Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 48 of 168
Found at i:13381115 original size:47 final size:46
Alignment explanation
Indices: 13381058--13381202 Score: 120
Period size: 47 Copynumber: 3.2 Consensus size: 46
13381048 ATAATACCAT
*
13381058 TTTATTATTAAGAATTTTATGAAATTATATATCACTATTAAATTATA
1 TTTAATATTAAGAATTTTATGAAATTATATATCA-TATTAAATTATA
** * * *
13381105 TTTAATATTAATTATTTTA--AATTGTATAAATTCATA-TAAGA--AAA
1 TTTAATATTAAGAATTTTATGAAAT-TATATA-TCATATTAA-ATTATA
* * *
13381149 TTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATA
1 TTTAATATTAAGAATTTTATGAAATTATATATCA-TATTAAATTATA
*
13381196 TGTAATA
1 TTTAATA
13381203 ATTATTATTT
Statistics
Matches: 73, Mismatches: 16, Indels: 18
0.68 0.15 0.17
Matches are distributed among these distances:
44 19 0.26
45 14 0.19
46 14 0.19
47 26 0.36
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (46 bp):
TTTAATATTAAGAATTTTATGAAATTATATATCATATTAAATTATA
Found at i:13381162 original size:91 final size:92
Alignment explanation
Indices: 13381039--13381229 Score: 278
Period size: 91 Copynumber: 2.1 Consensus size: 92
13381029 TTGATTTTAG
* * * *
13381039 TAAATTCATATAATACCATTTTATTATTAAGAATTTTATGAAATTATATATCACTATTAAATTAT
1 TAAATTCATATAAGACAAATTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTAT
* *
13381104 ATTTAAT-ATTAATTATTTTAAATTGTA
66 ATGTAATAATT-ATTATTTTAAATTATA
* *
13381131 TAAATTCATATAAGA-AAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTAT
1 TAAATTCATATAAGACAAATTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTAT
13381195 ATGTAATAATTATTATTTTAAATTATA
66 ATGTAATAATTATTATTTTAAATTATA
*
13381222 CAAATTCA
1 TAAATTCA
13381230 CAAAATATAA
Statistics
Matches: 89, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
91 72 0.81
92 17 0.19
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.47
Consensus pattern (92 bp):
TAAATTCATATAAGACAAATTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTAT
ATGTAATAATTATTATTTTAAATTATA
Found at i:13381386 original size:120 final size:120
Alignment explanation
Indices: 13381262--13381674 Score: 808
Period size: 120 Copynumber: 3.4 Consensus size: 120
13381252 AATTATTTTA
* *
13381262 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
13381327 ACAGTATCATATATTATGGTTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGGTTTGAGTAAATTCATATAAGAATATTAATTATTAAG
13381382 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
13381447 ACAGTATCATATATTATGGTTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGGTTTGAGTAAATTCATATAAGAATATTAATTATTAAG
13381502 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
13381567 ACAGTATCATATATTATGGTTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGGTTTGAGTAAATTCATATAAGAATATTAATTATTAAG
13381622 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
13381675 TAAATATGAT
Statistics
Matches: 291, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 291 1.00
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.49
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
ACAGTATCATATATTATGGTTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:13381422 original size:15 final size:15
Alignment explanation
Indices: 13381387--13381438 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
13381377 TTAAGAATTT
*
13381387 TATTAAATTAT-ATA
1 TATTTAATTATAATA
13381401 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
13381415 TATTTAATAATAAT-
1 TATTTAATTATAATA
13381429 TATGTTAATT
1 TAT-TTAATT
13381439 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:13381542 original size:15 final size:15
Alignment explanation
Indices: 13381507--13381558 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
13381497 TTAAGAATTT
*
13381507 TATTAAATTAT-ATA
1 TATTTAATTATAATA
13381521 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
13381535 TATTTAATAATAAT-
1 TATTTAATTATAATA
13381549 TATGTTAATT
1 TAT-TTAATT
13381559 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:13381657 original size:16 final size:16
Alignment explanation
Indices: 13381636--13381677 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
13381626 TTATTAAATT
*
13381636 ATATATTTTAATTATA
1 ATATATTTTAATAATA
13381652 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
13381667 AT-TATGTTTAA
1 ATATAT-TTTAA
13381678 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:13381662 original size:15 final size:15
Alignment explanation
Indices: 13381627--13381668 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
13381617 TTAAGAATTT
*
13381627 TATTAAATTAT-ATA
1 TATTTAATTATAATA
13381641 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
13381655 TATTTAATAATAAT
1 TATTTAATTATAAT
13381669 TATGTTTAAA
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:13381774 original size:147 final size:147
Alignment explanation
Indices: 13381611--13381883 Score: 503
Period size: 147 Copynumber: 1.9 Consensus size: 147
13381601 ATAAGAATAT
* *
13381611 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTA
13381676 AAATATGATTAAATTATTTACTATTGATATTAATAATCTTATTAAAATTTAAATAA-AATAATTT
66 AAATATGATTAAATTATTTACTATTGATATTAATAATCTTATTAAAATTT-AATAACAATAATTT
13381740 ACCAAAACAAATTTCTGC
130 ACCAAAACAAATTTCTGC
13381758 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTA
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTA
*
13381823 AAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAATAACAATAA
66 AAATATGATTAAATTATTTACTATTGATATTAATAATCTTATTAAAATTTAATAACAATAA
13381884 CAATAATCAT
Statistics
Matches: 122, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
146 5 0.04
147 117 0.96
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (147 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTA
AAATATGATTAAATTATTTACTATTGATATTAATAATCTTATTAAAATTTAATAACAATAATTTA
CCAAAACAAATTTCTGC
Found at i:13381798 original size:18 final size:17
Alignment explanation
Indices: 13381770--13381804 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
13381760 ATTATTAAGA
*
13381770 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
13381787 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
13381805 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:13382050 original size:45 final size:44
Alignment explanation
Indices: 13381964--13382058 Score: 145
Period size: 45 Copynumber: 2.1 Consensus size: 44
13381954 TTACACCTCT
*
13381964 ATTACATTCAACCAAACACAGGATTGCTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACACAGGATTGCTATTACACCTCTATTCC
***
13382008 ATTACATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCC
1 ATTACATTCAACCAAACACAGGA-TTGCTATTACACCTCTATTCC
13382053 ATTACA
1 ATTACA
13382059 CCTCTATTCC
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
44 20 0.43
45 26 0.57
ACGTcount: A:0.33, C:0.27, G:0.07, T:0.33
Consensus pattern (44 bp):
ATTACATTCAACCAAACACAGGATTGCTATTACACCTCTATTCC
Found at i:13382058 original size:16 final size:16
Alignment explanation
Indices: 13382037--13382122 Score: 136
Period size: 16 Copynumber: 5.4 Consensus size: 16
13382027 TTGATTTGCT
13382037 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
13382053 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
13382069 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
*
13382085 ATTACACCTCTAATCC
1 ATTACACCTCTATTCC
* *
13382101 AATACACCTCTAATCC
1 ATTACACCTCTATTCC
*
13382117 AATACA
1 ATTACA
13382123 GCGAACCAAA
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 68 1.00
ACGTcount: A:0.31, C:0.36, G:0.00, T:0.33
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:13389310 original size:41 final size:41
Alignment explanation
Indices: 13389253--13389343 Score: 139
Period size: 41 Copynumber: 2.2 Consensus size: 41
13389243 TCGACGAAGG
*
13389253 AGAAGAAAATTTACAACAAAAATCTATTCTAA-AGAAAATAAA
1 AGAA-AAAATCTACAACAAAAATCTATTCTAACA-AAAATAAA
*
13389295 AGAAAAAATCTACAACAAAACTCTATTCTAACAAAAATAAA
1 AGAAAAAATCTACAACAAAAATCTATTCTAACAAAAATAAA
13389336 AGAAAAAA
1 AGAAAAAA
13389344 AAAACCTAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
41 41 0.89
42 5 0.11
ACGTcount: A:0.64, C:0.12, G:0.05, T:0.19
Consensus pattern (41 bp):
AGAAAAAATCTACAACAAAAATCTATTCTAACAAAAATAAA
Found at i:13392177 original size:110 final size:109
Alignment explanation
Indices: 13392029--13392319 Score: 404
Period size: 109 Copynumber: 2.7 Consensus size: 109
13392019 CCGGCTTACA
* *
13392029 ATGCTGCTCACACAAGCTGTAGAGAATCCGCAACAGATGCAGGATCTCAAGCCATCGTTATGGTC
1 ATGCTGCTCACACAAGCTGTAGAGAATCTGCAACAGATGCAGGATCTC-AGCCATCGTTACGGTC
13392094 TGTATCATCT-GTATATAGTACCTGCTAAATAAACATCGGGTCACG
65 TGTATCA-CTGGTATATAGTACCTGCTAAATAAACATCGGGTCACG
* * * * * *
13392139 ATGCTGCTCACACAAGCAGTAGAAAATCTACAACAGATGTAGGATCTCAGCCATTGTTACGGTTT
1 ATGCTGCTCACACAAGCTGTAGAGAATCTGCAACAGATGCAGGATCTCAGCCATCGTTACGGTCT
*
13392204 GTATCACTGGTATATAGTACCTGCTAAATAATCATCGGGTCACG
66 GTATCACTGGTATATAGTACCTGCTAAATAAACATCGGGTCACG
* * * * * * * *
13392248 ATGTTGCTTACAAAAGTTGTACAGAATCTGCAACAGATGCAGGATCTTAGCCATCGCTACAGTCT
1 ATGCTGCTCACACAAGCTGTAGAGAATCTGCAACAGATGCAGGATCTCAGCCATCGTTACGGTCT
13392313 GTATCAC
66 GTATCAC
13392320 CGGCTCAAGG
Statistics
Matches: 157, Mismatches: 23, Indels: 3
0.86 0.13 0.02
Matches are distributed among these distances:
108 2 0.01
109 112 0.71
110 43 0.27
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (109 bp):
ATGCTGCTCACACAAGCTGTAGAGAATCTGCAACAGATGCAGGATCTCAGCCATCGTTACGGTCT
GTATCACTGGTATATAGTACCTGCTAAATAAACATCGGGTCACG
Found at i:13392409 original size:40 final size:40
Alignment explanation
Indices: 13392357--13392438 Score: 110
Period size: 40 Copynumber: 2.0 Consensus size: 40
13392347 ATACAAGGCC
* ** *
13392357 TGCTAGGCACAAAGCCTGATAAACACACTGGCACAAAGCT
1 TGCTAGGCACAAAGCCCGATAAACACACCAGCACAAAACT
* *
13392397 TGCTAGGTACAAAGCCCGATAAATACACCAGCACAAAACT
1 TGCTAGGCACAAAGCCCGATAAACACACCAGCACAAAACT
13392437 TG
1 TG
13392439 ATATTCACGT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.39, C:0.27, G:0.18, T:0.16
Consensus pattern (40 bp):
TGCTAGGCACAAAGCCCGATAAACACACCAGCACAAAACT
Found at i:13406103 original size:19 final size:19
Alignment explanation
Indices: 13406079--13406122 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
13406069 TGACGTATGT
*
13406079 TAGCTAGAGGACACTTATA
1 TAGCTAGAAGACACTTATA
*
13406098 TAGCTAGAAGACGCTTATA
1 TAGCTAGAAGACACTTATA
*
13406117 TGGCTA
1 TAGCTA
13406123 CATTACATGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.27
Consensus pattern (19 bp):
TAGCTAGAAGACACTTATA
Found at i:13409920 original size:35 final size:35
Alignment explanation
Indices: 13409851--13409931 Score: 103
Period size: 35 Copynumber: 2.3 Consensus size: 35
13409841 ATTCACTTGT
*
13409851 TAAGCATGCCATTATTACTGATTCTGAATAGCATGG
1 TAAGCATGCCATTATTACTGATTCTAAATAGCAT-G
*
13409887 TAAGCATGCCATTA-TACTGATTC-AAATTCGCATG
1 TAAGCATGCCATTATTACTGATTCTAAA-TAGCATG
13409921 TAAAGCATGCC
1 T-AAGCATGCC
13409932 TACCGAAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
34 4 0.10
35 23 0.56
36 14 0.34
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (35 bp):
TAAGCATGCCATTATTACTGATTCTAAATAGCATG
Found at i:13412276 original size:18 final size:18
Alignment explanation
Indices: 13412238--13412276 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
13412228 CCTATAAATA
*
13412238 ATATTACTAGCAACATTT
1 ATATTACTAACAACATTT
13412256 ATATTACTAAC-ACATTCT
1 ATATTACTAACAACATT-T
13412274 ATA
1 ATA
13412277 CATGCCATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.41, C:0.18, G:0.03, T:0.38
Consensus pattern (18 bp):
ATATTACTAACAACATTT
Found at i:13422409 original size:10 final size:10
Alignment explanation
Indices: 13422394--13422419 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
13422384 TTTCGTATAT
13422394 TGTTGAAAGG
1 TGTTGAAAGG
13422404 TGTTGAAAGG
1 TGTTGAAAGG
13422414 TGTTGA
1 TGTTGA
13422420 CCCTTCCTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.38, T:0.35
Consensus pattern (10 bp):
TGTTGAAAGG
Found at i:13428907 original size:11 final size:11
Alignment explanation
Indices: 13428870--13428912 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
13428860 ATTATTAACT
13428870 TTAA-GAAAAC
1 TTAATGAAAAC
13428880 TTATATGAAAAC
1 TTA-ATGAAAAC
* *
13428892 ATAATTAAAAC
1 TTAATGAAAAC
13428903 TTAATGAAAA
1 TTAATGAAAA
13428913 TGCTTTCTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
10 3 0.11
11 16 0.59
12 8 0.30
ACGTcount: A:0.58, C:0.07, G:0.07, T:0.28
Consensus pattern (11 bp):
TTAATGAAAAC
Found at i:13433333 original size:42 final size:42
Alignment explanation
Indices: 13433266--13433352 Score: 122
Period size: 42 Copynumber: 2.1 Consensus size: 42
13433256 TGAATACAAG
* * *
13433266 TCAGTGAGTTACACGACCTAGCACACGGGTGTGTGGGGCTAC
1 TCAGAGAGTTACACGACCTAGCACACGGGAGTGTGGGGCAAC
*
13433308 TCAGAGAGTTACACGGCC-AGTCACACGGGAGTGTGGGGCAAC
1 TCAGAGAGTTACACGACCTAG-CACACGGGAGTGTGGGGCAAC
13433350 TCA
1 TCA
13433353 AAGCATTACA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
41 2 0.05
42 38 0.95
ACGTcount: A:0.24, C:0.24, G:0.33, T:0.18
Consensus pattern (42 bp):
TCAGAGAGTTACACGACCTAGCACACGGGAGTGTGGGGCAAC
Found at i:13439310 original size:13 final size:13
Alignment explanation
Indices: 13439292--13439319 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
13439282 ATTTGATAAT
13439292 GGTATAAATTCTA
1 GGTATAAATTCTA
13439305 GGTATAAATTCTA
1 GGTATAAATTCTA
13439318 GG
1 GG
13439320 GTTTTATAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (13 bp):
GGTATAAATTCTA
Found at i:13440451 original size:21 final size:20
Alignment explanation
Indices: 13440423--13440461 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
13440413 TAGCATTTTG
* *
13440423 TTGAATGTTTAGTTTGTGAA
1 TTGAATGTATAATTTGTGAA
13440443 TTGACATGTATAATTTGTG
1 TTGA-ATGTATAATTTGTG
13440462 TAAGTTAACT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.26, C:0.03, G:0.23, T:0.49
Consensus pattern (20 bp):
TTGAATGTATAATTTGTGAA
Found at i:13454619 original size:34 final size:34
Alignment explanation
Indices: 13454578--13454646 Score: 95
Period size: 34 Copynumber: 2.0 Consensus size: 34
13454568 ACACGGTTAA
*
13454578 CCATCCAGCAGACTAG-ATGCTCGTATGAGCTAAT
1 CCATCCAGCACAC-AGAATGCTCGTATGAGCTAAT
* *
13454612 CCATCCAGTACACCGAATGCTCGTATGAGCTAAT
1 CCATCCAGCACACAGAATGCTCGTATGAGCTAAT
13454646 C
1 C
13454647 AATTTAGCAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
33 1 0.03
34 30 0.97
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (34 bp):
CCATCCAGCACACAGAATGCTCGTATGAGCTAAT
Found at i:13456612 original size:19 final size:19
Alignment explanation
Indices: 13456588--13456627 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
13456578 CATTTTCTAG
13456588 ATTTATTATTGAAGAATTA
1 ATTTATTATTGAAGAATTA
13456607 ATTTATTATTGAAGAATTA
1 ATTTATTATTGAAGAATTA
13456626 AT
1 AT
13456628 CTCCTTATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.47
Consensus pattern (19 bp):
ATTTATTATTGAAGAATTA
Found at i:13467573 original size:27 final size:27
Alignment explanation
Indices: 13467502--13467587 Score: 100
Period size: 27 Copynumber: 3.2 Consensus size: 27
13467492 TACAAATGAC
13467502 CCCACACGCCCGTGTGTGCCCGTGTGG
1 CCCACACGCCCGTGTGTGCCCGTGTGG
* ** * *
13467529 CCTACACGCTTGTATGTGCCTGTGTGG
1 CCCACACGCCCGTGTGTGCCCGTGTGG
* *
13467556 CCCACACACCCGTGTGTGCCCATGTGG
1 CCCACACGCCCGTGTGTGCCCGTGTGG
*
13467583 TCCAC
1 CCCAC
13467588 TCAGCCCAAA
Statistics
Matches: 46, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.12, C:0.37, G:0.28, T:0.23
Consensus pattern (27 bp):
CCCACACGCCCGTGTGTGCCCGTGTGG
Found at i:13485568 original size:41 final size:41
Alignment explanation
Indices: 13485531--13485638 Score: 162
Period size: 41 Copynumber: 2.6 Consensus size: 41
13485521 ACCAAAGTGT
* * *
13485531 AAACAGGGCCACGTATATGCAATTCAGGGGTATCAAAGTAC
1 AAACAGGGGCACATATGTGCAATTCAGGGGTATCAAAGTAC
** *
13485572 AAGTAGGGGCACATATGTGCAATTCAGGGGTATCGAAGTAC
1 AAACAGGGGCACATATGTGCAATTCAGGGGTATCAAAGTAC
13485613 AAACAGGGGCACATATGTGCAATTCA
1 AAACAGGGGCACATATGTGCAATTCA
13485639 TAGAATAATT
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 59 1.00
ACGTcount: A:0.35, C:0.18, G:0.27, T:0.20
Consensus pattern (41 bp):
AAACAGGGGCACATATGTGCAATTCAGGGGTATCAAAGTAC
Found at i:13494811 original size:30 final size:31
Alignment explanation
Indices: 13494756--13494823 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
13494746 ACCCTTAAAA
** * **
13494756 TATTTACACTATTGGTCCTTCAAATTTTTCG
1 TATTTACACTATTAATCCCTCAAATTTTGAG
13494787 TATTTACACT-TTAATCCCTCAAATTTTGAG
1 TATTTACACTATTAATCCCTCAAATTTTGAG
13494817 TATTTAC
1 TATTTAC
13494824 TCTTGGGCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 22 0.69
31 10 0.31
ACGTcount: A:0.26, C:0.19, G:0.07, T:0.47
Consensus pattern (31 bp):
TATTTACACTATTAATCCCTCAAATTTTGAG
Found at i:13504211 original size:28 final size:28
Alignment explanation
Indices: 13504179--13504236 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
13504169 CCAGACTCAT
13504179 TTACACGATGTTTATTGCCAATATAATC
1 TTACACGATGTTTATTGCCAATATAATC
*
13504207 TTACACGATGTTTATTGCCAATATTATC
1 TTACACGATGTTTATTGCCAATATAATC
13504235 TT
1 TT
13504237 TGAGATTTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.29, C:0.17, G:0.10, T:0.43
Consensus pattern (28 bp):
TTACACGATGTTTATTGCCAATATAATC
Found at i:13506046 original size:2 final size:2
Alignment explanation
Indices: 13506039--13506070 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
13506029 AAAATGATAT
13506039 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
13506071 TGCCGCCTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:13506443 original size:36 final size:36
Alignment explanation
Indices: 13506347--13506432 Score: 100
Period size: 36 Copynumber: 2.2 Consensus size: 36
13506337 ATTATTAAAT
*
13506347 TAATATTAGAATAATAATTTATTAATATTATTACATGATAA
1 TAATA-TA-AATAAT-ATTAATTAA-A-TATTACATGATAA
* *
13506388 TAATATAAATAATATTAATTAAATATTACATTATAG
1 TAATATAAATAATATTAATTAAATATTACATGATAA
13506424 TAATATAAA
1 TAATATAAA
13506433 ATTAGTTAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
36 20 0.48
37 1 0.02
38 8 0.19
39 6 0.14
40 2 0.05
41 5 0.12
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.42
Consensus pattern (36 bp):
TAATATAAATAATATTAATTAAATATTACATGATAA
Found at i:13506594 original size:19 final size:17
Alignment explanation
Indices: 13506570--13506612 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
13506560 TTCAATTAAA
13506570 TAAATATAATTCTTATATG
1 TAAATATAATT-TTAT-TG
* *
13506589 TAAATATGATTTTATTT
1 TAAATATAATTTTATTG
13506606 TAAATAT
1 TAAATAT
13506613 GATAATAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 8 0.36
18 4 0.18
19 10 0.45
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (17 bp):
TAAATATAATTTTATTG
Found at i:13506611 original size:17 final size:19
Alignment explanation
Indices: 13506570--13506615 Score: 60
Period size: 17 Copynumber: 2.5 Consensus size: 19
13506560 TTCAATTAAA
*
13506570 TAAATATAATTCTTATATG
1 TAAATATGATTCTTATATG
*
13506589 TAAATATGATT-TTAT-TT
1 TAAATATGATTCTTATATG
13506606 TAAATATGAT
1 TAAATATGAT
13506616 AATAATTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 11 0.44
18 4 0.16
19 10 0.40
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (19 bp):
TAAATATGATTCTTATATG
Found at i:13507827 original size:31 final size:30
Alignment explanation
Indices: 13507767--13507831 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 30
13507757 TACGTGATAA
13507767 TAATAAAAATAATATTAATTAAATATTAAT
1 TAATAAAAATAATATTAATTAAATATTAAT
*
13507797 TAATAAAATATATTATTAATATAAAT-TTAAT
1 TAATAAAA-ATAATATTAAT-TAAATATTAAT
13507828 TAAT
1 TAAT
13507832 TTGGTTTTAC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
30 8 0.25
31 19 0.59
32 5 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (30 bp):
TAATAAAAATAATATTAATTAAATATTAAT
Found at i:13508962 original size:26 final size:27
Alignment explanation
Indices: 13508912--13508962 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
13508902 TTAATTAGTA
* * *
13508912 AATATATTTTTTTAAAAATTATAAACG
1 AATATATTATTTAAAAAAATATAAACG
13508939 AATATATTATTTAAAAAAAT-TAAA
1 AATATATTATTTAAAAAAATATAAA
13508963 AAAATAAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 4 0.19
27 17 0.81
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (27 bp):
AATATATTATTTAAAAAAATATAAACG
Found at i:13511694 original size:2 final size:2
Alignment explanation
Indices: 13511687--13511711 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
13511677 ATATTTTCAC
13511687 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
13511712 AAGTTAAAAA
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:13513702 original size:49 final size:49
Alignment explanation
Indices: 13513630--13513729 Score: 200
Period size: 49 Copynumber: 2.0 Consensus size: 49
13513620 GCAGGAAAGA
13513630 AAGCATATATAACATGCATATACAAGATAAAAACCATCCATTCCAATTC
1 AAGCATATATAACATGCATATACAAGATAAAAACCATCCATTCCAATTC
13513679 AAGCATATATAACATGCATATACAAGATAAAAACCATCCATTCCAATTC
1 AAGCATATATAACATGCATATACAAGATAAAAACCATCCATTCCAATTC
13513728 AA
1 AA
13513730 ACCTCTTTCG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.48, C:0.22, G:0.06, T:0.24
Consensus pattern (49 bp):
AAGCATATATAACATGCATATACAAGATAAAAACCATCCATTCCAATTC
Found at i:13522884 original size:18 final size:18
Alignment explanation
Indices: 13522861--13522896 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
13522851 CTATAGACAT
13522861 CTAGTACCTTAGGGAAGG
1 CTAGTACCTTAGGGAAGG
13522879 CTAGTACCTTAGGGAAGG
1 CTAGTACCTTAGGGAAGG
13522897 TAGCTGTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.17, G:0.33, T:0.22
Consensus pattern (18 bp):
CTAGTACCTTAGGGAAGG
Found at i:13526792 original size:21 final size:21
Alignment explanation
Indices: 13526744--13526805 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
13526734 CAATCAGCAC
13526744 ACTCAGATGCATCCACAACAA
1 ACTCAGATGCATCCACAACAA
* *
13526765 AGC-CAGATGCATCCACACCAG
1 A-CTCAGATGCATCCACAACAA
*
13526786 ACTCAGACGC-TGCCACAACA
1 ACTCAGATGCAT-CCACAACA
13526806 CTCTTCAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
20 2 0.06
21 31 0.91
22 1 0.03
ACGTcount: A:0.37, C:0.37, G:0.15, T:0.11
Consensus pattern (21 bp):
ACTCAGATGCATCCACAACAA
Found at i:13532872 original size:17 final size:17
Alignment explanation
Indices: 13532850--13532882 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
13532840 GTTAGTGCAC
*
13532850 ATTGTCTTTGCATTTTT
1 ATTGTCATTGCATTTTT
13532867 ATTGTCATTGCATTTT
1 ATTGTCATTGCATTTT
13532883 AATGTTAGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.12, G:0.12, T:0.61
Consensus pattern (17 bp):
ATTGTCATTGCATTTTT
Found at i:13540566 original size:11 final size:11
Alignment explanation
Indices: 13540550--13540585 Score: 63
Period size: 11 Copynumber: 3.2 Consensus size: 11
13540540 TGTCACGCCA
13540550 AAATAAACCCC
1 AAATAAACCCC
13540561 AAATAAACCCC
1 AAATAAACCCC
13540572 AAAATAAACCCC
1 -AAATAAACCCC
13540584 AA
1 AA
13540586 GCCAGTTAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 13 0.54
12 11 0.46
ACGTcount: A:0.58, C:0.33, G:0.00, T:0.08
Consensus pattern (11 bp):
AAATAAACCCC
Found at i:13540576 original size:12 final size:12
Alignment explanation
Indices: 13540547--13540585 Score: 71
Period size: 12 Copynumber: 3.3 Consensus size: 12
13540537 AATTGTCACG
13540547 CCAAAATAAACC
1 CCAAAATAAACC
13540559 CC-AAATAAACC
1 CCAAAATAAACC
13540570 CCAAAATAAACC
1 CCAAAATAAACC
13540582 CCAA
1 CCAA
13540586 GCCAGTTAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 11 0.42
12 15 0.58
ACGTcount: A:0.56, C:0.36, G:0.00, T:0.08
Consensus pattern (12 bp):
CCAAAATAAACC
Found at i:13544744 original size:12 final size:12
Alignment explanation
Indices: 13544729--13544773 Score: 72
Period size: 12 Copynumber: 3.8 Consensus size: 12
13544719 TATTTATTTT
*
13544729 ATAATTTTTGTG
1 ATAATCTTTGTG
13544741 ATAATCTTTGTG
1 ATAATCTTTGTG
13544753 ATAATCTTTGTG
1 ATAATCTTTGTG
*
13544765 ATATTCTTT
1 ATAATCTTT
13544774 TGTCATCATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.24, C:0.07, G:0.13, T:0.56
Consensus pattern (12 bp):
ATAATCTTTGTG
Found at i:13547140 original size:28 final size:27
Alignment explanation
Indices: 13547109--13547165 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
13547099 AAATTCCTAT
13547109 TTGTGTTTTTATAAAAAAAAAATCATGA
1 TTGTGTTTTTAT-AAAAAAAAATCATGA
13547137 TTGTGTTTTTATAAAAAAAAATCATGA
1 TTGTGTTTTTATAAAAAAAAATCATGA
13547164 TT
1 TT
13547166 AAAGTTTGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 17 0.59
28 12 0.41
ACGTcount: A:0.44, C:0.04, G:0.11, T:0.42
Consensus pattern (27 bp):
TTGTGTTTTTATAAAAAAAAATCATGA
Found at i:13547172 original size:28 final size:28
Alignment explanation
Indices: 13547113--13547177 Score: 87
Period size: 27 Copynumber: 2.3 Consensus size: 28
13547103 TCCTATTTGT
**
13547113 GTTTTTATAAAAAAAAAATCATGATTGT
1 GTTTTTATAAAAAAAAAATCATGATTAA
13547141 GTTTTTAT-AAAAAAAAATCATGATTAAA
1 GTTTTTATAAAAAAAAAATCATGATT-AA
13547169 GTTTGTTAT
1 GTTT-TTAT
13547178 GATTATTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
27 17 0.52
28 12 0.36
29 4 0.12
ACGTcount: A:0.45, C:0.03, G:0.11, T:0.42
Consensus pattern (28 bp):
GTTTTTATAAAAAAAAAATCATGATTAA
Found at i:13551789 original size:20 final size:19
Alignment explanation
Indices: 13551765--13551812 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 19
13551755 TTTTCAACCC
* *
13551765 AAATTAATTATTTTCATTA
1 AAATTAATTAATTACATTA
* *
13551784 ATAATTATTTAATTACTTTA
1 A-AATTAATTAATTACATTA
13551804 AAATTAATT
1 AAATTAATT
13551813 TTCCAAAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (19 bp):
AAATTAATTAATTACATTA
Found at i:13553129 original size:4 final size:4
Alignment explanation
Indices: 13553120--13553164 Score: 54
Period size: 4 Copynumber: 10.8 Consensus size: 4
13553110 AATTTAGTTA
* *
13553120 AATT AATT AATTT AATT AATT AATTT AATT AATT GATT AAAT AAT
1 AATT AATT AA-TT AATT AATT AA-TT AATT AATT AATT AATT AAT
13553165 ATTTCTTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
4 27 0.77
5 8 0.23
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (4 bp):
AATT
Found at i:13553138 original size:13 final size:13
Alignment explanation
Indices: 13553120--13553153 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
13553110 AATTTAGTTA
13553120 AATTAATTAATTT
1 AATTAATTAATTT
13553133 AATTAATTAATTT
1 AATTAATTAATTT
13553146 AATTAATT
1 AATTAATT
13553154 GATTAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
AATTAATTAATTT
Found at i:13559060 original size:24 final size:24
Alignment explanation
Indices: 13559035--13559079 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
13559025 ATAACCTCTC
*
13559035 CCCCATTATCTC-CTAAAACAACT
1 CCCCATTAACTCGCTAAAACAACT
*
13559058 CCCTATTAACTCGCTAAAACAA
1 CCCCATTAACTCGCTAAAACAA
13559080 ATCTACTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.38, C:0.36, G:0.02, T:0.24
Consensus pattern (24 bp):
CCCCATTAACTCGCTAAAACAACT
Found at i:13568274 original size:16 final size:16
Alignment explanation
Indices: 13568243--13568276 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
13568233 ACGCATTGAA
**
13568243 ATCTTACTGTCTGTAT
1 ATCTTACTGTAAGTAT
13568259 ATCTTACTGTAAGTAT
1 ATCTTACTGTAAGTAT
13568275 AT
1 AT
13568277 TCCATAAGTC
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:0.15, G:0.12, T:0.47
Consensus pattern (16 bp):
ATCTTACTGTAAGTAT
Found at i:13569959 original size:21 final size:21
Alignment explanation
Indices: 13569919--13569959 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
13569909 GCTTTTGAAA
**
13569919 AGGAAGTTGCTGCTGCAGAAG
1 AGGAAGTTGCTGCTAAAGAAG
*
13569940 AGGAAGTTGTTGCTAAAGAA
1 AGGAAGTTGCTGCTAAAGAA
13569960 AAAAAAGTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.10, G:0.34, T:0.22
Consensus pattern (21 bp):
AGGAAGTTGCTGCTAAAGAAG
Found at i:13573774 original size:11 final size:11
Alignment explanation
Indices: 13573758--13573782 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
13573748 TTTTTGTAAA
13573758 TAAAACAAAAT
1 TAAAACAAAAT
13573769 TAAAACAAAAT
1 TAAAACAAAAT
13573780 TAA
1 TAA
13573783 GTAAAAGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.20
Consensus pattern (11 bp):
TAAAACAAAAT
Found at i:13574731 original size:21 final size:21
Alignment explanation
Indices: 13574705--13574747 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
13574695 TTCGGGTGGA
* *
13574705 TCAGCTTTTACGAGCTTCTGT
1 TCAGCTCTTACAAGCTTCTGT
13574726 TCAGCTCTTACAAGCTTCTGT
1 TCAGCTCTTACAAGCTTCTGT
13574747 T
1 T
13574748 GGCGTACTCG
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:0.16, C:0.26, G:0.16, T:0.42
Consensus pattern (21 bp):
TCAGCTCTTACAAGCTTCTGT
Found at i:13575609 original size:30 final size:31
Alignment explanation
Indices: 13575575--13575639 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 31
13575565 ACGGCCTGAG
* *
13575575 ACACGGA-CTTGTGTATCAGTAGTGTGTGAC
1 ACACGGAGCGTGTGTATCAGCAGTGTGTGAC
* *
13575605 ACAC-GAGCGTGTGTTTCAGCCGTGTGTGAC
1 ACACGGAGCGTGTGTATCAGCAGTGTGTGAC
13575635 ACACG
1 ACACG
13575640 ACCATACGAC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 2 0.07
30 27 0.93
ACGTcount: A:0.22, C:0.22, G:0.31, T:0.26
Consensus pattern (31 bp):
ACACGGAGCGTGTGTATCAGCAGTGTGTGAC
Found at i:13580438 original size:22 final size:20
Alignment explanation
Indices: 13580413--13580464 Score: 52
Period size: 22 Copynumber: 2.5 Consensus size: 20
13580403 AGTTGAAAAA
13580413 ATTCAACATTTTGTATATTATT
1 ATTCAA-ATTTTGTATA-TATT
*
13580435 ATTCTAAATTTTTTATATATT
1 ATTC-AAATTTTGTATATATT
13580456 -TTCATAATT
1 ATTCA-AATT
13580465 AACTTTCAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 1 0.04
20 7 0.26
21 4 0.15
22 13 0.48
23 2 0.07
ACGTcount: A:0.33, C:0.08, G:0.02, T:0.58
Consensus pattern (20 bp):
ATTCAAATTTTGTATATATT
Found at i:13580635 original size:31 final size:31
Alignment explanation
Indices: 13580597--13580655 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
13580587 TACTCTAGTC
*
13580597 AAATTAAATTTTGTAGACAATTTATATATTG
1 AAATTAAATTTTGTAAACAATTTATATATTG
13580628 AAATTAAATTTTGTAAACAATTTATATA
1 AAATTAAATTTTGTAAACAATTTATATA
13580656 AAAATTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (31 bp):
AAATTAAATTTTGTAAACAATTTATATATTG
Found at i:13583933 original size:19 final size:18
Alignment explanation
Indices: 13583898--13583932 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
13583888 TTATTTTTGT
13583898 TTTTGTTCTTTTCTTTTC
1 TTTTGTTCTTTTCTTTTC
13583916 TTTT-TTCTCTTTCTTTT
1 TTTTGTTCT-TTTCTTTT
13583933 TTATCTCTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (18 bp):
TTTTGTTCTTTTCTTTTC
Found at i:13583940 original size:15 final size:13
Alignment explanation
Indices: 13583906--13583934 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
13583896 GTTTTTGTTC
13583906 TTTTCT-TTTCTT
1 TTTTCTCTTTCTT
13583918 TTTTCTCTTTCTT
1 TTTTCTCTTTCTT
13583931 TTTT
1 TTTT
13583935 ATCTCTGTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTCTCTTTCTT
Found at i:13588962 original size:51 final size:50
Alignment explanation
Indices: 13588894--13589233 Score: 294
Period size: 51 Copynumber: 6.7 Consensus size: 50
13588884 TACCCGGTTG
* * *
13588894 ACATAGTAGCTTACACATAGTACTACACATGTGACCATTTTCATCCGATAC
1 ACATAGTAGCCTGCACATAGTACTACACATGTGACCA-TCTCATCCGATAC
* * * *
13588945 ACGTAGTAGCTTGCACATAGTACTACACATGTGATCGAAGCT-ATCC-AGTAC
1 ACATAGTAGCCTGCACATAGTACTACACATGTGA-C-CATCTCATCCGA-TAC
* * * *
13588996 GCATAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTCCGGTAC
1 ACATAGTAGCCTGCACATAGTACTACACATGTGACCATCTCA-TCCGATAC
* * * *
13589046 ACATAGTAGCCTGCACATAATACTACACACGTGACAATTTTCATCCGATAC
1 ACATAGTAGCCTGCACATAGTACTACACATGTGACCA-TCTCATCCGATAC
* * * * * * * *
13589097 ACGTAGTAGCCTCCACATAGTACTACACACGTGATCGAAGCT-ATTCGGTAT
1 ACATAGTAGCCTGCACATAGTACTACACATGTGA-C-CATCTCATCCGATAC
* * * * *
13589148 GCATAGTAGCCTACACATAGTACTACACATGCGACC-TGTCATTCCGATAT
1 ACATAGTAGCCTGCACATAGTACTACACATGTGACCATCTCA-TCCGATAC
* *
13589198 ACGTAGTAGCCTGCACATAGTACTACACACGTGACC
1 ACATAGTAGCCTGCACATAGTACTACACATGTGACC
13589234 TAGCAACTTC
Statistics
Matches: 234, Mismatches: 43, Indels: 25
0.77 0.14 0.08
Matches are distributed among these distances:
48 2 0.01
49 2 0.01
50 77 0.33
51 142 0.61
52 8 0.03
53 3 0.01
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.25
Consensus pattern (50 bp):
ACATAGTAGCCTGCACATAGTACTACACATGTGACCATCTCATCCGATAC
Found at i:13589104 original size:101 final size:100
Alignment explanation
Indices: 13588897--13589235 Score: 328
Period size: 101 Copynumber: 3.4 Consensus size: 100
13588887 CCGGTTGACA
* * * * * * *
13588897 TAGTAGCTTACACATAGTACTACACATGTGACCATTTTCA-TCCGATACACGTAGTAGCTTGCAC
1 TAGTAGCCTGCACATAGTACTACACACGTGACC--TATCATTCCGGTACACATAGTAGCCTGCAC
* * *
13588961 ATAGTACTACACATGTGATCGAAGCT-ATCC-AGTACGCA
64 ATAGTACTACACATGTGA-C-AATCTCATCCGA-TACACG
* *
13588999 TAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTCCGGTACACATAGTAGCCTGCACAT
1 TAGTAGCCTGCACATAGTACTACACACGTGACCTATCATTCCGGTACACATAGTAGCCTGCACAT
* * *
13589064 AATACTACACACGTGACAATTTTCATCCGATACACG
66 AGTACTACACATGTGACAA-TCTCATCCGATACACG
* ** * ** *
13589100 TAGTAGCCTCCACATAGTACTACACACGTGATCGAAGCTATT-CGGTATGCATAGTAGCCTACAC
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCTATC-ATTCCGGTACACATAGTAGCCTGCAC
* * * *
13589164 ATAGTACTACACATGCGAC-CTGTCATTCCGATATACG
64 ATAGTACTACACATGTGACAATCTCA-TCCGATACACG
13589201 TAGTAGCCTGCACATAGTACTACACACGTGACCTA
1 TAGTAGCCTGCACATAGTACTACACACGTGACCTA
13589236 GCAACTTCAC
Statistics
Matches: 199, Mismatches: 31, Indels: 16
0.81 0.13 0.07
Matches are distributed among these distances:
99 2 0.01
100 12 0.06
101 113 0.57
102 69 0.35
103 3 0.02
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.26
Consensus pattern (100 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCTATCATTCCGGTACACATAGTAGCCTGCACAT
AGTACTACACATGTGACAATCTCATCCGATACACG
Found at i:13589165 original size:152 final size:152
Alignment explanation
Indices: 13588894--13589232 Score: 534
Period size: 152 Copynumber: 2.2 Consensus size: 152
13588884 TACCCGGTTG
* * * * * *
13588894 ACATAGTAGCTTACACATAGTACTACACATGTGACCATTTTCATCCGATACACGTAGTAGCTTGC
1 ACATAGTAGCCTGCACATAGTACTACACACGTGACAATTTTCATCCGATACACGTAGTAGCCTCC
* *
13588959 ACATAGTACTACACATGTGATCGAAGCTATCCAGTACGCATAGTAGCCTGCACATAGTACTACAC
66 ACATAGTACTACACACGTGATCGAAGCTATCCAGTACGCATAGTAGCCTACACATAGTACTACAC
*
13589024 ATGCGACCTATCATTCCGGTAC
131 ATGCGACCTATCATTCCGATAC
*
13589046 ACATAGTAGCCTGCACATAATACTACACACGTGACAATTTTCATCCGATACACGTAGTAGCCTCC
1 ACATAGTAGCCTGCACATAGTACTACACACGTGACAATTTTCATCCGATACACGTAGTAGCCTCC
* * *
13589111 ACATAGTACTACACACGTGATCGAAGCTATTCGGTATGCATAGTAGCCTACACATAGTACTACAC
66 ACATAGTACTACACACGTGATCGAAGCTATCCAGTACGCATAGTAGCCTACACATAGTACTACAC
* *
13589176 ATGCGACCTGTCATTCCGATAT
131 ATGCGACCTATCATTCCGATAC
*
13589198 ACGTAGTAGCCTGCACATAGTACTACACACGTGAC
1 ACATAGTAGCCTGCACATAGTACTACACACGTGAC
13589233 CTAGCAACTT
Statistics
Matches: 170, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
152 170 1.00
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (152 bp):
ACATAGTAGCCTGCACATAGTACTACACACGTGACAATTTTCATCCGATACACGTAGTAGCCTCC
ACATAGTACTACACACGTGATCGAAGCTATCCAGTACGCATAGTAGCCTACACATAGTACTACAC
ATGCGACCTATCATTCCGATAC
Found at i:13591247 original size:27 final size:28
Alignment explanation
Indices: 13591217--13591278 Score: 108
Period size: 27 Copynumber: 2.2 Consensus size: 28
13591207 AATCAAACAG
13591217 AAATGAATAGAAATGGG-AAAAAATGGA
1 AAATGAATAGAAATGGGAAAAAAATGGA
*
13591244 AAATGAATAGAAATGGGAAAAAAATGGG
1 AAATGAATAGAAATGGGAAAAAAATGGA
13591272 AAATGAA
1 AAATGAA
13591279 AATGAAAATG
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 17 0.52
28 16 0.48
ACGTcount: A:0.60, C:0.00, G:0.26, T:0.15
Consensus pattern (28 bp):
AAATGAATAGAAATGGGAAAAAAATGGA
Found at i:13592450 original size:13 final size:12
Alignment explanation
Indices: 13592432--13592478 Score: 58
Period size: 13 Copynumber: 3.7 Consensus size: 12
13592422 GTTTTAAAAC
13592432 ATGTTTTCAAGTT
1 ATGTTTT-AAGTT
13592445 ATGTTTTTAAGTT
1 ATG-TTTTAAGTT
*
13592458 ATGTTTTAAATAT
1 ATGTTTTAAGT-T
13592471 ATGTTTTA
1 ATGTTTTA
13592479 TGTGTGCTCC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
12 7 0.23
13 20 0.65
14 4 0.13
ACGTcount: A:0.28, C:0.02, G:0.13, T:0.57
Consensus pattern (12 bp):
ATGTTTTAAGTT
Found at i:13596471 original size:6 final size:6
Alignment explanation
Indices: 13596460--13596510 Score: 102
Period size: 6 Copynumber: 8.5 Consensus size: 6
13596450 GAATTAATAT
13596460 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
13596508 TGT
1 TGT
13596511 GGGTATAATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.31, C:0.00, G:0.18, T:0.51
Consensus pattern (6 bp):
TGTATA
Found at i:13597855 original size:57 final size:57
Alignment explanation
Indices: 13597765--13597882 Score: 209
Period size: 57 Copynumber: 2.1 Consensus size: 57
13597755 TTTTCCATAA
* *
13597765 CATGTGTTAAATAAGCCTATTTAGTGTCGTTTTTAACCCTAGGTTAGTTGCCATCCT
1 CATGTGTTAAATAAACCTATTTAGTGTCATTTTTAACCCTAGGTTAGTTGCCATCCT
*
13597822 CATGTGTTAAATAAACCTATTTAGTGTCATTTTTAACCCTAGGTTAGTTTCCATCCT
1 CATGTGTTAAATAAACCTATTTAGTGTCATTTTTAACCCTAGGTTAGTTGCCATCCT
13597879 CATG
1 CATG
13597883 CTAAATGTTT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.41
Consensus pattern (57 bp):
CATGTGTTAAATAAACCTATTTAGTGTCATTTTTAACCCTAGGTTAGTTGCCATCCT
Found at i:13599403 original size:48 final size:48
Alignment explanation
Indices: 13599348--13599469 Score: 210
Period size: 48 Copynumber: 2.5 Consensus size: 48
13599338 AGTCACATAT
13599348 GTGGCACGGATTGTGTGCAGGCCACCAATATTCTGTTAAGATACAAGG
1 GTGGCACGGATTGTGTGCAGGCCACCAATATTCTGTTAAGATACAAGG
*
13599396 GTGGCACGGACTGTGTGCAGGCCACCAATATTCTGTTAAGATACAAGG
1 GTGGCACGGATTGTGTGCAGGCCACCAATATTCTGTTAAGATACAAGG
*
13599444 GTGGCACGGACTT-TGTGTAGGCCACC
1 GTGGCACGGA-TTGTGTGCAGGCCACC
13599470 GAGAGTCTAT
Statistics
Matches: 70, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
48 69 0.99
49 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.30, T:0.24
Consensus pattern (48 bp):
GTGGCACGGATTGTGTGCAGGCCACCAATATTCTGTTAAGATACAAGG
Found at i:13599495 original size:48 final size:48
Alignment explanation
Indices: 13599348--13599521 Score: 186
Period size: 48 Copynumber: 3.6 Consensus size: 48
13599338 AGTCACATAT
* * * * * * *
13599348 GTGGCACGGATTGTGTGCAGGCCACCAATATTCTGTTAAGATACAAGG
1 GTGGCACGGACTGTGTGTAGGCCACCGAGAGTCTATTAAGACACAAGG
* * * * * *
13599396 GTGGCACGGACTGTGTGCAGGCCACCAATATTCTGTTAAGATACAAGG
1 GTGGCACGGACTGTGTGTAGGCCACCGAGAGTCTATTAAGACACAAGG
* ** *
13599444 GTGGCACGGACTTTGTGTAGGCCACCGAGAGTCTATTATTACACAAAG
1 GTGGCACGGACTGTGTGTAGGCCACCGAGAGTCTATTAAGACACAAGG
*
13599492 GTGGTACGGACTGTGTGTAGGCCACCGAGA
1 GTGGCACGGACTGTGTGTAGGCCACCGAGA
13599522 AATCTGTTTT
Statistics
Matches: 113, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 113 1.00
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (48 bp):
GTGGCACGGACTGTGTGTAGGCCACCGAGAGTCTATTAAGACACAAGG
Found at i:13601188 original size:30 final size:30
Alignment explanation
Indices: 13601152--13601215 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
13601142 TATTTATTAT
*
13601152 GAATACAATATTTCTAGGATAAGTTGTAAA
1 GAATACAATATTTCCAGGATAAGTTGTAAA
*
13601182 GAATACAATATTTCCAGGATAGGTTGTAAA
1 GAATACAATATTTCCAGGATAAGTTGTAAA
13601212 GAAT
1 GAAT
13601216 TATAAAAGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.42, C:0.08, G:0.19, T:0.31
Consensus pattern (30 bp):
GAATACAATATTTCCAGGATAAGTTGTAAA
Found at i:13602168 original size:114 final size:114
Alignment explanation
Indices: 13601967--13602198 Score: 412
Period size: 114 Copynumber: 2.0 Consensus size: 114
13601957 TCTATGATAT
13601967 GTGATGAATTGACGGAAAAGGCCATGTTTTGACCATGACAATATATGGAAATGTGATTATGTGTT
1 GTGATGAATTGACGGAAAAGGCCATGTTTTGACCATGACAATATATGGAAATGTGATTATGTGTT
13602032 TCCGTGTAAGACAATAGCTGGGCTATGGCTTCGGTGTGTGATATGTGAC
66 TCCGTGTAAGACAATAGCTGGGCTATGGCTTCGGTGTGTGATATGTGAC
* *
13602081 GTGATGAATTGATGGAAAAGGCCATGTTTTGACCATGGCAATATATGGAAATGTGATTATGTGTT
1 GTGATGAATTGACGGAAAAGGCCATGTTTTGACCATGACAATATATGGAAATGTGATTATGTGTT
* *
13602146 TCCGTGTAAGAGC-ATAGTTGGGCTATGGCTTCGGTGTGTGATATGTGAT
66 TCCGTGTAAGA-CAATAGCTGGGCTATGGCTTCGGTGTGTGATATGTGAC
13602195 GTGA
1 GTGA
13602199 CGATGTGTAA
Statistics
Matches: 113, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
114 112 0.99
115 1 0.01
ACGTcount: A:0.26, C:0.11, G:0.30, T:0.33
Consensus pattern (114 bp):
GTGATGAATTGACGGAAAAGGCCATGTTTTGACCATGACAATATATGGAAATGTGATTATGTGTT
TCCGTGTAAGACAATAGCTGGGCTATGGCTTCGGTGTGTGATATGTGAC
Found at i:13602395 original size:186 final size:186
Alignment explanation
Indices: 13602081--13602417 Score: 629
Period size: 186 Copynumber: 1.8 Consensus size: 186
13602071 GATATGTGAC
* *
13602081 GTGATGAATTGATGGAAAAGGCCATGTTTTGACCATGGCAATATATGGAAATGTGATTATGTGTT
1 GTGATGAATTGACGGAAAAGGCCATGTTTTGACCATGGCAATATACGGAAATGTGATTATGTGTT
* *
13602146 TCCGTGTAAGAGCATAGTTGGGCTATGGCTTCGGTGTGTGATATGTGATGTGACGATGTGTAAGA
66 TCCGTGTAAGACCATAGCTGGGCTATGGCTTCGGTGTGTGATATGTGATGTGACGATGTGTAAGA
13602211 CCATAGTTATACTATGGCAATATAACGCAGGAGTGAGTACTTTTGTTCTATTATAT
131 CCATAGTTATACTATGGCAATATAACGCAGGAGTGAGTACTTTTGTTCTATTATAT
*
13602267 GTGATGAATTGACGGAAAATGCCATGTTTTGACCATGGCAATATACGGAAATGTGATTATGTGTT
1 GTGATGAATTGACGGAAAAGGCCATGTTTTGACCATGGCAATATACGGAAATGTGATTATGTGTT
13602332 TCCGTGTAAGACCATAGCTGGGCTATGGCTTCGGTGTGTGATATGTGATGTGACGATGTGTAAGA
66 TCCGTGTAAGACCATAGCTGGGCTATGGCTTCGGTGTGTGATATGTGATGTGACGATGTGTAAGA
13602397 CCATAGTTATACTATGGCAAT
131 CCATAGTTATACTATGGCAAT
13602418 GTGAAAACGA
Statistics
Matches: 146, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
186 146 1.00
ACGTcount: A:0.27, C:0.12, G:0.28, T:0.33
Consensus pattern (186 bp):
GTGATGAATTGACGGAAAAGGCCATGTTTTGACCATGGCAATATACGGAAATGTGATTATGTGTT
TCCGTGTAAGACCATAGCTGGGCTATGGCTTCGGTGTGTGATATGTGATGTGACGATGTGTAAGA
CCATAGTTATACTATGGCAATATAACGCAGGAGTGAGTACTTTTGTTCTATTATAT
Found at i:13605564 original size:48 final size:47
Alignment explanation
Indices: 13605433--13605602 Score: 169
Period size: 48 Copynumber: 3.6 Consensus size: 47
13605423 GGTCGCATAT
* * * *
13605433 GTGGTACGAACTGTGTGCAGGCCACCAATATTCTGTTAAGATACAAGG
1 GTGGCACGGACTGTGTGCAGGCCACCAAGATTCTGTT-ATATACAAGG
* * * *
13605481 ATGGCAGGGACTGTGTGCAGGCCACTAATATTCTGTTCATATACAAGG
1 GTGGCACGGACTGTGTGCAGGCCACCAAGATTCTGTT-ATATACAAGG
* * * * * *
13605529 GTGGCACAGACTATGTGCAGGCCACCGAGAGTCTGTTATTACACAAAG
1 GTGGCACGGACTGTGTGCAGGCCACCAAGATTCTGTTA-TATACAAGG
* *
13605577 GTGGTACGGACTGTGTGTAGGCCACC
1 GTGGCACGGACTGTGTGCAGGCCACC
13605603 GAGAAATCTG
Statistics
Matches: 100, Mismatches: 21, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
47 1 0.01
48 99 0.99
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (47 bp):
GTGGCACGGACTGTGTGCAGGCCACCAAGATTCTGTTATATACAAGG
Found at i:13612745 original size:57 final size:57
Alignment explanation
Indices: 13612641--13612759 Score: 172
Period size: 57 Copynumber: 2.1 Consensus size: 57
13612631 ATAGAAATGG
13612641 TGAAAATGGAGAAATGGGAAACATTTGGAAATGATCATGGTTCTCTCCAAAATGAAAA
1 TGAAAATGGAGAAAT-GGAAACATTTGGAAATGATCATGGTTCTCTCCAAAATGAAAA
*
13612699 TGAAAATGGAGAAAT-GAAATCATTTGGAAATGAAT-GTGGCTT-TCTCCAAAATGAAAA
1 TGAAAATGGAGAAATGGAAA-CATTTGGAAATG-ATCATGG-TTCTCTCCAAAATGAAAA
13612756 TGAA
1 TGAA
13612760 TTTATGTTTT
Statistics
Matches: 57, Mismatches: 1, Indels: 7
0.88 0.02 0.11
Matches are distributed among these distances:
56 4 0.07
57 34 0.60
58 19 0.33
ACGTcount: A:0.44, C:0.09, G:0.22, T:0.25
Consensus pattern (57 bp):
TGAAAATGGAGAAATGGAAACATTTGGAAATGATCATGGTTCTCTCCAAAATGAAAA
Found at i:13614181 original size:35 final size:39
Alignment explanation
Indices: 13614143--13614237 Score: 101
Period size: 39 Copynumber: 2.5 Consensus size: 39
13614133 CTTTATATAT
* *
13614143 TTGTCTTTTTGTCTTTTT-TT-CAT-TTAT-TTTTGTTT
1 TTGTTTTTTTGTCTTTTTCTTACATATTATGTTTTCTTT
*
13614178 TTGTTTTTATTTTCTTTTTCTTACATATTATGTTTTCTTT
1 TTGTTTTT-TTGTCTTTTTCTTACATATTATGTTTTCTTT
*
13614218 GTTGTTTTTTT-TATTTTTCT
1 -TTGTTTTTTTGTCTTTTTCT
13614238 ATATAGGTCC
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
35 7 0.14
36 9 0.18
37 2 0.04
38 3 0.06
39 12 0.24
40 9 0.18
41 8 0.16
ACGTcount: A:0.08, C:0.08, G:0.07, T:0.76
Consensus pattern (39 bp):
TTGTTTTTTTGTCTTTTTCTTACATATTATGTTTTCTTT
Found at i:13615879 original size:65 final size:65
Alignment explanation
Indices: 13615775--13615902 Score: 202
Period size: 65 Copynumber: 2.0 Consensus size: 65
13615765 TAGCTAAACA
* * **
13615775 TTAATCCTAAGTTGTATGTTAGATATGTCTTTCCATATTCAATATGCAATTGCGGTGTATCTTCT
1 TTAATCCTAAGTTGTATGTTAGATACGTCTATCCATATTCAATATGCAATTGCCATGTATCTTCT
* *
13615840 TTAATCCTAAGTTGTATGTTAGATACGTCTATGCATATTCAATATTCAATTGCCATGTATCTT
1 TTAATCCTAAGTTGTATGTTAGATACGTCTATCCATATTCAATATGCAATTGCCATGTATCTT
13615903 GTTGCTCAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
65 57 1.00
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.44
Consensus pattern (65 bp):
TTAATCCTAAGTTGTATGTTAGATACGTCTATCCATATTCAATATGCAATTGCCATGTATCTTCT
Found at i:13616808 original size:5 final size:5
Alignment explanation
Indices: 13616798--13616828 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
13616788 TTAGGTTTTC
13616798 TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT T
1 TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT T
13616829 AGAATATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TCTTT
Found at i:13618128 original size:27 final size:23
Alignment explanation
Indices: 13618074--13618118 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
13618064 TGCTAAAGCA
13618074 TGTAGGTTATGGATAAACCACCT
1 TGTAGGTTATGGATAAACCACCT
*
13618097 TGTAGGTTGTGGATAAACCACC
1 TGTAGGTTATGGATAAACCACC
13618119 AAATTTGTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (23 bp):
TGTAGGTTATGGATAAACCACCT
Found at i:13618961 original size:11 final size:11
Alignment explanation
Indices: 13618945--13618986 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 11
13618935 AAAGATGATC
13618945 AAAGAAAAGAG
1 AAAGAAAAGAG
13618956 AAAGAAAAGAG
1 AAAGAAAAGAG
13618967 -AAGAAGAAGTAG
1 AAAGAA-AAG-AG
13618979 TAAAGAAA
1 -AAAGAAA
13618987 TGTGTTTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 5 0.19
11 14 0.52
12 2 0.07
13 1 0.04
14 5 0.19
ACGTcount: A:0.69, C:0.00, G:0.26, T:0.05
Consensus pattern (11 bp):
AAAGAAAAGAG
Found at i:13621183 original size:33 final size:33
Alignment explanation
Indices: 13621133--13621212 Score: 106
Period size: 33 Copynumber: 2.4 Consensus size: 33
13621123 ACTTACCCTG
* * * *
13621133 TGTTTACTATCCTAGCAGACTGTCTCTGTTCTA
1 TGTTTACTGTCCCAGCAGACTATATCTGTTCTA
* *
13621166 TGTTTACTGTCCCAGCAGACTATATTTGTTCTG
1 TGTTTACTGTCCCAGCAGACTATATCTGTTCTA
13621199 TGTTTACTGTCCCA
1 TGTTTACTGTCCCA
13621213 ATGGATTGTA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.17, C:0.24, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTTTACTGTCCCAGCAGACTATATCTGTTCTA
Found at i:13626464 original size:26 final size:26
Alignment explanation
Indices: 13626430--13626479 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
13626420 ATCTTTAAAT
* *
13626430 TAATTTCACAAAATTTCAGAAAATCG
1 TAATATCACAAAATTCCAGAAAATCG
13626456 TAATATCACAAAATTCCAGAAAAT
1 TAATATCACAAAATTCCAGAAAAT
13626480 TGGTTCATGA
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:0.50, C:0.16, G:0.06, T:0.28
Consensus pattern (26 bp):
TAATATCACAAAATTCCAGAAAATCG
Found at i:13628314 original size:20 final size:20
Alignment explanation
Indices: 13628289--13628337 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
13628279 TTGTATGAAA
13628289 GTTACACGGCCTGGGGTAAT
1 GTTACACGGCCTGGGGTAAT
13628309 GTTACACGGCCTGGGGTAAT
1 GTTACACGGCCTGGGGTAAT
*
13628329 GTCACACGG
1 GTTACACGG
13628338 TCGTGTGACC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.20, C:0.22, G:0.35, T:0.22
Consensus pattern (20 bp):
GTTACACGGCCTGGGGTAAT
Found at i:13631950 original size:163 final size:163
Alignment explanation
Indices: 13631671--13631993 Score: 547
Period size: 163 Copynumber: 2.0 Consensus size: 163
13631661 AAGCCTAAAG
* *
13631671 TATTTGATGTCATAGAAAGAACTGAATTTGAGACAACGTAGATGGTTCGAGCTATTAGAAGATTA
1 TATTTGATGTCACAGAAAGAACTGAATTTGAGACAACGTAGATGGTTCGAGCTATTAAAAGATTA
* *
13631736 CGATTTGATCATCGACTATCATCTAGGAAAAGCTAATATTGTTGTTGATGCTTTAAGTAGAAAAT
66 CGATTTGATCATCGACTATCATCTAGGAAAAGCTAATATCGTTGCTGATGCTTTAAGTAGAAAAT
*
13631801 CTTTGTGTACCTTGAGAGCTTTGAATACTCAGT
131 CTTTGTGTACCTTGAGAGATTTGAATACTCAGT
* * *
13631834 TATTTGATGTCACAGAAAGAACTGAATTTGAGACAACGTAGATGGTTTGAGTTGTTAAAAGATTA
1 TATTTGATGTCACAGAAAGAACTGAATTTGAGACAACGTAGATGGTTCGAGCTATTAAAAGATTA
*
13631899 CGATTTGATCATCGACTATCATCTAGGAAAAGCTAATGTCGTTGCTGATGCTTTAAGTAGAAAAT
66 CGATTTGATCATCGACTATCATCTAGGAAAAGCTAATATCGTTGCTGATGCTTTAAGTAGAAAAT
* *
13631964 CTTTTTTTACCTTGAGAGATTTGAATACTC
131 CTTTGTGTACCTTGAGAGATTTGAATACTC
13631994 GATTGACATT
Statistics
Matches: 149, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
163 149 1.00
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (163 bp):
TATTTGATGTCACAGAAAGAACTGAATTTGAGACAACGTAGATGGTTCGAGCTATTAAAAGATTA
CGATTTGATCATCGACTATCATCTAGGAAAAGCTAATATCGTTGCTGATGCTTTAAGTAGAAAAT
CTTTGTGTACCTTGAGAGATTTGAATACTCAGT
Found at i:13632810 original size:14 final size:14
Alignment explanation
Indices: 13632791--13632830 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
13632781 TTGATTGCCA
13632791 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
13632805 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
13632819 GGAAAATGTTTT
1 GTAAAATGTTTT
13632831 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:13632839 original size:20 final size:20
Alignment explanation
Indices: 13632814--13632853 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
13632804 CGTAAAATGA
*
13632814 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
13632834 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
13632854 AGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:13632843 original size:34 final size:35
Alignment explanation
Indices: 13632799--13632865 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
13632789 CAGTAAAATG
* *
13632799 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTAGAAAATATTTTAC
*
13632833 TTTTCTGTAAAATGATTTACTAGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTAGAAAATATTTT
13632866 CTGCTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTAGAAAATATTTTAC
Found at i:13640358 original size:6 final size:6
Alignment explanation
Indices: 13640347--13640377 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
13640337 AAAACACAAT
13640347 TTGGCA TTGGCA TTGGCA TTGGCA TTGGCA T
1 TTGGCA TTGGCA TTGGCA TTGGCA TTGGCA T
13640378 CCCCCTTTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.16, G:0.32, T:0.35
Consensus pattern (6 bp):
TTGGCA
Found at i:13648474 original size:23 final size:21
Alignment explanation
Indices: 13648424--13648482 Score: 59
Period size: 23 Copynumber: 2.7 Consensus size: 21
13648414 AGGCATAATA
13648424 TTAAATTTAG-C-TTTTTTTT
1 TTAAATTTAGTCATTTTTTTT
13648443 TTATCAATTTAGTCATTTTTTTT
1 TTA--AATTTAGTCATTTTTTTT
*
13648466 AGTTAAATTTGGTCATT
1 --TTAAATTTAGTCATT
13648483 AACCTTATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
19 3 0.09
21 7 0.21
22 1 0.03
23 19 0.58
25 3 0.09
ACGTcount: A:0.24, C:0.07, G:0.08, T:0.61
Consensus pattern (21 bp):
TTAAATTTAGTCATTTTTTTT
Found at i:13648664 original size:14 final size:14
Alignment explanation
Indices: 13648628--13648654 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
13648618 ATAATTTAAA
13648628 ATTTAAAAAAAAGC
1 ATTTAAAAAAAAGC
13648642 ATTTAAAAAAAAG
1 ATTTAAAAAAAAG
13648655 TTCTTAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.04, G:0.07, T:0.22
Consensus pattern (14 bp):
ATTTAAAAAAAAGC
Found at i:13650038 original size:25 final size:25
Alignment explanation
Indices: 13650010--13650059 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
13650000 GGATTATAAG
13650010 ATAGGAGTACAAAATTCCTAAAAAT
1 ATAGGAGTACAAAATTCCTAAAAAT
13650035 ATAGGAGTACAAAATTCCTAAAAAT
1 ATAGGAGTACAAAATTCCTAAAAAT
13650060 TATGGTTTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.52, C:0.12, G:0.12, T:0.24
Consensus pattern (25 bp):
ATAGGAGTACAAAATTCCTAAAAAT
Found at i:13650375 original size:19 final size:19
Alignment explanation
Indices: 13650353--13650390 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
13650343 AAAATAAATG
*
13650353 GAAATAAAAAGAATAGAAA
1 GAAACAAAAAGAATAGAAA
*
13650372 GAAACGAAAAGAATAGAAA
1 GAAACAAAAAGAATAGAAA
13650391 TAATAGTTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.71, C:0.03, G:0.18, T:0.08
Consensus pattern (19 bp):
GAAACAAAAAGAATAGAAA
Found at i:13659581 original size:26 final size:27
Alignment explanation
Indices: 13659552--13659602 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
13659542 GACCGTAATG
*
13659552 CCCCTAGAGGGTAAATGACT-ATTTTT
1 CCCCTAGAAGGTAAATGACTGATTTTT
* *
13659578 CCCCTCGAATGTAAATGACTGATTT
1 CCCCTAGAAGGTAAATGACTGATTT
13659603 GTGCTATAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 17 0.81
27 4 0.19
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (27 bp):
CCCCTAGAAGGTAAATGACTGATTTTT
Found at i:13664310 original size:30 final size:30
Alignment explanation
Indices: 13664258--13664315 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
13664248 ACCTTTTATC
*
13664258 TTTCCCCAAAATTTTTACTCCC-TCCCACT
1 TTTCCCCAAAACTTTTACTCCCTTCCCACT
*
13664287 TTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTCCCC-AAAACTTTTACTCCCTTCCCA
13664316 TCCCACCTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 7 0.28
30 13 0.52
31 5 0.20
ACGTcount: A:0.21, C:0.40, G:0.00, T:0.40
Consensus pattern (30 bp):
TTTCCCCAAAACTTTTACTCCCTTCCCACT
Found at i:13687419 original size:22 final size:19
Alignment explanation
Indices: 13687394--13687435 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 19
13687384 TGATAATAAC
13687394 TAATATATAATTATATTTATTA
1 TAATATAT-ATTA-A-TTATTA
13687416 TAATATATATTAATTATTA
1 TAATATATATTAATTATTA
13687435 T
1 T
13687436 CAACTTTGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 7 0.35
20 1 0.05
21 4 0.20
22 8 0.40
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TAATATATATTAATTATTA
Found at i:13687426 original size:16 final size:15
Alignment explanation
Indices: 13687394--13687432 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
13687384 TGATAATAAC
13687394 TAATATATAATTATAT
1 TAAT-TATAATTATAT
*
13687410 TTATTATAATATATAT
1 TAATTATAAT-TATAT
13687426 TAATTAT
1 TAATTAT
13687433 TATCAACTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TAATTATAATTATAT
Found at i:13694606 original size:27 final size:27
Alignment explanation
Indices: 13694557--13694632 Score: 91
Period size: 27 Copynumber: 2.8 Consensus size: 27
13694547 GGACTTACTT
* * *
13694557 GTGTTTAATGTCC-CAGCGAACTACCCT
1 GTGTTTAATGTCCTGA-CGGACTACCCC
*
13694584 GTGTTTAATGTCCTGATGGACTACCCC
1 GTGTTTAATGTCCTGACGGACTACCCC
*
13694611 GTGTTTAGTGTCCTGACGGACT
1 GTGTTTAATGTCCTGACGGACT
13694633 CCATTGGTTG
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
27 41 0.98
28 1 0.02
ACGTcount: A:0.18, C:0.25, G:0.24, T:0.33
Consensus pattern (27 bp):
GTGTTTAATGTCCTGACGGACTACCCC
Found at i:13697047 original size:27 final size:27
Alignment explanation
Indices: 13696950--13697036 Score: 138
Period size: 27 Copynumber: 3.2 Consensus size: 27
13696940 ATTCGTGGGC
*
13696950 AAATGACCGAAATACCCCCAAAGGGTA
1 AAATGACTGAAATACCCCCAAAGGGTA
*
13696977 AAATGACTGAAACACCCCCAAAGGGTA
1 AAATGACTGAAATACCCCCAAAGGGTA
* *
13697004 AAATGACTGAAATACCCTCACAGGGTA
1 AAATGACTGAAATACCCCCAAAGGGTA
13697031 AAATGA
1 AAATGA
13697037 TTGTTATACC
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 55 1.00
ACGTcount: A:0.45, C:0.23, G:0.18, T:0.14
Consensus pattern (27 bp):
AAATGACTGAAATACCCCCAAAGGGTA
Found at i:13697432 original size:33 final size:33
Alignment explanation
Indices: 13697380--13697457 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 33
13697370 CGCATTATTG
* *
13697380 CACTGTACTTATTACTGTATTGGGCAAAGGCCCA
1 CACTGTAC-TGTTACTGTATAGGGCAAAGGCCCA
**
13697414 CACTGTACTGTTACTGTATAGGGCTCAGGCCCA
1 CACTGTACTGTTACTGTATAGGGCAAAGGCCCA
*
13697447 GACTGATACTG
1 CACTG-TACTG
13697458 CATGATTACT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
33 25 0.66
34 13 0.34
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.28
Consensus pattern (33 bp):
CACTGTACTGTTACTGTATAGGGCAAAGGCCCA
Found at i:13702414 original size:11 final size:11
Alignment explanation
Indices: 13702395--13702425 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
13702385 ATACATTTTC
13702395 ATTATTTATTA
1 ATTATTTATTA
*
13702406 ATTAATTATTA
1 ATTATTTATTA
13702417 ATTATTTAT
1 ATTATTTAT
13702426 ATTTTTAAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
ATTATTTATTA
Found at i:13708716 original size:46 final size:46
Alignment explanation
Indices: 13708646--13709002 Score: 459
Period size: 46 Copynumber: 8.2 Consensus size: 46
13708636 TTTGAGTACT
* *
13708646 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* *
13708692 TCTGATGAAGTGACAAATTGAT-A-----AG---T-GCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* *
13708728 TCTGATCAAGAGACAAAGTTATAAGTGGTAGCTTTAGCTACAC-TA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
13708773 TTCTGATCAAGTGACAAAGTGAT-A-----AG---TA-CTACACTTA
1 -TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* *
13708810 TATGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
13708856 TCTGATCAAGTGACAAAGTGATAAGTGTTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
13708902 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
13708948 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
13708994 TCTGATCAA
1 TCTGATCAA
13709003 CCCAACCGGC
Statistics
Matches: 272, Mismatches: 17, Indels: 44
0.82 0.05 0.13
Matches are distributed among these distances:
36 54 0.20
37 7 0.03
40 4 0.01
42 4 0.01
45 7 0.03
46 196 0.72
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (46 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
Found at i:13708723 original size:36 final size:36
Alignment explanation
Indices: 13708682--13708836 Score: 148
Period size: 36 Copynumber: 4.0 Consensus size: 36
13708672 GGTAGCTTTA
* * *
13708682 GCTACACTTATCTGATGAAGTGACAAATTGATAAGT
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
*
13708718 GCTACACTTATCTGATCAAGAGACAAAGTTATAAGTGGT
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAA---GT
* *
13708757 AGCTTTAGCTACACTATTCTGATCAAGTGACAAAGTGATAAGT
1 -GC--TA-C-AC-TTA-TCTGATCAAGAGACAAAGTGATAAGT
* *
13708800 ACTACACTTATATGATCAAGAGACAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
13708836 G
1 G
13708837 GTAGCTTTAG
Statistics
Matches: 97, Mismatches: 12, Indels: 20
0.75 0.09 0.16
Matches are distributed among these distances:
36 54 0.56
37 2 0.02
38 2 0.02
39 3 0.03
40 4 0.04
42 3 0.03
43 3 0.03
44 2 0.02
45 2 0.02
46 22 0.23
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.28
Consensus pattern (36 bp):
GCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
Found at i:13708785 original size:82 final size:82
Alignment explanation
Indices: 13708646--13708974 Score: 480
Period size: 82 Copynumber: 3.9 Consensus size: 82
13708636 TTTGAGTACT
* * *
13708646 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATGAAGTGACAAATT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGT
13708711 GATAAGTGCTACACTTA
66 GATAAGTGCTACACTTA
*
13708728 TCTGATCAAGAGACAAAGTTATAAGTGGTAGCTTTAGCTACAC-TATTCTGATCAAGTGACAAAG
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA-TCTGATCAAGTGACAAAG
*
13708792 TGATAAGTACTACACTTA
65 TGATAAGTGCTACACTTA
*
13708810 TATGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGT
13708875 GATAAGTGTTAGCTTTAGCTACACTTA
66 GAT-A-----AG---T-GCTACACTTA
* *
13708902 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAAGTGACAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGT
13708967 GATAAGTG
66 GATAAGTG
13708975 GTAGCCTTAG
Statistics
Matches: 224, Mismatches: 11, Indels: 24
0.86 0.04 0.09
Matches are distributed among these distances:
81 2 0.01
82 138 0.62
83 4 0.02
86 2 0.01
88 2 0.01
91 2 0.01
92 74 0.33
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (82 bp):
TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGT
GATAAGTGCTACACTTA
Found at i:13717261 original size:28 final size:28
Alignment explanation
Indices: 13717210--13717263 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
13717200 CAGTAACAGT
*
13717210 ACAGTGTGGGCCTTAGCCCAATACAGAA
1 ACAGTGTGGGCCTAAGCCCAATACAGAA
* *
13717238 ACAGTGTGGGCCTAAGCTCGATACAG
1 ACAGTGTGGGCCTAAGCCCAATACAG
13717264 TATCGGTATG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.30, C:0.24, G:0.28, T:0.19
Consensus pattern (28 bp):
ACAGTGTGGGCCTAAGCCCAATACAGAA
Found at i:13717662 original size:32 final size:32
Alignment explanation
Indices: 13717480--13717745 Score: 209
Period size: 32 Copynumber: 8.4 Consensus size: 32
13717470 GAATGGCTAC
* * * *
13717480 AAGCCATAAGT-ACAGTAATGTGATTGGCACA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
* * * *
13717511 AAGCCATCCGTAGCAGTGATATGATCGGCACA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
* * * * *
13717543 CAA-CTATCAGTAATGGTAA-CTGATTGACACA
1 -AAGCCATCAGTAACGGTAATATGATCGGCACA
* * * *
13717574 AAGCCATCAGTAGCAGTGATATGATCAGCACA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
* * *
13717606 CAA-CCATTAATAACAGTGAA-ATGATCGGCACA
1 -AAGCCATCAGTAACGGT-AATATGATCGGCACA
* *
13717638 CAGCCATCGGTAACGGTAATATGATCGGCACA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
* * * *
13717670 AAGCCATCACTACCGGTACTATGACCGGCACA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
* *
13717702 AAGCCATCAGTAACGGTACTATGATTGGCACA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
*
13717734 AAGCCATTAGTA
1 AAGCCATCAGTA
13717746 GCATCGCAGC
Statistics
Matches: 182, Mismatches: 45, Indels: 15
0.75 0.19 0.06
Matches are distributed among these distances:
30 2 0.01
31 32 0.18
32 143 0.79
33 5 0.03
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.20
Consensus pattern (32 bp):
AAGCCATCAGTAACGGTAATATGATCGGCACA
Found at i:13717726 original size:96 final size:95
Alignment explanation
Indices: 13717505--13717745 Score: 236
Period size: 96 Copynumber: 2.5 Consensus size: 95
13717495 TAATGTGATT
* * * * * * *
13717505 GGCACAAAGCCATCCGTAGCAGTGATATGATCGGCACACAACTATCAGTAATGGTAACTGATTGA
1 GGCACAAAGCCATCAGTAACAGTGATATGATCGGCACACAGCCATCAGTAACGGTAAATGATCGA
* * *
13717570 CACAAAGCCATCAGTAGCAGTGATATGATC
66 CACAAAGCCATCACTACCAGTGATATGACC
* * * * *
13717600 AGCACACAA-CCATTAATAACAGTGAAATGATCGGCACACAGCCATCGGTAACGGTAATATGATC
1 GGCACA-AAGCCATCAGTAACAGTGATATGATCGGCACACAGCCATCAGTAACGGTAA-ATGATC
* *
13717664 GGCACAAAGCCATCACTACCGGT-ACTATGACC
64 GACACAAAGCCATCACTACCAGTGA-TATGACC
* * * *
13717696 GGCACAAAGCCATCAGTAACGGT-ACTATGATTGGCACAAAGCCATTAGTA
1 GGCACAAAGCCATCAGTAACAGTGA-TATGATCGGCACACAGCCATCAGTA
13717746 GCATCGCAGC
Statistics
Matches: 115, Mismatches: 26, Indels: 9
0.77 0.17 0.06
Matches are distributed among these distances:
95 48 0.42
96 67 0.58
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.20
Consensus pattern (95 bp):
GGCACAAAGCCATCAGTAACAGTGATATGATCGGCACACAGCCATCAGTAACGGTAAATGATCGA
CACAAAGCCATCACTACCAGTGATATGACC
Found at i:13718023 original size:27 final size:27
Alignment explanation
Indices: 13717978--13718500 Score: 542
Period size: 27 Copynumber: 19.5 Consensus size: 27
13717968 GCAAAAAATA
*
13717978 GTCA-TTTACCC-ACCA-GGGCATTACA
1 GTCATTTTACCCTA-CAGGGGCATTACG
13718003 GTCATTTTACCCTACAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
** * * * *
13718030 ACCATTTTATCCTACAAGGGTATTAGG
1 GTCATTTTACCCTACAGGGGCATTACG
*
13718057 GTCATTTTACTCTACAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
13718084 GTCATTTTACCCTACAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
**
13718111 ACCATTTTACCCTACAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
** * * *
13718138 ACCATTTTATCCTACAGGGGTATTAGG
1 GTCATTTTACCCTACAGGGGCATTACG
*
13718165 GTCATTTTACTCTACAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
13718192 GTCATTTTACCCTACAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* *
13718219 ATCATTTTACCCTACAGGGGCATTACA
1 GTCATTTTACCCTACAGGGGCATTACG
* * *
13718246 GTCATTTTACCTTATAGGGGCATTATG
1 GTCATTTTACCCTACAGGGGCATTACG
*
13718273 GTCATTTTACCCTACAGGGGTATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* *
13718300 GTCATTTTACCCTACAGAGGTATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
**
13718327 GTCATTTTACCCTACAGGGGCATTATA
1 GTCATTTTACCCTACAGGGGCATTACG
* * *
13718354 ATCATTTTACCCTACAGGGGTATTAAG
1 GTCATTTTACCCTACAGGGGCATTACG
* * *
13718381 GTTATTTTACCCTATA-GGGCTATTTCG
1 GTCATTTTACCCTACAGGGGC-ATTACG
* * * * **
13718408 AT-ATTCTACCTTAC-GAGGGTATTTTG
1 GTCATTTTACCCTACAG-GGGCATTACG
* *
13718434 GTCATTTTACCCTA-TGGAGGCATTTCG
1 GTCATTTTACCCTACAGG-GGCATTACG
* * *
13718461 ATCATTTTACCTCT-C-GAGGGTATTTCG
1 GTCATTTTACC-CTACAG-GGGCATTACG
13718488 GTCATTTTACCCT
1 GTCATTTTACCCT
13718501 TCGAGGGTAT
Statistics
Matches: 419, Mismatches: 67, Indels: 23
0.82 0.13 0.05
Matches are distributed among these distances:
25 4 0.01
26 30 0.07
27 382 0.91
28 3 0.01
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.34
Consensus pattern (27 bp):
GTCATTTTACCCTACAGGGGCATTACG
Found at i:13720089 original size:63 final size:64
Alignment explanation
Indices: 13719982--13720111 Score: 192
Period size: 63 Copynumber: 2.0 Consensus size: 64
13719972 ATAGAAATTG
* *
13719982 TGAAAATAGAGAAATGGGAAATATTTGGAAATGATTATGGTTTTCTCCAAAATGAAAATGAAAA
1 TGAAAATAGAGAAATGGGAAATATTTGGAAATGAATATGATTTTCTCCAAAATGAAAATGAAAA
* * *
13720046 TGAAAATGGAGAAAT-GG-AATCATTTGGAAATGAATGTGATTTTCTCTAAAATGAAAATGAAAA
1 TGAAAATAGAGAAATGGGAAAT-ATTTGGAAATGAATATGATTTTCTCCAAAATGAAAATGAAAA
13720109 TGA
1 TGA
13720112 CTTGGAAATG
Statistics
Matches: 60, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
62 3 0.05
63 43 0.72
64 14 0.23
ACGTcount: A:0.46, C:0.05, G:0.21, T:0.28
Consensus pattern (64 bp):
TGAAAATAGAGAAATGGGAAATATTTGGAAATGAATATGATTTTCTCCAAAATGAAAATGAAAA
Found at i:13736626 original size:19 final size:19
Alignment explanation
Indices: 13736596--13736633 Score: 60
Period size: 18 Copynumber: 2.0 Consensus size: 19
13736586 AATATTTACA
13736596 ATTTTTTATT-AATTTGAT
1 ATTTTTTATTAAATTTGAT
13736614 ATTTTTTAGTTAAATTTGAT
1 ATTTTTTA-TTAAATTTGAT
13736634 TCTTCATCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
19 2 0.11
20 8 0.44
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (19 bp):
ATTTTTTATTAAATTTGAT
Found at i:13740498 original size:27 final size:27
Alignment explanation
Indices: 13740468--13740549 Score: 84
Period size: 27 Copynumber: 3.1 Consensus size: 27
13740458 AATGTGTTTT
13740468 TATTGCATGTTATTAAGTTGTCTTAAA
1 TATTGCATGTTATTAAGTTGTCTTAAA
* * *
13740495 TATTACA-GCTTA-TAAATATGT-TT--T
1 TATTGCATG-TTATTAAGT-TGTCTTAAA
13740519 TATTGCATGTTATTAAGTTGTCTTAAA
1 TATTGCATGTTATTAAGTTGTCTTAAA
13740546 TATT
1 TATT
13740550 ACAGCTTATA
Statistics
Matches: 42, Mismatches: 6, Indels: 14
0.68 0.10 0.23
Matches are distributed among these distances:
24 12 0.29
25 7 0.17
26 7 0.17
27 16 0.38
ACGTcount: A:0.30, C:0.07, G:0.12, T:0.50
Consensus pattern (27 bp):
TATTGCATGTTATTAAGTTGTCTTAAA
Found at i:13740531 original size:24 final size:23
Alignment explanation
Indices: 13740456--13740531 Score: 55
Period size: 24 Copynumber: 3.0 Consensus size: 23
13740446 TTATTCATGT
13740456 TAAATGTGTTTTTATTGCATGTTA
1 TAAAT-TGTTTTTATTGCATGTTA
* * *
13740480 TTAAGTTGTCTTAAATATTACA-GCTTA
1 -TAAATTGT-TT--TTATTGCATG-TTA
13740507 TAAATATGTTTTTATTGCATGTTA
1 TAAAT-TGTTTTTATTGCATGTTA
13740531 T
1 T
13740532 TAAGTTGTCT
Statistics
Matches: 39, Mismatches: 6, Indels: 13
0.67 0.10 0.22
Matches are distributed among these distances:
24 13 0.33
25 7 0.18
26 7 0.18
27 12 0.31
ACGTcount: A:0.29, C:0.07, G:0.13, T:0.51
Consensus pattern (23 bp):
TAAATTGTTTTTATTGCATGTTA
Found at i:13740532 original size:51 final size:51
Alignment explanation
Indices: 13740456--13740596 Score: 221
Period size: 51 Copynumber: 2.7 Consensus size: 51
13740446 TTATTCATGT
*
13740456 TAAATGTGTTTTTATTGCATGTTATTAAGTTGTCTTAAATATTACAGCTTA
1 TAAATATGTTTTTATTGCATGTTATTAAGTTGTCTTAAATATTACAGCTTA
13740507 TAAATATGTTTTTATTGCATGTTATTAAGTTGTCTTAAATATTACAGCTTA
1 TAAATATGTTTTTATTGCATGTTATTAAGTTGTCTTAAATATTACAGCTTA
*
13740558 TAAATATGTTTTTGTTATTGCATGTTTTTAA-TATGTCTT
1 TAAATATG--TTT-TTATTGCATGTTATTAAGT-TGTCTT
13740597 GTCCAACCGA
Statistics
Matches: 84, Mismatches: 2, Indels: 5
0.92 0.02 0.05
Matches are distributed among these distances:
51 58 0.69
53 4 0.05
54 22 0.26
ACGTcount: A:0.28, C:0.07, G:0.13, T:0.52
Consensus pattern (51 bp):
TAAATATGTTTTTATTGCATGTTATTAAGTTGTCTTAAATATTACAGCTTA
Found at i:13740558 original size:27 final size:27
Alignment explanation
Indices: 13740477--13740558 Score: 84
Period size: 27 Copynumber: 3.1 Consensus size: 27
13740467 TTATTGCATG
13740477 TTATTAAGTTGTCTTAAATATTACAGC
1 TTATTAAGTTGTCTTAAATATTACAGC
* * *
13740504 TTA-TAAATATGT-TT--TTATTGCATG-
1 TTATTAAGT-TGTCTTAAATATTACA-GC
13740528 TTATTAAGTTGTCTTAAATATTACAGC
1 TTATTAAGTTGTCTTAAATATTACAGC
13740555 TTAT
1 TTAT
13740559 AAATATGTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 14
0.68 0.10 0.23
Matches are distributed among these distances:
24 12 0.29
25 7 0.17
26 7 0.17
27 16 0.38
ACGTcount: A:0.32, C:0.09, G:0.11, T:0.49
Consensus pattern (27 bp):
TTATTAAGTTGTCTTAAATATTACAGC
Found at i:13742144 original size:20 final size:20
Alignment explanation
Indices: 13742115--13742162 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
13742105 GAACCACTCT
13742115 ATTT-CTTACTTATCATTCC
1 ATTTACTTACTTATCATTCC
* * *
13742134 GTTTACTTACTTTTCATTTC
1 ATTTACTTACTTATCATTCC
13742154 ATTTACTTA
1 ATTTACTTA
13742163 GCATAAGCCT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 3 0.12
20 21 0.88
ACGTcount: A:0.21, C:0.21, G:0.02, T:0.56
Consensus pattern (20 bp):
ATTTACTTACTTATCATTCC
Found at i:13756224 original size:20 final size:21
Alignment explanation
Indices: 13756176--13756228 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
13756166 TTTTCAGGTG
13756176 GTATCGATACCACTTAAAGGAA
1 GTATCGATACCAC-TAAAGGAA
* * *
13756198 ATATCGATACCA-TAGAGGCA
1 GTATCGATACCACTAAAGGAA
13756218 GTATCGATACC
1 GTATCGATACC
13756229 TACGTAACAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 16 0.59
22 11 0.41
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.23
Consensus pattern (21 bp):
GTATCGATACCACTAAAGGAA
Found at i:13756311 original size:12 final size:12
Alignment explanation
Indices: 13756296--13756320 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
13756286 TTTATGTTTG
13756296 TTTGTCGTATGT
1 TTTGTCGTATGT
13756308 TTTGTCGTATGT
1 TTTGTCGTATGT
13756320 T
1 T
13756321 AGTATAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.08, G:0.24, T:0.60
Consensus pattern (12 bp):
TTTGTCGTATGT
Found at i:13774006 original size:20 final size:20
Alignment explanation
Indices: 13773983--13774043 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
13773973 TAAGTAAATT
13773983 GAAAGATGTATAATCTTATA
1 GAAAGATGTATAATCTTATA
* *
13774003 GAAAGGT-TGATAA----ATT
1 GAAAGATGT-ATAATCTTATA
13774019 GAAAGATGTATAATCTTATA
1 GAAAGATGTATAATCTTATA
13774039 GAAAG
1 GAAAG
13774044 GTTGATGGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 12
0.66 0.09 0.26
Matches are distributed among these distances:
16 12 0.39
17 1 0.03
19 1 0.03
20 17 0.55
ACGTcount: A:0.46, C:0.03, G:0.20, T:0.31
Consensus pattern (20 bp):
GAAAGATGTATAATCTTATA
Found at i:13774018 original size:36 final size:36
Alignment explanation
Indices: 13773977--13774049 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
13773967 GGAAAATAAG
13773977 TAAATTGAAAGATGTATAATCTTATAGAAAGGTTGA
1 TAAATTGAAAGATGTATAATCTTATAGAAAGGTTGA
13774013 TAAATTGAAAGATGTATAATCTTATAGAAAGGTTGA
1 TAAATTGAAAGATGTATAATCTTATAGAAAGGTTGA
13774049 T
1 T
13774050 GGTTATACTT
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:0.44, C:0.03, G:0.19, T:0.34
Consensus pattern (36 bp):
TAAATTGAAAGATGTATAATCTTATAGAAAGGTTGA
Found at i:13777909 original size:24 final size:24
Alignment explanation
Indices: 13777870--13777965 Score: 95
Period size: 24 Copynumber: 4.0 Consensus size: 24
13777860 GACAAGTTGC
*
13777870 ACGTTATGTCCGAGCCACTCAATA
1 ACGTTATGTCCAAGCCACTCAATA
*
13777894 ACGTTATGCCCAAGCCACTCAATA
1 ACGTTATGTCCAAGCCACTCAATA
* * * *
13777918 GCATTGTGTTCAAGCCACTCAATA
1 ACGTTATGTCCAAGCCACTCAATA
* * *
13777942 ATG-TATTGGCCAAGCCATTCAATA
1 ACGTTA-TGTCCAAGCCACTCAATA
13777966 TCGCAGACAA
Statistics
Matches: 57, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
23 1 0.02
24 56 0.98
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (24 bp):
ACGTTATGTCCAAGCCACTCAATA
Found at i:13793883 original size:16 final size:16
Alignment explanation
Indices: 13793862--13793896 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
13793852 ACGATAACAT
*
13793862 GTTTATAGGCGGTCAA
1 GTTTATAGGAGGTCAA
13793878 GTTTATAGGAGGTCAA
1 GTTTATAGGAGGTCAA
13793894 GTT
1 GTT
13793897 CTTGGCACCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.26, C:0.09, G:0.31, T:0.34
Consensus pattern (16 bp):
GTTTATAGGAGGTCAA
Found at i:13794074 original size:14 final size:14
Alignment explanation
Indices: 13794055--13794081 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
13794045 TAGTTAAGTA
13794055 AATATTTTTATTTT
1 AATATTTTTATTTT
13794069 AATATTTTTATTT
1 AATATTTTTATTT
13794082 ACCTTCTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
AATATTTTTATTTT
Found at i:13802452 original size:8 final size:8
Alignment explanation
Indices: 13802441--13802468 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
13802431 AAAATAATAA
13802441 AATTATAG
1 AATTATAG
13802449 AATTATAG
1 AATTATAG
13802457 AATTATAG
1 AATTATAG
13802465 AATT
1 AATT
13802469 TACCCCACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (8 bp):
AATTATAG
Found at i:13804070 original size:36 final size:36
Alignment explanation
Indices: 13804022--13804484 Score: 361
Period size: 36 Copynumber: 12.7 Consensus size: 36
13804012 TAGTCAAAAC
*
13804022 CAACCTTTAAAAAAGGTTAGGATAGACTCGTCTAAGG
1 CAACC-TTAAAAAAGGTTGGGATAGACTCGTCTAAGG
* *
13804059 TAACCTT-AAAAAGGTTGGGATAGACCTTGTCTAAGG
1 CAACCTTAAAAAAGGTTGGGATAGA-CTCGTCTAAGG
* * * * * *
13804095 AAATCAT-AAAAAGGTTGGTATAGTCCTTGTCTAAGG
1 CAACCTTAAAAAAGGTTGGGATAG-ACTCGTCTAAGG
* * *
13804131 TAACTTTTAAAAACGGTTGGGATAGAGC-CGTCTAAGG
1 CAAC-CTTAAAAAAGGTTGGGATAGA-CTCGTCTAAGG
* * * * *
13804168 CAA-GTTTAAAAAGGTTGGAATAGACCTTGTCTAAGA
1 CAACCTTAAAAAAGGTTGGGATAGA-CTCGTCTAAGG
* *
13804204 CAACCTATAAAAAAAGGCTGGGATAGAC-CTATCTAAGG
1 CAACCT-T-AAAAAAGGTTGGGATAGACTC-GTCTAAGG
*
13804242 CAACCTTAAACAA-GTTGGGATAGAC-CATGTCTAAGG
1 CAACCTTAAAAAAGGTTGGGATAGACTC--GTCTAAGG
* * *
13804278 CAACCTTTAAAAAGGTTGGAATAGACTCGTTTAAGG
1 CAACCTTAAAAAAGGTTGGGATAGACTCGTCTAAGG
*
13804314 CAACCTT-AAAAAGGTTGGGATAGACCTTGTCTAAGG
1 CAACCTTAAAAAAGGTTGGGATAGA-CTCGTCTAAGG
** * * * * *
13804350 CAAATTTTAGAAAAGGTTGGGATAGACCCATTTAAAG
1 C-AACCTTAAAAAAGGTTGGGATAGACTCGTCTAAGG
* * *
13804387 CAACCTT-AAAAAGGTTGGGATAAATCTTGTCCAAGG
1 CAACCTTAAAAAAGGTTGGGATAGA-CTCGTCTAAGG
* * * *
13804423 AAACCTTTAAAAGAGGTTGGGATAAACCCGTCTAAGG
1 CAACC-TTAAAAAAGGTTGGGATAGACTCGTCTAAGG
* *
13804460 TAACCTT-AAAAAGATTGGGATAGAC
1 CAACCTTAAAAAAGGTTGGGATAGAC
13804485 ACGTATAATG
Statistics
Matches: 339, Mismatches: 68, Indels: 40
0.76 0.15 0.09
Matches are distributed among these distances:
35 92 0.27
36 117 0.35
37 53 0.16
38 62 0.18
39 15 0.04
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.25
Consensus pattern (36 bp):
CAACCTTAAAAAAGGTTGGGATAGACTCGTCTAAGG
Found at i:13804178 original size:73 final size:71
Alignment explanation
Indices: 13804022--13804484 Score: 464
Period size: 73 Copynumber: 6.4 Consensus size: 71
13804012 TAGTCAAAAC
* * * *
13804022 CAACCTTTAAAAAAGGTTAGGATAGA-CTCGTCTAAGGTAAC-CTTAAAAAGGTTGGGATAGACC
1 CAACC-TT-AAAAAGGTTGGGATAGACCTTGTCTAAGGCAACTTTTAAAAAGGTTGGGATAGACC
13804085 TTGTCTAAGG
64 --GTCTAAGG
* * * * * *
13804095 AAATCATAAAAAGGTTGGTATAGTCCTTGTCTAAGGTAACTTTTAAAAACGGTTGGGATAGAGCC
1 CAACCTTAAAAAGGTTGGGATAGACCTTGTCTAAGGCAACTTTTAAAAA-GGTTGGGATAGA-CC
13804160 GTCTAAGG
64 GTCTAAGG
** * * ** *
13804168 CAAGTTTAAAAAGGTTGGAATAGACCTTGTCTAAGACAACCTATAAAAAAAGGCTGGGATAGACC
1 CAACCTTAAAAAGGTTGGGATAGACCTTGTCTAAGGCAA-CT-TTTAAAAAGGTTGGGATAGACC
*
13804233 TATCTAAGG
64 -GTCTAAGG
* * *
13804242 CAACCTTAAACAA-GTTGGGATAGACCATGTCTAAGGCAACCTTTAAAAAGGTTGGAATAGACTC
1 CAACCTTAAA-AAGGTTGGGATAGACCTTGTCTAAGGCAACTTTTAAAAAGGTTGGGATAGAC-C
*
13804306 GTTTAAGG
64 GTCTAAGG
*
13804314 CAACCTTAAAAAGGTTGGGATAGACCTTGTCTAAGGCAAATTTTAGAAAAGGTTGGGATAGACCC
1 CAACCTTAAAAAGGTTGGGATAGACCTTGTCTAAGGCAACTTTTA-AAAAGGTTGGGATAGA-CC
* * *
13804379 ATTTAAAG
64 GTCTAAGG
* * * * * *
13804387 CAACCTTAAAAAGGTTGGGATAAATCTTGTCCAAGGAAACCTTTAAAAGAGGTTGGGATAAACCC
1 CAACCTTAAAAAGGTTGGGATAGACCTTGTCTAAGGCAACTTTTAAAA-AGGTTGGGATAGA-CC
13804452 GTCTAAGG
64 GTCTAAGG
* *
13804460 TAACCTTAAAAAGATTGGGATAGAC
1 CAACCTTAAAAAGGTTGGGATAGAC
13804485 ACGTATAATG
Statistics
Matches: 325, Mismatches: 52, Indels: 26
0.81 0.13 0.06
Matches are distributed among these distances:
71 16 0.05
72 80 0.25
73 155 0.48
74 64 0.20
75 10 0.03
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.25
Consensus pattern (71 bp):
CAACCTTAAAAAGGTTGGGATAGACCTTGTCTAAGGCAACTTTTAAAAAGGTTGGGATAGACCGT
CTAAGG
Done.