Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013775.1 Corchorus olitorius cultivar O-4 contig13808, 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: 14764
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.30
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:307 original size:27 final size:27
Alignment explanation
Indices: 244--368 Score: 173
Period size: 27 Copynumber: 4.7 Consensus size: 27
234 AATGAATTGA
* *
244 AAATGAC-AAAACGCCCCTGAAC-TAC
1 AAATGACTAAAATGCCCCTGAACGTGC
* *
269 AAATGACCAAAACGCCCCTGAACGTGC
1 AAATGACTAAAATGCCCCTGAACGTGC
*
296 AAATGACTAAAATGCCCCAGAACGTGC
1 AAATGACTAAAATGCCCCTGAACGTGC
*
323 AAATGACTAAAATGCCCCTAAACGTGC
1 AAATGACTAAAATGCCCCTGAACGTGC
*
350 AAATGACTAACATGCCCCT
1 AAATGACTAAAATGCCCCT
369 TATGTGACCC
Statistics
Matches: 91, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
25 7 0.08
26 15 0.16
27 69 0.76
ACGTcount: A:0.40, C:0.30, G:0.15, T:0.15
Consensus pattern (27 bp):
AAATGACTAAAATGCCCCTGAACGTGC
Found at i:484 original size:35 final size:35
Alignment explanation
Indices: 445--3028 Score: 2011
Period size: 35 Copynumber: 73.3 Consensus size: 35
435 TGTCTACAAG
* *
445 CCCTGGGTCAACTAAAATAAACTGAAGAGAGACCA
1 CCCTGGGTCAACTGAAATAAACTGAAGAAAGACCA
* **
480 CCCTGGATCAACTGAAATAAACTGAAGATCGACCA
1 CCCTGGGTCAACTGAAATAAACTGAAGAAAGACCA
* * * *
515 CCCTCGATCATTCT-AACATAAACTGAAGAAAGACTA
1 CCCTGGGTCA-ACTGAA-ATAAACTGAAGAAAGACCA
** * *
551 CCAAGGGTCAACTGAAATAAACTAAAGAAAGACCG
1 CCCTGGGTCAACTGAAATAAACTGAAGAAAGACCA
* * * * *
586 CCGTGGGTCAACTAAAATAAACTAAACAAAGACCG
1 CCCTGGGTCAACTGAAATAAACTGAAGAAAGACCA
** * *
621 CATTGGATCAACTGAAATAAACTGAAGAACGACCA
1 CCCTGGGTCAACTGAAATAAACTGAAGAAAGACCA
* * * *
656 CCCTCGATCATTCT-AACATAAACTGAAGATAGACCA
1 CCCTGGGTCA-ACTGAA-ATAAACTGAAGAAAGACCA
* * * *
692 GCCTTGGTCAACTGAAATAAACTGAAGTAAGACCG
1 CCCTGGGTCAACTGAAATAAACTGAAGAAAGACCA
* *
727 CCCTGGGTCAACTAAAATAAACTGAAGAACGACCA
1 CCCTGGGTCAACTGAAATAAACTGAAGAAAGACCA
* * * * *
762 CCCTTGATCATTCTGACATAAACTGAAGAAAATACCA
1 CCCTGGGTCA-ACTGAAATAAACTGAAG-AAAGACCA
* * * *
799 CCCTAGGTCAACTGAAATAAACTGAAGAATGATCG
1 CCCTGGGTCAACTGAAATAAACTGAAGAAAGACCA
** * **
834 CCCTGAATCAATTTTAATAAA-TGAAGAAAGACCA
1 CCCTGGGTCAACTGAAATAAACTGAAGAAAGACCA
** * * * *
868 TGCTAGATCAACTGAAATGAACTGGAGAACA-ACCA
1 CCCTGGGTCAACTGAAATAAACTGAAGAA-AGACCA
* * * * *
903 CCCTCGATCATTCTCACATAAACTGAAGAAAAGACCA
1 CCCTGGGTCA-ACTGAAATAAACTGAAG-AAAGACCA
* * *
940 CCCTAGGTCAACTGAAATAAACTGAAGAAAGAGCG
1 CCCTGGGTCAACTGAAATAAACTGAAGAAAGACCA
* * * *
975 CCCTAGGTCAACTGAAATAAACTGAAGAATGATCG
1 CCCTGGGTCAACTGAAATAAACTGAAGAAAGACCA
* * ** *
1010 CCCTAGATCAGTTGAAATAAACTGAAGAAAGACCG
1 CCCTGGGTCAACTGAAATAAACTGAAGAAAGACCA
* * * * *
1045 CGCTAGATCAACTGAAATGAACTAAAGAACA-ACCA
1 CCCTGGGTCAACTGAAATAAACTGAAGAA-AGACCA
* * * *
1080 CCCTCGATCATTCTGACATAAACTGAAGAAAGACCA
1 CCCTGGGTCA-ACTGAAATAAACTGAAGAAAGACCA
* ** * **
1116 CCCTAGGTCAACTGAAATAAACTGAACTAACACTGT
1 CCCTGGGTCAACTGAAATAAACTGAAGAAAGAC-CA
* * *
1152 CCC-GGGTCAACTAAAATAAAGTGAAGAACGACCA
1 CCCTGGGTCAACTGAAATAAACTGAAGAAAGACCA
* * * * * *
1186 CCCTCGATCAATTTAACATAAACTAAAGAAAGATCA
1 CCCTGGGTCAACTGAA-ATAAACTGAAGAAAGACCA
* * * * * *
1222 CGCTAGATCAACTGAAATAAACTAAAGTAAGACCG
1 CCCTGGGTCAACTGAAATAAACTGAAGAAAGACCA
*
1257 CCCTGGGTCAACTGAAATAAACTGAAGAATGACCA
1 CCCTGGGTCAACTGAAATAAACTGAAGAAAGACCA
* * * * *
1292 CCCTCGATCATTCTGACATAAACGGAAGAAAGACCA
1 CCCTGGGTCA-ACTGAAATAAACTGAAGAAAGACCA
* * * *
1328 CCATTGGTCAACTGAAATAAACTGAAGAAAAACCG
1 CCCTGGGTCAACTGAAATAAACTGAAGAAAGACCA
* *
1363 CCCTAGGTCAACTGAAATAAACTGAAGAACGACCA
1 CCCTGGGTCAACTGAAATAAACTGAAGAAAGACCA
* * * *
1398 CCCTCGATCATTCTGACATAAACTGAAGAAAGACCA
1 CCCTGGGTCA-ACTGAAATAAACTGAAGAAAGACCA
* * **
1434 CCATGGGTCAACTGAAATAACCTGAAGAAAGACTG
1 CCCTGGGTCAACTGAAATAAACTGAAGAAAGACCA
* * *
1469 TCTTGGGTCAACTGAACTAAACTGAAGAAAGACCA
1 CCCTGGGTCAACTGAAATAAACTGAAGAAAGACCA
* *
1504 CCCTGGGTCAACTGAAATAAACTGAAGAATGACCG
1 CCCTGGGTCAACTGAAATAAACTGAAGAAAGACCA
*
1539 CCCTGGGTCAACTGAAATAAACTGAAGAAAGACCG
1 CCCTGGGTCAACTGAAATAAACTGAAGAAAGACCA
* * * * *
1574 CCCTAGATCAATTGAAATAAACTAAAGAAAGACCG
1 CCCTGGGTCAACTGAAATAAACTGAAGAAAGACCA
* * *
1609 CCCTAGGTCAACTAAAATAAACTAAAGAAAGACCA
1 CCCTGGGTCAACTGAAATAAACTGAAGAAAGACCA
** * ** *
1644 CCCTGGAACAATTGAAATAAACTGAAGATCGACCC
1 CCCTGGGTCAACTGAAATAAACTGAAGAAAGACCA
*** * * *
1679 CCCTCCATCATTCTGACATAAACTGAAGAAAGACTA
1 CCCTGGGTCA-ACTGAAATAAACTGAAGAAAGACCA
** * * *
1715 CCAAGGGTCAACTGAAATAAACTAAAGAAAGATCG
1 CCCTGGGTCAACTGAAATAAACTGAAGAAAGACCA
* * **
1750 CCATGGGTCAACT-AATATAAACTAAAGAAAG--GT
1 CCCTGGGTCAACTGAA-ATAAACTGAAGAAAGACCA
* * * * **
1783 TCTTGGATCAACTGAAATAAATTGAA-AAACGATTA
1 CCCTGGGTCAACTGAAATAAACTGAAGAAA-GACCA
* * *
1818 CCCTCGATCATTCT-AACATAAACTGAAGAAAGACCA
1 CCCTGGGTCA-ACTGAA-ATAAACTGAAGAAAGACCA
* * *
1854 CCCTTGGTCAACTGAAATAAACTGAAGTAAGACCG
1 CCCTGGGTCAACTGAAATAAACTGAAGAAAGACCA
* * *
1889 CCTTGGGTCAACTAAAATAAACTGAAGAACGACCA
1 CCCTGGGTCAACTGAAATAAACTGAAGAAAGACCA
* * * *
1924 CCCTTGATCATTCTGACATAAACTGAAGAAAAGACCA
1 CCCTGGGTCA-ACTGAAATAAACTGAAG-AAAGACCA
** * * * *
1961 CCCTAAGTCAATTGAAATAAACTGAAGAATGATCG
1 CCCTGGGTCAACTGAAATAAACTGAAGAAAGACCA
* * ** * * *
1996 CCCTGGATCAATTTTAATGAACTGAAGATAGACCG
1 CCCTGGGTCAACTGAAATAAACTGAAGAAAGACCA
* * * *
2031 CGCTAGATCAACTGAAATGAACTGAAGAACA-ACCA
1 CCCTGGGTCAACTGAAATAAACTGAAGAA-AGACCA
* * * * *
2066 CCTTCGATCATTCTGACATAAACTGAAGAAAGACCA
1 CCCTGGGTCA-ACTGAAATAAACTGAAGAAAGACCA
* ** *
2102 CCCTAGGTCAACTGAAATAAACTGAATTAAGACCG
1 CCCTGGGTCAACTGAAATAAACTGAAGAAAGACCA
* * **
2137 CCCCGGGTCAACTGAAATAAACTGAATATCGACCA
1 CCCTGGGTCAACTGAAATAAACTGAAGAAAGACCA
* * * * *
2172 CCCTTGATCATTCTGACATAAACTGAAGAAACACCA
1 CCCTGGGTCA-ACTGAAATAAACTGAAGAAAGACCA
* * * *
2208 CCCTGGGTCAACTTAAATAAACTGAATAAAAACCG
1 CCCTGGGTCAACTGAAATAAACTGAAGAAAGACCA
* * *
2243 CCCTAGGTTAACTGAAATAAATTGAA-AAACGACCA
1 CCCTGGGTCAACTGAAATAAACTGAAGAAA-GACCA
* * * *
2278 CCCTTGATCATTCTGACATAAACTGAAGAAAGACCA
1 CCCTGGGTCA-ACTGAAATAAACTGAAGAAAGACCA
* * * * **
2314 CCCTTGTTCAACTGAAATAAATTGATGAAAGACTG
1 CCCTGGGTCAACTGAAATAAACTGAAGAAAGACCA
* * * *
2349 CCCTTGGTCAAGTGAAATAAACTGAAGAATGATC-
1 CCCTGGGTCAACTGAAATAAACTGAAGAAAGACCA
* * * * *
2383 CCATGGATCAATTGAAATAAACTAAAGAAAGACCG
1 CCCTGGGTCAACTGAAATAAACTGAAGAAAGACCA
* *
2418 CCCTGGATCAACT-AAATAAACTGAAGAATGACCA
1 CCCTGGGTCAACTGAAATAAACTGAAGAAAGACCA
* * * * *
2452 CCCTCGATCATTCTGACATAAACAGAAGAAAGACCA
1 CCCTGGGTCA-ACTGAAATAAACTGAAGAAAGACCA
* * * *
2488 TCCTGGGTCAACTGAAATATACTGAAGTAAGACCG
1 CCCTGGGTCAACTGAAATAAACTGAAGAAAGACCA
*
2523 CCCTGGGTCAACTGAAATAAACTGAAGAACGACCA
1 CCCTGGGTCAACTGAAATAAACTGAAGAAAGACCA
* * * * *
2558 CTCTCGATCATTCTGACATAAACTGAAGAAAGACCA
1 CCCTGGGTCA-ACTGAAATAAACTGAAGAAAGACCA
* * * *
2594 CCCTGGGTCAACTTATATAAACTTAAGAGAA-ACAA
1 CCCTGGGTCAACTGAAATAAACTGAAGA-AAGACCA
* * ** * *
2629 CACTAGGTGGATTGAAATAAACTGAAGAACGACCA
1 CCCTGGGTCAACTGAAATAAACTGAAGAAAGACCA
* * * * *
2664 CCCTTGATCATTCT-AACATAAATTAAAGAAAGACCA
1 CCCTGGGTCA-ACTGAA-ATAAACTGAAGAAAGACCA
* * *
2700 CCCTAGGTCAACTAAAATAAACTGAAGAAAGACCG
1 CCCTGGGTCAACTGAAATAAACTGAAGAAAGACCA
** *
2735 CCCTAAGTCAACTGAAATAAACTGAAGAAAGACCG
1 CCCTGGGTCAACTGAAATAAACTGAAGAAAGACCA
* * *
2770 TCCTAGGTCAACTGAAATAAACTGAAAAAAGACCA
1 CCCTGGGTCAACTGAAATAAACTGAAGAAAGACCA
* * *
2805 CCCTTGGTCAACTGAAATAAATTGAAGAAAGACCG
1 CCCTGGGTCAACTGAAATAAACTGAAGAAAGACCA
*
2840 CCCTGGGTCAACTGAAATAAACTGAA-AAACAACCA
1 CCCTGGGTCAACTGAAATAAACTGAAGAAA-GACCA
*** ** *
2875 CCCTCAATCATTTGGACATAAACTGAAGAAAAGACCA
1 CCCTGGGTCAACT-GAAATAAACTGAAG-AAAGACCA
* * * * * *
2912 GCCTGGGTCGACTGAAATAAATTGAAGTAAGATCG
1 CCCTGGGTCAACTGAAATAAACTGAAGAAAGACCA
* * * * * *
2947 CCATGGGTCAACTAAAATAAACTAAAGAATGATCG
1 CCCTGGGTCAACTGAAATAAACTGAAGAAAGACCA
* *
2982 CCCTGGATCAACTTGAAA-ATAACTGAAGAAAGACCG
1 CCCTGGGTCAAC-TGAAATA-AACTGAAGAAAGACCA
3018 CCCTGGGTCAA
1 CCCTGGGTCAA
3029 TATGAAACTA
Statistics
Matches: 2014, Mismatches: 480, Indels: 109
0.77 0.18 0.04
Matches are distributed among these distances:
32 3 0.00
33 19 0.01
34 91 0.05
35 1323 0.66
36 517 0.26
37 58 0.03
38 3 0.00
ACGTcount: A:0.42, C:0.22, G:0.17, T:0.19
Consensus pattern (35 bp):
CCCTGGGTCAACTGAAATAAACTGAAGAAAGACCA
Found at i:677 original size:106 final size:106
Alignment explanation
Indices: 456--3028 Score: 2016
Period size: 106 Copynumber: 24.3 Consensus size: 106
446 CCTGGGTCAA
* * * ** * *
456 CTAAAATAAACTGAAGAGAGACCACCCTGGATCAACTGAAATAAACTGAAGATCGACCACCCTCG
1 CTAACATAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTGG
* * * *** * *
521 ATCATTCT-AACATAAACTGAAGAAAGACTACCAAGGGTCA-A
66 ATCA-ACTGAA-ATAAACTGAAGAACGACCACCCTCGATCATT
* * * * * * **
562 CTGAA-ATAAACTAAAGAAAGACCGCCGTGGGTCAACTAAAATAAACTAAACAAAGACCGCATTG
1 CT-AACATAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTG
626 GATCAACTGAAATAAACTGAAGAACGACCACCCTCGATCATT
65 GATCAACTGAAATAAACTGAAGAACGACCACCCTCGATCATT
* * * *
668 CTAACATAAACTGAAGATAGACCAGCCTTGGTCAACTGAAATAAACTGAAGTAAGACCGCCCTGG
1 CTAACATAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTGG
* * *
733 GTCAACTAAAATAAACTGAAGAACGACCACCCTTGATCATT
66 ATCAACTGAAATAAACTGAAGAACGACCACCCTCGATCATT
* * * * *
774 CTGACATAAACTGAAGAAAATACCACCCTAGGTCAACTGAAATAAACTGAAGAATGATCGCCCTG
1 CTAACATAAACTGAAG-AAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTG
* * ** * ** * *
839 AATCAATTTTAATAAA-TGAAGAAAGACCATGCTAGATCA-A
65 GATCAACTGAAATAAACTGAAGAACGACCACCCTCGATCATT
* * * * * * * *
879 CTGAA-ATGAACTGGAGAACA-ACCACCCTCGATCATTCTCACATAAACTGAAGAAAAGACCACC
1 CT-AACATAAACTGAAGAA-AGACCACCCTGGGTCA-ACTGAAATAAACTGAAG-AAAGACCGCC
* * * * * *
942 CTAGG-TCAACTGAAATAAACTGAAGAAAGAGCGCCCTAGGTCA-A
62 CT-GGATCAACTGAAATAAACTGAAGAACGACCACCCTCGATCATT
* * * * * ** * *
986 CTGAA-ATAAACTGAAGAATGATCGCCCTAGATCAGTTGAAATAAACTGAAGAAAGACCGCGCTA
1 CT-AACATAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTG
* * *
1050 GATCAACTGAAATGAACTAAAGAACAACCACCCTCGATCATT
65 GATCAACTGAAATAAACTGAAGAACGACCACCCTCGATCATT
* * ** * *
1092 CTGACATAAACTGAAGAAAGACCACCCTAGGTCAACTGAAATAAACTGAACTAACACTGTCCC-G
1 CTAACATAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAGACCG-CCCTG
* * *
1156 GGTCAACTAAAATAAAGTGAAGAACGACCACCCTCGATCAATT
65 GATCAACTGAAATAAACTGAAGAACGACCACCCTCGATC-ATT
* * * * * * *
1199 -TAACATAAACTAAAGAAAGATCACGCTAGATCAACTGAAATAAACTAAAGTAAGACCGCCCTGG
1 CTAACATAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTGG
* *
1263 GTCAACTGAAATAAACTGAAGAATGACCACCCTCGATCATT
66 ATCAACTGAAATAAACTGAAGAACGACCACCCTCGATCATT
* * * * *
1304 CTGACATAAACGGAAGAAAGACCACCATTGGTCAACTGAAATAAACTGAAGAAAAACCGCCCTAG
1 CTAACATAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCT-G
1369 G-TCAACTGAAATAAACTGAAGAACGACCACCCTCGATCATT
65 GATCAACTGAAATAAACTGAAGAACGACCACCCTCGATCATT
* * * * * *
1410 CTGACATAAACTGAAGAAAGACCACCATGGGTCAACTGAAATAACCTGAAGAAAGACTGTCTTGG
1 CTAACATAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTGG
* * * * * *
1475 GTCAACTGAACTAAACTGAAGAAAGACCACCCTGGGTCA-A
66 ATCAACTGAAATAAACTGAAGAACGACCACCCTCGATCATT
* * *
1515 CTGAA-ATAAACTGAAGAATGACCGCCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTA
1 CT-AACATAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTG
* * * * * * *
1579 GATCAATTGAAATAAACTAAAGAAAGACCGCCCTAGGTCA-A
65 GATCAACTGAAATAAACTGAAGAACGACCACCCTCGATCATT
* * ** * ** * **
1620 CTAAAATAAACTAAAGAAAGACCACCCTGGAACAATTGAAATAAACTGAAGATCGACCCCCCTCC
1 CTAACATAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTGG
* * * * *** * *
1685 ATCATTCTGACATAAACTGAAGAAAGACTACCAAGGGTCA-A
66 ATCA-ACTGAAATAAACTGAAGAACGACCACCCTCGATCATT
* * * * * * *
1726 CTGAA-ATAAACTAAAGAAAGATCGCCATGGGTCAACT-AATATAAACTAAAGAAAG---GTTCT
1 CT-AACATAAACTGAAGAAAGACCACCCTGGGTCAACTGAA-ATAAACTGAAGAAAGACCG-CCC
* * **
1786 TGGATCAACTGAAATAAATTGAAAAACGATTACCCTCGATCATT
63 TGGATCAACTGAAATAAACTGAAGAACGACCACCCTCGATCATT
* * *
1830 CTAACATAAACTGAAGAAAGACCACCCTTGGTCAACTGAAATAAACTGAAGTAAGACCGCCTTGG
1 CTAACATAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTGG
* * *
1895 GTCAACTAAAATAAACTGAAGAACGACCACCCTTGATCATT
66 ATCAACTGAAATAAACTGAAGAACGACCACCCTCGATCATT
* ** * * *
1936 CTGACATAAACTGAAGAAAAGACCACCCTAAGTCAATTGAAATAAACTGAAGAATGATCGCCCTG
1 CTAACATAAACTGAAG-AAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTG
* ** * * * * *
2001 GATCAATTTTAATGAACTGAAGATA-GACCGCGCTAGATCA-A
65 GATCAACTGAAATAAACTGAAGA-ACGACCACCCTCGATCATT
* * * * * * *
2042 CTGAA-ATGAACTGAAGAACA-ACCACCTTCGATCATTCTGACATAAACTGAAGAAAGACCACCC
1 CT-AACATAAACTGAAGAA-AGACCACCCTGGGTCA-ACTGAAATAAACTGAAGAAAGACCGCCC
* * * *
2105 TAGG-TCAACTGAAATAAACTGAATTAA-GACCGCCC-CGGGTCA-A
63 T-GGATCAACTGAAATAAACTGAA-GAACGACCACCCTC-GATCATT
* ** * * * * * *
2148 CTGAA-ATAAACTGAATATCGACCACCCTTGATCATTCTGACATAAACTGAAGAAACACCACCCT
1 CT-AACATAAACTGAAGAAAGACCACCCTGGGTCA-ACTGAAATAAACTGAAGAAAGACCGCCCT
* * * ** * * * * *
2212 GGGTCAACTTAAATAAACTGAATAAAAACCGCCCTAGGTTA-A
64 GGATCAACTGAAATAAACTGAAGAACGACCACCCTCGATCATT
* * * * * *
2254 CTGAA-ATAAATTGAA-AAACGACCACCCTTGATCATTCTGACATAAACTGAAGAAAGACCACCC
1 CT-AACATAAACTGAAGAAA-GACCACCCTGGGTCA-ACTGAAATAAACTGAAGAAAGACCGCCC
* * * * * ** * * *
2317 TTGTTCAACTGAAATAAATTGATGAAAGACTGCCCTTGGTCAAGT
63 TGGATCAACTGAAATAAACTGAAGAACGACCACCCTCGATC-ATT
* * * * * * *
2362 -GAA-ATAAACTGAAGAATGATC-CCATGGATCAATTGAAATAAACTAAAGAAAGACCGCCCTGG
1 CTAACATAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTGG
*
2424 ATCAACT-AAATAAACTGAAGAATGACCACCCTCGATCATT
66 ATCAACTGAAATAAACTGAAGAACGACCACCCTCGATCATT
* * * * *
2464 CTGACATAAACAGAAGAAAGACCATCCTGGGTCAACTGAAATATACTGAAGTAAGACCGCCCTGG
1 CTAACATAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTGG
* *
2529 GTCAACTGAAATAAACTGAAGAACGACCACTCTCGATCATT
66 ATCAACTGAAATAAACTGAAGAACGACCACCCTCGATCATT
* * * * ** *
2570 CTGACATAAACTGAAGAAAGACCACCCTGGGTCAACTTATATAAACTTAAGAGAA-ACAACACTA
1 CTAACATAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGA-AAGACCGCCCT-
** * *
2634 GG-TGGATTGAAATAAACTGAAGAACGACCACCCTTGATCATT
64 GGATCAACTGAAATAAACTGAAGAACGACCACCCTCGATCATT
* * * * *
2676 CTAACATAAATTAAAGAAAGACCACCCTAGGTCAACTAAAATAAACTGAAGAAAGACCGCCCT-A
1 CTAACATAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTGG
* ** * * *
2740 AGTCAACTGAAATAAACTGAAGAAAGACCGTCCTAGGTCA-A
66 A-TCAACTGAAATAAACTGAAGAACGACCACCCTCGATCATT
* * *
2781 CTGAA-ATAAACTGAAAAAAGACCACCCTTGGTCAACTGAAATAAATTGAAGAAAGACCGCCCTG
1 CT-AACATAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTG
* * * *
2845 GGTCAACTGAAATAAACTGAAAAACAACCACCCTCAATCATT
65 GATCAACTGAAATAAACTGAAGAACGACCACCCTCGATCATT
* * * * * * *
2887 -TGGACATAAACTGAAGAAAAGACCAGCCTGGGTCGACTGAAATAAATTGAAGTAAGATCGCCAT
1 CT-AACATAAACTGAAG-AAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCT
* * * * * * *
2951 GGGTCAACTAAAATAAACTAAAGAATGATCGCCCTGGATCAACTT
64 GGATCAACTGAAATAAACTGAAGAACGACCACCCTCGATC-A-TT
* * *
2996 -GAAAAT-AACTGAAGAAAGACCGCCCTGGGTCAA
1 CTAACATAAACTGAAGAAAGACCACCCTGGGTCAA
3029 TATGAAACTA
Statistics
Matches: 2001, Mismatches: 401, Indels: 130
0.79 0.16 0.05
Matches are distributed among these distances:
102 2 0.00
103 51 0.03
104 111 0.06
105 404 0.20
106 1153 0.58
107 273 0.14
108 5 0.00
109 2 0.00
ACGTcount: A:0.42, C:0.22, G:0.17, T:0.19
Consensus pattern (106 bp):
CTAACATAAACTGAAGAAAGACCACCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCCTGG
ATCAACTGAAATAAACTGAAGAACGACCACCCTCGATCATT
Found at i:702 original size:141 final size:139
Alignment explanation
Indices: 444--3028 Score: 1837
Period size: 141 Copynumber: 18.3 Consensus size: 139
434 GTGTCTACAA
* * * * *
444 GCCCTGGGTCAACTAAAATAAACTGAAGAGAGACCACCCTGGATCAACTGAAATAAACTGAAGAT
1 GCCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCTTGGATCAACTGAAATAAACTGAAGAA
* * * * * *
509 CGACCACCCTCGATCATTCTAACATAAACTGAAGAAAGACTA-CCAAGGGTCAACTGAAATAAAC
66 AGACCACCCTAGGTCA-ACTAA-ATAAACTGAAGAAAGACCACCCTA-GGTCAACTGAAATAAAC
*
573 TAAAGAAAGACC
128 TGAAGAAAGACC
* * * * *
585 GCCGTGGGTCAACTAAAATAAACTAAACAAAGACCGCATTGGATCAACTGAAATAAACTGAAGAA
1 GCCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCTTGGATCAACTGAAATAAACTGAAGAA
* * * * * * *
650 CGACCACCCTCGATCATTCTAACATAAACTGAAGATAGACCAGCCTTGGTCAACTGAAATAAACT
66 AGACCACCCTAGGTCA-ACTAA-ATAAACTGAAGAAAGACCACCCTAGGTCAACTGAAATAAACT
*
715 GAAGTAAGACC
129 GAAGAAAGACC
* * * * *
726 GCCCTGGGTCAACTAAAATAAACTGAAGAACGACCACCCTT-GATCATTCTGACATAAACTGAAG
1 GCCCTGGGTCAACTGAAATAAACTGAAGAAAGACC-GCCTTGGATCA-ACTGAAATAAACTGAAG
* * * * * * **
790 AAAATACCACCCTAGGTCAACTGAAATAAACTGAAGAATGATCGCCCT-GAATCAATTTTAATAA
64 -AAAGACCACCCTAGGTCAACT-AAATAAACTGAAGAAAGACCACCCTAG-GTCAACTGAAATAA
854 A-TGAAGAAAGACC
126 ACTGAAGAAAGACC
*** * * * * * * * * * *
867 ATGCTAGATCAACTGAAATGAACTGGAGAACA-ACCACCCTCGATCATTCTCACATAAACTGAAG
1 GCCCTGGGTCAACTGAAATAAACTGAAGAA-AGACCGCCTTGGATCA-ACTGAAATAAACTGAAG
* *
931 AAAAGACCACCCTAGGTCAACTGAAATAAACTGAAGAAAGAGCGCCCTAGGTCAACTGAAATAAA
64 -AAAGACCACCCTAGGTCAACT-AAATAAACTGAAGAAAGACCACCCTAGGTCAACTGAAATAAA
* *
996 CTGAAGAATGATC
127 CTGAAGAAAGACC
* * ** * * *
1009 GCCCTAGATCAGTTGAAATAAACTGAAGAAAGACCGCGC-TAGATCAACTGAAATGAACTAAAGA
1 GCCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGC-CTTGGATCAACTGAAATAAACTGAAGA
* * * *
1073 ACA-ACCACCCTCGATCATTCTGACATAAACTGAAGAAAGACCACCCTAGGTCAACTGAAATAAA
65 A-AGACCACCCTAGGTCA-ACT-AAATAAACTGAAGAAAGACCACCCTAGGTCAACTGAAATAAA
** * *
1137 CTGAACTAACACT
127 CTGAAGAAAGACC
* * * * * * * * *
1150 GTCCC-GGGTCAACTAAAATAAAGTGAAGAACGACCACCCTCGATCAATTTAACATAAACTAAAG
1 G-CCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCTTGGATCAACTGAA-ATAAACTGAAG
* * * * * * *
1214 AAAGATCACGCTAGATCAACTGAAATAAACTAAAGTAAGACCGCCCTGGGTCAACTGAAATAAAC
64 AAAGACCACCCTAGGTCAACT-AAATAAACTGAAGAAAGACCACCCTAGGTCAACTGAAATAAAC
*
1279 TGAAGAATGACC
128 TGAAGAAAGACC
* * * * * * *
1291 ACCCTCGATCATTCTGACATAAACGGAAGAAAGACCACCATTGG-TCAACTGAAATAAACTGAAG
1 GCCCTGGGTCA-ACTGAAATAAACTGAAGAAAGACCGCC-TTGGATCAACTGAAATAAACTGAAG
* * * * * * *
1355 AAAAACCGCCCTAGGTCAACTGAAATAAACTGAAGAACGACCACCCTCGATCATTCTGACATAAA
64 AAAGACCACCCTAGGTCAACT-AAATAAACTGAAGAAAGACCACCCTAGGTCA-ACTGAAATAAA
1420 CTGAAGAAAGACC
127 CTGAAGAAAGACC
* * * * * * *
1433 ACCATGGGTCAACTGAAATAACCTGAAGAAAGACTGTCTTGGGTCAACTGAACTAAACTGAAGAA
1 GCCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCTTGGATCAACTGAAATAAACTGAAGAA
* * * *
1498 AGACCACCCTGGGTCAACTGAAATAAACTGAAGAATGACCGCCCTGGGTCAACTGAAATAAACTG
66 AGACCACCCTAGGTCAACT-AAATAAACTGAAGAAAGACCACCCTAGGTCAACTGAAATAAACTG
1563 AAGAAAGACC
130 AAGAAAGACC
* * * * * * *
1573 GCCCTAGATCAATTGAAATAAACTAAAGAAAGACCGCCCTAGG-TCAACTAAAATAAACTAAAGA
1 GCCCTGGGTCAACTGAAATAAACTGAAGAAAGACCG-CCTTGGATCAACTGAAATAAACTGAAGA
* * ** * *** * *
1637 AAGACCACCCT-GGAACAATTGAAATAAACTGAAGATCGACCCCCCTCCATCATTCTGACATAAA
65 AAGACCACCCTAGG-TCAACT-AAATAAACTGAAGAAAGACCACCCTAGGTCA-ACTGAAATAAA
*
1701 CTGAAGAAAGACT
127 CTGAAGAAAGACC
* ** * * * * *
1714 ACCAAGGGTCAACTGAAATAAACTAAAGAAAGATCGCCATGGGTCAACT-AATATAAACTAAAGA
1 GCCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCTTGGATCAACTGAA-ATAAACTGAAGA
*** * * ** * * *
1778 AAG---GTTCTTGGATCAACTGAAATAAATTGAA-AAACGATTACCCTCGATCATTCT-AACATA
65 AAGACCACCCTAGG-TCAACT-AAATAAACTGAAGAAA-GACCACCCTAGGTCA-ACTGAA-ATA
1838 AACTGAAGAAAGACC
125 AACTGAAGAAAGACC
* * * * *
1853 ACCCTTGGTCAACTGAAATAAACTGAAGTAAGACCGCCTTGGGTCAACTAAAATAAACTGAAGAA
1 GCCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCTTGGATCAACTGAAATAAACTGAAGAA
* * * * * * *
1918 CGACCACCCTTGATCATTCTGACATAAACTGAAGAAAAGACCACCCTAAGTCAATTGAAATAAAC
66 AGACCACCCTAGGTCA-ACT-AAATAAACTGAAG-AAAGACCACCCTAGGTCAACTGAAATAAAC
* *
1983 TGAAGAATGATC
128 TGAAGAAAGACC
* * ** * * * *
1995 GCCCTGGATCAATTTTAATGAACTGAAGATAGACCGCGC-TAGATCAACTGAAATGAACTGAAGA
1 GCCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGC-CTTGGATCAACTGAAATAAACTGAAGA
* * * * *
2059 ACA-ACCACCTTCGATCATTCTGACATAAACTGAAGAAAGACCACCCTAGGTCAACTGAAATAAA
65 A-AGACCACCCTAGGTCA-ACT-AAATAAACTGAAGAAAGACCACCCTAGGTCAACTGAAATAAA
**
2123 CTGAATTAAGACC
127 CTGAAGAAAGACC
* * ** * * *
2136 GCCCCGGGTCAACTGAAATAAACTGAATATCGACCACCCTT-GATCATTCTGACATAAACTGAAG
1 GCCCTGGGTCAACTGAAATAAACTGAAGAAAGACC-GCCTTGGATCA-ACTGAAATAAACTGAAG
* * * * * * *
2200 AAACACCACCCTGGGTCAACTTAAATAAACTGAATAAAAACCGCCCTAGGTTAACTGAAATAAAT
64 AAAGACCACCCTAGGTCAAC-TAAATAAACTGAAGAAAGACCACCCTAGGTCAACTGAAATAAAC
2265 TGAA-AAACGACC
128 TGAAGAAA-GACC
* * * * * * * * *
2277 ACCCTTGATCATTCTGACATAAACTGAAGAAAGACCACCCTT-GTTCAACTGAAATAAATTGATG
1 GCCCTGGGTCA-ACTGAAATAAACTGAAGAAAGACC-GCCTTGGATCAACTGAAATAAACTGAAG
** * * * * * *
2341 AAAGACTGCCCTTGGTCAAGTGAAATAAACTGAAGAATGATC-CCAT-GGATCAATTGAAATAAA
64 AAAGACCACCCTAGGTCAACT-AAATAAACTGAAGAAAGACCACCCTAGG-TCAACTGAAATAAA
*
2404 CTAAAGAAAGACC
127 CTGAAGAAAGACC
* * * * * * * *
2417 GCCCTGGATCAACT-AAATAAACTGAAGAATGACCACCCTCGATCATTCTGACATAAACAGAAGA
1 GCCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCTTGGATCA-ACTGAAATAAACTGAAGA
* * * * * *
2481 AAGACCATCCTGGGTCAACTGAAATATACTGAAGTAAGACCGCCCTGGGTCAACTGAAATAAACT
65 AAGACCACCCTAGGTCAACT-AAATAAACTGAAGAAAGACCACCCTAGGTCAACTGAAATAAACT
*
2546 GAAGAACGACC
129 GAAGAAAGACC
* * * * * * * * * * * *
2557 ACTCTCGATCATTCTGACATAAACTGAAGAAAGACCACCCTGGGTCAACTTATATAAACTTAAGA
1 GCCCTGGGTCA-ACTGAAATAAACTGAAGAAAGACCGCCTTGGATCAACTGAAATAAACTGAAGA
* * ** * * * * *
2622 GAA-ACAACACTAGGTGGATTGAAATAAACTGAAGAACGACCACCCTTGATCATTCT-AACATAA
65 -AAGACCACCCTAGGTCAACT-AAATAAACTGAAGAAAGACCACCCTAGGTCA-ACTGAA-ATAA
* *
2685 ATTAAAGAAAGACC
126 ACTGAAGAAAGACC
* * * * *
2699 ACCCTAGGTCAACTAAAATAAACTGAAGAAAGACCGCCCT-AAGTCAACTGAAATAAACTGAAGA
1 GCCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCTTGGA-TCAACTGAAATAAACTGAAGA
** * * *
2763 AAGACCGTCCTAGGTCAACTGAAATAAACTGAAAAAAGACCACCCTTGGTCAACTGAAATAAATT
65 AAGACCACCCTAGGTCAACT-AAATAAACTGAAGAAAGACCACCCTAGGTCAACTGAAATAAACT
2828 GAAGAAAGACC
129 GAAGAAAGACC
* * * ** ** *
2839 GCCCTGGGTCAACTGAAATAAACTGAA-AAACAACCACCCTCAATCATTTGGACATAAACTGAAG
1 GCCCTGGGTCAACTGAAATAAACTGAAGAAA-GACCGCCTTGGATCAACT-GAAATAAACTGAAG
* * * * * * * * * *
2903 AAAAGACCAGCCTGGGTCGACTGAAATAAATTGAAGTAAGATCGCCATGGGTCAACTAAAATAAA
64 -AAAGACCACCCTAGGTCAACT-AAATAAACTGAAGAAAGACCACCCTAGGTCAACTGAAATAAA
* * *
2968 CTAAAGAATGATC
127 CTGAAGAAAGACC
* * *
2981 GCCCTGGATCAACTTGAAA-ATAACTGAAGAAAGACCGCCCTGGGTCAA
1 GCCCTGGGTCAAC-TGAAATA-AACTGAAGAAAGACCGCCTTGGATCAA
3029 TATGAAACTA
Statistics
Matches: 1960, Mismatches: 414, Indels: 138
0.78 0.16 0.05
Matches are distributed among these distances:
137 3 0.00
138 26 0.01
139 160 0.08
140 267 0.14
141 965 0.49
142 479 0.24
143 54 0.03
144 6 0.00
ACGTcount: A:0.42, C:0.22, G:0.17, T:0.19
Consensus pattern (139 bp):
GCCCTGGGTCAACTGAAATAAACTGAAGAAAGACCGCCTTGGATCAACTGAAATAAACTGAAGAA
AGACCACCCTAGGTCAACTAAATAAACTGAAGAAAGACCACCCTAGGTCAACTGAAATAAACTGA
AGAAAGACC
Found at i:4338 original size:21 final size:23
Alignment explanation
Indices: 4312--4362 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
4302 CTAAAAACCT
4312 TTTTGAGAAAAA-C-ATTT-TTCC
1 TTTTGA-AAAAATCAATTTCTTCC
*
4333 TTTTGAAAAAATCAATTTCTTCT
1 TTTTGAAAAAATCAATTTCTTCC
4356 TTTTGAA
1 TTTTGAA
4363 CAATCCTTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 5 0.19
21 7 0.27
22 4 0.15
23 10 0.38
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.47
Consensus pattern (23 bp):
TTTTGAAAAAATCAATTTCTTCC
Found at i:4945 original size:14 final size:14
Alignment explanation
Indices: 4926--4976 Score: 61
Period size: 14 Copynumber: 3.6 Consensus size: 14
4916 CTCAAAAACC
4926 TTTTGAAAACTCAT
1 TTTTGAAAACTCAT
*
4940 TTTTGAAAAC-CTT
1 TTTTGAAAACTCAT
4953 TTCTTGAAAACAT-AT
1 TT-TTGAAAAC-TCAT
4968 TTTTGAAAA
1 TTTTGAAAA
4977 ATGTCTCTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
13 4 0.12
14 25 0.78
15 3 0.09
ACGTcount: A:0.37, C:0.12, G:0.08, T:0.43
Consensus pattern (14 bp):
TTTTGAAAACTCAT
Found at i:4985 original size:28 final size:28
Alignment explanation
Indices: 4928--4986 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
4918 CAAAAACCTT
* *
4928 TTGAAAACTCATTTTTGAAAACCTTTTC
1 TTGAAAACTCATTTTTGAAAACATTCTC
4956 TTGAAAACAT-ATTTTTGAAAA-ATGTCTC
1 TTGAAAAC-TCATTTTTGAAAACAT-TCTC
4984 TTG
1 TTG
4987 TTTTGACTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 1 0.04
28 25 0.93
29 1 0.04
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (28 bp):
TTGAAAACTCATTTTTGAAAACATTCTC
Found at i:12013 original size:7 final size:7
Alignment explanation
Indices: 12001--12049 Score: 62
Period size: 7 Copynumber: 6.9 Consensus size: 7
11991 GAGGCAACCC
12001 AATTTTT
1 AATTTTT
*
12008 AATTTTA
1 AATTTTT
*
12015 AATTTTC
1 AATTTTT
12022 AATTTTTT
1 AA-TTTTT
*
12030 AATTCTT
1 AATTTTT
12037 AATTTTT
1 AATTTTT
12044 AATTTT
1 AATTTT
12050 ATCTAACTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
7 30 0.83
8 6 0.17
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (7 bp):
AATTTTT
Found at i:12031 original size:22 final size:22
Alignment explanation
Indices: 12003--12049 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
11993 GGCAACCCAA
12003 TTTTTAATT-TTAAATTTTCAAT
1 TTTTTAATTCTT-AATTTTCAAT
*
12025 TTTTTAATTCTTAATTTTTAAT
1 TTTTTAATTCTTAATTTTCAAT
12047 TTT
1 TTT
12050 ATCTAACTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 21 0.91
23 2 0.09
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (22 bp):
TTTTTAATTCTTAATTTTCAAT
Done.