Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018402960.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_621.0, 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: 21525
ACGTcount: A:0.22, C:0.07, G:0.07, T:0.22
Warning! 8898 characters in sequence are not A, C, G, or T
Found at i:1465 original size:20 final size:20
Alignment explanation
Indices: 1418--1468 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
1408 NGTTTAACTT
*
1418 AAAACTAATTATGAGATTAA
1 AAAACTATTTATGAGATTAA
*
1438 AAAACTATTTATGGGATTAA
1 AAAACTATTTATGAGATTAA
1458 AAAACTATTTA
1 AAAACTATTTA
1469 AAGCGAGTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.51, C:0.06, G:0.10, T:0.33
Consensus pattern (20 bp):
AAAACTATTTATGAGATTAA
Found at i:2799 original size:171 final size:170
Alignment explanation
Indices: 2394--2805 Score: 445
Period size: 171 Copynumber: 2.4 Consensus size: 170
2384 NNNNNNNNNN
* * * * *
2394 AGTAATAAAGCTTTTGAAGGCATCGGTGACTATAAATGTAGTTTTCTTGCTAATTGGTATCTTTT
1 AGTAATAAGGCTTTTGAAGGCATCGGTGACTAGAAATGAACTTTTCTTGC-AAATGGTATCTTTT
* *
2459 TCTTCACGTTTCTGAAGACAAACATTCAATTATAATTAGTTTTAATAAAAAATATAAAGAAATTA
65 TCTTCACGTTTCTCAAGACAAACATGCAATTATAATTAGTTTTAATAAAAAATATAAAGAAATTA
* * * *
2524 AAATTAAAATCATTTATGAGGTTATAAAATCATTTAAAGCG
130 AAATTAAAACCAATTATGAGGTTAAAAAATCATTTAAAGCA
* ********** *
2565 AGTACTAAGGCTTTTGAAGGCATCGGTGACTANNNNNNNNNNTTTCTTGCTAATGGGTATCTTTT
1 AGTAATAAGGCTTTTGAAGGCATCGGTGACTAGAAATGAACTTTTCTTGCAAAT-GGTATCTTTT
* * *
2630 TCTTCACGTTTCTCTAGATAAACATGCAATTATAATTTA-TTTTAATAATAAATATAAA-AAATT
65 TCTTCACGTTTCTCAAGACAAACATGCAATTATAA-TTAGTTTTAATAAAAAATATAAAGAAA-T
* *
2693 TGAACTTAAAACCAATTATG-GGATTAAAAAA-CTATTTAAAGCA
128 TAAAATTAAAACCAATTATGAGG-TTAAAAAATC-ATTTAAAGCA
** * *
2736 AGTAATAAGGCTTTCAAAGGCATGGGTGACTAGAAATGAACTTTTCTTACAAATGGATATCTTTT
1 AGTAATAAGGCTTTTGAAGGCATCGGTGACTAGAAATGAACTTTTCTTGCAAATGG-TATCTTTT
2801 TCTTC
65 TCTTC
2806 NNNNNNNNNN
Statistics
Matches: 194, Mismatches: 41, Indels: 12
0.79 0.17 0.05
Matches are distributed among these distances:
170 10 0.05
171 181 0.93
172 3 0.02
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.36
Consensus pattern (170 bp):
AGTAATAAGGCTTTTGAAGGCATCGGTGACTAGAAATGAACTTTTCTTGCAAATGGTATCTTTTT
CTTCACGTTTCTCAAGACAAACATGCAATTATAATTAGTTTTAATAAAAAATATAAAGAAATTAA
AATTAAAACCAATTATGAGGTTAAAAAATCATTTAAAGCA
Found at i:4670 original size:171 final size:171
Alignment explanation
Indices: 4348--4709 Score: 456
Period size: 171 Copynumber: 2.1 Consensus size: 171
4338 NNNNNNNNNN
* * * * * *
4348 ATGAGGTTATAAAATTATTTAAAGTGAGTAATAAAGCTTTTGAAGGTATGGGTGATTATAAATAG
1 ATGAGGTTATAAAATCATTTAAAGCGACTAATAAAGCTTTTGAAGGTATGGATAACTATAAATAG
* * *
4413 ACTTTTCTTACCAATGGATATCTTTTTCTTTACGTTTCCCAAGACAAACATTCAATTATAATCAN
66 ACTTTTCTTACCAATGGATATCTTTGTCTTCACGTTTCCCAAGACAAACATTCAATTATAATCAG
********* *
4478 NNNNNNNNNAAAATATAAAAAAATTA-AAATTAAAATCATTT
131 TTTTAATAAAAAATATAAAAAAA-TACAAATTAAAATCAATT
*
4519 ATGAGGTTATAAAATCATTTAAAGCGACTAATAAAGCTTTTGAAGGTATGGATAACTATAAATTG
1 ATGAGGTTATAAAATCATTTAAAGCGACTAATAAAGCTTTTGAAGGTATGGATAACTATAAATAG
* * * ** * *
4584 ACTTTTCTTGCCAATGGATATCTTTGTCTTCATGTTTCTCAAGGTAAATATTCAATTATAATCTG
66 ACTTTTCTTACCAATGGATATCTTTGTCTTCACGTTTCCCAAGACAAACATTCAATTATAATCAG
*
4649 TTTTAATAAAAAATTTAAAAAAATACAAATTAAAATCAATT
131 TTTTAATAAAAAATATAAAAAAATACAAATTAAAATCAATT
4690 ATGAGGTTATAAAATCATTT
1 ATGAGGTTATAAAATCATTT
4710 NNNNNNNNNN
Statistics
Matches: 162, Mismatches: 28, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
170 2 0.01
171 160 0.99
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.36
Consensus pattern (171 bp):
ATGAGGTTATAAAATCATTTAAAGCGACTAATAAAGCTTTTGAAGGTATGGATAACTATAAATAG
ACTTTTCTTACCAATGGATATCTTTGTCTTCACGTTTCCCAAGACAAACATTCAATTATAATCAG
TTTTAATAAAAAATATAAAAAAATACAAATTAAAATCAATT
Found at i:10008 original size:171 final size:161
Alignment explanation
Indices: 9796--10109 Score: 322
Period size: 171 Copynumber: 1.9 Consensus size: 161
9786 TTTAATATTA
** * * *
9796 TTATTAAAACAAATTATAATTGTATGCTTATCTCGAGAAACATAAAGAAAAAGATACCCATTACC
1 TTATTAAAACAAATTATAATTAAATGCTTACCTCAAGAAACATAAAGAAAAAGATACCCAATACC
* * * *
9861 AAGAAAAGTGCATTTATAGTCACCGATGCCTTCAAAAACCTTATTACTCGCTTTAAATGATTTTA
66 AAGAAAAGTGAATTTATAGTCACCCATGCCTTCAAAAACCTTACTACTCACTTTAAATGATTTTA
9926 TAACCTCATANNNNNNNNNNATTTAGATTTTTTTAAATTTT
131 TAACCTCATA----------ATTTAGATTTTTTTAAATTTT
* * * * * * **
9967 TTATTAAAATAGATTATAATTAAATGTTTACCTCAAGAAACATGAAGAAAAAGATATCTAATGGC
1 TTATTAAAACAAATTATAATTAAATGCTTACCTCAAGAAACATAAAGAAAAAGATACCCAATACC
* * * * * * *
10032 AAGAAACGTTAATTTATAGTCGCCCATGCCTTCAAAAGCTTTACTACTCACTTTGATTGATTTTA
66 AAGAAAAGTGAATTTATAGTCACCCATGCCTTCAAAAACCTTACTACTCACTTTAAATGATTTTA
10097 TAACCTCATAATT
131 TAACCTCATAATT
10110 GATTTTGATT
Statistics
Matches: 119, Mismatches: 24, Indels: 10
0.78 0.16 0.07
Matches are distributed among these distances:
161 3 0.03
171 116 0.97
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.34
Consensus pattern (161 bp):
TTATTAAAACAAATTATAATTAAATGCTTACCTCAAGAAACATAAAGAAAAAGATACCCAATACC
AAGAAAAGTGAATTTATAGTCACCCATGCCTTCAAAAACCTTACTACTCACTTTAAATGATTTTA
TAACCTCATAATTTAGATTTTTTTAAATTTT
Found at i:12883 original size:171 final size:169
Alignment explanation
Indices: 12598--13364 Score: 760
Period size: 171 Copynumber: 4.5 Consensus size: 169
12588 NNNNNNNNNN
*
12598 ACAGATTATAATTGAATGTTTACCTTGAGAAATGTGAAGAAAAAGATATCCATTGGCAAAAAAAG
1 ACAGATTATAATTGAATGTTTACC-TGAGAAATGTGAAGAAAAAGATATCCATTGGCAAGAAAAG
* * * *
12663 TCTATTTATAGTCACCGATGTCTTCAAAAGCCTTATTA-TACGCTTTAAATGATTTTATAACCTT
65 TCTATTTATAGTCACCCATGCCTTCAAAAGCTTTATTACT-CGCTTTAAATGATTTTATAACCTC
* * *
12727 ATAATTGATTTTAAGTTAGATTTTTTTATGTTTTGTATCAAA
129 ATAATTGATTTTAA-TTAGATTTTTTTATATTTTTTATTAAA
* ****
12769 ACAGATTATAATTGAATGTTTACCATGAGAAAGGTGAAGAAAAAGATATCCATTGGCAAGANNNN
1 ACAGATTATAATTGAATGTTTACC-TGAGAAATGTGAAGAAAAAGATATCCATTGGCAAGAAAAG
****** ** * * *
12834 NNNNNNTATAGTCACCCATGCCTTTGAAAGCTTTATTACTTGTTTTAAATGATTTTATAAACTCA
65 TCTATTTATAGTCACCCATGCCTTCAAAAGCTTTATTACTCGCTTTAAATGATTTTATAACCTCA
*
12899 TAATT-A-ATT--TTA-ATTTTTTTATATTTTTTATTAAA
130 TAATTGATTTTAATTAGATTTTTTTATATTTTTTATTAAA
** ********* * ****
12934 ACAGATTGCAATTGAATGTTTNNNNNNNNNNACGTGAAGAAAAAGATATCCATTTATGAGAAAAG
1 ACAGATTATAATTGAATGTTT-ACCTGAGAAATGTGAAGAAAAAGATATCCATTGGCAAGAAAAG
** * * * ** *
12999 TCTATTTATAGTCACTAATGCCTTCAAAAACTTTATTGCTCACTTTAAATGATTTTATAATTTTA
65 TCTATTTATAGTCACCCATGCCTTCAAAAGCTTTATTACTCGCTTTAAATGATTTTATAACCTCA
* *
13064 TAATTGATTTTAATTTGAATTTTTTTATATTTTTTATTACA
130 TAATTGATTTTAATTAG-ATTTTTTTATATTTTTTATTAAA
* ** *
13105 ACAGCTTATAATTGAATGATTGCCTCTGA-AAATGTGAAGAAAAAGATATCCATT-ACTAAGAAA
1 ACAGATTATAATTGAATG-TTTAC-CTGAGAAATGTGAAGAAAAAGATATCCATTGGC-AAGAAA
* * * * * *
13168 AGTCCATTTATAGTCACCCATACCTTTCAAAAGCTTTATAACTGGCTTTAAATGAGTTTACAACC
63 AGTCTATTTATAGTCACCCATGCC-TTCAAAAGCTTTATTACTCGCTTTAAATGATTTTATAACC
*
13233 TCATAATTGATTTTAATTTAGGTTTTTTTATATTTTTTATTAAA
127 TCATAATTGATTTTAA-TTAGATTTTTTTATATTTTTTATTAAA
* * * *
13277 ACAGAGTATAATTGAATGTTTACCTCAAGAAAAGTGAAGAAAAA-AAATCCATTGGCAAGAAAAG
1 ACAGATTATAATTGAATGTTTACCT-GAGAAATGTGAAGAAAAAGATATCCATTGGCAAGAAAAG
*
13341 TCTATTTATAGTCACTCATGCCTT
65 TCTATTTATAGTCACCCATGCCTT
13365 NNNNNNNNNN
Statistics
Matches: 470, Mismatches: 110, Indels: 33
0.77 0.18 0.05
Matches are distributed among these distances:
165 116 0.25
166 4 0.01
167 2 0.00
169 4 0.01
170 6 0.01
171 234 0.50
172 101 0.21
173 3 0.01
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.38
Consensus pattern (169 bp):
ACAGATTATAATTGAATGTTTACCTGAGAAATGTGAAGAAAAAGATATCCATTGGCAAGAAAAGT
CTATTTATAGTCACCCATGCCTTCAAAAGCTTTATTACTCGCTTTAAATGATTTTATAACCTCAT
AATTGATTTTAATTAGATTTTTTTATATTTTTTATTAAA
Found at i:13783 original size:171 final size:170
Alignment explanation
Indices: 13468--14508 Score: 871
Period size: 171 Copynumber: 6.1 Consensus size: 170
13458 NNNNNNNTAG
** * **
13468 AAAAAAATTAAAATTAAAATCAATTACGAGGTTATAAAATCATTTAAAGCGGGTAACAAAGCTTT
1 AAAAAAATCCAAATTAAAATCAATTATGAGGTTATAAAATCATTTAAAGCCAGTAACAAAGCTTT
* * * * * * * * *
13533 TGAAGGCATGAGTGACGATAAATAGACTTTTCTTGCCAATGGATTTTTTTTTCTTTACCTTTCTC
66 TGAAGGCATGGGTGACTATAAATGGACTTTTCTTG-TAATAGATATCTTTTTCTTCACGTTTCTC
*
13598 GAGGTAAACATTCAATTATAATCTGTTTTAATAAAAAATAT
130 GAGGCAAACATTCAATTATAATCTGTTTTAATAAAAAATAT
********** * *
13639 AAAAAANNNNNNNNNNAAATCAATTATGAGGTTATAAAATCATTTAAAGCCAGTTATAAAGCTTT
1 AAAAAAATCCAAATTAAAATCAATTATGAGGTTATAAAATCATTTAAAGCCAGTAACAAAGCTTT
*
13704 TGAAGGTATGGGTGACTATAAATGGACTTTT-TTCAGTAATAGATATCTTTTTCTTCACGTTTCT
66 TGAAGGCATGGGTGACTATAAATGGACTTTTCTT--GTAATAGATATCTTTTTCTTCACGTTTCT
* * * *
13768 CAAGGCAATCATTCAATTATAATTTGTTTTAATGAAAAATAT
129 CGAGGCAAACATTCAATTATAATCTGTTTTAATAAAAAATAT
* * *
13810 AAAAAAATCCAAATTAAAATCAATTATAAGGTTATAAAATCATTTAAAGCGAGTAACAAAGTTTT
1 AAAAAAATCCAAATTAAAATCAATTATGAGGTTATAAAATCATTTAAAGCCAGTAACAAAGCTTT
** * * * * *
13875 TGAAGGCATTAGTGACTATAAATAGACTTTTCTCGTAAATAGATATTTTTTTCTTCATGTTTCTT
66 TGAAGGCATGGGTGACTATAAATGGACTTTTCTTGT-AATAGATATCTTTTTCTTCACGTTTCTC
* *
13940 GAGGCAAATATTCAATTACAATCTG-TTTAATAAAAAATAT
130 GAGGCAAACATTCAATTATAATCTGTTTTAATAAAAAATAT
* * ********** * *
13980 AAAAAAATTCAAATTAAAATCAATTATGAGTTTNNNNNNNNNNTTAAAGCAAGTAATAAAGCTTT
1 AAAAAAATCCAAATTAAAATCAATTATGAGGTTATAAAATCATTTAAAGCCAGTAACAAAGCTTT
** * ** * *
14045 CAAAGGCATGGGTGACTATAAATGGAATTTTCTTACCAATGGGTATCTTTTTCTTCACGTTTCT-
66 TGAAGGCATGGGTGACTATAAATGGACTTTTCTT-GTAATAGATATCTTTTTCTTCACGTTTCTC
* * *
14109 TAAGCTAAACATTCAATTATAATCTGTTTTAATAAAAAATGT
130 GAGGC-AAACATTCAATTATAATCTGTTTTAATAAAAAATAT
* * * ** *
14151 AAAAAAATCTAAATTTAAATCAATTATAAGGTTATAAAA-CTATTTAAAGCGTGTAA-AAGGCTT
1 AAAAAAATCCAAATTAAAATCAATTATGAGGTTATAAAATC-ATTTAAAGCCAGTAACAAAGCTT
* * * * * *
14214 TTGAAGACATAGGTTACT-TAAATGTACTTTTCTTGCTAATTGATATCTTTTTCTTCACATTTCT
65 TTGAAGGCATGGGTGACTATAAATGGACTTTTCTTG-TAATAGATATCTTTTTCTTCACGTTTCT
* * ***
14278 CGAGGTAAACA-TAAACTTATAATCTGTTTTAATTGTAAATAT
129 CGAGGCAAACATTCAA-TTATAATCTGTTTTAATAAAAAATAT
** ** * * ***********
14320 AAAAACGTTTAACTTAAAA-CTAATTATGAGATTGA-AAAA-CTATTTAAAGCGNNNNNNNNNNC
1 AAAAAAATCCAAATTAAAATC-AATTATGAGGTT-ATAAAATC-ATTTAAAGCCAGTAACAAAGC
* * * * * *
14382 TTTCGAAGGTATGGGTGACTAGAAATGGACCTTTCTTACTAATGGATATCTTTTTCTTCACGTTT
63 TTTTGAAGGCATGGGTGACTATAAATGGACTTTTCTT-GTAATAGATATCTTTTTCTTCACGTTT
* * *
14447 CTCAAGG-AAAGCGTTCAATTATAATCTATTTTAATAAAAAATAT
127 CTCGAGGCAAA-CATTCAATTATAATCTGTTTTAATAAAAAATAT
*
14491 AAAAAAATTCAAATTAAA
1 AAAAAAATCCAAATTAAA
14509 NNNNNNNNNN
Statistics
Matches: 684, Mismatches: 168, Indels: 36
0.77 0.19 0.04
Matches are distributed among these distances:
168 4 0.01
169 108 0.16
170 176 0.26
171 391 0.57
172 5 0.01
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.36
Consensus pattern (170 bp):
AAAAAAATCCAAATTAAAATCAATTATGAGGTTATAAAATCATTTAAAGCCAGTAACAAAGCTTT
TGAAGGCATGGGTGACTATAAATGGACTTTTCTTGTAATAGATATCTTTTTCTTCACGTTTCTCG
AGGCAAACATTCAATTATAATCTGTTTTAATAAAAAATAT
Found at i:14466 original size:340 final size:339
Alignment explanation
Indices: 13468--14508 Score: 995
Period size: 341 Copynumber: 3.1 Consensus size: 339
13458 NNNNNNNTAG
** ** *
13468 AAAAAAATTAAAATTAAAATCAATTACGAGGTTATAAAATCATTTAAAGCGGGTAACAAAGCTTT
1 AAAAAAATCCAAATTAAAATCAATTATAAGGTTATAAAATCATTTAAAGCGAGTAACAAAGCTTT
* * * * ** * * * * *
13533 TGAAGGCATGAGTGACGATAAATAGACTTTTCTTGCCAATGGATTTTTTTTTCTTTACCTTTCTC
66 TGAAGACATTAGTGACTATAAATAGACTTTTCTCGTAAATAGATATCTTTTTCTTCACATTTCTC
* * * **********
13598 GAGGTAAACATTCAATTATAATCTGTTTTAATAAAAAATATAAAAAANNNNNNNNNNAAATCAAT
131 GAGGCAAACATTAAATTACAATCTG-TTTAATAAAAAATATAAAAAAATTCAAATTAAAATCAAT
* * * *
13663 TATGAGGTT-ATAAAA-TCATTTAAAGCCAGTTATAAAGCTTTTGAAGGTATGGGTGACTATAAA
195 TATGAGATTGA-AAAACT-ATTTAAAGCAAGTAATAAAGCTTTCGAAGGTATGGGTGACTATAAA
* * * *
13726 TGGACTTTTTTCAGTAATAGATATCTTTTTCTTCACGTTTCTCAAGGCAATCATTCAATTATAAT
258 TGGACTTTCTT-ACTAATGGATATCTTTTTCTTCACGTTTCTCAAGG-AAACATTCAATTATAAT
* *
13791 TTGTTTTAATGAAAAATAT
321 CTGTTTTAATAAAAAATAT
*
13810 AAAAAAATCCAAATTAAAATCAATTATAAGGTTATAAAATCATTTAAAGCGAGTAACAAAGTTTT
1 AAAAAAATCCAAATTAAAATCAATTATAAGGTTATAAAATCATTTAAAGCGAGTAACAAAGCTTT
* * ** *
13875 TGAAGGCATTAGTGACTATAAATAGACTTTTCTCGTAAATAGATATTTTTTTCTTCATGTTTCTT
66 TGAAGACATTAGTGACTATAAATAGACTTTTCTCGTAAATAGATATCTTTTTCTTCACATTTCTC
* *
13940 GAGGCAAATATTCAATTACAATCTGTTTAATAAAAAATATAAAAAAATTCAAATTAAAATCAATT
131 GAGGCAAACATTAAATTACAATCTGTTTAATAAAAAATATAAAAAAATTCAAATTAAAATCAATT
* ********** * *
14005 ATGAGTTTNNNNNNNNNNTTAAAGCAAGTAATAAAGCTTTCAAAGGCATGGGTGACTATAAATGG
196 ATGAGATTGAAAAACTATTTAAAGCAAGTAATAAAGCTTTCGAAGGTATGGGTGACTATAAATGG
* * * * *
14070 AATTTTCTTACCAATGGGTATCTTTTTCTTCACGTTTCTTAAGCTAAACATTCAATTATAATCTG
261 -ACTTTCTTACTAATGGATATCTTTTTCTTCACGTTTCTCAAG-GAAACATTCAATTATAATCTG
*
14135 TTTTAATAAAAAATGT
324 TTTTAATAAAAAATAT
* * * *
14151 AAAAAAATCTAAATTTAAATCAATTATAAGGTTATAAAA-CTATTTAAAGCGTGTAA-AAGGCTT
1 AAAAAAATCCAAATTAAAATCAATTATAAGGTTATAAAATC-ATTTAAAGCGAGTAACAAAGCTT
* * *
14214 TTGAAGACA-TAGGTTACT-TAAAT-GTACTTTTCTTGCT-AATTGATATCTTTTTCTTCACATT
65 TTGAAGACATTA-GTGACTATAAATAG-ACTTTTCTCG-TAAATAGATATCTTTTTCTTCACATT
* * *** ** * *
14275 TCTCGAGGTAAACA-TAAACTTATAATCTGTTTTAATTGTAAATATAAAAACGTTTAACTTAAAA
127 TCTCGAGGCAAACATTAAA-TTACAATCTG-TTTAATAAAAAATATAAAAAAATTCAAATTAAAA
***********
14339 -CTAATTATGAGATTGAAAAACTATTTAAAGCGNNNNNNNNNNCTTTCGAAGGTATGGGTGACTA
190 TC-AATTATGAGATTGAAAAACTATTTAAAGCAAGTAATAAAGCTTTCGAAGGTATGGGTGACTA
* *
14403 GAAATGGACCTTTCTTACTAATGGATATCTTTTTCTTCACGTTTCTCAAGGAAAGCGTTCAATTA
254 TAAATGGA-CTTTCTTACTAATGGATATCTTTTTCTTCACGTTTCTCAAGGAAA-CATTCAATTA
*
14468 TAATCTATTTTAATAAAAAATAT
317 TAATCTGTTTTAATAAAAAATAT
*
14491 AAAAAAATTCAAATTAAA
1 AAAAAAATCCAAATTAAA
14509 NNNNNNNNNN
Statistics
Matches: 570, Mismatches: 116, Indels: 28
0.80 0.16 0.04
Matches are distributed among these distances:
338 4 0.01
339 61 0.11
340 173 0.30
341 191 0.34
342 141 0.25
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.36
Consensus pattern (339 bp):
AAAAAAATCCAAATTAAAATCAATTATAAGGTTATAAAATCATTTAAAGCGAGTAACAAAGCTTT
TGAAGACATTAGTGACTATAAATAGACTTTTCTCGTAAATAGATATCTTTTTCTTCACATTTCTC
GAGGCAAACATTAAATTACAATCTGTTTAATAAAAAATATAAAAAAATTCAAATTAAAATCAATT
ATGAGATTGAAAAACTATTTAAAGCAAGTAATAAAGCTTTCGAAGGTATGGGTGACTATAAATGG
ACTTTCTTACTAATGGATATCTTTTTCTTCACGTTTCTCAAGGAAACATTCAATTATAATCTGTT
TTAATAAAAAATAT
Found at i:18510 original size:171 final size:171
Alignment explanation
Indices: 18222--18544 Score: 459
Period size: 171 Copynumber: 1.9 Consensus size: 171
18212 NNNNNNNNNN
* * * * *
18222 TAAAGCGAGTAATAAGGCTTTTGAAGGCATCGGTGACTATAAATATACTTTTCTAGCTAATGGGT
1 TAAAGCGAGTAATAAGGCGTTCGAAGGCATCGGTGACTAGAAATAGACTTTTCTAGCTAATGGAT
* * ** * *
18287 ATCTTTTTCTTCATGTTTTTTGAGATAAACATACAATTATAATTTATTTTAATAATAAATATAAA
66 ATCTTTTTCTTCATATTTCTCAAGACAAACATACAATTATAATATATTTTAATAATAAATATAAA
* *
18352 AAATTTTAACATAAAACCAATTATGAGATTAAAAAGCTATT
131 AAAGTTCAACATAAAACCAATTATGAGATTAAAAAGCTATT
*
18393 TAAAGCGAGTAATAAGGCGTTCGAAGGCATGGGTGACTAGAAATAGACTTTTCTTA-CTAATGGA
1 TAAAGCGAGTAATAAGGCGTTCGAAGGCATCGGTGACTAGAAATAGACTTTTC-TAGCTAATGGA
* * *
18457 TATCTTTTTCTTCATATTTCTCAAGGCAAACATTCAATTATAATATGTTTTAATAATAAATATAA
65 TATCTTTTTCTTCATATTTCTCAAGACAAACATACAATTATAATATATTTTAATAATAAATATAA
* *
18522 AAAAGTTCAACTTAAAACTAATT
130 AAAAGTTCAACATAAAACCAATT
18545 NNNNNNNNNN
Statistics
Matches: 132, Mismatches: 19, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
171 130 0.98
172 2 0.02
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (171 bp):
TAAAGCGAGTAATAAGGCGTTCGAAGGCATCGGTGACTAGAAATAGACTTTTCTAGCTAATGGAT
ATCTTTTTCTTCATATTTCTCAAGACAAACATACAATTATAATATATTTTAATAATAAATATAAA
AAAGTTCAACATAAAACCAATTATGAGATTAAAAAGCTATT
Done.