Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_775 ID=scaffold_775-JGI_221_v2.0
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: 5763
ACGTcount: A:0.17, C:0.12, G:0.15, T:0.21
Warning! 1946 characters in sequence are not A, C, G, or T
Found at i:1183 original size:604 final size:604
Alignment explanation
Indices: 1--3173 Score: 3562
Period size: 604 Copynumber: 5.2 Consensus size: 604
* * *
1 TTCATATAATGGTTTTTTTAGTTGCGTTTCCTCGACGTGGTGTAACTCATTCATTATTTGCGTTT
1 TTCATATAAT-GTTTTTTTAGTTGCATTTTCTCGACGTGGTGTAACTCATTCGTTATTTGCGTTT
* * * * * *
66 TTTGAAGTAAATAATTTGAAACGATATTTGGTCGAATTTACATTTAAATTCGAGGCGCAAGTACG
65 TGTGAAATAAATAATTTGGAACGATATTTGGTCGAATTTGCATTCAAATTCGAGGCGCAAGTGCG
* * *
131 ATAAGGGGCAGCCTTTATATGAATAGATTGCGCAAGAGTTGATGGGTGCTATCATACCAGCACTA
130 ATAAGCGGCAGCCTTTATATGAATAGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCACTA
* * * * * *
196 ATGCACCGGATCCCGTCAGAACTCTGAAGTTAAGCGTGCTTGGGCGATAGTAGTACTAGGATTGG
195 ATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTT-GGAGAGAGTAGTACTAGGATGGG
* * * * *
261 TGACCTCTTGGGAAGTCCTCGTGTTGCACCCCTCCCATTTTATTACATATAAAGTTTTTATTTGG
259 TGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTCCCATTTTATTTCATATAATGGTTTT-TTTAG
*
326 TTGCATTTTCTCGACGTGGTGTAACTCATTCGTTATTTGCATTTTGTGAAATAAATAATTTGAAA
323 TTGCATTTTCTCGACGTGGTGTAACTCATTCGTTATTTGCGTTTTGTGAAATAAATAATTTGAAA
* * * * * *
391 CAATATTTGGTCAAATTGGCCTTTAAATTCGAGGCGCAAGTGCGATAAGGGGCAGCCTTCATATG
388 CGATATTTGGTCGAATTTGCATTCAAATTCGAGGCGCAAGTGCGATAAGGGGCAGCCTTTATATG
* *
456 AATAGATTGCGCAAGAGTTGACGGGAGCGATCATACCAGCACAAATGCACCGGATCCCATCAGAA
453 AATAGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAA
* * * *
521 CTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACTTCCTGGGAAGTCCACG
518 CTCTGCAGTTAAGCGTGCTTGGGCGATAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCG
*
586 TGTTGCACTCCTCCCATTTTAT
583 TGTTGCACCCCTCCCATTTTAT
*
608 TTCATATAATGTTTTTTTAGTTGCATTTTCTCGACTTGGTGTAACTCATTCGTTATTTGCGTTTT
1 TTCATATAATGTTTTTTTAGTTGCATTTTCTCGACGTGGTGTAACTCATTCGTTATTTGCGTTTT
* * *
673 GTGAAACAAATAATTTGGAACGATATTTGGTCGAATTTGTATTCAATTTCGAGGCGCAAGTGCGA
66 GTGAAATAAATAATTTGGAACGATATTTGGTCGAATTTGCATTCAAATTCGAGGCGCAAGTGCGA
*
738 TAAGCGGCAGCCTTTATATGAATAGATTGCGCAAGCGTTGACGGGTGCGATCATACCAGCACTAA
131 TAAGCGGCAGCCTTTATATGAATAGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCACTAA
*
803 TGCATCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGACGAGAGTAGTAC-AGGATGGGT
196 TGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGA-GAGAGTAGTACTAGGATGGGT
* *
867 GACCTCCTAGGAAGTCCTCGTGTTGCACCCCTCCCATTTTCTTTCATATAATGGTTTTTTTAGTT
260 GACCTCCTGGGAAGTCCTCGTGTTGCACCCCTCCCATTTTATTTCATATAATGGTTTTTTTAGTT
* * * * * *
932 GCGTTTCCTCGACGTGGTGTAACTCATTCATTATATGCGTTTTTTGAAGTAAATAATTTGAAACG
325 GCATTTTCTCGACGTGGTGTAACTCATTCGTTATTTGCGTTTTGTGAAATAAATAATTTGAAACG
* * *
997 ATATTTGGTCGAATTTACATTTAAATTCGAGGCGCAAGTACGATAAGGGGCAGCCTTTATATGAA
390 ATATTTGGTCGAATTTGCATTCAAATTCGAGGCGCAAGTGCGATAAGGGGCAGCCTTTATATGAA
* * *
1062 TAGATTGCGCAAGAGTTGATGGGTGCTATCATACCAGCACTAATGCACCGGATCCCGTCAGAACT
455 TAGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACT
* * *
1127 CTGAAGTTAAGCGTGCTTGGGCGATAGTAGTACTAGGATTGGTGACCTCTTGGGAAGTCCTCGTG
520 CTGCAGTTAAGCGTGCTTGGGCGATAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTG
1192 TTGCACCCCTCCCATTTTAT
585 TTGCACCCCTCCCATTTTAT
* * * *
1212 TACATATAAAGTTTTTATTTGGTTGCATTTTCTCGACGTGGTGTAACTCATTCGTTATTTGCATT
1 TTCATATAATG-TTTT-TTTAGTTGCATTTTCTCGACGTGGTGTAACTCATTCGTTATTTGCGTT
* * * * * *
1277 TTGTGAAATAAATAATTTGAAACAATATTTGGTCAAATTGGCCTTTAAATTCGAGGCGCAAGTGC
64 TTGTGAAATAAATAATTTGGAACGATATTTGGTCGAATTTGCATTCAAATTCGAGGCGCAAGTGC
* * * * *
1342 GATAAGGGGCAGCCTTCATATGAATAGATTGCGCAAGAGTTGACGGGAGCGATCATGCCAGCACA
129 GATAAGCGGCAGCCTTTATATGAATAGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCACT
******************************************************
1407 AATGCACCGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
194 AATGCACCGG-ATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGAGAGAGTAGTACTAGGATGG
****************************************************
1472 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAT-GTTTTTTTAG
258 GTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTCCCATTTTATTTCATATAATGGTTTTTTTAG
* * * ** *
1536 TTGCATTTGCTCGACGCGGTGTAACTCATTCGTTATTTGCGTTTCGTGAAGCAAATAATTTGGAA
323 TTGCATTTTCTCGACGTGGTGTAACTCATTCGTTATTTGCGTTTTGTGAAATAAATAATTTGAAA
* * *
1601 CGATATTTGGTCGAATTTGCATTCAAATTCGAGGCGCAAGTGCG--AACGGGCAACCTTTATATT
388 CGATATTTGGTCGAATTTGCATTCAAATTCGAGGCGCAAGTGCGATAAGGGGCAGCCTTTATATG
* * * * *
1664 AATAGATTGCGCTAGAGTTGACGGGTACGATCATACCAGCAGTAATGCACCGGATCCAATTAGAA
453 AATAGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAA
* * ** *
1729 CTCCGCAGTCAAGCGTGCCGGGGCGAGT-GTAGTACTAGGATGGGTGACCTCCTGAGAAGTCCTC
518 CTCTGCAGTTAAGCGTGCTTGGGCGA-TAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTC
1793 GTGTTGCACCCCTCCCATTTTAT
582 GTGTTGCACCCCTCCCATTTTAT
*
1816 TTCATATAATGTTTTTTTTAGTTGCATTTTCTCGACGTGGTGTAACTCATTCGTTATTAGCGTTT
1 TTCATATAATG-TTTTTTTAGTTGCATTTTCTCGACGTGGTGTAACTCATTCGTTATTTGCGTTT
* * * * *
1881 TGTGAAATACATAACTTGGAACGATATTTGGTCGAATTTGTATTTAAATTCGAGGCGCAAGTGCA
65 TGTGAAATAAATAATTTGGAACGATATTTGGTCGAATTTGCATTCAAATTCGAGGCGCAAGTGCG
* * * *
1946 ATAAGAGGCAGCCTATATATGAATAGATTGCGCAAGAGTTGACGGGTGTGATCATACTAGCACTA
130 ATAAGCGGCAGCCTTTATATGAATAGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCACTA
* *
2011 ATGCACCGGATCCCATCAGAACTCCGTAGTTAAACGTGCTTGGGAGAGAGTAGTACTAGGATGGG
195 ATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTT-GGAGAGAGTAGTACTAGGATGGG
* * *
2076 TGACTTTCTGGGAAGTCCTCGTGTTGCACCCCTCCCATTTTAATTCATATAATGGTTTTTTTAGT
259 TGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTCCCATTTTATTTCATATAATGGTTTTTTTAGT
* * * *
2141 TGCGTTTTCTCGACGTGGTGCAACACATTCGTTATTTGCGTTTTGTGAAATAAATAATTTGGAAC
324 TGCATTTTCTCGACGTGGTGTAACTCATTCGTTATTTGCGTTTTGTGAAATAAATAATTTGAAAC
* ** *
2206 GATATTTGGTCGAATTTGTATTCAGTTTCGAGGCGCAAGTGCGATAAGAGGCAGCCTTTATATGA
389 GATATTTGGTCGAATTTGCATTCAAATTCGAGGCGCAAGTGCGATAAGGGGCAGCCTTTATATGA
* *
2271 ATAGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCACAAATGCATCGGATCCCATCAGAAC
454 ATAGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAAC
* * *
2336 TCTGCAGTTAAGTGTGCTAGGGCGATAGTAGTACTAGGATGGGTGACCTACTGGGAAGTCCTCGT
519 TCTGCAGTTAAGCGTGCTTGGGCGATAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGT
* * *
2401 GATGCACCACTTCCATTTTAT
584 GTTGCACCCCTCCCATTTTAT
* * * *
2422 TTCATATAAT-TTTTTTT-GTTGCATTTGCTCCACCTGGTGTAACTCATTCGTTATTTGTGTTTT
1 TTCATATAATGTTTTTTTAGTTGCATTTTCTCGACGTGGTGTAACTCATTCGTTATTTGCGTTTT
** * * * * * * * *
2485 GCAAAATAAATAAATT-GAGTCGATATTTTGTCTAATTTGCCTTCAAATTCAATGTGCAAGTG-G
66 GTGAAATAAATAATTTGGA-ACGATATTTGGTCGAATTTGCATTCAAATTCGAGGCGCAAGTGCG
* * * *
2548 CATGAAG-AGCAGCCTTTATATGAATATATTGCGCAAGAGCTGACGGGTCCGATCATACCAGCAC
130 -AT-AAGCGGCAGCCTTTATATGAATAGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCAC
* * ** * *
2612 TAATGCTCCGGATCCCATCAGAACTCCGCAGTTAAGCATATTTGGGAGAGAGTAGAACTAGCATG
193 TAATGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTT-GGAGAGAGTAGTACTAGGATG
* *
2677 GGTGACCTCCTGAGAAGTCCTCGTGTTGCACCCCTCCCATTTTATTTCATATAATGTTTTTATTT
257 GGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTCCCATTTTATTTCATATAATGGTTTT-TTT
* * * * *
2742 AGTTGCATTTTCTCGAAGTGGTGTAACGCATTCGTTACTTACATTTTGTGAAATAAATAATTTGA
321 AGTTGCATTTTCTCGACGTGGTGTAACTCATTCGTTATTTGCGTTTTGTGAAATAAATAATTTGA
* * * * * *
2807 AACAATATTTGGTCGAATTTGTATTCAAAATCGAGGTTG-AAGTACGATAAGGGGCAGCCTTTTT
386 AACGATATTTGGTCGAATTTGCATTCAAATTCGAGG-CGCAAGTGCGATAAGGGGCAGCCTTTAT
* *
2871 ATGAATAGGTTGCGCAAGAGTTGACGGGTGCGATCATACCAGCACTAATGCACCTGATCCCATCA
450 ATGAATAGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCA
* * * * *
2936 GAACT-TCGAAGTGAAGCGTGCTTGGGGGAGAGTAGTACTAGGATGGGTGACCTCCTGGGAATTC
515 GAACTCT-GCAGTTAAGCGTGCTTGGGCGATAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTC
* *
3000 CACGTGTTGCACCCCTCCCTTTTTAT
579 CTCGTGTTGCACCCCTCCCATTTTAT
* * *
3026 TTCATGTAATGGTTTCTTTAGTTGCGTTTTCTCGACGTGGTGTAACTCATTCGTTATTTGCGTTT
1 TTCATATAAT-GTTTTTTTAGTTGCATTTTCTCGACGTGGTGTAACTCATTCGTTATTTGCGTTT
* *
3091 TGTGAAATAAATAATTTGGAACGATATTTGGTCGAATTTGTATTCAATTTCGAGGCGCAAGTGCG
65 TGTGAAATAAATAATTTGGAACGATATTTGGTCGAATTTGCATTCAAATTCGAGGCGCAAGTGCG
3156 ATAAGCGGCAGCCTTTAT
130 ATAAGCGGCAGCCTTTAT
3174 NNNNNNNNNN
Statistics
Matches: 2076, Mismatches: 467, Indels: 46
0.80 0.18 0.02
Matches are distributed among these distances:
602 2 0.00
603 423 0.20
604 809 0.39
605 69 0.03
606 657 0.32
607 113 0.05
608 3 0.00
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.31
Consensus pattern (604 bp):
TTCATATAATGTTTTTTTAGTTGCATTTTCTCGACGTGGTGTAACTCATTCGTTATTTGCGTTTT
GTGAAATAAATAATTTGGAACGATATTTGGTCGAATTTGCATTCAAATTCGAGGCGCAAGTGCGA
TAAGCGGCAGCCTTTATATGAATAGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCACTAA
TGCACCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGAGAGAGTAGTACTAGGATGGGTG
ACCTCCTGGGAAGTCCTCGTGTTGCACCCCTCCCATTTTATTTCATATAATGGTTTTTTTAGTTG
CATTTTCTCGACGTGGTGTAACTCATTCGTTATTTGCGTTTTGTGAAATAAATAATTTGAAACGA
TATTTGGTCGAATTTGCATTCAAATTCGAGGCGCAAGTGCGATAAGGGGCAGCCTTTATATGAAT
AGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTC
TGCAGTTAAGCGTGCTTGGGCGATAGTAGTACTAGGATGGGTGACCTCCTGGGAAGTCCTCGTGT
TGCACCCCTCCCATTTTAT
Found at i:3173 original size:907 final size:906
Alignment explanation
Indices: 1--3170 Score: 3735
Period size: 907 Copynumber: 3.5 Consensus size: 906
* *
1 TTCATATAATGGTTTTTTTAGTTGCGTTTCCTCGACGTGGTGTAACTCATTCATTATTTGCGTTT
1 TTCATATAATGGTTTTTTTAGTTGCATTTCCTCGACGTGGTGTAACTCATTCATTA-TTACGTTT
* *
66 TTTGAAGTAAATAATTTGAAACGATATTTGGTCGAATTTACATTTAAATTCGAGGCGCAAGTACG
65 TGTGAAATAAATAATTTGAAACGATATTTGGTCGAATTTACATTTAAATTCGAGGCGCAAGTACG
* *
131 ATAAGGGGCAGCCTTTATATGAATAGATTGCGCAAGAGTTGATGGGTGCTATCATACCAGCACTA
130 ATAAGGGGCAGCCTTTATATGAATAGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCACTA
* * *
196 ATGCACCGGATCCCGTCAGAACTCTGAAGTTAAGCGTGCTTGGGCGATAGTAGTACTAGGATTGG
195 ATGCACCGGATCCCATCAGAACTCTGAAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGG
* * *
261 TGACCTCTTGGGAAGTCCTCGTGTTGCACCCCTCCCATTTTATTACATATAAAGTTTTTATTTGG
260 TGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTCCCATTTTATTACATATAAAGTGTTTATTTAG
326 TTGCATTTTCTCGACGTGGTGTAACTCATTCGTTATTTGCATTTTGTGAAATAAATAATTTGAAA
325 TTGCATTTTCTCGACGTGGTGTAACTCATTCGTTATTTGCATTTTGTGAAATAAATAATTTGAAA
* *
391 CAATATTTGGTCAAATTGGCCTTTAAATTCGAGGCGCAAGTGCGATAAGGGGCAGCCTTCATATG
390 CAATATTTGGTCAAATTGGCATTCAAATTCGAGGCGCAAGTGCGATAAGGGGCAGCCTTCATATG
456 AATAGATTGCGCAAGAGTTGACGGGAGCGATCATACCAGCACAAATGCACCGGATCCCATCAGAA
455 AATAGATTGCGCAAGAGTTGACGGGAGCGATCATACCAGCACAAATGCACCGGATCCCATCAGAA
* * *
521 CTCCGCAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGTGACTTCCTGGGAAGTCCACG
520 CTCCGCAGTTAAGCGTGCTAGGGCGAGAGTAGTACTAGGATGGGTGACCTACTGGGAAGTCCACG
* * *
586 TGTTGCACTCCTCCCATTTTATTTCATATAATGTTTTTTTAGTTGCATTTTCTCGACTTGGTGTA
585 TGATGCAC-CCTCCCATTTTATTTCATATAATGTTTTTTTAGTTGCATTTGCTCGACCTGGTGTA
*
651 ACTCATTCGTTATTTGCGTTTTGTGAAACAAATAATTTGGAACGATATTTGGTCGAATTTGTATT
649 ACTCATTCGTTATTTGCGTTTTGTGAAACAAATAATTTGGAACGATATTTGGTCGAATTTGCATT
* *
716 CAATTTCGAGGCGCAAGTGCGAT-AAGCGGCAGCCTTTATATGAATAGATTGCGCAAGCGTTGAC
714 CAAATTCGAGGCGCAAGTGC-ATGAAG-GGCAGCCTTTATATGAATAGATTGCGCAAGAGTTGAC
*
780 GGGTGCGATCATACCAGCACTAATGCAT-CGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTT-
777 GGGTACGATCATACCAGCACTAATGC-TCCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTG
843 GGACGAGAGTAGTAC-AGGATGGGTGACCTCCT-AGGAAGTCCTCGTGTTGCACCCCTCCCATTT
841 GGA-GAGAGTAGTACTAGGATGGGTGACCTCCTGA-GAAGTCCTCGTGTTGCACCCCTCCCATTT
*
906 TCT
904 TAT
* *
909 TTCATATAATGGTTTTTTTAGTTGCGTTTCCTCGACGTGGTGTAACTCATTCATTATATGCGTTT
1 TTCATATAATGGTTTTTTTAGTTGCATTTCCTCGACGTGGTGTAACTCATTCATTAT-TACGTTT
* *
974 TTTGAAGTAAATAATTTGAAACGATATTTGGTCGAATTTACATTTAAATTCGAGGCGCAAGTACG
65 TGTGAAATAAATAATTTGAAACGATATTTGGTCGAATTTACATTTAAATTCGAGGCGCAAGTACG
* *
1039 ATAAGGGGCAGCCTTTATATGAATAGATTGCGCAAGAGTTGATGGGTGCTATCATACCAGCACTA
130 ATAAGGGGCAGCCTTTATATGAATAGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCACTA
* * *
1104 ATGCACCGGATCCCGTCAGAACTCTGAAGTTAAGCGTGCTTGGGCGATAGTAGTACTAGGATTGG
195 ATGCACCGGATCCCATCAGAACTCTGAAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGG
* * *
1169 TGACCTCTTGGGAAGTCCTCGTGTTGCACCCCTCCCATTTTATTACATATAAAGTTTTTATTTGG
260 TGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTCCCATTTTATTACATATAAAGTGTTTATTTAG
1234 TTGCATTTTCTCGACGTGGTGTAACTCATTCGTTATTTGCATTTTGTGAAATAAATAATTTGAAA
325 TTGCATTTTCTCGACGTGGTGTAACTCATTCGTTATTTGCATTTTGTGAAATAAATAATTTGAAA
* *
1299 CAATATTTGGTCAAATTGGCCTTTAAATTCGAGGCGCAAGTGCGATAAGGGGCAGCCTTCATATG
390 CAATATTTGGTCAAATTGGCATTCAAATTCGAGGCGCAAGTGCGATAAGGGGCAGCCTTCATATG
* ***********
1364 AATAGATTGCGCAAGAGTTGACGGGAGCGATCATGCCAGCACAAATGCACCGGNNNNNNNNNNNN
455 AATAGATTGCGCAAGAGTTGACGGGAGCGATCATACCAGCACAAATGCACCGG-ATCCCATCAGA
*****************************************************************
1429 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
519 ACTCCGCAGTTAAGCGTGCTAGGGCGAGAGTAGTACTAGGATGGGTGACCTACTGGGAAGTCCAC
******************************
1494 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNATGTTTTTTTAGTTGCATTTGCTCGACGC-GGTGT
584 GTGATGCACCCTCCCATTTTATTTCATATAATGTTTTTTTAGTTGCATTTGCTCGAC-CTGGTGT
* *
1558 AACTCATTCGTTATTTGCGTTTCGTGAAGCAAATAATTTGGAACGATATTTGGTCGAATTTGCAT
648 AACTCATTCGTTATTTGCGTTTTGTGAAACAAATAATTTGGAACGATATTTGGTCGAATTTGCAT
* * *
1623 TCAAATTCGAGGCGCAAGTGC--GAACGGGCAACCTTTATATTAATAGATTGCGCTAGAGTTGAC
713 TCAAATTCGAGGCGCAAGTGCATGAA-GGGCAGCCTTTATATGAATAGATTGCGCAAGAGTTGAC
* * * * * **
1686 GGGTACGATCATACCAGCAGTAATGCACCGGATCCAATTAGAACTCCGCAGTCAAGCGTGCCGGG
777 GGGTACGATCATACCAGCACTAATGCTCCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGG
* *
1751 GCGAGTGTAGTACTAGGATGGGTGACCTCCTGAGAAGTCCTCGTGTTGCACCCCTCCCATTTTAT
842 GAGAGAGTAGTACTAGGATGGGTGACCTCCTGAGAAGTCCTCGTGTTGCACCCCTCCCATTTTAT
* * *
1816 TTCATATAATGTTTTTTTTAGTTGCATTTTCTCGACGTGGTGTAACTCATTCGTTATTAGCGTTT
1 TTCATATAATGGTTTTTTTAGTTGCATTTCCTCGACGTGGTGTAACTCATTCATTATTA-CGTTT
* * * ** * *
1881 TGTGAAATACATAACTTGGAACGATATTTGGTCGAATTTGTATTTAAATTCGAGGCGCAAGTGCA
65 TGTGAAATAAATAATTTGAAACGATATTTGGTCGAATTTACATTTAAATTCGAGGCGCAAGTACG
* * * *
1946 ATAAGAGGCAGCCTATATATGAATAGATTGCGCAAGAGTTGACGGGTGTGATCATACTAGCACTA
130 ATAAGGGGCAGCCTTTATATGAATAGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCACTA
* * * *
2011 ATGCACCGGATCCCATCAGAACTCCGTAGTTAAACGTGCTTGGGAGAGAGTAGTACTAGGATGGG
195 ATGCACCGGATCCCATCAGAACTCTGAAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGG
* * * *
2076 TGACTTTCTGGGAAGTCCTCGTGTTGCACCCCTCCCATTTTAATT-CATATAATG-GTTTTTTTA
260 TGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTCCCATTTT-ATTACATATAAAGTGTTTATTTA
* * * * *
2139 GTTGCGTTTTCTCGACGTGGTGCAACACATTCGTTATTTGCGTTTTGTGAAATAAATAATTTGGA
324 GTTGCATTTTCTCGACGTGGTGTAACTCATTCGTTATTTGCATTTTGTGAAATAAATAATTTGAA
* * * * ** * *
2204 ACGATATTTGGTCGAATTTGTATTCAGTTTCGAGGCGCAAGTGCGATAAGAGGCAGCCTTTATAT
389 ACAATATTTGGTCAAATTGGCATTCAAATTCGAGGCGCAAGTGCGATAAGGGGCAGCCTTCATAT
* *
2269 GAATAGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCACAAATGCATCGGATCCCATCAGA
454 GAATAGATTGCGCAAGAGTTGACGGGAGCGATCATACCAGCACAAATGCACCGGATCCCATCAGA
* * * *
2334 ACTCTGCAGTTAAGTGTGCTAGGGCGATAGTAGTACTAGGATGGGTGACCTACTGGGAAGTCCTC
519 ACTCCGCAGTTAAGCGTGCTAGGGCGAGAGTAGTACTAGGATGGGTGACCTACTGGGAAGTCCAC
* *
2399 GTGATGCACCACTTCCATTTTATTTCATATAAT-TTTTTTT-GTTGCATTTGCTCCACCTGGTGT
584 GTGATGCACC-CTCCCATTTTATTTCATATAATGTTTTTTTAGTTGCATTTGCTCGACCTGGTGT
* ** * * * * * *
2462 AACTCATTCGTTATTTGTGTTTTGCAAAATAAATAAATT-GAGTCGATATTTTGTCTAATTTGCC
648 AACTCATTCGTTATTTGCGTTTTGTGAAACAAATAATTTGGA-ACGATATTTGGTCGAATTTGCA
* * * * * *
2526 TTCAAATTCAATGTGCAAGTGGCATGAAGAGCAGCCTTTATATGAATATATTGCGCAAGAGCTGA
712 TTCAAATTCGAGGCGCAAGT-GCATGAAGGGCAGCCTTTATATGAATAGATTGCGCAAGAGTTGA
* * **
2591 CGGGTCCGATCATACCAGCACTAATGCTCCGGATCCCATCAGAACTCCGCAGTTAAGCATATTTG
776 CGGGTACGATCATACCAGCACTAATGCTCCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTG
* *
2656 GGAGAGAGTAGAACTAGCATGGGTGACCTCCTGAGAAGTCCTCGTGTTGCACCCCTCCCATTTTA
841 GGAGAGAGTAGTACTAGGATGGGTGACCTCCTGAGAAGTCCTCGTGTTGCACCCCTCCCATTTTA
2721 T
906 T
* * * * * *
2722 TTCATATAATGTTTTTATTTAGTTGCATTTTCTCGAAGTGGTGTAACGCATTCGTTACTTACATT
1 TTCATATAATGGTTTT-TTTAGTTGCATTTCCTCGACGTGGTGTAACTCATTCATTA-TTACGTT
* ** * * *
2787 TTGTGAAATAAATAATTTGAAACAATATTTGGTCGAATTTGTATTCAAAATCGAGGTTG-AAGTA
64 TTGTGAAATAAATAATTTGAAACGATATTTGGTCGAATTTACATTTAAATTCGAGG-CGCAAGTA
* *
2851 CGATAAGGGGCAGCCTTTTTATGAATAGGTTGCGCAAGAGTTGACGGGTGCGATCATACCAGCAC
128 CGATAAGGGGCAGCCTTTATATGAATAGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCAC
* * *
2916 TAATGCACCTGATCCCATCAGAACT-TCGAAGTGAAGCGTGCTTGGGGGAGAGTAGTACTAGGAT
193 TAATGCACCGGATCCCATCAGAACTCT-GAAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGAT
* * * * * * *
2980 GGGTGACCTCCTGGGAATTCCACGTGTTGCACCCCTCCCTTTTTATTTCATGTAATG-GTTTCTT
257 GGGTGACCTCCTGGGAAGTCCTCGTGTTGCACCCCTCCCATTTTATTACATATAAAGTGTTTATT
* *
3044 TAGTTGCGTTTTCTCGACGTGGTGTAACTCATTCGTTATTTGCGTTTTGTGAAATAAATAATTTG
322 TAGTTGCATTTTCTCGACGTGGTGTAACTCATTCGTTATTTGCATTTTGTGAAATAAATAATTTG
* * * * * * *
3109 GAACGATATTTGGTCGAATTTGTATTCAATTTCGAGGCGCAAGTGCGATAAGCGGCAGCCTT
387 AAACAATATTTGGTCAAATTGGCATTCAAATTCGAGGCGCAAGTGCGATAAGGGGCAGCCTT
3171 TATNNNNNNN
Statistics
Matches: 1883, Mismatches: 357, Indels: 45
0.82 0.16 0.02
Matches are distributed among these distances:
903 3 0.00
904 87 0.05
905 9 0.00
906 440 0.23
907 718 0.38
908 626 0.33
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.31
Consensus pattern (906 bp):
TTCATATAATGGTTTTTTTAGTTGCATTTCCTCGACGTGGTGTAACTCATTCATTATTACGTTTT
GTGAAATAAATAATTTGAAACGATATTTGGTCGAATTTACATTTAAATTCGAGGCGCAAGTACGA
TAAGGGGCAGCCTTTATATGAATAGATTGCGCAAGAGTTGACGGGTGCGATCATACCAGCACTAA
TGCACCGGATCCCATCAGAACTCTGAAGTTAAGCGTGCTTGGGCGAGAGTAGTACTAGGATGGGT
GACCTCCTGGGAAGTCCTCGTGTTGCACCCCTCCCATTTTATTACATATAAAGTGTTTATTTAGT
TGCATTTTCTCGACGTGGTGTAACTCATTCGTTATTTGCATTTTGTGAAATAAATAATTTGAAAC
AATATTTGGTCAAATTGGCATTCAAATTCGAGGCGCAAGTGCGATAAGGGGCAGCCTTCATATGA
ATAGATTGCGCAAGAGTTGACGGGAGCGATCATACCAGCACAAATGCACCGGATCCCATCAGAAC
TCCGCAGTTAAGCGTGCTAGGGCGAGAGTAGTACTAGGATGGGTGACCTACTGGGAAGTCCACGT
GATGCACCCTCCCATTTTATTTCATATAATGTTTTTTTAGTTGCATTTGCTCGACCTGGTGTAAC
TCATTCGTTATTTGCGTTTTGTGAAACAAATAATTTGGAACGATATTTGGTCGAATTTGCATTCA
AATTCGAGGCGCAAGTGCATGAAGGGCAGCCTTTATATGAATAGATTGCGCAAGAGTTGACGGGT
ACGATCATACCAGCACTAATGCTCCGGATCCCATCAGAACTCCGCAGTTAAGCGTGCTTGGGAGA
GAGTAGTACTAGGATGGGTGACCTCCTGAGAAGTCCTCGTGTTGCACCCCTCCCATTTTAT
Found at i:5565 original size:303 final size:303
Alignment explanation
Indices: 5017--5713 Score: 1054
Period size: 303 Copynumber: 2.3 Consensus size: 303
5007 NNNNNNGGTA
* * * *
5017 CGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTCTGCAGTTAAGCGTGCTTGGACCAG
1 CGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGAAGTTAAGCGTGCTTGGGCGAG
* *
5082 AGTAGTACTAGGATGGGCGACCTCCTGAGAAGTCCTCGTGTTGCACCCCTCCCATTTTATTTCAT
66 AGTAGTACTAGGATGGGTGACCTCCTGAGAAGTCCTCGCGTTGCACCCCTCCCATTTTATTTCAT
* * * *
5147 ATAATGGTTTTTTTAGTTACGTTTTCTCGACGTGGTGTAACTCATTCATTTTTTGCGTTTTGTGA
131 ATAATGGTTTTTTTAGTTACATTTTCTCGACGTCGTGTAACTCATTCATTATTTACGTTTTGTGA
* * * *
5212 AGTAAATAATTTGAAACGATATTTGGTCGAATTTGCATTTAAATTCGAGGCGCAACTGTGATAAG
196 AATAAATAATTTGAAACGATATTTGGTCGAATTTGAATTCAAATTCGAGGCGCAACTGCGATAAG
* * * *
5277 GGGCAGCCGTTATATGAATAGCTTGCGCAAGAATTGACGGGTG
261 AGGCAGCCCTTATATGAATAGATTGCGCAAGAATTCACGGGTG
* * *
5320 GGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGAAGTTAAGCGTCCCTGGGCGAG
1 CGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGAAGTTAAGCGTGCTTGGGCGAG
* * *
5385 AGTAGTACTAGGATGGGTGACCTCCTGGGAGGTCCTCGCGTTGCACTCCTCCCATTTTATTTCAT
66 AGTAGTACTAGGATGGGTGACCTCCTGAGAAGTCCTCGCGTTGCACCCCTCCCATTTTATTTCAT
* * *
5450 ATAATGTTTTTTTTAGTTGCATTTTCTCGACGTCGTGTAACTCATTCGTTATTTACGTTTTGTGA
131 ATAATGGTTTTTTTAGTTACATTTTCTCGACGTCGTGTAACTCATTCATTATTTACGTTTTGTGA
** *
5515 AATAAATAATTTGAAACGATATTTTTTCGAATTTGAATTCAAATTCGAGGCGCAAGTGCGATAAG
196 AATAAATAATTTGAAACGATATTTGGTCGAATTTGAATTCAAATTCGAGGCGCAACTGCGATAAG
* *
5580 AGGCAGCCCTTATATGAATAGATTGCGCAAGAGTTCATGGGTG
261 AGGCAGCCCTTATATGAATAGATTGCGCAAGAATTCACGGGTG
* * *
5623 CGATCATACCAGTACTAATGCATCGTATCCCATCAGAACTCC-ACAGTTAAGCGTGCTTGGGCGA
1 CGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGA-AGTTAAGCGTGCTTGGGCGA
*
5687 GAGTAGTACTAGGATGGGTGACTTCCT
65 GAGTAGTACTAGGATGGGTGACCTCCT
5714 AGCGTGTTGC
Statistics
Matches: 354, Mismatches: 39, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
302 1 0.00
303 353 1.00
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (303 bp):
CGATCATACCAGCACTAATGCACCGGATCCCATCAGAACTCCGAAGTTAAGCGTGCTTGGGCGAG
AGTAGTACTAGGATGGGTGACCTCCTGAGAAGTCCTCGCGTTGCACCCCTCCCATTTTATTTCAT
ATAATGGTTTTTTTAGTTACATTTTCTCGACGTCGTGTAACTCATTCATTATTTACGTTTTGTGA
AATAAATAATTTGAAACGATATTTGGTCGAATTTGAATTCAAATTCGAGGCGCAACTGCGATAAG
AGGCAGCCCTTATATGAATAGATTGCGCAAGAATTCACGGGTG
Done.