Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397266.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_20.0, 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: 7441454
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 92215 characters in sequence are not A, C, G, or T
File 18 of 18
Found at i:7312551 original size:75 final size:76
Alignment explanation
Indices: 7312457--7312605 Score: 221
Period size: 75 Copynumber: 2.0 Consensus size: 76
7312447 TTAAGCCTTG
* * *
7312457 TGTTAATCAATTAAACCTATTTTATCTAACTTTTTTGTAACGCCTAGTACAACTTTAACTGATTG
1 TGTTAATCAATTAAACCTATTTTATCTAACTTTTGTATAACGCCCAGTACAACTTTAACTGATTG
7312522 AAG-CTCTTTA
66 AAGTCTCTTTA
* * *
7312532 TGTTAA-CTAATTAAACCTATTTTGTCTAACTTTTGTATAGCGCCCAGTACAGCTTTAACTGATT
1 TGTTAATC-AATTAAACCTATTTTATCTAACTTTTGTATAACGCCCAGTACAACTTTAACTGATT
7312596 GAAGTCTCTT
65 GAAGTCTCTT
7312606 GTTAATCGGT
Statistics
Matches: 66, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
74 1 0.02
75 60 0.91
76 5 0.08
ACGTcount: A:0.29, C:0.18, G:0.11, T:0.42
Consensus pattern (76 bp):
TGTTAATCAATTAAACCTATTTTATCTAACTTTTGTATAACGCCCAGTACAACTTTAACTGATTG
AAGTCTCTTTA
Found at i:7313130 original size:21 final size:21
Alignment explanation
Indices: 7313106--7313154 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
7313096 GATATTCATA
*
7313106 ACAATAAACTAGA-AATTGTTC
1 ACAATAAACCA-ACAATTGTTC
7313127 ACAATAAACCAACAATTGTTC
1 ACAATAAACCAACAATTGTTC
*
7313148 ACCATAA
1 ACAATAA
7313155 CCACATAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 1 0.04
21 24 0.96
ACGTcount: A:0.49, C:0.20, G:0.06, T:0.24
Consensus pattern (21 bp):
ACAATAAACCAACAATTGTTC
Found at i:7313400 original size:29 final size:29
Alignment explanation
Indices: 7313367--7313427 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
7313357 AGAATTTTAG
7313367 TAACTGATTATCAAAGTACCTTAATCAAC
1 TAACTGATTATCAAAGTACCTTAATCAAC
7313396 TAACTGATTATCAAAGTACCTTAATCAAC
1 TAACTGATTATCAAAGTACCTTAATCAAC
7313425 TAA
1 TAA
7313428 GACATGTCTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.43, C:0.20, G:0.07, T:0.31
Consensus pattern (29 bp):
TAACTGATTATCAAAGTACCTTAATCAAC
Found at i:7322143 original size:21 final size:22
Alignment explanation
Indices: 7322100--7322143 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
7322090 CTCTTAAGGT
*
7322100 AATTTAAAACAAAATGACATAA
1 AATTTAAAACAAAATAACATAA
* *
7322122 AATTTTAAA-AAAATAACTTAA
1 AATTTAAAACAAAATAACATAA
7322143 A
1 A
7322144 TTAAGTACTC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.64, C:0.07, G:0.02, T:0.27
Consensus pattern (22 bp):
AATTTAAAACAAAATAACATAA
Found at i:7343346 original size:6 final size:6
Alignment explanation
Indices: 7343335--7343359 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
7343325 TAAATCTAAC
7343335 AAACTA AAACTA AAACTA AAACTA A
1 AAACTA AAACTA AAACTA AAACTA A
7343360 TATAAAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.16, G:0.00, T:0.16
Consensus pattern (6 bp):
AAACTA
Found at i:7355299 original size:14 final size:14
Alignment explanation
Indices: 7355280--7355307 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
7355270 ATTATGTTCA
7355280 ATTGATCAAAAGGT
1 ATTGATCAAAAGGT
7355294 ATTGATCAAAAGGT
1 ATTGATCAAAAGGT
7355308 TGAATATTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.21, T:0.29
Consensus pattern (14 bp):
ATTGATCAAAAGGT
Found at i:7357203 original size:36 final size:35
Alignment explanation
Indices: 7357111--7357331 Score: 236
Period size: 35 Copynumber: 6.3 Consensus size: 35
7357101 TCTCAAGCAC
*
7357111 TTGATTAAAATTATTTAATTAAGTTA-T--GCCTAA
1 TTGATT-AAATTGTTTAATTAAGTTATTGGGCCTAA
*
7357144 TTCATTAAATTGTTTAATTAAGTTATTGGGCCTAA
1 TTGATTAAATTGTTTAATTAAGTTATTGGGCCTAA
* * *
7357179 TTGATTACACTTGTTTAATCAAGTTATTGGGCCTCA
1 TTGATTA-AATTGTTTAATTAAGTTATTGGGCCTAA
** * *
7357215 TTGATTAAATT-TGACAATTAACTTATTGAGCCTAA
1 TTGATTAAATTGT-TTAATTAAGTTATTGGGCCTAA
* * *
7357250 TTGATTAAATTTGTTTAATCAAGTTATTGAGTCTAA
1 TTGATTAAA-TTGTTTAATTAAGTTATTGGGCCTAA
* *
7357286 TT-ACTTAAATTGTTGAATTAAGTTATTGGACCTAA
1 TTGA-TTAAATTGTTTAATTAAGTTATTGGGCCTAA
7357321 TTGATTAAATT
1 TTGATTAAATT
7357332 AAACAATTAA
Statistics
Matches: 156, Mismatches: 23, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
32 18 0.12
33 6 0.04
34 1 0.01
35 71 0.46
36 59 0.38
37 1 0.01
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.44
Consensus pattern (35 bp):
TTGATTAAATTGTTTAATTAAGTTATTGGGCCTAA
Found at i:7357242 original size:71 final size:71
Alignment explanation
Indices: 7357111--7357329 Score: 245
Period size: 71 Copynumber: 3.1 Consensus size: 71
7357101 TCTCAAGCAC
* * * *
7357111 TTGATTAAAATTATTTAATTAAGTTA-T--GCCTAATT-CATTAAATTGTTTAATTAAGTTATTG
1 TTGATTAAACTTGTTTAATCAAGTTATTGAGCCTAATTAC-TTAAATTGTTGAATTAAGTTATTG
7357172 GGCCTAA
65 GGCCTAA
* * * *
7357179 TTGATTACACTTGTTTAATCAAGTTATTGGGCCTCATTGA-TTAAA-T-TTGACAATTAACTTAT
1 TTGATTAAACTTGTTTAATCAAGTTATTGAGCCTAATT-ACTTAAATTGTTG--AATTAAGTTAT
*
7357241 TGAGCCTAA
63 TGGGCCTAA
* *
7357250 TTGATTAAATTTGTTTAATCAAGTTATTGAGTCTAATTACTTAAATTGTTGAATTAAGTTATTGG
1 TTGATTAAACTTGTTTAATCAAGTTATTGAGCCTAATTACTTAAATTGTTGAATTAAGTTATTGG
*
7357315 ACCTAA
66 GCCTAA
7357321 TTGATTAAA
1 TTGATTAAA
7357330 TTAAACAATT
Statistics
Matches: 125, Mismatches: 16, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
68 22 0.18
69 3 0.02
70 2 0.02
71 94 0.75
72 1 0.01
73 3 0.02
ACGTcount: A:0.34, C:0.09, G:0.13, T:0.44
Consensus pattern (71 bp):
TTGATTAAACTTGTTTAATCAAGTTATTGAGCCTAATTACTTAAATTGTTGAATTAAGTTATTGG
GCCTAA
Found at i:7357309 original size:106 final size:106
Alignment explanation
Indices: 7357138--7357341 Score: 277
Period size: 106 Copynumber: 1.9 Consensus size: 106
7357128 ATTAAGTTAT
* * * *
7357138 GCCTAATTCATTAAATTGTTTAATTAAGTTATTGGGCCTAATTGATTACACTTGTTTAATCAAGT
1 GCCTAATTCATTAAATTGTTTAATCAAGTTATTGAGCCTAATTGATTACAATTGTTGAATCAAGT
* * **
7357203 TATTGGGCCTCATTGATTAAATTTGACAATTAACTTATTGA
66 TATTGGACCTAATTGATTAAATTAAACAATTAACTTATTGA
* * *
7357244 GCCTAATTGATTAAATTTGTTTAATCAAGTTATTGAGTCTAATT-ACTTA-AATTGTTGAATTAA
1 GCCTAATTCATTAAA-TTGTTTAATCAAGTTATTGAGCCTAATTGA-TTACAATTGTTGAATCAA
7357307 GTTATTGGACCTAATTGATTAAATTAAACAATTAA
64 GTTATTGGACCTAATTGATTAAATTAAACAATTAA
7357342 GTTAATTGGG
Statistics
Matches: 85, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
106 57 0.67
107 28 0.33
ACGTcount: A:0.34, C:0.10, G:0.13, T:0.42
Consensus pattern (106 bp):
GCCTAATTCATTAAATTGTTTAATCAAGTTATTGAGCCTAATTGATTACAATTGTTGAATCAAGT
TATTGGACCTAATTGATTAAATTAAACAATTAACTTATTGA
Found at i:7360746 original size:30 final size:31
Alignment explanation
Indices: 7360687--7360746 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
7360677 GTTCTTAAAT
7360687 TTTTATTTTGAGTCAAACTAAGCTCTTATAC
1 TTTTATTTTGAGTCAAACTAAGCTCTTATAC
*
7360718 TTTTATTTTGTA-TCAAA-TAAGCTTTTATA
1 TTTTATTTTG-AGTCAAACTAAGCTCTTATA
7360747 ACTAATAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 11 0.41
31 15 0.56
32 1 0.04
ACGTcount: A:0.30, C:0.12, G:0.08, T:0.50
Consensus pattern (31 bp):
TTTTATTTTGAGTCAAACTAAGCTCTTATAC
Found at i:7363759 original size:18 final size:18
Alignment explanation
Indices: 7363738--7363820 Score: 87
Period size: 18 Copynumber: 4.6 Consensus size: 18
7363728 TTAGGATTAG
7363738 CATCAAGAATAACCTCAA
1 CATCAAGAATAACCTCAA
* *
7363756 CATCAAAAAT-AGCTCCAA
1 CATCAAGAATAACCT-CAA
* * *
7363774 CAGCAAGAATAACTTCAG
1 CATCAAGAATAACCTCAA
* *
7363792 CATCAAGAACAACCCCAA
1 CATCAAGAATAACCTCAA
7363810 CATCAAGAATA
1 CATCAAGAATA
7363821 GTCTCATTGT
Statistics
Matches: 50, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
17 3 0.06
18 45 0.90
19 2 0.04
ACGTcount: A:0.49, C:0.28, G:0.08, T:0.14
Consensus pattern (18 bp):
CATCAAGAATAACCTCAA
Found at i:7363796 original size:36 final size:36
Alignment explanation
Indices: 7363741--7363820 Score: 97
Period size: 36 Copynumber: 2.2 Consensus size: 36
7363731 GGATTAGCAT
* * *
7363741 CAAGAATAACCTCAACATCAAAAATAGCTCCAACAG
1 CAAGAATAACCTCAACATCAAAAACAACCCCAACAG
* * * *
7363777 CAAGAATAACTTCAGCATCAAGAACAACCCCAACAT
1 CAAGAATAACCTCAACATCAAAAACAACCCCAACAG
7363813 CAAGAATA
1 CAAGAATA
7363821 GTCTCATTGT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.50, C:0.28, G:0.09, T:0.14
Consensus pattern (36 bp):
CAAGAATAACCTCAACATCAAAAACAACCCCAACAG
Found at i:7366371 original size:21 final size:19
Alignment explanation
Indices: 7366326--7366374 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 19
7366316 TTGAGCATAA
*
7366326 AAAAATTTATCTTTCAATG
1 AAAAATTTATCTTCCAATG
*
7366345 AGAAAATTTCATCTTCCGTATG
1 A-AAAATTT-ATCTTCC-AATG
7366367 AAAAATTT
1 AAAAATTT
7366375 TTTCATCTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 1 0.04
20 7 0.28
21 13 0.52
22 4 0.16
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.39
Consensus pattern (19 bp):
AAAAATTTATCTTCCAATG
Found at i:7375989 original size:18 final size:18
Alignment explanation
Indices: 7375966--7376001 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
7375956 CTTCCAACAA
7375966 TGGCATATAGGTCAGAGG
1 TGGCATATAGGTCAGAGG
*
7375984 TGGCATGTAGGTCAGAGG
1 TGGCATATAGGTCAGAGG
7376002 AAAACCTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.11, G:0.42, T:0.22
Consensus pattern (18 bp):
TGGCATATAGGTCAGAGG
Found at i:7382599 original size:144 final size:141
Alignment explanation
Indices: 7382326--7382754 Score: 346
Period size: 154 Copynumber: 2.9 Consensus size: 141
7382316 ATATGATTAT
** * * *
7382326 TTTTTTATTTTTTAGTTACTAATAATTTATAATTTATTTAAATATTAATAATTGATCATTCCAAT
1 TTTTTTATTTTTTAAATACTAATAATTTATAATTTATTCAAATATTAATAATTGATAATTACAAT
* * * *
7382391 GTTAATATTTATTTATAATTTAATCATCAGCATTACATAATATTAATATTTTATTATAATTTAAA
66 GTTAATATTTATTTATAATTAAATCATCAACATTACAAAATATTAATACTTTATTATAATTTAAA
7382456 TATCATTATGG
131 TATCATTATGG
*
7382467 TTTTTTATTTTTTTAAATATTAATAATTTATAATTTATTACAAATATTAATAATTGATAATTAAA
1 TTTTTTA-TTTTTTAAATACTAATAATTTATAATTTATT-CAAATATTAATAATTGATAATT---
* * * * * * *
7382532 ATAATGTT-AT-TTTATTTATCATTAAATTATTAATATTATAAAATATTAGTACTTTATTATAAT
61 ACAATGTTAATATTTATTTATAATTAAATCATCAACATTACAAAATATTAATACTTTATTATAAT
* **
7382595 TTAAATGTTATTATGATTATTT
126 TT-AA----A-TATCATTATGG
* * * * *
7382617 TTTAATTTATTTTATTTCTTAAATAATTATAATTTTTAATTTATT-TAAGATTAATAATTGATAA
1 TTT--TTTA---T-TTT-TTAAATACTAATAATTTATAATTTATTCAAATATTAATAATTGATAA
* * * * * *
7382681 TTTA-AATGTTAATATTTTATTTCTAATTTAATAATTAACATTATAAAGTATTAATA-TTTAATT
59 -TTACAATGTTAATA-TTTATTTATAATTAAATCATCAACATTACAAAATATTAATACTTT-A-T
7382744 TATAATTTAAA
120 TATAATTTAAA
7382755 ATATTAATCA
Statistics
Matches: 233, Mismatches: 32, Indels: 37
0.77 0.11 0.12
Matches are distributed among these distances:
141 7 0.03
142 28 0.12
143 20 0.09
144 45 0.19
145 4 0.02
146 6 0.03
149 1 0.00
150 12 0.05
151 6 0.03
152 7 0.03
153 3 0.01
154 56 0.24
155 14 0.06
156 24 0.10
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.53
Consensus pattern (141 bp):
TTTTTTATTTTTTAAATACTAATAATTTATAATTTATTCAAATATTAATAATTGATAATTACAAT
GTTAATATTTATTTATAATTAAATCATCAACATTACAAAATATTAATACTTTATTATAATTTAAA
TATCATTATGG
Found at i:7382633 original size:17 final size:17
Alignment explanation
Indices: 7382611--7382662 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 17
7382601 GTTATTATGA
7382611 TTATTTTTTAATTTATT
1 TTATTTTTTAATTTATT
* * *
7382628 TTATTTCTTAAATAATT
1 TTATTTTTTAATTTATT
* *
7382645 ATAATTTTTAATTTATT
1 TTATTTTTTAATTTATT
7382662 T
1 T
7382663 AAGATTAATA
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (17 bp):
TTATTTTTTAATTTATT
Found at i:7382698 original size:154 final size:157
Alignment explanation
Indices: 7382469--7382754 Score: 366
Period size: 154 Copynumber: 1.8 Consensus size: 157
7382459 CATTATGGTT
* *
7382469 TTTTATTTTTTTAAATATTAATAATTTATAATTTATTACAAATATTAATAATTGATAATTAAAAT
1 TTTTATTTTCTTAAATATTAATAATTTATAATTTATTA-AAAGATTAATAATTGATAATTAAAAT
** * * * *
7382534 AATGTTATTTTATTTATCATTAAATTATTAATATTATAAAATATTAGTACTTT-A-TTATAATTT
65 AATAATATTTTATTTATAATTAAATAATTAACATTATAAAATATTAATA-TTTAATTTATAATTT
7382597 AAATGTTATTATGATTATTTTTTAATTTA
129 AAATGTTATTATGATTATTTTTTAATTTA
* * *
7382626 TTTTA-TTTCTTAAATAATT-ATAATTTTTAATTTATT-TAAGATTAATAATTGATAATTTAAAT
1 TTTTATTTTCTTAAAT-ATTAATAATTTATAATTTATTAAAAGATTAATAATTGATAATTAAAAT
** * * *
7382688 GTTAATATTTTATTTCTAATTTAATAATTAACATTATAAAGTATTAATATTTAATTTATAATTTA
65 AATAATATTTTATTTATAATTAAATAATTAACATTATAAAATATTAATATTTAATTTATAATTTA
7382753 AA
130 AA
7382755 ATATTAATCA
Statistics
Matches: 110, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
153 3 0.03
154 62 0.56
155 12 0.11
156 25 0.23
157 8 0.07
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.53
Consensus pattern (157 bp):
TTTTATTTTCTTAAATATTAATAATTTATAATTTATTAAAAGATTAATAATTGATAATTAAAATA
ATAATATTTTATTTATAATTAAATAATTAACATTATAAAATATTAATATTTAATTTATAATTTAA
ATGTTATTATGATTATTTTTTAATTTA
Found at i:7382739 original size:42 final size:45
Alignment explanation
Indices: 7382689--7382771 Score: 118
Period size: 42 Copynumber: 1.9 Consensus size: 45
7382679 AATTTAAATG
* * *
7382689 TTAATATTTTATTTCTAATTTAATA-ATTAA-CATT-ATAAAGTA
1 TTAATATTTAATTTATAATTTAAAATATTAATCATTGATAAAGTA
7382731 TTAATATTTAATTTATAATTTAAAATATTAATCATTGATAA
1 TTAATATTTAATTTATAATTTAAAATATTAATCATTGATAA
7382772 GTAAAACATT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
42 22 0.63
43 5 0.14
44 4 0.11
45 4 0.11
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (45 bp):
TTAATATTTAATTTATAATTTAAAATATTAATCATTGATAAAGTA
Found at i:7384608 original size:27 final size:27
Alignment explanation
Indices: 7384578--7384631 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
7384568 TGATTATTAA
*
7384578 TTTTT-AAATATTTATAATTTATAATT
1 TTTTTAAAATATTAATAATTTATAATT
*
7384604 TTTTTAAAATATTAATAATTTATCATT
1 TTTTTAAAATATTAATAATTTATAATT
7384631 T
1 T
7384632 AAATATTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 5 0.20
27 20 0.80
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (27 bp):
TTTTTAAAATATTAATAATTTATAATT
Found at i:7384656 original size:25 final size:25
Alignment explanation
Indices: 7384622--7384671 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
7384612 ATATTAATAA
* **
7384622 TTTATCATTTAAATATTAATATTTT
1 TTTATAATTTAATCATTAATATTTT
7384647 TTTATAATTTAATCATTAATATTTT
1 TTTATAATTTAATCATTAATATTTT
7384672 AGGTATGATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (25 bp):
TTTATAATTTAATCATTAATATTTT
Found at i:7386870 original size:18 final size:18
Alignment explanation
Indices: 7386847--7386891 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
7386837 ATATAGATAT
7386847 CATTCAAATTCATGTTTC
1 CATTCAAATTCATGTTTC
* *
7386865 CATTCAAATTTATGTTTT
1 CATTCAAATTCATGTTTC
*
7386883 GATTCAAAT
1 CATTCAAAT
7386892 GCAAAGTGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.31, C:0.16, G:0.07, T:0.47
Consensus pattern (18 bp):
CATTCAAATTCATGTTTC
Found at i:7414082 original size:30 final size:30
Alignment explanation
Indices: 7414041--7414104 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
7414031 ATCTTCTTTA
*
7414041 TCATGATTTCTATAATCATTTTGAATCTCT
1 TCATAATTTCTATAATCATTTTGAATCTCT
*
7414071 TCATAATTTCTATGATCATTTTGAATCTCT
1 TCATAATTTCTATAATCATTTTGAATCTCT
7414101 TCAT
1 TCAT
7414105 TAACTTCTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.27, C:0.17, G:0.06, T:0.50
Consensus pattern (30 bp):
TCATAATTTCTATAATCATTTTGAATCTCT
Found at i:7415455 original size:30 final size:29
Alignment explanation
Indices: 7415419--7415476 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
7415409 TTTTTGTCAT
* *
7415419 AAGGGTTTATTTGATTTAAAATAAAAGTAA
1 AAGGGTTTATTTG-CTCAAAATAAAAGTAA
7415449 AAGGGTTTATTTGCTCAAAATAAAAGTA
1 AAGGGTTTATTTGCTCAAAATAAAAGTA
7415477 CAATAATTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 13 0.50
30 13 0.50
ACGTcount: A:0.45, C:0.03, G:0.17, T:0.34
Consensus pattern (29 bp):
AAGGGTTTATTTGCTCAAAATAAAAGTAA
Found at i:7417063 original size:18 final size:18
Alignment explanation
Indices: 7417020--7417063 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
7417010 GCATTTAAAA
7417020 TAAAAAAATAGTTTTTTT
1 TAAAAAAATAGTTTTTTT
* **
7417038 TAAGAAAATTTTTTTTTT
1 TAAAAAAATAGTTTTTTT
7417056 TAAAAAAA
1 TAAAAAAA
7417064 GAGCTTAAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (18 bp):
TAAAAAAATAGTTTTTTT
Found at i:7420792 original size:34 final size:33
Alignment explanation
Indices: 7420754--7420817 Score: 110
Period size: 34 Copynumber: 1.9 Consensus size: 33
7420744 ATTTATATAT
7420754 ACATATAAGCATATTACACTTAACATATAAATAA
1 ACATATAAGCATATTACA-TTAACATATAAATAA
*
7420788 ACATATAAGCATATTACATTACCATATAAA
1 ACATATAAGCATATTACATTAACATATAAA
7420818 AATAAAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 11 0.38
34 18 0.62
ACGTcount: A:0.52, C:0.16, G:0.03, T:0.30
Consensus pattern (33 bp):
ACATATAAGCATATTACATTAACATATAAATAA
Found at i:7425107 original size:22 final size:22
Alignment explanation
Indices: 7425064--7425108 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
7425054 CTTGTTCTTG
* *
7425064 GATTGAGTTTTATCTACGTGTT
1 GATTGAGCTTTATCTACATGTT
* *
7425086 GATTGAGCTTTATTTGCATGTT
1 GATTGAGCTTTATCTACATGTT
7425108 G
1 G
7425109 TTATGTCATC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.18, C:0.09, G:0.24, T:0.49
Consensus pattern (22 bp):
GATTGAGCTTTATCTACATGTT
Found at i:7428205 original size:17 final size:17
Alignment explanation
Indices: 7428185--7428218 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
7428175 GCTAAATCAA
7428185 ATATGATTTGATAGAGT
1 ATATGATTTGATAGAGT
*
7428202 ATATGATTTGATGGAGT
1 ATATGATTTGATAGAGT
7428219 CTTAAACAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.26, T:0.41
Consensus pattern (17 bp):
ATATGATTTGATAGAGT
Found at i:7434077 original size:19 final size:19
Alignment explanation
Indices: 7434053--7434089 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
7434043 CTGACTTTCT
7434053 ACCTAATTTCACCCCCTCG
1 ACCTAATTTCACCCCCTCG
*
7434072 ACCTAATTTCCCCCCCTC
1 ACCTAATTTCACCCCCTC
7434090 CCTTTCCTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.19, C:0.51, G:0.03, T:0.27
Consensus pattern (19 bp):
ACCTAATTTCACCCCCTCG
Found at i:7436847 original size:36 final size:36
Alignment explanation
Indices: 7436742--7436914 Score: 196
Period size: 36 Copynumber: 4.9 Consensus size: 36
7436732 NNNNNNNNNN
*
7436742 AGGCCCAATAACTTGATTAAACAAATTTAATCAATT
1 AGGCCCAATAACTTAATTAAACAAATTTAATCAATT
* **** *
7436778 AGGCTCAATAACTTAATT-CTTTAATTTAATCAATG
1 AGGCCCAATAACTTAATTAAACAAATTTAATCAATT
* *
7436813 AGGCCCAATAACTTGATTAAACAAATTTAGTCAATT
1 AGGCCCAATAACTTAATTAAACAAATTTAATCAATT
7436849 AGGCCCAATAACTTAATTAAAC-AATTTAA-CGAATT
1 AGGCCCAATAACTTAATTAAACAAATTTAATC-AATT
* *
7436884 AGG--C-ACAACTTAATTAAACAATTTTAATCAA
1 AGGCCCAATAACTTAATTAAACAAATTTAATCAA
7436915 GTGCTTGAGA
Statistics
Matches: 114, Mismatches: 19, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
32 14 0.12
33 9 0.08
34 2 0.02
35 41 0.36
36 48 0.42
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (36 bp):
AGGCCCAATAACTTAATTAAACAAATTTAATCAATT
Found at i:7436875 original size:71 final size:71
Alignment explanation
Indices: 7436742--7436914 Score: 219
Period size: 71 Copynumber: 2.5 Consensus size: 71
7436732 NNNNNNNNNN
* ****
7436742 AGGCCCAATAACTTGATTAAACAAATTTAATCAATTAGGCTCAATAACTTAATTCTTTAATTTAA
1 AGGCCCAATAACTTGATTAAACAAATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAA
7436807 TCAATG
66 TCAATG
*
7436813 AGGCCCAATAACTTGATTAAACAAATTTAGTCAATTAGGCCCAATAACTTAATTAAACAATTTAA
1 AGGCCCAATAACTTGATTAAACAAATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAA
*
7436878 -CGAATT
66 TC-AATG
* * *
7436884 AGG--C-ACAACTTAATTAAACAATTTTAATCAA
1 AGGCCCAATAACTTGATTAAACAAATTTAATCAA
7436915 GTGCTTGAGA
Statistics
Matches: 90, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
68 23 0.26
69 1 0.01
70 1 0.01
71 65 0.72
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (71 bp):
AGGCCCAATAACTTGATTAAACAAATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAA
TCAATG
Found at i:7439207 original size:14 final size:13
Alignment explanation
Indices: 7439184--7439216 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
7439174 TTAAACATTA
7439184 AGAATT-ATGTTT
1 AGAATTAATGTTT
7439196 GAGAATTAATGTTT
1 -AGAATTAATGTTT
7439210 AGAATTA
1 AGAATTA
7439217 TTGTGTGGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.42
Consensus pattern (13 bp):
AGAATTAATGTTT
Found at i:7439254 original size:85 final size:85
Alignment explanation
Indices: 7439161--7439352 Score: 260
Period size: 85 Copynumber: 2.3 Consensus size: 85
7439151 AATTTGTAAT
* * * *
7439161 TAATATGTTAGAATTAAACATTAAGAATTATGTTT-GAGAATTAATGTTTAGAATTATTGTGTGG
1 TAATATGTTAGAATTAAACATTAAAAATAATATTTAG-GAATTAATGTTGAGAATTATTGTGTGG
7439225 ATTTTTAATTAAAATGATTAG
65 ATTTTTAATTAAAATGATTAG
* * * *
7439246 TAATATGTTAGAATTAAATATTAAAAATAATATTTAGGAATTAATGTTGAGAATTATTTTTTTGA
1 TAATATGTTAGAATTAAACATTAAAAATAATATTTAGGAATTAATGTTGAGAATTATTGTGTGGA
*
7439311 TTTTTAATTAAAATGATTGG
66 TTTTTAATTAAAATGATTAG
* * *
7439331 CAATATGCTAGAATTAATCATT
1 TAATATGTTAGAATTAAACATT
7439353 GGAATTAATA
Statistics
Matches: 93, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
85 92 0.99
86 1 0.01
ACGTcount: A:0.40, C:0.02, G:0.14, T:0.44
Consensus pattern (85 bp):
TAATATGTTAGAATTAAACATTAAAAATAATATTTAGGAATTAATGTTGAGAATTATTGTGTGGA
TTTTTAATTAAAATGATTAG
Done.