Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 166 of 172
Found at i:54336299 original size:20 final size:19
Alignment explanation
Indices: 54336264--54336301 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
54336254 GTTTATAATT
*
54336264 TTTTTTATTGTGTTAATAA
1 TTTTTTATTGTATTAATAA
54336283 TTTTTTATTGTAATTAATA
1 TTTTTTATTGT-ATTAATA
54336302 TTTAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (19 bp):
TTTTTTATTGTATTAATAA
Found at i:54336304 original size:19 final size:18
Alignment explanation
Indices: 54336259--54336304 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
54336249 TACTAGTTTA
* *
54336259 TAATTTTTTTTATTGTGT
1 TAATATTTTTTATTGTAT
54336277 TAATAATTTTTTATTGTAAT
1 TAAT-ATTTTTTATTGT-AT
54336297 TAATATTT
1 TAATATTT
54336305 AAAAAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 4 0.17
19 15 0.62
20 5 0.21
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (18 bp):
TAATATTTTTTATTGTAT
Found at i:54352294 original size:8 final size:8
Alignment explanation
Indices: 54352283--54352307 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
54352273 CAAAAAGATG
54352283 AAAAAGAA
1 AAAAAGAA
54352291 AAAAAGAA
1 AAAAAGAA
54352299 AAAAAGAA
1 AAAAAGAA
54352307 A
1 A
54352308 TACGAAAGTA
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:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (8 bp):
AAAAAGAA
Found at i:54352670 original size:16 final size:17
Alignment explanation
Indices: 54352648--54352689 Score: 61
Period size: 16 Copynumber: 2.5 Consensus size: 17
54352638 CCTGGGGTTA
54352648 ATTTGGGTTAGTTTT-GG
1 ATTTGGGTT-GTTTTGGG
54352665 -TTTGGGTTGTTTTGGG
1 ATTTGGGTTGTTTTGGG
54352681 ATTTGGGTT
1 ATTTGGGTT
54352690 TTAAATTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 5 0.22
16 10 0.43
17 8 0.35
ACGTcount: A:0.07, C:0.00, G:0.38, T:0.55
Consensus pattern (17 bp):
ATTTGGGTTGTTTTGGG
Found at i:54352996 original size:108 final size:110
Alignment explanation
Indices: 54352830--54353051 Score: 342
Period size: 108 Copynumber: 2.0 Consensus size: 110
54352820 TTAATGGAAA
54352830 ACGAGTATAATCGGCGTGGTTTGGTGGTAAAACTTAACGAGTATAATAAAACTCAAATTTTCAAA
1 ACGAGTATAATCGGCGTGGTTTGGTGGTAAAACTT-A-GAGTATAATAAAACTCAAATTTTCAAA
* * * *
54352895 TTCAAAATCAAATTCTACCAAATGAGATTATTCTATATATAGAACAC
64 TTCAAAATCAAACTCTACCAAATGAGATTACTCCAGATATAGAACAC
* *
54352942 ACGAGTATAAAT-GG-GTGGTTTGGTGGTAAAACTT-GAGTATAATAAAATTCAAATTTTCAATT
1 ACGAGTAT-AATCGGCGTGGTTTGGTGGTAAAACTTAGAGTATAATAAAACTCAAATTTTCAAAT
54353004 TCAAAATCAAACTCTACCAAATGAGATTACTCCAGATATAGAACAC
65 TCAAAATCAAACTCTACCAAATGAGATTACTCCAGATATAGAACAC
54353050 AC
1 AC
54353052 AAACAGAAAA
Statistics
Matches: 103, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
108 70 0.68
111 20 0.19
112 10 0.10
113 3 0.03
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (110 bp):
ACGAGTATAATCGGCGTGGTTTGGTGGTAAAACTTAGAGTATAATAAAACTCAAATTTTCAAATT
CAAAATCAAACTCTACCAAATGAGATTACTCCAGATATAGAACAC
Found at i:54354613 original size:22 final size:22
Alignment explanation
Indices: 54354585--54354632 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
54354575 ATATACAAAT
54354585 AGGAGATCTAACATCTCAATTG
1 AGGAGATCTAACATCTCAATTG
54354607 AGGAGATCTAACATCTCAATTG
1 AGGAGATCTAACATCTCAATTG
54354629 AGGA
1 AGGA
54354633 CTATGGATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.25
Consensus pattern (22 bp):
AGGAGATCTAACATCTCAATTG
Found at i:54365313 original size:17 final size:18
Alignment explanation
Indices: 54365291--54365325 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
54365281 AAGAGTTTAA
*
54365291 TTTATAATTTATA-AATT
1 TTTATAATCTATATAATT
54365308 TTTATAATCTATATAATT
1 TTTATAATCTATATAATT
54365326 GGTTTGATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTATAATCTATATAATT
Found at i:54366483 original size:132 final size:132
Alignment explanation
Indices: 54366246--54366512 Score: 358
Period size: 132 Copynumber: 2.0 Consensus size: 132
54366236 TTGCCTTGCC
* * * * * *
54366246 TTAGAAACCACGAATGAAATTCCAAAGGGATATTCGATTATTTTGCGCAAAGGAGAAATTGTAAC
1 TTAGAAAACACGAACGAAATTCCAAAGAGACATTCGATTATTTTGCGCAAACGAGAAATTGCAAC
* * *
54366311 CCAACACGATAGGGCACAATTCCCCGAATTGCCAATTATCGAACA-CTTCATTCGTTTTAAA-AA
66 CCAACACGATAGGGCACAATTCCCCGAATTGCCAAATATCGAACATCGTC-TCCGTTTTAAAGAA
54366374 GTTT
130 -TTT
* * *
54366378 TTAGAAAACATGAACGAAATTCTAAAGAGACATTCGATTATTTTGGGCAAACGAGAAATTGCAAC
1 TTAGAAAACACGAACGAAATTCCAAAGAGACATTCGATTATTTTGCGCAAACGAGAAATTGCAAC
* * * *
54366443 CCAGCACGATAGGGCACGATTCTCCGAATTGCTAAATATCGAACATCGTCTCCGTTTTAAAGAAT
66 CCAACACGATAGGGCACAATTCCCCGAATTGCCAAATATCGAACATCGTCTCCGTTTTAAAGAAT
54366508 TT
131 TT
54366510 TTA
1 TTA
54366513 AACAAATGAT
Statistics
Matches: 117, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
132 112 0.96
133 5 0.04
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.27
Consensus pattern (132 bp):
TTAGAAAACACGAACGAAATTCCAAAGAGACATTCGATTATTTTGCGCAAACGAGAAATTGCAAC
CCAACACGATAGGGCACAATTCCCCGAATTGCCAAATATCGAACATCGTCTCCGTTTTAAAGAAT
TT
Found at i:54367358 original size:22 final size:22
Alignment explanation
Indices: 54367333--54367382 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
54367323 TATGTACACA
*
54367333 ATATATAATA-TATTAAAGATAT
1 ATATATAATATTAATAAA-ATAT
54367355 ATATATAATATTAATAAAATAT
1 ATATATAATATTAATAAAATAT
54367377 ATATAT
1 ATATAT
54367383 GTAGTATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 20 0.77
23 6 0.23
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (22 bp):
ATATATAATATTAATAAAATAT
Found at i:54367376 original size:20 final size:21
Alignment explanation
Indices: 54367332--54367382 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
54367322 GTATGTACAC
54367332 AATATATA-ATATATTAAAGA
1 AATATATATATATATTAAAGA
*
54367352 TATATATATA-ATATTAATA-A
1 AATATATATATATATTAA-AGA
54367372 AATATATATAT
1 AATATATATAT
54367383 GTAGTATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 24 0.92
21 2 0.08
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
AATATATATATATATTAAAGA
Found at i:54367618 original size:19 final size:18
Alignment explanation
Indices: 54367573--54367620 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
54367563 AAAGTAGGAC
54367573 ATAA-AATAATAAATAAT
1 ATAATAATAATAAATAAT
**
54367590 ATTTTAAATAATAAATAAT
1 ATAAT-AATAATAAATAAT
54367609 AATAATAATAAT
1 -ATAATAATAAT
54367621 GCAGAAACCA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
17 2 0.08
19 19 0.79
20 3 0.12
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
ATAATAATAATAAATAAT
Found at i:54369206 original size:136 final size:137
Alignment explanation
Indices: 54368940--54369533 Score: 897
Period size: 137 Copynumber: 4.3 Consensus size: 137
54368930 GGGATAGGGT
* * * *
54368940 TTGTTTCGATCTGCTCTACTGCAACTTCAGAGAGATGAGATCTGTGATTTATAGCTTCAGTCTGT
1 TTGTGTCGATCTACTCTACTGCAACTTCAGAGAGATGAGATCTGTGGTTTATAGCTTCAATCTGT
* * * * *
54369005 TCCAATGCAACTTCAGGGAGATAAGATCTGCTATC-TTAGTCTGCTCCACTGTAACTTTAGGAAG
66 TCCACTGCAACTTCAGGGAAATAAGATTTGCTATCTTTAGTCTGCTCCACTGCAACTTCAGGAAG
54369069 ATAAGAC
131 ATAAGAC
*
54369076 TTGTGTCAATCTACTCTACTGCAACTTCAGAGAGATGAG-TCTGTGGTTTATAGCTTCAATCTGT
1 TTGTGTCGATCTACTCTACTGCAACTTCAGAGAGATGAGATCTGTGGTTTATAGCTTCAATCTGT
* *
54369140 TCCACTGCAACTTCAGGGAAATAAGATTTGTTATCTTTAGTCAGCTCCACTGCAACTTCAGGAAG
66 TCCACTGCAACTTCAGGGAAATAAGATTTGCTATCTTTAGTCTGCTCCACTGCAACTTCAGGAAG
54369205 ATAAGAC
131 ATAAGAC
* *
54369212 TTGTGTCGATCTACTCTACTGCTACTTCAGAGAGATGAGATATGTGGTTTATAGCTTCAATCTGT
1 TTGTGTCGATCTACTCTACTGCAACTTCAGAGAGATGAGATCTGTGGTTTATAGCTTCAATCTGT
* * *
54369277 TCCATTGCAACTTCAGGGAAATAAGATTTACTATCTTTAGTCTGCTCCACTGCAACTTCAGGGAG
66 TCCACTGCAACTTCAGGGAAATAAGATTTGCTATCTTTAGTCTGCTCCACTGCAACTTCAGGAAG
54369342 ATAAGAC
131 ATAAGAC
* * *
54369349 TTGTGTTGATCTACTCTACTGCAACTTCAGAGAGATGAGATCAGTGGTTTATAGCTTCAACCTGT
1 TTGTGTCGATCTACTCTACTGCAACTTCAGAGAGATGAGATCTGTGGTTTATAGCTTCAATCTGT
* *
54369414 TCCACTGTAACTTCAGGGAAATAAGATTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAAGG-A
66 TCCACTGCAACTTCAGGGAAATAAGATTTGCTATCTTTAGTCTGCTCCACTGCAACTTC-AGGAA
54369478 GATAAGAC
130 GATAAGAC
* * * *
54369486 TTGTAACTTCGACCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGT
1 TTGT---GTCGATCTACTCTACTGCAACTTCAGAGAGATGAGATCTGT
54369534 AATTTTCAGA
Statistics
Matches: 417, Mismatches: 35, Indels: 8
0.91 0.08 0.02
Matches are distributed among these distances:
135 54 0.13
136 106 0.25
137 219 0.53
138 3 0.01
140 35 0.08
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (137 bp):
TTGTGTCGATCTACTCTACTGCAACTTCAGAGAGATGAGATCTGTGGTTTATAGCTTCAATCTGT
TCCACTGCAACTTCAGGGAAATAAGATTTGCTATCTTTAGTCTGCTCCACTGCAACTTCAGGAAG
ATAAGAC
Found at i:54369471 original size:45 final size:44
Alignment explanation
Indices: 54368985--54369534 Score: 287
Period size: 45 Copynumber: 12.2 Consensus size: 44
54368975 TGAGATCTGT
* * * *
54368985 GATTTATAGCTTCAGTCTGTTCCAATGCAACTTCAGGGAGATAA
1 GATTTGTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAA
* * * *
54369029 GATCTGCTATCTT-AGTCTGCTCCACTGTAACTTTAGGAAGATAA
1 GATTTG-TATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAA
* * * * * * *
54369073 GACTTG--T-GTCAATCTACTCTACTGCAACTTCAGAGAGATGA
1 GATTTGTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAA
* * *
54369114 G-TCTGTGGTTTATAGCTTCAATCTGTTCCACTGCAACTTCAGGGAAATAA
1 GAT-T-T-G--TAT--CTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAA
* * *
54369164 GATTTGTTATCTTTAGTCAGCTCCACTGCAACTTCAGGAAGATAA
1 GATTTG-TATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAA
* * * * * * * *
54369209 GACTTGTGTC--GA-TCTACTCTACTGCTACTTCAGAGAGATGA
1 GATTTGTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAA
* * * *
54369250 GATATGTGGTTTATAGCTTCAATCTGTTCCATTGCAACTTCAGGGAAATAA
1 GAT-T-T-G--TAT--CTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAA
* *
54369301 GATTTACTATCTTTAGTCTGCTCCACTGCAACTTCAGGGAGATAA
1 GATTT-GTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAA
* * * * * * *
54369346 GACTTG--TGTTGA-TCTACTCTACTGCAACTTCAGAGAGATGA
1 GATTTGTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAA
* ** * * *
54369387 GATCAGTGGTTTATAGCTTCAACCTGTTCCACTGTAACTTCAGGGAAATAA
1 GAT---T--TGTAT--CTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAA
*
54369438 GATTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAAGGAGATAA
1 GATTTG-TATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAA
* * * * *
54369483 GACTTGTAACTTC-GACCTGCTCTACTGCAACTTCAGAGAGATAA
1 GATTTGTATCTTCAG-TCTGCTCCACTGCAACTTCAGGGAGATAA
*
54369527 GATCTGTA
1 GATTTGTA
54369535 ATTTTCAGAC
Statistics
Matches: 375, Mismatches: 96, Indels: 70
0.69 0.18 0.13
Matches are distributed among these distances:
40 1 0.00
41 77 0.21
42 7 0.02
43 3 0.01
44 76 0.20
45 107 0.29
46 4 0.01
47 11 0.03
48 4 0.01
49 2 0.01
50 34 0.09
51 49 0.13
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (44 bp):
GATTTGTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAA
Found at i:54377088 original size:46 final size:46
Alignment explanation
Indices: 54377036--54377125 Score: 155
Period size: 46 Copynumber: 2.0 Consensus size: 46
54377026 TCTACACCAT
54377036 TCTTCGAGTTCTTTC-GAAAGCTCCACCCTTGTCTTTTCCGCTTCGC
1 TCTTCGAGTTCTTTCAG-AAGCTCCACCCTTGTCTTTTCCGCTTCGC
*
54377082 TCTTCGAGTTCTTTCAGAAGCTCCACCCTTGTCTTTTTCGCTTC
1 TCTTCGAGTTCTTTCAGAAGCTCCACCCTTGTCTTTTCCGCTTC
54377126 TACTACATCA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
46 41 0.98
47 1 0.02
ACGTcount: A:0.11, C:0.33, G:0.14, T:0.41
Consensus pattern (46 bp):
TCTTCGAGTTCTTTCAGAAGCTCCACCCTTGTCTTTTCCGCTTCGC
Found at i:54381288 original size:132 final size:132
Alignment explanation
Indices: 54381114--54381380 Score: 367
Period size: 132 Copynumber: 2.0 Consensus size: 132
54381104 TTGCATTGCC
* * * * *
54381114 TTAGAAACCACGAATGAAATTCCAAAGGGATATTCGATTATTTTGCGCAAAGGAGAAATTGCAAC
1 TTAGAAAACACGAACGAAATTCCAAAGAGACATTCGATTATTTTGCGCAAACGAGAAATTGCAAC
* * *
54381179 CCAGCACGATAAGGCACAATTCCCCGAATTGCCAATTATCGAACA-CTTCCTTCGTTTTAAA-AA
66 CCAGCACGATAAGGCACAATTCCCCGAATTGCCAAATATCGAACATCGT-CTCCGTTTTAAAGAA
54381242 GTTT
130 -TTT
* * *
54381246 TTAGAAAACATGAACGAAATTCTAAAGAGACATTCGATTATTTTGGGCAAACGAGAAATTGCAAC
1 TTAGAAAACACGAACGAAATTCCAAAGAGACATTCGATTATTTTGCGCAAACGAGAAATTGCAAC
* * * *
54381311 CCAGCACGATAGGGCACGATTCTCCGAATTGCTAAATATCGAACATCGTCTCCGTTTTAAAGAAT
66 CCAGCACGATAAGGCACAATTCCCCGAATTGCCAAATATCGAACATCGTCTCCGTTTTAAAGAAT
54381376 TT
131 TT
54381378 TTA
1 TTA
54381381 AACAAATGAT
Statistics
Matches: 118, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
132 114 0.97
133 4 0.03
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (132 bp):
TTAGAAAACACGAACGAAATTCCAAAGAGACATTCGATTATTTTGCGCAAACGAGAAATTGCAAC
CCAGCACGATAAGGCACAATTCCCCGAATTGCCAAATATCGAACATCGTCTCCGTTTTAAAGAAT
TT
Found at i:54382225 original size:22 final size:22
Alignment explanation
Indices: 54382197--54382246 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
54382187 TATGTACACA
*
54382197 ATATATAATA-TATTAAAGATAT
1 ATATATAATATTAATAAA-ATAT
54382219 ATATATAATATTAATAAAATAT
1 ATATATAATATTAATAAAATAT
54382241 ATATAT
1 ATATAT
54382247 GTAGTATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 20 0.77
23 6 0.23
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (22 bp):
ATATATAATATTAATAAAATAT
Found at i:54382240 original size:20 final size:21
Alignment explanation
Indices: 54382196--54382246 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
54382186 GTATGTACAC
54382196 AATATATA-ATATATTAAAGA
1 AATATATATATATATTAAAGA
*
54382216 TATATATATA-ATATTAATA-A
1 AATATATATATATATTAA-AGA
54382236 AATATATATAT
1 AATATATATAT
54382247 GTAGTATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 24 0.92
21 2 0.08
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
AATATATATATATATTAAAGA
Found at i:54387045 original size:21 final size:21
Alignment explanation
Indices: 54386978--54387055 Score: 88
Period size: 21 Copynumber: 3.8 Consensus size: 21
54386968 ACGCCAGAAA
*
54386978 AAGCTCG-AA-AGCTGAACAA
1 AAGCTCGTAAGAGCTGAACAG
* *
54386997 AAGCTCATAAGAGATGAACAG
1 AAGCTCGTAAGAGCTGAACAG
* *
54387018 AAACTCGTAAGAGCTTAACAG
1 AAGCTCGTAAGAGCTGAACAG
*
54387039 AAGCTCGTAACAGCTGA
1 AAGCTCGTAAGAGCTGA
54387056 TCCATCCAAT
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
19 6 0.13
20 2 0.04
21 39 0.83
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.15
Consensus pattern (21 bp):
AAGCTCGTAAGAGCTGAACAG
Found at i:54394950 original size:7 final size:7
Alignment explanation
Indices: 54394938--54394964 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
54394928 TGATTGGGTG
54394938 TTTGAAC
1 TTTGAAC
54394945 TTTGAAC
1 TTTGAAC
54394952 TTTGAAC
1 TTTGAAC
54394959 TTTGAA
1 TTTGAA
54394965 GCAGAGTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.44
Consensus pattern (7 bp):
TTTGAAC
Found at i:54398277 original size:23 final size:23
Alignment explanation
Indices: 54398251--54398299 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
54398241 ATCTTTGGAT
*
54398251 TGTCTATTTCGACTATTATTTTG
1 TGTCTATTTCGACTACTATTTTG
54398274 TGTCTATTTCGACTACTATTTTG
1 TGTCTATTTCGACTACTATTTTG
54398297 TGT
1 TGT
54398300 TTTTATTGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.16, C:0.14, G:0.14, T:0.55
Consensus pattern (23 bp):
TGTCTATTTCGACTACTATTTTG
Found at i:54401027 original size:14 final size:14
Alignment explanation
Indices: 54400999--54401031 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
54400989 AAGGAATGTT
54400999 ATTAGTAGATTAAA
1 ATTAGTAGATTAAA
54401013 ATTAG-AGATTAAA
1 ATTAGTAGATTAAA
*
54401026 AATAGT
1 ATTAGT
54401032 TTTTCTTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.52, C:0.00, G:0.15, T:0.33
Consensus pattern (14 bp):
ATTAGTAGATTAAA
Found at i:54411319 original size:21 final size:21
Alignment explanation
Indices: 54411287--54411327 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
54411277 GAACATTTGG
54411287 TGTATAGGCTAAGAA-AGGCCT
1 TGTATAGGCTAA-AACAGGCCT
54411308 TGTAT-GGCCTAAAACAGGCC
1 TGTATAGG-CTAAAACAGGCC
54411328 CATCGAGCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.22
Consensus pattern (21 bp):
TGTATAGGCTAAAACAGGCCT
Found at i:54424647 original size:137 final size:137
Alignment explanation
Indices: 54424395--54425356 Score: 1870
Period size: 137 Copynumber: 7.0 Consensus size: 137
54424385 TAGCCGTTGC
* * *
54424395 CTCTCTTGCTCATCTACAATGGTCAATATTTTCTAACATAAAACATATTAAAAAAAATAAGAACA
1 CTCTTTTGCTCATCTACAATGGTCAATATTTTCTAACATATAACATCTT-AAAAAAATAAGAACA
* *
54424460 GAACAAAGAATTTTCTTTTCACAAAAAAGATAACTAGTTGTTAGCTTAGCTACACTAGATGAAGT
65 GAGCAAACAATTTTCTTTTCACAAAAAAGATAACTAGTTGTTAGCTTAGCTACACTAGATGAAGT
54424525 TCAAATCA
130 TCAAATCA
54424533 CTCTTTTGCTCATCTACAATGGTCAATATTTTCTAACATATAACATCTTAAAAAAATAAGAACAG
1 CTCTTTTGCTCATCTACAATGGTCAATATTTTCTAACATATAACATCTTAAAAAAATAAGAACAG
54424598 AGCAAACAATTTTCTTTTCACAAAAAAGATAACTAGTTGTTAGCTTAGCTACACTAGATGAAGTT
66 AGCAAACAATTTTCTTTTCACAAAAAAGATAACTAGTTGTTAGCTTAGCTACACTAGATGAAGTT
54424663 CAAATCA
131 CAAATCA
54424670 CTCTTTTGCTCATCTACAATGGTCAATATTTTCTAACATATAACATCTTAAAAAAATAAGAACAG
1 CTCTTTTGCTCATCTACAATGGTCAATATTTTCTAACATATAACATCTTAAAAAAATAAGAACAG
54424735 AGCAAACAATTTTCTTTTCACAAAAAAGATAACTAGTTGTTAGCTTAGCTACACTAGATGAAGTT
66 AGCAAACAATTTTCTTTTCACAAAAAAGATAACTAGTTGTTAGCTTAGCTACACTAGATGAAGTT
54424800 CAAATCA
131 CAAATCA
54424807 CTCTTTTGCTCATCTACAATGGTCAATATTTTCTAACATATAACATCTTAAAAAAATAAGAACAG
1 CTCTTTTGCTCATCTACAATGGTCAATATTTTCTAACATATAACATCTTAAAAAAATAAGAACAG
54424872 AGCAAACAATTTTCTTTTCACAAAAAAGATAACTAGTTGTTAGCTTAGCTACACTAGATGAAGTT
66 AGCAAACAATTTTCTTTTCACAAAAAAGATAACTAGTTGTTAGCTTAGCTACACTAGATGAAGTT
54424937 CAAATCA
131 CAAATCA
54424944 CTCTTTTGCTCATCTACAATGGTCAATATTTTCTAACATATAACATCTTAAAAAAATAAGAACAG
1 CTCTTTTGCTCATCTACAATGGTCAATATTTTCTAACATATAACATCTTAAAAAAATAAGAACAG
54425009 AGCAAACAATTTTCTTTTCACAAAAAAGATAACTAGTTGTTAGCTTAGCTACACTAGATGAAGTT
66 AGCAAACAATTTTCTTTTCACAAAAAAGATAACTAGTTGTTAGCTTAGCTACACTAGATGAAGTT
54425074 CAAATCA
131 CAAATCA
54425081 CTCTTTTGCTCATCTACAATGGTCAATATTTTCTAACATATAACATCTTAAAAAAATAAGAACAG
1 CTCTTTTGCTCATCTACAATGGTCAATATTTTCTAACATATAACATCTTAAAAAAATAAGAACAG
54425146 AGCAAACAATTTTCTTTTCACAAAAAAGATAACTAGTTGTTAGCTTAGCTACACTAGATGAAGTT
66 AGCAAACAATTTTCTTTTCACAAAAAAGATAACTAGTTGTTAGCTTAGCTACACTAGATGAAGTT
54425211 CAAATCA
131 CAAATCA
54425218 CTCTTTTGCTCATCTACAATGGTCAATATTTTCTAACATATAACATCTTAAAAAAATAAGAACAG
1 CTCTTTTGCTCATCTACAATGGTCAATATTTTCTAACATATAACATCTTAAAAAAATAAGAACAG
54425283 AGCAAACAATTTTCTTTTCACAAAAAAGATAACTAGTTGTTAGCTTAGCTACACTAGATGAAGTT
66 AGCAAACAATTTTCTTTTCACAAAAAAGATAACTAGTTGTTAGCTTAGCTACACTAGATGAAGTT
54425348 CAAATCA
131 CAAATCA
54425355 CT
1 CT
54425357 AAAAATAAAA
Statistics
Matches: 819, Mismatches: 5, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
137 773 0.94
138 46 0.06
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.32
Consensus pattern (137 bp):
CTCTTTTGCTCATCTACAATGGTCAATATTTTCTAACATATAACATCTTAAAAAAATAAGAACAG
AGCAAACAATTTTCTTTTCACAAAAAAGATAACTAGTTGTTAGCTTAGCTACACTAGATGAAGTT
CAAATCA
Found at i:54429141 original size:15 final size:15
Alignment explanation
Indices: 54429121--54429149 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
54429111 TTCTTTTTCC
54429121 TAATATATTATTATT
1 TAATATATTATTATT
54429136 TAATATATTATTAT
1 TAATATATTATTAT
54429150 AGTCTTCAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TAATATATTATTATT
Found at i:54429370 original size:30 final size:30
Alignment explanation
Indices: 54429334--54429425 Score: 105
Period size: 30 Copynumber: 3.1 Consensus size: 30
54429324 AATCCTAAGA
*
54429334 TCCTGAATGACATATTGAGTCTTCCCAAGT
1 TCCTGAATGAGATATTGAGTCTTCCCAAGT
* * *
54429364 TCCTGAATAAGATATTGAGTCTTCCGAAGC
1 TCCTGAATGAGATATTGAGTCTTCCCAAGT
* * *
54429394 TCTTGAAAGAGATATT-AGGTCTTCTCAAGT
1 TCCTGAATGAGATATTGA-GTCTTCCCAAGT
54429424 TC
1 TC
54429426 TTAAACGTCC
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (30 bp):
TCCTGAATGAGATATTGAGTCTTCCCAAGT
Found at i:54430264 original size:20 final size:20
Alignment explanation
Indices: 54430209--54430257 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
54430199 TTGCTATTTA
54430209 TTTTAA-AAACTTTTTATTAT
1 TTTTAATAAA-TTTTTATTAT
54430229 TTTTAATAAATTTTTA-TAT
1 TTTTAATAAATTTTTATTAT
54430248 TGTTTAATAA
1 T-TTTAATAA
54430258 TTATTTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 4 0.15
20 20 0.74
21 3 0.11
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (20 bp):
TTTTAATAAATTTTTATTAT
Found at i:54432889 original size:21 final size:21
Alignment explanation
Indices: 54432865--54432922 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 21
54432855 AAAAAGTAAT
54432865 TTTTTAATTCTTTT-ATTTTTC
1 TTTTTAATT-TTTTCATTTTTC
** *
54432886 TTTTTTCTTTTTTCTTTTTTC
1 TTTTTAATTTTTTCATTTTTC
54432907 TTTTTACATTATTTTC
1 TTTTTA-ATT-TTTTC
54432923 TATCTTTATT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
20 4 0.14
21 18 0.62
22 2 0.07
23 5 0.17
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTTTAATTTTTTCATTTTTC
Found at i:54432892 original size:7 final size:7
Alignment explanation
Indices: 54432880--54432911 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
54432870 AATTCTTTTA
54432880 TTTTTCT
1 TTTTTCT
54432887 TTTTTCT
1 TTTTTCT
54432894 TTTTTCT
1 TTTTTCT
54432901 TTTTTCT
1 TTTTTCT
54432908 TTTT
1 TTTT
54432912 ACATTATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTCT
Found at i:54434016 original size:10 final size:10
Alignment explanation
Indices: 54434003--54434041 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
54433993 TTATTTTCAT
54434003 TTATCTTTAA
1 TTATCTTTAA
54434013 TTATCTTTAA
1 TTATCTTTAA
* *
54434023 TTATTTATTAT
1 TTATCT-TTAA
54434034 TTATCTTT
1 TTATCTTT
54434042 TAGAATTTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 17 0.68
11 8 0.32
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.67
Consensus pattern (10 bp):
TTATCTTTAA
Found at i:54434791 original size:17 final size:18
Alignment explanation
Indices: 54434759--54434792 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
54434749 TTTCCCTCAT
54434759 TTTAATTTCTGCAATTTA
1 TTTAATTTCTGCAATTTA
54434777 TTTAATTTC-GCAATTT
1 TTTAATTTCTGCAATTT
54434793 CCATTCACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.26, C:0.12, G:0.06, T:0.56
Consensus pattern (18 bp):
TTTAATTTCTGCAATTTA
Found at i:54437643 original size:22 final size:23
Alignment explanation
Indices: 54437615--54437662 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
54437605 CAATAAGAGG
*
54437615 AAAAACTT-AAATTTTATATGGA
1 AAAAACTTGAAATTTTATAAGGA
* *
54437637 AAAAACTTGGAATTTTGTAAGGA
1 AAAAACTTGAAATTTTATAAGGA
54437660 AAA
1 AAA
54437663 GCATTTTATC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.50, C:0.04, G:0.15, T:0.31
Consensus pattern (23 bp):
AAAAACTTGAAATTTTATAAGGA
Found at i:54437705 original size:19 final size:18
Alignment explanation
Indices: 54437665--54437713 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 18
54437655 AAGGAAAAGC
* *
54437665 ATTTTATCTTTTAAATTT
1 ATTTTATTTTTTAAATTA
54437683 ATTTTATTTTTTAGAATTA
1 ATTTTATTTTTTA-AATTA
54437702 ATTTTAATTTTT
1 ATTTT-ATTTTT
54437714 CTATAGTCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 12 0.44
19 9 0.33
20 6 0.22
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (18 bp):
ATTTTATTTTTTAAATTA
Found at i:54438204 original size:67 final size:67
Alignment explanation
Indices: 54438101--54438243 Score: 171
Period size: 67 Copynumber: 2.1 Consensus size: 67
54438091 ACCCCATAAT
*
54438101 CGAGCTATGATATTACACATTATACCCCATGTTTAATATCCTGACAGACTATTTATGTTGCCATA
1 CGAGCTATGATATTACACATTATACCCCATGTTTAATATCCTGACAGACTATTTACGTTGCCATA
54438166 GC
66 GC
* * * * * * * * *
54438168 CGAGTTATGATCTTACACCTTATATCCCAT-TGTTAATGTCTTGGCGGACTCTTTACGTTGCCAT
1 CGAGCTATGATATTACACATTATACCCCATGT-TTAATATCCTGACAGACTATTTACGTTGCCAT
*
54438232 GGC
65 AGC
54438235 CGAGCTATG
1 CGAGCTATG
54438244 GTTTAATGTC
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
66 1 0.02
67 62 0.98
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.35
Consensus pattern (67 bp):
CGAGCTATGATATTACACATTATACCCCATGTTTAATATCCTGACAGACTATTTACGTTGCCATA
GC
Found at i:54441429 original size:23 final size:24
Alignment explanation
Indices: 54441390--54441471 Score: 89
Period size: 23 Copynumber: 3.4 Consensus size: 24
54441380 TGTATCAAAT
54441390 TATTTAAATATAATTTATTATTTA-
1 TATTTAAA-ATAATTTATTATTTAG
54441414 TATTTAAAATAATTTATTATCATTAG
1 TATTTAAAATAATTTATTAT--TTAG
* *
54441440 T-TTTATAAATAATTTA-TATTAAT
1 TATTTA-AAATAATTTATTATTTAG
54441463 TATTTAAAA
1 TATTTAAAA
54441472 GATATTTAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
23 18 0.35
24 12 0.24
25 10 0.20
26 11 0.22
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (24 bp):
TATTTAAAATAATTTATTATTTAG
Found at i:54441449 original size:26 final size:23
Alignment explanation
Indices: 54441390--54441491 Score: 91
Period size: 24 Copynumber: 4.2 Consensus size: 23
54441380 TGTATCAAAT
54441390 TATTTAAATATAATTTATTATTTA
1 TATTTAAA-ATAATTTATTATTTA
54441414 TATTTAAAATAATTTATTATCATTA
1 TATTTAAAATAATTTATTAT--TTA
*
54441439 GT-TTTATAAATAATTTA-TATTAA
1 -TATTTA-AAATAATTTATTATTTA
* **
54441462 TTATTTAAAAGATATTTAAAATTTA
1 -TATTTAAAATA-ATTTATTATTTA
54441487 TATTT
1 TATTT
54441492 TATGTATTAT
Statistics
Matches: 66, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
23 19 0.29
24 22 0.33
25 14 0.21
26 11 0.17
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (23 bp):
TATTTAAAATAATTTATTATTTA
Found at i:54444789 original size:52 final size:52
Alignment explanation
Indices: 54444700--54444899 Score: 173
Period size: 52 Copynumber: 3.9 Consensus size: 52
54444690 GACGGAAAAG
* ** * *
54444700 ATGTGATATGTGCTTCCGTATAAGACTGTAGCAGGGCTATGGCATTGGTACA
1 ATGTGATATGTGATTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTACA
* ***
54444752 ATGTGAT-TCGTG-TTCCCGTATAAGACCATAGCTGGGCTATGACATCGGTGTG
1 ATGTGATAT-GTGATT-CCGTATAAGACCATAGCTGGGCTATGGCATCGGTACA
* * *
54444804 ATGTGATAATGTGATTCCGTATAAGACCATATCTAGGATATGGCATCGGT---
1 ATGTGAT-ATGTGATTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTACA
* * * *
54444854 A--TGATATGTGA-TCCGTGTAAGACCATGGCAGGGCTATGGCTTCGGT
1 ATGTGATATGTGATTCCGTATAAGACCATAGCTGGGCTATGGCATCGGT
54444900 GTGTGATGTG
Statistics
Matches: 124, Mismatches: 19, Indels: 16
0.78 0.12 0.10
Matches are distributed among these distances:
46 28 0.23
47 6 0.05
48 4 0.03
50 1 0.01
51 3 0.02
52 46 0.37
53 33 0.27
54 3 0.02
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.30
Consensus pattern (52 bp):
ATGTGATATGTGATTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTACA
Found at i:54444899 original size:46 final size:48
Alignment explanation
Indices: 54444767--54444879 Score: 122
Period size: 53 Copynumber: 2.3 Consensus size: 48
54444757 ATTCGTGTTC
* * *
54444767 CCGTATAAGACCATAGCTGGGCTATGACATCGGTGTGATGTGATAATGTGATT
1 CCGTATAAGACCATAGCTAGGATATGGCATC-G-GT-A--TGATAATGTGATT
*
54444820 CCGTATAAGACCATATCTAGGATATGGCATCGGTATGAT-ATGTGA-T
1 CCGTATAAGACCATAGCTAGGATATGGCATCGGTATGATAATGTGATT
*
54444866 CCGTGTAAGACCAT
1 CCGTATAAGACCAT
54444880 GGCAGGGCTA
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
46 14 0.25
47 6 0.11
48 4 0.07
50 1 0.02
51 2 0.04
52 1 0.02
53 27 0.49
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (48 bp):
CCGTATAAGACCATAGCTAGGATATGGCATCGGTATGATAATGTGATT
Found at i:54449987 original size:25 final size:25
Alignment explanation
Indices: 54449959--54450006 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
54449949 TTATAAAAAT
* *
54449959 AATAAAATAAATAAAACATAAAAGG
1 AATAAAACAAACAAAACATAAAAGG
*
54449984 AATAAAACAAACAAAGCATAAAA
1 AATAAAACAAACAAAACATAAAA
54450007 AGAAACAGAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.73, C:0.08, G:0.06, T:0.12
Consensus pattern (25 bp):
AATAAAACAAACAAAACATAAAAGG
Found at i:54452991 original size:20 final size:20
Alignment explanation
Indices: 54452966--54453006 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
54452956 GCCCCATGGC
54452966 CATGTCCCAAGCCACACGGG
1 CATGTCCCAAGCCACACGGG
*
54452986 CATGTCCCAGGCCACACGGG
1 CATGTCCCAAGCCACACGGG
54453006 C
1 C
54453007 GTATGCCCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.22, C:0.41, G:0.27, T:0.10
Consensus pattern (20 bp):
CATGTCCCAAGCCACACGGG
Found at i:54458452 original size:13 final size:13
Alignment explanation
Indices: 54458405--54458446 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
54458395 TAAAGTAATT
* *
54458405 AAATAAAATAAATA
1 AAATAAAAGAAA-G
54458419 AAATAAAAGAAAG
1 AAATAAAAGAAAG
54458432 AAATAAAAGAAAG
1 AAATAAAAGAAAG
54458445 AA
1 AA
54458447 TGAAAACGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
13 15 0.58
14 11 0.42
ACGTcount: A:0.79, C:0.00, G:0.10, T:0.12
Consensus pattern (13 bp):
AAATAAAAGAAAG
Found at i:54458492 original size:16 final size:16
Alignment explanation
Indices: 54458471--54458501 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
54458461 AGCAGGGAAA
*
54458471 GAAAGAAAGAAAAAGG
1 GAAAGAAAAAAAAAGG
54458487 GAAAGAAAAAAAAAG
1 GAAAGAAAAAAAAAG
54458502 AAAATTTAGG
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:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (16 bp):
GAAAGAAAAAAAAAGG
Found at i:54461340 original size:47 final size:47
Alignment explanation
Indices: 54461269--54461436 Score: 284
Period size: 47 Copynumber: 3.6 Consensus size: 47
54461259 GGTTGAGTTT
*
54461269 CGAACTCATTGAGTTGAGGT-CGAGTTCGTGAGATGTAACTAGGCATC
1 CGAACTCGTTGAGTTGA-GTCCGAGTTCGTGAGATGTAACTAGGCATC
*
54461316 CGAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCATC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATC
*
54461363 CGAACTCGTTGAGTTGAGTCCGAGTTTGTGAGATGTAACTAGGCATC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATC
*
54461410 CGAGCTCGTTGAGTTGAGTCCGAGTTC
1 CGAACTCGTTGAGTTGAGTCCGAGTTC
54461437 ACTTATGGAT
Statistics
Matches: 114, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
46 2 0.02
47 112 0.98
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (47 bp):
CGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCATC
Found at i:54466101 original size:4 final size:4
Alignment explanation
Indices: 54466092--54466142 Score: 102
Period size: 4 Copynumber: 12.8 Consensus size: 4
54466082 TGGTTTGACC
54466092 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
54466140 ACA
1 ACA
54466143 GAAGAAACAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 47 1.00
ACGTcount: A:0.51, C:0.25, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:54468370 original size:33 final size:33
Alignment explanation
Indices: 54468333--54468401 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
54468323 GGAGTTCATA
54468333 ATAAAAGAAG-GACCTTCAAGTCTGAGATTTATG
1 ATAAAAGAAGTGA-CTTCAAGTCTGAGATTTATG
* * *
54468366 ATAAAAGAAGTGATTTCAAGTCTGAGGTTTTTG
1 ATAAAAGAAGTGACTTCAAGTCTGAGATTTATG
54468399 ATA
1 ATA
54468402 TGAGCTTACA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 30 0.94
34 2 0.06
ACGTcount: A:0.38, C:0.09, G:0.22, T:0.32
Consensus pattern (33 bp):
ATAAAAGAAGTGACTTCAAGTCTGAGATTTATG
Found at i:54481502 original size:39 final size:38
Alignment explanation
Indices: 54481438--54481563 Score: 171
Period size: 39 Copynumber: 3.3 Consensus size: 38
54481428 TTTTTAACCT
* * *
54481438 GGATATTTTTCAGCACATAGCCTGCGGACCTCAAGTCC
1 GGATATATTTCAGCATATAGCCTGCGGACCTCATGTCC
* *
54481476 GGATATATTTCTAGCATATAGCCTGCGGATCTCATGTCA
1 GGATATATTTC-AGCATATAGCCTGCGGACCTCATGTCC
* *
54481515 GGATATTTTTCCAGCATATAGCCTGCGGACTTCATGTCC
1 GGATATATTT-CAGCATATAGCCTGCGGACCTCATGTCC
54481554 GGATATATTT
1 GGATATATTT
54481564 TCAATCTCAT
Statistics
Matches: 76, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
38 10 0.13
39 65 0.86
40 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.33
Consensus pattern (38 bp):
GGATATATTTCAGCATATAGCCTGCGGACCTCATGTCC
Found at i:54482609 original size:9 final size:9
Alignment explanation
Indices: 54482595--54482627 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
54482585 GTTAAGCGAA
54482595 TCGAGTTAT
1 TCGAGTTAT
*
54482604 TCGAGTTAA
1 TCGAGTTAT
54482613 TCGAGTTAT
1 TCGAGTTAT
54482622 TCGAGT
1 TCGAGT
54482628 CAACTCGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.24, C:0.12, G:0.24, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:54482616 original size:18 final size:18
Alignment explanation
Indices: 54482593--54482627 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
54482583 GAGTTAAGCG
54482593 AATCGAGTTATTCGAGTT
1 AATCGAGTTATTCGAGTT
54482611 AATCGAGTTATTCGAGT
1 AATCGAGTTATTCGAGT
54482628 CAACTCGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.11, G:0.23, T:0.37
Consensus pattern (18 bp):
AATCGAGTTATTCGAGTT
Found at i:54482708 original size:9 final size:9
Alignment explanation
Indices: 54482679--54482715 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
54482669 TGAGTTTTCG
54482679 AATTCGAAT
1 AATTCGAAT
*
54482688 AACTCGAAT
1 AATTCGAAT
54482697 AATTCGAAT
1 AATTCGAAT
*
54482706 AATTAGAAT
1 AATTCGAAT
54482715 A
1 A
54482716 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:54498223 original size:17 final size:17
Alignment explanation
Indices: 54498189--54498244 Score: 76
Period size: 17 Copynumber: 3.2 Consensus size: 17
54498179 AAATAAAATG
*
54498189 AAAAAAGTAGAAACATAT
1 AAAAAAGTA-AAAAATAT
54498207 AAAAAAGTAAAAAATAT
1 AAAAAAGTAAAAAATAT
*
54498224 AAAAAAGTAAATATATAT
1 AAAAAAGTAAA-AAATAT
54498242 AAA
1 AAA
54498245 TAAAAAAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
17 18 0.51
18 17 0.49
ACGTcount: A:0.71, C:0.02, G:0.07, T:0.20
Consensus pattern (17 bp):
AAAAAAGTAAAAAATAT
Found at i:54498252 original size:33 final size:33
Alignment explanation
Indices: 54498176--54498259 Score: 82
Period size: 35 Copynumber: 2.5 Consensus size: 33
54498166 TATAATAATC
54498176 TAAAAATAAA-ATGAAAAAAGTAGAAACATATAAA
1 TAAAAA-AAATAT-AAAAAAGTAGAAACATATAAA
* *
54498210 AAAGTAAAAAATATAAAAAAGTA-AATATATATAAA
1 TAA--AAAAAATATAAAAAAGTAGAA-ACATATAAA
*
54498245 TAAAAAAAATCTAAA
1 TAAAAAAAATATAAA
54498260 TTTTGATTAG
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
33 11 0.26
34 4 0.10
35 22 0.52
36 5 0.12
ACGTcount: A:0.71, C:0.02, G:0.06, T:0.20
Consensus pattern (33 bp):
TAAAAAAAATATAAAAAAGTAGAAACATATAAA
Found at i:54498801 original size:22 final size:22
Alignment explanation
Indices: 54498776--54498819 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
54498766 TAATCATATA
54498776 ATAAATTATTAATATAATAAAT
1 ATAAATTATTAATATAATAAAT
* * *
54498798 ATAATTTATTATTTTAATAAAT
1 ATAAATTATTAATATAATAAAT
54498820 TATTTAATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATAAATTATTAATATAATAAAT
Found at i:54498863 original size:13 final size:15
Alignment explanation
Indices: 54498845--54498885 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
54498835 TTTTATTTTG
54498845 ATAATA-AATTTTAA
1 ATAATATAATTTTAA
54498859 A-AATAATAATTTTAA
1 ATAAT-ATAATTTTAA
*
54498874 ATAATATTATTT
1 ATAATATAATTT
54498886 ACATATTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
13 3 0.13
14 2 0.09
15 15 0.65
16 3 0.13
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
ATAATATAATTTTAA
Found at i:54498866 original size:16 final size:16
Alignment explanation
Indices: 54498845--54498879 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
54498835 TTTTATTTTG
54498845 ATAATAAATTTTAAA-A
1 ATAAT-AATTTTAAATA
54498861 ATAATAATTTTAAATA
1 ATAATAATTTTAAATA
54498877 ATA
1 ATA
54498880 TTATTTACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
ATAATAATTTTAAATA
Found at i:54498932 original size:15 final size:15
Alignment explanation
Indices: 54498912--54498968 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
54498902 ATTCAATATT
54498912 AATATTTTAATAATA
1 AATATTTTAATAATA
*
54498927 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
54498946 AATATATTAATAATA
1 AATATTTTAATAATA
*
54498961 AATGTTTT
1 AATATTTT
54498969 GTAGTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:54504457 original size:33 final size:32
Alignment explanation
Indices: 54504410--54504516 Score: 117
Period size: 33 Copynumber: 3.3 Consensus size: 32
54504400 GGTGTACATT
* **
54504410 CCTTTCCAAGTGGTACACACAAAGTATACATTT
1 CCTTTTCAA-TGGTACACACAAAGTATACATAA
* *
54504443 CCTTTTCATATGGTATACACAAAGTATACCTAA
1 CCTTTTCA-ATGGTACACACAAAGTATACATAA
* *
54504476 CCTTTTCAA-GTGTACACACAAGGTGTACATAA
1 CCTTTTCAATG-GTACACACAAAGTATACATAA
54504508 CCTTTTCAA
1 CCTTTTCAA
54504517 ATTATACCAT
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
31 1 0.02
32 27 0.43
33 34 0.54
34 1 0.02
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32
Consensus pattern (32 bp):
CCTTTTCAATGGTACACACAAAGTATACATAA
Found at i:54509315 original size:54 final size:54
Alignment explanation
Indices: 54509233--54509337 Score: 201
Period size: 54 Copynumber: 1.9 Consensus size: 54
54509223 AGAAGGGTTC
*
54509233 AAAGCTTTTTGGAAAGGCAATCTGGTTACCATTGCTCATCGTCTTCCCTACCCT
1 AAAGCATTTTGGAAAGGCAATCTGGTTACCATTGCTCATCGTCTTCCCTACCCT
54509287 AAAGCATTTTGGAAAGGCAATCTGGTTACCATTGCTCATCGTCTTCCCTAC
1 AAAGCATTTTGGAAAGGCAATCTGGTTACCATTGCTCATCGTCTTCCCTAC
54509338 ACTGCAGTCA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.24, C:0.27, G:0.17, T:0.32
Consensus pattern (54 bp):
AAAGCATTTTGGAAAGGCAATCTGGTTACCATTGCTCATCGTCTTCCCTACCCT
Found at i:54513297 original size:32 final size:32
Alignment explanation
Indices: 54513256--54513322 Score: 125
Period size: 32 Copynumber: 2.1 Consensus size: 32
54513246 CATGAAGTAC
*
54513256 ATTGAATTGTCATTTGGGCTATAATTTTAAAA
1 ATTGAATTGTCATTTGGGCTACAATTTTAAAA
54513288 ATTGAATTGTCATTTGGGCTACAATTTTAAAA
1 ATTGAATTGTCATTTGGGCTACAATTTTAAAA
54513320 ATT
1 ATT
54513323 TAATGTTTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.34, C:0.07, G:0.15, T:0.43
Consensus pattern (32 bp):
ATTGAATTGTCATTTGGGCTACAATTTTAAAA
Found at i:54520071 original size:36 final size:36
Alignment explanation
Indices: 54520024--54520096 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
54520014 AATTGGTTTT
54520024 AATGAAATTAAAATTAGTGTTAATAGCAATGCGTAA
1 AATGAAATTAAAATTAGTGTTAATAGCAATGCGTAA
54520060 AATGAAATTAAAATTAGTGTTAATAGCAATGCGTAA
1 AATGAAATTAAAATTAGTGTTAATAGCAATGCGTAA
54520096 A
1 A
54520097 CATAATATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.48, C:0.05, G:0.16, T:0.30
Consensus pattern (36 bp):
AATGAAATTAAAATTAGTGTTAATAGCAATGCGTAA
Found at i:54521009 original size:25 final size:23
Alignment explanation
Indices: 54520965--54521011 Score: 58
Period size: 25 Copynumber: 2.0 Consensus size: 23
54520955 CAAAGTAAGA
*
54520965 AATTCTAAAATAAAATATAAAAC
1 AATTCTAAAATAAAACATAAAAC
*
54520988 AATTCTAACAAATAATACATAAAA
1 AATTCT-A-AAATAAAACATAAAA
54521012 AGGATTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 6 0.30
24 1 0.05
25 13 0.65
ACGTcount: A:0.64, C:0.11, G:0.00, T:0.26
Consensus pattern (23 bp):
AATTCTAAAATAAAACATAAAAC
Found at i:54521136 original size:21 final size:23
Alignment explanation
Indices: 54521089--54521142 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
54521079 CATTGAAGAT
**
54521089 AAAATAATATATAAAACTCTTTA
1 AAAATAATATATAAAACTAATTA
*
54521112 AAAATAATATAT-AAAC-AATTC
1 AAAATAATATATAAAACTAATTA
54521133 AAAAT-ATATA
1 AAAATAATATA
54521143 ATGTGTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.18
21 7 0.25
22 4 0.14
23 12 0.43
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.31
Consensus pattern (23 bp):
AAAATAATATATAAAACTAATTA
Found at i:54521195 original size:25 final size:25
Alignment explanation
Indices: 54521090--54521245 Score: 81
Period size: 24 Copynumber: 6.3 Consensus size: 25
54521080 ATTGAAGATA
* * *
54521090 AAATAATATATAAAACTCTT-TAA-
1 AAATAATATATAAAAATATTAAAAT
*
54521113 AAATAATATATAAACAAT-TCAAAAT
1 AAATAATATATAAA-AATATTAAAAT
* * *
54521138 ATATAATGTGTAAAAA-AGGTTTAAAAT
1 AAATAATATATAAAAATA---TTAAAAT
* * *
54521165 ACATAATATATGAAAATATTAAAGT
1 AAATAATATATAAAAATATTAAAAT
* *
54521190 AAATAATGTATAAAAAT-TTGAAAT
1 AAATAATATATAAAAATATTAAAAT
* ***
54521214 GAACGTTATATAAAAAT-TTAAAAT
1 AAATAATATATAAAAATATTAAAAT
*
54521238 AGATAATA
1 AAATAATA
54521246 ACAAAAAATG
Statistics
Matches: 97, Mismatches: 28, Indels: 15
0.69 0.20 0.11
Matches are distributed among these distances:
23 15 0.15
24 32 0.33
25 31 0.32
27 18 0.19
28 1 0.01
ACGTcount: A:0.57, C:0.04, G:0.07, T:0.32
Consensus pattern (25 bp):
AAATAATATATAAAAATATTAAAAT
Found at i:54521332 original size:14 final size:15
Alignment explanation
Indices: 54521315--54521396 Score: 68
Period size: 14 Copynumber: 5.5 Consensus size: 15
54521305 ATATAAGAAA
54521315 AATAATA-ATAAAAT
1 AATAATAGATAAAAT
54521329 AATAATAGTATATAAAT
1 AATAATAG-ATA-AAAT
*
54521346 AGA-AATAGA-AATAT
1 A-ATAATAGATAAAAT
54521360 AATAATAG-TAGAAAT
1 AATAATAGATA-AAAT
54521375 -ATAAATAGAT-AAAT
1 AAT-AATAGATAAAAT
54521389 AATAATAG
1 AATAATAG
54521397 TATTAGAATA
Statistics
Matches: 56, Mismatches: 2, Indels: 20
0.72 0.03 0.26
Matches are distributed among these distances:
13 1 0.02
14 28 0.50
15 11 0.20
16 5 0.09
17 10 0.18
18 1 0.02
ACGTcount: A:0.63, C:0.00, G:0.09, T:0.28
Consensus pattern (15 bp):
AATAATAGATAAAAT
Found at i:54521335 original size:17 final size:19
Alignment explanation
Indices: 54521315--54521395 Score: 61
Period size: 17 Copynumber: 4.5 Consensus size: 19
54521305 ATATAAGAAA
54521315 AATAATAATA-AAATA-AT
1 AATAATAATATAAATAGAT
*
54521332 AATAGT-ATATAAATAGA-
1 AATAATAATATAAATAGAT
54521349 AATAGA-AATAT-AATA-AT
1 AATA-ATAATATAAATAGAT
*
54521366 AGTAGA-AATATAAATAGAT
1 AATA-ATAATATAAATAGAT
54521385 AAATAATAATA
1 -AATAATAATA
54521396 GTATTAGAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 15
0.73 0.06 0.21
Matches are distributed among these distances:
16 4 0.08
17 28 0.55
18 9 0.18
19 3 0.06
20 7 0.14
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.28
Consensus pattern (19 bp):
AATAATAATATAAATAGAT
Found at i:54521358 original size:23 final size:24
Alignment explanation
Indices: 54521315--54521392 Score: 67
Period size: 23 Copynumber: 3.3 Consensus size: 24
54521305 ATATAAGAAA
*
54521315 AATAATAATA-AAATA-ATAATAGT
1 AATAATAGTAGAAATAGA-AATAGT
54521338 ATATAA-A-TAGAAATAGAAATA-T
1 A-ATAATAGTAGAAATAGAAATAGT
*
54521360 AATAATAGTAGAAATATAAATAGAT
1 AATAATAGTAGAAATAGAAATAG-T
54521385 AAATAATA
1 -AATAATA
54521393 ATAGTATTAG
Statistics
Matches: 46, Mismatches: 1, Indels: 13
0.77 0.02 0.22
Matches are distributed among these distances:
21 4 0.09
22 5 0.11
23 24 0.52
24 5 0.11
25 1 0.02
26 7 0.15
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (24 bp):
AATAATAGTAGAAATAGAAATAGT
Found at i:54521374 original size:29 final size:29
Alignment explanation
Indices: 54521325--54521398 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 29
54521315 AATAATAATA
*
54521325 AAATAATAATAGTATATAAATAGAAATAGA-
1 AAATAATAATAG--TAGAAATAGAAATAGAT
*
54521355 AATATAATAATAGTAGAAATATAAATAGAT
1 AA-ATAATAATAGTAGAAATAGAAATAGAT
54521385 AAATAATAATAGTA
1 AAATAATAATAGTA
54521399 TTAGAATAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
29 26 0.65
30 4 0.10
31 10 0.25
ACGTcount: A:0.62, C:0.00, G:0.09, T:0.28
Consensus pattern (29 bp):
AAATAATAATAGTAGAAATAGAAATAGAT
Found at i:54521407 original size:29 final size:27
Alignment explanation
Indices: 54521324--54521407 Score: 87
Period size: 29 Copynumber: 2.9 Consensus size: 27
54521314 AAATAATAAT
54521324 AAAATAATAATAGTATATAAATAGAAATAG
1 AAAATAATAATAGTAT-TAAAT--AAATAG
**
54521354 AAATATAATAATAGTAGAAATATAAATAG
1 AAA-ATAATAATAGTATTAA-ATAAATAG
54521383 ATAAATAATAATAGTATTAGAATAA
1 A-AAATAATAATAGTATTA-AATAA
54521408 CAGAATAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
29 24 0.52
30 8 0.17
31 14 0.30
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.29
Consensus pattern (27 bp):
AAAATAATAATAGTATTAAATAAATAG
Found at i:54525213 original size:23 final size:24
Alignment explanation
Indices: 54525185--54525241 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 24
54525175 ATTGAATCTT
*
54525185 AATTTTAAATTTTGAAAAA-AATA
1 AATTTTAAATTTTGAAAAATAAAA
*
54525208 AATTTTAAA--ATGAAAAATAAAA
1 AATTTTAAATTTTGAAAAATAAAA
*
54525230 AAATTTAAATTT
1 AATTTTAAATTT
54525242 AAATATGCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
21 7 0.26
22 11 0.41
23 9 0.33
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.37
Consensus pattern (24 bp):
AATTTTAAATTTTGAAAAATAAAA
Found at i:54528115 original size:16 final size:15
Alignment explanation
Indices: 54528077--54528119 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
54528067 AATGAAACAT
54528077 ACAAATTGAAATAAA
1 ACAAATTGAAATAAA
* *
54528092 ACTTAATTGAGATAAA
1 AC-AAATTGAAATAAA
54528108 ATCAAATTGAAA
1 A-CAAATTGAAA
54528120 GGGGGCAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
15 2 0.09
16 19 0.86
17 1 0.05
ACGTcount: A:0.58, C:0.07, G:0.09, T:0.26
Consensus pattern (15 bp):
ACAAATTGAAATAAA
Found at i:54540372 original size:33 final size:33
Alignment explanation
Indices: 54540333--54540398 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
54540323 CAAAATTATT
*
54540333 CCAAACCCAA-CTCGAATTAACCAAAACCAAAA
1 CCAAAACCAATCTCGAATTAACCAAAACCAAAA
54540365 CCAAAACCAATCTCGAATTAACCAAAACCAAAA
1 CCAAAACCAATCTCGAATTAACCAAAACCAAAA
54540398 C
1 C
54540399 TAACCCATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 9 0.28
33 23 0.72
ACGTcount: A:0.53, C:0.33, G:0.03, T:0.11
Consensus pattern (33 bp):
CCAAAACCAATCTCGAATTAACCAAAACCAAAA
Found at i:54543959 original size:20 final size:20
Alignment explanation
Indices: 54543936--54544012 Score: 63
Period size: 20 Copynumber: 3.9 Consensus size: 20
54543926 TTAATATTTT
54543936 TAAATCTTTAGATATTTTGA
1 TAAATCTTTAGATATTTTGA
54543956 TAAAGTCTTATA-ATA--TTGA
1 TAAA-TCTT-TAGATATTTTGA
* * *
54543975 TAAATCTTTAAAAATATT-A
1 TAAATCTTTAGATATTTTGA
*
54543994 GTAAATTTTTAGATATTTT
1 -TAAATCTTTAGATATTTT
54544013 AGTAAAAGTT
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
17 2 0.04
18 6 0.13
19 9 0.20
20 20 0.43
21 7 0.15
22 2 0.04
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (20 bp):
TAAATCTTTAGATATTTTGA
Found at i:54543971 original size:21 final size:17
Alignment explanation
Indices: 54543926--54543985 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 17
54543916 TAAGAATTTA
54543926 TTAATATTTTTAAATCT
1 TTAATATTTTTAAATCT
54543943 TTAGATATTTTGATAAAGTCT
1 TTA-ATATTTT--TAAA-TCT
**
54543964 TATAATATTGATAAATCT
1 T-TAATATTTTTAAATCT
54543982 TTAA
1 TTAA
54543986 AAATATTAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
17 6 0.17
18 11 0.31
19 4 0.11
20 4 0.11
21 9 0.25
22 2 0.06
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50
Consensus pattern (17 bp):
TTAATATTTTTAAATCT
Found at i:54560634 original size:29 final size:31
Alignment explanation
Indices: 54560584--54560644 Score: 83
Period size: 29 Copynumber: 2.0 Consensus size: 31
54560574 AAATTTCAGA
*
54560584 ACCATAATTTAAATTTCATATAT-ATAATTAC
1 ACCATAATTAAAATTTCATATATCA-AATTAC
54560615 ACCA-AATTAAAATTT-ATATATCAAATTAC
1 ACCATAATTAAAATTTCATATATCAAATTAC
54560644 A
1 A
54560645 TATTAAACCT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 13 0.46
30 11 0.39
31 4 0.14
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (31 bp):
ACCATAATTAAAATTTCATATATCAAATTAC
Found at i:54564492 original size:20 final size:20
Alignment explanation
Indices: 54564469--54564529 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 20
54564459 TATTTTAAAA
54564469 ATTAAAATTAAATTTTTATT
1 ATTAAAATTAAATTTTTATT
* *
54564489 ATTAATATAATAAATTTTGATT
1 ATTAA-A-ATTAAATTTTTATT
54564511 -TTATTAAATT-AATTTTTAT
1 ATTA--AAATTAAATTTTTAT
54564530 ATAAAAACCA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
20 13 0.39
21 6 0.18
22 13 0.39
23 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
ATTAAAATTAAATTTTTATT
Found at i:54583449 original size:30 final size:30
Alignment explanation
Indices: 54583409--54583465 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
54583399 ATAACTCATA
54583409 TTTAACAGAGATGGCAACGAGAAATTGACT
1 TTTAACAGAGATGGCAACGAGAAATTGACT
* *
54583439 TTTAATAGAGATGGCAACGAGAGATTG
1 TTTAACAGAGATGGCAACGAGAAATTG
54583466 GTCAGCGATG
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:0.39, C:0.11, G:0.26, T:0.25
Consensus pattern (30 bp):
TTTAACAGAGATGGCAACGAGAAATTGACT
Found at i:54585154 original size:71 final size:71
Alignment explanation
Indices: 54585038--54585252 Score: 430
Period size: 71 Copynumber: 3.0 Consensus size: 71
54585028 AATGAATACC
54585038 AAATATTACTTTTGTTGAAATGGCAGCTAGGGAGGATGTATGTATGGCCTTTTGGGTTTAAATCC
1 AAATATTACTTTTGTTGAAATGGCAGCTAGGGAGGATGTATGTATGGCCTTTTGGGTTTAAATCC
54585103 TATTTG
66 TATTTG
54585109 AAATATTACTTTTGTTGAAATGGCAGCTAGGGAGGATGTATGTATGGCCTTTTGGGTTTAAATCC
1 AAATATTACTTTTGTTGAAATGGCAGCTAGGGAGGATGTATGTATGGCCTTTTGGGTTTAAATCC
54585174 TATTTG
66 TATTTG
54585180 AAATATTACTTTTGTTGAAATGGCAGCTAGGGAGGATGTATGTATGGCCTTTTGGGTTTAAATCC
1 AAATATTACTTTTGTTGAAATGGCAGCTAGGGAGGATGTATGTATGGCCTTTTGGGTTTAAATCC
54585245 TATTTG
66 TATTTG
54585251 AA
1 AA
54585253 GCATGATTTT
Statistics
Matches: 144, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 144 1.00
ACGTcount: A:0.26, C:0.10, G:0.25, T:0.39
Consensus pattern (71 bp):
AAATATTACTTTTGTTGAAATGGCAGCTAGGGAGGATGTATGTATGGCCTTTTGGGTTTAAATCC
TATTTG
Found at i:54588261 original size:35 final size:34
Alignment explanation
Indices: 54588203--54588271 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 34
54588193 ATCAACAATT
* *
54588203 ATTTTTTTTTTAAATTAT-TTTTTTTATATTTTTA
1 ATTTTTTTTTGAAATTATATTTTTTGA-ATTTTTA
*
54588237 ATTTTTTTTTGAAGTTTATATTTTTTGAATTTTTA
1 ATTTTTTTTTGAA-ATTATATTTTTTGAATTTTTA
54588272 GATATTTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
34 12 0.40
35 11 0.37
36 7 0.23
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.72
Consensus pattern (34 bp):
ATTTTTTTTTGAAATTATATTTTTTGAATTTTTA
Found at i:54589621 original size:32 final size:32
Alignment explanation
Indices: 54589585--54589647 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
54589575 TTTTAACAAT
54589585 TTTCTAAATTATTTTAACATATTACCTTAAAA
1 TTTCTAAATTATTTTAACATATTACCTTAAAA
*
54589617 TTTCTAAATTATTTTAGCATATTACCTTAAA
1 TTTCTAAATTATTTTAACATATTACCTTAAA
54589648 CACTTTGATA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.38, C:0.13, G:0.02, T:0.48
Consensus pattern (32 bp):
TTTCTAAATTATTTTAACATATTACCTTAAAA
Found at i:54591940 original size:42 final size:42
Alignment explanation
Indices: 54591890--54592016 Score: 170
Period size: 42 Copynumber: 3.0 Consensus size: 42
54591880 CTTCATTTTC
** *
54591890 TCGATGCCATAGTTCAACTATGGTCTTACACATCTTCACATAA
1 TCGATGCCATAGCCCAACTATGGTCTTACACATATTCACAT-A
*
54591933 T-GATGCCATAGCCCAACTATGGTCTTACACATATTCATATA
1 TCGATGCCATAGCCCAACTATGGTCTTACACATATTCACATA
*
54591974 TCGATGCCATAGCCCAGCTATGGTCTTACACGA-A-TCACATA
1 TCGATGCCATAGCCCAACTATGGTCTTACAC-ATATTCACATA
54592015 TC
1 TC
54592017 TCACTGATGC
Statistics
Matches: 76, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
41 10 0.13
42 64 0.84
43 2 0.03
ACGTcount: A:0.30, C:0.27, G:0.13, T:0.30
Consensus pattern (42 bp):
TCGATGCCATAGCCCAACTATGGTCTTACACATATTCACATA
Found at i:54592111 original size:31 final size:31
Alignment explanation
Indices: 54592076--54592222 Score: 224
Period size: 31 Copynumber: 4.7 Consensus size: 31
54592066 CTTGTCACCT
*
54592076 GTAGCCGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
54592107 GTAGCCGGAGCTACCACTTTTCATTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
54592138 GTAGCCGGAA-CTACCACTTTTCACTGATCAG
1 GTAGCC-GAAGCTACCACTTTTCACTGATCAG
**
54592169 GTAGCAAAAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
54592200 GTAGCTGAAGCTACCACTTTTCA
1 GTAGCCGAAGCTACCACTTTTCA
54592223 TTTGTCATTT
Statistics
Matches: 105, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
30 2 0.02
31 101 0.96
32 2 0.02
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:54592303 original size:50 final size:51
Alignment explanation
Indices: 54592200--54592328 Score: 190
Period size: 50 Copynumber: 2.5 Consensus size: 51
54592190 CACTGATCAG
* * * *
54592200 GTAGCTGAAGCTACCACTTTTCATTTGTCATTTGTCATTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCATTTGTCATTGATCAGATAAGT
*
54592251 GTAGCCGAAGCTATCACTTATCACTT-TCACTTT-TCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCA-TTTGTCATTGATCAGATAAGT
54592301 GTAGCCGAAGCTATCACTTATCACTTGT
1 GTAGCCGAAGCTATCACTTATCACTTGT
54592329 TGCCATGGTC
Statistics
Matches: 71, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
50 45 0.63
51 26 0.37
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (51 bp):
GTAGCCGAAGCTATCACTTATCACTTGTCATTTGTCATTGATCAGATAAGT
Found at i:54608063 original size:27 final size:27
Alignment explanation
Indices: 54608033--54608116 Score: 77
Period size: 27 Copynumber: 3.1 Consensus size: 27
54608023 AAGCCCACCC
54608033 ATATTATTTTTATTTTTGAAAATATTT
1 ATATTATTTTTATTTTTGAAAATATTT
*
54608060 ATATTA-TATTA-TTTT-AATTTAATATTT
1 ATATTATTTTTATTTTTGAA---AATATTT
* *
54608087 A-ATAATTTTTATTTATTGAAAATTTTT
1 ATATTATTTTTATTT-TTGAAAATATTT
54608114 ATA
1 ATA
54608117 GAATCATCTT
Statistics
Matches: 45, Mismatches: 4, Indels: 15
0.70 0.06 0.23
Matches are distributed among these distances:
24 2 0.04
25 4 0.09
26 7 0.16
27 25 0.56
28 3 0.07
29 2 0.04
30 2 0.04
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (27 bp):
ATATTATTTTTATTTTTGAAAATATTT
Found at i:54608882 original size:16 final size:16
Alignment explanation
Indices: 54608861--54608892 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
54608851 TATTTTTTAA
54608861 TAAAATTTTTATATTT
1 TAAAATTTTTATATTT
54608877 TAAAATTTTTATATTT
1 TAAAATTTTTATATTT
54608893 GCTTTTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TAAAATTTTTATATTT
Found at i:54610113 original size:24 final size:24
Alignment explanation
Indices: 54610085--54610134 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
54610075 TTTTTTCCTC
* *
54610085 TTCCCTTTCCTTCTCT-CCTCTCTT
1 TTCCCTCTCCCTCTCTCCCT-TCTT
54610109 TTCCCTCTCCCTCTCTCCCTTCTT
1 TTCCCTCTCCCTCTCTCCCTTCTT
54610133 TT
1 TT
54610135 TCTTTAATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 20 0.87
25 3 0.13
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (24 bp):
TTCCCTCTCCCTCTCTCCCTTCTT
Found at i:54610121 original size:17 final size:18
Alignment explanation
Indices: 54610090--54610124 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
54610080 TCCTCTTCCC
*
54610090 TTTCCTTCTCTCCTCTCT
1 TTTCCCTCTCTCCTCTCT
54610108 TTTCCCTCTC-CCTCTCT
1 TTTCCCTCTCTCCTCTCT
54610125 CCCTTCTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTCCCTCTCTCCTCTCT
Found at i:54619606 original size:30 final size:30
Alignment explanation
Indices: 54619570--54619633 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
54619560 CAATTTTAAG
54619570 TATGGTTATAGCTTAGCCTAACATTTCTAC
1 TATGGTTATAGCTTAGCCTAACATTTCTAC
54619600 TATGGTTATAGCTTAGCCTAACATTTCTAC
1 TATGGTTATAGCTTAGCCTAACATTTCTAC
54619630 TATG
1 TATG
54619634 TTTTTGCAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.41
Consensus pattern (30 bp):
TATGGTTATAGCTTAGCCTAACATTTCTAC
Found at i:54629706 original size:13 final size:13
Alignment explanation
Indices: 54629684--54629720 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
54629674 ATCACCCCCA
*
54629684 CACCCTACTAAAT
1 CACCCCACTAAAT
54629697 CACCCCACTAAAT
1 CACCCCACTAAAT
54629710 CACCCCACTAA
1 CACCCCACTAA
54629721 CTCTATCACC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.38, C:0.46, G:0.00, T:0.16
Consensus pattern (13 bp):
CACCCCACTAAAT
Found at i:54629730 original size:30 final size:30
Alignment explanation
Indices: 54629695--54629765 Score: 97
Period size: 30 Copynumber: 2.4 Consensus size: 30
54629685 ACCCTACTAA
* *
54629695 ATCACCCCACTAAATCACCCCACTAACTCT
1 ATCACCCCACTAAACCACCCCACTAACTCC
* *
54629725 ATCACCCCACTAAACCATCCTACTAACTCC
1 ATCACCCCACTAAACCACCCCACTAACTCC
*
54629755 ATTACCCCACT
1 ATCACCCCACT
54629766 TGCCACTAAC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.32, C:0.46, G:0.00, T:0.21
Consensus pattern (30 bp):
ATCACCCCACTAAACCACCCCACTAACTCC
Found at i:54629778 original size:24 final size:24
Alignment explanation
Indices: 54629746--54629793 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
54629736 AAACCATCCT
*
54629746 ACTAACTCCATTACCCCACTTGCC
1 ACTAACTCCATCACCCCACTTGCC
54629770 ACTAACTCCATCACCCCACTTGCC
1 ACTAACTCCATCACCCCACTTGCC
54629794 TACAAAAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.25, C:0.48, G:0.04, T:0.23
Consensus pattern (24 bp):
ACTAACTCCATCACCCCACTTGCC
Found at i:54630887 original size:126 final size:126
Alignment explanation
Indices: 54630657--54630890 Score: 351
Period size: 126 Copynumber: 1.9 Consensus size: 126
54630647 TTCTCAATTG
* * * * * * * * *
54630657 TTTTTAAAATAATGGCAATGTTCGGTATTTAAAGACTTTGAAGAATCGTGCCCTAACGTATTGGG
1 TTTTCAAAATAAAGGCAATGGTCAGTATTTAAAGAATTCGAAGAATCATGCCCTAACGTACTGGC
* * *
54630722 TTTTGCTTTCTTTGTTTGTCTTGAATATTCGGATATCCTCTTACCAGTTCACTCTAAAAAA
66 TTTCGCTTTATTTGTTTGTCTTGAATATTCGAATATCCTCTTACCAGTTCACTCTAAAAAA
54630783 TTTTCAAAATAAAGGCAATGGTCAGTATTTAAAGAATTCGAAGAATCATGCCCTAACGTACTGGC
1 TTTTCAAAATAAAGGCAATGGTCAGTATTTAAAGAATTCGAAGAATCATGCCCTAACGTACTGGC
*
54630848 TTTCGCTTTATTTGTTTGTTTTGAATATTCGAATATCCTCTTA
66 TTTCGCTTTATTTGTTTGTCTTGAATATTCGAATATCCTCTTA
54630891 AGGCTAAAAC
Statistics
Matches: 95, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
126 95 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (126 bp):
TTTTCAAAATAAAGGCAATGGTCAGTATTTAAAGAATTCGAAGAATCATGCCCTAACGTACTGGC
TTTCGCTTTATTTGTTTGTCTTGAATATTCGAATATCCTCTTACCAGTTCACTCTAAAAAA
Found at i:54632237 original size:19 final size:19
Alignment explanation
Indices: 54632213--54632259 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
54632203 GACGTCTTCT
*
54632213 TTTGCATT-CATCCCATGCA
1 TTTGCATTACATCACAT-CA
54632232 TTTGCATTACATCACATCA
1 TTTGCATTACATCACATCA
*
54632251 TGTGCATTA
1 TTTGCATTA
54632260 ATTCAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.26, C:0.26, G:0.11, T:0.38
Consensus pattern (19 bp):
TTTGCATTACATCACATCA
Found at i:54634617 original size:18 final size:18
Alignment explanation
Indices: 54634584--54634618 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
54634574 TCAAATTTAA
* *
54634584 AAAAAAAAAGACAAAAGG
1 AAAAAAAAACAAAAAAGG
54634602 AAAAAAAAACAAAAAAG
1 AAAAAAAAACAAAAAAG
54634619 AAGAAAAGAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.83, C:0.06, G:0.11, T:0.00
Consensus pattern (18 bp):
AAAAAAAAACAAAAAAGG
Found at i:54634625 original size:18 final size:18
Alignment explanation
Indices: 54634584--54634625 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
54634574 TCAAATTTAA
* *
54634584 AAAAAAAAAGACAAAAGG
1 AAAAAAAAACACAAAAAG
54634602 AAAAAAAAACA-AAAAAG
1 AAAAAAAAACACAAAAAG
*
54634619 AAGAAAA
1 AAAAAAA
54634626 GATGCCAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.83, C:0.05, G:0.12, T:0.00
Consensus pattern (18 bp):
AAAAAAAAACACAAAAAG
Found at i:54635895 original size:23 final size:25
Alignment explanation
Indices: 54635869--54635915 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
54635859 TATCATTCAT
*
54635869 TTCATTATAT-CA-ATATTTTATGC
1 TTCATCATATCCATATATTTTATGC
*
54635892 TTCATCATTTCCATATATTTTATG
1 TTCATCATATCCATATATTTTATG
54635916 TATATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 2 0.10
25 10 0.50
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.53
Consensus pattern (25 bp):
TTCATCATATCCATATATTTTATGC
Found at i:54646076 original size:85 final size:85
Alignment explanation
Indices: 54645981--54646708 Score: 1232
Period size: 85 Copynumber: 8.6 Consensus size: 85
54645971 TGAATCCACA
*
54645981 CGCCTTAACCCCTTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCGCCGAGCAGT
1 CGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCGCCGAGCAGT
54646046 GGTGGAGCAGGTCGAAGACT
66 GGTGGAGCAGGTCGAAGACT
54646066 CGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCGCCGAGCAGT
1 CGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCGCCGAGCAGT
54646131 GGTGGAGCAGGTCGAAGACT
66 GGTGGAGCAGGTCGAAGACT
54646151 CGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCGCCGAGCAGT
1 CGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCGCCGAGCAGT
54646216 GGTGGAGCAGGTCGAAGACT
66 GGTGGAGCAGGTCGAAGACT
54646236 CGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCGCCGAGCAGT
1 CGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCGCCGAGCAGT
54646301 GGTGGAGCAGGTCGAAGACT
66 GGTGGAGCAGGTCGAAGACT
* * * *
54646321 CGCCTTAAGCCCCTAAGCAGTAGGGTAACAGGCTAAAGTTTACAGATTTGGGCTCACCGAGCAGT
1 CGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCGCCGAGCAGT
54646386 GGTGGAGCAGGTCGAAGA-T
66 GGTGGAGCAGGTCGAAGACT
*
54646405 CCGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCCT-GGCTCTCCGAGCA
1 -CGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGAT-CTGGGCTCGCCGAGCA
*
54646469 GTGGTGGAGTAGGTCGAAGACT
64 GTGGTGGAGCAGGTCGAAGACT
* * * *
54646491 CGCCTTAAGCCCCTAAGCAGTAGGGTAACAGGCTAAAGTTTACAGATTTGGGCTCACCGAGCAGT
1 CGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCGCCGAGCAGT
*
54646556 GGTGGAACAGGTCGAAGA-T
66 GGTGGAGCAGGTCGAAGACT
* *
54646575 CCGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCCT-GGCTCTCCGAACA
1 -CGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGAT-CTGGGCTCGCCGAGCA
*
54646639 GTGGTGGAGTAGGTCGAAGACT
64 GTGGTGGAGCAGGTCGAAGACT
* *
54646661 CGCCTTAATCCCCTAAGTAGTAGGGTAACAGGCTAAAA-TTACAGATCT
1 CGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCT
54646709 CATCCCACTA
Statistics
Matches: 611, Mismatches: 25, Indels: 16
0.94 0.04 0.02
Matches are distributed among these distances:
83 2 0.00
84 11 0.02
85 594 0.97
86 4 0.01
ACGTcount: A:0.28, C:0.24, G:0.28, T:0.20
Consensus pattern (85 bp):
CGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCGCCGAGCAGT
GGTGGAGCAGGTCGAAGACT
Found at i:54646987 original size:133 final size:135
Alignment explanation
Indices: 54646749--54647026 Score: 384
Period size: 133 Copynumber: 2.1 Consensus size: 135
54646739 ATTTCGACAA
* *
54646749 ATCTTATCTTCACTAAGCAGGAGTGAAGCAGATCAAATTTTGGCAAGTCTTATCTCCATGTAACG
1 ATCTTATCTTCACTAAGCAGGAGCGAAGCAAATCAAATTTTGGCAAGTCTTATCTCCATGTAACG
* * * *
54646814 GCAATGGAGTAGATTTCAGCCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCT-AA-AT
66 GCAATGGAGTAGATTCCAACCATCAGCCTTATCTTCACTGAGCAGAAGTGGAACAGGCTAAACAT
*
54646877 ACTAG
131 ACCAG
** * * * *
54646882 ATCTTATCTTCGTTGAGCAGGAGCGGAGCAAATCAAATTTTGATG-AA-TCTTATCTCTATGTAT
1 ATCTTATCTTCACTAAGCAGGAGCGAAGCAAATCAAATTTTG--GCAAGTCTTATCTCCATGTAA
*
54646945 CGGCAATGGAGTAGATTCCAATCATCAGCCTTATCTTCACTGAGCAGAAGTGGAACAGGCTAAAC
64 CGGCAATGGAGTAGATTCCAACCATCAGCCTTATCTTCACTGAGCAGAAGTGGAACAGGCTAAAC
54647010 ATACCAG
129 ATACCAG
54647017 ATCTTATCTT
1 ATCTTATCTT
54647027 TACTGGACAG
Statistics
Matches: 127, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
133 106 0.83
134 4 0.03
135 17 0.13
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (135 bp):
ATCTTATCTTCACTAAGCAGGAGCGAAGCAAATCAAATTTTGGCAAGTCTTATCTCCATGTAACG
GCAATGGAGTAGATTCCAACCATCAGCCTTATCTTCACTGAGCAGAAGTGGAACAGGCTAAACAT
ACCAG
Found at i:54647827 original size:26 final size:26
Alignment explanation
Indices: 54647791--54647840 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
54647781 TAGGGGATCG
*
54647791 CTTCCAGGATACATCCGTACCTATGT
1 CTTCCAGGATACATCCGTAACTATGT
*
54647817 CTTCCGGGATACATCCGTAACTAT
1 CTTCCAGGATACATCCGTAACTAT
54647841 ACCAAGCTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.24, C:0.30, G:0.16, T:0.30
Consensus pattern (26 bp):
CTTCCAGGATACATCCGTAACTATGT
Found at i:54648456 original size:126 final size:126
Alignment explanation
Indices: 54648298--54648526 Score: 386
Period size: 126 Copynumber: 1.8 Consensus size: 126
54648288 GTTTTAGCCT
*
54648298 TAAGAGGATATTCGAATATTCAAAACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATT
1 TAAGAGGATATCCGAATATTCAAAACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATT
* * * *
54648363 CTTCGAATTCTTTAAATACTGACCATTGCCTTTATTTTGAAATTTTTTTAGAGTGAACTGG
66 CTTCGAAGTCTTTAAATACCGAACATTGCCATTATTTTGAAATTTTTTTAGAGTGAACTGG
* * *
54648424 TAAGAGGATATCCGAATATTCAAGACAAACAAAGAAAGCGAAGCCCAGTACGTTAGGGCACTATT
1 TAAGAGGATATCCGAATATTCAAAACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATT
54648489 CTTCGAAGTCTTTAAATACCGAACATTGCCATTATTTT
66 CTTCGAAGTCTTTAAATACCGAACATTGCCATTATTTT
54648527 AAAAACAATT
Statistics
Matches: 95, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
126 95 1.00
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.29
Consensus pattern (126 bp):
TAAGAGGATATCCGAATATTCAAAACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATT
CTTCGAAGTCTTTAAATACCGAACATTGCCATTATTTTGAAATTTTTTTAGAGTGAACTGG
Found at i:54649047 original size:45 final size:45
Alignment explanation
Indices: 54648997--54649086 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 45
54648987 GAGAATAGAC
*
54648997 AAAGAAAACCTCTTTTGCTTTGATATTTGATTAATCTCAAAAAAA
1 AAAGAAAACCTATTTTGCTTTGATATTTGATTAATCTCAAAAAAA
* *
54649042 AAAGAAAACTTATTTTGCTTTGATATTTGATTAATCTCCAAAAAA
1 AAAGAAAACCTATTTTGCTTTGATATTTGATTAATCTCAAAAAAA
54649087 GAACTCCCCC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.37
Consensus pattern (45 bp):
AAAGAAAACCTATTTTGCTTTGATATTTGATTAATCTCAAAAAAA
Found at i:54649215 original size:29 final size:30
Alignment explanation
Indices: 54649167--54649236 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 30
54649157 TTTGTAGGCA
54649167 AGTGGGGTGATAGAGATAGT-GGATGATTT
1 AGTGGGGTGATAGAGATAGTGGGATGATTT
* * *
54649196 AGTGGGGTGATGGAGTTAGTGGGGTGATTT
1 AGTGGGGTGATAGAGATAGTGGGATGATTT
*
54649226 AGTGGGTTGAT
1 AGTGGGGTGAT
54649237 TTAGTAGGGT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 18 0.50
30 18 0.50
ACGTcount: A:0.21, C:0.00, G:0.46, T:0.33
Consensus pattern (30 bp):
AGTGGGGTGATAGAGATAGTGGGATGATTT
Found at i:54649229 original size:13 final size:13
Alignment explanation
Indices: 54649190--54649247 Score: 62
Period size: 13 Copynumber: 4.2 Consensus size: 13
54649180 AGATAGTGGA
54649190 TGATTTAGTGGGG
1 TGATTTAGTGGGG
54649203 TGATGGAGTTAGTGGGG
1 TGAT----TTAGTGGGG
*
54649220 TGATTTAGTGGGT
1 TGATTTAGTGGGG
*
54649233 TGATTTAGTAGGG
1 TGATTTAGTGGGG
54649246 TG
1 TG
54649248 TGGGGGTGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
13 25 0.66
17 13 0.34
ACGTcount: A:0.17, C:0.00, G:0.45, T:0.38
Consensus pattern (13 bp):
TGATTTAGTGGGG
Found at i:54649576 original size:13 final size:14
Alignment explanation
Indices: 54649551--54649592 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
54649541 TTATAATATG
54649551 TAAATTATATAAAA
1 TAAATTATATAAAA
54649565 TAAATT-TATAAAA
1 TAAATTATATAAAA
* *
54649578 -ACATTATACAAAA
1 TAAATTATATAAAA
54649591 TA
1 TA
54649593 TAAAATGTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 4 0.17
13 13 0.54
14 7 0.29
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (14 bp):
TAAATTATATAAAA
Found at i:54651387 original size:26 final size:27
Alignment explanation
Indices: 54651358--54651409 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
54651348 GTTTTTGAGT
*
54651358 TTAAT-TTTAATGAGAACTTTTAAAAA
1 TTAATGTTTAATGAAAACTTTTAAAAA
* *
54651384 TTAATGTTTAATTAAAATTTTTAAAA
1 TTAATGTTTAATGAAAACTTTTAAAA
54651410 TTTTGTGTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 5 0.23
27 17 0.77
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (27 bp):
TTAATGTTTAATGAAAACTTTTAAAAA
Found at i:54651410 original size:26 final size:26
Alignment explanation
Indices: 54651358--54651411 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
54651348 GTTTTTGAGT
*
54651358 TTAATTTTAATGAGAACTTTTAAAAA
1 TTAATTTTAATGAGAAATTTTAAAAA
* *
54651384 TTAATGTTTAATTA-AAATTTTTAAAA
1 TTAAT-TTTAATGAGAAATTTTAAAAA
54651410 TT
1 TT
54651412 TTGTGTAGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 17 0.71
27 7 0.29
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (26 bp):
TTAATTTTAATGAGAAATTTTAAAAA
Found at i:54675811 original size:30 final size:30
Alignment explanation
Indices: 54675748--54675811 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 30
54675738 TTTTATGTGA
*
54675748 AATTTAAACATTTTATTGAAATAATATTTT
1 AATTTAAACATTTTATTGAAATAATATTAT
*
54675778 AATTTAAATCACTTTTATT-TAATAA-ATTAT
1 AATTTAAA-CA-TTTTATTGAAATAATATTAT
54675808 AATT
1 AATT
54675812 AACAGTCTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 16 0.53
31 7 0.23
32 7 0.23
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.50
Consensus pattern (30 bp):
AATTTAAACATTTTATTGAAATAATATTAT
Found at i:54679374 original size:15 final size:15
Alignment explanation
Indices: 54679339--54679380 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
54679329 TTAAGAATTT
*
54679339 TATTAAATTAT-ATA
1 TATTTAATTATAATA
54679353 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
54679367 TATTTAATAATAAT
1 TATTTAATTATAAT
54679381 TATGTTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:54679411 original size:59 final size:59
Alignment explanation
Indices: 54679348--54679629 Score: 170
Period size: 60 Copynumber: 4.7 Consensus size: 59
54679338 TTATTAAATT
**
54679348 ATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTACCTTTTATAGTATC
1 ATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTAAATTTTATAGTATC
* * * * * * * * *
54679407 ATATATTATGATTTTAGTAAATTCATATAAGAA-TATTGATT--ATTAGAATTTTATTA-AATT
1 ATATATTTTAATTATAATATATTTA-ATAATAATTA-TG-TTAAATTA-AATTTTA-TAGTATC
* * *
54679467 ATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTATATTTTATAGTATC
1 ATATATTTTAATTATAATATATTTAATAATAATTATGTT-AAATTAAATTTTATAGTATC
* * * * * * * *
54679526 ATATATTATGATTTTAGTA-AATTATATAAGAA-TA--TTAATTATTAAGAATTTTATTA-AATT
1 ATATATTTTAATTATAATATATTTA-ATAATAATTATGTTAA--ATT-A-AATTTTA-TAGTATC
*
54679586 ATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAAT
1 ATATATTTTAATTATAATATATTTAATAATAATTATG-TTAAAT
54679630 ATGATTAAAT
Statistics
Matches: 161, Mismatches: 41, Indels: 39
0.67 0.17 0.16
Matches are distributed among these distances:
56 2 0.01
57 4 0.02
58 11 0.07
59 59 0.37
60 67 0.42
61 12 0.07
62 2 0.01
64 4 0.02
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (59 bp):
ATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTAAATTTTATAGTATC
Found at i:54679480 original size:18 final size:17
Alignment explanation
Indices: 54679454--54679488 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
54679444 GATTATTAGA
*
54679454 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
54679471 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
54679489 TTAATATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:54679500 original size:119 final size:120
Alignment explanation
Indices: 54679287--54679629 Score: 584
Period size: 119 Copynumber: 2.9 Consensus size: 120
54679277 NNNNNNNNNN
* *
54679287 ATATATTATGGTTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATAT
1 ATATATTATGATTTTAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATAT
* *
54679352 ATTTTAATTATAATATATTTAATAATAATTATGTTAAATTACCTTTTATAGTATC
66 ATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTACATTTTATAGTATC
*
54679407 ATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATT-AGAATTTTATTAAATTATAT
1 ATATATTATGATTTTAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATAT
* *
54679471 ATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTATATTTTATAGTATC
66 ATTTTAATTAAAATATATTTAATAATAATTATGTT-AAATTACATTTTATAGTATC
54679526 ATATATTATGATTTTAGTAAATT-ATATAAGAATATTAATTATTAAGAATTTTATTAAATTATAT
1 ATATATTATGATTTTAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATAT
54679590 ATTTTAATTAAAATATATTTAATAATAATTATGTTTAAAT
66 ATTTTAATTAAAATATATTTAATAATAATTATG-TTAAAT
54679630 ATGATTAAAT
Statistics
Matches: 210, Mismatches: 9, Indels: 8
0.93 0.04 0.04
Matches are distributed among these distances:
118 21 0.10
119 142 0.68
120 45 0.21
121 2 0.01
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (120 bp):
ATATATTATGATTTTAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATAT
ATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTACATTTTATAGTATC
Found at i:54679601 original size:18 final size:17
Alignment explanation
Indices: 54679573--54679607 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
54679563 ATTATTAAGA
*
54679573 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
54679590 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
54679608 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:54679717 original size:147 final size:149
Alignment explanation
Indices: 54679561--54679835 Score: 509
Period size: 147 Copynumber: 1.9 Consensus size: 149
54679551 ATAAGAATAT
*
54679561 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
*
54679626 AAATATGATTAAATTATTTATTATTGAT-ATTAATAATCTTATTAAAATTTAAATAA-AATAATT
66 AAATATGATTAAATTATTTATTATTGATAATAAATAATCTTATTAAAATTTAAATAACAATAATT
54679689 TACCAAAACAAATTTCTGC
131 TACCAAAACAAATTTCTGC
54679708 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
*
54679773 AAATATGATTAAATTATTTATTTTTGATAATAAATAATCTTATTAAAATTTAAATAACAATAA
66 AAATATGATTAAATTATTTATTATTGATAATAAATAATCTTATTAAAATTTAAATAACAATAA
54679836 CAATAATCAT
Statistics
Matches: 123, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
147 91 0.74
148 27 0.22
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (149 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
AAATATGATTAAATTATTTATTATTGATAATAAATAATCTTATTAAAATTTAAATAACAATAATT
TACCAAAACAAATTTCTGC
Found at i:54679748 original size:18 final size:17
Alignment explanation
Indices: 54679720--54679754 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
54679710 ATTATTAAGA
*
54679720 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
54679737 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
54679755 TAAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:54680008 original size:45 final size:44
Alignment explanation
Indices: 54679916--54680010 Score: 118
Period size: 45 Copynumber: 2.1 Consensus size: 44
54679906 TTACACCTCT
* * *
54679916 ATTACATTCAACCAAACACAGTTTTACTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACACAGATTTACTATTACACATCTATTCC
** * *
54679960 ATTACATTCAACCAAACAGTTGATTTGCTATTACACATCTATTTC
1 ATTACATTCAACCAAACA-CAGATTTACTATTACACATCTATTCC
54680005 ATTACA
1 ATTACA
54680011 CCTCTAATCC
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
44 18 0.42
45 25 0.58
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.36
Consensus pattern (44 bp):
ATTACATTCAACCAAACACAGATTTACTATTACACATCTATTCC
Found at i:54680026 original size:16 final size:16
Alignment explanation
Indices: 54680007--54680042 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
54679997 TCTATTTCAT
54680007 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
54680023 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
54680039 TACA
1 TACA
54680043 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:54680259 original size:30 final size:27
Alignment explanation
Indices: 54680211--54680278 Score: 73
Period size: 30 Copynumber: 2.4 Consensus size: 27
54680201 AATCTCAAAA
*
54680211 TTATATATAAATTTAATTTAATGTACAATT
1 TTATAAAT-AATTTAATTTAATGT--AATT
*
54680241 TTATAAATAATTTAAATTTTATGTAATT
1 TTATAAATAATTT-AATTTAATGTAATT
*
54680269 TTATACATAA
1 TTATAAATAA
54680279 ATTTTTTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 13 0.38
29 5 0.15
30 16 0.47
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (27 bp):
TTATAAATAATTTAATTTAATGTAATT
Found at i:54681071 original size:21 final size:23
Alignment explanation
Indices: 54681030--54681072 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
54681020 GTAATAAGAG
54681030 TAAATTATGCTAAATTAAATATC
1 TAAATTATGCTAAATTAAATATC
*
54681053 TAAATT-TGC-AAATTGAATAT
1 TAAATTATGCTAAATTAAATAT
54681073 AATATACCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 10 0.53
22 3 0.16
23 6 0.32
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (23 bp):
TAAATTATGCTAAATTAAATATC
Found at i:54682194 original size:32 final size:32
Alignment explanation
Indices: 54682153--54682491 Score: 635
Period size: 32 Copynumber: 10.6 Consensus size: 32
54682143 NNNNNNNNNN
54682153 GCTGGAAATTTTTTTGCTGCTGGAATTTTTTT
1 GCTGGAAATTTTTTTGCTGCTGGAATTTTTTT
54682185 GCTGGAAATTTTTTTGCTGCTGGAATTTTTTT
1 GCTGGAAATTTTTTTGCTGCTGGAATTTTTTT
54682217 GCTGGAAATTTTTTTGCTGCTGGAATTTTTTT
1 GCTGGAAATTTTTTTGCTGCTGGAATTTTTTT
54682249 GCTGGAAATTTTTTTGCTGCTGGAATTTTTTT
1 GCTGGAAATTTTTTTGCTGCTGGAATTTTTTT
54682281 GCTGGAAATTTTTTTGCTGCTGGAATTTTTTT
1 GCTGGAAATTTTTTTGCTGCTGGAATTTTTTT
54682313 GCTGGAAATTTTTTTGCTGCTGGAATTTTTTT
1 GCTGGAAATTTTTTTGCTGCTGGAATTTTTTT
54682345 GCTGGAAATTTTTTTGCTGCTGGAATTTTTTT
1 GCTGGAAATTTTTTTGCTGCTGGAATTTTTTT
54682377 GCTGGAAATTTTTTTGCTGCTGGAATTTTTTT
1 GCTGGAAATTTTTTTGCTGCTGGAATTTTTTT
54682409 GCTGGAAATTTTTTTGCTGCTGGAATTTTTTT
1 GCTGGAAATTTTTTTGCTGCTGGAATTTTTTT
*
54682441 GCTGGAAA-TTTTTTGTTGCTGGAATTTTTTT
1 GCTGGAAATTTTTTTGCTGCTGGAATTTTTTT
*
54682472 GGTGGAAAAATTTTTTTGCT
1 GCTGG--AAATTTTTTTGCT
54682492 TCCCCCCCCT
Statistics
Matches: 301, Mismatches: 3, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
31 26 0.09
32 264 0.88
33 3 0.01
34 8 0.03
ACGTcount: A:0.16, C:0.09, G:0.22, T:0.53
Consensus pattern (32 bp):
GCTGGAAATTTTTTTGCTGCTGGAATTTTTTT
Found at i:54682920 original size:25 final size:25
Alignment explanation
Indices: 54682889--54682936 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
54682879 TCTTTACTCA
54682889 TTGTCGTGTAACGAGAACAGAGTTG
1 TTGTCGTGTAACGAGAACAGAGTTG
*
54682914 TTGTCGTGTAACGAGAATAGAGT
1 TTGTCGTGTAACGAGAACAGAGT
54682937 AAAGACTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.29, C:0.10, G:0.31, T:0.29
Consensus pattern (25 bp):
TTGTCGTGTAACGAGAACAGAGTTG
Found at i:54683604 original size:54 final size:54
Alignment explanation
Indices: 54683522--54683830 Score: 528
Period size: 54 Copynumber: 5.7 Consensus size: 54
54683512 GACCCGAGGC
*
54683522 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGGAATTAAAAGGT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGGAATTAAAAGGT
*
54683576 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGGAATTAAAAGGT
* * *
54683630 TCAACCCACCTCTCGCAATATGAGTTGATTTTTGAAAACCAGAAATTAAAAGGT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGGAATTAAAAGGT
*
54683684 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGGAATTAAAAGGC
1 TCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACAGGAATTAAAAGGT
* *
54683739 TCAACTCACCTCTCGTAATATGAGTTGATTTTTGAAAAACAGGAATTAAAAGGC
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGGAATTAAAAGGT
54683793 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAA
1 TCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAA
54683831 CTTAACTTGA
Statistics
Matches: 243, Mismatches: 10, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
54 184 0.76
55 59 0.24
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (54 bp):
TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGGAATTAAAAGGT
Found at i:54683775 original size:109 final size:109
Alignment explanation
Indices: 54683518--54683830 Score: 547
Period size: 109 Copynumber: 2.9 Consensus size: 109
54683508 ATGTGACCCG
*
54683518 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGGAATTAAAAGGTTCAACTC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGGAATTAAAAGGTTCAACTC
54683583 ACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACAGAAATTAAA
66 ACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTAAA
* * * *
54683626 AGGTTCAACCCACCTCTCGCAATATGAGTTGATTTTTGAAAACCAGAAATTAAAAGGTTCAACTC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGGAATTAAAAGGTTCAACTC
*
54683691 ACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGGAATTAAA
66 ACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTAAA
* *
54683735 AGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTGAAAAACAGGAATTAAAAGGCTCAACTC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGGAATTAAAAGGTTCAACTC
54683800 ACCTCTCGCAATATGAGTTGATTTTTTGAAA
66 ACCTCTCGCAATATGAGTTGATTTTTTGAAA
54683831 CTTAACTTGA
Statistics
Matches: 192, Mismatches: 12, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
108 81 0.42
109 111 0.58
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (109 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGGAATTAAAAGGTTCAACTC
ACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTAAA
Found at i:54683791 original size:163 final size:163
Alignment explanation
Indices: 54683522--54683830 Score: 548
Period size: 163 Copynumber: 1.9 Consensus size: 163
54683512 GACCCGAGGC
* *
54683522 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGGAATTAAAAGGTTCAACTCACCT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGGAATTAAAAGGCTCAACTCACCT
*
54683587 CTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATG
66 CTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGCTCAACCCACCTCTCGCAATATG
54683652 AGTTGA-TTTTTGAAAACCAGAAATTAAAAGGT
131 AGTTGATTTTTTGAAAACCAGAAATTAAAAGGT
54683684 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGGAATTAAAAGGCTCAACTCACC
1 TCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACAGGAATTAAAAGGCTCAACTCACC
* * *
54683749 TCTCGTAATATGAGTTGATTTTTGAAAAACAGGAATTAAAAGGCTCAACTCACCTCTCGCAATAT
65 TCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGCTCAACCCACCTCTCGCAATAT
54683814 GAGTTGATTTTTTGAAA
130 GAGTTGATTTTTTGAAA
54683831 CTTAACTTGA
Statistics
Matches: 139, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
162 28 0.20
163 102 0.73
164 9 0.06
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (163 bp):
TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGGAATTAAAAGGCTCAACTCACCT
CTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAGGCTCAACCCACCTCTCGCAATATG
AGTTGATTTTTTGAAAACCAGAAATTAAAAGGT
Done.