Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014238.1 Corchorus olitorius cultivar O-4 contig14271, 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: 3951
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.34
Found at i:670 original size:321 final size:320
Alignment explanation
Indices: 8--3951 Score: 3599
Period size: 321 Copynumber: 12.0 Consensus size: 320
1 CGCGTTT
* * *
8 TTTTTTGCC-AAAACCGTGATGGTTAGTACATGATTTCCGCT-AAAACTGACCCGAAAAGTTTTT
1 TTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAAG-TTTT
* * * * * *
71 TTCTCTATTTTTTGCGAAATATTTAGAAAAAATATATAATTCAATGTCAAAAAGAGTGACGGGCT
65 TTCTCAATTTTTTGCAAAATATTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCT
* * *
136 TTTCACGCTTTTAATATCGTTTTTCCATTTGTTTCAGAATTAATTTCTAATTAAATC-AAAATTA
130 TTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAAA--A
** * * * * *
200 AGATTGTGATGCTCGTAAAAAGAAATCCTTATATCCAATGTGGATGACAATTGCTTCGATGAATA
193 AGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGGTTCGATGAATA
* * * * * * * *
265 AAGATATTTCAAGGAGTCTTTGTGCAAAAAAACCTGCAAAATTGAGCCAGCACTCCGGAACGTG
258 TAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAATTGAGCCGGGAC-CCGGAACGCG
** * * *
329 TTTTTAGCCAAAAACCGTGATTTTTAATACACGATTTCCGCT-AAAATTGACCCGAAAAGTTTTT
1 TTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAAGTTTTT
* * * * * *
393 CCTCAATTTTTTGTCATAATACTCAGAAAAAATATATAATTCAACGCCAAAAA-ATCGAAGTGGT
66 TCTCAATTTTTTG-CAAAATATTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACG-GGC
457 TTTTCACGCTTCTAATATCGTTTTTCCA-TTTTTTCCGAATTAATTTCTAATTAAATCGAAATAA
129 TTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAA-AA
* * * * *
521 ATATTCAGATGCTCGTGAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTAGATGAATA
193 AGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGGTTCGATGAATA
* * * * * * * *
586 TAGATATTTCAAGGAGT-TATTCTGCCAAAAATCATTCAAAACTGAGTCGGGGCCATGAAACTCA
258 TAGATATTTCAAGGAGTCT-TTCTGCCAAAAATCATGCAAAATTGAGCCGGGACC-CGGAACGCG
* *
650 TTTTTAGCCAAAAACCGTGATAGTTAGTACATGATTTCGGCTAAAAACTGACCCGAAAAGTTTAT
1 TTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAAGTTT-T
* * *
715 TTCTCAATTTTTTGCAAAATACTCAAAAAAAATATATAATTCAACTGCCAAAAAGATTGACGGCC
65 TTCTCAATTTTTTGCAAAATATTCAGAAAAAATATATAATTCAAC-GCCAAAAAGATTGACGGGC
* *
780 TTTTGACGCTTCTAATATCGTTTTTCCATTGTTTTTTTCCTAATTAATTTCTAATTAAATCGAAA
129 TTTTCACGCTTCTAATATCGTTTTTCCA---TTTTTTTCCGAATTAATTTCTAATTAAATCGAAA
* * ** * *
845 CAAGATTCAGATGCTCATAAAAACAAATTTTTATATACAATGTGGCTAAGATTTGGTTCGATGAA
191 AAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGGTTCGATGAA
* * *
910 TATAGATAATTCAAAGAGTCTTTGC-GCCAAAAATCATGCAAAATTGAGCCGAGACTCCGGAACG
256 TATAGATATTTCAAGGAGTCTTT-CTGCCAAAAATCATGCAAAATTGAGCCGGGAC-CCGGAACG
974 CG
319 CG
* * ** ** * *
976 TTTTTAGGCAAAAAACCAAATCG-TTTTTTCTCAAACGATTTCCGCTAAAAACTGACCCGAAAAG
1 TTTTTA-GCCAAAAACC--GT-GATGGTTAGT-ACACGATTTCGGCTAAAAACTGACCCGAAAAG
** ** * * *
1040 TTTTTTTCTCAATTTTTTGCGTAATATTTTGAAAAAATATATAATTCAATGTC-AAAAGAGTGAC
61 -TTTTTTCTCAATTTTTTGCAAAATATTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGAC
* * *
1104 GGGCTTTTCACGCTT-TCAATATCATTTTTCCATTTGTTTCTGAATTAATTTCTAATTAAATC-A
125 GGGCTTTTCACGCTTCT-AATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGA
* * * * * *
1167 AAACAAGATTGACATGCTCGTAAAAAGAAATCCTTATATCCAATGTAGATGACATTTGGTTCGAT
189 AAA-AAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGGTTCGAT
* * * * * * * *
1232 GAACAAAGATATTTCAAGGAGTCTTTGTGCAAAAAATCCTGCAAAATTGAACCGGCACTCCAGAA
253 GAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAATTGAGCCGGGAC-CCGGAA
1297 CGCG
317 CGCG
* ** *
1301 TTTTTAGCCAAAAACCGTGATGGTTAGTACACTATTTCCCCTAGAAACTGACCCGAAAAGTTTTT
1 TTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAAGTTTTT
* * * *** *
1366 TCTCAATGTTTTGCGAAATATTTAGAAAAAATATATAATTCAATATCAAAAAGAGTGACGGGCTT
66 TCTCAATTTTTTGCAAAATATTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTT
*
1431 TTCACGCTTCTAATATCGTTTTTCCATTTGTTTCCGAATTAATTTCTAATTAAATC-AAAACAAG
131 TTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAAA-AAG
* * * * * *
1495 ATTGAGATGCTCGTAAAAAGAAATCCTTATATCCAATGTGGATGACATTTGGTTCGTTGAATAAA
195 ATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGGTTCGATGAATATA
* * * * * *
1560 AATATTTCAAGGAGTCTTTGTGCAAAAAATCCTGCAAAATTGAGGCGGCACTCCGGAACGCG
260 GATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAATTGAGCCGGGAC-CCGGAACGCG
1622 TTTTTAGCCAAAAACCGTGATGGTTAGTACACCGATTTCGGCTAAAATTTTGCAAAAACTGACCC
1 TTTTTAGCCAAAAACCGTGATGGTTAGTACA-CGATTTCGGC--------T--AAAAACTGACCC
* * * * ** * *
1687 AAAAAGTTTTTCCTCAATTTTTTTTGCCAAAATACTCATAAGTAATATATAATTTAACGCAAAAA
55 GAAAAGTTTTTTCTCAA--TTTTTTG-CAAAATATTCAGAAAAAATATATAATTCAACGCCAAAA
* * * * * * * * *
1752 AAATTAAAGTGTTTTTCACGCTTCTAATATCATTTTT-CATTTTTTTTCTGAATCT-GTTTCCAA
117 AGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCCA-TTTTTTTCCGAAT-TAATTTCTAA
* * * * *
1815 TTAAATCGATACAAAGATTGAGATGCTCGTAAAAACAAATTCTTAAATCCATTGTGGCTGAGATT
180 TTAAATCGA-AAAAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATT
* * * ** * * **
1880 TTGTTAGATGAATATAAATATTTCAAGGAGTCTTTCTGCCAAAAATCATTTAAAACTGAGTCGTT
244 TGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAATTGAGCCGGG
* *
1945 ATCCGAAACGCG
309 ACCCGGAACGCG
* * * *
1957 TTTTTAGCCAAAAATCGTGATGGTTAGTACATGATTTCGGCTAAAAACTAACCCGAACAG-TTTT
1 TTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAAGTTTTT
* *
2021 TCTCAATTTTTTGCAAAATATT---------TATATAATTCAACACCAAAAATATTGACGGGCTT
66 TCTCAATTTTTTGCAAAATATTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTT
* *
2077 TTCACGCTTCTAAACTCTAATATCGTTTTTCCATTTTTTTCTGAATTAAATTCTAATTAAATCGA
131 TTCACG---CT----TCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGA
* * * * * *
2142 AATAAGGTTCGGATGCTCGTAAAAACAAATCCTTATATACAATGTGACAGAGATTTGGTTCGATG
189 AAAAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGGTTCGATG
*
2207 AATATAGATATTTCAAGGAGTCTTTAC-GCCAAAAATCATGCAAAATTGAGCCGGGAATCCGGAA
254 AATATAGATATTTCAAGGAGTCTTT-CTGCCAAAAATCATGCAAAATTGAGCCGGG-ACCCGGAA
2271 CGCG
317 CGCG
* * **
2275 TTTTT-GCCAAAAACCGTGATAGTTAGTACACGATTTCGTTGGCAAAAAAAAGAAAAAGAACACG
1 TTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTC---GGC-----TAA-AAACTG-AC-C-
* *
2339 ATTTCGGCTAAAA-TTGACCCGAAAAGTTTTTCCTCAATTTTTTGTCACAATACTCAGAAAAAAT
54 ----C-G--AAAAGTT------------TTTT-CTCAATTTTTTG-CAAAATATTCAGAAAAAAT
* * * *
2403 ATATAATTCAATGCCAAAAAAATTGAAGAGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTT
98 ATATAATTCAACGCCAAAAAGATTGACG-GGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTT
* * * *
2468 TTCCAAATTTAA-TTCTAATTAAATCGAAATAAAGATTCAGATGCTCGTGAAAACAAATTCTTAA
162 TTCCGAA-TTAATTTCTAATTAAATCGAAA-AAAGATTCAGATGCTCGTAAAAACAAATCCTTAT
* * * *
2532 ATCCATTGTGGCTGAGATTTTGTTAGATGAATATAAATATTTCAAGGAGTCTTTCTGCCAAAAAT
225 ATCCAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAAT
** * * ** * *
2597 CATTTAAAACTGAGTCGTTATCCGAAACGCG
290 CATGCAAAATTGAGCCGGGACCCGGAACGCG
* * * *
2628 TTTTTAGCCAAAAATCGTGATGGTTAGTACATGATTTCGGCTAAAAACTAACCCGAACAG-TTTT
1 TTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAAGTTTTT
* * * *
2692 TCTCAATTTTTTGCAAAATATTTAG-AAAAATATATAATTCAACACCAAAAATATTGACGCGCTT
66 TCTCAATTTTTTGCAAAATATTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTT
* *
2756 TTCACGCTTCTAAATTCTAATATCGTTTTTCCA-TTTTTTCTGAATTAAATTCTAATTAAATCGA
131 TTCACG---C----TTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGA
* * * * * *
2820 AACAAGGTTCGGATGCTCGTAAAAACAAATCCTTATATACAATGTGACAGAGATTTGGTTCGATG
189 AAAAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGGTTCGATG
*
2885 AATATAGATATTTCAAGGAGTCTTTAC-GCCAAAAATCATGCAAAATTGAGCCGGGAATCCGGAA
254 AATATAGATATTTCAAGGAGTCTTT-CTGCCAAAAATCATGCAAAATTGAGCCGGG-ACCCGGAA
2949 CGCG
317 CGCG
* * *
2953 TTTTT-GCAAAAAACTGTGATAGTTAGTACACGATTTCGTTGGCAAAAAAAAAGTACACGATTTC
1 TTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTC---GGC----------T-----A----
* * * * * *
3017 GGCTAAAATTGACCCGAAAAGTTTTTCCTCAGTTTTTTGTTACAATACTCAGAAAAAATATATAA
44 ----AAAACTGACCCGAAAAGTTTTTTCTCAATTTTTTG-CAAAATATTCAGAAAAAATATATAA
* * * *
3082 TTCAATGCCAAAAAAATTGAAGAGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGA
104 TTCAACGCCAAAAAGATTGACG-GGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGA
* * * * * * *
3147 ATTTATTTCTAATTAAATCGAAATAAAGATTCAAATGCTTGTAAAATCAAATACTTAAATCCATT
168 ATTAATTTCTAATTAAATCGAAA-AAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAAT
* *
3212 GTGGCTGAGA-----TT---TGAATATAGATATTTGAAGGAGTCTTTCTGCCAAAAATCATTCAA
232 GTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAA
* * * * **
3269 AACTGAACCAGGG-CCATGAAACTTG
297 AATTGAGCC-GGGACC-CGGAACGCG
* * *
3294 TTTTTAGCCAAAAACCGTGATAGTTAGTATACGATTTCGGCTAAAAACCGACCCGAAAAGTTTTT
1 TTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAAG-TTTT
*
3359 TTCTCAATTTTTTGCAAAATATTCAAAAAATATATTATATAATTCAACCGCCAAAAAGATTGACG
65 TTCTCAATTTTTTGCAAAATATTCAGAAAA-A-A-TATATAATTCAA-CGCCAAAAAGATTGACG
* * *
3424 GCCTTTTGACGCTTCTAATATCGTTTTTCCATTGTTTTTTTCCTAATTAATTTCTAATTAAATCG
126 GGCTTTTCACGCTTCTAATATCGTTTTTCCA---TTTTTTTCCGAATTAATTTCTAATTAAATCG
* * ** * *
3489 AAACAAGATTCAGATGCTCATAAAAACAAATTTTTATATACAATGTGGCTAAGATTTGGTTCGAT
188 AAAAAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGGTTCGAT
* * * *
3554 GAATATAGATAATTCAAAGAGTCTTTGC-GCCAAAAATCATGCAAAATTGAGCTGAGACTCCGGA
253 GAATATAGATATTTCAAGGAGTCTTT-CTGCCAAAAATCATGCAAAATTGAGCCGGGAC-CCGGA
3618 ACGCG
316 ACGCG
* * ** ** * *
3623 TTTTTAGGCAAAAAACCAAATCG-TTTTTTCTCAAACGATTTCCGCTAAAAACTGACCCGAAAAG
1 TTTTTA-GCCAAAAACC--GT-GATGGTTAGT-ACACGATTTCGGCTAAAAACTGACCCGAAAAG
** * * * *
3687 TTTTTTTCTCAATTTTTTGCGTAATATTTAGAAAAAATATATAATTCAATGTCAAAAAGAGTGAC
61 -TTTTTTCTCAATTTTTTGCAAAATATTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGAC
** * *
3752 GGGCTTTTCACGCTT-TCAATATCACTTTTCCATTTGTTTCTGAATTAATTTCTAATTAAATC-A
125 GGGCTTTTCACGCTTCT-AATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGA
* * * * * * *
3815 AAACAAGATTGACATACTCGTAAAAAGAAATCCTTATATCCAATGTAGATGACATTTGGTTCGAT
189 AAA-AAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGGTTCGAT
* * * * * * * *
3880 GAACAAAGATATTTCAAGGAGTCTTTGTGCAAAAAATCCTGCAAAATTGAACCGGCACTCCAGAA
253 GAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAATTGAGCCGGGAC-CCGGAA
3945 CGCG
317 CGCG
3949 TTT
1 TTT
Statistics
Matches: 2984, Mismatches: 458, Indels: 357
0.79 0.12 0.09
Matches are distributed among these distances:
311 32 0.01
314 2 0.00
316 27 0.01
317 145 0.05
318 59 0.02
319 51 0.02
320 105 0.04
321 502 0.17
322 215 0.07
323 64 0.02
324 161 0.05
325 188 0.06
326 269 0.09
327 50 0.02
328 41 0.01
329 104 0.03
330 93 0.03
331 4 0.00
332 32 0.01
333 62 0.02
334 18 0.01
335 124 0.04
336 105 0.04
337 4 0.00
338 1 0.00
339 3 0.00
340 2 0.00
341 58 0.02
342 33 0.01
343 1 0.00
344 4 0.00
345 3 0.00
346 2 0.00
347 19 0.01
348 34 0.01
349 51 0.02
350 21 0.01
351 19 0.01
352 8 0.00
353 92 0.03
354 139 0.05
357 2 0.00
359 25 0.01
360 10 0.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.34
Consensus pattern (320 bp):
TTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAAGTTTTT
TCTCAATTTTTTGCAAAATATTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTT
TTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAAAAAGA
TTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGGTTCGATGAATATAG
ATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAATTGAGCCGGGACCCGGAACGCG
Found at i:2588 original size:671 final size:664
Alignment explanation
Indices: 1676--3636 Score: 2778
Period size: 671 Copynumber: 2.9 Consensus size: 664
1666 AAATTTTGCA
* * * * * **
1676 AAAACTGACCCAAAAAGTTTTTCCTCAATTTTTTTTGCCAAAATACTCATAAGTAATATATAATT
1 AAAATTGACCCGAAAAGTTTTTCCTCAA--TTTTTTGTCACAATACTCAGAAAAAATATATAATT
* * * * *
1741 TAACGCAAAAAAAATT-AA-AGTGTTTTTCACGCTTCTAATATCATTTTT-CATTTTTTTTCTGA
64 CAATGCCAAAAAAATTGAAGAG-GTTTTTCACGCTTCTAATATCGTTTTTCCA-TTTTTTTCCGA
* * * * * *
1803 ATCTGTTTCCAATTAAATCGATACAAAGATTGAGATGCTCGTAAAAACAAATTCTTAAATCCATT
127 ATTTATTTCTAATTAAATCGAAATAAAGATTCAGATGCTCGT-AAAACAAATTCTTAAATCCATT
1868 GTGGCTGAGATTTTGTTAGATGAATATAAATATTTCAAGGAGTCTTTCTGCCAAAAATCATTTAA
191 GTGGCTGAGATTTTGTTAGATGAATATAAATATTTCAAGGAGTCTTTCTGCCAAAAATCATTTAA
1933 AACTGAGTCGTTATCCGAAACGCGTTTTTAGCCAAAAATCGTGATGGTTAGTACATGATTTCGGC
256 AACTGAGTCGTTATCCGAAACGCGTTTTTAGCCAAAAATCGTGATGGTTAGTACATGATTTCGGC
1998 TAAAAACTAACCCGAACAGTTTTTCTCAATTTTTTGCAAAATATTTATATAATTCAACACCAAAA
321 TAAAAACTAACCCGAACAGTTTTTCTCAATTTTTTGCAAAATATTTATATAATTCAACACCAAAA
2063 ATATTGACGGGCTTTTCACGCTTCTAAACTCTAATATCGTTTTTCCATTTTTTTCTGAATTAAAT
386 ATATTGACGGGCTTTTCACGCTTCTAAA-TCTAATATCGTTTTTCCATTTTTTTCTGAATTAAAT
*
2128 TCTAATTAAATCGAAATAAGGTTCGGATGCTCGTAAAAACAAATCCTTATATACAATGTGACAGA
450 TCTAATTAAATCGAAACAAGGTTCGGATGCTCGTAAAAACAAATCCTTATATACAATGTGACAGA
2193 GATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAATTGAGC
515 GATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAATTGAGC
2258 CGGGAATCCGGAACGCGTTTTTGCCAAAAACCGTGATAGTTAGTACACGATTTCGTTGGCAAAAA
580 CGGGAATCCGGAACGCGTTTTTGCCAAAAACCGTGATAGTTAGTACACGATTTCGTTGGC----A
2323 AAAGAAAAAGAACACGATTTCGGCT
641 AAA-AAAAAGAACACGATTTCGGCT
2348 AAAATTGACCCGAAAAGTTTTTCCTCAATTTTTTGTCACAATACTCAGAAAAAATATATAATTCA
1 AAAATTGACCCGAAAAGTTTTTCCTCAATTTTTTGTCACAATACTCAGAAAAAATATATAATTCA
*
2413 ATGCCAAAAAAATTGAAGAGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCAAATTT
66 ATGCCAAAAAAATTGAAGAGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTT
*
2478 AATTCTAATTAAATCGAAATAAAGATTCAGATGCTCGTGAAAACAAATTCTTAAATCCATTGTGG
131 ATTTCTAATTAAATCGAAATAAAGATTCAGATGCTCGT-AAAACAAATTCTTAAATCCATTGTGG
2543 CTGAGATTTTGTTAGATGAATATAAATATTTCAAGGAGTCTTTCTGCCAAAAATCATTTAAAACT
195 CTGAGATTTTGTTAGATGAATATAAATATTTCAAGGAGTCTTTCTGCCAAAAATCATTTAAAACT
2608 GAGTCGTTATCCGAAACGCGTTTTTAGCCAAAAATCGTGATGGTTAGTACATGATTTCGGCTAAA
260 GAGTCGTTATCCGAAACGCGTTTTTAGCCAAAAATCGTGATGGTTAGTACATGATTTCGGCTAAA
2673 AACTAACCCGAACAGTTTTTCTCAATTTTTTGCAAAATATTTAGAAAAATATATAATTCAACACC
325 AACTAACCCGAACAGTTTTTCTCAATTTTTTGCAAAATA-TT-------TATATAATTCAACACC
*
2738 AAAAATATTGACGCGCTTTTCACGCTTCTAAATTCTAATATCGTTTTTCCA-TTTTTTCTGAATT
382 AAAAATATTGACGGGCTTTTCACGCTTCTAAA-TCTAATATCGTTTTTCCATTTTTTTCTGAATT
2802 AAATTCTAATTAAATCGAAACAAGGTTCGGATGCTCGTAAAAACAAATCCTTATATACAATGTGA
446 AAATTCTAATTAAATCGAAACAAGGTTCGGATGCTCGTAAAAACAAATCCTTATATACAATGTGA
2867 CAGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAATT
511 CAGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAATT
* *
2932 GAGCCGGGAATCCGGAACGCGTTTTTGCAAAAAACTGTGATAGTTAGTACACGATTTCGTTGGCA
576 GAGCCGGGAATCCGGAACGCGTTTTTGCCAAAAACCGTGATAGTTAGTACACGATTTCGTTGGCA
*
2997 AAAAAAAAGTACACGATTTCGGCT
641 AAAAAAAAGAACACGATTTCGGCT
* *
3021 AAAATTGACCCGAAAAGTTTTTCCTCAGTTTTTTGTTACAATACTCAGAAAAAATATATAATTCA
1 AAAATTGACCCGAAAAGTTTTTCCTCAATTTTTTGTCACAATACTCAGAAAAAATATATAATTCA
3086 ATGCCAAAAAAATTGAAGAGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTT
66 ATGCCAAAAAAATTGAAGAGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTT
* * *
3151 ATTTCTAATTAAATCGAAATAAAGATTCAAATGCTTGTAAAATCAAATACTTAAATCCATTGTGG
131 ATTTCTAATTAAATCGAAATAAAGATTCAGATGCTCGTAAAA-CAAATTCTTAAATCCATTGTGG
* * *
3216 CTGAGA-----TT---TGAATATAGATATTTGAAGGAGTCTTTCTGCCAAAAATCATTCAAAACT
195 CTGAGATTTTGTTAGATGAATATAAATATTTCAAGGAGTCTTTCTGCCAAAAATCATTTAAAACT
** ** ** * * * *
3273 GAACCAG--GGCCATGAAACTTGTTTTTAGCCAAAAACCGTGATAGTTAGTATACGATTTCGGCT
260 GAGTC-GTTATCC--GAAACGCGTTTTTAGCCAAAAATCGTGATGGTTAGTACATGATTTCGGCT
** *
3336 AAAAACCGACCCGAAAAGTTTTTTTCTCAATTTTTTGCAAAATATTCAAAAAATATATTATATAA
322 AAAAACTAACCCGAACAG--TTTTTCTCAATTTTTTG---------C--AAAATAT-TTATATAA
* * * *
3401 TTCAACCGCCAAAAAGATTGACGGCCTTTTGACG---CT---TCTAATATCGTTTTTCCATTGTT
373 TTCAA-CACCAAAAATATTGACGGGCTTTTCACGCTTCTAAATCTAATATCGTTTTTCCA---TT
* * * * **
3460 TTTTTCCT-AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAAAAACAAATTTTT
434 TTTTT-CTGAATTAAATTCTAATTAAATCGAAACAAGGTTCGGATGCTCGTAAAAACAAATCCTT
* * * *
3524 ATATACAATGTGGCTA-AGATTTGGTTCGATGAATATAGATAATTCAAAGAGTCTTTGCGCCAAA
498 ATATACAATGTGAC-AGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTACGCCAAA
* * * *
3588 AATCATGCAAAATTGAGCTGAGACTCCGGAACGCGTTTTTAGGCAAAAA
562 AATCATGCAAAATTGAGCCGGGAATCCGGAACGCGTTTTT-GCCAAAAA
3637 ACCAAATCGT
Statistics
Matches: 1182, Mismatches: 70, Indels: 75
0.89 0.05 0.06
Matches are distributed among these distances:
664 2 0.00
665 49 0.04
666 78 0.07
668 19 0.02
670 196 0.17
671 276 0.23
672 48 0.04
673 232 0.20
674 4 0.00
677 1 0.00
678 205 0.17
679 72 0.06
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (664 bp):
AAAATTGACCCGAAAAGTTTTTCCTCAATTTTTTGTCACAATACTCAGAAAAAATATATAATTCA
ATGCCAAAAAAATTGAAGAGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTT
ATTTCTAATTAAATCGAAATAAAGATTCAGATGCTCGTAAAACAAATTCTTAAATCCATTGTGGC
TGAGATTTTGTTAGATGAATATAAATATTTCAAGGAGTCTTTCTGCCAAAAATCATTTAAAACTG
AGTCGTTATCCGAAACGCGTTTTTAGCCAAAAATCGTGATGGTTAGTACATGATTTCGGCTAAAA
ACTAACCCGAACAGTTTTTCTCAATTTTTTGCAAAATATTTATATAATTCAACACCAAAAATATT
GACGGGCTTTTCACGCTTCTAAATCTAATATCGTTTTTCCATTTTTTTCTGAATTAAATTCTAAT
TAAATCGAAACAAGGTTCGGATGCTCGTAAAAACAAATCCTTATATACAATGTGACAGAGATTTG
GTTCGATGAATATAGATATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAATTGAGCCGGGAA
TCCGGAACGCGTTTTTGCCAAAAACCGTGATAGTTAGTACACGATTTCGTTGGCAAAAAAAAAGA
ACACGATTTCGGCT
Found at i:3904 original size:326 final size:331
Alignment explanation
Indices: 3324--3951 Score: 822
Period size: 326 Copynumber: 1.9 Consensus size: 331
3314 TAGTTAGTAT
*
3324 ACGATTTCGGCTAAAAACCGACCCGAAAAGTTTTTTTCTCAATTTTTTGCAAAATATTCAAAAAA
1 ACGATTTCCGCTAAAAACCGACCCGAAAAGTTTTTTTCTCAATTTTTTGCAAAATATTCAAAAAA
* * **
3389 TATATTATATAATTCAACCGCCAAAAAGATTGACGGCCTTTTGACGCTTCTAATATCGTTTTTCC
66 TATATTATATAATTCAACCGCCAAAAAGAGTGACGGCCTTTTCACGCTTCTAATATCACTTTTCC
* * * *
3454 ATTGTTTTTTTCCTAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAAAAACAAA
131 A-T-TTTGTTTCCTAATTAATTTCTAATTAAATCAAAACAAGATTCACATACTCATAAAAACAAA
** * * * * *
3519 TTTTTATATACAATGTGGCTAAGATTTGGTTCGATGAATATAGATAATTCAAAGAGTCTTTGCGC
194 TCCTTATATACAATGTAGATAACATTTGGTTCGATGAACAAAGATAATTCAAAGAGTCTTTGCGC
* * * *
3584 CAAAAATCATGCAAAATTGAGCTGAG-ACTCCGGAACGCGTTTTTAGGCAAAAAACCAAATCGTT
259 AAAAAATCATGCAAAATTGAACCG-GCACTCCAGAACGCGTTTTTAGGCAAAAAACCAAATCGTT
3648 TTTTCTCAA
323 TTTTCTCAA
* ** * *
3657 ACGATTTCCGCTAAAAACTGACCCGAAAAGTTTTTTTCTCAATTTTTTGCGTAATATTTAGAAAA
1 ACGATTTCCGCTAAAAACCGACCCGAAAAGTTTTTTTCTCAATTTTTTGCAAAATATTCAAAAAA
* * *
3722 -A-A-TATATAATTCAA-TGTCAAAAAGAGTGACGGGCTTTTCACGCTT-TCAATATCACTTTTC
66 TATATTATATAATTCAACCGCCAAAAAGAGTGACGGCCTTTTCACGCTTCT-AATATCACTTTTC
* * *
3782 CA-TTTGTTT-CTGAATTAATTTCTAATTAAATCAAAACAAGATTGACATACTCGTAAAAAGAAA
130 CATTTTGTTTCCT-AATTAATTTCTAATTAAATCAAAACAAGATTCACATACTCATAAAAACAAA
* * * * *
3845 TCCTTATATCCAATGTAGATGACATTTGGTTCGATGAACAAAGATATTTCAAGGAGTCTTTGTGC
194 TCCTTATATACAATGTAGATAACATTTGGTTCGATGAACAAAGATAATTCAAAGAGTCTTTGCGC
*
3910 AAAAAATCCTGCAAAATTGAACCGGCACTCCAGAACGCGTTT
259 AAAAAATCATGCAAAATTGAACCGGCACTCCAGAACGCGTTT
Statistics
Matches: 255, Mismatches: 37, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
325 3 0.01
326 139 0.55
328 1 0.00
329 39 0.15
330 12 0.05
331 1 0.00
332 1 0.00
333 59 0.23
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (331 bp):
ACGATTTCCGCTAAAAACCGACCCGAAAAGTTTTTTTCTCAATTTTTTGCAAAATATTCAAAAAA
TATATTATATAATTCAACCGCCAAAAAGAGTGACGGCCTTTTCACGCTTCTAATATCACTTTTCC
ATTTTGTTTCCTAATTAATTTCTAATTAAATCAAAACAAGATTCACATACTCATAAAAACAAATC
CTTATATACAATGTAGATAACATTTGGTTCGATGAACAAAGATAATTCAAAGAGTCTTTGCGCAA
AAAATCATGCAAAATTGAACCGGCACTCCAGAACGCGTTTTTAGGCAAAAAACCAAATCGTTTTT
TCTCAA
Done.