Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A07
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: 93829987
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4250000 characters in sequence are not A, C, G, or T
File 295 of 295
Found at i:93634252 original size:6 final size:6
Alignment explanation
Indices: 93634241--93634265 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
93634231 AATTATTTAT
93634241 ATATTA ATATTA ATATTA ATATTA A
1 ATATTA ATATTA ATATTA ATATTA A
93634266 ATATATACTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
ATATTA
Found at i:93634686 original size:16 final size:17
Alignment explanation
Indices: 93634653--93634697 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 17
93634643 TACTATTACT
*
93634653 AATT-TAAAATTTTATA
1 AATTATAAAAATTTATA
93634669 AATTATAAAAATTT-TA
1 AATTATAAAAATTTATA
93634685 AA-T-TAAAAATTTA
1 AATTATAAAAATTTA
93634698 CTATTTTAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 9 0.35
15 1 0.04
16 8 0.31
17 8 0.31
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AATTATAAAAATTTATA
Found at i:93648072 original size:21 final size:20
Alignment explanation
Indices: 93648054--93648179 Score: 76
Period size: 20 Copynumber: 6.2 Consensus size: 20
93648044 TGCTTTCCGT
*
93648054 TTAGCTCTTATGAGCTTCCG
1 TTAGCTCTTATGAGCTTCAG
* * *
93648074 TTAACTCATATGAGTTTCAG
1 TTAGCTCTTATGAGCTTCAG
* * * * *
93648094 TTAACCCTTTTGGGGTTTCAG
1 TTAGCTCTTAT-GAGCTTCAG
*
93648115 TTCAGCTCTGATGAGCTTCAG
1 TT-AGCTCTTATGAGCTTCAG
* * *
93648136 TTAGC-CTT-CGGGCTTCCG
1 TTAGCTCTTATGAGCTTCAG
* *
93648154 TTTAGCACTTATGTGCTTCAG
1 -TTAGCTCTTATGAGCTTCAG
93648175 TTAGC
1 TTAGC
93648180 CTTCGAGCTA
Statistics
Matches: 80, Mismatches: 21, Indels: 10
0.72 0.19 0.09
Matches are distributed among these distances:
18 7 0.09
19 7 0.09
20 35 0.44
21 26 0.32
22 5 0.06
ACGTcount: A:0.17, C:0.22, G:0.21, T:0.39
Consensus pattern (20 bp):
TTAGCTCTTATGAGCTTCAG
Found at i:93648087 original size:20 final size:20
Alignment explanation
Indices: 93648048--93648098 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
93648038 CGTGTTTGCT
* *
93648048 TTCCGTTTAGCTCTTATGAGC
1 TTCCG-TTAACTCATATGAGC
*
93648069 TTCCGTTAACTCATATGAGT
1 TTCCGTTAACTCATATGAGC
*
93648089 TTCAGTTAAC
1 TTCCGTTAAC
93648099 CCTTTTGGGG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 21 0.81
21 5 0.19
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.41
Consensus pattern (20 bp):
TTCCGTTAACTCATATGAGC
Found at i:93648175 original size:39 final size:39
Alignment explanation
Indices: 93648129--93648229 Score: 166
Period size: 39 Copynumber: 2.6 Consensus size: 39
93648119 GCTCTGATGA
93648129 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
* *
93648168 GCTTCAGTTAGCCTTCGAGCTACCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
* *
93648207 GCTTCAGCTAGACTTCGGGCTTC
1 GCTTCAGTTAGCCTTCGGGCTTC
93648230 AGATGACGAT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.15, C:0.27, G:0.23, T:0.36
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
Found at i:93650015 original size:3 final size:3
Alignment explanation
Indices: 93650007--93650071 Score: 51
Period size: 3 Copynumber: 21.7 Consensus size: 3
93649997 GGGATTTAAA
* * * * * * *
93650007 AAT AAT AAT ATT AAT AAT GAT GAT AGT AAT ATT AAT AAT AAA AAT AAC
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
93650055 AAT AAT ACA- AAT AAT AA
1 AAT AAT A-AT AAT AAT AA
93650072 ATATTCTAAA
Statistics
Matches: 48, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
2 1 0.02
3 46 0.96
4 1 0.02
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:93650058 original size:21 final size:21
Alignment explanation
Indices: 93650003--93650058 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
93649993 AAGAGGGATT
93650003 TAAAAATAATAATATTAATAA
1 TAAAAATAATAATATTAATAA
* ** *
93650024 TGATGATAGTAATATTAATAA
1 TAAAAATAATAATATTAATAA
*
93650045 TAAAAATAACAATA
1 TAAAAATAATAATA
93650059 ATACAAATAA
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (21 bp):
TAAAAATAATAATATTAATAA
Found at i:93650246 original size:3 final size:3
Alignment explanation
Indices: 93650240--93650314 Score: 64
Period size: 3 Copynumber: 25.7 Consensus size: 3
93650230 AAAAGAAAAT
* * * * * *
93650240 ATA ATA ATG ATA ATA ATA ATA GTA AT- ACA ATA GTA ATA GTA ATA GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
93650287 ATA ATA ATA TTA ATA ATA AAA AT- ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
93650315 TAATTAATTT
Statistics
Matches: 54, Mismatches: 16, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
2 3 0.06
3 51 0.94
ACGTcount: A:0.59, C:0.01, G:0.07, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:93650257 original size:12 final size:12
Alignment explanation
Indices: 93650240--93650305 Score: 82
Period size: 12 Copynumber: 5.6 Consensus size: 12
93650230 AAAAGAAAAT
93650240 ATAATAAT-GATA
1 ATAATAATAG-TA
93650252 ATAATAATAGTA
1 ATAATAATAGTA
*
93650264 AT-ACAATAGTA
1 ATAATAATAGTA
*
93650275 ATAGTAATAGTA
1 ATAATAATAGTA
*
93650287 ATAATAATATTA
1 ATAATAATAGTA
93650299 ATAATAA
1 ATAATAA
93650306 AAATATAATT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
11 10 0.21
12 36 0.77
13 1 0.02
ACGTcount: A:0.58, C:0.02, G:0.08, T:0.33
Consensus pattern (12 bp):
ATAATAATAGTA
Found at i:93651473 original size:13 final size:15
Alignment explanation
Indices: 93651439--93651476 Score: 53
Period size: 13 Copynumber: 2.6 Consensus size: 15
93651429 CTTTGGATTG
93651439 TTTTGGTTATTATTTA
1 TTTTGGTT-TTATTTA
93651455 TTTTGGTTTT-TTT-
1 TTTTGGTTTTATTTA
93651468 TTTTGGTTT
1 TTTTGGTTT
93651477 AATGGGCCGG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 9 0.41
14 3 0.14
15 2 0.09
16 8 0.36
ACGTcount: A:0.08, C:0.00, G:0.16, T:0.76
Consensus pattern (15 bp):
TTTTGGTTTTATTTA
Found at i:93651961 original size:89 final size:88
Alignment explanation
Indices: 93651868--93652144 Score: 209
Period size: 89 Copynumber: 3.1 Consensus size: 88
93651858 CCAATGTAAT
* * *
93651868 TTCAGGGAGAAGAGATTTGTGGCTTCGATCTACTCTGCTGGAACTTCAAGGAGATAAGAATTGAT
1 TTCAGGGAGAAGAGATTTGTGGATTCAATCTACTCTACTGGAACTTCAAGGAGATAAGAATTG-T
93651933 AATTTCAATATGCTCCACAGCAAC
65 AATTTCAATATGCTCCACAGCAAC
* * * ** * * * * *
93651957 TTCAGGGAGATA-ATACTTGTGTATTTTATCCTGCTTTACTGCAACTTCAAAGAGATAAGGATTG
1 TTCAGGGAGA-AGAGATTTGTGGATTCAAT-CTACTCTACTGGAACTTCAAGGAGATAAGAATTG
*** * *
93652021 TGGCTTCGATATGCTCCA-ATGTAA-
64 TAATTTCAATATGCTCCACA-GCAAC
* * * * * * *
93652045 TATTAGGGAGAAGAGATTTGTAGTTTCAATCTACTCCATTGGAACTTCAAGGAGGTTAGAATTGG
1 T-TCAGGGAGAAGAGATTTGTGGATTCAATCTACTCTACTGGAACTTCAAGGAGATAAGAATT-G
*** *
93652110 TAATTTCAACCCGCTCCACTGCAAC
64 TAATTTCAATATGCTCCACAGCAAC
*
93652135 TTTAGGGAGA
1 TTCAGGGAGA
93652145 TAAGGTTGAT
Statistics
Matches: 137, Mismatches: 43, Indels: 16
0.70 0.22 0.08
Matches are distributed among these distances:
88 27 0.20
89 80 0.58
90 30 0.22
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (88 bp):
TTCAGGGAGAAGAGATTTGTGGATTCAATCTACTCTACTGGAACTTCAAGGAGATAAGAATTGTA
ATTTCAATATGCTCCACAGCAAC
Found at i:93651999 original size:178 final size:178
Alignment explanation
Indices: 93651702--93652147 Score: 493
Period size: 178 Copynumber: 2.5 Consensus size: 178
93651692 CAGAGAGGCT
* * * * * * * * *
93651702 AGATTTGTAGTTTTAATCTATTCCACTGCAACTTCAGGGAAATAAG-ATTCGTTATTTTCAGTC-
1 AGATTTGTAGCTTCAATCTACTCCACTGGAACTTCAAGGAGATAAGAATT-GATAATTTCA-ACA
* * * * * *** * *
93651765 TGCTTCACTGCAACTTTAGAGAGATAAGGTTTGTGTACTTTATCTTGCTCTACTGCAACTTCAGA
64 CGCTCCACAGCAACTTCAGGGAGATAATACTTGTGTACTTTATCCTGCTCTACTGCAACTTCAAA
* *
93651830 GTGATAAGGATTGTGGCTCCGATCTACTCCAATGTAAT-TTCAGGGAGAAG
129 GAGATAAGGATTGTGGCTCCGATATACTCCAATGTAATATT-AGGGAGAAG
* * ** * *
93651880 AGATTTGTGGCTTCGATCTACTCTGCTGGAACTTCAAGGAGATAAGAATTGATAATTTCAATATG
1 AGATTTGTAGCTTCAATCTACTCCACTGGAACTTCAAGGAGATAAGAATTGATAATTTCAACACG
* *
93651945 CTCCACAGCAACTTCAGGGAGATAATACTTGTGTATTTTATCCTGCTTTACTGCAACTTCAAAGA
66 CTCCACAGCAACTTCAGGGAGATAATACTTGTGTACTTTATCCTGCTCTACTGCAACTTCAAAGA
* *
93652010 GATAAGGATTGTGGCTTCGATATGCTCCAATGTAATATTAGGGAGAAG
131 GATAAGGATTGTGGCTCCGATATACTCCAATGTAATATTAGGGAGAAG
* * * * * *
93652058 AGATTTGTAGTTTCAATCTACTCCATTGGAACTTCAAGGAGGTTAGAATTGGTAATTTCAACCCG
1 AGATTTGTAGCTTCAATCTACTCCACTGGAACTTCAAGGAGATAAGAATTGATAATTTCAACACG
* *
93652123 CTCCACTGCAACTTTAGGGAGATAA
66 CTCCACAGCAACTTCAGGGAGATAA
93652148 GGTTGATGGC
Statistics
Matches: 222, Mismatches: 43, Indels: 6
0.82 0.16 0.02
Matches are distributed among these distances:
178 217 0.98
179 5 0.02
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (178 bp):
AGATTTGTAGCTTCAATCTACTCCACTGGAACTTCAAGGAGATAAGAATTGATAATTTCAACACG
CTCCACAGCAACTTCAGGGAGATAATACTTGTGTACTTTATCCTGCTCTACTGCAACTTCAAAGA
GATAAGGATTGTGGCTCCGATATACTCCAATGTAATATTAGGGAGAAG
Found at i:93652423 original size:143 final size:143
Alignment explanation
Indices: 93652162--93652435 Score: 315
Period size: 143 Copynumber: 1.9 Consensus size: 143
93652152 GATGGCTTAA
* * ** *
93652162 ATCTGCTCCACTGCAACTTCAGGAAGATAAGATTTGTTATAATTTGTAACTTTAATCTATTCCCT
1 ATCTGCTCCACTGCAACTTCAAGAAGATAAGATCTGCCATAATTTGTAACTTCAATCTATTCCCT
* * * ** * *
93652227 TGCAATATCAGGAAAACAAGATTCGTTGTCTTCAGTCTGCTCTGTTGCTACTTCAGGGAGATAAG
66 TGCAATATCAGGAAAACAAGATTCCTTGTCTTCAGCCTACTCTACTGATACTTCAAGGAGATAAG
93652292 ACTGGTGGATTTG
131 ACTGGTGGATTTG
* *
93652305 ATCTGCTCCACTGCAACTTCAAGAAGATAAGATCTGCCATTATTTGTAGCTTCAATCTATTCCAC
1 ATCTGCTCCACTGCAACTTCAAGAAGATAAGATCTGCCATAATTTGTAACTTCAATCTATTCC-C
* * *
93652370 -TGCAAT-TCCAGGGAAATAAGATTCACTT-TCTT-GGACCTACTCTACT-ATAACTTCAAGGAG
65 TTGCAATAT-CAGGAAAACAAGATTC-CTTGTCTTCAG-CCTACTCTACTGAT-ACTTCAAGGAG
93652430 ATAAGA
126 ATAAGA
93652436 TTTATAACTT
Statistics
Matches: 109, Mismatches: 17, Indels: 10
0.80 0.12 0.07
Matches are distributed among these distances:
142 3 0.03
143 103 0.94
144 3 0.03
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (143 bp):
ATCTGCTCCACTGCAACTTCAAGAAGATAAGATCTGCCATAATTTGTAACTTCAATCTATTCCCT
TGCAATATCAGGAAAACAAGATTCCTTGTCTTCAGCCTACTCTACTGATACTTCAAGGAGATAAG
ACTGGTGGATTTG
Found at i:93652478 original size:44 final size:44
Alignment explanation
Indices: 93652419--93652526 Score: 128
Period size: 44 Copynumber: 2.5 Consensus size: 44
93652409 CTCTACTATA
*
93652419 ACTTCA-AGGAGATAAGATTTATAACTTCAATATGCTCCGCTGCT
1 ACTTCAGA-GAGATAAGATTTATAACTTCAATATGCTCCACTGCT
* * * **
93652463 ACTTTAGAGAGATAAGATTTATGACTTCAATCTGCTTTACTGCT
1 ACTTCAGAGAGATAAGATTTATAACTTCAATATGCTCCACTGCT
* *
93652507 ACTTCAGGGAGATGAGATTT
1 ACTTCAGAGAGATAAGATTT
93652527 GTGGATTCAC
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
44 53 0.98
45 1 0.02
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.34
Consensus pattern (44 bp):
ACTTCAGAGAGATAAGATTTATAACTTCAATATGCTCCACTGCT
Found at i:93653464 original size:53 final size:53
Alignment explanation
Indices: 93653398--93653554 Score: 224
Period size: 53 Copynumber: 3.0 Consensus size: 53
93653388 GGAAGCATAG
* * *
93653398 CTCGAAATGAATAAATTAATCAAAGATAGCAAATGCAATAATAAGGAAATTAA
1 CTCGAAATGAATAAGTTAATCAAAGATAGAAAATGCAATAAGAAGGAAATTAA
* *
93653451 CTTGAAATGAATAAGTTAATCAAAGATAGAAAATGTAATAAGAAGGAAATTAA
1 CTCGAAATGAATAAGTTAATCAAAGATAGAAAATGCAATAAGAAGGAAATTAA
* * ** *
93653504 CTCGAAATAAATAAGTTAATTAAAGATAGAAAATATAATAAGAAGAAAATT
1 CTCGAAATGAATAAGTTAATCAAAGATAGAAAATGCAATAAGAAGGAAATT
93653555 GATTGAGAGT
Statistics
Matches: 94, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 94 1.00
ACGTcount: A:0.56, C:0.06, G:0.14, T:0.24
Consensus pattern (53 bp):
CTCGAAATGAATAAGTTAATCAAAGATAGAAAATGCAATAAGAAGGAAATTAA
Found at i:93658184 original size:5 final size:5
Alignment explanation
Indices: 93658176--93658200 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
93658166 ATACAATCAT
93658176 AAACA AAACA AAACA AAACA AAACA
1 AAACA AAACA AAACA AAACA AAACA
93658201 CGTCAGTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.20, G:0.00, T:0.00
Consensus pattern (5 bp):
AAACA
Found at i:93659765 original size:3 final size:3
Alignment explanation
Indices: 93659759--93659836 Score: 61
Period size: 3 Copynumber: 26.7 Consensus size: 3
93659749 AAAAAAAAAT
* * * * * *
93659759 ATA ATA ATG ATA ATA ATA ATA GTA AT- ACA ATA GTA ATA GTA ATA GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * *
93659806 ATA ATA ATA ATG TTA ATA ATA AAA AT- ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
93659837 TAATTAATTT
Statistics
Matches: 55, Mismatches: 18, Indels: 4
0.71 0.23 0.05
Matches are distributed among these distances:
2 3 0.05
3 52 0.95
ACGTcount: A:0.58, C:0.01, G:0.08, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:93659850 original size:28 final size:26
Alignment explanation
Indices: 93659806--93659857 Score: 68
Period size: 28 Copynumber: 1.9 Consensus size: 26
93659796 AGTAATAGTA
*
93659806 ATAATAATAATGTTAATAATAAAAAT
1 ATAATAATAATGTTAATAACAAAAAT
*
93659832 ATAATTAATTAATTTTAATAACAAAA
1 ATAA-TAA-TAATGTTAATAACAAAA
93659858 TAGCAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 4 0.18
27 3 0.14
28 15 0.68
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (26 bp):
ATAATAATAATGTTAATAACAAAAAT
Found at i:93664117 original size:14 final size:13
Alignment explanation
Indices: 93664098--93664145 Score: 55
Period size: 12 Copynumber: 3.8 Consensus size: 13
93664088 AAATAGAAGA
93664098 TATTATTTTAATTT
1 TATTATTTT-ATTT
*
93664112 TATTA-TTTATTA
1 TATTATTTTATTT
93664124 T-TTATTTTATTT
1 TATTATTTTATTT
*
93664136 TATTAATTTA
1 TATTATTTTA
93664146 GGATTAGGCT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 3 0.10
12 11 0.38
13 10 0.34
14 5 0.17
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TATTATTTTATTT
Found at i:93677548 original size:24 final size:24
Alignment explanation
Indices: 93677460--93677546 Score: 122
Period size: 24 Copynumber: 3.6 Consensus size: 24
93677450 AATTGACTTC
*
93677460 GGCACTATGTGTGC-AAATTTGAAT
1 GGCACTATGTGTGCGAAA-TTGTAT
93677484 GGCACTATGTGTGCGAAATTGTAT
1 GGCACTATGTGTGCGAAATTGTAT
* *
93677508 GGCACTATGTGTGCGGACTTGTAT
1 GGCACTATGTGTGCGAAATTGTAT
*
93677532 AGCACTATGTGTGCG
1 GGCACTATGTGTGCG
93677547 GATTTAAATG
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
24 55 0.95
25 3 0.05
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.32
Consensus pattern (24 bp):
GGCACTATGTGTGCGAAATTGTAT
Found at i:93677892 original size:24 final size:24
Alignment explanation
Indices: 93677864--93677928 Score: 103
Period size: 24 Copynumber: 2.7 Consensus size: 24
93677854 GCAAATTTGA
93677864 ATGGCACTATGTGTGCGAAATTGT
1 ATGGCACTATGTGTGCGAAATTGT
* *
93677888 ATGGCACTATGTGTGCGGACTTGT
1 ATGGCACTATGTGTGCGAAATTGT
*
93677912 ATAGCACTATGTGTGCG
1 ATGGCACTATGTGTGCG
93677929 GATTTAAATG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.22, C:0.15, G:0.31, T:0.32
Consensus pattern (24 bp):
ATGGCACTATGTGTGCGAAATTGT
Found at i:93678177 original size:382 final size:382
Alignment explanation
Indices: 93677471--93678234 Score: 1528
Period size: 382 Copynumber: 2.0 Consensus size: 382
93677461 GCACTATGTG
93677471 TGCAAATTTGAATGGCACTATGTGTGCGAAATTGTATGGCACTATGTGTGCGGACTTGTATAGCA
1 TGCAAATTTGAATGGCACTATGTGTGCGAAATTGTATGGCACTATGTGTGCGGACTTGTATAGCA
93677536 CTATGTGTGCGGATTTAAATGTCAATACGTATGTGAATTACTAAAGCACTATGTGTGTGGGTTAA
66 CTATGTGTGCGGATTTAAATGTCAATACGTATGTGAATTACTAAAGCACTATGTGTGTGGGTTAA
93677601 CATGGCACTATGGGTGCGAATTTCCTTGTTTGAGCATTACGTGAGCGAAATTAGTTGTTGATAAA
131 CATGGCACTATGGGTGCGAATTTCCTTGTTTGAGCATTACGTGAGCGAAATTAGTTGTTGATAAA
93677666 AATAAGATATTGGAGACATGAAAATTGAATCATAGGTACTTGGATGCATCTATTTCATCGTTGTT
196 AATAAGATATTGGAGACATGAAAATTGAATCATAGGTACTTGGATGCATCTATTTCATCGTTGTT
93677731 AAATATTGTAGGAAGGAATTAAGGTATTCGGTTATATGATACATTGAGTTAATGGTAAGACTTGA
261 AAATATTGTAGGAAGGAATTAAGGTATTCGGTTATATGATACATTGAGTTAATGGTAAGACTTGA
93677796 CTAGTAGTTGAATTGATAATTTCTGTAATCTATGGACCTTTCTAGTTTCTAGATCGA
326 CTAGTAGTTGAATTGATAATTTCTGTAATCTATGGACCTTTCTAGTTTCTAGATCGA
93677853 TGCAAATTTGAATGGCACTATGTGTGCGAAATTGTATGGCACTATGTGTGCGGACTTGTATAGCA
1 TGCAAATTTGAATGGCACTATGTGTGCGAAATTGTATGGCACTATGTGTGCGGACTTGTATAGCA
93677918 CTATGTGTGCGGATTTAAATGTCAATACGTATGTGAATTACTAAAGCACTATGTGTGTGGGTTAA
66 CTATGTGTGCGGATTTAAATGTCAATACGTATGTGAATTACTAAAGCACTATGTGTGTGGGTTAA
93677983 CATGGCACTATGGGTGCGAATTTCCTTGTTTGAGCATTACGTGAGCGAAATTAGTTGTTGATAAA
131 CATGGCACTATGGGTGCGAATTTCCTTGTTTGAGCATTACGTGAGCGAAATTAGTTGTTGATAAA
93678048 AATAAGATATTGGAGACATGAAAATTGAATCATAGGTACTTGGATGCATCTATTTCATCGTTGTT
196 AATAAGATATTGGAGACATGAAAATTGAATCATAGGTACTTGGATGCATCTATTTCATCGTTGTT
93678113 AAATATTGTAGGAAGGAATTAAGGTATTCGGTTATATGATACATTGAGTTAATGGTAAGACTTGA
261 AAATATTGTAGGAAGGAATTAAGGTATTCGGTTATATGATACATTGAGTTAATGGTAAGACTTGA
93678178 CTAGTAGTTGAATTGATAATTTCTGTAATCTATGGACCTTTCTAGTTTCTAGATCGA
326 CTAGTAGTTGAATTGATAATTTCTGTAATCTATGGACCTTTCTAGTTTCTAGATCGA
93678235 CATATTCAGT
Statistics
Matches: 382, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
382 382 1.00
ACGTcount: A:0.30, C:0.11, G:0.24, T:0.35
Consensus pattern (382 bp):
TGCAAATTTGAATGGCACTATGTGTGCGAAATTGTATGGCACTATGTGTGCGGACTTGTATAGCA
CTATGTGTGCGGATTTAAATGTCAATACGTATGTGAATTACTAAAGCACTATGTGTGTGGGTTAA
CATGGCACTATGGGTGCGAATTTCCTTGTTTGAGCATTACGTGAGCGAAATTAGTTGTTGATAAA
AATAAGATATTGGAGACATGAAAATTGAATCATAGGTACTTGGATGCATCTATTTCATCGTTGTT
AAATATTGTAGGAAGGAATTAAGGTATTCGGTTATATGATACATTGAGTTAATGGTAAGACTTGA
CTAGTAGTTGAATTGATAATTTCTGTAATCTATGGACCTTTCTAGTTTCTAGATCGA
Found at i:93693038 original size:3 final size:3
Alignment explanation
Indices: 93693030--93693062 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
93693020 CGGCTCTCTC
93693030 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
93693063 AATTCTAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:93698473 original size:27 final size:27
Alignment explanation
Indices: 93698439--93698493 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
93698429 GGTTAGAAAG
93698439 TAAGATTTTAATGTTTGGTTAATGGGA
1 TAAGATTTTAATGTTTGGTTAATGGGA
93698466 TAAGATTTTAATGTTTGGTTAATGGGA
1 TAAGATTTTAATGTTTGGTTAATGGGA
93698493 T
1 T
93698494 GTAAGACTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.00, G:0.25, T:0.45
Consensus pattern (27 bp):
TAAGATTTTAATGTTTGGTTAATGGGA
Found at i:93701954 original size:25 final size:25
Alignment explanation
Indices: 93701921--93701972 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
93701911 GTTATCTATT
*
93701921 AATATTTATATTAATACTAAATAAA
1 AATAATTATATTAATACTAAATAAA
*
93701946 AATAATTATATTAATATTAAATAAA
1 AATAATTATATTAATACTAAATAAA
93701971 AA
1 AA
93701973 ATAAAAAACC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (25 bp):
AATAATTATATTAATACTAAATAAA
Found at i:93703260 original size:10 final size:10
Alignment explanation
Indices: 93703245--93703304 Score: 70
Period size: 10 Copynumber: 6.0 Consensus size: 10
93703235 TAATTTTAGG
93703245 ATTTAT-TTT
1 ATTTATCTTT
93703254 CATTTATCTTT
1 -ATTTATCTTT
93703265 ATTTATCTTT
1 ATTTATCTTT
*
93703275 AATTATCTTT
1 ATTTATCTTT
*
93703285 AATTAT-TTGT
1 ATTTATCTT-T
93703295 ATTTATCTTT
1 ATTTATCTTT
93703305 TAGTATTTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
9 2 0.04
10 38 0.84
11 5 0.11
ACGTcount: A:0.23, C:0.08, G:0.02, T:0.67
Consensus pattern (10 bp):
ATTTATCTTT
Found at i:93710784 original size:24 final size:24
Alignment explanation
Indices: 93710757--93710841 Score: 80
Period size: 24 Copynumber: 3.3 Consensus size: 24
93710747 ACTGTTATAA
*
93710757 AAAATTATAAAATGCAAATTAATT
1 AAAATTATAAAATGAAAATTAATT
*
93710781 AAAATTATATAAATGAAAAATATATT
1 AAAATTATA-AAATGAAAATTA-ATT
* *
93710807 AAATAATATTAAAAAATTAAAATTAATT
1 --A-AA-ATTATAAAATGAAAATTAATT
93710835 AAAATTA
1 AAAATTA
93710842 CATAGATAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
24 13 0.26
25 12 0.24
26 4 0.08
28 4 0.08
29 12 0.24
30 5 0.10
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.34
Consensus pattern (24 bp):
AAAATTATAAAATGAAAATTAATT
Found at i:93710827 original size:18 final size:18
Alignment explanation
Indices: 93710804--93710873 Score: 51
Period size: 18 Copynumber: 3.9 Consensus size: 18
93710794 TGAAAAATAT
93710804 ATTAAATAATATTAAAAA
1 ATTAAATAATATTAAAAA
*
93710822 ATTAAA-ATTAATT--AAA
1 ATTAAATAAT-ATTAAAAA
*
93710838 ATTACATAGATA--AAAAA
1 ATTAAATA-ATATTAAAAA
93710855 ATTTAAATAATATTCAAAA
1 A-TTAAATAATATT-AAAA
93710874 TCTAAAATAA
Statistics
Matches: 39, Mismatches: 4, Indels: 16
0.66 0.07 0.27
Matches are distributed among these distances:
16 8 0.21
17 11 0.28
18 16 0.41
20 4 0.10
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.33
Consensus pattern (18 bp):
ATTAAATAATATTAAAAA
Found at i:93710867 original size:52 final size:54
Alignment explanation
Indices: 93710772--93710881 Score: 154
Period size: 54 Copynumber: 2.1 Consensus size: 54
93710762 TATAAAATGC
* *
93710772 AAATTAATTAAAATTATATAAATGAAAAATATATTAAATAATATTAAAAAAT-TA
1 AAATTAATTAAAATTACATAAATGAAAAAAATATTAAATAATATT-AAAAATCTA
* *
93710826 AAATTAATTAAAATTACATAGAT-AAAAAAAT-TTAAATAATATTCAAAATCTA
1 AAATTAATTAAAATTACATAAATGAAAAAAATATTAAATAATATTAAAAATCTA
93710878 AAAT
1 AAAT
93710882 AAACCGTTAC
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
51 5 0.10
52 18 0.35
53 7 0.14
54 21 0.41
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.34
Consensus pattern (54 bp):
AAATTAATTAAAATTACATAAATGAAAAAAATATTAAATAATATTAAAAATCTA
Found at i:93716042 original size:33 final size:33
Alignment explanation
Indices: 93716005--93716068 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
93715995 AATACATTGG
* *
93716005 AAATCAGCATGCAGGTGGTTTAAATACTATTCC
1 AAATCAGCATGCAGATGGTGTAAATACTATTCC
*
93716038 AAATCAGGATGCAGATGGTGTAAATACTATT
1 AAATCAGCATGCAGATGGTGTAAATACTATT
93716069 TCAACTGAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (33 bp):
AAATCAGCATGCAGATGGTGTAAATACTATTCC
Found at i:93721500 original size:21 final size:20
Alignment explanation
Indices: 93721476--93721515 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
93721466 TTTAGTTTAC
*
93721476 TTTAAATCCTAAACTCTAAAT
1 TTTAAACCCTAAA-TCTAAAT
*
93721497 TTTAAGCCCTAAATCTAAA
1 TTTAAACCCTAAATCTAAA
93721516 ATCCTAAACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.42, C:0.20, G:0.03, T:0.35
Consensus pattern (20 bp):
TTTAAACCCTAAATCTAAAT
Found at i:93728232 original size:21 final size:20
Alignment explanation
Indices: 93728192--93728233 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 20
93728182 AATATGTTTT
93728192 AAATTGAAATTTTATGATAG
1 AAATTGAAATTTTATGATAG
93728212 AAATTGAAAGGTTTT-TGATAG
1 AAATTGAAA--TTTTATGATAG
93728233 A
1 A
93728234 TAAACAACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 9 0.45
21 7 0.35
22 4 0.20
ACGTcount: A:0.43, C:0.00, G:0.19, T:0.38
Consensus pattern (20 bp):
AAATTGAAATTTTATGATAG
Found at i:93728917 original size:32 final size:32
Alignment explanation
Indices: 93728881--93729025 Score: 109
Period size: 32 Copynumber: 4.5 Consensus size: 32
93728871 AAAGGGTGAT
93728881 ACTTGAAAAGGATACATGTAC-CTAAATG-GTAC
1 ACTTGAAAAGGA-A-ATGTACACTAAATGTGTAC
***
93728913 ACTTGAAAAGGAAATGTACACTTTGTGTGTAC
1 ACTTGAAAAGGAAATGTACACTAAATGTGTAC
* ** *
93728945 ACTTGAAAAGGAAATGTACATTTTATGTATAC
1 ACTTGAAAAGGAAATGTACACTAAATGTGTAC
* * *
93728977 TATTTGAAAAGG-AATGTGCACCTCAA-GTGTAC
1 -ACTTGAAAAGGAAATGTACA-CTAAATGTGTAC
*
93729009 AATTGGAAAAGGGAAAT
1 ACTT-GAAAA-GGAAAT
93729026 ATCCATCGGA
Statistics
Matches: 93, Mismatches: 13, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
30 6 0.06
31 8 0.09
32 62 0.67
33 14 0.15
34 3 0.03
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.28
Consensus pattern (32 bp):
ACTTGAAAAGGAAATGTACACTAAATGTGTAC
Found at i:93728989 original size:33 final size:32
Alignment explanation
Indices: 93728910--93728990 Score: 117
Period size: 32 Copynumber: 2.5 Consensus size: 32
93728900 ACCTAAATGG
* *
93728910 TACACTTGAAAAGGAAATGTACACTTTGTGTG
1 TACACTTGAAAAGGAAATGTACACTTTATGTA
*
93728942 TACACTTGAAAAGGAAATGTACATTTTATGTA
1 TACACTTGAAAAGGAAATGTACACTTTATGTA
*
93728974 TACTATTTGAAAAGGAA
1 TAC-ACTTGAAAAGGAA
93728991 TGTGCACCTC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
32 32 0.73
33 12 0.27
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.32
Consensus pattern (32 bp):
TACACTTGAAAAGGAAATGTACACTTTATGTA
Found at i:93729496 original size:5 final size:5
Alignment explanation
Indices: 93729486--93729511 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
93729476 ATATTTTGAG
93729486 ATGAT ATGAT ATGAT ATGAT ATGAT A
1 ATGAT ATGAT ATGAT ATGAT ATGAT A
93729512 AGTATGTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.38
Consensus pattern (5 bp):
ATGAT
Found at i:93731040 original size:53 final size:51
Alignment explanation
Indices: 93730893--93731052 Score: 178
Period size: 52 Copynumber: 3.1 Consensus size: 51
93730883 TGACGGAAAA
* * * *
93730893 GATGTGATATGTGCTTCCGTATAAGACCATAGCAGGGCTATGGCATTGGTAC
1 GATGTGATATGTG-TTCCTTATAAGACCATAGCTGGGCTATGGCATCGGTAT
* * * *
93730945 AATGTGACT-CGTGTTCCTGTATAATACCATAGCTGGGCTATGGCATCGGTGT
1 GATGTGA-TATGTGTTCCT-TATAAGACCATAGCTGGGCTATGGCATCGGTAT
* *
93730997 GATGTGATAATGTGATTCCTTATAAGACCATATCTGGGATATGGCATCGGTAT
1 GATGTGAT-ATGTG-TTCCTTATAAGACCATAGCTGGGCTATGGCATCGGTAT
93731050 GAT
1 GAT
93731053 ATGTGATCCG
Statistics
Matches: 89, Mismatches: 14, Indels: 9
0.79 0.12 0.08
Matches are distributed among these distances:
51 5 0.06
52 43 0.48
53 36 0.40
54 5 0.06
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (51 bp):
GATGTGATATGTGTTCCTTATAAGACCATAGCTGGGCTATGGCATCGGTAT
Found at i:93732616 original size:18 final size:18
Alignment explanation
Indices: 93732593--93732627 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
93732583 GTGTTCCAAG
*
93732593 CCACACGGGCGTGTGTGA
1 CCACACGGGCATGTGTGA
93732611 CCACACGGGCATGTGTG
1 CCACACGGGCATGTGTG
93732628 GTACTGTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.29, G:0.37, T:0.17
Consensus pattern (18 bp):
CCACACGGGCATGTGTGA
Found at i:93733483 original size:28 final size:27
Alignment explanation
Indices: 93733434--93733491 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
93733424 GGCTTCATTA
*
93733434 TTATGGTTAAGGGTTCATTGTTTAAGGT
1 TTATGGTTAAGGGTTCAATG-TTAAGGT
* *
93733462 TTATGTTTAAGGG-TCTAATGTTAGGGT
1 TTATGGTTAAGGGTTC-AATGTTAAGGT
93733489 TTA
1 TTA
93733492 AAATTTAGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 11 0.42
28 15 0.58
ACGTcount: A:0.22, C:0.03, G:0.28, T:0.47
Consensus pattern (27 bp):
TTATGGTTAAGGGTTCAATGTTAAGGT
Found at i:93733516 original size:18 final size:19
Alignment explanation
Indices: 93733489--93733541 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
93733479 ATGTTAGGGT
* *
93733489 TTAAAATTTAGGGTTAAGG
1 TTAAAGTTTAAGGTTAAGG
*
93733508 -TAAAGTTTAAGGTTAGGG
1 TTAAAGTTTAAGGTTAAGG
93733526 TTAAGAGTTTAAGGTT
1 TTAA-AGTTTAAGGTT
93733542 TAAGTCGAGG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
18 15 0.52
19 3 0.10
20 11 0.38
ACGTcount: A:0.34, C:0.00, G:0.28, T:0.38
Consensus pattern (19 bp):
TTAAAGTTTAAGGTTAAGG
Found at i:93733833 original size:28 final size:28
Alignment explanation
Indices: 93733801--93733860 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
93733791 TTTTATTTTC
*
93733801 GTTTTAGGTTTCAAGTTTAGGGTTTAAT
1 GTTTTAGGTTTCAAGATTAGGGTTTAAT
*
93733829 GTTTTAGGTTTCAAGATTAGGGTTTTAT
1 GTTTTAGGTTTCAAGATTAGGGTTTAAT
93733857 GTTT
1 GTTT
93733861 AAGGCTTATG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.20, C:0.03, G:0.25, T:0.52
Consensus pattern (28 bp):
GTTTTAGGTTTCAAGATTAGGGTTTAAT
Found at i:93733852 original size:14 final size:14
Alignment explanation
Indices: 93733803--93733853 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
93733793 TTATTTTCGT
93733803 TTTA-GGTTTCAAG
1 TTTAGGGTTTCAAG
93733816 TTTAGGGTTT-AATG
1 TTTAGGGTTTCAA-G
93733830 TTTTA-GGTTTCAAG
1 -TTTAGGGTTTCAAG
*
93733844 ATTAGGGTTT
1 TTTAGGGTTT
93733854 TATGTTTAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
13 9 0.28
14 17 0.53
15 6 0.19
ACGTcount: A:0.22, C:0.04, G:0.25, T:0.49
Consensus pattern (14 bp):
TTTAGGGTTTCAAG
Found at i:93738431 original size:25 final size:25
Alignment explanation
Indices: 93738395--93738445 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
93738385 TAGAAGTTAT
93738395 TAAAGTTTAAACTCATATTTACATA
1 TAAAGTTTAAACTCATATTTACATA
*
93738420 TAAA-TTTAAAACTTATATTTACATA
1 TAAAGTTT-AAACTCATATTTACATA
93738445 T
1 T
93738446 TTATATGGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 3 0.12
25 21 0.88
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.43
Consensus pattern (25 bp):
TAAAGTTTAAACTCATATTTACATA
Found at i:93738820 original size:17 final size:16
Alignment explanation
Indices: 93738781--93738811 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
93738771 AAGTTTCATT
93738781 ATGAAAAATACGAGTA
1 ATGAAAAATACGAGTA
93738797 ATGAAAAATACGAGT
1 ATGAAAAATACGAGT
93738812 TCTGAAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.55, C:0.06, G:0.19, T:0.19
Consensus pattern (16 bp):
ATGAAAAATACGAGTA
Found at i:93743077 original size:13 final size:13
Alignment explanation
Indices: 93743059--93743105 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
93743049 GTAAATTTTG
93743059 ATGTTATTTATAA
1 ATGTTATTTATAA
*
93743072 ATGTTATTTATGTA
1 ATGTTATTTAT-AA
*
93743086 AT-TTATTAAATAA
1 ATGTTATT-TATAA
93743099 ATGTTAT
1 ATGTTAT
93743106 CAAATTAAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 19 0.68
14 9 0.32
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (13 bp):
ATGTTATTTATAA
Found at i:93744629 original size:30 final size:30
Alignment explanation
Indices: 93744595--93744666 Score: 93
Period size: 24 Copynumber: 2.6 Consensus size: 30
93744585 TTTGAATGTA
93744595 TTTGATTTGAATTACATTTGTTTGATGAAT
1 TTTGATTTGAATTACATTTGTTTGATGAAT
93744625 TTTGATTTG----A-A-TTGTTTGATGAAT
1 TTTGATTTGAATTACATTTGTTTGATGAAT
*
93744649 TTCGATTTGAATTACATT
1 TTTGATTTGAATTACATT
93744667 CGTCCAAGAC
Statistics
Matches: 35, Mismatches: 1, Indels: 12
0.73 0.02 0.25
Matches are distributed among these distances:
24 21 0.60
25 1 0.03
26 1 0.03
28 1 0.03
29 1 0.03
30 10 0.29
ACGTcount: A:0.26, C:0.04, G:0.17, T:0.53
Consensus pattern (30 bp):
TTTGATTTGAATTACATTTGTTTGATGAAT
Found at i:93761779 original size:31 final size:30
Alignment explanation
Indices: 93761743--93761800 Score: 89
Period size: 31 Copynumber: 1.9 Consensus size: 30
93761733 TATCCTATTC
*
93761743 CAGGGATATCCCGGTTGGAGGATATCCCTTA
1 CAGGGATATCCCGATTGG-GGATATCCCTTA
*
93761774 CAGGGATATCCCGATTGGGGTTATCCC
1 CAGGGATATCCCGATTGGGGATATCCC
93761801 ATTCGAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 8 0.32
31 17 0.68
ACGTcount: A:0.21, C:0.24, G:0.29, T:0.26
Consensus pattern (30 bp):
CAGGGATATCCCGATTGGGGATATCCCTTA
Found at i:93766134 original size:21 final size:22
Alignment explanation
Indices: 93766110--93766150 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
93766100 TTGTACAATT
*
93766110 TGTTATG-GTAATAAAATTGTG
1 TGTTATGCCTAATAAAATTGTG
93766131 TGTTATGCCTAATAAAATTG
1 TGTTATGCCTAATAAAATTG
93766151 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:93768325 original size:16 final size:16
Alignment explanation
Indices: 93768304--93768348 Score: 90
Period size: 16 Copynumber: 2.8 Consensus size: 16
93768294 CTTATTCGTG
93768304 CCAGGGATATCCCATT
1 CCAGGGATATCCCATT
93768320 CCAGGGATATCCCATT
1 CCAGGGATATCCCATT
93768336 CCAGGGATATCCC
1 CCAGGGATATCCC
93768349 GGTTCGTTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.24, C:0.33, G:0.20, T:0.22
Consensus pattern (16 bp):
CCAGGGATATCCCATT
Found at i:93777156 original size:31 final size:32
Alignment explanation
Indices: 93777106--93777172 Score: 127
Period size: 31 Copynumber: 2.1 Consensus size: 32
93777096 CTTTTCCAAC
93777106 TTTCATCAGTACGAGGAGAGCACCTATACAAG
1 TTTCATCAGTACGAGGAGAGCACCTATACAAG
93777138 TTTCATCAGTA-GAGGAGAGCACCTATACAAG
1 TTTCATCAGTACGAGGAGAGCACCTATACAAG
93777169 TTTC
1 TTTC
93777173 TTTCTTTCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 24 0.69
32 11 0.31
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (32 bp):
TTTCATCAGTACGAGGAGAGCACCTATACAAG
Found at i:93800825 original size:20 final size:21
Alignment explanation
Indices: 93800786--93800825 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
93800776 GTGTTTGGCT
* *
93800786 TTCCGTTTAGCTCTTATGAGC
1 TTCCGTTTAACTCATATGAGC
93800807 TTCCG-TTAACTCATATGAG
1 TTCCGTTTAACTCATATGAG
93800826 TTTCAGTTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.20, C:0.23, G:0.17, T:0.40
Consensus pattern (21 bp):
TTCCGTTTAACTCATATGAGC
Found at i:93800915 original size:37 final size:37
Alignment explanation
Indices: 93800864--93800959 Score: 124
Period size: 37 Copynumber: 2.6 Consensus size: 37
93800854 GCTCTGATGA
93800864 GCTTCAGTTA-CCTTCGGCTTCCGTTTAGCACTTATGT
1 GCTTCAG-TAGCCTTCGGCTTCCGTTTAGCACTTATGT
*
93800901 GCTTCAGTAGCCTTCGAG-TACCGTTTAGCACTTATGT
1 GCTTCAGTAGCCTTCG-GCTTCCGTTTAGCACTTATGT
* *
93800938 GCTTCACTAGACTTCGGGCTTC
1 GCTTCAGTAGCCTTC-GGCTTC
93800960 AGTGACGATG
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
36 2 0.04
37 45 0.88
38 4 0.08
ACGTcount: A:0.16, C:0.27, G:0.21, T:0.36
Consensus pattern (37 bp):
GCTTCAGTAGCCTTCGGCTTCCGTTTAGCACTTATGT
Found at i:93802940 original size:7 final size:7
Alignment explanation
Indices: 93802930--93802977 Score: 62
Period size: 7 Copynumber: 6.9 Consensus size: 7
93802920 CAAAAAAAAA
93802930 AAATAAT
1 AAATAAT
93802937 AAATAAT
1 AAATAAT
93802944 -AATAAT
1 AAATAAT
*
93802950 AAAAAAT
1 AAATAAT
*
93802957 ATAATAGT
1 A-AATAAT
93802965 AAATAAT
1 AAATAAT
93802972 AAATAA
1 AAATAA
93802978 AAAAAAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
6 6 0.17
7 24 0.69
8 5 0.14
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (7 bp):
AAATAAT
Found at i:93802949 original size:13 final size:13
Alignment explanation
Indices: 93802931--93802973 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
93802921 AAAAAAAAAA
93802931 AATAATAAATAAT
1 AATAATAAATAAT
*
93802944 AATAATAAAAAATAT
1 AATAAT-AAATA-AT
*
93802959 AATAGTAAATAAT
1 AATAATAAATAAT
93802972 AA
1 AA
93802974 ATAAAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
13 10 0.40
14 8 0.32
15 7 0.28
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (13 bp):
AATAATAAATAAT
Found at i:93802953 original size:25 final size:26
Alignment explanation
Indices: 93802922--93802983 Score: 79
Period size: 28 Copynumber: 2.3 Consensus size: 26
93802912 TGTAAATACA
*
93802922 AAAAAAAAAAATAATAAATAATAATAAT
1 AAAAAAAATAATAATAAATAAT-A-AAT
* *
93802950 AAAAAATATAATAGTAAATAATAAAT
1 AAAAAAAATAATAATAAATAATAAAT
93802976 AAAAAAAA
1 AAAAAAAA
93802984 AATTAATTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 10 0.33
27 1 0.03
28 19 0.63
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (26 bp):
AAAAAAAATAATAATAAATAATAAAT
Found at i:93804128 original size:13 final size:15
Alignment explanation
Indices: 93804094--93804131 Score: 53
Period size: 13 Copynumber: 2.6 Consensus size: 15
93804084 CTTTGGATTG
93804094 TTTTGGTTATTATTTA
1 TTTTGGTT-TTATTTA
93804110 TTTTGGTTTT-TTT-
1 TTTTGGTTTTATTTA
93804123 TTTTGGTTT
1 TTTTGGTTT
93804132 AATGGGCCGG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 9 0.41
14 3 0.14
15 2 0.09
16 8 0.36
ACGTcount: A:0.08, C:0.00, G:0.16, T:0.76
Consensus pattern (15 bp):
TTTTGGTTTTATTTA
Found at i:93804787 original size:177 final size:178
Alignment explanation
Indices: 93804355--93804799 Score: 502
Period size: 177 Copynumber: 2.5 Consensus size: 178
93804345 CAGAGAGGCT
* * * * * * * * * * *
93804355 AGATTTGTAGTTTTAATCTATTCCACTGCAACTTCAGGGAAATAAG-ATCGTTATTTTCAGTC-T
1 AGATTTGTAGCTTCAATCTACTCCACTGGAACTTCAAGGAGATAAGAATTGATAATTTCA-ACAC
* * ** * *
93804418 GCTTCACTGCAACTTTAGAGAGATAAGGTTTGTGTACTTTATCTTGCTCTACTGCAACTTCAGAG
65 GCTCCACTGCAACTTTAGGGAGATAAGACTTGTGTACTTTATCCTGCTCTACTGCAACTTCAAAG
* *
93804483 TGATAAGGATTGTGGCTCCGATCTACTCCAATGTAATTTCAGGGAGAAG
130 AGATAAGGATTGTGGCTCCGATATACTCCAATGTAATTTCAGGGAGAAG
* * ** * *
93804532 AGATTTGTGGCTTCGATCTACTCTGCTGGAACTTCAAGGAGATAAGAATTGATAATTTCAATATG
1 AGATTTGTAGCTTCAATCTACTCCACTGGAACTTCAAGGAGATAAGAATTGATAATTTCAACACG
* * * * *
93804597 CTCCACAGCAACTTCAGGGAGATAATACTTGTGTATTTTATCCTGCTTTACTGCAACTTCAAAGA
66 CTCCACTGCAACTTTAGGGAGATAAGACTTGTGTACTTTATCCTGCTCTACTGCAACTTCAAAGA
* *
93804662 GATAAGGATTGTGGCTTCGATATGCTCCAATGTAATATT-A-GGAGAAG
131 GATAAGGATTGTGGCTCCGATATACTCCAATGTAAT-TTCAGGGAGAAG
* * * * * *
93804709 AGATTTGTAGTTTCAATCTACTCCATTGGAACTTCAAGGAGGTTAGAATTGGTAATTTCAACCCG
1 AGATTTGTAGCTTCAATCTACTCCACTGGAACTTCAAGGAGATAAGAATTGATAATTTCAACACG
93804774 CTCCACTGCAACTTTAGGGAGATAAG
66 CTCCACTGCAACTTTAGGGAGATAAG
93804800 GTTGATGGCT
Statistics
Matches: 220, Mismatches: 45, Indels: 6
0.81 0.17 0.02
Matches are distributed among these distances:
177 119 0.54
178 99 0.45
179 2 0.01
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (178 bp):
AGATTTGTAGCTTCAATCTACTCCACTGGAACTTCAAGGAGATAAGAATTGATAATTTCAACACG
CTCCACTGCAACTTTAGGGAGATAAGACTTGTGTACTTTATCCTGCTCTACTGCAACTTCAAAGA
GATAAGGATTGTGGCTCCGATATACTCCAATGTAATTTCAGGGAGAAG
Found at i:93805079 original size:142 final size:142
Alignment explanation
Indices: 93804813--93805084 Score: 313
Period size: 143 Copynumber: 1.9 Consensus size: 142
93804803 GATGGCTTAA
* * ** *
93804813 ATCTGCTCCACTGCAACTTCAGGAAGATAAGATTTGTTATATTTGTAACTTTAATCTATTCCCTT
1 ATCTGCTCCACTGCAACTTCAAGAAGATAAGATCTGCCATATTTGTAACTTCAATCTATTCCCTT
* * * ** *
93804878 GCAATATCAGGAAAACAAGATTCGTTGTCTTCAGTCTGCTCTGTTGCTACTTCAGGGAGATAAGA
66 GCAATATCAGGAAAACAAGATTCCTTGTCTTCAGCCTACTCTACTGATACTTCAGGGAGATAAGA
93804943 CTGGTGGATTTG
131 CTGGTGGATTTG
*
93804955 ATCTGCTCCACTGCAACTTCAAGAAGATAAGATCTGCCATTATTTGTAGCTTCAATCTATTCCAC
1 ATCTGCTCCACTGCAACTTCAAGAAGATAAGATCTGCCA-TATTTGTAACTTCAATCTATTCC-C
* * *
93805020 -TGCAAT-TCCAGGGAAATAAGATTCACTT-TCTT-GGACCTACTCTACT-ATAACTTCA-GGAG
64 TTGCAATAT-CAGGAAAACAAGATTC-CTTGTCTTCAG-CCTACTCTACTGAT-ACTTCAGGGAG
93805079 ATAAGA
125 ATAAGA
93805085 TTTATAACTT
Statistics
Matches: 109, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
142 48 0.44
143 58 0.53
144 3 0.03
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (142 bp):
ATCTGCTCCACTGCAACTTCAAGAAGATAAGATCTGCCATATTTGTAACTTCAATCTATTCCCTT
GCAATATCAGGAAAACAAGATTCCTTGTCTTCAGCCTACTCTACTGATACTTCAGGGAGATAAGA
CTGGTGGATTTG
Found at i:93805124 original size:44 final size:44
Alignment explanation
Indices: 93805069--93805175 Score: 135
Period size: 44 Copynumber: 2.5 Consensus size: 44
93805059 CTCTACTATA
*
93805069 ACTTCAG-GAGATAAGATTTATAACTTCAATATGCTCCGCTGCT
1 ACTTCAGAGAGATAAGATTTATAACTTCAATATGCTCCACTGCT
* * * **
93805112 ACTTTAGAGAGATAAGATTTATGACTTCAATCTGCTTTACTGCT
1 ACTTCAGAGAGATAAGATTTATAACTTCAATATGCTCCACTGCT
* *
93805156 ACTTCAGGGAGATGAGATTT
1 ACTTCAGAGAGATAAGATTT
93805176 GTGGATTCAC
Statistics
Matches: 54, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
43 6 0.11
44 48 0.89
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.35
Consensus pattern (44 bp):
ACTTCAGAGAGATAAGATTTATAACTTCAATATGCTCCACTGCT
Found at i:93806158 original size:52 final size:52
Alignment explanation
Indices: 93806046--93806199 Score: 220
Period size: 52 Copynumber: 3.0 Consensus size: 52
93806036 GGAAGCATAG
* * *
93806046 CTCGAAATGAATAAATTAATCAAAGATAGCAAATGCAATAATAAGGAAATTAA
1 CTCGAAATGAATAAGTTAATCAAAGATAG-AAATGTAATAAGAAGGAAATTAA
*
93806099 CTTGAAATGAATAAGTTAATCAAAGATAGAAATGTAATAAGAAGGAAATTAA
1 CTCGAAATGAATAAGTTAATCAAAGATAGAAATGTAATAAGAAGGAAATTAA
* * * *
93806151 CTCGAAATAAATAAGTTAATTAAAGATAGAAATATAAT-AGAAGAAAATT
1 CTCGAAATGAATAAGTTAATCAAAGATAGAAATGTAATAAGAAGGAAATT
93806200 GATTGAGAGT
Statistics
Matches: 92, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
51 10 0.11
52 55 0.60
53 27 0.29
ACGTcount: A:0.55, C:0.06, G:0.14, T:0.25
Consensus pattern (52 bp):
CTCGAAATGAATAAGTTAATCAAAGATAGAAATGTAATAAGAAGGAAATTAA
Found at i:93812381 original size:3 final size:3
Alignment explanation
Indices: 93812375--93812448 Score: 55
Period size: 3 Copynumber: 25.7 Consensus size: 3
93812365 CAAAAAAAAT
* * * * * *
93812375 ATA ATA ATG ATA ATA ATA GTA AT- ACA ATA GTA ATA GTA ATA GTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
93812422 ATA ATA ATG TTA ATA ATA A-A AT- ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
93812449 TAATTAATTT
Statistics
Matches: 52, Mismatches: 16, Indels: 6
0.70 0.22 0.08
Matches are distributed among these distances:
2 5 0.10
3 47 0.90
ACGTcount: A:0.57, C:0.01, G:0.08, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:93812460 original size:26 final size:25
Alignment explanation
Indices: 93812419--93812470 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 25
93812409 AGTAATAGTA
*
93812419 ATAATAATAATGTTAATAATAAAAT
1 ATAATAATAATGTTAATAACAAAAT
93812444 ATAATTAATTAAT-TTAATAACAAAAT
1 ATAA-TAA-TAATGTTAATAACAAAAT
93812470 A
1 A
93812471 GCAAATAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 4 0.17
26 16 0.67
27 4 0.17
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (25 bp):
ATAATAATAATGTTAATAACAAAAT
Found at i:93816719 original size:14 final size:13
Alignment explanation
Indices: 93816700--93816747 Score: 55
Period size: 12 Copynumber: 3.8 Consensus size: 13
93816690 AAATAGAAGA
93816700 TATTATTTTAATTT
1 TATTATTTT-ATTT
*
93816714 TATTA-TTTATTA
1 TATTATTTTATTT
93816726 T-TTATTTTATTT
1 TATTATTTTATTT
*
93816738 TATTAATTTA
1 TATTATTTTA
93816748 GGATTAGGCT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 3 0.10
12 11 0.38
13 10 0.34
14 5 0.17
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TATTATTTTATTT
Done.