Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001876.1 Kokia drynarioides strain JFW-HI SEQ_113645, 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: 18546
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.31
Warning! 91 characters in sequence are not A, C, G, or T
Found at i:2288 original size:17 final size:18
Alignment explanation
Indices: 2266--2317 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 18
2256 NNNNNNNNNN
2266 TTTTTTTTCAATTTCT-T
1 TTTTTTTTCAATTTCTAT
*
2283 TTTTTTTTCAATCTCATAT
1 TTTTTTTTCAATTTC-TAT
* *
2302 TTTTCTTTCATTTTCT
1 TTTTTTTTCAATTTCT
2318 CTCATTATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
17 14 0.48
18 2 0.07
19 13 0.45
ACGTcount: A:0.13, C:0.15, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTTTTTCAATTTCTAT
Found at i:4465 original size:217 final size:216
Alignment explanation
Indices: 3013--7122 Score: 4186
Period size: 216 Copynumber: 19.2 Consensus size: 216
3003 AGAATCGAGT
* * * *
3013 GAGAAACAATTCTCATGTAAATAAGTTTTTAATTCTAAGACAAAAAGTTGTTTACATAATGACAA
1 GAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAA
* * * * *
3078 ACTATTTAGACCAAACGATGTGATTTCTCGAGCATGGAATGTTCGGAAAATTGCTCGAAGGAATG
66 ACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTAGAAGGAATG
* * * * *
3143 GATCGCCTTGAATGCTTTAAGGAACCGAAGCTATAAAAGAACTCGTAAAACTTTGACAAGTTTGG
131 GATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGG
*
3208 AAGTTC-GTTCAAGAACCAAGA
196 AAGTTCAG-CCAAGAACCAAGA
*
3229 GAGAAACAATTCTCACGTGAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAA
1 GAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAA
* * * * * * * *
3294 ACTATTTAAACCAAACGATGTGATTTCCCAAGAATGGAATGTTCGTAAAATTGATAGAAGAAATG
66 ACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTAGAAGGAATG
* *
3359 GA-CAGTCTTGAATACTTTATGGAACCGAAGTTATAAAAGAACTCTTAAAAGTTTGACAAGTTC-
131 GATC-GTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCG
* * *
3422 ---G----GCCAAGAATCGAGT
195 GAAGTTCAGCCAAGAACCAAGA
* *
3437 GAAAAACAATTCTCACGTAAATAAGTTTTTAATTTAAAGACCAAAAGTTGTTTACAAAATG----
1 GAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAA
* * ** * * * * *
3498 AC-ATTTAGATCAAATTATGTAATTTCTCGATCATGGAATGTTC-ATAAAATTCCTCGAAAGAAT
66 ACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGA-AAAATTGCTAGAAGGAAT
* *
3561 GGATCGTCTTGAATACTTTATGGAACCGAAGTTATAAAAGAACTCTTAAAAGTTTGACAAGTTCG
130 GGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCG
* * *
3626 GAAGTTCGGCCAAGAACCGAGT
195 GAAGTTCAGCCAAGAACCAAGA
* * ** *
3648 GAGAAACAATTCTCACGTAAATAAGTTTTTAGTTCAAAGACCGAAAGTTGTTTATGAAATTACAA
1 GAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAA
* * * * *
3713 ATTATTTAGACCAAACGATGCGACTTCCCGA-CAATAGAATGTTCGAAAAATTGCTAGAAGAAAT
66 ACTATTTAGACCAAATGATGCGATTTCCCGAGC-ATGGAATGTTCGAAAAATTGCTAGAAGGAAT
* * * * *
3777 GGATAGTCTTGAATACTTTATGGAACCAAAGTTATAAAAGAACTCGTAAAAATTTGACAAGTTTG
130 GGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCG
*
3842 GAAGTTCGGCCAAGAACCAAGA
195 GAAGTTCAGCCAAGAACCAAGA
* * *
3864 GAGAAACAATTCTCACGTAAATAAGTTTTTAATTTAAAGACCAAAACTTGTTTACAAAATGAAAA
1 GAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAA
* * * * * * *
3929 ACTATTTAGACCTAATAATTCGATTTCCCGAGCCTTGAATGTTCAAAAAATTGCTAGAAGAAATG
66 ACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTAGAAGGAATG
* *
3994 GATCGTCTTGAATACTTTAAGTAACTGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGG
131 GATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGG
*
4059 AAATTC-GACCAAGAACCAAGA
196 AAGTTCAG-CCAAGAACCAAGA
* * * * * * *
4080 GAGAAACAA-TCACACATAAAAAAGATTTTAATTCAAAGACCATAAGTTGTTTACAAAATTATAA
1 GAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAA
* * * * * *
4144 A-TAATTTAGACCAAATGATGCGATTTCCCAAGCATCGAATGTTCGGAAAATTTCTCGAAAGAAT
66 ACT-ATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTAGAAGGAAT
* * * *
4208 GGATCGTCTTGAAAACTTTAAGGAGCCAAAGTTATAAAAGAACAT-GTAAAAGTTTGACAAGTTT
130 GGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAAC-TCGTAAAAGTTTGACAAGTTC
4272 GGAAGTTCAGCCAAGAACCAAGA
194 GGAAGTTCAGCCAAGAACCAAGA
* * *
4295 GAGAAATAATTCTCACGTAAATAAGTTTTTAATTCAACGACCAAAAGTTGTTTACAAAATGATAA
1 GAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGA-CA
* * * * *
4360 AACTTTTTAGACCAAATTATGCGATTTCCTGAGCATGGAATGTTCGTAAAATTGCTAGAAGGAAC
65 AACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTAGAAGGAAT
* * * * * * *
4425 GAATCATCTTGAATACTTAAAGGAACCGAAATTATAAAAGAATTCGTAAAAGTTCGACAAGTTTG
130 GGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCG
*
4490 GAAGTTCATCCAAGAACCAAGA
195 GAAGTTCAGCCAAGAACCAAGA
* * *
4512 GAGAAAAAATTCTTACGTAAATAAGTTTTTAAATCAAAGACCAAAAGTTGTTTACAAAATGACAA
1 GAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAA
* * * * * * *
4577 ACTATTTGGACTAAATGATGCGCTTTCCTGAGCATGGAATGTTCGGAAAATTACTCGAAGGAATG
66 ACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTAGAAGGAATG
* * * * *
4642 AATCATCTTGAATA-TTGTAAGGAACCGAAGTTATAAATGAACTCGTAAAAGTTTGACAAGTCCA
131 GATCGTCTTGAATACTT-TAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCG
* ** *
4706 AAAGTTCCTCCAAGAACCAATA
195 GAAGTTCAGCCAAGAACCAAGA
* * *
4728 GAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACAAAAAAGTTGCTTACAAGATGACA
1 GAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGAC-CAAAAGTTGTTTACAAAATGACA
* * * * * *
4793 AACTATTTAGACCAAATGATGCAATTTCGCAAGCATGAAATATTCGAAAAATTGCTTGAAGGAAT
65 AACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTAGAAGGAAT
** * *
4858 CTATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCATAAAAATTTGACAAGCTT-
130 GGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAG-TTC
* *
4922 GAAAGTAC-GTCCAAGAACCAAGA
194 GGAAGTTCAG-CCAAGAACCAAGA
** * * * * **
4945 GAGAAACAATTCTCTTGGAAATAAGCTTTTAGTTCAAAGACCGAAAGTTGTTTATGAAATGACAA
1 GAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAA
* * * * * * * *
5010 ACTATTTAGACTAAACGATGTGATTTCCTGAGAATAGAATGTTCGGAAAATTTCTAGAA-GAATG
66 ACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTAGAAGGAATG
* * *
5074 GATAGTCTTGAAAACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTTGG
131 GATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGG
* *
5139 ATGTTCAGCCAAGAACTAAGA
196 AAGTTCAGCCAAGAACCAAGA
* * * * * *
5160 GAGAAACAATTCACACCTAAATAAGTTTTTAATTTAAGGACCAAAACTTGTTTACAAAACGACAA
1 GAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAA
* * * * * * * **
5225 ACTATTTAGACCTAATAATTCGATTTCCCAAGCCTTGAATGTTCAAAAAATTGCTAGAATAAATG
66 ACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTAGAAGGAATG
* * * * * *
5290 GATCGTCTTGAATACTTTAAGTAACCGGAGTTACAAAAGAACTTGTAAAAGTTTGATAGGTTCGG
131 GATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGG
*
5355 AAGTTCGGCCAAGAACCAAGA
196 AAGTTCAGCCAAGAACCAAGA
* * * * * * * ** *
5376 GAGAAACAGTTCACACATAAAGAAGATTTTAATTCAAAGAAAATTACAAATAATTG-AGACCAAA
1 GAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAG---A--CCAAA-AGTTGTTTACAAAA
* ** ** * ** *** * * *
5440 TGATGCGATTTCCTAAGCATTGAATATTTGA-AAAATTTCTCGAAAGAATGG-ATCGTCTTGAAA
60 TGA--CAAACTATTTAG-A-CCAA-A--TGATGCGATTTCCCG--AGCATGGAAT-GT-TCGAAA
* ** ** * *
5503 ACTT--T--AAGGAA-CCAAAG--TT--ATA----AAAGAACACGTAAAAGTT-TGACAAG---T
114 AATTGCTAGAAGGAATGGATCGTCTTGAATACTTTAAGGAAC-CG---AAGTTAT-AAAAGAACT
* ** * * *
5551 -TTGGAAGTTT----AG--C-CAAGA----------ACTAAGA
174 CGTAAAAGTTTGACAAGTTCGGAAGTTCAGCCAAGAACCAAGA
* * * *
5576 GAGAAATAATTCTCACGTAAATAAGTTTTTAATTCAAAGACAAAAAATTGTTTTCAAAATGACAA
1 GAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAA
* * * *
5641 ACAATTTAGACCAAATGATGCGATTTCCCGAAGCATGGATTGTTCGTAAAATTGCTCGAAGGAAT
66 ACTATTTAGACCAAATGATGCGATTTCCCG-AGCATGGAATGTTCGAAAAATTGCTAGAAGGAAT
* * * * * *
5706 GGATCGTCTTGAATACTGTAAGTAACCAAAGTTATAAAAGAATTCGTAAAAGTTTGATAAGTTCA
130 GGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCG
*
5771 GAAATTC-GTCCAAGAACC-A-A
195 GAAGTTCAG-CCAAGAACCAAGA
* * *
5791 GAGAAACAATTCTTACGTAAATAAGTTTTTAATTCAAAGTCCAAAAGTTGTTTAGAAAATGACAA
1 GAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAA
* * * * *
5856 ACTATTTAGACCAAATGATGTGCTTTCCTGATCATGGAATGTTCGGAAAA-TGTCTCA-AAGGAA
66 ACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTG-CT-AGAAGGAA
* * * *
5919 TCGATCATCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTGACTAGTTC
129 TGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTC
* * *
5984 GGAAGTACATCCAAGAACCAAGG
194 GGAAGTTCAGCCAAGAACCAAGA
* * *
6007 GAGAAACAATTCTCATGTAAATAAGTTTTTAATTTATAGACCAAAAGTTGTTTACAAAATGACAA
1 GAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAA
* * * * * * *
6072 ACTATTTAGACCAAACGATGCGATTCCCCGAGAATAGAATGTGC-AGAAAATTGATAGAAGAAAT
66 ACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGA-AAAATTGCTAGAAGGAAT
* * * ** * * * *
6136 GGATAGTCTTGAATACTTCATGGAATTGAAGTTATAATAGAACTCATAAAAGTTTGAAAAGTTTG
130 GGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCG
* * *
6201 AAAGTTCGGCCGAGAACCAAGA
195 GAAGTTCAGCCAAGAACCAAGA
6223 GAGAAACAATTCTCACGTAAATAAGTTTTTAA-T---AGACCAAAAGTTGTTTACAAAATGACAA
1 GAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAA
* * * * * * * *
6284 ACTATTTAGACCTAATAATTCGATTACCTGAGCCTTGAATGTTCGAAAAATTGCTAGAAGAAATG
66 ACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTAGAAGGAATG
* * * * *
6349 GATCGTCATGAATACTATAAGTAACCAAAGTTATAAAAGAACTCGTAAAAGTTTGGCAAGTTCGG
131 GATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGG
* **
6414 AAGTGCATACAAGAACCAAGA
196 AAGTTCAGCCAAGAACCAAGA
* * * * * **
6435 GAGAAATAATTCTCATGTAAATAAGTTTTTAGCTT-AAAGACCGAAAGTTTTTTATGAAATGACA
1 GAGAAACAATTCTCACGTAAATAAGTTTTTA-ATTCAAAGACCAAAAGTTGTTTACAAAATGACA
** * * * *
6499 AACTATTTAGACCAAATGATATGATTTCCCAAGCATTGAATGTTCGAAAAATTTCTTGGAA-GAA
65 AACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGC-TAGAAGGAA
* * * * * * *
6563 TGGATCGTTTTGAAAACTTTAAGGAACCAAAGTTATAAAAGAACACATAAAAGCTTGACAAGTTT
129 TGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTC
** * * *
6628 GGAACCTCAACCAAGAGCTAAGA
194 GGAAGTTCAGCCAAGAACCAAGA
* *
6651 GAGAAACAATTATCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGATAA
1 GAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAA
* * * * *
6716 AGCTTTTTAGACCAAATTATGCGATATCCCGAGCATGGAATGTTC-ATAAAGTTGCTCGAAGGAA
66 A-CTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGA-AAAATTGCTAGAAGGAA
* * * *
6780 TGGATCTTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACACGTAAAAGTTTAACAAGTCC
129 TGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTC
* ** *
6845 AGAAGTTCCTCCAAGAACTAAGA
194 GGAAGTTCAGCCAAGAACCAAGA
*
6868 GAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACAAAAAGTTGTTTACAAAATGACAA
1 GAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAA
* * * *
6933 ACTA-TTAGACCAAATGATGCTATTTCCCGAGCCTTGG-ATGTTCAAAAAATTGCTAGAAGAAAT
66 ACTATTTAGACCAAATGATGCGATTTCCCGAG-CATGGAATGTTCGAAAAATTGCTAGAAGGAAT
*
6996 GGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCA
130 GGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCG
*
7061 GAAG--CAAGTCTAAGAACCAAGA
195 GAAGTTC-AG-CCAAGAACCAAGA
* * * *
7083 GAGAAATAATTCTCATGTAAATAAGTTTTTAGTTTAAAGA
1 GAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGA
7123 ACTCGCATTG
Statistics
Matches: 3211, Mismatches: 566, Indels: 235
0.80 0.14 0.06
Matches are distributed among these distances:
187 7 0.00
188 12 0.00
189 9 0.00
190 1 0.00
191 8 0.00
192 3 0.00
193 5 0.00
194 7 0.00
195 10 0.00
196 12 0.00
197 2 0.00
199 2 0.00
200 51 0.02
203 107 0.03
204 5 0.00
206 1 0.00
207 3 0.00
208 67 0.02
209 1 0.00
210 3 0.00
211 68 0.02
212 176 0.05
213 5 0.00
214 101 0.03
215 605 0.19
216 1296 0.40
217 569 0.18
218 7 0.00
219 1 0.00
221 22 0.01
222 4 0.00
223 8 0.00
224 1 0.00
225 3 0.00
226 5 0.00
227 6 0.00
228 5 0.00
229 6 0.00
230 7 0.00
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (216 bp):
GAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAA
ACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTAGAAGGAATG
GATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGG
AAGTTCAGCCAAGAACCAAGA
Found at i:4553 original size:648 final size:648
Alignment explanation
Indices: 3013--7122 Score: 4697
Period size: 648 Copynumber: 6.4 Consensus size: 648
3003 AGAATCGAGT
* * * *
3013 GAGAAACAATTCTCATGTAAATAAGTTTTTAATTCTAAGACAAAAAGTTGTTTACATAATGACAA
1 GAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAA
* * * *
3078 ACTATTTAGACCAAACGATGTGATTT-CTCGAGCATGGAATGTTCGGAAAATTGCTCGAAGGAAT
66 ACTATTTAGACCAAATGATGCGATTTCCT-GAGCATGGAATGTTCGAAAAATTGCTAGAAGGAAT
* * ** *
3142 GGATCGCCTTGAATGCTTTAAGGAACCGAAGCTATAAAAGAACTCGTAAAACTTTGACAAGTTTG
130 GGATCGTCTTGAATACTTTAAGGAACCGAAATTATAAAAGAACTCGTAAAAGTTTGACAAGTTTG
* * *
3207 GAAGTTCGTTCAAGAACCAAGAGAGAAACAATTCTCACGTGAATAAGTTTTTAATTCAAAGACCA
195 GAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCA
* * *
3272 AAAGTTGTTTACAAAATGACAAACTATTTAAACCAAACGATGTGATTTCCCAAGAATGGAATGTT
260 AAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGTGATTTCCCAAGCATGGAATGTT
* * *
3337 CGTAAAATTGATAGAAGAAATGGA-CAGTCTTGAATACTTTATGGAACCGAAGTTATAAAAGAAC
325 CGAAAAATTGCTAGAAGAAATGGATC-GTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAAC
* * * * * *
3401 TCTTAAAAGTTTGACAAGTTC-G------G-CCAAGAATCGAGTGAAAAACAATTCTCACGTAAA
389 TCGTAAAAGTTTGACAAGTTCGGAAATTCGACCAAGAACCAAGAGAGAAACAATTCACACGTAAA
* * * *
3458 TAAGTTTTTAATTTAAAGACCAAAAGTTGTTTACAAAATG----AC-ATTTAGATCAAATTATGT
454 TAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGATAAACTATTTAGACCAAATGATGC
* * * * * * *
3518 AATTTCTCGATCATGGAATGTTCATAAAATTCCTCGAAAGAATGGATCGTCTTGAATACTTTATG
519 GATTTCCCAAGCATGGAATGTTCAAAAAATTGCTCGAAAGAATGGATCGTCTTGAATACTTTAAG
* * * * *
3583 GAACCGAAGTTATAAAAGAACTCTTAAAAGTTTGACAAGTTCGGAAGTTCGGCCAAGAACCGAGT
584 GAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTTGGAAGTTCAGCCAAGAACCAAGA
* * ** *
3648 GAGAAACAATTCTCACGTAAATAAGTTTTTAGTTCAAAGACCGAAAGTTGTTTATGAAATTACAA
1 GAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAA
* * * * * *
3713 ATTATTTAGACCAAACGATGCGACTTCCCGA-CAATAGAATGTTCGAAAAATTGCTAGAAGAAAT
66 ACTATTTAGACCAAATGATGCGATTTCCTGAGC-ATGGAATGTTCGAAAAATTGCTAGAAGGAAT
* * *
3777 GGATAGTCTTGAATACTTTATGGAACC-AAAGTTATAAAAGAACTCGTAAAAATTTGACAAGTTT
130 GGATCGTCTTGAATACTTTAAGGAACCGAAA-TTATAAAAGAACTCGTAAAAGTTTGACAAGTTT
** *
3841 GGAAGTTCGGCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTTAAAGACC
194 GGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACC
* * * * * * *
3906 AAAACTTGTTTACAAAATGAAAAACTATTTAGACCTAATAAT-TCGATTTCCCGAGCCTTGAATG
259 AAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGT-GATTTCCCAAGCATGGAATG
* * *
3970 TTCAAAAAATTGCTAGAAGAAATGGATCGTCTTGAATACTTTAAGTAACTGAAGTTATAAAAGAA
323 TTCGAAAAATTGCTAGAAGAAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAA
*
4035 CTCGTAAAAGTTTGACAAGTTCGGAAATTCGACCAAGAACCAAGAGAGAAACAA-TCACACATAA
388 CTCGTAAAAGTTTGACAAGTTCGGAAATTCGACCAAGAACCAAGAGAGAAACAATTCACACGTAA
* * * *
4099 AAAAGATTTTAATTCAAAGACCATAAGTTGTTTACAAAATTATAAA-TAATTTAGACCAAATGAT
453 ATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGATAAACT-ATTTAGACCAAATGAT
* ** * *
4163 GCGATTTCCCAAGCATCGAATGTTCGGAAAATTTCTCGAAAGAATGGATCGTCTTGAAAACTTTA
517 GCGATTTCCCAAGCATGGAATGTTCAAAAAATTGCTCGAAAGAATGGATCGTCTTGAATACTTTA
* *
4228 AGGAGCCAAAGTTATAAAAGAACAT-GTAAAAGTTTGACAAGTTTGGAAGTTCAGCCAAGAACCA
582 AGGAACCGAAGTTATAAAAGAAC-TCGTAAAAGTTTGACAAGTTTGGAAGTTCAGCCAAGAACCA
4292 AGA
646 AGA
* * *
4295 GAGAAATAATTCTCACGTAAATAAGTTTTTAATTCAACGACCAAAAGTTGTTTACAAAATGATAA
1 GAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGA-CA
* * * *
4360 AACTTTTTAGACCAAATTATGCGATTTCCTGAGCATGGAATGTTCGTAAAATTGCTAGAAGGAAC
65 AACTATTTAGACCAAATGATGCGATTTCCTGAGCATGGAATGTTCGAAAAATTGCTAGAAGGAAT
* * * * *
4425 GAATCATCTTGAATACTTAAAGGAACCGAAATTATAAAAGAATTCGTAAAAGTTCGACAAGTTTG
130 GGATCGTCTTGAATACTTTAAGGAACCGAAATTATAAAAGAACTCGTAAAAGTTTGACAAGTTTG
* * *
4490 GAAGTTCATCCAAGAACCAAGAGAGAAAAAATTCTTACGTAAATAAGTTTTTAAATCAAAGACCA
195 GAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCA
* * * * **
4555 AAAGTTGTTTACAAAATGACAAACTATTTGGACTAAATGATGCGCTTTCCTGAGCATGGAATGTT
260 AAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGTGATTTCCCAAGCATGGAATGTT
* * * * * * *
4620 CGGAAAATTACTCGAAGGAATGAATCATCTTGAATA-TTGTAAGGAACCGAAGTTATAAATGAAC
325 CGAAAAATTGCTAGAAGAAATGGATCGTCTTGAATACTT-TAAGGAACCGAAGTTATAAAAGAAC
** ** * *
4684 TCGTAAAAGTTTGACAAG-TCCAAAAGTTCCTCCAAGAACCAATAGAGAAACAATTCTCACGTAA
389 TCGTAAAAGTTTGACAAGTTCGGAAA-TTCGACCAAGAACCAAGAGAGAAACAATTCACACGTAA
* * * *
4748 ATAAGTTTTTAATTCAAAGACAAAAAAGTTGCTTACAAGATGACAAACTATTTAGACCAAATGAT
453 ATAAGTTTTTAATTCAAAGAC-CAAAAGTTGTTTACAAAATGATAAACTATTTAGACCAAATGAT
* * * * * * * **
4813 GCAATTTCGCAAGCATGAAATATTCGAAAAATTGCTTGAAGGAATCTATCGTCTTGAATACTTTA
517 GCGATTTCCCAAGCATGGAATGTTCAAAAAATTGCTCGAAAGAATGGATCGTCTTGAATACTTTA
* * * * *
4878 AGGAACCGAAGTTATAAAAGAACTCATAAAAATTTGACAAGCTTGAAAGTAC-GTCCAAGAACCA
582 AGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTTGGAAGTTCAG-CCAAGAACCA
4942 AGA
646 AGA
** * * * * **
4945 GAGAAACAATTCTCTTGGAAATAAGCTTTTAGTTCAAAGACCGAAAGTTGTTTATGAAATGACAA
1 GAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAA
* * * * * * *
5010 ACTATTTAGACTAAACGATGTGATTTCCTGAGAATAGAATGTTCGGAAAATTTCTAGAA-GAATG
66 ACTATTTAGACCAAATGATGCGATTTCCTGAGCATGGAATGTTCGAAAAATTGCTAGAAGGAATG
* * *
5074 GATAGTCTTGAAAACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTTGG
131 GATCGTCTTGAATACTTTAAGGAACCGAAATTATAAAAGAACTCGTAAAAGTTTGACAAGTTTGG
* * * * * * *
5139 ATGTTCAGCCAAGAACTAAGAGAGAAACAATTCACACCTAAATAAGTTTTTAATTTAAGGACCAA
196 AAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAA
* * * * * *
5204 AACTTGTTTACAAAACGACAAACTATTTAGACCTAATAAT-TCGATTTCCCAAGCCTTGAATGTT
261 AAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGT-GATTTCCCAAGCATGGAATGTT
* * * * *
5268 CAAAAAATTGCTAGAATAAATGGATCGTCTTGAATACTTTAAGTAACCGGAGTTACAAAAGAACT
325 CGAAAAATTGCTAGAAGAAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACT
* * * * * * * *
5333 TGTAAAAGTTTGATAGGTTCGGAAGTTCGGCCAAGAACCAAGAGAGAAACAGTTCACACATAAAG
390 CGTAAAAGTTTGACAAGTTCGGAAATTCGACCAAGAACCAAGAGAGAAACAATTCACACGTAAAT
* *
5398 AAGATTTTAATTCAAAG---AAAA-----TTAC--AA--AT--A--ATTGAGACCAAATGATGCG
455 AAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGATAAACTATTTAGACCAAATGATGCG
* * * ** * *
5447 ATTTCCTAAGCATTGAATATTTGAAAAATTTCTCGAAAGAATGGATCGTCTTGAAAACTTTAAGG
520 ATTTCCCAAGCATGGAATGTTCAAAAAATTGCTCGAAAGAATGGATCGTCTTGAATACTTTAAGG
* * * *
5512 AACCAAAGTTATAAAAGAACACGTAAAAGTTTGACAAGTTTGGAAGTTTAGCCAAGAACTAAGA
585 AACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTTGGAAGTTCAGCCAAGAACCAAGA
* * * *
5576 GAGAAATAATTCTCACGTAAATAAGTTTTTAATTCAAAGACAAAAAATTGTTTTCAAAATGACAA
1 GAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAA
* * * * *
5641 ACAATTTAGACCAAATGATGCGATTTCCCGAAGCATGGATTGTTCGTAAAATTGCTCGAAGGAAT
66 ACTATTTAGACCAAATGATGCGATTTCCTG-AGCATGGAATGTTCGAAAAATTGCTAGAAGGAAT
* * * * *
5706 GGATCGTCTTGAATACTGTAAGTAACC-AAAGTTATAAAAGAATTCGTAAAAGTTTGATAAGTTC
130 GGATCGTCTTGAATACTTTAAGGAACCGAAA-TTATAAAAGAACTCGTAAAAGTTTGACAAGTTT
* * * * *
5770 AGAAATTCGTCCAAGAACC-A-AGAGAAACAATTCTTACGTAAATAAGTTTTTAATTCAAAGTCC
194 GGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACC
* * ** *
5833 AAAAGTTGTTTAGAAAATGACAAACTATTTAGACCAAATGATGTGCTTTCCTGATCATGGAATGT
259 AAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGTGATTTCCCAAGCATGGAATGT
* * * * *
5898 TCGGAAAA-TGTCTCA-AAGGAATCGATCATCTTGAATACTTTAAGGAACCAAAGTTATAAAAGA
324 TCGAAAAATTG-CT-AGAAGAAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGA
* * * * * *
5961 ACTCGTAAAAGTTTGACTAGTTCGGAAGTAC-ATCCAAGAACCAAGGGAGAAACAATTCTCATGT
387 ACTCGTAAAAGTTTGACAAGTTCGGAAATTCGA-CCAAGAACCAAGAGAGAAACAATTCACACGT
* * * *
6025 AAATAAGTTTTTAATTTATAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAACGA
451 AAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGATAAACTATTTAGACCAAATGA
* * * * * * * * *
6090 TGCGATTCCCCGAGAATAGAATGTGCAGAAAATTGATAG-AAGAAATGGATAGTCTTGAATACTT
516 TGCGATTTCCCAAGCATGGAATGTTCAAAAAATTGCTCGAAAG-AATGGATCGTCTTGAATACTT
* * ** * * * * * *
6154 CATGGAATTGAAGTTATAATAGAACTCATAAAAGTTTGAAAAGTTTGAAAGTTCGGCCGAGAACC
580 TAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTTGGAAGTTCAGCCAAGAACC
6219 AAGA
645 AAGA
6223 GAGAAACAATTCTCACGTAAATAAGTTTTTAA-T---AGACCAAAAGTTGTTTACAAAATGACAA
1 GAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAA
* * * * * * *
6284 ACTATTTAGACCTAATAATTCGATTACCTGAGCCTTGAATGTTCGAAAAATTGCTAGAAGAAATG
66 ACTATTTAGACCAAATGATGCGATTTCCTGAGCATGGAATGTTCGAAAAATTGCTAGAAGGAATG
* * * * *
6349 GATCGTCATGAATACTATAAGTAACC-AAAGTTATAAAAGAACTCGTAAAAGTTTGGCAAGTTCG
131 GATCGTCTTGAATACTTTAAGGAACCGAAA-TTATAAAAGAACTCGTAAAAGTTTGACAAGTTTG
* * * * *
6413 GAAGTGCATACAAGAACCAAGAGAGAAATAATTCTCATGTAAATAAGTTTTTAGCTT-AAAGACC
195 GAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTA-ATTCAAAGACC
* * ** * *
6477 GAAAGTTTTTTATGAAATGACAAACTATTTAGACCAAATGATATGATTTCCCAAGCATTGAATGT
259 AAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGTGATTTCCCAAGCATGGAATGT
* * * * *
6542 TCGAAAAATTTCTTGGAAG-AATGGATCGTTTTGAAAACTTTAAGGAACCAAAGTTATAAAAGAA
324 TCGAAAAATTGC-TAGAAGAAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAA
* * * * ** * * *
6606 CACATAAAAGCTTGACAAGTTTGGAACCTCAACCAAGAGCTAAGAGAGAAACAATT-ATCACGTA
388 CTCGTAAAAGTTTGACAAGTTCGGAAATTCGACCAAGAACCAAGAGAGAAACAATTCA-CACGTA
* *
6670 AATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGATAAAGCTTTTTAGACCAAATTA
452 AATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGATAAA-CTATTTAGACCAAATGA
* * * * * *
6735 TGCGATATCCCGAGCATGGAATGTTCATAAAGTTGCTCGAAGGAATGGATCTTCTTGAATACTTT
516 TGCGATTTCCCAAGCATGGAATGTTCAAAAAATTGCTCGAAAGAATGGATCGTCTTGAATACTTT
* * *** ** *
6800 AAGGAACCGAAGTTATAAAAGAACACGTAAAAGTTTAACAAGTCCAGAAGTTCCTCCAAGAACTA
581 AAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTTGGAAGTTCAGCCAAGAACCA
6865 AGA
646 AGA
*
6868 GAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACAAAAAGTTGTTTACAAAATGACAA
1 GAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAA
* * * * *
6933 ACTA-TTAGACCAAATGATGCTATTTCCCGAGCCTTGG-ATGTTCAAAAAATTGCTAGAAGAAAT
66 ACTATTTAGACCAAATGATGCGATTTCCTGAG-CATGGAATGTTCGAAAAATTGCTAGAAGGAAT
* **
6996 GGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCA
130 GGATCGTCTTGAATACTTTAAGGAACCGAAATTATAAAAGAACTCGTAAAAGTTTGACAAGTTTG
* * * * *
7061 GAAG--CAAGTCTAAGAACCAAGAGAGAAATAATTCTCATGTAAATAAGTTTTTAGTTTAAAGA
195 GAAGTTC-A-TCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGA
7123 ACTCGCATTG
Statistics
Matches: 2907, Mismatches: 490, Indels: 143
0.82 0.14 0.04
Matches are distributed among these distances:
630 2 0.00
631 408 0.14
632 29 0.01
633 71 0.02
634 8 0.00
635 354 0.12
636 3 0.00
637 1 0.00
639 8 0.00
641 2 0.00
642 146 0.05
643 69 0.02
644 235 0.08
645 156 0.05
646 9 0.00
647 335 0.12
648 747 0.26
649 127 0.04
650 196 0.07
651 1 0.00
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (648 bp):
GAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAA
ACTATTTAGACCAAATGATGCGATTTCCTGAGCATGGAATGTTCGAAAAATTGCTAGAAGGAATG
GATCGTCTTGAATACTTTAAGGAACCGAAATTATAAAAGAACTCGTAAAAGTTTGACAAGTTTGG
AAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAA
AAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGTGATTTCCCAAGCATGGAATGTTC
GAAAAATTGCTAGAAGAAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTC
GTAAAAGTTTGACAAGTTCGGAAATTCGACCAAGAACCAAGAGAGAAACAATTCACACGTAAATA
AGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGATAAACTATTTAGACCAAATGATGCGA
TTTCCCAAGCATGGAATGTTCAAAAAATTGCTCGAAAGAATGGATCGTCTTGAATACTTTAAGGA
ACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTTGGAAGTTCAGCCAAGAACCAAGA
Found at i:7155 original size:15 final size:15
Alignment explanation
Indices: 7135--7182 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
7125 TCGCATTGGT
7135 GTGTTCGCAACCTGA
1 GTGTTCGCAACCTGA
* *
7150 GTGTTCGC-AGCTCCA
1 GTGTTCGCAACCT-GA
*
7165 GTGTTCGCAACATGA
1 GTGTTCGCAACCTGA
7180 GTG
1 GTG
7183 CTCACAACAC
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
14 3 0.12
15 21 0.81
16 2 0.08
ACGTcount: A:0.19, C:0.25, G:0.29, T:0.27
Consensus pattern (15 bp):
GTGTTCGCAACCTGA
Found at i:9692 original size:216 final size:216
Alignment explanation
Indices: 9311--10012 Score: 980
Period size: 216 Copynumber: 3.2 Consensus size: 216
9301 AGTTTAGAAG
* ** * *
9311 TTGCTCGAAGGAATGGATCCTCTTGAATACTTTAAGGAACCAAAGTTATTCAAGAACATGTAAAA
1 TTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAAAACTTGTAAAA
* *
9376 GTTTGACAAGTTCGAAAGTTCGA-CCAAGAACCAAGAGACAAACAATTCTCACGTAAATAAGTTT
66 GTTTGACAAGTTCGGAAGTTC-ATCCAAGAACCAAGAGACAAATAATTCTCACGTAAATAAGTTT
* * *
9440 TTAATTCAAGGACCAAAAGTTGTTTACAAAATGACAAACTATTTGGACCAAATGCTGTGATTTCC
130 TTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTGGACCAAATGATGCGATTTCC
*
9505 CGAGCATTGAATGTTCAAAAAA
195 CAAGCATTGAATGTTCAAAAAA
* * * * *
9527 TTGCTCAAAGGAATGGATCATCTTGAATACCTTAAGGAACCGAAGTTATAAAATAACTTGTAAAA
1 TTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAAAACTTGTAAAA
* *
9592 GTTTGACAAGTTCGGAAGTTCATCCAAGAATCAAGAGACAAATAATTCTTACGTAAATAAGTTTT
66 GTTTGACAAGTTCGGAAGTTCATCCAAGAACCAAGAGACAAATAATTCTCACGTAAATAAGTTTT
* *
9657 TAATTCAAAGACCAAAAGTTCTTTACAAAATGACAAACTATTTGGACCAAATGATGCGATTTCCT
131 TAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTGGACCAAATGATGCGATTTCCC
9722 AAGCA-TGAAATGTTTGCAAAAAA
196 AAGCATTG-AATG-TT-CAAAAAA
* * *
9745 TTACTCGAAGGAATGGATCGTCTTGAATATTTTAAGGAACCAAAGTTACAAAAAAACTTGTAAAA
1 TTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAAAACTTGTAAAA
* * * * * * * *
9810 GTTTAACAAGTTCAGAAGTTCGTCCAAGAACCAAAAGAGAAATCATTCTCATGTAAATAACTTTT
66 GTTTGACAAGTTCGGAAGTTCATCCAAGAACCAAGAGACAAATAATTCTCACGTAAATAAGTTTT
* *
9875 TAA-TCTAAAGA-CAAAAGTTGTTTACAAAATAACAAACTATTTAGACCAAATGATGCGATTTCC
131 TAATTC-AAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTGGACCAAATGATGCGATTTCC
* * *
9938 CAAACATGGAATGTTCGAAAAA
195 CAAGCATTGAATGTTCAAAAAA
* * *
9960 TTGCTCGAAGGAATGGATTGTCTTGAATACTTTAAGGAATCGAAGTTATAAAA
1 TTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAA
10013 GAATTGATGA
Statistics
Matches: 431, Mismatches: 49, Indels: 13
0.87 0.10 0.03
Matches are distributed among these distances:
215 56 0.13
216 186 0.43
217 61 0.14
218 128 0.30
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (216 bp):
TTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAAAACTTGTAAAA
GTTTGACAAGTTCGGAAGTTCATCCAAGAACCAAGAGACAAATAATTCTCACGTAAATAAGTTTT
TAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTGGACCAAATGATGCGATTTCCC
AAGCATTGAATGTTCAAAAAA
Found at i:11564 original size:5 final size:5
Alignment explanation
Indices: 11554--11600 Score: 85
Period size: 5 Copynumber: 9.4 Consensus size: 5
11544 AGGTTCGAAC
*
11554 AAGAA AAGAA AAGAA AAGAA AGGAA AAGAA AAGAA AAGAA AAGAA AA
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AA
11601 TATATCCTCA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 40 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:17707 original size:216 final size:215
Alignment explanation
Indices: 17319--18521 Score: 1318
Period size: 216 Copynumber: 5.7 Consensus size: 215
17309 CTATGATCAA
* * * * * *
17319 CCTTAAAGTATTCAAGACGATCCATTCCTTTGAGCAATTTTTCGAACGTTCCATGCTCGAGAAAT
1 CCTTAAAGTATTCAAGATGATCCATTCCTTCGAGGAA-TTTCCGAACATTCCATGCTCGGGAAAT
*
17384 CGCATCATTTGGTCCAAATAGTTTTTCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAACTT
65 CGCATCATTTGGTCCAAATAGTTTATCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAACTT
* * * *
17449 ATTTAGGTGAGAATTGTTTGTCTATTAGTCCTTGGCCGAACTTCCGAACTTGTCAAACTTTTTCG
130 ATTTACGTGAGAATTGTTTGTCTACTAGTCCTTGGCCGAACTTCCAAACTTGTCAAACTTTTACG
17514 AGTTCTTTTATAACTTCGGTT
195 AGTTCTTTTATAACTTCGGTT
*
17535 CCTTAAAGTATTC-AGAATGATCCATTCCTTCGAGGAAATTTCCGAACAATCCATGCAT-GGGAA
1 CCTTAAAGTATTCAAG-ATGATCCATTCCTTCGAGG-AATTTCCGAACATTCCATGC-TCGGGAA
* * ** * * * * *
17598 ATCGTATCATTAGGAACAAATAGTATATAATTTTGTAAACAACTTTTGGTGTTTGAATTTAAAAC
63 ATCGCATCATTTGGTCCAAATAGTTTATCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAAC
* * * *** *
17663 TTATTTACGTGAGAATTAATTT-TCTACTAGTTCTTGGTCGAACTTTTGAACTTGT-ATAACCTT
128 TTATTTACGTGAGAATT-GTTTGTCTACTAGTCCTTGGCCGAACTTCCAAACTTGTCA-AACTTT
17726 TACGAGTTCTTTTATAACCTT-GGTT
191 TACGAGTTCTTTTATAA-CTTCGGTT
* * * * *
17751 CCTTAAAGTATTCATGATGATCCATTCCTTCAAGGAATTCTCCAAACATTCCATTCTTGGGAAAT
1 CCTTAAAGTATTCAAGATGATCCATTCCTTCGAGGAATT-TCCGAACATTCCATGCTCGGGAAAT
*
17816 CGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTTGTCTTTGAA-TAAAAACTT
65 CGCATCATTTGGTCCAAATAGTTTATCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAACTT
* * * * *
17880 ATTTACGTGAGAATTATTTTTCTATTGGTCCTTGGCCAAACTTCCAAACTTGTCAAACTTTTACG
130 ATTTACGTGAGAATTGTTTGTCTACTAGTCCTTGGCCGAACTTCCAAACTTGTCAAACTTTTACG
*
17945 AGTTCTTTTATAACTTCGATT
195 AGTTCTTTTATAACTTCGGTT
* *
17966 CCGTAAAGTATTCAAGATGATCCATTCCTTCGAGGAATTTCTCGAACATTCCATGCTCGCGAAAT
1 CCTTAAAGTATTCAAGATGATCCATTCCTTCGAGGAATTTC-CGAACATTCCATGCTCGGGAAAT
* * *
18031 CGCATCATTTGGTCTAAATAGTTTCTCATTTTGTAAACAACTTTTTGTCTTTGAGTTAAAAACTT
65 CGCATCATTTGGTCCAAATAGTTTATCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAACTT
* * * * * *
18096 ATTTACGTGAGAATTGTTTGTCT-CATGGTTCTTGGCCGAGCTACCAAACTTGTCAAAGTCTTAC
130 ATTTACGTGAGAATTGTTTGTCTAC-TAGTCCTTGGCCGAACTTCCAAACTTGTCAAACTTTTAC
* ** * *
18160 GAATTCTTGAAAAACTTAGGTT
194 GAGTTCTTTTATAACTTCGGTT
* * * *
18182 CCTTAAAGTATTGAAGACGATCCA----TTC---G-A------AA-ATTCCATGCTCGAGAAATT
1 CCTTAAAGTATTCAAGATGATCCATTCCTTCGAGGAATTTCCGAACATTCCATGCTCGGGAAATC
* * *
18232 GCATCATTTGGT-CAAGTAGTTTGTCATTTTGTAAACAACCTTTTGTCTTTGAATTAAAAACTTA
66 GCATCATTTGGTCCAAATAGTTTATCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAACTTA
* * * * * * * * * * *
18296 TTTAGGTGAGAATTGGTCGTCT-CTTGGTTCTTGGACGAACATCCGAACTGGTAAAACTTGTACG
131 TTTACGTGAGAATTGTTTGTCTAC-TAGTCCTTGGCCGAACTTCCAAACTTGTCAAACTTTTACG
*
18360 AGTTCTTTTATAACTTAGGTT
195 AGTTCTTTTATAACTTCGGTT
* ** **
18381 CCTTAAAG-A--C--G--G-TCCTTTCCTTTTAGGAATTTTTTGAACATTCCATGCTCGGGAAAT
1 CCTTAAAGTATTCAAGATGATCCATTCCTTCGAGGAA-TTTCCGAACATTCCATGCTCGGGAAAT
* * * *
18438 CGCACCATTTGGTCCAAATAATTTGTCATTTTGTAAACAACTTTTTGGCTTTGAATTAAAAACTT
65 CGCATCATTTGGTCCAAATAGTTTATCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAACTT
18503 ATTTACGTGAGAATTGTTT
130 ATTTACGTGAGAATTGTTT
18522 CTCTCTTGGT
Statistics
Matches: 838, Mismatches: 117, Indels: 72
0.82 0.11 0.07
Matches are distributed among these distances:
191 3 0.00
192 1 0.00
194 1 0.00
195 2 0.00
198 2 0.00
199 123 0.15
200 29 0.03
201 2 0.00
206 2 0.00
207 28 0.03
208 64 0.08
209 1 0.00
212 3 0.00
214 9 0.01
215 188 0.22
216 370 0.44
217 10 0.01
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.39
Consensus pattern (215 bp):
CCTTAAAGTATTCAAGATGATCCATTCCTTCGAGGAATTTCCGAACATTCCATGCTCGGGAAATC
GCATCATTTGGTCCAAATAGTTTATCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAACTTA
TTTACGTGAGAATTGTTTGTCTACTAGTCCTTGGCCGAACTTCCAAACTTGTCAAACTTTTACGA
GTTCTTTTATAACTTCGGTT
Found at i:18095 original size:431 final size:427
Alignment explanation
Indices: 17319--18537 Score: 1416
Period size: 431 Copynumber: 2.9 Consensus size: 427
17309 CTATGATCAA
* * * * * *
17319 CCTTAAAGTATTCAAGACGATCCATTCCTTTGAGCAATTTTTCGAACGTTCCATGCTCGAGAAAT
1 CCTTAAAGTATTCATGAAGATCCATTCC-TTCAG-AA-TTTCCAAACATTCCATGCTCGAGAAAT
*
17384 CGCATCATTTGGTCCAAATAGTTTTTCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAACTT
63 CGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAACTT
* *
17449 ATTTAGGTGAGAATTGTTTGTCTATTAGTCCTTGGCCGAACTTCCGAACTTGTCAAACTTTTTCG
128 ATTTAGGTGAGAATTGTTTGTCTATTGGTCCTTGGCCGAACTTCCGAACTTGTCAAACTTTTACG
17514 AGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAGAATGATCCATTCCTTCGAGGAAATTTC-C
193 AGTTCTTTTATAACTTCGGTTCCTTAAAGTATTCAG-ATGATCCATTCCTTCGAGG-AATTTCTC
* * * * * *
17578 GAACAATCCATGCAT-GGGAAATCGTATCATTAGGAACAAATAGTATATAATTTTGTAAACAACT
256 GAACATTCCATGC-TCGGGAAATCGCATCATTTGG-TCAAATAGTTTATCATTTTGTAAACAACT
* * * *
17642 TTTGGTGTTTGAATTTAAAACTTATTTACGTGAGAATTAATTT-TCT-ACTAGTTCTTGGTCGAA
319 TTTTGTCTTTGAATTAAAAACTTATTTACGTGAGAATT-ATTTGTCTCA-TAGTTCTTGGCCGAA
**** * * * *
17705 CTTTTGAACTTGT-ATAAC-CTTTACGAGTTCTTTTATAACCTT-GGTT
382 CTACCAAACTTGTCA-AACTC-TTACGAATTC-TTGAAAAACTTAGGTT
* * * *
17751 CCTTAAAGTATTCATGATGATCCATTCCTTCAAGGAATTCTCCAAACATTCCATTCTTGGGAAAT
1 CCTTAAAGTATTCATGAAGATCCATTCCTTC-A-GAATT-TCCAAACATTCCATGCTCGAGAAAT
17816 CGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTTGTCTTTGAA-TAAAAACTT
63 CGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAACTT
* * * * *
17880 ATTTACGTGAGAATTATTTTTCTATTGGTCCTTGGCCAAACTTCCAAACTTGTCAAACTTTTACG
128 ATTTAGGTGAGAATTGTTTGTCTATTGGTCCTTGGCCGAACTTCCGAACTTGTCAAACTTTTACG
* *
17945 AGTTCTTTTATAACTTCGATTCCGTAAAGTATTCAAGATGATCCATTCCTTCGAGGAATTTCTCG
193 AGTTCTTTTATAACTTCGGTTCCTTAAAGTATTC-AGATGATCCATTCCTTCGAGGAATTTCTCG
* *
18010 AACATTCCATGCTCGCGAAATCGCATCATTTGGTCTAAATAGTTTCTCATTTTGTAAACAACTTT
257 AACATTCCATGCTCGGGAAATCGCATCATTTGGTC-AAATAGTTTATCATTTTGTAAACAACTTT
* * * *
18075 TTGTCTTTGAGTTAAAAACTTATTTACGTGAGAATTGTTTGTCTCATGGTTCTTGGCCGAGCTAC
321 TTGTCTTTGAATTAAAAACTTATTTACGTGAGAATTATTTGTCTCATAGTTCTTGGCCGAACTAC
*
18140 CAAACTTGTCAAAGTCTTACGAATTCTTGAAAAACTTAGGTT
386 CAAACTTGTCAAACTCTTACGAATTCTTGAAAAACTTAGGTT
* * *
18182 CCTTAAAGTA-T--TGAAGA-CGA-T-C--C---A-TTCGAAA-ATTCCATGCTCGAGAAATTGC
1 CCTTAAAGTATTCATGAAGATCCATTCCTTCAGAATTTCCAAACATTCCATGCTCGAGAAATCGC
* *
18234 ATCATTTGGT-CAAGTAGTTTGTCATTTTGTAAACAACCTTTTGTCTTTGAATTAAAAACTTATT
66 ATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAACTTATT
* * * * * * * * *
18298 TAGGTGAGAATTGGTCGTCTCTTGGTTCTTGGACGAACATCCGAACTGGTAAAACTTGTACGAGT
131 TAGGTGAGAATTGTTTGTCTATTGGTCCTTGGCCGAACTTCCGAACTTGTCAAACTTTTACGAGT
* * ** * *
18363 TCTTTTATAACTTAGGTTCCTTAAAG-A--C-G--G-TCCTTTCCTTTTAGGAATTTTTTGAACA
196 TCTTTTATAACTTCGGTTCCTTAAAGTATTCAGATGATCCATTCCTTCGAGGAATTTCTCGAACA
* * * *
18421 TTCCATGCTCGGGAAATCGCACCATTTGGTCCAAATAATTTGTCATTTTGTAAACAACTTTTTGG
261 TTCCATGCTCGGGAAATCGCATCATTTGGT-CAAATAGTTTATCATTTTGTAAACAACTTTTTGT
* * * *
18486 CTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTGG
325 CTTTGAATTAAAAACTTATTTACGTGAGAATTATTTGTCTCATAGTTCTTGG
18538 ATGAACAAT
Statistics
Matches: 690, Mismatches: 83, Indels: 53
0.84 0.10 0.06
Matches are distributed among these distances:
407 130 0.19
408 2 0.00
410 1 0.00
412 1 0.00
414 40 0.06
415 113 0.16
416 5 0.01
417 1 0.00
418 1 0.00
423 1 0.00
425 1 0.00
426 1 0.00
427 2 0.00
428 5 0.01
430 20 0.03
431 258 0.37
432 107 0.16
433 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.39
Consensus pattern (427 bp):
CCTTAAAGTATTCATGAAGATCCATTCCTTCAGAATTTCCAAACATTCCATGCTCGAGAAATCGC
ATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTTTTGTCTTTGAATTAAAAACTTATT
TAGGTGAGAATTGTTTGTCTATTGGTCCTTGGCCGAACTTCCGAACTTGTCAAACTTTTACGAGT
TCTTTTATAACTTCGGTTCCTTAAAGTATTCAGATGATCCATTCCTTCGAGGAATTTCTCGAACA
TTCCATGCTCGGGAAATCGCATCATTTGGTCAAATAGTTTATCATTTTGTAAACAACTTTTTGTC
TTTGAATTAAAAACTTATTTACGTGAGAATTATTTGTCTCATAGTTCTTGGCCGAACTACCAAAC
TTGTCAAACTCTTACGAATTCTTGAAAAACTTAGGTT
Found at i:18377 original size:199 final size:205
Alignment explanation
Indices: 17795--18544 Score: 671
Period size: 199 Copynumber: 3.6 Consensus size: 205
17785 GAATTCTCCA
* * *
17795 AACATTCCATTCTTGGGAAATCGCATCATTTGGTCCAAATAGTTTGTCATTTTGTAAACAACTTT
1 AACATTCCATGCTCGAGAAATCGCATCATTTGGT-CAAATAGTTTGTCATTTTGTAAACAACTTT
* ** * * * * *
17860 TTGTCTTTGAA-TAAAAACTTATTTACGTGAGAATTATTTTTCTATTGGTCCTTGGCCAAAC-TT
65 TTGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTCGTCTCTTGGTTCTTGGACGAACATA
* * * * ** * * * *
17923 CCAAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCGATTCCGTAAAGTATTCAAGATGATC
130 CCAAACTGGTAAAACTCTTACGAATTCTTGAAAAACTTAGGTTCC-T----TA---AAGACG-T-
*** * *
17988 CATTCCTTCGAGGAAT-TTCTCG
185 CATT-CGAAGACGAATCAT-TCG
* *
18010 AACATTCCATGCTCGCGAAATCGCATCATTTGGTCTAAATAGTTTCTCATTTTGTAAACAACTTT
1 AACATTCCATGCTCGAGAAATCGCATCATTTGGTC-AAATAGTTTGTCATTTTGTAAACAACTTT
* * * * *
18075 TTGTCTTTGAGTTAAAAACTTATTTACGTGAGAATTGTTTGTCTCATGGTTCTTGGCCGAGC-TA
65 TTGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTCGTCTCTTGGTTCTTGGACGAACATA
* * *
18139 CCAAACTTGTCAAAGTCTTACGAATTCTTGAAAAACTTAGGTTCCTT-AA-A-GT-ATT-GAAGA
130 CCAAACTGGTAAAACTCTTACGAATTCTTGAAAAACTTAGGTTCCTTAAAGACGTCATTCGAAGA
18199 CG-ATCCATTCG
195 CGAAT-CATTCG
* * * *
18210 AAAATTCCATGCTCGAGAAATTGCATCATTTGGTCAAGTAGTTTGTCATTTTGTAAACAACCTTT
1 AACATTCCATGCTCGAGAAATCGCATCATTTGGTCAAATAGTTTGTCATTTTGTAAACAACTTTT
* *
18275 TGTCTTTGAATTAAAAACTTATTTAGGTGAGAATTGGTCGTCTCTTGGTTCTTGGACGAACAT-C
66 TGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTCGTCTCTTGGTTCTTGGACGAACATAC
* * ** * * **
18339 CGAACTGGTAAAACT-TGTACGAGTTCTTTTATAACTTAGGTTCCTTAAAGACGGTCCTTTCCTT
131 CAAACTGGTAAAACTCT-TACGAATTCTTGAAAAACTTAGGTTCCTTAAAGAC-GT-CATT-CGA
** * ** *
18403 TTAGGAATTTTTTG
192 AGACGAATCATTCG
* * *
18417 AACATTCCATGCTCGGGAAATCGCACCATTTGGTCCAAATAATTTGTCATTTTGTAAACAACTTT
1 AACATTCCATGCTCGAGAAATCGCATCATTTGGT-CAAATAGTTTGTCATTTTGTAAACAACTTT
* *
18482 TTGGCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTC-TCTCTTGGTTCTTGGATGAACA
65 TTGTCTTTGAATTAAAAACTTATTTACGTGAGAATTG-TTCGTCTCTTGGTTCTTGGACGAACA
18545 AT
Statistics
Matches: 451, Mismatches: 67, Indels: 41
0.81 0.12 0.07
Matches are distributed among these distances:
198 1 0.00
199 120 0.27
200 41 0.09
201 2 0.00
202 3 0.01
203 2 0.00
204 1 0.00
205 3 0.01
206 1 0.00
207 37 0.08
208 85 0.19
209 2 0.00
211 1 0.00
214 1 0.00
215 70 0.16
216 81 0.18
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.38
Consensus pattern (205 bp):
AACATTCCATGCTCGAGAAATCGCATCATTTGGTCAAATAGTTTGTCATTTTGTAAACAACTTTT
TGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTCGTCTCTTGGTTCTTGGACGAACATAC
CAAACTGGTAAAACTCTTACGAATTCTTGAAAAACTTAGGTTCCTTAAAGACGTCATTCGAAGAC
GAATCATTCG
Done.