Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400435.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3632.0, 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: 7855
ACGTcount: A:0.21, C:0.08, G:0.07, T:0.23
Warning! 3199 characters in sequence are not A, C, G, or T
Found at i:2335 original size:171 final size:166
Alignment explanation
Indices: 2040--2704 Score: 505
Period size: 171 Copynumber: 4.0 Consensus size: 166
2030 NNNNNNNNNN
* * * ** *
2040 TTATAATCTAATAATTGATTTTAGGTTGAATTTTTTTTATTTTT-ATTTAAAACAGACAATAATT
1 TTATAATGTCATAATTGATTTTAAGTTGAATTTTTTACATTTTTCA-TTAAAATAGACAATAATT
* * * * * * *
2104 GAATGTCTATCTCTAGAAACGTTAA-AAAAAAGTATTCATTATCAAGAAAAGTCAATTTATAGTC
65 GAATGTCTACCTCAAGAAACGTGAAGAAAACA-CATTCATTAGCAAGAAAAGTCCATTTATAGTC
** *
2168 GTCTATTCTTTCAAAAACATTATTACTCACTTTAAATGGTT
129 ACCCATTC-TTC-AAAAC-TTATTACTCACTTTAAATGGTT
********** * *
2209 TTNNNNNNNNNNAATTGATTTTAAGTTGAATTTTTTAAGATTTTTCATTAAAATAGACTATAATT
1 TTATAATGTCATAATTGATTTTAAGTTGAATTTTTT-ACATTTTTCATTAAAATAGACAATAATT
* *
2274 GAATGTCTACCTCAAGAAACGAGAAGAGAAACACATTCATTAGAAAGAAAAGTCCATTTATAGTC
65 GAATGTCTACCTCAAGAAACGTGAAGA-AAACACATTCATTAGCAAGAAAAGTCCATTTATAGTC
******* * *
2339 ACCCATTCNNNNNNNNNNCTTGTTACTCACTTTAAATAGTT
129 ACCCATTC---TTCAAAACTTATTACTCACTTTAAATGGTT
* * *
2380 TTATAATGTCATAATT-ACCTTTAAGTTCAATTTTTTTACATTTTTCATTAAAATAGACCATAAT
1 TTATAATGTCATAATTGA-TTTTAAGTTGAA-TTTTTTACATTTTTCATTAAAATAGACAATAAT
* * * * *
2444 TGAATATCTACCTCAACAATCGTGAAGAAAAACGCATTCATTGGCAAGAAAAGTCCATTTATAGT
64 TGAATGTCTACCTCAAGAAACGTGAAG-AAAACACATTCATTAGCAAGAAAAGTCCATTTATAGT
*
2509 CACCCATTCTTCAAAGCCTTATTACTCACTTTAAATGGTT
128 CACCCATTCTTCAAA-ACTTATTACTCACTTTAAATGGTT
* * *
2549 TT-TAAATGTTCATAATTTATTTTAAGTTTATTTTTTTA-A-TTTTCATT-AAATAG---A-AAT
1 TTAT-AATG-TCATAATTGATTTTAAGTTGAATTTTTTACATTTTTCATTAAAATAGACAATAAT
* * * **
2606 TGATATGTCTACCT-AACAAA-GTGAAGAAAAAACAATTCA-TGGCAAAGATCA-TCCATTTATA
64 TGA-ATGTCTACCTCAAGAAACGTGAAGAAAACAC-ATTCATTAGC-AAGAAAAGTCCATTTATA
*
2667 GTCACCCATTCCTTCAAAAGTCTTGATTACTCGCTTTA
126 GTCACCCATT-CTTCAAAA--CTT-ATTACTCACTTTA
2705 GATGTATAGG
Statistics
Matches: 398, Mismatches: 78, Indels: 46
0.76 0.15 0.09
Matches are distributed among these distances:
160 29 0.07
161 23 0.06
162 14 0.04
163 22 0.06
166 6 0.02
167 8 0.02
168 2 0.01
169 59 0.15
170 61 0.15
171 162 0.41
172 12 0.03
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.38
Consensus pattern (166 bp):
TTATAATGTCATAATTGATTTTAAGTTGAATTTTTTACATTTTTCATTAAAATAGACAATAATTG
AATGTCTACCTCAAGAAACGTGAAGAAAACACATTCATTAGCAAGAAAAGTCCATTTATAGTCAC
CCATTCTTCAAAACTTATTACTCACTTTAAATGGTT
Found at i:3566 original size:171 final size:169
Alignment explanation
Indices: 2871--3822 Score: 616
Period size: 171 Copynumber: 5.6 Consensus size: 169
2861 TAATTTTATT
* * * *
2871 CTTCAAAAGCCTTATTGCTCATTTTAAATAGTTTTCTAATTTGATAATTGATTTTAAGTTG-ATT
1 CTTCAAAAGCCTTATTACACA-TTTAAATAGTTTTCTAATCTAATAATTGATTTTAAGTTGAATT
* *
2935 TTTTTACATTTTTGATGAAAACAGACAACAATTGACTATTTATCTCT-AGAAACATGAAGACAAA
65 TTTTTACATTTTTGATTAAAACAGACAATAATTGACTATTTATC-CTGAGAAACATGAAGACAAA
* * *
2999 AGCATTAATTGACAAGAAAACTCCATTTATAGTCACCCATTC
129 AGCATTAA-TGGCAAGAAAAGTCCATTTATACTCACCCATTC
********** * * ** *
3041 CTNNNNNNNNNNTATTACTCACTTTAAATAGTTTTTTAATCTCCTAATTGATTTTAGGTTGAATT
1 CTTCAAAAGCCTTATTACACA-TTTAAATAGTTTTCTAATCTAATAATTGATTTTAAGTTGAATT
* *********** * **
3106 GTTTTACATTTTTGATNNNNNNNNNNTATAATTGAATATTTA-CCTCGAGAAATGTGAAGA-AAA
65 TTTTTACATTTTTGATTAAAACAGACAATAATTGACTATTTATCCT-GAGAAACATGAAGACAAA
* * * * *
3169 CAGCATTGATTGGCGAGAAAAGTCTATTTATAGC-CTCTCATTC
129 -AGCATT-AATGGCAAGAAAAGTCCATTTATA-CTCACCCATTC
* * * * * **********
3212 CTTCAAAAGCCTAACTACTTGC-TTTAGATAGTTTTATAATCTAATAATTGATTTNNNNNNNNNN
1 CTTCAAAAGCCTTATTAC--ACATTTAAATAGTTTTCTAATCTAATAATTGATTTTAAGTTGAAT
* * * * * * * *
3276 TTTTTTACATTTTTGATTAAAAAAGATAATAATTAACTGTCTAT-CTCAAAAACCCTGAAGACAA
64 TTTTTTACATTTTTGATTAAAACAGACAATAATTGACTATTTATCCTGAGAAA-CATGAAGACAA
* * * * *
3340 AAGTATTCAATGGCAAGAAAAGTCTATTTAGAGC-CTCTCATTC
128 AAGCATT-AATGGCAAGAAAAGTCCATTTATA-CTCACCCATTC
3383 CTTCAAAAGCCTTATTACACATTTGAAATAGTTTTCTAATCTAATAATTGATTTTAAGTTGAATT
1 CTTCAAAAGCCTTATTACACATTT-AAATAGTTTTCTAATCTAATAATTGATTTTAAGTTGAATT
* * *
3448 TTTTTACATCTTTCATTAAAACAGACAATAATTGACTATTTATCCTGAGAAACTTGAAGACAAAA
65 TTTTTACATTTTTGATTAAAACAGACAATAATTGACTATTTATCCTGAGAAACATGAAGACAAAA
*
3513 GTATTCAATGGCAAGAAAAGTCCATTTATACTCACCCATTC
130 GCATT-AATGGCAAGAAAAGTCCATTTATACTCACCCATTC
* * *************
3554 CTTCAAAAGCCTTATTAGTCAC-TTTAAATGGTTTTCTAATCTCATAATTNNNNNNNNNNNNNAT
1 CTTCAAAAGCCTTATTA--CACATTTAAATAGTTTTCTAATCTAATAATTGATTTTAAGTTGAAT
* * * *
3618 TGTTTTATATTTTTGATT-AAACAGACTATAATTGAATATTTA-CCTCGAGAAACATGAAGA-AA
64 TTTTTTACATTTTTGATTAAAACAGACAATAATTGACTATTTATCCT-GAGAAACATGAAGACAA
** * * *
3680 AAAAATTAATTGACAAGAAAAGTCCATTTATAGTCACCCTTTC
128 AAGCATTAA-TGGCAAGAAAAGTCCATTTATACTCACCCATTC
* ** * * * * *
3723 CTTGAAAAGCCAAATTACTA-ACTTCAAATGGTTTTATAATCTAATAATTAATTTTAAGCTGAAT
1 CTTCAAAAGCCTTATTAC-ACA-TTTAAATAGTTTTCTAATCTAATAATTGATTTTAAGTTGAAT
* * * *
3787 ATTTTTACATTTTTTATTAAAACAGGCTATAATTGA
64 TTTTTTACATTTTTGATTAAAACAGACAATAATTGA
3823 ATGTNNNNNN
Statistics
Matches: 586, Mismatches: 173, Indels: 46
0.73 0.21 0.06
Matches are distributed among these distances:
167 1 0.00
168 3 0.01
169 97 0.17
170 107 0.18
171 361 0.62
172 13 0.02
173 4 0.01
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.36
Consensus pattern (169 bp):
CTTCAAAAGCCTTATTACACATTTAAATAGTTTTCTAATCTAATAATTGATTTTAAGTTGAATTT
TTTTACATTTTTGATTAAAACAGACAATAATTGACTATTTATCCTGAGAAACATGAAGACAAAAG
CATTAATGGCAAGAAAAGTCCATTTATACTCACCCATTC
Found at i:3754 original size:169 final size:157
Alignment explanation
Indices: 3466--3772 Score: 314
Period size: 169 Copynumber: 1.9 Consensus size: 157
3456 TCTTTCATTA
* * ** *
3466 AAACAGACAATAATTGACTATTTATCCTGAGAAACTTGAAGACAAAAGTATTCAATGGCAAGAAA
1 AAACAGACAATAATTGAATATTTATCCTGAGAAACATGAAGACAAAAAAATTCAATGACAAGAAA
** * * * *
3531 AGTCCATTTATACTCACCCATTCCTTCAAAAGCCTTATTAGTCACTTTAAATGGTTTTCTAATCT
66 AGTCCATTTATACTCACCCATTCCTTCAAAAGCCAAATTACTAACTTCAAATGGTTTTATAATCT
*
3596 CATAATTNNNNNNNNNNNNNATTGTTTTATATTTTTGATT
131 AATAATT-------------ATTGTTTTATATTTTTGATT
*
3636 AAACAGACTATAATTGAATATTTA-CCTCGAGAAACATGAAGA-AAAAAAATT-AATTGACAAGA
1 AAACAGACAATAATTGAATATTTATCCT-GAGAAACATGAAGACAAAAAAATTCAA-TGACAAGA
* * *
3698 AAAGTCCATTTATAGTCACCCTTTCCTTGAAAAGCCAAATTACTAACTTCAAATGGTTTTATAAT
64 AAAGTCCATTTATACTCACCCATTCCTTCAAAAGCCAAATTACTAACTTCAAATGGTTTTATAAT
3763 CTAATAATTA
129 CTAATAATTA
3773 ATTTTAAGCT
Statistics
Matches: 119, Mismatches: 16, Indels: 18
0.78 0.10 0.12
Matches are distributed among these distances:
156 1 0.01
168 2 0.02
169 81 0.68
170 35 0.29
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.32
Consensus pattern (157 bp):
AAACAGACAATAATTGAATATTTATCCTGAGAAACATGAAGACAAAAAAATTCAATGACAAGAAA
AGTCCATTTATACTCACCCATTCCTTCAAAAGCCAAATTACTAACTTCAAATGGTTTTATAATCT
AATAATTATTGTTTTATATTTTTGATT
Done.