Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401217.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4364.0, 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, 942
Length: 1570
ACGTcount: A:0.26, C:0.12, G:0.08, T:0.27
Warning! 418 characters in sequence are not A, C, G, or T
Found at i:368 original size:169 final size:170
Alignment explanation
Indices: 161--536 Score: 427
Period size: 169 Copynumber: 2.2 Consensus size: 170
151 NNNNNNNNNN
* * * ** *
161 AAAGCCCATTTATAGTCACCTAATCCTTTAAAAGCCTTATTA-TCCTCCCTAAATGGTTTAATAG
1 AAAGCCCATTTATAGTCACCCAAGCCTTCAAAAGCCTTATTACT-CTCCCTAAATAATTTAATAA
* ********** *
225 CCTTAAAATTGATTTTAAGT-NNNNNNNNNNACATTTTTGGTTAAAACAGATTATCATTGAATGT
65 CCTTAAAATTGATTCTAAGTAGAATGTTTTTACATTTTTGGTTAAAACAGATTATAATTGAATGT
*
289 TT-CTTTGCGAAACATGAAGAAA-AACCCATTCATCGGCAAGA
130 TTACTTTG-GAAACATGAAGAAAGAA-ACATTCATCGGCAAGA
* * * * *
330 AAAGCCCATTTATAGTTACCCAAGCCTTCAATAGCCTTATTACTCTCCTTACATAATTTTATAAC
1 AAAGCCCATTTATAGTCACCCAAGCCTTCAAAAGCCTTATTACTCTCCCTAAATAATTTAATAAC
* * **
395 CTTAAAATTGATTCTAAGTAGAATGTTTTTATATTTTTGTTTAAAACTTATTATAATTGAATGTT
66 CTTAAAATTGATTCTAAGTAGAATGTTTTTACATTTTTGGTTAAAACAGATTATAATTGAATGTT
*
460 TACCTTTGGAAACATGAAGAAAGAAACATTCATTGGCAAGA
131 TA-CTTTGGAAACATGAAGAAAGAAACATTCATCGGCAAGA
501 AAAGCCCATTTATAGTCACCCAAGCCTTCAAAAGCC
1 AAAGCCCATTTATAGTCACCCAAGCCTTCAAAAGCC
537 NNNNNNNNNN
Statistics
Matches: 171, Mismatches: 31, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
169 70 0.41
170 32 0.19
171 62 0.36
172 7 0.04
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.34
Consensus pattern (170 bp):
AAAGCCCATTTATAGTCACCCAAGCCTTCAAAAGCCTTATTACTCTCCCTAAATAATTTAATAAC
CTTAAAATTGATTCTAAGTAGAATGTTTTTACATTTTTGGTTAAAACAGATTATAATTGAATGTT
TACTTTGGAAACATGAAGAAAGAAACATTCATCGGCAAGA
Found at i:1569 original size:171 final size:169
Alignment explanation
Indices: 1050--1570 Score: 486
Period size: 171 Copynumber: 3.1 Consensus size: 169
1040 NNNNNNNNNN
* * * * * * *
1050 TAATTGAGTTTAAGTTGAATTTTTTTACATTTTTCATTAAAACTGATTTTAATTGCATTTTTACC
1 TAATTGATTTTAAGTTGAATTTTTTTACATTTTTCGTTAAAACAGATTATAATTGAATGTTT-CT
* ** * * * * *
1115 TTGGGAAACATGAAGAAAACCCATTCATTGACAAGAAAAGGCCATTTATTGTCACTCAAGTCTTG
65 TTGAGAAACATGAAGAAAATACATTCATTGGCAAGAAAAGCCCATTTATAGTCACTCAAGCCTTC
* *
1180 AAAAGCGTTATTATTCTCTTTAAATGATTTTATAATCTTA
130 AAAAGCATTATTACTCTCTTTAAATGATTTTATAATCTTA
* * * *
1220 TAATTTATTTTAAGTTGAATTTTTTTATATTTTTGGTTTAAAA-AGATTATAATTAAATGTATTC
1 TAATTGATTTTAAGTTGAATTTTTTTACATTTTTCG-TTAAAACAGATTATAATTGAATGT-TTC
* ********** * * * *
1284 TTTCANNNNNNNNNNGAAAATGCTATTCATTGGCAAGAAAAACCCATTTATACTCACCCAAGCCT
64 TTTGAGAAACATGAAGAAAATAC-ATTCATTGGCAAGAAAAGCCCATTTATAGTCACTCAAGCCT
* * * ****
1349 TCAAAAGCATTACTACTCTCTTTAAACGGTTTTAGGGCCTTA
128 TCAAAAGCATTATTACTCTCTTTAAATGATTTTATAATCTTA
* * * * *
1391 AAATTGATTTTAAGTTTAATTGTTTTGCATTTATCGTTAAAACAGATTATAATTGAATGTTTGCT
1 TAATTGATTTTAAGTTGAATTTTTTTACATTTTTCGTTAAAACAGATTATAATTGAATGTTT-CT
* * *
1456 TTGAGAAACATGAAGAAAAATACATTCAGTGGGAAGAAAAGCCCATTTATAGTCACTAAAGCCTT
65 TTGAGAAACATGAAG-AAAATACATTCATTGGCAAGAAAAGCCCATTTATAGTCACTCAAGCCTT
* * * *
1521 CAAAAGCCTTATTACTCTCTTCAAATAATTTTATAATCTCA
129 CAAAAGCATTATTACTCTCTTTAAATGATTTTATAATCTTA
1562 TAATTGATT
1 TAATTGATT
Statistics
Matches: 264, Mismatches: 81, Indels: 11
0.74 0.23 0.03
Matches are distributed among these distances:
170 60 0.23
171 198 0.75
172 6 0.02
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.39
Consensus pattern (169 bp):
TAATTGATTTTAAGTTGAATTTTTTTACATTTTTCGTTAAAACAGATTATAATTGAATGTTTCTT
TGAGAAACATGAAGAAAATACATTCATTGGCAAGAAAAGCCCATTTATAGTCACTCAAGCCTTCA
AAAGCATTATTACTCTCTTTAAATGATTTTATAATCTTA
Done.