Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015466.1 Corchorus olitorius cultivar O-4 contig15499, 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: 66744
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:1105 original size:317 final size:315
Alignment explanation
Indices: 260--2783 Score: 2184
Period size: 316 Copynumber: 8.0 Consensus size: 315
250 AATTCAACAC
260 CAAAAATACTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTAGAATTAATTTCT
1 CAAAAATACTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTAGAATTAATTTCT
325 AATTAAATCGAAACAAAATTTAGATGCTCGCAAAAATAAATCCTTAAATCCATTATGGCTTAGAT
66 AATTAAATCGAAACAAAATTTAGATGCTCGCAAAAATAAATCCTTAAATCCATTATGGCTTAGAT
* * *
390 TGGGTTAGATGAATATAGAAATTTTTAGTGGTCTTTTTCCAAAAAATCATACGAAACTGAGTCGG
131 T-GGTTAGATGAATATAGAAATTTTAAGGGGTCTTTTTCCAAAAAATCATGCGAAACTGAGTCGG
* * * * *
455 GGCCCCCAAATGGGTTTTTAGCCCCAAAACCGTGATAGTTGGTACGGAATTTCAGCCAAAAACTG
195 GGCTCCCAAACGCGTTTTTAGCCCCAAAACCGTGATAGTTAGTACAGAATTTCAGCCAAAAACTG
* * *
520 ACCTGAAATATTTTTTCATGAAATTTTTGCCACAATACTCAGAAAAAATATAAAATT
260 ACCCGAAA-AGTTTTTCATGAAATTTTTGCCACAATACTCAGAAAAAATATATAATT
*
577 CAAAAATACTGAAGGGTTTTTCATGCTTCTAATATCG-TTTTCCATTTTTTTAGAATTAATTTCT
1 CAAAAATACTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTAGAATTAATTTCT
*
641 ATTTAAATCGAAACAAAATTTAGATGCTCGCAAAAATAAATCCTTAAATCCATTATGGCTTAGAT
66 AATTAAATCGAAACAAAATTTAGATGCTCGCAAAAATAAATCCTTAAATCCATTATGGCTTAGAT
* * *
706 TGGATTAGATGAATATAGAAATTTTAAGGGGTCTTTTTACAAAAAATAATGTGAAACTGAGTCGG
131 TGG-TTAGATGAATATAGAAATTTTAAGGGGTCTTTTTCCAAAAAATCATGCGAAACTGAGTCGG
* * *
771 GGCCCCCAAATGCGTTTTTAGCCCCAAAACCGTGATAGTTGGTACAGAATTTCAGCCAAAAACTG
195 GGCTCCCAAACGCGTTTTTAGCCCCAAAACCGTGATAGTTAGTACAGAATTTCAGCCAAAAACTG
*
836 ACCCGAAAAAGTTTTTCATGAAATTTTTGCCACAATACTCAGAAAAAATATAAAATT
260 ACCCG-AAAAGTTTTTCATGAAATTTTTGCCACAATACTCAGAAAAAATATATAATT
* *
893 CAAAAATACTGAAGGGATTTTCATGCTTCTAATATCGTTTTTCCATTTTTTTAGAATTAATTTCT
1 CAAAAATACTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTAGAATTAATTTCT
*
958 ATTTAAATCGAAACAAAATTTAGATGCTCGCAAAAATAAATCCTTAAATCCATTATGGCTTAGAT
66 AATTAAATCGAAACAAAATTTAGATGCTCGCAAAAATAAATCCTTAAATCCATTATGGCTTAGAT
* * *
1023 TGGATTAGATGAATATAGAAATTTTAAGGGGTATTTTTCCAAAAAATAATGTGAAACTGAGTCGG
131 TGG-TTAGATGAATATAGAAATTTTAAGGGGTCTTTTTCCAAAAAATCATGCGAAACTGAGTCGG
* * *
1088 GGCGCCCAAACGCGTTTTTAGCCCCAAAACCGTGATAGTTAGTACACAATTTCAGCCAAAAAATG
195 GGCTCCCAAACGCGTTTTTAGCCCCAAAACCGTGATAGTTAGTACAGAATTTCAGCCAAAAACTG
* * * * * * **
1153 ACCCG-AAA-----T-A-AAAAGTGTT--CAAAATGAGCT-A-AATAAAATGTTAGCTGACC
260 ACCCGAAAAGTTTTTCATGAAATTTTTGCCACAAT-A-CTCAGAA-AAAAT-ATA--TAATT
* * ** * **
1203 CGAAAAGT-TTGACCGGTTTTTCACGCTTCTAATACCGTTTTTCCAATTTTTTTTTCTAATTAAT
1 C-AAAAATACTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCC-A--TTTTTTTAGAATTAAT
* * * * * *
1267 TTCTAATTAAATTGAATCAAAATTCAGATGCTCGTAAAAAACAAATCCTTATAA-ACA--ATGCG
62 TTCTAATTAAATCGAAACAAAATTTAGATGCTCG-CAAAAATAAATCCTTA-AATCCATTATG-G
* * * * ** ** * *
1329 GTTGAAAGTTGATTAGATGAATATA-AATATTTCAAGGATTC-TTCACGCCAAAAATCATGCAAA
124 CTT-AGA-TTGGTTAGATGAATATAGAA-ATTTTAAGGGGTCTTTTTC-CAAAAAATCATGCGAA
* ** * ** * *
1392 ATTGAGTCGGGGCTCCGGAACGCGTTTTTAG-CCAAAAACAATGATGGTTAGTACATG-ATTTCG
185 ACTGAGTCGGGGCTCCCAAACGCGTTTTTAGCCCCAAAACCGTGATAGTTAGTACA-GAATTTCA
* * *
1455 GCTACAATTTTGCAAAAACTGACCCGAAAAGTTTTTCTTCAATTTTTTGCCACAATACTCAGAAA
249 G---C-------CAAAAACTGACCCGAAAAGTTTTTCATGAAATTTTTGCCACAATACTCAGAAA
1520 AAATATATAATT
304 AAATATATAATT
*
1532 CAACACCAAAAATACTGAAGGTCTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTAGAATT
1 ------CAAAAATACTGAAGG-GTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTAGAATT
*
1597 AATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGCAAAAATAAATCCTTAAATCCATTATGG
59 AATTTCTAATTAAATCGAAACAAAATTTAGATGCTCGCAAAAATAAATCCTTAAATCCATTATGG
*
1662 CTTAGATTGGGTTAGATGAATATAGAAATTTTAAGTGGTCTTTTTCCAAAAAAATCATGCGAAAC
124 CTTAGATT-GGTTAGATGAATATAGAAATTTTAAGGGGTCTTTTTCC-AAAAAATCATGCGAAAC
* * * *
1727 TGAGTCGCGGC-CCTAAACGCGTTTTTAGTCCCAAAACCGTGATAGTTAGTACACAATTTCAGCC
187 TGAGTCGGGGCTCCCAAACGCGTTTTTAGCCCCAAAACCGTGATAGTTAGTACAGAATTTCAGCC
* * *
1791 GAAAAACTGACCCGAAAAAATATTTCTTGAAATTTTTGCCACAATACTCAGAAAAAATATATAAT
252 -AAAAACTGACCCG-AAAAGTTTTTCATGAAATTTTTGCCACAATACTCAGAAAAAATATATAAT
1856 T
315 T
* * ** * * * **
1857 CAACACCAAAAAGATTGACCGGCTTTTCACACTTCTAATACCGTTTTTCCATTTTTTTCTAATTA
1 ------CAAAAATACTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTAGAATTA
* * * * * *
1922 ATTTCTAATTAAATTGAATCAAGATTCAGATACTC-AAAAAATCACAAATCCTTATAA-CCA--A
60 ATTTCTAATTAAATCGAAACAAAATTTAGATGCTCGCAAAAAT---AAATCCTTA-AATCCATTA
* * ** *
1983 TGCGGTTGAGAGTTGGTTAGATGAATATA-AATATTTTAAGGAGTC---TTCGC-----GCCAAG
121 TG-GCTT-AGA-TTGGTTAGATGAATATAGAA-ATTTTAAGGGGTCTTTTTC-CAAAAAATCATG
* * ** * ** * *
2039 CAAAATTGAGTCGGGGCTCCGGAACGCATTTTTAG-CAAAAAACCGTGAT-TTTCGGCTAC--AA
181 CGAAACTGAGTCGGGGCTCCCAAACGCGTTTTTAGCCCCAAAACCGTGATAGTT-AG-TACAGAA
* * * * * *
2100 TTT-TG-CAAAAACTGACCCGAAAAGTTTTTCCT-CAA-TATT----CAACAC-C---AAAAAGA
244 TTTCAGCCAAAAACTGACCCGAAAAGTTTTTCATGAAATTTTTGCCACAATACTCAGAAAAAATA
* *
2153 T-TGA-C
309 TATAATT
***** * * * * * *
2158 CGGCTTTTC-G--CGCTTGTAAT-ATCG-TT-T--T-TCCTTTTT-C----TTCT--AATTAATT
1 CAAAAATACTGAAGGGTT-T-TTCA-CGCTTCTAATATCGTTTTTCCATTTTTTTAGAATTAATT
* * * * * * * * *
2207 TCTAATTAAATAGAATA-AAGATTCAGATACTCGTAAAAACAAATCCTTATATCCAATGTGG-TT
63 TCTAATTAAATCGAA-ACAAAATTTAGATGCTCGCAAAAATAAATCCTTAAATCCATTATGGCTT
* * * ** * *
2270 GAGAGTCGGTTAGATGAATATA-AATATTTCAAGGAGTC-TTCGCACCAAAAATCATGC-AAATT
127 -AGA-TTGGTTAGATGAATATAGAA-ATTTTAAGGGGTCTTTTTC-CAAAAAATCATGCGAAA-C
** * * * *
2332 TGAGTCGGGGCTCCGGAACGCTTTTTTAG-CCAAAAACCGTGATGGTTAGTACAAGATTTTC-GC
187 TGAGTCGGGGCTCCCAAACGCGTTTTTAGCCCCAAAACCGTGATAGTTAGTAC-AGAATTTCAGC
* * * * * *
2395 CTAAAAAATGACCCGATAATTTTTTC-T-CAATTTTCTGGCACAATACTCTA-AAAAAATTTAAT
251 C-AAAAACTGACCCGAAAAGTTTTTCATGAAATTTT-TGCCACAATACTC-AGAAAAAATAT-A-
*
2457 TCAATGC
311 T-AAT-T
* ** *
2464 CAAAAATATTGAACAGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTAGAAGTAATTTCT
1 CAAAAATACTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTAGAATTAATTTCT
* * * *
2529 AATTAAATCGAAACAAGATTTAAATGCTCGCAAAAACAAATCCTTAAATCCATTATGGCTTAAAT
66 AATTAAATCGAAACAAAATTTAGATGCTCGCAAAAATAAATCCTTAAATCCATTATGGCTTAGAT
* * *
2594 TAGGTTATATGAATATAGATATTTTAAGGGGTCTTTTTCCCAAAAATCATGCGAAACTGAGTCGG
131 T-GGTTAGATGAATATAGAAATTTTAAGGGGTCTTTTTCCAAAAAATCATGCGAAACTGAGTCGG
* * *
2659 GG-TCCCCAAACGTGTTTTTAGCCCCAAAACCGTGATAGTTAGTACACAATATCAGCCAAAAACT
195 GGCT-CCCAAACGCGTTTTTAGCCCCAAAACCGTGATAGTTAGTACAGAATTTCAGCCAAAAACT
* * *
2723 GACCCGAAAAAATTTTTCCTAAAATTTTTGCCACAATACTCAGAAAAAATATATAATT
259 GACCCG-AAAAGTTTTTCATGAAATTTTTGCCACAATACTCAGAAAAAATATATAATT
2781 CAA
1 CAA
2784 CACCAAAACC
Statistics
Matches: 1817, Mismatches: 248, Indels: 284
0.77 0.11 0.12
Matches are distributed among these distances:
279 1 0.00
280 50 0.03
281 1 0.00
282 41 0.02
283 5 0.00
284 3 0.00
286 6 0.00
287 47 0.03
288 3 0.00
289 11 0.01
290 6 0.00
291 23 0.01
292 5 0.00
293 4 0.00
294 3 0.00
295 1 0.00
296 5 0.00
297 1 0.00
300 6 0.00
302 2 0.00
303 8 0.00
304 1 0.00
306 11 0.01
307 16 0.01
308 14 0.01
309 5 0.00
310 33 0.02
311 10 0.01
312 12 0.01
313 89 0.05
314 92 0.05
315 11 0.01
316 299 0.16
317 272 0.15
318 36 0.02
319 156 0.09
320 44 0.02
321 21 0.01
322 6 0.00
323 23 0.01
324 89 0.05
325 69 0.04
326 41 0.02
327 4 0.00
329 3 0.00
330 1 0.00
331 13 0.01
332 64 0.04
333 109 0.06
334 8 0.00
335 6 0.00
336 27 0.01
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (315 bp):
CAAAAATACTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTAGAATTAATTTCT
AATTAAATCGAAACAAAATTTAGATGCTCGCAAAAATAAATCCTTAAATCCATTATGGCTTAGAT
TGGTTAGATGAATATAGAAATTTTAAGGGGTCTTTTTCCAAAAAATCATGCGAAACTGAGTCGGG
GCTCCCAAACGCGTTTTTAGCCCCAAAACCGTGATAGTTAGTACAGAATTTCAGCCAAAAACTGA
CCCGAAAAGTTTTTCATGAAATTTTTGCCACAATACTCAGAAAAAATATATAATT
Found at i:2187 original size:963 final size:925
Alignment explanation
Indices: 511--2791 Score: 2613
Period size: 925 Copynumber: 2.4 Consensus size: 925
501 GAATTTCAGC
* * * *
511 CAAAAACTGACCTGAAATATTTTTTCATGAAATTTTTGCCACAATACTCAGAAAAAATATAAAAT
1 CAAAAACTGACCCGAAA-ATTTTTTC-TCAATTTTTTGCCACAATACTCAGAAAAAATATATAAT
*
576 T----CAAAAATACTGAAGGGTTTTTCATGCTTCTAATATCG-TTTTCCATTTTTTTAGAATTAA
64 TCAACCAAAAATACTGAA-GGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTAGAATTAA
* *
636 TTTCTATTTAAATCGAAACAAAATTTAGATGCTCGCAAAAATAAATCCTTAAATCCATTATGGCT
128 TTTCTAATTAAATCGAAACAAGATTTAGATGCTCGCAAAAATAAATCCTTAAATCCATTATGGCT
* * * *
701 TAGATTGGATTAGATGAATATAGAAATTTTAAGGGGTCTTTTTACAAAAAATAATGTGAAACTGA
193 TAGATTGGGTTAGATGAATATAGAAATTTTAAGGGGTCTTTTTCCAAAAAATCATGCGAAACTGA
* * *
766 GTCGGGGCCCCCAAATGCGTTTTTAGCCCCAAAACCGTGATAGTTGGTACAGAATTTCAGCCAAA
258 GTCGGGGCCCCCAAACGCGTTTTTAGCCCCAAAACCGTGATAGTTAGTACACAATTTCAGCCAAA
* *
831 AACTGACCCGAAAAAGTTTTTCATGAAATTTTTGCCACAATACTCAGAAAAAATATAAAATT---
323 AACTGACCCGAAAAAATTTTTCATGAAATTTTTGCCACAATACTCAGAAAAAATATATAATTCAA
* * ** *
893 ---CAAAAATACTGAAGGGATTTTCATGCTTCTAATATCGTTTTTCCATTTTTTTAGAATTAATT
388 CACCAAAAAGACTGAACGGATTTTCACACTTCTAATACCGTTTTTCCATTTTTTTAGAATTAATT
* * * *
955 TCTATTTAAATCGAAACAAAATTTAGATGCTCGCAAAAATAAATCCTTAAATCCATTATGGCTTA
453 TCTAATTAAATCGAAACAAAATTCAGATACTCGAAAAAATAAATCCTTAAATCCA-TATGGCTTA
* ***
1020 GATTGGATTAGATGAATATAGAAATTTTAAGGGGTATTTTTCCAAAAAATAATGTGAAACTGAGT
517 GATTGGATTAGATGAATATAGAAATTTTAAGGAGTATTGCGCCAAAAAATAA-GT---A-TGAGT
* **
1085 CGGGGCGCCCAAACGCGTTTTTAGCCCCAAAACCGTGATAGTTAGTACACAATTTCAGCCAAAAA
577 CGGGGCGCCCAAACGCATTTTTAGCCAAAAAACCGTGATAGTTAGTACACAATTTCAGCCAAAAA
** * * * *
1150 ATGACCCGAAATAAAAAGTGTTCAAAATGAGCTAAATAAAATGTTAGCTGACCCGAAAAGTTTGA
642 ATGACCCGAAATAAAAAGTCCTCAAAATCAACTAAATAAAATGTGAGCTGACCCGAAAAGTATGA
*
1215 CCGGTTTTTCACGCTTCTAATACCGTTTTTCCAATTTTTTTTTCTAATTAATTTCTAATTAAATT
707 CCGG----T-----TT-T--T-CC-TTTTT-C---------TTCTAATTAATTTCTAATTAAATA
* *
1280 GAATCAAA-ATTCAGATGCTCGTAAAAAACAAATCCTTATAAACAATGCGGTTGAAAGTTGATTA
748 GAAT-AAAGATTCAGATACTCGT-AAAAACAAATCCTTATAAACAATGCGGTTGAAAGTCGATTA
* *
1344 GATGAATATAAATATTTCAAGGATTCTTCACGCCAAAAATCATGCAAAATTGAGTCGGGGCTCCG
811 GATGAATATAAATATTTCAAGGAGTCTTCACACCAAAAATCATGCAAAATTGAGTCGGGGCTCCG
*
1409 GAACGCGTTTTTAGCCAAAAACAATGATGGTTAGTACATGA-TTTCGGCTACAATTTT
876 GAACGCGTTTTTAGCCAAAAACAATGATGGTTAGTACAAGATTTTC-GC--C-----T
*
1466 GCAAAAACTGACCCGAAAAGTTTTTCTTCAATTTTTTGCCACAATACTCAGAAAAAATATATAAT
1 -CAAAAACTGACCCGAAAATTTTTTC-TCAATTTTTTGCCACAATACTCAGAAAAAATATATAAT
1531 TCAACACCAAAAATACTGAAGGTCTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTAGAAT
64 TC-A-ACCAAAAATACTGAAGG--TTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTAGAAT
1596 TAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGCAAAAATAAATCCTTAAATCCATTATG
125 TAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGCAAAAATAAATCCTTAAATCCATTATG
*
1661 GCTTAGATTGGGTTAGATGAATATAGAAATTTTAAGTGGTCTTTTTCCAAAAAAATCATGCGAAA
190 GCTTAGATTGGGTTAGATGAATATAGAAATTTTAAGGGGTCTTTTTCC-AAAAAATCATGCGAAA
* * *
1726 CTGAGTCGCGG-CCCTAAACGCGTTTTTAGTCCCAAAACCGTGATAGTTAGTACACAATTTCAGC
254 CTGAGTCGGGGCCCCCAAACGCGTTTTTAGCCCCAAAACCGTGATAGTTAGTACACAATTTCAGC
* *
1790 CGAAAAACTGACCCGAAAAAATATTTCTTGAAATTTTTGCCACAATACTCAGAAAAAATATATAA
319 C-AAAAACTGACCCGAAAAAATTTTTCATGAAATTTTTGCCACAATACTCAGAAAAAATATATAA
* * * **
1855 TTCAACACCAAAAAGATTGACCGGCTTTTCACACTTCTAATACCGTTTTTCCATTTTTTTCTAAT
383 TTCAACACCAAAAAGACTGAACGGATTTTCACACTTCTAATACCGTTTTTCCATTTTTTTAGAAT
* * *
1920 TAATTTCTAATTAAATTGAATCAAGATTCAGATACTC-AAAAAATCACAAATCCTTATAA-CCA-
448 TAATTTCTAATTAAATCGAAACAAAATTCAGATACTCGAAAAAAT---AAATCCTTA-AATCCAT
* * **
1982 ATGCGGTTGAGAGTTGG-TTAGATGAATATA-AATATTTTAAGGAGTCTTCGCGCCAAGCAA-AA
509 ATG-GCTT-AGA-TTGGATTAGATGAATATAGAA-ATTTTAAGGAGTATT-GCGCCAAAAAATAA
* ** * * *
2044 -T-TGAGTCGGGGCTCCGGAACGCATTTTTAG-CAAAAAACCGTGAT-TTTCG-GCTACAATTT-
569 GTATGAGTCGGGGCGCCCAAACGCATTTTTAGCCAAAAAACCGTGATAGTTAGTAC-ACAATTTC
* * ***** *
2103 TG-CAAAAACTGACCCGAAA-AGTTTTTCCTCAATATTCAAC-ACCAA-AAAGAT-TGACCGGCT
633 AGCCAAAAAATGACCCGAAATAAAAAGTCCTCAA-AATCAACTA--AATAAA-ATGTGA---GC-
** * *** *
2163 TTTCGCG-CTTGTAAT-ATC-GTTTTTCCTTTTTCTTCTAATTAATTTCTAATTAAATAGAATAA
690 TGACCCGAAAAGT-ATGACCGGTTTTTCCTTTTTCTTCTAATTAATTTCTAATTAAATAGAATAA
** * * *
2225 AGATTCAGATACTCGTAAAAACAAATCCTTATATCCAATGTGGTTGAGAGTCGGTTAGATGAATA
754 AGATTCAGATACTCGTAAAAACAAATCCTTATAAACAATGCGGTTGAAAGTCGATTAGATGAATA
* * *
2290 TAAATATTTCAAGGAGTCTTCGCACCAAAAATCATGCAAATTTGAGTCGGGGCTCCGGAACGCTT
819 TAAATATTTCAAGGAGTCTTCACACCAAAAATCATGCAAAATTGAGTCGGGGCTCCGGAACGCGT
**
2355 TTTTAGCCAAAAACCGTGATGGTTAGTACAAGATTTTCGCCT
884 TTTTAGCCAAAAACAATGATGGTTAGTACAAGATTTTCGCCT
* * * *
2397 -AAAAAATGACCCGATAATTTTTTCTCAATTTTCTGGCACAATACTCTA-AAAAAAT-T-TAATT
1 CAAAAACTGACCCGAAAATTTTTTCTCAATTTTTTGCCACAATACTC-AGAAAAAATATATAATT
* * *
2458 CAATGCCAAAAATATTGAACAGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTAGAAGTA
65 CAA--CCAAAAATACTGAA-GGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTAGAATTA
* *
2523 ATTTCTAATTAAATCGAAACAAGATTTAAATGCTCGCAAAAACAAATCCTTAAATCCATTATGGC
127 ATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGCAAAAATAAATCCTTAAATCCATTATGGC
* * * * *
2588 TTAAATTAGGTTATATGAATATAGATATTTTAAGGGGTCTTTTTCCCAAAAATCATGCGAAACTG
192 TTAGATTGGGTTAGATGAATATAGAAATTTTAAGGGGTCTTTTTCCAAAAAATCATGCGAAACTG
* * *
2653 AGTCGGGGTCCCCAAACGTGTTTTTAGCCCCAAAACCGTGATAGTTAGTACACAATATCAGCCAA
257 AGTCGGGGCCCCCAAACGCGTTTTTAGCCCCAAAACCGTGATAGTTAGTACACAATTTCAGCCAA
* *
2718 AAACTGACCCGAAAAAATTTTTCCTAAAATTTTTGCCACAATACTCAGAAAAAATATATAATTCA
322 AAACTGACCCGAAAAAATTTTTCATGAAATTTTTGCCACAATACTCAGAAAAAATATATAATTCA
2783 ACACCAAAA
387 ACACCAAAA
2792 CCGTGATAGT
Statistics
Matches: 1163, Mismatches: 119, Indels: 118
0.83 0.09 0.08
Matches are distributed among these distances:
924 99 0.09
925 197 0.17
926 19 0.02
927 2 0.00
928 27 0.02
929 22 0.02
931 1 0.00
936 1 0.00
938 138 0.12
939 44 0.04
948 1 0.00
949 5 0.00
950 2 0.00
951 1 0.00
953 1 0.00
954 2 0.00
955 43 0.04
956 16 0.01
959 1 0.00
960 9 0.01
961 38 0.03
962 26 0.02
963 187 0.16
964 103 0.09
965 30 0.03
969 6 0.01
970 82 0.07
971 5 0.00
972 43 0.04
973 12 0.01
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.32
Consensus pattern (925 bp):
CAAAAACTGACCCGAAAATTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTC
AACCAAAAATACTGAAGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTAGAATTAATTT
CTAATTAAATCGAAACAAGATTTAGATGCTCGCAAAAATAAATCCTTAAATCCATTATGGCTTAG
ATTGGGTTAGATGAATATAGAAATTTTAAGGGGTCTTTTTCCAAAAAATCATGCGAAACTGAGTC
GGGGCCCCCAAACGCGTTTTTAGCCCCAAAACCGTGATAGTTAGTACACAATTTCAGCCAAAAAC
TGACCCGAAAAAATTTTTCATGAAATTTTTGCCACAATACTCAGAAAAAATATATAATTCAACAC
CAAAAAGACTGAACGGATTTTCACACTTCTAATACCGTTTTTCCATTTTTTTAGAATTAATTTCT
AATTAAATCGAAACAAAATTCAGATACTCGAAAAAATAAATCCTTAAATCCATATGGCTTAGATT
GGATTAGATGAATATAGAAATTTTAAGGAGTATTGCGCCAAAAAATAAGTATGAGTCGGGGCGCC
CAAACGCATTTTTAGCCAAAAAACCGTGATAGTTAGTACACAATTTCAGCCAAAAAATGACCCGA
AATAAAAAGTCCTCAAAATCAACTAAATAAAATGTGAGCTGACCCGAAAAGTATGACCGGTTTTT
CCTTTTTCTTCTAATTAATTTCTAATTAAATAGAATAAAGATTCAGATACTCGTAAAAACAAATC
CTTATAAACAATGCGGTTGAAAGTCGATTAGATGAATATAAATATTTCAAGGAGTCTTCACACCA
AAAATCATGCAAAATTGAGTCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACAATGATGGTTAGT
ACAAGATTTTCGCCT
Found at i:2862 original size:104 final size:103
Alignment explanation
Indices: 2682--2999 Score: 582
Period size: 104 Copynumber: 3.1 Consensus size: 103
2672 GTTTTTAGCC
*
2682 CCAAAACCGTGATAGTTAGTACACAATATCAGCCAAAAACTGACCCGAAAAAATTTTTCCTAAAA
1 CCAAAACCGTGATAGTTAGTACACAATCTCAGCCAAAAACTGA-CCGAAAAAATTTTTCCTAAAA
2747 TTTTTGCCACAATACTCAGAAAAAATATATAATTCAACA
65 TTTTTGCCACAATACTCAGAAAAAATATATAATTCAACA
2786 CCAAAACCGTGATAGTTAGTACACAATCTCAGCCAAAAACTGACCTGAAAAAATTTTTCCTAAAA
1 CCAAAACCGTGATAGTTAGTACACAATCTCAGCCAAAAACTGACC-GAAAAAATTTTTCCTAAAA
*
2851 TTTTTGCCACAATACTCAGAGAAAATATATAATTCAACA
65 TTTTTGCCACAATACTCAGAAAAAATATATAATTCAACA
2890 CCAAAACCGTGATAGTTAGTACACAATCTCAGCCAAAAACTGATCCGAAAAAATTTTTCCTAAAA
1 CCAAAACCGTGATAGTTAGTACACAATCTCAGCCAAAAACTGA-CCGAAAAAATTTTTCCTAAAA
*
2955 TTTTTGCCACAATACTCAGAAAAACTATATAATTCAACA
65 TTTTTGCCACAATACTCAGAAAAAATATATAATTCAACA
2994 CCAAAA
1 CCAAAA
3000 AGATTGACCG
Statistics
Matches: 208, Mismatches: 4, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
103 2 0.01
104 204 0.98
105 2 0.01
ACGTcount: A:0.44, C:0.22, G:0.09, T:0.25
Consensus pattern (103 bp):
CCAAAACCGTGATAGTTAGTACACAATCTCAGCCAAAAACTGACCGAAAAAATTTTTCCTAAAAT
TTTTGCCACAATACTCAGAAAAAATATATAATTCAACA
Found at i:17454 original size:5 final size:5
Alignment explanation
Indices: 17446--17493 Score: 64
Period size: 5 Copynumber: 9.8 Consensus size: 5
17436 AAGAAATTTA
*
17446 AAAAC AAAAAA AAAAC AAAAC AAAA- AAAA- AAAAC AAAAC AAAAC AAAA
1 AAAAC -AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAA
17494 AGAACCTTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
4 8 0.21
5 27 0.69
6 4 0.10
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:17471 original size:23 final size:23
Alignment explanation
Indices: 17452--17494 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
17442 TTTAAAAACA
17452 AAAAA-AAAACAAAACAAAAAAA
1 AAAAACAAAACAAAACAAAAAAA
17474 AAAAACAAAACAAAACAAAAA
1 AAAAACAAAACAAAACAAAAA
17495 GAACCTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (23 bp):
AAAAACAAAACAAAACAAAAAAA
Found at i:17472 original size:18 final size:18
Alignment explanation
Indices: 17451--17494 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
17441 ATTTAAAAAC
17451 AAAAAAAAAACAAAACAA
1 AAAAAAAAAACAAAACAA
17469 AAAAAAAAAACAAAACAA
1 AAAAAAAAAACAAAACAA
17487 AACAAAAA
1 AA-AAAAA
17495 GAACCTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 20 0.80
19 5 0.20
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAACAAAACAA
Found at i:21988 original size:23 final size:24
Alignment explanation
Indices: 21943--21989 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
21933 GTCTATAAAC
21943 CAGAAAATGAATAGTTACTGTTAT
1 CAGAAAATGAATAGTTACTGTTAT
* *
21967 CAGACAATGATTAG-TACTGTTAT
1 CAGAAAATGAATAGTTACTGTTAT
21990 TTAAGGTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (24 bp):
CAGAAAATGAATAGTTACTGTTAT
Found at i:27627 original size:20 final size:20
Alignment explanation
Indices: 27602--27642 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
27592 ATAACCAGGT
*
27602 GCGCGACGCGGGTCGGATCC
1 GCGCGACGCGGATCGGATCC
27622 GCGCGACGCGGATCGGATCC
1 GCGCGACGCGGATCGGATCC
27642 G
1 G
27643 AATTAGTCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.12, C:0.34, G:0.44, T:0.10
Consensus pattern (20 bp):
GCGCGACGCGGATCGGATCC
Found at i:31062 original size:2 final size:2
Alignment explanation
Indices: 31055--31080 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
31045 AGACAAATAC
31055 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
31081 GGATCTCGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33415 original size:28 final size:29
Alignment explanation
Indices: 33382--33452 Score: 119
Period size: 28 Copynumber: 2.5 Consensus size: 29
33372 TTTAAGGAGT
33382 GTCCTTTAAGGTTTTTTTTTTGGCC-AGA
1 GTCCTTTAAGGTTTTTTTTTTGGCCAAGA
33410 GTCCTTTAAGGTTTTTTTTTTGGCCAAAGA
1 GTCCTTTAAGGTTTTTTTTTTGGCC-AAGA
33440 GT-CTTTAAGGTTT
1 GTCCTTTAAGGTTT
33453 ATATATATTA
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
28 25 0.61
29 11 0.27
30 5 0.12
ACGTcount: A:0.17, C:0.13, G:0.21, T:0.49
Consensus pattern (29 bp):
GTCCTTTAAGGTTTTTTTTTTGGCCAAGA
Found at i:38185 original size:25 final size:25
Alignment explanation
Indices: 38157--38208 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
38147 ACCTCTAATG
38157 ATTTCTTTATTCACAAAACTCGAAT
1 ATTTCTTTATTCACAAAACTCGAAT
38182 ATTTCTTTATTCACAAAACTCGAAT
1 ATTTCTTTATTCACAAAACTCGAAT
38207 AT
1 AT
38209 GTAATCTTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.37, C:0.19, G:0.04, T:0.40
Consensus pattern (25 bp):
ATTTCTTTATTCACAAAACTCGAAT
Found at i:38385 original size:17 final size:15
Alignment explanation
Indices: 38338--38437 Score: 72
Period size: 17 Copynumber: 6.9 Consensus size: 15
38328 GTAACTCCAC
38338 TTTGCAATTTAT--A
1 TTTGCAATTTATACA
* *
38351 TTT-CTATTT-TTCA
1 TTTGCAATTTATACA
38364 TTTGCAATTTACTACAA
1 TTTGCAATTTA-TAC-A
38381 TTTGCAATTTAT--A
1 TTTGCAATTTATACA
* *
38394 TTT-CTATTT-TTCA
1 TTTGCAATTTATACA
38407 TTTGCAATTTACTACAA
1 TTTGCAATTTA-TAC-A
38424 TTTGCAATTTATAC
1 TTTGCAATTTATAC
38438 TTGTATTATA
Statistics
Matches: 69, Mismatches: 6, Indels: 21
0.72 0.06 0.22
Matches are distributed among these distances:
11 2 0.03
12 10 0.14
13 15 0.22
14 10 0.14
16 8 0.12
17 24 0.35
ACGTcount: A:0.28, C:0.14, G:0.05, T:0.53
Consensus pattern (15 bp):
TTTGCAATTTATACA
Found at i:38399 original size:43 final size:43
Alignment explanation
Indices: 38338--38436 Score: 198
Period size: 43 Copynumber: 2.3 Consensus size: 43
38328 GTAACTCCAC
38338 TTTGCAATTTATATTTCTATTTTTCATTTGCAATTTACTACAA
1 TTTGCAATTTATATTTCTATTTTTCATTTGCAATTTACTACAA
38381 TTTGCAATTTATATTTCTATTTTTCATTTGCAATTTACTACAA
1 TTTGCAATTTATATTTCTATTTTTCATTTGCAATTTACTACAA
38424 TTTGCAATTTATA
1 TTTGCAATTTATA
38437 CTTGTATTAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 56 1.00
ACGTcount: A:0.28, C:0.13, G:0.05, T:0.54
Consensus pattern (43 bp):
TTTGCAATTTATATTTCTATTTTTCATTTGCAATTTACTACAA
Found at i:50879 original size:59 final size:59
Alignment explanation
Indices: 50804--50918 Score: 212
Period size: 59 Copynumber: 1.9 Consensus size: 59
50794 AGCATTAACA
*
50804 TCACGTGATAAAAATACGATTTTGATTTAGAAAATTCTCTCTTTCATATAATAAATATG
1 TCACGTGATAAAAATACAATTTTGATTTAGAAAATTCTCTCTTTCATATAATAAATATG
*
50863 TCACGTGATAAAAATACAATTTTGATTTAGAAAGTTCTCTCTTTCATATAATAAAT
1 TCACGTGATAAAAATACAATTTTGATTTAGAAAATTCTCTCTTTCATATAATAAAT
50919 GTGAAAGCTA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
59 54 1.00
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (59 bp):
TCACGTGATAAAAATACAATTTTGATTTAGAAAATTCTCTCTTTCATATAATAAATATG
Found at i:61518 original size:96 final size:96
Alignment explanation
Indices: 61350--61527 Score: 275
Period size: 96 Copynumber: 1.9 Consensus size: 96
61340 GTCCAAATAC
* * * * *
61350 CAAAGAGAGCTTCAGTTGACTATATTTAAGGGAACATCCATGCTGGAGAAAAAGGTGCAGCTGAT
1 CAAAGAGAGCTTCAATTGACAATATTTAAGGGAACATCCATGCCGGAGAAAAAAGTGCAGCCGAT
*
61415 ATCAGAATAGCTCTGTTTAAGTTCAAAATTT
66 ATCAGAATAGCTATGTTTAAGTTCAAAATTT
* *
61446 CAAAGGGAGCTTCAATTGACAATATTTAAGGGAACATTCATGCCGGAGAAAAAAGTGCAGCCGAT
1 CAAAGAGAGCTTCAATTGACAATATTTAAGGGAACATCCATGCCGGAGAAAAAAGTGCAGCCGAT
*
61511 ATTAGAATAGCTATGTT
66 ATCAGAATAGCTATGTT
61528 CATCTTTCCG
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
96 73 1.00
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (96 bp):
CAAAGAGAGCTTCAATTGACAATATTTAAGGGAACATCCATGCCGGAGAAAAAAGTGCAGCCGAT
ATCAGAATAGCTATGTTTAAGTTCAAAATTT
Found at i:62701 original size:11 final size:11
Alignment explanation
Indices: 62681--62715 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
62671 TTGACAGCGC
62681 AACAAAAACAA
1 AACAAAAACAA
**
62692 AATGAAAACAA
1 AACAAAAACAA
62703 AACAAAAACAA
1 AACAAAAACAA
62714 AA
1 AA
62716 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.80, C:0.14, G:0.03, T:0.03
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:66400 original size:19 final size:19
Alignment explanation
Indices: 66360--66396 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
66350 AATTTTTAAG
66360 TAAAAATTTAATATATAAA
1 TAAAAATTTAATATATAAA
66379 TAAAAATTTAATAT-TAAA
1 TAAAAATTTAATATATAAA
66397 ATAATTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAAAATTTAATATATAAA
Found at i:66704 original size:2 final size:2
Alignment explanation
Indices: 66697--66743 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
66687 TTCTTGCCAA
66697 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
66739 AT AT A
1 AT AT A
66744 C
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.