Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017822.1 Corchorus olitorius cultivar O-4 contig17855, 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: 3619
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Found at i:10 original size:2 final size:2
Alignment explanation
Indices: 4--45 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1 ATG
4 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
46 TAAGGAGTCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1347 original size:330 final size:328
Alignment explanation
Indices: 131--2653 Score: 2160
Period size: 330 Copynumber: 7.7 Consensus size: 328
121 GTTGGTATAT
* ** ** *
131 GATTTCGGCTAAAAATTTGCAAAAATTGATC-C-AATTTTTTTTTTCATTTTTTAGCCAAAATAC
1 GATTTCGGCT-AAATTTTGCAAAAATTGA-CACGAAAGTTTTTCCTCAATTTTTAGCCAAAATAC
* * **
194 TCATAAAAA-ATATATAATTCAACGCCAAAAAAATCGAAGGGTTTTTCACGCTTCTAATATCGTT
64 TCATAAAAATATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTCTAATATCGTT
* * * * * * * *
258 TTGCTTATTCTTT-CAAATTAAATTCTAATTAAATTGAAACATGATTGAAATGCTCTCGT-AAAA
129 TTTCCTATT-TTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATG--CTCGTAAAAA
* * *
321 CAAATCCTTAAATCCAATGTGGCTAAGATTTGGTTAGATGAATAT--ATATTTCAAGGAGTGTTG
191 CAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTG
* * * * *
384 CCACAAAAAATCATGCAAAACTGACCCGGGGCCCCAGAATGCGTTTTTAGCCAAATAACCGTGAT
256 GCGCCAAAAATCATGCAAAACTGAGCCGGGG--CCAGAACGCGTTTTTAGCCAAA-AACCGTGAT
449 G--T--TACAC
318 GATTAGTACAC
* * *
456 AATTTCGGCTAAAATTTTGCAAAAATTGACCACGAATA-TTTTTCCTTAATTTTTAGCCAGAATA
1 GATTTCGGCT-AAATTTTGCAAAAATTGA-CACGAA-AGTTTTTCCTCAATTTTTAGCCAAAATA
* * * * * * *
520 CTCAT-AGAATATATATAATTAAAAGCAAAAAAGATTGGAGGACTCTTCACGCTTTTAATATCGT
63 CTCATAAAAATATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTCTAATATCGT
* * * * * *
584 TTGTCTTATTTTTCTGAATTAACTTCTAATTAAATCAAAACAAGATT-ATGATGCTTGTAAAAAC
128 TTTTCCTATTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCA-GATGCTCGTAAAAAC
* * * *
648 CAATCCTTAAATTCAATGTGGCTGAGATTTGATTAGATGAATATAAATATTTCAAGGAGTCTCGG
192 AAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGG
* * *
713 CGCCAAAAATCATGCAAAACTAAGCTGGGGTCTC-GAAACCCGTTTTTAGCCAAAAACCGTGAT-
257 CGCCAAAAATCATGCAAAACTGAGCCGGGG-C-CAG-AACGCGTTTTTAGCCAAAAACCGTGATG
776 AGTTAGTACAC
319 A-TTAGTACAC
* * ** * **
787 GATTTCGGCTAAA-ATGGC-----CCGA-A--AAA-TTTTTCCGTCAAATTTT-GGAAATAATAC
1 GATTTCGGCTAAATTTTGCAAAAATTGACACGAAAGTTTTTCC-TCAATTTTTAGCCAA-AATAC
* * * * *
841 TCAT-AAAATATATATAATTTAACGTCAAAAAGATTGGAGGACTTTTCACGCTTTTATTATCGTT
64 TCATAAAAATATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTCTAATATCGTT
* * *
905 TTTCATATTTTT-TGAATTAATTTCTAATTAAATCG-AACAAGAGTCAGATGCTCGTAAAAACAA
129 TTTCCTATTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAA
* * * * * * * * *
968 ATTCTTAAATCCAATGTAGTTGAGATTTGATTTGATGAGTATGGATATTTTAAAGAGTCTTGACG
194 ATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCG
* * * * *
1033 CCAAAAATCATGCAAAACTTAGTCGGGGCCTGAACGCGTTTTTAGCGAAAAACCGTGATGATTAT
259 CCAAAAATCATGCAAAACTGAGCCGGGGCCAGAACGCGTTTTTAGCCAAAAACCGTGATGATTAG
1098 TACAC
324 TACAC
** * * *
1103 GATTTCGGCTAGAATTTTGCAAAAATTGAGTCGAAAGTTATTCACTCAATTTTTAGCCATAATAT
1 GATTTCGGCTA-AATTTTGCAAAAATTGACACGAAAGTTTTTC-CTCAATTTTTAGCCAAAATAC
* * * *
1168 TCATAAAAAT-TATATAATTCAATGCCAAAAAGATTGAAGGGCTTTTCATGCTTCTGATATCGTT
64 TCATAAAAATATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTCTAATATCGTT
* * * ***
1232 TTTCCTATTATTTTCCGAATTAATTTCTAATTAAATCAAAACATGATTCAGATGCTTG-ATTTAC
129 TTTCCTA-T-TTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAC
* * * * * * * *
1296 AAATCCTTAAATCCATTGTGGATGAGATTTGTTTAGATTACTATAGATATTTCAAAGTGTCTCGG
192 AAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGG
* * * * * ** * *
1361 CGCAAAAAATCATGCAATACTGAACCGGGACCCCGGAACGATTTTTTTGCAAAAAACCGTGATTT
257 CGCCAAAAATCATGCAAAACTGAGCCGGG--GCCAGAACGCGTTTTTAGCCAAAAACCGTGA--T
*
1426 CGATTAACGCACAC
318 -GATT-A-GTACAC
*
1440 GATTTCGGCTAATATTTTGCAAAAATTGACAAAC-AATAG-TTTTCCTCAATTTTT-GTCTAAAA
1 GATTTCGGCTAA-ATTTTGCAAAAATTGAC--ACGAA-AGTTTTTCCTCAATTTTTAG-CCAAAA
* * *
1502 TACTC-GAAAAATATATATAATTCAACACC-AAAAGTATTGAAGGACTTTTCACGCTTTTAATAT
61 TACTCATAAAAATATATATAATTCAACGCCAAAAAG-ATTGAAGGACTTTTCACGCTTCTAATAT
* * *
1565 CGTTTTT-C-A----T----ATTAA--TCTGATTAAATCGAAACATGATTCAAATGCTCGTAAAA
125 CGTTTTTCCTATTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAA
* * * * * * *
1618 A-AAAT-CTTAAATGCAATGTGGCTAAGATTTTATTAGATGAATAAAGTTATTTCAAGGAGTGTC
190 ACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTT
** * * * * * * *
1681 GGCGTAAAAAATCATGCAAAATTGAGCAAGTGCCCCGAAACGTGGTTTTAGCCAAAAACCGTGAT
255 GGCGCCAAAAATCATGCAAAACTGAGC-CGGGGCCAG-AACGCGTTTTTAGCCAAAAACCGTGAT
* *
1746 GGTAAGTACAC
318 GATTAGTACAC
* * * * * * * ** *
1757 GATTTTGCCTAAAATTTTGCAAAAAATGACCCGAAAAATTTGTCCTCAATTTTTGGATAATATAC
1 GATTTCGGCT-AAATTTTGCAAAAATTGACACG-AAAGTTTTTCCTCAATTTTTAGCCAAAATAC
* * * * * *
1822 TCAT-AAGATATATATAATTTAACGGCAAAAATATTGGAGGACTTTTCACGCTTTTAATATCGTT
64 TCATAAAAATATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTCTAATATCGTT
* * * * * * *
1886 TTTCATATTTTTCTGTATTAATTTCTAATTAAATCGGAACAAGATTTAGATTCTTGTAAAAACAA
129 TTTCCTATTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAA
** * * * * *
1951 ATTTTTAGATCCAATTTGGCTGAGATTTGATTAGATGAATAAAGATATCTCAAGGAGTCTTTGCG
194 ATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCG
* * ** *
2016 CCAAAAATCATGCAAAACTGAGCCGGGGTCCCAGAACGGGTTTTTATCCAAAAACTATGATGGTT
259 CCAAAAATCATGCAAAACTGAGCCGGGG--CCAGAACGCGTTTTTAGCCAAAAACCGTGATGATT
*
2081 ATTACAC
322 AGTACAC
* * * ** * *
2088 GATTTCGACTTAAATTTTGTAAAAATTGACCCGAAAGATAATTCCTCAATTTTTGGCTAAAATAC
1 GATTTCGGC-TAAATTTTGCAAAAATTGACACGAAAG-TTTTTCCTCAATTTTTAGCCAAAATAC
* * ** * * *
2153 TCATAAAAA-ATATATAAGTCAACGCCAAAAATATTGAAGGGTTTTTGATGTTTCTAATATCGTT
64 TCATAAAAATATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTCTAATATCGTT
* *
2217 TTTCCTA-TTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAATAA
129 TTTCCTATTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAA
* * * * * *
2281 ATCTTTAGATCTAATGTGGGTGAGATTTGATTAGAT-AAGTATAGATATTTCAAGTAGTCTTGGA
194 ATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAA-TATAGATATTTCAAGGAGTCTTGGC
* * * * *
2345 GCCAAAAATCATGCAAAATTGAGCCGGGTCCCCGGAAAGCGTTTTTAGCCAAAAAACCCTGATGG
258 GCCAAAAATCATGCAAAACTGAGCCGGG--GCCAGAACGCGTTTTTAGCC-AAAAACCGTGAT-G
*
2410 TTTGTTAGTACAC
319 ---ATTAGTACAC
* * * *
2423 GATTTCGGCTAAAATTTTGTAAAAATTGACACGAAAGATTTTTTTCTCAATTTTT-GGCTAAATA
1 GATTTCGGCT-AAATTTTGCAAAAATTGACACGAAAG--TTTTTCCTCAATTTTTAGCCAAAATA
* * *
2487 CTCAT-AAAA-ACATATAATTCAACGCTAAAAAGATTGAAGGGCATTTT-ACGCTT-TCAATATC
63 CTCATAAAAATATATATAATTCAACGCCAAAAAGATTGAAGGAC-TTTTCACGCTTCT-AATATC
* * ** * * * *
2548 GTATTTCTTATTTTTCTAAATTAATTTCTAATTAAATGGAAATAAGATTTAGATGCTCGTAATAA
126 GTTTTTCCTATTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA
* * *
2613 CAAATTCTTAAATCCAATGTTGCTGAGATTTGGTTAGATGA
191 CAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGA
2654 TGTAAAGTAT
Statistics
Matches: 1785, Mismatches: 317, Indels: 181
0.78 0.14 0.08
Matches are distributed among these distances:
315 1 0.00
316 46 0.03
317 111 0.06
318 112 0.06
319 35 0.02
320 82 0.05
321 4 0.00
322 90 0.05
323 38 0.02
324 4 0.00
325 37 0.02
326 56 0.03
327 198 0.11
328 67 0.04
329 43 0.02
330 255 0.14
331 246 0.14
332 33 0.02
333 1 0.00
334 52 0.03
335 142 0.08
336 29 0.02
337 94 0.05
338 6 0.00
339 3 0.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (328 bp):
GATTTCGGCTAAATTTTGCAAAAATTGACACGAAAGTTTTTCCTCAATTTTTAGCCAAAATACTC
ATAAAAATATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTCTAATATCGTTTT
TCCTATTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAAT
CCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCC
AAAAATCATGCAAAACTGAGCCGGGGCCAGAACGCGTTTTTAGCCAAAAACCGTGATGATTAGTA
CAC
Found at i:2380 original size:983 final size:966
Alignment explanation
Indices: 178--2559 Score: 2675
Period size: 983 Copynumber: 2.4 Consensus size: 966
168 TTTTTTTCAT
* *
178 TTTTTAGCCAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAAATCGAAGGGTTTTTCAC
1 TTTTTAGCCAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCAT
* * * * * * *
243 GCTTCTAATATCGTTTTGCTTATTCTTTCAAATTAAATTCTAATTAAATTGAAACATGATTGAAA
66 GCTTCTAATATCGTTTTTCCTATT-TTCCAAATTAATTTCTAATTAAATCGAAACATGATTCAGA
* * *
308 TGCTCTCGT-AAAACAAATCCTTAAATCCAATGTGGCTAAGATTTGGTTAGATGAATAT--ATAT
130 TG--CTCGTAAAAACAAATCCTTAAATCCAATGTGGATGAGATTTGATTAGAT-AATATAGATAT
* * * * * * *
370 TTCAAGGAGTGTTGCCA-CAAAAAATCATGCAAAACTGACCCGGGGCCCCAGAATGCGTTTTTAG
192 TTCAAGTAGTCTTG-GAGCAAAAAATCATGCAAAACTGAACCGGGACCCCGGAAAGCGTTTTTAG
* *
434 CCAAATAACCGTGA--TGTTA-CACA--ATTTCGGCTAAAATTTTGCAAAAATTGAC-CACGAAT
256 CCAAAAAACCGTGATTTGTTAGCACACGATTTCGGCTAAAATTTTGCAAAAATTGACAAAC-AAT
* * * * *
493 ATTTTTCCTTAATTTTTAGCCAGAATACTCATAGAATATATATAATT-AAAAGCAAAAAAGATTG
320 ATTTTTCCTCAATTTTT-GCTAAAATACTCATAAAATATATATAATTCAACA-CAAAAAAGATTG
* * *
557 GAGGACTCTTCACGCTTTTAATATCGTTTGTCTTATTTTTCTGAATTAACTTCTAATTAAATCAA
383 AAGGACTTTTCACGCTTTTAATATCGTTT-T-TCA------T--ATTAAC-TCTAATTAAATCAA
* * * * *
622 AACAAGATTATGATGCTTGTAAAAACCAATCCTTAAATTCAATGTGGCTGAGATTTGATTAGATG
437 AACAAGATTATAATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTAAGATTTGATTAGATG
* ** * *
687 AATATAAATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTAAGCTGGGGTCTCGAAAC
502 AATATAAATATTTCAAGGAGTCTCGGCGCAAAAAATCATGCAAAACTAAGCAAGGGCCCCGAAAC
* * * *
752 CCGTTTTTAGCCAAAAACCGTGATAGTTAGTACACGATTTCGGCTAAAATGGCCCGAAAAATTTT
567 CCGGTTTTAGCCAAAAACCGTGATAGTAAGTACACGATTTCGCCTAAAATGGCCCGAAAAATTTG
*
817 TCCGTCAAATTTTGGAAATAATACTCATAAAATATATATAATTTAACGTCAAAAAGATTGGAGGA
632 TCCGTCAAATTTTGGAAATAATACTCATAAAATATATATAATTTAACGGCAAAAAGATTGGAGGA
*
882 CTTTTCACGCTTTTATTATCGTTTTTCATATTTTTTGAATTAATTTCTAATTAAATCGAACAAGA
697 CTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTGAATTAATTTCTAATTAAATCGAACAAGA
* * * **
947 GTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTAGTTGAGATTTGATTTGATGAGTATGG
762 GTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTAGCTGAGATTTGATTAGATGAATAAAG
* * * * *
1012 ATATTTTAAAGAGTCTTGACGCCAAAAATCATGCAAAACTTAGTCGGGGCCTGAACGCGTTTTTA
827 ATATCTCAAAGAGTCTTGACGCCAAAAATCATGCAAAACTGAGCCGGGGCCAGAACGCGTTTTTA
* * * ** *
1077 GCGAAAAACCGTGATGATTATTACACGATTTCGGCTAGAATTTTGCAAAAATTGAGTCGAAAGTT
892 GCCAAAAACCATGATGATTATTACACGATTTCGACTAGAATTTTGCAAAAATTGACCCGAAAGTA
1142 ATTCACTCAA
957 ATTCACTCAA
* * * * * *
1152 TTTTTAGCCATAATATTCATAAAAATTATATAATTCAATGCCAAAAAGATTGAAGGGCTTTTCAT
1 TTTTTAGCCAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCAT
* * *
1217 GCTTCTGATATCGTTTTTCCTATTATTTTCCGAATTAATTTCTAATTAAATCAAAACATGATTCA
66 GCTTCTAATATCGTTTTTCC---TATTTTCCAAATTAATTTCTAATTAAATCGAAACATGATTCA
* *** * * *
1282 GATGCTTG-ATTTACAAATCCTTAAATCCATTGTGGATGAGATTTGTTTAGATTACTATAGATAT
128 GATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGATGAGATTTGATTAGA-TAATATAGATAT
* * * * ** *
1346 TTCAAAGT-GTCTCGGCGCAAAAAATCATGCAATACTGAACCGGGACCCCGGAACGATTTTTTTG
192 TTC-AAGTAGTCTTGGAGCAAAAAATCATGCAAAACTGAACCGGGACCCCGGAAAGCGTTTTTAG
*
1410 -CAAAAAACCGTGATTTCGATTAACGCACACGATTTCGGCTAATATTTTGCAAAAATTGACAAAC
256 CCAAAAAACCGTGATTT-G-TT-A-GCACACGATTTCGGCTAAAATTTTGCAAAAATTGACAAAC
* *
1474 AATAGTTTTCCTCAATTTTTGTCTAAAATACTCGA-AAAATATATATAATTCAACAC-CAAAAGT
317 AATATTTTTCCTCAATTTTTG-CTAAAATACTC-ATAAAATATATATAATTCAACACAAAAAAG-
* * *
1537 ATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTAA-TCTGATTAAATCGAAACATGA
379 ATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTAACTCTAATTAAATCAAAACAAGA
*
1601 TTCA-AATGCTCGTAAAAA-AAAT-CTTAAATGCAATGTGGCTAAGATTTTATTAGATGAATA-A
444 TT-ATAATGCTCGTAAAAACAAATCCTTAAATGCAATGTGGCTAAGATTTGATTAGATGAATATA
* * * * * * **
1662 AGTTATTTCAAGGAGTGTCGGCGTAAAAAATCATGCAAAATTGAGCAAGTGCCCCGAAACGTGGT
508 A-ATATTTCAAGGAGTCTCGGCGCAAAAAATCATGCAAAACTAAGCAAGGGCCCCGAAACCCGGT
* *
1727 TTTAGCCAAAAACCGTGATGGTAAGTACACGATTTTGCCTAAAATTTTGCAAAAAATGACCCGAA
572 TTTAGCCAAAAACCGTGATAGTAAGTACACGATTTCGCCTAAAA---TG--------G-CCCGAA
* * *
1792 AAATTTGTCC-TCAATTTTTGGATAAT-ATACTCATAAGATATATATAATTTAACGGCAAAAATA
625 AAATTTGTCCGTCAAATTTTGGA-AATAATACTCATAAAATATATATAATTTAACGGCAAAAAGA
*
1855 TTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGTATTAATTTCTAATTAAAT
689 TTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTT-TGAATTAATTTCTAATTAAAT
* * * * * * * *
1920 CGGAACAAGATTTAGATTCTTGTAAAAACAAATTTTTAGATCCAATTTGGCTGAGATTTGATTAG
753 C-GAACAAGAGTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTAGCTGAGATTTGATTAG
*
1985 ATGAATAAAGATATCTCAAGGAGTCTTTG-CGCCAAAAATCATGCAAAACTGAGCCGGGGTCCCA
817 ATGAATAAAGATATCTCAAAGAGTC-TTGACGCCAAAAATCATGCAAAACTGAGCCGGGG--CCA
* * * * *
2049 GAACGGGTTTTTATCCAAAAACTATGATGGTTATTACACGATTTCGACTTA-AATTTTGTAAAAA
879 GAACGCGTTTTTAGCCAAAAACCATGATGATTATTACACGATTTCGAC-TAGAATTTTGCAAAAA
2113 TTGACCCGAAAGATAATTC-CTCAA
943 TTGACCCGAAAG-TAATTCACTCAA
* * * * *
2137 TTTTTGGCTAAAATACTCATAAAAAATATATAAGTCAACGCCAAAAATATTGAAGGGTTTTTGAT
1 TTTTTAGCCAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCAT
* *
2202 GTTTCTAATATCGTTTTTCCTATTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTCAGAT
66 GCTTCTAATATCGTTTTTCCTATTTTCCAAATTAATTTCTAATTAAATCGAAACATGATTCAGAT
* * * * *
2267 GCTCGTAAAAATAAATCTTTAGATCTAATGTGGGTGAGATTTGATTAGATAAGTATAGATATTTC
131 GCTCGTAAAAACAAATCCTTAAATCCAATGTGGATGAGATTTGATTAGATAA-TATAGATATTTC
* * * *
2332 AAGTAGTCTTGGAGCCAAAAATCATGCAAAATTGAGCCGGGTCCCCGGAAAGCGTTTTTAGCCAA
195 AAGTAGTCTTGGAGCAAAAAATCATGCAAAACTGAACCGGGACCCCGGAAAGCGTTTTTAGCCAA
* * *
2397 AAAACCCTGATGGTTTGTTAGTACACGATTTCGGCTAAAATTTTGTAAAAATTGACACGAA-AGA
260 AAAA-CC-G-TGATTTGTTAGCACACGATTTCGGCTAAAATTTTGCAAAAATTGACA--AACA-A
* * * *
2461 T-TTTTTTCTCAATTTTTGGCT-AAATACTCATAAAA-ACATATAATTCAACGCTAAAAAGATTG
319 TATTTTTCCTCAATTTTT-GCTAAAATACTCATAAAATATATATAATTCAACACAAAAAAGATTG
* * * *
2523 AAGGGCATTTT-ACGCTTTCAATATCGTATTTCTTATT
383 AAGGAC-TTTTCACGCTTTTAATATCGTTTTTCATATT
2560 TTTCTAAATT
Statistics
Matches: 1181, Mismatches: 168, Indels: 110
0.81 0.12 0.08
Matches are distributed among these distances:
969 2 0.00
970 124 0.10
971 3 0.00
972 32 0.03
973 3 0.00
974 121 0.10
975 13 0.01
976 86 0.07
977 8 0.01
978 1 0.00
979 2 0.00
980 1 0.00
981 88 0.07
982 144 0.12
983 252 0.21
984 129 0.11
985 158 0.13
986 9 0.01
987 5 0.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (966 bp):
TTTTTAGCCAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCAT
GCTTCTAATATCGTTTTTCCTATTTTCCAAATTAATTTCTAATTAAATCGAAACATGATTCAGAT
GCTCGTAAAAACAAATCCTTAAATCCAATGTGGATGAGATTTGATTAGATAATATAGATATTTCA
AGTAGTCTTGGAGCAAAAAATCATGCAAAACTGAACCGGGACCCCGGAAAGCGTTTTTAGCCAAA
AAACCGTGATTTGTTAGCACACGATTTCGGCTAAAATTTTGCAAAAATTGACAAACAATATTTTT
CCTCAATTTTTGCTAAAATACTCATAAAATATATATAATTCAACACAAAAAAGATTGAAGGACTT
TTCACGCTTTTAATATCGTTTTTCATATTAACTCTAATTAAATCAAAACAAGATTATAATGCTCG
TAAAAACAAATCCTTAAATGCAATGTGGCTAAGATTTGATTAGATGAATATAAATATTTCAAGGA
GTCTCGGCGCAAAAAATCATGCAAAACTAAGCAAGGGCCCCGAAACCCGGTTTTAGCCAAAAACC
GTGATAGTAAGTACACGATTTCGCCTAAAATGGCCCGAAAAATTTGTCCGTCAAATTTTGGAAAT
AATACTCATAAAATATATATAATTTAACGGCAAAAAGATTGGAGGACTTTTCACGCTTTTAATAT
CGTTTTTCATATTTTTTGAATTAATTTCTAATTAAATCGAACAAGAGTCAGATGCTCGTAAAAAC
AAATTCTTAAATCCAATGTAGCTGAGATTTGATTAGATGAATAAAGATATCTCAAAGAGTCTTGA
CGCCAAAAATCATGCAAAACTGAGCCGGGGCCAGAACGCGTTTTTAGCCAAAAACCATGATGATT
ATTACACGATTTCGACTAGAATTTTGCAAAAATTGACCCGAAAGTAATTCACTCAA
Found at i:3397 original size:41 final size:42
Alignment explanation
Indices: 3259--3586 Score: 300
Period size: 41 Copynumber: 7.8 Consensus size: 42
3249 CAATAACCAA
* *
3259 AAAGTCC-CTAAACACATATATAACACAGGGGCA-ATTCTATTCC
1 AAAGTCCTC-AAACACA-ATATAACACAGGGGCACCTT-TATTAC
* *
3302 AAAAGTCCTCAAACACATATATAACACAGAGGCACCTATA-T-C
1 -AAAGTCCTCAAACACA-ATATAACACAGGGGCACCTTTATTAC
* * * *
3344 CAGGTCCCCAAACAC-ATATAACACAGGGGCGCCTTTATTAC
1 AAAGTCCTCAAACACAATATAACACAGGGGCACCTTTATTAC
* * *
3385 AAAGTCCTCAAACACATATATAACACAGAGGCATCTATA-T-C
1 AAAGTCCTCAAACACA-ATATAACACAGGGGCACCTTTATTAC
* *
3426 AAAGTTCC-CAAACACATATATAACACAGGGGCAACTCTATTAC
1 AAAG-TCCTCAAACACA-ATATAACACAGGGGCACCTTTATTAC
*
3469 AAAGTCCTCAAACACATATATAACACAGAGGCA--TTTA-TATC
1 AAAGTCCTCAAACACA-ATATAACACAGGGGCACCTTTATTA-C
* * *
3510 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
1 AAAGTCCTCAAACACA-ATATAACACAGGGGCACCTTTATTAC
*
3553 AAAAGTCCTCAAACACATATATAACACAGAGGCA
1 -AAAGTCCTCAAACACA-ATATAACACAGGGGCA
3587 TTTCTCCTTA
Statistics
Matches: 243, Mismatches: 26, Indels: 30
0.81 0.09 0.10
Matches are distributed among these distances:
39 19 0.08
40 3 0.01
41 93 0.38
42 9 0.04
43 52 0.21
44 65 0.27
45 2 0.01
ACGTcount: A:0.42, C:0.26, G:0.12, T:0.21
Consensus pattern (42 bp):
AAAGTCCTCAAACACAATATAACACAGGGGCACCTTTATTAC
Found at i:3473 original size:84 final size:85
Alignment explanation
Indices: 3259--3587 Score: 522
Period size: 84 Copynumber: 3.9 Consensus size: 85
3249 CAATAACCAA
* * *
3259 AAAGTCCCTAAACACATATATAACACAGGGGCAATTCTATTCCAAAAGTCCTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAAGTCCTCAAACACATATAT
*
3324 AACACAGAGGCACCTATATC
66 AACACAGAGGCATCTATATC
* * ** *
3344 CAGGTCCCCAAACAC--ATATAACACAGGGGCGCCTTTATTAC-AAAGTCCTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAAGTCCTCAAACACATATAT
3406 AACACAGAGGCATCTATATC
66 AACACAGAGGCATCTATATC
*
3426 AAAGTTCCCAAACACATATATAACACAGGGGCAACTCTATTAC-AAAGTCCTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAAGTCCTCAAACACATATAT
*
3490 AACACAGAGGCATTTATATC
66 AACACAGAGGCATCTATATC
*
3510 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAAGTCCTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAAGTCCTCAAACACATATAT
3575 AACACAGAGGCAT
66 AACACAGAGGCAT
3588 TTCTCCTTAT
Statistics
Matches: 223, Mismatches: 18, Indels: 6
0.90 0.07 0.02
Matches are distributed among these distances:
82 52 0.23
83 21 0.09
84 104 0.47
85 46 0.21
ACGTcount: A:0.42, C:0.26, G:0.12, T:0.21
Consensus pattern (85 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTACAAAAGTCCTCAAACACATATAT
AACACAGAGGCATCTATATC
Done.