGTTTC
Found at i:68751 original size:12 final size:12
Alignment explanation
Indices: 68734--68759 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
68724 ACCTTTTTCG
68734 TATACTGTTGGC
1 TATACTGTTGGC
68746 TATACTGTTGGC
1 TATACTGTTGGC
68758 TA
1 TA
68760 ATGGCTGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.19, C:0.15, G:0.23, T:0.42
Consensus pattern (12 bp):
TATACTGTTGGC
Found at i:76659 original size:38 final size:39
Alignment explanation
Indices: 76605--76683 Score: 151
Period size: 38 Copynumber: 2.1 Consensus size: 39
76595 GTATGATGGT
76605 CATCTGACCCATCAACGGTACTATCTCTACAGGTAGAGG
1 CATCTGACCCATCAACGGTACTATCTCTACAGGTAGAGG
76644 CATCTGA-CCATCAACGGTACTATCTCTACAGGTAGAGG
1 CATCTGACCCATCAACGGTACTATCTCTACAGGTAGAGG
76682 CA
1 CA
76684 CCGTCATTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
38 33 0.82
39 7 0.17
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (39 bp):
CATCTGACCCATCAACGGTACTATCTCTACAGGTAGAGG
Found at i:79013 original size:16 final size:16
Alignment explanation
Indices: 78992--79033 Score: 68
Period size: 16 Copynumber: 2.6 Consensus size: 16
78982 AAGTTAGCTC
78992 GAGATC-TCTCGGAGGT
1 GAGATCGTCT-GGAGGT
79008 GAGATCGTCTGGAGGT
1 GAGATCGTCTGGAGGT
79024 GAGATCGTCT
1 GAGATCGTCT
79034 TTTGCTAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 22 0.88
17 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.38, T:0.26
Consensus pattern (16 bp):
GAGATCGTCTGGAGGT
Found at i:82485 original size:25 final size:28
Alignment explanation
Indices: 82430--82484 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
82420 TTAAGCCTTA
*
82430 TTATTATTATTAGTTAAATAAAAAACTT
1 TTATTATTATTAGGTAAATAAAAAACTT
*
82458 TTATTATTATT-GGTAAA-AAATAACTT
1 TTATTATTATTAGGTAAATAAAAAACTT
82484 T
1 T
82485 AGCTTGGTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 9 0.36
27 5 0.20
28 11 0.44
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.47
Consensus pattern (28 bp):
TTATTATTATTAGGTAAATAAAAAACTT
Found at i:85516 original size:10 final size:10
Alignment explanation
Indices: 85501--85529 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
85491 GGTTTATTTG
85501 TTCATTTTAA
1 TTCATTTTAA
85511 TTCATTTTAA
1 TTCATTTTAA
85521 TTCATTTTA
1 TTCATTTTA
85530 TGTATAGGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.28, C:0.10, G:0.00, T:0.62
Consensus pattern (10 bp):
TTCATTTTAA
Found at i:85875 original size:64 final size:64
Alignment explanation
Indices: 85735--85883 Score: 171
Period size: 63 Copynumber: 2.3 Consensus size: 64
85725 TTTTTATATT
* *
85735 TTATCTTTG-TTTTAGGTATTTTAGTTTAAATAAGTTTTAGTATTTTAATTAGAATTTAGAATA
1 TTATATTTGTTTTTAGGTATTTTAGTTTAAATAAGTTTAAGTATTTTAATTAGAATTTAGAATA
* * *
85798 TTATATTAT-TTTTTAGGTATTTTGGTTTAAAT-AGTTTAAGTGTTTTAATTAGGATTTA-AGAT
1 TTATATT-TGTTTTTAGGTATTTTAGTTTAAATAAGTTTAAGTATTTTAATTAGAATTTAGA-AT
*
85860 G
64 A
* *
85861 TTTTAGTTTGTTTTTAGGAATTT
1 TTATA-TTTGTTTTTAGGTATTT
85884 GAAGGCTATA
Statistics
Matches: 73, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
62 1 0.01
63 36 0.49
64 36 0.49
ACGTcount: A:0.28, C:0.01, G:0.15, T:0.56
Consensus pattern (64 bp):
TTATATTTGTTTTTAGGTATTTTAGTTTAAATAAGTTTAAGTATTTTAATTAGAATTTAGAATA
Found at i:86193 original size:161 final size:161
Alignment explanation
Indices: 86022--86344 Score: 574
Period size: 161 Copynumber: 2.0 Consensus size: 161
86012 TTGGTTATGC
* *
86022 TTAGCTAATTTTCTTTCAAGCCGAAGGCTAAAGCGAAGGCTCAATTCTAAACGTGAGAATTGTAA
1 TTAGCTAATTTTCTTTCAAGCCGAAGGCTAAAACGAAGGCTCAATTCTAAACGTGAAAATTGTAA
* *
86087 GGTACTTAAATCGCTTTAGATTTTTCTCTCTGTTTTCTGAGCTTACTTTTCAAATCAAAACGATT
66 GGTACTTAAATCGCTTCAGATTTTTCTCTATGTTTTCTGAGCTTACTTTTCAAATCAAAACGATT
*
86152 TTGACATTGATCCGGATATTGTTATGGTTAA
131 TTGACATTGATCCGGATATTGTTACGGTTAA
*
86183 TTAGCTAATTTTCTTTCAAGCCGAAGGCTAAAACGAAGGCTCAATTTTAAACGTGAAAATTGTAA
1 TTAGCTAATTTTCTTTCAAGCCGAAGGCTAAAACGAAGGCTCAATTCTAAACGTGAAAATTGTAA
*
86248 GGTACTTAAATCGCTTCGGATTTTTCTCTATGTTTTCTGAGCTTACTTTTCAAATCAAAACGATT
66 GGTACTTAAATCGCTTCAGATTTTTCTCTATGTTTTCTGAGCTTACTTTTCAAATCAAAACGATT
*
86313 TTGACATTGGTCCGGATATTGTTACGGTTAA
131 TTGACATTGATCCGGATATTGTTACGGTTAA
86344 T
1 T
86345 GTTTGAAGAA
Statistics
Matches: 154, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
161 154 1.00
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (161 bp):
TTAGCTAATTTTCTTTCAAGCCGAAGGCTAAAACGAAGGCTCAATTCTAAACGTGAAAATTGTAA
GGTACTTAAATCGCTTCAGATTTTTCTCTATGTTTTCTGAGCTTACTTTTCAAATCAAAACGATT
TTGACATTGATCCGGATATTGTTACGGTTAA
Found at i:87170 original size:25 final size:25
Alignment explanation
Indices: 87132--87181 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
87122 TTGTTCTTCT
87132 TTTGGCTCTACTGAGCTAAAGAGAA
1 TTTGGCTCTACTGAGCTAAAGAGAA
*
87157 TTTGGCTCTGCTGAGCTAAAGAGAA
1 TTTGGCTCTACTGAGCTAAAGAGAA
87182 AATGTACAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (25 bp):
TTTGGCTCTACTGAGCTAAAGAGAA
Done.