Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr5
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: 43060996
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2186021 characters in sequence are not A, C, G, or T
File 118 of 128
Found at i:39244539 original size:21 final size:20
Alignment explanation
Indices: 39244512--39244569 Score: 55
Period size: 21 Copynumber: 2.9 Consensus size: 20
39244502 ATTAAATTGT
39244512 AAAATAAATTCTAAATTTTG
1 AAAATAAATTCTAAATTTTG
*** *
39244532 AGAAATAAGGGCTAAATTGTG
1 A-AAATAAATTCTAAATTTTG
*
39244553 AAAA-AAATTCAAAATTT
1 AAAATAAATTCTAAATTT
39244570 AGGGATTTAA
Statistics
Matches: 28, Mismatches: 9, Indels: 3
0.70 0.22 0.08
Matches are distributed among these distances:
19 8 0.29
20 4 0.14
21 16 0.57
ACGTcount: A:0.52, C:0.05, G:0.12, T:0.31
Consensus pattern (20 bp):
AAAATAAATTCTAAATTTTG
Found at i:39249904 original size:49 final size:50
Alignment explanation
Indices: 39249851--39249952 Score: 188
Period size: 49 Copynumber: 2.1 Consensus size: 50
39249841 CTTTAGGTTT
39249851 TATTATATATATTATTACATTGAAGGGGA-GGAAGCAAAACTACCATAAC
1 TATTATATATATTATTACATTGAAGGGGAGGGAAGCAAAACTACCATAAC
*
39249900 TATTATATATATTATTACATTGAAGGGGAGGGAAGCACAACTACCATAAC
1 TATTATATATATTATTACATTGAAGGGGAGGGAAGCAAAACTACCATAAC
39249950 TAT
1 TAT
39249953 GGTTGTTTTA
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
49 29 0.57
50 22 0.43
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (50 bp):
TATTATATATATTATTACATTGAAGGGGAGGGAAGCAAAACTACCATAAC
Found at i:39251766 original size:27 final size:27
Alignment explanation
Indices: 39251705--39251772 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
39251695 TAAAATAAGG
*
39251705 ATTT-AAAAATAAATATAAATAATGTT
1 ATTTAAAAAATAAATATAAATAATATT
*
39251731 ATTTTAAAAATAAATATAAATTACA-ATT
1 ATTTAAAAAATAAATATAAA-TA-ATATT
39251759 A-TTAAAAAATAAAT
1 ATTTAAAAAATAAAT
39251773 TCAAAAACAT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
26 4 0.11
27 27 0.73
28 5 0.14
29 1 0.03
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (27 bp):
ATTTAAAAAATAAATATAAATAATATT
Found at i:39261109 original size:15 final size:15
Alignment explanation
Indices: 39261067--39261110 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
39261057 AAGTGCCGGA
*
39261067 GGAGGTGGAGGGGGC
1 GGAGGTGGAGGAGGC
*
39261082 GGAGGTGGGGGAGGC
1 GGAGGTGGAGGAGGC
*
39261097 GGAGGCGGAGGAGG
1 GGAGGTGGAGGAGG
39261111 AGGTGGACGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.16, C:0.07, G:0.73, T:0.05
Consensus pattern (15 bp):
GGAGGTGGAGGAGGC
Found at i:39266442 original size:97 final size:98
Alignment explanation
Indices: 39266328--39266523 Score: 385
Period size: 97 Copynumber: 2.0 Consensus size: 98
39266318 CCATTTTAAA
39266328 ATTTTATAAATTATAAAGAGTCAAAAAAGAATTTTTATTTTTATTTTAGAGTAAAACCCTTACCC
1 ATTTTATAAATTATAAAGAGTCAAAAAAGAATTTTTATTTTTATTTTAGAGTAAAACCCTTACCC
39266393 ATGAAATATCATATCAACAAA-TTAACAATACT
66 ATGAAATATCATATCAACAAATTTAACAATACT
39266425 ATTTTATAAATTATAAAGAGTCAAAAAAGAATTTTTATTTTTATTTTAGAGTAAAACCCTTACCC
1 ATTTTATAAATTATAAAGAGTCAAAAAAGAATTTTTATTTTTATTTTAGAGTAAAACCCTTACCC
39266490 ATGAAATATCATATCAACAAATTTAACAATACT
66 ATGAAATATCATATCAACAAATTTAACAATACT
39266523 A
1 A
39266524 ATAATTAAAA
Statistics
Matches: 98, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
97 86 0.88
98 12 0.12
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (98 bp):
ATTTTATAAATTATAAAGAGTCAAAAAAGAATTTTTATTTTTATTTTAGAGTAAAACCCTTACCC
ATGAAATATCATATCAACAAATTTAACAATACT
Found at i:39268199 original size:27 final size:27
Alignment explanation
Indices: 39268143--39268199 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
39268133 GTATGGGGTA
* **
39268143 GGTGGAGCCTATCTGACAGGTGCGACT
1 GGTGGAGCCTATCTGACAAGCACGACT
*
39268170 GGTGGAGCCTATCTGACAAGCACGATT
1 GGTGGAGCCTATCTGACAAGCACGACT
39268197 GGT
1 GGT
39268200 TGAACAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.21, C:0.21, G:0.35, T:0.23
Consensus pattern (27 bp):
GGTGGAGCCTATCTGACAAGCACGACT
Found at i:39268413 original size:60 final size:60
Alignment explanation
Indices: 39268341--39268459 Score: 220
Period size: 60 Copynumber: 2.0 Consensus size: 60
39268331 ATACTAAACT
*
39268341 AAACACAACAATTTATAACATAATCCTAAATTACTAATAAATTAATTTTAAAATAATTAC
1 AAACACAACAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTAC
*
39268401 AAACACAACAATTTATAACATAATCTTAAATTACTAACAAATTAATTTTAAAATAATTA
1 AAACACAACAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTA
39268460 TAAAAAATAA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.54, C:0.13, G:0.00, T:0.34
Consensus pattern (60 bp):
AAACACAACAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTAC
Found at i:39268728 original size:25 final size:24
Alignment explanation
Indices: 39268684--39268733 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
39268674 TATATATTTA
39268684 AATATTTTAATAAAAATAAAATAAT
1 AATATTTTAATAAAAATAAAA-AAT
* * *
39268709 AATATTTTATTTAAAGTAAAAAAT
1 AATATTTTAATAAAAATAAAAAAT
39268733 A
1 A
39268734 TTTTAATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (24 bp):
AATATTTTAATAAAAATAAAAAAT
Found at i:39270972 original size:22 final size:21
Alignment explanation
Indices: 39270929--39270973 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
39270919 TACCTCAATT
* *
39270929 AATAAAAAAGATAAGGTGCTA
1 AATAAAAAAAATAAGGTCCTA
*
39270950 AATAAAAAAAATAAGATTCCTA
1 AATAAAAAAAATAAG-GTCCTA
39270972 AA
1 AA
39270974 ACGATGAACT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.62, C:0.07, G:0.11, T:0.20
Consensus pattern (21 bp):
AATAAAAAAAATAAGGTCCTA
Found at i:39292859 original size:23 final size:22
Alignment explanation
Indices: 39292825--39292870 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 22
39292815 TAATATCAAA
39292825 TAAAATAATATTATTATATTTT
1 TAAAATAATATTATTATATTTT
*
39292847 TAAAATATTTATTATTATATTTT
1 TAAAATA-ATATTATTATATTTT
39292870 T
1 T
39292871 TTTAATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TAAAATAATATTATTATATTTT
Found at i:39293857 original size:29 final size:27
Alignment explanation
Indices: 39293809--39293862 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 27
39293799 TAGTGCATGA
39293809 ATATATATACATATATATTATAAAAAT
1 ATATATATACATATATATTATAAAAAT
* *
39293836 ATATATATATATGTATGGATTATAAAA
1 ATATATATACATATAT--ATTATAAAA
39293863 TATGGAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 14 0.61
29 9 0.39
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.41
Consensus pattern (27 bp):
ATATATATACATATATATTATAAAAAT
Found at i:39294080 original size:15 final size:15
Alignment explanation
Indices: 39294057--39294087 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
39294047 AAATACATGG
39294057 TTATAATATTAATAA
1 TTATAATATTAATAA
*
39294072 TTATTATATTAATAA
1 TTATAATATTAATAA
39294087 T
1 T
39294088 AGTAATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TTATAATATTAATAA
Found at i:39294747 original size:16 final size:16
Alignment explanation
Indices: 39294726--39294756 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39294716 AGTAAATCGA
*
39294726 AGGAAAAAAATAAAAG
1 AGGAAAAAAACAAAAG
39294742 AGGAAAAAAACAAAA
1 AGGAAAAAAACAAAA
39294757 ATAAAATCAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.77, C:0.03, G:0.16, T:0.03
Consensus pattern (16 bp):
AGGAAAAAAACAAAAG
Found at i:39295960 original size:100 final size:100
Alignment explanation
Indices: 39295824--39296335 Score: 668
Period size: 100 Copynumber: 5.1 Consensus size: 100
39295814 GATTCGCTAT
* * * *
39295824 CTTCAGTCTAATTAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCCA
1 CTTCAGTCTATTTAATTGCAATGTCGGGGAAACAAGATTCGCCGTTGTAGCTTCAATCTGTTCCA
**
39295889 CTGCACCGCCAGGGAAGTAAGATTTGTCGTTGTGG
66 CTGCACCGCCAGGGAAGTAAGATTTACCGTTGTGG
* * * *
39295924 CTTCAGTCTTTTTAATTGTAATGTCGGGGAAGCAAGATTCGCCGTTGTACCTTCAATCTGTTCCA
1 CTTCAGTCTATTTAATTGCAATGTCGGGGAAACAAGATTCGCCGTTGTAGCTTCAATCTGTTCCA
*
39295989 CTGCACCGCCAGGGAAGTAAGATTCACCGTTGTGG
66 CTGCACCGCCAGGGAAGTAAGATTTACCGTTGTGG
* * * *
39296024 CTTCAATCTTTTTAATTGCAATGTCGGGGAAATAAGATTCACCGTTGTAGCTTCAATCTGTTCCA
1 CTTCAGTCTATTTAATTGCAATGTCGGGGAAACAAGATTCGCCGTTGTAGCTTCAATCTGTTCCA
* ** *
39296089 CTGCATCGCCAGGGAAGTAAGATTCGCTGTTGTGG
66 CTGCACCGCCAGGGAAGTAAGATTTACCGTTGTGG
* * *
39296124 CTTC-GATCTATTTAATTGCTATGTCGGGGAAACAATATTCGCCGTCGTAGCTTCAATCTGTTCC
1 CTTCAG-TCTATTTAATTGCAATGTCGGGGAAACAAGATTCGCCGTTGTAGCTTCAATCTGTTCC
* * * *
39296188 ACTACACTGCCAGGGAAGTAAGATTCACTGTTGTGG
65 ACTGCACCGCCAGGGAAGTAAGATTTACCGTTGTGG
* * ** * * *
39296224 CTTCAATCTATTTAATTGCAATGTCGGGGAAATACA-ATTTACTGTCGTAGCTTCAATCTGTTCT
1 CTTCAGTCTATTTAATTGCAATGTCGGGGAAACA-AGATTCGCCGTTGTAGCTTCAATCTGTTCC
* *
39296288 ACTACACTGCCAGGGAAGTAAGATTTACCGTTGTGG
65 ACTGCACCGCCAGGGAAGTAAGATTTACCGTTGTGG
*
39296324 CTTCAATCTATT
1 CTTCAGTCTATT
39296336 CCACTGTAAT
Statistics
Matches: 371, Mismatches: 38, Indels: 6
0.89 0.09 0.01
Matches are distributed among these distances:
100 370 1.00
101 1 0.00
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.32
Consensus pattern (100 bp):
CTTCAGTCTATTTAATTGCAATGTCGGGGAAACAAGATTCGCCGTTGTAGCTTCAATCTGTTCCA
CTGCACCGCCAGGGAAGTAAGATTTACCGTTGTGG
Found at i:39296349 original size:50 final size:50
Alignment explanation
Indices: 39295838--39296349 Score: 371
Period size: 50 Copynumber: 10.2 Consensus size: 50
39295828 AGTCTAATTA
* * * * *
39295838 ACTGCAATGTCGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCC
1 ACTGCAATGCCAGGGAAGTAAGATTCACCGTTGTAGCTTCAATCTGTTCC
** *** * * * **
39295888 ACTGCACCGCCAGGGAAGTAAGATTTGTCGTTGTGGCTTCAGTCTTTTTA
1 ACTGCAATGCCAGGGAAGTAAGATTCACCGTTGTAGCTTCAATCTGTTCC
* * * * * * *
39295938 ATTGTAATGTCGGGGAAGCAAGATTCGCCGTTGTACCTTCAATCTGTTCC
1 ACTGCAATGCCAGGGAAGTAAGATTCACCGTTGTAGCTTCAATCTGTTCC
** * * **
39295988 ACTGCACCGCCAGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTA
1 ACTGCAATGCCAGGGAAGTAAGATTCACCGTTGTAGCTTCAATCTGTTCC
* * * *
39296038 ATTGCAATGTCGGGGAAATAAGATTCACCGTTGTAGCTTCAATCTGTTCC
1 ACTGCAATGCCAGGGAAGTAAGATTCACCGTTGTAGCTTCAATCTGTTCC
* * * * * **
39296088 ACTGC-ATCGCCAGGGAAGTAAGATTCGCTGTTGTGGCTTCGATCTATTTA
1 ACTGCAAT-GCCAGGGAAGTAAGATTCACCGTTGTAGCTTCAATCTGTTCC
* * * * ** * * *
39296138 ATTGCTATGTCGGGGAAACAATATTCGCCGTCGTAGCTTCAATCTGTTCC
1 ACTGCAATGCCAGGGAAGTAAGATTCACCGTTGTAGCTTCAATCTGTTCC
* * * * * **
39296188 ACTACACTGCCAGGGAAGTAAGATTCACTGTTGTGGCTTCAATCTATTTA
1 ACTGCAATGCCAGGGAAGTAAGATTCACCGTTGTAGCTTCAATCTGTTCC
* * * * * * * *
39296238 ATTGCAATGTCGGGGAAATACA-ATTTACTGTCGTAGCTTCAATCTGTTCT
1 ACTGCAATGCCAGGGAAGTA-AGATTCACCGTTGTAGCTTCAATCTGTTCC
* * * * *
39296288 ACTACACTGCCAGGGAAGTAAGATTTACCGTTGTGGCTTCAATCTATTCC
1 ACTGCAATGCCAGGGAAGTAAGATTCACCGTTGTAGCTTCAATCTGTTCC
*
39296338 ACTGTAATGCCA
1 ACTGCAATGCCA
39296350 AAGAGATAGG
Statistics
Matches: 341, Mismatches: 117, Indels: 8
0.73 0.25 0.02
Matches are distributed among these distances:
49 3 0.01
50 335 0.98
51 3 0.01
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (50 bp):
ACTGCAATGCCAGGGAAGTAAGATTCACCGTTGTAGCTTCAATCTGTTCC
Found at i:39296646 original size:266 final size:254
Alignment explanation
Indices: 39296267--39297005 Score: 812
Period size: 250 Copynumber: 2.9 Consensus size: 254
39296257 ACAATTTACT
* * ** * ** * *
39296267 GTCGTAGCTTCAATCTGTTCTACTACACTGCCAGGGAAGTAAGATTTACCGTTGTGGCTTCAATC
1 GTCGTGGCTTCAATCTGGTCCCCTACACCGCCAGGGAAGTAAGATTCGCCGCTGCGGCTTCAATC
* * *
39296332 TATTCCACTGTAATGCCAAAGAGATAGGATTCGCTACCCACGGCCTTAATCCGCTCCACTTCAGC
66 CATTCCACTGTAATGCCAAAGAGATAGGATTCGCTGCCCACAGCCTTAATCCGCTCCACTTCAGC
* * *
39296397 TAATCTAAGTCTTAATGCCAGGGAGATAAGATTAACCGTCGTGGCTTCAATCTACTCCGCTGCAA
131 TAATCTAAGTCTTAACGCCAGGGAGATAAGATTCACCGTCGTGGCTTCAATCTGCTCCGCTGCAA
* * *
39296462 CGCTGGGGAAGTAAGATTCGCCATTGTGGCTTTAATCTACTTAACTGCTATATCGGGG-AACGAG
196 CGCCGGGGAAGTAAGATTC-CC-TTGTGG-TTT-AGCT-C-CAA-TG----A--GGGGAAACGAG
39296526 ATTCG-C
248 ATTCGTC
** ** *
39296532 TGTTTTGGCTTCAATCTGGTCCCCTACACCGCCATTGAAGTAAGATTCGTCG-TCGCGGCTTCAA
1 -GTCGTGGCTTCAATCTGGTCCCCTACACCGCCAGGGAAGTAAGATTCGCCGCT-GCGGCTTCAA
* * *
39296596 TCCGTTCCACTGTAATGCCAAAGAGATAGGATTTGCTGCCCACAGCCTTAATCCACTCCACTTCA
64 TCCATTCCACTGTAATGCCAAAGAGATAGGATTCGCTGCCCACAGCCTTAATCCGCTCCACTTCA
* *
39296661 GCTAAT-TCAAGTCTTAACGCCAGGGAGATAAGATTCTCCGACGTGGCTTCAATCTGCTCCGCTG
129 GCTAATCT-AAGTCTTAACGCCAGGGAGATAAGATTCACCGTCGTGGCTTCAATCTGCTCCGCTG
* * * *
39296725 CAACGCCGGAGAAGTAAGATT---TT-TCGTTTGGCTCCAATGAGGGGAAATGAGATTCGTC
193 CAACGCCGGGGAAGTAAGATTCCCTTGTGGTTTAGCTCCAATGAGGGGAAACGAGATTCGTC
* * *
39296783 GTCGTGGCTTCAATCTGGTCCCCTACACCGCTAGGGAAGTAAGATTCGCCGCTGCGGCTTTAACC
1 GTCGTGGCTTCAATCTGGTCCCCTACACCGCCAGGGAAGTAAGATTCGCCGCTGCGGCTTCAATC
* * *
39296848 CATTCCACTGTAATGCTAAAGAGATAGGATTCGCTGCCCACAGCTTTAATTCGCTCCACTTCAGC
66 CATTCCACTGTAATGCCAAAGAGATAGGATTCGCTGCCCACAGCCTTAATCCGCTCCACTTCAGC
* * * * * * * * *
39296913 TAATCCAAGTCTTAACACC-GAGGAGATAAGGTTCGCCATTGTGGCTTCAATCCGTTCCACTGCA
131 TAATCTAAGTCTTAACGCCAG-GGAGATAAGATTCACCGTCGTGGCTTCAATCTGCTCCGCTGCA
*
39296977 ACGCCAGGGAAGTAAGATTCACCGTTGTG
195 ACGCCGGGGAAGTAAGATTC-CC-TTGTG
39297006 ACTTCCATCT
Statistics
Matches: 402, Mismatches: 58, Indels: 36
0.81 0.12 0.07
Matches are distributed among these distances:
249 5 0.01
250 192 0.48
251 3 0.01
255 4 0.01
256 3 0.01
257 1 0.00
258 2 0.00
259 3 0.01
260 2 0.00
261 2 0.00
265 2 0.00
266 183 0.46
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (254 bp):
GTCGTGGCTTCAATCTGGTCCCCTACACCGCCAGGGAAGTAAGATTCGCCGCTGCGGCTTCAATC
CATTCCACTGTAATGCCAAAGAGATAGGATTCGCTGCCCACAGCCTTAATCCGCTCCACTTCAGC
TAATCTAAGTCTTAACGCCAGGGAGATAAGATTCACCGTCGTGGCTTCAATCTGCTCCGCTGCAA
CGCCGGGGAAGTAAGATTCCCTTGTGGTTTAGCTCCAATGAGGGGAAACGAGATTCGTC
Found at i:39298916 original size:21 final size:20
Alignment explanation
Indices: 39298891--39298930 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
39298881 GTAGAGGTTT
39298891 TTGTTTCTTT-TTATTTTTTTC
1 TTGTTT-TTTCTT-TTTTTTTC
39298912 TTGTTTTTTCTTTTTTTTT
1 TTGTTTTTTCTTTTTTTTT
39298931 GGATTAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.03, C:0.07, G:0.05, T:0.85
Consensus pattern (20 bp):
TTGTTTTTTCTTTTTTTTTC
Found at i:39306839 original size:3 final size:3
Alignment explanation
Indices: 39306831--39306921 Score: 98
Period size: 3 Copynumber: 30.7 Consensus size: 3
39306821 NNNNNNNAGA
*
39306831 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AC
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
39306878 AAT AGT AAT AAT GCAAT -AT AAC AAT ATT AAT AAT ATT AA- AAT AA
1 AAT AAT AAT AAT --AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
39306922 AAAAAACCTA
Statistics
Matches: 73, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
2 5 0.07
3 65 0.89
5 3 0.04
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:39311945 original size:5 final size:5
Alignment explanation
Indices: 39311935--39311964 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
39311925 AACTAAGAAC
39311935 CAGGG CAGGG CAGGG CAGGG CAGGG CAGGG
1 CAGGG CAGGG CAGGG CAGGG CAGGG CAGGG
39311965 GAAATGTGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.20, C:0.20, G:0.60, T:0.00
Consensus pattern (5 bp):
CAGGG
Found at i:39313419 original size:23 final size:24
Alignment explanation
Indices: 39313385--39313439 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 24
39313375 ATATATTATA
*
39313385 AATTTA-ATTTAAAT-TTTACAAAT
1 AATTTATA-TTAAATATTTAAAAAT
*
39313408 AATTTATATTAATTATTTAAAAAT
1 AATTTATATTAAATATTTAAAAAT
39313432 -ATTTATAT
1 AATTTATAT
39313440 ATTTCATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 19 0.68
24 9 0.32
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (24 bp):
AATTTATATTAAATATTTAAAAAT
Found at i:39315621 original size:3 final size:3
Alignment explanation
Indices: 39315613--39315670 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
39315603 TTAAAATGAC
39315613 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
39315661 ATA ATA ATA A
1 ATA ATA ATA A
39315671 AGACACGAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:39323299 original size:5 final size:5
Alignment explanation
Indices: 39323289--39323318 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
39323279 AACTAAGAAC
39323289 CAGGG CAGGG CAGGG CAGGG CAGGG CAGGG
1 CAGGG CAGGG CAGGG CAGGG CAGGG CAGGG
39323319 GAAATGTGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.20, C:0.20, G:0.60, T:0.00
Consensus pattern (5 bp):
CAGGG
Found at i:39324773 original size:23 final size:24
Alignment explanation
Indices: 39324739--39324793 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 24
39324729 ATATATTATA
*
39324739 AATTTA-ATTTAAAT-TTTACAAAT
1 AATTTATA-TTAAATATTTAAAAAT
*
39324762 AATTTATATTAATTATTTAAAAAT
1 AATTTATATTAAATATTTAAAAAT
39324786 -ATTTATAT
1 AATTTATAT
39324794 ATTTCATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 19 0.68
24 9 0.32
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (24 bp):
AATTTATATTAAATATTTAAAAAT
Found at i:39326975 original size:3 final size:3
Alignment explanation
Indices: 39326967--39327024 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
39326957 TTAAAATGAC
39326967 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
39327015 ATA ATA ATA A
1 ATA ATA ATA A
39327025 AGACACGAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:39331229 original size:25 final size:25
Alignment explanation
Indices: 39331201--39331281 Score: 92
Period size: 25 Copynumber: 3.2 Consensus size: 25
39331191 CCAAGAATGT
*
39331201 TTTACAGAGAGTTCGCCATAAAAAC
1 TTTACAGAGAGTTCGCCATAAAAGC
* *
39331226 TTTACAGA-ATATTCGCCATAAAGGC
1 TTTACAGAGA-GTTCGCCATAAAAGC
* * *
39331251 TTTATAGAGAGTTCACCACAAAAGC
1 TTTACAGAGAGTTCGCCATAAAAGC
39331276 TTTACA
1 TTTACA
39331282 AAATATTCAC
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
24 1 0.02
25 43 0.96
26 1 0.02
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (25 bp):
TTTACAGAGAGTTCGCCATAAAAGC
Found at i:39332640 original size:136 final size:135
Alignment explanation
Indices: 39332396--39332656 Score: 495
Period size: 136 Copynumber: 1.9 Consensus size: 135
39332386 ATCTTATAAG
*
39332396 GGATGCAATTGGGACACTAAGAGTAAAAAACGACCAGGAAATGACCAAATTGAAACACAATCAAT
1 GGATGCAATTGGGACACTAAGAGTAAAAAACGACCAAGAAATGACCAAATTGAAACACAATCAAT
39332461 GAAATGAGGTCGAATAAAAAATGTGGAAAAAGTTAAGGACTTATCATATTCTTTTGACTTTGTAA
66 GAAATGAGGTCGAATAAAAAATGTGGAAAAAGTTAAGGACTTATCATATTCTTTTG-CTTTGTAA
39332526 AAGCCT
130 AAGCCT
*
39332532 GGATGCAATTGGGACGCTAAGAGTAAAAAACGACCAAGAAATGACCAAATTGAAACACAATCAAT
1 GGATGCAATTGGGACACTAAGAGTAAAAAACGACCAAGAAATGACCAAATTGAAACACAATCAAT
39332597 GAAATGAGGTCGAATAAAAAATGTGGAAAAAGTTAAGGACTTATCATATTCTTTTGCTTT
66 GAAATGAGGTCGAATAAAAAATGTGGAAAAAGTTAAGGACTTATCATATTCTTTTGCTTT
39332657 TGAAAAACCA
Statistics
Matches: 123, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
135 4 0.03
136 119 0.97
ACGTcount: A:0.43, C:0.13, G:0.20, T:0.24
Consensus pattern (135 bp):
GGATGCAATTGGGACACTAAGAGTAAAAAACGACCAAGAAATGACCAAATTGAAACACAATCAAT
GAAATGAGGTCGAATAAAAAATGTGGAAAAAGTTAAGGACTTATCATATTCTTTTGCTTTGTAAA
AGCCT
Found at i:39333570 original size:12 final size:12
Alignment explanation
Indices: 39333553--39333582 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
39333543 ACAAAATCCG
39333553 AATTTAATTTCT
1 AATTTAATTTCT
*
39333565 AATTTAATTTTT
1 AATTTAATTTCT
39333577 AATTTA
1 AATTTA
39333583 TTTAATCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (12 bp):
AATTTAATTTCT
Found at i:39335054 original size:31 final size:30
Alignment explanation
Indices: 39335016--39335123 Score: 110
Period size: 31 Copynumber: 3.5 Consensus size: 30
39335006 TATTAAATTA
*
39335016 AATTTAATATTTATTTAGATAGTATTTTATT
1 AATTTAATATTTATATAGATA-TATTTTATT
* * * **
39335047 AACTTAATATTAATAT-GAGATATTAAATTT
1 AATTTAATATTTATATAGATATATTTTA-TT
*
39335077 AATTTAATATTTATCTAGATAATATTTTATT
1 AATTTAATATTTATATAGAT-ATATTTTATT
*
39335108 AATTTAATATTAATAT
1 AATTTAATATTTATAT
39335124 GATTAATTCT
Statistics
Matches: 60, Mismatches: 14, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
29 5 0.08
30 18 0.30
31 31 0.52
32 6 0.10
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.52
Consensus pattern (30 bp):
AATTTAATATTTATATAGATATATTTTATT
Found at i:39335075 original size:61 final size:61
Alignment explanation
Indices: 39335000--39335125 Score: 216
Period size: 61 Copynumber: 2.1 Consensus size: 61
39334990 ATATAATAAA
* *
39335000 ATGAGATATTAAATTAAATTTAATATTTATTTAGATAGTATTTTATTAACTTAATATTAAT
1 ATGAGATATTAAATTAAATTTAATATTTATCTAGATAATATTTTATTAACTTAATATTAAT
* *
39335061 ATGAGATATTAAATTTAATTTAATATTTATCTAGATAATATTTTATTAATTTAATATTAAT
1 ATGAGATATTAAATTAAATTTAATATTTATCTAGATAATATTTTATTAACTTAATATTAAT
39335122 ATGA
1 ATGA
39335126 TTAATTCTAA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (61 bp):
ATGAGATATTAAATTAAATTTAATATTTATCTAGATAATATTTTATTAACTTAATATTAAT
Found at i:39337992 original size:26 final size:24
Alignment explanation
Indices: 39337974--39338041 Score: 64
Period size: 29 Copynumber: 2.6 Consensus size: 24
39337964 AACAAATAAT
39337974 TTAAAAATTCTAAAATAACTAAAAA
1 TTAAAAATTC-AAAATAACTAAAAA
* *
39337999 TTCAAAATTCAAAATATATATAAAAAA
1 TTAAAAATTCAAAATA-A-CT-AAAAA
39338026 TCATAAAAATTCAAAA
1 T--TAAAAATTCAAAA
39338042 ATCATTATGA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
24 6 0.17
25 10 0.29
26 1 0.03
27 6 0.17
29 12 0.34
ACGTcount: A:0.63, C:0.09, G:0.00, T:0.28
Consensus pattern (24 bp):
TTAAAAATTCAAAATAACTAAAAA
Found at i:39342218 original size:106 final size:106
Alignment explanation
Indices: 39342033--39342238 Score: 340
Period size: 106 Copynumber: 1.9 Consensus size: 106
39342023 TATCGTTAAT
* *
39342033 TAAATCAAATTTTATGAAAAATGTATTCGTATTTCGAGTTAATCGGGAAGAAAATTATGCCTCAT
1 TAAATCAAATTTTATGAAAAATGTATTCGTATTTCGAGTTAATCGAGAAGAAAATTATGCCCCAT
39342098 AAGTTAGGACACGATGTCTCGAATCCCCAAAAATAAGAAAC
66 AAGTTAGGACACGATGTCTCGAATCCCCAAAAATAAGAAAC
* * * *
39342139 TAAATCAAATTTTATGAAGAATGTCTTCGTATTTCGAGTTAATCGAGAAGAGAATTATGCCCCGT
1 TAAATCAAATTTTATGAAAAATGTATTCGTATTTCGAGTTAATCGAGAAGAAAATTATGCCCCAT
* *
39342204 AAGTTAGGGCACGATGTCTCGAATCCCGAAAAATA
66 AAGTTAGGACACGATGTCTCGAATCCCCAAAAATA
39342239 GGAATGCTCA
Statistics
Matches: 92, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
106 92 1.00
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.29
Consensus pattern (106 bp):
TAAATCAAATTTTATGAAAAATGTATTCGTATTTCGAGTTAATCGAGAAGAAAATTATGCCCCAT
AAGTTAGGACACGATGTCTCGAATCCCCAAAAATAAGAAAC
Found at i:39348822 original size:33 final size:33
Alignment explanation
Indices: 39348775--39348848 Score: 103
Period size: 33 Copynumber: 2.2 Consensus size: 33
39348765 GATGAACTTT
* *
39348775 AGCCGAAAGTAGTGGAGTACGGCGGTGGATACG
1 AGCCGAGAGGAGTGGAGTACGGCGGTGGATACG
* * *
39348808 GGCCGAGAGGAGTGGAGTACGGTGGTGGATATG
1 AGCCGAGAGGAGTGGAGTACGGCGGTGGATACG
39348841 AGCCGAGA
1 AGCCGAGA
39348849 TGACTGTAGT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.26, C:0.14, G:0.46, T:0.15
Consensus pattern (33 bp):
AGCCGAGAGGAGTGGAGTACGGCGGTGGATACG
Found at i:39348860 original size:33 final size:33
Alignment explanation
Indices: 39348787--39348860 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 33
39348777 CCGAAAGTAG
* *
39348787 TGGAGTACGGCGGTGGATACGGGCCGAGAGGAG
1 TGGAGTACGGCGGTGGATACGAGCCGAGAGGAC
* * *
39348820 TGGAGTACGGTGGTGGATATGAGCCGAGATGAC
1 TGGAGTACGGCGGTGGATACGAGCCGAGAGGAC
*
39348853 TGTAGTAC
1 TGGAGTAC
39348861 CGAAGTGGTA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.23, C:0.14, G:0.45, T:0.19
Consensus pattern (33 bp):
TGGAGTACGGCGGTGGATACGAGCCGAGAGGAC
Found at i:39349814 original size:50 final size:50
Alignment explanation
Indices: 39349737--39349838 Score: 195
Period size: 50 Copynumber: 2.0 Consensus size: 50
39349727 GATGCCAAGA
*
39349737 ATAGCATTCGGTAAAGTGTCCATGACTGCAACAATATGAGGCATTCGCCT
1 ATAGCATTCGGTAAAGTGTCCACGACTGCAACAATATGAGGCATTCGCCT
39349787 ATAGCATTCGGTAAAGTGTCCACGACTGCAACAATATGAGGCATTCGCCT
1 ATAGCATTCGGTAAAGTGTCCACGACTGCAACAATATGAGGCATTCGCCT
39349837 AT
1 AT
39349839 GTCTACTACA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.25
Consensus pattern (50 bp):
ATAGCATTCGGTAAAGTGTCCACGACTGCAACAATATGAGGCATTCGCCT
Found at i:39350635 original size:18 final size:19
Alignment explanation
Indices: 39350609--39350644 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
39350599 AATTTTGAAT
39350609 TTCAGAATAAATAAAAATG
1 TTCAGAATAAATAAAAATG
39350628 TTCA-AATAAATAAAAAT
1 TTCAGAATAAATAAAAAT
39350645 CAAATAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.28
Consensus pattern (19 bp):
TTCAGAATAAATAAAAATG
Found at i:39350649 original size:15 final size:16
Alignment explanation
Indices: 39350609--39350652 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 16
39350599 AATTTTGAAT
39350609 TTCAGAATAAATAAAAA
1 TTCA-AATAAATAAAAA
39350626 TGTTCAAATAAATAAAAA
1 --TTCAAATAAATAAAAA
39350644 -TCAAATAAA
1 TTCAAATAAA
39350653 ATTACATCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.36
18 12 0.48
19 4 0.16
ACGTcount: A:0.64, C:0.07, G:0.05, T:0.25
Consensus pattern (16 bp):
TTCAAATAAATAAAAA
Found at i:39350661 original size:15 final size:16
Alignment explanation
Indices: 39350643--39350675 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
39350633 ATAAATAAAA
39350643 ATCAAAT-AAAATTAC
1 ATCAAATAAAAATTAC
*
39350658 ATCATATAAAAATTAC
1 ATCAAATAAAAATTAC
39350674 AT
1 AT
39350676 TAAAAAATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (16 bp):
ATCAAATAAAAATTAC
Found at i:39350795 original size:103 final size:104
Alignment explanation
Indices: 39350676--39350954 Score: 381
Period size: 103 Copynumber: 2.7 Consensus size: 104
39350666 AAAATTACAT
*
39350676 TAAAAAATCACAAAACACTAAACTAAACACTAACAATTTATATAACCTAATCATAAATTACTAAC
1 TAAAAAATCACAAAACACTAAACTAAACACTAACAATTTATAAAACCTAATCATAAATTACTAAC
39350741 AAAATAACTAT-AAATT-TTTTTAAAAAAAATACATTAC
66 AAAATAACTATAAAATTATTTTTAAAAAAAATACATTAC
* *
39350778 TAAAAAAATCACTAAACACATAAA-TAAACACTAACAATTTATAAAACCTAATCATAAATTAATA
1 T-AAAAAATCACAAAACAC-TAAACTAAACACTAACAATTTATAAAACCTAATCATAAATTACTA
* *
39350842 ACAAAATAACTATAAAATTATTTTTAAAAAAATTATATTAC
64 ACAAAATAACTATAAAATTATTTTTAAAAAAAATACATTAC
* * ** *
39350883 TAAAAAATCACAAAACTCTATACTAAACA-TCAACAA-TT-TGGAACCTAATCCCATAAATCACT
1 TAAAAAATCACAAAACACTAAACTAAACACT-AACAATTTATAAAACCTAAT--CATAAATTACT
39350945 AACAAAATAA
63 AACAAAATAA
39350955 ATAACTATAA
Statistics
Matches: 157, Mismatches: 12, Indels: 14
0.86 0.07 0.08
Matches are distributed among these distances:
102 10 0.06
103 73 0.46
104 54 0.34
105 20 0.13
ACGTcount: A:0.56, C:0.16, G:0.01, T:0.27
Consensus pattern (104 bp):
TAAAAAATCACAAAACACTAAACTAAACACTAACAATTTATAAAACCTAATCATAAATTACTAAC
AAAATAACTATAAAATTATTTTTAAAAAAAATACATTAC
Found at i:39351819 original size:35 final size:36
Alignment explanation
Indices: 39351776--39351847 Score: 128
Period size: 35 Copynumber: 2.0 Consensus size: 36
39351766 ACAATTTATA
*
39351776 ACCTAATCCCATAAATTACTAAC-AAATAAATAACT
1 ACCTAATCCCATAAATCACTAACAAAATAAATAACT
39351811 ACCTAATCCCATAAATCACTAACAAAATAAATAACT
1 ACCTAATCCCATAAATCACTAACAAAATAAATAACT
39351847 A
1 A
39351848 TAACAAAACA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
35 22 0.63
36 13 0.37
ACGTcount: A:0.53, C:0.24, G:0.00, T:0.24
Consensus pattern (36 bp):
ACCTAATCCCATAAATCACTAACAAAATAAATAACT
Found at i:39358967 original size:59 final size:59
Alignment explanation
Indices: 39358869--39358993 Score: 169
Period size: 59 Copynumber: 2.1 Consensus size: 59
39358859 ATATTTAAAT
* * * * *
39358869 ATGCAATAGTCAATCTGCGTTGCATGTTGCAAGTAAAGTGTATTGTCACTTTGTTTGGG
1 ATGCAATAGTCAATCTGCCTTGCATATTGCAAGTAAAGTGGATTGTCACTTTGTTAGGA
* * * *
39358928 ATGCAATAGTTAATTTGCCTTGCATATTGCAATTGAAGTGGATTGTCACTTTGTTAGGA
1 ATGCAATAGTCAATCTGCCTTGCATATTGCAAGTAAAGTGGATTGTCACTTTGTTAGGA
39358987 ATGCAAT
1 ATGCAAT
39358994 TCAGGATGGG
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (59 bp):
ATGCAATAGTCAATCTGCCTTGCATATTGCAAGTAAAGTGGATTGTCACTTTGTTAGGA
Found at i:39359388 original size:31 final size:30
Alignment explanation
Indices: 39359336--39359412 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 30
39359326 CACCCTAACT
* * *
39359336 ATATATATTGT-ATATCTTTTAGGAGTATATT
1 ATATATATT-TCATAT-ATTTAGGAATATATA
*
39359367 ATATATCTTTTCATATATTTAGGAATATATA
1 ATATAT-ATTTCATATATTTAGGAATATATA
39359398 ATATATATTTCATAT
1 ATATATATTTCATAT
39359413 TCATACGTGG
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
30 8 0.21
31 25 0.64
32 6 0.15
ACGTcount: A:0.36, C:0.05, G:0.08, T:0.51
Consensus pattern (30 bp):
ATATATATTTCATATATTTAGGAATATATA
Found at i:39363413 original size:30 final size:30
Alignment explanation
Indices: 39363397--39363936 Score: 1062
Period size: 30 Copynumber: 18.0 Consensus size: 30
39363387 CAATTCCACA
39363397 CCTATATTCATTATTCAATTACACTTAGTC
1 CCTATATTCATTATTCAATTACACTTAGTC
**
39363427 AATATATTCATTATTCAATTACACTTAGTC
1 CCTATATTCATTATTCAATTACACTTAGTC
39363457 CCTATATTCATTATTCAATTACACTTAGTC
1 CCTATATTCATTATTCAATTACACTTAGTC
39363487 CCTATATTCATTATTCAATTACACTTAGTC
1 CCTATATTCATTATTCAATTACACTTAGTC
39363517 CCTATATTCATTATTCAATTACACTTAGTC
1 CCTATATTCATTATTCAATTACACTTAGTC
39363547 CCTATATTCATTATTCAATTACACTTAGTC
1 CCTATATTCATTATTCAATTACACTTAGTC
39363577 CCTATATTCATTATTCAATTACACTTAGTC
1 CCTATATTCATTATTCAATTACACTTAGTC
39363607 CCTATATTCATTATTCAATTACACTTAGTC
1 CCTATATTCATTATTCAATTACACTTAGTC
39363637 CCTATATTCATTATTCAATTACACTTAGTC
1 CCTATATTCATTATTCAATTACACTTAGTC
39363667 CCTATATTCATTATTCAATTACACTTAGTC
1 CCTATATTCATTATTCAATTACACTTAGTC
39363697 CCTATATTCATTATTCAATTACACTTAGTC
1 CCTATATTCATTATTCAATTACACTTAGTC
39363727 CCTATATTCATTATTCAATTACACTTAGTC
1 CCTATATTCATTATTCAATTACACTTAGTC
39363757 CCTATATTCATTATTCAATTACACTTAGTC
1 CCTATATTCATTATTCAATTACACTTAGTC
39363787 CCTATATTCATTATTCAATTACACTTAGTC
1 CCTATATTCATTATTCAATTACACTTAGTC
39363817 CCTATATTCATTATTCAATTACACTTAGTC
1 CCTATATTCATTATTCAATTACACTTAGTC
39363847 CCTATATTCATTATTCAATTACACTTAGTC
1 CCTATATTCATTATTCAATTACACTTAGTC
39363877 CCTATATTCATTATTCAATTACACTTAGTC
1 CCTATATTCATTATTCAATTACACTTAGTC
39363907 CCTATATTCATTATTCAATTACACTTAGTC
1 CCTATATTCATTATTCAATTACACTTAGTC
39363937 AATTTCCCGA
Statistics
Matches: 506, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
30 506 1.00
ACGTcount: A:0.30, C:0.23, G:0.03, T:0.43
Consensus pattern (30 bp):
CCTATATTCATTATTCAATTACACTTAGTC
Found at i:39363420 original size:23 final size:22
Alignment explanation
Indices: 39363377--39363420 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
39363367 TTCTAAGTCG
39363377 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
39363400 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
39363421 TTAGTCAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:39364040 original size:45 final size:45
Alignment explanation
Indices: 39363983--39364068 Score: 145
Period size: 45 Copynumber: 1.9 Consensus size: 45
39363973 CTAGGTGGAT
* *
39363983 TCAGCACGTAGCAACCACCTTATTAATCAATGATGTCCGGTGGGA
1 TCAGCACATAGCAACCACCTTACTAATCAATGATGTCCGGTGGGA
*
39364028 TCAGCACATAGCAACCACCTTACTAATCAATGATGTTCGGT
1 TCAGCACATAGCAACCACCTTACTAATCAATGATGTCCGGT
39364069 TCACATAGCA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.26
Consensus pattern (45 bp):
TCAGCACATAGCAACCACCTTACTAATCAATGATGTCCGGTGGGA
Found at i:39364180 original size:51 final size:51
Alignment explanation
Indices: 39364125--39364302 Score: 245
Period size: 51 Copynumber: 3.5 Consensus size: 51
39364115 CCGATACACC
39364125 TAGTAGCCTGCACATAGTACTACACACGTGATCGAAACTATCTGGTATGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGATCGAAACTATCTGGTATGCA
* ** * * * *
39364176 TAGTAGCCTGCACATAGTACTACACATGTGA-CCTATC-ATTTCG-ATACA
1 TAGTAGCCTGCACATAGTACTACACACGTGATCGAAACTATCTGGTATGCA
*
39364224 CGTAGTAGCCTGCACATAGTACTACACACGTGATCGAAACTATCTGGTACGCA
1 --TAGTAGCCTGCACATAGTACTACACACGTGATCGAAACTATCTGGTATGCA
39364277 TAGTAGCCTGCACATAGTACTACACA
1 TAGTAGCCTGCACATAGTACTACACA
39364303 TGCGACCTAT
Statistics
Matches: 107, Mismatches: 15, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
48 4 0.04
49 4 0.04
50 33 0.31
51 59 0.55
52 4 0.04
53 3 0.03
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.25
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACACGTGATCGAAACTATCTGGTATGCA
Found at i:39364248 original size:101 final size:101
Alignment explanation
Indices: 39364085--39364317 Score: 396
Period size: 101 Copynumber: 2.3 Consensus size: 101
39364075 AGCAGGCTTT
*
39364085 ACATAGTACTACACATGTGACCATTACCA-TCCGATACACCTAGTAGCCTGCACATAGTACTACA
1 ACATAGTACTACACATGTGACC--TATCATTCCGATACACCTAGTAGCCTGCACATAGTACTACA
*
39364149 CACGTGATCGAAACTATCTGGTATGCATAGTAGCCTGC
64 CACGTGATCGAAACTATCTGGTACGCATAGTAGCCTGC
* *
39364187 ACATAGTACTACACATGTGACCTATCATTTCGATACACGTAGTAGCCTGCACATAGTACTACACA
1 ACATAGTACTACACATGTGACCTATCATTCCGATACACCTAGTAGCCTGCACATAGTACTACACA
39364252 CGTGATCGAAACTATCTGGTACGCATAGTAGCCTGC
66 CGTGATCGAAACTATCTGGTACGCATAGTAGCCTGC
*
39364288 ACATAGTACTACACATGCGACCTATCATTC
1 ACATAGTACTACACATGTGACCTATCATTC
39364318 NNNNNNNNNN
Statistics
Matches: 124, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
100 4 0.03
101 98 0.79
102 22 0.18
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.25
Consensus pattern (101 bp):
ACATAGTACTACACATGTGACCTATCATTCCGATACACCTAGTAGCCTGCACATAGTACTACACA
CGTGATCGAAACTATCTGGTACGCATAGTAGCCTGC
Found at i:39364795 original size:2 final size:2
Alignment explanation
Indices: 39364790--39364819 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
39364780 ATATGAAAAA
*
39364790 AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39364820 GTGATAGCCG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:39365014 original size:41 final size:41
Alignment explanation
Indices: 39364928--39365025 Score: 137
Period size: 41 Copynumber: 2.4 Consensus size: 41
39364918 CTATCTGATT
* *
39364928 AGCACTAAGTGTGCG-AACTAAATGATGAGGTTGAATATCG
1 AGCACTAAGTGTGCGAAACTAAATAATGAGGTTAAATATCG
*
39364968 AGCACTAAGTGTGCGAAACTAAATAATGATGTTAAATGA-CG
1 AGCACTAAGTGTGCGAAACTAAATAATGAGGTTAAAT-ATCG
*
39365009 GGCACTAAGTGTGCGAA
1 AGCACTAAGTGTGCGAA
39365026 GCTGAGATCA
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
40 15 0.29
41 36 0.69
42 1 0.02
ACGTcount: A:0.37, C:0.13, G:0.27, T:0.23
Consensus pattern (41 bp):
AGCACTAAGTGTGCGAAACTAAATAATGAGGTTAAATATCG
Found at i:39366753 original size:46 final size:46
Alignment explanation
Indices: 39366686--39366780 Score: 163
Period size: 46 Copynumber: 2.1 Consensus size: 46
39366676 GTTATAACCG
* *
39366686 GTAATGCCCCGTAATCCTATTTCGGCGACGATTATGGGTTACGGGT
1 GTAATGCCCCGTAACCCTATTTCGGCGACGATTACGGGTTACGGGT
*
39366732 GTAATGCCCCGTAACCCTATTTCGGCGACGATTACGGGTTAGGGGT
1 GTAATGCCCCGTAACCCTATTTCGGCGACGATTACGGGTTACGGGT
39366778 GTA
1 GTA
39366781 CAATTTAATG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.28
Consensus pattern (46 bp):
GTAATGCCCCGTAACCCTATTTCGGCGACGATTACGGGTTACGGGT
Found at i:39375265 original size:34 final size:38
Alignment explanation
Indices: 39375203--39375272 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 38
39375193 TTAATTCTTT
39375203 TTCTTTTATTTTCTTTTAACTTTCCCTTTTCTTTTTTG
1 TTCTTTTATTTTCTTTTAACTTTCCCTTTTCTTTTTTG
*
39375241 TTCTTTTA-TTTC-TTT-AGTTT-CCTTTTCTTTTT
1 TTCTTTTATTTTCTTTTAACTTTCCCTTTTCTTTTT
39375273 GTTTTCTTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
34 12 0.39
35 4 0.13
36 3 0.10
37 4 0.13
38 8 0.26
ACGTcount: A:0.07, C:0.17, G:0.03, T:0.73
Consensus pattern (38 bp):
TTCTTTTATTTTCTTTTAACTTTCCCTTTTCTTTTTTG
Found at i:39376228 original size:30 final size:29
Alignment explanation
Indices: 39376168--39376228 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 29
39376158 CAATTGAACC
*
39376168 AAAAATTTAAATTACAAAAAAGAAAGTTT
1 AAAAATTTAAAATACAAAAAAGAAAGTTT
* *
39376197 AAAAATTTTAAAATATAAATAA-AAAGATTT
1 AAAAA-TTTAAAATACAAAAAAGAAAG-TTT
39376227 AA
1 AA
39376229 TTGTAAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 9 0.33
30 18 0.67
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.30
Consensus pattern (29 bp):
AAAAATTTAAAATACAAAAAAGAAAGTTT
Found at i:39381096 original size:18 final size:19
Alignment explanation
Indices: 39381073--39381118 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
39381063 TATAATTTTA
*
39381073 AAAAATATAT-AATACATC
1 AAAAATATATAAAAACATC
39381091 AAAAATAT-TAAAAACATC
1 AAAAATATATAAAAACATC
*
39381109 AAAAAAATAT
1 AAAAATATAT
39381119 TTCCCAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 1 0.04
18 22 0.92
19 1 0.04
ACGTcount: A:0.67, C:0.09, G:0.00, T:0.24
Consensus pattern (19 bp):
AAAAATATATAAAAACATC
Found at i:39381237 original size:30 final size:30
Alignment explanation
Indices: 39381194--39381255 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
39381184 CTTAACAAGA
39381194 AAATGCCTCTAAAATAATAACAAAATTAAC
1 AAATGCCTCTAAAATAATAACAAAATTAAC
* *
39381224 AAATGTCTTTAAAATAATAACAAAATTAAC
1 AAATGCCTCTAAAATAATAACAAAATTAAC
39381254 AA
1 AA
39381256 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.58, C:0.13, G:0.03, T:0.26
Consensus pattern (30 bp):
AAATGCCTCTAAAATAATAACAAAATTAAC
Found at i:39381823 original size:18 final size:18
Alignment explanation
Indices: 39381789--39381823 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
39381779 GACATAGTTT
*
39381789 AAAATGAAAATTTTAAAG
1 AAAATGAAAATTGTAAAG
*
39381807 AAAATGAATATTGTAAA
1 AAAATGAAAATTGTAAA
39381824 AATGGATGTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.11, T:0.29
Consensus pattern (18 bp):
AAAATGAAAATTGTAAAG
Found at i:39388000 original size:28 final size:28
Alignment explanation
Indices: 39387960--39388064 Score: 133
Period size: 28 Copynumber: 3.8 Consensus size: 28
39387950 AACATGCCAA
39387960 AAAAAGGAAGCCTTTATGGCAATCTAAG
1 AAAAAGGAAGCCTTTATGGCAATCTAAG
*
39387988 AAAAAGGAAGCCTTTGTGGCAATCTAAG
1 AAAAAGGAAGCCTTTATGGCAATCTAAG
* ** *
39388016 -AAATGGAAGCCTTCGTGGCGATCTAA-
1 AAAAAGGAAGCCTTTATGGCAATCTAAG
*
39388042 AAAAATGGAAACCTTTATGGCAA
1 AAAAA-GGAAGCCTTTATGGCAA
39388065 ATCTTGTAAA
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
27 26 0.39
28 40 0.61
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.22
Consensus pattern (28 bp):
AAAAAGGAAGCCTTTATGGCAATCTAAG
Found at i:39392501 original size:23 final size:23
Alignment explanation
Indices: 39392458--39392503 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
39392448 AATATTCGGT
* *
39392458 ATATGTATTTGATAAGTATATAC
1 ATATGCATTTGATAAGAATATAC
39392481 ATATGCATTTGA-AATGAATATAC
1 ATATGCATTTGATAA-GAATATAC
39392504 CTCTGTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.41, C:0.07, G:0.13, T:0.39
Consensus pattern (23 bp):
ATATGCATTTGATAAGAATATAC
Found at i:39405463 original size:24 final size:22
Alignment explanation
Indices: 39405436--39405498 Score: 56
Period size: 24 Copynumber: 2.6 Consensus size: 22
39405426 CCCTTTAGAT
*
39405436 TTAGTCTTTACTTTTTCTTTTTTC
1 TTAGT-TTTACTTTTT-TTTGTTC
39405460 TTAGGTTTTACATTTTTTTTGTTC
1 TTA-GTTTTAC-TTTTTTTTGTTC
39405484 TT-GTTATTTACTTTT
1 TTAG-T-TTTACTTTT
39405499 ATGGAGAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
22 1 0.03
23 5 0.15
24 21 0.62
25 7 0.21
ACGTcount: A:0.11, C:0.11, G:0.08, T:0.70
Consensus pattern (22 bp):
TTAGTTTTACTTTTTTTTGTTC
Found at i:39431205 original size:21 final size:22
Alignment explanation
Indices: 39431162--39431207 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
39431152 AAATATTCGT
*
39431162 TAAAAAAAGAATAAATATGTACA
1 TAAAAAAACAATAAATA-GTACA
39431185 TAAAAAAACAATAAATA-TACA
1 TAAAAAAACAATAAATAGTACA
39431206 TA
1 TA
39431208 TATATATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 6 0.27
23 16 0.73
ACGTcount: A:0.67, C:0.07, G:0.04, T:0.22
Consensus pattern (22 bp):
TAAAAAAACAATAAATAGTACA
Found at i:39431230 original size:19 final size:20
Alignment explanation
Indices: 39431208--39431245 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
39431198 AATATACATA
*
39431208 TATATATAAAATA-ATTATG
1 TATATAAAAAATACATTATG
39431227 TATATAAAAAATACATTAT
1 TATATAAAAAATACATTAT
39431246 TTAATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (20 bp):
TATATAAAAAATACATTATG
Found at i:39432990 original size:45 final size:44
Alignment explanation
Indices: 39432939--39433063 Score: 178
Period size: 45 Copynumber: 2.8 Consensus size: 44
39432929 TTGTTTATTT
* * *
39432939 AGTCTGCCCCACTGCAATTTCATGGGGATAAGACTTGCTTTCTTG
1 AGTCTGCTCCACTGCAACTTCA-GGGGATAAGACTCGCTTTCTTG
*
39432984 AGTCTGCTCCACTGCAACTTCAGAGAGATAAGACTCGCTTTCTTG
1 AGTCTGCTCCACTGCAACTTCAG-GGGATAAGACTCGCTTTCTTG
*
39433029 GGTCTGCTCCACTGCAACTTCAGGGAGATAAGACT
1 AGTCTGCTCCACTGCAACTTCAGGG-GATAAGACT
39433064 AAATATGATA
Statistics
Matches: 72, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
44 2 0.03
45 70 0.97
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.29
Consensus pattern (44 bp):
AGTCTGCTCCACTGCAACTTCAGGGGATAAGACTCGCTTTCTTG
Found at i:39433131 original size:44 final size:44
Alignment explanation
Indices: 39433074--39433983 Score: 1718
Period size: 44 Copynumber: 20.7 Consensus size: 44
39433064 AAATATGATA
* * * *
39433074 TGCTCT-CTGCAACTTCAGAGAGATAAGATCT-GTGATTTTAATC
1 TGCTCTACTGCAACTTCAGGGAGATAGGAT-TATTGACTTTAATC
*
39433117 CGCTCCT-CTGCAACTTCAGGGAGATAGGATTATTGACTTTAATC
1 TGCT-CTACTGCAACTTCAGGGAGATAGGATTATTGACTTTAATC
39433161 TGCTCTACTGCAACTTCAGGGAGATAGGATTATTGACTTTAATC
1 TGCTCTACTGCAACTTCAGGGAGATAGGATTATTGACTTTAATC
39433205 TGCTCTACTGCAACTTCAGGGAGATAGGATTATTGACTTTAATC
1 TGCTCTACTGCAACTTCAGGGAGATAGGATTATTGACTTTAATC
39433249 TGCTCTACTGCAACTTCAGGGAGATAGGATTATTGACTTTAATC
1 TGCTCTACTGCAACTTCAGGGAGATAGGATTATTGACTTTAATC
39433293 TGCTCTACTGCAACTTCAGGGAGATAGGATTATTGACTTTAATC
1 TGCTCTACTGCAACTTCAGGGAGATAGGATTATTGACTTTAATC
39433337 TGCTCTACTGCAACTTCAGGGAGATAGGATTATTGACTTTAATC
1 TGCTCTACTGCAACTTCAGGGAGATAGGATTATTGACTTTAATC
39433381 TGCTCTACTGCAACTTCAGGGAGATAGGATTATTGACTTTAATC
1 TGCTCTACTGCAACTTCAGGGAGATAGGATTATTGACTTTAATC
39433425 TGCTCTACTGCAACTTCAGGGAGATAGGATTATTGACTTTAATC
1 TGCTCTACTGCAACTTCAGGGAGATAGGATTATTGACTTTAATC
39433469 TGCTCTACTGCAACTTCAGGGAGATAGGATTATTGACTTTAATC
1 TGCTCTACTGCAACTTCAGGGAGATAGGATTATTGACTTTAATC
39433513 TGCTCTACTGCAACTTCAGGGAGATAGGATTATTGACTTTAATC
1 TGCTCTACTGCAACTTCAGGGAGATAGGATTATTGACTTTAATC
39433557 TGCTCTACTGCAACTTCAGGGAGATAGGATTATTGACTTTAATC
1 TGCTCTACTGCAACTTCAGGGAGATAGGATTATTGACTTTAATC
39433601 TGCTCTACTGCAACTTCAGGGAGATAGGATTATTGACTTTAATC
1 TGCTCTACTGCAACTTCAGGGAGATAGGATTATTGACTTTAATC
39433645 TGCTCTACTGCAACTTCAGGGAGATAGGATTATTGACTTTAATC
1 TGCTCTACTGCAACTTCAGGGAGATAGGATTATTGACTTTAATC
39433689 TGCTCTACTGCAACTTCAGGGAGATAGGATTATTGACTTTAATC
1 TGCTCTACTGCAACTTCAGGGAGATAGGATTATTGACTTTAATC
39433733 TGCTCTACTGCAACTTCAGGGAGATAGGATTATTGACTTTAATC
1 TGCTCTACTGCAACTTCAGGGAGATAGGATTATTGACTTTAATC
39433777 TGCTCTACTGCAACTTCAGGGAGATAGGATTATTGACTTTAATC
1 TGCTCTACTGCAACTTCAGGGAGATAGGATTATTGACTTTAATC
39433821 TGCTCTACTGCAACTTCAGGGAGATAGGATTATTGACTTTAATC
1 TGCTCTACTGCAACTTCAGGGAGATAGGATTATTGACTTTAATC
39433865 TGCTCTACTGCAACTTCAGGGAGATAGGATTATTGACTTTAATC
1 TGCTCTACTGCAACTTCAGGGAGATAGGATTATTGACTTTAATC
39433909 TGCTCTACTGCAACTTCAGGGAGATAGGATTATTGACTTTAATC
1 TGCTCTACTGCAACTTCAGGGAGATAGGATTATTGACTTTAATC
* *
39433953 TGCTCCACTGCAACTTCAGGGAGATAAGATT
1 TGCTCTACTGCAACTTCAGGGAGATAGGATT
39433984 TGCCATTTTC
Statistics
Matches: 856, Mismatches: 8, Indels: 5
0.99 0.01 0.01
Matches are distributed among these distances:
43 6 0.01
44 850 0.99
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (44 bp):
TGCTCTACTGCAACTTCAGGGAGATAGGATTATTGACTTTAATC
Found at i:39434156 original size:50 final size:50
Alignment explanation
Indices: 39434020--39434183 Score: 150
Period size: 50 Copynumber: 3.3 Consensus size: 50
39434010 ATAGTTGCCA
* *
39434020 TCGTAGCTTCAATCTGTTCCACTACACCGCCA-GGAAAGTAAGATTCGCCG
1 TCGTAGCTTCAATCTGTTCAACTACACCGCCAGGGAAA-CAAGATTCGCCG
* ** * * * * * ** ***
39434070 TTGCGGCTTTAATCTTTTTAATTGCAATGTTGGGGAAACAAGATTCGCCG
1 TCGTAGCTTCAATCTGTTCAACTACACCGCCAGGGAAACAAGATTCGCCG
*
39434120 TCGTAGCTTCAATCTGTTCAACTACACCGCCAGGGAAACAAGATTCGCGG
1 TCGTAGCTTCAATCTGTTCAACTACACCGCCAGGGAAACAAGATTCGCCG
* *
39434170 TTGTGGCTTCAATC
1 TCGTAGCTTCAATC
39434184 CATTCCACTA
Statistics
Matches: 82, Mismatches: 31, Indels: 2
0.71 0.27 0.02
Matches are distributed among these distances:
50 77 0.94
51 5 0.06
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (50 bp):
TCGTAGCTTCAATCTGTTCAACTACACCGCCAGGGAAACAAGATTCGCCG
Found at i:39434379 original size:50 final size:49
Alignment explanation
Indices: 39434274--39434379 Score: 113
Period size: 50 Copynumber: 2.1 Consensus size: 49
39434264 TGCCAGGGAG
* * * *
39434274 ATAAGATTCGCCGTCGTGGCTTCAATCTGCTCCGCTACAATGCCAGGGA
1 ATAAGATTCGCCATCGTGGCTTCAATCTGCTCCACTACAATGCAAGGCA
* ** * *
39434323 AGTAAGATTCGCTATCGTGGCTTCAATCTTTTCCATTGCAATGTCAAGGCA
1 A-TAAGATTCGCCATCGTGGCTTCAATCTGCTCCACTACAATG-CAAGGCA
39434374 ATAAGA
1 ATAAGA
39434380 CTAATGTCTT
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
49 1 0.02
50 39 0.85
51 6 0.13
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (49 bp):
ATAAGATTCGCCATCGTGGCTTCAATCTGCTCCACTACAATGCAAGGCA
Found at i:39446905 original size:21 final size:22
Alignment explanation
Indices: 39446865--39446906 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
39446855 AATATTCGTT
*
39446865 AAAAAGAATAAATATGTACATGA
1 AAAAACAATAAATA-GTACATGA
39446888 AAAAACAATAAATA-TACAT
1 AAAAACAATAAATAGTACAT
39446907 ATATATGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
23 13 0.72
ACGTcount: A:0.64, C:0.07, G:0.07, T:0.21
Consensus pattern (22 bp):
AAAAACAATAAATAGTACATGA
Found at i:39448303 original size:11 final size:11
Alignment explanation
Indices: 39448289--39448328 Score: 50
Period size: 10 Copynumber: 3.8 Consensus size: 11
39448279 ATTTAGGTAT
39448289 TACAAAAATCA
1 TACAAAAATCA
39448300 TAC-AAAATCA
1 TACAAAAATCA
39448310 TA-AAAAAGT-A
1 TACAAAAA-TCA
39448320 TACAAAAAT
1 TACAAAAAT
39448329 ATTTAAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
10 17 0.65
11 9 0.35
ACGTcount: A:0.65, C:0.12, G:0.03, T:0.20
Consensus pattern (11 bp):
TACAAAAATCA
Found at i:39448433 original size:15 final size:16
Alignment explanation
Indices: 39448413--39448447 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
39448403 AATATTTTAA
39448413 AAATA-TATAAATTAC
1 AAATACTATAAATTAC
39448428 AAATATCTATAAATTAC
1 AAATA-CTATAAATTAC
39448445 AAA
1 AAA
39448448 AGCTAAAGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.28
17 13 0.72
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.31
Consensus pattern (16 bp):
AAATACTATAAATTAC
Found at i:39448607 original size:12 final size:12
Alignment explanation
Indices: 39448590--39448622 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
39448580 GGGGTTTAAA
39448590 TAAAAAATTATT
1 TAAAAAATTATT
39448602 T-AAAAATTATT
1 TAAAAAATTATT
*
39448613 AAAAAAATTA
1 TAAAAAATTA
39448623 CAAAATATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
TAAAAAATTATT
Found at i:39448656 original size:36 final size:35
Alignment explanation
Indices: 39448616--39448684 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 35
39448606 AATTATTAAA
39448616 AAAATTACAAAAT-ATTATAAAATATTATAAAAACAT
1 AAAATTACAAAATAATTA-AAAATA-TATAAAAACAT
39448652 AAAATTACAAAATAGATTAAAAATATATAAAAA
1 AAAATTACAAAATA-ATTAAAAATATATAAAAA
39448685 AAATTATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
36 21 0.68
37 6 0.19
38 4 0.13
ACGTcount: A:0.67, C:0.04, G:0.01, T:0.28
Consensus pattern (35 bp):
AAAATTACAAAATAATTAAAAATATATAAAAACAT
Found at i:39448657 original size:48 final size:48
Alignment explanation
Indices: 39448604--39448697 Score: 120
Period size: 48 Copynumber: 2.0 Consensus size: 48
39448594 AAATTATTTA
* * *
39448604 AAAATTATTAAAA-AAATTACAAAATAT-TATAAAATATTATAAAAACAT
1 AAAATTA-CAAAATAAATTA-AAAATATATAAAAAAAATTATAAAAACAT
*
39448652 AAAATTACAAAATAGATTAAAAATATATAAAAAAAATTATAAAAAC
1 AAAATTACAAAATAAATTAAAAATATATAAAAAAAATTATAAAAAC
39448698 CATTTTTTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
47 11 0.28
48 29 0.73
ACGTcount: A:0.67, C:0.04, G:0.01, T:0.28
Consensus pattern (48 bp):
AAAATTACAAAATAAATTAAAAATATATAAAAAAAATTATAAAAACAT
Found at i:39448684 original size:11 final size:11
Alignment explanation
Indices: 39448589--39448696 Score: 53
Period size: 12 Copynumber: 9.6 Consensus size: 11
39448579 TGGGGTTTAA
39448589 ATAAAAAATTAT
1 ATAAAAAA-TAT
* *
39448601 TTAAAAATTAT
1 ATAAAAAATAT
39448612 -TAAAAAA-AT
1 ATAAAAAATAT
*
39448621 -TACAAAATAT
1 ATAAAAAATAT
*
39448631 -TATAAAATATT
1 ATAAAAAATA-T
*
39448642 ATAAAAACATAAA
1 ATAAAAA-AT-AT
* *
39448655 ATTACAAAATAG
1 A-TAAAAAATAT
*
39448667 ATTAAAAATAT
1 ATAAAAAATAT
*
39448678 ATAAAAAAAATT
1 ATAAAAAATA-T
39448690 ATAAAAA
1 ATAAAAA
39448697 CCATTTTTTA
Statistics
Matches: 75, Mismatches: 14, Indels: 14
0.73 0.14 0.14
Matches are distributed among these distances:
9 8 0.11
10 16 0.21
11 19 0.25
12 21 0.28
13 5 0.07
14 6 0.08
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.30
Consensus pattern (11 bp):
ATAAAAAATAT
Found at i:39448696 original size:10 final size:10
Alignment explanation
Indices: 39448589--39448648 Score: 57
Period size: 10 Copynumber: 5.7 Consensus size: 10
39448579 TGGGGTTTAA
39448589 ATAAAAAATT
1 ATAAAAAATT
*
39448599 ATTTAAAAATT
1 A-TAAAAAATT
39448610 ATTAAAAAAATT
1 A-T-AAAAAATT
* *
39448622 ACAAAATATT
1 ATAAAAAATT
*
39448632 ATAAAATATT
1 ATAAAAAATT
39448642 ATAAAAA
1 ATAAAAA
39448649 CATAAAATTA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
10 23 0.55
11 11 0.26
12 8 0.19
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (10 bp):
ATAAAAAATT
Found at i:39450449 original size:20 final size:20
Alignment explanation
Indices: 39450412--39450452 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
39450402 GTTTCCATTG
* *
39450412 ATGTTAATTGAAGTTTTTGA
1 ATGTTAATGGAAGATTTTGA
*
39450432 ATGTTAATGGTAGATTTTGA
1 ATGTTAATGGAAGATTTTGA
39450452 A
1 A
39450453 GCTTAGAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.22, T:0.46
Consensus pattern (20 bp):
ATGTTAATGGAAGATTTTGA
Found at i:39457032 original size:35 final size:34
Alignment explanation
Indices: 39456986--39457094 Score: 112
Period size: 34 Copynumber: 3.2 Consensus size: 34
39456976 GAGCCCAGCT
* *
39456986 CTAGTTGGATAAACCAACGATATTTGCG-CCAAACA
1 CTAGTTCGATAAACCAACGA-ATGTGCGTCC-AACA
* * *
39457021 CTAGTTCGATAAACCAACGAATGTGTGTTCAGCA
1 CTAGTTCGATAAACCAACGAATGTGCGTCCAACA
* * * *
39457055 CTAGTTCGATAAACCCACGAATGTGTGTTCAGCA
1 CTAGTTCGATAAACCAACGAATGTGCGTCCAACA
39457089 CTAGTT
1 CTAGTT
39457095 AGAGAAACTG
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
34 47 0.70
35 20 0.30
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (34 bp):
CTAGTTCGATAAACCAACGAATGTGCGTCCAACA
Found at i:39457109 original size:34 final size:34
Alignment explanation
Indices: 39457019--39457094 Score: 143
Period size: 34 Copynumber: 2.2 Consensus size: 34
39457009 TTGCGCCAAA
39457019 CACTAGTTCGATAAACCAACGAATGTGTGTTCAG
1 CACTAGTTCGATAAACCAACGAATGTGTGTTCAG
*
39457053 CACTAGTTCGATAAACCCACGAATGTGTGTTCAG
1 CACTAGTTCGATAAACCAACGAATGTGTGTTCAG
39457087 CACTAGTT
1 CACTAGTT
39457095 AGAGAAACTG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (34 bp):
CACTAGTTCGATAAACCAACGAATGTGTGTTCAG
Found at i:39460099 original size:26 final size:26
Alignment explanation
Indices: 39460064--39460185 Score: 129
Period size: 26 Copynumber: 4.7 Consensus size: 26
39460054 AAACACCAGA
* * * *
39460064 AAATAGAAGCCTTTATGGCATATTTA
1 AAATGGAAGCCTTTGTGGCATATCTG
*
39460090 AAATGGAAG-CTTCTGTAGCATATCTG
1 AAATGGAAGCCTT-TGTGGCATATCTG
* * * *
39460116 ACATGGAAACCTTTGTGGCGTATTTG
1 AAATGGAAGCCTTTGTGGCATATCTG
* *
39460142 AAATGGAAACCTTTGTGGCGTATCTG
1 AAATGGAAGCCTTTGTGGCATATCTG
39460168 AAATGGAAGCCTTTGTGG
1 AAATGGAAGCCTTTGTGG
39460186 TGTATATGAA
Statistics
Matches: 81, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
25 3 0.04
26 75 0.93
27 3 0.04
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.32
Consensus pattern (26 bp):
AAATGGAAGCCTTTGTGGCATATCTG
Found at i:39460166 original size:52 final size:52
Alignment explanation
Indices: 39460064--39460196 Score: 142
Period size: 52 Copynumber: 2.6 Consensus size: 52
39460054 AAACACCAGA
* * * * * *
39460064 AAATAGAAGCCTTTATGGCATATTTAAAATGGAAGCTTCTGTAGCATATCTG
1 AAATGGAAACCTTTGTGGCGTATTTGAAATGGAACCTTCTGTAGCATATCTG
* * *
39460116 ACATGGAAACCTTTGTGGCGTATTTGAAATGGAAACCTT-TGTGGCGTATCTG
1 AAATGGAAACCTTTGTGGCGTATTTGAAATGG-AACCTTCTGTAGCATATCTG
* * *
39460168 AAATGGAAGCCTTTGTGGTGTATATGAAA
1 AAATGGAAACCTTTGTGGCGTATTTGAAA
39460197 AATGGCCCTT
Statistics
Matches: 67, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
52 62 0.93
53 5 0.07
ACGTcount: A:0.31, C:0.13, G:0.24, T:0.32
Consensus pattern (52 bp):
AAATGGAAACCTTTGTGGCGTATTTGAAATGGAACCTTCTGTAGCATATCTG
Found at i:39460190 original size:26 final size:26
Alignment explanation
Indices: 39460110--39460196 Score: 129
Period size: 26 Copynumber: 3.3 Consensus size: 26
39460100 TTCTGTAGCA
*
39460110 TATCTGACATGGAAACCTTTGTGGCG
1 TATCTGAAATGGAAACCTTTGTGGCG
*
39460136 TATTTGAAATGGAAACCTTTGTGGCG
1 TATCTGAAATGGAAACCTTTGTGGCG
* *
39460162 TATCTGAAATGGAAGCCTTTGTGGTG
1 TATCTGAAATGGAAACCTTTGTGGCG
*
39460188 TATATGAAA
1 TATCTGAAA
39460197 AATGGCCCTT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 55 1.00
ACGTcount: A:0.28, C:0.13, G:0.26, T:0.33
Consensus pattern (26 bp):
TATCTGAAATGGAAACCTTTGTGGCG
Found at i:39463853 original size:7 final size:7
Alignment explanation
Indices: 39463843--39463901 Score: 118
Period size: 7 Copynumber: 8.4 Consensus size: 7
39463833 TTAAAGGTTA
39463843 AAAGAAG
1 AAAGAAG
39463850 AAAGAAG
1 AAAGAAG
39463857 AAAGAAG
1 AAAGAAG
39463864 AAAGAAG
1 AAAGAAG
39463871 AAAGAAG
1 AAAGAAG
39463878 AAAGAAG
1 AAAGAAG
39463885 AAAGAAG
1 AAAGAAG
39463892 AAAGAAG
1 AAAGAAG
39463899 AAA
1 AAA
39463902 AGATTTACCT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 52 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (7 bp):
AAAGAAG
Found at i:39465599 original size:51 final size:50
Alignment explanation
Indices: 39465510--39465636 Score: 141
Period size: 51 Copynumber: 2.5 Consensus size: 50
39465500 TGATGGTCAC
* * * *
39465510 GTGTAGTACTATGTAG-AGGCTACTATGCGTACCGGATAGCT-TCGATCACGT
1 GTGTAGTACTATGT-GCAGGCTACTACGCGCACCAGATAG-TAT-GATCACAT
* * *
39465561 GTGTAGTACTATGTGCAGGCTACTACGTGCATCAGATAGTGATGGTCACAT
1 GTGTAGTACTATGTGCAGGCTACTACGCGCACCAGATAGT-ATGATCACAT
39465612 GTGTAGTACTATGTGCAGGCTACTA
1 GTGTAGTACTATGTGCAGGCTACTA
39465637 TGTGAACTGG
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
50 2 0.03
51 63 0.95
52 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (50 bp):
GTGTAGTACTATGTGCAGGCTACTACGCGCACCAGATAGTATGATCACAT
Found at i:39472385 original size:21 final size:22
Alignment explanation
Indices: 39472359--39472415 Score: 82
Period size: 21 Copynumber: 2.7 Consensus size: 22
39472349 AACAGTGGTG
*
39472359 GTGGTGAGATTAG-TTACTGTA
1 GTGGTGAGATTAGAATACTGTA
39472380 GTGGTGAGATT-GAATACTGTA
1 GTGGTGAGATTAGAATACTGTA
*
39472401 GCGGTGAGATTAGAA
1 GTGGTGAGATTAGAA
39472416 ATAGCGGTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
20 1 0.03
21 28 0.88
22 3 0.09
ACGTcount: A:0.28, C:0.05, G:0.35, T:0.32
Consensus pattern (22 bp):
GTGGTGAGATTAGAATACTGTA
Found at i:39472533 original size:33 final size:34
Alignment explanation
Indices: 39472466--39472533 Score: 93
Period size: 33 Copynumber: 2.0 Consensus size: 34
39472456 CGTTAGATTT
* *
39472466 AAATATTTTTAACTTATATTAATAATAAATAATA
1 AAATATATTTAAATTATATTAATAATAAATAATA
* *
39472500 AAATATATTTAAATTAT-TTTATATTAAATAATA
1 AAATATATTTAAATTATATTAATAATAAATAATA
39472533 A
1 A
39472534 TTAAACTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
33 15 0.50
34 15 0.50
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (34 bp):
AAATATATTTAAATTATATTAATAATAAATAATA
Found at i:39479724 original size:2 final size:2
Alignment explanation
Indices: 39479717--39479742 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
39479707 TGACTACTCA
39479717 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
39479743 GCGGGGTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39480980 original size:17 final size:18
Alignment explanation
Indices: 39480955--39480992 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
39480945 GTTTTATTGA
*
39480955 TTTCATTGTTTGTTTATT
1 TTTCATTGTTTATTTATT
39480973 TTTC-TTGTTTATTTATT
1 TTTCATTGTTTATTTATT
39480990 TTT
1 TTT
39480993 GTTCTTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.11, C:0.05, G:0.08, T:0.76
Consensus pattern (18 bp):
TTTCATTGTTTATTTATT
Found at i:39481000 original size:17 final size:17
Alignment explanation
Indices: 39480967--39481000 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
39480957 TCATTGTTTG
*
39480967 TTTATTTTTCTTGTTTA
1 TTTATTTTTCTTCTTTA
*
39480984 TTTATTTTTGTTCTTTA
1 TTTATTTTTCTTCTTTA
39481001 ATTTCTCTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.12, C:0.06, G:0.06, T:0.76
Consensus pattern (17 bp):
TTTATTTTTCTTCTTTA
Found at i:39481411 original size:19 final size:19
Alignment explanation
Indices: 39481387--39481423 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
39481377 TTTATTTTTA
*
39481387 TTTTTATTTTTTTAATTTC
1 TTTTTAATTTTTTAATTTC
39481406 TTTTTAATTTTTTAATTT
1 TTTTTAATTTTTTAATTT
39481424 GTTTATGACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTTAATTTTTTAATTTC
Found at i:39483868 original size:15 final size:15
Alignment explanation
Indices: 39483838--39483874 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
39483828 AATATTGGAC
*
39483838 TTTTAT-TATATTTA
1 TTTTATATATATATA
39483852 TTTTATATATATATA
1 TTTTATATATATATA
39483867 TTTTATAT
1 TTTTATAT
39483875 TTGGGTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 6 0.29
15 15 0.71
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTTATATATATATA
Found at i:39484210 original size:50 final size:50
Alignment explanation
Indices: 39484138--39484291 Score: 159
Period size: 50 Copynumber: 3.1 Consensus size: 50
39484128 TGTAATGTCG
*
39484138 GGGAAGCAAGATTTGCCATTGTAGCTTTAATTTGTTCCACTGCATTATCT
1 GGGAAGCAAGATTCGCCATTGTAGCTTTAATTTGTTCCACTGCATTATCT
* * ** * * * *
39484188 GGGAAGTAATATTCGCTGTTGTAGCTTTAATCTTCTT-GACTGCAATGT-T
1 GGGAAGCAAGATTCGCCATTGTAGCTTTAAT-TTGTTCCACTGCATTATCT
* * * *
39484237 GGGGAAGCAAGATTCGCCATTGTGGCTTTAATCTGCTCCACTACATTATCT
1 -GGGAAGCAAGATTCGCCATTGTAGCTTTAATTTGTTCCACTGCATTATCT
39484288 GGGA
1 GGGA
39484292 GATAAGGTCT
Statistics
Matches: 79, Mismatches: 21, Indels: 8
0.73 0.19 0.07
Matches are distributed among these distances:
49 3 0.04
50 71 0.90
51 5 0.06
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (50 bp):
GGGAAGCAAGATTCGCCATTGTAGCTTTAATTTGTTCCACTGCATTATCT
Found at i:39484634 original size:175 final size:174
Alignment explanation
Indices: 39484288--39484826 Score: 837
Period size: 175 Copynumber: 3.1 Consensus size: 174
39484278 TACATTATCT
* * * *
39484288 GGGAGATAAGGTCTGAAATTATTCGGTCTATTCCACTGTAATCTCAGGGAGATAATACCTGATAC
1 GGGAGATAAGATCTGAAATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGC
* **
39484353 GATCTGCTCTACTGTAACTTCAGAGA-TAAGATCCTTTATTTTAATCCACTCCACTGTAATCTCA
66 GATCTACTCTACTGTAACTTCAGAGAGTAAGATCCTTTATTTTAATCCGTTCCACTGTAATCTCA
* *
39484417 GGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCA
131 GGGAAATAGGATTACTGGCTTCAATCTGCTCCGCTGTAATCTCA
* *
39484461 GGGAGATAAGATCTAAAATTCTTCGGTCTATTCCACTGTAATCTTAGGGAGATAAGACCTGATGC
1 GGGAGATAAGATCTGAAATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGC
*
39484526 GATCTACTCTACTGTAACTTCAGAGAGGTAATATCCTTTATTTTAATCCGTTCCACTGTAATCTC
66 GATCTACTCTACTGTAACTTCAGAGA-GTAAGATCCTTTATTTTAATCCGTTCCACTGTAATCTC
* *
39484591 AGGGAAATAGGATTAGTGGCTTCAATCTGCTCTGCTGTAATCTCA
130 AGGGAAATAGGATTACTGGCTTCAATCTGCTCCGCTGTAATCTCA
* * *
39484636 AGGAGATAGGATCTGTAATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGC
1 GGGAGATAAGATCTGAAATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGC
* *
39484701 GATCTACTCTACTGTAACTTCAGAGAGATAAGATCTTTTATTTTAATCCGTTCCACTGTAATCTT
66 GATCTACTCTACTGTAACTTCAGAGAG-TAAGATCCTTTATTTTAATCCGTTCCACTGTAATCTC
* ** *
39484766 AGGGAAATAGGATTACTGGCTTCAATTTGCTCCATTGTAATCTTA
130 AGGGAAATAGGATTACTGGCTTCAATCTGCTCCGCTGTAATCTCA
*
39484811 GGGAGATAAGACCTGA
1 GGGAGATAAGATCTGA
39484827 TGCGATCTAC
Statistics
Matches: 331, Mismatches: 32, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
173 84 0.25
174 1 0.00
175 246 0.74
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.33
Consensus pattern (174 bp):
GGGAGATAAGATCTGAAATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGC
GATCTACTCTACTGTAACTTCAGAGAGTAAGATCCTTTATTTTAATCCGTTCCACTGTAATCTCA
GGGAAATAGGATTACTGGCTTCAATCTGCTCCGCTGTAATCTCA
Found at i:39484831 original size:129 final size:129
Alignment explanation
Indices: 39484667--39484950 Score: 496
Period size: 129 Copynumber: 2.2 Consensus size: 129
39484657 TTCGGTCTAT
* *
39484667 TCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAA
1 TCCACTGTAATCTTAGGGAGATAAGACCTGATGCGATCTACTATACTGTAACTTCAGAGAGATAA
* * *
39484732 GATCTTTTATTTTAATCCGTTCCACTGTAATCTTAGGGAAATAGGATTACTGGCTTCAATTTGC
66 GATCCTTTATTTTAATCCGTTCCACTGTAATCTCAGGGAAATAGGATTACTGGCTTCAATCTGC
*
39484796 TCCATTGTAATCTTAGGGAGATAAGACCTGATGCGATCTACTATACTGTAACTTCAGAGAGATAA
1 TCCACTGTAATCTTAGGGAGATAAGACCTGATGCGATCTACTATACTGTAACTTCAGAGAGATAA
*
39484861 GATCCTTTATTTTAATCTGTTCCACTGTAATCTCAGGGAAATAGGATTACTGGCTTCAATCTGC
66 GATCCTTTATTTTAATCCGTTCCACTGTAATCTCAGGGAAATAGGATTACTGGCTTCAATCTGC
*
39484925 TCCGCTGTAATCTTAGGGAGATAAGA
1 TCCACTGTAATCTTAGGGAGATAAGA
39484951 TCCACCACCT
Statistics
Matches: 146, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
129 146 1.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (129 bp):
TCCACTGTAATCTTAGGGAGATAAGACCTGATGCGATCTACTATACTGTAACTTCAGAGAGATAA
GATCCTTTATTTTAATCCGTTCCACTGTAATCTCAGGGAAATAGGATTACTGGCTTCAATCTGC
Found at i:39490882 original size:24 final size:24
Alignment explanation
Indices: 39490855--39490904 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
39490845 CTAGGCGGTG
39490855 ATAGTATTGGAGCATTAGCCAAGT
1 ATAGTATTGGAGCATTAGCCAAGT
39490879 ATAGTATTGGAGCATTAGCCAAGT
1 ATAGTATTGGAGCATTAGCCAAGT
39490903 AT
1 AT
39490905 TGCTTTATCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.30
Consensus pattern (24 bp):
ATAGTATTGGAGCATTAGCCAAGT
Found at i:39500493 original size:14 final size:14
Alignment explanation
Indices: 39500474--39500502 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
39500464 ACTAATGACT
39500474 ATTGAACACAGAAA
1 ATTGAACACAGAAA
39500488 ATTGAACACAGAAA
1 ATTGAACACAGAAA
39500502 A
1 A
39500503 GAGAAAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.14, G:0.14, T:0.14
Consensus pattern (14 bp):
ATTGAACACAGAAA
Found at i:39501042 original size:13 final size:14
Alignment explanation
Indices: 39501005--39501043 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
39500995 AGTATTGGAC
*
39501005 TTTTATTATATTTA
1 TTTTATTATATATA
39501019 TTTTATATATATATA
1 TTTTAT-TATATATA
39501034 TTTT-TTATAT
1 TTTTATTATAT
39501044 TTGGTTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 5 0.22
14 7 0.30
15 11 0.48
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTATTATATATA
Found at i:39505988 original size:16 final size:16
Alignment explanation
Indices: 39505967--39506000 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
39505957 CCAATATTCA
* *
39505967 ATTATCATATTTGCAC
1 ATTATCACATTTACAC
39505983 ATTATCACATTTACAC
1 ATTATCACATTTACAC
39505999 AT
1 AT
39506001 ATATATTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.21, G:0.03, T:0.41
Consensus pattern (16 bp):
ATTATCACATTTACAC
Found at i:39506085 original size:20 final size:19
Alignment explanation
Indices: 39506055--39506095 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
39506045 ATATATATAT
*
39506055 ATCAATTCAATCCATTTCA
1 ATCAATTCAATCCAATTCA
*
39506074 ATCAACTTCAATTCAATTCA
1 ATCAA-TTCAATCCAATTCA
39506094 AT
1 AT
39506096 AACAAAGTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (19 bp):
ATCAATTCAATCCAATTCA
Found at i:39506800 original size:16 final size:15
Alignment explanation
Indices: 39506781--39506826 Score: 58
Period size: 16 Copynumber: 3.0 Consensus size: 15
39506771 GCATGGCTTT
39506781 CTATTTATTTTATTA
1 CTATTTATTTTATTA
*
39506796 CCTATTTGTTTTATTA
1 -CTATTTATTTTATTA
39506812 -TACTTTATTTTATTA
1 CTA-TTTATTTTATTA
39506827 TATAATACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
14 2 0.07
15 11 0.41
16 14 0.52
ACGTcount: A:0.24, C:0.09, G:0.02, T:0.65
Consensus pattern (15 bp):
CTATTTATTTTATTA
Found at i:39506824 original size:15 final size:14
Alignment explanation
Indices: 39506782--39506829 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 14
39506772 CATGGCTTTC
39506782 TATTTATTTTATTA
1 TATTTATTTTATTA
*
39506796 CCTATTTGTTTTATTA
1 --TATTTATTTTATTA
39506812 TACTTTATTTTATTA
1 TA-TTTATTTTATTA
39506827 TAT
1 TAT
39506830 AATACATGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 3 0.10
15 13 0.45
16 13 0.45
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.67
Consensus pattern (14 bp):
TATTTATTTTATTA
Found at i:39512968 original size:17 final size:18
Alignment explanation
Indices: 39512943--39512983 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
39512933 GTTTTATTGA
*
39512943 TTTCGTTGTTTGTTT-ATT
1 TTTC-TTGTTTATTTAATT
39512961 TTTCTTGTTTATTTAATT
1 TTTCTTGTTTATTTAATT
39512979 TTTCT
1 TTTCT
39512984 CATTAATCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.10, C:0.07, G:0.10, T:0.73
Consensus pattern (18 bp):
TTTCTTGTTTATTTAATT
Found at i:39513390 original size:40 final size:42
Alignment explanation
Indices: 39513346--39513437 Score: 152
Period size: 43 Copynumber: 2.2 Consensus size: 42
39513336 TTTGATTTAT
*
39513346 TTTGGTAGATA-CC-AAAAGTAAATTTGAAAGAAATTAGTGA
1 TTTGGTAGATACCCAAAAAGTAAAATTGAAAGAAATTAGTGA
39513386 TTTGGTAGATACCCAGAAAAGTAAAATTGAAAGAAATTAGTGA
1 TTTGGTAGATACCCA-AAAAGTAAAATTGAAAGAAATTAGTGA
39513429 TTTGGTAGA
1 TTTGGTAGA
39513438 AGCAAAACTC
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
40 11 0.23
41 2 0.04
43 35 0.73
ACGTcount: A:0.43, C:0.05, G:0.22, T:0.29
Consensus pattern (42 bp):
TTTGGTAGATACCCAAAAAGTAAAATTGAAAGAAATTAGTGA
Found at i:39521765 original size:15 final size:15
Alignment explanation
Indices: 39521745--39521773 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
39521735 CATCAAAGAG
39521745 ATAGAATATACCAGC
1 ATAGAATATACCAGC
39521760 ATAGAATATACCAG
1 ATAGAATATACCAG
39521774 TAATCACATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.17, G:0.14, T:0.21
Consensus pattern (15 bp):
ATAGAATATACCAGC
Found at i:39524488 original size:35 final size:35
Alignment explanation
Indices: 39524431--39524562 Score: 183
Period size: 35 Copynumber: 3.7 Consensus size: 35
39524421 AATCTAACCA
* *
39524431 AAACACACCAGATGCTCATAAGAGCCAATCCATCTG
1 AAACACACCA-ATGCTCATAAGAGCTAATCCATCCG
* * *
39524467 AAACACACTAATGCTCGTAAGAGCTAATCCCTCCG
1 AAACACACCAATGCTCATAAGAGCTAATCCATCCG
* * *
39524502 AAACACACCAATGCTCATTAGAGCTAATCCTTCCA
1 AAACACACCAATGCTCATAAGAGCTAATCCATCCG
39524537 AAACACACCAATGCTCATAAGAGCTA
1 AAACACACCAATGCTCATAAGAGCTA
39524563 GTCTAACCGA
Statistics
Matches: 85, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
35 76 0.89
36 9 0.11
ACGTcount: A:0.39, C:0.30, G:0.12, T:0.19
Consensus pattern (35 bp):
AAACACACCAATGCTCATAAGAGCTAATCCATCCG
Found at i:39524573 original size:70 final size:71
Alignment explanation
Indices: 39524421--39524574 Score: 193
Period size: 70 Copynumber: 2.2 Consensus size: 71
39524411 AGTACCCAAC
* ** * *
39524421 AATCTAACCAAAACACACCAGATGCTCATAAGAGCCAATCCATCTGAAACACACTAATGCTCGTA
1 AATCTAACCGAAACACACCAGATGCTCATAAGAGCCAATCCATCCAAAACACACCAATGCTCATA
39524486 AGAGCT
66 AGAGCT
*** * * *
39524492 AATCCCTCCGAAACACACCA-ATGCTCATTAGAGCTAATCCTTCCAAAACACACCAATGCTCATA
1 AATCTAACCGAAACACACCAGATGCTCATAAGAGCCAATCCATCCAAAACACACCAATGCTCATA
39524556 AGAGCT
66 AGAGCT
*
39524562 AGTCTAACCGAAA
1 AATCTAACCGAAA
39524575 TAGAGAGTAT
Statistics
Matches: 68, Mismatches: 15, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
70 52 0.76
71 16 0.24
ACGTcount: A:0.40, C:0.30, G:0.12, T:0.19
Consensus pattern (71 bp):
AATCTAACCGAAACACACCAGATGCTCATAAGAGCCAATCCATCCAAAACACACCAATGCTCATA
AGAGCT
Found at i:39524594 original size:13 final size:13
Alignment explanation
Indices: 39524576--39524601 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39524566 TAACCGAAAT
39524576 AGAGAGTATAACA
1 AGAGAGTATAACA
39524589 AGAGAGTATAACA
1 AGAGAGTATAACA
39524602 TTTTTCAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.23, T:0.15
Consensus pattern (13 bp):
AGAGAGTATAACA
Found at i:39529818 original size:18 final size:18
Alignment explanation
Indices: 39529754--39529819 Score: 55
Period size: 18 Copynumber: 3.6 Consensus size: 18
39529744 ATCCAAGTCA
*
39529754 AATTAAA-AAAAAATAAAG
1 AATTAAATAAAAAAT-AAC
* * *
39529772 AAATAAAT-TAAAATAATT
1 AATTAAATAAAAAATAA-C
39529790 AATTAAGATAAAAAATAAC
1 AATTAA-ATAAAAAATAAC
39529809 AATTAAATAAA
1 AATTAAATAAA
39529820 TCAAAGATTA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
17 2 0.05
18 21 0.55
19 8 0.21
20 7 0.18
ACGTcount: A:0.71, C:0.02, G:0.03, T:0.24
Consensus pattern (18 bp):
AATTAAATAAAAAATAAC
Found at i:39531860 original size:30 final size:30
Alignment explanation
Indices: 39531825--39531884 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
39531815 AAATATTTTT
*
39531825 TTAAAAAATAATAAAATTATGAACAATAAA
1 TTAAAAAATAATAAAATTATGAAAAATAAA
39531855 TTAAAAAATAATAAAATTATGAAAAATAAA
1 TTAAAAAATAATAAAATTATGAAAAATAAA
39531885 AACTCTTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (30 bp):
TTAAAAAATAATAAAATTATGAAAAATAAA
Found at i:39531881 original size:18 final size:18
Alignment explanation
Indices: 39531828--39531883 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 18
39531818 TATTTTTTTA
39531828 AAAAATAATAAAATTATG
1 AAAAATAATAAAATTATG
*
39531846 ---AACAAT-AAATTA--
1 AAAAATAATAAAATTATG
39531858 AAAAATAATAAAATTATG
1 AAAAATAATAAAATTATG
39531876 AAAAATAA
1 AAAAATAA
39531884 AAACTCTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 12
0.68 0.05 0.27
Matches are distributed among these distances:
14 6 0.20
15 10 0.33
16 6 0.20
18 8 0.27
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.25
Consensus pattern (18 bp):
AAAAATAATAAAATTATG
Found at i:39532297 original size:13 final size:13
Alignment explanation
Indices: 39532279--39532303 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39532269 AGTTCTTGGT
39532279 CTAATCAATCCAA
1 CTAATCAATCCAA
39532292 CTAATCAATCCA
1 CTAATCAATCCA
39532304 TCTCGATTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.32, G:0.00, T:0.24
Consensus pattern (13 bp):
CTAATCAATCCAA
Found at i:39532769 original size:29 final size:29
Alignment explanation
Indices: 39532710--39532770 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
39532700 GTTTTAATTC
* *
39532710 TTTTCATAATTTTATGTTTTTAAATATAA
1 TTTTCATAATTTTATGTTTTCAAATAAAA
* * **
39532739 TTTTTATATTTTTATGTTTTCATTTAAAA
1 TTTTCATAATTTTATGTTTTCAAATAAAA
39532768 TTT
1 TTT
39532771 AACATTTAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (29 bp):
TTTTCATAATTTTATGTTTTCAAATAAAA
Found at i:39533339 original size:2 final size:2
Alignment explanation
Indices: 39533332--39533367 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
39533322 ACGATTCATT
*
39533332 CA CA CA CA CA CA CA CA CA CA CA CA CA TA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
39533368 TATATCTCTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.47, G:0.00, T:0.03
Consensus pattern (2 bp):
CA
Found at i:39535020 original size:42 final size:42
Alignment explanation
Indices: 39534974--39535070 Score: 115
Period size: 42 Copynumber: 2.3 Consensus size: 42
39534964 CAGAAACCTG
* *
39534974 TAAGGGTTGAACGGAAGCTC-ATAGAAGCTGAACGAAAACCCA
1 TAAGGGTTAAACGGAAGCTCAAAAG-AGCTGAACGAAAACCCA
** * *
39535016 TAAGGGTTAAATTGAAGCTCAAAAGAGCTGAATGGAAACCCA
1 TAAGGGTTAAACGGAAGCTCAAAAGAGCTGAACGAAAACCCA
*
39535058 TTAGGGTTAAACG
1 TAAGGGTTAAACG
39535071 AAAACTAATA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
42 42 0.93
43 3 0.07
ACGTcount: A:0.40, C:0.15, G:0.26, T:0.19
Consensus pattern (42 bp):
TAAGGGTTAAACGGAAGCTCAAAAGAGCTGAACGAAAACCCA
Found at i:39537078 original size:25 final size:25
Alignment explanation
Indices: 39536999--39537089 Score: 94
Period size: 25 Copynumber: 3.6 Consensus size: 25
39536989 ACATTTGCCG
***
39536999 TCAATTCATCCTTTTGCATTTTATGG
1 TCAATTCATCC-TTTGCATTTTACCA
** *
39537025 TCAATTTGTCCTTTGCA-TATACCA
1 TCAATTCATCCTTTGCATTTTACCA
*
39537049 TCAATTCATCCTTTGCATTTTACCT
1 TCAATTCATCCTTTGCATTTTACCA
*
39537074 TCAATTCATCATTTGC
1 TCAATTCATCCTTTGC
39537090 CACAGAACGA
Statistics
Matches: 53, Mismatches: 11, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
24 18 0.34
25 26 0.49
26 9 0.17
ACGTcount: A:0.22, C:0.24, G:0.08, T:0.46
Consensus pattern (25 bp):
TCAATTCATCCTTTGCATTTTACCA
Found at i:39538053 original size:9 final size:9
Alignment explanation
Indices: 39538039--39538065 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
39538029 CCACATTTAA
39538039 CATTTAATC
1 CATTTAATC
39538048 CATTTAATC
1 CATTTAATC
39538057 CATTTAATC
1 CATTTAATC
39538066 ACTATTTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.22, G:0.00, T:0.44
Consensus pattern (9 bp):
CATTTAATC
Found at i:39542564 original size:42 final size:42
Alignment explanation
Indices: 39542507--39542601 Score: 163
Period size: 42 Copynumber: 2.3 Consensus size: 42
39542497 GCTAGGCTCA
* *
39542507 AGCCTGATAAAAATTCACCGGCACTATGCATGCTAGGCTTTT
1 AGCCTGATATAAATTCACCGGCACTACGCATGCTAGGCTTTT
*
39542549 AGCCTGATATAAATTCACCGGCACTACGCCTGCTAGGCTTTT
1 AGCCTGATATAAATTCACCGGCACTACGCATGCTAGGCTTTT
39542591 AGCCTGATATA
1 AGCCTGATATA
39542602 TCACACTAGA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.28
Consensus pattern (42 bp):
AGCCTGATATAAATTCACCGGCACTACGCATGCTAGGCTTTT
Found at i:39542787 original size:32 final size:32
Alignment explanation
Indices: 39542751--39542828 Score: 120
Period size: 32 Copynumber: 2.4 Consensus size: 32
39542741 TATGTAAAAA
39542751 CATAATTTATATATTACTTTAAACATTGCTAT
1 CATAATTTATATATTACTTTAAACATTGCTAT
* *
39542783 CATAATTTATATATTATTTTAAACATTGTTAT
1 CATAATTTATATATTACTTTAAACATTGCTAT
39542815 CATACATTTCATAT
1 CATA-ATTT-ATAT
39542829 TCGACAATTA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
32 34 0.81
33 4 0.10
34 4 0.10
ACGTcount: A:0.37, C:0.12, G:0.03, T:0.49
Consensus pattern (32 bp):
CATAATTTATATATTACTTTAAACATTGCTAT
Found at i:39543813 original size:185 final size:186
Alignment explanation
Indices: 39543501--39543871 Score: 735
Period size: 185 Copynumber: 2.0 Consensus size: 186
39543491 TATGTTTTAT
39543501 TTTATTACATTAATTAACTAATTTACCATAATAACCTTTAATATTTAATTAACCAACATTATATC
1 TTTATTACATTAATTAACTAATTTACCATAATAACCTTTAATATTTAATTAACCAACATTATATC
39543566 ATAAGCCTATTACTGTCCATCAACATATTCCATGGTATAATTACAATATAAATACCTTCCATTAA
66 ATAAGCCTATTACTGTCCATCAACATATTCCATGGTATAATTACAATATAAATACCTTCCATTAA
39543631 AAGAACAAGTCAATTTAGCACTTTAAAAATTAGTTAGCAA-TTTTTACTTTTTACG
131 AAGAACAAGTCAATTTAGCACTTTAAAAATTAGTTAGCAATTTTTTACTTTTTACG
39543686 TTTATTACATTAATTAACTAATTTACCATAATAACCTTTAATATTTAATTAACCAACATTATATC
1 TTTATTACATTAATTAACTAATTTACCATAATAACCTTTAATATTTAATTAACCAACATTATATC
39543751 ATAAGCCTATTACTGTCCATCAACATATTCCATGGTATAATTACAATATAAATACCTTCCATTAA
66 ATAAGCCTATTACTGTCCATCAACATATTCCATGGTATAATTACAATATAAATACCTTCCATTAA
39543816 AAGAACAAGTCAATTTAGCACTTTAAAAATTAGTTAGCAATTTTTTACTTTTTACG
131 AAGAACAAGTCAATTTAGCACTTTAAAAATTAGTTAGCAATTTTTTACTTTTTACG
39543872 CGATTAAATC
Statistics
Matches: 185, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
185 170 0.92
186 15 0.08
ACGTcount: A:0.39, C:0.17, G:0.05, T:0.39
Consensus pattern (186 bp):
TTTATTACATTAATTAACTAATTTACCATAATAACCTTTAATATTTAATTAACCAACATTATATC
ATAAGCCTATTACTGTCCATCAACATATTCCATGGTATAATTACAATATAAATACCTTCCATTAA
AAGAACAAGTCAATTTAGCACTTTAAAAATTAGTTAGCAATTTTTTACTTTTTACG
Found at i:39552144 original size:11 final size:12
Alignment explanation
Indices: 39552113--39552143 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
39552103 GTAGGCAAAT
39552113 TTTTTTTTGCGG
1 TTTTTTTTGCGG
39552125 TTTTTTTTGCGG
1 TTTTTTTTGCGG
39552137 TTTTTTT
1 TTTTTTT
39552144 GTGCTTTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.00, C:0.06, G:0.19, T:0.74
Consensus pattern (12 bp):
TTTTTTTTGCGG
Found at i:39552165 original size:25 final size:24
Alignment explanation
Indices: 39552137--39552188 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
39552127 TTTTTTGCGG
*
39552137 TTTTT-TTGTGCTTTTTGCTTCTTT
1 TTTTTATTTTGCTTTTTG-TTCTTT
* *
39552161 TTTTTATTTTTCTTTTTGTTGTTT
1 TTTTTATTTTGCTTTTTGTTCTTT
39552185 TTTT
1 TTTT
39552189 AAAGAATAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 14 0.58
25 10 0.42
ACGTcount: A:0.02, C:0.08, G:0.10, T:0.81
Consensus pattern (24 bp):
TTTTTATTTTGCTTTTTGTTCTTT
Found at i:39568161 original size:21 final size:21
Alignment explanation
Indices: 39568137--39568195 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
39568127 AGTGCTAAAC
*
39568137 AGAAACCCGTAAGGGTTGAAT
1 AGAAACCCATAAGGGTTGAAT
* * * *
39568158 AGAAGCTCATAAGAGCTGAAT
1 AGAAACCCATAAGGGTTGAAT
39568179 AGAAACCCATAAGGGTT
1 AGAAACCCATAAGGGTT
39568196 AAACTCAAGC
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.41, C:0.15, G:0.25, T:0.19
Consensus pattern (21 bp):
AGAAACCCATAAGGGTTGAAT
Found at i:39568183 original size:42 final size:42
Alignment explanation
Indices: 39568123--39568241 Score: 141
Period size: 42 Copynumber: 2.8 Consensus size: 42
39568113 CACAGAATCA
* * * * *
39568123 CATAAGTGCTAAACAGAAACCCGTAAGGGTTGAA-TAGAAGCT
1 CATAAGAGCTGAACAGAAACCCATAAGGGTTAAACT-CAAGCT
*
39568165 CATAAGAGCTGAATAGAAACCCATAAGGGTTAAACTCAAGCT
1 CATAAGAGCTGAACAGAAACCCATAAGGGTTAAACTCAAGCT
* * *
39568207 CAAAAGAGCTGAACAAAAACCCATTAGGGTTAAAC
1 CATAAGAGCTGAACAGAAACCCATAAGGGTTAAAC
39568242 GGAAACTCAT
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
42 65 0.98
43 1 0.02
ACGTcount: A:0.44, C:0.18, G:0.20, T:0.18
Consensus pattern (42 bp):
CATAAGAGCTGAACAGAAACCCATAAGGGTTAAACTCAAGCT
Found at i:39575358 original size:18 final size:18
Alignment explanation
Indices: 39575319--39575363 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
39575309 CGTTCGATTC
39575319 CAAATCATTATTCATTTA
1 CAAATCATTATTCATTTA
*
39575337 CAAATTATTATTCAATTT-
1 CAAATCATTATTC-ATTTA
*
39575355 CAAAACATT
1 CAAATCATT
39575364 TTTCTTATTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (18 bp):
CAAATCATTATTCATTTA
Found at i:39578292 original size:15 final size:15
Alignment explanation
Indices: 39578267--39578301 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
39578257 GACTCTATTT
*
39578267 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
39578281 TAATTAATATTAAGA
1 TAATTAATATTAAGA
39578296 TAATTA
1 TAATTA
39578302 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Done.