Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007006.1 Hibiscus syriacus cultivar Beakdansim tig00018083_pilon, 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: 30501
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:1178 original size:179 final size:179
Alignment explanation
Indices: 615--1251 Score: 1082
Period size: 180 Copynumber: 3.6 Consensus size: 179
605 TTTTAAATGG
*
615 TATGGACATAAAGTACCGACACAATATTAAAAGTGTCGATA-AGGTTGTAGACCTATTCGCTCAT
1 TATGGACATAAAGTACCGACACAATATTAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCAT
679 -AACCGGTATATTTATACCGTTATATT--AAAATTATCTATTACATTAT-ATTATGGGTTCCGAT
66 AAACCGGTATATTTATACCGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGAT
*
740 GTGTAAATTTCGACACTTTTTTAAATCGTATCG-ACATTTTTCTTCCAA
131 GTGTAAATGTCGACACTTTTTTAAATCGTATCGCACATTTTTCTTCCAA
788 TAT-G--ATAAAGTACCGACACAATATTAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCAT
1 TATGGACATAAAGTACCGACACAATATTAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCAT
*
850 AGACCGGTATATTTATACCGGTTATATTAC-AAATTATCTATTACATTATAATTATGGGTTCCGA
66 AAACCGGTATATTTATACC-GTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGA
*
914 TGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
130 TGTGT-AAATGTCGACACTTTTTTAAATCGTATCG-CACATTTTTCTTCCAA
* * *
966 TATGGACATAAAGTACCGACACAATA-AAAAAGTGTCGATATAGGTTGTAGACCTATTGGCTCAT
1 TATGGACATAAAGTACCGACACAATATTAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCAT
1030 AAACC-GTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGA
66 AAACCGGTATATTTATACC-GTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGA
1094 TGTGTAAATGTCGACACTTTTTTAAATCGTATCGCACATTTTTCTTCCAA
130 TGTGTAAATGTCGACACTTTTTTAAATCGTATCGCACATTTTTCTTCCAA
1144 TATGGACATAAAGTACCGACACAATATTAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCAT
1 TATGGACATAAAGTACCGACACAATATTAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCAT
1209 AAGACCGGTATATTTATACCGTTATATTACAAAATTATCTATT
66 AA-ACCGGTATATTTATACCGTTATATTACAAAATTATCTATT
1252 TTATATAATA
Statistics
Matches: 436, Mismatches: 12, Indels: 25
0.92 0.03 0.05
Matches are distributed among these distances:
170 34 0.08
171 22 0.05
172 18 0.04
173 11 0.03
174 19 0.04
175 19 0.04
176 27 0.06
178 60 0.14
179 90 0.21
180 104 0.24
181 32 0.07
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (179 bp):
TATGGACATAAAGTACCGACACAATATTAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCAT
AAACCGGTATATTTATACCGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGAT
GTGTAAATGTCGACACTTTTTTAAATCGTATCGCACATTTTTCTTCCAA
Found at i:2719 original size:3 final size:3
Alignment explanation
Indices: 2711--2797 Score: 84
Period size: 3 Copynumber: 29.0 Consensus size: 3
2701 ACTTGTTTGG
* * * **
2711 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * * * *
2759 AGC TTC ATC GTC ATC ATC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
2798 GTCAGCTTCA
Statistics
Matches: 65, Mismatches: 19, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.24, C:0.34, G:0.06, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:2734 original size:18 final size:18
Alignment explanation
Indices: 2711--2812 Score: 87
Period size: 18 Copynumber: 5.7 Consensus size: 18
2701 ACTTGTTTGG
2711 ATCATCATCTTCATCATC
1 ATCATCATCTTCATCATC
* *
2729 ATCATCATCATCGTCATC
1 ATCATCATCTTCATCATC
* ** * *
2747 ATCTTCATCGCCAGCTTC
1 ATCATCATCTTCATCATC
* *
2765 ATCGTCATCATCATCATC
1 ATCATCATCTTCATCATC
* *
2783 ATCGTCATCTTCATCGTC
1 ATCATCATCTTCATCATC
* *
2801 AGCTTCATCTTC
1 ATCATCATCTTC
2813 TGCGACCGAT
Statistics
Matches: 67, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 67 1.00
ACGTcount: A:0.23, C:0.34, G:0.07, T:0.36
Consensus pattern (18 bp):
ATCATCATCTTCATCATC
Found at i:2778 original size:42 final size:42
Alignment explanation
Indices: 2719--2809 Score: 146
Period size: 42 Copynumber: 2.2 Consensus size: 42
2709 GGATCATCAT
*
2719 CTTCATCATCATCATCATCATCGTCATCATCTTCATCGCCAG
1 CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
* * *
2761 CTTCATCGTCATCATCATCATCATCGTCATCTTCATCGTCAG
1 CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
2803 CTTCATC
1 CTTCATC
2810 TTCTGCGACC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.22, C:0.35, G:0.08, T:0.35
Consensus pattern (42 bp):
CTTCATCATCATCATCATCATCATCATCATCTTCATCGCCAG
Found at i:4848 original size:196 final size:197
Alignment explanation
Indices: 4374--5617 Score: 2095
Period size: 195 Copynumber: 6.4 Consensus size: 197
4364 GATGATTTTG
*
4374 GGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGG-AAAAAATATC-AAACAAACT
1 GGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGAAAAAAATATCGACACAAACT
*
4437 ATATTAGTGTCGACACATTATTTAGACATA-T-TCTCATAAAACCGGTATTATTGTACC-GTTAG
66 ATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTTAG
*
4499 ATTGAAAAATTACATA-TACATTATACTTTTGGGTTCGATGATTTTGGGATCGACAC-GTTT-TA
131 ATTG-AAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATA
4561 TAT
195 TAT
*
4564 GGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAAAAAATATCGACACAAAC
1 GGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCT-GGAAAAAAATATCGACACAAAC
4629 TATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTTA
65 TATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTTA
4694 GATTGAAAATTACAT-TTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATA
130 GATTGAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATA
4758 TAT
195 TAT
* * *
4761 GGATCGACACGTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAAAAATATCGACACAAACT
1 GGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGAAAAAAATATCGACACAAACT
4826 ATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAT-ATTGTACCGGTTAG
66 ATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTTAG
4890 ATTGAAAATTACATATTACATTATAC-TTTGGGTTCGATGATTTTGGGATCGACACTTTTTATAT
131 ATTGAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATAT
4954 AT
196 AT
4956 GGATCGACACTTTATTGGTGCACC-TGTTTTTAATTCATTCTGGAAAAAAAATATCGACACAAAC
1 GGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGG-AAAAAAATATCGACACAAAC
*
5020 TATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATAATTGTACC-GTTA
65 TATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTTA
* *
5084 GATTAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTTTA
130 GATTGAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATA
5149 TAT
195 TAT
* *
5152 GGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGTAAAAAAAATATCGACACAAAC
1 GGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTG-GAAAAAAATATCGACACAAAC
*
5217 --TATTAGTGTCGACACATTATTTAGACTTATTCTCTCAT-AAACCGGTATAATTGTA-CGGTTA
65 TATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTTA
*
5278 GATTGAAAAATTACAGATTACA-T-TACTTTTGGGTTCGATGATTTTGGGATCGACAC-TTTT-T
130 GATTG-AAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTAT
5339 ATA-
194 ATAT
*
5342 GGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAAAAAATATCGACACAAAC
1 GGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGG-AAAAAAATATCGACACAAAC
*
5407 TATATTAGTGTCGACACATTATTTAGACTTATTCTCTCAT-AAACCGGTATAATTGTACCGGTTA
65 TATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTTA
*
5471 GATTAAAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTTGGGATCGACACTTTTTATA
130 GATTGAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATA
5535 TAT
195 TAT
*
5538 GGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAAAAATATCGACACAAACT
1 GGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGAAAAAAATATCGACACAAACT
*
5603 ATATTAGTATCGACA
66 ATATTAGTGTCGACA
5618 TGACCCTTAA
Statistics
Matches: 1006, Mismatches: 22, Indels: 47
0.94 0.02 0.04
Matches are distributed among these distances:
190 102 0.10
191 6 0.01
192 84 0.08
193 97 0.10
194 68 0.07
195 356 0.35
196 209 0.21
197 84 0.08
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (197 bp):
GGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGAAAAAAATATCGACACAAACT
ATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTTAG
ATTGAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATAT
AT
Found at i:4995 original size:391 final size:393
Alignment explanation
Indices: 4248--5617 Score: 2237
Period size: 391 Copynumber: 3.6 Consensus size: 393
4238 TTTAAATTAG
*
4248 TATCGACACAAAATATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
4313 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATT-AAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
4378 CGACAC--------T-T---T----A---T-T-GGTGCACCTTGTTTTTAATTCATTCTGG-AAA
130 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAA
*
4421 AAATATC-AAACAAACTATATTAGTGTCGACACATTATTTAGACATA-T-TCTCATAAAACCGGT
195 AAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGT
4483 ATTATTGTACC-GTTAGATTGAAAAATTACATA-TACATTATACTTTTGGGTTCGATGATTTTGG
260 A-TATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
* * *
4546 GATCGACACGTTTTATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAA
324 GATCGACACTTTTTATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGAAA
4611 AAAAA
389 AAAAA
4616 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
4681 ATTGTACCGGTTAGATTGAAAATTACAT-TTACATTATACTTTTGGGTTCGATGATTTTGGGATC
66 ATTGTACCGGTTAGATTAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
* *
4745 GACACTTTTTATATATGGATCGACACGTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAAA
131 GACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAAA
4810 AATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
196 AATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
4875 TATTGTACCGGTTAGATTG-AAAATTACATATTACATTATAC-TTTGGGTTCGATGATTTTGGGA
261 TATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
4938 TCGACACTTTTTATATATGGATCGACACTTTATTGGTGCACC-TGTTTTTAATTCATTCTGGAAA
326 TCGACAC-TTTT-TATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGAAA
5002 AAAAA
389 AAAAA
*
5007 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
5072 ATTGTACC-GTTAGATTAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
66 ATTGTACCGGTTAGATTAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
* *
5136 GACACTTTTTTTATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGTAAAAA
131 GACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTG-GAAAA
*
5201 AAATATCGACACAAAC--TATTAGTGTCGACACATTATTTAGACTTATTCTCTCAT-AAACCGGT
195 AAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGT
*
5263 ATAATTGTA-CGGTTAGATTGAAAAATTACAGATTACA-T-TACTTTTGGGTTCGATGATTTTGG
260 AT-ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
*
5325 GATCGACACTTTTTATA-GGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAA
324 GATCGACACTTTTTATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGAAA
5389 AAAAA
389 AAAAA
*
5394 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCAT-AAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
5458 ATTGTACCGGTTAGATTAAAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTTGGGATC
66 ATTGTACCGGTTAGATTAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
* *
5522 GACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTTTTTAATTCATTCTGGAAAAA
131 GACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAAA
*
5587 AATATCGACACAAACTATATTAGTATCGACA
196 AATATCGACACAAACTATATTAGTGTCGACA
5618 TGACCCTTAA
Statistics
Matches: 944, Mismatches: 20, Indels: 57
0.92 0.02 0.06
Matches are distributed among these distances:
366 41 0.04
367 10 0.01
368 81 0.09
374 1 0.00
375 1 0.00
378 1 0.00
382 1 0.00
385 21 0.02
386 108 0.11
387 171 0.18
388 17 0.02
389 89 0.09
390 126 0.13
391 229 0.24
392 47 0.05
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (393 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
GACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGAAAAA
AATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTA
TATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGA
TCGACACTTTTTATATGGATCGACACTTTATTGGTGCACCTTGTTTTTAATTCATTCTGGAAAAA
AAA
Found at i:5719 original size:18 final size:19
Alignment explanation
Indices: 5698--5738 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
5688 ATTCACATAA
5698 AAAAATAT-AATCGTATAC
1 AAAAATATAAATCGTATAC
* *
5716 AAAATTATAAATCTTATAC
1 AAAAATATAAATCGTATAC
5735 AAAA
1 AAAA
5739 TTAACTCGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.59, C:0.10, G:0.02, T:0.29
Consensus pattern (19 bp):
AAAAATATAAATCGTATAC
Found at i:9889 original size:20 final size:19
Alignment explanation
Indices: 9843--9889 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
9833 TCCGGTATCA
*
9843 TTTTACCGTTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
9862 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
9883 TTTTACC
1 TTTTACC
9890 TGTTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.19, C:0.17, G:0.09, T:0.55
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:10036 original size:20 final size:20
Alignment explanation
Indices: 10010--10055 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
10000 CACTTTTAAA
10010 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
10029 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
10050 TTTACC
1 TTTACC
10056 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:10537 original size:228 final size:227
Alignment explanation
Indices: 10121--10568 Score: 776
Period size: 228 Copynumber: 2.0 Consensus size: 227
10111 TTAAAACTGC
10121 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
1 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
* *
10186 TTAATTTAATAATTTAATTTACACAAAATTTTATTGATTGTTTTGATATTTTATAAAATATTATT
66 TTAATTTAATAATTTAATTTACACAAAAATTAATTGATTGTTTTGATATTTTATAAAATATTATT
* *
10251 TAGCATTTAAATTTAACAATATTAACCAAATATAATAATAAATATGTTTTCAACAGTGAAATAAG
131 TAGCATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCAACAGTGAAATAAG
*
10316 TATGGACACTTTTATAAAAATGATATATACTT
196 TATGGACACTTTTATAAAAAGGATATATACTT
10348 TTTTGAAAGTTATGTAATTTATGTTTCAAATTT-TTTAATAGTGTTTCATGTTTTCCACCTACAA
1 TTTT-AAAGTTATGTAATTTATGTTTC-AATTTATTTAATAGTGTTTCATGTTTTCCACCTACAA
*
10412 TATTAATTTAATAATTTCATTTACACAAAAAATTAATTGATTGTTTTGATATTTTATAAAATATT
64 TATTAATTTAATAATTTAATTTACAC-AAAAATTAATTGATTGTTTTGATATTTTATAAAATATT
*
10477 ATTTAG-ATTTTAAATTTAACAATATTAACTAAAGATAATAATAAATATATTTTC-ACAGTGAAA
128 ATTTAGCA-TTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCAACAGTGAAA
10540 TAAGTATGGACACTTTTATAAAAAGGATA
192 TAAGTATGGACACTTTTATAAAAAGGATA
10569 GATAATTTAC
Statistics
Matches: 210, Mismatches: 7, Indels: 7
0.94 0.03 0.03
Matches are distributed among these distances:
227 4 0.02
228 116 0.55
229 90 0.43
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.45
Consensus pattern (227 bp):
TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
TTAATTTAATAATTTAATTTACACAAAAATTAATTGATTGTTTTGATATTTTATAAAATATTATT
TAGCATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCAACAGTGAAATAAG
TATGGACACTTTTATAAAAAGGATATATACTT
Found at i:17539 original size:3 final size:3
Alignment explanation
Indices: 17531--17590 Score: 77
Period size: 3 Copynumber: 19.7 Consensus size: 3
17521 TATTTTATTT
* *
17531 ATA ATA AT- ATA ATA GTA ATA ATA ATA TTA ATA ATA ATA ATA ACTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA
17576 ATA ATA ATAA ATA AT
1 ATA ATA AT-A ATA AT
17591 TAAGACCCAG
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
2 2 0.04
3 42 0.84
4 6 0.12
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:18541 original size:21 final size:22
Alignment explanation
Indices: 18517--18567 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
18507 TGTCATTTGT
*
18517 ATAATTTACCTTT-TATTTTAA
1 ATAATTTACCTTTAAATTTTAA
* *
18538 ATAATTAACCTTTAAATTTTCA
1 ATAATTTACCTTTAAATTTTAA
18560 ATAATTTA
1 ATAATTTA
18568 TAATTATATG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 12 0.48
22 13 0.52
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.51
Consensus pattern (22 bp):
ATAATTTACCTTTAAATTTTAA
Found at i:18562 original size:22 final size:21
Alignment explanation
Indices: 18517--18565 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
18507 TGTCATTTGT
* *
18517 ATAATTTACCTTTTATTTTAA
1 ATAATTAACCTTTAATTTTAA
*
18538 ATAATTAACCTTTAAATTTTCA
1 ATAATTAACCTTT-AATTTTAA
18560 ATAATT
1 ATAATT
18566 TATAATTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.51
Consensus pattern (21 bp):
ATAATTAACCTTTAATTTTAA
Found at i:19182 original size:33 final size:33
Alignment explanation
Indices: 19117--19186 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
19107 CCTTTACAAC
* * *
19117 TCCCTAGTTTTTCACGGGCTAAACTAGAACCTT
1 TCCCTAGCTTTTCACGAGATAAACTAGAACCTT
* * *
19150 TCCCTAGCTTTTCACGAGATCAGCTAGTACCTT
1 TCCCTAGCTTTTCACGAGATAAACTAGAACCTT
19183 TCCC
1 TCCC
19187 CTTTACAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.21, C:0.31, G:0.14, T:0.33
Consensus pattern (33 bp):
TCCCTAGCTTTTCACGAGATAAACTAGAACCTT
Found at i:19922 original size:19 final size:20
Alignment explanation
Indices: 19877--19934 Score: 93
Period size: 19 Copynumber: 3.0 Consensus size: 20
19867 ATGTTTAATG
19877 AAAAA-GATACCAATTGTTT
1 AAAAAGGATACCAATTGTTT
19896 ACAAAAGGATACCAATTGTTT
1 A-AAAAGGATACCAATTGTTT
19917 -AAAAGGATACCAATTGTT
1 AAAAAGGATACCAATTGTT
19935 GGAAATATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
19 19 0.51
20 4 0.11
21 14 0.38
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (20 bp):
AAAAAGGATACCAATTGTTT
Done.