Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397268.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_81.0, 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: 6219335
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 77647 characters in sequence are not A, C, G, or T
File 13 of 13
Found at i:6153790 original size:7 final size:7
Alignment explanation
Indices: 6153752--6153798 Score: 51
Period size: 7 Copynumber: 6.9 Consensus size: 7
6153742 TTTTTTTTAA
6153752 AAAAAAT
1 AAAAAAT
*
6153759 AATAAAT
1 AAAAAAT
*
6153766 AATAAAT
1 AAAAAAT
*
6153773 AATAAAT
1 AAAAAAT
*
6153780 AAAATA-
1 AAAAAAT
6153786 AAAAAAT
1 AAAAAAT
6153793 AAAAAA
1 AAAAAA
6153799 AGCTGAAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
6 5 0.14
7 30 0.86
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (7 bp):
AAAAAAT
Found at i:6154428 original size:39 final size:40
Alignment explanation
Indices: 6154372--6154461 Score: 112
Period size: 39 Copynumber: 2.2 Consensus size: 40
6154362 ACCGAAGTAA
6154372 AGAAGAGGAAAGAAGGCTGCCGGCGCG-GAAAAAAAGAGAG
1 AGAAG-GGAAAGAAGGCTGCCGGCGCGAGAAAAAAAGAGAG
** *
6154412 AG-AGGGAAAGGAAGGCTGCCGGCTTGAGAAAGAAAGAGAG
1 AGAAGGGAAA-GAAGGCTGCCGGCGCGAGAAAAAAAGAGAG
*
6154452 GGAAGGGAAA
1 AGAAGGGAAA
6154462 CGCTGGCGGG
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
38 5 0.12
39 16 0.37
40 15 0.35
41 7 0.16
ACGTcount: A:0.43, C:0.10, G:0.42, T:0.04
Consensus pattern (40 bp):
AGAAGGGAAAGAAGGCTGCCGGCGCGAGAAAAAAAGAGAG
Found at i:6159037 original size:20 final size:20
Alignment explanation
Indices: 6158999--6159038 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
6158989 TCAAATCACT
* *
6158999 CATCATACATTTAATCATCC
1 CATCATACATTCAAACATCC
*
6159019 CATCATGCATTCAAACATCC
1 CATCATACATTCAAACATCC
6159039 TTCAAATTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.35, C:0.33, G:0.03, T:0.30
Consensus pattern (20 bp):
CATCATACATTCAAACATCC
Found at i:6163954 original size:22 final size:22
Alignment explanation
Indices: 6163904--6163966 Score: 74
Period size: 21 Copynumber: 2.9 Consensus size: 22
6163894 GAGCAACATT
*
6163904 TTCTTTAAAACCTCCGGGTACA
1 TTCTTCAAAACCTCCGGGTACA
* * *
6163926 -TCTTCAAAAGCTCTGGGTATA
1 TTCTTCAAAACCTCCGGGTACA
*
6163947 TTCTTCAAAACCTCCAGGTA
1 TTCTTCAAAACCTCCGGGTA
6163967 ATTAGTTTCT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
21 17 0.52
22 16 0.48
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (22 bp):
TTCTTCAAAACCTCCGGGTACA
Found at i:6163993 original size:24 final size:24
Alignment explanation
Indices: 6163966--6164014 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
6163956 ACCTCCAGGT
*
6163966 AATTAGTTTCTAGATTTCATTAAA
1 AATTAGTTTCTAGATTTCAGTAAA
*
6163990 AATTAGTTTTTAGATTTCAGTAAA
1 AATTAGTTTCTAGATTTCAGTAAA
6164014 A
1 A
6164015 GTTACGTAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.39, C:0.06, G:0.10, T:0.45
Consensus pattern (24 bp):
AATTAGTTTCTAGATTTCAGTAAA
Found at i:6164116 original size:147 final size:147
Alignment explanation
Indices: 6163843--6164137 Score: 414
Period size: 147 Copynumber: 2.0 Consensus size: 147
6163833 AATTTCAGAT
* *
6163843 AATTAGTTTCTAGATTTCATTAAAAGTTACGTAACCTCATTTAGAGATGAGGAGCAACATTTTCT
1 AATTAGTTTCTAGATTTCAGTAAAAGTTACGTAACCTCATTTAGAGATGAGGAGCAACACTTTCT
* *** *
6163908 TTAAAACCTCCGGGTACATCTTCAAAAGCTCTGGGTATATTCTTCAAAACCTCCAGGTAATTAG-
66 TTAAAACCTCCAGGTACATCTTCAAAAGCTCCAAGTATATCCTTCAAAACCTCCAGGTAATTAGT
6163972 TTTCTAGATTTCATTAAA
131 TTTC-AGATTTCATTAAA
* * * *
6163990 AATTAGTTTTTAGATTTCAGTAAAAGTTACGTAGCCTCATTTGGAGATGAGGAGCAACCCTTTCT
1 AATTAGTTTCTAGATTTCAGTAAAAGTTACGTAACCTCATTTAGAGATGAGGAGCAACACTTTCT
* * * *
6164055 TTAAAAGCTCTAGGTACATCTTCACAAGCTCCAAGTATATCCTTCAAAATCTCC-GGATAATTAG
66 TTAAAACCTCCAGGTACATCTTCAAAAGCTCCAAGTATATCCTTCAAAACCTCCAGG-TAATTAG
*
6164119 TTTTCAGATTTTATTAAA
130 TTTTCAGATTTCATTAAA
6164137 A
1 A
6164138 GTTACGTAAC
Statistics
Matches: 130, Mismatches: 16, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
146 2 0.02
147 124 0.95
148 4 0.03
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.35
Consensus pattern (147 bp):
AATTAGTTTCTAGATTTCAGTAAAAGTTACGTAACCTCATTTAGAGATGAGGAGCAACACTTTCT
TTAAAACCTCCAGGTACATCTTCAAAAGCTCCAAGTATATCCTTCAAAACCTCCAGGTAATTAGT
TTTCAGATTTCATTAAA
Found at i:6169355 original size:19 final size:19
Alignment explanation
Indices: 6169331--6169369 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
6169321 GCTAGAGGAA
6169331 AATTTTGAAATAAAATAAT
1 AATTTTGAAATAAAATAAT
* *
6169350 AATTTTTAGATAAAATAAT
1 AATTTTGAAATAAAATAAT
6169369 A
1 A
6169370 TCAAAATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (19 bp):
AATTTTGAAATAAAATAAT
Found at i:6180616 original size:8 final size:8
Alignment explanation
Indices: 6180595--6180669 Score: 64
Period size: 8 Copynumber: 9.2 Consensus size: 8
6180585 AAGTGAGAAG
6180595 AGAAAGGGA
1 AGAAA-GGA
*
6180604 A-AAAGAA
1 AGAAAGGA
6180611 AGAAAGGA
1 AGAAAGGA
*
6180619 AGAAATGA
1 AGAAAGGA
6180627 AGAAAGGA
1 AGAAAGGA
*
6180635 AGAAAAGA
1 AGAAAGGA
* *
6180643 GGAAGAAGA
1 AGAA-AGGA
6180652 A-AAAGGA
1 AGAAAGGA
6180659 AGGAAAGGA
1 A-GAAAGGA
6180668 AG
1 AG
6180670 GATCGGCTTA
Statistics
Matches: 54, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
7 7 0.13
8 35 0.65
9 12 0.22
ACGTcount: A:0.64, C:0.00, G:0.35, T:0.01
Consensus pattern (8 bp):
AGAAAGGA
Found at i:6188744 original size:15 final size:15
Alignment explanation
Indices: 6188724--6188753 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6188714 NNNNAAATAT
6188724 TCTTTGTTCTCTTTC
1 TCTTTGTTCTCTTTC
*
6188739 TCTTTGTTTTCTTTC
1 TCTTTGTTCTCTTTC
6188754 ACATGGTGGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.23, G:0.07, T:0.70
Consensus pattern (15 bp):
TCTTTGTTCTCTTTC
Found at i:6198639 original size:72 final size:72
Alignment explanation
Indices: 6198503--6198639 Score: 177
Period size: 72 Copynumber: 1.9 Consensus size: 72
6198493 AACATTGTCA
* ** * * **
6198503 CTTAGTCGACTAAGTCGTCTCTGTCTCTGAACTGAGTTTCTGGCAGTAGGCTCTTAGTTGACTAA
1 CTTAGTCCACTAAGTCGTCTCAATCTCTGAACTGAGTTTCTGACAGTAAGCTCTTAGTCAACTAA
6198568 CAAACTT
66 CAAACTT
* *
6198575 CTTAGTCCATTAAGTCGTTTCAATCTCTGAACCT-AGTTTCTGACAGTAAGCTCTTAGTCAACTA
1 CTTAGTCCACTAAGTCGTCTCAATCTCTGAA-CTGAGTTTCTGACAGTAAGCTCTTAGTCAACTA
6198639 A
65 A
6198640 TACTGTTTCT
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
72 53 0.96
73 2 0.04
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.35
Consensus pattern (72 bp):
CTTAGTCCACTAAGTCGTCTCAATCTCTGAACTGAGTTTCTGACAGTAAGCTCTTAGTCAACTAA
CAAACTT
Found at i:6202347 original size:15 final size:16
Alignment explanation
Indices: 6202321--6202353 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
6202311 TTTATGGATG
6202321 ATGCAGTTTGCTCTTA
1 ATGCAGTTTGCTCTTA
6202337 ATGCA-TTTGCTCTTA
1 ATGCAGTTTGCTCTTA
6202352 AT
1 AT
6202354 TTAGGGAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.21, C:0.18, G:0.15, T:0.45
Consensus pattern (16 bp):
ATGCAGTTTGCTCTTA
Found at i:6204980 original size:73 final size:73
Alignment explanation
Indices: 6204879--6205077 Score: 195
Period size: 73 Copynumber: 2.7 Consensus size: 73
6204869 TCAGTTCAAA
* * *
6204879 TTTTTAGACAG-AATGCTCTTAATAGACTAACATTGTCACTTAGTCGACTAAGTTGTCTCTGTCT
1 TTTTT-GACAGTAA-GCTCTTAGTAGACTAACATTGTCTCTTAGTCGACTAAGTCGTCTCTGTCT
6204943 CTGAACCTAG
64 CTGAACCTAG
* * * *** * * * * *
6204953 TTTTTGACAGTAGGCTCTTAGTTGACTAGCA-AAACTTCTTAATCAATTAAGTCGTTTTTGTCTC
1 TTTTTGACAGTAAGCTCTTAGTAGACTAACATTGTC-TCTTAGTCGACTAAGTCGTCTCTGTCTC
6205017 TGAACCTAG
65 TGAACCTAG
* * * *
6205026 TTTCTGGCAGTAAGTTCTTAGTCGACTAACATTGTCTCTTAGTCGACTAAGT
1 TTTTTGACAGTAAGCTCTTAGTAGACTAACATTGTCTCTTAGTCGACTAAGT
6205078 GTTCTCTATT
Statistics
Matches: 96, Mismatches: 26, Indels: 7
0.74 0.20 0.05
Matches are distributed among these distances:
72 1 0.01
73 88 0.92
74 7 0.07
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (73 bp):
TTTTTGACAGTAAGCTCTTAGTAGACTAACATTGTCTCTTAGTCGACTAAGTCGTCTCTGTCTCT
GAACCTAG
Done.