Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004050.1 Hibiscus syriacus cultivar Beakdansim tig00008849_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 73161
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:4560 original size:36 final size:36
Alignment explanation
Indices: 4508--4615 Score: 184
Period size: 36 Copynumber: 3.0 Consensus size: 36
4498 AGAACAACAG
*
4508 AACATCAACA-CACCAAGGATGGCTACGAAGGCAAC
1 AACATCGACACCACCAAGGATGGCTACGAAGGCAAC
4543 AACATCGACACCACCAAGGATGGCTACGAAGGCAAC
1 AACATCGACACCACCAAGGATGGCTACGAAGGCAAC
4579 AACATCGACACCACCAAGGATGGC-AGCGAAGGCAAC
1 AACATCGACACCACCAAGGATGGCTA-CGAAGGCAAC
4615 A
1 A
4616 TCATTAACAA
Statistics
Matches: 70, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
35 10 0.14
36 60 0.86
ACGTcount: A:0.41, C:0.30, G:0.22, T:0.07
Consensus pattern (36 bp):
AACATCGACACCACCAAGGATGGCTACGAAGGCAAC
Found at i:4679 original size:18 final size:18
Alignment explanation
Indices: 4631--4667 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
4621 AACAAAGCGG
* *
4631 ACAACAACAACAACGACA
1 ACAATAACAACAACGAAA
4649 ACAATAACAACAACGAAA
1 ACAATAACAACAACGAAA
4667 A
1 A
4668 TGAAAACAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.65, C:0.27, G:0.05, T:0.03
Consensus pattern (18 bp):
ACAATAACAACAACGAAA
Found at i:4913 original size:39 final size:38
Alignment explanation
Indices: 4814--4934 Score: 199
Period size: 38 Copynumber: 3.2 Consensus size: 38
4804 AGCACCAACT
* *
4814 CAGCCTTCTCCTTTGGAGCATAGGGATTCAGCTTACCAA
1 CAGCC-TCTTCTTTGGAGCATAGGGATTCAGCTCACCAA
4853 CAGCCTCTTCTTTGGAGCATAGGGATTCAGCTCACCAA
1 CAGCCTCTTCTTTGGAGCATAGGGATTCAGCTCACCAA
4891 CAGCCTCCTTCTTTGGAGCATA-GGATTCAGCTCACCAA
1 CAGCCT-CTTCTTTGGAGCATAGGGATTCAGCTCACCAA
4929 CAGCCT
1 CAGCCT
4935 GCTCCCCATG
Statistics
Matches: 79, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
38 59 0.75
39 20 0.25
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (38 bp):
CAGCCTCTTCTTTGGAGCATAGGGATTCAGCTCACCAA
Found at i:12441 original size:20 final size:20
Alignment explanation
Indices: 12397--12452 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
12387 TCGCGTTGCA
*
12397 AAATTCTCGTTGCGAAAACG
1 AAATTCGCGTTGCGAAAACG
*
12417 AAATTCGCGTTGCGAAATTCG
1 AAATTCGCGTTGCGAAA-ACG
*
12438 -AATTCGAGTTGCGAA
1 AAATTCGCGTTGCGAA
12453 TTTGAAAACT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
20 30 0.94
21 2 0.06
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (20 bp):
AAATTCGCGTTGCGAAAACG
Found at i:12822 original size:18 final size:16
Alignment explanation
Indices: 12801--12843 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 16
12791 GTAGAACTAG
12801 ATATTTTGGATGTATTTT
1 ATATTTT-GAT-TATTTT
12819 ATATTTAATGATTATTTT
1 ATATTT--TGATTATTTT
12837 ATATTTT
1 ATATTTT
12844 CAAAAATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 1 0.04
18 18 0.78
19 3 0.13
20 1 0.04
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.63
Consensus pattern (16 bp):
ATATTTTGATTATTTT
Found at i:14276 original size:18 final size:18
Alignment explanation
Indices: 14253--14310 Score: 98
Period size: 18 Copynumber: 3.2 Consensus size: 18
14243 GGTGGAGGAA
14253 GAGGAAGTAGAGATGGGT
1 GAGGAAGTAGAGATGGGT
14271 GAGGAAGTAGAGATGGGT
1 GAGGAAGTAGAGATGGGT
* *
14289 GAGGAAGAAGAGATGGGA
1 GAGGAAGTAGAGATGGGT
14307 GAGG
1 GAGG
14311 GAGAAGAGGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.36, C:0.00, G:0.52, T:0.12
Consensus pattern (18 bp):
GAGGAAGTAGAGATGGGT
Found at i:14315 original size:18 final size:18
Alignment explanation
Indices: 14253--14318 Score: 96
Period size: 18 Copynumber: 3.7 Consensus size: 18
14243 GGTGGAGGAA
*
14253 GAGGAAGTAGAGATGGGT
1 GAGGAAGAAGAGATGGGT
*
14271 GAGGAAGTAGAGATGGGT
1 GAGGAAGAAGAGATGGGT
*
14289 GAGGAAGAAGAGATGGGA
1 GAGGAAGAAGAGATGGGT
*
14307 GAGGGAGAAGAG
1 GAGGAAGAAGAG
14319 GGAGTAAAAG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.38, C:0.00, G:0.52, T:0.11
Consensus pattern (18 bp):
GAGGAAGAAGAGATGGGT
Found at i:14352 original size:18 final size:18
Alignment explanation
Indices: 14329--14377 Score: 53
Period size: 21 Copynumber: 2.6 Consensus size: 18
14319 GGAGTAAAAG
*
14329 AAGAGGAACATGAGGAAC
1 AAGAGGAACATGAAGAAC
14347 AAGAGGAGCAGCATGAAGAAC
1 AAGAGGA--A-CATGAAGAAC
*
14368 AAGATGAACA
1 AAGAGGAACA
14378 ACAGGTTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 9 0.35
19 1 0.04
20 1 0.04
21 15 0.58
ACGTcount: A:0.51, C:0.12, G:0.31, T:0.06
Consensus pattern (18 bp):
AAGAGGAACATGAAGAAC
Found at i:29687 original size:15 final size:15
Alignment explanation
Indices: 29655--29695 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
29645 GTCGATATTG
29655 AAAATAAA-TATT--
1 AAAATAAATTATTAA
*
29667 AAAATAATTTATTAA
1 AAAATAAATTATTAA
29682 AAAATAAATTATTA
1 AAAATAAATTATTA
29696 TTTATTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 7 0.29
13 4 0.17
15 13 0.54
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AAAATAAATTATTAA
Found at i:30598 original size:15 final size:15
Alignment explanation
Indices: 30556--30598 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
30546 CCTCGGTAAG
*
30556 TTTTCTTTTCTTCCT
1 TTTTCTTTTCTTTCT
*
30571 TTTTCTTTCCTTTC-
1 TTTTCTTTTCTTTCT
30585 TTTTCTGTTTCTTT
1 TTTTCT-TTTCTTT
30599 GCTGAGTTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 6 0.25
15 18 0.75
ACGTcount: A:0.00, C:0.23, G:0.02, T:0.74
Consensus pattern (15 bp):
TTTTCTTTTCTTTCT
Found at i:30696 original size:10 final size:10
Alignment explanation
Indices: 30667--30700 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
30657 CTCTGTGTTC
30667 TTTTCTCTTT
1 TTTTCTCTTT
30677 TCTTTC-CTTT
1 T-TTTCTCTTT
30687 TTTTCTCTTT
1 TTTTCTCTTT
30697 TTTT
1 TTTT
30701 TAGGTTCGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 4 0.18
10 14 0.64
11 4 0.18
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTCTCTTT
Found at i:31153 original size:3 final size:3
Alignment explanation
Indices: 31145--31247 Score: 160
Period size: 3 Copynumber: 35.3 Consensus size: 3
31135 TTAATATATT
31145 TAA TAA TAA T-A TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
31191 TAAA TAA TAA TAA T-A TAA T-A TAA TAA TAA TAA TAA TGA TAA TAA
1 T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
31235 TAA TAA TAA TAA T
1 TAA TAA TAA TAA T
31248 GATATGGGTA
Statistics
Matches: 93, Mismatches: 2, Indels: 10
0.89 0.02 0.10
Matches are distributed among these distances:
2 8 0.09
3 82 0.88
4 3 0.03
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:31199 original size:50 final size:49
Alignment explanation
Indices: 31145--31247 Score: 172
Period size: 50 Copynumber: 2.1 Consensus size: 49
31135 TTAATATATT
31145 TAATAATAATATAATA-ATATAATAATAATAATAATAATAATAATAATAAA
1 TAATAATAATATAATATA-ATAATAATAATAATAATAATAATAATAAT-AA
*
31195 TAATAATAATATAATATAATAATAATAATAATGATAATAATAATAATAA
1 TAATAATAATATAATATAATAATAATAATAATAATAATAATAATAATAA
31244 TAAT
1 TAAT
31248 GATATGGGTA
Statistics
Matches: 51, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
49 6 0.12
50 44 0.86
51 1 0.02
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (49 bp):
TAATAATAATATAATATAATAATAATAATAATAATAATAATAATAATAA
Found at i:31877 original size:111 final size:112
Alignment explanation
Indices: 31566--32326 Score: 1225
Period size: 111 Copynumber: 6.9 Consensus size: 112
31556 AGAATTATGC
* * *
31566 AAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTC-TCA-ATGAGTTCTTCTCAT
1 AAAAGGTTGAACAA-TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * *
31629 TATGAAC-TTCTCCGGAAAAGATAATCCATCAAGTGAT-GATTC-AGT
65 TATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGT
31674 AAAAGGTTGAACAATTCTTCTCATTATGAACTTCTTCTTCCTTC-TCAGATGAGTTCTTCTCATT
1 AAAAGGTTGAACAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
31738 ATGAACTTTCTCTGGAAAAGATGATCCATCAAATGAT-AATTCAAGT
66 ATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGT
31784 AAAAGGTTGAACAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGGTTGAACAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
31849 ATGAACTTTCTCTGGAAATGATGATCCATC-AATGATGGATTCAAGT
66 ATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGT
31895 AAAAGGTTG-ACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA-
1 AAAAGGTTGAAC-AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
31958 TA-GAACTTTC-CTGGAAATGATGATCCATCAAATGA-GGATTCAAGT
65 TATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGT
32003 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTT-TTCTTCTTCTTCAGATGAGTTCTTCTC
1 AAAAGGTTGAAC-AATTCTTCTCATTATGAACTTCTTCTTC--CTTCTTCAGATGAGTTCTTCTC
32067 ATTATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGT
63 ATTATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGT
32117 AAAAGGTTGAACAATTCTTCTCATTATGAACTTCTTC-TCCTTCTTCAGATGAGTTTCTTCTCAT
1 AAAAGGTTGAACAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG-TTCTTCTCAT
32181 TATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGT
65 TATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGT
*
32229 AAAAGGTTGAACAAATTCTTCTTATTATG-ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAAC-AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
32293 TATG-ACTTTCTCTGGAAATG-TCAATCCATCAAAT
65 TATGAACTTTCTCTGGAAATGAT-GATCCATCAAAT
32327 AATAGATTTG
Statistics
Matches: 623, Mismatches: 11, Indels: 35
0.93 0.02 0.05
Matches are distributed among these distances:
107 31 0.05
108 76 0.12
109 71 0.11
110 81 0.13
111 160 0.26
112 100 0.16
113 82 0.13
114 22 0.04
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (112 bp):
AAAAGGTTGAACAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGT
Found at i:31920 original size:221 final size:223
Alignment explanation
Indices: 31566--32312 Score: 1227
Period size: 221 Copynumber: 3.4 Consensus size: 223
31556 AGAATTATGC
* * * *
31566 AAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTC-TCA-ATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * *
31629 TATGAAC-TTCTCCGGAAAAGATAATCCATCAAGTGAT-GATTC-AGTAAAAGGTTGAACAATTC
66 TATGAACTTTCTCTGGAAATGATGATCCATCAA-TGATGGATTCAAGTAAAAGGTTGAACAATTC
31691 TTCTCATTATGAACTTCTTCTTCCTTC-TCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAA
130 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAA
* *
31755 AAGATGATCCATCAAATGATAATTCAAGT
195 ATGATGATCCATCAAATGATGATTCAAGT
31784 AAAAGGTTGAAC-AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
31848 TATGAACTTTCTCTGGAAATGATGATCCATCAATGATGGATTCAAGTAAAAGGTTG-ACAAATTC
66 TATGAACTTTCTCTGGAAATGATGATCCATCAATGATGGATTCAAGTAAAAGGTTGAAC-AATTC
31912 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA-TA-GAACTTTC-CTGGAA
130 TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAA
*
31974 ATGATGATCCATCAAATGAGGATTCAAGT
195 ATGATGATCCATCAAATGATGATTCAAGT
32003 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTT-TTCTTCTTCTTCAGATGAGTTCTTCTC
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC--CTTCTTCAGATGAGTTCTTCTC
32067 ATTATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGTAAAAGGTTGAACAAT
64 ATTATGAACTTTCTCTGGAAATGATGATCCATC-AATGATGGATTCAAGTAAAAGGTTGAACAAT
32132 TCTTCTCATTATGAACTTCTTC-TCCTTCTTCAGATGAGTTTCTTCTCATTATGAACTTTCTCTG
128 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG-TTCTTCTCATTATGAACTTTCTCTG
32196 GAAATGATGATCCATCAAATGATGGATTCAAGT
192 GAAATGATGATCCATCAAATGAT-GATTCAAGT
*
32229 AAAAGGTTGAACAAATTCTTCTTATTATG-ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
32293 TATG-ACTTTCTCTGGAAATG
66 TATGAACTTTCTCTGGAAATG
32313 TCAATCCATC
Statistics
Matches: 499, Mismatches: 12, Indels: 31
0.92 0.02 0.06
Matches are distributed among these distances:
217 29 0.06
218 14 0.03
219 73 0.15
220 61 0.12
221 117 0.23
222 77 0.15
223 20 0.04
224 36 0.07
225 32 0.06
226 40 0.08
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.39
Consensus pattern (223 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAATGATGATCCATCAATGATGGATTCAAGTAAAAGGTTGAACAATTCT
TCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAA
TGATGATCCATCAAATGATGATTCAAGT
Found at i:33319 original size:83 final size:83
Alignment explanation
Indices: 33056--33538 Score: 707
Period size: 83 Copynumber: 5.8 Consensus size: 83
33046 GTAGTTCCTA
* * *
33056 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAGGATGCTA-TGAGCACATTCATCTTCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATTCATCTTCTA
33120 AATTCAATGATTGGTTCTG
65 AATTCAATGATTGGTTCTG
* * * * *** *
33139 TCTAACTAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAAGTCTCCTTCATCCTCT
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT--GGCAAATTCATCTTCT
33204 AAATTCAATGATTGGTTCTG
64 AAATTCAATGATTGGTTCTG
* *
33224 CTAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATTTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAA
33289 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
*
33307 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATTTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAA
*
33372 ATTCAATGATTGGATCTG
66 ATTCAATGATTGGTTCTG
* * * *** *
33390 TCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAAGTCTCCTTCATCCTCT
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT--GGCAAATTCATCTTCT
33455 AAATTCAATGATTGGTTCTG
64 AAATTCAATGATTGGTTCTG
*
33475 CTAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTA
33539 GTTAATGTTT
Statistics
Matches: 357, Mismatches: 38, Indels: 10
0.88 0.09 0.02
Matches are distributed among these distances:
83 209 0.59
84 1 0.00
85 146 0.41
86 1 0.00
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.29
Consensus pattern (83 bp):
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAA
ATTCAATGATTGGTTCTG
Found at i:33336 original size:168 final size:167
Alignment explanation
Indices: 33058--33538 Score: 716
Period size: 168 Copynumber: 2.9 Consensus size: 167
33048 AGTTCCTACC
* *
33058 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAGGATGCTA-TGAGCACATTCATCTTCAAAA
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCACATTCATCTTCTAAA
* * *
33122 TTCAATGATTGGTTCTGTCTAACTAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTA
65 TTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT-
* *** *
33187 AGTCTCCTTCATCCTCTAAATTCAATGATTGGTTCTG-CT
129 -GGCAAATTCATCCTCTAAATTCAATGATTGGATCTGTCT
* *
33226 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATTTTCTAAAT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCATCTTCTAAAT
33291 TCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGG
66 TCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGG
**
33356 CAAATTCATTTTCTAAATTCAATGATTGGATCTGTCT
131 CAAATTCATCCTCTAAATTCAATGATTGGATCTGTCT
* * * *
33393 -AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAAGTCTCCTTCATCCTCTAA
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT--GGCACATTCATCTTCTAA
*
33457 ATTCAATGATTGGTTCTGCTAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
64 ATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
*
33522 GGCAAATTCATCTTCTA
129 GGCAAATTCATCCTCTA
33539 GTTAATGTTT
Statistics
Matches: 287, Mismatches: 22, Indels: 8
0.91 0.07 0.03
Matches are distributed among these distances:
166 73 0.25
167 2 0.01
168 210 0.73
169 2 0.01
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.29
Consensus pattern (167 bp):
AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCATCTTCTAAAT
TCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGG
CAAATTCATCCTCTAAATTCAATGATTGGATCTGTCT
Found at i:33499 original size:251 final size:251
Alignment explanation
Indices: 33056--33538 Score: 887
Period size: 251 Copynumber: 1.9 Consensus size: 251
33046 GTAGTTCCTA
* *
33056 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAGGATGCTATGAGCACATTCATCTTCAAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCAAA
* *
33121 ATTCAATGATTGGTTCTGTCTAACTAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
66 ATTCAATGATTGGATCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
33186 AAGTCTCCTTCATCCTCTAAATTCAATGATTGGTTCTGCTAAACCAGATCAGATAACTCAAAGAA
131 AAGTCTCCTTCATCCTCTAAATTCAATGATTGGTTCTGCTAAACCAGATCAGATAACTCAAAGAA
*
33251 CACTTCCAGAAGATGCTATTGGCAAATTCATTTTCTAAATTCAATGATTGGTTCTG
196 CACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAATGATTGGTTCTG
* *
33307 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATTCATTTTCTA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCAAATTCATCTTCAA
33371 AATTCAATGATTGGATCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
65 AATTCAATGATTGGATCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
33436 TAAGTCTCCTTCATCCTCTAAATTCAATGATTGGTTCTGCTAAACCAGATCAGATAACTCAAAGA
130 TAAGTCTCCTTCATCCTCTAAATTCAATGATTGGTTCTGCTAAACCAGATCAGATAACTCAAAGA
33501 ACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTA
195 ACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTA
33539 GTTAATGTTT
Statistics
Matches: 224, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
251 222 0.99
252 2 0.01
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.29
Consensus pattern (251 bp):
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCAAA
ATTCAATGATTGGATCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
AAGTCTCCTTCATCCTCTAAATTCAATGATTGGTTCTGCTAAACCAGATCAGATAACTCAAAGAA
CACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAATGATTGGTTCTG
Found at i:46078 original size:15 final size:15
Alignment explanation
Indices: 46040--46086 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
46030 TTTTCGTCGA
*
46040 TATTGAAAAATAAA-
1 TATTAAAAAATAAAT
*
46054 TATT--AAAATAATT
1 TATTAAAAAATAAAT
46067 TATTAAAAAATAAAT
1 TATTAAAAAATAAAT
46082 TATTA
1 TATTA
46087 TTTATTATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
12 7 0.25
13 4 0.14
14 4 0.14
15 13 0.46
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (15 bp):
TATTAAAAAATAAAT
Found at i:46165 original size:15 final size:16
Alignment explanation
Indices: 46130--46171 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
46120 TAAAAATATT
46130 TAAAAATATAAACAAG
1 TAAAAATATAAACAAG
*
46146 TAAAATTA-AAACAA-
1 TAAAAATATAAACAAG
46160 TAAAAAATATAA
1 T-AAAAATATAA
46172 CTAGAATGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 1 0.05
15 12 0.55
16 9 0.41
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.21
Consensus pattern (16 bp):
TAAAAATATAAACAAG
Found at i:47018 original size:15 final size:15
Alignment explanation
Indices: 46977--47018 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
46967 CCTCGGTAAG
*
46977 TTTCTTTTCTTCCTT
1 TTTCTTTTCTTTCTT
*
46992 TTTCTTTCCTTTC-T
1 TTTCTTTTCTTTCTT
47006 TTTCTGTTTCTTT
1 TTTCT-TTTCTTT
47019 GCTGAGTGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 6 0.26
15 17 0.74
ACGTcount: A:0.00, C:0.24, G:0.02, T:0.74
Consensus pattern (15 bp):
TTTCTTTTCTTTCTT
Found at i:47103 original size:12 final size:12
Alignment explanation
Indices: 47088--47128 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 12
47078 TCTCTCTGTG
47088 TTCTTTTCTCTT
1 TTCTTTTCTCTT
*
47100 TTCTTTCCT-TT
1 TTCTTTTCTCTT
*
47111 TTTTTTTCTCTT
1 TTCTTTTCTCTT
47123 TT-TTTT
1 TTCTTTT
47129 TAGGTTCGGG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
11 13 0.52
12 12 0.48
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (12 bp):
TTCTTTTCTCTT
Found at i:47129 original size:12 final size:12
Alignment explanation
Indices: 47091--47129 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
47081 CTCTGTGTTC
*
47091 TTTTCTCTTTTC
1 TTTTCTCTTTTT
*
47103 TTTCCT-TTTTT
1 TTTTCTCTTTTT
47114 TTTTCTCTTTTT
1 TTTTCTCTTTTT
47126 TTTT
1 TTTT
47130 AGGTTCGGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
11 9 0.39
12 14 0.61
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTCTCTTTTT
Found at i:47587 original size:3 final size:3
Alignment explanation
Indices: 47579--47702 Score: 212
Period size: 3 Copynumber: 41.3 Consensus size: 3
47569 TTAATATATT
*
47579 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
47627 TAA TAA TGA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
47675 TAA TGA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
47703 GATATGGGTA
Statistics
Matches: 113, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 113 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:49051 original size:24 final size:23
Alignment explanation
Indices: 49019--49074 Score: 85
Period size: 24 Copynumber: 2.4 Consensus size: 23
49009 CATTTAAATG
49019 ATAAACGAACACAAATGAACAAA
1 ATAAACGAACACAAATGAACAAA
* *
49042 CATAAACGAACATAAATGAACACA
1 -ATAAACGAACACAAATGAACAAA
49066 ATAAACGAA
1 ATAAACGAA
49075 TATTAACGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 9 0.30
24 21 0.70
ACGTcount: A:0.62, C:0.18, G:0.09, T:0.11
Consensus pattern (23 bp):
ATAAACGAACACAAATGAACAAA
Found at i:49089 original size:23 final size:23
Alignment explanation
Indices: 49019--49110 Score: 78
Period size: 24 Copynumber: 3.9 Consensus size: 23
49009 CATTTAAATG
* * *
49019 ATAAACGAACACAAATGAACAAA
1 ATAAACGAACATAAACGAACACA
*
49042 CATAAACGAACATAAATGAACACA
1 -ATAAACGAACATAAACGAACACA
* * *
49066 ATAAACGAATATTAACGAATACA
1 ATAAACGAACATAAACGAACACA
*
49089 A-ACGAATGAACATAAACGAACA
1 ATA--AACGAACATAAACGAACA
49111 TAAATGAAAA
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
22 1 0.02
23 20 0.36
24 35 0.62
ACGTcount: A:0.60, C:0.17, G:0.10, T:0.13
Consensus pattern (23 bp):
ATAAACGAACATAAACGAACACA
Found at i:49315 original size:24 final size:24
Alignment explanation
Indices: 49283--49338 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
49273 GATTAGGCTA
*
49283 AACATAAATGAACACACATAAACG
1 AACATAAATGAACACAAATAAACG
*
49307 AACATAAATGAACATAAATAAACG
1 AACATAAATGAACACAAATAAACG
49331 AACATAAA
1 AACATAAA
49339 CGAATATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.62, C:0.16, G:0.07, T:0.14
Consensus pattern (24 bp):
AACATAAATGAACACAAATAAACG
Found at i:49327 original size:14 final size:14
Alignment explanation
Indices: 49286--49338 Score: 51
Period size: 14 Copynumber: 4.1 Consensus size: 14
49276 TAGGCTAAAC
* * *
49286 ATAAATGAACACAC
1 ATAAACGAACATAA
49300 ATAAACGAACATAA
1 ATAAACGAACATAA
49314 AT----GAACATAA
1 ATAAACGAACATAA
49324 ATAAACGAACATAA
1 ATAAACGAACATAA
49338 A
1 A
49339 CGAATATATT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
10 10 0.31
14 22 0.69
ACGTcount: A:0.62, C:0.15, G:0.08, T:0.15
Consensus pattern (14 bp):
ATAAACGAACATAA
Found at i:53509 original size:22 final size:21
Alignment explanation
Indices: 53467--53506 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
53457 GAGTTTATTT
*
53467 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
53488 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
53507 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:57211 original size:20 final size:20
Alignment explanation
Indices: 57186--57257 Score: 90
Period size: 20 Copynumber: 3.6 Consensus size: 20
57176 TTTTCCGACT
57186 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
* * ***
57206 ATCGCAATACGAGTATGGCT
1 ATCGCAATGCGAATATGTAA
*
57226 ATCGCAACGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
57246 ATCGCAATGCGA
1 ATCGCAATGCGA
57258 TTATTACTAT
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.22
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:57231 original size:40 final size:40
Alignment explanation
Indices: 57182--57277 Score: 147
Period size: 40 Copynumber: 2.4 Consensus size: 40
57172 GCGATTTTCC
*
57182 GACTATCGCAATGCGAATATGTAAATCGCAATACGAGTAT
1 GACTATCGCAACGCGAATATGTAAATCGCAATACGAGTAT
* * *
57222 GGCTATCGCAACGCGAATATGTAAATCGCAATGCGATTAT
1 GACTATCGCAACGCGAATATGTAAATCGCAATACGAGTAT
*
57262 TACTATCGCAACGCGA
1 GACTATCGCAACGCGA
57278 TTCTGACTGT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (40 bp):
GACTATCGCAACGCGAATATGTAAATCGCAATACGAGTAT
Found at i:57269 original size:20 final size:20
Alignment explanation
Indices: 57183--57299 Score: 85
Period size: 20 Copynumber: 5.8 Consensus size: 20
57173 CGATTTTCCG
*
57183 ACTATCGCAATGCGAATATGT
1 ACTATCGCAATGCGATTAT-T
* * * *
57204 A-AATCGCAATACGAGTATG
1 ACTATCGCAATGCGATTATT
* * *
57223 GCTATCGCAACGCGAATATGT
1 ACTATCGCAATGCGATTAT-T
*
57244 A-AATCGCAATGCGATTATT
1 ACTATCGCAATGCGATTATT
* * *
57263 ACTATCGCAACGCGATTCTG
1 ACTATCGCAATGCGATTATT
*
57283 ACTGTCGCAATGCGATT
1 ACTATCGCAATGCGATT
57300 TTCAAAGCGC
Statistics
Matches: 73, Mismatches: 20, Indels: 7
0.73 0.20 0.07
Matches are distributed among these distances:
19 2 0.03
20 70 0.96
21 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (20 bp):
ACTATCGCAATGCGATTATT
Found at i:57500 original size:22 final size:22
Alignment explanation
Indices: 57474--57516 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
57464 GGCGACATCC
57474 GTCCCCATCTCCGACAAAATCA
1 GTCCCCATCTCCGACAAAATCA
*
57496 GTCCCCATCTCCGGCAAAATC
1 GTCCCCATCTCCGACAAAATC
57517 CATCTATCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.28, C:0.42, G:0.12, T:0.19
Consensus pattern (22 bp):
GTCCCCATCTCCGACAAAATCA
Found at i:57994 original size:20 final size:20
Alignment explanation
Indices: 57899--57992 Score: 100
Period size: 20 Copynumber: 4.8 Consensus size: 20
57889 GCGATTTTAG
57899 TTTCGCGTTGCGATTGTCA-
1 TTTCGCGTTGCGATTGTCAT
* *
57918 TTTCGCGTTGCGATAGTCAA
1 TTTCGCGTTGCGATTGTCAT
* * *
57938 ATTCGCATTGCGATAGTCAT
1 TTTCGCGTTGCGATTGTCAT
* * *
57958 TTTCGTGTTGTGATTTTCAT
1 TTTCGCGTTGCGATTGTCAT
*
57978 TTTCGTGTTGCGATT
1 TTTCGCGTTGCGATT
57993 TTAAGTTTCA
Statistics
Matches: 63, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
19 18 0.29
20 45 0.71
ACGTcount: A:0.15, C:0.17, G:0.23, T:0.45
Consensus pattern (20 bp):
TTTCGCGTTGCGATTGTCAT
Found at i:58001 original size:20 final size:20
Alignment explanation
Indices: 57958--58001 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
57948 CGATAGTCAT
* * *
57958 TTTCGTGTTGTGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
57978 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
57998 TTTC
1 TTTC
58002 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.11, C:0.11, G:0.20, T:0.57
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:59936 original size:20 final size:20
Alignment explanation
Indices: 59911--59977 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
59901 TAGTTTACTT
** *
59911 TCGCAACGCGAAAATGATTA
1 TCGCAACGCGAATTTGACTA
*
59931 TCGCAACGCGAATTTTACTA
1 TCGCAACGCGAATTTGACTA
59951 TCGCAACGCGAATTTGACTA
1 TCGCAACGCGAATTTGACTA
59971 TCGCAAC
1 TCGCAAC
59978 AAAAGAATCG
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (20 bp):
TCGCAACGCGAATTTGACTA
Found at i:60046 original size:20 final size:20
Alignment explanation
Indices: 60021--60096 Score: 143
Period size: 20 Copynumber: 3.8 Consensus size: 20
60011 GCGATTCTCT
60021 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
60041 CGTTGCGATAGTCATTTTTG
1 CGTTGCGATAGTCATTTTCG
60061 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
60081 CGTTGCGATAGTCATT
1 CGTTGCGATAGTCATT
60097 CATGTTGCGA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.16, C:0.18, G:0.25, T:0.41
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:60047 original size:34 final size:37
Alignment explanation
Indices: 60004--60090 Score: 108
Period size: 40 Copynumber: 2.4 Consensus size: 37
59994 GAAATGAAAA
*
60004 TCGCATTGCGAT-TC-TCT-CGTTGCGATAGTCATTT
1 TCGCGTTGCGATATCTTCTGCGTTGCGATAGTCATTT
*
60038 TCGCGTTGCGATAGTCATTTTTGCGTTGCGATAGTCATTT
1 TCGCGTTGCGATA-TC--TTCTGCGTTGCGATAGTCATTT
60078 TCGCGTTGCGATA
1 TCGCGTTGCGATA
60091 GTCATTCATG
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
34 11 0.24
36 2 0.04
39 2 0.04
40 30 0.67
ACGTcount: A:0.15, C:0.21, G:0.24, T:0.40
Consensus pattern (37 bp):
TCGCGTTGCGATATCTTCTGCGTTGCGATAGTCATTT
Found at i:62598 original size:18 final size:17
Alignment explanation
Indices: 62544--62592 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
62534 TTGGACTCCT
* *
62544 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TGA
62562 GAGTGCATCGATGCATGA
1 -AGTGCATCGATGCATGA
62580 AGTGCATTCGATG
1 AGTGCA-TCGATG
62593 TTTGAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATGA
Found at i:62695 original size:19 final size:19
Alignment explanation
Indices: 62671--62707 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
62661 TAATTAAATC
62671 AGAGTGCATCGATGCATGA
1 AGAGTGCATCGATGCATGA
62690 AGAGTGCATCGATGCATG
1 AGAGTGCATCGATGCATG
62708 GAATGCATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.30, C:0.16, G:0.32, T:0.22
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGA
Found at i:62744 original size:65 final size:63
Alignment explanation
Indices: 62546--62753 Score: 206
Period size: 65 Copynumber: 3.2 Consensus size: 63
62536 GGACTCCTAG
* * * * *
62546 TGCATCGGTGCACT-AAGAGTGCATCGATGCATGAAGTGCATTCGATGTTTGAA-AAATAGCCTG
1 TGCATCGATGCA-TGAAGAGTGCATCGATGCATGAA-TGCATTCGATGTTTCAATTAAT-TCATG
*
62609 G
63 A
* ** * * *
62610 TGCATCGATGCATGGATTGTGCATCGATGCATCAAATGCATTCGATGTTTTTAATTAAATCA-GA
1 TGCATCGATGCATGAAGAGTGCATCGATGCAT-GAATGCATTCGATG-TTTCAATTAATTCATGA
*
62674 GTGCATCGATGCATGAAGAGTGCATCGATGCATGGAATGCATTCGATGTTTCAATTTATTCATTG
1 -TGCATCGATGCATGAAGAGTGCATCGATGCAT-GAATGCATTCGATGTTTCAATTAATTCA-TG
62739 A
63 A
62740 TGCATCGATGCATG
1 TGCATCGATGCATG
62754 GTATTGATGC
Statistics
Matches: 118, Mismatches: 19, Indels: 13
0.79 0.13 0.09
Matches are distributed among these distances:
63 1 0.01
64 49 0.42
65 64 0.54
66 4 0.03
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (63 bp):
TGCATCGATGCATGAAGAGTGCATCGATGCATGAATGCATTCGATGTTTCAATTAATTCATGA
Found at i:62759 original size:21 final size:21
Alignment explanation
Indices: 62735--62774 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
62725 CAATTTATTC
62735 ATTGATGCATCGATGCATGGT
1 ATTGATGCATCGATGCATGGT
*
62756 ATTGATGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
62775 CTTTTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.33
Consensus pattern (21 bp):
ATTGATGCATCGATGCATGGT
Found at i:62781 original size:21 final size:21
Alignment explanation
Indices: 62735--62781 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
62725 CAATTTATTC
*
62735 ATTGATGCATCGATGCATGGT
1 ATTGATGCATCGATGCATGCT
*
62756 ATTGATGCATCGGTGCATGCT
1 ATTGATGCATCGATGCATGCT
*
62777 TTTGA
1 ATTGA
62782 AAAATTGATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.21, C:0.15, G:0.28, T:0.36
Consensus pattern (21 bp):
ATTGATGCATCGATGCATGCT
Found at i:65392 original size:24 final size:23
Alignment explanation
Indices: 65321--65400 Score: 94
Period size: 24 Copynumber: 3.5 Consensus size: 23
65311 CATGGTCTTG
*
65321 TGCATCGATGCACATTCAAGGCA
1 TGCATCGATGCACATTCAAGGGA
* *
65344 TGCATCGGTG--CA-TCATGCGGA
1 TGCATCGATGCACATTCAAG-GGA
65365 TGCATCGATGCACATTCAAAGGGA
1 TGCATCGATGCACATTC-AAGGGA
65389 TGCATCGATGCA
1 TGCATCGATGCA
65401 TTGTTAAGTG
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
20 4 0.09
21 13 0.28
23 11 0.23
24 17 0.36
25 2 0.04
ACGTcount: A:0.28, C:0.24, G:0.26, T:0.23
Consensus pattern (23 bp):
TGCATCGATGCACATTCAAGGGA
Found at i:65413 original size:44 final size:42
Alignment explanation
Indices: 65298--65420 Score: 122
Period size: 44 Copynumber: 2.8 Consensus size: 42
65288 AAAACCCGAC
* *
65298 GGATGCATCGATGCATGGTCTTGTGCATCGATGCACATTCAAG
1 GGATGCATCGATGCATTGT-TAGTGCATCGATGCACATTCAAG
* * **
65341 GCATGCATCGGTGCATCATG-CGGATGCATCGATGCACATTCAAAG
1 GGATGCATCGATGCAT--TGTTAG-TGCATCGATGCACATTC-AAG
*
65386 GGATGCATCGATGCATTGTTAAGTGCATCGGTGCA
1 GGATGCATCGATGCATTGTT-AGTGCATCGATGCA
65421 TTAAGCACAA
Statistics
Matches: 64, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
43 17 0.27
44 28 0.44
45 19 0.30
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.26
Consensus pattern (42 bp):
GGATGCATCGATGCATTGTTAGTGCATCGATGCACATTCAAG
Found at i:69051 original size:24 final size:24
Alignment explanation
Indices: 69005--69051 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
68995 GATTTTGAAT
* * **
69005 TTCCACCTTTTTCAAAATGTTTTG
1 TTCCAACTTTATCAAAAAATTTTG
69029 TTCCAACTTTATCAAAAAATTTT
1 TTCCAACTTTATCAAAAAATTTT
69052 AAGATCATCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.30, C:0.19, G:0.04, T:0.47
Consensus pattern (24 bp):
TTCCAACTTTATCAAAAAATTTTG
Found at i:69159 original size:15 final size:15
Alignment explanation
Indices: 69139--69176 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
69129 ACTCTTCTAG
69139 TTTGATTTGCAAATC
1 TTTGATTTGCAAATC
69154 TTTGATTTGCAAATC
1 TTTGATTTGCAAATC
69169 TTTGATTT
1 TTTGATTT
69177 TACTTTCAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.24, C:0.11, G:0.13, T:0.53
Consensus pattern (15 bp):
TTTGATTTGCAAATC
Found at i:71179 original size:63 final size:65
Alignment explanation
Indices: 71032--71211 Score: 200
Period size: 63 Copynumber: 2.9 Consensus size: 65
71022 TGGACTCCTA
* * *
71032 GTGCATCGGTGCACT-AAGAGTGCATCGATGCATGAAGTG-ATTCGATGTTTGAA--AAATAGCA
1 GTGCATCGATGCA-TGAAGAGTGCATCGATGCATGAAATGCATTCGATGTTTTAATTAAATAGCA
71093 T
65 T
*
71094 GTGCATCGATGCATG--GATGTGCATCGATGCATCAAATGCATTCGATGTTTTAATTAAATCAG-
1 GTGCATCGATGCATGAAGA-GTGCATCGATGCATGAAATGCATTCGATGTTTTAATTAAAT-AGC
71156 A-
64 AT
* *
71157 GTGCATCGATGC-TGAAGAGTGCATCGGTGCATGGAATGCATTCGAT-TTTTCAATT
1 GTGCATCGATGCATGAAGAGTGCATCGATGCATGAAATGCATTCGATGTTTT-AATT
71212 TATTCATTGA
Statistics
Matches: 102, Mismatches: 7, Indels: 17
0.81 0.06 0.13
Matches are distributed among these distances:
60 2 0.02
61 19 0.19
62 31 0.30
63 41 0.40
64 7 0.07
65 2 0.02
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATGAAGAGTGCATCGATGCATGAAATGCATTCGATGTTTTAATTAAATAGCAT
Found at i:71243 original size:21 final size:21
Alignment explanation
Indices: 71217--71256 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
71207 CAATTTATTC
71217 ATTGATGCATCGATGCATGGT
1 ATTGATGCATCGATGCATGGT
*
71238 ATTGATGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
71257 CTTTGAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.33
Consensus pattern (21 bp):
ATTGATGCATCGATGCATGGT
Done.