Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 109 of 318
Found at i:35006987 original size:134 final size:134
Alignment explanation
Indices: 35006456--35006979 Score: 865
Period size: 134 Copynumber: 3.9 Consensus size: 134
35006446 GAGATAAAAC
* * * * * * *
35006456 TATCAGCTTCAATGTACTCCACTGTAATCAGGGAGGTAAAATCTGCCGTCTTTAACCTACTTTGC
1 TATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCGC
*
35006521 TGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAATATAGGGAGATA
66 TGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAATACAGGGAGATA
35006586 GAGT
131 GAGT
*
35006590 TATCGGCTTCAATGTACTCCACTGTGGTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCGC
1 TATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCGC
35006655 TGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAATACAGGGAGATA
66 TGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAATACAGGGAGATA
35006720 GAGT
131 GAGT
* * *
35006724 TATCGGCTTCAATGTACTCCACTGTGGTCAGGGAGGTAAAATCTGTCATCTTTGATCTGCTTTGC
1 TATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCGC
*
35006789 TGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCTACTGCCAAATACAGGGAGATA
66 TGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAATACAGGGAGATA
35006854 GAGT
131 GAGT
* *
35006858 TATCGGTTTCAATGTACTCCACTGTAGTCACATGGAGGTAAAATCTGCCATCTTTGATCTGCTTC
1 TATCGGCTTCAATGTACTCCACTGTAGT--CAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTC
35006923 GCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTACTT-CAC-GCC-AATACA
64 GCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTA-TTCCACTGCCAAATACA
35006980 TGAAGATAAG
Statistics
Matches: 369, Mismatches: 18, Indels: 6
0.94 0.05 0.02
Matches are distributed among these distances:
134 288 0.78
135 3 0.01
136 76 0.21
137 2 0.01
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (134 bp):
TATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTTCGC
TGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAATACAGGGAGATA
GAGT
Found at i:35006991 original size:44 final size:44
Alignment explanation
Indices: 35006930--35007125 Score: 162
Period size: 44 Copynumber: 4.5 Consensus size: 44
35006920 TTCGCTGCCA
* * *
35006930 AATACAGGAAGGCAAGATCTGCAATCTTCAATCTACTTCACGCC
1 AATACAGGAAGACAAGATCTGCTATCTTCAATCTACTTCACACC
* * * * *
35006974 AATACATGAAGATAAGATCTGCTTTCTTCGATCTACTTCGCCACC
1 AATACAGGAAGACAAGATCTGCTATCTTCAATCTACTTC-ACACC
* ** * *
35007019 AGTATGGGAAGACAAGATCTGC-ATCGTCAATCCACTTC-CTACC
1 AATACAGGAAGACAAGATCTGCTATCTTCAATCTACTTCAC-ACC
* ** * * ** *
35007062 AATATAGGAAGACCGGACCTGTTATCTTTGATCTACTTCACGCC
1 AATACAGGAAGACAAGATCTGCTATCTTCAATCTACTTCACACC
*
35007106 AATACATGAAGACAAGATCT
1 AATACAGGAAGACAAGATCT
35007126 ACTTTAATGA
Statistics
Matches: 115, Mismatches: 33, Indels: 8
0.74 0.21 0.05
Matches are distributed among these distances:
42 1 0.01
43 19 0.17
44 74 0.64
45 21 0.18
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (44 bp):
AATACAGGAAGACAAGATCTGCTATCTTCAATCTACTTCACACC
Found at i:35009973 original size:62 final size:62
Alignment explanation
Indices: 35009869--35010052 Score: 298
Period size: 62 Copynumber: 3.0 Consensus size: 62
35009859 CTAAACTCGA
* *
35009869 CGTACTTTTGGATTTTAGGAAATTTATTGTAT-TCAATGAAATGTAATATTGATGCATGAACG
1 CGTATTTTTGGATTTTAGGAAATTTATTGTATGT-AATGAAATGTAATATTAATGCATGAACG
* *
35009931 CGTATTTTTGGATTTTAGGAAATTTATTGTATGTAATAAAATGTAATGTTAATGCATGAACG
1 CGTATTTTTGGATTTTAGGAAATTTATTGTATGTAATGAAATGTAATATTAATGCATGAACG
* *
35009993 CGTATTTTTGGATTTTAGGAAATTTATTGTATGTAATGAAATGTAATGTTAATGAATGAA
1 CGTATTTTTGGATTTTAGGAAATTTATTGTATGTAATGAAATGTAATATTAATGCATGAA
35010053 GAGATACGTG
Statistics
Matches: 115, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
62 114 0.99
63 1 0.01
ACGTcount: A:0.34, C:0.05, G:0.20, T:0.42
Consensus pattern (62 bp):
CGTATTTTTGGATTTTAGGAAATTTATTGTATGTAATGAAATGTAATATTAATGCATGAACG
Found at i:35016848 original size:14 final size:15
Alignment explanation
Indices: 35016824--35016852 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
35016814 TCTAATTACA
35016824 AGGATATTTAATAAC
1 AGGATATTTAATAAC
35016839 AGGA-ATTTAATAAC
1 AGGATATTTAATAAC
35016853 CAAATCTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (15 bp):
AGGATATTTAATAAC
Found at i:35020522 original size:31 final size:30
Alignment explanation
Indices: 35020487--35020551 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 30
35020477 AAATTTACAA
35020487 ATAACATATAAAGTTTAAAAC-TA-AATAAAAT
1 ATAACATATAAA---TAAAACATATAATAAAAT
*
35020518 ATAACATCTAAATAAAACATATAATAAAAT
1 ATAACATATAAATAAAACATATAATAAAAT
35020548 ATAA
1 ATAA
35020552 ATAAAACAGC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
28 6 0.19
29 2 0.06
30 12 0.39
31 11 0.35
ACGTcount: A:0.63, C:0.08, G:0.02, T:0.28
Consensus pattern (30 bp):
ATAACATATAAATAAAACATATAATAAAAT
Found at i:35020556 original size:11 final size:11
Alignment explanation
Indices: 35020526--35020559 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
35020516 ATATAACATC
35020526 TAAATAAAACA
1 TAAATAAAACA
*
35020537 TATAATAAAATA
1 TA-AATAAAACA
35020549 TAAATAAAACA
1 TAAATAAAACA
35020560 GCTTGAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (11 bp):
TAAATAAAACA
Found at i:35021785 original size:27 final size:27
Alignment explanation
Indices: 35021745--35021811 Score: 116
Period size: 27 Copynumber: 2.4 Consensus size: 27
35021735 TTTTGTGCAT
35021745 AAAAGAGGGTAAAGTGGAGTGACTTGAAG
1 AAAAG-GGG-AAAGTGGAGTGACTTGAAG
35021774 AAAAGGGGAAAGTGGAGTGACTTGAAG
1 AAAAGGGGAAAGTGGAGTGACTTGAAG
35021801 AAAAGGGGAAA
1 AAAAGGGGAAA
35021812 AGGAAGTTGG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
27 30 0.79
28 3 0.08
29 5 0.13
ACGTcount: A:0.45, C:0.03, G:0.39, T:0.13
Consensus pattern (27 bp):
AAAAGGGGAAAGTGGAGTGACTTGAAG
Found at i:35025400 original size:21 final size:21
Alignment explanation
Indices: 35025376--35025426 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 21
35025366 CCAAACCTTG
*
35025376 AGGTTTCGAGTTT-GGAATTTA
1 AGGTTTAGAGTTTAGG-ATTTA
35025397 AGGTTTAGAGTTTAGGATTTA
1 AGGTTTAGAGTTTAGGATTTA
35025418 AGGTTTAGA
1 AGGTTTAGA
35025427 TTCGAGGTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
21 26 0.93
22 2 0.07
ACGTcount: A:0.27, C:0.02, G:0.29, T:0.41
Consensus pattern (21 bp):
AGGTTTAGAGTTTAGGATTTA
Found at i:35027439 original size:10 final size:10
Alignment explanation
Indices: 35027424--35027455 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
35027414 TAAATACATT
35027424 TAATTAAAGA
1 TAATTAAAGA
35027434 TAATTAAAGA
1 TAATTAAAGA
35027444 TAATTAAA-A
1 TAATTAAAGA
35027453 TAA
1 TAA
35027456 AATCCTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.31
Consensus pattern (10 bp):
TAATTAAAGA
Found at i:35027481 original size:27 final size:26
Alignment explanation
Indices: 35027451--35027513 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
35027441 AGATAATTAA
35027451 AATAAAATCCTAAAATTAAATAATCCT
1 AATAAAATCCTAAAATT-AATAATCCT
* * * *
35027478 AATAATTATCTTAATATTAATTATCCT
1 AATAA-AATCCTAAAATTAATAATCCT
35027505 AATATAAAT
1 AATA-AAAT
35027514 AAAATGGAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
27 19 0.66
28 10 0.34
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (26 bp):
AATAAAATCCTAAAATTAATAATCCT
Found at i:35027500 original size:15 final size:15
Alignment explanation
Indices: 35027480--35027509 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
35027470 ATAATCCTAA
*
35027480 TAATTATCTTAATAT
1 TAATTATCCTAATAT
35027495 TAATTATCCTAATAT
1 TAATTATCCTAATAT
35027510 AAATAAAATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATTATCCTAATAT
Found at i:35030888 original size:42 final size:42
Alignment explanation
Indices: 35030828--35030931 Score: 109
Period size: 42 Copynumber: 2.5 Consensus size: 42
35030818 CCGAAGGCTG
* * * *
35030828 AACAAAAGCTCGTGAGAGCTAAAAAGAAACCCATAAGGGTTG
1 AACAGAAGCTCGTAAGAGCTAAAAAGAAACCCATAAAGGTTA
* * ** *
35030870 AACGGAAGCTCGTAAGAGCTGAACGGAAACCCGTAAAGGTTA
1 AACAGAAGCTCGTAAGAGCTAAAAAGAAACCCATAAAGGTTA
**
35030912 AACAGAAGCTCAAAAGAGCT
1 AACAGAAGCTCGTAAGAGCT
35030932 TAATTGAAAC
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.43, C:0.18, G:0.25, T:0.13
Consensus pattern (42 bp):
AACAGAAGCTCGTAAGAGCTAAAAAGAAACCCATAAAGGTTA
Found at i:35030904 original size:21 final size:21
Alignment explanation
Indices: 35030853--35030905 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
35030843 GAGCTAAAAA
* * *
35030853 GAAACCCATAAGGGTTGAACG
1 GAAACCCGTAAGAGCTGAACG
* *
35030874 GAAGCTCGTAAGAGCTGAACG
1 GAAACCCGTAAGAGCTGAACG
35030895 GAAACCCGTAA
1 GAAACCCGTAA
35030906 AGGTTAAACA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.38, C:0.21, G:0.28, T:0.13
Consensus pattern (21 bp):
GAAACCCGTAAGAGCTGAACG
Found at i:35031079 original size:19 final size:19
Alignment explanation
Indices: 35031055--35031095 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
35031045 TCCTCCAATG
*
35031055 TGATCAATTCATTAATTTT
1 TGATCAATTCATCAATTTT
35031074 TGATCAATTCATCAATTTT
1 TGATCAATTCATCAATTTT
35031093 TGA
1 TGA
35031096 ATGTACTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.32, C:0.12, G:0.07, T:0.49
Consensus pattern (19 bp):
TGATCAATTCATCAATTTT
Found at i:35035664 original size:22 final size:22
Alignment explanation
Indices: 35035628--35035669 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
35035618 AGCAACTTGA
*
35035628 TTTTTCTTTAGTTTCTTTTTTC
1 TTTTTCTTTAGTTTCCTTTTTC
**
35035650 TTTTTCTTTTTTTTCCTTTT
1 TTTTTCTTTAGTTTCCTTTT
35035670 CTGTTTACTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.02, C:0.14, G:0.02, T:0.81
Consensus pattern (22 bp):
TTTTTCTTTAGTTTCCTTTTTC
Found at i:35045255 original size:3 final size:3
Alignment explanation
Indices: 35045240--35045299 Score: 63
Period size: 3 Copynumber: 21.0 Consensus size: 3
35045230 TTCGGGAACA
* * * *
35045240 AAG AAG GAG AAG AAG AAA AAG AA- AAG AAG GAG AAG AAG GA- AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
35045286 -AG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG
35045300 GAGGAGCTGG
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
2 5 0.11
3 41 0.89
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:35046353 original size:13 final size:14
Alignment explanation
Indices: 35046335--35046394 Score: 61
Period size: 15 Copynumber: 4.2 Consensus size: 14
35046325 ATTTTTTGCT
35046335 AAAATAATATA-AA
1 AAAATAATATACAA
*
35046348 AAAATAAAATACGAA
1 AAAATAATATAC-AA
*
35046363 AATAAT-ATATTATAA
1 AA-AATAATA-TACAA
35046378 AAAATAATATACAA
1 AAAATAATATACAA
35046392 AAA
1 AAA
35046395 TATTTTACTT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
13 10 0.26
14 10 0.26
15 13 0.34
16 5 0.13
ACGTcount: A:0.72, C:0.03, G:0.02, T:0.23
Consensus pattern (14 bp):
AAAATAATATACAA
Found at i:35046353 original size:149 final size:149
Alignment explanation
Indices: 35045888--35046396 Score: 678
Period size: 149 Copynumber: 3.3 Consensus size: 149
35045878 TATAAAAAAT
* *
35045888 AAAAAATAAAATATGAAAATATTATATTTTAAAAAATAAAATACGAAAATAAAAAAATATGAACA
1 AAAAAATAAAATACGAAAATAATATATTTTAAAAAATAAAATACGAAAATAAAAAAA-A-G----
* *
35045953 AAGTGTCAAAGTGTCAAAGTCAGGGTTATTTATTAAATTAATATAAAAAACACTTAAATAATACA
60 AA--G--AAAGTGCCAAAATCAGGGTTATTTATTAAATTAATATAAAAAACACTTAAATAATACA
* *
35046018 TTTGAAACATTTTTAGCTAAAGTAATAT-
121 TTTGAAACATTTTTTGCTAAAATAATATA
* * * *
35046046 AAAAAATAAAATACGAAAATAATATATTTTAAAAAATAATATACAAAAATAAAAAAGACGAATAA
1 AAAAAATAAAATACGAAAATAATATATTTTAAAAAATAAAATACGAAAATAAAAAA-AAGAAGAA
* * **
35046111 AGTGCTAAAAGCAGGGTTATTTATTAAAAAAATATAAAAAAACACTTAAATAATACATTTGAAAC
65 AGTGCCAAAATCAGGGTTATTTATTAAATTAATAT-AAAAAACACTTAAATAATACATTTGAAAC
* * *
35046176 ATTATGTACTAAAATAATATA
129 ATTTTTTGCTAAAATAATATA
* * *
35046197 AAGAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATAGGAAAATAAAAAAAAGAAGAAA
1 AAAAAATAAAATACGAAAATAATATATTTTAAAAAATAAAATACGAAAATAAAAAAAAGAAGAAA
* *
35046262 ATGCCAAAATCAGGGTTGTTTATTAAATTAATATAAAAAACACTTAAATAATACATTTGAAACAT
66 GTGCCAAAATCAGGGTTATTTATTAAATTAATATAAAAAACACTTAAATAATACATTTGAAACAT
35046327 TTTTTGCTAAAATAATATA
131 TTTTTGCTAAAATAATATA
* * *
35046346 AAAAAATAAAATACGAAAATAATATATTATAAAAAATAATATACAAAAATA
1 AAAAAATAAAATACGAAAATAATATATTTTAAAAAATAAAATACGAAAATA
35046397 TTTTACTTAT
Statistics
Matches: 311, Mismatches: 37, Indels: 15
0.86 0.10 0.04
Matches are distributed among these distances:
149 124 0.40
150 79 0.25
151 52 0.17
153 2 0.01
157 1 0.00
158 52 0.17
159 1 0.00
ACGTcount: A:0.58, C:0.06, G:0.08, T:0.28
Consensus pattern (149 bp):
AAAAAATAAAATACGAAAATAATATATTTTAAAAAATAAAATACGAAAATAAAAAAAAGAAGAAA
GTGCCAAAATCAGGGTTATTTATTAAATTAATATAAAAAACACTTAAATAATACATTTGAAACAT
TTTTTGCTAAAATAATATA
Found at i:35046395 original size:13 final size:13
Alignment explanation
Indices: 35046335--35046396 Score: 54
Period size: 13 Copynumber: 4.5 Consensus size: 13
35046325 ATTTTTTGCT
*
35046335 AAAATAATATAAA
1 AAAATAATATACA
*
35046348 AAAATAAAATACGAA
1 AAAATAATATAC--A
35046363 AATAATATATTATA-A
1 AA-AATA-A-TATACA
35046378 AAAATAATATACA
1 AAAATAATATACA
35046391 AAAATA
1 AAAATA
35046397 TTTTACTTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
12 4 0.10
13 18 0.45
14 4 0.10
15 6 0.15
16 4 0.10
17 1 0.03
18 3 0.08
ACGTcount: A:0.71, C:0.03, G:0.02, T:0.24
Consensus pattern (13 bp):
AAAATAATATACA
Found at i:35047502 original size:18 final size:17
Alignment explanation
Indices: 35047479--35047514 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
35047469 ATAATAAATA
*
35047479 TATATTTTTATTTTTAAT
1 TATATTTATA-TTTTAAT
35047497 TATATTTATATTTTAAT
1 TATATTTATATTTTAAT
35047514 T
1 T
35047515 TTAATTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TATATTTATATTTTAAT
Found at i:35047553 original size:20 final size:19
Alignment explanation
Indices: 35047481--35047556 Score: 57
Period size: 20 Copynumber: 3.9 Consensus size: 19
35047471 AATAAATATA
* * *
35047481 TATTTTTATTTTTAA-TTA
1 TATTTATATTTTCAATTTT
35047499 TATTTATATTTT-AATTTT
1 TATTTATATTTTCAATTTT
* **
35047517 AATTTTAATATAATCAATTTT
1 TA-TTT-ATATTTTCAATTTT
35047538 TATTATATATTTTCAATTT
1 TATT-TATATTTTCAATTT
35047557 GTGTATTGTT
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
17 2 0.04
18 14 0.31
19 3 0.07
20 18 0.40
21 8 0.18
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (19 bp):
TATTTATATTTTCAATTTT
Found at i:35047586 original size:40 final size:40
Alignment explanation
Indices: 35047542--35047622 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 40
35047532 AATTTTTATT
35047542 ATATATTTTCAATTTGTGTATTGTTTTAAGAATTGTTTTA
1 ATATATTTTCAATTTGTGTATTGTTTTAAGAATTGTTTTA
** * * * * *
35047582 ATATATTTTTTATTTGTTTCTTTTTTTAATATTTGTTTTA
1 ATATATTTTCAATTTGTGTATTGTTTTAAGAATTGTTTTA
35047622 A
1 A
35047623 ATGTATTTGA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.25, C:0.02, G:0.09, T:0.64
Consensus pattern (40 bp):
ATATATTTTCAATTTGTGTATTGTTTTAAGAATTGTTTTA
Found at i:35048939 original size:72 final size:72
Alignment explanation
Indices: 35048802--35048940 Score: 181
Period size: 72 Copynumber: 1.9 Consensus size: 72
35048792 CGAGCTATCG
* * * *
35048802 CATTCACATTCGACTGATACTTCTTATCATCCGAATTTGGCGAGCAATGACTATTTCCCGGGCTC
1 CATTCACATTCGACTGATACTTCTTATCATCCGAATTTGCCGAGAAATAACTATTTCCCGAGCTC
35048867 GTCATCA
66 GTCATCA
** * * *
35048874 CATTCACATTCGGTTGATACTTCTTATCATCCGAATTTTCCG-GAAAATAACTATTTTCTGAGCT
1 CATTCACATTCGACTGATACTTCTTATCATCCGAATTTGCCGAG-AAATAACTATTTCCCGAGCT
35048938 CGT
65 CGT
35048941 TAGAGGGCGG
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
71 1 0.02
72 56 0.98
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.35
Consensus pattern (72 bp):
CATTCACATTCGACTGATACTTCTTATCATCCGAATTTGCCGAGAAATAACTATTTCCCGAGCTC
GTCATCA
Found at i:35049497 original size:17 final size:17
Alignment explanation
Indices: 35049477--35049515 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
35049467 AATACATTAC
35049477 AACATTAATCT-AATTGG
1 AACATTAAT-TAAATTGG
35049494 AACATTAATTAAATTGG
1 AACATTAATTAAATTGG
35049511 AACAT
1 AACAT
35049516 ACTATTACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 1 0.05
17 20 0.95
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.33
Consensus pattern (17 bp):
AACATTAATTAAATTGG
Found at i:35052736 original size:15 final size:16
Alignment explanation
Indices: 35052715--35052750 Score: 65
Period size: 15 Copynumber: 2.3 Consensus size: 16
35052705 ATGCAGTGAG
35052715 ATCTTGAGCTCTATGT
1 ATCTTGAGCTCTATGT
35052731 -TCTTGAGCTCTATGT
1 ATCTTGAGCTCTATGT
35052746 ATCTT
1 ATCTT
35052751 CCTCTAGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.17, C:0.19, G:0.17, T:0.47
Consensus pattern (16 bp):
ATCTTGAGCTCTATGT
Found at i:35053758 original size:42 final size:39
Alignment explanation
Indices: 35053689--35053767 Score: 104
Period size: 39 Copynumber: 1.9 Consensus size: 39
35053679 AGGGTTTACT
* * *
35053689 AACAATAATAATAACTAACAACAAAAAATAATAAAAATC
1 AACAATAATAATAACCAAAAACAAAAAACAATAAAAATC
35053728 AACAATAATAATAACAGCAAAAACACAAAAACAATAAAAA
1 AACAATAATAATAAC--CAAAAACA-AAAAACAATAAAAA
35053768 ATCCATTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
39 15 0.44
41 6 0.18
42 13 0.38
ACGTcount: A:0.71, C:0.14, G:0.01, T:0.14
Consensus pattern (39 bp):
AACAATAATAATAACCAAAAACAAAAAACAATAAAAATC
Found at i:35055382 original size:38 final size:38
Alignment explanation
Indices: 35055340--35055420 Score: 101
Period size: 38 Copynumber: 2.1 Consensus size: 38
35055330 ACTCTTTCAT
* * * *
35055340 ATTTTCTCTTCTTTTATCATTCCAATTTAGAAAAG-TTG
1 ATTTTCTCTCCTCTTATCATCCCAATTTA-AAAAGATTA
*
35055378 ATTTTCTCTCCTCTTATTATCCCAATTTAAAAAGATTA
1 ATTTTCTCTCCTCTTATCATCCCAATTTAAAAAGATTA
35055416 ATTTT
1 ATTTT
35055421 AAGCATTAAG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 5 0.14
38 32 0.86
ACGTcount: A:0.28, C:0.17, G:0.05, T:0.49
Consensus pattern (38 bp):
ATTTTCTCTCCTCTTATCATCCCAATTTAAAAAGATTA
Found at i:35055746 original size:17 final size:17
Alignment explanation
Indices: 35055724--35055758 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 17
35055714 CCCCAATCAT
35055724 TTTTTTATTATTAATATAA
1 TTTTTTA-T-TTAATATAA
35055743 TTTTTTATTTAATATA
1 TTTTTTATTTAATATA
35055759 TATAACATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 1 0.06
19 7 0.44
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTTTTATTTAATATAA
Found at i:35055761 original size:21 final size:19
Alignment explanation
Indices: 35055724--35055763 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
35055714 CCCCAATCAT
*
35055724 TTTTTTATTATTAATATAA
1 TTTTTTATTAATAATATAA
35055743 TTTTTTATTTAATATATATAA
1 TTTTTTA-TTAATA-ATATAA
35055764 CATAAGCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 5 0.28
21 6 0.33
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTTTATTAATAATATAA
Found at i:35065889 original size:23 final size:22
Alignment explanation
Indices: 35065838--35065889 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
35065828 CCTCGTCTTT
*
35065838 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
35065860 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
35065883 TTCTTTT
1 TTCTTTT
35065890 TCAAATTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:35065904 original size:18 final size:18
Alignment explanation
Indices: 35065883--35065921 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
35065873 TTTCTTCAAC
* *
35065883 TTCTTTTTCAAATTTCTT
1 TTCTGTTTCAAATTCCTT
*
35065901 TTCTGTTTCACATTCCTT
1 TTCTGTTTCAAATTCCTT
35065919 TTC
1 TTC
35065922 ACTCTCAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.13, C:0.23, G:0.03, T:0.62
Consensus pattern (18 bp):
TTCTGTTTCAAATTCCTT
Found at i:35068823 original size:14 final size:14
Alignment explanation
Indices: 35068804--35068834 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
35068794 TTTGATTGGT
*
35068804 GGAAAATATTTTCC
1 GGAAAATATTTTAC
35068818 GGAAAATATTTTAC
1 GGAAAATATTTTAC
35068832 GGA
1 GGA
35068835 TTTTCCAGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.10, G:0.19, T:0.32
Consensus pattern (14 bp):
GGAAAATATTTTAC
Found at i:35069329 original size:27 final size:27
Alignment explanation
Indices: 35069245--35069343 Score: 101
Period size: 27 Copynumber: 3.6 Consensus size: 27
35069235 AAAGGTATAT
35069245 TTTCTTGTCCATAGTTTTGTGAATCGG
1 TTTCTTGTCCATAGTTTTGTGAATCGG
* * ** * * *
35069272 TTTCTGGGT-TAGTTCTTTTTTGTTATTGG
1 TTTCT-TGTCCA-TAGTTTTGTG-AATCGG
35069301 TTTCTTGTCCATAGTTTTGTGAATCGG
1 TTTCTTGTCCATAGTTTTGTGAATCGG
35069328 TTTCTTGTCCATAGTT
1 TTTCTTGTCCATAGTT
35069344 AGAAAGATTT
Statistics
Matches: 54, Mismatches: 14, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
27 26 0.48
28 18 0.33
29 10 0.19
ACGTcount: A:0.12, C:0.13, G:0.21, T:0.54
Consensus pattern (27 bp):
TTTCTTGTCCATAGTTTTGTGAATCGG
Found at i:35071440 original size:26 final size:26
Alignment explanation
Indices: 35071411--35071468 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
35071401 CATCCTCAAA
*
35071411 CTATAATCTAGATATTAAATTGGTCT
1 CTATAATCTAGATATTAAACTGGTCT
*
35071437 CTATAATCTAGATTTTAAACTGGTCT
1 CTATAATCTAGATATTAAACTGGTCT
35071463 CTATAA
1 CTATAA
35071469 ATTTTGATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.41
Consensus pattern (26 bp):
CTATAATCTAGATATTAAACTGGTCT
Found at i:35071831 original size:20 final size:20
Alignment explanation
Indices: 35071806--35071845 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
35071796 AATATTTTTC
*
35071806 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
35071826 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
35071846 TTATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:35071852 original size:34 final size:35
Alignment explanation
Indices: 35071794--35071860 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
35071784 CAAACACCAG
* *
35071794 AAAATATTTTTCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
35071829 AAAACATTTTCCAG-AAATTATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
35071861 CATTTTACTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 16 0.57
35 12 0.43
ACGTcount: A:0.46, C:0.10, G:0.09, T:0.34
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:35076549 original size:32 final size:32
Alignment explanation
Indices: 35076513--35076581 Score: 77
Period size: 32 Copynumber: 2.2 Consensus size: 32
35076503 TGAAAAATCA
*
35076513 AATTTAAAAGGAAAT-TTTCAAATTATATATTT
1 AATTTAAAA-GAAATAATTCAAATTATATATTT
*** *
35076545 AATTTTGTAGAAATAATTCAATTTATATATTT
1 AATTTAAAAGAAATAATTCAAATTATATATTT
35076577 AATTT
1 AATTT
35076582 CAATATCTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 5 0.16
32 26 0.84
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48
Consensus pattern (32 bp):
AATTTAAAAGAAATAATTCAAATTATATATTT
Found at i:35080176 original size:23 final size:24
Alignment explanation
Indices: 35080138--35080186 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
35080128 AATTTTAAAA
* *
35080138 TCTAAAAATTAGAAAGATTAAATT
1 TCTAAAAATTAAAAAGATCAAATT
*
35080162 TCTAAAAA-TAAAAAGGTCAAATT
1 TCTAAAAATTAAAAAGATCAAATT
35080185 TC
1 TC
35080187 AAACGCACGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.53, C:0.08, G:0.08, T:0.31
Consensus pattern (24 bp):
TCTAAAAATTAAAAAGATCAAATT
Found at i:35081443 original size:49 final size:49
Alignment explanation
Indices: 35081371--35081471 Score: 202
Period size: 49 Copynumber: 2.1 Consensus size: 49
35081361 TATAAAAGTT
35081371 AGTAGTGGTGACTAAATAGAAAAAAACATGCGAAGAACAAAGCAGAACA
1 AGTAGTGGTGACTAAATAGAAAAAAACATGCGAAGAACAAAGCAGAACA
35081420 AGTAGTGGTGACTAAATAGAAAAAAACATGCGAAGAACAAAGCAGAACA
1 AGTAGTGGTGACTAAATAGAAAAAAACATGCGAAGAACAAAGCAGAACA
35081469 AGT
1 AGT
35081472 TCCCAACTAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.52, C:0.12, G:0.23, T:0.13
Consensus pattern (49 bp):
AGTAGTGGTGACTAAATAGAAAAAAACATGCGAAGAACAAAGCAGAACA
Found at i:35084888 original size:26 final size:28
Alignment explanation
Indices: 35084845--35084900 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 28
35084835 AGATAACTAC
35084845 TAATATATTAAAATATATTAATATAAAA
1 TAATATATTAAAATATATTAATATAAAA
* *
35084873 TAATAT-TTTAAA-ATATTAGTATAAAA
1 TAATATATTAAAATATATTAATATAAAA
35084899 TA
1 TA
35084901 TTTATTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 15 0.58
27 5 0.19
28 6 0.23
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (28 bp):
TAATATATTAAAATATATTAATATAAAA
Found at i:35084897 original size:13 final size:13
Alignment explanation
Indices: 35084859--35084902 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
35084849 ATATTAAAAT
35084859 ATATTAATATAAA
1 ATATTAATATAAA
* * *
35084872 ATAATATTTTAAA
1 ATATTAATATAAA
*
35084885 ATATTAGTATAAA
1 ATATTAATATAAA
35084898 ATATT
1 ATATT
35084903 TATTTTTTAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (13 bp):
ATATTAATATAAA
Found at i:35086113 original size:18 final size:19
Alignment explanation
Indices: 35086074--35086114 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
35086064 AAAAACTATA
35086074 ATATTTTTTTATGAATAAAT
1 ATATTTTTTTATGAAT-AAT
35086094 ATATTATTTTTAT-AAT-AT
1 ATATT-TTTTTATGAATAAT
35086112 ATA
1 ATA
35086115 GTACGGACAC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
18 5 0.25
20 8 0.40
21 7 0.35
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (19 bp):
ATATTTTTTTATGAATAAT
Found at i:35094350 original size:19 final size:19
Alignment explanation
Indices: 35094328--35094503 Score: 76
Period size: 19 Copynumber: 9.3 Consensus size: 19
35094318 AAAAATTAGA
35094328 AAAAAATATAAAAAAATAT
1 AAAAAATATAAAAAAATAT
* *
35094347 -AAAAATCATTAAAAAATGT
1 AAAAAAT-ATAAAAAAATAT
* ** * *
35094366 -AAAAATTTGTAAAATTTT
1 AAAAAATATAAAAAAATAT
*
35094384 ATAAAAATCGTAAAAAAAT-T
1 A-AAAAAT-ATAAAAAAATAT
* * *
35094404 ATAAAATATATAGAAATAT
1 AAAAAATATAAAAAAATAT
*
35094423 AAAAATTATAAAAAAAT-T
1 AAAAAATATAAAAAAATAT
* * * *
35094441 ATAAAGTCAT-AAGAATTAT
1 AAAAAAT-ATAAAAAAATAT
* *
35094460 ACAAAATATAAAGAAATAT
1 AAAAAATATAAAAAAATAT
**
35094479 -AAATTTCATAAAAAAATTAT
1 AAAAAAT-ATAAAAAAA-TAT
35094499 AAAAA
1 AAAAA
35094504 TTATCGTACC
Statistics
Matches: 115, Mismatches: 31, Indels: 20
0.69 0.19 0.12
Matches are distributed among these distances:
18 36 0.31
19 59 0.51
20 11 0.10
21 9 0.08
ACGTcount: A:0.65, C:0.03, G:0.04, T:0.28
Consensus pattern (19 bp):
AAAAAATATAAAAAAATAT
Found at i:35094350 original size:29 final size:30
Alignment explanation
Indices: 35094309--35094370 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
35094299 AATTTTTAAT
*
35094309 AAAAATCATAAAAATTAGAAAAAAATATAA
1 AAAAATCATAAAAATCAGAAAAAAATATAA
** *
35094339 AAAAAT-ATAAAAATCATTAAAAAATGTAA
1 AAAAATCATAAAAATCAGAAAAAAATATAA
35094368 AAA
1 AAA
35094371 TTTGTAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 22 0.79
30 6 0.21
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.21
Consensus pattern (30 bp):
AAAAATCATAAAAATCAGAAAAAAATATAA
Found at i:35094409 original size:10 final size:10
Alignment explanation
Indices: 35094309--35094445 Score: 67
Period size: 10 Copynumber: 14.2 Consensus size: 10
35094299 AATTTTTAAT
*
35094309 AAAAATCAT-
1 AAAAATTATA
*
35094318 AAAAATTAGA
1 AAAAATTATA
*
35094328 AAAAAATATA
1 AAAAATTATA
*
35094338 AAAAAATAT-
1 AAAAATTATA
*
35094347 AAAAATCATTA
1 AAAAATTA-TA
*
35094358 AAAAA-TGTA
1 AAAAATTATA
* *
35094367 AAAATTTGTA
1 AAAAATTATA
**
35094377 AAATTTTAT-
1 AAAAATTATA
35094386 AAAAATCGTA-A
1 AAAAAT--TATA
35094397 AAAAATTATA
1 AAAAATTATA
*
35094407 AAATA-TAT-
1 AAAAATTATA
*
35094415 AGAAA-TAT-
1 AAAAATTATA
35094423 AAAAATTATAA
1 AAAAATTAT-A
35094434 AAAAATTATA
1 AAAAATTATA
35094444 AA
1 AA
35094446 GTCATAAGAA
Statistics
Matches: 100, Mismatches: 17, Indels: 21
0.72 0.12 0.15
Matches are distributed among these distances:
8 10 0.10
9 31 0.31
10 37 0.37
11 22 0.22
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.28
Consensus pattern (10 bp):
AAAAATTATA
Found at i:35094433 original size:26 final size:27
Alignment explanation
Indices: 35094397--35094481 Score: 93
Period size: 28 Copynumber: 3.1 Consensus size: 27
35094387 AAAATCGTAA
35094397 AAAAATTAT-AAAATATATAGAAATAT
1 AAAAATTATAAAAATATATAGAAATAT
* *
35094423 AAAAATTATAAAAAAATTATA-AAGTCAT
1 AAAAATTATAAAAATA-TATAGAAAT-AT
* *
35094451 AAGAATTATACAAAATATAAAGAAATAT
1 AAAAATTATA-AAAATATATAGAAATAT
35094479 AAA
1 AAA
35094482 TTTCATAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
26 9 0.19
27 8 0.17
28 22 0.47
29 8 0.17
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (27 bp):
AAAAATTATAAAAATATATAGAAATAT
Found at i:35094470 original size:37 final size:37
Alignment explanation
Indices: 35094330--35094481 Score: 116
Period size: 37 Copynumber: 4.1 Consensus size: 37
35094320 AAATTAGAAA
* * * *
35094330 AAAATATAAAAAAATATAAAAATCATTAAAAAATGTA-
1 AAAATATATAGAAATATAAAAATTATAAAAAAAT-TAT
* * **
35094367 AAAATTTGTA-AAATTTTATAAAAATCGTAAAAAAATTAT
1 AAAATATATAGAAA---TATAAAAATTATAAAAAAATTAT
35094406 AAAATATATAGAAATATAAAAATTATAAAAAAATTAT
1 AAAATATATAGAAATATAAAAATTATAAAAAAATTAT
* * *
35094443 AAAGTCATA-AGAATTATACAAAA-TATAAAGAAA-TAT
1 AAAAT-ATATAGAAATATA-AAAATTATAAAAAAATTAT
35094479 AAA
1 AAA
35094482 TTTCATAAAA
Statistics
Matches: 96, Mismatches: 12, Indels: 15
0.78 0.10 0.12
Matches are distributed among these distances:
36 9 0.09
37 49 0.51
38 9 0.09
39 26 0.27
40 3 0.03
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (37 bp):
AAAATATATAGAAATATAAAAATTATAAAAAAATTAT
Found at i:35094483 original size:26 final size:25
Alignment explanation
Indices: 35094399--35094492 Score: 66
Period size: 26 Copynumber: 3.5 Consensus size: 25
35094389 AATCGTAAAA
*
35094399 AAATTAT-AAAATATATAGAAATAT
1 AAATTATAAAAATATAAAGAAATAT
**
35094423 AAAAATTATAAAAAAATTATAAAGTCATA-
1 --AAATTAT--AAAAA-TATAAAGAAATAT
35094452 AGAATTATACAAAATATAAAGAAATAT
1 A-AATTATA-AAAATATAAAGAAATAT
35094479 AAATTTCATAAAAA
1 AAA-TT-ATAAAAA
35094493 AATTATAAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 17
0.71 0.07 0.22
Matches are distributed among these distances:
26 20 0.37
27 12 0.22
28 9 0.17
29 4 0.07
30 9 0.17
ACGTcount: A:0.64, C:0.03, G:0.04, T:0.29
Consensus pattern (25 bp):
AAATTATAAAAATATAAAGAAATAT
Found at i:35094488 original size:37 final size:37
Alignment explanation
Indices: 35094383--35094507 Score: 121
Period size: 37 Copynumber: 3.3 Consensus size: 37
35094373 TGTAAAATTT
** *
35094383 TATAAAAATCGTAAAAAAATTATAAAAT-ATATAGAAA
1 TATAAAAATTATAAAAAAATTATAAAGTCATA-AGAAA
*
35094420 TATAAAAATTATAAAAAAATTATAAAGTCATAAGAAT
1 TATAAAAATTATAAAAAAATTATAAAGTCATAAGAAA
* * *
35094457 TATACAAAA-TATAAAGAAA-TATAAATTTCATAAAAAAA
1 TATA-AAAATTATAAAAAAATTATAAA-GTCAT-AAGAAA
35094495 TTATAAAAATTAT
1 -TATAAAAATTAT
35094508 CGTACCAAAA
Statistics
Matches: 74, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
36 6 0.08
37 46 0.62
38 15 0.20
39 7 0.09
ACGTcount: A:0.63, C:0.03, G:0.04, T:0.30
Consensus pattern (37 bp):
TATAAAAATTATAAAAAAATTATAAAGTCATAAGAAA
Found at i:35094502 original size:9 final size:9
Alignment explanation
Indices: 35094307--35094507 Score: 88
Period size: 9 Copynumber: 21.2 Consensus size: 9
35094297 TAAATTTTTA
*
35094307 ATAAAAATC
1 ATAAAAATT
35094316 ATAAAAATT
1 ATAAAAATT
* *
35094325 AGAAAAAAAT
1 A-TAAAAATT
*
35094335 ATAAAAAAAT
1 AT-AAAAATT
*
35094345 ATAAAAATC
1 ATAAAAATT
*
35094354 ATTAAAAAAT
1 A-TAAAAATT
*
35094364 GTAAAAATTT
1 ATAAAAA-TT
* *
35094374 GTAAAATTTT
1 ATAAAA-ATT
35094384 ATAAAAATCGT
1 ATAAAAAT--T
*
35094395 AAAAAAATT
1 ATAAAAATT
35094404 AT-AAAATAT
1 ATAAAAAT-T
*
35094413 ATAGAAA-T
1 ATAAAAATT
35094421 ATAAAAATT
1 ATAAAAATT
35094430 ATAAAAAAATT
1 AT--AAAAATT
* *
35094441 AT-AAAGTC
1 ATAAAAATT
*
35094449 ATAAGAATT
1 ATAAAAATT
35094458 ATACAAAA-T
1 ATA-AAAATT
*
35094467 ATAAAGAAAT
1 ATAAA-AATT
*
35094477 AT-AAATTT
1 ATAAAAATT
35094485 CATAAAAAAATT
1 -AT--AAAAATT
35094497 ATAAAAATT
1 ATAAAAATT
35094506 AT
1 AT
35094508 CGTACCAAAA
Statistics
Matches: 146, Mismatches: 26, Indels: 40
0.69 0.12 0.19
Matches are distributed among these distances:
8 22 0.15
9 55 0.38
10 45 0.31
11 19 0.13
12 5 0.03
ACGTcount: A:0.64, C:0.03, G:0.04, T:0.29
Consensus pattern (9 bp):
ATAAAAATT
Found at i:35094504 original size:28 final size:27
Alignment explanation
Indices: 35094398--35094504 Score: 80
Period size: 28 Copynumber: 3.9 Consensus size: 27
35094388 AAATCGTAAA
* *
35094398 AAAATTAT-AAAATA-TATAGAAATAT
1 AAAATTATAAAAAAATTATAAAAATAT
*
35094423 AAAAATTATAAAAAAATTAT-AAAGTCAT
1 -AAAATTATAAAAAAATTATAAAAAT-AT
*
35094451 AAGAATTAT-ACAAAA-TATAAAGAAATAT
1 AA-AATTATAAAAAAATTAT-AA-AAATAT
*
35094479 AAATTTCATAAAAAAATTATAAAAAT
1 AAAATT-ATAAAAAAATTATAAAAAT
35094505 TATCGTACCA
Statistics
Matches: 64, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
26 11 0.17
27 18 0.28
28 22 0.34
29 10 0.16
30 3 0.05
ACGTcount: A:0.64, C:0.03, G:0.04, T:0.29
Consensus pattern (27 bp):
AAAATTATAAAAAAATTATAAAAATAT
Found at i:35094690 original size:24 final size:25
Alignment explanation
Indices: 35094640--35094692 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
35094630 TCATTAAATT
*
35094640 TTTTTTATGATTTTTATAAAATTAAA
1 TTTTTTACGATTTTTATAAAA-TAAA
*
35094666 TTTTTTACGATTTTTATAGAA-AAA
1 TTTTTTACGATTTTTATAAAATAAA
35094690 TTT
1 TTT
35094693 ATAATTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 6 0.24
26 19 0.76
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.57
Consensus pattern (25 bp):
TTTTTTACGATTTTTATAAAATAAA
Found at i:35094939 original size:84 final size:84
Alignment explanation
Indices: 35094779--35094945 Score: 192
Period size: 84 Copynumber: 2.0 Consensus size: 84
35094769 TAATAAGAGT
* * * * *
35094779 AGGGGCTTAATTGCTTTTTTGAAAAATTTTGAGGATCTTTTTGATGCATTTTGAAAGTTTAATTA
1 AGGGGCTTAATTGCTTTTTTGAAAAAGTTTGAGGACCTTTTTGATGCATTCTGAAAGTTCAAGTA
*
35094844 CCCAATTGAGTG-AAAAAC
66 CCCAATCGAGTGCAAAAAC
* * **
35094862 AGGGGCTTAATTGCTTTTTTTGAAGAAGTTTGAGGGCCTTTTTGATTTATTCTGAAAGTTCAAGT
1 AGGGGCTTAATTGC-TTTTTTGAAAAAGTTTGAGGACCTTTTTGATGCATTCTGAAAGTTCAAGT
****
35094927 GTTTAATCGAGTGCAAAAA
65 ACCCAATCGAGTGCAAAAA
35094946 AAAAGGAGAG
Statistics
Matches: 68, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
83 14 0.21
84 49 0.72
85 5 0.07
ACGTcount: A:0.29, C:0.10, G:0.22, T:0.40
Consensus pattern (84 bp):
AGGGGCTTAATTGCTTTTTTGAAAAAGTTTGAGGACCTTTTTGATGCATTCTGAAAGTTCAAGTA
CCCAATCGAGTGCAAAAAC
Found at i:35097693 original size:16 final size:16
Alignment explanation
Indices: 35097672--35097710 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
35097662 AAATAATGCT
*
35097672 ATTACAGCTTTATTCC
1 ATTACAGCTCTATTCC
*
35097688 ATTACAGCTCTATTCT
1 ATTACAGCTCTATTCC
35097704 ATTACAG
1 ATTACAG
35097711 TGAACCAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.28, C:0.23, G:0.08, T:0.41
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:35098368 original size:23 final size:24
Alignment explanation
Indices: 35098338--35098387 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
35098328 TATTTCTTTT
* *
35098338 AAATATTTTAAAATTTACAATA-A
1 AAATATTTGAAAATTTAAAATATA
*
35098361 AAATATTTGAAATTTTAAAATATA
1 AAATATTTGAAAATTTAAAATATA
35098385 AAA
1 AAA
35098388 AAAATATATG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (24 bp):
AAATATTTGAAAATTTAAAATATA
Found at i:35099686 original size:3 final size:3
Alignment explanation
Indices: 35099680--35099706 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
35099670 CAACAACAAC
35099680 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
35099707 TTAAGACAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:35103834 original size:20 final size:19
Alignment explanation
Indices: 35103794--35103864 Score: 63
Period size: 20 Copynumber: 3.6 Consensus size: 19
35103784 AATTAAATAC
35103794 TAAAAAATATAAAAATATA
1 TAAAAAATATAAAAATATA
*
35103813 TAAAAAACTATTAAGAAT-TA
1 TAAAAAA-TA-TAAAAATATA
* * *
35103833 TAAATATTATTAAAATATAA
1 TAAAAAATATAAAAATAT-A
*
35103853 TAAAATATATAA
1 TAAAAAATATAA
35103865 CATTTAAGCT
Statistics
Matches: 39, Mismatches: 9, Indels: 7
0.71 0.16 0.13
Matches are distributed among these distances:
18 5 0.13
19 10 0.26
20 18 0.46
21 6 0.15
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.32
Consensus pattern (19 bp):
TAAAAAATATAAAAATATA
Found at i:35110598 original size:35 final size:35
Alignment explanation
Indices: 35110554--35110622 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
35110544 TAAAAGTTTT
35110554 TTATATAATATAAATTATATAAAAAAATAA-AAAAC
1 TTATATAATATAAA-TATATAAAAAAATAAGAAAAC
* *
35110589 TTATATAATATAAATATTTCAAAAAATAAGAAAA
1 TTATATAATATAAATATATAAAAAAATAAGAAAA
35110623 AAATAAATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
34 13 0.42
35 18 0.58
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (35 bp):
TTATATAATATAAATATATAAAAAAATAAGAAAAC
Found at i:35118602 original size:16 final size:17
Alignment explanation
Indices: 35118575--35118608 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
35118565 CCTACACTAC
*
35118575 AGAATCTTCATTTTAGA
1 AGAATCTTCATTTGAGA
35118592 AGAAT-TTCATTTGAGA
1 AGAATCTTCATTTGAGA
35118608 A
1 A
35118609 TCGGTGCCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (17 bp):
AGAATCTTCATTTGAGA
Found at i:35120999 original size:23 final size:23
Alignment explanation
Indices: 35120973--35121044 Score: 67
Period size: 23 Copynumber: 3.1 Consensus size: 23
35120963 TCACCATTGA
35120973 AACATGAATCATATATAGTTCTT
1 AACATGAATCATATATAGTTCTT
* * * *
35120996 AACATGAAATTATA-ACTAATAAC-A
1 AACATG-AATCATATA-TAGT-TCTT
35121020 AACATGAATCATATATAGTTCTT
1 AACATGAATCATATATAGTTCTT
35121043 AA
1 AA
35121045 GATGTAATAA
Statistics
Matches: 36, Mismatches: 8, Indels: 10
0.67 0.15 0.19
Matches are distributed among these distances:
22 1 0.03
23 18 0.50
24 16 0.44
25 1 0.03
ACGTcount: A:0.47, C:0.12, G:0.07, T:0.33
Consensus pattern (23 bp):
AACATGAATCATATATAGTTCTT
Found at i:35122286 original size:32 final size:32
Alignment explanation
Indices: 35122250--35122310 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
35122240 AGCTTTTGGT
35122250 TTTTTCATGTTGTCAAAGAGTTGAACAATAGA
1 TTTTTCATGTTGTCAAAGAGTTGAACAATAGA
*
35122282 TTTTTCGTGTTGTCAAAGAGTTGAACAAT
1 TTTTTCATGTTGTCAAAGAGTTGAACAAT
35122311 GAAAATAGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (32 bp):
TTTTTCATGTTGTCAAAGAGTTGAACAATAGA
Found at i:35127331 original size:14 final size:15
Alignment explanation
Indices: 35127295--35127331 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
35127285 AAAAATTTAA
35127295 AAATTAAAACTAATC
1 AAATTAAAACTAATC
35127310 AAATTAAAA-T-ATC
1 AAATTAAAACTAATC
35127323 AATATTAAA
1 AA-ATTAAA
35127332 TTTACAACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 5 0.24
14 7 0.33
15 9 0.43
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.30
Consensus pattern (15 bp):
AAATTAAAACTAATC
Found at i:35128420 original size:13 final size:13
Alignment explanation
Indices: 35128402--35128428 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
35128392 GTTTTGAGTG
35128402 ACAAATAGATTTT
1 ACAAATAGATTTT
35128415 ACAAATAGATTTT
1 ACAAATAGATTTT
35128428 A
1 A
35128429 GATATGAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.37
Consensus pattern (13 bp):
ACAAATAGATTTT
Found at i:35128522 original size:19 final size:20
Alignment explanation
Indices: 35128490--35128535 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 20
35128480 CGAAAAATAA
35128490 TTTCTGGAAAATAACTTACT
1 TTTCTGGAAAATAACTTACT
*
35128510 TTTCTGG-AAATAATTTACT
1 TTTCTGGAAAATAACTTACT
35128529 TTTCTGG
1 TTTCTGG
35128536 TGTTTGGATG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.46
Consensus pattern (20 bp):
TTTCTGGAAAATAACTTACT
Found at i:35131093 original size:25 final size:25
Alignment explanation
Indices: 35131064--35131111 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
35131054 TTATAATATG
* * *
35131064 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
35131089 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
35131112 GTTTATATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:35131178 original size:20 final size:20
Alignment explanation
Indices: 35131155--35131213 Score: 109
Period size: 20 Copynumber: 3.0 Consensus size: 20
35131145 TAAACATAGT
35131155 ATGTATGATATGCACATGAC
1 ATGTATGATATGCACATGAC
*
35131175 ATGTATGATATGCACATGAT
1 ATGTATGATATGCACATGAC
35131195 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
35131214 GGTATTCATA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (20 bp):
ATGTATGATATGCACATGAC
Found at i:35131195 original size:11 final size:11
Alignment explanation
Indices: 35131159--35131213 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
35131149 CATAGTATGT
35131159 ATGATATGCAC
1 ATGATATGCAC
* *
35131170 ATGACATG--T
1 ATGATATGCAC
35131179 ATGATATGCAC
1 ATGATATGCAC
*
35131190 ATGATATG--T
1 ATGATATGCAC
35131199 ATGATATGCAC
1 ATGATATGCAC
35131210 ATGA
1 ATGA
35131214 GGTATTCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:35131291 original size:24 final size:24
Alignment explanation
Indices: 35131264--35131479 Score: 299
Period size: 24 Copynumber: 9.0 Consensus size: 24
35131254 AAGGAAGTGC
*
35131264 AAAAGGGCTTATGCCCTAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
35131288 AAAAGGGCTTATGCCCTAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* * *
35131312 AAAAGGGCTTCTGCCCGAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
35131336 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* *
35131360 AAAAGGGCTTCTGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
*
35131384 AAAAGGGCTTCTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
35131408 AAAAGGGCTTATGCCCTAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* *
35131432 AAAAGGGCTTTTGCCCCAGTTTTT
1 AAAAGGGCTTATGCCCCAGTTATT
*
35131456 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
35131480 ATGATAAAGC
Statistics
Matches: 173, Mismatches: 17, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
24 163 0.94
25 10 0.06
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:35133985 original size:12 final size:12
Alignment explanation
Indices: 35133968--35133997 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
35133958 AAGGATGGGG
35133968 GAAGGGGAAGGA
1 GAAGGGGAAGGA
35133980 GAAGGGGAAGGA
1 GAAGGGGAAGGA
*
35133992 AAAGGG
1 GAAGGG
35133998 AAGATCAGGT
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:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (12 bp):
GAAGGGGAAGGA
Found at i:35134768 original size:61 final size:60
Alignment explanation
Indices: 35134650--35134800 Score: 139
Period size: 59 Copynumber: 2.5 Consensus size: 60
35134640 TTGGTCTAAT
* * *
35134650 AACAAATTTAGCGCTCTAATGTTTAC-ACATTCTATCAATTTGATCTTAAATATAAAAACTTC
1 AACAAATTTAGCCCT-TAATGTTTACAAAATTCTATCAATTTGATCTTAAATA-AAAAA-ATC
* *
35134712 AACAAATTTAGCCCTTAATGTTTACAAAATT-TGTC-ATTTTAGT-TTAAATTAAAAAAATC
1 AACAAATTTAGCCCTTAATGTTTACAAAATTCTATCAATTTGA-TCTTAAA-TAAAAAAATC
* * * **
35134771 AATAAAATTAGCCCTCAACATTTACAAAAT
1 AACAAATTTAGCCCTTAATGTTTACAAAAT
35134801 GATAAACTTT
Statistics
Matches: 76, Mismatches: 10, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
59 27 0.36
60 15 0.20
61 16 0.21
62 18 0.24
ACGTcount: A:0.42, C:0.16, G:0.06, T:0.36
Consensus pattern (60 bp):
AACAAATTTAGCCCTTAATGTTTACAAAATTCTATCAATTTGATCTTAAATAAAAAAATC
Found at i:35137455 original size:24 final size:23
Alignment explanation
Indices: 35137419--35137473 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
35137409 AAAAATCATG
*
35137419 TATCGGAAAGCTCAAGAGAGCTTA
1 TATCGGGAAGCTCAAGAGAGC-TA
* * *
35137443 TATCGGGATGCTCATGTGAGCTA
1 TATCGGGAAGCTCAAGAGAGCTA
*
35137466 TAACGGGA
1 TATCGGGA
35137474 CACTCTTGTG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 9 0.35
24 17 0.65
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (23 bp):
TATCGGGAAGCTCAAGAGAGCTA
Found at i:35148609 original size:17 final size:17
Alignment explanation
Indices: 35148587--35148621 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
35148577 TTGCTAAGTT
*
35148587 TTCCATATTACTGTTTC
1 TTCCATATTACTATTTC
35148604 TTCCATATTACTATTTC
1 TTCCATATTACTATTTC
35148621 T
1 T
35148622 CCCGTAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.20, C:0.23, G:0.03, T:0.54
Consensus pattern (17 bp):
TTCCATATTACTATTTC
Found at i:35151693 original size:43 final size:43
Alignment explanation
Indices: 35151645--35152014 Score: 429
Period size: 43 Copynumber: 8.6 Consensus size: 43
35151635 TTTATGTAAA
* *
35151645 AAACGCCACTAAAGAACATGACCTTTAGCAGCGCTTTTCCCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* * * * *
35151688 AAACGCCGCTAAAGAACATGACCTTCAGTGGCGCTTTTTCTAT
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* **
35151731 AAACGCCGCTAAAGAACATGACCTTTACCGGCATTTTTCCCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* * *
35151774 AAACGCCACTAAAGAACATGTCCTTTAGTGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* * * * *
35151817 AAACGCCGCTAAATAACACGTCATTTAGTGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAC
*
35151860 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTACCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* * ** *
35151903 AAATGCTGCTAAAGAACATGACCTTTAGCAACGTTTTTCCCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAC
* * * * * * *
35151946 AAAGGCCACTATA-AA-ATAGACCTTTAGCGACACTTTTCTCAT
1 AAACGCCGCTAAAGAACAT-GACCTTTAGCGGCGCTTTTCCCAC
*
35151988 AAACGCCGCTAAAAAACATGACCTTTA
1 AAACGCCGCTAAAGAACATGACCTTTA
35152015 AAAAAATAAA
Statistics
Matches: 275, Mismatches: 49, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
41 2 0.01
42 31 0.11
43 240 0.87
44 2 0.01
ACGTcount: A:0.32, C:0.29, G:0.15, T:0.25
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCCCAC
Found at i:35155945 original size:16 final size:17
Alignment explanation
Indices: 35155919--35155953 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
35155909 TATTAAAATA
35155919 TTAAATATTTAATTTTT
1 TTAAATATTTAATTTTT
35155936 TTAAAT-TTTAATTTTT
1 TTAAATATTTAATTTTT
35155952 TT
1 TT
35155954 GAAGATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TTAAATATTTAATTTTT
Found at i:35156628 original size:21 final size:21
Alignment explanation
Indices: 35156610--35156651 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
35156600 ATACTAAATT
*
35156610 CTAAATCCTAGTCCATAAACC
1 CTAAATCCTAGACCATAAACC
*
35156631 CTAAATCTTAGACCATAAACC
1 CTAAATCCTAGACCATAAACC
35156652 TACACCCTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.31, G:0.05, T:0.24
Consensus pattern (21 bp):
CTAAATCCTAGACCATAAACC
Found at i:35157023 original size:15 final size:14
Alignment explanation
Indices: 35157003--35157058 Score: 60
Period size: 15 Copynumber: 3.9 Consensus size: 14
35156993 CTAATATAAA
35157003 CCCTAAATCCCTATC
1 CCCTAAA-CCCTATC
*
35157018 CCCT-AACCACTAAC
1 CCCTAAACC-CTATC
*
35157032 CCTTAAACCCTATC
1 CCCTAAACCCTATC
35157046 CCCATAAACCCTA
1 CCC-TAAACCCTA
35157059 AATCATAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
13 2 0.06
14 15 0.44
15 17 0.50
ACGTcount: A:0.32, C:0.46, G:0.00, T:0.21
Consensus pattern (14 bp):
CCCTAAACCCTATC
Found at i:35157149 original size:14 final size:14
Alignment explanation
Indices: 35157128--35157176 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
35157118 CCCCAACACT
*
35157128 TAAACCATAAACCA
1 TAAACCATAATCCA
* *
35157142 TAATCCATAATCCC
1 TAAACCATAATCCA
*
35157156 TAACACCATAATCCG
1 TAA-ACCATAATCCA
35157171 TAAACC
1 TAAACC
35157177 TTAAAATAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
14 17 0.59
15 12 0.41
ACGTcount: A:0.45, C:0.33, G:0.02, T:0.20
Consensus pattern (14 bp):
TAAACCATAATCCA
Found at i:35157586 original size:40 final size:40
Alignment explanation
Indices: 35157542--35157727 Score: 223
Period size: 40 Copynumber: 4.7 Consensus size: 40
35157532 TTTTTTGCGA
* * * *
35157542 CGTTTTTGATAAAGCGTCACTAAAT-CTCGATCTATAGCGG
1 CGTTTTTCAAAAAGCGTCGCT-AATGCTCGACCTATAGCGG
* *
35157582 CGTTTTTCAAAAAGCGCCGCTAATGGTCGACCTATAGCGG
1 CGTTTTTCAAAAAGCGTCGCTAATGCTCGACCTATAGCGG
* *
35157622 CGTTTTTCAAAAAGC-ACTGCTAATGATCGACCTATAGCGG
1 CGTTTTTCAAAAAGCGTC-GCTAATGCTCGACCTATAGCGG
* * *
35157662 CGTTTTTTAAAAAGCGTCGCTAATGCTCAATCTATAGCGG
1 CGTTTTTCAAAAAGCGTCGCTAATGCTCGACCTATAGCGG
**
35157702 CGTTTTTCAAAAAGCACCGCTAATGC
1 CGTTTTTCAAAAAGCGTCGCTAATGC
35157728 CACTAAAGCT
Statistics
Matches: 127, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
39 4 0.03
40 122 0.96
41 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (40 bp):
CGTTTTTCAAAAAGCGTCGCTAATGCTCGACCTATAGCGG
Found at i:35157675 original size:80 final size:80
Alignment explanation
Indices: 35157568--35157726 Score: 255
Period size: 80 Copynumber: 2.0 Consensus size: 80
35157558 TCACTAAATC
* * *
35157568 TCGATCTATAGCGGCGTTTTTCAAAAAGCGCCGCTAATGGTCGACCTATAGCGGCGTTTTTCAAA
1 TCGACCTATAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCAACCTATAGCGGCGTTTTTCAAA
*
35157633 AAGCACTGCTAATGA
66 AAGCACCGCTAATGA
* * *
35157648 TCGACCTATAGCGGCGTTTTTTAAAAAGCGTCGCTAATGCTCAATCTATAGCGGCGTTTTTCAAA
1 TCGACCTATAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCAACCTATAGCGGCGTTTTTCAAA
35157713 AAGCACCGCTAATG
66 AAGCACCGCTAATG
35157727 CCACTAAAGC
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
80 72 1.00
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (80 bp):
TCGACCTATAGCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCAACCTATAGCGGCGTTTTTCAAA
AAGCACCGCTAATGA
Found at i:35157823 original size:40 final size:40
Alignment explanation
Indices: 35157774--35157882 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 40
35157764 ACATTTTTTG
* * *
35157774 CGGCGTTTTTCAAAAAGCGCAACTAATGGTCGACCTATAA
1 CGGCATTTTTCAAAAAGCGCCACTAATGCTCGACCTATAA
* * * * * *
35157814 CGTCATTTTTTAAAAAGCACCGCTAATGCTCGATCTATAG
1 CGGCATTTTTCAAAAAGCGCCACTAATGCTCGACCTATAA
*
35157854 CGGCGTTTTTCAAAAAGCGCCACTAATGC
1 CGGCATTTTTCAAAAAGCGCCACTAATGC
35157883 CACTAAAGCT
Statistics
Matches: 55, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (40 bp):
CGGCATTTTTCAAAAAGCGCCACTAATGCTCGACCTATAA
Found at i:35157900 original size:155 final size:155
Alignment explanation
Indices: 35157618--35158346 Score: 967
Period size: 155 Copynumber: 4.7 Consensus size: 155
35157608 TCGACCTATA
* * * *
35157618 GCGGCGTTTTTCAAAAAGCACTGCTAATGATCGACCTATAGCGGCGTTTTTTAAAAAGCGTCGCT
1 GCGGCGTTTTTCAAAAAGCGCAGCTAATGGTCGACCTATAGCGGCGTTTTTTAAAAAGCGCCGCT
* * *
35157683 AATGCTCAATCTATAGCGGCGTTTTTCAAAAAGCACCGCTAATGCCACTAAAGCTCAACACAAAA
66 AATGCTCGATCTATAGCGGCGTTTTTCAAAAAGCGCCACTAATGCCACTAAAGCTCAACACAAAA
** *
35157748 CGGCAGCGTTGTGC-TAACATTTTTT
131 CAACGGCGTTGTGCTTAA-ATTTTTT
* * * * *
35157773 GCGGCGTTTTTCAAAAAGCGCAACTAATGGTCGACCTATAACGTCATTTTTTAAAAAGCACCGCT
1 GCGGCGTTTTTCAAAAAGCGCAGCTAATGGTCGACCTATAGCGGCGTTTTTTAAAAAGCGCCGCT
35157838 AATGCTCGATCTATAGCGGCGTTTTTCAAAAAGCGCCACTAATGCCACTAAAGCTCAACACAAAA
66 AATGCTCGATCTATAGCGGCGTTTTTCAAAAAGCGCCACTAATGCCACTAAAGCTCAACACAAAA
* * *
35157903 CAATGGCGTTGTACTTAATTTTTTT
131 CAACGGCGTTGTGCTTAAATTTTTT
* * * * **
35157928 GTGGCGTTTTTCAAAAAGTGCTGCTAATGGTCGACCTATAGCGGCGTTTTTCAAAAAGCGTTGCT
1 GCGGCGTTTTTCAAAAAGCGCAGCTAATGGTCGACCTATAGCGGCGTTTTTTAAAAAGCGCCGCT
* * * * * * **
35157993 AATGGTCGACCTATAGCAGTGTTTTTTAAAAAGGGCCACTAATGCTGCTAAAG-TCAACACAAAA
66 AATGCTCGATCTATAGCGGCGTTTTTCAAAAAGCGCCACTAATGCCACTAAAGCTCAACACAAAA
** * * *
35158057 CGGCGGTGTTGTGCTAAAAATTTTT
131 CAACGGCGTTGTGCTTAAATTTTTT
* * *
35158082 GCGGCATTTTTCAAAAAACGCAGCTAATGGTCGACCTATAGCGACGTTTTTTAAAAAGCGCCGCT
1 GCGGCGTTTTTCAAAAAGCGCAGCTAATGGTCGACCTATAGCGGCGTTTTTTAAAAAGCGCCGCT
* *
35158147 AATGCTCGATCTATAGCGGCGTTTTTTAAAAAGCGCCACTAATGCCACTAAAGCTCAACACCAAA
66 AATGCTCGATCTATAGCGGCGTTTTTCAAAAAGCGCCACTAATGCCACTAAAGCTCAACACAAAA
* * * *
35158212 CAATGGAGTTATGCTTAATTTTTTT
131 CAACGGCGTTGTGCTTAAATTTTTT
* * *
35158237 GTGGCGTTTTTCAAAAAGCGCCGCTAATAGTCGACCTATAGCGGCGTTTTTTAAAAAGCGCCGCT
1 GCGGCGTTTTTCAAAAAGCGCAGCTAATGGTCGACCTATAGCGGCGTTTTTTAAAAAGCGCCGCT
* * *
35158302 AATGCTCTATCTATAGCAGCGTTTTTCAAAAAGCGCCGCTAATGC
66 AATGCTCGATCTATAGCGGCGTTTTTCAAAAAGCGCCACTAATGC
35158347 TTGATCTATA
Statistics
Matches: 492, Mismatches: 80, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
154 130 0.26
155 359 0.73
156 3 0.01
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.29
Consensus pattern (155 bp):
GCGGCGTTTTTCAAAAAGCGCAGCTAATGGTCGACCTATAGCGGCGTTTTTTAAAAAGCGCCGCT
AATGCTCGATCTATAGCGGCGTTTTTCAAAAAGCGCCACTAATGCCACTAAAGCTCAACACAAAA
CAACGGCGTTGTGCTTAAATTTTTT
Found at i:35157974 original size:40 final size:40
Alignment explanation
Indices: 35157930--35158025 Score: 147
Period size: 40 Copynumber: 2.4 Consensus size: 40
35157920 ATTTTTTTGT
*
35157930 GGCGTTTTTCAAAAAGTGCTGCTAATGGTCGACCTATAGC
1 GGCGTTTTTCAAAAAGCGCTGCTAATGGTCGACCTATAGC
*
35157970 GGCGTTTTTCAAAAAGCGTTGCTAATGGTCGACCTATAGC
1 GGCGTTTTTCAAAAAGCGCTGCTAATGGTCGACCTATAGC
* * *
35158010 AGTGTTTTTTAAAAAG
1 GGCGTTTTTCAAAAAG
35158026 GGCCACTAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (40 bp):
GGCGTTTTTCAAAAAGCGCTGCTAATGGTCGACCTATAGC
Found at i:35158138 original size:40 final size:40
Alignment explanation
Indices: 35158088--35158191 Score: 129
Period size: 40 Copynumber: 2.6 Consensus size: 40
35158078 TTTTGCGGCA
* *
35158088 TTTTTCAAAAAACGCAGCTAATGGTCGACCTATAGCGACG
1 TTTTTTAAAAAACGCAGCTAATGCTCGACCTATAGCGACG
* * * *
35158128 TTTTTTAAAAAGCGCCGCTAATGCTCGATCTATAGCGGCG
1 TTTTTTAAAAAACGCAGCTAATGCTCGACCTATAGCGACG
*
35158168 TTTTTTAAAAAGCGCCA-CTAATGC
1 TTTTTTAAAAAACG-CAGCTAATGC
35158192 CACTAAAGCT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
40 55 0.98
41 1 0.02
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (40 bp):
TTTTTTAAAAAACGCAGCTAATGCTCGACCTATAGCGACG
Found at i:35158180 original size:309 final size:310
Alignment explanation
Indices: 35157620--35158347 Score: 1125
Period size: 309 Copynumber: 2.4 Consensus size: 310
35157610 GACCTATAGC
* *
35157620 GGCGTTTTTCAAAAAGCACTGCTAATGATCGACCTATAGCGGCGTTTTTTAAAAAGCGTCGCTAA
1 GGCGTTTTTCAAAAAGCGCTGCTAATGGTCGACCTATAGCGGCGTTTTTTAAAAAGCGTCGCTAA
* * *
35157685 TGCTCAATCTATAGCGGCGTTTTTCAAAAAGCACCGCTAATGCCACTAAAGCTCAACACAAAACG
66 TGCTCAATCTATAGCAGCGTTTTTCAAAAAGCGCCGCTAATGCTACTAAAGCTCAACACAAAACG
* * * *
35157750 GCAGCGTTGTGCTAACATTTTTTGCGGCGTTTTTCAAAAAGCGCAACTAATGGTCGACCTATAAC
131 GCAGCGTTGTGCTAAAAATTTTTGCGGCATTTTTCAAAAAACGCAACTAATGGTCGACCTATAAC
*
35157815 GTCATTTTTTAAAAAGCACCGCTAATGCTCGATCTATAGCGGCGTTTTTCAAAAAGCGCCACTAA
196 GACATTTTTTAAAAAGCACCGCTAATGCTCGATCTATAGCGGCGTTTTTCAAAAAGCGCCACTAA
* *
35157880 TGCCACTAAAGCTCAACACAAAACAATGGCGTTGTACTTAATTTTTTTGT
261 TGCCACTAAAGCTCAACACAAAACAATGGAGTTATACTTAATTTTTTTGT
* * *
35157930 GGCGTTTTTCAAAAAGTGCTGCTAATGGTCGACCTATAGCGGCGTTTTTCAAAAAGCGTTGCTAA
1 GGCGTTTTTCAAAAAGCGCTGCTAATGGTCGACCTATAGCGGCGTTTTTTAAAAAGCGTCGCTAA
* * * * * * * *
35157995 TGGTCGACCTATAGCAGTGTTTTTTAAAAAGGGCCACTAATGCTGCTAAAG-TCAACACAAAACG
66 TGCTCAATCTATAGCAGCGTTTTTCAAAAAGCGCCGCTAATGCTACTAAAGCTCAACACAAAACG
* * * *
35158059 GCGGTGTTGTGCTAAAAATTTTTGCGGCATTTTTCAAAAAACGCAGCTAATGGTCGACCTATAGC
131 GCAGCGTTGTGCTAAAAATTTTTGCGGCATTTTTCAAAAAACGCAACTAATGGTCGACCTATAAC
* * *
35158124 GACGTTTTTTAAAAAGCGCCGCTAATGCTCGATCTATAGCGGCGTTTTTTAAAAAGCGCCACTAA
196 GACATTTTTTAAAAAGCACCGCTAATGCTCGATCTATAGCGGCGTTTTTCAAAAAGCGCCACTAA
* *
35158189 TGCCACTAAAGCTCAACACCAAACAATGGAGTTATGCTTAATTTTTTTGT
261 TGCCACTAAAGCTCAACACAAAACAATGGAGTTATACTTAATTTTTTTGT
* * *
35158239 GGCGTTTTTCAAAAAGCGCCGCTAATAGTCGACCTATAGCGGCGTTTTTTAAAAAGCGCCGCTAA
1 GGCGTTTTTCAAAAAGCGCTGCTAATGGTCGACCTATAGCGGCGTTTTTTAAAAAGCGTCGCTAA
*
35158304 TGCTCTATCTATAGCAGCGTTTTTCAAAAAGCGCCGCTAATGCT
66 TGCTCAATCTATAGCAGCGTTTTTCAAAAAGCGCCGCTAATGCT
35158348 TGATCTATAA
Statistics
Matches: 373, Mismatches: 45, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
309 273 0.73
310 100 0.27
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.29
Consensus pattern (310 bp):
GGCGTTTTTCAAAAAGCGCTGCTAATGGTCGACCTATAGCGGCGTTTTTTAAAAAGCGTCGCTAA
TGCTCAATCTATAGCAGCGTTTTTCAAAAAGCGCCGCTAATGCTACTAAAGCTCAACACAAAACG
GCAGCGTTGTGCTAAAAATTTTTGCGGCATTTTTCAAAAAACGCAACTAATGGTCGACCTATAAC
GACATTTTTTAAAAAGCACCGCTAATGCTCGATCTATAGCGGCGTTTTTCAAAAAGCGCCACTAA
TGCCACTAAAGCTCAACACAAAACAATGGAGTTATACTTAATTTTTTTGT
Found at i:35158294 original size:40 final size:40
Alignment explanation
Indices: 35158239--35158367 Score: 170
Period size: 40 Copynumber: 3.2 Consensus size: 40
35158229 ATTTTTTTGT
35158239 GGCGTTTTTCAAAAAGCGCCGCTAATAG-TCGACCTATAGC
1 GGCGTTTTTCAAAAAGCGCCGCTAAT-GCTCGACCTATAGC
* * *
35158279 GGCGTTTTTTAAAAAGCGCCGCTAATGCTCTATCTATAGC
1 GGCGTTTTTCAAAAAGCGCCGCTAATGCTCGACCTATAGC
* * * *
35158319 AGCGTTTTTCAAAAAGCGCCGCTAATGCTTGATCTATAAC
1 GGCGTTTTTCAAAAAGCGCCGCTAATGCTCGACCTATAGC
*
35158359 GGTGTTTTT
1 GGCGTTTTT
35158368 TGTCCATACA
Statistics
Matches: 78, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
39 1 0.01
40 77 0.99
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.32
Consensus pattern (40 bp):
GGCGTTTTTCAAAAAGCGCCGCTAATGCTCGACCTATAGC
Found at i:35158744 original size:14 final size:14
Alignment explanation
Indices: 35158725--35158760 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
35158715 GTAATCGGTA
35158725 AAATTTTCTTAATG
1 AAATTTTCTTAATG
35158739 AAATTTTCTTAATG
1 AAATTTTCTTAATG
35158753 AAATTTTC
1 AAATTTTC
35158761 ATACGTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.36, C:0.08, G:0.06, T:0.50
Consensus pattern (14 bp):
AAATTTTCTTAATG
Found at i:35161754 original size:42 final size:42
Alignment explanation
Indices: 35161695--35161878 Score: 168
Period size: 41 Copynumber: 4.5 Consensus size: 42
35161685 AATACTCGAT
*
35161695 ATCTCGCACACTAAGTGCCAAAATATAGCTGAAGCTATTAT-A
1 ATCTCGCACACTAAGTGCCAATATATAGCTGAAGCTATT-TCA
* ** *
35161737 ATCTCGCACACTAAGTG-CATTCCATAGCCGAAGCT-TTCTCA
1 ATCTCGCACACTAAGTGCCAATATATAGCTGAAGCTATT-TCA
* *
35161778 ACCTTGCACACTAAGTGCC-ATATATAGCTGAAGCTATTTCA
1 ATCTCGCACACTAAGTGCCAATATATAGCTGAAGCTATTTCA
** * * *
35161819 AT-TCGCACACTAAGTG-CTTTATATATCCGAAGCTATCTCGA
1 ATCTCGCACACTAAGTGCCAATATATAGCTGAAGCTATTTC-A
*
35161860 A--ACGCACACTAAGTGCCAA
1 ATCTCGCACACTAAGTGCCAA
35161879 ACATAGTTGA
Statistics
Matches: 115, Mismatches: 21, Indels: 13
0.77 0.14 0.09
Matches are distributed among these distances:
39 1 0.01
40 46 0.40
41 48 0.42
42 20 0.17
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.27
Consensus pattern (42 bp):
ATCTCGCACACTAAGTGCCAATATATAGCTGAAGCTATTTCA
Found at i:35161842 original size:40 final size:41
Alignment explanation
Indices: 35161698--35161875 Score: 152
Period size: 40 Copynumber: 4.4 Consensus size: 41
35161688 ACTCGATATC
* *
35161698 TCGCACACTAAGTGCCAAAATATAGCTGAAGCTATTAT-AAT
1 TCGCACACTAAGTG-CAATATATAGCCGAAGCTATTATCAAT
* ** *
35161739 CTCGCACACTAAGTGCATTCCATAGCCGAAGCT-TTCTCAACCT
1 -TCGCACACTAAGTGCAATATATAGCCGAAGCTATTATCAA--T
* *
35161782 T-GCACACTAAGTGCCATATATAGCTGAAGCTATT-TCAAT
1 TCGCACACTAAGTGCAATATATAGCCGAAGCTATTATCAAT
** * *
35161821 TCGCACACTAAGTGCTTTATATATCCGAAGCTA-TCTCGAA-
1 TCGCACACTAAGTGCAATATATAGCCGAAGCTATTATC-AAT
*
35161861 ACGCACACTAAGTGC
1 TCGCACACTAAGTGC
35161876 CAAACATAGT
Statistics
Matches: 113, Mismatches: 16, Indels: 16
0.78 0.11 0.11
Matches are distributed among these distances:
39 3 0.03
40 46 0.41
41 46 0.41
42 17 0.15
43 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.27
Consensus pattern (41 bp):
TCGCACACTAAGTGCAATATATAGCCGAAGCTATTATCAAT
Found at i:35161849 original size:81 final size:81
Alignment explanation
Indices: 35161699--35161884 Score: 243
Period size: 81 Copynumber: 2.3 Consensus size: 81
35161689 CTCGATATCT
*
35161699 CGCACACTAAGTGCCAAAATATAGCTGAAGCTATTATAATCTCGCACACTAAGTGCATTCCATAG
1 CGCACACTAAGTGCC-AAATATAGCTGAAGCTATTATAATCTCGCACACTAAGTGCATTACATAG
* *
35161764 CCGAAGCTTTCTC-AAC
65 CCGAAGCTATCTCGAAA
* * *
35161780 CTTGCACACTAAGTGCCATATATAGCTGAAGCTATT-TCAAT-TCGCACACTAAGTGCTTTATAT
1 C--GCACACTAAGTGCCAAATATAGCTGAAGCTATTAT-AATCTCGCACACTAAGTGCATTACAT
*
35161843 ATCCGAAGCTATCTCGAAA
63 AGCCGAAGCTATCTCGAAA
*
35161862 CGCACACTAAGTGCCAAACATAG
1 CGCACACTAAGTGCCAAATATAG
35161885 TTGATTTATC
Statistics
Matches: 92, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
80 20 0.22
81 34 0.37
82 24 0.26
83 14 0.15
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.26
Consensus pattern (81 bp):
CGCACACTAAGTGCCAAATATAGCTGAAGCTATTATAATCTCGCACACTAAGTGCATTACATAGC
CGAAGCTATCTCGAAA
Found at i:35169211 original size:40 final size:40
Alignment explanation
Indices: 35169097--35169234 Score: 147
Period size: 40 Copynumber: 3.4 Consensus size: 40
35169087 TCATACCGAA
*
35169097 CGCACACTAAGTGCCTTT-CATAGCCGAAGCT-TTCTCAACCT
1 CGCACACTAAGTGCCTTTATATAGCCGAAGCTATTC-CAA--T
* *
35169138 CGCACACTAAGTGCCATATATATAGCTGAAGCTATTCCAATT
1 CGCACACTAAGTGCC-TTTATATAGCCGAAGCTATTCCAA-T
* * *
35169180 CGCACACTAAATG-CTTTATATAGCCGAAGCTATCTCGAAA
1 CGCACACTAAGTGCCTTTATATAGCCGAAGCTAT-TCCAAT
35169220 CGCACACTAAGTGCC
1 CGCACACTAAGTGCC
35169235 AAATATAGTC
Statistics
Matches: 82, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
40 29 0.35
41 21 0.26
42 15 0.18
43 14 0.17
44 3 0.04
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.25
Consensus pattern (40 bp):
CGCACACTAAGTGCCTTTATATAGCCGAAGCTATTCCAAT
Found at i:35180853 original size:14 final size:15
Alignment explanation
Indices: 35180825--35180858 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
35180815 TAATTGAAGA
35180825 ATTTTTAGATATCAT
1 ATTTTTAGATATCAT
*
35180840 ATTTTTATAT-TCAT
1 ATTTTTAGATATCAT
35180854 ATTTT
1 ATTTT
35180859 AACATAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.62
Consensus pattern (15 bp):
ATTTTTAGATATCAT
Found at i:35180964 original size:23 final size:23
Alignment explanation
Indices: 35180934--35180978 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
35180924 TATTCAATTT
35180934 TGATTTGAACTTAAAATATTTTC
1 TGATTTGAACTTAAAATATTTTC
* *
35180957 TGATTTGAATTTAAATTATTTT
1 TGATTTGAACTTAAAATATTTT
35180979 TAGAGTGTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.33, C:0.04, G:0.09, T:0.53
Consensus pattern (23 bp):
TGATTTGAACTTAAAATATTTTC
Found at i:35184159 original size:129 final size:129
Alignment explanation
Indices: 35183929--35184186 Score: 507
Period size: 129 Copynumber: 2.0 Consensus size: 129
35183919 ATGGCTAGCT
35183929 GATCCCTACTATAGAAGTGACTATAGGCTGCCCTTTATTTGTGCAGCTAGATATATGGGAGTATG
1 GATCCCTACTATAGAAGTGACTATAGGCTGCCCTTTATTTGTGCAGCTAGATATATGGGAGTATG
35183994 TCAGATCCATGACTATCCTATAGTATATATGATTAAAATGTAGATTCCTTCATCTAATTCAGCA
66 TCAGATCCATGACTATCCTATAGTATATATGATTAAAATGTAGATTCCTTCATCTAATTCAGCA
*
35184058 GATCCCTACTATAGAAGTGACTATAGGCTGCCCTTTATTTGTGCAGTTAGATATATGGGAGTATG
1 GATCCCTACTATAGAAGTGACTATAGGCTGCCCTTTATTTGTGCAGCTAGATATATGGGAGTATG
35184123 TCAGATCCATGACTATCCTATAGTATATATGATTAAAATGTAGATTCCTTCATCTAATTCAGCA
66 TCAGATCCATGACTATCCTATAGTATATATGATTAAAATGTAGATTCCTTCATCTAATTCAGCA
35184187 CCGGCTGAAG
Statistics
Matches: 128, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
129 128 1.00
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.34
Consensus pattern (129 bp):
GATCCCTACTATAGAAGTGACTATAGGCTGCCCTTTATTTGTGCAGCTAGATATATGGGAGTATG
TCAGATCCATGACTATCCTATAGTATATATGATTAAAATGTAGATTCCTTCATCTAATTCAGCA
Found at i:35188089 original size:21 final size:21
Alignment explanation
Indices: 35188063--35188103 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
35188053 AGACGAGCAA
* *
35188063 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
35188084 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
35188104 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:35190956 original size:6 final size:6
Alignment explanation
Indices: 35190941--35190971 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
35190931 TAAATCAATG
*
35190941 AACACT AACACC AACACC AACACC AACACC A
1 AACACC AACACC AACACC AACACC AACACC A
35190972 TGGAAGTTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.52, C:0.45, G:0.00, T:0.03
Consensus pattern (6 bp):
AACACC
Found at i:35194032 original size:19 final size:21
Alignment explanation
Indices: 35194010--35194063 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
35194000 AATGTTAACA
35194010 TTTAAATAAATTTTTA-A-AG
1 TTTAAATAAATTTTTATATAG
* *
35194029 TTTAAATATTATTTTTATATAT
1 TTTAAATA-AATTTTTATATAG
35194051 TTTAAAT-AATTTT
1 TTTAAATAAATTTT
35194064 AATGATTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 8 0.28
20 12 0.41
21 1 0.03
22 8 0.28
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
TTTAAATAAATTTTTATATAG
Found at i:35201977 original size:13 final size:14
Alignment explanation
Indices: 35201951--35201978 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
35201941 TGCTTTTATT
35201951 AAAAATTAGAAAAA
1 AAAAATTAGAAAAA
35201965 AAAAATTAGAAAAA
1 AAAAATTAGAAAAA
35201979 TTTAAAATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (14 bp):
AAAAATTAGAAAAA
Found at i:35202041 original size:10 final size:10
Alignment explanation
Indices: 35202028--35202071 Score: 54
Period size: 11 Copynumber: 4.3 Consensus size: 10
35202018 ATAAAAAATT
35202028 AATTATTAAA
1 AATTATTAAA
35202038 AATTTATTAAA
1 AA-TTATTAAA
35202049 AATTA-TAAA
1 AATTATTAAA
*
35202058 AAATATATAAA
1 AATTAT-TAAA
35202069 AAT
1 AAT
35202072 CGTAAAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
9 8 0.28
10 5 0.17
11 16 0.55
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
AATTATTAAA
Found at i:35202044 original size:11 final size:11
Alignment explanation
Indices: 35202030--35202071 Score: 52
Period size: 10 Copynumber: 4.0 Consensus size: 11
35202020 AAAAAATTAA
35202030 TTATTAAAAAT
1 TTATTAAAAAT
35202041 TTATTAAAAA-
1 TTATTAAAAAT
*
35202051 TTATAAAAAAT
1 TTATTAAAAAT
*
35202062 ATA-TAAAAAT
1 TTATTAAAAAT
35202072 CGTAAAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 15 0.56
11 12 0.44
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
TTATTAAAAAT
Found at i:35202054 original size:21 final size:20
Alignment explanation
Indices: 35202028--35202088 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
35202018 ATAAAAAATT
* *
35202028 AATTATTAAAAATTTATTAAA
1 AATTATAAAAAATATA-TAAA
35202049 AATTATAAAAAATATATAAA
1 AATTATAAAAAATATATAAA
**
35202069 AATCGTAAAAAATATA-AAA
1 AATTATAAAAAATATATAAA
35202088 A
1 A
35202089 TTGTAAAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.11
20 18 0.50
21 14 0.39
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (20 bp):
AATTATAAAAAATATATAAA
Found at i:35202625 original size:87 final size:87
Alignment explanation
Indices: 35202456--35202650 Score: 209
Period size: 87 Copynumber: 2.2 Consensus size: 87
35202446 AATGAGAGCA
* * ** *
35202456 AGGGCTTAATTGTTTTTTTGAAAAATTTGGAGGGTCTTTTTGATGTATTTTGAAATTTCAAGTAC
1 AGGGCTTAATTGTTTTTTTGAAAAATTTGGAGGGCCTTTTGGATACATTTTGAAAGTTCAAGTAC
* * * *
35202521 CCAATTGTGTGGGAAAAAACA-G
66 CCAATGGAGT-GCAAAAAAAAGG
35202543 -GGGCTTAATTGATTTTTTT-AAAGAAGTTT-GAGGGCCTTTTGGATACATTTTGAAAGTTCAAG
1 AGGGCTTAATTG-TTTTTTTGAAA-AA-TTTGGAGGGCCTTTTGGATACATTTTGAAAGTTCAAG
* *
35202605 TGCTCAATGGAGTGCAAAAAAAAGG
63 TACCCAATGGAGTGCAAAAAAAAGG
35202630 AGGGCTTAATTGCTTCTTTTT
1 AGGGCTTAATTG-TT-TTTTT
35202651 TGTAAAAAAA
Statistics
Matches: 90, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
86 22 0.24
87 47 0.52
88 16 0.18
89 5 0.06
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (87 bp):
AGGGCTTAATTGTTTTTTTGAAAAATTTGGAGGGCCTTTTGGATACATTTTGAAAGTTCAAGTAC
CCAATGGAGTGCAAAAAAAAGG
Found at i:35204253 original size:26 final size:26
Alignment explanation
Indices: 35204189--35204253 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 26
35204179 ATCATTCTTC
*
35204189 ATATATTTGAAAACTTATTTTAAAAA
1 ATATTTTTGAAAACTTATTTTAAAAA
* * *
35204215 ATATTTATGAAAACTTTTTTTAAAGA
1 ATATTTTTGAAAACTTATTTTAAAAA
*
35204241 ATATTTTTTAAAA
1 ATATTTTTGAAAA
35204254 TAATCAGTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (26 bp):
ATATTTTTGAAAACTTATTTTAAAAA
Found at i:35206760 original size:20 final size:21
Alignment explanation
Indices: 35206731--35206769 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
35206721 CATATGACCA
*
35206731 AGTTGTCTTCG-CTCCAAACG
1 AGTTGACTTCGACTCCAAACG
35206751 AGTTGACTTCGACTCCAAA
1 AGTTGACTTCGACTCCAAA
35206770 ACAGACGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (21 bp):
AGTTGACTTCGACTCCAAACG
Found at i:35211006 original size:64 final size:64
Alignment explanation
Indices: 35210927--35211064 Score: 240
Period size: 64 Copynumber: 2.2 Consensus size: 64
35210917 ACAAAGCAAA
* *
35210927 GGCAATAACATACGGGAAAATATCATGACCAAGTCAGTACATTGGGCATTAGTTTATAAGGAAC
1 GGCAATAACATACGGGAAAATATCACGACCAAGTCAGTAAATTGGGCATTAGTTTATAAGGAAC
*
35210991 GGCAATAACATACGGGAAAATATCACGACCAAGTCAGTAAATTGGGCATTTGTTTATAAGGAAC
1 GGCAATAACATACGGGAAAATATCACGACCAAGTCAGTAAATTGGGCATTAGTTTATAAGGAAC
*
35211055 GCCAATAACA
1 GGCAATAACA
35211065 GTATTTTCTA
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 70 1.00
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.22
Consensus pattern (64 bp):
GGCAATAACATACGGGAAAATATCACGACCAAGTCAGTAAATTGGGCATTAGTTTATAAGGAAC
Found at i:35215786 original size:42 final size:42
Alignment explanation
Indices: 35215725--35215851 Score: 161
Period size: 42 Copynumber: 3.0 Consensus size: 42
35215715 CTTCGTTTTC
* * *
35215725 TCGATGCCGTAGCTCAACTATGGTCTTACACATCTTCACATAA
1 TCGATGCCATAGCCCAACTATGGTCTTACACATATTCACAT-A
*
35215768 T-GATGCCATAGCCCAACTATGGTCTTACACATATTCATATA
1 TCGATGCCATAGCCCAACTATGGTCTTACACATATTCACATA
* *
35215809 TCGATGCCATAGCCTAGCTATGGTCTTACACGA-A-TCACATA
1 TCGATGCCATAGCCCAACTATGGTCTTACAC-ATATTCACATA
35215850 TC
1 TC
35215852 TCACTGATGC
Statistics
Matches: 75, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
41 10 0.13
42 63 0.84
43 2 0.03
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (42 bp):
TCGATGCCATAGCCCAACTATGGTCTTACACATATTCACATA
Found at i:35215911 original size:47 final size:46
Alignment explanation
Indices: 35215810--35215933 Score: 149
Period size: 47 Copynumber: 2.7 Consensus size: 46
35215800 ATTCATATAT
* * * * * *
35215810 CGATGCCATAGCCTAGCTATGGTCTTACACGAATCACATATCTCAC
1 CGATGCCATATCCCAGATATGGTCTTATACGAAGCACATATCACAC
* * *
35215856 TGATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCACAC
1 CGATGCCATATCCCAGATATGGTCTTATAC-GAAGCACATATCACAC
*
35215903 CGATGCCATATCCCATATATGGTCTTATACG
1 CGATGCCATATCCCAGATATGGTCTTATACG
35215934 GAAATTACTT
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
46 26 0.39
47 40 0.61
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (46 bp):
CGATGCCATATCCCAGATATGGTCTTATACGAAGCACATATCACAC
Found at i:35215989 original size:31 final size:31
Alignment explanation
Indices: 35215959--35216068 Score: 193
Period size: 31 Copynumber: 3.5 Consensus size: 31
35215949 TTGTAGCCGG
* * *
35215959 AGCTACCACTATTCACTGATCAGGTAGCCGG
1 AGCTACCACTTTTCACTGATCAGGTAGCAGA
35215990 AGCTACCACTTTTCACTGATCAGGTAGCAGA
1 AGCTACCACTTTTCACTGATCAGGTAGCAGA
35216021 AGCTACCACTTTTCACTGATCAGGTAGCAGA
1 AGCTACCACTTTTCACTGATCAGGTAGCAGA
35216052 AGCTACCACTTTTCACT
1 AGCTACCACTTTTCACT
35216069 TGTCATTTGT
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 76 1.00
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.26
Consensus pattern (31 bp):
AGCTACCACTTTTCACTGATCAGGTAGCAGA
Found at i:35216149 original size:50 final size:50
Alignment explanation
Indices: 35216044--35216220 Score: 266
Period size: 50 Copynumber: 3.5 Consensus size: 50
35216034 CACTGATCAG
* * * * *
35216044 GTAGCAGAAGCTACCACTTTTCACTTGTCATTTGTCCCTGATCAGATAGGT
1 GTAGCCGAAGCTATCACTTATCACTT-TCATTTGTCCTTGATCAGATAAGT
*
35216095 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
*
35216145 GTAGCCGAAGCTA-CTACTTATCACTTTCATTTGTCCTTGATTAGATAAGT
1 GTAGCCGAAGCTATC-ACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
35216195 GTAGCCGAAGCTATCACTTATCACTT
1 GTAGCCGAAGCTATCACTTATCACTT
35216221 GTTGTCATGG
Statistics
Matches: 116, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
49 1 0.01
50 91 0.78
51 24 0.21
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.34
Consensus pattern (50 bp):
GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
Found at i:35220047 original size:26 final size:26
Alignment explanation
Indices: 35220018--35220069 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
35220008 GTATAAAACG
*
35220018 ATTTAAAAATAGATTATATATATAAA
1 ATTTAAAAATAGATAATATATATAAA
*
35220044 ATTTTAAAATAGATAATATATATAAA
1 ATTTAAAAATAGATAATATATATAAA
35220070 TATAAAAGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (26 bp):
ATTTAAAAATAGATAATATATATAAA
Found at i:35220075 original size:24 final size:26
Alignment explanation
Indices: 35220023--35220076 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
35220013 AAACGATTTA
* *
35220023 AAAATAGATTATATATATAAAATTTT
1 AAAATAGATAATATATATAAAATTAT
35220049 AAAATAGATAATATATAT-AAA-TAT
1 AAAATAGATAATATATATAAAATTAT
35220073 AAAA
1 AAAA
35220077 GTGTAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 6 0.23
25 3 0.12
26 17 0.65
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (26 bp):
AAAATAGATAATATATATAAAATTAT
Found at i:35220076 original size:32 final size:32
Alignment explanation
Indices: 35220032--35220095 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
35220022 AAAAATAGAT
* * * *
35220032 TATATATATAAAATTTTAAAATAGATAATATA
1 TATAAATATAAAAGTGTAAAATAAATAATATA
*
35220064 TATAAATATAAAAGTGTAAAATAAATATTATA
1 TATAAATATAAAAGTGTAAAATAAATAATATA
35220096 AAGAATATTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.38
Consensus pattern (32 bp):
TATAAATATAAAAGTGTAAAATAAATAATATA
Found at i:35220111 original size:24 final size:25
Alignment explanation
Indices: 35220080--35220138 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
35220070 TATAAAAGTG
* *
35220080 TAAAATAAAT-ATTAT-AAAGAATAT
1 TAAAATAAATAATAATAAAACAAT-T
35220104 TAAAATAAATAATAATAAAACAATT
1 TAAAATAAATAATAATAAAACAATT
35220129 TAAAATAAAT
1 TAAAATAAAT
35220139 GAAAAGAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
24 10 0.32
25 15 0.48
26 6 0.19
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (25 bp):
TAAAATAAATAATAATAAAACAATT
Found at i:35220176 original size:24 final size:24
Alignment explanation
Indices: 35220147--35220202 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
35220137 ATGAAAAGAG
*
35220147 TTTAAAATAAGGCATATGAAAT-AA
1 TTTAAAATAAGGAATAT-AAATCAA
*
35220171 TTTAAAATAAGTAATATAAATCAA
1 TTTAAAATAAGGAATATAAATCAA
35220195 TTTAAAAT
1 TTTAAAAT
35220203 TTATATACTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 4 0.14
24 25 0.86
ACGTcount: A:0.55, C:0.04, G:0.07, T:0.34
Consensus pattern (24 bp):
TTTAAAATAAGGAATATAAATCAA
Found at i:35224981 original size:18 final size:18
Alignment explanation
Indices: 35224958--35225001 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
35224948 TCAGTATTTT
35224958 GACCCACATGCTCATGTG
1 GACCCACATGCTCATGTG
35224976 GACCCACATGCTCATGTG
1 GACCCACATGCTCATGTG
*
35224994 GATCCACA
1 GACCCACA
35225002 CGGCCTAGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.25, C:0.34, G:0.20, T:0.20
Consensus pattern (18 bp):
GACCCACATGCTCATGTG
Found at i:35231219 original size:24 final size:25
Alignment explanation
Indices: 35231179--35231235 Score: 80
Period size: 24 Copynumber: 2.3 Consensus size: 25
35231169 GTTAATAATT
* * *
35231179 TTTTTTATAAATAAAAAATTTGTAG
1 TTTTTTATAAATAAAAAAATTATAA
35231204 TTTTTTATAAAT-AAAAAATTATAA
1 TTTTTTATAAATAAAAAAATTATAA
35231228 TTTTTTAT
1 TTTTTTAT
35231236 TTTTAAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 17 0.59
25 12 0.41
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (25 bp):
TTTTTTATAAATAAAAAAATTATAA
Found at i:35231232 original size:25 final size:25
Alignment explanation
Indices: 35231173--35231233 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
35231163 GTAAGTGTTA
35231173 ATAATTTTTTTTATAAATAAAAAATT
1 ATAA-TTTTTTTATAAATAAAAAATT
* *
35231199 -TGTAGTTTTTTATAAATAAAAAATT
1 AT-AATTTTTTTATAAATAAAAAATT
35231224 ATAATTTTTT
1 ATAATTTTTT
35231234 ATTTTTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
25 27 0.93
26 2 0.07
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.52
Consensus pattern (25 bp):
ATAATTTTTTTATAAATAAAAAATT
Found at i:35251073 original size:28 final size:28
Alignment explanation
Indices: 35251033--35251089 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
35251023 ACATTATCTA
*
35251033 AGTTAACAGAAAACTATGAAACCAAGGT
1 AGTTAAAAGAAAACTATGAAACCAAGGT
35251061 AGTTAAAAGAAAACTATGAAACCAAGGT
1 AGTTAAAAGAAAACTATGAAACCAAGGT
35251089 A
1 A
35251090 AACACATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.53, C:0.12, G:0.18, T:0.18
Consensus pattern (28 bp):
AGTTAAAAGAAAACTATGAAACCAAGGT
Found at i:35252310 original size:2 final size:2
Alignment explanation
Indices: 35252303--35252331 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
35252293 CATAATTTAA
35252303 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
35252332 GAGAGAGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35253107 original size:18 final size:17
Alignment explanation
Indices: 35253078--35253111 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
35253068 TATACTTATA
35253078 TTAATTATTAATTAAAC
1 TTAATTATTAATTAAAC
35253095 TTAATTAATTAATTAAA
1 TTAATT-ATTAATTAAA
35253112 ATTTTAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
TTAATTATTAATTAAAC
Found at i:35254866 original size:44 final size:44
Alignment explanation
Indices: 35254803--35254891 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
35254793 AATTTCGAAA
*
35254803 ATAAGCAACTAAGAACAATAATCACAACATTTATATTTTTAGTC
1 ATAAGCAACTAAAAACAATAATCACAACATTTATATTTTTAGTC
35254847 ATAAGCAACTAAAAACAATAATCACAACATTTATATTTTTAGTC
1 ATAAGCAACTAAAAACAATAATCACAACATTTATATTTTTAGTC
35254891 A
1 A
35254892 ATTTTATATA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.47, C:0.16, G:0.06, T:0.31
Consensus pattern (44 bp):
ATAAGCAACTAAAAACAATAATCACAACATTTATATTTTTAGTC
Done.