Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398491.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1786.0, 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: 5021
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.28
Warning! 1158 characters in sequence are not A, C, G, or T
Found at i:1621 original size:171 final size:171
Alignment explanation
Indices: 1323--1705 Score: 436
Period size: 171 Copynumber: 2.2 Consensus size: 171
1313 NNNNNNNNNN
* * * * *
1323 GAATTTTTTTACATTTTTTGTTATAAAAGG-CTATAATTGAATGTTTGCCTTGAGGAACATGAAG
1 GAATTTTTTTACATTTTTGGTTA-AAACGGATTATAATTGAATGTCTACCTTGAGGAACATGAAG
* * * * * *
1387 CAAAAGTCAACAATTGATACCAAAAGTCCATTTATAGTCACTCAGGCCTTCGAAAGGCTTATTAC
65 AAAAAGGCAACAATAGATACCAAAAGTCCATTTATAGTCACCCAGGCCTTCAAAAAGCTTATTAC
* *
1452 TCGCTTTAAATGGTTTTAT-TATCTCACAAAT-AATTTTAAGTT
130 TCACTTTAAATGGTTTTATAT-TATCACAAATGAA-TTTAAGTT
1494 GAATTTTTTTACATTTTTGGTTAAAACGGATTATAATTGAATGTCTACCTTGA-GAA-ATTAGAA
1 GAATTTTTTTACATTTTTGGTTAAAACGGATTATAATTGAATGTCTACCTTGAGGAACA-T-GAA
* * * * ** *
1557 GAAAAAGGCATTC-ATAGGTAGCAAAAGTGCATTTATAGTCACCCATTCCTTCAAAAATCTTATT
64 GAAAAAGGCA-ACAATAGATACCAAAAGTCCATTTATAGTCACCCAGGCCTTCAAAAAGCTTATT
* * *
1621 ACTCACTTTAAATGGTTTTATATTATCATAATTGAATTTAGGTT
128 ACTCACTTTAAATGGTTTTATATTATCACAAATGAATTTAAGTT
* * *
1665 GAATTGTTTTACATTTTTGGTTAGAACAGATTATAATTGAA
1 GAATTTTTTTACATTTTTGGTTAAAACGGATTATAATTGAA
1706 NNNNNNNNNN
Statistics
Matches: 180, Mismatches: 26, Indels: 12
0.83 0.12 0.06
Matches are distributed among these distances:
169 1 0.01
170 9 0.05
171 166 0.92
172 4 0.02
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.39
Consensus pattern (171 bp):
GAATTTTTTTACATTTTTGGTTAAAACGGATTATAATTGAATGTCTACCTTGAGGAACATGAAGA
AAAAGGCAACAATAGATACCAAAAGTCCATTTATAGTCACCCAGGCCTTCAAAAAGCTTATTACT
CACTTTAAATGGTTTTATATTATCACAAATGAATTTAAGTT
Found at i:1909 original size:232 final size:222
Alignment explanation
Indices: 1484--1937 Score: 484
Period size: 232 Copynumber: 2.0 Consensus size: 222
1474 CTCACAAATA
* * * *
1484 ATTTTAAGTTGAATTTTTTTACATTTTTGGTTAAAACGGATTATAATTGAATGTCTACCTTGAGA
1 ATTTTAAGTTGAAATGTTTTACATTTTTGGTTAAAACAGATTATAATTGAATGTCTACCTCGAGA
* ** *
1549 AATTAGAAGAAAAAGGCATTCATAGGTAGCAAAAGTGCATTTATAGTCACCCATTCCTTCAAAAA
66 AAATAGAAGAAAAAGGCATTCATAGGTAAAAAAAATGCATTTATAGTCACCCATTCCTTCAAAAA
* * ** * *
1614 TCTTATTACTCACTTTAAATGGTTTTATATTATCATAATTGAATTTAGGTTGAATTGTTTTACAT
131 CCATATTACTCACTTTAAATGGCCTTATA-TATCAAAATTGAATTTAAGTTGAATTGTTTTACAT
* *
1679 TTTTGGTTAGAACAGATTATAATTGAANNNNNNNNNNG
195 TTTTGGTTAGAAAAGACTATAATTGAA----------G
* * * * *
1717 ATTTTAGGTTGAAATGTTTTACATTTTTTGTTAAAATAGATTTTAATTGAATGTCTAGCTCGAGA
1 ATTTTAAGTTGAAATGTTTTACATTTTTGGTTAAAACAGATTATAATTGAATGTCTACCTCGAGA
* *
1782 AACATA-AAG-AAAAGTGCATTCATTGG-AAAAAAAATTCATTTATAGTCACCCATTCCTTCAAA
66 AA-ATAGAAGAAAAAG-GCATTCATAGGTAAAAAAAATGCATTTATAGTCACCCATTCCTTCAAA
* * *
1844 AGCCATATTACTCACTTTAAATGGCCTTATA-ATCCTAAAATTGATTTTAAGTTGAATTTTTTTA
129 AACCATATTACTCACTTTAAATGGCCTTATATAT-C-AAAATTGAATTTAAGTTGAATTGTTTTA
* * *
1908 CATTTTTTGTTATAAAAGGCTATAATTGAA
192 CATTTTTGGTTAGAAAAGACTATAATTGAA
1938 TGTTTGCCTT
Statistics
Matches: 188, Mismatches: 29, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
230 2 0.01
231 1 0.01
232 112 0.60
233 71 0.38
234 2 0.01
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.39
Consensus pattern (222 bp):
ATTTTAAGTTGAAATGTTTTACATTTTTGGTTAAAACAGATTATAATTGAATGTCTACCTCGAGA
AAATAGAAGAAAAAGGCATTCATAGGTAAAAAAAATGCATTTATAGTCACCCATTCCTTCAAAAA
CCATATTACTCACTTTAAATGGCCTTATATATCAAAATTGAATTTAAGTTGAATTGTTTTACATT
TTTGGTTAGAAAAGACTATAATTGAAG
Found at i:2067 original size:171 final size:170
Alignment explanation
Indices: 1716--2517 Score: 798
Period size: 171 Copynumber: 4.7 Consensus size: 170
1706 NNNNNNNNNN
* * * * * * *
1716 GATTTTAGGTTGAAATGTTTTACATTTTTTGTTAAAATAGATTTTAATTGAATGTCTAG-CTCGA
1 GATTTTAAGTTGAATTTTTTTACATTTTTGGTTAAAA-AGATTATAATTGAATGT-TTGCCTTGA
* *
1780 GAAACATAAAG-AAAAGTGCATTCATTGGA-AA-AAAAATTCATTTATAGTCACCCATTCCTTCA
64 GAAACATAAAGAAAAAGT-CATTCATT-GACAACAAAAGTCCATTTATAGTCACCCATTCCTTCA
* **
1842 AAAGCCATATTACTCACTTTAAATGGCCTTATAATC-C-TAAAATT
127 AAAGCCTTATTACTCACTTTAAATGGTTTTATAATCTCAT-AAA-T
* **
1886 GATTTTAAGTTGAATTTTTTTACATTTTTTGTTATAAAAGGCTATAATTGAATGTTTGCCTTGAG
1 GATTTTAAGTTGAATTTTTTTACATTTTTGGTTA-AAAAGATTATAATTGAATGTTTGCCTTGAG
* ** * *** *
1951 AAACATAAAGCAAAAGTCAACCATTGAC-ACAAAAAGTCCATTTATAGTCACTCGGACCTTCGAA
65 AAACATAAAGAAAAAGTCATTCATTGACAAC-AAAAGTCCATTTATAGTCACCCATTCCTTCAAA
* * * * *
2015 AGGCTTATTACTCGCTTTAAATAGTTTTATTATCTCACAAAT
129 AGCCTTATTACTCACTTTAAATGGTTTTATAATCTCATAAAT
* * ** * *
2057 GATTTTAAGTTGAATTTTTTTATATTTTTGGTTAAAACAAATTATAATTGAATGCGTACCTCGAG
1 GATTTTAAGTTGAATTTTTTTACATTTTTGGTTAAAA-AGATTATAATTGAATGTTTGCCTTGAG
** * * * * *
2122 AAATGTGAAGAAAAAGGCATTCATAGGCAACAAAAGTGCATTTATAGTCACCCATTCCTTCAAAA
65 AAACATAAAGAAAAAGTCATTCATTGACAACAAAAGTCCATTTATAGTCACCCATTCCTTCAAAA
** * *
2187 ATCTTATTACTCACTTTAAATGGTTTTATAATATCATAATT
130 GCCTTATTACTCACTTTAAATGGTTTTATAATCTCATAAAT
* * *
2228 GATTTTAAGTTGAATTTTTTTACATTTTTGGTTAGAACAGATTATAATTGAATGTTTTCCTTGGG
1 GATTTTAAGTTGAATTTTTTTACATTTTTGGTTA-AAAAGATTATAATTGAATGTTTGCCTTGAG
** * * * * *
2293 AAATGTGAAGAAAAAGAT-ATTCATTGGCAAGAAGAGTCTATTTATAGTCACCCATTCCTTCAAA
65 AAACATAAAGAAAAAG-TCATTCATTGACAACAAAAGTCCATTTATAGTCACCCATTCCTTCAAA
* * *
2357 AGCCTTATTACTCACTTTAAATGATTTTATAATTTCATAATT
129 AGCCTTATTACTCACTTTAAATGGTTTTATAATCTCATAAAT
* * * * *
2399 GATTTTAGGTTGAATTTTTTTACATTTTTGGTTAGAACAGAATATAATTGAGTGTCTGCCTT-AG
1 GATTTTAAGTTGAATTTTTTTACATTTTTGGTTA-AAAAGATTATAATTGAATGTTTGCCTTGAG
* * *
2463 AAA-ATGTGAAGAAAAAAGT-ATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCA
65 AAACA--TAAAG-AAAAAGTCATTCATTGACAACAAAAGTCCATTTATAGTCACCCA
2518 NNNNNNNNNN
Statistics
Matches: 533, Mismatches: 84, Indels: 29
0.83 0.13 0.04
Matches are distributed among these distances:
169 5 0.01
170 73 0.14
171 441 0.83
172 14 0.03
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.38
Consensus pattern (170 bp):
GATTTTAAGTTGAATTTTTTTACATTTTTGGTTAAAAAGATTATAATTGAATGTTTGCCTTGAGA
AACATAAAGAAAAAGTCATTCATTGACAACAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAG
CCTTATTACTCACTTTAAATGGTTTTATAATCTCATAAAT
Found at i:2340 original size:342 final size:342
Alignment explanation
Indices: 1716--2517 Score: 947
Period size: 342 Copynumber: 2.3 Consensus size: 342
1706 NNNNNNNNNN
* * * * * * *
1716 GATTTTAGGTTGAAATGTTTTACATTTTTTGTTAAAATAGATTTTAATTGAATGTCTAGCTCGAG
1 GATTTTAGGTTGAATTTTTTTACATTTTTGGTTAAAACAAATTATAATTGAATGTCTACCTCGAG
** * * *
1781 AAACATAAAG-AAAAGTGCATTCATTGG-AAAAAAAATTCATTTATAGTCACCCATTCCTTCAAA
66 AAATGTGAAGAAAAAG-GCATTCATTGGCAAAAAAAGTCCATTTATAGTCACCCATTCCTTCAAA
*
1844 AGCCATATTACTCACTTTAAATGGCCTTATAATCCTAAAATTGATTTTAAGTTGAATTTTTTTAC
130 AACCATATTACTCACTTTAAATGGCCTTATAATCCTAAAATTGATTTTAAGTTGAATTTTTTTAC
* * * *
1909 ATTTTTTGTTATAAAAGGCTATAATTGAATGTTTGCCTTGAGAAACATAAAGCAAAAGTCAACCA
195 ATTTTTGGTTAGAAAAGACTATAATTGAATGTTTGCCTTGAGAAACATAAAGAAAAAGTCAACCA
* * * * *
1974 TTGACACAAAAAGTCCATTTATAGTCACTCGGACCTTCGAAAGGCTTATTACTCGCTTTAAAT-A
260 TTGACACAAAAAGTCCATTTATAGTCACCCAGACCTTCAAAAGCCTTATTACTCACTTTAAATGA
*
2038 GTTTTATTATCTCACAAAT
325 -TTTTATAATCTCACAAAT
* *
2057 GATTTTAAGTTGAATTTTTTTATATTTTTGGTTAAAACAAATTATAATTGAATG-CGTACCTCGA
1 GATTTTAGGTTGAATTTTTTTACATTTTTGGTTAAAACAAATTATAATTGAATGTC-TACCTCGA
* * *
2121 GAAATGTGAAGAAAAAGGCATTCATAGGCAACAAAAGTGCATTTATAGTCACCCATTCCTTCAAA
65 GAAATGTGAAGAAAAAGGCATTCATTGGCAAAAAAAGTCCATTTATAGTCACCCATTCCTTCAAA
* * ** * *
2186 AATCTTATTACTCACTTTAAATGGTTTTATAAT-ATCATAATTGATTTTAAGTTGAATTTTTTTA
130 AACCATATTACTCACTTTAAATGGCCTTATAATCCT-AAAATTGATTTTAAGTTGAATTTTTTTA
* * * * ** * **
2250 CATTTTTGGTTAGAACAGATTATAATTGAATGTTTTCCTTGGGAAATGTGAAGAAAAAGAT-ATT
194 CATTTTTGGTTAGAAAAGACTATAATTGAATGTTTGCCTTGAGAAACATAAAGAAAAAG-TCAAC
* * * **
2314 CATTGGCA-AGAAGAGTCTATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTAAA
258 CATTGACACA-AAAAGTCCATTTATAGTCACCCAGACCTTCAAAAGCCTTATTACTCACTTTAAA
* * *
2378 TGATTTTATAATTTCATAATT
322 TGATTTTATAATCTCACAAAT
* * * *
2399 GATTTTAGGTTGAATTTTTTTACATTTTTGGTTAGAACAGAA-TATAATTGAGTGTCTGCCT-TA
1 GATTTTAGGTTGAATTTTTTTACATTTTTGGTTAAAACA-AATTATAATTGAATGTCTACCTCGA
* * *
2462 GAAAATGTGAAGAAAAAAGTATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCA
65 G-AAATGTGAAGAAAAAGGCATTCATTGGCAAAAAAAGTCCATTTATAGTCACCCA
2518 NNNNNNNNNN
Statistics
Matches: 390, Mismatches: 61, Indels: 19
0.83 0.13 0.04
Matches are distributed among these distances:
340 1 0.00
341 75 0.19
342 309 0.79
343 5 0.01
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.38
Consensus pattern (342 bp):
GATTTTAGGTTGAATTTTTTTACATTTTTGGTTAAAACAAATTATAATTGAATGTCTACCTCGAG
AAATGTGAAGAAAAAGGCATTCATTGGCAAAAAAAGTCCATTTATAGTCACCCATTCCTTCAAAA
ACCATATTACTCACTTTAAATGGCCTTATAATCCTAAAATTGATTTTAAGTTGAATTTTTTTACA
TTTTTGGTTAGAAAAGACTATAATTGAATGTTTGCCTTGAGAAACATAAAGAAAAAGTCAACCAT
TGACACAAAAAGTCCATTTATAGTCACCCAGACCTTCAAAAGCCTTATTACTCACTTTAAATGAT
TTTATAATCTCACAAAT
Found at i:3367 original size:64 final size:64
Alignment explanation
Indices: 3266--3386 Score: 156
Period size: 64 Copynumber: 1.9 Consensus size: 64
3256 ATTTATAGCT
* * * *
3266 ACCCATTCCTTCCAAAGCCTTATTACTCGTTCTAAATGGTTTTATAATATCATAATTGATAATC
1 ACCCATTCCTTCAAAAGCCATATTACTCGTTCTAAATGATTTTATAATATAATAATTGATAATC
* *
3330 ACCCATTCCTAT-AAAAGCCATATTACTCGCTT-TAAATGATTTTTTAATGTAATAATT
1 ACCCATTCCT-TCAAAAGCCATATTACTCG-TTCTAAATGATTTTATAATATAATAATT
3387 TGTTTTAAGT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
64 46 0.94
65 3 0.06
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (64 bp):
ACCCATTCCTTCAAAAGCCATATTACTCGTTCTAAATGATTTTATAATATAATAATTGATAATC
Found at i:3475 original size:234 final size:234
Alignment explanation
Indices: 3094--3556 Score: 544
Period size: 234 Copynumber: 2.0 Consensus size: 234
3084 TCCTTTATAG
* ** * *
3094 TCACCCATTCCTTGAAAAGCCTTATTACTCTTTTTAAATGGTTTTATAATCTCATAATTGATTTT
1 TCACCCATTCCTTGAAAAGCCATATTACTCGCTTTAAATGATTTTATAATCTAATAATTGATTTT
* *
3159 CAGTTGAATTTTTTTACATTTTTGGTGAAAAAAGACTAAATTGAATGTCTACCTCAAGAAACGTG
66 AAGTTGAATTTTTTTACATTTTTCGTGAAAAAAGACTAAATTGAATGTCTACCTCAAGAAACGTG
* * * *
3224 AAGAAAAAGGCATTCATTGACAAGAAAAGTGCATTTATAG-CTACCCATTCCTTCCAAAGCCTTA
131 AAGAAAAAGGCATTCATTGACAAGAAAAGTCCATTTATAGTC-ACCCATACATTCAAAAGCCTTA
3288 TTACTCG-TTCTAAATGGTTTTATAATATCATAATTGATAA
195 TTACTCGCTT-TAAATGGTTTTATAATATCATAATTGATAA
* *
3328 TCACCCATTCCTAT-AAAAGCCATATTACTCGCTTTAAATGATTTTTTAATGTAATAATTTG-TT
1 TCACCCATTCCT-TGAAAAGCCATATTACTCGCTTTAAATGATTTTATAATCTAATAA-TTGATT
*** * * * * **
3391 TTAAGTTTTTTTTTTTTTACATTTTTCGTTAAAACATACTCTAATTGAATGT-TCACCTTGAGAA
64 TTAAG-TTGAATTTTTTTACATTTTTCGTGAAAAAAGACT-AAATTGAATGTCT-ACCTCAAGAA
* * * * * * *
3455 ATGTG-A-ATAAAGGTATTCATTGGCAAGAAAAGTCCATTTATAGTCACTCGTACATTTAAAAGC
126 ACGTGAAGAAAAAGGCATTCATTGACAAGAAAAGTCCATTTATAGTCACCCATACATTCAAAAGC
*
3518 CTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATT
191 CTTATTACTCGCTTTAAATGGTTTTATAATATCATAATT
3557 AATTTAATTT
Statistics
Matches: 192, Mismatches: 30, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
234 134 0.70
235 36 0.19
236 22 0.11
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.40
Consensus pattern (234 bp):
TCACCCATTCCTTGAAAAGCCATATTACTCGCTTTAAATGATTTTATAATCTAATAATTGATTTT
AAGTTGAATTTTTTTACATTTTTCGTGAAAAAAGACTAAATTGAATGTCTACCTCAAGAAACGTG
AAGAAAAAGGCATTCATTGACAAGAAAAGTCCATTTATAGTCACCCATACATTCAAAAGCCTTAT
TACTCGCTTTAAATGGTTTTATAATATCATAATTGATAA
Found at i:3690 original size:171 final size:167
Alignment explanation
Indices: 3328--3782 Score: 493
Period size: 171 Copynumber: 2.7 Consensus size: 167
3318 TAATTGATAA
* * * * * *
3328 TCACCCATTCCTATAAAAGCCATATTACTCGCTTTAAATGATTTTTTAATGTAATAATTTGTTTT
1 TCACCCATTCCT-TAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAA-TTATTTT
** * **
3393 AAGTTTTTTTTTTTTTACATTTTTCGTTAAAACATACTCTAATTGAATGTTCACCTTGAGAAATG
64 AA-TTTTAATTTTTTTACATTTTTCGTTAAAACATACTATAATTGAATGTTCACCTCAAGAAATG
**
3458 TGAATAAAGGTATTCATTGGCAAGAAAAGTCCATTTATAG
128 TGAATAAAGCCATTCATTGGCAAGAAAAGTCCATTTATAG
* * * * *
3498 TCACTCGTACATTTAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTAATTTA
1 TCACCCATTC-CTTAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTATTTTA
**
3563 ATTTTAATTTGTTTTACATTTTTTATTAAAACATACTATAATTGAATGCTTC-CCTCAAGAACCA
65 ATTTTAATTT-TTTTACATTTTTCGTTAAAACATACTATAATTGAATG-TTCACCTCAAGAA--A
**
3627 TGTAGAA-AAAGCCATTCATTGAG-AAGAAAAGTTTATTTATAG
126 TGT-GAATAAAGCCATTCATTG-GCAAGAAAAGTCCATTTATAG
**
3669 TTTCCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTATTTTT
1 TCACCCATTCCTT-AAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTA-TTTT
* * * * * * * *
3734 AACTTGAATGTTTTTACAATTTTGGTTAAAACAGATTATAATTAAATGT
64 AATTTTAATTTTTTTACATTTTTCGTTAAAACATACTATAATTGAATGT
3783 CTACATTGAG
Statistics
Matches: 238, Mismatches: 38, Indels: 18
0.81 0.13 0.06
Matches are distributed among these distances:
168 7 0.03
169 48 0.20
170 52 0.22
171 116 0.49
172 15 0.06
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.42
Consensus pattern (167 bp):
TCACCCATTCCTTAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTATTTTAA
TTTTAATTTTTTTACATTTTTCGTTAAAACATACTATAATTGAATGTTCACCTCAAGAAATGTGA
ATAAAGCCATTCATTGGCAAGAAAAGTCCATTTATAG
Found at i:3817 original size:171 final size:171
Alignment explanation
Indices: 3512--3841 Score: 409
Period size: 171 Copynumber: 1.9 Consensus size: 171
3502 TCGTACATTT
* * *
3512 AAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTAATTTAATTTTAATTTGTTT
1 AAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTAATTTAACTTGAATGTGTTT
* * * * * * *
3577 TACATTTTTTATTAAAACATACTATAATTGAATGCTTCCCTCAAGAACCATGTAGAAAAAGCCAT
66 TACAATTTTGATTAAAACAGACTATAATTAAATGCTACACTCAAGAACCATGAAGAAAAAGCCAT
* *
3642 TCATTGAG-AAGAAAAGTTTATTTATAGTTTCCCATTCCTTC
131 TCATTG-GTAAGAAAACTCTATTTATAGTTTCCCATTCCTTC
*
3683 AAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTATTTTTAACTTGAATGT-TT
1 AAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTA-ATTTAACTTGAATGTGTT
* * ** *
3747 TTACAATTTTGGTTAAAACAGATTATAATTAAATGTCTACA-TTGAGAGA-CATGAAGGAAAATG
65 TTACAATTTTGATTAAAACAGACTATAATTAAATG-CTACACTCAAGA-ACCATGAA-GAAAAAG
*
3810 -TATTCATTGGTAAGAAAACTCTATTTATAGTT
127 CCATTCATTGGTAAGAAAACTCTATTTATAGTT
3842 ACTTATTNNN
Statistics
Matches: 135, Mismatches: 19, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
170 1 0.01
171 113 0.84
172 21 0.16
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (171 bp):
AAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTAATTTAACTTGAATGTGTTT
TACAATTTTGATTAAAACAGACTATAATTAAATGCTACACTCAAGAACCATGAAGAAAAAGCCAT
TCATTGGTAAGAAAACTCTATTTATAGTTTCCCATTCCTTC
Found at i:4116 original size:64 final size:64
Alignment explanation
Indices: 4010--4130 Score: 154
Period size: 64 Copynumber: 1.9 Consensus size: 64
4000 ACTTAAAACA
* * * * *
4010 AATTATTACATTAAAAAATCATTTAAAGTGAGTAATAGGGCTTTTA-TAGGAATGGGTGATTATC
1 AATTATGACATTAAAAAACCATTTAAAGCGAGTAATAAGGC-TTTAGAAGGAATGGGTGATTATC
* * *
4074 AATTATGATATTATAAAACCATTTAGAGCGAGTAATAAGGCTTTAGAAGGAATGGGT
1 AATTATGACATTAAAAAACCATTTAAAGCGAGTAATAAGGCTTTAGAAGGAATGGGT
4131 TGCTATAAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
63 4 0.08
64 44 0.92
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.33
Consensus pattern (64 bp):
AATTATGACATTAAAAAACCATTTAAAGCGAGTAATAAGGCTTTAGAAGGAATGGGTGATTATC
Done.