Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009210.1 Hibiscus syriacus cultivar Beakdansim tig00112797_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: 136780
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:11009 original size:59 final size:60
Alignment explanation
Indices: 10945--11109 Score: 136
Period size: 60 Copynumber: 2.8 Consensus size: 60
10935 TTACATCATA
* * * * *
10945 CATCCCTAAAATATAACCCTCATT-TTAATTAGT-TTTTAAGCTTTTAAATATTCTAATTC
1 CATCCCTAAAATATAACCCTCATTCTAAATTAATCCTTGAA-CTTTTAAACATTCTAATTC
* * * * * *
11004 CATCCCCAAACTATGACTCTCATTCTAAATTAATCCTTGAACTTTTGAACATTCTAATTT
1 CATCCCTAAAATATAACCCTCATTCTAAATTAATCCTTGAACTTTTAAACATTCTAATTC
* * * * * * * *
11064 CATCCCTACACTATGACCTTCTTTCTAAATTGATCTTTAAACTTTT
1 CATCCCTAAAATATAACCCTCATTCTAAATTAATCCTTGAACTTTT
11110 GAATCTTCCA
Statistics
Matches: 85, Mismatches: 19, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
59 20 0.24
60 61 0.72
61 4 0.05
ACGTcount: A:0.31, C:0.23, G:0.04, T:0.42
Consensus pattern (60 bp):
CATCCCTAAAATATAACCCTCATTCTAAATTAATCCTTGAACTTTTAAACATTCTAATTC
Found at i:11123 original size:60 final size:60
Alignment explanation
Indices: 10979--11133 Score: 170
Period size: 60 Copynumber: 2.6 Consensus size: 60
10969 TTAATTAGTT
* * * *
10979 TTTAAGCTTTTAAATATTCTAATTCCATCCCCAAACTATGACTCTCATTCTAAATTAATC
1 TTTAAACTTTTGAATCTTCTAATTTCATCCCCAAACTATGACTCTCATTCTAAATTAATC
* * * * * *
11039 CTTGAACTTTTGAA-CATTCTAATTTCATCCCTACACTATGAC-CTTCTTTCTAAATTGATC
1 TTTAAACTTTTGAATC-TTCTAATTTCATCCCCAAACTATGACTC-TCATTCTAAATTAATC
* *
11099 TTTAAACTTTTGAATCTTCCAATTTCATCCTCAAA
1 TTTAAACTTTTGAATCTTCTAATTTCATCCCCAAA
11134 TGCACCCAAA
Statistics
Matches: 76, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
59 1 0.01
60 74 0.97
61 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.05, T:0.41
Consensus pattern (60 bp):
TTTAAACTTTTGAATCTTCTAATTTCATCCCCAAACTATGACTCTCATTCTAAATTAATC
Found at i:11316 original size:29 final size:29
Alignment explanation
Indices: 11261--11316 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
11251 TTTGGGAGAC
* * *
11261 AATTGGAATGTTCAAAAAGTTTTGGATGA
1 AATTGAAATATTCAAAAAGTTTAGGATGA
11290 AATTGAAATATTC-AAAAGTTTAAGGAT
1 AATTGAAATATTCAAAAAGTTT-AGGAT
11317 TAATTTGGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 8 0.35
29 15 0.65
ACGTcount: A:0.43, C:0.04, G:0.20, T:0.34
Consensus pattern (29 bp):
AATTGAAATATTCAAAAAGTTTAGGATGA
Found at i:12017 original size:60 final size:61
Alignment explanation
Indices: 11936--12265 Score: 202
Period size: 59 Copynumber: 5.5 Consensus size: 61
11926 ATCTATTATG
* * * * *
11936 TTAAA-TTTTAAATATTCTAATTCT-ATCCCCAAACTATGACTCTCATTCTAAATTAATCC
1 TTAAACTTTTGAACATTCTAATTCTCATCCCTAAACTATAACCCTCATTCTAAATTAATCC
** **
11995 TTAAACTTTTGAACATTCTAATT-TCATCCCTAAACTATAACCCTC-TT-TAATATTGGTGA
1 TTAAACTTTTGAACATTCTAATTCTCATCCCTAAACTATAACCCTCATTCTAA-ATTAATCC
** * * * * *
12054 TTTTA-TGTT-AA-ATTTGAGTTAATTACATACATCCCTAAAGTATAACCCTCATTGTAAATTAG
1 TTAAACTTTTGAACA-TT---CTAATT-C-T-CATCCCTAAACTATAACCCTCATTCTAAATTAA
*
12116 TCT
59 TCC
* * * * * * * ** **
12119 TTAAGCTTTTAAATATTCTAATT-ACATCCCCACACTATGATTCTCACACTAAATTAATCC
1 TTAAACTTTTGAACATTCTAATTCTCATCCCTAAACTATAACCCTCATTCTAAATTAATCC
* *
12179 TT-AACTTTTGAACATTCTAATT-TCATCCCTAAACTATAACCCTCTTTCT-AATTGATCC
1 TTAAACTTTTGAACATTCTAATTCTCATCCCTAAACTATAACCCTCATTCTAAATTAATCC
*
12237 TTAAACTTTTGAATC-TTCCAATT-TCATCC
1 TTAAACTTTTGAA-CATTCTAATTCTCATCC
12266 TCAAGTGCAT
Statistics
Matches: 205, Mismatches: 48, Indels: 36
0.71 0.17 0.12
Matches are distributed among these distances:
56 1 0.00
57 4 0.02
58 16 0.08
59 73 0.36
60 65 0.32
63 1 0.00
64 25 0.12
65 9 0.04
66 6 0.03
67 4 0.02
68 1 0.00
ACGTcount: A:0.33, C:0.22, G:0.05, T:0.41
Consensus pattern (61 bp):
TTAAACTTTTGAACATTCTAATTCTCATCCCTAAACTATAACCCTCATTCTAAATTAATCC
Found at i:12785 original size:60 final size:60
Alignment explanation
Indices: 12659--12837 Score: 157
Period size: 60 Copynumber: 3.0 Consensus size: 60
12649 CGTTTGGGAG
* * ** *
12659 GAAATTGGAATGTTCAAAAGTTTGGGGACTAATTTAGAATGAAGGTCATAGTTTAAGGAT
1 GAAATTGAAATATTCAAAAGTTTAAGGACTAATTTAGAATGAAGATCATAGTTTAAGGAT
12719 GAAATTGAAATATTCAAAAGTTTAAGGACTAATTT-GAAATGATA-ATCATAGTTT-AGGAAT
1 GAAATTGAAATATTCAAAAGTTTAAGGACTAATTTAG-AATGA-AGATCATAGTTTAAGG-AT
* * ** * * * * * * * *
12779 GCAATTGGAGCATTTAAAATTTTATGGACCAATTTAAAATGAGGATCATACTTTGAGGA
1 GAAATTGAAATATTCAAAAGTTTAAGGACTAATTTAGAATGAAGATCATAGTTTAAGGA
12838 CACGTGATAC
Statistics
Matches: 97, Mismatches: 16, Indels: 12
0.78 0.13 0.10
Matches are distributed among these distances:
59 4 0.04
60 89 0.92
61 4 0.04
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.32
Consensus pattern (60 bp):
GAAATTGAAATATTCAAAAGTTTAAGGACTAATTTAGAATGAAGATCATAGTTTAAGGAT
Found at i:19713 original size:33 final size:33
Alignment explanation
Indices: 19671--19733 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
19661 GGCGACATCG
*
19671 AAGGTCTGCTGCAACAGACGTGGTGGATGCTCC
1 AAGGTCTGCTGCAACAGACGCGGTGGATGCTCC
* *
19704 AAGGTCTGCTGCATCAGATGCGGTGGATGC
1 AAGGTCTGCTGCAACAGACGCGGTGGATGC
19734 ATCCTCTGCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.21, C:0.22, G:0.35, T:0.22
Consensus pattern (33 bp):
AAGGTCTGCTGCAACAGACGCGGTGGATGCTCC
Found at i:59473 original size:19 final size:17
Alignment explanation
Indices: 59449--59483 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 17
59439 ACTAAAAGAT
59449 CAACCTTTCAGTTTTTTGG
1 CAACC-TTCA-TTTTTTGG
59468 CAACCTTCATTTTTTG
1 CAACCTTCATTTTTTG
59484 CTGTTTTAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 4 0.25
19 5 0.31
ACGTcount: A:0.17, C:0.23, G:0.11, T:0.49
Consensus pattern (17 bp):
CAACCTTCATTTTTTGG
Found at i:62527 original size:25 final size:25
Alignment explanation
Indices: 62501--62548 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
62491 ATATATATTA
62501 AAATA-AATATATTT-TTAATATAAT
1 AAATACAAT-TATTTATTAATATAAT
*
62525 AAATACAATTTTTTATTAATATAA
1 AAATACAATTATTTATTAATATAA
62549 AATGGGCCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
AAATACAATTATTTATTAATATAAT
Found at i:69357 original size:16 final size:18
Alignment explanation
Indices: 69334--69373 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
69324 ACTAATGGAT
69334 TTTA-ATGA-CAAAT-AA
1 TTTATATGATCAAATGAA
69349 TTTATATGATCAAATGAA
1 TTTATATGATCAAATGAA
*
69367 TCTATAT
1 TTTATAT
69374 ATTATATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 4 0.19
16 4 0.19
17 5 0.24
18 8 0.38
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.40
Consensus pattern (18 bp):
TTTATATGATCAAATGAA
Found at i:72500 original size:28 final size:28
Alignment explanation
Indices: 72469--72526 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
72459 TTATGTGTCT
72469 TATTTAAAG-TTTAAGAACTAA-AATTTTA
1 TATTTAAAGATTT-AGAA-TAATAATTTTA
*
72497 TATTTTAAGATTTAGAATAATAATTTTA
1 TATTTAAAGATTTAGAATAATAATTTTA
72525 TA
1 TA
72527 CTATCGGTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 3 0.11
28 21 0.78
29 3 0.11
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.47
Consensus pattern (28 bp):
TATTTAAAGATTTAGAATAATAATTTTA
Found at i:72834 original size:3 final size:3
Alignment explanation
Indices: 72814--72862 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
72804 AATTAAAAAC
* *
72814 AAT AAC AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
72862 A
1 A
72863 GAAAATTTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:74049 original size:54 final size:55
Alignment explanation
Indices: 73985--74093 Score: 193
Period size: 55 Copynumber: 2.0 Consensus size: 55
73975 GTTTGAGGAA
*
73985 GAAACAAAATTATGGCTCACTGAATT-GGGGAATTTAAGAAATCAGAAGTTAGGG
1 GAAACAAAATTAGGGCTCACTGAATTGGGGGAATTTAAGAAATCAGAAGTTAGGG
*
74039 GAAACAAAATTAGGGCTCACTGAATTGGGGGAATTTGAGAAATCAGAAGTTAGGG
1 GAAACAAAATTAGGGCTCACTGAATTGGGGGAATTTAAGAAATCAGAAGTTAGGG
74094 ATTTGGAAGG
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
54 25 0.48
55 27 0.52
ACGTcount: A:0.39, C:0.09, G:0.28, T:0.23
Consensus pattern (55 bp):
GAAACAAAATTAGGGCTCACTGAATTGGGGGAATTTAAGAAATCAGAAGTTAGGG
Found at i:76729 original size:6 final size:6
Alignment explanation
Indices: 76718--76742 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
76708 AGAAGATTAT
76718 ACCCGA ACCCGA ACCCGA ACCCGA A
1 ACCCGA ACCCGA ACCCGA ACCCGA A
76743 AATATTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCCGA
Found at i:76780 original size:35 final size:34
Alignment explanation
Indices: 76741--76826 Score: 145
Period size: 35 Copynumber: 2.5 Consensus size: 34
76731 CCCGAACCCG
* *
76741 AAAATATTTTATATATAATTAATATAAAATATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
76775 AAAAATATTATATATATAATTAATATAAAAAATAT
1 -AAAATATTATATATATAATTAATATAAAAAATAT
76810 AAAATATTATATATATA
1 AAAATATTATATATATA
76827 TATATAATCG
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
34 17 0.35
35 32 0.65
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (34 bp):
AAAATATTATATATATAATTAATATAAAAAATAT
Found at i:85201 original size:12 final size:12
Alignment explanation
Indices: 85184--85208 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
85174 AAGAGTTGAT
85184 AAGTTAAATTTG
1 AAGTTAAATTTG
85196 AAGTTAAATTTG
1 AAGTTAAATTTG
85208 A
1 A
85209 CTTGTCATCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (12 bp):
AAGTTAAATTTG
Found at i:86170 original size:15 final size:15
Alignment explanation
Indices: 86152--86186 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
86142 CGAGGGTATT
86152 GTAGTCATTCGGGAC
1 GTAGTCATTCGGGAC
*
86167 GTAGTCCTTCGGGAC
1 GTAGTCATTCGGGAC
86182 GTAGT
1 GTAGT
86187 GGTCCTTCGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.17, C:0.20, G:0.34, T:0.29
Consensus pattern (15 bp):
GTAGTCATTCGGGAC
Found at i:86193 original size:18 final size:18
Alignment explanation
Indices: 86159--86217 Score: 88
Period size: 18 Copynumber: 3.4 Consensus size: 18
86149 ATTGTAGTCA
86159 TTCGGGACGTA---GTCC
1 TTCGGGACGTAGTGGTCC
86174 TTCGGGACGTAGTGGTCC
1 TTCGGGACGTAGTGGTCC
86192 TTCGGGACGTAGTGGTCC
1 TTCGGGACGTAGTGGTCC
*
86210 TACGGGAC
1 TTCGGGAC
86218 ATATATAGCA
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
15 11 0.28
18 29 0.73
ACGTcount: A:0.14, C:0.24, G:0.37, T:0.25
Consensus pattern (18 bp):
TTCGGGACGTAGTGGTCC
Found at i:93453 original size:12 final size:12
Alignment explanation
Indices: 93416--93465 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
93406 ATTATTTAAA
93416 ATAA-TAAAATT
1 ATAATTAAAATT
*
93427 ATAATTACAATT
1 ATAATTAAAATT
*
93439 ATAATTAAAAAT
1 ATAATTAAAATT
* *
93451 ATAAATAACATT
1 ATAATTAAAATT
93463 ATA
1 ATA
93466 TCTAAATAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
11 4 0.12
12 28 0.88
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (12 bp):
ATAATTAAAATT
Found at i:98008 original size:5 final size:5
Alignment explanation
Indices: 97998--98048 Score: 63
Period size: 5 Copynumber: 10.8 Consensus size: 5
97988 CGACCGGTCT
* *
97998 GACCC GACCC GACCC GA-CC GA-CC GACTC GA-TC GACCC GACCC GACCC
1 GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACCC
98045 GACC
1 GACC
98049 GTTGACCGTT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
4 12 0.29
5 30 0.71
ACGTcount: A:0.22, C:0.53, G:0.22, T:0.04
Consensus pattern (5 bp):
GACCC
Found at i:98032 original size:13 final size:13
Alignment explanation
Indices: 98001--98049 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 13
97991 CCGGTCTGAC
98001 CCGACCCGACCCGA
1 CCGA-CCGACCCGA
*
98015 CCGACCGACTCGA
1 CCGACCGACCCGA
*
98028 TCGACCCGACCCGA
1 CCGA-CCGACCCGA
98042 CCCGACCG
1 -CCGACCG
98050 TTGACCGTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 11 0.38
14 15 0.52
15 3 0.10
ACGTcount: A:0.20, C:0.53, G:0.22, T:0.04
Consensus pattern (13 bp):
CCGACCGACCCGA
Found at i:105131 original size:19 final size:19
Alignment explanation
Indices: 105107--105149 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
105097 AAAACCGGTT
*
105107 TGACCGGTTCGAACAGGTC
1 TGACCGGTTCAAACAGGTC
*
105126 TGACCGGTTCAAACCGGTC
1 TGACCGGTTCAAACAGGTC
105145 TGACC
1 TGACC
105150 CGACCGACCC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.21, C:0.30, G:0.28, T:0.21
Consensus pattern (19 bp):
TGACCGGTTCAAACAGGTC
Found at i:105160 original size:9 final size:9
Alignment explanation
Indices: 105146--105182 Score: 58
Period size: 9 Copynumber: 4.1 Consensus size: 9
105136 AAACCGGTCT
105146 GACCCGACC
1 GACCCGACC
105155 GACCCGACC
1 GACCCGACC
105164 GA-CCGACCC
1 GACCCGA-CC
105173 GACCCGACC
1 GACCCGACC
105182 G
1 G
105183 TTGACCGTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 4 0.15
9 18 0.69
10 4 0.15
ACGTcount: A:0.22, C:0.54, G:0.24, T:0.00
Consensus pattern (9 bp):
GACCCGACC
Found at i:105161 original size:5 final size:5
Alignment explanation
Indices: 105146--105181 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
105136 AAACCGGTCT
105146 GACCC GA-CC GACCC GA-CC GA-CC GACCC GACCC GACC
1 GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACC
105182 GTTGACCGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 12 0.41
5 17 0.59
ACGTcount: A:0.22, C:0.56, G:0.22, T:0.00
Consensus pattern (5 bp):
GACCC
Found at i:105167 original size:13 final size:14
Alignment explanation
Indices: 105146--105182 Score: 67
Period size: 13 Copynumber: 2.7 Consensus size: 14
105136 AAACCGGTCT
105146 GACCCGACCGACCC
1 GACCCGACCGACCC
105160 GA-CCGACCGACCC
1 GACCCGACCGACCC
105173 GACCCGACCG
1 GACCCGACCG
105183 TTGACCGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 13 0.59
14 9 0.41
ACGTcount: A:0.22, C:0.54, G:0.24, T:0.00
Consensus pattern (14 bp):
GACCCGACCGACCC
Found at i:107033 original size:86 final size:86
Alignment explanation
Indices: 106882--107058 Score: 246
Period size: 86 Copynumber: 2.1 Consensus size: 86
106872 TCCTATTTGG
* *
106882 TGTCGATAAGTGGAGGTCACTCTCATTGGTTTTAGGCTAATCGATTATATTAATGGATTATAACC
1 TGTCGACAAGTGGAGGTCACTCTCATTGGTTTTAGGCTAATCGATTATATTAATGGATTACAACC
* *
106947 TTCCATATTTCAGTTTACCGA
66 TTCCACATCTCAGTTTACCGA
* * * * * *
106968 TGTCGACAAGTGGAGGTCACTCTCATTGGTTTTGGGCTATTCGGTTATATTGATTGATTGCAACC
1 TGTCGACAAGTGGAGGTCACTCTCATTGGTTTTAGGCTAATCGATTATATTAATGGATTACAACC
* *
107033 TTCCACATCTCGGTTTACTGA
66 TTCCACATCTCAGTTTACCGA
107054 TGTCG
1 TGTCG
107059 CAACAAAAAA
Statistics
Matches: 79, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
86 79 1.00
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.38
Consensus pattern (86 bp):
TGTCGACAAGTGGAGGTCACTCTCATTGGTTTTAGGCTAATCGATTATATTAATGGATTACAACC
TTCCACATCTCAGTTTACCGA
Found at i:110574 original size:23 final size:24
Alignment explanation
Indices: 110548--110599 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
110538 TTATTTATTA
*
110548 TTCATGAACATATTCGTTTA-ATG
1 TTCATAAACATATTCGTTTATATG
* *
110571 TTCATAAACGTATTCGTTTATTTG
1 TTCATAAACATATTCGTTTATATG
110595 TTCAT
1 TTCAT
110600 TTAGCGTTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 18 0.72
24 7 0.28
ACGTcount: A:0.27, C:0.13, G:0.12, T:0.48
Consensus pattern (24 bp):
TTCATAAACATATTCGTTTATATG
Found at i:110854 original size:38 final size:38
Alignment explanation
Indices: 110803--110882 Score: 133
Period size: 38 Copynumber: 2.1 Consensus size: 38
110793 GAAAACCGAG
110803 TAAACAAGCTTGTTCATGAACATAAATGAATGAGTCGA
1 TAAACAAGCTTGTTCATGAACATAAATGAATGAGTCGA
* * *
110841 TAAACATGCTTGTTCGTTAACATAAATGAATGAGTCGA
1 TAAACAAGCTTGTTCATGAACATAAATGAATGAGTCGA
110879 TAAA
1 TAAA
110883 TGAATCAGAC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.29
Consensus pattern (38 bp):
TAAACAAGCTTGTTCATGAACATAAATGAATGAGTCGA
Found at i:111651 original size:20 final size:20
Alignment explanation
Indices: 111628--111736 Score: 128
Period size: 20 Copynumber: 5.5 Consensus size: 20
111618 TTGCGATTTT
**
111628 TCAAATTCGCGTTGCGATAG
1 TCAAATTCGCAATGCGATAG
*
111648 TCAAATTCGCAATGCGAAAG
1 TCAAATTCGCAATGCGATAG
*
111668 TCAAATTCGCAACGCGATAG
1 TCAAATTCGCAATGCGATAG
** * *
111688 TCAAATTCGCAACACAAAAG
1 TCAAATTCGCAATGCGATAG
* *
111708 TCAAATTCGCAACGCGAAAG
1 TCAAATTCGCAATGCGATAG
111728 TCAAATTCG
1 TCAAATTCG
111737 TGTTGCGAAT
Statistics
Matches: 79, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 79 1.00
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (20 bp):
TCAAATTCGCAATGCGATAG
Found at i:111717 original size:60 final size:60
Alignment explanation
Indices: 111646--111793 Score: 192
Period size: 60 Copynumber: 2.5 Consensus size: 60
111636 GCGTTGCGAT
*
111646 AGTCAAATTCGCAATGCGAAAGTCAAATTCGCAACGCG-A-TAGTCAAATTCGCAACACAAA
1 AGTCAAATTCGCAACGCGAAAGTCAAATTCGCAACGCGAATTAGT-AAA-TCGCAACACAAA
**** * *
111706 AGTCAAATTCGCAACGCGAAAGTCAAATTCGTGTTGCGAATTTGTAAATCGCAACACAGA
1 AGTCAAATTCGCAACGCGAAAGTCAAATTCGCAACGCGAATTAGTAAATCGCAACACAAA
*
111766 AGTTAAATTCGCAACGCGAAAGTCAAAT
1 AGTCAAATTCGCAACGCGAAAGTCAAAT
111794 GTTTTTACGC
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
60 71 0.91
61 4 0.05
62 3 0.04
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.21
Consensus pattern (60 bp):
AGTCAAATTCGCAACGCGAAAGTCAAATTCGCAACGCGAATTAGTAAATCGCAACACAAA
Found at i:111744 original size:20 final size:20
Alignment explanation
Indices: 111641--111793 Score: 150
Period size: 20 Copynumber: 7.7 Consensus size: 20
111631 AATTCGCGTT
* *
111641 GCGATAGTCAAATTCGCAAT
1 GCGAAAGTCAAATTCGCAAC
111661 GCGAAAGTCAAATTCGCAAC
1 GCGAAAGTCAAATTCGCAAC
*
111681 GCGATAGTCAAATTCGCAAC
1 GCGAAAGTCAAATTCGCAAC
* *
111701 ACAAAAGTCAAATTCGCAAC
1 GCGAAAGTCAAATTCGCAAC
****
111721 GCGAAAGTCAAATTCGTGTT
1 GCGAAAGTCAAATTCGCAAC
*
111741 GCGAATTTGT-AAA-TCGCAAC
1 GCGAA--AGTCAAATTCGCAAC
* *
111761 AC-AGAAGTTAAATTCGCAAC
1 GCGA-AAGTCAAATTCGCAAC
111781 GCGAAAGTCAAAT
1 GCGAAAGTCAAAT
111794 GTTTTTACGC
Statistics
Matches: 106, Mismatches: 21, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
18 2 0.02
19 4 0.04
20 94 0.89
21 4 0.04
22 2 0.02
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.21
Consensus pattern (20 bp):
GCGAAAGTCAAATTCGCAAC
Found at i:111946 original size:22 final size:22
Alignment explanation
Indices: 111921--111971 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
111911 CTACGGCGTC
111921 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
* *
111943 ATCCATCCCCATTTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
111965 ATCCGTC
1 ATCCGTC
111972 TATCTCCATC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.24, C:0.43, G:0.12, T:0.22
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:112299 original size:20 final size:20
Alignment explanation
Indices: 112229--112292 Score: 110
Period size: 20 Copynumber: 3.2 Consensus size: 20
112219 CACAACGCGC
*
112229 TTTTCATTTTCGCGTTGCGC
1 TTTTCATTTTCGCGTTGCGA
*
112249 TTTTCATTTTCGCGTTGCAA
1 TTTTCATTTTCGCGTTGCGA
112269 TTTTCATTTTCGCGTTGCGA
1 TTTTCATTTTCGCGTTGCGA
112289 TTTT
1 TTTT
112293 AAGTTTCAGA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.09, C:0.20, G:0.17, T:0.53
Consensus pattern (20 bp):
TTTTCATTTTCGCGTTGCGA
Found at i:116016 original size:61 final size:62
Alignment explanation
Indices: 115916--116055 Score: 176
Period size: 66 Copynumber: 2.2 Consensus size: 62
115906 TTTTACATTG
*
115916 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGATTTA-TTTT-TTGATTAATTGATTTGTA
1 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTCTTGATTAATTGATTTGTA
* ** * *
115976 AAAGTTGATTTGTTTACTTTGATTTGTAAATAAGAATTATTTTTTTTCTTGTTTAATTGATTTGT
1 AAAGTTGATTTGTTTA-ATTGATGAGGAAATAAGAATTA---TTTTTCTTGATTAATTGATTTGT
116041 A
62 A
116042 AAAGTTGATTTGTT
1 AAAGTTGATTTGTT
116056 GTTCCTAAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
60 16 0.24
61 17 0.25
65 4 0.06
66 31 0.46
ACGTcount: A:0.30, C:0.01, G:0.16, T:0.52
Consensus pattern (62 bp):
AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTCTTGATTAATTGATTTGTA
Found at i:116163 original size:20 final size:20
Alignment explanation
Indices: 116140--116183 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
116130 AATAAGCGTT
* *
116140 GCGACAGTCAAATTTGCAAC
1 GCGAAAGTCAAATTCGCAAC
116160 GCGAAAGTCAAATTCGCAAC
1 GCGAAAGTCAAATTCGCAAC
116180 GCGA
1 GCGA
116184 TTTTTGGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.25, G:0.23, T:0.16
Consensus pattern (20 bp):
GCGAAAGTCAAATTCGCAAC
Found at i:116477 original size:39 final size:39
Alignment explanation
Indices: 116420--116504 Score: 116
Period size: 39 Copynumber: 2.2 Consensus size: 39
116410 ACTCAAGTTG
* *
116420 TAGATTTTGATTTCCTTTTGCTTGGCACCATATGAGATT
1 TAGATTTGGATTTCCTTTTGCTTGGCACCAAATGAGATT
* * *
116459 TAGATTTGGATTTTCTTTTTCTTGGCACCAAATGAGCTT
1 TAGATTTGGATTTCCTTTTGCTTGGCACCAAATGAGATT
*
116498 TGGATTT
1 TAGATTT
116505 TGATGAGCAT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.20, C:0.14, G:0.19, T:0.47
Consensus pattern (39 bp):
TAGATTTGGATTTCCTTTTGCTTGGCACCAAATGAGATT
Found at i:116539 original size:35 final size:35
Alignment explanation
Indices: 116500--116575 Score: 91
Period size: 35 Copynumber: 2.2 Consensus size: 35
116490 ATGAGCTTTG
*
116500 GATTTTGATGAGCA-TCGGAAGCATTTCGGACTTAT
1 GATTTTGATG-GCACTCAGAAGCATTTCGGACTTAT
* * *
116535 GATTTGGGTGGTACTCAGAAGCATTTCGGACTTAT
1 GATTTTGATGGCACTCAGAAGCATTTCGGACTTAT
*
116570 TATTTT
1 GATTTT
116576 TGTTATTATT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
34 2 0.06
35 32 0.94
ACGTcount: A:0.24, C:0.13, G:0.25, T:0.38
Consensus pattern (35 bp):
GATTTTGATGGCACTCAGAAGCATTTCGGACTTAT
Found at i:116918 original size:25 final size:25
Alignment explanation
Indices: 116884--116933 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
116874 ATTATTTTTC
*
116884 CAAATAATGTACCCATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
116909 CAAATAATGTACCCACAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
116934 TAATTGATTT
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:0.44, C:0.22, G:0.08, T:0.26
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:117078 original size:20 final size:20
Alignment explanation
Indices: 117050--117130 Score: 110
Period size: 20 Copynumber: 4.0 Consensus size: 20
117040 GTTTGCGATT
*
117050 TTGCGTTGCGAATTTGACTA
1 TTGCATTGCGAATTTGACTA
117070 TTGCATTGCGAATTTGACTA
1 TTGCATTGCGAATTTGACTA
* *
117090 TCGCATTGCGAATTTGTCT-
1 TTGCATTGCGAATTTGACTA
*
117109 TTCGCGTTGCGAATTTGACTA
1 TT-GCATTGCGAATTTGACTA
117130 T
1 T
117131 CGTAACGCTT
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
19 1 0.02
20 51 0.96
21 1 0.02
ACGTcount: A:0.20, C:0.17, G:0.22, T:0.41
Consensus pattern (20 bp):
TTGCATTGCGAATTTGACTA
Found at i:117119 original size:40 final size:40
Alignment explanation
Indices: 117055--117132 Score: 122
Period size: 40 Copynumber: 1.9 Consensus size: 40
117045 CGATTTTGCG
117055 TTGCGAATTTGACTATTGCATTGCGAATTTGACTATCGCA
1 TTGCGAATTTGACTATTGCATTGCGAATTTGACTATCGCA
* *
117095 TTGCGAATTTGTCT-TTCGCGTTGCGAATTTGACTATCG
1 TTGCGAATTTGACTATT-GCATTGCGAATTTGACTATCG
117133 TAACGCTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
39 2 0.06
40 33 0.94
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.40
Consensus pattern (40 bp):
TTGCGAATTTGACTATTGCATTGCGAATTTGACTATCGCA
Found at i:117480 original size:18 final size:18
Alignment explanation
Indices: 117457--117492 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
117447 AAACCTGTTG
117457 TGATTGAGATTTTGATTT
1 TGATTGAGATTTTGATTT
*
117475 TGATTGCGATTTTGATTT
1 TGATTGAGATTTTGATTT
117493 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.03, G:0.22, T:0.56
Consensus pattern (18 bp):
TGATTGAGATTTTGATTT
Found at i:120750 original size:20 final size:20
Alignment explanation
Indices: 120714--120886 Score: 127
Period size: 20 Copynumber: 8.6 Consensus size: 20
120704 ACTAAAACCT
*
120714 GTTGCGAAATT-AAATTCGC
1 GTTGCGAATTTGAAATTCGC
*
120733 GTTGCGAATTTGAAATTC-A
1 GTTGCGAATTTGAAATTCGC
**
120752 GTTGCGAATTTGACTTTCGC
1 GTTGCGAATTTGAAATTCGC
** * *
120772 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGAAATTCGC
*
120792 GTTGCGAATTTGGAAAATCGC
1 GTTGCGAATTT-GAAATTCGC
***
120813 AACGCGAATTT-ACATATTCGC
1 GTTGCGAATTTGA-A-ATTCGC
* ** *
120834 GTTGCGAAATTGAAAAACTGT
1 GTTGCGAATTTGAAATTC-GC
* *
120855 GTTGCGAAATTGGAATTCGC
1 GTTGCGAATTTGAAATTCGC
120875 GTTGCGAATTTG
1 GTTGCGAATTTG
120887 TTGGTCATTT
Statistics
Matches: 119, Mismatches: 28, Indels: 13
0.74 0.17 0.08
Matches are distributed among these distances:
19 27 0.23
20 50 0.42
21 41 0.34
22 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.35
Consensus pattern (20 bp):
GTTGCGAATTTGAAATTCGC
Found at i:130388 original size:2 final size:2
Alignment explanation
Indices: 130381--130406 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
130371 TTTCCGTTAA
130381 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
130407 TCCCTATATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:131755 original size:21 final size:21
Alignment explanation
Indices: 131731--131771 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
131721 ATATTTATTA
131731 ATATTTCTAATAATATAATAT
1 ATATTTCTAATAATATAATAT
* *
131752 ATATTTTTAATATTATAATA
1 ATATTTCTAATAATATAATA
131772 AACAATCAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
ATATTTCTAATAATATAATAT
Found at i:132060 original size:27 final size:25
Alignment explanation
Indices: 132019--132171 Score: 73
Period size: 27 Copynumber: 5.8 Consensus size: 25
132009 TAATATAATT
**
132019 TATAATATTTTTATTTCAATAAAAAA
1 TATAATATTAATATTT-AATAAAAAA
*
132045 TACTAATATTAATATTTGTATTAATAAAA
1 TA-TAATATTAATA-TT-TAATAA-AAAA
* *
132074 TTATAAAAATAATATTTAATAAAAAA
1 -TATAATATTAATATTTAATAAAAAA
* *
132100 TA-AATTATTTTAATATTT-TTAAAATA
1 TATAA-TA--TTAATATTTAATAAAAAA
*
132126 -ATAATATTAA-ATTTTATGATAAATAA
1 TATAATATTAATA-TTTA--ATAAAAAA
*
132152 TATATTTATT-ATATTTAATA
1 TATA-ATATTAATATTTAATA
132172 TTTGTAATAA
Statistics
Matches: 97, Mismatches: 14, Indels: 33
0.67 0.10 0.23
Matches are distributed among these distances:
22 1 0.01
23 7 0.07
24 2 0.02
25 9 0.09
26 19 0.20
27 30 0.31
28 13 0.13
29 14 0.14
30 2 0.02
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (25 bp):
TATAATATTAATATTTAATAAAAAA
Found at i:132337 original size:14 final size:14
Alignment explanation
Indices: 132318--132376 Score: 55
Period size: 14 Copynumber: 4.1 Consensus size: 14
132308 CAAGAAATGT
*
132318 AATTCATTTTCCAG
1 AATTCAATTTCCAG
* **
132332 AATTCAAATTATAG
1 AATTCAATTTCCAG
* *
132346 TAATTCATTTTCCAT
1 -AATTCAATTTCCAG
132361 AATTCAATTTCCAG
1 AATTCAATTTCCAG
132375 AA
1 AA
132377 AACCAATTAC
Statistics
Matches: 33, Mismatches: 11, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
14 24 0.73
15 9 0.27
ACGTcount: A:0.37, C:0.17, G:0.05, T:0.41
Consensus pattern (14 bp):
AATTCAATTTCCAG
Found at i:132940 original size:42 final size:43
Alignment explanation
Indices: 132881--132965 Score: 163
Period size: 42 Copynumber: 2.0 Consensus size: 43
132871 AATTGGGCAC
132881 ATAGTTTTTAAAATTTGCAATTTAGTAACTGG-CCTGATTTAG
1 ATAGTTTTTAAAATTTGCAATTTAGTAACTGGCCCTGATTTAG
132923 ATAGTTTTTAAAATTTGCAATTTAGTAACTGGCCCTGATTTAG
1 ATAGTTTTTAAAATTTGCAATTTAGTAACTGGCCCTGATTTAG
132966 GATGTTACAC
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 32 0.76
43 10 0.24
ACGTcount: A:0.31, C:0.11, G:0.16, T:0.42
Consensus pattern (43 bp):
ATAGTTTTTAAAATTTGCAATTTAGTAACTGGCCCTGATTTAG
Done.