Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007173.1 Hibiscus syriacus cultivar Beakdansim tig00018827_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: 1357898
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 9
Found at i:1323230 original size:13 final size:13
Alignment explanation
Indices: 1323214--1323258 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
1323204 GTAATAAATC
*
1323214 TATGACTCGCATT
1 TATGACACGCATT
1323227 TATGACACGCATT
1 TATGACACGCATT
1323240 TATGACACGCATT
1 TATGACACGCATT
*
1323253 AATGAC
1 TATGAC
1323259 GTTCTTTGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (13 bp):
TATGACACGCATT
Found at i:1323331 original size:85 final size:85
Alignment explanation
Indices: 1323237--1323531 Score: 422
Period size: 85 Copynumber: 3.5 Consensus size: 85
1323227 TATGACACGC
* *
1323237 ATTTATGACACGCAT-TAATGACGTT-CTTTGAGTGTCATTGAAGCCTCCGTCATAAATTAAGAT
1 ATTTATGACACGCATGT-ATGAC-TTACATTGCGTGTCATTGAAGCCTCCGTCATAAATTAAGAT
1323300 GACACACATTTGTGCGTCATAA
64 GACACACATTTGTGCGTCATAA
*
1323322 ATTTATGACACGCATGTATGACTTACATTGCGCGTCATTGAAG-CTCCGTCATAAATTAAGATGA
1 ATTTATGACACGCATGTATGACTTACATTGCGTGTCATTGAAGCCTCCGTCATAAATTAAGATGA
*
1323386 CACACATTTATGCGTCATAA
66 CACACATTTGTGCGTCATAA
* *
1323406 ATTTATGACACGCATGTATGACTTACATTGC-TCGTCATTGAAGCCCCCGTCATAAATCT--GCT
1 ATTTATGACACGCATGTATGACTTACATTGCGT-GTCATTGAAGCCTCCGTCATAAAT-TAAG-A
* *
1323468 TGACATACATTTGTGTGTCATAA
63 TGACACACATTTGTGCGTCATAA
*
1323491 ATTTATGACACGCATATATGACTTACATTGCGTGTCATTGA
1 ATTTATGACACGCATGTATGACTTACATTGCGTGTCATTGA
1323532 TTCACACGTC
Statistics
Matches: 192, Mismatches: 11, Indels: 14
0.88 0.05 0.06
Matches are distributed among these distances:
84 84 0.44
85 105 0.55
86 3 0.02
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (85 bp):
ATTTATGACACGCATGTATGACTTACATTGCGTGTCATTGAAGCCTCCGTCATAAATTAAGATGA
CACACATTTGTGCGTCATAA
Found at i:1323425 original size:28 final size:29
Alignment explanation
Indices: 1323368--1323425 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
1323358 ATTGAAGCTC
*
1323368 CGTCATAAATTAAGATGACACACATTTATG
1 CGTCATAAATT-AGATGACACACATGTATG
* *
1323398 CGTCATAAATT-TATGACACGCATGTATG
1 CGTCATAAATTAGATGACACACATGTATG
1323426 ACTTACATTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 14 0.56
30 11 0.44
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (29 bp):
CGTCATAAATTAGATGACACACATGTATG
Found at i:1323569 original size:85 final size:83
Alignment explanation
Indices: 1323237--1323571 Score: 329
Period size: 85 Copynumber: 4.0 Consensus size: 83
1323227 TATGACACGC
* * * *
1323237 ATTTATGACACGCAT-TAATGACGTT-CTTTGAGTGTCATTGAAGCCTCCGTCATAAATTAAGAT
1 ATTTATGACACGCATGT-ATGAC-TTACATTGCGTGTCATTGAAG-CACCGTCATAAA-TAAGAC
* *
1323300 GACACACATTTGTGCGTCATAA
62 GACAAACATTTGTGTGTCATAA
* * *
1323322 ATTTATGACACGCATGTATGACTTACATTGCGCGTCATTGAAGCTCCGTCATAAATTAAGATGAC
1 ATTTATGACACGCATGTATGACTTACATTGCGTGTCATTGAAGCACCGTCATAAA-TAAGACGAC
* * *
1323387 ACACATTTATGCGTCATAA
65 AAACATTTGTGTGTCATAA
* **
1323406 ATTTATGACACGCATGTATGACTTACATTGC-TCGTCATTGAAGCCCCCGTCATAAATCTG-CTT
1 ATTTATGACACGCATGTATGACTTACATTGCGT-GTCATTGAAG-CACCGTCATAAATAAGAC--
*
1323469 GACATACATTTGTGTGTCATAA
62 GACAAACATTTGTGTGTCATAA
* ** *
1323491 ATTTATGACACGCATATATGACTTACATTGCGTGTCATTGATTCACACGTCATTTAAA-AAGACC
1 ATTTATGACACGCATGTATGACTTACATTGCGTGTCATTGAAGCAC-CGTCA--TAAATAAGACG
* *
1323555 ACAAACGTTCGTGTGTC
63 ACAAACATTTGTGTGTC
1323572 GTGATTGTAT
Statistics
Matches: 217, Mismatches: 22, Indels: 22
0.83 0.08 0.08
Matches are distributed among these distances:
84 87 0.40
85 122 0.56
86 3 0.01
87 5 0.02
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.33
Consensus pattern (83 bp):
ATTTATGACACGCATGTATGACTTACATTGCGTGTCATTGAAGCACCGTCATAAATAAGACGACA
AACATTTGTGTGTCATAA
Found at i:1323598 original size:2 final size:2
Alignment explanation
Indices: 1323591--1323733 Score: 205
Period size: 2 Copynumber: 71.5 Consensus size: 2
1323581 TTTCAGAAAT
* * * *
1323591 TA TA TA TA TA TA GA GA TA TA TA AA TA TA AA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
1323633 TA TA TA TA TA TA TA AA TA TA GA TA TA TA TA TA AA TA TA AA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1323675 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1323717 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
1323734 TGTAGATTGA
Statistics
Matches: 125, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 125 1.00
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (2 bp):
TA
Found at i:1329621 original size:15 final size:15
Alignment explanation
Indices: 1329596--1329651 Score: 76
Period size: 15 Copynumber: 3.7 Consensus size: 15
1329586 GATGCTTTCT
*
1329596 TTTTCCTTCTTTGACA
1 TTTT-CTTCTTTGACG
1329612 TTTTCTTCTTTGACG
1 TTTTCTTCTTTGACG
*
1329627 TTTTCTTCTTAGACG
1 TTTTCTTCTTTGACG
*
1329642 TTGTCTTCTT
1 TTTTCTTCTT
1329652 ACCCCATGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
15 33 0.89
16 4 0.11
ACGTcount: A:0.09, C:0.21, G:0.11, T:0.59
Consensus pattern (15 bp):
TTTTCTTCTTTGACG
Found at i:1340700 original size:7 final size:7
Alignment explanation
Indices: 1340688--1340719 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
1340678 ATTGGAGCCT
1340688 AGGCGCA
1 AGGCGCA
1340695 AGGCGCA
1 AGGCGCA
1340702 AGGCGCA
1 AGGCGCA
1340709 AGGCGC-
1 AGGCGCA
1340715 AGGCG
1 AGGCG
1340720 TATTCCTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.20
7 20 0.80
ACGTcount: A:0.25, C:0.28, G:0.47, T:0.00
Consensus pattern (7 bp):
AGGCGCA
Found at i:1341154 original size:17 final size:17
Alignment explanation
Indices: 1341114--1341155 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
1341104 TAAATTAATT
1341114 TTATTAT-TAATTTAAA
1 TTATTATATAATTTAAA
*
1341130 ATATTTATATAATTTAAA
1 TTA-TTATATAATTTAAA
1341148 TTATTATA
1 TTATTATA
1341156 AAAAAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 2 0.09
17 9 0.41
18 11 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTATTATATAATTTAAA
Found at i:1341710 original size:16 final size:16
Alignment explanation
Indices: 1341689--1341728 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
1341679 TCTTCTTCTT
*
1341689 CTCTCCTCGTGGATAA
1 CTCTCCTCGTAGATAA
1341705 CTCTCCTCGTAGATAA
1 CTCTCCTCGTAGATAA
1341721 CTCTCCTC
1 CTCTCCTC
1341729 CATAACTCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.17, C:0.38, G:0.12, T:0.33
Consensus pattern (16 bp):
CTCTCCTCGTAGATAA
Found at i:1342793 original size:56 final size:56
Alignment explanation
Indices: 1342720--1342927 Score: 296
Period size: 56 Copynumber: 3.7 Consensus size: 56
1342710 TAAGTGTGCA
1342720 AAAAGCTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
1 AAAA-CTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
* *
1342777 AAAACTTAAGAAATTCATACTAAGTGGATGGATTTCTGTATGGGCACTATATGTGT
1 AAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
* ** * *
1342833 AAAACTAAAGAAATTCATACTAAGTGGATGAATTTTTGTATGGGTACTATATGTGC
1 AAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
* *
1342889 AAAAC-T-AGAAAATT-ATACTAAGTGTATAAATTTCCGTAT
1 AAAACTTAAG-AAATTCATACTAAGTGGATGAATTTCCGTAT
1342928 TGGTAACAGG
Statistics
Matches: 138, Mismatches: 12, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
54 23 0.17
55 5 0.04
56 106 0.77
57 4 0.03
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.33
Consensus pattern (56 bp):
AAAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTATATGTGT
Found at i:1343541 original size:10 final size:11
Alignment explanation
Indices: 1343519--1343562 Score: 65
Period size: 11 Copynumber: 4.2 Consensus size: 11
1343509 ACTTTTCACC
1343519 TTCT-TTTTCT
1 TTCTATTTTCT
1343529 TTCTATTTT-T
1 TTCTATTTTCT
1343539 TTCTATTTTCT
1 TTCTATTTTCT
*
1343550 TTCTATATTCT
1 TTCTATTTTCT
1343561 TT
1 TT
1343563 TCCCTAAGGC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
10 14 0.45
11 17 0.55
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.75
Consensus pattern (11 bp):
TTCTATTTTCT
Found at i:1343547 original size:21 final size:22
Alignment explanation
Indices: 1343519--1343564 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 22
1343509 ACTTTTCACC
1343519 TTCTTTTTCTTTCTAT-TT-TT
1 TTCTTTTTCTTTCTATATTCTT
1343539 TTCTATTTTCTTTCTATATTCTT
1 TTCT-TTTTCTTTCTATATTCTT
1343562 TTC
1 TTC
1343565 CCTAAGGCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 4 0.17
21 12 0.52
22 2 0.09
23 5 0.22
ACGTcount: A:0.09, C:0.17, G:0.00, T:0.74
Consensus pattern (22 bp):
TTCTTTTTCTTTCTATATTCTT
Found at i:1344154 original size:76 final size:74
Alignment explanation
Indices: 1344063--1344226 Score: 231
Period size: 74 Copynumber: 2.2 Consensus size: 74
1344053 TTAAACTCAA
*
1344063 ATTTAGGATAATATTTTAAACATTATA-TTTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGT
1 ATTTAGGATATTATTTT-AACATTATATTTTTATCTTTGTA-TTTAGTTTAAATAGG-TTTTAGT
1344127 ATTTTAATTAAG
63 ATTTTAATTAAG
* * * *
1344139 TTTTAGGATATTATTTTTATATTTTATTTTTATCTTTGTATTTAGTTTAAATAGGTTTTAGTATT
1 ATTTAGGATATTATTTTAACATTATATTTTTATCTTTGTATTTAGTTTAAATAGGTTTTAGTATT
*
1344204 TTAATTAGG
66 TTAATTAAG
*
1344213 ATTTAGAATATTAT
1 ATTTAGGATATTAT
1344227 ATTATTTTTT
Statistics
Matches: 79, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
74 30 0.38
75 21 0.27
76 28 0.35
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (74 bp):
ATTTAGGATATTATTTTAACATTATATTTTTATCTTTGTATTTAGTTTAAATAGGTTTTAGTATT
TTAATTAAG
Found at i:1344212 original size:19 final size:19
Alignment explanation
Indices: 1344184--1344246 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
1344174 TTGTATTTAG
*
1344184 TTTAAATAGGTTTTAGTAT
1 TTTAATTAGGTTTTAGTAT
* *
1344203 TTTAATTAGGATTTAGAAT
1 TTTAATTAGGTTTTAGTAT
* **
1344222 ATTATATTATTTTTTAGGTAT
1 TTTA-ATTAGGTTTTA-GTAT
1344243 TTTA
1 TTTA
1344247 GTTTAAATAG
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
19 19 0.58
20 8 0.24
21 6 0.18
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.56
Consensus pattern (19 bp):
TTTAATTAGGTTTTAGTAT
Found at i:1344224 original size:74 final size:77
Alignment explanation
Indices: 1344085--1344226 Score: 236
Period size: 74 Copynumber: 1.9 Consensus size: 77
1344075 ATTTTAAACA
* *
1344085 TTATATTTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGTTTTAGGATAT
1 TTATATTTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGATTTAGAATAT
1344150 TATTTTTATATT
66 TATTTTTATATT
*
1344162 TTAT-TTTTATCTTTGTA-TTTAGTTTAAATAGG-TTTTAGTATTTTAATTAGGATTTAGAATAT
1 TTATATTTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGATTTAGAATAT
1344224 TAT
66 TAT
1344227 ATTATTTTTT
Statistics
Matches: 62, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
74 30 0.48
75 15 0.24
76 13 0.21
77 4 0.06
ACGTcount: A:0.28, C:0.01, G:0.11, T:0.59
Consensus pattern (77 bp):
TTATATTTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGATTTAGAATAT
TATTTTTATATT
Found at i:1344262 original size:74 final size:74
Alignment explanation
Indices: 1344106--1344259 Score: 172
Period size: 74 Copynumber: 2.1 Consensus size: 74
1344096 CTTTGTATTT
* * *
1344106 TAGTTTAAATAGGTTTTTAGTATTTTAATTAAGTTTTAGGATATTATTTTTATATTTTATTTTTA
1 TAGTTTAAATAGGTTTTTAGTATTTTAATTAAGATTTAGAATATTATTATTATATTTTATTTTTA
* **
1344171 TCTTTGTATT
66 -CGTTGTAAA
* *
1344181 TAGTTTAAATAGG-TTTTAGTATTTTAATTAGGATTTAGAATATTA-TATTATTTTTTAGGTATT
1 TAGTTTAAATAGGTTTTTAGTATTTTAATTAAGATTTAGAATATTATTATTATATTTTA--T-TT
1344244 TTA-GTT-TAAA
63 TTACGTTGTAAA
1344254 TAGTTT
1 TAGTTT
1344260 TAAGTGTTTT
Statistics
Matches: 68, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
73 18 0.26
74 31 0.46
75 14 0.21
76 5 0.07
ACGTcount: A:0.29, C:0.01, G:0.12, T:0.58
Consensus pattern (74 bp):
TAGTTTAAATAGGTTTTTAGTATTTTAATTAAGATTTAGAATATTATTATTATATTTTATTTTTA
CGTTGTAAA
Found at i:1344893 original size:16 final size:17
Alignment explanation
Indices: 1344869--1344914 Score: 58
Period size: 16 Copynumber: 2.7 Consensus size: 17
1344859 AATCTCTTTA
*
1344869 ATTTGTTTATTTAATT-
1 ATTTTTTTATTTAATTC
1344885 ATTTTTTTATTTAATTC
1 ATTTTTTTATTTAATTC
*
1344902 TTATTTTTTATTT
1 AT-TTTTTTATTT
1344915 TAACCACAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 15 0.58
17 1 0.04
18 10 0.38
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (17 bp):
ATTTTTTTATTTAATTC
Found at i:1346681 original size:15 final size:15
Alignment explanation
Indices: 1346658--1346691 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1346648 CCAGCATAAA
*
1346658 AAGATGCACATCAGG
1 AAGACGCACATCAGG
1346673 AAGACGCACATCAGG
1 AAGACGCACATCAGG
1346688 AAGA
1 AAGA
1346692 ACAAGAGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.44, C:0.21, G:0.26, T:0.09
Consensus pattern (15 bp):
AAGACGCACATCAGG
Found at i:1348797 original size:93 final size:93
Alignment explanation
Indices: 1348638--1348825 Score: 367
Period size: 93 Copynumber: 2.0 Consensus size: 93
1348628 TAGCATGTAA
1348638 TCTACTTCAAAAGGATCAAGACTTTAACTTTAATTCAAAATGCAAAGAGTCTTTCGATTCATTAA
1 TCTACTTCAAAAGGATCAAGACTTTAACTTTAATTCAAAATGCAAAGAGTCTTTCGATTCATTAA
1348703 AGGAAAAGCTTATTTCAGCACCAATTGT
66 AGGAAAAGCTTATTTCAGCACCAATTGT
1348731 TCTACTTCAAAAGGATCAAGACTTTAACTTTAATTCAAAATGCAAAGAGTCTTTCGATTCATTAA
1 TCTACTTCAAAAGGATCAAGACTTTAACTTTAATTCAAAATGCAAAGAGTCTTTCGATTCATTAA
*
1348796 AGGAAAATCTTATTTCAGCACCAATTGT
66 AGGAAAAGCTTATTTCAGCACCAATTGT
1348824 TC
1 TC
1348826 AGCTGCCAGA
Statistics
Matches: 94, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 94 1.00
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (93 bp):
TCTACTTCAAAAGGATCAAGACTTTAACTTTAATTCAAAATGCAAAGAGTCTTTCGATTCATTAA
AGGAAAAGCTTATTTCAGCACCAATTGT
Found at i:1350631 original size:20 final size:20
Alignment explanation
Indices: 1350606--1350652 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
1350596 CATTTCGTTA
1350606 TATTTTTGTTTT-TATTTTTT
1 TATTTTTGTTTTAT-TTTTTT
*
1350626 TATTTTCGTTTTATTTTTTT
1 TATTTTTGTTTTATTTTTTT
1350646 TATTTTT
1 TATTTTT
1350653 TAGCGAACAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.11, C:0.02, G:0.04, T:0.83
Consensus pattern (20 bp):
TATTTTTGTTTTATTTTTTT
Found at i:1352513 original size:76 final size:75
Alignment explanation
Indices: 1352432--1352579 Score: 226
Period size: 76 Copynumber: 2.0 Consensus size: 75
1352422 TAAACTCAAA
1352432 TTTAGGATAATATTTTAAACATTATAT-TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTA
1 TTTAGGATAATATTTT-AACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGG-TTTTAGTA
*
1352496 TTTTTATTAAGT
64 TTTTAATTAAGT
* * * *
1352508 TTTAGGATATTATTTTTATATTTTATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTATT
1 TTTAGGATAATATTTTAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTATT
1352573 TTAATTA
66 TTAATTA
1352580 GAATTTAGAA
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
75 23 0.35
76 43 0.65
ACGTcount: A:0.28, C:0.03, G:0.10, T:0.59
Consensus pattern (75 bp):
TTTAGGATAATATTTTAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTATT
TTAATTAAGT
Found at i:1353886 original size:13 final size:13
Alignment explanation
Indices: 1353868--1353899 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1353858 ATATATAGAC
1353868 GAAAATGATTTTT
1 GAAAATGATTTTT
*
1353881 GAAAATGGTTTTT
1 GAAAATGATTTTT
1353894 GAAAAT
1 GAAAAT
1353900 ACATATAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41
Consensus pattern (13 bp):
GAAAATGATTTTT
Found at i:1353977 original size:36 final size:34
Alignment explanation
Indices: 1353909--1354197 Score: 255
Period size: 34 Copynumber: 8.2 Consensus size: 34
1353899 TACATATAAA
*
1353909 TATATAGTTTTTAAAACATTTTCGAAAATATATAT
1 TATATAGTTTTTAAAACATTTT-TAAAATATATAT
* *
1353944 TATATAGTTTATAAAACATTTTTAAAATTTATAT
1 TATATAGTTTTTAAAACATTTTTAAAATATATAT
* * *
1353978 AATATAGTTTTTGAAA-ATATTTGAAAATATCTATAT
1 TATATAGTTTTTAAAACAT-TTTTAAAATA--TATAT
* *
1354014 AATATAGTTTTTTGAAAACATTTTTTGAAAACATATAT
1 TATATAG-TTTTT-AAAACA-TTTTT-AAAATATATAT
* * * *
1354052 TATATA-ATTTGAAAGCATTTTTAAAATATATAA
1 TATATAGTTTTTAAAACATTTTTAAAATATATAT
* *
1354085 TATATAGTTTTTAAAAAATTTTTAAAATATATAA
1 TATATAGTTTTTAAAACATTTTTAAAATATATAT
*
1354119 TACA-AGTTTTTGAAAACATTTTTAAAAACTTATATAT
1 TATATAGTTTTT-AAAACATTTTT-AAAA--TATATAT
* *
1354156 ATATATAG-TTTAAAAATCA-TTTTGAAATATATAT
1 -TATATAGTTTTTAAAA-CATTTTTAAAATATATAT
1354190 ATATATAG
1 -TATATAG
1354198 CATAGTTTAC
Statistics
Matches: 211, Mismatches: 27, Indels: 33
0.78 0.10 0.12
Matches are distributed among these distances:
33 24 0.11
34 87 0.41
35 30 0.14
36 18 0.09
37 19 0.09
38 21 0.10
39 6 0.03
40 6 0.03
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (34 bp):
TATATAGTTTTTAAAACATTTTTAAAATATATAT
Found at i:1354039 original size:13 final size:13
Alignment explanation
Indices: 1354021--1354047 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1354011 TATAATATAG
1354021 TTTTTTGAAAACA
1 TTTTTTGAAAACA
1354034 TTTTTTGAAAACA
1 TTTTTTGAAAACA
1354047 T
1 T
1354048 ATATTATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.48
Consensus pattern (13 bp):
TTTTTTGAAAACA
Found at i:1355462 original size:2 final size:2
Alignment explanation
Indices: 1355455--1355489 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1355445 TTTCACTTAT
1355455 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1355490 TACATTAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1355546 original size:25 final size:24
Alignment explanation
Indices: 1355512--1355587 Score: 86
Period size: 25 Copynumber: 3.2 Consensus size: 24
1355502 TTTTCCCTCA
*
1355512 TTTTATTCTTTTTTGTTTATTATTT
1 TTTTA-TCTTTTTTATTTATTATTT
*
1355537 TTTTACTCTTTTTTCATTTA--A-CT
1 TTTTA-TCTTTTTT-ATTTATTATTT
1355560 TTTTATCTTTTTTATTTATTATTT
1 TTTTATCTTTTTTATTTATTATTT
1355584 TTTT
1 TTTT
1355588 TATAATTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
21 5 0.12
22 8 0.19
23 7 0.16
24 6 0.14
25 13 0.30
26 4 0.09
ACGTcount: A:0.14, C:0.08, G:0.01, T:0.76
Consensus pattern (24 bp):
TTTTATCTTTTTTATTTATTATTT
Found at i:1355568 original size:22 final size:22
Alignment explanation
Indices: 1355536--1355577 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1355526 GTTTATTATT
1355536 TTTTTACTCTTTTTTCATTTAAC
1 TTTTTACTCTTTTTT-ATTTAAC
1355559 TTTTTA-TCTTTTTTATTTA
1 TTTTTACTCTTTTTTATTTA
1355578 TTATTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 5 0.26
22 8 0.42
23 6 0.32
ACGTcount: A:0.17, C:0.12, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTTTACTCTTTTTTATTTAAC
Done.