Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011700.1 Corchorus capsularis cultivar CVL-1 contig11721, 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: 67226
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:119 original size:33 final size:33
Alignment explanation
Indices: 53--223 Score: 285
Period size: 33 Copynumber: 5.3 Consensus size: 33
43 TTCTTTCACG
* *
53 CAAAACAGAATTATTTTCAATGC---CATCAAC
1 CAAAACAGAATTATTTGCAATGCTATGATCAAC
83 CAAAACAGAATTATTTGCAATGCTATGATCAAC
1 CAAAACAGAATTATTTGCAATGCTATGATCAAC
*
116 CAAAACAGAATTATTTGCAATGTTATGATCAAC
1 CAAAACAGAATTATTTGCAATGCTATGATCAAC
149 CAAAACAGAATTATTTGCAATGCTATGATCAAC
1 CAAAACAGAATTATTTGCAATGCTATGATCAAC
*
182 CAAAACAGAATTATTTGCAATGCTATGATCGAC
1 CAAAACAGAATTATTTGCAATGCTATGATCAAC
215 CAAAACAGA
1 CAAAACAGA
224 TTTGTTTTCA
Statistics
Matches: 133, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
30 22 0.17
33 111 0.83
ACGTcount: A:0.43, C:0.19, G:0.12, T:0.26
Consensus pattern (33 bp):
CAAAACAGAATTATTTGCAATGCTATGATCAAC
Found at i:251 original size:66 final size:66
Alignment explanation
Indices: 53--256 Score: 236
Period size: 66 Copynumber: 3.1 Consensus size: 66
43 TTCTTTCACG
* * * * *
53 CAAAACAGAATTATTTTCAATGC---CATCAACCAAAACAGAATTATTTGCAATGCTATGATCAA
1 CAAAACAGAATTATTTGCAATGCTATGATCAACCAAAACAGAATTATTTGCAATACAATGAGCAA
115 C
66 C
* * * *
116 CAAAACAGAATTATTTGCAATGTTATGATCAACCAAAACAGAATTATTTGCAATGCTATGATCAA
1 CAAAACAGAATTATTTGCAATGCTATGATCAACCAAAACAGAATTATTTGCAATACAATGAGCAA
181 C
66 C
* * * * *
182 CAAAACAGAATTATTTGCAATGCTATGATCGACCAAAACAGATTTGTTTTC-ATCACAATTAGCA
1 CAAAACAGAATTATTTGCAATGCTATGATCAACCAAAACAGAATTATTTGCAAT-ACAATGAGCA
*
246 TC
65 AC
248 CAAAACAGA
1 CAAAACAGA
257 TTTAGTATCA
Statistics
Matches: 124, Mismatches: 13, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
63 21 0.17
65 2 0.02
66 101 0.81
ACGTcount: A:0.42, C:0.19, G:0.11, T:0.27
Consensus pattern (66 bp):
CAAAACAGAATTATTTGCAATGCTATGATCAACCAAAACAGAATTATTTGCAATACAATGAGCAA
C
Found at i:251 original size:99 final size:96
Alignment explanation
Indices: 53--256 Score: 257
Period size: 99 Copynumber: 2.1 Consensus size: 96
43 TTCTTTCACG
*
53 CAAAACAGAATTATTTTCAATGCCATCAACCAAAACAGAATTATTTGCAATGCTATGATCAACCA
1 CAAAACAGAATTATTTGCAATGCCATCAACCAAAACAGAATTATTTGCAATGCTATGATCAACCA
*** *
118 AAACAGAATTATTTGCAATGTTATGATCAAC
66 AAACAGAATTATTTGCAATACAATGAGCAAC
* *
149 CAAAACAGAATTATTTGCAATGCTATGATCAACCAAAACAGAATTATTTGCAATGCTATGATCGA
1 CAAAACAGAATTATTTGCAATGC---CATCAACCAAAACAGAATTATTTGCAATGCTATGATCAA
* * * * *
214 CCAAAACAGATTTGTTTTC-ATCACAATTAGCATC
63 CCAAAACAGAATTATTTGCAAT-ACAATGAGCAAC
248 CAAAACAGA
1 CAAAACAGA
257 TTTAGTATCA
Statistics
Matches: 92, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
96 22 0.24
98 2 0.02
99 68 0.74
ACGTcount: A:0.42, C:0.19, G:0.11, T:0.27
Consensus pattern (96 bp):
CAAAACAGAATTATTTGCAATGCCATCAACCAAAACAGAATTATTTGCAATGCTATGATCAACCA
AAACAGAATTATTTGCAATACAATGAGCAAC
Found at i:286 original size:33 final size:33
Alignment explanation
Indices: 249--313 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
239 ATTAGCATCC
249 AAAACAGATTTAGTATCATCACAAACAACACTT
1 AAAACAGATTTAGTATCATCACAAACAACACTT
* **
282 AAAACAGATTTAGTGTCATTGCAAACAACACT
1 AAAACAGATTTAGTATCATCACAAACAACACT
314 CAAATATCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.46, C:0.20, G:0.09, T:0.25
Consensus pattern (33 bp):
AAAACAGATTTAGTATCATCACAAACAACACTT
Found at i:328 original size:23 final size:24
Alignment explanation
Indices: 297--343 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
287 AGATTTAGTG
* *
297 TCATTGCAAACAACA-CTCAAATA
1 TCATCGCAAACAACATCTAAAATA
320 TCATCGCAAACAACATCTAAAATA
1 TCATCGCAAACAACATCTAAAATA
344 CTCTTTTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.49, C:0.26, G:0.04, T:0.21
Consensus pattern (24 bp):
TCATCGCAAACAACATCTAAAATA
Found at i:5620 original size:110 final size:110
Alignment explanation
Indices: 5416--5735 Score: 480
Period size: 110 Copynumber: 2.9 Consensus size: 110
5406 ATTGTTGATT
* *
5416 CAAAGATGGGTCATTTAATTTAGGAATGTTGGTGTTAGGGCCTTAAGTTTACTTATAAATAATGC
1 CAAA-ATGGGTCATTTGATTTAGGAATGTTGGTGTTAGGGCCTTAAGTTTACTTATAAATTATGC
* * ** *
5481 TTATCTATATTTAAGGATGAGTTCAGGTTATAAATTATTATGCTTA
65 TTATTTATATTTAAGGGTGAGTTTGGGTTATAAATTATTATACTTA
*
5527 CAAAATGGGTCATTTGATTTAGGAATGTTGGTGTTAGGGCCTTAAGTTTACTTATAAATTATGCA
1 CAAAATGGGTCATTTGATTTAGGAATGTTGGTGTTAGGGCCTTAAGTTTACTTATAAATTATGCT
* *
5592 TATTTATATTTAAGGGTGTGTTTGGGTTATAAACTATTATACTTA
66 TATTTATATTTAAGGGTGAGTTTGGGTTATAAATTATTATACTTA
* * * * *
5637 CAAAATAGGTTATTTGA-TTAGGAATGTTGGTGTTGGGGTCTTAATTTTACTTATAAATTATGCT
1 CAAAATGGGTCATTTGATTTAGGAATGTTGGTGTTAGGGCCTTAAGTTTACTTATAAATTATGCT
*
5701 TAGTTATATTTAAGGGTGAGTTTGGGTTATAAATT
66 TATTTATATTTAAGGGTGAGTTTGGGTTATAAATT
5736 TTGGTTCATT
Statistics
Matches: 190, Mismatches: 19, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
109 75 0.39
110 111 0.58
111 4 0.02
ACGTcount: A:0.30, C:0.07, G:0.21, T:0.42
Consensus pattern (110 bp):
CAAAATGGGTCATTTGATTTAGGAATGTTGGTGTTAGGGCCTTAAGTTTACTTATAAATTATGCT
TATTTATATTTAAGGGTGAGTTTGGGTTATAAATTATTATACTTA
Found at i:5736 original size:53 final size:51
Alignment explanation
Indices: 5573--5737 Score: 127
Period size: 53 Copynumber: 3.1 Consensus size: 51
5563 GGGCCTTAAG
*
5573 TTTACTTATAAATTATGCATATTTATATTTAAGGGTGTGTTTGGGTTATAAACT
1 TTTACTTATAAATTATGCTTA-TTATATTTAAGGGTG-GTTTGGGTTATAAA-T
* * * * * * * * *
5627 ATTATACTTACAAAATA-GGTTATT-TGATTAGGAATGTTGGTGTTGGGGTCTTAAT
1 -TT-TACTTATAAATTATGCTTATTAT-ATT--TAAGGGTGGT-TTGGGTTATAAAT
5682 TTTACTTATAAATTATGCTTAGTTATATTTAAGGGTGAGTTTGGGTTATAAAT
1 TTTACTTATAAATTATGCTTA-TTATATTTAAGGGTG-GTTTGGGTTATAAAT
5735 TTT
1 TTT
5738 GGTTCATTTG
Statistics
Matches: 82, Mismatches: 19, Indels: 20
0.68 0.16 0.17
Matches are distributed among these distances:
53 30 0.37
54 13 0.16
55 13 0.16
56 26 0.32
ACGTcount: A:0.29, C:0.05, G:0.19, T:0.47
Consensus pattern (51 bp):
TTTACTTATAAATTATGCTTATTATATTTAAGGGTGGTTTGGGTTATAAAT
Found at i:9952 original size:69 final size:69
Alignment explanation
Indices: 9841--9980 Score: 271
Period size: 69 Copynumber: 2.0 Consensus size: 69
9831 CACACTATTC
9841 TGAGGGAATGCAACAAATGAGAGAGACCATGGAGATCATCAAGAAGCAATTAGGTCAATTAGCAA
1 TGAGGGAATGCAACAAATGAGAGAGACCATGGAGATCATCAAGAAGCAATTAGGTCAATTAGCAA
9906 GTGA
66 GTGA
*
9910 TGAGGGAATGCAACAAATGAGAGAGACCATGGAGATCATCAAGAAGCAATTAGGTCAATTGGCAA
1 TGAGGGAATGCAACAAATGAGAGAGACCATGGAGATCATCAAGAAGCAATTAGGTCAATTAGCAA
9975 GTGA
66 GTGA
9979 TG
1 TG
9981 TGAGTGAGCT
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 70 1.00
ACGTcount: A:0.41, C:0.13, G:0.29, T:0.18
Consensus pattern (69 bp):
TGAGGGAATGCAACAAATGAGAGAGACCATGGAGATCATCAAGAAGCAATTAGGTCAATTAGCAA
GTGA
Found at i:23103 original size:19 final size:19
Alignment explanation
Indices: 23068--23105 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
23058 GTTAGAATTT
*
23068 AGAAAAAAAAGCGTAAAAA
1 AGAAAAAAAAGCATAAAAA
23087 AGAAAATAAAA-CATAAAAA
1 AGAAAA-AAAAGCATAAAAA
23106 TATATTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.76, C:0.05, G:0.11, T:0.08
Consensus pattern (19 bp):
AGAAAAAAAAGCATAAAAA
Found at i:25113 original size:105 final size:106
Alignment explanation
Indices: 24931--25187 Score: 364
Period size: 105 Copynumber: 2.5 Consensus size: 106
24921 TTTTCTAACG
* **
24931 CTTAAAATAAAATTTTAATTTTAATTT-GGGCTAAACTTAGTG-AATTAATTATATATTTTATTT
1 CTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAATTATATATTTTATTT
* *
24994 CTAAAACCCCATAACAAT-ATTATTAATTATGGAATTTACC
66 CTAAAACCCCATAACAATAATTACTAATTATGAAATTTACC
* * *
25034 CTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTATTT
1 CTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAATTATATATTTTATTT
* *
25099 CTAAAACCCTATAACAATAAATTACTAATTTTGAAATTTACC
66 CTAAAACCCCATAACAAT-AATTACTAATTATGAAATTTACC
*
25141 CTTAAAAGAAAAATAAAATTTT-A-TTGGGGC-AAACTTAGTGAAATTAA
1 CTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAA
25188 GGCTAAACTT
Statistics
Matches: 138, Mismatches: 12, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
103 24 0.17
104 31 0.22
105 42 0.30
106 1 0.01
107 40 0.29
ACGTcount: A:0.42, C:0.10, G:0.09, T:0.39
Consensus pattern (106 bp):
CTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAATTATATATTTTATTT
CTAAAACCCCATAACAATAATTACTAATTATGAAATTTACC
Found at i:38745 original size:41 final size:41
Alignment explanation
Indices: 38693--38810 Score: 136
Period size: 41 Copynumber: 3.0 Consensus size: 41
38683 ACAATTCAGC
* * *
38693 AAATCAAAACAGCAA-CAATAAATTTAGTTTCTCAAAATAGA
1 AAATCAAAACAGCAAGC-ATAAAATCAGTTTCTCAAAACAGA
* * *
38734 AAATCAAAACAGTAAGCATAAAATCAGTTTTTCAAAACAGC
1 AAATCAAAACAGCAAGCATAAAATCAGTTTCTCAAAACAGA
*
38775 AAATCAAAACAGCAAGCAT-TAA--AGTTTCTCAAAACA
1 AAATCAAAACAGCAAGCATAAAATCAGTTTCTCAAAACA
38811 ACAAGCATAA
Statistics
Matches: 67, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
38 13 0.19
40 2 0.03
41 51 0.76
42 1 0.01
ACGTcount: A:0.53, C:0.17, G:0.08, T:0.22
Consensus pattern (41 bp):
AAATCAAAACAGCAAGCATAAAATCAGTTTCTCAAAACAGA
Found at i:38783 original size:13 final size:13
Alignment explanation
Indices: 38765--38789 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38755 AATCAGTTTT
38765 TCAAAACAGCAAA
1 TCAAAACAGCAAA
38778 TCAAAACAGCAA
1 TCAAAACAGCAA
38790 GCATTAAAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.24, G:0.08, T:0.08
Consensus pattern (13 bp):
TCAAAACAGCAAA
Found at i:47844 original size:2 final size:2
Alignment explanation
Indices: 47837--47870 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
47827 TATAGATAAT
*
47837 TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
47871 GATGGGATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:49898 original size:16 final size:17
Alignment explanation
Indices: 49884--49941 Score: 59
Period size: 16 Copynumber: 3.4 Consensus size: 17
49874 TTATGATATC
49884 TTATTATATATAT-ATA
1 TTATTATATATATAATA
*
49900 -TATATATATATATATTGA
1 TTAT-TATATATATAAT-A
49918 TCTATTATATA-ATAATA
1 T-TATTATATATATAATA
49935 TTATTAT
1 TTATTAT
49942 TTTATAGTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
15 3 0.09
16 15 0.43
17 3 0.09
18 5 0.14
19 6 0.17
20 3 0.09
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (17 bp):
TTATTATATATATAATA
Found at i:49928 original size:2 final size:2
Alignment explanation
Indices: 49888--49914 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
49878 GATATCTTAT
49888 TA 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 TA T
49915 TGATCTATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:50542 original size:19 final size:19
Alignment explanation
Indices: 50503--50542 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
50493 ACCCTAACAT
*
50503 ATATAATAATAATATTATA
1 ATATAATAATAACATTATA
* *
50522 ATATAATAATCACATTTTA
1 ATATAATAATAACATTATA
50541 AT
1 AT
50543 TAAGACGTGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (19 bp):
ATATAATAATAACATTATA
Found at i:52433 original size:21 final size:22
Alignment explanation
Indices: 52407--52465 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 22
52397 TTGTACATGC
52407 ATGGTCAAACCCCAAAAGAT-A
1 ATGGTCAAACCCCAAAAGATAA
* *
52428 ATGGTCAAA-ACCAAAAGTTAA
1 ATGGTCAAACCCCAAAAGATAA
* *
52449 ATAGTCAAACCACAAAA
1 ATGGTCAAACCCCAAAA
52466 ACATCATTGT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 8 0.26
21 18 0.58
22 5 0.16
ACGTcount: A:0.53, C:0.20, G:0.12, T:0.15
Consensus pattern (22 bp):
ATGGTCAAACCCCAAAAGATAA
Found at i:52487 original size:54 final size:54
Alignment explanation
Indices: 52428--52657 Score: 199
Period size: 54 Copynumber: 4.3 Consensus size: 54
52418 CCAAAAGATA
*
52428 ATGGTCAAAACCAAAAGTTAAATAGTCAAACCACAAAAACATCATTGTACATGC
1 ATGGTCAAAACCCAAAGTTAAATAGTCAAACCACAAAAACATCATTGTACATGC
* * * * *
52482 ATGGTCAAACCCCAAAG-GATGAT-GATTAAACC-C--CAA-A-CATTGTACATGC
1 ATGGTCAAAACCCAAAGTTA-AATAG-TCAAACCACAAAAACATCATTGTACATGC
* * * *
52531 ATAGTCAAACCCCAAAGTTTAATAGTCAAACCA-TAAAACAATCATTGTACATGC
1 ATGGTCAAAACCCAAAGTTAAATAGTCAAACCACAAAAAC-ATCATTGTACATGC
* * * *
52585 ATGGTCAACACTCAAAGTTTAAA-AGTCAAACCACAAAAAGCATTTCATTGTATATAC
1 ATGGTCAAAACCCAAAG-TTAAATAGTCAAACCACAAAAA-CA--TCATTGTACATGC
*
52642 ATGGTCAAACCCCAAA
1 ATGGTCAAAACCCAAA
52658 TGTTGATCAA
Statistics
Matches: 138, Mismatches: 23, Indels: 27
0.73 0.12 0.14
Matches are distributed among these distances:
49 36 0.26
50 2 0.01
51 4 0.03
53 4 0.03
54 58 0.42
55 9 0.07
56 1 0.01
57 24 0.17
ACGTcount: A:0.44, C:0.22, G:0.12, T:0.22
Consensus pattern (54 bp):
ATGGTCAAAACCCAAAGTTAAATAGTCAAACCACAAAAACATCATTGTACATGC
Found at i:52804 original size:54 final size:55
Alignment explanation
Indices: 52664--52806 Score: 180
Period size: 54 Copynumber: 2.6 Consensus size: 55
52654 CAAATGTTGA
*
52664 TCAAACCCCAAAGTTCGATAGTCAAACCACAAAAAACATTATTATACATGCATAG
1 TCAAACCCCAAAGTTCGATAGTCAAACCACAAAAAACATCATTATACATGCATAG
* ** * * * * *
52719 TCAAACCACAAAGTTTAATAATAAAATCACAAAAAA-ATCATTGTACATGCATGG
1 TCAAACCCCAAAGTTCGATAGTCAAACCACAAAAAACATCATTATACATGCATAG
* *
52773 TCAACCCCCATAGTTCGATAGTCAAACCACAAAA
1 TCAAACCCCAAAGTTCGATAGTCAAACCACAAAA
52807 CCATTTTATC
Statistics
Matches: 71, Mismatches: 17, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
54 41 0.58
55 30 0.42
ACGTcount: A:0.46, C:0.23, G:0.09, T:0.22
Consensus pattern (55 bp):
TCAAACCCCAAAGTTCGATAGTCAAACCACAAAAAACATCATTATACATGCATAG
Found at i:52930 original size:53 final size:53
Alignment explanation
Indices: 52849--52987 Score: 197
Period size: 53 Copynumber: 2.6 Consensus size: 53
52839 AATGTTGGTT
*
52849 AAACCCCAAAGTTTGATAGTCAAACCACAAAAAATAATTGTACATGCATAGTC
1 AAACCCCAAAGTTTGATAATCAAACCACAAAAAATAATTGTACATGCATAGTC
* * * * *
52902 GAACCCCAAAGTTTAATATTCAAACCACAAAAAATCATTGTACATGCATGGTC
1 AAACCCCAAAGTTTGATAATCAAACCACAAAAAATAATTGTACATGCATAGTC
* * *
52955 AAACCTCAAAATTCGATAATCAAACCACAAAAA
1 AAACCCCAAAGTTTGATAATCAAACCACAAAAA
52988 GCATTTCATT
Statistics
Matches: 75, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
53 75 1.00
ACGTcount: A:0.47, C:0.22, G:0.09, T:0.22
Consensus pattern (53 bp):
AAACCCCAAAGTTTGATAATCAAACCACAAAAAATAATTGTACATGCATAGTC
Found at i:52980 original size:127 final size:128
Alignment explanation
Indices: 52719--52985 Score: 276
Period size: 127 Copynumber: 2.1 Consensus size: 128
52709 ACATGCATAG
* * * *
52719 TCAAACCACAAAGTTTAATAATAAAATCACAAAAAAATCATTGTACATGCATGGTCAACCCCCAT
1 TCAAACCACAAAGTTTAATAATAAAACCACAAAAAAATAATTGTACATGCATAGTCAACCCCCAA
* * * ** * * *
52784 AGTTCGATAGTCAAACCACAAAACCATTTTATCGTATGTGCATGGTCAAACCCCAAATGTTGGT
66 AGTTCAATAGTCAAACCACAAAA-CATATCATCGTACATGCATGGTCAAACCCAAAATGTCGAT
* * * *
52848 T-AAACCCCAAAGTTTGATAGTCAAACCAC-AAAAAATAATTGTACATGCATAGTCGAA-CCCCA
1 TCAAACCACAAAGTTTAATAATAAAACCACAAAAAAATAATTGTACATGCATAGTC-AACCCCCA
* * *
52910 AAGTTTAATATTCAAACCACAAAA-A-ATCATTGTACATGCATGGTCAAACCTCAAAAT-TCGAT
65 AAGTTCAATAGTCAAACCACAAAACATATCATCGTACATGCATGGTCAAACC-CAAAATGTCGAT
52972 AATCAAACCACAAA
1 --TCAAACCACAAA
52986 AAGCATTTCA
Statistics
Matches: 113, Mismatches: 20, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
124 23 0.20
125 6 0.05
126 1 0.01
127 57 0.50
128 25 0.22
129 1 0.01
ACGTcount: A:0.43, C:0.22, G:0.11, T:0.24
Consensus pattern (128 bp):
TCAAACCACAAAGTTTAATAATAAAACCACAAAAAAATAATTGTACATGCATAGTCAACCCCCAA
AGTTCAATAGTCAAACCACAAAACATATCATCGTACATGCATGGTCAAACCCAAAATGTCGAT
Found at i:53027 original size:181 final size:182
Alignment explanation
Indices: 52520--53058 Score: 737
Period size: 181 Copynumber: 3.0 Consensus size: 182
52510 AACCCCAAAC
* *
52520 ATTGTACATGCATAGTCAAACCCCAAAGTTTAATAGTCAAACCATAAAACAATCATTGTACATGC
1 ATTGTACATGCATAGTCAAACCCCAAAGTTTAATAATCAAACCACAAAA-AATCATTGTACATGC
* * *
52585 ATGGTC-AACACTCAAAGTT-TAAAAGTCAAACCACAAAAAGCATTTCATTGTATATACATGGTC
65 ATGGTCAAAC-CTCAAAGTTCGATAA-TCAAACCACAAAAAGCATTTCATTGTATATGCATGGTC
* * *
52648 AAACCCCAAATGTTGATCAAACCCCAAAGTTCGATAGTCAAACCACAAAAAACATT
128 AAACCCCAAATGTTGGTCAAACCCCAAAGTTTGATAGTCAAACCAC-AAAAACATA
* * * *
52704 ATTATACATGCATAGTCAAACCACAAAGTTTAATAATAAAATCACAAAAAAATCATTGTACATGC
1 ATTGTACATGCATAGTCAAACCCCAAAGTTTAATAATCAAACCAC-AAAAAATCATTGTACATGC
* * * * * * * *
52769 ATGGTCAACCCCCATAGTTCGATAGTCAAACCAC-AAAACCATTTTATCGTATGTGCATGGTCAA
65 ATGGTCAAACCTCAAAGTTCGATAATCAAACCACAAAAAGCATTTCATTGTATATGCATGGTCAA
*
52833 ACCCCAAATGTTGGTTAAACCCCAAAGTTTGATAGTCAAACCACAAAAA-ATA
130 ACCCCAAATGTTGGTCAAACCCCAAAGTTTGATAGTCAAACCACAAAAACATA
* *
52885 ATTGTACATGCATAGTCGAACCCCAAAGTTTAATATTCAAACCACAAAAAATCATTGTACATGCA
1 ATTGTACATGCATAGTCAAACCCCAAAGTTTAATAATCAAACCACAAAAAATCATTGTACATGCA
* *
52950 TGGTCAAACCTCAAAATTCGATAATCAAACCACAAAAAGCATTTCATTGTATATGCATGATCAAA
66 TGGTCAAACCTCAAAGTTCGATAATCAAACCACAAAAAGCATTTCATTGTATATGCATGGTCAAA
* * *
53015 CCCCATATGTTGGTCAAACACCAAA-TATTGATAGTCAAATCACA
131 CCCCAAATGTTGGTCAAACCCCAAAGT-TTGATAGTCAAACCACA
53059 TTAAACCTTA
Statistics
Matches: 309, Mismatches: 41, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
180 49 0.16
181 105 0.34
182 5 0.02
183 66 0.21
184 76 0.25
185 8 0.03
ACGTcount: A:0.42, C:0.22, G:0.11, T:0.25
Consensus pattern (182 bp):
ATTGTACATGCATAGTCAAACCCCAAAGTTTAATAATCAAACCACAAAAAATCATTGTACATGCA
TGGTCAAACCTCAAAGTTCGATAATCAAACCACAAAAAGCATTTCATTGTATATGCATGGTCAAA
CCCCAAATGTTGGTCAAACCCCAAAGTTTGATAGTCAAACCACAAAAACATA
Found at i:53496 original size:14 final size:14
Alignment explanation
Indices: 53477--53503 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
53467 ACATCGTATC
53477 TATTATAATTCATA
1 TATTATAATTCATA
53491 TATTATAATTCAT
1 TATTATAATTCAT
53504 TTATCAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (14 bp):
TATTATAATTCATA
Found at i:54883 original size:43 final size:43
Alignment explanation
Indices: 54834--54922 Score: 178
Period size: 43 Copynumber: 2.1 Consensus size: 43
54824 GTAATTACAC
54834 ATTTCCCTTCCTTAATTGTTTTAATCAATATTTAAGACTTTTA
1 ATTTCCCTTCCTTAATTGTTTTAATCAATATTTAAGACTTTTA
54877 ATTTCCCTTCCTTAATTGTTTTAATCAATATTTAAGACTTTTA
1 ATTTCCCTTCCTTAATTGTTTTAATCAATATTTAAGACTTTTA
54920 ATT
1 ATT
54923 AATTGCTTCT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.28, C:0.16, G:0.04, T:0.52
Consensus pattern (43 bp):
ATTTCCCTTCCTTAATTGTTTTAATCAATATTTAAGACTTTTA
Found at i:59462 original size:11 final size:11
Alignment explanation
Indices: 59442--59492 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
59432 AACCGTTTCC
59442 TTCTTCTTTTT
1 TTCTTCTTTTT
*
59453 TTCTTTTTTTT
1 TTCTTCTTTTT
*
59464 TTCTTC-CTTT
1 TTCTTCTTTTT
*
59474 TTCTT-TCTATT
1 TTCTTCT-TTTT
59485 TTCTTCTT
1 TTCTTCTT
59493 CATCTTCTCC
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
10 8 0.25
11 23 0.72
12 1 0.03
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (11 bp):
TTCTTCTTTTT
Found at i:59476 original size:21 final size:21
Alignment explanation
Indices: 59450--59490 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
59440 CCTTCTTCTT
* *
59450 TTTTTCTTTTTTTTTTCTTCC
1 TTTTTCTTTCTATTTTCTTCC
59471 TTTTTCTTTCTATTTTCTTC
1 TTTTTCTTTCTATTTTCTTC
59491 TTCATCTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTTTCTTTCTATTTTCTTCC
Found at i:62295 original size:29 final size:29
Alignment explanation
Indices: 62253--62313 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
62243 CACGGCCCAG
* *
62253 TGCAAGTAAAAGCCGCAAGAACGTATGCT
1 TGCAAGTAAAAGCCACAAAAACGTATGCT
*
62282 TGCAAGTAAGAGCCACAAAAACGTATGCT
1 TGCAAGTAAAAGCCACAAAAACGTATGCT
62311 TGC
1 TGC
62314 TCTCTCCACA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.18
Consensus pattern (29 bp):
TGCAAGTAAAAGCCACAAAAACGTATGCT
Found at i:66366 original size:27 final size:24
Alignment explanation
Indices: 66331--66383 Score: 63
Period size: 23 Copynumber: 2.1 Consensus size: 24
66321 GTAAATTGCC
66331 ATAGTTAATTGATATATACTAATTAATT
1 ATAGTTAATT-AT-TATA-TAATT-ATT
66359 ATAG-TAATTATTATATAATTATT
1 ATAGTTAATTATTATATAATTATT
66382 AT
1 AT
66384 TATTATTGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
23 5 0.20
24 5 0.20
25 4 0.16
26 2 0.08
27 5 0.20
28 4 0.16
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (24 bp):
ATAGTTAATTATTATATAATTATT
Found at i:66379 original size:11 final size:12
Alignment explanation
Indices: 66345--66383 Score: 53
Period size: 11 Copynumber: 3.2 Consensus size: 12
66335 TTAATTGATA
66345 TATACTAATTAAT
1 TATACTAATT-AT
*
66358 TATAGTAATTAT
1 TATACTAATTAT
66370 TATA-TAATTAT
1 TATACTAATTAT
66381 TAT
1 TAT
66384 TATTATTGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 10 0.40
12 6 0.24
13 9 0.36
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (12 bp):
TATACTAATTAT
Done.