Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004757.1 Hibiscus syriacus cultivar Beakdansim tig00010736_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: 106207
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:1302 original size:6 final size:6
Alignment explanation
Indices: 1291--1352 Score: 99
Period size: 6 Copynumber: 10.3 Consensus size: 6
1281 ATAAGAAGGT
*
1291 GGAGAA GGAGAA -GAGAGA GGAGAA GGAGAA GGAGAA GGATAA GGAGAA
1 GGAGAA GGAGAA GGAGA-A GGAGAA GGAGAA GGAGAA GGAGAA GGAGAA
1339 GGAGAA GGAGAA GG
1 GGAGAA GGAGAA GG
1353 GGGTTAACGA
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
5 4 0.08
6 44 0.85
7 4 0.08
ACGTcount: A:0.48, C:0.00, G:0.50, T:0.02
Consensus pattern (6 bp):
GGAGAA
Found at i:2492 original size:21 final size:20
Alignment explanation
Indices: 2466--2515 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
2456 GAATGTGTTT
*
2466 GATGTTGTTATAGCCGTTGGG
1 GATGTT-TTAGAGCCGTTGGG
* *
2487 GATGTTTTGGAGCCGTTTGG
1 GATGTTTTAGAGCCGTTGGG
2507 GATGATTTT
1 GATG-TTTT
2516 TCTACTCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.14, C:0.08, G:0.36, T:0.42
Consensus pattern (20 bp):
GATGTTTTAGAGCCGTTGGG
Found at i:2502 original size:20 final size:21
Alignment explanation
Indices: 2477--2515 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
2467 ATGTTGTTAT
2477 AGCCGTTGGGGATG-TTTTGG
1 AGCCGTTGGGGATGATTTTGG
*
2497 AGCCGTTTGGGATGATTTT
1 AGCCGTTGGGGATGATTTT
2516 TCTACTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.13, C:0.10, G:0.38, T:0.38
Consensus pattern (21 bp):
AGCCGTTGGGGATGATTTTGG
Found at i:13513 original size:2 final size:2
Alignment explanation
Indices: 13506--13536 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
13496 TTCATAAGTT
13506 TA TA TA 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 TA TA TA T
13537 CATAAAGTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:26039 original size:24 final size:24
Alignment explanation
Indices: 26010--26070 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
26000 TAATTTTATG
*
26010 TATGTTTGTTTATATT-TGTTCGTT
1 TATGTTCGTTTATATTCT-TTCGTT
*
26034 TGTGTTCGTTTATATTCTTTCGTT
1 TATGTTCGTTTATATTCTTTCGTT
*
26058 TATGTTCATTTAT
1 TATGTTCGTTTAT
26071 TATTTTAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 31 0.97
25 1 0.03
ACGTcount: A:0.13, C:0.08, G:0.15, T:0.64
Consensus pattern (24 bp):
TATGTTCGTTTATATTCTTTCGTT
Found at i:39337 original size:28 final size:29
Alignment explanation
Indices: 39291--39352 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 29
39281 TTTTTATTTT
*
39291 TAATAAAATTAGTGCATTCTATTAAAAATAA
1 TAATAAAATTA-TGCATTC-AATAAAAATAA
*
39322 TAATAAAATT-TG-ATTCAATATAAATAA
1 TAATAAAATTATGCATTCAATAAAAATAA
39349 TAAT
1 TAAT
39353 TATTTATGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 13 0.45
28 4 0.14
29 2 0.07
31 10 0.34
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (29 bp):
TAATAAAATTATGCATTCAATAAAAATAA
Found at i:45858 original size:19 final size:18
Alignment explanation
Indices: 45834--45878 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
45824 TTAAGTTTGA
*
45834 TTAATTTACTCAACTTAAT
1 TTAATTTACTCAA-ATAAT
*
45853 TTAATTCACTCAAATAAT
1 TTAATTTACTCAAATAAT
45871 TTCAATTT
1 TT-AATTT
45879 TTTTAACTCG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.38, C:0.16, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTTACTCAAATAAT
Found at i:46822 original size:66 final size:66
Alignment explanation
Indices: 46716--46841 Score: 234
Period size: 66 Copynumber: 1.9 Consensus size: 66
46706 TAATTTGGGA
46716 TGATTATGAAAATATGACACTTATCAATTCCCATTCACAAATTACAGTCATACATTTCATGAAAG
1 TGATTATGAAAATATGACACTTATCAATTCCCATTCACAAATTACAGTCATACATTTCATGAAAG
46781 G
66 G
* *
46782 TGATTATGAAAATATGACATTTATCAATTCCCATTCACAAATTATAGTCATACATTTCAT
1 TGATTATGAAAATATGACACTTATCAATTCCCATTCACAAATTACAGTCATACATTTCAT
46842 AATAACGGGC
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 58 1.00
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (66 bp):
TGATTATGAAAATATGACACTTATCAATTCCCATTCACAAATTACAGTCATACATTTCATGAAAG
G
Found at i:49950 original size:2 final size:2
Alignment explanation
Indices: 49943--50002 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
49933 TTCTTATGTT
49943 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
49985 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
50003 CCTATTTTCC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:51174 original size:10 final size:10
Alignment explanation
Indices: 51159--51192 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
51149 TTCATTTACC
51159 ATTTATTTTT
1 ATTTATTTTT
51169 ATTTATTTTT
1 ATTTATTTTT
*
51179 ATTTATTTCT
1 ATTTATTTTT
51189 ATTT
1 ATTT
51193 TACTAACGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (10 bp):
ATTTATTTTT
Found at i:60654 original size:50 final size:50
Alignment explanation
Indices: 60575--60670 Score: 138
Period size: 50 Copynumber: 1.9 Consensus size: 50
60565 AATACTTCGC
* ** *
60575 TTAGGATGAAAACCCGAGAGGGCGTCCTAAGTTGAAAAAAAAAAAAACGT
1 TTAGGATGAAAACCCGAAAGGGCACCCTAAATTGAAAAAAAAAAAAACGT
* *
60625 TTAGGGTGAAAACCCGAAAGGGCACCCTAAATTGAAAAAAGAAAAA
1 TTAGGATGAAAACCCGAAAGGGCACCCTAAATTGAAAAAAAAAAAA
60671 GAGGAAAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 40 1.00
ACGTcount: A:0.48, C:0.15, G:0.23, T:0.15
Consensus pattern (50 bp):
TTAGGATGAAAACCCGAAAGGGCACCCTAAATTGAAAAAAAAAAAAACGT
Found at i:61589 original size:105 final size:105
Alignment explanation
Indices: 61407--61866 Score: 884
Period size: 105 Copynumber: 4.4 Consensus size: 105
61397 AGGTTTCACC
*
61407 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTACAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
61472 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
61512 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
61577 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
61617 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
61682 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
**
61722 CAGAGCCAATTTCTGCTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
61787 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
61827 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
61867 GAAAACAACA
Statistics
Matches: 348, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 348 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.23
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
Found at i:63249 original size:2 final size:2
Alignment explanation
Indices: 63242--63267 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
63232 CTATTTATTC
63242 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
63268 TTGAATTTTT
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:63563 original size:2 final size:2
Alignment explanation
Indices: 63556--63625 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
63546 TTCTTATGTT
63556 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
63598 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
63626 CATTACCTAT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:65550 original size:23 final size:23
Alignment explanation
Indices: 65522--65568 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
65512 GTTTCTTTTT
*
65522 ATATTTGTTAGTAAATCCATTTA
1 ATATTTGTTAATAAATCCATTTA
* *
65545 ATATTTGTTAATATATTCATTTA
1 ATATTTGTTAATAAATCCATTTA
65568 A
1 A
65569 CGTTCACGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.51
Consensus pattern (23 bp):
ATATTTGTTAATAAATCCATTTA
Found at i:66544 original size:26 final size:26
Alignment explanation
Indices: 66510--66560 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
66500 ATTATATATA
*
66510 TATATATATATT-ATAAAATTTTATTC
1 TATAAATATATTCA-AAAATTTTATTC
*
66536 TATAAATATATTCAAAAGTTTTATT
1 TATAAATATATTCAAAAATTTTATT
66561 AAATTAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 21 0.95
27 1 0.05
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (26 bp):
TATAAATATATTCAAAAATTTTATTC
Found at i:67730 original size:39 final size:38
Alignment explanation
Indices: 67689--67837 Score: 131
Period size: 38 Copynumber: 4.1 Consensus size: 38
67679 ACTATGTAGT
*
67689 ATGTATGTATCTATGTATGTTTGTATAATTTATTAA--C
1 ATGTAT-TATCTATGTATGTATGTATAATTTATTAATGC
67726 --GTATGTA--TA--TAT--ATGTATAATTTATTAATGC
1 ATGTAT-TATCTATGTATGTATGTATAATTTATTAATGC
* * *
67757 ATGTATGTATATATTTATGTATGTATAATCTATTAATGC
1 ATGTAT-TATCTATGTATGTATGTATAATTTATTAATGC
* *
67796 ATGTATCATGC-ATGTACGTATGTATAATTTATTAATGC
1 ATGTATTAT-CTATGTATGTATGTATAATTTATTAATGC
67834 ATGT
1 ATGT
67838 CTCATAACCC
Statistics
Matches: 94, Mismatches: 7, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
29 15 0.16
31 4 0.04
33 9 0.10
35 9 0.10
37 3 0.03
38 30 0.32
39 24 0.26
ACGTcount: A:0.32, C:0.06, G:0.14, T:0.48
Consensus pattern (38 bp):
ATGTATTATCTATGTATGTATGTATAATTTATTAATGC
Found at i:67745 original size:29 final size:29
Alignment explanation
Indices: 67710--67768 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
67700 TATGTATGTT
*
67710 TGTATAATTTATTAACGTATGTATATATA
1 TGTATAATTTATTAACGCATGTATATATA
* *
67739 TGTATAATTTATTAATGCATGTATGTATA
1 TGTATAATTTATTAACGCATGTATATATA
67768 T
1 T
67769 ATTTATGTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.36, C:0.03, G:0.12, T:0.49
Consensus pattern (29 bp):
TGTATAATTTATTAACGCATGTATATATA
Found at i:67762 original size:19 final size:19
Alignment explanation
Indices: 67738--67837 Score: 85
Period size: 19 Copynumber: 5.2 Consensus size: 19
67728 ATGTATATAT
67738 ATGTATAATTTATTAATGC
1 ATGTATAATTTATTAATGC
* * * *
67757 ATGTATGTATATATTTATGT
1 ATGTAT-AATTTATTAATGC
*
67777 ATGTATAATCTATTAATGC
1 ATGTATAATTTATTAATGC
* ** * *
67796 ATGTATCATGCATGT-ACGT
1 ATGTATAATTTAT-TAATGC
67815 ATGTATAATTTATTAATGC
1 ATGTATAATTTATTAATGC
67834 ATGT
1 ATGT
67838 CTCATAACCC
Statistics
Matches: 60, Mismatches: 18, Indels: 6
0.71 0.21 0.07
Matches are distributed among these distances:
18 1 0.02
19 43 0.72
20 16 0.27
ACGTcount: A:0.33, C:0.07, G:0.14, T:0.46
Consensus pattern (19 bp):
ATGTATAATTTATTAATGC
Found at i:67829 original size:38 final size:38
Alignment explanation
Indices: 67737--67843 Score: 142
Period size: 38 Copynumber: 2.8 Consensus size: 38
67727 TATGTATATA
* * * *
67737 TATGTATAATTTATTAATGCATGTATGTATATATTTATG
1 TATGTATAATTTATTAATGCATGTAT-CATACATGTACG
* *
67776 TATGTATAATCTATTAATGCATGTATCATGCATGTACG
1 TATGTATAATTTATTAATGCATGTATCATACATGTACG
*
67814 TATGTATAATTTATTAATGCATGTCTCATA
1 TATGTATAATTTATTAATGCATGTATCATA
67844 ACCCATGTAT
Statistics
Matches: 59, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
38 34 0.58
39 25 0.42
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.46
Consensus pattern (38 bp):
TATGTATAATTTATTAATGCATGTATCATACATGTACG
Found at i:67925 original size:19 final size:18
Alignment explanation
Indices: 67901--67961 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 18
67891 TGGCGAATGC
67901 ATATATCATGTATGTATTT
1 ATATAT-ATGTATGTATTT
* *
67920 ATATATGTATGTAATATATTA
1 ATATA--TATGT-ATGTATTT
* *
67941 ATATGTATGTATGTATGT
1 ATATATATGTATGTATTT
67959 ATA
1 ATA
67962 AGTAATTTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
18 8 0.24
19 10 0.30
20 4 0.12
21 11 0.33
ACGTcount: A:0.36, C:0.02, G:0.13, T:0.49
Consensus pattern (18 bp):
ATATATATGTATGTATTT
Found at i:68141 original size:28 final size:27
Alignment explanation
Indices: 68099--68175 Score: 86
Period size: 28 Copynumber: 2.8 Consensus size: 27
68089 CATAAACTTT
*
68099 ATTTCAAACCCTATAAA-TTATATCATA
1 ATTTCAAACCATATAAACTT-TATCATA
68126 ATTTACAAACCATATAAACTTTATCATA
1 ATTT-CAAACCATATAAACTTTATCATA
*
68154 ATCTTCGAACTC-TATAAACTTT
1 AT-TTCAAAC-CATATAAACTTT
68176 TGTTCACAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 4 0.09
28 35 0.80
29 5 0.11
ACGTcount: A:0.42, C:0.19, G:0.01, T:0.38
Consensus pattern (27 bp):
ATTTCAAACCATATAAACTTTATCATA
Found at i:68885 original size:16 final size:15
Alignment explanation
Indices: 68864--68897 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
68854 TAATATTTAT
68864 CTGTTTCGAACCTGAA
1 CTGTTTCG-ACCTGAA
*
68880 CTGTTTTGACCTGAA
1 CTGTTTCGACCTGAA
68895 CTG
1 CTG
68898 ATATTGATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.35
Consensus pattern (15 bp):
CTGTTTCGACCTGAA
Found at i:70780 original size:43 final size:43
Alignment explanation
Indices: 70681--70849 Score: 198
Period size: 43 Copynumber: 4.0 Consensus size: 43
70671 TATAGCGACA
* * * *
70681 TTTTTGCCACAAACGCCAC-AATTCTCTTG-TCTTAGTGGCTTT
1 TTTTTACCACAAACGCCACTAATGCTATTGTTTTTAGTGGC-TT
* *
70723 TTTTTACCACAAACGCCGCTAATGCTATTGTTTTTAGTGGGTT
1 TTTTTACCACAAACGCCACTAATGCTATTGTTTTTAGTGGCTT
* * * *
70766 TTTTTACCACAAACGTCACTGATGCTATTGCTTTTAGTGGCCT
1 TTTTTACCACAAACGCCACTAATGCTATTGTTTTTAGTGGCTT
* **
70809 TTTTTGCCACAAACGCCGTTAATGCTATTGTTTTTAGTGGC
1 TTTTTACCACAAACGCCACTAATGCTATTGTTTTTAGTGGC
70850 ATTTGTAATA
Statistics
Matches: 107, Mismatches: 18, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
42 17 0.16
43 82 0.77
44 8 0.07
ACGTcount: A:0.20, C:0.22, G:0.17, T:0.41
Consensus pattern (43 bp):
TTTTTACCACAAACGCCACTAATGCTATTGTTTTTAGTGGCTT
Found at i:71386 original size:28 final size:28
Alignment explanation
Indices: 71346--71401 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
71336 TTGTCATCCG
*
71346 AGGCTGAATGTTGGTGCAACCCTACATA
1 AGGCTGAATGTTGATGCAACCCTACATA
*
71374 AGGCTGAGTGTTGATGCAACCCTACATA
1 AGGCTGAATGTTGATGCAACCCTACATA
71402 CAAAGTTGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (28 bp):
AGGCTGAATGTTGATGCAACCCTACATA
Found at i:74795 original size:23 final size:23
Alignment explanation
Indices: 74765--74816 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
74755 ACTCCTCTCT
*
74765 CCTTCCCCAACCTTTCTGCGTCC
1 CCTTCCCCAACCTTTCTGCCTCC
* *
74788 CCTTCCCCGACTTTTCTGCCTCC
1 CCTTCCCCAACCTTTCTGCCTCC
74811 CCTTCC
1 CCTTCC
74817 TCCTTCCCCC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.06, C:0.54, G:0.08, T:0.33
Consensus pattern (23 bp):
CCTTCCCCAACCTTTCTGCCTCC
Found at i:77266 original size:15 final size:15
Alignment explanation
Indices: 77246--77296 Score: 84
Period size: 15 Copynumber: 3.4 Consensus size: 15
77236 ATATTTAGTT
*
77246 GGGCGGGCGGATGTG
1 GGGCGGGCGGATGCG
77261 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
*
77276 GGGTGGGCGGATGCG
1 GGGCGGGCGGATGCG
77291 GGGCGG
1 GGGCGG
77297 ATAATGTCTC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.06, C:0.16, G:0.69, T:0.10
Consensus pattern (15 bp):
GGGCGGGCGGATGCG
Found at i:83214 original size:2 final size:2
Alignment explanation
Indices: 83207--83261 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
83197 TAGAGATCTT
83207 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
83249 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
83262 GATCTTGTTA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:87753 original size:2 final size:2
Alignment explanation
Indices: 87746--87776 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
87736 CACTAGTTTG
87746 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
87777 TTGTTGGGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:90509 original size:2 final size:2
Alignment explanation
Indices: 90477--90501 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
90467 TACCTCAATT
90477 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
90502 CAATATATCT
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:96059 original size:32 final size:32
Alignment explanation
Indices: 96013--96121 Score: 114
Period size: 31 Copynumber: 3.5 Consensus size: 32
96003 TTTTTACAAG
* * **
96013 TTTAAGGACTATTTTGTAATGGTTTGATAAGT
1 TTTAATGACCATTTTGTAATAATTTGATAAGT
*
96045 TTTAATGACCATTTTGTAACAATTTGATAAG-
1 TTTAATGACCATTTTGTAATAATTTGATAAGT
** * *
96076 TTTAATGATTATTTTATAATAATCTGATAA-T
1 TTTAATGACCATTTTGTAATAATTTGATAAGT
*
96107 TGTAATGACCATTTT
1 TTTAATGACCATTTT
96122 ATAACTTCTG
Statistics
Matches: 63, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
31 37 0.59
32 26 0.41
ACGTcount: A:0.33, C:0.06, G:0.14, T:0.47
Consensus pattern (32 bp):
TTTAATGACCATTTTGTAATAATTTGATAAGT
Found at i:96083 original size:31 final size:31
Alignment explanation
Indices: 96035--96146 Score: 115
Period size: 31 Copynumber: 3.6 Consensus size: 31
96025 TTTGTAATGG
*
96035 TTTGATAAGTTTTAATGACCATTTTGTAACAA
1 TTTGATAAG-TTTAATGACCATTTTATAACAA
** *
96067 TTTGATAAGTTTAATGATTATTTTATAATAA
1 TTTGATAAGTTTAATGACCATTTTATAACAA
*
96098 TCTGATAA-TTGTAATGACCATTTTATAAC--
1 TTTGATAAGTT-TAATGACCATTTTATAACAA
*
96127 TTCTGA-AACTTTAATGACCA
1 TT-TGATAAGTTTAATGACCA
96147 ATAAATTATT
Statistics
Matches: 68, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
29 12 0.18
30 7 0.10
31 40 0.59
32 9 0.13
ACGTcount: A:0.36, C:0.10, G:0.11, T:0.44
Consensus pattern (31 bp):
TTTGATAAGTTTAATGACCATTTTATAACAA
Found at i:104341 original size:31 final size:28
Alignment explanation
Indices: 104301--104473 Score: 217
Period size: 27 Copynumber: 6.0 Consensus size: 28
104291 TAAACCTGAC
104301 CCCGACCCGAATATCACACTTAAAAAAA
1 CCCGACCCGAATATCACACTTAAAAAAA
104329 CCGACAGACCCGAATATCACACTTAAAAAAA
1 CC--C-GACCCGAATATCACACTTAAAAAAA
* *
104360 -CCGACCTGAATATTACACTTAAAAAAA
1 CCCGACCCGAATATCACACTTAAAAAAA
*
104387 CCCGACCAACCCGAATATCAAACTT-AAAAAA
1 CCCG----ACCCGAATATCACACTTAAAAAAA
104418 CCCGACCCGAATATCACACTTAAAAAAA
1 CCCGACCCGAATATCACACTTAAAAAAA
*
104446 CCCGACCCGAATAGCGA-ACTTAAAAAAA
1 CCCGACCCGAATATC-ACACTTAAAAAAA
104474 TGACCCAACC
Statistics
Matches: 128, Mismatches: 7, Indels: 20
0.83 0.05 0.13
Matches are distributed among these distances:
27 39 0.30
28 37 0.29
29 1 0.01
30 2 0.02
31 35 0.27
32 14 0.11
ACGTcount: A:0.47, C:0.29, G:0.09, T:0.14
Consensus pattern (28 bp):
CCCGACCCGAATATCACACTTAAAAAAA
Found at i:104412 original size:59 final size:60
Alignment explanation
Indices: 104302--104452 Score: 245
Period size: 59 Copynumber: 2.6 Consensus size: 60
104292 AAACCTGACC
*
104302 CCGACCCGAATATCACACTTAAAAAAA-CCGA-CAGACCCGAATATCACACTTAAAAAAA
1 CCGACCCGAATATCACACTTAAAAAAACCCGACCAGACCCGAATATCAAACTTAAAAAAA
* * *
104360 CCGACCTGAATATTACACTTAAAAAAACCCGACCA-ACCCGAATATCAAACTTAAAAAAC
1 CCGACCCGAATATCACACTTAAAAAAACCCGACCAGACCCGAATATCAAACTTAAAAAAA
104419 CCGACCCGAATATCACACTTAAAAAAACCCGACC
1 CCGACCCGAATATCACACTTAAAAAAACCCGACC
104453 CGAATAGCGA
Statistics
Matches: 85, Mismatches: 6, Indels: 3
0.90 0.06 0.03
Matches are distributed among these distances:
58 25 0.29
59 58 0.68
60 2 0.02
ACGTcount: A:0.46, C:0.31, G:0.08, T:0.15
Consensus pattern (60 bp):
CCGACCCGAATATCACACTTAAAAAAACCCGACCAGACCCGAATATCAAACTTAAAAAAA
Found at i:104486 original size:59 final size:55
Alignment explanation
Indices: 104301--104473 Score: 215
Period size: 59 Copynumber: 3.0 Consensus size: 55
104291 TAAACCTGAC
104301 CCCGACCCGAATATCACACTTAAAAAAACCGACAGACCCGAATATCACACTTAAAAAAA
1 CCCGACCCGAATATCACACTTAAAAAAACC--C-GACCCGAATATCA-ACTTAAAAAAA
* *
104360 -CCGACCTGAATATTACACTTAAAAAAACCCGACCAACCCGAATATCAAACTT-AAAAAA
1 CCCGACCCGAATATCACACTTAAAAAAACCCG----ACCCGAATATC-AACTTAAAAAAA
*
104418 CCCGACCCGAATATCACACTTAAAAAAACCCGACCCGAATAGCGAACTTAAAAAAA
1 CCCGACCCGAATATCACACTTAAAAAAACCCGACCCGAATATC-AACTTAAAAAAA
104474 TGACCCAACC
Statistics
Matches: 101, Mismatches: 6, Indels: 17
0.81 0.05 0.14
Matches are distributed among these distances:
55 16 0.16
56 7 0.07
58 33 0.33
59 44 0.44
60 1 0.01
ACGTcount: A:0.47, C:0.29, G:0.09, T:0.14
Consensus pattern (55 bp):
CCCGACCCGAATATCACACTTAAAAAAACCCGACCCGAATATCAACTTAAAAAAA
Found at i:105415 original size:79 final size:79
Alignment explanation
Indices: 105291--105831 Score: 734
Period size: 79 Copynumber: 6.9 Consensus size: 79
105281 AATCTCAATG
* * * * *
105291 TTATTGATG-ATGTTTACGTCT-GTACGACTATCAAATCTAGATACATTGATGATCCAGGGAGAT
1 TTATTGATGTATGTTTATGT-TGGTGCGACTATCGAATCTCGATACATTGATGTTCCAGGGAGAT
*
105354 GTCTGAATCCCGGTA
65 GTCTGAATCCCGATA
* * * * *
105369 TTATTGATGTATGTTTATGTCGATGCGACTGTCGAATCTCGGTACATTGATGTTCCAGGGAGAAG
1 TTATTGATGTATGTTTATGTTGGTGCGACTATCGAATCTCGATACATTGATGTTCCAGGGAGATG
*
105434 TCTGAATCCCCATA
66 TCTGAATCCCGATA
* *
105448 TTATTGATGTATGTTTATGTTGGTGCGACAATCGAATCTCGATACATTGATGTTTCAGGGAGATG
1 TTATTGATGTATGTTTATGTTGGTGCGACTATCGAATCTCGATACATTGATGTTCCAGGGAGATG
*
105513 TCTGAATCCCGGTA
66 TCTGAATCCCGATA
* * * *
105527 TTATTGATGTATGTTTATGTTGGTTCTACTATCGAATCTCGATACATTGACGTTCCTGGGAGATG
1 TTATTGATGTATGTTTATGTTGGTGCGACTATCGAATCTCGATACATTGATGTTCCAGGGAGATG
*
105592 TCTGGATCCCG-TA
66 TCTGAATCCCGATA
* * * * * * *
105605 TTATTGATGTATGTTTATGTCGATGCAAATGTCGAATTTCGATACATTGATGTTCCATGGAGATG
1 TTATTGATGTATGTTTATGTTGGTGCGACTATCGAATCTCGATACATTGATGTTCCAGGGAGATG
105670 TCTGAATCCC-ATA
66 TCTGAATCCCGATA
* * *
105683 TCATTGATGTATGTTTATGTTGG-GCGACTATTGAATCTCGATGCATTGATGTTCCAGGGAGATG
1 TTATTGATGTATGTTTATGTTGGTGCGACTATCGAATCTCGATACATTGATGTTCCAGGGAGATG
105747 TCTGAAT-CCGATA
66 TCTGAATCCCGATA
* * *
105760 TTATTGATGTATGTTTATGTTGGTGCAACTATCGAATCTCGATACGTTGATGTTCCATGGAGATG
1 TTATTGATGTATGTTTATGTTGGTGCGACTATCGAATCTCGATACATTGATGTTCCAGGGAGATG
105825 TCTGAAT
66 TCTGAAT
105832 TACAGATCTT
Statistics
Matches: 403, Mismatches: 55, Indels: 10
0.86 0.12 0.02
Matches are distributed among these distances:
76 2 0.00
77 66 0.16
78 140 0.35
79 195 0.48
ACGTcount: A:0.24, C:0.15, G:0.23, T:0.37
Consensus pattern (79 bp):
TTATTGATGTATGTTTATGTTGGTGCGACTATCGAATCTCGATACATTGATGTTCCAGGGAGATG
TCTGAATCCCGATA
Found at i:105787 original size:155 final size:156
Alignment explanation
Indices: 105324--105831 Score: 709
Period size: 155 Copynumber: 3.2 Consensus size: 156
105314 ACGACTATCA
* *
105324 AATCTAGATACATTGATGATCCAGGGAGATGTCTGAATCCCGGTATTATTGATGTATGTTTATGT
1 AATCTCGATACATTGATGTTCCAGGGAGATGTCTGAATCCCGGTATTATTGATGTATGTTTATGT
* * * * * *
105389 CGATGCGACTGTCGAATCTCGGTACATTGATGTTCCAGGGAGAAGTCTGAATCCCCATATTATTG
66 TG-GGCGACTATCGAATCTCGATACATTGATGTTCCAGGGAGATGTCTGAATCCCGATATTATTG
105454 ATGTATGTTTATGTTGGTGCGACAA-TCG
130 ATGTATGTTTATGTTGGTGC-A-AATTCG
*
105482 AATCTCGATACATTGATGTTTCAGGGAGATGTCTGAATCCCGGTATTATTGATGTATGTTTATGT
1 AATCTCGATACATTGATGTTCCAGGGAGATGTCTGAATCCCGGTATTATTGATGTATGTTTATGT
* * * * *
105547 TGGTTCTACTATCGAATCTCGATACATTGACGTTCCTGGGAGATGTCTGGATCCCG-TATTATTG
66 TGG-GCGACTATCGAATCTCGATACATTGATGTTCCAGGGAGATGTCTGAATCCCGATATTATTG
* *
105611 ATGTATGTTTATGTCGATGCAAATGTCG
130 ATGTATGTTTATGTTGGTGCAAAT-TCG
* * * *
105639 AATTTCGATACATTGATGTTCCATGGAGATGTCTGAATCCC-ATATCATTGATGTATGTTTATGT
1 AATCTCGATACATTGATGTTCCAGGGAGATGTCTGAATCCCGGTATTATTGATGTATGTTTATGT
* *
105703 TGGGCGACTATTGAATCTCGATGCATTGATGTTCCAGGGAGATGTCTGAAT-CCGATATTATTGA
66 TGGGCGACTATCGAATCTCGATACATTGATGTTCCAGGGAGATGTCTGAATCCCGATATTATTGA
*
105767 TGTATGTTTATGTTGGTGCAACTATCG
131 TGTATGTTTATGTTGGTGCAAAT-TCG
* *
105794 AATCTCGATACGTTGATGTTCCATGGAGATGTCTGAAT
1 AATCTCGATACATTGATGTTCCAGGGAGATGTCTGAAT
105832 TACAGATCTT
Statistics
Matches: 312, Mismatches: 34, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
154 3 0.01
155 111 0.36
156 25 0.08
157 67 0.21
158 106 0.34
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (156 bp):
AATCTCGATACATTGATGTTCCAGGGAGATGTCTGAATCCCGGTATTATTGATGTATGTTTATGT
TGGGCGACTATCGAATCTCGATACATTGATGTTCCAGGGAGATGTCTGAATCCCGATATTATTGA
TGTATGTTTATGTTGGTGCAAATTCG
Done.