Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006473.1 Hibiscus syriacus cultivar Beakdansim tig00015689_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: 58709
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Found at i:3840 original size:54 final size:54
Alignment explanation
Indices: 3777--3889 Score: 201
Period size: 54 Copynumber: 2.1 Consensus size: 54
3767 ATGGGTTCTT
3777 TGCTTGCCCATGAGCACAAATTCAACAAGAATGAAG-AAACACATCCTCTAAAAC
1 TGCTTGCCCATGAGCACAAATTCAACAAGAATGAAGAAAACACA-CCTCTAAAAC
*
3831 TGCTTGCCCATGAGCACAAATTCAACAAGAATGAAGAAAACACACCTCTGAAAC
1 TGCTTGCCCATGAGCACAAATTCAACAAGAATGAAGAAAACACACCTCTAAAAC
3885 TGCTT
1 TGCTT
3890 TTCCATCAAA
Statistics
Matches: 57, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
54 50 0.88
55 7 0.12
ACGTcount: A:0.41, C:0.26, G:0.14, T:0.19
Consensus pattern (54 bp):
TGCTTGCCCATGAGCACAAATTCAACAAGAATGAAGAAAACACACCTCTAAAAC
Found at i:8508 original size:23 final size:23
Alignment explanation
Indices: 8482--8542 Score: 81
Period size: 21 Copynumber: 2.7 Consensus size: 23
8472 ATTTTACAAC
8482 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
8505 TACCTATTACA-T-TATAAGCGC
1 TACCTATTACATTATATAAACGA
*
8526 TACCTATTACATCATAT
1 TACCTATTACATTATAT
8543 TTTTACCTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 18 0.55
22 1 0.03
23 14 0.42
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:9005 original size:23 final size:23
Alignment explanation
Indices: 8953--9015 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
8943 ACTTTACAAC
8953 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* ** *
8976 TATCTATTACATTATATAAGTGT
1 TACCTATTACATTATATAAACGA
*
8999 TACCTATTACATCATAT
1 TACCTATTACATTATAT
9016 TTTACCTATT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.38, C:0.16, G:0.05, T:0.41
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:9120 original size:471 final size:476
Alignment explanation
Indices: 8083--9354 Score: 2257
Period size: 471 Copynumber: 2.7 Consensus size: 476
8073 TTATAATATG
*
8083 TTGAAAGTGTTCATACTTTTTAT-AAAATGATCGATAA-TTTTTTTAAAGTTATGTAATTTATGT
1 TTGAAAGTGTCCATACTTTTTATAAAAATGATCGA-AACTTTTTTTAAAGTTATGTAATTTATGT
*
8146 TTCAATTTTTTTAATAGTGTTTCATGTTTT-CACCTACAATATTAATTTAATAATTTCATTTGCA
65 TTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACA
* *
8210 CAAAAATTTATTTGA-TGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
130 AAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
8274 TAACCAAAGATAATAATAAATATGTAATATATGTTTATTGTTTTTAATTTAATAATAATATATAT
195 TAACCAAAGATAATAATAAATATGTAATATATGTTTATTGTTTTTAATTT-ATAATAATATATAT
*
8339 CGTAACGTAAAAAGTAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCA
259 CGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCA
8404 AAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATA
324 AAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATA
*
8469 GATATTTTACAACTACCTATTACATTATATAAACGATACCTATTACATTATAAGCGCTACCTATT
389 GATACTTTACAACTACCTATTACATTATATAAACGATACCTATTACATTATAAGCGCTACCTATT
8534 ACATCATATTTTTACCTATTATA
454 ACATCATATTTTTACCTATTATA
* * *
8557 TTGAAAGCGTCCATATTTTTTATAAAAAGGATCGAAAC-TTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAATGATCGAAACTTTTTTTAAAGTTATGTAATTTATGTT
8621 TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAA
66 TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAA
8686 AAAAAATTATTTGATTGTTTTGATA-TTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
131 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
8750 AACCAAAGATAATAATAAATATGTAATATATGTTTATTGTTTTTAA-TT-TAATAATATATATCG
196 AACCAAAGATAATAATAAATATGTAATATATGTTTATTGTTTTTAATTTATAATAATATATATCG
8813 TAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC-AA
261 TAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAA
*
8877 AGATAATCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGA
326 AGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGA
* * *
8942 TACTTTACAACTACCTATTACATTATATAAACGATATCTATTACATTATATAAGTGTTACCTATT
391 TACTTTACAACTACCTATTACATTATATAAACGATACCTATTACA-T-TATAAGCGCTACCTATT
9007 ACATCATA-TTTTACCTATTATA
454 ACATCATATTTTTACCTATTATA
9029 TTGAAAGTGTCCATACTTTTTATAAAAATGATCGAAACTTTTTTTAAAGTTATGTAA-TT-TGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAATGATCGAAACTTTTTTTAAAGTTATGTAATTTATGTT
*
9092 TTAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTAC-A
66 TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAA
9156 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATA-T
131 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
9220 AACCAAAGATAATAATAAATATGTAATATATGTTTATTGTTTTTAATTTAATAATAATATATATC
196 AACCAAAGATAATAATAAATATGTAATATATGTTTATTGTTTTTAATTT-ATAATAATATATATC
* *
9285 GTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCATTTAA
260 GTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAA
9350 AAGAT
325 AAGAT
9355 GTATATACCT
Statistics
Matches: 767, Mismatches: 19, Indels: 24
0.95 0.02 0.03
Matches are distributed among these distances:
470 73 0.10
471 214 0.28
472 128 0.17
473 116 0.15
474 85 0.11
475 141 0.18
476 10 0.01
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (476 bp):
TTGAAAGTGTCCATACTTTTTATAAAAATGATCGAAACTTTTTTTAAAGTTATGTAATTTATGTT
TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAA
AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATATT
AACCAAAGATAATAATAAATATGTAATATATGTTTATTGTTTTTAATTTATAATAATATATATCG
TAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAA
AGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGA
TACTTTACAACTACCTATTACATTATATAAACGATACCTATTACATTATAAGCGCTACCTATTAC
ATCATATTTTTACCTATTATA
Found at i:9382 original size:25 final size:25
Alignment explanation
Indices: 9354--9416 Score: 117
Period size: 25 Copynumber: 2.5 Consensus size: 25
9344 ATTTAAAAGA
*
9354 TGTATATACCTAAATATGTAGTTAT
1 TGTACATACCTAAATATGTAGTTAT
9379 TGTACATACCTAAATATGTAGTTAT
1 TGTACATACCTAAATATGTAGTTAT
9404 TGTACATACCTAA
1 TGTACATACCTAA
9417 TTTAATGATA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.40
Consensus pattern (25 bp):
TGTACATACCTAAATATGTAGTTAT
Found at i:12333 original size:200 final size:199
Alignment explanation
Indices: 11526--12949 Score: 2491
Period size: 200 Copynumber: 7.1 Consensus size: 199
11516 GATGTTTTTG
11526 GGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACAAAAAATATCGACACAAAC
1 GGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAC-AAAAATATCGACACAAAC
*
11591 TAACAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTA
65 TAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTA
*
11656 GATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATCGACACTTTTTA
130 GATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATCGACACTTTCTA
*
11721 AATAT
195 TATAT
* *
11726 GGATTGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAGCAAAATTATCGACACAAAC
1 GGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGA-CAAAAATATCGACACAAAC
* *
11791 T-AAAAAGTGTCGACAAATTATTTAGACATATTCTCTCATAAAACCGGTAAACTTGTACCGGTTA
65 TAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTA
*
11855 GATTGAAAAATTACATATTACATTGTACTTTTGG-TTTCGATGTTTTTGGGATCGACACTTTCTA
130 GATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATCGACACTTTCTA
11919 TATAT
195 TATAT
*
11924 AGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACAAAAAATATCGACACAAAC
1 GGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAC-AAAAATATCGACACAAAC
*
11989 TAACAAAGTGTCGACACATTATTTAGACATATTCTCT-A-AAAACCGGTATACTTGTACCGGTTA
65 TAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTA
*
12052 GATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATCGACACTTTTTA
130 GATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATCGACACTTTCTA
12117 TATAT
195 TATAT
12122 GGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAGCAAAAATATCGACACAAAC
1 GGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGA-CAAAAATATCGACACAAAC
* *
12187 TAAAAAAGTGTCGACAAATTATTTAGACATATTCTCTCATAAAACCGGTAAACTTGTACCGGTTA
65 TAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTA
*
12252 GATTGAAAAATTACATATTACATTGTACTTTTGGTTTTCGATGTTTTTGGGATCGACACTTTCTA
130 GATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATCGACACTTTCTA
*
12317 TATAA
195 TATAT
12322 GGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAAC
1 GGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGA-CAAAAATATCGACACAAAC
*
12387 TAACAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTA
65 TAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTA
12452 GATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATCGACACTTTCTA
130 GATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATCGACACTTTCTA
12517 TATAT
195 TATAT
* * *
12522 GGATCGACACTTTATGGTTGCACCCTATTTTCCATTCATTCTGGACCAAACTATCGACACAAACT
1 GGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACAAAAATATCGACACAAACT
* *
12587 AAAAAACTGTCGACAAATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAG
66 AAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAG
12652 ATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATCGACACGTTT-TA
131 ATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATCGACAC-TTTCTA
12716 TATAT
195 TATAT
12721 GGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCCAAAAA-ATCGACACAAA
1 GGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGA--CAAAAATATCGACACAAA
* *
12785 CTAAAAACGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTATACTTGTACCGGTT
64 CTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTT
* * *
12850 AGATTGAAAAATTACATATTACATTATACTTTTGGTTTCCGAAGTTTTTGGGATCGACACTTTTT
129 AGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATCGACACTTTCT
12915 ATATAT
194 ATATAT
*
12921 GGTTCGACACTTTATGGTTGCACCCTGTT
1 GGATCGACACTTTATGGTTGCACCCTGTT
12950 GGCCATATTG
Statistics
Matches: 1168, Mismatches: 45, Indels: 22
0.95 0.04 0.02
Matches are distributed among these distances:
197 58 0.05
198 226 0.19
199 320 0.27
200 559 0.48
201 5 0.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (199 bp):
GGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACAAAAATATCGACACAAACT
AAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAG
ATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATCGACACTTTCTAT
ATAT
Found at i:12727 original size:399 final size:400
Alignment explanation
Indices: 11526--12949 Score: 2603
Period size: 399 Copynumber: 3.6 Consensus size: 400
11516 GATGTTTTTG
11526 GGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACAAAAAATATCGACACAAAC
1 GGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACAAAAAATATCGACACAAAC
11591 TAACAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTA
66 TAACAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTA
11656 GATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATCGACACTTTTTA
131 GATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATCGACACTTTTTA
* * *
11721 AATATGGATTGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAGCAAAATTATCGACA
196 TATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAGCAAAAATATCGACA
11786 CAAACT-AAAAAGTGTCGACAAATTATTTAGACATATTCTCTCATAAAACCGGTAAACTTGTACC
261 CAAACTAAAAAAGTGTCGACAAATTATTTAGACATATTCTCTCATAAAACCGGTAAACTTGTACC
11850 GGTTAGATTGAAAAATTACATATTACATTGTACTTTTGG-TTTCGATGTTTTTGGGATCGACACT
326 GGTTAGATTGAAAAATTACATATTACATTGTACTTTTGGTTTTCGATGTTTTTGGGATCGACACT
11914 TTCTATATAT
391 TTCTATATAT
*
11924 AGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACAAAAAATATCGACACAAAC
1 GGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACAAAAAATATCGACACAAAC
11989 TAACAAAGTGTCGACACATTATTTAGACATATTCTCT-A-AAAACCGGTATACTTGTACCGGTTA
66 TAACAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTA
12052 GATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATCGACACTTTTTA
131 GATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATCGACACTTTTTA
12117 TATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAGCAAAAATATCGACA
196 TATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAGCAAAAATATCGACA
12182 CAAACTAAAAAAGTGTCGACAAATTATTTAGACATATTCTCTCATAAAACCGGTAAACTTGTACC
261 CAAACTAAAAAAGTGTCGACAAATTATTTAGACATATTCTCTCATAAAACCGGTAAACTTGTACC
12247 GGTTAGATTGAAAAATTACATATTACATTGTACTTTTGGTTTTCGATGTTTTTGGGATCGACACT
326 GGTTAGATTGAAAAATTACATATTACATTGTACTTTTGGTTTTCGATGTTTTTGGGATCGACACT
*
12312 TTCTATATAA
391 TTCTATATAT
*
12322 GGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACAAAC
1 GGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACAAAAAATATCGACACAAAC
12387 TAACAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTA
66 TAACAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTA
*
12452 GATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATCGACACTTTCTA
131 GATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATCGACACTTTTTA
* * *
12517 TATATGGATCGACACTTTATGGTTGCACCCTATTTTCCATTCATTCTGGA-CCAAACTATCGACA
196 TATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAGCAAAAATATCGACA
* *
12581 CAAACTAAAAAACTGTCGACAAATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACC
261 CAAACTAAAAAAGTGTCGACAAATTATTTAGACATATTCTCTCATAAAACCGGTAAACTTGTACC
*
12646 GGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATCGACACG
326 GGTTAGATTGAAAAATTACATATTACATTGTACTTTTGGTTTTCGATGTTTTTGGGATCGACAC-
12711 TTT-TATATAT
390 TTTCTATATAT
*
12721 GGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCCAAAAA-ATCGACACAAA
1 GGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGA-CAAAAAATATCGACACAAA
*
12785 CTAA-AAACGTGTCGACACATTATTTAGACATATTATCTCATAAAACCGGTATACTTGTACCGGT
65 CTAACAAA-GTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGT
* *
12849 TAGATTGAAAAATTACATATTACATTATACTTTTGGTTTCCGAAGTTTTTGGGATCGACACTTTT
129 TAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATCGACACTTTT
*
12914 TATATATGGTTCGACACTTTATGGTTGCACCCTGTT
194 TATATATGGATCGACACTTTATGGTTGCACCCTGTT
12950 GGCCATATTG
Statistics
Matches: 998, Mismatches: 21, Indels: 13
0.97 0.02 0.01
Matches are distributed among these distances:
396 158 0.16
397 98 0.10
398 238 0.24
399 356 0.36
400 148 0.15
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (400 bp):
GGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACAAAAAATATCGACACAAAC
TAACAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTA
GATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATCGACACTTTTTA
TATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAGCAAAAATATCGACA
CAAACTAAAAAAGTGTCGACAAATTATTTAGACATATTCTCTCATAAAACCGGTAAACTTGTACC
GGTTAGATTGAAAAATTACATATTACATTGTACTTTTGGTTTTCGATGTTTTTGGGATCGACACT
TTCTATATAT
Found at i:13079 original size:18 final size:18
Alignment explanation
Indices: 13056--13116 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
13046 TCTCATTCAT
*
13056 AATTATATTCACATACAA
1 AATTATAATCACATACAA
**
13074 AATTATAAATCGTATACAA
1 AATTAT-AATCACATACAA
**
13093 AATTATAAATCTTATACAA
1 AATTAT-AATCACATACAA
13112 AATTA
1 AATTA
13117 ACCCTACATT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
18 6 0.16
19 32 0.84
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.34
Consensus pattern (18 bp):
AATTATAATCACATACAA
Found at i:13092 original size:19 final size:19
Alignment explanation
Indices: 13068--13116 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
13058 TTATATTCAC
13068 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
13087 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
13106 ATACAAAATTA
1 ATACAAAATTA
13117 ACCCTACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:14945 original size:33 final size:33
Alignment explanation
Indices: 14908--14972 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
14898 CATCTTAATA
*
14908 TCACCCCTTAACACCCCAACTTCTTTCACCACC
1 TCACCCCTCAACACCCCAACTTCTTTCACCACC
* *
14941 TCACCCCTCAACACCTCTACTTCTTTCACCAC
1 TCACCCCTCAACACCCCAACTTCTTTCACCAC
14973 TCCATCTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.23, C:0.51, G:0.00, T:0.26
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACC
Found at i:15034 original size:21 final size:21
Alignment explanation
Indices: 15010--15050 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
15000 CTTATGTCTC
15010 TCAAGTGTATCTTCGACTCTA
1 TCAAGTGTATCTTCGACTCTA
* *
15031 TCAAGTTTCTCTTCGACTCT
1 TCAAGTGTATCTTCGACTCT
15051 TGATTGTCTT
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:0.20, C:0.27, G:0.12, T:0.41
Consensus pattern (21 bp):
TCAAGTGTATCTTCGACTCTA
Found at i:17118 original size:24 final size:24
Alignment explanation
Indices: 17081--17133 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
17071 CCGTTCTATC
17081 TATTTTCAGAGGATAT-TTAGCTTA
1 TATTTTCAGAGGATATGTTA-CTTA
** *
17105 TATTTTCATCGGATATGTTATTTA
1 TATTTTCAGAGGATATGTTACTTA
17129 TATTT
1 TATTT
17134 AATCGATACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.53
Consensus pattern (24 bp):
TATTTTCAGAGGATATGTTACTTA
Found at i:17721 original size:181 final size:180
Alignment explanation
Indices: 17245--17719 Score: 664
Period size: 182 Copynumber: 2.6 Consensus size: 180
17235 CGTACTTACG
* * * *
17245 AAAGTATCGACACTTTCAATATATCCGGTATCATTTTACCGGTTTTATCATTTTGATACTTGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCA-TTTCATACTGGTTT
* * * *
17310 TATCATATTTTTACCTTTTATATCGTTGTGGATCGATATATTTTTTTTTAAAGTATCGACACATT
65 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACA--TTTTTTAAAAGTATCGACACATT
*
17375 ATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATTCTTATAT
128 ATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
* *
17428 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTCGTACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCA-TTTCATACTGGTTT
* * *
17493 TATCATATTTTTACATGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
65 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
* *
17558 AGGAC-TTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
130 AGG-CGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
* * * * *
17610 AAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTTACCGGTTTTATCATTTCAATACTGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTC-ATACTGGTTT
* * *
17675 TGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTT
65 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
17720 AATTTGGATC
Statistics
Matches: 261, Mismatches: 28, Indels: 7
0.88 0.09 0.02
Matches are distributed among these distances:
181 72 0.28
182 95 0.36
183 94 0.36
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.43
Consensus pattern (180 bp):
AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTCATACTGGTTTT
ATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTATA
GGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
Found at i:25566 original size:18 final size:18
Alignment explanation
Indices: 25556--25596 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
25546 CCCGTTGACC
25556 TGACCCGACCCGACCCGT
1 TGACCCGACCCGACCCGT
25574 TGACCCGACCCGACCCGT
1 TGACCCGACCCGACCCGT
25592 TGACC
1 TGACC
25597 GGCGTTGACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.17, C:0.49, G:0.22, T:0.12
Consensus pattern (18 bp):
TGACCCGACCCGACCCGT
Found at i:25590 original size:23 final size:23
Alignment explanation
Indices: 25535--25590 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
25525 ACCGGTCATA
* *
25535 ACCCGACCCAACCCGTTGACCTG
1 ACCCGACCCGACCCGTTGACCCG
25558 ACCCGACCCGACCCGTTGACCCG
1 ACCCGACCCGACCCGTTGACCCG
25581 ACCCGACCCG
1 ACCCGACCCG
25591 TTGACCGGCG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.20, C:0.52, G:0.20, T:0.09
Consensus pattern (23 bp):
ACCCGACCCGACCCGTTGACCCG
Found at i:28054 original size:24 final size:24
Alignment explanation
Indices: 28027--28142 Score: 146
Period size: 24 Copynumber: 4.8 Consensus size: 24
28017 TTCAATTTGA
28027 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
* *
28051 ATTCTGATCTAATA-TCTGACATAG
1 ATTCTGATCTGATACT-TGACATGG
*
28075 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
* *
28099 ATTCTGATCTAATACTTGACCTGG
1 ATTCTGATCTGATACTTGACATGG
*
28123 AGTT-TGATATGATACTTGAC
1 A-TTCTGATCTGATACTTGAC
28143 CTGATTTATG
Statistics
Matches: 80, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
23 1 0.01
24 76 0.95
25 3 0.04
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:28081 original size:48 final size:48
Alignment explanation
Indices: 28027--28142 Score: 164
Period size: 48 Copynumber: 2.4 Consensus size: 48
28017 TTCAATTTGA
28027 ATTCTGATCTGATACTTGACATGGATTCTGATCTAATA-TCTGACATAG
1 ATTCTGATCTGATACTTGACATGGATTCTGATCTAATACT-TGACATAG
* * *
28075 ATTCTGATCTGATACTTGACTTGGATTCTGATCTAATACTTGACCTGG
1 ATTCTGATCTGATACTTGACATGGATTCTGATCTAATACTTGACATAG
*
28123 AGTT-TGATATGATACTTGAC
1 A-TTCTGATCTGATACTTGAC
28143 CTGATTTATG
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
48 59 0.95
49 3 0.05
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (48 bp):
ATTCTGATCTGATACTTGACATGGATTCTGATCTAATACTTGACATAG
Found at i:33966 original size:21 final size:20
Alignment explanation
Indices: 33870--34007 Score: 68
Period size: 21 Copynumber: 6.8 Consensus size: 20
33860 TAAAAACATA
*
33870 AAATAAAATAAAAAATATAT
1 AAATAAAATAAAAAATAAAT
**
33890 -AATAGTGAT-AAAAATATAA-
1 AAATA-AAATAAAAAATA-AAT
** * *
33909 AAATAAACCAAAGAAAAAAAC
1 AAATAAAATAAA-AAATAAAT
* * *
33930 ATATAAACTACAAAAATAACT
1 AAATAAAATA-AAAAATAAAT
33951 AAAATAAAATAAAAAATAAAT
1 -AAATAAAATAAAAAATAAAT
* *
33972 CAAA-GAAATAAAAAATGAAGT
1 -AAATAAAATAAAAAAT-AAAT
*
33993 AATTAAAATAAAAAA
1 AAATAAAATAAAAAA
34008 AGAAAAGGAA
Statistics
Matches: 87, Mismatches: 21, Indels: 19
0.69 0.17 0.15
Matches are distributed among these distances:
19 11 0.13
20 24 0.28
21 42 0.48
22 10 0.11
ACGTcount: A:0.72, C:0.05, G:0.04, T:0.19
Consensus pattern (20 bp):
AAATAAAATAAAAAATAAAT
Found at i:34106 original size:19 final size:20
Alignment explanation
Indices: 34079--34116 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
34069 AAACATAAAT
*
34079 AATACTAATATTAATAAAAA
1 AATACTAATAATAATAAAAA
34099 AATA-TAATAATAATAAAA
1 AATACTAATAATAATAAAA
34117 TAAAATAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (20 bp):
AATACTAATAATAATAAAAA
Found at i:34111 original size:16 final size:16
Alignment explanation
Indices: 34090--34124 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
34080 ATACTAATAT
*
34090 TAATAAAAAAATATAA
1 TAATAAAAAAATAAAA
*
34106 TAATAATAAAATAAAA
1 TAATAAAAAAATAAAA
34122 TAA
1 TAA
34125 GACTTTAGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
TAATAAAAAAATAAAA
Found at i:35254 original size:27 final size:27
Alignment explanation
Indices: 35208--35265 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 27
35198 GACAAAATGA
35208 AATAAAATAAAAAGTAAATAAATAA-AT
1 AATAAAATAAAAAGTAAAT-AATAATAT
*
35235 AATAATAATAAATAGT-AATAATAATAT
1 AATAA-AATAAAAAGTAAATAATAATAT
35262 AATA
1 AATA
35266 TATACTATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 5 0.18
27 14 0.50
28 9 0.32
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (27 bp):
AATAAAATAAAAAGTAAATAATAATAT
Found at i:35281 original size:7 final size:7
Alignment explanation
Indices: 35228--35283 Score: 53
Period size: 7 Copynumber: 8.1 Consensus size: 7
35218 AAAGTAAATA
*
35228 AATAAAT
1 AATATAT
35235 AATA-AT
1 AATATAT
*
35241 AATAAAT
1 AATATAT
*
35248 AGTA-AT
1 AATATAT
35254 AATAATAT
1 AAT-ATAT
35262 AATATAT
1 AATATAT
*
35269 ACTATAT
1 AATATAT
35276 AATATAT
1 AATATAT
35283 A
1 A
35284 TGTTTCAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
6 10 0.24
7 27 0.64
8 5 0.12
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (7 bp):
AATATAT
Found at i:36796 original size:16 final size:17
Alignment explanation
Indices: 36777--36809 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
36767 AAATTAAAAT
36777 GAAAGAAAAAAA-GAAA
1 GAAAGAAAAAAATGAAA
36793 GAAAGAAAAAAATGAAA
1 GAAAGAAAAAAATGAAA
36810 AGAGTTAGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (17 bp):
GAAAGAAAAAAATGAAA
Found at i:37894 original size:5 final size:5
Alignment explanation
Indices: 37885--37926 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
37875 AAAAAAGGGC
* *
37885 AATAA CATAA AATAA AATAA AA-AA TAAAAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA -AATAA AATAA AATAA AA
37927 AATATAATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
4 2 0.06
5 28 0.88
6 2 0.06
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.17
Consensus pattern (5 bp):
AATAA
Found at i:37910 original size:7 final size:7
Alignment explanation
Indices: 37898--37954 Score: 53
Period size: 7 Copynumber: 7.6 Consensus size: 7
37888 AACATAAAAT
37898 AAAATAA
1 AAAATAA
37905 AAAATAA
1 AAAATAA
*
37912 AAAA-AT
1 AAAATAA
37918 AAAATAA
1 AAAATAA
37925 AAAATATA
1 AAAATA-A
37933 ATAATGATAA
1 A-AA--ATAA
37943 AAAATATA
1 AAAATA-A
37951 AAAA
1 AAAA
37955 ATGAACCAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
6 5 0.12
7 21 0.50
8 7 0.17
9 4 0.10
10 2 0.05
11 3 0.07
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (7 bp):
AAAATAA
Found at i:37910 original size:12 final size:12
Alignment explanation
Indices: 37891--37936 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
37881 GGGCAATAAC
37891 ATAAAATAAAATA
1 ATAAAATAAAA-A
37904 A-AAAATAAAAAA
1 ATAAAAT-AAAAA
37916 ATAAAATAAAAA
1 ATAAAATAAAAA
*
37928 ATATAATAA
1 ATAAAATAA
37937 TGATAAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
12 20 0.67
13 10 0.33
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (12 bp):
ATAAAATAAAAA
Found at i:37918 original size:20 final size:20
Alignment explanation
Indices: 37893--38059 Score: 90
Period size: 20 Copynumber: 8.1 Consensus size: 20
37883 GCAATAACAT
37893 AAAATAAAATAAAAAATAAA
1 AAAATAAAATAAAAAATAAA
*
37913 AAAATAAAATAAAAAATATA
1 AAAATAAAATAAAAAATAAA
* *
37933 ATAAT--GATAAAAAATATAA
1 AAAATAAAATAAAAAATA-AA
* **
37952 AAAATGAACCAACGAAAA-AAA
1 AAAATAAAATAA--AAAATAAA
* *
37973 GAAATAAAAATTACAAAAAATAATT
1 AAAAT-AAAA-T--AAAAAATAA-A
37998 AAAATAAAATAAAAAATAAA
1 AAAATAAAATAAAAAATAAA
* * *
38018 TCAAA-GAAATAAAAAATGAAG
1 -AAAATAAAATAAAAAAT-AAA
* * *
38039 TAATTAAAATAAAAAAGAAA
1 AAAATAAAATAAAAAATAAA
38059 A
1 A
38060 GGAAAAAAAT
Statistics
Matches: 109, Mismatches: 24, Indels: 28
0.68 0.15 0.17
Matches are distributed among these distances:
18 10 0.09
19 5 0.05
20 38 0.35
21 32 0.29
22 3 0.03
23 9 0.08
24 6 0.06
25 6 0.06
ACGTcount: A:0.75, C:0.03, G:0.05, T:0.17
Consensus pattern (20 bp):
AAAATAAAATAAAAAATAAA
Found at i:37933 original size:9 final size:9
Alignment explanation
Indices: 37891--37956 Score: 55
Period size: 9 Copynumber: 7.0 Consensus size: 9
37881 GGGCAATAAC
*
37891 ATAAAATAAA
1 ATAAAA-AAT
37901 ATAAAAAAT
1 ATAAAAAAT
37910 A-AAAAAAT
1 ATAAAAAAT
37918 AAAATAAAAAAT
1 ---ATAAAAAAT
*
37930 AT-AATAAT
1 ATAAAAAAT
37938 GATAAAAAAT
1 -ATAAAAAAT
37948 ATAAAAAAT
1 ATAAAAAAT
37957 GAACCAACGA
Statistics
Matches: 47, Mismatches: 3, Indels: 13
0.75 0.05 0.21
Matches are distributed among these distances:
8 12 0.26
9 16 0.34
10 11 0.23
11 1 0.02
12 7 0.15
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (9 bp):
ATAAAAAAT
Found at i:38011 original size:21 final size:20
Alignment explanation
Indices: 37987--38054 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 20
37977 TAAAAATTAC
*
37987 AAAAAATAATTAAAATAAAAT
1 AAAAAATAAAT-AAATAAAAT
*
38008 AAAAAATAAATCAAA-GAAAT
1 AAAAAATAAAT-AAATAAAAT
* *
38028 AAAAAATGAAGTAATTAAAAT
1 AAAAAAT-AAATAAATAAAAT
38049 AAAAAA
1 AAAAAA
38055 GAAAAGGAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
20 13 0.33
21 26 0.67
ACGTcount: A:0.75, C:0.01, G:0.04, T:0.19
Consensus pattern (20 bp):
AAAAAATAAATAAATAAAAT
Found at i:38147 original size:3 final size:3
Alignment explanation
Indices: 38115--38171 Score: 57
Period size: 3 Copynumber: 19.7 Consensus size: 3
38105 AGTAAACATA
* * *
38115 AAT AAT ACT AAT ATT AAT AAA AAT -AT AAT AAT AAT AAT AAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
38160 AA- AAT AA- AAT AA
1 AAT AAT AAT AAT AA
38172 GACTTTAGGG
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
2 6 0.14
3 35 0.80
4 3 0.07
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:38170 original size:26 final size:25
Alignment explanation
Indices: 38098--38171 Score: 78
Period size: 26 Copynumber: 2.8 Consensus size: 25
38088 AAATGGAACA
*
38098 AATATAAAGTAAACAT-AAATAATACT
1 AATATAAA-TAAA-ATAAAATAATAAT
* *
38124 AATATTAATAAAAATATAATAATAAT
1 AATATAAAT-AAAATAAAATAATAAT
38150 AATAATAAATAAAATAAAATAA
1 AAT-ATAAATAAAATAAAATAA
38172 GACTTTAGGG
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
25 3 0.08
26 32 0.80
27 5 0.12
ACGTcount: A:0.68, C:0.03, G:0.01, T:0.28
Consensus pattern (25 bp):
AATATAAATAAAATAAAATAATAAT
Found at i:38899 original size:41 final size:41
Alignment explanation
Indices: 38838--38925 Score: 149
Period size: 41 Copynumber: 2.1 Consensus size: 41
38828 TTCCGTGATG
* *
38838 GATTCGATGATGTTTGGTTTACTGTTTTTGACGTTGGCTTC
1 GATTTGATGATGTTTGGTTTACTGTTTTCGACGTTGGCTTC
*
38879 GATTTGATGATGTTTGGTTTACTGTTTTCGATGTTGGCTTC
1 GATTTGATGATGTTTGGTTTACTGTTTTCGACGTTGGCTTC
38920 GATTTG
1 GATTTG
38926 TTCTCTGGTT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.12, C:0.10, G:0.27, T:0.50
Consensus pattern (41 bp):
GATTTGATGATGTTTGGTTTACTGTTTTCGACGTTGGCTTC
Found at i:38911 original size:21 final size:20
Alignment explanation
Indices: 38845--38913 Score: 54
Period size: 21 Copynumber: 3.4 Consensus size: 20
38835 ATGGATTCGA
38845 TGATGTTTGGTTTACTGTTTT
1 TGATGTTTGGTTTACTG-TTT
* *
38866 TGACG-TTGGCTT-C-GATTT
1 TGATGTTTGGTTTACTG-TTT
38884 GATGATGTTTGGTTTACTGTTT
1 --TGATGTTTGGTTTACTGTTT
38906 TCGATGTT
1 T-GATGTT
38914 GGCTTCGATT
Statistics
Matches: 37, Mismatches: 5, Indels: 12
0.69 0.09 0.22
Matches are distributed among these distances:
18 4 0.11
19 1 0.03
20 11 0.30
21 16 0.43
22 4 0.11
23 1 0.03
ACGTcount: A:0.12, C:0.09, G:0.26, T:0.54
Consensus pattern (20 bp):
TGATGTTTGGTTTACTGTTT
Found at i:39344 original size:3 final size:3
Alignment explanation
Indices: 39336--39375 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
39326 AAAGTAAATA
*
39336 AAT AAT AAT AAT AAT AAT AAAT ACT AAT AAT AAT -AT AAT A
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT A
39376 TATACTATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:39351 original size:16 final size:17
Alignment explanation
Indices: 39332--39375 Score: 65
Period size: 16 Copynumber: 2.7 Consensus size: 17
39322 ATGAAAAGTA
39332 AATAA-ATAATAATAAT
1 AATAATATAATAATAAT
*
39348 AATAATA-AATACTAAT
1 AATAATATAATAATAAT
39364 AATAATATAATA
1 AATAATATAATA
39376 TATACTATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 20 0.80
17 5 0.20
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (17 bp):
AATAATATAATAATAAT
Found at i:39356 original size:19 final size:19
Alignment explanation
Indices: 39332--39370 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
39322 ATGAAAAGTA
39332 AATAAATAATAATAATAAT
1 AATAAATAATAATAATAAT
*
39351 AATAAATACTAATAATAAT
1 AATAAATAATAATAATAAT
39370 A
1 A
39371 TAATATATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (19 bp):
AATAAATAATAATAATAAT
Found at i:39453 original size:37 final size:37
Alignment explanation
Indices: 39412--39673 Score: 220
Period size: 37 Copynumber: 7.2 Consensus size: 37
39402 TTTTTAAACT
* ** *
39412 TTATATTATTTTTCTAAAATGTTTCCAAAACTATGTA
1 TTATATTATTTTTCAAAAATGTTTTAAAAACTATATA
*
39449 TTATA-TAGTTTTCAAAAATGATTTT-AAAACTATATA
1 TTATATTATTTTTCAAAAATG-TTTTAAAAACTATATA
* *
39485 TTATATAATTTTTCAAAAATATTTTTAAAAACTATATA
1 TTATATTATTTTTCAAAAAT-GTTTTAAAAACTATATA
* * *
39523 TTATATAAGTTTTCAAAAATATTTTAAAAACTATATA
1 TTATATTATTTTTCAAAAATGTTTTAAAAACTATATA
* *
39560 TTATATATTTATTTTC-AAAAT-ATTTAAAAAC--TATA
1 TTATAT-TAT-TTTTCAAAAATGTTTTAAAAACTATATA
* * * *
39595 -TATA-TATTTCTAAAAAACCGTTTTCAAAACTATATA
1 TTATATTATTTTTCAAAAA-TGTTTTAAAAACTATATA
* *
39631 TTATA-TATATTTT-AAAAATATTTTCAAAAACTATTTA
1 TTATATTAT-TTTTCAAAAATGTTTT-AAAAACTATATA
*
39668 ATATAT
1 TTATAT
39674 ACAGAGAAAA
Statistics
Matches: 185, Mismatches: 25, Indels: 29
0.77 0.10 0.12
Matches are distributed among these distances:
31 3 0.02
32 6 0.03
34 12 0.06
35 4 0.02
36 36 0.19
37 81 0.44
38 38 0.21
39 5 0.03
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.46
Consensus pattern (37 bp):
TTATATTATTTTTCAAAAATGTTTTAAAAACTATATA
Found at i:42548 original size:35 final size:35
Alignment explanation
Indices: 42407--42562 Score: 98
Period size: 35 Copynumber: 4.6 Consensus size: 35
42397 ATTATATAAC
*
42407 AATACATTAAATAGTTATATCAATTGAAATTAATT
1 AATACATTAAATAGTTATATCAATTAAAATTAATT
** * **
42442 AATACATTAAATAG-T-TA-CAATTTCAGTTTTTAT
1 AATACATTAAATAGTTATATCAATTAAAATTAAT-T
** ** *
42475 AATATTTTTCAT--TTAATATGC-A-TAAAATT-A-C
1 AATACATTAAATAGTT-ATAT-CAATTAAAATTAATT
42506 AATACATTAAATAGTTATATCAATTAAAATTAATT
1 AATACATTAAATAGTTATATCAATTAAAATTAATT
42541 AATACATTTAAA-AGTTTATATC
1 AATACA-TTAAATAG-TTATATC
42563 TCTTATATAT
Statistics
Matches: 88, Mismatches: 19, Indels: 27
0.66 0.14 0.20
Matches are distributed among these distances:
31 9 0.10
32 15 0.17
33 20 0.23
34 8 0.09
35 23 0.26
36 13 0.15
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (35 bp):
AATACATTAAATAGTTATATCAATTAAAATTAATT
Found at i:42897 original size:21 final size:19
Alignment explanation
Indices: 42867--42911 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 19
42857 TGACACATGT
42867 TTTACCTAATTAGAGATTAAA
1 TTTACCTAATTA-A-ATTAAA
*
42888 TTTACTTAATTAAATTAAA
1 TTTACCTAATTAAATTAAA
*
42907 ATTAC
1 TTTAC
42912 AGCTAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 10 0.45
20 1 0.05
21 11 0.50
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.42
Consensus pattern (19 bp):
TTTACCTAATTAAATTAAA
Found at i:42911 original size:19 final size:21
Alignment explanation
Indices: 42868--42911 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 21
42858 GACACATGTT
*
42868 TTACCTAATTAGAGATTAAAT
1 TTACCTAATTAGAGATTAAAA
*
42889 TTACTTAATTA-A-ATTAAAA
1 TTACCTAATTAGAGATTAAAA
42908 TTAC
1 TTAC
42912 AGCTAAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 10 0.48
20 1 0.05
21 10 0.48
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (21 bp):
TTACCTAATTAGAGATTAAAA
Found at i:43528 original size:16 final size:16
Alignment explanation
Indices: 43503--43547 Score: 74
Period size: 16 Copynumber: 2.8 Consensus size: 16
43493 CAAGAGCCCT
43503 AGAGGTGACACTTTTG
1 AGAGGTGACACTTTTG
43519 AG-GAGTGACACTTTTG
1 AGAG-GTGACACTTTTG
43535 AGAGGTGACACTT
1 AGAGGTGACACTT
43548 GGATTAAGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 1 0.04
16 25 0.93
17 1 0.04
ACGTcount: A:0.27, C:0.13, G:0.31, T:0.29
Consensus pattern (16 bp):
AGAGGTGACACTTTTG
Found at i:49029 original size:200 final size:200
Alignment explanation
Indices: 48686--49090 Score: 715
Period size: 200 Copynumber: 2.0 Consensus size: 200
48676 AATGTAAATG
48686 AATTTAGATAGCCATTAACTGAAACCCTATTATCAAGATAGCCAAAATCATCAAAGACTGGCATC
1 AATTTAGATAGCCATTAACTGAAACCCTATTATCAAGATAGCCAAAATCATCAAAGACTGGCATC
48751 AACTCTCACAGAAAGCAACAAGAATACATTAGATCAATGGAACCCTCGCCAGAATAAAACTCTCA
66 AACTCTCACAGAAAGCAACAAGAATACATTAGATCAATGGAACCCTCGCCAGAATAAAACTCTCA
48816 CAAAATGCAAAAATGAC-CTAAAAAGAACAATT-AAAACCCCTAAATCATATTTTAGAATGATTT
131 CAAAATGCAAAAATG-CTCTAAAAAGAACAATTGAAAA-CCCTAAATCATATTTTAGAATGATTT
48879 CCTCCCC
194 CCTCCCC
*
48886 AATTTAGATAGCCATTAACTGAAACCCTATTATCAAGATAGCCAAAATCGTCAAAGACTGGCATC
1 AATTTAGATAGCCATTAACTGAAACCCTATTATCAAGATAGCCAAAATCATCAAAGACTGGCATC
* * *
48951 AACTCTCACAGAATGCAACAGGAATTCATTAGATCAATGGAACCCTCGCCAGAATAAAACTCTCA
66 AACTCTCACAGAAAGCAACAAGAATACATTAGATCAATGGAACCCTCGCCAGAATAAAACTCTCA
* *
49016 TAAAATGCAAAAATGCTCTAAAAAGAACAATTGAAAACCCTAATTCATATTTTAGAATGATTTCC
131 CAAAATGCAAAAATGCTCTAAAAAGAACAATTGAAAACCCTAAATCATATTTTAGAATGATTTCC
*
49081 TCCCT
196 TCCCC
49086 AATTT
1 AATTT
49091 TCAGCTCTCA
Statistics
Matches: 196, Mismatches: 7, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
199 1 0.01
200 191 0.97
201 4 0.02
ACGTcount: A:0.42, C:0.22, G:0.11, T:0.24
Consensus pattern (200 bp):
AATTTAGATAGCCATTAACTGAAACCCTATTATCAAGATAGCCAAAATCATCAAAGACTGGCATC
AACTCTCACAGAAAGCAACAAGAATACATTAGATCAATGGAACCCTCGCCAGAATAAAACTCTCA
CAAAATGCAAAAATGCTCTAAAAAGAACAATTGAAAACCCTAAATCATATTTTAGAATGATTTCC
TCCCC
Done.