Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012534.1 Corchorus olitorius cultivar O-4 contig12567, 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: 52712
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:1213 original size:21 final size:21
Alignment explanation
Indices: 1189--1228 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1179 CTCTTGTCAT
*
1189 TGGACCTAATGGCATCTTTAA
1 TGGACCAAATGGCATCTTTAA
*
1210 TGGATCAAATGGCATCTTT
1 TGGACCAAATGGCATCTTT
1229 GGCATCTCCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (21 bp):
TGGACCAAATGGCATCTTTAA
Found at i:11920 original size:22 final size:21
Alignment explanation
Indices: 11895--11943 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
11885 AAGTAACTTT
11895 TAAATCAAATATTAAATATATA
1 TAAATCAAAT-TTAAATATATA
* *
11917 TAAATTTAAGTTTAAATATATA
1 TAAA-TCAAATTTAAATATATA
11939 TAAAT
1 TAAAT
11944 TTAAGTATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.04
22 19 0.79
23 4 0.17
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (21 bp):
TAAATCAAATTTAAATATATA
Found at i:11944 original size:22 final size:22
Alignment explanation
Indices: 11906--11949 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
11896 AAATCAAATA
11906 TTAAATATATATAAATTTAAGT
1 TTAAATATATATAAATTTAAGT
11928 TTAAATATATATAAATTTAAGT
1 TTAAATATATATAAATTTAAGT
11950 ATAAGTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (22 bp):
TTAAATATATATAAATTTAAGT
Found at i:15121 original size:32 final size:34
Alignment explanation
Indices: 15055--15122 Score: 88
Period size: 32 Copynumber: 2.1 Consensus size: 34
15045 GTCCAACCCA
*
15055 ACTTGTCTGCCTATTAATTGTCTACTTTAATCTG
1 ACTTGTCTGCCTATTAATTGTCTACTTCAATCTG
*
15089 ACTTGTTCTG-CT-TTAATTG-CTTCTTCAATCTG
1 ACTTG-TCTGCCTATTAATTGTCTACTTCAATCTG
15121 AC
1 AC
15123 CTCTCAGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 13 0.42
33 7 0.23
34 7 0.23
35 4 0.13
ACGTcount: A:0.19, C:0.22, G:0.12, T:0.47
Consensus pattern (34 bp):
ACTTGTCTGCCTATTAATTGTCTACTTCAATCTG
Found at i:21881 original size:16 final size:17
Alignment explanation
Indices: 21860--21902 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
21850 TATTTACTGA
21860 AAATAATTATAATTAT-
1 AAATAATTATAATTATC
*
21876 AAATAATTATTATTATC
1 AAATAATTATAATTATC
*
21893 CAATAATTAT
1 AAATAATTAT
21903 CACTAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 15 0.62
17 9 0.38
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
AAATAATTATAATTATC
Found at i:28129 original size:32 final size:34
Alignment explanation
Indices: 28067--28134 Score: 97
Period size: 32 Copynumber: 2.1 Consensus size: 34
28057 GTCCAACCCA
28067 ACTTGTCTGCCTATTAATTGTCTGCTTCAATCTG
1 ACTTGTCTGCCTATTAATTGTCTGCTTCAATCTG
*
28101 ACTTGTTCTG-CT-TTAATTG-CTTCTTCAATCTG
1 ACTTG-TCTGCCTATTAATTGTCTGCTTCAATCTG
28133 AC
1 AC
28135 CTCTCAGGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
32 14 0.44
33 7 0.22
34 7 0.22
35 4 0.12
ACGTcount: A:0.18, C:0.24, G:0.13, T:0.46
Consensus pattern (34 bp):
ACTTGTCTGCCTATTAATTGTCTGCTTCAATCTG
Found at i:31470 original size:2 final size:2
Alignment explanation
Indices: 31463--31495 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
31453 GGTGAAAAGT
*
31463 TA TA TA TA TA TA TA AA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
31496 CATCAAACGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:33694 original size:952 final size:952
Alignment explanation
Indices: 32013--33919 Score: 3379
Period size: 952 Copynumber: 2.0 Consensus size: 952
32003 CAAATAAGAA
*
32013 AATATTTCTTAATGGATATCTTGAAACATAAAAATTCTCTTTTGAACCCTTCATGAAACTCGTAG
1 AATATTTCTTAATGGATATCTTGAAACATAAAAATTCCCTTTTGAACCCTTCATGAAACTCGTAG
* *
32078 ATCAAATTAACTTTCGGATTCTTCATGAAAGTCGTAGATCATATAGTAACCTTTTAATCGGCACT
66 ATCAAATTAACTTTCGGATTCTTCATGAAAGTCGTAGATCATACAGTAACC------TCGACACT
*
32143 TGAATGACTTAAATCGGACATGTGGATCGAAAATTATATGGGATTAAATAGACCAACAATTGAAA
125 TGAATAACTTAAATCGGACATGTGGATCGAAAATTATATGGGATTAAATAGACCAACAATTGAAA
*
32208 CGACCAAATTTAGGAAGCAGTTTTTTGAATTAAAACATAAAAGTTTGATCTTGAGTCCTTCATGA
190 CGACCAAATTTAGGAAGCAGTTTTTTGAATTAAAACATAAAAATTTGATCTTGAGTCCTTCATGA
*
32273 AAGTTGTAGATCATGAAATTACCTTTTAATAGACACATGAATCAACTTAATTGGACAAATAGAAT
255 AAGTTGTAGATCATGAAATTACCTTTTAATAGACACATGAATCAACTTAATTGGACAAATAGAAC
32338 AAAGAATAAAAAAATAAATCTGAAACGTTAGATTAAGATAGAATTTATTTGATAAAGAATCCAAA
320 AAAGAATAAAAAAATAAATCTGAAACGTTAGATTAAGATAGAATTTATTTGATAAAGAATCCAAA
* * *
32403 TAAGAGAATGGTTGTTAATGGAGATCTTGTACATAAAAACTCCCTTTTGAACACTTCATGATTTA
385 TAAGAAAATAGTTGTTAATGGAGATCTTGAACATAAAAACTCCCTTTTGAACACTTCATGATTTA
* *
32468 CTTCAATCCGAATGCTAGTTGTACATGAAATTTAACTCCCTTTTTTCGTTAACCGACACTTCAAT
450 CTTCAATCCGAAAGCTAGTTGTACATGAAATTTAACTCCCTTTTTTCATTAACCGACACTTCAAT
* * *
32533 AACTTCAATCGGACATGTGGACAAAAAATTATATGATATTAAATTGACCGGCAATCAAAACCACA
515 AACTTCAATCGGACATGTGGACAAAAAATTATACGATATGAAATTGAACGGCAATCAAAACCACA
*
32598 AAATTTCGGAAGCATTTTTTAGAATCAAAACATTAAAAGTGGCTTCTGAGTTCTGTATGAAAATT
580 AAAATTCGGAAGCATTTTTTAGAATCAAAACATTAAAAGTGGCTTCTGAGTTCTGTATGAAAATT
*
32663 GTAGATCATGAAATTACCTTTTAATAGACACTTGAATCACCTTAATCGGAAAAATAGGAAAAAAA
645 GTAGATCATGAAATTACCTTTTAATAGACACTTGAATCACCTCAATCGGAAAAATAGGAAAAAAA
*
32728 TACAAAATTAAATGTGAATATGTTAAATCATCCAACCTATAATTGTAAAGGACTAAATAGCATAA
710 TACAAAAATAAATGTGAATATGTTAAATCATCCAACCTATAATTGTAAAGGACTAAATAGCATAA
32793 AGCATAAAAGTATGAAGATCATTAGATAAATAATCCAACAAAAAAATATTAGTTTATAGAGAATG
775 AGCATAAAAGTATGAAGATCATTAGATAAATAATCCAACAAAAAAA-ATTAGTTTATAGAGAATG
*
32858 GGACCCACAAATAGTAAGATTTTCACAAAGTTCCCAAAATACCCTCAATCTTCAATCCAAATAAC
839 GGACCCACAAATAGTAAGATTTTCACAAAGTTCCCAAAATACCCTCAATCATCAATCCAAATAAC
*
32923 GAAAAAACCGAGCATAAAAGTACCAAAATAACCCTCCTTATTTGTATAT
904 GAAAAAACCGAGCATAAAAGTACCAAAATAACCCTCCTCATTTGTATAT
32972 AATATTTCTTAATGGATATCTTGAAACATAAAAATTCCCTTTTGAACCCTTCATGAAACTCGTAG
1 AATATTTCTTAATGGATATCTTGAAACATAAAAATTCCCTTTTGAACCCTTCATGAAACTCGTAG
* *
33037 ATCAAATTAACTTTCGGGTTCTTCATGAAAGTCGTATATCATACAGTAA-C-CGACACTTGAATA
66 ATCAAATTAACTTTCGGATTCTTCATGAAAGTCGTAGATCATACAGTAACCTCGACACTTGAATA
* *
33100 ACTTAAATCGGACATGTGGATCGAAAATTATATGGTATTAAATGGACCAACAATTGAAACGACCA
131 ACTTAAATCGGACATGTGGATCGAAAATTATATGGGATTAAATAGACCAACAATTGAAACGACCA
* * *
33165 AATTTAGGAATCATTTTTTTTTGAATTAAAACATAAAAATTTGCTCTTGAGTCCTTCATGAAAGT
196 AATTTAGGAAGCA--GTTTTTTGAATTAAAACATAAAAATTTGATCTTGAGTCCTTCATGAAAGT
33230 TGTAGATCATGAAATTACCTTTTAATAGACACATGAATCAACTTAATTGGACAAATAGAACAAAG
259 TGTAGATCATGAAATTACCTTTTAATAGACACATGAATCAACTTAATTGGACAAATAGAACAAAG
* *
33295 AAT-AAAAAATAAATCTGAAACGTTAGATTAAGATAGAATTTGTTTGATAAATAATCCAAATAAG
324 AATAAAAAAATAAATCTGAAACGTTAGATTAAGATAGAATTTATTTGATAAAGAATCCAAATAAG
*
33359 AAAATATTTGTTAATGGAGATCTTGAACATAAAAACTCCCTTTTGAACACTTCATGATTTACTTC
389 AAAATAGTTGTTAATGGAGATCTTGAACATAAAAACTCCCTTTTGAACACTTCATGATTTACTTC
33424 AATCCGAAAGCTAGTTGTACATGAAATTTAACTCCCTTTTTTCATTAACCGACACTTCAATAACT
454 AATCCGAAAGCTAGTTGTACATGAAATTTAACTCCCTTTTTTCATTAACCGACACTTCAATAACT
* *
33489 TCAATCGGACATGTGGATAAAAAATTATACGATATGAAATTGAACGGCAATCAAAACCATAAAAA
519 TCAATCGGACATGTGGACAAAAAATTATACGATATGAAATTGAACGGCAATCAAAACCACAAAAA
*
33554 TTCGGAAGCATTTTTTAGAATCAAAACATTAAAATTGGCTTCTGAGTTCTGTATGAAAATTGTAG
584 TTCGGAAGCATTTTTTAGAATCAAAACATTAAAAGTGGCTTCTGAGTTCTGTATGAAAATTGTAG
*
33619 ATCATGAAATTACCTTTTAATAGACACTTGAATCACCTCAATCGGACAAATAGGAAAAAAATACA
649 ATCATGAAATTACCTTTTAATAGACACTTGAATCACCTCAATCGGAAAAATAGGAAAAAAATACA
*
33684 AAAATAAATGTGAATATGTTAAATCATCCAACCTATAATTTTAAAGGACTAAATAGCATAAAGCA
714 AAAATAAATGTGAATATGTTAAATCATCCAACCTATAATTGTAAAGGACTAAATAGCATAAAGCA
* *
33749 TAAAAGTATGAGGATCATTAGATAAATAATCCAACAAAAAAAATTAGTTTATGGAGAATGGGACC
779 TAAAAGTATGAAGATCATTAGATAAATAATCCAACAAAAAAAATTAGTTTATAGAGAATGGGACC
*
33814 CACAAATAGTAAGATTTTCACAAAGTTCCCAAAATACCCTCATTCATCAATCCAAATAACGAAAA
844 CACAAATAGTAAGATTTTCACAAAGTTCCCAAAATACCCTCAATCATCAATCCAAATAACGAAAA
33879 AACCGAGCATAAAAGTACCAAAATAACCCTCCTCATTTGTA
909 AACCGAGCATAAAAGTACCAAAATAACCCTCCTCATTTGTA
33920 CATGAATTCA
Statistics
Matches: 909, Mismatches: 37, Indels: 12
0.95 0.04 0.01
Matches are distributed among these distances:
951 211 0.23
952 473 0.52
953 114 0.13
958 1 0.00
959 110 0.12
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.30
Consensus pattern (952 bp):
AATATTTCTTAATGGATATCTTGAAACATAAAAATTCCCTTTTGAACCCTTCATGAAACTCGTAG
ATCAAATTAACTTTCGGATTCTTCATGAAAGTCGTAGATCATACAGTAACCTCGACACTTGAATA
ACTTAAATCGGACATGTGGATCGAAAATTATATGGGATTAAATAGACCAACAATTGAAACGACCA
AATTTAGGAAGCAGTTTTTTGAATTAAAACATAAAAATTTGATCTTGAGTCCTTCATGAAAGTTG
TAGATCATGAAATTACCTTTTAATAGACACATGAATCAACTTAATTGGACAAATAGAACAAAGAA
TAAAAAAATAAATCTGAAACGTTAGATTAAGATAGAATTTATTTGATAAAGAATCCAAATAAGAA
AATAGTTGTTAATGGAGATCTTGAACATAAAAACTCCCTTTTGAACACTTCATGATTTACTTCAA
TCCGAAAGCTAGTTGTACATGAAATTTAACTCCCTTTTTTCATTAACCGACACTTCAATAACTTC
AATCGGACATGTGGACAAAAAATTATACGATATGAAATTGAACGGCAATCAAAACCACAAAAATT
CGGAAGCATTTTTTAGAATCAAAACATTAAAAGTGGCTTCTGAGTTCTGTATGAAAATTGTAGAT
CATGAAATTACCTTTTAATAGACACTTGAATCACCTCAATCGGAAAAATAGGAAAAAAATACAAA
AATAAATGTGAATATGTTAAATCATCCAACCTATAATTGTAAAGGACTAAATAGCATAAAGCATA
AAAGTATGAAGATCATTAGATAAATAATCCAACAAAAAAAATTAGTTTATAGAGAATGGGACCCA
CAAATAGTAAGATTTTCACAAAGTTCCCAAAATACCCTCAATCATCAATCCAAATAACGAAAAAA
CCGAGCATAAAAGTACCAAAATAACCCTCCTCATTTGTATAT
Found at i:35970 original size:36 final size:36
Alignment explanation
Indices: 35930--36101 Score: 158
Period size: 36 Copynumber: 4.8 Consensus size: 36
35920 CTTAAATGTC
* * *
35930 CTACTTAATTATCCGGAATTAAGTTCTTTATTGACT
1 CTACTTAATTACCCAGAATTAAGTTCTTTATCGACT
*
35966 CTACTTAATTACCCAGAATTAAGTTCCTTATCGACT
1 CTACTTAATTACCCAGAATTAAGTTCTTTATCGACT
* * **
36002 CTACTTAATTACCCAGAATTAACTTCTCTGACTATACT
1 CTACTTAATTACCCAGAATTAAGTTCT-TTA-TCGACT
*
36040 -TACTTAATTA-CCATGAATTAA-ATCTTTGA-CTGA-T
1 CTACTTAATTACCCA-GAATTAAGTTCTTT-ATC-GACT
* *
36074 TTACTTAATTACCCTGAATTAAG-TCTTT
1 CTACTTAATTACCCAGAATTAAGTTCTTT
36102 GACTGATTTT
Statistics
Matches: 114, Mismatches: 14, Indels: 17
0.79 0.10 0.12
Matches are distributed among these distances:
34 1 0.01
35 24 0.21
36 66 0.58
37 19 0.17
38 4 0.04
ACGTcount: A:0.31, C:0.20, G:0.08, T:0.41
Consensus pattern (36 bp):
CTACTTAATTACCCAGAATTAAGTTCTTTATCGACT
Found at i:36085 original size:35 final size:35
Alignment explanation
Indices: 36003--36110 Score: 130
Period size: 35 Copynumber: 3.0 Consensus size: 35
35993 TTATCGACTC
* *
36003 TACTTAATTACCCA-GAATTAACTTCTCTGACT-ATACT
1 TACTTAATTA-CCATGAATTAA-ATCTTTGACTGAT--T
36040 TACTTAATTACCATGAATTAAATCTTTGACTGATT
1 TACTTAATTACCATGAATTAAATCTTTGACTGATT
* *
36075 TACTTAATTACCCTGAATTAAGTCTTTGACTGATT
1 TACTTAATTACCATGAATTAAATCTTTGACTGATT
36110 T
1 T
36111 TAGTTAGGTC
Statistics
Matches: 65, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
35 35 0.54
36 11 0.17
37 19 0.29
ACGTcount: A:0.31, C:0.19, G:0.08, T:0.42
Consensus pattern (35 bp):
TACTTAATTACCATGAATTAAATCTTTGACTGATT
Found at i:36678 original size:36 final size:35
Alignment explanation
Indices: 36542--37145 Score: 773
Period size: 35 Copynumber: 17.0 Consensus size: 35
36532 CAAACAGCCC
36542 CTTAATTACCCTGAATTAAGTCTTTGACTGATTTA
1 CTTAATTACCCTGAATTAAGTCTTTGACTGATTTA
** * * *
36577 CTTAATTGTCCTGAATTAAGTTTTTTTACCGATTTTA
1 CTTAATTACCCTGAATTAAG-TCTTTGACTGA-TTTA
*
36614 CTTAATTACCCTAAATTAAGTCTTTGACTGATTTA
1 CTTAATTACCCTGAATTAAGTCTTTGACTGATTTA
* ** * *
36649 TTTAATTACCCAAAATTAAGTTCTCTGACT-ATACTTT
1 CTTAATTACCCTGAATTAAG-TCTTTGACTGAT--TTA
36686 CTTAATTACCAC-GAATTAAGTCTTTGACTGATTTA
1 CTTAATTACC-CTGAATTAAGTCTTTGACTGATTTA
*
36721 CTTAATTACCCTGAATTATGTCTTTGACTGATTTTA
1 CTTAATTACCCTGAATTAAGTCTTTGACTGA-TTTA
*
36757 CTTAATTACCCTGAATTAAGCCTTTGACTGATTTTA
1 CTTAATTACCCTGAATTAAGTCTTTGACTGA-TTTA
* *
36793 CTTAATTACCGTGAATTAAGTCTTTGACTGTTTTTA
1 CTTAATTACCCTGAATTAAGTCTTTGACTG-ATTTA
* * * *
36829 TTTAATTACCCTGAATTAACTCTTAGACCGATTTA
1 CTTAATTACCCTGAATTAAGTCTTTGACTGATTTA
* *
36864 CTTAATTAACCTGAATTAAGTCTTTGACCGATTTTA
1 CTTAATTACCCTGAATTAAGTCTTTGACTGA-TTTA
*
36900 CTTAATTACCCTGAATTAAGTCTTTGCCTGATTTA
1 CTTAATTACCCTGAATTAAGTCTTTGACTGATTTA
**
36935 CTTAATTACCCTGAATTAAGTCTTTGACTTTTTTTA
1 CTTAATTACCCTGAATTAAGTCTTTGAC-TGATTTA
*
36971 CTTAATTACCCTGAATTAA-TCTTTGACTAATTTA
1 CTTAATTACCCTGAATTAAGTCTTTGACTGATTTA
37005 CTTAATTACCCTGAATTAAGTCTTTGACTGATTTA
1 CTTAATTACCCTGAATTAAGTCTTTGACTGATTTA
* * *
37040 CTTAATTAACTTGAATTAAGTCTTTTACTGATTTA
1 CTTAATTACCCTGAATTAAGTCTTTGACTGATTTA
* ** **
37075 CTTGATTACGTTGAATTAAGTCTTTGACTTTTTTTA
1 CTTAATTACCCTGAATTAAGTCTTTGAC-TGATTTA
*
37111 CTTAATTACCCTGAATTAAGTCTTTAACTGATTTA
1 CTTAATTACCCTGAATTAAGTCTTTGACTGATTTA
37146 TGGATGCATA
Statistics
Matches: 496, Mismatches: 59, Indels: 28
0.85 0.10 0.05
Matches are distributed among these distances:
34 25 0.05
35 217 0.44
36 212 0.43
37 41 0.08
38 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.10, T:0.45
Consensus pattern (35 bp):
CTTAATTACCCTGAATTAAGTCTTTGACTGATTTA
Found at i:36790 original size:71 final size:71
Alignment explanation
Indices: 36542--37145 Score: 822
Period size: 71 Copynumber: 8.5 Consensus size: 71
36532 CAAACAGCCC
** * * *
36542 CTTAATTACCCTGAATTAAGTCTTTGACTGATTTACTTAATTGTCCTGAATTAAGTTTTTTTACC
1 CTTAATTACCCTGAATTAAGTCTTTGACTGATTTACTTAATTACCCTGAATTAAG-TCTTTGACT
36607 GATTTTA
65 GATTTTA
* * ** *
36614 CTTAATTACCCTAAATTAAGTCTTTGACTGATTTATTTAATTACCCAAAATTAAGTTCTCTGACT
1 CTTAATTACCCTGAATTAAGTCTTTGACTGATTTACTTAATTACCCTGAATTAAG-TCTTTGACT
36679 -ATACTTT-
65 GAT--TTTA
*
36686 CTTAATTACCAC-GAATTAAGTCTTTGACTGATTTACTTAATTACCCTGAATTATGTCTTTGACT
1 CTTAATTACC-CTGAATTAAGTCTTTGACTGATTTACTTAATTACCCTGAATTAAGTCTTTGACT
36750 GATTTTA
65 GATTTTA
* *
36757 CTTAATTACCCTGAATTAAGCCTTTGACTGATTTTACTTAATTACCGTGAATTAAGTCTTTGACT
1 CTTAATTACCCTGAATTAAGTCTTTGACTGA-TTTACTTAATTACCCTGAATTAAGTCTTTGACT
*
36822 GTTTTTA
65 GATTTTA
* * * * * *
36829 TTTAATTACCCTGAATTAACTCTTAGACCGATTTACTTAATTAACCTGAATTAAGTCTTTGACCG
1 CTTAATTACCCTGAATTAAGTCTTTGACTGATTTACTTAATTACCCTGAATTAAGTCTTTGACTG
36894 ATTTTA
66 ATTTTA
* *
36900 CTTAATTACCCTGAATTAAGTCTTTGCCTGATTTACTTAATTACCCTGAATTAAGTCTTTGACTT
1 CTTAATTACCCTGAATTAAGTCTTTGACTGATTTACTTAATTACCCTGAATTAAGTCTTTGACTG
*
36965 TTTTTA
66 ATTTTA
*
36971 CTTAATTACCCTGAATTAA-TCTTTGACTAATTTACTTAATTACCCTGAATTAAGTCTTTGACTG
1 CTTAATTACCCTGAATTAAGTCTTTGACTGATTTACTTAATTACCCTGAATTAAGTCTTTGACTG
37035 A-TTTA
66 ATTTTA
* * * * ** *
37040 CTTAATTAACTTGAATTAAGTCTTTTACTGATTTACTTGATTACGTTGAATTAAGTCTTTGACTT
1 CTTAATTACCCTGAATTAAGTCTTTGACTGATTTACTTAATTACCCTGAATTAAGTCTTTGACTG
*
37105 TTTTTA
66 ATTTTA
*
37111 CTTAATTACCCTGAATTAAGTCTTTAACTGATTTA
1 CTTAATTACCCTGAATTAAGTCTTTGACTGATTTA
37146 TGGATGCATA
Statistics
Matches: 469, Mismatches: 54, Indels: 19
0.87 0.10 0.04
Matches are distributed among these distances:
69 21 0.04
70 85 0.18
71 191 0.41
72 168 0.36
73 4 0.01
ACGTcount: A:0.28, C:0.17, G:0.10, T:0.45
Consensus pattern (71 bp):
CTTAATTACCCTGAATTAAGTCTTTGACTGATTTACTTAATTACCCTGAATTAAGTCTTTGACTG
ATTTTA
Found at i:41570 original size:27 final size:27
Alignment explanation
Indices: 41505--41575 Score: 72
Period size: 26 Copynumber: 2.7 Consensus size: 27
41495 GGTCACCTAG
** *
41505 GGGGCATTTTGGTCATTTTTACACTGA
1 GGGGCATTTTGGTCATTTGCACACTCA
** * *
41532 -GGGCATCCTGGTCATTTGCATATTCA
1 GGGGCATTTTGGTCATTTGCACACTCA
41558 GGGGCATTTTGGTCATTT
1 GGGGCATTTTGGTCATTT
41576 TAAGTCCACT
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
26 19 0.56
27 15 0.44
ACGTcount: A:0.17, C:0.17, G:0.27, T:0.39
Consensus pattern (27 bp):
GGGGCATTTTGGTCATTTGCACACTCA
Found at i:42106 original size:24 final size:25
Alignment explanation
Indices: 42077--42127 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
42067 TTATGTGAAC
*
42077 AATAAAATAAATAAACAAGA-AAAT
1 AATAAAATAAAGAAACAAGATAAAT
* *
42101 AATAAAATTAAGCAACAAGATAAAT
1 AATAAAATAAAGAAACAAGATAAAT
42126 AA
1 AA
42128 ATACTCCAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.18
Consensus pattern (25 bp):
AATAAAATAAAGAAACAAGATAAAT
Found at i:44659 original size:185 final size:185
Alignment explanation
Indices: 44340--44686 Score: 649
Period size: 185 Copynumber: 1.9 Consensus size: 185
44330 AATTACAGAG
44340 CAATTACAGAGCATCAACATAGCAGCAGAGGCAAGAGAAAGGACCAAAGTAGCTTGCAAGTTAAA
1 CAATTACAGAGCATCAACATAGCAGCAGAGGCAAGAGAAAGGACCAAAGTAGCTTGCAAGTTAAA
44405 AGTGCACACAAACCACAAGCAAATTCCCCAATAGCATTCAGTTATAAAATAGAATTGAGAAATTA
66 AGTGCACACAAACCACAAGCAAATTCCCCAATAGCATTCAGTTATAAAATAGAATTGAGAAATTA
*
44470 CCATGCTAGCTCACCATTCATCGCTATCTTCACTTAAAAACACCAAAATCAAAGA
131 CCATGCCAGCTCACCATTCATCGCTATCTTCACTTAAAAACACCAAAATCAAAGA
* * *
44525 CAATTATAGAGCATCAACATAGCAGCAGAGGCAGGAGAAAGGACCAAAGTAGCTTGCAGGTTAAA
1 CAATTACAGAGCATCAACATAGCAGCAGAGGCAAGAGAAAGGACCAAAGTAGCTTGCAAGTTAAA
*
44590 AGTGCACACAAACCACAAGCAAATTCCCCAATAGCATTTAGTTATAAAATAGAATTGAGAAATTA
66 AGTGCACACAAACCACAAGCAAATTCCCCAATAGCATTCAGTTATAAAATAGAATTGAGAAATTA
44655 CCATGCCAGCTCACCATTCATCGCTATCTTCA
131 CCATGCCAGCTCACCATTCATCGCTATCTTCA
44687 AAGCTGCACA
Statistics
Matches: 157, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
185 157 1.00
ACGTcount: A:0.41, C:0.22, G:0.16, T:0.20
Consensus pattern (185 bp):
CAATTACAGAGCATCAACATAGCAGCAGAGGCAAGAGAAAGGACCAAAGTAGCTTGCAAGTTAAA
AGTGCACACAAACCACAAGCAAATTCCCCAATAGCATTCAGTTATAAAATAGAATTGAGAAATTA
CCATGCCAGCTCACCATTCATCGCTATCTTCACTTAAAAACACCAAAATCAAAGA
Found at i:46571 original size:76 final size:75
Alignment explanation
Indices: 46423--46563 Score: 169
Period size: 76 Copynumber: 1.9 Consensus size: 75
46413 AAGGGCCCCA
* * * *
46423 ACTCCACTTGGGGCCCACATGGTTGTTCTGAACACCCATGTGGTTTGCTTGAGGACCCAGGTGGG
1 ACTCCACTTGGGGCCCACAAGGTTGTTCTGAACACCCATGTGGTTTGCCTGAGCACCCAGATGGG
46488 CAGTGTCACG
66 CAGTGTCACG
* * * *
46498 ACTCCAGTTGGGTGCCCTCAAGGTT-TGTCTGAAGACCCATGT-GTTTCGCCTGATCACCCAGAT
1 ACTCCACTTGGG-GCCCACAAGGTTGT-TCTGAACACCCATGTGGTTT-GCCTGAGCACCCAGAT
46561 GGG
63 GGG
46564 TTGTGTCATA
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
75 16 0.29
76 39 0.71
ACGTcount: A:0.18, C:0.27, G:0.29, T:0.26
Consensus pattern (75 bp):
ACTCCACTTGGGGCCCACAAGGTTGTTCTGAACACCCATGTGGTTTGCCTGAGCACCCAGATGGG
CAGTGTCACG
Done.