Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397304.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_4583.0, 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: 185427
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 1000 characters in sequence are not A, C, G, or T
Found at i:31 original size:18 final size:18
Alignment explanation
Indices: 4--73 Score: 59
Period size: 18 Copynumber: 3.7 Consensus size: 18
1 GAA
*
4 GGTGGGGGTGTTGTGGTT
1 GGTGGAGGTGTTGTGGTT
**
22 GGTGGAGGTGTTGCAGTT
1 GGTGGAGGTGTTGTGGTT
* **
40 GAAGGCGGAGGTGTTGTGGAA
1 ---GGTGGAGGTGTTGTGGTT
61 GGTGGAGGTGTTG
1 GGTGGAGGTGTTG
74 CTGTTGGAGG
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
18 27 0.68
21 13 0.32
ACGTcount: A:0.11, C:0.03, G:0.56, T:0.30
Consensus pattern (18 bp):
GGTGGAGGTGTTGTGGTT
Found at i:51 original size:21 final size:20
Alignment explanation
Indices: 25--79 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 20
15 TGTGGTTGGT
25 GGAGGTGTTGCAGTTGAAGGC
1 GGAGGTGTTGC-GTTGAAGGC
* *
46 GGAGGTGTT--GTGGAAGGT
1 GGAGGTGTTGCGTTGAAGGC
64 GGAGGTGTTGCTGTTG
1 GGAGGTGTTGC-GTTG
80 GAGGTGGTGG
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 16 0.57
21 12 0.43
ACGTcount: A:0.15, C:0.05, G:0.51, T:0.29
Consensus pattern (20 bp):
GGAGGTGTTGCGTTGAAGGC
Found at i:55 original size:39 final size:39
Alignment explanation
Indices: 1--106 Score: 113
Period size: 39 Copynumber: 2.7 Consensus size: 39
* * **
1 GAAGGTGGGGGTGTTGTGGTTGGTGGAGGTGTTGCAGTT
1 GAAGGCGGAGGTGTTGTGGAAGGTGGAGGTGTTGCAGTT
*
40 GAAGGCGGAGGTGTTGTGGAAGGTGGAGGTGTTGCTGTT
1 GAAGGCGGAGGTGTTGTGGAAGGTGGAGGTGTTGCAGTT
* * * ** *
79 GGAGGTGGTGGTGAAGTTGAAGGTGGAG
1 GAAGGCGGAGGTGTTGTGGAAGGTGGAG
107 TTATGGTGGT
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.15, C:0.03, G:0.54, T:0.28
Consensus pattern (39 bp):
GAAGGCGGAGGTGTTGTGGAAGGTGGAGGTGTTGCAGTT
Found at i:86 original size:21 final size:21
Alignment explanation
Indices: 22--91 Score: 83
Period size: 21 Copynumber: 3.5 Consensus size: 21
12 TGTTGTGGTT
*
22 GGTGGAGGTGTTGCAGTTGAA
1 GGTGGAGGTGTTGCTGTTGAA
*
43 GGCGGAGGTGTTG-TG--GAA
1 GGTGGAGGTGTTGCTGTTGAA
*
61 GGTGGAGGTGTTGCTGTTGGA
1 GGTGGAGGTGTTGCTGTTGAA
*
82 GGTGGTGGTG
1 GGTGGAGGTG
92 AAGTTGAAGG
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
18 15 0.37
19 2 0.05
20 1 0.02
21 23 0.56
ACGTcount: A:0.13, C:0.04, G:0.54, T:0.29
Consensus pattern (21 bp):
GGTGGAGGTGTTGCTGTTGAA
Found at i:3100 original size:7 final size:7
Alignment explanation
Indices: 3083--3166 Score: 50
Period size: 7 Copynumber: 12.4 Consensus size: 7
3073 CCAAAACCCG
3083 ACCCTTAA
1 ACCC-TAA
3091 ACCCTAA
1 ACCCTAA
*
3098 ACCC--G
1 ACCCTAA
*
3103 ACCCTTA
1 ACCCTAA
3110 ACCCTAA
1 ACCCTAA
**
3117 ACCC-CG
1 ACCCTAA
3123 ACCCT-A
1 ACCCTAA
*
3129 ACCCCAA
1 ACCCTAA
*
3136 ATCCTAA
1 ACCCTAA
* *
3143 ACCTTGA
1 ACCCTAA
*
3150 ACCCTGA
1 ACCCTAA
3157 ACCCTAA
1 ACCCTAA
3164 ACC
1 ACC
3167 AAAAATTAAA
Statistics
Matches: 58, Mismatches: 14, Indels: 9
0.72 0.17 0.11
Matches are distributed among these distances:
5 4 0.07
6 8 0.14
7 42 0.72
8 4 0.07
ACGTcount: A:0.35, C:0.45, G:0.05, T:0.15
Consensus pattern (7 bp):
ACCCTAA
Found at i:3114 original size:19 final size:19
Alignment explanation
Indices: 3076--3132 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 19
3066 CCAAAGCCCA
3076 AAACCCGACCCTTAAACCCT
1 AAACCCGACCCTT-AACCCT
3096 AAACCCGACCCTTAACCCT
1 AAACCCGACCCTTAACCCT
3115 AAACCCCGACCC-TAACCC
1 AAA-CCCGACCCTTAACCC
3133 CAAATCCTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
19 15 0.42
20 21 0.58
ACGTcount: A:0.33, C:0.49, G:0.05, T:0.12
Consensus pattern (19 bp):
AAACCCGACCCTTAACCCT
Found at i:4531 original size:30 final size:30
Alignment explanation
Indices: 4478--4534 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
4468 GCCATCTCAC
4478 TAAATAATAAATTTAAAATTTTAAAGATCT
1 TAAATAATAAATTTAAAATTTTAAAGATCT
**
4508 TAAA-AATAAATATTACTATTTTAAAGA
1 TAAATAATAAAT-TTAAAATTTTAAAGA
4535 CAATAAAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 7 0.29
30 17 0.71
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.39
Consensus pattern (30 bp):
TAAATAATAAATTTAAAATTTTAAAGATCT
Found at i:4542 original size:30 final size:29
Alignment explanation
Indices: 4478--4543 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 29
4468 GCCATCTCAC
*
4478 TAAATAATAAATTTAAAATTTTAAAGATCT
1 TAAA-AATAAATTTAAAATTTTAAAGATCA
**
4508 TAAAAATAAATATTACTATTTTAAAGA-CAA
1 TAAAAATAAAT-TTAAAATTTTAAAGATC-A
4538 TAAAAA
1 TAAAAA
4544 CAATTTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
29 8 0.26
30 23 0.74
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.35
Consensus pattern (29 bp):
TAAAAATAAATTTAAAATTTTAAAGATCA
Found at i:5195 original size:28 final size:28
Alignment explanation
Indices: 5155--5223 Score: 93
Period size: 28 Copynumber: 2.5 Consensus size: 28
5145 TGAGTTGCGG
* * *
5155 ATATATATATATATATGCACTCATATAT
1 ATATATATATATATATACACACACATAT
*
5183 ATATATATATATATTTACACACACATAT
1 ATATATATATATATATACACACACATAT
*
5211 ACATATATATATA
1 ATATATATATATA
5224 AAAAAAAGTC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.46, C:0.12, G:0.01, T:0.41
Consensus pattern (28 bp):
ATATATATATATATATACACACACATAT
Found at i:5396 original size:2 final size:2
Alignment explanation
Indices: 5383--5412 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5373 GGTATCAAAG
*
5383 AT AT AT AC 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
5413 GTATGTGTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5456 original size:14 final size:14
Alignment explanation
Indices: 5437--5472 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
5427 AGGTTTTGGA
* *
5437 TCTTGAGTCTCATG
1 TCTTGAATCTCAAG
5451 TCTTGAATCTCAAG
1 TCTTGAATCTCAAG
5465 TCTTGAAT
1 TCTTGAAT
5473 ATGTGTGTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.22, C:0.19, G:0.17, T:0.42
Consensus pattern (14 bp):
TCTTGAATCTCAAG
Found at i:19382 original size:2 final size:2
Alignment explanation
Indices: 19375--19406 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
19365 AAACAATAGA
19375 AT AT AT AT AT 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
19407 TTTGTGAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37205 original size:32 final size:33
Alignment explanation
Indices: 37169--37235 Score: 127
Period size: 32 Copynumber: 2.1 Consensus size: 33
37159 GCGTATTCTT
37169 TATTTTTGCAGGCCATTTATATAAATGGCA-AA
1 TATTTTTGCAGGCCATTTATATAAATGGCATAA
37201 TATTTTTGCAGGCCATTTATATAAATGGCATAA
1 TATTTTTGCAGGCCATTTATATAAATGGCATAA
37234 TA
1 TA
37236 ACATCAGCTC
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 30 0.88
33 4 0.12
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (33 bp):
TATTTTTGCAGGCCATTTATATAAATGGCATAA
Found at i:52988 original size:90 final size:90
Alignment explanation
Indices: 52833--53014 Score: 226
Period size: 90 Copynumber: 2.0 Consensus size: 90
52823 ATTAAGTCAA
* * * *
52833 TTACCTAATTTGTTACAACGAAAAATTAAAGACCAACTATTGAAATTCTTTTAAAATTTAGAGAT
1 TTACCTAATTTGTTAAAACAAAAAATTAAAGACCAACTATTGAAATCCTTTTAAAATTGAGAGAT
* *
52898 GATGAAAATAAAATAATACCAATAC
66 GATGAAAACAAAATAATACCAAAAC
* * *
52923 TTACCTGATTTTTTAAAACAAAAAATTAAA-ACTCAA-TCATTGAAATCCTTTTAAAGCTTGA-A
1 TTACCTAATTTGTTAAAACAAAAAATTAAAGAC-CAACT-ATTGAAATCCTTTTAAA-ATTGAGA
*
52985 GATGATGAAAACAAAATAATATCAAAAC
63 GATGATGAAAACAAAATAATACCAAAAC
53013 TT
1 TT
53015 GATAAATTAG
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
89 3 0.04
90 73 0.92
91 3 0.04
ACGTcount: A:0.48, C:0.13, G:0.08, T:0.31
Consensus pattern (90 bp):
TTACCTAATTTGTTAAAACAAAAAATTAAAGACCAACTATTGAAATCCTTTTAAAATTGAGAGAT
GATGAAAACAAAATAATACCAAAAC
Found at i:53029 original size:58 final size:58
Alignment explanation
Indices: 52967--53083 Score: 209
Period size: 58 Copynumber: 2.0 Consensus size: 58
52957 AATCATTGAA
*
52967 ATCCTTTTAAAGCTTGAAGATGATGAAAACAAAATAATATC-AAAACTTGATAAATTAG
1 ATCCTTTTAAAACTTGAAGATGATGAAAACAAAATAATA-CAAAAACTTGATAAATTAG
53025 ATCCTTTTAAAACTTGAAGATGATGAAAACAAAATAATACAAAAACTTGATAAATTAG
1 ATCCTTTTAAAACTTGAAGATGATGAAAACAAAATAATACAAAAACTTGATAAATTAG
53083 A
1 A
53084 GAATCGTGCT
Statistics
Matches: 57, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
57 1 0.02
58 56 0.98
ACGTcount: A:0.50, C:0.10, G:0.11, T:0.28
Consensus pattern (58 bp):
ATCCTTTTAAAACTTGAAGATGATGAAAACAAAATAATACAAAAACTTGATAAATTAG
Found at i:53140 original size:23 final size:23
Alignment explanation
Indices: 53113--53159 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
53103 TTATAAAAAT
53113 ATAACTTAAAAGAATAAATAAAG
1 ATAACTTAAAAGAATAAATAAAG
* *
53136 ATAACTTGAAAGAATAATTAAAG
1 ATAACTTAAAAGAATAAATAAAG
53159 A
1 A
53160 GAAGGAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.62, C:0.04, G:0.11, T:0.23
Consensus pattern (23 bp):
ATAACTTAAAAGAATAAATAAAG
Found at i:57789 original size:2 final size:2
Alignment explanation
Indices: 57782--57809 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
57772 TCTTGTCAAG
57782 AT AT AT 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
57810 TCTATAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60060 original size:24 final size:24
Alignment explanation
Indices: 60033--60090 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
60023 ATTTGGAGCA
*
60033 GGAGGTGGAGTCGGAGTTGGTGCT
1 GGAGGTGGAGTCGGAGGTGGTGCT
* * * *
60057 GGAGGAGGTGTCGGGGGTGGTGGT
1 GGAGGTGGAGTCGGAGGTGGTGCT
60081 GGAGGTGGAG
1 GGAGGTGGAG
60091 GTGTTGGGGG
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.12, C:0.05, G:0.62, T:0.21
Consensus pattern (24 bp):
GGAGGTGGAGTCGGAGGTGGTGCT
Found at i:60080 original size:27 final size:27
Alignment explanation
Indices: 60050--60104 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
60040 GAGTCGGAGT
*
60050 TGGTGCTGGAGGAGGTGTCGGGGGTGG
1 TGGTGCAGGAGGAGGTGTCGGGGGTGG
* * *
60077 TGGTGGAGGTGGAGGTGTTGGGGGTGG
1 TGGTGCAGGAGGAGGTGTCGGGGGTGG
60104 T
1 T
60105 TCAGGGCATG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.07, C:0.04, G:0.64, T:0.25
Consensus pattern (27 bp):
TGGTGCAGGAGGAGGTGTCGGGGGTGG
Found at i:60106 original size:99 final size:99
Alignment explanation
Indices: 59995--60235 Score: 286
Period size: 99 Copynumber: 2.4 Consensus size: 99
59985 GGTGGTGGGA
* * * * * *
59995 TTGGAGGTGGTTCGGGTCATGGTGGGGGATTTGGAGCAGGAGGTGGAGTCGGAGTTGGTGCTGGA
1 TTGGAGGTGGTTCGGGTCATGGTGGGGGATTTGGAGCTGGAGGTGGAGTAGGAGGTGGAGCAGCA
* * * *
60060 GGAGGTGTCGGGGGTGGTGGTGGAGGTGGAGGTG
66 GGAGGTGTCGGAGCTGATGGTGGAGGAGGAGGTG
* * * *
60094 TTGGGGGTGGTTCAGGG-CATGGTGGAGGTTTTGGAGCTGGAGGTGGAGTAGGTGGTGGAGCAGC
1 TTGGAGGTGGTTC-GGGTCATGGTGGGGGATTTGGAGCTGGAGGTGGAGTAGGAGGTGGAGCAGC
* *
60158 AGGAGGTGTTGGAGCTGATGGTGGAGGAGGAGTTG
65 AGGAGGTGTCGGAGCTGATGGTGGAGGAGGAGGTG
* * * *
60193 GTGGTGGTGGTTCAGGTCATGGTGGGGGCTTTGGAGCTGGAGG
1 TTGGAGGTGGTTCGGGTCATGGTGGGGGATTTGGAGCTGGAGG
60236 AGGTGTAAGT
Statistics
Matches: 119, Mismatches: 21, Indels: 4
0.83 0.15 0.03
Matches are distributed among these distances:
98 2 0.02
99 114 0.96
100 3 0.03
ACGTcount: A:0.13, C:0.07, G:0.55, T:0.25
Consensus pattern (99 bp):
TTGGAGGTGGTTCGGGTCATGGTGGGGGATTTGGAGCTGGAGGTGGAGTAGGAGGTGGAGCAGCA
GGAGGTGTCGGAGCTGATGGTGGAGGAGGAGGTG
Found at i:60382 original size:15 final size:15
Alignment explanation
Indices: 60364--60406 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
60354 GGTGTTGGAA
60364 TAGGAGGTGG-GGCTG
1 TAGGAGGTGGTGGC-G
60379 TAGGAGGTGGTGGCG
1 TAGGAGGTGGTGGCG
*
60394 GAGGAGGTGGTGG
1 TAGGAGGTGGTGG
60407 TGGTGGTGGC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 23 0.88
16 3 0.12
ACGTcount: A:0.14, C:0.05, G:0.63, T:0.19
Consensus pattern (15 bp):
TAGGAGGTGGTGGCG
Found at i:60528 original size:18 final size:18
Alignment explanation
Indices: 60505--60539 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
60495 AGGATTCGGA
60505 GTTGGAATTGGAATTGGT
1 GTTGGAATTGGAATTGGT
* *
60523 GTTGGAGTTGGAGTTGG
1 GTTGGAATTGGAATTGG
60540 CGCTGGTGCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.00, G:0.46, T:0.37
Consensus pattern (18 bp):
GTTGGAATTGGAATTGGT
Found at i:70224 original size:60 final size:60
Alignment explanation
Indices: 70155--70277 Score: 228
Period size: 60 Copynumber: 2.0 Consensus size: 60
70145 TGTTATGAGT
70155 AGGCATATGGTCTTAGTTGACATATCGTGTGTGCTATTGACTGCTGCTCATTTGAGTTTA
1 AGGCATATGGTCTTAGTTGACATATCGTGTGTGCTATTGACTGCTGCTCATTTGAGTTTA
* *
70215 AGGCATATGGTCTTAGTTGACATATCGTGTGTGCTATTGACTGCTGGTCGTTTGAGTTTA
1 AGGCATATGGTCTTAGTTGACATATCGTGTGTGCTATTGACTGCTGCTCATTTGAGTTTA
70275 AGG
1 AGG
70278 AGGAAGATCT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.20, C:0.14, G:0.28, T:0.39
Consensus pattern (60 bp):
AGGCATATGGTCTTAGTTGACATATCGTGTGTGCTATTGACTGCTGCTCATTTGAGTTTA
Found at i:74430 original size:2 final size:2
Alignment explanation
Indices: 74425--74517 Score: 168
Period size: 2 Copynumber: 46.0 Consensus size: 2
74415 TGTGTGTGTG
74425 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
74467 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A
*
74510 TA AA TA TA
1 TA TA TA TA
74518 CTTGTTTCAT
Statistics
Matches: 88, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
2 86 0.98
3 2 0.02
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (2 bp):
TA
Found at i:81882 original size:2 final size:2
Alignment explanation
Indices: 81875--81913 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
81865 AACCATGATC
81875 AT AT AT AT AT AT AT -T AT -T AT AT AT -T 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
81914 TATCAGTACT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.09
2 31 0.91
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:90383 original size:15 final size:18
Alignment explanation
Indices: 90375--90409 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
90365 CACCATCACC
*
90375 ACAACCACCACCACCTCG
1 ACAACCACCATCACCTCG
*
90393 ACAACCACCATCTCCTC
1 ACAACCACCATCACCTC
90410 CGCCACCTAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.54, G:0.03, T:0.11
Consensus pattern (18 bp):
ACAACCACCATCACCTCG
Found at i:105587 original size:2 final size:2
Alignment explanation
Indices: 105580--105604 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
105570 CCATCAAAAT
105580 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
105605 NNNNNNNNNN
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:107126 original size:3 final size:3
Alignment explanation
Indices: 107118--107147 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
107108 AAATGCTATG
107118 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
107148 TATCTTTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:110074 original size:5 final size:5
Alignment explanation
Indices: 110064--110092 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
110054 GGACCGCCTG
110064 GCCCT GCCCT GCCCT GCCCT GCCCT GCCC
1 GCCCT GCCCT GCCCT GCCCT GCCCT GCCC
110093 AGGTTTTGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.62, G:0.21, T:0.17
Consensus pattern (5 bp):
GCCCT
Found at i:132573 original size:18 final size:17
Alignment explanation
Indices: 132550--132584 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
132540 TTTGAGGAAT
132550 AAAAATAATTGTTAAATA
1 AAAAATAATT-TTAAATA
*
132568 AAAAATTATTTTAAATA
1 AAAAATAATTTTAAATA
132585 TCATTAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (17 bp):
AAAAATAATTTTAAATA
Found at i:132966 original size:4 final size:4
Alignment explanation
Indices: 132947--132992 Score: 51
Period size: 4 Copynumber: 11.2 Consensus size: 4
132937 ATCGTATGAG
132947 TAAA TAAA -ATAA -AAA TAAA TAAA TAAA TAAA TATAA TAATA TAAA T
1 TAAA TAAA TA-AA TAAA TAAA TAAA TAAA TAAA TA-AA TAA-A TAAA T
132993 TTAAAAAACT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
3 3 0.08
4 27 0.71
5 8 0.21
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (4 bp):
TAAA
Found at i:132976 original size:18 final size:17
Alignment explanation
Indices: 132947--132992 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 17
132937 ATCGTATGAG
132947 TAAATAAAATAAAAATAAA
1 TAAAT-AAATAAAAAT-AA
*
132966 TAAATAAATAAATATAA
1 TAAATAAATAAAAATAA
132983 TAATATAAAT
1 TAA-ATAAAT
132993 TTAAAAAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 5 0.20
18 15 0.60
19 5 0.20
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (17 bp):
TAAATAAATAAAAATAA
Found at i:140500 original size:2 final size:2
Alignment explanation
Indices: 140495--140526 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
140485 ATCGTACGTG
140495 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
140527 CACATACAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:142264 original size:24 final size:23
Alignment explanation
Indices: 142220--142265 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 23
142210 CAGATCATAT
142220 CCAAAATTTAATCATCATTCAATC
1 CCAAAATTTAATCAT-ATTCAATC
142244 CCAAAATTTCAATTCAT-TTCAA
1 CCAAAATTT-AA-TCATATTCAA
142266 CAAAAGTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
24 14 0.70
25 2 0.10
26 4 0.20
ACGTcount: A:0.41, C:0.24, G:0.00, T:0.35
Consensus pattern (23 bp):
CCAAAATTTAATCATATTCAATC
Found at i:153449 original size:12 final size:12
Alignment explanation
Indices: 153432--153456 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
153422 ATTACAGGGT
153432 GAGGAAGAAGAG
1 GAGGAAGAAGAG
153444 GAGGAAGAAGAG
1 GAGGAAGAAGAG
153456 G
1 G
153457 TTAAATTGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (12 bp):
GAGGAAGAAGAG
Found at i:162639 original size:2 final size:2
Alignment explanation
Indices: 162632--162656 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
162622 CACTGTTGGG
162632 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
162657 GAGAGAGAGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:162661 original size:2 final size:2
Alignment explanation
Indices: 162656--162684 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
162646 ATATATATAT
162656 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
162685 CTAAACAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:163666 original size:2 final size:2
Alignment explanation
Indices: 163659--163683 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
163649 AATATTCATC
163659 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
163684 AAAACATGGT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:172205 original size:62 final size:63
Alignment explanation
Indices: 172074--172221 Score: 151
Period size: 62 Copynumber: 2.4 Consensus size: 63
172064 AATTTATCTA
* * * * *
172074 TATTTTTATAACATTTTATAATTTCGCCTTTCCAATAAGTTTTAAATTCTTATAACTTGTTTT
1 TATTTTTATAAAATTTTATAATTTCGCCTTTCCAATAAGTTTAAAATTCTTATAACATATTGT
* * * *
172137 TGTTTTTA-AAAATTTTATAATTTCGTC-TTCGCAA-AAGGTTTAAAATTTTTTTAACATATTGT
1 TATTTTTATAAAATTTTATAATTTCGCCTTTC-CAATAA-GTTTAAAATTCTTATAACATATTGT
* *
172199 TATTTTTTTCAAA-TTTATAATTT
1 TATTTTTATAAAATTTTATAATTT
172222 TACACTTACA
Statistics
Matches: 70, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
61 5 0.07
62 55 0.79
63 10 0.14
ACGTcount: A:0.30, C:0.09, G:0.06, T:0.54
Consensus pattern (63 bp):
TATTTTTATAAAATTTTATAATTTCGCCTTTCCAATAAGTTTAAAATTCTTATAACATATTGT
Found at i:183147 original size:21 final size:22
Alignment explanation
Indices: 183121--183161 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
183111 TAGATTAGAT
183121 ATCTTTAATT-GAAAATTGATC
1 ATCTTTAATTAGAAAATTGATC
**
183142 ATCTTTTTTTAGAAAATTGA
1 ATCTTTAATTAGAAAATTGA
183162 AAGTATTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.46
Consensus pattern (22 bp):
ATCTTTAATTAGAAAATTGATC
Found at i:184372 original size:24 final size:25
Alignment explanation
Indices: 184345--184391 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
184335 TTTGTAATTT
184345 TAAACTTTA-AAATAAT-AATTTAAA
1 TAAA-TTTATAAATAATAAATTTAAA
*
184369 TAAATTTATAAATTATAAATTTA
1 TAAATTTATAAATAATAAATTTA
184392 TATTTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 4 0.20
24 10 0.50
25 6 0.30
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (25 bp):
TAAATTTATAAATAATAAATTTAAA
Done.