Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397279.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_239.0, 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: 2022356
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6073 characters in sequence are not A, C, G, or T
File 5 of 5
Found at i:1964771 original size:22 final size:22
Alignment explanation
Indices: 1964746--1964795 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
1964736 TTAGGCACTA
*
1964746 CGTGACTGGTTTTTATATATTG
1 CGTGACTGGTTGTTATATATTG
* *
1964768 CGTGACTTGTTGTTATGTATTG
1 CGTGACTGGTTGTTATATATTG
1964790 CGTGAC
1 CGTGAC
1964796 ATTAGGCTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.16, C:0.12, G:0.26, T:0.46
Consensus pattern (22 bp):
CGTGACTGGTTGTTATATATTG
Found at i:1964907 original size:203 final size:203
Alignment explanation
Indices: 1964563--1964945 Score: 531
Period size: 203 Copynumber: 1.9 Consensus size: 203
1964553 TTTTAGGCAC
* * *
1964563 TGCGTGACTATTTTTTATGTATTACGTGACATTGGGCTGTTACGTGACTGGTTATGTTGGCATAA
1 TGCGTGACTATTTGTTATGTATTACGTGACATTAGGCTATTACGTGACTGGTTATGTTGGCATAA
* *
1964628 TGTGAGTGGATATTATGCATTGAGTGACTAATTATTAGGTATTATGAGACTGCTGATGCATGACT
66 TGTGAGTGGATATTACGCATTGAGTGACTAATTATTAGGTATTACGAGACTGCTGATGCATGACT
* * *
1964693 TGTGCAATTCATCTATTGTTTTGAGGCTTTT-GTTCATTAGTTTTTAGGCACTACGTGACTGGTT
131 TGTGCAATTCATCTATTGTTTTAAGG-TTTTAGTTCACTAATTTTTAGGCACTACGTGACTGGTT
1964757 TTTATATAT
195 TTTATATAT
* * *
1964766 TGCGTGACT-TGTTGTTATGTATTGCGTGACATTAGGCTATTATGTGATTGGTTATGTTGGCATA
1 TGCGTGACTAT-TTGTTATGTATTACGTGACATTAGGCTATTACGTGACTGGTTATGTTGGCATA
* * * *
1964830 ATGTGAGTGGATATTACGCATTGAGTGACTTATTCTTAGGTATTGCGAGACTGAC-GGTG-AGTG
65 ATGTGAGTGGATATTACGCATTGAGTGACTAATTATTAGGTATTACGAGACTG-CTGATGCA-TG
** * *
1964893 ACTTGTTTAATTCATCTCTTGTTTTAAGGTTTTAGTTTACTAATTTTTAGGCA
128 ACTTGTGCAATTCATCTATTGTTTTAAGGTTTTAGTTCACTAATTTTTAGGCA
1964946 TTGCATGAAT
Statistics
Matches: 157, Mismatches: 19, Indels: 8
0.85 0.10 0.04
Matches are distributed among these distances:
202 6 0.04
203 150 0.96
204 1 0.01
ACGTcount: A:0.22, C:0.11, G:0.24, T:0.43
Consensus pattern (203 bp):
TGCGTGACTATTTGTTATGTATTACGTGACATTAGGCTATTACGTGACTGGTTATGTTGGCATAA
TGTGAGTGGATATTACGCATTGAGTGACTAATTATTAGGTATTACGAGACTGCTGATGCATGACT
TGTGCAATTCATCTATTGTTTTAAGGTTTTAGTTCACTAATTTTTAGGCACTACGTGACTGGTTT
TTATATAT
Found at i:1972606 original size:20 final size:19
Alignment explanation
Indices: 1972581--1972627 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
1972571 ATTAATAAAA
1972581 TTTATATTATAATTTAATTT
1 TTTATATTATAA-TTAATTT
**
1972601 TTTATAAAAATAATTAATTT
1 TTTAT-ATTATAATTAATTT
1972621 TTT-TATT
1 TTTATATT
1972628 TCGAATCAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
18 1 0.05
19 1 0.05
20 15 0.68
21 5 0.23
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTATATTATAATTAATTT
Found at i:1980177 original size:17 final size:18
Alignment explanation
Indices: 1980155--1980190 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1980145 CTTCATCTAC
*
1980155 AAAAATTTAATAAA-ATA
1 AAAAATATAATAAACATA
1980172 AAAAATATAATAAACATA
1 AAAAATATAATAAACATA
1980190 A
1 A
1980191 TTATTACAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (18 bp):
AAAAATATAATAAACATA
Found at i:1981465 original size:28 final size:28
Alignment explanation
Indices: 1981421--1981483 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 28
1981411 TGGTTCAAAA
* *
1981421 TTTTAAAATTTTGTAATTTCT-TTTGTT-T
1 TTTTAAAATATTATAATTT-TATTT-TTAT
1981449 TTTTAAAATATTATAATTTTATTTTTAT
1 TTTTAAAATATTATAATTTTATTTTTAT
1981477 TTTTAAA
1 TTTTAAA
1981484 TTTTTTTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 3 0.10
28 28 0.90
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (28 bp):
TTTTAAAATATTATAATTTTATTTTTAT
Found at i:1981499 original size:19 final size:20
Alignment explanation
Indices: 1981446--1981501 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 20
1981436 ATTTCTTTTG
* *
1981446 TTTTTTTAAAATATTATAAT
1 TTTTTTTATAATTTTATAAT
*
1981466 TTTATTTT-TATTTTTA-AAT
1 TTT-TTTTATAATTTTATAAT
1981485 TTTTTTTATAATTTTAT
1 TTTTTTTATAATTTTAT
1981502 CTTTACAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
18 4 0.14
19 13 0.45
20 8 0.28
21 4 0.14
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTTTTTATAATTTTATAAT
Found at i:1982054 original size:2 final size:2
Alignment explanation
Indices: 1982047--1982073 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1982037 TAGGGTTTAT
1982047 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 T
1982074 GGTTATGTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1986090 original size:94 final size:94
Alignment explanation
Indices: 1985981--1986168 Score: 315
Period size: 94 Copynumber: 2.0 Consensus size: 94
1985971 TAAAATGTTT
* *
1985981 TATATCGAAGTTTGTATAAATAATAAATAATTATAAATAATATGTTAGAAAATCT-AAGATGATA
1 TATATCAAAATTTGTATAAATAATAAATAATTATAAATAATATGTTAGAAAATCTAAAG-TGATA
*
1986045 ATTAATAAAGTTATTAAGTGTAATCATATA
65 ACTAATAAAGTTATTAAGTGTAATCATATA
* *
1986075 TATATCAAAATTTGTATAAATAATAACTAATTATAAATAATATGTTATAAAATCTAAAGTGATAA
1 TATATCAAAATTTGTATAAATAATAAATAATTATAAATAATATGTTAGAAAATCTAAAGTGATAA
1986140 CTAATAAAGTTATTAAGTGTAATCATATA
66 CTAATAAAGTTATTAAGTGTAATCATATA
1986169 AATAAAATTT
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
94 85 0.97
95 3 0.03
ACGTcount: A:0.49, C:0.04, G:0.09, T:0.37
Consensus pattern (94 bp):
TATATCAAAATTTGTATAAATAATAAATAATTATAAATAATATGTTAGAAAATCTAAAGTGATAA
CTAATAAAGTTATTAAGTGTAATCATATA
Found at i:1986200 original size:22 final size:22
Alignment explanation
Indices: 1986167--1986216 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
1986157 TGTAATCATA
1986167 TAAATAAAATTTAT-TATAAAT
1 TAAATAAAATTTATGTATAAAT
*
1986188 TAAAGTAATATTTATGTATAAAT
1 TAAA-TAAAATTTATGTATAAAT
1986211 TAAATA
1 TAAATA
1986217 TATGTATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 4 0.15
22 11 0.42
23 11 0.42
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (22 bp):
TAAATAAAATTTATGTATAAAT
Found at i:1986497 original size:16 final size:16
Alignment explanation
Indices: 1986476--1986509 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1986466 TAAATATATT
*
1986476 TTAAGTATATTATTAA
1 TTAAGTATATTAATAA
*
1986492 TTAAGTTTATTAATAA
1 TTAAGTATATTAATAA
1986508 TT
1 TT
1986510 TTTCTTAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (16 bp):
TTAAGTATATTAATAA
Found at i:1986524 original size:2 final size:2
Alignment explanation
Indices: 1986517--1986561 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
1986507 ATTTTTCTTA
* *
1986517 AT AT AT AT AC A- AA AT AT -T AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1986557 AT AT A
1 AT AT A
1986562 CAAACTAGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:2001522 original size:45 final size:45
Alignment explanation
Indices: 2001458--2001550 Score: 186
Period size: 45 Copynumber: 2.1 Consensus size: 45
2001448 TTCATATAGA
2001458 TGTAGTTGCTGAAGCTACAATTCATTCAGTGCAAGTTTTCTGTAG
1 TGTAGTTGCTGAAGCTACAATTCATTCAGTGCAAGTTTTCTGTAG
2001503 TGTAGTTGCTGAAGCTACAATTCATTCAGTGCAAGTTTTCTGTAG
1 TGTAGTTGCTGAAGCTACAATTCATTCAGTGCAAGTTTTCTGTAG
2001548 TGT
1 TGT
2001551 TATTCACAGC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.24, C:0.15, G:0.23, T:0.39
Consensus pattern (45 bp):
TGTAGTTGCTGAAGCTACAATTCATTCAGTGCAAGTTTTCTGTAG
Found at i:2002698 original size:16 final size:17
Alignment explanation
Indices: 2002647--2002700 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
2002637 ACGAGAGACC
2002647 TTATA-TAATATA-TAA
1 TTATATTAATATATTAA
* * *
2002662 TGATAAATAATATATTGA
1 TTAT-ATTAATATATTAA
2002680 TTATATTAAT-TATTAA
1 TTATATTAATATATTAA
2002696 TTATA
1 TTATA
2002701 AAAATTTATT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
15 3 0.10
16 11 0.35
17 12 0.39
18 5 0.16
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (17 bp):
TTATATTAATATATTAA
Found at i:2002710 original size:24 final size:22
Alignment explanation
Indices: 2002683--2002727 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2002673 ATATTGATTA
*
2002683 TATTAATTATTAATTATAAAAATT
1 TATTAATT-TTAA-AATAAAAATT
*
2002707 TATTTATTTTAAAATAAAAAT
1 TATTAATTTTAAAATAAAAAT
2002728 ATAAGAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 8 0.42
23 4 0.21
24 7 0.37
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TATTAATTTTAAAATAAAAATT
Found at i:2003027 original size:33 final size:33
Alignment explanation
Indices: 2002990--2003056 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
2002980 TTATACTATA
* *
2002990 TGATGTTAATATAACATGTTAACATATTATAAT
1 TGATGATAATATAACATGTTAACATATCATAAT
* ** *
2003023 TGATGATAATGTGTCATGTTAATATATCATAAT
1 TGATGATAATATAACATGTTAACATATCATAAT
2003056 T
1 T
2003057 AATAATGATA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.39, C:0.06, G:0.12, T:0.43
Consensus pattern (33 bp):
TGATGATAATATAACATGTTAACATATCATAAT
Found at i:2003449 original size:15 final size:16
Alignment explanation
Indices: 2003421--2003460 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
2003411 ACCAATTATT
2003421 ATATTTAGATAAATAA-
1 ATATTTA-ATAAATAAC
2003437 ATATTTAATAAATAAC
1 ATATTTAATAAATAAC
2003453 AT-TTTAAT
1 ATATTTAAT
2003461 CTATTTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (16 bp):
ATATTTAATAAATAAC
Found at i:2007136 original size:2 final size:2
Alignment explanation
Indices: 2007129--2007163 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2007119 GACCTAATTT
2007129 TA 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 TA T
2007164 TTGTAATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2010116 original size:21 final size:19
Alignment explanation
Indices: 2010085--2010126 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
2010075 GTCACTTTGA
*
2010085 TTAAAAAGATGGTAATCAG
1 TTAAAAAGATGATAATCAG
2010104 TTAATAAACGATGATAATCAG
1 TTAA-AAA-GATGATAATCAG
2010125 TT
1 TT
2010127 TGAAACAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
20 3 0.15
21 13 0.65
ACGTcount: A:0.45, C:0.07, G:0.17, T:0.31
Consensus pattern (19 bp):
TTAAAAAGATGATAATCAG
Found at i:2011860 original size:28 final size:29
Alignment explanation
Indices: 2011818--2011873 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
2011808 ATTTAAAAAA
* *
2011818 ATTTAAATAAGTTTTT-ATTTTTTATTGC
1 ATTTAAATAAATTTTTGAATTTTTATTGC
*
2011846 ATTTAATTAAATTTTTGAATTTTTATTG
1 ATTTAAATAAATTTTTGAATTTTTATTG
2011874 TGAGTTAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 14 0.58
29 10 0.42
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.61
Consensus pattern (29 bp):
ATTTAAATAAATTTTTGAATTTTTATTGC
Found at i:2013666 original size:19 final size:19
Alignment explanation
Indices: 2013644--2013705 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
2013634 TTTATCTTTA
2013644 AATATTTAATTTATTAATT
1 AATATTTAATTTATTAATT
* *
2013663 AATATATAATTT-TTATTT
1 AATATTTAATTTATTAATT
* *
2013681 AAAAAATTATAATTTATAAATT
1 --AATATT-TAATTTATTAATT
2013703 AAT
1 AAT
2013706 TATGAGAAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 7
0.70 0.15 0.15
Matches are distributed among these distances:
18 5 0.16
19 11 0.34
20 6 0.19
21 6 0.19
22 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
AATATTTAATTTATTAATT
Found at i:2013670 original size:38 final size:40
Alignment explanation
Indices: 2013622--2013705 Score: 109
Period size: 38 Copynumber: 2.1 Consensus size: 40
2013612 ATAAAACATG
* * * *
2013622 ATTAAGATATAATTTATCTTT-AAATATT-TAATTTATTA
1 ATTAATATATAATTTATATTTAAAAAATTATAATTTATAA
*
2013660 ATTAATATATAATTTTTATTTAAAAAATTATAATTTATAA
1 ATTAATATATAATTTATATTTAAAAAATTATAATTTATAA
2013700 ATTAAT
1 ATTAAT
2013706 TATGAGAAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
38 18 0.46
39 6 0.15
40 15 0.38
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (40 bp):
ATTAATATATAATTTATATTTAAAAAATTATAATTTATAA
Done.