Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398470.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1767.0, 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: 21649
ACGTcount: A:0.24, C:0.10, G:0.09, T:0.25
Warning! 6939 characters in sequence are not A, C, G, or T
Found at i:4287 original size:148 final size:150
Alignment explanation
Indices: 4017--4296 Score: 368
Period size: 148 Copynumber: 1.9 Consensus size: 150
4007 NNNNNNNNNN
* * *
4017 CAAAAGCCTTATTACTCTCTTTAAATGGTTTTATAACCTCATAATTGAATTAAGTTTAATTTATT
1 CAAAAGCCTTATTACTCTCTTTAAATGGTTTTATAACCTCAAAATTGAATTAAGGTTAAGTTATT
** * * ** *
4082 TTACATTTTTGGTTAAAACAGATTATAATTGAATGTTTGCGTTGAGAAAGATGAAGAAAAACCCA
66 TTACATTTTCAGTTAAAACAGATTATAATTGAATGTGTGCCTCAAGAAACATGAAGAAAAACCCA
4147 TTTATAGTCACCTAAGCCTT
131 TTTATAGTCACCTAAGCCTT
* * ** * * *
4167 CAAAAGCCTTATTATTCTCTTTGAATGGTTTTATAGTCTTAAAATTG-ATTTAGGTTGAGTT-TT
1 CAAAAGCCTTATTACTCTCTTTAAATGGTTTTATAACCTCAAAATTGAATTAAGGTTAAGTTATT
*
4230 TTACATTTTCAGTTAAAATAGATTATAATTGAATGTCGT-CCTCAAGAAACATGAAGAAAAACCC
66 TTACATTTTCAGTTAAAACAGATTATAATTGAATGT-GTGCCTCAAGAAACATGAAGAAAAACCC
4294 ATT
130 ATT
4297 NNNNNNNNNN
Statistics
Matches: 111, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
148 59 0.53
149 11 0.10
150 41 0.37
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (150 bp):
CAAAAGCCTTATTACTCTCTTTAAATGGTTTTATAACCTCAAAATTGAATTAAGGTTAAGTTATT
TTACATTTTCAGTTAAAACAGATTATAATTGAATGTGTGCCTCAAGAAACATGAAGAAAAACCCA
TTTATAGTCACCTAAGCCTT
Found at i:7118 original size:341 final size:332
Alignment explanation
Indices: 6477--7138 Score: 695
Period size: 341 Copynumber: 2.0 Consensus size: 332
6467 TTTTCTTGAA
* ** *
6477 GTTTCCTAAGGCAAACACTCAATTATAATCTAGTTTAACCAAAAATGTATCAAAACTCAACTTAA
1 GTTTCCAAAGGCAAACACTCAATTATAATCTAGTTTAACCAAAAACATATAAAAACTCAACTTAA
* * * *
6542 AATCAATTATAAGATTCTAAAACCATTTAAAGATAGTTATAAGGCTTTTGAAGACTTGGGTGTCT
66 AATCAATTATAAGACTATAAAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGACTTGGGTGTCT
* * *
6607 ATAAATGGGCTTTTCTTGCCAATGAATGGCTTTTTCTTCAGATTTCCCAAGGAAAACATTCAATT
131 ATAAAGGGGCTTTTCTTGCCAATGAATGGATTTTTCTTCAGATTTCCCAAGGAAAACACTCAATT
* * * ********** * *
6672 ATATTCTGTTTTAAACAAAAANNNNNNNNNNTTCAACTTAAAATCAATTTTGAGGTTATAAAACT
196 ATAATCTGGTTCAAACAAAAATGTGAAAACATTCAACTTAAAATCAATTCTGAGATTATAAAACT
* ** *
6737 ATTTAAGGAGTGTAACAAGGCTTTTAAAGGCTTTGGTGACTATAAATGGGCTTTTCCTGCCAATG
261 ATTTAACGAAAGTAACAAGGCTTTTAAAGGCTTGGGTGACTATAAATGGGCTTTTCCTGCCAATG
6802 ACNNNNNNNNNNTTCAT
326 AC----------TTCAT
* * *
6819 GTTTCCAAAGGTAAACATTCAATTATAATCT-GTTTTAACCAAAAACATA-AAACAATTCAACTT
1 GTTTCCAAAGGCAAACACTCAATTATAATCTAG-TTTAACCAAAAACATATAAA-AACTCAACTT
* * ***
6882 AAAATCAATTATGAGACTATAAAACCATTTAAAGAG-GATAATAAGGCTTTTGAAGGCTTGGNNN
64 AAAATCAATTATAAGACTATAAAACCATTTAAAGAGAG-TAATAAGGCTTTTGAAGACTTGGGTG
******* *
6946 NNNNNNNAGGGGC-TTTCTTGCCAATGAATGGATTTTTCTTCATG-TTTCCCAAGGCAAACACTC
128 TCTATAAAGGGGCTTTTCTTGCCAATGAATGGATTTTTCTTCA-GATTTCCCAAGGAAAACACTC
**
7009 AATTATAATCTGGTTCAATGAAAAATGTGAAAACATTCAACTTAAAATCAATTCTGAGATTATAA
192 AATTATAATCTGGTTCAAACAAAAATGTGAAAACATTCAACTTAAAATCAATTCTGAGATTATAA
* * * *
7074 AATTATTTAACGAAAGTAATAAGGCTTTTGAAGGCTTGGGTGACTATAAATGGGCTTTTCTTGCC
257 AACTATTTAACGAAAGTAACAAGGCTTTTAAAGGCTTGGGTGACTATAAATGGGCTTTTCCTGCC
7139 NNNNNNNNNN
Statistics
Matches: 264, Mismatches: 52, Indels: 9
0.81 0.16 0.03
Matches are distributed among these distances:
341 154 0.58
342 110 0.42
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.32
Consensus pattern (332 bp):
GTTTCCAAAGGCAAACACTCAATTATAATCTAGTTTAACCAAAAACATATAAAAACTCAACTTAA
AATCAATTATAAGACTATAAAACCATTTAAAGAGAGTAATAAGGCTTTTGAAGACTTGGGTGTCT
ATAAAGGGGCTTTTCTTGCCAATGAATGGATTTTTCTTCAGATTTCCCAAGGAAAACACTCAATT
ATAATCTGGTTCAAACAAAAATGTGAAAACATTCAACTTAAAATCAATTCTGAGATTATAAAACT
ATTTAACGAAAGTAACAAGGCTTTTAAAGGCTTGGGTGACTATAAATGGGCTTTTCCTGCCAATG
ACTTCAT
Found at i:7131 original size:170 final size:170
Alignment explanation
Indices: 6289--7138 Score: 650
Period size: 171 Copynumber: 5.0 Consensus size: 170
6279 GGTGACTATA
* * * * * *
6289 AATGGGTTTTTCTTCATCTTTCTCAAGGCAAACATTCAATTATAATCT-ATTCTAACCAAAAATA
1 AATGGCTTTTTCTTCATGTTTCCCAAGGCAAACACTCAATTATAATCTGGTT-TAACCAAAAATG
* * * * * * ***
6353 TAAAAAAATTAAACTTAAACTTAATTATGAGGTTATAAAACCATTTAAAGAGAGTAATAAGGNNN
65 T-AAAACATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGAAAGTAATAAGGCTT
********* * * *
6418 NNNNNNNAATGGGTGACTATAATTGGACTTTT-TGTCCCAATG
129 TTGAAGGCTTGGGTGACTATAAATGGGCTTTTCT-TGCCAATG
* * * * * *
6460 AGTGCCTTTTTCTTGAAGTTTCCTAAGGCAAACACTCAATTATAATCTAGTTTAACCAAAAATGT
1 AATGGCTTTTTCTTCATGTTTCCCAAGGCAAACACTCAATTATAATCTGGTTTAACCAAAAATGT
* * * * *
6525 ATCAAA-ACTCAACTTAAAATCAATTATAAGATTCTAAAACCATTTAAAGATAGTTATAAGGCTT
66 A--AAACATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGAAAGTAATAAGGCTT
* *
6589 TTGAAGACTTGGGTGTCTATAAATGGGCTTTTCTTGCCAATG
129 TTGAAGGCTTGGGTGACTATAAATGGGCTTTTCTTGCCAATG
* * * * * *
6631 AATGGCTTTTTCTTCA-GATTTCCCAAGGAAAACATTCAATTATATTCTGTTTTAAACAAAAANN
1 AATGGCTTTTTCTTCATG-TTTCCCAAGGCAAACACTCAATTATAATCTGGTTTAACCAAAAA-T
******** * * * * ** *
6695 NNNNNNNNTTCAACTTAAAATCAATTTTGAGGTTATAAAACTATTTAAGGAGTGTAACAAGGCTT
64 GTAAAACATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGAAAGTAATAAGGCTT
* * *
6760 TTAAAGGCTTTGGTGACTATAAATGGGCTTTTCCTGCCAATG
129 TTGAAGGCTTGGGTGACTATAAATGGGCTTTTCTTGCCAATG
*********** * * * * **
6802 ACNNNNNNNNNNTTCATGTTTCCAAAGGTAAACATTCAATTATAATCTGTTTTAACCAAAAACAT
1 AATGGCTTTTTCTTCATGTTTCCCAAGGCAAACACTCAATTATAATCTGGTTTAACCAAAAATGT
* *
6867 AAAACAATTCAACTTAAAATCAATTATGAGACTATAAAACCATTTAAAG-AGGATAATAAGGCTT
66 AAAAC-ATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGAAAG-TAATAAGGCTT
********** *
6931 TTGAAGGCTTGGNNNNNNNNNNAGGGGC-TTTCTTGCCAATG
129 TTGAAGGCTTGGGTGACTATAAATGGGCTTTTCTTGCCAATG
* * **
6972 AATGGATTTTTCTTCATGTTTCCCAAGGCAAACACTCAATTATAATCTGGTTCAATGAAAAATGT
1 AATGGCTTTTTCTTCATGTTTCCCAAGGCAAACACTCAATTATAATCTGGTTTAACCAAAAATGT
* ** *
7037 GAAAACATTCAACTTAAAATCAATTCTGAGATTATAAAATTATTTAACGAAAGTAATAAGGCTTT
66 -AAAACATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGAAAGTAATAAGGCTTT
7102 TGAAGGCTTGGGTGACTATAAATGGGCTTTTCTTGCC
130 TGAAGGCTTGGGTGACTATAAATGGGCTTTTCTTGCC
7139 NNNNNNNNNN
Statistics
Matches: 513, Mismatches: 153, Indels: 26
0.74 0.22 0.04
Matches are distributed among these distances:
170 126 0.25
171 380 0.74
172 7 0.01
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.32
Consensus pattern (170 bp):
AATGGCTTTTTCTTCATGTTTCCCAAGGCAAACACTCAATTATAATCTGGTTTAACCAAAAATGT
AAAACATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGAAAGTAATAAGGCTTTT
GAAGGCTTGGGTGACTATAAATGGGCTTTTCTTGCCAATG
Found at i:8046 original size:172 final size:171
Alignment explanation
Indices: 7624--8191 Score: 675
Period size: 172 Copynumber: 3.3 Consensus size: 171
7614 NNNNNNNNAT
* * * ** * ** *
7624 ATTATAATTGAATGTTAGCCTT-GAGAAACATA-AAGAAAAATCCATTTGTTTGCATTAAAAG-T
1 ATTATAATTAAATGTTTG-CTTCGAGAAACA-AGAAGAAAAACCCATTCATTGGCAAGAAAAGCC
* * * * * *
7686 CATTTATAGTCACCCAAGCCTTCAATAGCCTTATTACTCTCTTTAAATAGTTTTATAATCTCATA
64 CATTTATAGTCACCCAAGCCTTCAAAAGCCCTATTACTCACTTTAAATGGTTTTATAGTCCCATA
*
7751 ATTGATTTTAAGTTGAATGTTTTTATATTTTTAGTTAAAACAG
129 ATTGATTTTAAGTTGAATGTTTTTACATTTTTAGTTAAAACAG
* * ** * *
7794 ATTATAATTAAATGTTTGCCTTTG-GAAACATGAAGAAAAACATATTTATTGGAAAGAAAAGCCC
1 ATTATAATTAAATGTTTG-CTTCGAGAAACAAGAAGAAAAACCCATTCATTGGCAAGAAAAGCCC
*
7858 ATTTATAGTCACCCAAGCCTTCAAAAGCCCTATTACTCACTTTAAATGGTTTTATAGT-GCATTA
65 ATTTATAGTCACCCAAGCCTTCAAAAGCCCTATTACTCACTTTAAATGGTTTTATAGTCCCA-TA
* * *
7922 ATTGATTTTAAGCTGAATAGTTTTTACATTTTTAGTTCAAACAA
129 ATTGATTTTAAGTTGAAT-GTTTTTACATTTTTAGTTAAAACAG
* * *
7966 ATTATAATTGAATGTTTGCGTCGAGAAACAAGAAGAGAAACCCATTCATTGGCAAGAAAAGCCCA
1 ATTATAATTAAATGTTTGCTTCGAGAAACAAGAAGAAAAACCCATTCATTGGCAAGAAAAGCCCA
* *
8031 TTTATAGTCACCCAAGCCTTCGAAAGCCCTATTACTCACTTTAAATGGTTTTGTAGTCCCATAAT
66 TTTATAGTCACCCAAGCCTTCAAAAGCCCTATTACTCACTTTAAATGGTTTTATAGTCCCATAAT
*
8096 T-ATTTTTACGTTGAATGGTTTTTACATTCTTT-GTTAAAACAG
131 TGA-TTTTAAGTTGAAT-GTTTTTACATT-TTTAGTTAAAACAG
* * * *
8138 ATTGTAATTAAATGTTTTCTTTC-AGAAACATGAAGGAAAACCCATTCATTGGCA
1 ATTATAATTAAATGTTTGC-TTCGAGAAACAAGAAGAAAAACCCATTCATTGGCA
8192 CCCAAACATT
Statistics
Matches: 342, Mismatches: 46, Indels: 18
0.84 0.11 0.04
Matches are distributed among these distances:
170 49 0.14
171 78 0.23
172 208 0.61
173 7 0.02
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.36
Consensus pattern (171 bp):
ATTATAATTAAATGTTTGCTTCGAGAAACAAGAAGAAAAACCCATTCATTGGCAAGAAAAGCCCA
TTTATAGTCACCCAAGCCTTCAAAAGCCCTATTACTCACTTTAAATGGTTTTATAGTCCCATAAT
TGATTTTAAGTTGAATGTTTTTACATTTTTAGTTAAAACAG
Found at i:8906 original size:171 final size:171
Alignment explanation
Indices: 8345--9373 Score: 1166
Period size: 172 Copynumber: 6.1 Consensus size: 171
8335 TAGTTACCCC
* * *** * * * *
8345 AGCCTTATTACTCTCTTTAAACGATTTTATTGCCTTAAAATTGATTTTAAGTTTAATTGTTTTCA
1 AGCCTTATTACTCTCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATT-TTTTTA
* * ** * * *
8410 -ATTTTTGGTTAAAACGGATTATAATTGAATGTTTGCCTTGGGAAACATTAAGAAACACTCATTC
65 TATTTTTGGTTAAAACAGATTATAATTGAATGTTTACCTTTAGAAACATGAAGAAAAACACATTC
** * *
8474 ATTGGCTTGAAAAGCCCATTTATAGTCACCAAAGCTTTCAAA
130 ATTGGCAAGAAAAGCCCATTTATAGTCACCCAAGCCTTCAAA
* *
8516 AGCCTTATTACTCTCTTTAAATGGTTTTACAATCTCATAATTGAATTTAAGTTGAATTTGTTTTA
1 AGCCTTATTACTCTCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTT-TTTTA
* * *
8581 TATTTTTTGTTAAAACAGATTATCATTGAATGTTTACCTTTGGAAACATGAAGAAAAACACATTC
65 TATTTTTGGTTAAAACAGATTATAATTGAATGTTTACCTTTAGAAACATGAAGAAAAACACATTC
* * *
8646 ATTAGCAAGAAGAGCCCATTTATAGCCACCCAAGCCTTCAAA
130 ATTGGCAAGAAAAGCCCATTTATAGTCACCCAAGCCTTCAAA
* * * * *
8688 AGCCTTATTACT-TACTTTAAATGGTTTTGTAGTCTCATAAATGATTTTAAGCTGAATGGTTTTT
1 AGCCTTATTACTCT-CTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAAT-TTTTTT
** * * *
8752 ATATTTTTAATTAAAACAGATTATAATTGAATGTTTACCTTTAAAAACATGAAG-AAGACGCATT
64 ATATTTTTGGTTAAAACAGATTATAATTGAATGTTTACCTTTAGAAACATGAAGAAAAACACATT
** * *
8816 CATTCTCAAGAAAAGCCCATTTATAGTCACCCAAGCATTCAAT
129 CATTGGCAAGAAAAGCCCATTTATAGTCACCCAAGCCTTCAAA
* * *
8859 AGCCTTATTAGTCTCTTTAAATGGTTTTATAATCTCATAATTGATTTT-AGTTG-TTTTTTTTAC
1 AGCCTTATTACTCTCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTAT
* * * * *
8922 ATTTTTGGTTAAAACATATTATAATTGAATGTTTTCCTTTGGAAACATAAAGCAAAACACATTCA
66 ATTTTTGGTTAAAACAGATTATAATTGAATGTTTACCTTTAGAAACATGAAGAAAAACACATTCA
* * * **
8987 TTGGCCAGAAAGGCCCATTTACAGTCACCCAAGCCTTTGAA
131 TTGGCAAGAAAAGCCCATTTATAGTCACCCAAGCCTTCAAA
* * *
9028 AGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTAATTTTAAGTT-AAGTTTTTTGA
1 AGCCTTATTACTCTCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAA-TTTTTTTA
* * * * * *
9092 AATTTTTGGTTAAAACATATTATAATTGAGTGTTTCCCTTGAGAAACAT---GAAAAACCCATTC
65 TATTTTTGGTTAAAACAGATTATAATTGAATGTTTACCTTTAGAAACATGAAGAAAAACACATTC
9154 ATTGGCAAGAAAAGCCCATTTATAGTCACCCAAGCCTTCAAA
130 ATTGGCAAGAAAAGCCCATTTATAGTCACCCAAGCCTTCAAA
** * * *
9196 AGATTTATTACTCTCTTTAAATGGTTTTATAACCTCAAAATTGGTTTTAAGTTGAATTTTTTTAT
1 AGCCTTATTACTCTCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTAT
* * * * * * * **
9261 -CTTTTGGTTAAAAAAGATTATAATTGAATGTTTTCCTGGGTA-AACCA-GATGATAAAGTCATT
66 ATTTTTGGTTAAAACAGATTATAATTGAATGTTTACCT--TTAGAAACATGAAGAAAAACACATT
** * *
9323 CATTTTCAAGAAAAGCCTA-TTATAGTCACTCAAGCCTTCAAA
129 CATTGGCAAGAAAAGCCCATTTATAGTCACCCAAGCCTTCAAA
9365 AGCCTTATT
1 AGCCTTATT
9374 NNNNNNNNNN
Statistics
Matches: 728, Mismatches: 115, Indels: 32
0.83 0.13 0.04
Matches are distributed among these distances:
167 32 0.04
168 156 0.21
169 120 0.16
170 34 0.05
171 191 0.26
172 194 0.27
173 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (171 bp):
AGCCTTATTACTCTCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTAT
ATTTTTGGTTAAAACAGATTATAATTGAATGTTTACCTTTAGAAACATGAAGAAAAACACATTCA
TTGGCAAGAAAAGCCCATTTATAGTCACCCAAGCCTTCAAA
Found at i:14261 original size:170 final size:168
Alignment explanation
Indices: 13902--14548 Score: 548
Period size: 170 Copynumber: 3.8 Consensus size: 168
13892 NNNTTAAAGG
*
13902 CTTGGGTGACTATAAATGGGCTTTTCTTGCCAATGAATGGGTTTTTTCTTCATGTTTCTCC-AGG
1 CTTGGGTGACTATAAATGGGCTTTTCTTGTCAAT-AATGGG-TTTTTCTTCATGTTTC-CCAAGG
* *** * * * * * *
13966 AAAACCCACATTTATAATTTGTTTTAACCAAAAATGTAAAAAAAAACTAAACTTAAAATCAATTA
63 CAAACATTCAATTATAATCTGTTTTAA-CAAAAA-ATATAAAAAAATTCAA-TTAAAATCAATT-
*** * * * *******
14031 TGCGATTTTAAAACCATTTAAAGCA-AGTAATAAGGCTTNNNNNNN
124 TTAAAGTATAAAACCATTTAAA-AAGAGTAATAAGGCTTTTGAAAA
**** * * * * * * * ** *
14076 NNNAGGTGGCTATAAATAGACTTTTCTTGCCAATAAAGGGCCTTTTCTTCAGGTTTACTGAA-GA
1 CTTGGGTGACTATAAATGGGCTTTTCTTGTCAATAATGGG-TTTTTCTTCATGTTT-CCCAAGGC
*
14140 AAACATTCAATTATAATCTGTTTAAACAAAAAATATAAAAAAATTCAAGTT-AAATCAATTTTAA
64 AAACATTCAATTATAATCTGTTTTAACAAAAAATATAAAAAAATTCAA-TTAAAATCAATTTTAA
* * * *
14204 AGCTATAAAATCGTTTAAAGAGAGTAATAAGGCTTTTGAAAG
128 AG-TATAAAACCATTTAAAAAGAGTAATAAGGCTTTTGAAAA
* *
14246 CTTGGGTGACTATAAATGGGCTTTTCTCGTCAACGAATGGGTTTTTCTTCATGTTTCCCAAGGCA
1 CTTGGGTGACTATAAATGGGCTTTTCTTGTCAA-TAATGGGTTTTTCTTCATGTTTCCCAAGGCA
* * * * * * * *
14311 AACATTCAATTACAATCTTTTTTAACAACAAATATGAAAAAATCCAATATAAAATAAATTATGAG
65 AACATTCAATTATAATCTGTTTTAACAAAAAATATAAAAAAATTCAAT-TAAAATCAATT-TTAA
14376 AGTATAAAACCATTTAAAAAGAGTAATAAGGCTTTTGAAAA
128 AGTATAAAACCATTTAAAAAGAGTAATAAGGCTTTTGAAAA
* * * *
14417 CTTGGGTGATTATAAATGGGCTTTT-TTATCACTGAATGGGTTTTTCTTTATGTTTCCCAAGGCA
1 CTTGGGTGACTATAAATGGGCTTTTCTTGTCAAT-AATGGGTTTTTCTTCATGTTTCCCAAGGCA
* * * * *
14481 AAGATTCAATTATAATCTGTTTTAACCAAAAATGTTAAAAAATTCAACTTAAAATCAATTATAAA
65 AACATTCAATTATAATCTGTTTTAACAAAAAATATAAAAAAATTCAA-TTAAAATCAATTTTAAA
14546 GTA
129 GTA
14549 ATAAGGCTTT
Statistics
Matches: 376, Mismatches: 86, Indels: 27
0.77 0.18 0.06
Matches are distributed among these distances:
169 12 0.03
170 198 0.53
171 87 0.23
172 10 0.03
173 40 0.11
174 29 0.08
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.34
Consensus pattern (168 bp):
CTTGGGTGACTATAAATGGGCTTTTCTTGTCAATAATGGGTTTTTCTTCATGTTTCCCAAGGCAA
ACATTCAATTATAATCTGTTTTAACAAAAAATATAAAAAAATTCAATTAAAATCAATTTTAAAGT
ATAAAACCATTTAAAAAGAGTAATAAGGCTTTTGAAAA
Found at i:14573 original size:148 final size:149
Alignment explanation
Indices: 14397--14691 Score: 484
Period size: 149 Copynumber: 2.0 Consensus size: 149
14387 ATTTAAAAAG
* * *
14397 AGTAATAAGGCTTTTGAAAACTTGGGTGATTATAAATGGGCTTTT-TTATCACTGAATGGGTTTT
1 AGTAATAAGGCTTTTGAAAACTTGGGTGACTATAAATGGGCTTTTCTTATCAATGAATGAGTTTT
* * *
14461 TCTTTATGTTTCCCAAGGCAAAGATTCAATTATAATCTGTTTTAACCAAAAATGTTAAAAAATTC
66 TCTTCATGTTTCCCAAGGCAAACATTCAATTATAATCTGTTTTAACCAAAAATGTGAAAAAATTC
14526 AACTTAAAATCAATTATAA
131 AACTTAAAATCAATTATAA
** *
14545 AGTAATAAGGCTTTTGAAGGCTTGGGTGACTATAAATGGGCTTTTCTTGTCAATGAATGAGTTTT
1 AGTAATAAGGCTTTTGAAAACTTGGGTGACTATAAATGGGCTTTTCTTATCAATGAATGAGTTTT
* *
14610 TCTTCATTTTTCCCAAGGTAAACATTCAATTATAATCTGTTTTAACCAAAAATGTGAAAAAATTC
66 TCTTCATGTTTCCCAAGGCAAACATTCAATTATAATCTGTTTTAACCAAAAATGTGAAAAAATTC
14675 AACTTAAAATCAATTAT
131 AACTTAAAATCAATTAT
14692 TAGATTATAA
Statistics
Matches: 135, Mismatches: 11, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
148 42 0.31
149 93 0.69
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.38
Consensus pattern (149 bp):
AGTAATAAGGCTTTTGAAAACTTGGGTGACTATAAATGGGCTTTTCTTATCAATGAATGAGTTTT
TCTTCATGTTTCCCAAGGCAAACATTCAATTATAATCTGTTTTAACCAAAAATGTGAAAAAATTC
AACTTAAAATCAATTATAA
Found at i:14834 original size:171 final size:170
Alignment explanation
Indices: 14545--15052 Score: 651
Period size: 172 Copynumber: 3.0 Consensus size: 170
14535 TCAATTATAA
*
14545 AGTAATAAGGCTTTTGAAGGCTTGGGTGACTATAAATGGGCTTTTCTTGTCAATGAATGAGTTTT
1 AGTAATAAGGCTTTTGAAGGCTTGGGTGACTATAAATGGGCTTTTCTTGTCAATGAATGGGTTTT
*
14610 TCTTCAT-TTTTCCCAAGGTAAACATTCAATTATAATCTGTTTTAACCAAAAATGTGAAAAAATT
66 TCTTCATGTTTT-CCAAGGTAAACATTCAATTATAATCTGTTTTAACTAAAAATGT-AAAAAATT
* *
14674 CAACTTAAAATCAATTATTAGATTATAAAACCATTTAAAGCG
129 CAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAACG
* * **
14716 AGTAATAAGGCTTTTGTAGGATTGGGTGACTATAAATGGGCTTTTCTTGAGAATGAATGGGTTTT
1 AGTAATAAGGCTTTTGAAGGCTTGGGTGACTATAAATGGGCTTTTCTTGTCAATGAATGGGTTTT
* * *
14781 TCTTCATGTTTTTCAAGGTAAACATTTAATTATAATCTGTTTTAACTAAAAATGTAAAAAGCCTT
66 TCTTCATGTTTTCCAAGGTAAACATTCAATTATAATCTGTTTTAACTAAAAATGTAAAAA--ATT
* * * * * * *
14846 CAGCTTAAAAT-ACTTTATGGGACTACAAAACTATTTAAAATG
129 CAACTTAAAATCA-ATTATGAGATTATAAAACCATTTAAAACG
* * * * *
14888 AGTAATAAGGCTTTTAAAGGCTTGGGTGACTATCAATGGGCTTTTCTTCTCAATAAATGGCTTTT
1 AGTAATAAGGCTTTTGAAGGCTTGGGTGACTATAAATGGGCTTTTCTTGTCAATGAATGGGTTTT
* * * * * * * *
14953 TCTTCATGTTTCCCAATGCAAACATTCAATTACAATCTGTTTTAACTAAAAACGTAAGTAAGTTG
66 TCTTCATGTTTTCCAAGGTAAACATTCAATTATAATCTGTTTTAACTAAAAATGTAA-AAAATTC
* *
15018 AACTTAATATCAATTATGAGGTTATAAAACCATTT
130 AACTTAAAATCAATTATGAGATTATAAAACCATTT
15053 NNNNNNNNNN
Statistics
Matches: 286, Mismatches: 45, Indels: 12
0.83 0.13 0.03
Matches are distributed among these distances:
170 5 0.02
171 135 0.47
172 144 0.50
173 2 0.01
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (170 bp):
AGTAATAAGGCTTTTGAAGGCTTGGGTGACTATAAATGGGCTTTTCTTGTCAATGAATGGGTTTT
TCTTCATGTTTTCCAAGGTAAACATTCAATTATAATCTGTTTTAACTAAAAATGTAAAAAATTCA
ACTTAAAATCAATTATGAGATTATAAAACCATTTAAAACG
Found at i:15525 original size:172 final size:169
Alignment explanation
Indices: 15229--15804 Score: 757
Period size: 172 Copynumber: 3.4 Consensus size: 169
15219 NNNNNNNNNN
* * * * * *
15229 AAAATATAAAAAAATTCAACTTAAAATCAATTTTGAGGTTATAAAATCATTTAAATATACTAATA
1 AAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGAGAGTAATA
* *
15294 AGTCTTTTC-AAGGCTTGGATGACTATAAATGGGCTTTTCTTGCCAATGAATGGGTTTTTCTTCA
66 AGGC-TTTCGAAGGCTTGGATGACTATAAATGGGCTTTTCTTGCCAATAAAT-GGTTTTTCTTCA
*
15358 TGTTTCTCAAGGTAAACACTCAATTATAATCTGTTTTAACTA
129 TGTTTCTCAAGGTAAACATTCAATTATAATCTGTTTTAAC-A
* * * *
15400 AAAATATAAAAAAAACTT-AACTTAAAATTAATTATGAGATTATAAAATCATTAAAAGCGAGTAA
1 AAAATAT-AAAAAAA-TTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGAGAGTAA
*
15464 TAAGGCTTTCGAAGGCTTGGATGACTATAAATGGGCTTCTCTTGCCAATAAATGCGTTTTTCTTC
64 TAAGGCTTTCGAAGGCTTGGATGACTATAAATGGGCTTTTCTTGCCAATAAATG-GTTTTTCTTC
* *
15529 ATGTTT-TCAAAGGTAAACATTTAATTATAATCTATTTTAACCA
128 ATGTTTCTC-AAGGTAAACATTCAATTATAATCTGTTTTAA-CA
* *
15572 AAAATATAAAAAAAATTCACCTTAAAATCAATTATGATATTATAAAACCATTTAAAGA-ATGTAA
1 AAAATAT-AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGAGA-GTAA
* * * * *
15636 TAAGGCTTTTGAAGGCTTGGGTGACTATAAATGAGCTTTTCTTGCCAATAAATGGGTTTTCTTCT
64 TAAGGCTTTCGAAGGCTTGGATGACTATAAATGGGCTTTTCTTGCCAATAAATGGTTTTTCTTCA
* * *
15701 TGTTTCCCAAGGTAAATATTCAATTAAAATCTGTTTTAACA
129 TGTTTCTCAAGGTAAACATTCAATTATAATCTGTTTTAACA
* *
15742 AAAA-ATGAGAAAACATTCAACCTAAAATCAATTATGAGATTATAAAACCATTTAAAGAGAGTA
1 AAAATAT-A-AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGAGAGTA
15805 NNNNNNNNNN
Statistics
Matches: 358, Mismatches: 36, Indels: 23
0.86 0.09 0.06
Matches are distributed among these distances:
169 3 0.01
170 54 0.15
171 59 0.16
172 239 0.67
173 3 0.01
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (169 bp):
AAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGAGAGTAATA
AGGCTTTCGAAGGCTTGGATGACTATAAATGGGCTTTTCTTGCCAATAAATGGTTTTTCTTCATG
TTTCTCAAGGTAAACATTCAATTATAATCTGTTTTAACA
Found at i:16454 original size:171 final size:171
Alignment explanation
Indices: 16121--16462 Score: 389
Period size: 171 Copynumber: 2.0 Consensus size: 171
16111 NNNNNNNNNN
* * * *
16121 GTGACTATAAATGGGCTTTTCTTGCCAATGAATAGGTTTTTCTTCATGTTTCCCGAGGAATATAT
1 GTGACTATAAATGGGCTTTTCTTGCCAATGAATAGGTTTTTCTTCATCTTTCCCAAGGAAAACAT
* * ** * *
16186 TCAATAATAATCTGTTTTAATTAAAAATGTTAAAACATTCAACTTAAAATCAATTATGAGATTAT
66 TCAATAATAATATGTTCTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTAT
********** * *
16251 AAAACNNNNNNNNNNGAGTGATAAGACTTTTGAAGGCTTGG
131 AAAACTATTTAAATGGAGTAATAAGACTTTTGAAGGATTGG
* * * *
16292 GTGACTATAAATGGGTTTTTCTTGTCAATGAATTA-GTTTTTCTTCATCTTTCCTAATGAAAACA
1 GTGACTATAAATGGGCTTTTCTTGCCAATGAA-TAGGTTTTTCTTCATCTTTCCCAAGGAAAACA
* * *
16356 TTCAATTATAATATGTTCTAACCAAAAATGTAAAAAAATTCAACTTAAACTCAATTATGAGGTTA
65 TTCAATAATAATATGTTCTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTA
* *
16421 TAAAACTATTTAAATGGCGTAATAAGGCTTTTGAAGGATTGG
130 TAAAACTATTTAAATGGAGTAATAAGACTTTTGAAGGATTGG
16463 NNNNNNNNNN
Statistics
Matches: 139, Mismatches: 31, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
171 137 0.99
172 2 0.01
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.36
Consensus pattern (171 bp):
GTGACTATAAATGGGCTTTTCTTGCCAATGAATAGGTTTTTCTTCATCTTTCCCAAGGAAAACAT
TCAATAATAATATGTTCTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTAT
AAAACTATTTAAATGGAGTAATAAGACTTTTGAAGGATTGG
Found at i:17795 original size:171 final size:172
Alignment explanation
Indices: 17433--17882 Score: 435
Period size: 171 Copynumber: 2.6 Consensus size: 172
17423 GTAAAAAACC
* * * *
17433 TTAACTTAAAATCAATTATGAGATTATAAAACTATTTAA--AACGAGTACTAAGGCTTTTGAAGG
1 TTAACCTAAAATCAATTATGAGATTATAAAATTATTTAACCAA--AGTAATAAGCCTTTTGAAGG
** ********** * ** *
17496 CTTGGGTGGCTATAAANNNNNNNNNNTTGCCAATAAATGCATTTTCCTTCATGTTTCGAAAGGTA
64 CTTGGGTAACTATAAATGGGCTTTTCTTGCCAATGAATGGGTTTTCCTTCATGTTTCCAAAGGTA
* * *
17561 AACATTCAATTATAATCTGTTTTAACAAAAAATATAATAAAAAT
129 AACATTCAATTAAAATCTGTTTCAACAAAAAATATAAGAAAAAT
* * ********** * *
17605 TTAACTTAAAATCAATTATGATATTATAAAANNNNNNNNNNAATGTAATAAGGCTTTTGAAGGCT
1 TTAACCTAAAATCAATTATGAGATTATAAAATTATTTAACCAAAGTAATAAGCCTTTTGAAGGCT
* *
17670 TGGGTAATTATAAATGAGG-TTTTCTTGCCAATGAATGGGTTTT-CTTCATGTTTCCCAAGGTAA
66 TGGGTAACTATAAATG-GGCTTTTCTTGCCAATGAATGGGTTTTCCTTCATGTTTCCAAAGGTAA
* * *
17733 ATATTCAATTAAAATCTGTTTCAACAAAAAACTAT-GGAAACAT
130 ACATTCAATTAAAATCTGTTTCAACAAAAAA-TATAAGAAAAAT
17776 TCT-ACCTAAAATCAATTATGAGATTATAAAATTATTTAACCAAAGTAATAAGCCTTTTGAAGGC
1 T-TAACCTAAAATCAATTATGAGATTATAAAATTATTTAACCAAAGTAATAAGCCTTTTGAAGGC
17840 TTGGGTAACTATAAATGGGCTTTTCTTGCCAATGAATGGGTTT
65 TTGGGTAACTATAAATGGGCTTTTCTTGCCAATGAATGGGTTT
17883 NNNNNNNNNN
Statistics
Matches: 223, Mismatches: 49, Indels: 13
0.78 0.17 0.05
Matches are distributed among these distances:
170 2 0.01
171 138 0.62
172 81 0.36
174 2 0.01
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.34
Consensus pattern (172 bp):
TTAACCTAAAATCAATTATGAGATTATAAAATTATTTAACCAAAGTAATAAGCCTTTTGAAGGCT
TGGGTAACTATAAATGGGCTTTTCTTGCCAATGAATGGGTTTTCCTTCATGTTTCCAAAGGTAAA
CATTCAATTAAAATCTGTTTCAACAAAAAATATAAGAAAAAT
Found at i:18803 original size:170 final size:157
Alignment explanation
Indices: 18599--19180 Score: 412
Period size: 172 Copynumber: 3.4 Consensus size: 157
18589 CAATTATGAG
* *
18599 GTAATAAGGGTTTTGAAGGCTTGAGTGACTATAAATGGGCTTTTCTTGGCAATGAATGAGTTTTT
1 GTAATAAGGCTTTTGAAGGCTTG-GTGACTATAAATGGGCTTTTCTTGG-AATGAATGGGTTTTT
* * *
18664 CTTTATGTTTCCCAAGGCAAACATTCAATTATAATCTATTTTAACCAAAAAATGTGAAAATTCAA
64 CTTCATGTTTTCCAAGGCAAACATTCAATTATAATCT-TTTTAA-CTAAAAATGTGAAAATTCAA
* * * *
18729 CATAAAATCAATTATGAAATTATAANNNNNNNNNNAGCAA
127 CATAAAATCAATTATGAAACTACAA---------AAACAA
*
18769 GTAATAAGGCTTTTGAAGGCTTCGGTGACTATAAATGGACTTTTCTTGAGAATGAATGGGTTTGT
1 GTAATAAGGCTTTTGAAGGCTT-GGTGACTATAAATGGGCTTTTCTTG-GAATGAATGGGTTT-T
* * * * *
18834 T-TTCATGTTTTTCAAGACAAACATTCAAGTATAATCTGCTTTAACTAAAAATGTAAAAGCCATT
63 TCTTCATGTTTTCCAAGGCAAACATTCAATTATAATCT-TTTTAACTAAAAATGTGAAA---ATT
* * * ** * *
18898 CAGCTTAAAATCATTTATGGGACTACANNNNNNNNNNAAACGA
124 CAACATAAAATCAATTATGAAACTACA---------AAAACAA
* *
18941 GTAATAAGGCTTTTCAAGGCTTGGGTGACTATAAATGGGCTTTTCTTGTAAATGAATGGGTTTTT
1 GTAATAAGGCTTTTGAAGGCTT-GGTGACTATAAATGGGCTTTTCTTG-GAATGAATGGGTTTTT
*
19006 CTTCATGTTTTCCAAGGTAAACATTCAATTATAATCTTTTGTAACTAAAAATGTGAAAAAATTCA
64 CTTCATGTTTTCCAAGGCAAACATTCAATTATAATCTTTT-TAACTAAAAATGTG--AAAATTCA
* *** * ** *
19071 ACTTAAANNNNNNNNNNAGATTATAAAACCATTTAAAAA-GA
126 ACATAAA-------ATCA-ATTATGAAA-C-TACAAAAACAA
* * *
19112 GTAATAAGACTTTTGAAGGCTTGGGTGACTATAAATGGACTTTTCTTGCAAATGAATGGGTTTTT
1 GTAATAAGGCTTTTGAAGGCTT-GGTGACTATAAATGGGCTTTTCTTG-GAATGAATGGGTTTTT
19177 CTTC
64 CTTC
19181 NNNNNNNNNN
Statistics
Matches: 334, Mismatches: 49, Indels: 57
0.76 0.11 0.13
Matches are distributed among these distances:
169 12 0.04
170 92 0.28
171 86 0.26
172 132 0.40
174 3 0.01
178 1 0.00
179 5 0.01
180 1 0.00
181 2 0.01
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.34
Consensus pattern (157 bp):
GTAATAAGGCTTTTGAAGGCTTGGTGACTATAAATGGGCTTTTCTTGGAATGAATGGGTTTTTCT
TCATGTTTTCCAAGGCAAACATTCAATTATAATCTTTTTAACTAAAAATGTGAAAATTCAACATA
AAATCAATTATGAAACTACAAAAACAA
Done.