Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011081.1 Kokia drynarioides strain JFW-HI SEQ_126054, 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: 3729
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.39
Warning! 100 characters in sequence are not A, C, G, or T
Found at i:454 original size:216 final size:216
Alignment explanation
Indices: 4--456 Score: 577
Period size: 216 Copynumber: 2.1 Consensus size: 216
1 TTC
* * ** *
4 TTTCGCTCTTGGTTCTTGGACGAAGTATCGAACTTGTCAAACATTTACTAGTTCTTTTACAACTT
1 TTTCCCTCTTGGTTCTTGGACGAACTATCGAACACGTCAAACATTTACGAGTTCTTTTACAACTT
* * * *
69 CGATTCCTGAGAGTAGTCAAGATGATCCATTCCTTCGACCAATTTTCCGAGCATTCCATGATCAG
66 CGATTCCTGAGAGTAGTAAAGACGATCCATTCCTTCGACCAATTTTCCGAACATTCCATGACCAG
* * * * *
134 GATATCGTATCATTTGGTCTAAATAGTTTGTCATTTTGTACACAACTTTTGGTCTTTGAATTAAA
131 GAAATCGTATCATTTGATCTAAATAGTTTATCATTTCGTACACAACTTTTAGTCTTTGAATTAAA
* * *
199 AACTTTTTTACGTGGGAATTG
196 AACTTATTTACGTGAGAATTA
* * ** * * *
220 TTTCTCTATTTTTTCTTGGACGAACTTTCGAACACGTCAAACATTTTCGAGTTCTTTTATAACTT
1 TTTCCCTCTTGGTTCTTGGACGAACTATCGAACACGTCAAACATTTACGAGTTCTTTTACAACTT
* * * *
285 CGATTCCTGAGAGTATTAAAGACGATCCATTCCTTC-AGCCAATTTTTCGAACATTCCATGCCCG
66 CGATTCCTGAGAGTAGTAAAGACGATCCATTCCTTCGA-CCAATTTTCCGAACATTCCATGACCA
* * * *
349 GGAAATCGCT-TCGTTTGATTTAAATAGTTTATCATTTCGTATACAATTTTTAGTCTTTGAATTA
130 GGAAATCG-TATCATTTGATCTAAATAGTTTATCATTTCGTACACAACTTTTAGTCTTTGAATTA
*
413 AATACTTATTTACGTGAGAATTA
194 AAAACTTATTTACGTGAGAATTA
436 TTTCCCTCTTGGTTCTTGGAC
1 TTTCCCTCTTGGTTCTTGGAC
457 CAACATATGA
Statistics
Matches: 199, Mismatches: 36, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
215 1 0.01
216 197 0.99
217 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.40
Consensus pattern (216 bp):
TTTCCCTCTTGGTTCTTGGACGAACTATCGAACACGTCAAACATTTACGAGTTCTTTTACAACTT
CGATTCCTGAGAGTAGTAAAGACGATCCATTCCTTCGACCAATTTTCCGAACATTCCATGACCAG
GAAATCGTATCATTTGATCTAAATAGTTTATCATTTCGTACACAACTTTTAGTCTTTGAATTAAA
AACTTATTTACGTGAGAATTA
Found at i:973 original size:216 final size:216
Alignment explanation
Indices: 521--2374 Score: 1920
Period size: 216 Copynumber: 8.6 Consensus size: 216
511 NNNNNNNNNN
* * * * * * *
521 GTAAACAACTTTTGGTCATTGAATTAAAAACTTTTTTACATGGGAATTGTTTCTCTATTTGTTCT
1 GTAAACAAATTTTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAATTATTTCTCTCTTGGTTCT
* * *
586 TGGACAAACTTTCGAAC-ACGTCAAACATTTT-CGAGTTCTTTTATAACTTCGATTCCTGAGAGT
66 TGGACGAACTATCGAACTA-GTCAAAC-TTTTACAAGTTCTTTTATAACTTCGATTCCTGAGAGT
* * * * * *** * * *
649 ATTAAAGAAGATTCA-TTCCTTCAGCCAATTTTTCGAACATTCCATGCCCGGGAAATCGCTTCGT
129 ATTCAAGAAGATCCATTTCTTTGA-CCAATTTTTCGAAGATTCCATGATAGAGAAATCGCATCAT
* * *
713 TTGATTTAAATAGTTTATCATTTT
193 TTGGTATAAATAGTTTGTCATTTT
* * * * * *
737 GTATACAATTTTTAGTCTTTGAATTAAATACTTATTTACGTGAGAATTATTTCCCTCTTGGTTCT
1 GTAAACAAATTTTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAATTATTTCTCTCTTGGTTCT
* *
802 TGGACCAACATAT-GAACTAGTCAAACTTTTACAAGTTCTTTTATAACTTCGGTTCCTGAGAGTA
66 TGGACGAAC-TATCGAACTAGTCAAACTTTTACAAGTTCTTTTATAACTTCGATTCCTGAGAGTA
* * * *
866 TTCAAGAAGATCCATTTTCTTTGACCAATTTTTTGAAGATTCCATTATAGAGAAATCACAGCATT
130 TTCAAGAAGATCCA-TTTCTTTGACCAATTTTTCGAAGATTCCATGATAGAGAAATCGCATCATT
* *
931 TGGTAAAAATAGTTTGCCA-TTT
194 TGGTATAAATAGTTTGTCATTTT
* * * *
953 GTAAATAAATTTTGGTCTTTGAATTAAAAACTTTTTTACATTAGAATTCTTTCTCTCTTGGTTCT
1 GTAAACAAATTTTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAATTATTTCTCTCTTGGTTCT
* * * * * *
1018 TGGACGAAGTATCGAACTTGTCAAACATTTACTAGTTCTTTTACAACTTCGATTCCTGAGAGTAG
66 TGGACGAACTATCGAACTAGTCAAACTTTTACAAGTTCTTTTATAACTTCGATTCCTGAGAGTAT
* * * * *
1083 CCAAGATGATCCATTCCTTCGACCAATTTTTCG-AGCATTCCATGATCAG-GAAATCGTATCATT
131 TCAAGAAGATCCATTTCTTTGACCAATTTTTCGAAG-ATTCCATGAT-AGAGAAATCGCATCATT
* ** *
1146 TGGTCTAAATAGTTTGGAATTTC
194 TGGTATAAATAGTTTGTCATTTT
* * * * * * *
1169 GTAAACAACTTTTGGTCATTGAATTAAAAACTTTTTTACATGGGAATTGTTTCTCTATTTGTTCT
1 GTAAACAAATTTTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAATTATTTCTCTCTTGGTTCT
* * *
1234 TGGACAAACTTTCGAAC-ACGTCAAACATTTT-CGAGTTCTTTTATAACTTCGATTCCTGAGAGT
66 TGGACGAACTATCGAACTA-GTCAAAC-TTTTACAAGTTCTTTTATAACTTCGATTCCTGAGAGT
* * * * * *** * ** *
1297 ATTAAAGAAGATTCA-TTCCTTCAGCCAATTTTTCGAACATTCCATGCCCGGGAAATCGTTTCGT
129 ATTCAAGAAGATCCATTTCTTTGA-CCAATTTTTCGAAGATTCCATGATAGAGAAATCGCATCAT
* * * *
1361 TTGATTTAAATAGTTTATCACTTT
193 TTGGTATAAATAGTTTGTCATTTT
* * * * * *
1385 GTATACAATTTTTAGTCTTTGAATTAAATACTTATTTACGTGAGAATTATTTCCCTCTTGGTTCT
1 GTAAACAAATTTTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAATTATTTCTCTCTTGGTTCT
* *
1450 TGGACCAACATAT-GAACTAGTCAAACTTTTACAAGTTCTTTTATAACTTCGGTTCCTGAGAGTA
66 TGGACGAAC-TATCGAACTAGTCAAACTTTTACAAGTTCTTTTATAACTTCGATTCCTGAGAGTA
* * * *
1514 TTCAAGACGATCCAATTCTTTGACCAATTTTTTGAAGATTCCACT-ATAGAGAAATCGCAGCATT
130 TTCAAGAAGATCCATTTCTTTGACCAATTTTTCGAAGATTCCA-TGATAGAGAAATCGCATCATT
* *
1578 TGGTAAAAATAGTTTGCCA-TTT
194 TGGTATAAATAGTTTGTCATTTT
* * * *
1600 GTAAATAAATTTTGGTCTTTGAATTAAAAA-TTTTTTACATTAGAATTTTTTCTCTCTTGGTTCT
1 GTAAACAAATTTTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAATTATTTCTCTCTTGGTTCT
* * * * *
1664 TGGACGAAGTATCGAACTTGTCAAACATTTACAAGTTCTTTTACAACTTCGATTCCTGAGAGTAG
66 TGGACGAACTATCGAACTAGTCAAACTTTTACAAGTTCTTTTATAACTTCGATTCCTGAGAGTAT
* * * *
1729 TCAAGATGATCCATTCCTTCGACCAATTTTTCG-AGCATTCCATGATCAG-GAAATCGTATCATT
131 TCAAGAAGATCCATTTCTTTGACCAATTTTTCGAAG-ATTCCATGAT-AGAGAAATCGCATCATT
*
1792 TGGTCTAAATAGTTTGTCATTTT
194 TGGTATAAATAGTTTGTCATTTT
* * * * * **
1815 GTACACAACTTTTGGTCTTTGAATTAAAAACTTTTTTACGTGGGAATTGTTTCTCTATTTTTTCT
1 GTAAACAAATTTTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAATTATTTCTCTCTTGGTTCT
* *
1880 TGGACGAACTTTCGAAC-ACGTCAAACATTTT-CGAGTTCTTTTATAACTTCGATTCCTGAGAGT
66 TGGACGAACTATCGAACTA-GTCAAAC-TTTTACAAGTTCTTTTATAACTTCGATTCCTGAGAGT
* * * * *** *
1943 ATTAAAGACA-ATCCA-TTCCTTCAGCCAATTTTTCGAACATTCCATGCCCGGGAAATCG-ATTC
129 ATTCAAGA-AGATCCATTTCTTTGA-CCAATTTTTCGAAGATTCCATGATAGAGAAATCGCA-TC
* * * *
2005 GTTTGATTTAAATAGTTTATCATTTT
191 ATTTGGTATAAATAGTTTGTCATTTT
* * * * * * *
2031 GTATACAATTTTTAGACTTTGAATTAAATACTTATTTACGTGAGAATTATTTCCCTCTTGGTTCT
1 GTAAACAAATTTTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAATTATTTCTCTCTTGGTTCT
* * *
2096 TGGACCAACATAT-GAACTAGTCAAACTTTTACAAGTTCTTTTATAACTTTGGTTCCTGAGAGTA
66 TGGACGAAC-TATCGAACTAGTCAAACTTTTACAAGTTCTTTTATAACTTCGATTCCTGAGAGTA
* * * *
2160 TTCAAGATGATCCATTTCTTTGACCAATTTTTTGAAGATTCCATTAAAAATAGAGAAATCGCAGC
130 TTCAAGAAGATCCATTTCTTTGACCAATTTTTCGAAGATTCCA-T---GATAGAGAAATCGCATC
* *
2225 ATTTGGTAAAAATAGTTTGCCA-TTT
191 ATTTGGTATAAATAGTTTGTCATTTT
* *
2250 GTAAATAAATTTTGGTCTTTGAATTAAAAACTTTTTTACAGT-AGAATTCTTTCTCTCTTGGTTC
1 GTAAACAAATTTTGGTCTTTGAATTAAAAACTTTTTTAC-GTGAGAATTATTTCTCTCTTGGTTC
* * * * *
2314 TTGGACGAAGTATCGAACTTGTCAAACATTTACTAGTTCTTTTACAACTTCGATTCCTGAG
65 TTGGACGAACTATCGAACTAGTCAAACTTTTACAAGTTCTTTTATAACTTCGATTCCTGAG
2375 NNNNNNNNNN
Statistics
Matches: 1343, Mismatches: 251, Indels: 85
0.80 0.15 0.05
Matches are distributed among these distances:
213 6 0.00
214 149 0.11
215 138 0.10
216 834 0.62
217 75 0.06
218 9 0.01
219 104 0.08
220 27 0.02
221 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (216 bp):
GTAAACAAATTTTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAATTATTTCTCTCTTGGTTCT
TGGACGAACTATCGAACTAGTCAAACTTTTACAAGTTCTTTTATAACTTCGATTCCTGAGAGTAT
TCAAGAAGATCCATTTCTTTGACCAATTTTTCGAAGATTCCATGATAGAGAAATCGCATCATTTG
GTATAAATAGTTTGTCATTTT
Found at i:2008 original size:646 final size:647
Alignment explanation
Indices: 521--2374 Score: 3433
Period size: 646 Copynumber: 2.9 Consensus size: 647
511 NNNNNNNNNN
521 GTAAACAACTTTTGGTCATTGAATTAAAAACTTTTTTACATGGGAATTGTTTCTCTATTTGTTCT
1 GTAAACAACTTTTGGTCATTGAATTAAAAACTTTTTTACATGGGAATTGTTTCTCTATTTGTTCT
586 TGGACAAACTTTCGAACACGTCAAACATTTTCGAGTTCTTTTATAACTTCGATTCCTGAGAGTAT
66 TGGACAAACTTTCGAACACGTCAAACATTTTCGAGTTCTTTTATAACTTCGATTCCTGAGAGTAT
*
651 TAAAGAAGATTCATTCCTTCAGCCAATTTTTCGAACATTCCATGCCCGGGAAATCGCTTCGTTTG
131 TAAAGAAGATTCATTCCTTCAGCCAATTTTTCGAACATTCCATGCCCGGGAAATCGATTCGTTTG
716 ATTTAAATAGTTTATCATTTTGTATACAATTTTTAGTCTTTGAATTAAATACTTATTTACGTGAG
196 ATTTAAATAGTTTATCATTTTGTATACAATTTTTAGTCTTTGAATTAAATACTTATTTACGTGAG
781 AATTATTTCCCTCTTGGTTCTTGGACCAACATATGAACTAGTCAAACTTTTACAAGTTCTTTTAT
261 AATTATTTCCCTCTTGGTTCTTGGACCAACATATGAACTAGTCAAACTTTTACAAGTTCTTTTAT
846 AACTTCGGTTCCTGAGAGTATTCAAGAAGATCCATTTTCTTTGACCAATTTTTTGAAGATTCCAT
326 AACTTCGGTTCCTGAGAGTATTCAAGAAGATCCA-TTTCTTTGACCAATTTTTTGAAGATTCCAT
*
911 TATAGAGAAATCACAGCATTTGGTAAAAATAGTTTGCCATTTGTAAATAAATTTTGGTCTTTGAA
390 TATAGAGAAATCGCAGCATTTGGTAAAAATAGTTTGCCATTTGTAAATAAATTTTGGTCTTTGAA
976 TTAAAAACTTTTTTACATTAGAATTCTTTCTCTCTTGGTTCTTGGACGAAGTATCGAACTTGTCA
455 TTAAAAACTTTTTTACATTAGAATTCTTTCTCTCTTGGTTCTTGGACGAAGTATCGAACTTGTCA
1041 AACATTTACTAGTTCTTTTACAACTTCGATTCCTGAGAGTAGCCAAGATGATCCATTCCTTCGAC
520 AACATTTACTAGTTCTTTTACAACTTCGATTCCTGAGAGTAGCCAAGATGATCCATTCCTTCGAC
1106 CAATTTTTCGAGCATTCCATGATCAGGAAATCGTATCATTTGGTCTAAATAGTTTGGAATTTC
585 CAATTTTTCGAGCATTCCATGATCAGGAAATCGTATCATTTGGTCTAAATAGTTTGGAATTTC
1169 GTAAACAACTTTTGGTCATTGAATTAAAAACTTTTTTACATGGGAATTGTTTCTCTATTTGTTCT
1 GTAAACAACTTTTGGTCATTGAATTAAAAACTTTTTTACATGGGAATTGTTTCTCTATTTGTTCT
1234 TGGACAAACTTTCGAACACGTCAAACATTTTCGAGTTCTTTTATAACTTCGATTCCTGAGAGTAT
66 TGGACAAACTTTCGAACACGTCAAACATTTTCGAGTTCTTTTATAACTTCGATTCCTGAGAGTAT
*
1299 TAAAGAAGATTCATTCCTTCAGCCAATTTTTCGAACATTCCATGCCCGGGAAATCGTTTCGTTTG
131 TAAAGAAGATTCATTCCTTCAGCCAATTTTTCGAACATTCCATGCCCGGGAAATCGATTCGTTTG
*
1364 ATTTAAATAGTTTATCACTTTGTATACAATTTTTAGTCTTTGAATTAAATACTTATTTACGTGAG
196 ATTTAAATAGTTTATCATTTTGTATACAATTTTTAGTCTTTGAATTAAATACTTATTTACGTGAG
1429 AATTATTTCCCTCTTGGTTCTTGGACCAACATATGAACTAGTCAAACTTTTACAAGTTCTTTTAT
261 AATTATTTCCCTCTTGGTTCTTGGACCAACATATGAACTAGTCAAACTTTTACAAGTTCTTTTAT
* * *
1494 AACTTCGGTTCCTGAGAGTATTCAAGACGATCCAATTCTTTGACCAATTTTTTGAAGATTCCACT
326 AACTTCGGTTCCTGAGAGTATTCAAGAAGATCCATTTCTTTGACCAATTTTTTGAAGATTCCATT
1559 ATAGAGAAATCGCAGCATTTGGTAAAAATAGTTTGCCATTTGTAAATAAATTTTGGTCTTTGAAT
391 ATAGAGAAATCGCAGCATTTGGTAAAAATAGTTTGCCATTTGTAAATAAATTTTGGTCTTTGAAT
*
1624 TAAAAA-TTTTTTACATTAGAATTTTTTCTCTCTTGGTTCTTGGACGAAGTATCGAACTTGTCAA
456 TAAAAACTTTTTTACATTAGAATTCTTTCTCTCTTGGTTCTTGGACGAAGTATCGAACTTGTCAA
* *
1688 ACATTTACAAGTTCTTTTACAACTTCGATTCCTGAGAGTAGTCAAGATGATCCATTCCTTCGACC
521 ACATTTACTAGTTCTTTTACAACTTCGATTCCTGAGAGTAGCCAAGATGATCCATTCCTTCGACC
** *
1753 AATTTTTCGAGCATTCCATGATCAGGAAATCGTATCATTTGGTCTAAATAGTTTGTCATTTT
586 AATTTTTCGAGCATTCCATGATCAGGAAATCGTATCATTTGGTCTAAATAGTTTGGAATTTC
* * * *
1815 GTACACAACTTTTGGTCTTTGAATTAAAAACTTTTTTACGTGGGAATTGTTTCTCTATTTTTTCT
1 GTAAACAACTTTTGGTCATTGAATTAAAAACTTTTTTACATGGGAATTGTTTCTCTATTTGTTCT
*
1880 TGGACGAACTTTCGAACACGTCAAACATTTTCGAGTTCTTTTATAACTTCGATTCCTGAGAGTAT
66 TGGACAAACTTTCGAACACGTCAAACATTTTCGAGTTCTTTTATAACTTCGATTCCTGAGAGTAT
*
1945 TAAAGACA-ATCCATTCCTTCAGCCAATTTTTCGAACATTCCATGCCCGGGAAATCGATTCGTTT
131 TAAAGA-AGATTCATTCCTTCAGCCAATTTTTCGAACATTCCATGCCCGGGAAATCGATTCGTTT
*
2009 GATTTAAATAGTTTATCATTTTGTATACAATTTTTAGACTTTGAATTAAATACTTATTTACGTGA
195 GATTTAAATAGTTTATCATTTTGTATACAATTTTTAGTCTTTGAATTAAATACTTATTTACGTGA
2074 GAATTATTTCCCTCTTGGTTCTTGGACCAACATATGAACTAGTCAAACTTTTACAAGTTCTTTTA
260 GAATTATTTCCCTCTTGGTTCTTGGACCAACATATGAACTAGTCAAACTTTTACAAGTTCTTTTA
* *
2139 TAACTTTGGTTCCTGAGAGTATTCAAGATGATCCATTTCTTTGACCAATTTTTTGAAGATTCCAT
325 TAACTTCGGTTCCTGAGAGTATTCAAGAAGATCCATTTCTTTGACCAATTTTTTGAAGATTCCAT
2204 TAAAAATAGAGAAATCGCAGCATTTGGTAAAAATAGTTTGCCATTTGTAAATAAATTTTGGTCTT
390 T----ATAGAGAAATCGCAGCATTTGGTAAAAATAGTTTGCCATTTGTAAATAAATTTTGGTCTT
*
2269 TGAATTAAAAACTTTTTTACAGTAGAATTCTTTCTCTCTTGGTTCTTGGACGAAGTATCGAACTT
451 TGAATTAAAAACTTTTTTACATTAGAATTCTTTCTCTCTTGGTTCTTGGACGAAGTATCGAACTT
2334 GTCAAACATTTACTAGTTCTTTTACAACTTCGATTCCTGAG
516 GTCAAACATTTACTAGTTCTTTTACAACTTCGATTCCTGAG
2375 NNNNNNNNNN
Statistics
Matches: 1172, Mismatches: 28, Indels: 9
0.97 0.02 0.01
Matches are distributed among these distances:
646 554 0.47
647 100 0.09
648 356 0.30
650 71 0.06
651 91 0.08
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (647 bp):
GTAAACAACTTTTGGTCATTGAATTAAAAACTTTTTTACATGGGAATTGTTTCTCTATTTGTTCT
TGGACAAACTTTCGAACACGTCAAACATTTTCGAGTTCTTTTATAACTTCGATTCCTGAGAGTAT
TAAAGAAGATTCATTCCTTCAGCCAATTTTTCGAACATTCCATGCCCGGGAAATCGATTCGTTTG
ATTTAAATAGTTTATCATTTTGTATACAATTTTTAGTCTTTGAATTAAATACTTATTTACGTGAG
AATTATTTCCCTCTTGGTTCTTGGACCAACATATGAACTAGTCAAACTTTTACAAGTTCTTTTAT
AACTTCGGTTCCTGAGAGTATTCAAGAAGATCCATTTCTTTGACCAATTTTTTGAAGATTCCATT
ATAGAGAAATCGCAGCATTTGGTAAAAATAGTTTGCCATTTGTAAATAAATTTTGGTCTTTGAAT
TAAAAACTTTTTTACATTAGAATTCTTTCTCTCTTGGTTCTTGGACGAAGTATCGAACTTGTCAA
ACATTTACTAGTTCTTTTACAACTTCGATTCCTGAGAGTAGCCAAGATGATCCATTCCTTCGACC
AATTTTTCGAGCATTCCATGATCAGGAAATCGTATCATTTGGTCTAAATAGTTTGGAATTTC
Found at i:3401 original size:431 final size:432
Alignment explanation
Indices: 2425--3726 Score: 1358
Period size: 431 Copynumber: 3.0 Consensus size: 432
2415 NNNNNNNNNN
* * *
2425 TACGTGAGAATTATTTCCCTCTTGGTTCTTGGACCAACATAT-GAACTAGTCAAACTTTTACAAG
1 TACGAGAGAATTATTTCCCTCTTGGTTCTTGGACGAA-ATATCGAACTAGTCAAACATTTACAAG
* * *
2489 TTCTTTTATAACTTTGGTTCCTGAGAGTATTCAAGATGATCCATTTCTTTGACCAATTTTTTGAA
65 TTCTTTTATAAC-TTGGTTCCTGAGAGTATTCAAGATGATCCATTCCTTCGACCAATTTTTCGAA
* * * * ** * *
2554 GATTCCATTAAAAATAGAGAAATCGCAGCATTTGGTAAAAATAGTTTGCCA-TTTGTAAATAAAT
129 CATTCCA-T---GATCGGGAAATCGCTTCATTTGGTAAAAATAGTTTGTCATTTTGTAAACAAAT
* * * **
2618 TTTGGTCTTTGAATTAAAAACTTTTTTACATTAGAATTCTTTCTCTCTTGGTTCTTGGATGAA-A
190 TTTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAATTATTTCTCTCTTGGTTCTTGGACAAACA
* ** * * * ** *
2682 TATCGAACTTGTCAAAAATTGACTAGTTCTTTTACAACTTCGATTCCTGAGAGTAGCCAAGATGA
255 TATCGAACTAGTCAAACTTTTACAAGTTCTTTTATAACTTCGATTCCTGAGAGTATTCAAGACGA
* * * * *
2747 TCCA-TTCCTTCGACCAATTTTTCG-AGCATTCCATGATCAGGAAATCGTATCATTTGGTCAAAA
320 TCCATTTCTTTC-ACCAATTTTTCGAAG-ATTCCATTATCAGGAAATCGCAGCATTTGGTAAAAA
* * *
2810 TAGTTTGTCATTTTGTAAGCAACTTTTGGTCTTTGAATTAAAAACTTTTT
383 TAGTTTGCCATTTTGTAAACAAATTTTGGTCTTTGAATTAAAAACTTTTT
* * * * *
2860 TACGAGAGAATTATTTCTCTCTTGGTTCTTGGACGAACT-TCTGAACTGGTTAAACATTTTCAAG
1 TACGAGAGAATTATTTCCCTCTTGGTTCTTGGACGAAATATC-GAACTAGTCAAACATTTACAAG
* * *
2924 TTCTTTTATAACTTGTGTTCCTTAGAGTATTAAAGACGATCCATTCCTTC-AGCCAATTTTTCGA
65 TTCTTTTATAACTTG-GTTCCTGAGAGTATTCAAGATGATCCATTCCTTCGA-CCAATTTTTCGA
** * * ** * * *
2988 ACATTCCATGCCCGGGAAATCGCTTCGTTTGATTTAAATAGTTTATCATTTTGTATACAATTTTT
128 ACATTCCATGATCGGGAAATCGCTTCATTTGGTAAAAATAGTTTGTCATTTTGTAAACAAATTTT
* * * * *
3053 AGTCTTTGAATTAAATACTTATTTACGTGAGAATTATTTCCCTCTTGGTTCTTGGACCAACATAT
193 GGTCTTTGAATTAAAAACTTTTTTACGTGAGAATTATTTCTCTCTTGGTTCTTGGACAAACATAT
* *
3118 -GAACTAGTCAAACTTTTACAAGTTCTTTTATAACTTCGGTTCCTGAGAGTATTCAAGACGATAC
258 CGAACTAGTCAAACTTTTACAAGTTCTTTTATAACTTCGATTCCTGAGAGTATTCAAGACGATCC
* *
3182 ATTTCTTTTACCAATTTTTTGAAGATTCCATTAT-AGAGAAATCGCAGCATTTGGTAAAAATAGT
323 ATTTCTTTCACCAATTTTTCGAAGATTCCATTATCAG-GAAATCGCAGCATTTGGTAAAAATAGT
*
3246 TTGCCA-TTTGTAAATAAATTTTGGTCTTTGAATTAAAAACTTTTT
387 TTGCCATTTTGTAAACAAATTTTGGTCTTTGAATTAAAAACTTTTT
* * * * * *
3291 TAC-ATTAGAATTCTTTCGCTCTTGGTTCTTGGACGAAGTATCGAACTTGTCAAACATTTACTAG
1 TACGA-GAGAATTATTTCCCTCTTGGTTCTTGGACGAAATATCGAACTAGTCAAACATTTACAAG
* * ** * *
3355 TTCTTTTACAACTTCGATTCCTGAGAGTAGCCAAGATGATCCATTCCTTCGACTAATTTTTCGAG
65 TTCTTTTATAACTT-GGTTCCTGAGAGTATTCAAGATGATCCATTCCTTCGACCAATTTTTCGAA
* * * ** * *
3420 CATTACATGATCAGGAAATAG-TATCATTTGGTCGAAATCGTTTGTCATTTTGTAAACAACTTTT
129 CATTCCATGATCGGGAAATCGCT-TCATTTGGTAAAAATAGTTTGTCATTTTGTAAACAAATTTT
* * * * *
3484 GGTTTTTGAATTAAAAACTTTTTTACGTGGGAATTATTTCTCTATTTGTTCTTGGACAAAC-TTT
193 GGTCTTTGAATTAAAAACTTTTTTACGTGAGAATTATTTCTCTCTTGGTTCTTGGACAAACATAT
* * * *
3548 CAAAC-ACGTCAAACATTTTA-GAGTTCTTTTATAACTTCGATTCCTGAGAGTATTAAACACGAT
258 CGAACTA-GTCAAAC-TTTTACAAGTTCTTTTATAACTTCGATTCCTGAGAGTATTCAAGACGAT
* * * * ** * * **
3611 CCA-TTCCTTCAGCCAATTTTTCGAACATTCCATTACCGGGAAATCGCTTCGTTTGATTTAAATA
321 CCATTTCTTTCA-CCAATTTTTCGAAGATTCCATTATCAGGAAATCGCAGCATTTGGTAAAAATA
** * * * * *
3675 GTTTATCATTTTGTATACAATTTTTAGTCTTTGAATTAAATACTTATT
385 GTTTGCCATTTTGTAAACAAATTTTGGTCTTTGAATTAAAAACTTTTT
3723 TACG
1 TACG
3727 TGA
Statistics
Matches: 718, Mismatches: 128, Indels: 44
0.81 0.14 0.05
Matches are distributed among these distances:
430 11 0.02
431 365 0.51
432 213 0.30
433 12 0.02
434 6 0.01
435 111 0.15
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.40
Consensus pattern (432 bp):
TACGAGAGAATTATTTCCCTCTTGGTTCTTGGACGAAATATCGAACTAGTCAAACATTTACAAGT
TCTTTTATAACTTGGTTCCTGAGAGTATTCAAGATGATCCATTCCTTCGACCAATTTTTCGAACA
TTCCATGATCGGGAAATCGCTTCATTTGGTAAAAATAGTTTGTCATTTTGTAAACAAATTTTGGT
CTTTGAATTAAAAACTTTTTTACGTGAGAATTATTTCTCTCTTGGTTCTTGGACAAACATATCGA
ACTAGTCAAACTTTTACAAGTTCTTTTATAACTTCGATTCCTGAGAGTATTCAAGACGATCCATT
TCTTTCACCAATTTTTCGAAGATTCCATTATCAGGAAATCGCAGCATTTGGTAAAAATAGTTTGC
CATTTTGTAAACAAATTTTGGTCTTTGAATTAAAAACTTTTT
Found at i:3663 original size:647 final size:648
Alignment explanation
Indices: 2425--3729 Score: 2258
Period size: 647 Copynumber: 2.0 Consensus size: 648
2415 NNNNNNNNNN
2425 TACGTGAGAATTATTTCCCTCTTGGTTCTTGGACCAACATATGAACTAGTCAAACTTTTACAAGT
1 TACGTGAGAATTATTTCCCTCTTGGTTCTTGGACCAACATATGAACTAGTCAAACTTTTACAAGT
* * *
2490 TCTTTTATAACTTTGGTTCCTGAGAGTATTCAAGATGATCCATTTCTTTGACCAATTTTTTGAAG
66 TCTTTTATAACTTCGGTTCCTGAGAGTATTCAAGACGATACATTTCTTTGACCAATTTTTTGAAG
2555 ATTCCATTAAAAATAGAGAAATCGCAGCATTTGGTAAAAATAGTTTGCCATTTGTAAATAAATTT
131 ATTCCATT---AATAGAGAAATCGCAGCATTTGGTAAAAATAGTTTGCCATTTGTAAATAAATTT
* *
2620 TGGTCTTTGAATTAAAAACTTTTTTACATTAGAATTCTTTCTCTCTTGGTTCTTGGATGAAATAT
193 TGGTCTTTGAATTAAAAACTTTTTTACATTAGAATTCTTTCGCTCTTGGTTCTTGGACGAAATAT
2685 CGAACTTGTCAAAAATTGACTAGTTCTTTTACAACTTCGATTCCTGAGAGTAGCCAAGATGATCC
258 CGAACTTGTCAAAAATTGACTAGTTCTTTTACAACTTCGATTCCTGAGAGTAGCCAAGATGATCC
* *
2750 ATTCCTTCGACCAATTTTTCGAGCATTCCATGATCAGGAAATCGTATCATTTGGTCAAAATAGTT
323 ATTCCTTCGACCAATTTTTCGAGCATTACATGATCAGGAAATAGTATCATTTGGTCAAAATAGTT
*
2815 TGTCATTTTGTAAGCAACTTTTGGTCTTTGAATTAAAAACTTTTTTACGAGAGAATTATTTCTCT
388 TGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTTTTTACGAGAGAATTATTTCTCT
* * * ** * *
2880 CTTGGTTCTTGGACGAACTTCTGAACTGGTTAAACATTTTCAAGTTCTTTTATAACTTGTGTTCC
453 ATTGGTTCTTGGACAAACTTCTAAACACGTCAAACATTTTCAAGTTCTTTTATAACTTGTATTCC
* * *
2945 TTAGAGTATTAAAGACGATCCATTCCTTCAGCCAATTTTTCGAACATTCCATGCCCGGGAAATCG
518 TGAGAGTATTAAACACGATCCATTCCTTCAGCCAATTTTTCGAACATTCCATGACCGGGAAATCG
3010 CTTCGTTTGATTTAAATAGTTTATCATTTTGTATACAATTTTTAGTCTTTGAATTAAATACTTAT
583 CTTCGTTTGATTTAAATAGTTTATCATTTTGTATACAATTTTTAGTCTTTGAATTAAATACTTAT
3075 T
648 T
3076 TACGTGAGAATTATTTCCCTCTTGGTTCTTGGACCAACATATGAACTAGTCAAACTTTTACAAGT
1 TACGTGAGAATTATTTCCCTCTTGGTTCTTGGACCAACATATGAACTAGTCAAACTTTTACAAGT
*
3141 TCTTTTATAACTTCGGTTCCTGAGAGTATTCAAGACGATACATTTCTTTTACCAATTTTTTGAAG
66 TCTTTTATAACTTCGGTTCCTGAGAGTATTCAAGACGATACATTTCTTTGACCAATTTTTTGAAG
3206 ATTCCATT-ATAGAGAAATCGCAGCATTTGGTAAAAATAGTTTGCCATTTGTAAATAAATTTTGG
131 ATTCCATTAATAGAGAAATCGCAGCATTTGGTAAAAATAGTTTGCCATTTGTAAATAAATTTTGG
*
3270 TCTTTGAATTAAAAACTTTTTTACATTAGAATTCTTTCGCTCTTGGTTCTTGGACGAAGTATCGA
196 TCTTTGAATTAAAAACTTTTTTACATTAGAATTCTTTCGCTCTTGGTTCTTGGACGAAATATCGA
* *
3335 ACTTGTCAAACATTTACTAGTTCTTTTACAACTTCGATTCCTGAGAGTAGCCAAGATGATCCATT
261 ACTTGTCAAAAATTGACTAGTTCTTTTACAACTTCGATTCCTGAGAGTAGCCAAGATGATCCATT
* * *
3400 CCTTCGACTAATTTTTCGAGCATTACATGATCAGGAAATAGTATCATTTGGTCGAAATCGTTTGT
326 CCTTCGACCAATTTTTCGAGCATTACATGATCAGGAAATAGTATCATTTGGTCAAAATAGTTTGT
* * *
3465 CATTTTGTAAACAACTTTTGGTTTTTGAATTAAAAACTTTTTTACGTGGGAATTATTTCTCTATT
391 CATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTTTTTACGAGAGAATTATTTCTCTATT
*
3530 TGTTCTTGGACAAACTT-TCAAACACGTCAAACATTTT-AGAGTTCTTTTATAACTTCG-ATTCC
456 GGTTCTTGGACAAACTTCT-AAACACGTCAAACATTTTCA-AGTTCTTTTATAACTT-GTATTCC
*
3592 TGAGAGTATTAAACACGATCCATTCCTTCAGCCAATTTTTCGAACATTCCATTACCGGGAAATCG
518 TGAGAGTATTAAACACGATCCATTCCTTCAGCCAATTTTTCGAACATTCCATGACCGGGAAATCG
3657 CTTCGTTTGATTTAAATAGTTTATCATTTTGTATACAATTTTTAGTCTTTGAATTAAATACTTAT
583 CTTCGTTTGATTTAAATAGTTTATCATTTTGTATACAATTTTTAGTCTTTGAATTAAATACTTAT
3722 T
648 T
3723 TACGTGA
1 TACGTGA
Statistics
Matches: 621, Mismatches: 30, Indels: 10
0.94 0.05 0.02
Matches are distributed among these distances:
646 2 0.00
647 484 0.78
648 1 0.00
651 134 0.22
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.40
Consensus pattern (648 bp):
TACGTGAGAATTATTTCCCTCTTGGTTCTTGGACCAACATATGAACTAGTCAAACTTTTACAAGT
TCTTTTATAACTTCGGTTCCTGAGAGTATTCAAGACGATACATTTCTTTGACCAATTTTTTGAAG
ATTCCATTAATAGAGAAATCGCAGCATTTGGTAAAAATAGTTTGCCATTTGTAAATAAATTTTGG
TCTTTGAATTAAAAACTTTTTTACATTAGAATTCTTTCGCTCTTGGTTCTTGGACGAAATATCGA
ACTTGTCAAAAATTGACTAGTTCTTTTACAACTTCGATTCCTGAGAGTAGCCAAGATGATCCATT
CCTTCGACCAATTTTTCGAGCATTACATGATCAGGAAATAGTATCATTTGGTCAAAATAGTTTGT
CATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTTTTTACGAGAGAATTATTTCTCTATT
GGTTCTTGGACAAACTTCTAAACACGTCAAACATTTTCAAGTTCTTTTATAACTTGTATTCCTGA
GAGTATTAAACACGATCCATTCCTTCAGCCAATTTTTCGAACATTCCATGACCGGGAAATCGCTT
CGTTTGATTTAAATAGTTTATCATTTTGTATACAATTTTTAGTCTTTGAATTAAATACTTATT
Found at i:3727 original size:216 final size:215
Alignment explanation
Indices: 2425--3729 Score: 1303
Period size: 216 Copynumber: 6.0 Consensus size: 215
2415 NNNNNNNNNN
* *
2425 TACGTGAGAATTATTTCCCTCTTGGTTCTTGGACCAACATAT-GAACTAGTCAAAC-TTTTACAA
1 TACGTGAGAATTATTTCTCTCTTGGTTCTTGGACGAAC-TATCGAAC-AGTCAAACATTTTAC-A
* * * * * *
2488 GTTCTTTTATAACTTTGGTTCCTGAGAGTATTCAAGATGATCCATTTCTT-TGACCAATTTTTTG
63 GTTCTTTTATAACTTCGATTCCTGAGAGTATTCAAGACGATCCATTCCTTCAG-CCAATTTTTCG
* * * * ** * * *
2552 AAGATTCCATTAAAAATAGAGAAATCGCAGCATTTGGTAAAAATAGTTTGCCA-TTTGTAAATAA
127 AACATTCCA-T---GATCGGGAAATCGCTTCATTTGGTCAAAATAGTTTGTCATTTTGTAAACAA
*
2616 ATTTTGGTCTTTGAATTAAAAACTTTTT
188 CTTTTGGTCTTTGAATTAAAAACTTTTT
* * * * * * * *
2644 TACATTAGAATTCTTTCTCTCTTGGTTCTTGGATGAAATATCGAACTTGTCAAA-AATTGACTAG
1 TACGTGAGAATTATTTCTCTCTTGGTTCTTGGACGAACTATCGAAC-AGTCAAACATTTTAC-AG
* ** *
2708 TTCTTTTACAACTTCGATTCCTGAGAGTAGCCAAGATGATCCATTCCTTC-GACCAATTTTTCGA
64 TTCTTTTATAACTTCGATTCCTGAGAGTATTCAAGACGATCCATTCCTTCAG-CCAATTTTTCGA
* * *
2772 GCATTCCATGATCAGGAAATCG-TATCATTTGGTCAAAATAGTTTGTCATTTTGTAAGCAACTTT
128 ACATTCCATGATCGGGAAATCGCT-TCATTTGGTCAAAATAGTTTGTCATTTTGTAAACAACTTT
2836 TGGTCTTTGAATTAAAAACTTTTT
192 TGGTCTTTGAATTAAAAACTTTTT
* * *
2860 TACGAGAGAATTATTTCTCTCTTGGTTCTTGGACGAACT-TCTGAACTGGTTAAACATTTT-CAA
1 TACGTGAGAATTATTTCTCTCTTGGTTCTTGGACGAACTATC-GAAC-AGTCAAACATTTTAC-A
* * *
2923 GTTCTTTTATAACTT-GTGTTCCTTAGAGTATTAAAGACGATCCATTCCTTCAGCCAATTTTTCG
63 GTTCTTTTATAACTTCG-ATTCCTGAGAGTATTCAAGACGATCCATTCCTTCAGCCAATTTTTCG
** * * ** * * *
2987 AACATTCCATGCCCGGGAAATCGCTTCGTTTGATTTAAATAGTTTATCATTTTGTATACAATTTT
127 AACATTCCATGATCGGGAAATCGCTTCATTTGGTCAAAATAGTTTGTCATTTTGTAAACAACTTT
* * *
3052 TAGTCTTTGAATTAAATACTTATT
192 TGGTCTTTGAATTAAAAACTTTTT
* *
3076 TACGTGAGAATTATTTCCCTCTTGGTTCTTGGACCAACATAT-GAACTAGTCAAAC-TTTTACAA
1 TACGTGAGAATTATTTCTCTCTTGGTTCTTGGACGAAC-TATCGAAC-AGTCAAACATTTTAC-A
* * * * *
3139 GTTCTTTTATAACTTCGGTTCCTGAGAGTATTCAAGACGATACATTTCTTTTA-CCAATTTTTTG
63 GTTCTTTTATAACTTCGATTCCTGAGAGTATTCAAGACGATCCA-TTCCTTCAGCCAATTTTTCG
* * * * ** * * * *
3203 AAGATTCCATTATAGAGAAATCGCAGCATTTGGTAAAAATAGTTTGCCA-TTTGTAAATAAATTT
127 AACATTCCATGATCGGGAAATCGCTTCATTTGGTCAAAATAGTTTGTCATTTTGTAAACAACTTT
3267 TGGTCTTTGAATTAAAAACTTTTT
192 TGGTCTTTGAATTAAAAACTTTTT
* * * * * *
3291 TACATTAGAATTCTTTCGCTCTTGGTTCTTGGACGAAGTATCGAACTTGTCAAACA-TTTACTAG
1 TACGTGAGAATTATTTCTCTCTTGGTTCTTGGACGAACTATCGAAC-AGTCAAACATTTTAC-AG
* ** * *
3355 TTCTTTTACAACTTCGATTCCTGAGAGTAGCCAAGATGATCCATTCCTTC-GACTAATTTTTCGA
64 TTCTTTTATAACTTCGATTCCTGAGAGTATTCAAGACGATCCATTCCTTCAG-CCAATTTTTCGA
* * * * * *
3419 GCATTACATGATCAGGAAATAG-TATCATTTGGTCGAAATCGTTTGTCATTTTGTAAACAACTTT
128 ACATTCCATGATCGGGAAATCGCT-TCATTTGGTCAAAATAGTTTGTCATTTTGTAAACAACTTT
*
3483 TGGTTTTTGAATTAAAAACTTTTT
192 TGGTCTTTGAATTAAAAACTTTTT
* * * * * * *
3507 TACGTGGGAATTATTTCTCTATTTGTTCTTGGACAAACTTTCAAACACGTCAAACATTTTAGAGT
1 TACGTGAGAATTATTTCTCTCTTGGTTCTTGGACGAACTATCGAACA-GTCAAACATTTTACAGT
* *
3572 TCTTTTATAACTTCGATTCCTGAGAGTATTAAACACGATCCATTCCTTCAGCCAATTTTTCGAAC
65 TCTTTTATAACTTCGATTCCTGAGAGTATTCAAGACGATCCATTCCTTCAGCCAATTTTTCGAAC
* * * * ** * * * *
3637 ATTCCATTACCGGGAAATCGCTTCGTTTGATTTAAATAGTTTATCATTTTGTATACAATTTTTAG
130 ATTCCATGATCGGGAAATCGCTTCATTTGGTCAAAATAGTTTGTCATTTTGTAAACAACTTTTGG
* *
3702 TCTTTGAATTAAATACTTATT
195 TCTTTGAATTAAAAACTTTTT
3723 TACGTGA
1 TACGTGA
Statistics
Matches: 892, Mismatches: 169, Indels: 53
0.80 0.15 0.05
Matches are distributed among these distances:
214 8 0.01
215 201 0.23
216 549 0.62
217 19 0.02
218 5 0.01
219 110 0.12
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.40
Consensus pattern (215 bp):
TACGTGAGAATTATTTCTCTCTTGGTTCTTGGACGAACTATCGAACAGTCAAACATTTTACAGTT
CTTTTATAACTTCGATTCCTGAGAGTATTCAAGACGATCCATTCCTTCAGCCAATTTTTCGAACA
TTCCATGATCGGGAAATCGCTTCATTTGGTCAAAATAGTTTGTCATTTTGTAAACAACTTTTGGT
CTTTGAATTAAAAACTTTTT
Done.