Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014172.1 Corchorus olitorius cultivar O-4 contig14205, 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: 42362
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:1206 original size:21 final size:21
Alignment explanation
Indices: 1182--1294 Score: 158
Period size: 21 Copynumber: 5.4 Consensus size: 21
1172 CTTAGGCATT
*
1182 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
1203 TCCAATGATCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
* *
1224 TCCAATGAACTTGGAACCTGC
1 TCCAATGAGCTTGGAACCTTC
1245 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
1266 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
1287 TCCAATGA
1 TCCAATGA
1295 ACTTCTAGCA
Statistics
Matches: 85, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
20 2 0.02
21 83 0.98
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.28
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Found at i:2122 original size:29 final size:28
Alignment explanation
Indices: 2052--2183 Score: 178
Period size: 29 Copynumber: 4.6 Consensus size: 28
2042 AAGTGAACTT
*
2052 AAAATGACCAAAATGCCCCTGACTGTGC
1 AAAATGACCAAAATGCCCCTGAATGTGC
2080 -AAATGACCAAAATGCCCCTGAATGTGC
1 AAAATGACCAAAATGCCCCTGAATGTGC
2107 AGAAATGACCAAAATGCCCCTGAATGTGC
1 A-AAATGACCAAAATGCCCCTGAATGTGC
* * *
2136 AAAAATGACCATAATGCCCCTGGATTTTTG-
1 -AAAATGACCAAAATGCCCCT-GA-ATGTGC
2166 AAAATGACCAAAATGCCC
1 AAAATGACCAAAATGCCC
2184 ATAGGTGATC
Statistics
Matches: 94, Mismatches: 5, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
27 26 0.28
29 62 0.66
30 3 0.03
31 3 0.03
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (28 bp):
AAAATGACCAAAATGCCCCTGAATGTGC
Found at i:11185 original size:54 final size:54
Alignment explanation
Indices: 11126--11313 Score: 193
Period size: 54 Copynumber: 3.5 Consensus size: 54
11116 TGATCTTTTA
* *
11126 AAGTTTTCAGAGATCTAAGTTGATGTTCAAACGACCCTGTGCGGTCTTTCATAG
1 AAGTTTTCAGAGATCTAAGTTGATCTTCAAACGACCCTGTGCGGTTTTTCATAG
* * ** *
11180 AAGTTTTCAGAGGTTTAAGTTGATCTT-AAGTTGA-CCAGTGCGGTTTTTCATAG
1 AAGTTTTCAGAGATCTAAGTTGATCTTCAA-ACGACCCTGTGCGGTTTTTCATAG
* * *** * * *
11233 AAGCTTTT-AGAAATCTAGGTTGATCTTCTGGCGACCGTTTGCGGTTTTTCACAG
1 AAG-TTTTCAGAGATCTAAGTTGATCTTCAAACGACCCTGTGCGGTTTTTCATAG
*
11287 AAGTTTTCAGAGATTTAAGTTGATCTT
1 AAGTTTTCAGAGATCTAAGTTGATCTT
11314 TATATGACCC
Statistics
Matches: 107, Mismatches: 22, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
53 43 0.40
54 64 0.60
ACGTcount: A:0.24, C:0.15, G:0.23, T:0.38
Consensus pattern (54 bp):
AAGTTTTCAGAGATCTAAGTTGATCTTCAAACGACCCTGTGCGGTTTTTCATAG
Found at i:11401 original size:54 final size:54
Alignment explanation
Indices: 11341--11815 Score: 467
Period size: 54 Copynumber: 8.8 Consensus size: 54
11331 TCTTTTATAA
* * *
11341 AAGTTTTCGATGATCAGAGTTGATCCCCAGATGATCCAGTGCGGCCATTCCAAG
1 AAGTTTTCGATGATCAGAGTTGATCTCCAGATGATCCAGTGTGGTCATTCCAAG
* * * *
11395 ATGTTTTCAATGATACA-AGTTGATCTCCAGATGACCCAGTGTGGTCTTTCCAAG
1 AAGTTTTCGATGAT-CAGAGTTGATCTCCAGATGATCCAGTGTGGTCATTCCAAG
* * * *
11449 AAGTTTTTGACGATCAGAGTTGATCTCCATATGA-CCTAGTGTGGTCTTTCCAAG
1 AAGTTTTCGATGATCAGAGTTGATCTCCAGATGATCC-AGTGTGGTCATTCCAAG
* * * * *
11503 AAGTTTTCGACGATTAGAGTTGATCTCCTGATGATCCTGTGTGGTCTTTCCAAG
1 AAGTTTTCGATGATCAGAGTTGATCTCCAGATGATCCAGTGTGGTCATTCCAAG
* * * * *
11557 AAATTTTCGATGATTAGAGTTGATCCCCAAATGATCCAGTGTGGTGATTCCAAG
1 AAGTTTTCGATGATCAGAGTTGATCTCCAGATGATCCAGTGTGGTCATTCCAAG
* *
11611 ATA-TTTTCAATGATCAGAGTTGATCTCCAGATGACCCAGTGTGGTCATTCCAAG
1 A-AGTTTTCGATGATCAGAGTTGATCTCCAGATGATCCAGTGTGGTCATTCCAAG
* * * * ** * * * *
11665 AAGTTTTCAATGATCAAAGTTTATATTTAAATGATCCAGTGTGATCTTTCC-AT
1 AAGTTTTCGATGATCAGAGTTGATCTCCAGATGATCCAGTGTGGTCATTCCAAG
* * **** * *
11718 AAGTTTTTGATGATCAGAGTTGATCTCCA-ATTGATCTA-AACAGTCGTTTCAAG
1 AAGTTTTCGATGATCAGAGTTGATCTCCAGA-TGATCCAGTGTGGTCATTCCAAG
* * *
11771 AAGTTTTTGATGGTCAGAGTTGATCTCCAAATTGATCCAGTGTGG
1 AAGTTTTCGATGATCAGAGTTGATCTCCAGA-TGATCCAGTGTGG
11816 ACGCTGCAAG
Statistics
Matches: 348, Mismatches: 63, Indels: 19
0.81 0.15 0.04
Matches are distributed among these distances:
52 6 0.02
53 63 0.18
54 273 0.78
55 6 0.02
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (54 bp):
AAGTTTTCGATGATCAGAGTTGATCTCCAGATGATCCAGTGTGGTCATTCCAAG
Found at i:11472 original size:162 final size:162
Alignment explanation
Indices: 11304--11672 Score: 420
Period size: 162 Copynumber: 2.3 Consensus size: 162
11294 CAGAGATTTA
** * * * *
11304 AGTTGATCTTTATATGACCCGGTGTTGTCTTT-TATAAAAGTTTTCGATGATCAGAGTTGATCCC
1 AGTTGATCTCCATATGACCCAGTGTGGTCTTTCCA-AAAAGTTTTCGACGATCAGAGTTGATCCC
** * *
11368 CAGATGATCCAGTGCGGCCATTCCAAGATGTTTTCAATGA-TACAAGTTGATCTCCAGATGACCC
65 CAGATGATCCAGTGCGGCCATTCCAAGAAATTTTCAATGATTA-AAGTTGATCCCCAAATGACCC
* **
11432 AGTGTGGTCTTTCCAAGA-AGTTTTTGACGATCAG
129 AGTGTGGTCATTCCAAGATA-TTTTCAACGATCAG
* * * *
11466 AGTTGATCTCCATATGACCTAGTGTGGTCTTTCCAAGAAGTTTTCGACGATTAGAGTTGATCTCC
1 AGTTGATCTCCATATGACCCAGTGTGGTCTTTCCAAAAAGTTTTCGACGATCAGAGTTGATCCCC
* * * * * * * *
11531 TGATGATCCTGTGTGGTCTTTCCAAGAAATTTTCGATGATTAGAGTTGATCCCCAAATGATCCAG
66 AGATGATCCAGTGCGGCCATTCCAAGAAATTTTCAATGATTAAAGTTGATCCCCAAATGACCCAG
* *
11596 TGTGGTGATTCCAAGATATTTTCAATGATCAG
131 TGTGGTCATTCCAAGATATTTTCAACGATCAG
* * *
11628 AGTTGATCTCCAGATGACCCAGTGTGGTCATTCCAAGAAGTTTTC
1 AGTTGATCTCCATATGACCCAGTGTGGTCTTTCCAAAAAGTTTTC
11673 AATGATCAAA
Statistics
Matches: 174, Mismatches: 30, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
162 170 0.98
163 4 0.02
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (162 bp):
AGTTGATCTCCATATGACCCAGTGTGGTCTTTCCAAAAAGTTTTCGACGATCAGAGTTGATCCCC
AGATGATCCAGTGCGGCCATTCCAAGAAATTTTCAATGATTAAAGTTGATCCCCAAATGACCCAG
TGTGGTCATTCCAAGATATTTTCAACGATCAG
Found at i:16377 original size:21 final size:21
Alignment explanation
Indices: 16328--16368 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
16318 TTAAGGATAT
16328 GCAACAGCTAAAATCAAGGAG
1 GCAACAGCTAAAATCAAGGAG
*
16349 GCAGCAGCTAAAATCAAGGA
1 GCAACAGCTAAAATCAAGGA
16369 TTTAACAGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.46, C:0.20, G:0.24, T:0.10
Consensus pattern (21 bp):
GCAACAGCTAAAATCAAGGAG
Found at i:18185 original size:19 final size:19
Alignment explanation
Indices: 18161--18197 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
18151 AATTATTGGG
18161 ATTCGGAATAATGAAGGTA
1 ATTCGGAATAATGAAGGTA
*
18180 ATTCGGAATAATGGAGGT
1 ATTCGGAATAATGAAGGT
18198 GATCTCTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.05, G:0.30, T:0.27
Consensus pattern (19 bp):
ATTCGGAATAATGAAGGTA
Found at i:26667 original size:190 final size:191
Alignment explanation
Indices: 26329--26673 Score: 647
Period size: 190 Copynumber: 1.8 Consensus size: 191
26319 CACAAGGGTG
26329 GATTTCAATCTTAAAACAACTAGATTCGTATCAATTGGTAATCAGAGCATAGGTTGTCATCTTCA
1 GATTTCAATCTTAAAACAACTAGATTCGTATCAATTGGTAATCAGAGCATAGGTTGTCATCTTCA
26394 ATCGGTAAATCTATCCTTCTAATCATCTATCATCAAGTTTTTCATCCATCTCATTCATCAAAGTT
66 ATCGGTAAATCTATCCTTCTAATCATCTATCATCAAGTTTTTCATCCATCTCATTCATCAAAGTT
26459 CATATCGCAACTTTCAATTTTCAAGGAAGTTCAAGTCAACTTTGATAGATATTCAAGGCTA
131 CATATCGCAACTTTCAATTTTCAAGGAAGTTCAAGTCAACTTTGATAGATATTCAAGGCTA
* *
26520 GATTTGAATC-TAATACAACTAGATTCGTATCAATTGGTAATCAGAGCATAGGTTGTCATCTTCA
1 GATTTCAATCTTAAAACAACTAGATTCGTATCAATTGGTAATCAGAGCATAGGTTGTCATCTTCA
*
26584 ATCGGTAAATCTATCCTTCTATTCATCTATCATCAAGTTTTTCATCCATCTCATTCATCAAAGTT
66 ATCGGTAAATCTATCCTTCTAATCATCTATCATCAAGTTTTTCATCCATCTCATTCATCAAAGTT
*
26649 CTTATCGCAACTTTCAATTTTCAAG
131 CATATCGCAACTTTCAATTTTCAAG
26674 ATCTAAAAAT
Statistics
Matches: 150, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
190 141 0.94
191 9 0.06
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (191 bp):
GATTTCAATCTTAAAACAACTAGATTCGTATCAATTGGTAATCAGAGCATAGGTTGTCATCTTCA
ATCGGTAAATCTATCCTTCTAATCATCTATCATCAAGTTTTTCATCCATCTCATTCATCAAAGTT
CATATCGCAACTTTCAATTTTCAAGGAAGTTCAAGTCAACTTTGATAGATATTCAAGGCTA
Found at i:27146 original size:21 final size:21
Alignment explanation
Indices: 27120--27160 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
27110 TTGAAGCCCT
27120 ATTGGATAGAAGTGGTACTAA
1 ATTGGATAGAAGTGGTACTAA
**
27141 ATTGGATCTAAGTGGTACTA
1 ATTGGATAGAAGTGGTACTA
27161 GGGTTTCTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.07, G:0.27, T:0.32
Consensus pattern (21 bp):
ATTGGATAGAAGTGGTACTAA
Found at i:32616 original size:22 final size:22
Alignment explanation
Indices: 32589--32631 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
32579 ATGCAAGTGC
* *
32589 AAATGTGAGATAGATATGCAAA
1 AAATGTAAGATAAATATGCAAA
*
32611 AAATGTAATATAAATATGCAA
1 AAATGTAAGATAAATATGCAA
32632 GAGAACATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.53, C:0.05, G:0.16, T:0.26
Consensus pattern (22 bp):
AAATGTAAGATAAATATGCAAA
Found at i:32765 original size:26 final size:27
Alignment explanation
Indices: 32729--32804 Score: 109
Period size: 28 Copynumber: 2.8 Consensus size: 27
32719 AAGCTAGTAA
* *
32729 TGAAGTACAAAAGACCAAAGTG-CCCC
1 TGAAGTACAAATGACCAAAATGCCCCC
32755 TGAAGTACAAATGACCAAAATGCCCCCC
1 TGAAGTACAAATGACCAAAATG-CCCCC
32783 TGAAGTACAAATGACCAGAAAT
1 TGAAGTACAAATGACCA-AAAT
32805 TCACCTGGAT
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
26 20 0.44
28 21 0.47
29 4 0.09
ACGTcount: A:0.43, C:0.25, G:0.17, T:0.14
Consensus pattern (27 bp):
TGAAGTACAAATGACCAAAATGCCCCC
Found at i:33535 original size:150 final size:149
Alignment explanation
Indices: 33308--34337 Score: 1186
Period size: 150 Copynumber: 6.8 Consensus size: 149
33298 CAATAATCTG
* * * * * *
33308 ATAAAGCAATGATCCTAGACCATGATTAAAGAATAAAGC-AATGATCCTAAACCAGGATTAAAA-
1 ATAAAGTAATGATCCTAAACCAGGATT-AA-CATAGAGCTAAT-ATCCTCAACCAGGATTAAAAT
* * * *
33371 ACCAGCAACGATCCTCAACCAGGATTAAAGTGAAGCAATGATCCTAAACCAGGATTAAAATAAAG
63 A-AAGCAATGATCCTCAAACAGGATTAAAATGAAGCAATGATCCTAAA-CAGGATTAAAATAAAG
* *
33436 CAATGATCCTGAACCAGGATTAAA
126 CAATGATCCTCAAACAGGATTAAA
* * * * * *
33460 ATAAAGCAAAGATCCTCAAA-TAGGATTAAAAT-GAAG-TAATGATCCTAAACCAGGATTAACAT
1 ATAAAGTAATGATCCT-AAACCAGGATTAACATAG-AGCTAAT-ATCCTCAACCAGGATTAAAAT
* ** ** * * *
33522 AGAGCAAAT-ATCCTCATCCAGGAAAAAAATAAATCAATGATCCTCAAACAGGATTAAAATGAAG
63 AAAGC-AATGATCCTCAAACAGGATTAAAATGAAGCAATGATCCT-AAACAGGATTAAAATAAAG
*
33586 CAATAATCCTCAAACAGGATTAAA
126 CAATGATCCTCAAACAGGATTAAA
* ** * * *
33610 ATGAAGTAATGATCCTAAACCAGGATTAACATCCAGC-AACGATCCTCAACCAGGATTAAAGTGA
1 ATAAAGTAATGATCCTAAACCAGGATTAACATAGAGCTAA-TATCCTCAACCAGGATTAAAATAA
* *
33674 AGCAATGATCCTCAAACAGGATTAAAATGAAGCAATGATCTTCAAACAAGATTAAAATAAAGCAA
65 AGCAATGATCCTCAAACAGGATTAAAATGAAGCAATGATCCT-AAACAGGATTAAAATAAAGCAA
*
33739 TGATCCTAAAACAGGATTAAA
129 TGATCCTCAAACAGGATTAAA
* * * *
33760 ATAACGTAATTATCCTAAACCAGGATTAACATAGAGCTAATATCTTCAACCAGGATAAAAATAAA
1 ATAAAGTAATGATCCTAAACCAGGATTAACATAGAGCTAATATCCTCAACCAGGATTAAAATAAA
* *
33825 GCAATGATCCTCAAACGGGATTAAAATGAAGCAATGATCCTTAAACAGGATTAAAATAAAGCAAC
66 GCAATGATCCTCAAACAGGATTAAAATGAAGCAATGATCC-TAAACAGGATTAAAATAAAGCAAT
*
33890 GATCCTCAAACAAGATTAAA
130 GATCCTCAAACAGGATTAAA
* *
33910 ATAAAGTAATGATCCTAAACCAGGATTAACATAGAGCAAATATCCTCAACCAGGATAAAAATAAA
1 ATAAAGTAATGATCCTAAACCAGGATTAACATAGAGCTAATATCCTCAACCAGGATTAAAATAAA
* * * *
33975 GCAATGATCCTCAAACAGGATCAAAATGAAGAAATGATCCTAAAACGGGATTAAAATGAAGCAAT
66 GCAATGATCCTCAAACAGGATTAAAATGAAGCAATGATCCT-AAACAGGATTAAAATAAAGCAAT
*
34040 GATCCTTAAACAGGATTAAA
130 GATCCTCAAACAGGATTAAA
* * *
34060 ATGAAGTAATGATCCTAAACCAGGATTAACATAGAGCAAATATCCTCAACCAGGATAAAAATAAA
1 ATAAAGTAATGATCCTAAACCAGGATTAACATAGAGCTAATATCCTCAACCAGGATTAAAATAAA
* *
34125 GCAATGATCCTCAAACAGAATTAAAATGAAGCAATGATCCTCAAATAGGATTAAAAATGAAA-CA
66 GCAATGATCCTCAAACAGGATTAAAATGAAGCAATGATCCT-AAACAGGATT-AAAAT-AAAGCA
34189 ATGATCCTCAAACAGGATTAAA
128 ATGATCCTCAAACAGGATTAAA
* * * *
34211 ATAAA-TCAATGATCCTAAAACAGGATCAA-ACTA-ATG-TAATTATCCTAAACCAGGATTAACA
1 ATAAAGT-AATGATCCTAAACCAGGATTAACA-TAGA-GCTAA-TATCCTCAACCAGGATTAAAA
* * * * *
34272 TAAAGCAAAT-ATCCTCAACCGGGATAAAAATAAAGCAATGATCCTCAACCAGGATTAAAATAAA
62 TAAAGC-AATGATCCTCAAACAGGATTAAAATGAAGCAATGATCCT-AAACAGGATTAAAATAAA
34336 GC
125 GC
34338 TGATAAAGCA
Statistics
Matches: 764, Mismatches: 92, Indels: 46
0.85 0.10 0.05
Matches are distributed among these distances:
149 10 0.01
150 598 0.78
151 129 0.17
152 25 0.03
153 2 0.00
ACGTcount: A:0.48, C:0.17, G:0.14, T:0.21
Consensus pattern (149 bp):
ATAAAGTAATGATCCTAAACCAGGATTAACATAGAGCTAATATCCTCAACCAGGATTAAAATAAA
GCAATGATCCTCAAACAGGATTAAAATGAAGCAATGATCCTAAACAGGATTAAAATAAAGCAATG
ATCCTCAAACAGGATTAAA
Found at i:34332 original size:30 final size:30
Alignment explanation
Indices: 33308--34337 Score: 1050
Period size: 30 Copynumber: 34.2 Consensus size: 30
33298 CAATAATCTG
*
33308 ATAAAGCAATGATCCT-AGACCATGATTAAAGA
1 ATAAAGCAATGATCCTCA-ACCAGGATT-AA-A
*
33340 ATAAAGCAATGATCCTAAACCAGGATTAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
* *
33370 A-ACCAGCAACGATCCTCAACCAGGATTAAA
1 ATA-AAGCAATGATCCTCAACCAGGATTAAA
* * *
33400 GTGAAGCAATGATCCTAAACCAGGATTAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
*
33430 ATAAAGCAATGATCCTGAACCAGGATTAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
* **
33460 ATAAAGCAAAGATCCTCAAATAGGATTAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
* * * *
33490 ATGAAGTAATGATCCTAAACCAGGATTAAC
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
* * **
33520 ATAGAGCAAAT-ATCCTCATCCAGGAAAAAA
1 ATAAAGC-AATGATCCTCAACCAGGATTAAA
* *
33550 ATAAATCAATGATCCTCAAACAGGATTAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
* * *
33580 ATGAAGCAATAATCCTCAAACAGGATTAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
* * * *
33610 ATGAAGTAATGATCCTAAACCAGGATTAAC
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
** *
33640 ATCCAGCAACGATCCTCAACCAGGATTAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
* * *
33670 GTGAAGCAATGATCCTCAAACAGGATTAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
* * * *
33700 ATGAAGCAATGATCTTCAAACAAGATTAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
* *
33730 ATAAAGCAATGATCCTAAAACAGGATTAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
* * * * *
33760 ATAACGTAATTATCCTAAACCAGGATTAAC
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
* * *
33790 ATAGAGCTAAT-ATCTTCAACCAGGATAAAA
1 ATAAAGC-AATGATCCTCAACCAGGATTAAA
* *
33820 ATAAAGCAATGATCCTCAAACGGGATTAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
* * *
33850 ATGAAGCAATGATCCTTAAACAGGATTAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
* * *
33880 ATAAAGCAACGATCCTCAAACAAGATTAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
* * *
33910 ATAAAGTAATGATCCTAAACCAGGATTAAC
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
* *
33940 ATAGAGCAAAT-ATCCTCAACCAGGATAAAA
1 ATAAAGC-AATGATCCTCAACCAGGATTAAA
* *
33970 ATAAAGCAATGATCCTCAAACAGGATCAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
* * * * *
34000 ATGAAGAAATGATCCTAAAACGGGATTAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
* * *
34030 ATGAAGCAATGATCCTTAAACAGGATTAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
* * * *
34060 ATGAAGTAATGATCCTAAACCAGGATTAAC
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
* *
34090 ATAGAGCAAAT-ATCCTCAACCAGGATAAAA
1 ATAAAGC-AATGATCCTCAACCAGGATTAAA
* *
34120 ATAAAGCAATGATCCTCAAACAGAATTAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
* **
34150 ATGAAGCAATGATCCTCAAATAGGATTAAAA
1 ATAAAGCAATGATCCTCAACCAGGATT-AAA
*
34181 ATGAAA-CAATGATCCTCAAACAGGATTAAA
1 AT-AAAGCAATGATCCTCAACCAGGATTAAA
* * * *
34211 ATAAATCAATGATCCTAAAACAGGATCAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
* * * * * *
34241 CTAATGTAATTATCCTAAACCAGGATTAAC
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
* *
34271 ATAAAGCAAAT-ATCCTCAACCGGGATAAAA
1 ATAAAGC-AATGATCCTCAACCAGGATTAAA
34301 ATAAAGCAATGATCCTCAACCAGGATTAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
34331 ATAAAGC
1 ATAAAGC
34338 TGATAAAGCA
Statistics
Matches: 835, Mismatches: 147, Indels: 34
0.82 0.14 0.03
Matches are distributed among these distances:
29 19 0.02
30 747 0.89
31 42 0.05
32 26 0.03
33 1 0.00
ACGTcount: A:0.48, C:0.17, G:0.14, T:0.21
Consensus pattern (30 bp):
ATAAAGCAATGATCCTCAACCAGGATTAAA
Found at i:34705 original size:61 final size:62
Alignment explanation
Indices: 34622--34738 Score: 157
Period size: 61 Copynumber: 1.9 Consensus size: 62
34612 AACTGCAGAG
* * * * *
34622 AAGATCGCCCTGGATCTACTGAAGTAAATTTA-GGAAAGATCGCCCT-GAATCAATTAAAGAA
1 AAGATCGCCCTCGATCAACTGAAATAAATTAATGCAAAGATCGCCCTAG-ATCAATTAAAGAA
*
34683 AAGATCGCCTTCGATCAACTGAAATAAATTAATGCAAAGATCGCCCTAGATCAATT
1 AAGATCGCCCTCGATCAACTGAAATAAATTAATGCAAAGATCGCCCTAGATCAATT
34739 GAAATAAATT
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
61 27 0.56
62 20 0.42
63 1 0.02
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (62 bp):
AAGATCGCCCTCGATCAACTGAAATAAATTAATGCAAAGATCGCCCTAGATCAATTAAAGAA
Found at i:34882 original size:35 final size:36
Alignment explanation
Indices: 34678--34928 Score: 308
Period size: 36 Copynumber: 7.0 Consensus size: 36
34668 GAATCAATTA
* * * *
34678 AAGAAAAGATCGCCTTCGATCAACTGAAATAAA-TT
1 AAGAAAAGATCGCCCTGGATCAATTGAAATAAACTG
* * *
34713 AATGCAAAGATCGCCCTAGATCAATTGAAATAAATTG
1 AA-GAAAAGATCGCCCTGGATCAATTGAAATAAACTG
* *
34750 AAGAAAAGATTGCCCTGGATCAATTGAATTAAACTG
1 AAGAAAAGATCGCCCTGGATCAATTGAAATAAACTG
34786 AAGAAAAGATCGCCCTGGATCAATTGAAATAAACTG
1 AAGAAAAGATCGCCCTGGATCAATTGAAATAAACTG
*
34822 CAGAAAAGATCGCCCTGGATCAATTGAAATAAACTG
1 AAGAAAAGATCGCCCTGGATCAATTGAAATAAACTG
* * * * *
34858 AAG-AAACACCACTCTGGATCAATTGAAATAAGCTG
1 AAGAAAAGATCGCCCTGGATCAATTGAAATAAACTG
** *
34893 AAGAACTGGATCGCCCTGGATCAACTGAAATAAACT
1 AAGAA-AAGATCGCCCTGGATCAATTGAAATAAACT
34929 AAATAAAAAC
Statistics
Matches: 185, Mismatches: 27, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
35 32 0.17
36 128 0.69
37 25 0.14
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.22
Consensus pattern (36 bp):
AAGAAAAGATCGCCCTGGATCAATTGAAATAAACTG
Found at i:34958 original size:72 final size:72
Alignment explanation
Indices: 34761--34967 Score: 186
Period size: 72 Copynumber: 2.9 Consensus size: 72
34751 AGAAAAGATT
* * * * * * ** * *
34761 GCCCTGGATCAATTGAATTAAACTGAAGAAAAGATCGCCCTGGATCAATTGAAATAAACTGCAGA
1 GCCCTGGATCAACTGAAATAAACTAAAGAAAA-ACCACTCTGGATCAACCGAAATGAACTGAAGA
**
34826 A-AAGATC
65 ACTGGATC
* * * **
34833 GCCCTGGATCAATTGAAATAAACTGAAGAAACACCACTCTGGATCAATTGAAAT-AAGCTGAAGA
1 GCCCTGGATCAACTGAAATAAACTAAAGAAAAACCACTCTGGATCAACCGAAATGAA-CTGAAGA
34897 ACTGGATC
65 ACTGGATC
* * *
34905 GCCCTGGATCAACTGAAATAAACTAAATAAAAACCGCTAC-GGGTCAACCGAAATGAACTGAAG
1 GCCCTGGATCAACTGAAATAAACTAAAGAAAAACCACT-CTGGATCAACCGAAATGAACTGAAG
34968 CATCTGGAAT
Statistics
Matches: 115, Mismatches: 16, Indels: 8
0.83 0.12 0.06
Matches are distributed among these distances:
70 2 0.02
71 26 0.23
72 84 0.73
73 3 0.03
ACGTcount: A:0.42, C:0.20, G:0.19, T:0.19
Consensus pattern (72 bp):
GCCCTGGATCAACTGAAATAAACTAAAGAAAAACCACTCTGGATCAACCGAAATGAACTGAAGAA
CTGGATC
Found at i:34967 original size:107 final size:107
Alignment explanation
Indices: 34678--34967 Score: 269
Period size: 108 Copynumber: 2.7 Consensus size: 107
34668 GAATCAATTA
* * * * * * * * **
34678 AAGAAAAGATCGCCTTCGATCAACTGAAATAAATTAATGCAAAGATCGCCCTAGATCAATTGAAA
1 AAGAAAAGATCGCCCTGGATCAACTGAAATAAACTAAAGAAAAGACCGCACTGGATCAACCGAAA
* * *** * *
34743 TAAATTGAAGAAAAGATTGCCCTGGATCAATTGAATTAAACTG
66 TAAACTGAAG-AAACACCACTCTGGATCAATTGAAATAAACTG
* ** * * **
34786 AAGAAAAGATCGCCCTGGATCAATTGAAATAAACTGCAGAAAAGATCGCCCTGGATCAATTGAAA
1 AAGAAAAGATCGCCCTGGATCAACTGAAATAAACTAAAGAAAAGACCGCACTGGATCAACCGAAA
*
34851 TAAACTGAAGAAACACCACTCTGGATCAATTGAAATAAGCTG
66 TAAACTGAAGAAACACCACTCTGGATCAATTGAAATAAACTG
** * *
34893 AAGAACTGGATCGCCCTGGATCAACTGAAATAAACTAAATAAAA-ACCGCTAC-GGGTCAACCGA
1 AAGAA-AAGATCGCCCTGGATCAACTGAAATAAACTAAAGAAAAGACCGC-ACTGGATCAACCGA
*
34956 AATGAACTGAAG
64 AATAAACTGAAG
34968 CATCTGGAAT
Statistics
Matches: 151, Mismatches: 29, Indels: 5
0.82 0.16 0.03
Matches are distributed among these distances:
107 53 0.35
108 98 0.65
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.20
Consensus pattern (107 bp):
AAGAAAAGATCGCCCTGGATCAACTGAAATAAACTAAAGAAAAGACCGCACTGGATCAACCGAAA
TAAACTGAAGAAACACCACTCTGGATCAATTGAAATAAACTG
Found at i:36179 original size:21 final size:21
Alignment explanation
Indices: 36155--36194 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
36145 TATTTCAGTC
*
36155 ATTTCCTCCCTTTTTTCTTCA
1 ATTTCCTACCTTTTTTCTTCA
*
36176 ATTTCCTACTTTTTTTCTT
1 ATTTCCTACCTTTTTTCTT
36195 TTTTCTTTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.28, G:0.00, T:0.62
Consensus pattern (21 bp):
ATTTCCTACCTTTTTTCTTCA
Found at i:39527 original size:16 final size:16
Alignment explanation
Indices: 39502--39532 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39492 CAGATACTTA
39502 TGATGATTTGCATGAC
1 TGATGATTTGCATGAC
*
39518 TGATGCTTTGCATGA
1 TGATGATTTGCATGA
39533 ATGCATTCGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.13, G:0.26, T:0.39
Consensus pattern (16 bp):
TGATGATTTGCATGAC
Done.