Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A11
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: 114316535
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4920000 characters in sequence are not A, C, G, or T
File 356 of 356
Found at i:114076430 original size:14 final size:13
Alignment explanation
Indices: 114076408--114076460 Score: 63
Period size: 14 Copynumber: 4.0 Consensus size: 13
114076398 CTTTGAATCA
*
114076408 CTTCTTTTTATTTT
1 CTTC-TTTTCTTTT
*
114076422 CTTCATTTTCTTTC
1 CTTC-TTTTCTTTT
114076436 CTTCTTTTCTTTT
1 CTTCTTTTCTTTT
114076449 CTT-TTTTCTTTT
1 CTTCTTTTCTTTT
114076461 ATTTTCTTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
12 9 0.26
13 11 0.31
14 15 0.43
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.75
Consensus pattern (13 bp):
CTTCTTTTCTTTT
Found at i:114076457 original size:17 final size:18
Alignment explanation
Indices: 114076426--114076470 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
114076416 TATTTTCTTC
114076426 ATTTTCTTTCCTTCTTTT
1 ATTTTCTTTCCTTCTTTT
* *
114076444 CTTTTCTTT-TTTCTTTT
1 ATTTTCTTTCCTTCTTTT
114076461 ATTTTCTTTC
1 ATTTTCTTTC
114076471 TAACCAAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.76
Consensus pattern (18 bp):
ATTTTCTTTCCTTCTTTT
Found at i:114078484 original size:30 final size:31
Alignment explanation
Indices: 114078450--114078514 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
114078440 AGAAATTCTT
* *
114078450 ATTAAGCCCTTCAAA-TTTTTAAAAAATTTA
1 ATTAAACCCTTAAAAGTTTTTAAAAAATTTA
* * *
114078480 ATTAAACGCTTAAAAGTTTTTGAAAATTTTA
1 ATTAAACCCTTAAAAGTTTTTAAAAAATTTA
114078511 ATTA
1 ATTA
114078515 GATCCCTAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 12 0.41
31 17 0.59
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.42
Consensus pattern (31 bp):
ATTAAACCCTTAAAAGTTTTTAAAAAATTTA
Found at i:114100402 original size:69 final size:71
Alignment explanation
Indices: 114100313--114100447 Score: 168
Period size: 69 Copynumber: 1.9 Consensus size: 71
114100303 TAAAAGGTAA
**
114100313 TTTTAATCGTACATCGACTAGAAAATACTACCAT-ATCTCACTTCTTC-AT-TATTTTCATTAAA
1 TTTTAATCCCACATCGACTAGAAAATACTACCATAAT-TCACTTCTTCTATCTATTTTCATTAAA
114100375 ATATTAG
65 ATATTAG
* ** *
114100382 TTTTAATCCCACATTGACTAGCGAATACTACTATAATTCACTTCTTCTATCACTATTTTCATTAA
1 TTTTAATCCCACATCGACTAGAAAATACTACCATAATTCACTTCTTCTAT--CTATTTTCATTAA
114100447 A
64 A
114100448 CAAAATACTT
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
69 38 0.69
70 4 0.07
73 13 0.24
ACGTcount: A:0.33, C:0.21, G:0.05, T:0.41
Consensus pattern (71 bp):
TTTTAATCCCACATCGACTAGAAAATACTACCATAATTCACTTCTTCTATCTATTTTCATTAAAA
TATTAG
Found at i:114103108 original size:19 final size:21
Alignment explanation
Indices: 114103064--114103110 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 21
114103054 ATTGAGTGGT
114103064 TAATTAGACTTTAATTAAGTA
1 TAATTAGACTTTAATTAAGTA
*
114103085 AAATTAG-C-TTAATTAAG-A
1 TAATTAGACTTTAATTAAGTA
114103103 GTAATTAG
1 -TAATTAG
114103111 TGGAAAGGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 1 0.04
19 15 0.65
20 1 0.04
21 6 0.26
ACGTcount: A:0.45, C:0.04, G:0.13, T:0.38
Consensus pattern (21 bp):
TAATTAGACTTTAATTAAGTA
Found at i:114103442 original size:5 final size:5
Alignment explanation
Indices: 114103418--114103466 Score: 71
Period size: 5 Copynumber: 9.6 Consensus size: 5
114103408 AAGAAATTGT
* *
114103418 TATTA TATGA TATTA TTATTA TATTA TAGTA TATTA TATTA TATTA TAT
1 TATTA TATTA TATTA -TATTA TATTA TATTA TATTA TATTA TATTA TAT
114103467 AAATAAGTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
5 34 0.87
6 5 0.13
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (5 bp):
TATTA
Found at i:114104582 original size:15 final size:15
Alignment explanation
Indices: 114104562--114104618 Score: 98
Period size: 15 Copynumber: 3.9 Consensus size: 15
114104552 CGATGAATTT
114104562 ATTGAATTTATATTG
1 ATTGAATTTATATTG
*
114104577 ATTGAAATTATATTG
1 ATTGAATTTATATTG
114104592 ATTGAATTTATATTG
1 ATTGAATTTATATTG
114104607 ATTGAA-TTATAT
1 ATTGAATTTATAT
114104619 AATATATATG
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
14 6 0.15
15 34 0.85
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:114105021 original size:23 final size:23
Alignment explanation
Indices: 114104991--114105076 Score: 74
Period size: 21 Copynumber: 3.9 Consensus size: 23
114104981 GCTTTATCGA
*
114104991 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACTTCATGTGTCGTATT
* *
114105014 TCAGGCACCTCGTGTGTCGTA--
1 TCAGGCACTTCATGTGTCGTATT
* *
114105035 TCAGGCA-TCTCGTGTATCGT-TT
1 TCAGGCACT-TCATGTGTCGTATT
*
114105057 T-AGGCACTTTATGTGTCGTA
1 TCAGGCACTTCATGTGTCGTA
114105077 CTCTGATCAG
Statistics
Matches: 50, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
21 30 0.60
22 2 0.04
23 18 0.36
ACGTcount: A:0.16, C:0.21, G:0.24, T:0.38
Consensus pattern (23 bp):
TCAGGCACTTCATGTGTCGTATT
Found at i:114106613 original size:25 final size:25
Alignment explanation
Indices: 114106552--114106613 Score: 65
Period size: 24 Copynumber: 2.5 Consensus size: 25
114106542 TATGTCCACG
* *
114106552 AATATTAAACGAACATGTTCATGAAC
1 AATATT-AATGAACATGTTCACGAAC
*
114106578 -ATA-TAATTGAACATGTTTACGAAC
1 AATATTAA-TGAACATGTTCACGAAC
114106602 AATATTAATGAA
1 AATATTAATGAA
114106614 TAATAAACAA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
23 2 0.07
24 15 0.50
25 10 0.33
26 3 0.10
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.31
Consensus pattern (25 bp):
AATATTAATGAACATGTTCACGAAC
Found at i:114107348 original size:10 final size:10
Alignment explanation
Indices: 114107333--114107364 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
114107323 AAGATTAATG
114107333 AAAATTTCAA
1 AAAATTTCAA
114107343 AAAATTTCAA
1 AAAATTTCAA
*
114107353 AATATTTCAA
1 AAAATTTCAA
114107363 AA
1 AA
114107365 CTTCTAAGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.31
Consensus pattern (10 bp):
AAAATTTCAA
Found at i:114108260 original size:22 final size:23
Alignment explanation
Indices: 114108235--114108280 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
114108225 CAACTAAATT
114108235 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
114108257 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
114108280 A
1 A
114108281 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:114108286 original size:23 final size:23
Alignment explanation
Indices: 114108242--114108286 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
114108232 ATTAATTCAA
*
114108242 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
114108265 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
114108287 CACATATCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:114117110 original size:12 final size:12
Alignment explanation
Indices: 114117093--114117119 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
114117083 TAATATAACA
114117093 TAACATAACATG
1 TAACATAACATG
114117105 TAACATAACATG
1 TAACATAACATG
114117117 TAA
1 TAA
114117120 TGTGGTAGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.15, G:0.07, T:0.26
Consensus pattern (12 bp):
TAACATAACATG
Found at i:114117202 original size:25 final size:25
Alignment explanation
Indices: 114117160--114117228 Score: 81
Period size: 25 Copynumber: 2.8 Consensus size: 25
114117150 AAACCCTCAC
114117160 TAAATATATTTGTA-TAAATAA-AACA
1 TAAATATATTTGTATTAAA-AATAA-A
* *
114117185 TAAATA-ATTTTTATTAAAAATAAT
1 TAAATATATTTGTATTAAAAATAAA
114117209 TAAATATATTTGTATTAAAA
1 TAAATATATTTGTATTAAAA
114117229 CGCTCAGGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
24 14 0.37
25 24 0.63
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (25 bp):
TAAATATATTTGTATTAAAAATAAA
Found at i:114125321 original size:18 final size:17
Alignment explanation
Indices: 114125298--114125347 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
114125288 TTAAATATTC
*
114125298 TTAATTAAATTA-ATAAT
1 TTAATTAAAATATA-AAT
114125315 TTAAATTAAAATATAAAT
1 TT-AATTAAAATATAAAT
*
114125333 TTAATTAAAAAATAA
1 TTAATTAAAATATAA
114125348 GACCAATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 14 0.48
18 14 0.48
19 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TTAATTAAAATATAAAT
Found at i:114129418 original size:109 final size:109
Alignment explanation
Indices: 114129227--114129448 Score: 435
Period size: 109 Copynumber: 2.0 Consensus size: 109
114129217 ATGTCCAAGA
114129227 ATTGAACCTAAAAGCTAATGTCAACCAAGACATTATTTCAACGATTAAGAAAATTAAAGTATAAT
1 ATTGAACCTAAAAGCTAATGTCAACCAAGACATTATTTCAACGATTAAGAAAATTAAAGTATAAT
114129292 TGATTACACTGCTAATGGACTTTCATTAAATTTAAATATGTGAC
66 TGATTACACTGCTAATGGACTTTCATTAAATTTAAATATGTGAC
*
114129336 ATTGAACCTAAAATCTAATGTCAACCAAGACATTATTTCAACGATTAAGAAAATTAAAGTATAAT
1 ATTGAACCTAAAAGCTAATGTCAACCAAGACATTATTTCAACGATTAAGAAAATTAAAGTATAAT
114129401 TGATTACACTGCTAATGGACTTTCATTAAATTTAAATATGTGAC
66 TGATTACACTGCTAATGGACTTTCATTAAATTTAAATATGTGAC
114129445 ATTG
1 ATTG
114129449 TAATATTCAA
Statistics
Matches: 112, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
109 112 1.00
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.33
Consensus pattern (109 bp):
ATTGAACCTAAAAGCTAATGTCAACCAAGACATTATTTCAACGATTAAGAAAATTAAAGTATAAT
TGATTACACTGCTAATGGACTTTCATTAAATTTAAATATGTGAC
Found at i:114153838 original size:3 final size:3
Alignment explanation
Indices: 114153832--114153865 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
114153822 ATGATTCAAC
114153832 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
114153866 GAAGTCAAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:114156483 original size:13 final size:13
Alignment explanation
Indices: 114156465--114156499 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
114156455 GATGACCAAA
114156465 AAATTATTTTATG
1 AAATTATTTTATG
*
114156478 AAATTATGTTATG
1 AAATTATTTTATG
*
114156491 CAATTATTT
1 AAATTATTT
114156500 ATAATATTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.37, C:0.03, G:0.09, T:0.51
Consensus pattern (13 bp):
AAATTATTTTATG
Found at i:114172171 original size:3 final size:3
Alignment explanation
Indices: 114172163--114172190 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
114172153 AAAAGTGGGG
114172163 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
114172191 TAGCTTCAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:114184285 original size:16 final size:16
Alignment explanation
Indices: 114184261--114184297 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
114184251 AGTTTGGGCA
*
114184261 TGGAGTTTTTGTAAGG
1 TGGAATTTTTGTAAGG
114184277 TGGAATTTTTGTAAGG
1 TGGAATTTTTGTAAGG
114184293 TGGAA
1 TGGAA
114184298 GTGAAGAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.24, C:0.00, G:0.35, T:0.41
Consensus pattern (16 bp):
TGGAATTTTTGTAAGG
Found at i:114198358 original size:24 final size:24
Alignment explanation
Indices: 114198331--114198376 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
114198321 TTTTGAATAG
114198331 ATTA-ATTAATAAAATTATTTATGA
1 ATTACATTAAT-AAATTATTTATGA
*
114198355 ATTACATTAATAATTTATTTAT
1 ATTACATTAATAAATTATTTAT
114198377 TATCCTCACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (24 bp):
ATTACATTAATAAATTATTTATGA
Found at i:114209329 original size:17 final size:19
Alignment explanation
Indices: 114209293--114209332 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
114209283 ATACCCATCA
114209293 ATACCCATCATTACATTTTT
1 ATACCCATCA-TACATTTTT
114209313 ATACCCATCA-A-ATTTTT
1 ATACCCATCATACATTTTT
114209330 ATA
1 ATA
114209333 TAACCAATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 9 0.45
18 1 0.05
20 10 0.50
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (19 bp):
ATACCCATCATACATTTTT
Found at i:114210735 original size:6 final size:6
Alignment explanation
Indices: 114210724--114210755 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
114210714 GATGGCGTGG
*
114210724 TTTGCT TTTGCT TTTGCT TTTGCT TTAGCT TT
1 TTTGCT TTTGCT TTTGCT TTTGCT TTTGCT TT
114210756 ACCTTTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.03, C:0.16, G:0.16, T:0.66
Consensus pattern (6 bp):
TTTGCT
Found at i:114211319 original size:14 final size:14
Alignment explanation
Indices: 114211297--114211333 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
114211287 ATGCTACCCC
114211297 TTCTCTCTTTATCT
1 TTCTCTCTTTATCT
* *
114211311 TTTTCTCTTTTTCT
1 TTCTCTCTTTATCT
114211325 TTCTCTCTT
1 TTCTCTCTT
114211334 GCTTTCCTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.03, C:0.27, G:0.00, T:0.70
Consensus pattern (14 bp):
TTCTCTCTTTATCT
Found at i:114213588 original size:15 final size:15
Alignment explanation
Indices: 114213568--114213599 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
114213558 AAAGCTTTTT
114213568 TTGTTGTTGTTGCTA
1 TTGTTGTTGTTGCTA
114213583 TTGTTGTTGTTGCTA
1 TTGTTGTTGTTGCTA
114213598 TT
1 TT
114213600 CTATGTGTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.06, G:0.25, T:0.62
Consensus pattern (15 bp):
TTGTTGTTGTTGCTA
Found at i:114214799 original size:56 final size:56
Alignment explanation
Indices: 114214732--114214845 Score: 228
Period size: 56 Copynumber: 2.0 Consensus size: 56
114214722 AAAATATATA
114214732 AATATCTAGAATTAAATTTGTTATTATCTAATTAAAATTATGTACAATTTAAGGTT
1 AATATCTAGAATTAAATTTGTTATTATCTAATTAAAATTATGTACAATTTAAGGTT
114214788 AATATCTAGAATTAAATTTGTTATTATCTAATTAAAATTATGTACAATTTAAGGTT
1 AATATCTAGAATTAAATTTGTTATTATCTAATTAAAATTATGTACAATTTAAGGTT
114214844 AA
1 AA
114214846 ATTACTCCGA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (56 bp):
AATATCTAGAATTAAATTTGTTATTATCTAATTAAAATTATGTACAATTTAAGGTT
Found at i:114219559 original size:49 final size:49
Alignment explanation
Indices: 114219502--114219602 Score: 193
Period size: 49 Copynumber: 2.1 Consensus size: 49
114219492 AGCTAACAAC
114219502 AATGCTCGAGCACTCGTCGGAGGCTCTTTAAAAGTACAAATCATATTTA
1 AATGCTCGAGCACTCGTCGGAGGCTCTTTAAAAGTACAAATCATATTTA
*
114219551 AATGCTCGAGCATTCGTCGGAGGCTCTTTAAAAGTACAAATCATATTTA
1 AATGCTCGAGCACTCGTCGGAGGCTCTTTAAAAGTACAAATCATATTTA
114219600 AAT
1 AAT
114219603 CTCCAATAAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.30
Consensus pattern (49 bp):
AATGCTCGAGCACTCGTCGGAGGCTCTTTAAAAGTACAAATCATATTTA
Found at i:114222725 original size:61 final size:61
Alignment explanation
Indices: 114222650--114222775 Score: 252
Period size: 61 Copynumber: 2.1 Consensus size: 61
114222640 TTCCCTTTAA
114222650 ATATACCAATTTACCCAACCTTTATAAATTGACACATGATTACATCAAATATCTCACACTG
1 ATATACCAATTTACCCAACCTTTATAAATTGACACATGATTACATCAAATATCTCACACTG
114222711 ATATACCAATTTACCCAACCTTTATAAATTGACACATGATTACATCAAATATCTCACACTG
1 ATATACCAATTTACCCAACCTTTATAAATTGACACATGATTACATCAAATATCTCACACTG
114222772 ATAT
1 ATAT
114222776 GTTTCCCTTT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.40, C:0.24, G:0.05, T:0.32
Consensus pattern (61 bp):
ATATACCAATTTACCCAACCTTTATAAATTGACACATGATTACATCAAATATCTCACACTG
Found at i:114233102 original size:19 final size:19
Alignment explanation
Indices: 114233080--114233116 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
114233070 ACTTATTTAT
*
114233080 ATATAAAATATTATTAAAC
1 ATATAAAACATTATTAAAC
*
114233099 ATATGAAACATTATTAAA
1 ATATAAAACATTATTAAA
114233117 AAAACTTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (19 bp):
ATATAAAACATTATTAAAC
Found at i:114239652 original size:20 final size:20
Alignment explanation
Indices: 114239627--114239667 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
114239617 AATCAAGTTG
114239627 TAATATTTATAGTGTTACAA
1 TAATATTTATAGTGTTACAA
*
114239647 TAATATTTATATTGTTACAA
1 TAATATTTATAGTGTTACAA
114239667 T
1 T
114239668 GAAACATTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.49
Consensus pattern (20 bp):
TAATATTTATAGTGTTACAA
Found at i:114240898 original size:31 final size:31
Alignment explanation
Indices: 114240863--114240926 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
114240853 TTACAAAATG
*
114240863 GTCATTGAATTATTCAAAAATTTTCATTTAA
1 GTCATTGAACTATTCAAAAATTTTCATTTAA
** * *
114240894 GTCATTGAACTATTTGAAAGTTTTTATTTAA
1 GTCATTGAACTATTCAAAAATTTTCATTTAA
114240925 GT
1 GT
114240927 AATCGGTTTG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.34, C:0.08, G:0.11, T:0.47
Consensus pattern (31 bp):
GTCATTGAACTATTCAAAAATTTTCATTTAA
Found at i:114242579 original size:37 final size:37
Alignment explanation
Indices: 114242538--114242713 Score: 298
Period size: 37 Copynumber: 4.8 Consensus size: 37
114242528 TTTGAGTACT
114242538 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
*
114242575 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
*
114242612 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
*
114242649 TCTGATCAAGAGACAAAGTGATAAGTGGCTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
** *
114242686 TCTGATCAAGTGATAAAGTGATAAGTGG
1 TCTGATCAAGAAACAAAGTGATAAGTGG
114242714 TAGCTTCAGC
Statistics
Matches: 134, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 134 1.00
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (37 bp):
TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
Found at i:114242785 original size:45 final size:46
Alignment explanation
Indices: 114242676--114242799 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 46
114242666 GTGATAAGTG
* *
114242676 GCTACACTTATCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTCA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
*
114242722 GCTACACTTATCTGATCAAGTGGCAAAGTGATAAGTGGTAGCCT-A
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
114242767 GCTACACTTATCTGATCAAG-GAC-AAGTGATAAG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAG
114242800 AGGTCATATG
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
43 10 0.14
44 2 0.03
45 21 0.28
46 41 0.55
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (46 bp):
GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
Found at i:114265473 original size:2 final size:2
Alignment explanation
Indices: 114265466--114265493 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
114265456 TATGTCTGCT
114265466 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
114265494 AGAGAGAGAG
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:114265498 original size:2 final size:2
Alignment explanation
Indices: 114265493--114265519 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
114265483 GTGTGTGTGT
114265493 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
114265520 CAGGTTTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:114272199 original size:17 final size:17
Alignment explanation
Indices: 114272177--114272210 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
114272167 ACCTTCAGGT
114272177 TCTTGCTCCTCAACTAA
1 TCTTGCTCCTCAACTAA
*
114272194 TCTTGCTTCTCAACTAA
1 TCTTGCTCCTCAACTAA
114272211 CTGAATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.32, G:0.06, T:0.38
Consensus pattern (17 bp):
TCTTGCTCCTCAACTAA
Found at i:114281184 original size:73 final size:75
Alignment explanation
Indices: 114281107--114281247 Score: 205
Period size: 75 Copynumber: 1.9 Consensus size: 75
114281097 TAAAAATTAT
* * * * * *
114281107 AAATATTGGTAGGTTAATTTTACTATTATGC-CA-AAACAAATCACATCAACATGATTTAACTTA
1 AAATATTGGCAGGTGAATTTTACTATTATACTAAGAAAAAAATCACATCAACATGATTTAACATA
114281170 TAAAATATGC
66 TAAAATATGC
*
114281180 AAATATTGGCAGGTGAATTTTACTATTATACTAAGAAAAAAATCACGTCAACATGATTTAACATA
1 AAATATTGGCAGGTGAATTTTACTATTATACTAAGAAAAAAATCACATCAACATGATTTAACATA
114281245 TAA
66 TAA
114281248 GTGACTCGAT
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
73 28 0.47
74 1 0.02
75 30 0.51
ACGTcount: A:0.44, C:0.13, G:0.11, T:0.33
Consensus pattern (75 bp):
AAATATTGGCAGGTGAATTTTACTATTATACTAAGAAAAAAATCACATCAACATGATTTAACATA
TAAAATATGC
Found at i:114303860 original size:78 final size:78
Alignment explanation
Indices: 114303731--114303886 Score: 231
Period size: 78 Copynumber: 2.0 Consensus size: 78
114303721 CTCATATTCT
* * * *
114303731 ACCATTAAACCGTGATCCCTTGATCTCACCAGCTGGGAGGGTCGGTGATCATGTTGATAATGATC
1 ACCATTAAACCCTGATCCCTTGATCTCACCAGCTAGGAGAGTCGGTGATCATGTTGATAACGATC
*
114303796 ACCATGGAGTTTG
66 ACCATGGACTTTG
* * * *
114303809 ACCATTAAACCCTGATCGCTTGATCTCATCAGCTAGGAGAGTTGGTGATCATGTTGATAGCGATC
1 ACCATTAAACCCTGATCCCTTGATCTCACCAGCTAGGAGAGTCGGTGATCATGTTGATAACGATC
114303874 ACCATGGACTTTG
66 ACCATGGACTTTG
114303887 TGTACCAGAA
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
78 69 1.00
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (78 bp):
ACCATTAAACCCTGATCCCTTGATCTCACCAGCTAGGAGAGTCGGTGATCATGTTGATAACGATC
ACCATGGACTTTG
Found at i:114310708 original size:246 final size:247
Alignment explanation
Indices: 114310153--114310796 Score: 1184
Period size: 247 Copynumber: 2.6 Consensus size: 247
114310143 TTCATGAAAA
* *
114310153 GGGAACTGCATTTCTTACTTTTTTATCTTCATTTCCTTTTGCATATTTCTGAGATGCTCAATCCT
1 GGGAACTGCATTCCTTACTTTATTATCTTCATTTCCTTTTGCATATTTCTGAGATGCTCAATCCT
114310218 TCTAAATGAAAATTTACTAGCATACTCAGGTTCCACAAATTTACTATGCCACACTAAAAGGGGTT
66 TCTAAATGAAAATTTACTAGCATACTCAGGTTCCACAAATTTACTATGCCACACTAAAAGGGGTT
114310283 CAGGAAATCTATAATTGTTAAAAGTATTGTTGTGAATCACTAAAATTTTCCCATTGAGGAAAAAA
131 CAGGAAATCTATAATTGTTAAAAGTATTGTTGTGAATCACTAAAATTTTCCCATTGAGGAAAAAA
*
114310348 AGAAGGAAGGATTCGGATATCATCCGTCTAAATATTCCTTTTCTTAATTGAG
196 AGAAGGAAGGATTCGGATATCATCCGTCTAAATATTCCATTTCTTAATTGAG
114310400 GGGAACTGCATTCCTTACTTTATTATCTTCATTTCCTTTTGCATATTTCTGAGATGCTCAATCCT
1 GGGAACTGCATTCCTTACTTTATTATCTTCATTTCCTTTTGCATATTTCTGAGATGCTCAATCCT
*
114310465 TCTAAATGAAAATTTACTAGCATACTCAGGTTCCACAAATTTACTATGCCACACTAAAGGGGGTT
66 TCTAAATGAAAATTTACTAGCATACTCAGGTTCCACAAATTTACTATGCCACACTAAAAGGGGTT
114310530 CAGGAAATCTATAATTGTTAAAAGTATTGTTGTGAATCACTAAAATTTTCCCATTGAGGAAAAAA
131 CAGGAAATCTATAATTGTTAAAAGTATTGTTGTGAATCACTAAAATTTTCCCATTGAGGAAAAAA
*
114310595 AGGAGG-AGGATTCGGATATCATCCGTCTAAATATTCCATTTCTTAATTGAG
196 AGAAGGAAGGATTCGGATATCATCCGTCTAAATATTCCATTTCTTAATTGAG
** *
114310646 GGGAACTGTGTGT-GTTACTTTATTATCTTCATTTCCTTTTGCATATTTCTGAGATGCTCAATCC
1 GGGAACTGCAT-TCCTTACTTTATTATCTTCATTTCCTTTTGCATATTTCTGAGATGCTCAATCC
114310710 TTCTAAATGAAAATTTACTAGCATACTCAGGTTCCACAAATTTACTATGCCACACTAAAAGGGGT
65 TTCTAAATGAAAATTTACTAGCATACTCAGGTTCCACAAATTTACTATGCCACACTAAAAGGGGT
*
114310775 TCAGGATATCTATAATTGTTAA
130 TCAGGAAATCTATAATTGTTAA
114310797 TCTGATTGAG
Statistics
Matches: 386, Mismatches: 10, Indels: 3
0.97 0.03 0.01
Matches are distributed among these distances:
246 188 0.49
247 198 0.51
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.36
Consensus pattern (247 bp):
GGGAACTGCATTCCTTACTTTATTATCTTCATTTCCTTTTGCATATTTCTGAGATGCTCAATCCT
TCTAAATGAAAATTTACTAGCATACTCAGGTTCCACAAATTTACTATGCCACACTAAAAGGGGTT
CAGGAAATCTATAATTGTTAAAAGTATTGTTGTGAATCACTAAAATTTTCCCATTGAGGAAAAAA
AGAAGGAAGGATTCGGATATCATCCGTCTAAATATTCCATTTCTTAATTGAG
Found at i:114314053 original size:14 final size:13
Alignment explanation
Indices: 114314034--114314073 Score: 55
Period size: 14 Copynumber: 3.0 Consensus size: 13
114314024 GGGGTTTTTA
114314034 AAAAAATTATATAT
1 AAAAAATTA-ATAT
114314048 AAAAAA-TAATAT
1 AAAAAATTAATAT
114314060 AAAAAATTTAATAT
1 AAAAAA-TTAATAT
114314074 GCATGGGCTG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 10 0.42
13 2 0.08
14 12 0.50
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
AAAAAATTAATAT
Found at i:114314059 original size:12 final size:13
Alignment explanation
Indices: 114314034--114314066 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
114314024 GGGGTTTTTA
114314034 AAAAAATTATATAT
1 AAAAAA-TATATAT
114314048 AAAAAATA-ATAT
1 AAAAAATATATAT
114314060 AAAAAAT
1 AAAAAAT
114314067 TTAATATGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 11 0.58
13 2 0.11
14 6 0.32
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (13 bp):
AAAAAATATATAT
Done.