Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003206.1 Hibiscus syriacus cultivar Beakdansim tig00006746_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: 62100
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:1673 original size:31 final size:31
Alignment explanation
Indices: 1638--1703 Score: 132
Period size: 31 Copynumber: 2.1 Consensus size: 31
1628 CATCTTTTTT
1638 TCTATAATTCTTTTTACTCAACATTAATATA
1 TCTATAATTCTTTTTACTCAACATTAATATA
1669 TCTATAATTCTTTTTACTCAACATTAATATA
1 TCTATAATTCTTTTTACTCAACATTAATATA
1700 TCTA
1 TCTA
1704 ATTACGACTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.35, C:0.17, G:0.00, T:0.48
Consensus pattern (31 bp):
TCTATAATTCTTTTTACTCAACATTAATATA
Found at i:7596 original size:14 final size:14
Alignment explanation
Indices: 7579--7605 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
7569 CTGGGCAGAG
7579 TGCATCGATGCATA
1 TGCATCGATGCATA
7593 TGCATCGATGCAT
1 TGCATCGATGCAT
7606 CAAGGTTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (14 bp):
TGCATCGATGCATA
Found at i:7753 original size:64 final size:65
Alignment explanation
Indices: 7641--7795 Score: 158
Period size: 64 Copynumber: 2.4 Consensus size: 65
7631 GAAGGTGTAT
* * ** *
7641 CGATGCACATGTAGTGCATCGATGCA-CTCTTTTAAAATAAAAAGATCGAATGCA-ATTAGTGCA
1 CGATGCACAAGCAGTGCATCGATGCATCTCCATTAAAATAAAAACATCGAATGCATATTA-TGCA
*
7704 T
65 C
* * *
7705 CGATGCATAAGGCA-TGCATCGATGCATC-CCATTAATAAT-AAAACATCGAATGTATTTTATGC
1 CGATGCACAA-GCAGTGCATCGATGCATCTCCATTAA-AATAAAAACATCGAATGCATATTATGC
7767 AC
64 AC
*
7769 CGATGCACAAGTAGTGCATCGATGCAT
1 CGATGCACAAGCAGTGCATCGATGCAT
7796 ACCTTCATTA
Statistics
Matches: 75, Mismatches: 11, Indels: 10
0.78 0.11 0.10
Matches are distributed among these distances:
63 2 0.03
64 64 0.85
65 9 0.12
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (65 bp):
CGATGCACAAGCAGTGCATCGATGCATCTCCATTAAAATAAAAACATCGAATGCATATTATGCAC
Found at i:8213 original size:29 final size:29
Alignment explanation
Indices: 8170--8299 Score: 163
Period size: 29 Copynumber: 4.8 Consensus size: 29
8160 TATGTGATAT
8170 GAGAACATGACATGAGCTACATGATCACAA
1 GAGAA-ATGACATGAGCTACATGATCACAA
*
8200 GAGAAATGATATGAGCTACATGATCAC-A
1 GAGAAATGACATGAGCTACATGATCACAA
8228 -AG--A-GACATGAGCTAC---ATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
8250 GA-AAATGACATGAGCTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
*
8278 GAGAAATAACATGAG-TACATGA
1 GAGAAATGACATGAGCTACATGA
8300 ACATATAAAA
Statistics
Matches: 88, Mismatches: 3, Indels: 20
0.79 0.03 0.18
Matches are distributed among these distances:
21 5 0.06
22 1 0.01
23 1 0.01
24 12 0.14
25 13 0.15
27 2 0.02
28 17 0.19
29 32 0.36
30 5 0.06
ACGTcount: A:0.45, C:0.17, G:0.20, T:0.18
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGATCACAA
Found at i:8257 original size:49 final size:51
Alignment explanation
Indices: 8178--8281 Score: 167
Period size: 49 Copynumber: 2.0 Consensus size: 51
8168 ATGAGAACAT
*
8178 GACATGAGCTACATGATCACAAGAGAAATGATATGAGCTACATGATCACAAGA
1 GACATGAGCTACA--ATCACAAGAGAAATGACATGAGCTACATGATCACAAGA
8231 GACATGAGCTAC-ATCACAAGA-AAATGACATGAGCTACATGATCACAAGA
1 GACATGAGCTACAATCACAAGAGAAATGACATGAGCTACATGATCACAAGA
8280 GA
1 GA
8282 AATAACATGA
Statistics
Matches: 50, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
49 29 0.58
50 9 0.18
53 12 0.24
ACGTcount: A:0.44, C:0.18, G:0.20, T:0.17
Consensus pattern (51 bp):
GACATGAGCTACAATCACAAGAGAAATGACATGAGCTACATGATCACAAGA
Found at i:8402 original size:15 final size:15
Alignment explanation
Indices: 8384--8412 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
8374 GAGGGTATAA
8384 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGACG
8399 TAGTCCTTCGGGAC
1 TAGTCCTTCGGGAC
8413 ATATATGGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.28, G:0.31, T:0.28
Consensus pattern (15 bp):
TAGTCCTTCGGGACG
Found at i:14110 original size:21 final size:21
Alignment explanation
Indices: 14084--14124 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
14074 CTAGGCAGAG
14084 TTCATAGTGCATCGATGCATA
1 TTCATAGTGCATCGATGCATA
14105 TTCATAGTGCATCGATGCAT
1 TTCATAGTGCATCGATGCAT
14125 CAAGGTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.34
Consensus pattern (21 bp):
TTCATAGTGCATCGATGCATA
Found at i:14305 original size:63 final size:63
Alignment explanation
Indices: 14160--14313 Score: 154
Period size: 63 Copynumber: 2.4 Consensus size: 63
14150 GAAGGTGTAT
*** * * *
14160 CGATGCAC-AGATAGTGCATCGATGCACTTTTTTAAAATAAAAAGATTGAATGCAATTAGTGCAT
1 CGATGCACAAG-TAGTGCATCGATGCA-TCCATTAAAATAAAAACATCGAATGCAATTAGTGCAC
* * *
14224 CGATGCATAAGGCA-TGCATCGATGCATCCATTAATAAT-AAAACATCGAATGCATTTTA-TGCA
1 CGATGCACAA-GTAGTGCATCGATGCATCCATTAA-AATAAAAACATCGAATGCA-ATTAGTGCA
14286 C
63 C
14287 CGATGCACAAGTAGTGCATCGATGCAT
1 CGATGCACAAGTAGTGCATCGATGCAT
14314 ACCTTCATTA
Statistics
Matches: 74, Mismatches: 11, Indels: 11
0.77 0.11 0.11
Matches are distributed among these distances:
62 2 0.03
63 44 0.59
64 25 0.34
65 2 0.03
66 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (63 bp):
CGATGCACAAGTAGTGCATCGATGCATCCATTAAAATAAAAACATCGAATGCAATTAGTGCAC
Found at i:14731 original size:34 final size:29
Alignment explanation
Indices: 14689--14769 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
14679 TATGTGATAT
14689 GAGAACATGACATGAGCTACATGATCACAA
1 GAGAA-ATGACATGAGCTACATGATCACAA
14719 GAGAAATGACATGAGCTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
*
14748 GAGAAATGAAATGAG-TACATGA
1 GAGAAATGACATGAGCTACATGA
14770 ACATATAAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
28 7 0.14
29 38 0.76
30 5 0.10
ACGTcount: A:0.46, C:0.15, G:0.22, T:0.17
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGATCACAA
Found at i:14877 original size:15 final size:15
Alignment explanation
Indices: 14854--14887 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
14844 GAGGGTATAA
*
14854 TAGTTCTTCGGGACG
1 TAGTCCTTCGGGACG
*
14869 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGACG
14884 TAGT
1 TAGT
14888 GGTTCTACAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.18, G:0.32, T:0.35
Consensus pattern (15 bp):
TAGTCCTTCGGGACG
Found at i:19248 original size:23 final size:25
Alignment explanation
Indices: 19218--19269 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
19208 TTTACCCATT
19218 AATAAAAA-GTCATA-G-TTAAACTA
1 AATAAAAATGT-ATATGTTTAAACTA
19241 AATAAAAATGTATATGTTTAAACTA
1 AATAAAAATGTATATGTTTAAACTA
19266 AATA
1 AATA
19270 TATTTTTCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
23 11 0.42
24 3 0.12
25 12 0.46
ACGTcount: A:0.56, C:0.06, G:0.08, T:0.31
Consensus pattern (25 bp):
AATAAAAATGTATATGTTTAAACTA
Found at i:23711 original size:29 final size:30
Alignment explanation
Indices: 23663--23750 Score: 90
Period size: 29 Copynumber: 3.0 Consensus size: 30
23653 AAGAAGCTTG
** * *
23663 TCTCTATTTCTGCATTGCTACCTTTTAATG
1 TCTCTATTTGAGCACTGCTACCTTTTAATC
* *
23693 TCTGT-TTTGAGCACTGCTACTTTTTAATC
1 TCTCTATTTGAGCACTGCTACCTTTTAATC
*
23722 TCTCTATTTGAGCATTGCTA-CTTTCTAAT
1 TCTCTATTTGAGCACTGCTACCTTT-TAAT
23751 ATATAAGATT
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
29 26 0.55
30 21 0.45
ACGTcount: A:0.18, C:0.22, G:0.11, T:0.49
Consensus pattern (30 bp):
TCTCTATTTGAGCACTGCTACCTTTTAATC
Found at i:23734 original size:30 final size:30
Alignment explanation
Indices: 23663--23750 Score: 106
Period size: 30 Copynumber: 3.0 Consensus size: 30
23653 AAGAAGCTTG
** * *
23663 TCTCTATTTCTGCATTGCTACCTTTTAATG
1 TCTCTATTTGAGCATTGCTACTTTTTAATC
* *
23693 TCTGT-TTTGAGCACTGCTACTTTTTAATC
1 TCTCTATTTGAGCATTGCTACTTTTTAATC
*
23722 TCTCTATTTGAGCATTGCTACTTTCTAAT
1 TCTCTATTTGAGCATTGCTACTTTTTAAT
23751 ATATAAGATT
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
29 23 0.48
30 25 0.52
ACGTcount: A:0.18, C:0.22, G:0.11, T:0.49
Consensus pattern (30 bp):
TCTCTATTTGAGCATTGCTACTTTTTAATC
Found at i:32696 original size:23 final size:23
Alignment explanation
Indices: 32624--32688 Score: 112
Period size: 23 Copynumber: 2.8 Consensus size: 23
32614 ATACTTTACA
*
32624 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
32647 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
32670 ATATAAGCGCTACCTATTA
1 ATATAAGCGCTACCTATTA
32689 TATCATATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.38, C:0.22, G:0.06, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:33187 original size:23 final size:23
Alignment explanation
Indices: 33115--33179 Score: 112
Period size: 23 Copynumber: 2.8 Consensus size: 23
33105 ATACTTTACA
*
33115 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
33138 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
33161 ATATAAGCGCTACCTATTA
1 ATATAAGCGCTACCTATTA
33180 TATCATATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.38, C:0.22, G:0.06, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:33638 original size:23 final size:23
Alignment explanation
Indices: 33603--33675 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
33593 ATACTTTACA
*
33603 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
33626 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
33649 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
33672 ATAT
1 ATAT
33676 TTTTACTTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:33990 original size:489 final size:488
Alignment explanation
Indices: 32223--34016 Score: 3270
Period size: 488 Copynumber: 3.7 Consensus size: 488
32213 TTATAATATG
*
32223 TTGAAAGTGCCCATACTTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
1 TTGAAAGTGTCCATAC-TTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
* ** *
32288 TTCAA-TTTTTTAATAGTGTTTCATATTTTTTACCTACAATATTAATTTAATAATTTCATTTGCA
65 TTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACA
* *
32352 CAAAATATTATTTGATTGTTTT-ATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAT
130 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATAT
* *
32416 TAACCAAAGATAATAATAAATATGTAATATATATATTTTTTGTTTTTAATTTAATAATAATATAT
195 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATAT
* *
32481 ATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATTTTAAAACTCACT
260 ACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
32546 CAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATAAAAAGGA
325 CAAAAGATAA-CTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATAAAAAGGA
32611 TAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAA
389 TAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAA
32676 GCGCTACCTATTATATCATATTTTTACCTATTATA
454 GCGCTACCTATTATATCATATTTTTACCTATTATA
*
32711 TTGAAAGTGTCTATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
*
32776 TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTTATTTACAC
66 TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAC
32841 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATT
131 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATT
*
32906 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTTTTTTTTTAATTTAATAATAATATA
196 AACCAAAGATAATAATAAATATGTAATATATATGTTTA--TTGTTTTTAATTTAATAATAATATA
32971 TACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCAC
259 TACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCAC
*
33036 TCAAAAGATAATCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGG
324 TCAAAAGATAA-CTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATAAAAAGG
33101 ATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATA
388 ATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATA
33166 AGCGCTACCTATTATATCATATTTTTACCTATTATA
453 AGCGCTACCTATTATATCATATTTTTACCTATTATA
33202 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATAC-TTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
* * *
33266 TCAATTTTTTTAATAATGTTTTATGTTTTCCACCTACAATATTAATTTAATAATTTTATTTACAC
66 TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAC
33331 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATT
131 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATT
33396 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
196 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
* *
33461 CTGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATATTAAAACTCACTC
261 CCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
* *
33526 AAAAGATAACATTAAATTAATGTTTTCCACAGTGAAAAAAATATAGATACTTTTATAAAAAGGAT
326 AAAAGATAAC-TTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATAAAAAGGAT
33591 AGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAG
390 AGATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAG
* *
33656 CGCTACCTATTACATCATATTTTTACTTATTATA
455 CGCTACCTATTATATCATATTTTTACCTATTATA
* *
33690 TTGAAAGTGTCCATACTTTTTATAAAAGGGATCAATACTTTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
33755 TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAC
66 TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAC
33820 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATT
131 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATT
33885 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
196 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
*
33950 CCGCAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
261 CCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
34015 AA
326 AA
34017 CATATTAGGT
Statistics
Matches: 1265, Mismatches: 35, Indels: 11
0.96 0.03 0.01
Matches are distributed among these distances:
487 54 0.04
488 371 0.29
489 360 0.28
490 192 0.15
491 288 0.23
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.42
Consensus pattern (488 bp):
TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAC
AAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATT
AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
CCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC
AAAAGATAACTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATAAAAAGGATA
GATACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGC
GCTACCTATTATATCATATTTTTACCTATTATA
Found at i:34117 original size:87 final size:87
Alignment explanation
Indices: 34015--34234 Score: 413
Period size: 87 Copynumber: 2.5 Consensus size: 87
34005 AAACTCACTC
34015 AACATATTAGGTAACGCTTATATAATGTAATAGATAGCGCTTATATAATAAAATAGGTATTTAAC
1 AACATATTAGGTAACGCTTATATAATGTAATAGATAGCGCTTATATAATAAAATAGGTATTTAAC
*
34080 GGGAAATATTATCAAGTACAAT
66 GAGAAATATTATCAAGTACAAT
34102 AACATATTAGGTAACGCTTATATAATGTAATAGATAGCGCTTATATAATAAAATAGGTATTTAAC
1 AACATATTAGGTAACGCTTATATAATGTAATAGATAGCGCTTATATAATAAAATAGGTATTTAAC
34167 GAGAAATATTATCAAGTACAAT
66 GAGAAATATTATCAAGTACAAT
* *
34189 AACATATTAGGTAGCGCTTATATAATGTAATAGGTAGCGCTTATAT
1 AACATATTAGGTAACGCTTATATAATGTAATAGATAGCGCTTATAT
34235 TGACCTATTT
Statistics
Matches: 130, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
87 130 1.00
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (87 bp):
AACATATTAGGTAACGCTTATATAATGTAATAGATAGCGCTTATATAATAAAATAGGTATTTAAC
GAGAAATATTATCAAGTACAAT
Found at i:37658 original size:120 final size:120
Alignment explanation
Indices: 37445--37674 Score: 424
Period size: 120 Copynumber: 1.9 Consensus size: 120
37435 TTTTTCTTCC
*
37445 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCT
37510 AATAAAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
66 AATAAAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
*
37565 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCT
* *
37630 CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTA
66 AATAAAACCGGTATACTTATACCGGTTATATTACAAAATTATCTA
37675 AATGTCGACA
Statistics
Matches: 106, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
120 106 1.00
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (120 bp):
ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCT
AATAAAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
Found at i:38131 original size:183 final size:183
Alignment explanation
Indices: 37673--38304 Score: 1110
Period size: 183 Copynumber: 3.5 Consensus size: 183
37663 CAAAATTATC
37673 TAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCG
1 TAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCG
*
37738 ACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTAT
66 ACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTAT
37803 ACCGGTTATATTACAAAATTATCTATTACATTATAATTCT-GGTTCCGATGTG
131 ACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTG
37855 TAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCG
1 TAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCG
*
37920 ACACAATATTAAAAAGTGTCGATATAGGTTTTAGACCTATTCGCTCATAAAACCGGTATATTTAT
66 ACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTAT
*
37985 ACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTTCGATGTG
131 ACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTG
*
38038 TAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTTCATTCTGGACATAAAGTACCG
1 TAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCG
* *
38103 ACACAATATTAAAAAGTATCGATATAGGTTGTAGGCCTATTCGCTCATAAAACCGGTATATTTAT
66 ACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTAT
* * *
38168 ACCGATTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTTTTT
131 ACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATG---TG
* *
38224 TCAA--TCGACACTTTTTGAAAAGGTATCGACACA-TTTTCTTCCATTCTGGACATAAAGTACCG
1 TAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCG
38286 ACACAATATTAAAAAGTGT
66 ACACAATATTAAAAAGTGT
38305 GAAAACTTTG
Statistics
Matches: 431, Mismatches: 15, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
182 168 0.39
183 231 0.54
184 28 0.06
186 4 0.01
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.35
Consensus pattern (183 bp):
TAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCG
ACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTAT
ACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTG
Found at i:39517 original size:9 final size:9
Alignment explanation
Indices: 39502--39535 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
39492 TACTTGTTTG
39502 GATCATCAT
1 GATCATCAT
*
39511 CATCATCAT
1 GATCATCAT
39520 GATCATCAT
1 GATCATCAT
39529 GATCATC
1 GATCATC
39536 GTCAGCTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (9 bp):
GATCATCAT
Found at i:41403 original size:200 final size:200
Alignment explanation
Indices: 41019--41980 Score: 1606
Period size: 200 Copynumber: 4.8 Consensus size: 200
41009 AAACATTAAC
* * * * * *
41019 AGTGTCGATACA-TATTATATACC-AATCTCCCATAAACCCGATATACTTATACCGGTTAGATTG
1 AGTGTCGATACATTATT-TAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTG
* * *
41082 AAAAATTACCTAATACATTATACTTTTGGGTTTCGATGTTTATGGGATCGGCACTTTTTATATAT
65 AAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATAT
* * *
41147 GGATTGACACTTTATGGTTGCACCCTGTTTGACATTCATTCTGGACCAAAAATATCGACACAAAC
130 GGATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAAC
*
41212 TACAAA
195 TAAAAA
* *
41218 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTATCGGTTAGATTGA
1 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
41283 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
*
41348 GATTGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
131 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
41413 AAAAA
196 AAAAA
*
41418 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACTGGTATACTTGTACCGGTTAGATTGA
1 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
41483 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
* *
41548 GAACGGCACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
131 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
41613 AAAAA
196 AAAAA
* *
41618 AGTGTCGATACATTAGTTAGACTTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
1 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
* * *
41683 AAAATTACCTATTACATTATACTTATGGGTTTCAATGTTTATCGGATCGACAC-TTTTATATATT
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
* *
41747 GATCGACACTTTATTGTTGCACACTGTTTGACATTCATTCTGGACCAAAAATATCGACACAAACT
131 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
*
41812 ACAAA
196 AAAAA
* *
41817 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCAGTATACTTGTACCGATTAGATTGA
1 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
*
41882 AAAATTACCTATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
* *
41947 GATCGACACTTTATGGTTGCACCTTGTTTGCCAT
131 GATCGACACTTTATTGTTGCACCCTGTTTGCCAT
41981 ATTGTAAATT
Statistics
Matches: 717, Mismatches: 43, Indels: 5
0.94 0.06 0.01
Matches are distributed among these distances:
199 202 0.28
200 515 0.72
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (200 bp):
AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
AAAAA
Found at i:42225 original size:18 final size:18
Alignment explanation
Indices: 42202--42262 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
42192 TCTCATTCAT
*
42202 AATTATATTCACATACAA
1 AATTATAATCACATACAA
**
42220 AATTATAAATCGTATACAA
1 AATTAT-AATCACATACAA
**
42239 AATTATAAATCTTATACAA
1 AATTAT-AATCACATACAA
42258 AATTA
1 AATTA
42263 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:42238 original size:19 final size:19
Alignment explanation
Indices: 42214--42262 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
42204 TTATATTCAC
42214 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
42233 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
42252 ATACAAAATTA
1 ATACAAAATTA
42263 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:44160 original size:20 final size:20
Alignment explanation
Indices: 44123--44186 Score: 92
Period size: 21 Copynumber: 3.1 Consensus size: 20
44113 CCCCTTATGC
*
44123 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGT-TCTCTTCGACT
44144 CTCTCAAGTTCTCTTCGACT
1 CTCTCAAGTTCTCTTCGACT
*
44164 CTATCAAGTTTCTCTTCGACT
1 CTCTCAAG-TTCTCTTCGACT
44185 CT
1 CT
44187 TGATTGTCTT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
20 17 0.43
21 23 0.57
ACGTcount: A:0.17, C:0.31, G:0.11, T:0.41
Consensus pattern (20 bp):
CTCTCAAGTTCTCTTCGACT
Found at i:46582 original size:20 final size:20
Alignment explanation
Indices: 46536--46596 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
46526 ATCGGTAACG
46536 TTTTACCGGTTTTATCATTT
1 TTTTACCGGTTTTATCATTT
**
46556 TGATACCGGTTTTATCATTT
1 TTTTACCGGTTTTATCATTT
*
46576 TTTTACCTGG-TATATCATTT
1 TTTTACC-GGTTTTATCATTT
46596 T
1 T
46597 GGATCGATAC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
20 33 0.94
21 2 0.06
ACGTcount: A:0.18, C:0.15, G:0.11, T:0.56
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATTT
Found at i:46626 original size:180 final size:182
Alignment explanation
Indices: 46324--46792 Score: 669
Period size: 180 Copynumber: 2.6 Consensus size: 182
46314 CGTACTTACA
* *
46324 AAAGTATCGACACTTTCAATATATCCGGTATCGTTTTA-CGGTTTTATCATTTTGATACCGATTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * * * *
46388 TATCATATTTTTA-CTGTTATATCGTTGTGGATTGATATATTTTTTTTAAAGTATCGACACATTA
66 TATCATATTTTTACCTGTTATATCATTTTGGATCGATACA-TTTTTTAAAAGTATCGACACATTA
* *
46452 TAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
130 TAGGAGCTAAAACTGCTTATCTTTTAAATTCACAAAGTGTCGATCCTTATATT
46504 AAAGTATCGACACTTTCAATATAT-CGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
46568 TATCATTTTTTTACCTGGTATATCATTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCATTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
** *
46633 AGGATTTAAAACTGCTTATCTTTTAAATTCACGAAGTGTCGATCCTTATATT
131 AGGAGCTAAAACTGCTTATCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* * * * * * *
46685 AAAGTACCGACAC-TTAAATGTATCCGGTAGCGCTTTACCGGTTTTATCATTTTAATATCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
46749 TGTCATAGTTTTACCTGTTATATCATTTTGGATCGACACATTTT
66 TATCATATTTTTACCTGTTATATCATTTTGGATCGATACATTTT
46793 AATTTGGATC
Statistics
Matches: 258, Mismatches: 27, Indels: 7
0.88 0.09 0.02
Matches are distributed among these distances:
179 12 0.05
180 137 0.53
181 109 0.42
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (182 bp):
AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCATTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
AGGAGCTAAAACTGCTTATCTTTTAAATTCACAAAGTGTCGATCCTTATATT
Found at i:48074 original size:26 final size:27
Alignment explanation
Indices: 48012--48081 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 27
48002 ATGTTATTTT
* *
48012 ATTTTATTTTTA-TTTTTATTTTTAAC
1 ATTTTATTATTATTTTTTATTTCTAAC
48038 ATTTTACTTATTATTTTTTATTTCTAAC
1 ATTTTA-TTATTATTTTTTATTTCTAAC
* *
48066 CTTTT-TTATTCTTTTT
1 ATTTTATTATTATTTTT
48082 GCTTCTCTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
26 16 0.42
27 5 0.13
28 17 0.45
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.71
Consensus pattern (27 bp):
ATTTTATTATTATTTTTTATTTCTAAC
Found at i:51649 original size:23 final size:24
Alignment explanation
Indices: 51601--51651 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
51591 TTCTCTTGTG
* *
51601 ATCATGTATCTCATATCACTTTAT
1 ATCATGTATCTCATATCACGTCAT
*
51625 ATCATGT-TCTCATATCAGGTCAT
1 ATCATGTATCTCATATCACGTCAT
51648 ATCA
1 ATCA
51652 CATATCATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.29, C:0.22, G:0.08, T:0.41
Consensus pattern (24 bp):
ATCATGTATCTCATATCACGTCAT
Found at i:52084 original size:64 final size:63
Alignment explanation
Indices: 52004--52147 Score: 200
Period size: 64 Copynumber: 2.3 Consensus size: 63
51994 TATAAAAGGT
** * **
52004 ATTCGATGTATTATTATTGCTGGGATGCATCGATGCACTCCTTATGTATCGATGCACCAATTGC
1 ATTCGATGT-TTATTATTAATGGGATGCATCGATGCACTACTTATACATCGATGCACCAATTGC
**
52068 ATTCGATGTTTCATTATTAATGGGATGCATCGATGCACTACTTATACATCGATGCATGAATTGC
1 ATTCGATGTTT-ATTATTAATGGGATGCATCGATGCACTACTTATACATCGATGCACCAATTGC
52132 ATTCGATGTTT-TTATT
1 ATTCGATGTTTATTATT
52148 TTAAAAGAGT
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
62 5 0.07
63 2 0.03
64 65 0.90
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.39
Consensus pattern (63 bp):
ATTCGATGTTTATTATTAATGGGATGCATCGATGCACTACTTATACATCGATGCACCAATTGC
Found at i:52182 original size:64 final size:64
Alignment explanation
Indices: 52027--52189 Score: 188
Period size: 64 Copynumber: 2.5 Consensus size: 64
52017 TTATTGCTGG
* * *
52027 GATGCATCGATGCACT-CCTTATGTATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGG
1 GATGCATCGATGCACTACC-TATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGA
* * ** *
52091 GATGCATCGATGCACTACTTATACATCGATGCATGAATTGCATTCGATGTTTTTATT-TTAAA-A
1 GATGCATCGATGCACTACCTATGCATCGATGCACCAATTGCATTCGATG-TTTCATTATTAAAGA
* *
52154 GAGTGCATCGATGCACTACCAATGCATCGATACACC
1 GA-TGCATCGATGCACTACCTATGCATCGATGCACC
52190 TTCAAACAAT
Statistics
Matches: 82, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
63 2 0.02
64 73 0.89
65 7 0.09
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (64 bp):
GATGCATCGATGCACTACCTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGA
Found at i:61829 original size:21 final size:23
Alignment explanation
Indices: 61778--61829 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
61768 GATTCCACTG
61778 TGGGGGGAATCGGTTCCCCTTCA
1 TGGGGGGAATCGGTTCCCCTTCA
**
61801 AAGGGGGAATCGGTT-CCC-TCA
1 TGGGGGGAATCGGTTCCCCTTCA
61822 TGGGGGGA
1 TGGGGGGA
61830 TCGATCCCTC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 9 0.36
22 3 0.12
23 13 0.52
ACGTcount: A:0.17, C:0.21, G:0.40, T:0.21
Consensus pattern (23 bp):
TGGGGGGAATCGGTTCCCCTTCA
Done.