Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004914.1 Hibiscus syriacus cultivar Beakdansim tig00011064_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: 64532
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:5153 original size:2 final size:2
Alignment explanation
Indices: 5146--5173 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5136 ATTATATTAC
5146 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
5174 CTTAACCTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6922 original size:21 final size:21
Alignment explanation
Indices: 6884--6924 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
6874 AGAATTGAGA
* * *
6884 AAAATAAATTTAAGAAAAAAG
1 AAAATAAAGTAAAAAAAAAAG
6905 AAAATAAAGTAAAAAAAAAA
1 AAAATAAAGTAAAAAAAAAA
6925 AACAAACATG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (21 bp):
AAAATAAAGTAAAAAAAAAAG
Found at i:7291 original size:23 final size:23
Alignment explanation
Indices: 7238--7283 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
7228 TAAAAAAAGG
7238 ACAATTATCTTCAAACAGACATT
1 ACAATTATCTTCAAACAGACATT
*
7261 ACAATTATCTTCAAACATACATT
1 ACAATTATCTTCAAACAGACATT
7284 CTTTTTATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.43, C:0.22, G:0.02, T:0.33
Consensus pattern (23 bp):
ACAATTATCTTCAAACAGACATT
Found at i:15741 original size:16 final size:16
Alignment explanation
Indices: 15705--15743 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
15695 TGCGTGGCAT
*
15705 GCGTGTGCATAAGGTG
1 GCGTGTGCATAAGGAG
15721 GCGTGTGCATAAGGAG
1 GCGTGTGCATAAGGAG
*
15737 TCGTGTG
1 GCGTGTG
15744 TGTGATATGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.18, C:0.13, G:0.44, T:0.26
Consensus pattern (16 bp):
GCGTGTGCATAAGGAG
Found at i:23755 original size:13 final size:14
Alignment explanation
Indices: 23739--23769 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
23729 CACAATATGA
23739 TATTTTTTAAAT-T
1 TATTTTTTAAATAT
23752 TATTTTTTAAATAT
1 TATTTTTTAAATAT
23766 TATT
1 TATT
23770 ATATTTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TATTTTTTAAATAT
Found at i:23792 original size:23 final size:23
Alignment explanation
Indices: 23766--23811 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
23756 TTTTAAATAT
23766 TATTATATTT-ATAAAAAACTCTA
1 TATTAT-TTTAATAAAAAACTCTA
*
23789 TATTCTTTTAAATAAAAAACTCT
1 TATTATTTT-AATAAAAAACTCT
23812 CAAAATCCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 3 0.15
23 5 0.25
24 12 0.60
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (23 bp):
TATTATTTTAATAAAAAACTCTA
Found at i:24327 original size:25 final size:26
Alignment explanation
Indices: 24294--24344 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
24284 TAGATGATTT
24294 AAAAAAATACT-A-TAGACACATATTA
1 AAAAAAATA-TAATTAGACACATATTA
24319 AAAAAAATATAATTTAGACACATATT
1 AAAAAAATATAA-TTAGACACATATT
24345 TAGCCTATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 1 0.04
25 10 0.43
27 12 0.52
ACGTcount: A:0.59, C:0.10, G:0.04, T:0.27
Consensus pattern (26 bp):
AAAAAAATATAATTAGACACATATTA
Found at i:24751 original size:14 final size:14
Alignment explanation
Indices: 24732--24788 Score: 80
Period size: 14 Copynumber: 4.1 Consensus size: 14
24722 TCGGTTAAAT
24732 GTTCATTTATGTTC
1 GTTCATTTATGTTC
*
24746 GTTCATTTATGTTT
1 GTTCATTTATGTTC
*
24760 GTTCGA-TTATGTTA
1 GTTC-ATTTATGTTC
24774 GTTCATTTATGTTC
1 GTTCATTTATGTTC
24788 G
1 G
24789 AACATAAGAC
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
13 1 0.03
14 36 0.95
15 1 0.03
ACGTcount: A:0.16, C:0.11, G:0.18, T:0.56
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:32317 original size:21 final size:20
Alignment explanation
Indices: 32290--32388 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
32280 AATCAGTTTC
32290 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
32311 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
32332 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
32352 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
32373 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
32389 ACACATAAAT
Statistics
Matches: 61, Mismatches: 15, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
20 16 0.26
21 45 0.74
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:32417 original size:20 final size:20
Alignment explanation
Indices: 32355--32584 Score: 232
Period size: 20 Copynumber: 11.5 Consensus size: 20
32345 CGATTTTCCA
* ** *
32355 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
32375 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
32395 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
32415 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
32435 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
32455 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
32475 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
32495 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
32515 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
32535 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
32555 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
32575 AAATCACAAC
1 AAATCGCAAC
32585 ACTGAAATTT
Statistics
Matches: 176, Mismatches: 28, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 172 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:33306 original size:24 final size:24
Alignment explanation
Indices: 33267--33313 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
33257 AAATTTGGTC
33267 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
33291 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
33314 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:33505 original size:12 final size:12
Alignment explanation
Indices: 33488--33512 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
33478 ATATAATCCT
33488 GAAGAAGAAAAA
1 GAAGAAGAAAAA
33500 GAAGAAGAAAAA
1 GAAGAAGAAAAA
33512 G
1 G
33513 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:35854 original size:19 final size:19
Alignment explanation
Indices: 35835--36019 Score: 229
Period size: 19 Copynumber: 10.5 Consensus size: 19
35825 TCCCAACATG
35835 AAATCGCAATGCGGAAATGA
1 AAATCGCAATGC-GAAATGA
35855 AAATCGCAA--CG--A-GA
1 AAATCGCAATGCGAAATGA
*
35869 GAATCGCAATGCGAAATGA
1 AAATCGCAATGCGAAATGA
35888 AAATCGCAATGCGAAATGA
1 AAATCGCAATGCGAAATGA
35907 AAATCGCAA--CG--A-GA
1 AAATCGCAATGCGAAATGA
*
35921 GAATCGCAATGCGAAATGA
1 AAATCGCAATGCGAAATGA
35940 AAATCGCAATGCGAAATGA
1 AAATCGCAATGCGAAATGA
35959 AAATCGCAA--CG--A-GA
1 AAATCGCAATGCGAAATGA
*
35973 GAATCGCAATGCGAAATGA
1 AAATCGCAATGCGAAATGA
35992 AAATCGCAATGCGAAATGA
1 AAATCGCAATGCGAAATGA
36011 AAATCGCAA
1 AAATCGCAA
36020 CGAGAGAATC
Statistics
Matches: 144, Mismatches: 6, Indels: 31
0.80 0.03 0.17
Matches are distributed among these distances:
14 30 0.21
15 3 0.02
16 6 0.04
17 5 0.03
18 4 0.03
19 87 0.60
20 9 0.06
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14
Consensus pattern (19 bp):
AAATCGCAATGCGAAATGA
Found at i:35857 original size:33 final size:33
Alignment explanation
Indices: 35790--36000 Score: 215
Period size: 33 Copynumber: 6.2 Consensus size: 33
35780 CGGAAATTAC
35790 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACGATGA-AATCGCAATGCGAAATGAA
*
35823 AATCCCAAC-ATGAAATCGCAATGCGGAAATGAA
1 AATCGCAACGATGAAATCGCAATGC-GAAATGAA
35856 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACGATGA-AATCGCAATGCGAAATGAA
*
35889 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAG
1 AATCGCAA--CG--ATG-AAATCGCAATGCGAAATGAA
35922 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--CG--ATG-AAATCGCAATGCGAAATGAA
35960 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACGATGA-AATCGCAATGCGAAATGAA
35993 AATCGCAA
1 AATCGCAA
36001 TGCGAAATGA
Statistics
Matches: 158, Mismatches: 4, Indels: 32
0.81 0.02 0.16
Matches are distributed among these distances:
32 13 0.08
33 101 0.64
34 14 0.09
35 4 0.03
36 4 0.03
37 2 0.01
38 19 0.12
39 1 0.01
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.13
Consensus pattern (33 bp):
AATCGCAACGATGAAATCGCAATGCGAAATGAA
Found at i:36030 original size:33 final size:33
Alignment explanation
Indices: 35889--36041 Score: 159
Period size: 33 Copynumber: 4.5 Consensus size: 33
35879 GCGAAATGAA
35889 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
* *
35922 AATCGCAATGCGAAATGAAAATCGCAATGCGA-
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
* * * *
35954 AAT-GAAAAT-CGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCG-CAATGCGAAATGA-A-AATCGCAA--CG--A-GAG
35993 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
36026 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
36042 TATAAACGCA
Statistics
Matches: 98, Mismatches: 11, Indels: 22
0.75 0.08 0.17
Matches are distributed among these distances:
31 7 0.07
32 7 0.07
33 56 0.57
34 1 0.01
35 1 0.01
36 2 0.02
38 10 0.10
39 7 0.07
40 7 0.07
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.14
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:36057 original size:52 final size:52
Alignment explanation
Indices: 35835--36041 Score: 405
Period size: 52 Copynumber: 4.0 Consensus size: 52
35825 TCCCAACATG
35835 AAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGA
1 AAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGA
35888 AAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGA
1 AAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGA
35940 AAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGA
1 AAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGA
35992 AAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAT
1 AAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAT
36042 TATAAACGCA
Statistics
Matches: 154, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
52 142 0.92
53 12 0.08
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14
Consensus pattern (52 bp):
AAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGA
Found at i:36124 original size:72 final size:71
Alignment explanation
Indices: 36048--36182 Score: 261
Period size: 72 Copynumber: 1.9 Consensus size: 71
36038 AAATTATAAA
36048 CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCGCATTGCGATT
1 CGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATTTCGCATTGCGATT
36113 TTCATTT
65 TTCATTT
36120 CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGAT
1 CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGAT
36183 AGTCATTTTT
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
71 30 0.48
72 33 0.52
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (71 bp):
CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTT
TCATTT
Found at i:36147 original size:33 final size:33
Alignment explanation
Indices: 36048--36164 Score: 171
Period size: 33 Copynumber: 3.4 Consensus size: 33
36038 AAATTATAAA
36048 CGCATTGCGATTCTCTCGTTGCGATTTTCATTT
1 CGCATTGCGATTCTCTCGTTGCGATTTTCATTT
*
36081 CCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTT
1 -CGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTT
36120 CGCATTGCGATTCTCTCGTTGCGATTTTCATTT
1 CGCATTGCGATTCTCTCGTTGCGATTTTCATTT
36153 CGCATTGCGATT
1 CGCATTGCGATT
36165 TTCATTTCGC
Statistics
Matches: 76, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
33 27 0.36
34 10 0.13
35 4 0.05
36 6 0.08
37 4 0.05
38 10 0.13
39 15 0.20
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (33 bp):
CGCATTGCGATTCTCTCGTTGCGATTTTCATTT
Found at i:36190 original size:19 final size:19
Alignment explanation
Indices: 36066--36182 Score: 181
Period size: 19 Copynumber: 6.4 Consensus size: 19
36056 GATTCTCTCG
36066 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
36086 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
36105 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
36124 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
36138 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
36157 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
36176 TTGCGAT
1 TTGCGAT
36183 AGTCATTTTT
Statistics
Matches: 90, Mismatches: 2, Indels: 11
0.87 0.02 0.11
Matches are distributed among these distances:
14 6 0.07
16 7 0.08
17 7 0.08
19 55 0.61
20 15 0.17
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:36304 original size:14 final size:14
Alignment explanation
Indices: 36268--36304 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
36258 CATCAATTAC
*
36268 ACAAATCAACTTTT
1 ACAAATCATCTTTT
36282 ACAAATCATCTTTT
1 ACAAATCATCTTTT
36296 ACAAATCAT
1 ACAAATCAT
36305 TAAACAATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.43, C:0.22, G:0.00, T:0.35
Consensus pattern (14 bp):
ACAAATCATCTTTT
Found at i:38248 original size:20 final size:20
Alignment explanation
Indices: 38223--38288 Score: 91
Period size: 19 Copynumber: 3.4 Consensus size: 20
38213 TAGTTTACTT
* *
38223 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAACTCAAAA
38243 TCGCAACGCGAAAC-CAAAA
1 TCGCAACGCGAAACTCAAAA
*
38262 TCGCAACGCGAAA-TGAAAA
1 TCGCAACGCGAAACTCAAAA
38281 TCGCAACG
1 TCGCAACG
38289 ACAGAATCGC
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
19 29 0.69
20 13 0.31
ACGTcount: A:0.45, C:0.27, G:0.17, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAACTCAAAA
Found at i:38342 original size:19 final size:19
Alignment explanation
Indices: 38320--38448 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
38310 AAAATCGCAA
38320 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
38339 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
38353 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
38372 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
38386 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
38405 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
38424 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
38444 TGCGA
1 TGCGA
38449 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:38362 original size:33 final size:33
Alignment explanation
Indices: 38320--38411 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
38310 AAAATCGCAA
38320 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
38353 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
38386 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
38412 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:38612 original size:93 final size:93
Alignment explanation
Indices: 38496--38871 Score: 736
Period size: 93 Copynumber: 4.1 Consensus size: 93
38486 ATGGATTGCA
38496 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
38560 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
38588 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
38653 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
38681 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
38746 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
38774 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
38839 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
38867 TTACT
1 TTACT
38872 AAGCAATCTA
Statistics
Matches: 282, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
92 4 0.01
93 278 0.99
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:40596 original size:14 final size:14
Alignment explanation
Indices: 40577--40666 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
40567 TTGAAATGAA
40577 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
40591 AATCGCAACGCGAAATGAC
1 AATCGCAA--CG--A-GAG
40610 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
40624 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
40643 AATCGCAACGAGAG
1 AATCGCAACGAGAG
40657 AATCGCAACG
1 AATCGCAACG
40667 CGAAATGAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 20 0.32
ACGTcount: A:0.43, C:0.23, G:0.24, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:40614 original size:33 final size:33
Alignment explanation
Indices: 40569--40683 Score: 221
Period size: 33 Copynumber: 3.5 Consensus size: 33
40559 TCTTTTGGTT
40569 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
40602 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
40635 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
40668 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
40684 TGCGATTTTG
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.46, C:0.21, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:40615 original size:19 final size:19
Alignment explanation
Indices: 40591--40688 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
40581 GCAACGAGAG
*
40591 AATCGCAACGCGAAATGAC
1 AATCGCAACGCGAAATGAA
*
40610 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
40624 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
40643 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
40657 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
40676 AATCGCAATGCGA
1 AATCGCAACGCGA
40689 TTTTGGTTTC
Statistics
Matches: 64, Mismatches: 5, Indels: 20
0.72 0.06 0.22
Matches are distributed among these distances:
14 20 0.31
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 32 0.50
ACGTcount: A:0.44, C:0.22, G:0.23, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:40773 original size:20 final size:20
Alignment explanation
Indices: 40707--40802 Score: 122
Period size: 21 Copynumber: 4.8 Consensus size: 20
40697 TCGCGTTGCG
40707 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
40727 ATT-TCGCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
***
40746 ATTTCTCTCGTTGCGACAGTC
1 A-TTCTCTCGTTGCGATTTTC
40767 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
40787 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
40803 CTCTTCTGCA
Statistics
Matches: 64, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
19 16 0.25
20 22 0.34
21 26 0.41
ACGTcount: A:0.12, C:0.24, G:0.18, T:0.46
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:40790 original size:41 final size:40
Alignment explanation
Indices: 40708--40803 Score: 138
Period size: 41 Copynumber: 2.4 Consensus size: 40
40698 CGCGTTGCGA
***
40708 TTCTCTCGTTGCGATTTTCATTTCGCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGACAGTCATTTCGCGTTGCGATTTTCAT
*
40748 TTCTCTCGTTGCGACAGTCATTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGACAGTCATT-TCGCGTTGCGATTTTCAT
*
40789 TTATCTCGTTGCGAC
1 TTCTCTCGTTGCGAC
40804 TCTTCTGCAA
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
40 19 0.38
41 31 0.62
ACGTcount: A:0.11, C:0.25, G:0.18, T:0.46
Consensus pattern (40 bp):
TTCTCTCGTTGCGACAGTCATTTCGCGTTGCGATTTTCAT
Found at i:40924 original size:33 final size:33
Alignment explanation
Indices: 40882--40952 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
40872 AATACTAACT
*
40882 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
40915 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
40948 TGAAA
1 TGAAA
40953 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:41186 original size:22 final size:22
Alignment explanation
Indices: 41134--41188 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
41124 TGGTTGTGAG
**
41134 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
41156 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
41178 GGATTTCTTCG
1 GGATTTCTTCG
41189 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:41359 original size:20 final size:20
Alignment explanation
Indices: 41334--41527 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
41324 CTTTAAATAT
41334 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
41354 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
41376 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
41395 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
41415 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
41435 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
41455 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
41475 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
41495 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
41515 CGCGTTGCGATTT
1 CGCGTTGCGATTT
41528 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:41521 original size:60 final size:60
Alignment explanation
Indices: 41334--41527 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
41324 CTTTAAATAT
**
41334 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
41395 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
41455 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
41515 CGCGTTGCGATTT
1 CGCGTTGCGATTT
41528 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:41544 original size:21 final size:21
Alignment explanation
Indices: 41514--41596 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
41504 ATTTTCATAT
*
41514 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
41535 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
41556 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
41577 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
41597 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:41587 original size:42 final size:43
Alignment explanation
Indices: 41494--41592 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
41484 ATTTATGTGT
* *
41494 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
41535 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
41577 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
41593 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:49787 original size:13 final size:13
Alignment explanation
Indices: 49771--49795 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49761 AAATAAAAAT
49771 AAAAAAAAAAGAG
1 AAAAAAAAAAGAG
49784 AAAAAAAAAAGA
1 AAAAAAAAAAGA
49796 TGAATGACTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAGAG
Found at i:59482 original size:105 final size:105
Alignment explanation
Indices: 59294--59503 Score: 285
Period size: 105 Copynumber: 2.0 Consensus size: 105
59284 GAGTCGAGGG
* *
59294 TCTACGCGGTCCTTCGGGACATATAGGTATCCTATGGAACATCTATGAGGTCTTTTGAGACACGT
1 TCTACGCGGTCCTTCGAGACATATAGGTATCATATGGAACATCTATGAGGTCTTTTGAGACACGT
* *
59359 ATTTGGTCCTTAGCATATGTATATGATTCTTAAGGAATTT
66 ACTTGATCCTTAGCATATGTATATGATTCTTAAGGAATTT
* * * * * * * *
59399 TCTACGTGGTCCTTCGAGACGTATATGTATTATTTGGAGCATGTATGAGGTCTTTTGAGACACTT
1 TCTACGCGGTCCTTCGAGACATATAGGTATCATATGGAACATCTATGAGGTCTTTTGAGACACGT
* * *
59464 ACTTGATCTTTAGTATATGTATATGGTTCTTAAGGAATTT
66 ACTTGATCCTTAGCATATGTATATGATTCTTAAGGAATTT
59504 ATATGTGGTA
Statistics
Matches: 90, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
105 90 1.00
ACGTcount: A:0.24, C:0.15, G:0.22, T:0.39
Consensus pattern (105 bp):
TCTACGCGGTCCTTCGAGACATATAGGTATCATATGGAACATCTATGAGGTCTTTTGAGACACGT
ACTTGATCCTTAGCATATGTATATGATTCTTAAGGAATTT
Found at i:59578 original size:23 final size:24
Alignment explanation
Indices: 59532--59578 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
59522 CAATCTTATA
* *
59532 TGGCACTACGGTGCAAATTCTACG
1 TGGCACTACAGTGCAAATTATACG
*
59556 TGGCACTTCAGTGC-AATTATACG
1 TGGCACTACAGTGCAAATTATACG
59579 AGATGTGGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (24 bp):
TGGCACTACAGTGCAAATTATACG
Found at i:62287 original size:23 final size:24
Alignment explanation
Indices: 62243--62288 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
62233 CTAAATAATT
62243 AAAAAAATAAAAAAAAGGCAAGAGA
1 AAAAAAATAAAAAAAA-GCAAGAGA
* *
62268 AAAAAAATGAAATAAA-CAAGA
1 AAAAAAATAAAAAAAAGCAAGA
62289 TATAGGCAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 5 0.26
25 14 0.74
ACGTcount: A:0.76, C:0.04, G:0.13, T:0.07
Consensus pattern (24 bp):
AAAAAAATAAAAAAAAGCAAGAGA
Found at i:62502 original size:16 final size:15
Alignment explanation
Indices: 62472--62518 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
62462 CATAAGAATA
*
62472 ATTAAGAATATATAC
1 ATTAACAATATATAC
62487 ATTAACAATGATATAC
1 ATTAACAAT-ATATAC
*
62503 AAATAA-AATATATAC
1 -ATTAACAATATATAC
62518 A
1 A
62519 AAAAAGATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
14 1 0.04
15 14 0.50
16 9 0.32
17 4 0.14
ACGTcount: A:0.57, C:0.09, G:0.04, T:0.30
Consensus pattern (15 bp):
ATTAACAATATATAC
Found at i:62517 original size:15 final size:16
Alignment explanation
Indices: 62478--62520 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
62468 AATAATTAAG
*
62478 AATATATAC-ATTAAC
1 AATATATACAAATAAC
62493 AATGATATACAAATAA-
1 AAT-ATATACAAATAAC
62509 AATATATACAAA
1 AATATATACAAA
62521 AAAGATACGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 12 0.48
16 9 0.36
17 4 0.16
ACGTcount: A:0.60, C:0.09, G:0.02, T:0.28
Consensus pattern (16 bp):
AATATATACAAATAAC
Done.