Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010256.1 Corchorus capsularis cultivar CVL-1 contig10277, 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: 58614
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Found at i:2942 original size:59 final size:61
Alignment explanation
Indices: 2847--2962 Score: 173
Period size: 59 Copynumber: 1.9 Consensus size: 61
2837 TACTCTGATA
**
2847 TTTTTGGAACTTTGTTGGTTCTGATACAAGTTAGACCATAATCGAAATCAATTGTCATTGTC
1 TTTTTGGAACTTTGTT-GTTCTGATACAAGTTAGACCATAAAAGAAATCAATTGTCATTGTC
* *
2909 TTTTTGGAACTTTG-T-TTCTGATATATGTTAGACCATAAAAGAAATCAATTGTCA
1 TTTTTGGAACTTTGTTGTTCTGATACAAGTTAGACCATAAAAGAAATCAATTGTCA
2963 CCACTTTTCA
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
59 35 0.70
61 1 0.02
62 14 0.28
ACGTcount: A:0.30, C:0.13, G:0.16, T:0.41
Consensus pattern (61 bp):
TTTTTGGAACTTTGTTGTTCTGATACAAGTTAGACCATAAAAGAAATCAATTGTCATTGTC
Found at i:12401 original size:24 final size:24
Alignment explanation
Indices: 12369--12415 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
12359 AATCTAAGAC
12369 CTTATTTGAATGACCATGAATTAA
1 CTTATTTGAATGACCATGAATTAA
12393 CTTATTTGAATGACCATGAATTA
1 CTTATTTGAATGACCATGAATTA
12416 TTTTCGCTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (24 bp):
CTTATTTGAATGACCATGAATTAA
Found at i:29767 original size:111 final size:111
Alignment explanation
Indices: 29630--29917 Score: 446
Period size: 105 Copynumber: 2.6 Consensus size: 111
29620 GGAGCGGCGG
*
29630 AGATAAAGAAGGCGATGAAAGAAAGCAAAGAGAGCGTAGAAGAGCCAGAGATCACCGTAAAGGCA
1 AGATAAAGAAGGCGATGAAAGAAAGCAAAGAGAGCGTAGAAGAGCCAGAGATCACCGTAAAGGAA
29695 GTGGAAGCGATAAAAGATGTGTTGAGCAAGATAGGAGCAAAGATAA
66 GTGGAAGCGATAAAAGATGTGTTGAGCAAGATAGGAGCAAAGATAA
* *
29741 AGATAAAGAAGGCGATGAAAGAAAGCAAAGAGAGCGTAGAAGAGCTAGTGGA--A--GT---GGA
1 AGATAAAGAAGGCGATGAAAGAAAGCAAAGAGAGCGTAGAAGAGCCAG-AGATCACCGTAAAGGA
* * *
29799 AGCGGAATCGATAGAAGATGTGTTGAGCAAGATAGGAGCAAAGATAA
65 AGTGGAAGCGATAAAAGATGTGTTGAGCAAGATAGGAGCAAAGATAA
* *
29846 AGATAAAGAAGGCGATGAAAGAAAGCAAAGAGAGCGTAGAAGAGCCCGAGATCACCGTAAAGGTA
1 AGATAAAGAAGGCGATGAAAGAAAGCAAAGAGAGCGTAGAAGAGCCAGAGATCACCGTAAAGGAA
29911 GTGGAAG
66 GTGGAAG
29918 TGGAAGCCAT
Statistics
Matches: 157, Mismatches: 12, Indels: 16
0.85 0.06 0.09
Matches are distributed among these distances:
104 2 0.01
105 92 0.59
106 1 0.01
108 4 0.03
110 1 0.01
111 55 0.35
112 2 0.01
ACGTcount: A:0.45, C:0.10, G:0.33, T:0.12
Consensus pattern (111 bp):
AGATAAAGAAGGCGATGAAAGAAAGCAAAGAGAGCGTAGAAGAGCCAGAGATCACCGTAAAGGAA
GTGGAAGCGATAAAAGATGTGTTGAGCAAGATAGGAGCAAAGATAA
Found at i:29839 original size:105 final size:105
Alignment explanation
Indices: 29573--29890 Score: 419
Period size: 105 Copynumber: 3.0 Consensus size: 105
29563 ACCGTAAAGG
* * * * ****
29573 TAGTGGAAGTGGAAGCGGAAGCGATAGATGACGCGTTGAGCGAGATAGGAGC---GGCGGAGATA
1 TAGTGGAAGTGGAAGCGGAAGCGATAGAAGATGTGTTGAGCAAGATAGGAGCAAAGATAAAGATA
29635 AAGAAGGCGATGAAAGAAAGCAAAGAGAGCGTAGAAGAGC
66 AAGAAGGCGATGAAAGAAAGCAAAGAGAGCGTAGAAGAGC
* * * * *
29675 CAG-AGATCACCGTAAAGGCAGTGGAAGCGATAAAAGATGTGTTGAGCAAGATAGGAGCAAAGAT
1 TAGTGGA--A--GT---GGAAGCGGAAGCGATAGAAGATGTGTTGAGCAAGATAGGAGCAAAGAT
29739 AAAGATAAAGAAGGCGATGAAAGAAAGCAAAGAGAGCGTAGAAGAGC
59 AAAGATAAAGAAGGCGATGAAAGAAAGCAAAGAGAGCGTAGAAGAGC
*
29786 TAGTGGAAGTGGAAGCGGAATCGATAGAAGATGTGTTGAGCAAGATAGGAGCAAAGATAAAGATA
1 TAGTGGAAGTGGAAGCGGAAGCGATAGAAGATGTGTTGAGCAAGATAGGAGCAAAGATAAAGATA
29851 AAGAAGGCGATGAAAGAAAGCAAAGAGAGCGTAGAAGAGC
66 AAGAAGGCGATGAAAGAAAGCAAAGAGAGCGTAGAAGAGC
29891 CCGAGATCAC
Statistics
Matches: 186, Mismatches: 19, Indels: 19
0.83 0.08 0.08
Matches are distributed among these distances:
101 2 0.01
102 2 0.01
103 1 0.01
105 93 0.50
108 37 0.20
110 1 0.01
111 48 0.26
112 2 0.01
ACGTcount: A:0.43, C:0.10, G:0.35, T:0.12
Consensus pattern (105 bp):
TAGTGGAAGTGGAAGCGGAAGCGATAGAAGATGTGTTGAGCAAGATAGGAGCAAAGATAAAGATA
AAGAAGGCGATGAAAGAAAGCAAAGAGAGCGTAGAAGAGC
Found at i:32580 original size:1 final size:1
Alignment explanation
Indices: 32574--32598 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
32564 ATTAAGAATT
32574 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
32599 CATTGAGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:33704 original size:31 final size:31
Alignment explanation
Indices: 33669--33834 Score: 132
Period size: 31 Copynumber: 5.5 Consensus size: 31
33659 AGGGGCTAAT
33669 TGCTCAAATAAGGGTCTAACGTTTGTCAAAA
1 TGCTCAAATAAGGGTCTAACGTTTGTCAAAA
* * **
33700 TGCTCAAATAAGGGTCCGATC-TTT-T-AATT
1 TGCTCAAATAAGGGT-CTAACGTTTGTCAAAA
* *
33729 TGGC-CAAATAAGGGCCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGTCTAACGTTTGTCAAAA
** * **
33760 TGCTCAAATAAGGG-C-CCCATCTT-TCAATT
1 TGCTCAAATAAGGGTCTAACGT-TTGTCAAAA
*
33789 TGGC-CAAATAAGGGTCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGTCTAACGTTTGTCAAAA
33820 TGCTCAAATAAGGGT
1 TGCTCAAATAAGGGT
33835 TTGTCTCACA
Statistics
Matches: 101, Mismatches: 22, Indels: 24
0.69 0.15 0.16
Matches are distributed among these distances:
28 3 0.03
29 32 0.32
30 15 0.15
31 48 0.48
32 3 0.03
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (31 bp):
TGCTCAAATAAGGGTCTAACGTTTGTCAAAA
Found at i:33766 original size:60 final size:60
Alignment explanation
Indices: 33673--33834 Score: 279
Period size: 60 Copynumber: 2.7 Consensus size: 60
33663 GCTAATTGCT
* * *
33673 CAAATAAGGGTCTAACGTTTGTCAAAATGCTCAAATAAGGGTCCGATCTTTTAATTTGGC
1 CAAATAAGGGTCTAACGTTTGCCAAAATGCTCAAATAAGGGTCCCATCTTTCAATTTGGC
* *
33733 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCCATCTTTCAATTTGGC
1 CAAATAAGGGTCTAACGTTTGCCAAAATGCTCAAATAAGGGTCCCATCTTTCAATTTGGC
33793 CAAATAAGGGTCTAACGTTTGCCAAAATGCTCAAATAAGGGT
1 CAAATAAGGGTCTAACGTTTGCCAAAATGCTCAAATAAGGGT
33835 TTGTCTCACA
Statistics
Matches: 95, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 95 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (60 bp):
CAAATAAGGGTCTAACGTTTGCCAAAATGCTCAAATAAGGGTCCCATCTTTCAATTTGGC
Found at i:33900 original size:31 final size:31
Alignment explanation
Indices: 33865--33997 Score: 144
Period size: 31 Copynumber: 4.4 Consensus size: 31
33855 ACTAACATCG
33865 GGCCCTTATTTGAGCATTTTCGATAACATTA
1 GGCCCTTATTTGAGCATTTTCGATAACATTA
* *
33896 GGCCCTTATTTGAGTATTTTCGATAACGTTA
1 GGCCCTTATTTGAGCATTTTCGATAACATTA
* ** * * **
33927 GGCCCTTATTTGACCAAATT--AAAAGATCG
1 GGCCCTTATTTGAGCATTTTCGATAACATTA
* *
33956 GGCCCTTATTTGAGCATTTTCAATAACGTTA
1 GGCCCTTATTTGAGCATTTTCGATAACATTA
*
33987 TGCCCTTATTT
1 GGCCCTTATTT
33998 TGCCAGATTA
Statistics
Matches: 80, Mismatches: 20, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
29 21 0.26
31 59 0.74
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.38
Consensus pattern (31 bp):
GGCCCTTATTTGAGCATTTTCGATAACATTA
Found at i:33968 original size:60 final size:60
Alignment explanation
Indices: 33895--34059 Score: 208
Period size: 60 Copynumber: 2.8 Consensus size: 60
33885 CGATAACATT
33895 AGGCCCTTATTTGAGTATTTTCGATAACGTTAGGCCCTTATTTGACCAAATTAAAAGATC
1 AGGCCCTTATTTGAGTATTTTCGATAACGTTAGGCCCTTATTTGACCAAATTAAAAGATC
* * * * *
33955 GGGCCCTTATTTGAGCATTTTCAATAACGTTATGCCCTTATTTTG-CCAGATTAAAAGATC
1 AGGCCCTTATTTGAGTATTTTCGATAACGTTAGGCCCTTA-TTTGACCAAATTAAAAGATC
** * **
34015 AGATCCTTATTTGAGTATTTT-GACAAACGTTAGAACCTTATTTGA
1 AGGCCCTTATTTGAGTATTTTCGA-TAACGTTAGGCCCTTATTTGA
34060 ACAATTAGCC
Statistics
Matches: 88, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
59 5 0.06
60 79 0.90
61 4 0.05
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (60 bp):
AGGCCCTTATTTGAGTATTTTCGATAACGTTAGGCCCTTATTTGACCAAATTAAAAGATC
Found at i:41227 original size:15 final size:15
Alignment explanation
Indices: 41207--41238 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
41197 GCCGTCTCCA
41207 TCATCAACTTCACCG
1 TCATCAACTTCACCG
*
41222 TCATCAACTTCGCCG
1 TCATCAACTTCACCG
41237 TC
1 TC
41239 GGGATTGTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.22, C:0.41, G:0.09, T:0.28
Consensus pattern (15 bp):
TCATCAACTTCACCG
Found at i:41650 original size:17 final size:15
Alignment explanation
Indices: 41628--41661 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 15
41618 GCTGAAACCC
41628 AAAGGAAAGAAAAGGAG
1 AAAGG-AAGAAAA-GAG
41645 AAAGGAAGAAAAGAG
1 AAAGGAAGAAAAGAG
41660 AA
1 AA
41662 CTAGAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 7 0.41
17 5 0.29
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (15 bp):
AAAGGAAGAAAAGAG
Found at i:48521 original size:18 final size:18
Alignment explanation
Indices: 48498--48533 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
48488 AAGACTAGAA
48498 ATCAGATGAGCTTAGAGC
1 ATCAGATGAGCTTAGAGC
48516 ATCAGATGAGCTTAGAGC
1 ATCAGATGAGCTTAGAGC
48534 CAAACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.17, G:0.28, T:0.22
Consensus pattern (18 bp):
ATCAGATGAGCTTAGAGC
Found at i:49780 original size:129 final size:129
Alignment explanation
Indices: 49550--49806 Score: 487
Period size: 129 Copynumber: 2.0 Consensus size: 129
49540 GCATAAGGAG
49550 AAGAAGAAGCCAAAACAATGCCGCATGAAAAGCACTTCTCTAAACCAGTTGCCACTAGCAAGCAG
1 AAGAAGAAGCCAAAACAATGCCGCATGAAAAGCACTTCTCTAAACCAGTTGCCACTAGCAAGCAG
* *
49615 CCAACCTCAAATCAGCAATGTCCGTACCAGACAAGCTGAAGATTATAGCAAATCAAAGACTTAC
66 CCAACCTCAAATCAGCAATGTCCATACCAAACAAGCTGAAGATTATAGCAAATCAAAGACTTAC
*
49679 AAGAAGAAGCCAGAACAATGCCGCATGAAAAGCACTTCTCTAAACCAGTTGCCACTAGCAAGCAG
1 AAGAAGAAGCCAAAACAATGCCGCATGAAAAGCACTTCTCTAAACCAGTTGCCACTAGCAAGCAG
49744 CCAACCTCAAATCAGCAATGTCCATACCAAACAAGCTGAAGATTATAGCAAATCAAAGACTTA
66 CCAACCTCAAATCAGCAATGTCCATACCAAACAAGCTGAAGATTATAGCAAATCAAAGACTTA
49807 AATTCTAGCT
Statistics
Matches: 125, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
129 125 1.00
ACGTcount: A:0.42, C:0.26, G:0.16, T:0.16
Consensus pattern (129 bp):
AAGAAGAAGCCAAAACAATGCCGCATGAAAAGCACTTCTCTAAACCAGTTGCCACTAGCAAGCAG
CCAACCTCAAATCAGCAATGTCCATACCAAACAAGCTGAAGATTATAGCAAATCAAAGACTTAC
Found at i:54376 original size:16 final size:17
Alignment explanation
Indices: 54206--54407 Score: 239
Period size: 17 Copynumber: 12.1 Consensus size: 17
54196 ACTCACCCAA
*
54206 TACAAATACTCACCCGG
1 TACAAATACTCACCTGG
* *
54223 TACAAACACTCACCTGA
1 TACAAATACTCACCTGG
* *
54240 TACAAACACTCACCCGG
1 TACAAATACTCACCTGG
*
54257 TACAAATACTCACCGGG
1 TACAAATACTCACCTGG
*
54274 TACAAACACTCACCTGG
1 TACAAATACTCACCTGG
54291 TACAAATACTCACCTGG
1 TACAAATACTCACCTGG
*
54308 TACAAACACTCACCTGG
1 TACAAATACTCACCTGG
54325 TACAAATACTCACCTGG
1 TACAAATACTCACCTGG
* **
54342 TACAAACACTCTTCTGG
1 TACAAATACTCACCTGG
* *
54359 TGC-AATGCTCACCTGG
1 TACAAATACTCACCTGG
* *
54375 TGC-AATGCTCACCTGG
1 TACAAATACTCACCTGG
*
54391 TGC-AATACTCACCTGG
1 TACAAATACTCACCTGG
54407 T
1 T
54408 GAGATACTTA
Statistics
Matches: 164, Mismatches: 21, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
16 41 0.25
17 123 0.75
ACGTcount: A:0.32, C:0.33, G:0.14, T:0.21
Consensus pattern (17 bp):
TACAAATACTCACCTGG
Found at i:56305 original size:36 final size:36
Alignment explanation
Indices: 56258--56348 Score: 155
Period size: 36 Copynumber: 2.5 Consensus size: 36
56248 TGGTTGTAAT
*
56258 GCCGCTGGCCTTAGTCGCCCGATGCTTGGCTATAAC
1 GCCGCTGGCCTTAGTCGCCCAATGCTTGGCTATAAC
*
56294 GCCGCTGGCCTTAGTCGCCCAATGTTTGGCTATAAC
1 GCCGCTGGCCTTAGTCGCCCAATGCTTGGCTATAAC
*
56330 GCCGCTGGCCTAAGTCGCC
1 GCCGCTGGCCTTAGTCGCC
56349 TAATACATAA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 52 1.00
ACGTcount: A:0.14, C:0.34, G:0.27, T:0.24
Consensus pattern (36 bp):
GCCGCTGGCCTTAGTCGCCCAATGCTTGGCTATAAC
Found at i:57540 original size:27 final size:24
Alignment explanation
Indices: 57482--57542 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 24
57472 TGCGCCTCAG
57482 GGGAGACTCACATGTTGCGGGCTA
1 GGGAGACTCACATGTTGCGGGCTA
* *
57506 GAAGAGACTCACGTGTTGCGCGCGCTA
1 G-GGAGACTCACATGTTGCG-G-GCTA
57533 TGGGAGACTC
1 -GGGAGACTC
57543 CCTTGCTACG
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
24 1 0.03
25 16 0.53
26 1 0.03
27 11 0.37
28 1 0.03
ACGTcount: A:0.21, C:0.23, G:0.36, T:0.20
Consensus pattern (24 bp):
GGGAGACTCACATGTTGCGGGCTA
Found at i:57736 original size:13 final size:12
Alignment explanation
Indices: 57704--57735 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
57694 GCAATAACTA
*
57704 TAAAAAACTAAT
1 TAAAAAAATAAT
57716 TAAAAAAATAAT
1 TAAAAAAATAAT
57728 TAAAAAAA
1 TAAAAAAA
57736 AAAGATAAGG
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:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (12 bp):
TAAAAAAATAAT
Found at i:57907 original size:3 final size:3
Alignment explanation
Indices: 57883--57923 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
57873 TTAATGTGAG
* *
57883 TAA TAT TAA AAA TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
57924 AACATAACTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:58030 original size:15 final size:15
Alignment explanation
Indices: 58010--58260 Score: 151
Period size: 15 Copynumber: 15.7 Consensus size: 15
58000 GTTGTATGTT
58010 AGGGGAGACTCCCTC
1 AGGGGAGACTCCCTC
* *
58025 AGGGGAGACTTCCTTATT
1 AGGGGAGAC-TCC--CTC
* *
58043 ATGCGAGACTCCCTC
1 AGGGGAGACTCCCTC
58058 AGGGGAGACTCCCTC
1 AGGGGAGACTCCCTC
*
58073 AAGGGAGACTCCCTTGC
1 AGGGGAGACTCCC-T-C
* * *
58090 TATGCGAGACTCCTTC
1 -AGGGGAGACTCCCTC
*
58106 AGGGGAGACTCACTC
1 AGGGGAGACTCCCTC
*
58121 AGTGGAGACTCCCTTGC
1 AGGGGAGACTCCC-T-C
* *
58138 TATGCGAGACTCCCTC
1 -AGGGGAGACTCCCTC
**
58154 AAAGGAGACTCCCTTGC
1 AGGGGAGACTCCC-T-C
* * *
58171 TATGCGATACTCCCTC
1 -AGGGGAGACTCCCTC
* *
58187 AAGGGAGATTCCCTTGC
1 AGGGGAGACTCCC-T-C
* *
58204 TATGCGAGACTCCCTC
1 -AGGGGAGACTCCCTC
*
58220 AGGGGAGACTCCTTC
1 AGGGGAGACTCCCTC
*
58235 AGGTGAGACTCCCTC
1 AGGGGAGACTCCCTC
*
58250 AAGGGAGACTC
1 AGGGGAGACTC
58261 ACCAATCTAC
Statistics
Matches: 179, Mismatches: 42, Indels: 30
0.71 0.17 0.12
Matches are distributed among these distances:
15 110 0.61
16 11 0.06
17 11 0.06
18 47 0.26
ACGTcount: A:0.22, C:0.30, G:0.26, T:0.22
Consensus pattern (15 bp):
AGGGGAGACTCCCTC
Found at i:58056 original size:33 final size:33
Alignment explanation
Indices: 58014--58259 Score: 206
Period size: 33 Copynumber: 7.6 Consensus size: 33
58004 TATGTTAGGG
**
58014 GAGACTCCCTCAGGGGAGACTTCCTTATTATGC
1 GAGACTCCCTCAGGGGAGACTTCCTTGCTATGC
* * *
58047 GAGACTCCCTCAGGGGAGAC-TCCCT-C-AAGG
1 GAGACTCCCTCAGGGGAGACTTCCTTGCTATGC
* * * *
58077 GAGACTCCCTTGCTATGCGAGAC-TCCTT-C-AGGG
1 GAGACTCCC-T-C-AGGGGAGACTTCCTTGCTATGC
* * *
58110 GAGACTCACTCAGTGGAGACTCCCTTGCTATGC
1 GAGACTCCCTCAGGGGAGACTTCCTTGCTATGC
** *
58143 GAGACTCCCTCAAAGGAGACTCCCTTGCTATGC
1 GAGACTCCCTCAGGGGAGACTTCCTTGCTATGC
* *
58176 GATACTCCCTCAAGGGAGA-TTCCCTTGCTATGC
1 GAGACTCCCTCAGGGGAGACTT-CCTTGCTATGC
* *
58209 GAGACTCCCTCAGGGGAGAC-TCCTT-C-AGGT
1 GAGACTCCCTCAGGGGAGACTTCCTTGCTATGC
*
58239 GAGACTCCCTCAAGGGAGACT
1 GAGACTCCCTCAGGGGAGACT
58260 CACCAATCTA
Statistics
Matches: 178, Mismatches: 26, Indels: 20
0.79 0.12 0.09
Matches are distributed among these distances:
30 38 0.21
31 7 0.04
32 12 0.07
33 121 0.68
ACGTcount: A:0.22, C:0.30, G:0.26, T:0.22
Consensus pattern (33 bp):
GAGACTCCCTCAGGGGAGACTTCCTTGCTATGC
Found at i:58065 original size:48 final size:48
Alignment explanation
Indices: 58010--58167 Score: 235
Period size: 48 Copynumber: 3.3 Consensus size: 48
58000 GTTGTATGTT
* **
58010 AGGGGAGACTCCCTCAGGGGAGACTTCCTTATTATGCGAGACTCCCTC
1 AGGGGAGACTCCCTCAGGGGAGACTCCCTTGCTATGCGAGACTCCCTC
* *
58058 AGGGGAGACTCCCTCAAGGGAGACTCCCTTGCTATGCGAGACTCCTTC
1 AGGGGAGACTCCCTCAGGGGAGACTCCCTTGCTATGCGAGACTCCCTC
* *
58106 AGGGGAGACTCACTCAGTGGAGACTCCCTTGCTATGCGAGACTCCCTC
1 AGGGGAGACTCCCTCAGGGGAGACTCCCTTGCTATGCGAGACTCCCTC
**
58154 AAAGGAGACTCCCT
1 AGGGGAGACTCCCT
58168 TGCTATGCGA
Statistics
Matches: 98, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 98 1.00
ACGTcount: A:0.22, C:0.30, G:0.27, T:0.21
Consensus pattern (48 bp):
AGGGGAGACTCCCTCAGGGGAGACTCCCTTGCTATGCGAGACTCCCTC
Found at i:58228 original size:81 final size:80
Alignment explanation
Indices: 58014--58248 Score: 273
Period size: 81 Copynumber: 2.9 Consensus size: 80
58004 TATGTTAGGG
*
58014 GAGACTCCCTCAGGGGAGACTT-CCTTATTATGCGAGACTCCCTCAGGGGAGACTCCCTCAAGGG
1 GAGACTCCCTCAGGGGAGA-TTCCCTT-CTATGCGAGACTCCCTCAGGGGAGACTCCCTCAAGGG
58078 AGACTCCCTTGCTATGC
64 AGACTCCCTTGCTATGC
* * * * * *
58095 GAGACTCCTTCAGGGGAGACTCAC-TC-AGTG-GAGACTCCCTTGCTATGCGAGACTCCCTCAAA
1 GAGACTCCCTCAGGGGAGATTCCCTTCTA-TGCGAGACTCCC-T-C-AGGGGAGACTCCCTCAAG
58157 GGAGACTCCCTTGCTATGC
62 GGAGACTCCCTTGCTATGC
* * *
58176 GATACTCCCTCAAGGGAGATTCCCTTGCTATGCGAGACTCCCTCAGGGGAGACTCCTTC-AGGTG
1 GAGACTCCCTCAGGGGAGATTCCCTT-CTATGCGAGACTCCCTCAGGGGAGACTCCCTCAAGG-G
58240 AGACTCCCT
64 AGACTCCCT
58249 CAAGGGAGAC
Statistics
Matches: 128, Mismatches: 16, Indels: 20
0.78 0.10 0.12
Matches are distributed among these distances:
78 10 0.08
79 3 0.02
80 5 0.04
81 94 0.73
82 2 0.02
83 4 0.03
84 10 0.08
ACGTcount: A:0.21, C:0.31, G:0.25, T:0.23
Consensus pattern (80 bp):
GAGACTCCCTCAGGGGAGATTCCCTTCTATGCGAGACTCCCTCAGGGGAGACTCCCTCAAGGGAG
ACTCCCTTGCTATGC
Done.