Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr11
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: 61124829
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1263459 characters in sequence are not A, C, G, or T
File 193 of 205
Found at i:57167831 original size:47 final size:46
Alignment explanation
Indices: 57167777--57167927 Score: 185
Period size: 47 Copynumber: 3.2 Consensus size: 46
57167767 ATTCTATTTG
57167777 GCCTTTGTGGTGTATCTTGTATGTTGCCTTTGTGGCGTACTCTGATA
1 GCCTTTGTGGTGTAT-TTGTATGTTGCCTTTGTGGCGTACTCTGATA
* *
57167824 GCCTTTGTGGTGTATTCTGTATGTTGCCTTTGTAGCGTAATCTGATA
1 GCCTTTGTGGTGTATT-TGTATGTTGCCTTTGTGGCGTACTCTGATA
*** * * * *
57167871 ATATTTGGGGTGTATTTTGTATGTTGTCTTTGTGGTGTACTCTGGTA
1 GCCTTTGTGGTGTA-TTTGTATGTTGCCTTTGTGGCGTACTCTGATA
*
57167918 GCTTTTGTGG
1 GCCTTTGTGG
57167928 CTTATTCCGT
Statistics
Matches: 87, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
46 1 0.01
47 84 0.97
48 2 0.02
ACGTcount: A:0.12, C:0.13, G:0.28, T:0.47
Consensus pattern (46 bp):
GCCTTTGTGGTGTATTTGTATGTTGCCTTTGTGGCGTACTCTGATA
Found at i:57167867 original size:25 final size:25
Alignment explanation
Indices: 57167777--57167867 Score: 91
Period size: 25 Copynumber: 3.8 Consensus size: 25
57167767 ATTCTATTTG
*
57167777 GCCTTTGTGGTGT-ATCTTGTATGTT
1 GCCTTTGTGGCGTAATC-TGTATGTT
* *
57167802 GCCTTTGTGGCGTACTCTG-A--TA
1 GCCTTTGTGGCGTAATCTGTATGTT
* *
57167824 GCCTTTGTGGTGTATTCTGTATGTT
1 GCCTTTGTGGCGTAATCTGTATGTT
*
57167849 GCCTTTGTAGCGTAATCTG
1 GCCTTTGTGGCGTAATCTG
57167868 ATAATATTTG
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
22 18 0.34
23 1 0.02
24 1 0.02
25 31 0.58
26 2 0.04
ACGTcount: A:0.11, C:0.16, G:0.27, T:0.45
Consensus pattern (25 bp):
GCCTTTGTGGCGTAATCTGTATGTT
Found at i:57170834 original size:24 final size:24
Alignment explanation
Indices: 57170780--57170834 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
57170770 AAAAAAAATT
* *
57170780 CTATTTTTTACTATTTTGTTGCTA
1 CTATTTTTCACTATTATGTTGCTA
* *
57170804 ATTTTTTTCACTATTATGTTGCTA
1 CTATTTTTCACTATTATGTTGCTA
57170828 CTATTTT
1 CTATTTT
57170835 GTTATTATTG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.18, C:0.13, G:0.07, T:0.62
Consensus pattern (24 bp):
CTATTTTTCACTATTATGTTGCTA
Found at i:57170875 original size:19 final size:17
Alignment explanation
Indices: 57170851--57170885 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
57170841 ATTGTTTGAA
57170851 TATTATATAATTCTTGTTT
1 TATTAT-TAATT-TTGTTT
57170870 TATTATTAATTTTGTT
1 TATTATTAATTTTGTT
57170886 ACTATTTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 5 0.31
19 6 0.38
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.66
Consensus pattern (17 bp):
TATTATTAATTTTGTTT
Found at i:57170891 original size:18 final size:19
Alignment explanation
Indices: 57170851--57170891 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
57170841 ATTGTTTGAA
*
57170851 TATTATATAATTCTTGTTT
1 TATTATATAATTCTTGTTC
57170870 TATTAT-TAATT-TTGTTAC
1 TATTATATAATTCTTGTT-C
57170888 TATT
1 TATT
57170892 TTAGAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 5 0.25
18 9 0.45
19 6 0.30
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.63
Consensus pattern (19 bp):
TATTATATAATTCTTGTTC
Found at i:57182285 original size:25 final size:25
Alignment explanation
Indices: 57182200--57182288 Score: 67
Period size: 25 Copynumber: 3.6 Consensus size: 25
57182190 TTACCTTACA
* * * *
57182200 GGCTTTCCAGATAACTCGCAACAAG
1 GGCTTCCCAGATAATTCACCACAAG
*
57182225 GGCTTCCCA-A-ACTTTACACCACATAG
1 GGCTTCCCAGATA-ATT-CACCACA-AG
* *
57182251 GCCTT-TCAGATAATTCACCACAAG
1 GGCTTCCCAGATAATTCACCACAAG
57182275 GGCTTCCCAGATAA
1 GGCTTCCCAGATAA
57182289 CCTCGCCACA
Statistics
Matches: 48, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
23 1 0.02
24 8 0.17
25 29 0.60
26 9 0.19
27 1 0.02
ACGTcount: A:0.31, C:0.30, G:0.16, T:0.22
Consensus pattern (25 bp):
GGCTTCCCAGATAATTCACCACAAG
Found at i:57184397 original size:25 final size:25
Alignment explanation
Indices: 57184312--57184400 Score: 67
Period size: 25 Copynumber: 3.6 Consensus size: 25
57184302 TTACCTTACA
* * * *
57184312 GGCTTTCCAGATAACTCGCAACAAG
1 GGCTTCCCAGATAATTCACCACAAG
*
57184337 GGCTTCCCA-A-ACTTTACACCACATAG
1 GGCTTCCCAGATA-ATT-CACCACA-AG
* *
57184363 GCCTT-TCAGATAATTCACCACAAG
1 GGCTTCCCAGATAATTCACCACAAG
57184387 GGCTTCCCAGATAA
1 GGCTTCCCAGATAA
57184401 CCTCGCCACA
Statistics
Matches: 48, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
23 1 0.02
24 8 0.17
25 29 0.60
26 9 0.19
27 1 0.02
ACGTcount: A:0.31, C:0.30, G:0.16, T:0.22
Consensus pattern (25 bp):
GGCTTCCCAGATAATTCACCACAAG
Found at i:57188891 original size:27 final size:27
Alignment explanation
Indices: 57188859--57189230 Score: 333
Period size: 27 Copynumber: 13.8 Consensus size: 27
57188849 TCATCTCTTA
**
57188859 GGGGTATAACAGTCATTTTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
* ** * * *
57188886 GAGGTATTTTGGTCATTCTACCGTCTG
1 GGGGTATTTCAGTCATTTTACCCTATG
*
57188913 GGGGTATTTC-GATCATTCTACCCTATG
1 GGGGTATTTCAG-TCATTTTACCCTATG
** *
57188940 GGGGTATTTTGGTCATTTTACCTTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
* *
57188967 GGGCTATTTCAGTCATTTTACCTTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
* * * *
57188994 GGGGTATTTCGGTTATTTTATCTTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
*
57189021 GGGGTATTTCAGTTATTTTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
* *
57189048 AGGGTATTTCGGTCATTTTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
* * * *
57189075 AGGGTATTTC-GATTATTCTACCTTATG
1 GGGGTATTTCAG-TCATTTTACCCTATG
** *
57189102 GGGGTATTTTGGTCATTTTACCCTATA
1 GGGGTATTTCAGTCATTTTACCCTATG
* * * *
57189129 GAGGTTTTTGA-TTATTTTATCCC-ATG
1 GGGGTATTTCAGTCATTTTA-CCCTATG
57189155 GGGGTATTTC-GATCATTTTACCCTATG
1 GGGGTATTTCAG-TCATTTTACCCTATG
* *
57189182 AGGGTACTTT-GGTCATTTTACCCTATG
1 GGGGTA-TTTCAGTCATTTTACCCTATG
* *
57189209 AGGGTATTTTAGTCATTTTACC
1 GGGGTATTTCAGTCATTTTACC
57189231 TATTTTGGGG
Statistics
Matches: 285, Mismatches: 49, Indels: 22
0.80 0.14 0.06
Matches are distributed among these distances:
26 24 0.08
27 255 0.89
28 6 0.02
ACGTcount: A:0.19, C:0.16, G:0.22, T:0.43
Consensus pattern (27 bp):
GGGGTATTTCAGTCATTTTACCCTATG
Found at i:57188917 original size:54 final size:54
Alignment explanation
Indices: 57188859--57189231 Score: 378
Period size: 54 Copynumber: 6.9 Consensus size: 54
57188849 TCATCTCTTA
** * * * *
57188859 GGGGTATAACAGTCATTTTACCCTATGGAGGTATTTTGGTCATTCTACCGTCTG
1 GGGGTATTTCAGTCATTTTACCCTATGGGGGTATTTTGGTCATTTTACCTTATG
*
57188913 GGGGTATTTC-GATCATTCTACCCTATGGGGGTATTTTGGTCATTTTACCTTATG
1 GGGGTATTTCAG-TCATTTTACCCTATGGGGGTATTTTGGTCATTTTACCTTATG
* * * * *
57188967 GGGCTATTTCAGTCATTTTACCTTATGGGGGTATTTCGGTTATTTTATCTTATG
1 GGGGTATTTCAGTCATTTTACCCTATGGGGGTATTTTGGTCATTTTACCTTATG
* * * *
57189021 GGGGTATTTCAGTTATTTTACCCTATGAGGGTATTTCGGTCATTTTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATGGGGGTATTTTGGTCATTTTACCTTATG
* * * * * *
57189075 AGGGTATTTC-GATTATTCTACCTTATGGGGGTATTTTGGTCATTTTACCCTATA
1 GGGGTATTTCAG-TCATTTTACCCTATGGGGGTATTTTGGTCATTTTACCTTATG
* * * * * * *
57189129 GAGGTTTTTGA-TTATTTTATCCC-ATGGGGGTATTTCGATCATTTTACCCTATG
1 GGGGTATTTCAGTCATTTTA-CCCTATGGGGGTATTTTGGTCATTTTACCTTATG
* * * *
57189182 AGGGTACTTT-GGTCATTTTACCCTATGAGGGTATTTTAGTCATTTTACCT
1 GGGGTA-TTTCAGTCATTTTACCCTATGGGGGTATTTTGGTCATTTTACCT
57189232 ATTTTGGGGT
Statistics
Matches: 266, Mismatches: 45, Indels: 16
0.81 0.14 0.05
Matches are distributed among these distances:
53 42 0.16
54 223 0.84
55 1 0.00
ACGTcount: A:0.19, C:0.16, G:0.22, T:0.43
Consensus pattern (54 bp):
GGGGTATTTCAGTCATTTTACCCTATGGGGGTATTTTGGTCATTTTACCTTATG
Found at i:57188982 original size:81 final size:79
Alignment explanation
Indices: 57188870--57189233 Score: 406
Period size: 81 Copynumber: 4.5 Consensus size: 79
57188860 GGGTATAACA
** * *
57188870 GTCATTTTACCCTATGGAGGTATTTTGGTCATTCTACCGTCTGGGGGTATTTCGATCATTCTACC
1 GTCATTTTACCCTATGG-GGTATTTCAGTCATTTTACC-TATGGGGGTATTTCGATCATTCTACC
57188935 CTATGGGGGTATTTTG
64 CTATGGGGGTATTTTG
* * * * *
57188951 GTCATTTTACCTTATGGGGCTATTTCAGTCATTTTACCTTATGGGGGTATTTCGGTTATTTTATC
1 GTCATTTTACCCTATGGGG-TATTTCAGTCATTTTACC-TATGGGGGTATTTCGATCATTCTACC
* **
57189016 TTATGGGGGTATTTCA
64 CTATGGGGGTATTTTG
* * * *
57189032 GTTATTTTACCCTATGAGGGTATTTCGGTCATTTTACCCTATGAGGGTATTTCGATTATTCTACC
1 GTCATTTTACCCTATG-GGGTATTTCAGTCATTTTA-CCTATGGGGGTATTTCGATCATTCTACC
*
57189097 TTATGGGGGTATTTTG
64 CTATGGGGGTATTTTG
* * * * * *
57189113 GTCATTTTACCCTATAGAGGTTTTTGA-TTATTTTATCCCATGGGGGTATTTCGATCATTTTACC
1 GTCATTTTACCCTAT-GGGGTATTTCAGTCATTTTA-CCTATGGGGGTATTTCGATCATTCTACC
* *
57189177 CTATGAGGGTACTTTG
64 CTATGGGGGTATTTTG
*
57189193 GTCATTTTACCCTATGAGGGTATTTTAGTCATTTTACCTAT
1 GTCATTTTACCCTATG-GGGTATTTCAGTCATTTTACCTAT
57189234 TTTGGGGTCT
Statistics
Matches: 236, Mismatches: 41, Indels: 13
0.81 0.14 0.04
Matches are distributed among these distances:
79 1 0.00
80 72 0.31
81 157 0.67
82 6 0.03
ACGTcount: A:0.18, C:0.16, G:0.21, T:0.44
Consensus pattern (79 bp):
GTCATTTTACCCTATGGGGTATTTCAGTCATTTTACCTATGGGGGTATTTCGATCATTCTACCCT
ATGGGGGTATTTTG
Found at i:57193043 original size:16 final size:16
Alignment explanation
Indices: 57192993--57193047 Score: 53
Period size: 16 Copynumber: 3.5 Consensus size: 16
57192983 TTTCTAAAAA
57192993 TAATATTATT-TTAATT
1 TAATATT-TTATTAATT
* *
57193009 TATTATTTATATTGA--
1 TAATATTT-TATTAATT
57193024 TAATATTTTATTAATT
1 TAATATTTTATTAATT
57193040 TAATATTT
1 TAATATTT
57193048 ATGTGAGATA
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 5 0.16
15 8 0.26
16 15 0.48
17 3 0.10
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (16 bp):
TAATATTTTATTAATT
Found at i:57193096 original size:30 final size:29
Alignment explanation
Indices: 57192992--57193102 Score: 116
Period size: 30 Copynumber: 3.7 Consensus size: 29
57192982 TTTTCTAAAA
*
57192992 ATAATATTATTTTAATTTATTATTTATATTG
1 ATAATATTA-TTTAATTTAATATTTAT-TTG
* *
57193023 ATAATATTTTATTAATTTAATATTTATGTG
1 ATAATATTAT-TTAATTTAATATTTATTTG
*
57193053 A-GATATTAAATTTAATTTAATATTTATCTTG
1 ATAATATT--ATTTAATTTAATATTTAT-TTG
*
57193084 ATAAGATTATTTAATTTAA
1 ATAATATTATTTAATTTAA
57193103 CATTAATGTG
Statistics
Matches: 67, Mismatches: 8, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
29 5 0.07
30 31 0.46
31 27 0.40
32 4 0.06
ACGTcount: A:0.39, C:0.01, G:0.05, T:0.55
Consensus pattern (29 bp):
ATAATATTATTTAATTTAATATTTATTTG
Found at i:57203286 original size:13 final size:13
Alignment explanation
Indices: 57203268--57203292 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
57203258 TGGTTAGCAA
57203268 CAGTTAGTCATAG
1 CAGTTAGTCATAG
57203281 CAGTTAGTCATA
1 CAGTTAGTCATA
57203293 CAAGTATAAA
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:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
CAGTTAGTCATAG
Found at i:57209217 original size:9 final size:9
Alignment explanation
Indices: 57209203--57209236 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
57209193 AGTTTGATAA
57209203 TCGAATTAT
1 TCGAATTAT
57209212 TCGAATTAT
1 TCGAATTAT
*
57209221 TCGAGTTAT
1 TCGAATTAT
*
57209230 TTGAATT
1 TCGAATT
57209237 CAAAAACTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.29, C:0.09, G:0.15, T:0.47
Consensus pattern (9 bp):
TCGAATTAT
Found at i:57220405 original size:22 final size:22
Alignment explanation
Indices: 57220380--57220434 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
57220370 AAAATTAAAC
* *
57220380 TAAATATTAAAACTAATAAATT
1 TAAATATTAAAACTAAAAAAAT
*
57220402 TAAAT-TTAGAAATTAAAAAAAT
1 TAAATATTA-AAACTAAAAAAAT
57220424 TAAA-ATTAAAA
1 TAAATATTAAAA
57220435 TTGTGTTAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 6 0.21
22 22 0.79
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (22 bp):
TAAATATTAAAACTAAAAAAAT
Found at i:57222083 original size:70 final size:70
Alignment explanation
Indices: 57221994--57222133 Score: 237
Period size: 70 Copynumber: 2.0 Consensus size: 70
57221984 TGTGGATAGC
* *
57221994 GTTTGTTGCCTTTTTATATG-CTATCCATGGTTGTTTAAATGGATTAGATCGAGAATCGATTGAT
1 GTTTGTTACATTTTTATATGTC-ATCCATGGTTGTTTAAATGGATTAGATCGAGAATCGATTGAT
57222058 ATATCA
65 ATATCA
*
57222064 GTTTGTTACATTTTTATATGTCATCTATGGTTGTTTAAATGGATTAGATCGAGAATCGATTGATA
1 GTTTGTTACATTTTTATATGTCATCCATGGTTGTTTAAATGGATTAGATCGAGAATCGATTGATA
57222129 TATCA
66 TATCA
57222134 ATTCGATGAG
Statistics
Matches: 66, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
70 65 0.98
71 1 0.02
ACGTcount: A:0.27, C:0.10, G:0.19, T:0.44
Consensus pattern (70 bp):
GTTTGTTACATTTTTATATGTCATCCATGGTTGTTTAAATGGATTAGATCGAGAATCGATTGATA
TATCA
Found at i:57222579 original size:12 final size:12
Alignment explanation
Indices: 57222562--57222587 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
57222552 TATTTTTAAA
57222562 AAAGAAAAATTT
1 AAAGAAAAATTT
57222574 AAAGAAAAATTT
1 AAAGAAAAATTT
57222586 AA
1 AA
57222588 TTTAAAATAA
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:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (12 bp):
AAAGAAAAATTT
Found at i:57232053 original size:7 final size:7
Alignment explanation
Indices: 57232041--57232107 Score: 61
Period size: 7 Copynumber: 9.7 Consensus size: 7
57232031 CAGAAGAGTA
57232041 TTATTAT
1 TTATTAT
57232048 TTATTAT
1 TTATTAT
57232055 TTATTA-
1 TTATTAT
57232061 TT-TT-T
1 TTATTAT
*
57232066 TTATTTT
1 TTATTAT
*
57232073 TTACTATT
1 TTATTA-T
57232081 TTATTATT
1 TTATTA-T
57232089 TTATTAT
1 TTATTAT
57232096 TT-TATAT
1 TTAT-TAT
57232103 TTATT
1 TTATT
57232108 TTTTTGCATT
Statistics
Matches: 51, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
5 4 0.08
6 5 0.10
7 27 0.53
8 15 0.29
ACGTcount: A:0.24, C:0.01, G:0.00, T:0.75
Consensus pattern (7 bp):
TTATTAT
Found at i:57232070 original size:18 final size:17
Alignment explanation
Indices: 57232047--57232098 Score: 61
Period size: 18 Copynumber: 3.0 Consensus size: 17
57232037 AGTATTATTA
57232047 TTTATTATTTATTATTTT
1 TTTATT-TTTATTATTTT
*
57232065 TTTATTTTTTACTATTTT
1 TTTA-TTTTTATTATTTT
*
57232083 ATTA-TTTTATTATTTT
1 TTTATTTTTATTATTTT
57232099 ATATTTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 11 0.37
18 17 0.57
19 2 0.07
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTATTTTTATTATTTT
Found at i:57232071 original size:8 final size:8
Alignment explanation
Indices: 57232047--57232112 Score: 51
Period size: 8 Copynumber: 7.4 Consensus size: 8
57232037 AGTATTATTA
57232047 TTTATTATT
1 TTTATT-TT
57232056 TATTATTTT
1 T-TTATTTT
57232065 TTTATTTT
1 TTTATTTT
57232073 TTACTATTTT
1 TT--TATTTT
*
57232083 ATTATTTT
1 TTTATTTT
*
57232091 ATTATTTTAT
1 TTTA-TTT-T
57232101 ATTTATTTT
1 -TTTATTTT
57232110 TTT
1 TTT
57232113 GCATTCAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
8 22 0.45
9 8 0.16
10 16 0.33
11 3 0.06
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTATTTT
Found at i:57232090 original size:16 final size:16
Alignment explanation
Indices: 57232064--57232104 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
57232054 TTTATTATTT
57232064 TTTTATT-TTTTACTA
1 TTTTATTATTTTACTA
*
57232079 TTTTATTATTTTATTA
1 TTTTATTATTTTACTA
57232095 TTTTA-TATTT
1 TTTTATTATTT
57232105 ATTTTTTTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTATTATTTTACTA
Found at i:57232103 original size:18 final size:17
Alignment explanation
Indices: 57232039--57232109 Score: 76
Period size: 17 Copynumber: 4.1 Consensus size: 17
57232029 ATCAGAAGAG
57232039 TATTATTATTTATTA-TT
1 TATTATT-TTTATTATTT
57232056 TATTATTTTT-TTATTT
1 TATTATTTTTATTATTT
57232072 T-TTACTATTTTATTATTT
1 TATTA-T-TTTTATTATTT
57232090 TATTATTTTATATTTATTT
1 TATTATTTT-TA-TTATTT
57232109 T
1 T
57232110 TTTGCATTCA
Statistics
Matches: 47, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
15 6 0.13
16 7 0.15
17 14 0.30
18 10 0.21
19 10 0.21
ACGTcount: A:0.24, C:0.01, G:0.00, T:0.75
Consensus pattern (17 bp):
TATTATTTTTATTATTT
Found at i:57234329 original size:21 final size:22
Alignment explanation
Indices: 57234300--57234351 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
57234290 TGTAGTTTTC
*
57234300 TAGGAGAAAAATT-GGATGTGA
1 TAGGTGAAAAATTAGGATGTGA
* *
57234321 TAGGTGAAATATTAGGATTTGA
1 TAGGTGAAAAATTAGGATGTGA
57234343 TAGGTGAAA
1 TAGGTGAAA
57234352 GGTTGATGGG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 11 0.41
22 16 0.59
ACGTcount: A:0.40, C:0.00, G:0.31, T:0.29
Consensus pattern (22 bp):
TAGGTGAAAAATTAGGATGTGA
Found at i:57234479 original size:15 final size:15
Alignment explanation
Indices: 57234459--57234488 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
57234449 GGGTGGTTTC
57234459 CTTATTTTTTTTGGG
1 CTTATTTTTTTTGGG
57234474 CTTATTTTTTTTGGG
1 CTTATTTTTTTTGGG
57234489 TTTGAATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.07, C:0.07, G:0.20, T:0.67
Consensus pattern (15 bp):
CTTATTTTTTTTGGG
Found at i:57245375 original size:54 final size:54
Alignment explanation
Indices: 57245312--57245544 Score: 234
Period size: 54 Copynumber: 4.1 Consensus size: 54
57245302 AGTATCATAT
*
57245312 ATTATGATTTGAGTAAATTCATATAAAAATATTAATTATTAAGAATTTTATTAA
1 ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
*
57245366 ATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAA
1 ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
* * * * * * * * *
57245420 ATTATATATTTTAATTATAATAT-ATTTAATAATAATTATGTTAATTTATATTTTATAGTATCAT
1 ATTAT-GA-TTTGAGTA-AAT-TCATATAAGAAT-ATTA-ATT-ATTAAGAATTT-TA-T-T-A-
57245484 A
54 A
*
57245485 TATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAA
1 -ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
57245540 ATTAT
1 ATTAT
57245545 ATATTTTAAT
Statistics
Matches: 143, Mismatches: 22, Indels: 28
0.74 0.11 0.15
Matches are distributed among these distances:
54 62 0.43
55 2 0.01
56 7 0.05
57 12 0.08
58 5 0.03
59 4 0.03
60 16 0.11
61 4 0.03
62 5 0.03
63 12 0.08
64 7 0.05
65 2 0.01
66 5 0.03
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.48
Consensus pattern (54 bp):
ATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAA
Found at i:57245412 original size:28 final size:27
Alignment explanation
Indices: 57245327--57245412 Score: 63
Period size: 28 Copynumber: 3.1 Consensus size: 27
57245317 GATTTGAGTA
*
57245327 AATTCATATAAAAATATTAATTATTAAG
1 AATTCATAT-AAAATATTGATTATTAAG
* * *
57245355 AATT-TTATTAAAT-TATGA-T-TTGAG
1 AATTCATATAAAATAT-TGATTATTAAG
57245379 TAAATTCATATAAGAATATTGATTATTAAG
1 --AATTCATATAA-AATATTGATTATTAAG
57245409 AATT
1 AATT
57245413 TTATTAAATT
Statistics
Matches: 43, Mismatches: 7, Indels: 16
0.65 0.11 0.24
Matches are distributed among these distances:
24 4 0.09
25 2 0.05
26 10 0.23
27 7 0.16
28 14 0.33
29 2 0.05
30 4 0.09
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.43
Consensus pattern (27 bp):
AATTCATATAAAATATTGATTATTAAG
Found at i:57245449 original size:15 final size:15
Alignment explanation
Indices: 57245414--57245465 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
57245404 TTAAGAATTT
*
57245414 TATTAAATTAT-ATA
1 TATTTAATTATAATA
57245428 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
57245442 TATTTAATAATAAT-
1 TATTTAATTATAATA
57245456 TATGTTAATT
1 TAT-TTAATT
57245466 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:57245564 original size:16 final size:16
Alignment explanation
Indices: 57245543--57245587 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
57245533 TTATTAAATT
*
57245543 ATATATTTTAATTATA
1 ATATATTTTAATAATA
57245559 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
*
57245574 ATTATATTTAAATA
1 A-TATATTTTAATA
57245588 TGATTAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 10 0.40
16 9 0.36
17 6 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:57245593 original size:16 final size:16
Alignment explanation
Indices: 57245544--57245584 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
57245534 TATTAAATTA
*
57245544 TATATTTTAATTATAA-
1 TATA-TTTAATAATAAT
57245560 TATATTTAATAATAAT
1 TATATTTAATAATAAT
57245576 TATATTTAA
1 TATATTTAA
57245585 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TATATTTAATAATAAT
Found at i:57245794 original size:45 final size:43
Alignment explanation
Indices: 57245695--57245804 Score: 129
Period size: 45 Copynumber: 2.6 Consensus size: 43
57245685 TTTTCCATTA
57245695 TGCTATTACACCTCTATT-C---CATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATACATTCAACCAAACACAAGAT
* ***
57245734 TACTATTACACCTCTATTCCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCA-TACATTCAACCAAACACAAGA-T
57245779 TGCTATTACACCTCTATTCCAATACA
1 TGCTATTACACCTCTATTCC-ATACA
57245805 CCTCTATTCC
Statistics
Matches: 59, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
39 17 0.29
40 1 0.02
44 16 0.27
45 24 0.41
46 1 0.02
ACGTcount: A:0.34, C:0.29, G:0.05, T:0.33
Consensus pattern (43 bp):
TGCTATTACACCTCTATTCCATACATTCAACCAAACACAAGAT
Found at i:57245806 original size:16 final size:16
Alignment explanation
Indices: 57245785--57245835 Score: 84
Period size: 16 Copynumber: 3.2 Consensus size: 16
57245775 GATTTGCTAT
57245785 TACACCTCTATTCCAA
1 TACACCTCTATTCCAA
57245801 TACACCTCTATTCCAA
1 TACACCTCTATTCCAA
* *
57245817 TACACCCCTAATCCAA
1 TACACCTCTATTCCAA
57245833 TAC
1 TAC
57245836 TGCGAACCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.33, C:0.39, G:0.00, T:0.27
Consensus pattern (16 bp):
TACACCTCTATTCCAA
Found at i:57250557 original size:6 final size:6
Alignment explanation
Indices: 57250546--57250576 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
57250536 CATTATCAAC
57250546 ATATAA ATATAA ATATAA ATATAA ATATAA A
1 ATATAA ATATAA ATATAA ATATAA ATATAA A
57250577 AGGGAAAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
ATATAA
Found at i:57252558 original size:41 final size:42
Alignment explanation
Indices: 57252500--57252578 Score: 115
Period size: 41 Copynumber: 1.9 Consensus size: 42
57252490 ATGTTAACGC
* *
57252500 ATATCGATGCCACTGTCCCAAACAGGGTCTTATACGAATCAT
1 ATATCGATGCCAATGTCCCAAACAGGGTCTTACACGAATCAT
* *
57252542 ATAT-GATGCCAATGTCCCAGACATGGTCTTACACGAA
1 ATATCGATGCCAATGTCCCAAACAGGGTCTTACACGAA
57252579 ATCACACCTC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
41 29 0.88
42 4 0.12
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (42 bp):
ATATCGATGCCAATGTCCCAAACAGGGTCTTACACGAATCAT
Found at i:57252918 original size:123 final size:124
Alignment explanation
Indices: 57252722--57253075 Score: 541
Period size: 123 Copynumber: 2.9 Consensus size: 124
57252712 CAATTAATAT
57252722 CCATATACAAATCAAATTCGGCAATGTATATCTATATACAAATCAAATTCGGCAATGTATATCTA
1 CCATATACAAATCAAATTCGGCAATGTATATCTATATACAAATCAAATTCGGCAATGTATATCTA
* *
57252787 TATACAAATC-AATTCGGCAATGAATATCTATATACAAATCAAATTTGGTAATGTATAA
66 TATACAAATCAAATTCGGCAATGTATATCTATATACAAATCAAATTTGGCAATGTATAA
* * *
57252845 CCATATATAAATCAAATTCGGCAATGTATATCTATATACAAATCAAATTCGGCAATGTATAACCA
1 CCATATACAAATCAAATTCGGCAATGTATATCTATATACAAATCAAATTCGGCAATGTATATCTA
* * * *
57252910 TATCCAAATCAAATTCGGCAATGTATAACCATATACAAATCAAATTTGGCAATGTATAT
66 TATACAAATCAAATTCGGCAATGTATATCTATATACAAATCAAATTTGGCAATGTATAA
* * * * **
57252969 CTATATACAAATC-ACTTCGGCAATGTATATCTATAAACAAATCAATTTCGATAATGTATATCTA
1 CCATATACAAATCAAATTCGGCAATGTATATCTATATACAAATCAAATTCGGCAATGTATATCTA
* *
57253033 TAAACAAATCAAATTCGGCAATGTATATCTTTATACAAATCAA
66 TATACAAATCAAATTCGGCAATGTATATCTATATACAAATCAA
57253076 TTCGAAAATG
Statistics
Matches: 207, Mismatches: 23, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
123 153 0.74
124 54 0.26
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.31
Consensus pattern (124 bp):
CCATATACAAATCAAATTCGGCAATGTATATCTATATACAAATCAAATTCGGCAATGTATATCTA
TATACAAATCAAATTCGGCAATGTATATCTATATACAAATCAAATTTGGCAATGTATAA
Found at i:57253044 original size:185 final size:184
Alignment explanation
Indices: 57252699--57253100 Score: 601
Period size: 185 Copynumber: 2.2 Consensus size: 184
57252689 ATCCAATACT
* * *
57252699 CAAATCAATTCGACAAT-TAATATCCATATACAAATCAAATTCGGCAATGTATATCTATATACAA
1 CAAATCAATTCGACAATGT-ATAACCATATACAAATCAAATTCGGCAATGTATAACCATATACAA
*
57252763 ATCAAATTCGGCAATGTATATCTATATACAAATCAATTCGGCAATGAATATCTATATACAAATCA
65 ATCAAATTCGGCAATGTATATCTATATACAAATCAATTCGGCAATGAATATCTATAAACAAATCA
* * *
57252828 AATTTGGTAATGTATAACCATATATAAATCAAATTCGGCAATGTATATCTATATA
130 AATTTGATAATGTATAACCATAAACAAATCAAATTCGGCAATGTATATCTATATA
* *
57252883 CAAATCAAATTCGGCAATGTATAACCATATCCAAATCAAATTCGGCAATGTATAACCATATACAA
1 CAAATC-AATTCGACAATGTATAACCATATACAAATCAAATTCGGCAATGTATAACCATATACAA
* * *
57252948 ATCAAATTTGGCAATGTATATCTATATACAAATCACTTCGGCAATGTATATCTATAAACAAATC-
65 ATCAAATTCGGCAATGTATATCTATATACAAATCAATTCGGCAATGAATATCTATAAACAAATCA
* * *
57253012 AATTTCGATAATGTATATCTATAAACAAATCAAATTCGGCAATGTATATCTTTATA
130 AATTT-GATAATGTATAACCATAAACAAATCAAATTCGGCAATGTATATCTATATA
* *
57253068 CAAATCAATTCGAAAATGTATAAAACATATACA
1 CAAATCAATTCGACAATGTAT-AACCATATACA
57253101 TTAATTTCAA
Statistics
Matches: 195, Mismatches: 19, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
184 24 0.12
185 170 0.87
186 1 0.01
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.31
Consensus pattern (184 bp):
CAAATCAATTCGACAATGTATAACCATATACAAATCAAATTCGGCAATGTATAACCATATACAAA
TCAAATTCGGCAATGTATATCTATATACAAATCAATTCGGCAATGAATATCTATAAACAAATCAA
ATTTGATAATGTATAACCATAAACAAATCAAATTCGGCAATGTATATCTATATA
Found at i:57253086 original size:92 final size:92
Alignment explanation
Indices: 57252699--57253089 Score: 550
Period size: 92 Copynumber: 4.2 Consensus size: 92
57252689 ATCCAATACT
* * *
57252699 CAAATCAATTCGACAAT-TAATATCCATATACAAATCAAATTCGGCAATGTATATCTATATACAA
1 CAAATCAATTCGGCAATGT-ATATCCATATACAAATCAAATTCGGCAATGTATAACCATATACAA
57252763 ATCAAATTCGGCAATGTATATCTATATA
65 ATCAAATTCGGCAATGTATATCTATATA
* * * * *
57252791 CAAATCAATTCGGCAATGAATATCTATATACAAATCAAATTTGGTAATGTATAACCATATATAAA
1 CAAATCAATTCGGCAATGTATATCCATATACAAATCAAATTCGGCAATGTATAACCATATACAAA
57252856 TCAAATTCGGCAATGTATATCTATATA
66 TCAAATTCGGCAATGTATATCTATATA
* *
57252883 CAAATCAAATTCGGCAATGTATAACCATATCCAAATCAAATTCGGCAATGTATAACCATATACAA
1 CAAATC-AATTCGGCAATGTATATCCATATACAAATCAAATTCGGCAATGTATAACCATATACAA
*
57252948 ATCAAATTTGGCAATGTATATCTATATA
65 ATCAAATTCGGCAATGTATATCTATATA
* * * * ** * * *
57252976 CAAATCACTTCGGCAATGTATATCTATAAACAAATCAATTTCGATAATGTATATCTATAAACAAA
1 CAAATCAATTCGGCAATGTATATCCATATACAAATCAAATTCGGCAATGTATAACCATATACAAA
*
57253041 TCAAATTCGGCAATGTATATCTTTATA
66 TCAAATTCGGCAATGTATATCTATATA
**
57253068 CAAATCAATTCGAAAATGTATA
1 CAAATCAATTCGGCAATGTATA
57253090 AAACATATAC
Statistics
Matches: 265, Mismatches: 32, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
92 181 0.68
93 84 0.32
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.31
Consensus pattern (92 bp):
CAAATCAATTCGGCAATGTATATCCATATACAAATCAAATTCGGCAATGTATAACCATATACAAA
TCAAATTCGGCAATGTATATCTATATA
Found at i:57253100 original size:31 final size:31
Alignment explanation
Indices: 57252699--57253089 Score: 531
Period size: 31 Copynumber: 12.7 Consensus size: 31
57252689 ATCCAATACT
* *
57252699 CAAATC-AATTCGACAAT-TAATATCCATATA
1 CAAATCAAATTCGGCAATGT-ATATCTATATA
57252729 CAAATCAAATTCGGCAATGTATATCTATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
57252760 CAAATCAAATTCGGCAATGTATATCTATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
*
57252791 CAAATC-AATTCGGCAATGAATATCTATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* * * *
57252821 CAAATCAAATTTGGTAATGTATAACCATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
*
57252852 TAAATCAAATTCGGCAATGTATATCTATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* * *
57252883 CAAATCAAATTCGGCAATGTATAACCATATC
1 CAAATCAAATTCGGCAATGTATATCTATATA
* *
57252914 CAAATCAAATTCGGCAATGTATAACCATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
*
57252945 CAAATCAAATTTGGCAATGTATATCTATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* *
57252976 CAAATC-ACTTCGGCAATGTATATCTATAAA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* ** *
57253006 CAAATCAATTTCGATAATGTATATCTATAAA
1 CAAATCAAATTCGGCAATGTATATCTATATA
*
57253037 CAAATCAAATTCGGCAATGTATATCTTTATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
**
57253068 CAAATC-AATTCGAAAATGTATA
1 CAAATCAAATTCGGCAATGTATA
57253090 AAACATATAC
Statistics
Matches: 323, Mismatches: 34, Indels: 8
0.88 0.09 0.02
Matches are distributed among these distances:
30 76 0.24
31 246 0.76
32 1 0.00
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.31
Consensus pattern (31 bp):
CAAATCAAATTCGGCAATGTATATCTATATA
Found at i:57259287 original size:31 final size:31
Alignment explanation
Indices: 57259159--57259499 Score: 332
Period size: 31 Copynumber: 11.1 Consensus size: 31
57259149 ATCCAATACT
*
57259159 CAAATCAAA-TCGGCAATATATATATCCATATA
1 CAAATCAAATTCGGCAATGTATA-A-CCATATA
** * *
57259191 TGAATCAAATTCGGCAA--TATATCTATATA
1 CAAATCAAATTCGGCAATGTATAACCATATA
* * * * *
57259220 CAAATC-AATTTGGCAATGAATATCTAAATA
1 CAAATCAAATTCGGCAATGTATAACCATATA
* *
57259250 CAAATCAAATTCAGTAATGTATAACCATATA
1 CAAATCAAATTCGGCAATGTATAACCATATA
* * *
57259281 TAAATCAAATTCGGCAATGTATATCTATATA
1 CAAATCAAATTCGGCAATGTATAACCATATA
* *
57259312 CAAATCAAATTCTGCAATGTATAACCGTATA
1 CAAATCAAATTCGGCAATGTATAACCATATA
* *
57259343 CAGATCAAATTCAGCAATGTATAACCATATA
1 CAAATCAAATTCGGCAATGTATAACCATATA
* * *
57259374 CAAATCAAATTCGGCAATGTATATCTATAAA
1 CAAATCAAATTCGGCAATGTATAACCATATA
* * * * *
57259405 CAAATCAATTTCGGTAATGTATATCTATAAA
1 CAAATCAAATTCGGCAATGTATAACCATATA
** **
57259436 CAAATCAAATTCGGCAATGTATGTCTTTATA
1 CAAATCAAATTCGGCAATGTATAACCATATA
*
57259467 CAAATC-AATTCGGCAATGTATAAAACATATA
1 CAAATCAAATTCGGCAATGTAT-AACCATATA
57259498 CA
1 CA
57259500 TTTAATTTCA
Statistics
Matches: 258, Mismatches: 46, Indels: 11
0.82 0.15 0.03
Matches are distributed among these distances:
28 9 0.03
29 10 0.04
30 31 0.12
31 194 0.75
32 7 0.03
33 7 0.03
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.30
Consensus pattern (31 bp):
CAAATCAAATTCGGCAATGTATAACCATATA
Found at i:57259362 original size:93 final size:93
Alignment explanation
Indices: 57259159--57259488 Score: 393
Period size: 93 Copynumber: 3.6 Consensus size: 93
57259149 ATCCAATACT
* * **
57259159 CAAATCAAA-TCGGCAATATATATATCCATATATGAATCAAATTCGGCAA--TATATCTATATAC
1 CAAATCAAATTCAGCAATGTATA-A-CCATATACAAATCAAATTCGGCAATGTATATCTATATAC
* *
57259221 AAATC-AATT-TGGCAATGAATATCTAAATA
64 AAATCAAATTCT-GCAATGTATATCTATATA
* *
57259250 CAAATCAAATTCAGTAATGTATAACCATATATAAATCAAATTCGGCAATGTATATCTATATACAA
1 CAAATCAAATTCAGCAATGTATAACCATATACAAATCAAATTCGGCAATGTATATCTATATACAA
* **
57259315 ATCAAATTCTGCAATGTATAACCGTATA
66 ATCAAATTCTGCAATGTATATCTATATA
* *
57259343 CAGATCAAATTCAGCAATGTATAACCATATACAAATCAAATTCGGCAATGTATATCTATAAACAA
1 CAAATCAAATTCAGCAATGTATAACCATATACAAATCAAATTCGGCAATGTATATCTATATACAA
* * * *
57259408 ATCAATTTCGGTAATGTATATCTATAAA
66 ATCAAATTCTGCAATGTATATCTATATA
* ** **
57259436 CAAATCAAATTCGGCAATGTATGTCTTTATACAAATC-AATTCGGCAATGTATA
1 CAAATCAAATTCAGCAATGTATAACCATATACAAATCAAATTCGGCAATGTATA
57259489 AAACATATAC
Statistics
Matches: 208, Mismatches: 26, Indels: 9
0.86 0.11 0.04
Matches are distributed among these distances:
90 23 0.11
91 10 0.05
92 44 0.21
93 130 0.62
94 1 0.00
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.31
Consensus pattern (93 bp):
CAAATCAAATTCAGCAATGTATAACCATATACAAATCAAATTCGGCAATGTATATCTATATACAA
ATCAAATTCTGCAATGTATATCTATATA
Found at i:57270373 original size:19 final size:19
Alignment explanation
Indices: 57270332--57270396 Score: 64
Period size: 19 Copynumber: 3.5 Consensus size: 19
57270322 AATAAAAAGA
* *
57270332 AAAAATTA-GAAATAATAAC
1 AAAAATTATAAAATAA-AAT
57270351 AAAAATTATAAAATAAAAT
1 AAAAATTATAAAATAAAAT
57270370 -AAAATTATAATAA-AAAAT
1 AAAAATTATAA-AATAAAAT
*
57270388 CAAAATTAT
1 AAAAATTAT
57270397 TCAGAAAAGT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
18 15 0.37
19 20 0.49
20 6 0.15
ACGTcount: A:0.69, C:0.03, G:0.02, T:0.26
Consensus pattern (19 bp):
AAAAATTATAAAATAAAAT
Found at i:57271539 original size:23 final size:23
Alignment explanation
Indices: 57271495--57271541 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
57271485 TTATAAAATC
* *
57271495 AAATTAAATTATAAACAGATAAA
1 AAATTAAAATATAAACAAATAAA
**
57271518 AAATTAAAATATAATTAAATAAA
1 AAATTAAAATATAAACAAATAAA
57271541 A
1 A
57271542 CTCACACATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (23 bp):
AAATTAAAATATAAACAAATAAA
Found at i:57274689 original size:21 final size:21
Alignment explanation
Indices: 57274663--57274706 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
57274653 CGAAAATGTA
57274663 CAATTTTGATTAAGTGTTTAT
1 CAATTTTGATTAAGTGTTTAT
57274684 CAATTTTGATTAAGTGTTTAT
1 CAATTTTGATTAAGTGTTTAT
57274705 CA
1 CA
57274707 CTTTAGATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.30, C:0.07, G:0.14, T:0.50
Consensus pattern (21 bp):
CAATTTTGATTAAGTGTTTAT
Found at i:57281545 original size:23 final size:23
Alignment explanation
Indices: 57281519--57281573 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
57281509 GTCACCAACT
* * *
57281519 TTAAAATTCCCATTTAATTTTTA
1 TTAAAATTCCCATCTAATTCTCA
* *
57281542 TTAAAATTCTCATCTGATTCTCA
1 TTAAAATTCCCATCTAATTCTCA
57281565 TTAAAATTC
1 TTAAAATTC
57281574 ACATAACTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.35, C:0.16, G:0.02, T:0.47
Consensus pattern (23 bp):
TTAAAATTCCCATCTAATTCTCA
Found at i:57282698 original size:11 final size:11
Alignment explanation
Indices: 57282684--57282724 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
57282674 TTTTTATTTA
57282684 TTTTCTTTCTT
1 TTTTCTTTCTT
*
57282695 TTTTCTGTCTT
1 TTTTCTTTCTT
*
57282706 TTTT-TTT-GT
1 TTTTCTTTCTT
57282715 TTTTCTTTCT
1 TTTTCTTTCT
57282725 CTTCTTTTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
9 5 0.21
10 5 0.21
11 14 0.58
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.80
Consensus pattern (11 bp):
TTTTCTTTCTT
Found at i:57282707 original size:20 final size:21
Alignment explanation
Indices: 57282684--57282731 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
57282674 TTTTTATTTA
57282684 TTTTCTTTCT-TTTTTCTGTC
1 TTTTCTTTCTGTTTTTCTGTC
* *
57282704 TTTT-TTTTTGTTTTTCTTTC
1 TTTTCTTTCTGTTTTTCTGTC
*
57282724 TCTTCTTT
1 TTTTCTTT
57282732 TCAATTGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 4 0.17
20 16 0.70
21 3 0.13
ACGTcount: A:0.00, C:0.17, G:0.04, T:0.79
Consensus pattern (21 bp):
TTTTCTTTCTGTTTTTCTGTC
Found at i:57290518 original size:36 final size:36
Alignment explanation
Indices: 57290471--57290543 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
57290461 CACACTTAAA
57290471 CTTTTTTACATTTTTTAATTTAGTAGTCTCTATTGC
1 CTTTTTTACATTTTTTAATTTAGTAGTCTCTATTGC
57290507 CTTTTTTACATTTTTTAATTTAGTAGTCTCTATTGC
1 CTTTTTTACATTTTTTAATTTAGTAGTCTCTATTGC
57290543 C
1 C
57290544 ATGTAATTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.19, C:0.15, G:0.08, T:0.58
Consensus pattern (36 bp):
CTTTTTTACATTTTTTAATTTAGTAGTCTCTATTGC
Found at i:57295438 original size:51 final size:50
Alignment explanation
Indices: 57295308--57295496 Score: 238
Period size: 51 Copynumber: 3.7 Consensus size: 50
57295298 ACTATTATCA
* * *
57295308 TTCGATACACGTAGTAGCCTTCACATGGTACTACACACGTGATC-AAGTT
1 TTCGATACACGTAGTAGCCTTCACATAGTACTACACATGTGACCAAAGTT
*
57295357 TTACGATCCACGTAGTAGCCTTCACATAGTACTACACATGTGACCAAAGCTT
1 TT-CGATACACGTAGTAGCCTTCACATAGTACTACACATGTGACCAAAG-TT
* * * * *
57295409 TTTGGTACACGTAGTAGCCTTCACTTAGTACTACACATGTGACTATTA-TT
1 TTCGATACACGTAGTAGCCTTCACATAGTACTACACATGTGACCA-AAGTT
*
57295459 TATCGATACACGTTGTAGCCTTCACATAGTACTACACA
1 T-TCGATACACGTAGTAGCCTTCACATAGTACTACACA
57295497 CGTGTTCATC
Statistics
Matches: 121, Mismatches: 14, Indels: 8
0.85 0.10 0.06
Matches are distributed among these distances:
49 2 0.02
50 41 0.34
51 73 0.60
52 5 0.04
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (50 bp):
TTCGATACACGTAGTAGCCTTCACATAGTACTACACATGTGACCAAAGTT
Found at i:57303921 original size:41 final size:41
Alignment explanation
Indices: 57303791--57303913 Score: 156
Period size: 41 Copynumber: 3.0 Consensus size: 41
57303781 TTGCCTGATT
* *
57303791 TGATACACCGGCACAAAGCCTAATAGGCTCAAGGCCTGATA
1 TGATACACCGGCACAAAGCCTGATAGGCTCAAGGCCCGATA
* * * * *
57303832 TGATACACTGACACAAAGACTGCTAGGCTCAAGTCCCGATA
1 TGATACACCGGCACAAAGCCTGATAGGCTCAAGGCCCGATA
** *
57303873 TGATACACCGGCATGAAGCCTGTTAGGCTCAAGGCCCGATA
1 TGATACACCGGCACAAAGCCTGATAGGCTCAAGGCCCGATA
57303914 CAATACACTC
Statistics
Matches: 68, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
41 68 1.00
ACGTcount: A:0.32, C:0.27, G:0.23, T:0.19
Consensus pattern (41 bp):
TGATACACCGGCACAAAGCCTGATAGGCTCAAGGCCCGATA
Found at i:57309741 original size:24 final size:27
Alignment explanation
Indices: 57309696--57309753 Score: 70
Period size: 24 Copynumber: 2.3 Consensus size: 27
57309686 AGAACAACGG
* *
57309696 GGAGTAAA-AAAAATGAAGAAGAAA-A
1 GGAGAAAACAAAAATGAAAAAGAAAGA
57309721 -GAGAAAACAAAAAT-AAAAAGAAAGA
1 GGAGAAAACAAAAATGAAAAAGAAAGA
57309746 GGAGAAAA
1 GGAGAAAA
57309754 AGAATGAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
24 14 0.50
25 7 0.25
26 7 0.25
ACGTcount: A:0.71, C:0.02, G:0.22, T:0.05
Consensus pattern (27 bp):
GGAGAAAACAAAAATGAAAAAGAAAGA
Found at i:57318730 original size:12 final size:12
Alignment explanation
Indices: 57318713--57318743 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
57318703 CCACTATGCC
57318713 TCACATGGTCTG
1 TCACATGGTCTG
57318725 TCACATGGTCTG
1 TCACATGGTCTG
*
57318737 GCACATG
1 TCACATG
57318744 ATCGTGTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.29
Consensus pattern (12 bp):
TCACATGGTCTG
Found at i:57321460 original size:41 final size:41
Alignment explanation
Indices: 57321415--57321502 Score: 95
Period size: 41 Copynumber: 2.1 Consensus size: 41
57321405 GCTAGACACG
* * * *
57321415 ATACACAAGTACGAAGACTTCTAGGCTCAAGGCACGATACA
1 ATACACAAGCACGAAGACTACTAGACTCAAAGCACGATACA
** * * *
57321456 ATACACCGGCACGAAGCCTACTAGACTCAAAGCCCGATATA
1 ATACACAAGCACGAAGACTACTAGACTCAAAGCACGATACA
57321497 ATACAC
1 ATACAC
57321503 CCAACACATT
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.39, C:0.28, G:0.17, T:0.16
Consensus pattern (41 bp):
ATACACAAGCACGAAGACTACTAGACTCAAAGCACGATACA
Found at i:57321503 original size:41 final size:41
Alignment explanation
Indices: 57321425--57321503 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
57321415 ATACACAAGT
* * *
57321425 ACGAAGACTTCTAGGCTCAAGGCACGATACAATACACCGGC
1 ACGAAGACTACTAGACTCAAAGCACGATACAATACACCGGC
* * *
57321466 ACGAAGCCTACTAGACTCAAAGCCCGATATAATACACC
1 ACGAAGACTACTAGACTCAAAGCACGATACAATACACC
57321504 CAACACATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.37, C:0.30, G:0.18, T:0.15
Consensus pattern (41 bp):
ACGAAGACTACTAGACTCAAAGCACGATACAATACACCGGC
Found at i:57324102 original size:10 final size:8
Alignment explanation
Indices: 57324079--57324107 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
57324069 ATATTATCAT
57324079 TTCACACA
1 TTCACACA
57324087 TTCACACA
1 TTCACACA
57324095 TTCACACA
1 TTCACACA
57324103 TTCAC
1 TTCAC
57324108 TTTCATATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.34, C:0.38, G:0.00, T:0.28
Consensus pattern (8 bp):
TTCACACA
Found at i:57324993 original size:26 final size:26
Alignment explanation
Indices: 57324938--57325010 Score: 71
Period size: 26 Copynumber: 2.9 Consensus size: 26
57324928 GGAAAATTTT
* * *
57324938 CCTTTCTTTTCTTTTCTTTCTTCCTT
1 CCTTTTTTTTATTTTCTTTCTTCCTC
57324964 CCTTTTTTTTATTTTCCTTTCTTCC-C
1 CCTTTTTTTTATTTT-CTTTCTTCCTC
* *
57324990 CC-TTTATTTA-TTTGTTTCTTC
1 CCTTTTTTTTATTTTCTTTCTTC
57325011 AGCTCATGCT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
23 7 0.17
24 3 0.07
25 7 0.17
26 15 0.37
27 9 0.22
ACGTcount: A:0.04, C:0.27, G:0.01, T:0.67
Consensus pattern (26 bp):
CCTTTTTTTTATTTTCTTTCTTCCTC
Found at i:57334466 original size:18 final size:18
Alignment explanation
Indices: 57334445--57334488 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
57334435 TAATTGGATA
* *
57334445 TAGATACATATTTAGATT
1 TAGATACATAATCAGATT
*
57334463 TAGACACATAATCAGATT
1 TAGATACATAATCAGATT
57334481 TAGATACA
1 TAGATACA
57334489 ATTGCAAACA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.34
Consensus pattern (18 bp):
TAGATACATAATCAGATT
Found at i:57334716 original size:74 final size:74
Alignment explanation
Indices: 57334595--57334743 Score: 289
Period size: 74 Copynumber: 2.0 Consensus size: 74
57334585 ATGAGTCCAT
*
57334595 TCATCCAATCACACCAGTTTATGGTGGTATGCCACTTATAATAGTGCAGCTGATCTGCTAGACAA
1 TCATCCAATCACACCAGTTCATGGTGGTATGCCACTTATAATAGTGCAGCTGATCTGCTAGACAA
57334660 ATATTGCGG
66 ATATTGCGG
57334669 TCATCCAATCACACCAGTTCATGGTGGTATGCCACTTATAATAGTGCAGCTGATCTGCTAGACAA
1 TCATCCAATCACACCAGTTCATGGTGGTATGCCACTTATAATAGTGCAGCTGATCTGCTAGACAA
57334734 ATATTGCGG
66 ATATTGCGG
57334743 T
1 T
57334744 TTAATTGCCA
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (74 bp):
TCATCCAATCACACCAGTTCATGGTGGTATGCCACTTATAATAGTGCAGCTGATCTGCTAGACAA
ATATTGCGG
Found at i:57335961 original size:9 final size:9
Alignment explanation
Indices: 57335925--57335957 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
57335915 TAAAAATAAT
57335925 AATAAGAAA
1 AATAAGAAA
57335934 AATAAGAAA
1 AATAAGAAA
57335943 AATAA-ATAA
1 AATAAGA-AA
57335952 AATAAG
1 AATAAG
57335958 TAAATGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 1 0.05
9 21 0.95
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (9 bp):
AATAAGAAA
Found at i:57343772 original size:21 final size:22
Alignment explanation
Indices: 57343722--57343772 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
57343712 ACTGTGTGAC
* *
57343722 AAGGTACACAGCCATGTGGCTG
1 AAGGTACACACCCATGCGGCTG
*
57343744 AAGG-ACACACCCTTGCGGCTG
1 AAGGTACACACCCATGCGGCTG
57343765 -AGGTACAC
1 AAGGTACAC
57343773 GGTCGTACGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 3 0.12
21 18 0.72
22 4 0.16
ACGTcount: A:0.27, C:0.27, G:0.29, T:0.16
Consensus pattern (22 bp):
AAGGTACACACCCATGCGGCTG
Found at i:57347270 original size:15 final size:15
Alignment explanation
Indices: 57347250--57347281 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
57347240 CTACATCTCG
57347250 TCGCATATTTTACTC
1 TCGCATATTTTACTC
57347265 TCGCATATTTTACTC
1 TCGCATATTTTACTC
57347280 TC
1 TC
57347282 ACTGTTACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.19, C:0.28, G:0.06, T:0.47
Consensus pattern (15 bp):
TCGCATATTTTACTC
Found at i:57352728 original size:17 final size:17
Alignment explanation
Indices: 57352706--57352739 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
57352696 GATATTACTT
57352706 AAAATAAAAATAAATTA
1 AAAATAAAAATAAATTA
57352723 AAAATAAAAATAAATTA
1 AAAATAAAAATAAATTA
57352740 TAATTATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAATAAAAATAAATTA
Found at i:57352744 original size:6 final size:6
Alignment explanation
Indices: 57352735--57352761 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
57352725 AATAAAAATA
57352735 AATTAT AATTAT AATTAT AATTAT AAT
1 AATTAT AATTAT AATTAT AATTAT AAT
57352762 GATTTATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
AATTAT
Found at i:57353790 original size:15 final size:16
Alignment explanation
Indices: 57353770--57353804 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
57353760 TTAAACAAGG
57353770 TTAAAGATTAATT-AA
1 TTAAAGATTAATTAAA
*
57353785 TTAAAGTTTAATTAAA
1 TTAAAGATTAATTAAA
57353801 TTAA
1 TTAA
57353805 TTAAGGTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (16 bp):
TTAAAGATTAATTAAA
Found at i:57353804 original size:20 final size:19
Alignment explanation
Indices: 57353779--57353832 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
57353769 GTTAAAGATT
*
57353779 AATTAATTAAAGTTTAATTA
1 AATTAATT-AAGGTTAATTA
57353799 AATTAATTAAGGTTAATTA
1 AATTAATTAAGGTTAATTA
*
57353818 ACTTATAATTAAGGT
1 A-AT-TAATTAAGGT
57353833 ATAAAAGATA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 11 0.37
20 9 0.30
21 10 0.33
ACGTcount: A:0.46, C:0.02, G:0.09, T:0.43
Consensus pattern (19 bp):
AATTAATTAAGGTTAATTA
Found at i:57354956 original size:30 final size:30
Alignment explanation
Indices: 57354920--57355126 Score: 220
Period size: 30 Copynumber: 6.9 Consensus size: 30
57354910 TGAGTAACCA
*
57354920 CAATTATAATGTTAGCTTGTGTGAGCAATT
1 CAATTATAATGTCAGCTTGTGTGAGCAATT
* *
57354950 CAATTATAATGTCAGCTTGTTTGAGCAATC
1 CAATTATAATGTCAGCTTGTGTGAGCAATT
*
57354980 CGATTATAATGTCAGCTTGTGTGAG-AATT
1 CAATTATAATGTCAGCTTGTGTGAGCAATT
** *
57355009 CAATTATAATGTCAATTTGTGTGAGAAATT
1 CAATTATAATGTCAGCTTGTGTGAGCAATT
** * * * *
57355039 TGATTATAATGTCAGGTTATATGAGAAATT
1 CAATTATAATGTCAGCTTGTGTGAGCAATT
* * *
57355069 CGATTATAATGTGAGCTTGTGTGAG-AAAT
1 CAATTATAATGTCAGCTTGTGTGAGCAATT
* * *
57355098 CTAATTATAACGTCAACTTTTGTGAGCAA
1 C-AATTATAATGTCAGCTTGTGTGAGCAA
57355127 CCATAAAAAT
Statistics
Matches: 148, Mismatches: 26, Indels: 5
0.83 0.15 0.03
Matches are distributed among these distances:
29 29 0.20
30 117 0.79
31 2 0.01
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.38
Consensus pattern (30 bp):
CAATTATAATGTCAGCTTGTGTGAGCAATT
Found at i:57355073 original size:89 final size:89
Alignment explanation
Indices: 57354920--57355123 Score: 257
Period size: 89 Copynumber: 2.3 Consensus size: 89
57354910 TGAGTAACCA
* ** * * * *
57354920 CAATTATAATGTTAGCTTGTGTGAGCAATTCAATTATAATGTCAGCTTGTTTGAGCAATCCGATT
1 CAATTATAATGTCAATTTGTGTGAGAAATTCAATTATAATGTCAGCTTATATGAGAAATCCGATT
*
57354985 ATAATGTCAGCTTGTGTGAGAATT
66 ATAATGTCAGCTTGTGTGAGAAAT
** * *
57355009 CAATTATAATGTCAATTTGTGTGAGAAATTTGATTATAATGTCAGGTTATATGAGAAATTCGATT
1 CAATTATAATGTCAATTTGTGTGAGAAATTCAATTATAATGTCAGCTTATATGAGAAATCCGATT
*
57355074 ATAATGTGAGCTTGTGTGAGAAAT
66 ATAATGTCAGCTTGTGTGAGAAAT
*
57355098 CTAATTATAACGTCAACTTT-TGTGAG
1 C-AATTATAATGTCAA-TTTGTGTGAG
57355124 CAACCATAAA
Statistics
Matches: 99, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
89 77 0.78
90 19 0.19
91 3 0.03
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.38
Consensus pattern (89 bp):
CAATTATAATGTCAATTTGTGTGAGAAATTCAATTATAATGTCAGCTTATATGAGAAATCCGATT
ATAATGTCAGCTTGTGTGAGAAAT
Found at i:57367970 original size:29 final size:29
Alignment explanation
Indices: 57367923--57367979 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
57367913 ATTTAGCGCG
*
57367923 CTCTTTGTTTGATTGAAGCACTTTGGTGC
1 CTCTTTGTTTGATTAAAGCACTTTGGTGC
57367952 CTCTTTGTTTTGA-TAAAGCACTTTGGTG
1 CTCTTTG-TTTGATTAAAGCACTTTGGTG
57367980 TTGGTCTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 21 0.81
30 5 0.19
ACGTcount: A:0.16, C:0.16, G:0.23, T:0.46
Consensus pattern (29 bp):
CTCTTTGTTTGATTAAAGCACTTTGGTGC
Found at i:57370508 original size:18 final size:18
Alignment explanation
Indices: 57370481--57370523 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
57370471 CATATATTGA
57370481 TATATATT-AATTAATTTT
1 TATATATTAAATT-ATTTT
*
57370499 TATATTTTAAATTATTTT
1 TATATATTAAATTATTTT
*
57370517 TACATAT
1 TATATAT
57370524 ATTGCAATGA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (18 bp):
TATATATTAAATTATTTT
Found at i:57371113 original size:23 final size:23
Alignment explanation
Indices: 57371067--57371132 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
57371057 TTCAACTATG
*
57371067 ATTAAATTTAATC-ACT-TTAAT
1 ATTAAATTTAATCTAATATTAAT
57371088 ATTAAATTTAATCTAATATTAAT
1 ATTAAATTTAATCTAATATTAAT
* * *
57371111 ATTAGATTAAATTTAATATTAA
1 ATTAAATTTAATCTAATATTAA
57371133 ATCTTATTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.33
22 2 0.05
23 24 0.62
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (23 bp):
ATTAAATTTAATCTAATATTAAT
Found at i:57371192 original size:17 final size:16
Alignment explanation
Indices: 57371170--57371262 Score: 61
Period size: 17 Copynumber: 5.6 Consensus size: 16
57371160 CTACAAGGTA
57371170 AATATTAAATTAAATTT
1 AATATTAAATTAAA-TT
57371187 AATATTAAGA-TAATCACTCT
1 AATATTAA-ATTAA--A-T-T
*
57371207 AATATTAAATTAAA-A
1 AATATTAAATTAAATT
57371222 AATATT--ATTAAGA-T
1 AATATTAAATTAA-ATT
57371236 AAGTATTAAATTAAATTT
1 AA-TATTAAATTAAA-TT
57371254 AATATTAAA
1 AATATTAAA
57371263 CTATTAAAAT
Statistics
Matches: 62, Mismatches: 3, Indels: 22
0.71 0.03 0.25
Matches are distributed among these distances:
13 5 0.08
14 3 0.05
15 10 0.16
16 1 0.02
17 23 0.37
18 5 0.08
19 3 0.05
20 12 0.19
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (16 bp):
AATATTAAATTAAATT
Found at i:57382968 original size:37 final size:37
Alignment explanation
Indices: 57382927--57383102 Score: 298
Period size: 37 Copynumber: 4.8 Consensus size: 37
57382917 TTTGAGTACT
57382927 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
*
57382964 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
*
57383001 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
*
57383038 TCTGATCAAGAGACAAAGTGATAAGTGGCTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
** *
57383075 TCTGATCAAGTGATAAAGTGATAAGTGG
1 TCTGATCAAGAAACAAAGTGATAAGTGG
57383103 TAGCTTCAGC
Statistics
Matches: 134, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 134 1.00
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (37 bp):
TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
Found at i:57383174 original size:45 final size:46
Alignment explanation
Indices: 57383065--57383188 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 46
57383055 GTGATAAGTG
* *
57383065 GCTACACTTATCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTCA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
*
57383111 GCTACACTTATCTGATCAAGTGGCAAAGTGATAAGTGGTAGCCT-A
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
57383156 GCTACACTTATCTGATCAAG-GAC-AAGTGATAAG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAG
57383189 AGGTCATATG
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
43 10 0.14
44 2 0.03
45 21 0.28
46 41 0.55
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (46 bp):
GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
Found at i:57390666 original size:37 final size:37
Alignment explanation
Indices: 57390625--57390800 Score: 298
Period size: 37 Copynumber: 4.8 Consensus size: 37
57390615 TTTGAGTACT
57390625 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
*
57390662 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
*
57390699 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
*
57390736 TCTGATCAAGAGACAAAGTGATAAGTGGCTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
** *
57390773 TCTGATCAAGTGATAAAGTGATAAGTGG
1 TCTGATCAAGAAACAAAGTGATAAGTGG
57390801 TAGCTTCAGC
Statistics
Matches: 134, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 134 1.00
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (37 bp):
TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
Found at i:57390872 original size:45 final size:46
Alignment explanation
Indices: 57390763--57390886 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 46
57390753 GTGATAAGTG
* *
57390763 GCTACACTTATCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTCA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
*
57390809 GCTACACTTATCTGATCAAGTGGCAAAGTGATAAGTGGTAGCCT-A
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
57390854 GCTACACTTATCTGATCAAG-GAC-AAGTGATAAG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAG
57390887 AGGTCATATG
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
43 10 0.14
44 2 0.03
45 21 0.28
46 41 0.55
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (46 bp):
GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
Found at i:57392644 original size:17 final size:18
Alignment explanation
Indices: 57392617--57392651 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
57392607 AGTGAATGGG
57392617 TTTTTTAATTATATTTTA
1 TTTTTTAATTATATTTTA
*
57392635 TTTTTT-ATTATCTTTTA
1 TTTTTTAATTATATTTTA
57392652 ATAGTATGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTTAATTATATTTTA
Found at i:57396303 original size:19 final size:20
Alignment explanation
Indices: 57396268--57396309 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
57396258 ATATAAAATG
57396268 AAAGCAACTGAAAAACA-AA
1 AAAGCAACTGAAAAACAGAA
*
57396287 AAAGCAA-TGAGAGAACAGAA
1 AAAGCAACTGA-AAAACAGAA
57396307 AAA
1 AAA
57396310 ACCACAAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 3 0.15
19 12 0.60
20 5 0.25
ACGTcount: A:0.67, C:0.12, G:0.17, T:0.05
Consensus pattern (20 bp):
AAAGCAACTGAAAAACAGAA
Found at i:57397560 original size:40 final size:41
Alignment explanation
Indices: 57397479--57397561 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 41
57397469 CTTAAGTAGA
* *
57397479 ACCATATTTAATATAGTTTTTTAATGTGTTAATGAGTATTAT
1 ACCATATTTAATATAGTTTTTT-ATATGTTAAAGAGTATTAT
57397521 ACCATATTTAATATAGTTTTTT-TATGTTAAAGAGTATTAT
1 ACCATATTTAATATAGTTTTTTATATGTTAAAGAGTATTAT
57397561 A
1 A
57397562 AATTAATATA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
40 17 0.44
42 22 0.56
ACGTcount: A:0.35, C:0.05, G:0.11, T:0.49
Consensus pattern (41 bp):
ACCATATTTAATATAGTTTTTTATATGTTAAAGAGTATTAT
Found at i:57399234 original size:30 final size:29
Alignment explanation
Indices: 57399193--57399267 Score: 86
Period size: 25 Copynumber: 2.7 Consensus size: 29
57399183 TCTCGATATC
* *
57399193 CATAACTTTGACTTTCCAATATTTGATACA
1 CATATCTTTGACTTTCC-ATATTTAATACA
*
57399223 CATATCTTTGAC-TT---TATTTAATACC
1 CATATCTTTGACTTTCCATATTTAATACA
57399248 CATATCTTTGACTTTCCATA
1 CATATCTTTGACTTTCCATA
57399268 AATATGGATG
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
25 21 0.55
26 2 0.05
29 4 0.11
30 11 0.29
ACGTcount: A:0.29, C:0.21, G:0.05, T:0.44
Consensus pattern (29 bp):
CATATCTTTGACTTTCCATATTTAATACA
Found at i:57401593 original size:43 final size:43
Alignment explanation
Indices: 57401538--57401724 Score: 171
Period size: 43 Copynumber: 4.3 Consensus size: 43
57401528 TTTTAAAAAT
* * *
57401538 AAACGCCACTAAAGATCATGACCCTTAGCAGCGCTTTTACCAC
1 AAACGCCGCTAAAGACCATGACCCTTAGCGGCGCTTTTACCAC
* * * *
57401581 AAACGCCGCTAAAGACCATGAGCTTTAGTGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCATGACCCTTAGCGGCGCTTTTACCAC
* * * * *
57401624 AAACACCGCTAAAGACAATGA-ACTGTAACGGCGCTTTT-CCTAT
1 AAACGCCGCTAAAGACCATGACCCT-TAGCGGCGCTTTTACC-AC
* * * * *
57401667 AAATGCCGCTAAAAACCATGACCTTTAGCGGCGATTTTATCAC
1 AAACGCCGCTAAAGACCATGACCCTTAGCGGCGCTTTTACCAC
* *
57401710 AAGCGCCACTAAAGA
1 AAACGCCGCTAAAGA
57401725 ATAAACCTTT
Statistics
Matches: 112, Mismatches: 28, Indels: 8
0.76 0.19 0.05
Matches are distributed among these distances:
42 3 0.03
43 107 0.96
44 2 0.02
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.22
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCATGACCCTTAGCGGCGCTTTTACCAC
Found at i:57404369 original size:43 final size:43
Alignment explanation
Indices: 57404316--57404397 Score: 146
Period size: 43 Copynumber: 1.9 Consensus size: 43
57404306 GAAAAAAAAT
*
57404316 AGAACCAAAAGTTATTATATATGGTGCCTTCATTTTAAACTAC
1 AGAAACAAAAGTTATTATATATGGTGCCTTCATTTTAAACTAC
*
57404359 AGAAACAAAAGTTATTATATATGGTGCTTTCATTTTAAA
1 AGAAACAAAAGTTATTATATATGGTGCCTTCATTTTAAA
57404398 AGAGAAATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (43 bp):
AGAAACAAAAGTTATTATATATGGTGCCTTCATTTTAAACTAC
Found at i:57404404 original size:41 final size:41
Alignment explanation
Indices: 57404311--57404404 Score: 134
Period size: 43 Copynumber: 2.2 Consensus size: 41
57404301 TAAAAGAAAA
* *
57404311 AAAATAGAACCAAAAGTTATTATATATGGTGCCTTCATTTT
1 AAAACAGAAACAAAAGTTATTATATATGGTGCCTTCATTTT
*
57404352 AAACTACAGAAACAAAAGTTATTATATATGGTGCTTTCATTTT
1 AAA--ACAGAAACAAAAGTTATTATATATGGTGCCTTCATTTT
*
57404395 AAAAGAGAAA
1 AAAACAGAAA
57404405 TAAACCAGAC
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
41 9 0.19
43 38 0.81
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.33
Consensus pattern (41 bp):
AAAACAGAAACAAAAGTTATTATATATGGTGCCTTCATTTT
Found at i:57405797 original size:148 final size:149
Alignment explanation
Indices: 57405509--57406012 Score: 874
Period size: 148 Copynumber: 3.4 Consensus size: 149
57405499 TTTTGCGCCG
* * *
57405509 TTTTTCATAAAAGCGC-G-ACAAAAAAAGTCATTTTGAACAAAACTATGCCGTTTTGCTATGATA
1 TTTTTCATAAAAGCGCTGCA-AAAAAAATTCATTTTGAACAAAACTACGCCGTTTTGCTATGCTA
57405572 TGCTAAAA-GGGGCTATTTTTTTAAAGTAAAATTATTTTGTGGCGTTTTTTTATAAAAACGCCGC
65 TGCTAAAAGGGGGCTATTTTTTTAAAGTAAAATTATTTTGTGGCG-TTTTTTATAAAAACGCCGC
57405636 TATTGCTTACCTTTAGCGGCA
129 TATTGCTTACCTTTAGCGGCA
*
57405657 TTTTTCATAAAAGCGCTGCAAAAAAAATTCATTTTGAACAAAACTATGCCGTTTTGCTATGCTAT
1 TTTTTCATAAAAGCGCTGCAAAAAAAATTCATTTTGAACAAAACTACGCCGTTTTGCTATGCTAT
*
57405722 GCTAAAAGGGGGCT-TTTTTTTAAAGTAAAATTATTTTGTGGCGTTTTTTATATAAACGCCGCTA
66 GCTAAAAGGGGGCTATTTTTTTAAAGTAAAATTATTTTGTGGCGTTTTTTATAAAAACGCCGCTA
*
57405786 TTGCTTACCTTTAGCGGTA
131 TTGCTTACCTTTAGCGGCA
*
57405805 TTTTTCATAAAAGCGCTGCAAAAAAAATTCATTTTGAACAAAACTACACCGTTTTGCTATGCTAT
1 TTTTTCATAAAAGCGCTGCAAAAAAAATTCATTTTGAACAAAACTACGCCGTTTTGCTATGCTAT
57405870 GCTAAAAGGGGGCTATTTTTTTAAAGTAAAATTATTTTGTGGCGTTTTTTATAAAAACGCCGCTA
66 GCTAAAAGGGGGCTATTTTTTTAAAGTAAAATTATTTTGTGGCGTTTTTTATAAAAACGCCGCTA
*
57405935 TTGCTTACCTTTAGCGGCG
131 TTGCTTACCTTTAGCGGCA
*
57405954 TTTTTCATAAAAGCGCCGC-AAAAAAATTCATTTTGAACAAAACTACGCCGTTTTGCTAT
1 TTTTTCATAAAAGCGCTGCAAAAAAAATTCATTTTGAACAAAACTACGCCGTTTTGCTAT
57406013 TCTAAAAATT
Statistics
Matches: 341, Mismatches: 11, Indels: 8
0.95 0.03 0.02
Matches are distributed among these distances:
148 170 0.50
149 164 0.48
150 7 0.02
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (149 bp):
TTTTTCATAAAAGCGCTGCAAAAAAAATTCATTTTGAACAAAACTACGCCGTTTTGCTATGCTAT
GCTAAAAGGGGGCTATTTTTTTAAAGTAAAATTATTTTGTGGCGTTTTTTATAAAAACGCCGCTA
TTGCTTACCTTTAGCGGCA
Found at i:57406487 original size:14 final size:13
Alignment explanation
Indices: 57406468--57406516 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 13
57406458 AACCTTAATT
57406468 CCCTAACTCTTAAC
1 CCCTAACTC-TAAC
57406482 CCCTAACATCTAAC
1 CCCTAAC-TCTAAC
*
57406496 CCATAAACTCCTAAC
1 CCCT-AACT-CTAAC
57406511 CCCTAA
1 CCCTAA
57406517 ACCTTAAATC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
14 17 0.57
15 13 0.43
ACGTcount: A:0.35, C:0.43, G:0.00, T:0.22
Consensus pattern (13 bp):
CCCTAACTCTAAC
Found at i:57406802 original size:15 final size:15
Alignment explanation
Indices: 57406782--57406836 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
57406772 CCTAGCACGT
57406782 CTAACCCCTAAACCC
1 CTAACCCCTAAACCC
57406797 CTAACCCTCT-AACCC
1 CTAACCC-CTAAACCC
* * *
57406812 CTAAACCTTAAATCC
1 CTAACCCCTAAACCC
57406827 C-AACCCCTAA
1 CTAACCCCTAA
57406837 TCCATAATCC
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
14 8 0.24
15 23 0.70
16 2 0.06
ACGTcount: A:0.35, C:0.47, G:0.00, T:0.18
Consensus pattern (15 bp):
CTAACCCCTAAACCC
Found at i:57406818 original size:8 final size:7
Alignment explanation
Indices: 57406782--57406815 Score: 50
Period size: 8 Copynumber: 4.6 Consensus size: 7
57406772 CCTAGCACGT
57406782 CTAACCC
1 CTAACCC
57406789 CTAAACCC
1 CT-AACCC
57406797 CTAACCC
1 CTAACCC
57406804 TCTAACCC
1 -CTAACCC
57406812 CTAA
1 CTAA
57406816 ACCTTAAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
7 11 0.44
8 14 0.56
ACGTcount: A:0.32, C:0.50, G:0.00, T:0.18
Consensus pattern (7 bp):
CTAACCC
Found at i:57406850 original size:14 final size:14
Alignment explanation
Indices: 57406831--57406859 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
57406821 AAATCCCAAC
57406831 CCCTAATCCATAAT
1 CCCTAATCCATAAT
57406845 CCCTAATCCATAAT
1 CCCTAATCCATAAT
57406859 C
1 C
57406860 TATAAACCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.38, G:0.00, T:0.28
Consensus pattern (14 bp):
CCCTAATCCATAAT
Found at i:57407295 original size:73 final size:74
Alignment explanation
Indices: 57407125--57407299 Score: 271
Period size: 73 Copynumber: 2.4 Consensus size: 74
57407115 CTAAGCATTA
* *
57407125 GCGGCGCTTCCTTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGGGCGTTGTTTTGGCTT
1 GCGGCGCTTCCTTAAAAACGCCGCTAAATCCCCCAAAGCTCACAAAACGGACGTTGTTTTGGCTT
*
57407190 AGGTTTTTT
66 AGGTTCTTT
* * *
57407199 GCGGCGCTTGCTCAAAAATGCCGCTAAATCCCCCAAAGCTCACAAAAC-GACGTTGTTTTGGCTT
1 GCGGCGCTTCCTTAAAAACGCCGCTAAATCCCCCAAAGCTCACAAAACGGACGTTGTTTTGGCTT
57407263 AGGTTCTTT
66 AGGTTCTTT
* *
57407272 GCGGCGCTTTCTTGAAAACGCCGCTAAA
1 GCGGCGCTTCCTTAAAAACGCCGCTAAA
57407300 GCCCTGAGCA
Statistics
Matches: 91, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
73 47 0.52
74 44 0.48
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.27
Consensus pattern (74 bp):
GCGGCGCTTCCTTAAAAACGCCGCTAAATCCCCCAAAGCTCACAAAACGGACGTTGTTTTGGCTT
AGGTTCTTT
Found at i:57407312 original size:188 final size:185
Alignment explanation
Indices: 57407031--57407413 Score: 577
Period size: 188 Copynumber: 2.1 Consensus size: 185
57407021 TTATTTTTTT
* * *** *
57407031 CGCCGCTAAATCCCCGAAAGCTCACAAAATGACATCGTTTGGTTTTTTTTTTTGCGGCGCTTTCC
1 CGCCGCTAAATCCCCCAAAGCTCACAAAACGACATCGTTTGGTTAGGTTCTTTGCGGCGCTTTCC
*
57407096 TAAAAATGCCGCTAAAGACCTAAGCATTAGCGGCGCTTCCTTAAAAACGCCGCTAAATCCCCGAA
66 TAAAAACGCCGCTAAAGACCTAAGCATTAGCGGCGCTTCCTTAAAAACGCCGCTAAATCCCCGAA
* *
57407161 AGCTCACAAAACGGGCGTTGTTTTGGCTTAGGTTTTTTGCGGCGCTTGCTCAAAAA
131 AGCTCACAAAAC-GGCGTTGTTTTGGCTTAGGTTTTTTGCGACACTTGCTCAAAAA
* * *
57407217 TGCCGCTAAATCCCCCAAAGCTCACAAAACGACGTTGTTTTGGCTTAGGTTCTTTGCGGCGCTTT
1 CGCCGCTAAATCCCCCAAAGCTCACAAAACGACATCG-TTTGG-TTAGGTTCTTTGCGGCGCTTT
* * * * *
57407282 CTTGAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCG
64 CCTAAAAACGCCGCTAAAGACCTAAGCATTAGCGGCGCTTCCTTAAAAACGCCGCTAAATCCCCG
*
57407347 AAAGCTCACAAAACGGCGTTGTTTTGGCTTAGGTTTTTTGCGACACTTTCTCAAAAA
129 AAAGCTCACAAAACGGCGTTGTTTTGGCTTAGGTTTTTTGCGACACTTGCTCAAAAA
57407404 CGCCGCTAAA
1 CGCCGCTAAA
57407414 GCCCTGAGCA
Statistics
Matches: 176, Mismatches: 19, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
186 32 0.18
187 54 0.31
188 90 0.51
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.27
Consensus pattern (185 bp):
CGCCGCTAAATCCCCCAAAGCTCACAAAACGACATCGTTTGGTTAGGTTCTTTGCGGCGCTTTCC
TAAAAACGCCGCTAAAGACCTAAGCATTAGCGGCGCTTCCTTAAAAACGCCGCTAAATCCCCGAA
AGCTCACAAAACGGCGTTGTTTTGGCTTAGGTTTTTTGCGACACTTGCTCAAAAA
Found at i:57407404 original size:114 final size:114
Alignment explanation
Indices: 57407199--57407527 Score: 480
Period size: 114 Copynumber: 2.9 Consensus size: 114
57407189 TAGGTTTTTT
* * * *
57407199 GCGGCGCTTGCTCAAAAATGCCGCTAAATCCCCCAAAGCTCACAAAACGACGTTGTTTTGGCTTA
1 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGACGTTGTTTTGGCTTA
* **
57407264 GGTTCTTTGCGGCGCTTTCTTGAAAACGCCGCTAAAGCCCTGAGCATTA
66 GGTTTTTTGCGGCGCTTTCTAAAAAACGCCGCTAAAGCCCTGAGCATTA
*
57407313 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGGCGTTGTTTTGGCTTA
1 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGACGTTGTTTTGGCTTA
* * *
57407378 GGTTTTTTGCGACACTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTA
66 GGTTTTTTGCGGCGCTTTCTAAAAAACGCCGCTAAAGCCCTGAGCATTA
* * ** *
57407427 GCGGCGCTTTCCTT-AAAGCGCCACTAAATCCCCGAAAGCTCACAAAACGACGTCATTTTTGCTT
1 GCGGCGCTTT-CTTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGACGTTGTTTTGGCTT
* *
57407491 AGGTTTTTTGCGGCGCTTTTTAAAAAATGCCGCTAAA
65 AGGTTTTTTGCGGCGCTTTCTAAAAAACGCCGCTAAA
57407528 TCCCCCAAAG
Statistics
Matches: 193, Mismatches: 21, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
114 190 0.98
115 3 0.02
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.27
Consensus pattern (114 bp):
GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCACAAAACGACGTTGTTTTGGCTTA
GGTTTTTTGCGGCGCTTTCTAAAAAACGCCGCTAAAGCCCTGAGCATTA
Found at i:57407527 original size:73 final size:73
Alignment explanation
Indices: 57407430--57407600 Score: 229
Period size: 73 Copynumber: 2.3 Consensus size: 73
57407420 AGCATTAGCG
* * * *
57407430 GCGCTTTCCTT-AAAGCGCCACTAAATCCCCGAAAGCTCACAAAACGACGTCATTTTTGCTTAGG
1 GCGCTTT-CTTAAAAACGCCGCTAAATCCCCCAAAGCTCACAAAACGACGTCATTTTGGCTTAGG
* *
57407494 TTTTTTGCG
65 TTCTTTGCA
* * *
57407503 GCGCTTT-TTAAAAAATGCCGCTAAATCCCCCAAAGCTCACAAAACGATGTCGTTTTGGCTTAGG
1 GCGCTTTCTT-AAAAACGCCGCTAAATCCCCCAAAGCTCACAAAACGACGTCATTTTGGCTTAGG
57407567 TTCTTTGCA
65 TTCTTTGCA
57407576 GCGCTTTCTTAAAAACGCCGCTAAA
1 GCGCTTTCTTAAAAACGCCGCTAAA
57407601 GCTATTGTTC
Statistics
Matches: 85, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
71 2 0.02
73 81 0.95
74 2 0.02
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29
Consensus pattern (73 bp):
GCGCTTTCTTAAAAACGCCGCTAAATCCCCCAAAGCTCACAAAACGACGTCATTTTGGCTTAGGT
TCTTTGCA
Found at i:57407944 original size:18 final size:18
Alignment explanation
Indices: 57407921--57407956 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
57407911 CTTTCTATTT
57407921 TTCTAATAAAAGAAGTTG
1 TTCTAATAAAAGAAGTTG
57407939 TTCTAATAAAAGAAGTTG
1 TTCTAATAAAAGAAGTTG
57407957 AGGTGTAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.06, G:0.17, T:0.33
Consensus pattern (18 bp):
TTCTAATAAAAGAAGTTG
Found at i:57408030 original size:18 final size:18
Alignment explanation
Indices: 57408007--57408042 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
57407997 GTGAATGTGG
57408007 TTTTTTAATTATATTTTA
1 TTTTTTAATTATATTTTA
* *
57408025 TTTTTTTATTATCTTTTA
1 TTTTTTAATTATATTTTA
57408043 ATTGTGAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTTTAATTATATTTTA
Found at i:57412055 original size:22 final size:22
Alignment explanation
Indices: 57412030--57412121 Score: 141
Period size: 22 Copynumber: 4.2 Consensus size: 22
57412020 AAATTCAATA
57412030 TCAATTTCCTTCAAAAATTCTC
1 TCAATTTCCTTCAAAAATTCTC
57412052 TCAA-TTCCTTTCAAAAATTCTC
1 TCAATTTCC-TTCAAAAATTCTC
* *
57412074 TCAATTCCCTTCAAAACTTCTC
1 TCAATTTCCTTCAAAAATTCTC
*
57412096 TCAATTTCCTTCCAAAATTCTC
1 TCAATTTCCTTCAAAAATTCTC
57412118 TCAA
1 TCAA
57412122 ACTCTCAAAT
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
21 4 0.06
22 56 0.89
23 3 0.05
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.39
Consensus pattern (22 bp):
TCAATTTCCTTCAAAAATTCTC
Found at i:57412127 original size:30 final size:30
Alignment explanation
Indices: 57412093--57412151 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
57412083 TTCAAAACTT
* *
57412093 CTCTCAATTTCCTTCCAAAATTCTCTCAAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAAA
57412123 CTCTCAAATTCCTTCCAAAATCCTCTCAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAA
57412152 TTTCCTTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.36, G:0.00, T:0.34
Consensus pattern (30 bp):
CTCTCAAATTCCTTCCAAAATCCTCTCAAA
Found at i:57412127 original size:52 final size:51
Alignment explanation
Indices: 57412071--57412173 Score: 138
Period size: 52 Copynumber: 2.0 Consensus size: 51
57412061 TTCAAAAATT
* * *
57412071 CTCTC-AATTCCCTT-CAAAACTTCTCTCAATTTCCTTCCAAAATTCTCTCAAA
1 CTCTCAAATT-CCTTCCAAAA-TCCTCTCAATTTCCTTCAAAAAATCTC-CAAA
57412123 CTCTCAAATTCCTTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
57412174 TCCATATTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
51 4 0.09
52 33 0.72
53 9 0.20
ACGTcount: A:0.32, C:0.34, G:0.00, T:0.34
Consensus pattern (51 bp):
CTCTCAAATTCCTTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
Found at i:57412162 original size:21 final size:22
Alignment explanation
Indices: 57412123--57412164 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
57412113 TTCTCTCAAA
57412123 CTCTCAAATTCCTTCCAAAATC
1 CTCTCAAATTCCTTCCAAAATC
* *
57412145 CTCTCAATTTCCTTCAAAAA
1 CTCTCAAATTCCTTCCAAAA
57412165 ATCTCCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (22 bp):
CTCTCAAATTCCTTCCAAAATC
Found at i:57412257 original size:28 final size:30
Alignment explanation
Indices: 57412207--57412263 Score: 91
Period size: 28 Copynumber: 2.0 Consensus size: 30
57412197 TTAAATTTCA
57412207 TTTTTTTAAGAAAATTTTAAAATTTTTTAT
1 TTTTTTTAAGAAAATTTTAAAATTTTTTAT
*
57412237 TTTTTTTAA-ATAATTTT-AAATTTTTTA
1 TTTTTTTAAGAAAATTTTAAAATTTTTTA
57412264 ATATTTTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 10 0.38
29 7 0.27
30 9 0.35
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (30 bp):
TTTTTTTAAGAAAATTTTAAAATTTTTTAT
Found at i:57412270 original size:28 final size:30
Alignment explanation
Indices: 57412209--57412270 Score: 83
Period size: 28 Copynumber: 2.1 Consensus size: 30
57412199 AAATTTCATT
* *
57412209 TTTTTAAGAAAATTTTAAAATTTTTTATTT
1 TTTTTAAGAAAATTTTAAAATTTTTTAATA
*
57412239 TTTTTAA-ATAATTTT-AAATTTTTTAATA
1 TTTTTAAGAAAATTTTAAAATTTTTTAATA
57412267 TTTT
1 TTTT
57412271 CAACAATGGC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 15 0.52
29 7 0.24
30 7 0.24
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (30 bp):
TTTTTAAGAAAATTTTAAAATTTTTTAATA
Found at i:57412270 original size:29 final size:30
Alignment explanation
Indices: 57412208--57412270 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 30
57412198 TAAATTTCAT
*
57412208 TTTTTTAAGAAAATTTTAAAATTTTTTATT
1 TTTTTTAAGAAAATTTTAAAATTTTTTATA
*
57412238 TTTTTTAA-ATAATTTT-AAATTTTTTAATA
1 TTTTTTAAGAAAATTTTAAAATTTTTT-ATA
57412267 TTTT
1 TTTT
57412271 CAACAATGGC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 9 0.30
29 13 0.43
30 8 0.27
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (30 bp):
TTTTTTAAGAAAATTTTAAAATTTTTTATA
Found at i:57414575 original size:29 final size:29
Alignment explanation
Indices: 57414540--57414604 Score: 88
Period size: 23 Copynumber: 2.4 Consensus size: 29
57414530 ATTATTTGAC
57414540 TAAAAACCCTAACCCTAACCTAATTTAAT
1 TAAAAACCCTAACCCTAACCTAATTTAAT
57414569 T--AAA----AACCCTAACCTAATTTAAT
1 TAAAAACCCTAACCCTAACCTAATTTAAT
57414592 TAAAAACCCTAAC
1 TAAAAACCCTAAC
57414605 NTTCTCGAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 12
0.71 0.00 0.29
Matches are distributed among these distances:
23 20 0.67
25 3 0.10
27 3 0.10
29 4 0.13
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (29 bp):
TAAAAACCCTAACCCTAACCTAATTTAAT
Found at i:57414576 original size:23 final size:23
Alignment explanation
Indices: 57414550--57414604 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
57414540 TAAAAACCCT
57414550 AACCCTAACCTAATTTAATTAAA
1 AACCCTAACCTAATTTAATTAAA
57414573 AACCCTAACCTAATTTAATTAAA
1 AACCCTAACCTAATTTAATTAAA
57414596 AACCCTAAC
1 AACCCTAAC
57414605 NTTCTCGAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.27
Consensus pattern (23 bp):
AACCCTAACCTAATTTAATTAAA
Found at i:57414752 original size:23 final size:24
Alignment explanation
Indices: 57414746--57415273 Score: 626
Period size: 23 Copynumber: 21.8 Consensus size: 24
57414736 TAAAAACCCT
57414746 AACCCTAACCTAA-TTTAATTAAA
1 AACCCTAACCTAACTTTAATTAAA
57414769 AACCCTAACCTAA-TTTAATTAAA
1 AACCCTAACCTAACTTTAATTAAA
57414792 AACCCTAACCTAAC-TTAATTAAA
1 AACCCTAACCTAACTTTAATTAAA
57414815 AACCCTAACCTAACTTAATTAAATTAAA
1 AACCCTAACCTAAC-T--TT-AATTAAA
*
57414843 AACCCTAACATAAC-TTAATTAAA
1 AACCCTAACCTAACTTTAATTAAA
57414866 AACCCTAACCCT-AC-TTAATTAAA
1 AACCCTAA-CCTAACTTTAATTAAA
57414889 AACCCTAACCCTAACCTAATTTAATTAAA
1 AACCCTAA-CCTAA-C---TTTAATTAAA
57414918 AACCCTAACCTAA-TTTAATTAAA
1 AACCCTAACCTAACTTTAATTAAA
57414941 AACCCTAACCTAAC-TTAATTAAAAAAAA
1 AACCCTAACCTAACTTTAATT-----AAA
*
57414969 AACCCTAACATAAC-TTAATTAAA
1 AACCCTAACCTAACTTTAATTAAA
57414992 AACCCTAACCCTAATCTAATTTAATTAAA
1 AACCCTAA-CCTAA-C---TTTAATTAAA
57415021 AACCCTAACCTAA-TTTAATTAAA
1 AACCCTAACCTAACTTTAATTAAA
57415044 AACCCTAACCTAAC-TTAATTAAA
1 AACCCTAACCTAACTTTAATTAAA
*
57415067 AACCCTAACATAAC-TTAATTAAA
1 AACCCTAACCTAACTTTAATTAAA
*
57415090 AACCCTAACATAAC-TTAATTAAA
1 AACCCTAACCTAACTTTAATTAAA
*
57415113 AAACCTAACCTAACTTAATTAAATTAAA
1 AACCCTAACCTAAC-T--TT-AATTAAA
*
57415141 AACCCTAACATAA-TTTAATTAAA
1 AACCCTAACCTAACTTTAATTAAA
57415164 AACCCTAACCCT-AC-TTAATTAAA
1 AACCCTAA-CCTAACTTTAATTAAA
57415187 AACCCTAACCTAA-TTTAATTAAA
1 AACCCTAACCTAACTTTAATTAAA
57415210 AACCCTAACCTAA-TTTAATTAAA
1 AACCCTAACCTAACTTTAATTAAA
57415233 AACCCTAACCTAAC-TTAATTAAA
1 AACCCTAACCTAACTTTAATTAAA
* *
57415256 AAACCTAACCTAATTTTA
1 AACCCTAACCTAACTTTA
57415274 CTAACCATTA
Statistics
Matches: 456, Mismatches: 12, Indels: 73
0.84 0.02 0.13
Matches are distributed among these distances:
22 3 0.01
23 326 0.71
24 16 0.04
25 2 0.00
26 1 0.00
27 4 0.01
28 70 0.15
29 34 0.07
ACGTcount: A:0.49, C:0.23, G:0.00, T:0.28
Consensus pattern (24 bp):
AACCCTAACCTAACTTTAATTAAA
Found at i:57415325 original size:55 final size:55
Alignment explanation
Indices: 57415266--57415483 Score: 391
Period size: 55 Copynumber: 4.0 Consensus size: 55
57415256 AAACCTAACC
*
57415266 TAATTTTACTAACCATTAACACAATTGTTGGACTTAATAATTTAACATAATTTGA
1 TAATTTTACTAACCATTAACAAAATTGTTGGACTTAATAATTTAACATAATTTGA
*
57415321 TAATTTTACTAACCATTAACACAATTGTTGGACTTAATAATTTAACATAATTTGA
1 TAATTTTACTAACCATTAACAAAATTGTTGGACTTAATAATTTAACATAATTTGA
*
57415376 TAATTTTACTAACCATTAACAAAATTTTTGGACTTAATAATTTAACATAATTTGA
1 TAATTTTACTAACCATTAACAAAATTGTTGGACTTAATAATTTAACATAATTTGA
* *
57415431 TAATTTTACTAACCATTAACAAAATTTTTGGACTTAATAATTTTACATAATTT
1 TAATTTTACTAACCATTAACAAAATTGTTGGACTTAATAATTTAACATAATTT
57415484 TACATAATGT
Statistics
Matches: 160, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 160 1.00
ACGTcount: A:0.40, C:0.12, G:0.06, T:0.42
Consensus pattern (55 bp):
TAATTTTACTAACCATTAACAAAATTGTTGGACTTAATAATTTAACATAATTTGA
Found at i:57415428 original size:26 final size:26
Alignment explanation
Indices: 57415391--57415484 Score: 73
Period size: 26 Copynumber: 3.5 Consensus size: 26
57415381 TTACTAACCA
57415391 TTAACAAAATTTTTGGACTTAATAAT
1 TTAACAAAATTTTTGGACTTAATAAT
* * * * * *
57415417 TTAACATAATTTGAT-AATTTTACTAACCA
1 TTAACAAAATTT-TTGGA-CTTAATAA--T
57415446 TTAACAAAATTTTTGGACTTAATAAT
1 TTAACAAAATTTTTGGACTTAATAAT
* *
57415472 TTTACATAATTTT
1 TTAACAAAATTTT
57415485 ACATAATGTT
Statistics
Matches: 49, Mismatches: 14, Indels: 10
0.67 0.19 0.14
Matches are distributed among these distances:
26 23 0.47
27 7 0.14
28 7 0.14
29 12 0.24
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.45
Consensus pattern (26 bp):
TTAACAAAATTTTTGGACTTAATAAT
Found at i:57415482 original size:10 final size:10
Alignment explanation
Indices: 57415467--57415491 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
57415457 TTTGGACTTA
57415467 ATAATTTTAC
1 ATAATTTTAC
57415477 ATAATTTTAC
1 ATAATTTTAC
57415487 ATAAT
1 ATAAT
57415492 GTTAGATTTG
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:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (10 bp):
ATAATTTTAC
Found at i:57418854 original size:124 final size:123
Alignment explanation
Indices: 57418635--57418877 Score: 308
Period size: 124 Copynumber: 2.0 Consensus size: 123
57418625 CACGAGGGCG
* *** * *
57418635 CGATTTGACACTATTTGCTCAGAAACGTCAAAATTTTTTTTTCCTACATGACGAACTGTAGTGAA
1 CGATTTGACACTATTTACTCAGAAACGTCAAAAAAATTATTTCCTACATGACGAACTGTAGCGAA
* * *
57418700 ATCGCGTCCACGAGGGCGCGATTTCACAATTTCCTCTCATATAGCATCCTGGTATCAA
66 ATCGCGTCCACGAGGCCACGATTTCACAATTTCCTCTCAAATAGCATCCTGGTATCAA
* * * *
57418758 CGATTTTATACTATTTACTCAGAAAACGTCAAAAAAAATTATTTCTTACATGAC-CACTGTAGCG
1 CGATTTGACACTATTTACTCAG-AAACGTC-AAAAAAATTATTTCCTACATGACGAACTGTAGCG
* * * *
57418822 AAATCTCGTCCACGAGGCCACTATTTCACAATTTCTTCTTAAATAGCATCCTGGTA
64 AAATCGCGTCCACGAGGCCACGATTTCACAATTTCCTCTCAAATAGCATCCTGGTA
57418878 GAAGAGATTT
Statistics
Matches: 101, Mismatches: 17, Indels: 3
0.83 0.14 0.02
Matches are distributed among these distances:
123 19 0.19
124 64 0.63
125 18 0.18
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.32
Consensus pattern (123 bp):
CGATTTGACACTATTTACTCAGAAACGTCAAAAAAATTATTTCCTACATGACGAACTGTAGCGAA
ATCGCGTCCACGAGGCCACGATTTCACAATTTCCTCTCAAATAGCATCCTGGTATCAA
Found at i:57418895 original size:124 final size:123
Alignment explanation
Indices: 57418636--57418912 Score: 299
Period size: 124 Copynumber: 2.2 Consensus size: 123
57418626 ACGAGGGCGC
* * *** * *
57418636 GATTTGACACTATTTGCTCAGAAACGTCAAAATTTTTTTTTCCTACATGACGAACTGTAGTGAAA
1 GATTTCACACTATTTACTCAGAAACGTCAAAAAAATTATTTCCTACATGACGAACTGTAGCGAAA
* * * *
57418701 TCGCGTCCACGAGGGCGCGATTTCACAATTTCCTCTCATATAGCATCCTGGTATCAAC
66 TCGCGTCCACGAGGCCACGATTTCACAATTTCCTCTCAAATAGCATCCTGGTATCAAA
* * * *
57418759 GATTTTATACTATTTACTCAGAAAACGTCAAAAAAAATTATTTCTTACATGAC-CACTGTAGCGA
1 GATTTCACACTATTTACTCAG-AAACGTC-AAAAAAATTATTTCCTACATGACGAACTGTAGCGA
* * * * *
57418823 AATCTCGTCCACGAGGCCACTATTTCACAATTTCTTCTTAAATAGCATCCTGGTA-GAAGA
64 AATCGCGTCCACGAGGCCACGATTTCACAATTTCCTCTCAAATAGCATCCTGGTATCAA-A
* *
57418883 GATTTCCCACTATTTAAC-CAGATACGTCAA
1 GATTTCACACTATTT-ACTCAGAAACGTCAA
57418913 CTCGAAAAAA
Statistics
Matches: 127, Mismatches: 23, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
122 2 0.02
123 26 0.20
124 79 0.62
125 20 0.16
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.31
Consensus pattern (123 bp):
GATTTCACACTATTTACTCAGAAACGTCAAAAAAATTATTTCCTACATGACGAACTGTAGCGAAA
TCGCGTCCACGAGGCCACGATTTCACAATTTCCTCTCAAATAGCATCCTGGTATCAAA
Found at i:57420377 original size:17 final size:17
Alignment explanation
Indices: 57420355--57420387 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
57420345 TTACAAAATC
57420355 AAATCTTATAAGATTAT
1 AAATCTTATAAGATTAT
*
57420372 AAATCTTCTAAGATTA
1 AAATCTTATAAGATTA
57420388 GTTTCTATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.39
Consensus pattern (17 bp):
AAATCTTATAAGATTAT
Found at i:57427917 original size:16 final size:16
Alignment explanation
Indices: 57427896--57427947 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
57427886 TTTGGTTCGC
57427896 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
57427912 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* *
57427928 TGTAATGGAATAGAGG
1 TGTATTGGATTAGAGG
57427944 TGTA
1 TGTA
57427948 ATAGCAAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.29, C:0.00, G:0.37, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:57427994 original size:45 final size:44
Alignment explanation
Indices: 57427928--57428022 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
57427918 GGATTAGAGG
*
57427928 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAG-AAATCAACTGTTTGGTTGAA
* ***
57427973 TGTAATGGAATAGAGGCGTAATAGTAATCCTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
57428017 TGTAAT
1 TGTAAT
57428023 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 22 0.49
45 23 0.51
ACGTcount: A:0.33, C:0.06, G:0.27, T:0.34
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
Found at i:57428203 original size:18 final size:17
Alignment explanation
Indices: 57428182--57428216 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
57428172 TTATTATTAA
*
57428182 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
57428200 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
57428217 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:57432861 original size:22 final size:23
Alignment explanation
Indices: 57432835--57432879 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
57432825 TATTATTCTA
*
57432835 AATTTAATATATTTA-AAAAATT
1 AATTTAACATATTTATAAAAATT
* *
57432857 AATTTCACATTTTTATAAAAATT
1 AATTTAACATATTTATAAAAATT
57432880 TAAAAACCCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (23 bp):
AATTTAACATATTTATAAAAATT
Found at i:57433866 original size:24 final size:24
Alignment explanation
Indices: 57433839--57433901 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 24
57433829 GGTATACCAT
57433839 TTAAAATTATTTATAAATATT-AAA
1 TTAAAATTATTTATAAA-ATTAAAA
* *
57433863 TTAATAATAATTAATAAAATTAAAA
1 TTAA-AATTATTTATAAAATTAAAA
57433888 TATAAAA-TATTTAT
1 T-TAAAATTATTTAT
57433902 CAATTACATA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
24 12 0.38
25 17 0.53
26 3 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
TTAAAATTATTTATAAAATTAAAA
Found at i:57433961 original size:48 final size:48
Alignment explanation
Indices: 57433872--57433963 Score: 116
Period size: 48 Copynumber: 1.9 Consensus size: 48
57433862 ATTAATAATA
* * *
57433872 ATTAATAAAATTAAAATATAAAATATTTATCAATTACATAAATTACTC
1 ATTAATAAAATTAAAACATAAAATATCTATCAATTAAATAAATTACTC
*
57433920 ATTAATAAACATTAACACATAAAA-ATCTATC-ATTCAAATAAATT
1 ATTAATAAA-ATTAAAACATAAAATATCTATCAATT-AAATAAATT
57433964 CAAAATTAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
47 3 0.08
48 23 0.61
49 12 0.32
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.35
Consensus pattern (48 bp):
ATTAATAAAATTAAAACATAAAATATCTATCAATTAAATAAATTACTC
Found at i:57434121 original size:17 final size:17
Alignment explanation
Indices: 57434095--57434128 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
57434085 GAACGTGGTT
*
57434095 TTTTTGATTATATTTTA
1 TTTTTAATTATATTTTA
57434112 TTTTTAATTATATTTTA
1 TTTTTAATTATATTTTA
57434129 ATTGTGAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (17 bp):
TTTTTAATTATATTTTA
Found at i:57437600 original size:16 final size:16
Alignment explanation
Indices: 57437579--57437610 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
57437569 ATATTTTTAG
57437579 TATTTACCTTATAGTA
1 TATTTACCTTATAGTA
57437595 TATTTACCTTATAGTA
1 TATTTACCTTATAGTA
57437611 CAATATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.50
Consensus pattern (16 bp):
TATTTACCTTATAGTA
Found at i:57438887 original size:17 final size:17
Alignment explanation
Indices: 57438865--57438898 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
57438855 ATTACAAAAT
57438865 CAAATCTTATAAGATTA
1 CAAATCTTATAAGATTA
*
57438882 CAAATCTTCTAAGATTA
1 CAAATCTTATAAGATTA
57438899 GTTTTTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.15, G:0.06, T:0.35
Consensus pattern (17 bp):
CAAATCTTATAAGATTA
Found at i:57442163 original size:24 final size:24
Alignment explanation
Indices: 57442136--57442181 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
57442126 AAAAAGAAAC
*
57442136 AATTACCTTCACAATAATATAAAA
1 AATTACCTTCACAACAATATAAAA
57442160 AATTACCTTCACAACAATATAA
1 AATTACCTTCACAACAATATAA
57442182 TTTATTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.52, C:0.20, G:0.00, T:0.28
Consensus pattern (24 bp):
AATTACCTTCACAACAATATAAAA
Found at i:57446648 original size:17 final size:17
Alignment explanation
Indices: 57446626--57446659 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
57446616 ATAATTATTT
57446626 GCCTACTTTTGGTAATA
1 GCCTACTTTTGGTAATA
57446643 GCCTACTTTTGGTAATA
1 GCCTACTTTTGGTAATA
57446660 TTGAAGTAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.41
Consensus pattern (17 bp):
GCCTACTTTTGGTAATA
Found at i:57455430 original size:25 final size:25
Alignment explanation
Indices: 57455394--57455495 Score: 109
Period size: 25 Copynumber: 4.1 Consensus size: 25
57455384 GGACACACCA
* *
57455394 CAGCTCGA-ATGACCTTCCCATTGTT
1 CAGCTC-ACATGAGCTTCCCATTATT
*
57455419 CAGCTCACATGAGCTTCCCGA-TACT
1 CAGCTCACATGAGCTTCCC-ATTATT
**
57455444 CAGCTTGCATGAGCTTCCCATTATT
1 CAGCTCACATGAGCTTCCCATTATT
**
57455469 CAGCTCACATGAGCTTCCTGTTATT
1 CAGCTCACATGAGCTTCCCATTATT
57455494 CA
1 CA
57455496 ACTCGGAAGG
Statistics
Matches: 64, Mismatches: 10, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
24 2 0.03
25 61 0.95
26 1 0.02
ACGTcount: A:0.22, C:0.31, G:0.16, T:0.31
Consensus pattern (25 bp):
CAGCTCACATGAGCTTCCCATTATT
Found at i:57456637 original size:17 final size:17
Alignment explanation
Indices: 57456615--57456648 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
57456605 CTGGGATACG
57456615 GTCGTGTGTCCCTATTT
1 GTCGTGTGTCCCTATTT
57456632 GTCGTGTGTCCCTATTT
1 GTCGTGTGTCCCTATTT
57456649 TGAATGCCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.06, C:0.24, G:0.24, T:0.47
Consensus pattern (17 bp):
GTCGTGTGTCCCTATTT
Done.