Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005417.1 Hibiscus syriacus cultivar Beakdansim tig00012427_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: 80564
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:6131 original size:21 final size:21
Alignment explanation
Indices: 6093--6132 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
6083 AAAAAATTAC
*
6093 CTAAAATATTATTATTTTTAT
1 CTAAAATATTAATATTTTTAT
*
6114 CTAAAATATTAATGTTTTT
1 CTAAAATATTAATATTTTT
6133 TAACATTTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.55
Consensus pattern (21 bp):
CTAAAATATTAATATTTTTAT
Found at i:6183 original size:20 final size:20
Alignment explanation
Indices: 6158--6202 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
6148 AGTGTCCAAC
*
6158 AATAACGAAATCATAGAAAA
1 AATAACAAAATCATAGAAAA
* *
6178 AATAACAAAATGATAGAAAT
1 AATAACAAAATCATAGAAAA
6198 AATAA
1 AATAA
6203 TGTTTTCGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.67, C:0.07, G:0.09, T:0.18
Consensus pattern (20 bp):
AATAACAAAATCATAGAAAA
Found at i:10765 original size:30 final size:28
Alignment explanation
Indices: 10731--10793 Score: 76
Period size: 27 Copynumber: 2.2 Consensus size: 28
10721 TTTATTTTTT
* *
10731 ATAATTAAATATTTTTAAATTTTATAAAAA
1 ATAATTAAA-ATTATCAAA-TTTATAAAAA
10761 ATAATT-AAATTATCAAATTTATAAAAA
1 ATAATTAAAATTATCAAATTTATAAAAA
10788 A-AATTA
1 ATAATTA
10794 GATTAAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
26 4 0.13
27 11 0.37
28 7 0.23
29 2 0.07
30 6 0.20
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (28 bp):
ATAATTAAAATTATCAAATTTATAAAAA
Found at i:10808 original size:27 final size:28
Alignment explanation
Indices: 10747--10808 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 28
10737 AAATATTTTT
*
10747 AAATTTTATAAAAAATAATTAAATTATC
1 AAATTTTATAAAAAATAATTAAATTATA
*
10775 AAA-TTTATAAAAAA-AATTAGATTA-A
1 AAATTTTATAAAAAATAATTAAATTATA
10800 AAATGTTTA
1 AAAT-TTTA
10809 GCACCCCGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
25 3 0.10
26 9 0.30
27 15 0.50
28 3 0.10
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (28 bp):
AAATTTTATAAAAAATAATTAAATTATA
Found at i:13780 original size:21 final size:21
Alignment explanation
Indices: 13755--13798 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
13745 TCTTTTTTAA
13755 TTTTATGATGATATATACGTG
1 TTTTATGATGATATATACGTG
13776 TTTTATGATGATATATACGTG
1 TTTTATGATGATATATACGTG
13797 TT
1 TT
13799 ATACAGTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.27, C:0.05, G:0.18, T:0.50
Consensus pattern (21 bp):
TTTTATGATGATATATACGTG
Found at i:25839 original size:60 final size:60
Alignment explanation
Indices: 25717--25847 Score: 149
Period size: 60 Copynumber: 2.2 Consensus size: 60
25707 TATGATTCTA
* * *
25717 ATTCTAAATTAGTCTCTAAACTTTTAAATATTACAATTTTATTCTTAAATTATAAATGTC
1 ATTCTAAATTAGTCTCTAAACTTTCAAATATTACAATTTCATTCTTAAACTATAAATGTC
** * * *
25777 ATTCTAAATTAGTCAT-TAAACTTTCAAATATTTTAATTTCA-TCTTCAAACTATGACTTTC
1 ATTCTAAATTAGTC-TCTAAACTTTCAAATATTACAATTTCATTCTT-AAACTATAAATGTC
*
25837 ATTCTGAATTA
1 ATTCTAAATTA
25848 AGCAAAACCC
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
59 4 0.07
60 55 0.92
61 1 0.02
ACGTcount: A:0.37, C:0.14, G:0.04, T:0.46
Consensus pattern (60 bp):
ATTCTAAATTAGTCTCTAAACTTTCAAATATTACAATTTCATTCTTAAACTATAAATGTC
Found at i:26807 original size:20 final size:21
Alignment explanation
Indices: 26782--26820 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
26772 GGCTGCTGGA
26782 AACCGGTT-TAACCGGTTTTC
1 AACCGGTTCTAACCGGTTTTC
*
26802 AACCGGTTCTGACCGGTTT
1 AACCGGTTCTAACCGGTTT
26821 GACCTGTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.33
Consensus pattern (21 bp):
AACCGGTTCTAACCGGTTTTC
Found at i:26818 original size:10 final size:9
Alignment explanation
Indices: 26783--26881 Score: 63
Period size: 10 Copynumber: 10.3 Consensus size: 9
26773 GCTGCTGGAA
*
26783 ACCGGTTTA
1 ACCGGTTTG
*
26792 ACCGGTTTTCA
1 ACCGG-TTT-G
26803 ACCGGTTCTG
1 ACCGGTT-TG
26813 ACCGGTTTG
1 ACCGGTTTG
* *
26822 ACCTGTTTCA
1 ACCGGTTT-G
*
26832 ACCGGTTCG
1 ACCGGTTTG
*
26841 AACCGATTTG
1 -ACCGGTTTG
*
26851 ACCGGTCTG
1 ACCGGTTTG
*
26860 AACCAGTTTG
1 -ACCGGTTTG
*
26870 ACCGGTCTG
1 ACCGGTTTG
26879 ACC
1 ACC
26882 CGACCCGACC
Statistics
Matches: 70, Mismatches: 14, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
9 31 0.44
10 32 0.46
11 7 0.10
ACGTcount: A:0.18, C:0.28, G:0.24, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:26834 original size:29 final size:29
Alignment explanation
Indices: 26783--26881 Score: 103
Period size: 29 Copynumber: 3.4 Consensus size: 29
26773 GCTGCTGGAA
*
26783 ACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 ACCGGTTTGACCGG-TTTCAACCGGTTCTG
*
26813 ACCGGTTTGACCTGTTTCAACCGGTTC-G
1 ACCGGTTTGACCGGTTTCAACCGGTTCTG
* * * *
26841 AACCGATTTGACCGGTCTGAACCAGTT-TG
1 -ACCGGTTTGACCGGTTTCAACCGGTTCTG
*
26870 ACCGGTCTGACC
1 ACCGGTTTGACC
26882 CGACCCGACC
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
28 11 0.19
29 35 0.60
30 12 0.21
ACGTcount: A:0.18, C:0.28, G:0.24, T:0.29
Consensus pattern (29 bp):
ACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:26854 original size:19 final size:20
Alignment explanation
Indices: 26782--26879 Score: 64
Period size: 19 Copynumber: 5.0 Consensus size: 20
26772 GGCTGCTGGA
* * * *
26782 AACCGGTTTAACCGGTTTTC
1 AACCAGTTTGACCGGTTCTG
*
26802 AACCGGTTCTGACCGGTT-TG
1 AACCAGTT-TGACCGGTTCTG
* *
26822 -ACCTGTTTCAACCGGTTC-G
1 AACCAGTTT-GACCGGTTCTG
26841 AACC-GATTTGACCGG-TCTG
1 AACCAG-TTTGACCGGTTCTG
26860 AACCAGTTTGACCGG-TCTG
1 AACCAGTTTGACCGGTTCTG
26879 A
1 A
26880 CCCGACCCGA
Statistics
Matches: 66, Mismatches: 5, Indels: 15
0.77 0.06 0.17
Matches are distributed among these distances:
18 3 0.05
19 39 0.59
20 16 0.24
21 8 0.12
ACGTcount: A:0.19, C:0.27, G:0.24, T:0.30
Consensus pattern (20 bp):
AACCAGTTTGACCGGTTCTG
Found at i:26899 original size:17 final size:17
Alignment explanation
Indices: 26877--26915 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
26867 TTGACCGGTC
26877 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
26894 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
26911 TGACC
1 TGACC
26916 GTTGACCGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.18, C:0.46, G:0.23, T:0.13
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:28544 original size:60 final size:60
Alignment explanation
Indices: 28463--28607 Score: 150
Period size: 60 Copynumber: 2.4 Consensus size: 60
28453 ATTAGTCTCT
** *
28463 AAACTTTTAAATATTACAATTTTTTCCTT-AAACAATAATTTTCATTCTAAATTAATCATC
1 AAACTTTTAAATATTACAATTTCAT-CTTAAAACAATAACTTTCATTCTAAATTAATCATC
** * * * *
28523 AAACTTTTAAATATTTTAATTTCATCTTAAAACTATAACTTTCATTTTAAATTAGTC-CC
1 AAACTTTTAAATATTACAATTTCATCTTAAAACAATAACTTTCATTCTAAATTAATCATC
* *
28582 TAAACTTTTTGAATATTTCAATTTCA
1 -AAAC-TTTTAAATATTACAATTTCA
28608 CCCCAAAAAT
Statistics
Matches: 71, Mismatches: 11, Indels: 5
0.82 0.13 0.06
Matches are distributed among these distances:
59 4 0.06
60 49 0.69
61 18 0.25
ACGTcount: A:0.38, C:0.14, G:0.01, T:0.46
Consensus pattern (60 bp):
AAACTTTTAAATATTACAATTTCATCTTAAAACAATAACTTTCATTCTAAATTAATCATC
Found at i:28972 original size:3 final size:3
Alignment explanation
Indices: 28960--29018 Score: 111
Period size: 3 Copynumber: 20.0 Consensus size: 3
28950 ATCCTACGCT
28960 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
29007 ATA ATA ATA ATA
1 ATA ATA ATA ATA
29019 TTATTATTAT
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 53 0.96
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:29023 original size:3 final size:3
Alignment explanation
Indices: 29017--29058 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
29007 ATAATAATAA
29017 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
29059 AATAAAACAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:38652 original size:18 final size:18
Alignment explanation
Indices: 38626--38660 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
38616 TCAAAAGGAC
*
38626 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
38644 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
38661 CCGAATGGCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:39798 original size:12 final size:12
Alignment explanation
Indices: 39783--39821 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
39773 GATACGTTAC
39783 CTGAATTCTGTT
1 CTGAATTCTGTT
*
39795 CTG-ATTCTGAT
1 CTGAATTCTGTT
*
39806 CTGGATTCTGTT
1 CTGAATTCTGTT
39818 CTGA
1 CTGA
39822 TATCTGATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.15, C:0.18, G:0.21, T:0.46
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:39827 original size:12 final size:11
Alignment explanation
Indices: 39787--39827 Score: 55
Period size: 12 Copynumber: 3.5 Consensus size: 11
39777 CGTTACCTGA
39787 ATTCTGTTCTG
1 ATTCTGTTCTG
*
39798 ATTCTGATCTGG
1 ATTCTGTTCT-G
39810 ATTCTGTTCTG
1 ATTCTGTTCTG
39821 ATATCTG
1 AT-TCTG
39828 ATATGAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
11 12 0.46
12 14 0.54
ACGTcount: A:0.15, C:0.17, G:0.20, T:0.49
Consensus pattern (11 bp):
ATTCTGTTCTG
Found at i:40025 original size:2 final size:2
Alignment explanation
Indices: 40018--40082 Score: 94
Period size: 2 Copynumber: 32.0 Consensus size: 2
40008 GATGGGGGTG
* * *
40018 TA TA TA TA TA TA TGC TT TA AA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
40061 TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
40083 CTGGTTTTAT
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
2 56 0.98
3 1 0.02
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:42070 original size:18 final size:18
Alignment explanation
Indices: 42045--42091 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
42035 CGACTCGTTT
42045 ACCCGTTGACCCGACCCG
1 ACCCGTTGACCCGACCCG
*
42063 ACCTGTTGACCCGACCCG
1 ACCCGTTGACCCGACCCG
42081 ACCCGTTGACC
1 ACCCGTTGACC
42092 GTTGACCGGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.17, C:0.47, G:0.21, T:0.15
Consensus pattern (18 bp):
ACCCGTTGACCCGACCCG
Found at i:43437 original size:18 final size:18
Alignment explanation
Indices: 43411--43445 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
43401 TCAAAATGAC
*
43411 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
43429 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
43446 CCGGATGGCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:44571 original size:24 final size:23
Alignment explanation
Indices: 44544--44607 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
44534 ATTTCCGAAT
*
44544 TGAATTCTGTTCTGATACGTTACC
1 TGAATTCTGTTCTGATAC-TGACC
* * *
44568 TGAATTCTGTTATGATTCTGATC
1 TGAATTCTGTTCTGATACTGACC
*
44591 TGGATTCTGTTCTGATA
1 TGAATTCTGTTCTGATA
44608 TGTGATATGA
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
23 17 0.52
24 16 0.48
ACGTcount: A:0.20, C:0.16, G:0.19, T:0.45
Consensus pattern (23 bp):
TGAATTCTGTTCTGATACTGACC
Found at i:44619 original size:47 final size:48
Alignment explanation
Indices: 44530--44637 Score: 121
Period size: 47 Copynumber: 2.3 Consensus size: 48
44520 AAATATTTTA
* * * *
44530 TATGATTTCCGAAT-TGAATTCTGTTCTGATACGTTACCTGAATTCTGT
1 TATGATTTCTG-ATCTGGATTCTGTTCTGATACGTGACATGAATTCTGT
* * *
44578 TATGA-TTCTGATCTGGATTCTGTTCTGATATGTGATATGAATTTTGT
1 TATGATTTCTGATCTGGATTCTGTTCTGATACGTGACATGAATTCTGT
*
44625 TTTGATTTCTGAT
1 TATGATTTCTGAT
44638 ATCTCCTTTT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
46 2 0.04
47 36 0.72
48 12 0.24
ACGTcount: A:0.21, C:0.12, G:0.19, T:0.48
Consensus pattern (48 bp):
TATGATTTCTGATCTGGATTCTGTTCTGATACGTGACATGAATTCTGT
Found at i:44625 original size:24 final size:24
Alignment explanation
Indices: 44544--44639 Score: 81
Period size: 24 Copynumber: 4.0 Consensus size: 24
44534 ATTTCCGAAT
*
44544 TGAATTCTGTTCTGATA-C-GTTA
1 TGAATTCTGTTCTGATATCTGATA
* *
44566 CCTGAATTCTGTTATGAT-TCTGATC
1 --TGAATTCTGTTCTGATATCTGATA
* *
44591 TGGATTCTGTTCTGATATGTGATA
1 TGAATTCTGTTCTGATATCTGATA
* * *
44615 TGAATTTTGTTTTGATTTCTGATA
1 TGAATTCTGTTCTGATATCTGATA
44639 T
1 T
44640 CTCCTTTTAC
Statistics
Matches: 57, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
23 14 0.25
24 41 0.72
25 2 0.04
ACGTcount: A:0.21, C:0.11, G:0.19, T:0.49
Consensus pattern (24 bp):
TGAATTCTGTTCTGATATCTGATA
Found at i:44826 original size:2 final size:2
Alignment explanation
Indices: 44821--44860 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
44811 ATGCTTTAAA
44821 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
44861 TTTACTGGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46855 original size:13 final size:13
Alignment explanation
Indices: 46839--46880 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
46829 CGTTTACCCA
*
46839 ACCCGACCTTTTG
1 ACCCGACCTGTTG
* *
46852 ACCCGACCCGTTA
1 ACCCGACCTGTTG
46865 ACCCGACCTGTTG
1 ACCCGACCTGTTG
46878 ACC
1 ACC
46881 GTTGACCACT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.19, C:0.43, G:0.17, T:0.21
Consensus pattern (13 bp):
ACCCGACCTGTTG
Found at i:48205 original size:18 final size:18
Alignment explanation
Indices: 48182--48219 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
48172 TGTTCAAAAG
*
48182 GATTGAAGTAAATGATAA
1 GATTGAAGTAAATAATAA
*
48200 GATTGAATTAAATAATAA
1 GATTGAAGTAAATAATAA
48218 GA
1 GA
48220 CCGGATGGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.18, T:0.29
Consensus pattern (18 bp):
GATTGAAGTAAATAATAA
Found at i:49354 original size:12 final size:11
Alignment explanation
Indices: 49319--49403 Score: 55
Period size: 12 Copynumber: 7.3 Consensus size: 11
49309 TCCGAATTGA
49319 ATTCTGTTCTG
1 ATTCTGTTCTG
*
49330 ATAC-GTTACCTG
1 ATTCTGTT--CTG
49342 AATTCTGTTCTG
1 -ATTCTGTTCTG
*
49354 ATTCTGATCTGG
1 ATTCTGTTCT-G
*
49366 ATTCTATTCTG
1 ATTCTGTTCTG
* *
49377 ATATCTGATATG
1 AT-TCTGTTCTG
*
49389 AATTCTGTTTTG
1 -ATTCTGTTCTG
49401 ATT
1 ATT
49404 TCGGATATCT
Statistics
Matches: 57, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
10 3 0.05
11 18 0.32
12 28 0.49
13 5 0.09
14 3 0.05
ACGTcount: A:0.20, C:0.15, G:0.16, T:0.48
Consensus pattern (11 bp):
ATTCTGTTCTG
Found at i:49402 original size:24 final size:23
Alignment explanation
Indices: 49316--49403 Score: 88
Period size: 24 Copynumber: 3.7 Consensus size: 23
49306 ATTTCCGAAT
* *
49316 TGAATTCTGTTCTGATAC-GTTA
1 TGAATTCTGTTCTGATTCTGATA
*
49338 CCTGAATTCTGTTCTGATTCTGATC
1 --TGAATTCTGTTCTGATTCTGATA
* *
49363 TGGATTCTATTCTGATATCTGATA
1 TGAATTCTGTTCTGAT-TCTGATA
*
49387 TGAATTCTGTTTTGATT
1 TGAATTCTGTTCTGATT
49404 TCGGATATCT
Statistics
Matches: 53, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
23 15 0.28
24 36 0.68
25 2 0.04
ACGTcount: A:0.20, C:0.15, G:0.17, T:0.48
Consensus pattern (23 bp):
TGAATTCTGTTCTGATTCTGATA
Found at i:49410 original size:24 final size:24
Alignment explanation
Indices: 49302--49411 Score: 84
Period size: 24 Copynumber: 4.6 Consensus size: 24
49292 AAATATTTTA
*
49302 TCTGATTTCCGA-ATTGAATTCTGT
1 TCTGATTTCTGATA-TGAATTCTGT
* *
49326 TCTGA-TAC-GTTACCTGAATTCTGT
1 TCTGATTTCTGATA--TGAATTCTGT
* * *
49350 TCTGA-TTCTGATCTGGATTCTAT
1 TCTGATTTCTGATATGAATTCTGT
*
49373 TCTGATATCTGATATGAATTCTGT
1 TCTGATTTCTGATATGAATTCTGT
* *
49397 TTTGATTTCGGATAT
1 TCTGATTTCTGATAT
49412 CTCCGTTTAC
Statistics
Matches: 67, Mismatches: 15, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
22 1 0.01
23 16 0.24
24 48 0.72
25 2 0.03
ACGTcount: A:0.21, C:0.15, G:0.17, T:0.46
Consensus pattern (24 bp):
TCTGATTTCTGATATGAATTCTGT
Found at i:49598 original size:2 final size:2
Alignment explanation
Indices: 49593--49648 Score: 98
Period size: 2 Copynumber: 29.0 Consensus size: 2
49583 GCTTTAAAAA
49593 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
49634 AT -T AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
49649 TTTATGGAAC
Statistics
Matches: 52, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.04
2 50 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:69140 original size:48 final size:48
Alignment explanation
Indices: 69062--69156 Score: 154
Period size: 48 Copynumber: 2.0 Consensus size: 48
69052 CCAACCATAG
* * *
69062 GGTATTACTTTGTTGAGTCTCATGATTATTAAAAGTTACAAAATGATC
1 GGTATTACTTTGTTGAGTCCCACGACTATTAAAAGTTACAAAATGATC
*
69110 GGTATTACTTTGTTGAGTCCCCCGACTATTAAAAGTTACAAAATGAT
1 GGTATTACTTTGTTGAGTCCCACGACTATTAAAAGTTACAAAATGAT
69157 TATCCGACTA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.37
Consensus pattern (48 bp):
GGTATTACTTTGTTGAGTCCCACGACTATTAAAAGTTACAAAATGATC
Found at i:74430 original size:24 final size:24
Alignment explanation
Indices: 74403--74454 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
74393 TATGGAAACA
* *
74403 CAAAGGTTTAGTGCTT-AGAACATT
1 CAAAGCTTTAGGGCTTGA-AACATT
*
74427 CAAAGCTTTGGGGCTTGAAACATT
1 CAAAGCTTTAGGGCTTGAAACATT
74451 CAAA
1 CAAA
74455 ATTCTGGGGC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 23 0.96
25 1 0.04
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (24 bp):
CAAAGCTTTAGGGCTTGAAACATT
Found at i:75369 original size:42 final size:41
Alignment explanation
Indices: 75308--75399 Score: 121
Period size: 42 Copynumber: 2.2 Consensus size: 41
75298 CTCGAATAAC
* * *
75308 TCGTGTTTGTTTCATGTAATTTGTTTTTCGAAAAATATTTTT
1 TCGTGTTTGTTTCACGTAATTTGTTTTTAGAAAAAT-GTTTT
* *
75350 TCGTGTTTGTTTTACGTAATTTGTTTTTAGGAAAATGTTTT
1 TCGTGTTTGTTTCACGTAATTTGTTTTTAGAAAAATGTTTT
*
75391 TAGTGTTTG
1 TCGTGTTTG
75400 ATTGGAGGAA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 12 0.27
42 32 0.73
ACGTcount: A:0.20, C:0.05, G:0.18, T:0.57
Consensus pattern (41 bp):
TCGTGTTTGTTTCACGTAATTTGTTTTTAGAAAAATGTTTT
Found at i:75655 original size:26 final size:24
Alignment explanation
Indices: 75593--75655 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 24
75583 CATTTTAATC
75593 AAAATAT-TAATTATTAAAATATTT
1 AAAATATAT-ATTATTAAAATATTT
*
75617 AAAATATAT-TTATTAATAT-TTCT
1 AAAATATATATTATTAAAATATT-T
75640 AATAATATAATATTAT
1 AA-AATAT-ATATTAT
75656 ATTTTTATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.06
23 12 0.36
24 12 0.36
25 3 0.09
26 4 0.12
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAATATATATTATTAAAATATTT
Found at i:75736 original size:31 final size:30
Alignment explanation
Indices: 75621--75743 Score: 82
Period size: 31 Copynumber: 4.1 Consensus size: 30
75611 ATATTTAAAA
**
75621 TATATTTATTAATATTTCTAATAAT-ATAATAT
1 TATATTT-TTAAT-TTAATAATAATAAT-ATAT
75653 TATATTTTT-ATTATAATAA-AATAATCA-AT
1 TATATTTTTAATT-TAATAATAATAAT-ATAT
*
75682 TATA-TTATAA--TAAT-ATAAGATAATATAT
1 TATATTTTTAATTTAATAAT-A-ATAATATAT
*
75710 TATATTTTTAATTTAATAATATATAATAAAT
1 TATATTTTTAATTTAATAATA-ATAATATAT
75741 TAT
1 TAT
75744 TAATAAAATT
Statistics
Matches: 73, Mismatches: 7, Indels: 23
0.71 0.07 0.22
Matches are distributed among these distances:
25 1 0.01
26 4 0.05
27 2 0.03
28 14 0.19
29 16 0.22
30 9 0.12
31 18 0.25
32 9 0.12
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.50
Consensus pattern (30 bp):
TATATTTTTAATTTAATAATAATAATATAT
Found at i:75893 original size:22 final size:23
Alignment explanation
Indices: 75854--75900 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
75844 AATAATATTT
75854 TAATAAATATATTTAAAATATAA
1 TAATAAATATATTTAAAATATAA
*
75877 TAATTAATAT-TTTAAAATATAA
1 TAATAAATATATTTAAAATATAA
75899 TA
1 TA
75901 TAACATTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TAATAAATATATTTAAAATATAA
Found at i:76243 original size:29 final size:29
Alignment explanation
Indices: 76182--76243 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
76172 CTAGAAATGT
* * * *
76182 AATTCATTTTCTAGAATTTAAATTCCAAC
1 AATTCATTTTCCAAAATTCAAATTCCAAA
* *
76211 AATTCATTTTCCAAAATTCAATTTCTAAA
1 AATTCATTTTCCAAAATTCAAATTCCAAA
76240 AATT
1 AATT
76244 AAATTTAAGC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.40, C:0.16, G:0.02, T:0.42
Consensus pattern (29 bp):
AATTCATTTTCCAAAATTCAAATTCCAAA
Found at i:77066 original size:20 final size:19
Alignment explanation
Indices: 77018--77068 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
77008 AAATGACCAA
* *
77018 CAAATTCGTAACGCGATCT
1 CAAATTCGCAACGCGAACT
77037 CAAATTCGCAACGCGAACT
1 CAAATTCGCAACGCGAACT
*
77056 CCAATTTCGCAAC
1 -CAAATTCGCAAC
77069 ACATGTTTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.33, C:0.31, G:0.14, T:0.22
Consensus pattern (19 bp):
CAAATTCGCAACGCGAACT
Found at i:77102 original size:20 final size:20
Alignment explanation
Indices: 77079--77125 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 20
77069 ACATGTTTCA
77079 AAATCGCAACGCGAATAAGT
1 AAATCGCAACGCGAATAAGT
* *
77099 AAAT--C-ACGTGAATATGT
1 AAATCGCAACGCGAATAAGT
77116 AAATCGCAAC
1 AAATCGCAAC
77126 ACAGAAGTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 6
0.73 0.07 0.20
Matches are distributed among these distances:
17 14 0.64
18 1 0.05
19 1 0.05
20 6 0.27
ACGTcount: A:0.45, C:0.19, G:0.17, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGAATAAGT
Found at i:77481 original size:145 final size:145
Alignment explanation
Indices: 77226--77488 Score: 420
Period size: 145 Copynumber: 1.8 Consensus size: 145
77216 ATCGCAATGT
*
77226 GAATTTCATTTCCGCAACGCTAATTACCTATATCGGTAATTAGCGTTGAGAAATTCGAGTTGCGA
1 GAATTTCATTTCCGCAACGCTAATTACCTATATCGGTAATTAGCGTTGAGAAATTCAAGTTGCGA
* *
77291 ATTTGGAGAATTCGCGTTGTGATTTACATATTATCGTTGCAATTTAACTATTCACGTTGCGAATT
66 ATTTGGAGAATTCGCGTTGCGATTTACATATGATCGTTGCAATTTAACTATTCACGTTGCGAATT
77356 GGAAAATCGCTACGC
131 GGAAAATCGCTACGC
* * * *
77371 GAATTTCGTTTTCGCAACGCTAATTACCTATATCGGTAATT-GTCTTTGCGAAATTCAAGTTGCG
1 GAATTTCATTTCCGCAACGCTAATTACCTATATCGGTAATTAG-CGTTGAGAAATTCAAGTTGCG
** *
77435 AATTTGGAGAATTCGCGTTGCGATTTACATATGATCGTTGTGATTTACCTATTC
65 AATTTGGAGAATTCGCGTTGCGATTTACATATGATCGTTGCAATTTAACTATTC
77489 GCAACGCTAA
Statistics
Matches: 107, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
144 1 0.01
145 106 0.99
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.37
Consensus pattern (145 bp):
GAATTTCATTTCCGCAACGCTAATTACCTATATCGGTAATTAGCGTTGAGAAATTCAAGTTGCGA
ATTTGGAGAATTCGCGTTGCGATTTACATATGATCGTTGCAATTTAACTATTCACGTTGCGAATT
GGAAAATCGCTACGC
Found at i:77527 original size:105 final size:101
Alignment explanation
Indices: 77381--77689 Score: 293
Period size: 104 Copynumber: 3.0 Consensus size: 101
77371 GAATTTCGTT
* * *
77381 TTCGCAACGCTAATTACCTATATCGGTAATT-GTCTTTGCGAAATTCAAGTTGCGAATTTGGAGA
1 TTCGCAACGCTAATTACC-A-ATAGGTAATTAG-CGTTGCGAAATTCAAGTTGCGAATTTGGAAA
77445 ATTCGCGTTGCGATTTACATATGATCGTTGTGATTTACCTA
63 ATTCGCGTTGCGATTTACATATGATCGTTG-GATTT-CCTA
***
77486 TTCGCAACGCTAATTACCGAAGTAGGTAATTAGCGTTGCGAAATTCAAGTTGCGAA--AACAAAA
1 TTCGCAACGCTAATTACC-AA-TAGGTAATTAGCGTTGCGAAATTCAAGTTGCGAATTTGGAAAA
** * * * * * * *
77549 TTCGCAATGCGATTCTCCAAAATCGCAACG-CGAATTTCGTT
64 TTCGCGTTGCGATT-TAC-ATAT-G-ATCGTTGGATTTCCTA
* *
77590 TTCGCAACACTAATTACCAATATCGGTAATTAGCGTTGCGAAATTCGAGTTGCGAATTTGGAAAA
1 TTCGCAACGCTAATTACCAATA--GGTAATTAGCGTTGCGAAATTCAAGTTGCGAATTTGGAAAA
* *
77655 TTTGCGTTGCGATTTACATATTATCGTTGCGATTT
64 TTCGCGTTGCGATTTACATATGATCGTTG-GATTT
77690 TCCAATTACA
Statistics
Matches: 162, Mismatches: 30, Indels: 25
0.75 0.14 0.12
Matches are distributed among these distances:
102 5 0.03
103 18 0.11
104 60 0.37
105 58 0.36
106 18 0.11
107 3 0.02
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (101 bp):
TTCGCAACGCTAATTACCAATAGGTAATTAGCGTTGCGAAATTCAAGTTGCGAATTTGGAAAATT
CGCGTTGCGATTTACATATGATCGTTGGATTTCCTA
Found at i:77621 original size:104 final size:104
Alignment explanation
Indices: 77358--77646 Score: 295
Period size: 104 Copynumber: 2.8 Consensus size: 104
77348 TGCGAATTGG
* * *
77358 AAAATCGCTACGCGAATTTCGTTTTCGCAACGCTAATTACCTATATCGGTAATT-GTCTTTGCGA
1 AAAATCGCAACGCGAATTTCGTTTTCGCAACGCTAATTACCAATATCGGTAATTAG-CGTTGCGA
*** * **
77422 AATTCAAGTTGCGAATTTGGAGAATTCGCGTTGCGATTTAC
65 AATTCAAGTTGCGAA-TAACAAAATTCGCAATGCGATTTAC
* * * * * *
77463 -ATAT-G-ATCGTTGTGATTTACCTATTCGCAACGCTAATTACCGAAGTA--GGTAATTAGCGTT
1 AAAATCGCAACG-CG-AATTT-CGTTTTCGCAACGCTAATTACC-AA-TATCGGTAATTAGCGTT
*
77523 GCGAAATTCAAGTTGCGAA-AACAAAATTCGCAATGCGATTCTCC
61 GCGAAATTCAAGTTGCGAATAACAAAATTCGCAATGCGATT-TAC
*
77567 AAAATCGCAACGCGAATTTCGTTTTCGCAACACTAATTACCAATATCGGTAATTAGCGTTGCGAA
1 AAAATCGCAACGCGAATTTCGTTTTCGCAACGCTAATTACCAATATCGGTAATTAGCGTTGCGAA
*
77632 ATTCGAGTTGCGAAT
66 ATTCAAGTTGCGAAT
77647 TTGGAAAATT
Statistics
Matches: 147, Mismatches: 24, Indels: 26
0.75 0.12 0.13
Matches are distributed among these distances:
102 4 0.03
103 19 0.13
104 59 0.40
105 56 0.38
106 4 0.03
107 5 0.03
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.31
Consensus pattern (104 bp):
AAAATCGCAACGCGAATTTCGTTTTCGCAACGCTAATTACCAATATCGGTAATTAGCGTTGCGAA
ATTCAAGTTGCGAATAACAAAATTCGCAATGCGATTTAC
Found at i:77885 original size:20 final size:20
Alignment explanation
Indices: 77860--77924 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
77850 TTGTGTTGTT
*
77860 ATTTACATATTATCATTGCG
1 ATTTACATATTATCGTTGCG
* **
77880 ATTTACTTATTCGCGTTGCG
1 ATTTACATATTATCGTTGCG
* *
77900 AATTACATATTATCGTTGTG
1 ATTTACATATTATCGTTGCG
77920 ATTTA
1 ATTTA
77925 ACTATTCACG
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.46
Consensus pattern (20 bp):
ATTTACATATTATCGTTGCG
Found at i:77907 original size:40 final size:40
Alignment explanation
Indices: 77862--77943 Score: 112
Period size: 40 Copynumber: 2.0 Consensus size: 40
77852 GTGTTGTTAT
* *
77862 TTACATATTATCATTGCGATTT-ACTTATTCGCGTTGCGAA
1 TTACATATTATCATTGCGATTTAAC-TATTCACGTTGCAAA
* *
77902 TTACATATTATCGTTGTGATTTAACTATTCACGTTGCAAA
1 TTACATATTATCATTGCGATTTAACTATTCACGTTGCAAA
77942 TT
1 TT
77944 TTACTTTTGC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
40 35 0.95
41 2 0.05
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.44
Consensus pattern (40 bp):
TTACATATTATCATTGCGATTTAACTATTCACGTTGCAAA
Found at i:77977 original size:60 final size:59
Alignment explanation
Indices: 77913--78043 Score: 140
Period size: 60 Copynumber: 2.2 Consensus size: 59
77903 TACATATTAT
* *
77913 CGTTGTGATTTAACTATTC-ACGTTGCAAATTTT-ACTTTTGCATTGCGATTTTGAATTTCG
1 CGTTGTGATTTAACT-TTCGA-GTTGC-AATTTTGACTTTCGCATTGCGAATTTGAATTTCG
* * * * *
77973 CGTTGCTGTTTTGACTTTCGAGTTGCGATTTTGACTTTCGCGTTGCGAATTTGATTTTCG
1 CGTTG-TGATTTAACTTTCGAGTTGCAATTTTGACTTTCGCATTGCGAATTTGAATTTCG
*
78033 CGTTGCGATTT
1 CGTTGTGATTT
78044 TGGAACCTGT
Statistics
Matches: 59, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
59 9 0.15
60 41 0.69
61 9 0.15
ACGTcount: A:0.16, C:0.16, G:0.21, T:0.47
Consensus pattern (59 bp):
CGTTGTGATTTAACTTTCGAGTTGCAATTTTGACTTTCGCATTGCGAATTTGAATTTCG
Found at i:77984 original size:20 final size:20
Alignment explanation
Indices: 77941--78045 Score: 133
Period size: 20 Copynumber: 5.3 Consensus size: 20
77931 CACGTTGCAA
* *
77941 ATTTT-ACTTTTGCATTGCG
1 ATTTTGACTTTCGCGTTGCG
*
77960 ATTTTGAATTTCGCGTTGCTG
1 ATTTTGACTTTCGCGTTGC-G
*
77981 -TTTTGACTTTCGAGTTGCG
1 ATTTTGACTTTCGCGTTGCG
78000 ATTTTGACTTTCGCGTTGCG
1 ATTTTGACTTTCGCGTTGCG
* *
78020 AATTTGATTTTCGCGTTGCG
1 ATTTTGACTTTCGCGTTGCG
78040 ATTTTG
1 ATTTTG
78046 GAACCTGTGT
Statistics
Matches: 74, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
19 6 0.08
20 67 0.91
21 1 0.01
ACGTcount: A:0.13, C:0.15, G:0.23, T:0.49
Consensus pattern (20 bp):
ATTTTGACTTTCGCGTTGCG
Found at i:78591 original size:16 final size:16
Alignment explanation
Indices: 78570--78614 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
78560 TTTAAATTTT
78570 AAATA-TAAAAATATGC
1 AAATATTAAAAATAT-C
*
78586 AAATATTAAAAAAATC
1 AAATATTAAAAATATC
78602 -AATATTAAAAATA
1 AAATATTAAAAATA
78615 AAAAAAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 12 0.46
16 6 0.23
17 8 0.31
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (16 bp):
AAATATTAAAAATATC
Found at i:79792 original size:22 final size:22
Alignment explanation
Indices: 79764--79820 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
79754 GCATGTGAAC
79764 TTTGTCCCGAAAGACCTATGTA
1 TTTGTCCCGAAAGACCTATGTA
* * * *
79786 TTTGTCCTGAAGGACTTCTGTA
1 TTTGTCCCGAAAGACCTATGTA
79808 TATATGTCCCGAA
1 T-T-TGTCCCGAA
79821 TGACTGCGTC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
22 19 0.68
23 1 0.04
24 8 0.29
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (22 bp):
TTTGTCCCGAAAGACCTATGTA
Done.