Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003540.1 Kokia drynarioides strain JFW-HI SEQ_116385, 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: 2497
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.30
Found at i:1826 original size:427 final size:424
Alignment explanation
Indices: 1024--2497 Score: 1519
Period size: 427 Copynumber: 3.5 Consensus size: 424
1014 AGGTACCAAA
* * * ** *
1024 GTAAAAGTTTGACAAATTCAGAAGTTCGTCCTAGAAGAAAGAGAGAAACAATTCTCACGTAAATG
1 GTAAAAGTTTGACAAGTTCAGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATA
* * * * * *
1089 AGTTTTTAATTCAAAGACCAAAACATGTTTACAGTAATGACAAAATATTTACACAAAATGATTCA
66 AG--TTTAATTCAAAGACCAAAACTTGATAACA-AAATGA-AAAATATTTAGACAAAATGATGCA
* * * * *
1154 ATTTTTTGAGCATGGAATGTTCGGAAAATTGTTCGAAGGAATGGCTCGTCTTGAATACTTTTAAG
127 ATTTCTCGAGCATGGAATGTTCGGAAAATTGCTCGAAGGAATGGATAGTCTTGAATA-TTTTAAG
* * * ** *
1219 GAACCTAAGTAATAAAGGACCTTGTAAAATTTTGACAAGTTCTCCAGTTCATCCAAGAACCAAAG
191 GAACCGAAGT-ATAAAAGAAC-TGTAAAATTTTGACAAGTTCTGAAGTTCGTCC-AGAACCAAAG
* * * *
1284 AGAAACAATTCTCACATAAAT-ACGATTTTAATTCAAAGACACAAACTTCTTTAGAAAATGACAA
253 AGAAACAATTCTCACATAAATAAC-TTTTTAATTCAAAGACA-AAAATTGTTTACAAAATGACAA
** * *
1348 ACTATTTAGACCAAATGATGCGATTTATTGTGCATGGAATGTTCGGAAAATTGCTCGAAGGAATG
316 ACTATTTAGACCAAATGATGCGATTTCCTGAGCATGGAATGTTCAGAAAATTGCTCGAAGGAATG
* *
1413 GTTCATCTTGAATACATTAAGGAACCGAAGTTATAACAGAACTC
381 GTTCATCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTC
* * * *
1457 ATAAAAGTTTGACAAGTTCAGAACTTCGTTCAAGAACCAAGAGAGAAACAATTCTCACGTAAATA
1 GTAAAAGTTTGACAAGTTCAGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATA
* * * *
1522 AG-TT-ATTCAAAGACCAAAAGTTGAAAACAAAATGAAAAACTATTTAGACCAAATGATGCGATT
66 AGTTTAATTCAAAGACCAAAACTTGATAACAAAATGAAAAA-TATTTAGACAAAATGATGCAATT
** *
1585 TCTCGAGCATGGAATGTTCCAAAAATTGCTCGAAGGAATGGATAGTCTTCAATATTTTAAGGAAC
130 TCTCGAGCATGGAATGTTCGGAAAATTGCTCGAAGGAATGGATAGTCTTGAATATTTTAAGGAAC
*
1650 CGAAGTTATAAAAGAACTCGTAAAATTTTGACAAGTTCGGAAGTTCGTCTCAGAACCAATAGAGA
195 CGAAG-TATAAAAGAACT-GTAAAATTTTGACAAGTTCTGAAGTTCGTC-CAGAACCAA-AGAGA
* * ** * *
1715 ACCAATTCTTACATAAATAACTTTTTAATTC-AAGTTAAAAAGTTGATAACAAAATGACAAACTA
256 AACAATTCTCACATAAATAACTTTTTAATTCAAAGACAAAAA-TTGTTTACAAAATGACAAACTA
* * * * *
1779 TTTAGACAAAATTATACGATTTCCTGAGCATGGAATGTTCAGAAAATTGCTTGAAGGAATGGATC
320 TTTAGACCAAATGATGCGATTTCCTGAGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGGTTC
* * *
1844 TTCTTGAATTCTTTAAGGAACCAAAGTTATAAAAGAACTC
385 ATCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTC
* * *
1884 GTAACAA-TTTGACAAGTTCGGATGTTCATCCAAGAACCAAGAGTGAAACAATTCTCACGTAAAT
1 GTAA-AAGTTTGACAAGTTCAGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAAT
* ** * * *
1948 AATTTTTTAATTCAAAGA-CACAAACTTTTTTACAAAATGACAAACTATTTAGACCAAATGATGC
65 AA--GTTTAATTCAAAGACCA-AAACTTGATAACAAAATGA-AAAATATTTAGACAAAATGATGC
* * * * * * * * *
2012 AATTTCACGAGAAGGGAATGTTTGGAAAATTGCTCGAAGCAGTTGATTGTCTTGAATATGTTAAG
126 AATTTCTCGAGCATGGAATGTTCGGAAAATTGCTCGAAGGAATGGATAGTCTTGAATATTTTAAG
* * *
2077 GTACC----------A-AA--GTAAAAGTTTGACAAGTTCTGAAGTTAGTCCCAGAACCAAGAGA
191 GAACCGAAGTATAAAAGAACTGTAAAATTTTGACAAGTTCTGAAGTTCGT-CCAGAACCAA-AGA
* * * *
2129 GAAATAGTTCTCACGTAAATAAGTTTTTAATTCAAAGACAAAAATCTGTTTACAAAATGACAAAC
254 GAAACAATTCTCACATAAATAACTTTTTAATTCAAAGACAAAAAT-TGTTTACAAAATGACAAAC
* * **
2194 TATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTT-TGAAAAATTGCTCGAAGGAATTA
318 TATTTAGACCAAATGATGCGATTTCCTGAGCATGGAATGTTCAG-AAAATTGCTCGAAGGAATGG
* * * *
2258 TTCATCTTCAATA-TTTTATGAACCGAATTTATAAAAGAACTC
382 TTCATCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTC
* * *
2300 GTAAAAGTTTGACAAGTTC-GAAAGTTCATCTC-AGAACCAATAGAGAAACAATTCTCAAGTACA
1 GTAAAAGTTTGACAAGTTCAG-AAGTTCATC-CAAGAACCAAGAGAGAAACAATTCTCACGTAAA
* * * * *
2363 TAAGTTTTTAATTC-AAGATCAAAAGTTGATAGCAAAATGACAAATGATTTAGATAAAACT-ATG
64 TAAG--TTTAATTCAAAGACCAAAACTTGATAACAAAATGAAAAAT-ATTTAGACAAAA-TGATG
** *
2426 TGATTTC-CAGAGCATGGAATGTTTGGAAAATTGCTCGAAGGAATGGATCA-TCTTGAAT-TCTT
125 CAATTTCTC-GAGCATGGAATGTTCGGAAAATTGCTCGAAGGAATGGAT-AGTCTTGAATAT-TT
2488 TAAGGAACCG
187 TAAGGAACCG
Statistics
Matches: 871, Mismatches: 140, Indels: 77
0.80 0.13 0.07
Matches are distributed among these distances:
414 5 0.01
415 90 0.10
416 157 0.18
417 90 0.10
419 2 0.00
420 1 0.00
426 4 0.00
427 230 0.26
428 104 0.12
429 22 0.03
430 6 0.01
431 98 0.11
432 3 0.00
433 59 0.07
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.29
Consensus pattern (424 bp):
GTAAAAGTTTGACAAGTTCAGAAGTTCATCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATA
AGTTTAATTCAAAGACCAAAACTTGATAACAAAATGAAAAATATTTAGACAAAATGATGCAATTT
CTCGAGCATGGAATGTTCGGAAAATTGCTCGAAGGAATGGATAGTCTTGAATATTTTAAGGAACC
GAAGTATAAAAGAACTGTAAAATTTTGACAAGTTCTGAAGTTCGTCCAGAACCAAAGAGAAACAA
TTCTCACATAAATAACTTTTTAATTCAAAGACAAAAATTGTTTACAAAATGACAAACTATTTAGA
CCAAATGATGCGATTTCCTGAGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGGTTCATCTTG
AATACTTTAAGGAACCGAAGTTATAAAAGAACTC
Found at i:1837 original size:215 final size:216
Alignment explanation
Indices: 1024--2497 Score: 1387
Period size: 215 Copynumber: 6.9 Consensus size: 216
1014 AGGTACCAAA
* * * * ** *
1024 GTAAAAGTTTGACAAATTCAGAAGTTCGTC-CTAGAAGAAAGAGAGAAACAATTCTCACGTAAAT
1 GTAAAAGTTTGACAAGTTCGGAAGTTCATCTCAAGAACCAAGAGAGAAACAATTCTCACATAAAT
* * * ** * * * * * * *
1088 GAGTTTTTAATTCAAAGACCAAAACATGTTTACAGTAATGACAAAATATTTACACAAAATGATTC
66 AACTTTTTAATTCAAAGACAAAAAGTTGATAACA-AAATGACAAACTATTTAGACCAAATGATGC
* ** * * *
1153 AATTTTTTGAGCATGGAATGTTCGGAAAATTGTTCGAAGGAATGGCTCGTCTTGAATACTTTTAA
130 GATTTCCTGAGCATGGAATGTTCGGAAAATTGCTCGAAGGAATGGAT-ATCTTGAATA-TTTTAA
* * * * *
1218 GGAACCTAAGTAATAAAGGACCTT
193 GGAACCGAAGTTATAAAAGAACTC
* ***
1242 GTAAAATTTTGACAAGTTCTCCAGTTCATC-CAAGAACCAA-AGAGAAACAATTCTCACATAAAT
1 GTAAAAGTTTGACAAGTTCGGAAGTTCATCTCAAGAACCAAGAGAGAAACAATTCTCACATAAAT
* * * ** * *
1305 -ACGATTTTAATTCAAAGACACAAACTTCTTTAGAAAATGACAAACTATTTAGACCAAATGATGC
66 AAC-TTTTTAATTCAAAGACAAAAAGTTGATAACAAAATGACAAACTATTTAGACCAAATGATGC
** * * **
1369 GATTTATTGTGCATGGAATGTTCGGAAAATTGCTCGAAGGAATGGTTCATCTTGAATACATTAAG
130 GATTTCCTGAGCATGGAATGTTCGGAAAATTGCTCGAAGGAATGGAT-ATCTTGAATATTTTAAG
*
1434 GAACCGAAGTTATAACAGAACTC
194 GAACCGAAGTTATAAAAGAACTC
* * * * *
1457 ATAAAAGTTTGACAAGTTCAGAACTTCGT-TCAAGAACCAAGAGAGAAACAATTCTCACGTAAAT
1 GTAAAAGTTTGACAAGTTCGGAAGTTCATCTCAAGAACCAAGAGAGAAACAATTCTCACATAAAT
* * * *
1521 AA---GTT-ATTCAAAGACCAAAAGTTGAAAACAAAATGAAAAACTATTTAGACCAAATGATGCG
66 AACTTTTTAATTCAAAGACAAAAAGTTGATAACAAAATGACAAACTATTTAGACCAAATGATGCG
** *
1582 ATTT-CTCGAGCATGGAATGTTCCAAAAATTGCTCGAAGGAATGGATAGTCTTCAATATTTTAAG
131 ATTTCCT-GAGCATGGAATGTTCGGAAAATTGCTCGAAGGAATGGATA-TCTTGAATATTTTAAG
1646 GAACCGAAGTTATAAAAGAACTC
194 GAACCGAAGTTATAAAAGAACTC
* * * * *
1669 GTAAAATTTTGACAAGTTCGGAAGTTCGTCTC-AGAACCAATAGAGAACCAATTCTTACATAAAT
1 GTAAAAGTTTGACAAGTTCGGAAGTTCATCTCAAGAACCAAGAGAGAAACAATTCTCACATAAAT
** * * *
1733 AACTTTTTAATTC-AAGTTAAAAAGTTGATAACAAAATGACAAACTATTTAGACAAAATTATACG
66 AACTTTTTAATTCAAAGACAAAAAGTTGATAACAAAATGACAAACTATTTAGACCAAATGATGCG
* * *
1797 ATTTCCTGAGCATGGAATGTTCAGAAAATTGCTTGAAGGAATGGATCTTCTTGAAT-TCTTTAAG
131 ATTTCCTGAGCATGGAATGTTCGGAAAATTGCTCGAAGGAATGGAT-ATCTTGAATAT-TTTAAG
*
1861 GAACCAAAGTTATAAAAGAACTC
194 GAACCGAAGTTATAAAAGAACTC
* * *
1884 GTAACAA-TTTGACAAGTTCGGATGTTCATC-CAAGAACCAAGAGTGAAACAATTCTCACGTAAA
1 GTAA-AAGTTTGACAAGTTCGGAAGTTCATCTCAAGAACCAAGAGAGAAACAATTCTCACATAAA
* * * ** *
1947 TAATTTTTTAATTCAAAGACACAAACTTTTTTACAAAATGACAAACTATTTAGACCAAATGATGC
65 TAACTTTTTAATTCAAAGACAAAAAGTTGATAACAAAATGACAAACTATTTAGACCAAATGATGC
* * * * * * * * *
2012 AATTTCAC-GAGAAGGGAATGTTTGGAAAATTGCTCGAAGCAGTTGATTGTCTTGAATATGTTAA
130 GATTTC-CTGAGCATGGAATGTTCGGAAAATTGCTCGAAGGAATGGA-TATCTTGAATATTTTAA
*
2076 GGTACC-----------A-AA---
193 GGAACCGAAGTTATAAAAGAACTC
* * * * *
2085 GTAAAAGTTTGACAAGTTCTGAAGTT-AGTC-CCAGAACCAAGAGAGAAATAGTTCTCACGTAAA
1 GTAAAAGTTTGACAAGTTCGGAAGTTCA-TCTCAAGAACCAAGAGAGAAACAATTCTCACATAAA
* * *
2148 TAAGTTTTTAATTCAAAGACAAAAA-TCTGTTTACAAAATGACAAACTATTTAGACCAAATGATG
65 TAACTTTTTAATTCAAAGACAAAAAGT-TGATAACAAAATGACAAACTATTTAGACCAAATGATG
* * * * *
2212 CGATTTCCCGAGCATGGAATGTTTGAAAAATTGCTCGAAGGAAT-TATTCATCTTCAATATTTT-
129 CGATTTCCTGAGCATGGAATGTTCGGAAAATTGCTCGAAGGAATGGA-T-ATCTTGAATATTTTA
* *
2275 ATGAACCGAATTTATAAAAGAACTC
192 AGGAACCGAAGTTATAAAAGAACTC
* * *
2300 GTAAAAGTTTGACAAGTTCGAAAGTTCATCTC-AGAACCAATAGAGAAACAATTCTCA-AGTACA
1 GTAAAAGTTTGACAAGTTCGGAAGTTCATCTCAAGAACCAAGAGAGAAACAATTCTCACA-TAAA
* * **
2363 TAAGTTTTTAATTC-AAGATC-AAAAGTTGATAGCAAAATGACAAA-TGATTTAGATAAAACT-A
65 TAACTTTTTAATTCAAAGA-CAAAAAGTTGATAACAAAATGACAAACT-ATTTAGACCAAA-TGA
* * *
2424 TGTGATTTCCAGAGCATGGAATGTTTGGAAAATTGCTCGAAGGAATGGATCATCTTGAAT-TCTT
127 TGCGATTTCCTGAGCATGGAATGTTCGGAAAATTGCTCGAAGGAATGGAT-ATCTTGAATAT-TT
2488 TAAGGAACCG
190 TAAGGAACCG
Statistics
Matches: 1051, Mismatches: 155, Indels: 103
0.80 0.12 0.08
Matches are distributed among these distances:
200 13 0.01
201 158 0.15
204 2 0.00
205 1 0.00
211 3 0.00
212 178 0.17
213 6 0.01
214 92 0.09
215 314 0.30
216 202 0.19
217 51 0.05
218 31 0.03
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.29
Consensus pattern (216 bp):
GTAAAAGTTTGACAAGTTCGGAAGTTCATCTCAAGAACCAAGAGAGAAACAATTCTCACATAAAT
AACTTTTTAATTCAAAGACAAAAAGTTGATAACAAAATGACAAACTATTTAGACCAAATGATGCG
ATTTCCTGAGCATGGAATGTTCGGAAAATTGCTCGAAGGAATGGATATCTTGAATATTTTAAGGA
ACCGAAGTTATAAAAGAACTC
Found at i:2236 original size:201 final size:207
Alignment explanation
Indices: 701--2465 Score: 1091
Period size: 215 Copynumber: 8.3 Consensus size: 207
691 GACTCATATA
* ** **
701 ACAAAATGACAAACTATTTAGACAAAACAATGCGATTTCCCGAGCATGGAATGTTCAGAAAATTG
1 ACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTTGGAAAATTG
* * * * *
766 CTCGAAAG-AATGGA-TCATCCTGAAT-TCTTTAAGGAACCGAAGTTATAAAAGAAATCGTAAAA
66 CTCG-AAGCAAT-TATTCATCTTCAATAT-TGT-ATGAA-C---G-TATAAAAG-AA-CGTAAAA
* ** * * * *
828 GTTTGACAAGTTCAAAAGTTTGTCTCAGAACTAATAGAGAAACAATTCTCACATAAATAAGTTTT
120 GTTTGACAAGTTC-GAAGTTCATCCCAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTT
* *
893 TAATTCAAAGACACAAA-CTTTTTT
184 TAATTCAAAGACAAAAATC-TGTTT
* ** * *
917 ACAAAATGACAAAAGTATTTAGACCAAATGATGCGATTTTACGAGAATGGAATG-TTCGAAAATT
1 ACAAAATGAC-AAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTTGGAAAA-T
* * * * **
981 TGCTCGAAGGAATTGA-T-AGTCTTAAATACT-T-T-AA-G-GTACCA-AA-GTAAAAGTTTGAC
64 TGCTCGAAGCAATT-ATTCA-TCTTCAATATTGTATGAACGTATAAAAGAACGTAAAAGTTTGAC
* * * ** *
1037 AAATTCAGAAGTTCGTCCTAGAAGAAAGAGAGAAACAATTCTCACGTAAATGAGTTTTTAATTCA
127 AAGTTC-GAAGTTCATCCCAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCA
*
1102 AAGACCAAAA-CATGTTT
191 AAGACAAAAATC-TGTTT
* * * * * * *** *
1119 ACAGTAATGACAAAATATTTACACAAAATGATTCAATTTTTTGAGCATGGAATGTTCGGAAAATT
1 ACA-AAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTTGGAAAATT
* * *** * * * * * * *
1184 GTTCGAAGGAATGGCTCGTCTTGAATACTTTTAAGGAACCTAAGTAATAAAGGACCTTGTAAAAT
65 GCTCGAAGCAATTATTCATCTTCAATA-TTGT-ATGAA-C---GT-ATAAAAGAAC--GTAAAAG
** * * * *
1249 TTTGACAAGTTCTCCAGTTCATCCAAGAACCAA-AGAGAAACAATTCTCACATAAATACGATTTT
121 TTTGACAAGTTC-GAAGTTCATCCCAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTT
* *
1313 AATTCAAAGACACAAA-CTTCTTT
185 AATTCAAAGACAAAAATC-TGTTT
* *** * *
1336 AGAAAATGACAAACTATTTAGACCAAATGATGCGATTTATTGTGCATGGAATGTTCGGAAAATTG
1 ACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTTGGAAAATTG
* ** * * * * *
1401 CTCGAAGGAATGGTTCATCTTGAATACATT-AAGGAACCGAAGTTATAACAGAACTCATAAAAGT
66 CTCGAAGCAATTATTCATCTTCAAT--ATTGTATGAA-C---G-TATAAAAGAA--CGTAAAAGT
* * * *
1465 TTGACAAGTTCAGAACTTCGTTCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAG---TT-
122 TTGACAAGTTC-GAAGTTCATCCCAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTA
* ***
1526 ATTCAAAGACCAAAAGT-TGAAA
186 ATTCAAAGA-CAAAAATCTGTTT
* * ***
1548 ACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTCCAAAAATTG
1 ACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTTGGAAAATTG
* * * * *
1613 CTCGAAGGAATGGA-T-AGTCTTCAATATTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAT
66 CTCGAAGCAAT-TATTCA-TCTTCAATATTGT-ATGAA-C---G-TATAAAAGAA--CGTAAAAG
* * * * * * *
1676 TTTGACAAGTTCGGAAGTTCGTCTCAGAACCAATAGAGAACCAATTCTTACATAAATAACTTTTT
121 TTTGACAAGTTC-GAAGTTCATCCCAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTT
** * *
1741 AATTC-AAGTTAAAAAGT-TGATA
185 AATTCAAAGACAAAAA-TCTGTTT
* * * * **
1763 ACAAAATGACAAACTATTTAGACAAAATTATACGATTTCCTGAGCATGGAATGTTCAGAAAATTG
1 ACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTTGGAAAATTG
* * * * * * *
1828 CTTGAAGGAATGGA-TCTTCTTGAAT-TCTTTAAGGAACCAAAGTTATAAAAGAACTCGTAACAA
66 CTCGAAGCAAT-TATTCATCTTCAATAT-TGT-ATGAA-C---G-TATAAAAGAA--CGTAA-AA
* * * *
1891 -TTTGACAAGTTCGGATGTTCATCCAAGAACCAAGAGTGAAACAATTCTCACGTAAATAATTTTT
120 GTTTGACAAGTTC-GAAGTTCATCCCAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTT
* *
1955 TAATTCAAAGACACAAA-CTTTTTT
184 TAATTCAAAGACAAAAATC-TGTTT
* * * *
1979 ACAAAATGACAAACTATTTAGACCAAATGATGCAATTTCACGAGAAGGGAATGTTTGGAAAATTG
1 ACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTTGGAAAATTG
* * * * **
2044 CTCGAAGCAGTTGATT-GTCTTGAATA-TGT-T-AA-G-GTACCA-AA-GTAAAAGTTTGACAAG
66 CTCGAAGCAATT-ATTCATCTTCAATATTGTATGAACGTATAAAAGAACGTAAAAGTTTGACAAG
* *
2101 TTCTGAAGTT-AGTCCCAGAACCAAGAGAGAAATAGTTCTCACGTAAATAAGTTTTTAATTCAAA
130 TTC-GAAGTTCA-TCCCAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAA
2165 GACAAAAATCTGTTT
193 GACAAAAATCTGTTT
*
2180 ACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTTGAAAAATTG
1 ACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTTGGAAAATTG
* *
2245 CTCGAAGGAATTATTCATCTTCAATATTTTATGAACCGAATTTATAAAAGAACTCGTAAAAGTTT
66 CTCGAAGCAATTATTCATCTTCAATATTGTATGAA-CG----TATAAAAGAA--CGTAAAAGTTT
* * * *
2310 GACAAGTTCGAAAGTTCATCTCAGAACCAATAGAGAAACAATTCTCAAGTACATAAGTTTTTAAT
124 GACAAGTTCG-AAGTTCATCCCAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAAT
* *
2375 TC-AAGATCAAAAGT-TG-AT
188 TCAAAGA-CAAAAATCTGTTT
** * *
2393 AGCAAAATGACAAA-TGATTTAGATAAAACT-ATGTGATTTCCAGAGCATGGAATGTTTGGAAAA
1 A-CAAAATGACAAACT-ATTTAGACCAAA-TGATGCGATTTCCCGAGCATGGAATGTTTGGAAAA
2456 TTGCTCGAAG
63 TTGCTCGAAG
2466 GAATGGATCA
Statistics
Matches: 1259, Mismatches: 214, Indels: 154
0.77 0.13 0.09
Matches are distributed among these distances:
200 6 0.00
201 157 0.12
202 144 0.11
203 14 0.01
204 7 0.01
205 3 0.00
206 4 0.00
207 3 0.00
208 1 0.00
210 3 0.00
211 4 0.00
212 171 0.14
213 12 0.01
214 76 0.06
215 305 0.24
216 210 0.17
217 107 0.08
218 32 0.03
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.28
Consensus pattern (207 bp):
ACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTTGGAAAATTG
CTCGAAGCAATTATTCATCTTCAATATTGTATGAACGTATAAAAGAACGTAAAAGTTTGACAAGT
TCGAAGTTCATCCCAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGAC
AAAAATCTGTTT
Found at i:2468 original size:631 final size:626
Alignment explanation
Indices: 822--2496 Score: 1860
Period size: 631 Copynumber: 2.6 Consensus size: 626
812 AAAAGAAATC
* * * * * *
822 GTAAAAGTTTGACAAGTTCAAAAGTTTGTCTCAGAACTAATAGAGAAACAATTCTCACATAAATA
1 GTAAAAGTTTGACAAGTTCAGAAGTTAGTCCCAGAACCAAGAGAGAAACAATTCTCACGTAAATA
* * *
887 AGTTTTTAATTCAAAGACACAAA-CTTTTTTACAAAATGACAAAAGTATTTAGACCAAATGATGC
66 AGTTTTTAATTCAAAGACAAAAATC-TGTTTACAAAATGAC-AAACTATTTAGACCAAATGATGC
* * * * *
951 GATTTTACGAGAATGGAATGTTCGAAAATTTGCTCGAAGGAATTGATAGTCTTAAATA-CTT-T-
129 GATTTCACGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATT-ATAGTCTTCAATATTTTATG
* ** * ** *
1013 AA--G----GTACCA-AA---GTAAAAGTTTGACAAATTC-AGAAGTTCGTC-CTAGAAGAAAGA
193 AACCGAATTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGA-AAGTTCGTCTC-AGAACCAATA
* * * ** * *
1066 GAGAAACAATTCTCACGTAAATGAGTTTTTAATTCAAAGACCAAAACATGTTTACAGTAATGACA
256 GAGAAACAATTCTCAAGTAAATAAGTTTTTAATTC-AAGATCAAAAGTTG-ATACA-AAATGAC-
* * ** *
1131 AAATATTTACACAAAATGATTCAATTTTTTGAGCATGGAATGTTCGGAAAATTGTTCGAAGGAAT
317 AAATATTTAGACAAAAT-ATT-GATTTCCTGAGCATGGAATGTTCGGAAAATTGCTCGAAGGAAT
* * * * * * *
1196 GGCTCGTCTTGAATACTTTTAAGGAACCTAAGTAATAAAGGACCTTGTAAAATTTTGACAAGTTC
380 GGATCATCTTGAATTC-TTTAAGGAACCAAAGTAATAAAAGAACTCGTAAAATTTTGACAAGTTC
*
1261 TCCAGTTCATCCAAGAACCAAAGAGAAACAATTCTCACATAAATACGATTTTAATTCAAAGACAC
444 TCCAGTTCATCCAAGAACCAAAGAGAAACAATTCTCACATAAATAAGATTTTAATTCAAAGACAC
* * * * * *
1326 AAACTTCTTTAGAAAATGACAAACTATTTAGACCAAATGATGCGATTTATTGTGCATGGAATGTT
509 AAACTTCTTTACAAAATGACAAACTATTTAGACCAAATGATGCAATTTATCGAGAAGGGAATGTT
* *
1391 CGGAAAATTGCTCGAAGGAATGGTTCATCTTGAATACATTAAGGAACCGAAGTTATAACA
574 CGGAAAATTGCTCGAAGCAATGATTCATCTTGAATACATTAAGGAACC------A-AACA
* * * *
1451 GAACTCATAAAAGTTTGACAAGTTCAGAACTTCGTTCAAGAACCAAGAGAGAAACAATTCTCACG
1 G------TAAAAGTTTGACAAGTTCAGAAGTTAGTCCCAGAACCAAGAGAGAAACAATTCTCACG
* *** *
1516 TAAATAAG---TT-ATTCAAAGACCAAAAGT-TGAAAACAAAATGAAAAACTATTTAGACCAAAT
60 TAAATAAGTTTTTAATTCAAAGA-CAAAAATCTGTTTACAAAATGACAAACTATTTAGACCAAAT
* * *
1576 GATGCGATTTCTCGAGCATGGAATGTTCCAAAAATTGCTCGAAGGAATGGATAGTCTTCAATATT
124 GATGCGATTTCACGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAAT-TATAGTCTTCAATATT
* * *
1641 TTAAGGAACCGAAGTTATAAAAGAACTCGTAAAATTTTGACAAGTTCGGAAGTTCGTCTCAGAAC
188 TT-ATGAACCGAA-TTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCTCAGAAC
* * * * *
1706 CAATAGAGAACCAATTCTTACA-TAAATAACTTTTTAATTCAAGTTAAAAAGTTGATAACAAAAT
251 CAATAGAGAAACAATTCTCA-AGTAAATAAGTTTTTAATTCAAGATCAAAAGTTGAT-ACAAAAT
* * *
1770 GACAAACTATTTAGACAAAATTATACGATTTCCTGAGCATGGAATGTTCAGAAAATTGCTTGAAG
314 GACAAA-TATTTAGACAAAA-TAT-TGATTTCCTGAGCATGGAATGTTCGGAAAATTGCTCGAAG
* *
1835 GAATGGATCTTCTTGAATTCTTTAAGGAACCAAAGTTATAAAAGAACTCGTAACAA-TTTGACAA
376 GAATGGATCATCTTGAATTCTTTAAGGAACCAAAGTAATAAAAGAACTCGTAA-AATTTTGACAA
** * * **
1899 GTTC-GGATGTTCATCCAAGAACCAAGAGTGAAACAATTCTCACGTAAATAATTTTTTAATTCAA
440 GTTCTCCA-GTTCATCCAAGAACCAA-AGAGAAACAATTCTCACATAAATAAGATTTTAATTCAA
*
1963 AGACACAAACTTTTTTACAAAATGACAAACTATTTAGACCAAATGATGCAATTTCA-CGAGAAGG
503 AGACACAAACTTCTTTACAAAATGACAAACTATTTAGACCAAATGATGCAATTT-ATCGAGAAGG
* * * ** *
2027 GAATGTTTGGAAAATTGCTCGAAGCAGTTGATT-GTCTTGAATATGTTAAGGTACC-AA-A
567 GAATGTTCGGAAAATTGCTCGAAGCA-ATGATTCATCTTGAATACATTAAGGAACCAAACA
* * *
2085 GTAAAAGTTTGACAAGTTCTGAAGTTAGTCCCAGAACCAAGAGAGAAATAGTTCTCACGTAAATA
1 GTAAAAGTTTGACAAGTTCAGAAGTTAGTCCCAGAACCAAGAGAGAAACAATTCTCACGTAAATA
2150 AGTTTTTAATTCAAAGACAAAAATCTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGA
66 AGTTTTTAATTCAAAGACAAAAATCTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGA
* *
2215 TTTCCCGAGCATGGAATGTTTGAAAAATTGCTCGAAGGAATTATTCA-TCTTCAATATTTTATGA
131 TTTCACGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATTA-T-AGTCTTCAATATTTTATGA
*
2279 ACCGAATTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCATCTCAGAACCAATAGA
194 ACCGAA-TTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCTCAGAACCAATAGA
*
2344 GAAACAATTCTCAAGTACATAAGTTTTTAATTCAAGATCAAAAGTTGATAGCAAAATGACAAATG
258 GAAACAATTCTCAAGTAAATAAGTTTTTAATTCAAGATCAAAAGTTGATA-CAAAATGACAAAT-
* * *
2409 ATTTAGATAAAACTATGTGATTTCCAGAGCATGGAATGTTTGGAAAATTGCTCGAAGGAATGGAT
321 ATTTAGACAAAA-TAT-TGATTTCCTGAGCATGGAATGTTCGGAAAATTGCTCGAAGGAATGGAT
2474 CATCTTGAATTCTTTAAGGAACC
384 CATCTTGAATTCTTTAAGGAACC
2497 G
Statistics
Matches: 879, Mismatches: 121, Indels: 90
0.81 0.11 0.08
Matches are distributed among these distances:
628 59 0.07
629 1 0.00
630 75 0.09
631 226 0.26
632 103 0.12
633 1 0.00
634 4 0.00
635 59 0.07
636 1 0.00
641 4 0.00
642 62 0.07
643 203 0.23
644 18 0.02
645 62 0.07
646 1 0.00
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (626 bp):
GTAAAAGTTTGACAAGTTCAGAAGTTAGTCCCAGAACCAAGAGAGAAACAATTCTCACGTAAATA
AGTTTTTAATTCAAAGACAAAAATCTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGA
TTTCACGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATTATAGTCTTCAATATTTTATGAAC
CGAATTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCTCAGAACCAATAGAGAA
ACAATTCTCAAGTAAATAAGTTTTTAATTCAAGATCAAAAGTTGATACAAAATGACAAATATTTA
GACAAAATATTGATTTCCTGAGCATGGAATGTTCGGAAAATTGCTCGAAGGAATGGATCATCTTG
AATTCTTTAAGGAACCAAAGTAATAAAAGAACTCGTAAAATTTTGACAAGTTCTCCAGTTCATCC
AAGAACCAAAGAGAAACAATTCTCACATAAATAAGATTTTAATTCAAAGACACAAACTTCTTTAC
AAAATGACAAACTATTTAGACCAAATGATGCAATTTATCGAGAAGGGAATGTTCGGAAAATTGCT
CGAAGCAATGATTCATCTTGAATACATTAAGGAACCAAACA
Done.