Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004826.1 Hibiscus syriacus cultivar Beakdansim tig00010871_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: 58689
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.34
Found at i:2970 original size:11 final size:12
Alignment explanation
Indices: 2951--3029 Score: 61
Period size: 12 Copynumber: 6.6 Consensus size: 12
2941 AAACATAACT
*
2951 TATATATTTTCA
1 TATATATTTACA
2963 TA-ATATTTACA
1 TATATATTTACA
* *
2974 TATATATATATA
1 TATATATTTACA
* *
2986 TATATAATATATA
1 TATAT-ATTTACA
* *
2999 TATATATATATA
1 TATATATTTACA
* *
3011 TATATATATATA
1 TATATATTTACA
3023 TATATAT
1 TATATAT
3030 ATGCATCAAC
Statistics
Matches: 62, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
11 10 0.16
12 40 0.65
13 12 0.19
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.51
Consensus pattern (12 bp):
TATATATTTACA
Found at i:2980 original size:2 final size:2
Alignment explanation
Indices: 2973--3031 Score: 111
Period size: 2 Copynumber: 30.0 Consensus size: 2
2963 TAATATTTAC
2973 AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3014 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
3032 GCATCAACAA
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 55 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12612 original size:12 final size:12
Alignment explanation
Indices: 12595--12627 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
12585 TCATAACCTA
12595 TGTATATATGTG
1 TGTATATATGTG
12607 TGTATATATGTG
1 TGTATATATGTG
*
12619 TATATATAT
1 TGTATATAT
12628 ATACACATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.18, T:0.52
Consensus pattern (12 bp):
TGTATATATGTG
Found at i:14604 original size:40 final size:38
Alignment explanation
Indices: 14536--14613 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 38
14526 TCCATGCAGG
** *
14536 TGCCACGTGCTTGGTTTAACATTCCATTCGTATTGTCA
1 TGCCACGTGCTTGGGGTAACATCCCATTCGTATTGTCA
*
14574 TGCCACGTGCTTTGTGGGTAACATCCCATTCGTTTTGTCA
1 TGCCACGTGC-TTG-GGGTAACATCCCATTCGTATTGTCA
14614 CGACGTGCCA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 10 0.29
39 3 0.09
40 21 0.62
ACGTcount: A:0.17, C:0.24, G:0.21, T:0.38
Consensus pattern (38 bp):
TGCCACGTGCTTGGGGTAACATCCCATTCGTATTGTCA
Found at i:17871 original size:30 final size:30
Alignment explanation
Indices: 17816--17872 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
17806 AAGTTAACGG
**
17816 CATAGTTATTAAAAATAACTTAAAAATCCA
1 CATAGTTATTAAAAATAACAGAAAAATCCA
17846 CATAGTTATTAAAAATTAA-AGAAAAAT
1 CATAGTTATTAAAAA-TAACAGAAAAAT
17873 ATATTGAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 21 0.88
31 3 0.12
ACGTcount: A:0.56, C:0.09, G:0.05, T:0.30
Consensus pattern (30 bp):
CATAGTTATTAAAAATAACAGAAAAATCCA
Found at i:19364 original size:75 final size:75
Alignment explanation
Indices: 19241--19498 Score: 293
Period size: 75 Copynumber: 3.4 Consensus size: 75
19231 CTTAAATGGT
* ** * *
19241 TAAAATAAAATAGGCGCTACATATTATATTAAACTATCTACCAGTTTATTTGAAGGTTACTAATA
1 TAAAATAAAATAGGCGATACATATTACGTTAAACTATCTACTAGTTTATTTAAAGGTTACTAATA
* *
19306 ATGTAAATGG
66 ATATAAACGG
* * *
19316 TAAAATAAAATAGGCGATACATGTTACGTTAAAATATCTACTAGTTTATTTAAAGGTTACTATTA
1 TAAAATAAAATAGGCGATACATATTACGTTAAACTATCTACTAGTTTATTTAAAGGTTACTAATA
19381 ATATAAACGG
66 ATATAAACGG
* * * * * * * * *
19391 TAAAGTAAAATATGTGTTACTTATTACGTTAAACTAGCTATTGGTTTATTTAAAGTTTGA-TAAT
1 TAAAATAAAATAGGCGATACATATTACGTTAAACTATCTACTAGTTTATTTAAAGGTT-ACTAAT
19455 AATATAAACGG
65 AATATAAACGG
* * * *
19466 TAAAATAAAATAGGTGCTACCTATTATGTTAAA
1 TAAAATAAAATAGGCGATACATATTACGTTAAA
19499 TAAGTATTAC
Statistics
Matches: 155, Mismatches: 27, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
75 154 0.99
76 1 0.01
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (75 bp):
TAAAATAAAATAGGCGATACATATTACGTTAAACTATCTACTAGTTTATTTAAAGGTTACTAATA
ATATAAACGG
Found at i:19567 original size:98 final size:98
Alignment explanation
Indices: 19398--19596 Score: 281
Period size: 98 Copynumber: 2.0 Consensus size: 98
19388 CGGTAAAGTA
* * * * ** * * *
19398 AAATATGTGTTACTTATTACGTTAAACTAGCTATTGGTTTATTTAAAGTTTGATAATAATATAAA
1 AAATAAGTATTACCTATTACGTTAAACTAACTACCGATTTATTTAAAGGTTAATAATAATATAAA
** *
19463 CGGTAAAATAAAATAGGTGCTACCTATTATGTT
66 CGGTAAAATAAAATAGACGCTACCTATTACGTT
*
19496 AAATAAGTATTACCTATTACGTTAAACTAACTACCGATTTGTTTAAAGGTTAATAATAATATAAA
1 AAATAAGTATTACCTATTACGTTAAACTAACTACCGATTTATTTAAAGGTTAATAATAATATAAA
19561 CGGTAAAATAAAATAGACGCTACCTATTACGTT
66 CGGTAAAATAAAATAGACGCTACCTATTACGTT
19594 AAA
1 AAA
19597 CTAATTATCG
Statistics
Matches: 88, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
98 88 1.00
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.36
Consensus pattern (98 bp):
AAATAAGTATTACCTATTACGTTAAACTAACTACCGATTTATTTAAAGGTTAATAATAATATAAA
CGGTAAAATAAAATAGACGCTACCTATTACGTT
Found at i:20418 original size:105 final size:106
Alignment explanation
Indices: 20229--20513 Score: 356
Period size: 105 Copynumber: 2.7 Consensus size: 106
20219 TATTGGTGCA
* * * * * * * *
20229 ACCTAATATGTTAATATTTATTTATAACAAAATAAGAAATTAACATATTGTGTTGTCGTCGGATT
1 ACCTAACATGTTGATA-ATATTAATAACAAAATAAGTAATTAAC-TATT-TTTTATCGTCGAATT
* * *
20294 TCGAATGTCCCATCAGCTTAAACTTTAGTAACATTTTAGGCGCT
63 TCTAAGGTCCCATCAGCTTAAACTTTAGTAACATCTTAGGCGCT
*
20338 ATCTAACATGTTGATAATATTAATAACAAAATAAGTAATTAACT-TTTTTTATCGTCGAATTTCT
1 ACCTAACATGTTGATAATATTAATAACAAAATAAGTAATTAACTATTTTTTATCGTCGAATTTCT
* * *
20402 AAGGTCCTATCAGCTTAAACTTTGGTAATATCTTAGGCGCT
66 AAGGTCCCATCAGCTTAAACTTTAGTAACATCTTAGGCGCT
* * *
20443 ACCTAATATGTTGATAATATTAATAACAAATTAAGTAATTAACCTATTTTGTTATCGTCAAATTT
1 ACCTAACATGTTGATAATATTAATAACAAAATAAGTAATTAA-CTATTTT-TTATCGTCGAATTT
20508 CTAAGG
64 CTAAGG
20514 CATCATCAAC
Statistics
Matches: 154, Mismatches: 19, Indels: 7
0.86 0.11 0.04
Matches are distributed among these distances:
105 89 0.58
106 4 0.03
107 5 0.03
108 43 0.28
109 13 0.08
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (106 bp):
ACCTAACATGTTGATAATATTAATAACAAAATAAGTAATTAACTATTTTTTATCGTCGAATTTCT
AAGGTCCCATCAGCTTAAACTTTAGTAACATCTTAGGCGCT
Found at i:24661 original size:72 final size:71
Alignment explanation
Indices: 24539--24671 Score: 173
Period size: 70 Copynumber: 1.9 Consensus size: 71
24529 TCGAAATAAA
* * *
24539 AAAAAAACATGGAAAATGAGAAGGTCGCAAAGTATCAAAATTTTTCATAAATATCGATACTTTTA
1 AAAAAAACATGGAAAATGAGAAGCTCACAAAGTATCAAAATTTTTAATAAATATCGATACTTTTA
24604 AATTTT
66 AATTTT
*
24610 AAAAAAA-ATGGAAAATGAGAATGCT-ACAAAGTATC-AACTTTTTAAAAATAAATATCGATACT
1 AAAAAAACATGGAAAATGAGAA-GCTCACAAAGTATCAAAATTTTT---AATAAATATCGATACT
24672 ACGAGCTGAT
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
69 7 0.13
70 23 0.43
71 9 0.17
72 15 0.28
ACGTcount: A:0.50, C:0.10, G:0.12, T:0.29
Consensus pattern (71 bp):
AAAAAAACATGGAAAATGAGAAGCTCACAAAGTATCAAAATTTTTAATAAATATCGATACTTTTA
AATTTT
Found at i:25056 original size:76 final size:76
Alignment explanation
Indices: 24930--25088 Score: 239
Period size: 76 Copynumber: 2.1 Consensus size: 76
24920 CTTAACAGGT
* * *
24930 TAAAATAAAACAGGCTCAACCTATTACGTTAAACTAGCTATCTGTTTGTTTAAAGTTATAATAAT
1 TAAAATAAAACAGGCGCAACCTATTACGTTAAACTAGCTATCGGTTTGTTTAAAGATATAATAAT
*
24995 AATGTAAACAG
66 AATATAAACAG
* *
25006 TAAAATAAAATAGGCGCTACCTATTACGTTAAACTAGCT-TACGGTTTGTTTAAAGATATAATAA
1 TAAAATAAAACAGGCGCAACCTATTACGTTAAACTAGCTAT-CGGTTTGTTTAAAGATATAATAA
*
25070 TAATATAAACGG
65 TAATATAAACAG
25082 TAAAATA
1 TAAAATA
25089 TTTACAACTT
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
75 1 0.01
76 74 0.99
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (76 bp):
TAAAATAAAACAGGCGCAACCTATTACGTTAAACTAGCTATCGGTTTGTTTAAAGATATAATAAT
AATATAAACAG
Found at i:25135 original size:100 final size:100
Alignment explanation
Indices: 25006--25248 Score: 310
Period size: 100 Copynumber: 2.4 Consensus size: 100
24996 ATGTAAACAG
* *
25006 TAAAATAAAATAGGCGCTACCTATTACGTTAAACTAGCTTAC-GGTTTGTTTAAAGATATAATAA
1 TAAAATAAAATAGGCGCTACCTATTACGTTAAACTA-CCTACTGGCTTGTTTAAAGATATAATAA
* *
25070 TAATATAAACGGTAAAATATTTACAACTTAAC-CGAT
65 TAATATAAACGGAAAAATATTTACAACTTAACAAG-T
* * * *
25106 TAAAATGAAATAGCCGCTACCTATTACGTTAAACTACCTACTGGCTTGTTTAAAGGTATAATACT
1 TAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACTGGCTTGTTTAAAGATATAATAAT
* * *
25171 AATGTAAATGGAAAAATATTTATAACTTAACAAGT
66 AATATAAACGGAAAAATATTTACAACTTAACAAGT
* * * * *
25206 TAAAATAAAATAGGTGCTACCTAATATGTTAAAGTACCCACTG
1 TAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACTG
25249 ATTTGGTAAC
Statistics
Matches: 123, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
99 4 0.03
100 118 0.96
101 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.31
Consensus pattern (100 bp):
TAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACTGGCTTGTTTAAAGATATAATAAT
AATATAAACGGAAAAATATTTACAACTTAACAAGT
Found at i:25509 original size:109 final size:108
Alignment explanation
Indices: 25268--25537 Score: 366
Period size: 109 Copynumber: 2.5 Consensus size: 108
25258 CATTTTAGAC
25268 GCTACCTAATATGTTGATAATATTAATAACAAAATAAGTAATTAACATATTTTGTTATCGTCGAA
1 GCTACCTAATATGTTGATAATATTAATAACAAAATAAGTAATTAACATATTTTGTTATCGTCGAA
* * * * *
25333 TTTCTAAGGCCCCATCAGCTTTAACTTTGAAAATTTTTTAGGT
66 TTTCTAAGGCCCCATCAACTTAAACTTCGAAAATATATTAGGT
*
25376 GCTACCTAATATGTTGATAATATTAATAACAAAATAAGTAATTAATC-TATTTTTGTTATTGTC-
1 GCTACCTAATATGTTGATAATATTAATAACAAAATAAGTAATTAA-CATA-TTTTGTTATCGTCG
* *
25439 AGATTTCTAAGGCTCCATCAACTTAAACTCTCG-TAATATATTAGGT
64 A-ATTTCTAAGGCCCCATCAACTTAAACT-TCGAAAATATATTAGGT
* * * * *
25485 GTTACCTAATATGTTGATATTATTATTAACAAAATAAGTAATTTACTTATTTT
1 GCTACCTAATATGTTGATAATATTAATAACAAAATAAGTAATTAACATATTTT
25538 CTTAGTGTTT
Statistics
Matches: 145, Mismatches: 12, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
108 53 0.37
109 90 0.62
110 2 0.01
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.41
Consensus pattern (108 bp):
GCTACCTAATATGTTGATAATATTAATAACAAAATAAGTAATTAACATATTTTGTTATCGTCGAA
TTTCTAAGGCCCCATCAACTTAAACTTCGAAAATATATTAGGT
Found at i:26752 original size:17 final size:18
Alignment explanation
Indices: 26729--26777 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
26719 ATAATTTATA
26729 CTTTTATAATTTTTGA-TT
1 CTTTTATAATTTTT-ACTT
*
26747 -TTTTATAACTTTTACTT
1 CTTTTATAATTTTTACTT
*
26764 CTTTTTTAATTTTT
1 CTTTTATAATTTTT
26778 TTAATATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 1 0.04
17 14 0.54
18 11 0.42
ACGTcount: A:0.20, C:0.08, G:0.02, T:0.69
Consensus pattern (18 bp):
CTTTTATAATTTTTACTT
Found at i:26808 original size:19 final size:18
Alignment explanation
Indices: 26766--26810 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 18
26756 TTTTACTTCT
**
26766 TTTTTAATTTTTTTAATA
1 TTTTTAATTTTAATAATA
26784 TTTTTATATTTTAATAATA
1 TTTTTA-ATTTTAATAATA
26803 TTTTTAAT
1 TTTTTAAT
26811 AATTTCTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTTTAATTTTAATAATA
Found at i:26820 original size:19 final size:19
Alignment explanation
Indices: 26766--26824 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
26756 TTTTACTTCT
*
26766 TTTTTAAT-TTTTTTAATA
1 TTTTTAATATTTTATAATA
26784 TTTTT-ATATTTTAATAATA
1 TTTTTAATATTTT-ATAATA
* *
26803 TTTTTAATAATTTCTAAT-
1 TTTTTAATATTTTATAATA
26821 TTTT
1 TTTT
26825 ATTGAAAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
17 2 0.06
18 13 0.37
19 14 0.40
20 6 0.17
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTTTAATATTTTATAATA
Found at i:26822 original size:28 final size:28
Alignment explanation
Indices: 26770--26823 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
26760 ACTTCTTTTT
* *
26770 TAATTTTTTTAATATTTTTATATTTTAA
1 TAATATTTTTAATATTTCTATATTTTAA
26798 TAATATTTTTAATAATTTCTA-ATTTT
1 TAATATTTTTAAT-ATTTCTATATTTT
26824 TATTGAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 17 0.74
29 6 0.26
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (28 bp):
TAATATTTTTAATATTTCTATATTTTAA
Found at i:30433 original size:2 final size:2
Alignment explanation
Indices: 30420--30453 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
30410 TGCACCTTTC
* *
30420 AT AT AG AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30454 CCACACATAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (2 bp):
AT
Found at i:31264 original size:30 final size:30
Alignment explanation
Indices: 30878--31247 Score: 695
Period size: 30 Copynumber: 12.3 Consensus size: 30
30868 GAAGGACCTA
*
30878 TCCAGAGGTCACAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
* *
30908 TCCAGAGGTCACAAAGATCCTCGGTAACTA
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
30938 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
30968 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
30998 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
31028 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
31058 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
31088 TCTAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
31118 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
31148 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
31178 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
31208 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
31238 TCCATAGGTC
1 TCCAGAGGTC
31248 CCGAAGAACC
Statistics
Matches: 334, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 334 1.00
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.23
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:36015 original size:30 final size:30
Alignment explanation
Indices: 35660--35998 Score: 635
Period size: 30 Copynumber: 11.3 Consensus size: 30
35650 GAAGGACCTA
*
35660 TCCAGAGGTCACAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
35690 TCCAGAGGTCACAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
35720 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
35750 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
35780 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
35810 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
35840 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
35870 T-CAGAGGTCATAAAGATCCTCCGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
35899 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
35929 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
35959 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
35989 TCCATAGGTC
1 TCCAGAGGTC
35999 CCGAAGAACC
Statistics
Matches: 304, Mismatches: 4, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
29 28 0.09
30 276 0.91
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.23
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:36530 original size:24 final size:25
Alignment explanation
Indices: 36501--36548 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
36491 ATAATCATGC
*
36501 TACATACAAT-TTATGTCATGCATA
1 TACATACAATCATATGTCATGCATA
* *
36525 TACATATAATCATATTTCATGCAT
1 TACATACAATCATATGTCATGCAT
36549 TAAACATAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.40
Consensus pattern (25 bp):
TACATACAATCATATGTCATGCATA
Found at i:36907 original size:21 final size:21
Alignment explanation
Indices: 36877--36921 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
36867 ATTCTGTCGT
* *
36877 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
36898 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
36919 TTG
1 TTG
36922 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:37751 original size:26 final size:27
Alignment explanation
Indices: 37702--37759 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
37692 GACATGTTAC
**
37702 AATATATATATTATATGAGTTGTG-TA
1 AATATATATATTATATGAAATGTGATA
37728 AATATATATATATATAT-AAATGTGATA
1 AATATATATAT-TATATGAAATGTGATA
37755 AATAT
1 AATAT
37760 GTGAAATAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 16 0.57
27 12 0.43
ACGTcount: A:0.47, C:0.00, G:0.10, T:0.43
Consensus pattern (27 bp):
AATATATATATTATATGAAATGTGATA
Found at i:38067 original size:28 final size:26
Alignment explanation
Indices: 38036--38099 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 26
38026 ATGTGATTAG
38036 ATGAGAAATGAACATGAGATATATGAAT
1 ATGAGAAATG-ACATG-GATATATGAAT
* *
38064 ATGAATGAAATGATATGGTTATATGAAT
1 ATG-A-GAAATGACATGGATATATGAAT
38092 ATGAGAAA
1 ATGAGAAA
38100 AGGTATATGT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
26 4 0.12
27 1 0.03
28 16 0.50
29 5 0.16
30 6 0.19
ACGTcount: A:0.48, C:0.02, G:0.22, T:0.28
Consensus pattern (26 bp):
ATGAGAAATGACATGGATATATGAAT
Found at i:38074 original size:30 final size:28
Alignment explanation
Indices: 38040--38095 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
38030 GATTAGATGA
38040 GAAATGAACATGAGATATATGAATATGAAT
1 GAAATG-ACATG-GATATATGAATATGAAT
* *
38070 GAAATGATATGGTTATATGAATATGA
1 GAAATGACATGGATATATGAATATGA
38096 GAAAAGGTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 14 0.58
29 4 0.17
30 6 0.25
ACGTcount: A:0.46, C:0.02, G:0.21, T:0.30
Consensus pattern (28 bp):
GAAATGACATGGATATATGAATATGAAT
Found at i:38107 original size:28 final size:27
Alignment explanation
Indices: 38055--38108 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 27
38045 GAACATGAGA
*
38055 TATATGAATATGAATGAAATGATATGGT
1 TATATGAATATGAA-GAAAGGATATGGT
38083 TATATGAATATG-AGAAAAGGTATATG
1 TATATGAATATGAAG-AAAGG-ATATG
38109 TGATAAGATG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 1 0.04
27 5 0.22
28 17 0.74
ACGTcount: A:0.44, C:0.00, G:0.22, T:0.33
Consensus pattern (27 bp):
TATATGAATATGAAGAAAGGATATGGT
Found at i:38328 original size:32 final size:32
Alignment explanation
Indices: 38278--38470 Score: 284
Period size: 32 Copynumber: 6.1 Consensus size: 32
38268 CTTTCGAGAT
* * *
38278 ATATGGATA-GATTACCTATGTTATTCGGAAT
1 ATATGGACAGGATTACCTATGTTCTTCGGAAC
38309 ATATGGACAGGATTACCTATGTTCTTCGGAAC
1 ATATGGACAGGATTACCTATGTTCTTCGGAAC
38341 ATATGGACAGGATTACCTATGTTCTTCGGAAC
1 ATATGGACAGGATTACCTATGTTCTTCGGAAC
*
38373 ATATGGACATGATTACCTATGTTCTTCGGAAC
1 ATATGGACAGGATTACCTATGTTCTTCGGAAC
* * *
38405 ATATGAATAGGATTACCTATGTTCTCCGGAAC
1 ATATGGACAGGATTACCTATGTTCTTCGGAAC
* *
38437 ATATAGACA--ATTACCTATGTTATTCGGAAC
1 ATATGGACAGGATTACCTATGTTCTTCGGAAC
38467 ATAT
1 ATAT
38471 AGATAGGTCA
Statistics
Matches: 148, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
30 23 0.16
31 8 0.05
32 117 0.79
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.34
Consensus pattern (32 bp):
ATATGGACAGGATTACCTATGTTCTTCGGAAC
Found at i:42182 original size:24 final size:24
Alignment explanation
Indices: 42155--42200 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
42145 ATAAGTCTAG
*
42155 ATTTAATATCT-TGATACATGATTT
1 ATTTAATAT-TATGAAACATGATTT
42179 ATTTAATATTATGAAACATGAT
1 ATTTAATATTATGAAACATGAT
42201 ATGAATTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.46
Consensus pattern (24 bp):
ATTTAATATTATGAAACATGATTT
Found at i:42506 original size:2 final size:2
Alignment explanation
Indices: 42501--42538 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
42491 TATATATATA
42501 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
42539 ATAAATATGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:43121 original size:32 final size:32
Alignment explanation
Indices: 43063--43324 Score: 386
Period size: 32 Copynumber: 8.3 Consensus size: 32
43053 GTCTTTCGAG
* *
43063 ACATATGGATA-GATTACCTATATTCTTCGGA
1 ACATATGGACAGGATTACCTATGTTCTTCGGA
* *
43094 ACATATGGACATGATTATCTATGTTCTTCGGA
1 ACATATGGACAGGATTACCTATGTTCTTCGGA
*
43126 ATATATGGACAGGATTACCTATGTTCTTCGGA
1 ACATATGGACAGGATTACCTATGTTCTTCGGA
* *
43158 ATATATGGACAGGATTACCTATGTTCTTTGGA
1 ACATATGGACAGGATTACCTATGTTCTTCGGA
* *
43190 ACATATGGACATGATTACCTATGTTCTTCGAA
1 ACATATGGACAGGATTACCTATGTTCTTCGGA
*
43222 ACATATGGATAGGATTACCTATGTTCTTCGGA
1 ACATATGGACAGGATTACCTATGTTCTTCGGA
* * *
43254 ACATATGGACATGATTACCTATGTTCTCCAGA
1 ACATATGGACAGGATTACCTATGTTCTTCGGA
43286 ACATATGGACA--ATTACCTATGTTCTTCGGA
1 ACATATGGACAGGATTACCTATGTTCTTCGGA
43316 ACATATGGA
1 ACATATGGA
43325 TAGTCTCTTC
Statistics
Matches: 210, Mismatches: 20, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
30 26 0.12
31 10 0.05
32 174 0.83
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (32 bp):
ACATATGGACAGGATTACCTATGTTCTTCGGA
Found at i:44183 original size:4 final size:4
Alignment explanation
Indices: 44147--45805 Score: 3043
Period size: 4 Copynumber: 416.8 Consensus size: 4
44137 TGTAACAAAT
* * * * * *
44147 ATAC -TAC ATAT ATAC ATAT ATAC ATAT ATAC ATAC ATGC ATAT ATGC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * * * * *
44194 ATAT ATAC ATAC GTAC GTAC GTAC ATAC GTAC ATAC GTAC ATAC GTAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * *
44242 ATAC GTAC ATAC GTAC ATAC GTAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
44290 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
44338 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
44386 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* *
44434 ATAC ACAT ATAC ATAC ATAC ATAC ATAC ATAC AATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC -ATAC ATAC ATAC ATAC
44483 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
44531 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
44579 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
44627 ATAC ATAC ATAC ATAC ATAC ATAC ATAAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC AT-AC ATAC ATAC ATAC ATAC ATAC
44676 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A-AC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
44723 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC -TAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
44770 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
44818 -TAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
44865 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
44913 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
44961 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC -TAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
45008 ATAC ATAC ATAC ATAC -TAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
45055 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
45103 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC -TAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
45150 ATAC ATAC ATAC AT-- ATAC ATA- ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
45195 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
45243 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
45291 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
45339 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
45387 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC -TAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
45434 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
45482 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
45530 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
45578 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
45626 ATAC AGAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
45674 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
45722 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
45770 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATTAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC A-TAC ATA
45806 TACTCTATTC
Statistics
Matches: 1607, Mismatches: 34, Indels: 28
0.96 0.02 0.02
Matches are distributed among these distances:
2 2 0.00
3 27 0.02
4 1566 0.97
5 12 0.01
ACGTcount: A:0.49, C:0.25, G:0.01, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:46182 original size:18 final size:19
Alignment explanation
Indices: 46154--46248 Score: 97
Period size: 18 Copynumber: 5.0 Consensus size: 19
46144 CACTGAGTAT
46154 TTGTCCCGAAGGACCACTA
1 TTGTCCCGAAGGACCACTA
*
46173 -TGTCCTGAAGGACCACTGA
1 TTGTCCCGAAGGACCACT-A
* *
46192 TTGTTCCGAAGAACCACTA
1 TTGTCCCGAAGGACCACTA
*
46211 -TGTCCCAAAGGACCA-TA
1 TTGTCCCGAAGGACCACTA
*
46228 GTTTGTCCTGAAGGACCACTA
1 --TTGTCCCGAAGGACCACTA
46249 ATAATCTCTC
Statistics
Matches: 61, Mismatches: 9, Indels: 10
0.76 0.11 0.12
Matches are distributed among these distances:
17 2 0.03
18 28 0.46
19 2 0.03
20 27 0.44
21 2 0.03
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.23
Consensus pattern (19 bp):
TTGTCCCGAAGGACCACTA
Found at i:46202 original size:38 final size:38
Alignment explanation
Indices: 46154--46248 Score: 113
Period size: 38 Copynumber: 2.5 Consensus size: 38
46144 CACTGAGTAT
* **
46154 TTGTCCCGAAGGACCACTATGTCCTGAAGGACCACT-GA
1 TTGTTCCGAAGGACCACTATGTCCCAAAGGACCA-TAGA
* *
46192 TTGTTCCGAAGAACCACTATGTCCCAAAGGACCATAGT
1 TTGTTCCGAAGGACCACTATGTCCCAAAGGACCATAGA
46230 TTG-TCCTGAAGGACCACTA
1 TTGTTCC-GAAGGACCACTA
46249 ATAATCTCTC
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
37 4 0.08
38 45 0.92
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.23
Consensus pattern (38 bp):
TTGTTCCGAAGGACCACTATGTCCCAAAGGACCATAGA
Found at i:53768 original size:23 final size:23
Alignment explanation
Indices: 53717--53761 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
53707 ATGACTGAAT
53717 CTGTTTTGATGTATGTACTGTAA
1 CTGTTTTGATGTATGTACTGTAA
* *
53740 CTGTTTTGATGTCTGTATTGTA
1 CTGTTTTGATGTATGTACTGTA
53762 GTAGTTTACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.18, C:0.09, G:0.22, T:0.51
Consensus pattern (23 bp):
CTGTTTTGATGTATGTACTGTAA
Found at i:57184 original size:33 final size:33
Alignment explanation
Indices: 57142--57272 Score: 181
Period size: 33 Copynumber: 4.0 Consensus size: 33
57132 AGGAGGACCA
* *
57142 CCTCTTGCTCCTCTAGGCGAGTAGTCTTCCCTG
1 CCTCTTCCTCCTCTAGGAGAGTAGTCTTCCCTG
* *
57175 CCTCTTGCTCCTCTGGGAGAGTAGTCTTCCCTG
1 CCTCTTCCTCCTCTAGGAGAGTAGTCTTCCCTG
* *
57208 CCTCTTCCTCCTCTGGGAGAGTAATCTTCCCTG
1 CCTCTTCCTCCTCTAGGAGAGTAGTCTTCCCTG
* **
57241 CCTCTTCCTCCTCTAGAAGAAAAGTCTTCCCT
1 CCTCTTCCTCCTCTAGGAGAGTAGTCTTCCCT
57273 ACGAGGAGGA
Statistics
Matches: 89, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 89 1.00
ACGTcount: A:0.13, C:0.36, G:0.18, T:0.33
Consensus pattern (33 bp):
CCTCTTCCTCCTCTAGGAGAGTAGTCTTCCCTG
Done.