Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007793.1 Corchorus capsularis cultivar CVL-1 contig07814, 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: 102033
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:10097 original size:19 final size:19
Alignment explanation
Indices: 10061--10099 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
10051 AGCTTGGCCT
* **
10061 AAAAAAGAAAGAGGTTGCA
1 AAAAAAGAAAAAAATTGCA
10080 AAAAAAGAAAAAAATTGCA
1 AAAAAAGAAAAAAATTGCA
10099 A
1 A
10100 CGTCATGTAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.67, C:0.05, G:0.18, T:0.10
Consensus pattern (19 bp):
AAAAAAGAAAAAAATTGCA
Found at i:11945 original size:38 final size:38
Alignment explanation
Indices: 11900--12453 Score: 613
Period size: 38 Copynumber: 14.7 Consensus size: 38
11890 TCAAACTCAA
* * *
11900 AGCAATTATCAAGATCGATTGGAAACATGTTATCTTTC
1 AGCAATTATCAAGATCGACTGGAAACAGGTCATCTTTC
* * * * *
11938 AGTAATTATCGAG-TTGA-TCGAAAACAAGTCATCTTTC
1 AGCAATTATCAAGATCGACT-GGAAACAGGTCATCTTTC
*
11975 AGCAATCATCAA-AGTCGACTGGAAACAGGTCATCTTTC
1 AGCAATTATCAAGA-TCGACTGGAAACAGGTCATCTTTC
* *
12013 AGCATTTATCAAGATCGAGTGGAAACAGGTCATCTTTC
1 AGCAATTATCAAGATCGACTGGAAACAGGTCATCTTTC
* * * *
12051 AACAATCAT-TAGACTCGACTGGAAACGGGTCATCTTTC
1 AGCAATTATCAAGA-TCGACTGGAAACAGGTCATCTTTC
* * ***
12089 AGCAATTATCAAG-TTGATTGGAAACAGGTCATCTCAA
1 AGCAATTATCAAGATCGACTGGAAACAGGTCATCTTTC
* * *
12126 AGCAGTTATCAAGATCGACTAGAAATAGGTCATCTTTC
1 AGCAATTATCAAGATCGACTGGAAACAGGTCATCTTTC
* * * *
12164 AACAATTATCAAG-TTGATTGGAAACAGTTCATCTTTC
1 AGCAATTATCAAGATCGACTGGAAACAGGTCATCTTTC
* *
12201 AGCAATCATCATAG-TCGACTGGAAAAAGGTCATCTTTC
1 AGCAATTATCA-AGATCGACTGGAAACAGGTCATCTTTC
* * *
12239 AGCAGTTATCAAGATCGACTGGATACCGGTCATCTTTC
1 AGCAATTATCAAGATCGACTGGAAACAGGTCATCTTTC
*
12277 AGCAATCATC-AGAGTCGACTGGAAACAGGTCATCTTTC
1 AGCAATTATCAAGA-TCGACTGGAAACAGGTCATCTTTC
* * ***
12315 AGCAGTTATCAAGATCGACTGGAAACAGGTCGTCTCAA
1 AGCAATTATCAAGATCGACTGGAAACAGGTCATCTTTC
* *
12353 AGCAGTTATCAAGATCGACTGGAAACAGGTCATTTTTC
1 AGCAATTATCAAGATCGACTGGAAACAGGTCATCTTTC
* *
12391 AGCAATTATCAAG-TTGACTTGAAACAGGTCATCTTTC
1 AGCAATTATCAAGATCGACTGGAAACAGGTCATCTTTC
*
12428 AGCAGTTATCAAGATCGACTGGAAAC
1 AGCAATTATCAAGATCGACTGGAAAC
12454 TTTTCAGTTT
Statistics
Matches: 425, Mismatches: 78, Indels: 26
0.80 0.15 0.05
Matches are distributed among these distances:
36 1 0.00
37 126 0.30
38 291 0.68
39 7 0.02
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (38 bp):
AGCAATTATCAAGATCGACTGGAAACAGGTCATCTTTC
Found at i:12111 original size:113 final size:112
Alignment explanation
Indices: 11895--12453 Score: 652
Period size: 113 Copynumber: 4.9 Consensus size: 112
11885 CAACATCAAA
* * * * ** * * * *
11895 CTCAAAGCAATTATCAAGATCGATTGGAAACATGTTATCTTTCAGTAATTATCGAGTTGA-TCGA
1 CTCAAAGCAGTTATCAAGATCGACTGGAAACAGGTCATCTTTCAACAATCATCAAGTCGACT-GG
* *
11959 AAACAAGTCATCTTTCAGCAATCATCAAAGTCGACTGGAAACAGGTCAT
65 AAACAGGTCATCTTTCAGCAATTATC-AAGTCGACTGGAAACAGGTCAT
*** * * * *
12008 CTTTCAGCATTTATCAAGATCGAGTGGAAACAGGTCATCTTTCAACAATCATTAGACTCGACTGG
1 CTCAAAGCAGTTATCAAGATCGACTGGAAACAGGTCATCTTTCAACAATCATCA-AGTCGACTGG
* * *
12073 AAACGGGTCATCTTTCAGCAATTATCAAGTTGATTGGAAACAGGTCAT
65 AAACAGGTCATCTTTCAGCAATTATCAAGTCGACTGGAAACAGGTCAT
* * * * *
12121 CTCAAAGCAGTTATCAAGATCGACTAGAAATAGGTCATCTTTCAACAATTATCAAGTTGATTGGA
1 CTCAAAGCAGTTATCAAGATCGACTGGAAACAGGTCATCTTTCAACAATCATCAAGTCGACTGGA
* * *
12186 AACAGTTCATCTTTCAGCAATCATCATAGTCGACTGGAAAAAGGTCAT
66 AACAGGTCATCTTTCAGCAATTATCA-AGTCGACTGGAAACAGGTCAT
*** * * *
12234 CTTTCAGCAGTTATCAAGATCGACTGGATACCGGTCATCTTTCAGCAATCATCAGAGTCGACTGG
1 CTCAAAGCAGTTATCAAGATCGACTGGAAACAGGTCATCTTTCAACAATCATCA-AGTCGACTGG
* *
12299 AAACAGGTCATCTTTCAGCAGTTATCAAGATCGACTGGAAACAGGTCGT
65 AAACAGGTCATCTTTCAGCAATTATCAAG-TCGACTGGAAACAGGTCAT
* * * * *
12348 CTCAAAGCAGTTATCAAGATCGACTGGAAACAGGTCATTTTTCAGCAATTATCAAGTTGACTTGA
1 CTCAAAGCAGTTATCAAGATCGACTGGAAACAGGTCATCTTTCAACAATCATCAAGTCGACTGGA
*
12413 AACAGGTCATCTTTCAGCAGTTATCAAGATCGACTGGAAAC
66 AACAGGTCATCTTTCAGCAATTATCAAG-TCGACTGGAAAC
12454 TTTTCAGTTT
Statistics
Matches: 378, Mismatches: 63, Indels: 10
0.84 0.14 0.02
Matches are distributed among these distances:
112 31 0.08
113 222 0.59
114 124 0.33
115 1 0.00
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (112 bp):
CTCAAAGCAGTTATCAAGATCGACTGGAAACAGGTCATCTTTCAACAATCATCAAGTCGACTGGA
AACAGGTCATCTTTCAGCAATTATCAAGTCGACTGGAAACAGGTCAT
Found at i:12157 original size:75 final size:75
Alignment explanation
Indices: 11899--12453 Score: 573
Period size: 75 Copynumber: 7.4 Consensus size: 75
11889 ATCAAACTCA
* * * * * * * *
11899 AAGCAATTATCAAGATCGATTGGAAACATGTTATCTTTCAGTAATTATCGAGTTGATCGAAAACA
1 AAGCAATCATCAAGATCGACTGGAAACAGGTCATCTTTCAGCAATTATCAAGTTGATTGGAAACA
* *
11964 AGTCATCTTT
66 GGTCATCTCT
* * * *
11974 CAGCAATCATCAA-AGTCGACTGGAAACAGGTCATCTTTCAGCATTTATCAAGATCGAGTGGAAA
1 AAGCAATCATCAAGA-TCGACTGGAAACAGGTCATCTTTCAGCAATTATCAAG-TTGATTGGAAA
*
12038 CAGGTCATCTTT
64 CAGGTCATCTCT
* *
12050 CAA-CAATCAT-TAGACTCGACTGGAAACGGGTCATCTTTCAGCAATTATCAAGTTGATTGGAAA
1 -AAGCAATCATCAAGA-TCGACTGGAAACAGGTCATCTTTCAGCAATTATCAAGTTGATTGGAAA
*
12113 CAGGTCATCTCA
64 CAGGTCATCTCT
* * * * *
12125 AAGCAGTTATCAAGATCGACTAGAAATAGGTCATCTTTCAACAATTATCAAGTTGATTGGAAACA
1 AAGCAATCATCAAGATCGACTGGAAACAGGTCATCTTTCAGCAATTATCAAGTTGATTGGAAACA
* *
12190 GTTCATCTTT
66 GGTCATCTCT
* * * * * *
12200 CAGCAATCATCATAG-TCGACTGGAAAAAGGTCATCTTTCAGCAGTTATCAAGATCGACTGGATA
1 AAGCAATCATCA-AGATCGACTGGAAACAGGTCATCTTTCAGCAATTATCAAG-TTGATTGGAAA
* *
12264 CCGGTCATCTTT
64 CAGGTCATCTCT
* * * *
12276 CAGCAATCATC-AGAGTCGACTGGAAACAGGTCATCTTTCAGCAGTTATCAAGATCGACTGGAAA
1 AAGCAATCATCAAGA-TCGACTGGAAACAGGTCATCTTTCAGCAATTATCAAG-TTGATTGGAAA
* *
12340 CAGGTCGTCTCA
64 CAGGTCATCTCT
* * *
12352 AAGCAGTTATCAAGATCGACTGGAAACAGGTCATTTTTCAGCAATTATCAAGTTGACTT-GAAAC
1 AAGCAATCATCAAGATCGACTGGAAACAGGTCATCTTTCAGCAATTATCAAGTTGA-TTGGAAAC
*
12416 AGGTCATCTTT
65 AGGTCATCTCT
* * *
12427 CAGCAGTTATCAAGATCGACTGGAAAC
1 AAGCAATCATCAAGATCGACTGGAAAC
12454 TTTTCAGTTT
Statistics
Matches: 407, Mismatches: 61, Indels: 24
0.83 0.12 0.05
Matches are distributed among these distances:
74 5 0.01
75 204 0.50
76 194 0.48
77 4 0.01
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.28
Consensus pattern (75 bp):
AAGCAATCATCAAGATCGACTGGAAACAGGTCATCTTTCAGCAATTATCAAGTTGATTGGAAACA
GGTCATCTCT
Found at i:12516 original size:43 final size:43
Alignment explanation
Indices: 12451--12586 Score: 157
Period size: 43 Copynumber: 3.1 Consensus size: 43
12441 ATCGACTGGA
*
12451 AACTTTTCAGTTTTTCAGTTGCTTCAAAAAAAGGGCATTCCAAC
1 AACTTTTCAG-TTTTCAGTTGCTTCAAAAAAGGGGCATTCCAAC
** * * * * *
12495 AACTTTTTGGTTTTCAGTTGCTCCAAGAAGGGGGTATTCTAAC
1 AACTTTTCAGTTTTCAGTTGCTTCAAAAAAGGGGCATTCCAAC
* *
12538 AACTTTTCAGTTTTCAGTTGTTTTC-AAGAAGGGGCATTCCAAC
1 AACTTTTCAGTTTTCAGTTG-CTTCAAAAAAGGGGCATTCCAAC
12581 AACTTT
1 AACTTT
12587 CAACTCCAAA
Statistics
Matches: 74, Mismatches: 17, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
43 64 0.86
44 10 0.14
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (43 bp):
AACTTTTCAGTTTTCAGTTGCTTCAAAAAAGGGGCATTCCAAC
Found at i:15690 original size:39 final size:37
Alignment explanation
Indices: 15636--16123 Score: 395
Period size: 39 Copynumber: 13.1 Consensus size: 37
15626 CATATGCATC
*
15636 AGTAAACACAGTCAATAAGAACTTAATTCAGTGTGATTA
1 AGTAAACACAGTCAA-AAG-ACTTAATTCAGTGTAATTA
*
15675 AGTAAACACAATCAATAAGAACTTAATTCA-TGGTAATTA
1 AGTAAACACAGTCAA-AAG-ACTTAATTCAGT-GTAATTA
* * *
15714 AGTAAACACAGCCAGTAAAGTCTTAATTCAGGGTAATTA
1 AGTAAACACAGTCA--AAAGACTTAATTCAGTGTAATTA
* *
15753 AGTAAA-ATCAGT-AAATGACTTAATTCAGGGTAATTA
1 AGTAAACA-CAGTCAAAAGACTTAATTCAGTGTAATTA
* * *
15789 AGTAAA-ATCAG-C-CAAGACTTAATTCGGAGTAATTA
1 AGTAAACA-CAGTCAAAAGACTTAATTCAGTGTAATTA
15824 AGTAAACACAGTCAGCAAAGACTTAATTCA-TGTTAATTA
1 AGTAAACACAGTCA--AAAGACTTAATTCAGTG-TAATTA
15863 AGTAAACACAGTCAGCAAAGACTTAATTCAG-GATAATTA
1 AGTAAACACAGTCA--AAAGACTTAATTCAGTG-TAATTA
*
15902 AGTAAACACAATCAACAAAGACTTAATTCAGTGTAATTA
1 AGTAAACACAGTC-A-AAAGACTTAATTCAGTGTAATTA
* *
15941 AGTAAGATCA-A--C-AAAGACTTAATTTAGGGTAATTA
1 AGTAA-A-CACAGTCAAAAGACTTAATTCAGTGTAATTA
* *
15976 AGTAAGA-TCAGTC-AAAGACTTAATTTAG-GATAATTA
1 AGTAA-ACACAGTCAAAAGACTTAATTCAGTG-TAATTA
* *
16012 AGTAAA-AGTAGTC-AAAGACTTAATTCAGGGTAATTA
1 AGTAAACA-CAGTCAAAAGACTTAATTCAGTGTAATTA
* * * *
16048 AGTAAAAACAG-CCAATGACTTAATTCAGGGTAATTA
1 AGTAAACACAGTCAAAAGACTTAATTCAGTGTAATTA
*** * *
16084 AGTAAGGTCAAT--AAAGAACTTAATTCAGGGTAATTA
1 AGTAAACACAGTCAAAAG-ACTTAATTCAGTGTAATTA
16120 AGTA
1 AGTA
16124 GAGTTAATTA
Statistics
Matches: 391, Mismatches: 31, Indels: 57
0.82 0.06 0.12
Matches are distributed among these distances:
34 1 0.00
35 62 0.16
36 145 0.37
37 2 0.01
38 5 0.01
39 166 0.42
40 7 0.02
41 3 0.01
ACGTcount: A:0.45, C:0.12, G:0.16, T:0.27
Consensus pattern (37 bp):
AGTAAACACAGTCAAAAGACTTAATTCAGTGTAATTA
Found at i:15821 original size:35 final size:35
Alignment explanation
Indices: 15695--16195 Score: 450
Period size: 36 Copynumber: 13.7 Consensus size: 35
15685 ATCAATAAGA
*
15695 ACTTAATTCATGGTAATTAAGTAAACA-CAGCCAGTAAAG
1 ACTTAATTCAGGGTAATTAAGTAAA-ATCAG-C---AAAG
* *
15734 TCTTAATTCAGGGTAATTAAGTAAAATCAGTAAATG
1 ACTTAATTCAGGGTAATTAAGTAAAATCAGCAAA-G
*
15770 ACTTAATTCAGGGTAATTAAGTAAAATCAGCCAAG
1 ACTTAATTCAGGGTAATTAAGTAAAATCAGCAAAG
15805 ACTTAATTC-GGAGTAATTAAGTAAACACAGTCAGCAAAG
1 ACTTAATTCAGG-GTAATTAAGT-AA-A-A-TCAGCAAAG
* *
15844 ACTTAATTCATGTTAATTAAGTAAACACAGTCAGCAAAG
1 ACTTAATTCAGGGTAATTAAGT-AA-A-A-TCAGCAAAG
* *
15883 ACTTAATTCAGGATAATTAAGTAAACACAATCAACAAAG
1 ACTTAATTCAGGGTAATTAAGT--A-A-AATCAGCAAAG
* * *
15922 ACTTAATTCAGTGTAATTAAGTAAGATCAACAAAG
1 ACTTAATTCAGGGTAATTAAGTAAAATCAGCAAAG
* *
15957 ACTTAATTTAGGGTAATTAAGTAAGATCAGTCAAAG
1 ACTTAATTCAGGGTAATTAAGTAAAATCAG-CAAAG
* *
15993 ACTTAATTTAGGATAATTAAGTAAAAGT-AGTCAAAG
1 ACTTAATTCAGGGTAATTAAGTAAAA-TCAG-CAAAG
* *
16029 ACTTAATTCAGGGTAATTAAGTAAAAACAGCCAATG
1 ACTTAATTCAGGGTAATTAAGTAAAATCAG-CAAAG
** **
16065 ACTTAATTCAGGGTAATTAAGTAAGGTCAATAAAG
1 ACTTAATTCAGGGTAATTAAGTAAAATCAGCAAAG
* * * ***
16100 AACTTAATTCAGGGTAATTAAGTAGAGTTAATTAAG
1 -ACTTAATTCAGGGTAATTAAGTAAAATCAGCAAAG
* * * * **
16136 AACTTAATTCAGGGAAATTAAGTAGAGTGAATAAAG
1 -ACTTAATTCAGGGTAATTAAGTAAAATCAGCAAAG
16172 TACTTAATTCAGGGTAATTAAGTA
1 -ACTTAATTCAGGGTAATTAAGTA
16196 GAGTCAATAA
Statistics
Matches: 408, Mismatches: 40, Indels: 31
0.85 0.08 0.06
Matches are distributed among these distances:
34 2 0.00
35 63 0.15
36 214 0.52
37 3 0.01
38 2 0.00
39 117 0.29
40 4 0.01
41 3 0.01
ACGTcount: A:0.44, C:0.11, G:0.17, T:0.28
Consensus pattern (35 bp):
ACTTAATTCAGGGTAATTAAGTAAAATCAGCAAAG
Found at i:15996 original size:188 final size:184
Alignment explanation
Indices: 15636--16195 Score: 578
Period size: 188 Copynumber: 3.0 Consensus size: 184
15626 CATATGCATC
* *
15636 AGTAAACACAGTCA--ATAAGAACTTAATTCAGTGTGATTAAGTAAACACAATCA-ATAAGAACT
1 AGTAAACACAGTCAGCA-AAG-ACTTAATTCAGT-TAATTAAGTAAACACAGTCACA-AAG-ACT
** * * *
15698 TAATTCATGGTAATTAAGTAAACACAGCCAGTAAAGTCTTAATTCAGGGTAATTAAGTAAAATCA
61 TAATTCA-GGTAATTAAGTAAACACAATCA-AAAAGACTTAATTCAGGGTAATTAAGTAAGATCA
* * *
15763 GTAAATGACTTAATTCAGGGTAATTAAGTAAAATCAG-CCAAGACTTAATTCGGAGTAATTA
124 ATAAA-GACTTAATTCAGGGTAATTAAGTAAGATCAGTCAAAGACTTAATTCGGAGTAATTA
15824 AGTAAACACAGTCAGCAAAGACTTAATTCATGTTAATTAAGTAAACACAGTCAGCAAAGACTTAA
1 AGTAAACACAGTCAGCAAAGACTTAATTCA-GTTAATTAAGTAAACACAGTCA-CAAAGACTTAA
* *
15889 TTCAGGATAATTAAGTAAACACAATCAACAAAGACTTAATTCAGTGTAATTAAGTAAGATCAACA
64 TTCAGG-TAATTAAGTAAACACAATCAA-AAAGACTTAATTCAGGGTAATTAAGTAAGATCAATA
* *
15954 AAGACTTAATTTAGGGTAATTAAGTAAGATCAGTCAAAGACTTAATTTAGGA-TAATTA
127 AAGACTTAATTCAGGGTAATTAAGTAAGATCAGTCAAAGACTTAA-TTCGGAGTAATTA
* * *
16012 AGT-AA-A-AGT-AGTCAAAGACTTAATTCAGGGTAATTAAGTAAAAACAG-C-CAATGACTTAA
1 AGTAAACACAGTCAG-CAAAGACTTAATTCA-GTTAATTAAGTAAACACAGTCACAAAGACTTAA
*** * * *
16071 TTCAGGGTAATTAAGTAAGGTCAAT-AAAGA-ACTTAATTCAGGGTAATTAAGT-AGAGTTAATT
64 TTCA-GGTAATTAAGTAAACACAATCAAAAAGACTTAATTCAGGGTAATTAAGTAAGA-TCAATA
* * *
16133 AAGAACTTAATTCAGGGAAATTAAGT-AGAGTGAAT-AAAGTACTTAATTCAGG-GTAATTA
127 AAG-ACTTAATTCAGGGTAATTAAGTAAGA-TCAGTCAAAG-ACTTAATTC-GGAGTAATTA
16192 AGTA
1 AGTA
16196 GAGTCAATAA
Statistics
Matches: 323, Mismatches: 31, Indels: 43
0.81 0.08 0.11
Matches are distributed among these distances:
178 3 0.01
179 36 0.11
180 42 0.13
181 2 0.01
182 29 0.09
183 2 0.01
184 3 0.01
185 35 0.11
186 1 0.00
187 33 0.10
188 122 0.38
189 13 0.04
190 2 0.01
ACGTcount: A:0.45, C:0.11, G:0.16, T:0.28
Consensus pattern (184 bp):
AGTAAACACAGTCAGCAAAGACTTAATTCAGTTAATTAAGTAAACACAGTCACAAAGACTTAATT
CAGGTAATTAAGTAAACACAATCAAAAAGACTTAATTCAGGGTAATTAAGTAAGATCAATAAAGA
CTTAATTCAGGGTAATTAAGTAAGATCAGTCAAAGACTTAATTCGGAGTAATTA
Found at i:17804 original size:4 final size:4
Alignment explanation
Indices: 17790--17819 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
17780 CTCTAATCTA
*
17790 ATTT GTTT ATTT ATTT ATTT ATTT ATTT AT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT AT
17820 ATCGTCATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.73
Consensus pattern (4 bp):
ATTT
Found at i:21595 original size:31 final size:30
Alignment explanation
Indices: 21558--21687 Score: 136
Period size: 31 Copynumber: 4.3 Consensus size: 30
21548 TCCTTTTGTG
* *
21558 CACGTGGCATGCCAAGTGTCACTTTTTGGTA
1 CACGTGGCGTGACAA-TGTCACTTTTTGGTA
* *
21589 CACGTGGCGTGAC-ACGTCACTTTTTTGTA
1 CACGTGGCGTGACAATGTCACTTTTTGGTA
* * ** * *
21618 AACATGGCGTGACACGGGTCACTTTTTTGCA
1 CACGTGGCGTGACA-ATGTCACTTTTTGGTA
21649 CACGTGGCGTGACACATGTCACTTTTTGGTA
1 CACGTGGCGTGACA-ATGTCACTTTTTGGTA
21680 CACGTGGC
1 CACGTGGC
21688 ATGCCACGTC
Statistics
Matches: 82, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
29 24 0.29
30 1 0.01
31 57 0.70
ACGTcount: A:0.19, C:0.24, G:0.26, T:0.31
Consensus pattern (30 bp):
CACGTGGCGTGACAATGTCACTTTTTGGTA
Found at i:21607 original size:29 final size:30
Alignment explanation
Indices: 21575--21687 Score: 147
Period size: 31 Copynumber: 3.7 Consensus size: 30
21565 CATGCCAAGT
21575 GTCACTTTTTGGTACACGTGGCGTGACAC-
1 GTCACTTTTTGGTACACGTGGCGTGACACG
* * *
21604 GTCACTTTTTTGTAAACATGGCGTGACACGG
1 GTCACTTTTTGGTACACGTGGCGTGACAC-G
* * *
21635 GTCACTTTTTTGCACACGTGGCGTGACACAT
1 GTCACTTTTTGGTACACGTGGCGTGACAC-G
21666 GTCACTTTTTGGTACACGTGGC
1 GTCACTTTTTGGTACACGTGGC
21688 ATGCCACGTC
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
29 26 0.36
31 46 0.64
ACGTcount: A:0.19, C:0.23, G:0.26, T:0.33
Consensus pattern (30 bp):
GTCACTTTTTGGTACACGTGGCGTGACACG
Found at i:27837 original size:14 final size:14
Alignment explanation
Indices: 27814--27853 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
27804 CTATCTTCTT
27814 TCTTTCTTTTTTTC
1 TCTTTCTTTTTTTC
27828 TCTTT-TTTTTTT-
1 TCTTTCTTTTTTTC
*
27840 T-TTTCTTCTTTTC
1 TCTTTCTTTTTTTC
27853 T
1 T
27854 TTTTACAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
11 3 0.13
12 7 0.30
13 8 0.35
14 5 0.22
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.82
Consensus pattern (14 bp):
TCTTTCTTTTTTTC
Found at i:27838 original size:15 final size:16
Alignment explanation
Indices: 27809--27857 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 16
27799 TCTTTCTATC
27809 TTCT-TTCTTTCTTTTT
1 TTCTCTTCTTT-TTTTT
27825 TTCTCTT-TTTTTTTT
1 TTCTCTTCTTTTTTTT
*
27840 TTTTCTTCTTTTCTTTT
1 TTCTCTTCTTTT-TTTT
27857 T
1 T
27858 ACAATCATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
15 11 0.38
16 11 0.38
17 7 0.24
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (16 bp):
TTCTCTTCTTTTTTTT
Found at i:27841 original size:18 final size:19
Alignment explanation
Indices: 27807--27857 Score: 61
Period size: 17 Copynumber: 2.7 Consensus size: 19
27797 TTTCTTTCTA
* *
27807 TCTTCTTTCTTTCTTTTTT
1 TCTTCTTTTTTTTTTTTTT
27826 TC-TC-TTTTTTTTTTTTT
1 TCTTCTTTTTTTTTTTTTT
27843 TCTTCTTTTCTTTTT
1 TCTTCTTTT-TTTTT
27858 ACAATCATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 13 0.48
18 4 0.15
19 5 0.19
20 5 0.19
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (19 bp):
TCTTCTTTTTTTTTTTTTT
Found at i:36428 original size:218 final size:216
Alignment explanation
Indices: 35980--37324 Score: 1916
Period size: 210 Copynumber: 6.3 Consensus size: 216
35970 CTTATGATAA
* * * *
35980 TCAACTAATTAGGATGAAAATATGGATTAAAGCACGTTTAAAGTCAATCTTGGGTATATAAAAAA
1 TCAATTAATTAGGATGAAAATATGGATTAAAACACGTTTAAAGCCAATTTTGGGTATAT-AAAAA
* * * * * *
36045 ATGTCAATCTCTAAAAAATTTGGGGATGATGCTTATAATTATTT--GGATGATGGGAAATGATTT
65 ATGTCAATCTCGAAAGAATTTGGGGATGGTGCATATGATTATTTGGGGATGATGAGAAATGATTT
* *
36108 GGGTATAAATTATATCAGTTTGGGATACTGAATTTTGCATTTTGTTTAATTATTAGATGACACTA
130 GGGTATAAAGTATATCAGTTTGGGATACTGAACTTTGCATTTTGTTTAATTATTAGATGACACTA
36173 AATTCATATAGACGGGGTTTAT
195 AATTCATATAGACGGGGTTTAT
* * *
36195 TCAATTAATTAGGATGAAATTATGGATTAAAACACGTTTCAAGCCAATTTTTGGTATATAAAAAA
1 TCAATTAATTAGGATGAAAATATGGATTAAAACACGTTTAAAGCCAATTTTGGGTATAT-AAAAA
* * * *
36260 ATGTCAATTTCTAAAGAATTTGGCGATGGTGCTTATGATTATTTGGGGATGATGAGAAATGATTT
65 ATGTCAATCTCGAAAGAATTTGGGGATGGTGCATATGATTATTTGGGGATGATGAGAAATGATTT
* * **
36325 GGGTATAAAGTTTATTAGTTTAGGGATACTGAACTTTGCATTTTGAATAATTATTAGATGACACT
130 GGGTATAAAGTATATCAGTTT-GGGATACTGAACTTTGCATTTTGTTTAATTATTAGATGACACT
* *
36390 AAATTCATATAGACGAGATTTAT
194 AAATTCATATAGACGGGGTTTAT
* *
36413 TCAATTAATTAGGATGAAAATATGTATTAAAACACGTTTAAAGCCAATTTTGGGT-T-T-----T
1 TCAATTAATTAGGATGAAAATATGGATTAAAACACGTTTAAAGCCAATTTTGGGTATATAAAAAA
* * * *
36471 TGTCAATCTCGAAAGAATTTGGGGATGTTGTATATGATTGTTTGGGGATGATGAGAAATGATTTT
66 TGTCAATCTCGAAAGAATTTGGGGATGGTGCATATGATTATTTGGGGATGATGAGAAATGATTTG
* *
36536 GGTATAAAATATATCAGTTTGAGGATACTGAACTTTGTATTTTGTTTAATTATTAGATGACACTA
131 GGTATAAAGTATATCAGTTTG-GGATACTGAACTTTGCATTTTGTTTAATTATTAGATGACACTA
36601 AATTCATATAGACGGGGTTTAT
195 AATTCATATAGACGGGGTTTAT
* *
36623 TCAATTAATTAGGATGAAAATATGGATTAAAAAAACATTTAAAGCCAATTTTGGGTATATAAAAA
1 TCAATTAATTAGGATGAAAATATGGATT-AAAACACGTTTAAAGCCAATTTTGGGTATATAAAAA
*
36688 ATGTCAATCTCTAAAGAATTTGGGGATGGTGCATATGATTATTTGGGGATGATGAGAAATGATTT
65 ATGTCAATCTCGAAAGAATTTGGGGATGGTGCATATGATTATTTGGGGATGATGAGAAATGATTT
** * * *
36753 GAATATAAAGTATATCAGTTTAGGGATACTAAATTTTGCATTTTGTTTAATTATTAAATGACACT
130 GGGTATAAAGTATATCAGTTT-GGGATACTGAACTTTGCATTTTGTTTAATTATTAGATGACACT
36818 AAATTCATATAGACGGGGTTTAT
194 AAATTCATATAGACGGGGTTTAT
*
36841 TCAATTAATTAGGATGAAAATATGGATTAAAACACGTTTAAAGCCAATTTTGGG-AT-T-----T
1 TCAATTAATTAGGATGAAAATATGGATTAAAACACGTTTAAAGCCAATTTTGGGTATATAAAAAA
*
36899 TGTCAATCTCGAAAGAATTTGGGGATGGTGCAAATGATATATTTGGGGATGATGAGAAATGATTT
66 TGTCAATCTCGAAAGAATTTGGGGATGGTGCATATGAT-TATTTGGGGATGATGAGAAATGATTT
* *
36964 GGGTATAAAATATATCAGTTGGGGATACTGAACTTTGCATTTTGTTTAATTATTAGATGACACTA
130 GGGTATAAAGTATATCAGTTTGGGATACTGAACTTTGCATTTTGTTTAATTATTAGATGACACTA
37029 AATTCATATAGACGGGGTTTAT
195 AATTCATATAGACGGGGTTTAT
* *
37051 TCAATTAATTAGGATGAATATATGGATTAGAACACGTTTAAAGCCAATTTTGGGGT-T-T-----
1 TCAATTAATTAGGATGAAAATATGGATTAAAACACGTTTAAAGCCAATTTT-GGGTATATAAAAA
* * * *
37109 -TGTCAATCTCGGAAGAATTTGGGGATGGTGCATATGATTATTT-AGGATAATGATAAATGATTT
65 ATGTCAATCTCGAAAGAATTTGGGGATGGTGCATATGATTATTTGGGGATGATGAGAAATGATTT
* *
37172 GGGTATAAAGTATATCAGTTTGGGGATACTAAATTTTGCATTTTGTTTAATTATTAGATG-CAAC
130 GGGTATAAAGTATATCAGTTT-GGGATACTGAACTTTGCATTTTGTTTAATTATTAGATGAC-AC
*
37236 TAAATTCATATAGACAGGGTTTAT
193 TAAATTCATATAGACGGGGTTTAT
37260 TCAATTAATTAGGAT-AAACATATGGATTAAAACACGTTTAAAGCCAATTTTGGGTATATAAAAA
1 TCAATTAATTAGGATGAAA-ATATGGATTAAAACACGTTTAAAGCCAATTTTGGGTATATAAAAA
37324 A
65 A
37325 ATTTATATAT
Statistics
Matches: 1019, Mismatches: 84, Indels: 53
0.88 0.07 0.05
Matches are distributed among these distances:
208 43 0.04
209 114 0.11
210 346 0.34
211 73 0.07
212 1 0.00
213 1 0.00
215 98 0.10
216 3 0.00
217 61 0.06
218 278 0.27
219 1 0.00
ACGTcount: A:0.36, C:0.08, G:0.20, T:0.37
Consensus pattern (216 bp):
TCAATTAATTAGGATGAAAATATGGATTAAAACACGTTTAAAGCCAATTTTGGGTATATAAAAAA
TGTCAATCTCGAAAGAATTTGGGGATGGTGCATATGATTATTTGGGGATGATGAGAAATGATTTG
GGTATAAAGTATATCAGTTTGGGATACTGAACTTTGCATTTTGTTTAATTATTAGATGACACTAA
ATTCATATAGACGGGGTTTAT
Found at i:36992 original size:428 final size:426
Alignment explanation
Indices: 35980--37313 Score: 1983
Period size: 428 Copynumber: 3.1 Consensus size: 426
35970 CTTATGATAA
* * * *
35980 TCAACTAATTAGGATGAAAATATGGATTAAAGCACGTTTAAAGTCAATCTTGGGTATATAAAAAA
1 TCAATTAATTAGGATGAAAATATGGATTAAAACACGTTTAAAGCCAATTTTGGG-AT-T------
* * * * * *
36045 ATGTCAATCTCTAAAAAATTTGGGGATGATGCTTATAATTATTT--GGATGATGGGAAATGATTT
58 TTGTCAATCTCGAAAGAATTTGGGGATGATGCATATGATTATTTGGGGATGATGAGAAATGATTT
* * *
36108 GGGTATAAATTATATCAGTTTGGGATACTGAATTTTGCATTTTGTTTAATTATTAGATGACACTA
123 GGGTATAAAATATATCAGTTGGGGATACTGAACTTTGCATTTTGTTTAATTATTAGATGACACTA
* *
36173 AATTCATATAGACGGGGTTTATTCAATTAATTAGGATGAAATTATGGATTAAAACACGTTTCAAG
188 AATTCATATAGACGGGGTTTATTCAATTAATTAGGATGAAAATATGGATTAAAACACGTTTAAAG
* * * *
36238 CCAATTTTTGGTATATAAAAAAATGTCAATTTCTAAAGAATTTGGCGATGGTGCTTATGATTATT
253 CCAATTTTGGGTATAT-AAAAAATGTCAATCTCTAAAGAATTTGGGGATGGTGCATATGATTATT
* * * *
36303 TGGGGATGATGAGAAATGATTTGGGTATAAAGTTTATTAGTTTAGGGATACTGAACTTTGCATTT
317 TGGGGATGATGAGAAATGATTTGGGTATAAAGTATATCAGTTTAGGGATACTAAATTTTGCATTT
** * *
36368 TGAATAATTATTAGATGACACTAAATTCATATAGACGAGATTTAT
382 TGTTTAATTATTAGATGACACTAAATTCATATAGACGGGGTTTAT
* *
36413 TCAATTAATTAGGATGAAAATATGTATTAAAACACGTTTAAAGCCAATTTTGGGTTTTTGTCAAT
1 TCAATTAATTAGGATGAAAATATGGATTAAAACACGTTTAAAGCCAATTTTGGGATTTTGTCAAT
* * * *
36478 CTCGAAAGAATTTGGGGATGTTGTATATGATTGTTTGGGGATGATGAGAAATGATTTTGGTATAA
66 CTCGAAAGAATTTGGGGATGATGCATATGATTATTTGGGGATGATGAGAAATGATTTGGGTATAA
* *
36543 AATATATCAGTTTGAGGATACTGAACTTTGTATTTTGTTTAATTATTAGATGACACTAAATTCAT
131 AATATATCAG-TTGGGGATACTGAACTTTGCATTTTGTTTAATTATTAGATGACACTAAATTCAT
* *
36608 ATAGACGGGGTTTATTCAATTAATTAGGATGAAAATATGGATTAAAAAAACATTTAAAGCCAATT
195 ATAGACGGGGTTTATTCAATTAATTAGGATGAAAATATGGATT-AAAACACGTTTAAAGCCAATT
36673 TTGGGTATATAAAAAATGTCAATCTCTAAAGAATTTGGGGATGGTGCATATGATTATTTGGGGAT
259 TTGGGTATATAAAAAATGTCAATCTCTAAAGAATTTGGGGATGGTGCATATGATTATTTGGGGAT
**
36738 GATGAGAAATGATTTGAATATAAAGTATATCAGTTTAGGGATACTAAATTTTGCATTTTGTTTAA
324 GATGAGAAATGATTTGGGTATAAAGTATATCAGTTTAGGGATACTAAATTTTGCATTTTGTTTAA
*
36803 TTATTAAATGACACTAAATTCATATAGACGGGGTTTAT
389 TTATTAGATGACACTAAATTCATATAGACGGGGTTTAT
36841 TCAATTAATTAGGATGAAAATATGGATTAAAACACGTTTAAAGCCAATTTTGGGATTTTGTCAAT
1 TCAATTAATTAGGATGAAAATATGGATTAAAACACGTTTAAAGCCAATTTTGGGATTTTGTCAAT
* *
36906 CTCGAAAGAATTTGGGGATGGTGCAAATGATATATTTGGGGATGATGAGAAATGATTTGGGTATA
66 CTCGAAAGAATTTGGGGATGATGCATATGAT-TATTTGGGGATGATGAGAAATGATTTGGGTATA
36971 AAATATATCAGTTGGGGATACTGAACTTTGCATTTTGTTTAATTATTAGATGACACTAAATTCAT
130 AAATATATCAGTTGGGGATACTGAACTTTGCATTTTGTTTAATTATTAGATGACACTAAATTCAT
* *
37036 ATAGACGGGGTTTATTCAATTAATTAGGATGAATATATGGATTAGAACACGTTTAAAGCCAATTT
195 ATAGACGGGGTTTATTCAATTAATTAGGATGAAAATATGGATTAAAACACGTTTAAAGCCAATTT
** *
37101 TGGGGT-T-T------TGTCAATCTCGGAAGAATTTGGGGATGGTGCATATGATTATTT-AGGAT
260 T-GGGTATATAAAAAATGTCAATCTCTAAAGAATTTGGGGATGGTGCATATGATTATTTGGGGAT
* * *
37157 AATGATAAATGATTTGGGTATAAAGTATATCAGTTTGGGGATACTAAATTTTGCATTTTGTTTAA
324 GATGAGAAATGATTTGGGTATAAAGTATATCAGTTTAGGGATACTAAATTTTGCATTTTGTTTAA
*
37222 TTATTAGATG-CAACTAAATTCATATAGACAGGGTTTAT
389 TTATTAGATGAC-ACTAAATTCATATAGACGGGGTTTAT
37260 TCAATTAATTAGGAT-AAACATATGGATTAAAACACGTTTAAAGCCAATTTTGGG
1 TCAATTAATTAGGATGAAA-ATATGGATTAAAACACGTTTAAAGCCAATTTTGGG
37314 TATATAAAAA
Statistics
Matches: 830, Mismatches: 63, Indels: 30
0.90 0.07 0.03
Matches are distributed among these distances:
418 4 0.00
419 148 0.18
420 41 0.05
425 36 0.04
426 1 0.00
427 55 0.07
428 425 0.51
429 69 0.08
431 1 0.00
432 1 0.00
433 49 0.06
ACGTcount: A:0.35, C:0.08, G:0.20, T:0.37
Consensus pattern (426 bp):
TCAATTAATTAGGATGAAAATATGGATTAAAACACGTTTAAAGCCAATTTTGGGATTTTGTCAAT
CTCGAAAGAATTTGGGGATGATGCATATGATTATTTGGGGATGATGAGAAATGATTTGGGTATAA
AATATATCAGTTGGGGATACTGAACTTTGCATTTTGTTTAATTATTAGATGACACTAAATTCATA
TAGACGGGGTTTATTCAATTAATTAGGATGAAAATATGGATTAAAACACGTTTAAAGCCAATTTT
GGGTATATAAAAAATGTCAATCTCTAAAGAATTTGGGGATGGTGCATATGATTATTTGGGGATGA
TGAGAAATGATTTGGGTATAAAGTATATCAGTTTAGGGATACTAAATTTTGCATTTTGTTTAATT
ATTAGATGACACTAAATTCATATAGACGGGGTTTAT
Found at i:47181 original size:29 final size:29
Alignment explanation
Indices: 47149--47223 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 29
47139 TTGGTGTATC
47149 AAGTGCGGGTTGTGCACTTGTG-TTGATTT
1 AAGTGCGGGTTGTGCACTTG-GATTGATTT
*
47178 AAGTGCGGGTTGTGCACTTGGATTGTTTT
1 AAGTGCGGGTTGTGCACTTGGATTGATTT
* *
47207 GAGTGTGGGTT-TGCACT
1 AAGTGCGGGTTGTGCACT
47224 CGGTGTCAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
28 7 0.17
29 35 0.83
ACGTcount: A:0.13, C:0.11, G:0.36, T:0.40
Consensus pattern (29 bp):
AAGTGCGGGTTGTGCACTTGGATTGATTT
Found at i:54763 original size:20 final size:20
Alignment explanation
Indices: 54716--54765 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
54706 AAACCATATG
*
54716 GGGCGCCAAGCATGCCGCAT
1 GGGCGCCCAGCATGCCGCAT
54736 GGGCGCCCAGCATGCCGCAT
1 GGGCGCCCAGCATGCCGCAT
*
54756 TGGCGCCCAG
1 GGGCGCCCAG
54766 GGGAGTCGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.16, C:0.38, G:0.36, T:0.10
Consensus pattern (20 bp):
GGGCGCCCAGCATGCCGCAT
Found at i:56483 original size:42 final size:41
Alignment explanation
Indices: 56321--56488 Score: 164
Period size: 41 Copynumber: 4.0 Consensus size: 41
56311 AATGATTTAG
*
56321 AAAGTCAAACACAGTTAAAGTCTTAATTCATGG-TAATTAAG-
1 AAAGT-AAACACAGTTAAGGTCTTAATTCA-GGATAATTAAGA
* *
56362 AAAGTTAAACACAG-TCAGAGTCCTAATTCAGGATAATTAAGA
1 AAAG-TAAACACAGTTAAG-GTCTTAATTCAGGATAATTAAGA
* * * *
56404 AGAGCATACATAGTTAAGGTCTTAATTCATGGA-AATTAAGGA
1 AAAGTAAACACAGTTAAGGTCTTAATTCA-GGATAATTAA-GA
* **
56446 AAAGTAAACATAGTTAAGGTCTTAATTCACAATAATTAAGA
1 AAAGTAAACACAGTTAAGGTCTTAATTCAGGATAATTAAGA
56487 AA
1 AA
56489 GGTGATTACA
Statistics
Matches: 105, Mismatches: 14, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
40 4 0.04
41 57 0.54
42 44 0.42
ACGTcount: A:0.45, C:0.11, G:0.16, T:0.27
Consensus pattern (41 bp):
AAAGTAAACACAGTTAAGGTCTTAATTCAGGATAATTAAGA
Found at i:56579 original size:41 final size:41
Alignment explanation
Indices: 56534--57347 Score: 1220
Period size: 41 Copynumber: 19.9 Consensus size: 41
56524 AGTAAGAGTA
*
56534 AAGCACAGACTTAATTTCAAGGAAAGAAATTAGGTAAAGAT
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAT
*
56575 AAGCAGAGACTTAATTTCAAGGAAGGAAATTAGGTAAA-AT
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAT
* * *
56615 AAATCACGGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAA
1 -AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAT
*
56657 AAGCACGGACTTAATTTCAAGGAAGGAAATTAGGTAAAG-T
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAT
*
56697 ATAGCACAAACTTAATTTCAAGGAAGGAAATTAGGTAAAG-T
1 A-AGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAT
56738 AAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAG-T
1 -AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAT
* * *
56779 AAAGCACATACTTAATTTCAATGAAGGAAATTAGGTAAAGAA
1 -AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAT
56821 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAT
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAT
* * *
56862 AAGCACAGACTTAATTTCAAGAAAGGGAATTAGGTAAAGAA
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAT
* *
56903 AAGCACAGACTTAATTTCAATGAAGGAAATTAGTTAAAG-T
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAT
*
56943 AAAGCACAAACTTAATTTCAAGG-A-GAAATTAGGTAAAG-T
1 -AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAT
*
56982 AAAGCACAGACTTAAGTTCAAGGAAGGAAATTAGGTAAAG-T
1 -AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAT
*
57023 AAAGCACAGACTTAAGTTCAAGGAAGGAAATTAGGTAAAG-T
1 -AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAT
57064 AAAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAG-T
1 -AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAT
* *
57105 ATAGCACAAACTTAATTTCAAGGAAAGAAATTAGGTAAAG-T
1 A-AGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAT
* *
57146 AAAGCACAAACTTAATTTCAAGGAAGGAAATTAGGTAAAGAA
1 -AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAT
57188 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAT
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAT
57229 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAT
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAT
* * *
57270 AAGCACAGACTTAATTTGAAGGAAGGAAATTAGGTTAAGAA
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAT
*
57311 AAGCACAGATTTAATTTCAAGGAAGGAAATTAGGTAA
1 AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAA
57348 TTAATAAAGG
Statistics
Matches: 719, Mismatches: 43, Indels: 22
0.92 0.05 0.03
Matches are distributed among these distances:
39 35 0.05
40 6 0.01
41 675 0.94
42 3 0.00
ACGTcount: A:0.47, C:0.09, G:0.21, T:0.22
Consensus pattern (41 bp):
AAGCACAGACTTAATTTCAAGGAAGGAAATTAGGTAAAGAT
Found at i:57432 original size:36 final size:34
Alignment explanation
Indices: 57349--57448 Score: 134
Period size: 32 Copynumber: 2.9 Consensus size: 34
57339 ATTAGGTAAT
57349 TAATAAAGGGCTTAATTCAGGGTAATTAAGTAGAA
1 TAATAAA-GGCTTAATTCAGGGTAATTAAGTAGAA
*
57384 TAA-AGAA-G-TTAATTCAGGGTAATTAAGTAGAG
1 TAATA-AAGGCTTAATTCAGGGTAATTAAGTAGAA
57416 TCAATAAATGGCTTAATTCAGGGTAATTAAGTA
1 T-AATAAA-GGCTTAATTCAGGGTAATTAAGTA
57449 CTTTATTCAG
Statistics
Matches: 58, Mismatches: 1, Indels: 11
0.83 0.01 0.16
Matches are distributed among these distances:
32 24 0.41
33 5 0.09
34 2 0.03
35 6 0.10
36 21 0.36
ACGTcount: A:0.42, C:0.06, G:0.22, T:0.30
Consensus pattern (34 bp):
TAATAAAGGCTTAATTCAGGGTAATTAAGTAGAA
Found at i:57489 original size:32 final size:35
Alignment explanation
Indices: 57448--57550 Score: 113
Period size: 37 Copynumber: 2.9 Consensus size: 35
57438 GTAATTAAGT
* *
57448 ACTTTATTCAGGGTAATTAAGT-AG-AAT-AAATA
1 ACTTAATTCAAGGTAATTAAGTGAGCAATAAAATA
*
57480 ATTTAATTCAAGGTAATTAAGTGGAGTCAATAAAATA
1 ACTTAATTCAAGGTAATTAAGT-GAG-CAATAAAATA
*
57517 GCTTAATTCAAGGTAATTAAGTGGAGTCAATAAA
1 ACTTAATTCAAGGTAATTAAGT-GAG-CAATAAA
57551 GAACATTATC
Statistics
Matches: 61, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
32 19 0.31
34 2 0.03
36 3 0.05
37 37 0.61
ACGTcount: A:0.44, C:0.07, G:0.17, T:0.32
Consensus pattern (35 bp):
ACTTAATTCAAGGTAATTAAGTGAGCAATAAAATA
Found at i:57500 original size:54 final size:56
Alignment explanation
Indices: 57395--57501 Score: 155
Period size: 58 Copynumber: 1.9 Consensus size: 56
57385 AAAGAAGTTA
* * *
57395 ATTCAGGGTAATTAAGTAGAGTCAATAAATGGCTTAATTCAGGGTAATTAAGTACTTT
1 ATTCAGGGTAATTAAGTAGAATAAATAAAT-G-TTAATTCAAGGTAATTAAGTACTTT
57453 ATTCAGGGTAATTAAGTAGAATAAAT-AAT-TTAATTCAAGGTAATTAAGT
1 ATTCAGGGTAATTAAGTAGAATAAATAAATGTTAATTCAAGGTAATTAAGT
57502 GGAGTCAATA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
54 19 0.41
57 3 0.07
58 24 0.52
ACGTcount: A:0.40, C:0.07, G:0.19, T:0.35
Consensus pattern (56 bp):
ATTCAGGGTAATTAAGTAGAATAAATAAATGTTAATTCAAGGTAATTAAGTACTTT
Found at i:57500 original size:90 final size:91
Alignment explanation
Indices: 57363--57538 Score: 291
Period size: 90 Copynumber: 1.9 Consensus size: 91
57353 AAAGGGCTTA
* *
57363 ATTCAGGGTAATTAAGTAGAATAAAGAAGTTAATTCAGGGTAATTAAGTAGAGTCAAT-AAATGG
1 ATTCAGGGTAATTAAGTAGAATAAAGAAGTTAATTCAAGGTAATTAAGTAGAGTCAATAAAATAG
*
57427 CTTAATTCAGGGTAATTAAGTACTTT
66 CTTAATTCAAGGTAATTAAGTACTTT
* * *
57453 ATTCAGGGTAATTAAGTAGAATAAATAATTTAATTCAAGGTAATTAAGTGGAGTCAATAAAATAG
1 ATTCAGGGTAATTAAGTAGAATAAAGAAGTTAATTCAAGGTAATTAAGTAGAGTCAATAAAATAG
57518 CTTAATTCAAGGTAATTAAGT
66 CTTAATTCAAGGTAATTAAGT
57539 GGAGTCAATA
Statistics
Matches: 79, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
90 54 0.68
91 25 0.32
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.32
Consensus pattern (91 bp):
ATTCAGGGTAATTAAGTAGAATAAAGAAGTTAATTCAAGGTAATTAAGTAGAGTCAATAAAATAG
CTTAATTCAAGGTAATTAAGTACTTT
Found at i:58370 original size:32 final size:32
Alignment explanation
Indices: 58331--58431 Score: 132
Period size: 32 Copynumber: 3.2 Consensus size: 32
58321 TACATAAATA
* *
58331 GCCCCAAAATATTGATGTTCTCTGAATAAAAC
1 GCCCCAAAATAGTGGTGTTCTCTGAATAAAAC
*
58363 GCTCCAAAATAGTGGTGTTCTCTG-ATACAAAC
1 GCCCCAAAATAGTGGTGTTCTCTGAATA-AAAC
* * *
58395 GCCCCAAAATAGTGGCGTTCTCAGAAGAAAAC
1 GCCCCAAAATAGTGGTGTTCTCTGAATAAAAC
58427 GCCCC
1 GCCCC
58432 TACTTTGGGG
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
31 3 0.05
32 55 0.92
33 2 0.03
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.23
Consensus pattern (32 bp):
GCCCCAAAATAGTGGTGTTCTCTGAATAAAAC
Found at i:58474 original size:32 final size:31
Alignment explanation
Indices: 58359--58501 Score: 83
Period size: 32 Copynumber: 4.5 Consensus size: 31
58349 TCTCTGAATA
* * * * *
58359 AAACGCTCCAAAATAGTGGTGTTCTCTGATAC
1 AAACGCCCCAAAATAGGGGTGTTTTATGA-AG
* * *
58391 AAACGCCCCAAAATAGTGGCGTTCTCA-GAAG
1 AAACGCCCCAAAATAGGGGTGTT-TTATGAAG
* ** *
58422 AAAACGCCCCTACTTTGGGGTGTTTTATGAAG
1 -AAACGCCCCAAAATAGGGGTGTTTTATGAAG
* *
58454 AACACGCCCCAAAATAGGGGTGATTT-CGAAAGG
1 AA-ACGCCCCAAAATAGGGGTGTTTTATG-AA-G
*
58487 AAACGCCCCTAAATA
1 AAACGCCCCAAAATA
58502 TAAACTAATA
Statistics
Matches: 85, Mismatches: 20, Indels: 12
0.73 0.17 0.10
Matches are distributed among these distances:
31 6 0.07
32 76 0.89
33 3 0.04
ACGTcount: A:0.34, C:0.23, G:0.22, T:0.22
Consensus pattern (31 bp):
AAACGCCCCAAAATAGGGGTGTTTTATGAAG
Found at i:60020 original size:17 final size:18
Alignment explanation
Indices: 59993--60028 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
59983 ATTATAACTA
59993 TATATATATATATATTAT
1 TATATATATATATATTAT
60011 TATA-ATATATATATTAT
1 TATATATATATATATTAT
60028 T
1 T
60029 TTTGTCCCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TATATATATATATATTAT
Found at i:64534 original size:90 final size:90
Alignment explanation
Indices: 64379--64563 Score: 300
Period size: 90 Copynumber: 2.1 Consensus size: 90
64369 ACTGCATCAA
* * * * *
64379 ATCTGTTAATATTCTTCCTCACTTTCCCCATTTCGGTTTTTCCTTTGTTGGTCTTATTTTGTTCT
1 ATCTGTTAATATTCTGCCCCACTTTCCCCATGTCGGTTTTTCCTTTATTGGTCTTATTTTCTTCT
64444 ATAATTCTATTTTGTTGATTTTTAG
66 ATAATTCTATTTTGTTGATTTTTAG
*
64469 ATCTGTTAATATTCTGCCCCTCTCTT-CCCATGTCGGTTTTTCCTTTATTGGTCTTATTTTCTTC
1 ATCTGTTAATATTCTGCCCCACT-TTCCCCATGTCGGTTTTTCCTTTATTGGTCTTATTTTCTTC
64533 TATAATTCTATTTTGTTGATTTTTAG
65 TATAATTCTATTTTGTTGATTTTTAG
64559 ATCTG
1 ATCTG
64564 ATGGTTGTGT
Statistics
Matches: 88, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
90 86 0.98
91 2 0.02
ACGTcount: A:0.15, C:0.19, G:0.11, T:0.55
Consensus pattern (90 bp):
ATCTGTTAATATTCTGCCCCACTTTCCCCATGTCGGTTTTTCCTTTATTGGTCTTATTTTCTTCT
ATAATTCTATTTTGTTGATTTTTAG
Found at i:84284 original size:13 final size:13
Alignment explanation
Indices: 84266--84290 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
84256 GTTCTATATG
84266 TTTTTCTTTTTTC
1 TTTTTCTTTTTTC
84279 TTTTTCTTTTTT
1 TTTTTCTTTTTT
84291 TTCAGAGGGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTCTTTTTTC
Found at i:90929 original size:15 final size:15
Alignment explanation
Indices: 90909--90938 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
90899 ATTAATTGGA
90909 TCTCTGCTAGATTAG
1 TCTCTGCTAGATTAG
90924 TCTCTGCTAGATTAG
1 TCTCTGCTAGATTAG
90939 ATTTGATGAA
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:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (15 bp):
TCTCTGCTAGATTAG
Found at i:101253 original size:49 final size:49
Alignment explanation
Indices: 101139--101268 Score: 145
Period size: 49 Copynumber: 2.7 Consensus size: 49
101129 TTCAATCTTC
* * *
101139 AGTTTTTACCTGCTTTCCCCCAAAATGCCCTTCCCGGACAGAAGGCATT
1 AGTTTTTACCTGCTTTTCCCCAAAACGCCCTTCCCAGACAGAAGGCATT
* * * **
101188 AATTTTTACTTGCTTTTCCCTAAAACGCCCTTCCCAGATGGAAGGCACTT
1 AGTTTTTACCTGCTTTTCCCCAAAACGCCCTTCCCAGACAGAAGGCA-TT
* * *
101238 -GTTTTTACCTGCTTTTTCCGAAAAGGCCCTT
1 AGTTTTTACCTGCTTTTCCCCAAAACGCCCTT
101269 TCAGACAAAG
Statistics
Matches: 67, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
49 65 0.97
50 2 0.03
ACGTcount: A:0.22, C:0.29, G:0.15, T:0.34
Consensus pattern (49 bp):
AGTTTTTACCTGCTTTTCCCCAAAACGCCCTTCCCAGACAGAAGGCATT
Found at i:101571 original size:62 final size:62
Alignment explanation
Indices: 101419--101571 Score: 189
Period size: 62 Copynumber: 2.5 Consensus size: 62
101409 AAGTTTAGAA
* * ** ** *
101419 TTCCCAAAATACCCTTTCAGACAAAGGGCCAATTTTGTTACATCCTAGTGTATAGTTTCTAT
1 TTCCCAAAATACCCTTTCAGATAAAGGGTCAATTTTGCCACATCCTAGCATATAGTTTCAAT
* ** *
101481 TTCCCAAAATACCCTTTTAGATAAAGGGTCGGTTTTGCCACATCCTCGCATATAGTTTCAAT
1 TTCCCAAAATACCCTTTCAGATAAAGGGTCAATTTTGCCACATCCTAGCATATAGTTTCAAT
* *
101543 TTCCCAGAATACCCTTTCGGATAAAGGGT
1 TTCCCAAAATACCCTTTCAGATAAAGGGT
101572 AAGTCCAGTC
Statistics
Matches: 77, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
62 77 1.00
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.33
Consensus pattern (62 bp):
TTCCCAAAATACCCTTTCAGATAAAGGGTCAATTTTGCCACATCCTAGCATATAGTTTCAAT
Done.