Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016339.1 Corchorus olitorius cultivar O-4 contig16372, 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: 23876
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:869 original size:2 final size:2
Alignment explanation
Indices: 862--888 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
852 TAATATGTAG
862 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
889 TGTGGAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3685 original size:11 final size:11
Alignment explanation
Indices: 3666--3700 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
3656 CTCCACCAAA
3666 TTCTTTTTATT
1 TTCTTTTTATT
3677 TAT-TTTTTATT
1 T-TCTTTTTATT
3688 TTCTTTTTATT
1 TTCTTTTTATT
3699 TT
1 TT
3701 AAAAAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 1 0.05
11 20 0.91
12 1 0.05
ACGTcount: A:0.11, C:0.06, G:0.00, T:0.83
Consensus pattern (11 bp):
TTCTTTTTATT
Found at i:12083 original size:27 final size:27
Alignment explanation
Indices: 12053--12110 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
12043 TTTTAATACA
*
12053 TATTCTTTTAAG-TCATTTAACTTTTTT
1 TATTCTTTTAAGATCA-TCAACTTTTTT
* *
12080 TATTTTTTTAAGATGATCAACTTTTTT
1 TATTCTTTTAAGATCATCAACTTTTTT
12107 TATT
1 TATT
12111 AAGTATGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 25 0.93
28 2 0.07
ACGTcount: A:0.24, C:0.09, G:0.05, T:0.62
Consensus pattern (27 bp):
TATTCTTTTAAGATCATCAACTTTTTT
Found at i:12241 original size:15 final size:16
Alignment explanation
Indices: 12216--12245 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
12206 AATAATTATT
12216 TTTAGATTATAATATA
1 TTTAGATTATAATATA
12232 TTTA-ATTATAATAT
1 TTTAGATTATAATAT
12246 TATTATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGATTATAATATA
Found at i:15259 original size:333 final size:330
Alignment explanation
Indices: 13845--17020 Score: 2916
Period size: 333 Copynumber: 9.5 Consensus size: 330
13835 ATTACATCAA
** ** * * *
13845 CTAACCAAATCTCAGTAACATTGGATTTAATAATTTGTTTTTACGAGCATCTAAATCTTGATTCG
1 CTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCG
* * *
13910 ATTTAATTAGAAATTAATTTAGAAAAAATAAGAAATACGATATTAAAAGCGTGAAAAGCCCTCCA
66 ATTTAATTAGAAATTAATTCAGAAAAAATAAGAAAAACGATATTAAAAGCGTGAAAAGCCCTTCA
* * * *
13975 ATCTTTTTGTCGTTGAATTATATATTTTTATAAGTATTTTAGCCAAAAATTGAGCAGAAATCTTT
131 ATCTTTTTGGCGTTGAATTATATATTTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAATCTTT
* * * * *
14040 CGTGTCAATTTTTGCACAATTTTAGCCGAAATTGTGTACTAACTAACCATCATGTTTTTTTTTGG
196 CGTGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAAC-CATCA-CA-G----TTTTTAG
* * * ** * * * *
14105 CTAAAAACGCATTCCGCGGCCCCGGGTCAATTTAGCATAATTTTTGGCGCTGAGACTCCTTGAAA
254 CTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGC-CAGAGACTCCTTGAAA
14170 TATCTATATTCAT
318 TATCTATATTCAT
* * ** *
14183 CTAATAAAATGTTAGCCGCATTACTCAGTAACATTGGATTTAAGAATTTGTTTTTACGAGCATCT
1 C---T---A----A-CC-AAAT-CTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCT
* * * * *
14248 AAATCTTGATTCGATTTAATTAGAAATTAATTTAGAAAAAATAAGAAATACGATATTAAAAGCGT
53 GAATCATGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATAAGAAAAACGATATTAAAAGCGT
* * *
14313 GAAAAGCCCTCCAATCTTTTTGTCGTTGAATTATATATTTTTATAAGTATTTTAGCCAAAAATTG
118 GAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTATGAGTATTTTAGCCAAAAATTG
* * * *
14378 AGCAGAAATCTTTCGTGTCAATTTTTGCACAATTTTAGCCGAAATTGTGTACTAACTAACCATCA
183 AGGAAAAATCTTTCGTGTCAATTTTTGCAAAATTTTAGCCGAAATCGTG---T-ACTAACCATCA
* * * * ** * * * *
14443 C-GTTTTTTTGGGCTAAAAACGCATTCCGCGGCCCCGGGTCAATTTAGCATAATTTTTGGCGCTG
244 CAG--TTTTT-AGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGC-CAG
*
14507 AGACTTCTTGAAATATCTATATTCAT
305 AGACTCCTTGAAATATCTATATTCAT
** * * * * * *
14533 CTAATAAAATGTTAGCCGCATTGCATTTAAGGATTTGTTTTTATGAGCATCTGAATCTTGTTTCG
1 CTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCG
* * *
14598 ATTTAATTAGAAATTAAATCAGAAAAAA-AATGAAAAATGATATTAAAAGCGTGAAAAGCACTTC
66 ATTTAATTAGAAATTAATTCAGAAAAAATAA-GAAAAACGATATTAAAAGCGTGAAAAGCCCTTC
* * * * *
14662 AATATCTTTGGTGTTGAATTATATATTTTTTATGACTATTTTAGCTAAAAATTGA-GAAAATATC
130 AATCTTTTTGGCGTTGAATTATATA-TTTTTATGAGTATTTTAGCCAAAAATTGAGGAAAA-ATC
* * * * * * * *
14726 TTTCGAGTCAATTTTTACAAAATTTAAGTCAAAATCGTGTAATGACCATCACAATTTTT-GCCTA
193 TTTCGTGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTAG-CTA
** * * * * *
14790 ACAAA-GCAATGC-AGGCCCTCGGCTCAGTTTTGCATGATTTTTGGCCCCA-AGCCTCCTTGAGA
257 A-AAACGCGTTTCGGGGCCC-CGACTCAGTTTTGCATGATTTTTGG--CCAGAGACTCCTTGAAA
* *
14852 TATCCATATTTAT
318 TATCTATATTCAT
* * ** * * *
14865 CTAATCAAATCTCAGCCAAATTGGATTTAAAAATTTGTTTTTACGAGTATCTGAATCTTGTTTTG
1 CTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCG
* * * * * * *
14930 ATTTAATTAAAAATTAATTTAGAAAAAATAAGAAAAAAGAAATTAAAAGCGTGAAAAGTCATCCA
66 ATTTAATTAGAAATTAATTCAGAAAAAATAAGAAAAACGATATTAAAAGCGTGAAAAGCCCTTCA
* * * * *
14995 ATCTTTTTGGCGTTAAATTATATATATTTAATGAGCATTTTATCCAAAAATTGAGGAAAAAATAT
131 ATCTTTTTGGCGTTGAATTATATAT-TTTTATGAGTATTTTAGCCAAAAATTGAGG-AAAAATCT
** *** * *
15060 TTCGTGTC-ATCTTTTGCAAAATTTTAGCTAAAATCGTGTACTAACCATCGTGGTTTTTGGATAA
194 TTCGTGTCAAT-TTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTAGCTAA
* *
15124 AAACGCGTTTCGGGGCCCCGACTCAATTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATC
258 AAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGC-CAGAGACTCCTTGAAATATC
15189 TATATTCAT
322 TATATTCAT
** * * * * * *
15198 CTAATAAAATGTTAGCCCCATTGCATTTAAGGATTTATTTTTACGAGCATCTGAATCTTGTTTCG
1 CTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCG
* * * * * * *
15263 ATTTATTTAGACATTAATTCAGAGAAAATATGAAGAACGATATTAAAATCGTGAAAAGCCTTTCA
66 ATTTAATTAGAAATTAATTCAGAAAAAATAAGAAAAACGATATTAAAAGCGTGAAAAGCCCTTCA
* * * * * *
15328 ATCTTTTTGGTGTTGAATTATATATTTTTTATGAGTATTGTGGCTAAAATTTGAGGAAATATCTT
131 ATCTTTTTGGCGTTGAATTATATA-TTTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAATCTT
* * * *
15393 TCGGGTCAATTTTTGTAAAATTTTAGCCGAAATCGTGTAATAATCATTTTCCATCACAGTTTTAA
195 TCGTGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACT-A--A----CCATCACAGTTTTTA
* ** * * * *
15458 ACTAAAAAAACGTTTCGGGGCCTCGACTCAGTTTTGCATGATTTTTGGCAAGAAGACTTCTGGAA
253 GCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCCAG-AGACTCCTTGAA
* *
15523 ATATTTATATTTAT
317 ATATCTATATTCAT
* * *
15537 CTAACCAAATCTCAGCCACATTGGATTTAAGCATTTGTTTTTATGACCATCTGAATCATGTTTCG
1 CTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCG
* * ** * *
15602 ATTTTATTTGAAATTAATTCAGAAAAAATTTGAAAAACGATATTAGAAGCGTGAAAAACCCTTCA
66 ATTTAATTAGAAATTAATTCAGAAAAAATAAGAAAAACGATATTAAAAGCGTGAAAAGCCCTTCA
* * *
15667 ATATTTTTGGCTTTGAATTATATATATTTTATGAG-AGTTGTT-GCCCAAAATTGAGGAAAAAT-
131 ATCTTTTTGGCGTTGAATTATATAT-TTTTATGAGTA-TT-TTAGCCAAAAATTGAGGAAAAATC
* * ** * * *
15729 TTTCCG-GATCAATTTTTGCAAAATTTTAGCAGAAATCGTATACTTTCCATCACGGCTTTAAGCT
193 TTT-CGTG-TCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTAGCT
* * * * * * *
15793 AAAAACACGTTTCGGGACACCGACTTAGTTTTGCATGATTTTTTGCACAAAGATTCCTTGAAATA
256 AAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGC-CAGAGACTCCTTGAAATA
15858 T-TAATATTCAT
320 TCT-ATATTCAT
* * * * * * * * *
15869 ATGACCAAATCTCAGCCACTTTGGATTTAAGGACTTGTTTTTAAGAGCATTTGTATGATGTTTCT
1 CTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCG
* ** * *
15934 ATTTAATTCA-AAATTAATTGAGAAAAAAATTGGAAAAACGATATTAAAAGTC-TGAAAAACCTT
66 ATTTAATT-AGAAATTAATTCAG-AAAAAATAAGAAAAACGATATTAAAAG-CGTGAAAAGCCCT
* * * * * * * *
15997 TCAAGCTTTTCGTCTTTGAATTATATATTTTCGATGAGAATTGTGGCCAAAAATTGAGGAAAAAT
128 TCAATCTTTTTGGCGTTGAATTATATATTTT-TATGAGTATTTTAGCCAAAAATTGAGGAAAAAT
* * * * * * * *
16062 ATTCCG-GATCAATTTTTACAAAATTTTAGCTGAACTCGTGTACTATCCATCACTGTTTTAAGCT
192 CTTTCGTG-TCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTAGCT
* * *
16126 AAAAACGCGTTTCGAGGCCCCAACTCAGTTTTGCATGATTTTTGG-CACGAAGACTCCTTGAACT
256 AAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCCA-G-AGACTCCTTGAAAT
16190 ATCTATATTCAT
319 ATCTATATTCAT
* * *
16202 TTAACCAAATCTCAGCCACTTTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCC
1 CTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCG
* * ** * * **
16267 ATTTAATTCGAAATTAATTCTGAAAAAAATTGGAAAAACGATATTAGAAGCCTGAAAAATCCTTC
66 ATTTAATTAGAAATTAATTCAG-AAAAAATAAGAAAAACGATATTAAAAGCGTGAAAAGCCCTTC
* * * * * * *
16332 TATCTTTTTGTCTTTGAATTATATTTTTTTATGA-TAATTGTGGCCAAAAGTTGAGGAAAAATCT
130 AATCTTTTTGGCGTTGAATTATATATTTTTATGAGT-ATTTTAGCCAAAAATTGAGGAAAAATCT
* * ** *
16396 TTCG-GATC-AGTTTAGCAAAATTTTAGCCGAAATCGTGTACTTTCCATCACAGTTTTAAGCTAG
194 TTCGTG-TCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTAGCTA-
* * *
16459 AAAA-GCGTTTCGGGGCCCCTACTCAGTTTTGCATGATTTTTGGCAAGAAGACTTCTTGAAATAT
257 AAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCCAG-AGACTCCTTGAAATAT
* *
16523 TTATATTTAT
321 CTATATTCAT
* *
16533 CTAACCAAATCTCAGCCACATTGGATTTAAGGACTTGTTTTTACGACCAT-TGAATCATGTTTCG
1 CTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCG
* * ** * * *
16597 ATATT-ATTTGAAACTAATTCAGAAAAAATTGGAAAAACGATGTTAGAAGCGTGAAAAACCCTTC
66 AT-TTAATTAGAAATTAATTCAGAAAAAATAAGAAAAACGATATTAAAAGCGTGAAAAGCCCTTC
* ** * * * *
16661 GATCTTTTTGGATTTGAGTTATATATATTTTATGAG-AGTTGTGGCCAAAAATTGAGTAAAAA-C
130 AATCTTTTTGGCGTTGAATTATATAT-TTTTATGAGTA-TTTTAGCCAAAAATTGAGGAAAAATC
* * * ** * * *
16724 TTTCCTGATCAATTTTTGCAAAATTTTAGCAGAAATCGTATACTTTCCATCACGGCTTTAAGCTA
193 TTTCGTG-TCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTAGCTA
* * * * * *
16789 AAAACACGTTTCGGGACACCGACTTAGTTTTGCATGATTTTTTGCACAAAGACTCCTTGAAATAT
257 AAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGC-CAGAGACTCCTTGAAATAT
16854 -TAATATTCAT
321 CT-ATATTCAT
* * * * * *
16864 CTGACCAAATCTCAGCCACTTTGGATTTAAGGACTTGTTTTTACGAGCATTTGTATCATGTTTCT
1 CTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCG
* * ** * *
16929 ATTTAATTCA-AAATTAATTGAAAAAAAATTGGAAAAACGATATTAAAAGCCTGAAAA-CCTTTC
66 ATTTAATT-AGAAATTAATTCAGAAAAAATAAGAAAAACGATATTAAAAGCGTGAAAAGCCCTTC
* * * *
16992 AAGCTTTTCGTCTTTGAATTATATATTTT
130 AATCTTTTTGGCGTTGAATTATATATTTT
17021 CCATGATTTT
Statistics
Matches: 2405, Mismatches: 352, Indels: 170
0.82 0.12 0.06
Matches are distributed among these distances:
329 66 0.03
330 71 0.03
331 345 0.14
332 500 0.21
333 602 0.25
334 27 0.01
335 2 0.00
336 2 0.00
337 124 0.05
338 71 0.03
339 265 0.11
340 2 0.00
341 1 0.00
344 2 0.00
347 1 0.00
348 1 0.00
349 9 0.00
350 82 0.03
351 221 0.09
353 1 0.00
354 4 0.00
355 6 0.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Consensus pattern (330 bp):
CTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCG
ATTTAATTAGAAATTAATTCAGAAAAAATAAGAAAAACGATATTAAAAGCGTGAAAAGCCCTTCA
ATCTTTTTGGCGTTGAATTATATATTTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAATCTTT
CGTGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTAGCTAAAAA
CGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCCAGAGACTCCTTGAAATATCTATA
TTCAT
Found at i:16364 original size:665 final size:661
Alignment explanation
Indices: 13845--17020 Score: 2834
Period size: 665 Copynumber: 4.7 Consensus size: 661
13835 ATTACATCAA
* ** * ** * * * *
13845 CTAACCAAATCTCAGTAACATTGGATTTAATAATTTGTTTTTACGAGCATCTAAATCTTGATTCG
1 CTAACAAAATCTCAGCCACATTGCATTTAAGGACTTGTTTTTACGAGCATCTGAATCATGTTTCG
* * * * * * *
13910 ATTTAATTAGAAATTAATTTAGAAAAAATAAGAAATACGATATTAAAAGCGTGAAAAGCCCTCCA
66 ATTTATTTAGAAATTAATTCAGAAAAAAT-TGAAAAACGATATTAAAAGCGTGAAAAACCTTTCA
* * * * * * *
13975 ATCTTTTTGTCGTTGAATTATATA-TTTTTATAAGTATTTTAGCCAAAAATTGAGCAGAAATCTT
130 ATCTTTTGGT-GTTGAATTATATATTTTTTATGAGAATTGTGGCCAAAAATTGAGGAAAAATCTT
* * * * * *
14039 TCGTG-TCAATTTTTGCACAATTTTAGCCGAAATTGTGTACTAACTAACCATCA-TGTTTTTTTT
194 CCG-GATCAATTTTTACAAAATTTTAGCTGAAATCGTGTACT-A-T--CCATCACAG----TTTT
** * * * * ** * * * *
14102 TGGCTAAAAACGCATTCCGCGGCCCCGGGTCAATTTAGCATAATTTTTGGCGCTG-AGACTCCTT
250 AAGCTAAAAACACGTTTCGAGGCCCCGACTCAGTTTTGCATGATTTTTGGCAC-GAAGACTCCTT
* * **
14166 GAAATATCTATATTCATCTAATAAAATGTTAGCCGCATTACTCAGTAACATTGGATTTAAGAATT
314 GAAATATCTATATTCATC---T---A----A-CC-AAAT-CTCAGCCACATTGGATTTAAGAATT
* * * *
14231 TGTTTTTACGAGCATCTAAATCTTGATTCGATTTAATTAGAAATTAATTT-AGAAAAAATAAGAA
366 TGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATTAGAAATTAATTTGA-AAAAAATTAGAA
* * * * *
14295 ATACGATATTAAAAGCGTGAAAAGCCCTCCAATCTTTTTGTCGTTGAATTATATATTTTTAT-A-
430 AAACGATATTAAAAGCGTGAAAAACCCTTCAATCTTTTTGTCTTTGAATTATATTTTTTTATGAG
* * * * *
14358 AGTATTTTAGCCAAAAATTGAGCAGAAATCTTTCGTGTCAATTTTTGCACAATTTTAGCCGAAAT
495 AGT-TGTTAGCCAAAAATTGAGGAAAAATCTTTCGTGTC-ATTTTTGCAAAATTTTAGCAGAAA-
* * ** * * * **
14423 TGTGTACTAACTAACCATCACGTTTTTTTGGGCTAAAAACGCATTCCGCGGCCCCGGGTCAATTT
557 T-CGTA-T-ACTAACCATCACG--GTTTTAAGCTAAAAACGCGTTTCGGGGCCCCGACTCAATTT
* * * **
14488 AGCATAATTTTTGGCGCTGAGACTTCTTGAAATATCTATATTCAT
617 TGCATGATTTTTGGCACAAAGACTTCTTGAAATATCTATATTCAT
* * * * * * *
14533 CTAATAAAATGTTAGCCGCATTGCATTTAAGGATTTGTTTTTATGAGCATCTGAATCTTGTTTCG
1 CTAACAAAATCTCAGCCACATTGCATTTAAGGACTTGTTTTTACGAGCATCTGAATCATGTTTCG
* * * * *
14598 ATTTAATTAGAAATTAAATCAGAAAAAAAATGAAAAATGATATTAAAAGCGTGAAAAGCAC-TTC
66 ATTTATTTAGAAATTAATTCAG-AAAAAATTGAAAAACGATATTAAAAGCGTGAAAAAC-CTTTC
* ** * * *
14662 AATATCTTTGGTGTTGAATTATATATTTTTTATGACTATTTTAGCTAAAAATTGA-GAAAATATC
129 AATCT-TTTGGTGTTGAATTATATATTTTTTATGAGAATTGTGGCCAAAAATTGAGGAAAA-ATC
* * * * * *
14726 TTTC-GAGTCAATTTTTACAAAATTTAAG-TCAAAATCGTGTAATGA-CCATCACAATTTT-TGC
192 TTCCGGA-TCAATTTTTACAAAATTTTAGCT-GAAATCGTGTACT-ATCCATCACAGTTTTAAG-
* * * * * *
14787 CTAACAAAGCA--ATGC-AGGCCCTCGGCTCAGTTTTGCATGATTTTTGGCCCCAAGCCTCCTTG
253 CTAA-AAA-CACGTTTCGAGGCCC-CGACTCAGTTTTGCATGATTTTTGGCACGAAGACTCCTTG
* * * * * * *
14849 AGATATCCATATTTATCTAATCAAATCTCAGCCAAATTGGATTTAAAAATTTGTTTTTACGAGTA
315 AAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGAATTTGTTTTTACGAGCA
* * * * * *
14914 TCTGAATCTTGTTTTGATTTAATTAAAAATTAATTT-AGAAAAAATAAGAAAAAAGAAATTAAAA
380 TCTGAATCATGTTTCGATTTAATTAGAAATTAATTTGA-AAAAAATTAGAAAAACGATATTAAAA
** * * * * * * * *
14978 GCGTGAAAAGTCATCCAATCTTTTTGGCGTTAAATTATATATATTTAATGAGCA-TT-TTATCCA
444 GCGTGAAAAACCCTTCAATCTTTTTGTCTTTGAATTATAT-TTTTTTATGAG-AGTTGTTAGCCA
* *
15041 AAAATTGAGGAAAAAATATTTCGTGTCATCTTTTGCAAAATTTTAGCTA-AAATCGTGTACTAAC
507 AAAATTGAGG-AAAAATCTTTCGTGTCAT-TTTTGCAAAATTTTAGC-AGAAATCGTATACTAAC
** ** * *
15105 CATCGTGGTTTTTGGATAAAAACGCGTTTCGGGGCCCCGACTCAATTTTGCATGATTTTTGGCGC
569 CATCACGGTTTTAAGCTAAAAACGCGTTTCGGGGCCCCGACTCAATTTTGCATGATTTTTGGCAC
** *
15170 CGAGACTCCTTGAAATATCTATATTCAT
634 AAAGACTTCTTGAAATATCTATATTCAT
* * * * * * *
15198 CTAATAAAATGTTAGCCCCATTGCATTTAAGGATTTATTTTTACGAGCATCTGAATCTTGTTTCG
1 CTAACAAAATCTCAGCCACATTGCATTTAAGGACTTGTTTTTACGAGCATCTGAATCATGTTTCG
* * * * *
15263 ATTTATTTAGACATTAATTCAGAGAAAATATGAAGAACGATATTAAAATCGTGAAAAGCCTTTCA
66 ATTTATTTAGAAATTAATTCAGAAAAAAT-TGAAAAACGATATTAAAAGCGTGAAAAACCTTTCA
* * * *
15328 ATCTTTTTGGTGTTGAATTATATATTTTTTATGAGTATTGTGGCTAAAATTTGAGGAAATATCTT
130 ATC-TTTTGGTGTTGAATTATATATTTTTTATGAGAATTGTGGCCAAAAATTGAGGAAAAATCTT
* * ** * *
15393 TCGGGTCAATTTTTGTAAAATTTTAGCCGAAATCGTGTAATAATCATTTTCCATCACAGTTTTAA
194 CCGGATCAATTTTTACAAAATTTTAGCTGAAATCGTG---T-A-C--TATCCATCACAGTTTTAA
* * * * * * *
15458 ACTAAAAAAACGTTTCGGGGCCTCGACTCAGTTTTGCATGATTTTTGGCAAGAAGACTTCTGGAA
252 GCTAAAAACACGTTTCGAGGCCCCGACTCAGTTTTGCATGATTTTTGGCACGAAGACTCCTTGAA
* * * * *
15523 ATATTTATATTTATCTAACCAAATCTCAGCCACATTGGATTTAAGCATTTGTTTTTATGACCATC
317 ATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGAATTTGTTTTTACGAGCATC
* * * * *
15588 TGAATCATGTTTCGATTTTATTTGAAATTAA-TTCAGAAAAAATTTGAAAAACGATATTAGAAGC
382 TGAATCATGTTTCGATTTAATTAGAAATTAATTTGA-AAAAAATTAGAAAAACGATATTAAAAGC
* * * *
15652 GTGAAAAACCCTTCAATATTTTTGGCTTTGAATTATATATATTTTATGAGAGTTGTT-GCCCAAA
446 GTGAAAAACCCTTCAATCTTTTTGTCTTTGAATTATAT-TTTTTTATGAGAGTTGTTAGCCAAAA
**
15716 ATTGAGGAAAAAT-TTTCCG-GATCAATTTTTGCAAAATTTTAGCAGAAATCGTATACTTTCCAT
510 ATTGAGGAAAAATCTTT-CGTG-TC-ATTTTTGCAAAATTTTAGCAGAAATCGTATACTAACCAT
* * * * * * *
15779 CACGGCTTTAAGCTAAAAACACGTTTCGGGACACCGACTTAGTTTTGCATGATTTTTTGCACAAA
572 CACGGTTTTAAGCTAAAAACGCGTTTCGGGGCCCCGACTCAATTTTGCATGATTTTTGGCACAAA
15844 GA-TTCCTTGAAATAT-TAATATTCAT
637 GACTT-CTTGAAATATCT-ATATTCAT
* * * * * * * * * *
15869 ATGACCAAATCTCAGCCACTTTGGATTTAAGGACTTGTTTTTAAGAGCATTTGTATGATGTTTCT
1 CTAACAAAATCTCAGCCACATTGCATTTAAGGACTTGTTTTTACGAGCATCTGAATCATGTTTCG
* *
15934 ATTTAATTCA-AAATTAATTGAGAAAAAAATTGGAAAAACGATATTAAAAGTC-TGAAAAACCTT
66 ATTT-ATTTAGAAATTAATTCAG-AAAAAATT-GAAAAACGATATTAAAAG-CGTGAAAAACCTT
* * * **
15997 TCAAGCTTTTCGTCTTTGAATTATATATTTTCGATGAGAATTGTGGCCAAAAATTGAGGAAAAAT
127 TCAATCTTTTGGT-GTTGAATTATATATTTTTTATGAGAATTGTGGCCAAAAATTGAGGAAAAAT
* * *
16062 ATTCCGGATCAATTTTTACAAAATTTTAGCTGAACTCGTGTACTATCCATCACTGTTTTAAGCTA
191 CTTCCGGATCAATTTTTACAAAATTTTAGCTGAAATCGTGTACTATCCATCACAGTTTTAAGCTA
* * *
16127 AAAACGCGTTTCGAGGCCCCAACTCAGTTTTGCATGATTTTTGGCACGAAGACTCCTTGAACTAT
256 AAAACACGTTTCGAGGCCCCGACTCAGTTTTGCATGATTTTTGGCACGAAGACTCCTTGAAATAT
* * *
16192 CTATATTCATTTAACCAAATCTCAGCCACTTTGGATTTAAGGATTTGTTTTTACGAGCATCTGAA
321 CTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAA
* * * * *
16257 TCATGTTTCCATTTAATTCGAAATTAATTCTGAAAAAAATTGGAAAAACGATATTAGAAGCCTGA
386 TCATGTTTCGATTTAATTAGAAATTAATT-TGAAAAAAATTAGAAAAACGATATTAAAAGCGTGA
* * * * * *
16322 AAAATCCTTCTATCTTTTTGTCTTTGAATTATATTTTTTTATGATAATTG-TGGCCAAAAGTTGA
450 AAAACCCTTCAATCTTTTTGTCTTTGAATTATATTTTTTTATGAGAGTTGTTAGCCAAAAATTGA
* * * * ** *
16386 GGAAAAATCTTTCG-GATCAGTTTAGCAAAATTTTAGCCGAAATCGTGTACTTTCCATCACAGTT
515 GGAAAAATCTTTCGTG-TCATTTTTGCAAAATTTTAGCAGAAATCGTATACTAACCATCACGGTT
* *
16450 TTAAGCTAGAAAA-GCGTTTCGGGGCCCCTACTCAGTTTTGCATGATTTTTGGCA-AGAAGACTT
579 TTAAGCTA-AAAACGCGTTTCGGGGCCCCGACTCAATTTTGCATGATTTTTGGCACA-AAGACTT
* *
16513 CTTGAAATATTTATATTTAT
642 CTTGAAATATCTATATTCAT
* * *
16533 CTAACCAAATCTCAGCCACATTGGATTTAAGGACTTGTTTTTACGACCAT-TGAATCATGTTTCG
1 CTAACAAAATCTCAGCCACATTGCATTTAAGGACTTGTTTTTACGAGCATCTGAATCATGTTTCG
* * * *
16597 ATATTATTT-GAAACTAATTCAGAAAAAATTGGAAAAACGATGTTAGAAGCGTGAAAAACCCTTC
66 AT-TTATTTAGAAATTAATTCAGAAAAAATT-GAAAAACGATATTAAAAGCGTGAAAAACCTTTC
* * * * *
16661 GATCTTTTTGGAT-TTGAGTTATATATATTTTATGAGAGTTGTGGCCAAAAATTGAGTAAAAA-C
129 AATC-TTTTGG-TGTTGAATTATATATTTTTTATGAGAATTGTGGCCAAAAATTGAGGAAAAATC
* * * * * * *
16724 TTTCCTGATCAATTTTTGCAAAATTTTAGCAGAAATCGTATACTTTCCATCACGGCTTTAAGCTA
192 -TTCCGGATCAATTTTTACAAAATTTTAGCTGAAATCGTGTACTATCCATCACAGTTTTAAGCTA
* * * *
16789 AAAACACGTTTCG-GGACACCGACTTAGTTTTGCATGATTTTTTGCACAAAGACTCCTTGAAATA
256 AAAACACGTTTCGAGG-CCCCGACTCAGTTTTGCATGATTTTTGGCACGAAGACTCCTTGAAATA
* * * * *
16853 T-TAATATTCATCTGACCAAATCTCAGCCACTTTGGATTTAAGGACTTGTTTTTACGAGCATTTG
320 TCT-ATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGAATTTGTTTTTACGAGCATCTG
* * * *
16917 TATCATGTTTCTATTTAATTCA-AAATTAA-TTGAAAAAAAATTGGAAAAACGATATTAAAAGCC
384 AATCATGTTTCGATTTAATT-AGAAATTAATTTG-AAAAAAATTAGAAAAACGATATTAAAAGCG
* * * *
16980 TG-AAAACCTTTCAAGCTTTTCGTCTTTGAATTATATATTTT
447 TGAAAAACCCTTCAATCTTTTTGTCTTTGAATTATATTTTTT
17021 CCATGATTTT
Statistics
Matches: 2092, Mismatches: 325, Indels: 170
0.81 0.13 0.07
Matches are distributed among these distances:
660 35 0.02
661 36 0.02
662 275 0.13
663 32 0.02
664 159 0.08
665 466 0.22
666 70 0.03
667 14 0.01
668 3 0.00
669 131 0.06
670 33 0.02
671 223 0.11
672 338 0.16
673 8 0.00
676 1 0.00
679 1 0.00
681 6 0.00
682 56 0.03
683 3 0.00
684 1 0.00
685 6 0.00
687 1 0.00
688 120 0.06
689 74 0.04
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Consensus pattern (661 bp):
CTAACAAAATCTCAGCCACATTGCATTTAAGGACTTGTTTTTACGAGCATCTGAATCATGTTTCG
ATTTATTTAGAAATTAATTCAGAAAAAATTGAAAAACGATATTAAAAGCGTGAAAAACCTTTCAA
TCTTTTGGTGTTGAATTATATATTTTTTATGAGAATTGTGGCCAAAAATTGAGGAAAAATCTTCC
GGATCAATTTTTACAAAATTTTAGCTGAAATCGTGTACTATCCATCACAGTTTTAAGCTAAAAAC
ACGTTTCGAGGCCCCGACTCAGTTTTGCATGATTTTTGGCACGAAGACTCCTTGAAATATCTATA
TTCATCTAACCAAATCTCAGCCACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCATG
TTTCGATTTAATTAGAAATTAATTTGAAAAAAATTAGAAAAACGATATTAAAAGCGTGAAAAACC
CTTCAATCTTTTTGTCTTTGAATTATATTTTTTTATGAGAGTTGTTAGCCAAAAATTGAGGAAAA
ATCTTTCGTGTCATTTTTGCAAAATTTTAGCAGAAATCGTATACTAACCATCACGGTTTTAAGCT
AAAAACGCGTTTCGGGGCCCCGACTCAATTTTGCATGATTTTTGGCACAAAGACTTCTTGAAATA
TCTATATTCAT
Found at i:17227 original size:216 final size:216
Alignment explanation
Indices: 16815--17237 Score: 509
Period size: 216 Copynumber: 2.0 Consensus size: 216
16805 CACCGACTTA
*
16815 GTTTTGCATGATTTTTTGCACAAAGACTCCTTGAAATATTAATATTCATCTGACCAAATCTCAGC
1 GTTTTGCATGATTTTTTGCACAAAGACTCCTTGAAATATTAATATTCATCTAACCAAATCTCAGC
* ** * *
16880 CACTTTGGATTTAAGGACTTGTTTTTACGAGCATTTGTATCATGTTTCTATTTAATTCAAAATTA
66 CACATTGGATTTAAGGACTTACTTTTACGAGCATCTGAATCATGTTTCTATTTAATTCAAAATTA
* * * *
16945 ATTGAAAAAAAATTGGAAAAACGATATTAAAAGCCTGAAAACCTTTCAAGCTTTTCGTCTTTGAA
131 ATTGAAAAAAAATTGGAAAAAAGATATTAAAAGCCTGAAAACCTTACAAGCTTTTCGGCATTGAA
17010 TTATATATTTTCCATGATTTT
196 TTATATATTTTCCATGATTTT
* * ** *
17031 GTTTTGCATGATTTTTGGTGC-C-GAGACTCCTTGATATATTTTTATTCATCTAATCAAATCTCA
1 GTTTTGCATGATTTTT--TGCACAAAGACTCCTTGAAATATTAATATTCATCTAACCAAATCTCA
* * * * *
17094 GTCACATTGGATTTAAGGATTTACTTTTATGTGCATCTGAATCTTGTTTC-ATTTAATT-AGAAA
64 GCCACATTGGATTTAAGGACTTACTTTTACGAGCATCTGAATCATGTTTCTATTTAATTCA-AAA
* * * * *
17157 TTAATT-ATGAAAAAATAT-GAAAAAAGATATTAAAAGCGTGACAAGTCC-TACAATCTTTTTGG
128 TTAATTGA-AAAAAAAT-TGGAAAAAAGATATTAAAAGCCTGA-AA-ACCTTACAAGCTTTTCGG
17219 CATTGAATTATATATTTTC
189 CATTGAATTATATATTTTC
17238 TATGGGTATT
Statistics
Matches: 175, Mismatches: 25, Indels: 14
0.82 0.12 0.07
Matches are distributed among these distances:
214 2 0.01
215 45 0.26
216 122 0.70
217 3 0.02
218 3 0.02
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.40
Consensus pattern (216 bp):
GTTTTGCATGATTTTTTGCACAAAGACTCCTTGAAATATTAATATTCATCTAACCAAATCTCAGC
CACATTGGATTTAAGGACTTACTTTTACGAGCATCTGAATCATGTTTCTATTTAATTCAAAATTA
ATTGAAAAAAAATTGGAAAAAAGATATTAAAAGCCTGAAAACCTTACAAGCTTTTCGGCATTGAA
TTATATATTTTCCATGATTTT
Found at i:17644 original size:2 final size:2
Alignment explanation
Indices: 17637--17665 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
17627 AAATTACTAG
17637 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17666 TGTTTTCATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20892 original size:26 final size:25
Alignment explanation
Indices: 20857--20907 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 25
20847 GATTAGCTCA
20857 ATTAAACTATTCATTGCTTTTAATT
1 ATTAAACTATTCATTGCTTTTAATT
20882 ATTAGAACTATTCATTGCTTTTAATT
1 ATTA-AACTATTCATTGCTTTTAATT
20908 GGTATTGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 4 0.16
26 21 0.84
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.51
Consensus pattern (25 bp):
ATTAAACTATTCATTGCTTTTAATT
Found at i:22429 original size:15 final size:16
Alignment explanation
Indices: 22409--22438 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
22399 CATCATAATA
22409 AATCC-TTAAAAAATG
1 AATCCTTTAAAAAATG
22424 AATCCTTTAAAAAAT
1 AATCCTTTAAAAAAT
22439 ACATTCTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.53, C:0.13, G:0.03, T:0.30
Consensus pattern (16 bp):
AATCCTTTAAAAAATG
Done.