Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002402.1 Hibiscus syriacus cultivar Beakdansim tig00004913_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: 127585
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:11401 original size:30 final size:30
Alignment explanation
Indices: 11365--11426 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
11355 TAGCTACATA
11365 ATACTCAACATTCAATATAATTGTTAATTC
1 ATACTCAACATTCAATATAATTGTTAATTC
* * *
11395 ATACTCAACATTCATTATACTTGTTGATTC
1 ATACTCAACATTCAATATAATTGTTAATTC
11425 AT
1 AT
11427 GTTAAGTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.35, C:0.18, G:0.05, T:0.42
Consensus pattern (30 bp):
ATACTCAACATTCAATATAATTGTTAATTC
Found at i:29416 original size:15 final size:15
Alignment explanation
Indices: 29396--29425 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
29386 TACCTGCAAT
29396 GGTTGGTGCTGGTGC
1 GGTTGGTGCTGGTGC
29411 GGTTGGTGCTGGTGC
1 GGTTGGTGCTGGTGC
29426 TCTGGCTGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.13, G:0.53, T:0.33
Consensus pattern (15 bp):
GGTTGGTGCTGGTGC
Found at i:29450 original size:15 final size:15
Alignment explanation
Indices: 29397--29456 Score: 59
Period size: 15 Copynumber: 4.0 Consensus size: 15
29387 ACCTGCAATG
* *
29397 GTTGGTGCTGGTGCG
1 GTTGGTGCCGGTGCT
*
29412 GTTGGTGCTGGTGCT
1 GTTGGTGCCGGTGCT
*
29427 -CTGGCTGCCGGTGCT
1 GTTGG-TGCCGGTGCT
*
29442 GTTGGTGCCGCTGCT
1 GTTGGTGCCGGTGCT
29457 TTAAAAGGAG
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
14 3 0.08
15 32 0.84
16 3 0.08
ACGTcount: A:0.00, C:0.22, G:0.45, T:0.33
Consensus pattern (15 bp):
GTTGGTGCCGGTGCT
Found at i:30430 original size:102 final size:102
Alignment explanation
Indices: 30304--30855 Score: 604
Period size: 102 Copynumber: 5.4 Consensus size: 102
30294 GAAGCAATTA
* ** * * ** **
30304 AAGGAAGTGGTGATGGCAAGGGAAAAGGGAAAGGTGGGGGTCGTTTAAGTGGTGGTGGAGATGTT
1 AAGGAGGTGGTGATGGGGAGGGAAAAGGGAAAGGTGAGGGTAGTGCAAGTGGTGGTGGAGATACT
*
30369 GGTGGCTCTATTAAGGCTAGTTATGGAGGTAAAGTTG
66 GGTGGCTCTATTAAGGCTAGTTCTGGAGGTAAAGTTG
*
30406 AAGGAGGTGGTGATGGGGAAGGAAAAGGAAAAGGAAAAGGTGAGGGTAGTGCAAGTGGTGGTGGA
1 AAGGAGGTGGTGATGGGG-A-G----GGAAAAGGGAAAGGTGAGGGTAGTGCAAGTGGTGGTGGA
* * * *
30471 GACT-CTAGTGGCTCTATTAAGGCTAGTTTTGAAGGTGAAGTTG
60 GA-TACTGGTGGCTCTATTAAGGCTAGTTCTGGAGGTAAAGTTG
* * * * * *
30514 AAGGAGGTGGTGATGGGGAGGGAAAAGGAAAAGTTGATGGTAGTGCAAGTGGAGGTGAAGACACT
1 AAGGAGGTGGTGATGGGGAGGGAAAAGGGAAAGGTGAGGGTAGTGCAAGTGGTGGTGGAGATACT
*
30579 AGTGGCTCTATTAAGGCTAGTTCTGGAGGTAAAGTTG
66 GGTGGCTCTATTAAGGCTAGTTCTGGAGGTAAAGTTG
* * * ** * ** **
30616 AAGGAGGTGGTGATAGGGAGGGAAAAAGGAAAGTTGAGGGTAGCACAAATGGTGGTAAAGGCACT
1 AAGGAGGTGGTGATGGGGAGGGAAAAGGGAAAGGTGAGGGTAGTGCAAGTGGTGGTGGAGATACT
* *
30681 GGTGACTCTATTAAGGCTAGTTCTGGAGGTAAAATTG
66 GGTGGCTCTATTAAGGCTAGTTCTGGAGGTAAAGTTG
* * * * **
30718 AAGGAGGTGGTGATGGCGAGGGAAAAGGGAAAGTTGGGGGTAGTGCAAGCGGTGGTGGAGATGTT
1 AAGGAGGTGGTGATGGGGAGGGAAAAGGGAAAGGTGAGGGTAGTGCAAGTGGTGGTGGAGATACT
* * *
30783 GGTAGCTCTATTAAGGTTAGTTCT-AAGGGTAAAGTTG
66 GGTGGCTCTATTAAGGCTAGTTCTGGA-GGTAAAGTTG
* * *
30820 AAGGAAGTGGTGATGGAGAGGGAAAAGGGCAAGGTG
1 AAGGAGGTGGTGATGGGGAGGGAAAAGGGAAAGGTG
30856 GAGAGGTCGG
Statistics
Matches: 384, Mismatches: 57, Indels: 18
0.84 0.12 0.04
Matches are distributed among these distances:
101 1 0.00
102 290 0.76
103 1 0.00
104 1 0.00
106 1 0.00
107 1 0.00
108 88 0.23
109 1 0.00
ACGTcount: A:0.30, C:0.06, G:0.42, T:0.22
Consensus pattern (102 bp):
AAGGAGGTGGTGATGGGGAGGGAAAAGGGAAAGGTGAGGGTAGTGCAAGTGGTGGTGGAGATACT
GGTGGCTCTATTAAGGCTAGTTCTGGAGGTAAAGTTG
Found at i:31353 original size:54 final size:54
Alignment explanation
Indices: 31280--31406 Score: 218
Period size: 54 Copynumber: 2.4 Consensus size: 54
31270 AAGATGAGAT
* * *
31280 TGGTGGAACTGGTAGTGGAAGTGTTTCTGTTGAGGGAAAAGGGCAGGGTGTAGG
1 TGGTGCAAGTGGTGGTGGAAGTGTTTCTGTTGAGGGAAAAGGGCAGGGTGTAGG
*
31334 TGGTGCAAGTGGTGGTGGAAGTGTTTCTGTTGAGGGGAAAGGGCAGGGTGTAGG
1 TGGTGCAAGTGGTGGTGGAAGTGTTTCTGTTGAGGGAAAAGGGCAGGGTGTAGG
31388 TGGTGCAAGTGGTGGTGGA
1 TGGTGCAAGTGGTGGTGGA
31407 GACTCTGGTG
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 69 1.00
ACGTcount: A:0.20, C:0.06, G:0.49, T:0.26
Consensus pattern (54 bp):
TGGTGCAAGTGGTGGTGGAAGTGTTTCTGTTGAGGGAAAAGGGCAGGGTGTAGG
Found at i:33867 original size:74 final size:79
Alignment explanation
Indices: 33778--33935 Score: 227
Period size: 82 Copynumber: 2.0 Consensus size: 79
33768 TTGAAGGTGG
33778 TAAACACAAGGATC-A-ATG-G-TAGCAGACCTATAAACTGGATAACAGATACATGAACTAA-CC
1 TAAACACAAGGATCAAGATGAGCTAGCAGACCTATAAACTGGATAACAGATACATGAACTAACCC
33838 ATGAAAACCAGTGT
66 ATGAAAACCAGTGT
* *
33852 TAAACACAAGGATCAATGGATGCTAGCTAGCAGATCTATAAGCTGGATAACAGATACATGAACTA
1 TAAACACAAGGATCAA--GATG--AGCTAGCAGACCTATAAACTGGATAACAGATACATGAACTA
33917 ACCCATGAAAACCAGTGT
62 ACCCATGAAAACCAGTGT
33935 T
1 T
33936 TGTTTACGGA
Statistics
Matches: 73, Mismatches: 2, Indels: 9
0.87 0.02 0.11
Matches are distributed among these distances:
74 14 0.19
75 1 0.01
78 3 0.04
81 1 0.01
82 37 0.51
83 17 0.23
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.20
Consensus pattern (79 bp):
TAAACACAAGGATCAAGATGAGCTAGCAGACCTATAAACTGGATAACAGATACATGAACTAACCC
ATGAAAACCAGTGT
Found at i:34695 original size:39 final size:40
Alignment explanation
Indices: 34615--34704 Score: 112
Period size: 39 Copynumber: 2.3 Consensus size: 40
34605 CATGATACTG
* ** * *
34615 AAATAAAA-TAAAAACTAAAGTTTTTAACGGTGAGTATTA
1 AAATAAAACAAAAAACTAAAGTTTTTAACGCAGAGCACTA
*
34654 AAATAAAACAAAAAACTAAAGTTTTTAATGCAGA-CACTA
1 AAATAAAACAAAAAACTAAAGTTTTTAACGCAGAGCACTA
34693 AAATAAAACAAA
1 AAATAAAACAAA
34705 GGCTATTTAG
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
39 23 0.52
40 21 0.48
ACGTcount: A:0.58, C:0.09, G:0.09, T:0.24
Consensus pattern (40 bp):
AAATAAAACAAAAAACTAAAGTTTTTAACGCAGAGCACTA
Found at i:40144 original size:18 final size:18
Alignment explanation
Indices: 40121--40159 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
40111 TCTTACTCTC
40121 TTTGTTGTTTATATATGT
1 TTTGTTGTTTATATATGT
40139 TTTGTTGTTTATATATGT
1 TTTGTTGTTTATATATGT
40157 TTT
1 TTT
40160 CAGGGGTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.69
Consensus pattern (18 bp):
TTTGTTGTTTATATATGT
Found at i:40168 original size:20 final size:18
Alignment explanation
Indices: 40127--40169 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
40117 TCTCTTTGTT
**
40127 GTTTATATATGTTTTGTT
1 GTTTATATATGTTTTGGG
40145 GTTTATATATGTTTTCAGGG
1 GTTTATATATGTTTT--GGG
40165 GTTTA
1 GTTTA
40170 GCATTAGGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 15 0.71
20 6 0.29
ACGTcount: A:0.19, C:0.02, G:0.21, T:0.58
Consensus pattern (18 bp):
GTTTATATATGTTTTGGG
Found at i:45800 original size:21 final size:21
Alignment explanation
Indices: 45771--45824 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
45761 TTAATCTAGA
* * *
45771 GAACTATCGGCCCAGCGGAAT
1 GAACAATCGGCCAAGCAGAAT
45792 GAACAATCGGCCAAGCAGAAT
1 GAACAATCGGCCAAGCAGAAT
45813 GAACAATCGGCC
1 GAACAATCGGCC
45825 GACTCGGCTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.35, C:0.28, G:0.26, T:0.11
Consensus pattern (21 bp):
GAACAATCGGCCAAGCAGAAT
Found at i:48799 original size:31 final size:31
Alignment explanation
Indices: 48761--48914 Score: 274
Period size: 31 Copynumber: 5.0 Consensus size: 31
48751 GGGTCGAGGG
48761 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
48792 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
48823 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
48854 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
48885 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
48915 GTCCTTCGGG
Statistics
Matches: 120, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
31 119 0.99
32 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:50073 original size:58 final size:58
Alignment explanation
Indices: 50011--50134 Score: 239
Period size: 58 Copynumber: 2.1 Consensus size: 58
50001 ATAGTCGAGA
50011 GACCATTTATAACTTTTAATAATCAGGGAACTCAACAAAAAATGTCTTATAGTCAAAG
1 GACCATTTATAACTTTTAATAATCAGGGAACTCAACAAAAAATGTCTTATAGTCAAAG
*
50069 GACCATTTATAACTTTTAATAATCAGGGAACTCAATAAAAAATGTCTTATAGTCAAAG
1 GACCATTTATAACTTTTAATAATCAGGGAACTCAACAAAAAATGTCTTATAGTCAAAG
50127 GACCATTT
1 GACCATTT
50135 GTATACTTAA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 65 1.00
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.31
Consensus pattern (58 bp):
GACCATTTATAACTTTTAATAATCAGGGAACTCAACAAAAAATGTCTTATAGTCAAAG
Found at i:56655 original size:27 final size:27
Alignment explanation
Indices: 56595--56665 Score: 74
Period size: 27 Copynumber: 2.6 Consensus size: 27
56585 TAAGGTTCAT
* **
56595 GGGTATTTTGGTTATTTCAATACTTGA
1 GGGTATTTTAGTTATTTCAATACTCAA
*
56622 GGTTATTTTAGTTATTTCAA-AGCTCAA
1 GGGTATTTTAGTTATTTCAATA-CTCAA
56649 GGGTA-TTTAGATTATTT
1 GGGTATTTTAG-TTATTT
56666 TCTTTGATTC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
26 6 0.16
27 31 0.84
ACGTcount: A:0.25, C:0.07, G:0.20, T:0.48
Consensus pattern (27 bp):
GGGTATTTTAGTTATTTCAATACTCAA
Found at i:58913 original size:30 final size:30
Alignment explanation
Indices: 58879--59009 Score: 138
Period size: 30 Copynumber: 4.4 Consensus size: 30
58869 TCGCATGTAT
*
58879 ATGTCAGAACGGGGAGTTTATCCTATATAA
1 ATGTCAGAACGGGGAGTTTATCCTATACAA
** *
58909 ATGTCAGAACATGGAGTTTATCCTATATAA
1 ATGTCAGAACGGGGAGTTTATCCTATACAA
* * *
58939 ATGTTAGAACGGGGAGTTTATCAC-ATGCAT
1 ATGTCAGAACGGGGAGTTTATC-CTATACAA
* * * * *
58969 ATGTTAGAACGAGGAGTTTATCCCATGCAG
1 ATGTCAGAACGGGGAGTTTATCCTATACAA
58999 ATGTCAGAACG
1 ATGTCAGAACG
59010 AGTAATTTAC
Statistics
Matches: 88, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
29 1 0.01
30 86 0.98
31 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.29
Consensus pattern (30 bp):
ATGTCAGAACGGGGAGTTTATCCTATACAA
Found at i:61877 original size:4 final size:4
Alignment explanation
Indices: 61868--61895 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
61858 CTCAAAATAC
61868 TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG
61896 CATTTACGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:66349 original size:42 final size:42
Alignment explanation
Indices: 66303--66482 Score: 134
Period size: 42 Copynumber: 4.3 Consensus size: 42
66293 TTTTTTAGAC
*
66303 AAACGCCAC-ATAAAGGTTAAACA-ATAGCGGCGTTTATAGTAA
1 AAACGCCACAATAAA-G-TAAACATATAGCGGCATTTATAGTAA
* * * *
66345 AAACGCCGCAATATAGTAGACATGTAGCGGCATTTATAGTAA
1 AAACGCCACAATAAAGTAAACATATAGCGGCATTTATAGTAA
* * * * *
66387 AAACGCCGCAATATAGTAGACATGTAGCGGCGTTT-TAGCT-A
1 AAACGCCACAATAAAGTAAACATATAGCGGCATTTATAG-TAA
* * * * * * **
66428 AAACGCCGCAATATATTTAACATTTAGCGGCGTTTATACCAA
1 AAACGCCACAATAAAGTAAACATATAGCGGCATTTATAGTAA
*
66470 AAACGCCGCAATA
1 AAACGCCACAATA
66483 GAGTGGTAAA
Statistics
Matches: 121, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
41 40 0.33
42 77 0.64
43 4 0.03
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (42 bp):
AAACGCCACAATAAAGTAAACATATAGCGGCATTTATAGTAA
Found at i:66361 original size:19 final size:19
Alignment explanation
Indices: 66337--66404 Score: 57
Period size: 19 Copynumber: 3.4 Consensus size: 19
66327 TAGCGGCGTT
66337 TATAGTAAAAACGCCGCAA
1 TATAGTAAAAACGCCGCAA
* * *
66356 TATAGTAGACATGTA-GCGGCATT
1 TATAGTA-A-A--AACGCCGCA-A
66379 TATAGTAAAAACGCCGCAA
1 TATAGTAAAAACGCCGCAA
66398 TATAGTA
1 TATAGTA
66405 GACATGTAGC
Statistics
Matches: 37, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
19 15 0.41
20 6 0.16
21 2 0.05
22 6 0.16
23 8 0.22
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.24
Consensus pattern (19 bp):
TATAGTAAAAACGCCGCAA
Found at i:66456 original size:41 final size:42
Alignment explanation
Indices: 66327--66482 Score: 228
Period size: 42 Copynumber: 3.7 Consensus size: 42
66317 GGTTAAACAA
66327 TAGCGGCGTTTATAGTAAAAACGCCGCAATATAGTAGACATG
1 TAGCGGCGTTTATAGTAAAAACGCCGCAATATAGTAGACATG
*
66369 TAGCGGCATTTATAGTAAAAACGCCGCAATATAGTAGACATG
1 TAGCGGCGTTTATAGTAAAAACGCCGCAATATAGTAGACATG
* *
66411 TAGCGGCGTTT-TAGCT-AAAACGCCGCAATATATTTA-ACATT
1 TAGCGGCGTTTATAG-TAAAAACGCCGCAATATA-GTAGACATG
**
66452 TAGCGGCGTTTATACCAAAAACGCCGCAATA
1 TAGCGGCGTTTATAGTAAAAACGCCGCAATA
66483 GAGTGGTAAA
Statistics
Matches: 104, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
41 34 0.33
42 70 0.67
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (42 bp):
TAGCGGCGTTTATAGTAAAAACGCCGCAATATAGTAGACATG
Found at i:66458 original size:83 final size:84
Alignment explanation
Indices: 66327--66482 Score: 228
Period size: 83 Copynumber: 1.9 Consensus size: 84
66317 GGTTAAACAA
**
66327 TAGCGGCGTTTATAGTAAAAACGCCGCAATATAGTAGACATGTAGCGGCATTTATAGTAAAAACG
1 TAGCGGCGTTTATAGTAAAAACGCCGCAATATAGTAGACATGTAGCGGCATTTATACCAAAAACG
66392 CCGCAATATAGTAGACATG
66 CCGCAATATAGTAGACATG
* * *
66411 TAGCGGCGTTT-TAGCT-AAAACGCCGCAATATATTTA-ACATTTAGCGGCGTTTATACCAAAAA
1 TAGCGGCGTTTATAG-TAAAAACGCCGCAATATA-GTAGACATGTAGCGGCATTTATACCAAAAA
66473 CGCCGCAATA
64 CGCCGCAATA
66483 GAGTGGTAAA
Statistics
Matches: 65, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
83 51 0.78
84 14 0.22
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (84 bp):
TAGCGGCGTTTATAGTAAAAACGCCGCAATATAGTAGACATGTAGCGGCATTTATACCAAAAACG
CCGCAATATAGTAGACATG
Found at i:66505 original size:83 final size:83
Alignment explanation
Indices: 66344--66505 Score: 193
Period size: 83 Copynumber: 2.0 Consensus size: 83
66334 GTTTATAGTA
** *
66344 AAAACGCCGCAATATAGTAGACATGTAGCGGCATTTATAGTAAAAACGCCGCAATATAGTAGACA
1 AAAACGCCGCAATATAGTAGACATGTAGCGGCATTTATACCAAAAACGCCGCAATAGAGTAGACA
** * *
66409 TGTAGCGGCGTTTTAGCT
66 AATAGCAGAGTTTTAGCT
* * * *
66427 AAAACGCCGCAATATATTTA-ACATTTAGCGGCGTTTATACCAAAAACGCCGCAATAGAGTGGTA
1 AAAACGCCGCAATATA-GTAGACATGTAGCGGCATTTATACCAAAAACGCCGCAATAGAGTAG-A
66491 -AAATAGCAGAGTTTT
64 CAAATAGCAGAGTTTT
66506 TTGTATAAAT
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
83 63 0.95
84 3 0.05
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (83 bp):
AAAACGCCGCAATATAGTAGACATGTAGCGGCATTTATACCAAAAACGCCGCAATAGAGTAGACA
AATAGCAGAGTTTTAGCT
Found at i:67648 original size:52 final size:52
Alignment explanation
Indices: 67580--67738 Score: 291
Period size: 52 Copynumber: 3.1 Consensus size: 52
67570 TACTGAACAA
*
67580 TATGGTGAAGATTGTTTATGCATAAGTACTTTAATGTTTCTAAATTATAATG
1 TATGGTGAAGACTGTTTATGCATAAGTACTTTAATGTTTCTAAATTATAATG
*
67632 TATGTTGAAGACTGTTTATGCATAAGTACTTTAATGTTTCTAAATTATAATG
1 TATGGTGAAGACTGTTTATGCATAAGTACTTTAATGTTTCTAAATTATAATG
*
67684 TATGGTGAAGACTGTTTATGTATAAGTACTTTAATGTTTCTAAATTATAATG
1 TATGGTGAAGACTGTTTATGCATAAGTACTTTAATGTTTCTAAATTATAATG
67736 TAT
1 TAT
67739 TTTGTTGTTA
Statistics
Matches: 103, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 103 1.00
ACGTcount: A:0.33, C:0.06, G:0.16, T:0.45
Consensus pattern (52 bp):
TATGGTGAAGACTGTTTATGCATAAGTACTTTAATGTTTCTAAATTATAATG
Found at i:68017 original size:42 final size:40
Alignment explanation
Indices: 67967--68145 Score: 132
Period size: 41 Copynumber: 4.4 Consensus size: 40
67957 GCGGTTTTTT
*
67967 ACAAACGCCGCAATAGGTGTATTATATAGTCGCGTTCTTATA
1 ACAAACGCCGCAATAGGTGTATTAT-TAGTGGCGTT-TTATA
** *
68009 ACAAACGCCGCAAAATATTTGTATT-TTATTGGCGTTTTTAAATA
1 ACAAACGCCGC--AATAGGTGTATTATTAGTGGCG-TTTT--ATA
* ** *
68053 A-AAACGCCGCAAAAATTGT-TTATTAATGGCG-TTTATA
1 ACAAACGCCGCAATAGGTGTATTATTAGTGGCGTTTTATA
* * * * *
68090 ACAATCACCGCAATAGGTGTACTATATAGAGGCGTTTTTTA
1 ACAAACGCCGCAATAGGTGTATTAT-TAGTGGCGTTTTATA
*
68131 CCAAACGCCGCAATA
1 ACAAACGCCGCAATA
68146 TATTTGAATT
Statistics
Matches: 108, Mismatches: 19, Indels: 21
0.73 0.13 0.14
Matches are distributed among these distances:
37 4 0.04
38 13 0.12
39 6 0.06
40 8 0.07
41 32 0.30
42 19 0.18
43 12 0.11
44 14 0.13
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (40 bp):
ACAAACGCCGCAATAGGTGTATTATTAGTGGCGTTTTATA
Found at i:70174 original size:36 final size:37
Alignment explanation
Indices: 70134--70229 Score: 158
Period size: 36 Copynumber: 2.6 Consensus size: 37
70124 GCTATGCCTG
*
70134 CTGGTATGACTTCCCTTTTGCATCAATGTATG-CCCA
1 CTGGTATGACTTCCCTTTTGCATCAATCTATGCCCCA
**
70170 CTGGTATGACTTCCCTTTCACATCAATCTATGCCCCA
1 CTGGTATGACTTCCCTTTTGCATCAATCTATGCCCCA
70207 CTGGTATGACTTCCCTTTTGCAT
1 CTGGTATGACTTCCCTTTTGCAT
70230 GTTAGGTTCT
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
36 29 0.54
37 25 0.46
ACGTcount: A:0.19, C:0.30, G:0.15, T:0.36
Consensus pattern (37 bp):
CTGGTATGACTTCCCTTTTGCATCAATCTATGCCCCA
Found at i:70216 original size:37 final size:36
Alignment explanation
Indices: 70120--70224 Score: 147
Period size: 36 Copynumber: 2.9 Consensus size: 36
70110 TTGGTCAACC
* ** **
70120 TCAAGCTATGCCTGCTGGTATGACTTCCCTTTTGCA
1 TCAATCTATGCCCACTGGTATGACTTCCCTTTCACA
*
70156 TCAATGTATGCCCACTGGTATGACTTCCCTTTCACA
1 TCAATCTATGCCCACTGGTATGACTTCCCTTTCACA
70192 TCAATCTATGCCCCACTGGTATGACTTCCCTTT
1 TCAATCTATG-CCCACTGGTATGACTTCCCTTT
70225 TGCATGTTAG
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
36 39 0.64
37 22 0.36
ACGTcount: A:0.19, C:0.30, G:0.15, T:0.35
Consensus pattern (36 bp):
TCAATCTATGCCCACTGGTATGACTTCCCTTTCACA
Found at i:71146 original size:21 final size:21
Alignment explanation
Indices: 71122--71180 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
71112 TGATTTATTA
**
71122 TTATGGATTTTATTTTTCTTG
1 TTATGGATTTTAAGTTTCTTG
*
71143 TTATGGATTTTAAGTTTGTTG
1 TTATGGATTTTAAGTTTCTTG
* *
71164 TTATGGATGTCAAGTTT
1 TTATGGATTTTAAGTTT
71181 ATTGGAAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.19, C:0.03, G:0.20, T:0.58
Consensus pattern (21 bp):
TTATGGATTTTAAGTTTCTTG
Found at i:71396 original size:43 final size:43
Alignment explanation
Indices: 71383--71603 Score: 343
Period size: 43 Copynumber: 5.1 Consensus size: 43
71373 CTTTTGCAGT
* * *
71383 GTTTGTGGGAAAAACGTCGCTAAATCTCAAGACCTATTGCGAC
1 GTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTATTGCGGC
* *
71426 GTTTGTGGAAAAAACGCCGATAAATCTCAACACCTATTGCGGC
1 GTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTATTGCGGC
71469 GTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTATTGCGGC
1 GTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTATTGCGGC
* *
71512 GTTTGTGGGAAAAACGCCGCTAAATGTCAACACCTATTGTGGC
1 GTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTATTGCGGC
* * * *
71555 GTTTGTTGGAAAAATGCCGCCAAATATCAACACCTATTGCGGC
1 GTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTATTGCGGC
71598 GTTTGT
1 GTTTGT
71604 CCAACAAATG
Statistics
Matches: 164, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 164 1.00
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (43 bp):
GTTTGTGGGAAAAACGCCGCTAAATCTCAACACCTATTGCGGC
Found at i:71633 original size:86 final size:86
Alignment explanation
Indices: 71350--71644 Score: 306
Period size: 86 Copynumber: 3.4 Consensus size: 86
71340 GTTTGTTCTA
* * * * * * * * * *
71350 AAAAACGCCGCTATATA-CAAGATCTTTTGCAGTGTTTGTGGGAAAAACGTCGCTAAATCTCAAG
1 AAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTGGGAAAAACGCCGCCAAATATCAAC
* **
71414 ACCTATTGCGACGTTTGTGGA
66 ACCTATTGCGGCGTTTGTGCC
* * * *
71435 AAAAACGCCGATAAATCTCAACACCTATTGCGGCGTTTGTGGGAAAAACGCCGCTAAATCTCAAC
1 AAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTGGGAAAAACGCCGCCAAATATCAAC
**
71500 ACCTATTGCGGCGTTTGTGGG
66 ACCTATTGCGGCGTTTGTGCC
* * * *
71521 AAAAACGCCGCTAAATGTCAACACCTATTGTGGCGTTTGTTGGAAAAATGCCGCCAAATATCAAC
1 AAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTGGGAAAAACGCCGCCAAATATCAAC
71586 ACCTATTGCGGCGTTTGT-CC
66 ACCTATTGCGGCGTTTGTGCC
* * *** *
71606 AACAAATGCCGCTATATATCGTTACCTATTGCAGCGTTT
1 AA-AAACGCCGCTAAATATCAACACCTATTGCGGCGTTT
71645 TTTGTTACCA
Statistics
Matches: 179, Mismatches: 29, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
85 16 0.09
86 163 0.91
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (86 bp):
AAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTGGGAAAAACGCCGCCAAATATCAAC
ACCTATTGCGGCGTTTGTGCC
Found at i:71633 original size:129 final size:129
Alignment explanation
Indices: 71350--71644 Score: 344
Period size: 129 Copynumber: 2.3 Consensus size: 129
71340 GTTTGTTCTA
* * * * * * *
71350 AAAAACGCCGCTATATA-CAAGATCTTTTGCAGTGTTTGTGGGAAAAACGTCGCTAAATCTCAAG
1 AAAAACGCCGCTAAATATCAACACCTATTGCAGCGTTTGTGGGAAAAACGCCGCTAAATCTCAAC
* * **
71414 ACCTATTGCGACGTTTGTGGAAAAAACGCCGATAAATCTCAACACCTATTGCGGCGTTTGTGGG
66 ACCTATTGCGACGTTTGTGGAAAAAACGCCGACAAATATCAACACCTATTGCGGCGTTTGTGCC
* * *
71478 AAAAACGCCGCTAAATCTCAACACCTATTGCGGCGTTTGTGGGAAAAACGCCGCTAAATGTCAAC
1 AAAAACGCCGCTAAATATCAACACCTATTGCAGCGTTTGTGGGAAAAACGCCGCTAAATCTCAAC
* * * *
71543 ACCTATTGTGGCGTTTGTTGG-AAAAATGCCGCCAAATATCAACACCTATTGCGGCGTTTGT-CC
66 ACCTATTGCGACGTTTG-TGGAAAAAACGCCGACAAATATCAACACCTATTGCGGCGTTTGTGCC
* * ***
71606 AACAAATGCCGCTATATATCGTTACCTATTGCAGCGTTT
1 AA-AAACGCCGCTAAATATCAACACCTATTGCAGCGTTT
71645 TTTGTTACCA
Statistics
Matches: 139, Mismatches: 25, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
128 17 0.12
129 119 0.86
130 3 0.02
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (129 bp):
AAAAACGCCGCTAAATATCAACACCTATTGCAGCGTTTGTGGGAAAAACGCCGCTAAATCTCAAC
ACCTATTGCGACGTTTGTGGAAAAAACGCCGACAAATATCAACACCTATTGCGGCGTTTGTGCC
Found at i:80977 original size:16 final size:16
Alignment explanation
Indices: 80956--80988 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
80946 GAAGTGGTTT
80956 TAAGTGTGTTTTAAAA
1 TAAGTGTGTTTTAAAA
80972 TAAGTGTGTTTTAAAA
1 TAAGTGTGTTTTAAAA
80988 T
1 T
80989 GATAAATGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.45
Consensus pattern (16 bp):
TAAGTGTGTTTTAAAA
Found at i:81361 original size:22 final size:22
Alignment explanation
Indices: 81335--81376 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
81325 CAGATTGCTC
81335 AGAGGGAACCGATTCCCCCCCA
1 AGAGGGAACCGATTCCCCCCCA
*
81357 AGAGGGTACCGATTCCCCCC
1 AGAGGGAACCGATTCCCCCC
81377 TGAATGGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.24, C:0.40, G:0.24, T:0.12
Consensus pattern (22 bp):
AGAGGGAACCGATTCCCCCCCA
Found at i:86228 original size:20 final size:20
Alignment explanation
Indices: 86205--86292 Score: 70
Period size: 20 Copynumber: 4.3 Consensus size: 20
86195 TTGGGTATTA
*
86205 ATACCAACCTTTCGATATGG
1 ATACCAACCATTCGATATGG
* *
86225 ATACCCAA-TATTCAATATGG
1 ATA-CCAACCATTCGATATGG
** * *
86245 ATACCAGTTCATCCGGTATGG
1 ATACCA-ACCATTCGATATGG
* *
86266 ATACCAGCCATTCGATATGT
1 ATACCAACCATTCGATATGG
86286 ATACCAA
1 ATACCAA
86293 TTTATCGGTA
Statistics
Matches: 51, Mismatches: 14, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
19 3 0.06
20 30 0.59
21 18 0.35
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (20 bp):
ATACCAACCATTCGATATGG
Found at i:86266 original size:41 final size:41
Alignment explanation
Indices: 86220--86309 Score: 103
Period size: 41 Copynumber: 2.2 Consensus size: 41
86210 AACCTTTCGA
* *
86220 TATGGATACCCA-ATATTCAATATGGATACCAGTTCATCCGG
1 TATGGATACCCAGACATTCAATATGGATACCAATTCAT-CGG
* * * *
86261 TATGGATA-CCAGCCATTCGATATGTATACCAATTTATCGG
1 TATGGATACCCAGACATTCAATATGGATACCAATTCATCGG
86301 TATGGATAC
1 TATGGATAC
86310 AAGCCCACCG
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
40 14 0.34
41 27 0.66
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (41 bp):
TATGGATACCCAGACATTCAATATGGATACCAATTCATCGG
Found at i:86305 original size:61 final size:60
Alignment explanation
Indices: 86205--86332 Score: 141
Period size: 61 Copynumber: 2.1 Consensus size: 60
86195 TTGGGTATTA
* * ** *
86205 ATACCAACCTTTCGATATGGATACCCAATATTCAATATGGATACCAGTTCATCCGGTATGG
1 ATACCAACCATTCGATATGGATACCCAATATTCAATATGGATACAAGCCCA-CCGGTATCG
* * * **
86266 ATACCAGCCATTCGATATGTATA-CCAATTTATCGGTATGGATACAAGCCCACCGGTATCG
1 ATACCAACCATTCGATATGGATACCCAATAT-TCAATATGGATACAAGCCCACCGGTATCG
86326 ATACCAA
1 ATACCAA
86333 ATATCATATA
Statistics
Matches: 55, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
60 20 0.36
61 35 0.64
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.27
Consensus pattern (60 bp):
ATACCAACCATTCGATATGGATACCCAATATTCAATATGGATACAAGCCCACCGGTATCG
Found at i:87580 original size:2 final size:2
Alignment explanation
Indices: 87575--87602 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
87565 TTTATTAGTG
87575 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
87603 ATTTTGAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:90855 original size:115 final size:115
Alignment explanation
Indices: 90682--90901 Score: 315
Period size: 115 Copynumber: 1.9 Consensus size: 115
90672 GAAAAAATTA
* *
90682 TTAAATTTAATTCAAAATTGAATGAATAAATAAGAGAAATGGAAAAAGATGGTCAAAAACTAAAC
1 TTAAATTTAATTCAAAATTGAATGAATAAATAAAAGAAATGGAAAAAGATGGTCAAAAA-TAAAA
* *
90747 ATTTTATGAAATTAT-AAAATT-AGGGGCCTGAATTATAAATATAAAAATGG
65 AATTTATGAAATTATAAAAATTGAGGGCCCT-AATTATAAATATAAAAATGG
*
90797 TTAAATTTAATAT-AAAATTGAATGAATTAATAAAAGAAATGGAAAAA-AGTGGAT-AAAAATAA
1 TTAAATTTAAT-TCAAAATTGAATGAATAAATAAAAGAAATGGAAAAAGA-TGG-TCAAAAATAA
90859 AAAATTTATGAAATTATAAAAATTGAGGGCCCTAATTATAAAT
63 AAAATTTATGAAATTATAAAAATTGAGGGCCCTAATTATAAAT
90902 GGAAAAAATG
Statistics
Matches: 95, Mismatches: 5, Indels: 10
0.86 0.05 0.09
Matches are distributed among these distances:
114 19 0.20
115 67 0.71
116 9 0.09
ACGTcount: A:0.53, C:0.04, G:0.14, T:0.29
Consensus pattern (115 bp):
TTAAATTTAATTCAAAATTGAATGAATAAATAAAAGAAATGGAAAAAGATGGTCAAAAATAAAAA
ATTTATGAAATTATAAAAATTGAGGGCCCTAATTATAAATATAAAAATGG
Found at i:97714 original size:221 final size:221
Alignment explanation
Indices: 97331--97743 Score: 747
Period size: 221 Copynumber: 1.9 Consensus size: 221
97321 TGTGTTGTTG
* * *
97331 TGGCGTTGAATTGACCAAATACGGATCAGTTGAGACACCAAGTTATTCATCCAGACTGATGAGGA
1 TGGCGTTGAAATGACCAAATACGGATAAGTTAAGACACCAAGTTATTCATCCAGACTGATGAGGA
*
97396 GGGTGATGTTAAATGCAAACTTCTCTATGGAGTTGTTAGATGAATCCGATCATTTTGGCATGTGG
66 GGGTGATGTCAAATGCAAACTTCTCTATGGAGTTGTTAGATGAATCCGATCATTTTGGCATGTGG
97461 CAAGGCGAGGTGTTAGATGTTTTATTCCAACAAGGTCTAGACATCGCCATTGAAGAAGAAAATAT
131 CAAGGCGAGGTGTTAGATGTTTTATTCCAACAAGGTCTAGACATCGCCATTGAAGAAGAAAATAT
97526 CATGTTTGCTGTTGAATATTGTCCGT
196 CATGTTTGCTGTTGAATATTGTCCGT
*
97552 TGGCGTTGAAATGACCAAATACGGATAAGTTAAGACACCAAGTTCTTCATCCAGACTGATGAGGA
1 TGGCGTTGAAATGACCAAATACGGATAAGTTAAGACACCAAGTTATTCATCCAGACTGATGAGGA
*
97617 GGGTGATGTCAAATGCAAACTTCT-TGGTGGAGTTGTTAGATGAATCCGATCATTTTGGCATGTG
66 GGGTGATGTCAAATGCAAACTTCTCT-ATGGAGTTGTTAGATGAATCCGATCATTTTGGCATGTG
*
97681 GCAAGGTGAGGTGTTAGATGTTTTATTCCAACAAGGTCTAGACATCGCCATTGAAGAAGAAAA
130 GCAAGGCGAGGTGTTAGATGTTTTATTCCAACAAGGTCTAGACATCGCCATTGAAGAAGAAAA
97744 ACTTGTAGAT
Statistics
Matches: 184, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
220 1 0.01
221 183 0.99
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.29
Consensus pattern (221 bp):
TGGCGTTGAAATGACCAAATACGGATAAGTTAAGACACCAAGTTATTCATCCAGACTGATGAGGA
GGGTGATGTCAAATGCAAACTTCTCTATGGAGTTGTTAGATGAATCCGATCATTTTGGCATGTGG
CAAGGCGAGGTGTTAGATGTTTTATTCCAACAAGGTCTAGACATCGCCATTGAAGAAGAAAATAT
CATGTTTGCTGTTGAATATTGTCCGT
Found at i:101256 original size:19 final size:19
Alignment explanation
Indices: 101229--101265 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
101219 TGAGTGAACT
101229 GTTGAAGTCTGTTATGAAG
1 GTTGAAGTCTGTTATGAAG
*
101248 GTTGGAGTCTGTTATGAA
1 GTTGAAGTCTGTTATGAA
101266 TCTGTTATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.05, G:0.32, T:0.38
Consensus pattern (19 bp):
GTTGAAGTCTGTTATGAAG
Found at i:102421 original size:36 final size:36
Alignment explanation
Indices: 102369--102593 Score: 362
Period size: 36 Copynumber: 6.2 Consensus size: 36
102359 CTGCGTTTCT
* *
102369 AGTCAAACGGAAGGAGGCATCGGCACTTCCGATTCA
1 AGTCGAACGGAAGGAGGCATCGACACTTCCGATTCA
*
102405 AGTCGAACGGAAGGAGGCATCGGCACTTCCGATTCA
1 AGTCGAACGGAAGGAGGCATCGACACTTCCGATTCA
102441 AGTCGAACGGAAGGAGGCATCGACACTTCCGATTCA
1 AGTCGAACGGAAGGAGGCATCGACACTTCCGATTCA
102477 AGTCGAACGGAAGGAGGCATCGACACTTCCGATTCA
1 AGTCGAACGGAAGGAGGCATCGACACTTCCGATTCA
*
102513 AGTCGAACGGAAGGAGGCATC-AGCACTTCCGATTGA
1 AGTCGAACGGAAGGAGGCATCGA-CACTTCCGATTCA
* * *
102549 AATCGAACGGAAGGAAGCATCGACACTTCTGATTCA
1 AGTCGAACGGAAGGAGGCATCGACACTTCCGATTCA
*
102585 AATCGAACG
1 AGTCGAACG
102594 AACAGATGTA
Statistics
Matches: 180, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
35 1 0.01
36 178 0.99
37 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.28, T:0.17
Consensus pattern (36 bp):
AGTCGAACGGAAGGAGGCATCGACACTTCCGATTCA
Found at i:106334 original size:23 final size:23
Alignment explanation
Indices: 106308--106373 Score: 60
Period size: 27 Copynumber: 2.7 Consensus size: 23
106298 GTCTGATGTG
106308 GCAATTTCTAGAAGGTCCAGTCA
1 GCAATTTCTAGAAGGTCCAGTCA
* *
106331 GCAACAATCTTCTAGAAGATCTAGTCA
1 G---CAAT-TTCTAGAAGGTCCAGTCA
* *
106358 GCGACTTCTAGAAGGT
1 GCAATTTCTAGAAGGT
106374 GGACGGACAG
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
23 11 0.32
24 2 0.06
26 4 0.12
27 17 0.50
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (23 bp):
GCAATTTCTAGAAGGTCCAGTCA
Found at i:106343 original size:27 final size:26
Alignment explanation
Indices: 106309--106359 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
106299 TCTGATGTGG
*
106309 CAATTTCTAGAAGGTCCAGTCAGCAA
1 CAATTTCTAGAAGATCCAGTCAGCAA
*
106335 CAATCTTCTAGAAGATCTAGTCAGC
1 CAAT-TTCTAGAAGATCCAGTCAGC
106360 GACTTCTAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (26 bp):
CAATTTCTAGAAGATCCAGTCAGCAA
Found at i:112598 original size:13 final size:13
Alignment explanation
Indices: 112597--112639 Score: 77
Period size: 13 Copynumber: 3.3 Consensus size: 13
112587 CCGTTTACCC
112597 GACCCGACCCGTT
1 GACCCGACCCGTT
*
112610 TACCCGACCCGTT
1 GACCCGACCCGTT
112623 GACCCGACCCGTT
1 GACCCGACCCGTT
112636 GACC
1 GACC
112640 GTTGACCGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.16, C:0.47, G:0.21, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:112633 original size:18 final size:18
Alignment explanation
Indices: 112580--112620 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
112570 ACCGGTCACA
112580 ACCCGACCCGTTTACCCG
1 ACCCGACCCGTTTACCCG
112598 ACCCGACCCGTTTACCCG
1 ACCCGACCCGTTTACCCG
112616 ACCCG
1 ACCCG
112621 TTGACCCGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.17, C:0.51, G:0.17, T:0.15
Consensus pattern (18 bp):
ACCCGACCCGTTTACCCG
Found at i:115176 original size:24 final size:24
Alignment explanation
Indices: 115149--115243 Score: 118
Period size: 24 Copynumber: 4.0 Consensus size: 24
115139 ATTTCCGACT
** *
115149 TGAATTCTGTTCTGATAAATGACC
1 TGAATTCTGTTCTGATATCTGATC
*
115173 TGAATTCTGTTCTGATTTCTGATC
1 TGAATTCTGTTCTGATATCTGATC
* *
115197 TGGATTCTGTTCTGATATCTGTTC
1 TGAATTCTGTTCTGATATCTGATC
* *
115221 TGAATTCTGTTTTGATTTCTGAT
1 TGAATTCTGTTCTGATATCTGAT
115244 ATCTTCGTTT
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.19, C:0.15, G:0.18, T:0.48
Consensus pattern (24 bp):
TGAATTCTGTTCTGATATCTGATC
Found at i:115187 original size:12 final size:12
Alignment explanation
Indices: 115172--115241 Score: 79
Period size: 12 Copynumber: 5.8 Consensus size: 12
115162 GATAAATGAC
115172 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
115184 CTGATTTCTGAT
1 CTGAATTCTGTT
*
115196 CTGGATTCTGTT
1 CTGAATTCTGTT
115208 CTG-ATATCTGTT
1 CTGAAT-TCTGTT
115220 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
115232 TTGATTTCTG
1 CTGAATTCTG
115242 ATATCTTCGT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
11 2 0.04
12 45 0.92
13 2 0.04
ACGTcount: A:0.14, C:0.16, G:0.19, T:0.51
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:115240 original size:48 final size:48
Alignment explanation
Indices: 115135--115243 Score: 139
Period size: 48 Copynumber: 2.3 Consensus size: 48
115125 AAATATTTTA
* *
115135 TCTGATTTCCGA-CTTGAATTCTGTTCTGATAAATGACCTGAATTCTGT
1 TCTGATTTCTGATC-TGGATTCTGTTCTGATAAATGACCTGAATTCTGT
** **
115183 TCTGATTTCTGATCTGGATTCTGTTCTGATATCTGTTCTGAATTCTGT
1 TCTGATTTCTGATCTGGATTCTGTTCTGATAAATGACCTGAATTCTGT
*
115231 TTTGATTTCTGAT
1 TCTGATTTCTGAT
115244 ATCTTCGTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
48 52 0.98
49 1 0.02
ACGTcount: A:0.18, C:0.17, G:0.17, T:0.48
Consensus pattern (48 bp):
TCTGATTTCTGATCTGGATTCTGTTCTGATAAATGACCTGAATTCTGT
Found at i:117383 original size:13 final size:13
Alignment explanation
Indices: 117382--117438 Score: 71
Period size: 13 Copynumber: 4.3 Consensus size: 13
117372 CCGTTTACCC
117382 GACCCGACCCGTT
1 GACCCGACCCGTT
*
117395 TACCCGACCCGTT
1 GACCCGACCCGTT
117408 GA-CCGACCCGTT
1 GACCCGACCCGTT
*
117420 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
117435 GACC
1 GACC
117439 GTTGACCGGT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
12 12 0.32
13 14 0.37
15 12 0.32
ACGTcount: A:0.16, C:0.42, G:0.23, T:0.19
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:117383 original size:18 final size:18
Alignment explanation
Indices: 117360--117405 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
117350 ACCGGTCACA
117360 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTT
117378 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTT
117396 ACCCGACCCG
1 ACCCGACCCG
117406 TTGACCGACC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.17, C:0.52, G:0.17, T:0.13
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTT
Found at i:117415 original size:12 final size:12
Alignment explanation
Indices: 117385--117439 Score: 65
Period size: 12 Copynumber: 4.2 Consensus size: 12
117375 TTTACCCGAC
*
117385 CCGACCCGTTTA
1 CCGACCCGTTGA
117397 CCCGACCCGTTGA
1 -CCGACCCGTTGA
117410 CCGACCCGTTGA
1 CCGACCCGTTGA
117422 CCGTTGACCCGTTGA
1 CC---GACCCGTTGA
117437 CCG
1 CCG
117440 TTGACCGGTG
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
12 15 0.39
13 11 0.29
15 12 0.32
ACGTcount: A:0.15, C:0.42, G:0.24, T:0.20
Consensus pattern (12 bp):
CCGACCCGTTGA
Found at i:117427 original size:7 final size:7
Alignment explanation
Indices: 117415--117446 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
117405 GTTGACCGAC
117415 CCGTTGA
1 CCGTTGA
117422 CCGTTGA
1 CCGTTGA
117429 CCCGTTGA
1 -CCGTTGA
117437 CCGTTGA
1 CCGTTGA
117444 CCG
1 CCG
117447 GTGTTGACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.12, C:0.34, G:0.28, T:0.25
Consensus pattern (7 bp):
CCGTTGA
Found at i:117432 original size:15 final size:15
Alignment explanation
Indices: 117400--117445 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
117390 CCGTTTACCC
117400 GACCCGTTGACC---
1 GACCCGTTGACCGTT
117412 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
117427 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
117442 GACC
1 GACC
117446 GGTGTTGACC
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.39
15 19 0.61
ACGTcount: A:0.15, C:0.37, G:0.26, T:0.22
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:119974 original size:12 final size:12
Alignment explanation
Indices: 119959--120018 Score: 77
Period size: 12 Copynumber: 5.0 Consensus size: 12
119949 GATAAATGAC
119959 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
119971 CTGATTTCTGAT
1 CTGAATTCTGTT
*
119983 CTGGATTCTGTT
1 CTGAATTCTGTT
119995 CTG-ATATCTGTT
1 CTGAAT-TCTGTT
120007 CTGAATTCTGTT
1 CTGAATTCTGTT
120019 TTAATTTCTG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
11 2 0.05
12 37 0.90
13 2 0.05
ACGTcount: A:0.15, C:0.17, G:0.18, T:0.50
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:119978 original size:48 final size:48
Alignment explanation
Indices: 119922--120018 Score: 124
Period size: 48 Copynumber: 2.0 Consensus size: 48
119912 AAATATTTTA
119922 TCTGATTTCCGA-CTTGAATTCTGTTCTGATAAATGACCTGAATTCTGT
1 TCTGATTTCCGATC-TGAATTCTGTTCTGATAAATGACCTGAATTCTGT
* * ** **
119970 TCTGATTTCTGATCTGGATTCTGTTCTGATATCTGTTCTGAATTCTGT
1 TCTGATTTCCGATCTGAATTCTGTTCTGATAAATGACCTGAATTCTGT
120018 T
1 T
120019 TTAATTTCTG
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
48 41 0.98
49 1 0.02
ACGTcount: A:0.19, C:0.18, G:0.18, T:0.46
Consensus pattern (48 bp):
TCTGATTTCCGATCTGAATTCTGTTCTGATAAATGACCTGAATTCTGT
Found at i:120026 original size:48 final size:48
Alignment explanation
Indices: 119939--120030 Score: 130
Period size: 48 Copynumber: 1.9 Consensus size: 48
119929 TCCGACTTGA
*
119939 ATTCTGTTCTGATAAATGACCTGAATTCTGTTCTGATTTCTGATCTGG
1 ATTCTGTTCTGATAAATGACCTGAATTCTGTTCTAATTTCTGATCTGG
** ** *
119987 ATTCTGTTCTGATATCTGTTCTGAATTCTGTTTTAATTTCTGAT
1 ATTCTGTTCTGATAAATGACCTGAATTCTGTTCTAATTTCTGAT
120031 ATCTTCGTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 38 1.00
ACGTcount: A:0.20, C:0.15, G:0.16, T:0.49
Consensus pattern (48 bp):
ATTCTGTTCTGATAAATGACCTGAATTCTGTTCTAATTTCTGATCTGG
Found at i:120028 original size:24 final size:24
Alignment explanation
Indices: 119922--120030 Score: 112
Period size: 24 Copynumber: 4.5 Consensus size: 24
119912 AAATATTTTA
*
119922 TCTGATTTCCGA-CTTGAATTCTGT
1 TCTGATTTCTGATC-TGAATTCTGT
*** *
119946 TCTGATAAATGACCTGAATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
*
119970 TCTGATTTCTGATCTGGATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
* *
119994 TCTGATATCTGTTCTGAATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
* *
120018 TTTAATTTCTGAT
1 TCTGATTTCTGAT
120031 ATCTTCGTTT
Statistics
Matches: 68, Mismatches: 16, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
24 67 0.99
25 1 0.01
ACGTcount: A:0.19, C:0.17, G:0.17, T:0.48
Consensus pattern (24 bp):
TCTGATTTCTGATCTGAATTCTGT
Found at i:121354 original size:25 final size:24
Alignment explanation
Indices: 121325--121371 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
121315 ATTTTATGTT
121325 AGGATCGAATTTATAAAAATTTAAA
1 AGGATCG-ATTTATAAAAATTTAAA
*
121350 AGGATTGATTTATAAAAATTTA
1 AGGATCGATTTATAAAAATTTA
121372 GGGTCGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.49, C:0.02, G:0.13, T:0.36
Consensus pattern (24 bp):
AGGATCGATTTATAAAAATTTAAA
Found at i:122251 original size:35 final size:35
Alignment explanation
Indices: 122206--122284 Score: 97
Period size: 35 Copynumber: 2.3 Consensus size: 35
122196 CACTACAATC
* *
122206 ATTAATGACAACTTGTTGAACAG-GTCAAAAATACA
1 ATTATTGACAACTTGTTCAA-AGTGTCAAAAATACA
* *
122241 ATTATTGACAACTTGTTCAATGTGTCAAAAGTACA
1 ATTATTGACAACTTGTTCAAAGTGTCAAAAATACA
*
122276 ACTATTGAC
1 ATTATTGAC
122285 GTGGCCTGGA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
34 1 0.03
35 37 0.97
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.30
Consensus pattern (35 bp):
ATTATTGACAACTTGTTCAAAGTGTCAAAAATACA
Found at i:123165 original size:13 final size:14
Alignment explanation
Indices: 123139--123169 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
123129 GTGAAAATTT
123139 ATAAATATAAATAA
1 ATAAATATAAATAA
123153 ATAAATA-AAATAA
1 ATAAATATAAATAA
123166 ATAA
1 ATAA
123170 TAATTAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.59
14 7 0.41
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
ATAAATATAAATAA
Found at i:123539 original size:29 final size:31
Alignment explanation
Indices: 123504--123579 Score: 86
Period size: 29 Copynumber: 2.5 Consensus size: 31
123494 AAATACAAAT
* * *
123504 TAAAATTCAATGTTATAATTAA-ATAATTTC
1 TAAAATTCAATGATATAAATAATATAATATC
* *
123534 -AAAATT-TATAATATAAATAATATAATATC
1 TAAAATTCAATGATATAAATAATATAATATC
123563 TAAAATTCAATGATATA
1 TAAAATTCAATGATATA
123580 TGATATAGTT
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
28 10 0.28
29 13 0.36
30 6 0.17
31 7 0.19
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (31 bp):
TAAAATTCAATGATATAAATAATATAATATC
Found at i:123638 original size:35 final size:34
Alignment explanation
Indices: 123598--123675 Score: 131
Period size: 33 Copynumber: 2.3 Consensus size: 34
123588 TTTATCCTTA
123598 CTTAAAACACACAAATTCTTTTTTTGTAAATAGG
1 CTTAAAACACACAAATTCTTTTTTTGTAAATAGG
*
123632 CTTTAAA-ACACAAATTCTTTTTTTGTAAATAGG
1 CTTAAAACACACAAATTCTTTTTTTGTAAATAGG
123665 CTTAAATACAC
1 CTTAAA-ACAC
123676 TATTGCCTCA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
33 31 0.77
34 7 0.17
35 2 0.05
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (34 bp):
CTTAAAACACACAAATTCTTTTTTTGTAAATAGG
Found at i:124928 original size:30 final size:31
Alignment explanation
Indices: 124852--124937 Score: 88
Period size: 31 Copynumber: 2.8 Consensus size: 31
124842 TGAGGGACTA
* *
124852 AAATCGAACGAACCGATAACGTTAGAGATTG
1 AAATCGGACGGACCGATAACGTTAGAGATTG
* *
124883 AAATTGGATGGACCGATAATC-TTAGA-ACTT-
1 AAATCGGACGGACCGATAA-CGTTAGAGA-TTG
*
124913 AAATCGGACGGACCGATGACGTTAG
1 AAATCGGACGGACCGATAACGTTAG
124938 TGATCATTTC
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
29 1 0.02
30 21 0.47
31 22 0.49
32 1 0.02
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.22
Consensus pattern (31 bp):
AAATCGGACGGACCGATAACGTTAGAGATTG
Done.