Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011611.1 Corchorus olitorius cultivar O-4 contig11644, 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: 2647
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Found at i:376 original size:154 final size:154
Alignment explanation
Indices: 60--406 Score: 516
Period size: 154 Copynumber: 2.2 Consensus size: 154
50 TAGGCCATAG
* *
60 TCAACTAATCTCTCCAAAATGATTTATAGTTAGGCCTTAAACAATGGAAAGAAAAGCATTGAGGT
1 TCAACTAATCTCACCAAAATGA-TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGT
* * * *
125 TTGCCAAATGGAAGAATATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAATATAACAAGTGT
65 TTGCCAAATCGAAGAAGATTCAAAACGGAACTAATGGGCCCCGATAAGCCCAAAATAACAAGTGT
* *
190 TCCAAATGAGCTAAAAACTTTTAAG
130 TCCAAATGAGCTAAAAACTTTCAAA
* * *
215 TCGACTAATCTCACCAAAATGATTATAGTTAGGGCATAAACAATGGAAAGAATAGCATTGAGGTT
1 TCAACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTT
* * *
280 TGCCAAATCGAAGACGATTCAAATCTGAACTAATGGGCCCCGATAAGCCCAAAATAACAAGTGTT
66 TGCCAAATCGAAGAAGATTCAAAACGGAACTAATGGGCCCCGATAAGCCCAAAATAACAAGTGTT
* *
345 GCAAATGAGCTAAAATC-TTCACAA
131 CCAAATGAGCTAAAAACTTTCA-AA
*
369 TTAACTAATCTCACCAAAATGATTATAGTTAGGCCATA
1 TCAACTAATCTCACCAAAATGATTATAGTTAGGCCATA
407 GTCAACTAAT
Statistics
Matches: 172, Mismatches: 19, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
153 3 0.02
154 149 0.87
155 20 0.12
ACGTcount: A:0.40, C:0.18, G:0.17, T:0.24
Consensus pattern (154 bp):
TCAACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTT
TGCCAAATCGAAGAAGATTCAAAACGGAACTAATGGGCCCCGATAAGCCCAAAATAACAAGTGTT
CCAAATGAGCTAAAAACTTTCAAA
Found at i:584 original size:192 final size:193
Alignment explanation
Indices: 213--594 Score: 586
Period size: 192 Copynumber: 2.0 Consensus size: 193
203 AAAACTTTTA
* * *
213 AGTCGACTAATCTCACCAAAATGATTATAGTTAGGGCATAAACAATGGAAAGAATAGCATTGAGG
1 AGTCAACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG
* * * *
278 TTTGCCAAATCGAAGACGATTCAAATCTGAACTAATGGGCCCCGATAAGCCCAAAATAACAAGTG
66 TCTGCCAAATCGAAGAAGATTCAAAACTGAACTAACGGGCCCCGATAAGCCCAAAATAACAAGTG
* * *
343 TTGCAAATGAGCTAAAATCTTCACAATTAACTAATCTCACCAAAATGATTATAGTTAGGCCAT
131 TTCCAAATGAGCTAAAAACTTCACAATGAACTAATCTCACCAAAATGATTATAGTTAGGCCAT
* *
406 AGTCAACTAATCTCTCCAAAATGATTATAGTTAGGCCTTAAACAATGGAAAGAAAAGCATTGAGG
1 AGTCAACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG
* * * * *
471 TCTGCCAAATGGAAGAATATTCAAAAC-GGACTAACGGGCCCCGATAGGCCCAAAGTAACAAGTG
66 TCTGCCAAATCGAAGAAGATTCAAAACTGAACTAACGGGCCCCGATAAGCCCAAAATAACAAGTG
* *
535 TTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGC
131 TTCCAAATGAGCTAAAAACTTCACAATGAACTAATCTCACCAAAATGATTATAGTTAGGC
595 AATAAACAAT
Statistics
Matches: 170, Mismatches: 19, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
192 88 0.52
193 82 0.48
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.23
Consensus pattern (193 bp):
AGTCAACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG
TCTGCCAAATCGAAGAAGATTCAAAACTGAACTAACGGGCCCCGATAAGCCCAAAATAACAAGTG
TTCCAAATGAGCTAAAAACTTCACAATGAACTAATCTCACCAAAATGATTATAGTTAGGCCAT
Found at i:637 original size:347 final size:348
Alignment explanation
Indices: 1--753 Score: 1266
Period size: 347 Copynumber: 2.2 Consensus size: 348
*
1 ATGAGCTAAAAACTTCACAATCAACTAATCTCACCAAAATGATTATAGTTAGGCCATAGTCAACT
1 ATGAGCTAAAAACTTCACAATTAACTAATCTCACCAAAATGATTATAGTTAGGCCATAGTCAACT
*
66 AATCTCTCCAAAATGATTTATAGTTAGGCCTTAAACAATGGAAAGAAAAGCATTGAGGTTTGCCA
66 AATCTCTCCAAAATGATTTATAGTTAGGCCTTAAACAATGGAAAGAAAAGCATTGAGGTCTGCCA
*
131 AATGGAAGAATATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAATATAACAAGTGTTCCAAA
131 AATGGAAGAATATTCAAAACGGAACTAACGGGCCCCGATAGGCCCAATATAACAAGTGTTCCAAA
*
196 TGAGCTAAAAACTTTTAAGTCGACTAATCTCACCAAAATGATTATAGTTAGGGCATAAACAATGG
196 TGAGCTAAAAACTTTCAAGTCGACTAATCTCACCAAAATGATTATAGTTAGGGCATAAACAATGG
* * * *
261 AAAGAATAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAATC-TGAACTAATGGGCCCCGATA
261 AAAAAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGT-AACTAATGGGCCCCAATA
*
325 AGCCCAAAATAACAAGTGTTGCAA
325 AGCCCAAAATAACAAGTGTTCCAA
*
349 ATGAGCTAAAATCTTCACAATTAACTAATCTCACCAAAATGATTATAGTTAGGCCATAGTCAACT
1 ATGAGCTAAAAACTTCACAATTAACTAATCTCACCAAAATGATTATAGTTAGGCCATAGTCAACT
414 AATCTCTCCAAAATGA-TTATAGTTAGGCCTTAAACAATGGAAAGAAAAGCATTGAGGTCTGCCA
66 AATCTCTCCAAAATGATTTATAGTTAGGCCTTAAACAATGGAAAGAAAAGCATTGAGGTCTGCCA
478 AATGGAAGAATATTCAAAACGG-ACTAACGGGCCCCGATAGGCCCAA-AGTAACAAGTGTTCCAA
131 AATGGAAGAATATTCAAAACGGAACTAACGGGCCCCGATAGGCCCAATA-TAACAAGTGTTCCAA
*
541 ATGAGCTAAAAAC-TTCACAGTGGACTAATCTCACCAAAATGATTATAGTTA-GGCAATAAACAA
195 ATGAGCTAAAAACTTTCA-AGTCGACTAATCTCACCAAAATGATTATAGTTAGGGC-ATAAACAA
* *
604 TGGAAAAAAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCGCCA
258 TGG-AAAAAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTAACTAATGGGCCCCA
*
669 ATAGGCCCAAAATAACAAGTGTTCCAA
322 ATAAGCCCAAAATAACAAGTGTTCCAA
* * *
696 ATGAGCTAAAAACTTCACAGTTGACTAATCTCACCAAAATGATTATAGTTAGGTCATA
1 ATGAGCTAAAAACTTCACAATTAACTAATCTCACCAAAATGATTATAGTTAGGCCATA
754 AAGAATGGAA
Statistics
Matches: 382, Mismatches: 18, Indels: 11
0.93 0.04 0.03
Matches are distributed among these distances:
345 7 0.02
346 94 0.25
347 201 0.53
348 80 0.21
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.24
Consensus pattern (348 bp):
ATGAGCTAAAAACTTCACAATTAACTAATCTCACCAAAATGATTATAGTTAGGCCATAGTCAACT
AATCTCTCCAAAATGATTTATAGTTAGGCCTTAAACAATGGAAAGAAAAGCATTGAGGTCTGCCA
AATGGAAGAATATTCAAAACGGAACTAACGGGCCCCGATAGGCCCAATATAACAAGTGTTCCAAA
TGAGCTAAAAACTTTCAAGTCGACTAATCTCACCAAAATGATTATAGTTAGGGCATAAACAATGG
AAAAAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTAACTAATGGGCCCCAATAA
GCCCAAAATAACAAGTGTTCCAA
Found at i:707 original size:155 final size:152
Alignment explanation
Indices: 411--804 Score: 590
Period size: 155 Copynumber: 2.6 Consensus size: 152
401 GCCATAGTCA
* * * *
411 ACTAATCTCTCCAAAATGATTATAGTTAGGCCTTAAACAATGGAAAGAAAAGCATTGAGGTCTGC
1 ACTAATCTCACCAAAATGATTATAGTTAGG-CATAAACAATGGAAAAAAAAGCATTGAGGTTTGC
* ** * * *
476 CAAATGGAAGAATATTCAAAACGGACTAACGGGCCCCGATAGGCCCAAAGTAACAAGTGTTCCAA
65 CAAATCGAAGACGATTCAAAACGCACTAACGGGCCCCAATAGGCCCAAAATAACAAGTGTTCCAA
541 ATGAGCTAAAAACTTCACAGTGG
130 ATGAGCTAAAAACTTCACAGTGG
564 ACTAATCTCACCAAAATGATTATAGTTAGGCAATAAACAATGGAAAAAAAAAGCATTGAGGTTTG
1 ACTAATCTCACCAAAATGATTATAGTTAGGC-ATAAACAATGG-AAAAAAAAGCATTGAGGTTTG
* *
629 CCAAATCGAAGACGATTCAAAACGTCACTAATGGGCGCCAATAGGCCCAAAATAACAAGTGTTCC
64 CCAAATCGAAGACGATTCAAAACG-CACTAACGGGCCCCAATAGGCCCAAAATAACAAGTGTTCC
*
694 AAATGAGCTAAAAACTTCACAGTTG
128 AAATGAGCTAAAAACTTCACAGTGG
*
719 ACTAATCTCACCAAAATGATTATAGTTAGGTCATAAAGAATGGAAAAAAAAGCATTGAGGTTTCG
1 ACTAATCTCACCAAAATGATTATAGTTAGG-CATAAACAATGGAAAAAAAAGCATTGAGGTTT-G
* *
784 CCAAATCGATGACGATCCAAA
64 CCAAATCGAAGACGATTCAAA
805 TGAGCTAAAA
Statistics
Matches: 220, Mismatches: 16, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
152 1 0.00
153 39 0.18
154 60 0.27
155 119 0.54
156 1 0.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.22
Consensus pattern (152 bp):
ACTAATCTCACCAAAATGATTATAGTTAGGCATAAACAATGGAAAAAAAAGCATTGAGGTTTGCC
AAATCGAAGACGATTCAAAACGCACTAACGGGCCCCAATAGGCCCAAAATAACAAGTGTTCCAAA
TGAGCTAAAAACTTCACAGTGG
Found at i:889 original size:108 final size:107
Alignment explanation
Indices: 691--911 Score: 352
Period size: 108 Copynumber: 2.1 Consensus size: 107
681 TAACAAGTGT
* * *
691 TCCAAATGAGCTAAAAACTTCACAGTTGACTAATCTCACCAAAATGATTATAGTTAGGTCATAAA
1 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAGGATTATAGTTAGGCCATAAA
* * *
756 GAATGGAAAAAAAAGCATTGAGGTTTCGCCAAATCGATGACGA
66 CAATGGAAAAAAAAGAATTGAGGTTT-GCCAAATCGAAGACGA
799 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAGGATTATAGTTAGGCCATAAA
1 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAGGATTATAGTTAGGCCATAAA
* *
864 CAATGGAAAGAAAAGAATTGGGGTTTGCCAAATCGAAGACGA
66 CAATGGAAAAAAAAGAATTGAGGTTTGCCAAATCGAAGACGA
*
906 TTCAAA
1 TCCAAA
912 ACGTCACTAA
Statistics
Matches: 104, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
107 20 0.19
108 84 0.81
ACGTcount: A:0.42, C:0.17, G:0.19, T:0.23
Consensus pattern (107 bp):
TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAGGATTATAGTTAGGCCATAAA
CAATGGAAAAAAAAGAATTGAGGTTTGCCAAATCGAAGACGA
Found at i:1002 original size:262 final size:262
Alignment explanation
Indices: 536--1065 Score: 891
Period size: 262 Copynumber: 2.0 Consensus size: 262
526 TAACAAGTGT
*
536 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCAATAAA
1 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAGGATTATAGTTAGGCAATAAA
* *
601 CAATGGAAAAAAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCG
66 CAATGGAAAAAAAAAGAATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCC
* *
666 CCAATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTTGACTAATCTCACC
131 CCAATAGACCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACC
** * * * *
731 AAAATGATTATAGTTAGGTCATAAAGAATGGAAAAAAAAGCATTGAGGTTTCGCCAAATCGATGA
196 AAAATGATTATAAATAGGCCATAAACAATGGAAAAAAAAGCATTGAGGGTT-GCCAAATCGAAGA
796 CGA
260 CGA
*
799 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAGGATTATAGTTAGGCCATAAA
1 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAGGATTATAGTTAGGCAATAAA
* *
864 CAATGG-AAAGAAAAGAATTGGGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCC
66 CAATGGAAAAAAAAAGAATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCC
*
928 CCTATAGACCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACC
131 CCAATAGACCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACC
*
993 AAAATGATTATAAATAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGAC
196 AAAATGATTATAAATAGGCCATAAACAATGGAAAAAAAAGCATTGAGGGTTGCCAAATCGAAGAC
1058 GA
261 GA
*
1060 TTCAAA
1 TCCAAA
1066 ACAGAACTAA
Statistics
Matches: 250, Mismatches: 17, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
261 20 0.08
262 161 0.64
263 69 0.28
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.21
Consensus pattern (262 bp):
TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAGGATTATAGTTAGGCAATAAA
CAATGGAAAAAAAAAGAATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCC
CCAATAGACCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACC
AAAATGATTATAAATAGGCCATAAACAATGGAAAAAAAAGCATTGAGGGTTGCCAAATCGAAGAC
GA
Found at i:1094 original size:154 final size:153
Alignment explanation
Indices: 799--2647 Score: 2636
Period size: 154 Copynumber: 12.0 Consensus size: 153
789 TCGATGACGA
*
799 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAGGATTATAGTTAGGCCATAAA
1 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
* *
864 CAATGGAAAGAAAAGAATTGGGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCC
66 CAAT-GAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCC
* * *
929 CTATAGACCCAAAATAACAAGTGT
130 CGAAAGGCCCAAAATAACAAGTGT
**
953 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAAATAGGCCATAAA
1 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
* * *
1018 CAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACAG-AACTAATGGTCC
66 CAAT-GAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAC-GTCACTAATGGGCC
* *
1082 TCGAAACGCCCAAAATAACAAGTGT
129 CCGAAAGGCCCAAAATAACAAGTGT
1107 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
1 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
* * * *
1172 CAACTTAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCACTAATGGGACC
66 CAA-TGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCC
*
1237 CGATAGGCCCAAAAT-ACAAGTGT
130 CGAAAGGCCCAAAATAACAAGTGT
1260 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
1 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
*
1325 CAATGGAAAGAAAAGCATTTGTAGGTTTGCCAAATCGAAGTCGATTCAAAACGTCACTAAT-GGC
66 CAAT-GAAAGAAAAGCA-TTG-AGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGC
* * * *
1389 CCTGATAGGCCCAAGATAACAAATGT
128 CCCGAAAGGCCCAAAATAACAAGTGT
* * *
1415 TCCAAATAAGCTAAAAACTTCACAGTGGACTTATCTTACCAAAATGATTATAGTTAGGCCATAAA
1 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
* * * * * *
1480 CAACTTAAAGAGAAGCTTTGAGGTTTGCTAAATCGAAGACTATTCAAAACGTCATTAATGGGCCC
66 CAA-TGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCC
* * *
1545 CGATAGTCCCAAAATAAGAAGTGT
130 CGAAAGGCCCAAAATAACAAGTGT
* * * * *
1569 TCTAAATGAGCTAAAAACTTCACAGTGGACAAATCTAACCAAAATGATTATTGTGAGGCCATAAA
1 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
* * *
1634 CAATGGAAAGAAAAGCATTG-GGTTTTGCCAAATCGAAGATGATTCAAAACAG-AACTCATGGGC
66 CAAT-GAAAGAAAAGCATTGAGG-TTTGCCAAATCGAAGACGATTCAAAAC-GTCACTAATGGGC
1697 CCCGAAAGGCCCAAAATAACAAGTGT
128 CCCGAAAGGCCCAAAATAACAAGTGT
* *
1723 TCCAAAGGAGCTCAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATTATAGTTAGGCCAT
1 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATG---ATTATAGTTAGGCCAT
* * * * *
1788 AAACAATGGAAA-AAAAGCATTGGGGTTTGCCAAATTGACGACGATTCAAAACATAACTAATGGG
63 AAACAAT-GAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGG
1852 CCCCGAAAGGCCCAAAATAACAAGTGT
127 CCCCGAAAGGCCCAAAATAACAAGTGT
* * * *
1879 TCCAAATGAGTTAAAAACTTCCCAGTGGACTAATCTAACCAAAAGGATTATAGTTAGGCCATAAA
1 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
* * ** * *
1944 CTAATGAAAGAAAAGCATTGGGGTTTGCCAAATCGAAGGCGATTCAAAACGGAACGAATGTGCCC
66 C-AATGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCC
*
2009 CAAAAGGCCCAAAATAACAAGTGT
130 CGAAAGGCCCAAAATAACAAGTGT
* * *
2033 TCCAAATGAGCTAAAAACTTGAAAGTGGACTAATCTCACCAAAATGATTATAGTTGGGCCATAAA
1 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
* * * *
2098 CAACTTAGAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACAAATGGGCCC
66 CAA-TGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCC
*
2163 CGAAAGGCCCAAAATAACAAATGT
130 CGAAAGGCCCAAAATAACAAGTGT
* * *
2187 TCCAAATGAGGTAATAACTTCACAGTGGACTAATCTCACCAAAATTATTATAGTTAGGCCATAAA
1 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
*
2252 CAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGTCACTAATGGGCCC
66 CAAT-GAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCC
* * * *
2317 TGATAGG-CCAAGATAACAAATGT
130 CGAAAGGCCCAAAATAACAAGTGT
*
2340 TCCAAATAAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
1 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
* * * ** *
2405 CAACTTAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCAAAACAG-AACTAATGCTCT
66 CAA-TGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAC-GTCACTAATGGGCC
2469 CCGAAAGGCCCAAAATAACAAGTGT
129 CCGAAAGGCCCAAAATAACAAGTGT
* *
2494 TCCAAATGAGTTAAAAACTTCACAGTGGACTAATTTCACCAAAATGATTATAGTTAGGCCATAAA
1 TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
* *
2559 CAACT-TAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCC
66 CAA-TGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCC
* *
2623 CGATAGGCCCAAAATAACAAATGT
130 CGAAAGGCCCAAAATAACAAGTGT
2647 T
1 T
Statistics
Matches: 1520, Mismatches: 150, Indels: 51
0.88 0.09 0.03
Matches are distributed among these distances:
152 2 0.00
153 362 0.24
154 896 0.59
155 121 0.08
156 111 0.07
157 28 0.02
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (153 bp):
TCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
CAATGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCC
GAAAGGCCCAAAATAACAAGTGT
Found at i:1195 original size:416 final size:415
Alignment explanation
Indices: 411--1214 Score: 1258
Period size: 416 Copynumber: 1.9 Consensus size: 415
401 GCCATAGTCA
* * * *
411 ACTAATCTCTCCAAAATGATTATAGTTAGGCCTTAAACAATGGAAAGAAAAGCATTGAGGTCTGC
1 ACTAATCTCACCAAAAGGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGAATTGAGGTCTGC
* * * * *
476 CAAATGGAAGAATATTCAAAACGGACTAACGGGCCCCGATAGGCCCAAAGTAACAAGTGTTCCAA
66 CAAATCGAAGAAGATTCAAAACGCACTAACGGGCCCCGATAGACCCAAAATAACAAGTGTTCCAA
**
541 ATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCAATAAACAATG
131 ATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAAATAGGCAATAAACAATG
* *
606 GAAAAAAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCGCCAAT
196 GAAAAAAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGTAACTAATGGGCGCCAAT
* *
671 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTTGACTAATCTCACCAAAAT
261 ACGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT
* * *
736 GATTATAGTTAGGTCATAAAGAATGGAAAAAAAAGCATTGAGGTTTCGCCAAATCGATGACGATC
326 GATTATAGTTAGGCCATAAACAATGGAAAAAAAAGCATTGAGGTTT-GCCAAATCGAAGACGATC
801 CAAATGAGCTAAAAACTTCACAGTGG
390 CAAATGAGCTAAAAACTTCACAGTGG
* *
827 ACTAATCTCACCAAAAGGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGAATTGGGGTTTGC
1 ACTAATCTCACCAAAAGGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGAATTGAGGTCTGC
* * *
892 CAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCTATAGACCCAAAATAACAAGTGTTCCA
66 CAAATCGAAGAAGATTCAAAACG-CACTAACGGGCCCCGATAGACCCAAAATAACAAGTGTTCCA
*
957 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAAATAGGCCATAAACAAT
130 AATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAAATAGGCAATAAACAAT
* *
1022 GG-AAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACAG-AACTAATGGTC-CTC
195 GGAAAAAAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAAC-GTAACTAATGGGCGC-C
1084 GAA-ACGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCA
258 -AATACGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCA
* * *
1148 AAATGATTATAGTTAGGCCATAAACAACT-TAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGAC
322 AAATGATTATAGTTAGGCCATAAACAA-TGGAAAAAAAAGCATTGAGGTTTGCCAAATCGAAGAC
1212 GAT
386 GAT
1215 TCAATACGTC
Statistics
Matches: 354, Mismatches: 29, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
415 17 0.05
416 233 0.66
417 104 0.29
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.21
Consensus pattern (415 bp):
ACTAATCTCACCAAAAGGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGAATTGAGGTCTGC
CAAATCGAAGAAGATTCAAAACGCACTAACGGGCCCCGATAGACCCAAAATAACAAGTGTTCCAA
ATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAAATAGGCAATAAACAATG
GAAAAAAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGTAACTAATGGGCGCCAAT
ACGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT
GATTATAGTTAGGCCATAAACAATGGAAAAAAAAGCATTGAGGTTTGCCAAATCGAAGACGATCC
AAATGAGCTAAAAACTTCACAGTGG
Done.