Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020777.1 Corchorus olitorius cultivar O-4 contig20810, 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: 17063
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1109 original size:322 final size:321
Alignment explanation
Indices: 339--1585 Score: 1436
Period size: 322 Copynumber: 3.9 Consensus size: 321
329 TGGTAAAAAT
* * * * * * *
339 GACCAAAAAGATTTTTCCTCAATTTTTGGCAAAAACACTCATAAAAATATATATAATTCAACGCC
1 GACCCAAAA-ATTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAA-ATATATAATTCAACGCC
* * * * * **
404 AAAACGATTG--GAAGACTTTTCACACTTTTAATATCGTTTTTCATATTTTTTTCTTAA-AAATT
64 AAAAAGATTGACG-GGA-TTTTCACGCTTCTAATATCGTTTTTC-CATTTTTTTCCGAATAAATT
* * * * *
466 TCTAATTAAATCGAAACAAGATTCTGATGCAC-ATAAAAACAAATCCTTAAATCCAATGTGGCCT
126 TCTAATTAAATCGAAACAAGATTCAGATGCTCGA-AAAAACAAATCCTTATATCCAATAT-GACT
* * * ** * * *
530 -AGATTTGATTAGACT-AATAAAGA-AATTTCAAGGAGTCTCAGCACCAAAAACCATGCAAAACA
189 GAGATTTGGTTCGA-TGAATATAGATAA-TTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAACT
* * * * * *
592 GAGCCGTGAC-CCCAGAAGGCGTTTTTAGTCAAAATCCGTGAT-GTTAGTACACGATTTCGACTG
252 GAGCCGGGACTCCGA-AACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGACTA
*
655 AAAACT
316 AAAACC
* ** * * *
661 GACCC-GAAAGCTTCTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACTCGAA
1 GACCCAAAAATTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAA
* * * * *
725 AAAGATTAACGGGCTTTTCACGCTTCTTATATTGTTTTTTCATTTTTTTCCGAATAAATTTCTAA
66 AAAGATTGACGGGATTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATAAATTTCTAA
* * * * * * *
790 TTAAATCGAAATAAGATTCAGATGCTCGTAAAAACAAATCCTCATATTCAATGTGGCTGACATTT
131 TTAAATCGAAACAAGATTCAGATGCTCGAAAAAACAAATCCTTATATCCAATATGACTGAGATTT
* * * *
855 GGTTCGATGAATATAGATAAATCAAAGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGCCGGGG
196 GGTTCGATGAATATAGATAATTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAACTGAGCCGGGA
* *
920 CTCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTTGGCTAAAAACC
261 CTCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGACTAAAAACC
*
981 GACCCAAAAATTTTTATCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACACCA
1 GACCCAAAAATTTTT-TCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCA
* * *
1046 AAAAGATTGATGGGATTTTCACGCTTCTAATATCGTTTTTCCTTTTTTTTCCGAATTAATTTCTA
65 AAAAGATTGACGGGATTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATAAATTTCTA
* * **
1111 ATTAAATCGAAATAAAATAGAGATGCTCGAAAAAACAAATCCTTATATCCAATATGACTGAGATT
130 ATTAAATCGAAACAAGATTCAGATGCTCGAAAAAACAAATCCTTATATCCAATATGACTGAGATT
* * * * * *
1176 TGGTTCGATGAAAATAGATATTTCAAGGAGTCTTTGCGTCAAAAATCATGAAAAATTGAGCCGGA
195 TGGTTCGATGAATATAGATAATTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAACTGAGCCGGG
* * *
1241 ACTCCGGAACGCGTTTTTAGCCAAAAACCATGATGGTTAGTACACGATTTCGACTAAAAACG
260 ACTCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGACTAAAAACC
* * * *
1303 GAACCGAAAAGTTTTTTCTCAAATTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGTCA
1 G-ACCCAAAAATTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCA
* * *
1368 AAAACATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTA
65 AAAAGATTGACGGGATTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATAAATTTCTA
* * * *
1433 ATTAAGTCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCATATATTCAATATGACTGAGATT
130 ATTAAATCGAAACAAGATTCAGATGCTCGAAAAAACAAATCCTTATATCCAATATGACTGAGATT
* * * * * *
1498 TGGTTCCATGAATATAGATATTTCAAGGAGCCTTTACG-CAGAAAATCTTGCAAAACTGAACCGG
195 TGGTTCGATGAATATAGATAATTCAAGGAGTCTTTGCGCCA-AAAATCATGCAAAACTGAGCCGG
* * * *
1562 GGCCCCGGAACGTGTTTTTAGCCA
259 GACTCCGAAACGCGTTTTTAGCCA
1586 TAAGCCGCGA
Statistics
Matches: 794, Mismatches: 118, Indels: 26
0.85 0.13 0.03
Matches are distributed among these distances:
318 15 0.02
319 177 0.22
320 62 0.08
321 10 0.01
322 518 0.65
323 12 0.02
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (321 bp):
GACCCAAAAATTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAA
AAAGATTGACGGGATTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATAAATTTCTAA
TTAAATCGAAACAAGATTCAGATGCTCGAAAAAACAAATCCTTATATCCAATATGACTGAGATTT
GGTTCGATGAATATAGATAATTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAACTGAGCCGGGA
CTCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGACTAAAAACC
Found at i:3816 original size:569 final size:555
Alignment explanation
Indices: 2782--3842 Score: 1427
Period size: 569 Copynumber: 1.9 Consensus size: 555
2772 ATTGATGGTC
* *
2782 TTTTCACGCTTTTAATATCATTTTTCCAATTTTTTTCTGAATTAATTTCTAATTAAATCGAAACA
1 TTTTCACGCTTTAAATATCATTTTTCCAATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACA
* * *
2847 AGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTAACATTGGGTTTGATGAATA
66 AGATCCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTAACATTGGGTTAGATGAATA
* * ** * * *
2912 TAGATATTTCAAGGAGTCTTTGCGCAAAAAATCATGCAAAATTGAGTCGGGGTTCGGGAATGCGT
131 TAGATATTTCAAGGAGTCTTTGCGCAAAAAATAATGCAAAACTGAGTCGGGGCCCCGAAACGCGT
* *
2977 TTTTAGCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGATCCGAAAAGTTTATTC
196 TTTTAGCAAAAACCATGATGGTTAGTACACGATTTCAGCTAAAAACTGATCCGAAAAGTTTATTC
* ** * *
3042 TCAATTTTTTGCCACAATACTCAAAAAAGCTATATAATTCAACGCCAAAACGATTGACGGGCTTT
261 TCAATTTTTTGCCACAATACTAAAAAAAAATATATAATTCAACACCAAAAAGATTGACGGGCTTT
* * *
3107 CCATGCTTCTAATATCATTTTTCCATTTTTTTCCGAATTAATTTTTAATTAAATTGAAACAATAT
326 CCACGCTTCTAATATCATTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATTGAAACAAGAT
* * ** *
3172 TTAGATGCTCGTAAAAACAAATACTTAAATCGAACTTGGCTGGGATTTTGTTCGATGAATATAGA
391 TCAGATGCTCGTAAAAACAAATACTTAAATCCAACTTGGCTGACATTTGGTTCGATGAATATAGA
*
3237 TATTTCAAGGAGTATTTACGTCATAAA-TCATGCAAAAACAAAAACAAAAAGTATTTTCGGCAAA
456 TATTTCAAGGAGTATTTACGCCA-AAAGTCATGCAAAAACAAAAACAAAAAGTATTTTCGGCAAA
3301 AAATACACAATTCAACGCAAAAAAAAAATTGAAATA
520 AAATACACAATTCAACGCAAAAAAAAAATTGAAATA
* *
3337 TTTTCTCGCTTTAAATATCATTTTT-CTATTTTTTTCCGAATCT-ATTTCTAATTAAATCGAAAC
1 TTTTCACGCTTTAAATATCATTTTTCCAATTTTTTTCCGAAT-TAATTTCTAATTAAATCGAAAC
* * *
3400 AATATCCATATGCTCGTAAAAACAAATCCTTAAATCTAATGTGGCTGAGAGCCTGAGATT-GGTT
65 AAGATCCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCT-A-A--C----ATTGGGTT
*
3464 AGATGAATATAGATATTTCAAGGAGTCTTT-CTGCCAAAAAATAATGCAAAACTGAGTTGGGGCC
122 AGATGAATATAGATATTTCAAGGAGTCTTTGC-G-CAAAAAATAATGCAAAACTGAGTCGGGG-C
* *
3528 CCCGAAACGCGTTTTTAGCCCAAAAACTATGATGGTTAGTACATGATTTTCAGCTAAAAACTGA-
184 CCCGAAACGCGTTTTTAG--CAAAAACCATGATGGTTAGTACACGA-TTTCAGCTAAAAACTGAT
** * *
3592 CTCGAAATTTTTTTTTCATGAATTTTTTGCCACAATACTAAAAAAAAATATATAATTCAACACCA
246 C-CGAAA-AGTTTATTC-TCAATTTTTTGCCACAATACTAAAAAAAAATATATAATTCAACACCA
* * * *
3657 AAAAGATTGATGGTCTTTTCACGCTTTTAATATCATTTTTCCAATTTTTTTCCGAATTAATTTCT
308 AAAAGATTGACGGGCTTTCCACGCTTCTAATATCATTTTTCC-ATTTTTTTCCGAATTAATTTCT
* *
3722 AATTAAATTGAAACAAGATTCAGATGCTTGTAAAAACAAA-ACCTTATATCCAA-TGTGGCTGAC
372 AATTAAATTGAAACAAGATTCAGATGCTCGTAAAAACAAATA-CTTAAATCCAACT-TGGCTGAC
* * *
3785 ATTTGGTTTGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAGTCATGCAAAA
435 ATTTGGTTCGATGAATATAGATATTTCAAGGAGTATTTACGCCAAAAGTCATGCAAAA
3843 TTGAGTCGGG
Statistics
Matches: 435, Mismatches: 49, Indels: 30
0.85 0.10 0.06
Matches are distributed among these distances:
554 75 0.17
555 25 0.06
556 1 0.00
558 1 0.00
560 1 0.00
561 34 0.08
562 28 0.06
563 14 0.03
565 24 0.06
566 21 0.05
567 6 0.01
568 83 0.19
569 122 0.28
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (555 bp):
TTTTCACGCTTTAAATATCATTTTTCCAATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACA
AGATCCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTAACATTGGGTTAGATGAATA
TAGATATTTCAAGGAGTCTTTGCGCAAAAAATAATGCAAAACTGAGTCGGGGCCCCGAAACGCGT
TTTTAGCAAAAACCATGATGGTTAGTACACGATTTCAGCTAAAAACTGATCCGAAAAGTTTATTC
TCAATTTTTTGCCACAATACTAAAAAAAAATATATAATTCAACACCAAAAAGATTGACGGGCTTT
CCACGCTTCTAATATCATTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATTGAAACAAGAT
TCAGATGCTCGTAAAAACAAATACTTAAATCCAACTTGGCTGACATTTGGTTCGATGAATATAGA
TATTTCAAGGAGTATTTACGCCAAAAGTCATGCAAAAACAAAAACAAAAAGTATTTTCGGCAAAA
AATACACAATTCAACGCAAAAAAAAAATTGAAATA
Found at i:4001 original size:323 final size:326
Alignment explanation
Indices: 3337--4169 Score: 1027
Period size: 323 Copynumber: 2.5 Consensus size: 326
3327 AATTGAAATA
* * * *
3337 TTTTCTCGCTTTAAATATCATTTTTCTATTTTTTTCCGAATCT-ATTTCTAATTAAATCGAAACA
1 TTTTCACGCTTTTAATATCATTTTTCCATTTTTTTCCGAAT-TAATTTCTAATTAAATTGAAACA
* * * * * * *
3401 ATATCCATATGCTCGTAAAAACAAATCCTTAAATCTAATGTGGCTGAGAGCCTGAGATTGGTTAG
65 AGATTCAGATGCTTGTAAAAACAAAACCTTAAATCCAATGTGGCT--GA--C--A-TTTGGTTAG
* *
3466 ATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAAATAATGCAAAACTGAGTTGGGGCCCCC
123 ATGAATATAGATATTTCAAGGAGTCTTTC-GCC-AAAAATCATGCAAAACTGAGTCGGGGCCCCC
* * *
3531 GAAACGCGTTTTTAGCCCAAAAACTATGATGGTTAGTACATGATTTTCAGCTAAAAACTGACTCG
186 GAAACGCGTTTTTAGCCCAAAAACCATGATGGTTACTACACGATTTTCAGCTAAAAACTGACTCG
** * *
3596 AAATTTTTTTTTCATGAATTTTTTGCCACAATACTAAAAAAAAATATATAATTCAACACCAAAAA
251 AAATAGTTTTTTCATCAATTTTTTGCCACAATACTAAAAAAAAATATACAATTCAACACCAAAAA
* *
3661 GATTGATGGTC
316 GATTGACGGGC
3672 TTTTCACGCTTTTAATATCATTTTTCCAATTTTTTTCCGAATTAATTTCTAATTAAATTGAAACA
1 TTTTCACGCTTTTAATATCATTTTTCC-ATTTTTTTCCGAATTAATTTCTAATTAAATTGAAACA
* *
3737 AGATTCAGATGCTTGTAAAAACAAAACCTTATATCCAATGTGGCTGACATTTGGTTTGATGAATA
65 AGATTCAGATGCTTGTAAAAACAAAACCTTAAATCCAATGTGGCTGACATTTGGTTAGATGAATA
* * * * * *
3802 TAGATATTTCAAGGAGTCTTTGCGCCAAAAGTCATGCAAAATTGAGTCGGGG-CTCGGGAACGTG
130 TAGATATTTCAAGGAGTCTTT-CGCCAAAAATCATGCAAAACTGAGTCGGGGCCCCCGAAACGCG
*
3866 TTTTTAG-CCAAAAACCATGATGGTTACTACACGA-TTTCGGCTAAAAACTGA-TCCGAAA-AGT
194 TTTTTAGCCCAAAAACCATGATGGTTACTACACGATTTTCAGCTAAAAACTGACT-CGAAATAGT
* * * *
3927 TTTTTC-TCAATTTTTTGTCACAATACTCAGAAAAAATATACAATTCAACGCCAAAAAGATTGAC
258 TTTTTCATCAATTTTTTGCCACAATACTAAAAAAAAATATACAATTCAACACCAAAAAGATTGAC
3991 GGGC
323 GGGC
* * *
3995 TTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTTTAATTAAATTGAAACAA
1 TTTTCACGCTTTTAATATCATTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATTGAAACAA
* * * ** * * *
4060 GATTCAGATGCCTTGTAAAAACAAATA-CTTAAATCGAACGTGACTGGGATTT-ATTCGATAAAT
66 GATTCAGATG-CTTGTAAAAACAAA-ACCTTAAATCCAATGTGGCTGACATTTGGTTAGATGAAT
* *
4123 ATAGATATTTCAAGGAGTATTTACGTCAAAAATCATGCAAAACTGAG
129 ATAGATATTTCAAGGAGTCTTT-CGCCAAAAATCATGCAAAACTGAG
4170 CCAGTGCTAA
Statistics
Matches: 440, Mismatches: 52, Indels: 25
0.85 0.10 0.05
Matches are distributed among these distances:
322 97 0.22
323 112 0.25
324 9 0.02
325 21 0.05
326 24 0.05
327 15 0.03
328 22 0.05
329 38 0.09
330 2 0.00
332 1 0.00
334 2 0.00
335 25 0.06
336 72 0.16
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (326 bp):
TTTTCACGCTTTTAATATCATTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATTGAAACAA
GATTCAGATGCTTGTAAAAACAAAACCTTAAATCCAATGTGGCTGACATTTGGTTAGATGAATAT
AGATATTTCAAGGAGTCTTTCGCCAAAAATCATGCAAAACTGAGTCGGGGCCCCCGAAACGCGTT
TTTAGCCCAAAAACCATGATGGTTACTACACGATTTTCAGCTAAAAACTGACTCGAAATAGTTTT
TTCATCAATTTTTTGCCACAATACTAAAAAAAAATATACAATTCAACACCAAAAAGATTGACGGG
C
Found at i:4653 original size:29 final size:30
Alignment explanation
Indices: 4598--4658 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
4588 ATAATAATAT
* *
4598 TAATAAAAAAGTTGAATCATCTCAAAAAAA
1 TAATAAAAAAGTTAAATCATCTAAAAAAAA
* *
4628 TAATAAAAAAGTTAAATGA-CTAAAAAGAA
1 TAATAAAAAAGTTAAATCATCTAAAAAAAA
4657 TA
1 TA
4659 CTTCTTCAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 10 0.37
30 17 0.63
ACGTcount: A:0.62, C:0.07, G:0.08, T:0.23
Consensus pattern (30 bp):
TAATAAAAAAGTTAAATCATCTAAAAAAAA
Found at i:5640 original size:29 final size:30
Alignment explanation
Indices: 5601--5678 Score: 104
Period size: 29 Copynumber: 2.6 Consensus size: 30
5591 ACTTATAGCA
*
5601 TTTGGACATTTTGCCCCCTGAACT-TTAAT
1 TTTGGACATTTTGCCCCCTGAACTCTCAAT
* *
5630 TTTGGACATTTTACCCCTTGAACTCTCAAT
1 TTTGGACATTTTGCCCCCTGAACTCTCAAT
* *
5660 TTTGGACGTTTTGTCCCCT
1 TTTGGACATTTTGCCCCCT
5679 TTCAAGCGAT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 22 0.54
30 19 0.46
ACGTcount: A:0.18, C:0.26, G:0.14, T:0.42
Consensus pattern (30 bp):
TTTGGACATTTTGCCCCCTGAACTCTCAAT
Found at i:5892 original size:29 final size:30
Alignment explanation
Indices: 5833--5902 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 30
5823 ATCGTTTGAG
* * *
5833 AAGGGGTAAAATGTCCAAAATTGAGAGTTT
1 AAGGGGCAAAATGTACAAAATTGAGAATTT
*
5863 AGGGGGCAAAATGTACAAAATTGA-AATTT
1 AAGGGGCAAAATGTACAAAATTGAGAATTT
*
5892 AAGGGACAAAA
1 AAGGGGCAAAA
5903 CATCCAAACG
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 13 0.38
30 21 0.62
ACGTcount: A:0.46, C:0.07, G:0.26, T:0.21
Consensus pattern (30 bp):
AAGGGGCAAAATGTACAAAATTGAGAATTT
Found at i:5910 original size:29 final size:30
Alignment explanation
Indices: 5846--5910 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 30
5836 GGGTAAAATG
* * * **
5846 TCCAAAATTGAGAGTTTAGGGGGCAAAATG
1 TCCAAAATTGAGAATTTAAGGGACAAAACA
*
5876 TACAAAATTGA-AATTTAAGGGACAAAACA
1 TCCAAAATTGAGAATTTAAGGGACAAAACA
5905 TCCAAA
1 TCCAAA
5911 CGCTACAAGT
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
29 18 0.64
30 10 0.36
ACGTcount: A:0.46, C:0.12, G:0.20, T:0.22
Consensus pattern (30 bp):
TCCAAAATTGAGAATTTAAGGGACAAAACA
Found at i:8423 original size:51 final size:50
Alignment explanation
Indices: 8322--8424 Score: 120
Period size: 51 Copynumber: 2.0 Consensus size: 50
8312 GTTCTTCATA
* *
8322 TTTTTCTTGTTTAGATCTTGTCTCAGGACAATCAAACACTCTTTTAGTGT
1 TTTTTCTTGTTTAGATCTTGTCTCAGGACAATAAAACACTCTATTAGTGT
* * *
8372 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGAC-ATAAAAACACTGTATTCGTGT
1 TTTT-TCTTGTTT-AGATCTTGTCTCAGGACAAT-AAAACACTCTATTAGTGT
8423 TT
1 TT
8425 CTCTTTCAGA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
50 6 0.13
51 38 0.84
52 1 0.02
ACGTcount: A:0.21, C:0.19, G:0.14, T:0.46
Consensus pattern (50 bp):
TTTTTCTTGTTTAGATCTTGTCTCAGGACAATAAAACACTCTATTAGTGT
Found at i:11100 original size:42 final size:42
Alignment explanation
Indices: 11053--11139 Score: 147
Period size: 42 Copynumber: 2.1 Consensus size: 42
11043 GCTGTTACTA
* *
11053 CTCAAACAAGAAATCTAGTGCAGTTAAGGGATGATGGTAGAG
1 CTCAAACAAGAAATCCAGTGCAGTTAAGGGATGATGATAGAG
*
11095 CTCAAACACGAAATCCAGTGCAGTTAAGGGATGATGATAGAG
1 CTCAAACAAGAAATCCAGTGCAGTTAAGGGATGATGATAGAG
11137 CTC
1 CTC
11140 GCTTAAAGAC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.37, C:0.16, G:0.26, T:0.21
Consensus pattern (42 bp):
CTCAAACAAGAAATCCAGTGCAGTTAAGGGATGATGATAGAG
Found at i:12057 original size:16 final size:18
Alignment explanation
Indices: 12036--12073 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
12026 GTTGCAAGGG
12036 TGTCAAC-T-TGATTAAT
1 TGTCAACGTATGATTAAT
*
12052 TGTCAACGTATGCTTAAT
1 TGTCAACGTATGATTAAT
12070 TGTC
1 TGTC
12074 TTCGACATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
17 1 0.05
18 11 0.58
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (18 bp):
TGTCAACGTATGATTAAT
Found at i:16926 original size:15 final size:16
Alignment explanation
Indices: 16906--16935 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
16896 TTTATGATTA
16906 AAAAATAT-ATTTTTC
1 AAAAATATGATTTTTC
16921 AAAAATATGATTTTT
1 AAAAATATGATTTTT
16936 TAAATTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (16 bp):
AAAAATATGATTTTTC
Done.