Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011552.1 Corchorus olitorius cultivar O-4 contig11585, 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: 3226
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.24
Found at i:269 original size:21 final size:21
Alignment explanation
Indices: 245--286 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
235 ACATCTTAGG
245 CAACTCCGATGAGCTTGAAAC
1 CAACTCCGATGAGCTTGAAAC
*
266 CAACTCTGATGAGCTTGAAAC
1 CAACTCCGATGAGCTTGAAAC
287 TTCTTCCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.21
Consensus pattern (21 bp):
CAACTCCGATGAGCTTGAAAC
Found at i:682 original size:156 final size:156
Alignment explanation
Indices: 398--3226 Score: 4147
Period size: 156 Copynumber: 18.1 Consensus size: 156
388 GCGCATCACA
* *
398 AATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAAA-TTTACAATGGACTAATCTTACCAA
1 AATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAA-AAACTTCACAATGGACTAGTCTTACCAA
* *
462 AGTGATCATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACGA
65 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACGA
527 TTTTTAAAACCGAACTAATGGGCCCCG
130 TTTTTAAAACCGAACTAATGGGCCCCG
* * *
554 AATGGTCCAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCACAATGGACTAGTCTAACAAAA
1 AATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCACAATGGACTAGTCTTACCAAA
*
619 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGA-
66 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACGAT
* *
683 -TTCAAAACCGAACTAATGGACCCCG
131 TTTTAAAACCGAACTAATGGGCCCCG
* * *
708 AATGGCCCAAAATAACAAGTGTTCAAAATTAGCTAAGAACTTCACAATGGACTAATCTTACCAAA
1 AATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCACAATGGACTAGTCTTACCAAA
* * * * *
773 ATGATCATAGGTAGGCCATAAACAATGGAAAGAAAAGCATTATGGATTGCCAAATAGAAGACCAT
66 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACGAT
*
838 ATTTAAAACCGAACTAATGGGCCCCG
131 TTTTAAAACCGAACTAATGGGCCCCG
* * *
864 AATGGTCCAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCACAATGGACTAGTCTAACAAAA
1 AATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCACAATGGACTAGTCTTACCAAA
* *
929 ATGACTATAGTTAGGCCATAAACAATGAAAAGAAAAGCATTATGGTTTGCCAAATCGAAGATGAA
66 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAATCG-A-A-G--
*
994 ATCGAAGATGATTTTTAAAACCGAATTAATGGGCCCCG
126 A-C------GATTTTTAAAACCGAACTAATGGGCCCCG
* *
1032 AATGGTCCAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCACAATGGACTAGTCTAACCAAA
1 AATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCACAATGGACTAGTCTTACCAAA
* *
1097 ATGATTATAGTTAGGCCATAAATAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGAT
66 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACGAT
* *
1162 TTTTAAAACCGAAGTAATGGACCCCG
131 TTTTAAAACCGAACTAATGGGCCCCG
* * * *
1188 AATGGCCCAAAATAACAAGTGTTCAAAATTAGCTAAGAATTTCACAATGGACTAATCTTACCAAA
1 AATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCACAATGGACTAGTCTTACCAAA
* * *
1253 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAATCATTATGGATTGCCAAATAGAAGACGAT
66 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACGAT
*
1318 TTTTAAAACCGAACTAATGGGCCTCG
131 TTTTAAAACCGAACTAATGGGCCCCG
* * *
1344 AATGGTCCAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCACAATGGACTAGTCTAACAAAA
1 AATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCACAATGGACTAGTCTTACCAAA
* *
1409 ATGACTATAGTTAGGTCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACGAT
66 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACGAT
*
1474 TTTTAAAACCGAACGAATGGGCCCCG
131 TTTTAAAACCGAACTAATGGGCCCCG
* * * * *
1500 AATTGTCCAAAATAACAAGTGTTTAAAATGAGCTAAGAACTTCACAATGGACTAATCTTACCAAA
1 AATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCACAATGGACTAGTCTTACCAAA
* * *
1565 ATTACTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTCTGGTTTGCCAAATCGAAGACGA-
66 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACGAT
* * *
1629 -TTCAAAACCAAACTAATGGACCCCG
131 TTTTAAAACCGAACTAATGGGCCCCG
* *
1654 AACGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCACAATGGACTAATCTTACCAAA
1 AATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCACAATGGACTAGTCTTACCAAA
* * *
1719 ATGATTATAGTCAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACAAT
66 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACGAT
* * *
1784 TTTTCAAACCGAACTAAAGGGCCCTCT
131 TTTTAAAACCGAACTAATGGGCCC-CG
* * * * * * * *
1811 AATAGCTCAAAATAATAAGTGTTCAAAACGAGCTAAAAACGTCATAGTGGACTAATCTTACCAAA
1 AATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCACAATGGACTAGTCTTACCAAA
* *
1876 A-GAATTATAGTTAGGCCATAAACAATGGAAAGAAAAGAATTATGGTTTGCCAAATCGAAGACCA
66 ATG-ATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACGA
* *
1940 TTTTTAAAACAGAACTAACGGGCCCCG
130 TTTTTAAAACCGAACTAATGGGCCCCG
* ** * * * *
1967 AATGGTCCAAAACGACAGGTGTTCAAAACGAGCTAAGAACTTCACAACGGACTAGTCTTACCAAA
1 AATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCACAATGGACTAGTCTTACCAAA
* * * *
2032 ATGATTATTGTTAGGCCATAAACAATGGAGAGAAAAGCATTGTTGTTTGCCAAA-CTGAAGACGA
66 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAATC-GAAGACGA
* *
2096 TTTTTAAAACCTAACTAATGGGCCCCA
130 TTTTTAAAACCGAACTAATGGGCCCCG
* * * *
2123 AATGGCCCAAAATTACAAGTGTTCAAAATGAGCTAAGAACTTTACAATGGACTAATCTTACCAAA
1 AATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCACAATGGACTAGTCTTACCAAA
* * * *
2188 GTGATCATAGTTAGGCCATAAAGAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACTAT
66 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACGAT
2253 TTTTAAAACCGAACTAATGGGCCCCG
131 TTTTAAAACCGAACTAATGGGCCCCG
* * * *
2279 AATGGTCCAAAATAACAAGTGTTTAAAATGAGCTAAGAACTTCACAATGGACTAGTCTTACTAAA
1 AATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCACAATGGACTAGTCTTACCAAA
*
2344 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGA-
66 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACGAT
* *
2408 -TTCAAAACCGAACTAATGGACCCCG
131 TTTTAAAACCGAACTAATGGGCCCCG
* * * * *
2433 AACGGCCCAAAATAACAAGTCTTCAAACTGAGCTAAAAACTTCACAATGGACTAGTCTAACAAAA
1 AATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCACAATGGACTAGTCTTACCAAA
*
2498 ATGACTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACGAT
66 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACGAT
2563 TTTTAAAACCGAACTAATGGGCCCCG
131 TTTTAAAACCGAACTAATGGGCCCCG
* * * *
2589 AATGGTCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACACTGGACTAGTCTTACCGAA
1 AATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCACAATGGACTAGTCTTACCAAA
* * * * * *
2654 ATGATTATTGTTAGGCCATAAACAATGGAAAGAAATGCATTGTTGTTTACCAAACCGAAGACGA-
66 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACGAT
* *
2718 TTTT-AAACCAAACTAATGGACCCCG
131 TTTTAAAACCGAACTAATGGGCCCCG
* *
2743 AATGGCCCAAAATAACAAGTGTTCAAAATAAGCTAAGAACTTCACAATGGACTAGTCTTACCAAA
1 AATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCACAATGGACTAGTCTTACCAAA
2808 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACGAT
66 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACGAT
2873 TTTTAAAACCGAACTAATGGGCCCCGG
131 TTTTAAAACCGAACTAATGGGCCCC-G
* * * *
2900 AATGGTCCAAAATAACAAGGGTTCAAAATGAGCTAAAAACTTCACAATGGACTAGTCTAACAAAA
1 AATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCACAATGGACTAGTCTTACCAAA
*
2965 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGA-
66 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACGAT
* *
3029 -TTCAAAACCGAACTAATGGACCCCG
131 TTTTAAAACCGAACTAATGGGCCCCG
* *
3054 AATGGCCCAAAATAACAAGTGTTCAAAATAAGCTAAGAACTTCACAATGGACT-GATCTTACCAA
1 AATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCACAATGGACTAG-TCTTACCAA
* * *
3118 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAATGTTGTTTGCCAAATCGAAGACGA
65 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACGA
* * *
3183 TTTTTAAAAGCTAACTAATGGGCCTCG
130 TTTTTAAAACCGAACTAATGGGCCCCG
3210 AATGGCCCAAAATAACA
1 AATGGCCCAAAATAACA
Statistics
Matches: 2406, Mismatches: 237, Indels: 60
0.89 0.09 0.02
Matches are distributed among these distances:
153 1 0.00
154 680 0.28
155 34 0.01
156 1275 0.53
157 264 0.11
158 1 0.00
159 1 0.00
161 1 0.00
162 2 0.00
163 1 0.00
165 1 0.00
166 1 0.00
167 1 0.00
168 143 0.06
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.23
Consensus pattern (156 bp):
AATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCACAATGGACTAGTCTTACCAAA
ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACGAT
TTTTAAAACCGAACTAATGGGCCCCG
Found at i:963 original size:310 final size:311
Alignment explanation
Indices: 398--3226 Score: 4159
Period size: 310 Copynumber: 9.1 Consensus size: 311
388 GCGCATCACA
* * * *
398 AATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAAATTTACAATGGACTAATCTTACCAAA
1 AATGGTCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAGTCTTACCAAA
* * *
463 GTGATCATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACGAT
66 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGAT
* *
528 TTTTAAAACCGAACTAATGGGCCCCGAATGGTCCAAAATAACAAGTGTTCAAAATGAGCTAAAAA
131 TTTTAAAACCGAACTAATGGGCCCCGAATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAA
* *
593 CTTCACAATGGACTAGTCTAACAAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCA
196 CTTCACAATGGACTAGTCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCA
* * *
658 TTGTGGTTTGCCAAATCGAAGACGA-TTCAAAACCGAACTAATGGACCCCG
261 TTATGGTTTGCCAAATCGAAGACGATTTTAAAACCGAACTAATGGGCCCCG
* * *
708 AATGGCCCAAAATAACAAGTGTTCAAAATTAGCTAAGAACTTCACAATGGACTAATCTTACCAAA
1 AATGGTCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAGTCTTACCAAA
* * * * * *
773 ATGATCATAGGTAGGCCATAAACAATGGAAAGAAAAGCATTATGGATTGCCAAATAGAAGACCAT
66 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGAT
* * *
838 ATTTAAAACCGAACTAATGGGCCCCGAATGGTCCAAAATAACAAGTGTTCAAAATGAGCTAAAAA
131 TTTTAAAACCGAACTAATGGGCCCCGAATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAA
* * * *
903 CTTCACAATGGACTAGTCTAACAAAAATGACTATAGTTAGGCCATAAACAATGAAAAGAAAAGCA
196 CTTCACAATGGACTAGTCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCA
*
968 TTATGGTTTGCCAAATCGAAGATGAAATCGAAGATGATTTTTAAAACCGAATTAATGGGCCCCG
261 TTATGGTTTGCCAAATCG-A-A-G--A-C------GA-TTTTAAAACCGAACTAATGGGCCCCG
* *
1032 AATGGTCCAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCACAATGGACTAGTCTAACCAAA
1 AATGGTCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAGTCTTACCAAA
*
1097 ATGATTATAGTTAGGCCATAAATAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGAT
66 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGAT
* * *
1162 TTTTAAAACCGAAGTAATGGACCCCGAATGGCCCAAAATAACAAGTGTTCAAAATTAGCTAAGAA
131 TTTTAAAACCGAACTAATGGGCCCCGAATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAA
* * *
1227 TTTCACAATGGACTAATCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAATCA
196 CTTCACAATGGACTAGTCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCA
* * *
1292 TTATGGATTGCCAAATAGAAGACGATTTTTAAAACCGAACTAATGGGCCTCG
261 TTATGGTTTGCCAAATCGAAGACGA-TTTTAAAACCGAACTAATGGGCCCCG
* * *
1344 AATGGTCCAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCACAATGGACTAGTCTAACAAAA
1 AATGGTCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAGTCTTACCAAA
* * *
1409 ATGACTATAGTTAGGTCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACGAT
66 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGAT
* * * *
1474 TTTTAAAACCGAACGAATGGGCCCCGAATTGTCCAAAATAACAAGTGTTTAAAATGAGCTAAGAA
131 TTTTAAAACCGAACTAATGGGCCCCGAATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAA
* * *
1539 CTTCACAATGGACTAATCTTACCAAAATTACTATAGTTAGGCCATAAACAATGGAAAGAAAAGCA
196 CTTCACAATGGACTAGTCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCA
* * * *
1604 TTCTGGTTTGCCAAATCGAAGACGA-TTCAAAACCAAACTAATGGACCCCG
261 TTATGGTTTGCCAAATCGAAGACGATTTTAAAACCGAACTAATGGGCCCCG
* * * *
1654 AACGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCACAATGGACTAATCTTACCAAA
1 AATGGTCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAGTCTTACCAAA
* *
1719 ATGATTATAGTCAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACAAT
66 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGAT
* * * * * * * *
1784 TTTTCAAACCGAACTAAAGGGCCCTCTAATAGCTCAAAATAATAAGTGTTCAAAACGAGCTAAAA
131 TTTTAAAACCGAACTAATGGGCCC-CGAATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGA
* * * *
1849 ACGTCATAGTGGACTAATCTTACCAAAA-GAATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
195 ACTTCACAATGGACTAGTCTTACCAAAATG-ATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
* * * *
1913 AATTATGGTTTGCCAAATCGAAGACCATTTTTAAAACAGAACTAACGGGCCCCG
259 CATTATGGTTTGCCAAATCGAAGACGA-TTTTAAAACCGAACTAATGGGCCCCG
** * * *
1967 AATGGTCCAAAACGACAGGTGTTCAAAACGAGCTAAGAACTTCACAACGGACTAGTCTTACCAAA
1 AATGGTCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAGTCTTACCAAA
* * *
2032 ATGATTATTGTTAGGCCATAAACAATGGAGAGAAAAGCATTGTTGTTTGCCAAA-CTGAAGACGA
66 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATC-GAAGACGA
* * *
2096 TTTTTAAAACCTAACTAATGGGCCCCAAATGGCCCAAAATTACAAGTGTTCAAAATGAGCTAAGA
130 TTTTTAAAACCGAACTAATGGGCCCCGAATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGA
* * * * *
2161 ACTTTACAATGGACTAATCTTACCAAAGTGATCATAGTTAGGCCATAAAGAATGGAAAGAAAAGC
195 ACTTCACAATGGACTAGTCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC
*
2226 ATTATGGTTTGCCAAATCGAAGACTATTTTTAAAACCGAACTAATGGGCCCCG
260 ATTATGGTTTGCCAAATCGAAGACGA-TTTTAAAACCGAACTAATGGGCCCCG
* *
2279 AATGGTCCAAAATAACAAGTGTTTAAAATGAGCTAAGAACTTCACAATGGACTAGTCTTACTAAA
1 AATGGTCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAGTCTTACCAAA
2344 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGA-
66 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGAT
* * * * * *
2408 -TTCAAAACCGAACTAATGGACCCCGAACGGCCCAAAATAACAAGTCTTCAAACTGAGCTAAAAA
131 TTTTAAAACCGAACTAATGGGCCCCGAATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAA
* * *
2472 CTTCACAATGGACTAGTCTAACAAAAATGACTATAGTTAGGCCATAAACAATGGAAAGAAAAGCA
196 CTTCACAATGGACTAGTCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCA
2537 TTATGGTTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCG
261 TTATGGTTTGCCAAATCGAAGACGA-TTTTAAAACCGAACTAATGGGCCCCG
* *
2589 AATGGTCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACACTGGACTAGTCTTACCGAA
1 AATGGTCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAGTCTTACCAAA
* * * * *
2654 ATGATTATTGTTAGGCCATAAACAATGGAAAGAAATGCATTGTTGTTTACCAAACCGAAGACGA-
66 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGAT
* * *
2718 TTTT-AAACCAAACTAATGGACCCCGAATGGCCCAAAATAACAAGTGTTCAAAATAAGCTAAGAA
131 TTTTAAAACCGAACTAATGGGCCCCGAATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAA
2782 CTTCACAATGGACTAGTCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCA
196 CTTCACAATGGACTAGTCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCA
2847 TTATGGTTTGCCAAATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGG
261 TTATGGTTTGCCAAATCGAAGACGA-TTTTAAAACCGAACTAATGGGCCCC-G
* * * *
2900 AATGGTCCAAAATAACAAGGGTTCAAAATGAGCTAAAAACTTCACAATGGACTAGTCTAACAAAA
1 AATGGTCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAGTCTTACCAAA
2965 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGA-
66 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGAT
* * *
3029 -TTCAAAACCGAACTAATGGACCCCGAATGGCCCAAAATAACAAGTGTTCAAAATAAGCTAAGAA
131 TTTTAAAACCGAACTAATGGGCCCCGAATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAA
3093 CTTCACAATGGACT-GATCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC
196 CTTCACAATGGACTAG-TCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC
* * * * * *
3157 AATGTTGTTTGCCAAATCGAAGACGATTTTTAAAAGCTAACTAATGGGCCTCG
260 ATTATGGTTTGCCAAATCGAAGACGA-TTTTAAAACCGAACTAATGGGCCCCG
*
3210 AATGGCCCAAAATAACA
1 AATGGTCCAAAATAACA
Statistics
Matches: 2291, Mismatches: 203, Indels: 50
0.90 0.08 0.02
Matches are distributed among these distances:
310 898 0.39
311 403 0.18
312 550 0.24
313 158 0.07
315 1 0.00
316 1 0.00
318 1 0.00
319 1 0.00
321 1 0.00
322 3 0.00
323 1 0.00
324 273 0.12
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.23
Consensus pattern (311 bp):
AATGGTCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAGTCTTACCAAA
ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGAT
TTTTAAAACCGAACTAATGGGCCCCGAATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAA
CTTCACAATGGACTAGTCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCA
TTATGGTTTGCCAAATCGAAGACGATTTTAAAACCGAACTAATGGGCCCCG
Found at i:997 original size:12 final size:12
Alignment explanation
Indices: 980--1004 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
970 ATGGTTTGCC
980 AAATCGAAGATG
1 AAATCGAAGATG
992 AAATCGAAGATG
1 AAATCGAAGATG
1004 A
1 A
1005 TTTTTAAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.24, T:0.16
Consensus pattern (12 bp):
AAATCGAAGATG
Found at i:2155 original size:779 final size:775
Alignment explanation
Indices: 398--3226 Score: 4334
Period size: 779 Copynumber: 3.6 Consensus size: 775
388 GCGCATCACA
* *
398 AATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAAATTTACAATGGACTAATCTTACCAAA
1 AATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAATCTTACCAAA
* *
463 GTGATCATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACGAT
66 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACGAT
528 TTTTAAAACCGAACTAATGGGCCCCGAATGGTCCAAAATAACAAGTGTTCAAAATGAGCTAAAAA
131 TTTTAAAACCGAACTAATGGGCCCCGAATGGTCCAAAATAACAAGTGTTCAAAATGAGCTAAAAA
593 CTTCACAATGGACTAGTCTAACAAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCA
196 CTTCACAATGGACTAGTCTAACAAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCA
*
658 TTGTGGTTTGCCAAATCGAAGACGATTCAAAACCGAACTAATGGACCCCGAATGGCCCAAAATAA
261 TTATGGTTTGCCAAATCGAAGACGATTCAAAACCGAACTAATGGACCCCGAATGGCCCAAAATAA
* * *
723 CAAGTGTTCAAAATTAGCTAAGAACTTCACAATGGACTAATCTTACCAAAATGATCATAGGTAGG
326 CAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAATCTTACCAAAATGATTATAGTTAGG
* * * * *
788 CCATAAACAATGGAAAGAAAAGCATTATGGATTGCCAAATAGAAGACCATATTTAAAACCGAACT
391 CCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGA-C-GATTCAAAACCGAACT
* * *
853 AATGGGCCCCGAATGGTCCAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCACAATGGACTA
454 AATGGACCCCGAACGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCACAATGGACTA
*
918 GTCTAACAAAAATGACTATAGTTAGGCCATAAACAATGAAAAGAAAAGCATTATGGTTTGCCAAA
519 GTCTAACAAAAATGACTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAA
*
983 TCGAAGATGAAATCGAAGATGATTTTTAAAACCGAATTAATGGGCCCCGAATGGTCCAAAATAAC
584 TCG-A-A-G--A-C----A--ATTTTTAAAACCGAACTAATGGGCCCCGAATGGTCCAAAATAAC
*
1048 AAGTGTTCAAAATGAGCTAAAAACTTCACAATGGACTAGTCTAACCAAAATGATTATAGTTAGGC
637 AAGTGTTCAAAATGAGCTAAAAACTTCACAATGGACTAGTCTTACCAAAA-GATTATAGTTAGGC
* * *
1113 CATAAATAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGATTTTTAAAACCGAAGTA
701 CATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGATTTTTAAAACAGAACTA
1178 ATGGACCCCG
766 ATGGACCCCG
* *
1188 AATGGCCCAAAATAACAAGTGTTCAAAATTAGCTAAGAATTTCACAATGGACTAATCTTACCAAA
1 AATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAATCTTACCAAA
* * *
1253 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAATCATTATGGATTGCCAAATAGAAGACGAT
66 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACGAT
*
1318 TTTTAAAACCGAACTAATGGGCCTCGAATGGTCCAAAATAACAAGTGTTCAAAATGAGCTAAAAA
131 TTTTAAAACCGAACTAATGGGCCCCGAATGGTCCAAAATAACAAGTGTTCAAAATGAGCTAAAAA
* *
1383 CTTCACAATGGACTAGTCTAACAAAAATGACTATAGTTAGGTCATAAACAATGGAAAGAAAAGCA
196 CTTCACAATGGACTAGTCTAACAAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCA
* * * * *
1448 TTATGGTTTGCCAAATCGAAGACGATTTTTAAAACCGAACGAATGGGCCCCGAATTGTCCAAAAT
261 TTATGGTTTGCCAAATCGAAGACGA--TTCAAAACCGAACTAATGGACCCCGAATGGCCCAAAAT
* * *
1513 AACAAGTGTTTAAAATGAGCTAAGAACTTCACAATGGACTAATCTTACCAAAATTACTATAGTTA
324 AACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAATCTTACCAAAATGATTATAGTTA
* *
1578 GGCCATAAACAATGGAAAGAAAAGCATTCTGGTTTGCCAAATCGAAGACGATTCAAAACCAAACT
389 GGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGATTCAAAACCGAACT
1643 AATGGACCCCGAACGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCACAATGGACTA
454 AATGGACCCCGAACGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCACAATGGACTA
* * * * * *
1708 ATCTTACCAAAATGATTATAGTCAGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAA
519 GTCTAACAAAAATGACTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAA
* * * * *
1773 TCGAAGACAATTTTTCAAACCGAACTAAAGGGCCCTCTAATAG-CTCAAAATAATAAGTGTTCAA
584 TCGAAGACAATTTTTAAAACCGAACTAATGGGCCC-CGAATGGTC-CAAAATAACAAGTGTTCAA
* * * * *
1837 AACGAGCTAAAAACGTCATAGTGGACTAATCTTACCAAAAGAATTATAGTTAGGCCATAAACAAT
647 AATGAGCTAAAAACTTCACAATGGACTAGTCTTACCAAAAG-ATTATAGTTAGGCCATAAACAAT
* * * * *
1902 GGAAAGAAAAGAATTATGGTTTGCCAAATCGAAGACCATTTTTAAAACAGAACTAACGGGCCCCG
711 GGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGATTTTTAAAACAGAACTAATGGACCCCG
* ** * * * *
1967 AATGGTCCAAAACGACAGGTGTTCAAAACGAGCTAAGAACTTCACAACGGACTAGTCTTACCAAA
1 AATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAATCTTACCAAA
* * * *
2032 ATGATTATTGTTAGGCCATAAACAATGGAGAGAAAAGCATTGTTGTTTGCCAAA-CTGAAGACGA
66 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAATC-GAAGACGA
* * * * *
2096 TTTTTAAAACCTAACTAATGGGCCCCAAATGGCCCAAAATTACAAGTGTTCAAAATGAGCTAAGA
130 TTTTTAAAACCGAACTAATGGGCCCCGAATGGTCCAAAATAACAAGTGTTCAAAATGAGCTAAAA
* * * * * * *
2161 ACTTTACAATGGACTAATCTTACCAAAGTGATCATAGTTAGGCCATAAAGAATGGAAAGAAAAGC
195 ACTTCACAATGGACTAGTCTAACAAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC
* * * *
2226 ATTATGGTTTGCCAAATCGAAGACTATTTTTAAAACCGAACTAATGGGCCCCGAATGGTCCAAAA
260 ATTATGGTTTGCCAAATCGAAGACGA--TTCAAAACCGAACTAATGGACCCCGAATGGCCCAAAA
* * *
2291 TAACAAGTGTTTAAAATGAGCTAAGAACTTCACAATGGACTAGTCTTACTAAAATGATTATAGTT
323 TAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAATCTTACCAAAATGATTATAGTT
2356 AGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGATTCAAAACCGAAC
388 AGGCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGATTCAAAACCGAAC
* *
2421 TAATGGACCCCGAACGGCCCAAAATAACAAGTCTTCAAACTGAGCTAAAAACTTCACAATGGACT
453 TAATGGACCCCGAACGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCACAATGGACT
2486 AGTCTAACAAAAATGACTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAA
518 AGTCTAACAAAAATGACTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAA
*
2551 ATCGAAGACGATTTTTAAAACCGAACTAATGGGCCCCGAATGGTCCAAAATAACAAGTGTTCAAA
583 ATCGAAGACAATTTTTAAAACCGAACTAATGGGCCCCGAATGGTCCAAAATAACAAGTGTTCAAA
* * * *
2616 ATGAGCTAAGAACTTCACACTGGACTAGTCTTACCGAAATGATTATTGTTAGGCCATAAACAATG
648 ATGAGCTAAAAACTTCACAATGGACTAGTCTTACC-AAAAGATTATAGTTAGGCCATAAACAATG
* * * * *
2681 GAAAGAAATGCATTGTTGTTTACCAAACCGAAGACGA-TTTTAAACCA-AACTAATGGACCCCG
712 GAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGATTTTTAAAACAGAACTAATGGACCCCG
* *
2743 AATGGCCCAAAATAACAAGTGTTCAAAATAAGCTAAGAACTTCACAATGGACTAGTCTTACCAAA
1 AATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAATCTTACCAAA
2808 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACGAT
66 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACGAT
*
2873 TTTTAAAACCGAACTAATGGGCCCCGGAATGGTCCAAAATAACAAGGGTTCAAAATGAGCTAAAA
131 TTTTAAAACCGAACTAATGGGCCCC-GAATGGTCCAAAATAACAAGTGTTCAAAATGAGCTAAAA
2938 ACTTCACAATGGACTAGTCTAACAAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC
195 ACTTCACAATGGACTAGTCTAACAAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC
*
3003 ATTGTGGTTTGCCAAATCGAAGACGATTCAAAACCGAACTAATGGACCCCGAATGGCCCAAAATA
260 ATTATGGTTTGCCAAATCGAAGACGATTCAAAACCGAACTAATGGACCCCGAATGGCCCAAAATA
* *
3068 ACAAGTGTTCAAAATAAGCTAAGAACTTCACAATGGACTGATCTTACCAAAATGATTATAGTTAG
325 ACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAATCTTACCAAAATGATTATAGTTAG
* * * * *
3133 GCCATAAACAATGGAAAGAAAAGCAATGTTGTTTGCCAAATCGAAGACGATTTTTAAAAGCTAAC
390 GCCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGA--TTCAAAACCGAAC
* * *
3198 TAATGGGCCTCGAATGGCCCAAAATAACA
453 TAATGGACCCCGAACGGCCCAAAATAACA
Statistics
Matches: 1854, Mismatches: 173, Indels: 37
0.90 0.08 0.02
Matches are distributed among these distances:
775 144 0.08
776 154 0.08
777 162 0.09
778 131 0.07
779 710 0.38
780 1 0.00
784 1 0.00
785 1 0.00
787 1 0.00
788 1 0.00
789 1 0.00
790 409 0.22
791 1 0.00
792 137 0.07
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.23
Consensus pattern (775 bp):
AATGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAATCTTACCAAA
ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAATCGAAGACGAT
TTTTAAAACCGAACTAATGGGCCCCGAATGGTCCAAAATAACAAGTGTTCAAAATGAGCTAAAAA
CTTCACAATGGACTAGTCTAACAAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCA
TTATGGTTTGCCAAATCGAAGACGATTCAAAACCGAACTAATGGACCCCGAATGGCCCAAAATAA
CAAGTGTTCAAAATGAGCTAAGAACTTCACAATGGACTAATCTTACCAAAATGATTATAGTTAGG
CCATAAACAATGGAAAGAAAAGCATTGTGGTTTGCCAAATCGAAGACGATTCAAAACCGAACTAA
TGGACCCCGAACGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCACAATGGACTAGT
CTAACAAAAATGACTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTATGGTTTGCCAAATC
GAAGACAATTTTTAAAACCGAACTAATGGGCCCCGAATGGTCCAAAATAACAAGTGTTCAAAATG
AGCTAAAAACTTCACAATGGACTAGTCTTACCAAAAGATTATAGTTAGGCCATAAACAATGGAAA
GAAAAGCATTGTGGTTTGCCAAATCGAAGACGATTTTTAAAACAGAACTAATGGACCCCG
Done.