Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005219.1 Hibiscus syriacus cultivar Beakdansim tig00011818_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: 68703
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Found at i:478 original size:20 final size:20
Alignment explanation
Indices: 453--490 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
443 TCGTACAGGG
*
453 GGTATCGGTACCCCTTCAAT
1 GGTATCGATACCCCTTCAAT
*
473 GGTATCGATACCCTTTCA
1 GGTATCGATACCCCTTCA
491 TAAAATTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.29, G:0.18, T:0.32
Consensus pattern (20 bp):
GGTATCGATACCCCTTCAAT
Found at i:620 original size:20 final size:19
Alignment explanation
Indices: 576--620 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
566 TGAGCCTCGG
*
576 ATACTGTTTAAACAATATA
1 ATACTGTTCAAACAATATA
*
595 AGTACTGTTCAAACAGTATCA
1 A-TACTGTTCAAACAATAT-A
616 ATACT
1 ATACT
621 ATTTATATAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 1 0.05
20 19 0.86
21 2 0.09
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.33
Consensus pattern (19 bp):
ATACTGTTCAAACAATATA
Found at i:915 original size:18 final size:18
Alignment explanation
Indices: 855--915 Score: 50
Period size: 18 Copynumber: 3.2 Consensus size: 18
845 ATGTTTAATG
* *
855 AAAAGATACTAATTGTTA
1 AAAAAATACCAATTGTTA
* *
873 ACAAAAGGATATCAATTATTA
1 A-AAAA--ATACCAATTGTTA
894 AAAAAATACCAATTGTTGA
1 AAAAAATACCAATTGTT-A
913 AAA
1 AAA
916 TGTAAAATGT
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
18 11 0.33
19 7 0.21
20 4 0.12
21 11 0.33
ACGTcount: A:0.54, C:0.08, G:0.10, T:0.28
Consensus pattern (18 bp):
AAAAAATACCAATTGTTA
Found at i:3893 original size:19 final size:19
Alignment explanation
Indices: 3869--3905 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3859 TCGTACAGGG
*
3869 GGTATCGGTACCCCTTCAA
1 GGTATCGATACCCCTTCAA
*
3888 GGTATCGATACCCTTTCA
1 GGTATCGATACCCCTTCA
3906 TAAAATTCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.30, G:0.19, T:0.30
Consensus pattern (19 bp):
GGTATCGATACCCCTTCAA
Found at i:4025 original size:20 final size:20
Alignment explanation
Indices: 4000--4043 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
3990 TACTGTTAAT
4000 TACTGTTCAAACAATATCAG
1 TACTGTTCAAACAATATCAG
* *
4020 TACTGTTCAAACAGTATTAG
1 TACTGTTCAAACAATATCAG
4040 TACT
1 TACT
4044 ATTTATACAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.34
Consensus pattern (20 bp):
TACTGTTCAAACAATATCAG
Found at i:4310 original size:51 final size:51
Alignment explanation
Indices: 4255--4361 Score: 160
Period size: 51 Copynumber: 2.1 Consensus size: 51
4245 GTTATATTTT
* * *
4255 TTTATTTTATTCACTCACACCGGTGTAAGTATGTGTTAAGTGCTACACTTG
1 TTTATTTTATTCACTCACACCGATGTAAATATGAGTTAAGTGCTACACTTG
* * *
4306 TTTATTTTATTCACTTACACCGATGTAAATATGAGTTAAGTGCTACATTTT
1 TTTATTTTATTCACTCACACCGATGTAAATATGAGTTAAGTGCTACACTTG
4357 TTTAT
1 TTTAT
4362 AATATGAATT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.26, C:0.15, G:0.14, T:0.45
Consensus pattern (51 bp):
TTTATTTTATTCACTCACACCGATGTAAATATGAGTTAAGTGCTACACTTG
Found at i:4680 original size:21 final size:21
Alignment explanation
Indices: 4656--4705 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
4646 AACAGTGTTT
* *
4656 TAAAATAAATTAATTATTTTC
1 TAAAAGAAATTAATAATTTTC
*
4677 TAAAAGAAGTTAATAATTTT-
1 TAAAAGAAATTAATAATTTTC
*
4697 TAATAGAAA
1 TAAAAGAAA
4706 AACTTTTGGT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (21 bp):
TAAAAGAAATTAATAATTTTC
Found at i:4866 original size:21 final size:21
Alignment explanation
Indices: 4842--4896 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
4832 GATCCAAAAA
*
4842 ATCAAATATCCAAATTTTCGG
1 ATCAAATATCCAAATTTTCAG
** *
4863 ATCAAATATCTGAATTTTCAT
1 ATCAAATATCCAAATTTTCAG
*
4884 ATTAAATATCCAA
1 ATCAAATATCCAA
4897 TATCCGAATC
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.42, C:0.16, G:0.05, T:0.36
Consensus pattern (21 bp):
ATCAAATATCCAAATTTTCAG
Found at i:6265 original size:19 final size:18
Alignment explanation
Indices: 6234--6279 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
6224 TTTAATCTTT
*
6234 TATTTTGATTATTA-TAAA
1 TATTTTAATTATTACT-AA
6252 TATTATTAATTATTACTAA
1 TATT-TTAATTATTACTAA
6271 TATTTTAAT
1 TATTTTAAT
6280 AAAATATGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 9 0.36
19 15 0.60
20 1 0.04
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (18 bp):
TATTTTAATTATTACTAA
Found at i:21626 original size:31 final size:31
Alignment explanation
Indices: 21555--21626 Score: 72
Period size: 31 Copynumber: 2.3 Consensus size: 31
21545 AATACTATTA
* * * * **
21555 TGACCTTCAGATTTTTGATAAAATGTTATTT
1 TGACCTTTAAATTTTAGATAAAATATTAAAT
* *
21586 TAACTTTTAAATTTTAGATAAAATATTAAAT
1 TGACCTTTAAATTTTAGATAAAATATTAAAT
21617 TGACCTTTAA
1 TGACCTTTAA
21627 TTCAACAAAG
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (31 bp):
TGACCTTTAAATTTTAGATAAAATATTAAAT
Found at i:21923 original size:20 final size:21
Alignment explanation
Indices: 21898--21949 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 21
21888 TGATATTGTT
* *
21898 ATTTATAATTTT-TTGGATAG
1 ATTTATAATTTTATTGAATAA
21918 ATTTATAATATTTATTGAATAA
1 ATTTATAAT-TTTATTGAATAA
*
21940 ATTAATAATT
1 ATTTATAATT
21950 AAAATATATC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 9 0.33
21 4 0.15
22 14 0.52
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (21 bp):
ATTTATAATTTTATTGAATAA
Found at i:27636 original size:13 final size:13
Alignment explanation
Indices: 27618--27903 Score: 68
Period size: 13 Copynumber: 22.9 Consensus size: 13
27608 AAATTGAAAA
27618 ATATAATATATAT
1 ATATAATATATAT
*
27631 ATATAAAAT-TAT
1 ATATAATATATAT
27643 ATATAA-ACTATAT
1 ATATAATA-TATAT
* * *
27656 TTATATTATAAACT
1 ATATAATATATA-T
27670 ATATAAT-TAT-T
1 ATATAATATATAT
27681 ATA-AACTATATAT
1 ATATAA-TATATAT
27694 ATA-AAT-TATAT
1 ATATAATATATAT
* *
27705 TTAT-GTGCACTATAT
1 ATATAAT--A-TATAT
*
27720 ATATAA-ACTATGT
1 ATATAATA-TATAT
27733 ATATAA-ACTATAT
1 ATATAATA-TATAT
* * *
27746 TTATATTATAAACT
1 ATATAATATATA-T
27760 ATATAAT-TAT-T
1 ATATAATATATAT
*
27771 ATA-AGCTATATAT
1 ATATA-ATATATAT
*
27784 ATA-AAT-TATGT
1 ATATAATATATAT
27795 ATATAA-ACTATAT
1 ATATAATA-TATAT
*
27808 GTATAA-ACTATA-
1 ATATAATA-TATAT
27820 A-A-AAGTATATAGT
1 ATATAA-TATATA-T
* *
27833 TTATAAAATAT-T
1 ATATAATATATAT
*
27845 AT-TTATAT-TA-
1 ATATAATATATAT
*
27855 ATATAGTATATAT
1 ATATAATATATAT
* *
27868 AAAAAACTATATAT
1 ATATAA-TATATAT
*
27882 GTATAA-AT-TAT
1 ATATAATATATAT
27893 ATA-AATATATA
1 ATATAATATATA
27904 GTTTATCTGT
Statistics
Matches: 200, Mismatches: 39, Indels: 69
0.65 0.13 0.22
Matches are distributed among these distances:
10 10 0.05
11 46 0.23
12 29 0.14
13 76 0.38
14 29 0.14
15 10 0.05
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.43
Consensus pattern (13 bp):
ATATAATATATAT
Found at i:27701 original size:20 final size:20
Alignment explanation
Indices: 27640--27792 Score: 95
Period size: 18 Copynumber: 8.4 Consensus size: 20
27630 TATATAAAAT
27640 TATA-TATAAACTATAT-T-
1 TATATTATAAACTATATATA
27657 TATATTATAAACTATATA-A
1 TATATTATAAACTATATATA
27676 T-TATTATAAACTATATATA
1 TATATTATAAACTATATATA
* *
27695 TAAATTAT--A-T-T-TATG
1 TATATTATAAACTATATATA
** * * *
27710 TGCACTATATA-TATAAACTA
1 TATATTATAAACTATATA-TA
*
27730 TGTA-TATAAACTATAT-T-
1 TATATTATAAACTATATATA
27747 TATATTATAAACTATATA-A
1 TATATTATAAACTATATATA
*
27766 T-TATTATAAGCTATATATA
1 TATATTATAAACTATATATA
*
27785 TAAATTAT
1 TATATTAT
27793 GTATATAAAC
Statistics
Matches: 107, Mismatches: 13, Indels: 29
0.72 0.09 0.19
Matches are distributed among these distances:
15 8 0.07
16 1 0.01
17 10 0.09
18 58 0.54
19 12 0.11
20 18 0.17
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (20 bp):
TATATTATAAACTATATATA
Found at i:27742 original size:26 final size:26
Alignment explanation
Indices: 27618--27819 Score: 113
Period size: 25 Copynumber: 8.0 Consensus size: 26
27608 AAATTGAAAA
*
27618 ATATAATA-TATATATATAAAAT-TAT
1 ATATAA-ACTATATATATAAACTATAT
* * *
27643 ATATAAACTATAT-T-TATATTATAA
1 ATATAAACTATATATATAAACTATAT
27667 ACTATATAA-T-TAT-TATAAACTATAT
1 A-TATA-AACTATATATATAAACTATAT
* * **
27692 ATATAAATTATATTTATGTGCACTATAT
1 ATATAAACTATA--TATATAAACTATAT
*
27720 ATATAAACTATGTATATAAACTATAT
1 ATATAAACTATATATATAAACTATAT
* * *
27746 -T-TATATTATAAACTATATAA-T-TAT
1 ATATAAACTATATA-TATA-AACTATAT
* * *
27770 -TATAAGCTATATATATAAATTATGT
1 ATATAAACTATATATATAAACTATAT
*
27795 ATATAAACTATATGTATAAACTATA
1 ATATAAACTATATATATAAACTATA
27820 AAAAGTATAT
Statistics
Matches: 134, Mismatches: 27, Indels: 31
0.70 0.14 0.16
Matches are distributed among these distances:
23 8 0.06
24 30 0.22
25 41 0.31
26 35 0.26
27 1 0.01
28 19 0.14
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (26 bp):
ATATAAACTATATATATAAACTATAT
Found at i:27744 original size:90 final size:89
Alignment explanation
Indices: 27626--27792 Score: 298
Period size: 90 Copynumber: 1.9 Consensus size: 89
27616 AAATATAATA
27626 TATATATATAAAATTATATATAAACTATATTTATATTATAAACTATATAATTATTATAAACTATA
1 TATATATATAAAATTATATATAAACTATATTTATATTATAAACTATATAATTATTATAAACTATA
27691 TATATAAATTATATTTATGTGCAC
66 TATATAAATTATATTTATGTGCAC
* * *
27715 TATATATATAAACTATGTATATAAACTATATTTATATTATAAACTATATAATTATTATAAGCTAT
1 TATATATATAAAAT-TATATATAAACTATATTTATATTATAAACTATATAATTATTATAAACTAT
27780 ATATATAAATTAT
65 ATATATAAATTAT
27793 GTATATAAAC
Statistics
Matches: 74, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
89 13 0.18
90 61 0.82
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.45
Consensus pattern (89 bp):
TATATATATAAAATTATATATAAACTATATTTATATTATAAACTATATAATTATTATAAACTATA
TATATAAATTATATTTATGTGCAC
Found at i:27905 original size:73 final size:74
Alignment explanation
Indices: 27803--27940 Score: 197
Period size: 73 Copynumber: 1.9 Consensus size: 74
27793 GTATATAAAC
*
27803 TATATGTATAAACTATAAAAAGTATATAGTTTATAAAATATTATTTATATTAATATAGTATATAT
1 TATATGTATAAACTATAAAAAGTATATAGTTTATAAAATATAATTTATATTAATATAGTATATAT
27868 AAAAAACTA
66 AAAAAACTA
* * **** *
27877 TATATGTATAAATTATATAAA-TATATAGTTTATCTGTTATAATTTATATTTATATAGTATATAT
1 TATATGTATAAACTATAAAAAGTATATAGTTTATAAAATATAATTTATATTAATATAGTATATAT
27941 GTATGTATAA
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
73 37 0.66
74 19 0.34
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (74 bp):
TATATGTATAAACTATAAAAAGTATATAGTTTATAAAATATAATTTATATTAATATAGTATATAT
AAAAAACTA
Found at i:28329 original size:7 final size:7
Alignment explanation
Indices: 28319--28396 Score: 74
Period size: 7 Copynumber: 11.6 Consensus size: 7
28309 ATATATTATA
28319 TAAACCC
1 TAAACCC
28326 TAAACCC
1 TAAACCC
28333 TAAA-CC
1 TAAACCC
* *
28339 AAAATCC
1 TAAACCC
28346 TAAA--C
1 TAAACCC
*
28351 TAAAACCT
1 T-AAACCC
28359 TAAACCC
1 TAAACCC
28366 TAAA-CC
1 TAAACCC
*
28372 AAAACCC
1 TAAACCC
28379 TAAACCC
1 TAAACCC
*
28386 TAAACTC
1 TAAACCC
28393 TAAA
1 TAAA
28397 TTTTAAATCT
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
5 2 0.03
6 13 0.22
7 43 0.73
8 1 0.02
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (7 bp):
TAAACCC
Found at i:28349 original size:20 final size:19
Alignment explanation
Indices: 28319--28390 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 19
28309 ATATATTATA
*
28319 TAAACCCTAAACCCTAAACC
1 TAAACCCTAAA-CCAAAACC
* * *
28339 AAAATCCTAAACTAAAACC
1 TAAACCCTAAACCAAAACC
28358 TTAAACCCTAAACCAAAACCC
1 -TAAACCCTAAACCAAAA-CC
28379 TAAACCCTAAAC
1 TAAACCCTAAAC
28391 TCTAAATTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
19 6 0.14
20 35 0.81
21 2 0.05
ACGTcount: A:0.50, C:0.35, G:0.00, T:0.15
Consensus pattern (19 bp):
TAAACCCTAAACCAAAACC
Found at i:28363 original size:33 final size:33
Alignment explanation
Indices: 28320--28383 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
28310 TATATTATAT
*
28320 AAACCCTAAACCCTAAACCAAAATCCTAAACTA
1 AAACCCTAAACCCTAAACCAAAACCCTAAACTA
*
28353 AAACCTTAAACCCTAAACCAAAACCCTAAAC
1 AAACCCTAAACCCTAAACCAAAACCCTAAAC
28384 CCTAAACTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.52, C:0.34, G:0.00, T:0.14
Consensus pattern (33 bp):
AAACCCTAAACCCTAAACCAAAACCCTAAACTA
Found at i:28376 original size:13 final size:13
Alignment explanation
Indices: 28360--28384 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28350 CTAAAACCTT
28360 AAACCCTAAACCA
1 AAACCCTAAACCA
28373 AAACCCTAAACC
1 AAACCCTAAACC
28385 CTAAACTCTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.40, G:0.00, T:0.08
Consensus pattern (13 bp):
AAACCCTAAACCA
Found at i:28521 original size:37 final size:37
Alignment explanation
Indices: 28458--28528 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
28448 ATAGTTAATA
*
28458 TATATAATGTAACCTATGATATATGTATACATGTAAAC
1 TATATAATGTAACCTATGATACATGTAT-CATGTAAAC
*
28496 TATA-AATGTAACTTAT-AGTACATGTATCATGTA
1 TATATAATGTAACCTATGA-TACATGTATCATGTA
28529 TGTATAAACT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
36 7 0.23
37 19 0.63
38 4 0.13
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.38
Consensus pattern (37 bp):
TATATAATGTAACCTATGATACATGTATCATGTAAAC
Found at i:28556 original size:20 final size:19
Alignment explanation
Indices: 28517--28591 Score: 82
Period size: 20 Copynumber: 3.8 Consensus size: 19
28507 CTTATAGTAC
28517 ATGTATCATGTATGTATAAACT
1 ATGTAT-ATGTA--TATAAACT
28539 ATGTATAGTGTATATAAACT
1 ATGTATA-TGTATATAAACT
*
28559 ATGTATA--TATATAACCT
1 ATGTATATGTATATAAACT
28576 ATAGTATATGTATATA
1 AT-GTATATGTATATA
28592 TACAATCTAT
Statistics
Matches: 48, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
17 11 0.23
18 5 0.10
20 21 0.44
21 1 0.02
22 10 0.21
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.41
Consensus pattern (19 bp):
ATGTATATGTATATAAACT
Found at i:28601 original size:24 final size:23
Alignment explanation
Indices: 28558--28622 Score: 73
Period size: 24 Copynumber: 2.9 Consensus size: 23
28548 GTATATAAAC
*
28558 TATGTATATATATAACCTATAGTA
1 TATGTATATATA-AATCTATAGTA
*
28582 TATGTATATATACAATCTAT-TTA
1 TATGTATATATA-AATCTATAGTA
28605 TATGT-TATATAAAT-TATA
1 TATGTATATATAAATCTATA
28623 TATGTAACCT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
20 3 0.08
21 3 0.08
22 6 0.16
23 7 0.19
24 18 0.49
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (23 bp):
TATGTATATATAAATCTATAGTA
Found at i:28720 original size:21 final size:21
Alignment explanation
Indices: 28668--28720 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
28658 TAGTGTACTA
* *
28668 TATAGTTTATACTTTATAACC
1 TATAGTTTATAATTTATAAAC
* * *
28689 AATGGTATATAATTTATAAAC
1 TATAGTTTATAATTTATAAAC
28710 TATAGTTTATA
1 TATAGTTTATA
28721 TTAATGTACT
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.45
Consensus pattern (21 bp):
TATAGTTTATAATTTATAAAC
Found at i:28798 original size:6 final size:6
Alignment explanation
Indices: 28787--28937 Score: 57
Period size: 6 Copynumber: 24.3 Consensus size: 6
28777 CATATAATTT
* * * * *
28787 ATATTA ATATTA ATGTTA TAGACT- ATATTTT ATATTA ATATTA ATTATAA
1 ATATTA ATATTA ATATTA -ATATTA ATA-TTA ATATTA ATATTA A-TATTA
* *
28837 ATTATAA ACTATATT ATATTA ATA-TA AT-TTA ATATTA ATATT- A-ATT-
1 A-TATTA A-TAT-TA ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA
*
28883 ATATTA AT-TATA AT-TATA ATATTA ATTATTATA ATATTA ATTATAA
1 ATATTA ATAT-TA ATAT-TA ATATTA A-TA-T-TA ATATTA A-TATTA
28929 ATAGTTA AT
1 ATA-TTA AT
28938 TAATAAAAAT
Statistics
Matches: 115, Mismatches: 14, Indels: 31
0.72 0.09 0.19
Matches are distributed among these distances:
4 4 0.03
5 15 0.13
6 53 0.46
7 36 0.31
8 4 0.03
9 3 0.03
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.50
Consensus pattern (6 bp):
ATATTA
Found at i:28819 original size:31 final size:30
Alignment explanation
Indices: 28767--28859 Score: 104
Period size: 31 Copynumber: 3.1 Consensus size: 30
28757 CTATACTATA
28767 TAATTTATAACATATAATTTATATTAATAT
1 TAATTTATAACATATAATTTATATTAATAT
*
28797 TAATGTTATAGAC-TATATTTTATATTAATAT
1 TAAT-TTATA-ACATATAATTTATATTAATAT
**
28828 TAA-TTATAA-ATTATAAACTATATT-ATAT
1 TAATTTATAACA-TATAATTTATATTAATAT
28856 TAAT
1 TAAT
28860 ATAATTTAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
28 8 0.15
29 15 0.28
30 4 0.07
31 25 0.46
32 2 0.04
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.49
Consensus pattern (30 bp):
TAATTTATAACATATAATTTATATTAATAT
Found at i:28888 original size:15 final size:15
Alignment explanation
Indices: 28816--28939 Score: 93
Period size: 15 Copynumber: 8.2 Consensus size: 15
28806 AGACTATATT
28816 TTATATTAATATTAA
1 TTATATTAATATTAA
* *
28831 TTATAAATTATAAACTATA
1 TTAT--ATTA-ATATTA-A
28850 TTATATTAATA-TAA
1 TTATATTAATATTAA
28864 TTTAATATTAATATTAA
1 -TT-ATATTAATATTAA
28881 TTATATTAAT-TATAA
1 TTATATTAATAT-TAA
28896 -T-TA-TAATATTAA
1 TTATATTAATATTAA
28908 TTAT-TATAATATTAA
1 TTATAT-TAATATTAA
28923 TTATA--AATAGTTAA
1 TTATATTAATA-TTAA
28937 TTA
1 TTA
28940 ATAAAAATTA
Statistics
Matches: 91, Mismatches: 3, Indels: 31
0.73 0.02 0.25
Matches are distributed among these distances:
12 7 0.08
13 8 0.09
14 11 0.12
15 32 0.35
16 13 0.14
17 11 0.12
18 4 0.04
19 5 0.05
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (15 bp):
TTATATTAATATTAA
Found at i:28941 original size:33 final size:34
Alignment explanation
Indices: 28852--28931 Score: 105
Period size: 33 Copynumber: 2.5 Consensus size: 34
28842 AAACTATATT
* *
28852 ATATTAA-TAT-AATTTAATATTAA-TATTAATT
1 ATATTAATTATAAATATAATATTAATTATTAATA
*
28883 ATATTAATTATAATTATAATATTAATTATT-ATA
1 ATATTAATTATAAATATAATATTAATTATTAATA
28916 ATATTAATTATAAATA
1 ATATTAATTATAAATA
28932 GTTAATTAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
31 7 0.17
32 3 0.07
33 28 0.67
34 4 0.10
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (34 bp):
ATATTAATTATAAATATAATATTAATTATTAATA
Found at i:28943 original size:27 final size:25
Alignment explanation
Indices: 28822--28943 Score: 103
Period size: 27 Copynumber: 4.7 Consensus size: 25
28812 TATTTTATAT
28822 TAATATTAATTATA-AATTATAA--A
1 TAATATTAATTATATAATT-TAATTA
28845 CT-ATATTATATTAATATAATTTAA-TA
1 -TAATATTA-ATT-ATATAATTTAATTA
28871 TTAATATTAATTATATTAATTATAATTA
1 -TAATATTAATTATA-TAATT-TAATTA
28899 TAATATTAATTATTATAATATTAATTA
1 TAATATTAATTA-TATAAT-TTAATTA
28926 TAAATAGTTAATTA-ATAA
1 T-AATA-TTAATTATATAA
28944 AAATTATATA
Statistics
Matches: 85, Mismatches: 1, Indels: 21
0.79 0.01 0.20
Matches are distributed among these distances:
23 6 0.07
24 4 0.05
25 9 0.11
26 14 0.16
27 36 0.42
28 9 0.11
29 7 0.08
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (25 bp):
TAATATTAATTATATAATTTAATTA
Found at i:29404 original size:15 final size:15
Alignment explanation
Indices: 29383--29418 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
29373 AATCCTGCTG
29383 CCAATTCATTTTCTTT
1 CCAATTCATTTT-TTT
29399 -CAATTCATTTTTTT
1 CCAATTCATTTTTTT
29413 CCAATT
1 CCAATT
29419 TGTATTCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 3 0.16
15 16 0.84
ACGTcount: A:0.22, C:0.22, G:0.00, T:0.56
Consensus pattern (15 bp):
CCAATTCATTTTTTT
Found at i:29803 original size:18 final size:20
Alignment explanation
Indices: 29779--29836 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 20
29769 ATTTGATATA
29779 ATTTGTATACATGTATGT-T
1 ATTTGTATACATGTATGTAT
*
29798 -TTTGTA-CCTATGTATGATAT
1 ATTTGTATAC-ATGTATG-TAT
29818 AATTTGTATACATGTATGT
1 -ATTTGTATACATGTATGT
29837 GTGTACCTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
17 1 0.03
18 13 0.42
19 1 0.03
20 1 0.03
21 1 0.03
22 13 0.42
23 1 0.03
ACGTcount: A:0.28, C:0.07, G:0.16, T:0.50
Consensus pattern (20 bp):
ATTTGTATACATGTATGTAT
Found at i:29817 original size:40 final size:38
Alignment explanation
Indices: 29772--29865 Score: 134
Period size: 38 Copynumber: 2.4 Consensus size: 38
29762 TGTATGAATT
* *
29772 TGATATAATTTGTATACATGTATGTTTTTGTACCTATGTA
1 TGATATAATTTGTATACATGTATG--TGTGTACCTATGCA
29812 TGATATAATTTGTATACATGTATGTGTGTACCTATGCA
1 TGATATAATTTGTATACATGTATGTGTGTACCTATGCA
* *
29850 TAATATAATTTATATA
1 TGATATAATTTGTATA
29866 TAATGGAGAT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
38 26 0.52
40 24 0.48
ACGTcount: A:0.32, C:0.07, G:0.14, T:0.47
Consensus pattern (38 bp):
TGATATAATTTGTATACATGTATGTGTGTACCTATGCA
Found at i:29832 original size:22 final size:22
Alignment explanation
Indices: 29772--29835 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 22
29762 TGTATGAATT
29772 TGATATAATTTGTATACATGTA
1 TGATATAATTTGTATACATGTA
*
29794 TG-T-T--TTTGTA-CCTATGTA
1 TGATATAATTTGTATAC-ATGTA
29812 TGATATAATTTGTATACATGTA
1 TGATATAATTTGTATACATGTA
29834 TG
1 TG
29836 TGTGTACCTA
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
17 1 0.03
18 13 0.38
19 1 0.03
20 2 0.06
21 1 0.03
22 15 0.44
23 1 0.03
ACGTcount: A:0.30, C:0.06, G:0.16, T:0.48
Consensus pattern (22 bp):
TGATATAATTTGTATACATGTA
Found at i:32026 original size:23 final size:24
Alignment explanation
Indices: 32000--32049 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
31990 TTATTTTTTC
*
32000 TTTATATAAATTAAACTATA-TAA
1 TTTATATAAATCAAACTATATTAA
32023 TTTATATAAATCAAACTATATTAA
1 TTTATATAAATCAAACTATATTAA
32047 TTT
1 TTT
32050 TTTTTTGCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 19 0.76
24 6 0.24
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (24 bp):
TTTATATAAATCAAACTATATTAA
Found at i:32120 original size:13 final size:13
Alignment explanation
Indices: 32088--32114 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
32078 TAATTTACAT
32088 TTAAATAATTTTA
1 TTAAATAATTTTA
32101 TTAAATAATTTTA
1 TTAAATAATTTTA
32114 T
1 T
32115 ATAATAGGTA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTAAATAATTTTA
Found at i:32336 original size:16 final size:16
Alignment explanation
Indices: 32312--32374 Score: 99
Period size: 16 Copynumber: 3.9 Consensus size: 16
32302 TCATTTACAG
*
32312 GTCAAGTTAAAAACAA
1 GTCAGGTTAAAAACAA
*
32328 GTCAGGTTAAAAACAG
1 GTCAGGTTAAAAACAA
*
32344 GTCAGGTTAAAAACAT
1 GTCAGGTTAAAAACAA
32360 GTCAGGTTAAAAACA
1 GTCAGGTTAAAAACA
32375 GGTCGGGTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.48, C:0.13, G:0.19, T:0.21
Consensus pattern (16 bp):
GTCAGGTTAAAAACAA
Found at i:32344 original size:32 final size:32
Alignment explanation
Indices: 32308--32378 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
32298 CGGATCATTT
32308 ACAGGTCAAGTTAAAAACAAGTCAGGTTAAAA
1 ACAGGTCAAGTTAAAAACAAGTCAGGTTAAAA
* *
32340 ACAGGTCAGGTTAAAAACATGTCAGGTTAAAA
1 ACAGGTCAAGTTAAAAACAAGTCAGGTTAAAA
32372 ACAGGTC
1 ACAGGTC
32379 GGGTAATACC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.45, C:0.14, G:0.21, T:0.20
Consensus pattern (32 bp):
ACAGGTCAAGTTAAAAACAAGTCAGGTTAAAA
Found at i:38578 original size:31 final size:30
Alignment explanation
Indices: 38493--38598 Score: 97
Period size: 31 Copynumber: 3.4 Consensus size: 30
38483 GTCGAGGGTT
* **
38493 TACCTATGTTCTACGGAACATATGGACAAAA
1 TACCTATGTTCTAAGG-ACATATGGACAGTA
**
38524 TTACCTATGTAT-TTTGAGACATATGGACAGTA
1 -TACCTATGT-TCTAAG-GACATATGGACAGTA
*
38556 TACCTATGTTCTAAGGATCATATGGACAGTT
1 TACCTATGTTCTAAGGA-CATATGGACAGTA
*
38587 TACCTAGGTTCT
1 TACCTATGTTCT
38599 TCGGGACCTA
Statistics
Matches: 62, Mismatches: 8, Indels: 9
0.78 0.10 0.11
Matches are distributed among these distances:
30 3 0.05
31 34 0.55
32 23 0.37
33 2 0.03
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (30 bp):
TACCTATGTTCTAAGGACATATGGACAGTA
Found at i:54765 original size:23 final size:24
Alignment explanation
Indices: 54727--54776 Score: 75
Period size: 23 Copynumber: 2.1 Consensus size: 24
54717 AAAATTTAAA
* *
54727 TATTTTTTTTCATTTTTAATAATT
1 TATTTTTTATCATTTTTAAAAATT
54751 TATTTTTTATC-TTTTTAAAAATT
1 TATTTTTTATCATTTTTAAAAATT
54774 TAT
1 TAT
54777 AAATTTATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 14 0.58
24 10 0.42
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (24 bp):
TATTTTTTATCATTTTTAAAAATT
Found at i:56822 original size:13 final size:14
Alignment explanation
Indices: 56804--56837 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
56794 TAGTCTCTGT
56804 TTTATT-TTTTTTA
1 TTTATTCTTTTTTA
56817 TTTATTCTTTTTTA
1 TTTATTCTTTTTTA
56831 -TTATTCT
1 TTTATTCT
56838 GAACAGAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 13 0.65
14 7 0.35
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTATTCTTTTTTA
Found at i:59957 original size:14 final size:14
Alignment explanation
Indices: 59938--60008 Score: 70
Period size: 14 Copynumber: 4.7 Consensus size: 14
59928 GGATATAAAC
59938 GATTAGTTTATTAT
1 GATTAGTTTATTAT
59952 GATTAGTTTATTAT
1 GATTAGTTTATTAT
** *
59966 GATAATAAAGGATATAAAT
1 GAT--T--AGTTTAT-TAT
59985 GATTAGTTTATTAT
1 GATTAGTTTATTAT
59999 GATTAGTTTA
1 GATTAGTTTA
60009 CTAACTCATG
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
14 29 0.63
15 5 0.11
16 1 0.02
17 1 0.02
18 5 0.11
19 5 0.11
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (14 bp):
GATTAGTTTATTAT
Found at i:59975 original size:47 final size:47
Alignment explanation
Indices: 59901--60008 Score: 198
Period size: 47 Copynumber: 2.3 Consensus size: 47
59891 GTTCCTTTGG
*
59901 TTATGATTAGTTTATTATGATAGTAAAGGATATAAACGATTAGTTTA
1 TTATGATTAGTTTATTATGATAATAAAGGATATAAACGATTAGTTTA
*
59948 TTATGATTAGTTTATTATGATAATAAAGGATATAAATGATTAGTTTA
1 TTATGATTAGTTTATTATGATAATAAAGGATATAAACGATTAGTTTA
59995 TTATGATTAGTTTA
1 TTATGATTAGTTTA
60009 CTAACTCATG
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 59 1.00
ACGTcount: A:0.38, C:0.01, G:0.16, T:0.45
Consensus pattern (47 bp):
TTATGATTAGTTTATTATGATAATAAAGGATATAAACGATTAGTTTA
Found at i:64271 original size:12 final size:13
Alignment explanation
Indices: 64254--64322 Score: 63
Period size: 14 Copynumber: 5.3 Consensus size: 13
64244 TGTCTATTTT
64254 TATTATTA-ATTA
1 TATTATTATATTA
64266 TATTATTATTATTA
1 TATTATTA-TATTA
*
64280 TATTA-CATATT-
1 TATTATTATATTA
*
64291 TATTATATATAAATA
1 TATTAT-TAT-ATTA
*
64306 TATTATTTTATTA
1 TATTATTATATTA
64319 TATT
1 TATT
64323 TGCATTTACA
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
11 5 0.11
12 12 0.26
13 10 0.22
14 13 0.28
15 6 0.13
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (13 bp):
TATTATTATATTA
Found at i:64274 original size:18 final size:18
Alignment explanation
Indices: 64248--64318 Score: 65
Period size: 18 Copynumber: 3.8 Consensus size: 18
64238 AATTTTTGTC
*
64248 TATTTTTATTATTAATTA
1 TATTATTATTATTAATTA
64266 TATTATTATTATTATATTACA
1 TATTATTATTATTA-ATT--A
*
64287 TATTTATTA-TATATAAATA
1 TA-TTATTATTAT-TAATTA
64306 TATTATT-TTATTA
1 TATTATTATTATTA
64319 TATTTGCATT
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
17 2 0.04
18 21 0.47
19 6 0.13
21 8 0.18
22 8 0.18
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (18 bp):
TATTATTATTATTAATTA
Done.