Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 17 of 208
Found at i:5108855 original size:21 final size:21
Alignment explanation
Indices: 5108830--5108871 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5108820 CTGTTATGTC
*
5108830 AAATATAATTTGAACAATAAA
1 AAATATAATTTGAAAAATAAA
**
5108851 AAATATTTTTTGAAAAATAAA
1 AAATATAATTTGAAAAATAAA
5108872 TAAAATTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (21 bp):
AAATATAATTTGAAAAATAAA
Found at i:5108879 original size:21 final size:21
Alignment explanation
Indices: 5108838--5108879 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
5108828 TCAAATATAA
*
5108838 TTTGAACAATAAAAAATATTT
1 TTTGAAAAATAAAAAATATTT
5108859 TTTGAAAAATAAATAAA-ATTT
1 TTTGAAAAATAAA-AAATATTT
5108880 ATTTCGAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.38
Consensus pattern (21 bp):
TTTGAAAAATAAAAAATATTT
Found at i:5110774 original size:39 final size:40
Alignment explanation
Indices: 5110642--5110790 Score: 178
Period size: 40 Copynumber: 3.8 Consensus size: 40
5110632 TTTGTTATTC
* *
5110642 AAACGCCGCTATAGATCGAACATTAGCGGCGCTTCTTGAAA
1 AAACGCCGCTATAGATCGAGCATTAGCGGCGCTTC-TAAAA
* * **
5110683 AAA-GTCGTTATAGATCGAGCATTAGCGGCGCTTCTTGAA
1 AAACGCCGCTATAGATCGAGCATTAGCGGCGCTTCTAAAA
* *
5110722 AAACTCTGCTATAGATCGAGCATTAGCGGCGCTT-TAAAAA
1 AAACGCCGCTATAGATCGAGCATTAGCGGCGCTTCT-AAAA
*
5110762 AAACG-CGCTATAGATCAAGCATTAGCGGC
1 AAACGCCGCTATAGATCGAGCATTAGCGGC
5110791 TTTTTTCAAA
Statistics
Matches: 92, Mismatches: 14, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
39 29 0.32
40 60 0.65
41 3 0.03
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.23
Consensus pattern (40 bp):
AAACGCCGCTATAGATCGAGCATTAGCGGCGCTTCTAAAA
Found at i:5111434 original size:7 final size:7
Alignment explanation
Indices: 5111422--5111695 Score: 88
Period size: 7 Copynumber: 38.7 Consensus size: 7
5111412 AATATATACA
5111422 TTTAGGG
1 TTTAGGG
5111429 TTTAGGG
1 TTTAGGG
*
5111436 TGTA-GG
1 TTTAGGG
***
5111442 TTTATTA
1 TTTAGGG
*
5111449 TTTGGGG
1 TTTAGGG
***
5111456 TTTAAAA
1 TTTAGGG
*
5111463 TTTAAGG
1 TTTAGGG
* *
5111470 TTTATGA
1 TTTAGGG
*
5111477 TTTAGTG
1 TTTAGGG
* *
5111484 TTAAGAG
1 TTTAGGG
*
5111491 TTTAGTG
1 TTTAGGG
*
5111498 TTTACGG
1 TTTAGGG
5111505 TTTAGGG
1 TTTAGGG
*
5111512 TGTA-GG
1 TTTAGGG
*
5111518 TTTATGG
1 TTTAGGG
*
5111525 TTTAGTG
1 TTTAGGG
*
5111532 TTTAGTG
1 TTTAGGG
*
5111539 TGTAAGGG
1 T-TTAGGG
*
5111547 TTAAGGG
1 TTTAGGG
5111554 -TTAGGAG
1 TTTAGG-G
* *
5111561 CTTAGGAT
1 TTTAGG-G
5111569 TTATAGGG
1 TT-TAGGG
5111577 -TTATGGG
1 TTTA-GGG
*
5111584 CTTAGGG
1 TTTAGGG
5111591 TTTAGGG
1 TTTAGGG
*
5111598 GTTAGGAG
1 TTTAGG-G
* *
5111606 ATTAAGG
1 TTTAGGG
*
5111613 TTTAAGG
1 TTTAGGG
***
5111620 TTTAAAT
1 TTTAGGG
* *
5111627 TTTATGT
1 TTTAGGG
5111634 TTTAGGG
1 TTTAGGG
5111641 TTTAGTGG
1 TTTAG-GG
*
5111649 CTTAGGG
1 TTTAGGG
* *
5111656 TTTATGA
1 TTTAGGG
*
5111663 TTTAGTG
1 TTTAGGG
5111670 TTTAGGG
1 TTTAGGG
**
5111677 TTTAGTA
1 TTTAGGG
*
5111684 TTTATGG
1 TTTAGGG
5111691 TTTAG
1 TTTAG
5111696 CTAAAAACAT
Statistics
Matches: 196, Mismatches: 61, Indels: 20
0.71 0.22 0.07
Matches are distributed among these distances:
6 16 0.08
7 150 0.77
8 26 0.13
9 4 0.02
ACGTcount: A:0.22, C:0.01, G:0.32, T:0.45
Consensus pattern (7 bp):
TTTAGGG
Found at i:5111576 original size:23 final size:22
Alignment explanation
Indices: 5111547--5111619 Score: 78
Period size: 23 Copynumber: 3.3 Consensus size: 22
5111537 TGTGTAAGGG
5111547 TTAAGGGTTAGGAGCTTAGGAT
1 TTAAGGGTTAGGAGCTTAGGAT
*
5111569 TTATAGGGTTATGG-GCTTAGGGT
1 TTA-AGGGTTA-GGAGCTTAGGAT
* *
5111592 TTAGGGGTTAGGAGATTAAGG-T
1 TTAAGGGTTAGGAGCTT-AGGAT
5111614 TTAAGG
1 TTAAGG
5111620 TTTAAATTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
21 2 0.05
22 18 0.42
23 21 0.49
24 2 0.05
ACGTcount: A:0.25, C:0.03, G:0.38, T:0.34
Consensus pattern (22 bp):
TTAAGGGTTAGGAGCTTAGGAT
Found at i:5112247 original size:24 final size:24
Alignment explanation
Indices: 5112183--5112249 Score: 77
Period size: 23 Copynumber: 2.9 Consensus size: 24
5112173 CCCCACTCAG
* *
5112183 ATTTCCCCGATTTTATTT-CCCCA
1 ATTTCCCCAATTTCATTTCCCCCA
*
5112206 ATTT-TCCAA-TTCATTTTCCCCCA
1 ATTTCCCCAATTTCA-TTTCCCCCA
5112229 ATTTCCCCAATTTCATTTCCC
1 ATTTCCCCAATTTCATTTCCC
5112250 TAAATTCCCA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
21 3 0.08
22 6 0.17
23 13 0.36
24 10 0.28
25 4 0.11
ACGTcount: A:0.19, C:0.36, G:0.01, T:0.43
Consensus pattern (24 bp):
ATTTCCCCAATTTCATTTCCCCCA
Found at i:5112255 original size:24 final size:23
Alignment explanation
Indices: 5112183--5112258 Score: 75
Period size: 23 Copynumber: 3.3 Consensus size: 23
5112173 CCCCACTCAG
* *
5112183 ATTTCCCCGATTTTATTTCCCCA
1 ATTTCCCCAATTTCATTTCCCCA
*
5112206 ATTT-TCCAA-TTCATTTTCCCCCA
1 ATTTCCCCAATTTCA-TTT-CCCCA
*
5112229 ATTTCCCCAATTTCATTTCCCTA
1 ATTTCCCCAATTTCATTTCCCCA
*
5112252 AATTCCC
1 ATTTCCC
5112259 AACAGACTTG
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
21 3 0.07
22 6 0.14
23 23 0.53
24 7 0.16
25 4 0.09
ACGTcount: A:0.21, C:0.36, G:0.01, T:0.42
Consensus pattern (23 bp):
ATTTCCCCAATTTCATTTCCCCA
Found at i:5112415 original size:23 final size:22
Alignment explanation
Indices: 5112348--5112422 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
5112338 CCTCACTCAG
*
5112348 ATTTCCCGATTTTA-TTTCCCTA
1 ATTTCCCGATTTCATTTTCCC-A
* *
5112370 ATTTCCC-AATTCCTTTTCCCCCA
1 ATTTCCCGATTTCATTTT--CCCA
5112393 ATTTCCCCGATTTCATTTTCCCA
1 ATTT-CCCGATTTCATTTTCCCA
*
5112416 AATTCCC
1 ATTTCCC
5112423 AACTGACCTA
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
21 3 0.07
22 13 0.31
23 12 0.29
24 6 0.14
25 8 0.19
ACGTcount: A:0.19, C:0.36, G:0.03, T:0.43
Consensus pattern (22 bp):
ATTTCCCGATTTCATTTTCCCA
Found at i:5112452 original size:164 final size:165
Alignment explanation
Indices: 5112164--5112490 Score: 496
Period size: 164 Copynumber: 2.0 Consensus size: 165
5112154 CCGAATTTTG
*
5112164 TTAGTTTTCCCCCACTCAGATTTCCCCGATTTTATTTCCCCAATTTTCCAATTCATTTTCCCCCA
1 TTAGTTTTCCCCCACTCAGATTTCCCCGATTTTATTTCCCCAATTTCCCAATTCATTTTCCCCCA
* * *
5112229 ATTTCCCCAATTTCATTTCCCTAAATTCCCAACAGACTTGTCCAACGCCGCTACCGTCGCAATCG
66 ATTTCCCCAATTTCATTTCCCTAAATTCCCAACAGACCTATCCAACACCGCTACCGTCGCAATCG
*
5112294 TCTCCACTCTGGCAGTCACTCTGTCACCCGCTTAC
131 TCTCCACTCTAGCAGTCACTCTGTCACCCGCTTAC
* * *
5112329 TTAGTTTTCCCTCACTCAGATTT-CCCGATTTTATTTCCCTAATTTCCCAATTCCTTTTCCCCCA
1 TTAGTTTTCCCCCACTCAGATTTCCCCGATTTTATTTCCCCAATTTCCCAATTCATTTTCCCCCA
* * * * *
5112393 ATTTCCCCGATTTCATTTTCCC-AAATTCCCAACTGACCTATCCAACACCGTTGCCGTCGCAGTC
66 ATTTCCCCAATTTCA-TTTCCCTAAATTCCCAACAGACCTATCCAACACCGCTACCGTCGCAATC
* *
5112457 GTCTCCACTCTAGCGGTCGCTCTGTCACCCGCTT
130 GTCTCCACTCTAGCAGTCACTCTGTCACCCGCTT
5112491 CCTCTATTCA
Statistics
Matches: 146, Mismatches: 15, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
164 118 0.81
165 28 0.19
ACGTcount: A:0.19, C:0.37, G:0.10, T:0.34
Consensus pattern (165 bp):
TTAGTTTTCCCCCACTCAGATTTCCCCGATTTTATTTCCCCAATTTCCCAATTCATTTTCCCCCA
ATTTCCCCAATTTCATTTCCCTAAATTCCCAACAGACCTATCCAACACCGCTACCGTCGCAATCG
TCTCCACTCTAGCAGTCACTCTGTCACCCGCTTAC
Found at i:5114128 original size:21 final size:20
Alignment explanation
Indices: 5114104--5114186 Score: 70
Period size: 21 Copynumber: 4.3 Consensus size: 20
5114094 TCTTAACTTA
5114104 ATAACTTATATATATCATATC
1 ATAACTTATATATATC-TATC
5114125 ATAACTTATATA-A-CTCA-C
1 ATAACTTATATATATCT-ATC
* * *
5114143 ATAAC--ATACATAACT-TA
1 ATAACTTATATATATCTATC
5114160 ATAACTTATATATATCATATC
1 ATAACTTATATATATC-TATC
5114181 ATAACT
1 ATAACT
5114187 CACATAACTT
Statistics
Matches: 49, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
16 4 0.08
17 6 0.12
18 9 0.18
19 9 0.18
20 2 0.04
21 19 0.39
ACGTcount: A:0.46, C:0.17, G:0.00, T:0.37
Consensus pattern (20 bp):
ATAACTTATATATATCTATC
Found at i:5114188 original size:47 final size:52
Alignment explanation
Indices: 5114134--5114376 Score: 248
Period size: 52 Copynumber: 4.6 Consensus size: 52
5114124 CATAACTTAT
*
5114134 ATAACTCACATAACAT-ACATAACTTA-AT-A-AC-T-TATATATATCATATC
1 ATAACTCACATAAC-TCACATAACTTACATAATACATAAATATATATCATATC
* *
5114181 ATAACTCACATAACTTATATAACTTACATAATACATAAATATATATCATATC
1 ATAACTCACATAACTCACATAACTTACATAATACATAAATATATATCATATC
* *
5114233 ATAACTTACATAACTCACATAACTTACATGATACATAAATATATATCATA-C
1 ATAACTCACATAACTCACATAACTTACATAATACATAAATATATATCATATC
* *
5114284 ATAACTTACATAACTCACATAACTTACAAAGCTTACATAATACATAAATATATATAATATC
1 ATAACTCACATAACTCAC---A--T---AA-CTTACATAATACATAAATATATATCATATC
* * * *
5114345 ATAACTTATATAACTCTCATAACTTACGTAAT
1 ATAACTCACATAACTCACATAACTTACATAAT
5114377 TTACATAATA
Statistics
Matches: 169, Mismatches: 11, Indels: 27
0.82 0.05 0.13
Matches are distributed among these distances:
46 1 0.01
47 23 0.14
48 2 0.01
49 1 0.01
50 2 0.01
51 20 0.12
52 69 0.41
53 2 0.01
54 1 0.01
56 2 0.01
58 1 0.01
59 2 0.01
60 26 0.15
61 17 0.10
ACGTcount: A:0.47, C:0.19, G:0.01, T:0.33
Consensus pattern (52 bp):
ATAACTCACATAACTCACATAACTTACATAATACATAAATATATATCATATC
Found at i:5114244 original size:52 final size:52
Alignment explanation
Indices: 5114111--5114422 Score: 286
Period size: 61 Copynumber: 5.6 Consensus size: 52
5114101 TTAATAACTT
* * * *
5114111 ATATATATCATATCATAACTTATATAACTCACATAACATACATAACTTA-ATAA
1 ATATATATCATATCATAACTTACATAACTTATATAACTTACATAA--TACATAA
*
5114164 CTTATATATATCATATCATAACTCACATAACTTATATAACTTACATAATACATAA
1 ---ATATATATCATATCATAACTTACATAACTTATATAACTTACATAATACATAA
* * *
5114219 ATATATATCATATCATAACTTACATAACTCACATAACTTACATGATACATAA
1 ATATATATCATATCATAACTTACATAACTTATATAACTTACATAATACATAA
*
5114271 ATATATATCATA-CATAACTTACATAACTCACATAACTTACAAAGCTTACATAATACATAA
1 ATATATATCATATCATAACTTACATAACT----T-A--TA-TAA-CTTACATAATACATAA
* * *
5114331 ATATATATAATATCATAACTTATATAACTCTCATAACTTACGTAATTTACATAATACATAA
1 ATATATATCATATCATAACTTACATAA--CT--T-A--TA--TAACTTACATAATACATAA
*
5114392 ATATATATCATATCATAACTTGCATAACTTA
1 ATATATATCATATCATAACTTACATAACTTA
5114423 ATTATACTTA
Statistics
Matches: 221, Mismatches: 21, Indels: 28
0.82 0.08 0.10
Matches are distributed among these distances:
51 16 0.07
52 60 0.27
54 2 0.01
55 4 0.02
56 42 0.19
57 1 0.00
58 1 0.00
59 4 0.02
60 26 0.12
61 61 0.28
62 2 0.01
63 2 0.01
ACGTcount: A:0.46, C:0.18, G:0.01, T:0.35
Consensus pattern (52 bp):
ATATATATCATATCATAACTTACATAACTTATATAACTTACATAATACATAA
Found at i:5114261 original size:9 final size:9
Alignment explanation
Indices: 5114097--5114422 Score: 155
Period size: 9 Copynumber: 36.8 Consensus size: 9
5114087 CTTTGGATCT
5114097 TAACTTA-A
1 TAACTTACA
*
5114105 TAACTTATA
1 TAACTTACA
*
5114114 TATATCATATCA
1 TA-A-CTTA-CA
*
5114126 TAACTTATA
1 TAACTTACA
*
5114135 TAACTCACA
1 TAACTTACA
*
5114144 TAACATACA
1 TAACTTACA
5114153 TAACTTA-A
1 TAACTTACA
*
5114161 TAACTTATA
1 TAACTTACA
*
5114170 TATATCATATCA
1 TA-A-CTTA-CA
*
5114182 TAACTCACA
1 TAACTTACA
*
5114191 TAACTTATA
1 TAACTTACA
5114200 TAACTTACA
1 TAACTTACA
5114209 TAA--TACA
1 TAACTTACA
* *
5114216 TAA-ATATA
1 TAACTTACA
* *
5114224 TATCATATCA
1 TAACTTA-CA
5114234 TAACTTACA
1 TAACTTACA
*
5114243 TAACTCACA
1 TAACTTACA
5114252 TAACTTACA
1 TAACTTACA
*
5114261 TGA--TACA
1 TAACTTACA
* *
5114268 TAA-ATATA
1 TAACTTACA
* *
5114276 TATCATACA
1 TAACTTACA
5114285 TAACTTACA
1 TAACTTACA
*
5114294 TAACTCACA
1 TAACTTACA
5114303 TAACTTACA
1 TAACTTACA
5114312 -AAGCTTACA
1 TAA-CTTACA
5114321 TAA--TACA
1 TAACTTACA
* *
5114328 TAAATATATA
1 TAACT-TACA
5114338 TAA--TATCA
1 TAACTTA-CA
*
5114346 TAACTTATA
1 TAACTTACA
5114355 TAACTCT-CA
1 TAACT-TACA
*
5114364 TAACTTACG
1 TAACTTACA
*
5114373 TAATTTACA
1 TAACTTACA
5114382 TAA--TACA
1 TAACTTACA
* *
5114389 TAA-ATATA
1 TAACTTACA
* *
5114397 TATCATATCA
1 TAACTTA-CA
*
5114407 TAACTTGCA
1 TAACTTACA
5114416 TAACTTA
1 TAACTTA
5114423 ATTATACTTA
Statistics
Matches: 246, Mismatches: 46, Indels: 51
0.72 0.13 0.15
Matches are distributed among these distances:
7 29 0.12
8 37 0.15
9 137 0.56
10 29 0.12
11 8 0.03
12 6 0.02
ACGTcount: A:0.46, C:0.17, G:0.01, T:0.35
Consensus pattern (9 bp):
TAACTTACA
Found at i:5114336 original size:112 final size:107
Alignment explanation
Indices: 5114111--5114422 Score: 360
Period size: 112 Copynumber: 2.8 Consensus size: 107
5114101 TTAATAACTT
* *
5114111 ATATATATCATATCATAACTTATATAACTCACATAACATACATAACTTAATAACTTATATATATC
1 ATATATATCATATCATAACTTATATAACTCACATAACTTACATAAC-TAATAAATTATATATATC
*
5114176 ATATCATAACTCACATAACTTATATAACTTACATAATACATAA
65 ATATCATAACTCACATAACTTACATAACTTACATAATACATAA
* *
5114219 ATATATATCATATCATAACTTACATAACTCACATAACTTACATGA-TACATAAA-TATATATCAT
1 ATATATATCATATCATAACTTATATAACTCACATAACTTACATAACTA-ATAAATTATATAT-AT
5114282 ACATAACTTACATAACTCACATAACTTACA-AAGCTTACATAATACATAA
64 -CAT-A--T-CATAACTCACATAACTTACATAA-CTTACATAATACATAA
* * * * *
5114331 ATATATATAATATCATAACTTATATAACTCTCATAACTTACGTAATTTACATAATACATAAATAT
1 ATATATATCATATCATAACTTATATAACTCACATAACTTAC---A-TAAC-TAATAAAT-TATAT
**
5114396 ATATCATATCATAACTTGCATAACTTA
60 ATATCATATCATAACTCACATAACTTA
5114423 ATTATACTTA
Statistics
Matches: 175, Mismatches: 13, Indels: 27
0.81 0.06 0.13
Matches are distributed among these distances:
106 9 0.05
107 6 0.03
108 45 0.26
109 1 0.01
111 3 0.02
112 73 0.42
113 16 0.09
114 1 0.01
115 1 0.01
116 3 0.02
117 7 0.04
118 4 0.02
119 6 0.03
ACGTcount: A:0.46, C:0.18, G:0.01, T:0.35
Consensus pattern (107 bp):
ATATATATCATATCATAACTTATATAACTCACATAACTTACATAACTAATAAATTATATATATCA
TATCATAACTCACATAACTTACATAACTTACATAATACATAA
Found at i:5114342 original size:17 final size:17
Alignment explanation
Indices: 5114320--5114357 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
5114310 CAAAGCTTAC
5114320 ATAATA-CATAAATATAT
1 ATAATATCATAAAT-TAT
*
5114337 ATAATATCATAACTTAT
1 ATAATATCATAAATTAT
5114354 ATAA
1 ATAA
5114358 CTCTCATAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (17 bp):
ATAATATCATAAATTAT
Found at i:5116147 original size:12 final size:12
Alignment explanation
Indices: 5116130--5116155 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5116120 AAGATCGAGG
5116130 GATGAATCTGAT
1 GATGAATCTGAT
5116142 GATGAATCTGAT
1 GATGAATCTGAT
5116154 GA
1 GA
5116156 AGAGGATGAT
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:0.35, C:0.08, G:0.27, T:0.31
Consensus pattern (12 bp):
GATGAATCTGAT
Found at i:5118800 original size:16 final size:16
Alignment explanation
Indices: 5118763--5118802 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
5118753 TGACTCAAAT
* *
5118763 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
5118779 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
5118795 TAAAATTA
1 TAAAATTA
5118803 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:5118887 original size:9 final size:9
Alignment explanation
Indices: 5118875--5118918 Score: 65
Period size: 9 Copynumber: 5.1 Consensus size: 9
5118865 ATTATCAAAT
5118875 TATTAATTG
1 TATTAATTG
5118884 TATTAATTG
1 TATTAATTG
5118893 --TTAATTG
1 TATTAATTG
*
5118900 TATTGATTG
1 TATTAATTG
5118909 TATTAATTG
1 TATTAATTG
5118918 T
1 T
5118919 TGTAACAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
7 7 0.23
9 24 0.77
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:5118896 original size:16 final size:16
Alignment explanation
Indices: 5118872--5118909 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
5118862 AAAATTATCA
*
5118872 AATTATTAATTGTATT
1 AATTGTTAATTGTATT
5118888 AATTGTTAATTGTATT
1 AATTGTTAATTGTATT
*
5118904 GATTGT
1 AATTGT
5118910 ATTAATTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (16 bp):
AATTGTTAATTGTATT
Found at i:5120274 original size:27 final size:29
Alignment explanation
Indices: 5120244--5120300 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
5120234 AACTAAAAAC
5120244 TTAAACAT-AAAAA-TAAATATATATATT
1 TTAAACATAAAAAACTAAATATATATATT
*
5120271 TTAAACATAAAAAACTTAATATATATATT
1 TTAAACATAAAAAACTAAATATATATATT
5120300 T
1 T
5120301 AATATATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 8 0.30
28 5 0.19
29 14 0.52
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (29 bp):
TTAAACATAAAAAACTAAATATATATATT
Found at i:5121390 original size:13 final size:14
Alignment explanation
Indices: 5121374--5121402 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
5121364 TTTTAAATAT
5121374 TTATAATG-TTTAA
1 TTATAATGATTTAA
5121387 TTATAATGATTTAA
1 TTATAATGATTTAA
5121401 TT
1 TT
5121403 CTTTGTTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (14 bp):
TTATAATGATTTAA
Found at i:5122222 original size:43 final size:42
Alignment explanation
Indices: 5122175--5122305 Score: 146
Period size: 43 Copynumber: 3.2 Consensus size: 42
5122165 GAACGGTACT
*
5122175 TTTAGCGGTGTTTGTGA-AAAAGGCGCCGCTAAAGGTCATGTTC
1 TTTAGCGGCGTTTGTGACAAAA-GCGCCGCTAAA-GTCATGTTC
* * *
5122218 TTTAGCGGCGTTTGTGATAAAAGTGCCGTTAAAG----GTTC
1 TTTAGCGGCGTTTGTGACAAAAGCGCCGCTAAAGTCATGTTC
* *
5122256 TTTAGAGGCATTTGTGACAAAAGCGCCGCTAAAGTACATGTTC
1 TTTAGCGGCGTTTGTGACAAAAGCGCCGCTAAAGT-CATGTTC
5122299 TTTAGCG
1 TTTAGCG
5122306 ACATTGTCTA
Statistics
Matches: 73, Mismatches: 9, Indels: 12
0.78 0.10 0.13
Matches are distributed among these distances:
38 33 0.45
42 1 0.01
43 35 0.48
44 4 0.05
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.31
Consensus pattern (42 bp):
TTTAGCGGCGTTTGTGACAAAAGCGCCGCTAAAGTCATGTTC
Found at i:5122270 original size:38 final size:38
Alignment explanation
Indices: 5122214--5122289 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
5122204 TAAAGGTCAT
* * * * *
5122214 GTTCTTTAGCGGCGTTTGTGATAAAAGTGCCGTTAAAG
1 GTTCTTTAGAGGCATTTGTGACAAAAGCGCCGCTAAAG
5122252 GTTCTTTAGAGGCATTTGTGACAAAAGCGCCGCTAAAG
1 GTTCTTTAGAGGCATTTGTGACAAAAGCGCCGCTAAAG
5122290 TACATGTTCT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (38 bp):
GTTCTTTAGAGGCATTTGTGACAAAAGCGCCGCTAAAG
Found at i:5127852 original size:29 final size:29
Alignment explanation
Indices: 5127812--5127867 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
5127802 ATATGGACAA
5127812 GATCAAATTAGTCCCTCTATTATTAAATT
1 GATCAAATTAGTCCCTCTATTATTAAATT
* * *
5127841 GATCAATTTAGTCTCTTTATTATTAAA
1 GATCAAATTAGTCCCTCTATTATTAAA
5127868 AGGAATAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (29 bp):
GATCAAATTAGTCCCTCTATTATTAAATT
Found at i:5129459 original size:12 final size:12
Alignment explanation
Indices: 5129444--5129492 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
5129434 GAGGTGGTAT
5129444 TGGAGCTGGAAC
1 TGGAGCTGGAAC
*
5129456 TGGATCT-G-A-
1 TGGAGCTGGAAC
*
5129465 TGGAGCTGGAGC
1 TGGAGCTGGAAC
*
5129477 TGGAGCTGGAAT
1 TGGAGCTGGAAC
5129489 TGGA
1 TGGA
5129493 ATTGGTGGTG
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
9 6 0.21
10 2 0.07
11 1 0.03
12 20 0.69
ACGTcount: A:0.22, C:0.12, G:0.43, T:0.22
Consensus pattern (12 bp):
TGGAGCTGGAAC
Found at i:5129686 original size:6 final size:6
Alignment explanation
Indices: 5129603--5129682 Score: 67
Period size: 6 Copynumber: 13.8 Consensus size: 6
5129593 CTGGTGGTGG
* * * * * *
5129603 TGGAAC TGGAAC TGGAAT TGG--- TGGTAG TGGAGC TGGAGC TAGAAC
1 TGGAAC TGGAAC TGGAAC TGGAAC TGGAAC TGGAAC TGGAAC TGGAAC
* *
5129648 TGGAGC TGGAAC TGGAAC TGGAAC TGGAAT TGGAA
1 TGGAAC TGGAAC TGGAAC TGGAAC TGGAAC TGGAA
5129683 TTGGTGGTGG
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
3 3 0.05
6 58 0.95
ACGTcount: A:0.29, C:0.11, G:0.39, T:0.21
Consensus pattern (6 bp):
TGGAAC
Found at i:5129843 original size:18 final size:18
Alignment explanation
Indices: 5129810--5129844 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5129800 GAAGTGGTGG
*
5129810 AGCTAGTGGAGTTGGAAA
1 AGCTAGTGGAGGTGGAAA
*
5129828 AGCTAGTGGTGGTGGAA
1 AGCTAGTGGAGGTGGAA
5129845 CTGGTGGAGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.06, G:0.43, T:0.23
Consensus pattern (18 bp):
AGCTAGTGGAGGTGGAAA
Found at i:5134628 original size:18 final size:18
Alignment explanation
Indices: 5134605--5134645 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
5134595 CTACATATTT
5134605 TTTTATGTATAT-ACATTA
1 TTTTAT-TATATAACATTA
*
5134623 TTTTATTATATAATATTA
1 TTTTATTATATAACATTA
5134641 TTTTA
1 TTTTA
5134646 AGTTTTAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (18 bp):
TTTTATTATATAACATTA
Found at i:5137852 original size:20 final size:20
Alignment explanation
Indices: 5137827--5137887 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 20
5137817 TATGAACATT
5137827 AAATAAATTAATATAATAAA
1 AAATAAATTAATATAATAAA
* *
5137847 AAAT-AATTACATAGAA-CAA
1 AAATAAATTA-ATATAATAAA
* *
5137866 AAATAAATATAAAATTATAAA
1 AAATAAAT-TAATATAATAAA
5137887 A
1 A
5137888 GAATCAAATG
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
19 11 0.35
20 15 0.48
21 5 0.16
ACGTcount: A:0.69, C:0.03, G:0.02, T:0.26
Consensus pattern (20 bp):
AAATAAATTAATATAATAAA
Found at i:5139287 original size:23 final size:23
Alignment explanation
Indices: 5139260--5139304 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
5139250 TTTCCTAATG
* *
5139260 AAACCAAATTCAATGCCAAATCA
1 AAACCAAATCCAATACCAAATCA
5139283 AAACCAAATCCAATACCAAATC
1 AAACCAAATCCAATACCAAATC
5139305 GAGCTTCAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.53, C:0.29, G:0.02, T:0.16
Consensus pattern (23 bp):
AAACCAAATCCAATACCAAATCA
Found at i:5139304 original size:12 final size:12
Alignment explanation
Indices: 5139262--5139304 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
5139252 TCCTAATGAA
*
5139262 ACCAAATTCAAT
1 ACCAAATCCAAT
* *
5139274 GCCAAAT-CAAA
1 ACCAAATCCAAT
5139285 ACCAAATCCAAT
1 ACCAAATCCAAT
5139297 ACCAAATC
1 ACCAAATC
5139305 GAGCTTCAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
11 9 0.35
12 17 0.65
ACGTcount: A:0.51, C:0.30, G:0.02, T:0.16
Consensus pattern (12 bp):
ACCAAATCCAAT
Found at i:5145690 original size:30 final size:29
Alignment explanation
Indices: 5145651--5145756 Score: 88
Period size: 30 Copynumber: 3.5 Consensus size: 29
5145641 GGTGGAGACT
*
5145651 TTGGTAAAGGTGGTGGATATGGTGGTGGGA
1 TTGG-AAAGGTGGTGGATATGGTGGTGGAA
* * *
5145681 TTGGCAAAGGAGGAGG-TGTTGGTGGTGGAA
1 TTGG-AAAGGTGGTGGAT-ATGGTGGTGGAA
* * *
5145711 TTGGGAAAGGTGGTGGATACGGAGGTGGCA
1 TT-GGAAAGGTGGTGGATATGGTGGTGGAA
*
5145741 TAGGAAAGGGTGGTGG
1 TTGGAAA-GGTGGTGG
5145757 GATTGGCAAA
Statistics
Matches: 60, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
29 6 0.10
30 51 0.85
31 3 0.05
ACGTcount: A:0.23, C:0.03, G:0.51, T:0.24
Consensus pattern (29 bp):
TTGGAAAGGTGGTGGATATGGTGGTGGAA
Found at i:5145764 original size:78 final size:78
Alignment explanation
Indices: 5145671--5145960 Score: 458
Period size: 78 Copynumber: 3.7 Consensus size: 78
5145661 TGGTGGATAT
* * *
5145671 GGTGGTGGGATTGGCAAAGGAGGAGGTGTTGGTGGTGGAATTGGGAAA-GGTGGTGGATACGGAG
1 GGTGGTGGGATTGGCAAAGGAGGAGGTGTTGGAGGTGGAA-TCGGAAAGGGTGGAGGATACGGAG
5145735 GTGGCATAGGAAAG
65 GTGGCATAGGAAAG
*
5145749 GGTGGTGGGATTGGCAAAGGAGGAGGTGTTGGTGGTGGAATCGGAAAGGGTGGAGGATACGGAGG
1 GGTGGTGGGATTGGCAAAGGAGGAGGTGTTGGAGGTGGAATCGGAAAGGGTGGAGGATACGGAGG
*
5145814 TGGCATAGGAAAA
66 TGGCATAGGAAAG
5145827 GGTGGTGGGATTGGCAAAGGAGGAGGTGTTGGAGGTGGAATCGGAAAGGGTGGAGGATACGGAGG
1 GGTGGTGGGATTGGCAAAGGAGGAGGTGTTGGAGGTGGAATCGGAAAGGGTGGAGGATACGGAGG
*
5145892 TGGCATCGGAAAG
66 TGGCATAGGAAAG
* * * *
5145905 GGTGGTGGGATTGGCAAAGGAGGAGGAT-ATGGAGGTGGAATTGGTAAGGGAGGAGG
1 GGTGGTGGGATTGGCAAAGGAGGAGG-TGTTGGAGGTGGAATCGGAAAGGGTGGAGG
5145961 CCATGGAATT
Statistics
Matches: 200, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
77 6 0.03
78 193 0.96
79 1 0.00
ACGTcount: A:0.26, C:0.04, G:0.51, T:0.18
Consensus pattern (78 bp):
GGTGGTGGGATTGGCAAAGGAGGAGGTGTTGGAGGTGGAATCGGAAAGGGTGGAGGATACGGAGG
TGGCATAGGAAAG
Found at i:5145990 original size:36 final size:30
Alignment explanation
Indices: 5145905--5145990 Score: 82
Period size: 30 Copynumber: 2.7 Consensus size: 30
5145895 CATCGGAAAG
*
5145905 GGTGGTGGGATTGGCAAAGGAGGAGGATAT
1 GGTGGTGGGATTGGCAAGGGAGGAGGATAT
* * *
5145935 GGAGGTGGAATTGGTAAGGGAGGAGGCCATGGAATT
1 GGTGGTGGGATTGGCAAGGGAGGAGG--AT---A-T
5145971 GGTGGTGGGATTGGCAAGGG
1 GGTGGTGGGATTGGCAAGGG
5145991 TGGTGGAGTC
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
30 22 0.51
32 2 0.05
35 1 0.02
36 18 0.42
ACGTcount: A:0.24, C:0.05, G:0.51, T:0.20
Consensus pattern (30 bp):
GGTGGTGGGATTGGCAAGGGAGGAGGATAT
Found at i:5146022 original size:18 final size:18
Alignment explanation
Indices: 5146001--5146041 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
5145991 TGGTGGAGTC
*
5146001 GGTGGAGGAATTGGAAAG
1 GGTGGAGGAATTGGAAAA
* *
5146019 GGTGGCGGGATTGGAAAA
1 GGTGGAGGAATTGGAAAA
5146037 GGTGG
1 GGTGG
5146042 TGGATTTGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.27, C:0.02, G:0.54, T:0.17
Consensus pattern (18 bp):
GGTGGAGGAATTGGAAAA
Found at i:5146106 original size:24 final size:24
Alignment explanation
Indices: 5146076--5146140 Score: 78
Period size: 24 Copynumber: 2.7 Consensus size: 24
5146066 TGGATTTGGC
5146076 AAGGGTGGTGGTTTTGGAGGTGGA
1 AAGGGTGGTGGTTTTGGAGGTGGA
* ***
5146100 GTA-GGTGGTGGAGCTGGAGGTGGA
1 -AAGGGTGGTGGTTTTGGAGGTGGA
5146124 AAGGGTGGTGGTTTTGG
1 AAGGGTGGTGGTTTTGG
5146141 TGGAAATGGA
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
23 1 0.03
24 29 0.94
25 1 0.03
ACGTcount: A:0.15, C:0.02, G:0.55, T:0.28
Consensus pattern (24 bp):
AAGGGTGGTGGTTTTGGAGGTGGA
Found at i:5146691 original size:21 final size:23
Alignment explanation
Indices: 5146642--5146691 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 23
5146632 ATATATTCTC
* * *
5146642 TTTTATTCTCCTATTTTTGTTTC
1 TTTTATTCTCCTATTATTATTTA
5146665 TTTTATTCT-CT-TTATTATTTA
1 TTTTATTCTCCTATTATTATTTA
5146686 TTTTAT
1 TTTTAT
5146692 AACACGTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 13 0.54
22 2 0.08
23 9 0.38
ACGTcount: A:0.14, C:0.12, G:0.02, T:0.72
Consensus pattern (23 bp):
TTTTATTCTCCTATTATTATTTA
Found at i:5147065 original size:31 final size:29
Alignment explanation
Indices: 5147020--5147086 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 29
5147010 AAATGTTTAA
5147020 TATTTTTTTATTCAATTGGAATTTAGTT-TTC
1 TATTTTTTTATTCAA---GAATTTAGTTCTTC
*
5147051 TATTTTTATT-TTCAAGAATTTAGTTCTTT
1 TATTTTT-TTATTCAAGAATTTAGTTCTTC
5147080 TATTTTT
1 TATTTTT
5147087 CAAATTTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
28 10 0.30
29 9 0.27
31 12 0.36
32 2 0.06
ACGTcount: A:0.22, C:0.06, G:0.07, T:0.64
Consensus pattern (29 bp):
TATTTTTTTATTCAAGAATTTAGTTCTTC
Found at i:5153698 original size:18 final size:18
Alignment explanation
Indices: 5153675--5153717 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
5153665 GAATAAGTTT
5153675 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
5153693 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
5153711 TTAATTA
1 TTAATTA
5153718 CACCTTGTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:5155694 original size:62 final size:59
Alignment explanation
Indices: 5155603--5155728 Score: 157
Period size: 63 Copynumber: 2.1 Consensus size: 59
5155593 GTTGGTTACA
* *
5155603 TTTTTTCTTATTTTGATACTTAA-GTTTTTTTATTTGATTTGGTAC-TTGAACTTGACAACT
1 TTTTTTCTTATTTTGATACCTAAGGTTTTTTTATTTAATTT-G-ACGTTGAACTTGACAA-T
*
5155663 TTTTTTCTCCTATTTTGATACCTAAGGTTTTTTTTTTTAATTTGACGTTTGAACTTGACAAT
1 TTTTTTCT--TATTTTGATACCTAAGGTTTTTTTATTTAATTTGACG-TTGAACTTGACAAT
5155725 TTTT
1 TTTT
5155729 CCTAATTTGG
Statistics
Matches: 58, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
60 8 0.14
61 2 0.03
62 20 0.34
63 28 0.48
ACGTcount: A:0.21, C:0.11, G:0.11, T:0.57
Consensus pattern (59 bp):
TTTTTTCTTATTTTGATACCTAAGGTTTTTTTATTTAATTTGACGTTGAACTTGACAAT
Found at i:5157248 original size:28 final size:28
Alignment explanation
Indices: 5157192--5157251 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
5157182 GATTTCAATT
*
5157192 AAAATTATAAATTAAAACAATAATTTTA
1 AAAATTATAAATTAAAACAATAATCTTA
* *
5157220 AAAATTATCAATTAAAACATTACA-CTTA
1 AAAATTATAAATTAAAACAATA-ATCTTA
5157248 AAAA
1 AAAA
5157252 GTAATTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 27 0.96
29 1 0.04
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (28 bp):
AAAATTATAAATTAAAACAATAATCTTA
Found at i:5157293 original size:17 final size:17
Alignment explanation
Indices: 5157262--5157295 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5157252 GTAATTAAAA
* *
5157262 TATTATTATTTAAGTTT
1 TATTATTAATAAAGTTT
5157279 TATTATTAATAAAGTTT
1 TATTATTAATAAAGTTT
5157296 ATTGTAAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (17 bp):
TATTATTAATAAAGTTT
Found at i:5168645 original size:19 final size:20
Alignment explanation
Indices: 5168601--5168638 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
5168591 AATACATAAT
5168601 TATTTATTCGTAAAAATTTAC
1 TATTTATTCG-AAAAATTTAC
*
5168622 AATTTATTC-AAAAATTT
1 TATTTATTCGAAAAATTT
5168639 TATATTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 8 0.50
21 8 0.50
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.47
Consensus pattern (20 bp):
TATTTATTCGAAAAATTTAC
Found at i:5169176 original size:40 final size:41
Alignment explanation
Indices: 5169119--5169203 Score: 145
Period size: 40 Copynumber: 2.1 Consensus size: 41
5169109 AAAAAAAAGA
5169119 TTTGTGTTTTGCCGCTCTTTCTACTATTTTACTGTTG-TGT
1 TTTGTGTTTTGCCGCTCTTTCTACTATTTTACTGTTGTTGT
* *
5169159 TTTGTGTTTTGCTGCTCTTTCTTCTATTTTACTGTTGTTGT
1 TTTGTGTTTTGCCGCTCTTTCTACTATTTTACTGTTGTTGT
5169200 TTTG
1 TTTG
5169204 CTACTATTTC
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
40 35 0.83
41 7 0.17
ACGTcount: A:0.06, C:0.15, G:0.18, T:0.61
Consensus pattern (41 bp):
TTTGTGTTTTGCCGCTCTTTCTACTATTTTACTGTTGTTGT
Found at i:5171111 original size:34 final size:35
Alignment explanation
Indices: 5171056--5171122 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
5171046 CAAACACCAA
*
5171056 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
5171091 AAAACATTTTCCCG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
5171123 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:5175465 original size:25 final size:23
Alignment explanation
Indices: 5175416--5175468 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
5175406 TTTTTTGGGT
*
5175416 CAAAACAAAATATTTTCCTTTCA
1 CAAAACAAAATATTTTCCTTCCA
* *
5175439 CAAAATCAATATATTTTTCTTCCCA
1 CAAAA-CAAAATATTTTCCTT-CCA
5175464 CAAAA
1 CAAAA
5175469 AATTATTCGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 5 0.20
24 13 0.52
25 7 0.28
ACGTcount: A:0.43, C:0.23, G:0.00, T:0.34
Consensus pattern (23 bp):
CAAAACAAAATATTTTCCTTCCA
Found at i:5177960 original size:18 final size:18
Alignment explanation
Indices: 5177937--5177979 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
5177927 ACTCAATTCA
*
5177937 AACCCAAGTA-TTCAACCC
1 AACCCAAGTACCT-AACCC
*
5177955 AACCCAATTACCTAACCC
1 AACCCAAGTACCTAACCC
5177973 AACCCAA
1 AACCCAA
5177980 TCATAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 21 0.95
19 1 0.05
ACGTcount: A:0.42, C:0.42, G:0.02, T:0.14
Consensus pattern (18 bp):
AACCCAAGTACCTAACCC
Found at i:5178082 original size:9 final size:9
Alignment explanation
Indices: 5178068--5178126 Score: 82
Period size: 9 Copynumber: 6.6 Consensus size: 9
5178058 TGTAGTAATT
5178068 TAATTCGGG
1 TAATTCGGG
5178077 TAATTCGGG
1 TAATTCGGG
**
5178086 TAATTCGAT
1 TAATTCGGG
*
5178095 TAATTCGGT
1 TAATTCGGG
5178104 TAATTCGGG
1 TAATTCGGG
*
5178113 TAATTCGGT
1 TAATTCGGG
5178122 TAATT
1 TAATT
5178127 TTTAACAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 45 1.00
ACGTcount: A:0.25, C:0.10, G:0.24, T:0.41
Consensus pattern (9 bp):
TAATTCGGG
Found at i:5178091 original size:18 final size:18
Alignment explanation
Indices: 5178067--5178126 Score: 93
Period size: 18 Copynumber: 3.3 Consensus size: 18
5178057 ATGTAGTAAT
5178067 TTAATTCGGGTAATTCGG
1 TTAATTCGGGTAATTCGG
* **
5178085 GTAATTCGATTAATTCGG
1 TTAATTCGGGTAATTCGG
5178103 TTAATTCGGGTAATTCGG
1 TTAATTCGGGTAATTCGG
5178121 TTAATT
1 TTAATT
5178127 TTTAACAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.25, C:0.10, G:0.23, T:0.42
Consensus pattern (18 bp):
TTAATTCGGGTAATTCGG
Found at i:5178098 original size:27 final size:27
Alignment explanation
Indices: 5178067--5178126 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
5178057 ATGTAGTAAT
5178067 TTAATTCGGGTAATTCGGGTAATTCGA
1 TTAATTCGGGTAATTCGGGTAATTCGA
* *
5178094 TTAATTCGGTTAATTCGGGTAATTCGG
1 TTAATTCGGGTAATTCGGGTAATTCGA
5178121 TTAATT
1 TTAATT
5178127 TTTAACAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.25, C:0.10, G:0.23, T:0.42
Consensus pattern (27 bp):
TTAATTCGGGTAATTCGGGTAATTCGA
Found at i:5178235 original size:28 final size:28
Alignment explanation
Indices: 5178193--5178247 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
5178183 AATCAACCGA
** *
5178193 AAAAATTTCGGTTCGGTTAATTTTATTG
1 AAAAATTTCAATTCGGTTAATGTTATTG
5178221 AAAAATTTCAATTCGGTTAATGTTATT
1 AAAAATTTCAATTCGGTTAATGTTATT
5178248 TCGGGTCGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.45
Consensus pattern (28 bp):
AAAAATTTCAATTCGGTTAATGTTATTG
Found at i:5182487 original size:27 final size:27
Alignment explanation
Indices: 5182455--5182512 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 27
5182445 AAATATAAAA
5182455 AATAAAATTTAGTTAAA-ATAT-TGTTTT
1 AATAAAA--TAGTTAAATATATATGTTTT
*
5182482 AATAAAATAGTTAAATTTATATGTTTT
1 AATAAAATAGTTAAATATATATGTTTT
5182509 AATA
1 AATA
5182513 TTTTATTAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 8 0.29
26 3 0.11
27 17 0.61
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (27 bp):
AATAAAATAGTTAAATATATATGTTTT
Found at i:5199503 original size:26 final size:26
Alignment explanation
Indices: 5199467--5199526 Score: 113
Period size: 26 Copynumber: 2.3 Consensus size: 26
5199457 TTTAATATAC
5199467 AAAATATATATTTGATTAAAAATAAA
1 AAAATATATATTTGATTAAAAATAAA
5199493 AAAATATATATTTGATTAAAAATAAA
1 AAAATATATATTTGATTAAAAATAAA
5199519 AAAA-ATAT
1 AAAATATAT
5199527 TTTTTACTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 4 0.12
26 30 0.88
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (26 bp):
AAAATATATATTTGATTAAAAATAAA
Found at i:5200769 original size:3 final size:3
Alignment explanation
Indices: 5200761--5200816 Score: 85
Period size: 3 Copynumber: 18.7 Consensus size: 3
5200751 TTTTTAAATT
* * *
5200761 TTA TTA TTA TTA TTA TTA TTA TTA TTA TAA TTA TTA TTA ATA TTA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5200809 TTA TTA TT
1 TTA TTA TT
5200817 TCCATGTACA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:5200784 original size:18 final size:18
Alignment explanation
Indices: 5200761--5200816 Score: 94
Period size: 18 Copynumber: 3.1 Consensus size: 18
5200751 TTTTTAAATT
*
5200761 TTATTATTATTATTATTA
1 TTATTATTATAATTATTA
5200779 TTATTATTATAATTATTA
1 TTATTATTATAATTATTA
*
5200797 TTAATATTATAATTATTA
1 TTATTATTATAATTATTA
5200815 TT
1 TT
5200817 TCCATGTACA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTATTATTATAATTATTA
Found at i:5204406 original size:21 final size:21
Alignment explanation
Indices: 5204380--5204429 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
5204370 CTACAACTTA
* *
5204380 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGCGGCAACGAGAG
* *
5204401 AAGCAGAAGCTGCAACGAGAG
1 AAGCAGAGGCGGCAACGAGAG
5204422 AAGCAGAG
1 AAGCAGAG
5204430 CAGGCCAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.38, C:0.18, G:0.42, T:0.02
Consensus pattern (21 bp):
AAGCAGAGGCGGCAACGAGAG
Found at i:5204847 original size:42 final size:42
Alignment explanation
Indices: 5204801--5204901 Score: 184
Period size: 42 Copynumber: 2.4 Consensus size: 42
5204791 CACTATTTTT
5204801 CATGTTCTTTAGTGGCGCTTAAGAATAAACGCCGCTAAAGAA
1 CATGTTCTTTAGTGGCGCTTAAGAATAAACGCCGCTAAAGAA
5204843 CATGTTCTTTAGTGGCGCTTAAGAATAAACGCCGCTAAAGAA
1 CATGTTCTTTAGTGGCGCTTAAGAATAAACGCCGCTAAAGAA
* *
5204885 CATGATCTTTAGCGGCG
1 CATGTTCTTTAGTGGCG
5204902 TTTTTTTCTA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 57 1.00
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.27
Consensus pattern (42 bp):
CATGTTCTTTAGTGGCGCTTAAGAATAAACGCCGCTAAAGAA
Found at i:5204991 original size:43 final size:42
Alignment explanation
Indices: 5204830--5205075 Score: 330
Period size: 42 Copynumber: 5.8 Consensus size: 42
5204820 TAAGAATAAA
* * * ***** *
5204830 CGCCGCTAAAGAACATGTTCTTTAGTGGCGCTTAAGAATAAA
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
*
5204872 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
*
5204914 CGCCGCTAAAGTACATGGTCTTTAGCGGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
* * * *
5204956 CGCCGCTAAAGAACATTGTCTTTAGCAGCATTTTTTCCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
*
5204998 CGCCGCTAAAGAACATGGTCTTTAGAGGCGTTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCG-TTTTTTTCTAAG
*
5205041 CGCCGCTAAATAACATGGTCTTTAGCGGCGTTTTT
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTT
5205076 GTTTGTAAAC
Statistics
Matches: 180, Mismatches: 23, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
42 141 0.78
43 39 0.22
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (42 bp):
CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
Found at i:5210393 original size:8 final size:8
Alignment explanation
Indices: 5210380--5210404 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
5210370 ATTTGTGTGT
5210380 TCAATTTC
1 TCAATTTC
5210388 TCAATTTC
1 TCAATTTC
5210396 TCAATTTC
1 TCAATTTC
5210404 T
1 T
5210405 TCCACTATTT
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:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (8 bp):
TCAATTTC
Found at i:5211980 original size:13 final size:13
Alignment explanation
Indices: 5211962--5212050 Score: 133
Period size: 13 Copynumber: 6.8 Consensus size: 13
5211952 AGTTCTTCAT
5211962 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
5211975 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
* *
5211988 TGCTTTTCAAAAG
1 TGCTTTTGAGAAG
*
5212001 TGCTTTTCAGAAG
1 TGCTTTTGAGAAG
5212014 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
* *
5212027 TGCTTTTCAAAAG
1 TGCTTTTGAGAAG
5212040 TGCTTTTGAGA
1 TGCTTTTGAGA
5212051 CATTTGAGTG
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 68 1.00
ACGTcount: A:0.25, C:0.11, G:0.25, T:0.39
Consensus pattern (13 bp):
TGCTTTTGAGAAG
Found at i:5212016 original size:39 final size:39
Alignment explanation
Indices: 5211962--5212046 Score: 161
Period size: 39 Copynumber: 2.2 Consensus size: 39
5211952 AGTTCTTCAT
*
5211962 TGCTTTTGAGAAGTGCTTTTGAGAAGTGCTTTTCAAAAG
1 TGCTTTTCAGAAGTGCTTTTGAGAAGTGCTTTTCAAAAG
5212001 TGCTTTTCAGAAGTGCTTTTGAGAAGTGCTTTTCAAAAG
1 TGCTTTTCAGAAGTGCTTTTGAGAAGTGCTTTTCAAAAG
5212040 TGCTTTT
1 TGCTTTT
5212047 GAGACATTTG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.24, C:0.12, G:0.24, T:0.41
Consensus pattern (39 bp):
TGCTTTTCAGAAGTGCTTTTGAGAAGTGCTTTTCAAAAG
Found at i:5213231 original size:21 final size:21
Alignment explanation
Indices: 5213207--5213251 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
5213197 TAAGCTGACA
5213207 ACAAATTGAACAGCATTGCCT
1 ACAAATTGAACAGCATTGCCT
5213228 ACAAATTGAACAGCATTGCCT
1 ACAAATTGAACAGCATTGCCT
5213249 ACA
1 ACA
5213252 TACCAAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.40, C:0.24, G:0.13, T:0.22
Consensus pattern (21 bp):
ACAAATTGAACAGCATTGCCT
Found at i:5216585 original size:3 final size:3
Alignment explanation
Indices: 5216577--5216632 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
5216567 AATATAGTAT
5216577 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5216625 TTA TTA TT
1 TTA TTA TT
5216633 TCCATGTACA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5216889 original size:24 final size:24
Alignment explanation
Indices: 5216837--5216882 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
5216827 ATCCATGCAC
*
5216837 ATATACATATATTTTTTATAATAT
1 ATATACATATATTTTTTAAAATAT
5216861 ATATACATA-ATTTTTTAGAAAT
1 ATATACATATATTTTTTA-AAAT
5216883 TATTATAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.50
Consensus pattern (24 bp):
ATATACATATATTTTTTAAAATAT
Found at i:5218454 original size:16 final size:16
Alignment explanation
Indices: 5218429--5218463 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
5218419 TTGTGTTCTG
5218429 TTTTGGCTGCATGACA
1 TTTTGGCTGCATGACA
*
5218445 TTTTGTCTGCATGACA
1 TTTTGGCTGCATGACA
5218461 TTT
1 TTT
5218464 CATCATAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.17, C:0.17, G:0.20, T:0.46
Consensus pattern (16 bp):
TTTTGGCTGCATGACA
Found at i:5223338 original size:45 final size:45
Alignment explanation
Indices: 5222936--5223334 Score: 555
Period size: 45 Copynumber: 8.9 Consensus size: 45
5222926 GTCTGAAAAG
*
5222936 AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAAATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGAT
* * * *
5222981 AGCAAATCTTATCTTCTTGTATTGGCAGTGAAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGAT
* * *
5223026 AACAGATCTTGTCTTCCTGTATCGGCAGCGAAGTAGATCAAAGAT
1 AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGAT
* * *
5223071 AGCAGATCTTGTCTTCCTATATTGGTAGAGAAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGAT
* *
5223116 AGCAGATCTTGTCTTCCTGTATCGGCAGCGAAGTAGATCAAAGAT
1 AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGAT
* * * *
5223161 AGCATATATTGTCTTCCTATATTGGTAGCGAAGTAGATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGAT
* * *
5223206 AGCAGATCTTGTCTTCCTATATTGGCAGTGAAGTATATCGAAGAT
1 AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGAT
* * * *
5223251 AACAGATCTTGTCTTCCTATATTAGCAGCGAAGTAGATCAAAGAT
1 AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGAT
* * *
5223296 AACAGATCTTATTTTCCTGTATTGGCAGCGAAGTAGATC
1 AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
5223335 AAAGCGAAGC
Statistics
Matches: 311, Mismatches: 43, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 311 1.00
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.31
Consensus pattern (45 bp):
AGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGAT
Found at i:5225177 original size:3 final size:3
Alignment explanation
Indices: 5225169--5225215 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
5225159 AATATAGTAT
5225169 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5225216 TCCATGTACA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5225471 original size:24 final size:24
Alignment explanation
Indices: 5225419--5225464 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
5225409 ATCCATGCAC
*
5225419 ATATACATATATTTTTTATAATAT
1 ATATACATATATTTTTTAAAATAT
5225443 ATATACATA-ATTTTTTAGAAAT
1 ATATACATATATTTTTTA-AAAT
5225465 TATTATAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.50
Consensus pattern (24 bp):
ATATACATATATTTTTTAAAATAT
Found at i:5226192 original size:18 final size:18
Alignment explanation
Indices: 5226169--5226232 Score: 76
Period size: 18 Copynumber: 3.4 Consensus size: 18
5226159 ATATATTTAT
5226169 TTTTTTAATTTTAAAATA
1 TTTTTTAATTTTAAAATA
*
5226187 TTTTTTACATACTTTTTAAAT-
1 TTTTTT--A-A-TTTTAAAATA
5226208 TTTTTTAATTTTAAAATA
1 TTTTTTAATTTTAAAATA
5226226 TTTTTTA
1 TTTTTTA
5226233 TTTCTTTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
17 8 0.21
18 14 0.36
19 1 0.03
20 1 0.03
21 7 0.18
22 8 0.21
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTTTTAATTTTAAAATA
Found at i:5226272 original size:31 final size:30
Alignment explanation
Indices: 5226186--5226281 Score: 90
Period size: 29 Copynumber: 3.2 Consensus size: 30
5226176 ATTTTAAAAT
* *
5226186 ATTTTTTACATACTTTTTAA-A-TTTTTTTA
1 ATTTTTTA-ATATTTTTAAATACTTTTTTTA
** * * *
5226215 ATTTTAAAATATTTTTTATTTC-TTTTTTA
1 ATTTTTTAATATTTTTAAATACTTTTTTTA
5226244 ATTTTTTAATATTTTTAAAATACTTTTTTTA
1 ATTTTTTAATATTTTT-AAATACTTTTTTTA
5226275 ATTTTTT
1 ATTTTTT
5226282 TAATTTTAAT
Statistics
Matches: 53, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
28 9 0.17
29 27 0.51
30 3 0.06
31 14 0.26
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (30 bp):
ATTTTTTAATATTTTTAAATACTTTTTTTA
Found at i:5226281 original size:40 final size:38
Alignment explanation
Indices: 5226167--5226288 Score: 142
Period size: 39 Copynumber: 3.1 Consensus size: 38
5226157 AAATATATTT
*
5226167 ATTTTTTTAATTTTAAAATA-TTTTTTACATACTTTTTAA
1 ATTTTTTTAATTTTAAAATATTTTTTTA-AT-CTTTTTTA
*
5226206 ATTTTTTTAATTTTAAAATA-TTTTTTATTTCTTTTTTA
1 ATTTTTTTAATTTTAAAATATTTTTTTA-ATCTTTTTTA
*
5226244 ATTTTTTAATATTTTTAAAATACTTTTTTTAAT-TTTTTTA
1 ATTTTTT--TAATTTTAAAATA-TTTTTTTAATCTTTTTTA
5226284 ATTTT
1 ATTTT
5226289 AATTAAAATT
Statistics
Matches: 74, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
38 14 0.19
39 28 0.38
40 24 0.32
41 1 0.01
42 7 0.09
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (38 bp):
ATTTTTTTAATTTTAAAATATTTTTTTAATCTTTTTTA
Found at i:5226288 original size:8 final size:9
Alignment explanation
Indices: 5226167--5226288 Score: 52
Period size: 9 Copynumber: 12.6 Consensus size: 9
5226157 AAATATATTT
5226167 ATTTTTTTA
1 ATTTTTTTA
**
5226176 A-TTTTAAA
1 ATTTTTTTA
5226184 ATATTTTTTA
1 AT-TTTTTTA
*
5226194 CATACTTTTTAA
1 -AT--TTTTTTA
5226206 ATTTTTTTA
1 ATTTTTTTA
**
5226215 A-TTTTAAA
1 ATTTTTTTA
5226223 ATATTTTTTA
1 AT-TTTTTTA
*
5226233 TTTCTTTTTTA
1 -AT-TTTTTTA
5226244 A-TTTTTTA
1 ATTTTTTTA
5226252 ATATTTTTAAAATA
1 AT-TTTTT----TA
*
5226266 CTTTTTTTA
1 ATTTTTTTA
5226275 ATTTTTTTA
1 ATTTTTTTA
5226284 ATTTT
1 ATTTT
5226289 AATTAAAATT
Statistics
Matches: 84, Mismatches: 16, Indels: 26
0.67 0.13 0.21
Matches are distributed among these distances:
8 20 0.24
9 23 0.27
10 15 0.18
11 12 0.14
12 6 0.07
13 5 0.06
14 3 0.04
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (9 bp):
ATTTTTTTA
Found at i:5226375 original size:11 final size:11
Alignment explanation
Indices: 5226251--5226398 Score: 79
Period size: 11 Copynumber: 13.8 Consensus size: 11
5226241 TTAATTTTTT
5226251 AATATTTTTAA
1 AATATTTTTAA
**
5226262 AATACTTTTTTT
1 AATA-TTTTTAA
*
5226274 AAT-TTTTT-T
1 AATATTTTTAA
5226283 AAT-TTTAATTAA
1 AATATTT--TTAA
*
5226295 AATTTTAATTTAA
1 AATATT--TTTAA
5226308 AATA-TTTTAA
1 AATATTTTTAA
5226318 AATA---TTAA
1 AATATTTTTAA
5226326 AATATTTTTTAAA
1 AATA-TTTTT-AA
*
5226339 AATACTTTTTTA
1 AATA-TTTTTAA
5226351 AA-ATTTTT--
1 AATATTTTTAA
5226359 -A-A-TTTTAA
1 AATATTTTTAA
5226367 AATATTTTTAA
1 AATATTTTTAA
5226378 AATATTTTTAA
1 AATATTTTTAA
5226389 AATACTTTTT
1 AATA-TTTTT
5226399 TATTTTAAAA
Statistics
Matches: 113, Mismatches: 6, Indels: 35
0.73 0.04 0.23
Matches are distributed among these distances:
6 4 0.04
7 2 0.02
8 8 0.07
9 8 0.07
10 20 0.18
11 28 0.25
12 22 0.19
13 20 0.18
15 1 0.01
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (11 bp):
AATATTTTTAA
Found at i:5226375 original size:41 final size:39
Alignment explanation
Indices: 5226303--5226413 Score: 118
Period size: 40 Copynumber: 2.7 Consensus size: 39
5226293 AAAATTTTAA
*
5226303 TTTAAAATATTTTAAAATATTAAAATATTTTTTAAAAATACTTT
1 TTTAAAAT-TTTT--AATTTTAAAATATTTTTT-AAAATA-TTT
5226347 TTTAAAATTTTTAATTTTAAAATA-TTTTTAAAATATTT
1 TTTAAAATTTTTAATTTTAAAATATTTTTTAAAATATTT
* *
5226385 TTAAAATACTTTTTTATTTTAAAA-ATTTT
1 TTTAAA-A-TTTTTAATTTTAAAATATTTT
5226414 AAATAAAAAT
Statistics
Matches: 61, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
38 8 0.13
39 8 0.13
40 22 0.36
41 11 0.18
43 4 0.07
44 8 0.13
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (39 bp):
TTTAAAATTTTTAATTTTAAAATATTTTTTAAAATATTT
Found at i:5226412 original size:49 final size:48
Alignment explanation
Indices: 5226297--5226416 Score: 131
Period size: 49 Copynumber: 2.4 Consensus size: 48
5226287 TTAATTAAAA
*
5226297 TTTTAATTTAAAATATTTTAAAATATTAAAATATTTTTTAAAAATACTT
1 TTTTATTTTAAAA-ATTTTAAAATATTAAAATATTTTTTAAAAATACTT
*
5226346 TTTTAAAATTTT--TAATTTTAAAATATTTTTAAAATA-TTTTT-AAAATACTT
1 TTTT---ATTTTAAAAATTTTAAAATA---TTAAAATATTTTTTAAAAATACTT
5226396 TTTTATTTTAAAAATTTTAAA
1 TTTTATTTTAAAAATTTTAAA
5226417 TAAAAATGGG
Statistics
Matches: 60, Mismatches: 3, Indels: 16
0.76 0.04 0.20
Matches are distributed among these distances:
47 5 0.08
49 24 0.40
50 14 0.23
51 5 0.08
52 12 0.20
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (48 bp):
TTTTATTTTAAAAATTTTAAAATATTAAAATATTTTTTAAAAATACTT
Found at i:5226707 original size:20 final size:20
Alignment explanation
Indices: 5226682--5226721 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
5226672 CGTAAAATAA
*
5226682 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
5226702 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
5226722 AGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:5226711 original size:34 final size:35
Alignment explanation
Indices: 5226667--5226733 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
5226657 CAGTAAAATG
* *
5226667 TTTTCCGTAAAATAATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATAATTTACTAGAAAATATTTTAC
* *
5226701 TTTTCTGTAAAATGATTTACTAGAAAATATTTT
1 TTTTCCGTAAAATAATTTACTAGAAAATATTTT
5226734 CTGGTGTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 16 0.57
35 12 0.43
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATAATTTACTAGAAAATATTTTAC
Found at i:5231391 original size:9 final size:9
Alignment explanation
Indices: 5231373--5231415 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
5231363 TTTATAAAGT
*
5231373 TTTTTTATA
1 TTTTTAATA
5231382 TTTTTAATA
1 TTTTTAATA
5231391 TTTTTATATA
1 TTTTTA-ATA
*
5231401 TTTTTTATAA
1 TTTTTAAT-A
5231411 TTTTT
1 TTTTT
5231416 TGGGATGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
9 16 0.53
10 14 0.47
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (9 bp):
TTTTTAATA
Found at i:5231400 original size:19 final size:20
Alignment explanation
Indices: 5231372--5231415 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
5231362 TTTTATAAAG
*
5231372 TTTTTTTATATTTTTAAT-A
1 TTTTTATATATTTTTAATAA
*
5231391 TTTTTATATATTTTTTATAA
1 TTTTTATATATTTTTAATAA
5231411 TTTTT
1 TTTTT
5231416 TGGGATGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (20 bp):
TTTTTATATATTTTTAATAA
Found at i:5233289 original size:32 final size:33
Alignment explanation
Indices: 5233218--5233277 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
5233208 TTGTACGTAT
5233218 TATT-TTTTAAAATTTTAAAAATATTTATATTA
1 TATTATTTTAAAATTTTAAAAATATTTATATTA
*
5233250 TATTATTTTAATA-TTTAAAAAT-TTTATA
1 TATTATTTTAAAATTTTAAAAATATTTATA
5233278 CATTTTTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 6 0.23
32 13 0.50
33 7 0.27
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (33 bp):
TATTATTTTAAAATTTTAAAAATATTTATATTA
Found at i:5235542 original size:30 final size:29
Alignment explanation
Indices: 5235483--5235553 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 29
5235473 AAATAAAAAA
*
5235483 TTACCAAAATGTTATAACTTTTTTTTTAT
1 TTACCAAAATATTATAACTTTTTTTTTAT
**
5235512 TTACCAAAATATTAT-TTTTTTTTTGATTAT
1 TTACCAAAATATTATAACTTTTTTT--TTAT
*
5235542 TTACTAAAATAT
1 TTACCAAAATAT
5235554 ACCAAAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 7 0.19
29 14 0.39
30 15 0.42
ACGTcount: A:0.34, C:0.08, G:0.03, T:0.55
Consensus pattern (29 bp):
TTACCAAAATATTATAACTTTTTTTTTAT
Found at i:5235759 original size:18 final size:19
Alignment explanation
Indices: 5235722--5235760 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
5235712 TCAACTCATT
* *
5235722 TTTTTATTTAATAACTCTA
1 TTTTAATTTAATAACACTA
5235741 TTTTAATTTAATAA-ACTA
1 TTTTAATTTAATAACACTA
5235759 TT
1 TT
5235761 AAGTAATACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTTAATTTAATAACACTA
Found at i:5235939 original size:19 final size:19
Alignment explanation
Indices: 5235915--5235973 Score: 84
Period size: 19 Copynumber: 3.2 Consensus size: 19
5235905 TCTAATTAAG
5235915 TAATAACTCTATTTTAATT
1 TAATAACTCTATTTTAATT
* * *
5235934 TAATAA-ACTATTCTCATT
1 TAATAACTCTATTTTAATT
5235952 TAATAACTCTATTTTAATT
1 TAATAACTCTATTTTAATT
5235971 TAA
1 TAA
5235974 ATGAGAATAG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
18 15 0.45
19 18 0.55
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.49
Consensus pattern (19 bp):
TAATAACTCTATTTTAATT
Found at i:5235993 original size:18 final size:19
Alignment explanation
Indices: 5235970--5236016 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
5235960 CTATTTTAAT
* *
5235970 TTAAATGAGAATAG-TTTA
1 TTAAATGAAAATAGAGTTA
*
5235988 TTAAATTAAAATAGAGTTA
1 TTAAATGAAAATAGAGTTA
5236007 TTAAAT-AAAA
1 TTAAATGAAAA
5236017 AAATGAGTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 16 0.64
19 9 0.36
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.36
Consensus pattern (19 bp):
TTAAATGAAAATAGAGTTA
Found at i:5236024 original size:20 final size:19
Alignment explanation
Indices: 5235985--5236025 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
5235975 TGAGAATAGT
* *
5235985 TTATTAAATTAAAATAGAG
1 TTATTAAATAAAAAAAGAG
5236004 TTATTAAATAAAAAAATGAG
1 TTATTAAATAAAAAAA-GAG
5236024 TT
1 TT
5236026 GAAGGGGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.37
Consensus pattern (19 bp):
TTATTAAATAAAAAAAGAG
Found at i:5236282 original size:37 final size:37
Alignment explanation
Indices: 5236235--5236305 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
5236225 AGTATTACTT
5236235 AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
1 AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
*
5236272 AATATTTTATTAAATTAAAATAGAGTTATTAAAT
1 AATAGTTTATTAAATTAAAATAGAGTTATTAAAT
5236306 AAAAAATGTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (37 bp):
AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
Found at i:5236293 original size:18 final size:18
Alignment explanation
Indices: 5236235--5236309 Score: 71
Period size: 18 Copynumber: 4.1 Consensus size: 18
5236225 AGTATTACTT
*
5236235 AATAGTTTATTAAATTAA
1 AATAATTTATTAAATTAA
* * *
5236253 AATAGAGTTATTAAATGAG
1 AATA-ATTTATTAAATTAA
*
5236272 AATATTTTATTAAATTAA
1 AATAATTTATTAAATTAA
*
5236290 AATAGAGTTATTAAA-TAA
1 AATA-ATTTATTAAATTAA
5236308 AA
1 AA
5236310 AATGTGTTGA
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
18 23 0.51
19 22 0.49
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (18 bp):
AATAATTTATTAAATTAA
Found at i:5236310 original size:19 final size:19
Alignment explanation
Indices: 5236241--5236309 Score: 88
Period size: 19 Copynumber: 3.7 Consensus size: 19
5236231 ACTTAATAGT
5236241 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
* * **
5236260 TTATTAAATGAGAATA-TT
1 TTATTAAATTAAAATAGAG
5236278 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
5236297 TTATTAAA-TAAAA
1 TTATTAAATTAAAA
5236310 AATGTGTTGA
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
18 19 0.46
19 22 0.54
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (19 bp):
TTATTAAATTAAAATAGAG
Found at i:5236567 original size:14 final size:14
Alignment explanation
Indices: 5236525--5236567 Score: 50
Period size: 16 Copynumber: 2.9 Consensus size: 14
5236515 ATAACAAAAA
5236525 GTTATAATATTTTT
1 GTTATAATATTTTT
**
5236539 GTTAATTTTTATTTTT
1 GTT-A-TAATATTTTT
5236555 GTTATAATATTTT
1 GTTATAATATTTT
5236568 AGTAAAAAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
14 10 0.43
15 2 0.09
16 11 0.48
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (14 bp):
GTTATAATATTTTT
Found at i:5257388 original size:12 final size:12
Alignment explanation
Indices: 5257373--5257402 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
5257363 TTTTTTTTAA
5257373 TTTTAAAATACT
1 TTTTAAAATACT
5257385 TTTTAAAATACT
1 TTTTAAAATACT
5257397 TTTTAA
1 TTTTAA
5257403 TTTTTTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (12 bp):
TTTTAAAATACT
Found at i:5257427 original size:21 final size:21
Alignment explanation
Indices: 5257364--5257443 Score: 80
Period size: 20 Copynumber: 4.0 Consensus size: 21
5257354 ATTTTTTAAT
5257364 TTTTTTTAA-TTTTAAAATAC
1 TTTTTTTAATTTTTAAAATAC
** *
5257384 TTTTTAAAATACTTTT-TAAT--
1 TTTTTTTAAT--TTTTAAAATAC
5257404 TTTTTTTAA-TTTTAAAATAC
1 TTTTTTTAATTTTTAAAATAC
5257424 TTTTTTTAATTTTTAAAATA
1 TTTTTTTAATTTTTAAAATA
5257444 AAGTTTTGGT
Statistics
Matches: 47, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
17 4 0.09
18 3 0.06
20 23 0.49
21 10 0.21
22 3 0.06
23 4 0.09
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTTTTTAATTTTTAAAATAC
Found at i:5257450 original size:21 final size:20
Alignment explanation
Indices: 5257406--5257450 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
5257396 TTTTTAATTT
***
5257406 TTTTTAATTTTAAAATACTT
1 TTTTTAATTTTAAAATAAAG
5257426 TTTTTAATTTTTAAAATAAAG
1 TTTTTAA-TTTTAAAATAAAG
5257447 TTTT
1 TTTT
5257451 GGTATTTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (20 bp):
TTTTTAATTTTAAAATAAAG
Found at i:5259150 original size:18 final size:18
Alignment explanation
Indices: 5259109--5259153 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
5259099 TGATGATATT
*
5259109 GATATTGATGATAGTGAC
1 GATATTGATGATAGCGAC
*
5259127 GATATTGATGCTAGCGAC
1 GATATTGATGATAGCGAC
5259145 -ACTATTGAT
1 GA-TATTGAT
5259154 AGTGACCTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 1 0.04
18 23 0.96
ACGTcount: A:0.31, C:0.11, G:0.24, T:0.33
Consensus pattern (18 bp):
GATATTGATGATAGCGAC
Found at i:5262533 original size:20 final size:20
Alignment explanation
Indices: 5262494--5262533 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
5262484 GAAATTTTTC
**
5262494 AGTTTTGGGTTTTCTTTTGT
1 AGTTTTGGGTTTTCGGTTGT
*
5262514 AGTTTTGGGTTTTGGGTTGT
1 AGTTTTGGGTTTTCGGTTGT
5262534 TAATGGGCTT
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:0.05, C:0.03, G:0.33, T:0.60
Consensus pattern (20 bp):
AGTTTTGGGTTTTCGGTTGT
Found at i:5263293 original size:56 final size:56
Alignment explanation
Indices: 5263233--5263349 Score: 234
Period size: 56 Copynumber: 2.1 Consensus size: 56
5263223 CAATGTAAAC
5263233 ATTAAATTTAATTTAATTTTAAGATAACCACTTTAATATTAAATTAATAAAATATT
1 ATTAAATTTAATTTAATTTTAAGATAACCACTTTAATATTAAATTAATAAAATATT
5263289 ATTAAATTTAATTTAATTTTAAGATAACCACTTTAATATTAAATTAATAAAATATT
1 ATTAAATTTAATTTAATTTTAAGATAACCACTTTAATATTAAATTAATAAAATATT
5263345 ATTAA
1 ATTAA
5263350 GATAATTATT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 61 1.00
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (56 bp):
ATTAAATTTAATTTAATTTTAAGATAACCACTTTAATATTAAATTAATAAAATATT
Found at i:5263299 original size:31 final size:31
Alignment explanation
Indices: 5263264--5263366 Score: 87
Period size: 31 Copynumber: 3.5 Consensus size: 31
5263254 AGATAACCAC
5263264 TTTAATATTAAATTAATAAAATATTATTAAA
1 TTTAATATTAAATTAATAAAATATTATTAAA
* * ** *
5263295 TTTAAT-TT-AATT-TTAAGATA--A-CCAC
1 TTTAATATTAAATTAATAAAATATTATTAAA
5263320 TTTAATATTAAATTAATAAAATATTATTAAGA
1 TTTAATATTAAATTAATAAAATATTATTAA-A
5263352 --TAATTATTAAATTAA
1 TTTAA-TATTAAATTAA
5263367 ATTTAATATT
Statistics
Matches: 54, Mismatches: 10, Indels: 16
0.68 0.12 0.20
Matches are distributed among these distances:
25 7 0.13
26 3 0.06
27 4 0.07
28 12 0.22
29 4 0.07
30 6 0.11
31 18 0.33
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (31 bp):
TTTAATATTAAATTAATAAAATATTATTAAA
Found at i:5265235 original size:25 final size:26
Alignment explanation
Indices: 5265186--5265237 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
5265176 TTTAAAATAC
* * *
5265186 TTTTAAAATATTTTTTATTTTTTTAT
1 TTTTAAAATAATTTTTATGTGTTTAT
5265212 TTTTAAAATAATTTTT-TGTGTTTAT
1 TTTTAAAATAATTTTTATGTGTTTAT
5265237 T
1 T
5265238 AAAAATTGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 8 0.35
26 15 0.65
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (26 bp):
TTTTAAAATAATTTTTATGTGTTTAT
Found at i:5272576 original size:22 final size:22
Alignment explanation
Indices: 5272551--5272631 Score: 94
Period size: 22 Copynumber: 3.7 Consensus size: 22
5272541 CAACACGCCT
5272551 GTGTGGGAGGAGGCACAGGACC
1 GTGTGGGAGGAGGCACAGGACC
*
5272573 GTGTGGGAGGAGGCAC-GCGATC
1 GTGTGGGAGGAGGCACAG-GACC
*
5272595 ATGTGGGAGGAGGCACACGG-CC
1 GTGTGGGAGGAGGCACA-GGACC
**
5272617 GTGTACGAGGAGGCA
1 GTGTGGGAGGAGGCA
5272632 TATGGTCGTG
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
21 1 0.02
22 47 0.94
23 1 0.02
24 1 0.02
ACGTcount: A:0.22, C:0.19, G:0.48, T:0.11
Consensus pattern (22 bp):
GTGTGGGAGGAGGCACAGGACC
Found at i:5276208 original size:20 final size:20
Alignment explanation
Indices: 5276169--5276208 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
5276159 AACCCTTAAT
*
5276169 ATTACAAAAAAAAAAGCAAA
1 ATTACAAAAAAAAAACCAAA
*
5276189 ATTACAAAAAAAAGACCAAA
1 ATTACAAAAAAAAAACCAAA
5276209 TTAAACAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.72, C:0.12, G:0.05, T:0.10
Consensus pattern (20 bp):
ATTACAAAAAAAAAACCAAA
Found at i:5279185 original size:6 final size:6
Alignment explanation
Indices: 5279174--5279211 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
5279164 GATACATGTG
* *
5279174 CATATA CATATA CATATA CAGATA CAGATA CATATA CA
1 CATATA CATATA CATATA CATATA CATATA CATATA CA
5279212 GATATTACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.50, C:0.18, G:0.05, T:0.26
Consensus pattern (6 bp):
CATATA
Found at i:5279198 original size:18 final size:18
Alignment explanation
Indices: 5279163--5279215 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
5279153 ATGCAAAGAA
* * *
5279163 AGATACATGTGCATATAC
1 AGATACATATACAGATAC
*
5279181 ATATACATATACAGATAC
1 AGATACATATACAGATAC
5279199 AGATACATATACAGATA
1 AGATACATATACAGATA
5279216 TTACATAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.47, C:0.15, G:0.11, T:0.26
Consensus pattern (18 bp):
AGATACATATACAGATAC
Found at i:5279212 original size:12 final size:12
Alignment explanation
Indices: 5279163--5279215 Score: 61
Period size: 12 Copynumber: 4.4 Consensus size: 12
5279153 ATGCAAAGAA
* *
5279163 AGATACATGTGC
1 AGATACATATAC
*
5279175 ATATACATATAC
1 AGATACATATAC
* *
5279187 ATATACAGATAC
1 AGATACATATAC
5279199 AGATACATATAC
1 AGATACATATAC
5279211 AGATA
1 AGATA
5279216 TTACATAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.47, C:0.15, G:0.11, T:0.26
Consensus pattern (12 bp):
AGATACATATAC
Found at i:5287335 original size:31 final size:31
Alignment explanation
Indices: 5287297--5287373 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
5287287 CAAACGATAT
* *
5287297 AAAAATTATTAGAAATTC-TAAAATATTGTAA
1 AAAAATTATTA-AAAATCATAAAAGATTGTAA
*
5287328 AAAAATTATTAAAAATCATCAAAGATTGTAA
1 AAAAATTATTAAAAATCATAAAAGATTGTAA
*
5287359 AAGAATTATTAAAAA
1 AAAAATTATTAAAAA
5287374 ATTTAAAAAC
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 5 0.12
31 36 0.88
ACGTcount: A:0.58, C:0.04, G:0.06, T:0.31
Consensus pattern (31 bp):
AAAAATTATTAAAAATCATAAAAGATTGTAA
Found at i:5287633 original size:37 final size:37
Alignment explanation
Indices: 5287586--5287658 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 37
5287576 TAAAAGTTAC
*
5287586 AAAAATTATTAGAAATTC-TAAAATATTGTAAAAAAAT
1 AAAAATTATTAGAAA-TCATAAAAGATTGTAAAAAAAT
*
5287623 AAAATTTATTAGAAATCATAAAAGATTGTAAAAAAA
1 AAAAATTATTAGAAATCATAAAAGATTGTAAAAAAA
5287659 ATTATTAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
36 2 0.06
37 31 0.94
ACGTcount: A:0.60, C:0.03, G:0.07, T:0.30
Consensus pattern (37 bp):
AAAAATTATTAGAAATCATAAAAGATTGTAAAAAAAT
Found at i:5287762 original size:9 final size:10
Alignment explanation
Indices: 5287738--5287767 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
5287728 TTAATCAAAA
5287738 AAAAATATTTT
1 AAAAAT-TTTT
5287749 AAAAATTTTT
1 AAAAATTTTT
5287759 AAAAATTTT
1 AAAAATTTT
5287768 GAATAAACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 13 0.68
11 6 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
AAAAATTTTT
Found at i:5288310 original size:16 final size:17
Alignment explanation
Indices: 5288270--5288327 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 17
5288260 ATCTTTTTCC
**
5288270 ATTTTTAATAATTTAAAT
1 ATTTTT-ATAATTTGTAT
*
5288288 AATTTTTGTAATTT-TAT
1 -ATTTTTATAATTTGTAT
5288305 ATTTTTATAATTTGGTAT
1 ATTTTTATAATTT-GTAT
5288323 ATTTT
1 ATTTT
5288328 CTCTTTTACA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
16 12 0.35
17 2 0.06
18 14 0.41
19 6 0.18
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (17 bp):
ATTTTTATAATTTGTAT
Found at i:5290249 original size:2 final size:2
Alignment explanation
Indices: 5290242--5290266 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5290232 TCTGATGTAC
5290242 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 T
5290267 GAAGAAAGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5303755 original size:60 final size:60
Alignment explanation
Indices: 5303662--5303848 Score: 290
Period size: 60 Copynumber: 3.2 Consensus size: 60
5303652 ATGAATACAG
* * *
5303662 ATTCATCAGAAAGTTTTGGTGGAGCCTTCATCGGACTCTGTTCTTCTCTTGCTTCTTGAA
1 ATTCATCAGAAGGTTTTAGTGGAGACTTCATCGGACTCTGTTCTTCTCTTGCTTCTTGAA
* * *
5303722 ATTCATCAGAAGGTTTTAATGGAGACTTCATCGGACTCTGTTCTTCCCTTGCTTCATGAA
1 ATTCATCAGAAGGTTTTAGTGGAGACTTCATCGGACTCTGTTCTTCTCTTGCTTCTTGAA
*
5303782 ATTCATC---AGGTTTTAGTGGAGACTTCATTGGACTCTGTTCTTCTCTTGCTTCTTGAA
1 ATTCATCAGAAGGTTTTAGTGGAGACTTCATCGGACTCTGTTCTTCTCTTGCTTCTTGAA
5303839 ATTCATCAGA
1 ATTCATCAGA
5303849 GCTGGTACTC
Statistics
Matches: 114, Mismatches: 10, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
57 53 0.46
60 61 0.54
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.40
Consensus pattern (60 bp):
ATTCATCAGAAGGTTTTAGTGGAGACTTCATCGGACTCTGTTCTTCTCTTGCTTCTTGAA
Found at i:5303820 original size:57 final size:57
Alignment explanation
Indices: 5303674--5303847 Score: 267
Period size: 57 Copynumber: 3.0 Consensus size: 57
5303664 TCATCAGAAA
* *
5303674 GTTTTGGTGGAGCCTTCATCGGACTCTGTTCTTCTCTTGCTTCTTGAAATTCATCAGAAG
1 GTTTTAGTGGAGACTTCATCGGACTCTGTTCTTCTCTTGCTTCTTGAAATTCATC---AG
* * *
5303734 GTTTTAATGGAGACTTCATCGGACTCTGTTCTTCCCTTGCTTCATGAAATTCATCAG
1 GTTTTAGTGGAGACTTCATCGGACTCTGTTCTTCTCTTGCTTCTTGAAATTCATCAG
*
5303791 GTTTTAGTGGAGACTTCATTGGACTCTGTTCTTCTCTTGCTTCTTGAAATTCATCAG
1 GTTTTAGTGGAGACTTCATCGGACTCTGTTCTTCTCTTGCTTCTTGAAATTCATCAG
5303848 AGCTGGTACT
Statistics
Matches: 105, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
57 55 0.52
60 50 0.48
ACGTcount: A:0.18, C:0.21, G:0.20, T:0.41
Consensus pattern (57 bp):
GTTTTAGTGGAGACTTCATCGGACTCTGTTCTTCTCTTGCTTCTTGAAATTCATCAG
Found at i:5305586 original size:19 final size:20
Alignment explanation
Indices: 5305559--5305600 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
5305549 GAAACATTTA
5305559 TTTTAATGT-TTT-TAGTATT
1 TTTTAATGTATTTATA-TATT
*
5305578 TTTTGATGTATTTATATATT
1 TTTTAATGTATTTATATATT
5305598 TTT
1 TTT
5305601 AAAAATTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 8 0.40
20 10 0.50
21 2 0.10
ACGTcount: A:0.21, C:0.00, G:0.10, T:0.69
Consensus pattern (20 bp):
TTTTAATGTATTTATATATT
Found at i:5318061 original size:9 final size:10
Alignment explanation
Indices: 5318038--5318062 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
5318028 CCATAATTAT
5318038 TTTTTTACAA
1 TTTTTTACAA
5318048 TTTTTTACAA
1 TTTTTTACAA
5318058 TTTTT
1 TTTTT
5318063 CAAAGTCAGA
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:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTTTTACAA
Found at i:5318406 original size:23 final size:22
Alignment explanation
Indices: 5318363--5318406 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
5318353 TTCTAAGTCG
5318363 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
5318386 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
5318407 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:5319050 original size:2 final size:2
Alignment explanation
Indices: 5319045--5319093 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
5319035 ACACACACAC
5319045 AT AT 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 AT AT
5319087 AT AT AT A
1 AT AT AT A
5319094 CCAATCACAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5319635 original size:41 final size:40
Alignment explanation
Indices: 5319579--5319724 Score: 138
Period size: 41 Copynumber: 3.6 Consensus size: 40
5319569 TGATTCGATA
5319579 CACCGGC-TTATAGCCTGCTAGACCTATAGTCCGAAATGTAT
1 CACCGGCATTA-AGCCTGCTAGACCTATAGTCCGAAAT-TAT
* * *
5319620 CACCGGCATTAAGCCTGCTAGACGTAAAGTCTG-AATTAATT
1 CACCGGCATTAAGCCTGCTAGACCTATAGTCCGAAATT-A-T
* *
5319661 CACCGGCATTAAGCCTGCTAGGCAC-ATAG-CCTGAATTATAT
1 CACCGGCATTAAGCCTGCTAGAC-CTATAGTCC-GAAAT-TAT
**
5319702 CACCGGCATCCAGCCTGCTAGAC
1 CACCGGCATTAAGCCTGCTAGAC
5319725 AATAAGTCTG
Statistics
Matches: 87, Mismatches: 11, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
39 1 0.01
40 5 0.06
41 74 0.85
42 6 0.07
43 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (40 bp):
CACCGGCATTAAGCCTGCTAGACCTATAGTCCGAAATTAT
Found at i:5319732 original size:82 final size:82
Alignment explanation
Indices: 5319579--5319734 Score: 194
Period size: 82 Copynumber: 1.9 Consensus size: 82
5319569 TGATTCGATA
* * *
5319579 CACCGGCTTATAGCCTGCTAGACCTATAGTCCGAAATGTATCACCGGCATTAAGCCTGCTAGACG
1 CACCGGCTTATAGCCTGCTAGACCTATAGTCCGAAATATATCACCGGCATCAAGCCTGCTAGACA
5319644 TAAAGTCTGAATTAATT
66 TAAAGTCTGAATTAATT
* * *
5319661 CACCGGCATTA-AGCCTGCTAGGCAC-ATAG-CCTGAATTATATCACCGGCATCCAGCCTGCTAG
1 CACCGGC-TTATAGCCTGCTAGAC-CTATAGTCC-GAAATATATCACCGGCATCAAGCCTGCTAG
5319723 ACA-ATAAGTCTG
63 ACATA-AAGTCTG
5319735 GTTTACATTC
Statistics
Matches: 64, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
81 3 0.05
82 57 0.89
83 4 0.06
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (82 bp):
CACCGGCTTATAGCCTGCTAGACCTATAGTCCGAAATATATCACCGGCATCAAGCCTGCTAGACA
TAAAGTCTGAATTAATT
Found at i:5321706 original size:51 final size:51
Alignment explanation
Indices: 5321609--5321798 Score: 188
Period size: 51 Copynumber: 3.7 Consensus size: 51
5321599 CCGGGTTGTT
* *
5321609 ACATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCCGATAC
1 ACATAGTAGCCTGCACATAGTACTACACAAGTGACCATAACCATCCGATAC
* * * * * * * *
5321660 ACGTATTAGCCTACACATAGTACTCCACAAGTGATCGA-AACTATCCGGTAT
1 ACATAGTAGCCTGCACATAGTACTACACAAGTGA-CCATAACCATCCGATAC
* * * * *
5321711 GCATAGTAGCCTGCACATAGTACTACACATGCGACC-T-ATCATTCCGGTAC
1 ACATAGTAGCCTGCACATAGTACTACACAAGTGACCATAACCA-TCCGATAC
* *
5321761 ACGTAGTAGCCTGCACATAGTACTACACACGTGACCAT
1 ACATAGTAGCCTGCACATAGTACTACACAAGTGACCAT
5321799 CACTTTCACT
Statistics
Matches: 110, Mismatches: 25, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
49 2 0.02
50 40 0.36
51 66 0.60
52 2 0.02
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (51 bp):
ACATAGTAGCCTGCACATAGTACTACACAAGTGACCATAACCATCCGATAC
Found at i:5321818 original size:101 final size:101
Alignment explanation
Indices: 5321607--5321794 Score: 261
Period size: 101 Copynumber: 1.9 Consensus size: 101
5321597 AACCGGGTTG
* *
5321607 TTACATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCCGATACACGTATTAGCCT
1 TTACATAGTAGCCTGCACATAGTACTACACATGCGACCA-TACCATCCGATACACGTAGTAGCCT
* *
5321672 ACACATAGTACTCCACAAGTGATCGAAACTATCCGGT
65 ACACATAGTACTACACAAGTGATCCAAACTATCCGGT
* * * *
5321709 ATGCATAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTCCGGTACACGTAGTAGCCT
1 TTACATAGTAGCCTGCACATAGTACTACACATGCGACCATACCA-TCCGATACACGTAGTAGCCT
* *
5321773 GCACATAGTACTACACACGTGA
65 ACACATAGTACTACACAAGTGA
5321795 CCATCACTTT
Statistics
Matches: 76, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
100 4 0.05
101 37 0.49
102 35 0.46
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.24
Consensus pattern (101 bp):
TTACATAGTAGCCTGCACATAGTACTACACATGCGACCATACCATCCGATACACGTAGTAGCCTA
CACATAGTACTACACAAGTGATCCAAACTATCCGGT
Found at i:5325111 original size:18 final size:19
Alignment explanation
Indices: 5325090--5325134 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
5325080 CAAAAATTAA
5325090 TTATAAATTTTGA-ATTTT
1 TTATAAATTTTGAGATTTT
* *
5325108 TTATATATTTTTAGATTTT
1 TTATAAATTTTGAGATTTT
*
5325127 TTAAAAAT
1 TTATAAAT
5325135 ATACATTTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (19 bp):
TTATAAATTTTGAGATTTT
Found at i:5325305 original size:62 final size:62
Alignment explanation
Indices: 5325239--5325355 Score: 146
Period size: 62 Copynumber: 1.9 Consensus size: 62
5325229 GGACTTTTAT
**
5325239 ATTTTCTAAAATATATATTTAATTTAATTTTTAAAATATTTA-AACATTTTTAATATTCTTAG
1 ATTTTCTAAAATATATAAATAATTTAATTTTTAAAATATTTACAA-ATTTTTAATATTCTTAG
* * * * * *
5325301 ATTTTTTAAAATATTTAAATATTTTTATTTTTAAAATTTTTACAATTTTTTAATA
1 ATTTTCTAAAATATATAAATAATTTAATTTTTAAAATATTTACAAATTTTTAATA
5325356 ATTTATAAGT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
62 44 0.96
63 2 0.04
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.56
Consensus pattern (62 bp):
ATTTTCTAAAATATATAAATAATTTAATTTTTAAAATATTTACAAATTTTTAATATTCTTAG
Found at i:5325310 original size:28 final size:24
Alignment explanation
Indices: 5325277--5325342 Score: 69
Period size: 28 Copynumber: 2.5 Consensus size: 24
5325267 TTTTAAAATA
5325277 TTTAAACATTTTTAATATTCTTAGATTT
1 TTTAAA-ATTTTTAATATT-TT-GA-TT
* *
5325305 TTTAAAATATTTAAATATTTTTATT
1 TTTAAAAT-TTTTAATATTTTGATT
5325330 TTTAAAATTTTTA
1 TTTAAAATTTTTA
5325343 CAATTTTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
24 4 0.12
25 10 0.29
26 1 0.03
27 4 0.12
28 15 0.44
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (24 bp):
TTTAAAATTTTTAATATTTTGATT
Done.