Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397265.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_146.0, whole genome shotgun sequence
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: 8065533
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 116430 characters in sequence are not A, C, G, or T
File 12 of 18
Found at i:5014211 original size:136 final size:138
Alignment explanation
Indices: 5013967--5014240 Score: 326
Period size: 136 Copynumber: 2.0 Consensus size: 138
5013957 ATAATTTATT
* * * ** **
5013967 TAAAATATTAATAATTGATACTTTAAATATTAATTTTTTATTTATAATTTAATCATTAATGTTTT
1 TAAAATATTAATAATTGATAATTTAAATATTAATATTTTATTTAAAATTTAATCATTAACATCAT
* *
5014032 AAAATATTAATATTTTTTTAATGTAAATACTATTATGATTATTTATT-TTTATT-TTATT-TTTT
66 AAAATATTAATATTCTTATAATGTAAATACTATTATGATTATTTATTATTTATTGTT-TTATTTT
5014094 AAATATTAA
130 AAATATTAA
* *
5014103 TAAAATATTAATAATTGATAATTTACATATTAATATTTTCTTTAAAATTTAATCATTAACATCAT
1 TAAAATATTAATAATTGATAATTTAAATATTAATATTTTATTTAAAATTTAATCATTAACATCAT
* * * *
5014168 AAAATATTATTAATTAACTTATAAT-TTAA-A-TGTTATTATTATTTATTATTTATTGTTTTAGT
66 AAAATATTAAT-ATT--CTTATAATGTAAATACTATTATGATTATTTATTATTTATTGTTTTA-T
5014230 TTTAAATATTA
127 TTTAAATATTA
5014241 GTAATTTATA
Statistics
Matches: 116, Mismatches: 15, Indels: 11
0.82 0.11 0.08
Matches are distributed among these distances:
136 81 0.70
137 12 0.10
138 5 0.04
139 18 0.16
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (138 bp):
TAAAATATTAATAATTGATAATTTAAATATTAATATTTTATTTAAAATTTAATCATTAACATCAT
AAAATATTAATATTCTTATAATGTAAATACTATTATGATTATTTATTATTTATTGTTTTATTTTA
AATATTAA
Found at i:5016330 original size:4 final size:4
Alignment explanation
Indices: 5016317--5016350 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
5016307 ACATACATAG
*
5016317 ATGT ACGT ATGT ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
5016351 ATATATATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.26, C:0.03, G:0.24, T:0.47
Consensus pattern (4 bp):
ATGT
Found at i:5019242 original size:25 final size:27
Alignment explanation
Indices: 5019187--5019248 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 27
5019177 AAAATATAAA
5019187 TAAA-TAAATTTTTATTTTCTATCATAT
1 TAAATTAAATTTTTATTTTCTAT-ATAT
5019214 TAAATTAAATTTTTATATTTC-AT-T-T
1 TAAATTAAATTTTTAT-TTTCTATATAT
5019239 TAAATTAAAT
1 TAAATTAAAT
5019249 ATATTTTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
25 11 0.33
26 1 0.03
27 4 0.12
28 13 0.39
29 4 0.12
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (27 bp):
TAAATTAAATTTTTATTTTCTATATAT
Found at i:5019817 original size:2 final size:2
Alignment explanation
Indices: 5019810--5019834 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5019800 ATGCCAATTC
5019810 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5019835 GGTGAATTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5022715 original size:27 final size:27
Alignment explanation
Indices: 5022685--5022742 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
5022675 GTGACATGGC
* * *
5022685 GAAATATGACGAGTTGAATGTCCTGGT
1 GAAAGATGACAAGTTGAATATCCTGGT
* * *
5022712 GAAAGATGGCAATTTGAATATCGTGGT
1 GAAAGATGACAAGTTGAATATCCTGGT
5022739 GAAA
1 GAAA
5022743 CACAACAAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.34, C:0.09, G:0.29, T:0.28
Consensus pattern (27 bp):
GAAAGATGACAAGTTGAATATCCTGGT
Found at i:5028583 original size:16 final size:16
Alignment explanation
Indices: 5028538--5028569 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5028528 GGGTGGAGAA
*
5028538 CTGGAGATTGGAGAGT
1 CTGGAGAGTGGAGAGT
5028554 CTGGAGAGTGGAGAGT
1 CTGGAGAGTGGAGAGT
5028570 GGAGAGTATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.06, G:0.47, T:0.22
Consensus pattern (16 bp):
CTGGAGAGTGGAGAGT
Found at i:5028590 original size:23 final size:23
Alignment explanation
Indices: 5028531--5028590 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
5028521 GAGAAGAGGG
* *
5028531 TGGAGAACTGGAGATTGGAGAGTC
1 TGGAG-ACTGGAGAGTGGAGAGTA
*
5028555 TGGAGAGTGGAGAGTGGAGAGTA
1 TGGAGACTGGAGAGTGGAGAGTA
*
5028578 TGGAGACTAGAGA
1 TGGAGACTGGAGA
5028591 TAAGACGGCA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
23 26 0.84
24 5 0.16
ACGTcount: A:0.32, C:0.05, G:0.45, T:0.18
Consensus pattern (23 bp):
TGGAGACTGGAGAGTGGAGAGTA
Found at i:5029402 original size:24 final size:24
Alignment explanation
Indices: 5029384--5029429 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
5029374 TTATATATTT
5029384 TATTTTATTTCTTATTATAATACA
1 TATTTTATTTCTTATTATAATACA
*
5029408 TATTTTATTTTTTATTATAATA
1 TATTTTATTTCTTATTATAATA
5029430 TAAAATTAGT
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:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (24 bp):
TATTTTATTTCTTATTATAATACA
Found at i:5030871 original size:6 final size:6
Alignment explanation
Indices: 5030850--5030893 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
5030840 TAGCTATATT
* * *
5030850 AACATA ACATATA AACATA AACATA ATCATA AACATA AATATA A
1 AACATA A-ACATA AACATA AACATA AACATA AACATA AACATA A
5030894 GAGCGACTCG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
6 27 0.84
7 5 0.16
ACGTcount: A:0.64, C:0.14, G:0.00, T:0.23
Consensus pattern (6 bp):
AACATA
Found at i:5033113 original size:29 final size:29
Alignment explanation
Indices: 5033068--5033155 Score: 106
Period size: 29 Copynumber: 3.0 Consensus size: 29
5033058 AATGTAATAA
*
5033068 AATA-TTTTTGAATATGGCGTATAACAAC
1 AATATTTTTTTAATATGGCGTATAACAAC
* * * *
5033096 AATATTTTTTTAACATGGTGTGTAATAAC
1 AATATTTTTTTAATATGGCGTATAACAAC
*
5033125 AATATTTTTTTTAATATGGCATATAACAAC
1 AATA-TTTTTTTAATATGGCGTATAACAAC
5033155 A
1 A
5033156 TTTTTTAACC
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
28 4 0.08
29 23 0.48
30 21 0.44
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (29 bp):
AATATTTTTTTAATATGGCGTATAACAAC
Found at i:5033175 original size:56 final size:54
Alignment explanation
Indices: 5033060--5033176 Score: 130
Period size: 59 Copynumber: 2.1 Consensus size: 54
5033050 GGCATTAAAA
* **
5033060 TGTAATAAAATATTTTTGAATATGGCGTATAACAACAATATTTTTTTAACATGGTG
1 TGTAATAAAATATTTTTGAATATGGCATATAACAAC-A-ATTTTTTTAACATGACG
*
5033116 TGTAATAACAATATTTTTTTTAATATGGCATATAACAAC-A-TTTTTTAACCATGACG
1 TGTAATAA-AATA--TTTTTGAATATGGCATATAACAACAATTTTTTTAA-CATGACG
5033172 TGTAA
1 TGTAA
5033177 CATGTTTTTG
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
55 8 0.15
56 19 0.36
57 4 0.08
59 22 0.42
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.41
Consensus pattern (54 bp):
TGTAATAAAATATTTTTGAATATGGCATATAACAACAATTTTTTTAACATGACG
Found at i:5033252 original size:21 final size:21
Alignment explanation
Indices: 5033226--5033274 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
5033216 TACAATAGCA
5033226 TGTAACAACTTAACCATGACG
1 TGTAACAACTTAACCATGACG
* *
5033247 TGTAACAACTTAATCATGGCG
1 TGTAACAACTTAACCATGACG
5033268 TGTAACA
1 TGTAACA
5033275 TGTTTTTGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (21 bp):
TGTAACAACTTAACCATGACG
Found at i:5038416 original size:158 final size:159
Alignment explanation
Indices: 5038124--5038436 Score: 475
Period size: 158 Copynumber: 2.0 Consensus size: 159
5038114 ATGTAAAGGA
* * * *
5038124 GGATATAGGTGGCTGGCTTTGGATCTCAGCACAGAGGCATGTGGAGGACTTTGTGAGTACACGTT
1 GGATATAGGAGGCTGGCTTTGGATCTCAGCACAGAGGCATGTGAAGGACTCTGTGAGTACACATT
* * * * *
5038189 TACTTGAATTATACATACCTTATAGTCACAAATATTGTTTCAAAACGGTTGAATTGCAAAAAAAA
66 TACTTGAATGATACATACCTGATAGTCACAAAAATTGTGTCAAAACAGTTGAATTGCAAAAAAAA
5038254 CAATGCCAGTTCATATTATTGTAGCTGAT
131 CAATGCCAGTTCATATTATTGTAGCTGAT
* * *
5038283 GGATATAGGAGGCTGGCTTTGGATCTCTGCATAGAGGCATGT-AAGGACTCTGTGTGTACACATT
1 GGATATAGGAGGCTGGCTTTGGATCTCAGCACAGAGGCATGTGAAGGACTCTGTGAGTACACATT
* * * *
5038347 TACTTGAATGATACATAGCTGATAGTCACAAAAATTGTGTCGAAACAGTTGAATTGCAAATAAAG
66 TACTTGAATGATACATACCTGATAGTCACAAAAATTGTGTCAAAACAGTTGAATTGCAAAAAAAA
5038412 CAATGCCAGTTCATATTATTGTAGC
131 CAATGCCAGTTCATATTATTGTAGC
5038437 CATGGAACCA
Statistics
Matches: 138, Mismatches: 16, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
158 99 0.72
159 39 0.28
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.31
Consensus pattern (159 bp):
GGATATAGGAGGCTGGCTTTGGATCTCAGCACAGAGGCATGTGAAGGACTCTGTGAGTACACATT
TACTTGAATGATACATACCTGATAGTCACAAAAATTGTGTCAAAACAGTTGAATTGCAAAAAAAA
CAATGCCAGTTCATATTATTGTAGCTGAT
Found at i:5042122 original size:27 final size:27
Alignment explanation
Indices: 5042081--5042156 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 27
5042071 ACATTATGCC
* * *
5042081 GTTCCAAGCATGGAAGTGCCCAGGGTT
1 GTTCCAAGTACGGAAGTGCCCAGGGGT
*
5042108 GTTCCAAGTACGGAAGTGCTCAGGGGT
1 GTTCCAAGTACGGAAGTGCCCAGGGGT
* * *
5042135 GTTCTAAGTGCGGAAATGCCCA
1 GTTCCAAGTACGGAAGTGCCCA
5042157 AGGCCATTCT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.24, C:0.21, G:0.33, T:0.22
Consensus pattern (27 bp):
GTTCCAAGTACGGAAGTGCCCAGGGGT
Found at i:5042299 original size:2 final size:2
Alignment explanation
Indices: 5042292--5042318 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5042282 AACAAATCTG
5042292 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
5042319 GCGTTGTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5046152 original size:60 final size:60
Alignment explanation
Indices: 5046074--5046214 Score: 228
Period size: 60 Copynumber: 2.4 Consensus size: 60
5046064 TTCATTTATC
* * *
5046074 AAATCCATTAATACAACAATTCAAACCTCATACATTAAGTTAGAGATAAAGCCAATTTCT
1 AAATCCATAAATGCAACAATTCAAACCTCATACATTAAGCTAGAGATAAAGCCAATTTCT
* *
5046134 AAATCCATAAATGCAACAATTCAAACCTCATACTTTAAGCTAGAGATAAAGCCAATTTTT
1 AAATCCATAAATGCAACAATTCAAACCTCATACATTAAGCTAGAGATAAAGCCAATTTCT
*
5046194 AAATCTATAAATGCAACAATT
1 AAATCCATAAATGCAACAATT
5046215 TTTTCTACAT
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 75 1.00
ACGTcount: A:0.45, C:0.19, G:0.07, T:0.28
Consensus pattern (60 bp):
AAATCCATAAATGCAACAATTCAAACCTCATACATTAAGCTAGAGATAAAGCCAATTTCT
Found at i:5046352 original size:15 final size:15
Alignment explanation
Indices: 5046332--5046361 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5046322 ACTAACTTTT
5046332 TCATAAACATGCAAA
1 TCATAAACATGCAAA
*
5046347 TCATAAACTTGCAAA
1 TCATAAACATGCAAA
5046362 ACTAAATTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.20, G:0.07, T:0.23
Consensus pattern (15 bp):
TCATAAACATGCAAA
Found at i:5048688 original size:30 final size:30
Alignment explanation
Indices: 5048652--5048708 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
5048642 AATGGTATTG
5048652 TGCATATATAAGAACTTTATTCTTATGTTT
1 TGCATATATAAGAACTTTATTCTTATGTTT
* *
5048682 TGCATATATAGGAACTTTCTTCTTATG
1 TGCATATATAAGAACTTTATTCTTATG
5048709 AGGACATGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (30 bp):
TGCATATATAAGAACTTTATTCTTATGTTT
Found at i:5051178 original size:8 final size:8
Alignment explanation
Indices: 5051165--5051189 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
5051155 AAGCTAAGAG
5051165 ATCAAAAC
1 ATCAAAAC
5051173 ATCAAAAC
1 ATCAAAAC
5051181 ATCAAAAC
1 ATCAAAAC
5051189 A
1 A
5051190 CAAGATAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.64, C:0.24, G:0.00, T:0.12
Consensus pattern (8 bp):
ATCAAAAC
Found at i:5070881 original size:21 final size:22
Alignment explanation
Indices: 5070841--5070882 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
5070831 ATTCTTACTT
**
5070841 TAATTAGTTAAAAGCCATCCTC
1 TAATTAGTTAAAAGAAATCCTC
5070863 TAATTAGTT-AAAGAAATCCT
1 TAATTAGTTAAAAGAAATCCT
5070883 TAAAGTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (22 bp):
TAATTAGTTAAAAGAAATCCTC
Found at i:5073093 original size:2 final size:2
Alignment explanation
Indices: 5073086--5073120 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5073076 CAAGCCCGAT
5073086 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5073121 GCTAAGTAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5074107 original size:45 final size:44
Alignment explanation
Indices: 5073995--5074107 Score: 100
Period size: 45 Copynumber: 2.5 Consensus size: 44
5073985 ATCTTATGTT
* * * **
5073995 TACCAAAATACCAAAAACACCCTTTATTATAATTTAATAATATTA
1 TACCAAAATACGAAATAC-CCTTTTAGAATAATTTAATAATATTA
** * * ** *
5074040 TGTCAAAAGATGAAATTTCCTTTTAGAATAATTTAATAATATTT
1 TACCAAAATACGAAATACCCTTTTAGAATAATTTAATAATATTA
5074084 TCACCAAAATACGAAATACCCTTT
1 T-ACCAAAATACGAAATACCCTTT
5074108 ATTATAATTT
Statistics
Matches: 49, Mismatches: 18, Indels: 2
0.71 0.26 0.03
Matches are distributed among these distances:
44 23 0.47
45 26 0.53
ACGTcount: A:0.44, C:0.16, G:0.04, T:0.35
Consensus pattern (44 bp):
TACCAAAATACGAAATACCCTTTTAGAATAATTTAATAATATTA
Found at i:5074115 original size:44 final size:44
Alignment explanation
Indices: 5074013--5074119 Score: 117
Period size: 44 Copynumber: 2.4 Consensus size: 44
5074003 TACCAAAAAC
** *
5074013 ACCCTTTATTATAATTTAATAATATTATGTCAAAAGATGAAATT
1 ACCCTTTATTATAATTTAATAATATTATACCAAAAGACGAAATT
* * ** * *
5074057 TCCTTTTAGAATAATTTAATAATATTTTCACCAAAATACGAAA-T
1 ACCCTTTATTATAATTTAATAATATTAT-ACCAAAAGACGAAATT
5074101 ACCCTTTATTATAATTTAA
1 ACCCTTTATTATAATTTAA
5074120 AAATTAAGAT
Statistics
Matches: 49, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
44 39 0.80
45 10 0.20
ACGTcount: A:0.42, C:0.12, G:0.05, T:0.41
Consensus pattern (44 bp):
ACCCTTTATTATAATTTAATAATATTATACCAAAAGACGAAATT
Found at i:5076372 original size:32 final size:31
Alignment explanation
Indices: 5076336--5076416 Score: 105
Period size: 29 Copynumber: 2.7 Consensus size: 31
5076326 TATTGTTAAT
**
5076336 TATAAAAATTTAATTTATTTTAAAATAAAAAA
1 TATAAAAATTTAATTTA-AATAAAATAAAAAA
*
5076368 TATAAAAATTTAA-TTAAATATAATAAAAAA
1 TATAAAAATTTAATTTAAATAAAATAAAAAA
5076398 -ATAAAAA-TTAATTTAAATA
1 TATAAAAATTTAATTTAAATA
5076417 TATGTAAATA
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
28 4 0.09
29 14 0.31
30 11 0.24
31 3 0.07
32 13 0.29
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (31 bp):
TATAAAAATTTAATTTAAATAAAATAAAAAA
Found at i:5076405 original size:29 final size:30
Alignment explanation
Indices: 5076336--5076432 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
5076326 TATTGTTAAT
** *
5076336 TATAAAAATTTAATTTATTTTAAAATAAAAAA
1 TATAAAAA-TTAATTTA-AATATAATAAAAAA
5076368 TATAAAAATTTAA-TTAAATATAATAAAAAA
1 TATAAAAA-TTAATTTAAATATAATAAAAAA
* *
5076398 -ATAAAAATTAATTTAAATATATGTAAATAA
1 TATAAAAATTAATTTAAATATA-ATAAAAAA
5076428 TATAA
1 TATAA
5076433 GAGGTTTTTA
Statistics
Matches: 57, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
28 4 0.07
29 16 0.28
30 17 0.30
31 7 0.12
32 13 0.23
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (30 bp):
TATAAAAATTAATTTAAATATAATAAAAAA
Found at i:5081584 original size:33 final size:33
Alignment explanation
Indices: 5081542--5081605 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
5081532 CAAATTTGCA
*
5081542 TGTCATATCATCATCAATTATGATATATTAGCT
1 TGTCATATCATCATCAATTATAATATATTAGCT
* *
5081575 TGTCATATCATTATCAATTATAATATTTTAG
1 TGTCATATCATCATCAATTATAATATATTAG
5081606 TATTTCAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.34, C:0.12, G:0.08, T:0.45
Consensus pattern (33 bp):
TGTCATATCATCATCAATTATAATATATTAGCT
Found at i:5083146 original size:2 final size:2
Alignment explanation
Indices: 5083139--5083163 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5083129 GGAAGACGAC
5083139 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5083164 AATCATATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5085288 original size:21 final size:22
Alignment explanation
Indices: 5085253--5085296 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
5085243 CTCTTAAATT
5085253 AATTTAAAATAAAATAACCTAA
1 AATTTAAAATAAAATAACCTAA
* *
5085275 AATTT-AACTAAAATAACTTAA
1 AATTTAAAATAAAATAACCTAA
5085296 A
1 A
5085297 TTAATCACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (22 bp):
AATTTAAAATAAAATAACCTAA
Found at i:5089049 original size:12 final size:13
Alignment explanation
Indices: 5089030--5089065 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
5089020 CAGAATAGTT
5089030 TCTTGCTGCCTCC
1 TCTTGCTGCCTCC
5089043 T-TTGCTGCCT-C
1 TCTTGCTGCCTCC
5089054 TCTTGCTGCCTC
1 TCTTGCTGCCTC
5089066 AAAAATCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 2 0.10
12 18 0.86
13 1 0.05
ACGTcount: A:0.00, C:0.42, G:0.17, T:0.42
Consensus pattern (13 bp):
TCTTGCTGCCTCC
Found at i:5089743 original size:21 final size:22
Alignment explanation
Indices: 5089708--5089751 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
5089698 CTCTTAAAGT
5089708 AATTTAAAATAAAATAACCTAA
1 AATTTAAAATAAAATAACCTAA
* *
5089730 AATTT-AACTAAAATAACTTAA
1 AATTTAAAATAAAATAACCTAA
5089751 A
1 A
5089752 TTAATCACTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (22 bp):
AATTTAAAATAAAATAACCTAA
Found at i:5095464 original size:2 final size:2
Alignment explanation
Indices: 5095457--5095481 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5095447 TCAAATTTAG
5095457 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5095482 ATTGAGTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5095900 original size:2 final size:2
Alignment explanation
Indices: 5095893--5095923 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5095883 TAAAGCTTAA
5095893 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5095924 ACATAATTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5096468 original size:23 final size:22
Alignment explanation
Indices: 5096442--5096505 Score: 60
Period size: 21 Copynumber: 2.9 Consensus size: 22
5096432 TACTATAATT
5096442 AAATAATATTTTCATCAAAATAC
1 AAATAATATTTTCATCAAAAT-C
* *
5096465 AAAT-ATATTTT-ATCATAATT
1 AAATAATATTTTCATCAAAATC
* *
5096485 TAATAATATTTTGCATTAAAA
1 AAATAATATTTT-CATCAAAA
5096506 GATGAATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
20 3 0.09
21 14 0.42
22 7 0.21
23 9 0.27
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.42
Consensus pattern (22 bp):
AAATAATATTTTCATCAAAATC
Found at i:5096493 original size:21 final size:22
Alignment explanation
Indices: 5096436--5096541 Score: 81
Period size: 22 Copynumber: 4.8 Consensus size: 22
5096426 AACTTTTACT
5096436 ATAATTAAATAATATTTTCATC
1 ATAATTAAATAATATTTTCATC
* *
5096458 AAAATACAAAT-ATATTTT-ATC
1 ATAAT-TAAATAATATTTTCATC
* *
5096479 ATAATTTAATAATATTTTGCATT
1 ATAATTAAATAATATTTT-CATC
* * * * * *
5096502 AAAAGATGAATAAAATTTTTATT
1 ATAA-TTAAATAATATTTTCATC
5096525 ATAATTAAATAATATTT
1 ATAATTAAATAATATTT
5096542 AATATTAAAA
Statistics
Matches: 64, Mismatches: 15, Indels: 10
0.72 0.17 0.11
Matches are distributed among these distances:
20 3 0.05
21 14 0.22
22 21 0.33
23 15 0.23
24 11 0.17
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (22 bp):
ATAATTAAATAATATTTTCATC
Found at i:5096529 original size:46 final size:43
Alignment explanation
Indices: 5096422--5096541 Score: 132
Period size: 43 Copynumber: 2.7 Consensus size: 43
5096412 AATAAAATCA
* * *
5096422 AAATAACTTTTACTATAATTAAATAATATTTTCATCAAAATAC
1 AAATAAATTTTATTATAATTAAATAATATTTTCATCAAAAGAC
* * * * *
5096465 AAATATATTTTATCATAATTTAATAATATTTTGCATTAAAAGAT
1 AAATAAATTTTATTATAATTAAATAATATTTT-CATCAAAAGAC
*
5096509 GAATAAAATTTTTATTATAATTAAATAATATTT
1 AAAT-AAA-TTTTATTATAATTAAATAATATTT
5096542 AATATTAAAA
Statistics
Matches: 62, Mismatches: 12, Indels: 3
0.81 0.16 0.04
Matches are distributed among these distances:
43 27 0.44
44 11 0.18
45 2 0.03
46 22 0.35
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (43 bp):
AAATAAATTTTATTATAATTAAATAATATTTTCATCAAAAGAC
Found at i:5096639 original size:10 final size:10
Alignment explanation
Indices: 5096624--5096686 Score: 60
Period size: 10 Copynumber: 6.4 Consensus size: 10
5096614 ATATTCAAAT
5096624 AATAATATTA
1 AATAATATTA
5096634 AATAATATT-
1 AATAATATTA
** *
5096643 GTTTATAGTTA
1 AATAATA-TTA
5096654 AATAATATT-
1 AATAATATTA
5096663 AAT-ATATTA
1 AATAATATTA
5096672 AATAATATTTA
1 AATAATA-TTA
5096683 AATA
1 AATA
5096687 TTTTTATTTC
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
8 5 0.12
9 10 0.24
10 16 0.38
11 11 0.26
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.44
Consensus pattern (10 bp):
AATAATATTA
Found at i:5096656 original size:20 final size:18
Alignment explanation
Indices: 5096623--5096680 Score: 71
Period size: 20 Copynumber: 3.1 Consensus size: 18
5096613 TATATTCAAA
5096623 TAATAATATTAAATAATAT
1 TAAT-ATATTAAATAATAT
**
5096642 TGTTTATAGTTAAATAATAT
1 T-AATATA-TTAAATAATAT
5096662 TAATATATTAAATAATAT
1 TAATATATTAAATAATAT
5096680 T
1 T
5096681 TAAATATTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
18 12 0.36
19 8 0.24
20 13 0.39
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
TAATATATTAAATAATAT
Found at i:5098565 original size:3 final size:3
Alignment explanation
Indices: 5098557--5098599 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
5098547 TATCTTATAG
** *
5098557 TAA TAA TAA TGG TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
5098600 TCAGTTCATG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:5098580 original size:18 final size:18
Alignment explanation
Indices: 5098557--5098599 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
5098547 TATCTTATAG
*
5098557 TAATAATAATGGTAATAA
1 TAATAATAATAGTAATAA
5098575 TAATAATAATAGTAATAA
1 TAATAATAATAGTAATAA
5098593 TAATAAT
1 TAATAAT
5098600 TCAGTTCATG
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:0.58, C:0.00, G:0.07, T:0.35
Consensus pattern (18 bp):
TAATAATAATAGTAATAA
Found at i:5109477 original size:17 final size:16
Alignment explanation
Indices: 5109455--5109507 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
5109445 ACAATACCCC
5109455 TCCCTTTCCTTCCCTTT
1 TCCC-TTCCTTCCCTTT
5109472 TCCCTTCC-TCACCTTCT
1 TCCCTTCCTTC-CCTT-T
* *
5109489 TCCCTCCCTTCCATTT
1 TCCCTTCCTTCCCTTT
5109505 TCC
1 TCC
5109508 ATCCTAAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
15 2 0.06
16 12 0.39
17 15 0.48
18 2 0.06
ACGTcount: A:0.04, C:0.51, G:0.00, T:0.45
Consensus pattern (16 bp):
TCCCTTCCTTCCCTTT
Found at i:5124705 original size:3 final size:3
Alignment explanation
Indices: 5124697--5124729 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
5124687 ATTGCATATA
5124697 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
5124730 TTTCTACATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:5132553 original size:84 final size:84
Alignment explanation
Indices: 5132402--5132570 Score: 277
Period size: 84 Copynumber: 2.0 Consensus size: 84
5132392 AGAGATAGCA
* *
5132402 AGGACAACTTCATTTATGATTTCATCATAGACAAATAGCTTAAAATTGATGACTCTAGTTCTGAT
1 AGGACAACTTCATTTATGATTTCATCATAGACAAATAGCTTAAAATTGATGACTCGAGTTCTAAT
*
5132467 TGCTTTGGAAGTTAGACCT
66 TGCTTTAGAAGTTAGACCT
* *
5132486 AGGAGAACTTCATTTATGATTTCATCATAGACAAATAGCTTGAAATTGATGACTCCGA-TTCTAA
1 AGGACAACTTCATTTATGATTTCATCATAGACAAATAGCTTAAAATTGATGACT-CGAGTTCTAA
5132550 TTGCTTTAGAAGTTAGACCT
65 TTGCTTTAGAAGTTAGACCT
5132570 A
1 A
5132571 TTATAAATGT
Statistics
Matches: 79, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
84 77 0.97
85 2 0.03
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (84 bp):
AGGACAACTTCATTTATGATTTCATCATAGACAAATAGCTTAAAATTGATGACTCGAGTTCTAAT
TGCTTTAGAAGTTAGACCT
Found at i:5134235 original size:21 final size:22
Alignment explanation
Indices: 5134200--5134243 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
5134190 CTCTTAAAGT
5134200 AATTTAAAATAAAATAACTTAA
1 AATTTAAAATAAAATAACTTAA
*
5134222 AATTT-AACTAAAATAACTTAA
1 AATTTAAAATAAAATAACTTAA
5134243 A
1 A
5134244 TTAATCACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (22 bp):
AATTTAAAATAAAATAACTTAA
Found at i:5144122 original size:28 final size:30
Alignment explanation
Indices: 5144063--5144125 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
5144053 TGCATTTACC
* **
5144063 TAAACTCTTATATTTTTATTTTGAGTCAAA
1 TAAACTCTTATACTTTTATTTAAAGTCAAA
*
5144093 TAAACTCTTGTACTTTT-TTTAAAGT-AAA
1 TAAACTCTTATACTTTTATTTAAAGTCAAA
5144121 TAAAC
1 TAAAC
5144126 CTTTATGACT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 8 0.28
29 6 0.21
30 15 0.52
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.46
Consensus pattern (30 bp):
TAAACTCTTATACTTTTATTTAAAGTCAAA
Found at i:5144229 original size:33 final size:33
Alignment explanation
Indices: 5144191--5144267 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 33
5144181 AATGTTAATG
* *
5144191 TGACATGCTAAAATATCATAATTAATTATGATA
1 TGACATGCTAAAATATCATAACTAATAATGATA
* * *
5144224 TGACATGTTAATATATCATAACTGATAATGATA
1 TGACATGCTAAAATATCATAACTAATAATGATA
* *
5144257 TAATATGCTAA
1 TGACATGCTAA
5144268 TTGACATGAT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.09, G:0.10, T:0.36
Consensus pattern (33 bp):
TGACATGCTAAAATATCATAACTAATAATGATA
Found at i:5148571 original size:21 final size:21
Alignment explanation
Indices: 5148543--5148588 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
5148533 TTAAGTGATT
5148543 AATTTAAGTTATTTTA-GTTA
1 AATTTAAGTTATTTTATGTTA
*
5148563 AATTGTAAGTTATTTTATTTTA
1 AATT-TAAGTTATTTTATGTTA
5148585 AATT
1 AATT
5148589 ACTTTAAGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.17
21 12 0.52
22 7 0.30
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.57
Consensus pattern (21 bp):
AATTTAAGTTATTTTATGTTA
Found at i:5150072 original size:12 final size:12
Alignment explanation
Indices: 5150057--5150084 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
5150047 AATCCACTAA
5150057 ACTGGACTGAAG
1 ACTGGACTGAAG
5150069 ACTGGACTGAAG
1 ACTGGACTGAAG
5150081 ACTG
1 ACTG
5150085 AATCATCTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.18, G:0.32, T:0.18
Consensus pattern (12 bp):
ACTGGACTGAAG
Found at i:5151538 original size:22 final size:22
Alignment explanation
Indices: 5151503--5151558 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
5151493 AGTCGCGCAA
* *
5151503 CGCTGCGGCACTACTTCTCCAG
1 CGCTGCAGCGCTACTTCTCCAG
5151525 CGCTGCAGCGCTACTTCTCCAG
1 CGCTGCAGCGCTACTTCTCCAG
5151547 CGCTGCAGCGCT
1 CGCTGCAGCGCT
5151559 GAGCTCTCTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.12, C:0.41, G:0.25, T:0.21
Consensus pattern (22 bp):
CGCTGCAGCGCTACTTCTCCAG
Found at i:5154752 original size:3 final size:3
Alignment explanation
Indices: 5154746--5154787 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
5154736 TCATACGTTC
5154746 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5154788 AACTTGAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:5159445 original size:21 final size:20
Alignment explanation
Indices: 5159420--5159468 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
5159410 GAATTTGAAA
*
5159420 AAATCTAATCAAATTCAAATC
1 AAATCTAACCAAATT-AAATC
5159441 AAATCTTAACCAAATTAAATC
1 AAATC-TAACCAAATTAAATC
5159462 AAATCTA
1 AAATCTA
5159469 TGTAAATCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 2 0.08
21 15 0.58
22 9 0.35
ACGTcount: A:0.53, C:0.18, G:0.00, T:0.29
Consensus pattern (20 bp):
AAATCTAACCAAATTAAATC
Found at i:5161739 original size:16 final size:16
Alignment explanation
Indices: 5161718--5161766 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
5161708 GTTTTCTAGT
5161718 ATTAACTAGGTTCATG
1 ATTAACTAGGTTCATG
5161734 ATTAAC-ATGGTTCATG
1 ATTAACTA-GGTTCATG
* * *
5161750 AATAGCTAAGTTCATG
1 ATTAACTAGGTTCATG
5161766 A
1 A
5161767 CTATATTAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
15 1 0.04
16 26 0.93
17 1 0.04
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (16 bp):
ATTAACTAGGTTCATG
Found at i:5162653 original size:30 final size:30
Alignment explanation
Indices: 5162595--5162653 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
5162585 ATCGATTAAT
* *
5162595 AAAAAGATAAGAAAATCCAATTAATGAAAA
1 AAAAAGAGAAGAAAATCCAATCAATGAAAA
5162625 AAAAAGAGAAGAAAATCCAA-CAATTGAAA
1 AAAAAGAGAAGAAAATCCAATCAA-TGAAA
5162654 GCTAATTACC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 2 0.08
30 24 0.92
ACGTcount: A:0.66, C:0.08, G:0.12, T:0.14
Consensus pattern (30 bp):
AAAAAGAGAAGAAAATCCAATCAATGAAAA
Found at i:5162725 original size:14 final size:15
Alignment explanation
Indices: 5162697--5162725 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5162687 GTTTCAATGT
5162697 GAATTACATAGAAAA
1 GAATTACATAGAAAA
5162712 GAATTACA-AGAAAA
1 GAATTACATAGAAAA
5162726 TATTTGCTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.62, C:0.07, G:0.14, T:0.17
Consensus pattern (15 bp):
GAATTACATAGAAAA
Found at i:5164575 original size:97 final size:99
Alignment explanation
Indices: 5164406--5164603 Score: 346
Period size: 97 Copynumber: 2.0 Consensus size: 99
5164396 ATAACCCGAA
* *
5164406 ATCACAAACCTAAATCAAAGTTTCATCCTAGGCAGAGTTATTATAAAAGAAATTTCTAACAGGAT
1 ATCACAAACCTAAATC-AAGTTTCATCCTAGGCAGAGTTATTACAAAAGAAATTTCTAACAGGAC
*
5164471 CAGAAATCATAATGAAGAGATAAAATGCAGCCTTT
65 CAGAAATCATAATGAAGAGATAAAATGCAACCTTT
5164506 ATCACAAACCTAAATC-A-TTTCATCCTAGGCAGAGTTATTACAAAAGAAATTTCTAACAGGACC
1 ATCACAAACCTAAATCAAGTTTCATCCTAGGCAGAGTTATTACAAAAGAAATTTCTAACAGGACC
5164569 AGAAATCATAATGAAGAGATAAAATGCAACCTTT
66 AGAAATCATAATGAAGAGATAAAATGCAACCTTT
5164603 A
1 A
5164604 CAACCCAGTT
Statistics
Matches: 95, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
97 78 0.82
98 1 0.01
100 16 0.17
ACGTcount: A:0.44, C:0.17, G:0.13, T:0.25
Consensus pattern (99 bp):
ATCACAAACCTAAATCAAGTTTCATCCTAGGCAGAGTTATTACAAAAGAAATTTCTAACAGGACC
AGAAATCATAATGAAGAGATAAAATGCAACCTTT
Found at i:5174299 original size:2 final size:2
Alignment explanation
Indices: 5174292--5174317 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5174282 TGGCAAACAC
5174292 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
5174318 TCAAAAGTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:5175593 original size:28 final size:27
Alignment explanation
Indices: 5175538--5175602 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 27
5175528 TTAATTTAAA
*
5175538 ATAAAAATATAAAAAAATTTAAATTATT
1 ATAATAAT-TAAAAAAATTTAAATTATT
*
5175566 TTAATAATTAAAAAATATTTTAAA-TATT
1 ATAATAATTAAAAAA-A-TTTAAATTATT
*
5175594 ATATTAATT
1 ATAATAATT
5175603 TTAAAATTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
27 7 0.23
28 18 0.58
29 6 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (27 bp):
ATAATAATTAAAAAAATTTAAATTATT
Found at i:5175830 original size:3 final size:3
Alignment explanation
Indices: 5175822--5175847 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5175812 TTCACTAAAA
5175822 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
5175848 ATGATCATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:5186665 original size:29 final size:26
Alignment explanation
Indices: 5186605--5186673 Score: 75
Period size: 26 Copynumber: 2.5 Consensus size: 26
5186595 AGGAGCATCG
* *
5186605 ATTTTTTTAAATTAATAAATAATAAT
1 ATTTTTTAAAATTAATAAAAAATAAT
*
5186631 AGTTTTTAAAATTAATAAAAAATAAAATT
1 ATTTTTTAAAATTAATAAAAAAT--AA-T
*
5186660 ATTTTTTAATATTA
1 ATTTTTTAAAATTA
5186674 TTATATTATT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
26 20 0.57
28 2 0.06
29 13 0.37
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (26 bp):
ATTTTTTAAAATTAATAAAAAATAAT
Found at i:5190591 original size:30 final size:30
Alignment explanation
Indices: 5190539--5190635 Score: 101
Period size: 30 Copynumber: 3.3 Consensus size: 30
5190529 ATTATTAATC
* *
5190539 ATAAAAA-TT-ATTAGATTCAAAATAAATAT
1 ATAAAAATTTAATTA-ATTTAAAATAAAAAT
* *
5190568 ATAATAATTTATTTAATTTAAAATAAAAAT
1 ATAAAAATTTAATTAATTTAAAATAAAAAT
** *
5190598 ATAAAAATTTAATTAA-ACACAATAAAAAT
1 ATAAAAATTTAATTAATTTAAAATAAAAAT
5190627 ATAAAAATT
1 ATAAAAATT
5190636 CGAATCTTCT
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
29 25 0.44
30 29 0.51
31 3 0.05
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (30 bp):
ATAAAAATTTAATTAATTTAAAATAAAAAT
Found at i:5197109 original size:17 final size:18
Alignment explanation
Indices: 5197087--5197121 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
5197077 GATAAAAAGT
*
5197087 AAAAAATTTAAA-TTTAA
1 AAAAAAATTAAAGTTTAA
5197104 AAAAAAATTAAAGTTTAA
1 AAAAAAATTAAAGTTTAA
5197122 TTATAGTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (18 bp):
AAAAAAATTAAAGTTTAA
Found at i:5202094 original size:117 final size:119
Alignment explanation
Indices: 5201883--5202120 Score: 347
Period size: 117 Copynumber: 2.0 Consensus size: 119
5201873 GGAATTATAC
* * **
5201883 TGGCTGTTTTGGCTGCTGTTATGGTAATAGTTTATCTTTTTGGGTTTAAGTGATCAGCCCCTTTA
1 TGGCTGTTTTGGCTGCTGTTATAGTAATAGTTTATCTTCTACGGTTTAAGTGATCAGCCCCTTTA
5201948 TTGGTCTCTGAAACCAAATTAATGTTTGCAATTAACTTTAAATATCAGGTTCAA
66 TTGGTCTCTGAAACCAAATTAATGTTTGCAATTAACTTTAAATATCAGGTTCAA
* *
5202002 TGGCTGTTTTGGCTGCTGTTATAG-AATAGTTTATCTTCTACGGTTTATGT-ATCAGCTCCTTCT
1 TGGCTGTTTTGGCTGCTGTTATAGTAATAGTTTATCTTCTACGGTTTAAGTGATCAGCCCCTT-T
* * * * *
5202065 -TTGTTTTCTGGAAGCAAATTAATGTTTGCAATTAACTTTAAATATCAGGTTTAA
65 ATTGGTCTCTGAAACCAAATTAATGTTTGCAATTAACTTTAAATATCAGGTTCAA
5202119 TG
1 TG
5202121 TAGTCAGATT
Statistics
Matches: 107, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
117 61 0.57
118 23 0.21
119 23 0.21
ACGTcount: A:0.24, C:0.14, G:0.19, T:0.43
Consensus pattern (119 bp):
TGGCTGTTTTGGCTGCTGTTATAGTAATAGTTTATCTTCTACGGTTTAAGTGATCAGCCCCTTTA
TTGGTCTCTGAAACCAAATTAATGTTTGCAATTAACTTTAAATATCAGGTTCAA
Found at i:5206620 original size:33 final size:32
Alignment explanation
Indices: 5206583--5206657 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 32
5206573 TATTATTAAT
*
5206583 AAAAATTAAATTAATAAATTAAAGTTA-ATTTA
1 AAAAATTAAATTAA-AAATTAAAGCTATATTTA
* *
5206615 CAAAAAATAAATTAAAATTTAAAGCTATATTTA
1 -AAAAATTAAATTAAAAATTAAAGCTATATTTA
5206648 AAATAATTAA
1 AAA-AATTAA
5206658 TGAATTATGG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
32 13 0.36
33 23 0.64
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.35
Consensus pattern (32 bp):
AAAAATTAAATTAAAAATTAAAGCTATATTTA
Found at i:5207150 original size:1 final size:1
Alignment explanation
Indices: 5207144--5207182 Score: 78
Period size: 1 Copynumber: 39.0 Consensus size: 1
5207134 TTTTATTCTT
5207144 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
5207183 TCAATTCATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:5208635 original size:23 final size:22
Alignment explanation
Indices: 5208609--5208675 Score: 57
Period size: 23 Copynumber: 3.0 Consensus size: 22
5208599 TAATATATAT
5208609 TTTTTATTTTAAAATAAATAAAA
1 TTTTTATTTTAAAAT-AATAAAA
* *
5208632 -TTTTATTATTAACAATTAT-AAT
1 TTTTTATT-TTAA-AATAATAAAA
*
5208654 TTTTTATTTTTAAATTAATAAA
1 TTTTTA-TTTTAAAATAATAAA
5208676 TATTATATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
22 13 0.37
23 17 0.49
24 5 0.14
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (22 bp):
TTTTTATTTTAAAATAATAAAA
Found at i:5212606 original size:2 final size:2
Alignment explanation
Indices: 5212599--5212629 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5212589 TACTTGTTTT
5212599 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5212630 TTATCTTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5214234 original size:28 final size:28
Alignment explanation
Indices: 5214194--5214250 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
5214184 AAGAACCAGA
**
5214194 TAAGATTTGAGTTAATTTTTATTTATCT
1 TAAGATTTGAGTTAATTTCCATTTATCT
*
5214222 TAAGATTTGAGTTGATTTCCATTTATCT
1 TAAGATTTGAGTTAATTTCCATTTATCT
5214250 T
1 T
5214251 GCGGTCTGTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.26, C:0.07, G:0.12, T:0.54
Consensus pattern (28 bp):
TAAGATTTGAGTTAATTTCCATTTATCT
Found at i:5220162 original size:25 final size:23
Alignment explanation
Indices: 5220134--5220187 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
5220124 ATCAATAATT
*
5220134 ATAAAAATAATTATAATAAAACAAA
1 ATAAAAAT-ATCA-AATAAAACAAA
* *
5220159 ATAATAATATCAAATATAACAAA
1 ATAAAAATATCAAATAAAACAAA
5220182 A-AAAAA
1 ATAAAAA
5220188 GTTCAAAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
22 4 0.16
23 11 0.44
24 3 0.12
25 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.22
Consensus pattern (23 bp):
ATAAAAATATCAAATAAAACAAA
Found at i:5232958 original size:20 final size:20
Alignment explanation
Indices: 5232925--5232963 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5232915 TGAAAATGAC
*
5232925 GAAATATATGGATACATTTG
1 GAAATATATCGATACATTTG
*
5232945 GAAATGTATCGATACATTT
1 GAAATATATCGATACATTT
5232964 AGTTTCTAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.08, G:0.18, T:0.36
Consensus pattern (20 bp):
GAAATATATCGATACATTTG
Found at i:5254203 original size:34 final size:34
Alignment explanation
Indices: 5254134--5254208 Score: 98
Period size: 34 Copynumber: 2.2 Consensus size: 34
5254124 TGATCCTATC
* * *
5254134 AAAAAGC-ATTGTGAAGGTTTCGTTTAATCCTGT
1 AAAAAGCTATTGTGAAGGTTTCGCTCAATCCCGT
* *
5254167 AAAAAGCTATTGTGAAGGTTTTGCTCGATCCCGT
1 AAAAAGCTATTGTGAAGGTTTCGCTCAATCCCGT
5254201 AAAAAGCT
1 AAAAAGCT
5254209 CATTTCCCGT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
33 7 0.19
34 29 0.81
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (34 bp):
AAAAAGCTATTGTGAAGGTTTCGCTCAATCCCGT
Found at i:5256238 original size:32 final size:32
Alignment explanation
Indices: 5256183--5256250 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
5256173 ACTAAGTTGT
* * * *
5256183 CTCTGTCTTTGAACCCAGTTTTTGGCAGTAGA
1 CTCTGTCTCTAAACCCAGGTTTTGACAGTAGA
* *
5256215 CTCTGTCTCTAAACTCAGGTTTTGACAGTAGC
1 CTCTGTCTCTAAACCCAGGTTTTGACAGTAGA
5256247 CTCT
1 CTCT
5256251 TAGTCGACTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.37
Consensus pattern (32 bp):
CTCTGTCTCTAAACCCAGGTTTTGACAGTAGA
Found at i:5257086 original size:3 final size:3
Alignment explanation
Indices: 5257074--5257114 Score: 73
Period size: 3 Copynumber: 13.3 Consensus size: 3
5257064 TTTTTCTTTC
5257074 TAT TATT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
5257115 TATTTATTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:5258390 original size:109 final size:109
Alignment explanation
Indices: 5258276--5258495 Score: 440
Period size: 109 Copynumber: 2.0 Consensus size: 109
5258266 AAATTATTTG
5258276 ATTGATTCATGGAAAAAGAGAATCAGAGAAAGGGTGAAAATAGTGTGCAAAGAGGAAAAAAAATG
1 ATTGATTCATGGAAAAAGAGAATCAGAGAAAGGGTGAAAATAGTGTGCAAAGAGGAAAAAAAATG
5258341 TTGATGCTTTGTGGTTGCTATAAAAATTATAAAAGTTAAGATAA
66 TTGATGCTTTGTGGTTGCTATAAAAATTATAAAAGTTAAGATAA
5258385 ATTGATTCATGGAAAAAGAGAATCAGAGAAAGGGTGAAAATAGTGTGCAAAGAGGAAAAAAAATG
1 ATTGATTCATGGAAAAAGAGAATCAGAGAAAGGGTGAAAATAGTGTGCAAAGAGGAAAAAAAATG
5258450 TTGATGCTTTGTGGTTGCTATAAAAATTATAAAAGTTAAGATAA
66 TTGATGCTTTGTGGTTGCTATAAAAATTATAAAAGTTAAGATAA
5258494 AT
1 AT
5258496 CAAACCGAAT
Statistics
Matches: 111, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
109 111 1.00
ACGTcount: A:0.46, C:0.05, G:0.24, T:0.26
Consensus pattern (109 bp):
ATTGATTCATGGAAAAAGAGAATCAGAGAAAGGGTGAAAATAGTGTGCAAAGAGGAAAAAAAATG
TTGATGCTTTGTGGTTGCTATAAAAATTATAAAAGTTAAGATAA
Found at i:5259253 original size:18 final size:20
Alignment explanation
Indices: 5259230--5259277 Score: 73
Period size: 18 Copynumber: 2.5 Consensus size: 20
5259220 TAAAAATATT
5259230 TAAATATTATTTAA-TAT-A
1 TAAATATTATTTAATTATAA
*
5259248 TTAATATTATTTAATTATAA
1 TAAATATTATTTAATTATAA
5259268 TAAATATTAT
1 TAAATATTAT
5259278 AAAGAATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 13 0.50
19 3 0.12
20 10 0.38
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TAAATATTATTTAATTATAA
Found at i:5259290 original size:32 final size:31
Alignment explanation
Indices: 5259250--5259324 Score: 114
Period size: 32 Copynumber: 2.4 Consensus size: 31
5259240 TTAATATATT
*
5259250 AATATTATTTAATTATAATAAATATTATAAAG
1 AATATTATTTAA-TATAATAAATATAATAAAG
*
5259282 AATATTATTTGAATATAATAAATGTAATAAAG
1 AATATTATTT-AATATAATAAATATAATAAAG
5259314 AATATTATTTA
1 AATATTATTTA
5259325 GTATTATTNN
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
31 1 0.03
32 37 0.93
33 2 0.05
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (31 bp):
AATATTATTTAATATAATAAATATAATAAAG
Found at i:5271275 original size:14 final size:14
Alignment explanation
Indices: 5271256--5271285 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5271246 ATATTTTTTG
5271256 TTTTTGTTTCGTTT
1 TTTTTGTTTCGTTT
*
5271270 TTTTTGTTTTGTTT
1 TTTTTGTTTCGTTT
5271284 TT
1 TT
5271286 ATTTAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.03, G:0.13, T:0.83
Consensus pattern (14 bp):
TTTTTGTTTCGTTT
Found at i:5271433 original size:17 final size:17
Alignment explanation
Indices: 5271411--5271451 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
5271401 CAAGTTTGGT
5271411 ATGACTCTACCTATGGG
1 ATGACTCTACCTATGGG
5271428 ATGACTCTACCTATGGG
1 ATGACTCTACCTATGGG
5271445 ATGACTC
1 ATGACTC
5271452 CATTAGGGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.29
Consensus pattern (17 bp):
ATGACTCTACCTATGGG
Found at i:5272403 original size:16 final size:16
Alignment explanation
Indices: 5272382--5272415 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5272372 TTTCCCTTTA
*
5272382 ATTTATTTTTATTATT
1 ATTTATTATTATTATT
*
5272398 ATTTATTATTATTTTT
1 ATTTATTATTATTATT
5272414 AT
1 AT
5272416 CGATGTGTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
ATTTATTATTATTATT
Found at i:5273378 original size:52 final size:53
Alignment explanation
Indices: 5273297--5273402 Score: 146
Period size: 52 Copynumber: 2.0 Consensus size: 53
5273287 TTTATTTTTT
*
5273297 TAAGTGCATTTTATATAACTAGACATTTA-T-CTTTCCTA-TTTTTTATTCTACC
1 TAAGTGCATTTTATATAACTAAACATTTATTCCTTT-CTATTTTTTTATT-TACC
**
5273349 TAAGTGCATTTTATATAACTAAATGTTTATTCCTTTCTATTTTTTTATTTACC
1 TAAGTGCATTTTATATAACTAAACATTTATTCCTTTCTATTTTTTTATTTACC
5273402 T
1 T
5273403 TTTCTCATAA
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
52 26 0.54
53 9 0.19
54 13 0.27
ACGTcount: A:0.26, C:0.15, G:0.06, T:0.53
Consensus pattern (53 bp):
TAAGTGCATTTTATATAACTAAACATTTATTCCTTTCTATTTTTTTATTTACC
Found at i:5281904 original size:27 final size:26
Alignment explanation
Indices: 5281874--5281927 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 26
5281864 TTACTTTAAC
*
5281874 ATAAGT-TAAAAGATCATTATCTACAAG
1 ATAAGTATAAAA-ATCATTA-CTAAAAG
5281901 ATAAGTATAAAAATCATTACTAAAAG
1 ATAAGTATAAAAATCATTACTAAAAG
5281927 A
1 A
5281928 AATTTTTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 7 0.28
27 13 0.52
28 5 0.20
ACGTcount: A:0.54, C:0.09, G:0.09, T:0.28
Consensus pattern (26 bp):
ATAAGTATAAAAATCATTACTAAAAG
Found at i:5289823 original size:16 final size:16
Alignment explanation
Indices: 5289804--5289837 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
5289794 AATATATCAT
*
5289804 TTTTTATTAATCTTAC
1 TTTTTATTAATCCTAC
5289820 TTTTTATTAATCCTAC
1 TTTTTATTAATCCTAC
5289836 TT
1 TT
5289838 AATAGATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.15, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTTATTAATCCTAC
Found at i:5291239 original size:4 final size:4
Alignment explanation
Indices: 5291218--5291265 Score: 57
Period size: 4 Copynumber: 12.2 Consensus size: 4
5291208 ATAGCATATG
5291218 AATA AATA GAAT- AA-A AATA AATA AATA AATA AATA AA-A ATATA AATA
1 AATA AATA -AATA AATA AATA AATA AATA AATA AATA AATA A-ATA AATA
5291265 A
1 A
5291266 TAATACAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
3 6 0.15
4 28 0.72
5 5 0.13
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:5291268 original size:23 final size:23
Alignment explanation
Indices: 5291218--5291265 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
5291208 ATAGCATATG
5291218 AATAAATAGAATAAAAATAAATA
1 AATAAATAGAATAAAAATAAATA
5291241 AATAAATA-AATAAAAAT--ATA
1 AATAAATAGAATAAAAATAAATA
5291261 AATAA
1 AATAA
5291266 TAATACAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 8 0.32
22 9 0.36
23 8 0.32
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (23 bp):
AATAAATAGAATAAAAATAAATA
Found at i:5291270 original size:18 final size:20
Alignment explanation
Indices: 5291213--5291265 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 20
5291203 AACTTATAGC
*
5291213 ATATGAATAAATAGAATAAAA
1 ATATAAATAAATA-AATAAAA
5291234 ATAAATAAATAAATAAATAAAA
1 AT--ATAAATAAATAAATAAAA
5291256 ATATAAATAA
1 ATATAAATAA
5291266 TAATACAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 8 0.28
21 2 0.07
22 9 0.31
23 10 0.34
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.25
Consensus pattern (20 bp):
ATATAAATAAATAAATAAAA
Found at i:5294993 original size:18 final size:18
Alignment explanation
Indices: 5294967--5295026 Score: 95
Period size: 18 Copynumber: 3.4 Consensus size: 18
5294957 TGATCTCTTA
5294967 AATGC-TCTCAATCTTCG
1 AATGCTTCTCAATCTTCG
5294984 AATGCTTCTCAATCTTCG
1 AATGCTTCTCAATCTTCG
* *
5295002 AGTGCTTCTCAATTTTCG
1 AATGCTTCTCAATCTTCG
5295020 AATGCTT
1 AATGCTT
5295027 TCGAATGAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
17 5 0.13
18 34 0.87
ACGTcount: A:0.22, C:0.25, G:0.13, T:0.40
Consensus pattern (18 bp):
AATGCTTCTCAATCTTCG
Found at i:5295391 original size:81 final size:79
Alignment explanation
Indices: 5295267--5295510 Score: 298
Period size: 81 Copynumber: 3.1 Consensus size: 79
5295257 AATATGATTT
* * * ** * *
5295267 TTATCTCTAAATTAATATAATTA-TTAGAGATAATTTAAATGACCAATAATTAAATTTTGATTGG
1 TTATCTCTAAATTATTTTAATTATTTAGAGATAAATTGGATGACCAATAACTAATTTTTGATTGG
*
5295331 TCAAAAATATGAAGA
66 TC-AAAATATAAAGA
5295346 TTATCTCTAAATTATTTTAATATATTTAGAGATAAATTGGATGACCAATAACTAATTTTTTGATT
1 TTATCTCTAAATTATTTTAAT-TATTTAGAGATAAATTGGATGACCAATAACTAA-TTTTTGATT
*
5295411 GGTCAAAATATAAATA
64 GGTCAAAATATAAAGA
* * *
5295427 TTATCTCTAAATTATTTTGATTTATTTAGAGAT-AACTGGATGACCAATAACTAATTTTTCATTG
1 TTATCTCTAAATTATTTT-AATTATTTAGAGATAAATTGGATGACCAATAACTAATTTTTGATTG
* *
5295491 GTC-CAAT-TAAATA
65 GTCAAAATATAAAGA
5295504 TTATCTC
1 TTATCTC
5295511 AAGGGATAAA
Statistics
Matches: 148, Mismatches: 13, Indels: 10
0.87 0.08 0.06
Matches are distributed among these distances:
77 13 0.09
78 3 0.02
79 31 0.21
80 22 0.15
81 65 0.44
82 14 0.09
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.41
Consensus pattern (79 bp):
TTATCTCTAAATTATTTTAATTATTTAGAGATAAATTGGATGACCAATAACTAATTTTTGATTGG
TCAAAATATAAAGA
Found at i:5296482 original size:2 final size:2
Alignment explanation
Indices: 5296475--5296508 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5296465 GCTATGTTAA
5296475 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5296509 CATACAAGCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5296954 original size:38 final size:38
Alignment explanation
Indices: 5296893--5297041 Score: 151
Period size: 40 Copynumber: 3.9 Consensus size: 38
5296883 ACGATAGCAC
* *
5296893 TTATTGATCCTTGGGGGTGCTCTTTAAAATAGCACACGAT
1 TTATT-ATCCTT-GAGGTGCTCTTTATAATAGCACACGAT
* **
5296933 TTATTATCCTTGAGATGCTCTTTATAATAGCACTTG-T
1 TTATTATCCTTGAGGTGCTCTTTATAATAGCACACGAT
* * *
5296970 TTATCAT--TGGGAGGTGCTCTTTATACTAGCACACGAT
1 TTATTATCCT-TGAGGTGCTCTTTATAATAGCACACGAT
*
5297007 TTATTATCCTTGGAGGGTGCTCTTTGTAATAGCAC
1 TTATTATCCTT-GA-GGTGCTCTTTATAATAGCAC
5297042 TTGTTGATCC
Statistics
Matches: 88, Mismatches: 15, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
35 1 0.01
36 21 0.24
37 14 0.16
38 20 0.23
39 9 0.10
40 23 0.26
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.39
Consensus pattern (38 bp):
TTATTATCCTTGAGGTGCTCTTTATAATAGCACACGAT
Found at i:5296994 original size:36 final size:36
Alignment explanation
Indices: 5296873--5297077 Score: 153
Period size: 36 Copynumber: 5.6 Consensus size: 36
5296863 ATCCTCAAAG
** * * *
5296873 GGTGCTCTTTACGATAGCACTTATTGATCCTTGGG-
1 GGTGCTCTTTATAATAGCACTTGTTTATCATTGGGA
* ** * *
5296908 GGTGCTCTTTAAAATAGCACACGATTTATTATCCT-TGA
1 GGTGCTCTTTATAATAGCACTTG-TTTATCAT--TGGGA
*
5296946 GATGCTCTTTATAATAGCACTTGTTTATCATTGGGA
1 GGTGCTCTTTATAATAGCACTTGTTTATCATTGGGA
* ** * *
5296982 GGTGCTCTTTATACTAGCACACGATTTATTATCCTTGGA
1 GGTGCTCTTTATAATAGCACTTG-TTTATCAT--TGGGA
* * *
5297021 GGGTGCTCTTTGTAATAGCACTTGTTGATCCTTGGGA
1 -GGTGCTCTTTATAATAGCACTTGTTTATCATTGGGA
*
5297058 GGTGCTCTTTATACTAGCAC
1 GGTGCTCTTTATAATAGCAC
5297078 ACAATTTACA
Statistics
Matches: 130, Mismatches: 31, Indels: 17
0.73 0.17 0.10
Matches are distributed among these distances:
35 19 0.15
36 44 0.34
37 19 0.15
38 20 0.15
39 9 0.07
40 19 0.15
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (36 bp):
GGTGCTCTTTATAATAGCACTTGTTTATCATTGGGA
Found at i:5297063 original size:76 final size:75
Alignment explanation
Indices: 5296871--5297085 Score: 317
Period size: 76 Copynumber: 2.9 Consensus size: 75
5296861 TTATCCTCAA
** * * *
5296871 AGGGTGCTCTTTACGATAGCACTTATTGATCCTTGGG-GGTGCTCTTTAAAATAGCACACGATTT
1 AGGGTGCTCTTTATAATAGCACTTGTTGATCCTTGGGAGGTGCTCTTTATACTAGCACACGATTT
5296935 ATTATCCTTG
66 ATTATCCTTG
* * *
5296945 A-GATGCTCTTTATAATAGCACTTGTTTATCATTGGGAGGTGCTCTTTATACTAGCACACGATTT
1 AGGGTGCTCTTTATAATAGCACTTGTTGATCCTTGGGAGGTGCTCTTTATACTAGCACACGATTT
5297009 ATTATCCTTGG
66 ATTATCCTT-G
* *
5297020 AGGGTGCTCTTTGTAATAGCACTTGTTGATCCTTGGGAGGTGCTCTTTATACTAGCACACAATTT
1 AGGGTGCTCTTTATAATAGCACTTGTTGATCCTTGGGAGGTGCTCTTTATACTAGCACACGATTT
5297085 A
66 A
5297086 CAATCACCAT
Statistics
Matches: 125, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
73 29 0.23
74 35 0.28
75 2 0.02
76 59 0.47
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.38
Consensus pattern (75 bp):
AGGGTGCTCTTTATAATAGCACTTGTTGATCCTTGGGAGGTGCTCTTTATACTAGCACACGATTT
ATTATCCTTG
Found at i:5298588 original size:30 final size:31
Alignment explanation
Indices: 5298525--5298597 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
5298515 GATAATTACA
* *
5298525 TTCAATTTAGTCCCTATATTATAGAATTTTG
1 TTCAATTTAATCCCTATACTATAGAATTTTG
* * *
5298556 TTCAATTTAATCCTTGTACTATATAA-TTTG
1 TTCAATTTAATCCCTATACTATAGAATTTTG
5298586 TTCAATTTAATC
1 TTCAATTTAATC
5298598 TTTATATTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 16 0.43
31 21 0.57
ACGTcount: A:0.30, C:0.14, G:0.07, T:0.49
Consensus pattern (31 bp):
TTCAATTTAATCCCTATACTATAGAATTTTG
Found at i:5303005 original size:15 final size:15
Alignment explanation
Indices: 5302985--5303027 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
5302975 TATTAATTTT
*
5302985 TAAAAATTAAAATCA
1 TAAAAAATAAAATCA
5303000 TAAAAAATAAAATCTA
1 TAAAAAATAAAATC-A
**
5303016 TGTAAAATAAAA
1 TAAAAAATAAAA
5303028 AAGAAGAACA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 13 0.54
16 11 0.46
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (15 bp):
TAAAAAATAAAATCA
Found at i:5313852 original size:13 final size:14
Alignment explanation
Indices: 5313829--5313857 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
5313819 ATGAAATAAA
5313829 AAAAAAGAAAGATG
1 AAAAAAGAAAGATG
5313843 AAAAAA-AAAGATG
1 AAAAAAGAAAGATG
5313856 AA
1 AA
5313858 GCTTTAAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (14 bp):
AAAAAAGAAAGATG
Found at i:5315358 original size:21 final size:21
Alignment explanation
Indices: 5315309--5315359 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
5315299 GTTACACCTC
5315309 CAAAACCTACGATTACATTTT
1 CAAAACCTACGATTACATTTT
*
5315330 CTAAAACCTTCGGA-TACATTTT
1 C-AAAACCTAC-GATTACATTTT
5315352 CAAAACCT
1 CAAAACCT
5315360 CTAGATACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 8 0.30
22 17 0.63
23 2 0.07
ACGTcount: A:0.37, C:0.25, G:0.06, T:0.31
Consensus pattern (21 bp):
CAAAACCTACGATTACATTTT
Found at i:5315366 original size:21 final size:22
Alignment explanation
Indices: 5315322--5315370 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
5315312 AACCTACGAT
*
5315322 TACATTTTCTAAAACCTTCGGA
1 TACATTTTCTAAAACCTTCAGA
5315344 TACATTTTC-AAAACC-TCTAGA
1 TACATTTTCTAAAACCTTC-AGA
5315365 TACATT
1 TACATT
5315371 CTTATGGCAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 2 0.08
21 14 0.56
22 9 0.36
ACGTcount: A:0.35, C:0.22, G:0.06, T:0.37
Consensus pattern (22 bp):
TACATTTTCTAAAACCTTCAGA
Found at i:5315402 original size:167 final size:166
Alignment explanation
Indices: 5315219--5315640 Score: 452
Period size: 167 Copynumber: 2.5 Consensus size: 166
5315209 AAAAGCTCTG
* * * *
5315219 GGTAAGTAGTATTAATAATTCTTTAAAGTTACATAGCCTAATTTTGAGATGAAGAGCAACCTTTT
1 GGTAACTAGCATTAATATTTCTTTAAAGTTACATAGCCTAATTTTAAGATGAAGAGCAACCTTTT
** * * * *
5315284 CTTTTAAAACCTTTAGTTACACCTCCAAAACCTACGATTACATTTTCTAAAACC-TTCGGATACA
66 CTTTTAAAACCTCAAG-TACACCTCCAAAACATACAAATACATTTTCTAAAACCTTTAGG-TACA
* *
5315348 TTTTCAAAACCTCTAGATACATTCTTATGGCACTTCCGA
129 TTTTCAAAACCTCTAGATACATTCTTATGACACCT-CGA
* *** ** ** *
5315387 -GTAATTAGCATTAATATTTCTTTAAAGTTTTGTAGCCTTGTTTTAAGATGGGGAGCAACATTTT
1 GGTAACTAGCATTAATATTTCTTTAAAGTTACATAGCCTAATTTTAAGATGAAGAGCAACCTTTT
* * * *
5315451 CTTTTAAAACCCTCAAGTATATCTCGAAAACATCCAAATACATTTTCTAAAACCTTTAGGTACAT
66 CTTTTAAAA-CCTCAAGTACACCTCCAAAACATACAAATACATTTTCTAAAACCTTTAGGTACAT
* * * *
5315516 TTTCAAAATCTCTTGGTACATTCTTATGACACCTCTA
130 TTTCAAAACCTCTAGATACATTCTTATGACACCTCGA
* * * * *
5315553 GGTAACTAGCATTAATATTTCTTTAAAGTTACATAACCTCATTTAAAAATAAAGAGCAACCTTTT
1 GGTAACTAGCATTAATATTTCTTTAAAGTTACATAGCCTAATTTTAAGATGAAGAGCAACCTTTT
*
5315618 TTTCTATAAAACCTCCAAGTACA
66 CTT-T-TAAAACCT-CAAGTACA
5315641 TCTTTAAAAT
Statistics
Matches: 205, Mismatches: 43, Indels: 11
0.79 0.17 0.04
Matches are distributed among these distances:
166 2 0.01
167 178 0.87
168 13 0.06
169 12 0.06
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (166 bp):
GGTAACTAGCATTAATATTTCTTTAAAGTTACATAGCCTAATTTTAAGATGAAGAGCAACCTTTT
CTTTTAAAACCTCAAGTACACCTCCAAAACATACAAATACATTTTCTAAAACCTTTAGGTACATT
TTCAAAACCTCTAGATACATTCTTATGACACCTCGA
Found at i:5315533 original size:21 final size:22
Alignment explanation
Indices: 5315489--5315537 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
5315479 AACATCCAAA
5315489 TACATTTTCTAAAACCTTTAGG
1 TACATTTTCTAAAACCTTTAGG
*
5315511 TACATTTTC-AAAATCTCTT-GG
1 TACATTTTCTAAAACCT-TTAGG
5315532 TACATT
1 TACATT
5315538 CTTATGACAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 14 0.56
22 11 0.44
ACGTcount: A:0.31, C:0.18, G:0.08, T:0.43
Consensus pattern (22 bp):
TACATTTTCTAAAACCTTTAGG
Found at i:5315947 original size:17 final size:17
Alignment explanation
Indices: 5315908--5315948 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
5315898 TTACCATAGT
*
5315908 TTTATTTTTAATTGTTA
1 TTTATTTTAAATTGTTA
5315925 -TTATTTTAAATT-TTA
1 TTTATTTTAAATTGTTA
5315940 CTTTATTTT
1 -TTTATTTT
5315949 GTTTTTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 3 0.14
16 11 0.52
17 7 0.33
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (17 bp):
TTTATTTTAAATTGTTA
Found at i:5317333 original size:35 final size:34
Alignment explanation
Indices: 5317244--5317339 Score: 85
Period size: 35 Copynumber: 2.9 Consensus size: 34
5317234 AAATATGTAG
* *
5317244 TTTTAAA-AT-ATAAGATTAT-ATAAAATAAGGA
1 TTTTAAAGATAATAAGATTATAATATAATAAGAA
* *
5317275 TTTTCAAGATAATAA-ATAAATAATGATAATAA-AA
1 TTTTAAAGATAATAAGAT-TATAAT-ATAATAAGAA
5317309 TTTTTAAAGATAATAAGATTATAATAATAAT
1 -TTTTAAAGATAATAAGATTATAAT-ATAAT
5317340 GAATATAGAG
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
31 6 0.12
32 4 0.08
33 6 0.12
34 3 0.06
35 30 0.59
36 2 0.04
ACGTcount: A:0.55, C:0.01, G:0.07, T:0.36
Consensus pattern (34 bp):
TTTTAAAGATAATAAGATTATAATATAATAAGAA
Found at i:5317368 original size:23 final size:21
Alignment explanation
Indices: 5317329--5317374 Score: 56
Period size: 23 Copynumber: 2.1 Consensus size: 21
5317319 TAATAAGATT
5317329 ATAATAATAATGAATATAGAGA
1 ATAATAATAATGAATATA-AGA
* *
5317351 ATAATCAATAGTGGATATAAGA
1 ATAAT-AATAATGAATATAAGA
5317373 AT
1 AT
5317375 TAGTAATATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.54, C:0.02, G:0.15, T:0.28
Consensus pattern (21 bp):
ATAATAATAATGAATATAAGA
Found at i:5317865 original size:280 final size:281
Alignment explanation
Indices: 5317358--5317920 Score: 719
Period size: 280 Copynumber: 2.0 Consensus size: 281
5317348 AGAATAATCA
* *
5317358 ATAGTGGATATAAGAATTAGTAATATGTCATGCACTGTCATCACATTTAAATGTCATGGCATGTA
1 ATAGTGGACATAAGAATTAGTAATATGTCATGCACTCTCATCACATTTAAATGTCATGGCATGTA
* ** *
5317423 AACATTACATGCACAAGTTCAAGCTCCAATGATGGCACTTTTCGAGAGTGCTTGTGAAGACGAAT
66 AACATTACATGCACAAGTTAAAGCTCCAATGATGGCACTTTTCGAGAGTGCTTGCCAAGACGAAG
* * *
5317488 TTCTTCAAAAAATTTTCTAGATGAAAGGATATTTTGAGTCCCACCAGTTCGATGGGAGAGCTCGA
131 TTCTTCAAAAAATTTCCTAGATGAAAGGATATTTTAAGTCCCACCAGTTCGATGGGAGAGCTAGA
* * * * **
5317553 AGGACATCCTTAATAAAAAGCTTATGCTCGTATTAGGTTCTACATTC-TTGAAAAATATTATTTT
196 AGGACATCCTTAATAAAAAGCGTATACTCGTATGAGATTCTACATTCATAAAAAAATATTATTTT
* * *
5317617 TAAATGCGAACGACTATCCCG
261 CAAAGGCGAACGACTACCCCG
* * *
5317638 ATAGTGGACATAAGAATTGGTAGTATGTCATGCACTACT-ATCGCATTTAAATGTCATGGCATGT
1 ATAGTGGACATAAGAATTAGTAATATGTCATGCACT-CTCATCACATTTAAATGTCATGGCATGT
* * * * * *
5317702 AGACATTACGTGCACGAGTTAAAGC-CTCGATGATGAG-ACTTTTTGAGGGTGCTTGCCAAGAC-
65 AAACATTACATGCACAAGTTAAAGCTC-CAATGATG-GCACTTTTCGAGAGTGCTTGCCAAGACG
* * *
5317764 AAGTTCTTTCAAAAAA-TTCCTAGGTGAAAGGATATCTTTAAGTCCCACTAGTAT-GATGGGAGG
128 AAGTTC-TTCAAAAAATTTCCTAGATGAAAGGATAT-TTTAAGTCCCACCAGT-TCGATGGGAGA
* *
5317827 GCTTAGAA-GACATCCTTAATAAAAGGCGTCTACTCGTATGAGATTCTACATTCATAAAAAAATA
190 GC-TAGAAGGACATCCTTAATAAAAAGCGTATACTCGTATGAGATTCTACATTCATAAAAAAATA
5317891 TTATTTTCAAAGGCGAACGACTACCCCG
254 TTATTTTCAAAGGCGAACGACTACCCCG
5317919 AT
1 AT
5317921 GATGGGATTT
Statistics
Matches: 243, Mismatches: 32, Indels: 15
0.84 0.11 0.05
Matches are distributed among these distances:
279 23 0.09
280 178 0.73
281 42 0.17
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (281 bp):
ATAGTGGACATAAGAATTAGTAATATGTCATGCACTCTCATCACATTTAAATGTCATGGCATGTA
AACATTACATGCACAAGTTAAAGCTCCAATGATGGCACTTTTCGAGAGTGCTTGCCAAGACGAAG
TTCTTCAAAAAATTTCCTAGATGAAAGGATATTTTAAGTCCCACCAGTTCGATGGGAGAGCTAGA
AGGACATCCTTAATAAAAAGCGTATACTCGTATGAGATTCTACATTCATAAAAAAATATTATTTT
CAAAGGCGAACGACTACCCCG
Found at i:5320633 original size:2 final size:2
Alignment explanation
Indices: 5320626--5320653 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5320616 AATCTGAACA
5320626 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5320654 GTAGTTTTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5324429 original size:18 final size:17
Alignment explanation
Indices: 5324378--5324422 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 17
5324368 CGTGTTTAAA
5324378 TATATATAAGTGATAGATT
1 TATAT-TAA-TGATAGATT
5324397 TAATATTAATGATAGATT
1 T-ATATTAATGATAGATT
5324415 T-TATTAAT
1 TATATTAAT
5324423 ATGATAGTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 7 0.28
18 10 0.40
19 4 0.16
20 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (17 bp):
TATATTAATGATAGATT
Found at i:5331745 original size:76 final size:76
Alignment explanation
Indices: 5331631--5331778 Score: 219
Period size: 76 Copynumber: 1.9 Consensus size: 76
5331621 TTTAATTTTA
* * *
5331631 GGTGATCTATAAAAATAGGAAATTATTTCCTACTTTAAAAGCAATT-TCTAAAATTAAGGATAAA
1 GGTGATCTATAAAAATAGAAAATTATTTCCTACTTTAAAAGAAATTCT-TAAAATTAAGAATAAA
5331695 ATTTTAATCTCG
65 ATTTTAATCTCG
* *
5331707 GGTGAT-TCATAAAAATAGAAAATTATTTCTTACTTTAAAAGAAATTCTTAAAATTAAGAATAAT
1 GGTGATCT-ATAAAAATAGAAAATTATTTCCTACTTTAAAAGAAATTCTTAAAATTAAGAATAAA
5331771 ATTTTAAT
65 ATTTTAAT
5331779 TTGAGAAATT
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
75 1 0.02
76 63 0.97
77 1 0.02
ACGTcount: A:0.45, C:0.08, G:0.10, T:0.37
Consensus pattern (76 bp):
GGTGATCTATAAAAATAGAAAATTATTTCCTACTTTAAAAGAAATTCTTAAAATTAAGAATAAAA
TTTTAATCTCG
Found at i:5331799 original size:76 final size:76
Alignment explanation
Indices: 5331639--5331827 Score: 205
Period size: 76 Copynumber: 2.6 Consensus size: 76
5331629 TAGGTGATCT
* * *
5331639 ATAAAAATAGGAAATTATTTCCTACTTTAAAAGCAATTTCTAAAATTAAGGATAAAATTTTAATC
1 ATAAAAATAGAAAATTATTTCCTACTTTAAAAGAAATTTCTAAAATTAAGAATAAAATTTTAATC
* **
5331704 TCGGGTGATTC
66 TCGAGAAATTC
* *
5331715 ATAAAAATAGAAAATTATTTCTTACTTTAAAAGAAA-TTCTTAAAATTAAGAATAATATTTTAAT
1 ATAAAAATAGAAAATTATTTCCTACTTTAAAAGAAATTTC-TAAAATTAAGAATAAAATTTTAAT
*
5331779 -TTGAGAAATTC
65 CTCGAGAAATTC
* * *
5331790 AT----AT-G-AAATAATTTCCTATTTTAAAAGAAATTCCTAAA
1 ATAAAAATAGAAAATTATTTCCTACTTTAAAAGAAATTTCTAAA
5331828 GTTATGTGAT
Statistics
Matches: 98, Mismatches: 13, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
69 26 0.27
70 3 0.03
71 2 0.02
75 12 0.12
76 55 0.56
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.37
Consensus pattern (76 bp):
ATAAAAATAGAAAATTATTTCCTACTTTAAAAGAAATTTCTAAAATTAAGAATAAAATTTTAATC
TCGAGAAATTC
Found at i:5341412 original size:2 final size:2
Alignment explanation
Indices: 5341405--5341432 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5341395 TTAAAAGAAT
5341405 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5341433 ATTTCAAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5347335 original size:31 final size:31
Alignment explanation
Indices: 5347300--5347398 Score: 86
Period size: 31 Copynumber: 3.2 Consensus size: 31
5347290 CCAATTATGT
5347300 GAAAGTTATGGCGATTAAGCATGCTCTCAAA
1 GAAAGTTATGGCGATTAAGCATGCTCTCAAA
5347331 GAAAG-T-TGGC-ATTCAAG-AT--TC-CAATTA
1 GAAAGTTATGGCGATT-AAGCATGCTCTCAA--A
*
5347358 TGTGAAAGTTATGGCGATTAGGCATGCTCTCAAA
1 ---GAAAGTTATGGCGATTAAGCATGCTCTCAAA
5347392 GAAAGTT
1 GAAAGTT
5347399 GGCATTCAAG
Statistics
Matches: 54, Mismatches: 1, Indels: 26
0.67 0.01 0.32
Matches are distributed among these distances:
25 3 0.06
26 2 0.04
27 1 0.02
28 5 0.09
29 7 0.13
30 6 0.11
31 13 0.24
32 6 0.11
33 5 0.09
34 1 0.02
35 2 0.04
36 3 0.06
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.28
Consensus pattern (31 bp):
GAAAGTTATGGCGATTAAGCATGCTCTCAAA
Found at i:5347370 original size:61 final size:61
Alignment explanation
Indices: 5347275--5347417 Score: 277
Period size: 61 Copynumber: 2.3 Consensus size: 61
5347265 TTTGCTCTAC
5347275 TTGGCATTCAAGATTCCAATTATGTGAAAGTTATGGCGATTAAGCATGCTCTCAAAGAAAG
1 TTGGCATTCAAGATTCCAATTATGTGAAAGTTATGGCGATTAAGCATGCTCTCAAAGAAAG
*
5347336 TTGGCATTCAAGATTCCAATTATGTGAAAGTTATGGCGATTAGGCATGCTCTCAAAGAAAG
1 TTGGCATTCAAGATTCCAATTATGTGAAAGTTATGGCGATTAAGCATGCTCTCAAAGAAAG
5347397 TTGGCATTCAAGATTCCAATT
1 TTGGCATTCAAGATTCCAATT
5347418 TCTTTGTCTC
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
61 81 1.00
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (61 bp):
TTGGCATTCAAGATTCCAATTATGTGAAAGTTATGGCGATTAAGCATGCTCTCAAAGAAAG
Found at i:5347760 original size:22 final size:23
Alignment explanation
Indices: 5347728--5347793 Score: 80
Period size: 28 Copynumber: 2.7 Consensus size: 23
5347718 ATATAGAGTT
5347728 ATTTATACTTAATTTTGATAATA
1 ATTTATACTTAATTTTGATAATA
5347751 ATTTAACTTATACTTAATTTTGATAATA
1 A--T---TTATACTTAATTTTGATAATA
5347779 ATTTA-ACTTAATTTT
1 ATTTATACTTAATTTT
5347794 TGTGATAGTG
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
22 10 0.26
23 4 0.11
25 1 0.03
26 1 0.03
28 22 0.58
ACGTcount: A:0.38, C:0.06, G:0.03, T:0.53
Consensus pattern (23 bp):
ATTTATACTTAATTTTGATAATA
Found at i:5347762 original size:28 final size:28
Alignment explanation
Indices: 5347730--5347788 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
5347720 ATAGAGTTAT
5347730 TTATACTTAATTTTGATAATAATTTAAC
1 TTATACTTAATTTTGATAATAATTTAAC
5347758 TTATACTTAATTTTGATAATAATTTAAC
1 TTATACTTAATTTTGATAATAATTTAAC
5347786 TTA
1 TTA
5347789 ATTTTTGTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.39, C:0.07, G:0.03, T:0.51
Consensus pattern (28 bp):
TTATACTTAATTTTGATAATAATTTAAC
Found at i:5355902 original size:20 final size:20
Alignment explanation
Indices: 5355858--5355917 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
5355848 ATAATCAAAT
* * *
5355858 TAAATAAAATAAATATAAAAT
1 TAAAAAAAATAACTA-AAAAA
* * *
5355879 TAAAATAACTCACTAAAAAA
1 TAAAAAAAATAACTAAAAAA
5355899 TAAAAAAAATAACTAAAAA
1 TAAAAAAAATAACTAAAAA
5355918 TAACTAAATT
Statistics
Matches: 30, Mismatches: 9, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
20 20 0.67
21 10 0.33
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.22
Consensus pattern (20 bp):
TAAAAAAAATAACTAAAAAA
Found at i:5358461 original size:23 final size:23
Alignment explanation
Indices: 5358429--5358494 Score: 105
Period size: 23 Copynumber: 2.8 Consensus size: 23
5358419 TTGAGTTGCT
*
5358429 CAAGGCTGCAGTGCTAAGAGAGC
1 CAAGGTTGCAGTGCTAAGAGAGC
*
5358452 CAAGGTTGCAGTGCCAAGAGAGC
1 CAAGGTTGCAGTGCTAAGAGAGC
5358475 CAAGGTTGCAGTGCTGAAGA
1 CAAGGTTGCAGTGCT-AAGA
5358495 AAGTGTGGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
23 35 0.90
24 4 0.10
ACGTcount: A:0.30, C:0.20, G:0.35, T:0.15
Consensus pattern (23 bp):
CAAGGTTGCAGTGCTAAGAGAGC
Found at i:5369307 original size:20 final size:21
Alignment explanation
Indices: 5369284--5369329 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
5369274 ACATATTGAA
5369284 TAGTTTAA-TTTAAGTTATTT
1 TAGTTTAATTTTAAGTTATTT
*
5369304 TAGTTTAATTTTATGTTATTT
1 TAGTTTAATTTTAAGTTATTT
5369325 T-GTTT
1 TAGTTT
5369330 TAAATTACTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.24, C:0.00, G:0.11, T:0.65
Consensus pattern (21 bp):
TAGTTTAATTTTAAGTTATTT
Found at i:5379653 original size:20 final size:20
Alignment explanation
Indices: 5379616--5379653 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5379606 AGGAGAAAAG
*
5379616 TATAAAAATAAAATAAATTT
1 TATAAAAATAAAAAAAATTT
5379636 TATAAAAA-AAATAAAAAT
1 TATAAAAATAAA-AAAAAT
5379654 AAAGTACACT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (20 bp):
TATAAAAATAAAAAAAATTT
Found at i:5380388 original size:16 final size:16
Alignment explanation
Indices: 5380367--5380397 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5380357 ATTATATATG
5380367 TAATTTATAATTTATA
1 TAATTTATAATTTATA
*
5380383 TAATTTATACTTTAT
1 TAATTTATAATTTAT
5380398 GGTTAATTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (16 bp):
TAATTTATAATTTATA
Found at i:5381812 original size:2 final size:2
Alignment explanation
Indices: 5381805--5381844 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
5381795 TGCTAGCTAT
* *
5381805 TA TA TA TA TA TA TA TA TA TA T- TA AA TA TA TA TA CA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5381845 TTTTATCATC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:5381832 original size:21 final size:21
Alignment explanation
Indices: 5381802--5381844 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
5381792 CACTGCTAGC
* *
5381802 TATTATATATATATATATATA
1 TATTAAATATATATACATATA
5381823 TATTAAATATATATACATATA
1 TATTAAATATATATACATATA
5381844 T
1 T
5381845 TTTTATCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
TATTAAATATATATACATATA
Found at i:5384721 original size:10 final size:10
Alignment explanation
Indices: 5384706--5384780 Score: 57
Period size: 10 Copynumber: 7.4 Consensus size: 10
5384696 ATATTCAAAT
5384706 AATAATATTA
1 AATAATATTA
*
5384716 AATAATATTCTT
1 AATAATA-T-TA
*
5384728 TATAATATT-
1 AATAATATTA
* *
5384737 TATTATAGTTA
1 AATAATA-TTA
5384748 AATAATATT-
1 AATAATATTA
5384757 AAT-ATATTA
1 AATAATATTA
5384766 AATAATATTTA
1 AATAATA-TTA
5384777 AATA
1 AATA
5384781 TTTTTATTTC
Statistics
Matches: 53, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
8 5 0.09
9 12 0.23
10 15 0.28
11 14 0.26
12 7 0.13
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (10 bp):
AATAATATTA
Found at i:5384723 original size:45 final size:45
Alignment explanation
Indices: 5384661--5384754 Score: 154
Period size: 45 Copynumber: 2.1 Consensus size: 45
5384651 ATTAAATTTA
*
5384661 AATAATACTAAATAATATTCTTTATTATATTTATTATA-TTCAAAT
1 AATAATACTAAATAATATTCTTTATAATATTTATTATAGTT-AAAT
*
5384706 AATAATATTAAATAATATTCTTTATAATATTTATTATAGTTAAAT
1 AATAATACTAAATAATATTCTTTATAATATTTATTATAGTTAAAT
5384751 AATA
1 AATA
5384755 TTAATATATT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
45 44 0.96
46 2 0.04
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.48
Consensus pattern (45 bp):
AATAATACTAAATAATATTCTTTATAATATTTATTATAGTTAAAT
Found at i:5384755 original size:42 final size:41
Alignment explanation
Indices: 5384646--5384758 Score: 145
Period size: 45 Copynumber: 2.6 Consensus size: 41
5384636 CAAAATTTAT
* * *
5384646 TATTTATTAAATTTAAATAATACTAAATAATATTCTTTATTA
1 TATTTATTATA-TTAAATAATATTAAATAATATTCTTTATAA
5384688 TATTTATTATATTCAAATAATAATATTAAATAATATTCTTTATAA
1 TATTTATTATATT---A-AATAATATTAAATAATATTCTTTATAA
5384733 TATTTATTATAGTTAAATAATATTAA
1 TATTTATTATA-TTAAATAATATTAA
5384759 TATATTAAAT
Statistics
Matches: 63, Mismatches: 3, Indels: 10
0.83 0.04 0.13
Matches are distributed among these distances:
41 2 0.03
42 21 0.33
43 1 0.02
44 1 0.02
45 36 0.57
46 2 0.03
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.50
Consensus pattern (41 bp):
TATTTATTATATTAAATAATATTAAATAATATTCTTTATAA
Found at i:5384786 original size:10 final size:11
Alignment explanation
Indices: 5384656--5384780 Score: 61
Period size: 9 Copynumber: 11.8 Consensus size: 11
5384646 TATTTATTAA
5384656 ATTTAAATAAT
1 ATTTAAATAAT
*
5384667 A-CTAAATAAT
1 ATTTAAATAAT
** *
5384677 ATTCTTTATTAT
1 ATT-TAAATAAT
*
5384689 ATTT--ATTAT
1 ATTTAAATAAT
*
5384698 ATTCAAATAAT
1 ATTTAAATAAT
5384709 AATATTAAATAAT
1 -AT-TTAAATAAT
**
5384722 ATTCTTTATAAT
1 ATT-TAAATAAT
*
5384734 ATTT--ATTAT
1 ATTTAAATAAT
*
5384743 AGTTAAATAAT
1 ATTTAAATAAT
5384754 A-TT-AAT-AT
1 ATTTAAATAAT
5384762 A-TTAAATAAT
1 ATTTAAATAAT
5384772 ATTTAAATA
1 ATTTAAATA
5384781 TTTTTATTTC
Statistics
Matches: 89, Mismatches: 13, Indels: 24
0.71 0.10 0.19
Matches are distributed among these distances:
8 5 0.06
9 21 0.24
10 14 0.16
11 20 0.22
12 21 0.24
13 8 0.09
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (11 bp):
ATTTAAATAAT
Done.