Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007581.1 Kokia drynarioides strain JFW-HI SEQ_122211, 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: 2631
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Found at i:659 original size:216 final size:214
Alignment explanation
Indices: 2--1791 Score: 1353
Period size: 215 Copynumber: 8.4 Consensus size: 214
1 G
* ** *
2 TTCCTTAAAGTATTCAAGAGGATCGATTCCTTCGAGCAATTTTCTGAACATTCCATGCTCGGGAA
1 TTCCTTAAAGTATTCAAGATGATCGATTCCTTCGAGCAATTTTCCAAACATTCCA-GCTCGAGAA
* * * ***
67 ATTCCATCATTTGGACCAAATAGTTTGTCCTTTTGAAAAAAACTTTCAATCTTTGAATTAAAAAC
65 A-TGCATCATTTGGTCCAAATAGTTTGTCCTTTTGTAAAAAACTTTTGGTCTTTGAATTAAAAAC
* * ***
132 TTATTTACGTGAGAA-TGATTTCTCTCTTGGTTCTTGGCCGAATTTTTTAACTTTTCAAACTTTT
129 TTATTTATGTGAGAATTG-TTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTTTCAAACTTTT
*
196 TCGAGTTCCTTTATAACTTCGA
193 TCGAGTTCTTTTATAACTTCGA
* * * ** ** *
218 TTTCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTTAAACATTCCCTTCTCGGGAA
1 TTCCTTAAAGTATTCAAGATGATCGATTCCTTCGAGCAATTTTCCAAACATT-CCAGCTCGAGAA
* * * * * * *
283 ATCACATC-TTATGGTCCAAATAATATGTCATTTTGTAAAGAACTGTTGGTCTTTGGATTAAAAA
65 AT-GCATCATT-TGGTCCAAATAGTTTGTCCTTTTGTAAAAAACTTTTGGTCTTTGAATTAAAAA
* * * * * *
347 CTTATTTATTTGAGAATT-TTT-TCTCTTCGTTCTTGGCCAAACTTCCGAACTTGTGAAAATTTT
128 CTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTTTCAAACTTTT
*
410 TCTAGTTCTTTTATAACTTCGA
193 TCGAGTTCTTTTATAACTTCGA
* *
432 TTCCTTAAAGTAATCAAGATGATCGATTCCTCCCGA-CAATTTTCCAAACATTCCAGCCTCGAGA
1 TTCCTTAAAGTATTCAAGATGATCGATTCCT-TCGAGCAATTTTCCAAACATTCCAG-CTCGAGA
* * * * * * *
496 TATGACACCATTTGGTCCAAACAGTTTGTCCTTTTTTAAAAAACATTTGATCTTTGAATTAAAAG
64 AATG-CATCATTTGGTCCAAATAGTTTGTCCTTTTGTAAAAAACTTTTGGTCTTTGAATTAAAAA
* * * *
561 CTTATTTATGTAAGAATTGTTTCTCTCTTTGTTCTTGGCCGAACTTTCGAACTTTTTAAACTTTT
128 CTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTTTCAAACTTTT
*
626 TTGAGTTCTTTTATAACTTCGA
193 TCGAGTTCTTTTATAACTTCGA
* * * ** ** * ** *
648 TTCCTTAAAGTATTTAAGACGATCCATTATTTCGAATAATTTTTCGAAA-ATTCCATTATCGAAA
1 TTCCTTAAAGTATTCAAGATGATCGATTCCTTCGAGCAA-TTTTCCAAACATTCCA-GCTCGAGA
* * * * * * * *
712 AATCACATCATTTGGTCCAAAATAATCTGTCATTTTCTAAACAACTTTTGGTCATTGGATTAAAA
64 AAT-GCATCATTTGGTCC-AAATAGTTTGTCCTTTTGTAAAAAACTTTTGGTCTTTGAATTAAAA
* *
777 ACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAAATTTTCAAAATTT
127 ACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTTTCAAACTTT
* * * *
842 TTTGAGTTCTTTCACAACTTCGG
192 TTCGAGTTCTTTTATAACTTCGA
**** ** ** * * ** * * *
865 TTCCTTTCCTTCAAGCAATTTTTTGAAC-ATTCCATTATCGAG-AA-ATAGC-ATCATT--TGGT
1 TTCCTTAAAGT-ATTCAA---GATGATCGATTCC--T-TCGAGCAATTTTCCAAACATTCCAGCT
* * ** * * * * * * *** *
924 CCAAATAAAT-TTTCCTTTTGT--AAACAACTTTTAGT-CTTTGGATTAAAAAC--TAAAT-TAT
59 -C-GAGAAATGCATCATTTGGTCCAAA-TA-GTTT-GTCCTTTTG-TAAAAAACTTTTGGTCTTT
* * * * * * * **** ** * *
982 G---TGAGAA-TTGTTTCTCT----CTTGGTTCT-TGGACGAACTT--CCGAACTTGTCAAAC-T
118 GAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTT-CCGAACTT
*
1035 TT--------TTCGAGTTCTTTTAAAACTTCGA
182 TTCAAACTTTTTCGAGTTCTTTTATAACTTCGA
* * * *
1060 TTCCTTAAAGTATTCAAGAGGATCGATTCCTTCGAGCAATTTTCCTAACATTCGATGCTCGAAAA
1 TTCCTTAAAGTATTCAAGATGATCGATTCCTTCGAGCAATTTTCCAAACATTCCA-GCTCGAGAA
* * *
1125 ATCGCATCATTTGGTCAAAATAGTTTGTCCTTTTGTAACAAACTTTTGGTCTTTGAATTAAAAAA
65 AT-GCATCATTTGGTCCAAATAGTTTGTCCTTTTGTAAAAAACTTTTGGTCTTTGAATTAAAAAC
* *
1190 TTATTTACGTGAGAATGGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTTTCAAAC-TTTT
129 TTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTTTCAAACTTTTT
*
1254 CGAGTTCTTTTATAACTTCGT
194 CGAGTTCTTTTATAACTTCGA
* * * * * * * * *
1275 TTCCTTAAAGTAATAAAGATGATCCACTCCTTCGAGCAATTTTTCGAACATTACATTCTCGGGAA
1 TTCCTTAAAGTATTCAAGATGATCGATTCCTTCGAGCAATTTTCCAAACATTCCA-GCTCGAGAA
* * * * * * * *
1340 ATCGCATCTTTTGGTCTAAATAATCTGTCATTTTGTAAAGAAGTTTTGGTCTTTGGATTAAAAAC
65 AT-GCATCATTTGGTCCAAATAGTTTGTCCTTTTGTAAAAAACTTTTGGTCTTTGAATTAAAAAC
* **
1405 TTATTTATGTGAGAATTG-TTCGCTCTTGGTTCTTGGCCGAACTTCCGAACTTGACAAACTTTTT
129 TTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTTTCAAACTTTTT
* * *
1469 CGTGTTCTTTTATAACTCCGG
194 CGAGTTCTTTTATAACTTCGA
* * * * * *
1490 TTCTTTAAAGTATTCAAGAAGATCGATCCCTTCGAGCAATTTTTCAAACATTCTAGCCTCTAG-A
1 TTCCTTAAAGTATTCAAGATGATCGATTCCTTCGAGCAATTTTCCAAACATTCCAG-CTCGAGAA
* * *
1554 ATCGCACCATTTGGTCCAAATAGTTTGTCCTTTTGTAAAAAACTTTTGGCCTTTAAATTAAAAAC
65 AT-GCATCATTTGGTCCAAATAGTTTGTCCTTTTGTAAAAAACTTTTGGTCTTTGAATTAAAAAC
* **
1619 TTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCAAACTTTTGAACTTTTCAAACTTTTT
129 TTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTTTCAAACTTTTT
1684 CGAGTTCTTTTATAACTTCGA
194 CGAGTTCTTTTATAACTTCGA
* * * * *** ** * *
1705 TTCCTTAAAGTATTCAGGACGATTC-TTTCCTTGGAGCAATTTTTTGAACATTTGATTCTCGGGA
1 TTCCTTAAAGTATTCAAGATGA-TCGATTCCTTCGAGCAATTTTCCAAACATTCCA-GCTCGAGA
1769 AATTGCATCATTTGGTCCAAATA
64 AA-TGCATCATTTGGTCCAAATA
1792 ATCTGTTAGA
Statistics
Matches: 1214, Mismatches: 289, Indels: 142
0.74 0.18 0.09
Matches are distributed among these distances:
189 5 0.00
190 3 0.00
191 5 0.00
192 10 0.01
193 5 0.00
194 13 0.01
195 43 0.04
196 3 0.00
197 6 0.00
200 4 0.00
201 6 0.00
203 11 0.01
204 3 0.00
205 11 0.01
206 12 0.01
207 4 0.00
208 11 0.01
210 7 0.01
211 4 0.00
213 2 0.00
214 279 0.23
215 340 0.28
216 251 0.21
217 149 0.12
218 4 0.00
219 6 0.00
220 7 0.01
221 3 0.00
222 3 0.00
223 4 0.00
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (214 bp):
TTCCTTAAAGTATTCAAGATGATCGATTCCTTCGAGCAATTTTCCAAACATTCCAGCTCGAGAAA
TGCATCATTTGGTCCAAATAGTTTGTCCTTTTGTAAAAAACTTTTGGTCTTTGAATTAAAAACTT
ATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTTTCAAACTTTTTCG
AGTTCTTTTATAACTTCGA
Found at i:1018 original size:195 final size:196
Alignment explanation
Indices: 685--1065 Score: 561
Period size: 195 Copynumber: 1.9 Consensus size: 196
675 TATTTCGAAT
685 AATTTTTCGAAAATTCCATTATCGAAAAATCACATCATTTGGTCCAAAATAATCTGTCATTTTCT
1 AATTTTTCGAAAATTCCATTATCGAAAAATCACATCATTTGGTCCAAAATAATCTGTCATTTTCT
* * *
750 AAACAACTTTTGGTCATTGGATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTG
66 AAACAACTTTTAGTCATTGGATTAAAAACTAAATTATGTGAGAATTGTTTCTCTCTTGGTTCTTG
* * * * *
815 GCCGAACTTCCGAAATTTTCAAAATTTTTTGAGTTCTTTCACAACTTCGGTTCCTTTCCTTCAAG
131 GACGAACTTCCGAAATTGTCAAAATTTTTCGAGTTCTTTCAAAACTTCGATTCCTTTCCTTCAAG
880 C
196 C
* * * * *
881 AATTTTTTGAACATTCCATTATCGAGAAAT-AGCATCATTTGGTCC-AAATAAAT-TTTCCTTTT
1 AATTTTTCGAAAATTCCATTATCGAAAAATCA-CATCATTTGGTCCAAAAT-AATCTGTCATTTT
* *
943 GTAAACAACTTTTAGTCTTTGGATTAAAAACTAAATTATGTGAGAATTGTTTCTCTCTTGGTTCT
64 CTAAACAACTTTTAGTCATTGGATTAAAAACTAAATTATGTGAGAATTGTTTCTCTCTTGGTTCT
* * *
1008 TGGACGAACTTCCGAACTTGTCAAACTTTTTCGAGTTCTTTTAAAACTTCGATTCCTT
129 TGGACGAACTTCCGAAATTGTCAAAATTTTTCGAGTTCTTTCAAAACTTCGATTCCTT
1066 AAAGTATTCA
Statistics
Matches: 165, Mismatches: 18, Indels: 5
0.88 0.10 0.03
Matches are distributed among these distances:
195 122 0.74
196 43 0.26
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (196 bp):
AATTTTTCGAAAATTCCATTATCGAAAAATCACATCATTTGGTCCAAAATAATCTGTCATTTTCT
AAACAACTTTTAGTCATTGGATTAAAAACTAAATTATGTGAGAATTGTTTCTCTCTTGGTTCTTG
GACGAACTTCCGAAATTGTCAAAATTTTTCGAGTTCTTTCAAAACTTCGATTCCTTTCCTTCAAG
C
Found at i:1694 original size:430 final size:432
Alignment explanation
Indices: 2--2058 Score: 1983
Period size: 430 Copynumber: 4.9 Consensus size: 432
1 G
* * * *
2 TTCCTTAAAGTATTCAAGAGGATCGATTCCTTCGAGCAA-TTTTCTGAACATTCCATGCTCGGGA
1 TTCCTTAAAGTAATCAAGATGATCCATTCCTTCGAGCAATTTTTC-GAACATTCCATTCTCGGGA
* * * * *
66 AATTC-CATCATTTGGACCAAATAGTTTGTCCTTTTGAAAAAAACTTTCAATCTTTGAATTAAAA
65 AA-TCGCATCATTTGGTCCAAATAATCTGTCCTTTTGTAAAAAACTTTTAATCTTTGAATTAAAA
* * *** *
130 ACTTATTTACGTGAGAA-TGATTTCTCTCTTGGTTCTTGGCCGAATTTTTTAACTTTTCAAACTT
129 ACTTATTTATGTGAGAATTG-TTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTGTCAAACTT
* *
194 TTTCGAGTTCCTTTATAACTTCGATTTCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATT
193 TTTCGAGTTCTTTTATAACTTCGATTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATT
* ** ** * *
259 TTTTAAACATTCCCTTCTCGGGAAATCACATC-TTATGGTCCAAATAATATGTCATTTTGTAAAG
258 TTTCAAACATTCCAGTCTCGAAAAATCACATCATT-TGGTCCAAATAATTTGTCATTTTGTAAAA
* * * *
323 AACTGTTGGTCTTTGGATTAAAAACTTATTTATTTGAGAATT-TTT-TCTCTTCGTTCTTGGCCA
322 AACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCA
* * *
386 AACTTCCGAACTTGTGAAAATTTTTCTAGTTCTTTTATAACTTCGA
387 AACTTCCGAACTTTTCAAAATTTTTCGAGTTCTTTTATAACTTCGA
* * * * ** *
432 TTCCTTAAAGTAATCAAGATGATCGATTCCTCCCGA-CAATTTTCCAAACATTCCAGCCTCGAGA
1 TTCCTTAAAGTAATCAAGATGATCCATTCCT-TCGAGCAATTTTTCGAACATTCCATTCTCGGGA
* * * * * * * *
496 TAT-GACACCATTTGGTCCAAACAGTTTGTCCTTTTTTAAAAAACATTTGATCTTTGAATTAAAA
65 AATCG-CATCATTTGGTCCAAATAATCTGTCCTTTTGTAAAAAACTTTTAATCTTTGAATTAAAA
* * * * * *
560 GCTTATTTATGTAAGAATTGTTTCTCTCTTTGTTCTTGGCCGAACTTTCGAACTTTTTAAACTTT
129 ACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTGTCAAACTTT
* * ** **
625 TTTGAGTTCTTTTATAACTTCGATTCCTTAAAGTATTTAAGACGATCCATTATTTCGAATAATTT
194 TTCGAGTTCTTTTATAACTTCGATTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTT
* * * * *
690 TTCGAAA-ATTCCATTATCGAAAAATCACATCATTTGGTCCAAAATAATCTGTCATTTTCTAAAC
259 TTC-AAACATTCCAGTCTCGAAAAATCACATCATTTGGTCC-AAATAATTTGTCATTTTGTAAAA
* * *
754 AACTTTTGGTCATTGGATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCG
322 AACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCA
* *
819 AACTTCCGAAATTTTCAAAATTTTTTGAGTTC-----T---TTC-A
387 AACTTCCGAACTTTTCAAAATTTTTCGAGTTCTTTTATAACTTCGA
* * * * * * *
856 ---C---AACT--TC--G--GTTCCTTTCCTTCAAGCAATTTTTTGAACATTCCATTATCGAGAA
1 TTCCTTAAAGTAATCAAGATGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATTCTCGGGAA
* * * * *
909 ATAGCATCATTTGGTCCAAATAAAT-TTTCCTTTTGTAAACAACTTTTAGTCTTTGGATTAAAAA
66 ATCGCATCATTTGGTCCAAAT-AATCTGTCCTTTTGTAAAAAACTTTTAATCTTTGAATTAAAAA
* * *
973 CTAAATTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGACGAACTTCCGAACTTGTCAAACTTTT
130 CTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTGTCAAACTTTT
* * *
1038 TCGAGTTCTTTTAAAACTTCGATTCCTTAAAGTATTCAAGAGGATCGATTCCTTCGAGCAATTTT
195 TCGAGTTCTTTTATAACTTCGATTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTT
* * * * * * * *
1103 CCTAACATTCGA-TGCTCGAAAAATCGCATCATTTGGTCAAAATAGTTTGTCCTTTTGTAACAAA
260 TCAAACATTCCAGT-CTCGAAAAATCACATCATTTGGTCCAAATAATTTGTCATTTTGTAAAAAA
* * * *
1167 CTTTTGGTCTTTGAATTAAAAAATTATTTACGTGAGAATGGTTTCTCTCTTGGTTCTTGGCCGAA
324 CTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCAAA
* *
1232 CTTCCGAACTTTTC-AAACTTTTCGAGTTCTTTTATAACTTCGT
389 CTTCCGAACTTTTCAAAATTTTTCGAGTTCTTTTATAACTTCGA
* * *
1275 TTCCTTAAAGTAATAAAGATGATCCACTCCTTCGAGCAATTTTTCGAACATTACATTCTCGGGAA
1 TTCCTTAAAGTAATCAAGATGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATTCTCGGGAA
* * * * * ** *
1340 ATCGCATCTTTTGGTCTAAATAATCTGTCATTTTGTAAAGAAGTTTTGGTCTTTGGATTAAAAAC
66 ATCGCATCATTTGGTCCAAATAATCTGTCCTTTTGTAAAAAACTTTTAATCTTTGAATTAAAAAC
* *
1405 TTATTTATGTGAGAATTG-TTCGCTCTTGGTTCTTGGCCGAACTTCCGAACTTGACAAACTTTTT
131 TTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTGTCAAACTTTTT
* * * * * * *
1469 CGTGTTCTTTTATAACTCCGGTTCTTTAAAGTATTCAAGAAGATCGATCCCTTCGAGCAATTTTT
196 CGAGTTCTTTTATAACTTCGATTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTT
* * * * * * * *
1534 CAAACATTCTAGCCTC-TAGAATCGCACCATTTGGTCCAAATAGTTTGTCCTTTTGTAAAAAACT
261 CAAACATTCCAGTCTCGAAAAATCACATCATTTGGTCCAAATAATTTGTCATTTTGTAAAAAACT
* *
1598 TTTGGCCTTTAAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCAAACT
326 TTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCAAACT
** *
1663 TTTGAACTTTTCAAACTTTTTCGAGTTCTTTTATAACTTCGA
391 TCCGAACTTTTCAAAATTTTTCGAGTTCTTTTATAACTTCGA
* * * * * * * **
1705 TTCCTTAAAGTATTCAGGACGATTCTTTCCTTGGAGCAATTTTTTGAACATTTGATTCTCGGGAA
1 TTCCTTAAAGTAATCAAGATGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATTCTCGGGAA
*
1770 ATTGCATCATTTGGTCCAAATAA----T-C---TG----------TT-A-----G-ATTAAAAAC
66 ATCGCATCATTTGGTCCAAATAATCTGTCCTTTTGTAAAAAACTTTTAATCTTTGAATTAAAAAC
* * * ** * *
1810 TTATTTATGTGAGAATTATTTCTCTATTAGTTCTTAACCGAACTTCCAAACTTGTCAAACTTTTA
131 TTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTGTCAAACTTTTT
* * * * * * *
1875 CGAGTTCTTTTTTAACTTAGGTTCCTTAAAGTATTCAAGACCATCCATTCCGTCTAGTAA-TTTT
196 CGAGTTCTTTTATAACTTCGATTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTT
* * * * * * * * *
1939 CTGAACCTTTCA-TGCTGGAGAAATCGA-ATTATTTGGTCCAAATAGTTTGTCATTTCGTAAACA
261 C-AAACATTCCAGT-CTCGAAAAATC-ACATCATTTGGTCCAAATAATTTGTCATTTTGTAAAAA
* * * * * * *
2002 GCTTTTTGTCTTTGATTTAAAGACTTATTTACGTGTGAATTTTTTCTCT-TCTGGTTC
323 ACTTTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCT-TGGTTC
2059 CTTAAAGTAT
Statistics
Matches: 1358, Mismatches: 224, Indels: 113
0.80 0.13 0.07
Matches are distributed among these distances:
405 31 0.02
406 96 0.07
407 81 0.06
410 13 0.01
411 97 0.07
412 221 0.16
413 3 0.00
414 1 0.00
415 1 0.00
416 2 0.00
418 6 0.00
421 1 0.00
422 3 0.00
424 1 0.00
425 6 0.00
426 1 0.00
427 1 0.00
428 1 0.00
429 114 0.08
430 453 0.33
431 179 0.13
432 3 0.00
433 43 0.03
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (432 bp):
TTCCTTAAAGTAATCAAGATGATCCATTCCTTCGAGCAATTTTTCGAACATTCCATTCTCGGGAA
ATCGCATCATTTGGTCCAAATAATCTGTCCTTTTGTAAAAAACTTTTAATCTTTGAATTAAAAAC
TTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTCCGAACTTGTCAAACTTTTT
CGAGTTCTTTTATAACTTCGATTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTT
CAAACATTCCAGTCTCGAAAAATCACATCATTTGGTCCAAATAATTTGTCATTTTGTAAAAAACT
TTTGGTCTTTGAATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCAAACT
TCCGAACTTTTCAAAATTTTTCGAGTTCTTTTATAACTTCGA
Found at i:1975 original size:191 final size:191
Alignment explanation
Indices: 1610--1982 Score: 469
Period size: 191 Copynumber: 2.0 Consensus size: 191
1600 TGGCCTTTAA
* * * ** *** *
1610 ATTAAAAACTTATTTATGTGAGAATTGTTTCTCTCTTGGTTCTTGGCCAAACTTTTGAACTTTTC
1 ATTAAAAACTTATTTATGTGAGAATTATTTCTCTATTAGTTCTTAACCAAACTTCCAAACTTGTC
* * * * * * * *
1675 AAACTTTTTCGAGTTCTTTTATAACTTCGATTCCTTAAAGTATTCAGGACGATTCTTTCCTTGGA
66 AAACTTTTACGAGTTCTTTTATAACTTAGATTCCTTAAAGTATTCAAGACCATCCATTCCGTCGA
* * * * *
1740 GCAATTTTTTGAACATTTGATTCTCGGGAAATTGCATCATTTGGTCCAAATAATCTGTTAG
131 GCAATTTTCTGAACATTTCATGCTCGGGAAATCGAATCATTTGGTCCAAATAATCTGTTAG
*
1801 ATTAAAAACTTATTTATGTGAGAATTATTTCTCTATTAGTTCTTAACCGAACTTCCAAACTTGTC
1 ATTAAAAACTTATTTATGTGAGAATTATTTCTCTATTAGTTCTTAACCAAACTTCCAAACTTGTC
* * *
1866 AAACTTTTACGAGTTCTTTTTTAACTTAGGTTCCTTAAAGTATTCAAGACCATCCATTCCGTCTA
66 AAACTTTTACGAGTTCTTTTATAACTTAGATTCCTTAAAGTATTCAAGACCATCCATTCCGTCGA
* * *
1931 GTAATTTTCTGAACCTTTCATGCT-GGAGAAATCGAATTATTTGGTCCAAATA
131 GCAATTTTCTGAACATTTCATGCTCGG-GAAATCGAATCATTTGGTCCAAATA
1983 GTTTGTCATT
Statistics
Matches: 152, Mismatches: 29, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
190 2 0.01
191 150 0.99
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (191 bp):
ATTAAAAACTTATTTATGTGAGAATTATTTCTCTATTAGTTCTTAACCAAACTTCCAAACTTGTC
AAACTTTTACGAGTTCTTTTATAACTTAGATTCCTTAAAGTATTCAAGACCATCCATTCCGTCGA
GCAATTTTCTGAACATTTCATGCTCGGGAAATCGAATCATTTGGTCCAAATAATCTGTTAG
Found at i:2175 original size:160 final size:160
Alignment explanation
Indices: 1894--2190 Score: 362
Period size: 160 Copynumber: 1.9 Consensus size: 160
1884 TTTTAACTTA
* * * * *
1894 GGTTCCTTAAAGTATTCAAGACCATCCATTCCGTCTAGTAATTTTCTGAACCTTTCATGCTGGAG
1 GGTTCCTTAAAGTATTCAAGACCATCCATTCCGTCGAGCAATTTTCTGAACATTCCATGCTCGAG
* ** ** * * *
1959 AAATCGAATTATTTGGTCCAAATAGTTTGTCATTTCGTAAACAGCTTTTTGTCTTTGATTTAAAG
66 AAATCGAATCATTTAATCCAAATAGTTTGTCATTTCGTAAACAAATTTTAGTCTTTGAATTAAAA
2024 ACTTATTTACGTGTGAATTTTTTCTCTTCT
131 ACTTATTTACGTGTGAATTTTTTCTCTTCT
** * * *
2054 GGTTCCTTAAAGTATTCAAGATGATCCATTCCTTCGAGCAATTTTTTGAGCATTCCATGCTCGAG
1 GGTTCCTTAAAGTATTCAAGACCATCCATTCCGTCGAGCAATTTTCTGAACATTCCATGCTCGAG
* * * * * *
2119 AAATCGCATCATTTCAAT-GAAGTAGTTTGTTATTTTGTAAGCAAATTTTAGTCTTTGAATTAAA
66 AAATCGAATCATTT-AATCCAAATAGTTTGTCATTTCGTAAACAAATTTTAGTCTTTGAATTAAA
2183 AACTTATT
130 AACTTATT
2191 AACATTAGAA
Statistics
Matches: 112, Mismatches: 24, Indels: 2
0.81 0.17 0.01
Matches are distributed among these distances:
160 111 0.99
161 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.41
Consensus pattern (160 bp):
GGTTCCTTAAAGTATTCAAGACCATCCATTCCGTCGAGCAATTTTCTGAACATTCCATGCTCGAG
AAATCGAATCATTTAATCCAAATAGTTTGTCATTTCGTAAACAAATTTTAGTCTTTGAATTAAAA
ACTTATTTACGTGTGAATTTTTTCTCTTCT
Found at i:2433 original size:216 final size:207
Alignment explanation
Indices: 2056--2624 Score: 642
Period size: 216 Copynumber: 2.7 Consensus size: 207
2046 TCTCTTCTGG
* * * *
2056 TTCCTTAAAGTATTCAAGATGATCCATTCCTTCGAGCAATTTTTTGAGCATTCCATGCTCGAGAA
1 TTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCAAGCTCGAGAA
** * * * * *
2121 ATCGCATCATTTCAAT-GAAGTAGTTTGTTATTTTGTAAGCAAA-TTTTAGTCTTTGAATTAAAA
66 ATCGCATCATTT-GGTCCAAATAGTTTGTCATTTTGTAA-AAAACTTTTGGTCTTTGAATTAAAA
* * * * * * *
2184 ACTTATTAACATTAGAATTGTTTTTCTCTTGGTTCCTAGTC-GAACTTCCGAACTTTTCAAACTT
129 ACTTATTTACATGAGAATGGTTTCTCCCTTGGTT-CTAGACTGAACTTCCGAACTTGTCAAAC-T
2248 TTTCGAGTTCTATTATAGCTT
192 TTTCGAGTTCT-TT-TA---T
* * * * *
2269 CGATTCCTTATAGGATTCAAGACGATCCATTCCTTCGAGAAATTTTTCGAATATTCCAAGCTCGG
1 ---TTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCAAGCTCGA
* *
2334 GAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAAAAACTTTTGGTCCTAGAATTAAA
63 GAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAAAAACTTTTGGTCTTTGAATTAAA
* * *
2399 AACTTATTTACGTGAGAATGGTTTCTCCCTTGGTTCTTGACTGAACTTTCGAACTTGTCAAACTT
128 AACTTATTTACATGAGAATGGTTTCTCCCTTGGTTCTAGACTGAACTTCCGAACTTGTCAAACTT
2464 TTCGAGTTCTTTTAT
193 TTCGAGTTCTTTTAT
* * * * *
2479 TTGCTTAAAGTATTCAAGACGATCGATTCCTTCGAGCAATTTTCCAAACATT-CTAGCCTCGAGA
1 TTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCAAG-CTCGAGA
* * * * *
2543 AATCACACCATTTGGTCCAAATAGTTTGTCCTTTTGTAAAAAACTTTCGATCTTTGAATTAAAAA
65 AATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAAAAACTTTTGGTCTTTGAATTAAAAA
*
2608 CTTATTTATATGAGAAT
130 CTTATTTACATGAGAAT
2625 TATTTCT
Statistics
Matches: 302, Mismatches: 47, Indels: 17
0.83 0.13 0.05
Matches are distributed among these distances:
206 3 0.01
207 123 0.41
210 1 0.00
213 2 0.01
214 2 0.01
215 20 0.07
216 151 0.50
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (207 bp):
TTCCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTTTCGAACATTCCAAGCTCGAGAA
ATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAAAAACTTTTGGTCTTTGAATTAAAAAC
TTATTTACATGAGAATGGTTTCTCCCTTGGTTCTAGACTGAACTTCCGAACTTGTCAAACTTTTC
GAGTTCTTTTAT
Done.