Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015487.1 Corchorus capsularis cultivar CVL-1 contig15508, 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: 17040
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Found at i:7174 original size:332 final size:328
Alignment explanation
Indices: 6160--9312 Score: 2344
Period size: 332 Copynumber: 9.6 Consensus size: 328
6150 TTTTCAGTAA
* * ** * *
6160 AAAATACTCATAAAATATATATAATTCAACGCCAAACGGATTGGAGGATTTTTCACGCTTTTAAT
1 AAAATACTCATAAAATATATATAATTCAATGTCAAAAAGATTGAAGGACTTTTCACGCTTTTAAT
* * * * * * *
6225 ATCGTTTTTCATATTTTTC-AAAATTAATTTCTAATTAAATCAAAAGAAAATACAAATGCACATA
66 ATCGTTTTTCATATTTTTCTCAAA-TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATA
* * * * *
6289 AAAACAAATCCTTAAATCCAATATGCCCGAGATTTGATTAGATGAATAAAGATAATTCAAGGAGT
130 AAAACAAATCCTTAAATCTAATGTGGCTGAGATTTGATTAGATGAATAAAGATATTTCAAGGAGT
*
6354 CTAAT-GCCAAAAATCTTGCAAAA-TAGATCAGCCGTGACCCTGGAACGCGTTTTTAGCCAAAAA
195 CT--TGGCCAAAAATCATGCAAAACT-G---AG-CGTGACCCTGGAACGCGTTTTTAGCCAAAAA
* * * * *
6417 CCGCGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTTACCCGAAAGATATTTTCTT
253 CCGTGATGATTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGATCCGAAAGATATTTTCTC
6482 AATTTTTGGCT
318 AATTTTTGGCT
** ** * * * * * *
6493 AAAATACTCATAAAATATATATAATTTGACATCAAAAAGATTGAAGGGCATTTAATGCATCTAAT
1 AAAATACTCATAAAATATATATAATTCAATGTCAAAAAGATTGAAGGACTTTTCACGCTTTTAAT
* * * * *
6558 ATTGTTTTTCCTATTTTT-TCAAATTATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAA
66 ATCGTTTTTCATATTTTTCTCAAATAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAA
* * * * *
6622 AAACAAAT-CTTAAATTTAATGTGGCTGAAATTTGGTTAGATAAATATAGATATTTCAAGGAGTC
131 AAACAAATCCTTAAATCTAATGTGGCTGAGATTTGATTAGATGAATAAAGATATTTCAAGGAGTC
* ** ** * * * * * *
6686 TTGGCACAAAAATCAAGCAAAACTGAGCCCGACTATAGAACACGGTTTCAGGCGAAAACCGTGAT
196 TTGGC-CAAAAATCATGCAAAACTGAGCGTGACCCTGGAACGCGTTTTTAGCCAAAAACCGTGAT
* * * * * *
6751 GGTTAGTATATGATTTCGGTTAAAATTTTGCAAAAATTGA-CCCAAA-ATATTTTTCCTCGATTT
260 GATTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGATCCGAAAGATA-TTTT-CTCAATTT
* * *
6814 CTAGCG
323 TTGGCT
* * * * *
6820 AAAATACTCATAAAAAATATATAATTCATTGTCGAAAGGATTGGAGGACTTTTCACGCTTTTAAT
1 AAAATACTCATAAAATATATATAATTCAATGTCAAAAAGATTGAAGGACTTTTCACGCTTTTAAT
* * * *
6885 ATCGTTTTTCATATTTTTTCTCAAATAATTTCTTATTAAATCAAAACAAGATTCTGACT-CACAT
66 ATCGTTTTTCATA-TTTTTCTCAAATAATTTCTAATTAAATCGAAACAAGATTCAGA-TGCTCAT
* * *
6949 AAAAACAAATCCTTAAATCTAATGTGCCTGAGATTTGATTAGATTAATAAAGATACTTCAAGGAG
129 AAAAACAAATCCTTAAATCTAATGTGGCTGAGATTTGATTAGATGAATAAAGATATTTCAAGGAG
* * ** * * *
7014 TCTCGGACCAAAAAATCATGCAAAACGGAGACGTGACCCTAAAACGCATTTTTAGCAAAAAACTG
194 TCTTGG-CC-AAAAATCATGCAAAACTGAG-CGTGACCCTGGAACGCGTTTTTAGCCAAAAACCG
* * * *
7079 TAATGATTAGTAAACGATTTCGGCTACAATTTTGCAAAAATTCATCCGAAAGATATTTTCTCAAT
256 TGATGATTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGATCCGAAAGATATTTTCTCAAT
7144 TTTTGGCT
321 TTTTGGCT
* * * * *
7152 GAAATACTCATAATATATATATATATATATATAATTTGACATAAAAAAGATTGAATTG-CTTTTA
1 AAAATACTCATAA-A-ATATATATA-AT-T-CAA--TG---TCAAAAAGATTGAA-GGACTTTTC
* *
7216 ACGCTTCTAATATTGTTTTTCATA-TTTT-TCAAAGTAATTTCTAATTAAATCGAAACAAGATTC
55 ACGCTTTTAATATCGTTTTTCATATTTTTCTCAAA-TAATTTCTAATTAAATCGAAACAAGATTC
* * *
7279 AGATGCTCATAAAAACAAATCCTTAAATCTAATGTGGCTGAGATTTGGTGAGATGAATATAGATA
119 AGATGCTCATAAAAACAAATCCTTAAATCTAATGTGGCTGAGATTTGATTAGATGAATAAAGATA
* * *
7344 TTTCAAGGAGTCTTGGTACCAAAAATCATGCAAAACTGAATCG-AACCCTGGAACGCGGTTTTAG
184 TTTCAAGGAGTCTTGG--CCAAAAATCATGCAAAACTG-AGCGTGACCCTGGAACGCGTTTTTAG
*** * * * * *
7408 TTGAAAACCGTGATGATTAGTTCATGATTTCGACTAAAATTTTGCAAAAATTG-GCTCGAAATAT
246 CCAAAAACCGTGATGATTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGATC-CGAAAGAT
* * * *
7472 -TTTTCTTCGATTTCTAGCA
310 ATTTTC-TCAATTTTTGGCT
*** * * * *
7491 AAAATACTCATAAAA-ATATATAATTCAACACCCAAAA-ATTGAAAGCCTTTTTCACTCTTTTAA
1 AAAATACTCATAAAATATATATAATTCAATGTCAAAAAGATTGAAGGAC-TTTTCACGCTTTTAA
* *
7554 TATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATA
65 TATCGTTTTTCATATTTTTCTCAAATAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATA
* *
7619 AAAACAAATCATTAAAT-TCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAG
130 AAAACAAATCCTTAAATCT-AATGTGGCTGAGATTTGATTAGATGAATAAAGATATTTCAAGGAG
* * * * ** *
7683 TCTCGGCACCAAAAATCATGCAAAACTGAGTCG-GGCCCCGGAATGCGTTTTTAGCTGAAAATCG
194 TCTTGG--CCAAAAATCATGCAAAACTGAG-CGTGACCCTGGAACGCGTTTTTAGCCAAAAACCG
* *
7747 TGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGATCCGAAAGATTTTTTTCTTCA
256 TGATGATTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGATCCGAAAGA-TATTTTC-TCA
* *
7812 ATTGTTGGTT
319 ATTTTTGGCT
* * * *
7822 ACAATACTCATAAAATATATATAATTTAATGTCAAAAAGATATG-AGAACTTTTCATGCTTTTAA
1 AAAATACTCATAAAATATATATAATTCAATGTCAAAAAGAT-TGAAGGACTTTTCACGCTTTTAA
* * * * * *
7886 TAACGTTTTTCATATTTTTCTGAATTAATTTCTAGTTAAATTGAGACAAGATTC-GTATGCTCAT
65 TATCGTTTTTCATATTTTTCTCAAATAATTTCTAATTAAATCGAAACAAGATTCAG-ATGCTCAT
* * * * * * * * *
7950 AAAAACAAATTCTTGAATCCAATGTAGCTGAGATTAGCTTAAATGAA-AATGGAT-TTCTCAAAG
129 AAAAACAAATCCTTAAATCTAATGTGGCTGAGATTTGATTAGATGAATAA-AGATATT-TCAAGG
* * *
8013 AGTCTTGGCGTCAAAAATCATGCAAAACCT-AGC-TAGGGCCCCGGAATGCGTTTTTAGCCAAAA
192 AGTCTTGGC--CAAAAATCATGCAAAA-CTGAGCGT--GACCCTGGAACGCGTTTTTAGCCAAAA
* * * * * * *
8076 ACAGTAATGATTATTACACGATTTCGGCTAGAAGTTTACAAAAATTGA-CTCGAAAGTTATTTTC
252 ACCGTGATGATTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGATC-CGAAAGATATTTTC
** *
8140 TCAATTTTTACCC
316 TCAATTTTTGGCT
* ** * *
8153 ACAATACTCATAAAA-AGTATATAATTCAATG-CTAAAAAGATTGAAGGGTTTTTCATGCTTCTA
1 AAAATACTCATAAAATA-TATATAATTCAATGTC-AAAAAGATTGAAGGACTTTTCACGCTTTTA
* * * * *
8216 ATATTGTTTTTCCTATTATTT-TCCGAACTAATTTCTAATTAAATCGAAACATGATTCAGATGTT
64 ATATCGTTTTTCATATT-TTTCT-C-AAATAATTTCTAATTAAATCGAAACAAGATTCAGATGCT
** *** * * * **
8280 TGT-TTCACAAATCCTTAAAT-TCAATGTGGTTGAGATATGGTTAGATGAATGTAGATATTTCAA
126 CATAAAAACAAATCCTTAAATCT-AATGTGGCTGAGATTTGATTAGATGAATAAAGATATTTCAA
* * * * * * *
8343 GGAGTCTCTGCGCAAAAAATCATGCAATATTAAACCAG-GGCCCCGGAACGCGTTTTTAGCCAAA
190 GGAGTCT-TG-GCCAAAAATCATGCAAAACT-GAGC-GTGACCCTGGAACGCGTTTTTAGCCAAA
* * * * ** * *
8407 AAACGGGATTTCGACTAACATACACGATTGGGGCTAATATTTTGCAAAAATTGA-CCAGAAATAT
251 AACCGTGA--T-GA-TTA-GTACACGATTTCGGCTAAAATTTTGCAAAAATTGATCC-GAAAGAT
* *
8471 -TTTTCCTTAATTTTTGTCT
310 ATTTT-CTCAATTTTTGGCT
* * * * *
8490 AAAATACTCAT-AAATATATATAACTCAACT-CCAAAATGATTGGAGGACTTTTCACACTTTTAA
1 AAAATACTCATAAAATATATATAATTCAA-TGTCAAAAAGATTGAAGGACTTTTCACGCTTTTAA
* * * * * ** *
8553 TATCATTTTTCATATTTTTCTGAATTAATTTATAATTAAATCGAAACAAGATTAAGATGCTTGTG
65 TATCGTTTTTCATATTTTTCTCAAATAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATA
* * **
8618 AAAACAAATCCTTAAATGTAATGTGGCTG-G----GATT---TAAAT-AA-ATATTTTGAGGAGT
130 AAAACAAATCCTTAAATCTAATGTGGCTGAGATTTGATTAGATGAATAAAGATATTTCAAGGAGT
* * * * ** * *
8673 CTCGATGCTAAAAATCATACAAAACTGAGACGGGACACC-AAAACGCGTTTTTAGCAAAAAACCA
195 CTTG--GCCAAAAATCATGCAAAACTGAG-CGTGAC-CCTGGAACGCGTTTTTAGCCAAAAACCG
* * * ** * * **
8737 TGATGATTAGTACACTATTTCGG-AAATAATTTTGCAAAAAATGAT-AAAAAAAAATACTCTCAA
256 TGATGATTAGTACACGATTTCGGCTAA-AATTTTGCAAAAATTGATCCGAAAGATATTTTCTCAA
* *
8800 TTTTTAGCC
320 TTTTTGGCT
* * ** * * * * *
8809 ACAATATTCATAAAA-ATTATATAATTTTATGCCAAAAAAATAT-AAGGGCTTTTCATGCTTCTA
1 AAAATACTCATAAAATA-TATATAATTCAATGTCAAAAAGAT-TGAAGGACTTTTCACGCTTTTA
* * ** * * *
8872 ATATCGTTTTTTCTATTTTTTTTTC--CGAA--T-TAATGAAAACGAAACATGATTCAGATG-T-
64 ATATCG-TTTTTC-ATATTTTTCTCAAATAATTTCTAATTAAATCGAAACAAGATTCAGATGCTC
* * * * * * *
8930 -T---------T-GTAAAAAC-AA--TGGTTGAGATTCGGTTAGATGAATATAGATATTTCAAGG
127 ATAAAAACAAATCCTTAAATCTAATGTGGCTGAGATTTGATTAGATGAATAAAGATATTTCAAGG
* * * * * * *
8981 AGT-TTCGACGCCAAAAACCATTCAATATTGAAC-TGGACACC-GGAACGCGTTTTCAGCAAAAA
192 AGTCTT-G--GCCAAAAATCATGCAAAACTGAGCGT-GAC-CCTGGAACGCGTTTTTAGCCAAAA
** * * * * *
9043 AATGTGATGATTATTACACGATTTCGGCTAAAATTTTGCAAACATTGACCCGAAAGATATCTCCT
252 ACCGTGATGATTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGATCCGAAAGATATTTTCT
* *
9108 CATTTTTTAG-T
317 CAATTTTTGGCT
* ** *
9119 CATAATACTCATAAAA-ATTATATAATTCAATG-CAAAAAAGATTGAAGGGTTTTTCACACTTTT
1 -AAAATACTCATAAAATA-TATATAATTCAATGTC-AAAAAGATTGAAGGACTTTTCACGCTTTT
* * * *
9182 AATATCGTTTTTCGTATTTTT-T-GAATCAATTTCTAATTAAATCGAAACAAGATTTAAATGCTC
63 AATATCGTTTTTCATATTTTTCTCAAAT-AATTTCTAATTAAATCGAAACAAGATTCAGATGCTC
* * * * *
9245 ATAAAAATAAATCCTTAAATGC-AATGTGGCTAAGATTTCATTAGATGAATATAGATGTTTCAAG
127 ATAAAAACAAATCCTTAAAT-CTAATGTGGCTGAGATTTGATTAGATGAATAAAGATATTTCAAG
9309 GAGT
191 GAGT
9313 GCCGGGGCTC
Statistics
Matches: 2232, Mismatches: 452, Indels: 276
0.75 0.15 0.09
Matches are distributed among these distances:
301 5 0.00
302 1 0.00
303 2 0.00
304 4 0.00
305 1 0.00
306 3 0.00
308 1 0.00
309 10 0.00
310 74 0.03
311 106 0.05
312 1 0.00
313 22 0.01
314 2 0.00
316 2 0.00
317 23 0.01
318 1 0.00
319 27 0.01
320 69 0.03
321 9 0.00
322 10 0.00
323 1 0.00
324 3 0.00
325 59 0.03
326 17 0.01
327 147 0.07
328 38 0.02
329 283 0.13
330 69 0.03
331 188 0.08
332 379 0.17
333 197 0.09
334 56 0.03
335 32 0.01
336 68 0.03
337 59 0.03
338 7 0.00
339 94 0.04
340 120 0.05
341 4 0.00
342 37 0.02
343 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (328 bp):
AAAATACTCATAAAATATATATAATTCAATGTCAAAAAGATTGAAGGACTTTTCACGCTTTTAAT
ATCGTTTTTCATATTTTTCTCAAATAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAA
AAACAAATCCTTAAATCTAATGTGGCTGAGATTTGATTAGATGAATAAAGATATTTCAAGGAGTC
TTGGCCAAAAATCATGCAAAACTGAGCGTGACCCTGGAACGCGTTTTTAGCCAAAAACCGTGATG
ATTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGATCCGAAAGATATTTTCTCAATTTTTG
GCT
Found at i:7585 original size:669 final size:659
Alignment explanation
Indices: 6159--8040 Score: 2175
Period size: 669 Copynumber: 2.8 Consensus size: 659
6149 ATTTTCAGTA
* *
6159 AAAAATACTCATAAAATATATATAATTCAACGCCAAACGGATTGGAGGA-TTTTTCACGCTTTTA
1 AAAAATACTCATAAAA-ATATATAATTCAACCCCAAA-GGATT-GAAGACTTTTTCACGCTTTTA
* * * * *
6223 ATATCGTTTTTCATATTTTTCAAAATTAATTTCTAATTAAATCAAAAGAAAATACAAATGCACAT
63 ATATCGTTTTTCATATTTTTCTAAATTAATTTCTAATTAAATCAAAACAAGATTC-GATGCACAT
* * *
6288 AAAAACAAATCCTTAAATCCAATATGCCCGAGATTTGATTAGATGAATAAAGATAATTCAAGGAG
127 AAAAACAAATCCTTAAATCTAATGTGCCTGAGATTTGATTAGATGAATAAAGATAATTCAAGGAG
** * * * * *
6353 TCTAATG-CCAAAAATCTTGCAAAATAGATCAGCCGTGACCCTGGAACGCGTTTTTAGCCAAAAA
192 TCT-CGGACCAAAAATCATGCAAAA-CG--GAGACGTGACCCTGGAACGCGTTTTTAGCAAAAAA
* * * * *
6417 CCGCGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTTACCCGAAAGATATTTTCTT
253 CTGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTCATCCGAAAGATATTTTCTC
6482 AATTTTTGGCTAAAATACTC-----ATA-A-A-ATATATATAATTTGACATCAAAAAGATTGAAG
318 AATTTTTGGCTAAAATACTCATAAAATATATATATATATATAATTTGACATCAAAAAGATTGAA-
* * * *
6539 GGCATTTAATGCATCTAATATTGTTTTTCCTATTTTTTCAAATTATTTCTAATTAAATCGAAACA
382 -GCTTTTAATGCTTCTAATATTGTTTTTCATA-TTTTTCAAATAATTTCTAATTAAATCGAAACA
* * * * *
6604 AGATTCAGATACTCGTAAAAACAAATCTTAAATTTAATGTGGCTGAAATTTGGTTAGATAAATAT
445 AGATTCAGATGCTCATAAAAACAAATCTTAAATCTAATGTGGCTGAGATTTGGTTAGATGAATAT
* * *
6669 AGATATTTCAAGGAGTCTTGGCACAAAAATCAAGCAAAACTGAGCCCGACTATAGAACACGGTTT
510 AGATATTTCAAGGAGTCTTGGCACAAAAATCATGCAAAACTGAGACCGACCATAGAACACGGTTT
* **
6734 CAGGCGAAAACCGTGATGGTTAGTATATGATTTCGGTTAAAATTTTGCAAAAATTGACCCAAAAT
575 CAGGCGAAAACCGTGATGATTAGTATATGATTTCGACTAAAATTTTGCAAAAATTGACCCAAAAT
6799 ATTTTTCCTCGATTTCTAGC
640 ATTTTTCCTCGATTTCTAGC
* *** * *
6819 GAAAATACTCATAAAAAATATATAATTCATTGTCGAAAGGATTGGAGGAC-TTTTCACGCTTTTA
1 AAAAATACTCAT-AAAAATATATAATTCA-ACCCCAAAGGATT-GAAGACTTTTTCACGCTTTTA
*
6883 ATATCGTTTTTCATATTTTTTCTCAAA-TAATTTCTTATTAAATCAAAACAAGATTCTGACT-CA
63 ATATCGTTTTTCATA-TTTTTCT-AAATTAATTTCTAATTAAATCAAAACAAGATTC-GA-TGCA
* *
6946 CATAAAAACAAATCCTTAAATCTAATGTGCCTGAGATTTGATTAGATTAATAAAGATACTTCAAG
124 CATAAAAACAAATCCTTAAATCTAATGTGCCTGAGATTTGATTAGATGAATAAAGATAATTCAAG
** *
7011 GAGTCTCGGACCAAAAAATCATGCAAAACGGAGACGTGACCCTAAAACGCATTTTTAGCAAAAAA
189 GAGTCTCGGACC-AAAAATCATGCAAAACGGAGACGTGACCCTGGAACGCGTTTTTAGCAAAAAA
* * * *
7076 CTGTAATGATTAGTAAACGATTTCGGCTACAATTTTGCAAAAATTCATCCGAAAGATATTTTCTC
253 CTGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTCATCCGAAAGATATTTTCTC
* *
7141 AATTTTTGGCTGAAATACTCATAATATATATATATATATATATAATTTGACATAAAAAAGATTGA
318 AATTTTTGGCTAAAATACTCATAA-A-ATATATATATATATATAATTTGACATCAAAAAGATTGA
*
7206 ATTGCTTTTAACGCTTCTAATATTGTTTTTCATATTTTTCAAAGTAATTTCTAATTAAATCGAAA
381 A--GCTTTTAATGCTTCTAATATTGTTTTTCATATTTTTCAAA-TAATTTCTAATTAAATCGAAA
*
7271 CAAGATTCAGATGCTCATAAAAACAAATCCTTAAATCTAATGTGGCTGAGATTTGGTGAGATGAA
443 CAAGATTCAGATGCTCATAAAAACAAAT-CTTAAATCTAATGTGGCTGAGATTTGGTTAGATGAA
* * * * *
7336 TATAGATATTTCAAGGAGTCTTGGTACCAAAAATCATGCAAAACTGA-ATCGAACCCTGGAACGC
507 TATAGATATTTCAAGGAGTCTTGGCA-CAAAAATCATGCAAAACTGAGACCG-ACCATAGAACAC
* ** * *
7400 GGTTTTAGTTGAAAACCGTGATGATTAGT-TCATGATTTCGACTAAAATTTTGCAAAAATTGGCT
570 GGTTTCAGGCGAAAACCGTGATGATTAGTAT-ATGATTTCGACTAAAATTTTGCAAAAATTGACC
* *
7464 CGAAATATTTTTCTTCGATTTCTAGC
634 CAAAATATTTTTCCTCGATTTCTAGC
* * *
7490 AAAAATACTCATAAAAATATATAATTCAACACCCAAA-AATTGAAAGCCTTTTTCACTCTTTTAA
1 AAAAATACTCATAAAAATATATAATTCAAC-CCCAAAGGATTG-AAGACTTTTTCACGCTTTTAA
* * *
7554 TATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATA
64 TATCGTTTTTCATATTTTTCTAAATTAATTTCTAATTAAATCAAAACAAGATTC-GATGCACATA
* * * *
7619 AAAACAAATCATTAAAT-TCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAG
128 AAAACAAATCCTTAAATCT-AATGTGCCTGAGATTTGATTAGATGAATAAAGATAATTCAAGGAG
* * * * * **
7683 TCTCGGCACCAAAAATCATGCAAAACTGAGTCG-GGCCCCGGAATGCGTTTTTAGCTGAAAA-TC
192 TCTCGG-ACCAAAAATCATGCAAAACGGAGACGTGACCCTGGAACGCGTTTTTAGCAAAAAACT-
* *
7746 GTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGATCCGAAAGATTTTTTTCTTC
255 GTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTCATCCGAAAGA-TATTTTC-TC
* * *
7811 AATTGTTGGTTACAATACTCATAAAATATATATA-AT-T-TAA--TG---TCAAAAAGATATGAG
318 AATTTTTGGCTAAAATACTCATAAAATATATATATATATATAATTTGACATCAAAAAGAT-TGA-
* * * ** * * * *
7868 AACTTTTCATGCTTTTAATAACGTTTTTCATATTTTTCTGAATTAATTTCTAGTTAAATTGAGAC
381 AGCTTTTAATGCTTCTAATATTGTTTTTCATATTTTTC--AAATAATTTCTAATTAAATCGAAAC
* * * * * *
7933 AAGATTC-GTATGCTCATAAAAACAAATTCTTGAATCCAATGTAGCTGAGATTAGCTTAAATGAA
444 AAGATTCAG-ATGCTCATAAAAACAAA-TCTTAAATCTAATGTGGCTGAGATTTGGTTAGATGAA
* * * *
7997 AATGGAT-TTCTCAAAGAGTCTTGGCGTCAAAAATCATGCAAAAC
507 TATAGATATT-TCAAGGAGTCTTGGC-ACAAAAATCATGCAAAAC
8041 CTAGCTAGGG
Statistics
Matches: 1050, Mismatches: 131, Indels: 81
0.83 0.10 0.06
Matches are distributed among these distances:
659 104 0.10
660 107 0.10
661 221 0.21
662 22 0.02
663 2 0.00
665 3 0.00
666 4 0.00
667 4 0.00
668 93 0.09
669 241 0.23
670 133 0.13
671 116 0.11
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (659 bp):
AAAAATACTCATAAAAATATATAATTCAACCCCAAAGGATTGAAGACTTTTTCACGCTTTTAATA
TCGTTTTTCATATTTTTCTAAATTAATTTCTAATTAAATCAAAACAAGATTCGATGCACATAAAA
ACAAATCCTTAAATCTAATGTGCCTGAGATTTGATTAGATGAATAAAGATAATTCAAGGAGTCTC
GGACCAAAAATCATGCAAAACGGAGACGTGACCCTGGAACGCGTTTTTAGCAAAAAACTGTGATG
GTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTCATCCGAAAGATATTTTCTCAATTTTTG
GCTAAAATACTCATAAAATATATATATATATATAATTTGACATCAAAAAGATTGAAGCTTTTAAT
GCTTCTAATATTGTTTTTCATATTTTTCAAATAATTTCTAATTAAATCGAAACAAGATTCAGATG
CTCATAAAAACAAATCTTAAATCTAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAA
GGAGTCTTGGCACAAAAATCATGCAAAACTGAGACCGACCATAGAACACGGTTTCAGGCGAAAAC
CGTGATGATTAGTATATGATTTCGACTAAAATTTTGCAAAAATTGACCCAAAATATTTTTCCTCG
ATTTCTAGC
Found at i:9475 original size:300 final size:303
Alignment explanation
Indices: 9024--9596 Score: 739
Period size: 301 Copynumber: 1.9 Consensus size: 303
9014 TGGACACCGG
** * * *
9024 AACGCGTTTTCAGCAAAAAAATGTGATGATTATTACACGATTTCGGCTAAAATTTTGCAAACATT
1 AACGCGTTTTCAGCAAAAAAATGTGATGATTAGAACACGATTTCGGCTAAAATCTTGCAAAAAAT
* * * * *
9089 GACCCGAAAGATATCTCCTCATTTTTTAGTCATAATACTCATAAAAATTATATAATTCAATGCAA
66 GACCCGAAAGATATCCCCTCATTTATGAGTCAAAATACTCATAAAAATTATATAATTCAAGGCAA
*
9154 AAAAGATTGAAGGGTTTTTCACACTTTTAATATCGTTTTTCGTAT-TTTT-TGAATCAATTTCTA
131 AAAAGATTGAAGGGTTTTTCACACTTTTAATATCGTTTTT-GTATATTTTCTAAATCAATTTCTA
* *
9217 ATTAAATCGAAACAAGATTTAAATGCTCATAAAAATAAATCCTTAAATGCAATGTGGCTAAGATT
195 ATTAAATCGAAACAAGATTTAAATGCTCATAAAAACAAATCCTTAAATCCAATGTGGCTAAGATT
9282 TCATTAGATGAATATAGATGTTTCAAGGAGTGCCGGGGCTCTGA
260 TCATTAGATGAATATAGATGTTTCAAGGAGTGCCGGGGCTCTGA
* * *
9326 AACGCGTTTTTAGC-CAAAAATCGTGATGATTAGAACACGATTTTGGCTAAAA-CTTGCAAAAAA
1 AACGCGTTTTCAGCAAAAAAAT-GTGATGATTAGAACACGATTTCGGCTAAAATCTTGCAAAAAA
** * * *
9389 TGACCCGACAATTTTTCCCCT-ATTTATGGGT-AAAATACTCAT-AAAATATATATAATTTAAGG
65 TGACCCGA-AAGATATCCCCTCATTTATGAGTCAAAATACTCATAAAAAT-TATATAATTCAAGG
* * * *
9451 CCAAAAAGATTGGAGGAG-TTTTCACACTTTTAATATCGTTTTTTTATATTTTCTAAATTAATTT
128 CAAAAAAGATTGAAGG-GTTTTTCACACTTTTAATATCGTTTTTGTATATTTTCTAAATCAATTT
* ** ** * *
9515 CTAATTAAATCGAAACAAGATTTAGATGCTTGTAAAAACAAATTTTTAAATCCAATGTGTCTGAG
192 CTAATTAAATCGAAACAAGATTTAAATGCTCATAAAAACAAATCCTTAAATCCAATGTGGCTAAG
* *
9580 ATTTGATTAGATTAATA
257 ATTTCATTAGATGAATA
9597 CGGATATCTT
Statistics
Matches: 231, Mismatches: 34, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
299 8 0.03
300 65 0.28
301 110 0.48
302 48 0.21
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (303 bp):
AACGCGTTTTCAGCAAAAAAATGTGATGATTAGAACACGATTTCGGCTAAAATCTTGCAAAAAAT
GACCCGAAAGATATCCCCTCATTTATGAGTCAAAATACTCATAAAAATTATATAATTCAAGGCAA
AAAAGATTGAAGGGTTTTTCACACTTTTAATATCGTTTTTGTATATTTTCTAAATCAATTTCTAA
TTAAATCGAAACAAGATTTAAATGCTCATAAAAACAAATCCTTAAATCCAATGTGGCTAAGATTT
CATTAGATGAATATAGATGTTTCAAGGAGTGCCGGGGCTCTGA
Found at i:10129 original size:12 final size:12
Alignment explanation
Indices: 10112--10136 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
10102 CAAGGAAAAT
10112 TAATTAAGAAAG
1 TAATTAAGAAAG
10124 TAATTAAGAAAG
1 TAATTAAGAAAG
10136 T
1 T
10137 TAAAGAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.16, T:0.28
Consensus pattern (12 bp):
TAATTAAGAAAG
Found at i:11468 original size:19 final size:18
Alignment explanation
Indices: 11435--11470 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
11425 TTGAAATAAT
11435 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
11453 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
11471 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:13205 original size:28 final size:29
Alignment explanation
Indices: 13152--13230 Score: 133
Period size: 28 Copynumber: 2.8 Consensus size: 29
13142 ACACAAAACG
13152 GCCAAATAAGCCCCTGAACTCTAATTGCA
1 GCCAAATAAGCCCCTGAACTCTAATTGCA
*
13181 GCCAAATAAG-CCATGAACTCTAATTGCA
1 GCCAAATAAGCCCCTGAACTCTAATTGCA
*
13209 GCCAAGTAAGCCCCTGAACTCT
1 GCCAAATAAGCCCCTGAACTCT
13231 TAAAAAAGGC
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
28 26 0.57
29 20 0.43
ACGTcount: A:0.34, C:0.30, G:0.15, T:0.20
Consensus pattern (29 bp):
GCCAAATAAGCCCCTGAACTCTAATTGCA
Found at i:16481 original size:6 final size:6
Alignment explanation
Indices: 16470--16543 Score: 84
Period size: 6 Copynumber: 12.3 Consensus size: 6
16460 CAGCCGCACG
16470 ATCTAT ATC--T ATCTAT A-CTAT AATACTATAT ATCTAT ATCTAT ATCTAT
1 ATCTAT ATCTAT ATCTAT ATCTAT -AT-CT--AT ATCTAT ATCTAT ATCTAT
16519 ATCTAT ATCTAT ATCTAT A-CTAT AT
1 ATCTAT ATCTAT ATCTAT ATCTAT AT
16544 TAAAAAGTAC
Statistics
Matches: 60, Mismatches: 0, Indels: 16
0.79 0.00 0.21
Matches are distributed among these distances:
4 4 0.07
5 9 0.15
6 39 0.65
8 4 0.07
9 2 0.03
10 2 0.03
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.47
Consensus pattern (6 bp):
ATCTAT
Found at i:16713 original size:70 final size:70
Alignment explanation
Indices: 16631--16781 Score: 223
Period size: 70 Copynumber: 2.2 Consensus size: 70
16621 TTGTTTAGGT
* * * *
16631 TTTTA-TAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCTTTATAATT
1 TTTTACTA-TTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATATAATATCCTTATAACT
*
16695 ATTTTA
65 ATTATA
*
16701 TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATATAATATCCTTATAACTA
16766 TTATA
66 TTATA
*
16771 TTTTACCATTT
1 TTTTACTATTT
16782 CACTATTTTA
Statistics
Matches: 73, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
70 71 0.97
71 2 0.03
ACGTcount: A:0.37, C:0.12, G:0.01, T:0.50
Consensus pattern (70 bp):
TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATATAATATCCTTATAACTA
TTATA
Done.