Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014763.1 Corchorus olitorius cultivar O-4 contig14796, 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: 28124
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:45 original size:18 final size:17
Alignment explanation
Indices: 6--46 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
1 AGACT
6 CAAACTAACTGACTCAA
1 CAAACTAACTGACTCAA
* *
23 AAAACTAAACTGACTCGA
1 CAAACT-AACTGACTCAA
41 CAAACT
1 CAAACT
47 GACTAAACCC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.49, C:0.27, G:0.07, T:0.17
Consensus pattern (17 bp):
CAAACTAACTGACTCAA
Found at i:1947 original size:62 final size:62
Alignment explanation
Indices: 1871--1989 Score: 220
Period size: 62 Copynumber: 1.9 Consensus size: 62
1861 GGGTTCAGTG
*
1871 CAATGACCTCAATACCATGTAAGGTCTTGGGTATAAATCTTGTAAATGAAGAAAATAAAGTA
1 CAATGACCTCAATACCAAGTAAGGTCTTGGGTATAAATCTTGTAAATGAAGAAAATAAAGTA
*
1933 CAATGACCTCAATACTAAGTAAGGTCTTGGGTATAAATCTTGTAAATGAAGAAAATA
1 CAATGACCTCAATACCAAGTAAGGTCTTGGGTATAAATCTTGTAAATGAAGAAAATA
1990 GACACGCAGA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
62 55 1.00
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.28
Consensus pattern (62 bp):
CAATGACCTCAATACCAAGTAAGGTCTTGGGTATAAATCTTGTAAATGAAGAAAATAAAGTA
Found at i:8273 original size:27 final size:27
Alignment explanation
Indices: 8202--8273 Score: 67
Period size: 27 Copynumber: 2.6 Consensus size: 27
8192 TTTCCGATTG
*
8202 TATTCTTATTTTCAAATATATTTCTAAAT
1 TATTATTATTTT-AAA-ATATTTCTAAAT
**
8231 TATTATTATTAAAAAATATTT-T-AAT
1 TATTATTATTTTAAAATATTTCTAAAT
8256 TATTCCATTATTTTAAAA
1 TATT--ATTATTTTAAAA
8274 ATGGAAATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
25 7 0.19
26 1 0.03
27 16 0.44
28 3 0.08
29 9 0.25
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (27 bp):
TATTATTATTTTAAAATATTTCTAAAT
Found at i:9334 original size:10 final size:10
Alignment explanation
Indices: 9319--9366 Score: 78
Period size: 10 Copynumber: 4.8 Consensus size: 10
9309 TTTAGAAATA
9319 TATCTATATC
1 TATCTATATC
9329 TATCTATATC
1 TATCTATATC
* *
9339 AATCTATGTC
1 TATCTATATC
9349 TATCTATATC
1 TATCTATATC
9359 TATCTATA
1 TATCTATA
9367 AAAGTGCGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 34 1.00
ACGTcount: A:0.31, C:0.19, G:0.02, T:0.48
Consensus pattern (10 bp):
TATCTATATC
Found at i:11088 original size:20 final size:19
Alignment explanation
Indices: 11052--11099 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
11042 CAAGCTAATT
*
11052 CTAAAAATTTAAGCTTTAA
1 CTAAAAATTTAACCTTTAA
*
11071 CTAAAATATTTCACCTTTATA
1 CTAAAA-ATTTAACCTTTA-A
*
11092 TTAAAAAT
1 CTAAAAAT
11100 CAACTCAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 6 0.25
20 12 0.50
21 6 0.25
ACGTcount: A:0.46, C:0.12, G:0.02, T:0.40
Consensus pattern (19 bp):
CTAAAAATTTAACCTTTAA
Found at i:13923 original size:5 final size:5
Alignment explanation
Indices: 13913--13939 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
13903 CCCTAATGCC
13913 AAATA AAATA AAATA AAATA AAATA AA
1 AAATA AAATA AAATA AAATA AAATA AA
13940 TTGATTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:16739 original size:12 final size:12
Alignment explanation
Indices: 16724--16778 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 12
16714 CAGCCTGCCA
16724 GCCAGCACGCGG
1 GCCAGCACGCGG
16736 GCCAGCA--CGG
1 GCCAGCACGCGG
* ** **
16746 CCCAGCGTGCCA
1 GCCAGCACGCGG
16758 GCCAGCACGCGG
1 GCCAGCACGCGG
16770 GCCAGCACG
1 GCCAGCACG
16779 GCCCAGCGTG
Statistics
Matches: 32, Mismatches: 9, Indels: 4
0.71 0.20 0.09
Matches are distributed among these distances:
10 8 0.25
12 24 0.75
ACGTcount: A:0.18, C:0.44, G:0.36, T:0.02
Consensus pattern (12 bp):
GCCAGCACGCGG
Found at i:16786 original size:34 final size:34
Alignment explanation
Indices: 16710--16789 Score: 151
Period size: 34 Copynumber: 2.4 Consensus size: 34
16700 GCCAGGCGCA
*
16710 GGCCCAGCCTGCCAGCCAGCACGCGGGCCAGCAC
1 GGCCCAGCGTGCCAGCCAGCACGCGGGCCAGCAC
16744 GGCCCAGCGTGCCAGCCAGCACGCGGGCCAGCAC
1 GGCCCAGCGTGCCAGCCAGCACGCGGGCCAGCAC
16778 GGCCCAGCGTGC
1 GGCCCAGCGTGC
16790 TAGGCTTGGT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 45 1.00
ACGTcount: A:0.16, C:0.45, G:0.35, T:0.04
Consensus pattern (34 bp):
GGCCCAGCGTGCCAGCCAGCACGCGGGCCAGCAC
Found at i:16864 original size:16 final size:14
Alignment explanation
Indices: 16832--16899 Score: 52
Period size: 14 Copynumber: 4.8 Consensus size: 14
16822 AAGTTTTTTT
16832 TAAAA-AAAAAAAA
1 TAAAATAAAAAAAA
16845 TAAAATAAATAAATAA
1 TAAAATAAA-AAA-AA
*
16861 TAAAATAGAAAGGAAA
1 TAAAATA-AAA-AAAA
16877 T--AATAAAAAAAA
1 TAAAATAAAAAAAA
* *
16889 GAAAAGAAAAA
1 TAAAATAAAAA
16900 GGAAGAGAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 13
0.72 0.07 0.21
Matches are distributed among these distances:
12 3 0.07
13 8 0.18
14 14 0.32
15 3 0.07
16 13 0.30
17 3 0.07
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.13
Consensus pattern (14 bp):
TAAAATAAAAAAAA
Found at i:16908 original size:12 final size:12
Alignment explanation
Indices: 16883--16926 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
16873 GAAATAATAA
* *
16883 AAAAAAGAAAAG
1 AAAAAGGAAGAG
16895 AAAAAGGAAGAG
1 AAAAAGGAAGAG
* *
16907 AAAAAGAAAGGG
1 AAAAAGGAAGAG
16919 AAAAAGGA
1 AAAAAGGA
16927 TATAAGGAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (12 bp):
AAAAAGGAAGAG
Found at i:19269 original size:2 final size:2
Alignment explanation
Indices: 19258--19306 Score: 66
Period size: 2 Copynumber: 25.5 Consensus size: 2
19248 ATCTGACAAT
* *
19258 TA TA -A TA TA TA TG TA TA TA TG TA TA TA TA T- TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19298 TA TA TA TA T
1 TA TA TA TA T
19307 GCAATTCAAC
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (2 bp):
TA
Found at i:22938 original size:41 final size:41
Alignment explanation
Indices: 22843--22945 Score: 111
Period size: 41 Copynumber: 2.5 Consensus size: 41
22833 TTCCGGTTTA
* * *
22843 CAATTTGGTCCCTGATTTAAGTTAATATTTACTATTTGATG
1 CAATTTGATCCCTGATTTAGGTTAATAGTTACTATTTGATG
* * *
22884 CAATTT-AGCCCCTGATTTAGGATT-TTAGTTACTATTTGATT
1 CAATTTGA-TCCCTGATTTAGG-TTAATAGTTACTATTTGATG
22925 CAATTTGATCCCTGAGTTTAG
1 CAATTTGATCCCTGA-TTTAG
22946 AAATTATGCT
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
41 43 0.84
42 8 0.16
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.45
Consensus pattern (41 bp):
CAATTTGATCCCTGATTTAGGTTAATAGTTACTATTTGATG
Found at i:24227 original size:12 final size:12
Alignment explanation
Indices: 24210--24241 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
24200 TACCCCATGT
24210 AAACACGACACG
1 AAACACGACACG
24222 AAACACGACACG
1 AAACACGACACG
*
24234 ATACACGA
1 AAACACGA
24242 ATTGCCAGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.50, C:0.31, G:0.16, T:0.03
Consensus pattern (12 bp):
AAACACGACACG
Found at i:25486 original size:30 final size:30
Alignment explanation
Indices: 25447--26563 Score: 1691
Period size: 30 Copynumber: 37.1 Consensus size: 30
25437 TTAACTGAAG
* *
25447 AAGCAATGATCCT-AAACCAGGATTAAAATG
1 AAGCAATGATCCTCAAA-CAGGATTAACATA
* * * *
25477 AAGCCATGATCCTCAACCATGATTAAAATA
1 AAGCAATGATCCTCAAACAGGATTAACATA
* * *
25507 AGGTAATGATCCTC-AACTAGGATTAAAATA
1 AAGCAATGATCCTCAAAC-AGGATTAACATA
* *
25537 AAGCAATGATCCTCAAACATGATTTAATATA
1 AAGCAATGATCCTCAAACAGGA-TTAACATA
* * *
25568 AAGCAATGATCCTCAAACATGATTTAAAACA
1 AAGCAATGATCCTCAAACAGGA-TTAACATA
* * *
25599 AAGCAATGATCCT-AAATAGGGTTTAAAATA
1 AAGCAATGATCCTCAAACA-GGATTAACATA
* *
25629 AAGCAATGATCCTCGAACAAGATTAACATA
1 AAGCAATGATCCTCAAACAGGATTAACATA
*
25659 AAGCAATGCTCCTCAAACAGGATTAACATA
1 AAGCAATGATCCTCAAACAGGATTAACATA
*
25689 AAGCAATGATCCTCAAACAAGATTAACATA
1 AAGCAATGATCCTCAAACAGGATTAACATA
* * *
25719 AAGCAGTGCTCCTCAAACAGGATTAAAATA
1 AAGCAATGATCCTCAAACAGGATTAACATA
25749 AAGCAATGATCCTCAAACAGGATTAACATA
1 AAGCAATGATCCTCAAACAGGATTAACATA
25779 AAGCAATGATCCTCAAACAGGATTAACATA
1 AAGCAATGATCCTCAAACAGGATTAACATA
* *
25809 AAGCACTGATCCTCAAACAGGATTAAAATA
1 AAGCAATGATCCTCAAACAGGATTAACATA
25839 AAGCAATGATCCTCAAACAGGATTAACATA
1 AAGCAATGATCCTCAAACAGGATTAACATA
** * * * *
25869 AAGCTGTGACCCTCAAACAGGTTTAAAAGA
1 AAGCAATGATCCTCAAACAGGATTAACATA
25899 AAGCAATGATCCTCAAACAGGATTAACATA
1 AAGCAATGATCCTCAAACAGGATTAACATA
* *
25929 AAGCAATGATCCTCAAACATGATTAAAATA
1 AAGCAATGATCCTCAAACAGGATTAACATA
*
25959 AAGCAATGATCTTCAAACAGGATTAACATA
1 AAGCAATGATCCTCAAACAGGATTAACATA
*
25989 AAGCAATGATTCTCAAACAGGATTAACATA
1 AAGCAATGATCCTCAAACAGGATTAACATA
26019 AAGCAATGATCCTCAAACAGGATTAACATA
1 AAGCAATGATCCTCAAACAGGATTAACATA
*
26049 AAGCAGTGATCCTCAAACAGGATTAACATA
1 AAGCAATGATCCTCAAACAGGATTAACATA
*
26079 AAGCAATGATCCTCAAACAGGATTAAAAATA
1 AAGCAATGATCCTCAAACAGGATT-AACATA
*
26110 AAGCAGTGATCCTCAAACAGGATTAACATA
1 AAGCAATGATCCTCAAACAGGATTAACATA
* * *
26140 AAGCAGTGCTCCTCAAACAGGATTAAAATA
1 AAGCAATGATCCTCAAACAGGATTAACATA
*
26170 AAACAATGATCCTCAAACAGGATTAACATA
1 AAGCAATGATCCTCAAACAGGATTAACATA
*
26200 AAGCAATGATCCTCAAACAGGATTAAAATA
1 AAGCAATGATCCTCAAACAGGATTAACATA
26230 AAGCAATGATCCTCAAACAGGATTAACATA
1 AAGCAATGATCCTCAAACAGGATTAACATA
* *
26260 AAGCAATGATCCTCAAACGGGATTAAAATA
1 AAGCAATGATCCTCAAACAGGATTAACATA
26290 AAGCAATGATCCTCAAACAGGATTAACATA
1 AAGCAATGATCCTCAAACAGGATTAACATA
26320 AAGCAATGATCCTCAAACAGGATTAACATA
1 AAGCAATGATCCTCAAACAGGATTAACATA
* * *
26350 AAGCAGTGCTCCTCAAACAGGATTAAAATA
1 AAGCAATGATCCTCAAACAGGATTAACATA
26380 AAGCAATGATCCTCAAACAGGATTAACATA
1 AAGCAATGATCCTCAAACAGGATTAACATA
*
26410 AAGCAATGATCCTCAAACAGGATTAAAATA
1 AAGCAATGATCCTCAAACAGGATTAACATA
26440 AAGCAATGATCCTCAAACAGGATTAACATA
1 AAGCAATGATCCTCAAACAGGATTAACATA
* *
26470 AAGCAATGATCCTCAAACGGGATTAAAATA
1 AAGCAATGATCCTCAAACAGGATTAACATA
26500 AAGCAATGATCCTCAAACAGGATTAACATA
1 AAGCAATGATCCTCAAACAGGATTAACATA
26530 AAGCAATGATCCTCAAACAGGATTAACATA
1 AAGCAATGATCCTCAAACAGGATTAACATA
26560 AAGC
1 AAGC
26564 TGATAAAGCA
Statistics
Matches: 990, Mismatches: 90, Indels: 14
0.90 0.08 0.01
Matches are distributed among these distances:
29 2 0.00
30 902 0.91
31 86 0.09
ACGTcount: A:0.46, C:0.19, G:0.14, T:0.21
Consensus pattern (30 bp):
AAGCAATGATCCTCAAACAGGATTAACATA
Found at i:26894 original size:35 final size:35
Alignment explanation
Indices: 26825--27660 Score: 841
Period size: 35 Copynumber: 23.6 Consensus size: 35
26815 CATTTTGCAG
* *
26825 TCAATTGAAATAAACTGCAGAGAAGATCGCCCTGGA
1 TCAACTGAAATAAACTGAAGA-AAGATCGCCCTGGA
* * * * *
26861 TCTACTGAAGTAAATTGAGGAAAGATCGTCCTGGA
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
*
26896 TCAATTGAAATAAACTGAAGAAAAGATCGCCCTGGA
1 TCAACTGAAATAAACTGAAG-AAAGATCGCCCTGGA
*
26932 TCAAGTGAAATAAACTGAAGAAAAGATCGCCCTGGA
1 TCAACTGAAATAAACTGAAG-AAAGATCGCCCTGGA
* *
26968 TCAATTGAAATAAATTGAAGAAAAGATCGCCCTGGA
1 TCAACTGAAATAAACTGAAG-AAAGATCGCCCTGGA
*
27004 TCAACTGAAATAAACTGAAGAAAGACCGCCCTGGA
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
* * *
27039 TCAACTAAAATAAACTGAAGAAAGACCGCCCTGGG
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
*
27074 TCAACTGAAATAAACTGAAGAAAGGATCGCCCTAGA
1 TCAACTGAAATAAACTGAAGAAA-GATCGCCCTGGA
* * *
27110 TCAACTGAAATAAACTGAAGAAAAACCGCCCTGGG
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
** *
27145 TCAACAAAAATAAACTGAAGAAAGGATCACCCTGGA
1 TCAACTGAAATAAACTGAAGAAA-GATCGCCCTGGA
* * *
27181 TCAACTGAAGTAAAATGAAGAAAAGATCACCCTGGA
1 TCAACTGAAATAAACTGAAG-AAAGATCGCCCTGGA
* * * *
27217 TCAAACTGAAATAAACTGAA-ATAGGACCACCCTGGG
1 TC-AACTGAAATAAACTGAAGA-AAGATCGCCCTGGA
* * * * *
27253 TCAACTGAAATGAATTGAATAAGGATCGCCCTGAA
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
* * * * *
27288 TCAACTGAAGTGAATTGAAGAAAGACCGCCCTGGG
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
* * * *
27323 TCAGCTAAAATAAACTGAAGAAAGACCGCCCTGGG
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
* * * *
27358 TCAACTGAAATGAATTGAATAAGGATCGCCCTGGA
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
* * * *
27393 TCAACTGAATTGAACTGAAGAAA-AGCCGCCCTGGG
1 TCAACTGAAATAAACTGAAGAAAGA-TCGCCCTGGA
*
27428 TCAACTAAAATAAACTGAAGAAAGTATCGCCCTGGA
1 TCAACTGAAATAAACTGAAGAAAG-ATCGCCCTGGA
* * *
27464 TCAACTGAAGTAAAATGAAGAAAAGATCACCCTGGA
1 TCAACTGAAATAAACTGAAG-AAAGATCGCCCTGGA
* * * *
27500 TCAAACTGAAATAAACTGAA-ATAGGACCACCCTGGG
1 TC-AACTGAAATAAACTGAAGA-AAGATCGCCCTGGA
* * * *
27536 TCAACTGAAATGAATTGAATAAGGATCGCCCTGGA
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
* * * * *
27571 TCAACTGAAGTGAATTGAAGAAAGACCGCCCTGGG
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
* * * * * * *
27606 TCAGCTAAAATAAACTGAATAAAGACCACCTTGGG
1 TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
*
27641 TCAACTGAAATGAACTGAAG
1 TCAACTGAAATAAACTGAAG
27661 CGTCTAAAAT
Statistics
Matches: 675, Mismatches: 111, Indels: 29
0.83 0.14 0.04
Matches are distributed among these distances:
34 1 0.00
35 385 0.57
36 251 0.37
37 38 0.06
ACGTcount: A:0.42, C:0.19, G:0.21, T:0.18
Consensus pattern (35 bp):
TCAACTGAAATAAACTGAAGAAAGATCGCCCTGGA
Found at i:26905 original size:71 final size:71
Alignment explanation
Indices: 26825--27660 Score: 853
Period size: 71 Copynumber: 11.8 Consensus size: 71
26815 CATTTTGCAG
* * * * * * * *
26825 TCAATTGAAATAAACTGCAGAGAAGATCGCCCTGGATCTACTGAAGTAAATTGAGGAAAGATCGT
1 TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAGATCGC
26890 CCTGGA
66 CCTGGA
* *
26896 TCAATTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAAGTGAAATAAACTGAAGAAAAGATCG
1 TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAG-AAAGATCG
26961 CCCTGGA
65 CCCTGGA
* * *
26968 TCAATTGAAATAAATTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAGACCGC
1 TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAGATCGC
27033 CCTGGA
66 CCTGGA
* * *
27039 TCAACTAAAATAAACTGAAG-AAAGACCGCCCTGGGTCAACTGAAATAAACTGAAGAAAGGATCG
1 TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAA-GATCG
*
27103 CCCTAGA
65 CCCTGGA
* * ** *
27110 TCAACTGAAATAAACTGAAGAAAA-ACCGCCCTGGGTCAACAAAAATAAACTGAAGAAAGGATCA
1 TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAA-GATCG
27174 CCCTGGA
65 CCCTGGA
* * * * *
27181 TCAACTGAAGTAAAATGAAGAAAAGATCACCCTGGATCAAACTGAAATAAACTGAA-ATAGGACC
1 TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGATC-AACTGAAATAAACTGAAGA-AAGATC
* *
27245 ACCCTGGG
64 GCCCTGGA
* * * * * * * * *
27253 TCAACTGAAATGAATTGAA-TAAGGATCGCCCTGAATCAACTGAAGTGAATTGAAGAAAGACCGC
1 TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAGATCGC
*
27317 CCTGGG
66 CCTGGA
* * * * * * * *
27323 TCAGCTAAAATAAACTGAAG-AAAGACCGCCCTGGGTCAACTGAAATGAATTGAATAAGGATCGC
1 TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAGATCGC
27387 CCTGGA
66 CCTGGA
* * * * *
27393 TCAACTGAATTGAACTGAAGAAAAG-CCGCCCTGGGTCAACTAAAATAAACTGAAGAAAGTATCG
1 TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAG-ATCG
27457 CCCTGGA
65 CCCTGGA
* * * * *
27464 TCAACTGAAGTAAAATGAAGAAAAGATCACCCTGGATCAAACTGAAATAAACTGAA-ATAGGACC
1 TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGATC-AACTGAAATAAACTGAAGA-AAGATC
* *
27528 ACCCTGGG
64 GCCCTGGA
* * * * * * * *
27536 TCAACTGAAATGAATTGAA-TAAGGATCGCCCTGGATCAACTGAAGTGAATTGAAGAAAGACCGC
1 TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAGATCGC
*
27600 CCTGGG
66 CCTGGA
* * * * * * * *
27606 TCAGCTAAAATAAACTGAA-TAAAGACCACCTTGGGTCAACTGAAATGAACTGAAG
1 TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAG
27661 CGTCTAAAAT
Statistics
Matches: 651, Mismatches: 100, Indels: 29
0.83 0.13 0.04
Matches are distributed among these distances:
70 233 0.36
71 242 0.37
72 142 0.22
73 34 0.05
ACGTcount: A:0.42, C:0.19, G:0.21, T:0.18
Consensus pattern (71 bp):
TCAACTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAGATCGC
CCTGGA
Found at i:27216 original size:178 final size:178
Alignment explanation
Indices: 26847--27660 Score: 915
Period size: 178 Copynumber: 4.6 Consensus size: 178
26837 AACTGCAGAG
* * * * * * * *
26847 AAGATCGCCCTGGATCTACTGAAGTAAATTGAGGAAAGATCGTCCTGGATCAATTGAAATAAACT
1 AAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAGACCGCCCTGGGTCAACTGAAATAAACT
* * * * *
26912 GAAGAAAAGATCGCCCTGGATCAAGTGAAATAAACTGAAGAAAAGATCGCCCTGGATCAATTGAA
66 GAAGAAAGGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAAGACCGCCCTGGATCAACTAAA
* * * * * *
26977 ATAAATTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAACTGAAGA
131 ATAAACTGAAGAAAGGACCACCCTGGATCAACTGAAATAAATTGAATA
* *
27025 AAGACCGCCCTGGATCAACTAAAATAAACTGAAGAAAGACCGCCCTGGGTCAACTGAAATAAACT
1 AAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAGACCGCCCTGGGTCAACTGAAATAAACT
* * *
27090 GAAGAAAGGATCGCCCTAGATCAACTGAAATAAACTGAAGAAAA-ACCGCCCTGGGTCAACAAAA
66 GAAGAAAGGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAAGACCGCCCTGGATCAACTAAA
* * * *
27154 ATAAACTGAAGAAAGGATCACCCTGGATCAACTGAAGTAAAATGAAGAA
131 ATAAACTGAAGAAAGGACCACCCTGGATCAACTGAAATAAATTGAA-TA
* * * *
27203 AAGATCACCCTGGATCAAACTGAAATAAACTGAA-ATAGGACCACCCTGGGTCAACTGAAATGAA
1 AAGATCGCCCTGGATC-AACTGAAATAAACTGAAGA-AAGACCGCCCTGGGTCAACTGAAATAAA
* * * * * * * *
27267 TTGAA-TAAGGATCGCCCTGAATCAACTGAAGTGAATTGAAG-AAAGACCGCCCTGGGTCAGCTA
64 CTGAAGAAAGGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAAGACCGCCCTGGATCAACTA
* * *
27330 AAATAAACTGAAGAAA-GACCGCCCTGGGTCAACTGAAATGAATTGAATA
129 AAATAAACTGAAGAAAGGACCACCCTGGATCAACTGAAATAAATTGAATA
* * * *
27379 AGGATCGCCCTGGATCAACTGAATTGAACTGAAGAAA-AGCCGCCCTGGGTCAACTAAAATAAAC
1 AAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAGA-CCGCCCTGGGTCAACTGAAATAAAC
* * * * * *
27443 TGAAGAAAGTATCGCCCTGGATCAACTGAAGTAAAATGAAGAAAAGATCACCCTGGATCAAACTG
65 TGAAGAAAGGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAAGACCGCCCTGGATC-AACTA
* * *
27508 AAATAAACTGAA-ATAGGACCACCCTGGGTCAACTGAAATGAATTGAATA
129 AAATAAACTGAAGAAAGGACCACCCTGGATCAACTGAAATAAATTGAATA
* * * * * *
27557 AGGATCGCCCTGGATCAACTGAAGTGAATTGAAGAAAGACCGCCCTGGGTCAGCTAAAATAAACT
1 AAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAGACCGCCCTGGGTCAACTGAAATAAACT
* * * * * *
27622 GAATAAA-GACCACCTTGGGTCAACTGAAATGAACTGAAG
66 GAAGAAAGGATCGCCCTGGATCAACTGAAATAAACTGAAG
27661 CGTCTAAAAT
Statistics
Matches: 546, Mismatches: 79, Indels: 23
0.84 0.12 0.04
Matches are distributed among these distances:
174 1 0.00
175 41 0.08
176 47 0.09
177 124 0.23
178 287 0.53
179 46 0.08
ACGTcount: A:0.41, C:0.19, G:0.21, T:0.18
Consensus pattern (178 bp):
AAGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAGACCGCCCTGGGTCAACTGAAATAAACT
GAAGAAAGGATCGCCCTGGATCAACTGAAATAAACTGAAGAAAAGACCGCCCTGGATCAACTAAA
ATAAACTGAAGAAAGGACCACCCTGGATCAACTGAAATAAATTGAATA
Found at i:27469 original size:283 final size:283
Alignment explanation
Indices: 26825--27660 Score: 1226
Period size: 283 Copynumber: 2.9 Consensus size: 283
26815 CATTTTGCAG
* * * * * * * * * * *
26825 TCAATTGAAATAAACTGCAGAGAAGATCGCCCTGGATCTACTGAAGTAAATTGAGGAAAGATCGT
1 TCAACTGAAATAAACTGAAGA-AAAACCGCCCTGGGTCAACTAAAATAAACTGAAGAAAGATCGC
* * * * * *
26890 CCTGGATCAATTGAAATAAACTGAAGAAAAGATCGCCCTGGATC-AAGTGAAATAAACTGAAGAA
65 CCTGGATCAACTGAAGTAAAATGAAGAAAAGATCACCCTGGATCAAACTGAAATAAACTGAA-AT
* * * * * * * * * * *
26954 AAGATCGCCCTGGATCAATTGAAATAAATTGAAGAAAAGATCGCCCTGGATCAACTGAAATAAAC
129 AGGACCACCCTGGGTCAACTGAAATGAATTGAA-TAAGGATCGCCCTGGATCAACTGAAGTGAAT
* *
27019 TGAAGAAAGACCGCCCTGGATCAACTAAAATAAACTGAAGAAAGACCGCCCTGGGTCAACTGAAA
193 TGAAGAAAGACCGCCCTGGGTCAGCTAAAATAAACTGAAGAAAGACCGCCCTGGGTCAACTGAAA
*
27084 TAAACTGAAGAAAGGATCGCCCTAGA
258 TGAACTGAAGAAAGGATCGCCCTAGA
* *
27110 TCAACTGAAATAAACTGAAGAAAAACCGCCCTGGGTCAACAAAAATAAACTGAAGAAAGGATCAC
1 TCAACTGAAATAAACTGAAGAAAAACCGCCCTGGGTCAACTAAAATAAACTGAAGAAA-GATCGC
27175 CCTGGATCAACTGAAGTAAAATGAAGAAAAGATCACCCTGGATCAAACTGAAATAAACTGAAATA
65 CCTGGATCAACTGAAGTAAAATGAAGAAAAGATCACCCTGGATCAAACTGAAATAAACTGAAATA
*
27240 GGACCACCCTGGGTCAACTGAAATGAATTGAATAAGGATCGCCCTGAATCAACTGAAGTGAATTG
130 GGACCACCCTGGGTCAACTGAAATGAATTGAATAAGGATCGCCCTGGATCAACTGAAGTGAATTG
27305 AAGAAAGACCGCCCTGGGTCAGCTAAAATAAACTGAAGAAAGACCGCCCTGGGTCAACTGAAATG
195 AAGAAAGACCGCCCTGGGTCAGCTAAAATAAACTGAAGAAAGACCGCCCTGGGTCAACTGAAATG
* * *
27370 AATTGAA-TAAGGATCGCCCTGGA
260 AACTGAAGAAAGGATCGCCCTAGA
* * *
27393 TCAACTGAATTGAACTGAAGAAAAGCCGCCCTGGGTCAACTAAAATAAACTGAAGAAAGTATCGC
1 TCAACTGAAATAAACTGAAGAAAAACCGCCCTGGGTCAACTAAAATAAACTGAAGAAAG-ATCGC
27458 CCTGGATCAACTGAAGTAAAATGAAGAAAAGATCACCCTGGATCAAACTGAAATAAACTGAAATA
65 CCTGGATCAACTGAAGTAAAATGAAGAAAAGATCACCCTGGATCAAACTGAAATAAACTGAAATA
27523 GGACCACCCTGGGTCAACTGAAATGAATTGAATAAGGATCGCCCTGGATCAACTGAAGTGAATTG
130 GGACCACCCTGGGTCAACTGAAATGAATTGAATAAGGATCGCCCTGGATCAACTGAAGTGAATTG
* * *
27588 AAGAAAGACCGCCCTGGGTCAGCTAAAATAAACTGAATAAAGACCACCTTGGGTCAACTGAAATG
195 AAGAAAGACCGCCCTGGGTCAGCTAAAATAAACTGAAGAAAGACCGCCCTGGGTCAACTGAAATG
27653 AACTGAAG
260 AACTGAAG
27661 CGTCTAAAAT
Statistics
Matches: 500, Mismatches: 47, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
282 1 0.00
283 269 0.54
284 123 0.25
285 91 0.18
286 16 0.03
ACGTcount: A:0.42, C:0.19, G:0.21, T:0.18
Consensus pattern (283 bp):
TCAACTGAAATAAACTGAAGAAAAACCGCCCTGGGTCAACTAAAATAAACTGAAGAAAGATCGCC
CTGGATCAACTGAAGTAAAATGAAGAAAAGATCACCCTGGATCAAACTGAAATAAACTGAAATAG
GACCACCCTGGGTCAACTGAAATGAATTGAATAAGGATCGCCCTGGATCAACTGAAGTGAATTGA
AGAAAGACCGCCCTGGGTCAGCTAAAATAAACTGAAGAAAGACCGCCCTGGGTCAACTGAAATGA
ACTGAAGAAAGGATCGCCCTAGA
Done.