Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 118 of 187
Found at i:35534253 original size:19 final size:19
Alignment explanation
Indices: 35534229--35534269 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
35534219 TCAGAAAAGT
35534229 GGATGTTTGCTATGCAAGA
1 GGATGTTTGCTATGCAAGA
35534248 GGATGTTTGCTATGCAAGA
1 GGATGTTTGCTATGCAAGA
35534267 GGA
1 GGA
35534270 GATGGAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.27, C:0.10, G:0.34, T:0.29
Consensus pattern (19 bp):
GGATGTTTGCTATGCAAGA
Found at i:35536893 original size:18 final size:18
Alignment explanation
Indices: 35536862--35536914 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
35536852 TCATCAGTCG
* *
35536862 CATCTTTTTTCTCATCTA
1 CATCTTCTTCCTCATCTA
* **
35536880 CATCTTCTTCCTCAGCCG
1 CATCTTCTTCCTCATCTA
*
35536898 CATATTCTTCCTCATCT
1 CATCTTCTTCCTCATCT
35536915 GCGCCTTCAT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.15, C:0.36, G:0.04, T:0.45
Consensus pattern (18 bp):
CATCTTCTTCCTCATCTA
Found at i:35557981 original size:13 final size:13
Alignment explanation
Indices: 35557963--35557987 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35557953 GAATTAATAT
35557963 GTGTGAAAATTTC
1 GTGTGAAAATTTC
35557976 GTGTGAAAATTT
1 GTGTGAAAATTT
35557988 TATCGTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:35559145 original size:43 final size:42
Alignment explanation
Indices: 35559098--35559253 Score: 136
Period size: 43 Copynumber: 3.6 Consensus size: 42
35559088 TCCGATATGT
* *
35559098 GATTTCGTGTAAGACCACGTCTGGGACATTGGCCTCGATTTGA
1 GATTTCATGTAAGACCACGTCTGGGACATTGGCATCGATTT-A
* * * * * *
35559141 GATTTACGTGTAAGATCATGTCTAGGACATCGGCATCG-TATA
1 GATTT-CATGTAAGACCACGTCTGGGACATTGGCATCGATTTA
* * * *
35559183 CGATTTCATGTAAGACC-CTGTCTGGGATAGTGGCATCAATATTT
1 -GATTTCATGTAAGACCAC-GTCTGGGACATTGGCATCGAT-TTA
*
35559227 GATTACATGTAAGACCACGTCTGGGAC
1 GATTTCATGTAAGACCACGTCTGGGAC
35559254 GCTGGCATTG
Statistics
Matches: 89, Mismatches: 18, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
42 24 0.27
43 36 0.40
44 29 0.33
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (42 bp):
GATTTCATGTAAGACCACGTCTGGGACATTGGCATCGATTTA
Found at i:35562058 original size:18 final size:18
Alignment explanation
Indices: 35562035--35562073 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
35562025 AATGCAGAGT
35562035 GATAGTTTTGAAAATTTC
1 GATAGTTTTGAAAATTTC
35562053 GATAGTTTTGAAAATTTC
1 GATAGTTTTGAAAATTTC
35562071 GAT
1 GAT
35562074 CCCTCATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.44
Consensus pattern (18 bp):
GATAGTTTTGAAAATTTC
Found at i:35562858 original size:36 final size:35
Alignment explanation
Indices: 35562817--35562968 Score: 227
Period size: 36 Copynumber: 4.3 Consensus size: 35
35562807 ATCCACAGTT
* *
35562817 TTATGTTAGTTATGATATGATATATATTTGTGTAAG
1 TTATGTAAGTTATGATATGATATATATTTATGT-AG
35562853 TTATGTAAGTTATGATATGATATATATTTATGTA-
1 TTATGTAAGTTATGATATGATATATATTTATGTAG
*
35562887 TTATGTAAGTTATGATATGGTATATATTTATGTGAG
1 TTATGTAAGTTATGATATGATATATATTTATGT-AG
* *
35562923 CTATGTAAGTTATGATATGATATATATTTATATA-
1 TTATGTAAGTTATGATATGATATATATTTATGTAG
35562957 TTATGTAAGTTA
1 TTATGTAAGTTA
35562969 AGTAAGTTAT
Statistics
Matches: 107, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
34 43 0.40
35 3 0.03
36 61 0.57
ACGTcount: A:0.34, C:0.01, G:0.17, T:0.49
Consensus pattern (35 bp):
TTATGTAAGTTATGATATGATATATATTTATGTAG
Found at i:35562859 original size:9 final size:9
Alignment explanation
Indices: 35562847--35562988 Score: 55
Period size: 9 Copynumber: 16.2 Consensus size: 9
35562837 TATATATTTG
35562847 TGTAAGTTA
1 TGTAAGTTA
35562856 TGTAAGTTA
1 TGTAAGTTA
* *
35562865 TGATATGATA
1 TG-TAAGTTA
* *
35562875 TAT-ATTTA
1 TGTAAGTTA
35562883 TGT-A-TTA
1 TGTAAGTTA
35562890 TGTAAGTTA
1 TGTAAGTTA
* *
35562899 TGATATGGTA
1 TG-TAAGTTA
* *
35562909 TAT-ATTTA
1 TGTAAGTTA
* *
35562917 TGTGAGCTA
1 TGTAAGTTA
35562926 TGTAAGTTA
1 TGTAAGTTA
* *
35562935 TGATATGATA
1 TG-TAAGTTA
* *
35562945 TAT-ATTTA
1 TGTAAGTTA
*
35562953 TAT-A-TTA
1 TGTAAGTTA
35562960 TGTAAGTTA
1 TGTAAGTTA
*
35562969 AGTAAGTTA
1 TGTAAGTTA
*
35562978 TATAAGTTA
1 TGTAAGTTA
35562987 TG
1 TG
35562989 ATCCAAAGGT
Statistics
Matches: 96, Mismatches: 29, Indels: 16
0.68 0.21 0.11
Matches are distributed among these distances:
7 11 0.11
8 17 0.18
9 50 0.52
10 18 0.19
ACGTcount: A:0.35, C:0.01, G:0.18, T:0.46
Consensus pattern (9 bp):
TGTAAGTTA
Found at i:35562930 original size:70 final size:70
Alignment explanation
Indices: 35562817--35562968 Score: 250
Period size: 70 Copynumber: 2.2 Consensus size: 70
35562807 ATCCACAGTT
* * *
35562817 TTATGTTAGTTATGATATGATATATATTTGTGTAAGTTATGTAAGTTATGATATGATATATATTT
1 TTATGTAAGTTATGATATGATATATATTTATGTAAGCTATGTAAGTTATGATATGATATATATTT
*
35562882 ATGTA
66 ATATA
* *
35562887 TTATGTAAGTTATGATATGGTATATATTTATGTGAGCTATGTAAGTTATGATATGATATATATTT
1 TTATGTAAGTTATGATATGATATATATTTATGTAAGCTATGTAAGTTATGATATGATATATATTT
35562952 ATATA
66 ATATA
35562957 TTATGTAAGTTA
1 TTATGTAAGTTA
35562969 AGTAAGTTAT
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
70 76 1.00
ACGTcount: A:0.34, C:0.01, G:0.17, T:0.49
Consensus pattern (70 bp):
TTATGTAAGTTATGATATGATATATATTTATGTAAGCTATGTAAGTTATGATATGATATATATTT
ATATA
Found at i:35562988 original size:70 final size:70
Alignment explanation
Indices: 35562817--35562988 Score: 211
Period size: 70 Copynumber: 2.5 Consensus size: 70
35562807 ATCCACAGTT
* * * * * * * *
35562817 TTATGTTAGTTATGATATGATATATATTTGTGTAAGTTATGTAAGTTATGATATGATATATATTT
1 TTATGTAAGTTAAGATAAGGTATATAGTTATGTGAGCTATGTAAGTTATGATATGATATATATTT
*
35562882 ATGTA
66 ATATA
* * *
35562887 TTATGTAAGTTATGATATGGTATATATTTATGTGAGCTATGTAAGTTATGATATGATATATATTT
1 TTATGTAAGTTAAGATAAGGTATATAGTTATGTGAGCTATGTAAGTTATGATATGATATATATTT
35562952 ATATA
66 ATATA
*
35562957 TTATGTAAGTTAAG-TAAGTTATATAAGTTATG
1 TTATGTAAGTTAAGATAAGGTATAT-AGTTATG
35562989 ATCCAAAGGT
Statistics
Matches: 91, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
69 8 0.09
70 83 0.91
ACGTcount: A:0.34, C:0.01, G:0.17, T:0.48
Consensus pattern (70 bp):
TTATGTAAGTTAAGATAAGGTATATAGTTATGTGAGCTATGTAAGTTATGATATGATATATATTT
ATATA
Found at i:35563096 original size:13 final size:13
Alignment explanation
Indices: 35563078--35563104 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
35563068 TGATTATCAT
35563078 CTTTAAATTTTAA
1 CTTTAAATTTTAA
35563091 CTTTAAATTTTAA
1 CTTTAAATTTTAA
35563104 C
1 C
35563105 CCTTTAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (13 bp):
CTTTAAATTTTAA
Found at i:35563649 original size:19 final size:20
Alignment explanation
Indices: 35563622--35563659 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
35563612 TATCTTAAAT
35563622 TTTAAAATAAAAA-TAAAAA
1 TTTAAAATAAAAACTAAAAA
*
35563641 TTTAGAATAAAAACTAAAA
1 TTTAAAATAAAAACTAAAA
35563660 TAAATAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (20 bp):
TTTAAAATAAAAACTAAAAA
Found at i:35563660 original size:19 final size:18
Alignment explanation
Indices: 35563617--35563673 Score: 53
Period size: 19 Copynumber: 3.1 Consensus size: 18
35563607 CAAGTTATCT
*
35563617 TAAATTTTAAAATAAAAA
1 TAAAATTTAAAATAAAAA
*
35563635 TAAAAATTTAGAATAAAAA
1 T-AAAATTTAAAATAAAAA
*
35563654 CTAAAA-TAAATAATAAAAA
1 -TAAAATTTAA-AATAAAAA
35563673 T
1 T
35563674 TGGATTAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
18 4 0.12
19 27 0.84
20 1 0.03
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (18 bp):
TAAAATTTAAAATAAAAA
Found at i:35564142 original size:72 final size:72
Alignment explanation
Indices: 35564048--35564276 Score: 237
Period size: 72 Copynumber: 3.2 Consensus size: 72
35564038 ATAACAGAAT
* * *
35564048 AAATGGTTCTACTTAATATCAAAACTCAATAAGTTGAACTAAACTAACCTTTTTAAAAATTCATA
1 AAATGGTTTTACTTAATATCAAAACTCAATAAATTGAACTAAATTAACCTTTTTAAAAATTCATA
*
35564113 ATTGAAC
66 ATTAAAC
* * ** ** * * *
35564120 GAATGTTTTTACTTAATATCAAATTTCAATAAATCAAACTAAATTAAGC-TTCTGAAAATGT-AT
1 AAATGGTTTTACTTAATATCAAAACTCAATAAATTGAACTAAATTAACCTTTTTAAAAAT-TCAT
* *
35564183 AACTAAAT
65 AATTAAAC
* * **
35564191 AAATGGTTTCACTTAATATCAAAACTTAATAAATTGAACTAAATTAACCTTTTTAAAAACACATA
1 AAATGGTTTTACTTAATATCAAAACTCAATAAATTGAACTAAATTAACCTTTTTAAAAATTCATA
*
35564256 ATTAAAT
66 ATTAAAC
* *
35564263 AAACGATTTTACTT
1 AAATGGTTTTACTT
35564277 GATAATTAAT
Statistics
Matches: 122, Mismatches: 32, Indels: 6
0.76 0.20 0.04
Matches are distributed among these distances:
71 55 0.45
72 67 0.55
ACGTcount: A:0.45, C:0.13, G:0.06, T:0.35
Consensus pattern (72 bp):
AAATGGTTTTACTTAATATCAAAACTCAATAAATTGAACTAAATTAACCTTTTTAAAAATTCATA
ATTAAAC
Found at i:35564222 original size:71 final size:72
Alignment explanation
Indices: 35564035--35564249 Score: 215
Period size: 71 Copynumber: 3.0 Consensus size: 72
35564025 CTTTGTACTT
* * *
35564035 TGTATAAC-AGAATAAATGG-TTCTACTTAATATCAAAACTCAATAAGTTGAACTAAACTAACCT
1 TGTATAACTA-AATAAATGGTTTC-ACTTAATATCAAAACTTAATAAATTGAACTAAATTAACCT
*
35564098 TTTTAAAAA
64 TTCTAAAAA
* * ** * * * ** *
35564107 T-TCATAATTGAACGAATGTTTTTACTTAATATC-AAATTTCAATAAATCAAACTAAATTAAGC-
1 TGT-ATAACTAAATAAATGGTTTCACTTAATATCAAAACTT-AATAAATTGAACTAAATTAACCT
*
35564169 TTCTGAAAA
64 TTCTAAAAA
35564178 TGTATAACTAAATAAATGGTTTCACTTAATATCAAAACTTAATAAATTGAACTAAATTAACCTTT
1 TGTATAACTAAATAAATGGTTTCACTTAATATCAAAACTTAATAAATTGAACTAAATTAACCTTT
*
35564243 TTAAAAA
66 CTAAAAA
35564250 CACATAATTA
Statistics
Matches: 109, Mismatches: 27, Indels: 14
0.73 0.18 0.09
Matches are distributed among these distances:
71 56 0.51
72 51 0.47
73 2 0.02
ACGTcount: A:0.46, C:0.13, G:0.07, T:0.35
Consensus pattern (72 bp):
TGTATAACTAAATAAATGGTTTCACTTAATATCAAAACTTAATAAATTGAACTAAATTAACCTTT
CTAAAAA
Found at i:35567280 original size:27 final size:27
Alignment explanation
Indices: 35567241--35567307 Score: 98
Period size: 27 Copynumber: 2.5 Consensus size: 27
35567231 GTCGACGGCG
* *
35567241 ATGCAGCAAAGGGGACAATTGACAGTA
1 ATGCAGCAGAGGGGACAATCGACAGTA
* *
35567268 ATGCAGCAGAGGGGACAATCGACGGTG
1 ATGCAGCAGAGGGGACAATCGACAGTA
35567295 ATGCAGCAGAGGG
1 ATGCAGCAGAGGG
35567308 TCGGGGAAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.34, C:0.16, G:0.37, T:0.12
Consensus pattern (27 bp):
ATGCAGCAGAGGGGACAATCGACAGTA
Found at i:35567553 original size:41 final size:40
Alignment explanation
Indices: 35567463--35567556 Score: 116
Period size: 41 Copynumber: 2.3 Consensus size: 40
35567453 AAATGATACT
* *
35567463 TTGCAGCGTTTTTCTCATAGCGCCGCTAATGCTTGACCTT
1 TTGCAGCGTTTTTCTCATAACGCCGCTAATGCTTGACCTA
* * * *
35567503 TTGCAGCGTTTTTCTCATAAACGCCGTTACTGTTTTACCTA
1 TTGCAGCGTTTTTCTCAT-AACGCCGCTAATGCTTGACCTA
*
35567544 TTGCGGCGTTTTT
1 TTGCAGCGTTTTT
35567557 TGTTAGCGCC
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
40 18 0.39
41 28 0.61
ACGTcount: A:0.15, C:0.24, G:0.19, T:0.41
Consensus pattern (40 bp):
TTGCAGCGTTTTTCTCATAACGCCGCTAATGCTTGACCTA
Found at i:35581231 original size:17 final size:17
Alignment explanation
Indices: 35581209--35581272 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
35581199 AATCTTAGAG
35581209 TTCTAATTGTATACAGC
1 TTCTAATTGTATACAGC
* *
35581226 TTCTAATTGTGT-CTAAGAG
1 TTCTAATTGTATAC--AG-C
*
35581245 TTCTAATTGTATACAAC
1 TTCTAATTGTATACAGC
*
35581262 TTTTAATTGTA
1 TTCTAATTGTA
35581273 GCCTTTGATG
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
16 1 0.03
17 21 0.57
18 3 0.08
19 11 0.30
20 1 0.03
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.45
Consensus pattern (17 bp):
TTCTAATTGTATACAGC
Found at i:35581552 original size:47 final size:48
Alignment explanation
Indices: 35581476--35581569 Score: 163
Period size: 47 Copynumber: 2.0 Consensus size: 48
35581466 TGAGGGAATT
35581476 CTGTTGAATCCTTTATCATTGCAAGTTAGGCCGACTTAGGCGTTTTTG
1 CTGTTGAATCCTTTATCATTGCAAGTTAGGCCGACTTAGGCGTTTTTG
* *
35581524 CTGTTGAATCCTTT-TCATTGCGAGTTAGGCTGACTTAGGCGTTTTT
1 CTGTTGAATCCTTTATCATTGCAAGTTAGGCCGACTTAGGCGTTTTT
35581570 AAGCAAAGAA
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
47 30 0.68
48 14 0.32
ACGTcount: A:0.17, C:0.18, G:0.23, T:0.41
Consensus pattern (48 bp):
CTGTTGAATCCTTTATCATTGCAAGTTAGGCCGACTTAGGCGTTTTTG
Found at i:35583144 original size:42 final size:42
Alignment explanation
Indices: 35583085--35583168 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
35583075 TTGGACTAAG
35583085 CTTCCTAGATCAGGTTAATGCTCTTATTGCCCCGTCGAGCAA
1 CTTCCTAGATCAGGTTAATGCTCTTATTGCCCCGTCGAGCAA
35583127 CTTCCTAGATCAGGTTAATGCTCTTATTGCCCCGTCGAGCAA
1 CTTCCTAGATCAGGTTAATGCTCTTATTGCCCCGTCGAGCAA
35583169 TTACATAGTG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.21, C:0.29, G:0.19, T:0.31
Consensus pattern (42 bp):
CTTCCTAGATCAGGTTAATGCTCTTATTGCCCCGTCGAGCAA
Found at i:35586731 original size:47 final size:48
Alignment explanation
Indices: 35586647--35586740 Score: 136
Period size: 47 Copynumber: 2.0 Consensus size: 48
35586637 TGAGGGAATT
* *
35586647 CTGTTGAATCCTTTATCATTGCAAGTTAGGCCGACTTAGGCATTTTTG
1 CTGTTGAATCCTTTATCATTGCAAGTTAGGACAACTTAGGCATTTTTG
* * *
35586695 CTGTTGAATCCTTT-TCATTGCGAGTTAGGATAACTTAGGCGTTTTT
1 CTGTTGAATCCTTTATCATTGCAAGTTAGGACAACTTAGGCATTTTT
35586741 AAGGAAAGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
47 27 0.66
48 14 0.34
ACGTcount: A:0.20, C:0.17, G:0.21, T:0.41
Consensus pattern (48 bp):
CTGTTGAATCCTTTATCATTGCAAGTTAGGACAACTTAGGCATTTTTG
Found at i:35589347 original size:122 final size:123
Alignment explanation
Indices: 35589107--35589453 Score: 511
Period size: 122 Copynumber: 2.8 Consensus size: 123
35589097 TTATTTAGAG
*
35589107 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTATACCAGGATGCTATTTGAGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAG-AGAAATTGTG
*
35589172 AAA-TCGCGCCCTCGTGGACGCGGTTTGGCTACAGTAGGTCATGTAAGAAATAATCTTT
65 AAATTCGCGCCCTCGTGGACGCGATTTGGCTACAGTAGGTCATGTAAGAAATAATCTTT
*
35589230 TTGACGTTTCTGAGTAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAGAAATTGTGA
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAGAAATTGTGA
* * * * *
35589295 AATTC-TGTCCTCGTGGACGCGATTTTGCTACAGTTGGTCATGTAAGAAATAATTTTT
66 AATTCGCGCCCTCGTGGACGCGATTTGGCTACAGTAGGTCATGTAAGAAATAATCTTT
* * *
35589352 TTGAAGTTTCTGAGCAAATAGTATAAAATCGCTTCTCCCAGGATGCTATTTGAAAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTG-AGAGAAATTGTG
* * * * *
35589417 AAA-TCGCACCCTTGTGGACGCGGTTTTGCTGCAGTAG
65 AAATTCGCGCCCTCGTGGACGCGATTTGGCTACAGTAG
35589454 CAAGTTTGGG
Statistics
Matches: 202, Mismatches: 19, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
122 110 0.54
123 92 0.46
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (123 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAGAAATTGTGA
AATTCGCGCCCTCGTGGACGCGATTTGGCTACAGTAGGTCATGTAAGAAATAATCTTT
Found at i:35592543 original size:10 final size:10
Alignment explanation
Indices: 35592528--35592552 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
35592518 CAAATCTAAC
35592528 ATTATGTAAA
1 ATTATGTAAA
35592538 ATTATGTAAA
1 ATTATGTAAA
35592548 ATTAT
1 ATTAT
35592553 TAAGTCCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (10 bp):
ATTATGTAAA
Found at i:35592600 original size:55 final size:55
Alignment explanation
Indices: 35592536--35592716 Score: 326
Period size: 55 Copynumber: 3.3 Consensus size: 55
35592526 ACATTATGTA
35592536 AAATTATGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
1 AAATTATGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
* * *
35592591 AACTTATGTAAAATTATTTAGTCTAAAAATTGTGTTAATGGTTAGTAAAATTATC
1 AAATTATGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
*
35592646 AAATTATGTAAATTTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
1 AAATTATGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
35592701 AAATTATGTAAAATTA
1 AAATTATGTAAAATTA
35592717 GGTTAGGGTT
Statistics
Matches: 118, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 118 1.00
ACGTcount: A:0.43, C:0.05, G:0.12, T:0.40
Consensus pattern (55 bp):
AAATTATGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATC
Found at i:35592842 original size:117 final size:116
Alignment explanation
Indices: 35592711--35592950 Score: 421
Period size: 117 Copynumber: 2.1 Consensus size: 116
35592701 AAATTATGTA
*
35592711 AAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTT-GGGTTTAGGGTTTTTAATTAAATTA
1 AAATTAGGTTAGGGTTAGAGTTTTTAATTAAATTAGGTTAGGG-TTAGGGTTTTTAATTAAATTA
*
35592775 GGTTAGTGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGGTTTTTAATT
65 GGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGG-TTAGGGTTTTTAATT
*
35592828 AAATTAGGTTAGGGTTAGAGTTTTTAATTAAATTGGGTTAGGGTTAGGGTTTTTAATTAAATTAG
1 AAATTAGGTTAGGGTTAGAGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAG
35592893 GTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATT
66 GTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATT
35592944 -AATTAGG
1 AAATTAGG
35592951 GTTTTTAATT
Statistics
Matches: 119, Mismatches: 3, Indels: 4
0.94 0.02 0.03
Matches are distributed among these distances:
115 7 0.06
116 15 0.13
117 94 0.79
118 3 0.03
ACGTcount: A:0.28, C:0.00, G:0.27, T:0.45
Consensus pattern (116 bp):
AAATTAGGTTAGGGTTAGAGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAG
GTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATT
Found at i:35592951 original size:17 final size:18
Alignment explanation
Indices: 35592929--35592974 Score: 78
Period size: 17 Copynumber: 2.7 Consensus size: 18
35592919 TAGGTTAGGG
35592929 TTAGGGTTTTTAATT-AA
1 TTAGGGTTTTTAATTAAA
35592946 TTAGGGTTTTTAATTAAA
1 TTAGGGTTTTTAATTAAA
35592964 TTA-GGTTTTTA
1 TTAGGGTTTTTA
35592975 TTGCATCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 23 0.82
18 5 0.18
ACGTcount: A:0.28, C:0.00, G:0.17, T:0.54
Consensus pattern (18 bp):
TTAGGGTTTTTAATTAAA
Found at i:35592953 original size:29 final size:29
Alignment explanation
Indices: 35592711--35592950 Score: 421
Period size: 29 Copynumber: 8.3 Consensus size: 29
35592701 AAATTATGTA
35592711 AAATTAGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
35592740 AAATTAGGTT-GGGTTTAGGGTTTTTAATT
1 AAATTAGGTTAGGG-TTAGGGTTTTTAATT
*
35592769 AAATTAGGTTAGTGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
35592798 AAATTAGGTTAGGGTTTAGGGTTTTTAATT
1 AAATTAGGTTAGGG-TTAGGGTTTTTAATT
*
35592828 AAATTAGGTTAGGGTTAGAGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
*
35592857 AAATTGGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
35592886 AAATTAGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
35592915 AAATTAGGTTAGGGTTAGGGTTTTTAATT
1 AAATTAGGTTAGGGTTAGGGTTTTTAATT
35592944 -AATTAGG
1 AAATTAGG
35592951 GTTTTTAATT
Statistics
Matches: 202, Mismatches: 6, Indels: 7
0.94 0.03 0.03
Matches are distributed among these distances:
28 10 0.05
29 161 0.80
30 31 0.15
ACGTcount: A:0.28, C:0.00, G:0.27, T:0.45
Consensus pattern (29 bp):
AAATTAGGTTAGGGTTAGGGTTTTTAATT
Found at i:35593053 original size:36 final size:36
Alignment explanation
Indices: 35593013--35593127 Score: 92
Period size: 36 Copynumber: 3.2 Consensus size: 36
35593003 ATATCAAATA
*
35593013 ATATCAAAATAACTCGAAAAAATTTCTATGCCTATT
1 ATATCAAAATAACTCGAAAAAATTTCTATGCATATT
* **** * * *
35593049 ATATC-AAATAAACTTCTATTTTATTAC-AT-CAAATA
1 ATATCAAAAT-AAC-TCGAAAAAATTTCTATGCATATT
*
35593084 ATATCAAAATAACTCGAAAAAATTTCTATGCGTATT
1 ATATCAAAATAACTCGAAAAAATTTCTATGCATATT
*
35593120 ACATCAAA
1 ATATCAAA
35593128 TAAACTTCTA
Statistics
Matches: 55, Mismatches: 19, Indels: 10
0.65 0.23 0.12
Matches are distributed among these distances:
34 7 0.13
35 17 0.31
36 24 0.44
37 7 0.13
ACGTcount: A:0.46, C:0.16, G:0.04, T:0.34
Consensus pattern (36 bp):
ATATCAAAATAACTCGAAAAAATTTCTATGCATATT
Found at i:35593079 original size:25 final size:25
Alignment explanation
Indices: 35593045--35593155 Score: 83
Period size: 25 Copynumber: 4.6 Consensus size: 25
35593035 TTTCTATGCC
*
35593045 TATTATATCAAATAAACTTCTATTT
1 TATTACATCAAATAAACTTCTATTT
*
35593070 TATTACATCAAAT-AA-TATC-A--A
1 TATTACATCAAATAAACT-TCTATTT
* * * **
35593091 AATAAC-TCGAAA-AAATTTCTATGCG
1 TATTACATC-AAATAAACTTCTAT-TT
35593116 TATTACATCAAATAAACTTCTATTT
1 TATTACATCAAATAAACTTCTATTT
35593141 TATTACATCAAATAA
1 TATTACATCAAATAA
35593156 TAAATTTAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 20
0.69 0.10 0.21
Matches are distributed among these distances:
20 2 0.03
21 11 0.17
22 2 0.03
23 2 0.03
24 4 0.06
25 34 0.52
26 11 0.17
ACGTcount: A:0.45, C:0.14, G:0.03, T:0.38
Consensus pattern (25 bp):
TATTACATCAAATAAACTTCTATTT
Found at i:35593080 original size:71 final size:71
Alignment explanation
Indices: 35592973--35593157 Score: 325
Period size: 71 Copynumber: 2.6 Consensus size: 71
35592963 ATTAGGTTTT
* *
35592973 TATTGCATCAAATAGAACTTCTATTTTATTATATCAAATAATATCAAAATAACTCGAAAAAATTT
1 TATTACATCAAATA-AACTTCTATTTTATTACATCAAATAATATCAAAATAACTCGAAAAAATTT
35593038 CTATGCC
65 CTATGCC
*
35593045 TATTATATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCGAAAAAATTTC
1 TATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCGAAAAAATTTC
*
35593110 TATGCG
66 TATGCC
35593116 TATTACATCAAATAAACTTCTATTTTATTACATCAAATAATA
1 TATTACATCAAATAAACTTCTATTTTATTACATCAAATAATA
35593158 AATTTAAATA
Statistics
Matches: 108, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
71 96 0.89
72 12 0.11
ACGTcount: A:0.44, C:0.15, G:0.04, T:0.37
Consensus pattern (71 bp):
TATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCGAAAAAATTTC
TATGCC
Found at i:35593598 original size:18 final size:18
Alignment explanation
Indices: 35593554--35593599 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
35593544 GGATTCGGAA
* *
35593554 AGGATACATGTAAGGGTT
1 AGGATACATATAAGGGCT
*
35593572 AGGGTACATATAAGGGCT
1 AGGATACATATAAGGGCT
*
35593590 AGGAAACATA
1 AGGATACATA
35593600 CCTGGCATCA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.39, C:0.09, G:0.30, T:0.22
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:35595382 original size:31 final size:30
Alignment explanation
Indices: 35595346--35595411 Score: 105
Period size: 31 Copynumber: 2.2 Consensus size: 30
35595336 GCCATTGATG
35595346 AAAATATAAAAAAATATAAAATTATTTTTAA
1 AAAATATAAAAAAATATAAAATTA-TTTTAA
* *
35595377 AAAATATTAAAAAATATTAAATTATTTTAA
1 AAAATATAAAAAAATATAAAATTATTTTAA
35595407 AAAAT
1 AAAAT
35595412 GAAATTGAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
30 11 0.33
31 22 0.67
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (30 bp):
AAAATATAAAAAAATATAAAATTATTTTAA
Found at i:35595388 original size:10 final size:10
Alignment explanation
Indices: 35595346--35595411 Score: 53
Period size: 10 Copynumber: 6.5 Consensus size: 10
35595336 GCCATTGATG
*
35595346 AAAATATAAA
1 AAAATATTAA
35595356 AAAATA-TAA
1 AAAATATTAA
* *
35595365 AATTATTTTTAA
1 AA--AATATTAA
35595377 AAAATATTAA
1 AAAATATTAA
35595387 AAAATATTAA
1 AAAATATTAA
** *
35595397 ATTATTTTAA
1 AAAATATTAA
35595407 AAAAT
1 AAAAT
35595412 GAAATTGAGG
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
9 4 0.09
10 32 0.74
11 2 0.05
12 5 0.12
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
AAAATATTAA
Found at i:35595467 original size:29 final size:29
Alignment explanation
Indices: 35595435--35595523 Score: 75
Period size: 29 Copynumber: 3.3 Consensus size: 29
35595425 AATTGAAATT
35595435 AAATATGGATTTGAGAGAATTTTGGAAGG
1 AAATATGGATTTGAGAGAATTTTGGAAGG
* * **
35595464 AAAT-T-GA---GAG-GAA-ATTGAAATT
1 AAATATGGATTTGAGAGAATTTTGGAAGG
*
35595486 AAATATGGGTTTGAGAGAATTTTGGAAGG
1 AAATATGGATTTGAGAGAATTTTGGAAGG
*
35595515 AAATTTGGA
1 AAATATGGA
35595524 AGGAAATTGA
Statistics
Matches: 42, Mismatches: 11, Indels: 14
0.63 0.16 0.21
Matches are distributed among these distances:
22 9 0.21
23 4 0.10
24 4 0.10
27 5 0.12
28 4 0.10
29 16 0.38
ACGTcount: A:0.40, C:0.00, G:0.29, T:0.30
Consensus pattern (29 bp):
AAATATGGATTTGAGAGAATTTTGGAAGG
Found at i:35595468 original size:51 final size:51
Alignment explanation
Indices: 35595412--35595533 Score: 201
Period size: 51 Copynumber: 2.4 Consensus size: 51
35595402 TTTAAAAAAT
*
35595412 GAAATTGAGGGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
1 GAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
*
35595463 GAAATTGAGAGGAAATTGAAATTAAATATGGGTTTGAGAGAATTTTGGAAG
1 GAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
35595514 GAAATTTG-GAAGGAAATTGA
1 GAAA-TTGAG-AGGAAATTGA
35595534 GAGGATTAGA
Statistics
Matches: 67, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
51 54 0.81
52 13 0.19
ACGTcount: A:0.42, C:0.00, G:0.30, T:0.29
Consensus pattern (51 bp):
GAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
Found at i:35595523 original size:12 final size:12
Alignment explanation
Indices: 35595506--35595531 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
35595496 TTGAGAGAAT
35595506 TTTGGAAGGAAA
1 TTTGGAAGGAAA
35595518 TTTGGAAGGAAA
1 TTTGGAAGGAAA
35595530 TT
1 TT
35595532 GAGAGGATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (12 bp):
TTTGGAAGGAAA
Found at i:35597726 original size:2 final size:2
Alignment explanation
Indices: 35597719--35597746 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
35597709 AGATTTGTTT
35597719 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35597747 CTTACCTAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:35600706 original size:17 final size:18
Alignment explanation
Indices: 35600684--35600720 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
35600674 TTATTCTTTT
35600684 ATTCTTTCATCCA-AATC
1 ATTCTTTCATCCATAATC
*
35600701 ATTCTTTCATTCATAATC
1 ATTCTTTCATCCATAATC
35600719 AT
1 AT
35600721 ACTGTGCAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.30, C:0.24, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTCTTTCATCCATAATC
Found at i:35601451 original size:9 final size:9
Alignment explanation
Indices: 35601437--35601562 Score: 192
Period size: 9 Copynumber: 14.6 Consensus size: 9
35601427 GTTCAGACTC
*
35601437 AAAAATAAA
1 AAAAATCAA
35601446 AAAAATCAA
1 AAAAATCAA
35601455 AAAAATCAA
1 AAAAATCAA
35601464 AAAAATCAAA
1 AAAAATC-AA
35601474 AAAAATCAA
1 AAAAATCAA
35601483 AAAAATC-A
1 AAAAATCAA
35601491 AAAAATC-A
1 AAAAATCAA
35601499 AAAAATC-A
1 AAAAATCAA
35601507 AAAAATCAA
1 AAAAATCAA
35601516 AAAAATCAA
1 AAAAATCAA
35601525 AAAAATC-A
1 AAAAATCAA
35601533 AAAAATCAA
1 AAAAATCAA
35601542 AAAAATC--
1 AAAAATCAA
35601549 AAAAATCAA
1 AAAAATCAA
35601558 AAAAA
1 AAAAA
35601563 AAATCAAAGT
Statistics
Matches: 111, Mismatches: 1, Indels: 10
0.91 0.01 0.08
Matches are distributed among these distances:
7 7 0.06
8 32 0.29
9 63 0.57
10 9 0.08
ACGTcount: A:0.79, C:0.10, G:0.00, T:0.11
Consensus pattern (9 bp):
AAAAATCAA
Found at i:35601465 original size:17 final size:18
Alignment explanation
Indices: 35601437--35601562 Score: 192
Period size: 17 Copynumber: 7.3 Consensus size: 18
35601427 GTTCAGACTC
*
35601437 AAAAATAAAAAAAATCAA
1 AAAAATCAAAAAAATCAA
35601455 AAAAATCAAAAAAATCAAA
1 AAAAATCAAAAAAATC-AA
35601474 AAAAATCAAAAAAATC-A
1 AAAAATCAAAAAAATCAA
35601491 AAAAATC-AAAAAATC-A
1 AAAAATCAAAAAAATCAA
35601507 AAAAATCAAAAAAATCAA
1 AAAAATCAAAAAAATCAA
35601525 AAAAATC-AAAAAATCAA
1 AAAAATCAAAAAAATCAA
35601542 AAAAATC--AAAAATCAA
1 AAAAATCAAAAAAATCAA
35601558 AAAAA
1 AAAAA
35601563 AAATCAAAGT
Statistics
Matches: 104, Mismatches: 1, Indels: 8
0.92 0.01 0.07
Matches are distributed among these distances:
16 30 0.29
17 33 0.32
18 23 0.22
19 18 0.17
ACGTcount: A:0.79, C:0.10, G:0.00, T:0.11
Consensus pattern (18 bp):
AAAAATCAAAAAAATCAA
Found at i:35601577 original size:18 final size:19
Alignment explanation
Indices: 35601443--35601570 Score: 85
Period size: 19 Copynumber: 6.7 Consensus size: 19
35601433 ACTCAAAAAT
35601443 AAAAAAAATCAAAAA--AA
1 AAAAAAAATCAAAAATCAA
*
35601460 TCAAAAAAATCAAAAA--AA
1 -AAAAAAAATCAAAAATCAA
35601478 ATCAAAAAAATCAAAAAATCAAAA
1 A--AAAAAAATC-AAAAATC--AA
35601502 AATCAAAAAATCAAAAA--AA
1 AA--AAAAAATCAAAAATCAA
*
35601521 TCAAAAAAATCAAAAAATC--
1 -AAAAAAAATC-AAAAATCAA
35601540 -AAAAAAATCAAAAATCAA
1 AAAAAAAATCAAAAATCAA
35601558 AAAAAAAATCAAA
1 AAAAAAAATCAAA
35601571 GTCAAAATAG
Statistics
Matches: 91, Mismatches: 3, Indels: 31
0.73 0.02 0.25
Matches are distributed among these distances:
16 7 0.08
17 9 0.10
18 24 0.26
19 28 0.31
20 6 0.07
22 1 0.01
23 5 0.05
24 11 0.12
ACGTcount: A:0.78, C:0.11, G:0.00, T:0.11
Consensus pattern (19 bp):
AAAAAAAATCAAAAATCAA
Found at i:35601598 original size:21 final size:20
Alignment explanation
Indices: 35601574--35601625 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 20
35601564 AATCAAAGTC
35601574 AAAATAGGA-AAAAAGAAAAAG
1 AAAA-AGGAGAAAAAG-AAAAG
*
35601595 AAAAAAGAAGAAAAAGAAAAG
1 -AAAAAGGAGAAAAAGAAAAG
35601616 AAAAAGGAGA
1 AAAAAGGAGA
35601626 GGTCAAGGCG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 9 0.33
21 8 0.30
22 10 0.37
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (20 bp):
AAAAAGGAGAAAAAGAAAAG
Found at i:35601605 original size:16 final size:15
Alignment explanation
Indices: 35601582--35601619 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 15
35601572 TCAAAATAGG
35601582 AAAAAAGAAAAAGAA
1 AAAAAAGAAAAAGAA
35601597 AAAAGAAGAAAAAGAA
1 AAAA-AAGAAAAAGAA
35601613 AAGAAAA
1 AA-AAAA
35601620 AGGAGAGGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.19
16 15 0.71
17 2 0.10
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAAAGAA
Found at i:35601609 original size:11 final size:11
Alignment explanation
Indices: 35601583--35601621 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
35601573 CAAAATAGGA
35601583 AAAAAGAAAAAG
1 AAAAAG-AAAAG
*
35601595 AAAAA-AGAAG
1 AAAAAGAAAAG
35601605 AAAAAGAAAAG
1 AAAAAGAAAAG
35601616 AAAAAG
1 AAAAAG
35601622 GAGAGGTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 9 0.38
11 10 0.42
12 5 0.21
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:35602479 original size:9 final size:9
Alignment explanation
Indices: 35602467--35602499 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
35602457 AAAAAAAATG
35602467 ATGAAAAAA
1 ATGAAAAAA
35602476 ATG--AAAA
1 ATGAAAAAA
35602483 ATGAAAAAA
1 ATGAAAAAA
35602492 ATGAAAAA
1 ATGAAAAA
35602500 GTAAAAATGG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
7 7 0.32
9 15 0.68
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (9 bp):
ATGAAAAAA
Found at i:35602506 original size:16 final size:16
Alignment explanation
Indices: 35602467--35602499 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
35602457 AAAAAAAATG
35602467 ATGAAAAAAATGAAAA
1 ATGAAAAAAATGAAAA
35602483 ATGAAAAAAATGAAAA
1 ATGAAAAAAATGAAAA
35602499 A
1 A
35602500 GTAAAAATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (16 bp):
ATGAAAAAAATGAAAA
Found at i:35604507 original size:88 final size:88
Alignment explanation
Indices: 35604235--35605069 Score: 1365
Period size: 88 Copynumber: 9.5 Consensus size: 88
35604225 NNNNNNNNNN
*
35604235 GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGAAAGCGAAGCAGGTCGAAGACACAAACCTTGC
1 GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGC
35604300 CTCTCTCGGTTGTGATGGAGCTG
66 CTCTCTCGGTTGTGATGGAGCTG
* * *
35604323 GTTGAAGACAACAGATCTTGCCTTCCTGCATTGACAGTGAAGCA-GTCAAAGACACAAACCTTGC
1 GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGC
*
35604387 CTCCCTCGGTTGTGATGGAGCTG
66 CTCTCTCGGTTGTGATGGAGCTG
*
35604410 GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGATAGCGAAGCAGGTCGAAGACACAAACCTTGC
1 GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGC
*
35604475 CTCTCTCGGTTATGATGGAGCTG
66 CTCTCTCGGTTGTGATGGAGCTG
* *
35604498 GTTGAAGACAAAAGATCTTGCCTTCCTGCAGTGACAGTGAAGCAGGTCGAAGACACAAACCTTGC
1 GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGC
35604563 CTCTCTCGGTTGTGATGGAGCTG
66 CTCTCTCGGTTGTGATGGAGCTG
* * * *
35604586 GTTGAAGATAAAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGA-ACAAACATTTC
1 GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGC
35604650 CTCTCTCGGTTGTGATGGAGCTG
66 CTCTCTCGGTTGTGATGGAGCTG
* * *
35604673 GTTGAAGACAAAAGATCTTCCCTTCCTACTTTGACAGCGAAGCAGGTCGAAGACACAAACCTTGC
1 GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGC
35604738 CTCTCTCGGTTGTGATGGAGCTG
66 CTCTCTCGGTTGTGATGGAGCTG
* * *
35604761 GTTGAAGATAAAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGT
1 GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGC
35604826 CTCTCTCGGTTGTGATGGAGCTG
66 CTCTCTCGGTTGTGATGGAGCTG
*
35604849 GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGATACAAACCTTGC
1 GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGC
*
35604914 CTCTCTCGGTTGTGATGGAGCTT
66 CTCTCTCGGTTGTGATGGAGCTG
* * *
35604937 GTTGAAGA-AAACAGATCTTGTCTTCCTGCATTAACAGCGAAGCAGATCGAAGACACAAACCTTG
1 GTTGAAGACAAA-AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTG
35605001 CCTCTCTCGGTTGT-A-GCAGAGCTG
65 CCTCTCTCGGTTGTGATG--GAGCTG
* * *
35605025 GTTGAAGACAACAGATCTTCCCTTCCTGCATTGACAGCGGAGCAG
1 GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAG
35605070 ACTGAAGATA
Statistics
Matches: 692, Mismatches: 49, Indels: 12
0.92 0.07 0.02
Matches are distributed among these distances:
86 1 0.00
87 166 0.24
88 523 0.76
89 2 0.00
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (88 bp):
GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGC
CTCTCTCGGTTGTGATGGAGCTG
Found at i:35604714 original size:263 final size:264
Alignment explanation
Indices: 35604235--35605069 Score: 1365
Period size: 263 Copynumber: 3.2 Consensus size: 264
35604225 NNNNNNNNNN
*
35604235 GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGAAAGCGAAGCAGGTCGAAGACACAAACCTTGC
1 GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGC
* *
35604300 CTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAACAGATCTTGCCTTCCTGCATTGACAGTGAAG
66 CTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAG
* *
35604365 CA-GTCAAAGACACAAACCTTGCCTCCCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTT
131 CAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTT
* *
35604429 GCCTTCCTGCATTGATAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTATGATGGA
196 GCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTGTGATGGA
35604494 GCTG
261 GCTG
* *
35604498 GTTGAAGACAAAAGATCTTGCCTTCCTGCAGTGACAGTGAAGCAGGTCGAAGACACAAACCTTGC
1 GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGC
* *
35604563 CTCTCTCGGTTGTGATGGAGCTGGTTGAAGATAAAAGATCTTGCCTTCCTGTATTGACAGCGAAG
66 CTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAG
* *
35604628 CAGGTCGAAGA-ACAAACATTTCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTT
131 CAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTT
* * *
35604692 CCCTTCCTACTTTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTGTGATGGA
196 GCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTGTGATGGA
35604757 GCTG
261 GCTG
* * *
35604761 GTTGAAGATAAAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGT
1 GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGC
35604826 CTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAG
66 CTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAG
* *
35604891 CAGGTCGAAGATACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTTGTTGAAGA-AAACAGATCT
131 CAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAA-AGATCT
* * *
35604955 TGTCTTCCTGCATTAACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTCTCGGTTGT-A-GC
195 TGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTGTGATG-
35605018 AGAGCTG
259 -GAGCTG
* * *
35605025 GTTGAAGACAACAGATCTTCCCTTCCTGCATTGACAGCGGAGCAG
1 GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAG
35605070 ACTGAAGATA
Statistics
Matches: 530, Mismatches: 37, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
262 1 0.00
263 377 0.71
264 152 0.29
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (264 bp):
GTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGC
CTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAG
CAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTT
GCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTGTGATGGA
GCTG
Found at i:35606771 original size:3 final size:3
Alignment explanation
Indices: 35606765--35606806 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
35606755 TATTCAACTA
35606765 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
35606807 GTTGTTGTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:35606811 original size:3 final size:3
Alignment explanation
Indices: 35606805--35606838 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
35606795 ATTATTATTA
35606805 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
35606839 ATTTATTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:35606893 original size:2 final size:2
Alignment explanation
Indices: 35606886--35606923 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
35606876 TTAGATTTGT
35606886 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35606924 CTTACCTAGA
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):
TA
Found at i:35610540 original size:85 final size:85
Alignment explanation
Indices: 35610395--35610568 Score: 312
Period size: 85 Copynumber: 2.0 Consensus size: 85
35610385 TTGCACTCCT
35610395 GGTTTATCTTTGTTCTCACATTTTGTATATGCTTGCAGTGGCTTAAGATATATTTCTCCTATCTG
1 GGTTTATCTTTGTTCTCACATTTTGTATATGCTTGCAGTGGCTTAAGATATATTTCTCCTATCTG
35610460 CTGATTTCTTTATATTTTGC
66 CTGATTTCTTTATATTTTGC
* * *
35610480 GGTTTATCTTTGTTCTCACATTTTGTATATGCTTGCAGTGGGTTAATATATATTTTTCCTATCTG
1 GGTTTATCTTTGTTCTCACATTTTGTATATGCTTGCAGTGGCTTAAGATATATTTCTCCTATCTG
*
35610545 CTGATTTCTTTATGTTTTGC
66 CTGATTTCTTTATATTTTGC
35610565 GGTT
1 GGTT
35610569 CCCTATGGTC
Statistics
Matches: 85, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
85 85 1.00
ACGTcount: A:0.17, C:0.15, G:0.17, T:0.52
Consensus pattern (85 bp):
GGTTTATCTTTGTTCTCACATTTTGTATATGCTTGCAGTGGCTTAAGATATATTTCTCCTATCTG
CTGATTTCTTTATATTTTGC
Found at i:35612928 original size:17 final size:18
Alignment explanation
Indices: 35612908--35612954 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
35612898 ATATAAACTT
35612908 AAAATTCTAAAAA-CATA
1 AAAATTCTAAAAATCATA
* *
35612925 AAAAATCTAATAAATTATA
1 AAAATTCTAA-AAATCATA
*
35612944 AAAATTATAAA
1 AAAATTCTAAA
35612955 TTAGTAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 9 0.38
18 4 0.17
19 11 0.46
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (18 bp):
AAAATTCTAAAAATCATA
Found at i:35612985 original size:21 final size:21
Alignment explanation
Indices: 35612959--35613011 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
35612949 TATAAATTAG
*
35612959 TAAAAT-ATATTTAAAATTTTA
1 TAAAATCATA-TTAAAATTCTA
*
35612980 TAAAATCGTATTAAAATTCTA
1 TAAAATCATATTAAAATTCTA
35613001 TAAAAATCATA
1 T-AAAATCATA
35613012 AAAATTATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 17 0.63
22 10 0.37
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.40
Consensus pattern (21 bp):
TAAAATCATATTAAAATTCTA
Found at i:35613063 original size:10 final size:9
Alignment explanation
Indices: 35612908--35613071 Score: 75
Period size: 9 Copynumber: 17.4 Consensus size: 9
35612898 ATATAAACTT
*
35612908 AAAATTCTA
1 AAAATTATA
*
35612917 AAAA-CATA
1 AAAATTATA
* *
35612925 AAAAATCTA
1 AAAATTATA
35612934 ATAAATTATA
1 A-AAATTATA
35612944 AAAATTAT-
1 AAAATTATA
35612952 -AAATTAGT-
1 AAAATTA-TA
*
35612960 AAAATATATTT
1 AAAAT-TA-TA
*
35612971 AAAATTTTA
1 AAAATTATA
35612980 TAAAATCGTATTA
1 -AAAAT--TA-TA
*
35612993 AAATTCTATA
1 AAAAT-TATA
*
35613003 AAAATCATA
1 AAAATTATA
35613012 AAAATTATA
1 AAAATTATA
* *
35613021 AAAAGTATT
1 AAAATTATA
* * *
35613030 TAAAGTATT
1 AAAATTATA
35613039 AAAATTAATA
1 AAAATT-ATA
*
35613049 TAAATTTATA
1 -AAAATTATA
35613059 AAAATTATA
1 AAAATTATA
35613068 AAAA
1 AAAA
35613072 AAATCATAAA
Statistics
Matches: 120, Mismatches: 23, Indels: 24
0.72 0.14 0.14
Matches are distributed among these distances:
7 6 0.05
8 7 0.06
9 61 0.51
10 27 0.22
11 12 0.10
12 5 0.04
13 2 0.02
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (9 bp):
AAAATTATA
Found at i:35616284 original size:20 final size:22
Alignment explanation
Indices: 35616244--35616284 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
35616234 TCAGCAACCT
35616244 TTCTTCATTTGTTGGCTCTCTCA
1 TTCTTCATTTGTT-GCTCTCTCA
35616267 TTCTTCATTT-TT-CTCTCT
1 TTCTTCATTTGTTGCTCTCT
35616285 AAAACAAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
22 2 0.11
23 10 0.56
ACGTcount: A:0.07, C:0.27, G:0.07, T:0.59
Consensus pattern (22 bp):
TTCTTCATTTGTTGCTCTCTCA
Found at i:35619377 original size:84 final size:84
Alignment explanation
Indices: 35619236--35619406 Score: 324
Period size: 84 Copynumber: 2.0 Consensus size: 84
35619226 TGGGAAGAAT
*
35619236 GCAATATATGTCAAAGTCTGGAATTGAGCAGAGCTACCGGGAAAGTGTTAAACATGGACAAGAAA
1 GCAATATATGTCAAAGTCTGGAAATGAGCAGAGCTACCGGGAAAGTGTTAAACATGGACAAGAAA
35619301 TCCAAACCAGTTCTTTCAG
66 TCCAAACCAGTTCTTTCAG
35619320 GCAATATATGTCAAAGTCTGGAAATGAGCAGAGCTACCGGGAAAGTGTTAAACATGGACAAGAAA
1 GCAATATATGTCAAAGTCTGGAAATGAGCAGAGCTACCGGGAAAGTGTTAAACATGGACAAGAAA
*
35619385 TGCAAACCAGTTCTTTCAG
66 TCCAAACCAGTTCTTTCAG
35619404 GCA
1 GCA
35619407 TGGGGATGAT
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 85 1.00
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.22
Consensus pattern (84 bp):
GCAATATATGTCAAAGTCTGGAAATGAGCAGAGCTACCGGGAAAGTGTTAAACATGGACAAGAAA
TCCAAACCAGTTCTTTCAG
Found at i:35622237 original size:9 final size:9
Alignment explanation
Indices: 35622201--35622315 Score: 76
Period size: 9 Copynumber: 12.4 Consensus size: 9
35622191 ACATGTGGTA
35622201 AAAAATTAT
1 AAAAATTAT
35622210 AAAAA--AT
1 AAAAATTAT
*
35622217 AAAAATAAAT
1 AAAAAT-TAT
*
35622227 AAAAGTTAT
1 AAAAATTAT
35622236 AAAAATTATT
1 AAAAATTA-T
**
35622246 AAATTTTAAT
1 AAAAATT-AT
35622256 AAAAA-TATT
1 AAAAATTA-T
*
35622265 AAAAATTAGAA
1 AAAAATT--AT
35622276 AAAAATTAT
1 AAAAATTAT
**
35622285 AAAAATCGT
1 AAAAATTAT
35622294 AAAAA-TATT
1 AAAAATTA-T
35622303 AAAAATTAT
1 AAAAATTAT
35622312 AAAA
1 AAAA
35622316 TTGTATTAAT
Statistics
Matches: 82, Mismatches: 13, Indels: 22
0.70 0.11 0.19
Matches are distributed among these distances:
7 7 0.09
8 1 0.01
9 45 0.55
10 20 0.24
11 8 0.10
12 1 0.01
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.30
Consensus pattern (9 bp):
AAAAATTAT
Found at i:35622248 original size:19 final size:19
Alignment explanation
Indices: 35622201--35622315 Score: 89
Period size: 19 Copynumber: 6.2 Consensus size: 19
35622191 ACATGTGGTA
35622201 AAAAATTA-TAAAAA--AT
1 AAAAATTATTAAAAATTAT
* * *
35622217 AAAAATAAATAAAAGTTAT
1 AAAAATTATTAAAAATTAT
**
35622236 AAAAATTATTAAATTTTAAT
1 AAAAATTATTAAAAATT-AT
*
35622256 AAAAA-TATTAAAAATTAGAA
1 AAAAATTATTAAAAATT--AT
**
35622276 AAAAATTA-TAAAAATCGT
1 AAAAATTATTAAAAATTAT
35622294 AAAAA-TATTAAAAATTAT
1 AAAAATTATTAAAAATTAT
35622312 AAAA
1 AAAA
35622316 TTGTATTAAT
Statistics
Matches: 77, Mismatches: 15, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
16 7 0.09
17 7 0.09
18 17 0.22
19 24 0.31
20 20 0.26
21 2 0.03
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.30
Consensus pattern (19 bp):
AAAAATTATTAAAAATTAT
Found at i:35628933 original size:31 final size:32
Alignment explanation
Indices: 35628895--35628957 Score: 119
Period size: 31 Copynumber: 2.0 Consensus size: 32
35628885 AGGCAAATTA
35628895 CAAGAGTAATTGAATCCTAAT-AAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAAACTCTTT
35628926 CAAGAGTAATTGAATCCTAATAAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAAACTCTTT
35628958 AAAATTATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 21 0.68
32 10 0.32
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.32
Consensus pattern (32 bp):
CAAGAGTAATTGAATCCTAATAAAAACTCTTT
Found at i:35629057 original size:3 final size:3
Alignment explanation
Indices: 35629049--35629074 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
35629039 GAATTAAGTA
35629049 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
35629075 GATACATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:35629433 original size:18 final size:19
Alignment explanation
Indices: 35629410--35629445 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
35629400 TTTGGTACGA
*
35629410 TAATTTTA-ATTTTTTTAC
1 TAATTTTATATTTCTTTAC
35629428 TAATTTTATATTTCTTTA
1 TAATTTTATATTTCTTTA
35629446 TATTTTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.67
Consensus pattern (19 bp):
TAATTTTATATTTCTTTAC
Found at i:35629481 original size:48 final size:47
Alignment explanation
Indices: 35629429--35629559 Score: 149
Period size: 48 Copynumber: 2.7 Consensus size: 47
35629419 TTTTTTTACT
35629429 AATTTTATATTTCTTTATATTTTTTATAATTTTCTTAC-AACTTTATAA
1 AATTTTATATTT-TTTATATTTTTTATAATTTT-TTACGAACTTTATAA
* * **
35629477 AATTTTATATATTTCTATATATTTTATAATTTTTTACGATTTTTATAA
1 AATTTTATAT-TTTTTATATTTTTTATAATTTTTTACGAACTTTATAA
* * *
35629525 AATTTTACAATTTTTTA-ATTTTTAATAATATTTTA
1 AATTTTA-TATTTTTTATATTTTTTATAATTTTTTA
35629560 ACATTTTTTA
Statistics
Matches: 71, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
47 19 0.27
48 48 0.68
49 4 0.06
ACGTcount: A:0.34, C:0.05, G:0.01, T:0.60
Consensus pattern (47 bp):
AATTTTATATTTTTTATATTTTTTATAATTTTTTACGAACTTTATAA
Found at i:35629520 original size:19 final size:19
Alignment explanation
Indices: 35629498--35629569 Score: 67
Period size: 19 Copynumber: 3.8 Consensus size: 19
35629488 TTTCTATATA
*
35629498 TTTTATAATTTTTTACGAT
1 TTTTATAATTTTTTACAAT
**
35629517 TTTTATAAAATTTTACAAT
1 TTTTATAATTTTTTACAAT
* *
35629536 TTTT-TAATTTTTAATAAT
1 TTTTATAATTTTTTACAAT
35629554 ATTTTA-ACATTTTTTA
1 -TTTTATA-ATTTTTTA
35629570 TTAAAATTTA
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
18 10 0.24
19 25 0.60
20 7 0.17
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.61
Consensus pattern (19 bp):
TTTTATAATTTTTTACAAT
Found at i:35629523 original size:28 final size:26
Alignment explanation
Indices: 35629476--35629569 Score: 91
Period size: 28 Copynumber: 3.4 Consensus size: 26
35629466 CAACTTTATA
* *
35629476 AAATTTTATATATTTCTAT-ATATTTT
1 AAATTTTTTA-ATTTTTATAATATTTT
*
35629502 ATAATTTTTTACGATTTTTATAAAATTTT
1 A-AATTTTTTA--ATTTTTATAATATTTT
35629531 ACAATTTTTTAATTTTTAATAATATTTT
1 A-AATTTTTTAATTTTT-ATAATATTTT
35629559 AACATTTTTTA
1 AA-ATTTTTTA
35629570 TTAAAATTTA
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
26 1 0.02
27 15 0.26
28 25 0.44
29 16 0.28
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.60
Consensus pattern (26 bp):
AAATTTTTTAATTTTTATAATATTTT
Found at i:35629608 original size:49 final size:48
Alignment explanation
Indices: 35629470--35629598 Score: 124
Period size: 48 Copynumber: 2.6 Consensus size: 48
35629460 TTCTTACAAC
* * *
35629470 TTTATAAAATTTTATATATTTCTATATA-TTTT-ATAAT-TTTTTACGA-TT
1 TTTATAAAATTTTACA-ATTT-TTTA-ACTTTTAATAATATTTTAAC-ATTT
*
35629518 TTTATAAAATTTTACAATTTTTTAATTTTTAATAATATTTTAACATTT
1 TTTATAAAATTTTACAATTTTTTAACTTTTAATAATATTTTAACATTT
35629566 TTTATTAAAA-TTTACTAATTTTTATAACTTTTA
1 TTTA-TAAAATTTTAC-AATTTTT-TAACTTTTA
35629599 TTGAATTTTA
Statistics
Matches: 70, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
45 1 0.01
46 7 0.10
47 10 0.14
48 32 0.46
49 12 0.17
50 8 0.11
ACGTcount: A:0.36, C:0.05, G:0.01, T:0.59
Consensus pattern (48 bp):
TTTATAAAATTTTACAATTTTTTAACTTTTAATAATATTTTAACATTT
Found at i:35630017 original size:14 final size:14
Alignment explanation
Indices: 35629982--35630028 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
35629972 TATGATTATG
*
35629982 TTTAAA-TTTAGAG
1 TTTAAATTTTAGAA
*
35629995 TTTAGAATTTTGGAA
1 TTTA-AATTTTAGAA
35630010 TTTAAATTTTAGAA
1 TTTAAATTTTAGAA
35630024 CTTTA
1 -TTTA
35630029 TGATTTATGG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
13 4 0.14
14 11 0.39
15 13 0.46
ACGTcount: A:0.36, C:0.02, G:0.13, T:0.49
Consensus pattern (14 bp):
TTTAAATTTTAGAA
Found at i:35631866 original size:343 final size:342
Alignment explanation
Indices: 35631229--35631868 Score: 915
Period size: 343 Copynumber: 1.9 Consensus size: 342
35631219 GGTTTATAGA
* * * * *
35631229 TATTGAGGTACTAAATTTTTTCCTTCAAGGCTGACACCATGGTCTTGAGAGAATTATTCTTCTTA
1 TATTGAGCTACTAAATTTGTTCATTCAAGGCTGACACCATGGTCTTGAGAAAATCATTCTTCTTA
* * *
35631294 GTTAACTTCTCGATCTGATCATCCATAGCAACATTAAGGGTATTTCTCATTGCATCTTGATTGGA
66 GTCAACTTCTCGATCTAATCATCCATAGCAACATTAAGGGTATCTCTCATTGCATCTTGATTGGA
* * * * *
35631359 ATTGAGAGCTTTCACTTTATTATCCCTAAGCTTCTCTCTTATCAAGTCCAACTCATCGGTGCGTC
131 ACTGAGAGCCTTCAC-TTAGTATCCCTAAGCTTCTCTCTCATCAAGTCCAACTCATCGGTGCGCC
* * **
35631424 CCTCAATTATCTCGAGTGTTTCCTTCACACCACTTATGGATTCCTCGAGATTGCTCACCCGACCT
195 CCTCAATTACCTCGAGCGTTTCCTTCACACCACCCATGGATTCCTCGAGATTGCTCACCCGACCT
*
35631489 TCCAAAGCCGATAACATATCATTCGATATGCTATTTTCTTGGTCTTCTCATGGGTCTCCATCGAG
260 TCCAAAGCCGACAACATATCATTCGATATGCTATTTTCTTGGTCTTCTCATGGGTCTCCATCGAG
35631554 ACATTTTGTTCGTCTACT
325 ACATTTTGTTCGTCTACT
* *
35631572 TATTGAGCTACTAAATTTGTTCATTCAAGGTTGGCACCATGGTCTTGAGAAAATCATTCTTCTTA
1 TATTGAGCTACTAAATTTGTTCATTCAAGGCTGACACCATGGTCTTGAGAAAATCATTCTTCTTA
* * * * * *
35631637 GTCAACTTCTCGGTCTAATCATCTATGGCAGCATTGAGGGTCTCTCTCATTGCATCTTGATTGGA
66 GTCAACTTCTCGATCTAATCATCCATAGCAACATTAAGGGTATCTCTCATTGCATCTTGATTGGA
* *
35631702 ACTGAGAGCCTTCAC-TACGTAGTCCCTAAG-TTGCTCTCTCATCGAGTTCAACTCATCGGTGCG
131 ACTGAGAGCCTTCACTTA-GTA-TCCCTAAGCTT-CTCTCTCATCAAGTCCAACTCATCGGTGCG
* * *
35631765 CCCCTCAATTACCTCGAGCGTTTCCTTCACACCACCCATGGATTCCTCGAGATTGGTCACTCGCC
193 CCCCTCAATTACCTCGAGCGTTTCCTTCACACCACCCATGGATTCCTCGAGATTGCTCACCCGAC
** * *
35631830 CTTCCAAATTCGACAACATATCCTTCGATTTGCTATTTT
258 CTTCCAAAGCCGACAACATATCATTCGATATGCTATTTT
35631869 TCTAGTCTTC
Statistics
Matches: 259, Mismatches: 35, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
341 2 0.01
342 4 0.02
343 253 0.98
ACGTcount: A:0.23, C:0.26, G:0.16, T:0.35
Consensus pattern (342 bp):
TATTGAGCTACTAAATTTGTTCATTCAAGGCTGACACCATGGTCTTGAGAAAATCATTCTTCTTA
GTCAACTTCTCGATCTAATCATCCATAGCAACATTAAGGGTATCTCTCATTGCATCTTGATTGGA
ACTGAGAGCCTTCACTTAGTATCCCTAAGCTTCTCTCTCATCAAGTCCAACTCATCGGTGCGCCC
CTCAATTACCTCGAGCGTTTCCTTCACACCACCCATGGATTCCTCGAGATTGCTCACCCGACCTT
CCAAAGCCGACAACATATCATTCGATATGCTATTTTCTTGGTCTTCTCATGGGTCTCCATCGAGA
CATTTTGTTCGTCTACT
Found at i:35634250 original size:36 final size:38
Alignment explanation
Indices: 35634197--35634272 Score: 95
Period size: 36 Copynumber: 2.1 Consensus size: 38
35634187 AACACTAATA
**
35634197 ATAAAAAGTTATTAATAAATT-TAA-T-TTATATTTTAT
1 ATAAAAAGTTAAAAAT-AATTATAATTATTATATTTTAT
*
35634233 ATAAAAAGTTAAAAATAATTATAATTATTTTATTTTAT
1 ATAAAAAGTTAAAAATAATTATAATTATTATATTTTAT
35634271 AT
1 AT
35634273 TAATATTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
35 4 0.12
36 17 0.50
37 1 0.03
38 12 0.35
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (38 bp):
ATAAAAAGTTAAAAATAATTATAATTATTATATTTTAT
Found at i:35636230 original size:25 final size:25
Alignment explanation
Indices: 35636182--35636230 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
35636172 ATTAAATTAA
**
35636182 AAGACATAATTAATAAGTTCAATTT
1 AAGACATAATTAATAAGTGAAATTT
35636207 AAGACAT-ATTAATAAGCTGAAATT
1 AAGACATAATTAATAAG-TGAAATT
35636231 AAATTAACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.49, C:0.08, G:0.10, T:0.33
Consensus pattern (25 bp):
AAGACATAATTAATAAGTGAAATTT
Found at i:35636232 original size:24 final size:25
Alignment explanation
Indices: 35636182--35636232 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
35636172 ATTAAATTAA
* *
35636182 AAGACATAATTAATAAGTTCAATTT
1 AAGACATAATTAATAAGCTCAAATT
*
35636207 AAGACAT-ATTAATAAGCTGAAATT
1 AAGACATAATTAATAAGCTCAAATT
35636231 AA
1 AA
35636233 ATTAACTAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.51, C:0.08, G:0.10, T:0.31
Consensus pattern (25 bp):
AAGACATAATTAATAAGCTCAAATT
Found at i:35637236 original size:16 final size:16
Alignment explanation
Indices: 35637215--35637266 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
35637205 AGAATGGAAA
35637215 GAAAATTAGAAAGATG
1 GAAAATTAGAAAGATG
* *
35637231 GAAAATTA-AAAGGTA
1 GAAAATTAGAAAGATG
*
35637246 GAAAAAT-GAAAAGATG
1 GAAAATTAG-AAAGATG
35637262 GAAAA
1 GAAAA
35637267 ATATATTTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
15 11 0.38
16 18 0.62
ACGTcount: A:0.62, C:0.00, G:0.23, T:0.15
Consensus pattern (16 bp):
GAAAATTAGAAAGATG
Found at i:35637267 original size:16 final size:16
Alignment explanation
Indices: 35637224--35637268 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
35637214 AGAAAATTAG
*
35637224 AAAGATGG-AAAATTA
1 AAAGATGGAAAAATGA
* *
35637239 AAAGGTAGAAAAATGA
1 AAAGATGGAAAAATGA
35637255 AAAGATGGAAAAAT
1 AAAGATGGAAAAAT
35637269 ATATTTTTTC
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
15 6 0.25
16 18 0.75
ACGTcount: A:0.62, C:0.00, G:0.22, T:0.16
Consensus pattern (16 bp):
AAAGATGGAAAAATGA
Found at i:35641049 original size:2 final size:2
Alignment explanation
Indices: 35641042--35641078 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
35641032 CGTCCCCAAT
35641042 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
35641079 CATCGATAGC
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:35641610 original size:12 final size:12
Alignment explanation
Indices: 35641593--35641627 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
35641583 TTTTAATTAT
35641593 TTATTATTAAAA
1 TTATTATTAAAA
35641605 TTATTATTAAAA
1 TTATTATTAAAA
*
35641617 TCATTTATTAA
1 TTA-TTATTAA
35641628 TTTTGTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 14 0.67
13 7 0.33
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (12 bp):
TTATTATTAAAA
Found at i:35642478 original size:11 final size:11
Alignment explanation
Indices: 35642462--35642568 Score: 70
Period size: 11 Copynumber: 10.4 Consensus size: 11
35642452 ATTTTTTTAA
35642462 TTTTAAAATAC
1 TTTTAAAATAC
35642473 TTTTAAAATAC
1 TTTTAAAATAC
35642484 TTTTATTAAAT--
1 TTTTA--AAATAC
*
35642495 TTTT-TAA-A-
1 TTTTAAAATAC
**
35642503 TTTTAAAATTT
1 TTTTAAAATAC
35642514 TTTTAAAATAC
1 TTTTAAAATAC
35642525 TTTTAAAAT--
1 TTTTAAAATAC
** *
35642534 TTTT--TTTAA
1 TTTTAAAATAC
*
35642543 TTTTAAAATAT
1 TTTTAAAATAC
35642554 TTTTAAAATAC
1 TTTTAAAATAC
35642565 TTTT
1 TTTT
35642569 TTTAATTTTA
Statistics
Matches: 75, Mismatches: 11, Indels: 20
0.71 0.10 0.19
Matches are distributed among these distances:
7 1 0.01
8 6 0.08
9 10 0.13
11 54 0.72
13 4 0.05
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:35642505 original size:41 final size:41
Alignment explanation
Indices: 35642452--35642602 Score: 180
Period size: 41 Copynumber: 3.6 Consensus size: 41
35642442 ATTATTTTTT
* *
35642452 ATTTTTTTAATTTTAAAATACTTTTAAAATACTTTTATTAA
1 ATTTTTTAAATTTTAAAATATTTTTAAAATACTTTTATTAA
*
35642493 ATTTTTTAAATTTTAAAATTTTTTTAAAATACTTTTA--AA
1 ATTTTTTAAATTTTAAAATATTTTTAAAATACTTTTATTAA
* *
35642532 ATTTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAA
1 A-TTTTTTAAATTTTAAAATATTTTTAAAATACTTTTATTAA
* *
35642574 TTTTAATTTTAATTTTTAAAATAATTTTT
1 -ATT--TTTTAAATTTTAAAAT-ATTTTT
35642603 TGGTATTTAT
Statistics
Matches: 94, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
39 3 0.03
40 33 0.35
41 34 0.36
42 4 0.04
44 14 0.15
45 6 0.06
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (41 bp):
ATTTTTTAAATTTTAAAATATTTTTAAAATACTTTTATTAA
Found at i:35649510 original size:19 final size:18
Alignment explanation
Indices: 35649486--35649531 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
35649476 ACGCTCTTTT
* *
35649486 TGCATTCATTTCATGCATC
1 TGCATTCATGTCAT-CATA
35649505 TGCATTACATGTCATCATA
1 TGCATT-CATGTCATCATA
35649524 TGCATTCA
1 TGCATTCA
35649532 AGATTATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 2 0.08
19 15 0.62
20 7 0.29
ACGTcount: A:0.26, C:0.24, G:0.11, T:0.39
Consensus pattern (18 bp):
TGCATTCATGTCATCATA
Found at i:35658301 original size:44 final size:44
Alignment explanation
Indices: 35658238--35658609 Score: 234
Period size: 44 Copynumber: 8.0 Consensus size: 44
35658228 TAGATCACAT
* *
35658238 CAGATTGAAGCCAGAAATCTTATCTCCCTGAAATTACAGCAGAG
1 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAG
*
35658282 CAGATTGAAGCCAGTAATCTTATCTCCCTGAGATTACAGCGGAG
1 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAG
*** * *
35658326 CAGATT-AAAATA-AAGGATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCG
1 CAGATTGAAGCCAGAA--ATCTTATCTCCCTGAGA-TTAC---AGCG--GA--G
* * *
35658377 CATCAGATTGAAGCCAAAAATCTTATTTCCTTGAGATTACAGCGGAG
1 ---CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAG
* * * *
35658424 CAAATTGAAGCCAGTAATCCTATCTCCCTGAGATTACAGTGGAG
1 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAG
*** * *
35658468 CAGATT-AAAATA-AAGGATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCG
1 CAGATTGAAGCCAGAA--ATCTTATCTCCCTGAGA-TTAC---AGCG--GA--G
* *
35658519 CATCAAATTGAAGCCAGAAATCTTATCTCCTTGAGATTACAGCGGAG
1 ---CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAG
* * * *
35658566 CAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAG
1 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAG
35658610 TGGATTAAAA
Statistics
Matches: 252, Mismatches: 44, Indels: 64
0.70 0.12 0.18
Matches are distributed among these distances:
42 2 0.01
43 8 0.03
44 162 0.64
47 8 0.03
49 8 0.03
51 8 0.03
54 44 0.17
55 8 0.03
56 4 0.02
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (44 bp):
CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAG
Found at i:35658319 original size:98 final size:95
Alignment explanation
Indices: 35658200--35658610 Score: 253
Period size: 98 Copynumber: 4.3 Consensus size: 95
35658190 AAAATAAAGG
*
35658200 ATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCACATCAGATTGAAGCCAGAAATCTTATCTC
1 ATCTTATCTCCCTGAGA-TTACAGTAGAGTAGATCACA--A-ATTGAAGCCAGAAATCTTATCTC
35658264 CCTGAAATTACAGCAGAGCAGATTGAAGCCAGTA
62 CCTGAAATTACAGCAGAGCAGATTGAAGCCAGTA
** * * * *
35658298 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTA-AAA-T-AA---AG-GATCTTATCTCTCTG
1 ATCTTATCTCCCTGAGATTACAGTAGAGTAGATCACAAATTGAAGCCAGAAATCTTATCTCCCTG
* * **
35658356 AAGTTACAGTAGAGTAGATCGCATCAGATTGAAGCCAAAA
66 AAATTAC-----AGCAGA--G---CAGATTGAAGCCAGTA
* * * * *
35658396 ATCTTATTTCCTTGAGATTACAG-CG-G-AG----CAAATTGAAGCCAGTAATCCTATCTCCCTG
1 ATCTTATCTCCCTGAGATTACAGTAGAGTAGATCACAAATTGAAGCCAGAAATCTTATCTCCCTG
* ** * *** *
35658454 AGATTACAGTGGAGCAGATTAAAATAAAG-G
66 AAATTACAGCAGAGCAGATT-GAAGCCAGTA
*
35658484 ATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCGCATCAAATTGAAGCCAGAAATCTTATCTC
1 ATCTTATCTCCCTGAGA-TTACAGTAGAGTAGAT--CA-CAAATTGAAGCCAGAAATCTTATCTC
* * * *
35658548 CTTGAGATTACAGCGGAGCAGATTGAAGCTAGTA
62 CCTGAAATTACAGCAGAGCAGATTGAAGCCAGTA
* *
35658582 ATCCTATCTCCCTGAGATTACAGTGGAGT
1 ATCTTATCTCCCTGAGATTACAGTAGAGT
35658611 GGATTAAAAT
Statistics
Matches: 239, Mismatches: 42, Indels: 64
0.69 0.12 0.19
Matches are distributed among these distances:
87 1 0.00
88 43 0.18
89 6 0.03
90 1 0.00
91 3 0.01
92 5 0.02
93 12 0.05
94 3 0.01
95 4 0.02
96 1 0.00
97 8 0.03
98 150 0.63
99 2 0.01
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (95 bp):
ATCTTATCTCCCTGAGATTACAGTAGAGTAGATCACAAATTGAAGCCAGAAATCTTATCTCCCTG
AAATTACAGCAGAGCAGATTGAAGCCAGTA
Found at i:35658359 original size:142 final size:142
Alignment explanation
Indices: 35658103--35658666 Score: 941
Period size: 142 Copynumber: 4.0 Consensus size: 142
35658093 AAATAGGTTT
* * *
35658103 AAGCCACAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATGGAAGCTAGTAATCCTATCTCCC
1 AAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATCTCCC
35658168 TGAGATTACAGTGGAGC-GAATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGA
66 TGAGATTACAGTGGAGCAG-ATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGA
*
35658232 TCACATCAGATTG
130 TCGCATCAGATTG
* * *
35658245 AAGCCAGAAATCTTATCTCCCTGAAATTACAGCAGAGCAGATTGAAGCCAGTAATCTTATCTCCC
1 AAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATCTCCC
*
35658310 TGAGATTACAGCGGAGCAGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGAT
66 TGAGATTACAGTGGAGCAGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGAT
35658375 CGCATCAGATTG
131 CGCATCAGATTG
* * * *
35658387 AAGCCAAAAATCTTATTTCCTTGAGATTACAGCGGAGCAAATTGAAGCCAGTAATCCTATCTCCC
1 AAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATCTCCC
35658452 TGAGATTACAGTGGAGCAGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGAT
66 TGAGATTACAGTGGAGCAGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGAT
*
35658517 CGCATCAAATTG
131 CGCATCAGATTG
* *
35658529 AAGCCAGAAATCTTATCTCCTTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCC
1 AAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATCTCCC
** *
35658594 TGAGATTACAGTGGAGTGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTATAGTAGAGTAGAT
66 TGAGATTACAGTGGAGCAGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGAT
*
35658659 CGTATCAG
131 CGCATCAG
35658667 GTCTTATCTC
Statistics
Matches: 395, Mismatches: 26, Indels: 2
0.93 0.06 0.00
Matches are distributed among these distances:
142 394 1.00
143 1 0.00
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (142 bp):
AAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATCTCCC
TGAGATTACAGTGGAGCAGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGAT
CGCATCAGATTG
Found at i:35660708 original size:12 final size:13
Alignment explanation
Indices: 35660680--35660707 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
35660670 GTTTTATTTC
35660680 AAAGTTCCTAAAA
1 AAAGTTCCTAAAA
35660693 AAAGTTCCTAAAA
1 AAAGTTCCTAAAA
35660706 AA
1 AA
35660708 GGAGGCTTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.57, C:0.14, G:0.07, T:0.21
Consensus pattern (13 bp):
AAAGTTCCTAAAA
Found at i:35661714 original size:4 final size:4
Alignment explanation
Indices: 35661707--35661737 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
35661697 TATTAAAATT
35661707 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTA
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTA
35661738 TTCTTTCACG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:35665456 original size:23 final size:23
Alignment explanation
Indices: 35665422--35665469 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
35665412 GTTTGAATTA
35665422 TTTTGAGTTCGAGGCATTGAGGG
1 TTTTGAGTTCGAGGCATTGAGGG
*
35665445 TTTTAGAG-TCGAGTCATTGAGGG
1 TTTT-GAGTTCGAGGCATTGAGGG
35665468 TT
1 TT
35665470 ATAGTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 20 0.87
24 3 0.13
ACGTcount: A:0.19, C:0.08, G:0.35, T:0.38
Consensus pattern (23 bp):
TTTTGAGTTCGAGGCATTGAGGG
Found at i:35674196 original size:6 final size:6
Alignment explanation
Indices: 35674185--35674275 Score: 164
Period size: 6 Copynumber: 15.2 Consensus size: 6
35674175 TTACCAAAAC
35674185 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
* *
35674233 ATACAT ATACAT TTACAT TTACAT ATACAT ATACAT ATACAT A
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT A
35674276 CGGACATTAA
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 83 1.00
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.35
Consensus pattern (6 bp):
ATACAT
Found at i:35675897 original size:17 final size:15
Alignment explanation
Indices: 35675866--35675899 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 15
35675856 TGAACATGAA
35675866 ATTTTTTTTGTTTTT
1 ATTTTTTTTGTTTTT
35675881 ATTTTATTTTGTCTTTT
1 ATTTT-TTTTGT-TTTT
35675898 AT
1 AT
35675900 AATTGTCTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 6 0.35
17 6 0.35
ACGTcount: A:0.12, C:0.03, G:0.06, T:0.79
Consensus pattern (15 bp):
ATTTTTTTTGTTTTT
Found at i:35676302 original size:20 final size:20
Alignment explanation
Indices: 35676277--35676327 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
35676267 GTATCAATCT
*
35676277 GGTATCGATACT-TTTCTTAA
1 GGTATCGATA-TATTTCCTAA
35676297 GGTATCGATATATTTCCTAA
1 GGTATCGATATATTTCCTAA
*
35676317 GATATCGATAT
1 GGTATCGATAT
35676328 TCCTGGTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.41
Consensus pattern (20 bp):
GGTATCGATATATTTCCTAA
Found at i:35678605 original size:16 final size:16
Alignment explanation
Indices: 35678586--35678616 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
35678576 AAATAAATGG
*
35678586 AAGTTTAATTAAAATT
1 AAGTTAAATTAAAATT
35678602 AAGTTAAATTAAAAT
1 AAGTTAAATTAAAAT
35678617 AATGAAAAAC
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:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (16 bp):
AAGTTAAATTAAAATT
Found at i:35679603 original size:33 final size:33
Alignment explanation
Indices: 35679561--35679744 Score: 262
Period size: 33 Copynumber: 5.6 Consensus size: 33
35679551 TACTCTTTAT
* *
35679561 TTGGTGTGATGGTTGGTTTAACTCTTATGATCA
1 TTGGTGTGATGGTTGGATTAACTCTTATGAGCA
* *
35679594 TTGATGTGATGGTTGGTTTAACTCTTATGAGCA
1 TTGGTGTGATGGTTGGATTAACTCTTATGAGCA
35679627 TTGGTGTGATGGTTGGATTAACTCTTATGAGCA
1 TTGGTGTGATGGTTGGATTAACTCTTATGAGCA
* * *
35679660 TTGATGTGATGGTTGGATTAGCT-TCTATGAGAA
1 TTGGTGTGATGGTTGGATTAACTCT-TATGAGCA
* *
35679693 TTGGTGTGATGGTTCGATTAGCTCTTATGAGCA
1 TTGGTGTGATGGTTGGATTAACTCTTATGAGCA
*
35679726 TTGGTGTGATGGATGGATT
1 TTGGTGTGATGGTTGGATT
35679745 GGCTCGAGTG
Statistics
Matches: 137, Mismatches: 12, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
32 1 0.01
33 135 0.99
34 1 0.01
ACGTcount: A:0.20, C:0.08, G:0.30, T:0.41
Consensus pattern (33 bp):
TTGGTGTGATGGTTGGATTAACTCTTATGAGCA
Found at i:35679757 original size:33 final size:33
Alignment explanation
Indices: 35679561--35679777 Score: 258
Period size: 33 Copynumber: 6.5 Consensus size: 33
35679551 TACTCTTTAT
* * *
35679561 TTGGTGTGATGGTTGGTTTAACTCTTATGATCA
1 TTGGTGTGATGGTTGGATTAGCTCTTATGAGCA
* * *
35679594 TTGATGTGATGGTTGGTTTAACTCTTATGAGCA
1 TTGGTGTGATGGTTGGATTAGCTCTTATGAGCA
*
35679627 TTGGTGTGATGGTTGGATTAACTCTTATGAGCA
1 TTGGTGTGATGGTTGGATTAGCTCTTATGAGCA
* *
35679660 TTGATGTGATGGTTGGATTAGCT-TCTATGAGAA
1 TTGGTGTGATGGTTGGATTAGCTCT-TATGAGCA
*
35679693 TTGGTGTGATGGTTCGATTAGCTCTTATGAGCA
1 TTGGTGTGATGGTTGGATTAGCTCTTATGAGCA
* * *
35679726 TTGGTGTGATGGATGGATTGGCTC-GAGTGAGCA
1 TTGGTGTGATGGTTGGATTAGCTCTTA-TGAGCA
*
35679759 TCTGGTGTGTTTGGTTGGA
1 T-TGGTGTG-ATGGTTGGA
35679778 CTGATGATGT
Statistics
Matches: 163, Mismatches: 16, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
32 2 0.01
33 146 0.90
34 8 0.05
35 7 0.04
ACGTcount: A:0.19, C:0.09, G:0.32, T:0.40
Consensus pattern (33 bp):
TTGGTGTGATGGTTGGATTAGCTCTTATGAGCA
Found at i:35684118 original size:22 final size:22
Alignment explanation
Indices: 35684056--35684141 Score: 118
Period size: 22 Copynumber: 3.9 Consensus size: 22
35684046 ATTGTTCAAA
* **
35684056 CATGAGAGCTTAGTACGTGAAA
1 CATGAGAGCTTAGTACGTTAGC
35684078 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
35684100 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
* * *
35684122 CATGAGGGTTTAGTTCGTTA
1 CATGAGAGCTTAGTACGTTA
35684142 ATTTTAGATA
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 58 1.00
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAGC
Found at i:35699958 original size:25 final size:25
Alignment explanation
Indices: 35699898--35699958 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 25
35699888 CTCCTAAATT
35699898 TTAATTTAATTATCTAATTTTTCAA
1 TTAATTTAATTATCTAATTTTTCAA
*
35699923 TTTATTTAATTAT-TAATATTTT-ATA
1 TTAATTTAATTATCTAAT-TTTTCA-A
*
35699948 TTAATTAAATT
1 TTAATTTAATT
35699959 TTTGAGAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
24 5 0.16
25 26 0.84
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (25 bp):
TTAATTTAATTATCTAATTTTTCAA
Found at i:35702795 original size:16 final size:16
Alignment explanation
Indices: 35702774--35702807 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
35702764 AGTGCACTTA
35702774 AAATATGAACATGTTG
1 AAATATGAACATGTTG
35702790 AAATATGAACATGTTG
1 AAATATGAACATGTTG
35702806 AA
1 AA
35702808 TTTCAGTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.06, G:0.18, T:0.29
Consensus pattern (16 bp):
AAATATGAACATGTTG
Found at i:35706453 original size:22 final size:22
Alignment explanation
Indices: 35706428--35706473 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
35706418 GGTTCATGAG
*
35706428 TTGAACCAAAAATGATGTTAGT
1 TTGAACAAAAAATGATGTTAGT
*
35706450 TTGAACAAAAAATGATGTTGGT
1 TTGAACAAAAAATGATGTTAGT
35706472 TT
1 TT
35706474 TGGATGTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.39, C:0.07, G:0.20, T:0.35
Consensus pattern (22 bp):
TTGAACAAAAAATGATGTTAGT
Found at i:35708655 original size:18 final size:17
Alignment explanation
Indices: 35708634--35708693 Score: 61
Period size: 18 Copynumber: 3.5 Consensus size: 17
35708624 GAGAGCGTAA
35708634 AAAAAGAAAAAGAGACTG
1 AAAAAGAAAAAGAG-CTG
*
35708652 AAAAAG-AAACGAG-TG
1 AAAAAGAAAAAGAGCTG
* *
35708667 AAAAAGAAAGAGGGCTTG
1 AAAAAGAAAAAGAGC-TG
35708685 AAAAAGAAA
1 AAAAAGAAA
35708694 CGAGTGAAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
15 8 0.23
16 4 0.11
17 6 0.17
18 17 0.49
ACGTcount: A:0.63, C:0.05, G:0.25, T:0.07
Consensus pattern (17 bp):
AAAAAGAAAAAGAGCTG
Found at i:35708670 original size:15 final size:15
Alignment explanation
Indices: 35708650--35708701 Score: 61
Period size: 15 Copynumber: 3.3 Consensus size: 15
35708640 AAAAAGAGAC
35708650 TGAAAAAGAAACGAG
1 TGAAAAAGAAACGAG
35708665 TGAAAAAGAAA-GAGGG
1 TGAAAAAGAAACGA--G
35708681 CTTGAAAAAGAAACGAG
1 --TGAAAAAGAAACGAG
35708698 TGAA
1 TGAA
35708702 GAGAGTAATC
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
14 2 0.06
15 15 0.47
16 1 0.03
17 1 0.03
18 11 0.34
19 2 0.06
ACGTcount: A:0.56, C:0.06, G:0.29, T:0.10
Consensus pattern (15 bp):
TGAAAAAGAAACGAG
Found at i:35719381 original size:18 final size:18
Alignment explanation
Indices: 35719358--35719400 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
35719348 GAGTTAAACG
* *
35719358 AATCGAGTTGTTCGAGTT
1 AATCGAGTTATTCGAATT
35719376 AATCGAGTTATTCGAATT
1 AATCGAGTTATTCGAATT
35719394 AACTCGA
1 AA-TCGA
35719401 ATTTTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (18 bp):
AATCGAGTTATTCGAATT
Found at i:35720016 original size:19 final size:19
Alignment explanation
Indices: 35719980--35720032 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
35719970 TATATCTACT
35719980 ATTTATATTATTAAATTAA
1 ATTTATATTATTAAATTAA
*
35719999 ATTTCATATT-TTATATT--
1 ATTT-ATATTATTAAATTAA
*
35720016 ATTTATATTATTGAATT
1 ATTTATATTATTAAATT
35720033 GTTTAGTCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 5 0.17
17 9 0.31
19 10 0.34
20 5 0.17
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (19 bp):
ATTTATATTATTAAATTAA
Found at i:35738377 original size:30 final size:30
Alignment explanation
Indices: 35738342--35738561 Score: 187
Period size: 30 Copynumber: 7.3 Consensus size: 30
35738332 GTTGTCCCAA
** * *
35738342 CCCTTTTCATAGCTCGATAGCCGAAGTTAT
1 CCCTTTTCATAATTTGATAGCCGAAGCTAT
*
35738372 CCCTTTTTATAATTTGATAGCCGAAGCTAT
1 CCCTTTTCATAATTTGATAGCCGAAGCTAT
* *
35738402 CCCATTTCACAATTTGATAGCCGAAGCTAT
1 CCCTTTTCATAATTTGATAGCCGAAGCTAT
** * * * *
35738432 CCCTTTTCATTGTTCGATGGTCGTCA-CTAT
1 CCCTTTTCATAATTTGATAGCCG-AAGCTAT
* * * *
35738462 CCCTTTTCATTA-TTGAT-GATCGTCA-CCAT
1 CCCTTTTCATAATTTGATAG-CCG-AAGCTAT
* *
35738491 CCCTTTTCATAATTTGATAGCCGAGGTTAT
1 CCCTTTTCATAATTTGATAGCCGAAGCTAT
* *
35738521 TCCTTTTCATTATTTTGATAGCCGAAGCTAT
1 CCCTTTTCA-TAATTTGATAGCCGAAGCTAT
35738552 CCCTTTTCAT
1 CCCTTTTCAT
35738562 TAGCCAATGA
Statistics
Matches: 154, Mismatches: 30, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
28 1 0.01
29 24 0.16
30 101 0.66
31 28 0.18
ACGTcount: A:0.22, C:0.25, G:0.14, T:0.40
Consensus pattern (30 bp):
CCCTTTTCATAATTTGATAGCCGAAGCTAT
Found at i:35738492 original size:29 final size:30
Alignment explanation
Indices: 35738430--35738500 Score: 108
Period size: 29 Copynumber: 2.4 Consensus size: 30
35738420 AGCCGAAGCT
* * *
35738430 ATCCCTTTTCATTGTTCGATGGTCGTCACT
1 ATCCCTTTTCATTATTCGATGATCGTCACC
35738460 ATCCCTTTTCATTATT-GATGATCGTCACC
1 ATCCCTTTTCATTATTCGATGATCGTCACC
35738489 ATCCCTTTTCAT
1 ATCCCTTTTCAT
35738501 AATTTGATAG
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
29 23 0.61
30 15 0.39
ACGTcount: A:0.17, C:0.28, G:0.11, T:0.44
Consensus pattern (30 bp):
ATCCCTTTTCATTATTCGATGATCGTCACC
Found at i:35742447 original size:12 final size:12
Alignment explanation
Indices: 35742443--35742477 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
35742433 TATTTATTAT
35742443 TTTATTATTTTA
1 TTTATTATTTTA
35742455 TTTATTATTTTA
1 TTTATTATTTTA
35742467 TTT-TTATTTTA
1 TTTATTATTTTA
35742478 CTAAACCTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 8 0.35
12 15 0.65
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTATTATTTTA
Found at i:35742455 original size:20 final size:20
Alignment explanation
Indices: 35742430--35742468 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
35742420 GAGTAAGGTT
35742430 TTTTATTTATTATTTTATTA
1 TTTTATTTATTATTTTATTA
35742450 TTTTATTTATTATTTTATT
1 TTTTATTTATTATTTTATT
35742469 TTTATTTTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTTATTTATTATTTTATTA
Found at i:35747390 original size:20 final size:20
Alignment explanation
Indices: 35747365--35747412 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
35747355 ATACAGCGGT
35747365 GCCGGCGCCAGAGATCGGCG
1 GCCGGCGCCAGAGATCGGCG
35747385 GCCGGCGCCAGAGATCGGCG
1 GCCGGCGCCAGAGATCGGCG
35747405 GCCGGCGC
1 GCCGGCGC
35747413 GGTGGCCGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.12, C:0.38, G:0.46, T:0.04
Consensus pattern (20 bp):
GCCGGCGCCAGAGATCGGCG
Found at i:35747954 original size:4 final size:4
Alignment explanation
Indices: 35747933--35747973 Score: 55
Period size: 4 Copynumber: 10.0 Consensus size: 4
35747923 TTAATTAGTT
* *
35747933 TTTA TTTA TATA TATTA TTTA TTTA TTTA TTTA TTTT TTTA
1 TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA
35747974 ACAAATATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
4 29 0.91
5 3 0.09
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:35752904 original size:13 final size:14
Alignment explanation
Indices: 35752888--35752921 Score: 52
Period size: 13 Copynumber: 2.4 Consensus size: 14
35752878 AATAAATATA
35752888 TATTTTTT-ATTTT
1 TATTTTTTAATTTT
35752901 TATTTTTTAATTTT
1 TATTTTTTAATTTT
35752915 TAATTTT
1 T-ATTTT
35752922 AAAATACTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.42
14 6 0.32
15 5 0.26
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
TATTTTTTAATTTT
Found at i:35754855 original size:50 final size:50
Alignment explanation
Indices: 35754801--35754908 Score: 198
Period size: 50 Copynumber: 2.2 Consensus size: 50
35754791 ACCATTTCAA
*
35754801 TCCTTTTCATTAATACATGATATATTTTATTTGAACACTTACCATTCCTT
1 TCCTTTTCATTAATACATGATATATTTCATTTGAACACTTACCATTCCTT
*
35754851 TCCTTTTCATTAATACATGATATATTTCATTTGAACACTTACCGTTCCTT
1 TCCTTTTCATTAATACATGATATATTTCATTTGAACACTTACCATTCCTT
35754901 TCCTTTTC
1 TCCTTTTC
35754909 GTGCCCGTTG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
50 56 1.00
ACGTcount: A:0.25, C:0.22, G:0.05, T:0.48
Consensus pattern (50 bp):
TCCTTTTCATTAATACATGATATATTTCATTTGAACACTTACCATTCCTT
Found at i:35757112 original size:53 final size:53
Alignment explanation
Indices: 35757032--35757137 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
35757022 TATGTATAGA
35757032 CTGGTTAGTGGAACACCAAGCAGTTTAGAGTGTGCTTCTAAGAGGGTCACTCT
1 CTGGTTAGTGGAACACCAAGCAGTTTAGAGTGTGCTTCTAAGAGGGTCACTCT
35757085 CTGGTTAGTGGAACACCAAGCAGTTTAGAGTGTGCTTCTAAGAGGGTCACTCT
1 CTGGTTAGTGGAACACCAAGCAGTTTAGAGTGTGCTTCTAAGAGGGTCACTCT
35757138 GAAGACATCT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (53 bp):
CTGGTTAGTGGAACACCAAGCAGTTTAGAGTGTGCTTCTAAGAGGGTCACTCT
Found at i:35763039 original size:17 final size:19
Alignment explanation
Indices: 35763007--35763041 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
35762997 ATTATTATTT
35763007 TTTCATTTTTCTTCTCATC
1 TTTCATTTTTCTTCTCATC
35763026 TTTC-TTTTTC-TCTCAT
1 TTTCATTTTTCTTCTCAT
35763042 ATTTTCTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 6 0.38
19 4 0.25
ACGTcount: A:0.09, C:0.26, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTCATTTTTCTTCTCATC
Found at i:35763047 original size:18 final size:18
Alignment explanation
Indices: 35763005--35763054 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
35762995 GAATTATTAT
35763005 TTTTTCATTTTTCTTCTCA
1 TTTTTC-TTTTTCTTCTCA
*
35763024 TCTTTCTTTTTC-TCTCA
1 TTTTTCTTTTTCTTCTCA
35763041 TATTTTCTCTTTTC
1 T-TTTTCT-TTTTC
35763055 CACCACCTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 6 0.22
18 11 0.41
19 10 0.37
ACGTcount: A:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTTCTTTTTCTTCTCA
Found at i:35766636 original size:37 final size:37
Alignment explanation
Indices: 35766586--35766677 Score: 166
Period size: 37 Copynumber: 2.5 Consensus size: 37
35766576 TAAATAACCT
35766586 AGTGGTTAAGTGTGTGAATGTATTCCAAGTGGTTCCA
1 AGTGGTTAAGTGTGTGAATGTATTCCAAGTGGTTCCA
*
35766623 AGTGGTTAAGTGTGTGAATGTATTCGAAGTGGTTCCA
1 AGTGGTTAAGTGTGTGAATGTATTCCAAGTGGTTCCA
*
35766660 AGTGGTTAAGTGTCTGAA
1 AGTGGTTAAGTGTGTGAA
35766678 CACCCTTGCT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 53 1.00
ACGTcount: A:0.25, C:0.09, G:0.32, T:0.35
Consensus pattern (37 bp):
AGTGGTTAAGTGTGTGAATGTATTCCAAGTGGTTCCA
Found at i:35776505 original size:51 final size:50
Alignment explanation
Indices: 35776349--35776526 Score: 157
Period size: 51 Copynumber: 3.5 Consensus size: 50
35776339 CTAGGTCATG
* * *
35776349 TGTGTAGTACTATGTGCAGACTAATACGTGTATCGGAATG-ATA-GGTCGCA
1 TGTGTAGTACTATGTGCAG-CTACTACGTGTATCGG-ATGAAAATGGTCACA
* * * *** * *
35776399 TGTGTAGTACTATGTGCAAGCTACTATGCGTA-CTAGAT-AGCTTCGATCACT
1 TGTGTAGTACTATGTGC-AGCTACTACGTGTATC-GGATGAAAAT-GGTCACA
35776450 TGTGTAGTACTATGTGCAGCCTACTACGTGTATCGGATGAAAATGGTCACA
1 TGTGTAGTACTATGTGCAG-CTACTACGTGTATCGGATGAAAATGGTCACA
*
35776501 TGTGTAGTACCATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCA-GCTACTA
35776527 AGTGAACCGG
Statistics
Matches: 100, Mismatches: 19, Indels: 17
0.74 0.14 0.12
Matches are distributed among these distances:
49 3 0.03
50 29 0.29
51 64 0.64
52 4 0.04
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.31
Consensus pattern (50 bp):
TGTGTAGTACTATGTGCAGCTACTACGTGTATCGGATGAAAATGGTCACA
Found at i:35780246 original size:17 final size:17
Alignment explanation
Indices: 35780224--35780256 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
35780214 ACCACAATCT
35780224 ATGTAGTGGCATATGGC
1 ATGTAGTGGCATATGGC
35780241 ATGTAGTGGCATATGG
1 ATGTAGTGGCATATGG
35780257 AAGCAATATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.09, G:0.36, T:0.30
Consensus pattern (17 bp):
ATGTAGTGGCATATGGC
Found at i:35789058 original size:52 final size:52
Alignment explanation
Indices: 35789000--35789103 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
35788990 TTTAATTCAA
35789000 AAGCCATAAATTCATTTCAAAGTCATTTTCTTTTTTATTTTTCTTTTTCATT
1 AAGCCATAAATTCATTTCAAAGTCATTTTCTTTTTTATTTTTCTTTTTCATT
35789052 AAGCCATAAATTCATTTCAAAGTCATTTTCTTTTTTATTTTTCTTTTTCATT
1 AAGCCATAAATTCATTTCAAAGTCATTTTCTTTTTTATTTTTCTTTTTCATT
35789104 TTGGAGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.25, C:0.15, G:0.04, T:0.56
Consensus pattern (52 bp):
AAGCCATAAATTCATTTCAAAGTCATTTTCTTTTTTATTTTTCTTTTTCATT
Found at i:35789157 original size:57 final size:58
Alignment explanation
Indices: 35789090--35789209 Score: 179
Period size: 57 Copynumber: 2.1 Consensus size: 58
35789080 TCTTTTTTAT
* * *
35789090 TTTTCTTTTTCATTTTGGAGAAAACCACATTCATTTTCAAATATTTC-CATTTCTCCA
1 TTTTCATTTTCATTTTAGAGAAAACCACATTCATTTCCAAATATTTCTCATTTCTCCA
* * *
35789147 TTTTCATTTTCCTTTTAGAGAAAACCACATTCGTTTCCAAATGTTTCTCATTTCTCCA
1 TTTTCATTTTCATTTTAGAGAAAACCACATTCATTTCCAAATATTTCTCATTTCTCCA
35789205 TTTTC
1 TTTTC
35789210 GCCATTTCTA
Statistics
Matches: 56, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
57 41 0.73
58 15 0.27
ACGTcount: A:0.24, C:0.23, G:0.06, T:0.47
Consensus pattern (58 bp):
TTTTCATTTTCATTTTAGAGAAAACCACATTCATTTCCAAATATTTCTCATTTCTCCA
Found at i:35791557 original size:19 final size:19
Alignment explanation
Indices: 35791533--35791628 Score: 65
Period size: 19 Copynumber: 4.9 Consensus size: 19
35791523 ATCAAATATT
*
35791533 AAAAAT-TATTAAAATTTAG
1 AAAAATATA-TAAAAATTAG
35791552 AAAAATATATAAAAATTAG
1 AAAAATATATAAAAATTAG
*
35791571 AAATAAATAAATAAAAATCGTA-
1 -AA-AAATATATAAAAAT--TAG
35791593 AAAAAT-TATAAAATATATAG
1 AAAAATATATAAAA-AT-TAG
* *
35791613 AAATATA-AGAAAAATT
1 AAAAATATATAAAAATT
35791629 TTAAAATTTT
Statistics
Matches: 63, Mismatches: 6, Indels: 17
0.73 0.07 0.20
Matches are distributed among these distances:
18 1 0.02
19 25 0.40
20 20 0.32
21 15 0.24
23 2 0.03
ACGTcount: A:0.66, C:0.01, G:0.05, T:0.28
Consensus pattern (19 bp):
AAAAATATATAAAAATTAG
Found at i:35791584 original size:21 final size:19
Alignment explanation
Indices: 35791542--35791588 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 19
35791532 TAAAAATTAT
* *
35791542 TAAAATTTAGAAAAATATA
1 TAAAAATTAGAAAAATAAA
35791561 TAAAAATTAGAAATAAATAAA
1 TAAAAATTAG-AA-AAATAAA
35791582 TAAAAAT
1 TAAAAAT
35791589 CGTAAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 9 0.38
20 2 0.08
21 13 0.54
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (19 bp):
TAAAAATTAGAAAAATAAA
Found at i:35791777 original size:18 final size:19
Alignment explanation
Indices: 35791728--35791778 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 19
35791718 CAAAAAAACA
35791728 TTTTATAATTTTTCTATAT
1 TTTTATAATTTTTCTATAT
* *
35791747 TTTTATTGA-TTTT-TATTT
1 TTTTA-TAATTTTTCTATAT
*
35791765 TTTTATCATTTTTC
1 TTTTATAATTTTTC
35791779 GCCAATGTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
17 2 0.08
18 13 0.50
19 9 0.35
20 2 0.08
ACGTcount: A:0.20, C:0.06, G:0.02, T:0.73
Consensus pattern (19 bp):
TTTTATAATTTTTCTATAT
Found at i:35791952 original size:20 final size:21
Alignment explanation
Indices: 35791929--35791978 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
35791919 AAATTTTTTA
35791929 TATTTTTATTAAAATTTAA-T
1 TATTTTTATTAAAATTTAATT
*
35791949 TATTTTT-CTAAAATTTAATT
1 TATTTTTATTAAAATTTAATT
*
35791969 TATTATTATT
1 TATTTTTATT
35791979 TTTTAATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 10 0.40
20 14 0.56
21 1 0.04
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
TATTTTTATTAAAATTTAATT
Found at i:35792002 original size:19 final size:19
Alignment explanation
Indices: 35791943--35792004 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
35791933 TTTATTAAAA
**
35791943 TTTAATTATTTTTCTAAAA
1 TTTAATTATTTTTCTAATT
* *
35791962 TTTAATT-TATTAT-TATTT
1 TTTAATTAT-TTTTCTAATT
35791980 TTTAATTATTTTTCTAATT
1 TTTAATTATTTTTCTAATT
35791999 TTTAAT
1 TTTAAT
35792005 AAGAGTAGGG
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
18 13 0.38
19 21 0.62
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTAATTATTTTTCTAATT
Found at i:35793128 original size:4 final size:4
Alignment explanation
Indices: 35793119--35793149 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
35793109 AAGTTTTATT
35793119 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
35793150 TACTTAGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:35796047 original size:56 final size:56
Alignment explanation
Indices: 35795959--35796066 Score: 153
Period size: 56 Copynumber: 1.9 Consensus size: 56
35795949 GGATTACATG
* * *
35795959 TGTAAGACCATACCCCGACTATGACATCCGTTAAATTCTTCCATGACATTAACCAT
1 TGTAAGACCATACCCCGACTATGACATCCGTTAAAGTCTGCCAGGACATTAACCAT
* * * *
35796015 TGTAAGACCATAGCTCGACTATGGCATTCGTTAAAGTCTGCCAGGACATTAA
1 TGTAAGACCATACCCCGACTATGACATCCGTTAAAGTCTGCCAGGACATTAA
35796067 ACATGGGGAT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
56 45 1.00
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (56 bp):
TGTAAGACCATACCCCGACTATGACATCCGTTAAAGTCTGCCAGGACATTAACCAT
Done.