Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017891.1 Corchorus olitorius cultivar O-4 contig17924, 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: 33442
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:159 original size:13 final size:13
Alignment explanation
Indices: 141--165 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
131 AAACAATTGA
141 AAAGCACTTCTGG
1 AAAGCACTTCTGG
154 AAAGCACTTCTG
1 AAAGCACTTCTG
166 ATTTTCCGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (13 bp):
AAAGCACTTCTGG
Found at i:11640 original size:42 final size:44
Alignment explanation
Indices: 11589--11682 Score: 140
Period size: 45 Copynumber: 2.2 Consensus size: 44
11579 AGTGCATTAT
*
11589 CTAA-ATTCTACT-CT-ATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACTCCTCATCTCTAGATAATTCATCAAAATAAAG
*
11630 CTGATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTACTCCT-CATCTCTAGATAATTCATCAAAATAAAG
11675 CTAATATT
1 CTAATATT
11683 AATTTTTGCT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 3 0.07
42 8 0.17
43 2 0.04
45 33 0.72
ACGTcount: A:0.37, C:0.21, G:0.06, T:0.35
Consensus pattern (44 bp):
CTAATATTCTACTCCTCATCTCTAGATAATTCATCAAAATAAAG
Found at i:12919 original size:25 final size:25
Alignment explanation
Indices: 12883--12938 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
12873 CAAAAAAAAG
12883 TTCAAATAGAGCCTCCTCATCAATC
1 TTCAAATAGAGCCTCCTCATCAATC
*
12908 TTCAAATGGAGCCTCCTCATCAATC
1 TTCAAATAGAGCCTCCTCATCAATC
*
12933 CTCAAA
1 TTCAAA
12939 AGGGGCCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.32, C:0.32, G:0.09, T:0.27
Consensus pattern (25 bp):
TTCAAATAGAGCCTCCTCATCAATC
Found at i:12946 original size:25 final size:25
Alignment explanation
Indices: 12891--12946 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
12881 AGTTCAAATA
* *
12891 GAGCCTCCTCATCAATCTTCAAATG
1 GAGCCTCCTCATCAATCCTCAAAAG
12916 GAGCCTCCTCATCAATCCTCAAAAG
1 GAGCCTCCTCATCAATCCTCAAAAG
*
12941 GGGCCT
1 GAGCCT
12947 TTGGTAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.27, C:0.34, G:0.16, T:0.23
Consensus pattern (25 bp):
GAGCCTCCTCATCAATCCTCAAAAG
Found at i:20302 original size:18 final size:18
Alignment explanation
Indices: 20279--20314 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
20269 TATTAAAATT
20279 TGAGGGTATAAGAGGAAA
1 TGAGGGTATAAGAGGAAA
20297 TGAGGGTATAAGAGGAAA
1 TGAGGGTATAAGAGGAAA
20315 GTTAAGATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.39, T:0.17
Consensus pattern (18 bp):
TGAGGGTATAAGAGGAAA
Found at i:21337 original size:15 final size:15
Alignment explanation
Indices: 21300--21329 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
21290 TAGTCATACT
21300 ATACTAGTACTAGTA
1 ATACTAGTACTAGTA
21315 ATACTAGTACTAGTA
1 ATACTAGTACTAGTA
21330 TTATTAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (15 bp):
ATACTAGTACTAGTA
Found at i:24477 original size:12 final size:12
Alignment explanation
Indices: 24446--24485 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
24436 TTTTTCTGGT
*
24446 AATTTTAAGCAA
1 AATTTTAGGCAA
24458 AATTTTAGGCAA
1 AATTTTAGGCAA
*
24470 AATTTTAGGCGA
1 AATTTTAGGCAA
24482 AATT
1 AATT
24486 GTGTACTAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.42, C:0.07, G:0.15, T:0.35
Consensus pattern (12 bp):
AATTTTAGGCAA
Found at i:25407 original size:331 final size:331
Alignment explanation
Indices: 23057--27074 Score: 2681
Period size: 332 Copynumber: 12.1 Consensus size: 331
23047 TATTAAAAAT
* * * * * * ** *
23057 GTGAAAAGTCCTCCAATCTTTTTGCCATTAAATTATATATATTTTAGGAGTATTTTATCCAAAAA
1 GTGAAAAGTCCTTCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTGTGGCTAAAAA
* * * * * **
23122 TTGAGTAAAAATTTTTCGGGTC-TTTTTTGCAAAATTTTAGCCAAAATCGTGTGCT-ACCATCAC
66 TTGAGGAAAAA-CTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCAC
* * * * *
23185 GGTTTTTGGCTAAAAACGCGTT-TCGGGGCACC-AGCTCAGTTTTGCATGATTTTTGGCACCGAT
130 GGTTTTTGGCTAAAAACGCGTTCT-GGGGCCCCGA-CTTAGTTTTGCATGATTTTTGGCGCCAAG
* * * * * *
23248 ACTCCTTGAAATAACCATATTCATCTAAT-AAATTCTTTAGCCAAATTGCATTTAA-GATTTTTT
193 ACTCCTTGAAATATCTATATTTATCTAATCAAA-TC-TCAGCCACATTGGATTTAAGGA------
* * * *
23311 TTTTGTTTTTAACGAGCATCTGAATCATATTTTGATTTAATTAGAAATTAATTTAGAAAAAATAT
250 -TTTGTTTTT-ACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCA-AAAAAATAT
*
23376 G-AAAAACGATATTAAAAGC
312 GAAAAAACGATATTAGAAGC
* * * * * *
23395 GTCAAAA-TCCCTTCAATCTTTTTGTCATTGAATTATA-AAATTTTTATGAGTATTATGGCTGAA
1 GTGAAAAGT-CCTTCAATCTTTTTGGCGTTGAATTATATATA-TTTTATGAGTATTGTGGCTAAA
* * * * *
23458 AATTGAGGAAATATCTTTCGGGTCAATTTTTGCATAATTTTAGTCGAAATCGTGTAATAATCATC
64 AATTGAGGAAA-AACTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATC
* * * * *
23523 ACGGTTTTTGGCTAAAAGCGCGTTCTGGGG--CC-ATTTCAGTTTTGAAT-ATTTTTTGCGCGGA
128 ACGGTTTTTGGCTAAAAACGCGTTCTGGGGCCCCGACTT-AGTTTTGCATGATTTTTGGCGC-CA
* * *
23584 A-ACTCCTT-AAATTATCTATATTCATCTAACCAAATCCCAG-C-C-----A-TT---G--TT-T
191 AGACTCCTTGAAA-TATCTATATTTATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGT
* * * * *
23633 TTATA--AGCATCCGATTCATGTTTC-ATTTTAATTAGAAATTAATTCAGAAAAAATA-G-GAAA
255 TTTTACGAGCATCTGAATCTTGTTTCGA-TTTAATTAGAAATTAATTCA-AAAAAATATGAAAAA
*
23693 ACAATATTAGAAGC
318 ACGATATTAGAAGC
* * * *
23707 GTGAAAAGCCCTTTAATCTTTTTGACGTTGAATTATATAT-TTTTATGAGTATTGTGACTAAAAA
1 GTGAAAAGTCCTTCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTGTGGCTAAAAA
* * * ** * * *
23771 TTGAGGAAGAATA-TTTCGGGTCATTTTTTGCAAAATATTAGCCGAAATTATGCAACATCACGAT
66 TTGAGGAA-AA-ACTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTG-TA-ATAACCAT
**** * * * ** * * **** * * * * **
23835 -TTTTTTTTTTGCTAAAAAGGCATTCCAGGACCACGGGGCAGTATTACTTGATTTTTGTCATCAA
127 CACGGTTTTTGGCTAAAAACGCGTTCTGGGGCCCCGACTTAGTTTTGCATGATTTTTGGCGCCAA
* *
23899 GACTCCCTGAACTATCTATATTTATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTT
192 GACTCCTTGAAATATCTATATTTATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTT
* * * ** * *
23964 TTATGAGAATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAT-TAGGAAAAACT
257 TTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAAAAAAATAT-GAAAAAACG
24028 ATATTAGAAGC
321 ATATTAGAAGC
* * * * * *
24039 GTAAAAAATCCTTCAATATTTTTGGCGTAGAATTATATATATTTTTATTA-TAATT-TAG-TAAA
1 GTGAAAAGTCCTTCAATCTTTTTGGCGTTGAATTATATATA-TTTTATGAGT-ATTGTGGCT-AA
* * *
24101 AAATTTAGGAAATAACTTTCCG-GTCAATGTTTGCAAAATTTTAGCCGAAATCGTGTAATAATCA
63 AAATTGAGGAAA-AACTTT-CGAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCA
* * * * *
24165 TCACGGTTTTTGGCTAATAATGTGTTCCGAGGCCCCAAGAC--AGTTTTGCATGATTTTTGGCGC
126 TCACGGTTTTTGGCTAAAAACGCGTTCTGGGGCCCC--GACTTAGTTTTGCATGATTTTTGGCGC
* * * * * * * *
24228 TAAGACTACAT-AAGATATCCATATTCATTTAATCAAATCTCAGACACATTGCATTTAAGGATTT
189 CAAGACTCCTTGAA-ATATCTATATTTATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTT
* * *
24292 GTTTTTACGAGCATCTAAATCTTATTTCGATTTAATTAG-------TT-AGAAAAATATG-AAAA
253 GTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAAAAAAATATGAAAAA
* * *
24348 ACGATATGAAAATC
318 ACGATATTAGAAGC
* * * * * * *
24362 GTGAAACGTCCTCCAATCTTTTTGGCGTT-AAAT-TATATATTTCATGTGTATT-TAAGCCAAAA
1 GTGAAAAGTCCTTCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTGT-GGCTAAAA
* * * *
24424 ATTGAGG-AAAACTTTTTCTGGTAATTTTAAGCAAAATTTTAGGCAAAATTTTAGGCGAAATTGT
65 ATTGAGGAAAAAC--TTTC--G--A--GT---C--AATTTT-TGCAAAATTTTAGCCGAAATCGT
* * * **
24488 GTACTAACCATCACGGTTTTTTTATTTTTTTGTTAAAAACGCGTT-TCGGGGCCCAAACTCT-GT
116 GTAATAACCATCACGG---------TTTTTGGCTAAAAACGCGTTCT-GGGGCCCCGACT-TAGT
** * * * *
24551 TTTGCATGATTTTTGGCATCGAGACTCCTTGAAATATATATATATTCAGCTAATCAAATCTCAGT
170 TTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATAT-TT-ATCTAATCAAATCTCAGC
* * * **
24616 CACATTGCATTT-AGAGATTTGCTTTTACGAGCATCTGAATCTTATTTCGATTTAATTAGATTTT
233 CACATTGGATTTAAG-GATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATT
* * *
24680 AGTTCAGAAAAATATG-AAAAACGATATTAAAAGC
297 AATTCAAAAAAATATGAAAAAACGATATTAGAAGC
** * * * * * **
24714 GTGAAAAGT-AATCTAATATTTTTGGAGTTGAATTGTATATA---TATGATTATTTTGGAAAAAA
1 GTGAAAAGTCCTTC-AATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTGTGGCTAAAA
* *
24775 ATTGAGG-AAAACTATTTCTG-GTCAATTTTTGCAAAATATTAGCCGAAATCGTGTACATTAGTC
65 ATTGAGGAAAAAC--TTTC-GAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTA-A-TA-AC
* ** * * * * *
24838 GAAATCACGGTTTTTTCCTAAAAACGTGTTCCGGGGCCCCG-GTTCAGTGTTGCATGATTTTTTG
124 --CATCACGGTTTTTGGCTAAAAACGCGTTCTGGGGCCCCGACTT-AGTTTTGCATGATTTTTGG
* * * * * *
24902 CGTCGAGACTCCTTGAAATATCTATATTAATCTAAGCAAATCTCATCCACAATGGATTTAAGGAT
186 CGCCAAGACTCCTTGAAATATCTATATTTATCTAATCAAATCTCAGCCACATTGGATTTAAGGAT
*** * * * * *
24967 TTG-TAAAACAAGCATCTGAATCATGTTTTGATTTAATTAGAAATTAATTCGGAAAATAATAGGA
251 TTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTC--AAAAAAATATGA
* *
25031 AAAAATGATACTAGAAGC
314 AAAAACGATATTAGAAGC
* *
25049 AT-AAAAG-CCATTCAATCTTTATGGCGTTGAATTATATA-ATTTTATGAGTATTGTGGCTAAAA
1 GTGAAAAGTCC-TTCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTGTGGCTAAAA
* *
25111 CTTGAGGAAATAACTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAATCATCA
65 ATTGAGGAAA-AACTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCA
* * * *
25176 CGGTTTTTGGCTAAAAACGCGTTCTGGGGACCCGACTAAGTTTTGCATGATTTTTGGCACCAAAA
129 CGGTTTTTGGCTAAAAACGCGTTCTGGGGCCCCGACTTAGTTTTGCATGATTTTTGGCGCCAAGA
* * * * * * ** *
25241 CACTTTGAGATATCCATATTTATCTAATCAAATCTCAGCTACATTGGGTTTAATAATTTATTTTT
194 CTCCTTGAAATATCTATATTTATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTT
* ** *
25306 ACGAGCATTTGAATCTTGTTTTTATTTAATTAGAAATTAATTCAAAAAAATATGAAAAAATGATA
259 ACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAAAAAAATATGAAAAAACGATA
*
25371 TTAAAAGC
324 TTAGAAGC
* * * *
25379 GTGAAAAGTCCTCCAATCCTTTTGGCGTT-AA--AT-TATA---TAT-A-T-TTAT-GCCAAAAA
1 GTGAAAAGTCCTTCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTGTGGCTAAAAA
** * ** * **
25433 TTGACGGAAAATTTTTTC-AGGT-TATCAATTACAAAATTTTAGCCGAAATC--GT-AT-ACGTT
66 TTGA-GGAAAA-ACTTTCGA-GTCAAT-TTTTGCAAAATTTTAGCCGAAATCGTGTAATAAC-CA
* * * *
25492 TCACGGTTTTTGGCTAAAAATGCGTT-TCAGGACCCCGGCTTAGTTTTGCATGATTTTTGGCGCC
126 TCACGGTTTTTGGCTAAAAACGCGTTCT-GGGGCCCCGACTTAGTTTTGCATGATTTTTGGCGCC
* * * *
25556 GAGACTCCTTGAAATATCTATATTCATCTAATAAAATCTCAGCCACATTGAATTTAAGGATTT-T
190 AAGACTCCTTGAAATATCTATATTTATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGT
* * *
25620 TTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTAGAAAAAAAAATG-AATA
255 TTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA-TT-CAAAAAAATATGAAAAA
* *
25684 ACGAAATTAAAAGC
318 ACGATATTAGAAGC
* * * * * *
25698 GTGAAGAGTCCTTCAATTTTTTTGCCTTTTAATTATATATATATATATTCTATGAGTATTATGGC
1 GTGAAAAGTCCTTCAATCTTTTTGGC-GTTGA--AT-TATATATAT-TT-TATGAGTATTGTGGC
* * *
25763 CAAAAATGGAGGAAGAATA-TTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTG---T-A
60 TAAAAATTGAGGAA-AA-ACTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAA
* * * * * *
25823 CCATCACGGTTTTTTTTGGCTAAAAACGCGTTGTGGGCCCCCAAGTTAGTTTTGCACGATTTTTA
123 CCATCACGG---TTTTTGGCTAAAAACGCGTTCTGGGGCCCCGACTTAGTTTTGCATGATTTTTG
* * * * * * * * * *
25888 GTGGCAAAATTCGTTGAAGTATCTATATTCATCTAACCAAATCTTAGCCATATTGGATTTAAGGA
185 GCGCCAAGACTCCTTGAAATATCTATATTTATCTAATCAAATCTCAGCCACATTGGATTTAAGGA
* * * * *
25953 TTTGTTTTTACGAGCATTTGAATCATGTTTCAATTTAATTAGAAATAAATTTGAAAACAAATA-G
250 TTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA-TTCAAAA-AAATATG
* *
26017 GAAGAACGATATTAGAAG-
313 AAAAAACGATATTAGAAGC
* * *
26035 GTGAGAAGCCCTTCAATCTTTTTTGCGTTGATATTATATATATTTTTATGAGTATTGTGGCTAAA
1 GTGAAAAGTCCTTCAATCTTTTTGGCGTTGA-ATTATATATA-TTTTATGAGTATTGTGGCTAAA
* * * * *
26100 AATTGA-GAAAAATATTTCGGGTCAATTTTTGTAAAATTTTAGCCGAAATTGTGTACCGGT-ACC
64 AATTGAGGAAAAA-CTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTA---ATAACC
* * * * * *
26163 ATCATGTTTTTTTTGGCTAAAAACTCGTT-TCGGGG-CTCTAGGTTAGTTTTGCATGATTTTTGG
125 ATCACG--GTTTTTGGCTAAAAACGCGTTCT-GGGGCCCCGA-CTTAGTTTTGCATGATTTTTGG
* ** * * * *
26226 TGCCAAGACTTTTTAAAATATATATATATATATATATATTTATCTAACTAAATCTTAGCCACATT
186 CGCCAAGACTCCTT-GAA-ATATCTATAT-T-TATCTA---A--T--C-AAATCTCAGCCACATT
* * * ** * *
26291 GTATTTAAGGATTTGTTTGTACCAGTTTCTAAAT-TCTGTTTCGATTTAATCAGAAATTAATTTT
239 GGATTTAAGGATTTGTTTTTACGAGCATCTGAATCT-TGTTTCGATTTAATTAGAAATTAA--TT
* *
26355 GAAATAAAATA-GGAAAAACGATATTAGAAGC
301 CAAA-AAAATATGAAAAAACGATATTAGAAGC
* * * * * *
26386 GTGAAAAAAATGT-TTTCAATTTTTTTGGCGTTGAATTATTTATTTTTTATGAGTATTTTCGCTA
1 GTG---AAAA-GTCCTTCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTGTGGCTA
* *
26450 GAAAA-CGAGGAAAAATCTTTCGAGTCAATTTTTGCAAAA-TTTAGCCGAAATCGTGTACTAACC
62 -AAAATTGAGGAAAAA-CTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACC
** * ** * * * *
26513 ATCATAGTTATCAGCTAAAAATGCGTT-TTGGGCCCCGGCTTAGTTTTGCATGATTTTTGGTGCC
125 ATCACGGTTTTTGGCTAAAAACGCGTTCTGGGGCCCCGACTTAGTTTTGCATGATTTTTGGCGCC
* * * * * * *
26577 AAGACTCCTTGAAACATTTATATTCATCTAACCAAATCTCAGCCACATTAGATTTAAAGATTTGC
190 AAGACTCCTTGAAATATCTATATTTATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGT
* *
26642 TTTTACGAGCATCTGAATCTTGTTTCAATTTAATTAGAAATTAATTCGAAAAAAATA-GGAAAAA
255 TTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTC-AAAAAAATATGAAAAAA
*
26706 CAATATTAGAAGC
319 CGATATTAGAAGC
* * **** * * * *
26719 GTTAAAAGCCCTTCAATCTTTTTTATATCGAATTATATATTTTTTATGAGTATTTTAG-TCAAAA
1 GTGAAAAGTCCTTCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTGTGGCT-AAAA
* * * * * * * *
26783 ATCGAGGAAATATCTTTCGGGACAATTTTTACAAAATTTGAGCCGAAATTGTGTACTAACCATCA
65 ATTGAGGAAA-AACTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCA
** * * * *
26848 CGGTTTTTGGCTAAAAACGCGTTAC-AAGGCCACGGCTCTA-TTTGGCATGATTTTTGGCGCCGA
129 CGGTTTTTGGCTAAAAACGCGTT-CTGGGGCCCCGACT-TAGTTTTGCATGATTTTTGGCGCCAA
* * * * *
26911 GACTCCTTGAAATATCTTTATTTATCTAACCAAATCTCAACCACATTGTATTTAAGAATTT-TTT
192 GACTCCTTGAAATATCTATATTTATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTT
* * * * *
26975 TTATGTGCATCTAAATCTTTTTTCGATTTAATTAGAAATTAATTTAAAAAAAATTTATG-AAAAA
257 TTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA-TTCAAAAAAA--TATGAAAAAA
*
27039 TGATATTA-AAGTC
319 CGATATTAGAAG-C
*
27052 GTGAAAAGTCCTCCAATCTTTTT
1 GTGAAAAGTCCTTCAATCTTTTT
27075 TTGCATCTTT
Statistics
Matches: 2917, Mismatches: 547, Indels: 437
0.75 0.14 0.11
Matches are distributed among these distances:
311 63 0.02
312 69 0.02
313 49 0.02
314 9 0.00
315 39 0.01
316 7 0.00
317 3 0.00
318 44 0.02
319 148 0.05
320 26 0.01
321 37 0.01
322 40 0.01
323 41 0.01
324 9 0.00
325 6 0.00
326 4 0.00
327 7 0.00
328 7 0.00
329 12 0.00
330 109 0.04
331 254 0.09
332 393 0.13
333 200 0.07
334 74 0.03
335 190 0.07
336 90 0.03
337 216 0.07
338 159 0.05
339 58 0.02
340 42 0.01
341 7 0.00
342 57 0.02
343 9 0.00
344 78 0.03
345 9 0.00
346 2 0.00
347 36 0.01
348 19 0.01
349 64 0.02
350 39 0.01
351 36 0.01
352 86 0.03
353 42 0.01
354 27 0.01
355 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (331 bp):
GTGAAAAGTCCTTCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTGTGGCTAAAAA
TTGAGGAAAAACTTTCGAGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCACG
GTTTTTGGCTAAAAACGCGTTCTGGGGCCCCGACTTAGTTTTGCATGATTTTTGGCGCCAAGACT
CCTTGAAATATCTATATTTATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTAC
GAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAAAAAAATATGAAAAAACGATATT
AGAAGC
Found at i:28017 original size:46 final size:46
Alignment explanation
Indices: 27940--28033 Score: 161
Period size: 46 Copynumber: 2.0 Consensus size: 46
27930 GCCAATTTTC
* * *
27940 TTACATATATGAAACAGAATTTGGCACCCTTTGCTTAAAATTCACT
1 TTACACATATGAAACAGAATTCGGCAACCTTTGCTTAAAATTCACT
27986 TTACACATATGAAACAGAATTCGGCAACCTTTGCTTAAAATTCACT
1 TTACACATATGAAACAGAATTCGGCAACCTTTGCTTAAAATTCACT
28032 TT
1 TT
28034 CTGCACTTCA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.35, C:0.20, G:0.11, T:0.34
Consensus pattern (46 bp):
TTACACATATGAAACAGAATTCGGCAACCTTTGCTTAAAATTCACT
Done.