Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004951.1 Hibiscus syriacus cultivar Beakdansim tig00011133_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: 90040
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:1763 original size:567 final size:564
Alignment explanation
Indices: 918--2011 Score: 1602
Period size: 567 Copynumber: 1.9 Consensus size: 564
908 GTTGAATATG
* * * *
918 GTTTTGCTTGTTCTTGTTGCAATCCACCTTAGCTATGATACCACTGATAAGATACGGCCTAGCAT
1 GTTTTGCTTGTTATTCTTGCAATCCACCTTAGCTATGATACCACTGATAAGATACGACCTAACAT
* *
983 ACCTTGGAAGACAAGGATGTACCTTTGATTGTCCGATCTAGGAAAGCAACAAGGATCCTGCACAA
66 ACCTTGGAAGACAAGGATGTACCTTTGATTGACCGATCTAGGAAAACAACAAGGATCCTGCACAA
*
1048 ACAAGAAAACTCAAATAGAATGGCTAAATGGAATGGAAAGATATGGCAGCAGAATGGAAAAAATA
131 ACAAGAAAACTCAAATAGAATGGCTAAATGGAATGGAAAGATATGGCAGCAGAATAGAAAAAATA
* *
1113 TATATTGGTTATATTTAAAGGAAATGTGAAGTATGGTAGAATGGATATGATGGAAATGAATATGA
196 TATATTGGTGATATTT--AGGAAATGTGAAG-ATGGTAGAA-GGATATGATAGAAATGAATATGA
* *
1178 AAGATAATATCTCCAAGAAGACTCAAAGAAGAACCGATGTTAAAGAACAAAGACCCAGACTTTAT
257 AAGATAATATCTCCAAGAAGACTCAAAGAAGAAACAATGTTAAAGAACAAAGACCCAGACTTTAT
* * **
1243 -TTGCTTCTTAAAGGGGTGGTAAACAAGGACTTTGA-CCACTATCTATAAGGGATAGGAACCAAA
322 ATTACTTCTTAAAGGGGTGGTAAACAAGGACTTTGACCCACTATCTATAAGAGATAAAAACCAAA
*
1306 AGTATCA-GATGAATAGATGGGGTTGACACCACAAGCATAAGCTTGATAAGTCGATAAAGTTCAA
387 AGTATCAGGATAAATAGATGGGGTTGACACCACAAGCATAAGCTTGATAAGTCGATAAAGTTCAA
1370 TTAAGAACTAAAGAG-AAAACTCTCACAATATTTGATTAAAACAAGTATGCCTTAC-AATGAAAT
452 TTAA-AACTAAAGAGAAAAACTCTCACAATATTTGATT-AAACAAGTATGCCTTACAAATGAAAT
1433 ATGAAACCTATTTATAGAGTTTGAGAGAATGTGGTCGATGGTAAAGTATT
515 ATGAAACCTATTTATAGAGTTTGAGAGAATGTGGTCGATGGTAAAGTATT
* *
1483 GTTTTGCTTGTTATTCTTGCAATCCACCTTAGTTCTGATACCACTTGATAAGATACGACCTAACA
1 GTTTTGCTTGTTATTCTTGCAATCCACCTTAGCTATGATACCAC-TGATAAGATACGACCTAACA
* * *
1548 TTCCTTGGAAGATAAGGATGTACCTTTGATTGACTCGATCTAGGAAAACAATAAGGATCCTGCAC
65 TACCTTGGAAGACAAGGATGTACCTTTGATTGAC-CGATCTAGGAAAACAACAAGGATCCTGCAC
1613 AAACAAGAAAACTCAAAATAGAATGGCTAAATAGAAGTAATGGAATAGAAAGATATGGCAGCAGA
129 AAACAAGAAAACTC-AAATAGAATGGCTAAAT-G--G-AAT-G----GAAAGATATGGCAGCAGA
* * * ** *
1678 ATATATATATATATATATTGGGTGATATTT-TTAAA-G-GAA-ATGGT-GAA-G-TATGGTAG-A
184 ATAGA-AAAAATATATATT-GGTGATATTTAGGAAATGTGAAGATGGTAGAAGGATATGATAGAA
* *
1735 ATGAATATGAAAGATAGTATCTCCAAGAAGACTCAAAGAAGAAATAATGTTAAAGAACAAAGACC
247 ATGAATATGAAAGATAATATCTCCAAGAAGACTCAAAGAAGAAACAATGTTAAAGAACAAAGACC
*
1800 CAGACTTTATATTACTTCTTAAAGGGGTGGTAAATAAGGACTTTGACCCACTATCTATAAGAGAT
312 CAGACTTTATATTACTTCTTAAAGGGGTGGTAAACAAGGACTTTGACCCACTATCTATAAGAGAT
* * **
1865 AAAAATCAGAAGTATCAGGATAAATAGATGGGGTTGATGCCACAAGCATAAGCTTGATAAGTCGA
377 AAAAACCAAAAGTATCAGGATAAATAGATGGGGTTGACACCACAAGCATAAGCTTGATAAGTCGA
*
1930 TAAAGTTCAATTAAAACTAAAGAGAAAAACTCTCACAATATTTGATTAAACAAGTCTGCCTTACA
442 TAAAGTTCAATTAAAACTAAAGAGAAAAACTCTCACAATATTTGATTAAACAAGTATGCCTTACA
1995 AATGAAATATGAAACCT
507 AATGAAATATGAAACCT
2012 TATACGATCC
Statistics
Matches: 475, Mismatches: 35, Indels: 33
0.87 0.06 0.06
Matches are distributed among these distances:
565 40 0.08
566 49 0.10
567 114 0.24
568 56 0.12
569 58 0.12
570 97 0.20
571 4 0.01
572 8 0.02
573 1 0.00
574 3 0.01
575 1 0.00
576 3 0.01
577 21 0.04
578 11 0.02
579 9 0.02
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (564 bp):
GTTTTGCTTGTTATTCTTGCAATCCACCTTAGCTATGATACCACTGATAAGATACGACCTAACAT
ACCTTGGAAGACAAGGATGTACCTTTGATTGACCGATCTAGGAAAACAACAAGGATCCTGCACAA
ACAAGAAAACTCAAATAGAATGGCTAAATGGAATGGAAAGATATGGCAGCAGAATAGAAAAAATA
TATATTGGTGATATTTAGGAAATGTGAAGATGGTAGAAGGATATGATAGAAATGAATATGAAAGA
TAATATCTCCAAGAAGACTCAAAGAAGAAACAATGTTAAAGAACAAAGACCCAGACTTTATATTA
CTTCTTAAAGGGGTGGTAAACAAGGACTTTGACCCACTATCTATAAGAGATAAAAACCAAAAGTA
TCAGGATAAATAGATGGGGTTGACACCACAAGCATAAGCTTGATAAGTCGATAAAGTTCAATTAA
AACTAAAGAGAAAAACTCTCACAATATTTGATTAAACAAGTATGCCTTACAAATGAAATATGAAA
CCTATTTATAGAGTTTGAGAGAATGTGGTCGATGGTAAAGTATT
Found at i:4072 original size:23 final size:22
Alignment explanation
Indices: 4014--4073 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 22
4004 AAAATTCAGC
*
4014 AAAGAAAACAAAAGCACTCAAAA
1 AAAGAAAA-GAAAGCACTCAAAA
* * *
4037 GAAGAAATTGAAAGCACTTGAAAA
1 AAAGAAA-AGAAAGCAC-TCAAAA
4061 AAAGAAAAGAAAG
1 AAAGAAAAGAAAG
4074 AAAGAAAAGT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
23 18 0.62
24 11 0.38
ACGTcount: A:0.65, C:0.10, G:0.17, T:0.08
Consensus pattern (22 bp):
AAAGAAAAGAAAGCACTCAAAA
Found at i:5367 original size:24 final size:24
Alignment explanation
Indices: 5340--5391 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
5330 GACATGTCCT
* * *
5340 TTGACGTTCCAACAGCTATGCCAC
1 TTGACGTTCAAAAAGATATGCCAC
* *
5364 TTGATGTTCAAAAAGATGTGCCAC
1 TTGACGTTCAAAAAGATATGCCAC
5388 TTGA
1 TTGA
5392 AGTGCCAAGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (24 bp):
TTGACGTTCAAAAAGATATGCCAC
Found at i:15067 original size:17 final size:17
Alignment explanation
Indices: 15045--15084 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
15035 TAACCTTATA
15045 ATATATACTATTATATT
1 ATATATACTATTATATT
15062 ATATATACTATTATATT
1 ATATATACTATTATATT
*
15079 ACATAT
1 ATATAT
15085 CATTCTAAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATATACTATTATATT
Found at i:16065 original size:15 final size:17
Alignment explanation
Indices: 16042--16075 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
16032 TTAATATATG
16042 TTTAGTTTATTA-TTAT
1 TTTAGTTTATTAGTTAT
16058 TTTA-TTTATTAGTTAT
1 TTTAGTTTATTAGTTAT
16074 TT
1 TT
16076 AGGACCTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (17 bp):
TTTAGTTTATTAGTTAT
Found at i:16842 original size:9 final size:9
Alignment explanation
Indices: 16828--16863 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
16818 TATTTTTTTC
16828 AAAAAAACA
1 AAAAAAACA
16837 AAAAAAACA
1 AAAAAAACA
*
16846 AAAAAAGGCA
1 AAAAAA-ACA
16856 AAAAAAAC
1 AAAAAAAC
16864 CCCAAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.83, C:0.11, G:0.06, T:0.00
Consensus pattern (9 bp):
AAAAAAACA
Found at i:16857 original size:19 final size:17
Alignment explanation
Indices: 16827--16863 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 17
16817 CTATTTTTTT
16827 CAAAAAAACAAAAAAAA
1 CAAAAAAACAAAAAAAA
16844 CAAAAAAAGGCAAAAAAAA
1 CAAAAAAA--CAAAAAAAA
16863 C
1 C
16864 CCCAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.44
19 10 0.56
ACGTcount: A:0.81, C:0.14, G:0.05, T:0.00
Consensus pattern (17 bp):
CAAAAAAACAAAAAAAA
Found at i:20664 original size:15 final size:17
Alignment explanation
Indices: 20641--20674 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
20631 TTAATATATG
20641 TTTAGTTTATTA-TTAT
1 TTTAGTTTATTAGTTAT
20657 TTTA-TTTATTAGTTAT
1 TTTAGTTTATTAGTTAT
20673 TT
1 TT
20675 AGGACCTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (17 bp):
TTTAGTTTATTAGTTAT
Found at i:21286 original size:10 final size:10
Alignment explanation
Indices: 21271--21302 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
21261 AGTGATGTCA
21271 AAGGTAGCTG
1 AAGGTAGCTG
21281 AAGGTAGCTG
1 AAGGTAGCTG
*
21291 AATGTAGCTG
1 AAGGTAGCTG
21301 AA
1 AA
21303 CATAATGTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.34, C:0.09, G:0.34, T:0.22
Consensus pattern (10 bp):
AAGGTAGCTG
Found at i:21642 original size:91 final size:90
Alignment explanation
Indices: 21467--21647 Score: 211
Period size: 91 Copynumber: 2.0 Consensus size: 90
21457 CCTAGAACAC
* * * *
21467 CCATGTGCCTTGCATATGACCAGCCTCCATGTGCCTTGTATGTGGATCATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGACCAGCCCCCATGTACCTTGCATATGGATCATTTAGGCGCCAAGATG
* *
21532 AATAGTTCTCTCCTTATTCGGCCAAG
66 AATAGATCTATCC-TATTCGGCCAAG
** * * * *
21558 CCATGTGTTTTGCATGTGATCAGCCCCCATGTACCTTGCATATGGTTCATTTAGGTGCCAAGATG
1 CCATGTGCCTTGCATATGACCAGCCCCCATGTACCTTGCATATGGATCATTTAGGCGCCAAGATG
*
21623 AATGGCCATCTATCC-ATTCGGCCAA
66 AATAG--ATCTATCCTATTCGGCCAA
21648 TCACCATTAC
Statistics
Matches: 75, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
91 69 0.92
93 6 0.08
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.31
Consensus pattern (90 bp):
CCATGTGCCTTGCATATGACCAGCCCCCATGTACCTTGCATATGGATCATTTAGGCGCCAAGATG
AATAGATCTATCCTATTCGGCCAAG
Found at i:45017 original size:3 final size:3
Alignment explanation
Indices: 45009--45073 Score: 71
Period size: 3 Copynumber: 22.0 Consensus size: 3
44999 CATTAATTTT
* * *
45009 TTA TTA TTA TTA TTA TTT TTG TT- TTA TTA TTA TTA TTT TTA TTAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A
*
45054 TT- TTA GTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA
45074 AATAAATAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
2 4 0.08
3 46 0.87
4 3 0.06
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:45102 original size:11 final size:11
Alignment explanation
Indices: 45073--45111 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
45063 TATTATTATT
45073 AAATA-AATAAA
1 AAATATAAT-AA
*
45084 AAAAATAATAA
1 AAATATAATAA
45095 AAATATAATAA
1 AAATATAATAA
45106 AAATAT
1 AAATAT
45112 TACAAGGCCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 22 0.88
12 3 0.12
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (11 bp):
AAATATAATAA
Found at i:52157 original size:10 final size:10
Alignment explanation
Indices: 52142--52171 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
52132 GCAAAGAAAG
52142 AAGAAAAAAA
1 AAGAAAAAAA
52152 AAGAAAAAAA
1 AAGAAAAAAA
52162 AAGAGAAAAA
1 AAGA-AAAAA
52172 GGAAAATTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 14 0.74
11 5 0.26
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (10 bp):
AAGAAAAAAA
Found at i:52162 original size:12 final size:12
Alignment explanation
Indices: 52138--52171 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
52128 TCCAGCAAAG
52138 AAAGAAGAAAAAA
1 AAAGAA-AAAAAA
52151 AAAGAAAAAAAA
1 AAAGAAAAAAAA
*
52163 AGAGAAAAA
1 AAAGAAAAA
52172 GGAAAATTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 14 0.70
13 6 0.30
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAGAAAAAAAA
Found at i:57707 original size:76 final size:76
Alignment explanation
Indices: 57578--58264 Score: 1250
Period size: 76 Copynumber: 9.0 Consensus size: 76
57568 CTATTTCTCA
* *
57578 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGATGTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
57643 AGCCTTCGGGT
66 AGCCTTCGGGT
*
57654 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
57719 AGCCTTCGGGT
66 AGCCTTCGGGT
*
57730 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
57795 AGCCTTCGGGT
66 AGCCTTCGGGT
*
57806 CATCTGTAAGTCCTTCAGTGCATGATGCTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
57871 AGCCTTCGGGT
66 AGCCTTCGGGT
*
57882 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
57947 AGCCTTCGGGT
66 AGCCTTCGGGT
* *
57958 CATCTGTAAGTCCTTCAGTGCATGATGCTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
*
58023 AGCCTTAGGGT
66 AGCCTTCGGGT
58034 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
58099 AGCCTTCGGGT
66 AGCCTTCGGGT
58110 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
*
58175 AACCTTCGGGT
66 AGCCTTCGGGT
*
58186 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATTTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
*
58251 A-CCCTCGGGGT
66 AGCCTTC-GGGT
58262 CAT
1 CAT
58265 TCATAAGACC
Statistics
Matches: 591, Mismatches: 19, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
75 4 0.01
76 587 0.99
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
AGCCTTCGGGT
Found at i:58419 original size:3 final size:3
Alignment explanation
Indices: 58413--58474 Score: 72
Period size: 3 Copynumber: 21.0 Consensus size: 3
58403 TTAATTTTTT
* * * *
58413 TTA TTA TTA TTA TTT TTG TT- TTA TTA TTA TTA TTT TTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
58460 GTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
58475 AATAAATAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
2 2 0.04
3 48 0.96
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:58436 original size:17 final size:18
Alignment explanation
Indices: 58406--58474 Score: 70
Period size: 18 Copynumber: 3.9 Consensus size: 18
58396 GTATACATTA
*
58406 ATTTTTTTTATTATTATT
1 ATTTTTGTTATTATTATT
58424 ATTTTTGTT-TTATTATT
1 ATTTTTGTTATTATTATT
*
58441 ATTATTT-TTATTAATATT
1 ATT-TTTGTTATTATTATT
* * *
58459 AGTATTATTATTATTA
1 ATTTTTGTTATTATTA
58475 AATAAATAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
17 15 0.35
18 28 0.65
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (18 bp):
ATTTTTGTTATTATTATT
Found at i:58436 original size:20 final size:19
Alignment explanation
Indices: 58402--58449 Score: 78
Period size: 20 Copynumber: 2.5 Consensus size: 19
58392 AGCTGTATAC
*
58402 ATTAATTTTTTTTATTATT
1 ATTATTTTTTTTTATTATT
58421 ATTATTTTTGTTTTATTATT
1 ATTATTTTT-TTTTATTATT
58441 ATTATTTTT
1 ATTATTTTT
58450 ATTAATATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 8 0.30
20 19 0.70
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (19 bp):
ATTATTTTTTTTTATTATT
Found at i:58495 original size:11 final size:11
Alignment explanation
Indices: 58474--58508 Score: 61
Period size: 11 Copynumber: 3.1 Consensus size: 11
58464 TATTATTATT
58474 AAATAAATAAAA
1 AAAT-AATAAAA
58486 AAATAATAAAA
1 AAATAATAAAA
58497 AAATAATAAAA
1 AAATAATAAAA
58508 A
1 A
58509 TATTACAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 19 0.83
12 4 0.17
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (11 bp):
AAATAATAAAA
Found at i:58500 original size:19 final size:20
Alignment explanation
Indices: 58473--58510 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
58463 TTATTATTAT
*
58473 TAAATAAATAA-AAAAATAA
1 TAAAAAAATAATAAAAATAA
58492 TAAAAAAATAATAAAAATA
1 TAAAAAAATAATAAAAATA
58511 TTACAAGGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (20 bp):
TAAAAAAATAATAAAAATAA
Found at i:62439 original size:11 final size:11
Alignment explanation
Indices: 62423--62478 Score: 51
Period size: 11 Copynumber: 4.8 Consensus size: 11
62413 ATTGGAGTGC
62423 AAAAAGAAAAG
1 AAAAAGAAAAG
62434 AAAAAGACAAA-
1 AAAAAGA-AAAG
* *
62445 AAGAAGAATCAGAA
1 AAAAAGAA--A-AG
62459 AAAAAGAAAAG
1 AAAAAGAAAAG
62470 AAAAAGAAA
1 AAAAAGAAA
62479 TTCAAAAGAG
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
10 1 0.03
11 23 0.62
12 5 0.14
13 1 0.03
14 7 0.19
ACGTcount: A:0.79, C:0.04, G:0.16, T:0.02
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:65400 original size:2 final size:2
Alignment explanation
Indices: 65393--65446 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
65383 AGTTATTTTC
65393 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
65435 AT AT AT AT -T AT A
1 AT AT AT AT AT AT A
65447 CCTATAGTTA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:70699 original size:35 final size:37
Alignment explanation
Indices: 70628--70707 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
70618 ATACTATTTC
* *
70628 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCATATAT
*
70665 CATCACCATAGTCCATC-ACCA-TATCACGCATATAT
1 CATCACCATAATCCATCTACCATTATCACGCATATAT
70700 CATCACCA
1 CATCACCA
70708 AATTCTCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 21 0.52
36 3 0.08
37 16 0.40
ACGTcount: A:0.33, C:0.36, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCATATAT
Found at i:76342 original size:35 final size:37
Alignment explanation
Indices: 76275--76354 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
76265 ATACTATTTC
*
76275 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
* *
76312 CATCACCATAGTTCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
76347 CATCACCA
1 CATCACCA
76355 AATTCTCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 22 0.55
36 3 0.08
37 15 0.38
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.29
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:79933 original size:19 final size:20
Alignment explanation
Indices: 79909--79966 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 20
79899 TATCTTTTAT
79909 TTATTTCATTTT-ATT-CTTA
1 TTATTT-ATTTTCATTACTTA
79928 TTATTTATTTTCATTACTTA
1 TTATTTATTTTCATTACTTA
*
79948 -TA-TTATTATTCATTTCTTA
1 TTATTTATT-TTCATTACTTA
79967 AACCCATTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
18 10 0.29
19 21 0.60
20 4 0.11
ACGTcount: A:0.24, C:0.10, G:0.00, T:0.66
Consensus pattern (20 bp):
TTATTTATTTTCATTACTTA
Found at i:81288 original size:28 final size:29
Alignment explanation
Indices: 81257--81312 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
81247 TATTTTTTGC
81257 AGGACA-ATTCAAGAGA-CATGTCTTTTCA
1 AGGACAGATTCAAGA-ATCATGTCTTTTCA
*
81285 AGGAGATGATTCAAGAATCATGTCTTTT
1 AGGACA-GATTCAAGAATCATGTCTTTT
81313 GGAGGACTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 5 0.21
29 1 0.04
30 18 0.75
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (29 bp):
AGGACAGATTCAAGAATCATGTCTTTTCA
Found at i:83511 original size:13 final size:13
Alignment explanation
Indices: 83493--83519 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
83483 TGGCCAAAGA
83493 TGAAAAGGTATGT
1 TGAAAAGGTATGT
83506 TGAAAAGGTATGT
1 TGAAAAGGTATGT
83519 T
1 T
83520 AAAGGTGTTT
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:0.00, G:0.30, T:0.33
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:87311 original size:35 final size:35
Alignment explanation
Indices: 87261--87370 Score: 123
Period size: 35 Copynumber: 3.2 Consensus size: 35
87251 TAAGATACTA
*
87261 CCTA-AACATCACCATCTTCCATCACCATTTTACG
1 CCTATAACATCACCATCTTCCATCACCATTTCACG
* * * *
87295 CCTATAACATCACCATCTTCCATTACTATTGCACA
1 CCTATAACATCACCATCTTCCATCACCATTTCACG
* * * * *
87330 CCTATATCCTTACCATCTTCTATCATCATTTCACG
1 CCTATAACATCACCATCTTCCATCACCATTTCACG
87365 CCTATA
1 CCTATA
87371 TAACCACCAA
Statistics
Matches: 61, Mismatches: 14, Indels: 1
0.80 0.18 0.01
Matches are distributed among these distances:
34 4 0.07
35 57 0.93
ACGTcount: A:0.28, C:0.35, G:0.03, T:0.34
Consensus pattern (35 bp):
CCTATAACATCACCATCTTCCATCACCATTTCACG
Found at i:87539 original size:15 final size:15
Alignment explanation
Indices: 87519--87556 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
87509 TTGATAACAT
87519 TTCTTTCCATTTCAA
1 TTCTTTCCATTTCAA
*
87534 TTCTTTCCATTTCCA
1 TTCTTTCCATTTCAA
87549 TTCATTTC
1 TTC-TTTC
87557 TTTAATTATC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.16, C:0.29, G:0.00, T:0.55
Consensus pattern (15 bp):
TTCTTTCCATTTCAA
Found at i:87788 original size:18 final size:18
Alignment explanation
Indices: 87749--87787 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
87739 GTGCTGCAAC
87749 AAAAGCAACAAAAAGAAG
1 AAAAGCAACAAAAAGAAG
87767 AAAAGCAA-AAAGAA-AAG
1 AAAAGCAACAAA-AAGAAG
87784 AAAA
1 AAAA
87788 ATACTCCTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.77, C:0.08, G:0.15, T:0.00
Consensus pattern (18 bp):
AAAAGCAACAAAAAGAAG
Found at i:88989 original size:35 final size:36
Alignment explanation
Indices: 88930--88999 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 36
88920 AGATACAATC
*
88930 TGTCCATCACCATTATCATGCCTATATCATCACCAT
1 TGTCCATCACCATTATCACGCCTATATCATCACCAT
*
88966 TGTCCATCACCA-TATCACGCCTATATTATCACCA
1 TGTCCATCACCATTATCACGCCTATATCATCACCA
89000 ACTTCTAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 20 0.62
36 12 0.38
ACGTcount: A:0.29, C:0.34, G:0.06, T:0.31
Consensus pattern (36 bp):
TGTCCATCACCATTATCACGCCTATATCATCACCAT
Done.