Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016355.1 Corchorus olitorius cultivar O-4 contig16388, 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: 7364
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33
Found at i:1130 original size:340 final size:339
Alignment explanation
Indices: 5--2664 Score: 2238
Period size: 340 Copynumber: 7.8 Consensus size: 339
1 TTTC
* * *
5 TTTTGCAAAATTTTAGCCGTAAATCGTGTACGT---TATCAC-GATTTTTGTCTAAAAATGCGTT
1 TTTTGCAAAATTTTAGCCG-AAATCGTGTAC-TAACCATCACGGTTTTTTGGCTAAAAATGCGTT
* * *
66 TCGGGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTTCT-GAAAATATCTATATTCA
64 TCGGGGCCATGGCTCAGTTTTGCATGATTTTTGGCAGAATGACTTCTCG-AAATATCTATATTCA
*
130 TCTAATCAAATCTCTCAGCCACAATGCATTTACGGATTTATTTTTACAAGTATCTGAACCTTGTT
128 TCTAATCAAATCTCTCAGCCACAATGCATTTACGGATTTATTTTTACAAGTATCTGAATCTTGTT
* * * * * *
195 TCGATTTATTTATAAATAAATTCAGATAAAAATTGGAAAAACGATATTAAAAGTGTGAAAAACCC
193 TCGATTTAATTAGAAATAAATTCAGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCC
*
260 TAAAATAGTTTTGGCGTTGAATTATATGATTTTTCTGAGTATTGAGGCAAAAAATTGGGGAAAAA
258 TAAAATAGTTTTGGCGTTGAATTATATGATTTTTCTGAGTATTGTGGCAAAAAATTGGGGAAAAA
* *
325 CTTTTCGAATAAG-TTT
323 CTTTTCGGATCAGTTTT
* *
341 TTTTGCAAAATTTTAGCCGAAATCGTGTACTAAACATCACGGTTTTTTGGCTAAAAACGCGTTTC
1 TTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTGGCTAAAAATGCGTTTC
*
406 GGGGGCC-TGACTCAGTTTTGCATGATTTTTGGCAGAAAT-ACTTCTCGAAATATCTATATTCAT
66 -GGGGCCATGGCTCAGTTTTGCATGATTTTTGGCAG-AATGACTTCTCGAAATATCTATATTCAT
* * * *
469 TTAATCAAATCCCTCAGCCATAATGCATTTACGAATTTATTTTTACAAGTATCTGAATCTTGTTT
129 CTAATCAAATCTCTCAGCCACAATGCATTTACGGATTTATTTTTACAAGTATCTGAATCTTGTTT
* * * * **
534 CGATTTAAATAGAAAAAAAATTCAG--AAAAAATGGAAAAACGATATTTGAAGTGTGAAAAATTC
194 CGATTTAATTAG-AAATAAATTCAGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCC
* * * *
597 TGAAATATTTTTGCCGTTGAATTATATGATTTTTCTGAGTATTGTGGCAAGAAATTGGGGAAAAA
258 TAAAATAGTTTTGGCGTTGAATTATATGATTTTTCTGAGTATTGTGGCAAAAAATTGGGGAAAAA
*
662 ATTTTCGGATCAGTTTTTTT
323 CTTTTCGGATCAG---TTTT
* *
682 TTTTGTCAAAGTTTTAGCCGAAACCGTGTACTAACCATCACGGTTTTTTGGCTAAAAATGCGTTT
1 TTTTG-CAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTGGCTAAAAATGCGTTT
*
747 CGGGGCCATGGCTCAGTTTTGCATGATTTTTGGCAAAATGACTTCTCGAAATATCTATATTCATC
65 CGGGGCCATGGCTCAGTTTTGCATGATTTTTGGCAGAATGACTTCTCGAAATATCTATATTCATC
* * *
812 TAATCAACA-CTCTCAGCCACAATGCATTTACGGATTTAATTTTACGAGTATCTTAATCTTGTTT
130 TAATCAA-ATCTCTCAGCCACAATGCATTTACGGATTTATTTTTACAAGTATCTGAATCTTGTTT
* * *
876 CGATTTAATTGGAAATAAATTCAGAAAAAAAGTGGAAAAACGATATTAAAAGCGTGAAAAACCCT
194 CGATTTAATTAGAAATAAATTCAGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCT
* *
941 AAAATAGTTTTGGCGTTGAATTATATGATTTTTCTGAGTATTGAGGTAAAAAATTGGGGGAAAAA
259 AAAATAGTTTTGGCGTTGAATTATATGATTTTTCTGAGTATTGTGGCAAAAAATT-GGGGAAAAA
1006 CTTTTCGGATCAGTTTT
323 CTTTTCGGATCAGTTTT
*
1023 TTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTGGCTAAAAATGTGTTTC
1 TTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTGGCTAAAAATGCGTTTC
* *
1088 GGGGCCATGGCTCAGTTTTGCATGATTTTTGGCAGGATGACTTCTC-AAAGTATCTATACTCATC
66 GGGGCCATGGCTCAGTTTTGCATGATTTTTGGCAGAATGACTTCTCGAAA-TATCTATATTCATC
* *
1152 TAATCAAATCTCTCATCCACAATGCATTTACGGATTTATTTTTACAAGTATCTGAATCTTGTTTA
130 TAATCAAATCTCTCAGCCACAATGCATTTACGGATTTATTTTTACAAGTATCTGAATCTTGTTTC
* *** *** **** * * * * *
1217 GATTTAGACTA-AAAGTTCAAATAGGGGCTTGATCTTTAGGGAAAA-GGTCATT-TAAGGGCT-T
195 GATTTA-ATTAGAAA--T-AAAT-TCAG-AAAAAAAAT-GGAAAAACGAT-ATTAGAAGCG-TGA
** * ** * ** * *
1278 AAAATTC-AAAAAAGGTTAAATAAGTGTCCAACCTT-T-TCGATTTGGATCAAATAAGTACATT-
251 AAAACCCTAAAATA-GTT---TTGGCGTTGAA--TTATAT-GATTT--TTC---TGAGT--ATTG
* * * ** **
1339 T--CTATGAAATTTGTGGATAGTGGGA-TGTGCTTC-TCTCTAGTTTAT
302 TGGC-A-AAAAATTGGGGA-A---AAACT-T--TTCGGATC-AGTTT-T
* * * * * * *** *
1384 ATATATCCACAAATTTCATG--GAAAT-GTG--CT-TCTC-TCTA-GGTTATATATATAAACATT
1 -T-TTTGCA-AAATTTTA-GCCGAAATCGTGTACTAAC-CATC-ACGGTTTTTTGGCTAAA-AAT
* * *** * * * * * *
1441 TCATTATCCTGATTTGTTGAAAATGTCCACAAATTTCATGGAAATGTCCTTATTTGACCCA-AAT
59 GCGTT-T-C-G----G--GGCCATG-GCTC-AGTTT--T-G-CATG--ATT-TTTG--GCAGAAT
**** * ** * * * ** * *
1505 CGAAAAGGTTG-GGTACCTAT-TTGACCTTTTCTAAAGT-T-T-AGACC-CTTAAATGACCTTTT
104 -G-ACTTCTCGAAATATCTATATTCATCTAATC-AAA-TCTCTCAG-CCAC---AATG-CATTTA
** ** * *** *** * * * * *
1564 CCCA-AAAGGTCAGACCCCTATTTGAACTTTTAGCCTTAGATTTAATTGGAAATAAATTCAGAAA
160 CGGATTTA-TTTTTACAAGTATCTGAA-TCTT-G-TTTCGATTTAATTAGAAATAAATTCAGAAA
* * * *
1628 AAAAATGGAAAAATGATATTAGAAGCGTGAAAACCCCTAAAATAGTTTTGGAGTTAAATTATATG
221 AAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTAAAATAGTTTTGGCGTTGAATTATATG
* * *** *
1693 ATTTTTCTCAATATTGTGGCTTGAAATTGGGGAAAAACTTTTCGGGTCAG--TT
286 ATTTTTCTGAGTATTGTGGCAAAAAATTGGGGAAAAACTTTTCGGATCAGTTTT
* *
1745 TTTTGCAAAATTATAGCCGAAATCGTGTACTAACCATCACGG--TTTTGGCTAAAAACGCGTTTC
1 TTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTGGCTAAAAATGCGTTTC
* * *
1808 GGGGCCATGGCTAAGTTTTGCATGATTTTTGGCAGAAAGACTTCTTGAAATATCTATATTCATCT
66 GGGGCCATGGCTCAGTTTTGCATGATTTTTGGCAGAATGACTTCTCGAAATATCTATATTCATCT
* * * * *
1873 AATCAAATCTCTCAGCCACAATGGATTTACAGATTTTTTTTTACGAGTATCTGAGTCTTGTTTCG
131 AATCAAATCTCTCAGCCACAATGCATTTACGGATTTATTTTTACAAGTATCTGAATCTTGTTTCG
* **
1938 ATTTAATTAGAAATAAATTCAGAAAAAAAAAAT-GAAAAACGATAATAGAAGCGTGAAAAATTCT
196 ATTTAATTAGAAATAAATTCAG--AAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCT
* * * * *
2002 GAAATATTTTTAGTGTTGAATTATATGATTTTTATGAGTATTGTGGCAAAAAATTGGGTG-AAAA
259 AAAATAGTTTTGGCGTTGAATTATATGATTTTTCTGAGTATTGTGGCAAAAAATTGGG-GAAAAA
* *
2066 CTTTTCGGTTTAGTTTT
323 CTTTTCGGATCAGTTTT
* **
2083 CTTTGCAAAATTTTAGCCGAAATCGTGTACGT-----T-ACGGTTTTTTGGCTAAAAACACGTTT
1 TTTTGCAAAATTTTAGCCGAAATCGTGTAC-TAACCATCACGGTTTTTTGGCTAAAAATGCGTTT
* * * *
2142 CGGTGACC-TGACTCAGTTTTGCATGATTCTTGGCAGAAAGACTTCTCGAAATATCTATATTCAT
65 CGG-GGCCATGGCTCAGTTTTGCATGATTTTTGGCAGAATGACTTCTCGAAATATCTATATTCAT
*
2206 CTAATCAAATCTCTCAG-C-C-A--C----A---ATTTATTTTTACGAGTATCTGAATCTTGTTT
129 CTAATCAAATCTCTCAGCCACAATGCATTTACGGATTTATTTTTACAAGTATCTGAATCTTGTTT
* * **
2259 CGATTTAATTAGAAAAAAATTCAG-AAAAAAATGGAAAAACGATATTTGAAGCGTGAAAAATTCT
194 CGATTTAATTAGAAATAAATTCAGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCT
* * *
2323 GAAATATTTTTAGGCGTTGAATTATATGATTTTTCTGAGTAGTGTGGCAAAAAAATTGGGGAAAA
259 AAAATAGTTTT-GGCGTTGAATTATATGATTTTTCTGAGTATTGTGGC-AAAAAATTGGGGAAAA
* * *
2388 AATTTTCGGGTCA--TCT
322 ACTTTTCGGATCAGTTTT
* * * *
2404 TTTTACAAAATTTTAGCTGAAATCGTGTACTAACCATCAC-GATTTTTGGCTAAAAATGCATTTC
1 TTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTGGCTAAAAATGCGTTTC
* * *
2468 GGGGCCCTGGCTCAGTTGTGCATGA-TTTTGGCAGAATAACTTCTCGAAATATCTATATTCATCT
66 GGGGCCATGGCTCAGTTTTGCATGATTTTTGGCAGAATGACTTCTCGAAATATCTATATTCATCT
*
2532 AATCAAATCTCTCAGCCACAATGCATTTACTGATTTATTTTTACAAGTATCTGAATCTTGTTTCG
131 AATCAAATCTCTCAGCCACAATGCATTTACGGATTTATTTTTACAAGTATCTGAATCTTGTTTCG
* *
2597 ATTTAATTAGAAATAAATTCAGAAAAAAAAAATGGAAAAATGATATTATAAGCGTGAAAAACCCT
196 ATTTAATTAGAAATAAATTCAG--AAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCT
2662 AAA
259 AAA
2665 TATTATTAGT
Statistics
Matches: 1853, Mismatches: 312, Indels: 315
0.75 0.13 0.13
Matches are distributed among these distances:
320 9 0.00
321 69 0.04
322 33 0.02
323 76 0.04
324 54 0.03
325 40 0.02
326 4 0.00
327 1 0.00
329 1 0.00
332 1 0.00
333 6 0.00
334 3 0.00
335 126 0.07
336 164 0.09
337 121 0.07
338 184 0.10
339 71 0.04
340 194 0.10
341 51 0.03
342 180 0.10
343 89 0.05
344 27 0.01
345 19 0.01
346 11 0.01
347 1 0.00
348 7 0.00
349 10 0.01
350 3 0.00
351 6 0.00
353 1 0.00
354 9 0.00
355 6 0.00
356 3 0.00
357 3 0.00
358 9 0.00
359 25 0.01
360 24 0.01
361 9 0.00
362 10 0.01
363 15 0.01
364 12 0.01
365 3 0.00
366 2 0.00
367 2 0.00
369 8 0.00
370 11 0.01
371 7 0.00
372 1 0.00
373 1 0.00
374 3 0.00
375 5 0.00
376 6 0.00
377 9 0.00
378 6 0.00
379 21 0.01
380 28 0.02
381 14 0.01
382 20 0.01
383 4 0.00
384 3 0.00
385 12 0.01
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (339 bp):
TTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTTGGCTAAAAATGCGTTTC
GGGGCCATGGCTCAGTTTTGCATGATTTTTGGCAGAATGACTTCTCGAAATATCTATATTCATCT
AATCAAATCTCTCAGCCACAATGCATTTACGGATTTATTTTTACAAGTATCTGAATCTTGTTTCG
ATTTAATTAGAAATAAATTCAGAAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTAA
AATAGTTTTGGCGTTGAATTATATGATTTTTCTGAGTATTGTGGCAAAAAATTGGGGAAAAACTT
TTCGGATCAGTTTT
Found at i:3326 original size:98 final size:99
Alignment explanation
Indices: 3212--3389 Score: 304
Period size: 99 Copynumber: 1.8 Consensus size: 99
3202 AACTTTTTAA
* *
3212 ATTAAAATGGTAAAAATAAAATAATTATAAA-ATATTGAATTTAATTAAATGAAAATAAAGTTTT
1 ATTAAAATGGTAAAAATAAAATAATTATAAACATATTAAATTTAATTAAATAAAAATAAAGTTTT
3276 TAGTAGAATAAAACTGTATATTTTGAAAAAAAAT
66 TAGTAGAATAAAACTGTATATTTTGAAAAAAAAT
* * *
3310 ATTAAAATGGTAAAAATAAAGTAATTATAAACATATTAAATTTAATTGAATAAAAATAGAGTTTT
1 ATTAAAATGGTAAAAATAAAATAATTATAAACATATTAAATTTAATTAAATAAAAATAAAGTTTT
3375 TAGTAGAATAAAACT
66 TAGTAGAATAAAACT
3390 ATAATAGTTA
Statistics
Matches: 74, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
98 30 0.41
99 44 0.59
ACGTcount: A:0.54, C:0.02, G:0.10, T:0.34
Consensus pattern (99 bp):
ATTAAAATGGTAAAAATAAAATAATTATAAACATATTAAATTTAATTAAATAAAAATAAAGTTTT
TAGTAGAATAAAACTGTATATTTTGAAAAAAAAT
Found at i:3501 original size:2 final size:2
Alignment explanation
Indices: 3489--3530 Score: 52
Period size: 2 Copynumber: 21.5 Consensus size: 2
3479 AACTCGTACT
*
3489 TA TA T- TA TA TA TA TA GTA TA GA TA -A TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
3530 T
1 T
3531 TTTGTAATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
1 2 0.06
2 31 0.89
3 2 0.06
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (2 bp):
TA
Found at i:5679 original size:31 final size:31
Alignment explanation
Indices: 5643--5927 Score: 415
Period size: 31 Copynumber: 9.4 Consensus size: 31
5633 ACCTAAGAGA
5643 GAACTATATGCAATAACGATAGACCTAAAAT
1 GAACTATATGCAATAACGATAGACCTAAAAT
*
5674 GAACTATATGCAATAACGATAGACCTAAAAA
1 GAACTATATGCAATAACGATAGACCTAAAAT
5705 GAACTATATGCAATAACGATAGACCT--AA-
1 GAACTATATGCAATAACGATAGACCTAAAAT
*
5733 -AACTATATGCAATAACGATAGACCTATAAT
1 GAACTATATGCAATAACGATAGACCTAAAAT
*
5763 GAACTATATGCAATAACGATAGACCTATAAT
1 GAACTATATGCAATAACGATAGACCTAAAAT
5794 GAACTATATGCAATAACGATAGACCT--AA-
1 GAACTATATGCAATAACGATAGACCTAAAAT
*
5822 -AACTATATGCAATAACGATAAACCTAAAAT
1 GAACTATATGCAATAACGATAGACCTAAAAT
* *
5852 GAACTATATGCAATAACGACAGACCAAAAAT
1 GAACTATATGCAATAACGATAGACCTAAAAT
* * * *
5883 GAACTATACGCTATGATGATAGACCTAAAAAT
1 GAACTATATGCAATAACGATAGACCT-AAAAT
5915 GAACTATATGCAA
1 GAACTATATGCAA
5928 CAGCCATACT
Statistics
Matches: 232, Mismatches: 13, Indels: 17
0.89 0.05 0.06
Matches are distributed among these distances:
27 49 0.21
29 8 0.03
31 159 0.69
32 16 0.07
ACGTcount: A:0.48, C:0.17, G:0.13, T:0.22
Consensus pattern (31 bp):
GAACTATATGCAATAACGATAGACCTAAAAT
Found at i:5767 original size:58 final size:59
Alignment explanation
Indices: 5643--5910 Score: 339
Period size: 58 Copynumber: 4.5 Consensus size: 59
5633 ACCTAAGAGA
*
5643 GAACTATATGCAATAACGATAGACCTAAAATGAACTATATGCAATAACGATAGACCTAAAAA
1 GAACTATATGCAATAACGATAGACCT--AA-GAACTATATGCAATAACGATAGACCTAAAAT
*
5705 GAACTATATGCAATAACGATAGACCTAA-AACTATATGCAATAACGATAGACCTATAAT
1 GAACTATATGCAATAACGATAGACCTAAGAACTATATGCAATAACGATAGACCTAAAAT
5763 GAACTATATGCAATAACGATAGACCTATAATGAACTATATGCAATAACGATAGACCT--AA-
1 GAACTATATGCAATAACGATAGACC--TAA-GAACTATATGCAATAACGATAGACCTAAAAT
* * *
5822 -AACTATATGCAATAACGATAAACCTAAAATGAACTATATGCAATAACGACAGACCAAAAAT
1 GAACTATATGCAATAACGATAGACCT--AA-GAACTATATGCAATAACGATAGACCTAAAAT
* * * *
5883 GAACTATACGCTATGATGATAGACCTAA
1 GAACTATATGCAATAACGATAGACCTAA
5911 AAATGAACTA
Statistics
Matches: 186, Mismatches: 10, Indels: 22
0.85 0.05 0.10
Matches are distributed among these distances:
56 1 0.01
58 103 0.55
60 11 0.06
62 71 0.38
ACGTcount: A:0.48, C:0.17, G:0.13, T:0.22
Consensus pattern (59 bp):
GAACTATATGCAATAACGATAGACCTAAGAACTATATGCAATAACGATAGACCTAAAAT
Found at i:5798 original size:89 final size:89
Alignment explanation
Indices: 5644--5912 Score: 448
Period size: 89 Copynumber: 3.0 Consensus size: 89
5634 CCTAAGAGAG
*
5644 AACTATATGCAATAACGATAGACCTAAAATGAACTATATGCAATAACGATAGACCTAAAAAGAAC
1 AACTATATGCAATAACGATAGACCTAAAATGAACTATATGCAATAACGATAGACCTAAAATGAAC
5709 TATATGCAATAACGATAGACCTAA
66 TATATGCAATAACGATAGACCTAA
* *
5733 AACTATATGCAATAACGATAGACCTATAATGAACTATATGCAATAACGATAGACCTATAATGAAC
1 AACTATATGCAATAACGATAGACCTAAAATGAACTATATGCAATAACGATAGACCTAAAATGAAC
5798 TATATGCAATAACGATAGACCTAA
66 TATATGCAATAACGATAGACCTAA
* * *
5822 AACTATATGCAATAACGATAAACCTAAAATGAACTATATGCAATAACGACAGACCAAAAATGAAC
1 AACTATATGCAATAACGATAGACCTAAAATGAACTATATGCAATAACGATAGACCTAAAATGAAC
* * * *
5887 TATACGCTATGATGATAGACCTAA
66 TATATGCAATAACGATAGACCTAA
5911 AA
1 AA
5913 ATGAACTATA
Statistics
Matches: 168, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
89 168 1.00
ACGTcount: A:0.48, C:0.17, G:0.12, T:0.22
Consensus pattern (89 bp):
AACTATATGCAATAACGATAGACCTAAAATGAACTATATGCAATAACGATAGACCTAAAATGAAC
TATATGCAATAACGATAGACCTAA
Found at i:6484 original size:22 final size:22
Alignment explanation
Indices: 6451--6508 Score: 91
Period size: 22 Copynumber: 2.6 Consensus size: 22
6441 TATTCAACTG
6451 GACAAATAGGATTGCCTCCAC-
1 GACAAATAGGATTGCCTCCACA
*
6472 GAACAGATAGGATTGCCTCCACA
1 G-ACAAATAGGATTGCCTCCACA
6495 GACAAATAGGATTG
1 GACAAATAGGATTG
6509 TCCCCATGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 1 0.03
22 31 0.94
23 1 0.03
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.19
Consensus pattern (22 bp):
GACAAATAGGATTGCCTCCACA
Found at i:6521 original size:22 final size:21
Alignment explanation
Indices: 6452--6523 Score: 83
Period size: 22 Copynumber: 3.3 Consensus size: 21
6442 ATTCAACTGG
6452 ACAAATAGGATTGCCTCCACGA
1 ACAAATAGGATTGCCTCCA-GA
* *
6474 ACAGATAGGATTGCCTCCACA
1 ACAAATAGGATTGCCTCCAGA
6495 GACAAATAGGATTGTCC-CCATGA
1 -ACAAATAGGATTG-CCTCCA-GA
6518 ACAAAT
1 ACAAAT
6524 GAACTATAAC
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
21 1 0.02
22 39 0.91
23 3 0.07
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (21 bp):
ACAAATAGGATTGCCTCCAGA
Found at i:6581 original size:31 final size:31
Alignment explanation
Indices: 6545--7129 Score: 811
Period size: 31 Copynumber: 19.2 Consensus size: 31
6535 ATAGACCTGA
* **
6545 AACTATATGCAATACCGAAAGACCTAAAATG
1 AACTATATGCAATAACGATGGACCTAAAATG
*
6576 AACTATATGCAATAACGATAGACCT---A-G
1 AACTATATGCAATAACGATGGACCTAAAATG
* *
6603 AACAATATGCAATAACGATAGACCTAAAATG
1 AACTATATGCAATAACGATGGACCTAAAATG
*
6634 AACTATATGCAATAACGATAGACCTAAAATG
1 AACTATATGCAATAACGATGGACCTAAAATG
6665 AACTATATGCAATAACGATGGACCT-AAATG
1 AACTATATGCAATAACGATGGACCTAAAATG
6695 AACTATATGCAATAACGATGGACCT-AAATG
1 AACTATATGCAATAACGATGGACCTAAAATG
* *
6725 AGCTATATGCAATAACGATGGACCTAAAATT
1 AACTATATGCAATAACGATGGACCTAAAATG
*
6756 AACTATATGCAATAACGATAGACCTAAAATG
1 AACTATATGCAATAACGATGGACCTAAAATG
*
6787 AACTATATGCAATAACGATAGACCTAAAATG
1 AACTATATGCAATAACGATGGACCTAAAATG
*
6818 AACTATATGCAATAACGATAGACCTAAAATG
1 AACTATATGCAATAACGATGGACCTAAAATG
*
6849 AACTATATGCAATAACGATGGATCTAAAATG
1 AACTATATGCAATAACGATGGACCTAAAATG
*
6880 AACTATATGCAATAACGATGGATCT-AAATG
1 AACTATATGCAATAACGATGGACCTAAAATG
*
6910 AGCTATATGCAATAACGATGGACCTAAAATG
1 AACTATATGCAATAACGATGGACCTAAAATG
*
6941 AGCTATATGCAATAACGATGGACCTAAAATG
1 AACTATATGCAATAACGATGGACCTAAAATG
6972 AACTATATGCAATAACGATGGACCTAAAATG
1 AACTATATGCAATAACGATGGACCTAAAATG
* * * * * *
7003 AGCTATCTGCACCTAA-AAT-GAGCT-ATATG
1 AACTATATGCA-ATAACGATGGACCTAAAATG
*
7032 CAA-TA-A--CAATAACGATGGACCTAAACTAG
1 -AACTATATGCAATAACGATGGACCTAAAAT-G
* *
7061 AACTATATGCAATAACGATGTAACTAAAATG
1 AACTATATGCAATAACGATGGACCTAAAATG
*
7092 AGCTATATGCAATAACGATGGACCTAAAATG
1 AACTATATGCAATAACGATGGACCTAAAATG
7123 AACTATA
1 AACTATA
7130 CCTAAAATGA
Statistics
Matches: 503, Mismatches: 35, Indels: 32
0.88 0.06 0.06
Matches are distributed among these distances:
25 3 0.01
26 4 0.01
27 29 0.06
28 5 0.01
29 9 0.02
30 94 0.19
31 338 0.67
32 21 0.04
ACGTcount: A:0.45, C:0.16, G:0.15, T:0.23
Consensus pattern (31 bp):
AACTATATGCAATAACGATGGACCTAAAATG
Found at i:6793 original size:92 final size:93
Alignment explanation
Indices: 6547--7129 Score: 825
Period size: 92 Copynumber: 6.4 Consensus size: 93
6537 AGACCTGAAA
* * * *
6547 CTATATGCAATACCGAAAGACCTAAAATGAACTATATGCAATAACGATAGACCT---A-GAACAA
1 CTATATGCAATAACGATAGACCTAAAATGAACTATATGCAATAACGATGGACCTAAAATGAACTA
* *
6608 TATGCAATAACGATAGACCTAAAATGAA
66 TATGCAATAACGATGGACCTAAAATGAG
6636 CTATATGCAATAACGATAGACCTAAAATGAACTATATGCAATAACGATGGACCT-AAATGAACTA
1 CTATATGCAATAACGATAGACCTAAAATGAACTATATGCAATAACGATGGACCTAAAATGAACTA
6700 TATGCAATAACGATGGACCT-AAATGAG
66 TATGCAATAACGATGGACCTAAAATGAG
* * *
6727 CTATATGCAATAACGATGGACCTAAAATTAACTATATGCAATAACGATAGACCTAAAATGAACTA
1 CTATATGCAATAACGATAGACCTAAAATGAACTATATGCAATAACGATGGACCTAAAATGAACTA
* *
6792 TATGCAATAACGATAGACCTAAAATGAA
66 TATGCAATAACGATGGACCTAAAATGAG
*
6820 CTATATGCAATAACGATAGACCTAAAATGAACTATATGCAATAACGATGGATCTAAAATGAACTA
1 CTATATGCAATAACGATAGACCTAAAATGAACTATATGCAATAACGATGGACCTAAAATGAACTA
*
6885 TATGCAATAACGATGGATCT-AAATGAG
66 TATGCAATAACGATGGACCTAAAATGAG
* *
6912 CTATATGCAATAACGATGGACCTAAAATGAGCTATATGCAATAACGATGGACCTAAAATGAACTA
1 CTATATGCAATAACGATAGACCTAAAATGAACTATATGCAATAACGATGGACCTAAAATGAACTA
6977 TATGCAATAACGATGGACCTAAAATGAG
66 TATGCAATAACGATGGACCTAAAATGAG
* * * * * *
7005 CTATCTGCACCTAA-AAT-GAGCT-ATATGCAA-TA-A--CAATAACGATGGACCTAAACTAGAA
1 CTATATGCA-ATAACGATAGACCTAAAATG-AACTATATGCAATAACGATGGACCTAAAAT-GAA
* *
7063 CTATATGCAATAACGATGTAACTAAAATGAG
63 CTATATGCAATAACGATGGACCTAAAATGAG
*
7094 CTATATGCAATAACGATGGACCTAAAATGAACTATA
1 CTATATGCAATAACGATAGACCTAAAATGAACTATA
7130 CCTAAAATGA
Statistics
Matches: 444, Mismatches: 36, Indels: 25
0.88 0.07 0.05
Matches are distributed among these distances:
88 23 0.05
89 93 0.21
90 7 0.02
91 70 0.16
92 146 0.33
93 102 0.23
94 3 0.01
ACGTcount: A:0.45, C:0.16, G:0.15, T:0.23
Consensus pattern (93 bp):
CTATATGCAATAACGATAGACCTAAAATGAACTATATGCAATAACGATGGACCTAAAATGAACTA
TATGCAATAACGATGGACCTAAAATGAG
Found at i:7018 original size:20 final size:20
Alignment explanation
Indices: 6993--7033 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
6983 ATAACGATGG
*
6993 ACCTAAAATGAGCTATCTGC
1 ACCTAAAATGAGCTATATGC
7013 ACCTAAAATGAGCTATATGC
1 ACCTAAAATGAGCTATATGC
7033 A
1 A
7034 ATAACAATAA
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:0.39, C:0.22, G:0.15, T:0.24
Consensus pattern (20 bp):
ACCTAAAATGAGCTATATGC
Found at i:7134 original size:16 final size:16
Alignment explanation
Indices: 7113--7145 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
7103 ATAACGATGG
7113 ACCTAAAATGAACTAT
1 ACCTAAAATGAACTAT
*
7129 ACCTAAAATGAGCTAT
1 ACCTAAAATGAACTAT
7145 A
1 A
7146 TGCAATAACG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.48, C:0.18, G:0.09, T:0.24
Consensus pattern (16 bp):
ACCTAAAATGAACTAT
Found at i:7167 original size:31 final size:31
Alignment explanation
Indices: 7129--7273 Score: 254
Period size: 31 Copynumber: 4.7 Consensus size: 31
7119 AATGAACTAT
*
7129 ACCTAAAATGAGCTATATGCAATAACGATAG
1 ACCTAAAATGAACTATATGCAATAACGATAG
7160 ACCTAAAATGAACTATATGCAATAACGATAG
1 ACCTAAAATGAACTATATGCAATAACGATAG
7191 ACCTAAAATGAACTATATGCAATAACGATAG
1 ACCTAAAATGAACTATATGCAATAACGATAG
* * *
7222 ACCTAAAATGAGCTATATGCAATAACAATGG
1 ACCTAAAATGAACTATATGCAATAACGATAG
7253 ACCTAAAATGAACTATATGCA
1 ACCTAAAATGAACTATATGCA
7274 CCTAAAATGA
Statistics
Matches: 109, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 109 1.00
ACGTcount: A:0.47, C:0.17, G:0.14, T:0.23
Consensus pattern (31 bp):
ACCTAAAATGAACTATATGCAATAACGATAG
Found at i:7194 original size:78 final size:78
Alignment explanation
Indices: 7063--7207 Score: 247
Period size: 78 Copynumber: 1.9 Consensus size: 78
7053 TAAACTAGAA
* *
7063 CTATATGCAATAACGATGTAACTAAAATGAGCTATATGCAATAACGATGGACCTAAAATGAACTA
1 CTATATGCAATAACGATGTAACTAAAATGAACTATATGCAATAACGATAGACCTAAAATGAACTA
7128 TACCTAAAATGAG
66 TACCTAAAATGAG
*
7141 CTATATGCAATAACGATAG-ACCTAAAATGAACTATATGCAATAACGATAGACCTAAAATGAACT
1 CTATATGCAATAACGAT-GTAACTAAAATGAACTATATGCAATAACGATAGACCTAAAATGAACT
7205 ATA
65 ATA
7208 TGCAATAACG
Statistics
Matches: 63, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
78 62 0.98
79 1 0.02
ACGTcount: A:0.46, C:0.16, G:0.14, T:0.24
Consensus pattern (78 bp):
CTATATGCAATAACGATGTAACTAAAATGAACTATATGCAATAACGATAGACCTAAAATGAACTA
TACCTAAAATGAG
Found at i:7226 original size:62 final size:62
Alignment explanation
Indices: 7129--7364 Score: 287
Period size: 62 Copynumber: 3.9 Consensus size: 62
7119 AATGAACTAT
* *
7129 ACCTAAAATGAGCTATATGCAATAACGATAGACCTAAAATGAACTATATGCAATAACGATAG
1 ACCTAAAATGAACTATATGCAATAACGATAGACCTAAAATGAGCTATATGCAATAACGATAG
* *
7191 ACCTAAAATGAACTATATGCAATAACGATAGACCTAAAATGAGCTATATGCAATAACAATGG
1 ACCTAAAATGAACTATATGCAATAACGATAGACCTAAAATGAGCTATATGCAATAACGATAG
7253 ACCTAAAATGAACTATATG------C-----ACCTAAAATGAGCTATATGCAATAACGATAG
1 ACCTAAAATGAACTATATGCAATAACGATAGACCTAAAATGAGCTATATGCAATAACGATAG
*
7304 ACCTAAAATTAACCTAGAACTATATGCAATAACGATGGACCTAAAATGAGCTATATGCAAT
1 ACCT--AA--AA--T-GAACTATATGCAATAACGATAGACCTAAAATGAGCTATATGCAAT
Statistics
Matches: 150, Mismatches: 6, Indels: 29
0.81 0.03 0.16
Matches are distributed among these distances:
51 33 0.22
53 2 0.01
55 2 0.01
56 1 0.01
57 1 0.01
58 10 0.07
62 77 0.51
64 1 0.01
69 23 0.15
ACGTcount: A:0.46, C:0.17, G:0.14, T:0.23
Consensus pattern (62 bp):
ACCTAAAATGAACTATATGCAATAACGATAGACCTAAAATGAGCTATATGCAATAACGATAG
Found at i:7243 original size:260 final size:259
Alignment explanation
Indices: 6602--7242 Score: 364
Period size: 246 Copynumber: 2.5 Consensus size: 259
6592 GATAGACCTA
*
6602 GAACAATATGCAATAACGATAGACCTAAAATGAACTATATGCAATAACGATAGACCTAAAATGAA
1 GAACTATATGCAATAACGATAGACCT-AAATGAACTATATGCAATAACGATAGACCTAAAATGAA
* * *
6667 CTATATGCAATAACGATGGACCT-AAATGAACTATATGCAATAACGATGGACCT-AAATGAGCTA
65 CTATATGCAATAACGATAGACCTAAAATGAACTATATGCAATAACAATGGACCTAAAATGAACTA
* * * * * * * *
6730 TATGCA-ATAACGATGGACCTAAAAT-TAACTATATGCAATA-ACGATAGACCTAAAAT-GAACT
130 TATGCACCTAA-AAT-GAGCT-ATATGCAA-TA-A--CAATAGAC-ATAAAACTAAACTAGAACT
* * *
6791 ATATGCAATAACGATAGACCTAAAATGAACTATATGCAATAAC----GA--T---A-G------A
187 ATATGCAATAACGATGGAACTAAAATGAGCTATATGCAATAACGATGGACCTAAAATGAACTATA
6840 CCTAAAAT
252 CCTAAAAT
* * * * *
6848 GAACTATATGCAATAACGATGGATCTAAAATGAACTATATGCAATAACGATGGATCT-AAATGAG
1 GAACTATATGCAATAACGATAGACCT-AAATGAACTATATGCAATAACGATAGACCTAAAATGAA
* * *
6912 CTATATGCAATAACGATGGACCTAAAATGAGCTATATGCAATAACGATGGACCTAAAATGAACTA
65 CTATATGCAATAACGATAGACCTAAAATGAACTATATGCAATAACAATGGACCTAAAATGAACTA
* * * * * * * * * * * *
6977 TATGCA-ATAACGATGGACCTA-A---AATGAGCTATCTGCACCTAAAA-TGAGCTATATGCAAT
130 TATGCACCTAA-AAT-GAGCTATATGCAAT-AACAAT-AG-ACATAAAACTAAACTAGA-ACTAT
* * * * * * *
7036 A-ACAATAACGATGGACCTAAACTAGAACTATATGCAATAACGATGTAACTAAAATGAGCTATAT
189 ATGCAATAACGATGGAACTAAAAT-GAGCTATATGCAATAACGATGGACCTAAAATGAACTATA-
* *
7100 GCAATAACGAT
252 -C-CTAA-AAT
* * *
7111 GGACCTA-A---AATGAAC--TATACCTAAAATGAGCTATATGCAATAACGATAGACCTAAAATG
1 -GAACTATATGCAAT-AACGATAGACCT-AAATGAACTATATGCAATAACGATAGACCTAAAATG
* * *
7170 AACTATATGCAATAACGATAGACCTAAAATGAACTATATGCAATAACGATAGACCTAAAATGAGC
63 AACTATATGCAATAACGATAGACCTAAAATGAACTATATGCAATAACAATGGACCTAAAATGAAC
7235 TATATGCA
128 TATATGCA
7243 ATAACAATGG
Statistics
Matches: 325, Mismatches: 38, Indels: 50
0.79 0.09 0.12
Matches are distributed among these distances:
240 3 0.01
241 3 0.01
242 24 0.07
243 26 0.08
245 30 0.09
246 82 0.25
247 30 0.09
249 1 0.00
252 1 0.00
253 1 0.00
259 33 0.10
260 76 0.23
261 4 0.01
262 3 0.01
263 3 0.01
264 5 0.02
ACGTcount: A:0.45, C:0.16, G:0.15, T:0.23
Consensus pattern (259 bp):
GAACTATATGCAATAACGATAGACCTAAATGAACTATATGCAATAACGATAGACCTAAAATGAAC
TATATGCAATAACGATAGACCTAAAATGAACTATATGCAATAACAATGGACCTAAAATGAACTAT
ATGCACCTAAAATGAGCTATATGCAATAACAATAGACATAAAACTAAACTAGAACTATATGCAAT
AACGATGGAACTAAAATGAGCTATATGCAATAACGATGGACCTAAAATGAACTATACCTAAAAT
Found at i:7278 original size:20 final size:20
Alignment explanation
Indices: 7253--7293 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
7243 ATAACAATGG
7253 ACCTAAAATGAACTATATGC
1 ACCTAAAATGAACTATATGC
*
7273 ACCTAAAATGAGCTATATGC
1 ACCTAAAATGAACTATATGC
7293 A
1 A
7294 ATAACGATAG
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:0.44, C:0.20, G:0.12, T:0.24
Consensus pattern (20 bp):
ACCTAAAATGAACTATATGC
Found at i:7311 original size:31 final size:31
Alignment explanation
Indices: 7273--7364 Score: 103
Period size: 38 Copynumber: 2.7 Consensus size: 31
7263 AACTATATGC
7273 ACCTAAAATGAGCTATATGCAATAACGATAG
1 ACCTAAAATGAGCTATATGCAATAACGATAG
* *
7304 ACCTAAAATTAACCTAGAACTATATGCAATAACGATGG
1 ACCT--AA--AA--T-GAGCTATATGCAATAACGATAG
7342 ACCTAAAATGAGCTATATGCAAT
1 ACCTAAAATGAGCTATATGCAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
31 17 0.33
32 1 0.02
33 2 0.04
34 2 0.04
35 2 0.04
36 2 0.04
37 1 0.02
38 24 0.47
ACGTcount: A:0.45, C:0.17, G:0.14, T:0.24
Consensus pattern (31 bp):
ACCTAAAATGAGCTATATGCAATAACGATAG
Found at i:7319 original size:93 final size:93
Alignment explanation
Indices: 7083--7362 Score: 276
Period size: 93 Copynumber: 3.0 Consensus size: 93
7073 TAACGATGTA
* *
7083 ACTAAAATGAGCTATATGCAATAACGATGGACCTAAAATGAACTATACCTAAAATGAGCTATATG
1 ACTAAAATGAGCTATATGCAATAACGATAGACCTAAAAT----TAGACCTAAAATGAGCTATATG
*
7148 CAATAACGATAGACCTAAAATGAACTATATGC
62 CAATAACGATGGACCTAAAATGAACTATATGC
* * * * * *
7180 AATAACGATAGACCTA-A---AATGAACTATATG-CAATAACGA-TAGACCTAAAATGAGCTATA
1 ACTAA-AAT-GAGCTATATGCAAT-AACGATA-GAC-CTAA-AATTAGACCTAAAATGAGCTATA
*
7239 TGCAATAACAATGGACCTAAAATGAACTATATGC
60 TGCAATAACGATGGACCTAAAATGAACTATATGC
*
7273 ACCTAAAATGAGCTATATGCAATAACGATAGACCTAAAATTA-ACCT---A-GAACTATATGCAA
1 A-CTAAAATGAGCTATATGCAATAACGATAGACCTAAAATTAGACCTAAAATGAGCTATATGCAA
*
7333 TAACGATGGACCTAAAATGAGCTATATGC
65 TAACGATGGACCTAAAATGAACTATATGC
7362 A
1 A
7363 AT
Statistics
Matches: 151, Mismatches: 19, Indels: 34
0.74 0.09 0.17
Matches are distributed among these distances:
89 40 0.26
90 1 0.01
92 5 0.03
93 60 0.40
94 9 0.06
95 10 0.07
96 9 0.06
97 8 0.05
98 4 0.03
99 5 0.03
ACGTcount: A:0.46, C:0.17, G:0.14, T:0.23
Consensus pattern (93 bp):
ACTAAAATGAGCTATATGCAATAACGATAGACCTAAAATTAGACCTAAAATGAGCTATATGCAAT
AACGATGGACCTAAAATGAACTATATGC
Done.