Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010075.1 Corchorus capsularis cultivar CVL-1 contig10096, 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: 25818
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:932 original size:2 final size:2
Alignment explanation
Indices: 925--956 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
915 CTTATAAATG
925 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
957 GCAACAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2937 original size:332 final size:325
Alignment explanation
Indices: 2169--6985 Score: 2891
Period size: 332 Copynumber: 14.4 Consensus size: 325
2159 AAAGATGCCA
* * * * *
2169 AAAAAGATTGGAGGACTTTTCACGATTCTAATATCGTTTATCATATTTTTTTCTGAATTAATTTC
1 AAAAAGATTGAAGGACTTTTCACGCTTCTAATATCGTTTTTCCTA-TTTTTTCCGAATTAATTTC
* * * * * * *
2234 TAATTAAATCAAAATAAGATTCAGATGCACATAAAAACAAAT-CTTACATCCAATGTGGATGAGA
65 TAATTAAATCGAAACAAGATTCAAAT-CTCGT-AAAACAAATCCTTAAATCCAATGTGGCTGAGA
* * * * * *
2298 TTTGGTTAGATAAATAAAGATATTTCAAGGAGTCTCGGCGCCAAAAATTCATGCAAAACAAAACC
128 TTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAA-TCATGCAAAACTAAGCA
* * * * **
2363 GTGGCCCTGTAACACGTTTTTAGTCAAAAACGTGATGGTTGGTACACGATTTTTGCTAAAATTTT
192 G-GGCCC-GGAACGCGTTTTTAGCCAAAACCGTGAT-GTT-GTACACGATTTCGGCTAAAATTTT
* * * * * * *
2428 GTAAAAATTGACCCAAAAGATATTTCCTCAATTTTTGGCTAAAATACTTATAAAAAATATATAAT
253 GCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAGCAAAAATACTCATAAAAATTATATAAT
* * *
2493 TCGATATC
318 TCAACACC
* * * * *
2501 AAAAAGATTGAAGGGCTTTTAACGCTTCTAATATTGTTTTTCCTAATTTTCCCGAATTAATTTCT
1 AAAAAGATTGAAGGACTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCCGAATTAATTTCT
* *
2566 AATTAAATCGAAACAAGATTCAGATTCTCGTAAAAACAAATCCTTAAATCTAATGTGGCTGAGAT
66 AATTAAATCGAAACAAGATTCA-AATCTCGT-AAAACAAATCCTTAAATCCAATGTGGCTGAGAT
* * * * *
2631 TTGGTTAGATTAATATAAATATTTCAAGGAGTTTTGGCACCAAAAATCATGCAAAACTGAGCAGG
129 TTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTAAGCAGG
* * *
2696 GACTCGGAACTCGTTTTTAGCCGAAAACCGTGATGCTTAGTACACGATTTCGGCT-ATATTTTGC
194 G-CCCGGAACGCGTTTTTAGCC-AAAACCGTGATG-TT-GTACACGATTTCGGCTAAAATTTTGC
* * * *
2760 AAAAATTGACCCGAAAGATTTTTCCTCGATTTGTAGCAAAAATACTCATAAAAATTAAATAACTC
255 AAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAGCAAAAATACTCATAAAAATTATATAATTC
2825 AACACC
320 AACACC
* * * *
2831 AAAAA-ATTGAAAGTCTTTTTCACGCTTCTAATATCATTTTTCCTATTTTATTCCAAAATTAATT
1 AAAAAGATTGAAGGAC-TTTTCACGCTTCTAATATCGTTTTTCCTATTTT-TTCC-GAATTAATT
* * * **
2895 TTTGATTAAATCAAAACGGGATTTACAAAT-TCGTACAAACAAATCCTTAAAAAGAAATTCGCAC
63 TCTAATTAAATCGAAACAAGA-TT-CAAATCTCGTA-AAACAAATCCTT------AAA-T-----
**** * ** * * * *
2959 ACACACATACACACAGAGACAT-ATATATAT-ATATATATATATATT-AAGGAGTCTTGTCGCCA
113 -C-CA-AT-GTGGCTGAGATTTGGT-TAGATGA-ATATAGATAT-TTCAAGGAGTCTTGGCGCCA
** * * * * *
3021 AAAATCATGCAAAGTTCACCTAGAGCCCGGAACGCGCTTTTAGCCAAAAGAAAACCATGATG--G
171 AAAATCATGCAAAACTAAGC-AGGGCCCGGAACGCGTTTTTAGCC-----AAAACCGTGATGTTG
* * * * * *
3084 TACACGATTTCGGCTGAAATTTTACAAAAATTGACCCGAAATATATTT-CTCAATTTTTAGCCAC
230 TACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAGCAAA
*
3148 AATACTCATAAAAAATATATAATTCAACACC
295 AATACTCATAAAAATTATATAATTCAACACC
* * * *
3179 AAAAAGATTGAAGGGCTTCTCACGCTTCTAATATCGTTTTTCCT-TTTTTTTCAAATTAATTTCT
1 AAAAAGATTGAAGGACTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCCGAATTAATTTCT
** * * *
3243 AATTAAATTAAAACATGATTCAAATGCTCGTGAAAACAAATCCTTAAATCCAATGTAGCTAAGAT
66 AATTAAATCGAAACAAGATTCAAAT-CTCGT-AAAACAAATCCTTAAATCCAATGTGGCTGAGAT
* * * * * * * *
3308 TTGATTAGATGAATATAGATATTTCAAGGAATATT-GCAACTAAAAATCATGCAAAACTGACCCG
129 TTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGC-GCCAAAAATCATGCAAAACTAAGCAG
* * ***** * * * *
3372 GGACTCCAGAACGCG-TTTTAGGCAAAAAAAAAAAG-CG--CACGATTTCAGCTAAAATTTTGTA
193 GG-C-CCGGAACGCGTTTTTAGCCAAAACCGTGATGTTGTACACGATTTCGGCTAAAATTTTGCA
* *
3433 AAAATTGACCCGAAATATTTTTCCTCAATTTTTA--AACACAATACTCAT-AGAATATATATAAT
256 AAAATTGACCCGAAAGATTTTTCCTCAATTTTTAGCAA-A-AATACTCATAAAAAT-TATATAAT
*
3495 T-AAAAGCC
318 TCAACA-CC
* * * * *
3503 AAAAAGATTGGAGGACTCTTCACGCTTTTAATATCGTTTTTCATA-TTTTTCTGAATTAATTTCT
1 AAAAAGATTGAAGGACTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCCGAATTAATTTCT
* * *
3567 AATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATTCAATGTGGCCGAGAT
66 AATTAAATCGAAACAAGATTCAAAT-CTCGT-AAAACAAATCCTTAAATCCAATGTGGCTGAGAT
* * * * * *
3632 TTGATTAGATGAATATAGATATTTCAAGAAGTCTCGGTGCCAAAAATCATGTAAAACTAAGCCGG
129 TTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTAAG-CAG
* * * * *
3697 GGTCCCGAAACGCGTTTTAAGACCAAAACCGTGATTGTTAGTATACGATTTCAGTTAAAATTTTG
193 GG-CCCGGAACGCGTTTTTAG-CCAAAACCGTGA-TGTT-GTACACGATTTCGGCTAAAATTTTG
* * * * * *
3762 TAAAAAAATGATCCGAAAGATTTTTCCGTCAATTTTTGGCATAAATACTCAT-AATATATATATA
254 -CAAAAATTGACCCGAAAGATTTTTCC-TCAATTTTTAGCAAAAATACTCATAAAAAT-TATATA
* *
3826 ATTTAACGCC
316 ATTCAACACC
* * * * * * *
3836 AAAAGGATTGGATGACTTTTCATGCTTTTAATATCGTTTTT-C-ATATTTTCTGAATTAATTTCT
1 AAAAAGATTGAAGGACTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCCGAATTAATTTCT
* * * * *
3899 AATTAAATCGAAACAGGATTCAGATGCTCGTAAAATCAAATTCTTCAATCCAATGTAGCTGAGAT
66 AATTAAATCGAAACAAGATTCAAAT-CTCGTAAAA-CAAATCCTTAAATCCAATGTGGCTGAGAT
** * * * * * * * **
3964 TTTTTTAGATGAATATGGATATCTCAAAGAGTTTTGCCGTCAAAAATCATGCAAAACTTAGGTGG
129 TTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAAC-TAAGCAG
* * * * * ** *
4029 GGCATCGCAACGCATTTTTAGTCAAAAACCGTGATAATTGTTACACGATTTCGTTTAGAATTTTG
193 GGC-CCGGAACGCGTTTTTAG-CCAAAACCGTGAT-GTTG-TACACGATTTCGGCTAAAATTTTG
* ***
4094 CAAAAATTGACTCGAAAGTTATTTTT--TCAATTTTTAGCCTTAATACTCATAAAAATTATATAA
254 CAAAAATTGACCCGAAAG--ATTTTTCCTCAATTTTTAGCAAAAATACTCATAAAAATTATATAA
*
4157 TTCAACGCC
317 TTCAACACC
* * * * * *
4166 AAAAAAATTGAAAGG-TTTTTCATGCTTCTAGTATCGTTGTTCTTATTATTTTCCGAATTAATTT
1 AAAAAGATTG-AAGGACTTTTCACGCTTCTAATATCGTTTTTCCTATT-TTTTCCGAATTAATTT
* * * *** * * * *
4230 TTAATTAAATCGAAACATGATTCAAATGCTTGTTTCACAAATCTTTAAATCCATTTTGGATGAGA
64 CTAATTAAATCGAAACAAGATTCAAAT-CTCGTAAAACAAATCCTTAAATCCAATGTGGCTGAGA
* * * * * * * *
4295 TTTGGTTAGATTAATATAGATATTTCAAGAAGTCTCGGTGCAAAAAATCATGCAACATTGAACCG
128 TTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACT-AAGC-
* * * ** ** *
4360 AAGCCCCGGAACACGTTTTTAGGAAAAAAATTGTGATTTCGACTACCGTACACGATTTCGGCTAA
191 AGGGCCCGGAACGCGTTTTTA-G-CCAAAACCGTGA--T-G--T--TGTACACGATTTCGGCTAA
* * * * * * *
4425 TATTTTGCAACAATTGACCAGAAATAGTTTTCCTCAATTTTT-GTCTAAAAGACTCAT-AAAATA
247 AATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAG-CAAAAATACTCATAAAAAT-
*
4488 TATATAATTCAACTCC
310 TATATAATTCAACACC
* * * * * * * * *
4504 AAAAATATT-AGAGCATTTTTCACGTTTTTTAATANCGTTTTTCATATTTTTT-AGAATTACA-A
1 AAAAAGATTGA-AGGACTTTTCACG-CTTCTAATATCGTTTTTCCTATTTTTTCCGAATTA-ATT
* * * * *
4566 TCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAAAAAAATCTTTAAATGCAATGTGGCTG
63 TCTAATTAAATCGAAACAAGATTCAAAT-CTCGT--AAAACAAATCCTTAAATCCAATGTGGCTG
* * * * **
4631 AGATTTGATTAGATAAATAAATAAATATATATATATATATTTCAAGGAGTCTCGATGCCAAAAAT
125 AGATTTG----G-----T---TAGAT-GA-ATATAGATATTTCAAGGAGTCTTGGCGCCAAAAAT
* ** ** *
4696 CATGCAAAACTGAGTC-GGTGTCCCAAAACGCGTTTTTAGGGGGAAAAAACTGTGATTGTTAGTA
176 CATGCAAAACTAAG-CAGG-G-CCCGGAACGCGTTTTTA----GCCAAAACCGTGA-TGTT-GTA
* * ** *
4760 CACGATTTCGCCTAAAATTTTGCAAAAAAAATT-ACAC--AA-ATTTTTTTTCAATTTTTTA-CT
232 CACGATTTCGGCTAAAATTTTGC---AAAAATTGACCCGAAAGATTTTTCCTCAA-TTTTTAGCA
* * * *
4820 AAAATACACAT-GAAATATATATAATTTAACGCC
293 AAAATACTCATAAAAAT-TATATAATTCAACACC
* * * * * *
4853 AAAAAGATTGGAGGA-TGTTTCACGATTTTCATATCGTTTTTCATA-TTTTTCTGAATTAATTTC
1 AAAAAGATTGAAGGACT-TTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCCGAATTAATTTC
* * * *
4916 TATAATTAAATCGAAATATCGAAATCGGATTTAGATGCTCGTAAAATCAAATCATTAAATTCAAT
65 --TAATTAAATCG-AA-A-C--AA---GATTCAAAT-CTCGTAAAA-CAAATCCTTAAATCCAAT
* * * * ** ** *
4981 GTGTCTTAGATTTGATTAGATGAATATGGATACCTCAACTAGTCTTAGCGCCAAAAATCATGCAA
118 GTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAA
* * * * * *
5046 AACTAACCCGGAGCCCTGGAACACATTTTTAGCCAAAAACCATGATGATTATTACACGATTTCGG
183 AACTAAGCAGG-GCCC-GGAACGCGTTTTTAGCC-AAAACCGTGATG-TT-GTACACGATTTCGG
* * * * * * *
5111 CTAAATTTTTTCAAAAATTGACCGGAAACATATTTCCTAAATCTTTT-GCTAAAATTA-TCATAA
243 CTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAAT-TTTTAGC-AAAAATACTCATAA
* * ** *
5174 AAAATATATATTTTTACGCC
306 AAATTATATAATTCAACACC
* * * *
5194 AAAAATATTGAAGGATTTTTTACGCTTCTAATATCGTTTTTCCTACTTTTTTTCGAATTAATTTC
1 AAAAAGATTGAAGGACTTTTCACGCTTCTAATATCGTTTTTCCTA-TTTTTTCCGAATTAATTTC
* * * *
5259 TAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGACTGAAA
65 TAATTAAATCGAAACAAGATTCAAAT-CTCGT-AAAACAAATCCTTAAATCCAATGTGGCTGAGA
* * * * * ** *
5324 TTTGATTAGATGAATATAGATATTTCAAGGAATCTTGGTGCCAAAAATCATGCGATACTGACCCG
128 TTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACT-AAGCA
* * * * * *
5389 GGGTCCTGAACGTGTTTTTAGCACAAAAAAAATCGTGATGTTG--CACAATTTCGGCTTAATATT
192 GGGCCCGGAACGCGTTTTTAGC-C----AAAACCGTGATGTTGTACACGATTTCGGC-TAAAATT
* * * * * *
5452 TTGCAAAAAAAAATGCCCCTAAATATCTTTT-TTCAATTTTTAGTC-ACAATACTCATAAAAA-T
251 TTGC---AAAAATTGACCCGAAAGAT-TTTTCCTCAATTTTTAG-CAAAAATACTCATAAAAATT
*
5514 ATATAATTCAACGCC
311 ATATAATTCAACACC
* *
5529 AAAAAGATTGAAGGGGC-TTTCACGCTTCTAATACCGTTTTTCCCTATATTTTTCCGAATTAATT
1 AAAAAGATTGAA-GGACTTTTCACGCTTCTAATATCGTTTTT-CCTAT-TTTTTCCGAATTAATT
* * * * *
5593 TCTAATTAAAAT-GAAATATGATTCAGATACT--T---A-TAA-----AAA--CAA--TGGCTGG
63 TCTAATT-AAATCGAAACAAGATTCAAAT-CTCGTAAAACAAATCCTTAAATCCAATGTGGCTGA
* * * *
5642 GATTTGGGTTAGATGAATATAGGTATTTCAAGGAGTCTCGGCACCAAAAATCATTCAAAACTGAA
126 GATTT-GGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACT-AA
* * * * *
5707 --ATGGGCCCCGGAACGCGTTTTTAGTCAAAAACTGTGATGAT-TACACTATATCGGCTAAAATT
189 GCA-GGG-CCCGGAACGCGTTTTTAG-CCAAAACCGTGATGTTGTACACGATTTCGGCTAAAATT
* * * * * * *
5769 TTGTAAAAATTGACCCGAAAGATATTTT-ATTAATTTTTAACCATAATACTCATAAAAAATATAT
251 TTGCAAAAATTGACCCGAAAGAT-TTTTCCTCAATTTTTAGCAAAAATACTCATAAAAATTATAT
*
5833 AATTCAACGCC
315 AATTCAACACC
* * * * * * **
5844 AAAAATATTAAAGGGCTTTTGACGCTTTTAATATCGTTTTTCATATTTTTTCTAAATTAATTTCT
1 AAAAAGATTGAAGGACTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCCGAATTAATTTCT
* * * * * * *
5909 AATTTAAATCGAAACATGATTCAGATGCTCGTTAAAAAAAAAT-ATTAAATGCAATGTGGCTAAA
66 AA-TTAAATCGAAACAAGATTCAAAT-CTCG-T-AAAACAAATCCTTAAATCCAATGTGGCTGAG
** * * * * * *
5973 ATTTTTTTTAGATGAATATAGTTATTTCAAGGAGTGTCGGCGCCAAAAATCATGTAAAACTGAGT
127 A-TTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTAAGC
* * * ** * * * * *
6038 TGTTGCCCAGAAACGCGTTTTTAGTAAAAAGTCGTGATGGTTTGTACACAATTTTGGGTAAAGTT
191 AG-GGCCC-GGAACGCGTTTTTAGCCAAAA-CCGTGAT-G-TTGTACACGATTTCGGCTAAAATT
** * * ** * *
6103 TTGCAAAAAAAAGACCCGAAAAATTTTTCCTCAATTTTTGGTTAAAATACTC-CAAATATATATA
251 TTGC-AAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAGCAAAAATACTCATAAAAAT-TATA
* ***
6167 TAATTTAATGGC
314 TAATTCAACACC
* * * * *
6179 AAAAAGATTGGAGTACTTTTCACGCTTATAATATCGTTTTTCATA-TTTTT-CTATATTAATTTC
1 AAAAAGATTGAAGGACTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCCGA-ATTAATTTC
* * * * ***
6242 TAATTAAATCGAAACAAGATTTAGGCA-CTTGTAAAAATAAAAATTTAAATCCAATGTGGCTGAG
65 TAATTAAATCGAAACAAGATTCA--AATCTCGT-AAAACAAATCCTTAAATCCAATGTGGCTGAG
* * * * ** *
6306 ATTTGATTAGATGAACATAGATATCTAAAGGAGTCTTAACGCCAAAAATCATGCAAAACTGAGGC
127 ATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACT-AAGC
* ** * * * * * *
6371 GGGGCCACATAACACTTTTTTATACAAAAACTGTGATGGAT-TACACGATTTCGGCTAAAATTTT
191 AGGGCC-CGGAACGCGTTTTTA-GCCAAAACCGTGAT-GTTGTACACGATTTCGGCTAAAATTTT
* * * * * * *
6435 GTAAAAATTGACCCGAAAAATATTTCATCAATTTTT-GACTAAAATACTCATAAAAAATACATAA
253 GCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAG-CAAAAATACTCATAAAAATTATATAA
* *
6499 CTCAACGCC
317 TTCAACACC
* * * * * *
6508 AAAAAGATTGAAGGGCTTTTGACGTTTCTAATATTGTTTTTTCTATTTTTTCCAAATTAATTTCT
1 AAAAAGATTGAAGGACTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCCGAATTAATTTCT
* * * * * *
6573 AATTAAATCGAAACAAAATCCAGATACTCGTAAAGACAAATCTTTAAATCTAATGTGGGTGAGAT
66 AATTAAATCGAAACAAGATTCAAAT-CTCGTAAA-ACAAATCCTTAAATCCAATGTGGCTGAGAT
** * * * * * * *
6638 TTTATTAGATGAATATAGATATTTTAAGTAGTCTTTGGAGCCAGAAATCATGCAAAATTGAGCCG
129 TTGGTTAGATGAATATAGATATTTCAAGGAGTC-TTGGCGCCAAAAATCATGCAAAACTAAGCAG
** **
6703 GGTCCCGGAACGTATTTTTAGCCAAAAAACCGTGATGGTTTATTAGTAACACGATTTCAACTAAA
193 GG-CCCGGAACGCGTTTTTAGCC--AAAACCGTGAT-G----TT-GT-ACACGATTTCGGCTAAA
** * * *
6768 ATTTTGCAAAAATTGACATGAAAGATTTCTT-CTCAA--TTTAGCTAAAATACTCTTAACAA-TA
248 ATTTTGCAAAAATTGACCCGAAAGATTT-TTCCTCAATTTTTAGCAAAAATACTCATAAAAATTA
*
6829 TATAATTCAACGCC
312 TATAATTCAACACC
* * * * * * * * ** *
6843 AAAAATATTGGAGGGCTTTTTACGCTTTTAATATCATATTTCTTATTTTTTTCTAAATAAATTTC
1 AAAAAGATTGAAGGACTTTTCACGCTTCTAATATCGTTTTTCCTA-TTTTTTCCGAATTAATTTC
** * * * ** * * *
6908 TAATTAAATAAAAAAAAGATTCAGATACTCGTAAAAACAAATGCTTAAATTTAATTTTGCTGGGA
65 TAATTAAATCGAAACAAGATTCAAAT-CTCGT-AAAACAAATCCTTAAATCCAATGTGGCTGAGA
6973 TTTGGTTAGATGA
128 TTTGGTTAGATGA
6986 TGTAAAGTAT
Statistics
Matches: 3531, Mismatches: 713, Indels: 478
0.75 0.15 0.10
Matches are distributed among these distances:
313 24 0.01
314 70 0.02
315 47 0.01
317 21 0.01
318 10 0.00
320 12 0.00
321 65 0.02
322 7 0.00
323 47 0.01
324 208 0.06
325 12 0.00
326 9 0.00
327 1 0.00
328 10 0.00
329 156 0.04
330 391 0.11
331 207 0.06
332 509 0.14
333 288 0.08
334 59 0.02
335 193 0.05
336 186 0.05
337 64 0.02
338 137 0.04
339 56 0.02
340 38 0.01
341 77 0.02
342 13 0.00
343 72 0.02
344 3 0.00
345 46 0.01
346 5 0.00
347 14 0.00
348 182 0.05
349 98 0.03
350 42 0.01
351 8 0.00
352 18 0.01
353 63 0.02
354 2 0.00
355 13 0.00
356 6 0.00
357 27 0.01
358 15 0.00
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (325 bp):
AAAAAGATTGAAGGACTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCCGAATTAATTTCT
AATTAAATCGAAACAAGATTCAAATCTCGTAAAACAAATCCTTAAATCCAATGTGGCTGAGATTT
GGTTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTAAGCAGGGC
CCGGAACGCGTTTTTAGCCAAAACCGTGATGTTGTACACGATTTCGGCTAAAATTTTGCAAAAAT
TGACCCGAAAGATTTTTCCTCAATTTTTAGCAAAAATACTCATAAAAATTATATAATTCAACACC
Found at i:7206 original size:31 final size:30
Alignment explanation
Indices: 7139--7207 Score: 129
Period size: 30 Copynumber: 2.3 Consensus size: 30
7129 TCATAAGACC
7139 AATTTTTTTAAACATGTAAAGTATTAAACT
1 AATTTTTTTAAACATGTAAAGTATTAAACT
*
7169 AATTTTTTTAGACATGTAAAGTATTAAACT
1 AATTTTTTTAAACATGTAAAGTATTAAACT
7199 AATTTTTTT
1 AATTTTTTT
7208 CCTCAATGCT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.39, C:0.06, G:0.07, T:0.48
Consensus pattern (30 bp):
AATTTTTTTAAACATGTAAAGTATTAAACT
Found at i:7380 original size:15 final size:16
Alignment explanation
Indices: 7362--7391 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
7352 ATAAATAATA
7362 ATATTATAAT-TAAAT
1 ATATTATAATCTAAAT
7377 ATATTATAATCTAAA
1 ATATTATAATCTAAA
7392 AATAATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATTATAATCTAAAT
Found at i:10060 original size:85 final size:85
Alignment explanation
Indices: 9970--10128 Score: 291
Period size: 85 Copynumber: 1.9 Consensus size: 85
9960 GTAATATAGT
*
9970 AAAAATAAAATAGGTATAAGGATATTATATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAA
1 AAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAA
10035 AACTATAAAAGTAAAATGGG
66 AACTATAAAAGTAAAATGGG
* *
10055 AAAAATAAAATAGTTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGATTAA
1 AAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAA
10120 AACTATAAA
66 AACTATAAA
10129 GGTTTAAACA
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
85 71 1.00
ACGTcount: A:0.52, C:0.01, G:0.13, T:0.33
Consensus pattern (85 bp):
AAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAA
AACTATAAAAGTAAAATGGG
Found at i:11922 original size:106 final size:100
Alignment explanation
Indices: 11741--11926 Score: 264
Period size: 106 Copynumber: 1.8 Consensus size: 100
11731 ACAAGTCAAT
* * * *
11741 AGTAACATGACTATATATAGAGGACAATATAATTAAATACTATAAATATTTTTCATGTTTTCATA
1 AGTAACATGACTATATATAGAGGACAATATAATAAAAAACTATAAAAATTATTCATGTTTTCATA
11806 TATCTGGACATACAAGTTTAATTAAAACCGTAGTA
66 TATCTGGACATACAAGTTTAATTAAAACCGTAGTA
*
11841 AGTAACATGACTATATATATAGTAGAGAACAATATTATGAAAAAACTATAAAAATTATTCATGTT
1 AGTAACATGAC--TATATATAG-AG-G-ACAATATAAT-AAAAAACTATAAAAATTATTCATGTT
*
11906 TTCATATATCTTGACATACAA
60 TTCATATATCTGGACATACAA
11927 ACCTAATCAA
Statistics
Matches: 74, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
100 11 0.15
102 9 0.12
103 2 0.03
104 1 0.01
105 9 0.12
106 42 0.57
ACGTcount: A:0.44, C:0.11, G:0.10, T:0.35
Consensus pattern (100 bp):
AGTAACATGACTATATATAGAGGACAATATAATAAAAAACTATAAAAATTATTCATGTTTTCATA
TATCTGGACATACAAGTTTAATTAAAACCGTAGTA
Found at i:14913 original size:12 final size:12
Alignment explanation
Indices: 14896--14920 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
14886 AATATTCATC
14896 GAATGAGTCTTG
1 GAATGAGTCTTG
14908 GAATGAGTCTTG
1 GAATGAGTCTTG
14920 G
1 G
14921 GAGGGAAGCA
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:0.24, C:0.08, G:0.36, T:0.32
Consensus pattern (12 bp):
GAATGAGTCTTG
Found at i:16864 original size:39 final size:39
Alignment explanation
Indices: 16820--16894 Score: 105
Period size: 39 Copynumber: 1.9 Consensus size: 39
16810 GTCCCTCCTA
* *
16820 ATAATTAAGAAAACAAATTAAATTCAGGTTTAACCCCTG
1 ATAATTAAGAAAACAAATTAAATCCAGATTTAACCCCTG
** *
16859 ATAATTAAGGTAAGAAATTAAATCCAGATTTAACCC
1 ATAATTAAGAAAACAAATTAAATCCAGATTTAACCC
16895 TTAATTATAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 31 1.00
ACGTcount: A:0.47, C:0.15, G:0.11, T:0.28
Consensus pattern (39 bp):
ATAATTAAGAAAACAAATTAAATCCAGATTTAACCCCTG
Found at i:18165 original size:9 final size:10
Alignment explanation
Indices: 18150--18174 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
18140 AAAGGACAGA
18150 AAAAAAAAAC
1 AAAAAAAAAC
18160 AAAAAAAAAC
1 AAAAAAAAAC
18170 AAAAA
1 AAAAA
18175 CGAGAAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:22024 original size:14 final size:15
Alignment explanation
Indices: 21995--22038 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
21985 TGCCCCACTT
*
21995 TTTACACTTTTTCCC
1 TTTACACTTTTACCC
22010 TTTAC-CTTTTACCC
1 TTTACACTTTTACCC
22024 TTTTTACACTTTTAC
1 --TTTACACTTTTAC
22039 ACTGAGCATC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 8 0.32
15 5 0.20
16 5 0.20
17 7 0.28
ACGTcount: A:0.16, C:0.30, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTACACTTTTACCC
Found at i:22182 original size:32 final size:33
Alignment explanation
Indices: 22110--22193 Score: 98
Period size: 33 Copynumber: 2.6 Consensus size: 33
22100 CCATGGGCAG
* **
22110 GCCGCCCCAGTGGGGCGGCCTATTCATAGTGAA
1 GCCGCCCTAGTGGGGCGGCCTACCCATAGTGAA
* *
22143 GCCGCCCTAGTGGGGCGGCCTGCCCATGGT-AA
1 GCCGCCCTAGTGGGGCGGCCTACCCATAGTGAA
**
22175 GCCGCCCTCTTGGGGCGGC
1 GCCGCCCTAGTGGGGCGGC
22194 ACGGGTCATT
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
32 19 0.43
33 25 0.57
ACGTcount: A:0.12, C:0.35, G:0.37, T:0.17
Consensus pattern (33 bp):
GCCGCCCTAGTGGGGCGGCCTACCCATAGTGAA
Found at i:25749 original size:25 final size:27
Alignment explanation
Indices: 25697--25749 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
25687 TTACTCAACT
**
25697 AAAAACTCTATTTTTATTTTTCTGTAA
1 AAAAACTCTATTTTTATTTTAATGTAA
25724 AAAAACTCTATTTTTA-TTTAAT-TAA
1 AAAAACTCTATTTTTATTTTAATGTAA
25749 A
1 A
25750 TCTAATATCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 4 0.17
26 4 0.17
27 16 0.67
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (27 bp):
AAAAACTCTATTTTTATTTTAATGTAA
Done.