Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000950.1 Kokia drynarioides strain JFW-HI SEQ_112122, 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: 50492
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 3 characters in sequence are not A, C, G, or T
Found at i:1998 original size:216 final size:216
Alignment explanation
Indices: 1605--4395 Score: 3112
Period size: 216 Copynumber: 12.9 Consensus size: 216
1595 ACGCATTACA
* * * * * * *
1605 ATCGTCTTGAATACTTTAAAGAACTGAAGTTATAAAATAACTTGGAAAAGTTCGA-AAATTTGAA
1 ATCGTCTTGAATACTTTAAGGAACTGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAA
* * *
1669 AGTTCGGCCAAGAACCAAGAGAGAGACAATTCTCATGTAAATAAGTTTTTAATCCAAAGACCAAA
66 AGTTCGGCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAA
* * *
1734 AGTTGTTTACAAAATGACAAACTATTTGGACCAAATGATGCTATTTCCCGAGCATGGAGTGTTCG
131 AGTTGTTTACAAAATGACAAACTATTTGGACCAAATGATGCGATTTCTCGAGCATGGAATGTTCG
* *
1799 AAAAAATACTCGAAGGAATGG
196 AAAAATTGCTCGAAGGAATGG
** * * *
1820 ATAATCTTGAGTACTTTAAGGAACTGAAGTTATAAAAGAACTCGTAAAAGTTTTACAAGTTCAAA
1 ATCGTCTTGAATACTTTAAGGAACTGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAA
* * * * *
1885 AGCTT-GGCTAAGAACCAAGAGAGAAATAATCCTTACGTAAAAAAGTTTTTAATTCAAAGACCAA
66 AG-TTCGGCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAA
* * * * *
1949 AAGTTGTTTACAAAATGAAAAACTATTTAGACCAAATTATGTGATTTCCCGAGCATGGAATGTTC
130 AAGTTGTTTACAAAATGACAAACTATTTGGACCAAATGATGCGATTTCTCGAGCATGGAATGTTC
* *
2014 GGAAAATTGCTCGATGGAATGG
195 GAAAAATTGCTCGAAGGAATGG
* * * * **
2036 ATCATCTTGAATACTTTAAGGAAAC-GAAGTTATAAAATAACTTC-TAACAGTTGGGTAAGTTCG
1 ATCGTCTTGAATACTTTAAGG-AACTGAAGTTATAAAAGAAC-TCGTAAAAGTTTGACAAGTTCG
* * * *
2099 AAAGTTTGTCCAAGAACTAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACTA
64 AAAGTTCGGCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCA
* * * * *
2164 AAAGTTTTTTAGAAAATGACAAACTATTTTGACCAAATGATGTGATTTCTCAAGCATGGAATGTT
129 AAAGTTGTTTACAAAATGACAAACTATTTGGACCAAATGATGCGATTTCTCGAGCATGGAATGTT
* * *
2229 TGGAAAATTGCTCGAATGAATGG
194 CGAAAAATTGCTCGAAGGAATGG
* * ** * *
2252 ATCGTCTTGAATATTTTAAGGATC-GAAGTTATAAAAGAACTCAAAAAAGTTTGAAAAGTTCGGA
1 ATCGTCTTGAATACTTTAAGGAACTGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAA
* * * *
2316 AGTTCGACCAAGAACCAAGAGAGAAACAATTCTTATGTAAATAAGTTTTTAATCCAAAGACCAAA
66 AGTTCGGCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAA
* *
2381 ATTTGTTTACAAAATGACAAACTATTTGGACCAAATAATGCGATTTCTCGAGCATGGAATGTTCG
131 AGTTGTTTACAAAATGACAAACTATTTGGACCAAATGATGCGATTTCTCGAGCATGGAATGTTCG
* **
2446 GAAAATTGCTCGAAGGAATCA
196 AAAAATTGCTCGAAGGAATGG
* * *
2467 ATCATCTTGAATACTGTAAGGAAAC-GAAGTTATAAAAGAACTC-TAAAAAGTTTGAAAAGTTCG
1 ATCGTCTTGAATACTTTAAGG-AACTGAAGTTATAAAAGAACTCGT-AAAAGTTTGACAAGTTCG
* * ** * * *
2530 GATGTTCAACCAAGAACCAAGAGAGAAACAATTCTCATGTAAATAAGTTTTTAATCCAAACG-TC
64 AAAGTTCGGCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAA-GACC
* *
2594 AAAAGTTGTTTACAAAATGACAAACTATTTGGACCAAATGATCCGATTTCCCGAGCATGGAATGT
128 AAAAGTTGTTTACAAAATGACAAACTATTTGGACCAAATGATGCGATTTCTCGAGCATGGAATGT
* * *
2659 TCAAAAAATTGGTCAAAGGAATGG
193 TCGAAAAATTGCTCGAAGGAATGG
* * * *
2683 ATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCATAAAAGTTTTACAAGTTTGAA
1 ATCGTCTTGAATACTTTAAGGAACTGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAA
* * ** * *
2748 AGGTAGGCCAAGAA-CAAGGAGAGAAGTAATTCTCACGTAAATAAGTTTTTAATCCAAACACCAA
66 AGTTCGGCCAAGAACCAA-GAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAA
*
2812 AAGTTGTTTACAAAATGACAAACTATTTGGACCAAATGATCCGATTTCTCGAGCATGGAATGTTC
130 AAGTTGTTTACAAAATGACAAACTATTTGGACCAAATGATGCGATTTCTCGAGCATGGAATGTTC
* *
2877 GAAAAATTGGTCAAAGGAATGG
195 GAAAAATTGCTCGAAGGAATGG
* * * * *
2899 ATCATCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCATAAAAGTTTTACAAGTTCAAA
1 ATCGTCTTGAATACTTTAAGGAACTGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAA
* * * * *
2964 AGTTAGACCAAGAA-CAAGGAGAGAAATAATTCTCACGTAAATAAGTTTTTAATCCAAAGAACAA
66 AGTTCGGCCAAGAACCAA-GAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAA
* *
3028 AAGTTGTTTACAAATTGACAAACTATTTGGACCAAATGATGCGATTTCTCAAGCATGGAATGTTC
130 AAGTTGTTTACAAAATGACAAACTATTTGGACCAAATGATGCGATTTCTCGAGCATGGAATGTTC
3093 GAAAAATTGCTCGAAGGAATGG
195 GAAAAATTGCTCGAAGGAATGG
* * * * * *
3115 ATCGTCTCGAATGC--GAAGGAA-TGGATCGTCTTGAATACTTTAAGGAAC-CGAAGTTATAAAA
1 ATCGTCTTGAATACTTTAAGGAACT-GA-AG--TT--ATA----AAAGAACTC---G-TA-AAAG
* * * *
3176 TAACTCAT-AAAAGTTTTTACAAGTTCGGAAGTTTGGCCAAGAACCAACAGAGAAACAATT-TGC
51 T---T--TGACAA----------GTTCGAAAGTTCGGCCAAGAACCAAGAGAGAAACAATTCT-C
** *
3239 ACGTAAATAAGTTTTTAATTCAAAGACTGAAAGTTGTTTACAAAATGGCAAACTA-TT------A
100 ACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTGGACCAA
* * * *
3297 ATG-T--GATTTCTTGAGCATGTAATCTTCGAAAAAATT-CTCGAAGAAATGG
165 ATGATGCGATTTCTCGAGCATGGAATGTTCG-AAAAATTGCTCGAAGGAATGG
* * *
3346 ATTGTCTTGAATACTTTAA-GAAATCGAAGTTATAAAAGAACTCGTAAAAGTTTGA-AACGGTCG
1 ATCGTCTTGAATACTTTAAGGAACT-GAAGTTATAAAAGAACTCGTAAAAGTTTGACAA-GTTCG
* * * * * *
3409 GAAGTTCGACCTAGAACCTAA-AGAGAAACAATTCTCATGCAAATAAGTTTTTAATTCAAAGACT
64 AAAGTTCGGCCAAGAACC-AAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACC
* * * * * *
3473 AAAAGTTTTTTACAAAATGACAATCTATTTGGATCAAATGATGTGATTTTTCGAGCGTGGAATGT
128 AAAAGTTGTTTACAAAATGACAAACTATTTGGACCAAATGATGCGATTTCTCGAGCATGGAATGT
*
3538 TCGAAAAATTACTCGAAGGAATGG
193 TCGAAAAATTGCTCGAAGGAATGG
* * * * *
3562 ATCATTTTGAATACTTTAAGGAATTGAAGTTATAAAAGAATTCGTAAAAGTTTGAAAAGTTCGAA
1 ATCGTCTTGAATACTTTAAGGAACTGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAA
* * * * * *
3627 AGTTCAGCCAAAAACCAAGAGAGAAATAATTCTTACGTAAAAAAGTTTTTAATTTAAAGACCAAA
66 AGTTCGGCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAA
* * * * *
3692 AGTTGTTCACAAAATAAGAAATTATTTGGACCAAATGATGAGATTTCTCGAGCATGGAATGTTCG
131 AGTTGTTTACAAAATGACAAACTATTTGGACCAAATGATGCGATTTCTCGAGCATGGAATGTTCG
* * *
3757 AAAATTTGCTTGAAGGAATGA
196 AAAAATTGCTCGAAGGAATGG
* * * *
3778 ATCGTCTTGAATACTTTAAGGAATTGAAGTTGTAAAAGAACTTGTAAAAGTTTGACAAGTTTGAA
1 ATCGTCTTGAATACTTTAAGGAACTGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAA
* * * * * * * **
3843 AGTTCGGTCATA-AATCAAGAGAGAAATAATTTTCATGTAAATAAATTTTTAATTTAAAGACTGA
66 AGTTCGGCCA-AGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAA
* * *
3907 AAGTTGTGTACAAAATGTCAAACTATTTGGACCAAATGATGCGATTTCTTGAGCATGGAATGTTC
130 AAGTTGTTTACAAAATGACAAACTATTTGGACCAAATGATGCGATTTCTCGAGCATGGAATGTTC
* *
3972 -AGAGAATTGCTTGAAGGAATGG
195 GA-AAAATTGCTCGAAGGAATGG
* * *
3994 ATCGTCTTAAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGA
1 ATCGTCTTGAATACTTTAAGGAACTGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAA
* * *
4059 AGTTCGGCCAATAATCAAGAGAGAAACAATTCTCACGTAAATAAATTTTTAATTCAAAGACCAAA
66 AGTTCGGCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAA
* * * * *
4124 AGTTTTTTACAAAATGACAAACTATTTGGACTAGAA-GATGTGAATTCTCGAGCATGGAATGTTT
131 AGTTGTTTACAAAATGACAAACTATTTGGACCA-AATGATGCGATTTCTCGAGCATGGAATGTTC
* *
4188 GGAAAATTGCTCGAAGGAATTG
195 GAAAAATTGCTCGAAGGAATGG
* * * *
4210 ATCGTCTTTAATACTTTAAGAAACCGATA-TTATAAAAGAACTCGTAAAAGATTGACAAGTTCGA
1 ATCGTCTTGAATACTTTAAGGAACTGA-AGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGA
* * *
4274 AAGTTCGGTCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAAATCAA
65 AAGTTCGGCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAA
* * * * * *
4339 AACTTATTTACAAAATGAAAAACTATTTGGGCTAAATGATACGATTTCTCGAGCATG
130 AAGTTGTTTACAAAATGACAAACTATTTGGACCAAATGATGCGATTTCTCGAGCATG
4396 AAGTGTTTTA
Statistics
Matches: 2212, Mismatches: 290, Indels: 147
0.84 0.11 0.06
Matches are distributed among these distances:
206 81 0.04
207 5 0.00
213 4 0.00
214 11 0.00
215 254 0.11
216 1647 0.74
217 22 0.01
219 3 0.00
220 4 0.00
221 2 0.00
222 2 0.00
223 6 0.00
224 6 0.00
225 1 0.00
226 2 0.00
227 4 0.00
228 3 0.00
230 3 0.00
231 46 0.02
232 12 0.01
233 6 0.00
234 4 0.00
240 3 0.00
241 78 0.04
242 3 0.00
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.28
Consensus pattern (216 bp):
ATCGTCTTGAATACTTTAAGGAACTGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAA
AGTTCGGCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAA
AGTTGTTTACAAAATGACAAACTATTTGGACCAAATGATGCGATTTCTCGAGCATGGAATGTTCG
AAAAATTGCTCGAAGGAATGG
Found at i:3131 original size:24 final size:24
Alignment explanation
Indices: 3104--3150 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
3094 AAAAATTGCT
3104 CGAAGGAATGGATCGTCTCGAATG
1 CGAAGGAATGGATCGTCTCGAATG
*
3128 CGAAGGAATGGATCGTCTTGAAT
1 CGAAGGAATGGATCGTCTCGAAT
3151 ACTTTAAGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.30, C:0.15, G:0.32, T:0.23
Consensus pattern (24 bp):
CGAAGGAATGGATCGTCTCGAATG
Found at i:3667 original size:879 final size:855
Alignment explanation
Indices: 1605--4395 Score: 3182
Period size: 879 Copynumber: 3.2 Consensus size: 855
1595 ACGCATTACA
* * * * * * *
1605 ATCGTCTTGAATACTTTAA-AGAACTGAAGTTATAAAATAACTTGGAAAAGTTCGAAAATTTGAA
1 ATCGTCTTGAATACTTTAAGA-AAC-GAAGTTATAAAAGAACTCGTAAAAGTTTGAAAGTTCGGA
* * * *
1669 AGTTCGGCCAAGAACCAAGAGAGAGACAATTCTCATGTAAATAAGTTTTTAATCCAAAGACCAAA
64 AGTTCGACCAAGAACCAAGAGAGAAACAATTCTCATGTAAATAAGTTTTTAATTCAAAGACTAAA
* * * *
1734 AGTTGTTTACAAAATGACAAACTATTTGGACCAAATGATGCTATTTCCCGAGCATGGAGTGTTCG
129 AGTTATTTACAAAATGACAAACTATTTGGACCAAATGATCCGATTTCCCGAGCATGGAATGTTC-
* * * *
1799 AAAAAA-TACTCGAAGGAATGGATAATCTTGAGTACTTTAAGGAACTGAAGTTATAAAAGAACTC
193 AAAAAATTACTCAAAGGAATGGATCATCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTC
* * * * * * * * * *
1863 GTAAAAGTTTTACAAGTTCAAAAGCTTGGCTAAGAACCAA-GAGAGAAATAATCCTTACGTAAAA
258 ATAAAAGTTTGAAAAGTTCGAAAGGTAGGCCAA-AAACAAGGAGAGAAATAATTCTCACGTAAAA
* * * * * **
1927 AAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGAA-AAACTATTTAGACCAAATTATGT
322 AAGTTTTTAATCCAAACACCAAAAGTTGTTCACAAAAT-AACAAACTATTTGGACCAAATGATCA
* * * * *
1991 GATTTCCCGAGCATGGAATGTTCGGAAAATTGCTCGATGGAATGGATCATCTTGAATACTTTAAG
386 GATTTCTCGAGCATGGAATGTTCGAAAAATTGCTCAAAGGAATGAATCATCTTGAATACTTTAAG
* * * * ** * * *
2056 GAAACGAAGTTATAAAATAACTTC-TAACAGTTGGGTAAGTTCGAAAGTTTGTCCA-AGAA-CTA
451 GAACCGAAGTTATAAAAGAAC-TCATAAAAGTTTGACAAGTTCAAAAGTTAGACCATA-AATC-A
* * * * * *
2118 AGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACTAAAAGTTTTTTAGAAAATGA
513 AGAGAGAAATAATTCTCACGTAAATAAATTTTTAATCCAAAGACTAAAAGTTGTGTACAAAATGA
* * ** * *
2183 CAAACTATTTTGACCAAATGATGTGATTTCTCAAGCATGGAATGTTTGGAAAATTGC-TCGAATG
578 CAAACTATTTGGACCAAATGATGCGATTTCTCAAGCATGGAATGTTCAGAGAATTGCTTCGAAGG
* * * *
2247 AATGGATCGTCTTGAATATTTTAAGG-ATCGAAGTTATAAAAGAACTCAAAAAAGTTTGAAAAGT
643 AATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCATAAAAGTTTGACAAGT
* * * *
2311 TCGGAAGTTCGACCAAGAACCAAGAGAGAAACAATTCTTATGTAAATAAGTTTTTAATCCAAAGA
708 TCGGAAGTTCGGCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGA
* *
2376 CCAAAATTTGTTTACAAAATGACAAACTATTTGGACCAAATAATGCGATTTCTCGAGCATGGAAT
773 CCAAAAGTTGTTTACAAAATGACAAACTA-TT-------ATAATGTGATTTCTCGAGCATGGAAT
*
2441 GTTCGGAAAATTGCTCGAAGGAATCA
830 GTTCGGAAAATTGCTCGAAGGAATCG
* *
2467 ATCATCTTGAATACTGTAAGGAAACGAAGTTATAAAAGAACTC-TAAAAAGTTTGAAAAGTTCGG
1 ATCGTCTTGAATACTTTAA-GAAACGAAGTTATAAAAGAACTCGT-AAAAGTTTG-AAAGTTCGG
* * * *
2531 ATGTTCAACCAAGAACCAAGAGAGAAACAATTCTCATGTAAATAAGTTTTTAATCCAAACGTC-A
63 AAGTTCGACCAAGAACCAAGAGAGAAACAATTCTCATGTAAATAAGTTTTTAATTCAAA-GACTA
*
2595 AAAGTTGTTTACAAAATGACAAACTATTTGGACCAAATGATCCGATTTCCCGAGCATGGAATGTT
127 AAAGTTATTTACAAAATGACAAACTATTTGGACCAAATGATCCGATTTCCCGAGCATGGAATGTT
** *
2660 CAAAAAATTGGTCAAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACT
192 CAAAAAATTACTCAAAGGAATGGATCATCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACT
* * * * * *
2725 CATAAAAGTTTTACAAGTTTGAAAGGTAGGCCAAGAACAAGGAGAGAAGTAATTCTCACGTAAAT
257 CATAAAAGTTTGAAAAGTTCGAAAGGTAGGCCAAAAACAAGGAGAGAAATAATTCTCACGTAAAA
* * *
2790 AAGTTTTTAATCCAAACACCAAAAGTTGTTTACAAAATGACAAACTATTTGGACCAAATGATCCG
322 AAGTTTTTAATCCAAACACCAAAAGTTGTTCACAAAATAACAAACTATTTGGACCAAATGATCAG
* *
2855 ATTTCTCGAGCATGGAATGTTCGAAAAATTGGTCAAAGGAATGGATCATCTTGAATACTTTAAGG
387 ATTTCTCGAGCATGGAATGTTCGAAAAATTGCTCAAAGGAATGAATCATCTTGAATACTTTAAGG
*
2920 AACCGAAGTTATAAAAGAACTCATAAAAGTTTTACAAGTTCAAAAGTTAGACCA-AGAA-CAAGG
452 AACCGAAGTTATAAAAGAACTCATAAAAGTTTGACAAGTTCAAAAGTTAGACCATA-AATCAA-G
* * *
2983 AGAGAAATAATTCTCACGTAAATAAGTTTTTAATCCAAAGAAC-AAAAGTTGTTTACAAATTGAC
515 AGAGAAATAATTCTCACGTAAATAAATTTTTAATCCAAAG-ACTAAAAGTTGTGTACAAAATGAC
3047 AAACTATTTGGACCAAATGATGCGATTTCTCAAGCATGGAATGTTCGAAAAATTGCTCGAAGGAA
579 AAACTATTTGGACCAAATGATGCGATTTCTCAAGCATGGAATGTTC-----A------G-A-GAA
*
3112 TGGATCGTCTCGAATGCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAT
631 T---T-G-CT----T-CGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAG
* * *
3177 AACTCATAAAAGTTTTTACAAGTTCGGAAGTTTGGCCAAGAACCAACAGAGAAACAATT-TGCAC
686 AACTCATAAAAG-TTTGACAAGTTCGGAAGTTCGGCCAAGAACCAAGAGAGAAACAATTCT-CAC
** *
3241 GTAAATAAGTTTTTAATTCAAAGACTGAAAGTTGTTTACAAAATGGCAAACTA-T-TAATGTGAT
749 GTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTATAATGTGAT
* * * * * *
3304 TTCTTGAGCATGTAATCTTCGAAAAAATT-CTCGAAGAAATGG
814 TTCTCGAGCATGGAATGTTCG-GAAAATTGCTCGAAGGAATCG
* *
3346 ATTGTCTTGAATACTTTAAGAAATCGAAGTTATAAAAGAACTCGTAAAAGTTTGAAACGGTCGGA
1 ATCGTCTTGAATACTTTAAGAAA-CGAAGTTATAAAAGAACTCGTAAAAGTTTGAAA-GTTCGGA
* *
3411 AGTTCGACCTAGAACCTAA-AGAGAAACAATTCTCATGCAAATAAGTTTTTAATTCAAAGACTAA
64 AGTTCGACCAAGAACC-AAGAGAGAAACAATTCTCATGTAAATAAGTTTTTAATTCAAAGACTAA
* * * ** ** *
3475 AAGTTTTTTACAAAATGACAATCTATTTGGATCAAATGATGTGATTTTTCGAGCGTGGAATGTTC
128 AAGTTATTTACAAAATGACAAACTATTTGGACCAAATGATCCGATTTCCCGAGCATGGAATGTTC
* * * ** *
3540 GAAAAATTACTCGAAGGAATGGATCATTTTGAATACTTTAAGGAATTGAAGTTATAAAAGAATTC
193 AAAAAATTACTCAAAGGAATGGATCATCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTC
* * *
3605 GTAAAAGTTTGAAAAGTTCGAAAGTTCA-GCCAAAAACCAA-GAGAGAAATAATTCTTACGTAAA
258 ATAAAAGTTTGAAAAGTTCGAAAGGT-AGGCCAAAAA-CAAGGAGAGAAATAATTCTCACGTAAA
** * * * *
3668 AAAGTTTTTAATTTAAAGACCAAAAGTTGTTCACAAAATAAGAAATTATTTGGACCAAATGATGA
321 AAAGTTTTTAATCCAAACACCAAAAGTTGTTCACAAAATAACAAACTATTTGGACCAAATGATCA
* ** *
3733 GATTTCTCGAGCATGGAATGTTCGAAAATTTGCTTGAAGGAATGAATCGTCTTGAATACTTTAAG
386 GATTTCTCGAGCATGGAATGTTCGAAAAATTGCTCAAAGGAATGAATCATCTTGAATACTTTAAG
** * ** ** * **
3798 GAATTGAAGTTGTAAAAGAACTTGTAAAAGTTTGACAAGTTTGAAAGTTCGGTCATAAATCAAGA
451 GAACCGAAGTTATAAAAGAACTCATAAAAGTTTGACAAGTTCAAAAGTTAGACCATAAATCAAGA
* * ** * *
3863 GAGAAATAATTTTCATGTAAATAAATTTTTAATTTAAAGACTGAAAGTTGTGTACAAAATGTCAA
516 GAGAAATAATTCTCACGTAAATAAATTTTTAATCCAAAGACTAAAAGTTGTGTACAAAATGACAA
**
3928 ACTATTTGGACCAAATGATGCGATTTCTTGAGCATGGAATGTTCAGAGAATTGCTT-GAAGGAAT
581 ACTATTTGGACCAAATGATGCGATTTCTCAAGCATGGAATGTTCAGAGAATTGCTTCGAAGGAAT
* *
3992 GGATCGTCTTAAATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCG
646 GGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCATAAAAGTTTGACAAGTTCG
* * *
4057 GAAGTTCGGCCAATAATCAAGAGAGAAACAATTCTCACGTAAATAAATTTTTAATTCAAAGACCA
711 GAAGTTCGGCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCA
* *
4122 AAAGTTTTTTACAAAATGACAAACTATTTGGACTAGAAGATGTGAATTCTCGAGCATGGAATGTT
776 AAAGTTGTTTACAAAATGACAAACTA-TT--A-T---A-ATGTGATTTCTCGAGCATGGAATGTT
* *
4187 TGGAAAATTGCTCGAAGGAATTG
833 CGGAAAATTGCTCGAAGGAATCG
* * *
4210 ATCGTCTTTAATACTTTAAGAAACCGATA-TTATAAAAGAACTCGTAAAAGATTGACAAGTTCGA
1 ATCGTCTTGAATACTTTAAGAAA-CGA-AGTTATAAAAGAACTCGTAAAAGTTTGA-AAGTTCGG
** * *
4274 AAGTTCGGTCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAA-AATCA
63 AAGTTCGACCAAGAACCAAGAGAGAAACAATTCTCATGTAAATAAGTTTTTAATTCAAAGACT-A
* * * * * *
4338 AAACTTATTTACAAAATGAAAAACTATTTGGGCTAAATGATACGATTTCTCGAGCATG
127 AAAGTTATTTACAAAATGACAAACTATTTGGACCAAATGATCCGATTTCCCGAGCATG
4396 AAGTGTTTTA
Statistics
Matches: 1654, Mismatches: 210, Indels: 128
0.83 0.11 0.06
Matches are distributed among these distances:
854 92 0.06
855 58 0.04
856 1 0.00
857 1 0.00
860 1 0.00
861 2 0.00
862 57 0.03
863 500 0.30
864 191 0.12
865 3 0.00
866 4 0.00
867 1 0.00
868 1 0.00
874 2 0.00
875 1 0.00
876 3 0.00
878 11 0.01
879 558 0.34
880 18 0.01
881 1 0.00
886 1 0.00
887 31 0.02
888 26 0.02
889 90 0.05
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.28
Consensus pattern (855 bp):
ATCGTCTTGAATACTTTAAGAAACGAAGTTATAAAAGAACTCGTAAAAGTTTGAAAGTTCGGAAG
TTCGACCAAGAACCAAGAGAGAAACAATTCTCATGTAAATAAGTTTTTAATTCAAAGACTAAAAG
TTATTTACAAAATGACAAACTATTTGGACCAAATGATCCGATTTCCCGAGCATGGAATGTTCAAA
AAATTACTCAAAGGAATGGATCATCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCATA
AAAGTTTGAAAAGTTCGAAAGGTAGGCCAAAAACAAGGAGAGAAATAATTCTCACGTAAAAAAGT
TTTTAATCCAAACACCAAAAGTTGTTCACAAAATAACAAACTATTTGGACCAAATGATCAGATTT
CTCGAGCATGGAATGTTCGAAAAATTGCTCAAAGGAATGAATCATCTTGAATACTTTAAGGAACC
GAAGTTATAAAAGAACTCATAAAAGTTTGACAAGTTCAAAAGTTAGACCATAAATCAAGAGAGAA
ATAATTCTCACGTAAATAAATTTTTAATCCAAAGACTAAAAGTTGTGTACAAAATGACAAACTAT
TTGGACCAAATGATGCGATTTCTCAAGCATGGAATGTTCAGAGAATTGCTTCGAAGGAATGGATC
GTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTCATAAAAGTTTGACAAGTTCGGAAGT
TCGGCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGT
TGTTTACAAAATGACAAACTATTATAATGTGATTTCTCGAGCATGGAATGTTCGGAAAATTGCTC
GAAGGAATCG
Found at i:6433 original size:15 final size:15
Alignment explanation
Indices: 6398--6435 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
6388 TCTGAGTTAA
6398 TATTTTCTTTATTGC
1 TATTTTCTTTATTGC
*
6413 TGTTTTCTTT-TTGC
1 TATTTTCTTTATTGC
6427 TTATTTTCT
1 -TATTTTCT
6436 AGTGGAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 4 0.20
15 16 0.80
ACGTcount: A:0.08, C:0.13, G:0.08, T:0.71
Consensus pattern (15 bp):
TATTTTCTTTATTGC
Found at i:8343 original size:144 final size:136
Alignment explanation
Indices: 8076--8351 Score: 338
Period size: 135 Copynumber: 2.0 Consensus size: 136
8066 GTTTGAATCA
* * *
8076 TCATTTAGTAAAATGACTAGTCATTCTTCATTACTAGGTGCTTCTGTGTGTTACTTAAAGGATAT
1 TCATTTAGTAAAATGACTACTCATTCTTCATTACTAGGTGCTTCTGGGTATTACTTAAAGGATAT
* * * *
8141 AATCATCTTTTGGTAGCCATTTAAGAAACTTGGAAGGAAATATAAGTTTGAACTGAAATGTTGGT
66 AATCACCTTTGGGTAGCCATTGAAGAAACTTGAAAGGAAATATAAGTTTGAACTGAAATGTTGGT
8206 GTCTTG
131 GTCTTG
* * * *
8212 TCATTTAGTAAAATGACTACTCA-TCTTCATTATTAGGTGCTTTTGGGTATTGCTTGAAGGATAG
1 TCATTTAGTAAAATGACTACTCATTCTTCATTACTAGGTGCTTCTGGGTATTACTTAAAGGATA-
* * *
8276 GTTCATGGATCACCTTTGGGTAGTCATTGAAGAAGCTTCGAAAGAGAAATATTAGTTTGAACTGA
65 --T-A---ATCACCTTTGGGTAGCCATTGAAGAAACTT-GAAAG-GAAATATAAGTTTGAACTGA
8341 AATGTTGGTGT
122 AATGTTGGTGT
8352 ATAAGTGTTG
Statistics
Matches: 117, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
135 34 0.29
136 22 0.19
138 1 0.01
139 1 0.01
142 25 0.21
143 4 0.03
144 30 0.26
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.37
Consensus pattern (136 bp):
TCATTTAGTAAAATGACTACTCATTCTTCATTACTAGGTGCTTCTGGGTATTACTTAAAGGATAT
AATCACCTTTGGGTAGCCATTGAAGAAACTTGAAAGGAAATATAAGTTTGAACTGAAATGTTGGT
GTCTTG
Found at i:14460 original size:19 final size:19
Alignment explanation
Indices: 14433--14470 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
14423 TTCGTTAATG
* *
14433 GTGTCTGATTAGTGGAATC
1 GTGTATGATTAGTGAAATC
14452 GTGTATGATTAGTGAAATC
1 GTGTATGATTAGTGAAATC
14471 ATGTGTGCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.26, C:0.08, G:0.29, T:0.37
Consensus pattern (19 bp):
GTGTATGATTAGTGAAATC
Found at i:16210 original size:23 final size:23
Alignment explanation
Indices: 16184--16254 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 23
16174 ATCTCGATGA
16184 AATTTGGATTGTATTTAAAGAGT
1 AATTTGGATTGTATTTAAAGAGT
** *
16207 AATTT--A--AAATTTAAACAAGT
1 AATTTGGATTGTATTTAAA-GAGT
* *
16227 TATTTGGATTGTACTTAAAGAGT
1 AATTTGGATTGTATTTAAAGAGT
16250 AATTT
1 AATTT
16255 AAATTTTAAA
Statistics
Matches: 34, Mismatches: 9, Indels: 10
0.64 0.17 0.19
Matches are distributed among these distances:
19 7 0.21
20 7 0.21
21 1 0.03
22 1 0.03
23 12 0.35
24 6 0.18
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.42
Consensus pattern (23 bp):
AATTTGGATTGTATTTAAAGAGT
Found at i:16233 original size:43 final size:43
Alignment explanation
Indices: 16185--16269 Score: 152
Period size: 43 Copynumber: 2.0 Consensus size: 43
16175 TCTCGATGAA
*
16185 ATTTGGATTGTATTTAAAGAGTAATTTAAAATTTAAACAAGTT
1 ATTTGGATTGTACTTAAAGAGTAATTTAAAATTTAAACAAGTT
*
16228 ATTTGGATTGTACTTAAAGAGTAATTTAAATTTTAAACAAGT
1 ATTTGGATTGTACTTAAAGAGTAATTTAAAATTTAAACAAGT
16270 AATCTTAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.41, C:0.04, G:0.14, T:0.41
Consensus pattern (43 bp):
ATTTGGATTGTACTTAAAGAGTAATTTAAAATTTAAACAAGTT
Found at i:21715 original size:47 final size:47
Alignment explanation
Indices: 21654--21749 Score: 192
Period size: 47 Copynumber: 2.0 Consensus size: 47
21644 GAAGAATAAA
21654 GCTGGTGTTGTTTGTGTAGCATGTCATCTTGGTAAACAAAATAAATT
1 GCTGGTGTTGTTTGTGTAGCATGTCATCTTGGTAAACAAAATAAATT
21701 GCTGGTGTTGTTTGTGTAGCATGTCATCTTGGTAAACAAAATAAATT
1 GCTGGTGTTGTTTGTGTAGCATGTCATCTTGGTAAACAAAATAAATT
21748 GC
1 GC
21750 CTTTCACCAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.27, C:0.11, G:0.24, T:0.38
Consensus pattern (47 bp):
GCTGGTGTTGTTTGTGTAGCATGTCATCTTGGTAAACAAAATAAATT
Found at i:24328 original size:19 final size:18
Alignment explanation
Indices: 24288--24329 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
24278 TCTACTTTTT
*
24288 CTTTTTCTCTTGCTTCTT
1 CTTTTTCTCTTGCTTCTC
24306 CTTTCTTCTCTT-CTTCCTC
1 CTTT-TTCTCTTGCTT-CTC
24325 CTTTT
1 CTTTT
24330 CCACAGCACC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.00, C:0.33, G:0.02, T:0.64
Consensus pattern (18 bp):
CTTTTTCTCTTGCTTCTC
Found at i:25278 original size:46 final size:46
Alignment explanation
Indices: 25211--25302 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
25201 AATGACGGTA
25211 CATTGTATAATTGTTTGGATTGTTTCCGGTCCAAACAAAACCATCG
1 CATTGTATAATTGTTTGGATTGTTTCCGGTCCAAACAAAACCATCG
*
25257 CATTGTATAATTGTTTGGATTGTTTCCGGTCCAAACAGAACCATCG
1 CATTGTATAATTGTTTGGATTGTTTCCGGTCCAAACAAAACCATCG
25303 ATGCATAAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (46 bp):
CATTGTATAATTGTTTGGATTGTTTCCGGTCCAAACAAAACCATCG
Found at i:40029 original size:2 final size:2
Alignment explanation
Indices: 40024--40051 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
40014 CTCTCAGTCA
40024 AT AT AT AT 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
40052 GCACTGAGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46301 original size:193 final size:194
Alignment explanation
Indices: 45947--46304 Score: 440
Period size: 194 Copynumber: 1.9 Consensus size: 194
45937 GAAACTGATG
* * * * *
45947 CGATGGTTGAGGTACCGCATATGTTACGAGTTCTCGACAGCTCGTGTGAGTAGCATCGTGAGTCA
1 CGATGGTTGAGGTACCGCATATGTTACGAGTCCTCGAAAACTCATGTGAGTAGCATCGTGACTCA
* * * *
46012 AGAAATGAGAAAGAATCCAAGAATGGATTACAGGCCCTACGATGGTTGAGATTTATGCATAAGTG
66 AGAAATGAGAAAGAATCCAAGAATAGATTACAGGCCCTACGATGGTTGAGATCTATCCATAAGCG
*
46077 CATATTCTCGATAGTTAGTGTGAGCAGCATCATTACTGAAAAATTATATACACAGATATCGTAT
131 CATACTCTCGATAGTTAGTGTGAGCAGCATCATTACTGAAAAATTATATACACAGATATCGTAT
* * **
46141 CGATGGTTGAGGTATCGCATATGTTGCGAGTCCTCGAAAACTCATGTGAGTAGCATCGTGACTTG
1 CGATGGTTGAGGTACCGCATATGTTACGAGTCCTCGAAAACTCATGTGAGTAGCATCGTGACTCA
* * * * * * *
46206 GGAAA-GAGATATGGATCCTA-AATAGATTATAGGCCCTACGATGGTTNNNG-GA-CTATCCTTT
66 AGAAATGAGA-AAGAATCCAAGAATAGATTACAGGCCCTACGATGGTT---GAGATCTATCCATA
46267 A-CGCATACTCTCGATAAG-TAGTGTGAGCAGCATCATTA
127 AGCGCATACTCTCGAT-AGTTAGTGTGAGCAGCATCATTA
46305 GGGAACAGTT
Statistics
Matches: 138, Mismatches: 21, Indels: 11
0.81 0.12 0.06
Matches are distributed among these distances:
193 60 0.43
194 75 0.54
195 2 0.01
196 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (194 bp):
CGATGGTTGAGGTACCGCATATGTTACGAGTCCTCGAAAACTCATGTGAGTAGCATCGTGACTCA
AGAAATGAGAAAGAATCCAAGAATAGATTACAGGCCCTACGATGGTTGAGATCTATCCATAAGCG
CATACTCTCGATAGTTAGTGTGAGCAGCATCATTACTGAAAAATTATATACACAGATATCGTAT
Found at i:47214 original size:71 final size:71
Alignment explanation
Indices: 47096--47254 Score: 246
Period size: 71 Copynumber: 2.2 Consensus size: 71
47086 GCTTATGTAC
* * *
47096 TTGTATCGGTAGAAGCTGCAGGGTAGGACATTTTAGCTATTTGGAGTTTTTAGTACCGGTAGAAG
1 TTGTATCGGTAGAAGCTGCAGGGTAGGACATTTTAGCTATCTAGAGTTTTTAGTACCAGTAGAAG
47161 AATGAT
66 AATGAT
* * *
47167 TTGTATCAGTAGAAGCTGCAGGGTAGGACATTTTAGCTCTCTAGAGTTTTTAGTACTAGTAGAAG
1 TTGTATCGGTAGAAGCTGCAGGGTAGGACATTTTAGCTATCTAGAGTTTTTAGTACCAGTAGAAG
*
47232 CATGAT
66 AATGAT
*
47238 TTGTTTCGGTAGAAGCT
1 TTGTATCGGTAGAAGCT
47255 TTACTTGTAT
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
71 79 1.00
ACGTcount: A:0.26, C:0.11, G:0.28, T:0.35
Consensus pattern (71 bp):
TTGTATCGGTAGAAGCTGCAGGGTAGGACATTTTAGCTATCTAGAGTTTTTAGTACCAGTAGAAG
AATGAT
Found at i:48860 original size:2 final size:2
Alignment explanation
Indices: 48853--48887 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
48843 AATGATTGAA
48853 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
48888 AAATTGATCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.