Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020394.1 Corchorus olitorius cultivar O-4 contig20427, 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: 9343
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.35
Found at i:2132 original size:15 final size:16
Alignment explanation
Indices: 2114--2143 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2104 ATAAATAATA
2114 ATATTATAAT-TAAAT
1 ATATTATAATCTAAAT
2129 ATATTATAATCTAAA
1 ATATTATAATCTAAA
2144 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:3177 original size:28 final size:26
Alignment explanation
Indices: 3141--3196 Score: 67
Period size: 28 Copynumber: 2.1 Consensus size: 26
3131 ACGTGTTTAA
* *
3141 ATAAAAAAATATTAAAATAATTGAAATT
1 ATAAAAAAAAATT-AAAGAATT-AAATT
*
3169 ATAATAAAAAATTAAAGAATTAAATT
1 ATAAAAAAAAATTAAAGAATTAAATT
3195 AT
1 AT
3197 TATATTGTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 7 0.28
27 7 0.28
28 11 0.44
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (26 bp):
ATAAAAAAAAATTAAAGAATTAAATT
Found at i:4701 original size:25 final size:26
Alignment explanation
Indices: 4658--4707 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 26
4648 GGTACTGTAC
4658 AAATTGAATTTTTCTAAATAAAATAA
1 AAATTGAATTTTTCTAAATAAAATAA
4684 AAATTGAA-TTTTCTAAATAAAATA
1 AAATTGAATTTTTCTAAATAAAATA
4708 TTTTGATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 16 0.67
26 8 0.33
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (26 bp):
AAATTGAATTTTTCTAAATAAAATAA
Found at i:4894 original size:25 final size:27
Alignment explanation
Indices: 4842--4907 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
4832 AAAAGTACAC
*
4842 AAAATTATATTTTAATAGTGGCATAA-TT
1 AAAA-TATATTTTAATAATGGCA-AATTT
*
4870 AAAATATTTTTTAATAATGGC-AATTT
1 AAAATATATTTTAATAATGGCAAATTT
4896 AGAAATATATTT
1 A-AAATATATTT
4908 GGAGAAAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
25 2 0.06
26 3 0.09
27 24 0.73
28 4 0.12
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.44
Consensus pattern (27 bp):
AAAATATATTTTAATAATGGCAAATTT
Found at i:5897 original size:351 final size:351
Alignment explanation
Indices: 5248--5937 Score: 1021
Period size: 351 Copynumber: 2.0 Consensus size: 351
5238 ATTGCCAAGT
**
5248 CAGATGTCTTGAAGTCTAAATCTGATATTCTTAGACCCAAATTGTTAACATGGAAGCCCAAAGAA
1 CAGATGTCTTGAAACCTAAATCTGATATTCTTAGACCCAAATTGTTAACATGGAAGCCCAAAGAA
*
5313 GGAGTTCAAGACCAATCAGTAACTATGATGCAGTAATGATTCAGCCCTGATGCAGCATTGTTAAA
66 GGAGTCCAAGACCAATCAGTAACTATGATGCAGTAATGATTCAGCCCTGATGCAGCATTGTTAAA
* * *
5378 TCATATTTAAAGGAGGACTTAACAAGAGCAATTTTGGAAGAAAATTCATAACTTTTGATCCAGAG
131 TCATATTCAAAAGAGGACTTAACAAGAGCAATTTTGGAAGAAAATTCATAACTTTTGATCCAAAG
* ** * *
5443 CTCAGAAAAAATGCAAATGAGATGTCGTTGGAAAGAGAATTCCAAGATCTACAACTTTTATGTTA
196 CTCAGAAAAAATACAAATGAGATACCGTTGAAAAGAGAATTCCAAGACCTACAACTTTTATGTTA
* **
5508 CCTTGAGACCTGATTCTGCAGCTTCGATAGACGATTTTGACCTTAAAATTTCTAG-ATTGAATTG
261 CCTTGAGACCTAATTCTGCAGCTTCGATAGACGATTTTGACCTTAAAATTTCT-GTATAAAATTG
*
5572 ATCTTCTTCTAAACCGATGTGGAGAGC
325 ATCTTCTCCTAAACCGATGTGGAGAGC
* *
5599 CAGATGTCTTGAAACCTAAATCTGATATTCTTAGACCCAATTTGTTAATATGGAAGCCCAAAGAA
1 CAGATGTCTTGAAACCTAAATCTGATATTCTTAGACCCAAATTGTTAACATGGAAGCCCAAAGAA
* * *
5664 GGAGTCCAAGTCCAATCAGTAATTATGATGCAGTAATGGTTCAGCCCTGATGCAGCATTGTTAAA
66 GGAGTCCAAGACCAATCAGTAACTATGATGCAGTAATGATTCAGCCCTGATGCAGCATTGTTAAA
* * * *
5729 TCCTATTCAAAAGAGGACTTCACAAGAGCAGTTTTGGAAGAAAATTCATAACTTTTGATCTAAAG
131 TCATATTCAAAAGAGGACTTAACAAGAGCAATTTTGGAAGAAAATTCATAACTTTTGATCCAAAG
*
5794 CTCAG-AAAAATACAAATGATATACCGTTGAAAAGATG-ATTCCAAGACCTACAACTTTTATGTT
196 CTCAGAAAAAATACAAATGAGATACCGTTGAAAAGA-GAATTCCAAGACCTACAACTTTTATG-T
* * * * * *
5857 TACC-TGAAGACCTAATTCTTCAG-TTCTAGTGGATGATTTTGCCCTTGAAATTTCTGTATAAAA
259 TACCTTG-AGACCTAATTCTGCAGCTTCGA-TAGACGATTTTGACCTTAAAATTTCTGTATAAAA
5920 TTGATCTTCTCCTAAACC
322 TTGATCTTCTCCTAAACC
5938 AACTTGGAGA
Statistics
Matches: 303, Mismatches: 31, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
350 55 0.18
351 248 0.82
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.30
Consensus pattern (351 bp):
CAGATGTCTTGAAACCTAAATCTGATATTCTTAGACCCAAATTGTTAACATGGAAGCCCAAAGAA
GGAGTCCAAGACCAATCAGTAACTATGATGCAGTAATGATTCAGCCCTGATGCAGCATTGTTAAA
TCATATTCAAAAGAGGACTTAACAAGAGCAATTTTGGAAGAAAATTCATAACTTTTGATCCAAAG
CTCAGAAAAAATACAAATGAGATACCGTTGAAAAGAGAATTCCAAGACCTACAACTTTTATGTTA
CCTTGAGACCTAATTCTGCAGCTTCGATAGACGATTTTGACCTTAAAATTTCTGTATAAAATTGA
TCTTCTCCTAAACCGATGTGGAGAGC
Found at i:7845 original size:339 final size:331
Alignment explanation
Indices: 6351--9278 Score: 1706
Period size: 336 Copynumber: 8.8 Consensus size: 331
6341 TTGAAAAGAT
* * * * *
6351 GCCAAAAAGATTGGAGGACTTTTCACGATTTTAATATCGTTTTTCATATTTTTTCTGAATTGATT
1 GCCAAAAAGATTGAAGGACTTTTCACGCTTCTAATATCGTTTTTCATATTTTTTCCGAATTAATT
** * * * *
6416 TCTAATTAAATCGAAACAAGATTCGGATACAT-ATAAAAACAAATCCATAAATCCAATGTGGCTG
66 TCTAATTAAATCGAAACAAGATTCAAATGC-TCGTAAAAACAAATCCTTAAATCCAATGTAGCTG
** * * **
6480 AGATTTGGTTAGATGAATAAAGATATTTCAAGGAGTCTCGGCACCAAAAATCATGCAAAAC-AGA
130 AGATTTCATTAGATGAATATAGATATTTCAAGGAGTCTAGGTGCCAAAAATCATGCAAAACTA-A
* * * * * * * *
6544 -GCGGTGCCCCTGTAACGTGTTTTTAGCC--CAAAACCGTGATGGGTAGTACACGATTTCGGCTA
194 TCCGG-GCCCCAG-AACGCGTTTTAAGCCAAGAAAAAC-TGAT-GATAATACACGATTTCGGCTA
* * * * * * * * * * *
6606 AAATTTTGCAAAACTTGACCCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAA-AT
255 AAATTTTACAAAAATTGACCCAAAATATTTTTCCTCCAGTTTTAGCGACAATACTCAAAAAATAT
* *
6670 ATATAATTCTAT
320 ATATAATTCAAC
** * * * * * *
6682 ATCAAAAAGATTGAAGGGCTTTTAATGCTTCTAATATTG-TTTTCCTATTTTTTCCAAATTAATT
1 GCCAAAAAGATTGAAGGACTTTTCACGCTTCTAATATCGTTTTTCATATTTTTTCCGAATTAATT
* * * * * * * *
6746 TTTAATTAAATCGAAATAAGATTCAGATTCTCCTAAAAGCAAAT-CTTCAAATCTAATGTGGCTG
66 TCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTT-AAATCCAATGTAGCTG
** * * *** *
6810 AGATTTGGTTAGATGAATATAAATATTTCAAGGAGTCTTGCCACCAAAAATCATGTAAAACTAAG
130 AGATTTCATTAGATGAATATAGATATTTCAAGGAGTCTAGGTGCCAAAAATCATGCAAAACTAA-
* * * * * * * *
6875 T-CGGGCCCCAAAAGGCGTTTTTAGCC--GAAAACCGCGATGGTTAGTACATGATTTCGGCT-AA
194 TCCGGGCCCCAGAACGCGTTTTAAGCCAAGAAAAAC-TGAT-GATAATACACGATTTCGGCTAAA
* * * * * * * *
6936 ATTTTGCAAAAATTGACCCGAAAGATTTCTCCT--GGTTTTCTAGCGAAAATACTCATAAAAGTT
257 ATTTTACAAAAATTGACCCAAAATATTTTTCCTCCAG-TTT-TAGCGACAATACTCA-AAAAATA
*
6999 TA-ATAATTCGAC
319 TATATAATTCAAC
* * * * **
7011 GCCAAAAA-A-GGAAAGCCTTTTTCACGCTTCTAATATCGTTTTTCCTATTTTCTTTCAAAATTA
1 GCCAAAAAGATTGAAGGAC-TTTTCACGCTTCTAATATCGTTTTTCATA-TTT-TTTCCGAATTA
* * ** * * *
7074 ATTTCTGATTAAATCGAAACAAGATTTAAAAACTCGTACAAACAAATCCTTAAATACAATGTGGC
63 ATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATCCAATGTAGC
** * * * * * *
7139 TGAGATTTGGTTAGATGAATGTATG-TATGT--ATGA-TATA--T---ATATATCATGCAAAACT
128 TGAGATTTCATTAGATGAATATA-GATATTTCAAGGAGTCTAGGTGCCAAAAATCATGCAAAACT
* * * * ** * *
7195 AAGCTAGAGCCCCGGAACGC-------G---A-AATCA-TGATGGTAAT-CA--ATTTCGGCAAA
192 AATC-CGGGCCCCAGAACGCGTTTTAAGCCAAGAAAAACTGATGATAATACACGATTTCGGCTAA
* * * * * *
7245 AATTTTAGAACAATTGA-CCAAAATATTTTT-CTCAATTTTTAGCCACAATACTCATAAAATATA
256 AATTTTACAAAAATTGACCCAAAATATTTTTCCTCCAGTTTTAGCGACAATACTCAAAAAATATA
*
7308 TATAACTCAAC
321 TATAATTCAAC
* * * * * *
7319 GCCAAAAAGATTGAAGGGCTTCTCACGCTTCTAATATCGTTTTTCGTATTTGTTTTCAAATTAGT
1 GCCAAAAAGATTGAAGGACTTTTCACGCTTCTAATATCGTTTTTCATATTT-TTTCCGAATTAAT
* * *
7384 TTCTAATTAAATTGAAACATGATTCAAATGCTCGTAAAAACAAATCCTTAAATCCAATGTAGCTA
65 TTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATCCAATGTAGCTG
** * * * *
7449 AGATTTGGTTAGATGAATATAGATATTTCAAGGGATGT-T-GCTACTAAAAATCATGCAACACTA
130 AGATTTCATTAGATGAATATAGATATTTCAA-GGA-GTCTAGGTGCCAAAAATCATGCAAAACTA
* ** ** *
7512 ACCCGGAGCCCCAGAACGCGTTTTTGGCCAAGAAAAACTG-TGATCGTACATGATTTCGGCTAAA
193 ATCCGG-GCCCCAGAACGCGTTTTAAGCCAAGAAAAACTGATGATAATACACGATTTCGGCTAAA
*
7576 ATTTTACAAAAATTGACCCGAAATATTTTTCCTCCAGTTTTAGCGACAATACTCATATGATATAT
257 ATTTTACAAAAATTGACCCAAAATATTTTTCCTCCAGTTTTAGCGACAATACTC--A--A-A-A-
* *
7641 ATATATATATAATTAAAA
315 A-ATATATATAATTCAAC
* * * * *
7659 GCCTAAAAGATTGGAGGACTCTTCACGCTTTTAATATCGTTTTTCATA-TTTTTCCGAATTTATT
1 GCCAAAAAGATTGAAGGACTTTTCACGCTTCTAATATCGTTTTTCATATTTTTTCCGAA-TTAAT
* * ** * *
7723 TTCTAATTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAATCCTTAAATTGAATGTGGGTG
65 TTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATCCAATGTAGCTG
7788 AGATTTCATTAGATGAATATAGATATTTCAAGGAGTCTAGGTGCCAAAAATCATGCAAAACTAAT
130 AGATTTCATTAGATGAATATAGATATTTCAAGGAGTCTAGGTGCCAAAAATCATGCAAAACTAAT
* ** * * * *
7853 TCGGGGTCCAGAAACGCGTTTTAAGCCAA-AAACA-TGATGGTTAATGCACGATTTTGGCTAGAA
195 CCGGGCCCCAG-AACGCGTTTTAAGCCAAGAAAAACTGAT-GATAATACACGATTTCGGCTA-AA
* * ** * * * *
7916 TTTTGTAAAAAAAAAAGACCCGAAAA-ATTTTTCCGT-CAATTTTGGC-ATAAATAATCATAAAA
257 ATTT-T-ACAAAAATTGACCC-AAAATATTTTTCC-TCCAGTTTTAGCGA-CAATACTC--AAAA
* *
7978 AATATACATAATTTAAC
315 AATATATATAATTCAAC
* * * * * * *
7995 GCTAAAAGGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATA-TTTTGCTGAATTAAGT
1 GCCAAAAAGATTGAAGGACTTTTCACGCTTCTAATATCGTTTTTCATATTTTTTCCGAATTAATT
* * * * *
8059 TCTAATTAAACCGAAACAAGATTGAGATGCTCGTAAAAACAAATTCTTAAATTCAATTGTAGCTG
66 TCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATCCAA-TGTAGCTG
* * * * * * * * * * * * *
8124 ATATTTGATTAAATGGATGTGGATATCTCAAAGAGTTTTGGCGTCAAAAATCATGCAAAACTTAG
130 AGATTTCATTAGATGAATATAGATATTTCAAGGAGTCTAGGTGCCAAAAATCATGCAAAAC-TAA
* * * *
8189 TCAGGGCCCCGGAACGCGTTTTAAG-C--GAAAAACCGTGATGATTATTACACGATTTCGGCTAG
194 TCCGGGCCCCAGAACGCGTTTTAAGCCAAGAAAAA-C-TGATGA-TAATACACGATTTCGGCTAA
* * * *
8251 AATTTTACAAAAATTGACTCAAAAGTA-ATTTCCTCGAGTTTTAGCCG-CAATAGTCATAAAAAT
256 AATTTTACAAAAATTGACCCAAAA-TATTTTTCCTCCAGTTTTAG-CGACAATACTCA-AAAAAT
8314 -TATATAATTCAAC
318 ATATATAATTCAAC
* * *
8327 GCCAAAAAGATTGAAGGACTTTTCATGCTTCTAGTATCGTTTTTCCTATTATTTTCCGAATTAAT
1 GCCAAAAAGATTGAAGGACTTTTCACGCTTCTAATATCGTTTTTCATATT-TTTTCCGAATTAAT
* * *** * * *
8392 TTCTAATTAAATCGAAACATA-ATTCAAATCCTTGT-TTTACAAATCCTTAAATCCATTGTGGAT
65 TTCTAATTAAATCGAAACA-AGATTCAAATGCTCGTAAAAACAAATCCTTAAATCCAATGTAGCT
* *
8455 GAGATTTCATTAGA-GTAATATAGATATTTCAAGGAGTCTCAGGT-CAAAAAATCATGCAACACT
129 GAGATTTCATTAGATG-AATATAGATATTTCAAGGAGTCT-AGGTGCCAAAAATCATGCAAAACT
* * ** * * * *
8518 AAACCGGGGCCTGGAACGTGTTTTTAG---GGAAAAACCGTGATTTCGACTAACGTACGCGATTT
192 AATCCGGGCCCCAGAACGCGTTTTAAGCCAAGAAAAA-C-TGA--T-GA-TAA--TACACGATTT
* * * * * * *
8580 AGGCTAATATTTTGCAAAAATTGA-CCATAAATATTTTTCCAT--AATTTTTGTCTAAAATACTC
249 CGGCTAAAATTTTACAAAAATTGACCCA-AAATATTTTTCC-TCCAGTTTTAG-CGACAATACTC
*
8642 ATAAAATATATATAATTCAAC
311 AAAAAATATATATAATTCAAC
* * * * * * ** * *
8663 TCCATAAATATT-AGAGGACTTTTTACGCTTTTAAAATTTATTTTTTAT-TTTTTTCTGAATTAA
1 GCCAAAAAGATTGA-AGGACTTTTCACGCTTCTAATA-TCGTTTTTCATATTTTTTCCGAATTAA
** * * * ** * * *
8726 AATCTAAGTATATCGAAACAAGATTGAGGTGCTCGTAAAAACAAATCTTTAAATGCAATGTGGCT
64 TTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATCCAATGTAGCT
* * * * * * * * * *
8791 GAGATTTGATTAAATGAATACATATATTTCAAGGAGCCTCGATACTAAAAAACATGCAAAACTGA
129 GAGATTTCATTAGATGAATATAGATATTTCAAGGAGTCTAGGTGCCAAAAATCATGCAAAACT-A
* * * * * * *
8856 GTCGGGGACGC-GAAACGCGTTTTTAGCAAAAAAAAGAAAAAAAAAACTATGATGGTAACTACAC
193 ATCCGGGCCCCAG-AACGCGTTTTAAGC-----CAAG-----AAAAAC--TGATGATAA-TACAC
* * * * * * * * * *
8920 GATTTCGCCTAAAATTTTGCAAAAAATGA-CAAGAAAAATTTTTCCTCAATTTTTGGCTAAAATA
244 GATTTCGGCTAAAATTTTACAAAAATTGACCCA-AAATATTTTTCCTCCAGTTTTAGCGACAATA
** *
8984 CTCATGAAATATATATAATT-TAC
308 CTCAAAAAATATATATAATTCAAC
* * * * **
9007 GCCAAAAAGATTGGAGGACGTTTCACGATT-TACATATCATTTTTCATATTTTTTCTAAATTAAT
1 GCCAAAAAGATTGAAGGACTTTTCACGCTTCTA-ATATCGTTTTTCATATTTTTTCCGAATTAAT
* * **
9071 TTCTAATTAAATCGAAATAAGATAT-AGATGCTCGTAAAAACAAATCCTTAAATGAAATGT-GTC
65 TTCTAATTAAATCGAAACAAGAT-TCAAATGCTCGTAAAAACAAATCCTTAAATCCAATGTAG-C
* ** * * * *
9134 TGAGATTTGATTTCATGAATAT-GATATCTCAAGTAGTCTCAGCAT--CAAAAATCATGCAAAAT
128 TGAGATTTCATTAGATGAATATAGATATTTCAAGGAGTCT-AG-GTGCCAAAAATCATGCAAAAC
** * * * * * *
9196 TGACCCCGGGCCCTAGAACACATTTTTA-CC-A-AAAATCGTGATGATTATTAC-CGATTTCGGC
191 T-AATCCGGGCCCCAGAACGCGTTTTAAGCCAAGAAAAAC-TGATGA-TAATACACGATTTCGGC
9257 TAAAATTTTGA-AAAAATTGACC
253 TAAAATTTT-ACAAAAATTGACC
9279 GGAAAGATAT
Statistics
Matches: 2040, Mismatches: 420, Indels: 276
0.75 0.15 0.10
Matches are distributed among these distances:
307 7 0.00
308 123 0.06
309 49 0.02
310 21 0.01
311 4 0.00
312 5 0.00
313 5 0.00
315 3 0.00
316 28 0.01
317 1 0.00
323 17 0.01
324 10 0.00
326 1 0.00
327 15 0.01
328 95 0.05
329 82 0.04
330 171 0.08
331 165 0.08
332 124 0.06
333 30 0.01
334 76 0.04
335 116 0.06
336 294 0.14
337 62 0.03
338 22 0.01
339 147 0.07
340 60 0.03
341 2 0.00
342 37 0.02
343 61 0.03
344 114 0.06
345 73 0.04
346 9 0.00
347 1 0.00
348 1 0.00
349 1 0.00
350 8 0.00
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.33
Consensus pattern (331 bp):
GCCAAAAAGATTGAAGGACTTTTCACGCTTCTAATATCGTTTTTCATATTTTTTCCGAATTAATT
TCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATCCAATGTAGCTGA
GATTTCATTAGATGAATATAGATATTTCAAGGAGTCTAGGTGCCAAAAATCATGCAAAACTAATC
CGGGCCCCAGAACGCGTTTTAAGCCAAGAAAAACTGATGATAATACACGATTTCGGCTAAAATTT
TACAAAAATTGACCCAAAATATTTTTCCTCCAGTTTTAGCGACAATACTCAAAAAATATATATAA
TTCAAC
Found at i:8650 original size:668 final size:664
Alignment explanation
Indices: 6351--9331 Score: 1742
Period size: 668 Copynumber: 4.5 Consensus size: 664
6341 TTGAAAAGAT
* * * * * *
6351 GCCAAAAAGATTGGAGGACTTTTCACGATTTTAATATCGTTTTTCATATTTTTTCTGAA-TTGAT
1 GCCAAAAAGATTGAAGGACTCTTCACGCTTCTAATATCGTTTTTCATA-TTTTTCCGAATTTAAT
** * * *
6415 TTCTAATTAAATCGAAACAAGATTCGGATACAT-ATAAAAACAAATCCATAAATCCAATGTGGCT
65 TTCTAATTAAATCGAAACAAGATTCAAAT-CATCGTAAAAACAAATCCTTAAATCCAATGTGGAT
** * * ** * *
6479 GAGATTTGGTTAGATGAATAAAGATATTTCAAGGAGTCTCGGCACCAAAAATCATGCAAAAC-AG
129 GAGATTTCATTAGATGAATATAGATATTTCAAGGAGTCTAGGTGCAAAAAATCATGCAAAACTAA
* ** * * * * * * ** * * *
6543 AGCGGTGCCCCTGTAACGTGTTTTTAGCCCAAAACCGTGATGGGTAGTACACGATTTCGGCTAAA
194 ACCGG-GGTCCAGAAACGCGTTTTAAG-CCAAAAACATGATGACTAATACACGATTTAGGCTAGA
* * * * *
6608 ATTTTG-CAAAACTTGACCCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAA-ATA
257 ATTTTGAAAAAAATTGA-CCAAAATATTTTTCCTCAATTTTT-GC-AAAATACTCATAAAATATA
* * * * * * * * *
6671 TATAATTCTATA-TCAAAAAGATTGAAGGGCTTTTAATGCTTCTAATATTG-TTTTCCTATTTTT
319 TATAATTC-A-ACGCCAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATA-TTTT
** * * * * * * *
6734 TCCAAATTAATTTTTAATTAAATCGAAATAAGATTCAGATTCTCCTAAAAGCAAA-TCTTCAAAT
381 TCTGAATTAAGTTCTAATTAAATCGAAACAAGATTGAGATGCTCGTAAAAACAAATTCTT-AAAT
* * * * * * * * *
6798 CTAATGTGGCTGAGATTTGGTTAGATGAATATAAATATTTCAAG-GAGTCTTGCCACCAAAAATC
445 CCAATGTAGCTGAGATTTGATTAAATGAATATAGATATCTCAAGAGA-TGTTGCTACTAAAAATC
* * * * * * * * *
6862 ATGTAAAACTAAGTC-GG-GCCCCAAAAGGCGTTTTTAGCC-GAAAACCGCGATGGTTAGTACAT
509 ATGCAAAACTAA-CCAGGAGCCCCAGAACGCGTTTTAAGCCAGAAAAAC-TG-T-GATAGTACAC
* * * * *
6924 GATTTCGGCT-AAATTTTGCAAAAATTGACCC-GAA-AGATTT-CTCCTGGTTTTCTAGCGAAAA
570 GATTTCGGCTAAAATTTTACAAAAATTGACCCAAAATATATTTCCTCC-AG-TTT-TAGCGACAA
** *
6985 TACTC-AT-A-A-A-AGT-T-TA-ATAATTCGAC
632 TACTCAATGATATATA-TATATATATAATTAAAA
* * * * * * * *
7011 GCCAAAAA-A-GGAAAGCCTTTTTCACGCTTCTAATATCGTTTTTCCTATTTTCTTTCAAAATTA
1 GCCAAAAAGATTGAAGGAC-TCTTCACGCTTCTAATATCGTTTTTCATA-TTT-TTCCGAATTTA
* * * * *
7074 ATTTCTGATTAAATCGAAACAAGATTTAAA-AACTCGTACAAACAAATCCTTAAATACAATGTGG
63 ATTTCTAATTAAATCGAAACAAGATTCAAATCA-TCGTAAAAACAAATCCTTAAATCCAATGTGG
* ** * * * * * *
7138 CTGAGATTTGGTTAGATGAATGTATG-TATGT--ATGA-TATA--T---ATATATCATGCAAAAC
127 ATGAGATTTCATTAGATGAATATA-GATATTTCAAGGAGTCTAGGTGCAAAAAATCATGCAAAAC
* ** * * * * * * * * *
7194 TAAGCTAGAGCCCCGGAACGC-------G---AAATCATGATG-GTAAT-CA--ATTTCGGCAAA
191 TAAACCGGGGTCCAGAAACGCGTTTTAAGCCAAAAACATGATGACTAATACACGATTTAGGCTAG
* * *
7245 AATTTT-AGAACAATTGACCAAAATATTTTT-CTCAATTTTTAGCCACAATACTCATAAAATATA
256 AATTTTGAAAAAAATTGACCAAAATATTTTTCCTCAATTTTT-G-CAAAATACTCATAAAATATA
* * * * * *
7308 TATAACTCAACGCCAAAAAGATTGAAGGGCTTCTCACGCTTCTAATATCGTTTTTCGTATTTGTT
319 TATAATTCAACGCC-AAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTT-TT
* * * * * * *
7373 TTCAAATT-AGTTTCTAATTAAATTGAAACATGATTCAAATGCTCGTAAAAACAAATCCTTAAAT
382 CT-GAATTAAG-TTCTAATTAAATCGAAACAAGATTGAGATGCTCGTAAAAACAAATTCTTAAAT
* * * * *
7437 CCAATGTAGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGGATGTTGCTACTAAAAATCA
445 CCAATGTAGCTGAGATTTGATTAAATGAATATAGATATCTCAAGAGATGTTGCTACTAAAAATCA
* * ** * *
7502 TGCAACACTAACCCGGAGCCCCAGAACGCGTTTTTGGCCAAGAAAAACTGTGATCGTACATGATT
510 TGCAAAACTAACCAGGAGCCCCAGAACGCGTTTTAAGCC-AGAAAAACTGTGATAGTACACGATT
* *
7567 TCGGCTAAAATTTTACAAAAATTGACCCGAAATATTTTTCCTCCAGTTTTAGCGACAATACTCAT
574 TCGGCTAAAATTTTACAAAAATTGACCCAAAATATATTTCCTCCAGTTTTAGCGACAATACTCA-
7632 ATGATATATATATATATATAATTAAAA
638 ATGATATATATATATATATAATTAAAA
* * * *
7659 GCCTAAAAGATTGGAGGACTCTTCACGCTTTTAATATCGTTTTTCATATTTTTCCGAATTTATTT
1 GCCAAAAAGATTGAAGGACTCTTCACGCTTCTAATATCGTTTTTCATATTTTTCCGAATTTAATT
* * ** *
7724 TCTAATTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAATCCTTAAATTGAATGTGGGTGA
66 TCTAATTAAATCGAAACAAGATTCAAATCATCGTAAAAACAAATCCTTAAATCCAATGTGGATGA
* **
7789 GATTTCATTAGATGAATATAGATATTTCAAGGAGTCTAGGTGCCAAAAATCATGCAAAACTAATT
131 GATTTCATTAGATGAATATAGATATTTCAAGGAGTCTAGGTGCAAAAAATCATGCAAAACTAAAC
** * *
7854 CGGGGTCCAGAAACGCGTTTTAAGCCAAAAACATGATGGTTAATGCACGATTTTGGCTAGAATTT
196 CGGGGTCCAGAAACGCGTTTTAAGCCAAAAACATGATGACTAATACACGATTTAGGCTAGAATTT
** * *
7919 TGTAAAAAAAAAAGACCCGAAAA-ATTTTTCCGTCAATTTTGGCATAAATAATCATAAAAAATAT
261 TG--AAAAAAATTGA-CC-AAAATATTTTTCC-TCAATTTTTGCA-AAATACTCAT--AAAATAT
* * * *
7983 ACATAATTTAACGCTAAAAGGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTG
318 ATATAATTCAACGCCAAAA-GATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTT
* *
8048 CTGAATTAAGTTCTAATTAAACCGAAACAAGATTGAGATGCTCGTAAAAACAAATTCTTAAATTC
382 CTGAATTAAGTTCTAATTAAATCGAAACAAGATTGAGATGCTCGTAAAAACAAATTCTTAAATCC
* * * * *
8113 AATTGTAGCTGATATTTGATTAAATGGATGTGGATATCTCAA-AGAGTTTTGGCGT-C-AAAAAT
447 AA-TGTAGCTGAGATTTGATTAAATGAATATAGATATCTCAAGAGA-TGTT-GC-TACTAAAAAT
** * *
8175 CATGCAAAACTTAGTCAGG-GCCCCGGAACGCGTTTTAAG-C-GAAAAACCGTGATGATTATTAC
508 CATGCAAAAC-TAACCAGGAGCCCCAGAACGCGTTTTAAGCCAGAAAAA-C-TG-TGA-TAGTAC
* * *
8237 ACGATTTCGGCTAGAATTTTACAAAAATTGACTCAAAAGTA-ATTTCCTCGAGTTTTAGCCG-CA
568 ACGATTTCGGCTAAAATTTTACAAAAATTGACCCAAAA-TATATTTCCTCCAGTTTTAG-CGACA
* * *
8300 ATAGTC-AT-A-A-A-A-AT-TATATAATTCAAC
631 ATACTCAATGATATATATATATATATAATTAAAA
* * * *
8327 GCCAAAAAGATTGAAGGACTTTTCATGCTTCTAGTATCGTTTTTCCTATTATTTTCCGAA-TTAA
1 GCCAAAAAGATTGAAGGACTCTTCACGCTTCTAATATCGTTTTTCATA-T-TTTTCCGAATTTAA
* * *** *
8391 TTTCTAATTAAATCGAAACATA-ATTCAAATCCTTGT-TTTACAAATCCTTAAATCCATTGTGGA
64 TTTCTAATTAAATCGAAACA-AGATTCAAATCATCGTAAAAACAAATCCTTAAATCCAATGTGGA
*
8454 TGAGATTTCATTAGA-GTAATATAGATATTTCAAGGAGTCTCAGGT-CAAAAAATCATGCAACAC
128 TGAGATTTCATTAGATG-AATATAGATATTTCAAGGAGTCT-AGGTGCAAAAAATCATGCAAAAC
* * * * ** * *
8517 TAAACCGGGG-CCTGGAACGTGTTTTTAGGGAAAAACCGTGATTTCGACTAACGTACGCGATTTA
191 TAAACCGGGGTCCAGAAACGCGTTTTAAGCCAAAAA-CATGA--T-GACTAA--TACACGATTTA
*
8581 GGCTA-ATATTTTG-CAAAAATTGACCATAAATATTTTTCCAT-AATTTTTGTCTAAAATACTCA
250 GGCTAGA-ATTTTGAAAAAAATTGACCA-AAATATTTTTCC-TCAATTTTTG-C-AAAATACTCA
* * * * * **
8643 TAAAATATATATAATTCAACTCCATAAATATTAGAGGACTTTTTACGCTTTTAAAATTTATTTTT
310 TAAAATATATATAATTCAACGCCA-AAAGATTGGAGGACTTTTCACGCTTTTAATA-TCGTTTTT
* * ** * * *
8708 TATTTTTTTCTGAATTAAAATCTAAGTATATCGAAACAAGATTGAGGTGCTCGTAAAAACAAA-T
373 CATATTTTTCTGAATTAAGTTCTAATTAAATCGAAACAAGATTGAGATGCTCGTAAAAACAAATT
* * * * * * *
8772 CTTTAAATGCAATGTGGCTGAGATTTGATTAAATGAATACATATATTTCAAG-GA-GCCTCGATA
438 C-TTAAATCCAATGTAGCTGAGATTTGATTAAATGAATATAGATATCTCAAGAGATG--TTGCTA
* ** * * * * *
8835 CTAAAAAACATGCAAAACTGAGTC-GGGGACGC-GAAACGCGTTTTTAGCAAAAAAAAGAAAAAA
500 CTAAAAATCATGCAAAACT-AACCAGGAGCCCCAG-AACGCGTTTTAAGC------CAG-----A
* * * * * * * *
8898 AAAACTATGATGGTAACTACACGATTTCGCCTAAAATTTTGCAAAAAATGA-CAAGAAAAATTTT
552 AAAAC--TG-TGAT-AGTACACGATTTCGGCTAAAATTTTACAAAAATTGACCCA-AAATATATT
* * * * * *
8962 TCCTCAATTTTTGGCTAAAATACTC-ATGA-A-ATATATATA-AT--TT--AC
612 TCCTCCAGTTTTAGCGACAATACTCAATGATATATATATATATATAATTAAAA
* * * * * *
9007 GCCAAAAAGATTGGAGGACGT-TTCACGATT-TACATATCATTTTTCATATTTTTTCTAAATTAA
1 GCCAAAAAGATTGAAGGAC-TCTTCACGCTTCTA-ATATCGTTTTTCATATTTTTCCGAATTTAA
* * ** *
9070 TTTCTAATTAAATCGAAATAAGATAT-AGATGC-TCGTAAAAACAAATCCTTAAATGAAATGTGT
64 TTTCTAATTAAATCGAAACAAGAT-TCAAAT-CATCGTAAAAACAAATCCTTAAATCCAATGTGG
* * ** * * *
9133 CTGAGATTTGATTTCATGAATAT-GATATCTCAAGTAGTCTCAGCAT-C-AAAAATCATGCAAAA
127 ATGAGATTTCATTAGATGAATATAGATATTTCAAGGAGTCT-AG-GTGCAAAAAATCATGCAAAA
* * * * * * * * * * * *
9195 TTGACCCCGGGCCCTAG-AACACATTTTTA-CCAAAAATCGTGATGATTATTAC-CGATTTCGGC
190 CTAAACCGGGGTCC-AGAAACGCGTTTTAAGCCAAAAA-CATGATGACTAATACACGATTTAGGC
* * * * *
9257 TAAAATTTTG-AAAAAATTGACCGGAAAGATATTTCCTCAATTTTTGCTAAATTA-TCATAAAAT
253 TAGAATTTTGAAAAAAATTGACC-AAAATATTTTTCCTCAATTTTTGC-AAAATACTCATAAAAT
9320 AAATATATAATT
316 --ATATATAATT
9332 TTATCCCAAA
Statistics
Matches: 1841, Mismatches: 331, Indels: 285
0.75 0.13 0.12
Matches are distributed among these distances:
635 1 0.00
636 27 0.01
637 55 0.03
638 34 0.02
639 129 0.07
640 60 0.03
641 10 0.01
642 22 0.01
643 5 0.00
644 1 0.00
645 2 0.00
646 4 0.00
647 88 0.05
648 18 0.01
649 30 0.02
650 7 0.00
652 1 0.00
653 22 0.01
654 2 0.00
655 27 0.01
658 6 0.00
659 35 0.02
660 13 0.01
661 79 0.04
662 2 0.00
665 10 0.01
666 5 0.00
667 28 0.02
668 252 0.14
669 138 0.07
670 38 0.02
671 15 0.01
672 23 0.01
673 87 0.05
674 79 0.04
675 85 0.05
676 129 0.07
677 6 0.00
678 8 0.00
679 83 0.05
680 95 0.05
681 68 0.04
682 5 0.00
683 1 0.00
684 4 0.00
685 2 0.00
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.33
Consensus pattern (664 bp):
GCCAAAAAGATTGAAGGACTCTTCACGCTTCTAATATCGTTTTTCATATTTTTCCGAATTTAATT
TCTAATTAAATCGAAACAAGATTCAAATCATCGTAAAAACAAATCCTTAAATCCAATGTGGATGA
GATTTCATTAGATGAATATAGATATTTCAAGGAGTCTAGGTGCAAAAAATCATGCAAAACTAAAC
CGGGGTCCAGAAACGCGTTTTAAGCCAAAAACATGATGACTAATACACGATTTAGGCTAGAATTT
TGAAAAAAATTGACCAAAATATTTTTCCTCAATTTTTGCAAAATACTCATAAAATATATATAATT
CAACGCCAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAA
GTTCTAATTAAATCGAAACAAGATTGAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTAGCT
GAGATTTGATTAAATGAATATAGATATCTCAAGAGATGTTGCTACTAAAAATCATGCAAAACTAA
CCAGGAGCCCCAGAACGCGTTTTAAGCCAGAAAAACTGTGATAGTACACGATTTCGGCTAAAATT
TTACAAAAATTGACCCAAAATATATTTCCTCCAGTTTTAGCGACAATACTCAATGATATATATAT
ATATATAATTAAAA
Done.