Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005424.1 Hibiscus syriacus cultivar Beakdansim tig00012440_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: 85668
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:24575 original size:31 final size:30
Alignment explanation
Indices: 24539--24601 Score: 90
Period size: 31 Copynumber: 2.1 Consensus size: 30
24529 ATAATATGAT
*
24539 AAATTTTAATGACCATTTCATAATCATTTGA
1 AAATTTTAATGACCATTTCATAAT-ATGTGA
* *
24570 AAATTTTAATGACCGTTTTATAATATGTGA
1 AAATTTTAATGACCATTTCATAATATGTGA
24600 AA
1 AA
24602 GTTCATTAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 7 0.24
31 22 0.76
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.41
Consensus pattern (30 bp):
AAATTTTAATGACCATTTCATAATATGTGA
Found at i:26961 original size:45 final size:45
Alignment explanation
Indices: 26892--26988 Score: 185
Period size: 45 Copynumber: 2.2 Consensus size: 45
26882 GAATATAAAT
*
26892 ATTATTTAAAAGATTAATGTACCATCTCGCTAAAACATGTAACTA
1 ATTACTTAAAAGATTAATGTACCATCTCGCTAAAACATGTAACTA
26937 ATTACTTAAAAGATTAATGTACCATCTCGCTAAAACATGTAACTA
1 ATTACTTAAAAGATTAATGTACCATCTCGCTAAAACATGTAACTA
26982 ATTACTT
1 ATTACTT
26989 TCAATTATTT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 51 1.00
ACGTcount: A:0.41, C:0.16, G:0.08, T:0.34
Consensus pattern (45 bp):
ATTACTTAAAAGATTAATGTACCATCTCGCTAAAACATGTAACTA
Found at i:26971 original size:24 final size:24
Alignment explanation
Indices: 26898--26971 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
26888 AAATATTATT
26898 TAAAAGATTAATGTACCATCTCGC
1 TAAAAGATTAATGTACCATCTCGC
* * *
26922 TAAAACATGTAA-CTA--AT-TAC-T
1 TAAAAGAT-TAATGTACCATCT-CGC
26943 TAAAAGATTAATGTACCATCTCGC
1 TAAAAGATTAATGTACCATCTCGC
26967 TAAAA
1 TAAAA
26972 CATGTAACTA
Statistics
Matches: 37, Mismatches: 6, Indels: 14
0.65 0.11 0.25
Matches are distributed among these distances:
20 3 0.08
21 10 0.27
22 3 0.08
23 3 0.08
24 15 0.41
25 3 0.08
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.30
Consensus pattern (24 bp):
TAAAAGATTAATGTACCATCTCGC
Found at i:27262 original size:35 final size:34
Alignment explanation
Indices: 27216--27328 Score: 145
Period size: 35 Copynumber: 3.2 Consensus size: 34
27206 AAAACAATCC
*
27216 TCAATTTCATTCTAAACCACAAATTCCAAAGTAAT
1 TCAATTTCATTCTAAACC-CAAATTCCAAAATAAT
*
27251 TCAATTTCATTCTAAACCCTAAATTTCAAAATAAT
1 TCAATTTCATTCTAAACCC-AAATTCCAAAATAAT
* * * *
27286 TCAATTACATTATAAAACCCAAATTCTAAAATACT
1 TCAATTTCATTCT-AAACCCAAATTCCAAAATAAT
27321 TCAATTTC
1 TCAATTTC
27329 TGTCTTTTTT
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
34 1 0.01
35 61 0.90
36 6 0.09
ACGTcount: A:0.43, C:0.21, G:0.01, T:0.35
Consensus pattern (34 bp):
TCAATTTCATTCTAAACCCAAATTCCAAAATAAT
Found at i:27681 original size:20 final size:19
Alignment explanation
Indices: 27658--27700 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
27648 ATATTATTTC
*
27658 TATTATAATTAAAATATAAA
1 TATTACAATTAAAAT-TAAA
* *
27678 TATTACCATTATAATTAAA
1 TATTACAATTAAAATTAAA
27697 TATT
1 TATT
27701 TATTTACTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (19 bp):
TATTACAATTAAAATTAAA
Found at i:28428 original size:35 final size:34
Alignment explanation
Indices: 28380--28491 Score: 161
Period size: 35 Copynumber: 3.2 Consensus size: 34
28370 ATTCCTCCTT
* *
28380 AAATTGAAATATTTTAGAATTTGGGTTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGGG-TTTAGAATG
*
28415 TAATTGAATTATTTTGGAATTTAGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTT-GGGTTTAGAATG
*
28450 AAATTGAATTACTTTGGAATTTGGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTT-GGGTTTAGAATG
28485 AAATTGA
1 AAATTGA
28492 GGAATGTTTT
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
35 67 0.96
36 3 0.04
ACGTcount: A:0.35, C:0.01, G:0.22, T:0.42
Consensus pattern (34 bp):
AAATTGAATTATTTTGGAATTTGGGTTTAGAATG
Found at i:28654 original size:29 final size:30
Alignment explanation
Indices: 28598--28655 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
28588 TGCGGGACCA
* *
28598 TATTGCAAGTTGATTAAATGTTGGGGGACTG
1 TATTGCAAGTT-ATTAAAAGTTGAGGGACTG
28629 TATTGCAAGTT-TTAAAAGTTGAGGGAC
1 TATTGCAAGTTATTAAAAGTTGAGGGAC
28656 CTAAATGCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 14 0.56
31 11 0.44
ACGTcount: A:0.29, C:0.07, G:0.29, T:0.34
Consensus pattern (30 bp):
TATTGCAAGTTATTAAAAGTTGAGGGACTG
Found at i:46550 original size:21 final size:21
Alignment explanation
Indices: 46526--46573 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
46516 CCGTTTGTCT
*
46526 TTTTTTGGGTAAATTAATTCA
1 TTTTTCGGGTAAATTAATTCA
46547 TTTTTCGGGTAAATTAATTCA
1 TTTTTCGGGTAAATTAATTCA
46568 TTTTTC
1 TTTTTC
46574 CAGTTTTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.25, C:0.08, G:0.12, T:0.54
Consensus pattern (21 bp):
TTTTTCGGGTAAATTAATTCA
Found at i:53061 original size:24 final size:24
Alignment explanation
Indices: 53025--53113 Score: 80
Period size: 23 Copynumber: 3.8 Consensus size: 24
53015 AGCTCATATA
*
53025 AATTTGCATCGAAGTGCCACGTAG
1 AATTTGCACCGAAGTGCCACGTAG
* *
53049 AATTTGTC-CCGAAG-GAACGCGTAG
1 AATTTG-CACCGAAGTG-CCACGTAG
53073 AGA--TGCACCGAAGTGCCACGTAG
1 A-ATTTGCACCGAAGTGCCACGTAG
*
53096 AA-TTGCACCGTAGTGCCA
1 AATTTGCACCGAAGTGCCA
53114 TATAATATGT
Statistics
Matches: 53, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
22 2 0.04
23 30 0.57
24 19 0.36
25 2 0.04
ACGTcount: A:0.29, C:0.24, G:0.27, T:0.20
Consensus pattern (24 bp):
AATTTGCACCGAAGTGCCACGTAG
Found at i:53625 original size:54 final size:54
Alignment explanation
Indices: 53561--53738 Score: 284
Period size: 54 Copynumber: 3.3 Consensus size: 54
53551 GGTTTCCGTA
*
53561 TAAGGCGTGGGCACGGCTTATTCATTTTGAGCTATCGCAGAAAAGGTCTTCGGT
1 TAAGGCGTGGGCACGGCTTATTCATTTTGAGCTATCGCAGAAAAGGTCTTCAGT
53615 TAAGGCGTGGGCACGGCTTATTCATTTTGAGCTATCGCAGAAAAGGTCTTCAGT
1 TAAGGCGTGGGCACGGCTTATTCATTTTGAGCTATCGCAGAAAAGGTCTTCAGT
* * * * * * *
53669 TAAGGCGTGGGCACAGCTTATTCATTCTAAGCTATTGCATAAGAGGTCTTTAGT
1 TAAGGCGTGGGCACGGCTTATTCATTTTGAGCTATCGCAGAAAAGGTCTTCAGT
53723 TAAGGCGTGGGCACGG
1 TAAGGCGTGGGCACGG
53739 GTTACTAGTT
Statistics
Matches: 115, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 115 1.00
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (54 bp):
TAAGGCGTGGGCACGGCTTATTCATTTTGAGCTATCGCAGAAAAGGTCTTCAGT
Found at i:57214 original size:575 final size:572
Alignment explanation
Indices: 56072--57228 Score: 1848
Period size: 575 Copynumber: 2.0 Consensus size: 572
56062 CTAAATTCTC
* *
56072 TAGTATTGGGAGAAATCTAGAATGATTTGGAATGGTTTTGAAGCTAAATGGGTTATGGTACTTAT
1 TAGTATTGGGAGAAAGCTAGAATGATTTGGAATGATTTTGAAGCTAAATGGGTTATGGTACTTAT
* * * * *
56137 AGTTGAAGCTTAAGGATTAATCTTATAAATACCTTAAAGTATAATGACTAAATTTACAATTTTAC
66 AGTTGAAGCTTAAGGACTAATCTTATAAATACCCTAAAGTACAATAACTAAATGTACAATTTTAC
*
56202 CATTGCTAATTTTCAACAAAAACCAACCTTTTTTGACAATTTTTTCGATGAATTTTTTTTCTTAT
131 CATTGCTAATTTTCAACAAAAACCAACCTTTTTTAACAATTTTTTCGATGAATTTTTTTTC-T-T
*
56267 ATTATAACCTTTCGGTGCCACCAATTTCGGTGGCACTAATTTTCAACATCAAGTACAAGAGAAGA
194 ATTATAACCTTTCGGTGCCACCAATTTCGGTGGCACCAATTTTCAACATCAAGTACAAGAGAAGA
56332 CTATTATTTTCTCTACAAAGCTACAGGTTTCTACACGTTAGCTACAAAGTAAAAACTCATAGAAT
259 CTATTATTTTCTCTACAAAGCTACAGGTTTCTACACGTTAGCTACAAAGTAAAAACTCATAGAAT
56397 AGACATCATTAAATTTCAAAAAAATAGATTTTATTATACTTACGATATAATTGATTTCATCACAT
324 AGACATCATTAAATTTCAAAAAAATAGA-TTTATTATACTTACGATATAATTGATTTCATCACAT
56462 CTGATATGAATAAATGAAAATATTTAATATAAAAAATACATTTATAAAAATTATTCAAAAAATAA
388 CTGATATGAATAAATGAAAATATTTAATATAAAAAATACATTTATAAAAATTATTCAAAAAATAA
56527 CTTATAGGTGAGGTGAAAAGAAATTTATACATGAAATTAGTATTCTTGTATTTGAATCTTAAATA
453 CTTATAGGTGAGGTGAAAAGAAATTTATACATGAAATTAGTATTCTTGTATTTGAATCTTAAATA
* *
56592 ATAATTTTCAATTGTCATATTAAAATTTATGACAAAATAAGCAAAATTCTTTTAA
518 ATAATTTTCAATTGTCATATTAAAATTTATGACAAAATAAACAAAATTCTTTCAA
* *
56647 TAGTATTGGGAGAAAGCTAGAATGATTTGGGATGATTTTGAAGCTAAATGGGTTA-GAGTATTTA
1 TAGTATTGGGAGAAAGCTAGAATGATTTGGAATGATTTTGAAGCTAAATGGGTTATG-GTACTTA
**
56711 TAGTTGAAGCTTAAGGACTAATCTTATAAATACCCTAAAGTACAATAACTAAATGTGTAATTTTA
65 TAGTTGAAGCTTAAGGACTAATCTTATAAATACCCTAAAGTACAATAACTAAATGTACAATTTTA
* * *
56776 TCATTGCTAATTTTCAACAAAAGCCAA-CTCTTTTTAACAATTTTTTCGGTGGAATTTTTTTTC-
130 CCATTGCTAATTTTCAACAAAAACCAACCT-TTTTTAACAATTTTTTCGAT-GAATTTTTTTTCT
* *
56839 TATTATCAA-CTTTCAGTGGTTCAGCGCCACCAATTTCGGTGGCACCAATTTTTAACATCATGTA
193 TATTAT-AACCTTTC---GG-T----GCCACCAATTTCGGTGGCACCAATTTTCAACATCAAGTA
* *
56903 CAAGAGAAGACTATTATTTTCTCTACAAAGCTACATGTTTCTGCACGTTAGCTACAAAGTAAAAA
249 CAAGAGAAGACTATTATTTTCTCTACAAAGCTACAGGTTTCTACACGTTAGCTACAAAGTAAAAA
*
56968 CTCATAGAATA-ATCATCATTAAA-TTCCAAAAAA-A-A-TTATTATACTTACGATATAATTGAT
314 CTCATAGAATAGA-CATCATTAAATTTCAAAAAAATAGATTTATTATACTTACGATATAATTGAT
57028 TTCATCACATCTGATATGAATAAATGAAAATATTTAATATAAAAAATACATTTATAAAAATTATT
378 TTCATCACATCTGATATGAATAAATGAAAATATTTAATATAAAAAATACATTTATAAAAATTATT
* *
57093 CAACAAATAATTTATAGGTGAGGTGAAAAGAAATTTATACATGAAATTAGTATTCTTGTATTTGA
443 CAAAAAATAACTTATAGGTGAGGTGAAAAGAAATTTATACATGAAATTAGTATTCTTGTATTTGA
* *
57158 ATCTTAAATAATAA-TTTCAATTGTTATATTAAAATTTATGACAAGATAAACAAAATTCTTTCAA
508 ATCTTAAATAATAATTTTCAATTGTCATATTAAAATTTATGACAAAATAAACAAAATTCTTTCAA
*
57222 TAATATT
1 TAGTATT
57229 AATATCATTT
Statistics
Matches: 541, Mismatches: 28, Indels: 26
0.91 0.05 0.04
Matches are distributed among these distances:
573 11 0.02
574 5 0.01
575 211 0.39
576 181 0.33
577 1 0.00
578 1 0.00
579 1 0.00
580 10 0.02
581 120 0.22
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (572 bp):
TAGTATTGGGAGAAAGCTAGAATGATTTGGAATGATTTTGAAGCTAAATGGGTTATGGTACTTAT
AGTTGAAGCTTAAGGACTAATCTTATAAATACCCTAAAGTACAATAACTAAATGTACAATTTTAC
CATTGCTAATTTTCAACAAAAACCAACCTTTTTTAACAATTTTTTCGATGAATTTTTTTTCTTAT
TATAACCTTTCGGTGCCACCAATTTCGGTGGCACCAATTTTCAACATCAAGTACAAGAGAAGACT
ATTATTTTCTCTACAAAGCTACAGGTTTCTACACGTTAGCTACAAAGTAAAAACTCATAGAATAG
ACATCATTAAATTTCAAAAAAATAGATTTATTATACTTACGATATAATTGATTTCATCACATCTG
ATATGAATAAATGAAAATATTTAATATAAAAAATACATTTATAAAAATTATTCAAAAAATAACTT
ATAGGTGAGGTGAAAAGAAATTTATACATGAAATTAGTATTCTTGTATTTGAATCTTAAATAATA
ATTTTCAATTGTCATATTAAAATTTATGACAAAATAAACAAAATTCTTTCAA
Found at i:58099 original size:52 final size:52
Alignment explanation
Indices: 58030--58162 Score: 248
Period size: 52 Copynumber: 2.6 Consensus size: 52
58020 TTTTCATCTC
58030 TATGTACATATATTTGAATTTTCATTCACAACCAATGGGACTCCATCTCTTG
1 TATGTACATATATTTGAATTTTCATTCACAACCAATGGGACTCCATCTCTTG
* *
58082 TATGTACATATATTTGAATTTTCATTCACAGCCAATGGGATTCCATCTCTTG
1 TATGTACATATATTTGAATTTTCATTCACAACCAATGGGACTCCATCTCTTG
58134 TATGTACATATATTTGAATTTTCATTCAC
1 TATGTACATATATTTGAATTTTCATTCAC
58163 TCTCCTCATT
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 79 1.00
ACGTcount: A:0.29, C:0.19, G:0.11, T:0.41
Consensus pattern (52 bp):
TATGTACATATATTTGAATTTTCATTCACAACCAATGGGACTCCATCTCTTG
Found at i:59335 original size:20 final size:20
Alignment explanation
Indices: 59300--59357 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
59290 CGGGAAAAAG
*
59300 ATCTCCAAACGGCTATAATTC
1 ATCTCC-AATGGCTATAATTC
59321 ATCTCCAATGGCTATAATTC
1 ATCTCCAATGGCTATAATTC
*
59341 ATCTCTAATGGCTATAA
1 ATCTCCAATGGCTATAA
59358 ACGGCAACAA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
20 29 0.83
21 6 0.17
ACGTcount: A:0.33, C:0.24, G:0.10, T:0.33
Consensus pattern (20 bp):
ATCTCCAATGGCTATAATTC
Found at i:60286 original size:20 final size:20
Alignment explanation
Indices: 60261--60431 Score: 114
Period size: 20 Copynumber: 8.2 Consensus size: 20
60251 AATGACCAAC
*
60261 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTAAG
* *
60281 AAAATCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTAAG
*
60301 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TAAG
* ***
60321 ATAATCGCAACGCGATATTCC
1 AAAATCGCAACGCGAT-TAAG
*
60342 AAGAATCGCAATGCGATTAAG
1 AA-AATCGCAACGCGATTAAG
* ***
60363 AGAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TAAG
*
60384 AAGAATCGCAACGCGATTCAG
1 AA-AATCGCAACGCGATTAAG
60405 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
60427 AAAAT
1 AAAAT
60432 GAGTAAATTC
Statistics
Matches: 117, Mismatches: 23, Indels: 20
0.73 0.14 0.12
Matches are distributed among these distances:
18 1 0.01
20 69 0.59
21 12 0.10
22 35 0.30
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
AAAATCGCAACGCGATTAAG
Found at i:60351 original size:22 final size:20
Alignment explanation
Indices: 60323--60428 Score: 117
Period size: 20 Copynumber: 5.1 Consensus size: 20
60313 GTCAAAAGAT
60323 AATCGCAACGCGATATTCCAAG
1 AATCGCAACGCG--ATTCCAAG
* *
60345 AATCGCAATGCGATT-AAGAG
1 AATCGCAACGCGATTCCA-AG
60365 AATCGCAACGCGATCTTCCAAG
1 AATCGCAACGCGA--TTCCAAG
*
60387 AATCGCAACGCGATT-CAGAA
1 AATCGCAACGCGATTCCA-AG
60407 AATCGCAACGCGATTCCAAG
1 AATCGCAACGCGATTCCAAG
60427 AA
1 AA
60429 AATGAGTAAA
Statistics
Matches: 72, Mismatches: 6, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
19 3 0.04
20 38 0.53
21 2 0.03
22 28 0.39
23 1 0.01
ACGTcount: A:0.38, C:0.25, G:0.20, T:0.17
Consensus pattern (20 bp):
AATCGCAACGCGATTCCAAG
Found at i:60369 original size:42 final size:42
Alignment explanation
Indices: 60318--60428 Score: 163
Period size: 42 Copynumber: 2.7 Consensus size: 42
60308 CAACGGTCAA
* *
60318 AAGATAATCGCAACGCGATATTCCAAGAATCGCAATGCGATT
1 AAGAAAATCGCAACGCGATATTCCAAGAATCGCAACGCGATT
* *
60360 AAGAGAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATT
1 AAGAAAATCGCAACGCGATATTCCAAGAATCGCAACGCGATT
*
60402 CAGAAAATCGCAACGCG--ATTCCAAGAA
1 AAGAAAATCGCAACGCGATATTCCAAGAA
60429 AATGAGTAAA
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
40 9 0.14
42 54 0.86
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.17
Consensus pattern (42 bp):
AAGAAAATCGCAACGCGATATTCCAAGAATCGCAACGCGATT
Found at i:60538 original size:6 final size:6
Alignment explanation
Indices: 60527--60570 Score: 81
Period size: 6 Copynumber: 7.5 Consensus size: 6
60517 GACACGTATT
60527 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
60571 CGAGACGAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.13
6 33 0.87
ACGTcount: A:0.32, C:0.52, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:61089 original size:12 final size:11
Alignment explanation
Indices: 61059--61092 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 11
61049 CGCCGCCGTC
61059 TCGGGTCG-GG
1 TCGGGTCGTGG
61069 TCGGGTCGTGG
1 TCGGGTCGTGG
61080 TCGTGGTCGTGG
1 TCG-GGTCGTGG
61092 T
1 T
61093 AATGGTAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 8 0.36
11 5 0.23
12 9 0.41
ACGTcount: A:0.00, C:0.18, G:0.53, T:0.29
Consensus pattern (11 bp):
TCGGGTCGTGG
Found at i:61098 original size:6 final size:6
Alignment explanation
Indices: 61089--61113 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
61079 GTCGTGGTCG
61089 TGGTAA TGGTAA TGGTAA TGGTAA T
1 TGGTAA TGGTAA TGGTAA TGGTAA T
61114 ACGTGTCTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (6 bp):
TGGTAA
Found at i:61261 original size:40 final size:40
Alignment explanation
Indices: 61206--61418 Score: 286
Period size: 40 Copynumber: 5.2 Consensus size: 40
61196 GAATTTACTC
61206 ATTTTCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
*
61246 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
*
61286 ATTTTCTGAATCGCGTTGCGATT-TTCTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTT-GGAATCGCGTTGCG
*
61326 ATTCTT-GGAAGATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCG
* *
61370 ATTTTATGAATCGCATTGCGATTCTTGGAAGATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCG
*
61412 ATCTTCT
1 ATTTTCT
61419 TTTCAACGTT
Statistics
Matches: 156, Mismatches: 9, Indels: 14
0.87 0.05 0.08
Matches are distributed among these distances:
39 2 0.01
40 78 0.50
41 3 0.02
42 52 0.33
43 6 0.04
44 15 0.10
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (40 bp):
ATTTTCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
Found at i:61343 original size:22 final size:20
Alignment explanation
Indices: 61213--61413 Score: 232
Period size: 20 Copynumber: 9.8 Consensus size: 20
61203 CTCATTTTCT
61213 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
61233 GAATCGCGTTGCGATTTTCTT-
1 GAATCGCGTTGCGA--TTCTTG
61254 -AATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
*
61273 GAATCGCGTTGCGATT-TTCT
1 GAATCGCGTTGCGATTCTT-G
*
61293 GAATCGCGTTGCGATT-TTCT
1 GAATCGCGTTGCGATTCTT-G
61313 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
61333 GAAGATCGCGTTGCGATTCTTG
1 G-A-ATCGCGTTGCGATTCTTG
*
61355 GAAGATCGCGTTGCGATT-TTAT
1 G-A-ATCGCGTTGCGATTCTT-G
*
61377 GAATCGCATTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
61397 GAAGATCGCGTTGCGAT
1 G-A-ATCGCGTTGCGAT
61414 CTTCTTTTCA
Statistics
Matches: 163, Mismatches: 6, Indels: 22
0.85 0.03 0.12
Matches are distributed among these distances:
18 5 0.03
19 2 0.01
20 93 0.57
21 9 0.06
22 54 0.33
ACGTcount: A:0.17, C:0.19, G:0.28, T:0.36
Consensus pattern (20 bp):
GAATCGCGTTGCGATTCTTG
Found at i:61448 original size:20 final size:20
Alignment explanation
Indices: 61425--61475 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 20
61415 TTCTTTTCAA
* *
61425 CGTTGCGCTTTTCTAAATCG
1 CGTTGCGATTTTCTGAATCG
*
61445 CGTTGCG-GTTT-TGATATCG
1 CGTTGCGATTTTCTGA-ATCG
61464 CGTTGCGATTTT
1 CGTTGCGATTTT
61476 GTTGGTCATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 2 0.08
19 14 0.54
20 10 0.38
ACGTcount: A:0.12, C:0.20, G:0.25, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCTGAATCG
Found at i:61705 original size:15 final size:15
Alignment explanation
Indices: 61685--61716 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
61675 CCCGACCTAT
61685 AGAATACTGTTCAAA
1 AGAATACTGTTCAAA
*
61700 AGAATACTTTTCAAA
1 AGAATACTGTTCAAA
61715 AG
1 AG
61717 GAACTATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.28
Consensus pattern (15 bp):
AGAATACTGTTCAAA
Found at i:77130 original size:23 final size:23
Alignment explanation
Indices: 77104--77150 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
77094 ACAAATTAGA
* **
77104 TAGCGCTTATATAATGTAATAGG
1 TAGCACTTATATAATAAAATAGG
77127 TAGCACTTATATAATAAAATAGG
1 TAGCACTTATATAATAAAATAGG
77150 T
1 T
77151 TAATTACTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34
Consensus pattern (23 bp):
TAGCACTTATATAATAAAATAGG
Found at i:77213 original size:23 final size:22
Alignment explanation
Indices: 77109--77237 Score: 68
Period size: 23 Copynumber: 5.9 Consensus size: 22
77099 TTAGATAGCG
* *
77109 CTTATATAATGTAATAGGTAGCA
1 CTTATATAATATAATAGGTA-AA
* *
77132 CTTATATAATAAAATAGGTTAA
1 CTTATATAATATAATAGGTAAA
* * * *
77154 -TTACTGTAA-ACATTA-TTAAA
1 CTTA-TATAATATAATAGGTAAA
* * *
77174 CATA-ATAACATATTAGGTAACA
1 CTTATATAATATAATAGGTAA-A
**
77196 CTTATATAATATAATAGGTAGTG
1 CTTATATAATATAATAGGTA-AA
*
77219 CTTATATAATAAAATAGGT
1 CTTATATAATATAATAGGT
77238 TAATTACTAG
Statistics
Matches: 80, Mismatches: 19, Indels: 14
0.71 0.17 0.12
Matches are distributed among these distances:
19 3 0.04
20 8 0.10
21 12 0.15
22 9 0.11
23 48 0.60
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.36
Consensus pattern (22 bp):
CTTATATAATATAATAGGTAAA
Found at i:77224 original size:87 final size:87
Alignment explanation
Indices: 77090--77312 Score: 340
Period size: 87 Copynumber: 2.6 Consensus size: 87
77080 TATCAAGTAA
* * *
77090 AATAACAAATTAGATAGCGCTTATATAATGTAATAGGTAGCACTTATATAATAAAATAGGTTAAT
1 AATAACATATTAGGTAGCGCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAAT
* *
77155 TACT-GTAAACATTATTAAACAT
66 TACTAG-AAACATTATCAAACAC
* * * *
77177 AATAACATATTAGGTAACACTTATATAATATAATAGGTAGTGCTTATATAATAAAATAGGTTAAT
1 AATAACATATTAGGTAGCGCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAAT
*
77242 TACTAGAAACATTATCAAGCAC
66 TACTAGAAACATTATCAAACAC
77264 AATAACATATTAGGTAGCGCTTATATAATGTAATAGGTAGCGCTTATAT
1 AATAACATATTAGGTAGCGCTTATATAATGTAATAGGTAGCGCTTATAT
77313 TGACCTATTT
Statistics
Matches: 121, Mismatches: 14, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
87 120 0.99
88 1 0.01
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (87 bp):
AATAACATATTAGGTAGCGCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAAT
TACTAGAAACATTATCAAACAC
Found at i:77291 original size:23 final size:23
Alignment explanation
Indices: 77265--77312 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
77255 ATCAAGCACA
*
77265 ATAACATATTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
77288 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
77311 AT
1 AT
77313 TGACCTATTT
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:0.10, G:0.19, T:0.35
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:77972 original size:199 final size:197
Alignment explanation
Indices: 77330--78026 Score: 866
Period size: 198 Copynumber: 3.5 Consensus size: 197
77320 TTTTCTAACT
* * ** *
77330 AAACCGGTATATTTATACCGGTAACATTACAAATTTACATATTACATTATAATTATTGGTTTCGA
1 AAACTGGTATATTTATACCGGTTACATTGTAAATTTACATATTACATTATAATTATCGGTTTCGA
* *
77395 TATTTTTGGGATCGATAAAATTTTAAATGTATCGACACTTTATGTGTGCACCTCGTTGGGCATTC
66 TATTTTTGGGATCGAT-ACATTTTAAATGTATCGACACTTTATGTGTGCACCTCGTTAGGCATTC
* ** * * *
77460 ATTCTGAAAAAAAGTATTTACACTTTTTAAATTTGTGTCGATACATTATATTGACATATTCAATC
130 ATTCTGGAAAAAAGTATCGACACTTTTTAAATTTGTGTCAATACATTATGTTGACATATTCTATC
77525 ATA
195 ATA
* *
77528 TAA-TCGGTATATTTATACCGGTTACATTGTAAATTTACATATTACATTATAATTATCGGTTTTG
1 AAACT-GGTATATTTATACCGGTTACATTGTAAATTTACATATTACATTATAATTATCGGTTTCG
*
77592 ATATTTTTGGGATCGATACAATTTTAAATGTATCGACACTTTATGCGTGCACCTCGTTAGGCATT
65 ATATTTTTGGGATCGATAC-ATTTTAAATGTATCGACACTTTATGTGTGCACCTCGTTAGGCATT
* *** ** * * *
77657 CATTCTGGAAAAAAGTATCGACGCAAACTTAAA-ACGTGTCAATACATTATGTAGACATATTTTC
129 CATTCTGGAAAAAAGTATCGACAC-TTTTTAAATTTGTGTCAATACATTATGTTGACATATTCTA
77721 TCATA
193 TCATA
* * * *
77726 AAACCGGTATATTTCTACCAGG-TACATTGTAAATTTACCTATTACATTGTAATTATCGGTTTCG
1 AAACTGGTATATTTATACC-GGTTACATTGTAAATTTACATATTACATTATAATTATCGGTTTCG
* * * * *
77790 ATGTTTTT-GGATCGATACTTTTAATAAATGCATCAACACTTTATGTGTGCACCTCGTTTGGCAT
65 ATATTTTTGGGATCGATACATTT--TAAATGTATCGACACTTTATGTGTGCACCTCGTTAGGCAT
* * * *
77854 TCATTCTGGACAAAATGTATCGACACTTTTTAAATTTGTGTTAATATATTATGTTGACCTATTCT
128 TCATTCTGGA-AAAAAGTATCGACACTTTTTAAATTTGTGTCAATACATTATGTTGACATATTCT
77919 ATCATA
192 ATCATA
* * *
77925 AAACTGATATATTTATACTGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGA
1 AAACTGGTATATTTATACCGGTTACATTGTAAATTTACATATTACATTATAATTATCGGTTTCGA
* *
77990 TGTTTCTGGG-TCGATAC-TTTTAGAAAATGTATCGACA
66 TATTTTTGGGATCGATACATTTT---AAATGTATCGACA
78027 TATATGTTTA
Statistics
Matches: 427, Mismatches: 58, Indels: 27
0.83 0.11 0.05
Matches are distributed among these distances:
196 4 0.01
197 11 0.03
198 281 0.66
199 129 0.30
200 2 0.00
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (197 bp):
AAACTGGTATATTTATACCGGTTACATTGTAAATTTACATATTACATTATAATTATCGGTTTCGA
TATTTTTGGGATCGATACATTTTAAATGTATCGACACTTTATGTGTGCACCTCGTTAGGCATTCA
TTCTGGAAAAAAGTATCGACACTTTTTAAATTTGTGTCAATACATTATGTTGACATATTCTATCA
TA
Found at i:78312 original size:21 final size:21
Alignment explanation
Indices: 78273--78313 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
78263 CAGTAAAAAT
* *
78273 TACCTAAAACATTATTATTTC
1 TACCTAAAACATCAATATTTC
78294 TACCTAAAACATCAATATTT
1 TACCTAAAACATCAATATTT
78314 TTAAACATTT
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:0.41, C:0.20, G:0.00, T:0.39
Consensus pattern (21 bp):
TACCTAAAACATCAATATTTC
Found at i:78571 original size:109 final size:108
Alignment explanation
Indices: 78371--78575 Score: 295
Period size: 109 Copynumber: 1.9 Consensus size: 108
78361 AAATAACAAA
*
78371 ACCGGTAGCACTTTTACCGATTTTGTTAAGAAACCCGGTAAAATGCCAAAATAATAACAAAACCA
1 ACCGGTAGCACTTTTACCGATTTTGTTAAAAAACCCGGTAAAATGCCAAAATAATAACAAAACCA
*
78436 ATAGAAATAATGATGTTTTCGATAATTTTTACCGGTTTTGTTG
66 ATAGAAATAATGATGTATTCGATAATTTTTACCGGTTTTGTTG
** * * *
78479 ACCGGTAGTGCTTTTACC-AGTTTTGTTAAAAAAACTCGGTAAAATGTCAAAATAATTACAAAAC
1 ACCGGTAGCACTTTTACCGA-TTTTGTT-AAAAAACCCGGTAAAATGCCAAAATAATAACAAAAC
** *
78543 CGGTAGAAATAATGATGTATTCGGTAATTTTTA
64 CAATAGAAATAATGATGTATTCGATAATTTTTA
78576 GCCGTATATT
Statistics
Matches: 85, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
107 1 0.01
108 23 0.27
109 61 0.72
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (108 bp):
ACCGGTAGCACTTTTACCGATTTTGTTAAAAAACCCGGTAAAATGCCAAAATAATAACAAAACCA
ATAGAAATAATGATGTATTCGATAATTTTTACCGGTTTTGTTG
Done.