Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397332.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2675.0, 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: 54470
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.31
Warning! 5373 characters in sequence are not A, C, G, or T
Found at i:16403 original size:20 final size:21
Alignment explanation
Indices: 16370--16411 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
16360 AGTCATATGT
16370 TTCTTTCTTCTCAAA-ATTTC
1 TTCTTTCTTCTCAAATATTTC
16390 TTCTTTCCTT-TCAAATATTTC
1 TTCTTT-CTTCTCAAATATTTC
16411 T
1 T
16412 AACTTCATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.19, C:0.24, G:0.00, T:0.57
Consensus pattern (21 bp):
TTCTTTCTTCTCAAATATTTC
Found at i:21830 original size:15 final size:15
Alignment explanation
Indices: 21810--21863 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 15
21800 ATTACAATAC
* *
21810 AATGTGATTATAGGT
1 AATGTGATTACAAGT
*
21825 AATGTGATTGCAAGT
1 AATGTGATTACAAGT
* *
21840 AATGTGATTGCAAGC
1 AATGTGATTACAAGT
21855 AATGTGATT
1 AATGTGATT
21864 GTAGGGAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.33, C:0.06, G:0.26, T:0.35
Consensus pattern (15 bp):
AATGTGATTACAAGT
Found at i:21864 original size:15 final size:15
Alignment explanation
Indices: 21825--21864 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
21815 GATTATAGGT
*
21825 AATGTGATTGCAAGT
1 AATGTGATTGCAAGC
21840 AATGTGATTGCAAGC
1 AATGTGATTGCAAGC
21855 AATGTGATTG
1 AATGTGATTG
21865 TAGGGAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.33, C:0.07, G:0.28, T:0.33
Consensus pattern (15 bp):
AATGTGATTGCAAGC
Found at i:22049 original size:28 final size:28
Alignment explanation
Indices: 22017--22161 Score: 87
Period size: 26 Copynumber: 5.4 Consensus size: 28
22007 TCAAGTTTAA
*
22017 TATATTTATATTTTTTATTATTAATTTT
1 TATATATATATTTTTTATTATTAATTTT
* * *
22045 TATATAATGTCATTTCTTA--AATATATTTT
1 TATAT-ATAT-ATTTTTTATTATTA-ATTTT
* *
22074 TAATATGATATATTTTTTTTTATT-A-TTA
1 T-ATAT-ATATATTTTTTATTATTAATTTT
*
22102 T-TATA-ATATTTTGTATT-TT-ATTTT
1 TATATATATATTTTTTATTATTAATTTT
* *
22126 AATATTTATA-TTTTTATTATTAA-TTT
1 TATATATATATTTTTTATTATTAATTTT
22152 TATATA-ATAT
1 TATATATATAT
22162 CATATCTTAA
Statistics
Matches: 87, Mismatches: 18, Indels: 26
0.66 0.14 0.20
Matches are distributed among these distances:
23 3 0.03
24 12 0.14
25 14 0.16
26 15 0.17
27 1 0.01
28 11 0.13
29 15 0.17
30 14 0.16
31 2 0.02
ACGTcount: A:0.32, C:0.01, G:0.02, T:0.64
Consensus pattern (28 bp):
TATATATATATTTTTTATTATTAATTTT
Found at i:22153 original size:20 final size:20
Alignment explanation
Indices: 22089--22156 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 20
22079 TGATATATTT
* * *
22089 TTTTTTATTATTATTATAATA
1 TTTTATATTTTTATTATTA-A
*
22110 TTTTGTA-TTTTATT-TTAA
1 TTTTATATTTTTATTATTAA
22128 TATTTATATTTTTATTATTAA
1 T-TTTATATTTTTATTATTAA
22149 TTTTATAT
1 TTTTATAT
22157 AATATCATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
18 2 0.05
19 7 0.17
20 20 0.50
21 11 0.28
ACGTcount: A:0.29, C:0.00, G:0.01, T:0.69
Consensus pattern (20 bp):
TTTTATATTTTTATTATTAA
Found at i:22170 original size:107 final size:111
Alignment explanation
Indices: 22018--22234 Score: 327
Period size: 109 Copynumber: 2.0 Consensus size: 111
22008 CAAGTTTAAT
* * *
22018 ATATTTATATTTTTTATTATTAATTTTTATATAATGTCATTTCTTAAATATATTTTTAATATGAT
1 ATATTTATATTTTTTATTATTAATTTTTATATAATATCATATCTTAAAT-TATTTTTAATATCAT
* *
22083 ATATTTT-TTTTT-A-TTATTATTATAATATTTTGTATTTTATTTTA
65 ATATTTTATTTTTCATTTATTATTATAATATTATATATTTTATTTTA
*
22127 ATATTTATA-TTTTTATTATTAA-TTTTATATAATATCATATCTTAAATTATTTTTAATGTCATA
1 ATATTTATATTTTTTATTATTAATTTTTATATAATATCATATCTTAAATTATTTTTAATATCATA
*
22190 TATTTTATTTTTCATTTATTATTATAATCTTATATATTTTATTTT
66 TATTTTATTTTTCATTTATTATTATAATATTATATATTTTATTTT
22235 CATTTCTTTA
Statistics
Matches: 98, Mismatches: 7, Indels: 6
0.88 0.06 0.05
Matches are distributed among these distances:
106 20 0.20
107 28 0.29
108 14 0.14
109 36 0.37
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (111 bp):
ATATTTATATTTTTTATTATTAATTTTTATATAATATCATATCTTAAATTATTTTTAATATCATA
TATTTTATTTTTCATTTATTATTATAATATTATATATTTTATTTTA
Found at i:22246 original size:29 final size:32
Alignment explanation
Indices: 22172--22238 Score: 84
Period size: 34 Copynumber: 2.1 Consensus size: 32
22162 CATATCTTAA
*
22172 ATTATT-TTTAATGTCATATATTTTATTTTTC
1 ATTATTATTTAATCTCATATATTTTATTTTTC
*
22203 ATTTATTATTATAATCTTATATATTTTA-TTTTC
1 A-TTATTATT-TAATCTCATATATTTTATTTTTC
22236 ATT
1 ATT
22239 TCTTTAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
31 1 0.03
32 7 0.23
33 8 0.26
34 15 0.48
ACGTcount: A:0.28, C:0.06, G:0.01, T:0.64
Consensus pattern (32 bp):
ATTATTATTTAATCTCATATATTTTATTTTTC
Found at i:22367 original size:14 final size:14
Alignment explanation
Indices: 22350--22376 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
22340 ATCTTATATA
22350 TTTTATTTTAATTT
1 TTTTATTTTAATTT
22364 TTTTATTTTAATT
1 TTTTATTTTAATT
22377 ATAACATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTATTTTAATTT
Found at i:26475 original size:22 final size:22
Alignment explanation
Indices: 26437--26482 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
26427 TTATATGTAT
*
26437 TAACAAGATCTGATAAGGCATG
1 TAACAAGATCTGATAAGACATG
*
26459 TAACAAGA-CATGCTAAGACATG
1 TAACAAGATC-TGATAAGACATG
26481 TA
1 TA
26483 GTATATATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 20 0.95
ACGTcount: A:0.43, C:0.15, G:0.20, T:0.22
Consensus pattern (22 bp):
TAACAAGATCTGATAAGACATG
Found at i:27917 original size:72 final size:70
Alignment explanation
Indices: 27768--27923 Score: 158
Period size: 72 Copynumber: 2.2 Consensus size: 70
27758 TTTGACATCA
* *
27768 AACCTTTTTATACTAGGGTTAATTCCTCATAGATAATAAGCTTTCAATTAGCTACTAAATGCCAG
1 AACCTTTCTATACTAGGGTTAATTCCTCATAGATAATAAGCTTTCAATTAACTACTAAATGCCAG
27833 GGATC
66 GGATC
* * *
27838 AACCCTTTCTATACTAAGGGTTAA-TCCTTC-TAGGA-CATAGAGCTTTCCAGTTAACTACTAGA
1 AA-CCTTTCTATACT-AGGGTTAATTCC-TCATA-GATAATA-AGCTTT-CAATTAACTACTAAA
** *
27900 TGGTAGGGATT
60 TGCCAGGGATC
27911 AACCTTTCT-TACT
1 AACCTTTCTATACT
27924 TTAAAGGTTG
Statistics
Matches: 72, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
70 2 0.03
71 23 0.32
72 25 0.35
73 22 0.31
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (70 bp):
AACCTTTCTATACTAGGGTTAATTCCTCATAGATAATAAGCTTTCAATTAACTACTAAATGCCAG
GGATC
Found at i:28445 original size:55 final size:55
Alignment explanation
Indices: 28277--28449 Score: 129
Period size: 55 Copynumber: 3.1 Consensus size: 55
28267 GTCTTTGTTG
* * * * *
28277 GATAGGGTGAACAAGTTATGTGTCTCAACACATGTCTAGCA-GTATCG-CCCTTACTA
1 GATAGGGT-AACAAGTGATGTGACTTAACACACGTCTAGCACCT-T-GACCCTTACTA
* * * * * ** * *
28333 GATAAGGAG-AATAAGTGATGTGCCTTAGCACACATCTATCACC-AAAGCCTTTGCTA
1 GAT-AGG-GTAACAAGTGATGTGACTTAACACACGTCTAGCACCTTGA-CCCTTACTA
*
28389 GATAGGGTAACAAGTGATGTGACTTAACACACGTCTAGCACCTTGATCCTTACTA
1 GATAGGGTAACAAGTGATGTGACTTAACACACGTCTAGCACCTTGACCCTTACTA
28444 GATAGG
1 GATAGG
28450 ATGATAAAGC
Statistics
Matches: 87, Mismatches: 23, Indels: 15
0.70 0.18 0.12
Matches are distributed among these distances:
54 1 0.01
55 44 0.51
56 38 0.44
57 3 0.03
58 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (55 bp):
GATAGGGTAACAAGTGATGTGACTTAACACACGTCTAGCACCTTGACCCTTACTA
Found at i:28710 original size:58 final size:58
Alignment explanation
Indices: 28591--28791 Score: 201
Period size: 61 Copynumber: 3.4 Consensus size: 58
28581 CTTACTTATT
* * * *
28591 GCACCATAGCCCTTGCTAGTTAGGAAGAACAAGCATCTGTCTTACTTATTACACATGTCTA
1 GCACCAT-GCCCTTGCTAGATA-G-AGAACAAGCATGTGTCTTACTTATTGCACATATCTA
* * * *
28652 GCAACATAGCCCTTGCTAGATAG-GAACAAACATGTGTCGTACTTATTGCACATCTCTA
1 GCACCAT-GCCCTTGCTAGATAGAGAACAAGCATGTGTCTTACTTATTGCACATATCTA
* * *
28710 GCACCAT-CGCTTCGACTAGATAAGAATAACAAGCATGTGTCTTACATATTGCACATATCTA
1 GCACCATGCCCTT-G-CTAGAT-AG-AGAACAAGCATGTGTCTTACTTATTGCACATATCTA
*
28771 GCACCATG-CCTTGCAAGATAG
1 GCACCATGCCCTTGCTAGATAG
28792 GCCTCACAAG
Statistics
Matches: 118, Mismatches: 16, Indels: 15
0.79 0.11 0.10
Matches are distributed among these distances:
56 4 0.03
57 1 0.01
58 44 0.37
59 7 0.06
60 2 0.02
61 60 0.51
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.27
Consensus pattern (58 bp):
GCACCATGCCCTTGCTAGATAGAGAACAAGCATGTGTCTTACTTATTGCACATATCTA
Found at i:29515 original size:16 final size:16
Alignment explanation
Indices: 29485--29514 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29475 AACAAATTTA
29485 GATTTTGATTCTTTTG
1 GATTTTGATTCTTTTG
29501 GATTTTGATT-TTTT
1 GATTTTGATTCTTTT
29515 TTATATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.13, C:0.03, G:0.17, T:0.67
Consensus pattern (16 bp):
GATTTTGATTCTTTTG
Found at i:29851 original size:68 final size:68
Alignment explanation
Indices: 29742--29940 Score: 245
Period size: 68 Copynumber: 2.9 Consensus size: 68
29732 CACGTTTGGT
* * * * * *
29742 ATGATGAATGCCCTAAAATTATGTATATAATGTAAATTCCATATCCCATATGAGATGATTAAGTA
1 ATGATGAATGCCATGAGATTATGTATATAATGTATATTCCATATACCATATGAGATGATTAAGAA
**
29807 TGC
66 AAC
* * * *
29810 ATGATGAATGCCATGAGATTATTTATATGATGTATATTCCATATACCACATGAGATGATTTAGAA
1 ATGATGAATGCCATGAGATTATGTATATAATGTATATTCCATATACCATATGAGATGATTAAGAA
*
29875 AAT
66 AAC
* * * *
29878 ATGATGAATGTCATGAGATTATGTATATAATGTATTTTCCATATACCTTATGAGATGAATAAG
1 ATGATGAATGCCATGAGATTATGTATATAATGTATATTCCATATACCATATGAGATGATTAAG
29941 CATGTCTGTG
Statistics
Matches: 110, Mismatches: 21, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
68 110 1.00
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (68 bp):
ATGATGAATGCCATGAGATTATGTATATAATGTATATTCCATATACCATATGAGATGATTAAGAA
AAC
Found at i:30447 original size:20 final size:20
Alignment explanation
Indices: 30422--30465 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
30412 AATGTATAAG
30422 ATTCTTGAAAGTATCGATAC
1 ATTCTTGAAAGTATCGATAC
* *
30442 ATTCTTGAATGTATCGATAG
1 ATTCTTGAAAGTATCGATAC
30462 ATTC
1 ATTC
30466 ATTGCAAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.39
Consensus pattern (20 bp):
ATTCTTGAAAGTATCGATAC
Found at i:38558 original size:22 final size:22
Alignment explanation
Indices: 38530--38576 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
38520 CTTTTTTATG
38530 AAATATTATTCTCTATCTTTCA
1 AAATATTATTCTCTATCTTTCA
* * *
38552 AAATATTGTTCTTTATCTTTTA
1 AAATATTATTCTCTATCTTTCA
38574 AAA
1 AAA
38577 AAGAAAAGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.34, C:0.13, G:0.02, T:0.51
Consensus pattern (22 bp):
AAATATTATTCTCTATCTTTCA
Found at i:39813 original size:16 final size:16
Alignment explanation
Indices: 39759--39826 Score: 68
Period size: 16 Copynumber: 4.2 Consensus size: 16
39749 TCATTTTATT
39759 TTTAAAT-ATTAATAA
1 TTTAAATAATTAATAA
*
39774 TTTATAATATATTAAAAA
1 TTTA-AATA-ATTAATAA
* *
39792 TATAAATAATTGATAA
1 TTTAAATAATTAATAA
*
39808 TTTAAAT-ATTAATAT
1 TTTAAATAATTAATAA
39823 TTTA
1 TTTA
39827 TTTATACTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
15 14 0.33
16 15 0.35
17 4 0.09
18 10 0.23
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (16 bp):
TTTAAATAATTAATAA
Found at i:40391 original size:23 final size:23
Alignment explanation
Indices: 40361--40405 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
40351 GGAGAGAGTG
40361 TAACGACCTCTTCCCTCGATCGT
1 TAACGACCTCTTCCCTCGATCGT
40384 TAACGACCTCTTCCCTCGATCG
1 TAACGACCTCTTCCCTCGATCG
40406 AGACTATGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.18, C:0.40, G:0.13, T:0.29
Consensus pattern (23 bp):
TAACGACCTCTTCCCTCGATCGT
Found at i:43390 original size:18 final size:19
Alignment explanation
Indices: 43351--43397 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
43341 TTAATATTTT
43351 AATAATATTTTATTCATAA
1 AATAATATTTTATTCATAA
* *
43370 AATATTATTTTATT-TTAA
1 AATAATATTTTATTCATAA
43388 AATAAT-TTTT
1 AATAATATTTT
43398 TTACCTATCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 4 0.16
18 8 0.32
19 13 0.52
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (19 bp):
AATAATATTTTATTCATAA
Found at i:45013 original size:73 final size:74
Alignment explanation
Indices: 44865--45030 Score: 183
Period size: 73 Copynumber: 2.3 Consensus size: 74
44855 AAACAGAATA
* * * ** * * *
44865 CTCTTAGTCAAATAAC-ATGCTTTTTAGTTGATTAAGTCGTTTATGTCTTCTGATCCCAATTTTT
1 CTCTTAGTCGACTAACAATGCTTCTTAGTCAATTAAGTCGTTTATGTCGTCTGAACCCAATTTCT
*
44929 GGCAATGAG
66 GGCAATAAG
* *
44938 CTCTTAGTCGACTAACAATGCTTCTTAGTCAATTAAGTCGTTTCTGT-GTCTGAACCCAGTTTCT
1 CTCTTAGTCGACTAACAATGCTTCTTAGTCAATTAAGTCGTTTATGTCGTCTGAACCCAATTTCT
* *
45002 GGTAGTAAG
66 GGCAATAAG
* *
45011 CTCTTAATTGACTAACAATG
1 CTCTTAGTCGACTAACAATG
45031 TCTGTTGGCC
Statistics
Matches: 77, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
73 51 0.66
74 26 0.34
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.39
Consensus pattern (74 bp):
CTCTTAGTCGACTAACAATGCTTCTTAGTCAATTAAGTCGTTTATGTCGTCTGAACCCAATTTCT
GGCAATAAG
Done.