Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002611.1 Hibiscus syriacus cultivar Beakdansim tig00005277_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: 119130
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
File 2 of 2
Found at i:103406 original size:87 final size:88
Alignment explanation
Indices: 103280--103443 Score: 240
Period size: 87 Copynumber: 1.9 Consensus size: 88
103270 AAAAAACAAA
* * *
103280 AACAAATAAAAAATAGAAAACAATATAAGAATCAACTAATTCAAAGTCCTTCACATTAACGTAAA
1 AACAAATAAAAAACAGAAAACAATATAAGAATCAACTAATTCAAAGTACTTCACATTAACATAAA
103345 AATCAGCTAATATCCTTCACATC
66 AATCAGCTAATATCCTTCACATC
* * * * *
103368 AACAAAT-ACAAACAGAAAATAATATAATAATCAGCTAATTCAAAGTACTTCACATTAACATAAG
1 AACAAATAAAAAACAGAAAACAATATAAGAATCAACTAATTCAAAGTACTTCACATTAACATAAA
*
103432 AATTAGCTAATA
66 AATCAGCTAATA
103444 AAAAATAGAA
Statistics
Matches: 67, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
87 60 0.90
88 7 0.10
ACGTcount: A:0.52, C:0.17, G:0.06, T:0.24
Consensus pattern (88 bp):
AACAAATAAAAAACAGAAAACAATATAAGAATCAACTAATTCAAAGTACTTCACATTAACATAAA
AATCAGCTAATATCCTTCACATC
Found at i:103477 original size:20 final size:21
Alignment explanation
Indices: 103445--103483 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
103435 TAGCTAATAA
103445 AAAATAGAAAAACAGAAAAAT
1 AAAATAGAAAAACAGAAAAAT
103466 AAAATA-AAAAACAGAAAA
1 AAAATAGAAAAACAGAAAA
103484 TAAGATTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.79, C:0.05, G:0.08, T:0.08
Consensus pattern (21 bp):
AAAATAGAAAAACAGAAAAAT
Found at i:103630 original size:31 final size:31
Alignment explanation
Indices: 103603--103664 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
103593 AATAAAATAA
103603 AAAATAAAAAAACATATAAAATTTAAAAACAC
1 AAAAT-AAAAAACATATAAAATTTAAAAACAC
**
103635 AAAATAAAAAACATATAAAAAATAAAAACA
1 AAAATAAAAAACATATAAAATTTAAAAACA
103665 ATTATCAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
31 23 0.82
32 5 0.18
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (31 bp):
AAAATAAAAAACATATAAAATTTAAAAACAC
Found at i:103663 original size:17 final size:16
Alignment explanation
Indices: 103598--103685 Score: 63
Period size: 17 Copynumber: 5.3 Consensus size: 16
103588 ACAAAAATAA
103598 AATAAAAAATAAAAAAAC
1 AATAAAAAAT--AAAAAC
**
103616 ATATAAAATTTAAAAAC
1 A-ATAAAAAATAAAAAC
* *
103633 -ACAAAATA-AAAAAC
1 AATAAAAAATAAAAAC
103647 ATATAAAAAATAAAAAC
1 A-ATAAAAAATAAAAAC
**
103664 AATTATCAAATAAAAAC
1 AA-TAAAAAATAAAAAC
103681 AATAA
1 AATAA
103686 TAAACAATGA
Statistics
Matches: 56, Mismatches: 9, Indels: 12
0.73 0.12 0.16
Matches are distributed among these distances:
14 6 0.11
15 6 0.11
16 9 0.16
17 27 0.48
18 1 0.02
19 7 0.12
ACGTcount: A:0.74, C:0.08, G:0.00, T:0.18
Consensus pattern (16 bp):
AATAAAAAATAAAAAC
Found at i:103853 original size:19 final size:19
Alignment explanation
Indices: 103829--103869 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
103819 TGAATACCAG
103829 AAAAGAA-ATAAAAATACAA
1 AAAAGAATATAAAAATA-AA
103848 AAAAGAATATAAAAATAAA
1 AAAAGAATATAAAAATAAA
103867 AAA
1 AAA
103870 TATAAAAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.80, C:0.02, G:0.05, T:0.12
Consensus pattern (19 bp):
AAAAGAATATAAAAATAAA
Found at i:104939 original size:2 final size:2
Alignment explanation
Indices: 104932--105013 Score: 112
Period size: 2 Copynumber: 40.5 Consensus size: 2
104922 AGTCCTACGC
104932 AT 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 AT
* * *
104974 AT AT AT AT A- AT TT AT ACT TT AT ACT TT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT A
105014 CATACACTAA
Statistics
Matches: 71, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
1 1 0.01
2 68 0.96
3 2 0.03
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:105006 original size:49 final size:49
Alignment explanation
Indices: 104951--105057 Score: 155
Period size: 49 Copynumber: 2.2 Consensus size: 49
104941 TATATATATA
* *
104951 TATATATATATATATATATA-TATATATATATAATTT-ATACTTTATACTT
1 TATATATATATATACATACACTA-ATAT-TATAATTTAATACTTTATACTT
*
105000 TATATATATATATACATACACTAATATTATACTTTAATACTTTATACTT
1 TATATATATATATACATACACTAATATTATAATTTAATACTTTATACTT
105049 TATATATAT
1 TATATATAT
105058 TTTTTATACT
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
48 7 0.13
49 44 0.83
50 2 0.04
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.50
Consensus pattern (49 bp):
TATATATATATATACATACACTAATATTATAATTTAATACTTTATACTT
Found at i:105199 original size:19 final size:20
Alignment explanation
Indices: 105154--105218 Score: 73
Period size: 19 Copynumber: 3.4 Consensus size: 20
105144 GTGTGTGTGT
*
105154 ATATATGCTTATAATGTATA
1 ATATATACTTATAATGTATA
*
105174 TTATATACTTATAA-GTATA
1 ATATATACTTATAATGTATA
*
105193 ATGTATACTTAT-AT-TATA
1 ATATATACTTATAATGTATA
105211 TATATATA
1 -ATATATA
105219 TATATATAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
18 5 0.13
19 21 0.55
20 12 0.32
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.48
Consensus pattern (20 bp):
ATATATACTTATAATGTATA
Found at i:105324 original size:15 final size:13
Alignment explanation
Indices: 105201--105322 Score: 66
Period size: 13 Copynumber: 8.8 Consensus size: 13
105191 TAATGTATAC
105201 TTATATTATATATAT
1 TTATA-TATATA-AT
* *
105216 ATATATATATAAA
1 TTATATATATAAT
* *
105229 CTATAGTGTATAAT
1 TTATA-TATATAAT
*
105243 TTATATATATAGT
1 TTATATATATAAT
* *
105256 TTTTATATATAGT
1 TTATATATATAAT
* *
105269 TCATAT-TGTAAACT
1 TTATATATAT-AA-T
105283 ATGTAGTATATATAAT
1 -T-TA-TATATATAAT
*
105299 TTATATATATAGT
1 TTATATATATAAT
*
105312 TTACATATATA
1 TTATATATATA
105323 TATGGTATAT
Statistics
Matches: 83, Mismatches: 17, Indels: 16
0.72 0.15 0.14
Matches are distributed among these distances:
12 2 0.02
13 47 0.57
14 19 0.23
15 6 0.07
16 2 0.02
17 5 0.06
18 2 0.02
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.49
Consensus pattern (13 bp):
TTATATATATAAT
Found at i:106611 original size:17 final size:16
Alignment explanation
Indices: 106577--106623 Score: 76
Period size: 17 Copynumber: 2.9 Consensus size: 16
106567 AGTTTAAATA
106577 TTTTATTTTATTTTAT
1 TTTTATTTTATTTTAT
*
106593 TTTTAGTTTATTCTTAT
1 TTTTATTTTATT-TTAT
106610 TTTTATTTTATTTT
1 TTTTATTTTATTTT
106624 TTAATTAACC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 13 0.46
17 15 0.54
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.79
Consensus pattern (16 bp):
TTTTATTTTATTTTAT
Found at i:106624 original size:6 final size:5
Alignment explanation
Indices: 106575--106623 Score: 62
Period size: 5 Copynumber: 9.2 Consensus size: 5
106565 TAAGTTTAAA
*
106575 TATTT TATTT TATTT TATTTT TAGTT TATTCT TATTTT TATTT TATTT
1 TATTT TATTT TATTT TA-TTT TATTT TATT-T TA-TTT TATTT TATTT
106623 T
1 T
106624 TTAATTAACC
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
5 26 0.67
6 11 0.28
7 2 0.05
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (5 bp):
TATTT
Found at i:106624 original size:11 final size:11
Alignment explanation
Indices: 106575--106623 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
106565 TAAGTTTAAA
106575 TATTTTA-TTT
1 TATTTTATTTT
106585 TATTTTATTTT
1 TATTTTATTTT
* *
106596 TAGTTTATTCT
1 TATTTTATTTT
106607 TATTTT-TATTT
1 TATTTTAT-TTT
106618 TATTTT
1 TATTTT
106624 TTAATTAACC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
10 8 0.24
11 25 0.76
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (11 bp):
TATTTTATTTT
Found at i:106680 original size:17 final size:16
Alignment explanation
Indices: 106658--106706 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
106648 TTTTATTCAT
106658 TTTATTTTCTTTCTTTC
1 TTTATTTTCTTT-TTTC
*
106675 TTTATTTAT-TATTTTTG
1 TTTATTT-TCT-TTTTTC
106692 TTTATTTTCTTTTTT
1 TTTATTTTCTTTTTT
106707 ACTAACTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
16 6 0.21
17 19 0.68
18 3 0.11
ACGTcount: A:0.10, C:0.08, G:0.02, T:0.80
Consensus pattern (16 bp):
TTTATTTTCTTTTTTC
Found at i:112225 original size:72 final size:72
Alignment explanation
Indices: 112099--112239 Score: 228
Period size: 72 Copynumber: 2.0 Consensus size: 72
112089 ATACAGATGA
***
112099 TTTGTCTCACTTGAGACTGTTTTACTTGAAAGAAGATTTATTTCCCTTGTGATTGTCATTCTTAA
1 TTTGTCTCACTTGAGACTGTTTTACTTGAAAGAAGATTTATTTCCCTCAAGATTGTCATTCTTAA
112164 AACAGAC
66 AACAGAC
* **
112171 TTTGTCTCACTTGAGACTGTTTTACTTGAAAGAGGATTTATTTCCCTCAAGATTGTTTTTCTTAA
1 TTTGTCTCACTTGAGACTGTTTTACTTGAAAGAAGATTTATTTCCCTCAAGATTGTCATTCTTAA
112236 AACA
66 AACA
112240 AGATTTTATC
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
72 63 1.00
ACGTcount: A:0.26, C:0.16, G:0.15, T:0.43
Consensus pattern (72 bp):
TTTGTCTCACTTGAGACTGTTTTACTTGAAAGAAGATTTATTTCCCTCAAGATTGTCATTCTTAA
AACAGAC
Found at i:112245 original size:36 final size:36
Alignment explanation
Indices: 112108--112245 Score: 109
Period size: 36 Copynumber: 3.8 Consensus size: 36
112098 ATTTGTCTCA
* * *
112108 CTTGAGACTGTTTTACTTGAAAGAAGATTTATTTCC
1 CTTGAGATTGTTTTACTTAAAACAAGATTTATTTCC
* * * * *
112144 CTTGTGATTGTCATT-CTTAAAAC-AGACTTTGTCTCA
1 CTTGAGATTGT-TTTACTTAAAACAAGA-TTTATTTCC
* * * *
112180 CTTGAGACTGTTTTACTTGAAAGAGGATTTATTTCC
1 CTTGAGATTGTTTTACTTAAAACAAGATTTATTTCC
** *
112216 CTCAAGATTGTTTTTCTTAAAACAAGATTT
1 CTTGAGATTGTTTTACTTAAAACAAGATTT
112246 TATCTTGCTT
Statistics
Matches: 74, Mismatches: 24, Indels: 8
0.70 0.23 0.08
Matches are distributed among these distances:
35 5 0.07
36 65 0.88
37 4 0.05
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (36 bp):
CTTGAGATTGTTTTACTTAAAACAAGATTTATTTCC
Found at i:112377 original size:36 final size:36
Alignment explanation
Indices: 112330--112414 Score: 118
Period size: 36 Copynumber: 2.4 Consensus size: 36
112320 CATTAAAACA
** * *
112330 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
112366 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
*
112402 -TTCTCTTGAAACA
1 TTTCCCTTGAAACA
112415 TAAACATTGA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
35 12 0.27
36 32 0.73
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAG
Found at i:112513 original size:101 final size:102
Alignment explanation
Indices: 112253--112741 Score: 717
Period size: 101 Copynumber: 4.8 Consensus size: 102
112243 TTTTATCTTG
* * * * *
112253 CTTGAGATAGTTT-CCTTCGAAATAGGAAATTTTGTCTACCTTGAGATAGTTTCTCCTGGAACAT
1 CTTGAGATAGTTTCCCTT-G-AATA-CAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAT
112317 AAACATT-AAAACATTTCCCTTGAAATGAATTTTGTCTCT
63 AAACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCT
112356 CTTGAGATAGTTTCCCTTGAA-ACAAATTTTGTCTCCCTTGAGACAG-TTCTCTTGAAACATAAA
1 CTTGAGATAGTTTCCCTTGAATACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAA
112419 CATTGAAAACATTTCCCTTGAAATGAA-TTTGTCTCT
66 CATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCT
* * *
112455 CTTGAGATAGTTTCCCTCGAAGTAGAAATTTTGTCTCTCTTGAGACAG-TTCTCTTGAAACATAA
1 CTTGAGATAGTTTCCCTTGAA-TACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAA
*
112519 ACATTGAAAACA-TTCCCATGAAATGAATTTTGTCTCT
65 ACATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCT
** *
112556 CTTGAGATAGTTTCATTTTAAT-CAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAA
1 CTTGAGATAGTTTCCCTTGAATACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAA
*
112620 CATTGAAAACATTTCCCTTGAAATGAATTTTTATCTCT
66 CATTGAAAACATTTCCCTTGAAATGAA-TTTTGTCTCT
* *
112658 CTTGAGAAAGTTTCCCTTGAA-ACAAATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACATAAA
1 CTTGAGATAGTTTCCCTTGAATACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAA
*
112722 CTTTGAAAACAGTTTCCCTT
66 CATTGAAAACA-TTTCCCTT
112742 AAAACAAAAT
Statistics
Matches: 353, Mismatches: 23, Indels: 20
0.89 0.06 0.05
Matches are distributed among these distances:
99 70 0.20
100 86 0.24
101 92 0.26
102 79 0.22
103 22 0.06
104 4 0.01
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (102 bp):
CTTGAGATAGTTTCCCTTGAATACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAA
CATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCT
Found at i:112633 original size:201 final size:201
Alignment explanation
Indices: 112242--112739 Score: 738
Period size: 201 Copynumber: 2.5 Consensus size: 201
112232 TTAAAACAAG
*
112242 ATTTTATCT-TGCTTGAGATAGTTTCCTTCGAAATAGGAAATTTTGTCTACCTTGAGATAGTTTC
1 ATTTTATCTCT-CTTGAGATAGTTTCCCTCG-AATA-GAAATTTTGTCT-CCTTGAGATAGTTTC
* * *
112306 TCCTGGAACATAAACATT-AAAACATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTC
62 TCTTGAAACATAAACATTGAAAACATTTCCCATGAAATGAATTTTGTCTCTCTTGAGATAGTTTC
*
112370 CCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTCTCTTGAAACATAAACATTGAAAACATTTCC
127 ACTTGAAACAAATTTTGTCTCCCTTGAGACAGTTCTCTTGAAACATAAACATTGAAAACATTTCC
112435 CTTGAAATGA
192 CTTGAAATGA
* *
112445 A-TTTGTCTCTCTTGAGATAGTTTCCCTCGAAGTAGAAATTTTGTCTCTCTTGAGACAG-TTCTC
1 ATTTTATCTCTCTTGAGATAGTTTCCCTCGAA-TAGAAATTTTGTCTC-CTTGAGATAGTTTCTC
*
112508 TTGAAACATAAACATTGAAAACA-TTCCCATGAAATGAATTTTGTCTCTCTTGAGATAGTTTCAT
64 TTGAAACATAAACATTGAAAACATTTCCCATGAAATGAATTTTGTCTCTCTTGAGATAGTTTCAC
* *
112572 TTTAATCAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCC
129 TTGAAACAAATTTTGTCTCCCTTGAGACAG-TTCTCTTGAAACATAAACATTGAAAACATTTCCC
112637 TTGAAATGA
193 TTGAAATGA
* * *
112646 ATTTTTATCTCTCTTGAGAAAGTTTCCCTTGAA-ACAAATTTTGTCTCCCTTGAGATAGTTTCTC
1 A-TTTTATCTCTCTTGAGATAGTTTCCCTCGAATAGAAATTTTGTCT-CCTTGAGATAGTTTCTC
*
112710 TTGAAACATAAACTTTGAAAACAGTTTCCC
64 TTGAAACATAAACATTGAAAACA-TTTCCC
112740 TTAAAACAAA
Statistics
Matches: 268, Mismatches: 16, Indels: 21
0.88 0.05 0.07
Matches are distributed among these distances:
200 86 0.32
201 94 0.35
202 54 0.20
203 29 0.11
204 5 0.02
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (201 bp):
ATTTTATCTCTCTTGAGATAGTTTCCCTCGAATAGAAATTTTGTCTCCTTGAGATAGTTTCTCTT
GAAACATAAACATTGAAAACATTTCCCATGAAATGAATTTTGTCTCTCTTGAGATAGTTTCACTT
GAAACAAATTTTGTCTCCCTTGAGACAGTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTG
AAATGA
Found at i:112706 original size:36 final size:36
Alignment explanation
Indices: 112631--112717 Score: 111
Period size: 36 Copynumber: 2.4 Consensus size: 36
112621 ATTGAAAACA
* * *
112631 TTTCCCTTGAAATGAATTTTTATCTCTCTTGAGAAAG
1 TTTCCCTTGAAA-CAAATTTTATCTCCCTTGAGAAAG
* *
112668 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGATAG
1 TTTCCCTTGAAACAAATTTTATCTCCCTTGAGAAAG
*
112704 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
112718 TAAACTTTGA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
36 32 0.73
37 12 0.27
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTATCTCCCTTGAGAAAG
Found at i:112736 original size:30 final size:30
Alignment explanation
Indices: 112702--112758 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
112692 CCCTTGAGAT
* *
112702 AGTTTCTCTTGAAACATAAA-CTTTGAAAAC
1 AGTTTCCCTTAAAACA-AAATCTTTGAAAAC
112732 AGTTTCCCTTAAAACAAAATCTTTGAA
1 AGTTTCCCTTAAAACAAAATCTTTGAA
112759 TTTGTTTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 21 0.88
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.33
Consensus pattern (30 bp):
AGTTTCCCTTAAAACAAAATCTTTGAAAAC
Found at i:112848 original size:36 final size:36
Alignment explanation
Indices: 112763--112848 Score: 122
Period size: 36 Copynumber: 2.4 Consensus size: 36
112753 TTTGAATTTG
112763 TTTT-TCTTGAAACAAATTTTGTCTCCCTTGAGACA
1 TTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACA
* * *
112798 GTTTCT-TTAAAAACAAATTTTGTCTCTCTTGAGACA
1 TTTTCTCTT-GAAACAAATTTTGTCTCCCTTGAGACA
112834 TTTTCTCTTGAAACA
1 TTTTCTCTTGAAACA
112849 CAAAATCTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
35 5 0.12
36 36 0.84
37 2 0.05
ACGTcount: A:0.28, C:0.19, G:0.10, T:0.43
Consensus pattern (36 bp):
TTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACA
Found at i:112884 original size:68 final size:70
Alignment explanation
Indices: 112804--112966 Score: 183
Period size: 68 Copynumber: 2.4 Consensus size: 70
112794 GACAGTTTCT
* * * *
112804 TTAAAA-ACAAATTTTGTCTCTCTTGAGACATTTTCTCTTGAAAC-ACAAA-ATCTTTGAATTTA
1 TTAAAATA-AAATTTTGTCTCTCTTGAGACAGTTTCTCATGAAACAACAAATATCTTTGAAATCA
112866 TTTCCC
65 TTTCCC
* *
112872 TTAAAATAAAATTTTGTCTAC-CTTGAGACCGTTTCTCATGAAACAACAAATATCTTTGAAATCG
1 TTAAAATAAAATTTTGTCT-CTCTTGAGACAGTTTCTCATGAAACAACAAATATCTTTGAAATCA
112936 TTTCCC
65 TTTCCC
* * * *
112942 TTGAAAT-GAATTATGTCTCTTTTGA
1 TTAAAATAAAATTTTGTCTCTCTTGA
112967 TATAACTTCT
Statistics
Matches: 80, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
68 38 0.47
69 20 0.25
70 22 0.28
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.40
Consensus pattern (70 bp):
TTAAAATAAAATTTTGTCTCTCTTGAGACAGTTTCTCATGAAACAACAAATATCTTTGAAATCAT
TTCCC
Found at i:114470 original size:5 final size:5
Alignment explanation
Indices: 114460--114502 Score: 68
Period size: 5 Copynumber: 8.2 Consensus size: 5
114450 TAAGTTTAAA
114460 TATTT TATTT TATTT TATTT TATTCT TATTTT TATTT TATTT T
1 TATTT TATTT TATTT TATTT TATT-T TA-TTT TATTT TATTT T
114503 TTTAATTAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
5 28 0.78
6 6 0.17
7 2 0.06
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (5 bp):
TATTT
Found at i:114560 original size:21 final size:21
Alignment explanation
Indices: 114536--114582 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
114526 ATTGTATTCA
*
114536 TTTTA-TTTTCTTTCTTTTTAT
1 TTTTATTTTTCTTTATTTTT-T
*
114557 TTTTATTTTTGTTTATTTTTT
1 TTTTATTTTTCTTTATTTTTT
114578 TTTTA
1 TTTTA
114583 CTAACTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.11, C:0.04, G:0.02, T:0.83
Consensus pattern (21 bp):
TTTTATTTTTCTTTATTTTTT
Found at i:114571 original size:16 final size:15
Alignment explanation
Indices: 114537--114581 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
114527 TTGTATTCAT
*
114537 TTTATTTTCTTTCTT-
1 TTTATTTT-TTTTTTG
114552 TTTATTTTTATTTTTG
1 TTTATTTTT-TTTTTG
114568 TTTATTTTTTTTTT
1 TTTATTTTTTTTTT
114582 ACTAACTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 1 0.04
15 17 0.63
16 9 0.33
ACGTcount: A:0.09, C:0.04, G:0.02, T:0.84
Consensus pattern (15 bp):
TTTATTTTTTTTTTG
Found at i:115066 original size:8 final size:9
Alignment explanation
Indices: 115020--115071 Score: 61
Period size: 9 Copynumber: 5.7 Consensus size: 9
115010 AAATATAAAA
*
115020 TATACAGTT
1 TATATAGTT
115029 TATATAGTT
1 TATATAGTT
*
115038 CATATATAATT
1 --TATATAGTT
115049 TATATAGTT
1 TATATAGTT
115058 TAT-TAGTT
1 TATATAGTT
115066 TATATA
1 TATATA
115072 TATAATTCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
8 8 0.22
9 21 0.57
11 8 0.22
ACGTcount: A:0.37, C:0.04, G:0.08, T:0.52
Consensus pattern (9 bp):
TATATAGTT
Found at i:115073 original size:50 final size:50
Alignment explanation
Indices: 114992--115132 Score: 123
Period size: 50 Copynumber: 2.8 Consensus size: 50
114982 TATTATAATT
* * * **
114992 TATAATTATATAGTATATAAATA-TAAAATATACAGTTTATATAGTTCA-TA
1 TATAATTATATAGT-TATATATAGTTATATATA-AGTTTATATAGTAAACTA
* *
115042 TATAATTTATATAGTT-TAT-TAGTTTATATATATAATTCATAT-GTAAACTA
1 TATAA-TTATATAGTTATATATAG-TTATATATA-AGTTTATATAGTAAACTA
*
115092 TATAATTATTTAGTTATATATAGTTATATAT-AGTTTATATA
1 TATAATTATATAGTTATATATAGTTATATATAAGTTTATATA
115133 CTACTATGTA
Statistics
Matches: 73, Mismatches: 11, Indels: 15
0.74 0.11 0.15
Matches are distributed among these distances:
48 9 0.12
49 14 0.19
50 38 0.52
51 12 0.16
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48
Consensus pattern (50 bp):
TATAATTATATAGTTATATATAGTTATATATAAGTTTATATAGTAAACTA
Found at i:115081 original size:41 final size:40
Alignment explanation
Indices: 115029--115113 Score: 100
Period size: 41 Copynumber: 2.1 Consensus size: 40
115019 ATATACAGTT
* ** *
115029 TATATAGTTCATATATAATTTATATAGTT-TATTAGTTTATA
1 TATATAATTCATATATAAACTATATAATTAT-TTAG-TTATA
*
115070 TATATAATTCATATGTAAACTATATAATTATTTAGTTATA
1 TATATAATTCATATATAAACTATATAATTATTTAGTTATA
115110 TATA
1 TATA
115114 GTTATATATA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
40 9 0.24
41 28 0.74
42 1 0.03
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.51
Consensus pattern (40 bp):
TATATAATTCATATATAAACTATATAATTATTTAGTTATA
Found at i:115111 original size:2 final size:2
Alignment explanation
Indices: 115106--115562 Score: 96
Period size: 2 Copynumber: 231.0 Consensus size: 2
115096 ATTATTTAGT
* * *
115106 TA TA TA TA GT- TA TA TA TA GTT TA TA TA CTA CTA TG TA TA AA CTA
1 TA TA TA TA -TA TA TA TA TA -TA TA TA TA -TA -TA TA TA TA TA -TA
* * *
115150 TA TA TA TA T- TA TA TA AA T- TA -A CTC TA AA CTA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA
*
115190 TA TA TA -A TA TA CTA TA TA GTT TA TA TA -A CTA TA TA -A TA -A
1 TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA
* * *
115229 TA TA T- TA TA TA TA AA CTA TA TA T- TA TA CA -A TA TA TA AA CTA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA
* * * *
115270 TA GTT TA TA CA TA GTA -A TA TA TA GTA TA AA CTA TA TA GTT TA TA
1 TA -TA TA TA TA TA -TA TA TA TA TA -TA TA TA -TA TA TA -TA TA TA
* * * *
115314 TA TA TT TA TA T- TA -A TA AA T- TA TA -A TT TA TA CA TA GTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* ** *
115353 TA -A TT TA TA -A T- TA TA TA GTA TA TA TA TA -A GC TA TA TA GTT
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA
* * * * * *
115393 TA TA T- TG TA TA TA AA TA TA AA CTA TA TT TA TA AA CA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
* * *
115434 TA CA CTA TA TT TA TA TA TA TA TA TA TA -A TA CTA TG TA TA -A T-
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
* * * *
115475 TC TA AA T- TA TA TA TA CTA TA AA T- TA TA TA GTT TA T- TA TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA
* * * *
115516 AA TCA TA TA GTT TA TA TA TT TA GA TA T- TA T- TA TA TA -A TA TA
1 TA T-A TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
115557 TA TA TA
1 TA TA TA
115563 ATTATTTCAA
Statistics
Matches: 325, Mismatches: 72, Indels: 116
0.63 0.14 0.23
Matches are distributed among these distances:
1 32 0.10
2 256 0.79
3 37 0.11
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.46
Consensus pattern (2 bp):
TA
Found at i:115117 original size:10 final size:10
Alignment explanation
Indices: 115090--115132 Score: 56
Period size: 10 Copynumber: 4.6 Consensus size: 10
115080 ATATGTAAAC
*
115090 TATATAATTA
1 TATATAGTTA
115100 T-T-TAGTTA
1 TATATAGTTA
115108 TATATAGTTA
1 TATATAGTTA
115118 TATATAGTT-
1 TATATAGTTA
115127 TATATA
1 TATATA
115133 CTACTATGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
8 6 0.20
9 8 0.27
10 16 0.53
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (10 bp):
TATATAGTTA
Found at i:115125 original size:20 final size:19
Alignment explanation
Indices: 115019--115132 Score: 69
Period size: 20 Copynumber: 5.8 Consensus size: 19
115009 TAAATATAAA
*
115019 ATATACAGTTTATATAGTT
1 ATATATAGTTTATATAGTT
*
115038 CATATATAATTTATATAGTT
1 -ATATATAGTTTATATAGTT
115058 -TAT-TAGTTTATATA--T
1 ATATATAGTTTATATAGTT
* *
115073 ATAATTCATATGTAAACTATATAATT
1 AT-A-T-ATA-GT---TTATATAGTT
115099 AT-T-TAGTTATATATAGTT
1 ATATATAGTT-TATATAGTT
115117 ATATATAGTTTATATA
1 ATATATAGTTTATATA
115133 CTACTATGTA
Statistics
Matches: 74, Mismatches: 6, Indels: 29
0.68 0.06 0.27
Matches are distributed among these distances:
15 1 0.01
16 1 0.01
17 11 0.15
18 14 0.19
19 7 0.09
20 26 0.35
21 4 0.05
23 1 0.01
24 6 0.08
26 3 0.04
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.50
Consensus pattern (19 bp):
ATATATAGTTTATATAGTT
Found at i:115149 original size:11 final size:11
Alignment explanation
Indices: 115135--115271 Score: 56
Period size: 11 Copynumber: 12.5 Consensus size: 11
115125 TTTATATACT
*
115135 ACTATGTATAA
1 ACTATATATAA
*
115146 ACTATATATAT
1 ACTATATATAA
115157 A-T-TATATAA
1 ACTATATATAA
* *
115166 ATTA-ACTCTAA
1 ACTATA-TATAA
*
115177 ACTATAT-TAT
1 ACTATATATAA
115187 A-TATATAT-A
1 ACTATATATAA
*
115196 A-TATACTATAT
1 ACTATA-TATAA
* *
115207 AGTTTATAT-A
1 ACTATATATAA
115217 ACTATATAATAATA
1 ACTATAT-AT-A-A
*
115231 TATTATATATAA
1 -ACTATATATAA
*
115243 ACTATATATTAT
1 ACTATATA-TAA
*
115255 ACAATATATAA
1 ACTATATATAA
115266 ACTATA
1 ACTATA
115272 GTTTATACAT
Statistics
Matches: 94, Mismatches: 18, Indels: 28
0.67 0.13 0.20
Matches are distributed among these distances:
9 17 0.18
10 15 0.16
11 38 0.40
12 14 0.15
13 1 0.01
14 3 0.03
15 6 0.06
ACGTcount: A:0.49, C:0.07, G:0.01, T:0.42
Consensus pattern (11 bp):
ACTATATATAA
Found at i:115203 original size:23 final size:23
Alignment explanation
Indices: 115177--115290 Score: 66
Period size: 21 Copynumber: 5.0 Consensus size: 23
115167 TTAACTCTAA
115177 ACTATATTATATATATATAATAT
1 ACTATATTATATATATATAATAT
115200 ACTATA-TAGT-T-TATATAACTAT
1 ACTATATTA-TATATATATAA-TAT
*
115222 A-TAATAATATATTATATATAA-ACT
1 ACT-ATATTATA-TATATATAATA-T
* *
115246 A-TATATTATACA-ATAT-ATAA
1 ACTATATTATATATATATAATAT
*
115266 ACTATAGTT-TATACATAGTAATAT
1 ACTATA-TTATATATATA-TAATAT
115290 A
1 A
115291 TAGTATAAAC
Statistics
Matches: 72, Mismatches: 5, Indels: 27
0.69 0.05 0.26
Matches are distributed among these distances:
20 2 0.03
21 20 0.28
22 17 0.24
23 18 0.25
24 8 0.11
25 7 0.10
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (23 bp):
ACTATATTATATATATATAATAT
Found at i:115232 original size:27 final size:27
Alignment explanation
Indices: 115183--115261 Score: 76
Period size: 27 Copynumber: 3.0 Consensus size: 27
115173 CTAAACTATA
115183 TTATAT-A-TATATAATATACTATATAGT
1 TTATATAACTATATAATATACTATAT--T
115210 TTATATAACTATATAATA-A-TATATT
1 TTATATAACTATATAATATACTATATT
* * *
115235 ATATATAAACTATATATTATACAATAT
1 TTATAT-AACTATATAATATACTATAT
115262 ATAAACTATA
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
25 6 0.14
26 11 0.25
27 12 0.27
28 6 0.14
29 9 0.20
ACGTcount: A:0.48, C:0.05, G:0.01, T:0.46
Consensus pattern (27 bp):
TTATATAACTATATAATATACTATATT
Found at i:115313 original size:35 final size:32
Alignment explanation
Indices: 115258--115354 Score: 103
Period size: 35 Copynumber: 3.0 Consensus size: 32
115248 ATATTATACA
115258 ATATATAAAC-TATAGTTTATACATAGTAATAT
1 ATATATAAACTTATAGTTTATACATAGT-ATAT
* *
115290 ATAGTATAAACTATATAGTTTATATATA-TTTAT
1 ATA-TATAAACT-TATAGTTTATACATAGTATAT
*
115323 AT-TAATAAA-TTATAATTTATACATAGTATAT
1 ATAT-ATAAACTTATAGTTTATACATAGTATAT
115354 A
1 A
115355 ATTTATAATT
Statistics
Matches: 55, Mismatches: 5, Indels: 11
0.77 0.07 0.15
Matches are distributed among these distances:
30 13 0.24
31 7 0.13
32 8 0.15
33 12 0.22
34 1 0.02
35 14 0.25
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.44
Consensus pattern (32 bp):
ATATATAAACTTATAGTTTATACATAGTATAT
Found at i:115516 original size:21 final size:20
Alignment explanation
Indices: 115486--115534 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
115476 CTAAATTATA
*
115486 TATACTATAAATTATATAGTT
1 TATA-TATAAATCATATAGTT
115507 TATTATATAAATCATATAGTT
1 TA-TATATAAATCATATAGTT
115528 TATATAT
1 TATATAT
115535 TTAGATATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 5 0.19
21 19 0.73
22 2 0.08
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (20 bp):
TATATATAAATCATATAGTT
Found at i:116509 original size:38 final size:38
Alignment explanation
Indices: 116451--116534 Score: 125
Period size: 38 Copynumber: 2.2 Consensus size: 38
116441 ATTGGCATGG
*
116451 TAGGGTAAGGGGGTGTTGAAGGTCTTTCACCAAC-TCA
1 TAGGGTAAGGGGGTGTTGAAGGTCTCTCACCAACTTCA
*
116488 TAGGGTAAGGGGGGTGTTGAAGGTCTCTCGCCAACTTCA
1 TAGGGTAA-GGGGGTGTTGAAGGTCTCTCACCAACTTCA
116527 TATGGGTA
1 TA-GGGTA
116535 TGTCTCAACA
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
37 8 0.19
38 24 0.57
39 5 0.12
40 5 0.12
ACGTcount: A:0.23, C:0.15, G:0.35, T:0.27
Consensus pattern (38 bp):
TAGGGTAAGGGGGTGTTGAAGGTCTCTCACCAACTTCA
Done.