Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009922.1 Corchorus capsularis cultivar CVL-1 contig09943, 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: 27593
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:849 original size:94 final size:93
Alignment explanation
Indices: 687--918 Score: 304
Period size: 94 Copynumber: 2.5 Consensus size: 93
677 CAATTCAATT
687 AATGTTCATATATGAATAATACATGTTGAACCAATAAAAATCTTGTCTAAGCCGTAAATTCCAGT
1 AATGTTCATA-ATGAATAATACATGTTGAACCAATAAAAATCTTGTCTAAGCCGTAAATTCCAGT
* *
752 GAAATCCTCCTTCCGAGTTTTCTAAGAAC
65 GAAATCCGCCTTCAGAGTTTTCTAAGAAC
* * *
781 AATGTTCATGAATGAATAATACATGTTGAACCAATAATAATCTTTTGTAAGCCGTAAATTCC-GA
1 AATGTTCAT-AATGAATAATACATGTTGAACCAATAAAAATCTTGTCTAAGCCGTAAATTCCAG-
* *
845 TGAAATCCGCCTTCAGAGTTTTCTATGAGC
64 TGAAATCCGCCTTCAGAGTTTTCTAAGAAC
* * * ***
875 AATTTTAATTAATGAATAAAACATGTTGGGTCAATAAAAATCTT
1 AATGTTCA-TAATGAATAATACATGTTGAACCAATAAAAATCTT
919 CAATTCAATT
Statistics
Matches: 121, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
93 1 0.01
94 118 0.98
95 2 0.02
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (93 bp):
AATGTTCATAATGAATAATACATGTTGAACCAATAAAAATCTTGTCTAAGCCGTAAATTCCAGTG
AAATCCGCCTTCAGAGTTTTCTAAGAAC
Found at i:953 original size:148 final size:148
Alignment explanation
Indices: 781--1066 Score: 401
Period size: 148 Copynumber: 1.9 Consensus size: 148
771 TTCTAAGAAC
* * * *
781 AATGTTCATGAATGAATAATACATGTTGAACCAATAATAATCTTTTGTAAGCCGTAAATTCCGAT
1 AATGTTCATAAATGAATAATACATGTTGAACCAATAAAAATCTTGTATAAGCCGTAAATTCCGAT
* * * * * * **
846 GAAATCCGCCTTCAGAGTTTTCTATGAGCAATTTTAATTAATGAATAAAACATGTTGGGTCAATA
66 GAAAACCGCCTTAAGAGTTTTCTAAGAGCAATGTTAATAAATGAATAAAACATGCTGGACCAATA
911 AAAATCTTCAATTCAATT
131 AAAATCTTCAATTCAATT
** *
929 AATGTTCATAAATGAATAATACATGTTGGCCCAATAAAAATCTTGTATAAGCCGTAAATTCCGGT
1 AATGTTCATAAATGAATAATACATGTTGAACCAATAAAAATCTTGTATAAGCCGTAAATTCCGAT
* * * *
994 GAAAACCTCCTTAAGAGTTTTCTAAGAGCAATGTTCATAAATGAATGATACATGCTGGACCAATA
66 GAAAACCGCCTTAAGAGTTTTCTAAGAGCAATGTTAATAAATGAATAAAACATGCTGGACCAATA
1059 AAAATCTT
131 AAAATCTT
1067 TTGTAAGCCG
Statistics
Matches: 119, Mismatches: 19, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
148 119 1.00
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.32
Consensus pattern (148 bp):
AATGTTCATAAATGAATAATACATGTTGAACCAATAAAAATCTTGTATAAGCCGTAAATTCCGAT
GAAAACCGCCTTAAGAGTTTTCTAAGAGCAATGTTAATAAATGAATAAAACATGCTGGACCAATA
AAAATCTTCAATTCAATT
Found at i:1028 original size:242 final size:241
Alignment explanation
Indices: 602--1280 Score: 968
Period size: 242 Copynumber: 2.8 Consensus size: 241
592 GATAAAAATC
*
602 ATGAAATCCTCCTTCAGAGTTTTCTAAGAGCAATGTTTATAAATGAATGAAACATGTT-GAACCA
1 ATGAAATCCTCCTTCAGAGTTTTCTAAGAGCAAT-TTTATAAATGAATAAAACATGTTGGAA-CA
* *
666 ATAAAAATCTTCAATTCAATTAATGTTCATATATGAATAATACATGTTGAACCAATAAAAATCTT
64 ATAAAAATCTTCAATTCAATTAATGTTCATAAATGAATAATACATGTTGGACCAATAAAAATCTT
* * ** * *
731 GTCTAAGCCGTAAATTCCAGTGAAATCCTCCTTCCGAGTTTTCTAAGAACAATGTTCATGAATGA
129 GTATAAGCCGTAAATTCCGGTGAAATCCTCCTTAAGAGTTTTCTAAGAGCAATGTTCATAAATGA
* *
796 ATAATACATGTTGAACCAATAATAATCTTTTGTAAGCCGTAAATTCCG
194 ATAATACATGCTGAACCAATAAAAATCTTTTGTAAGCCGTAAATTCCG
* * * **
844 ATGAAATCCGCCTTCAGAGTTTTCTATGAGCAATTTTAATTAATGAATAAAACATGTTGGGTCAA
1 ATGAAATCCTCCTTCAGAGTTTTCTAAGAGCAATTTT-ATAAATGAATAAAACATGTTGGAACAA
*
909 TAAAAATCTTCAATTCAATTAATGTTCATAAATGAATAATACATGTTGGCCCAATAAAAATCTTG
65 TAAAAATCTTCAATTCAATTAATGTTCATAAATGAATAATACATGTTGGACCAATAAAAATCTTG
*
974 TATAAGCCGTAAATTCCGGTGAAAACCTCCTTAAGAGTTTTCTAAGAGCAATGTTCATAAATGAA
130 TATAAGCCGTAAATTCCGGTGAAATCCTCCTTAAGAGTTTTCTAAGAGCAATGTTCATAAATGAA
* *
1039 TGATACATGCTGGACCAATAAAAATCTTTTGTAAGCCGTAAATTCCG
195 TAATACATGCTGAACCAATAAAAATCTTTTGTAAGCCGTAAATTCCG
* * ** * *
1086 GTGAAATCCTCCTTTAGAG-TTTGAAAGAG-AACTATTCATAAATGAATAATACATGTTGGAACA
1 ATGAAATCCTCCTTCAGAGTTTTCTAAGAGCAA-T-TTTATAAATGAATAAAACATGTTGGAACA
* **
1149 ATAAAAATCTTCAATTCAATTAATGTTCATATAAATGAAAAATACACATTGGACCAATAAAAATC
64 ATAAAAATCTTCAATTCAATTAATGTTC--ATAAATGAATAATACATGTTGGACCAATAAAAATC
* * * * *
1214 TTGTGTAAGCCGTAAATTCCGGTGAAATCCTCTTTAAGAGCTTTCTAAAAGCAATTTTCATAAAT
127 TTGTATAAGCCGTAAATTCCGGTGAAATCCTCCTTAAGAGTTTTCTAAGAGCAATGTTCATAAAT
1279 GA
192 GA
1281 TTTATACAGG
Statistics
Matches: 390, Mismatches: 41, Indels: 11
0.88 0.09 0.02
Matches are distributed among these distances:
240 2 0.01
241 61 0.16
242 234 0.60
243 93 0.24
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.32
Consensus pattern (241 bp):
ATGAAATCCTCCTTCAGAGTTTTCTAAGAGCAATTTTATAAATGAATAAAACATGTTGGAACAAT
AAAAATCTTCAATTCAATTAATGTTCATAAATGAATAATACATGTTGGACCAATAAAAATCTTGT
ATAAGCCGTAAATTCCGGTGAAATCCTCCTTAAGAGTTTTCTAAGAGCAATGTTCATAAATGAAT
AATACATGCTGAACCAATAAAAATCTTTTGTAAGCCGTAAATTCCG
Found at i:1090 original size:94 final size:92
Alignment explanation
Indices: 929--1159 Score: 336
Period size: 94 Copynumber: 2.5 Consensus size: 92
919 CAATTCAATT
*
929 AATGTTCATAAATGAATAATACATGTTGGCCCAATAAAAATCTTGTATAAGCCGTAAATTCCGGT
1 AATGTTCATAAATGAATAATACATGTTGGACCAATAAAAATCTTGTATAAGCCGTAAATTCCGGT
*
994 GAAAACCTCCTTAAGAGTTTTCTAAGAG
66 GAAAACCTCCTTAAGAG-TTTCAAAGAG
* * * *
1022 CAATGTTCATAAATGAATGATACATGCTGGACCAATAAAAATCTTTTGTAAGCCGTAAATTCCGG
1 -AATGTTCATAAATGAATAATACATGTTGGACCAATAAAAATCTTGTATAAGCCGTAAATTCCGG
* * *
1087 TGAAATCCTCCTTTAGAGTTTGAAAGAG
65 TGAAAACCTCCTTAAGAGTTTCAAAGAG
* *
1115 AACTATTCATAAATGAATAATACATGTTGGAACAATAAAAATCTT
1 AA-TGTTCATAAATGAATAATACATGTTGGACCAATAAAAATCTT
1160 CAATTCAATT
Statistics
Matches: 123, Mismatches: 13, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
92 2 0.02
93 46 0.37
94 75 0.61
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (92 bp):
AATGTTCATAAATGAATAATACATGTTGGACCAATAAAAATCTTGTATAAGCCGTAAATTCCGGT
GAAAACCTCCTTAAGAGTTTCAAAGAG
Found at i:1570 original size:25 final size:26
Alignment explanation
Indices: 1530--1578 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
1520 GTCCATATTT
*
1530 ATTTTTTAAAT-TAAAATAATAATTAA
1 ATTTTTTAAATAAAAAATAA-AATTAA
1556 ATTTTTT-AATAAAAAATAAAATT
1 ATTTTTTAAATAAAAAATAAAATT
1579 TAAACATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
ATTTTTTAAATAAAAAATAAAATTAA
Found at i:2080 original size:149 final size:148
Alignment explanation
Indices: 1919--2198 Score: 422
Period size: 149 Copynumber: 1.9 Consensus size: 148
1909 ATGTTCATAA
*
1919 ATAAATGAATAATACATGTTGGACCAATAAAAATCTTTTGTAAGCCGTAAATTCCAG-CGAAAAC
1 ATAAATGAATAATACATGTTGGACCAATAAAAATCTTGTGTAAGCCGTAAATTCCAGTC-AAAAC
* *
1983 CTTC-TTCAGAGTTTTTTTAAGAGCAATGTTCATAAATGAATAAAACATGTT-AGACCAATAAAA
65 C-TCATTCAGAG-TTTTCTAAGAGCAATGTTCATAAATAAATAAAACATGTTGA-ACCAATAAAA
2046 ATCTTCAATTTAATTAATGTTC
127 ATCTTCAATTTAATTAATGTTC
* * * *
2068 ATAAATGAATAATAGATGTTGGACCAATAAAAATCTTGTGTAATCCGTAAATTCCGGTCAAATCC
1 ATAAATGAATAATACATGTTGGACCAATAAAAATCTTGTGTAAGCCGTAAATTCCAGTCAAAACC
* *
2133 TCATTCAGAGTTTTCTAAGAGTAATGTTCATAAATAAATAATACATGTTGAACCAATAAAAATCT
66 TCATTCAGAGTTTTCTAAGAGCAATGTTCATAAATAAATAAAACATGTTGAACCAATAAAAATCT
2198 T
131 T
2199 TTGTAAGCCG
Statistics
Matches: 119, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
148 52 0.44
149 66 0.55
150 1 0.01
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (148 bp):
ATAAATGAATAATACATGTTGGACCAATAAAAATCTTGTGTAAGCCGTAAATTCCAGTCAAAACC
TCATTCAGAGTTTTCTAAGAGCAATGTTCATAAATAAATAAAACATGTTGAACCAATAAAAATCT
TCAATTTAATTAATGTTC
Found at i:2225 original size:94 final size:93
Alignment explanation
Indices: 2061--2383 Score: 423
Period size: 94 Copynumber: 3.4 Consensus size: 93
2051 CAATTTAATT
* * *
2061 AATGTTCATAAATGAATAATAGATGTTGGACCAATAAAAATCTTGTGTAATCCGTAAATTCCGGT
1 AATGTTCATAAATGAATAATACATGTTGGACCAATAAAAATCTTTTGTAAACCGTAAATTCCGGT
* *
2126 CAAATCCTCATTCAGAGTTTTCTAAGAGT
66 GAAATCCTC-TTCAGAGTTTTCTAAGAGC
* * *
2155 AATGTTCATAAATAAATAATACATGTTGAACCAATAAAAATCTTTTGTAAGCCGTAAATTCCGGT
1 AATGTTCATAAATGAATAATACATGTTGGACCAATAAAAATCTTTTGTAAACCGTAAATTCCGGT
*
2220 GAAATCCTCCTTCAGAGTTTTGTAAGAGC
66 GAAATCCT-CTTCAGAGTTTTCTAAGAGC
* * ** *
2249 AATATTCATAAATGAATAATACATGTTGGATCAATAAAAATCAATTGTAAACCGTAAATTCTAGG
1 AATGTTCATAAATGAATAATACATGTTGGACCAATAAAAATCTTTTGTAAACCGTAAATTC-CGG
* *
2314 -GAATTCCTTCTTCAAAGTTTTCTAAGAGC
65 TGAAATCC-TCTTCAGAGTTTTCTAAGAGC
* * **
2343 AATGTTCATAAATGAATAACATATGTTGGATGAATAAAAAT
1 AATGTTCATAAATGAATAATACATGTTGGACCAATAAAAAT
2384 ATTCTGTGAG
Statistics
Matches: 203, Mismatches: 23, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
94 199 0.98
95 4 0.02
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.33
Consensus pattern (93 bp):
AATGTTCATAAATGAATAATACATGTTGGACCAATAAAAATCTTTTGTAAACCGTAAATTCCGGT
GAAATCCTCTTCAGAGTTTTCTAAGAGC
Found at i:3215 original size:26 final size:26
Alignment explanation
Indices: 3157--3216 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
3147 TGAACGAAAC
* *
3157 CTGAAATTTCTAAGAATGTAGTCTTT
1 CTGAATTTTCTAAGAATGTAGTCTTA
* *
3183 CTAAATTTTCTAAGAATGTGAG-GTTA
1 CTGAATTTTCTAAGAATGT-AGTCTTA
3209 CTGAATTT
1 CTGAATTT
3217 ATGTAGAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
26 26 0.93
27 2 0.07
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.42
Consensus pattern (26 bp):
CTGAATTTTCTAAGAATGTAGTCTTA
Found at i:3948 original size:22 final size:22
Alignment explanation
Indices: 3920--3965 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
3910 AAAAGTTACT
*
3920 AAAAC-TTAGTAAGCTTACTAAA
1 AAAACTTTA-TAAGCTCACTAAA
*
3942 AAAACTTTATAAGGTCACTAAA
1 AAAACTTTATAAGCTCACTAAA
3964 AA
1 AA
3966 CATAATAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.52, C:0.13, G:0.09, T:0.26
Consensus pattern (22 bp):
AAAACTTTATAAGCTCACTAAA
Found at i:11185 original size:31 final size:31
Alignment explanation
Indices: 11147--11208 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
11137 GGTTATCAGC
11147 CTCCAGATCTTTAGATCTTGGATGTTTGAGT
1 CTCCAGATCTTTAGATCTTGGATGTTTGAGT
11178 CTCCAGATCTTTAGATCTTGGATGTTTGAGT
1 CTCCAGATCTTTAGATCTTGGATGTTTGAGT
11209 TAGTTCAGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.19, C:0.16, G:0.23, T:0.42
Consensus pattern (31 bp):
CTCCAGATCTTTAGATCTTGGATGTTTGAGT
Found at i:12183 original size:147 final size:143
Alignment explanation
Indices: 11885--12205 Score: 353
Period size: 147 Copynumber: 2.2 Consensus size: 143
11875 ACATGTAAGC
* * * *
11885 AATGATCTAAATCTCGGAAACTTCCAAAAAATTATAACGGTTACTTGTAGATTATGATGTAAGCC
1 AATGATCTAAATCTCAGAAACTTCCAAACAATTATAACGGTTACTTGCAGATTACGATGTAAGCC
* ** *
11950 GTTTTTAAACGATCTAAATCTCGGAAACTGCCAAACAATTATAATGGTCACTTGCATATTACGAT
66 GTTTTTAAACGATCTAAATCTC-AAAACTGCCAAACAATTATAACAGTCACTTGCAGATTACGAT
*
12015 GTAAGTCGTTCTTA
130 GTAAGTCATTCTTA
* * * *
12029 AACGATCTAAATCTCAGAAACTTCCAAACAATTAT-GCAGGTTACTTGCATATTACGATGTAAGT
1 AATGATCTAAATCTCAGAAACTTCCAAACAATTATAAC-GGTTACTTGCAGATTACGATGTAAGC
* * * *
12093 TGTTCTTATTAAACGATCTAAATCGT-AAAGACTTCTAAACAATTATAACAGTTA-TCTGCAGAT
65 CG-T-TT-TTAAACGATCTAAATC-TCAAA-ACTGCCAAACAATTATAACAGTCACT-TGCAGAT
*
12156 TATGATGTAAGTCATTCTTA
124 TACGATGTAAGTCATTCTTA
* *
12176 AATGATCTAAATCGT-AGAGACTTCTAAACA
1 AATGATCTAAATC-TCAGAAACTTCCAAACA
12206 CGGTTACCTG
Statistics
Matches: 148, Mismatches: 21, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
143 1 0.01
144 55 0.37
145 1 0.01
146 5 0.03
147 84 0.57
148 2 0.01
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.33
Consensus pattern (143 bp):
AATGATCTAAATCTCAGAAACTTCCAAACAATTATAACGGTTACTTGCAGATTACGATGTAAGCC
GTTTTTAAACGATCTAAATCTCAAAACTGCCAAACAATTATAACAGTCACTTGCAGATTACGATG
TAAGTCATTCTTA
Found at i:12202 original size:72 final size:72
Alignment explanation
Indices: 11888--12205 Score: 331
Period size: 72 Copynumber: 4.4 Consensus size: 72
11878 TGTAAGCAAT
* * * * * *
11888 GATCTAAATCTCGGAAACTTCCAAAAAATTATAACGGTTACTTGTAGATTATGATGTAAGCCGTT
1 GATCTAAATCTCAGAAACTTCCAAACAATTATAACAGTTACTTGCAGATTACGATGTAAGTCGTT
*
11953 TTTAAAC
66 CTTAAAC
* * ** * *
11960 GATCTAAATCTCGGAAACTGCCAAACAATTATAATGGTCACTTGCATATTACGATGTAAGTCGTT
1 GATCTAAATCTCAGAAACTTCCAAACAATTATAACAGTTACTTGCAGATTACGATGTAAGTCGTT
12025 CTTAAAC
66 CTTAAAC
* * *
12032 GATCTAAATCTCAGAAACTTCCAAACAATTAT-GCAGGTTACTTGCATATTACGATGTAAGTTGT
1 GATCTAAATCTCAGAAACTTCCAAACAATTATAACA-GTTACTTGCAGATTACGATGTAAGTCGT
12096 TCTTATTAAAC
65 TC---TTAAAC
* *
12107 GATCTAAATCGT-A-AAGACTTCTAAACAATTATAACAGTTA-TCTGCAGATTATGATGTAAGTC
1 GATCTAAATC-TCAGAA-ACTTCCAAACAATTATAACAGTTACT-TGCAGATTACGATGTAAGTC
* *
12169 ATTCTTAAAT
63 GTTCTTAAAC
* *
12179 GATCTAAATCGT-AGAGACTTCTAAACA
1 GATCTAAATC-TCAGAAACTTCCAAACA
12206 CGGTTACCTG
Statistics
Matches: 213, Mismatches: 24, Indels: 18
0.84 0.09 0.07
Matches are distributed among these distances:
72 150 0.70
73 1 0.00
74 3 0.01
75 56 0.26
76 3 0.01
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (72 bp):
GATCTAAATCTCAGAAACTTCCAAACAATTATAACAGTTACTTGCAGATTACGATGTAAGTCGTT
CTTAAAC
Found at i:12274 original size:65 final size:64
Alignment explanation
Indices: 12124--12277 Score: 157
Period size: 65 Copynumber: 2.4 Consensus size: 64
12114 ATCGTAAAGA
* *
12124 CTTCTAAACAATTATAACAGTTATCTGCAGATTATGATGTAAGTCATTCTTAAATGATCTAAAT
1 CTTCTAAACAATTATAACGGTTACCTGCAGATTATGATGTAAGTCATTCTTAAATGATCTAAAT
* ** * * * ** * * *
12188 CGTAGAGAC-TTCTAAACACGGTTACCTGCAGATTATGATGTAAGTGGTTCTTGAATTATCTAAT
1 CTTCTAAACAAT-TATA-ACGGTTACCTGCAGATTATGATGTAAGTCATTCTTAAATGATCTAAA
12252 T
64 T
12253 GCTTCTAAACAATTATAACGGTTAC
1 -CTTCTAAACAATTATAACGGTTAC
12278 TTGTAGTCTA
Statistics
Matches: 67, Mismatches: 19, Indels: 7
0.72 0.20 0.08
Matches are distributed among these distances:
63 1 0.01
64 8 0.12
65 49 0.73
66 8 0.12
67 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.36
Consensus pattern (64 bp):
CTTCTAAACAATTATAACGGTTACCTGCAGATTATGATGTAAGTCATTCTTAAATGATCTAAAT
Found at i:12492 original size:72 final size:72
Alignment explanation
Indices: 12284--12654 Score: 311
Period size: 72 Copynumber: 5.3 Consensus size: 72
12274 TTACTTGTAG
* * * * **
12284 TCTAAATCGTAGAAACTTCCAAACCATTATAACGGTTACTTGCAGGTTATGATGTAAG-CATTCT
1 TCTAAATCGCAGAAACTTCCAAACAATTATAACGGTTACTTGCAGATTACGATGTAAGTTGTTCT
*
12348 TAAATGA
66 TAAACGA
* * * * ** ****
12355 TCTAGATTGCAGAAAATTCCAAATAATTATAACGGTTACTTGTGGATTACGATGTAAACCATTCT
1 TCTAAATCGCAGAAACTTCCAAACAATTATAACGGTTACTTGCAGATTACGATGTAAGTTGTTCT
*
12420 TAAAGGA
66 TAAACGA
* * * * *
12427 TCTAAATCGCGGAGACTTCCAAACAATTATAATGGTTACATGCAGAATACGATGTAAGTTGTTCT
1 TCTAAATCGCAGAAACTTCCAAACAATTATAACGGTTACTTGCAGATTACGATGTAAGTTGTTCT
*
12492 TAAACTA
66 TAAACGA
* * * * *
12499 T-TAAAATCACA-AGACTTCTAAACGATTATAACGGTTAC---C--A-T-C----TAAATTGTTC
1 TCT-AAATCGCAGAAACTTCCAAACAATTATAACGGTTACTTGCAGATTACGATGTAAGTTGTTC
*
12551 TTAAACGG
65 TTAAACGA
* * * * *
12559 TCTAAATCACATATACTTCCAAACAATTATAACGGTTACCTGCAGATTACAATGTAAGTTGTTCT
1 TCTAAATCGCAGAAACTTCCAAACAATTATAACGGTTACTTGCAGATTACGATGTAAGTTGTTCT
12624 TAAACGA
66 TAAACGA
*
12631 TCTAAATCGCAAAAACTTCCAAAC
1 TCTAAATCGCAGAAACTTCCAAAC
12655 GTGTAAGCAA
Statistics
Matches: 240, Mismatches: 45, Indels: 29
0.76 0.14 0.09
Matches are distributed among these distances:
60 24 0.10
61 25 0.10
64 2 0.01
65 1 0.00
66 2 0.01
67 1 0.00
68 2 0.01
71 72 0.30
72 111 0.46
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31
Consensus pattern (72 bp):
TCTAAATCGCAGAAACTTCCAAACAATTATAACGGTTACTTGCAGATTACGATGTAAGTTGTTCT
TAAACGA
Found at i:12598 original size:61 final size:60
Alignment explanation
Indices: 12485--12598 Score: 158
Period size: 61 Copynumber: 1.9 Consensus size: 60
12475 ACGATGTAAG
* * *
12485 TTGTTCTTAAACTATTAAAATCACAAGACTTCTAAACGATTATAACGGTTACCATCTAAA
1 TTGTTCTTAAACGATTAAAATCACAAGACTTCCAAACAATTATAACGGTTACCATCTAAA
* *
12545 TTGTTCTTAAACGGTCT-AAATCACATATACTTCCAAACAATTATAACGGTTACC
1 TTGTTCTTAAACGAT-TAAAATCACA-AGACTTCCAAACAATTATAACGGTTACC
12599 TGCAGATTAC
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
60 21 0.45
61 26 0.55
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (60 bp):
TTGTTCTTAAACGATTAAAATCACAAGACTTCCAAACAATTATAACGGTTACCATCTAAA
Found at i:25088 original size:7 final size:7
Alignment explanation
Indices: 25076--25100 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
25066 TTTTCTAACG
25076 TTTTTAC
1 TTTTTAC
25083 TTTTTAC
1 TTTTTAC
25090 TTTTTAC
1 TTTTTAC
25097 TTTT
1 TTTT
25101 CCTCTAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTTAC
Found at i:27217 original size:2 final size:2
Alignment explanation
Indices: 27210--27241 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
27200 ACTTATGATG
27210 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27242 TAAAGCTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.