Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014951.1 Corchorus capsularis cultivar CVL-1 contig14972, 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: 23548
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:1862 original size:13 final size:13
Alignment explanation
Indices: 1841--1870 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1831 GATCAAGTGT
*
1841 AAAAGTAAAAAGG
1 AAAAATAAAAAGG
1854 AAAAATAAAAAGG
1 AAAAATAAAAAGG
1867 AAAA
1 AAAA
1871 CAAATATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.07
Consensus pattern (13 bp):
AAAAATAAAAAGG
Found at i:9101 original size:21 final size:22
Alignment explanation
Indices: 9054--9101 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
9044 GTTCCAGCCA
**
9054 TCATT-TCCTTCTTCTTTTTCT
1 TCATTGTCCTTCTTCTAATTCT
9075 TC-TTGTCCTTCTTCTAATTC-
1 TCATTGTCCTTCTTCTAATTCT
9095 TCATTGT
1 TCATTGT
9102 TGTTCAATGG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.08, C:0.27, G:0.04, T:0.60
Consensus pattern (22 bp):
TCATTGTCCTTCTTCTAATTCT
Found at i:12817 original size:543 final size:544
Alignment explanation
Indices: 11778--12866 Score: 2011
Period size: 543 Copynumber: 2.0 Consensus size: 544
11768 GTTTATAGGA
*
11778 CAAATCCTGAAGAAACAAAGGAGCTAGAGAAGCAAGTTGGAGAGCTACTACAAAAAGGTTTTGTG
1 CAAATCATGAAGAAACAAAGGAGCTAGAGAAGCAAGTTGGAGAGCTACTACAAAAAGGTTTTGTG
* *
11843 CAGGAAAGCCTTTCTCCATGTGCAGTTCCTGTTTTGCTTGTTCCTAAGAAGGATGAAACTTGGAG
66 CAGGAAAGCCTTTCTCCATGTGCAATTCCTGCTTTGCTTGTTCCTAAGAAGGATGAAACTTGGAG
11908 AATGTGTGTTGATTGTAGAGCAGTAAACAACATAACGGTAAAGTATCGTCACCCTATTCCTAGAT
131 AATGTGTGTTGATTGTAGAGCAGTAAACAACATAACGGTAAAGTATCGTCACCCTATTCCTAGAT
*
11973 TAGATGATATGCTTGATGAATTGCATGGTGCTTGCTTATTTTCAAAGATTGATTTAAAGAGTGGT
196 TAGATGATATGCTTGATGAATTGCATGGTGCTTGCTTATTTTCAAAGATTGATTTAAAGAGTGGC
*
12038 TATCATCAAATTTGCATGAAAGAGGGTGATGAATGGAAAACTGCCTTTAAAACTAATCTAGGATT
261 TATCATCAAATTCGCATGAAAGAGGGTGATGAATGGAAAACTGCCTTTAAAACTAATCTAGGATT
12103 GTATGAATGGTTAGTTATGCCTTTTGGATTGACTAATGCAGCTAGTACTTTCATGAGGTTAATGA
326 GTATGAATGGTTAGTTATGCCTTTTGGATTGACTAATGCAGCTAGTACTTTCATGAGGTTAATGA
*
12168 ATCATGTTTTGAGAGCTTATATTTGCAAGTTTGTTGTTGTTTATTTTGATGATATACTTGTGTAT
391 ATCATGTTTTGAGAGCTTATATTGGCAAGTTTGTTGTTGTTTATTTTGATGATATACTTGTGTAT
*
12233 AGCCGAAACCTAGATGATCATATTAAGCACTTGCGTTGTGTGTTAGATGTACTTAGGGTTGAGAA
456 AGCCGAAACCTAGATGATCATATTAAGCACTTGCATTGTGTGTTAGATGTACTTAGGGTTGAGAA
12298 GTTGTATGCTAACCTTAAGAAGTG
521 GTTGTATGCTAACCTTAAGAAGTG
*
12322 CAAATCATGAAGAAACAAAGGAGCTAGAGAAGCAAGTTGGAGAGCTACTACAAAAGGGTTTTGTG
1 CAAATCATGAAGAAACAAAGGAGCTAGAGAAGCAAGTTGGAGAGCTACTACAAAAAGGTTTTGTG
12387 C-GAGAAAGCCTTTCTCCATGTGCAATTCCTGCTTTGCTTGTTCCTAAGAAGGATG-AACTTGGA
66 CAG-GAAAGCCTTTCTCCATGTGCAATTCCTGCTTTGCTTGTTCCTAAGAAGGATGAAACTTGGA
* *
12450 GAATGTGTGTTGATTGTAGAGCAGTAAACAACATAACGGTAAATTATCGTCACCCTATTCCTTGA
130 GAATGTGTGTTGATTGTAGAGCAGTAAACAACATAACGGTAAAGTATCGTCACCCTATTCCTAGA
*
12515 TTAGATGATATGCTTGATGAATTGCATGGTGCTTGCTTATTTTCACAGATTGATTTAAAGAGTGG
195 TTAGATGATATGCTTGATGAATTGCATGGTGCTTGCTTATTTTCAAAGATTGATTTAAAGAGTGG
*
12580 CTATCATCAAATTCGCATGAAAGAGGGTGATGAATGGAAAACTTCCTTTAAAACTAATCTAGGAT
260 CTATCATCAAATTCGCATGAAAGAGGGTGATGAATGGAAAACTGCCTTTAAAACTAATCTAGGAT
*
12645 TGTATGAATTGTTAGTTATGCCTTTTGGATTGACTAATGCAGCTAGTACTTTCATGAGGTTAATG
325 TGTATGAATGGTTAGTTATGCCTTTTGGATTGACTAATGCAGCTAGTACTTTCATGAGGTTAATG
12710 AATCATGTTTTGAGAGCTTATATTGGCAAGTTTGTTGTTGTTTATTTTGATGATATACTTGTGTA
390 AATCATGTTTTGAGAGCTTATATTGGCAAGTTTGTTGTTGTTTATTTTGATGATATACTTGTGTA
* * *
12775 TAGCCGAAACCTAGATGATTATATTAAGTACTTGCATTGTGTGTTAGATGTATTTAGGGTTGAGA
455 TAGCCGAAACCTAGATGATCATATTAAGCACTTGCATTGTGTGTTAGATGTACTTAGGGTTGAGA
12840 AGTTGTATGCTAACCTTAAGAAGTG
520 AGTTGTATGCTAACCTTAAGAAGTG
12865 CA
1 CA
12867 CCTTTTGCAC
Statistics
Matches: 528, Mismatches: 16, Indels: 3
0.97 0.03 0.01
Matches are distributed among these distances:
543 414 0.78
544 114 0.22
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.34
Consensus pattern (544 bp):
CAAATCATGAAGAAACAAAGGAGCTAGAGAAGCAAGTTGGAGAGCTACTACAAAAAGGTTTTGTG
CAGGAAAGCCTTTCTCCATGTGCAATTCCTGCTTTGCTTGTTCCTAAGAAGGATGAAACTTGGAG
AATGTGTGTTGATTGTAGAGCAGTAAACAACATAACGGTAAAGTATCGTCACCCTATTCCTAGAT
TAGATGATATGCTTGATGAATTGCATGGTGCTTGCTTATTTTCAAAGATTGATTTAAAGAGTGGC
TATCATCAAATTCGCATGAAAGAGGGTGATGAATGGAAAACTGCCTTTAAAACTAATCTAGGATT
GTATGAATGGTTAGTTATGCCTTTTGGATTGACTAATGCAGCTAGTACTTTCATGAGGTTAATGA
ATCATGTTTTGAGAGCTTATATTGGCAAGTTTGTTGTTGTTTATTTTGATGATATACTTGTGTAT
AGCCGAAACCTAGATGATCATATTAAGCACTTGCATTGTGTGTTAGATGTACTTAGGGTTGAGAA
GTTGTATGCTAACCTTAAGAAGTG
Found at i:19446 original size:435 final size:437
Alignment explanation
Indices: 17837--19751 Score: 2875
Period size: 435 Copynumber: 4.4 Consensus size: 437
17827 ATAAGAGTAG
* ** * *
17837 ACACTTGAATCATCTTAATCGGACAAATAAAACAAAAAATACAAA-AATAAAAG-CCAAAGCG-T
1 ACACTTGAATCACCTT-ATCGGACAAGCAAAACAAAAAATA-AAAGAATTAAAGTCGAAA-CGTT
* ** * * * *
17899 GAATCGTCCAAGACATAA-TTGTAAAGGATTAAATAACATAAATTTATAAAAGTAT-GAGGATCA
63 CAATCGTCCAACCCAGAATTTGTGATGGACTAAATAACATAAA-TTATAAAAGTATAG-GGATC-
* * * *
17962 TTTGATAAATAATCTAGTAAAAAAATATTTGTTTATGCAGACCAAGCATAAAAATCCATTCTTGA
125 TTTGATAAATAATCCAGTAAAAAAATATTTGTTTATGGAGACCAAACATAAAAATTCATTCTTGA
* * *
18027 ACCCTCCACGAAACTCATTAATCAAATCCAACTTTCAGGCCCTTAACGAAAGTCGTAAATCACAT
190 ACCCTCCACGAAACTCATTAATCAAATCCAGCTTTCAGGCCCTTAACGAAAGTCGTAGATCACAC
* * *
18092 AATAACCTTTTAACAGACACTTGAACAACCTCAATCGGACAAGTGGACTGAAACTTATACAATA-
255 AATAACCTTTTAACCGACACTTGAACAACCTCAATCGAACAAGTGGACCGAAACTTATACAATAT
*
18156 TAGATAGACCGGCAATCGAGAGCACAAAATTTCAGAAGTAATTTTTAGAATCAAAACATTAAAAT
320 TAGATAGACCGGCAATCGAGACCACAAAATTTCAGAAGTAATTTTTAGAATCAAAACATTAAAAT
* * *
18221 TGGCTTTTGAGTCCTTCATGGAATTTGTAGATCATAAAATTACCTTTTAATAGA
385 TGGCTTTTGAATCCTTCATGGAAGTTGTAGATCATGAAATTACCTTTTAATA-A
*
18275 A-ACTTGAATCACCTTGATCGGACAAGCAAATCAAAAAATAAAAGAATTAAAGTCGAAACGTTCA
1 ACACTTGAATCACCTT-ATCGGACAAGCAAAACAAAAAATAAAAGAATTAAAGTCGAAACGTTCA
* * *
18339 ATCGTCCAACCCAGAATTTGTGATGGACTAAATAGCATAAATTATAAAAGTGTATGGATCTTTTG
65 ATCGTCCAACCCAGAATTTGTGATGGACTAAATAACATAAATTATAAAAGTATAGGGATC-TTTG
* *
18404 ATAAATAAACCAGTAAAAAAATAATTGTTTATGGAGACCAAACATAAAAATTCATTCTTGAACCC
129 ATAAATAATCCAGTAAAAAAATATTTGTTTATGGAGACCAAACATAAAAATTCATTCTTGAACCC
** * * *
18469 TCTTCGAAACTCATTAATCAAATCCAGCTTTCAGGCTCTTAAAGAAAGTCATAGATCACACAATA
194 TCCACGAAACTCATTAATCAAATCCAGCTTTCAGGCCCTTAACGAAAGTCGTAGATCACACAATA
* * * *
18534 ACTTTTTAACCGACACTTGAACAACCTCAATCGGATAAGTGGACCGAAACTTATACAATATCAGA
259 ACCTTTTAACCGACACTTGAACAACCTCAATCGAACAAGTGGACCGAAACTTATACAATATTAGA
* *
18599 TAGATCGGCAATCGAGAGCACAAAATTTCAGAAGTAATTTTTAGAATCAAAACATTAAAATTGGC
324 TAGACCGGCAATCGAGACCACAAAATTTCAGAAGTAATTTTTAGAATCAAAACATTAAAATTGGC
*
18664 TTTTGAATCCTTCATGGAAGTTGTAGATCATGAAATTACCTTTTAATAG
389 TTTTGAATCCTTCATGGAAGTTGTAGATCATGAAATTACCTTTTAATAA
* *
18713 ACACTTGAATCACCTTGATCGGACAAGCAAAACGAAAAACAAAAGAATTAAAGTCGAAACGTTCA
1 ACACTTGAATCACCTT-ATCGGACAAGCAAAACAAAAAATAAAAGAATTAAAGTCGAAACGTTCA
** ** *
18778 ATCGTCCAGTCTTG-ATATTGTGATGGACTAAATAGCATAAATTATAAAAGTATAGGGATCTTTT
65 ATCGTCCAACCCAGAAT-TTGTGATGGACTAAATAACATAAATTATAAAAGTATAGGGATC-TTT
* *
18842 GATAAATAATACAGTAAAAAAAGTATTTGTTTATGGTGACCAAACATAAAAATTCATTCTTGAAC
128 GATAAATAATCCAGTAAAAAAA-TATTTGTTTATGGAGACCAAACATAAAAATTCATTCTTGAAC
*
18907 CCTCCACGATACTCATTAATCAAATCCAGCTTTCAGGCCCTTAACGAAAGTCGTAGATCACACAA
192 CCTCCACGAAACTCATTAATCAAATCCAGCTTTCAGGCCCTTAACGAAAGTCGTAGATCACACAA
18972 TAACCTTTTAACCGACACTTGAACAACCTCAATCGAACAAGTGGACCGAAACTTATACAATATTA
257 TAACCTTTTAACCGACACTTGAACAACCTCAATCGAACAAGTGGACCGAAACTTATACAATATTA
* * *
19037 GATAGACCAGCAATCGAGACCATAAAATTTCAGAAGTATTTTTTAGAATCAAAACATTAAAATTG
322 GATAGACCGGCAATCGAGACCACAAAATTTCAGAAGTAATTTTTAGAATCAAAACATTAAAATTG
* * *
19102 ACTTTTTAGTCCTTCATGGAAGTTGTAGATCATGAAATTACCTTTTAATAA
387 GCTTTTGAATCCTTCATGGAAGTTGTAGATCATGAAATTACCTTTTAATAA
19153 ACACTTGAATCACC-T-TCGGACAAGCAAAACAAAAAATAAAAGAATTAAAGTCGAAACGTTCAA
1 ACACTTGAATCACCTTATCGGACAAGCAAAACAAAAAATAAAAGAATTAAAGTCGAAACGTTCAA
*
19216 TCGTACAACCCAGAATTTGTGATGGACTAAATAACATAAATTATAAAAGTATAGGGATCTGTTGA
66 TCGTCCAACCCAGAATTTGTGATGGACTAAATAACATAAATTATAAAAGTATAGGGATCT-TTGA
19281 TAAATAATCCAGT-AAAAAATATTTGTTTATGGAGACCAAACATAAAAATTCATTCTTGAACCCT
130 TAAATAATCCAGTAAAAAAATATTTGTTTATGGAGACCAAACATAAAAATTCATTCTTGAACCCT
* *
19345 CCACGATACTCATTAATCAAATCCAGCTTTCGGGCCCTTAACGAAAGTCGTAGATCACACAATAA
195 CCACGAAACTCATTAATCAAATCCAGCTTTCAGGCCCTTAACGAAAGTCGTAGATCACACAATAA
* * *
19410 CCTTTTAACTGACACTTGAACAATCTCAATCGAACAAGTGGACCAAAACTTATACAATATTAGAT
260 CCTTTTAACCGACACTTGAACAACCTCAATCGAACAAGTGGACCGAAACTTATACAATATTAGAT
* ** * *
19475 AGACCGGAAATCGAGACCACAAAATTTCAGAACCATTTTTTAGAATTAAAACATTAAAATTGGCT
325 AGACCGGCAATCGAGACCACAAAATTTCAGAAGTAATTTTTAGAATCAAAACATTAAAATTGGCT
*
19540 TTTGAATCTTTCATGGAAGTTGTAGATCATGAAATTACCTTTTAATAA
390 TTTGAATCCTTCATGGAAGTTGTAGATCATGAAATTACCTTTTAATAA
* * *
19588 ACACTTGAATCACC-T-TCGGACAAGCAAAACAAAAAATAAAACAATTAAAGCCGAAAAGTTCAA
1 ACACTTGAATCACCTTATCGGACAAGCAAAACAAAAAATAAAAGAATTAAAGTCGAAACGTTCAA
* *
19651 TCGTCCAATCCAGAATTTGTGATGGACTAAATAACATAAATTATAAAAGTATAGGGACCATTTGA
66 TCGTCCAACCCAGAATTTGTGATGGACTAAATAACATAAATTATAAAAGTATAGGGATC-TTTGA
* ** *
19716 TAAATGATCCAACAAAAAAATATTTGTTTATTGAGA
130 TAAATAATCCAGTAAAAAAATATTTGTTTATGGAGA
19752 GCGGGACCCA
Statistics
Matches: 1356, Mismatches: 108, Indels: 28
0.91 0.07 0.02
Matches are distributed among these distances:
435 403 0.30
436 32 0.02
437 155 0.11
438 217 0.16
439 268 0.20
440 281 0.21
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (437 bp):
ACACTTGAATCACCTTATCGGACAAGCAAAACAAAAAATAAAAGAATTAAAGTCGAAACGTTCAA
TCGTCCAACCCAGAATTTGTGATGGACTAAATAACATAAATTATAAAAGTATAGGGATCTTTGAT
AAATAATCCAGTAAAAAAATATTTGTTTATGGAGACCAAACATAAAAATTCATTCTTGAACCCTC
CACGAAACTCATTAATCAAATCCAGCTTTCAGGCCCTTAACGAAAGTCGTAGATCACACAATAAC
CTTTTAACCGACACTTGAACAACCTCAATCGAACAAGTGGACCGAAACTTATACAATATTAGATA
GACCGGCAATCGAGACCACAAAATTTCAGAAGTAATTTTTAGAATCAAAACATTAAAATTGGCTT
TTGAATCCTTCATGGAAGTTGTAGATCATGAAATTACCTTTTAATAA
Found at i:19528 original size:875 final size:871
Alignment explanation
Indices: 17834--19746 Score: 2928
Period size: 875 Copynumber: 2.2 Consensus size: 871
17824 AACATAAGAG
* ** * *
17834 TAGACACTTGAATCATCTTAATCGGACAAATAAAACAAAAAATACAAAAATAAAAGCCAAAGCG-
1 TAGACACTTGAATCACCTT-ATCGGACAAGCAAAACAAAAAATA-AAAAATTAAAGCGAAA-CGT
* * * * *
17898 TGAATCGTCCAAGACAT-AATTGTAAAGGATTAAATAACATAAATTTATAAAAGTAT-GAGGATC
63 TCAATCGTCC-AGTCATGAATTGTGATGGACTAAATAACATAAA-TTATAAAAGTATAG-GGATC
*
17961 ATTTGATAAATAATCTAGTAAAAAAATATTTGTTTATGCAGACCAAGCATAAAAATCCATTCTTG
125 ATTTGATAAATAATC-AGTAAAAAAATATTTGTTTATGCAGACCAAACATAAAAATCCATTCTTG
18026 AACCCTCCACGAAACTCATTAATCAAATCCAACTTTCAGGCCCTTAACGAAAGTCGTAAATCACA
189 AACCCTCCACGAAACTCATTAATCAAATCCAACTTTCAGGCCCTTAACGAAAGTCGTAAATCACA
* * *
18091 TAATAACCTTTTAACAGACACTTGAACAACCTCAATCGGACAAGTGGACTGAAACTTATACAATA
254 CAATAACCTTTTAACAGACACTTGAACAACCTCAATCGAACAAGTGGACCGAAACTTATACAATA
* *
18156 TAGATAGACCGGCAATCGAGAGCACAAAATTTCAGAAGTAATTTTTAGAATCAAAACATTAAAAT
319 TAGATAGACCAGCAATCGAGACCACAAAATTTCAGAAGTAATTTTTAGAATCAAAACATTAAAAT
* *
18221 TGGCTTTTGAGTCCTTCATGGAATTTGTAGATCATAAAATTACCTTTTAATAGAAACTTGAATCA
384 TGACTTTTGAGTCCTTCATGGAAGTTGTAGATCATAAAATTACCTTTTAATAGAAACTTGAATCA
* *
18286 CCTTGATCGGACAAGCAAATCAAAAAATAAAAGAATTAAAGTCGAAACGTTCAATCGTCCAACCC
449 CCTT-ATCGGACAAGCAAAACAAAAAATAAAAGAATTAAAGTCGAAACGTTCAATCGTACAACCC
* * * *
18351 AGAATTTGTGATGGACTAAATAGCATAAATTATAAAAGTGTATGGATCTTTTGATAAATAAACCA
513 AGAATTTGTGATGGACTAAATAACATAAATTATAAAAGTATAGGGATCTGTTGATAAATAAACCA
**
18416 GTAAAAAAATAATTGTTTATGGAGACCAAACATAAAAATTCATTCTTGAACCCTCTTCGAAACTC
578 GTAAAAAAATAATTGTTTATGGAGACCAAACATAAAAATTCATTCTTGAACCCTCCACGAAACTC
* *
18481 ATTAATCAAATCCAGCTTTCAGGCTCTTAAAGAAAGTCATAGATCACACAATAACTTTTTAACCG
643 ATTAATCAAATCCAGCTTTCAGGCCCTTAAAGAAAGTCATAGATCACACAATAACCTTTTAACCG
* * * * *
18546 ACACTTGAACAACCTCAATCGGATAAGTGGACCGAAACTTATACAATATCAGATAGATCGGCAAT
708 ACACTTGAACAACCTCAATCGAACAAGTGGACCAAAACTTATACAATATCAGATAGACCGGAAAT
* **
18611 CGAGAGCACAAAATTTCAGAAGTAATTTTTAGAATCAAAACATTAAAATTGGCTTTTGAATCCTT
773 CGAGACCACAAAATTTCAGAACCAATTTTTAGAATCAAAACATTAAAATTGGCTTTTGAATCCTT
18676 CATGGAAGTTGTAGATCATGAAATTACCTTTTAA
838 CATGGAAGTTGTAGATCATGAAATTACCTTTTAA
* *
18710 TAGACACTTGAATCACCTTGATCGGACAAGCAAAACGAAAAACAAAAGAATTAAAGTCGAAACGT
1 TAGACACTTGAATCACCTT-ATCGGACAAGCAAAACAAAAAATAAAA-AATTAAAG-CGAAACGT
* * *
18775 TCAATCGTCCAGTCTTGATATTGTGATGGACTAAATAGCATAAATTATAAAAGTATAGGGATCTT
63 TCAATCGTCCAGTCATGA-ATTGTGATGGACTAAATAACATAAATTATAAAAGTATAGGGATCAT
** *
18840 TTGATAAATAATACAGTAAAAAAAGTATTTGTTTATGGTGACCAAACATAAAAATTCATTCTTGA
127 TTGATAAATAAT-CAGTAAAAAAA-TATTTGTTTATGCAGACCAAACATAAAAATCCATTCTTGA
* * *
18905 ACCCTCCACGATACTCATTAATCAAATCCAGCTTTCAGGCCCTTAACGAAAGTCGTAGATCACAC
190 ACCCTCCACGAAACTCATTAATCAAATCCAACTTTCAGGCCCTTAACGAAAGTCGTAAATCACAC
*
18970 AATAACCTTTTAACCGACACTTGAACAACCTCAATCGAACAAGTGGACCGAAACTTATACAATAT
255 AATAACCTTTTAACAGACACTTGAACAACCTCAATCGAACAAGTGGACCGAAACTTATACAATA-
* *
19035 TAGATAGACCAGCAATCGAGACCATAAAATTTCAGAAGTATTTTTTAGAATCAAAACATTAAAAT
319 TAGATAGACCAGCAATCGAGACCACAAAATTTCAGAAGTAATTTTTAGAATCAAAACATTAAAAT
* *
19100 TGACTTTTTAGTCCTTCATGGAAGTTGTAGATCATGAAATTACCTTTTAATA-AACACTTGAATC
384 TGACTTTTGAGTCCTTCATGGAAGTTGTAGATCATAAAATTACCTTTTAATAGAA-ACTTGAATC
19164 ACC-T-TCGGACAAGCAAAACAAAAAATAAAAGAATTAAAGTCGAAACGTTCAATCGTACAACCC
448 ACCTTATCGGACAAGCAAAACAAAAAATAAAAGAATTAAAGTCGAAACGTTCAATCGTACAACCC
*
19227 AGAATTTGTGATGGACTAAATAACATAAATTATAAAAGTATAGGGATCTGTTGATAAATAATCCA
513 AGAATTTGTGATGGACTAAATAACATAAATTATAAAAGTATAGGGATCTGTTGATAAATAAACCA
* *
19292 GT-AAAAAATATTTGTTTATGGAGACCAAACATAAAAATTCATTCTTGAACCCTCCACGATACTC
578 GTAAAAAAATAATTGTTTATGGAGACCAAACATAAAAATTCATTCTTGAACCCTCCACGAAACTC
* * * *
19356 ATTAATCAAATCCAGCTTTCGGGCCCTTAACGAAAGTCGTAGATCACACAATAACCTTTTAACTG
643 ATTAATCAAATCCAGCTTTCAGGCCCTTAAAGAAAGTCATAGATCACACAATAACCTTTTAACCG
* *
19421 ACACTTGAACAATCTCAATCGAACAAGTGGACCAAAACTTATACAATATTAGATAGACCGGAAAT
708 ACACTTGAACAACCTCAATCGAACAAGTGGACCAAAACTTATACAATATCAGATAGACCGGAAAT
* * *
19486 CGAGACCACAAAATTTCAGAACCATTTTTTAGAATTAAAACATTAAAATTGGCTTTTGAATCTTT
773 CGAGACCACAAAATTTCAGAACCAATTTTTAGAATCAAAACATTAAAATTGGCTTTTGAATCCTT
19551 CATGGAAGTTGTAGATCATGAAATTACCTTTTAA
838 CATGGAAGTTGTAGATCATGAAATTACCTTTTAA
* *
19585 TAAACACTTGAATCACC-T-TCGGACAAGCAAAACAAAAAATAAAACAATTAAAGCCGAAAAGTT
1 TAGACACTTGAATCACCTTATCGGACAAGCAAAACAAAAAATAAAA-AATTAAAG-CGAAACGTT
* *
19648 CAATCGTCCAATCCA-GAATTTGTGATGGACTAAATAACATAAATTATAAAAGTATAGGGACCAT
64 CAATCGTCCAGT-CATGAA-TTGTGATGGACTAAATAACATAAATTATAAAAGTATAGGGATCAT
* **
19712 TTGATAAATGATCCAACAAAAAAATATTTGTTTAT
127 TTGATAAATAAT-CAGTAAAAAAATATTTGTTTAT
19747 TGAGAGCGGG
Statistics
Matches: 945, Mismatches: 80, Indels: 29
0.90 0.08 0.03
Matches are distributed among these distances:
871 12 0.01
872 115 0.12
873 1 0.00
874 1 0.00
875 287 0.30
876 170 0.18
877 54 0.06
878 184 0.19
879 121 0.13
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.27
Consensus pattern (871 bp):
TAGACACTTGAATCACCTTATCGGACAAGCAAAACAAAAAATAAAAAATTAAAGCGAAACGTTCA
ATCGTCCAGTCATGAATTGTGATGGACTAAATAACATAAATTATAAAAGTATAGGGATCATTTGA
TAAATAATCAGTAAAAAAATATTTGTTTATGCAGACCAAACATAAAAATCCATTCTTGAACCCTC
CACGAAACTCATTAATCAAATCCAACTTTCAGGCCCTTAACGAAAGTCGTAAATCACACAATAAC
CTTTTAACAGACACTTGAACAACCTCAATCGAACAAGTGGACCGAAACTTATACAATATAGATAG
ACCAGCAATCGAGACCACAAAATTTCAGAAGTAATTTTTAGAATCAAAACATTAAAATTGACTTT
TGAGTCCTTCATGGAAGTTGTAGATCATAAAATTACCTTTTAATAGAAACTTGAATCACCTTATC
GGACAAGCAAAACAAAAAATAAAAGAATTAAAGTCGAAACGTTCAATCGTACAACCCAGAATTTG
TGATGGACTAAATAACATAAATTATAAAAGTATAGGGATCTGTTGATAAATAAACCAGTAAAAAA
ATAATTGTTTATGGAGACCAAACATAAAAATTCATTCTTGAACCCTCCACGAAACTCATTAATCA
AATCCAGCTTTCAGGCCCTTAAAGAAAGTCATAGATCACACAATAACCTTTTAACCGACACTTGA
ACAACCTCAATCGAACAAGTGGACCAAAACTTATACAATATCAGATAGACCGGAAATCGAGACCA
CAAAATTTCAGAACCAATTTTTAGAATCAAAACATTAAAATTGGCTTTTGAATCCTTCATGGAAG
TTGTAGATCATGAAATTACCTTTTAA
Found at i:19954 original size:2 final size:2
Alignment explanation
Indices: 19947--19988 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
19937 TAAAATATTT
*
19947 TA TA TA TA TA TA TA TA -A AA TA TA -A TA TA -A TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19986 TA T
1 TA T
19989 TGTTATAGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
1 3 0.08
2 33 0.92
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:20756 original size:113 final size:113
Alignment explanation
Indices: 20558--20785 Score: 420
Period size: 113 Copynumber: 2.0 Consensus size: 113
20548 GAACACAATA
* *
20558 GAGATCATGGAGAGGATGTGCAAGGACTGCAAGGAAGCAAGGACAAGCTTGAAGATCATGGAGAT
1 GAGATCATGGAGAGGATGTGAAAGGACTACAAGGAAGCAAGGACAAGCTTGAAGATCATGGAGAT
*
20623 TGCGCACAACTTGTTCCAAGCACCAAGGAGATGCCAAAGATGCCATTT
66 TGCGCACAACTTGTTCCAAGCACCAAGGAGATGCCAAAGACGCCATTT
*
20671 GAGATCATGGAGAGGATGTGAAAGGGCTACAAGGAAGCAAGGACAAGCTTGAAGATCATGGAGAT
1 GAGATCATGGAGAGGATGTGAAAGGACTACAAGGAAGCAAGGACAAGCTTGAAGATCATGGAGAT
20736 TGCGCACAACTTGTTCCAAGCACCAAGGAGATGCCAAAGACGCCATTT
66 TGCGCACAACTTGTTCCAAGCACCAAGGAGATGCCAAAGACGCCATTT
20784 GA
1 GA
20786 TCCATTAAAG
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
113 111 1.00
ACGTcount: A:0.35, C:0.18, G:0.29, T:0.17
Consensus pattern (113 bp):
GAGATCATGGAGAGGATGTGAAAGGACTACAAGGAAGCAAGGACAAGCTTGAAGATCATGGAGAT
TGCGCACAACTTGTTCCAAGCACCAAGGAGATGCCAAAGACGCCATTT
Done.