Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005801.1 Hibiscus syriacus cultivar Beakdansim tig00013605_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: 101330
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:1071 original size:23 final size:23
Alignment explanation
Indices: 1016--1082 Score: 93
Period size: 21 Copynumber: 3.0 Consensus size: 23
1006 CATTATTATA
1016 TGGCACTACGGTGCAATTCTAC-
1 TGGCACTACGGTGCAATTCTACG
*
1038 -GGCACTCCGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
1060 TGGCACTTCGGTGCAATTATACG
1 TGGCACTACGGTGCAATTCTACG
1083 AGCTCTGGTG
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
21 20 0.50
23 20 0.50
ACGTcount: A:0.21, C:0.27, G:0.25, T:0.27
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:6850 original size:22 final size:21
Alignment explanation
Indices: 6819--6866 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
6809 AAATGTTATA
* *
6819 AGATATAGAATATGAAATAAG
1 AGATATAGAACAAGAAATAAG
*
6840 AGATCATAGAACAAGAGATAAG
1 AGAT-ATAGAACAAGAAATAAG
6862 AGATA
1 AGATA
6867 GAAAGGATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 5 0.22
22 18 0.78
ACGTcount: A:0.56, C:0.04, G:0.21, T:0.19
Consensus pattern (21 bp):
AGATATAGAACAAGAAATAAG
Found at i:10719 original size:18 final size:18
Alignment explanation
Indices: 10696--10731 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
10686 ATGATGATAA
10696 TATTTTTTAAAAAAATAT
1 TATTTTTTAAAAAAATAT
*
10714 TATTTTTTAAAAATATAT
1 TATTTTTTAAAAAAATAT
10732 AAAAATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TATTTTTTAAAAAAATAT
Found at i:18958 original size:12 final size:12
Alignment explanation
Indices: 18941--18981 Score: 66
Period size: 12 Copynumber: 3.4 Consensus size: 12
18931 CATTAACTCA
18941 ATTAATAATTTT
1 ATTAATAATTTT
18953 ATTAATAATTTT
1 ATTAATAATTTT
18965 ATTAAT-ATTTT
1 ATTAATAATTTT
18976 AATTAA
1 -ATTAA
18982 AAATAAAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 5 0.18
12 23 0.82
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATTAATAATTTT
Found at i:21212 original size:60 final size:60
Alignment explanation
Indices: 21142--21277 Score: 159
Period size: 61 Copynumber: 2.2 Consensus size: 60
21132 AAAAGTTGGA
* * *
21142 GGATTAATTTAAAATGAGAGTCATAG-TTTGGGGATGAAATCAAAATAT-TTAAAAGTTTAT
1 GGATCAATTTAAAATGAGAGTCATAGATTTGAGGATGAAATCAAAATATCTAAAAAG--TAT
* * ***
21202 GGATCAATTTATAATGCGAGTCATAGATTTGAGGATGAAATTGTAATATCTAAAAAGTAT
1 GGATCAATTTAAAATGAGAGTCATAGATTTGAGGATGAAATCAAAATATCTAAAAAGTAT
21262 GAGATCAATTTAAAAT
1 G-GATCAATTTAAAAT
21278 AAAAGTTATA
Statistics
Matches: 64, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
60 27 0.42
61 31 0.48
62 6 0.09
ACGTcount: A:0.42, C:0.05, G:0.19, T:0.34
Consensus pattern (60 bp):
GGATCAATTTAAAATGAGAGTCATAGATTTGAGGATGAAATCAAAATATCTAAAAAGTAT
Found at i:38623 original size:13 final size:13
Alignment explanation
Indices: 38605--38633 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
38595 AATACAAATG
38605 AATATGAAGAAAA
1 AATATGAAGAAAA
38618 AATATGAAGAAAA
1 AATATGAAGAAAA
38631 AAT
1 AAT
38634 CGTTCTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.14, T:0.17
Consensus pattern (13 bp):
AATATGAAGAAAA
Found at i:45950 original size:21 final size:21
Alignment explanation
Indices: 45886--45950 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
45876 ACTTCGACTA
* *
45886 TCGCATTGCGA-TTTACATAT
1 TCGCATTGCGATTTTCCAAAT
** * *
45906 TCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATTTTCCAAAT
*
45927 TCGCGTTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
45948 TCG
1 TCG
45951 ACTATCGCAT
Statistics
Matches: 33, Mismatches: 11, Indels: 1
0.73 0.24 0.02
Matches are distributed among these distances:
20 11 0.33
21 22 0.67
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:45989 original size:69 final size:69
Alignment explanation
Indices: 45878--46009 Score: 264
Period size: 69 Copynumber: 1.9 Consensus size: 69
45868 CAACGCGAAC
45878 TTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCGAAGTTCGCGTTGCGATTTTC
1 TTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCGAAGTTCGCGTTGCGATTTTC
45943 CAAA
66 CAAA
45947 TTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCGAAGTTCGCGTTGCGATTT
1 TTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCGAAGTTCGCGTTGCGATTT
46010 ATTTCAAATT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 63 1.00
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (69 bp):
TTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCGAAGTTCGCGTTGCGATTTTC
CAAA
Found at i:46004 original size:21 final size:21
Alignment explanation
Indices: 45974--46049 Score: 68
Period size: 21 Copynumber: 3.6 Consensus size: 21
45964 GATTTACATA
45974 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCGAAG
* * *
45995 TTCGCGTTGCGATTTATTTC-AAA
1 TTCGCATTGCGA--TA-GTCGAAG
*
46018 TTCG--TTGCAATAGTCGAAG
1 TTCGCATTGCGATAGTCGAAG
46037 TTCGCATTGCGAT
1 TTCGCATTGCGAT
46050 TTATTCCCAA
Statistics
Matches: 42, Mismatches: 7, Indels: 12
0.69 0.11 0.20
Matches are distributed among these distances:
18 2 0.05
19 8 0.19
21 22 0.52
23 8 0.19
24 2 0.05
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCGAAG
Found at i:46085 original size:43 final size:42
Alignment explanation
Indices: 45955--46075 Score: 149
Period size: 42 Copynumber: 2.9 Consensus size: 42
45945 AATTCGACTA
*
45955 TCGCATTGCGATTTA---CATATTCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATTTATTCCAAATTCG--TTGCGATAGTCGAAGT
* * *
45996 TCGCGTTGCGATTTATTTCAAATTCGTTGCAATAGTCGAAGT
1 TCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGT
*
46038 TCGCATTGCGATTTATTCCCAAATTTGTTGCGATAGTC
1 TCGCATTGCGATTTATT-CCAAATTCGTTGCGATAGTC
46076 CAAAATCGCA
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
41 14 0.20
42 31 0.45
43 17 0.25
44 7 0.10
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (42 bp):
TCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGT
Found at i:46805 original size:21 final size:21
Alignment explanation
Indices: 46779--46911 Score: 157
Period size: 21 Copynumber: 6.4 Consensus size: 21
46769 ATTTTGGACT
46779 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* *
46800 ATCGCAACGAACTTGGACT--
1 ATCGCAACGAATTTGGAATAA
46819 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* * * *
46840 ATCGCAACGCGAACTTCGACTAT
1 ATCGCAA--CGAATTTGGAATAA
46863 AT--CAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
*
46882 ATCACAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
46903 ATCGCAACG
1 ATCGCAACG
46912 CGAACTTGGA
Statistics
Matches: 93, Mismatches: 13, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
19 29 0.31
21 52 0.56
23 12 0.13
ACGTcount: A:0.40, C:0.20, G:0.18, T:0.23
Consensus pattern (21 bp):
ATCGCAACGAATTTGGAATAA
Found at i:46827 original size:40 final size:40
Alignment explanation
Indices: 46772--46898 Score: 191
Period size: 40 Copynumber: 3.1 Consensus size: 40
46762 CGTTGCGATT
46772 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGAAC
46812 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAA--CGAAC
* ** * *
46854 TTCGACTATATCAACGAATTTGGAATAAATCACAACGAAT
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGAAC
46894 TTGGA
1 TTGGA
46899 ATAAATCGCA
Statistics
Matches: 79, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
40 43 0.54
42 36 0.46
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (40 bp):
TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGAAC
Found at i:46869 original size:42 final size:42
Alignment explanation
Indices: 46775--46890 Score: 173
Period size: 42 Copynumber: 2.8 Consensus size: 42
46765 TGCGATTTTG
* *
46775 GACTATCGCAACGAATTTGGAATAAATCGCAA--CGAACTTG
1 GACTATAGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
46815 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATAGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* *
46857 GACTATATCAACGAATTTGGAATAAATCACAACG
1 GACTATAGCAACGAATTTGGAATAAATCGCAACG
46891 AATTTGGAAT
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
40 32 0.46
42 38 0.54
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.22
Consensus pattern (42 bp):
GACTATAGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:47577 original size:23 final size:23
Alignment explanation
Indices: 47549--47606 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
47539 AAATTAATAA
47549 TATATTATGTAAAATGTTTCGAT
1 TATATTATGTAAAATGTTTCGAT
47572 TATATTATGTAAAATGTTTCGAT
1 TATATTATGTAAAATGTTTCGAT
47595 TATA--ATGTAAAA
1 TATATTATGTAAAA
47607 ATTATAACTA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
21 8 0.23
23 27 0.77
ACGTcount: A:0.40, C:0.03, G:0.12, T:0.45
Consensus pattern (23 bp):
TATATTATGTAAAATGTTTCGAT
Found at i:47649 original size:13 final size:13
Alignment explanation
Indices: 47620--47654 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
47610 ATAACTAATA
*
47620 ATATTAAAT-ATT
1 ATATTAAATAAAT
47632 ATATTAAATAAAT
1 ATATTAAATAAAT
47645 ATATTAAATA
1 ATATTAAATA
47655 TATTTATGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 9 0.43
13 12 0.57
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
ATATTAAATAAAT
Found at i:50967 original size:126 final size:126
Alignment explanation
Indices: 50742--51471 Score: 1381
Period size: 126 Copynumber: 5.8 Consensus size: 126
50732 CTATAATCGG
50742 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
50807 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAATACCTATTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAATACCTATTAT
50868 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
50933 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAATACCTATTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAATACCTATTAT
*
50994 TTCACTATTCACGTGAAGGCACGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
* *
51059 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAATACCTATTAT
51120 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
51185 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGTCACTAGATATATCAATACCTATTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAATACCTATTAT
51246 TTCACTATTCACGTGAAGGCGCGTTCCC-GGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
* *
51310 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGTCACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAATACCTATTAT
*
51371 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGACGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
51436 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGA
66 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGA
51472 ATAACTTAAA
Statistics
Matches: 592, Mismatches: 11, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
125 124 0.21
126 468 0.79
ACGTcount: A:0.22, C:0.26, G:0.19, T:0.32
Consensus pattern (126 bp):
TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAATACCTATTAT
Found at i:51917 original size:32 final size:32
Alignment explanation
Indices: 51872--51950 Score: 97
Period size: 32 Copynumber: 2.4 Consensus size: 32
51862 TTTCGAATAC
51872 TATAATTTATATTTAAATTTAAATTT-GAATAA
1 TATAATTTATATTT-AATTTAAATTTCGAATAA
* * *
51904 TATTATTTTTATTTTATTTTAAATTTCGAATAA
1 TATAATTTATA-TTTAATTTAAATTTCGAATAA
*
51937 TATAATTTGTATTT
1 TATAATTTATATTT
51951 TAAAAACATT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
32 22 0.55
33 18 0.45
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.57
Consensus pattern (32 bp):
TATAATTTATATTTAATTTAAATTTCGAATAA
Found at i:51951 original size:33 final size:33
Alignment explanation
Indices: 51850--51953 Score: 138
Period size: 33 Copynumber: 3.2 Consensus size: 33
51840 TAAGTTTAAA
*
51850 TTTAATGTTAAATTTCGAATACTATAATTTATAT
1 TTTAAT-TTAAATTTCGAATAATATAATTTATAT
* * *
51884 TTAAATTTAAATTT-GAATAATATTATTTTTAT
1 TTTAATTTAAATTTCGAATAATATAATTTATAT
* *
51916 TTTATTTTAAATTTCGAATAATATAATTTGTAT
1 TTTAATTTAAATTTCGAATAATATAATTTATAT
51949 TTTAA
1 TTTAA
51954 AAACATTTAT
Statistics
Matches: 60, Mismatches: 9, Indels: 3
0.83 0.12 0.04
Matches are distributed among these distances:
32 27 0.45
33 28 0.47
34 5 0.08
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (33 bp):
TTTAATTTAAATTTCGAATAATATAATTTATAT
Found at i:52562 original size:21 final size:21
Alignment explanation
Indices: 52474--52567 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
52464 TATGGTATAA
*
52474 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
52495 AA-CCTGGCGGGCTAGGCATGT
1 AACCCT-GCGGGCTAGGAATGT
52516 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
52537 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
52558 AACCCTGCGG
1 AACCCTGCGG
52568 AGATGGCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 3 0.04
21 63 0.91
22 3 0.04
ACGTcount: A:0.20, C:0.27, G:0.35, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:52597 original size:21 final size:21
Alignment explanation
Indices: 52571--52618 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
52561 CCTGCGGAGA
*
52571 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
52592 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
52613 GGGCAT
1 TGGCAT
52619 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:54381 original size:34 final size:32
Alignment explanation
Indices: 54336--54424 Score: 90
Period size: 34 Copynumber: 2.7 Consensus size: 32
54326 TTAATAATTC
54336 TAAATAAATAATAATTATATAAATATTATTTTAATA
1 TAAA-AAATAATAATTATATAAATA-TA--TTAATA
* * *
54372 -ATAAAATAATATTTACATAAATATATTAATA
1 TAAAAAATAATAATTATATAAATATATTAATA
* *
54403 TAAAAAATAATAACTATTTAAA
1 TAAAAAATAATAATTATATAAA
54425 AAAATACTAA
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
31 6 0.14
32 16 0.36
33 2 0.05
34 18 0.41
35 2 0.05
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.39
Consensus pattern (32 bp):
TAAAAAATAATAATTATATAAATATATTAATA
Found at i:54405 original size:14 final size:15
Alignment explanation
Indices: 54339--54411 Score: 51
Period size: 15 Copynumber: 4.7 Consensus size: 15
54329 ATAATTCTAA
54339 ATAAATAATAATT-AT
1 ATAAATAAT-ATTAAT
*
54354 ATAAATATTATTTTAAT
1 ATAAATA--ATATTAAT
* *
54371 AATAAAATAATATTTAC
1 -AT-AAATAATATTAAT
54388 ATAAAT-ATATTAAT
1 ATAAATAATATTAAT
*
54402 ATAAAAAATA
1 ATAAATAATA
54412 ATAACTATTT
Statistics
Matches: 45, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
14 11 0.24
15 14 0.31
16 4 0.09
17 9 0.20
18 2 0.04
19 5 0.11
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (15 bp):
ATAAATAATATTAAT
Found at i:55315 original size:20 final size:20
Alignment explanation
Indices: 55291--55364 Score: 139
Period size: 20 Copynumber: 3.7 Consensus size: 20
55281 TTGGTTCACG
*
55291 GAATGTAAGATTACCAGTGG
1 GAATGTAAGATTACCAGTGA
55311 GAATGTAAGATTACCAGTGA
1 GAATGTAAGATTACCAGTGA
55331 GAATGTAAGATTACCAGTGA
1 GAATGTAAGATTACCAGTGA
55351 GAATGTAAGATTAC
1 GAATGTAAGATTAC
55365 TGGGAATGTT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.39, C:0.09, G:0.26, T:0.26
Consensus pattern (20 bp):
GAATGTAAGATTACCAGTGA
Found at i:56093 original size:19 final size:20
Alignment explanation
Indices: 56069--56119 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
56059 AATGACCAAT
56069 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
56088 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
56108 AAAATCGCAACG
1 AAAATCGCAACG
56120 TTAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:56113 original size:20 final size:20
Alignment explanation
Indices: 56069--56326 Score: 117
Period size: 20 Copynumber: 12.6 Consensus size: 20
56059 AATGACCAAT
* *
56069 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
56088 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
56108 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
56128 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* * **
56148 AAAATCGCAATGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
56169 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
56192 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * * *
56212 AGAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * *
56232 ATAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* * *
56252 AGAGTCGCAACGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
56272 AGAGTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* *
56295 AAAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
*
56315 AGAATCGCAACG
1 AAAATCGCAACG
56327 TTGAAAATAA
Statistics
Matches: 188, Mismatches: 39, Indels: 23
0.75 0.16 0.09
Matches are distributed among these distances:
19 17 0.09
20 127 0.68
21 13 0.07
23 31 0.16
ACGTcount: A:0.39, C:0.19, G:0.22, T:0.19
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:56249 original size:40 final size:39
Alignment explanation
Indices: 56194--56324 Score: 145
Period size: 40 Copynumber: 3.2 Consensus size: 39
56184 TTTAGAAGAA
*
56194 AATCGCAATGCGATTGATAGAATCGCAATGCGATTGATAT
1 AATCGCAATGCGATTGA-AGAATCGCAATGCGATTGATAG
* * *
56234 AATCGCAATGCGATTGAGAGAGTCGCAACGCGATTGAGAG
1 AATCGCAATGCGATTGA-AGAATCGCAATGCGATTGATAG
* * *
56274 AGTCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTTATAG
1 AATCGCAATGCGA-TT-GAAG--AATCGCAATGCGATTGATAG
56317 AATCGCAA
1 AATCGCAA
56325 CGTTGAAAAT
Statistics
Matches: 75, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
40 46 0.61
41 4 0.05
42 2 0.03
43 23 0.31
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.22
Consensus pattern (39 bp):
AATCGCAATGCGATTGAAGAATCGCAATGCGATTGATAG
Found at i:56445 original size:6 final size:6
Alignment explanation
Indices: 56434--56466 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
56424 GACACGTATT
56434 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
56467 CGAGACGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:57156 original size:6 final size:6
Alignment explanation
Indices: 57147--57219 Score: 146
Period size: 6 Copynumber: 12.2 Consensus size: 6
57137 CGCCGCCGTC
57147 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
57195 TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG T
57220 AATACGTGTC
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 67 1.00
ACGTcount: A:0.00, C:0.16, G:0.49, T:0.34
Consensus pattern (6 bp):
TCGTGG
Found at i:57349 original size:20 final size:20
Alignment explanation
Indices: 57326--57663 Score: 169
Period size: 20 Copynumber: 16.6 Consensus size: 20
57316 TTATTTTCAA
57326 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
57346 CGTTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* * * *
57366 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* * * *
57386 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* * * *
57406 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* * * *
57426 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
*
57446 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
* * *
57469 CGTTGCGACTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
57489 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
57509 CATTGCGATTCTATCAATCG
1 CGTTGCGATTTTCTAAATCG
*
57529 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
** ** *
57552 CGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
* *
57573 CGTTGCGATTTTCT--TTTG
1 CGTTGCGATTTTCTAAATCG
*** **
57591 ACCGTTGCGATTTTCTTTTTAA
1 --CGTTGCGATTTTCTAAATCG
57613 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
57633 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCTAAATCG
57652 CGTTGCGATTTT
1 CGTTGCGATTTT
57664 ATTGGTCATT
Statistics
Matches: 267, Mismatches: 40, Indels: 23
0.81 0.12 0.07
Matches are distributed among these distances:
18 2 0.01
19 17 0.06
20 200 0.75
21 14 0.05
22 6 0.02
23 28 0.10
ACGTcount: A:0.17, C:0.24, G:0.20, T:0.39
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:57372 original size:40 final size:40
Alignment explanation
Indices: 57328--57559 Score: 293
Period size: 40 Copynumber: 5.7 Consensus size: 40
57318 ATTTTCAACG
* *
57328 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTAAATCGCATTGCGATTCTCTCAGTCGCA
* *
57368 TTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTAAATCGCATTGCGATTCTCTCAGTCGCA
* *
57408 TTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTAAATCGCATTGCGATTCTCTCAGTCGCA
* * *
57448 TTGCGATTTTCTTCTAAATCGCGTTGCGACTCTCTCAATCGCA
1 TTGCGA--TTC-TCTAAATCGCATTGCGATTCTCTCAGTCGCA
* * *
57491 TTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCA
1 TTGCGATTCTCTAAATCGCATTGCGATTCTCTCAGTCGCA
*
57531 TTGCGATTTTCTTCTAAATCGCGTTGCGA
1 TTGCGA--TTC-TCTAAATCGCATTGCGA
57560 ACTTGGAAGC
Statistics
Matches: 171, Mismatches: 15, Indels: 9
0.88 0.08 0.05
Matches are distributed among these distances:
40 115 0.67
41 3 0.02
42 6 0.04
43 47 0.27
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.37
Consensus pattern (40 bp):
TTGCGATTCTCTAAATCGCATTGCGATTCTCTCAGTCGCA
Found at i:57393 original size:60 final size:60
Alignment explanation
Indices: 57328--57538 Score: 287
Period size: 60 Copynumber: 3.5 Consensus size: 60
57318 ATTTTCAACG
* *
57328 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTAAATCGCATTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAGTCGCA
* *
57388 TTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTAAATCGCATTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAGTCGCA
* * * * * *
57448 TTGCGATTTTCTTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCA
1 TTGCGA--TTC-TCTAAATCGCATTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAGTCGCA
* *
57511 TTGCGATTCTATCAATCGCATTGCGATT
1 TTGCGATTCTCTAAATCGCATTGCGATT
57539 TTCTTCTAAA
Statistics
Matches: 132, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
60 77 0.58
61 3 0.02
62 3 0.02
63 49 0.37
ACGTcount: A:0.18, C:0.27, G:0.18, T:0.36
Consensus pattern (60 bp):
TTGCGATTCTCTAAATCGCATTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAGTCGCA
Found at i:57500 original size:83 final size:83
Alignment explanation
Indices: 57328--57559 Score: 335
Period size: 83 Copynumber: 2.8 Consensus size: 83
57318 ATTTTCAACG
* * * * *
57328 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAGTCGCATTGCGA--TTC-TCTCAGTCGCATT
1 TTGCGATTCTCTAAATCGCATTGCGATTCTCTCAGTCGCATTGCGATTTTCTTCTAAATCGCGTT
* *
57390 GCGATTCTCTCAGTCGCA
66 GCGACTCTCTCAATCGCA
* *
57408 TTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAGTCGCATTGCGATTTTCTTCTAAATCGCGTT
1 TTGCGATTCTCTAAATCGCATTGCGATTCTCTCAGTCGCATTGCGATTTTCTTCTAAATCGCGTT
57473 GCGACTCTCTCAATCGCA
66 GCGACTCTCTCAATCGCA
* * *
57491 TTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCATTGCGATTTTCTTCTAAATCGCGTT
1 TTGCGATTCTCTAAATCGCATTGCGATTCTCTCAGTCGCATTGCGATTTTCTTCTAAATCGCGTT
57556 GCGA
66 GCGA
57560 ACTTGGAAGC
Statistics
Matches: 135, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
80 42 0.31
82 3 0.02
83 90 0.67
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.37
Consensus pattern (83 bp):
TTGCGATTCTCTAAATCGCATTGCGATTCTCTCAGTCGCATTGCGATTTTCTTCTAAATCGCGTT
GCGACTCTCTCAATCGCA
Found at i:57653 original size:19 final size:20
Alignment explanation
Indices: 57613--57663 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
57603 TTCTTTTTAA
*
57613 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
57633 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
57652 CGTTGCGATTTT
1 CGTTGCGATTTT
57664 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:61441 original size:2 final size:2
Alignment explanation
Indices: 61434--61459 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
61424 ATTATAACCC
61434 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
61460 GAATGATCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61483 original size:21 final size:21
Alignment explanation
Indices: 61457--61499 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
61447 TATATATATA
*
61457 TATGAATGATCATAGATGAGG
1 TATGAATGACCATAGATGAGG
61478 TATGAATGACCATAGATGAGG
1 TATGAATGACCATAGATGAGG
61499 T
1 T
61500 CGAGTTTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.37, C:0.07, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGAATGACCATAGATGAGG
Found at i:62100 original size:21 final size:21
Alignment explanation
Indices: 62076--62115 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
62066 ATTTTATGTT
62076 TTTTAATAAT-TAAAGAATATA
1 TTTTAATAATATAAA-AATATA
62097 TTTTAATAATATAAAAATA
1 TTTTAATAATATAAAAATA
62116 AAAATCCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (21 bp):
TTTTAATAATATAAAAATATA
Found at i:64218 original size:2 final size:2
Alignment explanation
Indices: 64211--64237 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
64201 GAAATGCGTA
64211 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
64238 ATTTAAGGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:66476 original size:13 final size:12
Alignment explanation
Indices: 66441--66475 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
66431 ATATAGTATA
66441 ATTTTTAAAAAT
1 ATTTTTAAAAAT
66453 ATTTTTAAAAAT
1 ATTTTTAAAAAT
66465 ATTTTTAAAAA
1 ATTTTTAAAAA
66476 ACATGTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
ATTTTTAAAAAT
Found at i:66636 original size:41 final size:40
Alignment explanation
Indices: 66485--66636 Score: 104
Period size: 39 Copynumber: 3.9 Consensus size: 40
66475 AACATGTAAT
* *
66485 ATATATA-TTTTTTAAAA-ATCGGTTCTTGAAAATATGTAT-
1 ATATATAGTTTTTGAAAACATCGGTT-TTGAAAA-CTGTATA
* *
66524 ATA-ATATGGTTTTGAAAACA-CGCTTTTGAAAAC-GTATA
1 ATATATA-GTTTTTGAAAACATCGGTTTTGAAAACTGTATA
* *** *
66562 ATACATAG-TTTTGAAAACATATTTTTTTTAAAACGTGTATA
1 ATATATAGTTTTTGAAAACAT-CGGTTTTGAAAAC-TGTATA
*
66603 ATATATAGTTTTTTAAAA-ATCGGTTTTGGAAAAC
1 ATATATAGTTTTTGAAAACATCGGTTTT-GAAAAC
66637 ATATGATCGA
Statistics
Matches: 88, Mismatches: 14, Indels: 20
0.72 0.11 0.16
Matches are distributed among these distances:
37 15 0.17
38 7 0.08
39 22 0.25
40 16 0.18
41 20 0.23
42 8 0.09
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.41
Consensus pattern (40 bp):
ATATATAGTTTTTGAAAACATCGGTTTTGAAAACTGTATA
Found at i:68008 original size:60 final size:60
Alignment explanation
Indices: 67912--68112 Score: 267
Period size: 60 Copynumber: 3.4 Consensus size: 60
67902 ATCAAGTGAT
** * ***
67912 CATTTTGTAACTTTTAATAGTCAAGGGGCTCAACAAAGCTACTATCTCCGGTTAGAGGAC
1 CATTTTGTAACTTTTAATAGTTGAGGGGCTCAACAAAGCTACTCTCTATAGTTAGAGGAC
* * * *
67972 CAATTTGTAGCTTTTAATAGTTGAGGGGCTCAACAAAGCTACTCTTTATAGTTAGAGGAT
1 CATTTTGTAACTTTTAATAGTTGAGGGGCTCAACAAAGCTACTCTCTATAGTTAGAGGAC
* * * *
68032 CATTTTGTAACTTTTAATAATTGATGGCCTCAATAAAGCTACTCTCTATAGTTAGAGGAC
1 CATTTTGTAACTTTTAATAGTTGAGGGGCTCAACAAAGCTACTCTCTATAGTTAGAGGAC
*
68092 CATTTTATAACTTTTAATAGT
1 CATTTTGTAACTTTTAATAGT
68113 CGAGTGACTT
Statistics
Matches: 121, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 121 1.00
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (60 bp):
CATTTTGTAACTTTTAATAGTTGAGGGGCTCAACAAAGCTACTCTCTATAGTTAGAGGAC
Found at i:68830 original size:135 final size:132
Alignment explanation
Indices: 68522--68797 Score: 390
Period size: 135 Copynumber: 2.0 Consensus size: 132
68512 ACGATAACAT
* **
68522 TACATACGTTACATCATCAATTATGCATATGTGCAAATATCACATCAGCAATTTAAATGATCTTC
1 TACATACATTACA-CATCAA-TAAACATATGTGCAAATATCACATCAGCAATTTAAATGATCTTC
68587 ATCTAACATGAATTATTTTGATTAAAATTAATATTAGAAGTTAAAAACTTCAAAAATGGAAAAGG
64 ATCTAACATGAATTATTTTGATTAAAATTAATATTAGAAGTTAAAAACTTCAAAAATGGAAAAGG
68652 GTCA
129 GTCA
* **
68656 TTACATACGTTACATCATCAATTATGCATATGTGCAAATATCACATCAGCAATTTAAATGATCTT
1 -TACATACATTACA-CATCAA-TAAACATATGTGCAAATATCACATCAGCAATTTAAATGATCTT
68721 CATCTAACATGAATTATTTTGATTAAAAATTAATATATTAGAAGTTAAAACACTTCAAAAATAAT
63 CATCTAACATGAATTATTTTGATT-AAAATT-A-ATATTAGAAGTTAAAA-ACTTC--AAA-AAT
68786 GGAAAAGGGTCA
121 GGAAAAGGGTCA
68798 AATATATTAG
Statistics
Matches: 134, Mismatches: 0, Indels: 7
0.95 0.00 0.05
Matches are distributed among these distances:
135 88 0.66
136 6 0.04
137 1 0.01
138 16 0.12
139 5 0.04
141 3 0.02
142 15 0.11
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.33
Consensus pattern (132 bp):
TACATACATTACACATCAATAAACATATGTGCAAATATCACATCAGCAATTTAAATGATCTTCAT
CTAACATGAATTATTTTGATTAAAATTAATATTAGAAGTTAAAAACTTCAAAAATGGAAAAGGGT
CA
Found at i:68832 original size:47 final size:46
Alignment explanation
Indices: 68752--68846 Score: 181
Period size: 47 Copynumber: 2.0 Consensus size: 46
68742 ATTAAAAATT
68752 AATATATTAGAAGTTAAAACACTTCAAAAATAATGGAAAAGGGTCA
1 AATATATTAGAAGTTAAAACACTTCAAAAATAATGGAAAAGGGTCA
68798 AATATATTAGAAGTTAAAAACACTTCAAAAATAATGGAAAAGGGTCA
1 AATATATTAGAAGTT-AAAACACTTCAAAAATAATGGAAAAGGGTCA
68845 AA
1 AA
68847 ACGACATTGT
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
46 15 0.31
47 33 0.69
ACGTcount: A:0.54, C:0.08, G:0.15, T:0.23
Consensus pattern (46 bp):
AATATATTAGAAGTTAAAACACTTCAAAAATAATGGAAAAGGGTCA
Found at i:72475 original size:27 final size:26
Alignment explanation
Indices: 72418--72474 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 26
72408 CAATTGTTCC
* * *
72418 TTTTAATTTTTTTATTTTTTTTAAAA
1 TTTTAATTTTTATATTCTTATTAAAA
72444 TTTTAATTTTTATACTTCTTATTAATAA
1 TTTTAATTTTTATA-TTCTTATTAA-AA
72472 TTT
1 TTT
72475 ATTTTATCTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 13 0.50
27 8 0.31
28 5 0.19
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (26 bp):
TTTTAATTTTTATATTCTTATTAAAA
Found at i:76019 original size:16 final size:17
Alignment explanation
Indices: 76000--76032 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
75990 TCAATACAAA
76000 ATATAA-AATTTGAAAT
1 ATATAATAATTTGAAAT
76016 ATATAATAATTTGAAAT
1 ATATAATAATTTGAAAT
76033 TTTTAGAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (17 bp):
ATATAATAATTTGAAAT
Found at i:76617 original size:16 final size:16
Alignment explanation
Indices: 76588--76629 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
76578 GCTAAACTCG
76588 ACTCGTTG--CGTTAA
1 ACTCGTTGCTCGTTAA
76602 ACTCGTTGCTCGTTAA
1 ACTCGTTGCTCGTTAA
* *
76618 GCTCATTGCTCG
1 ACTCGTTGCTCG
76630 ACTTGTGCTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 8 0.33
16 16 0.67
ACGTcount: A:0.17, C:0.26, G:0.21, T:0.36
Consensus pattern (16 bp):
ACTCGTTGCTCGTTAA
Found at i:76638 original size:78 final size:79
Alignment explanation
Indices: 76545--76694 Score: 239
Period size: 78 Copynumber: 1.9 Consensus size: 79
76535 CATTAAATTT
76545 TTGCTCAACTTGTGCTCGTTAAAAAAAATTGTTGCTAAACTCGACTCGTTG-CGTTAAACTCGTT
1 TTGCTCAACTTGTGCTCGTTAAAAAAAATTGTTGCTAAACTCGACTCGTTGCCGTTAAACTCGTT
76609 GCTCGTTAAGCTCA
66 GCTCGTTAAGCTCA
* * * * *
76623 TTGCTCGACTTGTGCTCGTTAAAAAAAGTTGTTGCTCAACTCGACTTGTTGCTCGTTAAGCTCGT
1 TTGCTCAACTTGTGCTCGTTAAAAAAAATTGTTGCTAAACTCGACTCGTTGC-CGTTAAACTCGT
76688 TGCTCGT
65 TGCTCGT
76695 CTCGTCACTC
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
78 47 0.72
80 18 0.28
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.36
Consensus pattern (79 bp):
TTGCTCAACTTGTGCTCGTTAAAAAAAATTGTTGCTAAACTCGACTCGTTGCCGTTAAACTCGTT
GCTCGTTAAGCTCA
Found at i:78867 original size:23 final size:23
Alignment explanation
Indices: 78841--78889 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
78831 GGAAATGACA
78841 ATGGCCTAAATTGGCACTAGACT
1 ATGGCCTAAATTGGCACTAGACT
78864 ATGGCCTAAATTGGCACTAGACT
1 ATGGCCTAAATTGGCACTAGACT
78887 ATG
1 ATG
78890 TATGTATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (23 bp):
ATGGCCTAAATTGGCACTAGACT
Found at i:86511 original size:57 final size:56
Alignment explanation
Indices: 86393--86501 Score: 148
Period size: 57 Copynumber: 1.9 Consensus size: 56
86383 AGTGCACCGA
* *
86393 TGCATCAAGTGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGCTGG
1 TGCATCAAATGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGCATGGCTGG
* * *
86449 TGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGG
1 TGCATCAAATGCATTCGATG-TTTCA-AAATAGCCACAGTGCATCGATGCATGG
86502 TATGTGCATC
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
56 19 0.41
57 24 0.52
58 3 0.07
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (56 bp):
TGCATCAAATGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGCATGGCTGG
Found at i:86517 original size:56 final size:55
Alignment explanation
Indices: 86393--86518 Score: 139
Period size: 57 Copynumber: 2.2 Consensus size: 55
86383 AGTGCACCGA
*
86393 TGCATCAAGTGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGCTGG
1 TGCATCAA-TGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGCATGGCTGG
* * * *
86449 TGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGG-TATG
1 TGCATC-AATGCATTCGATG-TTTCA-AAATAGCCACAGTGCATCGATGCATGGCT-GG
*
86506 TGCATCGATGCAT
1 TGCATCAATGCAT
86519 GAAATGCATT
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
56 24 0.40
57 33 0.55
58 3 0.05
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (55 bp):
TGCATCAATGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGCATGGCTGG
Found at i:93135 original size:22 final size:21
Alignment explanation
Indices: 93093--93132 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
93083 AAGACTATTT
93093 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
**
93114 TCATTTTTGTATTTTGAAA
1 TCATTTTTCAATTTTGAAA
93133 ATAGAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:95093 original size:18 final size:17
Alignment explanation
Indices: 95039--95087 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
95029 TTGGACCCTT
* *
95039 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
95057 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
95075 AGTGCATTCGATG
1 AGTGCA-TCGATG
95088 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:95195 original size:65 final size:65
Alignment explanation
Indices: 95059--95218 Score: 182
Period size: 65 Copynumber: 2.5 Consensus size: 65
95049 TGCACTAAGA
* * *
95059 GTGCATCGATGCATCAAGTGCATTCGATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATACATGGCTG
* * * * *
95123 GTGCATCGATGCATCAAATGTATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTACAT-GTT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCACAGTGCATCGATACATGGCT
*
95186 AT
65 -G
* *
95188 GTGCATCGATGCATGAAATACATTCGATGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTT
95219 CAATTTAATT
Statistics
Matches: 81, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
64 29 0.36
65 49 0.60
66 3 0.04
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATACATGGCTG
Found at i:95257 original size:65 final size:63
Alignment explanation
Indices: 95059--95259 Score: 169
Period size: 65 Copynumber: 3.1 Consensus size: 63
95049 TGCACTAAGA
* * * *
95059 GTGCATCGATGCATCAAGTGCATTCGATGTTTCA-AAATAGC-CAGAGTGCATCGATGCATGGCT
1 GTGCATCGATGCATCAAATACATTCGATGTTTCATAAA-ATCTC--AGTGCATCGATGCATGGTT
95122 G
63 G
** * *
95123 GTGCATCGATGCATCAAATGTATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTACAT-GTTA
1 GTGCATCGATGCATCAAATACATTCGATG-TTTCATAAAAT-CTCAGTGCATCGATGCATGGTT-
*
95187 T
63 G
* **
95188 GTGCATCGATGCATGAAATACATTCGATG-TTCAATTTAAT-TCATGGTGCATCGATGCATGGAT
1 GTGCATCGATGCATCAAATACATTCGATGTTTC-ATAAAATCTCA--GTGCATCGATGCATGG-T
95251 TG
62 TG
95253 GTGCATC
1 GTGCATC
95260 ACTCTGAAAA
Statistics
Matches: 112, Mismatches: 15, Indels: 19
0.77 0.10 0.13
Matches are distributed among these distances:
62 3 0.03
63 3 0.03
64 46 0.41
65 53 0.47
66 6 0.05
67 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATACATTCGATGTTTCATAAAATCTCAGTGCATCGATGCATGGTTG
Found at i:97732 original size:31 final size:31
Alignment explanation
Indices: 97694--97790 Score: 167
Period size: 31 Copynumber: 3.1 Consensus size: 31
97684 AAGAGTCGAG
97694 AGTTTACCTAGGTTCTTCGGGACCTATGGAC
1 AGTTTACCTAGGTTCTTCGGGACCTATGGAC
97725 AGTTTACCTAGGTTCTTCGGGACCTATGGAC
1 AGTTTACCTAGGTTCTTCGGGACCTATGGAC
* * *
97756 AGTTTACCTAGGTTATTCGGGACTTATAGAC
1 AGTTTACCTAGGTTCTTCGGGACCTATGGAC
97787 AGTT
1 AGTT
97791 GTGACCTCTG
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 63 1.00
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.34
Consensus pattern (31 bp):
AGTTTACCTAGGTTCTTCGGGACCTATGGAC
Found at i:100779 original size:64 final size:62
Alignment explanation
Indices: 100684--100823 Score: 158
Period size: 64 Copynumber: 2.2 Consensus size: 62
100674 CACATTGAAT
* * *
100684 GTGCATCGATGCACTCTTTAAAGAAGAAACATCGAATGCAAATGGTGCATCGATGCATAAGG-A
1 GTGCATCGATGCACCCTTTAAAGAAGAAACATCAAAGGCAAATGGTGCATCGATGCAT--GGTA
* * * * *
100747 GTGCATCGATGCATCCCTTTAAA-ATGAAAACATCAAAGGTAATTTGTGTATCGATGCATGGTA
1 GTGCATCGATGCA-CCCTTTAAAGAAG-AAACATCAAAGGCAAATGGTGCATCGATGCATGGTA
100810 GTGCATCGATGCAC
1 GTGCATCGATGCAC
100824 ATGTTAAAGA
Statistics
Matches: 66, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
62 3 0.05
63 29 0.44
64 34 0.52
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.26
Consensus pattern (62 bp):
GTGCATCGATGCACCCTTTAAAGAAGAAACATCAAAGGCAAATGGTGCATCGATGCATGGTA
Found at i:100859 original size:20 final size:22
Alignment explanation
Indices: 100811--100868 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
100801 TGCATGGTAG
100811 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
*
100835 TGCATCGATGCACTG-T-AGCA
1 TGCATCGATGCACTGTTAAGAA
100855 TGCATCGATGCACT
1 TGCATCGATGCACT
100869 TCAAGGGGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Done.