Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019964.1 Corchorus olitorius cultivar O-4 contig19997, 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: 13564
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:2146 original size:330 final size:328
Alignment explanation
Indices: 575--2870 Score: 2033
Period size: 332 Copynumber: 6.9 Consensus size: 328
565 GACAATCTAG
* * * *
575 ATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAGTAGGAAAAACGATATTAGAAGCGTAA
1 ATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAA-TATGAAAAACGATATTAAAAGCGTGA
** ** * * * * * * *
640 AAAACCCTTTAATATTTTTGGCATTGAATTATATATTTTTTATAAGTATTTTACCCAAAAATTG-
65 AAAGTCCTCCAATTTTTTTGGCGTTAAATTATATATATTTTATGAGTATTTTAGCTAAAAATTGA
* * * * * * *
704 AGGAAATATCTTTCGGGCAATTTTTTGCAAAATTTTAGCAGAATTCTTGTAATAATC-ATCACGA
130 AGAAAAAAT-TTTCGGTC-ATTTTTTGCAAAATTTTAGCCGAAATC-TGTAGTAA-CAATCACGG
* * * ** ** * *
768 TTTATT-GCTAAAAATGTGTTCCAAGGCCCCGGGTCAGTTTTGCATGATTTTTGGCGCCACGAGT
191 TTT-TTGGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACT
* * * * *
832 CCTTGAGATATCCATATTCATCTAATCAAATCTCATG-CACATTGCATTTAAGGATTTGTTTTTA
255 CCTTGAAATATCTATATTCATCTAATCAAATCTTA-GCCACATTGGATTTAAGGATTT-TTTTAA
* *
896 CGACCATATGA
318 CGAGCATCTGA
* * *
907 ATCTTGTTTCAATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATGAAAAGTGTGA
1 ATCTTGTTTCGATTTAATTAGAAATTAATTCAG-AAAAATATGAAAAACGATATTAAAAGCGTGA
* * * *
972 AAAGTCCTCCAATTTTTTTGGTGCTAAATTATATATATTTCAAGAGTATTTTAGCTAAAAATT-A
65 AAAGTCCTCCAATTTTTTTGGCGTTAAATTATATATATTTTATGAGTATTTTAGCTAAAAATTGA
* * *
1036 AGGAAAAAAATTTTGGGTCATTTTTTGTAAAATTTTAGCCGAAAT-TGT-GT-ACCATCACGGTT
130 A-G-AAAAAATTTTCGGTCATTTTTTGCAAAATTTTAGCCGAAATCTGTAGTAACAATCACGG--
* ** * *
1098 TTTTTTGCT-AAAACGCGTTTCAAGGCCCC-AGCTCAGTTTTGCATGATTTTTGGCGTCGAGACT
191 TTTTTGGCTAAAAACGCGTTTCGGGGCCCCGA-CTCAGTTTTGCATGATTTTTGGCGCCAAGACT
* * *
1161 CCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTAC
255 CCTTGAAATATCTATATTCATCTAATCAAATCTTAGCCACATTGGATTTAAGGATTT-TTTTAAC
1226 GAGCATCTGA
319 GAGCATCTGA
* *
1236 ATCTTGTTTGGATTTAATTAGAAATTAATTGAGAAAAATATGAAAAACGATATTAAAAGCGTGAA
1 ATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAA
* *
1301 AAGTCCTCCAATCTTTTTGGAGTTGAAA-TATATATATTTTATGAGTATTTTAGGC-AAAAATTG
66 AAGTCCTCCAATTTTTTTGGCGTT-AAATTATATATATTTTATGAGTATTTTA-GCTAAAAATTG
* * * * *
1364 AGGAAAAATATTTAT-GGTCAATTTTTGCAAAATATTAGGCGAAATCGTGTACGTTAGTCGAAAT
129 AAGAAAAA-ATTT-TCGGTCATTTTTTGCAAAATTTTAGCCGAAATC-TGTA-G-TA-AC--AAT
* * ** ** * * * *
1428 CACGGTTTCTGG-----AA-GTGTTTCGGGAACCCGGTTCAGTATTGCACGATTTTTGGCACCGA
186 CACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCCAA
* ** * * *
1487 GAATCCTTGAAATATCTATATTTTTCTAACCAAAT-TTCAGCTACATTGGATTTAAGGA-TTTGT
251 GACTCCTTGAAATATCTATATTCATCTAATCAAATCTT-AGCCACATTGGATTTAAGGATTTTTT
* * *
1550 AAACCAACCATCTGA
315 TAA-CGAGCATCTGA
** * * * * *
1565 ATCACGTTTCGATTTAATTTGAAATTAATTCGGAAAATAATAGGAAAAACGATATTAGAAGCATG
1 ATCTTGTTTCGATTTAATTAGAAATTAATTCAG-AAA-AATATGAAAAACGATATTAAAAGCGTG
* * * *
1630 AAAAG-CCATTCAATTTTTTTGGCGTTGAAATTATATA-ATTTTTATGAGTATTGTGGCTAAGAA
64 AAAAGTCC-TCCAATTTTTTTGGCGTT-AAATTATATATA-TTTTATGAGTATTTTAGCTAAAAA
* * * * * *
1693 TTGAGGAAATAACTTTCGAGTCATTTTTTTG-TAAATTTCTAGCCGAAATCGTGTAATAATAATC
126 TTGAAGAAAAAATTTTCG-GTCA-TTTTTTGCAAAATTT-TAGCCGAAATC-TGTAGTAACAATC
* ** * * * * *
1757 ACGGTTTTTGGCTAAAAAAGCGTCCCGGGGCTTCTG-CTAAATTTTACATGATTTTTGGCGCCAA
187 ACGGTTTTTGGCTAAAAACGCGTTTCGGGGC-CCCGACTCAGTTTTGCATGATTTTTGGCGCCAA
* * * * * *
1821 GACT-CTTAGAGATATCCATATTCATCTAATCGAATCTTGGCTACATTGGATTTAAGAATTTTTT
251 GACTCCTT-GAAATATCTATATTCATCTAATCAAATCTTAGCCACATTGGATTTAAGGATTTTTT
*
1885 TAACGAGCATCTAA
315 TAACGAGCATCTGA
* *
1899 ATCTTGTTTCGATTTAATTAGAAAATAGTTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAA
1 ATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAA
* * * * *
1964 AAGTCCTCCAATCTTTTTGGTGTTAAATTATGTATATATTATGAGTATTTTAGCCAAAAATTGAA
66 AAGTCCTCCAATTTTTTTGGCGTTAAATTATATATATTTTATGAGTATTTTAGCTAAAAATTGAA
** * *
2029 GAAAAAATTTTCGGTTCATTTTTTGCAAAATTTTAGTTGAAATCATATAGTAACCATCACGGTTT
131 GAAAAAATTTTCGG-TCATTTTTTGCAAAATTTTAGCCGAAATC-TGTAGTAACAATCACGGTTT
* * * * * *
2094 TTGGCTAAAAGCGCATTTCGGGGCCCCGACTTAGTTTTACATGATATTTGGCGCCGAGACTCCTT
194 TTGGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTT
* * * * * * *
2159 GAAATATCTATATTCATCTAATAAAATCTCATCCATATTGAATTTAAGGATTTGTTTATACGAGT
259 GAAATATCTATATTCATCTAATCAAATCTTAGCCACATTGGATTTAAGGATTTTTTTA-ACGAGC
*
2224 TTCTGA
323 ATCTGA
* *
2230 ATTTTGTTTCGATTTAATTA-AAATTAATTCAGAAAAATTTGAAAAACGATATTAAAAGCGTGAA
1 ATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAA
* * *
2294 AAGTCCTCCAATTTTTTTGGCGTTCAATTATATATATTTTATGAGTATTGTGGCTAAAAATTGAG
66 AAGTCCTCCAATTTTTTTGGCGTTAAATTATATATATTTTATGAGTATTTTAGCTAAAAATT--G
* **
2359 AAAAAAAATATATTTCGGGTCAAATTTTGCAAAATTTTAGCCGAAAT-TGT-GT-ACAATCACGG
129 AAGAAAAA-AT-TTTC-GGTCATTTTTTGCAAAATTTTAGCCGAAATCTGTAGTAACAATCACGG
* * * * * * *
2421 CTTCTTTGGCTAAAAACGCATTTTGGGGCCCCGAGTCAGTTTTGTATGATTTTTGGTGGCAAAAC
191 -TT-TTTGGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGAC
* * *
2486 TCCTTGTAATATCTATATTCATATAACCAAATCTTAGCCACATTGGATTTAAGGATTTTTTTTTT
254 TCCTTGAAATATCTATATTCATCTAATCAAATCTTAGCCACATTGGATTTAAGGA----TTTTTT
*** *
2551 TTGTGAGCATTTTGA
315 TAACGAGCA-TCTGA
* * * * *
2566 ATCATGTTTCAATTTAATTAGAAATTAATT-TGAAAAAATAGGAAAAACGATATTAGAAGCGGTG
1 ATCTTGTTTCGATTTAATTAGAAATTAATTCAG-AAAAATATGAAAAACGATATTAAAAGC-GTG
* * * * * *
2630 ATAAGCCCTTCAA-TTTTTTGGCGTTGAATTATATAT-TCTTTATGAGTATTGTGGCTAAAAATT
64 AAAAGTCCTCCAATTTTTTTGGCGTTAAATTATATATAT-TTTATGAGTATTTTAGCTAAAAATT
* * * * * * *
2693 GAA-AACAAATATTTCGGGTCAATTTTTGCAAAATTTTAACCGAAATC-AT-GT-ACCATAATGG
128 GAAGAAAAAAT-TTTC-GGTCATTTTTTGCAAAATTTTAGCCGAAATCTGTAGTAACAATCA-CG
* ** * *
2754 GTTTTTGGCTAAAAACGTGTTTCGGGG-CCCGTGTCAGTTTTGCATGATTTTTTGCACCAAGACT
190 GTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACT
* * * * * *
2818 CCTTAAAATATATCTTTATTCATTTAACCAAAT-TTCAGGCACATTGTATTTAA
255 CCTT-GAA-ATATCTATATTCATCTAATCAAATCTT-AGCCACATTGGATTTAA
2871 TCAAAAACTA
Statistics
Matches: 1615, Mismatches: 274, Indels: 149
0.79 0.13 0.07
Matches are distributed among these distances:
327 6 0.00
328 136 0.08
329 194 0.12
330 330 0.20
331 180 0.11
332 344 0.21
333 129 0.08
334 143 0.09
335 24 0.01
336 29 0.02
337 87 0.05
338 13 0.01
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (328 bp):
ATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAA
AAGTCCTCCAATTTTTTTGGCGTTAAATTATATATATTTTATGAGTATTTTAGCTAAAAATTGAA
GAAAAAATTTTCGGTCATTTTTTGCAAAATTTTAGCCGAAATCTGTAGTAACAATCACGGTTTTT
GGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGA
AATATCTATATTCATCTAATCAAATCTTAGCCACATTGGATTTAAGGATTTTTTTAACGAGCATC
TGA
Found at i:2802 original size:993 final size:979
Alignment explanation
Indices: 579--2818 Score: 2592
Period size: 993 Copynumber: 2.3 Consensus size: 979
569 ATCTAGATCT
* * *
579 TGTTTCGATTTAATTAGAAATTAATTCGGAAAAAGTAGGAAAAACGATATTAGAAGCGTAAAAAA
1 TGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAG
* * * * ** * *
644 CCCTTTAATATTTTTGGCATTGAATTATATATTTTTTATAAGTATTTTACCCAAAAATTGAGGAA
66 CCCTTCAAT-TTTTTGGCGTTGAATTATATA-TTTTTATGAGTATTGTGGCTAAAAATTGAGAAA
* * * * * *
709 ATATCTTTCGGG-CAATTTTTTGCAAAATTTTAGCAGAATTCTTGTAATAATCATCACGATTTAT
129 AAATCTTTCGGGTCAA-TTTTTGCAAAATTTTAGCCGAAATCATGTAATAATAAT-ACGGTTT-T
* * * * * *
773 T-GCTAAAAATGTGTTCCAAGGCCCCGGGTCAGTTTTGCATGATTTTTGGCGCCACGAGTCCTTG
191 TGGCTAAAAAAGTGTTCC-GGGGCCCGTGTCAGTTTTGCATGATTTTTGGCGCCAAGACT-CTTG
* *
837 AGATATCCATATTCATCTAATCAAATCTCATGCACATTGCATTTAAGGATTTGTTTTTACGACCA
254 AGATATCCATATTCATCTAATCAAATCT-ATGCACATTGCATTTAAGAATTTGTTTTAACGACCA
* *
902 TATGAATCTTGTTTCAATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATGAAAAG
318 TATAAATCTTGTTTCAATTTAATTAGAAAATAATTCAGAAAAAATATGAAAAACGATATGAAAAG
* * *
967 TGTGAAAAGTCCTCCAATTTTTTTGGTGCTAAATTATATATATTTCAAGAGTATTTTAGCTAAAA
383 CGTGAAAAGTCCTCCAATCTTTTTGGTGCTAAATTATATATATTTCAAGAGTATTTTAGCCAAAA
* *
1032 ATTAAGGAAAAAAATTTTGGGTCATTTTTTGTAAAATTTTAGCCGAAATTGTGTACCATCACGGT
448 ATTAAGGAAAAAAATTTTGGGTCATTTTTTGCAAAATTTTAGCCGAAATTATGTACCATCACGG-
* * * * *
1097 TTTTTTTGCTAAAACGCGTTTCAAGGCCCCAGCTCAGTTTTGCATGATTTTTGGCGTCGAGACTC
512 TTTTTTGGCTAAAACGCATTTCAAGGCCCCAGCTCAGTTTTACATGATATTTGGCGCCGAGACTC
* * *
1162 CTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACG
577 CTTGAAATATCTATATTCATCTAATAAAATCTCAGCCACATTGAATTTAAGGATTTGTTTATACG
* *
1227 AGCATCTGAATCTTGTTTGGATTTAATTAGAAATTAATTGAGAAAAATATGAAAAACGATATTAA
642 AGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAA
* *
1292 AAGCGTGAAAAGTCCTCCAATCTTTTTGGAGTTGAAATATATATATTTTATGAGTATTTTAGGCA
707 AAGCGTGAAAAGTCCTCCAATCTTTTTGGAGTTCAAATATATATATTTTATGAGTATTGTAGGCA
* * *
1357 AAAATTGAGGAAAAATATTTATGGTCAATTTTTGCAAAATATTAGGCGAAATCGTGTACGTTAGT
772 AAAATTGAGAAAAAATATTTATGGTCAAATTTTGCAAAATATTAGCCGAAATC-TGTA-GTTAG-
**
1422 CGAAATCACGGTTTCTGGAAGTGTTTCGGGAACCCGGTTCAGTATTGCACGATTTTTGGCACCGA
834 C-AAATCACGGTTTCTGGAAGCATTTCGGGAACCCGGTTCAGTATTGCACGATTTTTGGCACCGA
* ** * *
1487 GAATCCTTGAAATATCTATATTTTTCTAACCAAATTTCAGCTACATTGGATTTAAGGATTTGTAA
898 AAATCCTTGAAATATCTATATTCATATAACCAAATTTCAGCCACATTGGATTTAAGGATTTGTAA
1552 ACCAACCATCTGAATCA
963 ACCAACCATCTGAATCA
* * *
1569 CGTTTCGATTTAATTTGAAATTAATTCGGAAAATAATAGGAAAAACGATATTAGAAGCATGAAAA
1 TGTTTCGATTTAATTAGAAATTAATTCGGAAAA-AATAGGAAAAACGATATTAGAAGCGTGAAAA
* *
1634 GCCATTCAATTTTTTTGGCGTTGAAATTATATAATTTTTATGAGTATTGTGGCTAAGAATTGAGG
65 GCCCTTCAA-TTTTTTGGCGTTG-AATTATAT-ATTTTTATGAGTATTGTGGCTAAAAATTGA-G
* * * * *
1699 AAATAA-CTTTCGAGTCATTTTTTTG-TAAATTTCTAGCCGAAATCGTGTAATAATAATCACGGT
126 AAAAAATCTTTCGGGTCA-ATTTTTGCAAAATTT-TAGCCGAAATCATGTAATAATAAT-ACGGT
* * * * * *
1762 TTTTGGCTAAAAAAGCGTCCCGGGGCTTC-TGCTAAATTTTACATGATTTTTGGCGCCAAGACTC
188 TTTTGGCTAAAAAAGTGTTCCGGGGC-CCGTG-TCAGTTTTGCATGATTTTTGGCGCCAAGACTC
* *
1826 TTAGAGATATCCATATTCATCTAATCGAATCT-TGGCTACATTGGATTTAAGAATTT-TTTTAAC
251 TT-GAGATATCCATATTCATCTAATCAAATCTAT-GC-ACATTGCATTTAAGAATTTGTTTTAAC
* * * * *
1889 GAGCATCTAAATCTTGTTTCGATTTAATTAGAAAATAGTTCAG-AAAAATATGAAAAACGATATT
313 GACCATATAAATCTTGTTTCAATTTAATTAGAAAATAATTCAGAAAAAATATGAAAAACGATATG
* * *
1953 AAAAGCGTGAAAAGTCCTCCAATCTTTTTGGTGTTAAATTATGTATATATT-ATGAGTATTTTAG
378 AAAAGCGTGAAAAGTCCTCCAATCTTTTTGGTGCTAAATTATATATAT-TTCAAGAGTATTTTAG
* **
2017 CCAAAAATTGAA-G-AAAAAATTTTCGGTTCATTTTTTGCAAAATTTTAGTTGAAATCATATAGT
442 CCAAAAATT-AAGGAAAAAAATTTT-GGGTCATTTTTTGCAAAATTTTAGCCGAAAT--TAT-GT
** *
2080 AACCATCACGG-TTTTTGGCTAAAAGCGCATTTCGGGGCCCC-GACTTAGTTTTACATGATATTT
502 -ACCATCACGGTTTTTTGGCTAAAA-CGCATTTCAAGGCCCCAG-CTCAGTTTTACATGATATTT
* *
2143 GGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATAAAATCTCATCCATATTGAATTTAAGG
564 GGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATAAAATCTCAGCCACATTGAATTTAAGG
** * *
2208 ATTTGTTTATACGAGTTTCTGAATTTTGTTTCGATTTAATTA-AAATTAATTCAGAAAAATTTGA
629 ATTTGTTTATACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGA
* * *
2272 AAAACGATATTAAAAGCGTGAAAAGTCCTCCAATTTTTTTGGCGTTCAATTATATATATTTTATG
694 AAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGAGTTCAAATATATATATTTTATG
*
2337 AGTATTGT-GGCTAAAAATTGAGAAAAAAAATATATT-TCGGGTCAAATTTTGCAAAATTTTAGC
759 AGTATTGTAGGC-AAAAATTGAG--AAAAAATAT-TTAT--GGTCAAATTTTGCAAAATATTAGC
* * **
2400 CGAAAT-TGT-G-TA-C-AATCACGGCTTCTTTGGCTAAAAACGCATTTTGGGGCCCCGAG-TCA
818 CGAAATCTGTAGTTAGCAAATCACGG-TT-TCTGG-----AA-GCATTTCGGGAACCCG-GTTCA
* * * *** *
2459 GTTTTGTATGATTTTTGGTGGC-AAAACTCCTTGTAATATCTATATTCATATAACCAAATCTT-A
874 GTATTGCACGATTTTTGGCACCGAAAA-TCCTTGAAATATCTATATTCATATAACCAAAT-TTCA
* ****** * *
2522 GCCACATTGGATTTAAGGATTTTTTTTTTTTGTGAGCATTTTGAATCA
937 GCCACATTGGATTTAAGGA----TTTGTAAACCAACCA-TCTGAATCA
* * *
2570 TGTTTCAATTTAATTAGAAATTAATT-TGAAAAAATAGGAAAAACGATATTAGAAGCGGTGATAA
1 TGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATAGGAAAAACGATATTAGAAGC-GTGAAAA
2634 GCCCTTCAATTTTTTGGCGTTGAATTATATATTCTTTATGAGTATTGTGGCTAAAAATTGA-AAA
65 GCCCTTCAATTTTTTGGCGTTGAATTATATATT-TTTATGAGTATTGTGGCTAAAAATTGAGAAA
* * ** *
2698 CAAATATTTCGGGTCAATTTTTGCAAAATTTTAACCGAAATCATGT-ACCATAAT-GGGTTTTTG
129 -AAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCATGTAATAATAATACGGTTTTTG
* * * *
2761 GCTAAAAACGTGTTTCGGGGCCCGTGTCAGTTTTGCATGATTTTTTGCACCAAGACTC
193 GCTAAAAAAGTGTTCCGGGGCCCGTGTCAGTTTTGCATGATTTTTGGCGCCAAGACTC
2819 CTTAAAATAT
Statistics
Matches: 1056, Mismatches: 143, Indels: 99
0.81 0.11 0.08
Matches are distributed among these distances:
988 8 0.01
989 2 0.00
990 46 0.04
991 158 0.15
992 108 0.10
993 267 0.25
994 156 0.15
995 27 0.03
996 88 0.08
997 54 0.05
998 49 0.05
999 37 0.04
1000 25 0.02
1001 31 0.03
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (979 bp):
TGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATAGGAAAAACGATATTAGAAGCGTGAAAAG
CCCTTCAATTTTTTGGCGTTGAATTATATATTTTTATGAGTATTGTGGCTAAAAATTGAGAAAAA
ATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCATGTAATAATAATACGGTTTTTGGCT
AAAAAAGTGTTCCGGGGCCCGTGTCAGTTTTGCATGATTTTTGGCGCCAAGACTCTTGAGATATC
CATATTCATCTAATCAAATCTATGCACATTGCATTTAAGAATTTGTTTTAACGACCATATAAATC
TTGTTTCAATTTAATTAGAAAATAATTCAGAAAAAATATGAAAAACGATATGAAAAGCGTGAAAA
GTCCTCCAATCTTTTTGGTGCTAAATTATATATATTTCAAGAGTATTTTAGCCAAAAATTAAGGA
AAAAAATTTTGGGTCATTTTTTGCAAAATTTTAGCCGAAATTATGTACCATCACGGTTTTTTGGC
TAAAACGCATTTCAAGGCCCCAGCTCAGTTTTACATGATATTTGGCGCCGAGACTCCTTGAAATA
TCTATATTCATCTAATAAAATCTCAGCCACATTGAATTTAAGGATTTGTTTATACGAGCATCTGA
ATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAA
AAGTCCTCCAATCTTTTTGGAGTTCAAATATATATATTTTATGAGTATTGTAGGCAAAAATTGAG
AAAAAATATTTATGGTCAAATTTTGCAAAATATTAGCCGAAATCTGTAGTTAGCAAATCACGGTT
TCTGGAAGCATTTCGGGAACCCGGTTCAGTATTGCACGATTTTTGGCACCGAAAATCCTTGAAAT
ATCTATATTCATATAACCAAATTTCAGCCACATTGGATTTAAGGATTTGTAAACCAACCATCTGA
ATCA
Found at i:4647 original size:22 final size:22
Alignment explanation
Indices: 4555--4924 Score: 100
Period size: 22 Copynumber: 16.6 Consensus size: 22
4545 ACTTTGCAGA
4555 TTATCAAAATTTCATAGTGTGGC
1 TTATCAAAATTTCATAGTGT-GC
* * *
4578 -AATCAAAATTTCATAATGTGG
1 TTATCAAAATTTCATAGTGTGC
* ***
4599 TTCT-AAAATTTTCATAGAAAG-
1 TTATCAAAA-TTTCATAGTGTGC
* *
4620 TAATCAAAATTTCATATTGTGC
1 TTATCAAAATTTCATAGTGTGC
** * *
4642 TTATCAAAATTTCATTTTGAGA
1 TTATCAAAATTTCATAGTGTGC
* * *
4664 TTAACAAAA-TTCTATAGGGAAG-
1 TTATCAAAATTTC-ATAGTG-TGC
* * *
4686 TTATC-AATTTTCCATAGGGAG-
1 TTATCAAAATTT-CATAGTGTGC
* *
4707 TTATCAAAATTTCATAGTATGA
1 TTATCAAAATTTCATAGTGTGC
* * *
4729 TTATCCAAATTTCATAGAGTACC
1 TTATCAAAATTTCATAGTGT-GC
** *** * *
4752 AAATCAGCCTTTCGCAATTAATGTGG
1 TTATCAAAATTT--C-A-TAGTGTGC
* * *
4778 TTATCAAAATTTTATAGTGAGG
1 TTATCAAAATTTCATAGTGTGC
* * *
4800 TCATCAAAATTAATTTCATA-TAGAGG
1 TTATC--AA--AATTTCATAGT-GTGC
* * *
4826 TTATCACAATTTTATAGTGTGT
1 TTATCAAAATTTCATAGTGTGC
4848 TTATCAAAATTTCATA-TG-G-
1 TTATCAAAATTTCATAGTGTGC
*
4867 TGATCAAAATTTCATAG-GATAG-
1 TTATCAAAATTTCATAGTG-T-GC
*
4889 TTATCAAAATTTCATAGTGTGA
1 TTATCAAAATTTCATAGTGTGC
* *
4911 GTATCAAAGTTTCA
1 TTATCAAAATTTCA
4925 CAGGGAGGTT
Statistics
Matches: 255, Mismatches: 65, Indels: 55
0.68 0.17 0.15
Matches are distributed among these distances:
19 16 0.06
20 1 0.00
21 36 0.14
22 157 0.62
23 12 0.05
24 3 0.01
25 2 0.01
26 24 0.09
27 4 0.02
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.38
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGTGC
Found at i:4655 original size:43 final size:44
Alignment explanation
Indices: 4555--4656 Score: 118
Period size: 43 Copynumber: 2.3 Consensus size: 44
4545 ACTTTGCAGA
*** *
4555 TTATCAAAATTTCATAGTGTGGCAATCAAAATTTCATAATGTGG
1 TTATCAAAATTTCATAGTAAAGCAATCAAAATTTCATAATGTGC
* * *
4599 TTCT-AAAATTTTCATAG-AAAGTAATCAAAATTTCATATTGTGC
1 TTATCAAAA-TTTCATAGTAAAGCAATCAAAATTTCATAATGTGC
4642 TTATCAAAATTTCAT
1 TTATCAAAATTTCAT
4657 TTTGAGATTA
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
43 33 0.69
44 15 0.31
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.39
Consensus pattern (44 bp):
TTATCAAAATTTCATAGTAAAGCAATCAAAATTTCATAATGTGC
Found at i:4938 original size:44 final size:41
Alignment explanation
Indices: 4848--4928 Score: 108
Period size: 41 Copynumber: 1.9 Consensus size: 41
4838 TATAGTGTGT
* *
4848 TTATCAAAATTTCATATGGTGATCAAAATTTCATAGGATAG
1 TTATCAAAATTTCATATGGAGATCAAAATTTCACAGGATAG
*
4889 TTATCAAAATTTCATAGTGTGAGTATCAAAGTTTCACAGG
1 TTATCAAAATTTCATA-TG-GAG-ATCAAAATTTCACAGG
4929 GAGGTTATCA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
41 16 0.47
42 2 0.06
43 2 0.06
44 14 0.41
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (41 bp):
TTATCAAAATTTCATATGGAGATCAAAATTTCACAGGATAG
Found at i:5142 original size:85 final size:85
Alignment explanation
Indices: 5042--5201 Score: 232
Period size: 85 Copynumber: 1.9 Consensus size: 85
5032 AAAAAGTCAC
* *
5042 ACAACATGTGTCAATGAAAATAAGCATATTTTTAGAAAATGCAAATGACAATGGAAT-AGAAATC
1 ACAACATGTGTCAATGAAAACAAGCATATTGTTAGAAAATGCAAATGACAATGGAATGA-AAATC
*
5106 TCAAACTAAAAATATAAGGCT
65 TCAAAATAAAAATATAAGGCT
* * * * *
5127 ACAATATGTGTCAATGAAAACAAGCATATTGTTAGAGAATGGATATGACAATGGAGTGAAAATCT
1 ACAACATGTGTCAATGAAAACAAGCATATTGTTAGAAAATGCAAATGACAATGGAATGAAAATCT
5192 CAAAATAAAA
66 CAAAATAAAA
5202 TAGATATGTT
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
85 65 0.98
86 1 0.02
ACGTcount: A:0.49, C:0.11, G:0.16, T:0.24
Consensus pattern (85 bp):
ACAACATGTGTCAATGAAAACAAGCATATTGTTAGAAAATGCAAATGACAATGGAATGAAAATCT
CAAAATAAAAATATAAGGCT
Found at i:7156 original size:26 final size:26
Alignment explanation
Indices: 7109--7159 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
7099 ACTATTAATA
* *
7109 ATAATATATAATAGAATTATTATTTT
1 ATAATATATAATAAAATCATTATTTT
7135 ATAATA-ATAATAAAACTCATTATTT
1 ATAATATATAATAAAA-TCATTATTT
7160 AATGAATACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (26 bp):
ATAATATATAATAAAATCATTATTTT
Found at i:12627 original size:26 final size:26
Alignment explanation
Indices: 12598--12650 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
12588 TAAATTCTGC
12598 TTTGACTTACTGTACAGAAATGTTAT
1 TTTGACTTACTGTACAGAAATGTTAT
12624 TTTGACTTACTGTACAGAAATGTTAT
1 TTTGACTTACTGTACAGAAATGTTAT
12650 T
1 T
12651 AATGTACTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.43
Consensus pattern (26 bp):
TTTGACTTACTGTACAGAAATGTTAT
Done.