Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 109 of 150
Found at i:33916007 original size:40 final size:42
Alignment explanation
Indices: 33915961--33916042 Score: 105
Period size: 40 Copynumber: 2.0 Consensus size: 42
33915951 GACAAAGCAG
* *
33915961 GAAAACGCTTTCTCAAGGAAGCGC-TT-TGTCCACGTGGACA
1 GAAAACGCGTCCTCAAGGAAGCGCTTTGTGTCCACGTGGACA
** *
33916001 GAAAACGCGTCCTTGAGGGAGCGCTTTGTGTCCACGTGGACA
1 GAAAACGCGTCCTCAAGGAAGCGCTTTGTGTCCACGTGGACA
33916043 AAGCGCTTCC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
40 19 0.54
41 2 0.06
42 14 0.40
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.22
Consensus pattern (42 bp):
GAAAACGCGTCCTCAAGGAAGCGCTTTGTGTCCACGTGGACA
Found at i:33916054 original size:40 final size:39
Alignment explanation
Indices: 33915980--33916058 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 39
33915970 TTCTCAAGGA
33915980 AGCGCTTTGTCCACGTGGACAGAAAACGCGTCCTTGAGGG
1 AGCGCTTTGTCCACGTGGACA-AAAACGCGTCCTTGAGGG
* *
33916020 AGCGCTTTGTGTCCACGTGGAC-AAAGCGCTTCCTTGAGG
1 AGCGC-TT-TGTCCACGTGGACAAAAACGCGTCCTTGAGG
33916059 AAACGTTTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
40 20 0.57
41 2 0.06
42 13 0.37
ACGTcount: A:0.20, C:0.25, G:0.32, T:0.23
Consensus pattern (39 bp):
AGCGCTTTGTCCACGTGGACAAAAACGCGTCCTTGAGGG
Found at i:33916480 original size:98 final size:95
Alignment explanation
Indices: 33916151--33916469 Score: 399
Period size: 97 Copynumber: 3.3 Consensus size: 95
33916141 AAAATAAGAG
* * * *
33916151 ATTAGGGTTTAGGGTTTCTTAATTAAATTAATTATAAATTTTTCAAAATTAGATTAGGGTTTCGT
1 ATTAGGGTTTAGGGTTACTTAATTAAATTAATTATAAATTTTTAAAAAATAGATTAGGGTTTAGT
* * *
33916216 GTTTATGG-TTTTAAGGAAAAATTAATTAA
66 GTTTAAGGTTTTTAAGGAAAAATAAAATAA
* *
33916245 ATTAGGGTTTAGGGTTACTTGAA-TAATTTAATTATAAATTTTTTAAAAATCAGATTAGGGTTTA
1 ATTAGGGTTTAGGGTTACTT-AATTAAATTAATTATAAATTTTTAAAAAAT-AGATTAGGGTTTA
* * *
33916309 GTGTTAAAGGTTTTTAAAGAAAAAATCAAATAA
64 GTGTTTAAGGTTTTT-AAGGAAAAATAAAATAA
** * * *
33916342 ATTAGGGTTTAAAGTTACATGAGTAAATTAATTATAAATTTTTAAAAAAAATAGATTAGGGTTTA
1 ATTAGGGTTTAGGGTTACTTAATTAAATTAATTATAAATTTTT--AAAAAATAGATTAGGGTTTA
*
33916407 GTGTTTAGGGTTTTTAAGGAAAAACTAAAATAA
64 GTGTTTAAGGTTTTTAAGGAAAAA-TAAAATAA
*
33916440 ATTAGGGTTTGGGGTTACTTAATTAAATTA
1 ATTAGGGTTTAGGGTTACTTAATTAAATTA
33916470 TTTGTTAATT
Statistics
Matches: 191, Mismatches: 26, Indels: 12
0.83 0.11 0.05
Matches are distributed among these distances:
94 43 0.23
95 22 0.12
96 5 0.03
97 58 0.30
98 57 0.30
99 6 0.03
ACGTcount: A:0.39, C:0.03, G:0.18, T:0.40
Consensus pattern (95 bp):
ATTAGGGTTTAGGGTTACTTAATTAAATTAATTATAAATTTTTAAAAAATAGATTAGGGTTTAGT
GTTTAAGGTTTTTAAGGAAAAATAAAATAA
Found at i:33916729 original size:126 final size:126
Alignment explanation
Indices: 33916480--33916774 Score: 434
Period size: 126 Copynumber: 2.4 Consensus size: 126
33916470 TTTGTTAATT
* * * *
33916480 TAAAA-AAGCTCCCACGTGGAC-TTTTTTTGCTACAGTAGTTACTGAAAAAATAATTTTGAGAAG
1 TAAAAGAAGCTCCCACGTGGACGCTATTTTGCTACAGTAGTTCCTGAAAAAATAATTTCGAGAAG
*
33916543 ACGTTTTTGAGCAAATAGTGGCAAAAACACTTTAAGCAGGATGCATTGTCAACAAAAGTAC
66 ACGTTTCTGAGCAAATAGTGGCAAAAACACTTTAAGCAGGATGCATTGTCAACAAAAGTAC
*
33916604 TAAAAGAAGCTCCCACGT-GACCGCTATTTTGCTACAGTAGTTCCTGAAAGAATAATTTCGAGAA
1 TAAAAGAAGCTCCCACGTGGA-CGCTATTTTGCTACAGTAGTTCCTGAAAAAATAATTTCGAGAA
* * * * * *
33916668 GACGTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGTAGGATGCTTTGTCAGCGAAAGTAC
65 GACGTTTCTGAGCAAATAGTGGCAAAAACACTTTAAGCAGGATGCATTGTCAACAAAAGTAC
* *
33916730 TGAAAGAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCCT
1 TAAAAGAAGCTCCCACGTGGACGCTATTTTGCTACAGTAGTTCCT
33916775 ATTTGGCCTT
Statistics
Matches: 153, Mismatches: 14, Indels: 6
0.88 0.08 0.03
Matches are distributed among these distances:
124 7 0.05
125 13 0.08
126 131 0.86
127 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (126 bp):
TAAAAGAAGCTCCCACGTGGACGCTATTTTGCTACAGTAGTTCCTGAAAAAATAATTTCGAGAAG
ACGTTTCTGAGCAAATAGTGGCAAAAACACTTTAAGCAGGATGCATTGTCAACAAAAGTAC
Found at i:33919889 original size:111 final size:110
Alignment explanation
Indices: 33919749--33919948 Score: 339
Period size: 111 Copynumber: 1.8 Consensus size: 110
33919739 TGTATTATTT
*
33919749 ATATTTTTTTAAATGAAAAATATAGAAATATTCAAAATATTACCATATTTAAAAGAATTTCTATT
1 ATATTTTATTAAATGAAAAATATAGAAATATTCAAAATATTACCATATTTAAAAGAATTTCTATT
*
33919814 TTATT-AAAATGATTAAAGTAAATTACAATTACTTTATTCAAAACA
66 TTATTAAAAAT-ATAAAAGTAAATTACAATTACTTTATTCAAAACA
* *
33919859 ATATTTTATTAAATGAAATAATATAGAAATATTTAAAATATTACCTTATTTAAAAGAATTTCTAT
1 ATATTTTATTAAATGAAA-AATATAGAAATATTCAAAATATTACCATATTTAAAAGAATTTCTAT
33919924 TTTATTAAAAATATAAAAGTAAATT
65 TTTATTAAAAATATAAAAGTAAATT
33919949 TCTATATTAT
Statistics
Matches: 84, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
110 17 0.20
111 62 0.74
112 5 0.06
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (110 bp):
ATATTTTATTAAATGAAAAATATAGAAATATTCAAAATATTACCATATTTAAAAGAATTTCTATT
TTATTAAAAATATAAAAGTAAATTACAATTACTTTATTCAAAACA
Found at i:33919950 original size:30 final size:33
Alignment explanation
Indices: 33919909--33920011 Score: 124
Period size: 34 Copynumber: 3.2 Consensus size: 33
33919899 TTACCTTATT
*
33919909 TAAAAGAATTTCTATTTTATTA-A-AAAT-ATA
1 TAAAATAATTTCTATTTTATTACAGAAATAATA
* *
33919939 -AAAGTAAATTTCTATATTATTACATGAAATAATA
1 TAAAAT-AATTTCTATTTTATTACA-GAAATAATA
33919973 TAAAATAATTTCTATTTTATTACATGAAATAATA
1 TAAAATAATTTCTATTTTATTACA-GAAATAATA
33920007 TAAAA
1 TAAAA
33920012 ATATTCAAAA
Statistics
Matches: 62, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
29 3 0.05
30 15 0.24
31 1 0.02
33 4 0.06
34 35 0.56
35 4 0.06
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.41
Consensus pattern (33 bp):
TAAAATAATTTCTATTTTATTACAGAAATAATA
Found at i:33919987 original size:34 final size:36
Alignment explanation
Indices: 33919933--33920011 Score: 135
Period size: 34 Copynumber: 2.2 Consensus size: 36
33919923 TTTTATTAAA
33919933 AATATAAAAGTAAATTTCTATATTATTACATGAAAT
1 AATATAAAAGTAAATTTCTATATTATTACATGAAAT
*
33919969 AATATAAAA-T-AATTTCTATTTTATTACATGAAAT
1 AATATAAAAGTAAATTTCTATATTATTACATGAAAT
33920003 AATATAAAA
1 AATATAAAA
33920012 ATATTCAAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
34 32 0.76
35 1 0.02
36 9 0.21
ACGTcount: A:0.52, C:0.05, G:0.04, T:0.39
Consensus pattern (36 bp):
AATATAAAAGTAAATTTCTATATTATTACATGAAAT
Found at i:33920456 original size:18 final size:18
Alignment explanation
Indices: 33920430--33920472 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
33920420 GACTAGAAAA
* * *
33920430 AGGAAACATATAAGAGTT
1 AGGATACATAAAAGAGCT
*
33920448 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGAGCT
33920466 AGGATAC
1 AGGATAC
33920473 GCACCTGGCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.47, C:0.09, G:0.26, T:0.19
Consensus pattern (18 bp):
AGGATACATAAAAGAGCT
Found at i:33937863 original size:29 final size:29
Alignment explanation
Indices: 33937799--33937863 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
33937789 CGATATTTAA
* * * *
33937799 TTATTTGGTATTGATATCATATTGATACT
1 TTATTTGGTATTGATACCAAATTAAGACT
*
33937828 TTATTTGGTATTGATACCAAATTAAGATT
1 TTATTTGGTATTGATACCAAATTAAGACT
*
33937857 TTGTTTG
1 TTATTTG
33937864 TTTACAAAAC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.28, C:0.06, G:0.15, T:0.51
Consensus pattern (29 bp):
TTATTTGGTATTGATACCAAATTAAGACT
Found at i:33940731 original size:18 final size:19
Alignment explanation
Indices: 33940691--33940733 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
33940681 TAATTAATGA
*
33940691 TTAATTAAATTATCAAATC
1 TTAATTAAATTAACAAATC
33940710 TTAATT-AATTAACATAAT-
1 TTAATTAAATTAACA-AATC
33940728 TTAATT
1 TTAATT
33940734 TTGAACTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (19 bp):
TTAATTAAATTAACAAATC
Found at i:33940944 original size:23 final size:23
Alignment explanation
Indices: 33940916--33940960 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
33940906 TTAATCACTT
33940916 TTTCAACTA-ATTATTTA-AACAAA
1 TTTCAA-TATATT-TTTATAACAAA
33940939 TTTCAATATATTTTTATAACAA
1 TTTCAATATATTTTTATAACAA
33940961 CCCCATAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (23 bp):
TTTCAATATATTTTTATAACAAA
Found at i:33943238 original size:42 final size:42
Alignment explanation
Indices: 33943174--33943262 Score: 169
Period size: 42 Copynumber: 2.1 Consensus size: 42
33943164 GGAAATGAGC
*
33943174 TTTTCAATAGAATATGAAACTAATTATTCAAGCTCAATAAAT
1 TTTTTAATAGAATATGAAACTAATTATTCAAGCTCAATAAAT
33943216 TTTTTAATAGAATATGAAACTAATTATTCAAGCTCAATAAAT
1 TTTTTAATAGAATATGAAACTAATTATTCAAGCTCAATAAAT
33943258 TTTTT
1 TTTTT
33943263 TTTCTCTTTT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (42 bp):
TTTTTAATAGAATATGAAACTAATTATTCAAGCTCAATAAAT
Found at i:33943287 original size:15 final size:15
Alignment explanation
Indices: 33943261--33943303 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
33943251 AATAAATTTT
*
33943261 TTTTTCTCTTTTTTATG
1 TTTTTCT-TTTCTT-TG
*
33943278 TTTTTCTTTTCTTTT
1 TTTTTCTTTTCTTTG
33943293 TTTTTCTTTTC
1 TTTTTCTTTTC
33943304 GATTTTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 12 0.50
16 5 0.21
17 7 0.29
ACGTcount: A:0.02, C:0.14, G:0.02, T:0.81
Consensus pattern (15 bp):
TTTTTCTTTTCTTTG
Found at i:33943309 original size:15 final size:15
Alignment explanation
Indices: 33943278--33943311 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
33943268 CTTTTTTATG
**
33943278 TTTTTCTTTTCTTTT
1 TTTTTCTTTTCGATT
33943293 TTTTTCTTTTCGATT
1 TTTTTCTTTTCGATT
33943308 TTTT
1 TTTT
33943312 ATTCTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.03, C:0.12, G:0.03, T:0.82
Consensus pattern (15 bp):
TTTTTCTTTTCGATT
Found at i:33943311 original size:17 final size:15
Alignment explanation
Indices: 33943257--33943319 Score: 65
Period size: 17 Copynumber: 3.9 Consensus size: 15
33943247 GCTCAATAAA
33943257 TTTTTTTTTCTCTTT-
1 TTTTTTTTTCT-TTTC
33943272 TTTATGTTTTTCTTTTC
1 TTT-T-TTTTTCTTTTC
33943289 TTTTTTTTTCTTTTC
1 TTTTTTTTTCTTTTC
*
33943304 GATTTTTTATTCTTTT
1 --TTTTTTTTTCTTTT
33943320 TTTAGAAAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
15 14 0.33
16 5 0.12
17 23 0.55
ACGTcount: A:0.05, C:0.11, G:0.03, T:0.81
Consensus pattern (15 bp):
TTTTTTTTTCTTTTC
Found at i:33944245 original size:8 final size:8
Alignment explanation
Indices: 33944172--33944228 Score: 51
Period size: 8 Copynumber: 6.6 Consensus size: 8
33944162 CAAGCAAACT
*
33944172 AATAAGAA
1 AATAAAAA
33944180 AATAAAAA
1 AATAAAAA
33944188 AATAAATAA
1 AATAAA-AA
33944197 GAATAAAAA
1 -AATAAAAA
*
33944206 GAGATAATAA
1 -A-ATAAAAA
*
33944216 AATAGAAA
1 AATAAAAA
33944224 AATAA
1 AATAA
33944229 CTGACAAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
8 22 0.54
9 7 0.17
10 12 0.29
ACGTcount: A:0.75, C:0.00, G:0.09, T:0.16
Consensus pattern (8 bp):
AATAAAAA
Found at i:33944325 original size:20 final size:20
Alignment explanation
Indices: 33944289--33944326 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
33944279 AAAGCAAAAG
*
33944289 CAAAAACAAAAACAAAATTA
1 CAAAAACAAAAAAAAAATTA
33944309 CAAAAA-AAATAAAAAAAT
1 CAAAAACAAA-AAAAAAAT
33944327 AACTAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.79, C:0.11, G:0.00, T:0.11
Consensus pattern (20 bp):
CAAAAACAAAAAAAAAATTA
Found at i:33948687 original size:44 final size:44
Alignment explanation
Indices: 33948632--33949132 Score: 272
Period size: 46 Copynumber: 11.7 Consensus size: 44
33948622 TTTTAATCCG
* *
33948632 CTCCACTGTAATATCAGGGAGATAGGATTATTGACTTCAATCTA
1 CTCCACTGTAATCTCAGGGAGATAAGATTATTGACTTCAATCTA
* ***
33948676 CTCCGCTGTAATCTCAGGGAGATAAGATCTGTAATT--CTTTGGTCTA
1 CTCCACTGTAATCTCAGGGAGATAAGA--T-T-ATTGACTTCAATCTA
* ** * *
33948722 TTCCACTGTAATCTCAGGGAGATAAGA--CCTGA-TGCCATCTA
1 CTCCACTGTAATCTCAGGGAGATAAGATTATTGACTTCAATCTA
* * * * ** *
33948763 CTCTACTGTAACCTCAGAGATATAAGATCCTT---TT-AATCCA
1 CTCCACTGTAATCTCAGGGAGATAAGATTATTGACTTCAATCTA
* *
33948803 CTCCATTGTAATCTCAGGGAGATAGGATTATTGACTTCAATCTA
1 CTCCACTGTAATCTCAGGGAGATAAGATTATTGACTTCAATCTA
* * **
33948847 CTCCGCTGTAATCTCAGGGAGATAAGATCT-TTAATTCTTCGGTCTA
1 CTCCACTGTAATCTCAGGGAGATAAGAT-TATTGA--CTTCAATCTA
* * **
33948893 TTCCACTGTAATCTCAGGGAGATAAGA-TCTT---TT-AATCCG
1 CTCCACTGTAATCTCAGGGAGATAAGATTATTGACTTCAATCTA
* * * * * *
33948932 TTCCACTGTAATCTCAGGGAAATAGGATTACTGGCTTCAATCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATTATTGACTTCAATCTA
* * ** **
33948976 CTCCGCTGTAATCTCAGGGAGATAAGATTTGAATCTCTTCGGTCTA
1 CTCCACTGTAATCTCAGGGAGATAAGA-TT-ATTGACTTCAATCTA
* * ** * *
33949022 TTCCACTGTAATCTCAGGAAGATAAGA--CCTGA-TGCGATCTA
1 CTCCACTGTAATCTCAGGGAGATAAGATTATTGACTTCAATCTA
* * * * ** **
33949063 CTCTATTGTAATTTCAGAGAGATAAGATCGTT---TT-AATCCG
1 CTCCACTGTAATCTCAGGGAGATAAGATTATTGACTTCAATCTA
*
33949103 CTCCACTGTAATCTCAGGGAGATAGGATTA
1 CTCCACTGTAATCTCAGGGAGATAAGATTA
33949133 CCGGCTTCAA
Statistics
Matches: 345, Mismatches: 87, Indels: 54
0.71 0.18 0.11
Matches are distributed among these distances:
39 27 0.08
40 59 0.17
41 57 0.17
42 1 0.00
43 7 0.02
44 86 0.25
45 5 0.01
46 99 0.29
47 1 0.00
48 3 0.01
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (44 bp):
CTCCACTGTAATCTCAGGGAGATAAGATTATTGACTTCAATCTA
Found at i:33948699 original size:84 final size:84
Alignment explanation
Indices: 33948587--33948875 Score: 296
Period size: 84 Copynumber: 3.4 Consensus size: 84
33948577 ACCTGATGCG
* * * * *
33948587 ATCTACTCTACTGTAATTTCAGAAAGATAAGATCATTTTAATCCGCTCCACTGTAATATCAGGGA
1 ATCTACTCCACTGTAATCTCAGAGAGATAAGATCATTTTAATCCACTCCACTGTAATCTCAGGGA
33948652 GATAGGATTATTGACTTCA
66 GATAGGATTATTGACTTCA
* * ** * *
33948671 ATCTACTCCGCTGTAATCTCAGGGAGATAAGATCTGTAATTCTTTGGTCTATTCCACTGTAATCT
1 ATCTACTCCACTGTAATCTCAGAGAGATAAGATC----A-T-TTTAATCCACTCCACTGTAATCT
* ** * *
33948736 CAGGGAGATAAGA--CCTGA-TGCC
60 CAGGGAGATAGGATTATTGACTTCA
* * * * *
33948758 ATCTACTCTACTGTAACCTCAGAGATATAAGATCCTTTTAATCCACTCCATTGTAATCTCAGGGA
1 ATCTACTCCACTGTAATCTCAGAGAGATAAGATCATTTTAATCCACTCCACTGTAATCTCAGGGA
33948823 GATAGGATTATTGACTTCA
66 GATAGGATTATTGACTTCA
* *
33948842 ATCTACTCCGCTGTAATCTCAGGGAGATAAGATC
1 ATCTACTCCACTGTAATCTCAGAGAGATAAGATC
33948876 TTTAATTCTT
Statistics
Matches: 159, Mismatches: 37, Indels: 18
0.74 0.17 0.08
Matches are distributed among these distances:
81 30 0.19
82 1 0.01
83 3 0.02
84 60 0.38
87 31 0.19
88 4 0.03
89 1 0.01
90 29 0.18
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (84 bp):
ATCTACTCCACTGTAATCTCAGAGAGATAAGATCATTTTAATCCACTCCACTGTAATCTCAGGGA
GATAGGATTATTGACTTCA
Found at i:33948822 original size:171 final size:171
Alignment explanation
Indices: 33948537--33948919 Score: 649
Period size: 171 Copynumber: 2.2 Consensus size: 171
33948527 TAAGATTCAA
* * *
33948537 AATTCTTCGGTCTATTCCACTGTAATCTCAGTGAGATAAAACCTGATGCGATCTACTCTACTGTA
1 AATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCCATCTACTCTACTGTA
** *
33948602 ATTTCAGAAAGATAAGATCATTTTAATCCGCTCCACTGTAATATCAGGGAGATAGGATTATTGAC
66 ACCTCAGAAAGATAAGATCATTTTAATCCACTCCACTGTAATATCAGGGAGATAGGATTATTGAC
33948667 TTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATCTGT
131 TTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATCTGT
*
33948708 AATTCTTTGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCCATCTACTCTACTGTA
1 AATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCCATCTACTCTACTGTA
* * * * *
33948773 ACCTCAGAGATATAAGATCCTTTTAATCCACTCCATTGTAATCTCAGGGAGATAGGATTATTGAC
66 ACCTCAGAAAGATAAGATCATTTTAATCCACTCCACTGTAATATCAGGGAGATAGGATTATTGAC
*
33948838 TTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATCTTT
131 TTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATCTGT
33948879 AATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGA
1 AATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGA
33948920 TCTTTTAATC
Statistics
Matches: 198, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
171 198 1.00
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (171 bp):
AATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCCATCTACTCTACTGTA
ACCTCAGAAAGATAAGATCATTTTAATCCACTCCACTGTAATATCAGGGAGATAGGATTATTGAC
TTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATCTGT
Found at i:33948947 original size:39 final size:41
Alignment explanation
Indices: 33948722--33949126 Score: 137
Period size: 44 Copynumber: 9.6 Consensus size: 41
33948712 CTTTGGTCTA
* * * **
33948722 TTCCACTGTAATCTCAGGGAGATAAGA-CCTGATGCCATCTA
1 TTCCACTGTAATCTCAGGGAGATAAGATACTG-TTCAATCCG
* * * * * * * *
33948763 CTCTACTGTAACCTCAGAGATATAAGATCCT-TTTAATCCA
1 TTCCACTGTAATCTCAGGGAGATAAGATACTGTTCAATCCG
* * * * **
33948803 CTCCATTGTAATCTCAGGGAGATAGGATTATTGACTTCAATCTA
1 TTCCACTGTAATCTCAGGGAGATAAGA-TACTG--TTCAATCCG
* *
33948847 CTCCGCTGTAATCTCAGGGAGATAAGAT-CT-TT-AATTCTTCGG
1 TTCCACTGTAATCTCAGGGAGATAAGATACTGTTCAA-TC--C-G
*
33948889 TCTATTCCACTGTAATCTCAGGGAGATAAGAT-CT-TTTAATCCG
1 ----TTCCACTGTAATCTCAGGGAGATAAGATACTGTTCAATCCG
* * *
33948932 TTCCACTGTAATCTCAGGGAAATAGGATTACTGGCTTCAATCTG
1 TTCCACTGTAATCTCAGGGAGATAAGA-TACT-G-TTCAATCCG
* * * ** **
33948976 CTCCGCTGTAATCTCAGGGAGATAAGATTTGAATCTCTTCGGTCTA
1 TTCCACTGTAATCTCAGGGAGATAAGA--T--A-CTGTTCAATCCG
* * * * **
33949022 TTCCACTGTAATCTCAGGAAGATAAGA-CCTGATGCGATCTA
1 TTCCACTGTAATCTCAGGGAGATAAGATACTG-TTCAATCCG
* * * * * *
33949063 CTCTATTGTAATTTCAGAGAGATAAGAT-C-GTTTTAATCCG
1 TTCCACTGTAATCTCAGGGAGATAAGATACTG-TTCAATCCG
*
33949103 CTCCACTGTAATCTCAGGGAGATA
1 TTCCACTGTAATCTCAGGGAGATA
33949127 GGATTACCGG
Statistics
Matches: 277, Mismatches: 62, Indels: 51
0.71 0.16 0.13
Matches are distributed among these distances:
38 2 0.01
39 29 0.10
40 54 0.19
41 55 0.20
42 4 0.01
43 2 0.01
44 62 0.22
45 2 0.01
46 62 0.22
47 3 0.01
48 2 0.01
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (41 bp):
TTCCACTGTAATCTCAGGGAGATAAGATACTGTTCAATCCG
Found at i:33948949 original size:129 final size:130
Alignment explanation
Indices: 33948767--33949048 Score: 433
Period size: 129 Copynumber: 2.2 Consensus size: 130
33948757 CATCTACTCT
* * * * *
33948767 ACTGTAACCTCAGAGATATAAGATCCTTTTAATCCACTCCATTGTAATCTCAGGGAGATAGGATT
1 ACTGTAATCTCAGGGAGATAAGATCCTTTTAATCCACTCCACTGTAATCTCAGGGAAATAGGATT
* *
33948832 ATTGACTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATCTTTAAT-TCTTCGGTCTATTC
66 ACTGACTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGAT-TTGAATCTCTTCGGTCTATTC
33948896 C
130 C
**
33948897 ACTGTAATCTCAGGGAGATAAGAT-CTTTTAATCCGTTCCACTGTAATCTCAGGGAAATAGGATT
1 ACTGTAATCTCAGGGAGATAAGATCCTTTTAATCCACTCCACTGTAATCTCAGGGAAATAGGATT
* *
33948961 ACTGGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTGAATCTCTTCGGTCTATTCC
66 ACTGACTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATTTGAATCTCTTCGGTCTATTCC
*
33949026 ACTGTAATCTCAGGAAGATAAGA
1 ACTGTAATCTCAGGGAGATAAGA
33949049 CCTGATGCGA
Statistics
Matches: 139, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
128 5 0.04
129 113 0.81
130 21 0.15
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (130 bp):
ACTGTAATCTCAGGGAGATAAGATCCTTTTAATCCACTCCACTGTAATCTCAGGGAAATAGGATT
ACTGACTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATTTGAATCTCTTCGGTCTATTCC
Found at i:33961551 original size:2 final size:2
Alignment explanation
Indices: 33961544--33961580 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
33961534 GTTTAAAATA
33961544 AT AT 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 AT AT A
33961581 CATGAAAGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:33964744 original size:17 final size:17
Alignment explanation
Indices: 33964722--33964767 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
33964712 GAAATCTTCA
*
33964722 TTAAATCCCTAAAATTT
1 TTAAATCCCTAAAATCT
*
33964739 TTAAAT-CCTTAAATCT
1 TTAAATCCCTAAAATCT
*
33964755 TGAAATCCCTAAA
1 TTAAATCCCTAAA
33964768 TCATTAGCAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
16 13 0.54
17 11 0.46
ACGTcount: A:0.41, C:0.20, G:0.02, T:0.37
Consensus pattern (17 bp):
TTAAATCCCTAAAATCT
Found at i:33965840 original size:33 final size:33
Alignment explanation
Indices: 33965775--33965885 Score: 95
Period size: 33 Copynumber: 3.4 Consensus size: 33
33965765 GTTGACTACT
*
33965775 GGGAGGGTGATGTTGAAGGGGT-GAAAGT-TGATG
1 GGGAGGGTGATGATGAAGGGGTAG-AA-TCTGATG
33965808 GGGAGGGTGATGATGAAGGGGTAGAATCTGATG
1 GGGAGGGTGATGATGAAGGGGTAGAATCTGATG
* * * ** *
33965841 GTGAAGGTGAT-CTGGAAAAGGTAGAATCT-AGTA
1 GGGAGGGTGATGAT-GAAGGGGTAGAATCTGA-TG
33965874 GGGAGGGTGATG
1 GGGAGGGTGATG
33965886 TAGGAGAGGT
Statistics
Matches: 64, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
32 3 0.05
33 60 0.94
34 1 0.02
ACGTcount: A:0.28, C:0.03, G:0.47, T:0.23
Consensus pattern (33 bp):
GGGAGGGTGATGATGAAGGGGTAGAATCTGATG
Found at i:33969478 original size:17 final size:16
Alignment explanation
Indices: 33969438--33969485 Score: 69
Period size: 16 Copynumber: 2.9 Consensus size: 16
33969428 GAATGCTAAT
*
33969438 GATTTAGGGATTTTAA
1 GATTTAGGGATTTAAA
33969454 GATTTAGGGATTTAAA
1 GATTTAGGGATTTAAA
*
33969470 TATTTTAGGGATTTAA
1 GA-TTTAGGGATTTAA
33969486 TGAAGATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 16 0.55
17 13 0.45
ACGTcount: A:0.33, C:0.00, G:0.23, T:0.44
Consensus pattern (16 bp):
GATTTAGGGATTTAAA
Found at i:33970923 original size:36 final size:36
Alignment explanation
Indices: 33970876--33971025 Score: 165
Period size: 36 Copynumber: 3.9 Consensus size: 36
33970866 GCTAAGCTAC
33970876 CACTTATCACTTTGTCACTTGATCAGATAAGTATAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAT
*
33970912 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCT
1 CACTTATCACTTTGTCACTTGATCAGATAA--GTA--T--A--T
* * *
33970956 ACCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
1 --CACTTATCACTTTGTCACTTGATCAGATAAGTATAT
*
33970994 CACTTATCACTTTTTCACTTGATCAGATAAGT
1 CACTTATCACTTTGTCACTTGATCAGATAAGT
33971026 GNNNNNNNNN
Statistics
Matches: 97, Mismatches: 7, Indels: 20
0.78 0.06 0.16
Matches are distributed among these distances:
36 59 0.61
38 3 0.03
40 2 0.02
42 2 0.02
44 3 0.03
46 28 0.29
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.38
Consensus pattern (36 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAT
Found at i:33970971 original size:82 final size:81
Alignment explanation
Indices: 33970826--33971026 Score: 325
Period size: 82 Copynumber: 2.5 Consensus size: 81
33970816 ATGGTCTTAC
* *
33970826 GTATGATCACTTATCA-TTTGTC-CCTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTT
1 GTAT-ATCACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTT
33970889 GTCACTTGATCAGATAA
65 GTCACTTGATCAGATAA
33970906 GTATATCACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTT
1 GTATATCACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCT-AAGCTACCACTTATCACTTT
*
33970971 GTCTCTTGATCAGATAA
65 GTCACTTGATCAGATAA
* *
33970988 GTGTAGCACTTATCACTTTTTCACTTGATCAGATAAGTG
1 GTATATCACTTATCACTTTTTCACTTGATCAGATAAGTG
33971027 NNNNNNNNNN
Statistics
Matches: 113, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
79 11 0.10
80 9 0.08
81 20 0.18
82 73 0.65
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.37
Consensus pattern (81 bp):
GTATATCACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAGCTACCACTTATCACTTTG
TCACTTGATCAGATAA
Found at i:33974579 original size:2 final size:2
Alignment explanation
Indices: 33974572--33974609 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
33974562 ATTACTGTTG
33974572 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33974610 TTCCAAAAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33974934 original size:19 final size:19
Alignment explanation
Indices: 33974892--33974927 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
33974882 TAATATATTA
33974892 TTTAATATTTGAATTTAAC
1 TTTAATATTTGAATTTAAC
33974911 TTTAATATTT-AATTTAA
1 TTTAATATTTGAATTTAA
33974928 TACTTAAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.56
Consensus pattern (19 bp):
TTTAATATTTGAATTTAAC
Found at i:33976172 original size:13 final size:13
Alignment explanation
Indices: 33976154--33976179 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
33976144 AGTCATTACG
33976154 TGATACATAATTA
1 TGATACATAATTA
33976167 TGATACATAATTA
1 TGATACATAATTA
33976180 AACATTTGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (13 bp):
TGATACATAATTA
Found at i:33980924 original size:24 final size:24
Alignment explanation
Indices: 33980888--33980942 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
33980878 GACACACCAC
* *
33980888 AGCTCACAAGAGCATCCCGTTATT
1 AGCTCTCAAGAGCATCCCGATATT
*
33980912 AGCTCTCATGAGCATCCCGATATT
1 AGCTCTCAAGAGCATCCCGATATT
*
33980936 GGCTCTC
1 AGCTCTC
33980943 TTAAGCTTCC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (24 bp):
AGCTCTCAAGAGCATCCCGATATT
Found at i:33981156 original size:24 final size:24
Alignment explanation
Indices: 33981089--33981181 Score: 116
Period size: 24 Copynumber: 3.8 Consensus size: 24
33981079 TTCTCGCTAT
* *
33981089 TGGCTCGCACGAGCTTCCCAATTA
1 TGGCTCGCATGAGCTTCCCGATTA
33981113 TGGCTCGCATGAGCTTCCCGATTA
1 TGGCTCGCATGAGCTTCCCGATTA
*
33981137 TGGCTCTCATGAGCTTCCCG-TTA
1 TGGCTCGCATGAGCTTCCCGATTA
* *
33981160 TACAGCTCGAATGAGCTTCCCG
1 T--GGCTCGCATGAGCTTCCCG
33981182 TTACATGGCT
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
23 4 0.07
24 41 0.67
25 16 0.26
ACGTcount: A:0.18, C:0.31, G:0.23, T:0.28
Consensus pattern (24 bp):
TGGCTCGCATGAGCTTCCCGATTA
Found at i:33981227 original size:30 final size:30
Alignment explanation
Indices: 33981172--33981252 Score: 121
Period size: 30 Copynumber: 2.8 Consensus size: 30
33981162 CAGCTCGAAT
* * *
33981172 GAGCTTCCC-GTTACATGGCTTGAGAGAGA
1 GAGCTTCCCATTTACGTGGCTCGAGAGAGA
33981201 GAGCTTCCCATTTACGTGGCTCGAGAGAGA
1 GAGCTTCCCATTTACGTGGCTCGAGAGAGA
33981231 GAGCTTCCCATTTACGT-GCTCG
1 GAGCTTCCCATTTACGTGGCTCG
33981253 TATGAACATT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
29 14 0.29
30 34 0.71
ACGTcount: A:0.21, C:0.25, G:0.28, T:0.26
Consensus pattern (30 bp):
GAGCTTCCCATTTACGTGGCTCGAGAGAGA
Found at i:33986156 original size:16 final size:17
Alignment explanation
Indices: 33986123--33986156 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
33986113 TCTAACTTGT
33986123 TTGAAAATGATATTTTA
1 TTGAAAATGATATTTTA
*
33986140 TTGAAAAT-ATTTTTTA
1 TTGAAAATGATATTTTA
33986156 T
1 T
33986157 CTACCGTTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (17 bp):
TTGAAAATGATATTTTA
Found at i:33990989 original size:41 final size:41
Alignment explanation
Indices: 33990930--33991081 Score: 187
Period size: 41 Copynumber: 3.7 Consensus size: 41
33990920 TTCTTACCTT
*
33990930 TCGGGGCTTTAACGGCGTTTTTGAAAAAGCGCCGCTAATGC
1 TCGGGGCTTTAACGGCGTTTCTGAAAAAGCGCCGCTAATGC
* * * * *
33990971 TTGGGGCTTTAGCGGCGTTTCTAAAAAAGCGTCGATAATGC
1 TCGGGGCTTTAACGGCGTTTCTGAAAAAGCGCCGCTAATGC
* * *
33991012 TCGGGGTTTTAACGACGTTTCTGAAAAAACGCCGCTAATGC
1 TCGGGGCTTTAACGGCGTTTCTGAAAAAGCGCCGCTAATGC
* * * *
33991053 TGGGGGCTTTAGCGGCGTTTTTGGAAAAG
1 TCGGGGCTTTAACGGCGTTTCTGAAAAAG
33991082 AGCTAAAAAC
Statistics
Matches: 90, Mismatches: 21, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
41 90 1.00
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.28
Consensus pattern (41 bp):
TCGGGGCTTTAACGGCGTTTCTGAAAAAGCGCCGCTAATGC
Found at i:33991611 original size:25 final size:25
Alignment explanation
Indices: 33991579--33991626 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
33991569 AGATTAATTA
* *
33991579 TTTTTTAATTTATATTTTAAATATG
1 TTTTTTAAGTTATATATTAAATATG
33991604 TTTTTTAAGTTATATATTAAATA
1 TTTTTTAAGTTATATATTAAATA
33991627 ATTTCATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.60
Consensus pattern (25 bp):
TTTTTTAAGTTATATATTAAATATG
Found at i:33991812 original size:14 final size:15
Alignment explanation
Indices: 33991782--33991819 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
33991772 GGGGATTATA
*
33991782 TATGGATTTAGGGAT
1 TATGGATTTAGGCAT
33991797 TATGGA-TTAGGCAT
1 TATGGATTTAGGCAT
33991811 TATGG-TTTA
1 TATGGATTTA
33991820 AGGGTTGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.26, C:0.03, G:0.29, T:0.42
Consensus pattern (15 bp):
TATGGATTTAGGCAT
Found at i:33991859 original size:21 final size:21
Alignment explanation
Indices: 33991789--33991885 Score: 70
Period size: 21 Copynumber: 4.6 Consensus size: 21
33991779 ATATATGGAT
* * * *
33991789 TTAGGGATTATGGATTAGGCA
1 TTAGGGTTTAGGGGTTAGGAA
* * * *
33991810 TTATGGTTTAAGGGTTGGGAT
1 TTAGGGTTTAGGGGTTAGGAA
*
33991831 TTAAGGTTTAGGGGTTAGGAA
1 TTAGGGTTTAGGGGTTAGGAA
* *
33991852 TTAGGG-TTAGGGGTTAAGAG
1 TTAGGGTTTAGGGGTTAGGAA
*
33991872 TCAGGGATTTAGGG
1 TTAGGG-TTTAGGG
33991886 TTTCAAGGGT
Statistics
Matches: 59, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 17 0.29
21 36 0.61
22 6 0.10
ACGTcount: A:0.25, C:0.02, G:0.39, T:0.34
Consensus pattern (21 bp):
TTAGGGTTTAGGGGTTAGGAA
Found at i:33991877 original size:20 final size:20
Alignment explanation
Indices: 33991838--33991877 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
33991828 GATTTAAGGT
* *
33991838 TTAGGGGTTAGGAATTAGGG
1 TTAGGGGTTAAGAATCAGGG
*
33991858 TTAGGGGTTAAGAGTCAGGG
1 TTAGGGGTTAAGAATCAGGG
33991878 ATTTAGGGTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.25, C:0.03, G:0.45, T:0.28
Consensus pattern (20 bp):
TTAGGGGTTAAGAATCAGGG
Found at i:33996347 original size:43 final size:43
Alignment explanation
Indices: 33996247--33996348 Score: 116
Period size: 43 Copynumber: 2.4 Consensus size: 43
33996237 GCGGAATGAC
* *
33996247 ACTTTTAGTGGCGTTTGTGAAAAAAGCGCCGCTAAAAGTCATG
1 ACTTTTAGCGGCGTTTGTGAAAAAAGCACCGCTAAAAGTCATG
* ** **
33996290 A-TCTATAGCGGCGTTTGTGGGAAAAGCACCGCTAAGGGTCATG
1 ACT-TTTAGCGGCGTTTGTGAAAAAAGCACCGCTAAAAGTCATG
*
33996333 ACTTTTAGCAGCGTTT
1 ACTTTTAGCGGCGTTT
33996349 ATTTTTAAAA
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
42 1 0.02
43 46 0.96
44 1 0.02
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.28
Consensus pattern (43 bp):
ACTTTTAGCGGCGTTTGTGAAAAAAGCACCGCTAAAAGTCATG
Found at i:33998910 original size:43 final size:44
Alignment explanation
Indices: 33998842--33998957 Score: 116
Period size: 43 Copynumber: 2.7 Consensus size: 44
33998832 ATTTATTGTA
*
33998842 CAATGCCAAC-GTCCCACAC-GTGGTCTTACAT-GT-ATTCACATAG
1 CAATGCC-ACTGTCCCACACAG-GGTCTTACATCGTAATT-ACAAAG
* * *
33998885 CGATGCCACTGTCCCACACAGGGTCTTA-TTCGTAATTACAAAT
1 CAATGCCACTGTCCCACACAGGGTCTTACATCGTAATTACAAAG
*
33998928 CAATTGCCACTATCCCACACAGGGTCTTAC
1 CAA-TGCCACTGTCCCACACAGGGTCTTAC
33998958 TCGAAAACAC
Statistics
Matches: 61, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
42 3 0.05
43 30 0.49
44 28 0.46
ACGTcount: A:0.28, C:0.31, G:0.16, T:0.26
Consensus pattern (44 bp):
CAATGCCACTGTCCCACACAGGGTCTTACATCGTAATTACAAAG
Found at i:34004912 original size:24 final size:24
Alignment explanation
Indices: 34004880--34004925 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
34004870 TTGGTCGTAC
34004880 AACTGGAGGTGCAACCAGAGGTTT
1 AACTGGAGGTGCAACCAGAGGTTT
**
34004904 AACTGGAGGTGCATTCAGAGGT
1 AACTGGAGGTGCAACCAGAGGT
34004926 GTATCTAGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.28, C:0.15, G:0.35, T:0.22
Consensus pattern (24 bp):
AACTGGAGGTGCAACCAGAGGTTT
Found at i:34004936 original size:24 final size:24
Alignment explanation
Indices: 34004880--34004937 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
34004870 TTGGTCGTAC
* *
34004880 AACTGGAGGTGCAACCAGAGGTTT
1 AACTAGAGGTGCAACCAGAGGTGT
* **
34004904 AACTGGAGGTGCATTCAGAGGTGT
1 AACTAGAGGTGCAACCAGAGGTGT
*
34004928 ATCTAGAGGT
1 AACTAGAGGT
34004938 TCAGGCCTGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.28, C:0.14, G:0.34, T:0.24
Consensus pattern (24 bp):
AACTAGAGGTGCAACCAGAGGTGT
Found at i:34017187 original size:5 final size:5
Alignment explanation
Indices: 34017173--34017211 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
34017163 CAGGCCTAGA
*
34017173 AAAAG AAAAAG AAAA- ATAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG -AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
34017212 AGGAAAGAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
4 3 0.10
5 22 0.73
6 5 0.17
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (5 bp):
AAAAG
Found at i:34017195 original size:15 final size:16
Alignment explanation
Indices: 34017173--34017219 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 16
34017163 CAGGCCTAGA
34017173 AAAAGAAAAAGAAAA-
1 AAAAGAAAAAGAAAAG
*
34017188 ATAAG-AAAAGAAAAG
1 AAAAGAAAAAGAAAAG
*
34017203 AAAAGAAAAAGGAAAG
1 AAAAGAAAAAGAAAAG
34017219 A
1 A
34017220 GAATGAGAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 9 0.33
15 8 0.30
16 10 0.37
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (16 bp):
AAAAGAAAAAGAAAAG
Found at i:34020054 original size:45 final size:44
Alignment explanation
Indices: 34019998--34020216 Score: 183
Period size: 45 Copynumber: 4.9 Consensus size: 44
34019988 ATACGCTTAA
* * * *
34019998 AAAAAGAGTAAGACTATAGTTGAAAGATGCTATGCCATCATGAT
1 AAAATGAGTAAGACCATAGCTGAAAGATGCTATGACATCATGAT
*
34020042 AAATATGAGTAAGACCATAGCTAAAAGATGCTATGACATCATGAT
1 AAA-ATGAGTAAGACCATAGCTGAAAGATGCTATGACATCATGAT
* * *
34020087 ATAAATGAGTACGACCAT-GACTGAAAGATGCTATGGCATCATGGT
1 A-AAATGAGTAAGACCATAG-CTGAAAGATGCTATGACATCATGAT
* * * * * * * *
34020132 AAACAAGACTAAGACCAT-GACTAAAAGACGTTGTGGCATCATGGT
1 AAA-ATGAGTAAGACCATAG-CTGAAAGATGCTATGACATCATGAT
* * *
34020177 AAACAAGACG-AAGACCATAGTTGAAAGACGCTATGACATC
1 AAA-ATGA-GTAAGACCATAGCTGAAAGATGCTATGACATC
34020217 CTAATAGTTT
Statistics
Matches: 147, Mismatches: 22, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
44 6 0.04
45 138 0.94
46 3 0.02
ACGTcount: A:0.42, C:0.16, G:0.21, T:0.22
Consensus pattern (44 bp):
AAAATGAGTAAGACCATAGCTGAAAGATGCTATGACATCATGAT
Found at i:34020193 original size:90 final size:90
Alignment explanation
Indices: 34019999--34020216 Score: 219
Period size: 90 Copynumber: 2.4 Consensus size: 90
34019989 TACGCTTAAA
* * * * * *
34019999 AAAAGAGTAAGACTATAGTTGAAAGATGCTATGCCATCATGATAAATATGAGTAAGACCATAGCT
1 AAAAGAGTAAGACCATAGCTGAAAGATGCTATGACATCATGATAAACAAGACTAAGACCATAGCT
*
34020064 AAAAGATGCTATGACATCATGATAT
66 AAAAGACGCTATGACATCATGATAT
* * * *
34020089 AAATGAGTACGACCAT-GACTGAAAGATGCTATGGCATCATGGTAAACAAGACTAAGACCAT-GA
1 AAAAGAGTAAGACCATAG-CTGAAAGATGCTATGACATCATGATAAACAAGACTAAGACCATAG-
* * * *
34020152 CTAAAAGACGTTGTGGCATCATGGTA-
64 CTAAAAGACGCTATGACATCATGATAT
* *
34020178 AACAAGACG-AAGACCATAGTTGAAAGACGCTATGACATC
1 AA-AAGA-GTAAGACCATAGCTGAAAGATGCTATGACATC
34020217 CTAATAGTTT
Statistics
Matches: 104, Mismatches: 19, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
89 4 0.04
90 98 0.94
91 2 0.02
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.22
Consensus pattern (90 bp):
AAAAGAGTAAGACCATAGCTGAAAGATGCTATGACATCATGATAAACAAGACTAAGACCATAGCT
AAAAGACGCTATGACATCATGATAT
Found at i:34024966 original size:41 final size:42
Alignment explanation
Indices: 34024907--34025038 Score: 164
Period size: 41 Copynumber: 3.2 Consensus size: 42
34024897 CTATCTTTCT
*
34024907 CCATGGTGGTGTTGCAGAGTTC-GAAGTTGATCCTT-CCTTCG
1 CCATGTTGGTGTTGCAGAGTTCGGAA-TTGATCCTTCCCTTCG
* * *
34024948 CCATGTTGGTATTACAGAGTTCGGAATTGGTCCTTCCCTT-G
1 CCATGTTGGTGTTGCAGAGTTCGGAATTGATCCTTCCCTTCG
* * *
34024989 TCATGTTGGTGTTGTAGAGTTCTGAATTGAT-CTTCCCTTCG
1 CCATGTTGGTGTTGCAGAGTTCGGAATTGATCCTTCCCTTCG
34025030 CCATGTTGG
1 CCATGTTGG
34025039 CATTTCAAAG
Statistics
Matches: 77, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
40 8 0.10
41 62 0.81
42 7 0.09
ACGTcount: A:0.15, C:0.20, G:0.27, T:0.38
Consensus pattern (42 bp):
CCATGTTGGTGTTGCAGAGTTCGGAATTGATCCTTCCCTTCG
Found at i:34025061 original size:41 final size:42
Alignment explanation
Indices: 34024929--34025093 Score: 121
Period size: 41 Copynumber: 4.0 Consensus size: 42
34024919 TGCAGAGTTC
* * *
34024929 GAAGTTGATCCTT-CCTTCGCCATGTTGGTATTACAGAGTTCG
1 GAAG-TGATCCTTCCCTTCGCCATGTTGGTATTTCAAAGTTTG
* * * * *
34024971 GAATTGGTCCTTCCCTT-GTCATGTTGGTGTTGT-AGAGTTCT-
1 GAAGTGATCCTTCCCTTCGCCATGTTGGTATT-TCAAAGTT-TG
* *
34025012 GAATTGAT-CTTCCCTTCGCCATGTTGGCATTTCAAAGTTTG
1 GAAGTGATCCTTCCCTTCGCCATGTTGGTATTTCAAAGTTTG
* *
34025053 GAAGTGAT-CTATCTC-TCTCCATGTTGGT-TTTGCAAAGTTTG
1 GAAGTGATCCT-TCCCTTCGCCATGTTGGTATTT-CAAAGTTTG
34025094 AAACTAATCT
Statistics
Matches: 100, Mismatches: 15, Indels: 17
0.76 0.11 0.13
Matches are distributed among these distances:
40 13 0.13
41 77 0.77
42 10 0.10
ACGTcount: A:0.18, C:0.19, G:0.23, T:0.40
Consensus pattern (42 bp):
GAAGTGATCCTTCCCTTCGCCATGTTGGTATTTCAAAGTTTG
Found at i:34025076 original size:82 final size:82
Alignment explanation
Indices: 34024896--34025091 Score: 211
Period size: 82 Copynumber: 2.4 Consensus size: 82
34024886 CATTACAAAT
* * *
34024896 TCTATCTTTCTCCATGGTGGTGTTGCAGAGTTCGAAGTTGATCCTTCCTTCGCCATGTTGGTATT
1 TCTATCTCTCTCCATGTTGGTGTTGCAGAGTTCGAAGTTGATCCTTCCTTCGCCATGTTGGCATT
* * *
34024961 ACAGAGTTCGGAATTGG
66 ACAAAGTTCGGAAGTGA
* * *
34024978 TCCT-TCCCT-TGTCATGTTGGTGTTGTAGAGTTCTGAA-TTGAT-CTTCCCTTCGCCATGTTGG
1 T-CTATCTCTCT-CCATGTTGGTGTTGCAGAGTTC-GAAGTTGATCCTT-CCTTCGCCATGTTGG
* *
34025039 CATTTCAAAGTTTGGAAGTGA
62 CATTACAAAGTTCGGAAGTGA
* *
34025060 TCTATCTCTCTCCATGTTGGTTTTGCAAAGTT
1 TCTATCTCTCTCCATGTTGGTGTTGCAGAGTT
34025092 TGAAACTAAT
Statistics
Matches: 92, Mismatches: 16, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
81 6 0.07
82 80 0.87
83 6 0.07
ACGTcount: A:0.17, C:0.20, G:0.23, T:0.40
Consensus pattern (82 bp):
TCTATCTCTCTCCATGTTGGTGTTGCAGAGTTCGAAGTTGATCCTTCCTTCGCCATGTTGGCATT
ACAAAGTTCGGAAGTGA
Found at i:34026146 original size:7 final size:7
Alignment explanation
Indices: 34026130--34026168 Score: 71
Period size: 7 Copynumber: 5.7 Consensus size: 7
34026120 ATTCTTGTTG
34026130 AAGT-AA
1 AAGTGAA
34026136 AAGTGAA
1 AAGTGAA
34026143 AAGTGAA
1 AAGTGAA
34026150 AAGTGAA
1 AAGTGAA
34026157 AAGTGAA
1 AAGTGAA
34026164 AAGTG
1 AAGTG
34026169 GATGGGATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 4 0.12
7 28 0.88
ACGTcount: A:0.56, C:0.00, G:0.28, T:0.15
Consensus pattern (7 bp):
AAGTGAA
Found at i:34029824 original size:43 final size:43
Alignment explanation
Indices: 34029756--34029854 Score: 146
Period size: 43 Copynumber: 2.3 Consensus size: 43
34029746 TAGCTCTCTC
*
34029756 TTATAACTACCATTAGTGTGCCTTAATTGGACATTTAGCGTGG
1 TTATAACTACCATTAGTGTGCCTTAATTGGACATTTAACGTGG
* * *
34029799 TTATGATTACCATTAGTGTTG-CTTAATTGGACATTTAACGTTG
1 TTATAACTACCATTAGTG-TGCCTTAATTGGACATTTAACGTGG
34029842 TTATAACTACCAT
1 TTATAACTACCAT
34029855 CAAACTTTCC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
43 47 0.96
44 2 0.04
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.40
Consensus pattern (43 bp):
TTATAACTACCATTAGTGTGCCTTAATTGGACATTTAACGTGG
Found at i:34030461 original size:47 final size:47
Alignment explanation
Indices: 34030410--34030553 Score: 131
Period size: 47 Copynumber: 3.1 Consensus size: 47
34030400 ATTATTAAGA
*
34030410 ATTTTATGAAATTATATATCATTATTAAATTATATTTAATATAAATT
1 ATTTTATGAAATTATATATAATTATTAAATTATATTTAATATAAATT
* * * * **
34030457 A-TTT-T-AAATTATACA-AATTCATATAAGA--AAATTTATTATCAAGA
1 ATTTTATGAAATTATATATAATT-AT-TAA-ATTATATTTAATATAAATT
*
34030501 ATTTTATGAAATTATATATTATTATTAAATTATATTTAATA-ATAATT
1 ATTTTATGAAATTATATATAATTATTAAATTATATTTAATATA-AATT
34030548 ATTTTA
1 ATTTTA
34030554 AATTATACAA
Statistics
Matches: 73, Mismatches: 14, Indels: 20
0.68 0.13 0.19
Matches are distributed among these distances:
43 3 0.04
44 23 0.32
45 8 0.11
46 8 0.11
47 28 0.38
48 3 0.04
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (47 bp):
ATTTTATGAAATTATATATAATTATTAAATTATATTTAATATAAATT
Found at i:34030491 original size:91 final size:91
Alignment explanation
Indices: 34030380--34030594 Score: 360
Period size: 91 Copynumber: 2.4 Consensus size: 91
34030370 TGGTTTTAGT
*
34030380 AAATTCATATAAGAATATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTATAT
1 AAATTCATATAAGAAAATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTATAT
34030445 TTAAT-ATAAATTATTTTAAATTATAC
66 TTAATAAT-AATTATTTTAAATTATAC
* *
34030471 AAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATAT
1 AAATTCATATAAGAAAATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTATAT
34030536 TTAATAATAATTATTTTAAATTATAC
66 TTAATAATAATTATTTTAAATTATAC
* * *
34030562 AAATTCATATAACAAAATTTATTAGTAATAATT
1 AAATTCATATAAGAAAATTTATTATTAAGAATT
34030595 ATTTTAAATT
Statistics
Matches: 116, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
91 114 0.98
92 2 0.02
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (91 bp):
AAATTCATATAAGAAAATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTATAT
TTAATAATAATTATTTTAAATTATAC
Found at i:34030729 original size:15 final size:16
Alignment explanation
Indices: 34030701--34030730 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
34030691 TAAATTCATA
34030701 TAAGAATATTTATTAT
1 TAAGAATATTTATTAT
34030717 TAAGAAT-TTTATTA
1 TAAGAATATTTATTA
34030731 AATTATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (16 bp):
TAAGAATATTTATTAT
Found at i:34030733 original size:130 final size:120
Alignment explanation
Indices: 34030601--34031010 Score: 757
Period size: 120 Copynumber: 3.4 Consensus size: 120
34030591 AATTATTTTA
*
34030601 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
*
34030666 ATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTTATTATTAAG
66 ATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
34030721 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
34030786 ATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
* *
34030841 AATTTTATTGAATTATATATTTTAATTAACATATATTTAATAATAATTATTTCAAATTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
* * *
34030906 ATAATATCATATATTATGATTTAATTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
34030961 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTAT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTAT
34031011 GTTAAAATAT
Statistics
Matches: 281, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 281 1.00
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
ATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
Found at i:34030750 original size:18 final size:17
Alignment explanation
Indices: 34030722--34030756 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
34030712 ATTATTAAGA
*
34030722 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
34030739 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
34030757 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:34030949 original size:37 final size:37
Alignment explanation
Indices: 34030908--34030979 Score: 85
Period size: 37 Copynumber: 1.9 Consensus size: 37
34030898 TATATTTTAT
*
34030908 AATA-TCATATATTATG-ATTTAATTAAATTCATATAAG
1 AATATTCAT-TATTAAGAATTTAATTAAATT-ATATAAG
* *
34030945 AATATTGATTATTAAGAATTTTATTAAATTATATA
1 AATATTCATTATTAAGAATTTAATTAAATTATATA
34030980 TTTTAATTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
37 15 0.50
38 15 0.50
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.46
Consensus pattern (37 bp):
AATATTCATTATTAAGAATTTAATTAAATTATATAAG
Found at i:34030990 original size:18 final size:17
Alignment explanation
Indices: 34030962--34030996 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
34030952 ATTATTAAGA
*
34030962 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
34030979 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
34030997 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:34031217 original size:44 final size:45
Alignment explanation
Indices: 34031153--34031249 Score: 126
Period size: 45 Copynumber: 2.2 Consensus size: 45
34031143 CTATTACACC
* *
34031153 TCCATTCCATTCAACTAAACACA-AGAA-TACTATTACGCCTCTAT
1 TCCATTACATTCAACCAAACA-ATAGAATTACTATTACGCCTCTAT
* * *
34031197 TCCATTACATTCAACCAAACAATTGAATTGCTATTACGGCTCTAT
1 TCCATTACATTCAACCAAACAATAGAATTACTATTACGCCTCTAT
34031242 TCCATTAC
1 TCCATTAC
34031250 CCCTCTATTC
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
43 1 0.02
44 22 0.48
45 23 0.50
ACGTcount: A:0.34, C:0.28, G:0.06, T:0.32
Consensus pattern (45 bp):
TCCATTACATTCAACCAAACAATAGAATTACTATTACGCCTCTAT
Found at i:34032157 original size:18 final size:18
Alignment explanation
Indices: 34032113--34032163 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
34032103 ATAAAATCAA
*
34032113 ATAATTATTTCAAATATT
1 ATAAATATTTCAAATATT
* *
34032131 ATTATTATTTCAAATATGT
1 ATAAATATTTCAAATAT-T
34032150 A-AAATATTTCAAAT
1 ATAAATATTTCAAAT
34032164 TTCATTGTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 27 0.93
19 2 0.07
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (18 bp):
ATAAATATTTCAAATATT
Found at i:34032402 original size:21 final size:20
Alignment explanation
Indices: 34032375--34032423 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
34032365 AGGAGTTATT
34032375 AATTAAAAAGATGAATTAAA
1 AATTAAAAAGATGAATTAAA
* *
34032395 AATATAAAAATATTAATTAAA
1 AAT-TAAAAAGATGAATTAAA
34032416 AATTAAAA
1 AATTAAAA
34032424 TAAAAGTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 8 0.31
21 18 0.69
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (20 bp):
AATTAAAAAGATGAATTAAA
Found at i:34037848 original size:6 final size:6
Alignment explanation
Indices: 34037837--34037871 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
34037827 AGGTTTCCAA
34037837 AAATGG AAATGG AAATGG AAATGG AAATGG AAATG
1 AAATGG AAATGG AAATGG AAATGG AAATGG AAATG
34037872 ATCCATTTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.51, C:0.00, G:0.31, T:0.17
Consensus pattern (6 bp):
AAATGG
Found at i:34041126 original size:7 final size:6
Alignment explanation
Indices: 34041096--34041125 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
34041086 GGTTTTCTCA
34041096 AAATGG AAATGG AAATGG AAATGAG AAATG
1 AAATGG AAATGG AAATGG AAATG-G AAATG
34041126 ATTCATTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.53, C:0.00, G:0.30, T:0.17
Consensus pattern (6 bp):
AAATGG
Found at i:34048938 original size:14 final size:15
Alignment explanation
Indices: 34048900--34048938 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
34048890 ACTGGACAAT
34048900 TAATAACAT-AGTCA
1 TAATAACATAAGTCA
*
34048914 TAATAGCATAAGTCA
1 TAATAACATAAGTCA
34048929 -AATAACATAA
1 TAATAACATAA
34048939 ATAAAGTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 17 0.77
15 5 0.23
ACGTcount: A:0.54, C:0.13, G:0.08, T:0.26
Consensus pattern (15 bp):
TAATAACATAAGTCA
Found at i:34054976 original size:31 final size:31
Alignment explanation
Indices: 34054941--34054999 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
34054931 TGTCAAGTGG
34054941 ACATAAA-AATAATAATTTTCTTATAAAATTC
1 ACATAAATAAT-ATAATTTTCTTATAAAATTC
* *
34054972 ACATAAATCATTTAATTTTCTTATAAAA
1 ACATAAATAATATAATTTTCTTATAAAA
34055000 AATTAAAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 23 0.92
32 2 0.08
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (31 bp):
ACATAAATAATATAATTTTCTTATAAAATTC
Found at i:34055155 original size:32 final size:32
Alignment explanation
Indices: 34055119--34055180 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
34055109 CCCTACAAAT
**
34055119 TTGTAGCAAATGACCCATTTCGGTAATTAATA
1 TTGTAGCAAACAACCCATTTCGGTAATTAATA
*
34055151 TTGTAGCAAACAACTCATTTCGGTAATTAA
1 TTGTAGCAAACAACCCATTTCGGTAATTAA
34055181 CTTGTATGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (32 bp):
TTGTAGCAAACAACCCATTTCGGTAATTAATA
Found at i:34055727 original size:111 final size:114
Alignment explanation
Indices: 34055498--34055729 Score: 305
Period size: 112 Copynumber: 2.1 Consensus size: 114
34055488 CCCTAAACCT
* *
34055498 TAAATAATAATTACAAATAAAAAATTACCTTTAAAACAAAATTTGTTGTTGCCTCCTCTCCTTCC
1 TAAATAACAATTACAAATAAAAAATTACCTTTAAAAAAAAATTTGTTGTTGCCTCCTCTCCTTCC
* * * * *
34055563 AAAATCACTAAATCAAACAAATAATAAGTAGCACAAAACCCTAAACAAG
66 AAAACCACAAAATAAAACAAATAATAAGTAGAACAAAACCCTAAACAAA
34055612 TAAATAACAATTACAAA-AAAAAA-TACCTTTAAAATAAAAATTT-TTGTTGCCTCCTCT-CTTC
1 TAAATAACAATTACAAATAAAAAATTACCTTTAAAA-AAAAATTTGTTGTTGCCTCCTCTCCTT-
* * *
34055673 CCAAAACCTCAAAATAAAAC-ACTAATAAGTA-AACTAAAACCTTAAACAAA
64 CCAAAACCACAAAATAAAACAAATAATAAGTAGAAC-AAAACCCTAAACAAA
34055723 TAAATAA
1 TAAATAA
34055730 TGATTAAAAA
Statistics
Matches: 105, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
110 2 0.02
111 33 0.31
112 41 0.39
113 13 0.12
114 16 0.15
ACGTcount: A:0.50, C:0.19, G:0.04, T:0.26
Consensus pattern (114 bp):
TAAATAACAATTACAAATAAAAAATTACCTTTAAAAAAAAATTTGTTGTTGCCTCCTCTCCTTCC
AAAACCACAAAATAAAACAAATAATAAGTAGAACAAAACCCTAAACAAA
Found at i:34061320 original size:4 final size:4
Alignment explanation
Indices: 34061311--34061336 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
34061301 TGTTCCCCTA
34061311 AATG AATG AATG AATG AATG AATG AA
1 AATG AATG AATG AATG AATG AATG AA
34061337 AGCCCTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.23, T:0.23
Consensus pattern (4 bp):
AATG
Found at i:34071457 original size:51 final size:51
Alignment explanation
Indices: 34071342--34071615 Score: 406
Period size: 51 Copynumber: 5.4 Consensus size: 51
34071332 CTTACGTATG
* * *
34071342 ATCACTTATCACTTGTCCCTGATCAGATAAATGTAGCT-AAGCTACCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
* *
34071392 ATCACTTGCCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCCCTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
* * *
34071443 ATCACTTGTTACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTATCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
*
34071494 ATCACTTGCCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
* * *
34071545 ATCACTTGTCACTTGTCACTGATTAGATAAGTGTAGCTGAAGCTATCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
* * *
34071596 ATCATTTGCCACTTGCCACT
1 ATCACTTGTCACTTGTCACT
34071616 TGCCACTTGT
Statistics
Matches: 202, Mismatches: 21, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
50 34 0.17
51 168 0.83
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.32
Consensus pattern (51 bp):
ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
Found at i:34071517 original size:102 final size:102
Alignment explanation
Indices: 34071342--34071615 Score: 460
Period size: 102 Copynumber: 2.7 Consensus size: 102
34071332 CTTACGTATG
* * * *
34071342 ATCACTTATCACTTGTCCCTGATCAGATAAATGTAGCT-AAGCTACCACTTATCACTTGCCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTGCCACTT
*
34071406 GTCACTGATCAGATAAGTGTAGCTAAAGCTACCCCTT
66 GTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
*
34071443 ATCACTTGTTACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTGCCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTGCCACTT
34071508 GTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
66 GTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
* *
34071545 ATCACTTGTCACTTGTCACTGATTAGATAAGTGTAGCTGAAGCTATCACTTATCATTTGCCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTGCCACTT
*
34071610 GCCACT
66 GTCACT
34071616 TGCCACTTGT
Statistics
Matches: 162, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
101 34 0.21
102 128 0.79
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.32
Consensus pattern (102 bp):
ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTGCCACTT
GTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
Found at i:34071616 original size:65 final size:65
Alignment explanation
Indices: 34071547--34071673 Score: 202
Period size: 65 Copynumber: 2.0 Consensus size: 65
34071537 TACCACTTAT
* * *
34071547 CACTTGTCACTTGTCACTGATTAGATAAGTGTAGCTGAAGCTA-TCACTTATCATTTGCCACTTG
1 CACTTGCCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACT-ACTTATCACTTGCCACTTG
34071611 C
65 C
*
34071612 CACTTGCCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACTACTTATCACTTGTCACT
1 CACTTGCCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACTACTTATCACTTGCCACT
34071674 GATCAGAAGT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
65 56 0.98
66 1 0.02
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.34
Consensus pattern (65 bp):
CACTTGCCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACTACTTATCACTTGCCACTTGC
Found at i:34075668 original size:50 final size:50
Alignment explanation
Indices: 34075553--34075801 Score: 336
Period size: 50 Copynumber: 4.8 Consensus size: 50
34075543 GATAATAACA
* **
34075553 TGCCAAAGCCATGTCCCAGACATGGTCTTACAGGGGATGTTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCATCTCGG
* *
34075604 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
34075654 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
34075704 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
34075759 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
34075802 TTACCCAAAT
Statistics
Matches: 176, Mismatches: 16, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
50 97 0.55
51 34 0.19
53 3 0.02
54 1 0.01
55 2 0.01
56 39 0.22
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:34075727 original size:100 final size:104
Alignment explanation
Indices: 34075552--34075801 Score: 373
Period size: 100 Copynumber: 2.4 Consensus size: 104
34075542 TGATAATAAC
* **
34075552 ATGCCAAAGCCATGTCCCAGACATGGTCTTACAGGGGATGTTCTCATCTCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGGTGCCCATGCCATG
* *
34075617 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
*
34075654 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCCATGCCATGT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCCATGCCATGT
34075718 CCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
66 CCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
34075759 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
34075802 TTACCCAAAT
Statistics
Matches: 134, Mismatches: 8, Indels: 8
0.89 0.05 0.05
Matches are distributed among these distances:
100 53 0.40
101 35 0.26
103 3 0.02
104 1 0.01
105 2 0.01
106 40 0.30
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:34075917 original size:13 final size:13
Alignment explanation
Indices: 34075896--34075927 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
34075886 GCTTGGATCA
*
34075896 TCATCAAATAAAT
1 TCATAAAATAAAT
34075909 TCATAAAATAAAT
1 TCATAAAATAAAT
34075922 TCATAA
1 TCATAA
34075928 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:34076174 original size:30 final size:30
Alignment explanation
Indices: 34076139--34076196 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
34076129 CCTCGACTCT
*
34076139 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
34076169 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
34076197 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:34079969 original size:8 final size:8
Alignment explanation
Indices: 34079958--34079994 Score: 67
Period size: 8 Copynumber: 4.8 Consensus size: 8
34079948 TATATTTTTG
34079958 TTTTATAA
1 TTTTATAA
34079966 TTTTATAA
1 TTTTATAA
34079974 TTTTATAA
1 TTTTATAA
34079982 -TTTATAA
1 TTTTATAA
34079989 TTTTAT
1 TTTTAT
34079995 TTTATTTCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 7 0.25
8 21 0.75
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (8 bp):
TTTTATAA
Found at i:34079987 original size:15 final size:16
Alignment explanation
Indices: 34079958--34079994 Score: 67
Period size: 15 Copynumber: 2.4 Consensus size: 16
34079948 TATATTTTTG
34079958 TTTTATAATTTTATAA
1 TTTTATAATTTTATAA
34079974 TTTTATAA-TTTATAA
1 TTTTATAATTTTATAA
34079989 TTTTAT
1 TTTTAT
34079995 TTTATTTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTATAATTTTATAA
Found at i:34080072 original size:26 final size:25
Alignment explanation
Indices: 34080025--34080080 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
34080015 TGAGTTGTTT
* **
34080025 TATTTTTATAATTTTATTTTTTTAAA
1 TATTTTTATAATTATA-AATTTTAAA
*
34080051 TATTTTTATAATTATAAATTTTGAA
1 TATTTTTATAATTATAAATTTTAAA
34080076 TATTT
1 TATTT
34080081 AGAATAATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 11 0.42
26 15 0.58
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (25 bp):
TATTTTTATAATTATAAATTTTAAA
Found at i:34081330 original size:27 final size:25
Alignment explanation
Indices: 34081299--34081368 Score: 90
Period size: 25 Copynumber: 2.8 Consensus size: 25
34081289 NNNTATTTAC
*
34081299 ATATACATATATAACAATATATTATAT
1 ATATACATATATAA-AATA-ATTACAT
*
34081326 ATATATATATATAAAATAATTACAT
1 ATATACATATATAAAATAATTACAT
34081351 ATATACATA-A-AAAATAAT
1 ATATACATATATAAAATAAT
34081369 GATTACTCTA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
23 8 0.20
24 1 0.03
25 14 0.35
26 4 0.10
27 13 0.32
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (25 bp):
ATATACATATATAAAATAATTACAT
Found at i:34081352 original size:23 final size:23
Alignment explanation
Indices: 34081295--34081368 Score: 76
Period size: 23 Copynumber: 3.0 Consensus size: 23
34081285 NNNNNNNTAT
*
34081295 TTACATATACATATATAACAATATA
1 TTACATATATATATATAA-AATA-A
*
34081320 TTATATATATATATATATAAAATAA
1 -T-TACATATATATATATAAAATAA
* *
34081345 TTACATATATACATAAAAAATAA
1 TTACATATATATATATAAAATAA
34081368 T
1 T
34081369 GATTACTCTA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
23 20 0.48
24 1 0.02
25 1 0.02
26 5 0.12
27 15 0.36
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (23 bp):
TTACATATATATATATAAAATAA
Found at i:34082373 original size:21 final size:21
Alignment explanation
Indices: 34082347--34082418 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
34082337 AATCATATCT
34082347 TCTAAGATTGTGTATATCATA
1 TCTAAGATTGTGTATATCATA
** **
34082368 TCTAAGATTGCATATATTTTA
1 TCTAAGATTGTGTATATCATA
*
34082389 TCTAAGA-T-TGCATATCATA
1 TCTAAGATTGTGTATATCATA
34082408 TCTAAGATTGT
1 TCTAAGATTGT
34082419 ATATCCTCGA
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
19 13 0.32
20 2 0.05
21 25 0.62
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.43
Consensus pattern (21 bp):
TCTAAGATTGTGTATATCATA
Found at i:34082382 original size:19 final size:19
Alignment explanation
Indices: 34082360--34082423 Score: 85
Period size: 19 Copynumber: 3.3 Consensus size: 19
34082350 AAGATTGTGT
34082360 ATATCATATCTAAGATTGC
1 ATATCATATCTAAGATTGC
34082379 ATAT-ATTTTATCTAAGATTGC
1 ATATCA---TATCTAAGATTGC
*
34082400 ATATCATATCTAAGATTGT
1 ATATCATATCTAAGATTGC
34082419 ATATC
1 ATATC
34082424 CTCGAAAATT
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
18 1 0.03
19 21 0.52
21 17 0.43
22 1 0.03
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.42
Consensus pattern (19 bp):
ATATCATATCTAAGATTGC
Found at i:34083994 original size:15 final size:15
Alignment explanation
Indices: 34083974--34084004 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
34083964 TGACTTGGCT
34083974 AAACACAGTTTTTGC
1 AAACACAGTTTTTGC
34083989 AAACACAGTTTTTGC
1 AAACACAGTTTTTGC
34084004 A
1 A
34084005 TTAGCTTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.32
Consensus pattern (15 bp):
AAACACAGTTTTTGC
Found at i:34084934 original size:20 final size:21
Alignment explanation
Indices: 34084888--34084965 Score: 124
Period size: 21 Copynumber: 3.7 Consensus size: 21
34084878 TTTGAAATGT
34084888 TTTATAATATTATTTTTTAAAA
1 TTTA-AATATTATTTTTTAAAA
34084910 TTTTAAATA-TATTTTTTAAAA
1 -TTTAAATATTATTTTTTAAAA
34084931 TTTAAATATTATTTTTTAAAA
1 TTTAAATATTATTTTTTAAAA
34084952 TTTAAATATT-TTTT
1 TTTAAATATTATTTT
34084966 AATAATATAA
Statistics
Matches: 54, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
20 12 0.22
21 34 0.63
22 4 0.07
23 4 0.07
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTAAATATTATTTTTTAAAA
Found at i:34085054 original size:10 final size:10
Alignment explanation
Indices: 34085041--34085114 Score: 53
Period size: 10 Copynumber: 7.1 Consensus size: 10
34085031 ATTTTAAATA
34085041 TTAAATTTTT
1 TTAAATTTTT
34085051 TTAAAATTTGTT
1 TT-AAATTT-TT
*
34085063 TTATAATATTT
1 TTA-AATTTTT
34085074 TT-AATTTGTT
1 TTAAATTT-TT
*
34085084 TTATAATATTT
1 TTA-AATTTTT
*
34085095 AT-AATTTTT
1 TTAAATTTTT
*
34085104 TTTAATTTTT
1 TTAAATTTTT
34085114 T
1 T
34085115 AAAAATATAT
Statistics
Matches: 51, Mismatches: 6, Indels: 14
0.72 0.08 0.20
Matches are distributed among these distances:
9 11 0.22
10 14 0.27
11 14 0.27
12 12 0.24
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (10 bp):
TTAAATTTTT
Found at i:34085081 original size:21 final size:21
Alignment explanation
Indices: 34085055--34085116 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
34085045 ATTTTTTTAA
34085055 AATTTGTTTTATAATATTTTT
1 AATTTGTTTTATAATATTTTT
*
34085076 AATTTGTTTTATAATATTTAT
1 AATTTGTTTTATAATATTTTT
34085097 AATTT-TTTT-TAAT-TTTTT
1 AATTTGTTTTATAATATTTTT
34085115 AA
1 AA
34085117 AAATATATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
18 6 0.15
19 4 0.10
20 4 0.10
21 25 0.64
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (21 bp):
AATTTGTTTTATAATATTTTT
Found at i:34085122 original size:30 final size:31
Alignment explanation
Indices: 34085062--34085130 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 31
34085052 TAAAATTTGT
* * *
34085062 TTTATAA-TATTTTTAATTTGTTTTATAATA
1 TTTATAATTTTTTTTAATTTGTTTAAAAATA
34085092 TTTATAATTTTTTTTAATTT-TTTAAAAATA
1 TTTATAATTTTTTTTAATTTGTTTAAAAATA
34085122 --TATAATTTT
1 TTTATAATTTT
34085131 AAAAATATGA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 9 0.26
30 15 0.43
31 11 0.31
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (31 bp):
TTTATAATTTTTTTTAATTTGTTTAAAAATA
Found at i:34085216 original size:29 final size:28
Alignment explanation
Indices: 34085169--34085253 Score: 75
Period size: 29 Copynumber: 2.9 Consensus size: 28
34085159 TGTTTTATAA
*
34085169 TATTTTAAATGT-ATATTTTAAATATTTTT
1 TATTTTAAAT-TAAT-TTTTAAATATTATT
34085198 TATTTTAAATATAATTTTTATAA-ATTATT
1 TATTTTAAAT-TAATTTTTA-AATATTATT
* *
34085227 AATTTTTAAATTAATTTTAAAGATATT
1 TA-TTTTAAATTAATTTTTAA-ATATT
34085254 CAAATGTTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
28 1 0.02
29 31 0.66
30 15 0.32
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (28 bp):
TATTTTAAATTAATTTTTAAATATTATT
Found at i:34088671 original size:30 final size:30
Alignment explanation
Indices: 34088636--34088738 Score: 102
Period size: 30 Copynumber: 3.5 Consensus size: 30
34088626 TGGTTGCTCT
* ** * *
34088636 GGGTGAAATGAACTCGAACTGCCTATGTCG
1 GGGTGATATGAACTCGAACCACCCATGTCC
*
34088666 GGGTGATACGAACTCGAACCACCCATGTCC
1 GGGTGATATGAACTCGAACCACCCATGTCC
***
34088696 GGGTGATATGAACTC-AAGCTGTCCA-GTCC
1 GGGTGATATGAACTCGAA-CCACCCATGTCC
34088725 GGGTGATATGAACT
1 GGGTGATATGAACT
34088739 ATTCTACGAC
Statistics
Matches: 62, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
29 20 0.32
30 42 0.68
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.22
Consensus pattern (30 bp):
GGGTGATATGAACTCGAACCACCCATGTCC
Found at i:34091385 original size:21 final size:20
Alignment explanation
Indices: 34091359--34091404 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
34091349 TTTATATTTT
*
34091359 AAATAAAGTCATATTTTTAAC
1 AAATAAAGTC-TATTTTTAAA
* *
34091380 AAATAAATTCTTTTTTTAAA
1 AAATAAAGTCTATTTTTAAA
34091400 AAATA
1 AAATA
34091405 TTGTTTTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (20 bp):
AAATAAAGTCTATTTTTAAA
Found at i:34091497 original size:21 final size:21
Alignment explanation
Indices: 34091464--34091507 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
34091454 ATTACTTTTT
*
34091464 AAAATTTTAAATAGAATTTAA
1 AAAAGTTTAAATAGAATTTAA
* * *
34091485 AAAAGTTTGAATATATTTTAA
1 AAAAGTTTAAATAGAATTTAA
34091506 AA
1 AA
34091508 TAATTAAAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.39
Consensus pattern (21 bp):
AAAAGTTTAAATAGAATTTAA
Found at i:34091685 original size:34 final size:36
Alignment explanation
Indices: 34091638--34091716 Score: 119
Period size: 34 Copynumber: 2.3 Consensus size: 36
34091628 TGTTTTATAT
*
34091638 TATTA-AAAAAATATATTTAAAATTTT-AAAAATAA
1 TATTATAAAAAATATATATAAAATTTTAAAAAATAA
*
34091672 T-TTTTAAAAAATATATATAAAATTTTAAAAAATAA
1 TATTATAAAAAATATATATAAAATTTTAAAAAATAA
34091707 TATTATAAAA
1 TATTATAAAA
34091717 CATTTCAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
33 2 0.05
34 21 0.54
35 9 0.23
36 7 0.18
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (36 bp):
TATTATAAAAAATATATATAAAATTTTAAAAAATAA
Found at i:34091695 original size:22 final size:22
Alignment explanation
Indices: 34091670--34091748 Score: 70
Period size: 23 Copynumber: 3.5 Consensus size: 22
34091660 TTTTAAAAAT
34091670 AATTTTTAAAAAATATATATAA
1 AATTTTTAAAAAATATATATAA
34091692 AA-TTTTAAAAAATAATATTATAA
1 AATTTTTAAAAAAT-ATA-TATAA
** * * * *
34091715 AACATTTCAAATATACATTTCAA
1 AATTTTTAAAAAATATATAT-AA
34091738 AATTTTTAAAA
1 AATTTTTAAAA
34091749 CCAATAATAA
Statistics
Matches: 45, Mismatches: 8, Indels: 7
0.75 0.13 0.12
Matches are distributed among these distances:
21 11 0.24
22 7 0.16
23 19 0.42
24 8 0.18
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (22 bp):
AATTTTTAAAAAATATATATAA
Found at i:34091697 original size:21 final size:23
Alignment explanation
Indices: 34091673--34091716 Score: 74
Period size: 21 Copynumber: 2.0 Consensus size: 23
34091663 TAAAAATAAT
34091673 TTTTAAAAAAT-ATA-TATAAAA
1 TTTTAAAAAATAATATTATAAAA
34091694 TTTTAAAAAATAATATTATAAAA
1 TTTTAAAAAATAATATTATAAAA
34091717 CATTTCAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 11 0.52
22 3 0.14
23 7 0.33
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
TTTTAAAAAATAATATTATAAAA
Found at i:34091776 original size:9 final size:8
Alignment explanation
Indices: 34091757--34091832 Score: 53
Period size: 9 Copynumber: 8.8 Consensus size: 8
34091747 AACCAATAAT
34091757 AAAAAATA
1 AAAAAATA
*
34091765 AATAAAACA
1 AA-AAAATA
*
34091774 AATAAATA
1 AAAAAATA
34091782 AAATAAATA
1 AAA-AAATA
*
34091791 AGGACAAATA
1 A--AAAAATA
*
34091801 AAAAACTTA
1 AAAAA-ATA
34091810 AAAAAAGTA
1 AAAAAA-TA
*
34091819 AATAAATA
1 AAAAAATA
34091827 AAAAAA
1 AAAAAA
34091833 ATTAAAAAGA
Statistics
Matches: 52, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
8 18 0.35
9 27 0.52
10 6 0.12
11 1 0.02
ACGTcount: A:0.76, C:0.04, G:0.04, T:0.16
Consensus pattern (8 bp):
AAAAAATA
Found at i:34091776 original size:13 final size:13
Alignment explanation
Indices: 34091744--34091791 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 13
34091734 TCAAAATTTT
*
34091744 TAAAACCAAT-AA
1 TAAAACAAATAAA
34091756 T-AAA-AAATAAA
1 TAAAACAAATAAA
34091767 TAAAACAAATAAA
1 TAAAACAAATAAA
*
34091780 TAAAATAAATAA
1 TAAAACAAATAA
34091792 GGACAAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
10 3 0.10
11 6 0.19
12 4 0.13
13 18 0.58
ACGTcount: A:0.75, C:0.06, G:0.00, T:0.19
Consensus pattern (13 bp):
TAAAACAAATAAA
Found at i:34091834 original size:9 final size:9
Alignment explanation
Indices: 34091751--34091850 Score: 51
Period size: 9 Copynumber: 10.9 Consensus size: 9
34091741 TTTTAAAACC
34091751 AATAATAAAA
1 AATAA-AAAA
*
34091761 AATAAATAA
1 AATAAAAAA
* *
34091770 AA-CAAATA
1 AATAAAAAA
*
34091778 AATAAAATA
1 AATAAAAAA
* *
34091787 AATAAGGACA
1 AATAA-AAAA
34091797 AATAAAAAA
1 AATAAAAAA
**
34091806 CTTAAAAAA
1 AATAAAAAA
* *
34091815 AGT-AAATA
1 AATAAAAAA
34091823 AATAAAAAA
1 AATAAAAAA
34091832 AATTAAAAAGA
1 AA-TAAAAA-A
*
34091843 AAGAAAAA
1 AATAAAAA
34091851 TGAAAAAGGA
Statistics
Matches: 68, Mismatches: 17, Indels: 10
0.72 0.18 0.11
Matches are distributed among these distances:
8 11 0.16
9 31 0.46
10 23 0.34
11 3 0.04
ACGTcount: A:0.76, C:0.03, G:0.05, T:0.16
Consensus pattern (9 bp):
AATAAAAAA
Found at i:34093610 original size:9 final size:9
Alignment explanation
Indices: 34093593--34093638 Score: 83
Period size: 9 Copynumber: 5.1 Consensus size: 9
34093583 TGAGTTTTCG
34093593 AATTCGAAT
1 AATTCGAAT
*
34093602 AACTCGAAT
1 AATTCGAAT
34093611 AATTCGAAT
1 AATTCGAAT
34093620 AATTCGAAT
1 AATTCGAAT
34093629 AATTCGAAT
1 AATTCGAAT
34093638 A
1 A
34093639 TCAAACTATA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 35 1.00
ACGTcount: A:0.46, C:0.13, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:34094653 original size:5 final size:5
Alignment explanation
Indices: 34094643--34094668 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
34094633 CTCGAAAATT
34094643 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
34094669 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:34098887 original size:15 final size:15
Alignment explanation
Indices: 34098867--34098895 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
34098857 GTATTGTTGC
34098867 TTGATAACACGGTGA
1 TTGATAACACGGTGA
34098882 TTGATAACACGGTG
1 TTGATAACACGGTG
34098896 TGTAAGGCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.28
Consensus pattern (15 bp):
TTGATAACACGGTGA
Found at i:34114444 original size:10 final size:10
Alignment explanation
Indices: 34114423--34114462 Score: 55
Period size: 10 Copynumber: 3.9 Consensus size: 10
34114413 TTCATTTAGT
34114423 TTTATATTTTA
1 TTTAT-TTTTA
34114434 TTTATTTTTA
1 TTTATTTTTA
34114444 TTTATTTTGT-
1 TTTATTTT-TA
34114454 TTTATTTTT
1 TTTATTTTT
34114463 TTATTTTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
9 1 0.04
10 21 0.75
11 6 0.21
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (10 bp):
TTTATTTTTA
Found at i:34116207 original size:29 final size:29
Alignment explanation
Indices: 34116174--34116240 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 29
34116164 CAAGTTTCAA
34116174 GAGCCACACGAGATAGACATAGGCCATGT
1 GAGCCACACGAGATAGACATAGGCCATGT
* ***
34116203 GAGCCACACGAGATGGACATAGGTTGTGT
1 GAGCCACACGAGATAGACATAGGCCATGT
34116232 GAGCCACAC
1 GAGCCACAC
34116241 ACGACCATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.31, C:0.24, G:0.30, T:0.15
Consensus pattern (29 bp):
GAGCCACACGAGATAGACATAGGCCATGT
Found at i:34117770 original size:40 final size:39
Alignment explanation
Indices: 34117720--34117795 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 39
34117710 GCACTGTACA
* *
34117720 TTTATTGTTTTATTGACTATTTT-TCTATTTTGTTATCTG
1 TTTATTGTTTTATTCA-TATTTTGTCTATTTTCTTATCTG
*
34117759 TTTATCTGTTTTATTCATTTTTTGTCTATTTTCTTAT
1 TTTAT-TGTTTTATTCATATTTTGTCTATTTTCTTAT
34117796 TAGTTTGCTC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
39 10 0.31
40 22 0.69
ACGTcount: A:0.14, C:0.09, G:0.08, T:0.68
Consensus pattern (39 bp):
TTTATTGTTTTATTCATATTTTGTCTATTTTCTTATCTG
Found at i:34118631 original size:5 final size:5
Alignment explanation
Indices: 34118612--34118649 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
34118602 AATAAAAATC
*
34118612 AAAAG ACAA- AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
34118650 TTATTTGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 3 0.10
5 27 0.90
ACGTcount: A:0.82, C:0.03, G:0.16, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:34119472 original size:29 final size:29
Alignment explanation
Indices: 34119430--34119496 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 29
34119420 CAAGTTTCAA
34119430 GAGCCACACGAGATAGACATAGGCCATGT
1 GAGCCACACGAGATAGACATAGGCCATGT
* ***
34119459 GAGCCACACGAGATGGACATAGGTTGTGT
1 GAGCCACACGAGATAGACATAGGCCATGT
34119488 GAGCCACAC
1 GAGCCACAC
34119497 ACGACCATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.31, C:0.24, G:0.30, T:0.15
Consensus pattern (29 bp):
GAGCCACACGAGATAGACATAGGCCATGT
Found at i:34123001 original size:15 final size:13
Alignment explanation
Indices: 34122978--34123020 Score: 52
Period size: 12 Copynumber: 3.2 Consensus size: 13
34122968 AAAAAAGAAC
34122978 ATTGAATTTTGAAA
1 ATTGAATTTT-AAA
34122992 ATTCGAATTTTTAAA
1 ATT-GAA-TTTTAAA
34123007 A-TGAATTTTAAA
1 ATTGAATTTTAAA
34123019 AT
1 AT
34123021 CCAAAATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
12 8 0.31
13 3 0.12
14 4 0.15
15 7 0.27
16 4 0.15
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.44
Consensus pattern (13 bp):
ATTGAATTTTAAA
Found at i:34125474 original size:30 final size:30
Alignment explanation
Indices: 34125434--34125509 Score: 125
Period size: 30 Copynumber: 2.5 Consensus size: 30
34125424 TTACGAGGAT
*
34125434 GTTCAGGAGCTTGGGAAGACTTGATATCTC
1 GTTCAGGAGCTTGGGAAGACTCGATATCTC
*
34125464 GTTTAGGAGCTTGGGAAGACTCGATATCTC
1 GTTCAGGAGCTTGGGAAGACTCGATATCTC
*
34125494 GTTCAGGATCTTGGGA
1 GTTCAGGAGCTTGGGA
34125510 TTGAGAAGAC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.22, C:0.16, G:0.32, T:0.30
Consensus pattern (30 bp):
GTTCAGGAGCTTGGGAAGACTCGATATCTC
Found at i:34125577 original size:36 final size:36
Alignment explanation
Indices: 34125478--34125577 Score: 105
Period size: 36 Copynumber: 2.8 Consensus size: 36
34125468 AGGAGCTTGG
* * *
34125478 GAAGA-CTCGATATCTCGTTCAGGATCTTGGGATTGA
1 GAAGACCT-GATATCTCATTCAGGAGCTTAGGATTGA
** *
34125514 GAAGACCCAATAT-TGCATTTAGGAGCTTAGGATTGA
1 GAAGACCTGATATCT-CATTCAGGAGCTTAGGATTGA
*
34125550 GAAGACCTGATATCTCATTCAGAAGCTT
1 GAAGACCTGATATCTCATTCAGGAGCTT
34125578 GGGAAGATCC
Statistics
Matches: 51, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
35 1 0.02
36 48 0.94
37 2 0.04
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (36 bp):
GAAGACCTGATATCTCATTCAGGAGCTTAGGATTGA
Found at i:34127476 original size:21 final size:20
Alignment explanation
Indices: 34127413--34127476 Score: 92
Period size: 21 Copynumber: 3.1 Consensus size: 20
34127403 CCTGATCAGT
34127413 ATACGACACATAAGTGCCTG
1 ATACGACACATAAGTGCCTG
* *
34127433 AAACGACACATGAGGTGCCTG
1 ATACGACACAT-AAGTGCCTG
34127454 ATACGACACATAAAGTGCCTG
1 ATACGACACAT-AAGTGCCTG
34127475 AT
1 AT
34127477 CGGCAAAGTC
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
20 10 0.26
21 28 0.74
ACGTcount: A:0.36, C:0.23, G:0.22, T:0.19
Consensus pattern (20 bp):
ATACGACACATAAGTGCCTG
Found at i:34127945 original size:8 final size:8
Alignment explanation
Indices: 34127934--34127958 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
34127924 TCCTTTTCTT
34127934 TTTCTTTC
1 TTTCTTTC
34127942 TTTCTTTC
1 TTTCTTTC
34127950 TTTCTTTC
1 TTTCTTTC
34127958 T
1 T
34127959 CCCCTGTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTCTTTC
Found at i:34128184 original size:5 final size:5
Alignment explanation
Indices: 34128176--34128236 Score: 67
Period size: 5 Copynumber: 12.6 Consensus size: 5
34128166 ATTTTACATG
*
34128176 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATATTTT ATAAT -TAA- ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA--AT ATAAT ATAAT ATAAT
34128226 AT-AT -TAAT ATA
1 ATAAT ATAAT ATA
34128237 TTTAAAACAT
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
3 1 0.02
4 10 0.21
5 33 0.69
7 4 0.08
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (5 bp):
ATAAT
Found at i:34129189 original size:21 final size:21
Alignment explanation
Indices: 34129128--34129237 Score: 87
Period size: 23 Copynumber: 5.1 Consensus size: 21
34129118 CCTGATCAGT
34129128 ATACGACACAT-AAGTGCCTA
1 ATACGACACATAAAGTGCCTA
* ** * * *
34129148 AAACGACACACGAGGTACCTG
1 ATACGACACATAAAGTGCCTA
34129169 ATACGACACATAAAGTGCCTGA
1 ATACGACACATAAAGTGCCT-A
* * **
34129191 GATATGACACATAAATTTTCTA
1 -ATACGACACATAAAGTGCCTA
34129213 ATGTACGACACATAAAGTGCCTA
1 A--TACGACACATAAAGTGCCTA
34129236 AT
1 AT
34129238 CGGCAAAGCC
Statistics
Matches: 66, Mismatches: 19, Indels: 9
0.70 0.20 0.10
Matches are distributed among these distances:
20 9 0.14
21 23 0.35
22 1 0.02
23 33 0.50
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.22
Consensus pattern (21 bp):
ATACGACACATAAAGTGCCTA
Found at i:34129939 original size:5 final size:5
Alignment explanation
Indices: 34129931--34129983 Score: 97
Period size: 5 Copynumber: 10.6 Consensus size: 5
34129921 ATTTTACATG
*
34129931 ATAAT ATAAT GTAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
34129981 ATA
1 ATA
34129984 TAATTAAATA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 46 1.00
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:34129994 original size:15 final size:17
Alignment explanation
Indices: 34129934--34130006 Score: 86
Period size: 15 Copynumber: 4.6 Consensus size: 17
34129924 TTACATGATA
*
34129934 ATATAATGTAATAT-A-
1 ATATAATATAATATAAT
34129949 ATATAATATAATAT-A-
1 ATATAATATAATATAAT
34129964 ATATAATATAATATAAT
1 ATATAATATAATATAAT
34129981 ATATAAT-TAA-ATAAT
1 ATATAATATAATATAAT
34129996 ATATTAATATA
1 ATA-TAATATA
34130007 TTTAAAACAT
Statistics
Matches: 53, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
15 36 0.68
16 8 0.15
17 9 0.17
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (17 bp):
ATATAATATAATATAAT
Found at i:34133766 original size:43 final size:41
Alignment explanation
Indices: 34133719--34133823 Score: 131
Period size: 43 Copynumber: 2.5 Consensus size: 41
34133709 TGTGATTTCA
34133719 TGTAAGACCATGTCTGGGACATTGACATCGAAGTGA-GAGAACG
1 TGTAAGACCATGTCTGGGACATTGACATCGAA-T-ATGAG-ACG
* * * *
34133762 TGTAAGACCATGTTTGGGACATTGGCATCGTATATGAGTCG
1 TGTAAGACCATGTCTGGGACATTGACATCGAATATGAGACG
*
34133803 TATAAGACCATGTCTGGGACA
1 TGTAAGACCATGTCTGGGACA
34133824 GTGGCATCAA
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
41 22 0.40
42 4 0.07
43 29 0.53
ACGTcount: A:0.30, C:0.16, G:0.29, T:0.26
Consensus pattern (41 bp):
TGTAAGACCATGTCTGGGACATTGACATCGAATATGAGACG
Found at i:34133821 original size:41 final size:43
Alignment explanation
Indices: 34133721--34133831 Score: 138
Period size: 41 Copynumber: 2.6 Consensus size: 43
34133711 TGATTTCATG
* *
34133721 TAAGACCATGTCTGGGACATTGACATCGAAGTGAGAGAACGTG
1 TAAGACCATGTCTGGGACATTGGCATCGAAGTGAGAGAACGTA
* * *
34133764 TAAGACCATGTTTGGGACATTGGCATCGTA-T-ATGAG-TCGTA
1 TAAGACCATGTCTGGGACATTGGCATCGAAGTGA-GAGAACGTA
*
34133805 TAAGACCATGTCTGGGACAGTGGCATC
1 TAAGACCATGTCTGGGACATTGGCATC
34133832 AAAATGTGTT
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
41 29 0.48
42 4 0.07
43 27 0.45
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.25
Consensus pattern (43 bp):
TAAGACCATGTCTGGGACATTGGCATCGAAGTGAGAGAACGTA
Found at i:34140669 original size:36 final size:35
Alignment explanation
Indices: 34140542--34140658 Score: 162
Period size: 35 Copynumber: 3.3 Consensus size: 35
34140532 ACTCTTTCTT
* *
34140542 TTGGTGTGTTTCGGTTGGACTAGCTCTTACGAGCA
1 TTGGTGTGTTTCGGATGGATTAGCTCTTACGAGCA
* * *
34140577 TTGGTGTGTTTCAGAGGGATTAGCTCTAACGAGCA
1 TTGGTGTGTTTCGGATGGATTAGCTCTTACGAGCA
* *
34140612 TTGGTGTGTTTCGGATGGATTGGCTCTTATGAGCA
1 TTGGTGTGTTTCGGATGGATTAGCTCTTACGAGCA
34140647 TTTGGTGTGTTT
1 -TTGGTGTGTTT
34140659 TCGTTGGATT
Statistics
Matches: 71, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
35 60 0.85
36 11 0.15
ACGTcount: A:0.15, C:0.13, G:0.32, T:0.39
Consensus pattern (35 bp):
TTGGTGTGTTTCGGATGGATTAGCTCTTACGAGCA
Found at i:34143975 original size:12 final size:12
Alignment explanation
Indices: 34143954--34143982 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
34143944 CCGCGTTGTA
34143954 TTCC-ATAAAAT
1 TTCCAATAAAAT
34143965 TTCCAATAAAAT
1 TTCCAATAAAAT
34143977 TTCCAA
1 TTCCAA
34143983 ATTGGCGTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.34
Consensus pattern (12 bp):
TTCCAATAAAAT
Done.