Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019404.1 Corchorus olitorius cultivar O-4 contig19437, 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: 42456
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:5494 original size:331 final size:328
Alignment explanation
Indices: 4772--5960 Score: 1206
Period size: 336 Copynumber: 3.6 Consensus size: 328
4762 TCGCCTAACC
* * * * *
4772 AAATCTTAGCAACATTGGATTTAAGAATCTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAA
1 AAATCTTAGCCACATTGGATTTAAAAATTTGTTTTTACAAGCATCTAAATCTTGTTTCGATTTAA
* * * **
4837 TTAGAAATTAATTTAGAAAAAATAAGAAATACGATATTAAAAGCGTAAAAAGCCC-TCTAATCTT
66 TTAGAAATTAATTAAG-AAAAATATGAAAAACGATATTAAAAGCGCCAAAAGCCCTTC-AATCTT
*
4901 TTTGCCGTTGAATTATATA-TTTTTATGAGTATTTT-AGCCAAAAATTGAGGAGAA-ATATTTCG
129 TTTGCCATTGAATTATATATTTTTTATGAGTATTTTGA-CCAAAAATTGAGGA-AATATATTTCG
* * * * *
4963 TGTCAATTTTTGTAAAATTTTAGTCGAAATCGTGTACTAACAAACCATCACGGTTTTTTTGCTAA
192 GGTCAATTTTTGTAAAATTTTAGCCGAAATCGTG---TAA-TAACCATCAC-G-TTTTTGGATAA
* * *
5028 AAACGCGTTCCGAGGA-ACCGGTTCAATTTTGCATGATTTTTGGC-TCCGAGACTACTTAAAATA
251 AAACGCGTT-TG-GGACACCGGCTCAATTTTGCATGATTTTTGGCGT-C-AGACTCCTTAAAATA
*
5091 TCTATATTCATCTAATC
312 TCTATATTCATCTAATA
* * * * **
5108 AAATCTCACCCAAATTAGATTTAAGGATTTGTTTTTACGAA-CATCTAAATCTTGTTTCGATTTA
1 AAATCTTAGCCACATTGGATTTAAAAATTTGTTTTTAC-AAGCATCTAAATCTTGTTTCGATTTA
* * * * *
5172 CTTAAAAATTAATT-TGGAAAATAGGAAAAACGATATTAGAAA-CGCCAAAAGCCCTTCAATCTT
65 ATTAGAAATTAATTAAGAAAAATATGAAAAACGATATTA-AAAGCGCCAAAAGCCCTTCAATCTT
* * * ** *
5235 TTTGGCGTTGAGTTATATATTTTTTATGAGTATTTTAGAAAAAAAATTGAGGAAATATCTTTCGG
129 TTTGCCATTGAATTATATATTTTTTATGAGTATTTT-GACCAAAAATTGAGGAAATATATTTCGG
**
5300 GTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAATAACCATCACTGTTTTTGGATTAAAAA-G
193 GTCAATTTTTGTAAAATTTTAGCCGAAATCGTGTAATAACCATCAC-GTTTTTGGA-TAAAAACG
* * * * *
5364 CATTATGGGACTCCGGCTCAGTTTTGCATGATTTTTGGCGTCAAGACTCCTTGAGATATCTATAT
256 CGTT-TGGGACACCGGCTCAATTTTGCATGATTTTTGGCGTC-AGACTCCTTAAAATATCTATAT
*
5429 TCATCTAATT
319 TCATCTAATA
*
5439 GAATCTTAGCCACATTGGATTTAAAAATTTGTTTTTACAAGCATCTAAATCTTGTTTCGATTTAA
1 AAATCTTAGCCACATTGGATTTAAAAATTTGTTTTTACAAGCATCTAAATCTTGTTTCGATTTAA
** * *
5504 TTAGAAATTAATTAAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGACCTCCAATCTTTT
66 TTAGAAATTAATTAAGAAAAATATGAAAAACGATATTAAAAGCGCCAAAAGCCCTTCAATCTTTT
* * * *
5569 TGCCATTAAATTATATATATATATATGTATTATGAGTATTTT-ATCAAACATTGAGG-AATAATT
131 TGCCATT-GA--AT-TATATAT-T-T-T-TTATGAGTATTTTGACCAAAAATTGAGGAAAT-ATA
* * * * *
5632 TTTCGGGTCATTTTTTTGTAAAATTTTAGCCAAAATTGTGTACTAACCATCACGGTTTTGAGATA
187 TTTCGGGTCA-ATTTTTGTAAAATTTTAGCCGAAATCGTGTAATAACCATCACGTTTTTG-GATA
* * * * *
5697 AAAACGCGTTTCGGGGCACCAGCTCAATTTTGCATCATTTTTGGCG-CCGACGGTCCTTCAAATA
250 AAAACGCGTTT-GGGACACCGGCTCAATTTTGCATGATTTTTGGCGTCAGAC--TCCTTAAAATA
5761 TCTATATTCATCTAATA
312 TCTATATTCATCTAATA
* ** * * ** *
5778 AAATTTTAGCCACATTTCATTT-AATA-TT-TTTTTACGAGCATCTTGATCATGTTTCGATTTAA
1 AAATCTTAGCCACATTGGATTTAAAAATTTGTTTTTACAAGCATCTAAATCTTGTTTCGATTTAA
* *
5840 TTAGAAATTAATTCAAAAAAAATATGAAAAACGATATTAAAAGCG-CAAAATCCCTTCAATCTTT
66 TTAGAAATTAATT-AAGAAAAATATGAAAAACGATATTAAAAGCGCCAAAAGCCCTTCAATCTTT
* * * * * *
5904 TTGGCATTGAATTAATATATTATTTATAAGTATTATGGCTAAAAATTGAGGAAATAT
130 TTGCCATTGAATT-ATATATTTTTTATGAGTATTTTGACCAAAAATTGAGGAAATAT
5961 TAGCCGAAAT
Statistics
Matches: 716, Mismatches: 105, Indels: 70
0.80 0.12 0.08
Matches are distributed among these distances:
329 11 0.02
330 18 0.03
331 137 0.19
332 64 0.09
333 12 0.02
334 52 0.07
335 26 0.04
336 186 0.26
337 41 0.06
338 41 0.06
339 115 0.16
340 13 0.02
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (328 bp):
AAATCTTAGCCACATTGGATTTAAAAATTTGTTTTTACAAGCATCTAAATCTTGTTTCGATTTAA
TTAGAAATTAATTAAGAAAAATATGAAAAACGATATTAAAAGCGCCAAAAGCCCTTCAATCTTTT
TGCCATTGAATTATATATTTTTTATGAGTATTTTGACCAAAAATTGAGGAAATATATTTCGGGTC
AATTTTTGTAAAATTTTAGCCGAAATCGTGTAATAACCATCACGTTTTTGGATAAAAACGCGTTT
GGGACACCGGCTCAATTTTGCATGATTTTTGGCGTCAGACTCCTTAAAATATCTATATTCATCTA
ATA
Found at i:6918 original size:337 final size:330
Alignment explanation
Indices: 6285--7761 Score: 1358
Period size: 337 Copynumber: 4.4 Consensus size: 330
6275 TTTTTTTTTC
* * *
6285 CATCTAATAAAATCTTAGCCACATTGCATTTAAGATTT-TTTTTACAAGCATCTG-ATCATATTT
1 CATCTAATCAAATCTTAGCCACATTGCATTTAAGATTTGTTTTTACAAGCATCTGAATCTTGTTT
* * ** *
6348 CGATTTAATTAGACATTATTTAAGAAAAATATGAAAAACGATATGT-AAAGCGTGAAAAGTCTTC
66 CGATTTAATTAGAAATTAATTCGGAAAAATATGAAAAACGATAT-TAAAAGCGTGAAAAGTCCTC
* * * ** *
6412 CAACATTTTTGGCGTTAAATTATATATATTTCATGAGTATTTCAGGCAAGTATTGAGGAAAAAT-
130 CAATATTTTTGGCGTTAAATTATATATATTTTATGAGTATTTTAGGCAAAAAATGAGGAAAAATA
* * * ** *
6476 TTTTCTGGTCATTTTTTTTTTGCAAAATTTTAGATGAAATCGTGTACTAACCATCACGGTTTTTT
195 TTTT-AGATCA----ATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTG
* ** * * * * * **
6541 GCTAAAAAAATGCGTTTTAGGG-CACCGGCTCTGTTTTGCATGATTTTTGGCGTCGAGGCTCCAA
255 GCTAAAAACA--CG-TTCCGGGACCCCGGTTCAGTTTTGCATGATTTTTGGCGTCAAGACTCCTT
*
6605 GAAATAT-AAGTATT
317 GAAATATCTA-TATT
* *
6619 CATCTAATCAAATCTTTA-CCACATTGCATTTGAAGATTT-TATTTTACGAGCATATGAATCTTG
1 CATCTAATCAAATC-TTAGCCACATTGCATTT-AAGATTTGT-TTTTACAAGCATCTGAATCTTG
*
6682 TTTCGATTTAATTAGAAATTAATTCGGAAAAATATGAAAAACGATATTAAAACCGTGAAAAGTCC
63 TTTCGATTTAATTAGAAATTAATTCGGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCC
* * * * * * *
6747 ACCAATATTTTTCGAGTTGAATTACATATATTTTATGAGTATTTTAGACAAAAAATGAGGAAAAC
128 TCCAATATTTTTGGCGTTAAATTATATATATTTTATGAGTATTTTAGGCAAAAAATGAGGAAAAA
* * * *
6812 TATTTCT-GATCAATTTTTGCAAAATATTAGTCGAAATCGTGTACGTTAGTCGAAATCACGGTTT
193 TATTT-TAGATCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAC--TA-AC--CATCACGGTTT
* * * * *
6876 TTGGCTAAAAACACGTTCCGGGACCTCGGTTCAGTGTTTGCATGATTTTTTGTGACAAAACTCCT
252 TTGGCTAAAAACACGTTCCGGGACCCCGGTTCAGT-TTTGCATGATTTTTGGCGTCAAGACTCCT
6941 TGAAATATCTATATT
316 TGAAATATCTATATT
* * * * * * *** **
6956 AATCTAACCAAATCTCATCCACAATGGATTTAAGGATTTG-TAAAACAAGCATCTGAATAATG-T
1 CATCTAATCAAATCTTAGCCACATTGCATTTAA-GATTTGTTTTTACAAGCATCTGAATCTTGTT
* * * * * * *
7019 TCGATTTAATTAAAAATTAATTCGGAAAATAATAGGAAAAACGGTATTAGAAGCATGAAAACTCA
65 TCGATTTAATTAGAAATTAATTCGG-AAA-AATATGAAAAACGATATTAAAAGCGTGAAAAGTCC
** * * * * *
7084 TTTAATTTTTTTGGCGTTGACTTATATA-ATTTTCATGAGTATTGT-GGCAAAAAATTGAGG--T
128 TCCAATATTTTTGGCGTTAAATTATATATATTTT-ATGAGTATTTTAGGCAAAAAA-TGAGGAAA
* * *
7145 AATATCTTTAGAGTCAATTTTTGCAAAATTCTAGCCGAAATCGTGTAATAATCATCACGGTTTTT
191 AATAT-TTTAGA-TCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTT
* ** * * ** * * * *
7210 CGCTAAAAACGGGTTCTGGGGCCCCGAATAAGTTTTGCATGATTTTTTGTGTCAAGACTCTTTGA
254 GGCTAAAAACACGTTCCGGGACCCCGGTTCAGTTTTGCATGATTTTTGGCGTCAAGACTCCTTGA
** *
7275 GTTATCCATATT
319 AATATCTATATT
* ** * * *
7287 CAT-TAAATCAAATCTCAGTTACATTGGATTTGAGAATTTGTTTTTACGAGCATCTGAATCTTGT
1 CATCT-AATCAAATCTTAGCCACATTGCATTTAAG-ATTTGTTTTTACAAGCATCTGAATCTTGT
* * *
7351 TTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAATGATATTTAAAA-CGTGAAAGGTCC
64 TTCGATTTAATTAGAAATTAATTCGGAAAAATATGAAAAACGATA-TTAAAAGCGTGAAAAGTCC
* * ** * * * * *
7415 TCAAATCTTTTTGTTGTTAAATTATTTATACTTTATGAGTA-TTTATGCCAAGAATTGACGGAAA
128 TCCAATATTTTTGGCGTTAAATTATATATATTTTATGAGTATTTTA-GGCAAAAAATGA-GGAAA
* * * *
7479 TAAAATTTTGGGTCATTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGG-TTTTG
191 -AATATTTTAGATCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTG
* * * *
7543 GCTAAAAACGCGTTTCGGGACCCCGACTT-AGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGA
255 GCTAAAAACACGTTCCGGGACCCCG-GTTCAGTTTTGCATGATTTTTGGCGTCAAGACTCCTTGA
*
7607 AATATCTATACT
319 AATATCTATATT
* * *
7619 CATCTTATCAAATTTTTGCCACATTG-ATTTTAAGGATTTGTTTTTACAAGCATCTGAATCTTGT
1 CATCTAATCAAATCTTAGCCACATTGCA-TTTAA-GATTTGTTTTTACAAGCATCTGAATCTTGT
* *
7683 TTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAGAGTCC
64 TTCGATTTAATTAGAAATTAATTC-GGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCC
7748 TCCAATATTTTTGG
128 TCCAATATTTTTGG
7762 TATTTAATTT
Statistics
Matches: 923, Mismatches: 177, Indels: 87
0.78 0.15 0.07
Matches are distributed among these distances:
330 4 0.00
331 119 0.13
332 216 0.23
333 137 0.15
334 30 0.03
335 54 0.06
336 64 0.07
337 273 0.30
338 25 0.03
339 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.37
Consensus pattern (330 bp):
CATCTAATCAAATCTTAGCCACATTGCATTTAAGATTTGTTTTTACAAGCATCTGAATCTTGTTT
CGATTTAATTAGAAATTAATTCGGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCC
AATATTTTTGGCGTTAAATTATATATATTTTATGAGTATTTTAGGCAAAAAATGAGGAAAAATAT
TTTAGATCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAA
AACACGTTCCGGGACCCCGGTTCAGTTTTGCATGATTTTTGGCGTCAAGACTCCTTGAAATATCT
ATATT
Found at i:8125 original size:281 final size:280
Alignment explanation
Indices: 7600--8137 Score: 648
Period size: 281 Copynumber: 1.9 Consensus size: 280
7590 GCGCCAAGAC
* * * * * *
7600 TCCTTGAAATATCTATACTCATCTTATCAAATTTTTGCCACATTGATTTTAAGGATTTGTTTTTA
1 TCCTTGAAATATCTATACTCATCTAACCAAATCTTAGCCACATTGATTTTAAGAATTTGTCTTTA
* * * * *
7665 CAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATAT
66 CAAGAATCTGAATCATGTTTCAATTTAATTAGAAATTAATTCAAAAAAAATAGGAAAAACGATAT
*
7730 TAAAAGCGTGAAGAGTCCTCCAATATTTTTGGTATTTAATTTTATATATATATATTCTATGAGCA
131 TAAAAGCGTGAAGAGTCCTCCAATATTTTTGGTATTGAA-TTTATATATATATATTCTATGAGCA
* *
7795 TTGTGGCTAAAAATTGAGGGAAAATATTTCGGGTTTGCAAAATTTTAGCCGAAATCGTGTACCAT
195 TTGTCGCTAAAAATTGAGGAAAAATATTTCGGGTTTGCAAAATTTTAGCCGAAATCGTGTACCAT
7860 CATGGTTTTGGTGGTCAACAT
260 CATGGTTTTGGTGGTCAACAT
* *
7881 TCCTTGAAATATCTATATTTATCTAACCAAATCTTAGCCACATTGGA-TTTAAGAATTTGTCTTT
1 TCCTTGAAATATCTATACTCATCTAACCAAATCTTAGCCACATT-GATTTTAAGAATTTGTCTTT
* *
7945 A-AGAGAATTTGAATCATGTTTCAATTTAATTAGAAATTAATTTGAAAAAAAATAGGAAAAACGA
65 ACA-AGAATCTGAATCATGTTTCAATTTAATTAGAAATTAA-TTCAAAAAAAATAGGAAAAACGA
* * * *
8009 TATTAGAAGCGTG-AGAAG-CCTTTCAATCTTTTTGGTGTTGAA-TTATATAT-T-T-TT-TATG
128 TATTAAAAGCGTGAAG-AGTCC-TCCAATATTTTTGGTATTGAATTTATATATATATATTCTATG
* * * *
8067 AGTATTTTCGCTAGAAATCT-AGGAAAAATCTTTCGGGTCAATTTTTGCAAAA-TTTAGCCGAAA
191 AGCATTGTCGCTAAAAAT-TGAGGAAAAATATTTCGGG------TTTGCAAAATTTTAGCCGAAA
8130 TCGTGTAC
249 TCGTGTAC
8138 TAACCATCAC
Statistics
Matches: 219, Mismatches: 26, Indels: 24
0.81 0.10 0.09
Matches are distributed among these distances:
276 33 0.15
277 3 0.01
278 1 0.00
279 1 0.00
280 9 0.04
281 110 0.50
282 62 0.28
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.38
Consensus pattern (280 bp):
TCCTTGAAATATCTATACTCATCTAACCAAATCTTAGCCACATTGATTTTAAGAATTTGTCTTTA
CAAGAATCTGAATCATGTTTCAATTTAATTAGAAATTAATTCAAAAAAAATAGGAAAAACGATAT
TAAAAGCGTGAAGAGTCCTCCAATATTTTTGGTATTGAATTTATATATATATATTCTATGAGCAT
TGTCGCTAAAAATTGAGGAAAAATATTTCGGGTTTGCAAAATTTTAGCCGAAATCGTGTACCATC
ATGGTTTTGGTGGTCAACAT
Found at i:8463 original size:612 final size:611
Alignment explanation
Indices: 7307--8425 Score: 1448
Period size: 612 Copynumber: 1.8 Consensus size: 611
7297 AATCTCAGTT
* * * * * *
7307 ACATTGGATTTGAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
1 ACATTGGATTTAAGAATTTGTCTTTAAGAGAATCTGAATCATGTTTCAATTTAATTAGAAATTAA
* * * * *
7372 TTCAGAAAAATATGAAAAATGATATTTAAAACGTGAAAGGTCCTCAAATCTTTTTGTTGTTAAAT
66 TTAAAAAAAATAGGAAAAACGATATTTAAAACGTGAAAGGTCCTCAAATCTTTTTGGTGTTAAAT
* * *
7437 TATTTATACTTTATGAGTATTTATGCCAAGAATTGACGGAAATAAAATTTTGGGTCATTTTTTGC
131 TATATATACTTTATGAGTATTTATGCCAAGAATTGACGGAAATAAAATTTCGGGTCAATTTTTGC
* *
7502 AAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTGGCTAAAAACGCGTTTCGGGACCCC
196 AAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTGGCTAAAAACACGTTCCGGGACCCC
* * ** * *
7567 GACTTAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATACTCATCTTATCAAAT
261 GACTCAATTTTGCATGATTTTTGAAGCCAAGACTCCTTGAAATATCTATACTCATCTAACCAAAT
* ** *
7632 TTTTGCCACATTGATTTTAAGGATTTGTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAG
326 CTCAGCCACATTGATTTTAAGGATTTGTCTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAG
* * * * *
7697 AAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAGAGTCCTCCAATATTTTTGG
391 AAATTAATTCAGAAAAAATAGGAAAAACAATATTAAAAGCGTGAAAAGCCCTCCAATATTTTTGA
** * *
7762 TATTTAATTTTATATATATATATTCTATGAGCATTGTGGCTAAAAATTGAGGGAAAATATTTCGG
456 TATCGAA-TTTATATATATATATTCTATGAGCATTGTAGCCAAAAATTGA-GGAAAATATTTCGG
*
7827 GTTTGCAAAATTTTAGCCGAAATCGTGTACCATCATGGTTTTGGTGGTCAACATTCCTTGAAATA
519 GTTTGCAAAATTTTAGCCGAAATCGCGTACCATCATGGTTTTGGTGGTCAACATTCCTTGAAATA
7892 TCTATATTTATCTAACCAAATCTTAGCC
584 TCTATATTTATCTAACCAAATCTTAGCC
*
7920 ACATTGGATTTAAGAATTTGTCTTTAAGAGAATTTGAATCATGTTTCAATTTAATTAGAAATTAA
1 ACATTGGATTTAAGAATTTGTCTTTAAGAGAATCTGAATCATGTTTCAATTTAATTAGAAATTAA
*
7985 TTTGAAAAAAAATAGGAAAAACGATA-TTAGAAGCGTGAGAA-G-CCTTTC-AATCTTTTTGGTG
66 -TT-AAAAAAAATAGGAAAAACGATATTTA-AAACGTGA-AAGGTCC--TCAAATCTTTTTGGTG
* ** * **
8046 TTGAATTATATATTTTTTATGAGTATTT-T-CGCTAGAAATCT-A-GGAAA-AATCTTTCGGGTC
125 TTAAATTATATATACTTTATGAGTATTTATGC-CAAG-AAT-TGACGGAAATAAAATTTCGGGTC
8106 AATTTTTGCAAAA-TTTAGCCGAAATCGTGTACTAACCATCACGGTTTTCGGCTAAAAACACGTT
187 AATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTT-GGCTAAAAACACGTT
* * * *
8170 CCGGG-GCCCGGCTCAATTTTGCATGATTTTTTAAGCCAAGACTCCTTGAAATATCTATATTCAT
251 CCGGGACCCCGACTCAATTTTGCATGATTTTTGAAGCCAAGACTCCTTGAAATATCTATACTCAT
*
8234 CTAACCAAATCTCAGCCACATTAGA-TTTAAGGATTTGTCTTTACGAGCATCTGAATCTTGTTTC
316 CTAACCAAATCTCAGCCACATT-GATTTTAAGGATTTGTCTTTACAAGCATCTGAATCTTGTTTC
* * * * * *
8298 GATTTAATTAGAAATTAATTCGGAAAAAAATAGGAAAAATAATATTAGAAGTGTTAAAAGCCCTT
380 GATTTAATTAGAAATTAATTCAG-AAAAAATAGGAAAAACAATATTAAAAGCGTGAAAAGCCCTC
* * * *
8363 CAAT-TTTTTTATATCGAA-TTATATAT-T-T-TT-TATGAGTATTTTAGCCCAAAATTGA-GAA
444 CAATATTTTTGATATCGAATTTATATATATATATTCTATGAGCATTGTAGCCAAAAATTGAGGAA
8421 AATAT
509 AATAT
8426 CTTTCTGGTC
Statistics
Matches: 436, Mismatches: 58, Indels: 33
0.83 0.11 0.06
Matches are distributed among these distances:
604 8 0.02
606 20 0.05
607 2 0.00
608 1 0.00
609 1 0.00
610 8 0.02
612 172 0.39
613 137 0.31
614 16 0.04
615 66 0.15
616 5 0.01
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (611 bp):
ACATTGGATTTAAGAATTTGTCTTTAAGAGAATCTGAATCATGTTTCAATTTAATTAGAAATTAA
TTAAAAAAAATAGGAAAAACGATATTTAAAACGTGAAAGGTCCTCAAATCTTTTTGGTGTTAAAT
TATATATACTTTATGAGTATTTATGCCAAGAATTGACGGAAATAAAATTTCGGGTCAATTTTTGC
AAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTGGCTAAAAACACGTTCCGGGACCCC
GACTCAATTTTGCATGATTTTTGAAGCCAAGACTCCTTGAAATATCTATACTCATCTAACCAAAT
CTCAGCCACATTGATTTTAAGGATTTGTCTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAG
AAATTAATTCAGAAAAAATAGGAAAAACAATATTAAAAGCGTGAAAAGCCCTCCAATATTTTTGA
TATCGAATTTATATATATATATTCTATGAGCATTGTAGCCAAAAATTGAGGAAAATATTTCGGGT
TTGCAAAATTTTAGCCGAAATCGCGTACCATCATGGTTTTGGTGGTCAACATTCCTTGAAATATC
TATATTTATCTAACCAAATCTTAGCC
Found at i:8493 original size:331 final size:331
Alignment explanation
Indices: 7881--8702 Score: 1059
Period size: 331 Copynumber: 2.5 Consensus size: 331
7871 TGGTCAACAT
* * *
7881 TCCTTGAAATATCTATATTTATCTAACCAAATCTTAGCCACATTGGATTTAAGAATTTGTCTTTA
1 TCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTCTTTA
* * * * * * *
7946 AGAGAATTTGAATCATGTTTCAATTTAATTAGAAATTAATTTGAAAAAAAATAGGAAAAACGATA
66 AGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATAGGAAAAACAATA
* * * ** * * *
8011 TTAGAAGCGTGAGAAGCCTTTCAATCTTTTTGGTGTTGAATTATATATTTTTTATGAGTATTTTC
131 TTAGAAGTGTGAAAAGCCCTTCAAT-TTTTTTATATCGAATTATATATTTTTTATGAGTATTTTA
* *
8076 GCTAGAAATCTAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTAGCCGAAATCGTGTACTAA
195 GCCAGAAATCTAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTAGCCGAAATCGCGTACTAA
* * * *
8141 CCATCACGGTTTTCGGCTAAAAACACGTTCCGGGGCC-CGGCTCAATTTTGCATGATTTTTTAAG
260 CCATCACGCTTTTCGGCTAAAAACACGTTACAGGGCCACGGCTCAATTTTGCATGATTTTTGAAG
8205 CCAAGAC
325 CCAAGAC
*
8212 TCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTAGATTTAAGGATTTGTCTTTA
1 TCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTCTTTA
* *
8277 CGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATAGGAAAAATAATA
66 AGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATAGGAAAAACAATA
*
8342 TTAGAAGTGTTAAAAGCCCTTCAATTTTTTTATATCGAATTATATATTTTTTATGAGTATTTTAG
131 TTAGAAGTGTGAAAAGCCCTTCAATTTTTTTATATCGAATTATATATTTTTTATGAGTATTTTAG
* *
8407 CCCA-AAAT-T-GAGAAAATATCTTTCTGGTCAATTTTTTCAAAATTTTAGCCGAAATCGCGTAC
196 -CCAGAAATCTAG-GAAAA-ATCTTTCGGGTCAATTTTTGCAAAA-TTTAGCCGAAATCGCGTAC
* * **
8469 TAACCATCACAGCTTTT-TGCTAAAAACATGTTACAGGGCCACGGCTCTGTTTTGCATGATTTTT
257 TAACCATCAC-GCTTTTCGGCTAAAAACACGTTACAGGGCCACGGCTCAATTTTGCATGATTTTT
** *
8533 GGTGCCGAGAC
321 GAAGCCAAGAC
* * * *
8544 TCCTTGAAATATC-ATTATTCA-CATAATCAAATTTCAGCCACATTGGATTTAAGGATTTATTTT
1 TCCTTGAAATATCTA-TATTCATC-TAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTCTT
* * * * *
8607 TATGTGCATCTGAATCTTGTTTCGATTTAATTAAAAATTAATTCAG-AAAAAATATG-AAAACAA
64 TAAGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATAGGAAAAACAA
* * * *
8670 TATTAAAAGTGTGAAAAGTCCTTTAATCTTTTT
129 TATTAGAAGTGTGAAAAGCCCTTCAATTTTTTT
8703 GGTGTTGAAT
Statistics
Matches: 430, Mismatches: 53, Indels: 17
0.86 0.11 0.03
Matches are distributed among these distances:
328 1 0.00
329 6 0.01
330 96 0.22
331 198 0.46
332 129 0.30
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (331 bp):
TCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTCTTTA
AGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATAGGAAAAACAATA
TTAGAAGTGTGAAAAGCCCTTCAATTTTTTTATATCGAATTATATATTTTTTATGAGTATTTTAG
CCAGAAATCTAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTAGCCGAAATCGCGTACTAAC
CATCACGCTTTTCGGCTAAAAACACGTTACAGGGCCACGGCTCAATTTTGCATGATTTTTGAAGC
CAAGAC
Found at i:27186 original size:2 final size:2
Alignment explanation
Indices: 27179--27214 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
27169 AGGTTAAAAG
* *
27179 GA GA GA GA GA GA AA GA GA GA GA GA AA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
27215 ATAGAAACAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (2 bp):
GA
Found at i:27197 original size:12 final size:12
Alignment explanation
Indices: 27180--27215 Score: 72
Period size: 12 Copynumber: 3.0 Consensus size: 12
27170 GGTTAAAAGG
27180 AGAGAGAGAGAA
1 AGAGAGAGAGAA
27192 AGAGAGAGAGAA
1 AGAGAGAGAGAA
27204 AGAGAGAGAGAA
1 AGAGAGAGAGAA
27216 TAGAAACAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (12 bp):
AGAGAGAGAGAA
Found at i:38783 original size:17 final size:18
Alignment explanation
Indices: 38746--38784 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
38736 GGGAGTAAAC
38746 AAAAGCTTCATATTTTAA
1 AAAAGCTTCATATTTTAA
38764 AAAAGCTTCATATTTTAA
1 AAAAGCTTCATATTTTAA
38782 AAA
1 AAA
38785 TACTAAACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.49, C:0.10, G:0.05, T:0.36
Consensus pattern (18 bp):
AAAAGCTTCATATTTTAA
Found at i:39180 original size:13 final size:13
Alignment explanation
Indices: 39147--39173 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
39137 CTGCATAAAA
39147 TAATTAATAGTAT
1 TAATTAATAGTAT
39160 TAATTAATAGTAT
1 TAATTAATAGTAT
39173 T
1 T
39174 GCATAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (13 bp):
TAATTAATAGTAT
Found at i:42425 original size:2 final size:2
Alignment explanation
Indices: 42418--42456 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
42408 GAAATGTACA
42418 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.