Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016240.1 Corchorus capsularis cultivar CVL-1 contig16261, 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: 23410
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.33
Found at i:92 original size:49 final size:49
Alignment explanation
Indices: 10--110 Score: 157
Period size: 49 Copynumber: 2.1 Consensus size: 49
1 GTTTATCCA
* * * *
10 AGTTTATGTTAGAATGATCGATTCAGTTGACCCAGGGTGGTTTTTCTTC
1 AGTTCATGTCAGAATGATCGATTCAGTCGACCCAGGGTGGTCTTTCTTC
*
59 AGTTCATGTCAGAATGATCGATTCGGTCGACCCAGGGTGGTCTTTCTTC
1 AGTTCATGTCAGAATGATCGATTCAGTCGACCCAGGGTGGTCTTTCTTC
108 AGT
1 AGT
111 AGTTTCCACG
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.37
Consensus pattern (49 bp):
AGTTCATGTCAGAATGATCGATTCAGTCGACCCAGGGTGGTCTTTCTTC
Found at i:254 original size:33 final size:34
Alignment explanation
Indices: 190--259 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
180 TGGTTTCCAG
* *
190 TTGATCCAGGGTGGTCTTTATCAGGTTATTCA-GT
1 TTGATCCAGGGTGGTCTTCATCAAG-TATTCATGT
224 TTGATCCAGGGTGGTCTTCATCAAAG-ATTCATGT
1 TTGATCCAGGGTGGTCTTCATC-AAGTATTCATGT
258 TT
1 TT
260 AAATTTAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
33 5 0.16
34 25 0.78
35 2 0.06
ACGTcount: A:0.20, C:0.16, G:0.24, T:0.40
Consensus pattern (34 bp):
TTGATCCAGGGTGGTCTTCATCAAGTATTCATGT
Found at i:482 original size:64 final size:63
Alignment explanation
Indices: 424--656 Score: 197
Period size: 64 Copynumber: 3.7 Consensus size: 63
414 AATTCTGTTG
*
424 AAGA-GTTTCATTTCAAATCCTGCTTAAGGTCTCTGGTCGAGAGTTTCTTGTTTCAATTCCAA
1 AAGATGTTTCATTTAAAATCCTGCTTAAGGTCTCTGGTCGAGAGTTTCTTGTTTCAATTCCAA
* * * * * * **
486 AATATTGTTTCATTTTAAATCCTGCTTGAGGTCTCTAGTCCAAAGTTTCTTGTTTCAATT--TT
1 AAGA-TGTTTCATTTAAAATCCTGCTTAAGGTCTCTGGTCGAGAGTTTCTTGTTTCAATTCCAA
* ** ** ** * *
548 AA-ATCTTGTC-TTCCAAATCCTAATCGAGGTCTCTAGTCGAGAATTTCTTGTTTCAATTCCAA
1 AAGATGTT-TCATTTAAAATCCTGCTTAAGGTCTCTGGTCGAGAGTTTCTTGTTTCAATTCCAA
* * * * *
610 AATATTGTTTCATTTTAAATCCTGCTTGAGATCTCTAGTCGAGAGTT
1 AAGA-TGTTTCATTTAAAATCCTGCTTAAGGTCTCTGGTCGAGAGTT
657 ATCAATTCTA
Statistics
Matches: 136, Mismatches: 27, Indels: 14
0.77 0.15 0.08
Matches are distributed among these distances:
60 43 0.32
61 3 0.02
62 7 0.05
63 3 0.02
64 80 0.59
ACGTcount: A:0.25, C:0.18, G:0.15, T:0.42
Consensus pattern (63 bp):
AAGATGTTTCATTTAAAATCCTGCTTAAGGTCTCTGGTCGAGAGTTTCTTGTTTCAATTCCAA
Found at i:690 original size:58 final size:58
Alignment explanation
Indices: 606--771 Score: 192
Period size: 57 Copynumber: 2.9 Consensus size: 58
596 TGTTTCAATT
** * *
606 CCAAAATATTGTTTCATTTT-AAATCCTGCTTGAGATCTCTAGTCGAGAGTTATCAAT
1 CCAAAATCCTGTTTCATTTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTATCAAC
* * * * * * *
663 TCTAAGTCCTGTTTCATTTTCAAATCCTGCTCGAGGTCTCTAATTGAGAGTTTTCAAC
1 CCAAAATCCTGTTTCATTTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTATCAAC
* * *
721 CCAAAATCTTGTTTCA-TTTCAAATCCTGCTTGAGGTCTCTAGCCAAGAGTT
1 CCAAAATCCTGTTTCATTTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTT
772 TCTGTTTCAA
Statistics
Matches: 88, Mismatches: 20, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
57 45 0.51
58 43 0.49
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (58 bp):
CCAAAATCCTGTTTCATTTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTATCAAC
Found at i:760 original size:57 final size:57
Alignment explanation
Indices: 606--761 Score: 195
Period size: 58 Copynumber: 2.7 Consensus size: 57
596 TGTTTCAATT
* * * * *
606 CCAAAATATTGTTTCATTTTAAATCCTGCTTGAGATCTCTAGTCGAGAGTTATCAAT
1 CCAAAATCTTGTTTCATTTCAAATCCTGCTTGAGGTCTCTAATCGAGAGTTATCAAC
* * * * * * *
663 TCTAAGTCCTGTTTCATTTTCAAATCCTGCTCGAGGTCTCTAATTGAGAGTTTTCAAC
1 CCAAAATCTTGTTTCA-TTTCAAATCCTGCTTGAGGTCTCTAATCGAGAGTTATCAAC
721 CCAAAATCTTGTTTCATTTCAAATCCTGCTTGAGGTCTCTA
1 CCAAAATCTTGTTTCATTTCAAATCCTGCTTGAGGTCTCTA
762 GCCAAGAGTT
Statistics
Matches: 81, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
57 35 0.43
58 46 0.57
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (57 bp):
CCAAAATCTTGTTTCATTTCAAATCCTGCTTGAGGTCTCTAATCGAGAGTTATCAAC
Found at i:6750 original size:48 final size:48
Alignment explanation
Indices: 6679--6807 Score: 204
Period size: 48 Copynumber: 2.7 Consensus size: 48
6669 TCCATAAATA
* *
6679 CAGTAGTAAGTTTAATTCAGAGTAATTAAGCTAAGAAGAAAAAGTAAC
1 CAGTAATAAGTTTAATTTAGAGTAATTAAGCTAAGAAGAAAAAGTAAC
*
6727 CAGTAATAAGTTTAATTTAGAGTAATTAAGCTAAGAAGAAAAAGTAAT
1 CAGTAATAAGTTTAATTTAGAGTAATTAAGCTAAGAAGAAAAAGTAAC
* * *
6775 TAGTAATTAGTTTAATTTTGAGTAATTAAGCTA
1 CAGTAATAAGTTTAATTTAGAGTAATTAAGCTA
6808 GAAAGTAAAG
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 75 1.00
ACGTcount: A:0.46, C:0.05, G:0.17, T:0.32
Consensus pattern (48 bp):
CAGTAATAAGTTTAATTTAGAGTAATTAAGCTAAGAAGAAAAAGTAAC
Found at i:6856 original size:19 final size:18
Alignment explanation
Indices: 6832--6925 Score: 66
Period size: 19 Copynumber: 4.9 Consensus size: 18
6822 AGTAAATAGT
6832 AGTAATTAGCTTAATTCAG
1 AGTAATTAGCTTAA-TCAG
6851 AGTAATTAAG-TTAATCAAG
1 AGTAATT-AGCTTAATC-AG
** ** *
6870 AAGTAAAAAGAGTAATCACT
1 -AGTAATTAGCTTAATCA-G
6890 AGTAATTAGCTTAATTCAG
1 AGTAATTAGCTTAA-TCAG
6909 AGTAATTAAG-TTAATCA
1 AGTAATT-AGCTTAATCA
6926 AGAAGTAAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 15
0.71 0.11 0.18
Matches are distributed among these distances:
18 5 0.08
19 37 0.63
20 17 0.29
ACGTcount: A:0.45, C:0.09, G:0.15, T:0.32
Consensus pattern (18 bp):
AGTAATTAGCTTAATCAG
Found at i:6896 original size:58 final size:58
Alignment explanation
Indices: 6818--7482 Score: 548
Period size: 58 Copynumber: 11.7 Consensus size: 58
6808 GAAAGTAAAG
6818 AAAGAGTAAAT-AGTAGTAATTAGCTTAATTCAGAGTAATTAAGTTAATCAAGAAGTAA
1 AAAGAGT-AATCAGTAGTAATTAGCTTAATTCAGAGTAATTAAGTTAATCAAGAAGTAA
*
6876 AAAGAGTAATCACTAGTAATTAGCTTAATTCAGAGTAATTAAGTTAATCAAGAAGTAA
1 AAAGAGTAATCAGTAGTAATTAGCTTAATTCAGAGTAATTAAGTTAATCAAGAAGTAA
* * * *
6934 AAGGAGTAAAC-GTTGTAATTAGCTTAATTAAGAGTAATTAAGTTAATCAAGAAGTAA
1 AAAGAGTAATCAGTAGTAATTAGCTTAATTCAGAGTAATTAAGTTAATCAAGAAGTAA
* * * * *
6991 AAGGAGTAAACAATTGTAATTAGCTTCATTCAGAGTAATTAAGTTAATCAAGAAGTAA
1 AAAGAGTAATCAGTAGTAATTAGCTTAATTCAGAGTAATTAAGTTAATCAAGAAGTAA
* * * *
7049 AAGGAGTAATCAGTAGTAATTAGCCTAATTTAGAGTAATTAAGTCAATCAAGAAGTAA
1 AAAGAGTAATCAGTAGTAATTAGCTTAATTCAGAGTAATTAAGTTAATCAAGAAGTAA
* * *
7107 AAAGAGTAATCGGTAGTAATTAGTTTAATTCAGAGCAATTAAGTTAATCAAGAAGTAA
1 AAAGAGTAATCAGTAGTAATTAGCTTAATTCAGAGTAATTAAGTTAATCAAGAAGTAA
* * * * * * *
7165 AAAGAGGAGTAATTAGTAAATTGGTTTAATTCAGAGTAATTAAGCT-A--AA-AAGTAA
1 AAAGAGTAATCAGTAGT-AATTAGCTTAATTCAGAGTAATTAAGTTAATCAAGAAGTAA
* * * * *
7220 AAGGAGGAGTAATTAGTA--AATTGGTTTAATT-ATGGGTAATTAAGCT-A--AA-AAGTAA
1 AA--A-GAGTAATCAGTAGTAATTAGCTTAATTCA-GAGTAATTAAGTTAATCAAGAAGTAA
* * * *
7275 AAGGAGGAGTAATCAGTA--AATTAGTTTAATTCTGAGTAATTAA---ACT-AAAAAGTAAA
1 AA--A-GAGTAATCAGTAGTAATTAGCTTAATTCAGAGTAATTAAGTTAATCAAGAAGT-AA
* * * *
7331 AGAAGGAATAATCAGTA--AATTGGTTTAATTCAGAGTAATTAAGCTAA--AAG--GTAAA
1 A-AA-GAGTAATCAGTAGTAATTAGCTTAATTCAGAGTAATTAAGTTAATCAAGAAGT-AA
* * ** * *
7386 AGAAGGATTAATTAGTAG--ATTAGCCAAATTCAGAGTAATTAAGCTAA-AAAGTAA--AA
1 A-AA-GAGTAATCAGTAGTAATTAGCTTAATTCAGAGTAATTAAGTTAATCAAG-AAGTAA
* *
7442 GAAAGAGTAATGAGTA-T-ATTAGTTTAATTCAGAGTAATTAA
1 -AAAGAGTAATCAGTAGTAATTAGCTTAATTCAGAGTAATTAA
7483 ACTAAAAAGA
Statistics
Matches: 527, Mismatches: 57, Indels: 49
0.83 0.09 0.08
Matches are distributed among these distances:
54 3 0.01
55 196 0.37
56 12 0.02
57 62 0.12
58 229 0.43
59 25 0.05
ACGTcount: A:0.46, C:0.06, G:0.19, T:0.29
Consensus pattern (58 bp):
AAAGAGTAATCAGTAGTAATTAGCTTAATTCAGAGTAATTAAGTTAATCAAGAAGTAA
Found at i:6976 original size:115 final size:116
Alignment explanation
Indices: 6821--7166 Score: 541
Period size: 115 Copynumber: 3.0 Consensus size: 116
6811 AGTAAAGAAA
* *
6821 GAGTAAATAGTAGTAATTAGCTTAATTCAGAGTAATTAAGTTAATCAAGAAGTAAAAAGAGTAAT
1 GAGTAAACAGTAGTAATTAGCTTAATTAAGAGTAATTAAGTTAATCAAGAAGTAAAAAGAGTAAT
*
6886 CACTAGTAATTAGCTTAATTCAGAGTAATTAAGTTAATCAAGAAGTAAAAG
66 CAATAGTAATTAGCTTAATTCAGAGTAATTAAGTTAATCAAGAAGTAAAAG
* * *
6937 GAGTAAAC-GTTGTAATTAGCTTAATTAAGAGTAATTAAGTTAATCAAGAAGTAAAAGGAGTAAA
1 GAGTAAACAGTAGTAATTAGCTTAATTAAGAGTAATTAAGTTAATCAAGAAGTAAAAAGAGTAAT
* *
7001 CAATTGTAATTAGCTTCATTCAGAGTAATTAAGTTAATCAAGAAGTAAAAG
66 CAATAGTAATTAGCTTAATTCAGAGTAATTAAGTTAATCAAGAAGTAAAAG
* * * *
7052 GAGTAATCAGTAGTAATTAGCCTAATTTAGAGTAATTAAGTCAATCAAGAAGTAAAAAGAGTAAT
1 GAGTAAACAGTAGTAATTAGCTTAATTAAGAGTAATTAAGTTAATCAAGAAGTAAAAAGAGTAAT
** * *
7117 CGGTAGTAATTAGTTTAATTCAGAGCAATTAAGTTAATCAAGAAGTAAAA
66 CAATAGTAATTAGCTTAATTCAGAGTAATTAAGTTAATCAAGAAGTAAAA
7167 AGAGGAGTAA
Statistics
Matches: 208, Mismatches: 21, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
115 107 0.51
116 101 0.49
ACGTcount: A:0.46, C:0.07, G:0.18, T:0.29
Consensus pattern (116 bp):
GAGTAAACAGTAGTAATTAGCTTAATTAAGAGTAATTAAGTTAATCAAGAAGTAAAAAGAGTAAT
CAATAGTAATTAGCTTAATTCAGAGTAATTAAGTTAATCAAGAAGTAAAAG
Found at i:6979 original size:19 final size:21
Alignment explanation
Indices: 6948--6990 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 21
6938 AGTAAACGTT
*
6948 GTAATT-AGCTTAATTAAG-A
1 GTAATTAAGCTTAATCAAGAA
6967 GTAATTAAG-TTAATCAAGAA
1 GTAATTAAGCTTAATCAAGAA
6987 GTAA
1 GTAA
6991 AAGGAGTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.47, C:0.05, G:0.16, T:0.33
Consensus pattern (21 bp):
GTAATTAAGCTTAATCAAGAA
Found at i:7024 original size:173 final size:174
Alignment explanation
Indices: 6833--7208 Score: 558
Period size: 173 Copynumber: 2.2 Consensus size: 174
6823 GTAAATAGTA
6833 GTAATTAGCTTAATTCAGAGTAATTAAGTTAATCAAGAAGTAAAAAGAGTAATCACTAGTAATTA
1 GTAATTAGCTTAATTCAGAGTAATTAAGTTAATCAAGAAGTAAAAAGAGTAATCACTAGTAATTA
* * * *
6898 GCTTAATTCAGAGTAATTAAGTTAATCAAGAAGTAAAAGGAGTAAAC-GTTGTAATTAGCTTAAT
66 GCCTAATTCAGAGTAATTAAGTCAATCAAGAAGTAAAAAGAGTAAACGGTAGTAATTAGCTTAAT
*
6962 TAAGAGTAATTAAGTTAATCAAGAAGTAAAAGGAGTAAACAATT
131 TAAGAGCAATTAAGTTAATCAAGAAGTAAAAGGAGTAAACAATT
* * *
7006 GTAATTAGCTTCATTCAGAGTAATTAAGTTAATCAAGAAGTAAAAGGAGTAATCAGTAGTAATTA
1 GTAATTAGCTTAATTCAGAGTAATTAAGTTAATCAAGAAGTAAAAAGAGTAATCACTAGTAATTA
* * *
7071 GCCTAATTTAGAGTAATTAAGTCAATCAAGAAGTAAAAAGAGTAATCGGTAGTAATTAGTTTAAT
66 GCCTAATTCAGAGTAATTAAGTCAATCAAGAAGTAAAAAGAGTAAACGGTAGTAATTAGCTTAAT
* * * **
7136 TCAGAGCAATTAAGTTAATCAAGAAGTAAAAAGAG-GAGTAATT
131 TAAGAGCAATTAAGTTAATCAAGAAGTAAAAGGAGTAAACAATT
* *
7179 AGTAAATTGGTTTAATTCAGAGTAATTAAG
1 -GT-AATTAGCTTAATTCAGAGTAATTAAG
7209 CTAAAAAGTA
Statistics
Matches: 181, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
173 109 0.60
174 49 0.27
175 23 0.13
ACGTcount: A:0.45, C:0.07, G:0.18, T:0.30
Consensus pattern (174 bp):
GTAATTAGCTTAATTCAGAGTAATTAAGTTAATCAAGAAGTAAAAAGAGTAATCACTAGTAATTA
GCCTAATTCAGAGTAATTAAGTCAATCAAGAAGTAAAAAGAGTAAACGGTAGTAATTAGCTTAAT
TAAGAGCAATTAAGTTAATCAAGAAGTAAAAGGAGTAAACAATT
Found at i:7233 original size:28 final size:28
Alignment explanation
Indices: 7198--7287 Score: 87
Period size: 28 Copynumber: 3.2 Consensus size: 28
7188 GTTTAATTCA
7198 GAGTAATTAAGCTAAAAAGTAAAAGGAG
1 GAGTAATTAAGCTAAAAAGTAAAAGGAG
** ** **
7226 GAGTAATT-AG-TAAATTGGTTTAATTATG
1 GAGTAATTAAGCTAAA-AAGTAAAAGGA-G
7254 G-GTAATTAAGCTAAAAAGTAAAAGGAG
1 GAGTAATTAAGCTAAAAAGTAAAAGGAG
7281 GAGTAAT
1 GAGTAAT
7288 CAGTAAATTA
Statistics
Matches: 45, Mismatches: 12, Indels: 10
0.67 0.18 0.15
Matches are distributed among these distances:
26 4 0.09
27 15 0.33
28 22 0.49
29 4 0.09
ACGTcount: A:0.47, C:0.02, G:0.24, T:0.27
Consensus pattern (28 bp):
GAGTAATTAAGCTAAAAAGTAAAAGGAG
Found at i:7234 original size:55 final size:55
Alignment explanation
Indices: 6687--7548 Score: 567
Period size: 55 Copynumber: 15.5 Consensus size: 55
6677 TACAGTAGTA
* ** *
6687 AGTTTAATTCAGAGTAATTAAGCTAAGAAG--AAA--A--AGTAACCAGT-AATA
1 AGTTTAATTCAGAGTAATTAAGCTAAAAAGTAAAAGGAGGAGTAATTAGTAAATT
* *
6735 AGTTTAATTTAGAGTAATTAAGCTAAGAAG--AAA--A--AGTAATTAGT-AATT
1 AGTTTAATTCAGAGTAATTAAGCTAAAAAGTAAAAGGAGGAGTAATTAGTAAATT
** * * * *
6783 AGTTTAATTTTGAGTAATTAAGCTAGAAAGT-AAAGAAAGAGTAAATAGTAGTAATT
1 AGTTTAATTCAGAGTAATTAAGCTAAAAAGTAAAAGGAGGAGTAATTAGTA--AATT
* * * * * * *
6839 AGCTTAATTCAGAGTAATTAAGTTAATCAAGAAGTAAAAAGAGTAATCACTAGT-AATT
1 AGTTTAATTCAGAGTAATTAAGCT-A--AA-AAGTAAAAGGAGGAGTAATTAGTAAATT
* * *
6897 AGCTTAATTCAGAGTAATTAAGTTAATCAAGAAGTAAAAGGAGTA--AACGTT-GT-AATT
1 AGTTTAATTCAGAGTAATTAAGCT-A--AA-AAGTAAAAGGAGGAGTAA--TTAGTAAATT
* * * * **
6954 AGCTTAATTAAGAGTAATTAAGTTAATCAAGAAGTAAAAGGAGTAAACAATT-GT-AATT
1 AGTTTAATTCAGAGTAATTAAGCT-A--AA-AAGTAAAAGGAG-GAGTAATTAGTAAATT
* * * * * * *
7012 AGCTTCATTCAGAGTAATTAAGTTAATCAAGAAGTAAAAGGAGTAATCAGTAGT-AATT
1 AGTTTAATTCAGAGTAATTAAGCT-A--AA-AAGTAAAAGGAGGAGTAATTAGTAAATT
** * *
7070 AGCCTAATTTAGAGTAATTAAGTCAATCAAGAAGTAAAA--A-GAGTAATCGGTAGT-AATT
1 AGTTTAATTCAGAGTAATTAAG-C--T-AAAAAGTAAAAGGAGGAGTAAT---TAGTAAATT
* * *
7128 AGTTTAATTCAGAGCAATTAAGTTAATCAAGAAGTAAAAAGAGGAGTAATTAGTAAATT
1 AGTTTAATTCAGAGTAATTAAGCT-A--AA-AAGTAAAAGGAGGAGTAATTAGTAAATT
*
7187 GGTTTAATTCAGAGTAATTAAGCTAAAAAGTAAAAGGAGGAGTAATTAGTAAATT
1 AGTTTAATTCAGAGTAATTAAGCTAAAAAGTAAAAGGAGGAGTAATTAGTAAATT
* * *
7242 GGTTTAATT-ATGGGTAATTAAGCTAAAAAGTAAAAGGAGGAGTAATCAGTAAATT
1 AGTTTAATTCA-GAGTAATTAAGCTAAAAAGTAAAAGGAGGAGTAATTAGTAAATT
* * * * *
7297 AGTTTAATTCTGAGTAATTAAACTAAAAAGTAAAAGAAGGAATAATCAGTAAATT
1 AGTTTAATTCAGAGTAATTAAGCTAAAAAGTAAAAGGAGGAGTAATTAGTAAATT
* * * * *
7352 GGTTTAATTCAGAGTAATTAAGCTAAAAGGTAAAAGAAGGATTAATTAGTAGATT
1 AGTTTAATTCAGAGTAATTAAGCTAAAAAGTAAAAGGAGGAGTAATTAGTAAATT
*** * * * *
7407 AGCCAAATTCAGAGTAATTAAGCTAAAAAGTAAAAGAAAGAGTAATGAGTATATT
1 AGTTTAATTCAGAGTAATTAAGCTAAAAAGTAAAAGGAGGAGTAATTAGTAAATT
* * * *
7462 AGTTTAATTCAGAGTAATTAAACTAAAAAG-AGTAAAGGAAAGAGTAACTAGTAGATT
1 AGTTTAATTCAGAGTAATTAAGCTAAAAAGTA--AAAGG-AGGAGTAATTAGTAAATT
* * *
7519 TGTTTAATTCAGAGTAATTAAACTGAAAAG
1 AGTTTAATTCAGAGTAATTAAGCTAAAAAG
7549 GAGTAAAAAT
Statistics
Matches: 691, Mismatches: 86, Indels: 65
0.82 0.10 0.08
Matches are distributed among these distances:
48 71 0.10
49 3 0.00
51 1 0.00
53 9 0.01
54 2 0.00
55 251 0.36
56 32 0.05
57 97 0.14
58 171 0.25
59 27 0.04
60 7 0.01
61 20 0.03
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.29
Consensus pattern (55 bp):
AGTTTAATTCAGAGTAATTAAGCTAAAAAGTAAAAGGAGGAGTAATTAGTAAATT
Found at i:13306 original size:16 final size:16
Alignment explanation
Indices: 13258--13381 Score: 132
Period size: 16 Copynumber: 7.9 Consensus size: 16
13248 CAGTTTTTTT
13258 GGGTCATTCGGGT-TAC
1 GGGTCATTCGGGTCT-C
*
13274 GAGTCA-TCTGGGT-TC
1 GGGTCATTC-GGGTCTC
*
13289 GGGTTATTCGGGTCTC
1 GGGTCATTCGGGTCTC
*
13305 GGGTCATACGGGTCTC
1 GGGTCATTCGGGTCTC
* *
13321 GGGTCATTCGAGTTTC
1 GGGTCATTCGGGTCTC
*
13337 AGGTCATTCGGGTCTC
1 GGGTCATTCGGGTCTC
*
13353 GGGTCATTCGGGTTTC
1 GGGTCATTCGGGTCTC
13369 GGGTC--TCGGGTCT
1 GGGTCATTCGGGTCT
13382 ACCGGGTCTC
Statistics
Matches: 91, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
14 7 0.08
15 11 0.12
16 73 0.80
ACGTcount: A:0.10, C:0.21, G:0.36, T:0.33
Consensus pattern (16 bp):
GGGTCATTCGGGTCTC
Found at i:13308 original size:7 final size:7
Alignment explanation
Indices: 13296--13395 Score: 74
Period size: 7 Copynumber: 12.9 Consensus size: 7
13286 TTCGGGTTAT
13296 TCGGGTC
1 TCGGGTC
13303 TCGGGTC
1 TCGGGTC
13310 ATACGGGTC
1 -T-CGGGTC
13319 TCGGGTC
1 TCGGGTC
* *
13326 ATTCGAGTT
1 --TCGGGTC
*
13335 TCAGGTC
1 TCGGGTC
13342 ATTCGGGTC
1 --TCGGGTC
13351 TCGGGTC
1 TCGGGTC
*
13358 ATTCGGGTT
1 --TCGGGTC
13367 TCGGGTC
1 TCGGGTC
13374 TCGGGTC
1 TCGGGTC
13381 TACCGGGTC
1 T--CGGGTC
13390 TCGGGT
1 TCGGGT
13396 TGGGCGGGTT
Statistics
Matches: 75, Mismatches: 8, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
7 43 0.57
8 2 0.03
9 30 0.40
ACGTcount: A:0.08, C:0.24, G:0.37, T:0.31
Consensus pattern (7 bp):
TCGGGTC
Found at i:13316 original size:9 final size:8
Alignment explanation
Indices: 13258--13395 Score: 62
Period size: 7 Copynumber: 17.5 Consensus size: 8
13248 CAGTTTTTTT
13258 GGGTCATTC
1 GGGTCA-TC
*
13267 GGGTTA-C
1 GGGTCATC
*
13274 GAGTCATC
1 GGGTCATC
13282 TGGGT--TC
1 -GGGTCATC
*
13289 GGGTTATTC
1 GGGTCA-TC
13298 GGGTC-TC
1 GGGTCATC
13305 GGGTCATAC
1 GGGTCAT-C
13314 GGGTC-TC
1 GGGTCATC
13321 GGGTCATTC
1 GGGTCA-TC
* *
13330 GAGT-TTC
1 GGGTCATC
*
13337 AGGTCATTC
1 GGGTCA-TC
13346 GGGTC-TC
1 GGGTCATC
13353 GGGTCATTC
1 GGGTCA-TC
*
13362 GGGT-TTC
1 GGGTCATC
13369 GGGTC-TC
1 GGGTCATC
*
13376 GGGTCTACC
1 GGGTC-ATC
13385 GGGTC-TC
1 GGGTCATC
13392 GGGT
1 GGGT
13396 TGGGCGGGTT
Statistics
Matches: 99, Mismatches: 14, Indels: 34
0.67 0.10 0.23
Matches are distributed among these distances:
6 4 0.04
7 49 0.49
8 3 0.03
9 43 0.43
ACGTcount: A:0.09, C:0.22, G:0.37, T:0.32
Consensus pattern (8 bp):
GGGTCATC
Found at i:13389 original size:32 final size:31
Alignment explanation
Indices: 13258--13381 Score: 153
Period size: 32 Copynumber: 4.0 Consensus size: 31
13248 CAGTTTTTTT
* *
13258 GGGTCATTCGGGTTACGAGTCATCTGGGT-TC
1 GGGTCATTCGGGTTTCGGGTCATC-GGGTCTC
* *
13289 GGGTTATTCGGGTCTCGGGTCATACGGGTCTC
1 GGGTCATTCGGGTTTCGGGTCAT-CGGGTCTC
* *
13321 GGGTCATTCGAGTTTCAGGTCATTCGGGTCTC
1 GGGTCATTCGGGTTTCGGGTCA-TCGGGTCTC
13353 GGGTCATTCGGGTTTCGGGTC-TCGGGTCT
1 GGGTCATTCGGGTTTCGGGTCATCGGGTCT
13382 ACCGGGTCTC
Statistics
Matches: 80, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
30 8 0.10
31 23 0.29
32 48 0.60
33 1 0.01
ACGTcount: A:0.10, C:0.21, G:0.36, T:0.33
Consensus pattern (31 bp):
GGGTCATTCGGGTTTCGGGTCATCGGGTCTC
Found at i:13866 original size:21 final size:21
Alignment explanation
Indices: 13841--13888 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
13831 TTGCCAATTT
13841 ATAATAGGTAAAATCATAACA
1 ATAATAGGTAAAATCATAACA
* *
13862 ATAATTGGTAAAATTATAACA
1 ATAATAGGTAAAATCATAACA
13883 ATAATA
1 ATAATA
13889 TAAATTGTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.56, C:0.06, G:0.08, T:0.29
Consensus pattern (21 bp):
ATAATAGGTAAAATCATAACA
Found at i:14177 original size:53 final size:52
Alignment explanation
Indices: 14092--14192 Score: 150
Period size: 53 Copynumber: 1.9 Consensus size: 52
14082 GACGTGGCAC
* *
14092 GCCACGTGTACCAAAAAGTGACATGTAGCACGCCACATGTACTAAAAAGTCGT
1 GCCACATGTACCAAAAAGTGACATGTA-CACGCCACATGTACCAAAAAGTCGT
14145 GCCACATGTACCAAAAAGTGACACATGT-CACGCCACATGTACCAAAAA
1 GCCACATGTACCAAAAAGTG--ACATGTACACGCCACATGTACCAAAAA
14193 ATGACACGCG
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
53 38 0.86
55 6 0.14
ACGTcount: A:0.39, C:0.27, G:0.18, T:0.17
Consensus pattern (52 bp):
GCCACATGTACCAAAAAGTGACATGTACACGCCACATGTACCAAAAAGTCGT
Found at i:14211 original size:31 final size:31
Alignment explanation
Indices: 14144--14242 Score: 117
Period size: 31 Copynumber: 3.2 Consensus size: 31
14134 TAAAAAGTCG
* * *
14144 TGCCACATGTACCAAAAAGTGACACATGTCA
1 TGCCACATGTACCAAAAAATGACACGTGACA
* * *
14175 CGCCACATGTACCAAAAAATGACACGCGGCA
1 TGCCACATGTACCAAAAAATGACACGTGACA
** *
14206 TGCCACATGTTTCAAAAAATGGCACGTGACA
1 TGCCACATGTACCAAAAAATGACACGTGACA
14237 TGCCAC
1 TGCCAC
14243 GTGCACAAAA
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 57 1.00
ACGTcount: A:0.36, C:0.28, G:0.18, T:0.17
Consensus pattern (31 bp):
TGCCACATGTACCAAAAAATGACACGTGACA
Found at i:14544 original size:16 final size:16
Alignment explanation
Indices: 14523--14610 Score: 97
Period size: 16 Copynumber: 5.5 Consensus size: 16
14513 AGTTAATGTC
*
14523 TCGGGTTATTCGGGTT
1 TCGGGTCATTCGGGTT
* * *
14539 TCGGGTCATACGGATC
1 TCGGGTCATTCGGGTT
14555 TCGGGTCATTCGGGTT
1 TCGGGTCATTCGGGTT
*
14571 TCGGGTCA-TCTGGATT
1 TCGGGTCATTC-GGGTT
* *
14587 ACGGGTCATTCGGGTC
1 TCGGGTCATTCGGGTT
14603 TCGGGTCA
1 TCGGGTCA
14611 GCTGGATTAT
Statistics
Matches: 58, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
15 2 0.03
16 54 0.93
17 2 0.03
ACGTcount: A:0.11, C:0.20, G:0.35, T:0.33
Consensus pattern (16 bp):
TCGGGTCATTCGGGTT
Found at i:14558 original size:32 final size:32
Alignment explanation
Indices: 14521--14617 Score: 135
Period size: 32 Copynumber: 3.0 Consensus size: 32
14511 CCAGTTAATG
*
14521 TCTCGGGTTATTCGGGTTTCGGGTCATAC-GGA
1 TCTCGGGTCATTCGGGTTTCGGGTCAT-CTGGA
14553 TCTCGGGTCATTCGGGTTTCGGGTCATCTGGA
1 TCTCGGGTCATTCGGGTTTCGGGTCATCTGGA
* *
14585 T-TACGGGTCATTCGGGTCTCGGGTCAGCTGGA
1 TCT-CGGGTCATTCGGGTTTCGGGTCATCTGGA
14617 T
1 T
14618 TATGGATTAA
Statistics
Matches: 60, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
31 2 0.03
32 58 0.97
ACGTcount: A:0.11, C:0.21, G:0.35, T:0.33
Consensus pattern (32 bp):
TCTCGGGTCATTCGGGTTTCGGGTCATCTGGA
Found at i:17224 original size:1 final size:1
Alignment explanation
Indices: 17218--17247 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
17208 GTTTAAAACG
17218 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
17248 ATGAATTCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:18373 original size:17 final size:18
Alignment explanation
Indices: 18346--18381 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
18336 CTCCCCATAC
18346 TACCTAGGTAGTATGAGG
1 TACCTAGGTAGTATGAGG
18364 TACC-AGGTAGTATGAGG
1 TACCTAGGTAGTATGAGG
18381 T
1 T
18382 GATAGGTTGC
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:0.28, C:0.11, G:0.33, T:0.28
Consensus pattern (18 bp):
TACCTAGGTAGTATGAGG
Found at i:20589 original size:16 final size:16
Alignment explanation
Indices: 20541--20602 Score: 61
Period size: 16 Copynumber: 3.9 Consensus size: 16
20531 ACTTTTTGGA
20541 TTCAGGTTCGGGTTTT
1 TTCAGGTTCGGGTTTT
* * * *
20557 TTCGGGTTTGAGCTTT
1 TTCAGGTTCGGGTTTT
*
20573 TTCAGATTCGGGTTTT
1 TTCAGGTTCGGGTTTT
* *
20589 TTCGGGTTCAGGTT
1 TTCAGGTTCGGGTT
20603 CAGGCGGGTT
Statistics
Matches: 34, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.08, C:0.13, G:0.31, T:0.48
Consensus pattern (16 bp):
TTCAGGTTCGGGTTTT
Found at i:21144 original size:21 final size:22
Alignment explanation
Indices: 21120--21164 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
21110 CGAAACTGAA
*
21120 TTGCTAAATACCGTCCC-CTTT
1 TTGCTAAATACCGCCCCACTTT
**
21141 TTGCTATTTACCGCCCCACTTT
1 TTGCTAAATACCGCCCCACTTT
21163 TT
1 TT
21165 ACACTTTTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.16, C:0.33, G:0.09, T:0.42
Consensus pattern (22 bp):
TTGCTAAATACCGCCCCACTTT
Found at i:23032 original size:41 final size:39
Alignment explanation
Indices: 22985--23362 Score: 208
Period size: 41 Copynumber: 9.6 Consensus size: 39
22975 TCTTTCAAGC
* * *
22985 GTTGGCATCCGTTGGCCTTCTTGAAGAAAAAGTATCCAAAT
1 GTTGGCATCGGTTGGCCTTCTT-AA-AAAAAGTTTCCAAAA
* * *
23026 GTTGGCATCGGTTGGCCTTC-TAAAAATA-TTTTC-AGA
1 GTTGGCATCGGTTGGCCTTCTTAAAAAAAGTTTCCAAAA
* * * **
23062 GTCGGTATCTGTTGGCCTTCTCTAAAAATCAAGTTTTATAAAA
1 GTTGGCATCGGTTGGCCTTCT-TAAAAA--AAG-TTTCCAAAA
* * * *
23105 GTCGGCATCAGTTGGCCTTCTTTAAAATTGAA-TTTTCAAAA
1 GTTGGCATCGGTTGGCCTTC-TTAAAA--AAAGTTTCCAAAA
* *
23146 GTTGGCATCGGTTGGCCTTCTTGAAGAAAAAGTATCCAAAT
1 GTTGGCATCGGTTGGCCTTCTT-AA-AAAAAGTTTCCAAAA
* * *
23187 GTTGGCATCGGTTGGCCTTC-T-AAAAATGTTTTC-AGA
1 GTTGGCATCGGTTGGCCTTCTTAAAAAAAGTTTCCAAAA
* * * *
23223 GTCGGTATCTGTTGGCCTTCTCTAAAAATCAAGTTT-TATAATA
1 GTTGGCATCGGTTGGCCTTCT-TAAAAA--AAGTTTCCA-AA-A
* * *
23266 GTCGGCATCAGTTGGCCTTCTTTAAAATCGAA-TTTCC-AAA
1 GTTGGCATCGGTTGGCCTTC-TTAAAA--AAAGTTTCCAAAA
* * **
23306 GTTGGTATCGGTTGGCCTT-GT--AACGAGTTTCC-AAA
1 GTTGGCATCGGTTGGCCTTCTTAAAAAAAGTTTCCAAAA
23341 GTTGGCATCGGTTGGCCTTCTT
1 GTTGGCATCGGTTGGCCTTCTT
23363 CTTTTTTAAA
Statistics
Matches: 263, Mismatches: 47, Indels: 59
0.71 0.13 0.16
Matches are distributed among these distances:
34 1 0.00
35 26 0.10
36 39 0.15
37 11 0.04
38 13 0.05
39 6 0.02
40 24 0.09
41 79 0.30
42 9 0.03
43 53 0.20
44 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (39 bp):
GTTGGCATCGGTTGGCCTTCTTAAAAAAAGTTTCCAAAA
Found at i:23119 original size:43 final size:41
Alignment explanation
Indices: 23029--23292 Score: 176
Period size: 43 Copynumber: 6.6 Consensus size: 41
23019 TCCAAATGTT
* * *
23029 GGCATCGGTTGGCC-T-TCTAAAAAT-A--TTTTCAGAGTC
1 GGCATCAGTTGGCCTTCTCTAAAAATAAGTTTTTAAAAGTC
* *
23065 GGTATCTGTTGGCCTTCTCTAAAAATCAAGTTTTATAAAAGTC
1 GGCATCAGTTGGCCTTCTCTAAAAAT-AAGTTTT-TAAAAGTC
* * * *
23108 GGCATCAGTTGGCCTTCTTTAAAATTGAA-TTTTCAAAAGTT
1 GGCATCAGTTGGCCTTCTCTAAAAAT-AAGTTTTTAAAAGTC
* * ** * *
23149 GGCATCGGTTGGCCTTCT-TGAAGAAA-AAGTATCCAAATGTT
1 GGCATCAGTTGGCCTTCTCT-AA-AAATAAGTTTTTAAAAGTC
* * *
23190 GGCATCGGTTGGCC-T-TCTAAAAAT--G-TTTTCAGAGTC
1 GGCATCAGTTGGCCTTCTCTAAAAATAAGTTTTTAAAAGTC
* * *
23226 GGTATCTGTTGGCCTTCTCTAAAAATCAAGTTTTATAATAGTC
1 GGCATCAGTTGGCCTTCTCTAAAAAT-AAGTTTT-TAAAAGTC
*
23269 GGCATCAGTTGGCCTTCTTTAAAA
1 GGCATCAGTTGGCCTTCTCTAAAA
23293 TCGAATTTCC
Statistics
Matches: 179, Mismatches: 30, Indels: 31
0.75 0.12 0.13
Matches are distributed among these distances:
36 28 0.16
37 3 0.02
38 21 0.12
39 3 0.02
40 6 0.03
41 49 0.27
42 12 0.07
43 57 0.32
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.35
Consensus pattern (41 bp):
GGCATCAGTTGGCCTTCTCTAAAAATAAGTTTTTAAAAGTC
Found at i:23250 original size:161 final size:160
Alignment explanation
Indices: 22985--23324 Score: 617
Period size: 161 Copynumber: 2.1 Consensus size: 160
22975 TCTTTCAAGC
*
22985 GTTGGCATCCGTTGGCCTTCTTGAAGAAAAAGTATCCAAATGTTGGCATCGGTTGGCCTTCTAAA
1 GTTGGCATCGGTTGGCCTTCTTGAAGAAAAAGTATCCAAATGTTGGCATCGGTTGGCCTTCTAAA
23050 AATATTTTCAGAGTCGGTATCTGTTGGCCTTCTCTAAAAATCAAGTTTTATAAAAGTCGGCATCA
66 AATATTTTCAGAGTCGGTATCTGTTGGCCTTCTCTAAAAATCAAGTTTTATAAAAGTCGGCATCA
*
23115 GTTGGCCTTCTTTAAAATTGAATTTTCAAAA
131 GTTGGCCTTCTTTAAAATCGAA-TTTCAAAA
23146 GTTGGCATCGGTTGGCCTTCTTGAAGAAAAAGTATCCAAATGTTGGCATCGGTTGGCCTTCTAAA
1 GTTGGCATCGGTTGGCCTTCTTGAAGAAAAAGTATCCAAATGTTGGCATCGGTTGGCCTTCTAAA
* *
23211 AATGTTTTCAGAGTCGGTATCTGTTGGCCTTCTCTAAAAATCAAGTTTTATAATAGTCGGCATCA
66 AATATTTTCAGAGTCGGTATCTGTTGGCCTTCTCTAAAAATCAAGTTTTATAAAAGTCGGCATCA
*
23276 GTTGGCCTTCTTTAAAATCGAATTTCCAAA
131 GTTGGCCTTCTTTAAAATCGAATTTCAAAA
*
23306 GTTGGTATCGGTTGGCCTT
1 GTTGGCATCGGTTGGCCTT
23325 GTAACGAGTT
Statistics
Matches: 173, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
160 25 0.14
161 148 0.86
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (160 bp):
GTTGGCATCGGTTGGCCTTCTTGAAGAAAAAGTATCCAAATGTTGGCATCGGTTGGCCTTCTAAA
AATATTTTCAGAGTCGGTATCTGTTGGCCTTCTCTAAAAATCAAGTTTTATAAAAGTCGGCATCA
GTTGGCCTTCTTTAAAATCGAATTTCAAAA
Found at i:23358 original size:118 final size:118
Alignment explanation
Indices: 23102--23361 Score: 278
Period size: 118 Copynumber: 2.2 Consensus size: 118
23092 AAGTTTTATA
* * * * *
23102 AAAGTCGGCATCAGTTGGCCTTCTTTAAAATTGAATTTTCAAAAGTTGGCATCGGTTGGCCTTCT
1 AAAGTCGGCATCAGTTGGCCTTCTCTAAAAATCAATTTTCAAAAGTCGGCATCAGTTGGCCTTCT
*
23167 TGAAGAAAAAGTATCCAAATGTTGGCATCGGTTGGCCTTCTAAAAATGTTTTC
66 TGAAGAAAAAGTATCCAAATGTTGGCATCGGTTGGCCTTCTAAAAATGTTTCC
* * *
23220 AGAGTCGGTATCTGTTGGCCTTCTCTAAAAATCAAGTTTT-ATAATAGTCGGCATCAGTTGGCCT
1 AAAGTCGGCATCAGTTGGCCTTCTCTAAAAATCAA-TTTTCA-AA-AGTCGGCATCAGTTGGCCT
* * * * * **
23284 TCTTTAA-AATCGAA-TTTCCAAA-GTTGGTATCGGTTGGCCTTGTAACGA-GTTTCC
63 TCTTGAAGAA--AAAGTATCCAAATGTTGGCATCGGTTGGCCTTCTAAAAATGTTTCC
* *
23338 AAAGTTGGCATCGGTTGGCCTTCT
1 AAAGTCGGCATCAGTTGGCCTTCT
23362 TCTTTTTTAA
Statistics
Matches: 117, Mismatches: 20, Indels: 10
0.80 0.14 0.07
Matches are distributed among these distances:
118 55 0.47
119 30 0.26
120 30 0.26
121 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (118 bp):
AAAGTCGGCATCAGTTGGCCTTCTCTAAAAATCAATTTTCAAAAGTCGGCATCAGTTGGCCTTCT
TGAAGAAAAAGTATCCAAATGTTGGCATCGGTTGGCCTTCTAAAAATGTTTCC
Found at i:23393 original size:19 final size:19
Alignment explanation
Indices: 23369--23405 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
23359 TCTTCTTTTT
23369 TAAAAAAA-AATAATAATAA
1 TAAAAAAATAATAA-AATAA
23388 TAAAAAAATAATAAAATA
1 TAAAAAAATAATAAAATA
23406 TGGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (19 bp):
TAAAAAAATAATAAAATAA
Found at i:23394 original size:17 final size:16
Alignment explanation
Indices: 23372--23405 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
23362 TCTTTTTTAA
23372 AAAAAAATAATAATAAT
1 AAAAAAATAATAA-AAT
23389 AAAAAAATAATAAAAT
1 AAAAAAATAATAAAAT
23405 A
1 A
23406 TGGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (16 bp):
AAAAAAATAATAAAAT
Done.