Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019695.1 Corchorus olitorius cultivar O-4 contig19728, 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: 19317
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:647 original size:332 final size:329
Alignment explanation
Indices: 8--2339 Score: 1028
Period size: 332 Copynumber: 7.1 Consensus size: 329
1 GAGACGT
* * * * *
8 GTTTTTAGCAAAATA-TCGTGATGGTTATTACACGATTTTGGCTAAAATTTTGCAAAAACTGACC
1 GTTTTTAGCAAAAAACT-GTGATGGTTAGTACACGATTTTGACTAAAACTTTGCAAAAATTGACC
* ** * *
72 CGAAAATTTTTTTTCCTCAATTCTTTGCCACAACACTCTG-AAAAATCTATAATTGAACCCCAAA
65 CGAAAA--TTTTTTCCTCAATTCTTTGCCACAATACTAAGAAAAAATATATAATTCAA-CCCAAA
* * * * * **
136 AAATTTGAAGGGCTTTTAACGTTTCAAATATTGTTTTTCTAATTTTTTTTTCAGAATCAATTTTT
127 AAAATTGAAGGGCTTTTCACGCTTCAAATATCGTTTTTCTAA---TTTTTTCCG-AT-TTTTTTT
* * * * * *
201 -AATTAAATCGAAATAAGATTCAGATGGTCGTAAAAAGAGATCCTTAA-ATCCAATGTTGCTGAG
187 CAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCC-TAATA-ACAATGTGGCTGAG
* * * * * ** *
264 A-TTTGTCTTGATAAATATAGATAATTCAAGGAGTCTTTAGTCCAAAAATCATGCAAAATTGGGT
250 ATTTTGT-TAGATGAATATATATATTTCAAGGAGTCTTTAGTCCAAAAATCATGCAAAACTAAGC
** *
328 CG-GAATTCCGGAACGC
314 CGAG-ACCCCGAAACGC
* * *
344 AG-TTTTAGCAAAAAACTGTGATGGTTAGTAAACGATTTCGACTAAAACTTTGTAAAAATTGACC
1 -GTTTTTAGCAAAAAACTGTGATGGTTAGTACACGATTTTGACTAAAACTTTGCAAAAATTGACC
* *
408 CGAAAAGTTTTTCCACAATTCTTTGCCACAATACTAAGAAAAAATATATAATTCAACGCCAAAAA
65 CGAAAATTTTTTCCTCAATTCTTTGCCACAATACTAAGAAAAAATATATAATTCAAC-CCAAAAA
*
473 AATTGAAGGG-TTTTCACGCTTCTAATATCGTTTTTCTAATTTTTTCCGTATTTTTTTTCAAATT
129 AATTGAAGGGCTTTTCACGCTTCAAATATCGTTTTTCTAATTTTTTCCG-ATTTTTTTTC-AATT
* * * * * **
537 ATATCGAAACAAGATTCGGTTGCTTGTAGAAACCTATCCTGAATAACAATGTGGCTGAGATTTTG
192 AAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCT-AATAACAATGTGGCTGAGATTTTG
* * *
602 TTCGATGAATATATATATTTGAAGGAGTCTTTACG-CCAAAAATCATGCAAAACTAAGCCGAGGC
256 TTAGATGAATATATATATTTCAAGGAGTCTTTA-GTCCAAAAATCATGCAAAACTAAGCCGAGAC
666 CCCGAAACGC
320 CCCGAAACGC
* * * * *
676 GTTTTTAGCAAAAAAACCGTGATAGTTAGTACACGATTTTGACTAAAACTTTACAAAAATTTACT
1 GTTTTTAGC-AAAAAACTGTGATGGTTAGTACACGATTTTGACTAAAACTTTGCAAAAATTGACC
* * * *
741 CGAAATTTTTTTCCTCAATTCTTTGCCACAATATCCAA-AAAAAATATAAAATTCAACCCCAAAA
65 CGAAAATTTTTTCCTCAATTCTTTGCCACAATA-CTAAGAAAAAATATATAATTCAACCCAAAAA
* * * * * *
805 AATTGAAGGGTTTTTCACGCTTCAAATATCGTTTTTC-CATTTATACCGAATTTATTTCTAATTA
129 AATTGAAGGGCTTTTCACGCTTCAAATATCGTTTTTCTAATTTTTTCCGATTTTTTTTC-AATTA
* * * *
869 AATCGAAACACGATTCAGATGCTCGTAAAAACAAATCCT-TTAATCCATAGTGGCTGAGATTTGG
193 AATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTAATAA-CAAT-GTGGCTGAGATTTTG
* *
933 TTAGATGAAATATATATATATATATATTTCAAGGAGTCTTT-CTGCCAAAAATCATGTAAAACTG
256 TTAGATG--------A-ATATATATATTTCAAGGAGTCTTTAGT-CCAAAAATCATGCAAAACT-
* ** *
997 AA-CCGGGGTCCCGAAATGC
310 AAGCCGAGACCCCGAAACGC
* ** * * * ** **
1016 GTTTTAAGCCTAAAACCGTGAT-GTTAAAAACTGACGCGAATTTTTTTCTCAATTCTTTGCAAAA
1 GTTTTTAGCAAAAAACTGTGATGGTT----AGT-ACACG-A-TTTTGACT-AAAACTTTGCAAAA
* ** * * *** * * * * ** * **
1080 TATT---CAGAAAA-AATAT-AT-AATTCAACGCCAAAAAAAT-TG-ACGAGT-T-T--TTCATG
58 -ATTGACCCGAAAATTTTTTCCTCAATTCTTTGCCACAATACTAAGAAAAAATATATAATTCAAC
**** * * * * * * * * **
1133 CTTCTAAAA-T---CGTCTTTT----C--C--AT-T--TTTTCCGATTTAATTT-CTAATTTAAT
122 CCAAAAAAATTGAAGGGCTTTTCACGCTTCAAATATCGTTTTTCTAATT-TTTTCCGATTTTTTT
* ** * * * ** * * *
1182 TGAA--ACAA--GATTC-AGATGC--ACG-T--AAAAACA-AATCCGTTAAT-CCATTGTGGCTG
186 TCAATTA-AATCGAAACAAGATTCAGATGCTCGTAAAA-ACAAATC-CTAATAACAATGTGGCTG
* * * ** * *
1235 GGATTTGGTTAGATGAATATAGATATTTCAAACAGTCTTTA-TGCCAAAAAACCATGCAAAACTG
248 AGATTTTGTTAGATGAATATATATATTTCAAGGAGTCTTTAGT-CC-AAAAATCATGCAAAACTA
** * * *
1299 AGATGAG-GCCCGATACAC
311 AGCCGAGACCCCGAAACGC
* * * *
1317 GTTTTTAACCAAAAAACCGTGATGGTTAGTACACGA-TTT---T--AGC--T--AAAAACTGACC
1 GTTTTT-AGCAAAAAACTGTGATGGTTAGTACACGATTTTGACTAAAACTTTGCAAAAATTGACC
* * *
1372 CGAAAATTTTTT-CTTAATT-TTTCACCACAATAC-ACATAAAAAATATATAATTCAACACCAAA
65 CGAAAATTTTTTCCTCAATTCTTT-GCCACAATACTA-AGAAAAAATATATAATTCAAC-CCAAA
* * * * * * * *
1434 AAGATTGAAGGGATTTCCACGCTTCTAATATCGTTTTTC--CTTTCTTCCGAATTTATTTCTAAT
127 AAAATTGAAGGGCTTTTCACGCTTCAAATATCGTTTTTCTAATTTTTTCCGATTTTTTTTC-AAT
* * * * * * * *
1497 TAAATCGATACCAGATTCAAAAGCGCATAAAAACAAATCCTTAA-ATTCAATGTGGTTGAGA-TT
191 TAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCC-TAATA-ACAATGTGGCTGAGATTT
* * * * * *
1560 TGATTAGATGAATATAGATATTTCAAGGAGACTTTAAG-CCAAAAACCATGCAAAATTGAGACGA
254 TG-TTAGATGAATATATATATTTCAAGGAGTCTTT-AGTCCAAAAATCATGCAAAACTAAGCCGA
*
1624 GGCCCCG-AACGC
317 GACCCCGAAACGC
* ** * ** * *
1636 GTTTTTAGCCAAAAACAATGATGATTAGTACACGA-TTT--C---GGC--TG--AAAACTGACTC
1 GTTTTTAGCAAAAAACTGTGATGGTTAGTACACGATTTTGACTAAAACTTTGCAAAAATTGACCC
* * * * *
1691 GAAAACTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTGAATGCCAAAAAA
66 GAAAATTTTTTCCTCAATTCTTTGCCACAATACTAAGAAAAAATATATAATTCAA-CCCAAAAAA
* * * ** * *
1756 ATTGAAGGGTTTTTCACGCTTCTAATATC-ATTTTCCCATTTTTTCCCCGAATTTATTTCTAATT
130 ATTGAAGGGCTTTTCACGCTTCAAATATCGTTTTTCTAATTTTTT--CCGATTTTTTTTC-AATT
* * * * * *
1820 AAATCCAAACAAGATTTAGATGCTCGTAAAAACAAATCTTTAA-ATCCAATGTGGCTGGGATTTG
192 AAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATC-CTAATA-ACAATGTGGCTGAGATTTT
* * * * * * **
1884 GTTCGATGAATATAGATATCTCAACGAGTCTTTA-TGCCAAAAATCATGTAAAACTGAGTTG-G-
255 GTTAGATGAATATATATATTTCAAGGAGTCTTTAGT-CCAAAAATCATGCAAAACTAAGCCGAGA
*** *
1946 GGTC-TAACGC
319 CCCCGAAACGC
* * * * * * *
1956 GATTTTAGCCAAAAAAAACCGTGA---TTAATAAACGATTTCGGCTAAAATTTTGCAAAAACTT-
1 GTTTTTAG-C--AAAAAACTGTGATGGTTAGTACACGATTTTGACTAAAACTTTGCAAAAA-TTG
* **
2017 ACCCGAAAATTTTTTCCTCAATTCTTTGCCACAATACTTAGAAAAAATATATAATTCAACATAAA
62 ACCCGAAAATTTTTTCCTCAATTCTTTGCCACAATACTAAGAAAAAATATATAATTCAAC-CCAA
* * ** * **
2082 AAAAATTTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTTTCCGAATTTAATTC
126 AAAAA-TTGAAGGGCTTTTCACGCTTCAAATATCGTTTTT-C-TAATTTTTTCCGATTTTTTTTC
* * * *
2147 TAATTAAATCAAAACAAGATTCAGATGCTCGTAAAAAGAAATCCTTAA-ATCTATTGTGGCTGAG
188 -AATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCC-TAATAAC-AATGTGGCTGAG
* ** * * * * * *
2211 ATTTGGTTAGACAAATATAGATATTTCAATGTGTCTTTA-TGCCAAAAATCATACAAAACTGAGT
250 ATTTTGTTAGATGAATATATATATTTCAAGGAGTCTTTAGT-CCAAAAATCATGCAAAACTAAGC
* * *
2275 TG-GGCCCCGACACGC
314 CGAGACCCCGAAACGC
* * ** * *
2290 GTTTTTAACCAAAAACCTTGATGATTATTAGTACACGATTTCGGCTAAAA
1 GTTTTT-AGCAAAAAAC-TG-TGATGGTTAGTACACGATTTTGACTAAAA
2340 ACTAACCCGA
Statistics
Matches: 1531, Mismatches: 322, Indels: 284
0.72 0.15 0.13
Matches are distributed among these distances:
284 2 0.00
285 4 0.00
287 7 0.00
288 3 0.00
289 11 0.01
291 3 0.00
292 2 0.00
293 1 0.00
295 7 0.00
296 4 0.00
297 2 0.00
298 4 0.00
299 2 0.00
300 4 0.00
301 38 0.02
302 31 0.02
303 3 0.00
304 1 0.00
306 1 0.00
308 4 0.00
309 12 0.01
310 23 0.02
311 16 0.01
312 3 0.00
313 6 0.00
314 7 0.00
316 6 0.00
317 3 0.00
318 57 0.04
319 114 0.07
320 83 0.05
321 17 0.01
322 115 0.08
323 15 0.01
325 1 0.00
327 1 0.00
328 2 0.00
329 3 0.00
330 73 0.05
331 111 0.07
332 270 0.18
333 131 0.09
334 76 0.05
335 41 0.03
336 58 0.04
337 23 0.02
338 4 0.00
339 15 0.01
340 63 0.04
341 14 0.01
342 3 0.00
343 6 0.00
344 5 0.00
345 6 0.00
346 11 0.01
347 3 0.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (329 bp):
GTTTTTAGCAAAAAACTGTGATGGTTAGTACACGATTTTGACTAAAACTTTGCAAAAATTGACCC
GAAAATTTTTTCCTCAATTCTTTGCCACAATACTAAGAAAAAATATATAATTCAACCCAAAAAAA
TTGAAGGGCTTTTCACGCTTCAAATATCGTTTTTCTAATTTTTTCCGATTTTTTTTCAATTAAAT
CGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTAATAACAATGTGGCTGAGATTTTGTTAGA
TGAATATATATATTTCAAGGAGTCTTTAGTCCAAAAATCATGCAAAACTAAGCCGAGACCCCGAA
ACGC
Found at i:2123 original size:322 final size:318
Alignment explanation
Indices: 1041--2450 Score: 1165
Period size: 322 Copynumber: 4.4 Consensus size: 318
1031 CCGTGATGTT
* * * *
1041 AAAAACTGACGCG--AATTTTTTTCTCAATTCTTTG-CAAAATATTCAGAAAAAATATATAATTC
1 AAAAACTGACCCGAAAATTTTTTCCTCAATT-TTTGCCACAATACTCAGAAAAAATATATAATTC
* * * * *
1103 AACGCCAAAAAAATTGACGAGTTTTTCATGCTTCTAAAATCGTCTTTTCCATTTTTTCCG-ATTT
65 AACACCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGT-TTTTCC------TCCGAATTT
* ** * *
1167 AATTTCTAATTTAATTGAAACAAGATTCAGATGCACGTAAAAACAAATCCGTT-AATCCATTGTG
123 -ATTTCTAATTAAATCAAAACAAGATTCAGATGCTCGTAAAAACAAATCC-TTAAATCCAATGTG
* *
1231 GCTGGGATTTGGTTAGATGAATATAGATATTTCAAAC-AGTCTTTATGCCAAAAAACCATGCAAA
186 GCTGAGATTTGGTTAGATGAATATAGATATTTC-AACGAGTCTTTATGCC-AAAAATCATGCAAA
* * * * * * * * **
1295 ACTGAGATGAGG-CCCGATACACGTTTTTAACC-AAAAAACCGTGATGGTTAGTACACGATTTTA
249 ACTGAGTTG-GGCCCCGA-ACGCGATTTTAGCCAAAAAAAAC--GATGATTAATAAACGATTTCG
1358 GC----T--
310 GCATTTTGC
* * * *
1361 AAAAACTGACCCGAAAATTTTTT-CTTAATTTTTCACCACAATACACATAAAAAATATATAATTC
1 AAAAACTGACCCGAAAATTTTTTCCTCAATTTTT-GCCACAATACTCAGAAAAAATATATAATTC
* * *
1425 AACACCAAAAAGATTGAAGGGATTTCCACGCTTCTAATATCGTTTTTCCTTTCTTCCGAATTTAT
65 AACACCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTT-C---C-TCCGAATTTAT
* * * * * * * * *
1490 TTCTAATTAAATCGATACCAGATTCAAAAGCGCATAAAAACAAATCCTTAAATTCAATGTGGTTG
125 TTCTAATTAAATCAAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTG
* * * * * *
1555 AGATTTGATTAGATGAATATAGATATTTCAAGGAGACTTTAAGCCAAAAACCATGCAAAATTGAG
190 AGATTTGGTTAGATGAATATAGATATTTCAACGAGTCTTTATGCCAAAAATCATGCAAAACTGAG
** * * * * *
1620 ACGAGGCCCCGAACGCGTTTTTAGCCAAAAACAATGATGATTAGTACACGATTTCGGC----TG-
255 TTG-GGCCCCGAACGCGATTTTAGCCAAAAAAAACGATGATTAATAAACGATTTCGGCATTTTGC
* * *
1680 -AAAACTGACTCGAAAACTTTTTCCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTG
1 AAAAACTGACCCGAAAATTTTTTCCTCAA-TTTTTGCCACAATACTCAGAAAAAATATATAATTC
** * *
1744 AATGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCATTTTCCCATTTTTTCCCCGAATT
65 AACACCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCC------T--CCGAATT
* * *
1809 TATTTCTAATTAAATCCAAACAAGATTTAGATGCTCGTAAAAACAAATCTTTAAATCCAATGTGG
122 TATTTCTAATTAAATCAAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGG
* * * *
1874 CTGGGATTTGGTTCGATGAATATAGATATCTCAACGAGTCTTTATGCCAAAAATCATGTAAAACT
187 CTGAGATTTGGTTAGATGAATATAGATATTTCAACGAGTCTTTATGCCAAAAATCATGCAAAACT
** *
1939 GAGTTGGG-GTCTAACGCGATTTTAGCCAAAAAAAACCG-TGATTAATAAACGATTTCGGCTAAA
252 GAGTTGGGCCCCGAACGCGATTTTAGCCAAAAAAAA-CGATGATTAATAAACGATTTCGGC----
2002 ATTTTGC
312 ATTTTGC
* *
2009 AAAAACTTACCCGAAAATTTTTTCCTCAATTCTTTGCCACAATACTTAGAAAAAATATATAATTC
1 AAAAACTGACCCGAAAATTTTTTCCTCAATT-TTTGCCACAATACTCAGAAAAAATATATAATTC
**
2074 AACATAAAAAAAATTTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTTTCCGAA
65 AACACCAAAAAAA-TTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCC---------TCCGAA
* * * *
2139 TTTAATTCTAATTAAATCAAAACAAGATTCAGATGCTCGTAAAAAGAAATCCTTAAATCTATTGT
120 TTTATTTCTAATTAAATCAAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGT
** * * *
2204 GGCTGAGATTTGGTTAGACAAATATAGATATTTCAATGTGTCTTTATGCCAAAAATCATACAAAA
185 GGCTGAGATTTGGTTAGATGAATATAGATATTTCAACGAGTCTTTATGCCAAAAATCATGCAAAA
* * **** *
2269 CTGAGTTGGGCCCCGACACGCGTTTTTAACCAAAAACCTTGATGATTATTAGTACACGATTTCGG
250 CTGAGTTGGGCCCCGA-ACGCGATTTTAGCCAAAAAAAACGATGATTA--A-TAAACGATTTCGG
2334 C----T--
311 CATTTTGC
* * *
2336 AAAAACTAACCCGAAAAGTTTTTT-CTCAATTTTTTTTG-CAAAATATTCAGAAAAAAATATATA
1 AAAAACTGACCCGAAAA-TTTTTTCCTCAA---TTTTTGCCACAATACTCAG-AAAAAATATATA
* * ** ** *
2399 ATTCAACGCCAAAAAGATTGACTGG-CCTTCACGCTTATAATATCGTTTTTCC
61 ATTCAACACCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCC
2451 AATTTTTTTC
Statistics
Matches: 903, Mismatches: 137, Indels: 93
0.80 0.12 0.08
Matches are distributed among these distances:
315 1 0.00
318 42 0.05
319 110 0.12
320 168 0.19
321 17 0.02
322 188 0.21
325 1 0.00
327 45 0.05
328 23 0.03
329 32 0.04
330 67 0.07
331 34 0.04
332 129 0.14
333 3 0.00
334 29 0.03
336 1 0.00
337 13 0.01
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (318 bp):
AAAAACTGACCCGAAAATTTTTTCCTCAATTTTTGCCACAATACTCAGAAAAAATATATAATTCA
ACACCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCTCCGAATTTATTTCTAA
TTAAATCAAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTT
GGTTAGATGAATATAGATATTTCAACGAGTCTTTATGCCAAAAATCATGCAAAACTGAGTTGGGC
CCCGAACGCGATTTTAGCCAAAAAAAACGATGATTAATAAACGATTTCGGCATTTTGC
Found at i:2478 original size:11 final size:11
Alignment explanation
Indices: 2446--2485 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
2436 TAATATCGTT
**
2446 TTTCCAATTTT
1 TTTCCAATTAA
2457 TTTCCGAATTAA
1 TTTCC-AATTAA
2469 TTTCCAATTAA
1 TTTCCAATTAA
2480 TTTCCA
1 TTTCCA
2486 TTGCAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
11 17 0.65
12 9 0.35
ACGTcount: A:0.28, C:0.20, G:0.03, T:0.50
Consensus pattern (11 bp):
TTTCCAATTAA
Found at i:3566 original size:330 final size:328
Alignment explanation
Indices: 2965--5170 Score: 2097
Period size: 332 Copynumber: 6.7 Consensus size: 328
2955 AATAGAAACA
* * * * * *
2965 ACACGATTTCAGG-TAAAGTTTTGCAAAAATTGTCCCGAAAAATATTTCCTCAATTTTTTGCTAA
1 ACACGATTTC-GGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAGCGAA
* * * * * * * *
3029 AATACTCATAAAAAATATATAACTCGACATCAAAAATATTGGAA-GGCTTGTAACGCTTCTGATA
65 AATACTCATAAAAAATATATAATTCAACACCAAAAAGATT-GAAGGGCTTTTCACGCTTTTAATA
* * * *
3093 TTGTTTTTCCT-TTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATACAAATGCTCGTAA
129 TCGTTTTTCCTATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAA
* * *
3157 AAACAAATCCTTAAGTCCAATGTGGCTGAGATTTGGTTAGATGAATATAAATATTTCAAGGAGTC
194 AAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTC
* * * * * * *
3222 TTGGCACAAAAAATCATACAAAACTGAGTCAAGCCCCAGAATGTGTTTTTAGCCGAAAA-GTG-T
259 TTGGCGCCAAAAATCATGCAAAACTGAGCCAGGCCCC-GAACGCGTTTTTAGCC-AAAACGTGAT
3285 GATGAGT
322 GATGAGT
* * * *
3292 ACACGATTTCGACTAAAATTTTGCAAAACTTGACCCGAAAGATTTTTCCTCAATTTCTAACGAAA
1 ACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAGCGAAA
* * * * *
3357 ATACTCATAAAAAATATATAATTCAACACCAAAAA-AATGAAAGTCTTTTTCACGCTTATAATAA
66 ATACTCATAAAAAATATATAATTCAACACCAAAAAGATTGAAGGGC-TTTTCACGCTTTTAATAT
** * * * * * *
3421 CGTTTTTCCTACTTTATTTCCAAATTACTTTCTGATGAAATCGAAACAAGATTTAGTTGTTCGTA
130 CGTTTTTCCTA-TTT-TTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTA
* *
3486 AAAACAAATCCTTAAATCCAATGTGGCTAAGATTTTATTAGATGAATATAGATATTTCAAGGAGT
193 AAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGT
** * * * * * * * **
3551 CTTAACGCCAAAAATCATACAACACTAACCCGGGGCCCTGGAACGCGTTTTTGGCCAAAATATCG
258 CTTGGCGCCAAAAATCATGCAAAACTGAGCC-AGGCCC-CGAACGCGTTTTTAGCCAAAACGT-G
3616 -TGATG-GT
320 ATGATGAGT
* * * *
3623 ACACGATTTCGGCTGATAA-TTTGTAAAAATTGACCCG--A-A-TTTTCCTCAATTTTTAGCCAC
1 ACACGATTTCGGCT-AAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAGCGAA
* * * *
3683 AATACCCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTCTCACGCTTCTAATAT
65 AATACTCATAAAAAATATATAATTCAACACCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATAT
* *
3748 TGTTTTTCCTATATTTTTCTGAATTAATTTCTAATTAAATCGAAACATGATTCAGATG---GT--
130 CGTTTTTCCTAT-TTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAA
* * * **
3808 -------T--GTAAA-ACAA--TGGCTGGGATTT-AGTTAGATGAATAGGGATATTTCAAGGAGT
194 AAACAAATCCTTAAATCCAATGTGGCTGAGATTTGA-TTAGATGAATATAGATATTTCAAGGAGT
* * * * * * * * **
3860 GTCGGCACC-AAAATCATGGAAAACAGAACCGGGCCCTAGAACGTATTTTTAG-CAAACACCGTG
258 CTTGGCGCCAAAAATCATGCAAAACTGAGCCAGGCCC-CGAACGCGTTTTTAGCCAAA-A-CGTG
* *
3923 ATGATTATT
320 ATGATGAGT
* *
3932 ACACAATTTCGGCTAAAATTTTGTAAAAATTGACCCGAAAGATATTTT-CTCAATTTTTAGCCG-
1 ACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGAT-TTTTCCTCAATTTTTAG-CGA
* * * * *
3995 CAATACTCATAAAGAATATATAATTCAACACCAAAAAGATTGAAGGAC-ATTCATGCTTTTAATA
64 AAATACTCATAAAAAATATATAATTCAACACCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATA
* * *
4059 TC-ATTTTCCATATTTTTTCTTAATGAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTA
129 TCGTTTTTCC-TATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTA
* * * * *
4123 AAAGCAATTTTACTTAAATGCAATGTGGCTAAGATTAT-ATTAGATGAATATAGATATTTCAAGG
193 AAAACAA--ATCCTTAAATCCAATGTGGCTGAGATT-TGATTAGATGAATATAGATATTTCAAGG
* ** *
4187 AGTCTCGGCGCCAAAAATCATGCAAAACTGAGCCGAAACCCCGACACACGTTTTTAGCCAAAAAC
255 AGTCTTGGCGCCAAAAATCATGCAAAACTGAGCC-AGGCCCCGA-ACGCGTTTTTAGCC-AAAA-
* *
4252 CGTGATGGTTAGT
316 CGTGATGATGAGT
* *
4265 ACACGATTTTGGCTAAAATTTTGCAAAAAGTT-ACCCGAAAGATTTCTCCTCAATTTTT-G-GAT
1 ACACGATTTCGGCTAAAATTTTGCAAAAA-TTGACCCGAAAGATTTTTCCTCAATTTTTAGCGA-
* * * * *
4327 AAATTACTCATAAAATATAAATAATTTAACACCAAAAAGATTGGAGGACTTTTCACGCTTTTAAT
64 AAA-TACTCATAAAAAATATATAATTCAACACCAAAAAGATTGAAGGGCTTTTCACGCTTTTAAT
* * *
4392 ATCGTTTTTCATATTTTTTCTGAATTAGTTTCTAATTAAATCGAAACAAGATTCAGATGCTCATA
128 ATCGTTTTTCCTATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTA
* * * * * * *
4457 AAAACAAATCATCAAATGCAATGTAGCTGAGATTTGATTATATGAATATGGATATATCAAGGAAG
193 AAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGG-AG
* *** * * *
4522 CCTTGGCGCCAAAAATCATGCAAAACTGAGTTGGGGCCCGAAACGCTTTTTTAGCCAAAAATGGT
257 TCTTGGCGCCAAAAATCATGCAAAACTGAGCCAGGCCCCG-AACGCGTTTTTAGCC-AAAA-CGT
* * *
4587 GATGGTTATT
319 GATGATGAGT
* * * ** * *
4597 ACATGATTTCGGCTAAAATTTTGTAAAAATTGATCTAAAAGATTTTTCCTCAATTTTTGGCTAAA
1 ACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAGCGAAA
* * *
4662 ATACTCATAAAAAATATATATTTCAACGCCAAAAAGATTGAAGGGCTTTTGACG-TTTATAATAT
66 ATACTCATAAAAAATATATAATTCAACACCAAAAAGATTGAAGGGCTTTTCACGCTTT-TAATAT
* *
4726 CGTTTTTCCTATTTTTT-TCGAATTAGTTTCTAATTAAATCGAAACAAGATTCGGATGCTCGTAA
130 CGTTTTTCCTATTTTTTCT-GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAA
* ** *
4790 AAACAAATCCTTAAATCCAATATGGCTGAGATTTGATTAGATGAATATAGATATTTCAAATACTC
194 AAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTC
* * * * * * *
4855 TCGGAGTCAAAAATCATGCAAAATTGAGGCAGGTCCCCGGAATGCGTTTTTAGCAGAAAACCGTG
259 TTGGCGCCAAAAATCATGCAAAACTGAGCCAGG-CCCC-GAACGCGTTTTTAGC-CAAAA-CGTG
*
4920 ATGGTTTGTTATAGT
320 AT-G-ATG----AGT
* * * * * * *
4935 ACAAGATTTCGGCTAAAATTTTGCAAAAATTGACACAAAAGATTTCTCCTCAGTTTTTGGCTAAA
1 ACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAGCGAAA
* * * * *
5000 ATACTCAT-AAAAATATATAATTCAACGCCAAAAAGATTGGAGAGTTTTTCACGCTTTTAATATT
66 ATACTCATAAAAAATATATAATTCAACACCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATC
* * * *
5064 GTATTACTTATTTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAA
131 GTTTTTCCTATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAA
* * * * *
5129 ACAAATTCTTAAATCTAATGTTGCTGAGTTTTGGTTAGATGA
196 ACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGA
5171 TGTAAAGTAT
Statistics
Matches: 1553, Mismatches: 249, Indels: 144
0.80 0.13 0.07
Matches are distributed among these distances:
306 4 0.00
307 20 0.01
308 24 0.02
309 72 0.05
311 52 0.03
312 21 0.01
313 56 0.04
314 8 0.01
323 2 0.00
325 4 0.00
326 41 0.03
327 189 0.12
328 11 0.01
329 4 0.00
330 170 0.11
331 106 0.07
332 336 0.22
333 138 0.09
334 79 0.05
335 5 0.00
337 139 0.09
338 72 0.05
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (328 bp):
ACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAGCGAAA
ATACTCATAAAAAATATATAATTCAACACCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATC
GTTTTTCCTATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAA
ACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTT
GGCGCCAAAAATCATGCAAAACTGAGCCAGGCCCCGAACGCGTTTTTAGCCAAAACGTGATGATG
AGT
Found at i:11587 original size:25 final size:25
Alignment explanation
Indices: 11559--11674 Score: 169
Period size: 25 Copynumber: 4.6 Consensus size: 25
11549 CGCTCATGTT
* * *
11559 CTTGTGTTTGAAAAACGAGCCTGTG
1 CTTGCGTTTGGAAAACGAACCTGTG
11584 CTTGCGTTTGGAAAACGAACCTGTG
1 CTTGCGTTTGGAAAACGAACCTGTG
11609 CTTGCGTTTGGAAAACGAACCTGTG
1 CTTGCGTTTGGAAAACGAACCTGTG
* * *
11634 CTTGCGTTTGGCAAGCGAGCCTGTG
1 CTTGCGTTTGGAAAACGAACCTGTG
*
11659 CTTGCGTTTAGAAAAC
1 CTTGCGTTTGGAAAAC
11675 ACATAGGCTA
Statistics
Matches: 82, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 82 1.00
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.29
Consensus pattern (25 bp):
CTTGCGTTTGGAAAACGAACCTGTG
Found at i:15220 original size:327 final size:326
Alignment explanation
Indices: 14445--17307 Score: 2374
Period size: 327 Copynumber: 8.7 Consensus size: 326
14435 CGTTTTTTTA
* * *
14445 GTACACGATTTCGGTTAAAATTTTGCAAAAAATGACCCGAAAGA-TATTTCCTCAATTTTTGGCT
1 GTACACGATTTCGGCTAAAATTTTGCAAAAAATGACCCGAAAAATTA-TTCCTCAATTTTTAGCT
* * * *
14509 AAAATACTCATAAAAAATATATAATTCGACACCAAAAAGATTGAAGGGCTTTTAACGCTTCTAAT
65 AAAATACTCAT-AAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAAT
* ** * * * *
14574 ATTGTTTTTCCA-ATTTTTATCCAAATTAATGTCTAATTAAATTGAAACAAAATTCAGATGCTCG
129 ATCGTTTTT-CATA-TTTT-TCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTTG
* * * *
14638 TAAAAATAAATCCCTAAA-TCTAATGTGTCTGAGATTTGGTTAGATGAATATAGATATTTCAAGG
191 TAAAAACAAATCCTTAAATTC-AATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGG
* * * *
14702 A-T-T--GCACCATAAATCATGCAAAACTGAGCCGGGCCCCGGAACGCATTTTTAG-CAGAAAAC
255 AGTCTCGGCGCCAAAAATCATGCAAAACTAAGCCGGGCCCCGGAACGCGTTTTTAGCCA-AAAAC
14762 CGTGATGATC
319 CGTGAT-A-C
* * * * * * * * * *
14772 AATACACGATTTCGGATAAAGTTTTGCAAAAATTGATCCGAAAGATTTTTCCTCGATTTATAACT
1 -GTACACGATTTCGGCTAAAATTTTGCAAAAAATGACCCGAAAAATTATTCCTCAATTTTTAGCT
* * ***
14837 AAAATACTCATAAAAA-ACTATAATTCAATGCCAAAAAAAATTGAAACCCTTTTTCACGCTTTTA
65 AAAATACTCATAAAAATA-TATAATTCAACGCC-AAAAAGATTGAAGGGC-TTTTCACGCTTTTA
* * *
14901 ATATCGTTTTTCATATTTTTGTGAATTAATTTCTAATTAAATCTAAACAAGATTCAGATGCTCGT
127 ATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTTGT
14966 AAAAACAAATCCTTAAATTCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAG
192 AAAAACAAATCCTTAAATTCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAG
* * * ** * * *
15031 TCTCGGTGTCAAAAATCATACAAAACTAAGCTAGGTCCCGGAACACGTTTTTAGCCGAAAACCGT
257 TCTCGGCGCCAAAAATCATGCAAAACTAAGCCGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGT
15096 -A-AC
322 GATAC
* *
15099 GTACACGATTTCGGCTAAAATTTTGCAAAAAAATGACCCAAAAAATTATTCCGTCAATTTTTGGC
1 GTACACGATTTCGGCTAAAATTTTGC-AAAAAATGACCCGAAAAATTATTCC-TCAATTTTTAGC
* *
15164 TAAAATACTCATAAAATATATATAATTCAACGCCAAAAAAATTGGAGGGCTTTTCACGCTTTTAA
64 TAAAATACTCATAAAA-ATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAA
* * * *
15229 TATCGTTTTTCATATTTTTTTGAATTAATTTTTAATTAAATCGAAACAAGATTCAGATGGTTATA
128 TATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTTGTA
* * *
15294 AAAA-AAATTCTTAAA-TC-------C--A-A--T--TTA-A-GAATATGGATATCTT-AAAGAG
193 AAAACAAATCCTTAAATTCAATGTGGCTGAGATTTGATTAGATGAATATAGATAT-TTCAAGGAG
* * * * *
15340 TCTTGGCGCCAAAAATCATGCAAAACTTAGCCGGGGCCTCGGAACGCGTTTTCAGCCAAAAAAAA
257 TCTCGGCGCCAAAAATCATGCAAAACTAAGCC-GGGCCCCGGAACGCGTTTTTAGCC--AAAAAC
*
15405 CGTGATGATTA
319 CGTGAT-A--C
* * * *
15416 TTACACGATTTCGATCGGCTAGAATTTTGC-AAAAATCGACTCG-AAAGTTATTTCCTCAATTTT
1 GTACACGA-TT---TCGGCTAAAATTTTGCAAAAAAT-GACCCGAAAAATTA-TTCCTCAATTTT
* * * * *
15479 TAGCCACAATACTCATAAAAATTATATAATTCAATGCCAAAAAGATTGAAGGGCTTTTTATGCTT
60 TAGCTAAAATACTCATAAAAA-TATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTT
* * * * *
15544 CTAATATCGTTTTTCCTATTAATTTCCGAATTAATTTTTAATTAAATCGAAACATGATTCAGATG
124 TTAATATCGTTTTTCATATT--TTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATG
*** * * * * * *
15609 CTTGT-TTTACAAATCCTAAAATCCAATTTGGCTGAAATTTGGTTAGATGAATGTAGATATTTCA
187 CTTGTAAAAACAAATCCTTAAATTCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCA
* * * * ** *
15673 AGGAATCTCGGCG-CAAAAATTCATGCAACATTGAA-CCTGAGCCTAGGAACACGTTTTTAGCCA
252 AGGAGTCTCGGCGCCAAAAA-TCATGCAAAACT-AAGCC-GGGCCCCGGAACGCGTTTTTAGCCA
*
15736 AAAATCGTGATTTCGACTAGC
314 AAAA-C-CG---T-GA-TA-C
* * * * * * * *
15757 GTACACGATTTTGGCTAATATTTTGCAAAAATTGACCAGAAATATTTTTTCTCAAATTTT-GTCT
1 GTACACGATTTCGGCTAAAATTTTGCAAAAAATGACCCGAAAAATTATTCCTCAATTTTTAG-CT
* * * *
15821 AAAATACGT-ATAAAATATATATAATTCAACTCAAAAAAGATTTG-AGGACTTTTTACGCTTTTA
65 AAAATAC-TCATAAAA-ATATATAATTCAACGCCAAAAAGA-TTGAAGGGCTTTTCACGCTTTTA
*
15884 ATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTCAATCGAAACAAGATTCAGATGCTTGT
127 ATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTTGT
* * * * *
15949 AAAAAAACAAATCCTTAAATGCAATATGGCTGAGACTTCATTAGATGAATATAGATATTTCAAAG
192 --AAAAACAAATCCTTAAATTCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGG
* * * * **
16014 AGTCTCGACGCCAAAAATCATGCAAAA-TTAGCCGGGACTCCGAAACGCGTTTTTAGTAAAGAAA
255 AGTCTCGGCGCCAAAAATCATGCAAAACTAAGCCGGG-CCCCGGAACGCGTTTTTAG-CCA-AAA
*
16078 ATCGTGATGGTTA-
317 ACCGTGA----TAC
* ** * *
16091 GTACACGATTTCAGCTAAAATTTTGCAAAAAAATGACCAAAAAAATTATTCCTCATTTTTTAAAC
1 GTACACGATTTCGGCTAAAATTTTGC-AAAAAATGACCCGAAAAATTATTCCTCAATTTTT-AGC
* * * ** *
16156 -ATAATACTCATAAAATATATATAATTCAACACTAAAAAGATTGAAGAACTTTTCACGCTTCTAA
64 TAAAATACTCATAAAA-ATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAA
* * * * * * * * *
16220 TATTGTTTTTCCTACTTTCTCCGAATTAAGTTCTAATTAAAACGAAACATGATTCAAATGTTTGT
128 TATCGTTTTTCATA-TTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTTGT
* * * *
16285 -------AA-----AAA--CAA--TGGTTGGGATTTGGTTAGATGAACATAGATATTTCAAGGAG
192 AAAAACAAATCCTTAAATTCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAG
* * ** * * *
16334 TCTCGGTGCCAAAAATCATTCAAAGTTGAA-CCAGGTCCCGGAACGCATTTTTAGCCAAAAACCC
257 TCTCGGCGCCAAAAATCATGCAAAACT-AAGCCGGGCCCCGGAACGCGTTTTTAGCCAAAAA-CC
*
16398 TAATGATTA-
320 --GTGA-TAC
* * * * *
16407 TTACACGATTTCAGCTAAAATTTTGTAAAAATTGACCCGAAAGATATT-TT-TTCAATTTTTAGC
1 GTACACGATTTCGGCTAAAATTTTGCAAAAAATGACCCGAAA-A-ATTATTCCTCAATTTTTAGC
* * * * *
16470 CATAATACTCATAGAAAATATATAATTCAATGTCAAAAAGATTGAAGTGCTTTTCACGCTTTTAA
64 TAAAATACTCATA-AAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAA
* * * * *
16535 TATCGTTTTTCATATTTTTTCTAAATTAATTTCTAATTAAATTGAAACAATATTTAGATGCTCGT
128 TATCGTTTTTCATA-TTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTTGT
* * * * * * *
16600 AAAAACATATCCTTAAATGCAATGTGGCTAATAATTT-ATTAGATGAGTATAGACATTTCAAAGA
192 AAAAACAAATCCTTAAATTCAATGTGGCTGA-GATTTGATTAGATGAATATAGATATTTCAAGGA
* * * ** *
16664 GTGTCGGCG-CAAAAACCATGCAAAAC-AGAGCCGGGACCCCGAAACATGTTTTTATCCAAAAAA
256 GTCTCGGCGCCAAAAATCATGCAAAACTA-AGCCGGG-CCCCGGAACGCGTTTTTAGCC-AAAAA
*
16727 TCGTGATGGGTTA-
318 CCGTGA-----TAC
* * * * ** * *
16740 GTACACGATTTTGGCTAAAATTTTGCAATAAAT-AACCTAAATTTTTTTCC-CAATTTTT-GATA
1 GTACACGATTTCGGCTAAAATTTTGCAAAAAATGACCCGAAAAATTATTCCTCAATTTTTAGCTA
* * * *
16802 AAATACTCATAAAGTATATATAATTTAACGCCAAAAAGATTGGAGGACTTTTCACGCTTTTAATA
66 AAATACTCATAAA-AATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATA
*
16867 TCGTTTTTCATATTTTTGC-GAATTAATTTCTAATTAAATCGAAACAAGACTCAGATGCTTGTAA
130 TCGTTTTTCATATTTTT-CTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTTGTAA
* * * * * * *
16931 AAACAAATTCTTAAATCCAATGTGACTGAGATTTTATCAGATGAATATGGATATTTTAAGGAGTC
194 AAACAAATCCTTAAATTCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTC
* * ** * *
16996 TTGGCGTCAAAAATCATGCAAAACTAAGCCGGAGCCCTAGAACGCTTTTTTAGCCAAAAACTGTG
259 TCGGCGCCAAAAATCATGCAAAACTAAGCCGG-GCCCCGGAACGCGTTTTTAGCCAAAAACCGTG
*
17061 ATGGTTATA
323 A----TA-C
* * * * * *
17070 TTACACGATTTCGGCTAAAATTTTGTAAAAATTAACCCGAAATA-TATTTCCTCAATTTTTGGCT
1 GTACACGATTTCGGCTAAAATTTTGCAAAAAATGACCCGAAAAATTA-TTCCTCAATTTTTAGCT
* * *
17134 AAAATACTCATAAAAATATATAATTCAACGCCAAAAAGATTGGAGGGCTTTTTACACTTTTAATA
65 AAAATACTCATAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATA
* * * * * *
17199 TCGTATTTCATATTTTTTCTAAATTAATTTTTAATTAAATCGAAATAAGATTCATATGCTCGTAA
130 TCGTTTTTCATA-TTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTTGTAA
* * * * * *
17264 AAGCAAATTCTTAAATACAATGTTGCTCAGATTTGGTTAGATGA
194 AAACAAATCCTTAAATTCAATGTGGCTGAGATTTGATTAGATGA
17308 TGTAAAGTAT
Statistics
Matches: 2038, Mismatches: 363, Indels: 263
0.77 0.14 0.10
Matches are distributed among these distances:
309 42 0.02
310 22 0.01
311 3 0.00
312 7 0.00
313 2 0.00
314 2 0.00
315 126 0.06
316 38 0.02
317 12 0.01
318 74 0.04
319 101 0.05
320 13 0.01
321 67 0.03
322 5 0.00
325 2 0.00
326 34 0.02
327 216 0.11
328 131 0.06
329 154 0.08
330 155 0.08
331 119 0.06
332 83 0.04
333 128 0.06
334 29 0.01
335 135 0.07
336 57 0.03
337 120 0.06
338 136 0.07
339 11 0.01
340 2 0.00
341 8 0.00
342 3 0.00
343 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (326 bp):
GTACACGATTTCGGCTAAAATTTTGCAAAAAATGACCCGAAAAATTATTCCTCAATTTTTAGCTA
AAATACTCATAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATAT
CGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTTGTAAAA
ACAAATCCTTAAATTCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTC
GGCGCCAAAAATCATGCAAAACTAAGCCGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATA
C
Found at i:17707 original size:13 final size:14
Alignment explanation
Indices: 17675--17720 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
17665 ATCTAAAAAT
*
17675 AATTATTAGAAGTA-
1 AATTATTAG-ATTAC
17689 AATTATTA-ATTAC
1 AATTATTAGATTAC
17702 AATTA-TAGATTAC
1 AATTATTAGATTAC
17715 AATTAT
1 AATTAT
17721 AGTGGGTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
12 5 0.18
13 15 0.54
14 8 0.29
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.41
Consensus pattern (14 bp):
AATTATTAGATTAC
Found at i:18758 original size:5 final size:5
Alignment explanation
Indices: 18748--18774 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
18738 AGCATTACTC
18748 TTATT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TT
18775 TTATATTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:19283 original size:2 final size:2
Alignment explanation
Indices: 19276--19314 Score: 69
Period size: 2 Copynumber: 19.0 Consensus size: 2
19266 TCCCTGGTAT
19276 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
19315 AGT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Done.