Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012935.1 Corchorus capsularis cultivar CVL-1 contig12956, 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: 1839
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.22
Found at i:97 original size:50 final size:49
Alignment explanation
Indices: 12--115 Score: 138
Period size: 50 Copynumber: 2.1 Consensus size: 49
2 ACTTGAAAAC
* * *
12 AACTGAAGAAAGACCGCCCTGCATCGACTGAATCGATCATT-TAGACATA
1 AACTTAAGAAAGACCACCCTGCATCAACTGAATCGATCATTCTA-ACATA
**
61 AACTTAAGAAAGACCACCCTCGGGTCAACTGAATCGATCATTCTAACATA
1 AACTTAAGAAAGACCACCCT-GCATCAACTGAATCGATCATTCTAACATA
111 AACTT
1 AACTT
116 CTAATAAACT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
49 18 0.38
50 28 0.58
51 2 0.04
ACGTcount: A:0.38, C:0.25, G:0.15, T:0.22
Consensus pattern (49 bp):
AACTTAAGAAAGACCACCCTGCATCAACTGAATCGATCATTCTAACATA
Found at i:308 original size:49 final size:49
Alignment explanation
Indices: 251--352 Score: 168
Period size: 49 Copynumber: 2.1 Consensus size: 49
241 ACTTGAAAAC
* *
251 AACTGAAGAAAGACCGCCCTGCGTCGACTGAATCGATCATTCTGACATA
1 AACTGAAGAAAGACCACCCTGCGTCAACTGAATCGATCATTCTGACATA
* *
300 AACTGAAGAAAGACCACCCTGGGTCAACTTAATCGATCATTCTGACATA
1 AACTGAAGAAAGACCACCCTGCGTCAACTGAATCGATCATTCTGACATA
349 AACT
1 AACT
353 TCGAAAAAAC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (49 bp):
AACTGAAGAAAGACCACCCTGCGTCAACTGAATCGATCATTCTGACATA
Found at i:309 original size:120 final size:120
Alignment explanation
Indices: 1--712 Score: 1056
Period size: 120 Copynumber: 5.9 Consensus size: 120
**
1 AACTTGAAAACAACTGAAGAAAGACCGCCCTGCATCGACTGAATCGATCATT-TAGACATAAACT
1 AACTTGAAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCT-GACATAAACT
* * *
65 TAAGAAAGACCACCCTCGGGTCAACTGAATCGATCATTCTAACATAAACTTCTAATA
65 GAAGAAAGACCACCCT-GGGTCAACTGAATCGATCATTCTGACATAAACTTCGAATA
* * * *
122 AACTTG-AAACAACTTAA-AAAGACCGGCCTGGGTCGACTGAATCGATCATTCTGACATACACTT
1 AACTTGAAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTG
* * *
185 AAGAAAAACCACCCTGGGTCAACTGAATTGATCATTCTGACATTAACTT-GAATTA
66 AAGAAAGACCACCCTGGGTCAACTGAATCGATCATTCTGACATAAACTTCGAA-TA
*
240 AACTTGAAAACAACTGAAGAAAGACCGCCCTGCGTCGACTGAATCGATCATTCTGACATAAACTG
1 AACTTGAAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTG
* *
305 AAGAAAGACCACCCTGGGTCAACTTAATCGATCATTCTGACATAAACTTCGAAAA
66 AAGAAAGACCACCCTGGGTCAACTGAATCGATCATTCTGACATAAACTTCGAATA
* * *
360 AACTTGAAAACAACTTAAAAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATACACTG
1 AACTTGAAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTG
* *
425 AAGAAA-ACCACCCTGGGTCAACTGAATTGATCATTCTGACATAAACATCGAATA
66 AAGAAAGACCACCCTGGGTCAACTGAATCGATCATTCTGACATAAACTTCGAATA
* * * *
479 AACTTGAAAACAACTGAAAAAAGACCGCCTTGGGTCGACTGAATCGATCATTCTGACATACACTT
1 AACTTGAAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTG
* * *
544 AAGAAAGACCACCTTGGGTCAACTAAATTGATCATTCTGACATAAACTTCGAATA
66 AAGAAAGACCACCCTGGGTCAACTGAATCGATCATTCTGACATAAACTTCGAATA
* * *
599 AACTTGAAAACAATTGAAAGAAAGACCGCCCTAGGTAGACTGAATCGATCATTCTGACATAAACT
1 AACTTGAAAACAACTG-AAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACT
* * *
664 GAAGAAACACCACCCTAGGTCAACTGAATCGATCATTCTAACATAAACT
65 GAAGAAAGACCACCCTGGGTCAACTGAATCGATCATTCTGACATAAACT
713 GAAGAAAGAC
Statistics
Matches: 537, Mismatches: 47, Indels: 14
0.90 0.08 0.02
Matches are distributed among these distances:
117 2 0.00
118 39 0.07
119 176 0.33
120 226 0.42
121 94 0.18
ACGTcount: A:0.39, C:0.23, G:0.16, T:0.23
Consensus pattern (120 bp):
AACTTGAAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTG
AAGAAAGACCACCCTGGGTCAACTGAATCGATCATTCTGACATAAACTTCGAATA
Found at i:559 original size:49 final size:49
Alignment explanation
Indices: 498--592 Score: 145
Period size: 49 Copynumber: 1.9 Consensus size: 49
488 ACAACTGAAA
* * * *
498 AAAGACCGCCTTGGGTCGACTGAATCGATCATTCTGACATACACTTAAG
1 AAAGACCACCTTGGGTCAACTAAATCGATCATTCTGACATAAACTTAAG
*
547 AAAGACCACCTTGGGTCAACTAAATTGATCATTCTGACATAAACTT
1 AAAGACCACCTTGGGTCAACTAAATCGATCATTCTGACATAAACTT
593 CGAATAAACT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 41 1.00
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (49 bp):
AAAGACCACCTTGGGTCAACTAAATCGATCATTCTGACATAAACTTAAG
Found at i:690 original size:49 final size:49
Alignment explanation
Indices: 616--810 Score: 293
Period size: 49 Copynumber: 4.0 Consensus size: 49
606 AAACAATTGA
*
616 AAGAAAGACCGCCCTAGGT-AGACTGAATCGATCATTCTGACATAAACTG
1 AAGAAAGACCACCCTAGGTCA-ACTGAATCGATCATTCTGACATAAACTG
* *
665 AAGAAACACCACCCTAGGTCAACTGAATCGATCATTCTAACATAAACTG
1 AAGAAAGACCACCCTAGGTCAACTGAATCGATCATTCTGACATAAACTG
* * * *
714 AAGAAAGACCGCCCTAGGTCGACTGAATCGATCATTTTGACATAAATTG
1 AAGAAAGACCACCCTAGGTCAACTGAATCGATCATTCTGACATAAACTG
* *
763 AAGAAAGACCACCCTGGGTCAACTAAATCGATCATTCTGACATAAACT
1 AAGAAAGACCACCCTAGGTCAACTGAATCGATCATTCTGACATAAACT
811 TCGAATAAAC
Statistics
Matches: 130, Mismatches: 15, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
49 129 0.99
50 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.22
Consensus pattern (49 bp):
AAGAAAGACCACCCTAGGTCAACTGAATCGATCATTCTGACATAAACTG
Found at i:785 original size:98 final size:98
Alignment explanation
Indices: 616--810 Score: 327
Period size: 98 Copynumber: 2.0 Consensus size: 98
606 AAACAATTGA
616 AAGAAAGACCGCCCTAGGTAGACTGAATCGATCATTCTGACATAAACTGAAGAAACACCACCCTA
1 AAGAAAGACCGCCCTAGGTAGACTGAATCGATCATTCTGACATAAACTGAAGAAACACCACCCTA
*
681 GGTCAACTGAATCGATCATTCTAACATAAACTG
66 GGTCAACTAAATCGATCATTCTAACATAAACTG
* * * * *
714 AAGAAAGACCGCCCTAGGTCGACTGAATCGATCATTTTGACATAAATTGAAGAAAGACCACCCTG
1 AAGAAAGACCGCCCTAGGTAGACTGAATCGATCATTCTGACATAAACTGAAGAAACACCACCCTA
*
779 GGTCAACTAAATCGATCATTCTGACATAAACT
66 GGTCAACTAAATCGATCATTCTAACATAAACT
811 TCGAATAAAC
Statistics
Matches: 90, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
98 90 1.00
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.22
Consensus pattern (98 bp):
AAGAAAGACCGCCCTAGGTAGACTGAATCGATCATTCTGACATAAACTGAAGAAACACCACCCTA
GGTCAACTAAATCGATCATTCTAACATAAACTG
Found at i:915 original size:48 final size:49
Alignment explanation
Indices: 832--927 Score: 158
Period size: 48 Copynumber: 2.0 Consensus size: 49
822 TGAAAACAAC
* *
832 TGAAAAAAGACCGCCCTGGGTCGACTAAATCGATCATTCTGACATAAAG
1 TGAAAAAAGACCACCCTGGGTCAACTAAATCGATCATTCTGACATAAAG
*
881 TGAAAAAAGACCACCCT-GGTCAACTGAATCGATCATTCTGACATAAA
1 TGAAAAAAGACCACCCTGGGTCAACTAAATCGATCATTCTGACATAAA
928 CTTCGAATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
48 28 0.64
49 16 0.36
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.21
Consensus pattern (49 bp):
TGAAAAAAGACCACCCTGGGTCAACTAAATCGATCATTCTGACATAAAG
Found at i:958 original size:120 final size:120
Alignment explanation
Indices: 709--1524 Score: 830
Period size: 120 Copynumber: 6.4 Consensus size: 120
699 TTCTAACATA
* * * * *
709 AACTGAAGAAAGACCGCCCTAGGTCGACTGAATCGATCATTTTGACATAAATTGAAGAAAGACCA
1 AACTGAAAAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTGAAAAAAGACCA
*
774 CCCTGGGTCAACTAAATCGATCATTCTGACATAAACTTCGAATAAACTTGAAAAC
66 CCCTGGGTCAACTGAATCGATCATTCTGACATAAACTTCGAATAAACTTGAAAAC
* *
829 AACTGAAAAAAGACCGCCCTGGGTCGACTAAATCGATCATTCTGACATAAAGTGAAAAAAGACCA
1 AACTGAAAAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTGAAAAAAGACCA
894 CCCT-GGTCAACTGAATCGATCATTCTGACATAAACTTCGAATAAACTTGAAAAC
66 CCCTGGGTCAACTGAATCGATCATTCTGACATAAACTTCGAATAAACTTGAAAAC
* *
948 AACTGAAAAAAAGACCGCCCTGGGTCGATTGAATCGATCATTCTGACATAAACT-AAAGAAAAAC
1 AACTG-AAAAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTGAAA-AAAGAC
1012 CACCCTGGGTCAACTGAATCGATCATTCTGACATAAACTTCGAATAAACTTGAAAAC
64 CACCCTGGGTCAACTGAATCGATCATTCTGACATAAACTTCGAATAAACTTGAAAAC
* *
1069 AACTGAAAAAAAGACCGCCCTGCGTCGACTGAATCGATCATTCTGACATAAACTTGGATAAACGT
1 AACTG-AAAAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAAC-T-GA-AAA--A
* * * * * **
1134 GGA-AACTACTGAAGAAAGACCACCCTGGGTCGACTGAATAGATCATTCTGACATAAACTTCGAA
60 AGACCAC-CCTG--G---G-TCA-ACTGAATC---------GATCATTCTGACATAAACTTCGAA
*
1198 TAACCTTGAAAAC
108 TAAACTTGAAAAC
* * **
1211 AACTGAAGAAAGACCGCCCTGGGTCGACTGAATTGATCATTCTGACATAAACTTGGATAAACGTG
1 AACTGAAAAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAAC-T-GA-AAA--AA
* * * * ** *
1276 GA-AACTACTGAAGAAAGACCACCCTGGGTCGACCGAATCGATAATTCTGACATAAACTTGGAAT
61 GACCAC-CCTG--G---G-TCA-ACTGAATC----G-ATC----ATTCTGACATAAACTTCGAAT
*
1340 AAACTGGAAAAC
109 AAACTTGAAAAC
* *
1352 AACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTGAAGAAAGACCA
1 AACTGAAAAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTGAAAAAAGACCA
* *
1417 CCCTAGGTCAACTAAATCGATCATTCTGACATAAACTTCGAATAAACTTGAAAAC
66 CCCTGGGTCAACTGAATCGATCATTCTGACATAAACTTCGAATAAACTTGAAAAC
* * *
1472 AATTGAAGAAAGACCACCCTGGGTCGACTGAATCGATCATTCTGACATAAACT
1 AACTGAAAAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACT
1525 TGGATTAAAC
Statistics
Matches: 616, Mismatches: 48, Indels: 64
0.85 0.07 0.09
Matches are distributed among these distances:
119 57 0.09
120 201 0.33
121 101 0.16
122 1 0.00
124 5 0.01
125 5 0.01
126 4 0.01
128 1 0.00
129 4 0.01
130 2 0.00
131 2 0.00
132 2 0.00
133 5 0.01
134 1 0.00
136 6 0.01
137 5 0.01
138 2 0.00
139 2 0.00
140 1 0.00
141 168 0.27
142 41 0.07
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (120 bp):
AACTGAAAAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTGAAAAAAGACCA
CCCTGGGTCAACTGAATCGATCATTCTGACATAAACTTCGAATAAACTTGAAAAC
Found at i:1030 original size:49 final size:50
Alignment explanation
Indices: 948--1050 Score: 156
Period size: 49 Copynumber: 2.1 Consensus size: 50
938 ACTTGAAAAC
* * *
948 AACTGAAAAAAAGACCGCCCTGGGTCGATTGAATCGATCATTCTGACATA
1 AACTGAAAAAAAGACCACCCTGGGTCAACTGAATCGATCATTCTGACATA
998 AACT-AAAGAAAA-ACCACCCTGGGTCAACTGAATCGATCATTCTGACATA
1 AACTGAAA-AAAAGACCACCCTGGGTCAACTGAATCGATCATTCTGACATA
1047 AACT
1 AACT
1051 TCGAATAAAC
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
49 41 0.84
50 8 0.16
ACGTcount: A:0.39, C:0.23, G:0.17, T:0.21
Consensus pattern (50 bp):
AACTGAAAAAAAGACCACCCTGGGTCAACTGAATCGATCATTCTGACATA
Found at i:1154 original size:191 final size:189
Alignment explanation
Indices: 881--1781 Score: 1029
Period size: 191 Copynumber: 4.6 Consensus size: 189
871 TGACATAAAG
* * * * *
881 TGAAAAAAGACCACCCTGGTCAACTGAATCGATCATTCTGACATAAACTTCGAATAAACTTGAAA
1 TGAAGAAAGACCACCCTGGTCGACTGAATCGATCATTCTGACATAAACTT-GGATAAACGTGGAA
* * *
946 ACAACTGAAAAAAAGACCGCCCTGGGTCGATTGAATCGATCATTCTGACATAAACTAAAGAAAAA
65 ACAACTG-AAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTGAAGAAAAA
1011 CCACCCTGGGTCAACTGAATCGATCATTCTGACATAAACTTCGAATAAACTTGAAAACAAC
129 CCACCCTGGGTCAACTGAATCGATCATTCTGACATAAACTTCGAATAAACTTGAAAACAAC
* *
1072 TGAAAAAAAGACCGCCCTGCGTCGACTGAATCGATCATTCTGACATAAACTTGGATAAACGTGGA
1 TG-AAGAAAGACCACCCTG-GTCGACTGAATCGATCATTCTGACATAAACTTGGATAAACGTGGA
* * * *
1137 AACTACTGAAGAAAGACCACCCTGGGTCGACTGAATAGATCATTCTGACATAAACTTCGAATAAC
64 AACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAAC-T-GAAGAA-
* * * ** * ** * * * *
1202 CTTGAAAACA-ACTGAAGAAAGACCGCCCTGGGTCGA--CTGA-ATTGATCATTCTGACATAAAC
126 ----AAACCACCCTG-GGTCA-ACTG-AATCGATC-ATTCTGACA-TAAAC-TTC-GA-ATAAAC
1263 TTGGATAAACGTGGAAACTAC
179 TT-GA-AAAC------A--AC
* *
1284 TGAAGAAAGACCACCCTGGGTCGACCGAATCGATAATTCTGACATAAACTTGGAATAAAC-TGGA
1 TGAAGAAAGACCACCCT-GGTCGACTGAATCGATCATTCTGACATAAACTTGG-ATAAACGTGG-
*
1348 AAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTGAAGAAAG
63 AAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTGAAGAAAA
* * *
1413 ACCACCCTAGGTCAACTAAATCGATCATTCTGACATAAACTTCGAATAAACTTGAAAACAAT
128 ACCACCCTGGGTCAACTGAATCGATCATTCTGACATAAACTTCGAATAAACTTGAAAACAAC
* *
1475 TGAAGAAAGACCACCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGGATTAAACTTGAA
1 TGAAGAAAGACCACCCT-GGTCGACTGAATCGATCATTCTGACATAAACTTGGA-TAAACGTGGA
* * *
1540 AACAACTGAAGAAAGATCGCCCTAGGTCGACTGAATCGATCATTCTGACATAAACTGAAGAAAGA
64 AACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTGAAGAAAAA
* * * **
1605 CCTCCCTGGGTCAACTGAATCGATCATTCTGACATAAACTTGGAATAAACTTTAAAATGAC
129 CCACCCTGGGTCAACTGAATCGATCATTCTGACATAAACTTCGAATAAACTTGAAAACAAC
* *
1666 TGAAGAAAGACCGCCCTGGTCGACTGAATTGATCATTCTGACATAAACTTGGATAAACGTGGAAA
1 TGAAGAAAGACCACCCTGGTCGACTGAATCGATCATTCTGACATAAACTTGGATAAACGTGGAAA
* ** *
1731 CTACTGAAGAAAGACAACCCTGGGTCGACCGAATCGATCATTCTGACATAA
66 CAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAA
1782 CTTGAAATAA
Statistics
Matches: 603, Mismatches: 71, Indels: 74
0.81 0.09 0.10
Matches are distributed among these distances:
189 55 0.09
190 36 0.06
191 235 0.39
192 35 0.06
193 36 0.06
197 3 0.00
198 8 0.01
199 14 0.02
200 9 0.01
201 11 0.02
202 11 0.02
203 9 0.01
204 13 0.02
205 7 0.01
206 2 0.00
210 6 0.01
211 49 0.08
212 64 0.11
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (189 bp):
TGAAGAAAGACCACCCTGGTCGACTGAATCGATCATTCTGACATAAACTTGGATAAACGTGGAAA
CAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTGAAGAAAAACC
ACCCTGGGTCAACTGAATCGATCATTCTGACATAAACTTCGAATAAACTTGAAAACAAC
Found at i:1242 original size:71 final size:70
Alignment explanation
Indices: 998--1404 Score: 580
Period size: 71 Copynumber: 5.8 Consensus size: 70
988 TTCTGACATA
* * *
998 AACTAAAGAAAAACCACCCTGGGTCAACTGAATCGATCATTCTGACATAAACTTCGAATAAACTT
1 AACTGAAGAAAGACCACCCTGGGTCGACTGAATCGATCATTCTGACATAAACTT-GAATAAACTT
1063 GAAAAC
65 GAAAAC
* * * * *
1069 AACTGAAAAAAAGACCGCCCTGCGTCGACTGAATCGATCATTCTGACATAAACTTGGATAAACGT
1 AACTG-AAGAAAGACCACCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGAATAAACTT
*
1134 GGAAAC
65 GAAAAC
* * *
1140 TACTGAAGAAAGACCACCCTGGGTCGACTGAATAGATCATTCTGACATAAACTTCGAATAACCTT
1 AACTGAAGAAAGACCACCCTGGGTCGACTGAATCGATCATTCTGACATAAACTT-GAATAAACTT
1205 GAAAAC
65 GAAAAC
* * * *
1211 AACTGAAGAAAGACCGCCCTGGGTCGACTGAATTGATCATTCTGACATAAACTTGGATAAACGTG
1 AACTGAAGAAAGACCACCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGAATAAACTTG
*
1276 GAAAC
66 AAAAC
* * * *
1281 TACTGAAGAAAGACCACCCTGGGTCGACCGAATCGATAATTCTGACATAAACTTGGAATAAACTG
1 AACTGAAGAAAGACCACCCTGGGTCGACTGAATCGATCATTCTGACATAAACTT-GAATAAACTT
1346 GAAAAC
65 GAAAAC
*
1352 AACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACT
1 AACTGAAGAAAGACCACCCTGGGTCGACTGAATCGATCATTCTGACATAAACT
1405 GAAGAAAGAC
Statistics
Matches: 295, Mismatches: 38, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
70 106 0.36
71 145 0.49
72 44 0.15
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (70 bp):
AACTGAAGAAAGACCACCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGAATAAACTTG
AAAAC
Found at i:1289 original size:141 final size:141
Alignment explanation
Indices: 1003--1404 Score: 696
Period size: 141 Copynumber: 2.8 Consensus size: 141
993 ACATAAACTA
* *
1003 AAGAAAAACCACCCTGGGTCAACTGAATCGATCATTCTGACATAAACTTCGAATAAACTTGAAAA
1 AAGAAAGACCACCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTCGAATAAACTTGAAAA
* *
1068 CAACTGAAAAAAAGACCGCCCTGCGTCGACTGAATCGATCATTCTGACATAAACTTGGATAAACG
66 CAACTG-AAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGGATAAACG
1133 TGGAAACTACTG
130 TGGAAACTACTG
* *
1145 AAGAAAGACCACCCTGGGTCGACTGAATAGATCATTCTGACATAAACTTCGAATAACCTTGAAAA
1 AAGAAAGACCACCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTCGAATAAACTTGAAAA
*
1210 CAACTGAAGAAAGACCGCCCTGGGTCGACTGAATTGATCATTCTGACATAAACTTGGATAAACGT
66 CAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGGATAAACGT
1275 GGAAACTACTG
131 GGAAACTACTG
* * * *
1286 AAGAAAGACCACCCTGGGTCGACCGAATCGATAATTCTGACATAAACTTGGAATAAACTGGAAAA
1 AAGAAAGACCACCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTCGAATAAACTTGAAAA
1351 CAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACT
66 CAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACT
1405 GAAGAAAGAC
Statistics
Matches: 246, Mismatches: 14, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
141 179 0.73
142 67 0.27
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (141 bp):
AAGAAAGACCACCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTCGAATAAACTTGAAAA
CAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGGATAAACGT
GGAAACTACTG
Found at i:1435 original size:49 final size:49
Alignment explanation
Indices: 1352--1453 Score: 168
Period size: 49 Copynumber: 2.1 Consensus size: 49
1342 ACTGGAAAAC
* * * *
1352 AACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATA
1 AACTGAAGAAAGACCACCCTAGGTCAACTAAATCGATCATTCTGACATA
1401 AACTGAAGAAAGACCACCCTAGGTCAACTAAATCGATCATTCTGACATA
1 AACTGAAGAAAGACCACCCTAGGTCAACTAAATCGATCATTCTGACATA
1450 AACT
1 AACT
1454 TCGAATAAAC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.21
Consensus pattern (49 bp):
AACTGAAGAAAGACCACCCTAGGTCAACTAAATCGATCATTCTGACATA
Found at i:1520 original size:71 final size:71
Alignment explanation
Indices: 1401--1595 Score: 318
Period size: 71 Copynumber: 2.7 Consensus size: 71
1391 TTCTGACATA
* *
1401 AACTGAAGAAAGACCACCCTAGGTCAACTAAATCGATCATTCTGACATAAACTTCGAATAAACTT
1 AACTGAAGAAAGACCACCCTAGGTCGACTGAATCGATCATTCTGACATAAACTTCGAATAAACTT
1466 GAAAAC
66 GAAAAC
* * * *
1472 AATTGAAGAAAGACCACCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGGATTAAACTT
1 AACTGAAGAAAGACCACCCTAGGTCGACTGAATCGATCATTCTGACATAAACTTCGAATAAACTT
1537 GAAAAC
66 GAAAAC
* *
1543 AACTGAAGAAAGATCGCCCTAGGTCGACTGAATCGATCATTCTGACATAAACT
1 AACTGAAGAAAGACCACCCTAGGTCGACTGAATCGATCATTCTGACATAAACT
1596 GAAGAAAGAC
Statistics
Matches: 114, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
71 114 1.00
ACGTcount: A:0.39, C:0.22, G:0.16, T:0.23
Consensus pattern (71 bp):
AACTGAAGAAAGACCACCCTAGGTCGACTGAATCGATCATTCTGACATAAACTTCGAATAAACTT
GAAAAC
Found at i:1599 original size:120 final size:119
Alignment explanation
Indices: 1475--1714 Score: 399
Period size: 120 Copynumber: 2.0 Consensus size: 119
1465 TGAAAACAAT
* *
1475 TGAAGAAAGACCACCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGGATTAAACTTGAA
1 TGAAGAAAGACCACCCTGGGTCAACTGAATCGATCATTCTGACATAAACTTGGAATAAACTTGAA
*
1540 AACAACTGAAGAAAGATCGCCCTAGGTCGACTGAATCGATCATTCTGACATAAAC
66 AACAACTGAAGAAAGACCGCCCT-GGTCGACTGAATCGATCATTCTGACATAAAC
* *
1595 TGAAGAAAGACCTCCCTGGGTCAACTGAATCGATCATTCTGACATAAACTTGGAATAAACTTTAA
1 TGAAGAAAGACCACCCTGGGTCAACTGAATCGATCATTCTGACATAAACTTGGAATAAACTTGAA
** *
1660 AATGACTGAAGAAAGACCGCCCTGGTCGACTGAATTGATCATTCTGACATAAAC
66 AACAACTGAAGAAAGACCGCCCTGGTCGACTGAATCGATCATTCTGACATAAAC
1714 T
1 T
1715 TGGATAAACG
Statistics
Matches: 112, Mismatches: 8, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
119 31 0.28
120 81 0.72
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (119 bp):
TGAAGAAAGACCACCCTGGGTCAACTGAATCGATCATTCTGACATAAACTTGGAATAAACTTGAA
AACAACTGAAGAAAGACCGCCCTGGTCGACTGAATCGATCATTCTGACATAAAC
Found at i:1622 original size:49 final size:49
Alignment explanation
Indices: 1543--1644 Score: 168
Period size: 49 Copynumber: 2.1 Consensus size: 49
1533 ACTTGAAAAC
* *
1543 AACTGAAGAAAGATCGCCCTAGGTCGACTGAATCGATCATTCTGACATA
1 AACTGAAGAAAGACCGCCCTAGGTCAACTGAATCGATCATTCTGACATA
* *
1592 AACTGAAGAAAGACCTCCCTGGGTCAACTGAATCGATCATTCTGACATA
1 AACTGAAGAAAGACCGCCCTAGGTCAACTGAATCGATCATTCTGACATA
1641 AACT
1 AACT
1645 TGGAATAAAC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.23
Consensus pattern (49 bp):
AACTGAAGAAAGACCGCCCTAGGTCAACTGAATCGATCATTCTGACATA
Found at i:1708 original size:70 final size:70
Alignment explanation
Indices: 1593--1839 Score: 329
Period size: 70 Copynumber: 3.5 Consensus size: 70
1583 TCTGACATAA
* * *
1593 ACTGAAGAAAGACCTCCCTGGGTCAACTGAATCGATCATTCTGACATAAACTTGGAATAAACTTT
1 ACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGGAATAAACTTG
1658 AAAAT
66 AAAAT
*
1663 GACTGAAGAAAGACCGCCCT-GGTCGACTGAATTGATCATTCTGACATAAACTTGG-ATAAACGT
1 -ACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGGAATAAAC-T
* *
1726 GGAAACT
64 TGAAAAT
** * *
1733 ACTGAAGAAAGACAACCCTGGGTCGACCGAATCGATCATTCTGACAT-AACTTGAAATAAACTTG
1 ACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGGAATAAACTTG
*
1797 AAAACA
66 AAAA-T
**
1803 ACTGAAGAAAGACCGCCCTGCATCGACTGAATCGATC
1 ACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATC
Statistics
Matches: 153, Mismatches: 19, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
69 34 0.22
70 101 0.66
71 18 0.12
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (70 bp):
ACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGGAATAAACTTG
AAAAT
Done.