Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000513.1 Hibiscus syriacus cultivar Beakdansim tig00000977_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: 76154
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:280 original size:49 final size:49
Alignment explanation
Indices: 200--376 Score: 169
Period size: 49 Copynumber: 3.5 Consensus size: 49
190 TTCATGCTAC
* *
200 AAAAAAGTGTAGCACTAAACACATACGTACACC-GTGTAAGTGATAAAA
1 AAAAAAGTGTAGCACTTAACACATACTTACACCGGTGTAAGTGATAAAA
* * * *
248 TATAAAAGTGTAGTACTTAACACATATTTACACCTGTGTAAGTGAAATAAATAAA
1 -AAAAAAGTGTAGCACTTAACACATACTTACACCGGTGTAAGTG--AT--A-AAA
* *
303 AAAAAAGTGTAGCATTTAACACATACTTACACCGGTGTGAGTGA-ATAAA
1 AAAAAAGTGTAGCACTTAACACATACTTACACCGGTGTAAGTGATA-AAA
* * * *
352 CAAAAAGTATGGTACTTAACACATA
1 AAAAAAGTGTAGCACTTAACACATA
377 TTTATATCGG
Statistics
Matches: 106, Mismatches: 16, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
49 53 0.50
50 9 0.08
52 3 0.03
54 38 0.36
55 3 0.03
ACGTcount: A:0.46, C:0.14, G:0.15, T:0.25
Consensus pattern (49 bp):
AAAAAAGTGTAGCACTTAACACATACTTACACCGGTGTAAGTGATAAAA
Found at i:322 original size:54 final size:54
Alignment explanation
Indices: 202--357 Score: 180
Period size: 54 Copynumber: 3.0 Consensus size: 54
192 CATGCTACAA
* * *
202 AAAAGTGTAGCACTAAACACATACGTACACC-GTGTAAGTG-AT--A-AAATAT
1 AAAAGTGTAGCACTTAACACATACTTACACCGGTGTAAGTGAATAAATAAAAAT
* * *
251 AAAAGTGTAGTACTTAACACATATTTACACCTGTGTAAGTGAAATAAATAAAAA-
1 AAAAGTGTAGCACTTAACACATACTTACACCGGTGTAAGTG-AATAAATAAAAAT
* * *
305 AAAAGTGTAGCATTTAACACATACTTACACCGGTGTGAGTGAATAAACAAAAA
1 AAAAGTGTAGCACTTAACACATACTTACACCGGTGTAAGTGAATAAATAAAAA
358 GTATGGTACT
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
49 27 0.30
50 9 0.10
52 2 0.02
53 11 0.12
54 37 0.41
55 4 0.04
ACGTcount: A:0.46, C:0.14, G:0.15, T:0.24
Consensus pattern (54 bp):
AAAAGTGTAGCACTTAACACATACTTACACCGGTGTAAGTGAATAAATAAAAAT
Found at i:392 original size:103 final size:103
Alignment explanation
Indices: 200--393 Score: 257
Period size: 103 Copynumber: 1.9 Consensus size: 103
190 TTCATGCTAC
* *
200 AAAAAAGTGTAGCACTAAACACATACGTACACCGTGTAAGTGATAAAATATAAAAGTGTAGTACT
1 AAAAAAGTGTAGCACTAAACACATACGTACACCGTGTAAGTGATAAAACATAAAAGTATAGTACT
* *
265 TAACACATATTTACACCTGTGTAAGTGAAATAAATAAA
66 TAACACATATTTACACCGGCGTAAGTGAAATAAATAAA
* * * * *
303 AAAAAAGTGTAGCATTTAACACATACTTACACCGGTGTGAGTGA-ATAAACA-AAAAGTATGGTA
1 AAAAAAGTGTAGCACTAAACACATACGTACACC-GTGTAAGTGATA-AAACATAAAAGTATAGTA
* *
366 CTTAACACATATTTATATCGGCGTAAGT
64 CTTAACACATATTTACACCGGCGTAAGT
394 ATGTACATCT
Statistics
Matches: 78, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
103 65 0.83
104 13 0.17
ACGTcount: A:0.44, C:0.14, G:0.16, T:0.26
Consensus pattern (103 bp):
AAAAAAGTGTAGCACTAAACACATACGTACACCGTGTAAGTGATAAAACATAAAAGTATAGTACT
TAACACATATTTACACCGGCGTAAGTGAAATAAATAAA
Found at i:2987 original size:827 final size:826
Alignment explanation
Indices: 1386--3023 Score: 3124
Period size: 827 Copynumber: 2.0 Consensus size: 826
1376 CGGGTATCTT
*
1386 CACATCTAAAACTCAGAAAACATCATACTTCTTTCTAGAAATAGATGGGGAGATAAAGGTAACAA
1 CACATATAAAACTCAGAAAACATCATACTTCTTTCTAGAAATAGATGGGGAGATAAAGGTAACAA
1451 TCGGAAGTATATAAGCATCAGTAAAGAGAAAAATATATAGAATTTGCCAGAAAACAAAACAAAGG
66 TCGGAAGTATATAAGCATCAGTAAAGAGAAAAATATATAGAATTTGCCAGAAAACAAAACAAAGG
*
1516 TTTCTATGCAATTTTTGAAAAAAAAGTGTAATAGCAGAAGTAATGGGTTTTCCAAGAAGAACCCT
131 TTTCTATGCAATTTCTGAAAAAAAAGTGTAATAGCAGAAGTAATGGGTTTTCCAAGAAGAACCCT
*
1581 GATGTGATCCAATTCAGCATCATGGATATTCCACCCTTACAAGGGAAGAGACTTTCTAACTTTAC
196 AATGTGATCCAATTCAGCATCATGGATATTCCACCCTTACAAGGGAAGAGACTTTCTAACTTTAC
1646 ACATATATGATTATTTTATAGTTATTTTCATCTACATATATTATATCTATAGTTATTATGATGAT
261 ACATATATGATTATTTTATAGTTATTTTCATCTACATATATTATATCTATAGTTATTATGATGA-
1711 AACCTATCCATTAATATGTGAAATATAAGTTATCATAATATACTATAGTTCACATTCTATATAAT
325 AACCTATCCATTAATATGTGAAATATAAGTTATCATAATATACTATAGTTCACATTCTATATAAT
1776 ACATTATAAGTTCATTTACTTAGTTTATTTCTTTATGTTATGCATGTAGGCACATTCGGCCAGTA
390 ACATTATAAGTTCATTTACTTAGTTTATTTCTTTATGTTATGCATGTAGGCACATTCGGCCAGTA
1841 CTTGGGAGCTACATTGGAGCTAAATGGAGCATGCAAAAGCAAGGATACTTACATGGGAACGATTA
455 CTTGGGAGCTACATTGGAGCTAAATGGAGCATGCAAAAGCAAGGATACTTACATGGGAACGATTA
1906 GGAGAGCATAAGGAGCAAATTCGTGAAAAGTTGTTTTGAGGCCGTAAGCTCATAGCTGGATTGAG
520 GGAGAGCATAAGGAGCAAATTCGTGAAAAGTTGTTTTGAGGCCGTAAGCTCATAGCTGGATTGAG
*
1971 CTGAAGATTTGAGCTACAAGATGACCTCATTTCAGCTAGGGAGTTGTACCATTATCATCACCACT
585 CTGAAGATTTGAGCTACAAGATGACCTCATTTCAGCTAGGGAGTTGTACCATCATCATCACCACT
*
2036 TAGGACACTTCAAATATGTCCTAAGTTAAAATTTGTGAAATCGTACCTTTTCGCGAATAGTTGCC
650 TAGGACACTTCAAATATGTCCTAAGTCAAAATTTGTGAAATCGTACCTTTTCGCGAATAGTTGCC
2101 AACTCAAGAGGTACCTTTTCACAAGGAGCTGCCATAATGTTCACCATGCTACAAGTCACCTATGG
715 AACTCAAGAGGTACCTTTTCACAAGGAGCTGCCATAATGTTCACCATGCTACAAGTCACCTATGG
2166 TCAGCTCACCTTTAGCTCATTCACACCATAAATATATAGAATTTGCC
780 TCAGCTCACCTTTAGCTCATTCACACCATAAATATATAGAATTTGCC
2213 CACATATAAAACTCAAGAAAACATCATACTTCTTTCTAGAAATAGATGGGGAGATAAAGGTAACA
1 CACATATAAAACTC-AGAAAACATCATACTTCTTTCTAGAAATAGATGGGGAGATAAAGGTAACA
2278 ATCGGAAGTATATAAGCATCAGTAAAGAGAAAAATATATAGAATTTGCCAGAAAACAAAACAAAG
65 ATCGGAAGTATATAAGCATCAGTAAAGAGAAAAATATATAGAATTTGCCAGAAAACAAAACAAAG
2343 GTTTCTATGCAATTTCTG-AAAAAAAGTGTAATAGCAGAAGTAATGGGTTTTCCAAGAAGAACCC
130 GTTTCTATGCAATTTCTGAAAAAAAAGTGTAATAGCAGAAGTAATGGGTTTTCCAAGAAGAACCC
2407 TAATGTGATCCAA-TCAGCATCATGGA-ATTCCACCCTTACAAGGGAAGAGACTTTCTAACTTTA
195 TAATGTGATCCAATTCAGCATCATGGATATTCCACCCTTACAAGGGAAGAGACTTTCTAACTTTA
2470 CACATATATATGATTATTTTATAGTTATTTTCATCTACATATATTATATCTATAGTTATTATGAT
260 CAC--ATATATGATTATTTTATAGTTATTTTCATCTACATATATTATATCTATAGTTATTATGAT
2535 G-AACCTATCCATTAATATGTGAAATATAAGTTATCATAATATACTATAGTTCACATTCTTATAT
323 GAAACCTATCCATTAATATGTGAAATATAAGTTATCATAATATACTATAGTTCACATTC-TATAT
2599 AATACATTATATAAGTTCATTTACTTAGTTTATTTCTTTATGTTATGCATGTAGGCACATTCGGC
387 AATACA-T-TATAAGTTCATTTACTTAGTTTATTTCTTTATGTTATGCATGTAGGCACATTCGGC
2664 CAGTACTTGGGAGCTACATTGGAGCTAAATGGAGCATGCAAAAGCAAGGATACTTACATGGGAAC
450 CAGTACTTGGGAGCTACATTGGAGCTAAATGGAGCATGCAAAAGCAAGGATACTTACATGGGAAC
*
2729 GATTAGGAGAGCATAAGGAG-TAATTCGTGAAAAGTTGTTTTGAGGCCGTAAGCTCATAGCTGGA
515 GATTAGGAGAGCATAAGGAGCAAATTCGTGAAAAGTTGTTTTGAGGCCGTAAGCTCATAGCTGGA
2793 TTGAGCTGAAGATTTGAGCTACAAGATGACCTCATTTCAGCTAGGGAGTTGTACCATCATCATCA
580 TTGAGCTGAAGATTTGAGCTACAAGATGACCTCATTTCAGCTAGGGAGTTGTACCATCATCATCA
2858 CCACTTAGGACACTTCAAATATGTCCTAAGTCAAAATTTGTGAAATCGTACCTTTTCGCGAATAG
645 CCACTTAGGACACTTCAAATATGTCCTAAGTCAAAATTTGTGAAATCGTACCTTTTCGCGAATAG
2923 TTGCCAACTCAAGAGGTACCTTTTCACAAGGAGCTGCCATAATGTTCACCATGCTACAAGTCACC
710 TTGCCAACTCAAGAGGTACCTTTTCACAAGGAGCTGCCATAATGTTCACCATGCTACAAGTCACC
2988 TATGGTCAGCTCACCTTTAGCTCATTCACACCATAA
775 TATGGTCAGCTCACCTTTAGCTCATTCACACCATAA
3024 GTAGCTCAAA
Statistics
Matches: 799, Mismatches: 6, Indels: 12
0.98 0.01 0.01
Matches are distributed among these distances:
825 97 0.12
826 24 0.03
827 405 0.51
828 273 0.34
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (826 bp):
CACATATAAAACTCAGAAAACATCATACTTCTTTCTAGAAATAGATGGGGAGATAAAGGTAACAA
TCGGAAGTATATAAGCATCAGTAAAGAGAAAAATATATAGAATTTGCCAGAAAACAAAACAAAGG
TTTCTATGCAATTTCTGAAAAAAAAGTGTAATAGCAGAAGTAATGGGTTTTCCAAGAAGAACCCT
AATGTGATCCAATTCAGCATCATGGATATTCCACCCTTACAAGGGAAGAGACTTTCTAACTTTAC
ACATATATGATTATTTTATAGTTATTTTCATCTACATATATTATATCTATAGTTATTATGATGAA
ACCTATCCATTAATATGTGAAATATAAGTTATCATAATATACTATAGTTCACATTCTATATAATA
CATTATAAGTTCATTTACTTAGTTTATTTCTTTATGTTATGCATGTAGGCACATTCGGCCAGTAC
TTGGGAGCTACATTGGAGCTAAATGGAGCATGCAAAAGCAAGGATACTTACATGGGAACGATTAG
GAGAGCATAAGGAGCAAATTCGTGAAAAGTTGTTTTGAGGCCGTAAGCTCATAGCTGGATTGAGC
TGAAGATTTGAGCTACAAGATGACCTCATTTCAGCTAGGGAGTTGTACCATCATCATCACCACTT
AGGACACTTCAAATATGTCCTAAGTCAAAATTTGTGAAATCGTACCTTTTCGCGAATAGTTGCCA
ACTCAAGAGGTACCTTTTCACAAGGAGCTGCCATAATGTTCACCATGCTACAAGTCACCTATGGT
CAGCTCACCTTTAGCTCATTCACACCATAAATATATAGAATTTGCC
Found at i:6915 original size:2 final size:2
Alignment explanation
Indices: 6872--6898 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6862 ATCCTAACTA
6872 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
6899 CCTTTGAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13592 original size:16 final size:16
Alignment explanation
Indices: 13571--13615 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
13561 TGGAAAATCA
*
13571 TGTATTTGCCCCTCCT
1 TGTATTTTCCCCTCCT
13587 TGTATTTTCCCCTCCT
1 TGTATTTTCCCCTCCT
13603 TGTATTTTCCCCT
1 TGTATTTTCCCCT
13616 TTTACCCTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.07, C:0.36, G:0.09, T:0.49
Consensus pattern (16 bp):
TGTATTTTCCCCTCCT
Found at i:16325 original size:2 final size:2
Alignment explanation
Indices: 16318--16350 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
16308 ATCACAAAAT
16318 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16351 TGCAATAATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19609 original size:20 final size:20
Alignment explanation
Indices: 19562--19610 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
19552 TATTTGTAGG
*
19562 TATCGATACTACATGAACAT
1 TATCGATACTACATGAACAA
* * *
19582 TATGGATATTGCATGAACAA
1 TATCGATACTACATGAACAA
19602 TATCGATAC
1 TATCGATAC
19611 CATAAGGCAA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (20 bp):
TATCGATACTACATGAACAA
Found at i:19684 original size:35 final size:35
Alignment explanation
Indices: 19641--19710 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
19631 ATTCTTCATG
*
19641 GGGTATCGATACCGAA-GTGGTAGCATCGGTACCAT
1 GGGTATCGATACC-AAGGTGGAAGCATCGGTACCAT
*
19676 GGGTATCGATACCAAGGTGGAAGTATCGGTACCAT
1 GGGTATCGATACCAAGGTGGAAGCATCGGTACCAT
19711 TCTTACAATG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
34 2 0.06
35 30 0.94
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.23
Consensus pattern (35 bp):
GGGTATCGATACCAAGGTGGAAGCATCGGTACCAT
Found at i:20838 original size:23 final size:23
Alignment explanation
Indices: 20811--20866 Score: 78
Period size: 23 Copynumber: 2.4 Consensus size: 23
20801 CAGGTAAGAG
*
20811 ATGAAAGTATGTGAT-TGTATGAT
1 ATGAAAGTATGT-ATATATATGAT
*
20834 ATGAAAGTATGTATATATATGTT
1 ATGAAAGTATGTATATATATGAT
20857 ATGAAAGTAT
1 ATGAAAGTAT
20867 ATCACTGCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 2 0.07
23 28 0.93
ACGTcount: A:0.39, C:0.00, G:0.21, T:0.39
Consensus pattern (23 bp):
ATGAAAGTATGTATATATATGAT
Found at i:24244 original size:3 final size:3
Alignment explanation
Indices: 24236--24294 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
24226 ATGTTAGCAA
24236 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
24284 AAT AAT AAT AA
1 AAT AAT AAT AA
24295 ATGTTAAATA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:24327 original size:23 final size:22
Alignment explanation
Indices: 24301--24415 Score: 89
Period size: 23 Copynumber: 5.2 Consensus size: 22
24291 ATAAATGTTA
24301 AATAAATCAAAGAAGAAAAAAAT
1 AATAAATCAAAGAA-AAAAAAAT
*
24324 AATAAATCAAAG-CAAAAAAAT
1 AATAAATCAAAGAAAAAAAAAT
* *
24345 -ATAAAT-AAATAAATAAAAAT
1 AATAAATCAAAGAAAAAAAAAT
*
24365 AA-AAAGTCAAAGGAAAAATAAAT
1 AATAAA-TCAAA-GAAAAAAAAAT
*
24388 AA-AAATTAAAAAGAACAAAAAAA-
1 AATAAA-T-CAAAGAA-AAAAAAAT
24411 AATAA
1 AATAA
24416 GAAAAGTTAG
Statistics
Matches: 74, Mismatches: 10, Indels: 15
0.75 0.10 0.15
Matches are distributed among these distances:
19 3 0.04
20 16 0.22
21 10 0.14
22 3 0.04
23 31 0.42
24 11 0.15
ACGTcount: A:0.75, C:0.04, G:0.06, T:0.15
Consensus pattern (22 bp):
AATAAATCAAAGAAAAAAAAAT
Found at i:24348 original size:20 final size:20
Alignment explanation
Indices: 24302--24382 Score: 74
Period size: 20 Copynumber: 3.9 Consensus size: 20
24292 TAAATGTTAA
24302 ATAAATCAAAGAAGAAAAAAAT
1 ATAAATCAAAG--GAAAAAAAT
*
24324 AATAAATCAAAGCAAAAAAAT
1 -ATAAATCAAAGGAAAAAAAT
**
24345 ATAAAT-AAATAAATAAAAAT
1 ATAAATCAAAGGAA-AAAAAT
*
24365 AAAAAGTCAAAGGAAAAA
1 ATAAA-TCAAAGGAAAAA
24383 TAAATAAAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
19 5 0.10
20 16 0.33
21 12 0.24
22 5 0.10
23 11 0.22
ACGTcount: A:0.73, C:0.05, G:0.07, T:0.15
Consensus pattern (20 bp):
ATAAATCAAAGGAAAAAAAT
Found at i:24358 original size:14 final size:14
Alignment explanation
Indices: 24318--24393 Score: 50
Period size: 14 Copynumber: 5.4 Consensus size: 14
24308 CAAAGAAGAA
24318 AAAAAT-AATAAAT
1 AAAAATAAATAAAT
* ** *
24331 CAAAGCAAAAAAAT
1 AAAAATAAATAAAT
*
24345 ATAAATAAATAAAT
1 AAAAATAAATAAAT
*
24359 AAAAATAAA-AAGT
1 AAAAATAAATAAAT
24372 CAAAGGAA-AAATAAAT
1 -AAA--AATAAATAAAT
24388 AAAAAT
1 AAAAAT
24394 TAAAAAGAAC
Statistics
Matches: 45, Mismatches: 12, Indels: 11
0.66 0.18 0.16
Matches are distributed among these distances:
13 8 0.18
14 26 0.58
15 6 0.13
16 5 0.11
ACGTcount: A:0.74, C:0.04, G:0.05, T:0.17
Consensus pattern (14 bp):
AAAAATAAATAAAT
Found at i:24410 original size:29 final size:28
Alignment explanation
Indices: 24351--24415 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 28
24341 AAATATAAAT
*
24351 AAATAAATAAAAATAAAAAGTCAAAGGAA
1 AAATAAATAAAAATAAAAAGACAAA-GAA
*
24380 AAATAAATAAAAATTAAAAAGAACAAAAAA
1 AAATAAATAAAAA-TAAAAAG-ACAAAGAA
24410 AAATAA
1 AAATAA
24416 GAAAAGTTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
29 13 0.41
30 15 0.47
31 4 0.12
ACGTcount: A:0.77, C:0.03, G:0.06, T:0.14
Consensus pattern (28 bp):
AAATAAATAAAAATAAAAAGACAAAGAA
Found at i:24412 original size:30 final size:30
Alignment explanation
Indices: 24351--24450 Score: 89
Period size: 29 Copynumber: 3.4 Consensus size: 30
24341 AAATATAAAT
* *
24351 AAATAAATAAAAA-TAAAAAG-TCAAAGGAA
1 AAATAAATAAAAATTAAAAAGAACAAA-AAA
24380 AAATAAATAAAAATTAAAAAGAACAAAAAA
1 AAATAAATAAAAATTAAAAAGAACAAAAAA
* * *** *
24410 AAAT-AAGAAAAGTTAGTTAGAAGAAAAATA
1 AAATAAATAAAAATTAAAAAGAACAAAAA-A
24440 AAATAAATAAA
1 AAATAAATAAA
24451 CAAAAAATTA
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
29 31 0.53
30 18 0.31
31 9 0.16
ACGTcount: A:0.73, C:0.02, G:0.09, T:0.16
Consensus pattern (30 bp):
AAATAAATAAAAATTAAAAAGAACAAAAAA
Found at i:24498 original size:16 final size:16
Alignment explanation
Indices: 24477--24512 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
24467 TAGCAATAAT
24477 AAAATAAATGAAAACA
1 AAAATAAATGAAAACA
*
24493 AAAATAAATGAAAATA
1 AAAATAAATGAAAACA
24509 AAAA
1 AAAA
24513 AATTGTGTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.78, C:0.03, G:0.06, T:0.14
Consensus pattern (16 bp):
AAAATAAATGAAAACA
Found at i:24551 original size:5 final size:5
Alignment explanation
Indices: 24541--24579 Score: 53
Period size: 5 Copynumber: 7.6 Consensus size: 5
24531 AGATAATAAG
24541 AAATA AAATAA AAATA ATAA-A AAATA AAATA AAATA AAA
1 AAATA AAAT-A AAATA A-AATA AAATA AAATA AAATA AAA
24580 AAGGATCAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
4 2 0.06
5 22 0.71
6 7 0.23
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:24559 original size:21 final size:21
Alignment explanation
Indices: 24533--24581 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
24523 AAATAGCCAG
*
24533 ATAATAAGAAATAAAATAAAA
1 ATAATAAAAAATAAAATAAAA
24554 ATAATAAAAAATAAAAT-AAA
1 ATAATAAAAAATAAAATAAAA
24574 ATAA-AAAA
1 ATAATAAAA
24582 GGATCAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 4 0.15
20 7 0.26
21 16 0.59
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (21 bp):
ATAATAAAAAATAAAATAAAA
Found at i:25102 original size:22 final size:24
Alignment explanation
Indices: 25072--25120 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 24
25062 TGGGTTTTGT
*
25072 TTGTTGTTTCGTG-GGT-TTGTTG
1 TTGTGGTTTCGTGAGGTATTGTTG
*
25094 TTGTGGTTTTGTGATGGTATTGTTG
1 TTGTGGTTTCGTGA-GGTATTGTTG
25119 TT
1 TT
25121 CGATCTGTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 11 0.50
24 3 0.14
25 8 0.36
ACGTcount: A:0.04, C:0.02, G:0.35, T:0.59
Consensus pattern (24 bp):
TTGTGGTTTCGTGAGGTATTGTTG
Found at i:26683 original size:20 final size:20
Alignment explanation
Indices: 26658--26708 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
26648 TGGAGCGTGG
26658 GGGGAATCGGTACCCCCTAT
1 GGGGAATCGGTACCCCCTAT
26678 GGGGAATCGGTACCCCCTAT
1 GGGGAATCGGTACCCCCTAT
*
26698 GGAGAATCGGT
1 GGGGAATCGGT
26709 TCCCTAAGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.22, C:0.25, G:0.33, T:0.20
Consensus pattern (20 bp):
GGGGAATCGGTACCCCCTAT
Found at i:41064 original size:20 final size:20
Alignment explanation
Indices: 41037--41090 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
41027 ATACTGACAT
41037 GGAA-GTATCGATACCAAGA
1 GGAAGGTATCGATACCAAGA
*
41056 GGGAGGTATCGATACCAAGA
1 GGAAGGTATCGATACCAAGA
41076 GGAAGGTATCGATAC
1 GGAAGGTATCGATAC
41091 TGTAATGGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 3 0.09
20 29 0.91
ACGTcount: A:0.37, C:0.15, G:0.31, T:0.17
Consensus pattern (20 bp):
GGAAGGTATCGATACCAAGA
Found at i:47661 original size:23 final size:21
Alignment explanation
Indices: 47609--47670 Score: 81
Period size: 23 Copynumber: 2.9 Consensus size: 21
47599 TTTTGGTGCA
*
47609 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
*
47629 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
47650 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
47671 ACAGGGGAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.28
21 9 0.25
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.35, G:0.26, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:47678 original size:21 final size:21
Alignment explanation
Indices: 47652--47691 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
47642 CCCCCTTTGA
*
47652 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
47673 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
47692 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:49641 original size:9 final size:8
Alignment explanation
Indices: 49618--49669 Score: 54
Period size: 9 Copynumber: 6.4 Consensus size: 8
49608 TTGTTTCAAC
49618 TTTTTGGA
1 TTTTTGGA
49626 TATTTTGGA
1 T-TTTTGGA
49635 TTGTTT-GA
1 TT-TTTGGA
49643 TTTTGTGGA
1 TTTT-TGGA
*
49652 TTGTTGGA
1 TTTTTGGA
49660 -TTTTGGA
1 TTTTTGGA
49667 TTT
1 TTT
49670 ATGAATAGTG
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
7 8 0.22
8 13 0.35
9 16 0.43
ACGTcount: A:0.13, C:0.00, G:0.27, T:0.60
Consensus pattern (8 bp):
TTTTTGGA
Found at i:49653 original size:17 final size:17
Alignment explanation
Indices: 49621--49664 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
49611 TTTCAACTTT
49621 TTGGATATTT-TGGATTG
1 TTGGAT-TTTGTGGATTG
*
49638 TTTGATTTTGTGGATTG
1 TTGGATTTTGTGGATTG
49655 TTGGATTTTG
1 TTGGATTTTG
49665 GATTTATGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.14, C:0.00, G:0.30, T:0.57
Consensus pattern (17 bp):
TTGGATTTTGTGGATTG
Found at i:51686 original size:53 final size:53
Alignment explanation
Indices: 51617--51725 Score: 182
Period size: 53 Copynumber: 2.1 Consensus size: 53
51607 CTATGTGTAC
*
51617 TTTCGACACTACGTGTGCATCCATGGTATTCATAATGAGTTTTTGAATTACCA
1 TTTCGACACTACGTGTGCATCCATGGTATTCATAATGAGTTTGTGAATTACCA
* * *
51670 TTTCGGCACTATGTGTGCATCCATGGTATTCGTAATGAGTTTGTGAATTACCA
1 TTTCGACACTACGTGTGCATCCATGGTATTCATAATGAGTTTGTGAATTACCA
51723 TTT
1 TTT
51726 TGTTACCTTA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.39
Consensus pattern (53 bp):
TTTCGACACTACGTGTGCATCCATGGTATTCATAATGAGTTTGTGAATTACCA
Found at i:53109 original size:18 final size:18
Alignment explanation
Indices: 53078--53112 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
53068 TCATTCAGGA
*
53078 TGATGACGAGGATGATGT
1 TGATGACGACGATGATGT
*
53096 TGATGGCGACGATGATG
1 TGATGACGACGATGATG
53113 CATCGGAGGC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.09, G:0.40, T:0.26
Consensus pattern (18 bp):
TGATGACGACGATGATGT
Found at i:54766 original size:25 final size:26
Alignment explanation
Indices: 54737--54792 Score: 73
Period size: 24 Copynumber: 2.2 Consensus size: 26
54727 TAAACTATTA
*
54737 AATATTTGAAAACAATACAAAAT-ATT
1 AATATTTAAAAAC-ATACAAAATAATT
54763 -ATA-TTAAAAACATACAAAATAATT
1 AATATTTAAAAACATACAAAATAATT
54787 AATATT
1 AATATT
54793 GATCATGTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
23 9 0.35
24 10 0.38
25 6 0.23
26 1 0.04
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.32
Consensus pattern (26 bp):
AATATTTAAAAACATACAAAATAATT
Found at i:54777 original size:23 final size:26
Alignment explanation
Indices: 54745--54792 Score: 75
Period size: 23 Copynumber: 2.0 Consensus size: 26
54735 TAAATATTTG
54745 AAAACAATACAAAAT-ATT-ATATTA
1 AAAACAATACAAAATAATTAATATTA
54769 AAAAC-ATACAAAATAATTAATATT
1 AAAACAATACAAAATAATTAATATT
54793 GATCATGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 9 0.41
24 8 0.36
25 5 0.23
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.29
Consensus pattern (26 bp):
AAAACAATACAAAATAATTAATATTA
Found at i:55597 original size:7 final size:7
Alignment explanation
Indices: 55585--55613 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
55575 TGGTGCAACA
55585 CTTATTC
1 CTTATTC
55592 CTTATTC
1 CTTATTC
55599 CTTATTC
1 CTTATTC
55606 CTTATTC
1 CTTATTC
55613 C
1 C
55614 ATGTCTGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.31, G:0.00, T:0.55
Consensus pattern (7 bp):
CTTATTC
Found at i:56017 original size:2 final size:2
Alignment explanation
Indices: 56010--56036 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
56000 AATAATCTTA
56010 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
56037 CCGACAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:73600 original size:15 final size:15
Alignment explanation
Indices: 73565--73601 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
73555 TTAACTGTAT
*
73565 TCATTTATGTTTTTA
1 TCATTTATGTTTTCA
73580 TACATTTATGTTTTCA
1 T-CATTTATGTTTTCA
73596 TCATTT
1 TCATTT
73602 GAGTTAATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.22, C:0.11, G:0.05, T:0.62
Consensus pattern (15 bp):
TCATTTATGTTTTCA
Found at i:75562 original size:13 final size:13
Alignment explanation
Indices: 75530--75576 Score: 62
Period size: 13 Copynumber: 3.7 Consensus size: 13
75520 TGCGTCATAA
*
75530 ATTTATTACACGC
1 ATTTATGACACGC
75543 A-TTATGACACGC
1 ATTTATGACACGC
75555 ATTTATGACGA-GC
1 ATTTATGAC-ACGC
75568 ATTTATGAC
1 ATTTATGAC
75577 GCTCATTGCG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
12 11 0.35
13 19 0.61
14 1 0.03
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (13 bp):
ATTTATGACACGC
Found at i:75583 original size:13 final size:13
Alignment explanation
Indices: 75530--75583 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
75520 TGCGTCATAA
* *
75530 ATTTATTACACGC
1 ATTTATGACGCGC
*
75543 A-TTATGACACGC
1 ATTTATGACGCGC
*
75555 ATTTATGACGAGC
1 ATTTATGACGCGC
*
75568 ATTTATGACGCTC
1 ATTTATGACGCGC
75581 ATT
1 ATT
75584 GCGCGTCATT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
12 11 0.31
13 24 0.69
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (13 bp):
ATTTATGACGCGC
Found at i:75741 original size:2 final size:2
Alignment explanation
Indices: 75734--75787 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
75724 GTATTTCGTA
*
75734 AT AT AT AT AT AT CT 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
75776 AT AT AT AT AT AT
1 AT AT AT AT AT AT
75788 TGTAGATTGA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.