Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 113 of 279
Found at i:35743879 original size:54 final size:54
Alignment explanation
Indices: 35743820--35743930 Score: 143
Period size: 54 Copynumber: 2.1 Consensus size: 54
35743810 AGCATGGCTG
*
35743820 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* * * * * *
35743874 CCAGAACAGATATATGTGGCAGGGCCACCAGATCCGATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
35743928 CCA
1 CCA
35743931 AAACGCTTCC
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
54 32 0.65
55 17 0.35
ACGTcount: A:0.34, C:0.24, G:0.24, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:35745588 original size:26 final size:26
Alignment explanation
Indices: 35745552--35745661 Score: 170
Period size: 26 Copynumber: 4.2 Consensus size: 26
35745542 CATGAAATTC
35745552 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
35745578 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
*
35745604 TTATCAT-AGAACATTTACCTAACCTA
1 TTATCATGA-AACATTTACCTAACCCA
*
35745630 TTATCATTG-AACATTTACCTAACCTA
1 TTATCA-TGAAACATTTACCTAACCCA
35745656 TTATCA
1 TTATCA
35745662 ATTTGTACCA
Statistics
Matches: 80, Mismatches: 1, Indels: 6
0.92 0.01 0.07
Matches are distributed among these distances:
25 1 0.01
26 78 0.98
27 1 0.01
ACGTcount: A:0.37, C:0.25, G:0.04, T:0.35
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:35747120 original size:43 final size:42
Alignment explanation
Indices: 35747063--35747171 Score: 130
Period size: 42 Copynumber: 2.6 Consensus size: 42
35747053 AATGCCAACG
* * *
35747063 TCCCAGACATGGTCTTACATGTAATGAAATATCGATGCC-ACTG
1 TCCCAGACAGGGTCTTACATGTAATCAAATA-CGATGCCGA-TA
** *
35747106 TCCCAGTTAGGGTCTTACATGAAATCAAATACGATGCCGATA
1 TCCCAGACAGGGTCTTACATGTAATCAAATACGATGCCGATA
*
35747148 TCCCAGACATGGTCTTACATGTAA
1 TCCCAGACAGGGTCTTACATGTAA
35747172 ATCTCAAATC
Statistics
Matches: 55, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
42 28 0.51
43 27 0.49
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (42 bp):
TCCCAGACAGGGTCTTACATGTAATCAAATACGATGCCGATA
Found at i:35756765 original size:30 final size:30
Alignment explanation
Indices: 35756731--35756791 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
35756721 TTCCCGAGCC
*
35756731 TAGGGGTAAAAGTGTAAATATGCAAAAGTT
1 TAGGGGAAAAAGTGTAAATATGCAAAAGTT
* * * *
35756761 TAGGGGAAAAATTGTAATTTTGCCAAAGTT
1 TAGGGGAAAAAGTGTAAATATGCAAAAGTT
35756791 T
1 T
35756792 TGAGTTAAGG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.39, C:0.05, G:0.25, T:0.31
Consensus pattern (30 bp):
TAGGGGAAAAAGTGTAAATATGCAAAAGTT
Found at i:35759480 original size:21 final size:21
Alignment explanation
Indices: 35759454--35759498 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
35759444 AATTGACTCG
35759454 ATTTATTCGATATGGAATTAA
1 ATTTATTCGATATGGAATTAA
35759475 ATTTATTCGATATGGAATTAA
1 ATTTATTCGATATGGAATTAA
35759496 ATT
1 ATT
35759499 AGGTGGTCGT
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:0.38, C:0.04, G:0.13, T:0.44
Consensus pattern (21 bp):
ATTTATTCGATATGGAATTAA
Found at i:35760136 original size:31 final size:30
Alignment explanation
Indices: 35760098--35760169 Score: 117
Period size: 31 Copynumber: 2.4 Consensus size: 30
35760088 TGTTTTAATA
*
35760098 AATTTAATATTTATCTAGATAGTATTTTATT
1 AATTTAATATTTATCTAGATAATATTTT-TT
*
35760129 AATTTAATATTTATTTAGATAATATTTTTT
1 AATTTAATATTTATCTAGATAATATTTTTT
35760159 AATTTAATATT
1 AATTTAATATT
35760170 AATGTGATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
30 13 0.33
31 26 0.67
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.57
Consensus pattern (30 bp):
AATTTAATATTTATCTAGATAATATTTTTT
Found at i:35760141 original size:15 final size:15
Alignment explanation
Indices: 35760123--35760169 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
35760113 TAGATAGTAT
35760123 TTTATTAATTTAATA
1 TTTATTAATTTAATA
* **
35760138 TTTATTTAGATAATA
1 TTTATTAATTTAATA
*
35760153 TTTTTTAATTTAATA
1 TTTATTAATTTAATA
35760168 TT
1 TT
35760170 AATGTGATTA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (15 bp):
TTTATTAATTTAATA
Found at i:35760166 original size:35 final size:34
Alignment explanation
Indices: 35760079--35760172 Score: 113
Period size: 31 Copynumber: 2.8 Consensus size: 34
35760069 ACTTTTCTAA
*
35760079 AGATAATATTGTTTTAATAAATTTAATATTTATCT
1 AGATAATATT-TTTTAATTAATTTAATATTTATCT
* *
35760114 AGATAGTA--TTTT-ATTAATTTAATATTTATTT
1 AGATAATATTTTTTAATTAATTTAATATTTATCT
35760145 AGATAATATTTTTTAATTTAATATTAAT
1 AGATAATATTTTTTAA-TTAAT-TTAAT
35760173 GTGATTAATT
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
31 24 0.48
32 4 0.08
33 4 0.08
34 1 0.02
35 12 0.24
36 5 0.10
ACGTcount: A:0.39, C:0.01, G:0.05, T:0.54
Consensus pattern (34 bp):
AGATAATATTTTTTAATTAATTTAATATTTATCT
Found at i:35769135 original size:2 final size:2
Alignment explanation
Indices: 35769128--35769160 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
35769118 GGGAATACTA
35769128 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
35769161 AGCAGTAGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:35769898 original size:26 final size:26
Alignment explanation
Indices: 35769869--35769918 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
35769859 TTAACATCAG
* *
35769869 AAACTCGAATCTTAAATCCTAAACTT
1 AAACTCGAAACTCAAATCCTAAACTT
**
35769895 AAACTTTAAACTCAAATCCTAAAC
1 AAACTCGAAACTCAAATCCTAAAC
35769919 ACCAAGAGAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.46, C:0.24, G:0.02, T:0.28
Consensus pattern (26 bp):
AAACTCGAAACTCAAATCCTAAACTT
Found at i:35770072 original size:22 final size:24
Alignment explanation
Indices: 35770033--35770086 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 24
35770023 ACAAAATTAC
*
35770033 AAAAATTATATATTAATAAT-ATAA
1 AAAAATTATATATAAAT-ATCATAA
*
35770057 AAAAATTAT-TA-AAATATCATTA
1 AAAAATTATATATAAATATCATAA
35770079 AAAAATTA
1 AAAAATTA
35770087 AAAAATTCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 2 0.07
22 14 0.52
23 2 0.07
24 9 0.33
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (24 bp):
AAAAATTATATATAAATATCATAA
Found at i:35777899 original size:22 final size:22
Alignment explanation
Indices: 35777874--35777918 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
35777864 TATATTAAGT
35777874 ATACCTTAGTTTCAGTTAGTTA
1 ATACCTTAGTTTCAGTTAGTTA
35777896 ATACCTTAGTTTCAGTTAGTTA
1 ATACCTTAGTTTCAGTTAGTTA
35777918 A
1 A
35777919 GTTTCTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.44
Consensus pattern (22 bp):
ATACCTTAGTTTCAGTTAGTTA
Found at i:35778156 original size:54 final size:54
Alignment explanation
Indices: 35778070--35778320 Score: 220
Period size: 54 Copynumber: 4.6 Consensus size: 54
35778060 TGGATTCACG
** ** * * * **
35778070 GATTTACGATCGCAACCTCCCA-TATACAAGATTTTCAAAATTTTATGGTTCATT
1 GATTTACGATCGCAACCTCTTACT-TATGAGATTTTCAAAATATCATGATTTGTT
** * *
35778124 GATTTACGATCGTGACCTCTTACTTATGAGATTTTCAGAATATCATGATTTGTC
1 GATTTACGATCGCAACCTCTTACTTATGAGATTTTCAAAATATCATGATTTGTT
* * * *
35778178 GATTTACGATGGCAAACT-TCTACTTATGAGATTTTCAGAATCTCACT-ATTTGTT
1 GATTTACGATCGCAACCTCT-TACTTATGAGATTTTCAAAATATCA-TGATTTGTT
* * * ** *
35778232 GATTTATGATCGCAACCTCTTACTTATGAGATTTTTAAAATCTCGCGATTTGTC
1 GATTTACGATCGCAACCTCTTACTTATGAGATTTTCAAAATATCATGATTTGTT
* * *
35778286 GATTTACGATTGCAACCTCCTACTTATAAGATTTT
1 GATTTACGATCGCAACCTCTTACTTATGAGATTTT
35778321 TAGAATCTTA
Statistics
Matches: 161, Mismatches: 31, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
53 1 0.01
54 157 0.98
55 3 0.02
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (54 bp):
GATTTACGATCGCAACCTCTTACTTATGAGATTTTCAAAATATCATGATTTGTT
Found at i:35778259 original size:108 final size:108
Alignment explanation
Indices: 35778121--35778380 Score: 306
Period size: 108 Copynumber: 2.4 Consensus size: 108
35778111 TTTATGGTTC
** * *
35778121 ATTGATTTACGATCGTGACCTCTTACTTATGAGATTTTCAGAATATCATGATTTGTCGATTTACG
1 ATTGATTTACGATCGCAACCTCTTACTTATGAGATTTTCAAAATATCACGATTTGTCGATTTACG
* *
35778186 ATGGCAAACTTCTACTTATGAGATTTTCAGAATCTCACTA-TTT
66 ATGGCAAACTCCTACTTATAAGATTTTCAGAATCTCAC-AGTTT
* * * * *
35778229 GTTGATTTATGATCGCAACCTCTTACTTATGAGATTTTTAAAATCTCGCGATTTGTCGATTTACG
1 ATTGATTTACGATCGCAACCTCTTACTTATGAGATTTTCAAAATATCACGATTTGTCGATTTACG
* * * *
35778294 ATTGCAACCTCCTACTTATAAGATTTTTAGAATCTTACAGTTT
66 ATGGCAAACTCCTACTTATAAGATTTTCAGAATCTCACAGTTT
** * * * **
35778337 ATCAATTTAGGATCGCAACCTCTCATTTACAAGATTTTCAAAAT
1 ATTGATTTACGATCGCAACCTCTTACTTATGAGATTTTCAAAAT
35778381 CTTGTGGTTT
Statistics
Matches: 127, Mismatches: 24, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
107 1 0.01
108 126 0.99
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (108 bp):
ATTGATTTACGATCGCAACCTCTTACTTATGAGATTTTCAAAATATCACGATTTGTCGATTTACG
ATGGCAAACTCCTACTTATAAGATTTTCAGAATCTCACAGTTT
Found at i:35778321 original size:54 final size:54
Alignment explanation
Indices: 35778124--35778358 Score: 256
Period size: 54 Copynumber: 4.4 Consensus size: 54
35778114 ATGGTTCATT
** * * *
35778124 GATTTACGATCGTGACCTCTTACTTATGAGATTTTCAGAATATCATGATTTGTC
1 GATTTACGATCGCAACCTCCTACTTATGAGATTTTCAGAATCTCACGATTTGTC
* * * * *
35778178 GATTTACGATGGCAAACTTCTACTTATGAGATTTTCAGAATCTCACTATTTGTT
1 GATTTACGATCGCAACCTCCTACTTATGAGATTTTCAGAATCTCACGATTTGTC
* * * * *
35778232 GATTTATGATCGCAACCTCTTACTTATGAGATTTTTAAAATCTCGCGATTTGTC
1 GATTTACGATCGCAACCTCCTACTTATGAGATTTTCAGAATCTCACGATTTGTC
* * * * *
35778286 GATTTACGATTGCAACCTCCTACTTATAAGATTTTTAGAATCTTAC-AGTTTATC
1 GATTTACGATCGCAACCTCCTACTTATGAGATTTTCAGAATCTCACGA-TTTGTC
* *
35778340 AATTTAGGATCGCAACCTC
1 GATTTACGATCGCAACCTC
35778359 TCATTTACAA
Statistics
Matches: 149, Mismatches: 31, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
53 1 0.01
54 148 0.99
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.40
Consensus pattern (54 bp):
GATTTACGATCGCAACCTCCTACTTATGAGATTTTCAGAATCTCACGATTTGTC
Found at i:35778371 original size:54 final size:54
Alignment explanation
Indices: 35778071--35778383 Score: 175
Period size: 54 Copynumber: 5.8 Consensus size: 54
35778061 GGATTCACGG
* * * * * * * **
35778071 ATTTACGATCGCAACCTCCCA-TATACAAGATTTTCAAAATTTTATGGTTCATTG
1 ATTTACGATCGCAACCTCTCACT-TATAAGATTTTTAAAATCTTACGATTTATCA
** * * * * * * * * *
35778125 ATTTACGATCGTGACCTCTTACTTATGAGATTTTCAGAATATCATGATTTGTCG
1 ATTTACGATCGCAACCTCTCACTTATAAGATTTTTAAAATCTTACGATTTATCA
* * * * * * * * **
35778179 ATTTACGATGGCAAACT-TCTACTTATGAGATTTTCAGAATCTCACTATTTGTTG
1 ATTTACGATCGCAACCTCTC-ACTTATAAGATTTTTAAAATCTTACGATTTATCA
* * * ** * *
35778233 ATTTATGATCGCAACCTCTTACTTATGAGATTTTTAAAATCTCGCGATTTGTCG
1 ATTTACGATCGCAACCTCTCACTTATAAGATTTTTAAAATCTTACGATTTATCA
* *
35778287 ATTTACGATTGCAACCTC-CTACTTATAAGATTTTTAGAATCTTAC-AGTTTATCA
1 ATTTACGATCGCAACCTCTC-ACTTATAAGATTTTTAAAATCTTACGA-TTTATCA
* * * *
35778341 ATTTAGGATCGCAACCTCTCATTTACAAGATTTTCAAAATCTT
1 ATTTACGATCGCAACCTCTCACTTATAAGATTTTTAAAATCTT
35778384 GTGGTTTATC
Statistics
Matches: 207, Mismatches: 46, Indels: 12
0.78 0.17 0.05
Matches are distributed among these distances:
53 2 0.01
54 202 0.98
55 3 0.01
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.40
Consensus pattern (54 bp):
ATTTACGATCGCAACCTCTCACTTATAAGATTTTTAAAATCTTACGATTTATCA
Found at i:35778391 original size:54 final size:54
Alignment explanation
Indices: 35778233--35778437 Score: 164
Period size: 54 Copynumber: 3.8 Consensus size: 54
35778223 CTATTTGTTG
* * * * * * *
35778233 ATTTATGATCGCAACCTCTTACTTATGAGATTTTTAAAATCTCGCGATTTGTCG
1 ATTTACGATCGCAACCTCTCACTTATAAGATTTTTAAAATCTTGCGGTTTATCA
* * * *
35778287 ATTTACGATTGCAACCTC-CTACTTATAAGATTTTTAGAATCTTACAGTTTATCA
1 ATTTACGATCGCAACCTCTC-ACTTATAAGATTTTTAAAATCTTGCGGTTTATCA
* * * * * *
35778341 ATTTAGGATCGCAACCTCTCATTTACAAGATTTTCAAAATCTTGTGGTTTATCG
1 ATTTACGATCGCAACCTCTCACTTATAAGATTTTTAAAATCTTGCGGTTTATCA
* * * * * *
35778395 ATATGCAATCGCAACCTAC-CGCTTACAAGA-TTTTAGAATCTTG
1 ATTTACGATCGCAACCT-CTCACTTATAAGATTTTTAAAATCTTG
35778438 TTGATGCCAA
Statistics
Matches: 119, Mismatches: 29, Indels: 7
0.77 0.19 0.05
Matches are distributed among these distances:
53 11 0.09
54 106 0.89
55 2 0.02
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (54 bp):
ATTTACGATCGCAACCTCTCACTTATAAGATTTTTAAAATCTTGCGGTTTATCA
Found at i:35778396 original size:108 final size:108
Alignment explanation
Indices: 35778138--35778436 Score: 262
Period size: 108 Copynumber: 2.8 Consensus size: 108
35778128 TACGATCGTG
* ** * * ** * * * *
35778138 ACCTCTTACTTATGAGATTTTCAGAATATCATGATTTGTCGATTTACGATGGCAAACTTCTACTT
1 ACCTCTCACTTACAAGATTTTCAAAATCTCGCGATTTATCGATTTACGATCGCAACCTCCTACTT
* * * * ** *
35778203 ATGAGATTTTCAGAATCTCACTATTTGTTGATTTATGATCGCA
66 ATAAGATTTTTAGAATCTTACTATTTATCAATTTAGGATCGCA
* ** * * *
35778246 ACCTCTTACTTATGAGATTTTTAAAATCTCGCGATTTGTCGATTTACGATTGCAACCTCCTACTT
1 ACCTCTCACTTACAAGATTTTCAAAATCTCGCGATTTATCGATTTACGATCGCAACCTCCTACTT
35778311 ATAAGATTTTTAGAATCTTAC-AGTTTATCAATTTAGGATCGCA
66 ATAAGATTTTTAGAATCTTACTA-TTTATCAATTTAGGATCGCA
* * * * * * * *
35778354 ACCTCTCATTTACAAGATTTTCAAAATCTTGTGGTTTATCGATATGCAATCGCAACCTACC-GCT
1 ACCTCTCACTTACAAGATTTTCAAAATCTCGCGATTTATCGATTTACGATCGCAACCT-CCTACT
*
35778418 TACAAGA-TTTTAGAATCTT
65 TATAAGATTTTTAGAATCTT
35778437 GTTGATGCCA
Statistics
Matches: 159, Mismatches: 30, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
107 13 0.08
108 144 0.91
109 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (108 bp):
ACCTCTCACTTACAAGATTTTCAAAATCTCGCGATTTATCGATTTACGATCGCAACCTCCTACTT
ATAAGATTTTTAGAATCTTACTATTTATCAATTTAGGATCGCA
Found at i:35778803 original size:24 final size:23
Alignment explanation
Indices: 35778775--35778998 Score: 142
Period size: 24 Copynumber: 9.4 Consensus size: 23
35778765 GCACAGGTGG
35778775 CATAATTTTCTGCTGTATAGCTCA
1 CATAATTTTCTGCTGTATAGCT-A
* * **
35778799 TATAATTTTCTACTACATAGCTAA
1 CATAATTTTCTGCTGTATAGCT-A
* *
35778823 CATAATTTTCTGTTGTATAGCTTG
1 CATAATTTTCTGCTGTATAGC-TA
* *
35778847 CATAATTTTCTGCTGCACAGCTA
1 CATAATTTTCTGCTGTATAGCTA
* * *
35778870 GCATAATTTTCTGTTGTATAGTTT
1 -CATAATTTTCTGCTGTATAGCTA
* * * *
35778894 CATATTTTTTTGTTGTAGAGCTA
1 CATAATTTTCTGCTGTATAGCTA
* * ** *
35778917 GCATAATCTTCTACTCCACAGCTA
1 -CATAATTTTCTGCTGTATAGCTA
* * *
35778941 GCATAATTTTCTGCTATACAGTTTA
1 -CATAATTTTCTGCTGTATAG-CTA
* * *
35778966 CATAATTTTCTACTGCACAGCTA
1 CATAATTTTCTGCTGTATAGCTA
35778989 GCATAATTTT
1 -CATAATTTT
35778999 TTGTTGTAGA
Statistics
Matches: 153, Mismatches: 42, Indels: 10
0.75 0.20 0.05
Matches are distributed among these distances:
23 21 0.14
24 129 0.84
25 3 0.02
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.43
Consensus pattern (23 bp):
CATAATTTTCTGCTGTATAGCTA
Found at i:35778803 original size:48 final size:48
Alignment explanation
Indices: 35778725--35778890 Score: 188
Period size: 48 Copynumber: 3.4 Consensus size: 48
35778715 TCACCAGTTC
* * * * * *
35778725 GCATAATTTTTTTACTGTATAGTTCGTATAAATTTCTACTGCACAGGTG
1 GCATAA-TTTTCTGCTGTATAGCTCGTATAATTTTCTACTGCACAGCTA
* * *
35778774 GCATAATTTTCTGCTGTATAGCTCATATAATTTTCTACTACATAGCTA
1 GCATAATTTTCTGCTGTATAGCTCGTATAATTTTCTACTGCACAGCTA
* * * * *
35778822 ACATAATTTTCTGTTGTATAGCTTGCATAATTTTCTGCTGCACAGCTA
1 GCATAATTTTCTGCTGTATAGCTCGTATAATTTTCTACTGCACAGCTA
*
35778870 GCATAATTTTCTGTTGTATAG
1 GCATAATTTTCTGCTGTATAG
35778891 TTTCATATTT
Statistics
Matches: 99, Mismatches: 18, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
48 93 0.94
49 6 0.06
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (48 bp):
GCATAATTTTCTGCTGTATAGCTCGTATAATTTTCTACTGCACAGCTA
Found at i:35778947 original size:119 final size:120
Alignment explanation
Indices: 35778774--35779023 Score: 324
Period size: 119 Copynumber: 2.1 Consensus size: 120
35778764 TGCACAGGTG
* * * * * * * *
35778774 GCATAATTTTCTGCTGTATAGCTCA-TATAATTTTCTACTACATAGCTAACATAATTTTCTGTTG
1 GCATAATTTTTTGTTGTAGAGCT-AGCATAATCTTCTACTACACAGCTAACATAATTTTCTGCTA
* * * *
35778838 TATAGCTTGCATAATTTTCTGCTGCACAGCTAGCATAATTTTCTGTTGTATAGTTT
65 TACAGCTTACATAATTTTCTACTGCACAGCTAGCATAATTTTCTGTTGTAGAGTTT
* * *
35778894 -CATATTTTTTTGTTGTAGAGCTAGCATAATCTTCTACTCCACAGCTAGCATAATTTTCTGCTAT
1 GCATAATTTTTTGTTGTAGAGCTAGCATAATCTTCTACTACACAGCTAACATAATTTTCTGCTAT
* *
35778958 ACAGTTTACATAATTTTCTACTGCACAGCTAGCATAATTTTTTGTTGTAGAGTTT
66 ACAGCTTACATAATTTTCTACTGCACAGCTAGCATAATTTTCTGTTGTAGAGTTT
35779013 GCATAATTTTT
1 GCATAATTTTT
35779024 CGCTACACAA
Statistics
Matches: 110, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
118 1 0.01
119 100 0.91
120 9 0.08
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.44
Consensus pattern (120 bp):
GCATAATTTTTTGTTGTAGAGCTAGCATAATCTTCTACTACACAGCTAACATAATTTTCTGCTAT
ACAGCTTACATAATTTTCTACTGCACAGCTAGCATAATTTTCTGTTGTAGAGTTT
Found at i:35778964 original size:71 final size:72
Alignment explanation
Indices: 35778822--35778995 Score: 215
Period size: 71 Copynumber: 2.4 Consensus size: 72
35778812 TACATAGCTA
* * * * * * *
35778822 ACATAATTTTCTGTTGTATAGCTTGCATAATTTTCTGCTGCACAGCTAGCATAATTTTCTGTTGT
1 ACATAATTTTCTGTTGTAGAGCTAGCATAATCTTCTACTCCACAGCTAGCATAATTTTCTGCTAT
*
35778887 ATAGTTT
66 ACAGTTT
* *
35778894 -CATATTTTTTTGTTGTAGAGCTAGCATAATCTTCTACTCCACAGCTAGCATAATTTTCTGCTAT
1 ACATAATTTTCTGTTGTAGAGCTAGCATAATCTTCTACTCCACAGCTAGCATAATTTTCTGCTAT
35778958 ACAGTTT
66 ACAGTTT
** * *
35778965 ACATAATTTTCTACTGCACAGCTAGCATAAT
1 ACATAATTTTCTGTTGTAGAGCTAGCATAAT
35778996 TTTTTGTTGT
Statistics
Matches: 85, Mismatches: 16, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
71 61 0.72
72 24 0.28
ACGTcount: A:0.26, C:0.18, G:0.13, T:0.42
Consensus pattern (72 bp):
ACATAATTTTCTGTTGTAGAGCTAGCATAATCTTCTACTCCACAGCTAGCATAATTTTCTGCTAT
ACAGTTT
Found at i:35779047 original size:48 final size:48
Alignment explanation
Indices: 35778894--35779048 Score: 177
Period size: 48 Copynumber: 3.2 Consensus size: 48
35778884 TGTATAGTTT
* * * * *
35778894 CATATTTTTTTGTTGTAGAGCTAGCATAATCTTCTACTCCACAGCTAG
1 CATAATTTTTTGTTGTAGAGTTTGCATAATTTTCTACTACACAGCTAG
* * * * * *
35778942 CATAATTTTCTGCTATACAGTTTACATAATTTTCTACTGCACAGCTAG
1 CATAATTTTTTGTTGTAGAGTTTGCATAATTTTCTACTACACAGCTAG
* *
35778990 CATAATTTTTTGTTGTAGAGTTTGCATAATTTT-TCGCTACACAACTAG
1 CATAATTTTTTGTTGTAGAGTTTGCATAATTTTCT-ACTACACAGCTAG
35779038 CATAATTTTTT
1 CATAATTTTTT
35779049 ACTACATAGC
Statistics
Matches: 88, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
47 1 0.01
48 87 0.99
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.43
Consensus pattern (48 bp):
CATAATTTTTTGTTGTAGAGTTTGCATAATTTTCTACTACACAGCTAG
Found at i:35779758 original size:12 final size:12
Alignment explanation
Indices: 35779741--35779774 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
35779731 TTCCCTTTAA
35779741 AATAGTAAA-ATT
1 AATAGTAAAGA-T
35779753 AATAGTAAAGAT
1 AATAGTAAAGAT
35779765 AATAGTAAAG
1 AATAGTAAAG
35779775 GAGAAGTAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 20 0.95
13 1 0.05
ACGTcount: A:0.59, C:0.00, G:0.15, T:0.26
Consensus pattern (12 bp):
AATAGTAAAGAT
Found at i:35780664 original size:10 final size:10
Alignment explanation
Indices: 35780649--35780680 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
35780639 TAAATACATT
35780649 TAATTAAAGA
1 TAATTAAAGA
35780659 TAATTAAAGA
1 TAATTAAAGA
35780669 TAATTAAA-A
1 TAATTAAAGA
35780678 TAA
1 TAA
35780681 AATCCTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.31
Consensus pattern (10 bp):
TAATTAAAGA
Found at i:35780692 original size:19 final size:18
Alignment explanation
Indices: 35780668--35780711 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
35780658 ATAATTAAAG
35780668 ATAATTAAAATAAAATCCTA
1 ATAATTAAAAT--AATCCTA
*
35780688 A-AATTTAAATAATCCTA
1 ATAATTAAAATAATCCTA
35780705 ATAATTA
1 ATAATTA
35780712 TCCTAATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
17 8 0.38
18 4 0.19
19 8 0.38
20 1 0.05
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (18 bp):
ATAATTAAAATAATCCTA
Found at i:35780726 original size:15 final size:15
Alignment explanation
Indices: 35780706--35780735 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
35780696 ATAATCCTAA
35780706 TAATTATCCTAATAT
1 TAATTATCCTAATAT
35780721 TAATTATCCTAATAT
1 TAATTATCCTAATAT
35780736 AAATAAAATG
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:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (15 bp):
TAATTATCCTAATAT
Found at i:35782268 original size:39 final size:38
Alignment explanation
Indices: 35782179--35782274 Score: 120
Period size: 39 Copynumber: 2.5 Consensus size: 38
35782169 ATCCTTGTTG
* * *
35782179 TAATTATTGTAATTATAATTTATGATCGAATATTATTA
1 TAATTATTGTAATTATAATTTATCATCAAACATTATTA
* * *
35782217 TAACTATTGTAATTGTAATTTTTCAGTCAAACATTATTA
1 TAATTATTGTAATTATAATTTATCA-TCAAACATTATTA
*
35782256 TAATTATGGTAATTATAAT
1 TAATTATTGTAATTATAAT
35782275 CGATTAATTG
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
38 21 0.44
39 27 0.56
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.48
Consensus pattern (38 bp):
TAATTATTGTAATTATAATTTATCATCAAACATTATTA
Found at i:35783562 original size:38 final size:39
Alignment explanation
Indices: 35783512--35783593 Score: 112
Period size: 38 Copynumber: 2.1 Consensus size: 39
35783502 CAATTTGATC
* * *
35783512 TAATTTGATTCTTGTACATAATGTCATTATTTAGCCATA
1 TAATTTGATTCTTCTACAGAATATCATTATTTAGCCATA
* *
35783551 TAATTT-ATTCTTCTACAGAATATCATTATTTATCCTTA
1 TAATTTGATTCTTCTACAGAATATCATTATTTAGCCATA
35783589 TAATT
1 TAATT
35783594 GACACTTTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
38 32 0.84
39 6 0.16
ACGTcount: A:0.32, C:0.13, G:0.06, T:0.49
Consensus pattern (39 bp):
TAATTTGATTCTTCTACAGAATATCATTATTTAGCCATA
Found at i:35785680 original size:41 final size:43
Alignment explanation
Indices: 35785620--35785961 Score: 448
Period size: 41 Copynumber: 8.3 Consensus size: 43
35785610 GACGTTTTTT
** *
35785620 AAAACGCCGCTAAAAA-CAGAGCAACAGCGGCG-TTTTAGTAA
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGTAA
*
35785661 AAAATGCCGCTAAAAA-CAGAGCATTAGCGGCGCTTTTGGT--
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGTAA
* *
35785701 AAAACGCCGCTAAAAACCAGAGCATTAACGACGCTTTTGGT--
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGTAA
*
35785742 AAAACACCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT--
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGTAA
* *
35785783 AAAACGCCGCTAAAAACCAGAGCATTAACGACGCTTTTGGT--
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGTAA
*
35785824 AAAACACCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT--
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGTAA
* *
35785865 AAAACGCCGCTAAAAACCAGAGCATTAACGACGCTTTTGGT--
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGTAA
*
35785906 AAAACACCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT--
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGTAA
35785947 AAAACGCCGCTAAAA
1 AAAACGCCGCTAAAA
35785962 GTCATATAAC
Statistics
Matches: 276, Mismatches: 23, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
40 15 0.05
41 255 0.92
42 6 0.02
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.19
Consensus pattern (43 bp):
AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGTAA
Found at i:35785780 original size:82 final size:82
Alignment explanation
Indices: 35785598--35785961 Score: 594
Period size: 82 Copynumber: 4.5 Consensus size: 82
35785588 TTTTAAAATA
* * * ** * * *
35785598 CAGAGCAATAGCGACG-TTTT-TTAAAACGCCGCTAAAAA-CAGAGCAACAGCGGCG-TTTTAGT
1 CAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAAACCAGAGCATTAACGACGCTTTTGGT
*
35785659 AAAAAATGCCGCTAAAAA-
66 AAAACA--CCGCTAAAAAC
35785677 CAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAAACCAGAGCATTAACGACGCTTTTGGT
1 CAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAAACCAGAGCATTAACGACGCTTTTGGT
35785742 AAAACACCGCTAAAAAC
66 AAAACACCGCTAAAAAC
35785759 CAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAAACCAGAGCATTAACGACGCTTTTGGT
1 CAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAAACCAGAGCATTAACGACGCTTTTGGT
35785824 AAAACACCGCTAAAAAC
66 AAAACACCGCTAAAAAC
35785841 CAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAAACCAGAGCATTAACGACGCTTTTGGT
1 CAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAAACCAGAGCATTAACGACGCTTTTGGT
35785906 AAAACACCGCTAAAAAC
66 AAAACACCGCTAAAAAC
35785923 CAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAA
1 CAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAA
35785962 GTCATATAAC
Statistics
Matches: 271, Mismatches: 9, Indels: 7
0.94 0.03 0.02
Matches are distributed among these distances:
79 14 0.05
80 4 0.01
81 27 0.10
82 215 0.79
83 11 0.04
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.20
Consensus pattern (82 bp):
CAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAAACCAGAGCATTAACGACGCTTTTGGT
AAAACACCGCTAAAAAC
Found at i:35785818 original size:123 final size:123
Alignment explanation
Indices: 35785598--35785961 Score: 540
Period size: 123 Copynumber: 3.0 Consensus size: 123
35785588 TTTTAAAATA
* * ** *
35785598 CAGAGCAATAGCGACG-TTTT-TTAAAACGCCGCTAAAAA-CAGAGCAACAGCGGCG-TTTTAGT
1 CAGAGCATTAGCGACGCTTTTGGTAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
*
35785659 AAAAAATGCCGCTAAAAA-CAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAAAC
66 --AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAAAC
* *
35785718 CAGAGCATTAACGACGCTTTTGGTAAAACACCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
1 CAGAGCATTAGCGACGCTTTTGGTAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
* * *
35785783 AAAACGCCGCTAAAAACCAGAGCATTAACGACGCTTTTGGTAAAACACCGCTAAAAAC
66 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAAAC
* * *
35785841 CAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAAACCAGAGCATTAACGACGCTTTTGGT
1 CAGAGCATTAGCGACGCTTTTGGTAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
*
35785906 AAAACACCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAA
66 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAA
35785962 GTCATATAAC
Statistics
Matches: 219, Mismatches: 20, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
120 14 0.06
121 4 0.02
122 31 0.14
123 164 0.75
124 6 0.03
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.20
Consensus pattern (123 bp):
CAGAGCATTAGCGACGCTTTTGGTAAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGT
AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAAAC
Found at i:35786141 original size:14 final size:14
Alignment explanation
Indices: 35786119--35786163 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
35786109 TTAATTATCA
*
35786119 TTATAGTTTAAGGT
1 TTATGGTTTAAGGT
*
35786133 TTATGGTTTAAGAT
1 TTATGGTTTAAGGT
* *
35786147 ATATGGTTTAGGGT
1 TTATGGTTTAAGGT
35786161 TTA
1 TTA
35786164 AGCAGGTTTA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.49
Consensus pattern (14 bp):
TTATGGTTTAAGGT
Found at i:35786154 original size:21 final size:21
Alignment explanation
Indices: 35786130--35786214 Score: 71
Period size: 21 Copynumber: 3.7 Consensus size: 21
35786120 TATAGTTTAA
*
35786130 GGTTTATGGTTTAAGATATAT
1 GGTTTAGGGTTTAAGATATAT
*
35786151 GGTTTAGGGTTTAAGCAGGTTTAT
1 GGTTTAGGGTTTAAG-A--TATAT
*
35786175 GAGTTAACTATGGTTTAAGATATAT
1 G-GTT---TAGGGTTTAAGATATAT
*
35786200 AGTTTAGGGTTTAAG
1 GGTTTAGGGTTTAAG
35786215 GTTTAAGAGT
Statistics
Matches: 51, Mismatches: 6, Indels: 14
0.72 0.08 0.20
Matches are distributed among these distances:
21 24 0.47
22 1 0.02
24 8 0.16
25 7 0.14
27 1 0.02
28 10 0.20
ACGTcount: A:0.28, C:0.02, G:0.27, T:0.42
Consensus pattern (21 bp):
GGTTTAGGGTTTAAGATATAT
Found at i:35786192 original size:49 final size:46
Alignment explanation
Indices: 35786134--35786229 Score: 147
Period size: 49 Copynumber: 2.0 Consensus size: 46
35786124 GTTTAAGGTT
* *
35786134 TATGGTTTAAGATATATGGTTTAGGGTTTAAGCAGGTTTATGAGTTAAC
1 TATGGTTTAAGATATATAGTTTAGGGTTT-A--AGGTTTAAGAGTTAAC
35786183 TATGGTTTAAGATATATAGTTTAGGGTTTAAGGTTTAAGAGTTAAC
1 TATGGTTTAAGATATATAGTTTAGGGTTTAAGGTTTAAGAGTTAAC
35786229 T
1 T
35786230 TGTATTTGAA
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
46 16 0.36
48 1 0.02
49 28 0.62
ACGTcount: A:0.30, C:0.03, G:0.25, T:0.42
Consensus pattern (46 bp):
TATGGTTTAAGATATATAGTTTAGGGTTTAAGGTTTAAGAGTTAAC
Found at i:35786279 original size:14 final size:15
Alignment explanation
Indices: 35786252--35786280 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
35786242 TTTGTGATGA
35786252 ATTATGATTTTAGGG
1 ATTATGATTTTAGGG
35786267 ATTATGA-TTTAGGG
1 ATTATGATTTTAGGG
35786281 TTTAAGGGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.28, C:0.00, G:0.28, T:0.45
Consensus pattern (15 bp):
ATTATGATTTTAGGG
Found at i:35791204 original size:4 final size:4
Alignment explanation
Indices: 35791195--35791222 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
35791185 CAGCTGTTTC
35791195 TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG
35791223 CTAAATGGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:35798755 original size:17 final size:18
Alignment explanation
Indices: 35798714--35798756 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
35798704 TGTATTTACT
35798714 TATTATATAAGTAAATAG
1 TATTATATAAGTAAATAG
*
35798732 TAATATA-AAGTAAAATA-
1 TATTATATAAGT-AAATAG
35798749 TATTATAT
1 TATTATAT
35798757 TATTTAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (18 bp):
TATTATATAAGTAAATAG
Found at i:35798854 original size:16 final size:17
Alignment explanation
Indices: 35798826--35798869 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 17
35798816 AACGATTAGC
35798826 AGGGAAAGAAAGAATGAAAA
1 AGGGAAAGAAA-AA-G-AAA
35798846 AGGGAAAGAAAAAGAAA
1 AGGGAAAGAAAAAGAAA
35798863 AGGGAAA
1 AGGGAAA
35798870 ATTAGGTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.42
18 1 0.04
19 2 0.08
20 11 0.46
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.02
Consensus pattern (17 bp):
AGGGAAAGAAAAAGAAA
Found at i:35799720 original size:6 final size:6
Alignment explanation
Indices: 35799713--35799746 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
35799703 ATTATGATTG
* *
35799713 TTACTG TTACTA TTACTA TTACTA TTACTG TTAC
1 TTACTA TTACTA TTACTA TTACTA TTACTA TTAC
35799747 CCTATAGTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.26, C:0.18, G:0.06, T:0.50
Consensus pattern (6 bp):
TTACTA
Found at i:35799734 original size:12 final size:12
Alignment explanation
Indices: 35799713--35799746 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
35799703 ATTATGATTG
35799713 TTACTGTTACTA
1 TTACTGTTACTA
*
35799725 TTACTATTACTA
1 TTACTGTTACTA
35799737 TTACTGTTAC
1 TTACTGTTAC
35799747 CCTATAGTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.26, C:0.18, G:0.06, T:0.50
Consensus pattern (12 bp):
TTACTGTTACTA
Found at i:35803447 original size:130 final size:131
Alignment explanation
Indices: 35803269--35803670 Score: 411
Period size: 132 Copynumber: 3.1 Consensus size: 131
35803259 AGAATTTTTT
* * * * * * *
35803269 TTTTGTAAAA-ACATGAGTGAAAAC-CTAAAGGAATATTCAACTGCTTTGAACCAACGAGAAATC
1 TTTT-TAAAAGACATGAGTG-AAACTCTAAAGGGATATTCGATTACTTTGAGCAAACGAGAAATT
* * * * * *
35803332 GTAACCTAGCACGATAGCGTACGATTCT-CGAATTGCCAAATATCGAACATCGCTTATGTTTAAA
64 GCAACCCAACACGTTAGAGCACGATTCTACGAATTGCCAAATATCGAACATCGCTTATGTTTAAA
35803396 GAA
129 GAA
* * *
35803399 TTTTTAAAAGACATGGGTGAAACTCTAAAGGGATCTTCGATTACTTTGAGCAAACAAGAAATTGC
1 TTTTTAAAAGACATGAGTGAAACTCTAAAGGGATATTCGATTACTTTGAGCAAACGAGAAATTGC
* * * *
35803464 AACCCAACACGTTAGAGCACGATTCTGCGAATTGTCAAATGTCGAACATCACCCTTAT-TTTAAA
66 AACCCAACACGTTAGAGCACGATTCTACGAATTGCCAAATATCGAACAT--CGCTTATGTTTAAA
*
35803528 GGA
129 GAA
** * * * * * *
35803531 TTTTTGGAAGACATAAGTGAAATTTTGAAGGGATATTCGATTATTTTGAGCAAACGCGAAATTGC
1 TTTTTAAAAGACATGAGTGAAACTCTAAAGGGATATTCGATTACTTTGAGCAAACGAGAAATTGC
* * *
35803596 AACCCAACACGTTAGGGCACGATTCTACGAATTGCCAAATATCAAATC-TCGTCTT-CGTTTTAA
66 AACCCAACACGTTAGAGCACGATTCTACGAATTGCCAAATATCGAA-CATCG-CTTATG-TTTAA
35803659 AGAA
128 AGAA
35803663 TTTTTAAA
1 TTTTTAAA
35803671 TGAATAATTA
Statistics
Matches: 222, Mismatches: 41, Indels: 16
0.80 0.15 0.06
Matches are distributed among these distances:
129 9 0.04
130 65 0.29
131 23 0.10
132 118 0.53
133 7 0.03
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Consensus pattern (131 bp):
TTTTTAAAAGACATGAGTGAAACTCTAAAGGGATATTCGATTACTTTGAGCAAACGAGAAATTGC
AACCCAACACGTTAGAGCACGATTCTACGAATTGCCAAATATCGAACATCGCTTATGTTTAAAGA
A
Found at i:35804017 original size:14 final size:14
Alignment explanation
Indices: 35803998--35804028 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
35803988 CAACACGACA
35803998 TAAAAATAATGGAC
1 TAAAAATAATGGAC
*
35804012 TAAAAATGATGGAC
1 TAAAAATAATGGAC
35804026 TAA
1 TAA
35804029 CAATCAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.55, C:0.06, G:0.16, T:0.23
Consensus pattern (14 bp):
TAAAAATAATGGAC
Found at i:35804463 original size:19 final size:19
Alignment explanation
Indices: 35804439--35804478 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
35804429 TTGAATTATT
35804439 TTTATTACAAATGATGGAC
1 TTTATTACAAATGATGGAC
35804458 TTTATTACAAATGATGGAC
1 TTTATTACAAATGATGGAC
35804477 TT
1 TT
35804479 AAAAGCATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (19 bp):
TTTATTACAAATGATGGAC
Found at i:35806038 original size:22 final size:22
Alignment explanation
Indices: 35805978--35806038 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
35805968 TTCATTTTTC
**
35805978 CTATTTGCTGTTG-TCCTGTTG
1 CTATTTGCTGTTGTTTTTGTTG
* * *
35805999 CCATTTGCTTGTTTTTTTTGTTT
1 CTATTTGC-TGTTGTTTTTGTTG
35806022 CTATTTGCTGTTGTTTT
1 CTATTTGCTGTTGTTTT
35806039 CTTGTCTGTT
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
21 7 0.23
22 12 0.39
23 12 0.39
ACGTcount: A:0.05, C:0.15, G:0.18, T:0.62
Consensus pattern (22 bp):
CTATTTGCTGTTGTTTTTGTTG
Found at i:35806227 original size:14 final size:15
Alignment explanation
Indices: 35806208--35806240 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
35806198 TTTATATATT
35806208 TTTTG-TATTTTTTG
1 TTTTGTTATTTTTTG
*
35806222 TTTTGTTTTTTTTTG
1 TTTTGTTATTTTTTG
35806237 TTTT
1 TTTT
35806241 TGGTGTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.03, C:0.00, G:0.12, T:0.85
Consensus pattern (15 bp):
TTTTGTTATTTTTTG
Found at i:35806236 original size:24 final size:24
Alignment explanation
Indices: 35806206--35806251 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
35806196 GCTTTATATA
*
35806206 TTTTTTGTATTTT-TTGTTTTGTTT
1 TTTTTTGT-TTTTGGTGTTTTGTTT
35806230 TTTTTTGTTTTTGGTGTTTTGT
1 TTTTTTGTTTTTGGTGTTTTGT
35806252 GTTTGCACGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.02, C:0.00, G:0.17, T:0.80
Consensus pattern (24 bp):
TTTTTTGTTTTTGGTGTTTTGTTT
Found at i:35810306 original size:38 final size:38
Alignment explanation
Indices: 35810251--35810329 Score: 140
Period size: 38 Copynumber: 2.1 Consensus size: 38
35810241 AAATTAATTA
*
35810251 TATTAATTATTATTAAATAAATAAAAGAAAGACAAGTG
1 TATTAATTATTAGTAAATAAATAAAAGAAAGACAAGTG
*
35810289 TATTAATTATTAGTAAATAAATAAAAGAAAGGCAAGTG
1 TATTAATTATTAGTAAATAAATAAAAGAAAGACAAGTG
35810327 TAT
1 TAT
35810330 GGTAAAAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.53, C:0.03, G:0.13, T:0.32
Consensus pattern (38 bp):
TATTAATTATTAGTAAATAAATAAAAGAAAGACAAGTG
Found at i:35811649 original size:40 final size:40
Alignment explanation
Indices: 35811526--35811661 Score: 120
Period size: 40 Copynumber: 3.5 Consensus size: 40
35811516 CGACCTTGAG
* *
35811526 TCGATGAGACACTGGGTGTCACTATATTTCTTCGGATA-GAT
1 TCGATGAGACACTGGGTGTCACTATATTACTTC-GA-ACTAT
** ** *
35811567 TCGATGAGGTACTGGGTACCAC--T-TTACTTCG-ACTAGG
1 TCGATGAGACACTGGGTGTCACTATATTACTTCGAACTA-T
* *
35811604 CCGATGAGACACTGGGTGTCACTATATTGCTTCGAACTAT
1 TCGATGAGACACTGGGTGTCACTATATTACTTCGAACTAT
*
35811644 TCGATGAGGCACTGGGTG
1 TCGATGAGACACTGGGTG
35811662 CCATTCCGGT
Statistics
Matches: 73, Mismatches: 16, Indels: 13
0.72 0.16 0.13
Matches are distributed among these distances:
35 1 0.01
36 1 0.01
37 18 0.25
38 6 0.08
39 2 0.03
40 23 0.32
41 22 0.30
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (40 bp):
TCGATGAGACACTGGGTGTCACTATATTACTTCGAACTAT
Found at i:35818009 original size:34 final size:33
Alignment explanation
Indices: 35817939--35818056 Score: 116
Period size: 34 Copynumber: 3.5 Consensus size: 33
35817929 GTCGTTCAGT
* * *
35817939 TGAAAATTTATTAAATGTACTCTAATTGTTTTTCA
1 TGAAAATTTA-TAAAAGTA-TTTAATTGTTTATCA
35817974 TGAAAATTTATAAAAGTATTATAATTGTTTATCA
1 TGAAAATTTATAAAAGTATT-TAATTGTTTATCA
* * * *
35818008 TG--AATAT-TAAATGTACTTTGATTTTTTATCA
1 TGAAAATTTATAAAAGTA-TTTAATTGTTTATCA
35818039 TGAAAATTTATAAAAGTA
1 TGAAAATTTATAAAAGTA
35818057 GTAATTTTTA
Statistics
Matches: 69, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
31 20 0.29
32 6 0.09
33 5 0.07
34 28 0.41
35 10 0.14
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.46
Consensus pattern (33 bp):
TGAAAATTTATAAAAGTATTTAATTGTTTATCA
Found at i:35818670 original size:9 final size:9
Alignment explanation
Indices: 35818652--35818699 Score: 51
Period size: 10 Copynumber: 4.9 Consensus size: 9
35818642 AGTTTTTTTA
35818652 TTATAATTT
1 TTATAATTT
*
35818661 TTATAGTTTT
1 TTATA-ATTT
35818671 TCTATAATTT
1 T-TATAATTT
35818681 TTATAATATT
1 TTATAAT-TT
35818691 TTAATAATT
1 TT-ATAATT
35818700 ATTAAACTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
9 11 0.33
10 13 0.39
11 9 0.27
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (9 bp):
TTATAATTT
Found at i:35818697 original size:20 final size:20
Alignment explanation
Indices: 35818654--35818699 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
35818644 TTTTTTTATT
* *
35818654 ATAATTTTTATAGTTTTTCT
1 ATAATTTTTATAATTTTTCA
35818674 ATAATTTTTATAATATTTT-A
1 ATAATTTTTATAAT-TTTTCA
35818694 ATAATT
1 ATAATT
35818700 ATTAAACTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (20 bp):
ATAATTTTTATAATTTTTCA
Found at i:35823662 original size:14 final size:13
Alignment explanation
Indices: 35823645--35823686 Score: 52
Period size: 11 Copynumber: 3.3 Consensus size: 13
35823635 CATTTAATAT
35823645 AATAAATAATTTAA
1 AATAAATAA-TTAA
35823659 AATAAAT-A-TAA
1 AATAAATAATTAA
*
35823670 AACAAATAATTAA
1 AATAAATAATTAA
35823683 AATA
1 AATA
35823687 TTTATAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
11 9 0.38
12 1 0.04
13 7 0.29
14 7 0.29
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAAATAATTAA
Found at i:35823696 original size:25 final size:25
Alignment explanation
Indices: 35823648--35823695 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
35823638 TTAATATAAT
35823648 AAATAATTTAAAATAAATATAAAAC
1 AAATAATTTAAAATAAATATAAAAC
**
35823673 AAATAA-TTAAAATATTTATAAAA
1 AAATAATTTAAAATAAATATAAAA
35823696 ATATTATGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (25 bp):
AAATAATTTAAAATAAATATAAAAC
Found at i:35833867 original size:24 final size:24
Alignment explanation
Indices: 35833812--35833859 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
35833802 TCCTTTCCTC
35833812 TTAATTATACACTTGAACAATATT
1 TTAATTATACACTTGAACAATATT
35833836 TTAATTATACACTTGAACAATATT
1 TTAATTATACACTTGAACAATATT
35833860 GTTGTTATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.12, G:0.04, T:0.42
Consensus pattern (24 bp):
TTAATTATACACTTGAACAATATT
Found at i:35834134 original size:13 final size:13
Alignment explanation
Indices: 35834116--35834160 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
35834106 ATGTAAAAAC
35834116 AATTTAAAATATA
1 AATTTAAAATATA
35834129 AATTTATTAAA-A-A
1 AATTTA--AAATATA
35834142 AATTTAAAATATA
1 AATTTAAAATATA
35834155 AATTTA
1 AATTTA
35834161 TTAATATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
11 3 0.11
12 1 0.04
13 20 0.71
14 1 0.04
15 3 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AATTTAAAATATA
Found at i:35834140 original size:26 final size:26
Alignment explanation
Indices: 35834100--35834164 Score: 103
Period size: 26 Copynumber: 2.4 Consensus size: 26
35834090 TAAATCATTG
*
35834100 AAATATATGTAAAAACAATTTAAAATAT
1 AAATTTAT-TAAAAA-AATTTAAAATAT
35834128 AAATTTATTAAAAAAATTTAAAATAT
1 AAATTTATTAAAAAAATTTAAAATAT
35834154 AAATTTATTAA
1 AAATTTATTAA
35834165 TATATATAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
26 23 0.64
27 6 0.17
28 7 0.19
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (26 bp):
AAATTTATTAAAAAAATTTAAAATAT
Found at i:35834173 original size:18 final size:18
Alignment explanation
Indices: 35834150--35834192 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
35834140 AAAATTTAAA
35834150 ATATAAATTTATTAATAT
1 ATATAAATTTATTAATAT
35834168 ATATAAATTTATTAATAT
1 ATATAAATTTATTAATAT
*
35834186 ATGTAAA
1 ATATAAA
35834193 AATAACTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
ATATAAATTTATTAATAT
Found at i:35834300 original size:19 final size:20
Alignment explanation
Indices: 35834272--35834313 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
35834262 CAAACACCAA
35834272 AAAAGCAAATCA-TTTCCAG
1 AAAAGCAAATCATTTTCCAG
* *
35834291 AAAAGTAAATTATTTTCCAG
1 AAAAGCAAATCATTTTCCAG
35834311 AAA
1 AAA
35834314 TCATTTTTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.50, C:0.14, G:0.10, T:0.26
Consensus pattern (20 bp):
AAAAGCAAATCATTTTCCAG
Found at i:35834849 original size:25 final size:25
Alignment explanation
Indices: 35834821--35834872 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
35834811 TTTGGCTTGA
*
35834821 CATTTACTAAGCAATATCAGATATT
1 CATTTACTAAGCAATATCAAATATT
* *
35834846 CATTTATTAGGCAATATCAAATATT
1 CATTTACTAAGCAATATCAAATATT
35834871 CA
1 CA
35834873 AATTAATCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.37
Consensus pattern (25 bp):
CATTTACTAAGCAATATCAAATATT
Found at i:35836316 original size:41 final size:42
Alignment explanation
Indices: 35836230--35836320 Score: 103
Period size: 41 Copynumber: 2.2 Consensus size: 42
35836220 TATATAATTC
**
35836230 TTTAATTTTATTATTTTTAAAATAATTAAAAAATAATTTGGA
1 TTTAATTTTATTATTTTTAAAATAATTAAAAAATAATTTAAA
* * * * * *
35836272 TTTATTTTTATTATTTTT-ATATATTTTAAAAGTTATTTAAA
1 TTTAATTTTATTATTTTTAAAATAATTAAAAAATAATTTAAA
35836313 TTTAATTT
1 TTTAATTT
35836321 CAAAAGATGA
Statistics
Matches: 40, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
41 23 0.57
42 17 0.43
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.58
Consensus pattern (42 bp):
TTTAATTTTATTATTTTTAAAATAATTAAAAAATAATTTAAA
Found at i:35836707 original size:15 final size:15
Alignment explanation
Indices: 35836687--35836717 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
35836677 CTATTTTCTG
*
35836687 TTTTTTTTTCCTTTA
1 TTTTTTATTCCTTTA
35836702 TTTTTTATTCCTTTA
1 TTTTTTATTCCTTTA
35836717 T
1 T
35836718 CAGCAGCACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTTTATTCCTTTA
Found at i:35841481 original size:41 final size:42
Alignment explanation
Indices: 35841431--35841509 Score: 115
Period size: 41 Copynumber: 1.9 Consensus size: 42
35841421 CTGAAACTTG
* *
35841431 AGGGCTGAACAGAAGCACATAAGTGCT-AATGGAAACCCATA
1 AGGGCTGAACAGAAGCACATAAGAGCTGAATGAAAACCCATA
* *
35841472 AGGGTTGAACAGAAGCTCATAAGAGCTGAATGAAAACC
1 AGGGCTGAACAGAAGCACATAAGAGCTGAATGAAAACC
35841510 TAATAGGTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
41 24 0.73
42 9 0.27
ACGTcount: A:0.42, C:0.18, G:0.25, T:0.15
Consensus pattern (42 bp):
AGGGCTGAACAGAAGCACATAAGAGCTGAATGAAAACCCATA
Found at i:35841501 original size:21 final size:21
Alignment explanation
Indices: 35841434--35841501 Score: 57
Period size: 21 Copynumber: 3.3 Consensus size: 21
35841424 AAACTTGAGG
*
35841434 GCTGAACAGAAGCACATAAGT
1 GCTGAACAGAAGCACATAAGA
** * * *
35841455 GCT-AATGGAAACCCATAAGG
1 GCTGAACAGAAGCACATAAGA
* *
35841475 GTTGAACAGAAGCTCATAAGA
1 GCTGAACAGAAGCACATAAGA
35841496 GCTGAA
1 GCTGAA
35841502 TGAAAACCTA
Statistics
Matches: 34, Mismatches: 12, Indels: 2
0.71 0.25 0.04
Matches are distributed among these distances:
20 14 0.41
21 20 0.59
ACGTcount: A:0.41, C:0.18, G:0.25, T:0.16
Consensus pattern (21 bp):
GCTGAACAGAAGCACATAAGA
Found at i:35845249 original size:12 final size:12
Alignment explanation
Indices: 35845226--35845282 Score: 63
Period size: 12 Copynumber: 5.2 Consensus size: 12
35845216 CCAAAATTTT
35845226 TTTATT-TAAAA
1 TTTATTATAAAA
35845237 TTTATTATAAAA
1 TTTATTATAAAA
*
35845249 TATA-TA-AAAA
1 TTTATTATAAAA
35845259 TTTATTATAAAA
1 TTTATTATAAAA
35845271 --TA-TATAAAA
1 TTTATTATAAAA
35845280 TTT
1 TTT
35845283 TAGTGTAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
9 7 0.18
10 9 0.23
11 11 0.28
12 12 0.31
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
TTTATTATAAAA
Found at i:35845259 original size:22 final size:22
Alignment explanation
Indices: 35845233--35845284 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
35845223 TTTTTTATTT
35845233 AAAATTTATTATAAAATATATA
1 AAAATTTATTATAAAATATATA
35845255 AAAATTTATTATAAAATATATA
1 AAAATTTATTATAAAATATATA
*
35845277 AAATTTTA
1 AAAATTTA
35845285 GTGTAAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
AAAATTTATTATAAAATATATA
Found at i:35845291 original size:22 final size:22
Alignment explanation
Indices: 35845233--35845292 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
35845223 TTTTTTATTT
*
35845233 AAAATTTATTATAAAATATATA
1 AAAATTTAGTATAAAATATATA
*
35845255 AAAATTTATTATAAAATATATA
1 AAAATTTAGTATAAAATATATA
* *
35845277 AAATTTTAGTGTAAAA
1 AAAATTTAGTATAAAA
35845293 ATACTTTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (22 bp):
AAAATTTAGTATAAAATATATA
Found at i:35853554 original size:13 final size:13
Alignment explanation
Indices: 35853536--35853563 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
35853526 AAACGAACTT
35853536 CAAAATAATTATG
1 CAAAATAATTATG
35853549 CAAAATAATTATG
1 CAAAATAATTATG
35853562 CA
1 CA
35853564 GATGAAAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.11, G:0.07, T:0.29
Consensus pattern (13 bp):
CAAAATAATTATG
Found at i:35855107 original size:27 final size:27
Alignment explanation
Indices: 35855077--35855131 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
35855067 TATCATTTTC
35855077 ATAATTGACACATTAGTATGAGTAACA
1 ATAATTGACACATTAGTATGAGTAACA
35855104 ATAATTGACACATTAGTATGAGTAACA
1 ATAATTGACACATTAGTATGAGTAACA
35855131 A
1 A
35855132 CAAAAATGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.45, C:0.11, G:0.15, T:0.29
Consensus pattern (27 bp):
ATAATTGACACATTAGTATGAGTAACA
Found at i:35864343 original size:28 final size:28
Alignment explanation
Indices: 35864311--35864367 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
35864301 GTAAGATAGA
35864311 AAATAATAATAAATTAATTTATTTTTTT
1 AAATAATAATAAATTAATTTATTTTTTT
35864339 AAATAATAATAAATTAATTTATTTTTTT
1 AAATAATAATAAATTAATTTATTTTTTT
35864367 A
1 A
35864368 TATTGTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
AAATAATAATAAATTAATTTATTTTTTT
Found at i:35867372 original size:21 final size:18
Alignment explanation
Indices: 35867335--35867385 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 18
35867325 TAAGAAATAT
35867335 AAAT-TTTTGAATTTTTA
1 AAATATTTTGAATTTTTA
35867352 CAAATATTTTGAATTTTTTTA
1 -AAATATTTTGAA--TTTTTA
35867373 AAATTATTTTGAA
1 AAA-TATTTTGAA
35867386 GCTTTATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.14
19 7 0.24
20 3 0.10
21 15 0.52
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.55
Consensus pattern (18 bp):
AAATATTTTGAATTTTTA
Found at i:35867989 original size:43 final size:43
Alignment explanation
Indices: 35867922--35868010 Score: 144
Period size: 43 Copynumber: 2.1 Consensus size: 43
35867912 AAGATGATAC
*
35867922 CAAGAGAATAATACCTTTATGATATAAGTACAATATACTCTAA
1 CAAGAAAATAATACCTTTATGATATAAGTACAATATACTCTAA
*
35867965 CAAGAAAATAATACCTTTGA-GATATAAGTATAATATACTCTAA
1 CAAGAAAATAATACCTTT-ATGATATAAGTACAATATACTCTAA
35868008 CAA
1 CAA
35868011 TTGACATAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
43 42 0.98
44 1 0.02
ACGTcount: A:0.48, C:0.13, G:0.09, T:0.29
Consensus pattern (43 bp):
CAAGAAAATAATACCTTTATGATATAAGTACAATATACTCTAA
Found at i:35871232 original size:5 final size:5
Alignment explanation
Indices: 35871222--35871248 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
35871212 CATATTTATT
35871222 ATTGA ATTGA ATTGA ATTGA ATTGA AT
1 ATTGA ATTGA ATTGA ATTGA ATTGA AT
35871249 GCTGAATGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41
Consensus pattern (5 bp):
ATTGA
Found at i:35871414 original size:43 final size:43
Alignment explanation
Indices: 35871366--35871487 Score: 156
Period size: 43 Copynumber: 2.8 Consensus size: 43
35871356 GCCGAGATGA
* * *
35871366 GATTACATGTAAGACCATGTTTGGGACATTGGCAT-TTTATTGT
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATCGTTA-TAT
* *
35871409 GATTACATGTAAGATCATGTCTAGGACATTGGCATCGTTATAT
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATCGTTATAT
***
35871452 GATTTTGTGTAAGACCATGTCTGGGACATTGGCATC
1 GATTACATGTAAGACCATGTCTGGGACATTGGCATC
35871488 AATATGATAT
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
43 65 0.96
44 3 0.04
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (43 bp):
GATTACATGTAAGACCATGTCTGGGACATTGGCATCGTTATAT
Found at i:35871506 original size:43 final size:42
Alignment explanation
Indices: 35871372--35871528 Score: 140
Period size: 43 Copynumber: 3.7 Consensus size: 42
35871362 ATGAGATTAC
* * * *
35871372 ATGTAAGACCATGTTTGGGACATTGGCATTTTATTGTGAT-TAC
1 ATGTAAGACCATGTCTGGGACATTGGCA-TCTA-TATGATATAT
* * *
35871415 ATGTAAGATCATGTCTAGGACATTGGCATCGTTATATGAT-TTT
1 ATGTAAGACCATGTCTGGGACATTGGCATC--TATATGATATAT
* *
35871458 GTGTAAGACCATGTCTGGGACATTGGCATCAATATGATATAAT
1 ATGTAAGACCATGTCTGGGACATTGGCATCTATATGATAT-AT
** *
35871501 ATGTAAGACCACATCTGGGATA-TGGCAT
1 ATGTAAGACCATGTCTGGGACATTGGCAT
35871529 TGTATGAGCT
Statistics
Matches: 94, Mismatches: 16, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
41 7 0.07
42 8 0.09
43 77 0.82
44 2 0.02
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.34
Consensus pattern (42 bp):
ATGTAAGACCATGTCTGGGACATTGGCATCTATATGATATAT
Found at i:35874412 original size:44 final size:42
Alignment explanation
Indices: 35874345--35874501 Score: 151
Period size: 43 Copynumber: 3.7 Consensus size: 42
35874335 TGTGTTTTTG
* * *
35874345 TGTAAGACCATGTCTGGGGCGTTGGCATCGACTTATGATTTACG
1 TGTAAGACCACGTCTGGGACGTTGGCATCGA-TT-TGATTTACA
*
35874389 TGTAATACCACGTCTGGGACGTTGGCATCGTATTTGATTT-CA
1 TGTAAGACCACGTCTGGGACGTTGGCATCG-ATTTGATTTACA
*
35874431 TGTAAGACC-CTGTCTGGGATAG-TGGCATCGATATTTGA-TTACA
1 TGTAAGACCAC-GTCTGGGA-CGTTGGCATCG--ATTTGATTTACA
* * *
35874474 TGTAAGCCCACATCTGGGACATTGGCAT
1 TGTAAGACCACGTCTGGGACGTTGGCAT
35874502 TGTACAAGCT
Statistics
Matches: 96, Mismatches: 10, Indels: 15
0.79 0.08 0.12
Matches are distributed among these distances:
41 1 0.01
42 27 0.28
43 37 0.39
44 30 0.31
45 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (42 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCGATTTGATTTACA
Found at i:35877338 original size:20 final size:20
Alignment explanation
Indices: 35877313--35877357 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
35877303 AGGGACTAAA
* *
35877313 ATGAAAAGTTGTAAAATTTG
1 ATGAAAAATTCTAAAATTTG
*
35877333 ATGAAAAATTCTAAAATTTT
1 ATGAAAAATTCTAAAATTTG
35877353 ATGAA
1 ATGAA
35877358 TATATGTGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.49, C:0.02, G:0.13, T:0.36
Consensus pattern (20 bp):
ATGAAAAATTCTAAAATTTG
Found at i:35882617 original size:12 final size:12
Alignment explanation
Indices: 35882600--35882629 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
35882590 CATGATATTC
35882600 AATTTATCAATT
1 AATTTATCAATT
35882612 AATTTATCAATT
1 AATTTATCAATT
35882624 -ATTTAT
1 AATTTAT
35882630 GATTTAATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.33
12 12 0.67
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (12 bp):
AATTTATCAATT
Found at i:35883497 original size:19 final size:19
Alignment explanation
Indices: 35883454--35883499 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
35883444 TAAGTTTAGT
*
35883454 AATTAATTAATCCTAATTA
1 AATTAATTAAACCTAATTA
** *
35883473 GCTTAATTAAACTTAATTA
1 AATTAATTAAACCTAATTA
35883492 AATTAATT
1 AATTAATT
35883500 TTAATCATAA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.43
Consensus pattern (19 bp):
AATTAATTAAACCTAATTA
Found at i:35887261 original size:50 final size:51
Alignment explanation
Indices: 35887183--35887311 Score: 190
Period size: 50 Copynumber: 2.5 Consensus size: 51
35887173 GACCATGGCA
*
35887183 ACAAGTGATAAGTGATAGCTTCGACTACACTTATCTGATCAA-GAAAAAGTG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAATGAAAAA-TG
*
35887234 A-AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAATGACAAATG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAATGAAAAATG
* * *
35887284 ACAAGTGAAAAGTGGTAGCTTCAGCTAC
1 ACAAGTGATAAGTGATAGCTTCGGCTAC
35887312 CTGATCAGTG
Statistics
Matches: 71, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
50 42 0.59
51 29 0.41
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (51 bp):
ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAATGAAAAATG
Found at i:35887325 original size:31 final size:31
Alignment explanation
Indices: 35887287--35887404 Score: 184
Period size: 31 Copynumber: 3.8 Consensus size: 31
35887277 ACAAATGACA
* *
35887287 AGTGAAAAGTGGTAGCTTCAGCTACCTGATC
1 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
35887318 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
35887349 AGTGAAAAGTGGTAG-TACCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCT-CCGGCTACCTGATC
* *
35887380 AGTGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTCCGGCTAC
35887405 AAGTGACAAG
Statistics
Matches: 81, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
30 1 0.01
31 79 0.98
32 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
Found at i:35887567 original size:49 final size:47
Alignment explanation
Indices: 35887454--35887594 Score: 167
Period size: 49 Copynumber: 3.0 Consensus size: 47
35887444 ATGGCATCGG
* * * * * * *
35887454 TGTGATATATATAAGACCATATCTGTGATATGGCATCA-GTGAGATA
1 TGTGATACATGTAAGACCATAGCTGGGCTATGGCATCATATGTGATA
* *
35887500 TGTGATCCGTGTAAGACCATAGCTGGGCTATGGCATCGATATGTGATA
1 TGTGATACATGTAAGACCATAGCTGGGCTATGGCATC-ATATGTGATA
35887548 TGTGATTACATGTAAGACCATAGCTGGGCTATGGCATCATTATGTGA
1 TGTGA-TACATGTAAGACCATAGCTGGGCTATGGCATCA-TATGTGA
35887595 AGATGTGTAA
Statistics
Matches: 80, Mismatches: 11, Indels: 5
0.83 0.11 0.05
Matches are distributed among these distances:
46 30 0.38
47 1 0.01
48 12 0.15
49 37 0.46
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (47 bp):
TGTGATACATGTAAGACCATAGCTGGGCTATGGCATCATATGTGATA
Found at i:35891159 original size:26 final size:28
Alignment explanation
Indices: 35891114--35891171 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
35891104 AACTAATTCT
**
35891114 AATTTCCAATCTTTGTTTTTA-CTCTTC
1 AATTTCCAATCTTTAATTTTACCTCTTC
*
35891141 AATTTCC-ATCTTTAATTTTACCTTTTC
1 AATTTCCAATCTTTAATTTTACCTCTTC
35891168 AATT
1 AATT
35891172 GTTTATCCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 11 0.41
27 16 0.59
ACGTcount: A:0.22, C:0.21, G:0.02, T:0.55
Consensus pattern (28 bp):
AATTTCCAATCTTTAATTTTACCTCTTC
Found at i:35891569 original size:19 final size:18
Alignment explanation
Indices: 35891541--35891591 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
35891531 AAAAAAATTT
*
35891541 AAAATTAAAAATCAT-TAA
1 AAAAATAAAAAT-ATATAA
35891559 AAAAATAAAAATATATAA
1 AAAAATAAAAATATATAA
35891577 AAAAAT-AAAATATAT
1 AAAAATAAAAATATAT
35891592 TTTAAATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
17 11 0.35
18 20 0.65
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (18 bp):
AAAAATAAAAATATATAA
Found at i:35891580 original size:17 final size:17
Alignment explanation
Indices: 35891556--35891591 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
35891546 TAAAAATCAT
35891556 TAAAAAAATAAAAATATA
1 TAAAAAAAT-AAAATATA
35891574 TAAAAAAATAAAATATA
1 TAAAAAAATAAAATATA
35891591 T
1 T
35891592 TTTAAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (17 bp):
TAAAAAAATAAAATATA
Found at i:35891915 original size:13 final size:12
Alignment explanation
Indices: 35891888--35891912 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35891878 GACAGTAAAA
35891888 TAAAATATTTTT
1 TAAAATATTTTT
35891900 TAAAATATTTTT
1 TAAAATATTTTT
35891912 T
1 T
35891913 TAATCGAACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TAAAATATTTTT
Found at i:35892935 original size:30 final size:31
Alignment explanation
Indices: 35892899--35892962 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
35892889 TTTGATTCAT
*
35892899 AAATTTTGATT-TAGTACAATTATATACGTG
1 AAATTTTGATTGTAGTACAATTATATACATG
* * *
35892929 AAATTTTGGTTGTGGTTCAATTATATACATG
1 AAATTTTGATTGTAGTACAATTATATACATG
35892960 AAA
1 AAA
35892963 CTTCAATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 10 0.34
31 19 0.66
ACGTcount: A:0.36, C:0.06, G:0.16, T:0.42
Consensus pattern (31 bp):
AAATTTTGATTGTAGTACAATTATATACATG
Found at i:35893731 original size:19 final size:18
Alignment explanation
Indices: 35893709--35893759 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 18
35893699 TTTTATGTTT
35893709 ATAAATTAAAATATATTT-A
1 ATAAATTAAAAT-T-TTTAA
*
35893728 ATAATTTTAAAATTTTTAA
1 ATAA-ATTAAAATTTTTAA
*
35893747 ATAAATAAAAATT
1 ATAAATTAAAATT
35893760 CCTTAAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 10 0.37
19 10 0.37
20 7 0.26
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
ATAAATTAAAATTTTTAA
Found at i:35905739 original size:27 final size:26
Alignment explanation
Indices: 35905709--35905759 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
35905699 TAAATTTAAG
*
35905709 ATCTAATCTTTATACATCAACTTTTTT
1 ATCTAAT-TTGATACATCAACTTTTTT
* *
35905736 ATCTAATTTGGTACCTCAACTTTT
1 ATCTAATTTGATACATCAACTTTT
35905760 ACAACGTCCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 14 0.67
27 7 0.33
ACGTcount: A:0.27, C:0.20, G:0.04, T:0.49
Consensus pattern (26 bp):
ATCTAATTTGATACATCAACTTTTTT
Found at i:35906705 original size:17 final size:17
Alignment explanation
Indices: 35906683--35906725 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
35906673 GCCCTCCCAA
35906683 AAAAAAAAAACCTAACC
1 AAAAAAAAAACCTAACC
35906700 AAAAAAAAAACCTAACC
1 AAAAAAAAAACCTAACC
35906717 AAAAAAAAA
1 AAAAAAAAA
35906726 GAAAAACCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.77, C:0.19, G:0.00, T:0.05
Consensus pattern (17 bp):
AAAAAAAAAACCTAACC
Found at i:35906706 original size:22 final size:21
Alignment explanation
Indices: 35906681--35906750 Score: 94
Period size: 22 Copynumber: 3.5 Consensus size: 21
35906671 AAGCCCTCCC
35906681 AAAAAAAAAAAACCTAACC--
1 AAAAAAAAAAAACCTAACCAA
35906700 --AAAAAAAAAACCTAACCAA
1 AAAAAAAAAAAACCTAACCAA
*
35906719 AAAAAAAGAAAAACCTAACCCA
1 AAAAAAA-AAAAACCTAACCAA
35906741 AAAAAAAAAA
1 AAAAAAAAAA
35906751 CCAAGAAACC
Statistics
Matches: 45, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
17 17 0.38
21 8 0.18
22 20 0.44
ACGTcount: A:0.76, C:0.19, G:0.01, T:0.04
Consensus pattern (21 bp):
AAAAAAAAAAAACCTAACCAA
Found at i:35907704 original size:16 final size:15
Alignment explanation
Indices: 35907680--35907714 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
35907670 TAATTATTAT
35907680 TATTCTAATATTTTGA
1 TATTCTAATATTTT-A
*
35907696 TATTTTAATATTTTA
1 TATTCTAATATTTTA
35907711 TATT
1 TATT
35907715 ATTCACATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (15 bp):
TATTCTAATATTTTA
Found at i:35919760 original size:74 final size:73
Alignment explanation
Indices: 35919661--35920227 Score: 852
Period size: 74 Copynumber: 7.7 Consensus size: 73
35919651 TGATGTTTTT
* * **
35919661 ATTTCTGTTTCAAAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGG
1 ATTTCTGTTTTAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGG
35919726 TAATTTCA
66 TAATTTCA
35919734 ATTTCTGTTGTTAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAG
1 ATTTCTGTT-TTAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAG
35919799 GTAATTTCA
65 GTAATTTCA
35919808 ATTTCTGTTGTTAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAG
1 ATTTCTGTT-TTAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAG
35919873 GTAATTTCA
65 GTAATTTCA
35919882 ATTTCTGTTGTTAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAG
1 ATTTCTGTT-TTAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAG
35919947 GTAATTTCA
65 GTAATTTCA
* * * * *
35919956 ATTTCTGTTTT-CAAAATTCAACTCGTATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGG
1 ATTTCTGTTTTAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGG
* *
35920020 TATTTTAA
66 TAATTTCA
* ** *
35920028 ATTTTTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGA
1 ATTTCTG-TTTT-AAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGA
35920093 GGTAATTTCA
64 GGTAATTTCA
* ** *
35920103 ATTTCTGTTTT-CAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTC-GAGACACGCTGAG
1 ATTTCTGTTTTAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAG-GACACGCTGAG
35920166 GTAATTTCA
65 GTAATTTCA
* ** *
35920175 ATTTCTGTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAG
1 ATTTCTGTTTTAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAG
35920228 ATCACACATG
Statistics
Matches: 458, Mismatches: 29, Indels: 13
0.92 0.06 0.03
Matches are distributed among these distances:
71 1 0.00
72 127 0.28
73 51 0.11
74 222 0.48
75 57 0.12
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (73 bp):
ATTTCTGTTTTAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGG
TAATTTCA
Found at i:35922160 original size:16 final size:15
Alignment explanation
Indices: 35922136--35922170 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
35922126 TAATTATTAT
35922136 TATTCTAATATTTTGA
1 TATTCTAATATTTT-A
*
35922152 TATTTTAATATTTTA
1 TATTCTAATATTTTA
35922167 TATT
1 TATT
35922171 ATTCACATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (15 bp):
TATTCTAATATTTTA
Found at i:35927556 original size:27 final size:27
Alignment explanation
Indices: 35927508--35927666 Score: 166
Period size: 27 Copynumber: 5.9 Consensus size: 27
35927498 GCGAGGCTGC
* *
35927508 CAGATATTGTGAC-GAAGTCACCAGATA
1 CAGATATTGTGGCAG-AGCCACCAGATA
* *
35927535 CAGATATTGTGGCGGAGCCACCA-AAA
1 CAGATATTGTGGCAGAGCCACCAGATA
*
35927561 CAGATTTATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
* *
35927588 CAGATAATTGTGGCATAGCCACCAG-GA
1 CAGAT-ATTGTGGCAGAGCCACCAGATA
35927615 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
*
35927642 CAGATATTTGTGGCATAGCCACCAG
1 CAGATA-TTGTGGCAGAGCCACCAG
35927667 GACGCTTCCT
Statistics
Matches: 112, Mismatches: 12, Indels: 16
0.80 0.09 0.11
Matches are distributed among these distances:
26 10 0.09
27 98 0.88
28 4 0.04
ACGTcount: A:0.33, C:0.22, G:0.25, T:0.20
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACCAGATA
Found at i:35927666 original size:54 final size:53
Alignment explanation
Indices: 35927526--35927669 Score: 216
Period size: 54 Copynumber: 2.7 Consensus size: 53
35927516 GTGACGAAGT
** ** *
35927526 CACCAGATACAGATATTGTGGCGGAGCCACCAAAACAGATTTATGTGGCAGAGC
1 CACCAGAT-CAGATATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
35927580 CACCAGATCAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
1 CACCAGATCAGAT-ATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
35927634 CACCAGATCAGATATTTGTGGCATAGCCACCAGGAC
1 CACCAGATCAGATA-TTGTGGCATAGCCACCAGGAC
35927670 GCTTCCTCCA
Statistics
Matches: 83, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
53 6 0.07
54 77 0.93
ACGTcount: A:0.33, C:0.24, G:0.25, T:0.19
Consensus pattern (53 bp):
CACCAGATCAGATATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
Found at i:35940628 original size:16 final size:16
Alignment explanation
Indices: 35940607--35940663 Score: 105
Period size: 16 Copynumber: 3.6 Consensus size: 16
35940597 TTTGGTTCGC
35940607 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
35940623 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
35940639 TGTAATGGATTAGAGG
1 TGTATTGGATTAGAGG
35940655 TGTATTGGA
1 TGTATTGGA
35940664 ATATTGGAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.26, C:0.00, G:0.37, T:0.37
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:35940935 original size:16 final size:16
Alignment explanation
Indices: 35940898--35940939 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
35940888 TTAATCATAT
*
35940898 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
35940914 TT-AAATATATTATAA
1 TTAAAATATATTATAA
35940929 TTAAAATATAT
1 TTAAAATATAT
35940940 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:35940946 original size:14 final size:15
Alignment explanation
Indices: 35940907--35940948 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
35940897 TTTAAACATA
*
35940907 ATTATTATTAAATAT
1 ATTATAATTAAATAT
35940922 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
35940936 A-TATAATTTAATA
1 ATTATAATTAAATA
35940949 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:35940964 original size:15 final size:16
Alignment explanation
Indices: 35940944--35940973 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
35940934 ATATATAATT
35940944 TAATAAA-ATTCTTAA
1 TAATAAATATTCTTAA
35940959 TAATAAATATTCTTA
1 TAATAAATATTCTTA
35940974 TATGAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (16 bp):
TAATAAATATTCTTAA
Found at i:35940998 original size:61 final size:61
Alignment explanation
Indices: 35940933--35941120 Score: 197
Period size: 61 Copynumber: 3.1 Consensus size: 61
35940923 TTATAATTAA
35940933 AATATATAATTTAATAAAATTCTTAATAATAAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATAAATATTCTTATATGAATTTACTCAAATCAT
* * * * * * * * ** * *
35940994 AATATATGATACT-ATAAAA-T-ATAA-ATTAACATAATTATTAT-TAAATATATTTTAATTAA
1 AATATATAAT-TTAATAAAATTCTTAATAATAA-AT-ATTCTTATATGAATTTACTCAAATCAT
*
35941053 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATAAATATTCTTATATGAATTTACTCAAATCAT
35941114 AATATAT
1 AATATAT
35941121 GATACTATAA
Statistics
Matches: 94, Mismatches: 25, Indels: 16
0.70 0.19 0.12
Matches are distributed among these distances:
58 5 0.05
59 31 0.33
60 16 0.17
61 38 0.40
62 4 0.04
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (61 bp):
AATATATAATTTAATAAAATTCTTAATAATAAATATTCTTATATGAATTTACTCAAATCAT
Found at i:35941050 original size:120 final size:120
Alignment explanation
Indices: 35940901--35941130 Score: 442
Period size: 120 Copynumber: 1.9 Consensus size: 120
35940891 ATCATATTTA
35940901 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATAAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATAAA
35940966 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
* *
35941021 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATAAA
35941086 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAA
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAA
35941131 TTTACTCAAA
Statistics
Matches: 108, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 108 1.00
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.43
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATAAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
Found at i:35941059 original size:18 final size:17
Alignment explanation
Indices: 35941038--35941072 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
35941028 TTATTATTAA
*
35941038 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
35941056 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
35941073 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:35946934 original size:43 final size:41
Alignment explanation
Indices: 35946854--35946938 Score: 102
Period size: 43 Copynumber: 2.0 Consensus size: 41
35946844 TTTATAAATT
35946854 TAATAACAAAAATAAAAAATTTTTCAATTGTCAATATAATA
1 TAATAACAAAAATAAAAAATTTTTCAATTGTCAATATAATA
* *
35946895 TAATAATAAATAATAAATAATATTTTCATTATT-TC-ATATAATA
1 TAATAACAAA-AATAAAAAAT-TTTTCA--ATTGTCAATATAATA
35946938 T
1 T
35946939 CATACAATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
41 9 0.24
42 9 0.24
43 15 0.39
44 2 0.05
45 3 0.08
ACGTcount: A:0.53, C:0.06, G:0.01, T:0.40
Consensus pattern (41 bp):
TAATAACAAAAATAAAAAATTTTTCAATTGTCAATATAATA
Found at i:35958253 original size:51 final size:50
Alignment explanation
Indices: 35958198--35958357 Score: 248
Period size: 51 Copynumber: 3.2 Consensus size: 50
35958188 TTAATCACAT
35958198 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCT-AAGCTACCACTTATCAC
* *
35958249 TTATCACTTGTCACTGATCAGATAAGAGTAGCTAAGCTACCACTTATCAT
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAGCTACCACTTATCAC
* * *
35958299 TTGTCACTTATCACTGATCAGATAAGTGTAGCTGAGGCTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCT-AAGCTACCACTTATCAC
*
35958350 TTGTCACT
1 TTATCACT
35958358 GATCAGAAGT
Statistics
Matches: 101, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
50 46 0.46
51 55 0.54
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (50 bp):
TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAGCTACCACTTATCAC
Found at i:35962504 original size:13 final size:14
Alignment explanation
Indices: 35962488--35962523 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
35962478 CAATCTCATA
35962488 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
35962501 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
35962514 TCTC-ATTTCA
1 TCTCAATTTCA
35962524 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:35962513 original size:18 final size:19
Alignment explanation
Indices: 35962475--35962515 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
35962465 TGGTTCATGT
35962475 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
35962494 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
35962512 TTTC
1 TTTC
35962516 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:35963038 original size:18 final size:19
Alignment explanation
Indices: 35963012--35963050 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
35963002 TTTCAATTCA
35963012 ATTCAAATAATCAATATAT
1 ATTCAAATAATCAATATAT
*
35963031 ATTC-AATATTCAATATAT
1 ATTCAAATAATCAATATAT
35963049 AT
1 AT
35963051 ATCTATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTCAAATAATCAATATAT
Found at i:35964375 original size:5 final size:5
Alignment explanation
Indices: 35964365--35964421 Score: 62
Period size: 5 Copynumber: 11.0 Consensus size: 5
35964355 TTACTTATTT
* *
35964365 ATATA ATATAA TATATA ATATA ATATA CTATA ATATA ATAATA ATTTA
1 ATATA ATAT-A -ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA
35964413 ATAT- ATATA
1 ATATA ATATA
35964422 TTTTAACACA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 7 0.16
7 4 0.09
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:35964381 original size:12 final size:12
Alignment explanation
Indices: 35964364--35964419 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
35964354 TTTACTTATT
35964364 TATATAATATAA
1 TATATAATATAA
35964376 TATATAATATAATA
1 TATATAATAT-A-A
35964390 TACTATAATATAA
1 TA-TATAATATAA
*
35964403 TA-ATAATTTAA
1 TATATAATATAA
35964414 TATATA
1 TATATA
35964420 TATTTTAACA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 10 0.26
12 13 0.33
13 4 0.10
14 4 0.10
15 8 0.21
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (12 bp):
TATATAATATAA
Found at i:35964434 original size:26 final size:26
Alignment explanation
Indices: 35964366--35964421 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
35964356 TACTTATTTA
*
35964366 TATAATATAATATATAATATAATATAC
1 TATAATATAACA-ATAATATAATATAC
* *
35964393 TATAATATAATAATAATTTAATATA-
1 TATAATATAACAATAATATAATATAC
35964418 TATA
1 TATA
35964422 TTTTAACACA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
25 4 0.14
26 12 0.43
27 12 0.43
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (26 bp):
TATAATATAACAATAATATAATATAC
Found at i:35966155 original size:24 final size:22
Alignment explanation
Indices: 35966128--35966194 Score: 62
Period size: 24 Copynumber: 2.8 Consensus size: 22
35966118 ACGAACACCT
35966128 AAAAACCTAGAAATTTAAAAACAG
1 AAAAACCTA-AAATTTAAAAA-AG
* *
35966152 AAAAACCTCCAAAAATTAAAAAAT
1 AAAAACCT--AAAATTTAAAAAAG
*
35966176 AAAAACCCAAAAATTTAAA
1 AAAAA-CCTAAAATTTAAA
35966195 TTAAATTAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
23 9 0.25
24 14 0.39
25 12 0.33
26 1 0.03
ACGTcount: A:0.66, C:0.15, G:0.03, T:0.16
Consensus pattern (22 bp):
AAAAACCTAAAATTTAAAAAAG
Found at i:35967357 original size:18 final size:17
Alignment explanation
Indices: 35967335--35967375 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
35967325 TTCTTATAAT
*
35967335 TTTTTTTATAATTTATA
1 TTTTTTTATAAATTATA
*
35967352 TGTTTTTTCTAAATTATA
1 T-TTTTTTATAAATTATA
35967370 TTTTTT
1 TTTTTT
35967376 CTAAATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (17 bp):
TTTTTTTATAAATTATA
Found at i:35968094 original size:20 final size:19
Alignment explanation
Indices: 35968052--35968109 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 19
35968042 TTGGAGTTTA
*
35968052 AATTGAGTTAAACAACAAAG
1 AATTGATTTAAACAA-AAAG
35968072 AATTGATTTAAACAAAAATG
1 AATTGATTTAAACAAAAA-G
* *
35968092 AATCGATTTGAACAAAAA
1 AATTGATTTAAACAAAAA
35968110 AAGAATCAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 3 0.09
20 31 0.91
ACGTcount: A:0.55, C:0.09, G:0.12, T:0.24
Consensus pattern (19 bp):
AATTGATTTAAACAAAAAG
Found at i:35968115 original size:21 final size:20
Alignment explanation
Indices: 35968059--35968116 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
35968049 TTAAATTGAG
* *
35968059 TTAAACAACAAAGAATTGAT
1 TTAAACAAAAAAGAATCGAT
*
35968079 TTAAACAAAAATGAATCGAT
1 TTAAACAAAAAAGAATCGAT
*
35968099 TTGAACAAAAAAAGAATC
1 TTAAAC-AAAAAAGAATC
35968117 AATTCAACAG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 22 0.69
21 10 0.31
ACGTcount: A:0.57, C:0.10, G:0.10, T:0.22
Consensus pattern (20 bp):
TTAAACAAAAAAGAATCGAT
Found at i:35968410 original size:14 final size:15
Alignment explanation
Indices: 35968391--35968425 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
35968381 TTTAATTTTC
*
35968391 AAAATTTCAAAAA-A
1 AAAATTTAAAAAATA
35968405 AAAATTTAAAAAATA
1 AAAATTTAAAAAATA
35968420 AAAATT
1 AAAATT
35968426 GCATTTTGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAATTTAAAAAATA
Found at i:35968484 original size:30 final size:29
Alignment explanation
Indices: 35968421--35968522 Score: 116
Period size: 30 Copynumber: 3.4 Consensus size: 29
35968411 TAAAAAATAA
* *
35968421 AAATTGCATTTTGACCCCTAAACTTT-TCCT
1 AAATTTCATTTTGA-CCCTAAACTTTCT-TT
35968451 AAATTTCATTTTGACCCTTAAACTTTCTTT
1 AAATTTCATTTTGACCC-TAAACTTTCTTT
* * *
35968481 AAATTTCACTTAGACTCCTAAACTTTCATT
1 AAATTTCATTTTGAC-CCTAAACTTTCTTT
35968511 AAATTTCATTTT
1 AAATTTCATTTT
35968523 AATCCTAATT
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
29 3 0.05
30 56 0.90
31 3 0.05
ACGTcount: A:0.29, C:0.22, G:0.04, T:0.45
Consensus pattern (29 bp):
AAATTTCATTTTGACCCTAAACTTTCTTT
Found at i:35968896 original size:3 final size:3
Alignment explanation
Indices: 35968890--35968924 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
35968880 GTGTAGGAGG
35968890 AGA AGA AGA AGA AGA AGA AGA AGAA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AG-A AGA AGA AGA A
35968925 AGAAAAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:35981164 original size:70 final size:70
Alignment explanation
Indices: 35980966--35981433 Score: 373
Period size: 70 Copynumber: 6.8 Consensus size: 70
35980956 CTTTACAAGG
35980966 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
35981031 TTAAA
66 TTAAA
* * **
35981036 AGAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCCAGACACGTTGAGGTATTTTTACCTTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
35981101 TTAAA
66 TTAAA
* * ** * ** *
35981106 AAAATCAACTCCTATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTT-AGTTTA
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTT-
*
35981170 TGTT--T
65 T-TTAAA
* ** ** * *** * *
35981175 TAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCT--TTTC-C-TT----T-TTGTT---TTTC
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
*
35981228 A----
66 TTAAA
* * * * *
35981229 -AAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATT-T
35981293 GTTGTCAAAAA
65 -TT-T---AAA
* *
35981304 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAA-ATTT
**
35981369 GCTTTTCA
65 --TTTAAA
* *
35981377 AAATTCAATTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTT
35981434 CAATTTCTGT
Statistics
Matches: 320, Mismatches: 51, Indels: 51
0.76 0.12 0.12
Matches are distributed among these distances:
53 30 0.09
55 1 0.00
56 1 0.00
57 1 0.00
58 3 0.01
60 4 0.01
61 2 0.01
62 2 0.01
65 2 0.01
66 2 0.01
67 1 0.00
69 33 0.10
70 117 0.37
71 2 0.01
73 56 0.17
76 58 0.18
77 5 0.02
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (70 bp):
AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
TTAAA
Found at i:35981354 original size:76 final size:76
Alignment explanation
Indices: 35981228--35981532 Score: 395
Period size: 73 Copynumber: 4.0 Consensus size: 76
35981218 TTTGTTTTTC
* * *
35981228 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCT
*
35981293 GTTGTCAAAAA
66 GTTTTCAAAAA
*
35981304 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCT
35981369 GCTTTTC----A
66 G-TTTTCAAAAA
* *
35981377 AAATTCAATTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCT
35981442 GTTTTCAAAAAAA
66 GTTTTC--AAAAA
* ** * * *
35981455 AAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTC-GGTTCACATGCTGAGGTATTTTCAATT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAG---ACACGTTGAGGTATTTTCAATT
*
35981519 TCTGTTTTTAAAAA
63 TCTGTTTTCAAAAA
35981533 NNNNNNNNNN
Statistics
Matches: 202, Mismatches: 17, Indels: 18
0.85 0.07 0.08
Matches are distributed among these distances:
72 5 0.02
73 64 0.32
76 62 0.31
77 5 0.02
78 38 0.19
80 28 0.14
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (76 bp):
AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCT
GTTTTCAAAAA
Done.