Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000304.1 Hibiscus syriacus cultivar Beakdansim tig00000573_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: 68738
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:3626 original size:22 final size:22
Alignment explanation
Indices: 3597--3651 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
3587 ATCTACACTC
*
3597 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
*
3619 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
3641 TTCAAAGATGA
1 TTCAAAGATGA
3652 AAACTTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCTCTT
Found at i:4473 original size:76 final size:76
Alignment explanation
Indices: 4331--5076 Score: 1245
Period size: 76 Copynumber: 9.9 Consensus size: 76
4321 CTATTTCCCA
*
4331 CATCTGTAAGTCCTGCAGTGCATGATGTTTCC-AAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
4395 AGCCTTCGGGT
66 AGCCTTCGGGT
4406 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
4471 AGCCTTCGGGT
66 AGCCTTCGGGT
*
4482 CATCTGTAAGTTCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
4547 AGCCTTCGGGT
66 AGCCTTCGGGT
4558 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
4623 AGCCTTCGGGT
66 AGCCTTCGGGT
*
4634 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGAGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
4699 AACCTTAGGGT
66 AGCCTTCGGGT
* *
4710 CATCTGCAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGTTTTTTTGATG-TTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAG-CTTTTTGATGTTTTCA
*
4774 AAGCCTTAGGGT
65 AAGCCTTCGGGT
4786 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAG-TTTTTGATG-TTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
4849 AGCCTTAGGGT
66 AGCCTTCGGGT
* * *
4860 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGAAGCTTTTTAATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
4925 A-CCCTCAGGGT
66 AGCCTTC-GGGT
* * *
4936 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGAGAGCTTTTTAATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
5001 A-CCCTCAGGGT
66 AGCCTTC-GGGT
* *
5012 CATTTGTAAGTCCTGCAGTGCATGATGTTT-CAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
5076 A
66 A
5077 CCCTCATGAT
Statistics
Matches: 645, Mismatches: 21, Indels: 10
0.95 0.03 0.01
Matches are distributed among these distances:
74 72 0.11
75 75 0.12
76 489 0.76
77 9 0.01
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGT
Found at i:5255 original size:3 final size:3
Alignment explanation
Indices: 5247--5304 Score: 62
Period size: 3 Copynumber: 18.0 Consensus size: 3
5237 TTTTACTTAA
* *
5247 ATT ATT ATT ATT ATT ATA AAT ATT ATT ATT ATT ATTT ATAT ATAT ATAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT AT-T AT-T AT-T
5296 ATT ATT ATT
1 ATT ATT ATT
5305 TAATAAATAT
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
3 35 0.71
4 14 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:5272 original size:15 final size:15
Alignment explanation
Indices: 5252--5316 Score: 64
Period size: 15 Copynumber: 4.3 Consensus size: 15
5242 CTTAAATTAT
5252 TATTATTATTATAAA
1 TATTATTATTATAAA
*
5267 TATTATTATTAT-TA
1 TATTATTATTATAAA
*
5281 T-TTA-TATATATATA
1 TATTATTAT-TATAAA
5295 TATTATTATTTAATAAA
1 TATTATTA-TT-ATAAA
5312 TATTA
1 TATTA
5317 CAAACCCAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
12 3 0.07
13 6 0.14
14 5 0.12
15 15 0.36
16 3 0.07
17 10 0.24
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TATTATTATTATAAA
Found at i:5272 original size:18 final size:19
Alignment explanation
Indices: 5244--5281 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
5234 TTATTTTACT
5244 TAAATTATTATTATTATTA
1 TAAATTATTATTATTATTA
5263 TAAA-TATTATTATTATTA
1 TAAATTATTATTATTATTA
5281 T
1 T
5282 TTATATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TAAATTATTATTATTATTA
Found at i:6851 original size:111 final size:112
Alignment explanation
Indices: 6729--6951 Score: 242
Period size: 111 Copynumber: 2.0 Consensus size: 112
6719 CATAAATTAC
* * *
6729 TTTTAATAATTATGTTTTAATATATATTTATTTA-TTTTTAATAT-AAGAAATG-GCAGTCTTAA
1 TTTTAATAATTATATATT-A-AT-TATTTATTTATTTTTTAATATCAAGAAAAGAGCAGTCTTAA
* * *
6791 -AAAACTGGATGTCTATTTTCTGATATTTTTAAATAAAT-AATATCTTATTG
63 GAAAACTAGAAGTC--TTTTCTGATATTTCTAAATAAATAAATATCTTATTG
* * *
6841 TTTTAA-AATTATATATTAATTGTTTATTTATTTTTTAATATCGAAGAAAAGAGCTGTCTTAAGG
1 TTTTAATAATTATATATTAATTATTTATTTATTTTTTAATATC-AAGAAAAGAGCAGTCTTAAGA
* * *
6905 CACCTAGAAGTCTTTTCTGATATTTCTAAATAAATAAATATTTTATT
65 AAACTAGAAGTCTTTTCTGATATTTCTAAATAAATAAATATCTTATT
6952 TATTTTATAT
Statistics
Matches: 93, Mismatches: 12, Indels: 12
0.79 0.10 0.10
Matches are distributed among these distances:
108 9 0.10
109 12 0.13
110 1 0.01
111 38 0.41
112 25 0.27
113 8 0.09
ACGTcount: A:0.36, C:0.07, G:0.09, T:0.48
Consensus pattern (112 bp):
TTTTAATAATTATATATTAATTATTTATTTATTTTTTAATATCAAGAAAAGAGCAGTCTTAAGAA
AACTAGAAGTCTTTTCTGATATTTCTAAATAAATAAATATCTTATTG
Found at i:6854 original size:21 final size:22
Alignment explanation
Indices: 6825--6865 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
6815 ATTTTTAAAT
*
6825 AAATAATATCTT-ATTGTTTTA
1 AAATAATATATTAATTGTTTTA
*
6846 AAATTATATATTAATTGTTT
1 AAATAATATATTAATTGTTT
6866 ATTTATTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (22 bp):
AAATAATATATTAATTGTTTTA
Found at i:6974 original size:17 final size:17
Alignment explanation
Indices: 6952--6987 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
6942 ATATTTTATT
6952 TATTTTATATATAAATA
1 TATTTTATATATAAATA
* *
6969 TATTTTTTATATAATTA
1 TATTTTATATATAAATA
6986 TA
1 TA
6988 ACTTTGAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TATTTTATATATAAATA
Found at i:9921 original size:144 final size:144
Alignment explanation
Indices: 9661--9940 Score: 560
Period size: 144 Copynumber: 1.9 Consensus size: 144
9651 AGCACCAAAG
9661 ATGTAAGTCCATGTCCTCTTGTCCAGATTGTCATTTATGTAATATATGTTGCTGTAATAGCAAAA
1 ATGTAAGTCCATGTCCTCTTGTCCAGATTGTCATTTATGTAATATATGTTGCTGTAATAGCAAAA
9726 CAAAAGATACCCAGCATCAGGGAATTTATTGTCAGGGTGCATGCATGATGATGATTCCTCTCTCT
66 CAAAAGATACCCAGCATCAGGGAATTTATTGTCAGGGTGCATGCATGATGATGATTCCTCTCTCT
9791 CTCTCTAAATATAT
131 CTCTCTAAATATAT
9805 ATGTAAGTCCATGTCCTCTTGTCCAGATTGTCATTTATGTAATATATGTTGCTGTAATAGCAAAA
1 ATGTAAGTCCATGTCCTCTTGTCCAGATTGTCATTTATGTAATATATGTTGCTGTAATAGCAAAA
9870 CAAAAGATACCCAGCATCAGGGAATTTATTGTCAGGGTGCATGCATGATGATGATTCCTCTCTCT
66 CAAAAGATACCCAGCATCAGGGAATTTATTGTCAGGGTGCATGCATGATGATGATTCCTCTCTCT
9935 CTCTCT
131 CTCTCT
9941 CTCTCTAAAT
Statistics
Matches: 136, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
144 136 1.00
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (144 bp):
ATGTAAGTCCATGTCCTCTTGTCCAGATTGTCATTTATGTAATATATGTTGCTGTAATAGCAAAA
CAAAAGATACCCAGCATCAGGGAATTTATTGTCAGGGTGCATGCATGATGATGATTCCTCTCTCT
CTCTCTAAATATAT
Found at i:10847 original size:2 final size:2
Alignment explanation
Indices: 10842--10868 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
10832 TTGAGGGGGG
10842 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
10869 CATACATACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13696 original size:26 final size:26
Alignment explanation
Indices: 13633--13687 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
13623 AGCTCATTTA
13633 TATATACATCAAC--ATATATTCATG
1 TATATACATCAACATATATATTCATG
13657 TATATACATCAACATATATATTCATG
1 TATATACATCAACATATATATTCATG
13683 TATAT
1 TATAT
13688 TATGTAACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 13 0.45
26 16 0.55
ACGTcount: A:0.42, C:0.15, G:0.04, T:0.40
Consensus pattern (26 bp):
TATATACATCAACATATATATTCATG
Found at i:14140 original size:23 final size:23
Alignment explanation
Indices: 14080--14148 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
14070 CACCACAGCT
* * *
14080 CGTATAATTGCACCAAAGTACCA
1 CGTAGAATTGCACCGAAGTGCCA
*
14103 CGTAGAATTGCACCGGAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
*
14126 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
14149 TATAATAATG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:15701 original size:21 final size:21
Alignment explanation
Indices: 15659--15719 Score: 104
Period size: 21 Copynumber: 2.9 Consensus size: 21
15649 TTCGCTTGAG
*
15659 GGGTATCGATTCCCCATTGAAT
1 GGGTACCGATTCCCC-TTGAAT
15681 GGGTACCGATTCCCCTTGAAT
1 GGGTACCGATTCCCCTTGAAT
15702 GGGTACCGATTCCCCTTG
1 GGGTACCGATTCCCCTTG
15720 CCTAGAAATC
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
21 24 0.63
22 14 0.37
ACGTcount: A:0.18, C:0.28, G:0.25, T:0.30
Consensus pattern (21 bp):
GGGTACCGATTCCCCTTGAAT
Found at i:20156 original size:30 final size:31
Alignment explanation
Indices: 20120--20179 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
20110 CTTAGCTTTA
**
20120 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
20150 TATTATGTTTACATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
20180 GGCAGCATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 23 0.85
31 4 0.15
ACGTcount: A:0.30, C:0.08, G:0.08, T:0.53
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:21102 original size:19 final size:20
Alignment explanation
Indices: 21078--21118 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
21068 AATTTATCTG
*
21078 CATT-AAAATTATGTATTTT
1 CATTAAAAATCATGTATTTT
*
21097 CATTAAAAATCATGTTTTTT
1 CATTAAAAATCATGTATTTT
21117 CA
1 CA
21119 AAGGGGTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.37, C:0.10, G:0.05, T:0.49
Consensus pattern (20 bp):
CATTAAAAATCATGTATTTT
Found at i:21866 original size:12 final size:11
Alignment explanation
Indices: 21840--21899 Score: 50
Period size: 12 Copynumber: 5.0 Consensus size: 11
21830 ATTGGAGTGC
21840 AAAAAG-AAAA
1 AAAAAGAAAAA
*
21850 GAAAAGACAAAA
1 AAAAAGA-AAAA
21862 AAAAAGAAAAA
1 AAAAAGAAAAA
21873 AAAATTTAGAAAAGA
1 AAAA---AGAAAA-A
21888 AGAAAAGAAAAA
1 A-AAAAGAAAAA
21900 GAAGTTCAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
10 5 0.12
11 8 0.20
12 11 0.27
13 6 0.15
14 6 0.15
15 2 0.05
16 3 0.07
ACGTcount: A:0.80, C:0.02, G:0.13, T:0.05
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:21911 original size:26 final size:26
Alignment explanation
Indices: 21863--21917 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
21853 AAGACAAAAA
*
21863 AAAAGAAAAAAAAATTTAGAAAAGAAG
1 AAAAGAAAAAAAAATTCAGAAAAG-AG
* *
21890 AAAAGAAAAAGAAGTTCA-AAAAGAG
1 AAAAGAAAAAAAAATTCAGAAAAGAG
21915 AAA
1 AAA
21918 GCAAGCCAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 5 0.20
26 5 0.20
27 15 0.60
ACGTcount: A:0.73, C:0.02, G:0.16, T:0.09
Consensus pattern (26 bp):
AAAAGAAAAAAAAATTCAGAAAAGAG
Found at i:23176 original size:24 final size:24
Alignment explanation
Indices: 23149--23216 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
23139 GACATGTCCT
* *
23149 TTGACGTTCCAACAGTTATGCCAC
1 TTGAAGTTCCAAAAGTTATGCCAC
* * *
23173 TTGAAGTTCAAAAAGATATGTCAC
1 TTGAAGTTCCAAAAGTTATGCCAC
*
23197 TTGAAGTGCCAAAAGTTATG
1 TTGAAGTTCCAAAAGTTATG
23217 ATCATTGAAG
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (24 bp):
TTGAAGTTCCAAAAGTTATGCCAC
Found at i:23232 original size:24 final size:23
Alignment explanation
Indices: 23156--23232 Score: 75
Period size: 24 Copynumber: 3.2 Consensus size: 23
23146 CCTTTGACGT
* *
23156 TCCAACAGTTATGCCACTTGAAG
1 TCCAAAAGTTATGTCACTTGAAG
* *
23179 TTCAAAAAGATATGTCACTTGAAG
1 -TCCAAAAGTTATGTCACTTGAAG
23203 TGCCAAAAGTTATGATCA-TTGAAG
1 T-CCAAAAGTTATG-TCACTTGAAG
23227 CTCCAA
1 -TCCAA
23233 GTTCATTACA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
23 1 0.02
24 39 0.89
25 4 0.09
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.27
Consensus pattern (23 bp):
TCCAAAAGTTATGTCACTTGAAG
Found at i:24312 original size:30 final size:31
Alignment explanation
Indices: 24260--24319 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
24250 CTTAGCTTTA
**
24260 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
**
24290 TATTATGTTTGTATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
24320 GGCAGCATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.28, C:0.07, G:0.10, T:0.55
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:25261 original size:19 final size:20
Alignment explanation
Indices: 25237--25279 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
25227 AGCATTTATC
*
25237 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
25256 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
25276 TTCA
1 TTCA
25280 AAGAGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:27163 original size:29 final size:30
Alignment explanation
Indices: 27092--27151 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
27082 CAATTTAAGG
*
27092 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACGTGAATTGAATTTA
27123 CAAAATGTTTTTGGACGT-AATTGAATTTA
1 CAAAATGTTTTTGGACGTGAATTGAATTTA
27152 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.42
Consensus pattern (30 bp):
CAAAATGTTTTTGGACGTGAATTGAATTTA
Found at i:27268 original size:22 final size:22
Alignment explanation
Indices: 27242--27286 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
27232 TTCAAGATTG
* *
27242 CCCAGGGGGTATAGATTCCCCC
1 CCCAGGGGGTACAGATACCCCC
27264 CCCAGGGGGTACAGATACCCCC
1 CCCAGGGGGTACAGATACCCCC
27286 C
1 C
27287 TGCAGGTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.40, G:0.27, T:0.13
Consensus pattern (22 bp):
CCCAGGGGGTACAGATACCCCC
Found at i:27350 original size:21 final size:21
Alignment explanation
Indices: 27324--27364 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
27314 AAATGTCCAG
27324 GGGGGTACCGATTCCCCCCCA
1 GGGGGTACCGATTCCCCCCCA
27345 GGGGGTACCGATTCCCCCCC
1 GGGGGTACCGATTCCCCCCC
27365 CTGTTCAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.12, C:0.44, G:0.29, T:0.15
Consensus pattern (21 bp):
GGGGGTACCGATTCCCCCCCA
Found at i:27426 original size:20 final size:21
Alignment explanation
Indices: 27401--27442 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
27391 ATTTGAATAT
*
27401 TATGAA-GGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
27421 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
27442 T
1 T
27443 CTATTCTGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:27508 original size:20 final size:22
Alignment explanation
Indices: 27470--27509 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
27460 TTTGAGTATA
27470 AAAATCATCCCCAAACGGCTCT
1 AAAATCATCCCCAAACGGCTCT
27492 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
27510 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCT
Found at i:27763 original size:34 final size:32
Alignment explanation
Indices: 27724--27793 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
27714 TTTTGTAAAG
*
27724 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
27758 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
27790 GGGA
1 GGGA
27794 GTTTGTAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:29978 original size:60 final size:60
Alignment explanation
Indices: 29896--30015 Score: 231
Period size: 60 Copynumber: 2.0 Consensus size: 60
29886 ATTTTTCAAA
29896 TGTTTTGTTATATCAAAAAGGGGGAGATTGTTAAACTATGTTTCGATATAACAATTTAAG
1 TGTTTTGTTATATCAAAAAGGGGGAGATTGTTAAACTATGTTTCGATATAACAATTTAAG
*
29956 TGTTTTGTTATATCAAAAAGGGGGAGATTGTTAAACTATGTTTTGATATAACAATTTAAG
1 TGTTTTGTTATATCAAAAAGGGGGAGATTGTTAAACTATGTTTCGATATAACAATTTAAG
30016 GCAAAATGGT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.35, C:0.06, G:0.20, T:0.39
Consensus pattern (60 bp):
TGTTTTGTTATATCAAAAAGGGGGAGATTGTTAAACTATGTTTCGATATAACAATTTAAG
Found at i:30046 original size:34 final size:30
Alignment explanation
Indices: 30008--30076 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 30
29998 TTGATATAAC
*
30008 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACGT-AATTG
30042 AATTT-ACAAAATGTTTTTGGACGTAATTG
1 AATTTAACAAAATGTTTTTGGACGTAATTG
30071 AATTTA
1 AATTTA
30077 TTCAAAGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 10 0.30
30 11 0.33
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.19, T:0.41
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACGTAATTG
Found at i:30088 original size:29 final size:30
Alignment explanation
Indices: 30017--30076 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
30007 CAATTTAAGG
*
30017 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACGTGAATTGAATTTA
30048 CAAAATGTTTTTGGACGT-AATTGAATTTA
1 CAAAATGTTTTTGGACGTGAATTGAATTTA
30077 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.42
Consensus pattern (30 bp):
CAAAATGTTTTTGGACGTGAATTGAATTTA
Found at i:30219 original size:15 final size:15
Alignment explanation
Indices: 30199--30228 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
30189 CCCCCCCAGG
30199 GGGTACAGATACCCC
1 GGGTACAGATACCCC
30214 GGGTACAGATACCCC
1 GGGTACAGATACCCC
30229 CCCAGGGGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.33, G:0.27, T:0.13
Consensus pattern (15 bp):
GGGTACAGATACCCC
Found at i:30256 original size:22 final size:21
Alignment explanation
Indices: 30189--30250 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
30179 AGATTCCCCC
30189 CCCCCCCAGGGGGTACAGATA
1 CCCCCCCAGGGGGTACAGATA
30210 ---CCCC---GGGTACAGATA
1 CCCCCCCAGGGGGTACAGATA
30225 CCCCCCCAGGGGGTACAGATA
1 CCCCCCCAGGGGGTACAGATA
30246 CCCCC
1 CCCCC
30251 TGCAGGTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
15 11 0.31
18 8 0.23
21 16 0.46
ACGTcount: A:0.23, C:0.42, G:0.26, T:0.10
Consensus pattern (21 bp):
CCCCCCCAGGGGGTACAGATA
Found at i:30326 original size:20 final size:21
Alignment explanation
Indices: 30284--30327 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
30274 AACAGAATGT
30284 CCAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
*
30305 CCAGTGGGTACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
30326 CC
1 CC
30328 TGTTCAACAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.45, G:0.25, T:0.16
Consensus pattern (21 bp):
CCAGGGGGTACCGATTCCCCC
Found at i:30389 original size:21 final size:21
Alignment explanation
Indices: 30363--30405 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
30353 ATTTGAATAT
*
30363 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
30384 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
30405 T
1 T
30406 CTATTCTGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:30726 original size:34 final size:32
Alignment explanation
Indices: 30687--30756 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
30677 TTTTGTAAAG
*
30687 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
30721 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
30753 GGGA
1 GGGA
30757 GTTTGTAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:34766 original size:8 final size:8
Alignment explanation
Indices: 34753--34793 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
34743 CTCATTTTCA
34753 GAGAATTT
1 GAGAATTT
34761 GAGAATTT
1 GAGAATTT
*
34769 -AGAGTTT
1 GAGAATTT
*
34776 GGGAATTT
1 GAGAATTT
34784 GAGAATTT
1 GAGAATTT
34792 GA
1 GA
34794 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:35092 original size:128 final size:128
Alignment explanation
Indices: 34864--35748 Score: 1628
Period size: 128 Copynumber: 6.9 Consensus size: 128
34854 TAATCGGAGT
34864 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
34929 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
34992 ACTATTCACATGAAGGCGCGTTCCCGGGGGAGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
*
35057 CATTGCCCTATTATGTCACTCACGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
35120 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
35185 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *
35248 ACTATTCATATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
35313 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
35376 ACTATTCACATGAAGGCGCGTTCCTGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
*
35441 CATTGCCCTATTATTTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *** *
35504 TC-AGGGGACATGAAGGCGCGTTCCCGGGGGGGCGCCTTCCATTATTTCGTCAGAGAATATGTTA
1 ACTA-TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTA
35568 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
65 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *
35632 ACTATTCACATGAAGGCGCGTTCCCGGGGGGGCGCCTTCCATTATTTCATCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
*
35697 CATTGCCCTATTATGTCACTCATGTCCCTCAGGGACACTAGATATATCAGTA
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
35749 AATCAGGTAA
Statistics
Matches: 732, Mismatches: 23, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
127 1 0.00
128 730 1.00
129 1 0.00
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (128 bp):
ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
Found at i:36187 original size:34 final size:34
Alignment explanation
Indices: 36149--36248 Score: 130
Period size: 33 Copynumber: 3.0 Consensus size: 34
36139 AAATTTAATG
*
36149 TTAAATTTTGAATACTATAATTTATATTTTAAAT
1 TTAAATTTTGAATAATATAATTTATATTTTAAAT
* * * *
36183 TTAAA-TTTGAATAATATTATTTTTATTTTTATT
1 TTAAATTTTGAATAATATAATTTATATTTTAAAT
* *
36216 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTTGAATAATATAATTTATATTTTAAA
36249 AACATTTATC
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
33 28 0.51
34 27 0.49
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (34 bp):
TTAAATTTTGAATAATATAATTTATATTTTAAAT
Found at i:36856 original size:21 final size:21
Alignment explanation
Indices: 36768--36861 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
36758 TATGGTATAA
*
36768 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
36789 AA-CCTGGCGGGCTAGGCATGT
1 AACCCT-GCGGGCTAGGAATGT
36810 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
36831 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
36852 AACCCTGCGG
1 AACCCTGCGG
36862 AGATGGCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 3 0.04
21 63 0.91
22 3 0.04
ACGTcount: A:0.20, C:0.27, G:0.35, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:36891 original size:21 final size:21
Alignment explanation
Indices: 36865--36912 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
36855 CCTGCGGAGA
*
36865 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
36886 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
36907 GGGCAT
1 TGGCAT
36913 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:38509 original size:18 final size:17
Alignment explanation
Indices: 38442--38515 Score: 58
Period size: 17 Copynumber: 4.2 Consensus size: 17
38432 TACATTATAA
* *
38442 AAAATAAAAATTAATAT
1 AAAATAAAAATAAATTT
* * * *
38459 AAATTCATAATAACTTT
1 AAAATAAAAATAAATTT
38476 AAAATAAAAATAAATTT
1 AAAATAAAAATAAATTT
* *
38493 AAATATTAAAATTAATTAT
1 AAA-ATAAAAATAAATT-T
38512 AAAA
1 AAAA
38516 AATATTATCA
Statistics
Matches: 43, Mismatches: 12, Indels: 3
0.74 0.21 0.05
Matches are distributed among these distances:
17 27 0.63
18 12 0.28
19 4 0.09
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAATAAAAATAAATTT
Found at i:38678 original size:34 final size:31
Alignment explanation
Indices: 38635--38723 Score: 97
Period size: 34 Copynumber: 2.7 Consensus size: 31
38625 TTAATAATTC
*
38635 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAAAAAATAATAATTATATAAATA-TA--TTAA
* *
38669 TAAAAAAATAATATTTACATAAATATATTAA
1 TAAAAAAATAATAATTATATAAATATATTAA
* *
38700 TATAAAAAATAATAACTATTTAAA
1 TA-AAAAAATAATAATTATATAAA
38724 AAAATACTAA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
31 6 0.13
32 17 0.36
33 2 0.04
34 22 0.47
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (31 bp):
TAAAAAAATAATAATTATATAAATATATTAA
Found at i:38680 original size:31 final size:33
Alignment explanation
Indices: 38638--38712 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 33
38628 ATAATTCTAA
* * *
38638 ATAAATAATAATTATATAAAT-ATTATTTTAAT
1 ATAAAAAATAATTATATAAATAAATATATTAAT
* *
38670 A-AAAAAATAA-TATTTACATAAATATATTAAT
1 ATAAAAAATAATTATATAAATAAATATATTAAT
38701 ATAAAAAATAAT
1 ATAAAAAATAAT
38713 AACTATTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
30 7 0.20
31 18 0.51
32 10 0.29
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (33 bp):
ATAAAAAATAATTATATAAATAAATATATTAAT
Found at i:38739 original size:34 final size:35
Alignment explanation
Indices: 38670--38745 Score: 95
Period size: 34 Copynumber: 2.2 Consensus size: 35
38660 TTATTTTAAT
* * *
38670 AAAAA-AATAATATTTACATAAATATATTAATATA
1 AAAAATAATAATATTTACATAAAAATACTAACATA
38704 AAAAATAATAACTATTTA-A-AAAAATACTAACATA
1 AAAAATAATAA-TATTTACATAAAAATACTAACATA
38738 AAAAATAA
1 AAAAATAA
38746 ATTTCTTACC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
34 25 0.68
35 6 0.16
36 6 0.16
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (35 bp):
AAAAATAATAATATTTACATAAAAATACTAACATA
Found at i:42572 original size:25 final size:24
Alignment explanation
Indices: 42521--42573 Score: 63
Period size: 26 Copynumber: 2.2 Consensus size: 24
42511 ATTTTCTAAA
*
42521 AAAATATAATATATACGGTTTTCG
1 AAAATATAATATATACAGTTTTCG
*
42545 AAAATATATATATTATATAGTTTT-G
1 AAAATATA-ATA-TATACAGTTTTCG
42570 AAAA
1 AAAA
42574 CATTTCGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 8 0.32
25 8 0.32
26 9 0.36
ACGTcount: A:0.47, C:0.04, G:0.09, T:0.40
Consensus pattern (24 bp):
AAAATATAATATATACAGTTTTCG
Found at i:42592 original size:64 final size:63
Alignment explanation
Indices: 42501--42662 Score: 175
Period size: 64 Copynumber: 2.6 Consensus size: 63
42491 ATAGTATAAT
* * **** *
42501 TTTTGAAAATATTTTCTAAAA-AAATATAATATATACGGTTTTCGAAAATATATATATTATATAG
1 TTTTGAAAACA-TTTCTAAAATATATATAATATATAAAAATTT-GAAAATATATATAATATATAG
* * * *
42565 TTTTGAAAACATTTCGAAAATATATATAGTTTTAAAAAAATTTGAAAATATATATAATATATAG
1 TTTTGAAAACATTTCTAAAATATATATA-ATATATAAAAATTTGAAAATATATATAATATATAG
*
42629 TTTTGAAAACGTTT-TAAAATATATATAATATATA
1 TTTTGAAAACATTTCTAAAATATATATAATATATA
42663 GCTTTTGAAA
Statistics
Matches: 80, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
62 4 0.05
63 20 0.25
64 49 0.61
65 7 0.09
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.41
Consensus pattern (63 bp):
TTTTGAAAACATTTCTAAAATATATATAATATATAAAAATTTGAAAATATATATAATATATAG
Found at i:42612 original size:28 final size:29
Alignment explanation
Indices: 42558--42620 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
42548 ATATATATAT
* *
42558 TATATAGTTTTGAAAACATTTCGAAAATA
1 TATATAGTTTTAAAAAAATTTCGAAAATA
42587 TATATAGTTTTAAAAAAATTT-GAAAATA
1 TATATAGTTTTAAAAAAATTTCGAAAATA
42615 TATATA
1 TATATA
42621 ATATATAGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 13 0.41
29 19 0.59
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.40
Consensus pattern (29 bp):
TATATAGTTTTAAAAAAATTTCGAAAATA
Found at i:42632 original size:35 final size:35
Alignment explanation
Indices: 42586--42700 Score: 149
Period size: 35 Copynumber: 3.2 Consensus size: 35
42576 TTTCGAAAAT
42586 ATATATAGTTTTAAAAAAATTTGAAAATATATATA
1 ATATATAGTTTTAAAAAAATTTGAAAATATATATA
* ** *
42621 ATATATAGTTTTGAAAACGTTTTAAAATATATATA
1 ATATATAGTTTTAAAAAAATTTGAAAATATATATA
* *
42656 ATATATAGCTTTTGAAAAAAAATTGAAAACATATATA
1 ATATATAG-TTTT-AAAAAAATTTGAAAATATATATA
42693 TATATATA
1 -ATATATA
42701 TATTATATTG
Statistics
Matches: 67, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
35 39 0.58
36 4 0.06
37 17 0.25
38 7 0.10
ACGTcount: A:0.51, C:0.03, G:0.07, T:0.39
Consensus pattern (35 bp):
ATATATAGTTTTAAAAAAATTTGAAAATATATATA
Found at i:42698 original size:47 final size:47
Alignment explanation
Indices: 42647--42750 Score: 138
Period size: 47 Copynumber: 2.2 Consensus size: 47
42637 ACGTTTTAAA
42647 ATATATATAATATATAGCTTTTGAAAAAAAATTGAAAACATATATAT
1 ATATATATAATATATAGCTTTTGAAAAAAAATTGAAAACATATATAT
* * * * * **
42694 ATATATATATTATATTGTTTTTTAAAACATTTTGAAAACATATATAT
1 ATATATATAATATATAGCTTTTGAAAAAAAATTGAAAACATATATAT
42741 A-ATATATAAT
1 ATATATATAAT
42751 TTTTAAAACA
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
46 8 0.16
47 41 0.84
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (47 bp):
ATATATATAATATATAGCTTTTGAAAAAAAATTGAAAACATATATAT
Found at i:42726 original size:11 final size:11
Alignment explanation
Indices: 42712--42811 Score: 56
Period size: 11 Copynumber: 8.2 Consensus size: 11
42702 ATTATATTGT
42712 TTTTTAAAACA
1 TTTTTAAAACA
*
42723 TTTTGAAAACA
1 TTTTTAAAACA
* *
42734 TATATATAATATATAA
1 T-T-TTTAA-A-A-CA
42750 TTTTTAAAACA
1 TTTTTAAAACA
42761 TTTTTAAAACA
1 TTTTTAAAACA
* *
42772 TATATATAATATATA
1 T-T-TTTAA-A-ACA
42787 GTTTTTAAAACA
1 -TTTTTAAAACA
*
42799 TTTTGAAAACA
1 TTTTTAAAACA
42810 TT
1 TT
42812 ATATAGGTTT
Statistics
Matches: 68, Mismatches: 11, Indels: 20
0.69 0.11 0.20
Matches are distributed among these distances:
11 36 0.53
12 5 0.07
13 9 0.13
14 10 0.15
15 5 0.07
16 3 0.04
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (11 bp):
TTTTTAAAACA
Found at i:42763 original size:38 final size:38
Alignment explanation
Indices: 42694--42816 Score: 185
Period size: 38 Copynumber: 3.2 Consensus size: 38
42684 ACATATATAT
* **
42694 ATATATATATTATATTGTTTTTTAAAACATTTTGAAAAC
1 ATATATATAATATA-TAATTTTTAAAACATTTTGAAAAC
*
42733 ATATATATAATATATAATTTTTAAAACATTTTTAAAAC
1 ATATATATAATATATAATTTTTAAAACATTTTGAAAAC
*
42771 ATATATATAATATATAGTTTTTAAAACATTTTGAAAAC
1 ATATATATAATATATAATTTTTAAAACATTTTGAAAAC
42809 AT-TATATA
1 ATATATATA
42817 GGTTTTGAAA
Statistics
Matches: 78, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
37 6 0.08
38 59 0.76
39 13 0.17
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (38 bp):
ATATATATAATATATAATTTTTAAAACATTTTGAAAAC
Found at i:42846 original size:31 final size:30
Alignment explanation
Indices: 42779--42847 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 30
42769 ACATATATAT
*
42779 AATATATAGTTTTTAAAACATTTTGAAAAC
1 AATATATAGTTTTGAAAACATTTTGAAAAC
* *
42809 ATTATATAGGTTTTGAAAACATTTTTTAAAA-
1 AATATATA-GTTTTGAAAACA-TTTTGAAAAC
42840 AATATATA
1 AATATATA
42848 ATGTATAGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 7 0.21
31 18 0.55
32 8 0.24
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.42
Consensus pattern (30 bp):
AATATATAGTTTTGAAAACATTTTGAAAAC
Found at i:42938 original size:3 final size:3
Alignment explanation
Indices: 42914--42952 Score: 51
Period size: 3 Copynumber: 12.0 Consensus size: 3
42904 TTTTTTGAAA
42914 ATT ATAT ATT ATAT AGTT ATT ATT ATT ATT ATT ATT ATT
1 ATT AT-T ATT AT-T A-TT ATT ATT ATT ATT ATT ATT ATT
42953 TATTGTTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
3 25 0.76
4 7 0.21
5 1 0.03
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:42961 original size:7 final size:7
Alignment explanation
Indices: 42914--42980 Score: 50
Period size: 7 Copynumber: 9.4 Consensus size: 7
42904 TTTTTTGAAA
*
42914 ATTATAT
1 ATTATTT
*
42921 ATTATAT
1 ATTATTT
42928 AGTTA-TT
1 A-TTATTT
42935 ATTA-TT
1 ATTATTT
42941 ATTA-TT
1 ATTATTT
42947 ATTATTT
1 ATTATTT
*
42954 ATTGTTT
1 ATTATTT
42961 ATTTCATTT
1 A-TT-ATTT
42970 ATTTATTT
1 A-TTATTT
42978 ATT
1 ATT
42981 TTGTTTGTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
6 15 0.28
7 21 0.40
8 10 0.19
9 7 0.13
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.66
Consensus pattern (7 bp):
ATTATTT
Found at i:44500 original size:4 final size:4
Alignment explanation
Indices: 44491--44533 Score: 59
Period size: 4 Copynumber: 10.0 Consensus size: 4
44481 GATCCTCTAC
44491 ATTT ATTT ATTT ATTT ATTT ATTT ATTAT ATATT ATTTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATT-T AT-TT A-TTT ATTT
44534 TAATTTTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
4 26 0.72
5 8 0.22
6 2 0.06
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:44579 original size:2 final size:2
Alignment explanation
Indices: 44572--44612 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
44562 AACCTTATTT
44572 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
44613 TGTATTTTAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:55936 original size:38 final size:38
Alignment explanation
Indices: 55885--55973 Score: 169
Period size: 38 Copynumber: 2.3 Consensus size: 38
55875 AAAAAAACAA
55885 TAATGACTAAATAGATTAAAATGGATTTTTATATAGTG
1 TAATGACTAAATAGATTAAAATGGATTTTTATATAGTG
55923 TAATGACTAAATAGATTAAAATGGATTTTTATATAGTG
1 TAATGACTAAATAGATTAAAATGGATTTTTATATAGTG
*
55961 TAAAGACTAAATA
1 TAATGACTAAATA
55974 AACTCTGATC
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 50 1.00
ACGTcount: A:0.45, C:0.03, G:0.15, T:0.37
Consensus pattern (38 bp):
TAATGACTAAATAGATTAAAATGGATTTTTATATAGTG
Found at i:55964 original size:22 final size:22
Alignment explanation
Indices: 55901--55964 Score: 52
Period size: 22 Copynumber: 3.2 Consensus size: 22
55891 CTAAATAGAT
55901 TAAAATGGATTTTTATATAGTG
1 TAAAATGGATTTTTATATAGTG
* *
55923 T--AAT-GA---CTAAATAGAT-
1 TAAAATGGATTTTTATATAG-TG
55939 TAAAATGGATTTTTATATAGTG
1 TAAAATGGATTTTTATATAGTG
55961 TAAA
1 TAAA
55965 GACTAAATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 16
0.60 0.08 0.32
Matches are distributed among these distances:
16 7 0.23
17 1 0.03
18 3 0.10
19 4 0.13
20 3 0.10
21 1 0.03
22 11 0.37
ACGTcount: A:0.42, C:0.02, G:0.16, T:0.41
Consensus pattern (22 bp):
TAAAATGGATTTTTATATAGTG
Found at i:57926 original size:15 final size:15
Alignment explanation
Indices: 57906--57956 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
57896 ATTATTAGCC
*
57906 TATTTTATTTTATTT
1 TATTTTATTTTATAT
57921 TATTTTATTTTATAT
1 TATTTTATTTTATAT
* *
57936 TATATTATATTA-AT
1 TATTTTATTTTATAT
*
57950 CATTTTA
1 TATTTTA
57957 ACTATTTGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
14 7 0.23
15 24 0.77
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (15 bp):
TATTTTATTTTATAT
Found at i:57947 original size:5 final size:5
Alignment explanation
Indices: 57906--57943 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
57896 ATTATTAGCC
* *
57906 TATTT TATTT TATTT TATTT TATTT TATAT TATAT TAT
1 TATTT TATTT TATTT TATTT TATTT TATTT TATTT TAT
57944 ATTAATCATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (5 bp):
TATTT
Found at i:64069 original size:13 final size:14
Alignment explanation
Indices: 64053--64081 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
64043 TTTTCTACTG
64053 TACTTTT-AAAAGT
1 TACTTTTCAAAAGT
64066 TACTTTTCAAAAGT
1 TACTTTTCAAAAGT
64080 TA
1 TA
64082 TACCAAACTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (14 bp):
TACTTTTCAAAAGT
Done.