Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020648.1 Corchorus olitorius cultivar O-4 contig20681, 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: 7230
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.34
Found at i:458 original size:81 final size:81
Alignment explanation
Indices: 313--506 Score: 221
Period size: 81 Copynumber: 2.4 Consensus size: 81
303 CGTTGAATCC
* * * * * * *
313 AATGTTGCATTTACTGCATATTACCTAATTTACCCTTGCAAGTTGGAGGGGTGTCGGTGAGTAAG
1 AATGTTGCATTTACTGCAAATTACCTAATTTAACCTTGCAAGTGGGAAGAGAGACGGTGAGTAAG
378 TCCC-TTCATTAAA-CT
66 TCCCATT-ATTAAACCT
* * * * *
393 AAATTTTGCATTAACTGCAAATTACCTAATTTAACTTTGCAAGTGGGAAGAGAGAGGGTGGGTAA
1 -AATGTTGCATTTACTGCAAATTACCTAATTTAACCTTGCAAGTGGGAAGAGAGACGGTGAGTAA
*
458 GTCCCATTGTTAAACCT
65 GTCCCATTATTAAACCT
* *
475 AATGTAGCATTTACTGCACATTACCTAATTTA
1 AATGTTGCATTTACTGCAAATTACCTAATTTA
507 CTCTTACAAT
Statistics
Matches: 94, Mismatches: 17, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
81 90 0.96
82 4 0.04
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.34
Consensus pattern (81 bp):
AATGTTGCATTTACTGCAAATTACCTAATTTAACCTTGCAAGTGGGAAGAGAGACGGTGAGTAAG
TCCCATTATTAAACCT
Found at i:628 original size:134 final size:135
Alignment explanation
Indices: 400--645 Score: 354
Period size: 134 Copynumber: 1.8 Consensus size: 135
390 ACTAAATTTT
* * *
400 GCATTAACTGCAAATTACCTAATTTAACTTTGCAAGTGGGAAGAGAGAGGGTGGGTAAGTCCCAT
1 GCATTAACTGCAAATTACCTAATTTAACCTTGCAAGTGGGAAGAGAGAGGGTGAGTAAGTCACAT
* * *
465 TGTTAAACCTAATGTAGCATTTACTGCACATTACCTAATTTACTCTTACAATTGTGTTAAACCCA
66 TGTTAAACCCAATATAGCATTTACAGCACATTACCTAATTTACTCTTACAATTGTGTTAAACCCA
530 ATGTA
131 ATGTA
* * * *
535 GCATTTACTGCACATTA-CTAATTTAACCTTGCAAGTGGG-AGTAGATAGGGTGATTAAGTCAC-
1 GCATTAACTGCAAATTACCTAATTTAACCTTGCAAGTGGGAAG-AGAGAGGGTGAGTAAGTCACA
*
597 TTCGTTAAACCCAATATAGGATTTACAGCACATTACCTAATTTACTCTT
65 TT-GTTAAACCCAATATAGCATTTACAGCACATTACCTAATTTACTCTT
646 TCAAATGGGA
Statistics
Matches: 98, Mismatches: 11, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
133 4 0.04
134 79 0.81
135 15 0.15
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (135 bp):
GCATTAACTGCAAATTACCTAATTTAACCTTGCAAGTGGGAAGAGAGAGGGTGAGTAAGTCACAT
TGTTAAACCCAATATAGCATTTACAGCACATTACCTAATTTACTCTTACAATTGTGTTAAACCCA
ATGTA
Found at i:715 original size:215 final size:215
Alignment explanation
Indices: 156--726 Score: 632
Period size: 216 Copynumber: 2.7 Consensus size: 215
146 AGTGTGGGTA
* * * * **
156 AGTAAGTCCCATCGTTAAACCTAATATAACATTTACTGCACATTACCTGATTTAAGCTTGCAAGT
1 AGTAAGTCCCTTCGTTAAACCAAATATAGCATTTACTGCACATTACCTAATTTACTCTTGCAAGT
* ** * *
221 GGGAGGAG-AGTGTGTGAGTATA-TCCCTTCGTTAAACCTAATGTGGCATTTACTGCACATTACC
66 GGGAAGAGAAAAG-GTGAGTA-AGTCCCTTTGTTAAACCTAATGTAGCATTTACTGCACATTACC
* * * * * *
284 TAATTTACCCTTACACTTTCGTTGAATCCAATGTTGCATTTACTGCATATTACCTAATTTACCCT
129 TAATTTACCCTTACAATTTCGTTAAACCCAATGTAGCATTTACTGCACATTACCTAATTTAACCT
* * *
349 TGCAAGTTGGAGGGGTGTCGGTG
194 TGCAAGTGGGAGAGATG-CGGTG
* * * * * *
372 AGTAAGTCCCTTCATTAAACTAAATTTTGCATTAACTGCAAATTACCTAATTTAACT-TTGCAAG
1 AGTAAGTCCCTTCGTTAAACCAAATATAGCATTTACTGCACATTACCTAATTT-ACTCTTGCAAG
* * * *
436 TGGGAAGAGAGAGGGTGGGTAAGTCCCATTGTTAAACCTAATGTAGCATTTACTGCACATTACCT
65 TGGGAAGAGAAAAGGTGAGTAAGTCCCTTTGTTAAACCTAATGTAGCATTTACTGCACATTACCT
*
501 AATTTACTCTTACAATTGT-GTTAAACCCAATGTAGCATTTACTGCACATTA-CTAATTTAACCT
130 AATTTACCCTTACAATT-TCGTTAAACCCAATGTAGCATTTACTGCACATTACCTAATTTAACCT
564 TGCAAGTGGGAGTAGATAG-GGTG
194 TGCAAGTGGGAG-AGAT-GCGGTG
* * * * * * *
587 ATTAAGTCACTTCGTTAAACCCAATATAGGATTTACAGCACATTACCTAATTTACTCTTTCAAAT
1 AGTAAGTCCCTTCGTTAAACCAAATATAGCATTTACTGCACATTACCTAATTTACTCTTGCAAGT
* * * * * * *
652 GGGATGAGAAAAGGTGAGTAAGTCCCTTTGTTAAACCCAATCTAGAATTTGCTACAAATTACCTA
66 GGGAAGAGAAAAGGTGAGTAAGTCCCTTTGTTAAACCTAATGTAGCATTTACTGCACATTACCTA
717 ATTTACCCTT
131 ATTTACCCTT
727 GCAAGTGGGA
Statistics
Matches: 293, Mismatches: 55, Indels: 15
0.81 0.15 0.04
Matches are distributed among these distances:
214 3 0.01
215 138 0.47
216 148 0.51
217 4 0.01
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (215 bp):
AGTAAGTCCCTTCGTTAAACCAAATATAGCATTTACTGCACATTACCTAATTTACTCTTGCAAGT
GGGAAGAGAAAAGGTGAGTAAGTCCCTTTGTTAAACCTAATGTAGCATTTACTGCACATTACCTA
ATTTACCCTTACAATTTCGTTAAACCCAATGTAGCATTTACTGCACATTACCTAATTTAACCTTG
CAAGTGGGAGAGATGCGGTG
Found at i:839 original size:164 final size:163
Alignment explanation
Indices: 601--900 Score: 386
Period size: 164 Copynumber: 1.8 Consensus size: 163
591 AGTCACTTCG
* * * * *
601 TTAAACCCAATATAGGATTTACAGCACATTACCTAATTTACTCTTTCAAATGGGATGAGAAAAGG
1 TTAAACCCAATATAGCATTTACAGCACATTACCTAATTTACCCTTGCAAATGAGAGGAGAAAAGG
** *
666 TGAGTAAGTCCCTTTGTTAAACCCAATCTAGAATTTGCTACAAATTACCTAATTTACCCTTGCAA
66 TGAGTAAGTCCCTCCGTTAAACCCAATCTAGAATTTACTACAAATTACCTAATTTACCCTTGCAA
731 GTGGGACACATTACCAAATTTACCCTTACACCT
131 GTGGGACACATTACCAAATTTACCCTTACACCT
* * * * *
764 TTAAACCCAATGTATCATTTACTGCACATTTTCCTAATTTACCCTTGCAAGTGAGAGGA-AAAAG
1 TTAAACCCAATATAGCATTTACAGCACA-TTACCTAATTTACCCTTGCAAATGAGAGGAGAAAA-
* * ** * * * *
828 GGTGAGTAAGTCCCTCCGTTAAACCTAATGTAGCTTTTATTGCATATTAGCTAATTTACCCTTGC
64 GGTGAGTAAGTCCCTCCGTTAAACCCAATCTAGAATTTACTACAAATTACCTAATTTACCCTTGC
893 AAGTGGGA
129 AAGTGGGA
901 GAAGAGATAG
Statistics
Matches: 114, Mismatches: 21, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
163 28 0.25
164 86 0.75
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (163 bp):
TTAAACCCAATATAGCATTTACAGCACATTACCTAATTTACCCTTGCAAATGAGAGGAGAAAAGG
TGAGTAAGTCCCTCCGTTAAACCCAATCTAGAATTTACTACAAATTACCTAATTTACCCTTGCAA
GTGGGACACATTACCAAATTTACCCTTACACCT
Found at i:918 original size:81 final size:80
Alignment explanation
Indices: 520--1049 Score: 331
Period size: 81 Copynumber: 6.5 Consensus size: 80
510 TTACAATTGT
* * * * *
520 GTTAAACCCAATGTAGCATTTACTGCACATTA-CTAATTTAACCTTGCAAGTGGGAGTAGATAGG
1 GTTAAACCCAATGTAACATTTACTGCACATTACCTAATTTACCCTTGCAAGTGGGAG-AAAAAGA
* * *
584 GTGATTAAGTCACTTC
65 GTGAGTAAGTCCCTCC
* ** * * * *
600 GTTAAACCCAATATAGGATTTACAGCACATTACCTAATTTACTCTTTCAAATGGGATGAGAAAAG
1 GTTAAACCCAATGTAACATTTACTGCACATTACCTAATTTACCCTTGCAAGTGGGA-GA-AAAAG
**
665 -GTGAGTAAGTCCCTTT
64 AGTGAGTAAGTCCCTCC
* * * * *
681 GTTAAACCCAATCTAGA-ATTTGCTACAAATTACCTAATTTACCCTTGCAAGTGGGACACATTAC
1 GTTAAACCCAATGTA-ACATTTACTGCACATTACCTAATTTACCCTTGCAAGTGGGAGA-A--A-
* ** ** *
745 CAA-A-T--TTACCCTTACACC
61 -AAGAGTGAGTA-AGTCCCTCC
* * * *
763 TTTAAACCCAATGTATCATTTACTGCACATTTTCCTAATTTACCCTTGCAAGTGAGAGGAAAAAG
1 GTTAAACCCAATGTAACATTTACTGCACA-TTACCTAATTTACCCTTGCAAGTGGGA-GAAAAAG
*
828 GGTGAGTAAGTCCCTCC
64 AGTGAGTAAGTCCCTCC
* * * * * * * *
845 GTTAAACCTAATGTAGCTTTTATTGCATATTAGCTAATTTACCCTTGCAAGTGGGAGAAGAGATA
1 GTTAAACCCAATGTAACATTTACTGCACATTACCTAATTTACCCTTGCAAGTGGGAGAA-AAAGA
* * * *
910 GTGGGTAAGTTCTTTC
65 GTGAGTAAGTCCCTCC
* ** * *
926 GTTATACCCAATGTAACATTTACTGCACATTACCTAATTTAAACTTGCAAGTAGGAG-GAAAGAG
1 GTTAAACCCAATGTAACATTTACTGCACATTACCTAATTTACCCTTGCAAGTGGGAGAAAAAGA-
* * * *
990 GTTAAATAACTCCCTTC
65 G-TGAGTAAGTCCCTCC
* * * *
1007 GTTAAA-CCAACTGTAGCATTTAATTCACATTACCGAATTTACC
1 GTTAAACCCAA-TGTAACATTTACTGCACATTACCTAATTTACC
1050 ATTACACCTT
Statistics
Matches: 340, Mismatches: 89, Indels: 41
0.72 0.19 0.09
Matches are distributed among these distances:
79 5 0.01
80 39 0.11
81 208 0.61
82 56 0.16
83 29 0.09
84 3 0.01
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (80 bp):
GTTAAACCCAATGTAACATTTACTGCACATTACCTAATTTACCCTTGCAAGTGGGAGAAAAAGAG
TGAGTAAGTCCCTCC
Found at i:960 original size:245 final size:243
Alignment explanation
Indices: 521--977 Score: 553
Period size: 245 Copynumber: 1.9 Consensus size: 243
511 TACAATTGTG
* * * *
521 TTAAACCCAATGTAGCATTTACTGCACATTACTAATTTAACCTTGCAAGTGGGAGTAGATAGGGT
1 TTAAACCCAATGTAGCATTTACTGCACATTACTAATTTAACCTTGCAAGTGAGAGGAAAAAGGGT
* * * * *
586 GATTAAGTCACTTCGTTAAACCCAATATAGGATTTACAGCACATTACCTAATTTACTCTTTCAAA
66 GAGTAAGTCACTCCGTTAAACCCAATATAGCATTTACAGCACATTACCTAATTTACCCTTGCAAA
*
651 TGGGATGAGAAAAGGTGAGTAAGTCCCTTTGTTAAACCCAATCTAGAATTTGCTACAAATTACCT
131 TGGGATGAGAAAAGGTGAGTAAGTCCCTTTGTTAAACCCAATCTAGAATTTACTACAAATTACCT
**
716 AATTTACCCTTGCAAGTGGGACACATTACCAAATTTACCCTTACACCT
196 AATTTAAACTTGCAAGTGGGACACATTACCAAATTTACCCTTACACCT
* * *
764 TTAAACCCAATGTATCATTTACTGCACATTTTCCTAATTTACCCTTGCAAGTGAGAGGAAAAAGG
1 TTAAACCCAATGTAGCATTTACTGCACA--TTACTAATTTAACCTTGCAAGTGAGAGGAAAAAGG
* * * * ** * *
829 GTGAGTAAGTCCCTCCGTTAAACCTAATGTAGCTTTTATTGCATATTAGCTAATTTACCCTTGCA
64 GTGAGTAAGTCACTCCGTTAAACCCAATATAGCATTTACAGCACATTACCTAATTTACCCTTGCA
* * * * * * * *
894 AGTGGGA-GAAGAGATA-GTGGGTAAGT-TCTTTCGTTATACCCAATGTA-ACATTTACTGCACA
129 AATGGGATG-AGA-AAAGGTGAGTAAGTCCCTTT-GTTAAACCCAATCTAGA-ATTTACTACAAA
955 TTACCTAATTTAAACTTGCAAGT
190 TTACCTAATTTAAACTTGCAAGT
978 AGGAGGAAAG
Statistics
Matches: 177, Mismatches: 31, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
243 27 0.15
244 6 0.03
245 142 0.80
246 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (243 bp):
TTAAACCCAATGTAGCATTTACTGCACATTACTAATTTAACCTTGCAAGTGAGAGGAAAAAGGGT
GAGTAAGTCACTCCGTTAAACCCAATATAGCATTTACAGCACATTACCTAATTTACCCTTGCAAA
TGGGATGAGAAAAGGTGAGTAAGTCCCTTTGTTAAACCCAATCTAGAATTTACTACAAATTACCT
AATTTAAACTTGCAAGTGGGACACATTACCAAATTTACCCTTACACCT
Found at i:1093 original size:54 final size:54
Alignment explanation
Indices: 1002--1109 Score: 137
Period size: 54 Copynumber: 2.0 Consensus size: 54
992 TAAATAACTC
* ** *
1002 CCTTCGTTAAACCAACTGTAGCATTTAATTCACATTACCGAATTT-ACCATTACA
1 CCTTCGTTAAACCAAATGTAGCATTTAATGAAAATTACCGAATTTAACC-TTACA
** *
1056 CCTTCGTTAAACCAAATGTAGCATTTTCTGAAAATTACCTAATTTAACCTTACA
1 CCTTCGTTAAACCAAATGTAGCATTTAATGAAAATTACCGAATTTAACCTTACA
1110 AGTGGGAGGA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
54 43 0.93
55 3 0.07
ACGTcount: A:0.34, C:0.24, G:0.07, T:0.34
Consensus pattern (54 bp):
CCTTCGTTAAACCAAATGTAGCATTTAATGAAAATTACCGAATTTAACCTTACA
Found at i:1394 original size:81 final size:81
Alignment explanation
Indices: 1089--1755 Score: 275
Period size: 81 Copynumber: 8.2 Consensus size: 81
1079 TTTTCTGAAA
* ** * * * *
1089 ATTACCTAATTTAACCTTACAAGTGGGAGGAAG-GAGGGTGAGTAAGTCCCTTCGTT-AACCTAA
1 ATTACCTAATTTAACCTTGCAAGTGGGA-GAAGAGAAAGTGAATAAGTTCCTTCATTAAACCCAA
* * * *
1152 TATGGCA-TTAACTGCAC
65 TGTAGAATTTAA-TACAC
* * * **
1169 ATTACCTAATTTACTTACCCTTGCAAGTGGGAG--GAGAAAGGGTAAGTAAATCCCTTTGTTAAA
1 ATTACCTAATTTA---A-CCTTGCAAGTGGGAGAAGAGAAAGTG-AA-TAAGTTCCTTCATTAAA
* * * * *
1232 CCTATTGTACGATTTTTATTGCA-
60 CCCAATGTA-GA-ATTTAATACAC
** * * * * * *
1255 ATTACCTTTTTTACCCTTGCAAGTGGGAGGAGATAAAGTGAGTAAGTTCTTTCGTTAAA-CCACA
1 ATTACCTAATTTAACCTTGCAAGTGGGAGAAGAGAAAGTGAATAAGTTCCTTCATTAAACCCA-A
* *
1319 TGTA-ACATTTAATGCAT
65 TGTAGA-ATTTAATACAC
* * * *
1336 ATTACCTAATTTAACTTTGCAAGTGGGATAAGAGAAGGTGAATAATTTCCTTCATTAAACCCAAT
1 ATTACCTAATTTAACCTTGCAAGTGGGAGAAGAGAAAGTGAATAAGTTCCTTCATTAAACCCAAT
*
1401 GTAGAATTTACTACAC
66 GTAGAATTTAATACAC
* * * * ** * * * *
1417 ATTACCTAATTTACCCTTCCAAGTGGGAGGACAGAGGGTGAGTAACTTCATTCGTTAAACCC-AT
1 ATTACCTAATTTAACCTTGCAAGTGGGAGAAGAGAAAGTGAATAAGTTCCTTCATTAAACCCAAT
* ** *
1481 -TAGCATTTTTTGA-AA
66 GTAGAATTTAAT-ACAC
* * * * ** ** * * **
1496 ATTACCTAATTTACCCTTACAAGTGGGGGGAGAGAGGGTGGGTGAGTCCCTTTGTTAAACCCAAT
1 ATTACCTAATTTAACCTTGCAAGTGGGAGAAGAGAAAGTGAATAAGTTCCTTCATTAAACCCAAT
* * *
1561 GTAGAATTTATTTCAT
66 GTAGAATTTAATACAC
* * * * ** * * * **
1577 ATTACCTAATTTACCCTTGTAACTGAGACTAGAGAGAGTGAGTATG-TCCTTTTGTTAAACCCAA
1 ATTACCTAATTTAACCTTGCAAGTGGGAGAAGAGAAAGTGAATAAGTTCC-TTCATTAAACCCAA
1641 TGTAGCAA-TTACA-ACAC
65 TGTAG-AATTTA-ATACAC
* * * * * * * * * *
1658 ATTACGTAATTTAACATTACAAGTGGGAGGAGAGAAGGTGAGTGAGTCCCTTCGTTAAACCTAAT
1 ATTACCTAATTTAACCTTGCAAGTGGGAGAAGAGAAAGTGAATAAGTTCCTTCATTAAACCCAAT
** * *
1723 GTATCATTTATTGCAC
66 GTAGAATTTAATACAC
1739 ATTACCTAATTT-ACCTT
1 ATTACCTAATTTAACCTT
1756 CACACCTTCG
Statistics
Matches: 452, Mismatches: 108, Indels: 54
0.74 0.18 0.09
Matches are distributed among these distances:
79 62 0.14
80 34 0.08
81 249 0.55
82 44 0.10
83 4 0.01
84 32 0.07
85 8 0.02
86 12 0.03
87 4 0.01
88 3 0.01
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32
Consensus pattern (81 bp):
ATTACCTAATTTAACCTTGCAAGTGGGAGAAGAGAAAGTGAATAAGTTCCTTCATTAAACCCAAT
GTAGAATTTAATACAC
Found at i:1460 original size:162 final size:161
Alignment explanation
Indices: 1056--1753 Score: 570
Period size: 162 Copynumber: 4.3 Consensus size: 161
1046 TACCATTACA
* * * * *
1056 CCTTCGTTAAACCAAATGTAGCATTT-TCTGA-AAATTACCTAATTTAACCTTACAAGTGGGAGG
1 CCTTCGTTAAACCCAATGTAGAATTTAT-T-ACACATTACCTAATTTACCCTTGCAAGTGGGAGG
* * * * *
1119 A-AGGAGGGTGAGTAAGTCCCTTCGTT-AACCTAATATGGCA-TTAACTGCACATTACCTAATTT
64 AGA-GAGAGTGAGTAAGTCCTTTCGTTAAACC-CATGTAGCATTTAA-TGCACATTACCTAATTT
* *
1181 ACTTACCCTTGCAAGTGGGAGGAGA-AAGG-GTAAGTAAATC
126 A---A-CCTTACAAGTGGGAGGAGAGAAGGTG-AA-TAAGTC
* * * * * **
1221 CCTTTGTTAAACCTATTGTACGATTTTTATTGCA-ATTACCTTTTTTACCCTTGCAAGTGGGAGG
1 CCTTCGTTAAACCCAATGTA-GA-ATTTATTACACATTACCTAATTTACCCTTGCAAGTGGGAGG
* * * * *
1285 AGATAAAGTGAGTAAGTTCTTTCGTTAAACCACATGTAACATTTAATGCATATTACCTAATTTAA
64 AGAGAGAGTGAGTAAGTCCTTTCGTTAAACC-CATGTAGCATTTAATGCACATTACCTAATTTAA
* * ** * *
1350 CTTTGCAAGTGGGATAAGAGAAGGTGAATAATTT
128 CCTTACAAGTGGGAGGAGAGAAGGTGAATAAGTC
* * * *
1384 CCTTCATTAAACCCAATGTAGAATTTACTACACATTACCTAATTTACCCTTCCAAGTGGGAGGAC
1 CCTTCGTTAAACCCAATGTAGAATTTATTACACATTACCTAATTTACCCTTGCAAGTGGGAGGAG
* * * * ** * * *
1449 AGAGGGTGAGTAACTTCATTCGTTAAACCCAT-TAGCATTTTTTGAAAATTACCTAATTTACCCT
66 AGAGAGTGAGTAAGTCCTTTCGTTAAACCCATGTAGCATTTAATGCACATTACCTAATTTAACCT
* * ** *
1513 TACAAGTGGGGGGAGAGAGGGTGGGTGAGTC
131 TACAAGTGGGAGGAGAGAAGGTGAATAAGTC
* * * * * * **
1544 CCTTTGTTAAACCCAATGTAGAATTTATTTCATATTACCTAATTTACCCTTGTAACTGAGACTAG
1 CCTTCGTTAAACCCAATGTAGAATTTATTACACATTACCTAATTTACCCTTGCAAGTGGGAGGAG
* * * * *
1609 AGAGAGTGAGTATGTCCTTTTGTTAAACCCAATGTAGCAATTACA-ACACATTACGTAATTTAAC
66 AGAGAGTGAGTAAGTCCTTTCGTTAAACCC-ATGTAGCATTTA-ATGCACATTACCTAATTTAAC
* * *
1673 ATTACAAGTGGGAGGAGAGAAGGTGAGTGAGTC
129 CTTACAAGTGGGAGGAGAGAAGGTGAATAAGTC
* ** *
1706 CCTTCGTTAAACCTAATGTATCATTTATTGCACATTACCTAATTTACC
1 CCTTCGTTAAACCCAATGTAGAATTTATTACACATTACCTAATTTACC
1754 TTCACACCTT
Statistics
Matches: 425, Mismatches: 95, Indels: 29
0.77 0.17 0.05
Matches are distributed among these distances:
160 123 0.29
161 12 0.03
162 146 0.34
163 36 0.08
164 7 0.02
165 18 0.04
166 46 0.11
167 32 0.08
168 5 0.01
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (161 bp):
CCTTCGTTAAACCCAATGTAGAATTTATTACACATTACCTAATTTACCCTTGCAAGTGGGAGGAG
AGAGAGTGAGTAAGTCCTTTCGTTAAACCCATGTAGCATTTAATGCACATTACCTAATTTAACCT
TACAAGTGGGAGGAGAGAAGGTGAATAAGTC
Found at i:1580 original size:241 final size:243
Alignment explanation
Indices: 1192--1753 Score: 545
Period size: 241 Copynumber: 2.3 Consensus size: 243
1182 CTTACCCTTG
* * * * * * *
1192 CAAGTGGGAGGAGA-AAGGGTAAGTAAATCCCTTTGTTAAACCTATTGTA-CGATTTTTATTG-C
1 CAAGTGGGAGGACAGAA-GGTGAGTAACTCCATTCGTTAAACCTAATGTAGC-A--TTTATTGAA
** * * *
1254 AATTACCTTTTTTACCCTTGCAAGTGGGAGGAGATAAAGTGAGTAAGTTCTTTCGTTAAACCACA
62 AATTACCTAATTTACCCTTACAAGTGGGAGGAGAGAAAGTGAGTAAGTCCTTTCGTTAAACCACA
* * *
1319 TGTAACATTTAATGCATATTACCTAATTTAACTTTGCAAGTGGGA-TA-AGAGAAGGTGAATAAT
127 TGTAACATTTAATGCATATTACCTAATTTAACCTTGCAACTGAGACTAGAGAG-A-GTGAAT-AT
* * * * *
1382 TTCC-TTCATTAAACCCAATGTAG-AATTTACTACACATTACCTAATTTACCCTTC
189 GTCCTTTCATTAAACCCAATGTAGCAA-TTACAACACATTACCTAATTTAACATTA
* * * *
1436 CAAGTGGGAGGACAGAGGGTGAGTAACTTCATTCGTTAAACC-CAT-TAGCATTTTTTGAAAATT
1 CAAGTGGGAGGACAGAAGGTGAGTAACTCCATTCGTTAAACCTAATGTAGCATTTATTGAAAATT
* ** * *
1499 ACCTAATTTACCCTTACAAGTGGGGGGAGAGAGGGTGGGTGAGTCCCTTT-GTTAAACC-CAATG
66 ACCTAATTTACCCTTACAAGTGGGAGGAGAGAAAGTGAGTAAGT-CCTTTCGTTAAACCAC-ATG
* * * * *
1562 TAGA-ATTTATTTCATATTACCTAATTTACCCTTGTAACTGAGACTAGAGAGAGTGAGTATGTCC
129 TA-ACATTTAATGCATATTACCTAATTTAACCTTGCAACTGAGACTAGAGAGAGTGAATATGTCC
** *
1626 TTTTGTTAAACCCAATGTAGCAATTACAACACATTACGTAATTTAACATTA
193 TTTCATTAAACCCAATGTAGCAATTACAACACATTACCTAATTTAACATTA
* * * * * * *
1677 CAAGTGGGAGGAGAGAAGGTGAGTGAGTCCCTTCGTTAAACCTAATGTATCATTTATTGCACATT
1 CAAGTGGGAGGACAGAAGGTGAGTAACTCCATTCGTTAAACCTAATGTAGCATTTATTGAAAATT
1742 ACCTAATTTACC
66 ACCTAATTTACC
1754 TTCACACCTT
Statistics
Matches: 258, Mismatches: 48, Indels: 25
0.78 0.15 0.08
Matches are distributed among these distances:
240 12 0.05
241 165 0.64
242 15 0.06
243 32 0.12
244 33 0.13
245 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (243 bp):
CAAGTGGGAGGACAGAAGGTGAGTAACTCCATTCGTTAAACCTAATGTAGCATTTATTGAAAATT
ACCTAATTTACCCTTACAAGTGGGAGGAGAGAAAGTGAGTAAGTCCTTTCGTTAAACCACATGTA
ACATTTAATGCATATTACCTAATTTAACCTTGCAACTGAGACTAGAGAGAGTGAATATGTCCTTT
CATTAAACCCAATGTAGCAATTACAACACATTACCTAATTTAACATTA
Found at i:2130 original size:81 final size:81
Alignment explanation
Indices: 1774--2303 Score: 476
Period size: 81 Copynumber: 6.5 Consensus size: 81
1764 CGATAAATTC
* * * * * * *
1774 AATGTAGAATTTAATACACATTACCTAATTTAACCTTGCAAGTGAGATAAGAGAGGGT-AGGTAA
1 AATGTAGCATTTACTGCACATTACCTAATTTACCCTTGCAAGTGGGAGAAGAGTGGGTGA-GT-A
* * *
1838 GGTCCCAT-GTTAAACCC
64 TGTCCCTTCGTTAAACCT
* * * ** * * * * ** * **
1855 AACGTAGAATTTATTGTGCAGTATCTAATTTACCTTTGCATGTGGGAGGTGTGTGGGTGAGTAAC
1 AATGTAGCATTTACTGCACATTACCTAATTTACCCTTGCAAGTGGGAGAAGAGTGGGTGAGTATG
*
1920 TCCCTTCGTTAAACCC
66 TCCCTTCGTTAAACCT
* ** * * * *
1936 AATTTTTCATTTACTGCACACATTACCTAATTTAACCTTGCAAGTGGAAGGAA-AGAGGGTGGGT
1 AATGTAGCATTTACTG--CACATTACCTAATTTACCCTTGCAAGTGGGA-GAAGAGTGGGTGAGT
** *
2000 AAATCCTTTCGTTAAACC-
63 ATGTCCCTTCGTTAAACCT
* * *
2018 CATGTTGCATTTACTGCACATTACCTAATTTACCCTTGCAAGTGGGAGAAGAGCGGGTGAGTATG
1 AATGTAGCATTTACTGCACATTACCTAATTTACCCTTGCAAGTGGGAGAAGAGTGGGTGAGTATG
*
2083 TCCCTTCGTTAAGCCT
66 TCCCTTCGTTAAACCT
* * *
2099 AATGTAGCATTTACTGCAAATTACCTAATTTACCCATGCTAGTGGGA-AAGGAGTGGGAGTGAGT
1 AATGTAGCATTTACTGCACATTACCTAATTTACCCTTGCAAGTGGGAGAA-GAGT-GG-GTGAGT
2163 GAGTAAGTCCCTTCGTTAAACCT
63 -A-T--GTCCCTTCGTTAAACCT
* * * *
2186 AATGTAGCATTTTCTGCACATTACCTAATTTACCTTTGCAAATGGGAGGAGAGTGGGTGAGTATG
1 AATGTAGCATTTACTGCACATTACCTAATTTACCCTTGCAAGTGGGAGAAGAGTGGGTGAGTATG
*
2251 TTCCTTCGTTAAACCT
66 TCCCTTCGTTAAACCT
* *
2267 AATGTAGCATTTATTGCACATCACCTAATTTACCCTT
1 AATGTAGCATTTACTGCACATTACCTAATTTACCCTT
2304 ACACCTTCAT
Statistics
Matches: 364, Mismatches: 70, Indels: 30
0.78 0.15 0.06
Matches are distributed among these distances:
79 3 0.01
80 60 0.16
81 157 0.43
82 16 0.04
83 54 0.15
84 3 0.01
85 7 0.02
86 2 0.01
87 61 0.17
88 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (81 bp):
AATGTAGCATTTACTGCACATTACCTAATTTACCCTTGCAAGTGGGAGAAGAGTGGGTGAGTATG
TCCCTTCGTTAAACCT
Found at i:2246 original size:168 final size:161
Alignment explanation
Indices: 1879--2301 Score: 504
Period size: 168 Copynumber: 2.6 Consensus size: 161
1869 TGTGCAGTAT
* * * ** * * **
1879 CTAATTTACCTTTGCATGTGGGAGGTGTGTGGGTGAGTAACTCCCTTCGTTAAACCCAATTTTTC
1 CTAATTTACCTTTGCAAGTGGGAGGAGAGTGGGTGAGTATGTCCCTTCGTTAAACCTAATGTAGC
* * * *
1944 ATTTACTGCACACATTACCTAATTTAACCTTGCAAGTGGAAGGAAAGAGGGTGGGTAAATCCTTT
66 ATTTACTGCA-A-ATTACCTAATTTACCCATGCAAGTGGAAGGAAAGAGGGTGAGTAAATCCCTT
* *
2009 CGTTAAACCCATGTTGCATTTACTGCACATTAC
129 CGTTAAACCAATGTAGCATTTACTGCACATTAC
* * * *
2042 CTAATTTACCCTTGCAAGTGGGAGAAGAGCGGGTGAGTATGTCCCTTCGTTAAGCCTAATGTAGC
1 CTAATTTACCTTTGCAAGTGGGAGGAGAGTGGGTGAGTATGTCCCTTCGTTAAACCTAATGTAGC
* ** *
2107 ATTTACTGCAAATTACCTAATTTACCCATGCTAGTGGGAAAGGAGTGGGAGTGAGTGAGTAAGTC
66 ATTTACTGCAAATTACCTAATTTACCCATGCAAGT-GG-AAGGA--AAGAG-G-GTGAGTAAATC
*
2172 CCTTCGTTAAACCTAATGTAGCATTTTCTGCACATTAC
125 CCTTCGTTAAACC-AATGTAGCATTTACTGCACATTAC
* *
2210 CTAATTTACCTTTGCAAATGGGAGGAGAGTGGGTGAGTATGTTCCTTCGTTAAACCTAATGTAGC
1 CTAATTTACCTTTGCAAGTGGGAGGAGAGTGGGTGAGTATGTCCCTTCGTTAAACCTAATGTAGC
* * *
2275 ATTTATTGCACATCACCTAATTTACCC
66 ATTTACTGCAAATTACCTAATTTACCC
2302 TTACACCTTC
Statistics
Matches: 220, Mismatches: 33, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
161 21 0.10
162 3 0.01
163 67 0.30
165 3 0.01
166 1 0.00
167 21 0.10
168 104 0.47
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.32
Consensus pattern (161 bp):
CTAATTTACCTTTGCAAGTGGGAGGAGAGTGGGTGAGTATGTCCCTTCGTTAAACCTAATGTAGC
ATTTACTGCAAATTACCTAATTTACCCATGCAAGTGGAAGGAAAGAGGGTGAGTAAATCCCTTCG
TTAAACCAATGTAGCATTTACTGCACATTAC
Found at i:2317 original size:54 final size:54
Alignment explanation
Indices: 2253--2356 Score: 145
Period size: 54 Copynumber: 1.9 Consensus size: 54
2243 TGAGTATGTT
* * *
2253 CCTTCGTTAAACCTAATGTAGCATTTATTGCACATCACCTAATTTACCCTTACA
1 CCTTCATTAAACCCAATGTAGCATTTACTGCACATCACCTAATTTACCCTTACA
* * * *
2307 CCTTCATTAAACCCAATGTTGCATTTACTGCATATTATCTAATTTACCCT
1 CCTTCATTAAACCCAATGTAGCATTTACTGCACATCACCTAATTTACCCT
2357 CGCAAGTGGG
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 43 1.00
ACGTcount: A:0.29, C:0.27, G:0.07, T:0.38
Consensus pattern (54 bp):
CCTTCATTAAACCCAATGTAGCATTTACTGCACATCACCTAATTTACCCTTACA
Found at i:2414 original size:135 final size:135
Alignment explanation
Indices: 2172--2433 Score: 326
Period size: 135 Copynumber: 1.9 Consensus size: 135
2162 TGAGTAAGTC
* * * * *
2172 CCTTCGTTAAACCTAATGTAGCATTTTCTGCACATTACCTAATTTACCTTTGCAAATGGGAGGAG
1 CCTTCATTAAACCCAATGTAGCATTTACTGCACATTACCTAATTTACCCTCGCAAATGGGAGGAG
* * * * * * * *
2237 AGTGGGTGAGTATGTTCCTTCGTTAAACCTAATGTAGCATTTATTGCACATCACCTAATTTACCC
66 AGTGGGTAAGTAAGTCCCTTAGTTAAACCCAATGTAGCATTTACTACAAATCACCTAATTTACCC
2302 TTACA
131 TTACA
* * * * *
2307 CCTTCATTAAACCCAATGTTGCATTTACTGCATATTATCTAATTTACCCTCGCAAGTGGGAGGGG
1 CCTTCATTAAACCCAATGTAGCATTTACTGCACATTACCTAATTTACCCTCGCAAATGGGAGGAG
* * * *
2372 AGTTGGTAAGTAAGTCCCTTAGTTAAACCCAATTTTGCATTTACTACAAATTACCTAATTTA
66 AGTGGGTAAGTAAGTCCCTTAGTTAAACCCAATGTAGCATTTACTACAAATCACCTAATTTA
2434 ACTTTGCAAG
Statistics
Matches: 105, Mismatches: 22, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
135 105 1.00
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.35
Consensus pattern (135 bp):
CCTTCATTAAACCCAATGTAGCATTTACTGCACATTACCTAATTTACCCTCGCAAATGGGAGGAG
AGTGGGTAAGTAAGTCCCTTAGTTAAACCCAATGTAGCATTTACTACAAATCACCTAATTTACCC
TTACA
Found at i:2478 original size:81 final size:81
Alignment explanation
Indices: 2313--2497 Score: 208
Period size: 81 Copynumber: 2.3 Consensus size: 81
2303 TACACCTTCA
* * * * * **
2313 TTAAACCCAATGTTGCATTTACTGCATATTATCTAATTTACCCTCGCAAGTGGGAGGGGAGTTGG
1 TTAAACCCAATGTTGCATTTACTACAAATTACCTAATTTAACCTCGCAAGTGGGAGGAGAGAGGG
* *
2378 TAAGTAAGTCCCTTAG
66 TAAGTAAATCCCATAG
* * *
2394 TTAAACCCAATTTTGCATTTACTACAAATTACCTAATTTAACTTTGCAAGTGGGAGGAGAGAGGG
1 TTAAACCCAATGTTGCATTTACTACAAATTACCTAATTTAACCTCGCAAGTGGGAGGAGAGAGGG
** *
2459 TGGGTAAATCCCATCG
66 TAAGTAAATCCCATAG
* * *
2475 TTAAACCTAATGTAGCATATACT
1 TTAAACCCAATGTTGCATTTACT
2498 GCACATTTTA
Statistics
Matches: 85, Mismatches: 19, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
81 85 1.00
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (81 bp):
TTAAACCCAATGTTGCATTTACTACAAATTACCTAATTTAACCTCGCAAGTGGGAGGAGAGAGGG
TAAGTAAATCCCATAG
Found at i:2485 original size:216 final size:219
Alignment explanation
Indices: 2085--2503 Score: 533
Period size: 216 Copynumber: 1.9 Consensus size: 219
2075 TGAGTATGTC
* * * *
2085 CCTTCGTTAAGCCTAATGTAGCATTTACTGCAAATTACCTAATTTACCCATGCTAGTGGGAAAGG
1 CCTTCATTAAACCCAATGTAGCATTTACTGCAAATTACCTAATTTACCCATGCAAGT-GG--AGG
* * * * * *
2150 AGTGGGAGTGAGTGAGTAAGTCCCTTCGTTAAACCTAATGTAGCATTTTCTGCACATTACCTAAT
63 AGTGGGAGTGAGTAAGTAAGTCCCTTAGTTAAACCCAATGTAGCATTTACTACAAATTACCTAAT
* * ** * * *
2215 TTACCTTTGCAAATGGGAGGAGAGTGGGTGAGTATGTTCCTTCGTTAAACCTAATGTAGCATTTA
128 TTAACTTTGCAAATGGGAGGAGAGAGGGTGAGTAAATCCCATCGTTAAACCTAATGTAGCATATA
*
2280 TTGCACATCACCTAATTTACCCTTACA
193 CTGCACATCACCTAATTTACCCTTACA
* * *
2307 CCTTCATTAAACCCAATGTTGCATTTACTGCATATTATCTAATTTACCC-TCGCAAGT-G-GGAG
1 CCTTCATTAAACCCAATGTAGCATTTACTGCAAATTACCTAATTTACCCAT-GCAAGTGGAGGAG
* *
2369 -GGGAGTTG-GTAAGTAAGTCCCTTAGTTAAACCCAATTTTGCATTTACTACAAATTACCTAATT
65 TGGGAG-TGAGTAAGTAAGTCCCTTAGTTAAACCCAATGTAGCATTTACTACAAATTACCTAATT
* *
2432 TAACTTTGCAAGTGGGAGGAGAGAGGGTGGGTAAATCCCATCGTTAAACCTAATGTAGCATATAC
129 TAACTTTGCAAATGGGAGGAGAGAGGGTGAGTAAATCCCATCGTTAAACCTAATGTAGCATATAC
2497 TGCACAT
194 TGCACAT
2504 TTTATATGCA
Statistics
Matches: 170, Mismatches: 25, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
216 114 0.67
217 6 0.04
220 1 0.01
221 1 0.01
222 48 0.28
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.32
Consensus pattern (219 bp):
CCTTCATTAAACCCAATGTAGCATTTACTGCAAATTACCTAATTTACCCATGCAAGTGGAGGAGT
GGGAGTGAGTAAGTAAGTCCCTTAGTTAAACCCAATGTAGCATTTACTACAAATTACCTAATTTA
ACTTTGCAAATGGGAGGAGAGAGGGTGAGTAAATCCCATCGTTAAACCTAATGTAGCATATACTG
CACATCACCTAATTTACCCTTACA
Found at i:3573 original size:16 final size:16
Alignment explanation
Indices: 3552--3585 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3542 ATTGATGACA
*
3552 TTGTTTTTATAATTGT
1 TTGTTTTCATAATTGT
*
3568 TTGTTTTCCTAATTGT
1 TTGTTTTCATAATTGT
3584 TT
1 TT
3586 TGGTTATGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.15, C:0.06, G:0.12, T:0.68
Consensus pattern (16 bp):
TTGTTTTCATAATTGT
Found at i:4396 original size:18 final size:18
Alignment explanation
Indices: 4373--4407 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
4363 TTCATGCCAC
*
4373 CAAAACATGATCATTGTT
1 CAAAACATGAACATTGTT
4391 CAAAACATGAACATTGT
1 CAAAACATGAACATTGT
4408 CGACGAGGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.29
Consensus pattern (18 bp):
CAAAACATGAACATTGTT
Done.