Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012652.1 Kokia drynarioides strain JFW-HI SEQ_127663, 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: 13388
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Warning! 100 characters in sequence are not A, C, G, or T
Found at i:407 original size:216 final size:216
Alignment explanation
Indices: 2--1766 Score: 1952
Period size: 216 Copynumber: 8.2 Consensus size: 216
1 A
** * * * *
2 AACTTGACATCCTTTTATGAGTTCTTCTATAACTTCGATTTCTTAGAGTATTCAAGACAATCCAT
1 AACTTGACAAACTTTTACGAGTTCTTCTATAACTTCGATTCCTTAAAGTATTCATGACAATCCAT
* ** ** * * *
67 TCCTTAGAGCAATTTTTTTAACATTCCATGCTCGGGAAATCATATAATTTGGTCTAAATACTTTG
66 TCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTTGTCTAAATAGTTTG
* * * * *
132 TCATTTTCTAAACAACTTTTGGTCTTTCAATCAAAAACTTATTTACGTGAGAGTTGTTTCTCTGT
131 TCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCT
197 TGGTTCTTGGACGAACTTCTG
196 TGGTTCTTGGACGAACTTCTG
* *
218 AACTTGGA-AAACTTTTACCAGTTCATCTATAACTTTC-ATTCCTTAAAGTATTCATGACAATCC
1 AACTT-GACAAACTTTTACGAGTTCTTCTATAAC-TTCGATTCCTTAAAGTATTCATGACAATCC
* * *
281 ATTCCTTCAAGCAATATTTCGAACATTCCATGCTCGGGAAATCGCATCATTTGGTCTAAATAGTT
64 ATTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTTGTCTAAATAGTT
* * * *
346 TGCCATTTTGTAAACAACTTTTGGTCTTTAAATTAAAATCTTATTTACGTGAGAATTGTTTCTCG
129 TGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCT
* *
411 CTTTGTTCTTGGACGAACTTCCG
194 CTTGGTTCTTGGACGAACTTCTG
*** * * * * * *
434 AACTTGATGTAGTTTTGCAAGTTCTTTTAAAACTTC-AGTTCCTTAAAGTATTCATGACGATCCA
1 AACTTGACAAACTTTTACGAGTTCTTCTATAACTTCGA-TTCCTTAAAGTATTCATGACAATCCA
* * *
498 TTCCTTCGAGCAATTTTTCAAACATTCCATGCAT-GCGAAATTGCATCATTTTGTCTAAATAGTT
65 TTCCTTCGAGCAATTTTTCGAACATTCCATGC-TCGGGAAATCGCATCATTTTGTCTAAATAGTT
* * * *
562 TGTCATTTTCTAAACAACTTTTGGTCTTTGAATTAAAAACCTATTTACGTGAGAGTTGTTTTTCT
129 TGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCT
* * **
627 CTTGGTTCTTAGATGAACTTCCA
194 CTTGGTTCTTGGACGAACTTCTG
* * * * ** *
650 AACTTGACAAAATTTTACAAGTTCTTCAATAACTTCGGTTTTTTAAAGTATTCAGGACAATCCAT
1 AACTTGACAAACTTTTACGAGTTCTTCTATAACTTCGATTCCTTAAAGTATTCATGACAATCCAT
* * * * * *
715 TCCTTCGAGCAATTTTTTGAATATTCCATGCTCGAGAAATCTCATCATTTGGTCTAAATACTTTG
66 TCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTTGTCTAAATAGTTTG
* * * * *
780 TCATTTTCTAAACTACTTTTGGTCTTTGAATGAAAAACTTATTTACGTGAGAGA-TGTTTTTATC
131 TCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGA-ATTGTTTCTCTC
* * **
844 TTGGTTCTTTGACAAACTTCCC
195 TTGGTTCTTGGACGAACTTCTG
* * * * *
866 AACTTGGCAAACATTTACGAGTTCTTTTATTACTTC-AGTT-CTATAAAGTATTCATGACGATCC
1 AACTTGACAAACTTTTACGAGTTCTTCTATAACTTCGA-TTCCT-TAAAGTATTCATGACAATCC
* * * * * * *
929 ATTCCTTCGAGCAA-TTTTCTGAACATTTCGTGCTTGGGAAATCGCATCATTTTTTCTATACAAT
64 ATTCCTTCGAGCAATTTTTC-GAACATTCCATGCTCGGGAAATCGCATCATTTTGTCTAAATAGT
* * * * *
993 TTATCATTTGGTAAACAACTTTTGGTCTTTGAATGAGAAACTTATTTACATGAGAATTGTTTCTC
128 TTGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTC
* * * * *
1058 TCTTGGATATTAGATGAACTTCTA
193 TCTTGGTTCTTGGACGAACTTCTG
* * *
1082 AACTTGACAAACTTTGACGAGTTCTTTCAATAACTTCGATTCTTTAAAGTATTCATGACAATCCA
1 AACTTGACAAACTTTTACGAGTTC-TTCTATAACTTCGATTCCTTAAAGTATTCATGACAATCCA
* * * * *
1147 TTCCTTCAAGCAATTTTTCGAACATTTCATGCTTGGGAAATCGCATCCTTTTTTCTAAACTA-TT
65 TTCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTTGTCTAAA-TAGTT
* * * *
1211 TGTCATTTGGTAAACAACTTTTGGTCTTTGAATGAAAAACTTATTTACATGAGAATTGTTTCTCG
129 TGTCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCT
*** * *
1276 CTTGGAAATTGGATGAACTTCTA
194 CTTGGTTCTTGGACGAACTTCTG
* * * * * * *
1299 AACTTGACAAACTTTGATGACTTATTCTATAACTTCGGTTCTTTAAAGTATTCATGACGATCCAT
1 AACTTGACAAACTTTTACGAGTTCTTCTATAACTTCGATTCCTTAAAGTATTCATGACAATCCAT
** * * *
1364 TCCTTCGAGCAATTTTTTAAACATTCCATGCTTGGGAAATCACATCATTTTTTCTAAATAGTTTG
66 TCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTTGTCTAAATAGTTTG
* * * *
1429 TCATTTGGTATACAACTTTTGGTCATTGAATTAAAAACTTATTTACGTGAGAATT-TATTATCTC
131 TCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGT-TTCTCTC
* * *
1493 TTGGATCATGGACAAACTTCTG
195 TTGGTTCTTGGACGAACTTCTG
* * * * * *
1515 AACTTCACAAACTTTTACTAGTTGTTCTATAACTTTGGTTCATTAAAGTATTCATGACAATCCAT
1 AACTTGACAAACTTTTACGAGTTCTTCTATAACTTCGATTCCTTAAAGTATTCATGACAATCCAT
* * * * * *
1580 TCCTTCGAGTAA-TTTTCTGAACATTCCATGCTCAGGAAATCGAATAATTTAGTTTAAATAGTTT
66 TCCTTCGAGCAATTTTTC-GAACATTCCATGCTCGGGAAATCGCATCATTTTGTCTAAATAGTTT
* * * *
1644 GTCATTTTGTAAACAACTTTTGGTCTATAAATTAAAAAAGTTATTTACGTGAGAGTTGTTTCTCA
130 GTCATTTTGTAAACAACTTTTGGTCTTTGAATT-AAAAACTTATTTACGTGAGAATTGTTTCTC-
* * *
1709 T-TTTGTTCTTGGACAAACTTTTG
193 TCTTGGTTCTTGGACGAACTTCTG
* * *
1732 AACTTGACAAAGTTTTACGAGTTCTTTTAAAACTT
1 AACTTGACAAACTTTTACGAGTTCTTCTATAACTT
1767 TAGTTCCTGA
Statistics
Matches: 1324, Mismatches: 202, Indels: 45
0.84 0.13 0.03
Matches are distributed among these distances:
215 20 0.02
216 1030 0.78
217 264 0.20
218 10 0.01
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (216 bp):
AACTTGACAAACTTTTACGAGTTCTTCTATAACTTCGATTCCTTAAAGTATTCATGACAATCCAT
TCCTTCGAGCAATTTTTCGAACATTCCATGCTCGGGAAATCGCATCATTTTGTCTAAATAGTTTG
TCATTTTGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTTCTCTCT
TGGTTCTTGGACGAACTTCTG
Found at i:3972 original size:50 final size:50
Alignment explanation
Indices: 3895--4015 Score: 134
Period size: 50 Copynumber: 2.4 Consensus size: 50
3885 TGTCATCCAT
* * * *
3895 TAACTCTCATGATCAGTTAAGTTTGCATCATAAATAATGACACGCATTAAG
1 TAACTCACATG-TTAGTTAAATATGCATCATAAATAATGACACGCATTAAG
* ** * * *
3946 TAACTTACATGTTAGTTAAATATGCATCATAAATCCTGTCATGCATTATG
1 TAACTCACATGTTAGTTAAATATGCATCATAAATAATGACACGCATTAAG
*
3996 TAACTCCCATGTTAGTTAAA
1 TAACTCACATGTTAGTTAAA
4016 GTTTGCNNNN
Statistics
Matches: 58, Mismatches: 12, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
50 49 0.84
51 9 0.16
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (50 bp):
TAACTCACATGTTAGTTAAATATGCATCATAAATAATGACACGCATTAAG
Found at i:4390 original size:50 final size:50
Alignment explanation
Indices: 4313--4444 Score: 147
Period size: 50 Copynumber: 2.6 Consensus size: 50
4303 TGTCATCCAT
* * *
4313 TAACTCTCATGATCAGTTAAGTTTGCATCATAAATAATGACACGCATTAAG
1 TAACTCACATG-TTAGTTAAATTTGCATCATAAATAATGACACGCATTAAG
* * ** * * *
4364 TAACTTACATGTTAGTTAAATATGCATCATAAATCCTGTCATGCATTATG
1 TAACTCACATGTTAGTTAAATTTGCATCATAAATAATGACACGCATTAAG
*
4414 TAACTCCCATGTTAGTTAAAGTTTGCATCAT
1 TAACTCACATGTTAGTTAAA-TTTGCATCAT
4445 TAATCAAGTC
Statistics
Matches: 67, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
50 49 0.73
51 18 0.27
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (50 bp):
TAACTCACATGTTAGTTAAATTTGCATCATAAATAATGACACGCATTAAG
Found at i:4495 original size:50 final size:50
Alignment explanation
Indices: 4433--4547 Score: 221
Period size: 50 Copynumber: 2.3 Consensus size: 50
4423 TGTTAGTTAA
4433 AGTTTGCATCATTAATCAAGTCATGCATTTAGTAATCCATTAGTTCATTT
1 AGTTTGCATCATTAATCAAGTCATGCATTTAGTAATCCATTAGTTCATTT
4483 AGTTTGCATCATTAATCAAGTCATGCATTTAGTAATCCATTAGTTCATTT
1 AGTTTGCATCATTAATCAAGTCATGCATTTAGTAATCCATTAGTTCATTT
*
4533 AGTTTGCATCTTTAA
1 AGTTTGCATCATTAA
4548 ACCATTCATT
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 64 1.00
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.43
Consensus pattern (50 bp):
AGTTTGCATCATTAATCAAGTCATGCATTTAGTAATCCATTAGTTCATTT
Found at i:8497 original size:50 final size:51
Alignment explanation
Indices: 8431--8568 Score: 138
Period size: 50 Copynumber: 2.7 Consensus size: 51
8421 ATGATCAGTT
* *
8431 AAGTTTGCATCATAAATAATGACATGCATTAAGTAACTTACATGTTAGTCA
1 AAGTATGCATCATAAATAATGACATGCATTAAGTAACTCACATGTTAGTCA
** * * *
8482 AA-TATGCATCATAAATCCT-ATCATGCATTATGTAACTCCCATGTTAGTTA
1 AAGTATGCATCATAAATAATGA-CATGCATTAAGTAACTCACATGTTAGTCA
* * *
8532 AAGTTTGCATCATTAAATCAA-GTCATGCATTTAGTAA
1 AAGTATGCATCA-TAAAT-AATGACATGCATTAAGTAA
8569 TCCATTAGTT
Statistics
Matches: 69, Mismatches: 13, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
49 1 0.01
50 41 0.59
51 10 0.14
52 17 0.25
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (51 bp):
AAGTATGCATCATAAATAATGACATGCATTAAGTAACTCACATGTTAGTCA
Found at i:11643 original size:216 final size:215
Alignment explanation
Indices: 10831--12908 Score: 2033
Period size: 216 Copynumber: 9.7 Consensus size: 215
10821 CAAGAACCCC
* * * * *
10831 TAGTTTGCCATTTTGTAAACAACTTTTGGTCTCTAAATTAAAATCTTATTTACGTGAGAATTGTT
1 TAGTTTGTCATTTTCTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTT
* ** * ** * * * *
10896 TCTCTCTTTTTTCTTGGACGAACCTCTGAACTTGATGAAGC----A--AGTTCTTTTAAAACTTC
66 CCTCTCTTGGTTCTTGGACGAACTTCCAAACTTGA-CAAACTTTTACGAGTTCTTCTATAACTTC
** * * * * ** *
10955 AATTCCTTAAAGTATTCATGACGATCCATTCCTTCTAGCAAATTTTTCAAACATTCCAAGCACGA
130 GGTTCTTTAAAGTATTCATGACGATCCATTCCTTCGAGC-AA-TTTTCGAACATTCCATGCTTGG
*
11020 GAAATCTCATCATTTTGTCTAAA
193 GAAATCGCATCATTTTGTCTAAA
* ** * * *
11043 TTGTTTGTCATTTTCTAAACAACTTTTTATCTTTGAATTAAAAACCTATTTACGCGAGAGTTG-T
1 TAGTTTGTCATTTTCTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTT
* * * * * * *
11107 CTTTCTCTTGCTTCTTAGATGAACTTCCAAGCTTGACAAACTTTTACGAGTTC-TCAATAACTTT
66 C-CTCTCTTGGTTCTTGGACGAACTTCCAAACTTGACAAACTTTTACGAGTTCTTCTATAACTTC
* * * * *
11171 GGTT-TCTTAAAGTATTCAGGACAATTCATTCCTTAGAGCAATTTGTTGAACATTCCATGCTTGG
130 GGTTCT-TTAAAGTATTCATGACGATCCATTCCTTCGAGCAATTT-TCGAACATTCCATGCTTGG
*
11235 GAAATCGCATCATTTGGTCTAAA
193 GAAATCGCATCATTTTGTCTAAA
* * * * * *
11258 TACTTTGTCATTTTCTAAACTACTTTTCGTCTTTGAATGAAAAACTTATTCAC--GAGAGTTG-T
1 TAGTTTGTCATTTTCTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTT
* * * *** * *
11320 CTCTATCTTGGTTCTTAGACAAACTTTTGAACTTGGCAAACTTTTACGAGTTCTTTTATAACTTC
66 C-CTCTCTTGGTTCTTGGACGAACTTCCAAACTTGACAAACTTTTACGAGTTCTTCTATAACTTC
* * * *
11385 AGTT-TCATAAAGTATTCATGACCATCCATTCCTTCGAGCAATTTTACGAACATTTCATGCTTGG
130 GGTTCT-TTAAAGTATTCATGACGATCCATTCCTTCGAGCAATTTT-CGAACATTCCATGCTTGG
* *
11449 GAAATTGCATCATTTTTTCTAAA
193 GAAATCGCATCATTTTGTCTAAA
** * *
11472 CTA-TTTGTCATTTGGTAAACAACTTTTGGTCTTTGAATGAAAAACTTATTTACATGAGAATTGT
1 -TAGTTTGTCATTTTCTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGT
* * * * *
11536 TCCTCTCTTGGATATTGGATGAACTTCTAAACTTGACAAACTTTGACGAGTTCTTCTATAACTTC
65 TCCTCTCTTGGTTCTTGGACGAACTTCCAAACTTGACAAACTTTTACGAGTTCTTCTATAACTTC
* * *
11601 GGCTCTTTAAAGTATTCATGACGATCCATTCCTTCGAGCAATTTTCTAAACATTCCATGCATGGG
130 GGTTCTTTAAAGTATTCATGACGATCCATTCCTTCGAGCAATTTTC-GAACATTCCATGCTTGGG
* *
11666 AAATCACATCATTTTCTCTAAA
194 AAATCGCATCATTTTGTCTAAA
* ** * *
11688 TAGTTTATCATTTGGTATACAACTTTTGGTCATTGAATTAAAAAACTTATTTACGTGAGAATT-T
1 TAGTTTGTCATTTTCTAAACAACTTTTGGTCTTTGAATT-AAAAACTTATTTACGTGAGAATTGT
** * ** * * * * *
11752 ATTATCTCTTGGATCAAGGACAAACTTCCGAACTTTACAAACTTTTACCAGTTGTTCTATAACTT
65 -TCCTCTCTTGGTTCTTGGACGAACTTCCAAACTTGACAAACTTTTACGAGTTCTTCTATAACTT
* * * * * * **
11817 TGGTTCATTAAAGTATTCATGACGATCC-TTTCTTCAAGCAATTTTTCGGACATTCCAAGCACGG
129 CGGTTCTTTAAAGTATTCATGACGATCCATTCCTTCGAGCAA-TTTTCGAACATTCCATGCTTGG
* * * *
11881 GGAACCGCATCATTCTGCCTAAA
193 GAAATCGCATCATTTTGTCTAAA
* * * * **
11904 TAGTTTTTCATTTTCTAAA-AACTTTTGGTCTATAAATTAAAAAATTATTTACGTGAGTGTTGTT
1 TAGTTTGTCATTTTCTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTT
* * * * *
11968 TCTCTCATT-GTTCTTGGACGAACTTCCGAACTTGACGAAGTTTTACGAGTTCTTCTAAAACTTC
66 CCTCTC-TTGGTTCTTGGACGAACTTCCAAACTTGACAAACTTTTACGAGTTCTTCTATAACTTC
* * * * * * **
12032 AGTTCCTTAAAGTATTCATGACGATCCGTTCCTTCTAGCAATTTTTCGAACTTTCCGTGCACGGG
130 GGTTCTTTAAAGTATTCATGACGATCCATTCCTTCGAGCAA-TTTTCGAACATTCCATGCTTGGG
12097 AAATCGCATCATTTTGTCTAAA
194 AAATCGCATCATTTTGTCTAAA
* ** * * *
12119 TTGTTTGTCATTTTCTAAACAACTTTTTATCTTTGAATTAAAAACCTATTTACGCGAGATTTG-T
1 TAGTTTGTCATTTTCTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTT
* * * * * * * *
12183 CTTTCTCTTGCTTCTTAGATGAATTTCCAAGCTTGACAAACTTTTACGAGTTCTTCAATAACTTT
66 C-CTCTCTTGGTTCTTGGACGAACTTCCAAACTTGACAAACTTTTACGAGTTCTTCTATAACTTC
* * * * *
12248 GGTT-TCTGAAAGTATTCAGGACAATCCATTCCTTAGAGCAATTTGTTGAACATTCCATGCTTGG
130 GGTTCT-TTAAAGTATTCATGACGATCCATTCCTTCGAGCAATTT-TCGAACATTCCATGCTTGG
*
12312 GAAATC-CTATCATTTGGTCTAAA
193 GAAATCGC-ATCATTTTGTCTAAA
* * * * * *
12335 TACTTTGTCATTTTCTAAACTACTTTTCGTCTTTGAATGAAAAACTTATTCACGTGAGAGTTGTT
1 TAGTTTGTCATTTTCTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTT
* * * * * * * *
12400 TCTATCTTGGTTCTTAGACGAACTTTCGAACTTGGCAAACTTTTACGAGTTCTTTTATAACTTCA
66 CCTCTCTTGGTTCTTGGACGAACTTCCAAACTTGACAAACTTTTACGAGTTCTTCTATAACTTCG
** * * * *
12465 GTTCCATAAAGTATTCATGACCATCCATTCCTTCGACCAATTTTTCGAACATTTCGTGCTTGGGA
131 GTTCTTTAAAGTATTCATGACGATCCATTCCTTCGAGCAA-TTTTCGAACATTCCATGCTTGGGA
*
12530 AATCGCATCATTTTTTCTAAA
195 AATCGCATCATTTTGTCTAAA
** * * *
12551 CTA-TTTGTCATTTGGTAAACAACTTTTGGTCTTTGAATGAAAATCTTATTTACATGAGAATTGT
1 -TAGTTTGTCATTTTCTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGT
* * * * * *
12615 TCCTCTCTTGGATATTGGATGAACTTCTAAACTTGACAAACTTTGACGAGCTCTTCTATAACTTC
65 TCCTCTCTTGGTTCTTGGACGAACTTCCAAACTTGACAAACTTTTACGAGTTCTTCTATAACTTC
* *
12680 GGCTCTTTAAAGTATTCATGACGATCCATTCCTTCGAACAATTTTCTGAACATTCCATGCTTGGG
130 GGTTCTTTAAAGTATTCATGACGATCCATTCCTTCGAGCAATTTTC-GAACATTCCATGCTTGGG
* *
12745 AAATCACATCATTTTCTCTAAA
194 AAATCGCATCATTTTGTCTAAA
** * *
12767 TAGTTTGTCATTTGGTATACAACTTTTGGTCATTGAATTAAAAACTTATTTACGTGAGAATT-TA
1 TAGTTTGTCATTTTCTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGT-
** * * * * * * *
12831 TTATCTCTTGGATCATGGACAAACTTCCAAACTTTACAAACTTTTACCAGTTATTCTATAACTTT
65 TCCTCTCTTGGTTCTTGGACGAACTTCCAAACTTGACAAACTTTTACGAGTTCTTCTATAACTTC
*
12896 GGTTCATTAAAGT
130 GGTTCTTTAAAGT
12909 TATAAATAGT
Statistics
Matches: 1534, Mismatches: 294, Indels: 72
0.81 0.15 0.04
Matches are distributed among these distances:
211 4 0.00
212 77 0.05
213 53 0.03
214 225 0.15
215 187 0.12
216 870 0.57
217 118 0.08
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.40
Consensus pattern (215 bp):
TAGTTTGTCATTTTCTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTT
CCTCTCTTGGTTCTTGGACGAACTTCCAAACTTGACAAACTTTTACGAGTTCTTCTATAACTTCG
GTTCTTTAAAGTATTCATGACGATCCATTCCTTCGAGCAATTTTCGAACATTCCATGCTTGGGAA
ATCGCATCATTTTGTCTAAA
Found at i:12140 original size:647 final size:640
Alignment explanation
Indices: 10833--12908 Score: 2169
Period size: 647 Copynumber: 3.2 Consensus size: 640
10823 AGAACCCCTA
* * * * * *
10833 GTTTGCCATTTTGTAAACAACTTTTGGTCTCTAAATTAAAATCTTATTTACGTGAGAATTGTTTC
1 GTTTGTCATTTGGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTCC
*** * * ** ** * * * **
10898 TCTCTTTTTTCTTGGACGAACCTCTGAACTTGATGAA----G-CAAGTTCTTTTAAAACTTCAAT
66 TCTCTTGGATATTGGACGAACTTCCAAACTTGACAAACTTTGACGAGTTCTTCTATAACTTCGGT
* * * * *
10958 TCCTTAAAGTATTCATGACGATCCATTCCTTCTAGCAAATTTTTCAAACATTCCAAGCACGAGAA
131 TCTTTAAAGTATTCATGACGATCCATTCCTTCGAGC-AATTTTT-AAACATTCCATGCATGGGAA
* **
11023 ATCTCATCATTTTGTCTAAATTGTTTGTCATTTTCTAAACAACTTTTTATCTTTGAATTAAAAAC
194 ATC-CATCATTTTGTCTAAATAGTTTGTCATTTTCTAAACAACTTTTCGTCTTTGAATTAAAAAC
* * * *
11088 CTATTTACGCGAGAGTTGTCTTTCTCTTGCTTCTTAGATGAACTTCC-AAGCTTGACAAACTTTT
258 TTATTTACGTGAGAGTTGT-TTTCTCTTGGTTCTTAGACGAACTTCCGAA-CTTGACAAACTTTT
* * * *
11152 ACGAGTTCTCAATAACTTTGGTTTC-TTAAAGTATTCAGGACAATTCATTCCTT-AGAGCAATTT
321 ACGAGTTTTCTATAACTTTGG-TTCATTAAAGTATTCATGACAA-TCCTTCCTTCA-AGCAATTT
*
11215 GTT-GAACATTCCATGCTTGGGAAATCGCATCATTTGGTCTAAATACTTTGTCATTTTCTAAACT
383 -TTCGAACATTCCATGCTTGGGAAATCGCATCATTT-GTCTAAATA-TTTGTCATTTTCTAAACA
* * * * * *
11279 ACTTTTCGTCTTTGAATGAAAAACTTATTCAC-GAGAGTTGTCTCTATCTTGGTTCTTAGACAAA
445 ACTTTTGGTCTTTGAATGAAAAACTTATTTACTGAGAGTTGTTTCTCTCTTGGTTCTTGGACGAA
* * * * * *
11343 CTTTTGAACTTGGCAAACTTTTACGAGTTCTTTTATAACTTCAGTTTCATAAAGTATTCATGACC
510 CTTCTGAACTTGACAAACTTTTACGAGTTCTTCTATAACTTCAGTTCCTTAAAGTATTCATGACG
* * *
11408 ATCCATTCCTTCGAGCAATTTTACGAACATTT-CATGCTTGGGAAATTGCATCATTTTTTCTAAA
575 ATCCATTCCTTCGAGCAATTTTTCGAAC-TTTCCATGCTTGGGAAATCGCATCATTTTCTCTAAA
*
11472 CT
639 TT
* * *
11474 ATTTGTCATTTGGTAAACAACTTTTGGTCTTTGAATGAAAAACTTATTTACATGAGAATTGTTCC
1 GTTTGTCATTTGGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTCC
* * *
11539 TCTCTTGGATATTGGATGAACTTCTAAACTTGACAAACTTTGACGAGTTCTTCTATAACTTCGGC
66 TCTCTTGGATATTGGACGAACTTCCAAACTTGACAAACTTTGACGAGTTCTTCTATAACTTCGGT
11604 TCTTTAAAGTATTCATGACGATCCATTCCTTCGAGCAATTTTCTAAACATTCCATGCATGGGAAA
131 TCTTTAAAGTATTCATGACGATCCATTCCTTCGAGCAATTTT-TAAACATTCCATGCATGGGAAA
* * ** * * *
11669 TCACATCATTTTCTCTAAATAGTTTATCATTTGGTATACAACTTTTGGTCATTGAATTAAAAAAC
195 TC-CATCATTTTGTCTAAATAGTTTGTCATTTTCTAAACAACTTTTCGTCTTTGAATT-AAAAAC
* * * * *
11734 TTATTTACGTGAGAATT-TATTATCTCTTGGATC-AAGGACAAACTTCCGAACTTTACAAACTTT
258 TTATTTACGTGAGAGTTGT-TT-TCTCTTGGTTCTTA-GACGAACTTCCGAACTTGACAAACTTT
* * *
11797 TACCAGTTGTTCTATAACTTTGGTTCATTAAAGTATTCATGACGATCCTTTCTTCAAGCAATTTT
320 TACGAGTT-TTCTATAACTTTGGTTCATTAAAGTATTCATGACAATCCTTCCTTCAAGCAATTTT
* * ** * * * *
11862 TCGGACATTCCAAGCACGGGGAACCGCATCATTCTGCCTAAATAGTTTTTCATTTTCTAAA-AAC
384 TCGAACATTCCATGCTTGGGAAATCGCATCATT-TGTCTAAATA-TTTGTCATTTTCTAAACAAC
* * * * *
11926 TTTTGGTCTATAAATTAAAAAATTATTTACGTGAGTGTTGTTTCTCTCATT-GTTCTTGGACGAA
447 TTTTGGTCTTTGAATGAAAAACTTATTTAC-TGAGAGTTGTTTCTCTC-TTGGTTCTTGGACGAA
* * * *
11990 CTTCCGAACTTGACGAAGTTTTACGAGTTCTTCTAAAACTTCAGTTCCTTAAAGTATTCATGACG
510 CTTCTGAACTTGACAAACTTTTACGAGTTCTTCTATAACTTCAGTTCCTTAAAGTATTCATGACG
* * * ** *
12055 ATCCGTTCCTTCTAGCAATTTTTCGAACTTTCCGTGCACGGGAAATCGCATCATTTTGTCTAAAT
575 ATCCATTCCTTCGAGCAATTTTTCGAACTTTCCATGCTTGGGAAATCGCATCATTTTCTCTAAAT
12120 T
640 T
** ** * * *
12121 GTTTGTCATTTTCTAAACAACTTTTTATCTTTGAATTAAAAACCTATTTACGCGAGATTTG-TCT
1 GTTTGTCATTTGGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTC-
* ** * * * * * * * *
12185 TTCTCTTGCTTCTTAGATGAATTTCCAAGCTTGACAAACTTTTACGAGTTCTTCAATAACTTTGG
65 CTCTCTTGGATATTGGACGAACTTCCAAACTTGACAAACTTTGACGAGTTCTTCTATAACTTCGG
* * * * * *
12250 TT-TCTGAAAGTATTCAGGACAATCCATTCCTTAGAGCAATTTGTTGAACATTCCATGCTTGGGA
130 TTCT-TTAAAGTATTCATGACGATCCATTCCTTCGAGCAATTT-TTAAACATTCCATGCATGGGA
* * * *
12314 AATCCTATCATTTGGTCTAAATACTTTGTCATTTTCTAAACTACTTTTCGTCTTTGAATGAAAAA
193 AATCC-ATCATTTTGTCTAAATAGTTTGTCATTTTCTAAACAACTTTTCGTCTTTGAATTAAAAA
* * * *
12379 CTTATTCACGTGAGAGTTGTTTCTATCTTGGTTCTTAGACGAACTTTCGAACTTGGCAAACTTTT
257 CTTATTTACGTGAGAGTTGTTT-TCTCTTGGTTCTTAGACGAACTTCCGAACTTGACAAACTTTT
* ** * * *
12444 ACGAGTTCTTTTATAACTTCAGTTCCA-TAAAGTATTCATGACCATCCATTCCTTCGACCAATTT
321 ACGAGTT-TTCTATAACTTTGGTT-CATTAAAGTATTCATGACAATCC-TTCCTTCAAGCAATTT
* * * **
12508 TTCGAACATTTCGTGCTTGGGAAATCGCATCATTTTTTCTAAACTATTTGTCATTTGGTAAACAA
383 TTCGAACATTCCATGCTTGGGAAATCGCATCA-TTTGTCTAAA-TATTTGTCATTTTCTAAACAA
* * * * * *
12573 CTTTTGGTCTTTGAATGAAAATCTTATTTACATGAGAATTGTTCCTCTCTTGGATATTGGATGAA
446 CTTTTGGTCTTTGAATGAAAAACTTATTTAC-TGAGAGTTGTTTCTCTCTTGGTTCTTGGACGAA
* * * * * *
12638 CTTCTAAACTTGACAAACTTTGACGAGCTCTTCTATAACTTCGGCTCTTTAAAGTATTCATGACG
510 CTTCTGAACTTGACAAACTTTTACGAGTTCTTCTATAACTTCAGTTCCTTAAAGTATTCATGACG
* * *
12703 ATCCATTCCTTCGAACAA-TTTTCTGAACATTCCATGCTTGGGAAATCACATCATTTTCTCTAAA
575 ATCCATTCCTTCGAGCAATTTTTC-GAACTTTCCATGCTTGGGAAATCGCATCATTTTCTCTAAA
*
12767 TA
639 TT
* * *
12769 GTTTGTCATTTGGTATACAACTTTTGGTCATTGAATTAAAAACTTATTTACGTGAGAATT-TATT
1 GTTTGTCATTTGGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGT-TC
* * * * * * *
12833 ATCTCTTGGATCA-TGGACAAACTTCCAAACTTTACAAACTTTTACCAGTTATTCTATAACTTTG
65 CTCTCTTGGAT-ATTGGACGAACTTCCAAACTTGACAAACTTTGACGAGTTCTTCTATAACTTCG
*
12897 GTTCATTAAAGT
129 GTTCTTTAAAGT
12909 TATAAATAGT
Statistics
Matches: 1175, Mismatches: 224, Indels: 65
0.80 0.15 0.04
Matches are distributed among these distances:
641 84 0.07
645 105 0.09
646 275 0.23
647 436 0.37
648 274 0.23
649 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.40
Consensus pattern (640 bp):
GTTTGTCATTTGGTAAACAACTTTTGGTCTTTGAATTAAAAACTTATTTACGTGAGAATTGTTCC
TCTCTTGGATATTGGACGAACTTCCAAACTTGACAAACTTTGACGAGTTCTTCTATAACTTCGGT
TCTTTAAAGTATTCATGACGATCCATTCCTTCGAGCAATTTTTAAACATTCCATGCATGGGAAAT
CCATCATTTTGTCTAAATAGTTTGTCATTTTCTAAACAACTTTTCGTCTTTGAATTAAAAACTTA
TTTACGTGAGAGTTGTTTTCTCTTGGTTCTTAGACGAACTTCCGAACTTGACAAACTTTTACGAG
TTTTCTATAACTTTGGTTCATTAAAGTATTCATGACAATCCTTCCTTCAAGCAATTTTTCGAACA
TTCCATGCTTGGGAAATCGCATCATTTGTCTAAATATTTGTCATTTTCTAAACAACTTTTGGTCT
TTGAATGAAAAACTTATTTACTGAGAGTTGTTTCTCTCTTGGTTCTTGGACGAACTTCTGAACTT
GACAAACTTTTACGAGTTCTTCTATAACTTCAGTTCCTTAAAGTATTCATGACGATCCATTCCTT
CGAGCAATTTTTCGAACTTTCCATGCTTGGGAAATCGCATCATTTTCTCTAAATT
Found at i:13072 original size:98 final size:98
Alignment explanation
Indices: 12901--13087 Score: 277
Period size: 98 Copynumber: 1.9 Consensus size: 98
12891 ACTTTGGTTC
* *
12901 ATTAAAGTTATAAATAGTTTCCGAACATACCAGGCACGGGGAATTGCATCATTCTGCATAAATAG
1 ATTAAAGTTATAAATAGTTTCCGAACATACCAGGCACGGGAAATCGCATCATTCTGCATAAATAG
*
12966 TTTTTCATTTCCTAAACAACTTTTGGTTTATAA
66 TTTGTCATTTCCTAAACAACTTTTGGTTTATAA
* * * * *
12999 ATTAAAGTTATAAATAGTTTCCGAACATTCCATGCACTGGAAATCGCATCATTTTGTC-TAAATT
1 ATTAAAGTTATAAATAGTTTCCGAACATACCAGGCACGGGAAATCGCATCATTCTG-CATAAATA
*
13063 GTTTGTCATTTTCTAAACAACTTTT
65 GTTTGTCATTTCCTAAACAACTTTT
13088 TATCTTTGAA
Statistics
Matches: 79, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
98 78 0.99
99 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.38
Consensus pattern (98 bp):
ATTAAAGTTATAAATAGTTTCCGAACATACCAGGCACGGGAAATCGCATCATTCTGCATAAATAG
TTTGTCATTTCCTAAACAACTTTTGGTTTATAA
Done.