Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003648.1 Hibiscus syriacus cultivar Beakdansim tig00007754_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: 52087
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.33
Found at i:3352 original size:14 final size:14
Alignment explanation
Indices: 3333--3363 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3323 TCTTCTCATT
*
3333 TCTCTATTTCTCTC
1 TCTCTATCTCTCTC
3347 TCTCTATCTCTCTC
1 TCTCTATCTCTCTC
3361 TCT
1 TCT
3364 AAAATAGAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.06, C:0.39, G:0.00, T:0.55
Consensus pattern (14 bp):
TCTCTATCTCTCTC
Found at i:4238 original size:10 final size:10
Alignment explanation
Indices: 4223--4259 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
4213 GAGTCTTGTA
4223 ATAATAATAT
1 ATAATAATAT
4233 ATAATAATAT
1 ATAATAATAT
*
4243 -T-ATTATAT
1 ATAATAATAT
4251 ATAATAATA
1 ATAATAATA
4260 CAATATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
8 6 0.26
9 2 0.09
10 15 0.65
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
ATAATAATAT
Found at i:4592 original size:93 final size:96
Alignment explanation
Indices: 4495--4669 Score: 257
Period size: 97 Copynumber: 1.8 Consensus size: 96
4485 AAATGATTTG
* * ** *
4495 CTTCACTACTCTTTTGTGAAGGTTGAA-T-TTAAC-TGAGAAGAATTTGTTTCACTACTCTTCTA
1 CTTCACTACTCTTATATGAAGGTTGAATTATTAACTTGAGAAGAACCTGTTTCACTACTCTTCCA
4557 TGAAGATCAGATTCGAGGTTCGCTTGAATTA
66 TGAAGATCAGATTCGAGGTTCGCTTGAATTA
*
4588 CTTCACTACTCTTATATGAAGGTTGAATTGATTGACTTGAGAAGAACCTGTTTCACTACTCTTCC
1 CTTCACTACTCTTATATGAAGGTTGAATT-ATTAACTTGAGAAGAACCTGTTTCACTACTCTTCC
*
4653 ATGAAGATTAGATTCGA
65 ATGAAGATCAGATTCGA
4670 AGTTGGGATA
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
93 25 0.35
94 1 0.01
96 4 0.06
97 41 0.58
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (96 bp):
CTTCACTACTCTTATATGAAGGTTGAATTATTAACTTGAGAAGAACCTGTTTCACTACTCTTCCA
TGAAGATCAGATTCGAGGTTCGCTTGAATTA
Found at i:4657 original size:97 final size:91
Alignment explanation
Indices: 4495--4767 Score: 279
Period size: 93 Copynumber: 2.9 Consensus size: 91
4485 AAATGATTTG
* * *
4495 CTTCACTACTCTTTTGTGAAGGTTGAAT--TTAAC-TGAGAAGAATTTGTTTCACTACTCTTCTA
1 CTTCACTACTCTTTTATGAAGGTTGAATGATTGACTTGAGAAGAATCTGTTTCACTACTCTTCTA
4557 TGAAGATCAGATTCGAGGTTCGCTTGAATTA
66 TGAAGATCAGATTCGAGGTT-G---GAA-TA
* * *
4588 CTTCACTACTCTTATATGAAGGTTGAATTGATTGACTTGAGAAGAACCTGTTTCACTACTCTTCC
1 CTTCACTACTCTTTTATGAAGGTTGAA-TGATTGACTTGAGAAGAATCTGTTTCACTACTCTTCT
* * *
4653 ATGAAGATTAGATTCGAAGTTGGGATA
65 ATGAAGATCAGATTCGAGGTTGGAATA
* *
4680 CTTCACTACT-TTTTCGA-GAAGGCTGAAAATGATTGACTTGA-ACAGAATCTATTTCACTACTC
1 CTTCACTACTCTTTT--ATGAAGGTTG--AATGATTGACTTGAGA-AGAATCTGTTTCACTACTC
* * *
4742 TTTTATGATGGTCAGATTCGAGGTTG
61 TTCTATGAAGATCAGATTCGAGGTTG
4768 ATTTACTTCC
Statistics
Matches: 152, Mismatches: 19, Indels: 18
0.80 0.10 0.10
Matches are distributed among these distances:
91 3 0.02
92 20 0.13
93 77 0.51
94 3 0.02
96 5 0.03
97 44 0.29
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (91 bp):
CTTCACTACTCTTTTATGAAGGTTGAATGATTGACTTGAGAAGAATCTGTTTCACTACTCTTCTA
TGAAGATCAGATTCGAGGTTGGAATA
Found at i:4787 original size:93 final size:92
Alignment explanation
Indices: 4541--4794 Score: 253
Period size: 93 Copynumber: 2.7 Consensus size: 92
4531 GAAGAATTTG
* **
4541 TTTCACTACTCTTCTATGAAGATCAGATTCGAGGTTCGCTTGAATTACTTCACTACTCTTATATG
1 TTTCACTACTCTTCTATGAAGATCAGATTCGA-G---G-TTGAATTACTTCACTACTTTTCGATG
* * *
4606 AAGGTTGAATTGATTGACTTGAGAAGAACCTG
61 AAGGCTGAAATGATTGACTTGAGAAGAACCTA
* * * *
4638 TTTCACTACTCTTCCATGAAGATTAGATTCGAAGTTGGGA-TACTTCACTACTTTTTCGA-GAAG
1 TTTCACTACTCTTCTATGAAGATCAGATTCGAGGTT-GAATTACTTCACTAC-TTTTCGATGAAG
*
4701 GCTGAAAATGATTGACTTGA-ACAGAATCTA
64 GCTG-AAATGATTGACTTGAGA-AGAACCTA
* * * * *
4731 TTTCACTACTCTTTTATGATGGTCAGATTCGAGGTTGATTTACTTCCACTACTTTTCCATGAAG
1 TTTCACTACTCTTCTATGAAGATCAGATTCGAGGTTGAATTACTT-CACTACTTTTCGATGAAG
4795 AGTTCTTACA
Statistics
Matches: 130, Mismatches: 20, Indels: 17
0.78 0.12 0.10
Matches are distributed among these distances:
92 22 0.17
93 68 0.52
94 10 0.08
97 30 0.23
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.37
Consensus pattern (92 bp):
TTTCACTACTCTTCTATGAAGATCAGATTCGAGGTTGAATTACTTCACTACTTTTCGATGAAGGC
TGAAATGATTGACTTGAGAAGAACCTA
Found at i:4873 original size:20 final size:20
Alignment explanation
Indices: 4850--4928 Score: 113
Period size: 20 Copynumber: 4.0 Consensus size: 20
4840 CTAATAGATG
*
4850 ACCCGAAGGATTTACAAATT
1 ACCCGAAGGCTTTACAAATT
*
4870 ACCCGAAGGCTTTACAAAAT
1 ACCCGAAGGCTTTACAAATT
*
4890 ACCCGAAGGCTTTACAAATG
1 ACCCGAAGGCTTTACAAATT
* *
4910 ACCCGGAGGCTTTATAAAT
1 ACCCGAAGGCTTTACAAAT
4929 AACCTGGAGG
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.23
Consensus pattern (20 bp):
ACCCGAAGGCTTTACAAATT
Found at i:4937 original size:20 final size:20
Alignment explanation
Indices: 4850--4941 Score: 96
Period size: 20 Copynumber: 4.6 Consensus size: 20
4840 CTAATAGATG
* * *
4850 ACCCGAAGGATTTACAAATT
1 ACCCGGAGGCTTTACAAATA
*
4870 ACCCGAAGGCTTTACAAA-A
1 ACCCGGAGGCTTTACAAATA
* *
4889 TACCCGAAGGCTTTACAAATG
1 -ACCCGGAGGCTTTACAAATA
*
4910 ACCCGGAGGCTTTATAAATA
1 ACCCGGAGGCTTTACAAATA
*
4930 ACCTGGAGGCTT
1 ACCCGGAGGCTT
4942 GACCCGAATG
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
20 63 1.00
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.23
Consensus pattern (20 bp):
ACCCGGAGGCTTTACAAATA
Found at i:8115 original size:21 final size:21
Alignment explanation
Indices: 8091--8207 Score: 103
Period size: 21 Copynumber: 5.4 Consensus size: 21
8081 CACTGAAGTG
8091 CCACATAATTATCCCGAAGGA
1 CCACATAATTATCCCGAAGGA
* *
8112 CCACATAATTTTGCACCGAAGTA
1 CCACATAATTAT-C-CCGAAGGA
* *
8135 CCATATAGGTT-TGCACCGAAGTG-
1 CCACATA-ATTAT-C-CCGAAG-GA
* *
8158 CCACATATTTATCTCGAAGGA
1 CCACATAATTATCCCGAAGGA
8179 CCACATAATTATCCCGAAGGA
1 CCACATAATTATCCCGAAGGA
*
8200 CCATATAA
1 CCACATAA
8208 ACCCTCGACT
Statistics
Matches: 79, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
20 1 0.01
21 42 0.53
22 4 0.05
23 30 0.38
24 2 0.03
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.24
Consensus pattern (21 bp):
CCACATAATTATCCCGAAGGA
Found at i:8137 original size:23 final size:23
Alignment explanation
Indices: 8077--8188 Score: 90
Period size: 23 Copynumber: 5.0 Consensus size: 23
8067 CAACTCGTAA
* *
8077 TTTGCACTGAAGTGCCACATAAT
1 TTTGCACCGAAGTACCACATAAT
* *
8100 TAT-C-CCGAAGGACCACATAAT
1 TTTGCACCGAAGTACCACATAAT
* **
8121 TTTGCACCGAAGTACCATATAGG
1 TTTGCACCGAAGTACCACATAAT
*
8144 TTTGCACCGAAGTGCCACAT-AT
1 TTTGCACCGAAGTACCACATAAT
* *
8166 TTAT-C-TCGAAGGACCACATAAT
1 TT-TGCACCGAAGTACCACATAAT
8188 T
1 T
8189 ATCCCGAAGG
Statistics
Matches: 69, Mismatches: 16, Indels: 9
0.73 0.17 0.10
Matches are distributed among these distances:
21 27 0.39
22 8 0.12
23 34 0.49
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (23 bp):
TTTGCACCGAAGTACCACATAAT
Found at i:8185 original size:67 final size:65
Alignment explanation
Indices: 8077--8206 Score: 197
Period size: 67 Copynumber: 2.0 Consensus size: 65
8067 CAACTCGTAA
* * *
8077 TTTGCACTGAAGTGCCACATAATTATCCCGAAGGACCACATAATTTTGCACCGAAGTACCATATA
1 TTTGCACCGAAGTGCCACATAATTATCCCGAAGGACCACATAATTAT-C-CCGAAGGACCATATA
8142 GG
64 GG
* *
8144 TTTGCACCGAAGTGCCACATATTTATCTCGAAGGACCACATAATTATCCCGAAGGACCATATA
1 TTTGCACCGAAGTGCCACATAATTATCCCGAAGGACCACATAATTATCCCGAAGGACCATATA
8207 AACCCTCGAC
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
65 14 0.24
66 1 0.02
67 43 0.74
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (65 bp):
TTTGCACCGAAGTGCCACATAATTATCCCGAAGGACCACATAATTATCCCGAAGGACCATATAGG
Found at i:20691 original size:618 final size:620
Alignment explanation
Indices: 19513--20764 Score: 2276
Period size: 618 Copynumber: 2.0 Consensus size: 620
19503 ATAGTTTGAA
* *
19513 ATCAAATGAATACGGGTAAATAGTTAATTAAATTATTTACTTTATATTATTTAATTATATTTTAA
1 ATCAAATAAATACGGGTAAATAGTTAATTAAATTATTTACTTTATATTATTTAATTATATTGTAA
* * * * *
19578 ATTTCGATGTAAGTTTGAAATTTAATAATATTATGTAGTTAAATGGTGGATGATATATGACATAT
66 ATTTCGATGTAAGTCTGAAATTTAATAATATTATGCAATTAAATGATGGATGATATATGACACAT
*
19643 GTACTCCTAAATTACAACAATTAGCAATTAAAGTGCTTAGTCAAACAACTTCTGCATCAAATTGC
131 GTACTCCTAAATTACAACAATTAGCAATTAAAGTGATTAGTCAAACAACTTCTGCATCAAATTGC
* *
19708 GAACGAAACTGGATCACATTAAGCTATATTCACACCTAATTGAGAAACAGTTGAAATACAATAAA
196 GAACGAAACTGGAGCACATTAAGCTATATTCACACCTAATCGAGAAACAGTTGAAATACAATAAA
19773 ATTGAGAAACTAGTGTTTGCTTATTACAATATAAGGCTTAATATGAGGCATCAATAAATAATGAG
261 ATTGAGAAACTAGTGTTTGCTTATTACAATATAAGGCTTAATATGAGGCATCAATAAATAATGAG
19838 AATTGATAATATAAACGCTATTTACAATCCTATCAGTCTTTATCATATCTTTAAAGAAGTTGATT
326 AATTGATAATATAAACGCTATTTACAATCCTATCAGTCTTTATCATATCTTTAAAGAAGTTGATT
19903 CACTATCAAAATGACTTTAAGAGAAAGAGTGTCCATTGTTAGACGGTGAAAATGACGGTGTGTTC
391 CACTATCAAAATGACTTTAAGAGAAAGAGTGTCCATTGTTAGACGGTGAAAATGACGGTGTGTTC
19968 CCTGTGGATACATAAGATGATGAAATGAATGTTAATGATCAATCTCAACAACAAAATTTATCTCA
456 CCTGTGGATACATAAGATGATGAAATGAATGTTAATGATCAATCTCAACAACAAAATTTATCTCA
*
20033 TTCAAGTTCTAGTGCAATGCCAAGTCAAATTATTGATGGGCTAGATGGTGGTGGTTTAAGTCCAA
521 TTCAAGTTCTAGTGCAATGCCAAGTCAAATTAGTGATGGGCTAGATGGTGGTGGTTTAAGTCCAA
** *
20098 TTGATGAGGGTGATATGCAGAGTGGTAATGGAGGC
586 TTGATGAGGGTGATATAAAAAGTGGTAATGGAGGC
20133 ATCAAATAAATACGGGTAAATAGTTAATTAAATTATTTACTTTATATTATTTAATTATATTGTAA
1 ATCAAATAAATACGGGTAAATAGTTAATTAAATTATTTACTTTATATTATTTAATTATATTGTAA
*
20198 ATTTCGATGTAAGTCTGAAATTTAATAATATTATGCAATTAAGTGATGGATGATATATGACACAT
66 ATTTCGATGTAAGTCTGAAATTTAATAATATTATGCAATTAAATGATGGATGATATATGACACAT
*
20263 GTACTCCTAAATTACAATAATTAGCAATTAAAGTGATTAGTC-AACAACTTCTGCATCAAATTGC
131 GTACTCCTAAATTACAACAATTAGCAATTAAAGTGATTAGTCAAACAACTTCTGCATCAAATTGC
20327 GAACGAAACTGGAGCACATTCAA-CTATATTCACACCTAATCGAGAAACAGTTGAAATACAATAA
196 GAACGAAACTGGAGCACATT-AAGCTATATTCACACCTAATCGAGAAACAGTTGAAATACAATAA
20391 AATTGAGAAACTAGTGTTTGCTTATTACAATATAAGGCTTAATATGAGGCATCAAT-AATAATGA
260 AATTGAGAAACTAGTGTTTGCTTATTACAATATAAGGCTTAATATGAGGCATCAATAAATAATGA
20455 GAATTGATAATATAAACGCTATTTACAATCCTATCAGTCTTTATCATATCTTTAAAGAAGTTGAT
325 GAATTGATAATATAAACGCTATTTACAATCCTATCAGTCTTTATCATATCTTTAAAGAAGTTGAT
* * *
20520 TCACTATCAAAATGGCTTTAAGAGAAAGTGTGTCCATTGTTAGATGGTGAAAATGACGGTGTGTT
390 TCACTATCAAAATGACTTTAAGAGAAAGAGTGTCCATTGTTAGACGGTGAAAATGACGGTGTGTT
* *
20585 CCCTGTGGATACATAAGATGATGAAATGAATGTTGATGATCAATTTCAACAACAAAATTTATCTC
455 CCCTGTGGATACATAAGATGATGAAATGAATGTTAATGATCAATCTCAACAACAAAATTTATCTC
*
20650 ATTCAAGTTCTAGTGCAATGCCAAGTCAAATTGGTGATGGGCTAGATGGTGGTGGTTTAAGTCCA
520 ATTCAAGTTCTAGTGCAATGCCAAGTCAAATTAGTGATGGGCTAGATGGTGGTGGTTTAAGTCCA
20715 ATTGATGAGGGTGATATAAAAAGTGGTAATGGAGGC
585 ATTGATGAGGGTGATATAAAAAGTGGTAATGGAGGC
20751 ATCAAATAAATACG
1 ATCAAATAAATACG
20765 ACACATGCCA
Statistics
Matches: 609, Mismatches: 22, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
618 308 0.51
619 137 0.22
620 164 0.27
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (620 bp):
ATCAAATAAATACGGGTAAATAGTTAATTAAATTATTTACTTTATATTATTTAATTATATTGTAA
ATTTCGATGTAAGTCTGAAATTTAATAATATTATGCAATTAAATGATGGATGATATATGACACAT
GTACTCCTAAATTACAACAATTAGCAATTAAAGTGATTAGTCAAACAACTTCTGCATCAAATTGC
GAACGAAACTGGAGCACATTAAGCTATATTCACACCTAATCGAGAAACAGTTGAAATACAATAAA
ATTGAGAAACTAGTGTTTGCTTATTACAATATAAGGCTTAATATGAGGCATCAATAAATAATGAG
AATTGATAATATAAACGCTATTTACAATCCTATCAGTCTTTATCATATCTTTAAAGAAGTTGATT
CACTATCAAAATGACTTTAAGAGAAAGAGTGTCCATTGTTAGACGGTGAAAATGACGGTGTGTTC
CCTGTGGATACATAAGATGATGAAATGAATGTTAATGATCAATCTCAACAACAAAATTTATCTCA
TTCAAGTTCTAGTGCAATGCCAAGTCAAATTAGTGATGGGCTAGATGGTGGTGGTTTAAGTCCAA
TTGATGAGGGTGATATAAAAAGTGGTAATGGAGGC
Found at i:20880 original size:13 final size:13
Alignment explanation
Indices: 20844--20883 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
20834 GGGTAAATAG
*
20844 TTAATTAAATTAT
1 TTAATTATATTAT
*
20857 TTATTTTATATTAT
1 TTA-ATTATATTAT
20871 TTAATTATATTAT
1 TTAATTATATTAT
20884 AAATTTTGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTAATTATATTAT
Found at i:30778 original size:609 final size:609
Alignment explanation
Indices: 29904--31133 Score: 1973
Period size: 609 Copynumber: 2.0 Consensus size: 609
29894 ATAGTTTTAA
*
29904 ATCAAATGAATACGGGTAAATAGTTAATTAAATTATTTACTTTATACTATTTAATTATATTGTAA
1 ATCAAATAAATACGGGTAAATAGTTAATTAAATTATTTACTTTATACTATTTAATTATATTGTAA
29969 ATTTCGATGTAAGTTTGAAACTTATATATTATGCAGTTAAGTGGTGGATGATATATGACACATGT
66 ATTTCGATGTAAGTTTGAAACTTATATATTATGCAGTTAAGTGGTGGATGATATATGACACATGT
* *
30034 ACTCCTACATTACAACAATTTGCAATTAAAGTGCTTAGTCAAACAATTCTACATCAAATTGCGAA
131 ACTCCTAAATTACAACAATTAGCAATTAAAGTGCTTAGTCAAACAATTCTACATCAAATTGCGAA
*
30099 CGAAACTGGAGCACATTCAGCTATATTCACACCTAATCGAGAAACAATTGAAATACAATAATATT
196 CGAAACTGGAGCACATTCAGCTATATTCACACCTAATCGAGAAACAATTGAAATACAATAAAATT
30164 GAGAAACTAGTGTTTGCTTATTACAATATAAGGCTTAAAATGAGGCATCAATAAATAATGAGAAT
261 GAGAAACTAGTGTTTGCTTATTACAATATAAGGCTTAAAATGAGGCATCAATAAATAATGAGAAT
30229 TGATAATATAACGCTATTTACAATCCTATCAGT-TTTATCATATC-TTAAAGAAGTTGATTCACT
326 TGATAATATAACGCTATTTACAATCCTATCAGTCTTTATCATATCTTTAAAGAAGTTGATTCACT
*
30292 ATCAAAATGACTTTAAGAGAATGA-TGTCCATTGTTAGATGGTGAAAATGACGGTGTGTTCCCTG
391 ATC-AAATGACTTT-A-AGAATGAGTGTCCATTGTTAGATGGTGAAAATAAC-G-GTGTTCCCTG
30356 TGGATACATAAGATG-GAAATG-ATGTTGATGATCAATCTCAACAAAAAAATTTATCTCATCATT
451 TGGATACATAAGATGAGAAATGAATGTTGATGATCAATCTCAAC-AAAAAATTTA--TC-TCATT
*
30419 CAAGTTCTAGTGCAATGCCAAGTAAAATTGGTGATGGGCTAGATAG-GGTGGTTTAAGTCCAATT
512 CAAGTTCTAGTGCAACGCCAAGTAAAATTGGTGATGGGCTAGATAGTGGTGGTTTAAGTCCAATT
* * * *
30483 GATGAGGGTGATATAAAGAGTGGTAATGGAGGC
577 GATGAGGATAATAGAAAGAGCGGTAATGGAGGC
* * *
30516 ATCAAATAAATACTGGTAATTAGTTAATT-AA-TATTTACTTTATATTA-TTAA-T-TATTGTAA
1 ATCAAATAAATACGGGTAAATAGTTAATTAAATTATTTACTTTATACTATTTAATTATATTGTAA
*
30576 ATTTCGATGTAAGTTTGAAATTTAATAATATTATGCAGTTAAGTGGTGGATGATATATGACACAT
66 ATTTCGATGTAAGTTTGAAACTT-AT-ATATTATGCAGTTAAGTGGTGGATGATATATGACACAT
*
30641 GTACTCCTAAATTACAACAATTAGCAATTAAAGTGCTTAGTCAAACAACTTCTGCATCAAATTGC
129 GTACTCCTAAATTACAACAATTAGCAATTAAAGTGCTTAGTCAAACAA-TTCTACATCAAATTGC
*
30706 GAACGAAACTGGAGCACATTCAGCTATATTCACACCTATTCGAGAAACAATTGAAATAC-ATAAA
193 GAACGAAACTGGAGCACATTCAGCTATATTCACACCTAATCGAGAAACAATTGAAATACAATAAA
* * *
30770 ATTGAGAAACTAGTGTTTGGTTATTATAATATAAGGCTTAATATGAGGCATCAATAAATAATGAG
258 ATTGAGAAACTAGTGTTTGCTTATTACAATATAAGGCTTAAAATGAGGCATCAATAAATAATGAG
* *
30835 AATTGATAATATAACGCTATTTACAATCCTATCAGTCTTTATCATATCTTTGAAGAAGTTTATTC
323 AATTGATAATATAACGCTATTTACAATCCTATCAGTCTTTATCATATCTTTAAAGAAGTTGATTC
*
30900 ACTATCAAATGACTTTAAGAATGAGTGTCCATTGTTAGATGGTGAAAATAACGGTGTTGCCTGTG
388 ACTATCAAATGACTTTAAGAATGAGTGTCCATTGTTAGATGGTGAAAATAACGGTGTTCCCTGTG
* * *
30965 GATACATCAGATGATGAAATGAATGTTGATGATCAATCTCAACGACAAATTTATCTCATTCAAGT
453 GATACATAAGATGA-GAAATGAATGTTGATGATCAATCTCAACAAAAAATTTATCTCATTCAAGT
* * * *
31030 TCTAGTGCAACGCCAAGTAAAATTGGTGATGGGCTCGATTGTGGTGGTTTAATTCCAATTGATTA
517 TCTAGTGCAACGCCAAGTAAAATTGGTGATGGGCTAGATAGTGGTGGTTTAAGTCCAATTGATGA
*
31095 GGATAATAGACAGAGCGGTAATGGAGGC
582 GGATAATAGAAAGAGCGGTAATGGAGGC
*
31123 A-CCAATAAATA
1 ATCAAATAAATA
31134 ATGAGAATTG
Statistics
Matches: 577, Mismatches: 31, Indels: 26
0.91 0.05 0.04
Matches are distributed among these distances:
606 57 0.10
607 100 0.17
608 11 0.02
609 231 0.40
610 130 0.23
611 22 0.04
612 26 0.05
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (609 bp):
ATCAAATAAATACGGGTAAATAGTTAATTAAATTATTTACTTTATACTATTTAATTATATTGTAA
ATTTCGATGTAAGTTTGAAACTTATATATTATGCAGTTAAGTGGTGGATGATATATGACACATGT
ACTCCTAAATTACAACAATTAGCAATTAAAGTGCTTAGTCAAACAATTCTACATCAAATTGCGAA
CGAAACTGGAGCACATTCAGCTATATTCACACCTAATCGAGAAACAATTGAAATACAATAAAATT
GAGAAACTAGTGTTTGCTTATTACAATATAAGGCTTAAAATGAGGCATCAATAAATAATGAGAAT
TGATAATATAACGCTATTTACAATCCTATCAGTCTTTATCATATCTTTAAAGAAGTTGATTCACT
ATCAAATGACTTTAAGAATGAGTGTCCATTGTTAGATGGTGAAAATAACGGTGTTCCCTGTGGAT
ACATAAGATGAGAAATGAATGTTGATGATCAATCTCAACAAAAAATTTATCTCATTCAAGTTCTA
GTGCAACGCCAAGTAAAATTGGTGATGGGCTAGATAGTGGTGGTTTAAGTCCAATTGATGAGGAT
AATAGAAAGAGCGGTAATGGAGGC
Found at i:31396 original size:307 final size:304
Alignment explanation
Indices: 30814--31428 Score: 948
Period size: 307 Copynumber: 2.0 Consensus size: 304
30804 GGCTTAATAT
* *
30814 GAGGCATCAATAAATAATGAGAATTGATAATATAACGCTATTTACAATCCTATCAGTCTTTATCA
1 GAGGCACCAATAAATAATGAGAATTGATAATATAACACTATTTACAATCCTATCAGTCTTTATCA
* *
30879 TATCTTTGAAGAAGTTTATTCACTATCAAATGACTTTAAGAATGAGTGTCCATTGTTAGATGGTG
66 TATCTTTAAAGAAGTTGATTCACTATCAAATGACTTTAAGAATGAGTGTCCATTGTTAGATGGTG
* *
30944 AAAATAACGGTGTTGCCTGTGGATACATCAGATGATGAAATGAATGTTGATGATCAATCTCAACG
131 AAAATAACGGTGTTGCCTGTGGATACATAAGATGATGAAATGAATGTTGATGATCAATCTCAACA
* * * *
31009 ACAAATTTATCTCATTCAAGTTCTAGTGCAACGCCAAGTAAAATTGGTGATGGGCTCGATTGTGG
196 AAAAATTTATCTCATTCAAGTTCTAGGGCAACGCCAAGTAAAATTGGTGATGGGCTAGATGGTGG
* *
31074 TGGTTTAATTCCAATTGATTAGGATAATAGACAGAGCGGTAATG
261 TGGTTTAAGTCCAATTGATGAGGATAATAGACAGAGCGGTAATG
*
31118 GAGGCACCAATAAATAATGAGAATTGATAATATAAACACTATTTACAATCCTATCAGTTTTTATC
1 GAGGCACCAATAAATAATGAGAATTGATAATAT-AACACTATTTACAATCCTATCAGTCTTTATC
*
31183 TTATCTTTAAAG-AGTTGATTCACTATCAAAATGACTTTAAGAGAATGAGTGTCCATTG-TAGAT
65 ATATCTTTAAAGAAGTTGATTCACTATC-AAATGACTTT-A-AGAATGAGTGTCCATTGTTAGAT
* *
31246 GGTGAAAATGACGGTGTGTTCCTGTGGATACATAAGA-GATGAAATGAATGTTGATGATCAATCT
127 GGTGAAAATAACGGTGT-TGCCTGTGGATACATAAGATGATGAAATGAATGTTGATGATCAATCT
* *
31310 CAACAAAAAAATTTATCTCATTCAAGTTCTAGGGCAATGCCAAGTCAAATTGGTGATGGGCTAGA
191 CAAC-AAAAAATTTATCTCATTCAAGTTCTAGGGCAACGCCAAGTAAAATTGGTGATGGGCTAGA
* * * * *
31375 TGGTGGTTGTTTAAGTCCAATTGATGAGGGTGATATACAGAGTGGTAATG
255 TGGTGGTGGTTTAAGTCCAATTGATGAGGATAATAGACAGAGCGGTAATG
31425 GAGG
1 GAGG
31429 ATTCAAATAA
Statistics
Matches: 282, Mismatches: 23, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
304 46 0.16
305 49 0.17
306 53 0.19
307 134 0.48
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (304 bp):
GAGGCACCAATAAATAATGAGAATTGATAATATAACACTATTTACAATCCTATCAGTCTTTATCA
TATCTTTAAAGAAGTTGATTCACTATCAAATGACTTTAAGAATGAGTGTCCATTGTTAGATGGTG
AAAATAACGGTGTTGCCTGTGGATACATAAGATGATGAAATGAATGTTGATGATCAATCTCAACA
AAAAATTTATCTCATTCAAGTTCTAGGGCAACGCCAAGTAAAATTGGTGATGGGCTAGATGGTGG
TGGTTTAAGTCCAATTGATGAGGATAATAGACAGAGCGGTAATG
Found at i:32150 original size:13 final size:13
Alignment explanation
Indices: 32117--32153 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
32107 GGGTAAATAG
32117 TTAATTA-ATTA-
1 TTAATTATATTAT
*
32128 TTATTTATATTAT
1 TTAATTATATTAT
32141 TTAATTATATTAT
1 TTAATTATATTAT
32154 AATTTTGATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 6 0.27
12 4 0.18
13 12 0.55
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTAATTATATTAT
Found at i:35593 original size:960 final size:953
Alignment explanation
Indices: 33716--35622 Score: 2985
Period size: 957 Copynumber: 2.0 Consensus size: 953
33706 AGGCACCAAA
* * *
33716 AACATACTTTTGAAGGTTTTCTTTGGGTAGGAGATCAAAATTTTAGTAACATTGGTTATAGTGGT
1 AACATACTTTCGAAGGTTTTCTTTGGGTAGGAGATCAAAATTTTAGTAACATTGGGTATAGTGAT
* *
33781 TCATCTACTGATAATCAAATCATTAATTTCAATTTGGAGTGGAGTATTCTAAGAATATTGACAGA
66 TCATCTACTGATAATCAAATCATCAATTTCAATTTAGAGTGGAGTATTCTAAGAATATTGACAGA
* *
33846 AACATTAGAAGACACAAGATTAGATTGAAATTTAGAACCTTCTTTGATAATCAAATCAAATTGGT
131 AACATTAGAAGACACAAGATTAGATTGAAAATTAGAAACTTCTTTGATAATCAAATCAAATTGGT
** *
33911 GAATTAGGTTAGATTCAATACTATTATTTTTAACTTAGTTAAATATTTTAAATTGAATTATTTTT
196 GAATTAGGTTAGATTCAATACTATTATTTGCAACTTAGTTAAATATTTAAAATTGAA-TATTTTT
33976 CTCATTTTCACTCAAACTTTTATTTATGCAAATGTTACTATTTAAAGTAAACTGAGACATTCGAC
260 CTCATTTTCACTCAAACTTTTATTTATGCAAATGTTACTATTTAAAGTAAACTGAGACATTCGAC
* *
34041 ACTTCACAAGCACAAATAGTTTGGAATCAAATGAATATGGGTAAATAACTAATTAATTATTTACT
325 ACTTCACAAGCACAAATAGTTTGAAATCAAA-GAATACGGGTAAATAACTAATTAATTATTTACT
* * * *
34106 TTATATTATTTAATTATATTGTACATTTTTATGTAAGTTTGAAATTATAATATTATGCAGTTGAG
389 TTATATTATGTAATTATATTGTAAATTTTGATGTAAGTTTGAAATTATAATATTATGCAGTTAAG
* * *
34171 TGTGAATGATATATGACACATGTATTTCCTAAATTACAATAATTAGCAATTAAAGTGCTTAGTCA
454 TGTGAATGATATAAGACACATGTATCTCCTAAATTACAACAATTAGCAATTAAAGTGCTTAGTCA
* * * *
34236 AACAACTTTTGCATCAAATTACGAACGATACTGGAGCACATTCAGATATATTCACACCTAATCAA
519 AACAACTTCTACATCAAATTACGAACGAAACTGAAGCACATTCAGATATATTCACACCTAATCAA
* * * *
34301 GAAACAGTTGAAATATAAAAAATTGAGAAACTAGTGTTTACTTGTTACAACATAAGGCTTAAACT
584 GAAACAATTGAAATACAAAAAATTGAGAAACTAGTGTTTACTTATTACAACATAAGGCTTAAAAT
* * * *
34366 GAGGCGTCAATAAAGAATGAGCATTGATAATATAAACGCTAGTTACATTCCTAGCAGACTTGATC
649 GAGGCATCAATAAAGAATGAGCATTGATAATATAAACGCTAGTTACAATCCTACCAGACATGATC
* *
34431 ATATCTTTGAAGATGTTGATCCACTATCAGAATGAGTTTAAGAGAAAGAGAGTCCATTGTTAGAT
714 ATATCTTTGAAAATGTTGATCCACTATCAGAATGAGTTTAAGAGAAAGAGAGTCCATTATTAGAT
* * *
34496 GGTGAAAATTACAGTGTGTTGCATGTGGATACATCAGATGATGAAATGAATGTTGATGATAAATC
779 GATGAAAATGACAGTGTGTTGCATGTGGATACATCAGATGATAAAATGAATGTTGATGATAAATC
* *
34561 TCAACAAGAAAATTTATCTCATTCAAGTTCTAGTGCAACGCCAAGTCAAATTGGTGATGGGCTCG
844 TCAACAACAAAATTTATCTCATTCAAGTTCTACTGCAACGCCAAGTCAAATTGGTGATGGGCTCG
34626 ATGGTGGTGGTTTAAGTCCAAATGATGAGGATGATAGACAGAGTT
909 ATGGTGGTGGTTTAAGTCCAAATGATGAGGATGATAGACAGAGTT
34671 AACATACTTTCG-AGGTTTTTCTTTGGGTAGGAGATCAAAATTTTAGTAACATTGGGTATAGTGA
1 AACATACTTTCGAAGG-TTTTCTTTGGGTAGGAGATCAAAATTTTAGTAACATTGGGTATAGTGA
* *
34735 TTCATCTACTGATAATCAAATCATCAATTTCAATTTAGAGTTGAGTATTCTAAGAATATATTGAT
65 TTCATCTACTGATAATCAAATCATCAATTTCAATTTAGAGTGGAGTATTCTAAG-A-ATATTGAC
*
34800 GGAAACATTAGAAGACA-AAGATTAGTGATTGAAAGATTAGAAACTT-TATTGATAATCAAATCA
128 AGAAACATTAGAAGACACAAGATTA--GATTGAAA-ATTAGAAACTTCT-TTGATAATCAAATCA
34863 AATTGGTGAATTAGGTTAGATTCAAATACTATTATTTGCAACTTAGTTAAATAATTTAAAATTGA
189 AATTGGTGAATTAGGTTAGATTC-AATACTATTATTTGCAACTTAGTTAAAT-ATTTAAAATTGA
* *
34928 A-ATTTTTCTCA-TTTCACTCAATCTTTTATTTATGCAAATGTTTCTATTTAAAAGTAAACATGA
252 ATATTTTTCTCATTTTCACTCAAACTTTTATTTATGCAAATGTTACTATTT-AAAGTAAAC-TGA
* **
34991 GACATTCGACACTTTACAAGCACAAATAGTTTGAAATCAAA-AATACGGGTAAATAGTTAATTAA
315 GACATTCGACACTTCACAAGCACAAATAGTTTGAAATCAAAGAATACGGGTAAATAACTAATTAA
35055 TTATTTACTTTATATTATGTAATTATATTGTAAATTTTGATGTAAGTTTGAAATTTAATAATATT
380 TTATTTACTTTATATTATGTAATTATATTGTAAATTTTGATGTAAGTTTGAAA-TT-ATAATATT
* * *
35120 ATGCAGTTAAGTGGTGGATGATATAAGGCATATGT-TCTCCTAAATTACAAACAATTAGCAATTA
443 ATGCAGTTAAGT-GTGAATGATATAAGACACATGTATCTCCTAAATTAC-AACAATTAGCAATTA
* * *
35184 AAGTTCTTAGTTAAACAACTTCTACATCAAATTACGAACGAAACTGAAGCACATTCA-CTATATT
506 AAGTGCTTAGTCAAACAACTTCTACATCAAATTACGAACGAAACTGAAGCACATTCAGATATATT
* *
35248 CACACCTAATCAAGAAACAATTGAAATACAAAAAATTGAGAAACTAGTGTTTTATTTATTACAAT
571 CACACCTAATCAAGAAACAATTGAAATACAAAAAATTGAGAAACTAGTG-TTTACTTATTACAAC
*
35313 ATAAGGCTTAAAATGAGGCATCAATAAAGAATGAGCATTGATAATATAAATGCTAGTTACAATCC
635 ATAAGGCTTAAAATGAGGCATCAATAAAGAATGAGCATTGATAATATAAACGCTAGTTACAATCC
*
35378 TACCAGTCATGATC-TATCTTTGAAAATGTTGATCCACTAT-AGAATGAGTTTAAGAG-AAG-GA
700 TACCAGACATGATCATATCTTTGAAAATGTTGATCCACTATCAGAATGAGTTTAAGAGAAAGAGA
* *
35439 TTCCATTATTAGATGATGAAAATGACAGTGTGTTGCCAT-TGGATATATCAGATGATAAAATGAA
765 GTCCATTATTAGATGATGAAAATGACAGTGTGTTG-CATGTGGATACATCAGATGATAAAATGAA
* * * *
35503 TGTTGATGATCAATCTCAACAACAATATTTGTCTCATTCAAGTTCTACTGCAACTCCAAGTCAAA
829 TGTTGATGATAAATCTCAACAACAAAATTTATCTCATTCAAGTTCTACTGCAACGCCAAGTCAAA
*
35568 TTGGTGATGGGCTCGATGGTGGTGGTTTAAGTCCAATTGATGAGGATGATAGACA
894 TTGGTGATGGGCTCGATGGTGGTGGTTTAAGTCCAAATGATGAGGATGATAGACA
35623 AAGTGGTAAT
Statistics
Matches: 872, Mismatches: 63, Indels: 32
0.90 0.07 0.03
Matches are distributed among these distances:
954 3 0.00
955 108 0.12
956 8 0.01
957 192 0.22
958 121 0.14
959 84 0.10
960 177 0.20
961 179 0.21
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.34
Consensus pattern (953 bp):
AACATACTTTCGAAGGTTTTCTTTGGGTAGGAGATCAAAATTTTAGTAACATTGGGTATAGTGAT
TCATCTACTGATAATCAAATCATCAATTTCAATTTAGAGTGGAGTATTCTAAGAATATTGACAGA
AACATTAGAAGACACAAGATTAGATTGAAAATTAGAAACTTCTTTGATAATCAAATCAAATTGGT
GAATTAGGTTAGATTCAATACTATTATTTGCAACTTAGTTAAATATTTAAAATTGAATATTTTTC
TCATTTTCACTCAAACTTTTATTTATGCAAATGTTACTATTTAAAGTAAACTGAGACATTCGACA
CTTCACAAGCACAAATAGTTTGAAATCAAAGAATACGGGTAAATAACTAATTAATTATTTACTTT
ATATTATGTAATTATATTGTAAATTTTGATGTAAGTTTGAAATTATAATATTATGCAGTTAAGTG
TGAATGATATAAGACACATGTATCTCCTAAATTACAACAATTAGCAATTAAAGTGCTTAGTCAAA
CAACTTCTACATCAAATTACGAACGAAACTGAAGCACATTCAGATATATTCACACCTAATCAAGA
AACAATTGAAATACAAAAAATTGAGAAACTAGTGTTTACTTATTACAACATAAGGCTTAAAATGA
GGCATCAATAAAGAATGAGCATTGATAATATAAACGCTAGTTACAATCCTACCAGACATGATCAT
ATCTTTGAAAATGTTGATCCACTATCAGAATGAGTTTAAGAGAAAGAGAGTCCATTATTAGATGA
TGAAAATGACAGTGTGTTGCATGTGGATACATCAGATGATAAAATGAATGTTGATGATAAATCTC
AACAACAAAATTTATCTCATTCAAGTTCTACTGCAACGCCAAGTCAAATTGGTGATGGGCTCGAT
GGTGGTGGTTTAAGTCCAAATGATGAGGATGATAGACAGAGTT
Found at i:42961 original size:12 final size:13
Alignment explanation
Indices: 42938--42975 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
42928 AGGTAAATAG
*
42938 TTAATTAAATTAT
1 TTAATTATATTAT
*
42951 TTACTT-TATTAT
1 TTAATTATATTAT
42963 TTAATTATATTAT
1 TTAATTATATTAT
42976 ACATTTTGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (13 bp):
TTAATTATATTAT
Found at i:46352 original size:14 final size:15
Alignment explanation
Indices: 46325--46364 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
46315 GGGTAAATAG
46325 TTAATTA-A-ATTAT
1 TTAATTATATATTAT
*
46338 TTACTT-TATATTAT
1 TTAATTATATATTAT
46352 TTAATTATATATT
1 TTAATTATATATT
46365 CTAAATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 6 0.27
14 10 0.45
15 6 0.27
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (15 bp):
TTAATTATATATTAT
Done.