Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005490.1 Hibiscus syriacus cultivar Beakdansim tig00012634_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: 54751
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3935 original size:32 final size:32
Alignment explanation
Indices: 3883--3960 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 32
3873 GCCAAAACCT
* * *
3883 GATCGGTTGGTTTTCGGGTCAAGTTAAAATCG
1 GATCGATTGGTTTTCAGGTCAAGTTAAAATCA
* * *
3915 GATTGATTGGTTTTCAGGTCAGGTTAATATCA
1 GATCGATTGGTTTTCAGGTCAAGTTAAAATCA
*
3947 TATCGATTGGTTTT
1 GATCGATTGGTTTT
3961 GAGTCGGATT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.22, C:0.10, G:0.27, T:0.41
Consensus pattern (32 bp):
GATCGATTGGTTTTCAGGTCAAGTTAAAATCA
Found at i:6362 original size:35 final size:35
Alignment explanation
Indices: 6316--6390 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
6306 TTCATGTTCA
6316 AAATTCCAAAATACTTCAATTACATTCTAAACCCC
1 AAATTCCAAAATACTTCAATTACATTCTAAACCCC
* * *
6351 AAATTCTAAAATACTTTAATTACATTCTAAACCCT
1 AAATTCCAAAATACTTCAATTACATTCTAAACCCC
6386 AAATT
1 AAATT
6391 AAAGTATTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.44, C:0.23, G:0.00, T:0.33
Consensus pattern (35 bp):
AAATTCCAAAATACTTCAATTACATTCTAAACCCC
Found at i:7385 original size:90 final size:90
Alignment explanation
Indices: 7232--7413 Score: 337
Period size: 90 Copynumber: 2.0 Consensus size: 90
7222 ATAATCCTTC
* *
7232 ATATCAAATATTATTTTGAAATGATTTAGAAGTTATCGGACATAGAAATGATATTTTAACTGAGG
1 ATATCAAATAATATTTTGAAATGATTTAGAAGTTATCAGACATAGAAATGATATTTTAACTGAGG
7297 AAATATTATATTGAATTATTAAACT
66 AAATATTATATTGAATTATTAAACT
*
7322 ATATCGAATAATATTTTGAAATGATTTAGAAGTTATCAGACATAGAAATGATATTTTAACTGAGG
1 ATATCAAATAATATTTTGAAATGATTTAGAAGTTATCAGACATAGAAATGATATTTTAACTGAGG
7387 AAATATTATATTGAATTATTAAACT
66 AAATATTATATTGAATTATTAAACT
7412 AT
1 AT
7414 TACTAAAGGT
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
90 89 1.00
ACGTcount: A:0.43, C:0.05, G:0.13, T:0.38
Consensus pattern (90 bp):
ATATCAAATAATATTTTGAAATGATTTAGAAGTTATCAGACATAGAAATGATATTTTAACTGAGG
AAATATTATATTGAATTATTAAACT
Found at i:11190 original size:9 final size:9
Alignment explanation
Indices: 11134--11266 Score: 85
Period size: 9 Copynumber: 14.6 Consensus size: 9
11124 ATACTATATA
*
11134 ATATAATAT
1 ATATAATTT
*
11143 ATATGAACTAT
1 ATAT-AA-TTT
*
11154 ATATAAATT
1 ATATAATTT
11163 ATATAATTT
1 ATATAATTT
*
11172 ATAT-A-CT
1 ATATAATTT
*
11179 ATATAGTTT
1 ATATAATTT
11188 ATATGAATTAT
1 ATAT-AATT-T
*
11199 ATATAAATT
1 ATATAATTT
*
11208 GTATAATTT
1 ATATAATTT
*
11217 ATAT-A-CT
1 ATATAATTT
*
11224 ATATAGTTT
1 ATATAATTT
11233 ATATGAATTAT
1 ATAT-AATT-T
*
11244 ATATAAATT
1 ATATAATTT
*
11253 GTATAATTT
1 ATATAATTT
11262 ATATA
1 ATATA
11267 TATATAGTTA
Statistics
Matches: 95, Mismatches: 19, Indels: 20
0.71 0.14 0.15
Matches are distributed among these distances:
7 10 0.11
8 2 0.02
9 50 0.53
10 16 0.17
11 17 0.18
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.47
Consensus pattern (9 bp):
ATATAATTT
Found at i:11192 original size:45 final size:45
Alignment explanation
Indices: 11142--11353 Score: 262
Period size: 45 Copynumber: 4.9 Consensus size: 45
11132 TAATATAATA
11142 TATATGAACTATATATAAATTATATAATTTATATACTATATAGTT
1 TATATGAACTATATATAAATTATATAATTTATATACTATATAGTT
* *
11187 TATATGAATTATATATAAATTGTATAATTTATATACTATATAGTT
1 TATATGAACTATATATAAATTATATAATTTATATACTATATAGTT
* *
11232 TATATGAATTATATATAAATTGTATAATTTATATA-TATATAG--
1 TATATGAACTATATATAAATTATATAATTTATATACTATATAGTT
* *
11274 T-TA--AACTATATATAAACTATACATAAATTATATA-T-TATAGTT
1 TATATGAACTATATATAAA-T-TATATAATTTATATACTATATAGTT
* * *
11316 TATATGAAATATATATAAACTATATAA-TTAGATACTAT
1 TATATGAACTATATATAAATTATATAATTTATATACTAT
11354 GTAAATTATA
Statistics
Matches: 148, Mismatches: 10, Indels: 19
0.84 0.06 0.11
Matches are distributed among these distances:
39 12 0.08
40 6 0.04
41 15 0.10
42 8 0.05
43 9 0.06
44 8 0.05
45 90 0.61
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (45 bp):
TATATGAACTATATATAAATTATATAATTTATATACTATATAGTT
Found at i:11244 original size:16 final size:16
Alignment explanation
Indices: 11162--11246 Score: 54
Period size: 16 Copynumber: 5.4 Consensus size: 16
11152 ATATATAAAT
* *
11162 TATATAATTTATATAC
1 TATATAGTTTATATAA
11178 TATATAGTTTATATGAA
1 TATATAGTTTATAT-AA
11195 T-TATA---TATA-AA
1 TATATAGTTTATATAA
* * *
11206 TTGTATAATTTATATAC
1 -TATATAGTTTATATAA
11223 TATATAGTTTATATGAA
1 TATATAGTTTATAT-AA
11240 TTATATA
1 -TATATA
11247 TAAATTGTAT
Statistics
Matches: 54, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
11 2 0.04
12 1 0.02
13 8 0.15
16 33 0.61
17 4 0.07
18 6 0.11
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.49
Consensus pattern (16 bp):
TATATAGTTTATATAA
Found at i:11283 original size:13 final size:11
Alignment explanation
Indices: 11275--11341 Score: 64
Period size: 11 Copynumber: 6.0 Consensus size: 11
11265 TATATATAGT
11275 TAAACTATATA
1 TAAACTATATA
*
11286 TAAACTATACA
1 TAAACTATATA
*
11297 TAAATTATATA
1 TAAACTATATA
* * *
11308 TTATAGTTTATA
1 -TAAACTATATA
11320 TGAAA-TATATA
1 T-AAACTATATA
11331 TAAACTATATA
1 TAAACTATATA
11342 ATTAGATACT
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
10 3 0.07
11 32 0.71
12 10 0.22
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.40
Consensus pattern (11 bp):
TAAACTATATA
Found at i:11444 original size:16 final size:15
Alignment explanation
Indices: 11401--11434 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
11391 TTCAAAGTAT
*
11401 ATACTATACGTATGA
1 ATACTATATGTATGA
11416 ATACTATATGTATGA
1 ATACTATATGTATGA
11431 ATAC
1 ATAC
11435 ATTCATGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (15 bp):
ATACTATATGTATGA
Found at i:12013 original size:91 final size:90
Alignment explanation
Indices: 11821--12015 Score: 232
Period size: 91 Copynumber: 2.1 Consensus size: 90
11811 ATGTGTTCAT
* * * *
11821 CCTTGTTCATCCCCAAAACACTCATTTGATCTTTACAAACAACAAAACTCAAGATCAAACCTATT
1 CCTTGTTCAT-CCCAAAACACTCATTCGATCCTCACAAACAACAAAACCCAAGATCAAACCTATT
*
11886 TTTTCGATCAAACACCCAAAATTCAA
65 TTTTCGATCAAACACCCAAAACTCAA
* * ** *
11912 -CTTGTATTCATCTCAAAACCCTCATTCGATCCTCATTAACACCAAAACCCAAGATCAAACC-AG
1 CCTTG--TTCATCCCAAAACACTCATTCGATCCTCACAAACAACAAAACCCAAGATCAAACCTA-
*
11975 TTTTTTCGTTCAAACACCCAAAACTCAA
63 TTTTTTCGATCAAACACCCAAAACTCAA
12003 CCCTTGTTCATCC
1 -CCTTGTTCATCC
12016 GTGTTCATCC
Statistics
Matches: 87, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
90 5 0.06
91 73 0.84
92 5 0.06
93 4 0.05
ACGTcount: A:0.36, C:0.31, G:0.05, T:0.28
Consensus pattern (90 bp):
CCTTGTTCATCCCAAAACACTCATTCGATCCTCACAAACAACAAAACCCAAGATCAAACCTATTT
TTTCGATCAAACACCCAAAACTCAA
Found at i:12346 original size:48 final size:45
Alignment explanation
Indices: 12291--12455 Score: 174
Period size: 48 Copynumber: 3.5 Consensus size: 45
12281 AGTATTGTTC
12291 ATCTTCTCTAACCCTAAATCTAA-TCAAGA-TCTTCCTCTTCTTCTATTT
1 ATCTTCTCTAACCCTAAATCTAACT-AAGACTCTT--T-TTCTTCT-TTT
* *
12339 ATCTTCTCTAACACTAAATCTAACTGAGACTCTTATTATTCTTCTTTT
1 ATCTTCTCTAACCCTAAATCTAACTAAGACTC-T-TT-TTCTTCTTTT
* * * *
12387 ATTTTCTTTAACCCTAAAT-TAACTAAGACTCTTTATCTTTTGTTT
1 ATCTTCTCTAACCCTAAATCTAACTAAGACTCTTTTTCTTCT-TTT
12432 ATCTTCTCTAACCCTAAATCTAAC
1 ATCTTCTCTAACCCTAAATCTAAC
12456 CGATATTATT
Statistics
Matches: 100, Mismatches: 11, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
44 5 0.05
45 22 0.22
46 5 0.05
47 11 0.11
48 44 0.44
49 11 0.11
50 1 0.01
51 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.03, T:0.45
Consensus pattern (45 bp):
ATCTTCTCTAACCCTAAATCTAACTAAGACTCTTTTTCTTCTTTT
Found at i:21461 original size:27 final size:25
Alignment explanation
Indices: 21431--21513 Score: 91
Period size: 25 Copynumber: 3.3 Consensus size: 25
21421 TGAAAATAAA
21431 AATAAAATATTTTTAAATTAAGTTAAT
1 AATAAAATATTTTT-AA-TAAGTTAAT
* *
21458 AATAGAATATATTTAATAAGTTAAT
1 AATAAAATATTTTTAATAAGTTAAT
21483 -ATAAAAATATTTTT--TAAGTTAAT
1 AAT-AAAATATTTTTAATAAGTTAAT
*
21506 AAAAAAAT
1 AATAAAAT
21514 TTATATACTA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
23 14 0.29
24 3 0.06
25 18 0.37
26 2 0.04
27 12 0.24
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (25 bp):
AATAAAATATTTTTAATAAGTTAAT
Found at i:21500 original size:23 final size:23
Alignment explanation
Indices: 21447--21517 Score: 83
Period size: 23 Copynumber: 3.1 Consensus size: 23
21437 ATATTTTTAA
*
21447 ATTAAGTTAATAATAGAATATATTT
1 ATTAAGTTAAT-ATA-AAAATATTT
*
21472 AATAAGTTAATATAAAAATATTT
1 ATTAAGTTAATATAAAAATATTT
*
21495 TTTAAGTTAATA-AAAAA-ATTT
1 ATTAAGTTAATATAAAAATATTT
21516 AT
1 AT
21518 ATACTAAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
21 5 0.12
22 5 0.12
23 18 0.44
24 3 0.07
25 10 0.24
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (23 bp):
ATTAAGTTAATATAAAAATATTT
Found at i:22524 original size:38 final size:40
Alignment explanation
Indices: 22472--22547 Score: 95
Period size: 38 Copynumber: 1.9 Consensus size: 40
22462 CATTGTTTAC
*
22472 TATATAGATGAAAAA-AT-A-TTATTTAATATATATATATA
1 TATATAGATAAAAAATATGATTTATTTAATATA-ATATATA
* *
22510 TATATATATAAAAAATATGATTTTTTTAATATAATATA
1 TATATAGATAAAAAATATGATTTATTTAATATAATATA
22548 CTGTGTATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
38 13 0.41
39 2 0.06
40 6 0.19
41 11 0.34
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (40 bp):
TATATAGATAAAAAATATGATTTATTTAATATAATATATA
Found at i:29463 original size:16 final size:16
Alignment explanation
Indices: 29442--29475 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
29432 ACACTACGGG
29442 TGCACAATTGTTTCAT
1 TGCACAATTGTTTCAT
29458 TGCACAATTGTTTCAT
1 TGCACAATTGTTTCAT
29474 TG
1 TG
29476 AATTTCTGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.24, C:0.18, G:0.15, T:0.44
Consensus pattern (16 bp):
TGCACAATTGTTTCAT
Found at i:38027 original size:35 final size:33
Alignment explanation
Indices: 37988--38072 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 33
37978 GTATCTCAGT
37988 TAATTTTGTT-TATTACCATTTAATATCAGTTATTG
1 TAATTTTGTTATATTACCATTTAATA-C--TTATTG
*
38023 TAATTTGGTTATCATTTACCATTTAATACTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATACTTATTG
* *
38058 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
38073 TAAAATTATT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.56
36 1 0.02
37 2 0.05
38 13 0.30
ACGTcount: A:0.27, C:0.08, G:0.11, T:0.54
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATACTTATTG
Found at i:41688 original size:42 final size:42
Alignment explanation
Indices: 41642--41736 Score: 154
Period size: 42 Copynumber: 2.3 Consensus size: 42
41632 CGGTACCTGC
* *
41642 CCCGCGCTATATATAATTATAAAGGTCAGACGCGGCCCTTAA
1 CCCGCGCTATATATAATTATAAAGGTCAGACGCGACCCCTAA
**
41684 CCCGCGCTATATATAATTATAAAGGTCAGGTGCGACCCCTAA
1 CCCGCGCTATATATAATTATAAAGGTCAGACGCGACCCCTAA
41726 CCCGCGCTATA
1 CCCGCGCTATA
41737 CCCTACGTGG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.23
Consensus pattern (42 bp):
CCCGCGCTATATATAATTATAAAGGTCAGACGCGACCCCTAA
Found at i:43594 original size:21 final size:21
Alignment explanation
Indices: 43544--43594 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
43534 AACCGCTTCG
* *
43544 TGAGCCTGGTGCGGATGGTGT
1 TGAGCCTGGTGCAGATGGTGC
*
43565 TAAGCCTGGTGCAGATGGTGC
1 TGAGCCTGGTGCAGATGGTGC
*
43586 TGAGACTGG
1 TGAGCCTGG
43595 ACTATTCATT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.16, C:0.16, G:0.43, T:0.25
Consensus pattern (21 bp):
TGAGCCTGGTGCAGATGGTGC
Found at i:47641 original size:4 final size:4
Alignment explanation
Indices: 47632--47664 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
47622 AATCATGCAT
47632 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA T
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA T
47665 TATTACTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
TAAA
Found at i:47806 original size:12 final size:12
Alignment explanation
Indices: 47789--47846 Score: 50
Period size: 12 Copynumber: 5.1 Consensus size: 12
47779 AAAACAATTA
47789 ATTAAATAAAAT
1 ATTAAATAAAAT
47801 ATT-AA-AAAAT
1 ATTAAATAAAAT
*
47811 -TTAAATAAATT
1 ATTAAATAAAAT
* *
47822 ACTAAAAAAAAT
1 ATTAAATAAAAT
* *
47834 ACTAAATATAAT
1 ATTAAATAAAAT
47846 A
1 A
47847 AAATATATCT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 7 0.19
11 6 0.16
12 22 0.59
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (12 bp):
ATTAAATAAAAT
Found at i:47815 original size:21 final size:21
Alignment explanation
Indices: 47790--47830 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
47780 AAACAATTAA
*
47790 TTAAATAAAATATTAAAAAAT
1 TTAAATAAAATACTAAAAAAT
*
47811 TTAAATAAATTACTAAAAAA
1 TTAAATAAAATACTAAAAAA
47831 AATACTAAAT
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:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (21 bp):
TTAAATAAAATACTAAAAAAT
Found at i:48587 original size:33 final size:33
Alignment explanation
Indices: 48540--48614 Score: 143
Period size: 33 Copynumber: 2.3 Consensus size: 33
48530 AAAATCATGA
48540 TTGAA-AGAGTAACCATCTCAACAAAGAGGAAG
1 TTGAAGAGAGTAACCATCTCAACAAAGAGGAAG
48572 TTGAAGAGAGTAACCATCTCAACAAAGAGGAAG
1 TTGAAGAGAGTAACCATCTCAACAAAGAGGAAG
48605 TTGAAGAGAG
1 TTGAAGAGAG
48615 AGCATGCGAT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
32 5 0.12
33 37 0.88
ACGTcount: A:0.45, C:0.13, G:0.25, T:0.16
Consensus pattern (33 bp):
TTGAAGAGAGTAACCATCTCAACAAAGAGGAAG
Found at i:53158 original size:126 final size:127
Alignment explanation
Indices: 52525--53270 Score: 1215
Period size: 127 Copynumber: 5.9 Consensus size: 127
52515 TAATCGGAGT
* *
52525 ACTATTCACATGAAGGCGCGTTCCCGGGGTGCGCATTCCATTATTTCGTCAGAGAATATGTTATC
1 ACTATTCACATGAAGGCGCGTTCCCGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATC
52590 ATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAG--ATATCAGTACCTATTATTTC
66 ATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
52650 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGTCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCC-GGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
52715 CATTGCCCTATTATGTCACTCATGTCCCTC-GGGACACTAGATATATCAGTACCTATTATTTC
65 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
52777 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCC-GGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
52842 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
65 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *
52905 ACTATTCACATGAAGGTGCGTTCCCGGGGCGCGCCTTCCATTATTTCGTTAGAGAATATGTTATC
1 ACTATTCACATGAAGGCGCGTTCCCGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATC
52970 ATTGCCC---TATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 ATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *** *
53029 TC-AGGGGACATGAAGGCGCGTTCCTGGGGGCGCGCCTTCCATTATTTC-TCAGAGAATATGTTA
1 ACTA-TTCACATGAAGGCGCGTTCC-CGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTA
53092 TCATTGCCCTATTATGTCACTCATGT-CCTCGGGGACACTAGATATATCAGTACCTATTATTTC
64 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* **** * *
53155 TC-AGGGGGCATGAAGGCGCGTTCCCAGGGCGCGCCTTCCGTTATTTCGTCAGAGAATATGTTAT
1 ACTA-TTCACATGAAGGCGCGTTCCCGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
53219 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
65 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
53271 ATCAGGTAAA
Statistics
Matches: 591, Mismatches: 19, Indels: 20
0.94 0.03 0.03
Matches are distributed among these distances:
123 1 0.00
124 92 0.16
125 77 0.13
126 167 0.28
127 198 0.34
128 56 0.09
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.32
Consensus pattern (127 bp):
ACTATTCACATGAAGGCGCGTTCCCGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATC
ATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
Found at i:54295 original size:21 final size:20
Alignment explanation
Indices: 54268--54337 Score: 95
Period size: 21 Copynumber: 3.4 Consensus size: 20
54258 GGTATAAAAC
*
54268 CCTGCGGGCTAGGCATGTAA
1 CCTGCGGGCTAGGAATGTAA
54288 CCTGGCGGGCTAGGAATGTAA
1 CCT-GCGGGCTAGGAATGTAA
*
54309 CCCTGCGGGCTCGGAATGTAA
1 -CCTGCGGGCTAGGAATGTAA
54330 CCCTGCGG
1 -CCTGCGG
54338 AGATGGCATA
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
20 3 0.07
21 40 0.87
22 3 0.07
ACGTcount: A:0.19, C:0.27, G:0.36, T:0.19
Consensus pattern (20 bp):
CCTGCGGGCTAGGAATGTAA
Found at i:54367 original size:21 final size:21
Alignment explanation
Indices: 54341--54388 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
54331 CCTGCGGAGA
*
54341 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
54362 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
54383 GGGCAT
1 TGGCAT
54389 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Done.