Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006882.1 Hibiscus syriacus cultivar Beakdansim tig00017545_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: 84751
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:10296 original size:17 final size:16
Alignment explanation
Indices: 10274--10324 Score: 56
Period size: 13 Copynumber: 3.3 Consensus size: 16
10264 TTTTTTAAAT
10274 AAATAAATATGCAATAA
1 AAATAAATAT-CAATAA
10291 AAATAAAT-T-AA-AA
1 AAATAAATATCAATAA
10304 AAATAAA-ATTCAATAA
1 AAATAAATA-TCAATAA
10320 AAATA
1 AAATA
10325 TAATGTAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
13 9 0.30
14 3 0.10
15 2 0.07
16 8 0.27
17 8 0.27
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.24
Consensus pattern (16 bp):
AAATAAATATCAATAA
Found at i:10302 original size:30 final size:30
Alignment explanation
Indices: 10268--10334 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 30
10258 TATTCATTTT
*
10268 TTAAATAAATAAATATGCAATAAAAATA-AA
1 TTAAAAAAATAAA-ATGCAATAAAAATATAA
*
10298 TTAAAAAAATAAAATTCAATAAAAATATAA
1 TTAAAAAAATAAAATGCAATAAAAATATAA
10328 TGTAAAA
1 T-TAAAA
10335 CTAAAAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 13 0.39
30 15 0.45
31 5 0.15
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.27
Consensus pattern (30 bp):
TTAAAAAAATAAAATGCAATAAAAATATAA
Found at i:10768 original size:26 final size:24
Alignment explanation
Indices: 10726--10782 Score: 71
Period size: 26 Copynumber: 2.3 Consensus size: 24
10716 CAACAGTTAA
*
10726 TAATATTTATTCATTTTTAATAAAAT
1 TAATATTTAATCATTTTT--TAAAAT
10752 TAATATTTAAT-ATTTTTTTAAAAT
1 TAATATTTAATCA-TTTTTTAAAAT
10776 TAATATT
1 TAATATT
10783 AGAAAGAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 13 0.45
25 1 0.03
26 15 0.52
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (24 bp):
TAATATTTAATCATTTTTTAAAAT
Found at i:10773 original size:24 final size:26
Alignment explanation
Indices: 10726--10782 Score: 82
Period size: 24 Copynumber: 2.3 Consensus size: 26
10716 CAACAGTTAA
*
10726 TAATATTTATTCATTTTTAATAAAAT
1 TAATATTTAATCATTTTTAATAAAAT
*
10752 TAATATTTAAT-ATTTTT-TTAAAAT
1 TAATATTTAATCATTTTTAATAAAAT
10776 TAATATT
1 TAATATT
10783 AGAAAGAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 13 0.45
25 6 0.21
26 10 0.34
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (26 bp):
TAATATTTAATCATTTTTAATAAAAT
Found at i:10889 original size:11 final size:10
Alignment explanation
Indices: 10830--10887 Score: 71
Period size: 10 Copynumber: 5.7 Consensus size: 10
10820 CTTTACATTA
10830 TATTTTTATT
1 TATTTTTATT
* *
10840 GAATTTTATT
1 TATTTTTATT
* *
10850 CATTTTAATT
1 TATTTTTATT
10860 TATTTTTATTT
1 TATTTTTA-TT
10871 TATTTTTATT
1 TATTTTTATT
10881 TATTTTT
1 TATTTTT
10888 TAAAAAAGTG
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
10 30 0.75
11 10 0.25
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (10 bp):
TATTTTTATT
Found at i:11532 original size:20 final size:21
Alignment explanation
Indices: 11509--11548 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
11499 TTAATTTTGG
*
11509 ATAAATTAT-GATTTTAGTAC
1 ATAAATTATCAATTTTAGTAC
11529 ATAAATTATCAATTTTAGTA
1 ATAAATTATCAATTTTAGTA
11549 TGCTTGAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
ATAAATTATCAATTTTAGTAC
Found at i:14716 original size:28 final size:28
Alignment explanation
Indices: 14659--14715 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
14649 AAAAAATTTG
* *
14659 AATAATTTAAGTATCTATTTTTACATAA
1 AATAATTTAAGTACCTATTTTAACATAA
* *
14687 AATACTTTAGGTACCTATTTTAAC-TAA
1 AATAATTTAAGTACCTATTTTAACATAA
14714 AA
1 AA
14716 AGATAATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 5 0.20
28 20 0.80
ACGTcount: A:0.42, C:0.11, G:0.05, T:0.42
Consensus pattern (28 bp):
AATAATTTAAGTACCTATTTTAACATAA
Found at i:14730 original size:31 final size:29
Alignment explanation
Indices: 14685--14760 Score: 89
Period size: 31 Copynumber: 2.6 Consensus size: 29
14675 ATTTTTACAT
*
14685 AAAATACTTTAGGTACCTATTTTAACTAAA
1 AAAATATTTTAGGTACCTATTTTAA-TAAA
* ** *
14715 AAGATAATTTTAGGTATTTATTTTGATAAA
1 AAAAT-ATTTTAGGTACCTATTTTAATAAA
14745 AAAATATTTTAGGTAC
1 AAAATATTTTAGGTAC
14761 TTAATTAAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
29 10 0.26
30 12 0.32
31 16 0.42
ACGTcount: A:0.42, C:0.07, G:0.11, T:0.41
Consensus pattern (29 bp):
AAAATATTTTAGGTACCTATTTTAATAAA
Found at i:16496 original size:21 final size:21
Alignment explanation
Indices: 16461--16510 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
16451 TTATGGTAAT
*
16461 TTTAAAAAATATATATTTAAAA
1 TTTAAAAAATATATAATT-AAA
*
16483 TTTAAAAAAT-TATAATTATA
1 TTTAAAAAATATATAATTAAA
16503 TTTAAAAA
1 TTTAAAAA
16511 GCACAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 10 0.38
21 6 0.23
22 10 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TTTAAAAAATATATAATTAAA
Found at i:17386 original size:29 final size:29
Alignment explanation
Indices: 17353--17408 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
17343 TCCCAACACA
*
17353 TAGGTCACCATGCCCTCCGGGCGACCTTG
1 TAGGTCACCATGCACTCCGGGCGACCTTG
*
17382 TAGGTCGCCATGCACTCCGGGCGACCT
1 TAGGTCACCATGCACTCCGGGCGACCT
17409 ACCCTTGCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.14, C:0.38, G:0.29, T:0.20
Consensus pattern (29 bp):
TAGGTCACCATGCACTCCGGGCGACCTTG
Found at i:17445 original size:23 final size:23
Alignment explanation
Indices: 17419--17483 Score: 87
Period size: 23 Copynumber: 2.8 Consensus size: 23
17409 ACCCTTGCTC
17419 GCTCGCTCGGATGCCCTCGCATA
1 GCTCGCTCGGATGCCCTCGCATA
17442 GCTCGCTC-GACTGCCCTCGCATA
1 GCTCGCTCGGA-TGCCCTCGCATA
* * *
17465 GCTTGGTCGGATGGCCTCG
1 GCTCGCTCGGATGCCCTCG
17484 GAGACTCTCG
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
22 2 0.05
23 33 0.89
24 2 0.05
ACGTcount: A:0.11, C:0.37, G:0.29, T:0.23
Consensus pattern (23 bp):
GCTCGCTCGGATGCCCTCGCATA
Found at i:27150 original size:22 final size:22
Alignment explanation
Indices: 27109--27150 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
27099 TCGAATTGTG
* *
27109 ATTTTATAAATTCGACTCGAAA
1 ATTTTATAAATTCAAATCGAAA
*
27131 ATTTTTTAAATTCAAATCGA
1 ATTTTATAAATTCAAATCGA
27151 GTTGTAAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.40
Consensus pattern (22 bp):
ATTTTATAAATTCAAATCGAAA
Found at i:31921 original size:19 final size:19
Alignment explanation
Indices: 31894--31941 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
31884 TGTATCGAAG
31894 TCCTCAAATTA-CAATTTTCA
1 TCCT-AAATTATCAATTTT-A
*
31914 TCCTAAATTATGAATTTTA
1 TCCTAAATTATCAATTTTA
31933 TCCTAAATT
1 TCCTAAATT
31942 GGTTACTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.35, C:0.19, G:0.02, T:0.44
Consensus pattern (19 bp):
TCCTAAATTATCAATTTTA
Found at i:34305 original size:32 final size:32
Alignment explanation
Indices: 34260--34336 Score: 138
Period size: 32 Copynumber: 2.4 Consensus size: 32
34250 TAACTCATTT
34260 GAAG-GTTTTATCGCCTCTTGAGTCGATTCGG
1 GAAGAGTTTTATCGCCTCTTGAGTCGATTCGG
34291 GAAGAGTTTTATCGCCTCTTGAGTCGATTCGG
1 GAAGAGTTTTATCGCCTCTTGAGTCGATTCGG
*
34323 GAAGAGTTATATCG
1 GAAGAGTTTTATCG
34337 ATTATTAAAG
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
31 4 0.09
32 40 0.91
ACGTcount: A:0.21, C:0.17, G:0.29, T:0.34
Consensus pattern (32 bp):
GAAGAGTTTTATCGCCTCTTGAGTCGATTCGG
Found at i:39362 original size:20 final size:21
Alignment explanation
Indices: 39337--39375 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
39327 TTTTGGTGCA
*
39337 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
39357 GAGGGAACCGATTCCCCCC
1 GAGGGAACCGATTCCCCCC
39376 ACAGGGGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.21, C:0.38, G:0.26, T:0.15
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:41339 original size:9 final size:8
Alignment explanation
Indices: 41316--41367 Score: 54
Period size: 9 Copynumber: 6.4 Consensus size: 8
41306 TTGTTTCAAC
41316 TTTTTGGA
1 TTTTTGGA
41324 TATTTTGGA
1 T-TTTTGGA
41333 TTGTTT-GA
1 TT-TTTGGA
41341 TTTTGTGGA
1 TTTT-TGGA
*
41350 TTGTTGGA
1 TTTTTGGA
41358 -TTTTGGA
1 TTTTTGGA
41365 TTT
1 TTT
41368 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:41351 original size:17 final size:17
Alignment explanation
Indices: 41319--41362 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
41309 TTTCAACTTT
41319 TTGGATATTT-TGGATTG
1 TTGGAT-TTTGTGGATTG
*
41336 TTTGATTTTGTGGATTG
1 TTGGATTTTGTGGATTG
41353 TTGGATTTTG
1 TTGGATTTTG
41363 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:45981 original size:31 final size:30
Alignment explanation
Indices: 45912--45982 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 30
45902 GAAAAGAAAC
*
45912 TCAGGGACTAATATGGGGATATAGCCAAAA
1 TCAGGGACTAATATGGGGAAATAGCCAAAA
* *
45942 TCATGGACTAATAT-GGGAAACGTAGCTAAAA
1 TCAGGGACTAATATGGGGAAA--TAGCCAAAA
45973 TCAGGGACTA
1 TCAGGGACTA
45983 GACGAATCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 5 0.14
30 13 0.37
31 17 0.49
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.21
Consensus pattern (30 bp):
TCAGGGACTAATATGGGGAAATAGCCAAAA
Found at i:47477 original size:37 final size:37
Alignment explanation
Indices: 47427--47500 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
47417 TAGGCGGGTG
47427 GCCGAATTCGGGGCTTATTTTTTATCTTTGATGAATA
1 GCCGAATTCGGGGCTTATTTTTTATCTTTGATGAATA
47464 GCCGAATTCGGGGCTTATTTTTTATCTTTGATGAATA
1 GCCGAATTCGGGGCTTATTTTTTATCTTTGATGAATA
47501 CTTGTTGCCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.22, C:0.14, G:0.22, T:0.43
Consensus pattern (37 bp):
GCCGAATTCGGGGCTTATTTTTTATCTTTGATGAATA
Found at i:48540 original size:14 final size:14
Alignment explanation
Indices: 48521--48551 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
48511 TATTTATGGG
48521 ATATCGAACTCTTT
1 ATATCGAACTCTTT
*
48535 ATATCGAGCTCTTT
1 ATATCGAACTCTTT
48549 ATA
1 ATA
48552 ACTTGACCCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.42
Consensus pattern (14 bp):
ATATCGAACTCTTT
Found at i:50925 original size:25 final size:25
Alignment explanation
Indices: 50891--50945 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
50881 TTCTTATAGA
* *
50891 CATCATACACCAAGTTCGAATACGG
1 CATCATACACCAAATTCAAATACGG
50916 CATCATACACCAAATTCAAATACGG
1 CATCATACACCAAATTCAAATACGG
*
50941 TATCA
1 CATCA
50946 CTCAACCCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.40, C:0.27, G:0.11, T:0.22
Consensus pattern (25 bp):
CATCATACACCAAATTCAAATACGG
Found at i:53239 original size:29 final size:29
Alignment explanation
Indices: 53206--53285 Score: 74
Period size: 30 Copynumber: 2.8 Consensus size: 29
53196 TTCGTCTTAT
53206 CTAAAGTTTTTTTT-TGTCAAAATAAATAC
1 CTAAAGTTTTTTTTAT-TCAAAATAAATAC
* ** *
53235 CTAAACTTGTTTTTTATTCAAAATAGGTGC
1 CTAAAGTT-TTTTTTATTCAAAATAAATAC
* *
53265 CTAAAGTGTTTTTGA-TCAAAA
1 CTAAAGTTTTTTTTATTCAAAA
53286 CAGGTATCTA
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
28 6 0.14
29 13 0.31
30 22 0.52
31 1 0.02
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.42
Consensus pattern (29 bp):
CTAAAGTTTTTTTTATTCAAAATAAATAC
Found at i:53285 original size:28 final size:28
Alignment explanation
Indices: 53216--53299 Score: 80
Period size: 28 Copynumber: 3.0 Consensus size: 28
53206 CTAAAGTTTT
** *
53216 TTTTTG-TCAAAATAAATACCTAAACTTG
1 TTTTTGATCAAAATAGGTACCTAAA-GTG
* *
53244 TTTTTTATTCAAAATAGGTGCCTAAAGTG
1 TTTTTGA-TCAAAATAGGTACCTAAAGTG
* *
53273 TTTTTGATCAAAACAGGTATCTAAAGT
1 TTTTTGATCAAAATAGGTACCTAAAGT
53300 ATTCAATTTT
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
28 22 0.49
29 8 0.18
30 15 0.33
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.39
Consensus pattern (28 bp):
TTTTTGATCAAAATAGGTACCTAAAGTG
Found at i:54234 original size:60 final size:60
Alignment explanation
Indices: 54159--54297 Score: 165
Period size: 60 Copynumber: 2.3 Consensus size: 60
54149 AATAAAAGGG
* * *
54159 TAAAAG-TACACAAATGGTCCTCCAACTATAGGATATTGCTTTATTTAGTTCCATGAA-TAT
1 TAAAAGTTACA-AAATGGTCCTCCAACCATAGGATATTGCTTTATTGAG-TCCATCAACTAT
* * * * * *
54219 TAAAAGTTATAAAATGGTCCTTCGACCATAGGATGTTGCTTTGTTGAGTCCCTCAACTAT
1 TAAAAGTTACAAAATGGTCCTCCAACCATAGGATATTGCTTTATTGAGTCCATCAACTAT
54279 TAAAAGTTACAAAATGGTC
1 TAAAAGTTACAAAATGGTC
54298 ACCTGACTAT
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
59 6 0.09
60 58 0.87
61 3 0.04
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Consensus pattern (60 bp):
TAAAAGTTACAAAATGGTCCTCCAACCATAGGATATTGCTTTATTGAGTCCATCAACTAT
Found at i:55953 original size:411 final size:412
Alignment explanation
Indices: 55164--55980 Score: 1564
Period size: 411 Copynumber: 2.0 Consensus size: 412
55154 GTTTCTAAAA
55164 TAAAATGTTGAGTTTCAAAATGCTCTAAAAAAGGAAAAAGGGCCAAAGTGTCAACTCTATCAAAT
1 TAAAATGTTGAGTTTCAAAATGCTCTAAAAAAGGAAAAAGGGCCAAAGTGTCAACTCTATCAAAT
55229 GTTAGGAGCCTTTTTGCCCTAAAATGAAACGTTATGGGTCAAAATAATCCAAAAAATATAAGGAC
66 GTTAGGAGCCTTTTTGCCCTAAAATGAAACGTTATGGGTCAAAATAATCCAAAAAATATAAGGAC
*
55294 TAAAATGATCATTTTGATAAATGTTGGCAGCTAATTTTGGTATTATGTCTTAAAAATATTATTAT
131 TAAAATGATCATTTTGATAAATGTTGGCAGCTAATTTTGGTATTATGCCTTAAAAATATTATTAT
55359 CTTTTAAGATTTTATGTTTGAGCCCGACATTTGCAAATATGTATAAACATTCATTGTCAAATAAC
196 CTTTTAAGATTTTATGTTTGAGCCCGACATTTGCAAATATGTATAAACATTCATTGTCAAATAAC
55424 TGGGAGTCTTTCGACGATATAATATCTTATAGTCCTCTTAAATTAATCAAATAATATATTTAAAC
261 TGGGAGTCTTTCGACGATATAATATCTTATAGTCCTCTTAAATTAATCAAATAATATATTTAAAC
*
55489 ATTGAGACGTCGCACTAACCAAGTGACTTTCGTAGTAAAGGAATTGTTGTTATTCCTAAGGACTC
326 ATTGAGACGTCGCACTAACCAAGTGACTTTCGTAGTAAAGGAATTGTTGTTATTCCTAAGAACTC
55554 GGGTTCGAGCACTATAGATGTT
391 GGGTTCGAGCACTATAGATGTT
55576 TAAAATGTTGAGTTTCAAAATGCTCT-AAAAAGGAAAAAGGGCCAAAGTGTCAACTCTATCAAAT
1 TAAAATGTTGAGTTTCAAAATGCTCTAAAAAAGGAAAAAGGGCCAAAGTGTCAACTCTATCAAAT
55640 GTTAGGAGCCTTTTTGCCCTAAAATGAAACGTTATGGGTCAAAATAATCCAAAAAATATAAGGAC
66 GTTAGGAGCCTTTTTGCCCTAAAATGAAACGTTATGGGTCAAAATAATCCAAAAAATATAAGGAC
*
55705 TGAAATGATCATTTTGATAAATGTTGGCAGCTAATTTTGGTATTATGCCTTAAAAATATTATTAT
131 TAAAATGATCATTTTGATAAATGTTGGCAGCTAATTTTGGTATTATGCCTTAAAAATATTATTAT
*
55770 CTTTTAAGATTTTATGTTTGAGCCCGACATTTGCAAATATGTATAAGCATTCATTGTCAAATAAC
196 CTTTTAAGATTTTATGTTTGAGCCCGACATTTGCAAATATGTATAAACATTCATTGTCAAATAAC
55835 TGGGAGTCTTTCGACGATATAATATCTTATAGTCCTCTTAAATTAATCAAATAATATATTTAAAC
261 TGGGAGTCTTTCGACGATATAATATCTTATAGTCCTCTTAAATTAATCAAATAATATATTTAAAC
* *
55900 ATTGAGACGTCGCACTAACCAAGTGACTTTCGTAGTAAAGGAATTGTTGTTATTTCTATGAACTC
326 ATTGAGACGTCGCACTAACCAAGTGACTTTCGTAGTAAAGGAATTGTTGTTATTCCTAAGAACTC
*
55965 GGGTTTGAGCACTATA
391 GGGTTCGAGCACTATA
55981 AATATCAGGG
Statistics
Matches: 398, Mismatches: 7, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
411 372 0.93
412 26 0.07
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.34
Consensus pattern (412 bp):
TAAAATGTTGAGTTTCAAAATGCTCTAAAAAAGGAAAAAGGGCCAAAGTGTCAACTCTATCAAAT
GTTAGGAGCCTTTTTGCCCTAAAATGAAACGTTATGGGTCAAAATAATCCAAAAAATATAAGGAC
TAAAATGATCATTTTGATAAATGTTGGCAGCTAATTTTGGTATTATGCCTTAAAAATATTATTAT
CTTTTAAGATTTTATGTTTGAGCCCGACATTTGCAAATATGTATAAACATTCATTGTCAAATAAC
TGGGAGTCTTTCGACGATATAATATCTTATAGTCCTCTTAAATTAATCAAATAATATATTTAAAC
ATTGAGACGTCGCACTAACCAAGTGACTTTCGTAGTAAAGGAATTGTTGTTATTCCTAAGAACTC
GGGTTCGAGCACTATAGATGTT
Found at i:56317 original size:3 final size:3
Alignment explanation
Indices: 56309--56347 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
56299 TTATACGCAT
56309 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
56348 TCGACAACTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:64704 original size:29 final size:29
Alignment explanation
Indices: 64662--64724 Score: 126
Period size: 29 Copynumber: 2.2 Consensus size: 29
64652 AATCATTTCA
64662 GTAACTAATATGATCTTCGAGATTCGACG
1 GTAACTAATATGATCTTCGAGATTCGACG
64691 GTAACTAATATGATCTTCGAGATTCGACG
1 GTAACTAATATGATCTTCGAGATTCGACG
64720 GTAAC
1 GTAAC
64725 GTCTAGATCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (29 bp):
GTAACTAATATGATCTTCGAGATTCGACG
Found at i:67211 original size:2 final size:2
Alignment explanation
Indices: 67204--67247 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
67194 TAAATAATAA
67204 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
67246 AT
1 AT
67248 TTAGATGTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:69910 original size:25 final size:24
Alignment explanation
Indices: 69863--69934 Score: 76
Period size: 23 Copynumber: 3.0 Consensus size: 24
69853 TTAAACTTTA
* *
69863 ATTTTATTTA-TATTTTCTAAAAACT
1 ATTTT-TTTATTATTTTATGAAAA-T
69888 ATTTTTTTATTATTTTATGAAAAT
1 ATTTTTTTATTATTTTATGAAAAT
* *
69912 A-ATTTATATTATTTTATGAAAAT
1 ATTTTTTTATTATTTTATGAAAAT
69935 TTGATCTCTT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
23 20 0.48
24 6 0.14
25 16 0.38
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (24 bp):
ATTTTTTTATTATTTTATGAAAAT
Found at i:70858 original size:35 final size:35
Alignment explanation
Indices: 70781--70862 Score: 103
Period size: 35 Copynumber: 2.3 Consensus size: 35
70771 GATATTCGAG
*
70781 GTTTAGGGTTTAGGATATATTATTCATGTCTTAGA
1 GTTTAGGGTTTAGGATATATTATTCAGGTCTTAGA
* * * *
70816 GTCTAGGGTTTAGGATCTATTATTTAGGTTTTA-A
1 GTTTAGGGTTTAGGATATATTATTCAGGTCTTAGA
70850 GATTTAGGGTTTA
1 G-TTTAGGGTTTA
70863 AGGTTTAAAG
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
34 2 0.05
35 38 0.95
ACGTcount: A:0.24, C:0.05, G:0.24, T:0.46
Consensus pattern (35 bp):
GTTTAGGGTTTAGGATATATTATTCAGGTCTTAGA
Found at i:73451 original size:20 final size:20
Alignment explanation
Indices: 73426--73464 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
73416 AGATTACGCA
73426 GGGGTACAGATTCCCCCCTG
1 GGGGTACAGATTCCCCCCTG
**
73446 GGGGTATTGATTCCCCCCT
1 GGGGTACAGATTCCCCCCT
73465 AAAGAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.33, G:0.28, T:0.26
Consensus pattern (20 bp):
GGGGTACAGATTCCCCCCTG
Found at i:74140 original size:31 final size:31
Alignment explanation
Indices: 74102--74182 Score: 135
Period size: 31 Copynumber: 2.6 Consensus size: 31
74092 AGGGTCGAGG
*
74102 GTTTACCTATGTTTTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGATT
74133 GTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGATT
* *
74164 GATTACCTAGGTTCTTCGG
1 GTTTACCTATGTTCTTCGG
74183 AATCTATGGA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.19, C:0.16, G:0.23, T:0.42
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGATT
Found at i:74191 original size:31 final size:31
Alignment explanation
Indices: 74104--74192 Score: 108
Period size: 31 Copynumber: 2.9 Consensus size: 31
74094 GGTCGAGGGT
* * * *
74104 TTACCTATGTTTTTCGGGACATATGGATTGT
1 TTACCTAGGTTCTTCGGAACATATGGATTGA
* *
74135 TTACCTATGTTCTTCGGGACATATGGATTGA
1 TTACCTAGGTTCTTCGGAACATATGGATTGA
74166 TTACCTAGGTTCTTCGGAATC-TATGGA
1 TTACCTAGGTTCTTCGGAA-CATATGGA
74193 CTGGTCCTTC
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
31 52 0.98
32 1 0.02
ACGTcount: A:0.21, C:0.16, G:0.22, T:0.40
Consensus pattern (31 bp):
TTACCTAGGTTCTTCGGAACATATGGATTGA
Found at i:74932 original size:21 final size:22
Alignment explanation
Indices: 74906--74948 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
74896 GTAGCAGTAA
*
74906 TGTAGCA-GGGTATCGGTTCCC
1 TGTAGCAGGGGAATCGGTTCCC
74927 TGTAGCAGGGGAATCGGTTCCC
1 TGTAGCAGGGGAATCGGTTCCC
74949 CTCTGACATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.16, C:0.23, G:0.35, T:0.26
Consensus pattern (22 bp):
TGTAGCAGGGGAATCGGTTCCC
Found at i:75021 original size:24 final size:22
Alignment explanation
Indices: 74981--75027 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 22
74971 AACATTCGGG
74981 TACTGTTCACGGTACTGGTCAT
1 TACTGTTCACGGTACTGGTCAT
*
75003 TACTGTTCATACGGTACTGTTCAT
1 TACTGTTC--ACGGTACTGGTCAT
75027 T
1 T
75028 GTTCATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 8 0.36
24 14 0.64
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.40
Consensus pattern (22 bp):
TACTGTTCACGGTACTGGTCAT
Found at i:77871 original size:52 final size:54
Alignment explanation
Indices: 77785--77892 Score: 148
Period size: 52 Copynumber: 2.0 Consensus size: 54
77775 CTCTGCAAAT
*** *
77785 TAATTAATGAGATTAGTCAATAATCTATGGC-AA-ATGTAAACGAGATTGTGTG
1 TAATTAATGAGATTAGTCAATAATCTACCACAAATATGTAAACAAGATTGTGTG
* *
77837 TAATTAATGGGATTAGTCAATAATCTCCCACAAATATGTAAACAAGATTGTGTG
1 TAATTAATGAGATTAGTCAATAATCTACCACAAATATGTAAACAAGATTGTGTG
77891 TA
1 TA
77893 TGGCTGAGTG
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
52 26 0.54
53 2 0.04
54 20 0.42
ACGTcount: A:0.39, C:0.10, G:0.19, T:0.32
Consensus pattern (54 bp):
TAATTAATGAGATTAGTCAATAATCTACCACAAATATGTAAACAAGATTGTGTG
Found at i:78244 original size:12 final size:12
Alignment explanation
Indices: 78227--78251 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
78217 CAAGAACCCC
78227 ACCCACTCCTTA
1 ACCCACTCCTTA
78239 ACCCACTCCTTA
1 ACCCACTCCTTA
78251 A
1 A
78252 GTAGCTCCGT
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:0.28, C:0.48, G:0.00, T:0.24
Consensus pattern (12 bp):
ACCCACTCCTTA
Found at i:79119 original size:114 final size:114
Alignment explanation
Indices: 78964--79665 Score: 1064
Period size: 114 Copynumber: 6.0 Consensus size: 114
78954 TGTTCGAGAG
* * * *
78964 ATTGTTTTATATGAAAAAAAATGAAGCTTGATTATTGTTTTCTTATGTTTGTTTCAGAAATTTAG
1 ATTGTTTTATATG-AAAAGAATGAAGCTTGGTTATGGTTTTCCTATGTTTGTTTCAGAAATTTAG
*
79029 GAGAATTGGGATGTTTGCAATCATTCTTGCCTCTGAATAGCATGGTCAAA
65 GAGAATTGGGATGTTTCCAATCATTCTTGCCTCTGAATAGCATGGTCAAA
79079 ATTGTTTTATATGAAAAGAATGAAGCTTGGTTATGGTTTTCCTATGTTTGTTTCAGAAATTTAGG
1 ATTGTTTTATATGAAAAGAATGAAGCTTGGTTATGGTTTTCCTATGTTTGTTTCAGAAATTTAGG
79144 AGAATTGGGATGTTTCCAATCATTCTTGCCTCTGAATAGCATGGTCGTGGTCAAA
66 AGAATTGGGATGTTTCCAATCATTCTTGCCTCTGAATAGCA------TGGTCAAA
* *
79199 ATTGTTTGATATGAAAAGAATGAAGCTCGGTTATGGTTTTCCTATAATCCTATGTTTGTTTCAGA
1 ATTGTTTTATATGAAAAGAATGAAGCTTGGTTATGG---T--T-T--TCCTATGTTTGTTTCAGA
*
79264 AATTTAGGAGAATTGGGATGTTTCCAGTCATTCTTGCCTCTGAATAGCATGGTCAAA
58 AATTTAGGAGAATTGGGATGTTTCCAATCATTCTTGCCTCTGAATAGCATGGTCAAA
79321 ATTGTTTTATATGAAAAGAATGAAGCTTGGTTATGGTTTTCCTATGTTTGTTTCAGAAATTTAGG
1 ATTGTTTTATATGAAAAGAATGAAGCTTGGTTATGGTTTTCCTATGTTTGTTTCAGAAATTTAGG
*
79386 AGAATTGGGATGTTTCCAATCATTCTTGCCTCTGAATAGCGTGGTCAAA
66 AGAATTGGGATGTTTCCAATCATTCTTGCCTCTGAATAGCATGGTCAAA
* *
79435 ATTGTTTGATATGAAAAGAATGAAGCTCGGTTATGGTTTTCCTATAATCCTATGTTTGTTTCAGA
1 ATTGTTTTATATGAAAAGAATGAAGCTTGGTTATGG---T--T-T--TCCTATGTTTGTTTCAGA
*
79500 AATTTAGGAGAATTGGGATGTTTCCAGTCATTCTTGCCTCTGAATAGCATGGTCAAA
58 AATTTAGGAGAATTGGGATGTTTCCAATCATTCTTGCCTCTGAATAGCATGGTCAAA
* *
79557 ATTGTTTTATTTGAAAA-AATGAAGCTTGATTATGGTTTTCCTATGTTTGTTTCAGAAATTTAGG
1 ATTGTTTTATATGAAAAGAATGAAGCTTGGTTATGGTTTTCCTATGTTTGTTTCAGAAATTTAGG
79621 AGAATTGGGATGTTTCCAATCATTCTTGCCTCTGAATAGCATGGT
66 AGAATTGGGATGTTTCCAATCATTCTTGCCTCTGAATAGCATGGT
79666 TCCCACAGCT
Statistics
Matches: 544, Mismatches: 21, Indels: 46
0.89 0.03 0.08
Matches are distributed among these distances:
113 70 0.13
114 195 0.36
115 14 0.03
116 2 0.00
117 2 0.00
118 1 0.00
119 2 0.00
120 43 0.08
121 16 0.03
122 130 0.24
123 1 0.00
125 1 0.00
126 1 0.00
128 66 0.12
ACGTcount: A:0.28, C:0.12, G:0.21, T:0.39
Consensus pattern (114 bp):
ATTGTTTTATATGAAAAGAATGAAGCTTGGTTATGGTTTTCCTATGTTTGTTTCAGAAATTTAGG
AGAATTGGGATGTTTCCAATCATTCTTGCCTCTGAATAGCATGGTCAAA
Found at i:79559 original size:236 final size:236
Alignment explanation
Indices: 79007--79665 Score: 1212
Period size: 242 Copynumber: 2.8 Consensus size: 236
78997 ATTGTTTTCT
* *
79007 TATGTTTGTTTCAGAAATTTAGGAGAATTGGGATGTTTGCAATCATTCTTGCCTCTGAATAGCAT
1 TATGTTTGTTTCAGAAATTTAGGAGAATTGGGATGTTTCCAGTCATTCTTGCCTCTGAATAGCAT
79072 GGTCAAAATTGTTTTATATGAAAAGAATGAAGCTTGGTTATGGTTTTCCTATGTTTGTTTCAGAA
66 GGTCAAAATTGTTTTATATGAAAAGAATGAAGCTTGGTTATGGTTTTCCTATGTTTGTTTCAGAA
79137 ATTTAGGAGAATTGGGATGTTTCCAATCATTCTTGCCTCTGAATAGCATGGTCGTGGTCAAAATT
131 ATTTAGGAGAATTGGGATGTTTCCAATCATTCTTGCCTCTGAAT---A--G-CGTGGTCAAAATT
79202 GTTTGATATGAAAAGAATGAAGCTCGGTTATGGTTTTCCTATAATCC
190 GTTTGATATGAAAAGAATGAAGCTCGGTTATGGTTTTCCTATAATCC
79249 TATGTTTGTTTCAGAAATTTAGGAGAATTGGGATGTTTCCAGTCATTCTTGCCTCTGAATAGCAT
1 TATGTTTGTTTCAGAAATTTAGGAGAATTGGGATGTTTCCAGTCATTCTTGCCTCTGAATAGCAT
79314 GGTCAAAATTGTTTTATATGAAAAGAATGAAGCTTGGTTATGGTTTTCCTATGTTTGTTTCAGAA
66 GGTCAAAATTGTTTTATATGAAAAGAATGAAGCTTGGTTATGGTTTTCCTATGTTTGTTTCAGAA
79379 ATTTAGGAGAATTGGGATGTTTCCAATCATTCTTGCCTCTGAATAGCGTGGTCAAAATTGTTTGA
131 ATTTAGGAGAATTGGGATGTTTCCAATCATTCTTGCCTCTGAATAGCGTGGTCAAAATTGTTTGA
79444 TATGAAAAGAATGAAGCTCGGTTATGGTTTTCCTATAATCC
196 TATGAAAAGAATGAAGCTCGGTTATGGTTTTCCTATAATCC
79485 TATGTTTGTTTCAGAAATTTAGGAGAATTGGGATGTTTCCAGTCATTCTTGCCTCTGAATAGCAT
1 TATGTTTGTTTCAGAAATTTAGGAGAATTGGGATGTTTCCAGTCATTCTTGCCTCTGAATAGCAT
* *
79550 GGTCAAAATTGTTTTATTTGAAAA-AATGAAGCTTGATTATGGTTTTCCTATGTTTGTTTCAGAA
66 GGTCAAAATTGTTTTATATGAAAAGAATGAAGCTTGGTTATGGTTTTCCTATGTTTGTTTCAGAA
*
79614 ATTTAGGAGAATTGGGATGTTTCCAATCATTCTTGCCTCTGAATAGCATGGT
131 ATTTAGGAGAATTGGGATGTTTCCAATCATTCTTGCCTCTGAATAGCGTGGT
79666 TCCCACAGCT
Statistics
Matches: 412, Mismatches: 5, Indels: 7
0.97 0.01 0.02
Matches are distributed among these distances:
235 90 0.22
236 148 0.36
237 1 0.00
239 1 0.00
242 172 0.42
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.39
Consensus pattern (236 bp):
TATGTTTGTTTCAGAAATTTAGGAGAATTGGGATGTTTCCAGTCATTCTTGCCTCTGAATAGCAT
GGTCAAAATTGTTTTATATGAAAAGAATGAAGCTTGGTTATGGTTTTCCTATGTTTGTTTCAGAA
ATTTAGGAGAATTGGGATGTTTCCAATCATTCTTGCCTCTGAATAGCGTGGTCAAAATTGTTTGA
TATGAAAAGAATGAAGCTCGGTTATGGTTTTCCTATAATCC
Found at i:82637 original size:27 final size:27
Alignment explanation
Indices: 82599--82661 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
82589 GCAGTTGATC
*
82599 ATTCGGCTCATATCCCTCTCCTGAGAG
1 ATTCGACTCATATCCCTCTCCTGAGAG
*
82626 ATTCGACTCATATCCCTCTGCTGAGAG
1 ATTCGACTCATATCCCTCTCCTGAGAG
82653 ATTCGACTC
1 ATTCGACTC
82662 CGGTTCGCGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.21, C:0.32, G:0.17, T:0.30
Consensus pattern (27 bp):
ATTCGACTCATATCCCTCTCCTGAGAG
Done.