Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A04
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: 82679320
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4050000 characters in sequence are not A, C, G, or T
File 255 of 255
Found at i:82536941 original size:29 final size:29
Alignment explanation
Indices: 82536885--82536941 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
82536875 TCAAAATTAC
* *
82536885 GTAATTTTATACAATAATTTTATTTTTGT
1 GTAATTTTATACAAAAATTTTATATTTGT
*
82536914 GTAATTTTATATATAAAATTTT-TATTTG
1 GTAATTTTATACA-AAAATTTTATATTTG
82536942 ATTTAAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 17 0.71
30 7 0.29
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.58
Consensus pattern (29 bp):
GTAATTTTATACAAAAATTTTATATTTGT
Found at i:82548573 original size:23 final size:23
Alignment explanation
Indices: 82548547--82548592 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
82548537 GTAAAGAAAG
82548547 ATTACTTGAAACACTGCTTCTTT
1 ATTACTTGAAACACTGCTTCTTT
82548570 ATTACTTGAAACACTGCTTCTTT
1 ATTACTTGAAACACTGCTTCTTT
82548593 CTTTTGTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.22, G:0.09, T:0.43
Consensus pattern (23 bp):
ATTACTTGAAACACTGCTTCTTT
Found at i:82569077 original size:18 final size:18
Alignment explanation
Indices: 82569054--82569088 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
82569044 GCGCTCTCGT
82569054 TCTCTTTCCTTCTCCCGC
1 TCTCTTTCCTTCTCCCGC
82569072 TCTCTTTCCTTCTCCCG
1 TCTCTTTCCTTCTCCCG
82569089 TCGCTCCAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.00, C:0.49, G:0.06, T:0.46
Consensus pattern (18 bp):
TCTCTTTCCTTCTCCCGC
Found at i:82578709 original size:21 final size:21
Alignment explanation
Indices: 82578676--82578715 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
82578666 ATAACATCAT
*
82578676 AAATTTATAAATTGATTATTG
1 AAATTTATAAATTCATTATTG
82578697 AAATTTA-ATAATTCATTAT
1 AAATTTATA-AATTCATTAT
82578716 AAATTAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (21 bp):
AAATTTATAAATTCATTATTG
Found at i:82578879 original size:32 final size:32
Alignment explanation
Indices: 82578843--82578903 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
82578833 TTATAAACTT
*
82578843 ATAAATTAATCACTTGAATTTAATAACTCGTG
1 ATAAATTAATCAATTGAATTTAATAACTCGTG
* * *
82578875 ATAAATTAATTAATTTAATTTGATAACTC
1 ATAAATTAATCAATTGAATTTAATAACTC
82578904 TTATTGATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.41
Consensus pattern (32 bp):
ATAAATTAATCAATTGAATTTAATAACTCGTG
Found at i:82578983 original size:154 final size:148
Alignment explanation
Indices: 82578719--82579110 Score: 468
Period size: 154 Copynumber: 2.6 Consensus size: 148
82578709 TCATTATAAA
* * *
82578719 TTAATTAATTAATTTCATTTGATAACTCATATTGATTAATTGAGTAATTTGTTAAATTTATTAAC
1 TTAATTAATTAATTTAATTTGATAACTCATATTGATTAATTGAG---CTTGTTAAATTTATAAAC
* * * * * *
82578784 TTTATAATTTATCATATTAATAAATATATTCTACTGTGAGGTTGAAATATTATAAACTTATAAAT
63 TTTATAATTAATCATGTGAA-AAATGTATTCTACTATGAGGTTGAAACATTATAAACTTATAAAT
*
82578849 TAATCACTTGAATTTAATAACT
127 TAATCACTTAAATTTAATAACT
* *
82578871 CGTGATAAATTAATTAATTTAATTTGATAACTCTTATTGATTAATTGAGCTTGTTAGATTTATAA
1 --T--T-AATTAATTAATTTAATTTGATAACTCATATTGATTAATTGAGCTTGTTAAATTTATAA
*
82578936 ACTTTATAATTAATCATGTGAAAGAATGTATTCTACTATGAGTTTGAAACATTATAAACTTATAA
61 ACTTTATAATTAATCATGTGAAA-AATGTATTCTACTATGAGGTTGAAACATTATAAACTTATAA
* *
82579001 ATTGATTACTTAAATTTAATAACT
125 ATTAATCACTTAAATTTAATAACT
* * * * *
82579025 TTAA-T--TT-ATTTAATTTGATAACTCATACTGATTAATTAAGCTTGTTATATTTATGAACGTT
1 TTAATTAATTAATTTAATTTGATAACTCATATTGATTAATTGAGCTTGTTAAATTTATAAACTTT
*
82579086 GTAATTAATCATGTGAAATAATGTA
66 ATAATTAATCATGTGAAA-AATGTA
82579111 AAATAAAATA
Statistics
Matches: 211, Mismatches: 23, Indels: 17
0.84 0.09 0.07
Matches are distributed among these distances:
145 71 0.34
146 2 0.01
148 1 0.00
149 2 0.01
150 1 0.00
152 1 0.00
153 1 0.00
154 91 0.43
156 1 0.00
157 40 0.19
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.45
Consensus pattern (148 bp):
TTAATTAATTAATTTAATTTGATAACTCATATTGATTAATTGAGCTTGTTAAATTTATAAACTTT
ATAATTAATCATGTGAAAAATGTATTCTACTATGAGGTTGAAACATTATAAACTTATAAATTAAT
CACTTAAATTTAATAACT
Found at i:82584882 original size:19 final size:20
Alignment explanation
Indices: 82584860--82584900 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
82584850 ATTTAATTTC
*
82584860 TATTTTTTATT-TTTAAAAA
1 TATTTTATATTATTTAAAAA
82584879 TATTTTATATTAGTTTAAAAA
1 TATTTTATATTA-TTTAAAAA
82584900 T
1 T
82584901 TTATTTAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 10 0.53
21 9 0.47
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (20 bp):
TATTTTATATTATTTAAAAA
Found at i:82592205 original size:39 final size:40
Alignment explanation
Indices: 82592162--82592241 Score: 137
Period size: 40 Copynumber: 2.0 Consensus size: 40
82592152 TATTTGAGTG
82592162 AAAATTATATAATTT-ACTGGATGAAA-TATATATTAATAA
1 AAAATTATATAATTTAACTGGAT-AAACTATATATTAATAA
82592201 AAAATTATATAATTTAACTGGATAAACTATATATTAATAA
1 AAAATTATATAATTTAACTGGATAAACTATATATTAATAA
82592241 A
1 A
82592242 TACACTTATG
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
39 18 0.46
40 21 0.54
ACGTcount: A:0.53, C:0.04, G:0.06, T:0.38
Consensus pattern (40 bp):
AAAATTATATAATTTAACTGGATAAACTATATATTAATAA
Found at i:82592237 original size:20 final size:20
Alignment explanation
Indices: 82592167--82592237 Score: 51
Period size: 20 Copynumber: 3.5 Consensus size: 20
82592157 GAGTGAAAAT
*
82592167 TATATAATTTACTGGATGAAA
1 TATATAATTAACTGGAT-AAA
* *
82592188 TATAT-ATTAA-T-AAAAAA
1 TATATAATTAACTGGATAAA
82592205 TTATATAATTTAACTGGATAAA
1 -TATATAA-TTAACTGGATAAA
82592227 CTATAT-ATTAA
1 -TATATAATTAA
82592238 TAAATACACT
Statistics
Matches: 39, Mismatches: 6, Indels: 11
0.70 0.11 0.20
Matches are distributed among these distances:
17 3 0.08
18 6 0.15
19 2 0.05
20 12 0.31
21 7 0.18
22 9 0.23
ACGTcount: A:0.49, C:0.04, G:0.07, T:0.39
Consensus pattern (20 bp):
TATATAATTAACTGGATAAA
Found at i:82593498 original size:52 final size:53
Alignment explanation
Indices: 82593428--82593532 Score: 185
Period size: 52 Copynumber: 2.0 Consensus size: 53
82593418 ACCTCTTTTG
82593428 CTTCTTTGTTTGAATTTTGTTTATTTTTCATGCTTTAATTTTGGCTT-TTTAT
1 CTTCTTTGTTTGAATTTTGTTTATTTTTCATGCTTTAATTTTGGCTTCTTTAT
* *
82593480 CTTCTTTGTTTGAATTTTGTTTATTTTTTATGCTTTAATTTTGGTTTCTTTAT
1 CTTCTTTGTTTGAATTTTGTTTATTTTTCATGCTTTAATTTTGGCTTCTTTAT
82593533 TTTTGATCAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
52 45 0.90
53 5 0.10
ACGTcount: A:0.13, C:0.09, G:0.11, T:0.67
Consensus pattern (53 bp):
CTTCTTTGTTTGAATTTTGTTTATTTTTCATGCTTTAATTTTGGCTTCTTTAT
Found at i:82593519 original size:24 final size:24
Alignment explanation
Indices: 82593440--82593522 Score: 80
Period size: 24 Copynumber: 3.3 Consensus size: 24
82593430 TCTTTGTTTG
*
82593440 AATTTTGTTTATTTTTCATGCTTT
1 AATTTTGTTTATTTTTTATGCTTT
*
82593464 AATTTTGGCTTT-TTATCTTCTTTG-TTT
1 AATTTT-G-TTTATT-T-TT-TATGCTTT
82593491 GAATTTTGTTTATTTTTTATGCTTT
1 -AATTTTGTTTATTTTTTATGCTTT
82593516 AATTTTG
1 AATTTTG
82593523 GTTTCTTTAT
Statistics
Matches: 48, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
24 16 0.33
25 8 0.17
26 8 0.17
27 8 0.17
28 8 0.17
ACGTcount: A:0.16, C:0.07, G:0.11, T:0.66
Consensus pattern (24 bp):
AATTTTGTTTATTTTTTATGCTTT
Found at i:82597690 original size:25 final size:24
Alignment explanation
Indices: 82597644--82597691 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
82597634 GTAGAAGTGT
*
82597644 AATAAAAATATATATATATAAAAC
1 AATAAAAATATATATACATAAAAC
* *
82597668 AATATAAATGATATATACCTAAAA
1 AATAAAAAT-ATATATACATAAAA
82597692 TACGAATAGC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.29
Consensus pattern (24 bp):
AATAAAAATATATATACATAAAAC
Found at i:82598324 original size:41 final size:41
Alignment explanation
Indices: 82598261--82598344 Score: 116
Period size: 41 Copynumber: 2.0 Consensus size: 41
82598251 TCTTTTCCTA
*
82598261 GGCAAGTGGGGTAATGAGGTTAGTGGAGTGATGGAATTAGT
1 GGCAAGTAGGGTAATGAGGTTAGTGGAGTGATGGAATTAGT
* * *
82598302 GGCAAGTAGGGTGATG-GAGTTAGTGGGGTGATGGAGTTAGT
1 GGCAAGTAGGGTAATGAG-GTTAGTGGAGTGATGGAATTAGT
82598343 GG
1 GG
82598345 TCGGTTTAGT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
40 1 0.03
41 37 0.97
ACGTcount: A:0.24, C:0.02, G:0.48, T:0.26
Consensus pattern (41 bp):
GGCAAGTAGGGTAATGAGGTTAGTGGAGTGATGGAATTAGT
Found at i:82598332 original size:17 final size:17
Alignment explanation
Indices: 82598310--82598344 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
82598300 GTGGCAAGTA
82598310 GGGTGATGGAGTTAGTG
1 GGGTGATGGAGTTAGTG
82598327 GGGTGATGGAGTTAGTG
1 GGGTGATGGAGTTAGTG
82598344 G
1 G
82598345 TCGGTTTAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.00, G:0.54, T:0.29
Consensus pattern (17 bp):
GGGTGATGGAGTTAGTG
Found at i:82598842 original size:18 final size:19
Alignment explanation
Indices: 82598819--82598882 Score: 53
Period size: 18 Copynumber: 3.4 Consensus size: 19
82598809 TACCGTGATT
82598819 TGAAGCT-CGAATGCTAAC
1 TGAAGCTACGAATGCTAAC
82598837 TGAAGCATAC-AAGTGCTAAAC
1 TGAAGC-TACGAA-TGCT-AAC
* * *
82598858 GGAAG-TCCGAAGGCTAAC
1 TGAAGCTACGAATGCTAAC
82598876 TGAAGCT
1 TGAAGCT
82598883 CATCGAGTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 11
0.71 0.08 0.22
Matches are distributed among these distances:
18 13 0.36
19 9 0.25
20 7 0.19
21 7 0.19
ACGTcount: A:0.36, C:0.20, G:0.25, T:0.19
Consensus pattern (19 bp):
TGAAGCTACGAATGCTAAC
Found at i:82611756 original size:20 final size:21
Alignment explanation
Indices: 82611729--82611773 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
82611719 CTTAAATTAT
82611729 TAAAAAAATTAAAATTTA-TGA
1 TAAAAAAA-TAAAATTTATTGA
*
82611750 TAAAAAAATATAATTTATTGA
1 TAAAAAAATAAAATTTATTGA
82611771 TAA
1 TAA
82611774 TAGTGTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (21 bp):
TAAAAAAATAAAATTTATTGA
Found at i:82637174 original size:23 final size:22
Alignment explanation
Indices: 82637138--82637183 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
82637128 ATTAATTTTT
*
82637138 AGAAATTATGGAAAAATATTAA
1 AGAAATTATAGAAAAATATTAA
*
82637160 AGAAAGTTATAGAAAATTATTAA
1 AGAAA-TTATAGAAAAATATTAA
82637183 A
1 A
82637184 ATGATAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.59, C:0.00, G:0.13, T:0.28
Consensus pattern (22 bp):
AGAAATTATAGAAAAATATTAA
Found at i:82644456 original size:24 final size:25
Alignment explanation
Indices: 82644409--82644490 Score: 82
Period size: 24 Copynumber: 3.4 Consensus size: 25
82644399 CCATGTAACC
*
82644409 GGAAGCTCATA-AGAGTC-ATAATCG
1 GGAAGCTCA-AGAGAGCCAATAATCG
82644433 GGAAGCTCAAGCA-AGCCAAT-ATCG
1 GGAAGCTCAAG-AGAGCCAATAATCG
* * *
82644457 GGAAGCTCCAGAGAGCCATTAATTG
1 GGAAGCTCAAGAGAGCCAATAATCG
82644482 GGAAGCTCA
1 GGAAGCTCA
82644491 TGAAAGAGCC
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
23 2 0.04
24 32 0.67
25 14 0.29
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (25 bp):
GGAAGCTCAAGAGAGCCAATAATCG
Found at i:82644566 original size:25 final size:25
Alignment explanation
Indices: 82644510--82644626 Score: 87
Period size: 25 Copynumber: 4.7 Consensus size: 25
82644500 CTTTAATTTA
* * *
82644510 GAAGCTCGTAAGAGC-AATATGTCGG
1 GAAGCTCATAAGAGCTAA-ATATCAG
* *
82644535 GATGCTCATAAGAGCTAAATAACAG
1 GAAGCTCATAAGAGCTAAATATCAG
* * * *
82644560 GAAGCTCGTGAGAGCCAAATTTCAG
1 GAAGCTCATAAGAGCTAAATATCAG
* *
82644585 GAAGCTCAAAAGAGC-CAATATC-G
1 GAAGCTCATAAGAGCTAAATATCAG
*
82644608 AGATGCTCATAAGAGCTAA
1 -GAAGCTCATAAGAGCTAA
82644627 TAATGGGATG
Statistics
Matches: 70, Mismatches: 19, Indels: 6
0.74 0.20 0.06
Matches are distributed among these distances:
23 1 0.01
24 18 0.26
25 49 0.70
26 2 0.03
ACGTcount: A:0.38, C:0.18, G:0.25, T:0.19
Consensus pattern (25 bp):
GAAGCTCATAAGAGCTAAATATCAG
Found at i:82654828 original size:14 final size:13
Alignment explanation
Indices: 82654809--82654870 Score: 52
Period size: 14 Copynumber: 4.5 Consensus size: 13
82654799 GTTTACAAGT
82654809 AAAATATTTTTCGG
1 AAAATATTTTT-GG
82654823 AAAATAATTTTTGG
1 AAAAT-ATTTTTGG
* *
82654837 AAAATAATTTCTGA
1 AAAAT-ATTTTTGG
* *
82654851 AAAATAATTTCTGA
1 AAAAT-ATTTTTGG
82654865 AAAATA
1 AAAATA
82654871 ATTTACTTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
13 1 0.02
14 38 0.84
15 6 0.13
ACGTcount: A:0.48, C:0.05, G:0.10, T:0.37
Consensus pattern (13 bp):
AAAATATTTTTGG
Found at i:82654852 original size:27 final size:28
Alignment explanation
Indices: 82654817--82654874 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
82654807 GTAAAATATT
* *
82654817 TTTCGG-AAAATAATTTTTGGAAAATAA
1 TTTCGGAAAAATAATTTCTGAAAAATAA
*
82654844 TTTCTGAAAAATAATTTCTGAAAAATAA
1 TTTCGGAAAAATAATTTCTGAAAAATAA
82654872 TTT
1 TTT
82654875 ACTTTTCTGG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (28 bp):
TTTCGGAAAAATAATTTCTGAAAAATAA
Found at i:82654871 original size:14 final size:14
Alignment explanation
Indices: 82654823--82654874 Score: 86
Period size: 14 Copynumber: 3.7 Consensus size: 14
82654813 TATTTTTCGG
* *
82654823 AAAATAATTTTTGG
1 AAAATAATTTCTGA
82654837 AAAATAATTTCTGA
1 AAAATAATTTCTGA
82654851 AAAATAATTTCTGA
1 AAAATAATTTCTGA
82654865 AAAATAATTT
1 AAAATAATTT
82654875 ACTTTTCTGG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 36 1.00
ACGTcount: A:0.50, C:0.04, G:0.08, T:0.38
Consensus pattern (14 bp):
AAAATAATTTCTGA
Found at i:82655177 original size:19 final size:19
Alignment explanation
Indices: 82655153--82655193 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
82655143 GTAACTATCA
82655153 TTCTTACAAATCAAGCAGT
1 TTCTTACAAATCAAGCAGT
82655172 TTCTTACAAATCAAGCAGT
1 TTCTTACAAATCAAGCAGT
82655191 TTC
1 TTC
82655194 AGTTACTAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.34, C:0.22, G:0.10, T:0.34
Consensus pattern (19 bp):
TTCTTACAAATCAAGCAGT
Found at i:82656887 original size:18 final size:18
Alignment explanation
Indices: 82656861--82656924 Score: 78
Period size: 18 Copynumber: 3.6 Consensus size: 18
82656851 ATTGAAACTT
*
82656861 CAACTTATAAATGAACAA
1 CAACATATAAATGAACAA
82656879 CAACATATAAATGAACAA
1 CAACATATAAATGAACAA
*
82656897 CAAC-TCCCTAAA-GAACAA
1 CAACAT--ATAAATGAACAA
82656915 CAACATATAA
1 CAACATATAA
82656925 CTTATTTCAT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
17 4 0.10
18 31 0.77
19 5 0.12
ACGTcount: A:0.56, C:0.22, G:0.05, T:0.17
Consensus pattern (18 bp):
CAACATATAAATGAACAA
Found at i:82657677 original size:48 final size:47
Alignment explanation
Indices: 82657606--82657699 Score: 170
Period size: 48 Copynumber: 2.0 Consensus size: 47
82657596 TTCAGATCAG
*
82657606 TCAGGGAAAAGAAGAAGAAGAAGAAAAAGTCGTACCCAAAAACCAATT
1 TCAGGGAAAAGAAGAAGAAGAAGAAAAAGCCGTACCC-AAAACCAATT
82657654 TCAGGGAAAAGAAGAAGAAGAAGAAAAAGCCGTACCCAAAACCAAT
1 TCAGGGAAAAGAAGAAGAAGAAGAAAAAGCCGTACCCAAAACCAAT
82657700 CTTACAGAAC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
47 9 0.20
48 36 0.80
ACGTcount: A:0.54, C:0.16, G:0.21, T:0.09
Consensus pattern (47 bp):
TCAGGGAAAAGAAGAAGAAGAAGAAAAAGCCGTACCCAAAACCAATT
Found at i:82664857 original size:32 final size:32
Alignment explanation
Indices: 82664816--82664881 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
82664806 CAGGTATCTA
82664816 TCATAAGTTCTGACCATTTCATTTATGTTCTT
1 TCATAAGTTCTGACCATTTCATTTATGTTCTT
82664848 TCATAAGTTCTGACCATTTCATTTATGTTCTT
1 TCATAAGTTCTGACCATTTCATTTATGTTCTT
82664880 TC
1 TC
82664882 TTTTGGTCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.21, C:0.20, G:0.09, T:0.50
Consensus pattern (32 bp):
TCATAAGTTCTGACCATTTCATTTATGTTCTT
Found at i:82664869 original size:18 final size:18
Alignment explanation
Indices: 82664816--82664869 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
82664806 CAGGTATCTA
82664816 TCATAAGTTCTGACCATT
1 TCATAAGTTCTGACCATT
* **
82664834 TCAT---TTATGTTC-TT
1 TCATAAGTTCTGACCATT
82664848 TCATAAGTTCTGACCATT
1 TCATAAGTTCTGACCATT
82664866 TCAT
1 TCAT
82664870 TTATGTTCTT
Statistics
Matches: 26, Mismatches: 6, Indels: 8
0.65 0.15 0.20
Matches are distributed among these distances:
14 6 0.23
15 5 0.19
17 5 0.19
18 10 0.38
ACGTcount: A:0.24, C:0.20, G:0.09, T:0.46
Consensus pattern (18 bp):
TCATAAGTTCTGACCATT
Found at i:82668086 original size:21 final size:22
Alignment explanation
Indices: 82668062--82668102 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
82668052 TTGTACAATT
*
82668062 TGTTATG-GTAATAAAATTGTG
1 TGTTATGCCTAATAAAATTGTG
82668083 TGTTATGCCTAATAAAATTG
1 TGTTATGCCTAATAAAATTG
82668103 ATGAATGGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.34, C:0.05, G:0.20, T:0.41
Consensus pattern (22 bp):
TGTTATGCCTAATAAAATTGTG
Found at i:82677980 original size:46 final size:46
Alignment explanation
Indices: 82677962--82678118 Score: 140
Period size: 46 Copynumber: 3.3 Consensus size: 46
82677952 TGACAAGTGG
* * *
82677962 AAAGTGATAAGTAATAGCT-TCGGCTATACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGATAGCTAT-AGCTACACTTATCTGATCAAGTGAC
*
82678008 AAAGTGATAAGTGATAGCT-TCGGCTACACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGATAGCTAT-AGCTACACTTATCTGATCAAGTGAC
* * **
82678054 AAGTGAAAAGTGATAAGTGATAGCT-TCGGCTATACTTATCTGATCAAGAAAC
1 ------AAAGTGATAAGTGATAGCTAT-AGCTACACTTATCTGATCAAGTGAC
82678106 AAAGTGATAAGTG
1 AAAGTGATAAGTG
82678119 GCTACACTTA
Statistics
Matches: 100, Mismatches: 5, Indels: 12
0.85 0.04 0.10
Matches are distributed among these distances:
46 57 0.57
52 43 0.43
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (46 bp):
AAAGTGATAAGTGATAGCTATAGCTACACTTATCTGATCAAGTGAC
Found at i:82677981 original size:52 final size:51
Alignment explanation
Indices: 82677910--82678101 Score: 277
Period size: 52 Copynumber: 3.8 Consensus size: 51
82677900 ATCAAGTGAC
* **
82677910 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGT-G
* *
82677962 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC-----
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
82678008 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
*
82678059 AAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAG
1 -AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAG
82678102 AAACAAAGTG
Statistics
Matches: 126, Mismatches: 8, Indels: 12
0.86 0.05 0.08
Matches are distributed among these distances:
46 44 0.35
52 82 0.65
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (51 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
Found at i:82678016 original size:98 final size:98
Alignment explanation
Indices: 82677896--82678119 Score: 385
Period size: 98 Copynumber: 2.3 Consensus size: 98
82677886 TTTGAGTACT
*
82677896 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
*
82677961 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
* *
82677994 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
*
82678059 AAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
**
82678092 TCTGATCAAGAAACAAAGTGATAAGTGG
1 TCTGATCAAGTGACAAAGTGATAAGTGG
82678120 CTACACTTAT
Statistics
Matches: 118, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 118 1.00
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (98 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
Found at i:82678128 original size:37 final size:37
Alignment explanation
Indices: 82678081--82678190 Score: 170
Period size: 37 Copynumber: 3.0 Consensus size: 37
82678071 TGATAGCTTC
*
82678081 GGCTATACTTATCTGATCAAGAAACAAAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
*
82678118 GGCTACACTTATCTGATCAAGAAACAAAGTGATAGGT
1 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
**
82678155 GGCTACACTTATCTGATC-AGGGAC-AAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
82678190 G
1 G
82678191 ATCATACGTA
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
35 11 0.16
36 4 0.06
37 53 0.78
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.25
Consensus pattern (37 bp):
GGCTACACTTATCTGATCAAGAAACAAAGTGATAAGT
Done.