Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011956.1 Corchorus capsularis cultivar CVL-1 contig11977, 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: 64803
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:249 original size:40 final size:40
Alignment explanation
Indices: 195--312 Score: 220
Period size: 40 Copynumber: 3.0 Consensus size: 40
185 CCGCTTATTC
*
195 CCAGT-TTGCCCTTCCCCACCGGAAGGTGTTGTTTAGTTT
1 CCAGTCTTGCCCTTCCTCACCGGAAGGTGTTGTTTAGTTT
234 CCAGTCTTGCCCTTCCTCACCGGAAGGTGTTGTTTAGTTT
1 CCAGTCTTGCCCTTCCTCACCGGAAGGTGTTGTTTAGTTT
274 CCAGTCTTGCCCTTCCTCACCGGAAGGTGTTGTTTAGTT
1 CCAGTCTTGCCCTTCCTCACCGGAAGGTGTTGTTTAGTT
313 GTCTAATTAC
Statistics
Matches: 77, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
39 5 0.06
40 72 0.94
ACGTcount: A:0.13, C:0.28, G:0.23, T:0.36
Consensus pattern (40 bp):
CCAGTCTTGCCCTTCCTCACCGGAAGGTGTTGTTTAGTTT
Found at i:3676 original size:20 final size:21
Alignment explanation
Indices: 3647--3685 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
3637 AAAATAGGGT
3647 AAAAACGTATATAAAAATAAC
1 AAAAACGTATATAAAAATAAC
3668 AAAAA-GTATATAAAAATA
1 AAAAACGTATATAAAAATA
3686 GCTATAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.69, C:0.05, G:0.05, T:0.21
Consensus pattern (21 bp):
AAAAACGTATATAAAAATAAC
Found at i:7780 original size:33 final size:33
Alignment explanation
Indices: 7711--7817 Score: 117
Period size: 33 Copynumber: 3.2 Consensus size: 33
7701 CGCCTAGCGA
* * * *
7711 TGGCCGGT-TGTGGCCGGACATGTCCATGTAGCG
1 TGGCCGGTGT-TGGCCGGGCATCTCCAAGTCGCG
* * *
7744 TGGCCGGTGTTGGTCGGGCATCTCCGAGTCGTG
1 TGGCCGGTGTTGGCCGGGCATCTCCAAGTCGCG
* *
7777 TGGCCGGTGTTGGCCGGGCTTCTCCAAGTCGCA
1 TGGCCGGTGTTGGCCGGGCATCTCCAAGTCGCG
7810 TGGCCGGT
1 TGGCCGGT
7818 CACTAGTGCT
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
33 60 0.98
34 1 0.02
ACGTcount: A:0.08, C:0.26, G:0.40, T:0.25
Consensus pattern (33 bp):
TGGCCGGTGTTGGCCGGGCATCTCCAAGTCGCG
Found at i:26677 original size:2 final size:2
Alignment explanation
Indices: 26670--26708 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
26660 AGATTTGAAC
* *
26670 AT AT AT AT AT AT GT AT AT AT AT AT AT AT AT GT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
26709 CTCTATATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
AT
Found at i:26693 original size:18 final size:18
Alignment explanation
Indices: 26670--26708 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
26660 AGATTTGAAC
26670 ATATATATATATGTATAT
1 ATATATATATATGTATAT
26688 ATATATATATATGTATAT
1 ATATATATATATGTATAT
26706 ATA
1 ATA
26709 CTCTATATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (18 bp):
ATATATATATATGTATAT
Found at i:28886 original size:15 final size:15
Alignment explanation
Indices: 28845--28888 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
28835 GGCCAAACAT
28845 AATTTTACATTTAA-
1 AATTTTACATTTAAC
*
28859 AA-TTTA-TTTTAAC
1 AATTTTACATTTAAC
28872 AATTTTACATTTAAC
1 AATTTTACATTTAAC
28887 AA
1 AA
28889 ATCTTATTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
12 5 0.20
13 6 0.24
14 6 0.24
15 8 0.32
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.48
Consensus pattern (15 bp):
AATTTTACATTTAAC
Found at i:31733 original size:2 final size:2
Alignment explanation
Indices: 31728--31824 Score: 52
Period size: 2 Copynumber: 52.0 Consensus size: 2
31718 ATAAAGTTAT
* *
31728 TA TA TA TA TA TA TA TA TA GT- TC CA -A TA T- TA TA T- 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
* * *
31767 TA TA TA T- TT TA TT TGA TA TA TGA TA TA AA TA TA -A TA TA T- TA
1 TA TA TA TA TA TA TA T-A TA TA T-A TA TA TA TA TA TA TA TA TA TA
31808 T- TA TA TA TA -A T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
31825 CTACAATTAT
Statistics
Matches: 75, Mismatches: 7, Indels: 26
0.69 0.06 0.24
Matches are distributed among these distances:
1 10 0.13
2 61 0.81
3 4 0.05
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:31741 original size:23 final size:23
Alignment explanation
Indices: 31715--31821 Score: 62
Period size: 23 Copynumber: 4.5 Consensus size: 23
31705 CCACTTCTTT
31715 TATATAAAGTTATTATATA-TATA
1 TATATAAA-TTATTATATATTATA
* *
31738 TATATATAGTTCCAATATTATATTATA
1 TATATA-AATT--ATTA-TATATTATA
* *
31765 TATATATATT-TTATTTGA-TATA
1 TATATAAATTATTATAT-ATTATA
*
31787 TGATATAAA-TATAATATATTAT-
1 T-ATATAAATTATTATATATTATA
31809 TATATATAATTAT
1 TATATA-AATTAT
31822 ATACTACAAT
Statistics
Matches: 64, Mismatches: 9, Indels: 22
0.67 0.09 0.23
Matches are distributed among these distances:
21 5 0.08
22 12 0.19
23 27 0.42
24 1 0.02
25 3 0.05
26 6 0.09
27 10 0.16
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (23 bp):
TATATAAATTATTATATATTATA
Found at i:32912 original size:2 final size:2
Alignment explanation
Indices: 32905--32929 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
32895 TTATTATTAT
32905 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
32930 GATAATCTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:38398 original size:24 final size:24
Alignment explanation
Indices: 38371--38448 Score: 120
Period size: 24 Copynumber: 3.2 Consensus size: 24
38361 AACATATTGT
*
38371 GGCGTCCAGACGCCCCTATTTTGC
1 GGCGTCCAGACGCCACTATTTTGC
*
38395 GGCGTCCAGACGCCACTATTGTGC
1 GGCGTCCAGACGCCACTATTTTGC
* *
38419 GGCGTCCAGACGCCACTATTTGGG
1 GGCGTCCAGACGCCACTATTTTGC
38443 GGCGTC
1 GGCGTC
38449 TGGACGCCGC
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.14, C:0.33, G:0.31, T:0.22
Consensus pattern (24 bp):
GGCGTCCAGACGCCACTATTTTGC
Found at i:38564 original size:32 final size:32
Alignment explanation
Indices: 38509--38606 Score: 151
Period size: 32 Copynumber: 3.1 Consensus size: 32
38499 TAAATGTAGC
* *
38509 GGCGTTTTGTTCTTTATACGCCGCTATATAAG
1 GGCGATTTGTTCTTTAGACGCCGCTATATAAG
* * *
38541 GGCGCTTTGTTCTTCAGATGCCGCTATATAAG
1 GGCGATTTGTTCTTTAGACGCCGCTATATAAG
38573 GGCGATTTGTTCTTTAGACGCCGCTATATAAG
1 GGCGATTTGTTCTTTAGACGCCGCTATATAAG
38605 GG
1 GG
38607 TATACCCCAA
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 59 1.00
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (32 bp):
GGCGATTTGTTCTTTAGACGCCGCTATATAAG
Found at i:41043 original size:27 final size:27
Alignment explanation
Indices: 41005--41094 Score: 153
Period size: 27 Copynumber: 3.3 Consensus size: 27
40995 CGACCCGAGG
*
41005 CGAAGTGGGAGGATCCACTGCTGGGGT
1 CGAAGTGGGAGGATCCACTGCTAGGGT
*
41032 CGAAGTGGGAGGATCCACTGCTTGGGT
1 CGAAGTGGGAGGATCCACTGCTAGGGT
*
41059 CGAAGTGGGAGGATCCACTTCTAGGGT
1 CGAAGTGGGAGGATCCACTGCTAGGGT
41086 CGAAGTGGG
1 CGAAGTGGG
41095 GAGAGCTGGA
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 60 1.00
ACGTcount: A:0.20, C:0.18, G:0.42, T:0.20
Consensus pattern (27 bp):
CGAAGTGGGAGGATCCACTGCTAGGGT
Found at i:41888 original size:33 final size:34
Alignment explanation
Indices: 41826--41903 Score: 140
Period size: 33 Copynumber: 2.3 Consensus size: 34
41816 AAACCCATGG
41826 GAAACATGACAGTGCGCCAAAAAAAAAAAAGACAA
1 GAAACATGACAGTGCGCC-AAAAAAAAAAAGACAA
41861 GAAACATGACAGTGCGCC-AAAAAAAAAAGACAA
1 GAAACATGACAGTGCGCCAAAAAAAAAAAGACAA
41894 GAAACATGAC
1 GAAACATGAC
41904 GGTAACTTTC
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
33 25 0.58
35 18 0.42
ACGTcount: A:0.58, C:0.18, G:0.18, T:0.06
Consensus pattern (34 bp):
GAAACATGACAGTGCGCCAAAAAAAAAAAGACAA
Found at i:42416 original size:18 final size:20
Alignment explanation
Indices: 42379--42416 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
42369 GAATCCACCG
*
42379 ATGTGTGCAAAATTGTCAAC
1 ATGTGTGCAAAATTGCCAAC
42399 ATGTG-GCAAAATT-CCAAC
1 ATGTGTGCAAAATTGCCAAC
42417 TGCAAGGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 8 0.47
20 5 0.29
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.26
Consensus pattern (20 bp):
ATGTGTGCAAAATTGCCAAC
Found at i:42897 original size:10 final size:10
Alignment explanation
Indices: 42882--42906 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
42872 GAGGACTCTA
42882 GAATTTTCTG
1 GAATTTTCTG
42892 GAATTTTCTG
1 GAATTTTCTG
42902 GAATT
1 GAATT
42907 GTGCAGGAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:45156 original size:10 final size:10
Alignment explanation
Indices: 45138--45189 Score: 59
Period size: 10 Copynumber: 4.8 Consensus size: 10
45128 CTGATTGCAT
45138 GGCATTGGCCG
1 GGCA-TGGCCG
45149 GGCATGGCCG
1 GGCATGGCCG
45159 GGCATGGTGCGCG
1 GGCAT-G-GC-CG
*
45172 GACATGGCCG
1 GGCATGGCCG
45182 GGCATGGC
1 GGCATGGC
45190 TTGGTGCCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
10 20 0.56
11 7 0.19
12 3 0.08
13 6 0.17
ACGTcount: A:0.12, C:0.27, G:0.48, T:0.13
Consensus pattern (10 bp):
GGCATGGCCG
Found at i:52206 original size:30 final size:30
Alignment explanation
Indices: 52170--52266 Score: 106
Period size: 30 Copynumber: 3.1 Consensus size: 30
52160 CATCGCATGC
*
52170 GCCATCGCATGGGGCAACCGGCCACAACTG
1 GCCATCGCATGGGGCAACCGACCACAACTG
* *
52200 GCCATCGCATCGGGCATCAACCGACCACAACCG
1 GCCATCGCAT-GGG--GCAACCGACCACAACTG
* *
52233 ACCATCGCATGGGGCATCC-ACGCACAACTG
1 GCCATCGCATGGGGCAACCGAC-CACAACTG
52263 GCCA
1 GCCA
52267 ATGGATCCTT
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
29 2 0.04
30 24 0.44
31 3 0.05
32 3 0.05
33 23 0.42
ACGTcount: A:0.26, C:0.39, G:0.25, T:0.10
Consensus pattern (30 bp):
GCCATCGCATGGGGCAACCGACCACAACTG
Found at i:52228 original size:33 final size:32
Alignment explanation
Indices: 52184--52266 Score: 98
Period size: 33 Copynumber: 2.6 Consensus size: 32
52174 TCGCATGGGG
52184 CAACCGGCCACAACTGGCCATCGCATCGGGCAT
1 CAACC-GCCACAACTGGCCATCGCATCGGGCAT
* * *
52217 CAACCGACCACAACCGACCATCGCATGGGGCAT
1 CAACCG-CCACAACTGGCCATCGCATCGGGCAT
*
52250 CCA-CG-CACAACTGGCCA
1 CAACCGCCACAACTGGCCA
52267 ATGGATCCTT
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
30 10 0.23
32 3 0.07
33 30 0.70
ACGTcount: A:0.28, C:0.41, G:0.22, T:0.10
Consensus pattern (32 bp):
CAACCGCCACAACTGGCCATCGCATCGGGCAT
Found at i:58883 original size:33 final size:32
Alignment explanation
Indices: 58786--58890 Score: 111
Period size: 33 Copynumber: 3.2 Consensus size: 32
58776 TTGCAAAGAG
* *
58786 TGTTTTAGATGTTGTTTGCGATGATATTAAACC
1 TGTTTTAG-TGTTGTTTGCGATGATACTAAATC
* * * * *
58819 TAATTTGAGTGTTGTTTGCAATAACACTAAATC
1 T-GTTTTAGTGTTGTTTGCGATGATACTAAATC
*
58852 TGTTTTAAGTGTTGTTTGTGATGATACTAAATC
1 TGTTTT-AGTGTTGTTTGCGATGATACTAAATC
58885 TGTTTT
1 TGTTTT
58891 GGATGCTAAT
Statistics
Matches: 57, Mismatches: 13, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
32 3 0.05
33 49 0.86
34 5 0.09
ACGTcount: A:0.26, C:0.09, G:0.19, T:0.47
Consensus pattern (32 bp):
TGTTTTAGTGTTGTTTGCGATGATACTAAATC
Found at i:58953 original size:33 final size:33
Alignment explanation
Indices: 58916--59023 Score: 173
Period size: 33 Copynumber: 3.3 Consensus size: 33
58906 TGAAAACAAA
58916 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
58949 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
* * * *
58982 TCTGTTTTTGTTGATTATAGCATT-AAAAAAAT
1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
59014 TCTGTTTTGG
1 TCTGTTTTGG
59024 GTGAAAAGAA
Statistics
Matches: 70, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
32 15 0.21
33 55 0.79
ACGTcount: A:0.27, C:0.10, G:0.18, T:0.45
Consensus pattern (33 bp):
TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
Found at i:61318 original size:984 final size:982
Alignment explanation
Indices: 59368--61333 Score: 3363
Period size: 984 Copynumber: 2.0 Consensus size: 982
59358 AGGGGGAGGG
*
59368 AATGATGCGCCCAAGGCTTATCATGAAGGGAATGATGCGCCAAGGACTTATTATGGACTTGAAGA
1 AATGATGCGCCAAAGGCTTATCATGAAGGGAATGATGCGCCAAGGACTTATTATGGACTTGAAGA
59433 CAAGCATGGAGAGCATGGAAAGGATGTGCAAGGGCTGCCAGGAAGCATGGAGATGCATGAAGATC
66 CAAGCATGGAGAGCATGGAAAGGATGTGCAAGGGCTGCCAGGAAGCATGGAGATGCATGAAGATC
59498 ATGGAGATATTGATGATCATGTTCCAAGCACCAAAAGGATGCCATTCGATCCATTGAAGATGCCA
131 ATGGAGATATTGATGATCATGTTCCAAGCACCAAAAGGATGCCATTCGATCCATTGAAGATGCCA
59563 TTAGGTCCGATGACAAGAGCAAGAGCTAAGAGATTCAAGGATGCACTCATGGGCCTTGTTCGAAC
196 TTAGGTCCGATGACAAGAGCAAGAGCTAAGAGATTCAAGGATGCACTCATGGGCCTTGTTCGAAC
59628 TCATCTTGAAGACTTGAAGACCATTGAAGTTCAATTGAAGAGCTTTGGTGATGATTTGGGCAAGA
261 TCATCTTGAAGACTTGAAGACCATTGAAGTTCAATTGAAGAGCTTTGGTGATGATTTGGGCAAGA
*
59693 AATTACCAATCAATTACATGTTCATCACTTTACTTTTATTGATTCTAGATGGCCGGATTGACATA
326 AATTACCAATCAATTACATGTTCATCACTTTACTTCTATTGATTCTAGATGGCCGGATTGACATA
*
59758 TGGCATAAGCCCATTATCATTAGTTATCTTTGTTTGGGCTTAATTCTATCTTAGATTAGCTTATT
391 CGGCATAAGCCCATTATCATTAGTTATCTTTGTTTGGGCTTAATTCTATCTTAGATTAGCTTATT
* *
59823 TTTAAGTTTGGACCTTATTTGGATTGGGCCTTGGTTGACTAAGTCCAATCCTTGTTTAATTATGT
456 TTTAAGTTTGGACCTTATCTGGATTGGGCCTTGGTTAACTAAGTCCAATCCTTGTTTAATTATGT
59888 CTTTATTTCCTTTTCCTAGTAGGGCTTGGACTAGTTTTTCCCTAGCCTTTATATTTGGACGAAAA
521 CTTTATTTCCTTTTCCTAGTAGGGCTTGGACTAGTTTTTCCCTAGCCTTTATATTTGGACGAAAA
59953 TTAGGATTTATTTTAGGATTTTGGTTGACCCTATCACTATATAAGGCCACAAATATCTCTTGTAA
586 TTAGGATTTATTTTAGGATTTTGGTTGACCCTATCACTATATAAGGCCACAAATATCTCTTGTAA
***
60018 AAGTAGAAGTTGAGTTGATTAATAAAGTTGAGGATTATTTTCCCAAATTGATTATCTTAGCTTCA
651 AAGTAGAAGTTGAGTTGATTAATAAAGTTGAGGATTATACACCCAAATTGATTATCTTAGCTTCA
60083 TTGTTCTAGTTTGAGCAAACTTAGGGTTCTTCAATCTTGTAGAGTCCTAGCAAACAATTAGGTTG
716 TTGTTCTAGTTTGAGCAAACTTAGGGTTCTTCAATCTTGTAGAGTCCTAGCAAACAATTAGGTTG
* * * *
60148 TGATTGCTTAATTGTTTGTGAATCTTGTGATCTTAGGTGTTCATGTGGAGGTCGACTTGGAGGTT
781 TGATTGCTTAATTGTTTGTGAATCTTGTGATCTTAGGAGTTCATGTGCAGGTCGAATTGGAGGCT
* * * * ** *
60213 TAAGGCCGACGAACGAAGGAAGATTTATCAAGTGAAGATTGTCGACATACTCATCTAGAAGTTTG
846 TAAGGCCGACGAAAGAAGGAAGAATAACCAAGTGAAGATCATCGACATACACATCTAGAAGTTTG
** * * * * *
60278 GTGATTCAAGTTGATCTTAGGCGGGTCTCTAAGGTGGATTTGGTCCGATATACAACTAGATTCGT
911 AAGATTCAAGTCGATCTTAGGCGGATCTCAAAGGTAGATTTGATCCGATATACAACTAGATTCGT
*
60343 ATTAATT
976 ATCAATT
60350 AATGATGCGCCAAAGGCTTATCATGAAGGGAATGATGCGCCAAGGACTTATTATGGACTTGAAGA
1 AATGATGCGCCAAAGGCTTATCATGAAGGGAATGATGCGCCAAGGACTTATTATGGACTTGAAGA
*
60415 CAAGCATGGAGAGCATGGAAAGGATTTGCAAGGGCTGCCAGGAAGCATGGAGATGCATGAAGATC
66 CAAGCATGGAGAGCATGGAAAGGATGTGCAAGGGCTGCCAGGAAGCATGGAGATGCATGAAGATC
60480 ATGGAGATATTGATGATCATGTTCCAAGCACCAAAAGGATGCCATTCGATCCATTGAAGATGCCA
131 ATGGAGATATTGATGATCATGTTCCAAGCACCAAAAGGATGCCATTCGATCCATTGAAGATGCCA
*
60545 TTAGGTCCGATGACATGAGCAAGAGCTAAGAGATTCAAGGATGCACTCATGGGCCTTGTTCGAAC
196 TTAGGTCCGATGACAAGAGCAAGAGCTAAGAGATTCAAGGATGCACTCATGGGCCTTGTTCGAAC
60610 TCATCTTGAAGACTTGAAGACCATTGAAGTTCAATTGAAGAGCTTTGGTGATGATTTGGGCAAGA
261 TCATCTTGAAGACTTGAAGACCATTGAAGTTCAATTGAAGAGCTTTGGTGATGATTTGGGCAAGA
60675 AATTACCAATCAATTACATGTTCATCACTTTACTTGCTATTGATTCTAGATGGCCGGTATTGACA
326 AATTACCAATCAATTACATGTTCATCACTTTACTT-CTATTGATTCTAGATGGCCGG-ATTGACA
* *
60740 TACGGCTTGAGCCCATTATCATTAGTTATCTTTGTTTGGGCTTAATTCTATCTTAGATTAGCTTA
389 TACGGCATAAGCCCATTATCATTAGTTATCTTTGTTTGGGCTTAATTCTATCTTAGATTAGCTTA
60805 TTTTTAAGTTTGGACCTTATCTGGATTGGGCCTTGGTTAACTAAGTCCAATCCTTGTTTAATTAT
454 TTTTTAAGTTTGGACCTTATCTGGATTGGGCCTTGGTTAACTAAGTCCAATCCTTGTTTAATTAT
60870 GTCTTTATTTCCTTTTCCTAGTAGGGCTTGGACTAGTTTTTCCCTAGCCTTTATATTTGGACGAA
519 GTCTTTATTTCCTTTTCCTAGTAGGGCTTGGACTAGTTTTTCCCTAGCCTTTATATTTGGACGAA
* *
60935 AATTAGGATTTATTTTAGGATTTTGGTTGACCCTATCACTATATAAGGCCACCAATATGTCTTGT
584 AATTAGGATTTATTTTAGGATTTTGGTTGACCCTATCACTATATAAGGCCACAAATATCTCTTGT
* * *
61000 AAAATTTGAAGTTGAGTTGATTAATAAAGTTGAGGTTTATACACCCAAATTGATTATCTTAGCTT
649 AAAAGTAGAAGTTGAGTTGATTAATAAAGTTGAGGATTATACACCCAAATTGATTATCTTAGCTT
61065 CATTGTTCTAGTTTGAGCAAACTTAGGGTTCTTCAATCTTGTAGAGTCCTAGCAAACAATTAGGT
714 CATTGTTCTAGTTTGAGCAAACTTAGGGTTCTTCAATCTTGTAGAGTCCTAGCAAACAATTAGGT
*
61130 TGTGATTGCTTAATTGTTTGTGAATCTTGTGATCTT-GAGAGTTCAAT-TGCAGGTCTAATT-GA
779 TGTGATTGCTTAATTGTTTGTGAATCTTGTGATCTTAG-GAGTTC-ATGTGCAGGTCGAATTGGA
* * * ** *
61192 GTGCTTAAGTCCGATGAAAG-AGGAGGAATAACCTTGTGAAGGTCATCGACATACACATCTAGAA
842 G-GCTTAAGGCCGACGAAAGAAGGAAGAATAACCAAGTGAAGATCATCGACATACACATCTAGAA
* * * *
61256 G-TTGAAGAAGTTCAAGTCGA-CTTTGGTGGATATTCAAAGGGTAGATTTGAAT-CTAT-TACAA
906 GTTTGAAG-A-TTCAAGTCGATCTTAGGCGGAT-CTCAAA-GGTAGATTTG-ATCCGATATACAA
61317 CTAGATTCGTATCAATT
966 CTAGATTCGTATCAATT
61334 CAAGTGGGAA
Statistics
Matches: 927, Mismatches: 47, Indels: 18
0.93 0.05 0.02
Matches are distributed among these distances:
982 361 0.39
983 68 0.07
984 483 0.52
985 14 0.02
986 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (982 bp):
AATGATGCGCCAAAGGCTTATCATGAAGGGAATGATGCGCCAAGGACTTATTATGGACTTGAAGA
CAAGCATGGAGAGCATGGAAAGGATGTGCAAGGGCTGCCAGGAAGCATGGAGATGCATGAAGATC
ATGGAGATATTGATGATCATGTTCCAAGCACCAAAAGGATGCCATTCGATCCATTGAAGATGCCA
TTAGGTCCGATGACAAGAGCAAGAGCTAAGAGATTCAAGGATGCACTCATGGGCCTTGTTCGAAC
TCATCTTGAAGACTTGAAGACCATTGAAGTTCAATTGAAGAGCTTTGGTGATGATTTGGGCAAGA
AATTACCAATCAATTACATGTTCATCACTTTACTTCTATTGATTCTAGATGGCCGGATTGACATA
CGGCATAAGCCCATTATCATTAGTTATCTTTGTTTGGGCTTAATTCTATCTTAGATTAGCTTATT
TTTAAGTTTGGACCTTATCTGGATTGGGCCTTGGTTAACTAAGTCCAATCCTTGTTTAATTATGT
CTTTATTTCCTTTTCCTAGTAGGGCTTGGACTAGTTTTTCCCTAGCCTTTATATTTGGACGAAAA
TTAGGATTTATTTTAGGATTTTGGTTGACCCTATCACTATATAAGGCCACAAATATCTCTTGTAA
AAGTAGAAGTTGAGTTGATTAATAAAGTTGAGGATTATACACCCAAATTGATTATCTTAGCTTCA
TTGTTCTAGTTTGAGCAAACTTAGGGTTCTTCAATCTTGTAGAGTCCTAGCAAACAATTAGGTTG
TGATTGCTTAATTGTTTGTGAATCTTGTGATCTTAGGAGTTCATGTGCAGGTCGAATTGGAGGCT
TAAGGCCGACGAAAGAAGGAAGAATAACCAAGTGAAGATCATCGACATACACATCTAGAAGTTTG
AAGATTCAAGTCGATCTTAGGCGGATCTCAAAGGTAGATTTGATCCGATATACAACTAGATTCGT
ATCAATT
Found at i:63325 original size:32 final size:32
Alignment explanation
Indices: 63273--63350 Score: 90
Period size: 32 Copynumber: 2.5 Consensus size: 32
63263 GGCACTTGAC
* *
63273 CGGCCATCGAATAGGG--CAACCGGCCACAA-
1 CGGCCATCGCATGGGGATCAACCGGCCACAAT
* *
63302 CTGGGCATCGCATGGGGATCAACCGTCCACAAT
1 C-GGCCATCGCATGGGGATCAACCGGCCACAAT
63335 CGGCCATCGCATGGGG
1 CGGCCATCGCATGGGG
63351 CATCCGCGCA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
29 1 0.03
30 12 0.30
32 26 0.65
33 1 0.03
ACGTcount: A:0.24, C:0.32, G:0.31, T:0.13
Consensus pattern (32 bp):
CGGCCATCGCATGGGGATCAACCGGCCACAAT
Found at i:63369 original size:30 final size:30
Alignment explanation
Indices: 63271--63370 Score: 96
Period size: 30 Copynumber: 3.3 Consensus size: 30
63261 CGGGCACTTG
* *
63271 ACCGGCCATCGAATAGGGCAACCG-GCCACA
1 ACCGGCCATCGCATGGGGCAACCGCG-CACA
* *
63301 ACTGGGCATCGCATGGGGATCAACCGTC-CACA
1 ACCGGCCATCGCATGGGG--CAACCG-CGCACA
* *
63333 ATCGGCCATCGCATGGGGCATCCGCGCACA
1 ACCGGCCATCGCATGGGGCAACCGCGCACA
63363 ACCGGCCA
1 ACCGGCCA
63371 ATGGATCCTT
Statistics
Matches: 56, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
29 1 0.02
30 30 0.54
32 25 0.45
ACGTcount: A:0.25, C:0.36, G:0.28, T:0.11
Consensus pattern (30 bp):
ACCGGCCATCGCATGGGGCAACCGCGCACA
Done.