Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005105.1 Hibiscus syriacus cultivar Beakdansim tig00011474_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: 58216
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:439 original size:185 final size:191
Alignment explanation
Indices: 67--775 Score: 906
Period size: 185 Copynumber: 3.7 Consensus size: 191
57 CCATTTAAAT
* **
67 TGGACACAAAGTATCGACACAAATT-AAAAAG-GTTGAACTTCATGTACACCATTTT-TCATAAA
1 TGGACACAAAGTATCGACACAAATTAAAAAAGTGTCGAACTTCATGTACACTGTTTTCTCATAAA
*
129 CCGGTGTATTTAG-ACGGTTAGATTGATAATTTACCTATTA-ATTATAATTATGGGTCTCGATGT
66 CCGGTGTATTTAGAACGGTTAGATTGATAATTTACCTATTACATTATAA-TATAGGTCTCGATG-
192 TTTTGGGATCGATACTTTTATACAGTATCGACACATTATGGTGACCTTGGTAAGGAAATCATTC
129 TTTTGGGATCGATACTTTTATA-AGTATCGACACATTATGGTGACCTTGGTAAGGAAATCATTC
256 TGGACACAAAGTATCGACACAAATTAAAAAAGTGTCGATACTTCATGTACACTGTTTTCTCATAA
1 TGGACACAAAGTATCGACACAAATTAAAAAAGTGTCGA-ACTTCATGTACACTGTTTTCTCATAA
*
321 ACCAGTGTATTTAGAACGGTTAGA-TGATAA-TTACCTATTA-ATTATAATATAGGTCTCGATGT
65 ACCGGTGTATTTAGAACGGTTAGATTGATAATTTACCTATTACATTATAATATAGGTCTCGATGT
* *
383 TTTGGGATCGATACTTTT-T-A-TACCGA-ACATTATGGTGACCTTGGTAAGGAAATCATTT
130 TTTGGGATCGATACTTTTATAAGTATCGACACATTATGGTGACCTTGGTAAGGAAATCATTC
*
441 TGGACACAAAGTATCGACACAAATTTAAAAAGTGTCG-ACTTCATGTACACCTGTTTTCTCATAA
1 TGGACACAAAGTATCGACACAAATTAAAAAAGTGTCGAACTTCATGTACA-CTGTTTTCTCATAA
* * * * *
505 A-CGGTGTATTTAGACCGGTTAGA-T-CTAATTTACCTATTACATTATAGTTATGGGTCTCCAT-
65 ACCGGTGTATTTAGAACGGTTAGATTGATAATTTACCTATTACATTATA-ATATAGGTCTCGATG
* *
566 TTTTGGGATCGATACGTTTTATAAATGTATCGACACATTCCAT-G-CA-CTTGGTAAAGAAAATC
129 TTTTGGGATCGATAC-TTTTAT-AA-GTATCGACACATT--ATGGTGACCTTGGT-AAGGAAATC
628 ATTC
188 ATTC
* *
632 TGGACACAAAGTATGGGATCGACACAAATTAAACAAGTGTCGATACTTTATGTACACTGTTTTCT
1 TGGACACAAAG--T---ATCGACACAAATTAAAAAAGTGTCGA-ACTTCATGTACACTGTTTTCT
*
697 CATAAACCGGTGTATTTAGACCGGTTAGATTGATAATTTACC--TTACATTATAAT-TATGGTTC
60 CATAAACCGGTGTATTTAGAACGGTTAGATTGATAATTTACCTATTACATTATAATATA-GG-TC
*
759 TCGATATTTTGGGATCG
123 TCGATGTTTTGGGATCG
776 CACAAATTAA
Statistics
Matches: 463, Mismatches: 25, Indels: 54
0.85 0.05 0.10
Matches are distributed among these distances:
182 3 0.01
183 43 0.09
184 36 0.08
185 82 0.18
186 6 0.01
187 1 0.00
188 1 0.00
189 26 0.06
190 36 0.08
191 45 0.10
192 35 0.08
193 28 0.06
194 9 0.02
196 24 0.05
197 18 0.04
198 49 0.11
199 12 0.03
200 9 0.02
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (191 bp):
TGGACACAAAGTATCGACACAAATTAAAAAAGTGTCGAACTTCATGTACACTGTTTTCTCATAAA
CCGGTGTATTTAGAACGGTTAGATTGATAATTTACCTATTACATTATAATATAGGTCTCGATGTT
TTGGGATCGATACTTTTATAAGTATCGACACATTATGGTGACCTTGGTAAGGAAATCATTC
Found at i:2265 original size:15 final size:16
Alignment explanation
Indices: 2245--2280 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
2235 TCATTAGGAT
2245 TAATATC-TTTCATGA
1 TAATATCTTTTCATGA
2260 TAATATCTTTTCATGA
1 TAATATCTTTTCATGA
2276 -AATAT
1 TAATAT
2281 TTAAATATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.36, C:0.11, G:0.06, T:0.47
Consensus pattern (16 bp):
TAATATCTTTTCATGA
Found at i:4337 original size:18 final size:18
Alignment explanation
Indices: 4311--4345 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
4301 AAGTACATAT
*
4311 ACCCTTTGGTTGCTTTCC
1 ACCCATTGGTTGCTTTCC
4329 ACCCATTGGTTGCTTTC
1 ACCCATTGGTTGCTTTC
4346 TACCAATTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.09, C:0.31, G:0.17, T:0.43
Consensus pattern (18 bp):
ACCCATTGGTTGCTTTCC
Found at i:4354 original size:18 final size:18
Alignment explanation
Indices: 4316--4354 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
4306 CATATACCCT
*
4316 TTGGTTGCTTTCCACCCA
1 TTGGTTGCTTTCCACCAA
*
4334 TTGGTTGCTTTCTACCAA
1 TTGGTTGCTTTCCACCAA
4352 TTG
1 TTG
4355 ATTCATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.13, C:0.26, G:0.18, T:0.44
Consensus pattern (18 bp):
TTGGTTGCTTTCCACCAA
Found at i:5487 original size:140 final size:137
Alignment explanation
Indices: 5250--5568 Score: 452
Period size: 140 Copynumber: 2.3 Consensus size: 137
5240 ACTTAATTTA
* *
5250 TCGACACTTT-AA-ATAT-CGGTATCTTTTTACCGGTTTTATCATTTCGAGACCTCTTTTGTCAT
1 TCGACACTTTCAATATATCCGGTAGCTTTTTACCGGTTTTATCATTTCGAGACCTCGTTTGTCAT
*
5312 ATTATTACCGGATATATTACTATGGATCGATACATTTGTATAAAGTATCGACA-CTTTTCAGGCG
66 ATTATTACCGGATATATTACTATGGATCGACACATTTGTATAAAGTATCGACACCTTTT-AGGCG
5376 CTATAACTTCTT
130 CTATAA---C-T
5388 CTCGACACTTTCAATATATCCGGTAGCTTTTTACCGGTTTTATCATTTCGAGA-C-CGTTTGTCA
1 -TCGACACTTTCAATATATCCGGTAGCTTTTTACCGGTTTTATCATTTCGAGACCTCGTTTGTCA
* * * *
5451 TATTATTACCTGTTATATTGCTATGGATCGACACATTTTTATAAAGTATCGACACCTTTTAGGCG
65 TATTATTACCGGATATATTACTATGGATCGACACATTTGTATAAAGTATCGACACCTTTTAGGCG
*
5516 CTGTAACT
130 CTATAACT
**
5524 TCGACACTTTCAATATATCCGGTAGCGCTTTACCGGTTTTATCAT
1 TCGACACTTTCAATATATCCGGTAGCTTTTTACCGGTTTTATCAT
5569 ATTTTTACAT
Statistics
Matches: 166, Mismatches: 10, Indels: 12
0.88 0.05 0.06
Matches are distributed among these distances:
135 43 0.26
136 1 0.01
137 1 0.01
139 10 0.06
140 69 0.42
141 10 0.06
142 32 0.19
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (137 bp):
TCGACACTTTCAATATATCCGGTAGCTTTTTACCGGTTTTATCATTTCGAGACCTCGTTTGTCAT
ATTATTACCGGATATATTACTATGGATCGACACATTTGTATAAAGTATCGACACCTTTTAGGCGC
TATAACT
Found at i:7285 original size:41 final size:40
Alignment explanation
Indices: 7232--7331 Score: 114
Period size: 41 Copynumber: 2.4 Consensus size: 40
7222 TTTTATTTTT
* *
7232 ATATTATTAAATATATTTATTTAATTA-TTAAAAATATAA-AG
1 ATATTA-TAAATATATTAATTTAA-TAGTT-AAAATATAATAA
*
7273 ATATTATAAAATATATTAATTTAATAGTTTAAATATAATAA
1 ATATTAT-AAATATATTAATTTAATAGTTAAAATATAATAA
7314 ATAGTTATAAATATATTA
1 ATA-TTATAAATATATTA
7332 TTCTAAAATA
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
40 11 0.21
41 37 0.71
42 4 0.08
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (40 bp):
ATATTATAAATATATTAATTTAATAGTTAAAATATAATAA
Found at i:17717 original size:15 final size:14
Alignment explanation
Indices: 17638--17734 Score: 52
Period size: 15 Copynumber: 6.4 Consensus size: 14
17628 TATTATATTT
*
17638 TATTAAAACTAAAA
1 TATTAAAATTAAAA
* *
17652 TAATTATAAATTATAT
1 T-ATTA-AAATTAAAA
*
17668 TAATTAATTATTAAAA
1 T-ATTAA-AATTAAAA
*
17684 TAATAATATTATTAAAA
1 TATTAA-A--ATTAAAA
*
17701 TATTGAAAATTATAA
1 TATT-AAAATTAAAA
17716 TATTAAAA-TAAGAA
1 TATTAAAATTAA-AA
17730 TATTA
1 TATTA
17735 TATTATATTA
Statistics
Matches: 65, Mismatches: 11, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
13 2 0.03
14 12 0.18
15 20 0.31
16 18 0.28
17 11 0.17
18 2 0.03
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.40
Consensus pattern (14 bp):
TATTAAAATTAAAA
Found at i:17731 original size:14 final size:14
Alignment explanation
Indices: 17676--17734 Score: 61
Period size: 14 Copynumber: 4.4 Consensus size: 14
17666 ATTAATTAAT
17676 TATTAAAATAATAA
1 TATTAAAATAATAA
*
17690 TATT--ATTAA-AA
1 TATTAAAATAATAA
*
17701 TATTGAAAATTATAA
1 TATT-AAAATAATAA
*
17716 TATTAAAATAAGAA
1 TATTAAAATAATAA
17730 TATTA
1 TATTA
17735 TATTATATTA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
11 6 0.17
12 4 0.11
14 20 0.56
15 6 0.17
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (14 bp):
TATTAAAATAATAA
Found at i:23976 original size:56 final size:56
Alignment explanation
Indices: 23911--24093 Score: 278
Period size: 56 Copynumber: 3.3 Consensus size: 56
23901 CATATTTTTC
23911 TAGATATATTCGATTTCGGAGTCCATATTTTTATGATTCTTAATGGCAACAACTGA
1 TAGATATATTCGATTTCGGAGTCCATATTTTTATGATTCTTAATGGCAACAACTGA
* * * * * * *
23967 TAGATATATTTGATTTTGG-GACCCTTATTTTTATGCTTATTAATGGTAACAACTGA
1 TAGATATATTCGATTTCGGAG-TCCATATTTTTATGATTCTTAATGGCAACAACTGA
*
24023 TAGATATATTCGATTCCGGAGTCCATATTTTTATGATTCTTAATGGCAACAACTGA
1 TAGATATATTCGATTTCGGAGTCCATATTTTTATGATTCTTAATGGCAACAACTGA
24079 TAGATATATTCGATT
1 TAGATATATTCGATT
24094 GAGAATGAAA
Statistics
Matches: 110, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
55 1 0.01
56 108 0.98
57 1 0.01
ACGTcount: A:0.30, C:0.13, G:0.16, T:0.41
Consensus pattern (56 bp):
TAGATATATTCGATTTCGGAGTCCATATTTTTATGATTCTTAATGGCAACAACTGA
Found at i:24400 original size:21 final size:20
Alignment explanation
Indices: 24320--24401 Score: 67
Period size: 21 Copynumber: 4.0 Consensus size: 20
24310 CGCAAATCAG
24320 TTTCCAGATTCGCAATGCGAT
1 TTTCCA-ATTCGCAATGCGAT
* * *
24341 TAT-GACTATCGCAATGCGAT
1 TTTCCAAT-TCGCAATGCGAT
* **
24361 TTTCCAATTTTGCGTTGCGAT
1 TTTCCAA-TTCGCAATGCGAT
24382 TTTCCCAATTCGCAATGCGA
1 TTT-CCAATTCGCAATGCGA
24402 ATAAGTAAAT
Statistics
Matches: 45, Mismatches: 12, Indels: 8
0.69 0.18 0.12
Matches are distributed among these distances:
19 1 0.02
20 15 0.33
21 24 0.53
22 5 0.11
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.35
Consensus pattern (20 bp):
TTTCCAATTCGCAATGCGAT
Found at i:24416 original size:20 final size:21
Alignment explanation
Indices: 24391--24442 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
24381 TTTTCCCAAT
*
24391 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
24411 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
24432 TCGCAATGCGA
1 TCGCAATGCGA
24443 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:24455 original size:41 final size:41
Alignment explanation
Indices: 24428--24525 Score: 151
Period size: 41 Copynumber: 2.4 Consensus size: 41
24418 GCGAATTTGG
*
24428 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* *
24469 AAAATCGCAACGCGATACTGACTTTCGCAACGAGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* *
24510 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
24526 TTTCAAAGCG
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.23, G:0.17, T:0.20
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:24456 original size:20 final size:20
Alignment explanation
Indices: 24431--24525 Score: 77
Period size: 20 Copynumber: 4.7 Consensus size: 20
24421 AATTTGGAAA
* *
24431 ATCGCAATGCGATACTGAC-T
1 ATCGCAACGCGATAAT-ACAT
*
24451 ATCGCAACGCGATAATACAAA
1 ATCGCAACGCGATAATAC-AT
*
24472 ATCGCAACGCGATACTGAC-T
1 ATCGCAACGCGATAAT-ACAT
* *
24492 TTCGCAACGAGATAATACAT
1 ATCGCAACGCGATAATACAT
*
24512 AATCGCAATGCGAT
1 -ATCGCAACGCGAT
24526 TTTCAAAGCG
Statistics
Matches: 59, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
19 4 0.07
20 28 0.47
21 25 0.42
22 2 0.03
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGATAATACAT
Found at i:24709 original size:22 final size:22
Alignment explanation
Indices: 24684--24727 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
24674 CCATCTCTCA
24684 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
24706 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
24728 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:25024 original size:20 final size:20
Alignment explanation
Indices: 24975--25033 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
24965 TTTATTCTCT
* **
24975 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTGTCATTTTCG
24995 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
* *
25015 TGTTGCGATTTTCATTTTC
1 CGTTGCGATTGTCATTTTC
25034 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.15, C:0.19, G:0.22, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTGTCATTTTCG
Found at i:26373 original size:18 final size:18
Alignment explanation
Indices: 26352--26399 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
26342 TTCACTTCGG
26352 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
26370 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
26388 GAGCCATCACCT
1 GAGCCATCACCT
26400 GATCGACCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.46, G:0.12, T:0.15
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:26988 original size:19 final size:20
Alignment explanation
Indices: 26934--26989 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
26924 TAGTTTACTT
* *
26934 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
26954 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
*
26974 TCGCAATGC-GAAATGA
1 TCGCAACGCGGAAATGA
26990 AAATCGTAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 6 0.19
20 25 0.81
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:26995 original size:19 final size:19
Alignment explanation
Indices: 26973--27069 Score: 88
Period size: 19 Copynumber: 5.6 Consensus size: 19
26963 GGAAATGGCT
26973 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
26992 ATCGTAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
27006 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
27025 ATCGCAAT--G--AT-AAA
1 ATCGCAATGCGAAATGAAA
**
27039 ATCGCAACACGAAATGAAA
1 ATCGCAATGCGAAATGAAA
27058 ATCGCAATGCGA
1 ATCGCAATGCGA
27070 TTTGTGTTTC
Statistics
Matches: 61, Mismatches: 7, Indels: 20
0.69 0.08 0.23
Matches are distributed among these distances:
14 19 0.31
15 3 0.05
16 3 0.05
17 3 0.05
18 3 0.05
19 30 0.49
ACGTcount: A:0.47, C:0.19, G:0.19, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:27065 original size:33 final size:33
Alignment explanation
Indices: 26973--27066 Score: 143
Period size: 33 Copynumber: 2.8 Consensus size: 33
26963 GGAAATGGCT
* *
26973 ATCGCAATGCGAAATGAAAATCGTAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAATGACAAA
*
27006 ATCGCAATGCGAAATGAAAATCGCAATGATAAA
1 ATCGCAATGCGAAATGAAAATCGCAATGACAAA
**
27039 ATCGCAACACGAAATGAAAATCGCAATG
1 ATCGCAATGCGAAATGAAAATCGCAATG
27067 CGATTTGTGT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.48, C:0.18, G:0.18, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAATGACAAA
Found at i:27081 original size:19 final size:19
Alignment explanation
Indices: 27076--27141 Score: 79
Period size: 19 Copynumber: 3.7 Consensus size: 19
27066 GCGATTTGTG
*
27076 TTTCGCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
27095 TTTCGCATTGCGA-TTT--
1 TTTCGCATTGCGATTTTCA
*
27111 TGTCG--TTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
27128 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
27142 AGCCATTTCC
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
14 6 0.15
15 3 0.08
16 4 0.10
17 4 0.10
18 3 0.08
19 19 0.49
ACGTcount: A:0.12, C:0.20, G:0.21, T:0.47
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:27164 original size:20 final size:20
Alignment explanation
Indices: 27126--27200 Score: 98
Period size: 20 Copynumber: 3.8 Consensus size: 20
27116 TTGCGATTTT
*
27126 CATTT-CGCATTGCGATAGC
1 CATTTCCGCGTTGCGATAGC
*
27145 CATTTCCGCGTTGTGATAGC
1 CATTTCCGCGTTGCGATAGC
* *
27165 CATTTCCGCGTTGCAATAGT
1 CATTTCCGCGTTGCGATAGC
*
27185 CATTTTCGCGTTGCGA
1 CATTTCCGCGTTGCGA
27201 AAGTAAGTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
19 5 0.10
20 43 0.90
ACGTcount: A:0.17, C:0.25, G:0.23, T:0.35
Consensus pattern (20 bp):
CATTTCCGCGTTGCGATAGC
Found at i:27211 original size:20 final size:20
Alignment explanation
Indices: 27188--27226 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
27178 CAATAGTCAT
27188 TTTCGCGTTGCGAAAGTAAG
1 TTTCGCGTTGCGAAAGTAAG
*
27208 TTTCGTGTTGCGAAAGTAA
1 TTTCGCGTTGCGAAAGTAA
27227 ACTATTCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.13, G:0.28, T:0.33
Consensus pattern (20 bp):
TTTCGCGTTGCGAAAGTAAG
Found at i:27620 original size:21 final size:20
Alignment explanation
Indices: 27568--27628 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 20
27558 GACTCACATG
27568 TCATCCCTCAAGAGTCCCCT
1 TCATCCCTCAAGAGTCCCCT
* ** *
27588 CCAATCGTTCAAGAGGCCCCT
1 TC-ATCCCTCAAGAGTCCCCT
27609 ATCATCCCTCAAGAGTCCCC
1 -TCATCCCTCAAGAGTCCCC
27629 CCTCACCGTT
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
20 1 0.03
21 29 0.94
22 1 0.03
ACGTcount: A:0.23, C:0.43, G:0.13, T:0.21
Consensus pattern (20 bp):
TCATCCCTCAAGAGTCCCCT
Found at i:27627 original size:42 final size:42
Alignment explanation
Indices: 27568--27656 Score: 126
Period size: 42 Copynumber: 2.1 Consensus size: 42
27558 GACTCACATG
* *
27568 TCATCCCTCAAGAGTCCCCTCC-AATCGTTCAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCCC-CCTAACCGTTCAAGAGGCCACTA
* *
27610 TCATCCCTCAAGAGTCCCCCCTCACCGTTCAAGAGGCCACTG
1 TCATCCCTCAAGAGTCCCCCCTAACCGTTCAAGAGGCCACTA
27652 TCATC
1 TCATC
27657 GTTGAAGAGG
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
41 2 0.05
42 40 0.95
ACGTcount: A:0.22, C:0.42, G:0.15, T:0.21
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCCCCCTAACCGTTCAAGAGGCCACTA
Found at i:27659 original size:21 final size:21
Alignment explanation
Indices: 27591--27671 Score: 72
Period size: 21 Copynumber: 3.9 Consensus size: 21
27581 GTCCCCTCCA
27591 ATCGTTCAAGAGGCCCCTATC
1 ATCGTTCAAGAGGCCCCTATC
** * **
27612 ATCCCTCAAGAGTCCCCCCTC
1 ATCGTTCAAGAGGCCCCTATC
* * *
27633 ACCGTTCAAGAGGCCACTGTC
1 ATCGTTCAAGAGGCCCCTATC
* *
27654 ATCGTTGAAGAGGTCCCT
1 ATCGTTCAAGAGGCCCCT
27672 CCCACCATTC
Statistics
Matches: 44, Mismatches: 16, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.22, C:0.36, G:0.20, T:0.22
Consensus pattern (21 bp):
ATCGTTCAAGAGGCCCCTATC
Found at i:29099 original size:14 final size:14
Alignment explanation
Indices: 29065--29103 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
29055 TTGATTGTTT
29065 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
29079 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
29093 TGTTGATTTGT
1 AATTGATTTGT
29104 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:29267 original size:19 final size:19
Alignment explanation
Indices: 29243--29326 Score: 115
Period size: 19 Copynumber: 4.7 Consensus size: 19
29233 GCAACGAGAG
29243 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
29262 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
29281 AATCACAATGCGAAATGGA
1 AATCGCAATGCGAAATGAA
29300 AATCGCAA--CG--A-GAA
1 AATCGCAATGCGAAATGAA
29314 AATCGCAATGCGA
1 AATCGCAATGCGA
29327 TTTTCATTTC
Statistics
Matches: 58, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
14 10 0.17
15 1 0.02
16 2 0.03
17 2 0.03
19 43 0.74
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:29957 original size:41 final size:41
Alignment explanation
Indices: 29906--30043 Score: 147
Period size: 41 Copynumber: 3.4 Consensus size: 41
29896 AACTTTGAAA
* * *
29906 ATCGCATTGCGATTTTGTATTATCTCGTTGCAATAGTCAGA
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCAATAGTCAGT
* ** **
29947 ATCTCGTTGCGA--AAGTCAGAATCGCGTTGCGAA-AGTCAGT
1 ATCGCGTTGCGATTTTGT-ATTATCGCGTTGC-AATAGTCAGT
*
29987 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCAATAGTCAGT
*
30028 ATCGCATTGCGATTTT
1 ATCGCGTTGCGATTTT
30044 CCAAATTCGC
Statistics
Matches: 77, Mismatches: 15, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
39 2 0.03
40 28 0.36
41 45 0.58
42 2 0.03
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (41 bp):
ATCGCGTTGCGATTTTGTATTATCGCGTTGCAATAGTCAGT
Found at i:30032 original size:20 final size:20
Alignment explanation
Indices: 29926--30040 Score: 115
Period size: 20 Copynumber: 5.7 Consensus size: 20
29916 GATTTTGTAT
* *
29926 TATCTCGTTGCAATAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
29946 AATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
29966 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
29986 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAG
30007 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
30027 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
30041 TTTCCAAATT
Statistics
Matches: 81, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
19 3 0.04
20 62 0.77
21 14 0.17
22 2 0.02
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.32
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:30059 original size:41 final size:41
Alignment explanation
Indices: 29906--30061 Score: 127
Period size: 41 Copynumber: 3.8 Consensus size: 41
29896 AACTTTGAAA
** * * * *
29906 ATCGCATTGCGATTTTGTATTATCTCGTTGCAATAGTCAGA
1 ATCGCATTGCGATTTTCAAATATCGCGTTGCGATAGTCAGT
* * *** * *
29947 ATCTCGTTGCGAAAGTCAGA-ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTCAAATATCGCGTTGCGATAGTCAGT
* ** *
29987 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCATTGCGATTTTCAAATATCGCGTTGCGATAGTCAGT
*
30028 ATCGCATTGCGATTTTCCAAAT-TCGCATTGCGAT
1 ATCGCATTGCGATTTT-CAAATATCGCGTTGCGAT
30062 TTACTTATTC
Statistics
Matches: 86, Mismatches: 27, Indels: 4
0.74 0.23 0.03
Matches are distributed among these distances:
40 28 0.33
41 56 0.65
42 2 0.02
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (41 bp):
ATCGCATTGCGATTTTCAAATATCGCGTTGCGATAGTCAGT
Found at i:37132 original size:29 final size:29
Alignment explanation
Indices: 37090--37178 Score: 160
Period size: 29 Copynumber: 3.1 Consensus size: 29
37080 CTACAGTGAG
*
37090 CTTGGAGGTCGCCATGGCATCTGAGCGAC
1 CTTGGAGGTCGCCATGGCATCCGAGCGAC
*
37119 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1 CTTGGAGGTCGCCATGGCATCCGAGCGAC
37148 CTTGGAGGTCGCCATGGCATCCGAGCGAC
1 CTTGGAGGTCGCCATGGCATCCGAGCGAC
37177 CT
1 CT
37179 GTGGGGTGTT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 57 1.00
ACGTcount: A:0.16, C:0.30, G:0.35, T:0.19
Consensus pattern (29 bp):
CTTGGAGGTCGCCATGGCATCCGAGCGAC
Found at i:37488 original size:10 final size:10
Alignment explanation
Indices: 37475--37548 Score: 62
Period size: 10 Copynumber: 7.0 Consensus size: 10
37465 CCAACACGCT
37475 GGCCATCCGA
1 GGCCATCCGA
37485 GGCCATCTGACCGA
1 GGCCA--T--CCGA
37499 GGCCATCCGAA
1 GGCCATCCG-A
*
37510 AG-CATCCGA
1 GGCCATCCGA
*
37519 TGCCATCCGA
1 GGCCATCCGA
37529 GAG-CATCCGA
1 G-GCCATCCGA
37539 GGCCATCCGA
1 GGCCATCCGA
37549 ACGAGCTATG
Statistics
Matches: 53, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
9 3 0.06
10 36 0.68
11 3 0.06
12 2 0.04
14 9 0.17
ACGTcount: A:0.24, C:0.36, G:0.27, T:0.12
Consensus pattern (10 bp):
GGCCATCCGA
Found at i:37523 original size:20 final size:20
Alignment explanation
Indices: 37495--37549 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
37485 GGCCATCTGA
37495 CCGAGGCCATCCGAAAGCAT
1 CCGAGGCCATCCGAAAGCAT
* *
37515 CCGATGCCATCCGAGAGCAT
1 CCGAGGCCATCCGAAAGCAT
37535 CCGAGGCCATCCGAA
1 CCGAGGCCATCCGAA
37550 CGAGCTATGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.27, C:0.36, G:0.25, T:0.11
Consensus pattern (20 bp):
CCGAGGCCATCCGAAAGCAT
Found at i:37568 original size:23 final size:23
Alignment explanation
Indices: 37536--37617 Score: 119
Period size: 23 Copynumber: 3.6 Consensus size: 23
37526 CGAGAGCATC
*
37536 CGAGGCCATCCGAACGAGCTATG
1 CGAGGGCATCCGAACGAGCTATG
*
37559 TGAGGGCATCCGAACGAGCTATG
1 CGAGGGCATCCGAACGAGCTATG
* *
37582 CGAGGGCAACCGAGCGAGCTATG
1 CGAGGGCATCCGAACGAGCTATG
*
37605 CGAGGGAATCCGA
1 CGAGGGCATCCGA
37618 GCAACCGAGC
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 52 1.00
ACGTcount: A:0.27, C:0.26, G:0.35, T:0.12
Consensus pattern (23 bp):
CGAGGGCATCCGAACGAGCTATG
Found at i:37688 original size:10 final size:10
Alignment explanation
Indices: 37667--37723 Score: 60
Period size: 10 Copynumber: 5.4 Consensus size: 10
37657 CCTACCCTCG
*
37667 CTCGGTTGCC
1 CTCGGATGCC
*
37677 CTCGGATTCC
1 CTCGGATGCC
*
37687 CTCGCATAGCTC
1 CTCGGAT-GC-C
37699 GCTCGGATGCC
1 -CTCGGATGCC
37710 CTCGGATGCC
1 CTCGGATGCC
37720 CTCG
1 CTCG
37724 CATAGCTCGT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
10 28 0.72
11 2 0.05
12 3 0.08
13 6 0.15
ACGTcount: A:0.09, C:0.40, G:0.26, T:0.25
Consensus pattern (10 bp):
CTCGGATGCC
Found at i:37704 original size:33 final size:33
Alignment explanation
Indices: 37663--37747 Score: 134
Period size: 33 Copynumber: 2.6 Consensus size: 33
37653 GCGACCTACC
* *
37663 CTCGCTCGGTTGCCCTCGGATTCCCTCGCATAG
1 CTCGCTCGGATGCCCTCGGATGCCCTCGCATAG
37696 CTCGCTCGGATGCCCTCGGATGCCCTCGCATAG
1 CTCGCTCGGATGCCCTCGGATGCCCTCGCATAG
* *
37729 CTCGTTCGGATGGCCTCGG
1 CTCGCTCGGATGCCCTCGG
37748 TCGGATGGCC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.09, C:0.38, G:0.28, T:0.25
Consensus pattern (33 bp):
CTCGCTCGGATGCCCTCGGATGCCCTCGCATAG
Found at i:37751 original size:14 final size:14
Alignment explanation
Indices: 37729--37758 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
37719 CCTCGCATAG
*
37729 CTCGTTCGGATGGC
1 CTCGGTCGGATGGC
37743 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
37757 CT
1 CT
37759 TGGATGCCCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.07, C:0.30, G:0.37, T:0.27
Consensus pattern (14 bp):
CTCGGTCGGATGGC
Found at i:38140 original size:14 final size:14
Alignment explanation
Indices: 38123--38149 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
38113 CATCCGAAGC
38123 CATCCGACCGAGGG
1 CATCCGACCGAGGG
38137 CATCCGACCGAGG
1 CATCCGACCGAGG
38150 CTATTCGAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.37, G:0.33, T:0.07
Consensus pattern (14 bp):
CATCCGACCGAGGG
Found at i:38247 original size:29 final size:29
Alignment explanation
Indices: 38205--38282 Score: 147
Period size: 29 Copynumber: 2.7 Consensus size: 29
38195 ACGCGAGGAG
38205 CAGGAGTGCATGGCGACCTACAAGGTCGC
1 CAGGAGTGCATGGCGACCTACAAGGTCGC
38234 CAGGAGTGCATGGCGACCTACAAGGTCGC
1 CAGGAGTGCATGGCGACCTACAAGGTCGC
*
38263 CCGGAGTGCATGGCGACCTA
1 CAGGAGTGCATGGCGACCTA
38283 TGCTGGGAAG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.23, C:0.28, G:0.35, T:0.14
Consensus pattern (29 bp):
CAGGAGTGCATGGCGACCTACAAGGTCGC
Found at i:38525 original size:2 final size:2
Alignment explanation
Indices: 38478--38505 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
38468 AAATTAATGA
38478 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
38506 CTAAATTCAT
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:38527 original size:17 final size:17
Alignment explanation
Indices: 38501--38535 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
38491 TATATATATA
*
38501 TATATCTAAATTCATGT
1 TATATATAAATTCATGT
38518 TATATATAAATTCATGT
1 TATATATAAATTCATGT
38535 T
1 T
38536 TCTAAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.37, C:0.09, G:0.06, T:0.49
Consensus pattern (17 bp):
TATATATAAATTCATGT
Found at i:41696 original size:21 final size:20
Alignment explanation
Indices: 41667--41707 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
41657 AGGTGGCCCG
41667 TTATATTTTAATAATAAAATA
1 TTATATTTTAATAA-AAAATA
*
41688 TTATTTTTTAATAAAAAATA
1 TTATATTTTAATAAAAAATA
41708 AAAAAAACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTATATTTTAATAAAAAATA
Found at i:58172 original size:30 final size:30
Alignment explanation
Indices: 57967--58216 Score: 244
Period size: 30 Copynumber: 8.5 Consensus size: 30
57957 AAATAAAAAT
*
57967 AACAGAAACTTAAAGGACTAAAATAGCTAA
1 AACAGAAAGTTAAAGGACTAAAATAGCTAA
* * *
57997 AATAGAAAGTTAAATGACTAAAA-ATCTAA
1 AACAGAAAGTTAAAGGACTAAAATAGCTAA
* * * *
58026 AATAGAAAGCTAAGGGATTAAAATAG-TAAA
1 AACAGAAAGTTAAAGGACTAAAATAGCT-AA
* * *
58056 AACATAAAGCTAAAGGACCAAAATAGCTAA
1 AACAGAAAGTTAAAGGACTAAAATAGCTAA
*
58086 AACAGAAACTTACAAGG-CTAAAATAG-TAA
1 AACAGAAAGTTA-AAGGACTAAAATAGCTAA
* *
58115 AAGCAAAAACTTAAAGGACTAAAATAGCTAA
1 AA-CAGAAAGTTAAAGGACTAAAATAGCTAA
* *
58146 AACAGAAAGTTCAAGGACCAAAATAGCTAA
1 AACAGAAAGTTAAAGGACTAAAATAGCTAA
* * * *
58176 AATAGGAA-TCAAAGAACT-AAATAGC-AA
1 AACAGAAAGTTAAAGGACTAAAATAGCTAA
58203 AACAGAAAGTTAAA
1 AACAGAAAGTTAAA
Statistics
Matches: 180, Mismatches: 32, Indels: 18
0.78 0.14 0.08
Matches are distributed among these distances:
27 8 0.04
28 11 0.06
29 40 0.22
30 111 0.62
31 10 0.06
ACGTcount: A:0.57, C:0.12, G:0.14, T:0.17
Consensus pattern (30 bp):
AACAGAAAGTTAAAGGACTAAAATAGCTAA
Found at i:58172 original size:90 final size:89
Alignment explanation
Indices: 57967--58177 Score: 232
Period size: 89 Copynumber: 2.4 Consensus size: 89
57957 AAATAAAAAT
* * * * *
57967 AACAGAAACTTAAAGGACTAAAATAGCTAAAATAGAAAGTTAAATGACTAAAAATCTAAAATAGA
1 AACAGAAAGTTAAAGGACCAAAATAGCTAAAACAGAAACTTAAATGACTAAAAATCTAAAACAGA
* * *
58032 AAGCTAAGGGATTAAAATAGTAAA
66 AAACTAAAGGACTAAAATAGTAAA
* * * *
58056 AACATAAAGCTAAAGGACCAAAATAGCTAAAACAGAAACTTACAA-GGCT-AAAATAGTAAAAGC
1 AACAGAAAGTTAAAGGACCAAAATAGCTAAAACAGAAACTTA-AATGACTAAAAAT-CTAAAA-C
58119 A-AAAACTTAAAGGACTAAAATAGCT-AA
63 AGAAAAC-TAAAGGACTAAAATAG-TAAA
*
58146 AACAGAAAGTTCAAGGACCAAAATAGCTAAAA
1 AACAGAAAGTTAAAGGACCAAAATAGCTAAAA
58178 TAGGAATCAA
Statistics
Matches: 102, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
88 5 0.05
89 48 0.47
90 48 0.47
91 1 0.01
ACGTcount: A:0.57, C:0.12, G:0.14, T:0.17
Consensus pattern (89 bp):
AACAGAAAGTTAAAGGACCAAAATAGCTAAAACAGAAACTTAAATGACTAAAAATCTAAAACAGA
AAACTAAAGGACTAAAATAGTAAA
Done.