Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 140 of 206
Found at i:42851910 original size:53 final size:53
Alignment explanation
Indices: 42851830--42851970 Score: 264
Period size: 53 Copynumber: 2.7 Consensus size: 53
42851820 CTTTTTCTAT
42851830 TTAGAAAAAGAATTCTATCTAAATAATAAATAAATTCAAGTGGGTGTTCATTA
1 TTAGAAAAAGAATTCTATCTAAATAATAAATAAATTCAAGTGGGTGTTCATTA
* *
42851883 TTAGAAAAAGAATTCTATCTAAATAATAAATAAATTGAAGTGGGTGTTCATTG
1 TTAGAAAAAGAATTCTATCTAAATAATAAATAAATTCAAGTGGGTGTTCATTA
42851936 TTAGAAAAAGAATTCTATCTAAATAATAAATAAAT
1 TTAGAAAAAGAATTCTATCTAAATAATAAATAAAT
42851971 ACAATCCCCC
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 86 1.00
ACGTcount: A:0.48, C:0.06, G:0.13, T:0.33
Consensus pattern (53 bp):
TTAGAAAAAGAATTCTATCTAAATAATAAATAAATTCAAGTGGGTGTTCATTA
Found at i:42854542 original size:18 final size:18
Alignment explanation
Indices: 42854519--42854554 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
42854509 TGATTTTTTT
*
42854519 TTTTACTTTTCATATTTG
1 TTTTACTGTTCATATTTG
*
42854537 TTTTACTGTTCATGTTTG
1 TTTTACTGTTCATATTTG
42854555 GGATCTATGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.11, G:0.11, T:0.64
Consensus pattern (18 bp):
TTTTACTGTTCATATTTG
Found at i:42857350 original size:6 final size:5
Alignment explanation
Indices: 42857333--42857366 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
42857323 AACAGATTCG
*
42857333 TAAAA CAAAA TAAAAA TAAAA TAAAA TAAAA TAA
1 TAAAA TAAAA T-AAAA TAAAA TAAAA TAAAA TAA
42857367 TAAAAACGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (5 bp):
TAAAA
Found at i:42857358 original size:16 final size:16
Alignment explanation
Indices: 42857333--42857363 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
42857323 AACAGATTCG
42857333 TAAAACAAAATAAAAA
1 TAAAACAAAATAAAAA
*
42857349 TAAAATAAAATAAAA
1 TAAAACAAAATAAAA
42857364 TAATAAAAAC
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:0.81, C:0.03, G:0.00, T:0.16
Consensus pattern (16 bp):
TAAAACAAAATAAAAA
Found at i:42858172 original size:50 final size:50
Alignment explanation
Indices: 42858116--42858361 Score: 172
Period size: 50 Copynumber: 4.9 Consensus size: 50
42858106 ACTGTGATGT
* *
42858116 CGGGGAAGCAAGATTCGCCATTATGGCTTTAATCTGTTCCACTGCACCGC
1 CGGGGAAGCAAGATTCGCCATTGTGGCTTTAATCTGTTCCACTGCAACGC
* * ** * * ** * * *
42858166 CAGGGAAGTAAGATTCGCTGTTGTAGCTTTAATCTTTTGAACTACAATGT
1 CGGGGAAGCAAGATTCGCCATTGTGGCTTTAATCTGTTCCACTGCAACGC
* * * * *
42858216 CGGGGAAGCAAGATTCACCGA-TGTGGCCTTAATCTGTTCCATTGCATCAC
1 CGGGGAAGCAAGATTCGCC-ATTGTGGCTTTAATCTGTTCCACTGCAACGC
* * * ** * * ** * *
42858266 CTGGGAGGTAAGATTCGCTGTTGTAGCTTTAATCTTTTGAACTGCAATGT
1 CGGGGAAGCAAGATTCGCCATTGTGGCTTTAATCTGTTCCACTGCAACGC
* **
42858316 CGGGGAAGCAAGATTCACCGA-TGCAGCTTTAATCTGTTCCACTGCA
1 CGGGGAAGCAAGATTCGCC-ATTGTGGCTTTAATCTGTTCCACTGCA
42858362 TCACCTGAGG
Statistics
Matches: 138, Mismatches: 55, Indels: 6
0.69 0.28 0.03
Matches are distributed among these distances:
50 138 1.00
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (50 bp):
CGGGGAAGCAAGATTCGCCATTGTGGCTTTAATCTGTTCCACTGCAACGC
Found at i:42858367 original size:100 final size:100
Alignment explanation
Indices: 42858112--42858368 Score: 392
Period size: 100 Copynumber: 2.6 Consensus size: 100
42858102 CTTAACTGTG
* * * *
42858112 ATGTCGGGGAAGCAAGATTCGCC-AT-TATGGCTTTAATCTGTTCCACTGCACCGCCAGGGAAGT
1 ATGTCGGGGAAGCAAGATTCACCGATGTA--GCTTTAATCTGTTCCACTGCATCACCTGGGAAGT
42858175 AAGATTCGCTGTTGTAGCTTTAATCTTTTGAACTACA
64 AAGATTCGCTGTTGTAGCTTTAATCTTTTGAACTACA
* * * *
42858212 ATGTCGGGGAAGCAAGATTCACCGATGTGGCCTTAATCTGTTCCATTGCATCACCTGGGAGGTAA
1 ATGTCGGGGAAGCAAGATTCACCGATGTAGCTTTAATCTGTTCCACTGCATCACCTGGGAAGTAA
*
42858277 GATTCGCTGTTGTAGCTTTAATCTTTTGAACTGCA
66 GATTCGCTGTTGTAGCTTTAATCTTTTGAACTACA
*
42858312 ATGTCGGGGAAGCAAGATTCACCGATGCAGCTTTAATCTGTTCCACTGCATCACCTG
1 ATGTCGGGGAAGCAAGATTCACCGATGTAGCTTTAATCTGTTCCACTGCATCACCTG
42858369 AGGGATAAGA
Statistics
Matches: 142, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
100 139 0.98
101 2 0.01
102 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (100 bp):
ATGTCGGGGAAGCAAGATTCACCGATGTAGCTTTAATCTGTTCCACTGCATCACCTGGGAAGTAA
GATTCGCTGTTGTAGCTTTAATCTTTTGAACTACA
Found at i:42858379 original size:50 final size:49
Alignment explanation
Indices: 42858225--42858380 Score: 127
Period size: 50 Copynumber: 3.1 Consensus size: 49
42858215 TCGGGGAAGC
* * * *
42858225 AAGATTCACCGATGTGGCCTTAATCTGTTCCATTGCATCACCTGGGAGGT
1 AAGATTCACCGATGTAGCTTTAATCTGTTCCACTGCATCACCTGGG-GAT
* * * * ** ** *
42858275 AAGATTCGCTGTTGTAGCTTTAATCTTTTGAACTGCA--ATGTCGGGGAAGC
1 AAGATTCACCGATGTAGCTTTAATCTGTTCCACTGCATCACCT-GGGG-A-T
*
42858325 AAGATTCACCGATGCAGCTTTAATCTGTTCCACTGCATCACCTGAGGGAT
1 AAGATTCACCGATGTAGCTTTAATCTGTTCCACTGCATCACCTG-GGGAT
42858375 AAGATT
1 AAGATT
42858381 TGCTTCTTCG
Statistics
Matches: 77, Mismatches: 23, Indels: 12
0.69 0.21 0.11
Matches are distributed among these distances:
48 3 0.04
49 3 0.04
50 64 0.83
51 2 0.03
52 5 0.06
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31
Consensus pattern (49 bp):
AAGATTCACCGATGTAGCTTTAATCTGTTCCACTGCATCACCTGGGGAT
Found at i:42858538 original size:44 final size:44
Alignment explanation
Indices: 42858475--42858977 Score: 237
Period size: 44 Copynumber: 10.8 Consensus size: 44
42858465 CCTTTATTTT
* * *
42858475 AATCCGCTCCACTATAATCTCAGGGAGATAGGATTACTAGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
* * * *
42858519 AATCTTCTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
* * * * *
42858563 AATCTGATGCGATCTACTCTACTGTAACCTCAGAGAGATAAGA-TCCT-GTATTTT
1 AATC---T--G--CT-C-C-ACTGTAATCTCAGGGAGATAAGATTACTAG--CTTC
* * *
42858617 AATCCGCTCCACTGTAATCTCATGGAGATAGGATTACTAGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
* * * *
42858661 CATCTGCTCCTCTGTAATCTCAAGGAGATAAGATTTCTAGCTGCAATC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCT----TC
* * * * * *
42858709 TAATGTGATCTACTCTACTGTAACCTCAGAGAGATAAGATCCT-TTA-TTTT
1 -AATCTG--CT-C-C-ACTGTAATCTCAGGGAGATAAGAT--TACTAGCTTC
*
42858759 AATCCGCTCCACTGTAATCTCAGGGAGA-AAGGATTACTAGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAA-GATTACTAGCTTC
* * * * *
42858803 CACCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
* ** * * *
42858847 AATCTGATGTGATCTACTCTACTGTAACCTCAAAGAGATAAGATCCT-TTA-TTTT
1 AATC-----TG--CT-C-C-ACTGTAATCTCAGGGAGATAAGAT--TACTAGCTTC
* * * *
42858901 AATCCGGTCCACTGTAATTTCAGGGAGATAGGATTACTAGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
* *
42858945 CATCTGCTCCGCTGTAATCTCAGGGAGATAAGA
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGA
42858978 CTTGTTTTCT
Statistics
Matches: 339, Mismatches: 76, Indels: 88
0.67 0.15 0.17
Matches are distributed among these distances:
42 2 0.01
43 6 0.02
44 204 0.60
45 8 0.02
46 4 0.01
47 6 0.02
48 2 0.01
49 12 0.04
50 1 0.00
51 6 0.02
52 4 0.01
53 6 0.02
54 73 0.22
55 3 0.01
56 2 0.01
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (44 bp):
AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
Found at i:42858680 original size:142 final size:142
Alignment explanation
Indices: 42858424--42858977 Score: 946
Period size: 142 Copynumber: 3.9 Consensus size: 142
42858414 GGGATAAGAC
* *
42858424 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTA
1 CTGATGCGATCTACTCTACTGTAACCTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
* *
42858489 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTTCTCCGCTGTAATCTCAGGGAGATAAGATT
66 TAATCTCAGGGAGATAGGATTACTAGCTTCCATCTGCTCCGCTGTAATCTCAGGGAGATAAGATT
42858554 TCTGGCTTCAAT
131 TCTGGCTTCAAT
*
42858566 CTGATGCGATCTACTCTACTGTAACCTCAGAGAGATAAGATCCTGTATTTTAATCCGCTCCACTG
1 CTGATGCGATCTACTCTACTGTAACCTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
* * *
42858631 TAATCTCATGGAGATAGGATTACTAGCTTCCATCTGCTCCTCTGTAATCTCAAGGAGATAAGATT
66 TAATCTCAGGGAGATAGGATTACTAGCTTCCATCTGCTCCGCTGTAATCTCAGGGAGATAAGATT
* *
42858696 TCTAGCTGCAAT
131 TCTGGCTTCAAT
* *
42858708 CTAATGTGATCTACTCTACTGTAACCTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
1 CTGATGCGATCTACTCTACTGTAACCTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
* *
42858773 TAATCTCAGGGAGAAAGGATTACTAGCTTCCACCTGCTCCGCTGTAATCTCAGGGAGATAAGATT
66 TAATCTCAGGGAGATAGGATTACTAGCTTCCATCTGCTCCGCTGTAATCTCAGGGAGATAAGATT
42858838 TCTGGCTTCAAT
131 TCTGGCTTCAAT
* * *
42858850 CTGATGTGATCTACTCTACTGTAACCTCAAAGAGATAAGATCCTTTATTTTAATCCGGTCCACTG
1 CTGATGCGATCTACTCTACTGTAACCTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
*
42858915 TAATTTCAGGGAGATAGGATTACTAGCTTCCATCTGCTCCGCTGTAATCTCAGGGAGATAAGA
66 TAATCTCAGGGAGATAGGATTACTAGCTTCCATCTGCTCCGCTGTAATCTCAGGGAGATAAGA
42858978 CTTGTTTTCT
Statistics
Matches: 386, Mismatches: 26, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
142 386 1.00
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (142 bp):
CTGATGCGATCTACTCTACTGTAACCTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
TAATCTCAGGGAGATAGGATTACTAGCTTCCATCTGCTCCGCTGTAATCTCAGGGAGATAAGATT
TCTGGCTTCAAT
Found at i:42860439 original size:7 final size:7
Alignment explanation
Indices: 42860420--42860466 Score: 55
Period size: 7 Copynumber: 6.9 Consensus size: 7
42860410 TTAGCCTTTC
42860420 CATTTTT
1 CATTTTT
42860427 -ACTTTTT
1 CA-TTTTT
42860434 CATTTTT
1 CATTTTT
42860441 CCATTTTT
1 -CATTTTT
42860449 CA-TTTT
1 CATTTTT
42860455 CA-TTTT
1 CATTTTT
42860461 CATTTT
1 CATTTT
42860467 CCCTTTTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
6 13 0.36
7 15 0.42
8 8 0.22
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.68
Consensus pattern (7 bp):
CATTTTT
Found at i:42860441 original size:22 final size:21
Alignment explanation
Indices: 42860416--42860460 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
42860406 CCCCTTAGCC
*
42860416 TTTCCATTTTTACTTTTTCATT
1 TTTCCATTTTT-CATTTTCATT
42860438 TTTCCATTTTTCATTTTCATT
1 TTTCCATTTTTCATTTTCATT
42860459 TT
1 TT
42860461 CATTTTCCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.13, C:0.18, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTCCATTTTTCATTTTCATT
Found at i:42861420 original size:47 final size:52
Alignment explanation
Indices: 42861316--42861420 Score: 114
Period size: 46 Copynumber: 2.1 Consensus size: 52
42861306 ATTTTTTCCT
* *
42861316 TTTTTCTTTTTTCCTTCTCTCCTTTTTTATTTTCATTTTGACTTTAATTTTTC
1 TTTTTCTTTTTTCCTTCTCT-CTTTTTTATCTTCATTTTGACTTTAATTTTTA
* *
42861369 TTTTTC-TTTTT-CTTCTCT-TTTTTT-TCTT-ATTTT-ATTTTGATTTTTGA
1 TTTTTCTTTTTTCCTTCTCTCTTTTTTATCTTCATTTTGACTTTAATTTTT-A
42861416 TTTTT
1 TTTTT
42861421 TTGAATCGGA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
46 10 0.21
47 10 0.21
48 3 0.06
49 6 0.13
51 7 0.15
52 5 0.11
53 6 0.13
ACGTcount: A:0.09, C:0.14, G:0.03, T:0.74
Consensus pattern (52 bp):
TTTTTCTTTTTTCCTTCTCTCTTTTTTATCTTCATTTTGACTTTAATTTTTA
Found at i:42866875 original size:19 final size:21
Alignment explanation
Indices: 42866840--42866880 Score: 68
Period size: 19 Copynumber: 2.0 Consensus size: 21
42866830 ATTTTTTTTC
42866840 AAAAGTCACAATGTTTTAAAT
1 AAAAGTCACAATGTTTTAAAT
42866861 AAAA-TCACAAT-TTTTAAAT
1 AAAAGTCACAATGTTTTAAAT
42866880 A
1 A
42866881 TAAGAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 9 0.45
20 7 0.35
21 4 0.20
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.34
Consensus pattern (21 bp):
AAAAGTCACAATGTTTTAAAT
Found at i:42866894 original size:17 final size:18
Alignment explanation
Indices: 42866869--42866907 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
42866859 ATAAAATCAC
* *
42866869 AATTTTTAAATATAAGAA
1 AATTTTAAAATATAAAAA
42866887 AATTTTAAAATATAAAAA
1 AATTTTAAAATATAAAAA
42866905 AAT
1 AAT
42866908 CCATATATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (18 bp):
AATTTTAAAATATAAAAA
Found at i:42867334 original size:23 final size:23
Alignment explanation
Indices: 42867287--42867335 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
42867277 ATTTTTTGGC
* *
42867287 TTTGTTTTAGAATTTTATGTATT
1 TTTGTTTTAAAATTTTATATATT
*
42867310 TTTGTTTTAAAATTTTCTAT-TT
1 TTTGTTTTAAAATTTTATATATT
42867332 TTTG
1 TTTG
42867336 AAAATTTTCC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 6 0.26
23 17 0.74
ACGTcount: A:0.20, C:0.02, G:0.10, T:0.67
Consensus pattern (23 bp):
TTTGTTTTAAAATTTTATATATT
Found at i:42871365 original size:71 final size:70
Alignment explanation
Indices: 42871239--42871859 Score: 523
Period size: 71 Copynumber: 8.8 Consensus size: 70
42871229 AACTGAAAGC
* * * * * * * * * * *
42871239 TTTTAACTCTCGCTAATTGTTTGGGGAGCTACAGCCTTAAACCTATAAGCTTTAAAGTGACAATT
1 TTTTAACTCTTGCTAACTATTTGGGGGGCTGCGGTCTTAAA-CTTTGAGCCTTAAAGTGACAGTT
42871304 GGGAGT
65 GGGAGT
* * * * * *
42871310 TTTTAACTGTTGCTAACTGTTTGGAGGGTTGCAGTCTTAAACTTTCGAGCCTTAAAGTGATAGTT
1 TTTTAACTCTTGCTAACTATTTGGGGGGCTGCGGTCTTAAACTTT-GAGCCTTAAAGTGACAGTT
*
42871375 GGGAGC
65 GGGAGT
* * * * *
42871381 TTTTAACTCTCT-TTAACTATTTGGGGGG-TGTGGTTTTAAAC-CTGCAAGCCTTAAAGTGATAG
1 TTTTAACTCT-TGCTAACTATTTGGGGGGCTGCGGTCTTAAACTTTG--AGCCTTAAAGTGACAG
*
42871443 TTAGGAGT
63 TTGGGAGT
* * * * *
42871451 TTTTAACTCTTACTAATTATTTGGGGGGCTGCGGTCTTAAACTTTTGAGCCTTAAAGTGATAATC
1 TTTTAACTCTTGCTAACTATTTGGGGGGCTGCGGTCTTAAAC-TTTGAGCCTTAAAGTGACAGTT
* *
42871516 GAGAGC
65 GGGAGT
** * * ** *
42871522 TTTTAACTCTCACTAACTATTTGGGGGGCTGCAGTCTTAGACCTACGAGCATTAAAGTGACAGTT
1 TTTTAACTCTTGCTAACTATTTGGGGGGCTGCGGTCTTA-AACTTTGAGCCTTAAAGTGACAGTT
*
42871587 TGGAGT
65 GGGAGT
** * * *
42871593 TTTTAACTCTTGCTAACTGCTTGGGCGGTTGCGGTCTTAAACCTTTGAGCCTTAAAGTGATAGTT
1 TTTTAACTCTTGCTAACTATTTGGGGGGCTGCGGTCTTAAA-CTTTGAGCCTTAAAGTGACAGTT
42871658 GGGAGT
65 GGGAGT
** * * * *
42871664 TTTTAACTCTCACTTACTATTTGGGGGGCTACGGTCTTAAACCTGTGAGTCTTAAAGTGACAGTT
1 TTTTAACTCTTGCTAACTATTTGGGGGGCTGCGGTCTTAAA-CTTTGAGCCTTAAAGTGACAGTT
*
42871729 GGGAGC
65 GGGAGT
** * * * **
42871735 TTTTAACTCACGCTAACTATTTGGGGGGCTACGGTATTAAACCTATGAGCCTTAATA-TGACACC
1 TTTTAACTCTTGCTAACTATTTGGGGGGCTGCGGTCTTAAA-CTTTGAGCCTTAA-AGTGACAGT
42871799 TGGGAGT
64 TGGGAGT
* * * * *
42871806 TTTTAACT-TTCGCTAACTATTTGAGGAGTTGCAGTCTTAAACTTGGGAGCCTTA
1 TTTTAACTCTT-GCTAACTATTTGGGGGGCTGCGGTCTTAAACTT-TGAGCCTTA
42871860 GTTTTGATAA
Statistics
Matches: 446, Mismatches: 91, Indels: 26
0.79 0.16 0.05
Matches are distributed among these distances:
68 1 0.00
69 2 0.00
70 62 0.14
71 375 0.84
72 4 0.01
73 2 0.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (70 bp):
TTTTAACTCTTGCTAACTATTTGGGGGGCTGCGGTCTTAAACTTTGAGCCTTAAAGTGACAGTTG
GGAGT
Found at i:42871640 original size:142 final size:141
Alignment explanation
Indices: 42871236--42871847 Score: 636
Period size: 142 Copynumber: 4.3 Consensus size: 141
42871226 AACAACTGAA
* * * * * *
42871236 AGCTTTTAACTCTCGCTAATTGTTTGGGGAGCTACAGCCTTAAACCTATAAGCTTTAAAGTGACA
1 AGCTTTTAACTCTCACTAACTATTTGGGGGGCTACAGTCTTAAACCTACAAGC-TTAAAGTGACA
* * * * * *
42871301 ATTGGGAGTTTTTAACTGTTGCTAACTGTTTGGAGGGTTGCAGTCTTAAA-CTTTCGAGCCTTAA
65 GTTGGGAGTTTTTAACTCTTGCTAACTATTTGGGGGGCTGCGGTCTTAAACCTTT-GAGCCTTAA
42871365 AGTGATAGTTGGG
129 AGTGATAGTTGGG
** *** * * *
42871378 AGCTTTTAACTCTCTTTAACTATTTGGGGGG-TGTGGTTTTAAACCTGCAAGCCTTAAAGTGATA
1 AGCTTTTAACTCTCACTAACTATTTGGGGGGCTACAGTCTTAAACCTACAAG-CTTAAAGTGACA
* * * *
42871442 GTTAGGAGTTTTTAACTCTTACTAATTATTTGGGGGGCTGCGGTCTTAAACTTTTGAGCCTTAAA
65 GTTGGGAGTTTTTAACTCTTGCTAACTATTTGGGGGGCTGCGGTCTTAAACCTTTGAGCCTTAAA
* * *
42871507 GTGATAATCGAG
130 GTGATAGTTGGG
* * *
42871519 AGCTTTTAACTCTCACTAACTATTTGGGGGGCTGCAGTCTTAGACCTACGAGCATTAAAGTGACA
1 AGCTTTTAACTCTCACTAACTATTTGGGGGGCTACAGTCTTAAACCTACAAGC-TTAAAGTGACA
* ** * *
42871584 GTTTGGAGTTTTTAACTCTTGCTAACTGCTTGGGCGGTTGCGGTCTTAAACCTTTGAGCCTTAAA
65 GTTGGGAGTTTTTAACTCTTGCTAACTATTTGGGGGGCTGCGGTCTTAAACCTTTGAGCCTTAAA
42871649 GTGATAGTTGGG
130 GTGATAGTTGGG
* * * ***
42871661 AGTTTTTAACTCTCACTTACTATTTGGGGGGCTACGGTCTTAAACCTGTGAGTCTTAAAGTGACA
1 AGCTTTTAACTCTCACTAACTATTTGGGGGGCTACAGTCTTAAACCTACAAG-CTTAAAGTGACA
* ** * * *
42871726 GTTGGGAGCTTTTAACTCACGCTAACTATTTGGGGGGCTACGGTATTAAACCTATGAGCCTTAAT
65 GTTGGGAGTTTTTAACTCTTGCTAACTATTTGGGGGGCTGCGGTCTTAAACCTTTGAGCCTTAA-
* **
42871791 A-TGACACCTGGG
129 AGTGATAGTTGGG
* * * * * * *
42871803 AGTTTTTAACTTTCGCTAACTATTTGAGGAGTTGCAGTCTTAAAC
1 AGCTTTTAACTCTCACTAACTATTTGGGGGGCTACAGTCTTAAAC
42871848 TTGGGAGCCT
Statistics
Matches: 389, Mismatches: 75, Indels: 12
0.82 0.16 0.03
Matches are distributed among these distances:
141 113 0.29
142 274 0.70
143 2 0.01
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.35
Consensus pattern (141 bp):
AGCTTTTAACTCTCACTAACTATTTGGGGGGCTACAGTCTTAAACCTACAAGCTTAAAGTGACAG
TTGGGAGTTTTTAACTCTTGCTAACTATTTGGGGGGCTGCGGTCTTAAACCTTTGAGCCTTAAAG
TGATAGTTGGG
Found at i:42871692 original size:213 final size:212
Alignment explanation
Indices: 42871239--42871847 Score: 657
Period size: 213 Copynumber: 2.9 Consensus size: 212
42871229 AACTGAAAGC
* * * * * * * * *
42871239 TTTTAACTCTCGCTAATTGTTTGGGGAGCTACAGCCTTAAACCTATAAGCTTTAAAGTGACAATT
1 TTTTAACTCTCACTAACTATTTGGGGGGCTACGGTCTTAAACCTGTGAGCCTTAAAGTGACAATT
* * * * * * * *
42871304 GGGAGTTTTTAACTGTTGCTAACTGTTTGGAGGGTTGCAGTCTTAAACTTTCGAGCCTTAAAGTG
66 GGGAGCTTTTAACTCTCGCTAACTATTTGGGGGGCTGCAGTCTTAAACCTACGAGCCTTAAAGTG
* * * * * *
42871369 ATAGTTGGGAGCTTTTAACTCTCT-TTAACTATTTGGGGGGTGTGGTTTTAAACCTGCAAGCCTT
131 ACAGTTGGGAGTTTTTAACTCT-TGCTAACTACTTGGGGGGTGCGGTCTTAAACCTGCAAGCCTT
42871433 AAAGTGATAGTTAGGAGT
195 AAAGTGATAGTTAGGAGT
* * * * * * *
42871451 TTTTAACTCTTACTAATTATTTGGGGGGCTGCGGTCTTAAACTTTTGAGCCTTAAAGTGATAATC
1 TTTTAACTCTCACTAACTATTTGGGGGGCTACGGTCTTAAACCTGTGAGCCTTAAAGTGACAATT
* * * *
42871516 GAGAGCTTTTAACTCTCACTAACTATTTGGGGGGCTGCAGTCTTAGACCTACGAGCATTAAAGTG
66 GGGAGCTTTTAACTCTCGCTAACTATTTGGGGGGCTGCAGTCTTAAACCTACGAGCCTTAAAGTG
* * * ***
42871581 ACAGTTTGGAGTTTTTAACTCTTGCTAACTGCTTGGGCGGTTGCGGTCTTAAACCTTTGAGCCTT
131 ACAGTTGGGAGTTTTTAACTCTTGCTAACTACTTGGG-GGGTGCGGTCTTAAACCTGCAAGCCTT
*
42871646 AAAGTGATAGTTGGGAGT
195 AAAGTGATAGTTAGGAGT
* * *
42871664 TTTTAACTCTCACTTACTATTTGGGGGGCTACGGTCTTAAACCTGTGAGTCTTAAAGTGACAGTT
1 TTTTAACTCTCACTAACTATTTGGGGGGCTACGGTCTTAAACCTGTGAGCCTTAAAGTGACAATT
* * * * *
42871729 GGGAGCTTTTAACTCACGCTAACTATTTGGGGGGCTACGGTATTAAACCTATGAGCCTTAATA-T
66 GGGAGCTTTTAACTCTCGCTAACTATTTGGGGGGCTGCAGTCTTAAACCTACGAGCCTTAA-AGT
** * * * *
42871793 GACACCTGGGAGTTTTTAACT-TTCGCTAACTATTTGAGGAGTTGCAGTCTTAAAC
130 GACAGTTGGGAGTTTTTAACTCTT-GCTAACTACTTG-GGGGGTGCGGTCTTAAAC
42871848 TTGGGAGCCT
Statistics
Matches: 328, Mismatches: 64, Indels: 9
0.82 0.16 0.02
Matches are distributed among these distances:
211 1 0.00
212 136 0.41
213 188 0.57
214 3 0.01
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (212 bp):
TTTTAACTCTCACTAACTATTTGGGGGGCTACGGTCTTAAACCTGTGAGCCTTAAAGTGACAATT
GGGAGCTTTTAACTCTCGCTAACTATTTGGGGGGCTGCAGTCTTAAACCTACGAGCCTTAAAGTG
ACAGTTGGGAGTTTTTAACTCTTGCTAACTACTTGGGGGGTGCGGTCTTAAACCTGCAAGCCTTA
AAGTGATAGTTAGGAGT
Found at i:42875953 original size:21 final size:21
Alignment explanation
Indices: 42875929--42875970 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
42875919 TCTAGTGGTT
42875929 ATATTGTATTTTTGGTGTTTA
1 ATATTGTATTTTTGGTGTTTA
42875950 ATATTGTATTTTTGGTGTTTA
1 ATATTGTATTTTTGGTGTTTA
42875971 CTCTTTTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.19, T:0.62
Consensus pattern (21 bp):
ATATTGTATTTTTGGTGTTTA
Found at i:42880586 original size:42 final size:42
Alignment explanation
Indices: 42880532--42880631 Score: 139
Period size: 42 Copynumber: 2.4 Consensus size: 42
42880522 CTATACGAAT
* *
42880532 GGCACTGAGTGTGCGAAA-ATAAAATGACGATGTTGAATAACG
1 GGCACTAAGTGTGCGAAACA-AAAATGACGATGTCGAATAACG
* *
42880574 GGCACTAAGTGTGTGAAACAAAAATGACGATGTCGAGTAACG
1 GGCACTAAGTGTGCGAAACAAAAATGACGATGTCGAATAACG
*
42880616 GGCACTAAGTCTGCGA
1 GGCACTAAGTGTGCGA
42880632 TACCAAGATC
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
42 50 0.98
43 1 0.02
ACGTcount: A:0.36, C:0.15, G:0.29, T:0.20
Consensus pattern (42 bp):
GGCACTAAGTGTGCGAAACAAAAATGACGATGTCGAATAACG
Found at i:42882571 original size:20 final size:19
Alignment explanation
Indices: 42882534--42882575 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
42882524 GTTGTTTTTA
42882534 ATGTAAATGAATTAATATAT
1 ATGTAAATGAATTAATAT-T
*
42882554 ATGTAAATGTATCT-ATATT
1 ATGTAAATGAAT-TAATATT
42882573 ATG
1 ATG
42882576 ACGAATTGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 4 0.20
20 15 0.75
21 1 0.05
ACGTcount: A:0.43, C:0.02, G:0.12, T:0.43
Consensus pattern (19 bp):
ATGTAAATGAATTAATATT
Found at i:42886218 original size:26 final size:26
Alignment explanation
Indices: 42886182--42886231 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
42886172 CTGATCAAAA
42886182 AGGGGTTGCTAAGTGCAGATTCCCCG
1 AGGGGTTGCTAAGTGCAGATTCCCCG
**
42886208 AGGGGTTGCTAAGTGTTGATTCCC
1 AGGGGTTGCTAAGTGCAGATTCCC
42886232 TGAATTATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.18, C:0.20, G:0.34, T:0.28
Consensus pattern (26 bp):
AGGGGTTGCTAAGTGCAGATTCCCCG
Found at i:42886220 original size:67 final size:68
Alignment explanation
Indices: 42886141--42886272 Score: 178
Period size: 67 Copynumber: 2.0 Consensus size: 68
42886131 ATTGAATGTA
42886141 AGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGA-TCAAAAAGG-GGTTGCTAAGTGCAGATTC
1 AGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGATTC-AAAAGGTGGTTGCTAAGTGCAGATTC
42886204 CCCG
65 CCCG
** * * * * *
42886208 AGGGGTTGCTAAGTGTTGATTCCCTGAATTATTGATTCTAAAGGTGGTTGCTAAGTGCTGATTCC
1 AGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGATTCAAAAGGTGGTTGCTAAGTGCAGATTCC
42886273 ATCATATCCT
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
67 35 0.62
68 21 0.38
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (68 bp):
AGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGATTCAAAAGGTGGTTGCTAAGTGCAGATTCC
CCG
Found at i:42886300 original size:43 final size:41
Alignment explanation
Indices: 42886208--42886313 Score: 113
Period size: 43 Copynumber: 2.5 Consensus size: 41
42886198 AGATTCCCCG
* * * *
42886208 AGGGGTTGCTAAGTGTTGATTCCCTGAATTATTGATTCTAA
1 AGGGGTTGCTAAGTGCTGATTCCATCAATCATTGATTCTAA
* *
42886249 AGGTGGTTGCTAAGTGCTGATTCCATCATATCCTTGATTGTTAA
1 AGG-GGTTGCTAAGTGCTGATTCCATCA-ATCATTGATT-CTAA
* *
42886293 AGGGGTTGCTATGTACTGATT
1 AGGGGTTGCTAAGTGCTGATT
42886314 TCCCGTATCA
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
41 3 0.06
42 21 0.39
43 24 0.44
44 6 0.11
ACGTcount: A:0.23, C:0.13, G:0.25, T:0.39
Consensus pattern (41 bp):
AGGGGTTGCTAAGTGCTGATTCCATCAATCATTGATTCTAA
Found at i:42890099 original size:65 final size:65
Alignment explanation
Indices: 42889995--42890182 Score: 349
Period size: 65 Copynumber: 2.9 Consensus size: 65
42889985 AGCAATAATT
* *
42889995 AATTTAGCCACAACTCTCCATAAAAAATTATCGAATCTCAATGAAATAAGGAATAGAATAAAGCA
1 AATTTAGCCACAACCCTCCATACAAAATTATCGAATCTCAATGAAATAAGGAATAGAATAAAGCA
42890060 AATTTAGCCACAACCCTCCATACAAAATTATCGAATCTCAATGAAATAAGGAATAGAATAAAGCA
1 AATTTAGCCACAACCCTCCATACAAAATTATCGAATCTCAATGAAATAAGGAATAGAATAAAGCA
*
42890125 AATTTAGCCACAACCCTCCATACAAAATTATCGAATCTCAATGAAATAAGAAATAGAA
1 AATTTAGCCACAACCCTCCATACAAAATTATCGAATCTCAATGAAATAAGGAATAGAA
42890183 GCCAATCAAC
Statistics
Matches: 120, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 120 1.00
ACGTcount: A:0.48, C:0.19, G:0.10, T:0.22
Consensus pattern (65 bp):
AATTTAGCCACAACCCTCCATACAAAATTATCGAATCTCAATGAAATAAGGAATAGAATAAAGCA
Found at i:42894926 original size:32 final size:32
Alignment explanation
Indices: 42894845--42894930 Score: 88
Period size: 32 Copynumber: 2.7 Consensus size: 32
42894835 TTTTGCTAAT
* *
42894845 CATCC-AGCTCCTTTTGTTCACA-CCAATGGAC
1 CATCCAAG-TCCTGTTGTTCACACCCAAAGGAC
* **
42894876 CATTCACTTCCTGTTGTTCACACCCAAAGGAC
1 CATCCAAGTCCTGTTGTTCACACCCAAAGGAC
42894908 CATCCAAGTCCATG-TGTTCACAC
1 CATCCAAGTCC-TGTTGTTCACAC
42894931 TAAAGACTCT
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
31 17 0.39
32 25 0.57
33 2 0.05
ACGTcount: A:0.24, C:0.35, G:0.13, T:0.28
Consensus pattern (32 bp):
CATCCAAGTCCTGTTGTTCACACCCAAAGGAC
Found at i:42895746 original size:17 final size:18
Alignment explanation
Indices: 42895703--42895750 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
42895693 GTTTGAAGAA
* *
42895703 TATAAAAATAATATCGAT
1 TATAAAAAAAATATCGAG
42895721 TA-AAGAAAAAAT-TCGAG
1 TATAA-AAAAAATATCGAG
42895738 TATAAAAAAAATA
1 TATAAAAAAAATA
42895751 CAAATCTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
17 15 0.60
18 10 0.40
ACGTcount: A:0.62, C:0.04, G:0.08, T:0.25
Consensus pattern (18 bp):
TATAAAAAAAATATCGAG
Found at i:42898837 original size:50 final size:50
Alignment explanation
Indices: 42898671--42898858 Score: 153
Period size: 50 Copynumber: 3.6 Consensus size: 50
42898661 GGGAATGAGA
* * **
42898671 TCCCATGTAAGACCAAGTCTGGGAAATGGCATTGGCATTATTGAGGTTATGAGAGG
1 TCCCATGTAAGACCAAGTCTGGGACATGGCATGGGCACCA---A---TATGAGAGG
* * * * * * *
42898727 TCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAGATGTGAGG
1 TCCCATGTAAGACCAAGTCTGGGACATGGCATGGGCACCAATATGAGAGG
** * **
42898777 TCCCCCGTAAGATCAAGTCTGGGACATGGCATGGGCACCAATATGAGAAC
1 TCCCATGTAAGACCAAGTCTGGGACATGGCATGGGCACCAATATGAGAGG
*
42898827 TCCCATGTAAGACCATA-TCTGGGATATGGCAT
1 TCCCATGTAAGACCA-AGTCTGGGACATGGCAT
42898859 TGGTAGTACA
Statistics
Matches: 106, Mismatches: 25, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
50 71 0.67
51 1 0.01
53 1 0.01
56 33 0.31
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (50 bp):
TCCCATGTAAGACCAAGTCTGGGACATGGCATGGGCACCAATATGAGAGG
Found at i:42899139 original size:20 final size:20
Alignment explanation
Indices: 42899114--42899162 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
42899104 TGAGTTATTT
42899114 AAGTAAGCAAGTAAGCAAAC
1 AAGTAAGCAAGTAAGCAAAC
* *
42899134 AAGTAAG-AGAGTAAGTAAAG
1 AAGTAAGCA-AGTAAGCAAAC
42899154 AAG-AAGCAA
1 AAGTAAGCAA
42899163 AGACCATGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.57, C:0.08, G:0.24, T:0.10
Consensus pattern (20 bp):
AAGTAAGCAAGTAAGCAAAC
Found at i:42900867 original size:49 final size:49
Alignment explanation
Indices: 42900807--42900906 Score: 191
Period size: 49 Copynumber: 2.0 Consensus size: 49
42900797 AGAAAAAGAA
42900807 AAAAAAAGATAGTGAATCCAGAAAGTGGAATTTCTATGCGAGAGAAAAG
1 AAAAAAAGATAGTGAATCCAGAAAGTGGAATTTCTATGCGAGAGAAAAG
*
42900856 AAAAAAGGATAGTGAATCCAGAAAGTGGAATTTCTATGCGAGAGAAAAG
1 AAAAAAAGATAGTGAATCCAGAAAGTGGAATTTCTATGCGAGAGAAAAG
42900905 AA
1 AA
42900907 GATTCAGAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.49, C:0.08, G:0.25, T:0.18
Consensus pattern (49 bp):
AAAAAAAGATAGTGAATCCAGAAAGTGGAATTTCTATGCGAGAGAAAAG
Found at i:42914105 original size:19 final size:17
Alignment explanation
Indices: 42914077--42914116 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 17
42914067 GTGAATTGAT
42914077 AATG-AATTGAATTGAGA
1 AATGAAATTGAA-TGAGA
42914094 ATATGAAATTGAATGAGA
1 A-ATGAAATTGAATGAGA
42914112 AATGA
1 AATGA
42914117 TATATGTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 5 0.24
18 9 0.43
19 7 0.33
ACGTcount: A:0.50, C:0.00, G:0.23, T:0.28
Consensus pattern (17 bp):
AATGAAATTGAATGAGA
Found at i:42919250 original size:42 final size:42
Alignment explanation
Indices: 42919203--42919474 Score: 325
Period size: 42 Copynumber: 6.5 Consensus size: 42
42919193 TTGAGATTTT
* *
42919203 AGACTTTACGCCTAGCAGGCTTATTGCTAGTGAAACAATATC
1 AGACTTTACGTCTAGCAGGCTTAATGCTAGTGAAACAATATC
* * *
42919245 AGACTTTACGTCTAGCAGGCTTAATGCCAGTGAAATAATTTC
1 AGACTTTACGTCTAGCAGGCTTAATGCTAGTGAAACAATATC
* *
42919287 AGACTTTACGTCTAGTAGGCTTATTGCTAGTGAAACAATATC
1 AGACTTTACGTCTAGCAGGCTTAATGCTAGTGAAACAATATC
* * *
42919329 AGACTTTACGTCTAGCAGGCTTAATGCCT-GTGAAATAATTTT
1 AGACTTTACGTCTAGCAGGCTTAATG-CTAGTGAAACAATATC
* **
42919371 AGACTTTACGTCTAGCAGGCTTAATACCGGTGAAACAATATC
1 AGACTTTACGTCTAGCAGGCTTAATGCTAGTGAAACAATATC
* * * *
42919413 AGACTTTACATCTAGCATGCTTAATTC-AGGTGAAAC-ATTTC
1 AGACTTTACGTCTAGCAGGCTTAATGCTA-GTGAAACAATATC
* * *
42919454 AGACTATATGTCTAGTAGGCT
1 AGACTTTACGTCTAGCAGGCT
42919475 AAGTGTCGGT
Statistics
Matches: 197, Mismatches: 30, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
41 21 0.11
42 174 0.88
43 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Consensus pattern (42 bp):
AGACTTTACGTCTAGCAGGCTTAATGCTAGTGAAACAATATC
Found at i:42919344 original size:84 final size:84
Alignment explanation
Indices: 42919198--42919474 Score: 387
Period size: 84 Copynumber: 3.3 Consensus size: 84
42919188 TGAAATTGAG
* *
42919198 ATTTTAGACTTTACGCCTAGCAGGCTTATTGCTAGTGAAACAATATCAGACTTTACGTCTAGCAG
1 ATTTCAGACTTTACGTCTAGCAGGCTTATTGCTAGTGAAACAATATCAGACTTTACGTCTAGCAG
42919263 GCTTAATGCCAGTGAAATA
66 GCTTAATGCCAGTGAAATA
*
42919282 ATTTCAGACTTTACGTCTAGTAGGCTTATTGCTAGTGAAACAATATCAGACTTTACGTCTAGCAG
1 ATTTCAGACTTTACGTCTAGCAGGCTTATTGCTAGTGAAACAATATCAGACTTTACGTCTAGCAG
*
42919347 GCTTAATGCCTGTGAAATA
66 GCTTAATGCCAGTGAAATA
* * * ** * *
42919366 ATTTTAGACTTTACGTCTAGCAGGCTTAATACCGGTGAAACAATATCAGACTTTACATCTAGCAT
1 ATTTCAGACTTTACGTCTAGCAGGCTTATTGCTAGTGAAACAATATCAGACTTTACGTCTAGCAG
* *
42919431 GCTTAAT-TCAGGTGAAA-C
66 GCTTAATGCCA-GTGAAATA
* * *
42919449 ATTTCAGACTATATGTCTAGTAGGCT
1 ATTTCAGACTTTACGTCTAGCAGGCT
42919475 AAGTGTCGGT
Statistics
Matches: 173, Mismatches: 19, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
83 23 0.13
84 150 0.87
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Consensus pattern (84 bp):
ATTTCAGACTTTACGTCTAGCAGGCTTATTGCTAGTGAAACAATATCAGACTTTACGTCTAGCAG
GCTTAATGCCAGTGAAATA
Found at i:42927437 original size:42 final size:42
Alignment explanation
Indices: 42927389--42927656 Score: 333
Period size: 42 Copynumber: 6.4 Consensus size: 42
42927379 AATTGAGATT
* * * *
42927389 TCAGACTTTACGCCTAACAGACTTATTGCCAGTGAAACAATA
1 TCAGACTTTACGTCTAGCAGACTTAATGCCGGTGAAACAATA
** *
42927431 TCAGACTTTACGTCTAGCA-AGCTTAATGCCGGTGAAATTATT
1 TCAGACTTTACGTCTAGCAGA-CTTAATGCCGGTGAAACAATA
* *
42927473 TCAGACTTTACGTCTAGCAGACTTATTGCCAGTGAAACAATA
1 TCAGACTTTACGTCTAGCAGACTTAATGCCGGTGAAACAATA
* * *
42927515 TCAGACTTTACATCTAGCAGGCTTAATGCTGGTGAAACAATA
1 TCAGACTTTACGTCTAGCAGACTTAATGCCGGTGAAACAATA
* * *
42927557 TTAGACTTTACGTCTAGCAGGCTTAATGCCCGTGAAACAATA
1 TCAGACTTTACGTCTAGCAGACTTAATGCCGGTGAAACAATA
* * *
42927599 TCAAACTTTACGTCTAGCAGGCTTAATGCCGGTGAAAC-ATT
1 TCAGACTTTACGTCTAGCAGACTTAATGCCGGTGAAACAATA
* *
42927640 TCAGACTATATGTCTAG
1 TCAGACTTTACGTCTAG
42927657 TAGGTTAAGT
Statistics
Matches: 196, Mismatches: 28, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
41 17 0.09
42 178 0.91
43 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (42 bp):
TCAGACTTTACGTCTAGCAGACTTAATGCCGGTGAAACAATA
Found at i:42927531 original size:84 final size:83
Alignment explanation
Indices: 42927386--42927656 Score: 391
Period size: 84 Copynumber: 3.2 Consensus size: 83
42927376 TGAAATTGAG
* * *
42927386 ATTTCAGACTTTACGCCTAACAGACTTATTGCCAGTGAAACAATATCAGACTTTACGTCTAGCAA
1 ATTTCAGACTTTACGTCTAGCAGACTTATTGCCAGTGAAACAATATCAGACTTTACGTCTAGCAG
*
42927451 GCTTAATGCCGGTGAAATT
66 GCTTAATGCCGGTGAAA-A
*
42927470 ATTTCAGACTTTACGTCTAGCAGACTTATTGCCAGTGAAACAATATCAGACTTTACATCTAGCAG
1 ATTTCAGACTTTACGTCTAGCAGACTTATTGCCAGTGAAACAATATCAGACTTTACGTCTAGCAG
*
42927535 GCTTAATGCTGGTGAAACA
66 GCTTAATGCCGGTGAAA-A
* * * *
42927554 ATATT-AGACTTTACGTCTAGCAGGCTTAATGCCCGTGAAACAATATCAAACTTTACGTCTAGCA
1 AT-TTCAGACTTTACGTCTAGCAGACTTATTGCCAGTGAAACAATATCAGACTTTACGTCTAGCA
*
42927618 GGCTTAATGCCGGTGAAAC
65 GGCTTAATGCCGGTGAAAA
* *
42927637 ATTTCAGACTATATGTCTAG
1 ATTTCAGACTTTACGTCTAG
42927657 TAGGTTAAGT
Statistics
Matches: 169, Mismatches: 16, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
82 2 0.01
83 15 0.09
84 150 0.89
85 2 0.01
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.30
Consensus pattern (83 bp):
ATTTCAGACTTTACGTCTAGCAGACTTATTGCCAGTGAAACAATATCAGACTTTACGTCTAGCAG
GCTTAATGCCGGTGAAAA
Found at i:42934391 original size:28 final size:28
Alignment explanation
Indices: 42934360--42934420 Score: 122
Period size: 28 Copynumber: 2.2 Consensus size: 28
42934350 AATAATATGT
42934360 CATTCTGCTACATTATGATAACTTAGTA
1 CATTCTGCTACATTATGATAACTTAGTA
42934388 CATTCTGCTACATTATGATAACTTAGTA
1 CATTCTGCTACATTATGATAACTTAGTA
42934416 CATTC
1 CATTC
42934421 CTAGTAATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.39
Consensus pattern (28 bp):
CATTCTGCTACATTATGATAACTTAGTA
Found at i:42938206 original size:41 final size:41
Alignment explanation
Indices: 42938133--42938265 Score: 185
Period size: 41 Copynumber: 3.2 Consensus size: 41
42938123 CAATGTTTCA
* * * *
42938133 CACACTAATTGTCAATCATATAGCCGAAGCTATTATAATTCCG
1 CACACTAAGTGTC-AT-ACATAGCCAAAGCTATTATAATTCTG
42938176 CACACTAAGTGTCATACATAGCCAAAGCTATTATAATTCTG
1 CACACTAAGTGTCATACATAGCCAAAGCTATTATAATTCTG
* * *
42938217 CACATTAAGTGTCTTACATAGCCAAAACTATTATAATTCTG
1 CACACTAAGTGTCATACATAGCCAAAGCTATTATAATTCTG
42938258 CACACTAA
1 CACACTAA
42938266 CAGCATGTTT
Statistics
Matches: 82, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
41 68 0.83
42 2 0.02
43 12 0.15
ACGTcount: A:0.37, C:0.23, G:0.11, T:0.30
Consensus pattern (41 bp):
CACACTAAGTGTCATACATAGCCAAAGCTATTATAATTCTG
Found at i:42941569 original size:16 final size:16
Alignment explanation
Indices: 42941548--42941589 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
42941538 TTATTAAATT
*
42941548 ATATATTTTAATTATA
1 ATATATTTTAATAATA
42941564 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
42941579 AT-TATGTTTAA
1 ATATAT-TTTAA
42941590 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:42941574 original size:15 final size:15
Alignment explanation
Indices: 42941539--42941580 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
42941529 TTAAGAATTT
*
42941539 TATTAAATTAT-ATA
1 TATTTAATTATAATA
42941553 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
42941567 TATTTAATAATAAT
1 TATTTAATTATAAT
42941581 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:42941814 original size:45 final size:44
Alignment explanation
Indices: 42941734--42941823 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 44
42941724 ACCTCTATTC
*
42941734 CATTCAACCAAACACAAGATTACTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTACTATTACGCCTCTAATCCATTA
* *
42941778 CATTCAACCAAACA-ATTGATTTGCTATTACGCCTCTAATCCATTA
1 CATTCAACCAAACACA-AGA-TTACTATTACGCCTCTAATCCATTA
42941823 C
1 C
42941824 GCCTCTATTC
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
43 1 0.02
44 16 0.39
45 24 0.59
ACGTcount: A:0.34, C:0.29, G:0.06, T:0.31
Consensus pattern (44 bp):
CATTCAACCAAACACAAGATTACTATTACGCCTCTAATCCATTA
Found at i:42941824 original size:16 final size:16
Alignment explanation
Indices: 42941803--42941835 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
42941793 TTGATTTGCT
42941803 ATTACGCCTCTAATCC
1 ATTACGCCTCTAATCC
*
42941819 ATTACGCCTCTATTCC
1 ATTACGCCTCTAATCC
42941835 A
1 A
42941836 ATACAGCGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.36, G:0.06, T:0.33
Consensus pattern (16 bp):
ATTACGCCTCTAATCC
Found at i:42944031 original size:15 final size:15
Alignment explanation
Indices: 42944011--42944042 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
42944001 CATTTCACTA
*
42944011 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
42944026 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
42944041 TT
1 TT
42944043 TGCATGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:42950792 original size:18 final size:19
Alignment explanation
Indices: 42950761--42950804 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
42950751 TCTTAGAAAT
42950761 CTTAGGATACCCTACTTGA
1 CTTAGGATACCCTACTTGA
*
42950780 CTTAGGA-ACCCTATTTGA
1 CTTAGGATACCCTACTTGA
*
42950798 TTTAGGA
1 CTTAGGA
42950805 GAAGGTTACT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.34
Consensus pattern (19 bp):
CTTAGGATACCCTACTTGA
Found at i:42964549 original size:17 final size:16
Alignment explanation
Indices: 42964506--42964552 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
42964496 AATTTAAAAT
*
42964506 AATTTTTGAATTAGTG
1 AATTTTTGATTTAGTG
*
42964522 AATTTTTTGATTTATTG
1 AA-TTTTTGATTTAGTG
42964539 AATTTTGTGATTTA
1 AATTTT-TGATTTA
42964553 AAAAGAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 6 0.22
17 21 0.78
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (16 bp):
AATTTTTGATTTAGTG
Found at i:42965458 original size:46 final size:46
Alignment explanation
Indices: 42965391--42965483 Score: 152
Period size: 46 Copynumber: 2.0 Consensus size: 46
42965381 CATGGCAAAG
**
42965391 TGTGAAACGTAGGTATGGTA-TTTCAGTGAAGAAAACCATACTGAGT
1 TGTGAAAAATAGGTATGGTATTTTC-GTGAAGAAAACCATACTGAGT
42965437 TGTGAAAAATAGGTATGGTATTTTCGTGAAGAAAACCATACTGAGT
1 TGTGAAAAATAGGTATGGTATTTTCGTGAAGAAAACCATACTGAGT
42965483 T
1 T
42965484 ATAGCAATGT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
46 40 0.91
47 4 0.09
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.30
Consensus pattern (46 bp):
TGTGAAAAATAGGTATGGTATTTTCGTGAAGAAAACCATACTGAGT
Found at i:42980194 original size:20 final size:21
Alignment explanation
Indices: 42980157--42980196 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
42980147 ATGTACCTAT
*
42980157 TGGTGTGTAGGGTAGATGGAGA
1 TGGTGTGTAGCG-AGATGGAGA
42980179 TGGTGTGTAGCG-GATGGA
1 TGGTGTGTAGCGAGATGGA
42980197 ATAGGAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
22 11 0.65
ACGTcount: A:0.20, C:0.03, G:0.50, T:0.28
Consensus pattern (21 bp):
TGGTGTGTAGCGAGATGGAGA
Found at i:42981207 original size:68 final size:67
Alignment explanation
Indices: 42981098--42981267 Score: 182
Period size: 68 Copynumber: 2.5 Consensus size: 67
42981088 TTCTCTAGTT
* * *** * *
42981098 AATATGAGATTAAAATTAACTTTTTAATTAAAATGGTGAAGAAGTAAGTTATGTGAGTATTC-TT
1 AATATG-GATTAAAATTAACTTTTTAATGAAAGTAACGAAGAAGTAAGCTATG-AAGTATTCTTT
*
42981162 AGCC
64 AACC
* *
42981166 AATGTGGAATTAAAATTAACTTTTTAATGAAAGTAACGAAGAAGTGAGCTATGAAGTATTCTTTA
1 AATATGG-ATTAAAATTAACTTTTTAATGAAAGTAACGAAGAAGTAAGCTATGAAGTATTCTTTA
*
42981231 ATC
65 ACC
*
42981234 AATATGGATTAAAACTAA-TCTTTTAATGAAAGTA
1 AATATGGATTAAAATTAACT-TTTTAATGAAAGTA
42981268 GTGAAAAAAT
Statistics
Matches: 86, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
66 1 0.01
67 32 0.37
68 53 0.62
ACGTcount: A:0.42, C:0.06, G:0.16, T:0.35
Consensus pattern (67 bp):
AATATGGATTAAAATTAACTTTTTAATGAAAGTAACGAAGAAGTAAGCTATGAAGTATTCTTTAA
CC
Found at i:42984977 original size:25 final size:24
Alignment explanation
Indices: 42984932--42984994 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 24
42984922 TGTCGTCACT
*
42984932 TATAAAA-AAATTATTAGTATCTTA
1 TATAAAATAAATTATTAATATC-TA
42984956 TATTAAAATAAATT-TTAATATCTA
1 TA-TAAAATAAATTATTAATATCTA
42984980 TA-AAAATAAAATTAT
1 TATAAAAT-AAATTAT
42984995 AGATTTTAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 5 0.15
23 5 0.15
24 7 0.21
25 12 0.35
26 5 0.15
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (24 bp):
TATAAAATAAATTATTAATATCTA
Found at i:42987000 original size:19 final size:20
Alignment explanation
Indices: 42986978--42987019 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
42986968 ATAAAAGTTA
* *
42986978 TTTTCTTGATTTAAAG-ATT
1 TTTTCTTGAATAAAAGCATT
*
42986997 TTTTTTTGAATAAAAGCATT
1 TTTTCTTGAATAAAAGCATT
42987017 TTT
1 TTT
42987020 GGAAGTTTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.29, C:0.05, G:0.10, T:0.57
Consensus pattern (20 bp):
TTTTCTTGAATAAAAGCATT
Found at i:42993398 original size:2 final size:2
Alignment explanation
Indices: 42993382--42993425 Score: 63
Period size: 2 Copynumber: 22.0 Consensus size: 2
42993372 CTCACGAGTA
*
42993382 AT AT GAT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42993424 AT
1 AT
42993426 TGCATACCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
1 1 0.03
2 35 0.92
3 2 0.05
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
AT
Found at i:42998814 original size:31 final size:31
Alignment explanation
Indices: 42998777--42998837 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
42998767 GATAATTTTA
42998777 AAGAGTTTTATTAGGATTCAATTACTCTTGG
1 AAGAGTTTTATTAGGATTCAATTACTCTTGG
42998808 AAGAGTTTTATTAGGATTCAATTACTCTTG
1 AAGAGTTTTATTAGGATTCAATTACTCTTG
42998838 TAATTTGCCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.30, C:0.10, G:0.18, T:0.43
Consensus pattern (31 bp):
AAGAGTTTTATTAGGATTCAATTACTCTTGG
Found at i:43007962 original size:46 final size:45
Alignment explanation
Indices: 43007680--43008830 Score: 433
Period size: 44 Copynumber: 26.7 Consensus size: 45
43007670 TTTGTTTTAA
* * * *
43007680 TCTGCTCCACTGTAATCTCAGGGAGATAGGAT-T-ACTAGCTTCAA
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAT-TCTTCAG
* * *
43007724 TCTGCTCCGCTGTAATCTCAGGGAGATAAGTTCTGAAATTCTTCGG
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATCTG-AATTCTTCAG
* * * * * *
43007770 TCTGTTCCACTGTAATCTCAGGGAAATAAGACCT-AGTGC--GA-
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAATTCTTCAG
* * * * *
43007811 TCTACTCTACTGTAA-CTTCAGAGAGGATAAGATCCTTG-GTT-TT-AA
1 TCTGCTCCACTGTAATC-TCAGGGA-GATAAGAT-C-TGAATTCTTCAG
* * * * * *
43007856 TCCGCTCCACTATAATCTCAGGGAGATAGGAT-T-ACTAGCTTCAA
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAT-TCTTCAG
* * *
43007900 TCTGGTCCGCTGTAATCTTAGGGAGATAAGATCTGAAATTCTTCAG
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATCTG-AATTCTTCAG
* * * * * *
43007946 TCTGTTCCACTGTAATCTCAGGGAAATAAGACCTG-GTGC--GA-
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAATTCTTCAG
* * * * *
43007987 TCTGCTCTACTGTAA-CTTTAGAGAGATAAGATC------CTTTAA
1 TCTGCTCCACTGTAATC-TCAGGGAGATAAGATCTGAATTCTTCAG
* * * * * *
43008026 TCCGCTCTACTGTAATCTCAGGGAGATAGGAT-T-ACTATATTCAA
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAT-TCTTCAG
*
43008070 TCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGCAATTCTTCGG
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATCTG-AATTCTTCAG
* * * * * *
43008116 TCTGTTCCACTGTAATCTCAGGGAAATAAGACCTG-GTAC--GA-
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAATTCTTCAG
* * * *
43008157 TCTGCTCTACTGTAA-CTTCAGAGAGATAAGATC------CTTTAA
1 TCTGCTCCACTGTAATC-TCAGGGAGATAAGATCTGAATTCTTCAG
* * * * *
43008196 TCCGCTCCACTGTAATCTCAGGGAGATAGGAT-T-ACTATATTCAA
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAT-TCTTCAG
* * *
43008240 TTTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGCAATTCTTCGG
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATCTG-AATTCTTCAG
* * * * * *
43008286 TCTGTTCCACCGTAATCTCAGGGAAATAAGACCTG--TGC--GA-
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAATTCTTCAG
* * * * * *
43008326 TCTACTCTACTGTAA-CTTCAGAGAGATATGATCCTTG-GTT-TT-AA
1 TCTGCTCCACTGTAATC-TCAGGGAGATAAGAT-C-TGAATTCTTCAG
* * * * *
43008370 TCCGCTCCACTGTAATATCAGGGAGATAGGAT-T-ACTAGT-TTCAA
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGA--ATTCTTCAG
* *
43008414 TCTAG-TCCGCTGTAATCTCAGGGAGATAAGATCTGAAAATCTTCAG
1 TCT-GCTCCACTGTAATCTCAGGGAGATAAGATCTG-AATTCTTCAG
* * * * * *
43008460 TCTGTTCCACTGTAATCTCAGGGAAATAAGACCTG-GTGC--GA-
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAATTCTTCAG
* * *
43008501 TCTGCTCCACTGTAA-CTTCAGAGAGATAAGATC------CTTTAA
1 TCTGCTCCACTGTAATC-TCAGGGAGATAAGATCTGAATTCTTCAG
* * * * *
43008540 TCCGCTCCACTGTAATCTCAGGGAGATAGGAT-T-ACTATATTCAA
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAT-TCTTCAG
43008584 TCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGCAATTCTTC-G
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATCTG-AATTCTTCAG
** * * * * *
43008629 ATCTATTCCACTGTAATCTCAGGGAAATAAGACCTG-GTGC--GA-
1 -TCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAATTCTTCAG
* * * * *
43008671 TCTGCTCTACTCTAA-CTTCAGAGAGATAAGATC------CTTTAA
1 TCTGCTCCACTGTAATC-TCAGGGAGATAAGATCTGAATTCTTCAG
* * * * * *
43008710 TCCGCTCCACTGTAATCTCAGGCAGATAGGAT-T-ACTATATTCAA
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAT-TCTTCAG
* *
43008754 TCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGCAATTCTTCGG
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGATCTG-AATTCTTCAG
* * *
43008800 TCTGTTCCACTGTAATCTTAGGGAAATAAGA
1 TCTGCTCCACTGTAATCTCAGGGAGATAAGA
43008831 CCTGTATAAT
Statistics
Matches: 828, Mismatches: 184, Indels: 188
0.69 0.15 0.16
Matches are distributed among these distances:
36 4 0.00
38 4 0.00
39 104 0.13
40 31 0.04
41 124 0.15
42 10 0.01
43 10 0.01
44 262 0.32
45 28 0.03
46 238 0.29
47 13 0.02
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (45 bp):
TCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAATTCTTCAG
Found at i:43008112 original size:170 final size:170
Alignment explanation
Indices: 43007600--43008834 Score: 1918
Period size: 170 Copynumber: 7.2 Consensus size: 170
43007590 TTCAATGTAC
* * ** * * * *
43007600 TCCACTGTAACCACAGGGAGGTAAAACCTGATGCGATCTACTCTACTGTAACTTCAGTGAGATAA
1 TCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCTGCTCTACTGTAACTTCAGAGAGATAA
* **
43007665 GATCCTTTGTTTTAATCTGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCT
66 GATCC-----TTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTATATTCAATCTGCT
* *
43007730 CCGCTGTAATCTCAGGGAGATAAGTTCTGAAATTCTTCGGTCTGT
126 CCGCTGTAATCTCAGGGAGATAAGATCTGCAATTCTTCGGTCTGT
* *
43007775 TCCACTGTAATCTCAGGGAAATAAGACCTAGTGCGATCTACTCTACTGTAACTTCAGAGAGGATA
1 TCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCTGCTCTACTGTAACTTCAGAGA-GATA
* ** *
43007840 AGATCCTTGGTTTTAATCCGCTCCACTATAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGG
65 AGATCC-----TTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTATATTCAATCTGC
* * *
43007905 TCCGCTGTAATCTTAGGGAGATAAGATCTGAAATTCTTCAGTCTGT
125 TCCGCTGTAATCTCAGGGAGATAAGATCTGCAATTCTTCGGTCTGT
*
43007951 TCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCTGCTCTACTGTAACTTTAGAGAGATAA
1 TCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCTGCTCTACTGTAACTTCAGAGAGATAA
* *
43008016 GATCCTTTAATCCGCTCTACTGTAATCTCAGGGAGATAGGATTACTATATTCAATCTGCTCCACT
66 GATCCTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTATATTCAATCTGCTCCGCT
43008081 GTAATCTCAGGGAGATAAGATCTGCAATTCTTCGGTCTGT
131 GTAATCTCAGGGAGATAAGATCTGCAATTCTTCGGTCTGT
*
43008121 TCCACTGTAATCTCAGGGAAATAAGACCTGGTACGATCTGCTCTACTGTAACTTCAGAGAGATAA
1 TCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCTGCTCTACTGTAACTTCAGAGAGATAA
*
43008186 GATCCTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTATATTCAATTTGCTCCGCT
66 GATCCTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTATATTCAATCTGCTCCGCT
43008251 GTAATCTCAGGGAGATAAGATCTGCAATTCTTCGGTCTGT
131 GTAATCTCAGGGAGATAAGATCTGCAATTCTTCGGTCTGT
* * *
43008291 TCCACCGTAATCTCAGGGAAATAAGACCT-GTGCGATCTACTCTACTGTAACTTCAGAGAGATAT
1 TCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCTGCTCTACTGTAACTTCAGAGAGATAA
*
43008355 GATCCTTGGTTTTAATCCGCTCCACTGTAATATCAGGGAGATAGGATTACTAGT-TTCAATCTAG
66 GATCC-----TTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTA-TATTCAATCT-G
* * *
43008419 -TCCGCTGTAATCTCAGGGAGATAAGATCTGAAAATCTTCAGTCTGT
124 CTCCGCTGTAATCTCAGGGAGATAAGATCTGCAATTCTTCGGTCTGT
*
43008465 TCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCTGCTCCACTGTAACTTCAGAGAGATAA
1 TCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCTGCTCTACTGTAACTTCAGAGAGATAA
*
43008530 GATCCTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTATATTCAATCTGCTCCACT
66 GATCCTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTATATTCAATCTGCTCCGCT
* *
43008595 GTAATCTCAGGGAGATAAGATCTGCAATTCTTCGATCTAT
131 GTAATCTCAGGGAGATAAGATCTGCAATTCTTCGGTCTGT
*
43008635 TCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCTGCTCTACTCTAACTTCAGAGAGATAA
1 TCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCTGCTCTACTGTAACTTCAGAGAGATAA
*
43008700 GATCCTTTAATCCGCTCCACTGTAATCTCAGGCAGATAGGATTACTATATTCAATCTGCTCCGCT
66 GATCCTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTATATTCAATCTGCTCCGCT
43008765 GTAATCTCAGGGAGATAAGATCTGCAATTCTTCGGTCTGT
131 GTAATCTCAGGGAGATAAGATCTGCAATTCTTCGGTCTGT
*
43008805 TCCACTGTAATCTTAGGGAAATAAGACCTG
1 TCCACTGTAATCTCAGGGAAATAAGACCTG
43008835 TATAATGAAC
Statistics
Matches: 990, Mismatches: 59, Indels: 27
0.92 0.05 0.03
Matches are distributed among these distances:
169 39 0.04
170 566 0.57
174 119 0.12
175 101 0.10
176 165 0.17
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (170 bp):
TCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCTGCTCTACTGTAACTTCAGAGAGATAA
GATCCTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTATATTCAATCTGCTCCGCT
GTAATCTCAGGGAGATAAGATCTGCAATTCTTCGGTCTGT
Found at i:43008644 original size:514 final size:515
Alignment explanation
Indices: 43007600--43008835 Score: 2132
Period size: 514 Copynumber: 2.4 Consensus size: 515
43007590 TTCAATGTAC
* * ** * * * *
43007600 TCCACTGTAACCACAGGGAGGTAAAACCTGATGCGATCTACTCTACTGTAACTTCAGTGAGATAA
1 TCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCTGCTCTACTGTAACTTCAGAGAGATAA
* **
43007665 GATCCTTTGTTTTAATCTGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCT
66 GATCC-----TTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTATATTCAATCTGCT
* *
43007730 CCGCTGTAATCTCAGGGAGATAAGTTCTGAAATTCTTCGGTCTGTTCCACTGTAATCTCAGGGAA
126 CCGCTGTAATCTCAGGGAGATAAGATCTGCAATTCTTCGGTCTGTTCCACTGTAATCTCAGGGAA
43007795 ATAAGACCTAGTGCGATCTACTCTACTGTAACTTCAGAGAGGATAAGATCCTTGGTTTTAATCCG
191 ATAAGACCT-GTGCGATCTACTCTACTGTAACTTCAGAGAGGATAAGATCCTTGGTTTTAATCCG
* * *
43007860 CTCCACTATAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGGTCCGCTGTAATCTTAGGGAG
255 CTCCACTATAATATCAGGGAGATAGGATTACTAGCTTCAATCTAGTCCGCTGTAATCTCAGGGAG
*
43007925 ATAAGATCTGAAATTCTTCAGTCTGTTCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCT
320 ATAAGATCTGAAAATCTTCAGTCTGTTCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCT
* * *
43007990 GCTCTACTGTAACTTTAGAGAGATAAGATCCTTTAATCCGCTCTACTGTAATCTCAGGGAGATAG
385 GCTCCACTGTAACTTCAGAGAGATAAGATCCTTTAATCCGCTCCACTGTAATCTCAGGGAGATAG
* *
43008055 GATTACTATATTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGCAATTCTTCGGTCTG
450 GATTACTATATTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGCAATTCTTCGATCTA
43008120 T
515 T
*
43008121 TCCACTGTAATCTCAGGGAAATAAGACCTGGTACGATCTGCTCTACTGTAACTTCAGAGAGATAA
1 TCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCTGCTCTACTGTAACTTCAGAGAGATAA
*
43008186 GATCCTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTATATTCAATTTGCTCCGCT
66 GATCCTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTATATTCAATCTGCTCCGCT
*
43008251 GTAATCTCAGGGAGATAAGATCTGCAATTCTTCGGTCTGTTCCACCGTAATCTCAGGGAAATAAG
131 GTAATCTCAGGGAGATAAGATCTGCAATTCTTCGGTCTGTTCCACTGTAATCTCAGGGAAATAAG
*
43008316 ACCTGTGCGATCTACTCTACTGTAACTTCAGAGA-GATATGATCCTTGGTTTTAATCCGCTCCAC
196 ACCTGTGCGATCTACTCTACTGTAACTTCAGAGAGGATAAGATCCTTGGTTTTAATCCGCTCCAC
* *
43008380 TGTAATATCAGGGAGATAGGATTACTAGTTTCAATCTAGTCCGCTGTAATCTCAGGGAGATAAGA
261 TATAATATCAGGGAGATAGGATTACTAGCTTCAATCTAGTCCGCTGTAATCTCAGGGAGATAAGA
43008445 TCTGAAAATCTTCAGTCTGTTCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCTGCTCCA
326 TCTGAAAATCTTCAGTCTGTTCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCTGCTCCA
43008510 CTGTAACTTCAGAGAGATAAGATCCTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTAC
391 CTGTAACTTCAGAGAGATAAGATCCTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTAC
43008575 TATATTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGCAATTCTTCGATCTAT
456 TATATTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGCAATTCTTCGATCTAT
*
43008635 TCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCTGCTCTACTCTAACTTCAGAGAGATAA
1 TCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCTGCTCTACTGTAACTTCAGAGAGATAA
*
43008700 GATCCTTTAATCCGCTCCACTGTAATCTCAGGCAGATAGGATTACTATATTCAATCTGCTCCGCT
66 GATCCTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTATATTCAATCTGCTCCGCT
*
43008765 GTAATCTCAGGGAGATAAGATCTGCAATTCTTCGGTCTGTTCCACTGTAATCTTAGGGAAATAAG
131 GTAATCTCAGGGAGATAAGATCTGCAATTCTTCGGTCTGTTCCACTGTAATCTCAGGGAAATAAG
43008830 ACCTGT
196 ACCTGT
43008836 ATAATGAACC
Statistics
Matches: 681, Mismatches: 34, Indels: 7
0.94 0.05 0.01
Matches are distributed among these distances:
514 468 0.69
515 30 0.04
516 122 0.18
521 61 0.09
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.31
Consensus pattern (515 bp):
TCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCTGCTCTACTGTAACTTCAGAGAGATAA
GATCCTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTATATTCAATCTGCTCCGCT
GTAATCTCAGGGAGATAAGATCTGCAATTCTTCGGTCTGTTCCACTGTAATCTCAGGGAAATAAG
ACCTGTGCGATCTACTCTACTGTAACTTCAGAGAGGATAAGATCCTTGGTTTTAATCCGCTCCAC
TATAATATCAGGGAGATAGGATTACTAGCTTCAATCTAGTCCGCTGTAATCTCAGGGAGATAAGA
TCTGAAAATCTTCAGTCTGTTCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCTGCTCCA
CTGTAACTTCAGAGAGATAAGATCCTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTAC
TATATTCAATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGCAATTCTTCGATCTAT
Found at i:43010909 original size:14 final size:14
Alignment explanation
Indices: 43010890--43010919 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
43010880 TGACCTCTCC
*
43010890 TTTTCTTTTTCTTT
1 TTTTCTCTTTCTTT
43010904 TTTTCTCTTTCTTT
1 TTTTCTCTTTCTTT
43010918 TT
1 TT
43010920 CCCCTATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTCTCTTTCTTT
Found at i:43017549 original size:30 final size:27
Alignment explanation
Indices: 43017498--43017557 Score: 66
Period size: 30 Copynumber: 2.1 Consensus size: 27
43017488 AAATCTATCC
*
43017498 TTTTATTATTATTATTATTATTTAACTAA
1 TTTTATTATTATCATTATTATTT--CTAA
* *
43017527 TTTTATTTATTCTCATTTTTATTTCTAA
1 TTTTA-TTATTATCATTATTATTTCTAA
43017555 TTT
1 TTT
43017558 GTGTTTCTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 7 0.26
29 5 0.19
30 15 0.56
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.67
Consensus pattern (27 bp):
TTTTATTATTATCATTATTATTTCTAA
Found at i:43025786 original size:24 final size:24
Alignment explanation
Indices: 43025754--43025800 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
43025744 TTTATTGAAA
* *
43025754 TATTGAGTGGCTTGTCCACAACGC
1 TATTAAGTGGCTTGACCACAACGC
*
43025778 TATTAAGTGGTTTGACCACAACG
1 TATTAAGTGGCTTGACCACAACG
43025801 ATACAAGTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (24 bp):
TATTAAGTGGCTTGACCACAACGC
Found at i:43042758 original size:26 final size:26
Alignment explanation
Indices: 43042707--43042774 Score: 73
Period size: 26 Copynumber: 2.6 Consensus size: 26
43042697 CTACTTTAGC
*
43042707 AATACTTTTAAAAAGTGCTATGGAGA
1 AATACTTTTGAAAAGTGCTATGGAGA
* * * *
43042733 AATGCTTTTGAAAAGTGTTTTTGAGA
1 AATACTTTTGAAAAGTGCTATGGAGA
* *
43042759 ATTATTTTTGAAAAGT
1 AATACTTTTGAAAAGT
43042775 TTGGTTTAAG
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.37, C:0.04, G:0.19, T:0.40
Consensus pattern (26 bp):
AATACTTTTGAAAAGTGCTATGGAGA
Found at i:43045739 original size:27 final size:27
Alignment explanation
Indices: 43045709--43045851 Score: 216
Period size: 27 Copynumber: 5.3 Consensus size: 27
43045699 CCAAAATAGA
* *
43045709 TAAAATGACCAAAATACCCTCATAGGG
1 TAAAATGACCGAAATACCCCCATAGGG
*** *
43045736 TAAAATGAAAAAAATACCCTCATAGGG
1 TAAAATGACCGAAATACCCCCATAGGG
43045763 TAAAATGACCGAAATACCCCCATAGGG
1 TAAAATGACCGAAATACCCCCATAGGG
*
43045790 TAAAATGATCGAAATA-CCCCATAGGG
1 TAAAATGACCGAAATACCCCCATAGGG
43045816 TAAAATGACCGAAATACCCCCATAGGG
1 TAAAATGACCGAAATACCCCCATAGGG
43045843 TAAAATGAC
1 TAAAATGAC
43045852 TGTTATACCC
Statistics
Matches: 107, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
26 25 0.23
27 82 0.77
ACGTcount: A:0.45, C:0.21, G:0.17, T:0.17
Consensus pattern (27 bp):
TAAAATGACCGAAATACCCCCATAGGG
Found at i:43045835 original size:53 final size:54
Alignment explanation
Indices: 43045709--43045850 Score: 232
Period size: 53 Copynumber: 2.6 Consensus size: 54
43045699 CCAAAATAGA
* *
43045709 TAAAATGACCAAAATACCCTCATAGGGTAAAATGAAAAAAATACCCTCATAGGG
1 TAAAATGACCGAAATACCCCCATAGGGTAAAATGAAAAAAATACCCTCATAGGG
***
43045763 TAAAATGACCGAAATACCCCCATAGGGTAAAATGATCGAAATACCC-CATAGGG
1 TAAAATGACCGAAATACCCCCATAGGGTAAAATGAAAAAAATACCCTCATAGGG
43045816 TAAAATGACCGAAATACCCCCATAGGGTAAAATGA
1 TAAAATGACCGAAATACCCCCATAGGGTAAAATGA
43045851 CTGTTATACC
Statistics
Matches: 83, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
53 42 0.51
54 41 0.49
ACGTcount: A:0.45, C:0.20, G:0.17, T:0.18
Consensus pattern (54 bp):
TAAAATGACCGAAATACCCCCATAGGGTAAAATGAAAAAAATACCCTCATAGGG
Found at i:43045876 original size:80 final size:83
Alignment explanation
Indices: 43045706--43045878 Score: 221
Period size: 80 Copynumber: 2.1 Consensus size: 83
43045696 ACCCCAAAAT
*
43045706 AGATAAAATGACCAAAATACCCTCATAGGGTAAAATGAAAAAAATACCCTCATAGGGTAAAATGA
1 AGATAAAATGACCAAAATACCCTCATAGGGTAAAATGAAAAAAATACCCCCATAGGGTAAAATGA
43045771 CCGAAATACCCCCATAGG
66 CCGAAATACCCCCATAGG
* * ***
43045789 -G-TAAAATGATCGAAATACCC-CATAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGA
1 AGATAAAATGACCAAAATACCCTCATAGGGTAAAATGAAAAAAATACCCCCATAGGGTAAAATGA
* **
43045851 CTGTTATA-CCCC-TAGG
66 CCGAAATACCCCCATAGG
*
43045867 AGATTAAATGAC
1 AGATAAAATGAC
43045879 TGTTATGGCC
Statistics
Matches: 77, Mismatches: 11, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
78 4 0.05
79 5 0.06
80 50 0.65
81 17 0.22
82 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.19
Consensus pattern (83 bp):
AGATAAAATGACCAAAATACCCTCATAGGGTAAAATGAAAAAAATACCCCCATAGGGTAAAATGA
CCGAAATACCCCCATAGG
Found at i:43048188 original size:21 final size:21
Alignment explanation
Indices: 43048162--43048205 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
43048152 GAAGTTCGAG
*
43048162 TTGTATCTGTAGAAC-CCATAA
1 TTGTATCGGTAGAACTCC-TAA
43048183 TTGTATCGGTAGAACTCCTAA
1 TTGTATCGGTAGAACTCCTAA
43048204 TT
1 TT
43048206 CTACTAATAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (21 bp):
TTGTATCGGTAGAACTCCTAA
Found at i:43051063 original size:20 final size:20
Alignment explanation
Indices: 43051040--43051077 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
43051030 AGTGATTTTT
43051040 GGAAAAATTAATTTTGATCA
1 GGAAAAATTAATTTTGATCA
43051060 GGAAAAATTAATTTTGAT
1 GGAAAAATTAATTTTGAT
43051078 TAAGTAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.03, G:0.16, T:0.37
Consensus pattern (20 bp):
GGAAAAATTAATTTTGATCA
Found at i:43051093 original size:21 final size:20
Alignment explanation
Indices: 43051041--43051090 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
43051031 GTGATTTTTG
*
43051041 GAAAAATTAATTTTGATCAG
1 GAAAAATTAATTTTGATCAA
*
43051061 GAAAAATTAATTTTGATTAA
1 GAAAAATTAATTTTGATCAA
*
43051081 GTAAAATTAA
1 GAAAAATTAA
43051091 ATTCATCAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.50, C:0.02, G:0.12, T:0.36
Consensus pattern (20 bp):
GAAAAATTAATTTTGATCAA
Found at i:43061914 original size:50 final size:50
Alignment explanation
Indices: 43061856--43062038 Score: 181
Period size: 50 Copynumber: 3.6 Consensus size: 50
43061846 TTCGATACAC
* *
43061856 GTAGTAGCCTTCACATAGTACTACACATGTGATCAAACTTTTCGGTTCAT
1 GTAGTAGCCTGCACATAGTACTACACACGTGATCAAACTTTTCGGTTCAT
* * * *
43061906 GTAGTAGCCTGCACATAGTACTACAAACGTGATCGAAGTTATCTGG-T-AT
1 GTAGTAGCCTGCACATAGTACTACACACGTGATCAAACTTTTC-GGTTCAT
* * *** * * * *
43061955 GCATAGTAGCCTGCACATAGTACTACACATGTGACCTTTCATTCCGGTACAC
1 G--TAGTAGCCTGCACATAGTACTACACACGTGATCAAACTTTTCGGTTCAT
*
43062007 GTAGTAGCCTACACATAGTACTACACACGTGA
1 GTAGTAGCCTGCACATAGTACTACACACGTGA
43062039 CCATCACTTT
Statistics
Matches: 108, Mismatches: 20, Indels: 10
0.78 0.14 0.07
Matches are distributed among these distances:
49 3 0.03
50 69 0.64
51 34 0.31
52 2 0.02
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (50 bp):
GTAGTAGCCTGCACATAGTACTACACACGTGATCAAACTTTTCGGTTCAT
Found at i:43062011 original size:101 final size:101
Alignment explanation
Indices: 43061857--43062038 Score: 265
Period size: 101 Copynumber: 1.8 Consensus size: 101
43061847 TCGATACACG
* * * * * * *
43061857 TAGTAGCCTTCACATAGTACTACACATGTGATCAAACTTTTCGGTTCATGTAGTAGCCTGCACAT
1 TAGTAGCCTGCACATAGTACTACACATGTGACCAAACATTCCGGTACACGTAGTAGCCTACACAT
43061922 AGTACTACAAACGTGATCGAAGTTATCTGGTATGCA
66 AGTACTACAAACGTGATCGAAGTTATCTGGTATGCA
***
43061958 TAGTAGCCTGCACATAGTACTACACATGTGACCTTTCATTCCGGTACACGTAGTAGCCTACACAT
1 TAGTAGCCTGCACATAGTACTACACATGTGACCAAACATTCCGGTACACGTAGTAGCCTACACAT
*
43062023 AGTACTACACACGTGA
66 AGTACTACAAACGTGA
43062039 CCATCACTTT
Statistics
Matches: 70, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
101 70 1.00
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.29
Consensus pattern (101 bp):
TAGTAGCCTGCACATAGTACTACACATGTGACCAAACATTCCGGTACACGTAGTAGCCTACACAT
AGTACTACAAACGTGATCGAAGTTATCTGGTATGCA
Found at i:43078971 original size:75 final size:75
Alignment explanation
Indices: 43078803--43078971 Score: 162
Period size: 75 Copynumber: 2.3 Consensus size: 75
43078793 GGTTTATCCA
* * *** * *
43078803 ACTAGCACTCGGTGCAAACACCATTGGTTCATCCAACTAGAGCTGTGCTCACATTTAATATCATC
1 ACTAGCACTGGGAGCAAACATTGTTGGTTCATCCAACTAGAGCTGGGCTCACATTCAATATCATC
*
43078868 AGTATATCAG
66 AGTATACCAG
** * * * *
43078878 ACTAGCGTTGGGCGCAAACATTGTTGGTTTATCCAACTAGGGCTGGGCTCACATTCAATA-CTGT
1 ACTAGCACTGGGAGCAAACATTGTTGGTTCATCCAACTAGAGCTGGGCTCACATTCAATATC-AT
*
43078942 CAGT-TAACCTG
65 CAGTAT-ACCAG
*
43078953 ACTAGCACTGGGATCAAAC
1 ACTAGCACTGGGAGCAAAC
43078972 TCCTTTACGG
Statistics
Matches: 74, Mismatches: 18, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
74 2 0.03
75 72 0.97
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.27
Consensus pattern (75 bp):
ACTAGCACTGGGAGCAAACATTGTTGGTTCATCCAACTAGAGCTGGGCTCACATTCAATATCATC
AGTATACCAG
Found at i:43081182 original size:26 final size:26
Alignment explanation
Indices: 43081139--43081205 Score: 98
Period size: 26 Copynumber: 2.6 Consensus size: 26
43081129 TTACATCATC
* *
43081139 ACTCACACGAACTGTGAAATAGGCCT
1 ACTCACACGAGCTATGAAATAGGCCT
*
43081165 ACTCACACGAGCTATGAAATGGGCCT
1 ACTCACACGAGCTATGAAATAGGCCT
*
43081191 GCTCACACGAGCTAT
1 ACTCACACGAGCTAT
43081206 AAGTCAGAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.31, C:0.28, G:0.21, T:0.19
Consensus pattern (26 bp):
ACTCACACGAGCTATGAAATAGGCCT
Found at i:43089918 original size:30 final size:30
Alignment explanation
Indices: 43089882--43089942 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
43089872 ATACATTTCA
* *
43089882 AACATTAATATAACATAACATAAGGCATTC
1 AACATTAACAAAACATAACATAAGGCATTC
43089912 AACATTAACAAAACATAACATAAGGCATTC
1 AACATTAACAAAACATAACATAAGGCATTC
43089942 A
1 A
43089943 TTCACATGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.52, C:0.18, G:0.07, T:0.23
Consensus pattern (30 bp):
AACATTAACAAAACATAACATAAGGCATTC
Found at i:43091174 original size:20 final size:20
Alignment explanation
Indices: 43091149--43091197 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
43091139 GAACCACTCA
43091149 ATTTACTTACTC-CTCATTCC
1 ATTTACTTACTCTC-CATTCC
*
43091169 ATTTACTTACTTTCCATTCC
1 ATTTACTTACTCTCCATTCC
43091189 ATTTACTTA
1 ATTTACTTA
43091198 GCATAAGCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 26 0.96
21 1 0.04
ACGTcount: A:0.22, C:0.29, G:0.00, T:0.49
Consensus pattern (20 bp):
ATTTACTTACTCTCCATTCC
Found at i:43092226 original size:20 final size:19
Alignment explanation
Indices: 43092190--43092233 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
43092180 GTCAATTTGT
43092190 CATAATATGGATACATTCA
1 CATAATATGGATACATTCA
* * *
43092209 CATATATATTGATTCATTTA
1 CATA-ATATGGATACATTCA
43092229 CATAA
1 CATAA
43092234 AAAAACATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.39
Consensus pattern (19 bp):
CATAATATGGATACATTCA
Found at i:43110815 original size:21 final size:21
Alignment explanation
Indices: 43110789--43110828 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
43110779 TTTAATATAA
43110789 TAATACATT-ATTATATTATTT
1 TAATACATTAATTA-ATTATTT
*
43110810 TAATACTTTAATTAATTAT
1 TAATACATTAATTAATTAT
43110829 GACCCAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (21 bp):
TAATACATTAATTAATTATTT
Found at i:43113265 original size:2 final size:2
Alignment explanation
Indices: 43113258--43113290 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
43113248 AATCATTTTA
43113258 AT AT 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 AT AT A
43113291 CTCTCTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:43119652 original size:16 final size:16
Alignment explanation
Indices: 43119631--43119661 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
43119621 TCATCAAACA
*
43119631 AAGAAAGATTACGCCC
1 AAGAAAGAGTACGCCC
43119647 AAGAAAGAGTACGCC
1 AAGAAAGAGTACGCC
43119662 TTAGAGTATT
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:0.45, C:0.23, G:0.23, T:0.10
Consensus pattern (16 bp):
AAGAAAGAGTACGCCC
Found at i:43122583 original size:21 final size:21
Alignment explanation
Indices: 43122526--43122586 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
43122516 TTGATCAGTG
** *
43122526 TTGAACGACGTTGACCGATCG
1 TTGAACGACGTTGATTGATCA
*
43122547 TTGACCCGACGTTGATTGATCA
1 TTGA-ACGACGTTGATTGATCA
43122569 TTGAACGACGTTGATTGA
1 TTGAACGACGTTGATTGA
43122587 CTATGTGGTG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 17 0.50
22 17 0.50
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.30
Consensus pattern (21 bp):
TTGAACGACGTTGATTGATCA
Found at i:43122717 original size:23 final size:23
Alignment explanation
Indices: 43122678--43122743 Score: 59
Period size: 22 Copynumber: 3.0 Consensus size: 23
43122668 ATAAATATAA
* *
43122678 TTTTA-AAAAATTAAAAATAGTT
1 TTTTATAAAATTTTAAAATAGTT
43122700 TTTTATAAAATTTTAAAATA-TAT
1 TTTTATAAAATTTTAAAATAGT-T
**
43122723 AATTAT-AAATTTTAAAA-AGTT
1 TTTTATAAAATTTTAAAATAGTT
43122744 AAAATAATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
21 2 0.05
22 18 0.49
23 17 0.46
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (23 bp):
TTTTATAAAATTTTAAAATAGTT
Found at i:43140735 original size:136 final size:136
Alignment explanation
Indices: 43140491--43140759 Score: 398
Period size: 136 Copynumber: 2.0 Consensus size: 136
43140481 ATACATTCAT
* * *
43140491 GCAGACAACCTTCTTTGTGTTAGCCAAACATGGGTCCGTTTTCAAAGATCAATCATTCCTTTTAT
1 GCAGACAACCTTCTTTGTGTTAGCCAAACACGGGTCCGTATTCAAAGATCAATCATTCCTTTCAT
* *
43140556 TTCCTTAGTCATGCTAGCTAGTCTGGTTTGTAATGTACCTGCCTTACCT-GAGGCCACATAACCA
66 TTCCTTAGCCATGCTAGCTAGTCTGGTTTGCAATGTACCTGCCTTA-CTAGAGGCCACATAACCA
43140620 TTGTCAA
130 TTGTCAA
* * * ** *
43140627 GCAGACAACCTTCTTTGTGTTGGCCAAACCCGGTTTTGTATTCAGAGATCAA-CAATTCCTTTCA
1 GCAGACAACCTTCTTTGTGTTAGCCAAACACGGGTCCGTATTCAAAGATCAATC-ATTCCTTTCA
*
43140691 TTTCCTTTGCCATGCTAGCTAGTCTGGTTTGCAATGTACCTGCCTTACTAGAGGCCACATAACCA
65 TTTCCTTAGCCATGCTAGCTAGTCTGGTTTGCAATGTACCTGCCTTACTAGAGGCCACATAACCA
43140756 TTGT
130 TTGT
43140760 TCATATACTA
Statistics
Matches: 119, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
135 3 0.03
136 116 0.97
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.34
Consensus pattern (136 bp):
GCAGACAACCTTCTTTGTGTTAGCCAAACACGGGTCCGTATTCAAAGATCAATCATTCCTTTCAT
TTCCTTAGCCATGCTAGCTAGTCTGGTTTGCAATGTACCTGCCTTACTAGAGGCCACATAACCAT
TGTCAA
Found at i:43144211 original size:20 final size:20
Alignment explanation
Indices: 43144188--43144235 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
43144178 AACCACTCCT
43144188 TTTACTTACTTACCATTCCA
1 TTTACTTACTTACCATTCCA
*
43144208 TTTACTTACTTTCCATTCCA
1 TTTACTTACTTACCATTCCA
43144228 TTTACTTA
1 TTTACTTA
43144236 GTATAAGCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.23, C:0.27, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTACTTACTTACCATTCCA
Found at i:43146023 original size:19 final size:18
Alignment explanation
Indices: 43145993--43146028 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
43145983 ACTTTTGTTT
43145993 TATTTATTTATTTTAACC
1 TATTTATTTATTTTAACC
43146011 TATTTACTTTATTTTAAC
1 TATTTA-TTTATTTTAAC
43146029 AATAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.28, C:0.11, G:0.00, T:0.61
Consensus pattern (18 bp):
TATTTATTTATTTTAACC
Found at i:43153239 original size:20 final size:20
Alignment explanation
Indices: 43153214--43153258 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
43153204 TAAATACACA
43153214 TAATTACAACT-AGACACAAT
1 TAATTA-AACTAAGACACAAT
**
43153234 TAATTAAGTTAAGACACAAT
1 TAATTAAACTAAGACACAAT
43153254 TAATT
1 TAATT
43153259 CGGTTGGACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.49, C:0.13, G:0.07, T:0.31
Consensus pattern (20 bp):
TAATTAAACTAAGACACAAT
Found at i:43156261 original size:26 final size:26
Alignment explanation
Indices: 43156204--43156272 Score: 79
Period size: 26 Copynumber: 2.7 Consensus size: 26
43156194 TTTACATGAA
* *
43156204 TGCTCACATGAGTTGTGAAATGGGTC
1 TGCTCACACGAGCTGTGAAATGGGTC
*
43156230 TACTCACACGAGCTGTGAAATGGG-C
1 TGCTCACACGAGCTGTGAAATGGGTC
43156255 TTGCTCACAC-AGGCTGTG
1 -TGCTCACACGA-GCTGTG
43156273 GGTCGAAATG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
25 2 0.05
26 35 0.95
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.26
Consensus pattern (26 bp):
TGCTCACACGAGCTGTGAAATGGGTC
Found at i:43159057 original size:53 final size:54
Alignment explanation
Indices: 43158975--43159080 Score: 160
Period size: 53 Copynumber: 2.0 Consensus size: 54
43158965 AGTCCATGGC
* * *
43158975 ACCATATCGTGTAATACCATAACTAGTGGGTTATGGTATCATA-TGGAAAGAAT
1 ACCATATCATGTAAGACCATAACTAGTGGGTTATGGCATCATATTGGAAAGAAT
* *
43159028 ACCATATCATGTAAGACCATAATTTGTGGGTTATGGCATCATATTGGAAAGAA
1 ACCATATCATGTAAGACCATAACTAGTGGGTTATGGCATCATATTGGAAAGAA
43159081 CTAAGGGGGT
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
53 38 0.81
54 9 0.19
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (54 bp):
ACCATATCATGTAAGACCATAACTAGTGGGTTATGGCATCATATTGGAAAGAAT
Found at i:43160360 original size:30 final size:30
Alignment explanation
Indices: 43160326--43160537 Score: 170
Period size: 30 Copynumber: 7.1 Consensus size: 30
43160316 TGACCAATGG
43160326 AAAGGGATAGCTTCGACTATCAAATTATGA
1 AAAGGGATAGCTTCGACTATCAAATTATGA
* *
43160356 AAAGGGAT-GACTT-TAGCTATCGAATTATGA
1 AAAGGGATAG-CTTCGA-CTATCAAATTATGA
* *
43160386 AAAGGGATAGCTTCGGCTATCAAATTATAAA
1 AAAGGGATAGCTTCGACTATCAAATTAT-GA
* *
43160417 AAAGGGATAG-TGACGACCATCAACA--ATGA
1 AAAGGGATAGCT-TCGACTATCAA-ATTATGA
* * *
43160446 AAAGGGAT-GGTGACGACCATCAACA--ATGA
1 AAAGGGATAGCT-TCGACTATCAA-ATTATGA
* * * *
43160475 AAAGGGATGGCTTCGGCAATCAAAATATGA
1 AAAGGGATAGCTTCGACTATCAAATTATGA
* *
43160505 AAAGGGATAGCTTCGACTATCGAACTATGA
1 AAAGGGATAGCTTCGACTATCAAATTATGA
43160535 AAA
1 AAA
43160538 AGGGTGGTAA
Statistics
Matches: 152, Mismatches: 19, Indels: 22
0.79 0.10 0.11
Matches are distributed among these distances:
28 2 0.01
29 46 0.30
30 83 0.55
31 20 0.13
32 1 0.01
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.22
Consensus pattern (30 bp):
AAAGGGATAGCTTCGACTATCAAATTATGA
Found at i:43160458 original size:29 final size:29
Alignment explanation
Indices: 43160416--43160484 Score: 129
Period size: 29 Copynumber: 2.4 Consensus size: 29
43160406 CAAATTATAA
*
43160416 AAAAGGGATAGTGACGACCATCAACAATG
1 AAAAGGGATGGTGACGACCATCAACAATG
43160445 AAAAGGGATGGTGACGACCATCAACAATG
1 AAAAGGGATGGTGACGACCATCAACAATG
43160474 AAAAGGGATGG
1 AAAAGGGATGG
43160485 CTTCGGCAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.29, T:0.13
Consensus pattern (29 bp):
AAAAGGGATGGTGACGACCATCAACAATG
Found at i:43160496 original size:29 final size:29
Alignment explanation
Indices: 43160430--43160537 Score: 110
Period size: 29 Copynumber: 3.7 Consensus size: 29
43160420 GGGATAGTGA
* *
43160430 CGACCATCAACAATGAAAAGGGATGG-TGA
1 CGACAATCAACAATGAAAAGGGATGGCT-T
*
43160459 CGACCATCAACAATGAAAAGGGATGGCTT
1 CGACAATCAACAATGAAAAGGGATGGCTT
* * *
43160488 CGGCAATCAAAATATGAAAAGGGATAGCTT
1 CGACAATCAACA-ATGAAAAGGGATGGCTT
* *
43160518 CGACTATCGAACTATGAAAA
1 CGACAATC-AACAATGAAAA
43160538 AGGGTGGTAA
Statistics
Matches: 67, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
29 35 0.52
30 30 0.45
31 2 0.03
ACGTcount: A:0.42, C:0.18, G:0.23, T:0.18
Consensus pattern (29 bp):
CGACAATCAACAATGAAAAGGGATGGCTT
Found at i:43161938 original size:27 final size:27
Alignment explanation
Indices: 43161900--43161952 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
43161890 GGTGTTACAG
* *
43161900 GAAGTCTTTGTGGCAATCTATGAAAAT
1 GAAGCCTTTGTGGCAATCTATAAAAAT
43161927 GAAGCCTTTGTGGCAATCTATAAAAA
1 GAAGCCTTTGTGGCAATCTATAAAAA
43161953 CAAATGCCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (27 bp):
GAAGCCTTTGTGGCAATCTATAAAAAT
Found at i:43162128 original size:27 final size:27
Alignment explanation
Indices: 43162098--43162149 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
43162088 TGGAAGAATA
*
43162098 ATATGCATGGCGAACTCTAAAGGAAAG
1 ATATGCATGGCAAACTCTAAAGGAAAG
* * *
43162125 ATATGTATGGTAAACTGTAAAGGAA
1 ATATGCATGGCAAACTCTAAAGGAA
43162150 TGGCTCCATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.42, C:0.10, G:0.25, T:0.23
Consensus pattern (27 bp):
ATATGCATGGCAAACTCTAAAGGAAAG
Found at i:43167125 original size:6 final size:6
Alignment explanation
Indices: 43167114--43167147 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
43167104 GTTTTCTTCT
43167114 AAATGA AAATGA AAATGA AAATAGA GAAATGA AA
1 AAATGA AAATGA AAATGA AAAT-GA -AAATGA AA
43167148 TCATTTGGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 18 0.69
7 4 0.15
8 4 0.15
ACGTcount: A:0.68, C:0.00, G:0.18, T:0.15
Consensus pattern (6 bp):
AAATGA
Found at i:43167172 original size:63 final size:65
Alignment explanation
Indices: 43167050--43167188 Score: 178
Period size: 63 Copynumber: 2.2 Consensus size: 65
43167040 ATGTTGAATC
* * * * *
43167050 AAATGAAAAT-ATAAATAGAAATGGAGAAATGAGAAACATTTGGAAATTATTATGGTTTTCTTCT
1 AAATGAAAATGATAAATAGAAATAGAGAAATGAGAAACATTTGGAAATGAATATGGTTTTCTCCA
* *
43167114 AAATGAAAATGA-AAAT-GAAAATAGAGAAATGA-AATCATTTGGAAATGAATGTGGTTTTCTCC
1 AAATGAAAATGATAAATAG-AAATAGAGAAATGAGAAACATTTGGAAATGAATATGGTTTTCTCC
43167176 A
65 A
43167177 AAATGAAAATGA
1 AAATGAAAATGA
43167189 CTTGGAAATG
Statistics
Matches: 66, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
63 38 0.58
64 27 0.41
65 1 0.02
ACGTcount: A:0.48, C:0.05, G:0.18, T:0.29
Consensus pattern (65 bp):
AAATGAAAATGATAAATAGAAATAGAGAAATGAGAAACATTTGGAAATGAATATGGTTTTCTCCA
Found at i:43173399 original size:50 final size:50
Alignment explanation
Indices: 43173324--43173465 Score: 176
Period size: 50 Copynumber: 2.8 Consensus size: 50
43173314 ATTTGGGTAA
*
43173324 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * *
43173374 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCTATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * * * *
43173424 AGAACTCTCATGCAAGACCATATCTGGGATATGGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
43173466 GTACAAGAAA
Statistics
Matches: 78, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 78 1.00
ACGTcount: A:0.25, C:0.23, G:0.30, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:43177749 original size:40 final size:40
Alignment explanation
Indices: 43177683--43177826 Score: 159
Period size: 40 Copynumber: 3.6 Consensus size: 40
43177673 ACCAAAGTAT
* * *
43177683 AAACA-GGGCACGTATGAGCGTCCAGGGGTACTGAAATAC
1 AAACAGGGGCACGTATGTGCATTCAGGGGTACTGAAATAC
* *
43177722 AAACAGGGGAACGTATGTGCATTCAGGGGTAC-CAAAGTAC
1 AAACAGGGGCACGTATGTGCATTCAGGGGTACTGAAA-TAC
* * * *
43177762 AAATAGGGGCACATATGTGCATTCAGAGGTA-TCGAAGTAC
1 AAACAGGGGCACGTATGTGCATTCAGGGGTACT-GAAATAC
*
43177802 AAACAGGGGCACGTATGTGCTTTCA
1 AAACAGGGGCACGTATGTGCATTCA
43177827 TTCATTAGTT
Statistics
Matches: 87, Mismatches: 14, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
39 8 0.09
40 77 0.89
41 2 0.02
ACGTcount: A:0.33, C:0.18, G:0.29, T:0.19
Consensus pattern (40 bp):
AAACAGGGGCACGTATGTGCATTCAGGGGTACTGAAATAC
Found at i:43177810 original size:80 final size:79
Alignment explanation
Indices: 43177663--43177826 Score: 204
Period size: 80 Copynumber: 2.1 Consensus size: 79
43177653 ATACTATTTG
* * * * *
43177663 ATTCAGGGTTACCAAAGTATAAACAGGGCACGTATGAGCGTCCAGGGGTACTGAAATACAAACAG
1 ATTCAGGGGTACCAAAGTACAAACAGGGCACATATGAGCATCCAGAGGTACTGAAATACAAACAG
43177728 GGGAACGTATGTGC
66 GGGAACGTATGTGC
* * * *
43177742 ATTCAGGGGTACCAAAGTACAAATAGGGGCACATATGTGCATTCAGAGGTA-TCGAAGTACAAAC
1 ATTCAGGGGTACCAAAGTACAAACA-GGGCACATATGAGCATCCAGAGGTACT-GAAATACAAAC
*
43177806 AGGGGCACGTATGTGC
64 AGGGGAACGTATGTGC
*
43177822 TTTCA
1 ATTCA
43177827 TTCATTAGTT
Statistics
Matches: 72, Mismatches: 11, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
79 23 0.32
80 49 0.68
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.21
Consensus pattern (79 bp):
ATTCAGGGGTACCAAAGTACAAACAGGGCACATATGAGCATCCAGAGGTACTGAAATACAAACAG
GGGAACGTATGTGC
Found at i:43184015 original size:14 final size:15
Alignment explanation
Indices: 43183988--43184017 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
43183978 GCCCGGTCCC
43183988 AAAACCAAATAAATA
1 AAAACCAAATAAATA
43184003 AAAACCAAA-AAATA
1 AAAACCAAATAAATA
43184017 A
1 A
43184018 TAATCTCAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.77, C:0.13, G:0.00, T:0.10
Consensus pattern (15 bp):
AAAACCAAATAAATA
Found at i:43192654 original size:231 final size:231
Alignment explanation
Indices: 43192226--43192682 Score: 643
Period size: 231 Copynumber: 2.0 Consensus size: 231
43192216 CCTGTATTCT
* * *
43192226 CGTATTAGGCCCTCGATTAGAGATTTTTGACGGATGAGTGAACACCACTCACCGTTATTGTAGGA
1 CGTATTAGGCCCTCAATTAGAGA-TTTTGACGAATGAGTGAACACCACTCACCCTTATTGTAGGA
* *
43192291 TTACTCTTGTAAGATAGTTCGACTGAACCTTCCCTCATCAGGTAGTTTGAATGGATATTTCTAGA
65 TTACTCTTGTAAGATAGTTCAACTGAACCTTCCCTCATAAGGTAGTTTGAATGGATATTTCTAGA
*
43192356 GGTAGATAGTCCCTGACGAACTATCTAACCCCTAGATTGTATAAGGTGTACTTTCCATTTATAAG
130 GGTAGATAATCCCTGACGAACTATCTAACCCCTAGATTGTATAAGGTGTACTTTCCATTTATAAG
* **
43192421 AAAAATCCTTAATGGATTTTGCAACACTAGATATTTGA
195 -AAAATCCTGAATGGATTTCACAACACTAGATATTTGA
* *
43192459 CGTATTAGGCCTTCAATTAGAGA-TTTGACGAATG-GATGAACACCACTCACCCTTATTGTTGGA
1 CGTATTAGGCCCTCAATTAGAGATTTTGACGAATGAG-TGAACACCACTCACCCTTATTGTAGGA
* * *
43192522 TTACTCTTGTAAGATATTTCAACTGAACCTT-CTTCCATAAGGTAGTTTGAATTGATATTTCTAG
65 TTACTCTTGTAAGATAGTTCAACTGAACCTTCCCT-CATAAGGTAGTTTGAATGGATATTTCTAG
** * * **
43192586 AGGTAGATAATCCCTGGTGAACTATCTCATCTTTAGATTGTATAAGGTGTAC-TTCTCATTTATA
129 AGGTAGATAATCCCTGACGAACTATCTAACCCCTAGATTGTATAAGGTGTACTTTC-CATTTATA
* *
43192650 AGAAAATCCTGACTGTATTTCACAACACTAGAT
193 AGAAAATCCTGAATGGATTTCACAACACTAGAT
43192683 GGTCCAAATG
Statistics
Matches: 199, Mismatches: 22, Indels: 9
0.87 0.10 0.04
Matches are distributed among these distances:
230 32 0.16
231 146 0.73
233 21 0.11
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (231 bp):
CGTATTAGGCCCTCAATTAGAGATTTTGACGAATGAGTGAACACCACTCACCCTTATTGTAGGAT
TACTCTTGTAAGATAGTTCAACTGAACCTTCCCTCATAAGGTAGTTTGAATGGATATTTCTAGAG
GTAGATAATCCCTGACGAACTATCTAACCCCTAGATTGTATAAGGTGTACTTTCCATTTATAAGA
AAATCCTGAATGGATTTCACAACACTAGATATTTGA
Found at i:43193769 original size:26 final size:26
Alignment explanation
Indices: 43193712--43193785 Score: 87
Period size: 26 Copynumber: 2.8 Consensus size: 26
43193702 AAAAATCAAG
43193712 TGCCTTTGTGGCAATCTATGAAATGGA
1 TGCCTTTGTGGCAATC-ATGAAATGGA
* *
43193739 AGCCTTTGTGGCGTATC-TGAAATGGA
1 TGCCTTTGTGGC-AATCATGAAATGGA
*
43193765 TGCCTTTGTGGCTAATAATGA
1 TGCCTTTGTGGC-AATCATGA
43193786 CAGGAACATC
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
26 22 0.56
27 14 0.36
28 3 0.08
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.34
Consensus pattern (26 bp):
TGCCTTTGTGGCAATCATGAAATGGA
Found at i:43194012 original size:27 final size:27
Alignment explanation
Indices: 43193967--43194023 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
43193957 AAATATATAT
*
43193967 ATATGGAAAATTCTAAAGGAATGGAAC
1 ATATGGAAAACTCTAAAGGAATGGAAC
* *
43193994 ATATGGCAAACTCTGAAGGAATGGAAC
1 ATATGGAAAACTCTAAAGGAATGGAAC
43194021 ATA
1 ATA
43194024 ATGGTTAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.46, C:0.11, G:0.23, T:0.21
Consensus pattern (27 bp):
ATATGGAAAACTCTAAAGGAATGGAAC
Found at i:43204146 original size:38 final size:37
Alignment explanation
Indices: 43204104--43204199 Score: 99
Period size: 35 Copynumber: 2.6 Consensus size: 37
43204094 CACTCTAGAA
*
43204104 AGCTTGTAGATAACAATTTTCATGGTGTCACTCTGTAG
1 AGCTTGT-GATAACAATTTTCATGGTGTCACTCCGTAG
* * *
43204142 AGCTTGT-AT-ACTATTTCCATGGTGTTACTCCGTAG
1 AGCTTGTGATAACAATTTTCATGGTGTCACTCCGTAG
*
43204177 AGTCTATG-GATAACCATTTTCAT
1 AG-CT-TGTGATAACAATTTTCAT
43204200 CCTATCGTCT
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
35 24 0.50
36 4 0.08
37 4 0.08
38 16 0.33
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.39
Consensus pattern (37 bp):
AGCTTGTGATAACAATTTTCATGGTGTCACTCCGTAG
Found at i:43213877 original size:27 final size:27
Alignment explanation
Indices: 43213836--43214004 Score: 187
Period size: 27 Copynumber: 6.3 Consensus size: 27
43213826 CGAAAAGGTT
** *
43213836 GTAAAATTATTGAAATACCCTCGAAGA
1 GTAAAATTACCGAAATACCCTCGAAGG
43213863 GTAAAATTACCGAAATACCCTCGAAGG
1 GTAAAATTACCGAAATACCCTCGAAGG
* * *
43213890 GTAAAATTACTGGAACACCCTCGAAGG
1 GTAAAATTACCGAAATACCCTCGAAGG
* * *
43213917 GTAAAATGATCGAAATACCC-CTAAAGG
1 GTAAAATTACCGAAATACCCTC-GAAGG
***
43213944 GTAAAATTATTTAAATACCCTCGAAGG
1 GTAAAATTACCGAAATACCCTCGAAGG
* * *
43213971 GTAAAATGACCGAAATACCCTTGATGG
1 GTAAAATTACCGAAATACCCTCGAAGG
43213998 GTAAAAT
1 GTAAAAT
43214005 GATCGTAACA
Statistics
Matches: 118, Mismatches: 22, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
26 1 0.01
27 116 0.98
28 1 0.01
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.22
Consensus pattern (27 bp):
GTAAAATTACCGAAATACCCTCGAAGG
Found at i:43213911 original size:54 final size:54
Alignment explanation
Indices: 43213836--43214004 Score: 232
Period size: 54 Copynumber: 3.1 Consensus size: 54
43213826 CGAAAAGGTT
* *
43213836 GTAAAATTATTGAAATACCCTCGAAGAGTAAAATTACCGAAATACCCTCGAAGG
1 GTAAAATTATTGAAATACCCTCGAAGGGTAAAATGACCGAAATACCCTCGAAGG
* * * * *
43213890 GTAAAATTACTGGAACACCCTCGAAGGGTAAAATGATCGAAATACCC-CTAAAGG
1 GTAAAATTATTGAAATACCCTCGAAGGGTAAAATGACCGAAATACCCTC-GAAGG
* * *
43213944 GTAAAATTATTTAAATACCCTCGAAGGGTAAAATGACCGAAATACCCTTGATGG
1 GTAAAATTATTGAAATACCCTCGAAGGGTAAAATGACCGAAATACCCTCGAAGG
43213998 GTAAAAT
1 GTAAAAT
43214005 GATCGTAACA
Statistics
Matches: 98, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
53 1 0.01
54 97 0.99
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.22
Consensus pattern (54 bp):
GTAAAATTATTGAAATACCCTCGAAGGGTAAAATGACCGAAATACCCTCGAAGG
Found at i:43214005 original size:27 final size:27
Alignment explanation
Indices: 43213847--43214061 Score: 184
Period size: 27 Copynumber: 8.0 Consensus size: 27
43213837 TAAAATTATT
* *
43213847 GAAATACCCTCGAAGAGTAAAATTACC
1 GAAATACCCTCGAAGGGTAAAATGACC
* *
43213874 GAAATACCCTCGAAGGGTAAAATTACT
1 GAAATACCCTCGAAGGGTAAAATGACC
* * *
43213901 GGAACACCCTCGAAGGGTAAAATGATC
1 GAAATACCCTCGAAGGGTAAAATGACC
* * **
43213928 GAAATACCC-CTAAAGGGTAAAATTATT
1 GAAATACCCTC-GAAGGGTAAAATGACC
*
43213955 TAAATACCCTCGAAGGGTAAAATGACC
1 GAAATACCCTCGAAGGGTAAAATGACC
* * *
43213982 GAAATACCCTTGATGGGTAAAATGATC
1 GAAATACCCTCGAAGGGTAAAATGACC
* * **
43214009 GTAACACCCAT-TTAGGGTAAAATGACC
1 GAAATACCC-TCGAAGGGTAAAATGACC
* * *
43214036 GTAATGCCC-CAATAGGGTAAAATGAC
1 GAAATACCCTCGA-AGGGTAAAATGAC
43214062 TGTGATGCCC
Statistics
Matches: 152, Mismatches: 31, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
26 1 0.01
27 149 0.98
28 2 0.01
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.21
Consensus pattern (27 bp):
GAAATACCCTCGAAGGGTAAAATGACC
Found at i:43214026 original size:54 final size:54
Alignment explanation
Indices: 43213836--43214036 Score: 210
Period size: 54 Copynumber: 3.7 Consensus size: 54
43213826 CGAAAAGGTT
* * * * * *
43213836 GTAAAATTATTGAAATACCCTCGAAGAGTAAAATTACCGAAATACCCTCGAAGG
1 GTAAAATTATCGTAACACCCTCGAAGGGTAAAATGACCGAAATACCCTTGAAGG
* * * *
43213890 GTAAAATTA-CTGGAACACCCTCGAAGGGTAAAATGATCGAAATACCCCTAAAGG
1 GTAAAATTATC-GTAACACCCTCGAAGGGTAAAATGACCGAAATACCCTTGAAGG
* * *
43213944 GTAAAATTAT-TTAAATACCCTCGAAGGGTAAAATGACCGAAATACCCTTGATGG
1 GTAAAATTATCGT-AACACCCTCGAAGGGTAAAATGACCGAAATACCCTTGAAGG
* **
43213998 GTAAAATGATCGTAACACCCAT-TTAGGGTAAAATGACCG
1 GTAAAATTATCGTAACACCC-TCGAAGGGTAAAATGACCG
43214037 TAATGCCCCA
Statistics
Matches: 121, Mismatches: 21, Indels: 10
0.80 0.14 0.07
Matches are distributed among these distances:
54 119 0.98
55 2 0.02
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.22
Consensus pattern (54 bp):
GTAAAATTATCGTAACACCCTCGAAGGGTAAAATGACCGAAATACCCTTGAAGG
Found at i:43214026 original size:81 final size:81
Alignment explanation
Indices: 43213875--43214031 Score: 215
Period size: 81 Copynumber: 1.9 Consensus size: 81
43213865 AAAATTACCG
* * * * *
43213875 AAATACCCTCGAAGGGTAAAATTACTGGAACACCCTCGAAGGGTAAAATGATCGAAATACCCCTA
1 AAATACCCTCGAAGGGTAAAATGACCGAAACACCCTCGAAGGGTAAAATGATCGAAACACCCATA
43213940 AAGGGTAAAATTATTT
66 AAGGGTAAAATTATTT
* * * * *
43213956 AAATACCCTCGAAGGGTAAAATGACCGAAATACCCTTGATGGGTAAAATGATCGTAACACCCATT
1 AAATACCCTCGAAGGGTAAAATGACCGAAACACCCTCGAAGGGTAAAATGATCGAAACACCCATA
*
43214021 TAGGGTAAAAT
66 AAGGGTAAAAT
43214032 GACCGTAATG
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
81 65 1.00
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.22
Consensus pattern (81 bp):
AAATACCCTCGAAGGGTAAAATGACCGAAACACCCTCGAAGGGTAAAATGATCGAAACACCCATA
AAGGGTAAAATTATTT
Found at i:43214069 original size:27 final size:27
Alignment explanation
Indices: 43214021--43214089 Score: 102
Period size: 27 Copynumber: 2.6 Consensus size: 27
43214011 AACACCCATT
*
43214021 TAGGGTAAAATGACCGTAATGCCCCAA
1 TAGGGTAAAATGACTGTAATGCCCCAA
* **
43214048 TAGGGTAAAATGACTGTGATGCCCCTG
1 TAGGGTAAAATGACTGTAATGCCCCAA
43214075 TAGGGTAAAATGACT
1 TAGGGTAAAATGACT
43214090 ATTTTACCCC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.23
Consensus pattern (27 bp):
TAGGGTAAAATGACTGTAATGCCCCAA
Found at i:43214099 original size:27 final size:27
Alignment explanation
Indices: 43214021--43214110 Score: 72
Period size: 27 Copynumber: 3.3 Consensus size: 27
43214011 AACACCCATT
** * * **
43214021 TAGGGTAAAATGACCGTAATGCCCCAA
1 TAGGGTAAAATGACTATGATACCCCTG
* *
43214048 TAGGGTAAAATGACTGTGATGCCCCTG
1 TAGGGTAAAATGACTATGATACCCCTG
**
43214075 TAGGGTAAAATGACTATTTTACCCCTG
1 TAGGGTAAAATGACTATGATACCCCTG
* *
43214102 GAGGTTAAA
1 TAGGGTAAA
43214111 TGATTGATTT
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (27 bp):
TAGGGTAAAATGACTATGATACCCCTG
Found at i:43214202 original size:24 final size:24
Alignment explanation
Indices: 43214106--43214203 Score: 97
Period size: 24 Copynumber: 4.1 Consensus size: 24
43214096 CCCCTGGAGG
* *
43214106 TTAAATGATTGATTTGCCTGTGAT
1 TTAAATGATTAATTTGTCTGTGAT
* * * * *
43214130 GTAAATGATTGATTTATCCGAGAT
1 TTAAATGATTAATTTGTCTGTGAT
* * *
43214154 GTAAATGACTAATTTGTCAGTGAT
1 TTAAATGATTAATTTGTCTGTGAT
*
43214178 TTAAATGAATAATTTGTCTGTGAT
1 TTAAATGATTAATTTGTCTGTGAT
43214202 TT
1 TT
43214204 GTATGACTGA
Statistics
Matches: 61, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 61 1.00
ACGTcount: A:0.31, C:0.07, G:0.19, T:0.43
Consensus pattern (24 bp):
TTAAATGATTAATTTGTCTGTGAT
Found at i:43214319 original size:27 final size:27
Alignment explanation
Indices: 43214279--43214344 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
43214269 ATGGAGGAAG
* *
43214279 TACTG-TACTGGTGGCTTTGCCACA-A
1 TACTGTTACTGGTGGCTTGGCAACATA
*
43214304 TCACTGTTACTTGTGGCTTGGCAACATA
1 T-ACTGTTACTGGTGGCTTGGCAACATA
43214332 TACTGTTACTGGT
1 TACTGTTACTGGT
43214345 AGATTTGCTG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
25 1 0.03
26 4 0.12
27 27 0.79
28 2 0.06
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.36
Consensus pattern (27 bp):
TACTGTTACTGGTGGCTTGGCAACATA
Found at i:43214435 original size:32 final size:31
Alignment explanation
Indices: 43214390--43214576 Score: 203
Period size: 32 Copynumber: 5.8 Consensus size: 31
43214380 GCGATGCTAT
* * *
43214390 TGATGACTTTGTGCTGATCATATTACCATTAC
1 TGATGGCTGTGTGC-GATCATATTACTATTAC
*
43214422 TGATGGCTGTGTGCCGATCATATTACCATTAC
1 TGATGGCTGTGTG-CGATCATATTACTATTAC
* *
43214454 TGATGGCTGTATGACGATCATATTACTACTAC
1 TGATGGCTGTGTG-CGATCATATTACTATTAC
* * * *
43214486 TTATGGCTTTGTGTTGATCATACTACTATTAC
1 TGATGGCTGTGTG-CGATCATATTACTATTAC
*
43214518 TGATGGCTGTGTGGCGATCATATTACTACTAC
1 TGATGGCTGTGT-GCGATCATATTACTATTAC
* *
43214550 TGATGGCTTTGTGCCAATCATATTACT
1 TGATGGCTGTGTG-CGATCATATTACT
43214577 GTACTTATTG
Statistics
Matches: 132, Mismatches: 20, Indels: 6
0.84 0.13 0.04
Matches are distributed among these distances:
31 1 0.01
32 129 0.98
33 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.39
Consensus pattern (31 bp):
TGATGGCTGTGTGCGATCATATTACTATTAC
Found at i:43214492 original size:64 final size:64
Alignment explanation
Indices: 43214405--43214575 Score: 243
Period size: 64 Copynumber: 2.7 Consensus size: 64
43214395 ACTTTGTGCT
* * *
43214405 GATCATATTACCATTACTGATGGCTGTGTGCCGATCATATTACCATTACTGATGGCTGTATGAC
1 GATCATATTACTACTACTGATGGCTTTGTGCCGATCATATTACCATTACTGATGGCTGTATGAC
* ** * * * *
43214469 GATCATATTACTACTACTTATGGCTTTGTGTTGATCATACTACTATTACTGATGGCTGTGTGGC
1 GATCATATTACTACTACTGATGGCTTTGTGCCGATCATATTACCATTACTGATGGCTGTATGAC
*
43214533 GATCATATTACTACTACTGATGGCTTTGTGCCAATCATATTAC
1 GATCATATTACTACTACTGATGGCTTTGTGCCGATCATATTAC
43214576 TGTACTTATT
Statistics
Matches: 92, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
64 92 1.00
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (64 bp):
GATCATATTACTACTACTGATGGCTTTGTGCCGATCATATTACCATTACTGATGGCTGTATGAC
Found at i:43214570 original size:96 final size:95
Alignment explanation
Indices: 43214396--43214589 Score: 271
Period size: 96 Copynumber: 2.0 Consensus size: 95
43214386 CTATTGATGA
* *
43214396 CTTTGTGCTGATCATATTACCATTACTGATGGCTGTGTGCCGATCATATTACCATTACTGATGGC
1 CTTTGTGCTGATCATACTACCATTACTGATGGCTGTGTGCCGATCATATTACCACTACTGATGGC
*
43214461 TGTATGACGATCATATTACTACTACTTATGG
66 TGTATGACAATCATATTACT-CTACTTATGG
* * * *
43214492 CTTTGTGTTGATCATACTACTATTACTGATGGCTGTGTGGCGATCATATTACTACTACTGATGGC
1 CTTTGTGCTGATCATACTACCATTACTGATGGCTGTGTGCCGATCATATTACCACTACTGATGGC
* * * * *
43214557 TTTGTGCCAATCATATTACTGTACTTATTG
66 TGTATGACAATCATATTACTCTACTTATGG
43214587 CTT
1 CTT
43214590 GTGGCCATTC
Statistics
Matches: 86, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
95 11 0.13
96 75 0.87
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.40
Consensus pattern (95 bp):
CTTTGTGCTGATCATACTACCATTACTGATGGCTGTGTGCCGATCATATTACCACTACTGATGGC
TGTATGACAATCATATTACTCTACTTATGG
Found at i:43218083 original size:387 final size:388
Alignment explanation
Indices: 43217367--43218141 Score: 1345
Period size: 387 Copynumber: 2.0 Consensus size: 388
43217357 TAATATAGAT
* * * * *
43217367 TCTAGAAGATATGTTTTGATGTTGTATACTCGAGTTAGAAGGTAGTTGGGAAAGATATCTACCGT
1 TCTAGAAAATATGTGTCGATGTTGTATACTCGAGTTACAAGGTAGTTGGGAAAGATATCTACCAT
* *
43217432 TAGCTGAATTCGCTTATAACAACAATTATCAATCCAATATTATAACGGCACTATTTGAAGCATTA
66 TAGCTGAATTCACTTATAACAACAATTATCAATCCAATATTATAACGGCACCATTTGAAGCATTA
* *
43217497 TACAGAAGAAAATGTAAGACACCGTTGCATTGGTTTGAGCTAAGCGAATCCAAAATGGTAGGGAT
131 TACAGAAGAAAACGTAAGACACCGTTGCATTGGTCTGAGCTAAGCGAATCCAAAATGGTAGGGAT
* *
43217562 TGATTTGATTCGAGAAATTGAGGATAAGGTTTGAGGTATTCAAGATTGTTTGAAAGTTGCATCTA
196 TGATTTGATTCGAAAAATTGAGGATAAGGTTTGAGGTATTCAAGATTGTTTGAAAGTTGCATATA
* * **
43217627 ATCGTCAGAAGTCGCATGCAGATCTGAAAATAAAAGATATACAATTTGTTGTTGGATATCGGGTA
261 ATCGTCAGAAGTCGCACGCAAATCTGAAAATAAAAGATATACAATTTGTTGTTGGATATCGCCTA
43217692 CTTTTAAAAGTTTTT-TGTGGAAGAAAGTGCCACAATTCGGTAATAAAGGAAAGTTGAGTCTG
326 CTTTTAAAAGTTTTTCTGTGGAAGAAAGTGCCACAATTCGGTAATAAAGGAAAGTTGAGTCTG
*
43217754 TCTAGAAAATATGTGTCGATGTTGTATACTTGAGTTACAAGGTAGTTGGGAAAGATATCTACCAT
1 TCTAGAAAATATGTGTCGATGTTGTATACTCGAGTTACAAGGTAGTTGGGAAAGATATCTACCAT
*
43217819 TAGCTGAATTCACTTATAACAACAATTATCAATCCAATATTATAATGGCACCATTTGAAGCATTA
66 TAGCTGAATTCACTTATAACAACAATTATCAATCCAATATTATAACGGCACCATTTGAAGCATTA
*
43217884 TACAGAAGAAAACGTAAGACACCGTTGTATTGGTCTGAGCTAAGCGAATCCAAAATGGTAGGGAT
131 TACAGAAGAAAACGTAAGACACCGTTGCATTGGTCTGAGCTAAGCGAATCCAAAATGGTAGGGAT
*
43217949 TGATTTGATTCGAAAAATTGAGGATAAGGTTTGAGGTATTCAAGATTGTTTGAAAGTTGCATATG
196 TGATTTGATTCGAAAAATTGAGGATAAGGTTTGAGGTATTCAAGATTGTTTGAAAGTTGCATATA
*
43218014 ATCGTCAGAAGTCGCACGCAAATTTGAAAATAAAAGATATACAATTTGTTGTTGGATATCGCCTA
261 ATCGTCAGAAGTCGCACGCAAATCTGAAAATAAAAGATATACAATTTGTTGTTGGATATCGCCTA
* *
43218079 CTTTTAAAAGTTTTTCTGTGGAAGAAAGTGCCATAATTGGGTAATAAAGGAAAGTTGAGTCTG
326 CTTTTAAAAGTTTTTCTGTGGAAGAAAGTGCCACAATTCGGTAATAAAGGAAAGTTGAGTCTG
43218142 AGATTTATCG
Statistics
Matches: 365, Mismatches: 22, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
387 320 0.88
388 45 0.12
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.31
Consensus pattern (388 bp):
TCTAGAAAATATGTGTCGATGTTGTATACTCGAGTTACAAGGTAGTTGGGAAAGATATCTACCAT
TAGCTGAATTCACTTATAACAACAATTATCAATCCAATATTATAACGGCACCATTTGAAGCATTA
TACAGAAGAAAACGTAAGACACCGTTGCATTGGTCTGAGCTAAGCGAATCCAAAATGGTAGGGAT
TGATTTGATTCGAAAAATTGAGGATAAGGTTTGAGGTATTCAAGATTGTTTGAAAGTTGCATATA
ATCGTCAGAAGTCGCACGCAAATCTGAAAATAAAAGATATACAATTTGTTGTTGGATATCGCCTA
CTTTTAAAAGTTTTTCTGTGGAAGAAAGTGCCACAATTCGGTAATAAAGGAAAGTTGAGTCTG
Found at i:43220469 original size:20 final size:19
Alignment explanation
Indices: 43220446--43220499 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 19
43220436 GTTAATCCTC
43220446 GTTTTATTAAGTTAATTAAA
1 GTTTTATTAAGTTAATT-AA
* *
43220466 GTTTAATTTAGTTAATTAA
1 GTTTTATTAAGTTAATTAA
*
43220485 GATTTATTAAGTTAA
1 GTTTTATTAAGTTAA
43220500 CCTAAATGTA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (19 bp):
GTTTTATTAAGTTAATTAA
Found at i:43220499 original size:19 final size:19
Alignment explanation
Indices: 43220448--43220499 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
43220438 TAATCCTCGT
43220448 TTTATTAAGTTAATTAAAG
1 TTTATTAAGTTAATTAAAG
*
43220467 TTTAATTTAGTTAATT-AAG
1 TTT-ATTAAGTTAATTAAAG
43220486 ATTTATTAAGTTAA
1 -TTTATTAAGTTAA
43220500 CCTAAATGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (19 bp):
TTTATTAAGTTAATTAAAG
Found at i:43226138 original size:21 final size:21
Alignment explanation
Indices: 43226114--43226166 Score: 90
Period size: 20 Copynumber: 2.6 Consensus size: 21
43226104 TAATTAGCTA
*
43226114 ATTTAGTTAATCATGTTTTAT
1 ATTTAATTAATCATGTTTTAT
43226135 ATTTAATT-ATCATGTTTTAT
1 ATTTAATTAATCATGTTTTAT
43226155 ATTTAATTAATC
1 ATTTAATTAATC
43226167 TCAATTAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 20 0.67
21 10 0.33
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.57
Consensus pattern (21 bp):
ATTTAATTAATCATGTTTTAT
Found at i:43227206 original size:27 final size:27
Alignment explanation
Indices: 43227176--43227338 Score: 159
Period size: 27 Copynumber: 6.0 Consensus size: 27
43227166 GGACAGTCCA
* * *
43227176 TACATAGTTCGCCACAAAAGTTTTTCT
1 TACAGAGTTCGCCACAAAGGCTTTTCT
* ***
43227203 TACAAAGTTTTACACAAAGGCTTTTCT
1 TACAGAGTTCGCCACAAAGGCTTTTCT
* *
43227230 TTCAGAGTTTGCCACAAAGGCTTTAT-T
1 TACAGAGTTCGCCACAAAGGCTTT-TCT
* *
43227257 TTCAGAGTTTGCCACAAAGGCTTTTCT
1 TACAGAGTTCGCCACAAAGGCTTTTCT
**
43227284 TTTAGAGTTCGCCACAAAGGCTTTTC-
1 TACAGAGTTCGCCACAAAGGCTTTTCT
* *
43227310 TATCAAAGTTCACCACAAAGGCTTTTCT
1 TA-CAGAGTTCGCCACAAAGGCTTTTCT
43227338 T
1 T
43227339 TCCTCACGTG
Statistics
Matches: 116, Mismatches: 16, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
26 2 0.02
27 112 0.97
28 2 0.02
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (27 bp):
TACAGAGTTCGCCACAAAGGCTTTTCT
Found at i:43227273 original size:54 final size:54
Alignment explanation
Indices: 43227181--43227340 Score: 191
Period size: 54 Copynumber: 3.0 Consensus size: 54
43227171 GTCCATACAT
* * *
43227181 AGTTCGCCACAAAAGTTTTTCT-TACAAAGTTTTA-CACAAAGGCTTTTCTTTCAG
1 AGTTCGCCACAAAGGCTTTTCTAT-CAAAG-TTCACCACAAAGGCTTTTCTTTCAG
* * * ** *
43227235 AGTTTGCCACAAAGGCTTTAT-TTTCAGAGTTTGCCACAAAGGCTTTTCTTTTAG
1 AGTTCGCCACAAAGGCTTT-TCTATCAAAGTTCACCACAAAGGCTTTTCTTTCAG
43227289 AGTTCGCCACAAAGGCTTTTCTATCAAAGTTCACCACAAAGGCTTTTCTTTC
1 AGTTCGCCACAAAGGCTTTTCTATCAAAGTTCACCACAAAGGCTTTTCTTTC
43227341 CTCACGTGTT
Statistics
Matches: 90, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
53 4 0.04
54 84 0.93
55 2 0.02
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (54 bp):
AGTTCGCCACAAAGGCTTTTCTATCAAAGTTCACCACAAAGGCTTTTCTTTCAG
Found at i:43230016 original size:20 final size:20
Alignment explanation
Indices: 43229991--43230030 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
43229981 TAGTGGAAAT
*
43229991 ACAGAGGCACCGAAGTGCAA
1 ACAGAGGCACAGAAGTGCAA
*
43230011 ACAGAGGCACATAAGTGCAA
1 ACAGAGGCACAGAAGTGCAA
43230031 TCCCATACAA
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:0.42, C:0.23, G:0.28, T:0.07
Consensus pattern (20 bp):
ACAGAGGCACAGAAGTGCAA
Found at i:43233030 original size:20 final size:20
Alignment explanation
Indices: 43233002--43233040 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
43232992 GCCCAAAAGT
*
43233002 GCAATCAGAGGCACTGAAGA
1 GCAAACAGAGGCACTGAAGA
*
43233022 GCAAACAGAGGTACTGAAG
1 GCAAACAGAGGCACTGAAG
43233041 TGAAAACCCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.18, G:0.31, T:0.10
Consensus pattern (20 bp):
GCAAACAGAGGCACTGAAGA
Found at i:43233047 original size:20 final size:20
Alignment explanation
Indices: 43233007--43233047 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
43232997 AAAGTGCAAT
*
43233007 CAGAGGCACTGAAGAGCAAA
1 CAGAGGCACTGAAGAGAAAA
* *
43233027 CAGAGGTACTGAAGTGAAAA
1 CAGAGGCACTGAAGAGAAAA
43233047 C
1 C
43233048 CCGTACAAGC
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:0.44, C:0.17, G:0.29, T:0.10
Consensus pattern (20 bp):
CAGAGGCACTGAAGAGAAAA
Found at i:43252130 original size:8 final size:8
Alignment explanation
Indices: 43252118--43252149 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
43252108 CTTCTTCTCC
43252118 TTTTCTTT
1 TTTTCTTT
*
43252126 CTTTCTTT
1 TTTTCTTT
43252134 TTTTCTTT
1 TTTTCTTT
43252142 TTTTCTTT
1 TTTTCTTT
43252150 ATTTAATTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (8 bp):
TTTTCTTT
Found at i:43252201 original size:3 final size:3
Alignment explanation
Indices: 43252195--43252245 Score: 50
Period size: 3 Copynumber: 17.0 Consensus size: 3
43252185 TTCCTTTCTT
* * * *
43252195 TTA TTA TTA TTA TTA CTA -TA ATA ATA ATA TTTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
43252240 TTA TTA
1 TTA TTA
43252246 ACTTTATATA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 2 0.05
3 40 0.91
4 2 0.05
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Done.