Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014754.1 Kokia drynarioides strain JFW-HI SEQ_129793, 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: 104367
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:2277 original size:22 final size:21
Alignment explanation
Indices: 2238--2287 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
2228 TTTTCCATTT
* *
2238 TTTCTGCTCTCTTGTATTTCC
1 TTTCTTCTCTCTTCTATTTCC
*
2259 TTTCTTCTCCTCTTCTATTTTC
1 TTTCTTCT-CTCTTCTATTTCC
2281 -TTCTTCT
1 TTTCTTCT
2288 TTTTTTAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 14 0.56
22 11 0.44
ACGTcount: A:0.04, C:0.30, G:0.04, T:0.62
Consensus pattern (21 bp):
TTTCTTCTCTCTTCTATTTCC
Found at i:2569 original size:33 final size:33
Alignment explanation
Indices: 2494--2572 Score: 83
Period size: 33 Copynumber: 2.4 Consensus size: 33
2484 TACTATATTT
* *
2494 AAATATTTAAAATATAGTTTATATAATCTTATT
1 AAATATTTAAAATATAGTTAATATAATCTTATG
*
2527 AAATTTTTAAAATA-A-TTAATATTAATTACTTA-G
1 AAATATTTAAAATATAGTTAATA-TAA-T-CTTATG
2560 AAATATTTAAAAT
1 AAATATTTAAAAT
2573 TAATATTTCA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
31 5 0.13
32 4 0.10
33 26 0.67
34 4 0.10
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (33 bp):
AAATATTTAAAATATAGTTAATATAATCTTATG
Found at i:7811 original size:28 final size:28
Alignment explanation
Indices: 7789--7922 Score: 146
Period size: 28 Copynumber: 4.8 Consensus size: 28
7779 GTAAGCATAC
* **
7789 CAAAGCTCTACCTGAGCTAT-AAGAGGT
1 CAAAGCTCTACCTGAGCTATAAACAAAT
* * *
7816 CAAAGCTCTACCTAAGCTATAAATAGAT
1 CAAAGCTCTACCTGAGCTATAAACAAAT
* *
7844 CCAAGCTCTACCTGAGCTATAAATAAAT
1 CAAAGCTCTACCTGAGCTATAAACAAAT
* *
7872 CAAAGCTCTA-CTCAAGTTATAAACAAAT
1 CAAAGCTCTACCT-GAGCTATAAACAAAT
*
7900 CAAAGCTCTACCCGAGCTATAAA
1 CAAAGCTCTACCTGAGCTATAAA
7923 TAGAGTATCG
Statistics
Matches: 91, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
27 21 0.23
28 69 0.76
29 1 0.01
ACGTcount: A:0.40, C:0.24, G:0.13, T:0.23
Consensus pattern (28 bp):
CAAAGCTCTACCTGAGCTATAAACAAAT
Found at i:7906 original size:56 final size:56
Alignment explanation
Indices: 7789--7924 Score: 177
Period size: 56 Copynumber: 2.4 Consensus size: 56
7779 GTAAGCATAC
* ** * *
7789 CAAAGCTCTACCTGAGCTAT-AAGAGGTCAAAGCTCTACCTAAGCTATAAATAGAT
1 CAAAGCTCTACCTGAGCTATAAATAAATCAAAGCTCTACCTAAGCTATAAACAAAT
* *
7844 CCAAGCTCTACCTGAGCTATAAATAAATCAAAGCTCTA-CTCAAGTTATAAACAAAT
1 CAAAGCTCTACCTGAGCTATAAATAAATCAAAGCTCTACCT-AAGCTATAAACAAAT
*
7900 CAAAGCTCTACCCGAGCTATAAATA
1 CAAAGCTCTACCTGAGCTATAAATA
7925 GAGTATCGCT
Statistics
Matches: 70, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
55 21 0.30
56 49 0.70
ACGTcount: A:0.40, C:0.24, G:0.12, T:0.24
Consensus pattern (56 bp):
CAAAGCTCTACCTGAGCTATAAATAAATCAAAGCTCTACCTAAGCTATAAACAAAT
Found at i:10125 original size:16 final size:15
Alignment explanation
Indices: 10104--10157 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
10094 ATAACACAGA
10104 GTAATTGAATGAAAGT
1 GTAATT-AATGAAAGT
*
10120 GTAATT-ATTAAAGT
1 GTAATTAATGAAAGT
*
10134 AGTAATTATATGAAAAT
1 -GTAATTA-ATGAAAGT
10151 GTAATTA
1 GTAATTA
10158 CAAAAAATTG
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
14 7 0.22
15 6 0.19
16 13 0.41
17 6 0.19
ACGTcount: A:0.46, C:0.00, G:0.17, T:0.37
Consensus pattern (15 bp):
GTAATTAATGAAAGT
Found at i:10140 original size:15 final size:14
Alignment explanation
Indices: 10115--10157 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
10105 TAATTGAATG
10115 AAAGTGTAATTATT
1 AAAGTGTAATTATT
10129 AAAGTAGTAATTATAT
1 AAAGT-GTAATTAT-T
*
10145 GAAAATGTAATTA
1 -AAAGTGTAATTA
10158 CAAAAAATTG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 5 0.20
15 8 0.32
16 8 0.32
17 4 0.16
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.37
Consensus pattern (14 bp):
AAAGTGTAATTATT
Found at i:10895 original size:26 final size:26
Alignment explanation
Indices: 10866--10931 Score: 105
Period size: 26 Copynumber: 2.5 Consensus size: 26
10856 TGAAATTTTC
* *
10866 TCGAATCGAGTCGAGTGTTATGGAAT
1 TCGAATCGAGTCGAGTGTGATGAAAT
10892 TCGAATCGAGTCGAGTGTGATGAAAT
1 TCGAATCGAGTCGAGTGTGATGAAAT
*
10918 TCGAATCGAATCGA
1 TCGAATCGAGTCGA
10932 ATTGAATATA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.30, C:0.14, G:0.29, T:0.27
Consensus pattern (26 bp):
TCGAATCGAGTCGAGTGTGATGAAAT
Found at i:11630 original size:160 final size:158
Alignment explanation
Indices: 11428--11785 Score: 372
Period size: 172 Copynumber: 2.2 Consensus size: 158
11418 AAGGGTGGGA
* * * *
11428 AGTAAAAGTTTAGGG-GGAAAATAAAATGTTTTGAG-GGTT-T-T-GGGGAGTAAAATTTTGGAG
1 AGTAAAAGTTTTGGGAGGAAAATAAAAAGTTTTAAGAGTTTGTATGGGGGAGTAAAATTTTGGAG
* * *
11488 GAAAAATAATAAAAAAATTTGGGAGGAGGGAATGAGTTTGGGGTAGATGGAGGGTTG-GATGGGA
66 GAAAAATAATAAAAAAAATT--GA-G-GGAAATGAGTTTGGGGTAGATGG-GGGGTGAGATGGGA
*
11552 GGAGAGTAAAAGTTTTTGTGAGGAAAGTGAG-AGAG
126 GGAGAGTAAAAG-TTTTGAG-GGAAAGTGAGAAG-G
11587 AGTAAAAGTTTTGGGAGGAAAATAAAAAGTTTTAAGAGTTTTGGGGGAAAATAAATGGGGGGAGT
1 AGTAAAAGTTTTGGGAGGAAAATAAAAAGTTTTAAGAG-TTT----G----T--AT-GGGGGAGT
* *
11652 AAAATTTTGGAGGGAAAATATTAAAAAAAATTGAGGGAAATGAGTTTGGGGTAGATGGGGGGTGA
54 AAAATTTTGGAGGAAAAATAATAAAAAAAATTGAGGGAAATGAGTTTGGGGTAGATGGGGGGTGA
*
11717 GATGGGAGGAGAGTAAAAGTTTTGAGGGAAAGTGGGAAGG
119 GATGGGAGGAGAGTAAAAGTTTTGAGGGAAAGTGAGAAGG
11757 AGTAAAAGTTTTGGGA-GAAAAGTAAAAAG
1 AGTAAAAGTTTTGGGAGGAAAA-TAAAAAG
11786 GTTCAAAGTT
Statistics
Matches: 168, Mismatches: 11, Indels: 29
0.81 0.05 0.14
Matches are distributed among these distances:
159 14 0.08
160 18 0.11
161 1 0.01
162 2 0.01
169 5 0.03
170 33 0.20
171 14 0.08
172 41 0.24
173 1 0.01
174 3 0.02
176 36 0.21
ACGTcount: A:0.39, C:0.00, G:0.37, T:0.24
Consensus pattern (158 bp):
AGTAAAAGTTTTGGGAGGAAAATAAAAAGTTTTAAGAGTTTGTATGGGGGAGTAAAATTTTGGAG
GAAAAATAATAAAAAAAATTGAGGGAAATGAGTTTGGGGTAGATGGGGGGTGAGATGGGAGGAGA
GTAAAAGTTTTGAGGGAAAGTGAGAAGG
Found at i:11936 original size:18 final size:18
Alignment explanation
Indices: 11902--11947 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
11892 ATTCATAAAA
*
11902 AATTCGAGTTGACTCGAAT
1 AATTCGA-TTAACTCGAAT
11921 AATTCGATTAACTCGAAT
1 AATTCGATTAACTCGAAT
*
11939 AACTCGATT
1 AATTCGATT
11948 CGTTTAACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 18 0.72
19 7 0.28
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (18 bp):
AATTCGATTAACTCGAAT
Found at i:17014 original size:30 final size:30
Alignment explanation
Indices: 16971--17029 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
16961 GTGGGTGGGA
*
16971 TGAGAGGAGAGTAAAAGTTTTAGGAGGAAAG
1 TGAGAGGAGAGTAAAAGTGTT-GGAGGAAAG
*
17002 TGAGATGA-AGTAAAAGTGTTGGAGGAAA
1 TGAGAGGAGAGTAAAAGTGTTGGAGGAAA
17030 TTAAAAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 8 0.31
30 11 0.42
31 7 0.27
ACGTcount: A:0.42, C:0.00, G:0.37, T:0.20
Consensus pattern (30 bp):
TGAGAGGAGAGTAAAAGTGTTGGAGGAAAG
Found at i:17201 original size:21 final size:22
Alignment explanation
Indices: 17177--17220 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
17167 GGGGGAGAGT
*
17177 GGGAAAGAATA-AAAGTTTTGG
1 GGGAAAGAATATAAAGGTTTGG
17198 GGGAAAGAATATAAAGGTTTGG
1 GGGAAAGAATATAAAGGTTTGG
17220 G
1 G
17221 AGTTTGGGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.41, C:0.00, G:0.36, T:0.23
Consensus pattern (22 bp):
GGGAAAGAATATAAAGGTTTGG
Found at i:18457 original size:23 final size:23
Alignment explanation
Indices: 18380--18530 Score: 105
Period size: 23 Copynumber: 6.6 Consensus size: 23
18370 TATACAGAAC
* *
18380 AAACAGAGAGTAC-CAAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
18402 -AACAGAGA--ACACATAAGTGCT
1 AAACAGAGAGCACACA-AAGTGCT
* *
18423 GGGTAACAGAGAGCACACACAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
* *
18449 AAACAGAGAGTACACAAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
* *
18472 AATCAGAGAGCACACAAACTGCT
1 AAACAGAGAGCACACAAAGTGCT
** * *
18495 AGTCAGAGAGCACGA-GACGTGCT
1 AAACAGAGAGCAC-ACAAAGTGCT
*
18518 AAACAGAAAGCAC
1 AAACAGAGAGCAC
18531 GCTAGTGTTC
Statistics
Matches: 103, Mismatches: 17, Indels: 17
0.75 0.12 0.12
Matches are distributed among these distances:
19 2 0.02
20 2 0.02
21 14 0.14
23 65 0.63
24 1 0.01
25 8 0.08
26 6 0.06
27 5 0.05
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:18502 original size:69 final size:68
Alignment explanation
Indices: 18380--18524 Score: 181
Period size: 69 Copynumber: 2.1 Consensus size: 68
18370 TATACAGAAC
* *
18380 AAACAGAGAGTACCAAAGTACTAACAGAGAACACATAAGTGCTGGGTAACAGAGAGCAC-ACACA
1 AAACAGAGAGTACCAAAGTACTAACAGAGAACACATAACTGCTGAGT-ACAGAGAGCACGACAC-
18444 GTGCT
64 GTGCT
*
18449 AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACACA-AACTGCT-AGT-CAGAGAGCACGAG
1 AAACAGAGAGTAC-CAAAGTACTAA-CAGAGA--ACACATAACTGCTGAGTACAGAGAGCACGAC
18511 ACGTGCT
62 ACGTGCT
18518 AAACAGA
1 AAACAGA
18525 AAGCACGCTA
Statistics
Matches: 68, Mismatches: 3, Indels: 10
0.84 0.04 0.12
Matches are distributed among these distances:
69 35 0.51
70 14 0.21
71 8 0.12
72 6 0.09
73 5 0.07
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (68 bp):
AAACAGAGAGTACCAAAGTACTAACAGAGAACACATAACTGCTGAGTACAGAGAGCACGACACGT
GCT
Found at i:24533 original size:62 final size:62
Alignment explanation
Indices: 24457--24583 Score: 227
Period size: 62 Copynumber: 2.0 Consensus size: 62
24447 TCAAACAATC
* *
24457 TCTGACTATTTTCTAGCCATTGTTCAACTTCTGTTGGATCATCATCTTTATTTCCTTTGAAT
1 TCTGACTATTTTCTAGCCATTATTCAACTTCTGCTGGATCATCATCTTTATTTCCTTTGAAT
*
24519 TCTGACTATTTTCTAGCCATTATTCAACTTCTGCTGGATCATCATCTTTCTTTCCTTTGAAT
1 TCTGACTATTTTCTAGCCATTATTCAACTTCTGCTGGATCATCATCTTTATTTCCTTTGAAT
24581 TCT
1 TCT
24584 TCGGCTCCAT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.19, C:0.23, G:0.10, T:0.48
Consensus pattern (62 bp):
TCTGACTATTTTCTAGCCATTATTCAACTTCTGCTGGATCATCATCTTTATTTCCTTTGAAT
Found at i:25685 original size:23 final size:23
Alignment explanation
Indices: 25659--25761 Score: 118
Period size: 23 Copynumber: 4.4 Consensus size: 23
25649 AGTGCTGGGT
25659 AACAGAGAGCACACACAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
*
25682 AACAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
***
25705 GTTAGAGAGCACACACAGTGCTAA
1 AACAGAGAGCACACACAGTGCT-A
*
25729 TAACAGAGAGCACGAGAC-GTGCTA
1 -AACAGAGAGCAC-ACACAGTGCTA
*
25753 AATAGAGAG
1 AACAGAGAG
25762 TGCGCTAGTG
Statistics
Matches: 67, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
23 48 0.72
24 2 0.03
25 14 0.21
26 3 0.04
ACGTcount: A:0.43, C:0.20, G:0.25, T:0.12
Consensus pattern (23 bp):
AACAGAGAGCACACACAGTGCTA
Found at i:25690 original size:48 final size:48
Alignment explanation
Indices: 25633--25741 Score: 143
Period size: 48 Copynumber: 2.3 Consensus size: 48
25623 ACCAAAGTAG
* *
25633 TAACAGAGAGCACA-TAAGTGCTGGGTAACAGAGAGCACACACAGTGCT-A
1 TAACAGAGAGCACACAAAGTGCT-AGT--CAGAGAGCACACACAGTGCTAA
*
25682 -AACAGAGAGCACACAAAGTGCTAGTTAGAGAGCACACACAGTGCTAA
1 TAACAGAGAGCACACAAAGTGCTAGTCAGAGAGCACACACAGTGCTAA
25729 TAACAGAGAGCAC
1 TAACAGAGAGCAC
25742 GAGACGTGCT
Statistics
Matches: 54, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
46 19 0.35
47 1 0.02
48 27 0.50
49 7 0.13
ACGTcount: A:0.41, C:0.21, G:0.25, T:0.13
Consensus pattern (48 bp):
TAACAGAGAGCACACAAAGTGCTAGTCAGAGAGCACACACAGTGCTAA
Found at i:25751 original size:48 final size:46
Alignment explanation
Indices: 25662--25761 Score: 130
Period size: 48 Copynumber: 2.1 Consensus size: 46
25652 GCTGGGTAAC
**
25662 AGAGAGCACACACAGTGCTAAACAGAGAGCACACAAAGTGCTAGTT
1 AGAGAGCACACACAGTGCTAAACAGAGAGCACACAAAGTGCTAAAT
* *
25708 AGAGAGCACACACAGTGCTAATAACAGAGAGCACGA-GACGTGCTAAAT
1 AGAGAGCACACACAGTGCT-A-AACAGAGAGCAC-ACAAAGTGCTAAAT
25756 AGAGAG
1 AGAGAG
25762 TGCGCTAGTG
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
46 19 0.40
47 1 0.02
48 26 0.55
49 1 0.02
ACGTcount: A:0.42, C:0.20, G:0.26, T:0.12
Consensus pattern (46 bp):
AGAGAGCACACACAGTGCTAAACAGAGAGCACACAAAGTGCTAAAT
Found at i:25761 original size:25 final size:25
Alignment explanation
Indices: 25633--25741 Score: 120
Period size: 23 Copynumber: 4.5 Consensus size: 25
25623 ACCAAAGTAG
* **
25633 TAACAGAGAGCACATA-AGTGCTGGG
1 TAACAGAGAGCACACACAGTGCT-AA
25658 TAACAGAGAGCACACACAGTGCT-A
1 TAACAGAGAGCACACACAGTGCTAA
* *
25682 -AACAGAGAGCACACAAAGTGCTAG
1 TAACAGAGAGCACACACAGTGCTAA
*
25706 T--TAGAGAGCACACACAGTGCTAA
1 TAACAGAGAGCACACACAGTGCTAA
25729 TAACAGAGAGCAC
1 TAACAGAGAGCAC
25742 GAGACGTGCT
Statistics
Matches: 71, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
23 41 0.58
25 24 0.34
26 6 0.08
ACGTcount: A:0.41, C:0.21, G:0.25, T:0.13
Consensus pattern (25 bp):
TAACAGAGAGCACACACAGTGCTAA
Found at i:29306 original size:49 final size:49
Alignment explanation
Indices: 29253--30118 Score: 640
Period size: 49 Copynumber: 17.8 Consensus size: 49
29243 CCCTGAAAAC
* *
29253 ATGAAGGGAAAGATTGAAGCCGCAATGGCGAATCTTGTACCCTCGAGAT
1 ATGAAGGGAAAGATTGAAGCCGCAACGGCGAATCTTGTACCCTAGAGAT
* * * *
29302 ATGAAGGGAAAGATTGAAACCGCAATGGTGAATCTTGTACCTTAGAGAT
1 ATGAAGGGAAAGATTGAAGCCGCAACGGCGAATCTTGTACCCTAGAGAT
* * *
29351 GTGATGGGAAAGATTGAAGCCGCAACGACGAATCTTGTACCCTAGAGAT
1 ATGAAGGGAAAGATTGAAGCCGCAACGGCGAATCTTGTACCCTAGAGAT
* * * * * ** *
29400 ATGAAGGGAAAGGTTGAAGCTGTAACGACGAACCTAATACCCTAAAGA-
1 ATGAAGGGAAAGATTGAAGCCGCAACGGCGAATCTTGTACCCTAGAGAT
* * * *
29448 ATTGGAGGGAAAGATTGAAGCCGAAACGGCGAACCTTGTACCTTAGAGAT
1 A-TGAAGGGAAAGATTGAAGCCGCAACGGCGAATCTTGTACCCTAGAGAT
* * * * * *
29498 ATGATGAGAAAGATTGAAGCCGTAATGACGAATCTTGTACCTTAGAGAT
1 ATGAAGGGAAAGATTGAAGCCGCAACGGCGAATCTTGTACCCTAGAGAT
* * ** * *
29547 GTGATGGGAAAGATTGAAGTTGCAATGGTGAATCTTGTACCCTAGAGAT
1 ATGAAGGGAAAGATTGAAGCCGCAACGGCGAATCTTGTACCCTAGAGAT
* * * * * *
29596 ATGGA-TGAAAGGTTGAA---G---CGGCGAACCTTATACCATAGAGAT
1 ATGAAGGGAAAGATTGAAGCCGCAACGGCGAATCTTGTACCCTAGAGAT
* * *** * * * * *
29638 GTGAAGGGAAAGGTTGAAATAGCGATGGTGAACCTTGTACCTTAGAGAT
1 ATGAAGGGAAAGATTGAAGCCGCAACGGCGAATCTTGTACCCTAGAGAT
* ** * * * *
29687 ATGATGGGAAAGATTGAAGTTGCAATGGCGAATGTTGTACCTTAAAGAT
1 ATGAAGGGAAAGATTGAAGCCGCAACGGCGAATCTTGTACCCTAGAGAT
* * * * * *
29736 GTGATA-GGAACA-ATTGAAGTCGTAACGACGAATCTTGTAACCTAGATAT
1 ATGA-AGGGAA-AGATTGAAGCCGCAACGGCGAATCTTGTACCCTAGAGAT
* * * * * * * * *
29785 ATGGAGGGAATGGTTAAAGCCAC-GCGGCGAATCTTATCCCCTAGACAT
1 ATGAAGGGAAAGATTGAAGCCGCAACGGCGAATCTTGTACCCTAGAGAT
* * * * * * * *
29833 GTGGAGGGAAAGGTTGAAGTCGCAACGACGAACCTTATACCTTAGAGAT
1 ATGAAGGGAAAGATTGAAGCCGCAACGGCGAATCTTGTACCCTAGAGAT
* * * * * *
29882 GTGATGAGAAAGATTGAAGCCGCAACAGCGAATCTTATACCCTAAAGAT
1 ATGAAGGGAAAGATTGAAGCCGCAACGGCGAATCTTGTACCCTAGAGAT
* * * * ** * * * *
29931 GTGAAGGGAAAGGTTAAAGCCGTAGTGGTGAACCTTATACCTTAGAGAT
1 ATGAAGGGAAAGATTGAAGCCGCAACGGCGAATCTTGTACCCTAGAGAT
* * * *
29980 GTGATGGGAAAGATTGAAGCCGTAACGGCGAATCTTATACCCTAGAGAT
1 ATGAAGGGAAAGATTGAAGCCGCAACGGCGAATCTTGTACCCTAGAGAT
* * * * * * *
30029 ATGGAGGGAAAGGTTGAAGTCGCAACGAC-AAACTTTTTACCTTAGAGAT
1 ATGAAGGGAAAGATTGAAGCCGCAACGGCGAATC-TTGTACCCTAGAGAT
* *
30078 GTGAAGGGAAAGATTGAAGCCGCAACGGCGAATCTTATACC
1 ATGAAGGGAAAGATTGAAGCCGCAACGGCGAATCTTGTACC
30119 TTGAAGATGA
Statistics
Matches: 647, Mismatches: 154, Indels: 32
0.78 0.18 0.04
Matches are distributed among these distances:
42 22 0.03
43 11 0.02
45 1 0.00
46 1 0.00
48 52 0.08
49 555 0.86
50 5 0.01
ACGTcount: A:0.34, C:0.15, G:0.28, T:0.23
Consensus pattern (49 bp):
ATGAAGGGAAAGATTGAAGCCGCAACGGCGAATCTTGTACCCTAGAGAT
Found at i:29458 original size:98 final size:98
Alignment explanation
Indices: 29257--30118 Score: 717
Period size: 98 Copynumber: 8.9 Consensus size: 98
29247 GAAAACATGA
* * * * * *
29257 AGGGAAAGATTGAAGCCGCAATGGCGAATCTTGTACCCTCGAGATATGAAGGGAAAGATTGAAAC
1 AGGGAAAGATTGAAGTCGCAACGGCGAACCTTGTACCTTAGAGATATGAAGGGAAAGATTGAAGC
* * * *
29322 CGCAATGGTGAATCTTGTACCTTAGAGATGT-G
66 CGCAACGGCGAATCTTATACCCTAGAGATGTGG
* * * * *
29354 ATGGGAAAGATTGAAGCCGCAACGACGAATCTTGTACCCTAGAGATATGAAGGGAAAGGTTGAAG
1 A-GGGAAAGATTGAAGTCGCAACGGCGAACCTTGTACCTTAGAGATATGAAGGGAAAGATTGAAG
* * * * * *
29419 CTGTAACGACGAACCTAATACCCTAAAGAAT-TGG
65 CCGCAACGGCGAATCTTATACCCTAGAG-ATGTGG
* * * *
29453 AGGGAAAGATTGAAGCCGAAACGGCGAACCTTGTACCTTAGAGATATGATGAGAAAGATTGAAGC
1 AGGGAAAGATTGAAGTCGCAACGGCGAACCTTGTACCTTAGAGATATGAAGGGAAAGATTGAAGC
* * * * *
29518 CGTAATGACGAATCTTGTACCTTAGAGATGT-G
66 CGCAACGGCGAATCTTATACCCTAGAGATGTGG
* * * * * * * *
29550 ATGGGAAAGATTGAAGTTGCAATGGTGAATCTTGTACCCTAGAGATATGGA-TGAAAGGTTGAA-
1 A-GGGAAAGATTGAAGTCGCAACGGCGAACCTTGTACCTTAGAGATATGAAGGGAAAGATTGAAG
* * *
29613 --G---CGGCGAACCTTATACCATAGAGATGTGA
65 CCGCAACGGCGAATCTTATACCCTAGAGATGTGG
* * * * * * * *
29642 AGGGAAAGGTTGAAATAGCGATGGTGAACCTTGTACCTTAGAGATATGATGGGAAAGATTGAAGT
1 AGGGAAAGATTGAAGTCGCAACGGCGAACCTTGTACCTTAGAGATATGAAGGGAAAGATTGAAGC
* * * * * *
29707 TGCAATGGCGAATGTTGTACCTTAAAGATGT-G
66 CGCAACGGCGAATCTTATACCCTAGAGATGTGG
* * * * * * * * *
29739 ATAGGAACA-ATTGAAGTCGTAACGACGAATCTTGTAACC-TAGATATATGGAGGGAATGGTTAA
1 A-GGGAA-AGATTGAAGTCGCAACGGCGAACCTTGT-ACCTTAGAGATATGAAGGGAAAGATTGA
* * * *
29802 AGCCAC-GCGGCGAATCTTATCCCCTAGACATGTGG
63 AGCCGCAACGGCGAATCTTATACCCTAGAGATGTGG
* * * * * *
29837 AGGGAAAGGTTGAAGTCGCAACGACGAACCTTATACCTTAGAGATGTGATGAGAAAGATTGAAGC
1 AGGGAAAGATTGAAGTCGCAACGGCGAACCTTGTACCTTAGAGATATGAAGGGAAAGATTGAAGC
* * *
29902 CGCAACAGCGAATCTTATACCCTAAAGATGTGA
66 CGCAACGGCGAATCTTATACCCTAGAGATGTGG
* * * * ** * * * *
29935 AGGGAAAGGTTAAAGCCGTAGTGGTGAACCTTATACCTTAGAGATGTGATGGGAAAGATTGAAGC
1 AGGGAAAGATTGAAGTCGCAACGGCGAACCTTGTACCTTAGAGATATGAAGGGAAAGATTGAAGC
* *
30000 CGTAACGGCGAATCTTATACCCTAGAGATATGG
66 CGCAACGGCGAATCTTATACCCTAGAGATGTGG
* * * * * *
30033 AGGGAAAGGTTGAAGTCGCAACGACAAACTTTTTACCTTAGAGATGTGAAGGGAAAGATTGAAGC
1 AGGGAAAGATTGAAGTCGCAACGGCGAACCTTGTACCTTAGAGATATGAAGGGAAAGATTGAAGC
30098 CGCAACGGCGAATCTTATACC
66 CGCAACGGCGAATCTTATACC
30119 TTGAAGATGA
Statistics
Matches: 610, Mismatches: 135, Indels: 39
0.78 0.17 0.05
Matches are distributed among these distances:
91 62 0.10
92 11 0.02
94 1 0.00
95 1 0.00
96 4 0.01
97 82 0.13
98 441 0.72
99 8 0.01
ACGTcount: A:0.34, C:0.15, G:0.28, T:0.23
Consensus pattern (98 bp):
AGGGAAAGATTGAAGTCGCAACGGCGAACCTTGTACCTTAGAGATATGAAGGGAAAGATTGAAGC
CGCAACGGCGAATCTTATACCCTAGAGATGTGG
Found at i:30225 original size:42 final size:43
Alignment explanation
Indices: 30131--30225 Score: 108
Period size: 42 Copynumber: 2.3 Consensus size: 43
30121 GAAGATGAGG
* * *
30131 AGAAG-TAGATTGAAGCCACAAAGGTGAATATCAATACTGTAG
1 AGAAGCTAGATTAAAGCCACAAAGGCGAATATCAATACTGTAA
*
30173 AGAAGC-AGATTAAAGCCACAAAGGCGAATCTCAA-AGCTGTAA
1 AGAAGCTAGATTAAAGCCACAAAGGCGAATATCAATA-CTGTAA
*
30215 AG-GGCTAGATT
1 AGAAGCTAGATT
30226 GAAGTTGCAA
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
41 3 0.07
42 42 0.93
ACGTcount: A:0.42, C:0.15, G:0.24, T:0.19
Consensus pattern (43 bp):
AGAAGCTAGATTAAAGCCACAAAGGCGAATATCAATACTGTAA
Found at i:31004 original size:14 final size:14
Alignment explanation
Indices: 30975--31007 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
30965 GAAGACAGAG
30975 ACAAAAGCAAAGAA
1 ACAAAAGCAAAGAA
30989 ACAAACAGCAAA-AA
1 ACAAA-AGCAAAGAA
31003 ACAAA
1 ACAAA
31008 TTACTATGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.73, C:0.18, G:0.09, T:0.00
Consensus pattern (14 bp):
ACAAAAGCAAAGAA
Found at i:31137 original size:4 final size:4
Alignment explanation
Indices: 31128--32621 Score: 1674
Period size: 4 Copynumber: 378.8 Consensus size: 4
31118 TTATGATTTT
*
31128 CATA CATA CATA CATA CATA CATA CATA CATG CATA CATA CA-A GCATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA -CATA
* * *
31176 CATA CATA AATA CATA CATA CATC CATC CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * *
31224 CATA CATC CATA CATA CATA CATG CATA CATA CATA CATG CATA CATG
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* *
31272 CATA CATA CATG CATA CATA CATG CATA CAT- CTATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA C-ATA CATA CATA CATA
* * *
31320 CATA CATA CATG CATA CATA CAT- -ATA CATG CATA CA-A GCATA CATG
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA -CATA CATA
* * * * *
31366 CATG CATG CATG CATA CGTA CATA CATAGA CAGA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CAT--A CATA CATA CATA CATA CATA
* * *
31416 CATT CAAA CATA CA-A GCATA CATA C--A CATA CATG CATA CATA CATA
1 CATA CATA CATA CATA -CATA CATA CATA CATA CATA CATA CATA CATA
* * * * *
31462 CACA CAAA CATG CATA CATA C--A CATA CATG CATA CATA TATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
31508 CAAA CATA CATA CATA CATA CATA CATA CATA CATA CATA CA-A GCATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA -CATA
* *
31556 CATA C--A CATA CATG CATA CA-A GCATA CATA C--A CATA CATT CATA
1 CATA CATA CATA CATA CATA CATA -CATA CATA CATA CATA CATA CATA
* * *
31600 CATG CATA CATA CATA CATA CATA CATA CATA CATA CATG CATA CATG
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * *
31648 CATA CATA TAAA CATA CATA CATG CATA CATA CTTA CATA CATC CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * *
31696 CATA CATA CATA CATG CATA CAGA CATA CATA CATA CA-A GCATA TATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA -CATA CATA
* *
31744 C--A CATA CATG CATA CA-A GCATA CATA C--A CATA CATG CATA CA-A
1 CATA CATA CATA CATA CATA -CATA CATA CATA CATA CATA CATA CATA
* *
31787 GCATA CATA CAT- -ATA CATG CATA CA-A GCATA CATA C--A CATA CATG
1 -CATA CATA CATA CATA CATA CATA CATA -CATA CATA CATA CATA CATA
* * * *
31832 CATA CATG CATA CATA CATA CAAA CATC CATA CATA CATA CATG CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* *
31880 CATG CATA CATG CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* *
31928 CATA CATA CATA CA-A GCATA CATA C--A CATA CATG CATA AATA CATA
1 CATA CATA CATA CATA -CATA CATA CATA CATA CATA CATA CATA CATA
* *
31974 CATA CA-A GCATG CATA CATA C--A CATA CAAA CATA CATA CATA CATA
1 CATA CATA -CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * *
32020 CATA CATC CATA CATA CA-A GTATA CATA CTTA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA -CATA CATA CATA CATA CATA CATA CATA
* * * *
32068 CATA CATT CATA CATT CATA CATA CGTA CATA CATA CATG CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * *
32116 AATA CATA CATA CATA CAGA CATA CATG CATA CATA CATA CATG CATG
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * ** * *
32164 CATG CATA CATA CATA TATG CACG CATG CATG CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* *
32212 CATA CATA CATA CATA CATA CATA CGTA CATA CATA CATA CGTA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * *
32260 CA-A AACA CGTA CATA CATA CATA CATA CATA CATA CATA CACA CTTA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * *
32307 CATA CAGA CATA CACA CATA CATA CAGA CAGA CATA CTTG CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* *
32355 CATA CATA CATA CATG CATA CATA CATA CATA CATA CATA CATA CAAA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * *
32403 CATA CATA CATG CATA CATA CATA CATG CATA CATA CATA CATA CATG
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * *
32451 CATG CGTA CATA CATA CATA CATA CATA CATA CATG CATG CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * *
32499 CATA CATA CATA GATA CATA GATA CATA CATA CATA CATA CTTA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * *
32547 CATA CCTA CATA CATA CATA CATA CATA CATA CTTA CATA CATA CCTA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* *
32595 CATA CATA CTTA CGTA CATA CATA CAT
1 CATA CATA CATA CATA CATA CATA CAT
32622 TTTTCTTTTA
Statistics
Matches: 1260, Mismatches: 179, Indels: 102
0.82 0.12 0.07
Matches are distributed among these distances:
2 22 0.02
3 15 0.01
4 1208 0.96
5 12 0.01
6 3 0.00
ACGTcount: A:0.46, C:0.25, G:0.05, T:0.24
Consensus pattern (4 bp):
CATA
Found at i:32969 original size:30 final size:31
Alignment explanation
Indices: 32917--32988 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 31
32907 TTTATGAAAT
32917 TTTTTAAAATTAAACCCCTTTTATTTT-TTC
1 TTTTTAAAATTAAACCCCTTTTATTTTATTC
* *
32947 ATTTTTCAAATTAAA-TCCTTTTATTTTATTC
1 -TTTTTAAAATTAAACCCCTTTTATTTTATTC
*
32978 TTTTTGAAATT
1 TTTTTAAAATT
32989 TTCCCTTTAC
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 21 0.57
31 16 0.43
ACGTcount: A:0.28, C:0.12, G:0.01, T:0.58
Consensus pattern (31 bp):
TTTTTAAAATTAAACCCCTTTTATTTTATTC
Found at i:39359 original size:194 final size:195
Alignment explanation
Indices: 39027--39416 Score: 710
Period size: 194 Copynumber: 2.0 Consensus size: 195
39017 CAATTATTCG
*
39027 AAAAAGAGTGAGGTAGGTGCTGAAATGTGGCATTCGGAAACTAGCTTAACCACTCCTCAGTCGCA
1 AAAAAGAGTGAGGTAGGTGCTGAAAGGTGGCATTCGGAAACTAGCTTAACCACTCCTCAGTCGCA
**
39092 ACCCCCTTATTCAGTCTTTCCCTTATATTTGTTTTCGGAAAGTTTCCTCTTTCTCAAGTACCTCA
66 ACCCCCTTATTCAGTCTTTCCCTTATATTTGTTTTCAAAAAGTTTCCTCTTTCTCAAGTACCTCA
*
39157 AATCTAGTAACCGACATTCCTTAAGTACGTCTCAAAATATCTCTATTCTACGCTCGTCCCTAGAA
131 AATCTAGTAACCGACATTCCTTAAGTACGTCTCAAAATATCTCTATTCTACGCTCATCCCTAGAA
*
39222 AAAAAGAGTGAGGTAGGTGTTGAAAGGTGGCATTCGGAAACTAGCTTAACCACTCCTCAGTCGCA
1 AAAAAGAGTGAGGTAGGTGCTGAAAGGTGGCATTCGGAAACTAGCTTAACCACTCCTCAGTCGCA
39287 ACCCCC-TATTCAGTCTTTCCCTTATATTTGTTTTCAAAAAGTTTCCTCTTTCTCAAGTACCTCA
66 ACCCCCTTATTCAGTCTTTCCCTTATATTTGTTTTCAAAAAGTTTCCTCTTTCTCAAGTACCTCA
**
39351 AATCTAGTAACCGACATTCCTTAAGTACGTCTCGGAATATCTCTATTCTACGCTCATCCCTAGAA
131 AATCTAGTAACCGACATTCCTTAAGTACGTCTCAAAATATCTCTATTCTACGCTCATCCCTAGAA
39416 A
1 A
39417 GTCCTCCCCT
Statistics
Matches: 188, Mismatches: 7, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
194 119 0.63
195 69 0.37
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (195 bp):
AAAAAGAGTGAGGTAGGTGCTGAAAGGTGGCATTCGGAAACTAGCTTAACCACTCCTCAGTCGCA
ACCCCCTTATTCAGTCTTTCCCTTATATTTGTTTTCAAAAAGTTTCCTCTTTCTCAAGTACCTCA
AATCTAGTAACCGACATTCCTTAAGTACGTCTCAAAATATCTCTATTCTACGCTCATCCCTAGAA
Found at i:40508 original size:9 final size:9
Alignment explanation
Indices: 40494--40538 Score: 90
Period size: 9 Copynumber: 5.0 Consensus size: 9
40484 TGACTAAATT
40494 ATAAATGTC
1 ATAAATGTC
40503 ATAAATGTC
1 ATAAATGTC
40512 ATAAATGTC
1 ATAAATGTC
40521 ATAAATGTC
1 ATAAATGTC
40530 ATAAATGTC
1 ATAAATGTC
40539 CACTCTTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 36 1.00
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.33
Consensus pattern (9 bp):
ATAAATGTC
Found at i:41869 original size:195 final size:193
Alignment explanation
Indices: 41531--41886 Score: 491
Period size: 195 Copynumber: 1.8 Consensus size: 193
41521 CGATGCAATC
* * * *
41531 GCTAAAGTACCGCATATGTTGCGAGACCTCGACAGCTCGTGTGAGCAGCATCGTGAATTGAAAAT
1 GCTAAAGTACCGCATATGTTGCAAGACCTCGACAGCTCGTGTAAGCAGCATCATGAATAGAAAAT
* *
41596 GAGAAATGAATTCAAGAATGGATTACAGACCCTACGATGGCTGGGATTTATGCATAAGTACACAT
66 GAGAAATGAAATCAAAAATGGATTACAGACCCTACGATGGCTGGGATTTATGCATAAGTACACAT
41661 TCTCGACAGCTCGTGTGAGCAGCATCATTAGGGAAACAATTATATGCATAGATACCGTATCGATG
131 TCTCGACAGCTCGTGT--GCAGCATCATTAGGGAAACAATTATATGCATAGATACCGTATCGATG
* * * * *
41726 GCTAAGGTACCGCATATGTTGCAAGTCCTTGATAGCTCGTGTAAGCAGCATCATGAGTCAGAAAA
1 GCTAAAGTACCGCATATGTTGCAAGACCTCGACAGCTCGTGTAAGCAGCATCATGAAT-AGAAAA
* * * * * * *
41791 -GAGATATGAAATCAAAAATGGATTATAGGCTCTACGATGGCTGGGATTTATGCTTGAA-TGCAT
65 TGAGAAATGAAATCAAAAATGGATTACAGACCCTACGATGGCTGGGATTTATGCAT-AAGTACAC
*
41854 ATTCTCGACAGCTCGTGTGCAGCATCGTTAGGG
129 ATTCTCGACAGCTCGTGTGCAGCATCATTAGGG
41887 GACAGTTTAC
Statistics
Matches: 140, Mismatches: 19, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
193 14 0.10
195 119 0.85
196 7 0.05
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (193 bp):
GCTAAAGTACCGCATATGTTGCAAGACCTCGACAGCTCGTGTAAGCAGCATCATGAATAGAAAAT
GAGAAATGAAATCAAAAATGGATTACAGACCCTACGATGGCTGGGATTTATGCATAAGTACACAT
TCTCGACAGCTCGTGTGCAGCATCATTAGGGAAACAATTATATGCATAGATACCGTATCGATG
Found at i:42720 original size:21 final size:21
Alignment explanation
Indices: 42672--42723 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
42662 AAAGTTTTTA
*
42672 GTATCGGTAGAAGCATGACAT
1 GTATCGGTAGAAGCATCACAT
* *
42693 GTTTCGGTAGAAGTCA-CACTT
1 GTATCGGTAGAAG-CATCACAT
42714 GTATCGGTAG
1 GTATCGGTAG
42724 CATTGTCTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (21 bp):
GTATCGGTAGAAGCATCACAT
Found at i:44850 original size:52 final size:52
Alignment explanation
Indices: 44744--44909 Score: 201
Period size: 52 Copynumber: 3.2 Consensus size: 52
44734 TATGATTTTG
* * * * *
44744 GCTCGTAAAAACGTAATTCTG-TT-TGGCTCATAAGAGCGTAATTCGGTCTG
1 GCTCGTAAGAGCGTAATTCTGATTCTGGCTCATAAGAGTGTAATTCTGTCTA
*
44794 GCTCGTAAGAGCGTAATTCTGATTCTGGCTCACAAGAGTGTAATTCTGTCTA
1 GCTCGTAAGAGCGTAATTCTGATTCTGGCTCATAAGAGTGTAATTCTGTCTA
* * * * * * *
44846 GCTCGTAAGAGCATAATTCTGATTCTAGCTCGTAAAATTATAATTCTATCTA
1 GCTCGTAAGAGCGTAATTCTGATTCTGGCTCATAAGAGTGTAATTCTGTCTA
44898 GCTCGTAAGAGC
1 GCTCGTAAGAGC
44910 TAAACTCTAT
Statistics
Matches: 100, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
50 19 0.19
51 2 0.02
52 79 0.79
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.33
Consensus pattern (52 bp):
GCTCGTAAGAGCGTAATTCTGATTCTGGCTCATAAGAGTGTAATTCTGTCTA
Found at i:44880 original size:27 final size:26
Alignment explanation
Indices: 44744--44909 Score: 142
Period size: 25 Copynumber: 6.5 Consensus size: 26
44734 TATGATTTTG
* * *
44744 GCTCGTAAAAACGTAATTCTGTT-TG
1 GCTCGTAAGAGCGTAATTCTGTTCTA
* * *
44769 GCTCATAAGAGCGTAATTC-GGTCTG
1 GCTCGTAAGAGCGTAATTCTGTTCTA
*
44794 GCTCGTAAGAGCGTAATTCTGATTCTG
1 GCTCGTAAGAGCGTAATTCTG-TTCTA
** *
44821 GCTCACAAGAGTGTAATTCTG-TCTA
1 GCTCGTAAGAGCGTAATTCTGTTCTA
*
44846 GCTCGTAAGAGCATAATTCTGATTCTA
1 GCTCGTAAGAGCGTAATTCTG-TTCTA
* *** *
44873 GCTCGTAAAATTATAATTCT-ATCTA
1 GCTCGTAAGAGCGTAATTCTGTTCTA
44898 GCTCGTAAGAGC
1 GCTCGTAAGAGC
44910 TAAACTCTAT
Statistics
Matches: 115, Mismatches: 21, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
24 2 0.02
25 69 0.60
26 1 0.01
27 43 0.37
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.33
Consensus pattern (26 bp):
GCTCGTAAGAGCGTAATTCTGTTCTA
Found at i:44903 original size:25 final size:25
Alignment explanation
Indices: 44834--44905 Score: 90
Period size: 27 Copynumber: 2.8 Consensus size: 25
44824 CACAAGAGTG
* *
44834 TAATTCTGTCTAGCTCGTAAGAGCA
1 TAATTCTATCTAGCTCGTAAAAGCA
**
44859 TAATTCTGATTCTAGCTCGTAAAATTA
1 TAATTCT-A-TCTAGCTCGTAAAAGCA
44886 TAATTCTATCTAGCTCGTAA
1 TAATTCTATCTAGCTCGTAA
44906 GAGCTAAACT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.46
26 1 0.02
27 21 0.51
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.38
Consensus pattern (25 bp):
TAATTCTATCTAGCTCGTAAAAGCA
Found at i:44918 original size:25 final size:26
Alignment explanation
Indices: 44794--44941 Score: 110
Period size: 25 Copynumber: 5.7 Consensus size: 26
44784 ATTCGGTCTG
* *
44794 GCTCGTAAGAGC-GTAATTCTGATTCTG
1 GCTCGTAAGAGCTATAATTCT-A-TCTA
** * *
44821 GCTCACAAGAG-TGTAATTCTGTCTA
1 GCTCGTAAGAGCTATAATTCTATCTA
44846 GCTCGTAAGAGC-ATAATTCTGATTCTA
1 GCTCGTAAGAGCTATAATTCT-A-TCTA
**
44873 GCTCGTAA-AATTATAATTCTATCTA
1 GCTCGTAAGAGCTATAATTCTATCTA
* *
44898 GCTCGTAAGAGCTA-AACTCTATCTGG
1 GCTCGTAAGAGCTATAATTCTATCT-A
*
44924 GCTCGTATGAGCTA-AATT
1 GCTCGTAAGAGCTATAATT
44942 TCTAGAAGAC
Statistics
Matches: 98, Mismatches: 16, Indels: 15
0.76 0.12 0.12
Matches are distributed among these distances:
25 40 0.41
26 21 0.21
27 37 0.38
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (26 bp):
GCTCGTAAGAGCTATAATTCTATCTA
Found at i:56035 original size:32 final size:32
Alignment explanation
Indices: 55999--56063 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
55989 GCATTCTCAT
55999 ATCATATATGCATGACATGTTTTTCGATTCTA
1 ATCATATATGCATGACATGTTTTTCGATTCTA
56031 ATCATATATGCATGACATGTTTTTCGATTCTA
1 ATCATATATGCATGACATGTTTTTCGATTCTA
56063 A
1 A
56064 CTTTTTTAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.43
Consensus pattern (32 bp):
ATCATATATGCATGACATGTTTTTCGATTCTA
Found at i:62365 original size:51 final size:52
Alignment explanation
Indices: 62269--62366 Score: 128
Period size: 52 Copynumber: 1.9 Consensus size: 52
62259 AGATCTGATA
* **
62269 TTTTATATAAAAATAAATATTTATTTAAATTGATTTTGTTTAAATCTGGTGT
1 TTTTACATAAAAATAAATATTTATTTAAATTGATTTTGTACAAATCTGGTGT
* *
62321 TTTTACATAAACAA-AAATATTTGTTTATATT-ATTTTGTACAAATCT
1 TTTTACATAAA-AATAAATATTTATTTAAATTGATTTTGTACAAATCT
62367 TATATTTAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
51 13 0.32
52 25 0.62
53 2 0.05
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50
Consensus pattern (52 bp):
TTTTACATAAAAATAAATATTTATTTAAATTGATTTTGTACAAATCTGGTGT
Found at i:62717 original size:79 final size:81
Alignment explanation
Indices: 62520--62730 Score: 208
Period size: 79 Copynumber: 2.6 Consensus size: 81
62510 AATTTAAGTC
* * *
62520 GAATAAA--TTTGTTTCTGGATTTATT-CTCGCCGTTTAACAGATTTCATTATATTTTGATTTTG
1 GAATAAATCTTTGTTTCGGGATTTATTCCT-GCCGTTCAACAGA-TT--TTAT-TTTTGATTTGG
*
62582 TTTCCAAAACAAGAATAAGTT
61 TTTCCAAAACAAGAATAAATT
* *
62603 GAATAAATCTTT-TTT-GAGATTTATTCCTGCTGTTCAACAGATTTTATTTTT-ATTTGGTTTCC
1 GAATAAATCTTTGTTTCGGGATTTATTCCTGCCGTTCAACAGATTTTATTTTTGATTTGGTTTCC
62665 -AAACAAGAATTAAAATT
66 AAAACAAGAA-T-AAATT
* *
62682 -AA-ACAAT-TTTGTTTCGGGATTTATTCCTACCGTTCAACAGATTTGATTT
1 GAATA-AATCTTTGTTTCGGGATTTATTCCTGCCGTTCAACAGATTTTATTT
62731 GATTTGATTT
Statistics
Matches: 110, Mismatches: 10, Indels: 20
0.79 0.07 0.14
Matches are distributed among these distances:
77 13 0.12
78 19 0.17
79 38 0.35
80 4 0.04
82 2 0.02
83 26 0.24
84 5 0.05
85 3 0.03
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.45
Consensus pattern (81 bp):
GAATAAATCTTTGTTTCGGGATTTATTCCTGCCGTTCAACAGATTTTATTTTTGATTTGGTTTCC
AAAACAAGAATAAATT
Found at i:70796 original size:19 final size:19
Alignment explanation
Indices: 70761--70797 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
70751 CCTAGTTATT
* *
70761 TTTTTTTATTTTTATAGAG
1 TTTTTTTATTATGATAGAG
70780 TTTTTTTATTATGATAGA
1 TTTTTTTATTATGATAGA
70798 TTGATTAAGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.11, T:0.65
Consensus pattern (19 bp):
TTTTTTTATTATGATAGAG
Found at i:71125 original size:26 final size:26
Alignment explanation
Indices: 71073--71125 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
71063 TTATTAGCAC
*
71073 TATATCTTAATTATCAAAATAATTTA
1 TATATCTTAATTATCAAAATAAGTTA
* * *
71099 TATATGTTAATTATCTAAATTAGTTA
1 TATATCTTAATTATCAAAATAAGTTA
71125 T
1 T
71126 TATTTTGAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.49
Consensus pattern (26 bp):
TATATCTTAATTATCAAAATAAGTTA
Found at i:71901 original size:30 final size:31
Alignment explanation
Indices: 71865--71942 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
71855 CAATCAAAAA
* *
71865 TATAAAAAGCAAAAGA-TGAAATGAAACAAT
1 TATAAAAAGAAAAAGACTAAAATGAAACAAT
* *
71895 TATAAAAATAAAAGGACTAAAATGAAACAAT
1 TATAAAAAGAAAAAGACTAAAATGAAACAAT
71926 TATTAAAGAAGAAAAAG
1 TA-TAAA-AAGAAAAAG
71943 GTTGATTAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
30 13 0.33
31 15 0.38
32 4 0.10
33 7 0.18
ACGTcount: A:0.64, C:0.05, G:0.13, T:0.18
Consensus pattern (31 bp):
TATAAAAAGAAAAAGACTAAAATGAAACAAT
Found at i:72945 original size:13 final size:14
Alignment explanation
Indices: 72921--72950 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
72911 AACTATTCAA
72921 TTTTAACTTTTTTT
1 TTTTAACTTTTTTT
72935 TTTTAACTTTTTTT
1 TTTTAACTTTTTTT
72949 TT
1 TT
72951 GTCACCAGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.07, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTAACTTTTTTT
Found at i:78845 original size:125 final size:127
Alignment explanation
Indices: 78600--78829 Score: 313
Period size: 127 Copynumber: 1.8 Consensus size: 127
78590 AATCCTTCTT
* * *
78600 CGCAAATGGATCAACTCTAAAGACAACCCAACAACAAAATCAACATTTTTAAACTAATAAATCTC
1 CGCAAATGGATCAACACCAAAGACAACCCAACAACAAAATCAACATATTTAAACTAATAAATCTC
**
78665 TTTCTAGGATACCCAAACCGCAATTAAAGCTTAAATCAACAATGAAATAAAAAGTAATTACA
66 TTTCTAAAATACCCAAACCGCAATTAAAGCTTAAATCAACAATGAAATAAAAAGTAATTACA
* ** * *
78727 CGCAAATGGATCAGCACCAAAGAGTATCCAACAACAGAATCAA-A-ATTTAAACTAATAAATCTC
1 CGCAAATGGATCAACACCAAAGACAACCCAACAACAAAATCAACATATTTAAACTAATAAATCTC
* *
78790 TTTCTAAAATACCCCAAACCGTAATTGAAGGC-TAAATCAA
66 TTTCTAAAATA-CCCAAACCGCAATT-AAAGCTTAAATCAA
78830 TGAAGAAAAG
Statistics
Matches: 89, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
125 27 0.30
126 22 0.25
127 40 0.45
ACGTcount: A:0.47, C:0.22, G:0.09, T:0.22
Consensus pattern (127 bp):
CGCAAATGGATCAACACCAAAGACAACCCAACAACAAAATCAACATATTTAAACTAATAAATCTC
TTTCTAAAATACCCAAACCGCAATTAAAGCTTAAATCAACAATGAAATAAAAAGTAATTACA
Found at i:80110 original size:20 final size:21
Alignment explanation
Indices: 80061--80110 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
80051 GTTTAAAATG
80061 TTATTTTTATATCATAATATT
1 TTATTTTTATATCATAATATT
**
80082 TTAGCTTTATGA-CAT-ATATT
1 TTATTTTTAT-ATCATAATATT
80102 TTATTTTTA
1 TTATTTTTA
80111 AAATATAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 12 0.50
21 11 0.46
22 1 0.04
ACGTcount: A:0.30, C:0.06, G:0.04, T:0.60
Consensus pattern (21 bp):
TTATTTTTATATCATAATATT
Found at i:80725 original size:29 final size:29
Alignment explanation
Indices: 80691--80747 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
80681 TCCACCTTGA
* *
80691 CACGAATTCTCAATGAACAAGTTATTCAC
1 CACGAACTCTCAACGAACAAGTTATTCAC
*
80720 CACGAACTCTCAACGAACAAGTTCTTCA
1 CACGAACTCTCAACGAACAAGTTATTCA
80748 GCTCTTCCAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.37, C:0.28, G:0.11, T:0.25
Consensus pattern (29 bp):
CACGAACTCTCAACGAACAAGTTATTCAC
Found at i:82410 original size:37 final size:36
Alignment explanation
Indices: 82361--82436 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 36
82351 ATTCCAAAAA
82361 TAATATTATTTTAATAGT-TTAATATTAAATTTAAT-T
1 TAATATTATTTTAATAGTATT-ATATT-AATTTAATAT
*
82397 TAATACTTATTTTAATAGTATTTTATTAATTTAATAT
1 TAATA-TTATTTTAATAGTATTATATTAATTTAATAT
82434 TAA
1 TAA
82437 AGTGATTATC
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
36 13 0.36
37 21 0.58
38 2 0.06
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (36 bp):
TAATATTATTTTAATAGTATTATATTAATTTAATAT
Found at i:82434 original size:11 final size:11
Alignment explanation
Indices: 82361--82436 Score: 52
Period size: 12 Copynumber: 6.8 Consensus size: 11
82351 ATTCCAAAAA
*
82361 TAATATTATTT
1 TAATATTAATT
82372 TAATAGTTTAATAT
1 TAATA--TTAAT-T
82386 TAA-ATTTAATT
1 TAATA-TTAATT
*
82397 TAATACTTATTT
1 TAATA-TTAATT
*
82409 TAATAGT-ATT
1 TAATATTAATT
82419 T--TATTAATT
1 TAATATTAATT
82428 TAATATTAA
1 TAATATTAA
82437 AGTGATTATC
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
8 3 0.06
9 4 0.08
10 3 0.06
11 16 0.31
12 17 0.33
13 5 0.10
14 4 0.08
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (11 bp):
TAATATTAATT
Found at i:84966 original size:12 final size:12
Alignment explanation
Indices: 84949--84985 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
84939 CACTGGCTTG
84949 AGTTGTATCGAT
1 AGTTGTATCGAT
84961 AGTTGTATC-AT
1 AGTTGTATCGAT
84972 AG--GTATCGAT
1 AGTTGTATCGAT
84982 AGTT
1 AGTT
84986 CTACTTACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
9 5 0.23
10 4 0.18
11 4 0.18
12 9 0.41
ACGTcount: A:0.27, C:0.08, G:0.24, T:0.41
Consensus pattern (12 bp):
AGTTGTATCGAT
Found at i:93565 original size:3 final size:3
Alignment explanation
Indices: 93559--93592 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
93549 ACCACCACCA
93559 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
93593 TGACGTTGGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:95455 original size:30 final size:31
Alignment explanation
Indices: 95421--95501 Score: 96
Period size: 30 Copynumber: 2.7 Consensus size: 31
95411 ACTACATTTA
95421 ACAAAACAGTCACTCAACTT-T-GAAAATGTG
1 ACAAAACAGTCACTCAACTTATCGAAAA-GTG
* * *
95451 ACAAAACAATCACTGAAGTTATCGAAAAGTG
1 ACAAAACAGTCACTCAACTTATCGAAAAGTG
*
95482 ACAAAACAGTC-CTCTACTTA
1 ACAAAACAGTCACTCAACTTA
95502 CTATTCATTT
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
30 23 0.55
31 14 0.33
32 5 0.12
ACGTcount: A:0.44, C:0.21, G:0.12, T:0.22
Consensus pattern (31 bp):
ACAAAACAGTCACTCAACTTATCGAAAAGTG
Found at i:96764 original size:20 final size:20
Alignment explanation
Indices: 96735--96778 Score: 61
Period size: 22 Copynumber: 2.1 Consensus size: 20
96725 AATAGAAGAG
*
96735 AAAGAAAATAAAAAGAAAGTTA
1 AAAGAATATAAAAA-AAA-TTA
96757 AAAGAATATAAAAAAAATTA
1 AAAGAATATAAAAAAAATTA
96777 AA
1 AA
96779 TTGCTTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.24
21 3 0.14
22 13 0.62
ACGTcount: A:0.75, C:0.00, G:0.09, T:0.16
Consensus pattern (20 bp):
AAAGAATATAAAAAAAATTA
Found at i:101420 original size:14 final size:15
Alignment explanation
Indices: 101401--101436 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
101391 TTAAAAATAT
101401 TTTTTTTTTATTT-C
1 TTTTTTTTTATTTAC
*
101415 TTTTTTTTTTTTTAC
1 TTTTTTTTTATTTAC
101430 TTTTTTT
1 TTTTTTT
101437 CGGCAACTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.06, C:0.06, G:0.00, T:0.89
Consensus pattern (15 bp):
TTTTTTTTTATTTAC
Found at i:101420 original size:15 final size:15
Alignment explanation
Indices: 101400--101436 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
101390 TTTAAAAATA
101400 TTTTTTTTTTATTT-C
1 TTTTTTTTTT-TTTAC
101415 TTTTTTTTTTTTTAC
1 TTTTTTTTTTTTTAC
101430 TTTTTTT
1 TTTTTTT
101437 CGGCAACTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 3 0.14
15 18 0.86
ACGTcount: A:0.05, C:0.05, G:0.00, T:0.89
Consensus pattern (15 bp):
TTTTTTTTTTTTTAC
Found at i:101518 original size:13 final size:12
Alignment explanation
Indices: 101499--101559 Score: 50
Period size: 13 Copynumber: 4.8 Consensus size: 12
101489 AAAGATAGTC
101499 AAATCAGTTAAT
1 AAATCAGTTAAT
**
101511 AGAATCAGTTGGTT
1 A-AATCAGTT-AAT
101525 AAATCAGTTAAT
1 AAATCAGTTAAT
* *
101537 AGAATTAGTTGAT
1 A-AATCAGTTAAT
101550 CAAATCAGTT
1 -AAATCAGTT
101560 TGTAACACCC
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
12 3 0.08
13 32 0.84
14 3 0.08
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.34
Consensus pattern (12 bp):
AAATCAGTTAAT
Found at i:101535 original size:26 final size:26
Alignment explanation
Indices: 101497--101559 Score: 99
Period size: 26 Copynumber: 2.4 Consensus size: 26
101487 TCAAAGATAG
*
101497 TCAAATCAGTTAATAGAATCAGTTGG
1 TCAAATCAGTTAATAGAATCAGTTGA
* *
101523 TTAAATCAGTTAATAGAATTAGTTGA
1 TCAAATCAGTTAATAGAATCAGTTGA
101549 TCAAATCAGTT
1 TCAAATCAGTT
101560 TGTAACACCC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.35
Consensus pattern (26 bp):
TCAAATCAGTTAATAGAATCAGTTGA
Found at i:104343 original size:2 final size:2
Alignment explanation
Indices: 104338--104367 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
104328 ATTTTATTTC
104338 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.