Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397262.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_67.0, 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: 8984705
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 112788 characters in sequence are not A, C, G, or T
File 20 of 20
Found at i:8861737 original size:29 final size:31
Alignment explanation
Indices: 8861670--8861740 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 31
8861660 TCCACTCCTA
8861670 CCGATTCCCCCCGGCCCCTTCCCCCACGAGTC
1 CCGATTCCCCCCGGCCCC-TCCCCCACGAGTC
* *
8861702 CCG-TTCCCCCCTGCCCC-CTCCCACGAGT-
1 CCGATTCCCCCCGGCCCCTCCCCCACGAGTC
*
8861730 CGGATTCCCCC
1 CCGATTCCCCC
8861741 TGCAGGCCTG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
28 2 0.06
29 17 0.49
31 13 0.37
32 3 0.09
ACGTcount: A:0.08, C:0.59, G:0.15, T:0.17
Consensus pattern (31 bp):
CCGATTCCCCCCGGCCCCTCCCCCACGAGTC
Found at i:8889482 original size:16 final size:17
Alignment explanation
Indices: 8889463--8889497 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
8889453 ATCATAGTAT
8889463 ATTATTTATTTATT-TA
1 ATTATTTATTTATTGTA
8889479 ATTATTTATTTATTGTA
1 ATTATTTATTTATTGTA
8889496 AT
1 AT
8889498 ATTACCATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (17 bp):
ATTATTTATTTATTGTA
Found at i:8902737 original size:3 final size:3
Alignment explanation
Indices: 8902731--8902760 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
8902721 ATAACGGTGG
*
8902731 TGA TGA TGA TGA AGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
8902761 CGACGATGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.37, C:0.00, G:0.33, T:0.30
Consensus pattern (3 bp):
TGA
Found at i:8902768 original size:9 final size:9
Alignment explanation
Indices: 8902756--8902781 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
8902746 TGATGATGAT
8902756 GATGACGAC
1 GATGACGAC
8902765 GATGACGAC
1 GATGACGAC
8902774 GATGACGA
1 GATGACGA
8902782 TAAATCGAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.19, G:0.35, T:0.12
Consensus pattern (9 bp):
GATGACGAC
Found at i:8906606 original size:45 final size:45
Alignment explanation
Indices: 8906452--8906593 Score: 214
Period size: 45 Copynumber: 3.2 Consensus size: 45
8906442 GCTATCTACT
* * * * *
8906452 GCAAAACAGAACGGAGAAGGTGC-GGTGTGGCGGTGCGATCTGCG
1 GCAAAACAGAACGGAAAAGGTACGGGTGCGGCTGTGAGATCTGCG
*
8906496 GCAAACCAGAACGGAAAAGGTACGGGTGCGGCTGTGAGATCTGCG
1 GCAAAACAGAACGGAAAAGGTACGGGTGCGGCTGTGAGATCTGCG
*
8906541 GCAAAACAGAACGGAAAAGGTACGGGTGCGGCTGTGAGATCTGTG
1 GCAAAACAGAACGGAAAAGGTACGGGTGCGGCTGTGAGATCTGCG
8906586 GCAAAACA
1 GCAAAACA
8906594 AAATGGAGAA
Statistics
Matches: 89, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
44 20 0.22
45 69 0.78
ACGTcount: A:0.30, C:0.18, G:0.38, T:0.13
Consensus pattern (45 bp):
GCAAAACAGAACGGAAAAGGTACGGGTGCGGCTGTGAGATCTGCG
Found at i:8906753 original size:124 final size:125
Alignment explanation
Indices: 8906533--8906764 Score: 315
Period size: 124 Copynumber: 1.9 Consensus size: 125
8906523 GCGGCTGTGA
* * * *
8906533 GATCTGCGGCAAAACAGAACGGAAAAGGTACGGGTGCGGCTGTGAGATCTGTGGCAAAACAAAAT
1 GATCTGCGACAAAACAGAACGAAAAAGGTACGGGTGCGGCGGTGAGATCTGCGGCAAAACAAAAT
*
8906598 GGAGAAGGTGCGGATGCAATCTCGCGGTGTGGT-GTGTGATCTGCGAGGCTGGGTGGTGT
66 GGAGAAGGTGCGGATGCAATCTCGCGGTGTGGTGGTGCGATCTGCGAGGCTGGGTGGTGT
* *** * * *
8906657 GATCTGCGACAAACCAGAACGAAAAAGGTGTTGGTGCGGCGGTGAGATTTGCGGTAAAACAGAAT
1 GATCTGCGACAAAACAGAACGAAAAAGGTACGGGTGCGGCGGTGAGATCTGCGGCAAAACAAAAT
* *
8906722 GGAGAAGGTGCGGGTGCGATCT-GCGGGTGTGGTGGTGCGATCT
66 GGAGAAGGTGCGGATGCAATCTCGC-GGTGTGGTGGTGCGATCT
8906765 ACGATAAACT
Statistics
Matches: 92, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
123 2 0.02
124 82 0.89
125 8 0.09
ACGTcount: A:0.25, C:0.15, G:0.40, T:0.20
Consensus pattern (125 bp):
GATCTGCGACAAAACAGAACGAAAAAGGTACGGGTGCGGCGGTGAGATCTGCGGCAAAACAAAAT
GGAGAAGGTGCGGATGCAATCTCGCGGTGTGGTGGTGCGATCTGCGAGGCTGGGTGGTGT
Found at i:8908442 original size:21 final size:21
Alignment explanation
Indices: 8908412--8908485 Score: 69
Period size: 21 Copynumber: 3.5 Consensus size: 21
8908402 TAAGTTACGT
* *
8908412 AATGTTCAAAGTTAGTCACAC
1 AATGTACAAAGTTAGTCACGC
* *
8908433 AATGTACAAAGTAAATCACGC
1 AATGTACAAAGTTAGTCACGC
*
8908454 AATGCTTA-AAAATTAGTCACGC
1 AATG--TACAAAGTTAGTCACGC
*
8908476 AATGTCCAAA
1 AATGTACAAA
8908486 AATCACCAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
20 1 0.02
21 24 0.57
22 15 0.36
23 2 0.05
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.24
Consensus pattern (21 bp):
AATGTACAAAGTTAGTCACGC
Found at i:8915028 original size:10 final size:11
Alignment explanation
Indices: 8915014--8915055 Score: 59
Period size: 12 Copynumber: 3.8 Consensus size: 11
8915004 ACAACATACA
*
8915014 AAAACCAAGCC
1 AAAACCAAACC
8915025 -AAACCAAACC
1 AAAACCAAACC
8915035 AAAACCAAAACC
1 AAAACC-AAACC
8915047 AAAACCAAA
1 AAAACCAAA
8915056 ACCTGTCAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
10 9 0.32
11 8 0.29
12 11 0.39
ACGTcount: A:0.64, C:0.33, G:0.02, T:0.00
Consensus pattern (11 bp):
AAAACCAAACC
Found at i:8915041 original size:6 final size:6
Alignment explanation
Indices: 8915025--8915058 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
8915015 AAACCAAGCC
8915025 AAACC- AAACCA AAACCA AAACCA AAACCA AAACC
1 AAACCA AAACCA AAACCA AAACCA AAACCA AAACC
8915059 TGTCAATCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.18
6 23 0.82
ACGTcount: A:0.65, C:0.35, G:0.00, T:0.00
Consensus pattern (6 bp):
AAACCA
Found at i:8925363 original size:24 final size:24
Alignment explanation
Indices: 8925304--8925363 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
8925294 TGAAGGCCCA
*
8925304 TCTCATTCTGCAGAGGATTGATGT
1 TCTCATTCTGCAGAGGATTAATGT
* *
8925328 TCTCAGTCTGCAGAGGGTTAATGT
1 TCTCATTCTGCAGAGGATTAATGT
* *
8925352 TTTCATTTTGCA
1 TCTCATTCTGCA
8925364 TGGGATGAGG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.20, C:0.17, G:0.23, T:0.40
Consensus pattern (24 bp):
TCTCATTCTGCAGAGGATTAATGT
Found at i:8931415 original size:29 final size:29
Alignment explanation
Indices: 8931383--8931441 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
8931373 GCAATTTCAT
*
8931383 CAATTTTATGTTTTGATAGCATGTCCTCC
1 CAATTTTATGTTTTGATAGCATGACCTCC
*
8931412 CAATTTTATGTTTTGATAGCTTGACCTCC
1 CAATTTTATGTTTTGATAGCATGACCTCC
8931441 C
1 C
8931442 CTTTTCTGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.20, C:0.22, G:0.14, T:0.44
Consensus pattern (29 bp):
CAATTTTATGTTTTGATAGCATGACCTCC
Found at i:8933021 original size:2 final size:2
Alignment explanation
Indices: 8933014--8933046 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
8933004 CTCCTGTTTG
*
8933014 CT CT CT CT CT CT CT CT CT CT CT CT CA CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
8933047 ATGTTTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.03, C:0.52, G:0.00, T:0.45
Consensus pattern (2 bp):
CT
Found at i:8934556 original size:104 final size:104
Alignment explanation
Indices: 8934371--8934578 Score: 308
Period size: 104 Copynumber: 2.0 Consensus size: 104
8934361 AGGTATAGTC
* * *
8934371 TCTCTCATAACAATATCAACTTAAGTTCAAGCCAATAAAAATTAAAAGAATAACTAGGAAGACCG
1 TCTCTCATAACAATATCAACTTAAGTTCAAGCCAACAAAAATCAAAAGAATAACAAGGAAGACCG
*
8934436 AGCACTGATGAGATGCTCATTTATATATTCGAAACATAA
66 AGCACTGATGAAATGCTCATTTATATATTCGAAACATAA
* * * * * * *
8934475 TCTCTCATAACAATTTCAACTTATGTTCATGTCACCAAAAATCAATAGAATAACAAGGAAGATCG
1 TCTCTCATAACAATATCAACTTAAGTTCAAGCCAACAAAAATCAAAAGAATAACAAGGAAGACCG
*
8934540 AGCACTGATGAAATGCTCATTTATATATTTGAAACATAA
66 AGCACTGATGAAATGCTCATTTATATATTCGAAACATAA
8934579 ATGCTTCTGT
Statistics
Matches: 92, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
104 92 1.00
ACGTcount: A:0.43, C:0.17, G:0.12, T:0.28
Consensus pattern (104 bp):
TCTCTCATAACAATATCAACTTAAGTTCAAGCCAACAAAAATCAAAAGAATAACAAGGAAGACCG
AGCACTGATGAAATGCTCATTTATATATTCGAAACATAA
Found at i:8949785 original size:2 final size:2
Alignment explanation
Indices: 8949778--8949818 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
8949768 TGTTATCAAT
8949778 AG AG AG AG AG AG AG AG AG A- AG -G A- AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
8949817 AG
1 AG
8949819 GGTAAACTGG
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 3 0.08
2 33 0.92
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:8951574 original size:5 final size:5
Alignment explanation
Indices: 8951564--8951590 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
8951554 CTTCAGAGCA
8951564 GTTGC GTTGC GTTGC GTTGC GTTGC GT
1 GTTGC GTTGC GTTGC GTTGC GTTGC GT
8951591 GGTCGTCTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.19, G:0.41, T:0.41
Consensus pattern (5 bp):
GTTGC
Found at i:8958084 original size:9 final size:9
Alignment explanation
Indices: 8958070--8958098 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
8958060 GATGGTGAGC
8958070 TTTTTTTA-
1 TTTTTTTAT
8958078 TTTTTTTAT
1 TTTTTTTAT
8958087 TTTTTTTAT
1 TTTTTTTAT
8958096 TTT
1 TTT
8958099 GTGTAGTCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:8961422 original size:18 final size:19
Alignment explanation
Indices: 8961382--8961421 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
8961372 AACCAAATTG
8961382 AAAA-TTTTGTTCTCTCAT
1 AAAACTTTTGTTCTCTCAT
8961400 AAAACTTTTGTTCTCTCAT
1 AAAACTTTTGTTCTCTCAT
8961419 AAA
1 AAA
8961422 CTGGTATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.33, C:0.17, G:0.05, T:0.45
Consensus pattern (19 bp):
AAAACTTTTGTTCTCTCAT
Found at i:8967188 original size:6 final size:6
Alignment explanation
Indices: 8967177--8967236 Score: 97
Period size: 6 Copynumber: 10.3 Consensus size: 6
8967167 ACGCAGTAGA
8967177 TCCCAT TCCCAT TCCCAT TCCCAT TCCCAT TCCCAT TCCCAT TCCC-T
1 TCCCAT TCCCAT TCCCAT TCCCAT TCCCAT TCCCAT TCCCAT TCCCAT
*
8967224 T-CCAT TCCTAT TC
1 TCCCAT TCCCAT TC
8967237 GGGAAAATAT
Statistics
Matches: 51, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
4 2 0.04
5 4 0.08
6 45 0.88
ACGTcount: A:0.15, C:0.48, G:0.00, T:0.37
Consensus pattern (6 bp):
TCCCAT
Found at i:8968995 original size:3 final size:3
Alignment explanation
Indices: 8968982--8969021 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
8968972 TTAATGAGAG
*
8968982 AGA AG- AGA AGA AGA AGA AGA AGA AGA AGG AGA AGA A-A AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
8969022 CAGCGTGATA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 4 0.12
3 29 0.88
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:8972945 original size:3 final size:3
Alignment explanation
Indices: 8972937--8972961 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
8972927 GGGAGTTGAC
8972937 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
8972962 GTAGTAGACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:8974845 original size:23 final size:23
Alignment explanation
Indices: 8974819--8974866 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
8974809 ACTTAAAATA
* * *
8974819 ATAAATAAAGATAATTTGAAAGT
1 ATAAATAAAGAAAAATAGAAAGT
*
8974842 ATAATTAAAGAAAAATAGAAAGT
1 ATAAATAAAGAAAAATAGAAAGT
8974865 AT
1 AT
8974867 TTAGGGGAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.60, C:0.00, G:0.12, T:0.27
Consensus pattern (23 bp):
ATAAATAAAGAAAAATAGAAAGT
Found at i:8980334 original size:2 final size:2
Alignment explanation
Indices: 8980327--8980359 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
8980317 NNNNNNNNNN
8980327 TA TA TA TA 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 TA TA TA TA T
8980360 GGCCACTTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.