Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397285.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_299.0, 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: 1083202
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.33
Warning! 21736 characters in sequence are not A, C, G, or T
File 4 of 4
Found at i:1000768 original size:5 final size:5
Alignment explanation
Indices: 1000758--1000801 Score: 56
Period size: 5 Copynumber: 9.2 Consensus size: 5
1000748 TTTAACTTAC
* *
1000758 TTTAT TTTAT TTTAT TTTAT TAT-T TTTAT TTT-T ATTAT TTTAT T
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT T
1000802 ATTAACACTC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
4 6 0.18
5 27 0.82
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTAT
Found at i:1000776 original size:15 final size:15
Alignment explanation
Indices: 1000758--1000801 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 15
1000748 TTTAACTTAC
1000758 TTTATTTTATTTTAT
1 TTTATTTTATTTTAT
*
1000773 TTTATTAT-TTTTAT
1 TTTATTTTATTTTAT
*
1000787 TTT-TATTATTTTAT
1 TTTATTTTATTTTAT
1000801 T
1 T
1000802 ATTAACACTC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
13 2 0.08
14 16 0.64
15 7 0.28
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTATTTTATTTTAT
Found at i:1000799 original size:14 final size:14
Alignment explanation
Indices: 1000764--1000801 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
1000754 TTACTTTATT
1000764 TTATTTTA-TTTTA
1 TTATTTTATTTTTA
1000777 TTATTTTTATTTTTA
1 TTA-TTTTATTTTTA
1000792 TTATTTTATT
1 TTATTTTATT
1000802 ATTAACACTC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 3 0.13
14 12 0.52
15 8 0.35
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
TTATTTTATTTTTA
Found at i:1000799 original size:23 final size:24
Alignment explanation
Indices: 1000758--1000804 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
1000748 TTTAACTTAC
*
1000758 TTTATTTTATTTTATTTTATTATT
1 TTTATTTTATATTATTTTATTATT
1000782 TTTATTTT-TATTATTTTATTATT
1 TTTATTTTATATTATTTTATTATT
1000805 AACACTCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (24 bp):
TTTATTTTATATTATTTTATTATT
Found at i:1004233 original size:15 final size:15
Alignment explanation
Indices: 1004197--1004230 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1004187 GTTGATTAGT
*
1004197 TTAATTTAATTTATT
1 TTAATTTAATTTATG
1004212 TTAATTTAATTTTATG
1 TTAATTTAA-TTTATG
1004228 TTA
1 TTA
1004231 TTTTTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (15 bp):
TTAATTTAATTTATG
Found at i:1009291 original size:2 final size:2
Alignment explanation
Indices: 1009284--1009308 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1009274 AGTTGCTGCC
1009284 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1009309 GTGCAAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1010321 original size:25 final size:25
Alignment explanation
Indices: 1010287--1010345 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 25
1010277 CGGTTTGTGA
* * *
1010287 TTATATGTGGCAGGGCCATGAGTTG
1 TTATACGTGGCAAGGCCACGAGTTG
*
1010312 TTATACGTGGCAAGGCTACGAGTTG
1 TTATACGTGGCAAGGCCACGAGTTG
*
1010337 ATATACGTG
1 TTATACGTG
1010346 ATTGTGACCA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.24, C:0.14, G:0.32, T:0.31
Consensus pattern (25 bp):
TTATACGTGGCAAGGCCACGAGTTG
Found at i:1015009 original size:21 final size:20
Alignment explanation
Indices: 1014979--1015017 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1014969 TTGAAAAACC
1014979 ATAGTCGACTATAGCCCATAT
1 ATAGTCGACTATA-CCCATAT
*
1015000 ATAGTTGACTATACCCAT
1 ATAGTCGACTATACCCAT
1015018 TAGTTTCTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.31
Consensus pattern (20 bp):
ATAGTCGACTATACCCATAT
Found at i:1022800 original size:21 final size:22
Alignment explanation
Indices: 1022771--1022814 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1022761 AAATGATTAA
1022771 TTTAAGTTATTTTA-GTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
* *
1022792 TTTAGGTTATTTTATTTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
1022814 T
1 T
1022815 ACTTTAAGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (22 bp):
TTTAAGTTATTTTATGTTAAAT
Found at i:1039064 original size:11 final size:12
Alignment explanation
Indices: 1039048--1039076 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
1039038 ACCATACAAG
1039048 AAAAGAAAAA-A
1 AAAAGAAAAAGA
1039059 AAAAGAAAAAGA
1 AAAAGAAAAAGA
1039071 AAAAGA
1 AAAAGA
1039077 CATGAGGTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 10 0.59
12 7 0.41
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAAGA
Found at i:1039075 original size:6 final size:6
Alignment explanation
Indices: 1039048--1039076 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
1039038 ACCATACAAG
1039048 AAAAGA AAAA-A AAAAGA AAAAGA AAAAGA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
1039077 CATGAGGTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:1045637 original size:21 final size:22
Alignment explanation
Indices: 1045612--1045655 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
1045602 AAGTGATTAA
1045612 TTTAAGTTATTTTA-GTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
*
1045633 TTTAAGTTATTTTATTTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
1045655 T
1 T
1045656 ACTTTAAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (22 bp):
TTTAAGTTATTTTATGTTAAAT
Found at i:1050343 original size:18 final size:18
Alignment explanation
Indices: 1050322--1050364 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
1050312 CTTGTCATAT
1050322 TCTTCTTCAGCTTCATCA
1 TCTTCTTCAGCTTCATCA
* * *
1050340 TCTTCATCATCTTCGTCA
1 TCTTCTTCAGCTTCATCA
*
1050358 CCTTCTT
1 TCTTCTT
1050365 TATTATGTTC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.14, C:0.35, G:0.05, T:0.47
Consensus pattern (18 bp):
TCTTCTTCAGCTTCATCA
Found at i:1062025 original size:2 final size:2
Alignment explanation
Indices: 1062018--1062060 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
1062008 TTAGAAAGAA
* *
1062018 AG AG AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1062060 A
1 A
1062061 CTTAATAACT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1062029 original size:14 final size:14
Alignment explanation
Indices: 1062010--1062060 Score: 84
Period size: 14 Copynumber: 3.6 Consensus size: 14
1062000 GGTAAGGATT
*
1062010 AGAAAGAAAGAGAG
1 AGAAAGAGAGAGAG
1062024 AGAAAGAGAGAGAG
1 AGAAAGAGAGAGAG
*
1062038 AGAGAGAGAGAGAG
1 AGAAAGAGAGAGAG
1062052 AGAAAGAGA
1 AGAAAGAGA
1062061 CTTAATAACT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 34 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (14 bp):
AGAAAGAGAGAGAG
Found at i:1063343 original size:29 final size:29
Alignment explanation
Indices: 1063282--1063349 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
1063272 ACCTAATCCT
* *
1063282 TGAAAAGGCAAAAGGTTATGTCTGATCCT
1 TGAAAAGGCAAAAGGTTATGTCTGATACG
* *
1063311 TGAAAAGG-AAAAGGTTATGTTTGCTTACG
1 TGAAAAGGCAAAAGGTTATGTCTG-ATACG
1063340 TGAAAAGGCA
1 TGAAAAGGCA
1063350 TTGTGTGGGT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 14 0.42
29 18 0.55
30 1 0.03
ACGTcount: A:0.37, C:0.10, G:0.26, T:0.26
Consensus pattern (29 bp):
TGAAAAGGCAAAAGGTTATGTCTGATACG
Found at i:1064284 original size:19 final size:21
Alignment explanation
Indices: 1064246--1064284 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1064236 CTTTAAACTA
1064246 ATTATCATCGTTTCTTAATTG
1 ATTATCATCGTTTCTTAATTG
1064267 ATTATCATC-TTT-TTAATT
1 ATTATCATCGTTTCTTAATT
1064285 AAAGTCATCC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 3 0.17
21 9 0.50
ACGTcount: A:0.26, C:0.13, G:0.05, T:0.56
Consensus pattern (21 bp):
ATTATCATCGTTTCTTAATTG
Found at i:1066083 original size:21 final size:21
Alignment explanation
Indices: 1066059--1066109 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
1066049 TAAAGTATAG
1066059 AGGTGCTTGAAACTATAATAT
1 AGGTGCTTGAAACTATAATAT
1066080 AGGTGCTTGAAACTATAATAT
1 AGGTGCTTGAAACTATAATAT
1066101 AGGTGCTTG
1 AGGTGCTTG
1066110 CTTAGGAGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.33, C:0.10, G:0.24, T:0.33
Consensus pattern (21 bp):
AGGTGCTTGAAACTATAATAT
Found at i:1067729 original size:71 final size:71
Alignment explanation
Indices: 1067648--1067802 Score: 199
Period size: 71 Copynumber: 2.2 Consensus size: 71
1067638 TTTAACCTAT
* * * * *
1067648 CAAGGTCGACTATA-TCTCTTCTATAGTTGACTATGGCAATTCTTCAACTTGATTTTTTTGGT-T
1 CAAGGTCGACTATACT-TCCTCTATAGTCGACTATGGCAATTC-TAAACTTGATTTTCTTGATCT
1067711 TTCTAG-AA
64 TT-TAGAAA
*
1067719 CAAGGTCGACTATACTTCCTCTATAGTCGACTATGGCTATTCTAAACTTGATTTTCTTGATCTTT
1 CAAGGTCGACTATACTTCCTCTATAGTCGACTATGGCAATTCTAAACTTGATTTTCTTGATCTTT
*
1067784 TTGAAA
66 TAGAAA
1067790 CAAGGTCGACTAT
1 CAAGGTCGACTAT
1067803 GTTTTCTTTC
Statistics
Matches: 74, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
70 18 0.24
71 55 0.74
72 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.41
Consensus pattern (71 bp):
CAAGGTCGACTATACTTCCTCTATAGTCGACTATGGCAATTCTAAACTTGATTTTCTTGATCTTT
TAGAAA
Found at i:1067822 original size:71 final size:70
Alignment explanation
Indices: 1067648--1067827 Score: 170
Period size: 71 Copynumber: 2.5 Consensus size: 70
1067638 TTTAACCTAT
* * * * *
1067648 CAAGGTCGACTATATCTC-TTCTATAGTTGACTATGGCAATTCTTCAACTTGATTTTTTTGGTTT
1 CAAGGTCGACTATATTTCTTTCTA-A-TTGACTATGGCTATTCTTAAACTTGATTTTCTTGATTT
1067712 TCTAGAA
64 TCTAGAA
* * *
1067719 CAAGGTCGACTATACTTC-CTCTATAGTCGACTATGGCTATTC-TAAACTTGATTTTCTTGATCT
1 CAAGGTCGACTATATTTCTTTCTA-A-TTGACTATGGCTATTCTTAAACTTGATTTTCTTGAT-T
*
1067782 TT-TTGAAA
63 TTCTAG-AA
* *
1067790 CAAGGTCGACTATGTTTTCTTTCTAATTGACTAAGGCT
1 CAAGGTCGACTAT-ATTTCTTTCTAATTGACTATGGCT
1067828 TTATGATCTT
Statistics
Matches: 91, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
70 18 0.20
71 65 0.71
72 4 0.04
73 4 0.04
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.42
Consensus pattern (70 bp):
CAAGGTCGACTATATTTCTTTCTAATTGACTATGGCTATTCTTAAACTTGATTTTCTTGATTTTC
TAGAA
Found at i:1070063 original size:4 final size:4
Alignment explanation
Indices: 1070054--1070083 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
1070044 AGAGAAGGGG
*
1070054 AGAA AGAA AGAA AGAA AGAA AGGA AGAA AG
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AG
1070084 GGGGAAGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:1073543 original size:18 final size:18
Alignment explanation
Indices: 1073503--1073543 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
1073493 TAATTTATTT
1073503 AAAAA-AATACAACATAA
1 AAAAATAATACAACATAA
*
1073520 ATAAATAATACAAACA-AA
1 AAAAATAATAC-AACATAA
1073538 AAAAAT
1 AAAAAT
1073544 TTGTTAAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 4 0.20
18 12 0.60
19 4 0.20
ACGTcount: A:0.76, C:0.10, G:0.00, T:0.15
Consensus pattern (18 bp):
AAAAATAATACAACATAA
Found at i:1074520 original size:46 final size:46
Alignment explanation
Indices: 1074428--1074624 Score: 274
Period size: 46 Copynumber: 4.5 Consensus size: 46
1074418 AAATTGAACT
*
1074428 TCGACTTTGTGAAGCTTGA--G-G-A--TGAGAGATTATAAGATCA
1 TCGACTTTGTGAAGCTTGAGGGTGAAGGTGAGAGATTATAAGATCG
*
1074468 TCGACTTTGTGAAGCTTGAGGGTGAAGGTGAGAGATTATAGGATCG
1 TCGACTTTGTGAAGCTTGAGGGTGAAGGTGAGAGATTATAAGATCG
* *
1074514 TAGACTTTGTGAAACTTGAGGGTG-A---G-G-GATTATAAGATCG
1 TCGACTTTGTGAAGCTTGAGGGTGAAGGTGAGAGATTATAAGATCG
1074554 TCGACTTTGTGAAGCTTGAGGGTGAAGGTGAGAGATTATAAGATCG
1 TCGACTTTGTGAAGCTTGAGGGTGAAGGTGAGAGATTATAAGATCG
1074600 TCGACTTTGTGAAGCTTGAGGGTGA
1 TCGACTTTGTGAAGCTTGAGGGTGA
1074625 GAGATTAGAG
Statistics
Matches: 138, Mismatches: 7, Indels: 18
0.85 0.04 0.11
Matches are distributed among these distances:
40 53 0.38
41 2 0.01
42 2 0.01
43 1 0.01
44 2 0.01
45 2 0.01
46 76 0.55
ACGTcount: A:0.28, C:0.09, G:0.34, T:0.29
Consensus pattern (46 bp):
TCGACTTTGTGAAGCTTGAGGGTGAAGGTGAGAGATTATAAGATCG
Found at i:1074575 original size:86 final size:86
Alignment explanation
Indices: 1074430--1074631 Score: 350
Period size: 86 Copynumber: 2.3 Consensus size: 86
1074420 ATTGAACTTC
*
1074430 GACTTTGTGAAGCTTGAGGATGAGAGATTATAAGATCATCGACTTTGTGAAGCTTGAGGGTGAAG
1 GACTTTGTGAAGCTTGAGGGTGAGAGATTATAAGATCATCGACTTTGTGAAGCTTGAGGGTGAAG
*
1074495 GTGAGAGATTATAGGATCGTA
66 GTGAGAGATTATAAGATCGTA
* * *
1074516 GACTTTGTGAAACTTGAGGGTGAGGGATTATAAGATCGTCGACTTTGTGAAGCTTGAGGGTGAAG
1 GACTTTGTGAAGCTTGAGGGTGAGAGATTATAAGATCATCGACTTTGTGAAGCTTGAGGGTGAAG
*
1074581 GTGAGAGATTATAAGATCGTC
66 GTGAGAGATTATAAGATCGTA
1074602 GACTTTGTGAAGCTTGAGGGTGAGAGATTA
1 GACTTTGTGAAGCTTGAGGGTGAGAGATTA
1074632 GAGGATTGTG
Statistics
Matches: 108, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
86 108 1.00
ACGTcount: A:0.29, C:0.08, G:0.34, T:0.29
Consensus pattern (86 bp):
GACTTTGTGAAGCTTGAGGGTGAGAGATTATAAGATCATCGACTTTGTGAAGCTTGAGGGTGAAG
GTGAGAGATTATAAGATCGTA
Found at i:1077491 original size:3 final size:3
Alignment explanation
Indices: 1077483--1077525 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
1077473 AAAAGAGTAG
1077483 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1077526 GCTCATAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Done.