Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009213.1 Hibiscus syriacus cultivar Beakdansim tig00112800_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: 747713
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:637493 original size:25 final size:25
Alignment explanation
Indices: 637446--637495 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
637436 TTTATTATTA
* *
637446 TATTTTTTTAATATTTTAATAATAT
1 TATTATTTTAATATATTAATAATAT
637471 TATTATTTTAATA-ATTAATTAATAT
1 TATTATTTTAATATATTAA-TAATAT
637496 AATCAATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (25 bp):
TATTATTTTAATATATTAATAATAT
Found at i:637657 original size:14 final size:15
Alignment explanation
Indices: 637620--637649 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
637610 ATTTTAATAG
637620 TAATATTAACATAAA
1 TAATATTAACATAAA
637635 TAATATTAA-ATAAA
1 TAATATTAACATAAA
637649 T
1 T
637650 TATTTTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (15 bp):
TAATATTAACATAAA
Found at i:637670 original size:19 final size:20
Alignment explanation
Indices: 637646--637683 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
637636 AATATTAAAT
637646 AAATTATT-TTAATATTTTA
1 AAATTATTATTAATATTTTA
*
637665 AAATTATTATTATTATTTT
1 AAATTATTATTAATATTTT
637684 TTAATAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
AAATTATTATTAATATTTTA
Found at i:640889 original size:28 final size:28
Alignment explanation
Indices: 640845--640898 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
640835 TTCGAAACGG
*
640845 TTCGAATTTTCGAGTCAAATTTAAGTTA
1 TTCGAATCTTCGAGTCAAATTTAAGTTA
*
640873 TTCGAATCTTCGTGTCAAATTTAAGT
1 TTCGAATCTTCGAGTCAAATTTAAGT
640899 GTGACATCTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.43
Consensus pattern (28 bp):
TTCGAATCTTCGAGTCAAATTTAAGTTA
Found at i:644774 original size:31 final size:31
Alignment explanation
Indices: 644736--644798 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
644726 GAAACAGAGG
644736 TGGAATTAGAGTTAAGGTTAAGATTTGGAGA
1 TGGAATTAGAGTTAAGGTTAAGATTTGGAGA
644767 TGGAATTAGAGTTAAGGTTAAGATTTGGAGA
1 TGGAATTAGAGTTAAGGTTAAGATTTGGAGA
644798 T
1 T
644799 TTTTTTTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.33
Consensus pattern (31 bp):
TGGAATTAGAGTTAAGGTTAAGATTTGGAGA
Found at i:647331 original size:2 final size:2
Alignment explanation
Indices: 647324--647368 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
647314 ATCTGATCTT
647324 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
647366 TA T
1 TA T
647369 TTATTTATTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:647661 original size:34 final size:33
Alignment explanation
Indices: 647623--647699 Score: 99
Period size: 29 Copynumber: 2.4 Consensus size: 33
647613 AATTTTGTTA
*
647623 AATAATATAATAAATTGATTTCTAGAATTGCAT
1 AATAATATAATAAATTGATTTCAAGAATTGCAT
*
647656 --T-A-ATAATAAATTGGTTTCAAGAATTGCATT
1 AATAATATAATAAATTGATTTCAAGAATTGCA-T
647686 AATAATATAATAAA
1 AATAATATAATAAA
647700 ATTTAGGTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
29 24 0.65
30 2 0.05
31 1 0.03
32 1 0.03
33 1 0.03
34 8 0.22
ACGTcount: A:0.48, C:0.05, G:0.09, T:0.38
Consensus pattern (33 bp):
AATAATATAATAAATTGATTTCAAGAATTGCAT
Found at i:647667 original size:29 final size:29
Alignment explanation
Indices: 647629--647692 Score: 110
Period size: 29 Copynumber: 2.2 Consensus size: 29
647619 GTTAAATAAT
*
647629 ATAATAAATTGATTTCTAGAATTGCATTA
1 ATAATAAATTGATTTCAAGAATTGCATTA
*
647658 ATAATAAATTGGTTTCAAGAATTGCATTA
1 ATAATAAATTGATTTCAAGAATTGCATTA
647687 ATAATA
1 ATAATA
647693 TAATAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (29 bp):
ATAATAAATTGATTTCAAGAATTGCATTA
Found at i:648802 original size:18 final size:18
Alignment explanation
Indices: 648781--648825 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
648771 ACCAGGGAGT
648781 GATCCTAAGCCAGATTGA
1 GATCCTAAGCCAGATTGA
648799 GATCCTAAGCCAGATTGA
1 GATCCTAAGCCAGATTGA
*
648817 GAACCTAAG
1 GATCCTAAG
648826 AAGGAAGGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.20
Consensus pattern (18 bp):
GATCCTAAGCCAGATTGA
Found at i:654109 original size:21 final size:21
Alignment explanation
Indices: 654061--654110 Score: 57
Period size: 24 Copynumber: 2.3 Consensus size: 21
654051 TTGTGTTTCA
654061 TATT-ATAATTTTTATTATTT
1 TATTAATAATTTTTATTATTT
*
654081 TAAAATTAATATTTTTTATTATTT
1 T---ATTAATAATTTTTATTATTT
654105 TATTAA
1 TATTAA
654111 AATGAACCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
20 1 0.04
21 5 0.20
23 3 0.12
24 16 0.64
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TATTAATAATTTTTATTATTT
Found at i:662883 original size:21 final size:21
Alignment explanation
Indices: 662854--662898 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
662844 AGAATATTTA
*
662854 TAAATTTAAGTTTATTTCTT-T
1 TAAAATTAA-TTTATTTCTTAT
*
662875 TAAAATTAATTTTTTTCTTAT
1 TAAAATTAATTTATTTCTTAT
662896 TAA
1 TAA
662899 CATAAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.60
Consensus pattern (21 bp):
TAAAATTAATTTATTTCTTAT
Found at i:665838 original size:37 final size:37
Alignment explanation
Indices: 665780--665883 Score: 127
Period size: 37 Copynumber: 2.8 Consensus size: 37
665770 CTTTTCGTCA
* * *
665780 TACTAGGATTCAAACTCCTAAAAATAGGATATAATTT
1 TACTATGATTCAAACTCCTAAAAATAGGATAGAATTC
* * * *
665817 TGCTATGATTCAAACTTCTAAAAATATGATAGAGTTC
1 TACTATGATTCAAACTCCTAAAAATAGGATAGAATTC
* *
665854 TACTATGATTTAAACTCCTAAAGATAGGAT
1 TACTATGATTCAAACTCCTAAAAATAGGAT
665884 CCACAAGCAC
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 55 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (37 bp):
TACTATGATTCAAACTCCTAAAAATAGGATAGAATTC
Found at i:666352 original size:2 final size:2
Alignment explanation
Indices: 666345--666369 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
666335 AATTAGTTAT
666345 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 T
666370 TCATACTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:666509 original size:14 final size:14
Alignment explanation
Indices: 666464--666572 Score: 78
Period size: 14 Copynumber: 7.5 Consensus size: 14
666454 TTTTCTTTGC
666464 ATTTTTATTATTAT
1 ATTTTTATTATTAT
* *
666478 -GTTATATTTATTATT
1 ATTTTTA-TTATTA-T
*
666493 ATTTTTACTATTAT
1 ATTTTTATTATTAT
* *
666507 ATTTTCCTTTTATTCT
1 ATTTT--TATTATTAT
666523 ACTTATTTA-TATTAT
1 A-TT-TTTATTATTAT
* * *
666538 ATATGTATTTTTAT
1 ATTTTTATTATTAT
666552 ATTTTTATTATTAT
1 ATTTTTATTATTAT
666566 ATTTTTA
1 ATTTTTA
666573 CTTTCTCTTT
Statistics
Matches: 71, Mismatches: 16, Indels: 16
0.69 0.16 0.16
Matches are distributed among these distances:
13 7 0.10
14 36 0.51
15 12 0.17
16 12 0.17
17 2 0.03
18 2 0.03
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.67
Consensus pattern (14 bp):
ATTTTTATTATTAT
Found at i:666637 original size:21 final size:22
Alignment explanation
Indices: 666599--666673 Score: 82
Period size: 23 Copynumber: 3.3 Consensus size: 22
666589 ATTATTCTTG
*
666599 TATTATTACTTGTATTATTTATAT-
1 TATTATT--TTGT-TTATATATATA
666623 TATTATTTTGTTTATATATATA
1 TATTATTTTGTTTATATATATA
666645 TATATATATTT-TTTATATATATA
1 TAT-TAT-TTTGTTTATATATATA
666668 TATTAT
1 TATTAT
666674 ATTTTATATA
Statistics
Matches: 47, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
21 9 0.19
22 10 0.21
23 18 0.38
24 10 0.21
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.63
Consensus pattern (22 bp):
TATTATTTTGTTTATATATATA
Found at i:666659 original size:23 final size:21
Alignment explanation
Indices: 666613--666691 Score: 88
Period size: 22 Copynumber: 3.6 Consensus size: 21
666603 ATTACTTGTA
*
666613 TTATTTATATTATTAT-TTTGT
1 TTATATATATTATTATATTT-T
666634 TTATATATATATATATATATTTT
1 TTATATATAT-TAT-TATATTTT
666657 TTATATATATATATTATATTTT
1 TTATATATAT-TATTATATTTT
* *
666679 ATATATTTATTAT
1 TTATATATATTAT
666692 ACCTATTATA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.23
22 19 0.37
23 18 0.35
24 3 0.06
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (21 bp):
TTATATATATTATTATATTTT
Found at i:666703 original size:2 final size:2
Alignment explanation
Indices: 666635--666684 Score: 52
Period size: 2 Copynumber: 26.5 Consensus size: 2
666625 TTATTTTGTT
* *
666635 TA TA TA TA TA TA TA TA TA T- TT TT TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
666675 T- TT TA TA TA T
1 TA TA TA TA TA T
666685 TTATTATACC
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
1 3 0.07
2 40 0.93
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (2 bp):
TA
Found at i:666705 original size:29 final size:30
Alignment explanation
Indices: 666635--666706 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 30
666625 TTATTTTGTT
* * *
666635 TATATATATA-TATATATATTTTTTATATA
1 TATATATATATTTTATATATTTATTATACA
*
666664 TATATATTATATTTTATATATTTATTATACC
1 TATATA-TATATTTTATATATTTATTATACA
666695 TAT-TATATATTT
1 TATATATATATTT
666707 GTTTTTTTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 13 0.35
30 6 0.16
31 18 0.49
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (30 bp):
TATATATATATTTTATATATTTATTATACA
Found at i:666819 original size:2 final size:2
Alignment explanation
Indices: 666814--666880 Score: 93
Period size: 2 Copynumber: 34.5 Consensus size: 2
666804 TTTATTATTG
* * *
666814 AT AT AT AT TT TT AT -T AT AT AT AT AT -T TT 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
666854 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
666881 CACAAGTTAA
Statistics
Matches: 60, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
1 2 0.03
2 58 0.97
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
AT
Found at i:667146 original size:23 final size:25
Alignment explanation
Indices: 667110--667159 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 25
667100 TCTTTTCGTC
667110 ATTTAATTTATTAA-T-TTATATAT
1 ATTTAATTTATTAATTATTATATAT
* *
667133 ATTTACTTTTTTAATTATTATATAT
1 ATTTAATTTATTAATTATTATATAT
667158 AT
1 AT
667160 ATATATATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 12 0.52
24 1 0.04
25 10 0.43
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (25 bp):
ATTTAATTTATTAATTATTATATAT
Found at i:667243 original size:28 final size:28
Alignment explanation
Indices: 667212--667275 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 28
667202 GTTTTATTTA
*
667212 TTATCTTTTTTTTCTTTTTA-TATA-TATT
1 TTATCTTTTATTT-TTTTTACT-TACTATT
667240 TTAT-TATTTATTTTTTTTACTTACTATT
1 TTATCT-TTTATTTTTTTTACTTACTATT
667268 TTATCTTT
1 TTATCTTT
667276 GCTTTCTTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
27 9 0.29
28 21 0.68
29 1 0.03
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.73
Consensus pattern (28 bp):
TTATCTTTTATTTTTTTTACTTACTATT
Found at i:667816 original size:17 final size:17
Alignment explanation
Indices: 667794--667828 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
667784 TAATTTTTAA
*
667794 AATAATTAAAATTATAT
1 AATAATTAAAATAATAT
667811 AATAATTAAAATAATAT
1 AATAATTAAAATAATAT
667828 A
1 A
667829 TTTTGATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
AATAATTAAAATAATAT
Found at i:672175 original size:26 final size:27
Alignment explanation
Indices: 672124--672183 Score: 104
Period size: 26 Copynumber: 2.3 Consensus size: 27
672114 TCGGGTCAAG
*
672124 TTTGGGTCGTGTGGAGGATGTAAAATT
1 TTTGGGTCGGGTGGAGGATGTAAAATT
672151 TTTGGGTCGGGTGG-GGATGTAAAATT
1 TTTGGGTCGGGTGGAGGATGTAAAATT
672177 TTTGGGT
1 TTTGGGT
672184 TGGTTCGGGT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 19 0.59
27 13 0.41
ACGTcount: A:0.18, C:0.03, G:0.40, T:0.38
Consensus pattern (27 bp):
TTTGGGTCGGGTGGAGGATGTAAAATT
Found at i:677989 original size:53 final size:53
Alignment explanation
Indices: 677903--678020 Score: 139
Period size: 53 Copynumber: 2.2 Consensus size: 53
677893 TACAAATAAA
* * **
677903 ATTTTAAGGCGGATACCATCAGTAAAATAAGTAACAAATTGAAGAAAACTCATG
1 ATTTTAAGGTGGACACCATCAGTAAAATAAGTAACAAATCAAAGAAAACTCA-G
* * * *
677957 -TTTTAAGGTGGACACCGTTAGTAAAATGAGTAACTAATCAAAGAAAACTCAG
1 ATTTTAAGGTGGACACCATCAGTAAAATAAGTAACAAATCAAAGAAAACTCAG
*
678009 ATTTTAGGGTGG
1 ATTTTAAGGTGG
678021 GCATGAAAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
52 1 0.02
53 53 0.98
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.26
Consensus pattern (53 bp):
ATTTTAAGGTGGACACCATCAGTAAAATAAGTAACAAATCAAAGAAAACTCAG
Found at i:679960 original size:6 final size:6
Alignment explanation
Indices: 679946--679981 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
679936 AAGAGTATAG
* *
679946 TGAACA TGAATA TGAACA TGAACA CGAACA TGAACA
1 TGAACA TGAACA TGAACA TGAACA TGAACA TGAACA
679982 CAAATGTTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.50, C:0.17, G:0.17, T:0.17
Consensus pattern (6 bp):
TGAACA
Found at i:680250 original size:143 final size:143
Alignment explanation
Indices: 679979--680263 Score: 446
Period size: 142 Copynumber: 2.0 Consensus size: 143
679969 ACGAACATGA
* *
679979 ACACAAATGTTGAGAAAGCCCTACATGCACACATATAAAAACTTTTGATACTTTTTGTTTATTAT
1 ACACAAATGTTGAGAAAGCCCTACATGCACACATATAAAAACGTTTGATACCTTTTGTTTATTAT
* * **
680044 TTTTCGGGTAAACTGTGGAAGTAATCCTCTTTATTTTAGGTCTGATTGATTTTGGTCAATA-TTT
66 TTTTCGGGTAAACTATGCAAGTAATCCTCTTTATTTTAGGTCTGATCAATTTTGGTCAATATTTT
680108 TTTAATTAAATGC
131 TTTAATTAAATGC
* *
680121 ACACAAATGTTGATAAATCCCTACATGCACACATATAAAAACGTTTGATACCTTTTGTTTATTTA
1 ACACAAATGTTGAGAAAGCCCTACATGCACACATATAAAAACGTTTGATACCTTTTGTTTA-TTA
* * * *
680186 TTTTTCGGGTAAACTATGCCAGTAGTCCTCTTTGTTTTAGGTCTGATCAATTTTGGTCACTATTT
65 TTTTTCGGGTAAACTATGCAAGTAATCCTCTTTATTTTAGGTCTGATCAATTTTGGTCAATATTT
680251 TTTTAATTAAATG
130 TTTTAATTAAATG
680264 TACTTGATCC
Statistics
Matches: 129, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
142 57 0.44
143 57 0.44
144 15 0.12
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.42
Consensus pattern (143 bp):
ACACAAATGTTGAGAAAGCCCTACATGCACACATATAAAAACGTTTGATACCTTTTGTTTATTAT
TTTTCGGGTAAACTATGCAAGTAATCCTCTTTATTTTAGGTCTGATCAATTTTGGTCAATATTTT
TTTAATTAAATGC
Found at i:704542 original size:236 final size:238
Alignment explanation
Indices: 704127--704603 Score: 613
Period size: 236 Copynumber: 2.0 Consensus size: 238
704117 GTTAAAACCC
* *
704127 TTAAGCTGTATATTTCTCAATAATATCAGTTTATAGGAGACTCCATGCATCCGATCCCGACAAGA
1 TTAAGCTGTATATTTCTCAATAATATCAGTTTATAGGAGACACCATGCATCCAATCCCGACAAGA
* * * * *
704192 TTGATCAAGCGTTTACCGTTTTTACTGTTATAATTCGACTTTTCATAACAGTATGTATACGATGG
66 TTGATCAAGCGTTCACCG-TTTTACTGTTATAATTCAACTTTTCATAACAATATATATACAATGG
* * *
704257 AGTCAGTATCTTGTCTGTGTTTTGGTGGAGTTTCCTAGCAACATCCCAGAACTGGTAAATTAACA
130 AGTCAGTATCTTGTCGGTGTTTGGGTGGAGTTTCCTAGCAACATCCCAGAACTGGTAAATCAACA
* *
704322 AAGATGGAGTTCCC-TTGCTCTCTCGTCCCTCTTTATATCACCA
195 AAAATGGAGTTCCCTTTGCACTCTCGTCCCTCTTTATATCACCA
* * * * * *
704365 TTAAGCTGTATATTTCTCGATAATATCAGTTCTATCGGAGGCACCGTGCATCCAATCCCGTCACG
1 TTAAGCTGTATATTTCTCAATAATATCAGTT-TATAGGAGACACCATGCATCCAATCCCGACAAG
* * * *
704430 ATTGATCGAGTGTTCACCG-TTT-CTGTTATAATTCAATTGTTTCATAACAATATATATGCAATG
65 ATTGATCAAGCGTTCACCGTTTTACTGTTATAATTCAACT-TTTCATAACAATATATATACAATG
* * * * *
704493 GAGT-AGGTATCTTGTGGGTG-TTGGGTGGAGTTTCCTATCAACTTCCCAGAACTTGTACATCAA
129 GAGTCA-GTATCTTGTCGGTGTTTGGGTGGAGTTTCCTAGCAACATCCCAGAACTGGTAAATCAA
* * *
704556 CAAAAATGGAGTTCCCTTTGCACTTTCGTGCCTCTTTATATCATCA
193 CAAAAATGGAGTTCCCTTTGCACTCTCGTCCCTCTTTATATCACCA
704602 TT
1 TT
704604 GAATCAAACT
Statistics
Matches: 205, Mismatches: 30, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
236 67 0.33
237 66 0.32
238 30 0.15
239 42 0.20
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.36
Consensus pattern (238 bp):
TTAAGCTGTATATTTCTCAATAATATCAGTTTATAGGAGACACCATGCATCCAATCCCGACAAGA
TTGATCAAGCGTTCACCGTTTTACTGTTATAATTCAACTTTTCATAACAATATATATACAATGGA
GTCAGTATCTTGTCGGTGTTTGGGTGGAGTTTCCTAGCAACATCCCAGAACTGGTAAATCAACAA
AAATGGAGTTCCCTTTGCACTCTCGTCCCTCTTTATATCACCA
Found at i:706070 original size:34 final size:34
Alignment explanation
Indices: 706006--706071 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
705996 AACCACCATC
**
706006 TCTTCTTCTTCTTCTTCTATTTTCTCAGCCATTT
1 TCTTCTTCTTCTTCTTCTATTGGCTCAGCCATTT
*
706040 TCTTCTTCTTCTTCTTCT-TCTGGCTGAGCCAT
1 TCTTCTTCTTCTTCTTCTAT-TGGCTCAGCCAT
706072 GGAGCACTGG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 1 0.04
34 27 0.96
ACGTcount: A:0.08, C:0.30, G:0.08, T:0.55
Consensus pattern (34 bp):
TCTTCTTCTTCTTCTTCTATTGGCTCAGCCATTT
Found at i:706614 original size:24 final size:24
Alignment explanation
Indices: 706587--706666 Score: 97
Period size: 24 Copynumber: 3.3 Consensus size: 24
706577 ACACACACAT
*
706587 ATGTATGTATATACATATGCATGC
1 ATGTATGTATGTACATATGCATGC
* * * *
706611 ATGTACGTACGTACATATGTATGT
1 ATGTATGTATGTACATATGCATGC
*
706635 ATGTATGTATGTATATATGCATGC
1 ATGTATGTATGTACATATGCATGC
*
706659 ATGCATGT
1 ATGTATGT
706667 GAAGAAAGCT
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (24 bp):
ATGTATGTATGTACATATGCATGC
Found at i:710907 original size:16 final size:16
Alignment explanation
Indices: 710886--710926 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
710876 AAAGAGTTCT
710886 ACTCGATTTAAAATCA
1 ACTCGATTTAAAATCA
*
710902 ACTCGATTCAAAATCA
1 ACTCGATTTAAAATCA
*
710918 ACTCAATTT
1 ACTCGATTT
710927 TTAAGTGGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.41, C:0.22, G:0.05, T:0.32
Consensus pattern (16 bp):
ACTCGATTTAAAATCA
Found at i:711722 original size:28 final size:28
Alignment explanation
Indices: 711684--711744 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 28
711674 TTTAATAAAA
** *
711684 AAAAACTTAATTTATTTAAAAAAAAATC
1 AAAAACTTAATGAAATTAAAAAAAAATC
* *
711712 AAAAATTTAATGAAATTAAAAAAAACTC
1 AAAAACTTAATGAAATTAAAAAAAAATC
711740 AAAAA
1 AAAAA
711745 AACTAGAATC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.66, C:0.07, G:0.02, T:0.26
Consensus pattern (28 bp):
AAAAACTTAATGAAATTAAAAAAAAATC
Found at i:719753 original size:12 final size:12
Alignment explanation
Indices: 719738--719763 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
719728 TTAATAAAGA
719738 AGATTCTAAATT
1 AGATTCTAAATT
719750 AGATTCTAAATT
1 AGATTCTAAATT
719762 AG
1 AG
719764 GGGGGGGGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (12 bp):
AGATTCTAAATT
Found at i:721822 original size:10 final size:10
Alignment explanation
Indices: 721784--721832 Score: 53
Period size: 10 Copynumber: 4.9 Consensus size: 10
721774 TCATCATACT
721784 AAATTCTCTC
1 AAATTCTCTC
*
721794 AATTTCTCTC
1 AAATTCTCTC
*
721804 AACTTCTCTC
1 AAATTCTCTC
* *
721814 AAATACTCTT
1 AAATTCTCTC
*
721824 ATATTCTCT
1 AAATTCTCT
721833 GTTTAAGGTA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
10 32 1.00
ACGTcount: A:0.27, C:0.29, G:0.00, T:0.45
Consensus pattern (10 bp):
AAATTCTCTC
Found at i:721881 original size:9 final size:9
Alignment explanation
Indices: 721869--721902 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
721859 TAATATTTTG
721869 TATTTAATT
1 TATTTAATT
*
721878 TATTTAA-G
1 TATTTAATT
721886 TATTTAATT
1 TATTTAATT
721895 TATTTAAT
1 TATTTAAT
721903 ATTTTACATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (9 bp):
TATTTAATT
Found at i:721908 original size:17 final size:17
Alignment explanation
Indices: 721868--721906 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
721858 TTAATATTTT
721868 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
721885 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
721902 -TATTT
1 GTATTT
721907 TACATAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (17 bp):
GTATTTAATTTATTTAA
Found at i:722864 original size:3 final size:3
Alignment explanation
Indices: 722856--722891 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
722846 TATAAACGTC
722856 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATTT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT AT
722892 ACCATCCAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:740392 original size:25 final size:25
Alignment explanation
Indices: 740364--740422 Score: 86
Period size: 24 Copynumber: 2.4 Consensus size: 25
740354 TTTTTATTTT
740364 TTATTA-ATCTAAAGTGATTACAAAA
1 TTATTATAT-TAAAGTGATTACAAAA
740389 TTA-TATATTAAAGTGATTACAAAA
1 TTATTATATTAAAGTGATTACAAAA
740413 TTATATATAT
1 TTAT-TATAT
740423 ATGTGTGTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
24 21 0.68
25 5 0.16
26 5 0.16
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.41
Consensus pattern (25 bp):
TTATTATATTAAAGTGATTACAAAA
Found at i:740401 original size:24 final size:24
Alignment explanation
Indices: 740373--740420 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
740363 TTTATTAATC
740373 TAAAGTGATTACAAAATTATATAT
1 TAAAGTGATTACAAAATTATATAT
740397 TAAAGTGATTACAAAATTATATAT
1 TAAAGTGATTACAAAATTATATAT
740421 ATATGTGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.04, G:0.08, T:0.38
Consensus pattern (24 bp):
TAAAGTGATTACAAAATTATATAT
Done.