Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009112.1 Hibiscus syriacus cultivar Beakdansim tig00112593_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: 40861
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:1826 original size:742 final size:743
Alignment explanation
Indices: 1--2112 Score: 4163
Period size: 742 Copynumber: 2.8 Consensus size: 743
1 CAGAGTGTTAACTTAGCAATCAGATTCCATATGCTGAAAACTTCATGTTTATGTTTCAGACAGAT
1 CAGAGTGTTAACTTAGCAATCAGATTCCATATGCTGAAAACTTCATGTTTATGTTTCAGACAGAT
66 GAATAATTTCCTTCAAATTTGGCTCTGTATGTTCAATGTGTATTATTTAACCTGGTTAATGGTAA
66 GAATAATTTCCTTCAAATTTGGCTCTGTATGTTCAATGTGTATTATTTAACCTGGTTAATGGTAA
131 GATATAAACTGCACCTACCTCACTCTGCCTGTTCCAAAATTGATGTACTTCAAGCACTTTGGAAA
131 GATATAAACTGCACCTACCTCACTCTGCCTGTTCCAAAATTGATGTACTTCAAGCACTTTGGAAA
196 TTTTGTACATTATTGATGCTTTGTTTCATAGAAAGGTATAATGAGGATTTCCTTTTCTAGCTTAC
196 TTTTGTACATTATTGATGCTTTGTTTCATAGAAAGGTATAATGAGGATTTCCTTTTCTAGCTTAC
261 CTTTCCTTTCTCTTATCTTTTGGTCAAAATTCTCATAGAAAAAAATTGCAAGTTAAAAACCTTGT
261 CTTTCCTTTCTCTTATCTTTTGGTCAAAATTCTCATAGAAAAAAATTGCAAGTTAAAAACCTTGT
*
326 TCTTGATCCAAGCTTAGTGAAGAAAATAAATAAGGTTGTGCAGTTTGTCAACCATAACCTCAAAA
326 TCTTGATCCAAGCGTAGTGAAGAAAATAAATAAGGTTGTGCAGTTTGTCAACCATAACCTCAAAA
391 GGATATTGGGTGGGTGCTTGACTATAAAAGAAGCAATTTACTTCCTACCTATTGGTGTAATTAGC
391 GGATATTGGGTGGGTGCTTGACTATAAAAGAAGCAATTTACTTCCTACCTATTGGTGTAATTAGC
456 CATATGATCGTCAAATTACTGGGAGAATGGAAACAGGAGTGCGTGCCTAGGACTTTGAACCTCAT
456 CATATGATCGTCAAATTACTGGGAGAATGGAAACAGGAGTGCGTGCCTAGGACTTTGAACCTCAT
521 AATTCAAAACAAGTGTAGTTTTATATACAACTCAAACAATAACTAGGGTGTTAATCAATAGGAGT
521 AATTCAAAACAAGTGTAGTTTTATATACAACTCAAACAATAACTAGGGTGTTAATCAATAGGAGT
*
586 GCTGTTGGCCTTTTTTCTGTTTTAATGCTATATATGTAGTTTTATATACATTTTTTTCTTCTTTT
586 GCTATTGGCCTTTTTTCTGTTTTAATGCTATATATGTAG-TTTATATACATTTTTTTCTTCTTTT
651 ATGCAACATTCTGATTAAAACTTCAATGCATATTAACCTCACTTCAATAGTCAACTTTCTGACTG
650 ATGCAACATTCTGATTAAAACTTCAATGCATATTAACCTCACTTCAATAGTCAACTTTCTGACTG
716 AAACATGTCTCTGGTTCACCTGGTCTACC
715 AAACATGTCTCTGGTTCACCTGGTCTACC
745 CAGAGTGTTAACTTAGCAATCAGATTCCATATGCTGAAAACTTCATGTTTATGTTTCAGACAGAT
1 CAGAGTGTTAACTTAGCAATCAGATTCCATATGCTGAAAACTTCATGTTTATGTTTCAGACAGAT
*
810 GAATAATTTCCTTCAAATTTGGCTCTATATGTTCAATGTGTATTATTTAACCTGGTTAATGGTAA
66 GAATAATTTCCTTCAAATTTGGCTCTGTATGTTCAATGTGTATTATTTAACCTGGTTAATGGTAA
875 GATATAAACTGCACCTACCTCACTCTGCCTGTTCCAAAATTGATGTACTTCAAGCACTTTGGAAA
131 GATATAAACTGCACCTACCTCACTCTGCCTGTTCCAAAATTGATGTACTTCAAGCACTTTGGAAA
940 TTTTGTACATTATTGATGCTTTGTTTCATAGAAAGGTATAATGAGGATTTCCTTTTCTAGCTTAC
196 TTTTGTACATTATTGATGCTTTGTTTCATAGAAAGGTATAATGAGGATTTCCTTTTCTAGCTTAC
1005 CTTTCCTTTCTCTTATCTTTTGGTCAAAATTCTCATAGAAAAAAATTGCAAGTTAAAAACCTTGT
261 CTTTCCTTTCTCTTATCTTTTGGTCAAAATTCTCATAGAAAAAAATTGCAAGTTAAAAACCTTGT
1070 TCTTGATCCAAGCGTAGTGAAGAAAATAAATAAGGTTGTGCAGTTTGTCAACCATAACCTCAAAA
326 TCTTGATCCAAGCGTAGTGAAGAAAATAAATAAGGTTGTGCAGTTTGTCAACCATAACCTCAAAA
1135 GGATATTGGGTGGGTGCTTGACTATAAAAGAAGCAATTTACTTCCTACCTATTGGTGTAATTAGC
391 GGATATTGGGTGGGTGCTTGACTATAAAAGAAGCAATTTACTTCCTACCTATTGGTGTAATTAGC
1200 CATATGATCGTCAAATTACTGGGAGAATGGAAACAGGAGTGCGTGCCTAGGACTTTGAACCTCAT
456 CATATGATCGTCAAATTACTGGGAGAATGGAAACAGGAGTGCGTGCCTAGGACTTTGAACCTCAT
1265 AATTCAAAACAAGTGTAGTTTTATATACAACTCAAACAATAACTAGGGTGTTAATCAATAGGAGT
521 AATTCAAAACAAGTGTAGTTTTATATACAACTCAAACAATAACTAGGGTGTTAATCAATAGGAGT
1330 GCTATTGGCCTTTTTTCTGTTTT-ATGCTATATATGTAGTTTATATACATTTTTTTCTTCTTTTA
586 GCTATTGGCCTTTTTTCTGTTTTAATGCTATATATGTAGTTTATATACATTTTTTTCTTCTTTTA
1394 TGCAACATTCTGATTAAAACTTCAATGCATATTAACCTCACTTCAATAGTCAACTTTCTGACTGA
651 TGCAACATTCTGATTAAAACTTCAATGCATATTAACCTCACTTCAATAGTCAACTTTCTGACTGA
1459 AACATGTCTCTGGTTCACCTGGTCTACC
716 AACATGTCTCTGGTTCACCTGGTCTACC
1487 CAGAGTGTTAACTTAGCAATCAGATTCCATATGCTGAAAACTTCATGTTTATGTTTCAGACAGAT
1 CAGAGTGTTAACTTAGCAATCAGATTCCATATGCTGAAAACTTCATGTTTATGTTTCAGACAGAT
*
1552 GAATAATTTCCTTCAAATTTGGCTCTGTATGTTCAATGTGTATTATTTATCCTGGTTAATGGTAA
66 GAATAATTTCCTTCAAATTTGGCTCTGTATGTTCAATGTGTATTATTTAACCTGGTTAATGGTAA
1617 GATATAAACTGCACCTACCTCACTCTGCCTGTTCCAAAATTGATGTACTTCAAGCACTTTGGAAA
131 GATATAAACTGCACCTACCTCACTCTGCCTGTTCCAAAATTGATGTACTTCAAGCACTTTGGAAA
1682 TTTTGTACATTATTGATGCTTTGTTTCATAGAAAGGTATAATGAGGATTTCCTTTTCTAGCTTAC
196 TTTTGTACATTATTGATGCTTTGTTTCATAGAAAGGTATAATGAGGATTTCCTTTTCTAGCTTAC
1747 CTTTCCTTTCTCTTATCTTTTGGTCAAAATTCTCATAGAAAAAAATTGCAAGTTAAAAACCTTGT
261 CTTTCCTTTCTCTTATCTTTTGGTCAAAATTCTCATAGAAAAAAATTGCAAGTTAAAAACCTTGT
1812 TCTTGATCCAAGCGTAGTGAAGAAAATAAATAAGGTTGTGCAGTTTGTCAACCATAACCTCAAAA
326 TCTTGATCCAAGCGTAGTGAAGAAAATAAATAAGGTTGTGCAGTTTGTCAACCATAACCTCAAAA
1877 GGATATTGGGTGGGTGCTTGACTATAAAAGAAGCAATTTACTTCCTACCTATTGGTGTAATTAGC
391 GGATATTGGGTGGGTGCTTGACTATAAAAGAAGCAATTTACTTCCTACCTATTGGTGTAATTAGC
1942 CATATGATCGTCAAATTACTGGGAGAATGGAAACAGGAGTGCGTGCCTAGGACTTTGAACCTCAT
456 CATATGATCGTCAAATTACTGGGAGAATGGAAACAGGAGTGCGTGCCTAGGACTTTGAACCTCAT
2007 AATTCAAAACAAGTGTAGTTTTATATACAACTCAAACAATAACTAGGGTGTTAATCAATAGGAGT
521 AATTCAAAACAAGTGTAGTTTTATATACAACTCAAACAATAACTAGGGTGTTAATCAATAGGAGT
*
2072 GCTATTGGCCTTTTTTCTGTTTTAATGCTATATATGGAGTT
586 GCTATTGGCCTTTTTTCTGTTTTAATGCTATATATGTAGTT
2113 GCTGAGAATT
Statistics
Matches: 1361, Mismatches: 6, Indels: 3
0.99 0.00 0.00
Matches are distributed among these distances:
742 725 0.53
743 31 0.02
744 605 0.44
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (743 bp):
CAGAGTGTTAACTTAGCAATCAGATTCCATATGCTGAAAACTTCATGTTTATGTTTCAGACAGAT
GAATAATTTCCTTCAAATTTGGCTCTGTATGTTCAATGTGTATTATTTAACCTGGTTAATGGTAA
GATATAAACTGCACCTACCTCACTCTGCCTGTTCCAAAATTGATGTACTTCAAGCACTTTGGAAA
TTTTGTACATTATTGATGCTTTGTTTCATAGAAAGGTATAATGAGGATTTCCTTTTCTAGCTTAC
CTTTCCTTTCTCTTATCTTTTGGTCAAAATTCTCATAGAAAAAAATTGCAAGTTAAAAACCTTGT
TCTTGATCCAAGCGTAGTGAAGAAAATAAATAAGGTTGTGCAGTTTGTCAACCATAACCTCAAAA
GGATATTGGGTGGGTGCTTGACTATAAAAGAAGCAATTTACTTCCTACCTATTGGTGTAATTAGC
CATATGATCGTCAAATTACTGGGAGAATGGAAACAGGAGTGCGTGCCTAGGACTTTGAACCTCAT
AATTCAAAACAAGTGTAGTTTTATATACAACTCAAACAATAACTAGGGTGTTAATCAATAGGAGT
GCTATTGGCCTTTTTTCTGTTTTAATGCTATATATGTAGTTTATATACATTTTTTTCTTCTTTTA
TGCAACATTCTGATTAAAACTTCAATGCATATTAACCTCACTTCAATAGTCAACTTTCTGACTGA
AACATGTCTCTGGTTCACCTGGTCTACC
Found at i:7000 original size:36 final size:36
Alignment explanation
Indices: 6896--7002 Score: 151
Period size: 36 Copynumber: 3.0 Consensus size: 36
6886 TTAAACTAAG
* * *
6896 AATAAGTCTAGTTACCAAGTGACATGACTTATTATT
1 AATAAGTCTATTTATCAAGTGACATGACTTATTGTT
* *
6932 AATTAGTCTATTTATCAAGTGTCATGACTTATTGTT
1 AATAAGTCTATTTATCAAGTGACATGACTTATTGTT
* *
6968 AATAAGTCTATTTATCAAGTGACATAATTTATTGT
1 AATAAGTCTATTTATCAAGTGACATGACTTATTGT
7003 AAATTGTATT
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 62 1.00
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (36 bp):
AATAAGTCTATTTATCAAGTGACATGACTTATTGTT
Found at i:17769 original size:14 final size:14
Alignment explanation
Indices: 17740--17795 Score: 66
Period size: 14 Copynumber: 4.1 Consensus size: 14
17730 CGTTCGTGAA
17740 CGTTCGATTATATGTT
1 CGTTC-ATT-TATGTT
17756 CGTTCATTTA---T
1 CGTTCATTTATGTT
17767 -GTTCATTTATGTT
1 CGTTCATTTATGTT
17780 CGTTCATTTATGTT
1 CGTTCATTTATGTT
17794 CG
1 CG
17796 AACAGATGGT
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
10 9 0.25
11 1 0.03
13 1 0.03
14 17 0.47
15 3 0.08
16 5 0.14
ACGTcount: A:0.16, C:0.14, G:0.16, T:0.54
Consensus pattern (14 bp):
CGTTCATTTATGTT
Found at i:17782 original size:24 final size:26
Alignment explanation
Indices: 17741--17796 Score: 98
Period size: 24 Copynumber: 2.2 Consensus size: 26
17731 GTTCGTGAAC
17741 GTTCGATTATATGTTCGTTCATTTAT
1 GTTCGATTATATGTTCGTTCATTTAT
17767 GTTC-ATT-TATGTTCGTTCATTTAT
1 GTTCGATTATATGTTCGTTCATTTAT
17791 GTTCGA
1 GTTCGA
17797 ACAGATGGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
24 21 0.72
25 4 0.14
26 4 0.14
ACGTcount: A:0.18, C:0.12, G:0.16, T:0.54
Consensus pattern (26 bp):
GTTCGATTATATGTTCGTTCATTTAT
Found at i:18079 original size:13 final size:13
Alignment explanation
Indices: 18063--18112 Score: 61
Period size: 13 Copynumber: 4.1 Consensus size: 13
18053 TGTTGCTCGT
18063 TTATGTTCATTTA
1 TTATGTTCATTTA
*
18076 TTATGTTC--GT-
1 TTATGTTCATTTA
18086 TTATGTTCATTTA
1 TTATGTTCATTTA
*
18099 TTATGTTCGTTTA
1 TTATGTTCATTTA
18112 T
1 T
18113 GTTTGTTCGT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
10 8 0.26
11 1 0.03
12 1 0.03
13 21 0.68
ACGTcount: A:0.18, C:0.08, G:0.12, T:0.62
Consensus pattern (13 bp):
TTATGTTCATTTA
Found at i:18089 original size:23 final size:23
Alignment explanation
Indices: 18059--18115 Score: 114
Period size: 23 Copynumber: 2.5 Consensus size: 23
18049 TTTGTGTTGC
18059 TCGTTTATGTTCATTTATTATGT
1 TCGTTTATGTTCATTTATTATGT
18082 TCGTTTATGTTCATTTATTATGT
1 TCGTTTATGTTCATTTATTATGT
18105 TCGTTTATGTT
1 TCGTTTATGTT
18116 TGTTCGTTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.16, C:0.09, G:0.14, T:0.61
Consensus pattern (23 bp):
TCGTTTATGTTCATTTATTATGT
Found at i:19493 original size:25 final size:25
Alignment explanation
Indices: 19460--19516 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
19450 TTTGCTATGA
*
19460 ATATCATTTATATTTAG-GAATGAAT
1 ATATAATTT-TATTTAGAGAATGAAT
* *
19485 ATATAATTTTATTTTGAGAGTGAAT
1 ATATAATTTTATTTAGAGAATGAAT
*
19510 TTATAAT
1 ATATAAT
19517 ATTTTAAAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 6 0.22
25 21 0.78
ACGTcount: A:0.39, C:0.02, G:0.12, T:0.47
Consensus pattern (25 bp):
ATATAATTTTATTTAGAGAATGAAT
Found at i:28749 original size:25 final size:25
Alignment explanation
Indices: 28721--28779 Score: 91
Period size: 25 Copynumber: 2.4 Consensus size: 25
28711 GAAAGGGTAA
28721 AAAAAATTTAATCTTTGAACTTCAT
1 AAAAAATTTAATCTTTGAACTTCAT
* *
28746 AAAAAATTTAATCTTTGAATTTTAT
1 AAAAAATTTAATCTTTGAACTTCAT
*
28771 ATAAAATTT
1 AAAAAATTT
28780 TAATTATAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (25 bp):
AAAAAATTTAATCTTTGAACTTCAT
Found at i:29403 original size:23 final size:23
Alignment explanation
Indices: 29377--29424 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
29367 ATAAAGTACA
*
29377 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
29400 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
29423 AT
1 AT
29425 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:30175 original size:18 final size:18
Alignment explanation
Indices: 30152--30188 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
30142 CGAAATATAT
30152 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
30170 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
30188 A
1 A
30189 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:30418 original size:23 final size:23
Alignment explanation
Indices: 30392--30456 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
30382 ATGCGAGATA
30392 GATACCTATTACATTATATAAAC
1 GATACCTATTACATTATATAAAC
**
30415 GATACCTATTACATTATATAAGG
1 GATACCTATTACATTATATAAAC
* *
30438 GCTACCTATTACATCATAT
1 GATACCTATTACATTATAT
30457 GTTTACCTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.35
Consensus pattern (23 bp):
GATACCTATTACATTATATAAAC
Found at i:30837 original size:21 final size:20
Alignment explanation
Indices: 30807--30860 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 20
30797 GATAGACACT
*
30807 TTACAATATAACCATTACCTA
1 TTACATTATAACCA-TACCTA
*
30828 TTACATTATATAAACGATACCTA
1 TTACA-T-TAT-AACCATACCTA
30851 TTACATTATA
1 TTACATTATA
30861 TAAGGGCTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
20 1 0.04
21 8 0.29
22 1 0.04
23 14 0.50
24 4 0.14
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.37
Consensus pattern (20 bp):
TTACATTATAACCATACCTA
Found at i:30848 original size:23 final size:23
Alignment explanation
Indices: 30822--30884 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
30812 ATATAACCAT
30822 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
30845 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
30868 TACCTATTACATCATAT
1 TACCTATTACATTATAT
30885 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:31264 original size:429 final size:428
Alignment explanation
Indices: 30394--31412 Score: 1988
Period size: 429 Copynumber: 2.4 Consensus size: 428
30384 GCGAGATAGA
30394 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
1 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
*
30459 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAACTTA
66 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
30524 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTAATAA
131 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTAATAA
30589 TTTCATTTGCACAAAAAATATTTGATTGTTTTTATATTTTATAAATATTATTTAGAATTTTTAAT
196 TTTCATTTGCACAAAAAATATTTGATTGTTTTTATATTTTATAAATATTATTTAGAATTTTTAAT
30654 TTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAAT
261 TTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAAT
30719 ATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACA
326 ATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACA
30784 CTTTTATAAAAAGGATAGACACTTTACAATATAACCAT
391 CTTTTATAAAAAGGATAGACACTTTACAATATAACCAT
30822 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
1 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
30887 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
66 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
30952 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATA
131 TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGA-TTAATA
31017 ATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTAGAATTTTT
195 ATTTCATTTGCACAAAAAA-TATTTGATTGTTTTTATATTTTAT-AAATATTATTTAGAATTTTT
31082 AATTTAATAAT-A-ATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATT
258 AATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATT
31145 AATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGG
323 AATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGG
31210 ACACTTTTATAAAAAGGATAGACACTTTACAATATAACCAT
388 ACACTTTTATAAAAAGGATAGACACTTTACAATATAACCAT
31251 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
1 TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
31316 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
66 TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
31381 TGTAATTTATGTTTCAATTTTTTTAACAGTGT
131 TGTAATTTATGTTTCAATTTTTTTAACAGTGT
31413 ACTGCGAATT
Statistics
Matches: 587, Mismatches: 1, Indels: 5
0.99 0.00 0.01
Matches are distributed among these distances:
428 187 0.32
429 344 0.59
430 25 0.04
431 31 0.05
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.40
Consensus pattern (428 bp):
TACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGT
TTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTA
TGTAATTTATGTTTCAATTTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTAATAA
TTTCATTTGCACAAAAAATATTTGATTGTTTTTATATTTTATAAATATTATTTAGAATTTTTAAT
TTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAAT
ATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACA
CTTTTATAAAAAGGATAGACACTTTACAATATAACCAT
Found at i:31266 original size:21 final size:20
Alignment explanation
Indices: 31236--31289 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 20
31226 GATAGACACT
*
31236 TTACAATATAACCATTACCTA
1 TTACATTATAACCA-TACCTA
*
31257 TTACATTATATAAACGATACCTA
1 TTACA-T-TAT-AACCATACCTA
31280 TTACATTATA
1 TTACATTATA
31290 TAAGGGCTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
20 1 0.04
21 8 0.29
22 1 0.04
23 14 0.50
24 4 0.14
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.37
Consensus pattern (20 bp):
TTACATTATAACCATACCTA
Found at i:31277 original size:23 final size:23
Alignment explanation
Indices: 31251--31313 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
31241 ATATAACCAT
31251 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
31274 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
31297 TACCTATTACATCATAT
1 TACCTATTACATTATAT
31314 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:34180 original size:184 final size:184
Alignment explanation
Indices: 33871--34724 Score: 1604
Period size: 184 Copynumber: 4.7 Consensus size: 184
33861 TTTTAAATGG
* *
33871 TATGGACATAAAGTACCGACACAATATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
*
33936 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
34001 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
34055 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
34120 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
34185 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
34239 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
34304 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
*
34369 GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
* *
34423 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTGGCTCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
* *
34488 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTTC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
34553 GATGTGT-AAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
34606 TATGGACAT-AAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
**
34670 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTTTATTATAAT
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAAT
34725 ATGTTGAAAG
Statistics
Matches: 656, Mismatches: 14, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
182 105 0.16
183 54 0.08
184 497 0.76
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (184 bp):
TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
Found at i:36200 original size:3 final size:3
Alignment explanation
Indices: 36192--36278 Score: 84
Period size: 3 Copynumber: 29.0 Consensus size: 3
36182 ACTTGTTTGG
* * * **
36192 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * * * *
36240 AGC TTC ATC GTC ATC ATC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
36279 GTCAGCTTCA
Statistics
Matches: 65, Mismatches: 19, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.24, C:0.34, G:0.06, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:36215 original size:18 final size:18
Alignment explanation
Indices: 36192--36293 Score: 87
Period size: 18 Copynumber: 5.7 Consensus size: 18
36182 ACTTGTTTGG
36192 ATCATCATCTTCATCATC
1 ATCATCATCTTCATCATC
* *
36210 ATCATCATCATCGTCATC
1 ATCATCATCTTCATCATC
* ** * *
36228 ATCTTCATCGCCAGCTTC
1 ATCATCATCTTCATCATC
* *
36246 ATCGTCATCATCATCATC
1 ATCATCATCTTCATCATC
* *
36264 ATCGTCATCTTCATCGTC
1 ATCATCATCTTCATCATC
* *
36282 AGCTTCATCTTC
1 ATCATCATCTTC
36294 TGCGACCGAT
Statistics
Matches: 67, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 67 1.00
ACGTcount: A:0.23, C:0.34, G:0.07, T:0.36
Consensus pattern (18 bp):
ATCATCATCTTCATCATC
Found at i:36259 original size:42 final size:42
Alignment explanation
Indices: 36200--36290 Score: 146
Period size: 42 Copynumber: 2.2 Consensus size: 42
36190 GGATCATCAT
*
36200 CTTCATCATCATCATCATCATCGTCATCATCTTCATCGCCAG
1 CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
* * *
36242 CTTCATCGTCATCATCATCATCATCGTCATCTTCATCGTCAG
1 CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
36284 CTTCATC
1 CTTCATC
36291 TTCTGCGACC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.22, C:0.35, G:0.08, T:0.35
Consensus pattern (42 bp):
CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
Found at i:38738 original size:199 final size:199
Alignment explanation
Indices: 37746--39752 Score: 3627
Period size: 200 Copynumber: 10.1 Consensus size: 199
37736 TTTAAATTAG
* *
37746 TATCGACACAAAATATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
37811 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTC---GA-TTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
37872 CGACACTTTTTAAATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
37937 AAAA
196 AAAA
37941 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
38006 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
38071 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAA
131 CGACAC-TTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGGAA
38136 AAAAA
195 AAAAA
38141 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
38206 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
38271 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAA
131 CGACAC-TTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGGAA
38336 AAAAA
195 AAAAA
38341 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
38406 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
38471 CGACACTTTTTAAATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
38536 AAAA
196 AAAA
38540 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTA-T-TCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
38603 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
38668 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAA
131 CGACAC-TTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGG-A
38733 AAAAAA
194 AAAAAA
38739 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
38804 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
38869 CGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCTTG-TTTTAATTCATTCTGGG-A
131 CGACAC-TTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGGAA
38932 AAAAA
195 AAAAA
38937 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
39002 ATTGTACCGGTTAGATTGAAAAATTACATATTAC-TTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
39066 CGACAC-TTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGG-GAA
39130 AAAAA
195 AAAAA
39135 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
39200 ATTGTA-CGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
39264 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
39329 AAAA
196 AAAA
*
39333 TATCGACACAAACTATATTAGTATCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
* *
39398 ATTGTACCGGTTAGATTGAAAAATTACAGATTACATTATACTTTTGGTTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
39463 CGACACTTTTTATATAT-GATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCT-GGAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
39526 AAAA
196 AAAA
*
39530 TATCCACACAAACTATATTAGTGTCG--ACATTATTTAGA-TTATTCTCTCAT-AAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
*
39591 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
39656 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTG-TTTTAATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
39720 AAAA
196 AAAA
*
39724 TATCGACACAAACTATATTAGTATCGACA
1 TATCGACACAAACTATATTAGTGTCGACA
39753 TGACCCTTAA
Statistics
Matches: 1761, Mismatches: 32, Indels: 37
0.96 0.02 0.02
Matches are distributed among these distances:
193 104 0.06
194 69 0.04
195 161 0.09
196 17 0.01
197 182 0.10
198 394 0.22
199 295 0.17
200 412 0.23
201 127 0.07
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (199 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
AAAA
Found at i:39877 original size:19 final size:19
Alignment explanation
Indices: 39834--39877 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
39824 ATTCACATAA
*
39834 AAAAATATAAATCGTATAC
1 AAAATTATAAATCGTATAC
*
39853 -AAATTATAAATCTTATAC
1 AAAATTATAAATCGTATAC
39871 AAAATTA
1 AAAATTA
39878 ACTCGACATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.32
Consensus pattern (19 bp):
AAAATTATAAATCGTATAC
Done.