Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015336.1 Corchorus olitorius cultivar O-4 contig15369, 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: 61243
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:598 original size:321 final size:320
Alignment explanation
Indices: 1--2179 Score: 2242
Period size: 321 Copynumber: 6.7 Consensus size: 320
** * * * *
1 AATATCTATATTCATCTAATTAAATCTCAGCCATATTGGAATGAAGAATTTGTTTTTACGAGCAT
1 AATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCAT
* * * *
66 CTGAATCTTGTTTCAATTTAATTTGAAATAAAA-TCAGGGAAAAAAAAGGGAAAAACGATATCAA
66 CTGAATCTTGTTTCGATTTAA-TT-AAA-AAAAGTC--GG-AAAAAAATGGAAAAACGATATTAG
* * * *
130 AAGAGTG-AAAATCCTTCAATTTTTTTGGCGTTGAATCATATATTTTTTCTGAGTATTCTGG-AA
125 AAGCGTGAAAAACCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAA
* * * * * *
193 AAAATTGAGGAAAAA-CTTTTCGGGTCAATTTTTGCAAAATTTAAGCCGATATCATGTACTAACC
190 AAAATTGAGAAAAAATTTTTTCAGGTC-A--GTT------TTT-AGCCGAAATCGTGTACTAACC
* *
257 ATCCCGGTTTTCGGCTAAAAACGCGTTTCGGGACCTGAGTCAGTTTTGAATGATTTTTGGCAGAA
245 ATCACGGTTTTCGGCTAAAAACGCGTTTCGGGACCTGACTCAGTTTTGAATGATTTTTGGCAGAA
322 AGACTCCTTGA
310 AGACTCCTTGA
* * * *
333 AATATCTATATTCATCTAACCAAATCTAAGCCACATTAGATTTCACGGATTTATTTTTACGAGCA
1 AATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTT-AAGGATTTGTTTTTACGAGCA
* * * *
398 CCTAAATCTTGTTTCGATTTAATTAAAAAAAGTCGGAAAAAAA-GGAAAAATGATATTAGAAGTG
65 TCTGAATCTTGTTTCGATTTAATTAAAAAAAGTCGGAAAAAAATGGAAAAACGATATTAGAAGCG
* * * * * *
462 TGAAAAATCCTTCCATTTTTTTTGGCATTGAGTTATACATTTTTTCTGAGTGTTGTGGCAAAAAA
130 TGAAAAACCCTT-CAATTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAA
* * * *
527 TAGAGAAAAAATTTTTTCAGATCAGTTTTTAGCCGAAATCATGTACTAACCATCACGGTTTTCGA
194 TTGAGAAAAAATTTTTTCAGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTCGG
592 CTAAAAACGCGTTTCGGGACCTGACTCAGTTTTGAATGATTTTTGGCAGAAAGACTCCTTGA
259 CTAAAAACGCGTTTCGGGACCTGACTCAGTTTTGAATGATTTTTGGCAGAAAGACTCCTTGA
* **
654 AATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTACGGATTTGTTTTTACGAGTTT
1 AATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCAT
* * ** * * * *
719 CTGAATTTTGTTTCGATATTATTTGAAATTAATTTGGACAAAAAAATGGAAAACCGATATTGGAA
66 CTGAATCTTGTTTCGAT-TTAATT-AAAAAAAGTCGG--AAAAAAATGGAAAAACGATATTAGAA
* * * * * * *
784 GCCTGAAAAGA-CCATCACTCTTTTTGGCGTTGAGTTAAATATTTTTTATGAGTATTGTGGCAAA
127 GCGTGAAAA-ACCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAA
* * *
848 AAATTGAGAAAAAA-TTTTTCGGGTCAGTTTTTAGCCGAAAATCGTGTACCAACTATCACGGTTT
191 AAATTGAGAAAAAATTTTTTCAGGTCAGTTTTTAGCCG-AAATCGTGTACTAACCATCACGGTTT
* * *
912 TCGGCTAAAAACGCGTTTCCGGACCTGACTCACTTTTGAATGGTTTTTGGCAGAAAGACTCCTTG
255 TCGGCTAAAAACGCGTTTCGGGACCTGACTCAGTTTTGAATGATTTTTGGCAGAAAGACTCCTTG
977 A
320 A
* *
978 AATATCTATATTCATCTAACCAAATCTCAGCCACATTAGATTTCACGGATTTGTTTTTACGAGCA
1 AATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTT-AAGGATTTGTTTTTACGAGCA
* * * *
1043 CCTAAATCTTGTTTCGATTTAATTAAAAAAAGTCGGAAAAAAATGGAAAAATGATATTAGAAGTG
65 TCTGAATCTTGTTTCGATTTAATTAAAAAAAGTCGGAAAAAAATGGAAAAACGATATTAGAAGCG
* * * * *
1108 TGAAAAATCCTTCAATTTTTTTGGCGTTGAGTTATATATTTTTTCTGAATATT-TTGCAAAAAAA
130 TGAAAAACCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAAT
* * * * * * * *
1172 TGAG-ATAAA-CTTTTCGGGTTAGTTTTTAACCGAAATCGTGTAATAACCATCACGATTTTTGGC
195 TGAGAAAAAATTTTTTCAGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTCGGC
* ** *
1235 TAAAAACGCATTTC-GGATCC---CGGAGTTTTGAATGATTTTTGGCAGAAAGACTCCTTTA
260 TAAAAACGCGTTTCGGGA-CCTGACTCAGTTTTGAATGATTTTTGGCAGAAAGACTCCTTGA
* * *
1293 AATATCTATATTCATCTAACAAAATCTCAGCCACAATGGATTTAAGAATTTGTTTTTACGAGCAT
1 AATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCAT
* * * * *
1358 CTCAATCTTTGTTTCGATTTCATTAGAAATAAGTTCGAAAAAAAAGAGAAGAAAAACGATATTAG
66 CTGAATC-TTGTTTCGATTTAATTA-AAAAAAG-TCGGAAAAAAA-TG--GAAAAACGATATTAG
* *
1423 AAGCCTGAAAAACCCTTCAATTTTTTTGGCGTTAAATTATATA--TTTTCTGAGTATTGTGGCAA
125 AAGCGTGAAAAACCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAA
* * ** *
1486 AAAATTGAGCAAAAACTTTTCGGGTT-AGTTTTTGCAAAATTTTAGCCGAAATTGTGTACTAACC
190 AAAATTGAG-AAAAAATTTT----TTCAG---GT-C-AGTTTTTAGCCGAAATCGTGTACTAACC
* * * * * * *
1550 ATCACGGTTTTTGGCTAAAAACACGTTCCGGAGCCCCGACTCAATTTTGCATGATTTTTGGC-GT
245 ATCACGGTTTTCGGCTAAAAACGCGTTTCGG-GACCTGACTCAGTTTTGAATGATTTTTGGCAG-
1614 AAAGACTCCTTGA
308 AAAGACTCCTTGA
* * *
1627 AATAT-TCATATTCATCGAACCAAATGC-CAGCCACATTGGATATAAGGATTTGTTTTTACGAGT
1 AATATCT-ATATTCATCTAACCAAAT-CTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGC
** *
1690 ATCTGAATCTTGTTTCGATTTAATTAGACATTAATTCGGTAAAAAAATGGAAAAACGATATTAGA
64 ATCTGAATCTTGTTTCGATTTAATTA-A-AAAAAGTCGG-AAAAAAATGGAAAAACGATATTAGA
* *
1755 AGCGTGAAGAAACCCTTCAATTTTTTTGGCGTTAAATTATATATTTTTTCTGAGTATTGTGACAA
126 AGCGTGAA-AAACCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAA
* ** * * * *
1820 AAAAATGAGAAAAAAAACTTTTCGGGCCAGTTTTTGAAAAATTTTAGCCGAAATTGTGTACTCAT
190 AAAATTGAG-AAAAAATTTTTTCAGGTCAG----T------TTTTAGCCGAAATCGTGTACT-AA
* ** * * * * * * * *
1885 TCAAAATTGGTTTTTGGTTAAAAACGTGTTCCGGGGACC-CACCTCAATTTTGCATGATTTTTGG
243 CCATCA-CGGTTTTCGGCTAAAAACGCGTTTC-GGGACCTGA-CTCAGTTTTGAATGATTTTTGG
1949 CAGAAAGACTCCTTGA
305 CAGAAAGACTCCTTGA
** *
1965 AATATCTGCATTCATCTAACCAAATCTCAGCCACATTGGATATAAGGATTTGTTTTTACGAGCAT
1 AATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCAT
* **
2030 CTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAAAAAAAGATAATGGAAAAACGATATTAGA
66 CTGAATCTTGTTTCGATTTAATTA-AAA-AAAGTC-GGAAAA-A-AATGGAAAAACGATATTAGA
* * *
2095 AGTGTGAAAAACCCTTCAATTTTTTTGGCGTTGAATTATATAATTTTTT-TGAGCATTGTAGCAA
126 AGCGTGAAAAACCCTTCAATTTTTTTGGCGTTGAATTATAT-ATTTTTTCTGAGTATTGTGGCAA
* * *
2159 AAATTTGAGGAAAAACTTTTT
190 AAAATTGAGAAAAAATTTTTT
2180 GGGTCAATTT
Statistics
Matches: 1574, Mismatches: 202, Indels: 136
0.82 0.11 0.07
Matches are distributed among these distances:
314 25 0.02
315 89 0.06
316 6 0.00
317 13 0.01
318 54 0.03
319 37 0.02
320 99 0.06
321 211 0.13
322 13 0.01
323 29 0.02
324 194 0.12
325 60 0.04
326 4 0.00
327 20 0.01
328 19 0.01
329 40 0.03
330 70 0.04
331 40 0.03
332 73 0.05
333 61 0.04
334 137 0.09
335 1 0.00
336 21 0.01
337 7 0.00
338 161 0.10
339 56 0.04
340 34 0.02
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.35
Consensus pattern (320 bp):
AATATCTATATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCAT
CTGAATCTTGTTTCGATTTAATTAAAAAAAGTCGGAAAAAAATGGAAAAACGATATTAGAAGCGT
GAAAAACCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATT
GAGAAAAAATTTTTTCAGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTCGGCT
AAAAACGCGTTTCGGGACCTGACTCAGTTTTGAATGATTTTTGGCAGAAAGACTCCTTGA
Found at i:2702 original size:687 final size:682
Alignment explanation
Indices: 1532--3688 Score: 2661
Period size: 687 Copynumber: 3.1 Consensus size: 682
1522 AAATTTTAGC
* * * * * *
1532 CGAAATTGTGTACTAACCATCACGGTTTTTGGCTAAAAA-CACGTTCCGGAGCCCCGACTCAATT
1 CGAAATCGTGTACTAACCATCACGGTTTTTGGC-AAAAACCGCGTTCCGAAGTCTCGGCTCAATT
*
1596 TTGCATGATTTTTGGCGTAAAGACTCCTTGAAATAT-TCATATTCATCGAACCAAATGC-CAGCC
65 TTGCATGATTTTTGGCG-AAAGACTCATTGAAATATCT-ATATTCATCGAACCAAAT-CTCAGCC
*
1659 ACATTGGATATAAGGA-TTTGTTTTTACGAGTATCTGAATCTTGTTTCGATTTAATTAGACATTA
127 ACATTGGATATAAGGATTTTGTTTTTACGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATTA
* * * * *
1723 ATTCGG-TAAAAA-AATGGAAAAACGATATTAGAAGCGTGAAGAAACCCTTCAATTTTTTTGGCG
192 ATTCGGAAAAAAATAATGGAAAAACGATATTAGAAGCATGAA-AAGCCCATCAATCTTTTTGGCG
* * * * *
1786 TTAAATTATATATTTTTTCTGAGTATTGTGACAAAAAAATGAGAAAAAAAACTTTTCGGGCCAGT
256 TTGAATTATATATTTTTTATGAGTATTTTG-CAAAAAATTGAG---AAAAACTTTTCGGGTCAG-
* * * *
1851 TTTTGAAAAATTTTAGCCGAAATTGTGTACTCATTCAAAATTGGTTTTTGGTTAAAAACGTGTTC
316 ---T------TTTTAGCCGAAATTGTGTACT-A-ACATAA-TGGTTTTTGGCTAAAAACGTGTTT
* **
1916 CGGGGACCC-ACCTCAATTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTGCATTCAT
369 CAGGG-CCCGA-CTCAATTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCAT
* *
1980 CTAACCAAATCTCAGCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCG
432 CTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCG
* * *
2045 ATTTAATTAGAAATAAATTCAAAAAAAGATAATGGAAAAACGATATT-AGAAGTGTGAAAAACCC
497 ATTTAATTAGAAATAAATTC-AGAAAA-A-AATGGGAAAACGATATTGA-AAGCGTGAAAAACCC
* *
2109 TTCAA-TTTTTTTGGCGTTGAATTATATAATTTTTT-TGAGCATTGTAG-C-AAAAATTTGAGGA
558 TTCAATTTTTTTTGGCGTTGAATTATAT-ATTTTTTCTGAGTATTGT-GTCAAAAAAATTGAGGA
** * *
2170 AAAACTTTTTGGGTCAATTTTTGCAAAATTTTCGTCGAAATCGTGTACTTTTTGTTTTGGCCAA
621 AAAACTTTTCAGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTTTTT-TTTT-GCCAA
* * * * *
2234 CGCAATTGTGTACTAACCATCACGGTTTTTTGCCTAAAAA-CGCGTTCTGGAGTCTCGGCTCAAT
1 CGAAATCGTGTACTAACCATCACGG-TTTTTGGC-AAAAACCGCGTTCCGAAGTCTCGGCTCAAT
* * * * *
2298 TTGGCATGATTTTTGGCG-CAGACTCTTTGAAATATCTATATTAATCAAACCAAATCTCAGCCAC
64 TTTGCATGATTTTTGGCGAAAGACTCATTGAAATATCTATATTCATCGAACCAAATCTCAGCCAC
* ** *
2362 ATTGTATATAAAAATTTTGTTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
129 ATTGGATATAAGGATTTTG-TTTTTACGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
** * *
2427 TTCGGAAAAAAATAATGGAAAAACGATATTAGAAGCAACAAAAGGCCGTCAATCTTTTTGGCGTT
193 TTCGGAAAAAAATAATGGAAAAACGATATTAGAAGCATGAAAAGCCCATCAATCTTTTTGGCGTT
* * *
2492 GAATTAT-TTTTTTTTTTGAATATTTTGCAAAAAATTGAGAAAAACTTTTCGGGTCAGTTTTTAG
258 GAATTATATATTTTTTATGAGTATTTTGCAAAAAATTGAGAAAAACTTTTCGGGTCAGTTTTTAG
* * * * ** *
2556 CCGAAATCGTGTACTAACCATCATGATTTTTGGCTAAAAACGAGTTTCATAGCCCTGACTCAGTT
323 CCGAAATTGTGTACTAA-CATAATGGTTTTTGGCTAAAAACGTGTTTCAGGGCCC-GACTCAATT
** *
2621 TTTAATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCAC
386 TTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCAC
* * *
2686 AATGGATTTAAGGATTTGTTTTTACCAGCATCCAAATCTTTGTTTCGATTTAATTAGAAATAAAT
451 ATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATC-TTGTTTCGATTTAATTAGAAATAAAT
2751 TCAGAAAAAAATGGGAAAACGATATTGAAAGCGTG-AAAACCCTTTCAATTTTTTTTGGCGTTGA
515 TCAGAAAAAAATGGGAAAACGATATTGAAAGCGTGAAAAACCC-TTCAATTTTTTTTGGCGTTGA
* *
2815 ATTATATATTTTTTCTGAGTATTGTGTCAAAAAAATTGAGGAAAAACTTTTCATGTCAAGTTTTG
579 ATTATATATTTTTTCTGAGTATTGTGTCAAAAAAATTGAGGAAAAACTTTTCAGGTCAATTTTTG
* *
2880 CAAAATTTTAGCCGAAATTGTGCACTTTTTTTTTTGCCAA
644 CAAAATTTTAGCCGAAATCGTGTAC-TTTTTTTTTGCCAA
* *
2920 CGAAATCGTGTACTAACTATCACGGTTTTTGGCAAAAACCGTGTTCCGAAGTCTCGGCTCAATTT
1 CGAAATCGTGTACTAACCATCACGGTTTTTGGCAAAAACCGCGTTCCGAAGTCTCGGCTCAATTT
*
2985 TGCATGATTTTCGGCGTAAAGACTCATTGAAATATCTATATTCATCGAACCAAATCTCAGCCAGC
66 TGCATGATTTTTGGCG-AAAGACTCATTGAAATATCTATATTCATCGAACCAAATCT----CAGC
* * * * * *
3050 CACATTGGATTTAAGGATTTTCTTTTTACGAGTTTCTGAATTTTGTTTTGATTTAATTTGAAATT
126 CACATTGGATATAAGGATTTTGTTTTTACGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATT
* * * *
3115 AATTTGGAAAAAAAT--TGGAAAACCGATATTAGAAACCTGAAAAGCCCATCAATCTTTTTGGCG
191 AATTCGGAAAAAAATAATGGAAAAACGATATTAGAAGCATGAAAAGCCCATCAATCTTTTTGGCG
* * * *
3178 TTGAATTATATATTTTTTATGAGTATTGTGGCAAAAAATTGAGAAAGAATTTTTTGGGTTAGTTT
256 TTGAATTATATATTTTTTATGAGTATT-TTGCAAAAAATTGAGAAA-AACTTTTCGGGTCAGTTT
* * * * *
3243 TTAGCCGAAATTGTTTAC--ACGTTACGGTTTTTGGCTAAAAACGTGTTTCAGGGCCCCGATTCA
319 TTAGCCGAAATTGTGTACTAACATAATGGTTTTTGGCTAAAAACGTGTTTCAGGG-CCCGACTCA
* * * *
3306 ATTTTGCAT-TTTTTTGGCAGAAAGAATCTTTGAAATATCTATATTCATCTAACCAAATCTTAGC
383 ATTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGC
* * * * * * *
3370 TACATTAGATTCACGGATTTGTTTTTATGAGCACCTAAATCTTGTTTCGATTAAATTA-AAA-AA
448 CACATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATAA
* ** *
3433 A-TCGGAAAAAAATGGGAAAACGATGCTGAAAGCGTGAAAACCCCTTCAATTTTTTTTGGCGTTG
513 ATTCAGAAAAAAATGGGAAAACGATATTGAAAGCGTGAAAAACCCTTCAATTTTTTTTGGCGTTG
3497 AATTATATATTTTTTCTGAGTATTGTGTCAAAAAAATTGAGGAAAAACTTTTCAGGTCAATTTTT
578 AATTATATATTTTTTCTGAGTATTGTGTCAAAAAAATTGAGGAAAAACTTTTCAGGTCAATTTTT
*
3562 GCAAAATTTTAGCCGAAATCGTATACTTTTTTTTTGCCAA
643 GCAAAATTTTAGCCGAAATCGTGTACTTTTTTTTTGCCAA
* * * *
3602 CGAAATCGTATACTAACTATCACGGTTTTTGGCAAAAACCGCGTTCTGAAGTCTCGGCTCAGTTT
1 CGAAATCGTGTACTAACCATCACGGTTTTTGGCAAAAACCGCGTTCCGAAGTCTCGGCTCAATTT
3667 TGCATGATTTTTGGCGTAAAGA
66 TGCATGATTTTTGGCG-AAAGA
3689 TTAGTGGCAA
Statistics
Matches: 1278, Mismatches: 147, Indels: 80
0.85 0.10 0.05
Matches are distributed among these distances:
682 96 0.08
683 138 0.11
684 21 0.02
685 82 0.06
686 80 0.06
687 299 0.23
688 126 0.10
689 38 0.03
690 69 0.05
691 52 0.04
695 1 0.00
699 17 0.01
700 1 0.00
701 49 0.04
702 40 0.03
703 113 0.09
704 31 0.02
705 25 0.02
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (682 bp):
CGAAATCGTGTACTAACCATCACGGTTTTTGGCAAAAACCGCGTTCCGAAGTCTCGGCTCAATTT
TGCATGATTTTTGGCGAAAGACTCATTGAAATATCTATATTCATCGAACCAAATCTCAGCCACAT
TGGATATAAGGATTTTGTTTTTACGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTC
GGAAAAAAATAATGGAAAAACGATATTAGAAGCATGAAAAGCCCATCAATCTTTTTGGCGTTGAA
TTATATATTTTTTATGAGTATTTTGCAAAAAATTGAGAAAAACTTTTCGGGTCAGTTTTTAGCCG
AAATTGTGTACTAACATAATGGTTTTTGGCTAAAAACGTGTTTCAGGGCCCGACTCAATTTTGCA
TGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGG
ATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATAAATTCAGAA
AAAAATGGGAAAACGATATTGAAAGCGTGAAAAACCCTTCAATTTTTTTTGGCGTTGAATTATAT
ATTTTTTCTGAGTATTGTGTCAAAAAAATTGAGGAAAAACTTTTCAGGTCAATTTTTGCAAAATT
TTAGCCGAAATCGTGTACTTTTTTTTTGCCAA
Found at i:22370 original size:26 final size:26
Alignment explanation
Indices: 22354--22409 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
22344 CGACAGCTAT
22354 TGCCAAACCAATAATACGACAACCAC
1 TGCCAAACCAATAATACGACAACCAC
22380 TGCCAAACCAATAATACGACAACCAC
1 TGCCAAACCAATAATACGACAACCAC
22406 TGCC
1 TGCC
22410 TAAGAAGTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.43, C:0.36, G:0.09, T:0.12
Consensus pattern (26 bp):
TGCCAAACCAATAATACGACAACCAC
Found at i:40363 original size:134 final size:134
Alignment explanation
Indices: 40123--40394 Score: 544
Period size: 134 Copynumber: 2.0 Consensus size: 134
40113 AAAAAAGAAA
40123 AAATGAGAGAAATGTTCGATCAGATATTTGGGTCGGTTTTCCAACTCCATTTTCTCTCTAAGATC
1 AAATGAGAGAAATGTTCGATCAGATATTTGGGTCGGTTTTCCAACTCCATTTTCTCTCTAAGATC
40188 ATTACTTTGAAAGCGATCAAAGAGTTGCAACCATAGCAAAAAAAAGGAAGAGCATCTTTTTGCAT
66 ATTACTTTGAAAGCGATCAAAGAGTTGCAACCATAGCAAAAAAAAGGAAGAGCATCTTTTTGCAT
40253 ACGG
131 ACGG
40257 AAATGAGAGAAATGTTCGATCAGATATTTGGGTCGGTTTTCCAACTCCATTTTCTCTCTAAGATC
1 AAATGAGAGAAATGTTCGATCAGATATTTGGGTCGGTTTTCCAACTCCATTTTCTCTCTAAGATC
40322 ATTACTTTGAAAGCGATCAAAGAGTTGCAACCATAGCAAAAAAAAGGAAGAGCATCTTTTTGCAT
66 ATTACTTTGAAAGCGATCAAAGAGTTGCAACCATAGCAAAAAAAAGGAAGAGCATCTTTTTGCAT
40387 ACGG
131 ACGG
40391 AAAT
1 AAAT
40395 TAAACAGAGA
Statistics
Matches: 138, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
134 138 1.00
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (134 bp):
AAATGAGAGAAATGTTCGATCAGATATTTGGGTCGGTTTTCCAACTCCATTTTCTCTCTAAGATC
ATTACTTTGAAAGCGATCAAAGAGTTGCAACCATAGCAAAAAAAAGGAAGAGCATCTTTTTGCAT
ACGG
Found at i:51798 original size:31 final size:31
Alignment explanation
Indices: 51760--51858 Score: 105
Period size: 31 Copynumber: 3.3 Consensus size: 31
51750 AGTATCTAAA
* *
51760 TAGTCCCTGTATTATTGAAAAAAGATCATTT
1 TAGTCCCTGTATTATTGAAAAAAAATCAATT
* ***
51791 TAGTCCCTCTATTA-TG-AAATCTATCAATT
1 TAGTCCCTGTATTATTGAAAAAAAATCAATT
*
51820 TAGTCCCTGTACTATT-AAAAAACAATCAATT
1 TAGTCCCTGTATTATTGAAAAAA-AATCAATT
51851 TAGTCCCT
1 TAGTCCCT
51859 CTATGAAATA
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
29 21 0.38
30 6 0.11
31 28 0.51
ACGTcount: A:0.34, C:0.19, G:0.09, T:0.37
Consensus pattern (31 bp):
TAGTCCCTGTATTATTGAAAAAAAATCAATT
Found at i:53648 original size:30 final size:31
Alignment explanation
Indices: 53606--53683 Score: 115
Period size: 30 Copynumber: 2.5 Consensus size: 31
53596 CTTTCCCCTT
53606 AATCTCTCTTTCAAGAATTGTGCCAAAAAAA
1 AATCTCTCTTTCAAGAATTGTGCCAAAAAAA
* *
53637 ATAT-T-TCTTTCATGATTTGTGCCAAAAAAA
1 A-ATCTCTCTTTCAAGAATTGTGCCAAAAAAA
53667 AATCTCTCTTTCAAGAA
1 AATCTCTCTTTCAAGAA
53684 ACTGCAAATC
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
29 2 0.05
30 25 0.62
31 11 0.28
32 2 0.05
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (31 bp):
AATCTCTCTTTCAAGAATTGTGCCAAAAAAA
Found at i:53668 original size:31 final size:30
Alignment explanation
Indices: 53610--53683 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 30
53600 CCCCTTAATC
53610 TCTCTTTCAAGAATTGTGCCAAAAAAAATA
1 TCTCTTTCAAGAATTGTGCCAAAAAAAATA
* * * *
53640 TTTCTTTCATGATTTGTGCCAAAAAAAAATC
1 TCTCTTTCAAGAATTGTGCC-AAAAAAAATA
53671 TCTCTTTCAAGAA
1 TCTCTTTCAAGAA
53684 ACTGCAAATC
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
30 17 0.47
31 19 0.53
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (30 bp):
TCTCTTTCAAGAATTGTGCCAAAAAAAATA
Found at i:54012 original size:7 final size:7
Alignment explanation
Indices: 54000--54025 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
53990 TCAATATCTC
54000 TTTTCAA
1 TTTTCAA
54007 TTTTCAA
1 TTTTCAA
54014 TTTTCAA
1 TTTTCAA
54021 TTTTC
1 TTTTC
54026 TGATATCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (7 bp):
TTTTCAA
Found at i:54372 original size:197 final size:197
Alignment explanation
Indices: 54037--54433 Score: 758
Period size: 197 Copynumber: 2.0 Consensus size: 197
54027 GATATCTAAT
54037 CAACTATGGTAATCCTAGGCAATGGATTTGTTGAAAGAATTAGGTCTTCTTGCACTAGGGTCGAC
1 CAACTATGGTAATCCTAGGCAATGGATTTGTTGAAAGAATTAGGTCTTCTTGCACTAGGGTCGAC
54102 AAACTTACAGCGGCAAGAACCGCAGAAAGAAACACCATAGGGCAGTTGAAGGGTTTAATTTACCG
66 AAACTTACAGCGGCAAGAACCGCAGAAAGAAACACCATAGGGCAGTTGAAGGGTTTAATTTACCG
*
54167 TAACATAGTGGATTTTAACAAAGTTTCCAATGACCGAATCCTGCAAAATGTTGAGCCTGAAACTC
131 TAACATAGTGGATTTTAACAAAGTTTCCAATGACCGAATCCTACAAAATGTTGAGCCTGAAACTC
54232 AA
196 AA
54234 CAACTATGGTAATCCTAGGCAATGGATTTGTTGAAAGAATTAGGTCTTCTTGCACTAGGGTCGAC
1 CAACTATGGTAATCCTAGGCAATGGATTTGTTGAAAGAATTAGGTCTTCTTGCACTAGGGTCGAC
* *
54299 AAACTTACAGCGGCAAGAACCGCCGAAAGAAACACCATAGGGCGGTTGAAGGGTTTAATTTACCG
66 AAACTTACAGCGGCAAGAACCGCAGAAAGAAACACCATAGGGCAGTTGAAGGGTTTAATTTACCG
*
54364 TAACATAGTGGATTTTGACAAAGTTTCCAATGACCGAATCCTACAAAATGTTGAGCCTGAAACTC
131 TAACATAGTGGATTTTAACAAAGTTTCCAATGACCGAATCCTACAAAATGTTGAGCCTGAAACTC
54429 AA
196 AA
54431 CAA
1 CAA
54434 TTGATTTATA
Statistics
Matches: 196, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
197 196 1.00
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (197 bp):
CAACTATGGTAATCCTAGGCAATGGATTTGTTGAAAGAATTAGGTCTTCTTGCACTAGGGTCGAC
AAACTTACAGCGGCAAGAACCGCAGAAAGAAACACCATAGGGCAGTTGAAGGGTTTAATTTACCG
TAACATAGTGGATTTTAACAAAGTTTCCAATGACCGAATCCTACAAAATGTTGAGCCTGAAACTC
AA
Found at i:55353 original size:13 final size:13
Alignment explanation
Indices: 55335--55373 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
55325 ATATAATAGT
55335 ATAGTAAGATA-A
1 ATAGTAAGATATA
55347 GATAGTAAGATATA
1 -ATAGTAAGATATA
*
55361 ATAGTAAAATATA
1 ATAGTAAGATATA
55374 TAGGTGCGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 23 0.96
14 1 0.04
ACGTcount: A:0.56, C:0.00, G:0.15, T:0.28
Consensus pattern (13 bp):
ATAGTAAGATATA
Found at i:56502 original size:31 final size:31
Alignment explanation
Indices: 56459--56527 Score: 120
Period size: 31 Copynumber: 2.2 Consensus size: 31
56449 TACATCTTAG
56459 GTCCCTGAATATTAATTAATTGTGCAAATAA
1 GTCCCTGAATATTAATTAATTGTGCAAATAA
* *
56490 GTCCTTGAATATTAATTAATTGTGCAATTAA
1 GTCCCTGAATATTAATTAATTGTGCAAATAA
56521 GTCCCTG
1 GTCCCTG
56528 TAATCAAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.38
Consensus pattern (31 bp):
GTCCCTGAATATTAATTAATTGTGCAAATAA
Found at i:60871 original size:21 final size:21
Alignment explanation
Indices: 60839--60888 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
60829 CGGGTTGAAG
* *
60839 AAGAAGAAAAAAGAAAAGGGAA
1 AAGAAAAAAAAACAAAA-GGAA
60861 AAGAAAAAAAAACAAAAGGAA
1 AAGAAAAAAAAACAAAAGGAA
*
60882 AGGAAAA
1 AAGAAAA
60889 GCTAAATGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 10 0.40
22 15 0.60
ACGTcount: A:0.76, C:0.02, G:0.22, T:0.00
Consensus pattern (21 bp):
AAGAAAAAAAAACAAAAGGAA
Done.