Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2417
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: 59515
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:10581 original size:44 final size:40
Alignment explanation
Indices: 10488--10621 Score: 130
Period size: 44 Copynumber: 3.3 Consensus size: 40
10478 GCTACTCGTT
* * *
10488 CAAATGCCTTCGGACATAGCCC-GATTATAGTAACT-GCGCA
1 CAAATGCCTTCGGGCTTACCCCGGATT-TAGTAACTCGCG-A
*
10528 CAATTGCCTTCGGGACTTAAACCCCGGATTTAGTAAACTCGCGA
1 CAAATGCCTTCGGG-CTT--ACCCCGGATTTAGT-AACTCGCGA
* * *
10572 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGC-A
1 CAAATGCCTTCGGGCTTACCCCGGATTTAGTAACTCGCGA
10611 CAAATGCCTTC
1 CAAATGCCTTC
10622 AAATCTTAGT
Statistics
Matches: 80, Mismatches: 8, Indels: 13
0.79 0.08 0.13
Matches are distributed among these distances:
39 12 0.15
40 18 0.22
41 14 0.17
43 11 0.14
44 22 0.28
45 3 0.04
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGCTTACCCCGGATTTAGTAACTCGCGA
Found at i:13223 original size:37 final size:39
Alignment explanation
Indices: 13146--13247 Score: 129
Period size: 37 Copynumber: 2.6 Consensus size: 39
13136 ATAAGCCTTT
13146 GAAGGCATTTTGTTGCGAGATTACTAAATTCCGGGCTAAG-CC
1 GAAGGCA-TTTG-TGCGAG-TTACT-AATTCCGGGCTAAGCCC
*
13188 GAAGGCATTTGTGCGAGTTACTAA-TCCGGGTTAAGCCC
1 GAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCC
*
13226 GAAGGCAATT-TGCGAGTTACTA
1 GAAGGCATTTGTGCGAGTTACTA
13248 TATCGGCGCT
Statistics
Matches: 57, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
37 22 0.39
38 13 0.23
39 5 0.09
40 6 0.11
41 4 0.07
42 7 0.12
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.27
Consensus pattern (39 bp):
GAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCC
Found at i:23657 original size:40 final size:40
Alignment explanation
Indices: 23594--23775 Score: 242
Period size: 40 Copynumber: 4.6 Consensus size: 40
23584 AACCCAAGTA
* * *
23594 CCTTCAGGATTTAG-CCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
* *
23633 CCTTCGGGACATAGCCCGGATATAGTCAATAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
23673 CCTTCGGGACTTAGCCCTGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
* * * *
23713 CCTTCAGGACTTAGCCCGGATATAGTCACTATCATAAAAG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
23753 CATTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
23776 CATTCGAATA
Statistics
Matches: 126, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
39 11 0.09
40 114 0.90
41 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:27031 original size:46 final size:45
Alignment explanation
Indices: 26951--27121 Score: 152
Period size: 45 Copynumber: 3.8 Consensus size: 45
26941 AAAACTACAA
* * *
26951 ATCTGATCTTCGCTGAG-AAGAGCGGAGCAAATCAAATTTCGGTAG
1 ATCTTATC-TCGCTGAGCAAGAGCGGAGCAGATCAAATTTCGGCAG
**
26996 ATCTTATCTTCGCTGAGCAAGAGCGGAGCAGATCAAATTTTAGCAG
1 ATCTTATC-TCGCTGAGCAAGAGCGGAGCAGATCAAATTTCGGCAG
* * * * *
27042 ATCTCATCCCGCTG-GCAGGAGTGGAAG-AGATTAAATTTCGGCAG
1 ATCTTATCTCGCTGAGCAAGAGCGG-AGCAGATCAAATTTCGGCAG
* * * *
27086 ATCCTATCTCCCTAAGC-AGTAGTGGAGCAGATCAAA
1 ATCTTATCTCGCTGAGCAAG-AGCGGAGCAGATCAAA
27122 GACAATGAGC
Statistics
Matches: 102, Mismatches: 19, Indels: 10
0.78 0.15 0.08
Matches are distributed among these distances:
44 34 0.33
45 37 0.36
46 31 0.30
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.24
Consensus pattern (45 bp):
ATCTTATCTCGCTGAGCAAGAGCGGAGCAGATCAAATTTCGGCAG
Found at i:27199 original size:90 final size:86
Alignment explanation
Indices: 27083--27294 Score: 282
Period size: 90 Copynumber: 2.4 Consensus size: 86
27073 TAAATTTCGG
*
27083 CAGATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACAATGAGCCTTAACCCCCTAAGCA
1 CAGATCCTATCTCCCTAAGCAATAGTGGAGCAGATCAAAGACAATGAGCCTTAA-CCCCTAAGCA
*
27148 GTAGGGTAA-TAGGCGAGAAAATGA
65 GTAGGGTAACT-GAC-AGAAAAT-A
* *** *
27172 CAGATCTTTATCTCCCTAAGCAATAGTGGAGCAGATCAAAGATGGTGAGTCTTAACCCCTAAGCA
1 CAGATC-CTATCTCCCTAAGCAATAGTGGAGCAGATCAAAGACAATGAGCCTTAACCCCTAAGCA
*
27237 GTAGGGTAACTGACTGAAAATA
65 GTAGGGTAACTGACAGAAAATA
* *
27259 CAGATCCTATTTCCCTAAGCAATAGTGGAGCGGATC
1 CAGATCCTATCTCCCTAAGCAATAGTGGAGCAGATC
27295 GAAAATGGCA
Statistics
Matches: 110, Mismatches: 11, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
86 27 0.25
87 7 0.06
88 6 0.05
89 27 0.25
90 43 0.39
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.22
Consensus pattern (86 bp):
CAGATCCTATCTCCCTAAGCAATAGTGGAGCAGATCAAAGACAATGAGCCTTAACCCCTAAGCAG
TAGGGTAACTGACAGAAAATA
Found at i:27461 original size:46 final size:46
Alignment explanation
Indices: 27405--27559 Score: 136
Period size: 46 Copynumber: 3.3 Consensus size: 46
27395 TAGGCTTTAA
*
27405 CTCCCTAAGCAATAGGGTAAAAGGCTAGAGGATTACAAGATCTTAT
1 CTCCCTAAGCAGTAGGGTAAAAGGCTAGAGGATTACAAGATCTTAT
* ** * * * * * *
27451 CTCCCTAAGCAGCAGCGG-AGCAGATCGAAGATGG-TGAGCAGGCT-TTAA
1 CTCCCTAAGCAGTAG-GGTAAAAG-GC-TAGA-GGATTA-CAAGATCTTAT
*
27499 CTCCCTAAGCAGTAGGGTAAAAGGCTGGAGGATTACAAGATCTTAT
1 CTCCCTAAGCAGTAGGGTAAAAGGCTAGAGGATTACAAGATCTTAT
*
27545 CTCCCTAAGTAGTAG
1 CTCCCTAAGCAGTAG
27560 TGGAGCAGAT
Statistics
Matches: 80, Mismatches: 21, Indels: 16
0.68 0.18 0.14
Matches are distributed among these distances:
45 6 0.08
46 37 0.46
47 6 0.08
48 25 0.31
49 6 0.08
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (46 bp):
CTCCCTAAGCAGTAGGGTAAAAGGCTAGAGGATTACAAGATCTTAT
Found at i:27578 original size:94 final size:92
Alignment explanation
Indices: 27083--27577 Score: 473
Period size: 94 Copynumber: 5.5 Consensus size: 92
27073 TAAATTTCGG
* * ** *
27083 CAGATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACAATGAGC---C-TTAACCCCCTA
1 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGATGAGCAGGCTTTAACTCCCTA
* * * *
27144 AGCAGTAGGGTAATAGGCGAGAAAATGA
66 AGCAGTAGGGTAAAAGGC-TGAAGATTA
* * * *
27172 CAGATCTTTATCTCCCTAAGCAATAGTGGAGCAGATCAAAGATG--GTG-AGTC-TTAAC-CCCT
1 CAGATC-TTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGATGAGCAGGCTTTAACTCCCT
** * *
27232 AAGCAGTAGGGTAACTGACTGAA-AATA
65 AAGCAGTAGGGTAAAAGGCTGAAGATTA
* * * * * * * *
27259 CAGATCCTATTTCCCTAAGCAATAGTGGAGCGGATCGAA-A--ATG-GCAAGCTTTATCTTCCTG
1 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGATGAGCAGGCTTTAACTCCCTA
* *
27320 AGCAGCAGTGG-AGCAA-GCTGAAGATTA
66 AGCAGTAG-GGTA-AAAGGCTGAAGATTA
** *
27347 CAGATCTTATCTCCCTAAGCAGCGGTGGAGCAGATCGAAGATGATGAGTAGGCTTTAACTCCCTA
1 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGATGAGCAGGCTTTAACTCCCTA
* *
27412 AGCAATAGGGTAAAAGGCTAGAGGATTA
66 AGCAGTAGGGTAAAAGGCT-GAAGATTA
* * *
27440 CAAGATCTTATCTCCCTAAGCAGCAGCGGAGCAGATCGAAGATGGTGAGCAGGCTTTAACTCCCT
1 C-AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGATGAGCAGGCTTTAACTCCCT
*
27505 AAGCAGTAGGGTAAAAGGCTGGAGGATTA
65 AAGCAGTAGGGTAAAAGGCT-GAAGATTA
*
27534 CAAGATCTTATCTCCCTAAGTAGTAGTGGAGCAGATCGAAGATG
1 C-AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATG
27578 GCAAACCTTA
Statistics
Matches: 336, Mismatches: 50, Indels: 35
0.80 0.12 0.08
Matches are distributed among these distances:
84 1 0.00
85 4 0.01
86 33 0.10
87 24 0.07
88 43 0.13
89 27 0.08
90 39 0.12
91 7 0.02
92 23 0.07
93 8 0.02
94 127 0.38
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.22
Consensus pattern (92 bp):
CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGATGAGCAGGCTTTAACTCCCTA
AGCAGTAGGGTAAAAGGCTGAAGATTA
Found at i:27698 original size:44 final size:44
Alignment explanation
Indices: 27083--27701 Score: 152
Period size: 44 Copynumber: 13.8 Consensus size: 44
27073 TAAATTTCGG
* ** *
27083 CAGATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACAA
1 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATAA
* * * * ** *** * *
27127 -TGAGCCTTAACCCCCTAAGCAGTAG-GGTAATAGGCGAGAAAATGA
1 CAGA-TCTTATCTCCCTAAGCAGTAGTGG-AGCA-GATTGAAGATAA
* ** *
27172 CAGATCTTTATCTCCCTAAGCAATAGTGGAGCAGATCAAAGAT-G
1 CAGATC-TTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATAA
** * * * * *
27216 GTGAGTCTTAAC-CCCTAAGCAGTAG-GGTAACTGACTGAAAAT-A
1 CAGA-TCTTATCTCCCTAAGCAGTAGTGG-AGCAGATTGAAGATAA
* * * * * * **
27259 CAGATCCTATTTCCCTAAGCAATAGTGGAGCGGATCGAAAATGG
1 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATAA
* * * * * *
27303 CA-AGCTTTATCTTCCTGAGCAGCAGTGGAGCA-AGCTGAAGATTA
1 CAGATC-TTATCTCCCTAAGCAGTAGTGGAGCAGA-TTGAAGATAA
** * *
27347 CAGATCTTATCTCCCTAAGCAGCGGTGGAGCAGATCGAAGATGAT
1 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGAT-AA
* * * * ** * * * *
27392 GAGTAGGCTTTAACTCCCTAAGCAATAG-GGTAAAAGGCTAGAGGATTA
1 CAG-A-TC-TTATCTCCCTAAGCAGTAGTGG-AGCA-GATTGAAGATAA
* * * *
27440 CAAGATCTTATCTCCCTAAGCAGCAGCGGAGCAGATCGAAGATGGTGAG
1 C-AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGA---T-AA
* * ** * * * *
27489 CAG-GCTTTAACTCCCTAAGCAGTAG-GGTAAAAGGCTGGAGGATTA
1 CAGATC-TTATCTCCCTAAGCAGTAGTGG-AGCA-GATTGAAGATAA
* * **
27534 CAAGATCTTATCTCCCTAAGTAGTAGTGGAGCAGATCGAAGATGG
1 C-AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATAA
* * * * * * *
27579 CAAACCTTATCTCTCTAA--AGTTGCAGAGAGCAGGTTGAAG-TTA
1 CAGATCTTATCTCCCTAAGCAGTAG-TG-GAGCAGATTGAAGATAA
* * ** *
27622 CA-AGTCTTATCTCTCTGAAGCCGTAGCAGAGCATATTGAAGATAA
1 CAGA-TCTTATCTCCCT-AAGCAGTAGTGGAGCAGATTGAAGATAA
27667 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGAT
1 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGAT
27702 CGAAAATACC
Statistics
Matches: 397, Mismatches: 137, Indels: 82
0.64 0.22 0.13
Matches are distributed among these distances:
42 11 0.03
43 66 0.17
44 137 0.35
45 48 0.12
46 65 0.16
47 14 0.04
48 40 0.10
49 16 0.04
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (44 bp):
CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATAA
Found at i:29349 original size:23 final size:22
Alignment explanation
Indices: 29322--29369 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
29312 CTTTTTGGAA
* *
29322 TTTTATTTATGTATTATTGTATT
1 TTTTATATATGTATT-TTATATT
*
29345 TTTTATATATTTATTTTATATT
1 TTTTATATATGTATTTTATATT
29367 TTT
1 TTT
29370 AATACATATC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.73
Consensus pattern (22 bp):
TTTTATATATGTATTTTATATT
Found at i:38464 original size:27 final size:27
Alignment explanation
Indices: 38433--38486 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
38423 ACCATTCCAG
*
38433 GATGTTGTAGGGGATGACCCGCAAATA
1 GATGTTGTAGGGGATGACCCACAAATA
38460 GATGTTGTAGGGGATGACCCACAAATA
1 GATGTTGTAGGGGATGACCCACAAATA
38487 TATGCATGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.31, T:0.22
Consensus pattern (27 bp):
GATGTTGTAGGGGATGACCCACAAATA
Found at i:48105 original size:22 final size:23
Alignment explanation
Indices: 48053--48105 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 23
48043 TAAATGATGG
*
48053 ATGCCTATTGAGTTATAATATGTA
1 ATGCC-ATTGAGTTATAAAATGTA
48077 ATG-CATT-AGTTAGTAAAATGT-
1 ATGCCATTGAGTTA-TAAAATGTA
48098 ATGCCATT
1 ATGCCATT
48106 TATTTGTGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 8 0.31
22 14 0.54
23 1 0.04
24 3 0.12
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.40
Consensus pattern (23 bp):
ATGCCATTGAGTTATAAAATGTA
Found at i:48905 original size:39 final size:40
Alignment explanation
Indices: 48795--49013 Score: 268
Period size: 40 Copynumber: 5.5 Consensus size: 40
48785 TTCGAATGAT
*
48795 ATCCGGGTTAGGTCCCGAAGGCATTTGTGCGAGTTACTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
48835 ATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
* * * *
48875 TTCTGGGCTAAG-CCAGAAGGCA-TTGATGCGAGTTACTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTTG-TGCGAGTTACTAA
*
48914 ATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATG
1 ATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-A
* * * *
48955 A-CCGGGCTATGTCCCGAAGGCATTTGAGCGAG-TAGCTAT
1 ATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTAA
* *
48994 ATCC-GGTTAAATTCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
49014 TATGTGATTC
Statistics
Matches: 155, Mismatches: 18, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
38 3 0.02
39 46 0.30
40 102 0.66
41 4 0.03
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (40 bp):
ATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
Found at i:48962 original size:79 final size:81
Alignment explanation
Indices: 48797--49013 Score: 277
Period size: 79 Copynumber: 2.7 Consensus size: 81
48787 CGAATGATAT
* * *
48797 CCGGGTTAGGTCCCGAAGGCATTTG-TGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTT
1 CCGGGCTAAGTCCAGAAGGCATTTGATGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTT
*
48861 GTGCGAGTTACTAATT
66 GTGCGAGTTACTAATA
*
48877 CTGGGCTAAG-CCAGAAGGCA-TTGATGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTT
1 CCGGGCTAAGTCCAGAAGGCATTTGATGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTT
48940 GTGCGAGTTACT-ATGA
66 GTGCGAGTTACTAAT-A
* * * * *
48956 CCGGGCTATGTCCCGAAGGCATTTGA-GCGAG-TAGCTATATCC-GGTTAAATTCCGAAGG
1 CCGGGCTAAGTCCAGAAGGCATTTGATGCGAGTTA-CTAAATCCGGGTTAAGTCCCGAAGG
49014 TATGTGATTC
Statistics
Matches: 121, Mismatches: 11, Indels: 11
0.85 0.08 0.08
Matches are distributed among these distances:
78 5 0.04
79 84 0.69
80 28 0.23
81 4 0.03
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.26
Consensus pattern (81 bp):
CCGGGCTAAGTCCAGAAGGCATTTGATGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTT
GTGCGAGTTACTAATA
Found at i:51722 original size:47 final size:47
Alignment explanation
Indices: 51670--52310 Score: 1038
Period size: 47 Copynumber: 13.6 Consensus size: 47
51660 GATAATTGTG
* *
51670 ATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
51717 ATGTGAAAGTGTATA-ATGTGATAA-G-CGAATGG-CAATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
51760 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
51809 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
51858 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
51905 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
51952 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
51999 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
52046 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
52095 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
52144 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
52191 ATGTGAAAGTGTATATATGTGATGAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* * * * * * *
52238 ATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGG
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
52285 ATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGAAAGTGTATATATGTGATAAG
52311 TCCCGAAGGG
Statistics
Matches: 562, Mismatches: 24, Indels: 16
0.93 0.04 0.03
Matches are distributed among these distances:
43 21 0.04
44 6 0.01
45 5 0.01
46 18 0.03
47 342 0.61
48 6 0.01
49 164 0.29
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:52144 original size:286 final size:283
Alignment explanation
Indices: 51670--52310 Score: 1140
Period size: 286 Copynumber: 2.3 Consensus size: 283
51660 GATAATTGTG
* *
51670 ATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAATG
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAATG
51735 TGATAA-GCGAATGGCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCC
66 TGATAAGGCGAATGGCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCC
51799 GATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
131 GATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
*
51864 AAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATA
196 AAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATA
51929 AGGCCTAATGGCCGATGTGATGA
261 AGGCCTAATGGCCGATGTGATGA
51952 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA-AT
52017 GTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATG
65 GTGATAAGG-CGAATGG-CAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATG
52082 GCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATG
128 GCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATG
52147 TGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTG
193 TGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTG
*
52212 ATGAGGCCTAATGGCCGATGTGATGA
258 ATAAGGCCTAATGGCCGATGTGATGA
* * * * * * *
52238 ATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAAT
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT-AAT
52303 GTGATAAG
65 GTGATAAG
52311 TCCCGAAGGG
Statistics
Matches: 343, Mismatches: 11, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
282 60 0.17
283 9 0.03
284 1 0.00
285 7 0.02
286 265 0.77
287 1 0.00
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (283 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAATG
TGATAAGGCGAATGGCAATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCC
GATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
AAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATA
AGGCCTAATGGCCGATGTGATGA
Found at i:54787 original size:118 final size:117
Alignment explanation
Indices: 54576--54859 Score: 408
Period size: 118 Copynumber: 2.4 Consensus size: 117
54566 CAAAGCTTCA
*
54576 TGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTACCGGGCTAAGTC
1 TGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTACCGGGCTAAGTC
* * *
54641 CCGAAGAGCATCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCG
66 CCGAAGAGCATCATGCTAGTAATATATCCGGGCTAA-ACCCGAAGAGCATTCG
* * *
54694 TGCTAGTGATGTATCCGGACTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCGGGCTAAGTT
1 TGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTACCGGGCTAAGTC
* *
54759 CCGAAGAGCATTC-TGCTAGTAATATATCCGTGCTAAACTCGAAGAGCATTCG
66 CCGAAGAGCA-TCATGCTAGTAATATATCCGGGCTAAACCCGAAGAGCATTCG
* * * * * *
54811 TGCTGGTGTTATATCCGGGCTAGGTCCCGAAGAGCAATCATGCTGGTGA
1 TGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA
54860 CGTGTATTCG
Statistics
Matches: 149, Mismatches: 16, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
117 56 0.38
118 91 0.61
119 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (117 bp):
TGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTACCGGGCTAAGTC
CCGAAGAGCATCATGCTAGTAATATATCCGGGCTAAACCCGAAGAGCATTCG
Found at i:54855 original size:40 final size:40
Alignment explanation
Indices: 54572--54859 Score: 397
Period size: 39 Copynumber: 7.3 Consensus size: 40
54562 GCGTCAAAGC
54572 TTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCA
1 TTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCA
*
54612 TTCGTGCTAGTGATGTA-CCGGGCTAAGTCCCGAAGAGCA
1 TTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCA
54651 -TCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCA
1 TTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCA
* *
54690 TTCGTGCTAGTGATGTATCCGGACTAAGTCCCGAAGAGCA
1 TTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCA
*
54730 TTCATGCTAGTGATGTAT-CGGGCTAAGTTCCGAAGAGCA
1 TTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCA
* * * * *
54769 TTC-TGCTAGTAATATATCCGTGCTAA-ACTCGAAGAGCA
1 TTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCA
* * * * *
54807 TTCGTGCTGGTGTTATATCCGGGCTAGGTCCCGAAGAGCA
1 TTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCA
* *
54847 ATCATGCTGGTGA
1 TTCATGCTAGTGA
54860 CGTGTATTCG
Statistics
Matches: 220, Mismatches: 23, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
38 39 0.18
39 91 0.41
40 90 0.41
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TTCATGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCA
Found at i:55065 original size:25 final size:24
Alignment explanation
Indices: 55019--55072 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 24
55009 TGTGTAATAA
55019 CGAATGAATAGAGCACTATGTGTG
1 CGAATGAATAGAGCACTATGTGTG
* * *
55043 TGAATGATTAGAGGCACTGTGTGTG
1 CGAATGAATAGA-GCACTATGTGTG
55068 CGAAT
1 CGAAT
55073 TCCTTTTAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 10 0.40
25 15 0.60
ACGTcount: A:0.30, C:0.11, G:0.31, T:0.28
Consensus pattern (24 bp):
CGAATGAATAGAGCACTATGTGTG
Found at i:58484 original size:49 final size:47
Alignment explanation
Indices: 58419--59079 Score: 590
Period size: 49 Copynumber: 13.6 Consensus size: 47
58409 ATAATTGTGG
* *
58419 ATGTGAATGTATATATATGTGATAAGGCCTAAATGGCCGATGTGAATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCT-AATGGCCGATGTG-ATGA
* * *
58468 ATGTGCAAGTGTATATATGTGATAAGG-CGAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
58514 ATGTG-AAGTGTATATATATGTGATAAGGCCT-AT-GCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
58560 ATGTG-AAGTGTTATAATATAGTGATAAGGCCTAATTGCCGATGTGATGA
1 ATGTGAAAGTG-TAT-ATAT-GTGATAAGGCCTAATGGCCGATGTGATGA
* *
58609 ATGTGAAAGTGTATATATGTGAATCAGGCCCGAAATGGCCAGATGTGGATGA
1 ATGTGAAAGTGTATATATGTG-ATAAGG-CC-TAATGGCC-GATGT-GATGA
58661 ATGTGACAAGTGGTATATATGTGGA-AAGGCCTCAATGGCC-ATGTGATGA
1 ATGTGA-AAGT-GTATATATGT-GATAAGGCCT-AATGGCCGATGTGATGA
58710 ATGGTGAAAGTTGTATAATATGTGAT-AGGCCTAATGGCCGATGTGATG-
1 AT-GTGAAAG-TGTAT-ATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
58758 ATGTGAAACAGTGGTATATATGTGATAA-G-CGAAT-GCCAATGTGATGA
1 ATGTG-AA-AGT-GTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
58805 ATGTGAAAGTGTAATATTGATAGTGTTAATGTATAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGT-ATA-T-AT-GTG---A--TA-AGGCCTAATGGCCGATGTGATGA
*
58862 ATGTGAAATGTATATATATGTGATAAGGCCTAAATGGCCGATGTGATTGA
1 ATGTGAAA-GTGTATATATGTGATAAGGCCT-AATGGCCGATGTGA-TGA
* *
58912 ATGTGAACACGTGTATATAGTATTGATAAGGTCTAAT-GCCGATGTGAATGA
1 ATGTGAA-A-GTGTATATA-T-GTGATAAGGCCTAATGGCCGATGTG-ATGA
*
58963 ATGTG--AGTGT-TAATTATGTGATGAGGCCTAA-GGCCGATGTGATG-
1 ATGTGAAAGTGTAT-A-TATGTGATAAGGCCTAATGGCCGATGTGATGA
* * * * *
59007 ATGTGAACAGTGTAT-TATGTGA-CAGGCCGAGTGGCCAAACGTGAATG-
1 ATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCC-GATGTG-ATGA
*
59054 ATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGAAAGTGTATATATGTGATAAG
59080 TCTCGGAAGG
Statistics
Matches: 521, Mismatches: 32, Indels: 119
0.78 0.05 0.18
Matches are distributed among these distances:
44 13 0.02
45 28 0.05
46 81 0.16
47 86 0.17
48 50 0.10
49 100 0.19
50 36 0.07
51 33 0.06
52 25 0.05
53 19 0.04
54 15 0.03
55 4 0.01
56 5 0.01
57 23 0.04
58 3 0.01
ACGTcount: A:0.32, C:0.09, G:0.29, T:0.30
Consensus pattern (47 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:58711 original size:150 final size:143
Alignment explanation
Indices: 58419--59013 Score: 597
Period size: 150 Copynumber: 4.0 Consensus size: 143
58409 ATAATTGTGG
*
58419 ATGTGAA-TGTATATATATGTGATAAGGCCTAAATGGCCGATGTGAATGAATGTGCA-AGTGTAT
1 ATGTGAAGTGTATATATATGTGATAAGGCCTAAATGGCCGATGTG-ATGAATGTGAACAGTGTAT
*
58482 ATATGTGATAAGGCGAATGGCCAATGTGATGAATGTG-AAGTGTATATATATGTGATAAGGCCT-
65 ATATGTGAT-AGGCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGTGA-AAGGCCTA
58545 AT-GCCGATGTGATGA
128 ATGGCCGATGTGATGA
*
58560 ATGTGAAGTGT-TATAATATAGTGATAAGGCCT-AATTGCCGATGTGATGAATGTGAA-AGTGTA
1 ATGTGAAGTGTATAT-ATAT-GTGATAAGGCCTAAATGGCCGATGTGATGAATGTGAACAGTGTA
58622 TATATGTGAATCAGGCCCGAAATGGCCAGATGTGGATGAATGTGACAAGTGGTATATATGTG-GA
64 TATATGTG-AT-AGG--CG-AATGGCCA-ATGT-GATGAATGTGA-AAGT-GTATATATGTGTGA
58686 AAGGCCTCAATGGCC-ATGTGATGA
120 AAGGCCT-AATGGCCGATGTGATGA
58710 ATGGTGAAAGTTGTATA-ATATGTGAT-AGGCCT-AATGGCCGATGTGATG-ATGTGAAACAGTG
1 AT-GTG-AAG-TGTATATATATGTGATAAGGCCTAAATGGCCGATGTGATGAATGTG-AACAGT-
*
58771 GTATATATGTGATAAGCGAAT-GCCAATGTGATGAATGTGAAAGTGTAATATTGATAGTGTTAAT
61 GTATATATGTGATAGGCGAATGGCCAATGTGATGAATGTGAAAGTGT-ATA-T-AT-GTG----T
*
58835 GTATAGGCCTAATGGCCGATGTGATGA
118 G-AAAGGCCTAATGGCCGATGTGATGA
*
58862 ATGTGAAATGTATATATATGTGATAAGGCCTAAATGGCCGATGTGATTGAATGTGAACACGTGTA
1 ATGTGAAGTGTATATATATGTGATAAGGCCTAAATGGCCGATGTGA-TGAATGTGAACA-GTGTA
* * *
58927 TATAGTATTGATAAGGTCTAAT-GCCGATGTGAATGAATGTG--AGTGT-TAATTATGTGATG--
64 TATA-T-GTGAT-AGG-CGAATGGCCAATGTG-ATGAATGTGAAAGTGTAT-A-TATGTG-TGAA
58986 AGGCCTAA-GGCCGATGTGATG-
121 AGGCCTAATGGCCGATGTGATGA
59007 ATGTGAA
1 ATGTGAA
59014 CAGTGTATTA
Statistics
Matches: 397, Mismatches: 12, Indels: 86
0.80 0.02 0.17
Matches are distributed among these distances:
141 34 0.09
142 26 0.07
143 19 0.05
144 14 0.04
145 21 0.05
146 24 0.06
147 21 0.05
148 9 0.02
149 17 0.04
150 62 0.16
151 33 0.08
152 50 0.13
153 19 0.05
154 13 0.03
155 7 0.02
156 7 0.02
157 12 0.03
158 9 0.02
ACGTcount: A:0.32, C:0.09, G:0.29, T:0.30
Consensus pattern (143 bp):
ATGTGAAGTGTATATATATGTGATAAGGCCTAAATGGCCGATGTGATGAATGTGAACAGTGTATA
TATGTGATAGGCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGTGAAAGGCCTAATG
GCCGATGTGATGA
Found at i:58864 original size:57 final size:49
Alignment explanation
Indices: 58839--59013 Score: 163
Period size: 46 Copynumber: 3.6 Consensus size: 49
58829 GTTAATGTAT
*
58839 AGGCCT-AATGGCCGATGTGATGAATGTGAAATGTATATATATGTGATA
1 AGGCCTAAATGGCCGATGTGATGAATGTGAAATGTATATATATGTAATA
*
58887 AGGCCTAAATGGCCGATGTGATTGAATGTGAACACGTGTATATAGTAT-TGATA
1 AGGCCTAAATGGCCGATGTGA-TGAATGTGAA-A--TGTATATA-TATGTAATA
* * * *
58940 AGGTCT-AAT-GCCGATGTGAATGAATGTG-AGTGT-TA-ATTATGTGATG
1 AGGCCTAAATGGCCGATGTG-ATGAATGTGAAATGTATATA-TATGTAATA
58986 AGGCCT-AA-GGCCGATGTGATG-ATGTGAA
1 AGGCCTAAATGGCCGATGTGATGAATGTGAA
59014 CAGTGTATTA
Statistics
Matches: 112, Mismatches: 5, Indels: 23
0.80 0.04 0.16
Matches are distributed among these distances:
44 5 0.04
45 8 0.07
46 22 0.20
47 3 0.03
48 6 0.05
49 14 0.12
50 11 0.10
51 18 0.16
52 4 0.04
53 18 0.16
54 3 0.03
ACGTcount: A:0.31, C:0.10, G:0.29, T:0.30
Consensus pattern (49 bp):
AGGCCTAAATGGCCGATGTGATGAATGTGAAATGTATATATATGTAATA
Done.