Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007200.1 Hibiscus syriacus cultivar Beakdansim tig00018999_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: 414581
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:351836 original size:10 final size:10
Alignment explanation
Indices: 351816--351871 Score: 78
Period size: 10 Copynumber: 5.6 Consensus size: 10
351806 ACGGGTCGTG
351816 ACCGGTC-AA
1 ACCGGTCAAA
351825 ACCGGTCAAA
1 ACCGGTCAAA
351835 ACCGGTTCAAA
1 ACCGG-TCAAA
*
351846 ACCGGTTAAA
1 ACCGGTCAAA
*
351856 ACTGGTCAAA
1 ACCGGTCAAA
351866 ACCGGT
1 ACCGGT
351872 TTCCAGCGTT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
9 7 0.17
10 24 0.59
11 10 0.24
ACGTcount: A:0.36, C:0.27, G:0.21, T:0.16
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:351864 original size:20 final size:20
Alignment explanation
Indices: 351816--351872 Score: 80
Period size: 21 Copynumber: 2.9 Consensus size: 20
351806 ACGGGTCGTG
*
351816 ACCGGTC-AAACCGGTCAAA
1 ACCGGTCAAAACCGGTTAAA
351835 ACCGGTTCAAAACCGGTTAAA
1 ACCGG-TCAAAACCGGTTAAA
*
351856 ACTGGTCAAAACCGGTT
1 ACCGGTCAAAACCGGTT
351873 TCCAGCGTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 5 0.15
20 14 0.41
21 15 0.44
ACGTcount: A:0.35, C:0.26, G:0.21, T:0.18
Consensus pattern (20 bp):
ACCGGTCAAAACCGGTTAAA
Found at i:357908 original size:46 final size:45
Alignment explanation
Indices: 357815--357908 Score: 100
Period size: 46 Copynumber: 2.1 Consensus size: 45
357805 TTATATTACA
* * * * *
357815 TTTAAAAATATATTTTTAAAAATTTATAACTATCACTAATGTATT
1 TTTAAAAATATATTTTAAAAAATTTAAAACTATAAATAATATATT
* *
357860 TTTAATAATATAATTTTAAAAAATTTAAAATTATAATATAATAT-TT
1 TTTAAAAATAT-ATTTTAAAAAATTTAAAACTATAA-ATAATATATT
357906 TTT
1 TTT
357909 CGAGTAGTTC
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
45 10 0.25
46 25 0.62
47 5 0.12
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (45 bp):
TTTAAAAATATATTTTAAAAAATTTAAAACTATAAATAATATATT
Found at i:358069 original size:2 final size:2
Alignment explanation
Indices: 358062--358114 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
358052 TTTACACCCC
358062 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 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
358104 TA TA TA TA TA T
1 TA TA TA TA TA T
358115 CAAAAAGAAC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:365436 original size:32 final size:32
Alignment explanation
Indices: 365383--365454 Score: 83
Period size: 32 Copynumber: 2.2 Consensus size: 32
365373 TAAGTTGACC
* * **
365383 CTTGGGTAGGCTCCGATGCCCCGAGAAACTTT
1 CTTGGGTAGGCTCCGAGGCCCCAAGAAACTCA
*
365415 CTTGGGTAGGCTCTC-AGGCCCCAAGACACTCA
1 CTTGGGTAGGCTC-CGAGGCCCCAAGAAACTCA
365447 CTTGGGTA
1 CTTGGGTA
365455 AATCGTAGGA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
32 33 0.97
33 1 0.03
ACGTcount: A:0.19, C:0.29, G:0.28, T:0.24
Consensus pattern (32 bp):
CTTGGGTAGGCTCCGAGGCCCCAAGAAACTCA
Found at i:367488 original size:17 final size:17
Alignment explanation
Indices: 367468--367500 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
367458 CACGTAAGTC
367468 TACGCG-ATCCCTATGTG
1 TACGCGTAT-CCTATGTG
367485 TACGCGTATCCTATGT
1 TACGCGTATCCTATGT
367501 CTCTCTCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.18, C:0.27, G:0.21, T:0.33
Consensus pattern (17 bp):
TACGCGTATCCTATGTG
Found at i:367855 original size:17 final size:17
Alignment explanation
Indices: 367835--367871 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
367825 AAATATTTAG
367835 ATATATTTAATAATATA
1 ATATATTTAATAATATA
* *
367852 ATATTTTTAATATTATA
1 ATATATTTAATAATATA
367869 ATA
1 ATA
367872 AAATAATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATATATTTAATAATATA
Found at i:367958 original size:21 final size:20
Alignment explanation
Indices: 367917--367962 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
367907 TATTGTTATT
367917 TTAATAATATATAATAATTA
1 TTAATAATATATAATAATTA
* * *
367937 TTAATAAATTTATATTATTTA
1 TTAAT-AATATATAATAATTA
367958 TTAAT
1 TTAAT
367963 TTCATATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TTAATAATATATAATAATTA
Found at i:368024 original size:25 final size:26
Alignment explanation
Indices: 367826--368019 Score: 82
Period size: 25 Copynumber: 7.8 Consensus size: 26
367816 TAATTATTAA
*
367826 AATATTTAGATATATT-TAATAATAT
1 AATATTTATATATATTATAATAATAT
* *
367851 AATATTTTTA-ATATTATAATAAAAT
1 AATATTTATATATATTATAATAATAT
*
367876 -A-ATTAAT-TATATTATAAT-ATAT
1 AATATTTATATATATTATAATAATAT
* * *
367898 AAGATATTATATTGTTATTTTAATAATAT
1 AATAT-TTATA-T-ATATTATAATAATAT
* *
367927 -ATA-ATA-AT-TATTAATAA-ATTTAT
1 AATATTTATATATATT-ATAATA-ATAT
*
367950 ATTATTTAT-TA-ATT-TCATATAA-AT
1 AATATTTATATATATTAT-A-ATAATAT
* *
367974 AATATTTAAAT-TATTAATAATGA-AT
1 AATATTTATATATATT-ATAATAATAT
367999 AATATTTATATATATT-TAATA
1 AATATTTATATATATTATAATA
368020 TAATAGTCTA
Statistics
Matches: 125, Mismatches: 21, Indels: 47
0.65 0.11 0.24
Matches are distributed among these distances:
22 8 0.06
23 22 0.18
24 25 0.20
25 46 0.37
26 8 0.06
27 2 0.02
28 10 0.08
29 4 0.03
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (26 bp):
AATATTTATATATATTATAATAATAT
Found at i:368203 original size:18 final size:18
Alignment explanation
Indices: 368176--368214 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
368166 TAATAAAATT
368176 ATAAAAATAA-TATTTTA
1 ATAAAAATAATTATTTTA
368193 ATAATAAATAATTATTTTA
1 ATAA-AAATAATTATTTTA
368212 ATA
1 ATA
368215 TTTTAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 4 0.20
18 6 0.30
19 10 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATAAAAATAATTATTTTA
Found at i:368238 original size:27 final size:27
Alignment explanation
Indices: 368183--368238 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
368173 ATTATAAAAA
* *
368183 TAATATTTTAATAATAAATAATTATTT
1 TAATATTTTAAAAATAAATAATTAATT
368210 TAATATTTTAAAAAT-AATAATTAAATT
1 TAATATTTTAAAAATAAATAATT-AATT
368237 TA
1 TA
368239 TAATAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 7 0.27
27 19 0.73
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (27 bp):
TAATATTTTAAAAATAAATAATTAATT
Found at i:368249 original size:22 final size:24
Alignment explanation
Indices: 368183--368251 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 24
368173 ATTATAAAAA
*
368183 TAATATTTTAATAATAAATAATTATTT
1 TAATA-TTT-ATAATAAATAA-TATAT
368210 TAATATTT-TAA-AAATAATA-AT
1 TAATATTTATAATAAATAATATAT
368231 TAA-ATTTATAATAAATAATAT
1 TAATATTTATAATAAATAATAT
368252 TATTTATTGT
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
20 4 0.11
21 7 0.18
22 10 0.26
23 6 0.16
24 3 0.08
26 3 0.08
27 5 0.13
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
TAATATTTATAATAAATAATATAT
Found at i:368256 original size:19 final size:19
Alignment explanation
Indices: 368174--368258 Score: 59
Period size: 21 Copynumber: 4.2 Consensus size: 19
368164 ATTAATAAAA
368174 TTATAAAAATAATATT--T
1 TTATAAAAATAATATTAAT
*
368191 TAATAATAAATAATTATTTTAAT
1 TTATAA-AAATAA-TA--TTAAT
*
368214 ATTTTAAAAATAATAATTAAAT
1 -TTATAAAAATAAT-ATT-AAT
368236 TTATAATAAATAATATT-AT
1 TTATAA-AAATAATATTAAT
368255 TTAT
1 TTAT
368259 TGTATTTTAA
Statistics
Matches: 54, Mismatches: 4, Indels: 18
0.71 0.05 0.24
Matches are distributed among these distances:
17 5 0.09
18 6 0.11
19 8 0.15
21 12 0.22
22 11 0.20
23 8 0.15
24 4 0.07
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TTATAAAAATAATATTAAT
Found at i:370756 original size:21 final size:21
Alignment explanation
Indices: 370732--370779 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
370722 AGGTTTTCCC
* *
370732 TTGATGCAGCCAGGATGTCCT
1 TTGATGCAGCAAGGATGTCAT
370753 TTGATGCAGCAAGGATGTCAT
1 TTGATGCAGCAAGGATGTCAT
370774 TTGATG
1 TTGATG
370780 ATCCGAGGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGATGCAGCAAGGATGTCAT
Found at i:373092 original size:22 final size:23
Alignment explanation
Indices: 373015--373086 Score: 75
Period size: 22 Copynumber: 3.3 Consensus size: 23
373005 TTTAGTATCA
373015 TTTTAATAA-A-AATATTAATA-
1 TTTTAATAATATAATATTAATAT
* *
373035 -ATTAA-AATATATTTATTAATAT
1 TTTTAATAATATA-ATATTAATAT
373057 TTTTAATAATATAATATT-ATAT
1 TTTTAATAATATAATATTAATAT
373079 TTTTAATA
1 TTTTAATA
373087 TCATAACAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
18 2 0.05
19 5 0.12
20 1 0.02
21 8 0.19
22 12 0.29
23 8 0.19
24 6 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TTTTAATAATATAATATTAATAT
Found at i:373130 original size:23 final size:24
Alignment explanation
Indices: 373089--373137 Score: 82
Period size: 23 Copynumber: 2.1 Consensus size: 24
373079 TTTTAATATC
373089 ATAACAATATGATATGATATTATA
1 ATAACAATATGATATGATATTATA
*
373113 ATAATAATAT-ATATGATATTATA
1 ATAACAATATGATATGATATTATA
373136 AT
1 AT
373138 CTTGTTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 15 0.62
24 9 0.38
ACGTcount: A:0.51, C:0.02, G:0.06, T:0.41
Consensus pattern (24 bp):
ATAACAATATGATATGATATTATA
Found at i:379438 original size:2 final size:2
Alignment explanation
Indices: 379431--379473 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
379421 TATTTAAAAC
379431 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
379473 A
1 A
379474 GCACACAAGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:380377 original size:12 final size:13
Alignment explanation
Indices: 380360--380473 Score: 89
Period size: 12 Copynumber: 9.1 Consensus size: 13
380350 TTCAAAGAGG
380360 TTTTATAT-TTAA
1 TTTTATATATTAA
380372 TTTTATATATTATA
1 TTTTATATATTA-A
*
380386 TTTGAT-T-TTAA
1 TTTTATATATTAA
380397 TTTTA-ATATTAA
1 TTTTATATATTAA
* *
380409 TTTTTTA-AATAA
1 TTTTATATATTAA
* *
380421 -ATTAAATATTAA
1 TTTTATATATTAA
*
380433 TTTTTTAATATTATA
1 TTTTAT-ATATTA-A
*
380448 TTATATATATTAA
1 TTTTATATATTAA
380461 TTTTA-ATATTAA
1 TTTTATATATTAA
380473 T
1 T
380474 AATAATTTTT
Statistics
Matches: 79, Mismatches: 14, Indels: 18
0.71 0.13 0.16
Matches are distributed among these distances:
11 9 0.11
12 35 0.44
13 12 0.15
14 18 0.23
15 5 0.06
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (13 bp):
TTTTATATATTAA
Found at i:380386 original size:19 final size:18
Alignment explanation
Indices: 380362--380412 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
380352 CAAAGAGGTT
380362 TTATATTTAATTTTATATA
1 TTATATTTAATTTTA-ATA
* *
380381 TTATATTTGATTTTAATT
1 TTATATTTAATTTTAATA
380399 TTA-ATATTAATTTT
1 TTATAT-TTAATTTT
380413 TTAAATAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 2 0.07
18 12 0.43
19 14 0.50
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (18 bp):
TTATATTTAATTTTAATA
Found at i:380428 original size:24 final size:24
Alignment explanation
Indices: 380401--380509 Score: 106
Period size: 24 Copynumber: 4.7 Consensus size: 24
380391 TTTTAATTTT
380401 AATATTAATTTTTTAAATAAATTA
1 AATATTAATTTTTTAAATAAATTA
*
380425 AATATTAATTTTTTAATATTATATTA
1 AATATTAATTTTTTAA-A-TAAATTA
380451 TATATATTAA--TTTT-AAT--ATT-
1 -A-ATATTAATTTTTTAAATAAATTA
*
380471 AATAATAA-TTTTTAAATAAATTA
1 AATATTAATTTTTTAAATAAATTA
*
380494 AATATTAATCTTTTAA
1 AATATTAATTTTTTAA
380510 TATTATATTA
Statistics
Matches: 71, Mismatches: 4, Indels: 20
0.75 0.04 0.21
Matches are distributed among these distances:
18 6 0.08
19 5 0.07
20 3 0.04
21 3 0.04
22 3 0.04
23 8 0.11
24 23 0.32
25 2 0.03
26 10 0.14
27 1 0.01
28 7 0.10
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (24 bp):
AATATTAATTTTTTAAATAAATTA
Found at i:380447 original size:69 final size:69
Alignment explanation
Indices: 380367--380535 Score: 243
Period size: 69 Copynumber: 2.4 Consensus size: 69
380357 AGGTTTTATA
* * * *
380367 TTTAATTTTATATAT-TATATTTGATTTTAATTTTAATATTAATTTTTTAAATAAATTAAATATT
1 TTTAATATTATATATATATATTTAATTTTAATATTAATAATAA-TTTTTAAATAAATTAAATATT
*
380431 AATTT
65 AATCT
380436 TTTAATATTATAT-TATATATATTAATTTTAATATTAATAATAATTTTTAAATAAATTAAATATT
1 TTTAATATTATATATATATAT-TTAATTTTAATATTAATAATAATTTTTAAATAAATTAAATATT
380500 AATCT
65 AATCT
*
380505 TTTAATATTATATTATAGATATTTAATTTTA
1 TTTAATATTATA-TATATATATTTAATTTTA
380536 TATCATATAA
Statistics
Matches: 90, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
68 1 0.01
69 54 0.60
70 29 0.32
71 6 0.07
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (69 bp):
TTTAATATTATATATATATATTTAATTTTAATATTAATAATAATTTTTAAATAAATTAAATATTA
ATCT
Found at i:380450 original size:26 final size:27
Alignment explanation
Indices: 380395--380472 Score: 94
Period size: 26 Copynumber: 3.0 Consensus size: 27
380385 ATTTGATTTT
*
380395 AATTTTAATATTAATTTTTTAA-A-TA
1 AATTATAATATTAATTTTTTAATATTA
380420 AATTA-AATATTAATTTTTTAATATTA
1 AATTATAATATTAATTTTTTAATATTA
*
380446 TATTATATATATTAA--TTTTAATATTA
1 AATTATA-ATATTAATTTTTTAATATTA
380472 A
1 A
380473 TAATAATTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
24 16 0.35
25 5 0.11
26 17 0.37
27 1 0.02
28 7 0.15
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
AATTATAATATTAATTTTTTAATATTA
Found at i:380469 original size:21 final size:21
Alignment explanation
Indices: 380445--380548 Score: 60
Period size: 21 Copynumber: 4.9 Consensus size: 21
380435 TTTTAATATT
380445 ATATTATATATATTAATTTTA
1 ATATTATATATATTAATTTTA
380466 ATATTA-ATA-A-TAATTTTTAA
1 ATATTATATATATTAA-TTTT-A
380486 ATAAATTA-A-ATATTAATCTTTTA
1 AT--ATTATATATATTAA--TTTTA
380509 ATATTATAT-TA-TAGATATTTA
1 ATATTATATATATTA-AT-TTTA
* *
380530 ATTTTATATCATATAAATT
1 ATATTATAT-ATATTAATT
380549 ATTTTATATA
Statistics
Matches: 66, Mismatches: 3, Indels: 27
0.69 0.03 0.28
Matches are distributed among these distances:
18 3 0.05
19 5 0.08
20 7 0.11
21 25 0.38
22 11 0.17
23 10 0.15
24 5 0.08
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (21 bp):
ATATTATATATATTAATTTTA
Found at i:380479 original size:12 final size:12
Alignment explanation
Indices: 380393--380532 Score: 55
Period size: 14 Copynumber: 11.5 Consensus size: 12
380383 ATATTTGATT
*
380393 TTAATTTTAATA
1 TTAATTATAATA
*
380405 TTAATTTTTTAA-A
1 TTAA--TTATAATA
*
380418 TAAATTA-AATA
1 TTAATTATAATA
*
380429 TTAATTTTTTAATA
1 TTAA--TTATAATA
380443 TTATATTATATATA
1 TTA-ATTATA-ATA
*
380457 TTAATTTTAATA
1 TTAATTATAATA
*
380469 TTAATAATAAT-
1 TTAATTATAATA
380480 TT--TTA-AATA
1 TTAATTATAATA
380489 --AATTA-AATA
1 TTAATTATAATA
*
380498 TTAATCTTTTAATA
1 TTAA--TTATAATA
380512 TTATATTATAGATA
1 TTA-ATTATA-ATA
380526 TTTAATT
1 -TTAATT
380533 TTATATCATA
Statistics
Matches: 98, Mismatches: 11, Indels: 36
0.68 0.08 0.25
Matches are distributed among these distances:
8 3 0.03
9 9 0.09
10 2 0.02
11 10 0.10
12 16 0.16
13 21 0.21
14 32 0.33
15 5 0.05
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (12 bp):
TTAATTATAATA
Found at i:380590 original size:20 final size:19
Alignment explanation
Indices: 380530--380591 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
380520 TAGATATTTA
*
380530 ATTTTATATCA-TATAAATT
1 ATTTTATAT-ATTATTAATT
*
380549 ATTTTATATATTATTAA-A
1 ATTTTATATATTATTAATT
380567 ATTTTATAT-TTATTTTAATT
1 ATTTTATATATTA--TTAATT
380587 ATTTT
1 ATTTT
380592 GATTTAAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 3 0.08
18 10 0.28
19 18 0.50
20 5 0.14
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTATATATTATTAATT
Found at i:381062 original size:31 final size:31
Alignment explanation
Indices: 381027--381086 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
381017 TAGTTGTATG
* *
381027 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATATCAGGATTGTAAAACTAA
381058 AATTATTTAAATATCAGGATTGTAAAACT
1 AATTATTTAAATATCAGGATTGTAAAACT
381087 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.45, C:0.07, G:0.08, T:0.40
Consensus pattern (31 bp):
AATTATTTAAATATCAGGATTGTAAAACTAA
Found at i:385139 original size:21 final size:21
Alignment explanation
Indices: 385113--385166 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
385103 GCGTTGCATT
385113 TCGCGTTGCGATAATTGAAAA
1 TCGCGTTGCGATAATTGAAAA
*
385134 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAATTGAAAA
385155 TCGCGTTGCGAT
1 TCGCGTTGCGAT
385167 TTTCCATTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAATTGAAAA
Found at i:385183 original size:20 final size:20
Alignment explanation
Indices: 385155--385429 Score: 265
Period size: 20 Copynumber: 13.6 Consensus size: 20
385145 TAGTTGAAAA
*
385155 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCAGT
* *
385175 TCGCATTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCAGT
385195 TCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
* *
385215 TCGCGTTGCGATAGTCTACAGT
1 TCGCGTTGCGAT--TTTCCAGT
*
385237 T-GTCGTTGCGATTTTCCAAAT
1 TCG-CGTTGCGATTTTCC-AGT
* *
385258 T--CGTTGCGATAGTCTACAGT
1 TCGCGTTGCGAT--TTTCCAGT
*
385278 T-GCCGTTGCGATTTTCCAAAT
1 TCG-CGTTGCGATTTTCC-AGT
* *
385299 T--CGTTGCGATTTTTCATT
1 TCGCGTTGCGATTTTCCAGT
385317 TCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
* ** **
385337 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCAGT
*
385358 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCAGT
*
385378 TCGCGTTGCAATTTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
385398 TCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
385418 TCGCGTTGCGAT
1 TCGCGTTGCGAT
385430 AGTTAAAAAA
Statistics
Matches: 212, Mismatches: 31, Indels: 24
0.79 0.12 0.09
Matches are distributed among these distances:
18 3 0.01
19 22 0.10
20 137 0.65
21 25 0.12
22 25 0.12
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.40
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCAGT
Found at i:385243 original size:22 final size:22
Alignment explanation
Indices: 385218--385289 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
385208 TTCCAGTTCG
385218 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* * **
385240 CGTTGCGAT--TTTCCAAAT-T
1 CGTTGCGATAGTCTACAGTTGT
*
385259 CGTTGCGATAGTCTACAGTTGC
1 CGTTGCGATAGTCTACAGTTGT
385281 CGTTGCGAT
1 CGTTGCGAT
385290 TTTCCAAATT
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
19 10 0.26
20 5 0.13
21 5 0.13
22 18 0.47
ACGTcount: A:0.18, C:0.21, G:0.25, T:0.36
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:385263 original size:19 final size:19
Alignment explanation
Indices: 385239--385334 Score: 86
Period size: 19 Copynumber: 4.8 Consensus size: 19
385229 TCTACAGTTG
385239 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
** * *
385258 TCGTTGCGATAGTCTACAGT
1 TCGTTGCGATTTTCCA-AAT
385278 TGCCGTTGCGATTTTCCAAAT
1 T--CGTTGCGATTTTCCAAAT
* *
385299 TCGTTGCGATTTTTC-ATT
1 TCGTTGCGATTTTCCAAAT
385317 TCGCGTTGCGATTTTCCA
1 T--CGTTGCGATTTTCCA
385335 GTTCGCGTTG
Statistics
Matches: 60, Mismatches: 11, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
18 3 0.05
19 26 0.43
20 16 0.27
21 3 0.05
22 12 0.20
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.42
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:385263 original size:61 final size:60
Alignment explanation
Indices: 385180--385409 Score: 245
Period size: 61 Copynumber: 3.8 Consensus size: 60
385170 CCATTTCGCA
*
385180 TTGCGATTTTCCATTTCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTCTACAGTTGTCG
1 TTGCGATTTTCCATTTC-CGTTGCGATTTTCCAGTTCGCGTTGCGATAGT-TACAATTGTCG
* * * * * *
385242 TTGCGATTTTCCAAATT-CGTTGCGATAGTCTACAGTT-GCCGTTGCGAT-TTTCCAAAT-TCG
1 TTGCGATTTTCC-ATTTCCGTTGCGAT--TTTCCAGTTCG-CGTTGCGATAGTTACAATTGTCG
* * *
385302 TTGCGATTTTTCATTTCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAAATCG-CG
1 TTGCGATTTTCCATTTC-CGTTGCGATTTTCCAGTTCGCGTTGCGATAGTT-ACAATTGTCG
*
385363 TTGCGATTTTCCATTTCGCGTTGCAATTTTCCAGTTCGCGTTGCGAT
1 TTGCGATTTTCCATTTC-CGTTGCGATTTTCCAGTTCGCGTTGCGAT
385410 TTTCCAGTTC
Statistics
Matches: 140, Mismatches: 18, Indels: 21
0.78 0.10 0.12
Matches are distributed among these distances:
59 19 0.14
60 17 0.12
61 71 0.51
62 14 0.10
63 19 0.14
ACGTcount: A:0.16, C:0.22, G:0.23, T:0.40
Consensus pattern (60 bp):
TTGCGATTTTCCATTTCCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTACAATTGTCG
Found at i:385372 original size:41 final size:40
Alignment explanation
Indices: 385134--385437 Score: 251
Period size: 41 Copynumber: 7.5 Consensus size: 40
385124 TAATTGAAAA
*
385134 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATAGTT-AAAATCGCGTTGCGATTTTCCAGT
* * * **
385175 TCGCATTGCGAT-TTTCCATTTCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATAGTT-AAAATCGCGTTGCGATTTTCCAGT
* * * *
385215 TCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAAT
1 TCGCGTTGCGATAGT-TAAAATCG-CGTTGCGATTTTCC-AGT
* * * *
385258 T--CGTTGCGATAGTCTACAGTTGCCGTTGCGATTTTCCAAAT
1 TCGCGTTGCGATAGT-TAAAATCG-CGTTGCGATTTTCC-AGT
** * **
385299 T--CGTTGCGATTTTTCATTTCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATAGTTAAAATCGCGTTGCGATTTTCCAGT
*
385337 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATAGTT-AAAATCGCGTTGCGATTTTCCAGT
* * * **
385378 TCGCGTTGCAAT-TTTCCAGTTCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATAGTT-AAAATCGCGTTGCGATTTTCCAGT
385418 TCGCGTTGCGATAGTTAAAA
1 TCGCGTTGCGATAGTTAAAA
385438 AAAAGATTTT
Statistics
Matches: 213, Mismatches: 42, Indels: 17
0.78 0.15 0.06
Matches are distributed among these distances:
38 3 0.01
39 14 0.07
40 81 0.38
41 97 0.46
42 15 0.07
43 3 0.01
ACGTcount: A:0.17, C:0.21, G:0.23, T:0.39
Consensus pattern (40 bp):
TCGCGTTGCGATAGTTAAAATCGCGTTGCGATTTTCCAGT
Found at i:386187 original size:22 final size:22
Alignment explanation
Indices: 386158--386251 Score: 97
Period size: 22 Copynumber: 4.5 Consensus size: 22
386148 AATTTGGAAA
386158 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* *
386180 TTCGCAACAACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * **
386202 ATCGCAACG--AA-TTTGGAAA
1 ATCGCAACGACAACTGTAGACT
*
386221 ATCGCAACGAC-ATTGTAGACT
1 ATCGCAACGACAACTGTAGACT
386242 ATCGCAACGA
1 ATCGCAACGA
386252 AAATGGAAAA
Statistics
Matches: 57, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
19 13 0.23
20 3 0.05
21 14 0.25
22 27 0.47
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.20
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:386209 original size:19 final size:20
Alignment explanation
Indices: 386136--386252 Score: 76
Period size: 22 Copynumber: 5.7 Consensus size: 20
386126 TTTTTTTTTA
* *
386136 ACTATCGCAACGAA-TTTGG
1 ACTATCGCAACGAACTGTAG
**
386155 AAAATCGCAACGACAACTGTAG
1 ACTATCGCAACG--AACTGTAG
* *
386177 ACTTTCGCAACAACAACTGTAG
1 ACTATCGCAAC--GAACTGTAG
* *
386199 ACTATCGCAACGAA-TTTGG
1 ACTATCGCAACGAACTGTAG
** *
386218 AAAATCGCAACGACATTGTAG
1 ACTATCGCAACGA-ACTGTAG
386239 ACTATCGCAACGAA
1 ACTATCGCAACGAA
386253 AATGGAAAAT
Statistics
Matches: 73, Mismatches: 18, Indels: 13
0.70 0.17 0.12
Matches are distributed among these distances:
19 24 0.33
20 4 0.05
21 16 0.22
22 29 0.40
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (20 bp):
ACTATCGCAACGAACTGTAG
Found at i:386243 original size:40 final size:40
Alignment explanation
Indices: 386194--386300 Score: 137
Period size: 40 Copynumber: 2.6 Consensus size: 40
386184 CAACAACAAC
**
386194 TGTAGACTATCGCAACGAATTTGGAAAATCGCAACGAC-AT
1 TGTAGACTATCGCAACGAAAATGGAAAATCGCAACG-CGAT
386234 TGTAGACTATCGCAACGAAAATGGAAAATCGCAACGCGAT
1 TGTAGACTATCGCAACGAAAATGGAAAATCGCAACGCGAT
* *
386274 TTTCA-ACTATCGCAACGCGAAATGGAA
1 TGT-AGACTATCGCAACG-AAAATGGAA
386301 CGCGAATTTG
Statistics
Matches: 60, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
39 1 0.02
40 50 0.83
41 9 0.15
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (40 bp):
TGTAGACTATCGCAACGAAAATGGAAAATCGCAACGCGAT
Found at i:386266 original size:19 final size:19
Alignment explanation
Indices: 386202--386269 Score: 73
Period size: 19 Copynumber: 3.5 Consensus size: 19
386192 ACTGTAGACT
*
386202 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAAATTGGAAA
* **
386221 ATCGCAACGACATTGTAGACT
1 ATCGCAACGAAATTG--GAAA
*
386242 ATCGCAACGAAAATGGAAA
1 ATCGCAACGAAATTGGAAA
386261 ATCGCAACG
1 ATCGCAACG
386270 CGATTTTCAA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
19 24 0.62
21 15 0.38
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.18
Consensus pattern (19 bp):
ATCGCAACGAAATTGGAAA
Found at i:389039 original size:14 final size:14
Alignment explanation
Indices: 389020--389052 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
389010 CGTCCATGAA
389020 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
389034 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
389048 CGTTC
1 CGTTC
389053 ATTTATGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.06, C:0.18, G:0.27, T:0.48
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:389058 original size:14 final size:14
Alignment explanation
Indices: 389020--389061 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
389010 CGTCCATGAA
*
389020 CGTTCGGTTATGTT
1 CGTTCAGTTATGTT
*
389034 CGTTCGGTTATGTT
1 CGTTCAGTTATGTT
*
389048 CGTTCATTTATGTT
1 CGTTCAGTTATGTT
389062 TAACCAAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.10, C:0.14, G:0.24, T:0.52
Consensus pattern (14 bp):
CGTTCAGTTATGTT
Found at i:413209 original size:40 final size:38
Alignment explanation
Indices: 413165--413240 Score: 125
Period size: 40 Copynumber: 1.9 Consensus size: 38
413155 TAGAGTGTAG
413165 TTTTTGTTTCATTTTAGTACCCGCTGTTAAAAATTTTAGT
1 TTTTTGTTTCATTTTAGTACCC-CT-TTAAAAATTTTAGT
*
413205 TTTTTGTTTCATTTTAGTACCCCTTTCAAAATTTTA
1 TTTTTGTTTCATTTTAGTACCCCTTTAAAAATTTTA
413241 CGTTGAGTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
38 11 0.31
39 2 0.06
40 22 0.63
ACGTcount: A:0.22, C:0.14, G:0.09, T:0.54
Consensus pattern (38 bp):
TTTTTGTTTCATTTTAGTACCCCTTTAAAAATTTTAGT
Found at i:414002 original size:2 final size:2
Alignment explanation
Indices: 413995--414581 Score: 1061
Period size: 2 Copynumber: 299.0 Consensus size: 2
413985 TTGTGAAGTT
413995 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA -A GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
414036 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
414078 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
414120 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
414162 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
414204 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
414246 GA GA GA GA GA GA GA GA GA GA GA GA GA GA -A GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
414287 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
414329 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
414371 GA G- GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
414412 GA GA GA GA GA GA GA GA G- GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
*
414453 GA GA GA GA GA GA G- GA -A GA GA G- GA GA GA GA GA GG GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
*
414492 GA G- GA GA GA GA GA G- GA GA GA GA GA GA GA GA G- GG GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
* *
414531 GA TA GA GA GA GG GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
414573 GA G- GA GA GA
1 GA GA GA GA GA
Statistics
Matches: 567, Mismatches: 7, Indels: 22
0.95 0.01 0.04
Matches are distributed among these distances:
1 11 0.02
2 556 0.98
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Done.