Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012395.1 Kokia drynarioides strain JFW-HI SEQ_127399, 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: 119698
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Warning! 25 characters in sequence are not A, C, G, or T
Found at i:4637 original size:12 final size:12
Alignment explanation
Indices: 4616--4644 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
4606 GAGATGAAGG
4616 TTTT-GGAGTGT
1 TTTTGGGAGTGT
4627 TTTTGGGAGTGT
1 TTTTGGGAGTGT
4639 TTTTGG
1 TTTTGG
4645 ATGCACGAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.07, C:0.00, G:0.38, T:0.55
Consensus pattern (12 bp):
TTTTGGGAGTGT
Found at i:4769 original size:7 final size:7
Alignment explanation
Indices: 4757--4781 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
4747 AAATAGACCT
4757 AATTTTA
1 AATTTTA
4764 AATTTTA
1 AATTTTA
4771 AATTTTA
1 AATTTTA
4778 AATT
1 AATT
4782 ATTTAAGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
AATTTTA
Found at i:4803 original size:17 final size:16
Alignment explanation
Indices: 4765--4848 Score: 71
Period size: 16 Copynumber: 5.1 Consensus size: 16
4755 CTAATTTTAA
* *
4765 ATTTTAAATTTTAAATT
1 ATTTTAAA-TTGAATTT
4782 A-TTTAAGATTGAATTT
1 ATTTTAA-ATTGAATTT
*
4798 ATTTTAAATTTAATCTT
1 ATTTTAAATTGAAT-TT
**
4815 ATTTTGAGTTTGAATTT
1 ATTTT-AAATTGAATTT
*
4832 ATTTTAAATTAAATTT
1 ATTTTAAATTGAATTT
4848 A
1 A
4849 AACTTTTAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 9
0.75 0.12 0.12
Matches are distributed among these distances:
16 27 0.50
17 21 0.39
18 6 0.11
ACGTcount: A:0.37, C:0.01, G:0.06, T:0.56
Consensus pattern (16 bp):
ATTTTAAATTGAATTT
Found at i:4803 original size:33 final size:35
Alignment explanation
Indices: 4765--4841 Score: 106
Period size: 34 Copynumber: 2.3 Consensus size: 35
4755 CTAATTTTAA
4765 ATTTTAAATTTTAA-ATTA-TTTAAGATTGAATTT
1 ATTTTAAATTTTAATATTATTTTAAGATTGAATTT
* * *
4798 ATTTTAAA-TTTAATCTTATTTTGAGTTTGAATTT
1 ATTTTAAATTTTAATATTATTTTAAGATTGAATTT
4832 ATTTTAAATT
1 ATTTTAAATT
4842 AAATTTAAAC
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
32 5 0.13
33 11 0.29
34 21 0.55
35 1 0.03
ACGTcount: A:0.35, C:0.01, G:0.06, T:0.57
Consensus pattern (35 bp):
ATTTTAAATTTTAATATTATTTTAAGATTGAATTT
Found at i:6802 original size:29 final size:29
Alignment explanation
Indices: 6768--6921 Score: 168
Period size: 29 Copynumber: 5.3 Consensus size: 29
6758 TTCAAAACTC
* * *
6768 ACATTTTGGCCCTCAAACTTCTTAAAATT
1 ACATTTTTGCCCTCGAACTTCTAAAAATT
* * *
6797 ACATTTTT-TCCTCAAACTTCTCAAAAAAT
1 ACATTTTTGCCCTCGAACTTCT-AAAAATT
* *
6826 ACATTTTTTCCCTCGAACTTCCAAAAATT
1 ACATTTTTGCCCTCGAACTTCTAAAAATT
* * *
6855 ACATTTTTACCCCCGAACTTCCAAAAATT
1 ACATTTTTGCCCTCGAACTTCTAAAAATT
6884 ACATTTTTTGCTCC-CGAACTTCTAAAAATT
1 ACA-TTTTTGC-CCTCGAACTTCTAAAAATT
6914 ACATTTTT
1 ACATTTTT
6922 TTGAATTTTC
Statistics
Matches: 109, Mismatches: 12, Indels: 8
0.84 0.09 0.06
Matches are distributed among these distances:
28 12 0.11
29 61 0.56
30 34 0.31
31 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.04, T:0.38
Consensus pattern (29 bp):
ACATTTTTGCCCTCGAACTTCTAAAAATT
Found at i:6832 original size:58 final size:57
Alignment explanation
Indices: 6768--6922 Score: 186
Period size: 58 Copynumber: 2.7 Consensus size: 57
6758 TTCAAAACTC
* * * *
6768 ACATTTTGGCCCTCAAACTTCTTAAAATTACATTTTTTCCTCAAACTTCTCAAAAAAT
1 ACATTTTTGCCCTCGAACTTCTAAAAATTACATTTTTTCCCCAAACTTC-CAAAAAAT
* * * * *
6826 ACATTTTTTCCCTCGAACTTCCAAAAATTACATTTTTACCCCCGAACTTCCAAAAATT
1 ACATTTTTGCCCTCGAACTTCTAAAAATTACATTTTT-TCCCCAAACTTCCAAAAAAT
6884 ACATTTTTTGCTCC-CGAACTTCTAAAAATTACATTTTTT
1 ACA-TTTTTGC-CCTCGAACTTCTAAAAATTACATTTTTT
6923 TGAATTTTCT
Statistics
Matches: 82, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
58 42 0.51
59 38 0.46
60 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.04, T:0.39
Consensus pattern (57 bp):
ACATTTTTGCCCTCGAACTTCTAAAAATTACATTTTTTCCCCAAACTTCCAAAAAAT
Found at i:7062 original size:97 final size:98
Alignment explanation
Indices: 6945--7135 Score: 305
Period size: 97 Copynumber: 2.0 Consensus size: 98
6935 AAAATATTTA
* * *
6945 AAATCGAGGTAATATTCCTTTATTTCGGGTTTTGAAAATTTGTGCCTTAACTTATTGGGCGCGA-
1 AAATCGAGGTAATATTCCTTTATTTCGAGTTTTGAAAATTTGTGCCTTAACTTACTAGGCGCGAT
7009 TTTTTCTTCAAA-TCGGGATAATCAAATACCCTT
66 TTTTTCTTCAAACT-GGGATAATCAAATACCCTT
* *
7042 AAATTGAGGTAATATTCCTTTATTTCGAGTTTTGAAAATTTGTGCCTTAACTTACTAGGTGCGAT
1 AAATCGAGGTAATATTCCTTTATTTCGAGTTTTGAAAATTTGTGCCTTAACTTACTAGGCGCGAT
*
7107 TTTTTCTTCAAACTGGGATAATCGAATAC
66 TTTTTCTTCAAACTGGGATAATCAAATAC
7136 TCTTTTTCAA
Statistics
Matches: 86, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
97 59 0.69
98 26 0.30
99 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (98 bp):
AAATCGAGGTAATATTCCTTTATTTCGAGTTTTGAAAATTTGTGCCTTAACTTACTAGGCGCGAT
TTTTTCTTCAAACTGGGATAATCAAATACCCTT
Found at i:15167 original size:39 final size:39
Alignment explanation
Indices: 15123--16070 Score: 466
Period size: 39 Copynumber: 24.3 Consensus size: 39
15113 TGAAGATTCG
* *
15123 ATCTCTTACCCCGAGCTTGGGGCAGATCCCCATCAGTCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGTCA
* * **
15162 ATCTCTTACCCCGAACCCT-GGGTAGATTGCAGCCAT---TTG
1 ATCTCTTACCCCG-AGCCTGGGGCAGA-T-CA-CCATCAGTCA
* * * * ** * **
15201 ATCTCTTATCTCAACGCCTGGGGTAGAT-TGCAGTCATTTG
1 ATCTCTTACCCCGA-GCCTGGGGCAGATCACCA-TCAGTCA
* * **
15241 ATCTCTTACCCCAAGCTTGGGGCAGATCACCATCAACCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGTCA
* * * * *
15280 ATATCTTACCCCGAGGCTAGGGCAAATTGCAGCCATC---CG
1 ATCTCTTACCCCGAGCCTGGGGCAGA-T-CA-CCATCAGTCA
*
15319 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGTCA
* * * *
15358 ATCTCTTGCCCCGAGCCTAGGGCAGATCCCCATTAG-CGA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGTC-A
* * * * *
15397 ATCTCTTACCCTGATCATGGAGCAGATTGCAGCCAT---TCG
1 ATCTCTTACCCCGAGCCTGGGGCAGA-T-CA-CCATCAGTCA
* * * * * *
15436 ATCTTTTACCCCGAGCTTTGGGCAAATCACCATTAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGTCA
* * ** * * *
15475 ATCTCTTACCTCGAGCTTGGGGCAGATTGCAATTATTCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGTCA
* * *
15514 ATCTCTTACCTCGAGCTTGGGGCAGATCACCATCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGTCA
* * ** * * * *
15553 ATCTCTTACCTCGAGCCTGGGGCAAAT-TGCAACCGACTG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGTC-A
*
15592 ATCTCTTACCCCGAGCCTGAGGCAGATCACCATCAG-CAA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGTC-A
* * * * * *
15631 ATCTCTTACCCCAATCATGGGGCAGATTA-CAGCCATTCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCA-TCAGTCA
* * ** * *
15670 ATCTTTTATCCCGAGCCTAAGGTAGATCACCATCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGTCA
* *** * *
15709 ATCTCTTACCCCGAGCCTGGGGTAGAT-TGTAGTTATTCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCA-TCAGTCA
* * *
15748 ATCTCTTACCCCGA-CCTTTGGGCAGATTGTAGCCAT---TCG
1 ATCTCTTACCCCGAGCC-TGGGGCAGA-T-CA-CCATCAGTCA
* *
15787 ATCTCTTACCCCGAGCTTGGGGTAGATCACCATCAG-CAA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGTC-A
* * * * *
15826 ATCTCTTACCCCGATCATAGGGCAGATTA-CAGTCATTCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCA-TCAGTCA
* * * *
15865 ATCTCTTACCACGAGCCTAGGGTAGATCACCATCAGTAA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGTCA
* * ** * * * *
15904 ATCTCTTACCCTGAGCCTGAGGCAGATTGCAACCATTCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGTCA
* * *
15943 ATCTTTTCCCCCGAGCTTGGGGCAGATCACCATCAGTCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGTCA
* * ** ** * * *
15982 ATCTCTTAACCCGAG-CTAGAGATAGATTGCAACCATTCA
1 ATCTCTTACCCCGAGCCT-GGGGCAGATCACCATCAGTCA
* * ** * *
16021 ATCTTTTACCCCGAGCTTCAGGCAGATCATCATCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGTCA
16060 ATCTCTTACCC
1 ATCTCTTACCC
16071 TGATCATGGG
Statistics
Matches: 674, Mismatches: 189, Indels: 92
0.71 0.20 0.10
Matches are distributed among these distances:
36 15 0.02
37 6 0.01
38 19 0.03
39 571 0.85
40 44 0.07
41 4 0.01
42 14 0.02
43 1 0.00
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGTCA
Found at i:15406 original size:117 final size:116
Alignment explanation
Indices: 15123--16070 Score: 598
Period size: 117 Copynumber: 8.1 Consensus size: 116
15113 TGAAGATTCG
* * * * * *
15123 ATCTCTTACCCCGAGCTTGGGGCAGATCCCCATCAGTCAATCTCTTACCCCGAACCCT-GGGTAG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATTAG-CAATCTCTTACCCCG-AGCTTAGGGCAG
* * * * * ** ****
15187 ATTGCAGCCATTTGATCTCTTATCTCAACGCCTGGGGTAGAT-TGCAGTCATTTG
64 ATTGCAGCCATTCGATCTCTTACCCCGA-GCCTGGGGCAGATCACCA-TCAGCCA
* * * * * *
15241 ATCTCTTACCCCAAGCTTGGGGCAGATCACCATCAACCAATATCTTACCCCGAGGC-TAGGGCAA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCAT-TAGCAATCTCTTACCCCGA-GCTTAGGGCAG
*
15305 ATTGCAGCCATCCGATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCA
64 ATTGCAGCCATTCGATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCA
* * * * * *
15358 ATCTCTTGCCCCGAGCCTAGGGCAGATCCCCATTAGCGAATCTCTTACCCTGATCAT-GGAGCAG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATTAGC-AATCTCTTACCCCGAGCTTAGG-GCAG
* * * * *
15422 ATTGCAGCCATTCGATCTTTTACCCCGAGCTTTGGGCAAATCACCATTAGCCA
64 ATTGCAGCCATTCGATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCA
* * ** * * * *
15475 ATCTCTTACCTCGAGCTTGGGGCAGATTGCAATTATTCAATCTCTTACCTCGAGCTTGGGGCAGA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATTA-GCAATCTCTTACCCCGAGCTTAGGGCAGA
* * ** * * **
15540 -T-CA-CCA-TCAGCCAATCTCTTACCTCGAGCCTGGGGCAAAT-TGCAACCGACTG
65 TTGCAGCCATTC-G---ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAG-CCA
* * * * * *
15592 ATCTCTTACCCCGAGCCTGAGGCAGATCACCATCAGCAAATCTCTTACCCCAATCATGGGGCAGA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATTAGC-AATCTCTTACCCCGAGCTTAGGGCAGA
* * * * ** *
15657 TTACAGCCATTCAATCTTTTATCCCGAGCCTAAGGTAGATCACCATCAGCCA
65 TTGCAGCCATTCGATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCA
* *** * * *
15709 ATCTCTTACCCCGAGCCTGGGGTAGAT-TGTAGTTATTCAATCTCTTACCCCGACCTTTGGGCAG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCA-TTA-GCAATCTCTTACCCCGAGCTTAGGGCAG
* * * *
15773 ATTGTAGCCATTCGATCTCTTACCCCGAGCTTGGGGTAGATCACCATCAGCAA
64 ATTGCAGCCATTCGATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCA
* * * * * * *
15826 ATCTCTTACCCCGATCATAGGGCAGATTACAGTCATT--CAATCTCTTACCACGAGCCTAGGGTA
1 ATCTCTTACCCCGAGCCTGGGGCAGA-T-CA-CCATTAGCAATCTCTTACCCCGAGCTTAGGGCA
* * ** * * ** *
15889 GA-T-CA-CCA-TCAGTAAATCTCTTACCCTGAGCCTGAGGCAGATTGCAACCATTCG
63 GATTGCAGCCATTC-G---ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCA
* * * * * **
15943 ATCTTTTCCCCCGAGCTTGGGGCAGATCACCATCAGTCAATCTCTTAACCCGAGC-TAGAGATAG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATTAG-CAATCTCTTACCCCGAGCTTAG-GGCAG
* * * * ** *
16007 ATTGCAACCATTCAATCTTTTACCCCGAGCTTCAGGCAGATCATCATCAGCCA
64 ATTGCAGCCATTCGATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCA
16060 ATCTCTTACCC
1 ATCTCTTACCC
16071 TGATCATGGG
Statistics
Matches: 636, Mismatches: 156, Indels: 77
0.73 0.18 0.09
Matches are distributed among these distances:
113 4 0.01
114 11 0.02
115 5 0.01
116 16 0.03
117 496 0.78
118 86 0.14
119 5 0.01
120 8 0.01
121 5 0.01
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (116 bp):
ATCTCTTACCCCGAGCCTGGGGCAGATCACCATTAGCAATCTCTTACCCCGAGCTTAGGGCAGAT
TGCAGCCATTCGATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCA
Found at i:16551 original size:17 final size:17
Alignment explanation
Indices: 16526--16586 Score: 79
Period size: 17 Copynumber: 3.6 Consensus size: 17
16516 TTAAAATTTT
16526 ATTTA-TTTAAGTTTGA
1 ATTTATTTTAAGTTTGA
* *
16542 ATTTATTTTAAATTTAA
1 ATTTATTTTAAGTTTGA
* *
16559 ACTTATTTTGAGTTTGA
1 ATTTATTTTAAGTTTGA
16576 ATTTATTTTAA
1 ATTTATTTTAA
16587 ATTAAATTTA
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
16 5 0.14
17 31 0.86
ACGTcount: A:0.33, C:0.02, G:0.08, T:0.57
Consensus pattern (17 bp):
ATTTATTTTAAGTTTGA
Found at i:17029 original size:25 final size:25
Alignment explanation
Indices: 16992--17041 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
16982 AAACTTATCC
* *
16992 TCGAAATATATACAGAGACCAACAA
1 TCGAAATATATACAGAAACAAACAA
17017 TCGAAATCA-ATACAGAAACAAACAA
1 TCGAAAT-ATATACAGAAACAAACAA
17042 ATAGCACTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 21 0.95
26 1 0.05
ACGTcount: A:0.56, C:0.20, G:0.10, T:0.14
Consensus pattern (25 bp):
TCGAAATATATACAGAAACAAACAA
Found at i:17457 original size:17 final size:17
Alignment explanation
Indices: 17435--17469 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
17425 ATCAAGAAAT
17435 ATTAATA-ATAAATAAAA
1 ATTAATATATAAA-AAAA
17452 ATTAATATATAAAAAAA
1 ATTAATATATAAAAAAA
17469 A
1 A
17470 GAGTGATAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
ATTAATATATAAAAAAA
Found at i:17708 original size:22 final size:22
Alignment explanation
Indices: 17682--17732 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
17672 TAGATCTGGG
*
17682 CTAGATCAGGTTCGATCTAGAC
1 CTAGATCAGGTTCGATCTAAAC
*
17704 CTAGATCGGGTTCGATCTAAAC
1 CTAGATCAGGTTCGATCTAAAC
17726 CTAGATC
1 CTAGATC
17733 TGATTTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (22 bp):
CTAGATCAGGTTCGATCTAAAC
Found at i:18487 original size:30 final size:30
Alignment explanation
Indices: 18453--18524 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
18443 AGCTATCCAC
** * *
18453 AAATCATATTTTGACCCTTACACTTTTCAA
1 AAATCATATTTTGACCCCCAAACTTCTCAA
*
18483 AAATCACATTTTGACCCCCAAACTTCTCAA
1 AAATCATATTTTGACCCCCAAACTTCTCAA
*
18513 AAATTATATTTT
1 AAATCATATTTT
18525 TCCTTTAAAC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.38
Consensus pattern (30 bp):
AAATCATATTTTGACCCCCAAACTTCTCAA
Found at i:18594 original size:28 final size:29
Alignment explanation
Indices: 18474--18615 Score: 112
Period size: 29 Copynumber: 4.9 Consensus size: 29
18464 TGACCCTTAC
* * *
18474 ACTTTTCAAAAATCACATTTTGACCCCCAA
1 ACTTCTCAAAAATTACATTTTTA-CCCCAA
* **
18504 ACTTCTCAAAAATTATATTTTT-CCTTTAA
1 ACTTCTCAAAAATTACATTTTTACC-CCAA
* * **
18533 ACTTCTCAAAAATTACAATTTTATCGCTGA
1 ACTTCTCAAAAATTACATTTTTA-CCCCAA
*
18563 ACTTC-CAAAAATTACATTTTTACCCCAT
1 ACTTCTCAAAAATTACATTTTTACCCCAA
* *
18591 ACTTC-C-AAAATCACGTTTTTACCCC
1 ACTTCTCAAAAATTACATTTTTACCCC
18616 GAATTTTCCT
Statistics
Matches: 91, Mismatches: 18, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
27 17 0.19
28 10 0.11
29 38 0.42
30 25 0.27
31 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.37
Consensus pattern (29 bp):
ACTTCTCAAAAATTACATTTTTACCCCAA
Found at i:18609 original size:27 final size:28
Alignment explanation
Indices: 18563--18615 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
18553 TTATCGCTGA
*
18563 ACTTCCAAAAATTACATTTTTACCCCAT
1 ACTTCCAAAAATCACATTTTTACCCCAT
*
18591 ACTTCC-AAAATCACGTTTTTACCCC
1 ACTTCCAAAAATCACATTTTTACCCC
18616 GAATTTTCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 17 0.74
28 6 0.26
ACGTcount: A:0.32, C:0.32, G:0.02, T:0.34
Consensus pattern (28 bp):
ACTTCCAAAAATCACATTTTTACCCCAT
Found at i:29807 original size:24 final size:24
Alignment explanation
Indices: 29783--29829 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
29773 ACAATTCAAT
29783 TTTATCTTA-ATTTGC-TCTGACAA
1 TTTATCTTATATTTGCAT-TGACAA
*
29806 TTTATTTTATATTTGCATTGACAA
1 TTTATCTTATATTTGCATTGACAA
29830 ATTAACTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 8 0.38
24 12 0.57
25 1 0.05
ACGTcount: A:0.28, C:0.13, G:0.09, T:0.51
Consensus pattern (24 bp):
TTTATCTTATATTTGCATTGACAA
Found at i:37001 original size:11 final size:11
Alignment explanation
Indices: 36985--37022 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
36975 TATAAAAAAC
36985 AAAAAAACAAA
1 AAAAAAACAAA
36996 AAAAAAAC-AA
1 AAAAAAACAAA
*
37006 AGAAAAACAGAA
1 AAAAAAACA-AA
37018 AAAAA
1 AAAAA
37023 TATATTGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
10 9 0.39
11 8 0.35
12 6 0.26
ACGTcount: A:0.87, C:0.08, G:0.05, T:0.00
Consensus pattern (11 bp):
AAAAAAACAAA
Found at i:38573 original size:24 final size:23
Alignment explanation
Indices: 38537--38583 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
38527 ACAATTCAAT
* *
38537 TTTATCTTAATTTTCTTTGACAA
1 TTTATCTTAATTTGCATTGACAA
*
38560 TTTATTTTATATTTGCATTGACAA
1 TTTATCTTA-ATTTGCATTGACAA
38584 ATTAACTCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.28, C:0.11, G:0.06, T:0.55
Consensus pattern (23 bp):
TTTATCTTAATTTGCATTGACAA
Found at i:40986 original size:27 final size:27
Alignment explanation
Indices: 40883--40986 Score: 102
Period size: 27 Copynumber: 3.9 Consensus size: 27
40873 ATTAAAGTAT
* * * *
40883 GCCACAAAGGCAATTCACTTAGTGTAC
1 GCCACAAAGGCTATTCATTTAGAGTTC
40910 GCCACAAAGGCTATTCATTTAGA-TTAC
1 GCCACAAAGGCTATTCATTTAGAGTT-C
* * * *
40937 ACCACAAGGGTTATTCTTTTAGAGTTC
1 GCCACAAAGGCTATTCATTTAGAGTTC
* *
40964 GGCACAAAGGCTATTCTTTTAGA
1 GCCACAAAGGCTATTCATTTAGA
40987 TAGTATCATG
Statistics
Matches: 63, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
26 1 0.02
27 60 0.95
28 2 0.03
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (27 bp):
GCCACAAAGGCTATTCATTTAGAGTTC
Found at i:43686 original size:36 final size:37
Alignment explanation
Indices: 43641--43715 Score: 107
Period size: 37 Copynumber: 2.1 Consensus size: 37
43631 GTTTCTGAGT
* *
43641 ATTTTAATAATATTTTC-TTTCTATAATGTTTTACAC
1 ATTTTAATAATATTTGCTTTTCTATAATGTTCTACAC
* *
43677 ATTTTAATAATATTTGCTTTTTTATAGTGTTCTACAC
1 ATTTTAATAATATTTGCTTTTCTATAATGTTCTACAC
43714 AT
1 AT
43716 GCTATCGATA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
36 16 0.47
37 18 0.53
ACGTcount: A:0.29, C:0.11, G:0.05, T:0.55
Consensus pattern (37 bp):
ATTTTAATAATATTTGCTTTTCTATAATGTTCTACAC
Found at i:44089 original size:114 final size:113
Alignment explanation
Indices: 43969--44196 Score: 438
Period size: 114 Copynumber: 2.0 Consensus size: 113
43959 AACCTATTTT
43969 AAGTGTAATTCAACGCTCTTTTTTTGGGTACATATATCAATGGGCTTTACCATAAGTAGGAATGT
1 AAGTGTAATTCAACGCTCTTTTTTTGGGTACATATATCAATGGGCTTTACCATAAGTAGGAATGT
44034 GATAACTACCGTGTTAGAGTGGTTCATGTTTCTAAAAGGGCGTAGGTGA
66 GATAACTACCGTGTTAGAGTGGTTCATGTTT-TAAAAGGGCGTAGGTGA
44083 AAGTGTAATTCAACGCTCTTTTTTTGGGTACATATATCAATGGGCTTTACCATAAGTAGGAATGT
1 AAGTGTAATTCAACGCTCTTTTTTTGGGTACATATATCAATGGGCTTTACCATAAGTAGGAATGT
*
44148 GATAACTACCGTGTTAGAGTGGTTCATGTTTTTAAAGGGCGTAGGTGA
66 GATAACTACCGTGTTAGAGTGGTTCATGTTTTAAAAGGGCGTAGGTGA
44196 A
1 A
44197 TCCTCCTTTT
Statistics
Matches: 113, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
113 17 0.15
114 96 0.85
ACGTcount: A:0.28, C:0.13, G:0.25, T:0.35
Consensus pattern (113 bp):
AAGTGTAATTCAACGCTCTTTTTTTGGGTACATATATCAATGGGCTTTACCATAAGTAGGAATGT
GATAACTACCGTGTTAGAGTGGTTCATGTTTTAAAAGGGCGTAGGTGA
Found at i:51038 original size:27 final size:27
Alignment explanation
Indices: 51007--51075 Score: 138
Period size: 27 Copynumber: 2.6 Consensus size: 27
50997 ATAATTGAAT
51007 AAACATAATCATAGTCCTACTGAAGAC
1 AAACATAATCATAGTCCTACTGAAGAC
51034 AAACATAATCATAGTCCTACTGAAGAC
1 AAACATAATCATAGTCCTACTGAAGAC
51061 AAACATAATCATAGT
1 AAACATAATCATAGT
51076 ATGATCAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.46, C:0.20, G:0.10, T:0.23
Consensus pattern (27 bp):
AAACATAATCATAGTCCTACTGAAGAC
Found at i:57056 original size:38 final size:38
Alignment explanation
Indices: 57005--57284 Score: 212
Period size: 38 Copynumber: 7.4 Consensus size: 38
56995 ATATAATTAA
* * *
57005 ATGTTTATTGGGCTTTATGCTTAGTAGACTTTATGCCG
1 ATGTTTATCGGGCTTTATGCCTAGCAGACTTTATGCCG
* * * *
57043 ATGTTTATCGGGCTTTGTGCTTAGCA-AGTTTTATG-CT
1 ATGTTTATCGGGCTTTATGCCTAGCAGA-CTTTATGCCG
* *
57080 AGTGTTTATCGGGCTTTATGCCTAACAGGCTTTATGCCG
1 A-TGTTTATCGGGCTTTATGCCTAGCAGACTTTATGCCG
* * * * * * *
57119 GTGTTTATCAGACTTTGTGCCTAGTAGGCTTTATGTCG
1 ATGTTTATCGGGCTTTATGCCTAGCAGACTTTATGCCG
* * * * *
57157 -TGTTTATCGAGCTTTGTTCCTAGTAAGA-TTTATGCCA
1 ATGTTTATCGGGCTTTATGCCTAG-CAGACTTTATGCCG
*
57194 ATGTTTATCGGGCTTTGA-GCCTAGCATG-CTTTATGTCG
1 ATGTTTATCGGGCTTT-ATGCCTAGCA-GACTTTATGCCG
* * * * **
57232 ATGTTTATCGGGCTTTGTACCTAGCAGGCTATATGTTG
1 ATGTTTATCGGGCTTTATGCCTAGCAGACTTTATGCCG
*
57270 ATGTTTATCGTGCTT
1 ATGTTTATCGGGCTT
57285 AGTGTGTAGC
Statistics
Matches: 194, Mismatches: 37, Indels: 22
0.77 0.15 0.09
Matches are distributed among these distances:
37 31 0.16
38 162 0.84
39 1 0.01
ACGTcount: A:0.17, C:0.16, G:0.24, T:0.42
Consensus pattern (38 bp):
ATGTTTATCGGGCTTTATGCCTAGCAGACTTTATGCCG
Found at i:57205 original size:113 final size:114
Alignment explanation
Indices: 57017--57284 Score: 315
Period size: 113 Copynumber: 2.4 Consensus size: 114
57007 GTTTATTGGG
* * * * * * * * *
57017 CTTTATGCTTAGTAGACTTTATGCCGATGTTTATCGGGCTTTGTGCTTAGCAAGTTTTATGCTAG
1 CTTTGTGCCTAGTAGGCTTTATGTCGATGTTTATCGAGCTTTGTGCCTAGCAAGATTTATGCCAA
*
57082 TGTTTATCGGGCTTT-ATGCCTAACAGGCTTTATGCCGGTGTTTATCAGA
66 TGTTTATCGGGCTTTGA-GCCTAACAGGCTTTATGCCGATGTTTATCAGA
* *
57131 CTTTGTGCCTAGTAGGCTTTATGTCG-TGTTTATCGAGCTTTGTTCCTAGTAAGATTTATGCCAA
1 CTTTGTGCCTAGTAGGCTTTATGTCGATGTTTATCGAGCTTTGTGCCTAGCAAGATTTATGCCAA
* * * * *
57195 TGTTTATCGGGCTTTGAGCCTAGCATGCTTTATGTCGATGTTTATCGGG
66 TGTTTATCGGGCTTTGAGCCTAACAGGCTTTATGCCGATGTTTATCAGA
* * * * *
57244 CTTTGTACCTAGCAGGCTATATGTTGATGTTTATCGTGCTT
1 CTTTGTGCCTAGTAGGCTTTATGTCGATGTTTATCGAGCTT
57285 AGTGTGTAGC
Statistics
Matches: 130, Mismatches: 22, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
113 94 0.72
114 36 0.28
ACGTcount: A:0.18, C:0.17, G:0.24, T:0.42
Consensus pattern (114 bp):
CTTTGTGCCTAGTAGGCTTTATGTCGATGTTTATCGAGCTTTGTGCCTAGCAAGATTTATGCCAA
TGTTTATCGGGCTTTGAGCCTAACAGGCTTTATGCCGATGTTTATCAGA
Found at i:57299 original size:151 final size:151
Alignment explanation
Indices: 57026--57300 Score: 340
Period size: 151 Copynumber: 1.8 Consensus size: 151
57016 GCTTTATGCT
* * * * *
57026 TAGTAGACTTTATGCCGATGTTTATCGGGCTTTGTGCTTAGCAAGTTTTATGCTAGTGTTTATCG
1 TAGTAGACTTTATGCCAATGTTTATCGGGCTTTGAGCCTAGCAAGCTTTATGCGAGTGTTTATCG
* * * * *
57091 GGCTTTATGCCTAACAGGCTTTATGCCGGTGTTTATCAGACTTTGTGCCTAGTAGGCTTTATGTC
66 GGCTTTATACCTAACAGGCTATATGCCGATGTTTATCAGACTTAGTGCCTAGCAGGCTTTATGTC
57156 GTGTTTATCGAGCTTTGTTCC
131 GTGTTTATCGAGCTTTGTTCC
*
57177 TAGTAAGA-TTTATGCCAATGTTTATCGGGCTTTGAGCCTAGCATGCTTTATGTCGA-TGTTTAT
1 TAGT-AGACTTTATGCCAATGTTTATCGGGCTTTGAGCCTAGCAAGCTTTATG-CGAGTGTTTAT
* * ** * **
57240 CGGGCTTTGTACCTAGCAGGCTATATGTTGATGTTTATC-GTGCTTAGTGTGTAGCAGGCTT
64 CGGGCTTTATACCTAACAGGCTATATGCCGATGTTTATCAG-ACTTAGTGCCTAGCAGGCTT
57301 CGTGCTGTGG
Statistics
Matches: 103, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
150 1 0.01
151 97 0.94
152 5 0.05
ACGTcount: A:0.18, C:0.16, G:0.25, T:0.41
Consensus pattern (151 bp):
TAGTAGACTTTATGCCAATGTTTATCGGGCTTTGAGCCTAGCAAGCTTTATGCGAGTGTTTATCG
GGCTTTATACCTAACAGGCTATATGCCGATGTTTATCAGACTTAGTGCCTAGCAGGCTTTATGTC
GTGTTTATCGAGCTTTGTTCC
Found at i:62359 original size:38 final size:38
Alignment explanation
Indices: 62317--62584 Score: 236
Period size: 38 Copynumber: 7.1 Consensus size: 38
62307 TTTATCAGGT
*
62317 TTTGTGCCTAGCAGACTTTATGCTAGTATTTATCGAGC
1 TTTGTGCCTAGCAGACTTTATGCTAGTGTTTATCGAGC
* * ** * *
62355 TTTGTGCCTAGCAGACTATGTGCCGGTGTTTATTGGGC
1 TTTGTGCCTAGCAGACTTTATGCTAGTGTTTATCGAGC
* * ** * *
62393 TTTGTGCCTAGTAGGCTTTATGCCGGTGTTTATTGGGC
1 TTTGTGCCTAGCAGACTTTATGCTAGTGTTTATCGAGC
62431 TTTGTGCCTAGCA-AGCTTTATGTCT-GTGTTTATCGAGC
1 TTTGTGCCTAGCAGA-CTTTATG-CTAGTGTTTATCGAGC
* * * * *
62469 TTTGTGCCTAACAGACTTTAT-TTTGATGTTTATTGGGC
1 TTTGTGCCTAGCAGACTTTATGCTAG-TGTTTATCGAGC
* * * *
62507 TTTGTGCCTAGTAGGCTATATGCTAGTATTTATCGAGC
1 TTTGTGCCTAGCAGACTTTATGCTAGTGTTTATCGAGC
* * * * * *
62545 TTAGTGCCTAGCAGGCTTTGTGCCAGTGGTTATCAAGC
1 TTTGTGCCTAGCAGACTTTATGCTAGTGTTTATCGAGC
62583 TT
1 TT
62585 AATGCCTAAC
Statistics
Matches: 187, Mismatches: 37, Indels: 12
0.79 0.16 0.05
Matches are distributed among these distances:
36 1 0.01
37 1 0.01
38 181 0.97
39 4 0.02
ACGTcount: A:0.17, C:0.17, G:0.26, T:0.40
Consensus pattern (38 bp):
TTTGTGCCTAGCAGACTTTATGCTAGTGTTTATCGAGC
Found at i:62505 original size:114 final size:113
Alignment explanation
Indices: 62317--62595 Score: 317
Period size: 114 Copynumber: 2.4 Consensus size: 113
62307 TTTATCAGGT
* * * *
62317 TTTGTGCCTAGC-AGACTTTATGCTAGTATTTATCGAGCTTTGTGCCTAGCAGACTATGTGCCGG
1 TTTGTGCCTAGCAAG-CTTTATGCT-GTGTTTATCGAGCTTTGTGCCTAACAGACTATATGCCGA
* * * * *
62381 TGTTTATTGGGCTTTGTGCCTAGTAGGCTTTATGCCGGTGTTTATTGGGC
64 TGTTTATTGGGCTTTGTGCCTAGTAGGCTATATGCCAGTATTTATCGAGC
* ***
62431 TTTGTGCCTAGCAAGCTTTATGTCTGTGTTTATCGAGCTTTGTGCCTAACAGACTTTATTTTGAT
1 TTTGTGCCTAGCAAGCTTTATG-CTGTGTTTATCGAGCTTTGTGCCTAACAGACTATATGCCGAT
*
62496 GTTTATTGGGCTTTGTGCCTAGTAGGCTATATGCTAGTATTTATCGAGC
65 GTTTATTGGGCTTTGTGCCTAGTAGGCTATATGCCAGTATTTATCGAGC
* * * * * * **
62545 TTAGTGCCTAGCAGGCTTTGTGCCAGTGGTTATCAAGCTTAATGCCTAACA
1 TTTGTGCCTAGCAAGCTTTATG-CTGTGTTTATCGAGCTTTGTGCCTAACA
62596 AGCTCCTTGC
Statistics
Matches: 140, Mismatches: 23, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
114 136 0.97
115 4 0.03
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.39
Consensus pattern (113 bp):
TTTGTGCCTAGCAAGCTTTATGCTGTGTTTATCGAGCTTTGTGCCTAACAGACTATATGCCGATG
TTTATTGGGCTTTGTGCCTAGTAGGCTATATGCCAGTATTTATCGAGC
Found at i:64212 original size:12 final size:12
Alignment explanation
Indices: 64197--64229 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
64187 CGAAAAGCAT
*
64197 AAAATAAAGTAG
1 AAAATAAAATAG
64209 AAAATAAAATAG
1 AAAATAAAATAG
64221 AAAATAAAA
1 AAAATAAAA
64230 GCAAGATTTG
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:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (12 bp):
AAAATAAAATAG
Found at i:67402 original size:12 final size:12
Alignment explanation
Indices: 67380--67420 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
67370 TTGAATTTTG
67380 AAAGCATAAAATA
1 AAAG-ATAAAATA
67393 AAAGATAAAATA
1 AAAGATAAAATA
* *
67405 AAATAGAAAATA
1 AAAGATAAAATA
67417 AAAG
1 AAAG
67421 CAAAAGTTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
12 21 0.84
13 4 0.16
ACGTcount: A:0.73, C:0.02, G:0.10, T:0.15
Consensus pattern (12 bp):
AAAGATAAAATA
Found at i:67407 original size:17 final size:17
Alignment explanation
Indices: 67385--67419 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
67375 TTTTGAAAGC
67385 ATAAAATA-AAAGATAAA
1 ATAAAATAGAAA-ATAAA
67402 ATAAAATAGAAAATAAA
1 ATAAAATAGAAAATAAA
67419 A
1 A
67420 GCAAAAGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.82
18 3 0.18
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (17 bp):
ATAAAATAGAAAATAAA
Found at i:71890 original size:12 final size:12
Alignment explanation
Indices: 71873--71905 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
71863 GGAATTGTAT
*
71873 AAAATAAAGTAG
1 AAAATAAAATAG
71885 AAAATAAAATAG
1 AAAATAAAATAG
71897 AAAATAAAA
1 AAAATAAAA
71906 GCAAGATTTG
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:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (12 bp):
AAAATAAAATAG
Found at i:73775 original size:21 final size:21
Alignment explanation
Indices: 73751--73797 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
73741 CTTAACTTTT
73751 ATTTGTTATTGA-T-TTGTTTCA
1 ATTT-TTATTGACTCTT-TTTCA
*
73772 ATTTTTGTTGACTCTTTTTCA
1 ATTTTTATTGACTCTTTTTCA
73793 ATTTT
1 ATTTT
73798 CCTTTAGGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 6 0.26
21 15 0.65
22 2 0.09
ACGTcount: A:0.17, C:0.09, G:0.11, T:0.64
Consensus pattern (21 bp):
ATTTTTATTGACTCTTTTTCA
Found at i:90018 original size:17 final size:17
Alignment explanation
Indices: 89996--90028 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
89986 TTTGAAAGTA
89996 TAAAATA-AAAGATAAAC
1 TAAAATAGAAA-ATAAAC
90013 TAAAATAGAAAATAAA
1 TAAAATAGAAAATAAA
90029 GGAAAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.73, C:0.03, G:0.06, T:0.18
Consensus pattern (17 bp):
TAAAATAGAAAATAAAC
Found at i:102200 original size:22 final size:22
Alignment explanation
Indices: 102175--102217 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
102165 AAAATATTTC
102175 ATTA-ATAAATTGGGTTTAATTA
1 ATTATATAAATTGGG-TTAATTA
*
102197 ATTATTTAAATTGGGTTAATT
1 ATTATATAAATTGGGTTAATT
102218 TTATTCTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (22 bp):
ATTATATAAATTGGGTTAATTA
Found at i:106240 original size:33 final size:33
Alignment explanation
Indices: 106194--106259 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
106184 ATCTTTATGC
* *
106194 CTTAAATTGAAAATGATTTTTA-TACAGGGGGAG
1 CTTAAATTCAAAATGACTTTTATTA-AGGGGGAG
*
106227 CTTAATTTCAAAATGACTTTTATTAAGGGGGAG
1 CTTAAATTCAAAATGACTTTTATTAAGGGGGAG
106260 AAATATATTC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 27 0.93
34 2 0.07
ACGTcount: A:0.35, C:0.08, G:0.23, T:0.35
Consensus pattern (33 bp):
CTTAAATTCAAAATGACTTTTATTAAGGGGGAG
Found at i:108161 original size:19 final size:20
Alignment explanation
Indices: 108117--108162 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
108107 TTTGTTTCTA
108117 CTTATTTTTCTTCTTCTTTT
1 CTTATTTTTCTTCTTCTTTT
*
108137 -TGATTTTTC-TCTAT-TTTT
1 CTTATTTTTCTTCT-TCTTTT
108155 CTTATTTT
1 CTTATTTT
108163 GTCAAGACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.09, C:0.15, G:0.02, T:0.74
Consensus pattern (20 bp):
CTTATTTTTCTTCTTCTTTT
Found at i:113001 original size:12 final size:12
Alignment explanation
Indices: 112984--113022 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
112974 GGGTTTAATC
112984 AAACTAAAAATT
1 AAACTAAAAATT
112996 AAACTAAATAATT
1 AAACTAAA-AATT
*
113009 -AACTAAAAAAT
1 AAACTAAAAATT
113020 AAA
1 AAA
113023 AATAAACTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
11 3 0.12
12 17 0.71
13 4 0.17
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (12 bp):
AAACTAAAAATT
Found at i:117155 original size:14 final size:14
Alignment explanation
Indices: 117136--117165 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
117126 ATAAAATTTT
*
117136 TTGCTTTTCTTTGA
1 TTGCTTTACTTTGA
117150 TTGCTTTACTTTGA
1 TTGCTTTACTTTGA
117164 TT
1 TT
117166 TGTTATATGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.10, C:0.13, G:0.13, T:0.63
Consensus pattern (14 bp):
TTGCTTTACTTTGA
Done.