Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013548.1 Corchorus olitorius cultivar O-4 contig13581, 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: 40559
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Found at i:633 original size:154 final size:154
Alignment explanation
Indices: 1--3458 Score: 3510
Period size: 154 Copynumber: 22.1 Consensus size: 154
* * * * *
1 TATAGTTAGGCCATAAACAATGG-AAG-AAAGAAATGAGGATTGCCAAATCGAAGACCATTCAGA
1 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAA
** * *
64 ACGTCACTGATGGGCCCTCGATAGGCCCAAAATAACAGGTGTTCCAAATGAGCTAAAAACTTCAC
66 ACGGAACTAATGGGCCC-CGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCA-
* *
129 AA-TGGATTAATCTCACCAAAATGAT
129 AAGTGGACTAATCTTACCAAAATGAT
* * * *
154 TATAGTTAGGCCATAAACAATGGAAAGAAAAGAAATAAGGTTTGCCAAATCGAAGACGATTCAAA
1 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAA
** * * *
219 ACGTCACTAAT-GGCTCCGATGGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACA
66 ACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAA
* * *
283 GTGGACTAATCTCACCAACATTAT
131 GTGGACTAATCTTACCAAAATGAT
* * * *
307 TATAGTTAGGCTATAAACAATGGAAAGAAAAGAAATGAGGTTTGCC-AATCGAAGAACGATTCAA
1 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAG-ACGATTCAA
* * * * *
371 AATGTCAATTCATGGGCCCCGATAGGCCCAAAATAACAAGTGGTTCCAAATGTGCTAAAAAACTT
65 AACG-GAACTAATGGGCCCCGATAGGCCCAAAATAACAAGT-GTTCCAAATGAGCT-AAAAACTT
* *
436 CACAGTGGACTAATCTCACCAAAATGAT
127 CAAAGTGGACTAATCTTACCAAAATGAT
* * * *
464 TATAGTTAGGCCATAAATACTGGAAAGAAGAGCATTGATGGTTGCCAAATCGAAGACGATTCAAA
1 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAA
* * ** * **
529 ATGGAACTAGTGGGCCCCGATAGGCCCAAAATAACAAGTGTTTTAAATGAGTTAAAAACCACAAA
66 ACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAA
594 GTGGACTAATCTTACCAAAATGAT
131 GTGGACTAATCTTACCAAAATGAT
* * * * * **
618 TATAGTTAGGTCATAAACATTGGAAAGAAGTAGTATTGAGGGTTGCCAAATCGAACACGATAAAA
1 TATAGTTAGGCCATAAACAATGGAAAGAA-AAGCATTGAGGGTTGCCAAATCGAAGACGAT-TCA
* ** * *
683 AAACGGAACTAATAGGCCTTGATATGCCCAAAATTACAAGTGTTCCAAATGAGCTAAAAACTTCA
64 AAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCA
*
748 AAGTGAACTAATCTTACCAAAATGAT
129 AAGTGGACTAATCTTACCAAAATGAT
* * **
774 TATAGTTAGGTCATAAACATTGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATAAAAA
1 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAA
* * * *
839 ACGGAACTAATAGGCCTCGATATGCCCAAAATTACAAGTGTTCCAAATGAGCTAAAAACTTCAAA
66 ACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAA
904 GTGGACTAATCTTACCAAAATGAT
131 GTGGACTAATCTTACCAAAATGAT
* * *
928 TATAGTTAGGTCATAAACATTGGAAAGAAAAGCATTGAAGGTTGCCAAATCGAAGACGATTCAAA
1 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAA
*
993 ACGGAACTAATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAA
66 ACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAA
1058 GTGGACTAATCTTACCAAAATGAT
131 GTGGACTAATCTTACCAAAATGAT
* * *
1082 TATAGTTAGGCCATAAACAATAGAAAGAAAAGCATTAAGGGTTGCCAAACCGAACG-CGATTCAA
1 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAA-GACGATTC-A
* * *
1146 AAATGGAACTAATGGGCCTCGATAAGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCA
64 AAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCA
1211 AAGTGGACTAATCTTACCAAAATGAT
129 AAGTGGACTAATCTTACCAAAATGAT
* * *
1237 TATAGTTAGGTCATAATCATTGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAA
1 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAA
* * *
1302 ACGGAACTAATGGGCCCCGATAGGCCTAAAATAACAAGTGTTCCAAATGAACTAAAAACGTCACT
66 ACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCA--
** *
1367 AA-TGGAC--CCCGATAGGCCAAAAT-A-
129 AAGTGGACTAATC-TTA--CCAAAATGAT
* * * * * * ** * * *** * *
1391 AAAAGTGT-TGCAAATGAGCTAA---AAACTTCAAAGTGACT-AATCTTACCAAAAT-GATTATA
1 TATAGT-TAGGC-CATAAAC-AATGGAAA--GAAAAG-CATTGAGGGTTGCC-AAATCGA--AGA
* ** ** *** ** *
1450 -GTTAGGTCATAAACATTGGAAAGAA-AAGCATTGAGGTTTG-CC-AAAT--CGAAGACGATT-C
57 CG--A-TTCA-AAAC---GGAACTAATGGGCCCCGA--TAGGCCCAAAATAAC-AAG-TG-TTCC
** * ** * * * **** *
1508 AAAAAAAC--GGAAC-T-AATG-GGCCCCAATAGGCCCAAAAT-AA
110 AAATGAGCTAAAAACTTCAAAGTGG-ACTAATCTTACCAAAATGAT
* * * * **
1548 CA-AGGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATG-ATT-ATAGTTA
1 TATA-GTT----A-G-GCCATAAA---CA-A-TGG---AA----A-GAAAA-GCATTGAGGGTT-
*** * * * * **
1610 GGCCATAAAT--AATG--GAAAGAAAA--GCATTGATGGTTGCCAAATCGA-AGACGATTCAAAA
44 -GCC--AAATCGAA-GACGATTCAAAACGGAACTAATGG--GCC---CCGATAG--G-CCCAAAA
* ** * ** * *** *
1668 TGGAACTAGTGGGCCCCAAT-AGGCCCAAAA--TAACAAGTGTTTTAAATGAGTTAAAAACCACA
97 T--AACAAGT-GTTCCAAATGA-GCTAAAAACTTCA-AAGTGGACT-AAT--CTT----ACCA-A
*
1730 AAGTGGAC
149 AA-T-GAT
* * *
1738 TA-ATCTTA--CCAAAATGATTATAGTTAGGTCATAA-ACATTGGAAAGAAAAGCATTGAGGGTT
1 TATA-GTTAGGCCATAA--A-CA-A--T-GG--A-AAGA-A----------AAGCATTGAGGGTT
* * * * *
1799 GTCAAATCGAAGACGATTCAAAACAGAACTAATGGGCCTCGATATGCCCAAAATAAGAAGTGTTC
44 GCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTC
*
1864 CAAATGAGATAAAAACTTCAAAGTGGACTAATCTTACCAAAATGAT
109 CAAATGAGCTAAAAACTTCAAAGTGGACTAATCTTACCAAAATGAT
* * *
1910 TATAGTTAGGTCATAAACATTGGAAAGAAAAGCATTGAGGGTTGCCGAATCGAAGACGATTCAAA
1 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAA
* * *
1975 ACAGAACTAATGGGCCTCGATATGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAA
66 ACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAA
**
2040 GTTTACTAATCTTACCAAAATGAT
131 GTGGACTAATCTTACCAAAATGAT
* * * *
2064 TGTAGTTAGGTCATAAACATTGGAAAGTAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAA
1 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAA
*
2129 ACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACA
66 ACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAA
**
2194 GTGGACTAATCCCACCAAAATGAT
131 GTGGACTAATCTTACCAAAATGAT
* *
2218 TATAGTTAGGCCATATACAATGGAAAGAAAAGCATTGAGGGTTGACAAATCGAAGACGATTCAAA
1 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAA
* * *
2283 ACGTCAA-TAATGGGCCCCGATAGG-CCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCAC
66 ACG-GAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAA
* * * *
2346 AGTGGACTGATATCACTAAAATGAT
130 AGTGGACTAATCTTACCAAAATGAT
*
2371 TATAGTTAGGTCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAA
1 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAA
* * *
2436 ACGGAACTAATGGGCCACGATAGGCCCAAAATAACAAGTGTGCCAAATGAGCTAAAAACTTCACA
66 ACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAA
*
2501 GTGGACTAATCTCACCAAAATGAT
131 GTGGACTAATCTTACCAAAATGAT
2525 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAA
1 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAA
* * * * *
2590 ACGGAACTAATGGGCCCCGATAGGCCCAGAATAACAAGTGTGCCAAATGACCTAAAAATTTCACA
66 ACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAA
*
2655 GTGGACTAATCTCACCAAAATGAT
131 GTGGACTAATCTTACCAAAATGAT
* *
2679 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTTAG-CAAATTGAAGACGATTAA
1 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGG-TT-GCCAAATCGAAGACGATTCA
* *
2743 AAACGGAACTAATGGGCCCCGATATGCCCAAAATAACAAGTGTTCCAAATGAGCTAAACACTTCA
64 AAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCA
*
2808 CAA-TGGACTAATCTCACCAAAATGAT
129 -AAGTGGACTAATCTTACCAAAATGAT
*
2834 TATAGTTAGGCCATTAACAATGGAAAGAAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAA
1 TATAGTTAGGCCATAAACAATGGAAAG-AAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAA
* *
2899 AACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAG-GTTCCAAATGAGCTAAAAACTTGAC
65 AACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAA
*
2963 AGTGGACTAATCTCACCAAAATGAT
130 AGTGGACTAATCTTACCAAAATGAT
* * *
2988 TATAGTTAGGCCATAAATAATGGAAAGAAAAGCATTGATGGTTGCCAAATCGAAGATGATTCAAA
1 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAA
* * * * **
3053 ATGGAACTAATGGACCCCGATAGGCCCAAAATAACAAGTGTTTCAAATGAGTTAAAAACCACAAA
66 ACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAA
3118 GTGGACTAATCTTACCAAAATGAT
131 GTGGACTAATCTTACCAAAATGAT
* * *
3142 TATAGTTAGGTCATAAACATTGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAG
1 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAA
* * *
3207 ACGGAACTAATGGGCCTCGATAGGCCCAAAATAACAAGTGTTTCAAATGAGCTAAAAATTTCAAA
66 ACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAA
3272 GTGGACTAATCTTACCAAAATGAT
131 GTGGACTAATCTTACCAAAATGAT
* * *
3296 TATAGTTAGGTCATAAACATTGGAAAGAAAAGCATTGATGGTTGCCAAATCGAAGACGATTCAAA
1 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAA
* * *
3361 ACGGAACTAATGGGCCTCGATAGGCCCAAAATAAGAAGTGTTCCAAATGAGCTAAAAAGTTCAAA
66 ACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAA
3426 GTGGACTAATCTTACCAAAATGAT
131 GTGGACTAATCTTACCAAAATGAT
3450 TATAGTTAG
1 TATAGTTAG
3459 TGATACGAAT
Statistics
Matches: 2835, Mismatches: 321, Indels: 297
0.82 0.09 0.09
Matches are distributed among these distances:
152 11 0.00
153 360 0.13
154 1434 0.51
155 485 0.17
156 199 0.07
157 91 0.03
158 10 0.00
159 4 0.00
160 8 0.00
161 3 0.00
162 18 0.01
163 11 0.00
164 6 0.00
165 7 0.00
167 2 0.00
168 3 0.00
170 4 0.00
171 5 0.00
172 12 0.00
173 6 0.00
174 14 0.00
175 8 0.00
176 12 0.00
177 6 0.00
178 4 0.00
179 5 0.00
180 5 0.00
181 14 0.00
182 20 0.01
183 4 0.00
184 10 0.00
185 1 0.00
186 12 0.00
187 5 0.00
188 6 0.00
189 14 0.00
190 9 0.00
191 7 0.00
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.22
Consensus pattern (154 bp):
TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAA
ACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAA
GTGGACTAATCTTACCAAAATGAT
Found at i:1413 original size:56 final size:57
Alignment explanation
Indices: 1307--1416 Score: 177
Period size: 56 Copynumber: 1.9 Consensus size: 57
1297 TCAAAACGGA
* *
1307 ACTAATGGGCCCCGATAGGCCTAAAATAACAAGTGTTCCAAATGAACTAAAAACGTC
1 ACTAATGGACCCCGATAGGCCTAAAATAAAAAGTGTTCCAAATGAACTAAAAACGTC
* *
1364 ACTAATGGACCCCGATAGGCC-AAAATAAAAAGTGTTGCAAATGAGCTAAAAAC
1 ACTAATGGACCCCGATAGGCCTAAAATAAAAAGTGTTCCAAATGAACTAAAAAC
1417 TTCAAAGTGA
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
56 29 0.59
57 20 0.41
ACGTcount: A:0.43, C:0.21, G:0.18, T:0.18
Consensus pattern (57 bp):
ACTAATGGACCCCGATAGGCCTAAAATAAAAAGTGTTCCAAATGAACTAAAAACGTC
Found at i:1598 original size:209 final size:209
Alignment explanation
Indices: 1173--1576 Score: 659
Period size: 209 Copynumber: 1.9 Consensus size: 209
1163 CTCGATAAGC
*
1173 CCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTAATCTTACCAAAATGATT
1 CCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTAATCTTACCAAAATGATT
*
1238 ATAGTTAGGTCATAATCATTGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAA
66 ATAGTTAGGTCATAAACATTGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAA
* *
1303 CGGAACTAATGGGCCCCGATAGGCCTAAAATAACAAGTGTTCCAAATGAACTAAAAACGTCACTA
131 CGGAACTAATGGGCCCCAATAGGCCCAAAATAACAAGTGTTCCAAATGAACTAAAAACGTCACTA
* **
1368 ATGGACCCCGATAGG
196 ATGGA-CCCAATACA
*
1383 CCAAAATAAAAAGTGTTGCAAATGAGCTAAAAACTTCAAAGT-GACTAATCTTACCAAAATGATT
1 CCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTAATCTTACCAAAATGATT
*
1447 ATAGTTAGGTCATAAACATTGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAA
66 ATAGTTAGGTCATAAACATTGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTC---A
* *
1512 AAACGGAACTAATGGGCCCCAATAGGCCCAAAATAACAAG-GTTCCAAATGAGCTAAAAACTTCA
128 AAACGGAACTAATGGGCCCCAATAGGCCCAAAATAACAAGTGTTCCAAATGAACTAAAAACGTCA
1576 C
193 C
1577 AGTGGACTAA
Statistics
Matches: 183, Mismatches: 8, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
209 81 0.44
210 40 0.22
211 23 0.13
212 39 0.21
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.21
Consensus pattern (209 bp):
CCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTAATCTTACCAAAATGATT
ATAGTTAGGTCATAAACATTGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAA
CGGAACTAATGGGCCCCAATAGGCCCAAAATAACAAGTGTTCCAAATGAACTAAAAACGTCACTA
ATGGACCCAATACA
Found at i:2533 original size:461 final size:461
Alignment explanation
Indices: 1356--3458 Score: 3266
Period size: 461 Copynumber: 4.6 Consensus size: 461
1346 AAATGAACTA
* *
1356 AAAACGTC-ACTAATGGACCCCGATAGGCCAAAATAAAAAGTGTTGCAAATGAGCTAAAAACTTC
1 AAAACG-CAACTAATGGGCCCCGATAGGCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTC
1420 AAAGT-GACTAATCTTACCAAAATGATTATAGTTAGGTCATAAACATTGGAAAGAAAAGCATTGA
65 AAAGTGGACTAATCTTACCAAAATGATTATAGTTAGGTCATAAACATTGGAAAGAAAAGCATTGA
* *
1484 GGTTTGCCAAATCGAAGACGATTCAAAAAAACGGAACTAATGGGCCCCAATAGGCCCAAAATAAC
130 GGGTTGCCAAATCGAAGACGATTC---AAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAAC
1549 AAG-GTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGC
192 AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGC
* * * *
1613 CATAAATAATGGAAAGAAAAGCATTGATGGTTGCCAAATCGAAGACGATTCAAAATGGAACTAGT
257 CATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAAT
* ** *
1678 GGGCCCCAATAGGCCCAAAATAACAAGTGTTTTAAATGAGTTAAAAACCACAAAGTGGACTAATC
322 GGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACCACAAAGTGGACTAATC
* * * *
1743 TTACCAAAATGATTATAGTTAGGTCATAAACATTGGAAAGAAAAGCATTGAGGGTTGTCAAATCG
387 TCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGACAAATCG
1808 AAGACGATTC
452 AAGACGATTC
* * * *
1818 AAAACAG-AACTAATGGGCCTCGATATGCCCAAAATAAGAAGTGTTCCAAATGAGATAAAAACTT
1 AAAAC-GCAACTAATGGGCCCCGATA-GGCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTT
1882 CAAAGTGGACTAATCTTACCAAAATGATTATAGTTAGGTCATAAACATTGGAAAGAAAAGCATTG
64 CAAAGTGGACTAATCTTACCAAAATGATTATAGTTAGGTCATAAACATTGGAAAGAAAAGCATTG
* * * *
1947 AGGGTTGCCGAATCGAAGACGATTCAAAACAGAACTAATGGGCCTCGATATGCCCAAAATAACAA
129 AGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAA
* ** * * *
2012 GTGTTCCAAATGAGCTAAAAACTTCAAAGTTTACTAATCTTACCAAAATGATTGTAGTTAGGTCA
194 GTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCA
* *
2077 TAAACATTGGAAAGTAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGG
259 TAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGG
** * *
2142 GCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCCC
324 GCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACCACAAAGTGGACTAATCTC
*
2207 ACCAAAATGATTATAGTTAGGCCATATACAATGGAAAGAAAAGCATTGAGGGTTGACAAATCGAA
389 ACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGACAAATCGAA
2272 GACGATTC
454 GACGATTC
2280 AAAACGTCAA-TAATGGGCCCCGATAGGCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTC
1 AAAACG-CAACTAATGGGCCCCGATAGGCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTC
* * * * * *
2344 ACAGTGGACTGATATCACTAAAATGATTATAGTTAGGTCATAAACAATGGAAAGAAAAGCATTGA
65 AAAGTGGACTAATCTTACCAAAATGATTATAGTTAGGTCATAAACATTGGAAAGAAAAGCATTGA
*
2409 GGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCACGATAGGCCCAAAATAACAAG
130 GGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAG
*
2474 TGTGCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
195 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
2539 AAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGG
260 AAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGG
* * * *** *
2604 CCCCGATAGGCCCAGAATAACAAGTGTGCCAAATGACCTAAAAATTTCACAGTGGACTAATCTCA
325 CCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACCACAAAGTGGACTAATCTCA
* *
2669 CCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTTAGCAAATTGAA
390 CCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGA-CAAATCGAA
*
2734 GACGATTA
454 GACGATTC
* * * *
2742 AAAACGGAACTAATGGGCCCCGATATGCCCAAAATAACAAGTGTTCCAAATGAGCTAAACACTTC
1 AAAACGCAACTAATGGGCCCCGATA-GGCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTC
* * * *
2807 ACAA-TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATTAACAATGGAAAGAAAAAGCATT
65 A-AAGTGGACTAATCTTACCAAAATGATTATAGTTAGGTCATAAACATTGGAAAG-AAAAGCATT
2871 GAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACA
128 GAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACA
*
2936 AG-GTTCCAAATGAGCTAAAAACTTGACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCC
193 AGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCC
* * * *
3000 ATAAATAATGGAAAGAAAAGCATTGATGGTTGCCAAATCGAAGATGATTCAAAATGGAACTAATG
258 ATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATG
* * *
3065 GACCCCGATAGGCCCAAAATAACAAGTGTTTCAAATGAGTTAAAAACCACAAAGTGGACTAATCT
323 GGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACCACAAAGTGGACTAATCT
* * * *
3130 TACCAAAATGATTATAGTTAGGTCATAAACATTGGAAAGAAAAGCATTGAGGGTTGCCAAATCGA
388 CACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGACAAATCGA
3195 AGACGATTC
453 AGACGATTC
* * * * * *
3204 AAGACGGAACTAATGGGCCTCGATAGGCCCAAAATAACAAGTGTTTCAAATGAGCTAAAAATTTC
1 AAAACGCAACTAATGGGCCCCGATAGG-CCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTC
3269 AAAGTGGACTAATCTTACCAAAATGATTATAGTTAGGTCATAAACATTGGAAAGAAAAGCATTGA
65 AAAGTGGACTAATCTTACCAAAATGATTATAGTTAGGTCATAAACATTGGAAAGAAAAGCATTGA
* * *
3334 TGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCTCGATAGGCCCAAAATAAGAAG
130 GGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAG
* * *
3399 TGTTCCAAATGAGCTAAAAAGTTCAAAGTGGACTAATCTTACCAAAATGATTATAGTTAG
195 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAG
3459 TGATACGAAT
Statistics
Matches: 1506, Mismatches: 120, Indels: 30
0.91 0.07 0.02
Matches are distributed among these distances:
461 506 0.34
462 490 0.33
463 353 0.23
464 157 0.10
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (461 bp):
AAAACGCAACTAATGGGCCCCGATAGGCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCA
AAGTGGACTAATCTTACCAAAATGATTATAGTTAGGTCATAAACATTGGAAAGAAAAGCATTGAG
GGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGT
GTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATA
AACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGC
CCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACCACAAAGTGGACTAATCTCAC
CAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGACAAATCGAAGA
CGATTC
Found at i:4292 original size:21 final size:21
Alignment explanation
Indices: 4268--4315 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
4258 CTTAGGCAAT
4268 TCCAATGAGCTTGAAACCTT-C
1 TCCAATGAGCTTGAAA-CTTGC
*
4289 TCCAATGAGCTTGGAACTTGC
1 TCCAATGAGCTTGAAACTTGC
4310 TCCAAT
1 TCCAAT
4316 CATCTCCTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 3 0.12
21 22 0.88
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (21 bp):
TCCAATGAGCTTGAAACTTGC
Found at i:5173 original size:21 final size:21
Alignment explanation
Indices: 5149--5191 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
5139 AATTCCAGTA
*
5149 AGCTTGAAACCTT-CTCCAATG
1 AGCTCGAAA-CTTGCTCCAATG
*
5170 AGCTCGGAACTTGCTCCAATG
1 AGCTCGAAACTTGCTCCAATG
5191 A
1 A
5192 TCTCCTAGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.26
Consensus pattern (21 bp):
AGCTCGAAACTTGCTCCAATG
Found at i:6999 original size:33 final size:34
Alignment explanation
Indices: 6927--7024 Score: 105
Period size: 33 Copynumber: 2.9 Consensus size: 34
6917 CTATGACCAA
** *
6927 CTAAAACAGAA-TTGTTTTCATCACAATTAGCAGC
1 CTAAAACAGAATTTG-TTTCATCACAAACAACAGC
*
6961 C-AAAACAGAATTTGTTTCATCACAAACAATA-C
1 CTAAAACAGAATTTGTTTCATCACAAACAACAGC
*
6993 CTAAAACAG-ATTTAGTGTCATCACAAACAACA
1 CTAAAACAGAATTT-GTTTCATCACAAACAACA
7025 CTCAAATTAG
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
32 6 0.11
33 45 0.82
34 4 0.07
ACGTcount: A:0.44, C:0.21, G:0.09, T:0.26
Consensus pattern (34 bp):
CTAAAACAGAATTTGTTTCATCACAAACAACAGC
Found at i:7040 original size:33 final size:33
Alignment explanation
Indices: 6962--7066 Score: 97
Period size: 33 Copynumber: 3.2 Consensus size: 33
6952 ATTAGCAGCC
* *
6962 AAAACAGAATTT-GTTTCATCACAAACAATACCT
1 AAAACAG-ATTTAGTATCATCACAAACAACACCT
*
6995 AAAACAGATTTAGTGTCATCACAAACAACA-CT
1 AAAACAGATTTAGTATCATCACAAACAACACCT
** * ** *
7027 CAAATTAGGTTTAGTATCATTGCAAACAACATCT
1 -AAAACAGATTTAGTATCATCACAAACAACACCT
7061 AAAACA
1 AAAACA
7067 CTCTTTGCAA
Statistics
Matches: 59, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
32 6 0.10
33 51 0.86
34 2 0.03
ACGTcount: A:0.46, C:0.20, G:0.09, T:0.26
Consensus pattern (33 bp):
AAAACAGATTTAGTATCATCACAAACAACACCT
Found at i:10579 original size:32 final size:33
Alignment explanation
Indices: 10543--10607 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
10533 GGAGGAGCGA
*
10543 CGTCAT-GCGATGGCGCCCTGTTGGGGCGCCGT
1 CGTCATGGCGATGGCGCCCTGTTGGAGCGCCGT
*
10575 CGTCATGGCGATGGCGCCTTGTTGGAGCGCCGT
1 CGTCATGGCGATGGCGCCCTGTTGGAGCGCCGT
10608 AAATTTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 6 0.20
33 24 0.80
ACGTcount: A:0.08, C:0.29, G:0.40, T:0.23
Consensus pattern (33 bp):
CGTCATGGCGATGGCGCCCTGTTGGAGCGCCGT
Found at i:11086 original size:27 final size:27
Alignment explanation
Indices: 11023--11090 Score: 102
Period size: 27 Copynumber: 2.5 Consensus size: 27
11013 AAGGGATAAA
*
11023 GAGGCTGAGGCTGCTCGGATGTATAGG
1 GAGGCGGAGGCTGCTCGGATGTATAGG
*
11050 GAGGCTGAGGCTGCTCGGATGTATAGG
1 GAGGCGGAGGCTGCTCGGATGTATAGG
11077 GAGAG-GGAGGCTGC
1 GAG-GCGGAGGCTGC
11091 CGCTGGTGCT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
27 38 0.97
28 1 0.03
ACGTcount: A:0.19, C:0.15, G:0.47, T:0.19
Consensus pattern (27 bp):
GAGGCGGAGGCTGCTCGGATGTATAGG
Found at i:11089 original size:33 final size:27
Alignment explanation
Indices: 11023--11079 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
11013 AAGGGATAAA
11023 GAGGCTGAGGCTGCTCGGATGTATAGG
1 GAGGCTGAGGCTGCTCGGATGTATAGG
11050 GAGGCTGAGGCTGCTCGGATGTATAGG
1 GAGGCTGAGGCTGCTCGGATGTATAGG
11077 GAG
1 GAG
11080 AGGGAGGCTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.19, C:0.14, G:0.46, T:0.21
Consensus pattern (27 bp):
GAGGCTGAGGCTGCTCGGATGTATAGG
Found at i:14349 original size:33 final size:33
Alignment explanation
Indices: 14293--14399 Score: 101
Period size: 33 Copynumber: 3.2 Consensus size: 33
14283 CGCCCTCTAA
** * *
14293 GGGCGGCATC-CACATGGTGACGCCGCCCTCCTTG
1 GGGCGGCATCAC-CATGGCCACGCCGCCCACC-GG
* *
14327 GGG-GGCATGACCATGTCCACGCCGCCCACCGG
1 GGGCGGCATCACCATGGCCACGCCGCCCACCGG
* **
14359 GGGCGGCATCCCCATGGCCACGCCGCCCACCAA
1 GGGCGGCATCACCATGGCCACGCCGCCCACCGG
14392 GGGCGGCA
1 GGGCGGCA
14400 CCGACCATTT
Statistics
Matches: 60, Mismatches: 11, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
32 4 0.07
33 52 0.87
34 4 0.07
ACGTcount: A:0.15, C:0.41, G:0.34, T:0.10
Consensus pattern (33 bp):
GGGCGGCATCACCATGGCCACGCCGCCCACCGG
Found at i:22629 original size:18 final size:21
Alignment explanation
Indices: 22604--22658 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
22594 GCGTTTGTGG
*
22604 CTTCTTCTCGGCGTTTTGCCT
1 CTTCTTCTCGGCGTTTCGCCT
22625 CTTCTTCTCGGCGTTTCGCCT
1 CTTCTTCTCGGCGTTTCGCCT
*
22646 CTTCATCTCGGCG
1 CTTCTTCTCGGCG
22659 CACTAATTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.02, C:0.36, G:0.20, T:0.42
Consensus pattern (21 bp):
CTTCTTCTCGGCGTTTCGCCT
Found at i:28626 original size:12 final size:12
Alignment explanation
Indices: 28571--28626 Score: 55
Period size: 12 Copynumber: 4.9 Consensus size: 12
28561 CATGTCAAGC
* *
28571 AAAATTCAAAGA
1 AAAATTAAAATA
*
28583 AAAATTAAAGTA
1 AAAATTAAAATA
28595 AAAATT-AAA-A
1 AAAATTAAAATA
*
28605 ATAA-TAAAATA
1 AAAATTAAAATA
28616 AAAATTAAAAT
1 AAAATTAAAAT
28627 TAAACATGCA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
9 1 0.03
10 7 0.20
11 6 0.17
12 21 0.60
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.23
Consensus pattern (12 bp):
AAAATTAAAATA
Found at i:35118 original size:35 final size:36
Alignment explanation
Indices: 35071--35163 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 36
35061 GGAACTTTGA
* *
35071 AAAACTGAATGGGAACTTTCCC-AGTTT-GAAAACTT
1 AAAACTG-ATGGGAACTTTCCCAAATTTAAAAAACTT
*
35106 AAAAGCTGATGGGAATTTTCCCAAATTTAAAAAAAACTT
1 AAAA-CTGATGGGAACTTTCCCAAATTT--AAAAAACTT
*
35145 AAAACTGGTGGGAACTTTC
1 AAAACTGATGGGAACTTTC
35164 ACAATTAGAG
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
35 17 0.35
36 7 0.15
38 13 0.27
39 11 0.23
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (36 bp):
AAAACTGATGGGAACTTTCCCAAATTTAAAAAACTT
Found at i:35178 original size:39 final size:39
Alignment explanation
Indices: 35099--35183 Score: 102
Period size: 39 Copynumber: 2.2 Consensus size: 39
35089 TCCCAGTTTG
* * *
35099 AAAACTTAAAAGCTGATGGGAATTTTCCCAAATTTAAAA
1 AAAACTTAAAAGCTGATGGGAACTTTCACAAATTGAAAA
*
35138 AAAACTTAAAA-CTGGTGGGAACTTTCAC-AATTAGAGAAA
1 AAAACTTAAAAGCTGATGGGAACTTTCACAAATT-GA-AAA
35177 AAAACTT
1 AAAACTT
35184 GATGAAATTC
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
37 4 0.10
38 15 0.38
39 21 0.52
ACGTcount: A:0.47, C:0.13, G:0.14, T:0.26
Consensus pattern (39 bp):
AAAACTTAAAAGCTGATGGGAACTTTCACAAATTGAAAA
Found at i:35986 original size:18 final size:17
Alignment explanation
Indices: 35959--35995 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 17
35949 AAAAAATAGG
35959 AAGAAAAAAGAAAAAAA
1 AAGAAAAAAGAAAAAAA
35976 AAGAAAGAAAGAAAAAAA
1 AAGAAA-AAAGAAAAAAA
35994 AA
1 AA
35996 AAGCAACTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (17 bp):
AAGAAAAAAGAAAAAAA
Found at i:35997 original size:21 final size:21
Alignment explanation
Indices: 35948--35998 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
35938 TAATAATAAC
* *
35948 AAAAAAATAGGAAGAAAAAAG
1 AAAAAAAAAGAAAGAAAAAAG
*
35969 AAAAAAAAAGAAAGAAAGAA-
1 AAAAAAAAAGAAAGAAAAAAG
35989 AAAAAAAAAG
1 AAAAAAAAAG
35999 CAACTAGAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 10 0.37
21 17 0.63
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (21 bp):
AAAAAAAAAGAAAGAAAAAAG
Found at i:38686 original size:2 final size:2
Alignment explanation
Indices: 38679--38723 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
38669 CTGAAAGTAG
38679 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
38721 AC A
1 AC A
38724 TATATATATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:38728 original size:2 final size:2
Alignment explanation
Indices: 38723--38761 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
38713 ACACACACAC
38723 AT AT AT AT AT AT AT AT AT -T 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 AT AT AT AT
38762 CAACGTTAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Done.