Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009328.1 Kokia drynarioides strain JFW-HI SEQ_124035, 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: 2668
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Found at i:452 original size:215 final size:215
Alignment explanation
Indices: 1--2665 Score: 2545
Period size: 215 Copynumber: 12.4 Consensus size: 215
* * * *
1 ACGAACATAT-GAACTAGTCAAACTTTTACAAGTTCTTTTATAACTTCGGTTCCTCAGAGTATTC
1 ACGAACATATCGAACTAGTCAAACATTTACGAGTTCTTTTATAACTTCGATTCCTGAGAGTATTC
* * * * * * *
65 AAGACGATCCATTTCTTTGATCGATTTTTTGAAG-ATTCCATTATCGAGAAATCGCAGCATTCT-
66 AAGACGATCCATTCCTTTGACCAATTTTTCG-AGCATTCCATGATCG-GAAATCGTATCATT-TG
* * * *
128 GT-AAAATAGTTTGCCA-TTTGTAAATAAA-TTTTGGTCTTTGAATTAAAAACTTTTTTACATTA
128 GTCTAAATAGTTTGTCATTTTGT--ATAAATTTTTGGTCTTTGAATTAAAAACTTTTTTACGTGA
*
190 GAATTCTTTCTCTCTTGGTTCTTGG
191 GAATTATTTCTCTCTTGGTTCTTGG
* * * * * **
215 ACGAA-GTTTCGAACTTGTCAAACATTTACTAGTTCTTTTACAACTTCGATTCCTGAGAGTAGCC
1 ACGAACATATCGAACTAGTCAAACATTTACGAGTTCTTTTATAACTTCGATTCCTGAGAGTATTC
*
279 AAGATGATCCATTCCTTTGACCAATTTTTCGAGCATTCCATGATCAGGAAATCGTATCATTTGGT
66 AAGACGATCCATTCCTTTGACCAATTTTTCGAGCATTCCATGATC-GGAAATCGTATCATTTGGT
* * * * *
344 CTAAATAGTTAGTCATTTTGTATAAATTTTTAGTCTTTGAATTAAATACTTATTTATGTGAGAAT
130 CTAAATAGTTTGTCATTTTGTATAAATTTTTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAAT
*
409 TATTTCCCTCTTGGTTCTTGG
195 TATTTCTCTCTTGGTTCTTGG
* * * * * *
430 ACGAACATAT-GAACTAGTCAAACTTTTACAAGTTTTTTTATAACTTCGGTTTCTCAGAGTATTC
1 ACGAACATATCGAACTAGTCAAACATTTACGAGTTCTTTTATAACTTCGATTCCTGAGAGTATTC
* * * * * *
494 AAGACGATCCATTTCTTTGACCTATTTTTTGAAG-ATTCCATTATCGAGAAATCGCAGCATCTT-
66 AAGACGATCCATTCCTTTGACCAATTTTTCG-AGCATTCCATGATCG-GAAATCGTATCAT-TTG
** * ** *
557 GTAAAAATAGTTTGCCA-TTTGTAAATAAATTTTT-GTCTTTGAATTAAAAACTTTTTTAAATTA
128 GTCTAAATAGTTTGTCATTTTGT--ATAAATTTTTGGTCTTTGAATTAAAAACTTTTTTACGTGA
* * *
620 GAATTCTTTCTCTCTTGTTTCCTGG
191 GAATTATTTCTCTCTTGGTTCTTGG
* * * * * * **
645 ACGAA-GTATCGAACTTGTTAAACATTTACTAGTTCTTTTACAACTTCGCTTCCTGAGAGTAGCC
1 ACGAACATATCGAACTAGTCAAACATTTACGAGTTCTTTTATAACTTCGATTCCTGAGAGTATTC
* * * *
709 AAGATGATCCATTCCTTCGACCAATTTTTCTAGCATTCAATGATCAGGAAATCGTATCATTTGGT
66 AAGACGATCCATTCCTTTGACCAATTTTTCGAGCATTCCATGATC-GGAAATCGTATCATTTGGT
* * * * * *
774 CTAAATCGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAGTAAAAAACTTTTTTACGTGGGAA
130 CTAAATAGTTTGTCATTTTGTATA-AATTTTTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAA
* * **
839 TTGTTTCTCTATTTTTTCTTGG
194 TTATTTCTCTCTTGGTTCTTGG
* * * *
861 ACGAAC-TTTCAAAC-ACGTCAAACATTTGCGAGTTCTTTTATAACTTCGATTCTTGAGAGTATT
1 ACGAACATATCGAACTA-GTCAAACATTTACGAGTTCTTTTATAACTTCGATTCCTGAGAGTATT
* * * * ** *
924 AAAGACGATTCATTCC-TTCAGCCAATTTTTCGAACATTCCATGCCCGGGAAATCGCT-TCGTTT
65 CAAGACGATCCATTCCTTTGA-CCAATTTTTCGAGCATTCCATGATC-GGAAATCG-TATCATTT
* * * * * * * *
987 GATTTAAATCGTTTATCATTTTGTATAAATTTTTAGTCTTTGAATTAAATACTTATTTACGAGAG
127 GGTCTAAATAGTTTGTCATTTTGTATAAATTTTTGGTCTTTGAATTAAAAACTTTTTTACGTGAG
1052 AATTATTTCTCTCTTGGTTCTTGG
192 AATTATTTCTCTCTTGGTTCTTGG
* *
1076 ACGAA-AT-TCTGAACTGGTTAAACATTTACGAGTTCTTTTATAACTTCGATTCCTGAGAGTATT
1 ACGAACATATC-GAACTAGTCAAACATTTACGAGTTCTTTTATAACTTCGATTCCTGAGAGTATT
* * * * * ** * *
1139 AAAGACGATCCATTCC-TTCAGCCATTTTTTCGAACATTCTATGCCCGTGAAATCCCT-TCGTTT
65 CAAGACGATCCATTCCTTTGA-CCAATTTTTCGAGCATTCCATGATCG-GAAAT-CGTATCATTT
* * * * * * *
1202 GATTTAAATAGTTTATCATTTTGTATAAATTTTTAGTCTTTGAATTAAATACTTATTTATGTGAG
127 GGTCTAAATAGTTTGTCATTTTGTATAAATTTTTGGTCTTTGAATTAAAAACTTTTTTACGTGAG
*
1267 AATTATTTCCCTCTTGGTTCTTGG
192 AATTATTTCTCTCTTGGTTCTTGG
* * * *
1291 ACGAACATAT-GAACTAGTCAAACTTTTACAAGTTCTTTTATAACTTCGGTTCCTCAGAGTATTC
1 ACGAACATATCGAACTAGTCAAACATTTACGAGTTCTTTTATAACTTCGATTCCTGAGAGTATTC
* * * * * * *
1355 AAGACGATCCATTTCTTTGACCGATTTTTTGAAG-ATTCCATTATCGAGAAATCGCAGCATTTTG
66 AAGACGATCCATTCCTTTGACCAATTTTTCG-AGCATTCCATGATCG-GAAATCGTATCATTTGG
** * *
1419 TAAAAATAGTTTGCCA-TTTGTAAATAAA-TTTTGGTCTTTGAATTAAAAACTTTTTTACACT-A
129 TCTAAATAGTTTGTCATTTTGT--ATAAATTTTTGGTCTTTGAATTAAAAACTTTTTTAC-GTGA
*
1481 GAATTCTTTCTCTCTTGGTTCCTT-G
191 GAATTATTTCTCTCTTGGTT-CTTGG
* * * * * **
1506 ACGAA-GTATCGAACTTGTTAAACATTTACTAGTTCTTTTACAACTTCGATTCCTGAGAGTAGCC
1 ACGAACATATCGAACTAGTCAAACATTTACGAGTTCTTTTATAACTTCGATTCCTGAGAGTATTC
** * *
1570 AAGGTGATCCATTCCTTCGACCAATTTTTCGAGCATTCAATGATCAGGAAATCGTATCATTTGGT
66 AAGACGATCCATTCCTTTGACCAATTTTTCGAGCATTCCATGATC-GGAAATCGTATCATTTGGT
* * * * * *
1635 CTAAATCGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAGTAAAAAACTTTTTTACGTGGGAA
130 CTAAATAGTTTGTCATTTTGTATA-AATTTTTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAA
* * **
1700 TTGTTTCTCTATTTTTTCTTGG
194 TTATTTCTCTCTTGGTTCTTGG
* * *
1722 ACGAAC-TTTCGAAC-ACGTCAAACATTTGCGAGTTCTTTTATAACTTCGATTCTTGAGAGTATT
1 ACGAACATATCGAACTA-GTCAAACATTTACGAGTTCTTTTATAACTTCGATTCCTGAGAGTATT
* * * * * ** *
1785 AAAGATGATTCATTCC-TTCAGCCAATTTTTCGAACATTCCATGCCCGGGAAATCGCT-TCGTTT
65 CAAGACGATCCATTCCTTTGA-CCAATTTTTCGAGCATTCCATGATC-GGAAATCG-TATCATTT
* * * * * * * * *
1848 GATTTAATTCGTTTATCATTTTGTATAAATTTTTAGTCTTTGAATTAAATACTTATTTACGAGAG
127 GGTCTAAATAGTTTGTCATTTTGTATAAATTTTTGGTCTTTGAATTAAAAACTTTTTTACGTGAG
1913 AATTATTTCTCTCTTGGTTCTTGG
192 AATTATTTCTCTCTTGGTTCTTGG
* *
1937 ACGAA-AT-TCTGAACTGGTTAAACATTTACGAGTTCTTTTATAACTTCGATTCCTGAGAGTATT
1 ACGAACATATC-GAACTAGTCAAACATTTACGAGTTCTTTTATAACTTCGATTCCTGAGAGTATT
* * * * ** *
2000 AAAGACGATCCATTCC-TTCAGCCATTTTTTCGAACATTCCATGCCCGGGAAATCGCT-TCGTTT
65 CAAGACGATCCATTCCTTTGA-CCAATTTTTCGAGCATTCCATGATC-GGAAATCG-TATCATTT
* * * * * *
2063 GATTTAAATAGTTTATCATTTTGTATACAATTTTTAGTCTTTGAATTAAATACTTATTTACGTGA
127 GGTCTAAATAGTTTGTCATTTTGTATA-AATTTTTGGTCTTTGAATTAAAAACTTTTTTACGTGA
* *
2128 GAATTATTTCCCTCTTGGATCTTGG
191 GAATTATTTCTCTCTTGGTTCTTGG
* * * *
2153 ACGAACATAT-GAACTAGACAAAC-TCTTACAAGTTCTTTTATAACTTCGGTTCCTTAGAGTATT
1 ACGAACATATCGAACTAGTCAAACAT-TTACGAGTTCTTTTATAACTTCGATTCCTGAGAGTATT
* * * * * * *
2216 CAAGACTATCCATTTCTTTGACCAATTTTTTGAAG-AGTCCATTATCGAGAAATCGCAGCATTTG
65 CAAGACGATCCATTCCTTTGACCAATTTTTCG-AGCATTCCATGATCG-GAAATCGTATCATTTG
** * * * *
2280 GTAAAAATAGTTTGCCAATTTGTAAATAAA-TTTTGGTCTTTGAATTAAAAACTTTTTTACATTA
128 GTCTAAATAGTTTGTCATTTTGT--ATAAATTTTTGGTCTTTGAATTAAAAACTTTTTTACGTGA
*
2344 GAATTCTTTCTCTCTTGGTTCTTGG
191 GAATTATTTCTCTCTTGGTTCTTGG
* * * * **
2369 ACGAA-GTATCGAACTTGTCAAACATTTACTAGTTCTTTTACAACTTCGATTCCTGAGAGTAGCC
1 ACGAACATATCGAACTAGTCAAACATTTACGAGTTCTTTTATAACTTCGATTCCTGAGAGTATTC
* * *
2433 AAGATGATCCATTCCTTCGACCAATTTTTCGAGCATTCCATGATTAGGAAATCGTATCATTTGGT
66 AAGACGATCCATTCCTTTGACCAATTTTTCGAGCATTCCATGA-TCGGAAATCGTATCATTTGGT
* * * * * * * *
2498 CTAAATCGTTTGACATTTTGTAAACAACTTTCGGTCTTTGAATTAATAACTTTTTTATGTGGGAA
130 CTAAATAGTTTGTCATTTTGTATA-AATTTTTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAA
* * *
2563 TTGTTTCTCTATTTGTTCTTGG
194 TTATTTCTCTCTTGGTTCTTGG
* * * * *
2585 ACGAAC-TTTCTAAC-ACGTCAAACATTTTCGATTTCTTTTATAACTTCGATTCGTGAGAGTATT
1 ACGAACATATCGAACTA-GTCAAACATTTACGAGTTCTTTTATAACTTCGATTCCTGAGAGTATT
* *
2648 AAAGACGATTCATTCCTT
65 CAAGACGATCCATTCCTT
2666 CAG
Statistics
Matches: 2030, Mismatches: 350, Indels: 140
0.81 0.14 0.06
Matches are distributed among these distances:
213 5 0.00
214 141 0.07
215 1040 0.51
216 826 0.41
217 14 0.01
218 4 0.00
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (215 bp):
ACGAACATATCGAACTAGTCAAACATTTACGAGTTCTTTTATAACTTCGATTCCTGAGAGTATTC
AAGACGATCCATTCCTTTGACCAATTTTTCGAGCATTCCATGATCGGAAATCGTATCATTTGGTC
TAAATAGTTTGTCATTTTGTATAAATTTTTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAATT
ATTTCTCTCTTGGTTCTTGG
Found at i:1408 original size:646 final size:644
Alignment explanation
Indices: 1--2661 Score: 2676
Period size: 646 Copynumber: 4.1 Consensus size: 644
* *
1 ACGAACATATGAACTAGTCAAACTTTTACAAGTTCTTTTATAACTTCGGTTCCTCAGAGTATTCA
1 ACGAACATATGAACTAGTCAAACTTTTACAAGTTCTTTTATAACTTCGATTCCTGAGAGTATTCA
* *
66 AGACGATCCATTTCTTTGATCGATTTTTTGAAGATTCCATTATCGAGAAATCGCAGCATTCT-GT
66 AGACGATCCATTTCTTTGACCGATTTTTTGAAGATTCCATGATCGAGAAATCGCAGCATT-TGGT
* * *
130 AAAATAGTTTGCCATTTGTAAATAAATTTTGGTCTTTGAATTAAAAACTTTTTTACATTAGAATT
130 AAAATAGTTTGCCATTTGTAAACAAATTTTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAATT
* * *
195 CTTTCTCTCTTGGTTCTTGGACGAAGTTTCGAACTTGTCAAACATTTACTAGTTCTTTTACAACT
195 CTTTCTCTCTTGGTTCTTGGACGAACTATCGAACATGTCAAACATTTACTAGTTCTTTTACAACT
* *
260 TCGATTCCTGAGAGTAGCCAAGATGATCCATTCCTTTGACCAATTTTTCGAGCATTCCATGATCA
260 TCGATTCCTGAGAGTAGCCAAGACGATCCATTCCTTTGACCAATTTTTCGAACATTCCATGATCA
325 GGAAATCGTATCATTTGGTCTAAATAG-TTAGTCATTTTGTATAAATTTTTAGTCTTTGAATTAA
325 GGAAATCGTATCATTTGGTCTAAATAGTTTA-TCATTTTGTATAAATTTTTAGTCTTTGAATTAA
* * * * *
389 ATACTTATTTATGTGAGAATTATTTCCCTCTTGGTTCTTGGACGAACA-TATGAACTAGTCAAAC
389 AAACTTATTTACGAGAGAATTATTTCTCTCTTGGTTCTTGGACGAA-ATTCTGAACTAGTCAAAC
* * * * * * * * * *
453 TTTTACAAGTTTTTTTATAACTTCGGTTTCTCAGAGTATTCAAGACGATCCATTTCTT-TGACCT
453 ATTTACGAGTTCTTTTATAACTTCGATTCCTGAGAGTATTAAAGACGATCCATTCCTTCAGACCA
* * *** * ** ** **
517 ATTTTTTGAAGATTCCATTATCGAGAAATCGCAGCATCTTG-TAAAAATAGTTTGCCA-TTTGTA
518 ATTTTTCGAACATTCCATGCCCG-GAAATCCCTTCAT-TTGATTTAAATAGTTTATCATTTTGT-
* * ** * * * *
580 AATAAATTTTT-GTCTTTGAATTAAAAACTTTTTTAAATTAGAATTCTTTCTCTCTTGTTTCCTG
580 -ATAAATTTTTAGTCTTTGAATTAAATACTTATTTATGTGAGAATTATTTCTCTCTTGGTTCTTG
644 G
644 G
* * * * * * * **
645 ACGAA-GTATCGAACTTGTTAAACATTTACTAGTTCTTTTACAACTTCGCTTCCTGAGAGTAGCC
1 ACGAACATAT-GAACTAGTCAAACTTTTACAAGTTCTTTTATAACTTCGATTCCTGAGAGTATTC
* * * * * * *
709 AAGATGATCCATTCCTTCGACCAATTTTTCT--AGCATTCAATGATC-AGGAAATCGTATCATTT
65 AAGACGATCCATTTCTTTGACCGATTTTT-TGAAG-ATTCCATGATCGA-GAAATCGCAGCATTT
* * * * * * *
771 GGTCTAAATCGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAGTAAAAAACTTTTTTACGTGG
127 GGT-AAAATAGTTTGCCA-TTTGTAAACAAATTTTGGTCTTTGAATTAAAAACTTTTTTACGTGA
* * ** * * * * *
836 GAATTGTTTCTCTATTTTTTCTTGGACGAACTTTCAAACACGTCAAACATTTGCGAGTTCTTTTA
190 GAATTCTTTCTCTCTTGGTTCTTGGACGAACTATCGAACATGTCAAACATTTACTAGTTCTTTTA
* * *** * *
901 TAACTTCGATTCTTGAGAGTATTAAAGACGATTCATTCC-TTCAGCCAATTTTTCGAACATTCCA
255 CAACTTCGATTCCTGAGAGTAGCCAAGACGATCCATTCCTTTGA-CCAATTTTTCGAACATTCCA
** * * * * *
965 TGCCCGGGAAATCGCT-TCGTTTGATTTAAATCGTTTATCATTTTGTATAAATTTTTAGTCTTTG
319 TGATCAGGAAATCG-TATCATTTGGTCTAAATAGTTTATCATTTTGTATAAATTTTTAGTCTTTG
* *
1029 AATTAAATACTTATTTACGAGAGAATTATTTCTCTCTTGGTTCTTGGACGAAATTCTGAACTGGT
383 AATTAAAAACTTATTTACGAGAGAATTATTTCTCTCTTGGTTCTTGGACGAAATTCTGAACTAGT
*
1094 TAAACATTTACGAGTTCTTTTATAACTTCGATTCCTGAGAGTATTAAAGACGATCCATTCCTTCA
448 CAAACATTTACGAGTTCTTTTATAACTTCGATTCCTGAGAGTATTAAAGACGATCCATTCCTTCA
* * *
1159 G-CCATTTTTTCGAACATTCTATGCCCGTGAAATCCCTTCGTTTGATTTAAATAGTTTATCATTT
513 GACCAATTTTTCGAACATTCCATGCCCG-GAAATCCCTTCATTTGATTTAAATAGTTTATCATTT
*
1223 TGTATAAATTTTTAGTCTTTGAATTAAATACTTATTTATGTGAGAATTATTTCCCTCTTGGTTCT
577 TGTATAAATTTTTAGTCTTTGAATTAAATACTTATTTATGTGAGAATTATTTCTCTCTTGGTTCT
1288 TGG
642 TGG
* *
1291 ACGAACATATGAACTAGTCAAACTTTTACAAGTTCTTTTATAACTTCGGTTCCTCAGAGTATTCA
1 ACGAACATATGAACTAGTCAAACTTTTACAAGTTCTTTTATAACTTCGATTCCTGAGAGTATTCA
* *
1356 AGACGATCCATTTCTTTGACCGATTTTTTGAAGATTCCATTATCGAGAAATCGCAGCATTTTGTA
66 AGACGATCCATTTCTTTGACCGATTTTTTGAAGATTCCATGATCGAGAAATCGCAGCATTTGGT-
* *
1421 AAAATAGTTTGCCATTTGTAAATAAATTTTGGTCTTTGAATTAAAAACTTTTTTACACT-AGAAT
130 AAAATAGTTTGCCATTTGTAAACAAATTTTGGTCTTTGAATTAAAAACTTTTTTAC-GTGAGAAT
* * *
1485 TCTTTCTCTCTTGGTTCCTT-GACGAAGTATCGAACTTGTTAAACATTTACTAGTTCTTTTACAA
194 TCTTTCTCTCTTGGTT-CTTGGACGAACTATCGAACATGTCAAACATTTACTAGTTCTTTTACAA
** * * *
1549 CTTCGATTCCTGAGAGTAGCCAAGGTGATCCATTCCTTCGACCAATTTTTCGAGCATTCAATGAT
258 CTTCGATTCCTGAGAGTAGCCAAGACGATCCATTCCTTTGACCAATTTTTCGAACATTCCATGAT
* * * * * * *
1614 CAGGAAATCGTATCATTTGGTCTAAATCGTTTGTCATTTTGTAAACAACTTTTGGTCTTTGAGTA
323 CAGGAAATCGTATCATTTGGTCTAAATAGTTTATCATTTTGTATA-AATTTTTAGTCTTTGAATT
* * * * * ** *
1679 AAAAACTTTTTTACGTGGGAATTGTTTCTCTATTTTTTCTTGGACGAACTT-TCGAAC-ACGTCA
387 AAAAACTTATTTACGAGAGAATTATTTCTCTCTTGGTTCTTGGACGAAATTCT-GAACTA-GTCA
* * * *
1742 AACATTTGCGAGTTCTTTTATAACTTCGATTCTTGAGAGTATTAAAGATGATTCATTCCTTCAG-
450 AACATTTACGAGTTCTTTTATAACTTCGATTCCTGAGAGTATTAAAGACGATCCATTCCTTCAGA
* * * *
1806 CCAATTTTTCGAACATTCCATGCCCGGGAAATCGCTTCGTTTGATTTAATTCGTTTATCATTTTG
515 CCAATTTTTCGAACATTCCATGCCC-GGAAATCCCTTCATTTGATTTAAATAGTTTATCATTTTG
* *
1871 TATAAATTTTTAGTCTTTGAATTAAATACTTATTTACGAGAGAATTATTTCTCTCTTGGTTCTTG
579 TATAAATTTTTAGTCTTTGAATTAAATACTTATTTATGTGAGAATTATTTCTCTCTTGGTTCTTG
1936 G
644 G
* * * * * *
1937 ACGAA-ATTCTGAACTGGTTAAACATTTACGAGTTCTTTTATAACTTCGATTCCTGAGAGTATTA
1 ACGAACA-TATGAACTAGTCAAACTTTTACAAGTTCTTTTATAACTTCGATTCCTGAGAGTATTC
* * * ** * ** *
2001 AAGACGATCCA-TTCCTTCAGCC-ATTTTTTCGAACATTCCATGCCCGGGAAATCGCTTCGTTTG
65 AAGACGATCCATTTCTTTGA-CCGATTTTTT-GAAGATTCCATGATCGAGAAATCGCAGCATTTG
* * ** * * * * *
2064 ATTTAAATAGTTTATCATTTTGTATACAATTTTTAGTCTTTGAATTAAATACTTATTTACGTGAG
128 -GTAAAATAGTTTGCCA-TTTGTAAACAAATTTTGGTCTTTGAATTAAAAACTTTTTTACGTGAG
* * * * *
2129 AATTATTTCCCTCTTGGATCTTGGACGAACATAT-GAAC-TAGACAAAC-TCTTACAAGTTCTTT
191 AATTCTTTCTCTCTTGGTTCTTGGACGAAC-TATCGAACAT-GTCAAACAT-TTACTAGTTCTTT
* * * ** * * * * *
2191 TATAACTTCGGTTCCTTAGAGTATTCAAGACTATCCATTTCTTTGACCAATTTTTTGAAGAGTCC
253 TACAACTTCGATTCCTGAGAGTAGCCAAGACGATCCATTCCTTTGACCAATTTTTCGAACATTCC
* * * ** ** * *
2256 ATTATC-GAGAAATCGCAGCATTTGGTAAAAATAGTTTGCCAATTTGTAAATAAA-TTTTGGTCT
318 ATGATCAG-GAAATCGTATCATTTGGTCTAAATAGTTTATCATTTTGT--ATAAATTTTTAGTCT
* * * *
2319 TTGAATTAAAAACTTTTTTAC-ATTAGAATTCTTTCTCTCTTGGTTCTTGGACGAAGTATC-GAA
380 TTGAATTAAAAACTTATTTACGA-GAGAATTATTTCTCTCTTGGTTCTTGGACGAAAT-TCTGAA
* * * *** *
2382 CTTGTCAAACATTTACTAGTTCTTTTACAACTTCGATTCCTGAGAGTAGCCAAGATGATCCATTC
443 CTAGTCAAACATTTACGAGTTCTTTTATAACTTCGATTCCTGAGAGTATTAAAGACGATCCATTC
* *** * * * *
2447 CTTC-GACCAATTTTTCGAGCATTCCATGATTAGGAAAT-CGTATCATTTGGTCTAAATCGTTTG
508 CTTCAGACCAATTTTTCGAACATTCCATG-CCCGGAAATCCCT-TCATTTGATTTAAATAGTTT-
* * ** * * *
2510 A-CATTTTGTAAACAACTTTCGGTCTTTGAATT-AATAACTTTTTTATGTGGGAATTGTTTCTCT
570 ATCATTTTGTATA-AATTTTTAGTCTTTGAATTAAAT-ACTTATTTATGTGAGAATTATTTCTCT
* *
2573 ATTTGTTCTTGG
633 CTTGGTTCTTGG
* * * * *
2585 ACGAAC-TTTCTAAC-ACGTCAAACATTTT-CGATTTCTTTTATAACTTCGATTCGTGAGAGTAT
1 ACGAACATAT-GAACTA-GTCAAAC-TTTTACAAGTTCTTTTATAACTTCGATTCCTGAGAGTAT
* *
2647 TAAAGACGATTCATT
63 TCAAGACGATCCATT
2662 CCTTCAG
Statistics
Matches: 1669, Mismatches: 293, Indels: 105
0.81 0.14 0.05
Matches are distributed among these distances:
643 7 0.00
644 98 0.06
645 220 0.13
646 864 0.52
647 361 0.22
648 113 0.07
649 6 0.00
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (644 bp):
ACGAACATATGAACTAGTCAAACTTTTACAAGTTCTTTTATAACTTCGATTCCTGAGAGTATTCA
AGACGATCCATTTCTTTGACCGATTTTTTGAAGATTCCATGATCGAGAAATCGCAGCATTTGGTA
AAATAGTTTGCCATTTGTAAACAAATTTTGGTCTTTGAATTAAAAACTTTTTTACGTGAGAATTC
TTTCTCTCTTGGTTCTTGGACGAACTATCGAACATGTCAAACATTTACTAGTTCTTTTACAACTT
CGATTCCTGAGAGTAGCCAAGACGATCCATTCCTTTGACCAATTTTTCGAACATTCCATGATCAG
GAAATCGTATCATTTGGTCTAAATAGTTTATCATTTTGTATAAATTTTTAGTCTTTGAATTAAAA
ACTTATTTACGAGAGAATTATTTCTCTCTTGGTTCTTGGACGAAATTCTGAACTAGTCAAACATT
TACGAGTTCTTTTATAACTTCGATTCCTGAGAGTATTAAAGACGATCCATTCCTTCAGACCAATT
TTTCGAACATTCCATGCCCGGAAATCCCTTCATTTGATTTAAATAGTTTATCATTTTGTATAAAT
TTTTAGTCTTTGAATTAAATACTTATTTATGTGAGAATTATTTCTCTCTTGGTTCTTGG
Found at i:1822 original size:861 final size:860
Alignment explanation
Indices: 151--2668 Score: 4321
Period size: 861 Copynumber: 2.9 Consensus size: 860
141 CCATTTGTAA
* * * * *
151 ATAAA-TTTTGGTCTTTGAATTAAAAACTTTTTTAC-ATTAGAATTCTTTCTCTCTTGGTTCTTG
1 ATAAATTTTTAGTCTTTGAATTAAATACTTATTTACGA-GAGAATTATTTCTCTCTTGGTTCTTG
* * * * * **
214 GACGAAGTT-TCGAACTTGTCAAACATTTACTAGTTCTTTTACAACTTCGATTCCTGAGAGTAGC
65 GACGAAATTCT-GAACTGGTTAAACATTTACGAGTTCTTTTATAACTTCGATTCCTGAGAGTATT
* * * * * * * * *
278 CAAGATGATCCATTCCTT-TGACCAATTTTTCGAGCATTCCATGATCAGGAAAT-CGTATCATTT
129 AAAGACGATCCATTCCTTCAG-CCATTTTTTCGAACATTCCATG-CCCGGAAATCCCT-TCGTTT
* *
341 GGTCTAAATAG-TTAGTCATTTTGTATAAATTTTTAGTCTTTGAATTAAATACTTATTTATGTGA
191 GATTTAAATAGTTTA-TCATTTTGTATAAATTTTTAGTCTTTGAATTAAATACTTATTTATGTGA
*
405 GAATTATTTCCCTCTTGGTTCTTGGACGAACATATGAACTAGTCAAACTTTTACAAGTTTTTTTA
255 GAATTATTTCCCTCTTGGTTCTTGGACGAACATATGAACTAGTCAAACTTTTACAAGTTCTTTTA
* *
470 TAACTTCGGTTTCTCAGAGTATTCAAGACGATCCATTTCTTTGACCTATTTTTTGAAGATTCCAT
320 TAACTTCGGTTCCTCAGAGTATTCAAGACGATCCATTTCTTTGACCAATTTTTTGAAGATTCCAT
* *
535 TATCGAGAAATCGCAGCATCTTGTAAAAATAGTTTGCCATTTGTAAATAAATTTTTGTCTTTGAA
385 TATCGAGAAATCGCAGCATTTTGTAAAAATAGTTTGCCATTTGTAAATAAATTTTGGTCTTTGAA
* * *
600 TTAAAAACTTTTTTAAATTAGAATTCTTTCTCTCTTGTTTCCTGGACGAAGTATCGAACTTGTTA
450 TTAAAAACTTTTTTACATTAGAATTCTTTCTCTCTTGGTTCCTTGACGAAGTATCGAACTTGTTA
*
665 AACATTTACTAGTTCTTTTACAACTTCGCTTCCTGAGAGTAGCCAAGATGATCCATTCCTTCGAC
515 AACATTTACTAGTTCTTTTACAACTTCGATTCCTGAGAGTAGCCAAGATGATCCATTCCTTCGAC
*
730 CAATTTTTCTAGCATTCAATGATCAGGAAATCGTATCATTTGGTCTAAATCGTTTGTCATTTTGT
580 CAATTTTTCGAGCATTCAATGATCAGGAAATCGTATCATTTGGTCTAAATCGTTTGTCATTTTGT
795 AAACAACTTTTGGTCTTTGAGTAAAAAACTTTTTTACGTGGGAATTGTTTCTCTATTTTTTCTTG
645 AAACAACTTTTGGTCTTTGAGTAAAAAACTTTTTTACGTGGGAATTGTTTCTCTATTTTTTCTTG
860 GACGAACTTTCAAACACGTCAAACATTTGCGAGTTCTTTTATAACTTCGATTCTTGAGAGTATTA
710 GACGAACTTTCAAACACGTCAAACATTTGCGAGTTCTTTTATAACTTCGATTCTTGAGAGTATTA
925 AAGACGATTCATTCCTTCAGCCAATTTTTCGAACATTCCATGCCCGGGAAATCGCTTCGTTTGAT
775 AAGACGATTCATTCCTTCAGCCAATTTTTCGAACATTCCATGCCCGGGAAATCGCTTCGTTTGAT
990 TTAAATCGTTTATCATTTTGT
840 TTAAATCGTTTATCATTTTGT
1011 ATAAATTTTTAGTCTTTGAATTAAATACTTATTTACGAGAGAATTATTTCTCTCTTGGTTCTTGG
1 ATAAATTTTTAGTCTTTGAATTAAATACTTATTTACGAGAGAATTATTTCTCTCTTGGTTCTTGG
1076 ACGAAATTCTGAACTGGTTAAACATTTACGAGTTCTTTTATAACTTCGATTCCTGAGAGTATTAA
66 ACGAAATTCTGAACTGGTTAAACATTTACGAGTTCTTTTATAACTTCGATTCCTGAGAGTATTAA
*
1141 AGACGATCCATTCCTTCAGCCATTTTTTCGAACATTCTATGCCCGTGAAATCCCTTCGTTTGATT
131 AGACGATCCATTCCTTCAGCCATTTTTTCGAACATTCCATGCCCG-GAAATCCCTTCGTTTGATT
1206 TAAATAGTTTATCATTTTGTATAAATTTTTAGTCTTTGAATTAAATACTTATTTATGTGAGAATT
195 TAAATAGTTTATCATTTTGTATAAATTTTTAGTCTTTGAATTAAATACTTATTTATGTGAGAATT
1271 ATTTCCCTCTTGGTTCTTGGACGAACATATGAACTAGTCAAACTTTTACAAGTTCTTTTATAACT
260 ATTTCCCTCTTGGTTCTTGGACGAACATATGAACTAGTCAAACTTTTACAAGTTCTTTTATAACT
*
1336 TCGGTTCCTCAGAGTATTCAAGACGATCCATTTCTTTGACCGATTTTTTGAAGATTCCATTATCG
325 TCGGTTCCTCAGAGTATTCAAGACGATCCATTTCTTTGACCAATTTTTTGAAGATTCCATTATCG
1401 AGAAATCGCAGCATTTTGTAAAAATAGTTTGCCATTTGTAAATAAATTTTGGTCTTTGAATTAAA
390 AGAAATCGCAGCATTTTGTAAAAATAGTTTGCCATTTGTAAATAAATTTTGGTCTTTGAATTAAA
*
1466 AACTTTTTTACACTAGAATTCTTTCTCTCTTGGTTCCTTGACGAAGTATCGAACTTGTTAAACAT
455 AACTTTTTTACATTAGAATTCTTTCTCTCTTGGTTCCTTGACGAAGTATCGAACTTGTTAAACAT
*
1531 TTACTAGTTCTTTTACAACTTCGATTCCTGAGAGTAGCCAAGGTGATCCATTCCTTCGACCAATT
520 TTACTAGTTCTTTTACAACTTCGATTCCTGAGAGTAGCCAAGATGATCCATTCCTTCGACCAATT
1596 TTTCGAGCATTCAATGATCAGGAAATCGTATCATTTGGTCTAAATCGTTTGTCATTTTGTAAACA
585 TTTCGAGCATTCAATGATCAGGAAATCGTATCATTTGGTCTAAATCGTTTGTCATTTTGTAAACA
1661 ACTTTTGGTCTTTGAGTAAAAAACTTTTTTACGTGGGAATTGTTTCTCTATTTTTTCTTGGACGA
650 ACTTTTGGTCTTTGAGTAAAAAACTTTTTTACGTGGGAATTGTTTCTCTATTTTTTCTTGGACGA
* *
1726 ACTTTCGAACACGTCAAACATTTGCGAGTTCTTTTATAACTTCGATTCTTGAGAGTATTAAAGAT
715 ACTTTCAAACACGTCAAACATTTGCGAGTTCTTTTATAACTTCGATTCTTGAGAGTATTAAAGAC
*
1791 GATTCATTCCTTCAGCCAATTTTTCGAACATTCCATGCCCGGGAAATCGCTTCGTTTGATTTAAT
780 GATTCATTCCTTCAGCCAATTTTTCGAACATTCCATGCCCGGGAAATCGCTTCGTTTGATTTAAA
1856 TCGTTTATCATTTTGT
845 TCGTTTATCATTTTGT
1872 ATAAATTTTTAGTCTTTGAATTAAATACTTATTTACGAGAGAATTATTTCTCTCTTGGTTCTTGG
1 ATAAATTTTTAGTCTTTGAATTAAATACTTATTTACGAGAGAATTATTTCTCTCTTGGTTCTTGG
1937 ACGAAATTCTGAACTGGTTAAACATTTACGAGTTCTTTTATAACTTCGATTCCTGAGAGTATTAA
66 ACGAAATTCTGAACTGGTTAAACATTTACGAGTTCTTTTATAACTTCGATTCCTGAGAGTATTAA
*
2002 AGACGATCCATTCCTTCAGCCATTTTTTCGAACATTCCATGCCCGGGAAATCGCTTCGTTTGATT
131 AGACGATCCATTCCTTCAGCCATTTTTTCGAACATTCCATGCCC-GGAAATCCCTTCGTTTGATT
*
2067 TAAATAGTTTATCATTTTGTATACAATTTTTAGTCTTTGAATTAAATACTTATTTACGTGAGAAT
195 TAAATAGTTTATCATTTTGTATA-AATTTTTAGTCTTTGAATTAAATACTTATTTATGTGAGAAT
* * *
2132 TATTTCCCTCTTGGATCTTGGACGAACATATGAACTAGACAAACTCTTACAAGTTCTTTTATAAC
259 TATTTCCCTCTTGGTTCTTGGACGAACATATGAACTAGTCAAACTTTTACAAGTTCTTTTATAAC
* * *
2197 TTCGGTTCCTTAGAGTATTCAAGACTATCCATTTCTTTGACCAATTTTTTGAAGAGTCCATTATC
324 TTCGGTTCCTCAGAGTATTCAAGACGATCCATTTCTTTGACCAATTTTTTGAAGATTCCATTATC
*
2262 GAGAAATCGCAGCATTTGGTAAAAATAGTTTGCCAATTTGTAAATAAATTTTGGTCTTTGAATTA
389 GAGAAATCGCAGCATTTTGTAAAAATAGTTTGCC-ATTTGTAAATAAATTTTGGTCTTTGAATTA
*
2327 AAAACTTTTTTACATTAGAATTCTTTCTCTCTTGGTT-CTTGGACGAAGTATCGAACTTGTCAAA
453 AAAACTTTTTTACATTAGAATTCTTTCTCTCTTGGTTCCTT-GACGAAGTATCGAACTTGTTAAA
2391 CATTTACTAGTTCTTTTACAACTTCGATTCCTGAGAGTAGCCAAGATGATCCATTCCTTCGACCA
517 CATTTACTAGTTCTTTTACAACTTCGATTCCTGAGAGTAGCCAAGATGATCCATTCCTTCGACCA
* * *
2456 ATTTTTCGAGCATTCCATGATTAGGAAATCGTATCATTTGGTCTAAATCGTTTGACATTTTGTAA
582 ATTTTTCGAGCATTCAATGATCAGGAAATCGTATCATTTGGTCTAAATCGTTTGTCATTTTGTAA
* * * * * *
2521 ACAACTTTCGGTCTTTGAATTAATAACTTTTTTATGTGGGAATTGTTTCTCTATTTGTTCTTGGA
647 ACAACTTTTGGTCTTTGAGTAAAAAACTTTTTTACGTGGGAATTGTTTCTCTATTTTTTCTTGGA
* * * *
2586 CGAACTTTCTAACACGTCAAACATTTTCGATTTCTTTTATAACTTCGATTCGTGAGAGTATTAAA
712 CGAACTTTCAAACACGTCAAACATTTGCGAGTTCTTTTATAACTTCGATTCTTGAGAGTATTAAA
2651 GACGATTCATTCCTTCAG
777 GACGATTCATTCCTTCAG
Statistics
Matches: 1580, Mismatches: 67, Indels: 19
0.95 0.04 0.01
Matches are distributed among these distances:
860 7 0.00
861 1014 0.64
862 208 0.13
863 351 0.22
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.41
Consensus pattern (860 bp):
ATAAATTTTTAGTCTTTGAATTAAATACTTATTTACGAGAGAATTATTTCTCTCTTGGTTCTTGG
ACGAAATTCTGAACTGGTTAAACATTTACGAGTTCTTTTATAACTTCGATTCCTGAGAGTATTAA
AGACGATCCATTCCTTCAGCCATTTTTTCGAACATTCCATGCCCGGAAATCCCTTCGTTTGATTT
AAATAGTTTATCATTTTGTATAAATTTTTAGTCTTTGAATTAAATACTTATTTATGTGAGAATTA
TTTCCCTCTTGGTTCTTGGACGAACATATGAACTAGTCAAACTTTTACAAGTTCTTTTATAACTT
CGGTTCCTCAGAGTATTCAAGACGATCCATTTCTTTGACCAATTTTTTGAAGATTCCATTATCGA
GAAATCGCAGCATTTTGTAAAAATAGTTTGCCATTTGTAAATAAATTTTGGTCTTTGAATTAAAA
ACTTTTTTACATTAGAATTCTTTCTCTCTTGGTTCCTTGACGAAGTATCGAACTTGTTAAACATT
TACTAGTTCTTTTACAACTTCGATTCCTGAGAGTAGCCAAGATGATCCATTCCTTCGACCAATTT
TTCGAGCATTCAATGATCAGGAAATCGTATCATTTGGTCTAAATCGTTTGTCATTTTGTAAACAA
CTTTTGGTCTTTGAGTAAAAAACTTTTTTACGTGGGAATTGTTTCTCTATTTTTTCTTGGACGAA
CTTTCAAACACGTCAAACATTTGCGAGTTCTTTTATAACTTCGATTCTTGAGAGTATTAAAGACG
ATTCATTCCTTCAGCCAATTTTTCGAACATTCCATGCCCGGGAAATCGCTTCGTTTGATTTAAAT
CGTTTATCATTTTGT
Done.