Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017873.1 Corchorus olitorius cultivar O-4 contig17906, 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: 5802
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Found at i:1176 original size:14 final size:15
Alignment explanation
Indices: 1157--1189 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1147 TATAATATCG
1157 TTTTCCCTATTT-TT
1 TTTTCCCTATTTATT
*
1171 TTTTCCGTATTTATT
1 TTTTCCCTATTTATT
1186 TTTT
1 TTTT
1190 TGTGAGACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.09, C:0.15, G:0.03, T:0.73
Consensus pattern (15 bp):
TTTTCCCTATTTATT
Found at i:1871 original size:333 final size:331
Alignment explanation
Indices: 16--3609 Score: 2910
Period size: 332 Copynumber: 10.8 Consensus size: 331
6 TAAGACGGAG
** * *
16 CCCGGAACGCGTTTTTAGCAAAAAACTATGACGGTTAGTACACGATTTCGGCAAAAATTTTAG-A
1 CCCGGAACGCGTTTTTAGC-AAAAACCCTGATGGTTAGTACACGATTTCGGCTAAAATTTT-GCA
* * *
80 AAAATTGACCCG-AAAG-----------TTTTT-GCCAAAATACTCA-AGAAAAAAAATACAATT
64 AAAATTGTCCCGAAAAGTTTTTCCTCAATTTTTGGACAAAATACTCATA-AAAAAATATACAATT
* * * * *
131 CACGCTAAAAAGATTGAAGGGCTTTTCAGGCTTCTAATACCATTTTTCATATATTTTT-CTGAAT
128 CACACCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCATAT-TTTTTCCTGAAT
*
195 TAATTTCTAATAAAATC-AAAGCAAGATTCCGATGCTCGTAAAAACCAATCCTTAAATCCAATGT
192 TAATTTCTAATAAAATCGAAA-CAAGATTCCGATGCTCGTAAAAACAAATCCTTAAATCCAATGT
* * * * * *
259 GGTTGAGATTTGGTTAGATGATTATAGATATTTCAAAGAGTCTGGCCGGCAAAAAATCAAGCAAA
256 GGCTAAGATTTTGTTAGATGAATATAGATATTTCAAGGAGTCTGGGCGGC-AAAAATCAAGCAAA
* *
324 ACTGAGCCGAGGT
320 ACTGAGCTG-GGC
* * * * * *
337 CCCGAAATGCGTTTTCAGCAAAAACCCTGATGGTTAGTTCATGATTTCGGCTAAAATTTTACAAA
1 CCCGGAACGCGTTTTTAGCAAAAACCCTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAA
* ** * * * * * * *
402 AATGGATCCAAAAAAATTTATCCACAATTTTTGGCCAAAATAATC-GAGAAAAATATACAATTCA
66 AATTG-TCCCGAAAAGTTTTTCCTCAATTTTTGGACAAAATACTCATAAAAAAATATACAATTCA
*
466 CGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCATATTTGTTTCC-GAATTA
130 CACCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCATATTT-TTTCCTGAATTA
* * * * *
530 ATTTCTAATAAAATCAAAACAATATTCCGATGCTCGTAAAAACAAATCCTTAAATTCATTGTGAC
194 ATTTCTAATAAAATCGAAACAAGATTCCGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGC
* * **
595 TAAGATTTAGTTAGATGAATATAGATATTTCAAGGAGTCTGCGCCCCAAAAATCATA-CAAAACT
259 TAAGATTTTGTTAGATGAATATAGATATTTCAAGGAGTCTGGGCGGCAAAAATCA-AGCAAAACT
* *
659 GTGACTGAG-
323 GAG-CTGGGC
* ** * * * * * *
668 CCCGGAACGCG-TTTTAACAAAAAACTGTGACGATTTGTACATGGTTTCGGCTAAAATTTTACAA
1 CCCGGAACGCGTTTTTAGC-AAAAACCCTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAA
* * * * * * * **
732 AAATAGACTCGAAAAATTTTTCCTCAATTTTCGGCCAAAATACTCAT-AAAAAATATATAGCTCA
65 AAATTGTCCCGAAAAGTTTTTCCTCAATTTTTGGACAAAATACTCATAAAAAAATATACAATTCA
* * ** * *
796 CCGCCAAAAATATTGAAGGGCTTTTCACGC-TCTAATATCGTTTCCCTTATTTTTTTCTGAATTA
130 -CACCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCATATTTTTTCCTGAATTA
* * * * * *
860 ATTTATAATTAAAGCGAAACAAGATT-CGAATGCTCGTAAAACCAAATCTTTTAATCCAATGTGG
194 ATTTCTAATAAAATCGAAACAAGATTCCG-ATGCTCGTAAAAACAAATCCTTAAATCCAATGTGG
* * * *
924 CTGAGATTTTGTTAGATTATTATAGATATTTCAAGGAGTCTGGGCGGAAAAAATCAAGCAAAACT
258 CTAAGATTTTGTTAGATGAATATAGATATTTCAAGGAGTCTGGGCGGCAAAAATCAAGCAAAACT
989 GAGCTGGGGC
323 GAGCT-GGGC
* * * *
999 CCTGGAGCGCG-TTTTATGC--AAA-----A-----AGTACATGATCTCGGCTAAAATTTTGCAA
1 CCCGGAACGCGTTTTTA-GCAAAAACCCTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAA
** * * * *
1051 AAATTGTCCAAAAAATTTTTTCCTAAATTTTTGGACACAATACTCATAAAGAAATATACAATTCC
65 AAATTGTCCCGAAAAGTTTTTCCTCAATTTTTGGACAAAATACTCATAAAAAAATATACAATT-C
* * * * *
1116 ACACCGAAAAGATTGAAGGGCTTTTCATGCTTATAATATCGTTTTCCCTATTTTTTTTTCC-GTA
129 ACACCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTT-TC-A-TATTTTTTCCTG-A
** * * *
1180 TTTATTTTTTTGTGAGACATGTATTGAATATCCTTCCGACTAATTAAATTGAAACCAATTTCTGA
190 ---ATTAATTTCT---A-A--TA---AA-A----T-CGA--AA--CAA--G------A-TTCCGA
* * * * *
1245 TGCTCGTAAAAACAAATCCTTAAATCCATTGTGGTTAAGATTTGGTTAGATGAATACAAATATTT
224 TGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTAAGATTTTGTTAGATGAATATAGATATTT
* *
1310 CAAGGAGTCTGGGCAGCAAAACTCAAGCAAAACTGAGCTGGGGC
289 CAAGGAGTCTGGGCGGCAAAAATCAAGCAAAACTGAGCT-GGGC
* * * *
1354 CCCGGAATGCGTTTTTAGCAAAAACCCTGATGGTTAATACATGATTTCGGCTAAAATTTTGCCAA
1 CCCGGAACGCGTTTTTAGCAAAAACCCTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAA
* * * * * * *
1419 AATGTGAT-CCG-AAAGATTTTCCCCTCAATTTTTAGCCATAGTACTC-GAGAAAAATATACAAT
66 AAT-TG-TCCCGAAAAG-TTTT-TCCTCAATTTTTGGACAAAATACTCATAAAAAAATATACAAT
* * * *
1481 TGA-AGCAAAAAAGATTGAAGGACTTTTCACGCTTCTAATATCATTTTTCATATTTTTTCCTGAA
127 TCACA-CCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCATATTTTTTCCTGAA
* * ** * * *
1545 TTAATTTCTAATTAAAGCGAAACAAGATTCAAATGCTCGTAAAAACAAATCTTTTAATCTAATGT
191 TTAATTTCTAATAAAATCGAAACAAGATTCCGATGCTCGTAAAAACAAATCCTTAAATCCAATGT
* * ** *
1610 GGCTAAGATTTTGTTAGATTAATATAGATACTTCAAGGAGTCTAAGCGGAAAAAATCAAGCAAAA
256 GGCTAAGATTTTGTTAGATGAATATAGATATTTCAAGGAGTCTGGGCGGCAAAAATCAAGCAAAA
* *
1675 CTGAGCTTGAC
321 CTGAGCTGGGC
** * * * * * * *
1686 CTTGAAACGCGTTTTTAGCAAAAACCTTGTTGATTAGTACACGTTTTCGACTAAAATTTTGCACA
1 CCCGGAACGCGTTTTTAGCAAAAACCCTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAA
* * *
1751 AATTGTCCCGAAACGTTTTTCCTCAATTTTTGGACACAATACTCATAAAAAAATATATAATTCGA
66 AATTGTCCCGAAAAGTTTTTCCTCAATTTTTGGACAAAATACTCATAAAAAAATATACAATTC-A
* * * * *
1816 CACCGAAAAGATTGAAGGGCTTTTCATGCTTCTAATTTCGTTTTCCCTAATTTTTTCC--ATATT
130 CACCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCAT-ATTTTTTCCTGA-ATT
* * * * * *
1879 TATTTCTGATTAAATCGAAA-ATGATTTCTGATGCTCGTAAAAACAAATCCTTAAATCTAATGTG
193 AATTTCTAATAAAATCGAAACAAGA-TTCCGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
* * * * * * *
1943 GTTGAGATTTGGTTAGATGAATGTAAACATTTGAAGGAGTCTGGGCGGCAAAAATCAAGCAAAAC
257 GCTAAGATTTTGTTAGATGAATATAGATATTTCAAGGAGTCTGGGCGGCAAAAATCAAGCAAAAC
*
2008 TGAG-TCGGAC
322 TGAGCT-GGGC
* * * *
2018 CCCGGAACACGTTTTTAGCAAAAATCCTGATGGTTTGTACACGATTTCGGCGAAAATTTTGCAAA
1 CCCGGAACGCGTTTTTAGCAAAAACCCTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAA
* * * * * *
2083 AATTGAT-CCG-AAAGATTTTGT-CTCAATTTTTAGCCATAATACTCA-AGAAAAATGTACGATT
66 AATTG-TCCCGAAAAG-TTTT-TCCTCAATTTTTGGACAAAATACTCATAAAAAAATATACAATT
** *
2144 CATGCAAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCATATTTGTTT-CTGAAT
128 CACACCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCATATTT-TTTCCTGAAT
* *
2208 TAATTTCTAATAAAATCAAAACAAGATTCCAATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
192 TAATTTCTAATAAAATCGAAACAAGATTCCGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
* * * * * *
2273 GCTAAG-TTTTAGTTAGGTGAATAAAGATATTTCAAGGAGTCTGCGCGCCAAAAGTCATGCAAAA
257 GCTAAGATTTT-GTTAGATGAATATAGATATTTCAAGGAGTCTGGGCGGCAAAAATCAAGCAAAA
* *
2337 ATGAGAC-GGGG
321 CTGAG-CTGGGC
* ** * ** * * * * * *
2348 CCCGAAACATGATTTTAGCAAAAATCTGTGACGGTTAGCACACGATTTCGACTAAGATTATACAA
1 CCCGGAACGCGTTTTTAGCAAAAA-CCCTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAA
* ** * * * * *
2413 AAATTGACGTGAAAAATTTTTCCTCAAATTTTTGTA-AAAAGTACTC--GAGAAAATTTACAATT
65 AAATTGTCCCGAAAAGTTTTTCCTC-AATTTTTGGACAAAA-TACTCATAAAAAAATATACAATT
*** * *
2475 CTTGCCAAAAATATTGAAGGGCTTTTCACGCTTCTAATATCTTTTTTCATATTTGTTT-CTGAAT
128 CACACCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCATATTT-TTTCCTGAAT
* * * * *
2539 TTATTTCTAAGAAAATC-AGAACAAGATTCCGATGCTCGTCAAAACAAATCCTCAAATCCATTGT
192 TAATTTCTAATAAAATCGA-AACAAGATTCCGATGCTCGTAAAAACAAATCCTTAAATCCAATGT
* ** * * * * *
2603 GGCTAAGATTTCGTTAGATGAATATAGATATTTGGAGAAGTTTGCGCGCCAAAAATCATGCAAAA
256 GGCTAAGATTTTGTTAGATGAATATAGATATTTCAAGGAGTCTGGGCGGCAAAAATCAAGCAAAA
* * *
2668 TTGA-CAAGGGT
321 CTGAGC-TGGGC
* * * ** * * * * *
2679 CCCTGAACACGTTTTTAGTAAAAAAACTATGATAGTTAGTACACAATTTCGCCTAAACTTTTACA
1 CCCGGAACGCGTTTTTAG--CAAAAACCCTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCA
* * * * * * *
2744 AAAATGGACCCAAAAATTTTTTCCTCAATTTTTGG-CTAGAATACTCGTAAAAAATATATA-ACT
64 AAAATTGTCCCGAAAAGTTTTTCCTCAATTTTTGGAC-AAAATACTCATAAAAAA-ATATACAAT
* * * *
2807 TAACACCAAAAAGATTGAAGGGCTGTTCACGCTTCTAATATCGTTTTTCTTATTTTTT-TTGAAT
127 TCACACCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCATATTTTTTCCTGAAT
* * * *** * * * *
2871 TAATTTCTAATTAAAGCGAAATAAGATTAAAAATGCTCGTAAAAACAATTCTTTTAATCCAATAT
192 TAATTTCTAATAAAATCGAAACAAGATT-CCGATGCTCGTAAAAACAAATCCTTAAATCCAATGT
* * *
2936 GGCTGAGATTTTGTTAGATTAATATAGATATTTCAAGGAGTCTGGGTGG-AAAAATCAAGCAAAA
256 GGCTAAGATTTTGTTAGATGAATATAGATATTTCAAGGAGTCTGGGCGGCAAAAATCAAGCAAAA
3000 CTGAGCTGGGGC
321 CTGAGCT-GGGC
* * * * * *
3012 CCTGAAACGCGTTTTTAGCAAAAACCCTGATGGTTAGTATACGTTTTTGGCTAAACTTTTGCAAA
1 CCCGGAACGCGTTTTTAGCAAAAACCCTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAA
* * * **
3077 AATTGTCCTGAAAATTTTTTCCTCAATTTTTGGACACAATACTCAT-AAAAGGTATACAATTCGA
66 AATTGTCCCGAAAAGTTTTTCCTCAATTTTTGGACAAAATACTCATAAAAAAATATACAATTC-A
* * * * *
3141 CACCGAAAAGATTGAAGGGCTTTTCATGCTTCTAATTTCG-ATTTCACTAATTTTTTTCC-GTAT
130 CACCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCA-T-A-TTTTTTCCTGAAT
* * * * * *
3204 TTATTTATAACAAAAAT-GAAAC-CGATTTCTGATGCTCGAAAAAACAAATCCTTAAATCCAATG
192 TAATTTCTAA-TAAAATCGAAACAAGA-TTCCGATGCTCGTAAAAACAAATCCTTAAATCCAATG
* * * * * * * * *
3267 TGGTTGAGATTTGGTTAGATTAATATAGATATTTCAAGGAGTTTGGGTGACAAAATTCAAGAAAA
255 TGGCTAAGATTTTGTTAGATGAATATAGATATTTCAAGGAGTCTGGGCGGCAAAAATCAAGCAAA
*
3332 ACTGGGTCTGGGC
320 ACTGAG-CTGGGC
* * *
3345 CCCGGAATGTGTTTTTACCAAAAACCCTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAA
1 CCCGGAACGCGTTTTTAGCAAAAACCCTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAA
* * * * * * * *
3410 AATTGACCCG-AAAGATTTTGCCTCAA-TTTTGGAGCCATAATATTC-GAGAAAAATATACGACT
66 AATTGTCCCGAAAAG-TTTTTCCTCAATTTTTGGA--CAAAATACTCATAAAAAAATATACAATT
* * * * *
3472 CA-AGCCAAAAAGATTGAAGTGCTTTTCATGCTTCTAATATAGTTTTTCATATATGTTTGC-GAA
128 CACA-CCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCATAT-TTTTTCCTGAA
* * * * * * *
3535 TTAATTTCTAAGAAAA-CTAAAACAAGATTCTGATCCTCGTAAAAACAAATCCTCAAATCGATTG
191 TTAATTTCTAATAAAATC-GAAACAAGATTCCGATGCTCGTAAAAACAAATCCTTAAATCCAATG
3599 TGGCTAAGATT
255 TGGCTAAGATT
3610 GCGTTATATG
Statistics
Matches: 2621, Mismatches: 503, Indels: 287
0.77 0.15 0.08
Matches are distributed among these distances:
319 62 0.02
320 78 0.03
321 32 0.01
322 5 0.00
323 1 0.00
324 10 0.00
327 7 0.00
329 25 0.01
330 391 0.15
331 520 0.20
332 588 0.22
333 576 0.22
334 50 0.02
336 2 0.00
337 1 0.00
340 1 0.00
342 5 0.00
344 4 0.00
346 5 0.00
348 1 0.00
351 1 0.00
352 2 0.00
354 1 0.00
355 109 0.04
356 6 0.00
357 4 0.00
358 1 0.00
361 7 0.00
362 1 0.00
364 10 0.00
365 2 0.00
366 2 0.00
367 70 0.03
368 21 0.01
369 20 0.01
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (331 bp):
CCCGGAACGCGTTTTTAGCAAAAACCCTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAA
AATTGTCCCGAAAAGTTTTTCCTCAATTTTTGGACAAAATACTCATAAAAAAATATACAATTCAC
ACCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCATATTTTTTCCTGAATTAAT
TTCTAATAAAATCGAAACAAGATTCCGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTA
AGATTTTGTTAGATGAATATAGATATTTCAAGGAGTCTGGGCGGCAAAAATCAAGCAAAACTGAG
CTGGGC
Found at i:1921 original size:332 final size:328
Alignment explanation
Indices: 16--5372 Score: 2939
Period size: 333 Copynumber: 16.2 Consensus size: 328
6 TAAGACGGAG
* ** * *
16 CCCGGAACGCGTTTTTAGCAAAAAACTATGACGGTTAGTACACGATTTCGGCAAAAATTTTAG-A
1 CCCGAAACGCGTTTTTAGC-AAAAACCCTGATGGTTAGTACACGATTTCGGCTAAAATTTT-GCA
* * * *
80 AAAATTGACCCGAAAGTTTTTGC-C---------A-A-AATACTCAAGAAAAAAAATACAATTCA
64 AAAATTGTCCCGAAAGTTTTTCCTCAATTTTTGGACATAATACTCTA-AAAAAATATACAATTCA
* * * * * *
133 CGCTAAAAAGATTGAAGGGCTTTTCAGGCTTCTAATACCATTTTTCATATATTTTTCTGAATTAA
128 CACCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCATAT-TTTTTC-CAATTAA
* *
198 TTTCTAATAAAATC-AAAGCAAGA-TTCCGATGCTCGTAAAAACCAATCCTTAAATCCAATGTGG
191 TTTCTAATAAAATCGAAA-CAAGATTTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGG
* * * * *
261 TTGAGATTTGGTTAGATGATTATAGATATTTCAAAGAGTCTGGCCGGCAAAAAATCAAGCAAAAC
255 CTAAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTGGGCGGC-AAAAATCAAGCAAAAC
* *
326 TGAGCCGAGGT
319 TGAGCTG-GGC
* * * * *
337 CCCGAAATGCGTTTTCAGCAAAAACCCTGATGGTTAGTTCATGATTTCGGCTAAAATTTTACAAA
1 CCCGAAACGCGTTTTTAGCAAAAACCCTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAA
* ** * * * * * * * *
402 AATGGATCCAAAAAAATTTATCCACAATTTTTGGCCAAAATAATCGAGAAAAATATACAATTCAC
66 AATTG-TCC-CGAAAGTTTTTCCTCAATTTTTGGACATAATACTCTAAAAAAATATACAATTCAC
*
467 GCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCATATTTGTTTCCGAATTAAT
129 ACCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCATATTT-TTTCC-AATTAAT
* * * * * *
532 TTCTAATAAAATCAAAACAATA-TTCCGATGCTCGTAAAAACAAATCCTTAAATTCATTGTGACT
192 TTCTAATAAAATCGAAACAAGATTTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCT
* * **
596 AAGATTTAGTTAGATGAATATAGATATTTCAAGGAGTCTGCGCCCCAAAAATCATA-CAAAACTG
257 AAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTGGGCGGCAAAAATCA-AGCAAAACTG
* *
660 TGACTGAG-
321 AG-CTGGGC
* * ** * * * * * *
668 CCCGGAACGCG-TTTTAACAAAAAACTGTGACGATTTGTACATGGTTTCGGCTAAAATTTTACAA
1 CCCGAAACGCGTTTTTAGC-AAAAACCCTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAA
* * * * * * * * **
732 AAATAGACTCGAAAAATTTTTCCTCAATTTTCGGCCAAAATACTC-ATAAAAAATATATAGCTCA
65 AAATTGTCCCG-AAAGTTTTTCCTCAATTTTTGGACATAATACTCTA-AAAAAATATACAATTCA
* * ** * *
796 CCGCCAAAAATATTGAAGGGCTTTTCACGC-TCTAATATCGTTTCCCTTATTTTTTTCTGAATTA
128 -CACCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCATA-TTTTTTC-CAATTA
* * * * * *
860 ATTTATAATTAAAGCGAAACAAGA-TTC-GAATGCTCGTAAAACCAAATCTTTTAATCCAATGTG
190 ATTTCTAATAAAATCGAAACAAGATTTCTG-ATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
* * * * *
923 GCTGAGATTTTGTTAGATTATTATAGATATTTCAAGGAGTCTGGGCGGAAAAAATCAAGCAAAAC
254 GCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTGGGCGGCAAAAATCAAGCAAAAC
988 TGAGCTGGGGC
319 TGAGCT-GGGC
* * * * *
999 CCTGGAGCGCG-TTTTATGC--AAA-----A-----AGTACATGATCTCGGCTAAAATTTTGCAA
1 CCCGAAACGCGTTTTTA-GCAAAAACCCTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAA
** * * * *
1051 AAATTGTCCAAAAAATTTTTTCCTAAATTTTTGGACACAATACTCATAAAGAAATATACAATTCC
65 AAATTGTCC-CGAAAGTTTTTCCTCAATTTTTGGACATAATACTC-TAAAAAAATATACAATT-C
* * * * * *
1116 ACACCGAAAAGATTGAAGGGCTTTTCATGCTTATAATATCGTTTTCCCTATTTTTTTTTCCGTAT
127 ACACCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTT-TC-A-TATTTTTTCC--AA
* * ** * *** * * **
1181 TTATTTTTTTGTGAGACAT-GTATTGAATATCCTTCCGA--CTAATTAAATTGAAACCAATTTCT
187 TTAATTTCTAAT-A-AAATCG-AAACAAGAT--TTCTGATGCT-CGT-AA---AAA-CAA-----
* ** * * * * * *
1243 GATGCTCGTAAAAACAA-AT-CCTTAAATCCATTGTGGTTAAGATTTG-GT-TAGATGAATACAA
236 -AT-C-CTTAAATCCAATGTGGC-T-AA--GATT-TGGTT-AGA--TGAATATAGAT-ATTTCAA
** * *
1304 ATATTTCAAGGAGTCTGGGCAGCAAAACTCAAGCAAAACTGAGCTGGGGC
289 GGA-GTC-TGG-G-C--GGCA--AAAA-TCAAGCAAAACTGAGCT-GGGC
* * * * *
1354 CCCGGAATGCGTTTTTAGCAAAAACCCTGATGGTTAATACATGATTTCGGCTAAAATTTTGCCAA
1 CCCGAAACGCGTTTTTAGCAAAAACCCTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAA
* * * * * * *
1419 AATGTGAT-CCGAAAGATTTTCCCCTCAATTTTTAGCCATAGTACTCGAGAAAAATATACAATTG
66 AAT-TG-TCCCGAAAG-TTTT-TCCTCAATTTTTGGACATAATACTCTAAAAAAATATACAATTC
* * *
1483 A-AGCAAAAAAGATTGAAGGACTTTTCACGCTTCTAATATCATTTTTCATATTTTTTCCTGAATT
127 ACA-CCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCATATTTTTTCC--AATT
* * ** * * *
1547 AATTTCTAATTAAAGCGAAACAAGA-TTCAAATGCTCGTAAAAACAAATCTTTTAATCTAATGTG
189 AATTTCTAATAAAATCGAAACAAGATTTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
* * * ** *
1611 GCTAAGATTTTGTTAGATTAATATAGATACTTCAAGGAGTCTAAGCGGAAAAAATCAAGCAAAAC
254 GCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTGGGCGGCAAAAATCAAGCAAAAC
* *
1676 TGAGCTTGAC
319 TGAGCTGGGC
** * * * * * *
1686 CTTGAAACGCGTTTTTAGCAAAAACCTTGTTGATTAGTACACGTTTTCGACTAAAATTTTGCACA
1 CCCGAAACGCGTTTTTAGCAAAAACCCTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAA
* *
1751 AATTGTCCCGAAACGTTTTTCCTCAATTTTTGGACACAATACTCATAAAAAAATATATAATTCGA
66 AATTGTCCCGAAA-GTTTTTCCTCAATTTTTGGACATAATACTC-TAAAAAAATATACAATTC-A
* * * * * *
1816 CACCGAAAAGATTGAAGGGCTTTTCATGCTTCTAATTTCGTTTTCCCTAATTTTTTCCATATTTA
128 CACCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCAT-ATTTTTTCCA-ATTAA
* * * * *
1881 TTTCTGATTAAATCGAAA-ATGATTTCTGATGCTCGTAAAAACAAATCCTTAAATCTAATGTGGT
191 TTTCTAATAAAATCGAAACAAGATTTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGC
* * * * *
1945 TGAGATTTGGTTAGATGAATGTAAACATTTGAAGGAGTCTGGGCGGCAAAAATCAAGCAAAACTG
256 TAAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTGGGCGGCAAAAATCAAGCAAAACTG
*
2010 AG-TCGGAC
321 AGCT-GGGC
* * * * *
2018 CCCGGAACACGTTTTTAGCAAAAATCCTGATGGTTTGTACACGATTTCGGCGAAAATTTTGCAAA
1 CCCGAAACGCGTTTTTAGCAAAAACCCTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAA
* * * *
2083 AATTGAT-CCGAAAGATTTTGT-CTCAATTTTTAGCCATAATACTC-AAGAAAAATGTACGATTC
66 AATTG-TCCCGAAAG-TTTT-TCCTCAATTTTTGGACATAATACTCTAA-AAAAATATACAATTC
** * *
2145 ATGCAAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCATATTTGTTTCTGAATTA
127 ACACCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCATATTT-TTTC-CAATTA
* **
2210 ATTTCTAATAAAATCAAAACAAGA-TTCCAATGCTCGTAAAAACAAATCCTTAAATCCAATGTGG
190 ATTTCTAATAAAATCGAAACAAGATTTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGG
* * * * * * * * *
2274 CTAAGTTTTAGTTAGGTGAATAAAGATATTTCAAGGAGTCTGCGCGCCAAAAGTCATGCAAAAAT
255 CTAAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTGGGCGGCAAAAATCAAGCAAAACT
*
2339 GAGAC-GGGG
320 GAG-CTGGGC
** * ** * * * * * *
2348 CCCGAAACATGATTTTAGCAAAAATCTGTGACGGTTAGCACACGATTTCGACTAAGATTATACAA
1 CCCGAAACGCGTTTTTAGCAAAAA-CCCTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAA
* ** * * * * * *
2413 AAATTGACGTGAAAAATTTTTCCTCAAATTTTTGTA-AAAAGTACTC-GAGAAAATTTACAATTC
65 AAATTGTCCCG-AAAGTTTTTCCTC-AATTTTTGGACATAA-TACTCTAAAAAAATATACAATTC
*** * * * *
2476 TTGCCAAAAATATTGAAGGGCTTTTCACGCTTCTAATATCTTTTTTCATATTTGTTTCTGAATTT
127 ACACCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCATATTT-TTTC-CAATTA
* * * * *
2541 ATTTCTAAGAAAATC-AGAACAAGA-TTCCGATGCTCGTCAAAACAAATCCTCAAATCCATTGTG
190 ATTTCTAATAAAATCGA-AACAAGATTTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
* ** * * * * * *
2604 GCTAAGATTTCGTTAGATGAATATAGATATTTGGAGAAGTTTGCGCGCCAAAAATCATGCAAAAT
254 GCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTGGGCGGCAAAAATCAAGCAAAAC
*
2669 TGA-CAAGGGTC
319 TGAGC-TGGG-C
* * * ** * * * * *
2680 CCTG-AACACGTTTTTAGTAAAAAAACTATGATAGTTAGTACACAATTTCGCCTAAACTTTTACA
1 CCCGAAACGCGTTTTTAG--CAAAAACCCTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCA
* * * * * *
2744 AAAATGGACCCAAAAATTTTTTCCTCAATTTTTGG-CTAGAATACTCGTAAAAAATATATA-ACT
64 AAAATTGTCCC-GAAAGTTTTTCCTCAATTTTTGGAC-ATAATACTC-TAAAAAA-ATATACAAT
* * * **
2807 TAACACCAAAAAGATTGAAGGGCTGTTCACGCTTCTAATATCGTTTTTCTTATTTTTTTTGAATT
125 TCACACCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCATA-TTTTTTCCAATT
* * * **** * * * *
2872 AATTTCTAATTAAAGCGAAATAAGATTAAAAATGCTCGTAAAAACAATTCTTTTAATCCAATATG
189 AATTTCTAATAAAATCGAAACAAGATTTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
* * * *
2937 GCTGAGATTTTGTTAGATTAATATAGATATTTCAAGGAGTCTGGGTGG-AAAAATCAAGCAAAAC
254 GCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTGGGCGGCAAAAATCAAGCAAAAC
3001 TGAGCTGGGGC
319 TGAGCT-GGGC
* * * * *
3012 CCTGAAACGCGTTTTTAGCAAAAACCCTGATGGTTAGTATACGTTTTTGGCTAAACTTTTGCAAA
1 CCCGAAACGCGTTTTTAGCAAAAACCCTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAA
* * * **
3077 AATTGTCCTGAAAATTTTTTCCTCAATTTTTGGACACAATACTC-ATAAAAGGTATACAATTCGA
66 AATTGTCCCG-AAAGTTTTTCCTCAATTTTTGGACATAATACTCTA-AAAAAATATACAATTC-A
* * * * *
3141 CACCGAAAAGATTGAAGGGCTTTTCATGCTTCTAATTTCG-ATTTCACTAATTTTTTTCCGTATT
128 CACCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCA-T-A-TTTTTTCC-AATT
* * * * *
3205 TATTTATAACAAAAAT-GAAAC-CGATTTCTGATGCTCGAAAAAACAAATCCTTAAATCCAATGT
189 AATTTCTAA-TAAAATCGAAACAAGATTTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATGT
* * * * * * * *
3268 GGTTGAGATTTGGTTAGATTAATATAGATATTTCAAGGAGTTTGGGTGACAAAATTCAAGAAAAA
253 GGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTGGGCGGCAAAAATCAAGCAAAA
*
3333 CTGGGTCTGGGC
318 CTGAG-CTGGGC
* * * *
3345 CCCGGAATGTGTTTTTACCAAAAACCCTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAA
1 CCCGAAACGCGTTTTTAGCAAAAACCCTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAA
* * * * * * *
3410 AATTGACCCGAAAGATTTTGCCTCAA-TTTTGGAGCCATAATATTCGAGAAAAATATACGACTCA
66 AATTGTCCCGAAAG-TTTTTCCTCAATTTTTGGA--CATAATACTCTAAAAAAATATACAATTCA
* * * * *
3474 -AGCCAAAAAGATTGAAGTGCTTTTCATGCTTCTAATATAGTTTTTCATATATGTTTGCGAATTA
128 CA-CCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCATAT-T-TTTTCCAATTA
* * * * * *
3538 ATTTCTAAGAAAA-CTAAAACAAGA-TTCTGATCCTCGTAAAAACAAATCCTCAAATCGATTGTG
190 ATTTCTAATAAAATC-GAAACAAGATTTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
* * * ** * *** * *** **
3601 GCTAAGA-TTGCGTTATATGCA-A-GGA-GCTGCACTAAGACTGGGGCTCGG-AACGCGTTTTTA
254 GCTAAGATTTG-GTTAGATGAATATAGATATTTCAAGGAGTCT-GGG--CGGCAA---AAATCAA
* * *
3661 GCAAAGA--AATCTGTG-
312 GCAAA-ACTGAGCTGGGC
* * * ** * ** * * ** *
3676 ACGGTTAGTATACGATTTCGGCTAAAA---T--T--TT-GCA-AAAATTGATC--CGAAAGATTT
1 CCCG--A-AACGCGTTTTTAGCAAAAACCCTGATGGTTAGTACACGATT--TCGGCTAAA-ATTT
*** * * * ** **** * * * * * *
3730 TGTCTCAATTTTTGGCCAGAATA-CTCATGAAAAATATAT-AAC-TCA-ACGCCT-AAAAGAT-T
60 TG---CAAAAATTGTCCCGAA-AGTTTTTCCTCAATTTTTGGACATAATAC-TCTAAAAAAATAT
** **** * * * *** * * *
3789 GA-AGGTCTTTTC---ACGCTTCTAATATCGTTT-----TTCT--TAT-TTTTTTCTGA-ATTAA
120 -ACAATTCACACCAAAAAGATT-GAAGGGCTTTTCACGCTTCTAATATCGTTTTTC--ATATT-T
* ** ** * * * *
3841 TTTCTAATTAAAGTGAAATAAGATTC----C-A-A------ATGCTCGTAAAAACAATTCTTTTA
180 TTTCCAATTAATTTCTAATAA-AATCGAAACAAGATTTCTGATGCTCGTAAAAACAAATCCTTAA
* * * * * *
3894 ATCCAATATGGCTGAGATTTTGTTAGATTAATATAGGTATTTCAAGGAGTCTGGGCGGAAAAAAT
244 ATCCAATGTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTGGGCGGCAAAAAT
*
3959 CAAGCAAAACTGAGTTGGGGC
309 CAAGCAAAACTGAGCT-GGGC
* * * * * * **
3980 CCTGGAACGCGTTTTTAGTAAAAACCGTGATGGTTAGTACACGTTTTCAGCTAATCTTTTGCAAA
1 CCCGAAACGCGTTTTTAGCAAAAACCCTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAA
* * **
4045 AATTGTCCCGAAAATTTTTGCCTCAATTTTTGGACACAATACTC-ATAAAATGTATACAATTCGA
66 AATTGTCCCGAAAGTTTTT-CCTCAATTTTTGGACATAATACTCTA-AAAAAATATACAATTC-A
** * * * * *
4109 CACTGAAAATATTGAAGGGCTTTTCATGCATT-TAATTTCG-ATTTCACTAATTTTTTTCCGTAT
128 CACCAAAAAGATTGAAGGGCTTTTCACGC-TTCTAATATCGTTTTTCA-T-A-TTTTTTCC-AAT
* * *
4172 TTATTTCTAATAAAAAT-GAAAC-TGATTTCTGATGCTCGTAAAAATAAATCCTTAAATCCAATG
188 TAATTTCTAAT-AAAATCGAAACAAGATTTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATG
* * * * * *
4235 TGGTTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTTTGGGTGACAAAAATCAAGAAAA
252 TGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTGGGCGGCAAAAATCAAGCAAA
* *
4300 ACTGGGCCGGGAC
317 ACTGAGCTGGG-C
* * *
4313 CTCGGAATGCGTTTTTAGCAAAAACCCTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAA
1 CCCGAAACGCGTTTTTAGCAAAAACCCTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAA
** * * * * * * * * *
4378 AATTAACCCGAAAGATTTTGCCTCAAATTTTAGCCATAATATTCGAGAAAAATATACGACTCA-A
66 AATTGTCCCGAAAG-TTTTTCCTCAATTTTTGGACATAATACTCTAAAAAAATATACAATTCACA
* * * *
4442 GCCAAAAAGATTGAAGGGCTTTTCATGCTTCCAATATAGTTTTTCACATTTGTTTCCGAATTAAT
130 -CCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCATATTT-TTTCC-AATTAAT
* * * * * *
4507 TTCTAAGAAAATCAAAACAAGA-TTCTGATCCTCGTAAAAACAAATCCTCAAATCGATTGTGGCT
192 TTCTAATAAAATCGAAACAAGATTTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCT
* * * * * * *
4571 AAGATTTCGTTAGATGAATACAGATATGTCAAGGAGTCTGCGC-GCAAAAAATCATGGAAAACTA
257 AAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTGGGCGGC-AAAAATCAAGCAAAACTG
4635 AGAC-GGG-
321 AG-CTGGGC
* * ** * *
4642 CCCAAAACGCGTTATTAGCAAAAAAAAACTGTGACGGTTAGTACACGATTTCGGCTAAAATTTTA
1 CCCGAAACGCGTTTTTAGC----AAAAACCCTGATGGTTAGTACACGATTTCGGCTAAAATTTTG
* * * * ** ** * * * * * *
4707 TAAAAGTGGACTCAAAAAAATTTTCCTCAATTTTTTGCCAGAATACTCGT-AAAATATATATAAC
62 CAAAAATTGTC-CCGAAAGTTTTTCCTCAATTTTTGGACATAATACTC-TAAAAAAATATACAAT
* * * * *
4771 TCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTCTTTTTTGTTTTTCTG
125 TC-ACACCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTC--ATAT-TTTTTC-C
* * * ** * * *
4836 AATTAATTTCTAATTAAAGCGAAACAAGA-TCCAAATGCTCGTAAAAACAATTCTTTTAATCCAA
185 AATTAATTTCTAATAAAATCGAAACAAGATTTCTGATGCTCGTAAAAACAAATCCTTAAATCCAA
* * * *
4900 TGTGGCTGAGATTTTGTTAGACT-AATATAGATATTTCAAGGAGTCTGGGCAGAAAAAATCAAGC
250 TGTGGCTAAGATTTGGTTAGA-TGAATATAGATATTTCAAGGAGTCTGGGCGGCAAAAATCAAGC
*
4964 AAAACTGAGCTGGGGA
314 AAAACTGAGCT-GGGC
* * * * * * *
4980 ACTGTAACGCGTTTTTTGTAAAAACTCTGATGGTTAACGTACACGTTTTCAGG-TAAAATTTTGC
1 CCCGAAACGCGTTTTTAGCAAAAACCCTGATGGTT-A-GTACACGATTTC-GGCTAAAATTTTGC
* * * * * **
5044 TAAGATTTTTCC-AAA----------AATTTTTGGACACAATACTC-ATAAAAGGTATACAATTC
63 AAAAATTGTCCCGAAAGTTTTTCCTCAATTTTTGGACATAATACTCTA-AAAAAATATACAATTC
* * * * * **
5097 GACACCGAAAATATTGAAGGGCTTTTCATGCTTCTAATTTCG-ATTTCACTAATTTTTTTTAGTA
127 -ACACCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCA-T-ATTTTTTCCA--A
* * * *
5161 TTTATTTCTAATAAAA-CTGAAAC-CGATTTCTTATGCTCGTAAAAAGAAATCCTTAAATCCAAT
187 TTAATTTCTAATAAAATC-GAAACAAGATTTCTGATGCTCGTAAAAACAAATCCTTAAATCCAAT
* * * * * *
5224 GTGGTTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTTTGGGTGACAAAAATCAAGAAA
251 GTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTGGGCGGCAAAAATCAAGCAA
* *
5289 AACTGTGCCGGGGC
316 AACTGAG-CTGGGC
* * * *
5303 CCCGGAATGCGTTTTTAGCAAAAACCCTGATGGTTAATACCCGATTTCGGCTAAAATTTTGCAAA
1 CCCGAAACGCGTTTTTAGCAAAAACCCTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAA
5368 AATTG
66 AATTG
5373 GCTGAGATTT
Statistics
Matches: 3824, Mismatches: 915, Indels: 594
0.72 0.17 0.11
Matches are distributed among these distances:
300 1 0.00
301 18 0.00
302 2 0.00
303 44 0.01
304 8 0.00
305 5 0.00
306 21 0.01
307 5 0.00
308 7 0.00
309 10 0.00
310 15 0.00
311 4 0.00
313 21 0.01
314 12 0.00
315 5 0.00
316 4 0.00
319 61 0.02
320 86 0.02
321 71 0.02
322 26 0.01
323 170 0.04
324 85 0.02
325 12 0.00
326 16 0.00
327 7 0.00
328 5 0.00
329 58 0.02
330 412 0.11
331 645 0.17
332 639 0.17
333 763 0.20
334 135 0.04
335 5 0.00
336 141 0.04
337 9 0.00
338 13 0.00
339 4 0.00
340 3 0.00
341 10 0.00
342 7 0.00
343 11 0.00
344 8 0.00
345 11 0.00
346 7 0.00
347 10 0.00
348 5 0.00
349 4 0.00
350 1 0.00
352 3 0.00
354 4 0.00
355 35 0.01
356 8 0.00
357 3 0.00
359 6 0.00
360 1 0.00
361 2 0.00
362 7 0.00
363 1 0.00
364 18 0.00
365 1 0.00
366 2 0.00
367 70 0.02
368 21 0.01
369 20 0.01
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (328 bp):
CCCGAAACGCGTTTTTAGCAAAAACCCTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAA
AATTGTCCCGAAAGTTTTTCCTCAATTTTTGGACATAATACTCTAAAAAAATATACAATTCACAC
CAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCATATTTTTTCCAATTAATTTCT
AATAAAATCGAAACAAGATTTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTAAGA
TTTGGTTAGATGAATATAGATATTTCAAGGAGTCTGGGCGGCAAAAATCAAGCAAAACTGAGCTG
GGC
Found at i:5507 original size:146 final size:146
Alignment explanation
Indices: 5229--5518 Score: 393
Period size: 146 Copynumber: 2.0 Consensus size: 146
5219 CCAATGTGGT
** *
5229 TGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTTTGGGTGACAAAAATCAAGAAAAACTG
1 TGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCCGGGGGACAAAAATCAAGAAAAACTG
* * * * *
5294 TGCCGGGGCCCCGGAATGCGTTTTTAGCAAAAACCCTGATGGTTAATACCCGATTTCGGCTAAAA
66 AGCCGGGGCACCGGAACGCGTTTTTAGCAAAAACCCTGATGGTTAATACACGATTTCAGCTAAAA
5359 TTTTGCAAAAATTGGC
131 TTTTGCAAAAATTGGC
* * *
5375 TGAGATTTTGTTAGATTAATATAGATATTTCAAGGAGTCCGGGCGGA-AAAAATCAAGCAAAACT
1 TGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCCGGG-GGACAAAAATCAAGAAAAACT
** * * * * * *
5439 GAGTTGGGGCACTGGAACGCGTTTTTAGTAAAAACCGTGATGGTTAGTACACGTTTTCAGCTAGA
65 GAGCCGGGGCACCGGAACGCGTTTTTAGCAAAAACCCTGATGGTTAATACACGATTTCAGCTAAA
5504 ATTTTGCAAAAATTG
130 ATTTTGCAAAAATTG
5519 TCCCCAAAAT
Statistics
Matches: 124, Mismatches: 19, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
146 122 0.98
147 2 0.02
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (146 bp):
TGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCCGGGGGACAAAAATCAAGAAAAACTG
AGCCGGGGCACCGGAACGCGTTTTTAGCAAAAACCCTGATGGTTAATACACGATTTCAGCTAAAA
TTTTGCAAAAATTGGC
Done.