Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A12
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: 102106374
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3186644 characters in sequence are not A, C, G, or T
File 86 of 311
Found at i:27409623 original size:45 final size:44
Alignment explanation
Indices: 27409539--27409623 Score: 116
Period size: 45 Copynumber: 1.9 Consensus size: 44
27409529 ATGTAATCTG
* *
27409539 AACTCATTGAGTTGTGTCTGAGTTCATGATATATGTGACATCGA
1 AACTCATTGAGTTGTGTCTAAGTTCATGATATATATGACATCGA
* * *
27409583 AACTCCTTGAGTTGTGGTCTAAGTTCGTGATATGTATGACA
1 AACTCATTGAGTTGT-GTCTAAGTTCATGATATATATGACA
27409624 CATGTTTTGG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
44 14 0.40
45 21 0.60
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (44 bp):
AACTCATTGAGTTGTGTCTAAGTTCATGATATATATGACATCGA
Found at i:27422487 original size:24 final size:23
Alignment explanation
Indices: 27422434--27422490 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 23
27422424 GCATGCTCAG
*
27422434 ATTCATCATGTGAATAAATCAAAA
1 ATTCATCA-ATGAATAAATCAAAA
*
27422458 AATCATCAATGAATACAA-CAACAA
1 ATTCATCAATGAATA-AATCAA-AA
27422482 ATTCATCAA
1 ATTCATCAA
27422491 GATACGGTCC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
23 9 0.32
24 19 0.68
ACGTcount: A:0.53, C:0.18, G:0.05, T:0.25
Consensus pattern (23 bp):
ATTCATCAATGAATAAATCAAAA
Found at i:27436998 original size:42 final size:43
Alignment explanation
Indices: 27436952--27437056 Score: 103
Period size: 43 Copynumber: 2.5 Consensus size: 43
27436942 CGATGCCTTA
*
27436952 TCCCAGACAGGGTCTTACACG-AAA-CT-AGATACGA-TGCC-GATG
1 TCCCAGACACGGTCTTACACGTAAATCTCA-AT-C-ATTGCCTG-TG
** *
27436994 TCCCAGACTTGGTCTTATACGTAAATCTCAATCATTGCCTGTG
1 TCCCAGACACGGTCTTACACGTAAATCTCAATCATTGCCTGTG
27437037 TCCCAGACACGGTCTTACAC
1 TCCCAGACACGGTCTTACAC
27437057 AATATCTCAG
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
42 19 0.37
43 27 0.52
44 5 0.10
45 1 0.02
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.26
Consensus pattern (43 bp):
TCCCAGACACGGTCTTACACGTAAATCTCAATCATTGCCTGTG
Found at i:27448778 original size:48 final size:48
Alignment explanation
Indices: 27448700--27448985 Score: 214
Period size: 48 Copynumber: 6.0 Consensus size: 48
27448690 AGGGTAAATT
* * * * * * *
27448700 GCCGATGTCATGTCCAAGACATTGTTTTACACTGGCTCACATGTCGAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAAG
* * * ****
27448748 GTCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAAGGTG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAAG
* * * * * * * *
27448796 GCCGTTGCTATATCTCAGACATGATTTTACACTAGCACACATATCAAC
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAAG
* * * * * * *
27448844 ACCGATGTCATGTCCCAGACATGGCCTTATACTAGCAAACATATCAAT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAAG
* * * * * **
27448892 GTCGATGCCATGTCCCAAACATGGTCCTACACTGGCTCTCATAAT-TTG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACACAT-ATCAAG
**
27448940 GCCGATGCCATGTCTTAGACATGGTCTTACACTGGCACACATATCA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCA
27448986 CCCAATTGTC
Statistics
Matches: 177, Mismatches: 59, Indels: 4
0.74 0.25 0.02
Matches are distributed among these distances:
47 2 0.01
48 173 0.98
49 2 0.01
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (48 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCAAG
Found at i:27451234 original size:21 final size:21
Alignment explanation
Indices: 27451210--27451279 Score: 54
Period size: 21 Copynumber: 3.2 Consensus size: 21
27451200 TGATTTGAAC
27451210 TCATTGAGTTGTGGTCTGAGT
1 TCATTGAGTTGTGGTCTGAGT
**
27451231 TCATAAT-A-TATGTGGCATCTGAAC
1 TCAT--TGAGT-TGTGG--TCTGAGT
*
27451255 TCATTGAGTTATGGTCTGAGT
1 TCATTGAGTTGTGGTCTGAGT
27451276 TCAT
1 TCAT
27451280 AATGTATATG
Statistics
Matches: 37, Mismatches: 5, Indels: 14
0.66 0.09 0.25
Matches are distributed among these distances:
21 14 0.38
22 7 0.19
23 6 0.16
24 10 0.27
ACGTcount: A:0.23, C:0.13, G:0.24, T:0.40
Consensus pattern (21 bp):
TCATTGAGTTGTGGTCTGAGT
Found at i:27453239 original size:21 final size:22
Alignment explanation
Indices: 27453210--27453257 Score: 80
Period size: 21 Copynumber: 2.2 Consensus size: 22
27453200 TATTGGTGGC
*
27453210 TGAGTATGAAAAGAGATATTTT
1 TGAGTATGAAAAAAGATATTTT
27453232 TGAG-ATGAAAAAAGATATTTT
1 TGAGTATGAAAAAAGATATTTT
27453253 TGAGT
1 TGAGT
27453258 TTGTATCAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (22 bp):
TGAGTATGAAAAAAGATATTTT
Found at i:27464714 original size:37 final size:35
Alignment explanation
Indices: 27464664--27464740 Score: 109
Period size: 37 Copynumber: 2.1 Consensus size: 35
27464654 TTATTACGAA
* *
27464664 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATC-CC-CACGAAGTCATCGG
*
27464701 GTCTTACCCGGACAAAATCCCCACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACGAAGTCATCGG
27464736 GTCTT
1 GTCTT
27464741 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
35 17 0.46
36 2 0.05
37 18 0.49
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (35 bp):
GTCTTACCCGGACAAAATCCCCACGAAGTCATCGG
Found at i:27465009 original size:47 final size:47
Alignment explanation
Indices: 27464859--27465142 Score: 455
Period size: 47 Copynumber: 6.1 Consensus size: 47
27464849 CCCTTCGGGA
* * * * * * *
27464859 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
27464906 CCTGTCACATATATACACTTTCACATTCA-CACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
27464952 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
27464999 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
27465046 CTTATCACA-ATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
27465092 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
27465139 CTTA
1 CTTA
27465143 CTATCATTTC
Statistics
Matches: 220, Mismatches: 15, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
46 85 0.39
47 135 0.61
ACGTcount: A:0.28, C:0.30, G:0.10, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:27465018 original size:93 final size:94
Alignment explanation
Indices: 27464859--27465142 Score: 455
Period size: 93 Copynumber: 3.0 Consensus size: 94
27464849 CCCTTCGGGA
* * * * * * * * *
27464859 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
27464924 TTTCACATTCA-CACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
*
27464952 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATTACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
27465017 TTTCACATTCATCACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
*
27465046 CTTATCACA-ATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
27465110 TTTCACATTCATCACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
27465139 CTTA
1 CTTA
27465143 CTATCATTTC
Statistics
Matches: 178, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
93 152 0.85
94 26 0.15
ACGTcount: A:0.28, C:0.30, G:0.10, T:0.32
Consensus pattern (94 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGC
Found at i:27465111 original size:140 final size:140
Alignment explanation
Indices: 27464859--27465142 Score: 453
Period size: 140 Copynumber: 2.0 Consensus size: 140
27464849 CCCTTCGGGA
* * * * * *
27464859 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATACAC
27464924 TTTCACATTCACACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCG
66 TTTCACATTCACACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCG
27464989 GCCATTAGGC
131 GCCATTAGGC
* * * *
27464999 CTTATTACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACA-ATATACAC
1 CTTATCACATATATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATACAC
*
27465063 TTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCA-CACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
27465128 GGCCATTAGGC
130 GGCCATTAGGC
27465139 CTTA
1 CTTA
27465143 CTATCATTTC
Statistics
Matches: 132, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
139 19 0.14
140 113 0.86
ACGTcount: A:0.28, C:0.30, G:0.10, T:0.32
Consensus pattern (140 bp):
CTTATCACATATATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATACAC
TTTCACATTCACACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCG
GCCATTAGGC
Found at i:27467383 original size:26 final size:26
Alignment explanation
Indices: 27467347--27467400 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 26
27467337 ATATGATGGC
27467347 TAATTATTAG-TGACTCGGTTTAGTGG
1 TAATTATTAGATGACTCGGTTT-GTGG
27467373 TAATTATTAGTATGACTCGGTTTGTGG
1 TAATTATTAG-ATGACTCGGTTTGTGG
27467400 T
1 T
27467401 CCCGAAACCA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
26 10 0.38
27 5 0.19
28 11 0.42
ACGTcount: A:0.22, C:0.07, G:0.26, T:0.44
Consensus pattern (26 bp):
TAATTATTAGATGACTCGGTTTGTGG
Found at i:27468689 original size:40 final size:41
Alignment explanation
Indices: 27468632--27468738 Score: 105
Period size: 41 Copynumber: 2.6 Consensus size: 41
27468622 CAGCATGATT
* * *
27468632 TGCTCTTCGGGATTTAGCACGGATATA-TCACTAC-CA-CGAA
1 TGCTCTTCGGAACTTAGC-CGGATATAGTAACT-CGCACCGAA
*
27468672 TGCTCTTCGGAACTTAGCCCGGATTTAGTAACTCGCACCGAA
1 TGCTCTTCGGAACTTAG-CCGGATATAGTAACTCGCACCGAA
*
27468714 TGC-CTTCGGATCTTAGTCCGGATAT
1 TGCTCTTCGGAACTTAG-CCGGATAT
27468739 GGCACTTAGC
Statistics
Matches: 56, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
40 23 0.41
41 26 0.46
42 7 0.12
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.29
Consensus pattern (41 bp):
TGCTCTTCGGAACTTAGCCGGATATAGTAACTCGCACCGAA
Found at i:27469146 original size:28 final size:29
Alignment explanation
Indices: 27469081--27469159 Score: 90
Period size: 28 Copynumber: 2.7 Consensus size: 29
27469071 CTTAATAATC
*
27469081 AACCACGCACACTTAGTGCCATGTACTTTA
1 AACC-CGCACACTTAGTGCCATGCACTTTA
*
27469111 AACTCGCACACTT-GTGCCATGCA-TTTCA
1 AACCCGCACACTTAGTGCCATGCACTTT-A
*
27469139 AGCCCGCAACACTTAGTGCCA
1 AACCCGC-ACACTTAGTGCCA
27469160 ATCTCACAAC
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
27 3 0.07
28 15 0.36
29 15 0.36
30 9 0.21
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCACTTTA
Found at i:27471102 original size:37 final size:37
Alignment explanation
Indices: 27471052--27471130 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
27471042 TTATTACGAA
* * *
27471052 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
27471089 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
27471126 GTCTT
1 GTCTT
27471131 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:27471416 original size:46 final size:47
Alignment explanation
Indices: 27471249--27471532 Score: 464
Period size: 47 Copynumber: 6.1 Consensus size: 47
27471239 CCCTTCGGGA
* * * * * * *
27471249 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
27471296 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
27471343 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
27471390 CTTAT-ACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
27471436 CTTATCACACATATACACTTTCACATTCATCACATCGG-CATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
27471482 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
27471529 CTTA
1 CTTA
27471533 CTATCATTTC
Statistics
Matches: 222, Mismatches: 13, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
46 91 0.41
47 131 0.59
ACGTcount: A:0.28, C:0.31, G:0.10, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:27471426 original size:93 final size:94
Alignment explanation
Indices: 27471249--27471532 Score: 464
Period size: 93 Copynumber: 3.0 Consensus size: 94
27471239 CCCTTCGGGA
* * * * * * * * *
27471249 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
27471314 TTTCACATTCATCACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
27471343 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT-ACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
27471407 TTTCACATTCATCACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
*
27471436 CTTATCACACATATACACTTTCACATTCATCACATCGG-CATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
27471500 TTTCACATTCATCACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
27471529 CTTA
1 CTTA
27471533 CTATCATTTC
Statistics
Matches: 179, Mismatches: 10, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
92 13 0.07
93 123 0.69
94 43 0.24
ACGTcount: A:0.28, C:0.31, G:0.10, T:0.32
Consensus pattern (94 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGC
Found at i:27474987 original size:40 final size:38
Alignment explanation
Indices: 27474934--27475072 Score: 125
Period size: 40 Copynumber: 3.5 Consensus size: 38
27474924 CATGATTGCT
* * *
27474934 CTTCGGGATTTAGCACGGATATATCACTAGCACGAATGC
1 CTTCGGAACTTAGCCCGGATATATCACTAGCAC-AATGC
* * *
27474973 TCTTCGGAACTTAGCCCGGATTTAGTAACTCGCACCAATGC
1 -CTTCGGAACTTAGCCCGGATATA-TCACTAGCA-CAATGC
* * * *
27475014 CTTCGGATCTTAGTCCGGATATGGTCACTTAGCACAAAGC
1 CTTCGGAACTTAGCCCGGATAT-ATCAC-TAGCACAATGC
*
27475054 CTTCGGGACTTAGCCCGGA
1 CTTCGGAACTTAGCCCGGA
27475073 CATCATTCGA
Statistics
Matches: 79, Mismatches: 16, Indels: 8
0.77 0.16 0.08
Matches are distributed among these distances:
40 62 0.78
41 16 0.20
42 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (38 bp):
CTTCGGAACTTAGCCCGGATATATCACTAGCACAATGC
Found at i:27475414 original size:29 final size:29
Alignment explanation
Indices: 27475375--27475453 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
27475365 CTTAATAATC
*
27475375 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
27475405 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
27475434 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
27475454 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:27475496 original size:43 final size:43
Alignment explanation
Indices: 27475435--27475537 Score: 206
Period size: 43 Copynumber: 2.4 Consensus size: 43
27475425 TGCATTTCAA
27475435 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
27475478 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
27475521 GCCCGCACACTTAGTGC
1 GCCCGCACACTTAGTGC
27475538 TGAAAACCAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.26, C:0.36, G:0.16, T:0.22
Consensus pattern (43 bp):
GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
Found at i:27477433 original size:37 final size:37
Alignment explanation
Indices: 27477383--27477461 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
27477373 TTATTACGAA
* * *
27477383 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
27477420 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
27477457 GTCTT
1 GTCTT
27477462 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:27477747 original size:46 final size:47
Alignment explanation
Indices: 27477580--27477863 Score: 464
Period size: 47 Copynumber: 6.1 Consensus size: 47
27477570 CCCTTCGGGA
* * * * * * *
27477580 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
27477627 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
27477674 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
27477721 CTTAT-ACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
27477767 CTTATCACACATATACACTTTCACATTCATCACATCGG-CATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
27477813 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
27477860 CTTA
1 CTTA
27477864 CTATCATTTC
Statistics
Matches: 222, Mismatches: 13, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
46 91 0.41
47 131 0.59
ACGTcount: A:0.28, C:0.31, G:0.10, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:27477757 original size:93 final size:94
Alignment explanation
Indices: 27477580--27477863 Score: 464
Period size: 93 Copynumber: 3.0 Consensus size: 94
27477570 CCCTTCGGGA
* * * * * * * * *
27477580 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
27477645 TTTCACATTCATCACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
27477674 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT-ACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
27477738 TTTCACATTCATCACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
*
27477767 CTTATCACACATATACACTTTCACATTCATCACATCGG-CATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
27477831 TTTCACATTCATCACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
27477860 CTTA
1 CTTA
27477864 CTATCATTTC
Statistics
Matches: 179, Mismatches: 10, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
92 13 0.07
93 123 0.69
94 43 0.24
ACGTcount: A:0.28, C:0.31, G:0.10, T:0.32
Consensus pattern (94 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGC
Found at i:27482398 original size:44 final size:46
Alignment explanation
Indices: 27482338--27482505 Score: 141
Period size: 46 Copynumber: 3.7 Consensus size: 46
27482328 TATGCATGCT
*
27482338 GATGCATGTCCTAGACATGTCTTACACTAGCACAACTCT-T-A-GCC
1 GATGCATGTCCCAGACATGTCTTACACTAGC-CAACTCTGTAAGGCC
** * * * *
27482382 GATGTGTGTCCCAGACACGTCTTACACTGGCTATCTCTGTCAAGGCC
1 GATGCATGTCCCAGACATGTCTTACACTAGCCAACTCTGT-AAGGCC
* * * *
27482429 GATGCATGTCCCAGACATGTCTTACTCT-GGC-ACTCATAGTATGGCT
1 GATGCATGTCCCAGACATGTCTTACACTAGCCAACTC-T-GTAAGGCC
* *
27482475 GAAGTATGTCCCAGACATGTCTTAC-CTAGCC
1 GATGCATGTCCCAGACATGTCTTACACTAGCC
27482506 CTTGTCTGGA
Statistics
Matches: 98, Mismatches: 19, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
43 5 0.05
44 27 0.28
45 5 0.05
46 32 0.33
47 29 0.30
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (46 bp):
GATGCATGTCCCAGACATGTCTTACACTAGCCAACTCTGTAAGGCC
Found at i:27482442 original size:47 final size:44
Alignment explanation
Indices: 27482338--27482461 Score: 133
Period size: 47 Copynumber: 2.8 Consensus size: 44
27482328 TATGCATGCT
* *
27482338 GATGCATGTCCTAGACATGTCTTACACTAGCACAACTCTTAGCC
1 GATGCATGTCCCAGACATGTCTTACACTGGCACAACTCTTAGCC
** * * *
27482382 GATGTGTGTCCCAGACACGTCTTACACTGGC-TATCTCTGTCAAGGCC
1 GATGCATGTCCCAGACATGTCTTACACTGGCACAACTCT-T--A-GCC
*
27482429 GATGCATGTCCCAGACATGTCTTACTCTGGCAC
1 GATGCATGTCCCAGACATGTCTTACACTGGCAC
27482462 TCATAGTATG
Statistics
Matches: 63, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
43 5 0.08
44 27 0.43
46 1 0.02
47 30 0.48
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (44 bp):
GATGCATGTCCCAGACATGTCTTACACTGGCACAACTCTTAGCC
Found at i:27486505 original size:42 final size:42
Alignment explanation
Indices: 27486446--27486530 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
27486436 GATACATAAC
* *
27486446 CTCATTGACCCGTCCTTCTTTTTCACAAAAAGCACTGGAGCA
1 CTCATCGACCCATCCTTCTTTTTCACAAAAAGCACTGGAGCA
27486488 CTCATCGACCCATCCTTCTTTTTCACAAAAAGCACTGGAGCA
1 CTCATCGACCCATCCTTCTTTTTCACAAAAAGCACTGGAGCA
27486530 C
1 C
27486531 CCCATGGTGA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.27, C:0.33, G:0.13, T:0.27
Consensus pattern (42 bp):
CTCATCGACCCATCCTTCTTTTTCACAAAAAGCACTGGAGCA
Found at i:27490015 original size:44 final size:46
Alignment explanation
Indices: 27489947--27490114 Score: 143
Period size: 46 Copynumber: 3.7 Consensus size: 46
27489937 TATGCGTGCT
*
27489947 GATGCATGTCCCAGACATGACTTACACTAGCACATCTCT-T-A-GCC
1 GATGCATGTCCCAGACATGTCTTACACTAGC-CATCTCTGTCAGGCC
* * * *
27489991 GATGCGTGTCCCAGACACGTCTTACACTGGCTATCTCTGTCGAGGCC
1 GATGCATGTCCCAGACATGTCTTACACTAGCCATCTCTGTC-AGGCC
* * * *
27490038 GTTGCATGTCCCAGACATGTCTTACTCT-GGCA-CTCATAGT-ATGGCT
1 GATGCATGTCCCAGACATGTCTTACACTAGCCATCTC-T-GTCA-GGCC
* *
27490084 GAAGTATGTCCCAGACATGTCTTAC-CTAGCC
1 GATGCATGTCCCAGACATGTCTTACACTAGCC
27490115 CTTGTCTGGA
Statistics
Matches: 100, Mismatches: 16, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
43 6 0.06
44 28 0.28
45 6 0.06
46 31 0.31
47 29 0.29
ACGTcount: A:0.22, C:0.30, G:0.21, T:0.27
Consensus pattern (46 bp):
GATGCATGTCCCAGACATGTCTTACACTAGCCATCTCTGTCAGGCC
Found at i:27490051 original size:47 final size:44
Alignment explanation
Indices: 27489947--27490070 Score: 142
Period size: 47 Copynumber: 2.8 Consensus size: 44
27489937 TATGCGTGCT
* *
27489947 GATGCATGTCCCAGACATGACTTACACTAGCACATCTCTTAGCC
1 GATGCATGTCCCAGACATGTCTTACACTGGCACATCTCTTAGCC
* * *
27489991 GATGCGTGTCCCAGACACGTCTTACACTGGC-TATCTCTGTCGAGGCC
1 GATGCATGTCCCAGACATGTCTTACACTGGCACATCTCT-T--A-GCC
* *
27490038 GTTGCATGTCCCAGACATGTCTTACTCTGGCAC
1 GATGCATGTCCCAGACATGTCTTACACTGGCAC
27490071 TCATAGTATG
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
43 6 0.09
44 28 0.43
46 1 0.02
47 30 0.46
ACGTcount: A:0.21, C:0.31, G:0.21, T:0.27
Consensus pattern (44 bp):
GATGCATGTCCCAGACATGTCTTACACTGGCACATCTCTTAGCC
Found at i:27492472 original size:46 final size:46
Alignment explanation
Indices: 27492383--27492603 Score: 168
Period size: 46 Copynumber: 4.8 Consensus size: 46
27492373 GTATATCTAT
* * * *
27492383 GCCGATGCCATATCCCAAACATGGTCTTACACT-GAC-ACATCTCGTA-
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAG-CTTCGTCTCGTAG
*
27492429 GCCGATGCATGTGCCAGACATGTCTTACACTAGCTTACGTCTCG-AG
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTT-CGTCTCGTAG
* * * * *
27492475 GCCAATGCATGTCCCAGACATGTCTTACACCAGCACTCGTCTC-AAT
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGC-TTCGTCTCGTAG
* * * * *
27492521 GTCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAAT-GT-T
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCT-TCGT-CTCGTAG
*
27492569 GCCGATGCATGTCCCAGACATGGCTTACACTAGCT
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCT
27492604 AACACGAGTG
Statistics
Matches: 143, Mismatches: 21, Indels: 22
0.77 0.11 0.12
Matches are distributed among these distances:
44 11 0.08
45 13 0.09
46 68 0.48
47 29 0.20
48 21 0.15
49 1 0.01
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (46 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTAGCTTCGTCTCGTAG
Found at i:27494004 original size:44 final size:44
Alignment explanation
Indices: 27493936--27494037 Score: 186
Period size: 44 Copynumber: 2.3 Consensus size: 44
27493926 TTTAAACATT
*
27493936 CGCACACTTAGTGCTTAAAGGTTAGCTAATGCTAGAACGATTTC
1 CGCACACTTAGTGCTTAAAAGTTAGCTAATGCTAGAACGATTTC
27493980 CGCACACTTAGTGCTTAAAAGTTAGCTAATGCTAGAACGATTTC
1 CGCACACTTAGTGCTTAAAAGTTAGCTAATGCTAGAACGATTTC
*
27494024 CACACACTTAGTGC
1 CGCACACTTAGTGC
27494038 AAACTCAATT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
44 56 1.00
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (44 bp):
CGCACACTTAGTGCTTAAAAGTTAGCTAATGCTAGAACGATTTC
Found at i:27498401 original size:40 final size:40
Alignment explanation
Indices: 27498348--27498423 Score: 98
Period size: 40 Copynumber: 1.9 Consensus size: 40
27498338 CGGCTAAGAA
*
27498348 TGGCACTTAGTGTGCGGTTTGAAATAGCTTCAGCTAAATG
1 TGGCACTTAGTGTGCGATTTGAAATAGCTTCAGCTAAATG
* * ** *
27498388 TGGCTCTTGGTGTGCGATTTGTGATAGCTTCGGCTA
1 TGGCACTTAGTGTGCGATTTGAAATAGCTTCAGCTA
27498424 TATATATATG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 30 1.00
ACGTcount: A:0.18, C:0.16, G:0.30, T:0.36
Consensus pattern (40 bp):
TGGCACTTAGTGTGCGATTTGAAATAGCTTCAGCTAAATG
Found at i:27498483 original size:2 final size:2
Alignment explanation
Indices: 27498432--27498469 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
27498422 TATATATATA
27498432 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
27498470 GCACTTAGTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:27502773 original size:36 final size:37
Alignment explanation
Indices: 27502725--27502797 Score: 98
Period size: 36 Copynumber: 2.0 Consensus size: 37
27502715 TGGCAATACA
27502725 TGTGAGTACGTGTAAGACCATAG-CTGGG-CTATGGCAT
1 TGTGAGTACGTGTAAGACCAT-GTCTGGGAC-ATGGCAT
*
27502762 TGTGA-TACGTGTAATACCATGTCTGGGACATGGCAT
1 TGTGAGTACGTGTAAGACCATGTCTGGGACATGGCAT
27502798 CGATATGAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
35 1 0.03
36 26 0.79
37 6 0.18
ACGTcount: A:0.25, C:0.16, G:0.30, T:0.29
Consensus pattern (37 bp):
TGTGAGTACGTGTAAGACCATGTCTGGGACATGGCAT
Found at i:27502867 original size:48 final size:48
Alignment explanation
Indices: 27502796--27502893 Score: 144
Period size: 48 Copynumber: 2.0 Consensus size: 48
27502786 GGGACATGGC
* *
27502796 ATCGATATGAGATCCTGTGTAAGACCATATTTGGGATATGGCATCGGT
1 ATCGATATGAGATACTGTGTAAGACCATATCTGGGATATGGCATCGGT
* *
27502844 ATCGATATGAGATTACT-TGTAAGACTATATCTGGGATATGGCTTCGGT
1 ATCGATATGAGA-TACTGTGTAAGACCATATCTGGGATATGGCATCGGT
27502892 AT
1 AT
27502894 GAGATTTCGT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
48 42 0.93
49 3 0.07
ACGTcount: A:0.28, C:0.13, G:0.26, T:0.34
Consensus pattern (48 bp):
ATCGATATGAGATACTGTGTAAGACCATATCTGGGATATGGCATCGGT
Found at i:27502908 original size:42 final size:42
Alignment explanation
Indices: 27502731--27502993 Score: 139
Period size: 42 Copynumber: 6.3 Consensus size: 42
27502721 TACATGTGAG
* * *
27502731 TACGTGTAAGACCATAGCTGGGCTATGG---C-AT-TGTGA-
1 TACGTGTAAGACCATATCTGGGATATGGCTTCGATATGAGAT
* * * *
27502767 TACGTGTAATACCATGTCTGGGACATGGCATCGATATGAGA-
1 TACGTGTAAGACCATATCTGGGATATGGCTTCGATATGAGAT
* *
27502808 TCCTGTGTAAGACCATATTTGGGATATGGCATCGGTATCGATATGAGAT
1 TAC-GTGTAAGACCATATCTGGGATATGG---C--T-TCGATATGAGAT
* * *
27502857 TACTTGTAAGACTATATCTGGGATATGGCTTCGGTATGAGAT
1 TACGTGTAAGACCATATCTGGGATATGGCTTCGATATGAGAT
* * * ** ** * *
27502899 TTCGTGTAAGACCTTGTCTAAGATGCGGCATCGATATGTGAT
1 TACGTGTAAGACCATATCTGGGATATGGCTTCGATATGAGAT
* * * * * * *
27502941 TTCGT-AAAGACCATGTCTGGGACATGGCATCGATGTGAAACT
1 TACGTGTAAGACCATATCTGGGATATGGCTTCGATATGAGA-T
27502983 T-CGTGTAAGAC
1 TACGTGTAAGAC
27502994 TAAAGTTGGA
Statistics
Matches: 172, Mismatches: 40, Indels: 24
0.73 0.17 0.10
Matches are distributed among these distances:
36 23 0.13
39 1 0.01
40 2 0.01
41 34 0.20
42 74 0.43
43 1 0.01
45 2 0.01
48 33 0.19
49 2 0.01
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (42 bp):
TACGTGTAAGACCATATCTGGGATATGGCTTCGATATGAGAT
Found at i:27504863 original size:45 final size:44
Alignment explanation
Indices: 27504766--27504885 Score: 122
Period size: 45 Copynumber: 2.8 Consensus size: 44
27504756 CTTTCTCAAA
* * *
27504766 TCACCGGCATT-TCGCCTGTTAGGCTTG-AGGCCCTATATCAGT
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCTATATCAGT
27504808 TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCTA-AT-AGT
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCTATATCAGT
** * *
27504850 ACCTCACCGGCATTATAGTTTGCTAAGCTCAAAGGC
1 ---TCACCGGCATTATAGCCTGCTAGGCTCGAAGGC
27504886 TCGAATAATC
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
42 14 0.21
43 15 0.23
44 8 0.12
45 29 0.44
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.27
Consensus pattern (44 bp):
TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCTATATCAGT
Found at i:27505270 original size:43 final size:43
Alignment explanation
Indices: 27505222--27505333 Score: 181
Period size: 43 Copynumber: 2.6 Consensus size: 43
27505212 CCGGCATTAC
*
27505222 GCCTGCTAGGCACGAAGGCCCGAATACATATCACC-GACACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCAG-CACGAA
* *
27505265 GCCTGCTAGGCATGAAGGCCCGAATACACATCACCAGCACTAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCAGCACGAA
27505308 GCCTGCTAGGCACGAAGGCCCGAATA
1 GCCTGCTAGGCACGAAGGCCCGAATA
27505334 TAGTACCAAC
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
43 63 0.98
44 1 0.02
ACGTcount: A:0.31, C:0.32, G:0.24, T:0.12
Consensus pattern (43 bp):
GCCTGCTAGGCACGAAGGCCCGAATACACATCACCAGCACGAA
Found at i:27511059 original size:2 final size:2
Alignment explanation
Indices: 27511006--27511045 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
27510996 GCTATATATA
27511006 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
27511046 GCATTTAGTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:27519962 original size:23 final size:23
Alignment explanation
Indices: 27519935--27519981 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
27519925 AGTGAATGAA
27519935 TGCATATGGGTAAGCATGAAATC
1 TGCATATGGGTAAGCATGAAATC
27519958 TGCATATGGGTAAGCATGAAATC
1 TGCATATGGGTAAGCATGAAATC
27519981 T
1 T
27519982 ATGGAAACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.13, G:0.26, T:0.28
Consensus pattern (23 bp):
TGCATATGGGTAAGCATGAAATC
Found at i:27529517 original size:43 final size:43
Alignment explanation
Indices: 27529422--27529528 Score: 126
Period size: 43 Copynumber: 2.5 Consensus size: 43
27529412 ATCAAGATGT
* * * * *
27529422 GATTACATGTAAGACTATGTCTGGGACATTGCCATTGTATTGT
1 GATTACGTGTAAGACCATGTCTGGGACATTGCCATCGTAATGC
*
27529465 GATTACGTGTAAGACCATGTCTGGGACATTGGCATCGTTAAT-C
1 GATTACGTGTAAGACCATGTCTGGGACATTGCCATCG-TAATGC
* *
27529508 GATTTCGTGTAAGACCTTGTC
1 GATTACGTGTAAGACCATGTC
27529529 CAGGATAGTG
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
43 52 0.95
44 3 0.05
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (43 bp):
GATTACGTGTAAGACCATGTCTGGGACATTGCCATCGTAATGC
Found at i:27536686 original size:14 final size:16
Alignment explanation
Indices: 27536662--27536694 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
27536652 ATTTTCTGTG
27536662 TTTATTATGTGT-AAA
1 TTTATTATGTGTGAAA
27536677 TTTA-TATGTGTGAAA
1 TTTATTATGTGTGAAA
27536692 TTT
1 TTT
27536695 TTGTGTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (16 bp):
TTTATTATGTGTGAAA
Found at i:27537297 original size:28 final size:26
Alignment explanation
Indices: 27537258--27537309 Score: 68
Period size: 28 Copynumber: 1.9 Consensus size: 26
27537248 GAATTTGAGT
**
27537258 AATTAGGGCTAATTTGTAAAATAATA
1 AATTAGGGCTAAAATGTAAAATAATA
27537284 AATTGAGGGACTAAAATGTAAAATAA
1 AATT-AGGG-CTAAAATGTAAAATAA
27537310 ATGAAATGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 4 0.18
27 4 0.18
28 14 0.64
ACGTcount: A:0.50, C:0.04, G:0.17, T:0.29
Consensus pattern (26 bp):
AATTAGGGCTAAAATGTAAAATAATA
Found at i:27537935 original size:56 final size:56
Alignment explanation
Indices: 27537846--27537981 Score: 227
Period size: 56 Copynumber: 2.4 Consensus size: 56
27537836 ACCATGGCAT
* *
27537846 CGATATATGTGTGCGAGTAAGACCAAGTTTAATACGTTGGCATCGATATGTGATTC
1 CGATATATGTGTGCGAGTAAGACCAAGTTTAATACATTGGCATCGATATGTGATTA
* *
27537902 CGTTATATGTGTGCGAGTAAGACCACGTTTAATACATTGGCATCGATATGTGATTA
1 CGATATATGTGTGCGAGTAAGACCAAGTTTAATACATTGGCATCGATATGTGATTA
*
27537958 CGATATATGTGTGTGAGTAAGACC
1 CGATATATGTGTGCGAGTAAGACC
27537982 CTACCTAGGA
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
56 74 1.00
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.32
Consensus pattern (56 bp):
CGATATATGTGTGCGAGTAAGACCAAGTTTAATACATTGGCATCGATATGTGATTA
Found at i:27537999 original size:56 final size:55
Alignment explanation
Indices: 27537846--27538014 Score: 178
Period size: 56 Copynumber: 3.0 Consensus size: 55
27537836 ACCATGGCAT
* * * ** *
27537846 CGATATATGTGTGCGAGTAAGACCAAGTTTAATACGTTGGCATCGATATGTGATTC
1 CGATATATGTGTGCGAGTAAGACCACG-CTAAGACAATGGCATCGATATGTGATTA
* * * *
27537902 CGTTATATGTGTGCGAGTAAGACCACGTTTAATACATTGGCATCGATATGTGATTA
1 CGATATATGTGTGCGAGTAAGACCACG-CTAAGACAATGGCATCGATATGTGATTA
* * *
27537958 CGATATATGTGTGTGAGTAAGACCCTAC-CTAGGACAATGGCATCGATATATGATTA
1 CGATATATGTGTGCGAGTAAGA-CC-ACGCTAAGACAATGGCATCGATATGTGATTA
27538014 C
1 C
27538015 ATGTAAGACC
Statistics
Matches: 100, Mismatches: 11, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
56 96 0.96
57 2 0.02
58 2 0.02
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (55 bp):
CGATATATGTGTGCGAGTAAGACCACGCTAAGACAATGGCATCGATATGTGATTA
Found at i:27541582 original size:49 final size:48
Alignment explanation
Indices: 27541426--27541597 Score: 184
Period size: 48 Copynumber: 3.6 Consensus size: 48
27541416 AAATGCTGAC
** * *
27541426 GCCATGTCCCAGACATGGTCTTACACTGGCTAGCA-CATTGAAGTTGAC
1 GCCATGTCCCAGACA-GGTCTTACACTGGCTCCCATCATTGAAGTAGAT
* * * * * * **
27541474 GTCGTGTCCCAGATAGGTCTTACACTGACTCCCATAATTGAGGCCGAT
1 GCCATGTCCCAGACAGGTCTTACACTGGCTCCCATCATTGAAGTAGAT
* * *
27541522 GCCATGTCCCAGACAGGTCTTACACTGGCTCTCATCTATCGATGTAGAT
1 GCCATGTCCCAGACAGGTCTTACACTGGCTCCCATC-ATTGAAGTAGAT
27541571 GCCATGTCCCAGACAGGTCTTACACTG
1 GCCATGTCCCAGACAGGTCTTACACTG
27541598 ACACACAACA
Statistics
Matches: 101, Mismatches: 21, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
47 16 0.16
48 50 0.50
49 35 0.35
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.26
Consensus pattern (48 bp):
GCCATGTCCCAGACAGGTCTTACACTGGCTCCCATCATTGAAGTAGAT
Found at i:27545505 original size:49 final size:49
Alignment explanation
Indices: 27545432--27545617 Score: 246
Period size: 49 Copynumber: 3.8 Consensus size: 49
27545422 TAGCCGAAGC
* *
27545432 TATCTGGTACGCATAATAGCCTGCACTTAGTACTACACATGCGACCAAT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
* * * *
27545481 AATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGATCACAGT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGA-C-CAAT
* * *
27545532 TTTCAGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
** *
27545581 TATCCAGTACACGTAGTAGCCTGCACTTAGTACTACA
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACA
27545618 TACGTGATCT
Statistics
Matches: 117, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
49 74 0.63
50 2 0.02
51 41 0.35
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.27
Consensus pattern (49 bp):
TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
Found at i:27545610 original size:100 final size:100
Alignment explanation
Indices: 27545437--27545626 Score: 326
Period size: 100 Copynumber: 1.9 Consensus size: 100
27545427 GAAGCTATCT
**
27545437 GGTACGCATAATAGCCTGCACTTAGTACTACACATGCGACCAATAATCTGGTACACGTAGTAGCC
1 GGTACGCATAATAGCCTGCACTTAGTACTACACATGCGACCAATAATCCAGTACACGTAGTAGCC
*
27545502 TGCACTTAGTACTACACATGTGATCACAGTTTTCA
66 TGCACTTAGTACTACACACGTGATCACAGTTTTCA
* *
27545537 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCAGTACACGTAGTAGCC
1 GGTACGCATAATAGCCTGCACTTAGTACTACACATGCGACCAATAATCCAGTACACGTAGTAGCC
*
27545602 TGCACTTAGTACTACATACGTGATC
66 TGCACTTAGTACTACACACGTGATC
27545627 TCACAATAGT
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
100 84 1.00
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.26
Consensus pattern (100 bp):
GGTACGCATAATAGCCTGCACTTAGTACTACACATGCGACCAATAATCCAGTACACGTAGTAGCC
TGCACTTAGTACTACACACGTGATCACAGTTTTCA
Found at i:27548144 original size:15 final size:15
Alignment explanation
Indices: 27548088--27548152 Score: 64
Period size: 15 Copynumber: 4.4 Consensus size: 15
27548078 TAAAGATAAC
*
27548088 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
*
27548102 AAGAAATCTA-AGATA
1 AAGAAATCCAGA-ATA
*
27548117 GAA-AAACCCAGAATA
1 -AAGAAATCCAGAATA
27548132 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
27548147 AAGAAA
1 AAGAAA
27548153 CCCAAGATAC
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
14 10 0.24
15 28 0.68
16 3 0.07
ACGTcount: A:0.63, C:0.12, G:0.14, T:0.11
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:27548154 original size:30 final size:31
Alignment explanation
Indices: 27548088--27548156 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 31
27548078 TAAAGATAAC
* *
27548088 AAGAAAACC-GAATAAAGAAATCTAAGATAG
1 AAGAAACCCAGAATAAAGAAATCCAAGATAG
27548118 AA-AAACCCAGAATAAAGAAATCC-AGAATA-
1 AAGAAACCCAGAATAAAGAAATCCAAG-ATAG
27548147 AAGAAACCCA
1 AAGAAACCCA
27548157 AGATACGATA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
29 9 0.26
30 25 0.74
ACGTcount: A:0.61, C:0.16, G:0.13, T:0.10
Consensus pattern (31 bp):
AAGAAACCCAGAATAAAGAAATCCAAGATAG
Found at i:27551226 original size:49 final size:49
Alignment explanation
Indices: 27551153--27551340 Score: 250
Period size: 49 Copynumber: 3.8 Consensus size: 49
27551143 TAACCGAAGC
*
27551153 TATCTGGTACACATAATAGCCTGCACTTAGTACTACACATGCGACCAAT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
* * * * * *
27551202 AATCTGGTACACGTAGTAACCTGCACTTAGTACTACACACGTGATCACAGT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGA-C-CAAT
* * *
27551253 TTTCGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
* *
27551302 TATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACA
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACA
27551341 CGTGATCTCA
Statistics
Matches: 117, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
49 76 0.65
50 2 0.02
51 39 0.33
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.26
Consensus pattern (49 bp):
TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
Found at i:27551276 original size:100 final size:100
Alignment explanation
Indices: 27551158--27551347 Score: 335
Period size: 100 Copynumber: 1.9 Consensus size: 100
27551148 GAAGCTATCT
*
27551158 GGTACACATAATAGCCTGCACTTAGTACTACACATGCGACCAATAATCTGGTACACGTAGTAACC
1 GGTACACATAATAGCCTGCACTTAGTACTACACATGCGACCAATAATCCGGTACACGTAGTAACC
27551223 TGCACTTAGTACTACACACGTGATCACAGTTTTCG
66 TGCACTTAGTACTACACACGTGATCACAGTTTTCG
* * * *
27551258 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCC
1 GGTACACATAATAGCCTGCACTTAGTACTACACATGCGACCAATAATCCGGTACACGTAGTAACC
27551323 TGCACTTAGTACTACACACGTGATC
66 TGCACTTAGTACTACACACGTGATC
27551348 TCACAATAGT
Statistics
Matches: 85, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
100 85 1.00
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.25
Consensus pattern (100 bp):
GGTACACATAATAGCCTGCACTTAGTACTACACATGCGACCAATAATCCGGTACACGTAGTAACC
TGCACTTAGTACTACACACGTGATCACAGTTTTCG
Found at i:27557670 original size:18 final size:18
Alignment explanation
Indices: 27557647--27557683 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
27557637 GAAGAAAAAG
27557647 AATGATCTTTTTGGGTTA
1 AATGATCTTTTTGGGTTA
27557665 AATGATCTTTTTGGGTTA
1 AATGATCTTTTTGGGTTA
27557683 A
1 A
27557684 CTCAATCTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.05, G:0.22, T:0.49
Consensus pattern (18 bp):
AATGATCTTTTTGGGTTA
Found at i:27559378 original size:26 final size:29
Alignment explanation
Indices: 27559328--27559385 Score: 77
Period size: 27 Copynumber: 2.1 Consensus size: 29
27559318 AAACTCAAAA
*
27559328 TAAACAAGGAAAAAATCTATTTCATA-TAT
1 TAAACAA-GAAAAAATCTATCTCATACTAT
27559357 TAAACAA-AAAAAAT-TATCTCATACTAT
1 TAAACAAGAAAAAATCTATCTCATACTAT
27559384 TA
1 TA
27559386 GCAATTTGTC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 8 0.30
27 12 0.44
29 7 0.26
ACGTcount: A:0.53, C:0.12, G:0.03, T:0.31
Consensus pattern (29 bp):
TAAACAAGAAAAAATCTATCTCATACTAT
Found at i:27560385 original size:14 final size:14
Alignment explanation
Indices: 27560368--27560421 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
27560358 CCCAAACTCA
27560368 GAACCTCAAACCTT
1 GAACCTCAAACCTT
*
27560382 GAA-CTCAAACCAT
1 GAACCTCAAACCTT
* *
27560395 GAACCTTAAACTTT
1 GAACCTCAAACCTT
* *
27560409 TAACCTCGAACCT
1 GAACCTCAAACCT
27560422 CGAGGTTGGG
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
13 12 0.39
14 19 0.61
ACGTcount: A:0.37, C:0.31, G:0.07, T:0.24
Consensus pattern (14 bp):
GAACCTCAAACCTT
Found at i:27575676 original size:6 final size:6
Alignment explanation
Indices: 27575665--27575689 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
27575655 TTCTCTTTTA
27575665 TTTCTT TTTCTT TTTCTT TTTCTT T
1 TTTCTT TTTCTT TTTCTT TTTCTT T
27575690 CTTTTCTTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTCTT
Found at i:27581197 original size:17 final size:17
Alignment explanation
Indices: 27581177--27581209 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
27581167 AGAAAATGTC
27581177 TTTAA-AATAATAACAAA
1 TTTAACAATAA-AACAAA
27581194 TTTAACAATAAAACAA
1 TTTAACAATAAAACAA
27581210 GTGTTATACA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.27
Consensus pattern (17 bp):
TTTAACAATAAAACAAA
Found at i:27583581 original size:40 final size:40
Alignment explanation
Indices: 27583523--27583600 Score: 147
Period size: 40 Copynumber: 1.9 Consensus size: 40
27583513 TGAAAGTATG
27583523 TCTCTTTAACAACCGATGTTACCGAAAAATGACGCATCTA
1 TCTCTTTAACAACCGATGTTACCGAAAAATGACGCATCTA
*
27583563 TCTCTTTAACAACTGATGTTACCGAAAAATGACGCATC
1 TCTCTTTAACAACCGATGTTACCGAAAAATGACGCATC
27583601 CCTTTTAGTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.35, C:0.24, G:0.13, T:0.28
Consensus pattern (40 bp):
TCTCTTTAACAACCGATGTTACCGAAAAATGACGCATCTA
Found at i:27586488 original size:17 final size:16
Alignment explanation
Indices: 27586457--27586487 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
27586447 TTCAAAATAC
*
27586457 CTTAAACCCTAAAAAT
1 CTTAAAACCTAAAAAT
27586473 CTTAAAACCTAAAAA
1 CTTAAAACCTAAAAA
27586488 AAATAAAAAG
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:0.55, C:0.23, G:0.00, T:0.23
Consensus pattern (16 bp):
CTTAAAACCTAAAAAT
Found at i:27587272 original size:21 final size:22
Alignment explanation
Indices: 27587239--27587290 Score: 72
Period size: 21 Copynumber: 2.4 Consensus size: 22
27587229 TACTCCATAC
*
27587239 TAATTTTTATGAATTTT-TTTT
1 TAATTTTTATGAATTTTAATTT
27587260 TATATTTTT-TGAATTTTAATTT
1 TA-ATTTTTATGAATTTTAATTT
27587282 TAATTTTTA
1 TAATTTTTA
27587291 AATTATTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 16 0.59
22 11 0.41
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (22 bp):
TAATTTTTATGAATTTTAATTT
Found at i:27588373 original size:6 final size:6
Alignment explanation
Indices: 27588362--27588395 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
27588352 TATCCAGAAT
27588362 AGATGC AGATGC AGATGC AGATGC AGATGC AGAT
1 AGATGC AGATGC AGATGC AGATGC AGATGC AGAT
27588396 ATTCTTAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.35, C:0.15, G:0.32, T:0.18
Consensus pattern (6 bp):
AGATGC
Found at i:27590510 original size:14 final size:15
Alignment explanation
Indices: 27590491--27590519 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
27590481 ATATTTAGAT
27590491 AAATTA-TTAATTGA
1 AAATTATTTAATTGA
27590505 AAATTATTTAATTGA
1 AAATTATTTAATTGA
27590520 TAAGATTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (15 bp):
AAATTATTTAATTGA
Found at i:27591014 original size:21 final size:20
Alignment explanation
Indices: 27590989--27591060 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 20
27590979 CATGTTTACT
27590989 TTCTGTTTAGCTCTCATGAGA
1 TTCTGTTTAGCTCT-ATGAGA
* *
27591010 TTCTGTTTAACTCATATGAGT
1 TTCTGTTTAGCTC-TATGAGA
* *
27591031 TTCCT-TTCAGCTCTATTGAGC
1 TT-CTGTTTAGCTCTA-TGAGA
27591052 TTCTGTTTA
1 TTCTGTTTA
27591061 ACCCTTATGG
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
20 4 0.10
21 34 0.83
22 3 0.07
ACGTcount: A:0.18, C:0.19, G:0.15, T:0.47
Consensus pattern (20 bp):
TTCTGTTTAGCTCTATGAGA
Found at i:27591056 original size:42 final size:42
Alignment explanation
Indices: 27590988--27591140 Score: 132
Period size: 42 Copynumber: 3.6 Consensus size: 42
27590978 TCATGTTTAC
* * * *
27590988 TTTCTGTTTAGCTCTCA-TGAGATTCTGTTTAACTCATATGAG
1 TTTCCGTTCAGCTCT-ATTGAGCTTCTGTTTAACCCATATGAG
* * *
27591030 TTTCCTTTCAGCTCTATTGAGCTTCTGTTTAACCCTTATGGG
1 TTTCCGTTCAGCTCTATTGAGCTTCTGTTTAACCCATATGAG
* * * *
27591072 TTTCCGTTCAGCTCT-TACGAGCTTCTGTTCAACCCTTATGGG
1 TTTCCGTTCAGCTCTAT-TGAGCTTCTGTTTAACCCATATGAG
* * *
27591114 TTTCTGTTTAGGTCTCA-TGAGCTTCTG
1 TTTCCGTTCAGCTCT-ATTGAGCTTCTG
27591141 ATCATCTTTC
Statistics
Matches: 93, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
41 2 0.02
42 91 0.98
ACGTcount: A:0.16, C:0.22, G:0.18, T:0.44
Consensus pattern (42 bp):
TTTCCGTTCAGCTCTATTGAGCTTCTGTTTAACCCATATGAG
Found at i:27591118 original size:21 final size:21
Alignment explanation
Indices: 27591052--27591121 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
27591042 TCTATTGAGC
*
27591052 TTCTGTTTAACCCTTATGGGT
1 TTCTGTTCAACCCTTATGGGT
* * * * * *
27591073 TTCCGTTCAGCTCTTACGAGC
1 TTCTGTTCAACCCTTATGGGT
27591094 TTCTGTTCAACCCTTATGGGT
1 TTCTGTTCAACCCTTATGGGT
27591115 TTCTGTT
1 TTCTGTT
27591122 TAGGTCTCAT
Statistics
Matches: 36, Mismatches: 13, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (21 bp):
TTCTGTTCAACCCTTATGGGT
Found at i:27593353 original size:17 final size:17
Alignment explanation
Indices: 27593331--27593373 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
27593321 AATTTTCCAA
*
27593331 AGTAATAATGTAATATT
1 AGTAATAACGTAATATT
27593348 AGTAATAACGTAATATT
1 AGTAATAACGTAATATT
27593365 AGTAGATAA
1 AGTA-ATAA
27593374 AAAATTGATA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 20 0.83
18 4 0.17
ACGTcount: A:0.49, C:0.02, G:0.14, T:0.35
Consensus pattern (17 bp):
AGTAATAACGTAATATT
Found at i:27593783 original size:90 final size:91
Alignment explanation
Indices: 27593674--27593862 Score: 301
Period size: 90 Copynumber: 2.1 Consensus size: 91
27593664 TGTATTTGTA
* * *
27593674 CTATTATA-TATTATATTAATTTAGGCTTCAATTAACTAACTTTAAATTTTAAACGGTAGCTTAA
1 CTATTGTACTATTATATTAATTTAGGCTTCAATTAACTAACTTTAAAGTTTAAAAGGTAGCTTAA
27593738 CAAAC-TTTTTTTTGTTTAATTTATG
66 CAAACTTTTTTTTTGTTTAATTTATG
* *
27593763 CTATTGTACTATTATATTAATTTAGGCTTCAATTAACTAACTTTAAAGTTTAAAATGTAGTTTAA
1 CTATTGTACTATTATATTAATTTAGGCTTCAATTAACTAACTTTAAAGTTTAAAAGGTAGCTTAA
*
27593828 CATACTTTTTTTTTGTTTAATTTATG
66 CAAACTTTTTTTTTGTTTAATTTATG
*
27593854 CTGTTGTAC
1 CTATTGTAC
27593863 CTGTACTATT
Statistics
Matches: 91, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
89 7 0.08
90 56 0.62
91 28 0.31
ACGTcount: A:0.32, C:0.10, G:0.09, T:0.49
Consensus pattern (91 bp):
CTATTGTACTATTATATTAATTTAGGCTTCAATTAACTAACTTTAAAGTTTAAAAGGTAGCTTAA
CAAACTTTTTTTTTGTTTAATTTATG
Found at i:27599415 original size:17 final size:18
Alignment explanation
Indices: 27599393--27599440 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 18
27599383 ATCGAAGGAG
27599393 TAAAAAGAAGAAAAAA-A
1 TAAAAAGAAGAAAAAAGA
*
27599410 TAAAAAGAAAGAAAAAAGG
1 TAAAAAG-AAGAAAAAAGA
27599429 TAAAGAAGAAGA
1 TAAA-AAGAAGA
27599441 GTTTTGAACG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 7 0.26
18 9 0.33
19 8 0.30
20 3 0.11
ACGTcount: A:0.75, C:0.00, G:0.19, T:0.06
Consensus pattern (18 bp):
TAAAAAGAAGAAAAAAGA
Found at i:27605710 original size:24 final size:23
Alignment explanation
Indices: 27605683--27605731 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
27605673 ATTATATTAG
*
27605683 TATTTATTCAATTATTAATAATTT
1 TATTTATTCAATTA-TAAGAATTT
* *
27605707 TATTTATTTATTTATAAGAATTT
1 TATTTATTCAATTATAAGAATTT
27605730 TA
1 TA
27605732 AAATAATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (23 bp):
TATTTATTCAATTATAAGAATTT
Found at i:27610663 original size:104 final size:103
Alignment explanation
Indices: 27610370--27610670 Score: 323
Period size: 103 Copynumber: 2.9 Consensus size: 103
27610360 TAGTCTTAAT
* * * *
27610370 TTAACTCAGCTAACTCAAAAAATTCAAGTTGTGAGCTTAACTCAACTAACCTTTAAGCATAAGCT
1 TTAACTCAGCTAACTCAAAAAATTCAGGTTGAGAGCTTAACTCAGCTAACCTTTAAACATAAGCT
* * * ** *
27610435 GGGAACATAGGTTCACGAGCTATTTCAGATTTCCAAGC
66 GGGAACGTAGGTTCGCGAGCTGTTTTGGACTTCCAAGC
* * * * * ** * *
27610473 TTAACTCAACTAACTAAAAAAATTCAGGTTGCGAGTTTAACTTAGCTAACCTTTAAATGTTAGTT
1 TTAACTCAGCTAACTCAAAAAATTCAGGTTGAGAGCTTAACTCAGCTAACCTTTAAACATAAGCT
* *
27610538 GGGAACGTAGGTCCGCGAGCTGTTTTGGACTTGCAAGC
66 GGGAACGTAGGTTCGCGAGCTGTTTTGGACTTCCAAGC
* * *
27610576 TTGACTCAGCTAACTCAAAAATATTTAGGTTGAGAGCTTAACTCAGCTAACCTTTAAACATCAGC
1 TTAACTCAGCTAACTCAAAAA-ATTCAGGTTGAGAGCTTAACTCAGCTAACCTTTAAACATAAGC
* * * * * *
27610641 TAGTAATGTAAGTTCGCAAGCTGTCTTGGA
65 TGGGAACGTAGGTTCGCGAGCTGTTTTGGA
27610671 GTTGTGAGCA
Statistics
Matches: 159, Mismatches: 38, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
103 101 0.64
104 58 0.36
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (103 bp):
TTAACTCAGCTAACTCAAAAAATTCAGGTTGAGAGCTTAACTCAGCTAACCTTTAAACATAAGCT
GGGAACGTAGGTTCGCGAGCTGTTTTGGACTTCCAAGC
Found at i:27610768 original size:40 final size:40
Alignment explanation
Indices: 27610708--27610811 Score: 109
Period size: 40 Copynumber: 2.6 Consensus size: 40
27610698 AAACATTAGT
* * * ***
27610708 TGGGAACGTAGGTCCGCGAGCTGTGTTGGAGTTTATCAGC
1 TGGGAACATAGGTCCACGAGCTATGCCAGAGTTTATCAGC
27610748 TGGGAACATAGGTCCACGAGCTATGCCAGAGTTTATCAGC
1 TGGGAACATAGGTCCACGAGCTATGCCAGAGTTTATCAGC
* * * * *
27610788 TAGGAGCGTAGGTTCGCGAGCTAT
1 TGGGAACATAGGTCCACGAGCTAT
27610812 CATGGAATTG
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 53 1.00
ACGTcount: A:0.22, C:0.19, G:0.34, T:0.25
Consensus pattern (40 bp):
TGGGAACATAGGTCCACGAGCTATGCCAGAGTTTATCAGC
Found at i:27611003 original size:143 final size:144
Alignment explanation
Indices: 27610742--27611081 Score: 371
Period size: 143 Copynumber: 2.4 Consensus size: 144
27610732 GTTGGAGTTT
* * * *** * * *
27610742 ATCAGCTGGGAACATAGGTCCACGAGCTATGCCAGAGTTTATCAGCTAGGAGCGTAGGTTCGCGA
1 ATCAGCTGGGAACGTAGGTTCACGAGTTATGTTGGAGTTTATCAGCTAGGAACGTACGTTCACGA
* ** * *
27610807 GCTATCATGGAATTGCAAGCTTAACTCAACTAACTCAAGTAAATGGAGGTTGTGAGCAT-ACTCA
66 GCTATCATAGAATTGCAAGCTTAACTCAACTAACTCAAGTAAATAAAAGTTGTGAACATAACTCA
*
27610871 GCTAACCTTTAAAC
131 GATAACCTTTAAAC
* *
27610885 ATCAGCTGGGAACGTAGGTTCACGAGTTATGTTGGAGTTTATCAGCTGGGAATGTACG-TCTACG
1 ATCAGCTGGGAACGTAGGTTCACGAGTTATGTTGGAGTTTATCAGCTAGGAACGTACGTTC-ACG
* * * * * *
27610949 AGCTGTCTTAGAGTTGCGAGCTTAACTCAGCTAACTCGAA-TAAATAAAATTTGTGAACATAACT
65 AGCTATCATAGAATTGCAAGCTTAACTCAACTAACTC-AAGTAAATAAAAGTTGTGAACATAACT
27611013 CAGATAACCTTTAAAC
129 CAGATAACCTTTAAAC
* ** * * * *
27611029 ATCAGCTGGGAATGTAGGTTTGCGAGTTATATTGGTGTTTATTAACTAGGAAC
1 ATCAGCTGGGAACGTAGGTTCACGAGTTATGTTGGAGTTTATCAGCTAGGAAC
27611082 AAAGCTTCGT
Statistics
Matches: 162, Mismatches: 32, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
142 2 0.01
143 96 0.59
144 64 0.40
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (144 bp):
ATCAGCTGGGAACGTAGGTTCACGAGTTATGTTGGAGTTTATCAGCTAGGAACGTACGTTCACGA
GCTATCATAGAATTGCAAGCTTAACTCAACTAACTCAAGTAAATAAAAGTTGTGAACATAACTCA
GATAACCTTTAAAC
Found at i:27611096 original size:144 final size:142
Alignment explanation
Indices: 27610819--27611084 Score: 327
Period size: 144 Copynumber: 1.9 Consensus size: 142
27610809 TATCATGGAA
** * * *
27610819 TTGCAAGCTTAACTCAACTAACTCAAGTAAATGGAGGTTGTGAGCATACTCAGCTAACCTTTAAA
1 TTGCAAGCTTAACTCAACTAACTCAAGTAAATAAAAGTTGTGAACATACTCAGATAACCTTTAAA
* * * ***
27610884 CATCAGCTGGGAACGTAGGTTCACGAGTTATGTTGGAGTTTATCAGCTGGGAATGTACGTCTACG
66 CATCAGCTGGGAACGTAGGTTCACGAGTTATATTGGAGTTTATCAACTAGGAACAAACGTCTA-G
27610949 AGCTGTCTTAGAG
130 AGCTGTCTTAGAG
* * *
27610962 TTGCGAGCTTAACTCAGCTAACTCGAA-TAAATAAAATTTGTGAACATAACTCAGATAACCTTTA
1 TTGCAAGCTTAACTCAACTAACTC-AAGTAAATAAAAGTTGTGAACAT-ACTCAGATAACCTTTA
* ** * *
27611026 AACATCAGCTGGGAATGTAGGTTTGCGAGTTATATTGGTGTTTATTAACTAGGAACAAA
64 AACATCAGCTGGGAACGTAGGTTCACGAGTTATATTGGAGTTTATCAACTAGGAACAAA
27611085 GCTTCGTGAG
Statistics
Matches: 102, Mismatches: 19, Indels: 3
0.82 0.15 0.02
Matches are distributed among these distances:
143 37 0.36
144 65 0.64
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.30
Consensus pattern (142 bp):
TTGCAAGCTTAACTCAACTAACTCAAGTAAATAAAAGTTGTGAACATACTCAGATAACCTTTAAA
CATCAGCTGGGAACGTAGGTTCACGAGTTATATTGGAGTTTATCAACTAGGAACAAACGTCTAGA
GCTGTCTTAGAG
Found at i:27614679 original size:281 final size:281
Alignment explanation
Indices: 27614169--27614727 Score: 657
Period size: 281 Copynumber: 2.0 Consensus size: 281
27614159 TTGAGTACAC
* * *
27614169 CTTATATTAACTATGTCTACAAACTAGAAGGCATGCACAATGTACAGATATCTAAATTCTCACCT
1 CTTATATTAACGATGTCTAAAAACTAGAAGGCATGCACAATGTACAGATATCTAAATTCTCACCC
* *
27614234 ATCCCAGATGAGAGTATTGGGCTGCCAGTGTCCAGCGTCCAGTTCAAGTTAGCCCCGAATATAAA
66 ATCCCAGATGAAAGTATTGGGCTGCCAGTGTCCAGCGTCCAGTTCAAGTTAGCCCCGAACATAAA
* * *
27614299 CTTGCATCGTGTCCCGAAAGGTCATCCAACTTTCACTCAAATACACACCAAAATGGATGTTCAGG
131 CTTGCACCGCGTCCCGAAAGGTCATCCAACTTTCACTCAAATACACACCAAAATGGATATTCAGG
* * * *
27614364 AAAGAGACAATCAATAGAGGTTTTTCAAGTACTGTAGAAACCCAGAGCATACGAAGGCAACATGT
196 AAAGAGACAATCAACAAAGGTTTATCAAGTACTGTAGAAACCCAGAGCATACAAAGGCAACATGT
*
27614429 TCCG-TATTGAGGGATACACGT
261 T-CGATATTAAGGGATACACGT
* * *
27614450 CTTATATTAACGATG-CGTAAAAACTAGAAGGCATGCACAATGTA-TGAATATCTGAATTCTGAC
1 CTTATATTAACGATGTC-TAAAAACTAGAAGGCATGCACAATGTACAG-ATATCTAAATTCTCAC
* * *
27614513 CCATCCCAGATGAAAGTA-TGTGGTTGCTAGTGTCCAGCGCTCCA-TTCAAGTTGGCCCCGAACA
64 CCATCCCAGATGAAAGTATTG-GGCTGCCAGTGTCCAGCG-TCCAGTTCAAGTTAGCCCCGAACA
* ** * * *** ** * *
27614576 TGAACTTGTGCCGCGTCCCGAAAGGTCGTCTGAA-TTTCACTTGGATACGTACTAATATGGATAT
127 TAAACTTGCACCGCGTCCCGAAAGGTCATC-CAACTTTCACTCAAATACACACCAAAATGGATAT
* * * * *
27614640 TC-GAGAGAGAGACAATCAACAAAGG-TTATGAGGGTACTGTAGAAATCCAGGGCATACAAAGGC
191 TCAG-GAAAGAGACAATCAACAAAGGTTTATCA-AGTACTGTAGAAACCCAGAGCATACAAAGGC
*
27614703 ATCATGTTCGATATTAAGGGATACA
254 AACATGTTCGATATTAAGGGATACA
27614728 TTGAGGCCTC
Statistics
Matches: 233, Mismatches: 37, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
280 11 0.05
281 216 0.93
282 6 0.03
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (281 bp):
CTTATATTAACGATGTCTAAAAACTAGAAGGCATGCACAATGTACAGATATCTAAATTCTCACCC
ATCCCAGATGAAAGTATTGGGCTGCCAGTGTCCAGCGTCCAGTTCAAGTTAGCCCCGAACATAAA
CTTGCACCGCGTCCCGAAAGGTCATCCAACTTTCACTCAAATACACACCAAAATGGATATTCAGG
AAAGAGACAATCAACAAAGGTTTATCAAGTACTGTAGAAACCCAGAGCATACAAAGGCAACATGT
TCGATATTAAGGGATACACGT
Found at i:27615337 original size:24 final size:24
Alignment explanation
Indices: 27615310--27615372 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 24
27615300 ACCCTCGTAC
*
27615310 TCATCTTCATCTCCA-CATTGGTCT
1 TCATCTTCATCTCCACCATCGG-CT
*
27615334 TCATATTCAGT-TCCACCATCGGCT
1 TCATCTTCA-TCTCCACCATCGGCT
*
27615358 TCATCTTCGTCTCCA
1 TCATCTTCATCTCCA
27615373 TCGCTTTCCT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
23 1 0.03
24 25 0.78
25 6 0.19
ACGTcount: A:0.17, C:0.35, G:0.10, T:0.38
Consensus pattern (24 bp):
TCATCTTCATCTCCACCATCGGCT
Found at i:27617006 original size:25 final size:24
Alignment explanation
Indices: 27616977--27617024 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
27616967 GCACTACCGC
*
27616977 AGCTCTGTGTGAGCGTCCTGATATA
1 AGCTCT-TATGAGCGTCCTGATATA
* *
27617002 AGCTCTTATGGGCTTCCTGATAT
1 AGCTCTTATGAGCGTCCTGATAT
27617025 GGCTTGCTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.19, C:0.21, G:0.25, T:0.35
Consensus pattern (24 bp):
AGCTCTTATGAGCGTCCTGATATA
Found at i:27629949 original size:46 final size:46
Alignment explanation
Indices: 27629896--27629986 Score: 182
Period size: 46 Copynumber: 2.0 Consensus size: 46
27629886 CTGGAAAAAG
27629896 TTAACCATTTTCGTCTTAAGAACCTCAGGGTCAAAAATCCATTCTA
1 TTAACCATTTTCGTCTTAAGAACCTCAGGGTCAAAAATCCATTCTA
27629942 TTAACCATTTTCGTCTTAAGAACCTCAGGGTCAAAAATCCATTCT
1 TTAACCATTTTCGTCTTAAGAACCTCAGGGTCAAAAATCCATTCT
27629987 CCATCAGTAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.33
Consensus pattern (46 bp):
TTAACCATTTTCGTCTTAAGAACCTCAGGGTCAAAAATCCATTCTA
Found at i:27640551 original size:40 final size:40
Alignment explanation
Indices: 27640492--27640708 Score: 321
Period size: 40 Copynumber: 5.5 Consensus size: 40
27640482 GGATTGATAA
27640492 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
27640531 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
27640571 CCGGGCCAAGTCCCGAAGGCAATTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
27640611 CCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * **
27640651 CCGGGCTAAGTCCCGAAGGCATTTGAGTGAGTGGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
**
27640691 CC-GGCTAAACCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
27640709 TACTTGGTTT
Statistics
Matches: 163, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
39 24 0.15
40 139 0.85
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.23
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:27643008 original size:19 final size:18
Alignment explanation
Indices: 27642986--27643039 Score: 63
Period size: 19 Copynumber: 2.9 Consensus size: 18
27642976 TAGTGCATAG
*
27642986 TGGCACACGAAGCGCATCT
1 TGGCACAC-AAGCGCATCC
**
27643005 TGGCACACAAATTGCATCC
1 TGGCACAC-AAGCGCATCC
27643024 TGGCACACAAGCGCAT
1 TGGCACACAAGCGCAT
27643040 AAACCTGTAC
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
18 6 0.21
19 23 0.79
ACGTcount: A:0.30, C:0.31, G:0.22, T:0.17
Consensus pattern (18 bp):
TGGCACACAAGCGCATCC
Found at i:27643550 original size:6 final size:6
Alignment explanation
Indices: 27643539--27643563 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
27643529 AATTTCCATC
27643539 AATTCA AATTCA AATTCA AATTCA A
1 AATTCA AATTCA AATTCA AATTCA A
27643564 GAAAATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (6 bp):
AATTCA
Found at i:27652350 original size:67 final size:68
Alignment explanation
Indices: 27652237--27652369 Score: 250
Period size: 67 Copynumber: 2.0 Consensus size: 68
27652227 GGGCCTAGTC
27652237 GAAACAGTGGTTTCGGGACCACTATTTCGAGGCCAGAGAAAATTATTTTAGTATTATTTTATGTG
1 GAAACAGTGGTTTCGGGACCACTATTTCGAGGCCAGAGAAAATTATTTTAGTATTATTTTATGTG
27652302 TCG
66 TCG
*
27652305 GAAA-AGTGGTTTCGGGACCACTATTTTGAGGCCAGAGAAAATTATTTTAGTATTATTTTATGTG
1 GAAACAGTGGTTTCGGGACCACTATTTCGAGGCCAGAGAAAATTATTTTAGTATTATTTTATGTG
27652369 T
66 T
27652370 TATAATATAA
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
67 60 0.94
68 4 0.06
ACGTcount: A:0.29, C:0.11, G:0.23, T:0.37
Consensus pattern (68 bp):
GAAACAGTGGTTTCGGGACCACTATTTCGAGGCCAGAGAAAATTATTTTAGTATTATTTTATGTG
TCG
Found at i:27660124 original size:19 final size:17
Alignment explanation
Indices: 27660092--27660127 Score: 54
Period size: 19 Copynumber: 2.0 Consensus size: 17
27660082 ATTTGGATAA
27660092 ATTATTAATTGATAAAT
1 ATTATTAATTGATAAAT
27660109 ATTATTTAATTTGATAAAT
1 ATTA-TTAA-TTGATAAAT
27660128 TAATTAGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 4 0.24
19 9 0.53
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (17 bp):
ATTATTAATTGATAAAT
Found at i:27660129 original size:17 final size:16
Alignment explanation
Indices: 27660082--27660129 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 16
27660072 AGCCTAGAAT
27660082 ATTTGGATAAATTATTA
1 ATTT-GATAAATTATTA
27660099 A-TTGATAAATATTATTTA
1 ATTTGAT-AA-ATTA-TTA
27660117 ATTTGATAAATTA
1 ATTTGATAAATTA
27660130 ATTAGTTAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
15 3 0.11
16 4 0.15
17 9 0.33
18 6 0.22
19 5 0.19
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (16 bp):
ATTTGATAAATTATTA
Found at i:27660758 original size:26 final size:27
Alignment explanation
Indices: 27660702--27660768 Score: 77
Period size: 26 Copynumber: 2.6 Consensus size: 27
27660692 TGATATATGA
*
27660702 CTCTTTGTGAGCTT-CTCATTGATTGG
1 CTCTTTGTGAGCTTCCTCATTGAATGG
*
27660728 CTCTTTGTGAGCTTCCTGATT-AATGG
1 CTCTTTGTGAGCTTCCTCATTGAATGG
* *
27660754 GTCTTCG-GAGCTTCC
1 CTCTTTGTGAGCTTCC
27660769 CAATATTGGC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
25 8 0.22
26 23 0.64
27 5 0.14
ACGTcount: A:0.12, C:0.22, G:0.24, T:0.42
Consensus pattern (27 bp):
CTCTTTGTGAGCTTCCTCATTGAATGG
Found at i:27660860 original size:24 final size:24
Alignment explanation
Indices: 27660833--27660894 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
27660823 ATGCTTTACG
*
27660833 GAGCTACCCGTTATTGGCTCGTAT
1 GAGCTTCCCGTTATTGGCTCGTAT
* *
27660857 GAGCTTCCTGATTA-TGGCTCTTAT
1 GAGCTTCCCG-TTATTGGCTCGTAT
27660881 GAGCTTCCCGTTAT
1 GAGCTTCCCGTTAT
27660895 ACAACTCGGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
23 3 0.09
24 26 0.81
25 3 0.09
ACGTcount: A:0.16, C:0.24, G:0.23, T:0.37
Consensus pattern (24 bp):
GAGCTTCCCGTTATTGGCTCGTAT
Found at i:27662903 original size:30 final size:30
Alignment explanation
Indices: 27662867--27662994 Score: 118
Period size: 30 Copynumber: 4.3 Consensus size: 30
27662857 GGCTATCAAT
27662867 TATGAAAAGGGATGGTGACGACCATCGAAC
1 TATGAAAAGGGATGGTGACGACCATCGAAC
* * * *
27662897 TATGAAAAGGAATGGCT-TC-AGCTAT-GAAAT
1 TATGAAAAGGGATGG-TGACGA-CCATCG-AAC
*
27662927 TATGAAAAGGGATGGTGACGACCATTGAAC
1 TATGAAAAGGGATGGTGACGACCATCGAAC
* * * * *
27662957 AATGAAAAGGGTTGGTGACGACGATCAAAT
1 TATGAAAAGGGATGGTGACGACCATCGAAC
27662987 TATGAAAA
1 TATGAAAA
27662995 AAGATAGCTT
Statistics
Matches: 77, Mismatches: 15, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
29 3 0.04
30 71 0.92
31 3 0.04
ACGTcount: A:0.40, C:0.12, G:0.27, T:0.21
Consensus pattern (30 bp):
TATGAAAAGGGATGGTGACGACCATCGAAC
Found at i:27662987 original size:60 final size:60
Alignment explanation
Indices: 27662864--27662994 Score: 167
Period size: 60 Copynumber: 2.2 Consensus size: 60
27662854 TTTGGCTATC
* * * *
27662864 AATTATGAAAAGGGATGGTGACGACCATCGAACTATGAAAAGGAATGGCTTCAGCTATGA
1 AATTATGAAAAGGGATGGTGACGACCATCGAACAATGAAAAGGAATGGCTACAGCGATCA
* **
27662924 AATTATGAAAAGGGATGGTGACGACCATTGAACAATGAAAAGGGTTGG-TGAC-GACGATCA
1 AATTATGAAAAGGGATGGTGACGACCATCGAACAATGAAAAGGAATGGCT-ACAG-CGATCA
27662984 AATTATGAAAA
1 AATTATGAAAA
27662995 AAGATAGCTT
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
59 2 0.03
60 60 0.97
ACGTcount: A:0.40, C:0.11, G:0.27, T:0.21
Consensus pattern (60 bp):
AATTATGAAAAGGGATGGTGACGACCATCGAACAATGAAAAGGAATGGCTACAGCGATCA
Found at i:27663018 original size:30 final size:30
Alignment explanation
Indices: 27662984--27663060 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 30
27662974 ACGACGATCA
* * *
27662984 AATTATGAAAAAAGATAGCTTCGGTTATCG
1 AATTATGAAAAAAGATAACCTCGGCTATCG
*
27663014 AATTATGAAAAAGGATAACCTCGGCTATCG
1 AATTATGAAAAAAGATAACCTCGGCTATCG
* *
27663044 AATAAAGAAAAAGAGAT
1 AATTATGAAAAA-AGAT
27663061 GTGTCAACCA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
30 36 0.92
31 3 0.08
ACGTcount: A:0.47, C:0.10, G:0.19, T:0.23
Consensus pattern (30 bp):
AATTATGAAAAAAGATAACCTCGGCTATCG
Found at i:27664123 original size:12 final size:12
Alignment explanation
Indices: 27664106--27664133 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
27664096 GTCAGGTTGT
27664106 CACACGACCTAG
1 CACACGACCTAG
27664118 CACACGACCTAG
1 CACACGACCTAG
27664130 CACA
1 CACA
27664134 TGGTTGTGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.36, C:0.43, G:0.14, T:0.07
Consensus pattern (12 bp):
CACACGACCTAG
Found at i:27666760 original size:20 final size:20
Alignment explanation
Indices: 27666736--27666800 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
27666726 AAGCCACCAG
27666736 TAATGCAGATAAGCTGCCAA
1 TAATGCAGATAAGCTGCCAA
* ** ** *
27666756 AAATGTGGATAAGCCACCAG
1 TAATGCAGATAAGCTGCCAA
*
27666776 TAATGCAGACAAGCTGCCAA
1 TAATGCAGATAAGCTGCCAA
27666796 TAATG
1 TAATG
27666801 TGGAGAAGAG
Statistics
Matches: 32, Mismatches: 13, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.18
Consensus pattern (20 bp):
TAATGCAGATAAGCTGCCAA
Found at i:27666774 original size:40 final size:40
Alignment explanation
Indices: 27666719--27666804 Score: 145
Period size: 40 Copynumber: 2.1 Consensus size: 40
27666709 CACACCAGTT
*
27666719 TGTGGACAAGCCACCAGTAATGCAGATAAGCTGCCAAAAA
1 TGTGGACAAGCCACCAGTAATGCAGACAAGCTGCCAAAAA
* *
27666759 TGTGGATAAGCCACCAGTAATGCAGACAAGCTGCCAATAA
1 TGTGGACAAGCCACCAGTAATGCAGACAAGCTGCCAAAAA
27666799 TGTGGA
1 TGTGGA
27666805 GAAGAGACTA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.37, C:0.21, G:0.24, T:0.17
Consensus pattern (40 bp):
TGTGGACAAGCCACCAGTAATGCAGACAAGCTGCCAAAAA
Found at i:27666833 original size:40 final size:40
Alignment explanation
Indices: 27666719--27666841 Score: 138
Period size: 40 Copynumber: 3.1 Consensus size: 40
27666709 CACACCAGTT
* * *
27666719 TGTGGACAAGCCACCAGTAATGCAGATAAGCTGCCAAAAA
1 TGTGGAGAAGACACCAGTAATGCAGATAAGCTGCCAATAA
* * *
27666759 TGTGGATAAGCCACCAGTAATGCAGACAAGCTGCCAATAA
1 TGTGGAGAAGACACCAGTAATGCAGATAAGCTGCCAATAA
* * * * * *
27666799 TGTGGAGAAGAGACTAGTAGTGCAAATAAACTGCCAGTAA
1 TGTGGAGAAGACACCAGTAATGCAGATAAGCTGCCAATAA
27666839 TGT
1 TGT
27666842 AGAAAAGCTA
Statistics
Matches: 71, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 71 1.00
ACGTcount: A:0.38, C:0.19, G:0.24, T:0.19
Consensus pattern (40 bp):
TGTGGAGAAGACACCAGTAATGCAGATAAGCTGCCAATAA
Found at i:27667040 original size:38 final size:38
Alignment explanation
Indices: 27666973--27667045 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
27666963 GTACAGTAAG
* *
27666973 CATGATTAAAACATGCAATTAGTAGTAGAATTAGTAGA
1 CATGATTAAAACATGCAATAAGTAGTAGAAATAGTAGA
* *
27667011 CATGATTTAAACATGCGATAAGT-GATAGAAATAGT
1 CATGATTAAAACATGCAATAAGTAG-TAGAAATAGT
27667046 GGCATGAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 1 0.03
38 29 0.97
ACGTcount: A:0.44, C:0.08, G:0.19, T:0.29
Consensus pattern (38 bp):
CATGATTAAAACATGCAATAAGTAGTAGAAATAGTAGA
Found at i:27669470 original size:16 final size:16
Alignment explanation
Indices: 27669446--27669479 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
27669436 AATTTACCAT
*
27669446 TTGGAGAACTTTAAGG
1 TTGGAGAACTCTAAGG
*
27669462 TTGGCGAACTCTAAGG
1 TTGGAGAACTCTAAGG
27669478 TT
1 TT
27669480 TGACAGACTT
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:0.12, G:0.29, T:0.32
Consensus pattern (16 bp):
TTGGAGAACTCTAAGG
Found at i:27672380 original size:43 final size:43
Alignment explanation
Indices: 27672319--27672520 Score: 278
Period size: 43 Copynumber: 4.7 Consensus size: 43
27672309 TTAGTGGCAT
* *
27672319 TAAAGAACGTGACCTTTAGCAGCGCTTTTCACATAAACGCCGC
1 TAAAGAACGTGACCTTTAGCGGCGCTTTTCACACAAACGCCGC
* * *
27672362 TAAAGAACATGACCTTTAGCGGTGCTTTTCACACAAATGCCGC
1 TAAAGAACGTGACCTTTAGCGGCGCTTTTCACACAAACGCCGC
* * *
27672405 TAAAGAACGTGACCTTTAACGGCGCTTTTCACACAAACACTGC
1 TAAAGAACGTGACCTTTAGCGGCGCTTTTCACACAAACGCCGC
* * * * * *
27672448 TAAAGAACATGACTTTTAGTGGCGCTTCTCTCAAAAACGCCGC
1 TAAAGAACGTGACCTTTAGCGGCGCTTTTCACACAAACGCCGC
27672491 TAAAGAACGTGACCTTTAGCGGCGCTTTTC
1 TAAAGAACGTGACCTTTAGCGGCGCTTTTC
27672521 TTACAAACAC
Statistics
Matches: 135, Mismatches: 24, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 135 1.00
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (43 bp):
TAAAGAACGTGACCTTTAGCGGCGCTTTTCACACAAACGCCGC
Found at i:27673248 original size:14 final size:14
Alignment explanation
Indices: 27673229--27673271 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
27673219 AGTAACAATG
27673229 AATTAAACCATTAT
1 AATTAAACCATTAT
*
27673243 AATTAAACTATTAT
1 AATTAAACCATTAT
*
27673257 GATTAAA-CATTAT
1 AATTAAACCATTAT
27673270 AA
1 AA
27673272 ATATTTAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
13 6 0.24
14 19 0.76
ACGTcount: A:0.51, C:0.09, G:0.02, T:0.37
Consensus pattern (14 bp):
AATTAAACCATTAT
Found at i:27677410 original size:12 final size:12
Alignment explanation
Indices: 27677393--27677434 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
27677383 CTTGACTGTG
27677393 CCTCATATTCAT
1 CCTCATATTCAT
*
27677405 CCTCAT-TCACAT
1 CCTCATAT-TCAT
*
27677417 CTTCATATTCAT
1 CCTCATATTCAT
27677429 CCTCAT
1 CCTCAT
27677435 TCACATCTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
11 1 0.04
12 22 0.92
13 1 0.04
ACGTcount: A:0.24, C:0.36, G:0.00, T:0.40
Consensus pattern (12 bp):
CCTCATATTCAT
Found at i:27677427 original size:24 final size:24
Alignment explanation
Indices: 27677395--27677449 Score: 101
Period size: 24 Copynumber: 2.2 Consensus size: 24
27677385 TGACTGTGCC
27677395 TCATATTCATCCTCATTCACATCT
1 TCATATTCATCCTCATTCACATCT
27677419 TCATATTCATCCTCATTCACATCT
1 TCATATTCATCCTCATTCACATCT
27677443 TCTATAT
1 TC-ATAT
27677450 GTCTATTCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 26 0.87
25 4 0.13
ACGTcount: A:0.25, C:0.31, G:0.00, T:0.44
Consensus pattern (24 bp):
TCATATTCATCCTCATTCACATCT
Found at i:27678087 original size:72 final size:72
Alignment explanation
Indices: 27677970--27678114 Score: 272
Period size: 72 Copynumber: 2.0 Consensus size: 72
27677960 ATGGTAAGCA
27677970 TTATAAGGATAAACCAGATTAATCATTGAAGAGGTTCTACTAGGTGTACACTCTCCATGGAAAAT
1 TTATAAGGATAAACCAGATTAATCATTGAAGAGGTTCTACTAGGTGTACACTCTCCATGGAAAAT
*
27678035 CTATTTT
66 CCATTTT
*
27678042 TTATAAGGATAAACCAGATTAATCATTGAAGAGGTTCTACTAGGTGTACACTCTTCATGGAAAAT
1 TTATAAGGATAAACCAGATTAATCATTGAAGAGGTTCTACTAGGTGTACACTCTCCATGGAAAAT
27678107 CCATTTT
66 CCATTTT
27678114 T
1 T
27678115 ATACCCCCGA
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 71 1.00
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (72 bp):
TTATAAGGATAAACCAGATTAATCATTGAAGAGGTTCTACTAGGTGTACACTCTCCATGGAAAAT
CCATTTT
Found at i:27678397 original size:9 final size:9
Alignment explanation
Indices: 27678383--27678597 Score: 286
Period size: 9 Copynumber: 23.9 Consensus size: 9
27678373 TAAGTATAAT
27678383 TAAGTTATG
1 TAAGTTATG
27678392 TAAGTTATG
1 TAAGTTATG
27678401 TAAGTTATG
1 TAAGTTATG
*
27678410 TGAGTTATG
1 TAAGTTATG
*
27678419 TGAGTTATG
1 TAAGTTATG
* *
27678428 TGAGGTATG
1 TAAGTTATG
*
27678437 TAAGTTGTG
1 TAAGTTATG
27678446 TAAGTTATG
1 TAAGTTATG
*
27678455 TGAGTTATG
1 TAAGTTATG
27678464 TAAGTTATG
1 TAAGTTATG
*
27678473 TAAGGTATG
1 TAAGTTATG
27678482 TAAGTTATG
1 TAAGTTATG
*
27678491 TGAGTTATG
1 TAAGTTATG
*
27678500 TGAGTTATG
1 TAAGTTATG
* *
27678509 TGAGGTATG
1 TAAGTTATG
*
27678518 TAAGTTGTG
1 TAAGTTATG
27678527 TAAGTTATG
1 TAAGTTATG
*
27678536 TGAGTTATG
1 TAAGTTATG
27678545 TAAGTTATG
1 TAAGTTATG
*
27678554 TAAGGTATG
1 TAAGTTATG
27678563 TAAGTTATG
1 TAAGTTATG
27678572 TAAGTTATG
1 TAAGTTATG
*
27678581 TAAGTTCTG
1 TAAGTTATG
*
27678590 TGAGTTAT
1 TAAGTTAT
27678598 TTGAATCAAC
Statistics
Matches: 183, Mismatches: 23, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 183 1.00
ACGTcount: A:0.28, C:0.00, G:0.29, T:0.43
Consensus pattern (9 bp):
TAAGTTATG
Found at i:27679610 original size:20 final size:20
Alignment explanation
Indices: 27679587--27679637 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
27679577 TTTCAACTTT
*
27679587 GATTTGGGGAAAAATTTAGG
1 GATTTGGGGAAAAAGTTAGG
27679607 GATTTGGGG-AAAAGTTAGG
1 GATTTGGGGAAAAAGTTAGG
27679626 GATTTGGGGAAA
1 GATTTGGGGAAA
27679638 TTTTGTTAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 18 0.62
20 11 0.38
ACGTcount: A:0.33, C:0.00, G:0.39, T:0.27
Consensus pattern (20 bp):
GATTTGGGGAAAAAGTTAGG
Found at i:27680125 original size:148 final size:148
Alignment explanation
Indices: 27679849--27680150 Score: 371
Period size: 148 Copynumber: 2.0 Consensus size: 148
27679839 GCATAGTCCA
* * *
27679849 TTGCAGTGTTTTGTACAAAACGCCACTAATAACAAGGCTAAAACGACGACGTTTTCTGAAATCTT
1 TTGCGGTGTTTTGGACAAAACGCCACTAATAACAAGGCTAAAACGACGACGTTTTCTGAAATCCT
* * * *
27679914 AATACATACTTGTGGCATTTTATGTAAGCGCCACTAAATACAAAGCATAAAACGGCGCAATTTTG
66 AATACATACTTGCGGCATTTTACGTAAGCGCCACTAAAAACAAAGCATAAAACGACGCAATTTTG
* *
27679979 GAAACACTTAACATATAT
131 CAAACACTTAACACATAT
* * * *
27679997 TTGCGGTGTTTTGGGCAAAATGCCACTAATAACAAGGCT-AAACGATGTCG-TTTC-GAGAACTC
1 TTGCGGTGTTTTGGACAAAACGCCACTAATAACAAGGCTAAAACGACGACGTTTTCTGA-AA-TC
* *
27680059 CTAATACATATTTGCGGCATTTTTAACG-AAGCGCCACTAAAAACAAAGCATAAAATGACGTC-A
64 CTAATACATACTTGCGGCA-TTTT-ACGTAAGCGCCACTAAAAACAAAGCATAAAACGACG-CAA
* *
27680122 TTTTGCTAACACTTAACACATGT
126 TTTTGCAAACACTTAACACATAT
27680145 TTGCGG
1 TTGCGG
27680151 CATTTTTGTT
Statistics
Matches: 132, Mismatches: 17, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
145 2 0.02
146 6 0.05
147 27 0.20
148 94 0.71
149 3 0.02
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (148 bp):
TTGCGGTGTTTTGGACAAAACGCCACTAATAACAAGGCTAAAACGACGACGTTTTCTGAAATCCT
AATACATACTTGCGGCATTTTACGTAAGCGCCACTAAAAACAAAGCATAAAACGACGCAATTTTG
CAAACACTTAACACATAT
Found at i:27680709 original size:7 final size:7
Alignment explanation
Indices: 27680687--27680872 Score: 58
Period size: 7 Copynumber: 26.1 Consensus size: 7
27680677 ATTTATTATC
27680687 AGGGTTT
1 AGGGTTT
*
27680694 AGAGTTTT
1 AG-GGTTT
27680702 AGGGTTT
1 AGGGTTT
*
27680709 ATGGTTT
1 AGGGTTT
27680716 AGGGTTT
1 AGGGTTT
* *
27680723 AAAGGCTTA
1 --AGGGTTT
*
27680732 AGGATTT
1 AGGGTTT
*
27680739 A-GTTTCT
1 AGGGTT-T
*
27680746 AGAGTTT
1 AGGGTTT
*
27680753 AAGGTTTT
1 -AGGGTTT
27680761 AGGGTTT
1 AGGGTTT
*
27680768 ATGGTTT
1 AGGGTTT
*
27680775 GGGGTTT
1 AGGGTTT
*
27680782 AAAGGTTT
1 -AGGGTTT
* **
27680790 AAGGAAT
1 AGGGTTT
*
27680797 A--GTTC
1 AGGGTTT
27680802 ATGGG-TT
1 A-GGGTTT
*
27680809 AGGATTT
1 AGGGTTT
27680816 AGGGGTTT
1 A-GGGTTT
*
27680824 -GGCTTT
1 AGGGTTT
**
27680830 AGATTTT
1 AGGGTTT
*
27680837 AAGGTTT
1 AGGGTTT
*
27680844 AGGGATT
1 AGGGTTT
*
27680851 AGGCTTT
1 AGGGTTT
*
27680858 AGAGTTT
1 AGGGTTT
27680865 AGGGTTT
1 AGGGTTT
27680872 A
1 A
27680873 AGGGCTAAAA
Statistics
Matches: 126, Mismatches: 40, Indels: 26
0.66 0.21 0.14
Matches are distributed among these distances:
5 2 0.02
6 10 0.08
7 85 0.67
8 24 0.19
9 5 0.04
ACGTcount: A:0.23, C:0.03, G:0.32, T:0.42
Consensus pattern (7 bp):
AGGGTTT
Found at i:27680788 original size:15 final size:14
Alignment explanation
Indices: 27680687--27680790 Score: 75
Period size: 15 Copynumber: 7.1 Consensus size: 14
27680677 ATTTATTATC
*
27680687 AGGGTTTAGAGTTTT
1 AGGGTTTA-AGGTTT
*
27680702 AGGGTTTATGGTTT
1 AGGGTTTAAGGTTT
*
27680716 AGGGTTTAAAGGCTTA
1 AGGGTTT-AAGG-TTT
* *
27680732 AGGATTT-AGTTTCT
1 AGGGTTTAAGGTT-T
*
27680746 AGAGTTTAAGGTTTT
1 AGGGTTTAAGG-TTT
*
27680761 AGGGTTTATGGTTT
1 AGGGTTTAAGGTTT
*
27680775 GGGGTTTAAAGGTTT
1 AGGGTTT-AAGGTTT
27680790 A
1 A
27680791 AGGAATAGTT
Statistics
Matches: 68, Mismatches: 15, Indels: 12
0.72 0.16 0.13
Matches are distributed among these distances:
13 2 0.03
14 27 0.40
15 29 0.43
16 10 0.15
ACGTcount: A:0.22, C:0.02, G:0.32, T:0.44
Consensus pattern (14 bp):
AGGGTTTAAGGTTT
Found at i:27680855 original size:28 final size:28
Alignment explanation
Indices: 27680813--27680872 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
27680803 TGGGTTAGGA
* * *
27680813 TTTAGGGGTTTGGCTTTAGATTTTAAGG
1 TTTAGGGATTAGGCTTTAGAGTTTAAGG
*
27680841 TTTAGGGATTAGGCTTTAGAGTTTAGGG
1 TTTAGGGATTAGGCTTTAGAGTTTAAGG
27680869 TTTA
1 TTTA
27680873 AGGGCTAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.20, C:0.03, G:0.32, T:0.45
Consensus pattern (28 bp):
TTTAGGGATTAGGCTTTAGAGTTTAAGG
Found at i:27681907 original size:40 final size:40
Alignment explanation
Indices: 27681821--27681914 Score: 116
Period size: 40 Copynumber: 2.4 Consensus size: 40
27681811 TTTTTTGCAG
* *
27681821 CATTTTTCAAAAAGCACCGCTAATGGTTGACCTATAGTGG
1 CATTTTTCAAAAAGCACCGCTAATGGTTGACCTATAGCGA
* * * * * *
27681861 CGTTTTTTAAAAAGCGCCGCTAGTGTTTGATCTATAGCGA
1 CATTTTTCAAAAAGCACCGCTAATGGTTGACCTATAGCGA
27681901 CATTTTTCAAAAAG
1 CATTTTTCAAAAAG
27681915 TGCCTCTAAT
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (40 bp):
CATTTTTCAAAAAGCACCGCTAATGGTTGACCTATAGCGA
Found at i:27682059 original size:40 final size:40
Alignment explanation
Indices: 27681976--27682063 Score: 104
Period size: 40 Copynumber: 2.2 Consensus size: 40
27681966 TTTTTTTGCA
* * * *
27681976 GCGTTTATCAAAAAGCGTCGCTTATACTCAATCTATAGCG
1 GCGTTTTTCAAAAAGCGTCGCTAATACTCAATATATAGAG
* * * *
27682016 GCGTTTTTCAGAAAGCGTCGCTAATGCTCGATATATGGAG
1 GCGTTTTTCAAAAAGCGTCGCTAATACTCAATATATAGAG
27682056 GCGTTTTT
1 GCGTTTTT
27682064 TAACCAAACG
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (40 bp):
GCGTTTTTCAAAAAGCGTCGCTAATACTCAATATATAGAG
Found at i:27682063 original size:156 final size:151
Alignment explanation
Indices: 27681707--27682051 Score: 343
Period size: 156 Copynumber: 2.3 Consensus size: 151
27681697 AATTTTTTTA
* * * * **
27681707 CGGCATTTTTCAAAAAGGGCCGCTAATGGTTGACCTATAGTAG-CATTTTTAAAAAGCGCCGCTA
1 CGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGATATATAG-AGACATTTTTAAAAAGCGCCGCTA
* * *
27681771 ATGCCACTAAAACTCAACAGAAAAGCGTTGTGCTTAATTTTTTTTTGCAGCATTTTTCAAAAAGC
65 ATGCCACTAAAACTCAACAGAAAAGCGCTATGCTTAATTTTTTTTTGCAGCATTTATCAAAAAGC
** **
27681836 ACCGCTAATGGTTGACCTATAG
130 ACCGCTAATACTCAACCTATAG
* * * * * * * * *
27681858 TGGCGTTTTTTAAAAAGCGCCGCTAGTGTTTGATCTATAGCGACATTTTTCAAAAAGTGCCTCTA
1 CGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGATATATAGAGACATTTTT-AAAAAGCGCCGCTA
* *
27681923 ATGCCACTAAAACTCAACATAAAACGACGGCACTATGCTTAA-TTTTTTTTGCAGCGTTTATCAA
65 ATGCCACTAAAACTCAACAGAAAA-G-C-G--CTATGCTTAATTTTTTTTTGCAGCATTTATCAA
** * *
27681987 AAAGCGTCGCTTATACTCAATCTATAG
125 AAAGCACCGCTAATACTCAACCTATAG
* *
27682014 CGGCGTTTTTCAGAAAGCGTCGCTAATGCTCGATATAT
1 CGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGATATAT
27682052 GGAGGCGTTT
Statistics
Matches: 156, Mismatches: 31, Indels: 9
0.80 0.16 0.05
Matches are distributed among these distances:
150 1 0.01
151 40 0.26
152 35 0.22
153 1 0.01
154 1 0.01
155 1 0.01
156 69 0.44
157 8 0.05
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (151 bp):
CGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGATATATAGAGACATTTTTAAAAAGCGCCGCTAA
TGCCACTAAAACTCAACAGAAAAGCGCTATGCTTAATTTTTTTTTGCAGCATTTATCAAAAAGCA
CCGCTAATACTCAACCTATAG
Found at i:27682995 original size:68 final size:67
Alignment explanation
Indices: 27682782--27683000 Score: 195
Period size: 68 Copynumber: 3.2 Consensus size: 67
27682772 GATGCCACAA
* ** * * * * *
27682782 CCTAGCTATGGTTTTACATGGTATGAACCCATGTTTAATGTCCTAATGAACTCCTTATGTTGCCA
1 CCTAGCTATGGTCTTACATAATATAAACCCATGTTTAATGTCTTAAAG-ACTCCATATATTGCCA
*
27682847 AAG
65 TAG
* * * * *** * * *
27682850 CCCAGTTATGGTCTTACACAATATAAACTCATGTTTAATGTTCTGGTAGACTCCATTTATTACCT
1 CCTAGCTATGGTCTTACATAATATAAACCCATGTTTAATG-TCTTAAAGACTCCATATATTGCCA
*
27682915 TAA
65 TAG
* * *
27682918 CCTAACTATGGTCTTACATAATATAAACCCATGTTTAATGTCTTAACAGACTTCATATATTGTCA
1 CCTAGCTATGGTCTTACATAATATAAACCCATGTTTAATGTCTTAA-AGACTCCATATATTGCCA
27682983 TAG
65 TAG
*
27682986 CTTAGCTATGGTCTT
1 CCTAGCTATGGTCTT
27683001 CCACATTAAA
Statistics
Matches: 113, Mismatches: 36, Indels: 4
0.74 0.24 0.03
Matches are distributed among these distances:
67 3 0.03
68 107 0.95
69 3 0.03
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (67 bp):
CCTAGCTATGGTCTTACATAATATAAACCCATGTTTAATGTCTTAAAGACTCCATATATTGCCAT
AG
Found at i:27693954 original size:14 final size:14
Alignment explanation
Indices: 27693935--27693963 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
27693925 TTTTTTTAAG
27693935 TCCAAAAATACTTA
1 TCCAAAAATACTTA
27693949 TCCAAAAATACTTA
1 TCCAAAAATACTTA
27693963 T
1 T
27693964 TTTAGTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.31
Consensus pattern (14 bp):
TCCAAAAATACTTA
Found at i:27695614 original size:48 final size:47
Alignment explanation
Indices: 27695540--27695768 Score: 214
Period size: 48 Copynumber: 4.8 Consensus size: 47
27695530 CTTGCACACT
* * * *
27695540 AAGTGCTCACATCATGGCCCGAAGCCAACA-CAATATATCTCGCACCCA
1 AAGTGCTAATATCATGGCCC-AAGCCAA-ATCAATATAACTCGCACCCG
* * *
27695588 AAGTGCTAATATCATGGCTCATAGCCAAATCAATGA-AGCTCGCACCTG
1 AAGTGCTAATATCATGGCCCA-AGCCAAATCAAT-ATAACTCGCACCCG
* * * * *
27695636 AAGTG-TCGATATCATGGCTCAAAGCCAAATTAAAATAACTCGCACCTG
1 AAGTGCT-AATATCATGGC-CCAAGCCAAATCAATATAACTCGCACCCG
*
27695684 AAGTGCCAATATCATGGCCCAAAGCCAAATCAA-AGTAACTCGCACCCG
1 AAGTGCTAATATCATGGCCC-AAGCCAAATCAATA-TAACTCGCACCCG
* *
27695732 AAGTTCCAATATCATGGCCCGAAGCCAAATCAATATA
1 AAGTGCTAATATCATGGCCC-AAGCCAAATCAATATA
27695769 TCCCCTAATG
Statistics
Matches: 152, Mismatches: 19, Indels: 20
0.80 0.10 0.10
Matches are distributed among these distances:
47 6 0.04
48 143 0.94
49 3 0.02
ACGTcount: A:0.36, C:0.28, G:0.16, T:0.20
Consensus pattern (47 bp):
AAGTGCTAATATCATGGCCCAAGCCAAATCAATATAACTCGCACCCG
Found at i:27695710 original size:96 final size:96
Alignment explanation
Indices: 27695550--27695761 Score: 250
Period size: 96 Copynumber: 2.2 Consensus size: 96
27695540 AAGTGCTCAC
* * * * * * *
27695550 ATCATGGCCCGAAGCCAACA-CAATATATCTCGCACCCAAAGTGCTAATATCATGGCTCATAGCC
1 ATCATGGCCCAAAGCCAA-ATTAAAATAACTCGCACCCAAAGTGCCAATATCATGGCCCAAAGCC
* * *
27695614 AAATCAATG-AAGCTCGCACCTGAAGTGT-CGAT
65 AAATCAAAGTAA-CTCGCACCCGAAGT-TCCAAT
* **
27695646 ATCATGGCTCAAAGCCAAATTAAAATAACTCGCACCTGAAGTGCCAATATCATGGCCCAAAGCCA
1 ATCATGGCCCAAAGCCAAATTAAAATAACTCGCACCCAAAGTGCCAATATCATGGCCCAAAGCCA
27695711 AATCAAAGTAACTCGCACCCGAAGTTCCAAT
66 AATCAAAGTAACTCGCACCCGAAGTTCCAAT
*
27695742 ATCATGGCCCGAAGCCAAAT
1 ATCATGGCCCAAAGCCAAAT
27695762 CAATATATCC
Statistics
Matches: 98, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
95 2 0.02
96 94 0.96
97 2 0.02
ACGTcount: A:0.36, C:0.28, G:0.17, T:0.19
Consensus pattern (96 bp):
ATCATGGCCCAAAGCCAAATTAAAATAACTCGCACCCAAAGTGCCAATATCATGGCCCAAAGCCA
AATCAAAGTAACTCGCACCCGAAGTTCCAAT
Found at i:27698344 original size:46 final size:45
Alignment explanation
Indices: 27698291--27698460 Score: 202
Period size: 46 Copynumber: 3.7 Consensus size: 45
27698281 AACCCGCCCC
*
27698291 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGC-TTCGCATCCA
* * * *
27698337 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAG-TTACA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--GCTTCGCATCCA
* * *
27698383 TTCA-CGAACTCGGACTCAACTCAACGAGTTC-GACATTCGCATCCA
1 -TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGC-TTCGCATCCA
27698428 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG
27698461 ATGCTCAACC
Statistics
Matches: 103, Mismatches: 14, Indels: 14
0.79 0.11 0.11
Matches are distributed among these distances:
43 1 0.01
44 4 0.04
45 30 0.29
46 62 0.60
47 4 0.04
48 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (45 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCTTCGCATCCA
Found at i:27698452 original size:91 final size:92
Alignment explanation
Indices: 27698296--27698464 Score: 304
Period size: 91 Copynumber: 1.8 Consensus size: 92
27698286 GCCCCTAAGT
* *
27698296 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
27698361 CGAGTTCGGATGCCTAGTTACATTCAC
66 CGAGTTCGGATGCCTAGTTACATTCAC
*
27698388 GAACTCGGACTCAACTCAACGAGTTC-GACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
27698452 CGAGTTCGGATGC
66 CGAGTTCGGATGC
27698465 TCAACCATCC
Statistics
Matches: 74, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
91 49 0.66
92 25 0.34
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.21
Consensus pattern (92 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTCAC
Found at i:27698922 original size:30 final size:30
Alignment explanation
Indices: 27698888--27698947 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
27698878 ATTTAATACG
27698888 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
27698918 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
27698948 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:27706492 original size:30 final size:30
Alignment explanation
Indices: 27706458--27706514 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
27706448 ATTTAATACG
27706458 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * * *
27706488 AACTTTTGCATAATTATACTTTTGCCC
1 AACTTTGGAAAAATTACACTTTTGCCC
27706515 TTAGGCTCGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.30, C:0.23, G:0.09, T:0.39
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:27710814 original size:28 final size:28
Alignment explanation
Indices: 27710774--27710829 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
27710764 GAGGAATACA
*
27710774 CAAAAGATAGCGTGCTTGTCAATTGCTG
1 CAAAAGATAGCGTGCTTCTCAATTGCTG
27710802 CAAAAGATAGCGTGCTTCTCAATTGCTG
1 CAAAAGATAGCGTGCTTCTCAATTGCTG
27710830 TCACAGTTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.29
Consensus pattern (28 bp):
CAAAAGATAGCGTGCTTCTCAATTGCTG
Found at i:27715470 original size:20 final size:22
Alignment explanation
Indices: 27715419--27715466 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
27715409 AAAAAAATAA
* *
27715419 AAAATTTATTTTTTTAATTTAT
1 AAAATTTATTTTTATAATATAT
27715441 GAAAATTTATTTTTATAATATAT
1 -AAAATTTATTTTTATAATATAT
27715464 AAA
1 AAA
27715467 TTATAGATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 3 0.13
23 20 0.87
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (22 bp):
AAAATTTATTTTTATAATATAT
Found at i:27715521 original size:17 final size:18
Alignment explanation
Indices: 27715499--27715537 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
27715489 AGGAAAAATA
27715499 AAAAAATT-TAAA-ATAAT
1 AAAAAATTCTAAATAT-AT
27715516 AAAAAATTCTAAATATAT
1 AAAAAATTCTAAATATAT
27715534 AAAA
1 AAAA
27715538 TTATAGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 8 0.40
18 10 0.50
19 2 0.10
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (18 bp):
AAAAAATTCTAAATATAT
Found at i:27718569 original size:25 final size:24
Alignment explanation
Indices: 27718536--27718703 Score: 90
Period size: 25 Copynumber: 6.8 Consensus size: 24
27718526 GTAAACACGG
27718536 AATTCTCTGAAAAGCCTTTGTGGC
1 AATTCTCTGAAAAGCCTTTGTGGC
*
27718560 AATTACTCTGGAACA-CCTTTGTGGC
1 AATT-CTCT-GAAAAGCCTTTGTGGC
* * * *
27718585 AATTTTTTTG-AAA-CATAGTTGTGGTG
1 AA-TTCTCTGAAAAGCCT--TTGTGG-C
*
27718611 AATTCTCTGAAAAGCCTTTGTGGAA
1 AATTCTCTGAAAAGCCTTTGTGG-C
* * * * *
27718636 AATACTTTGGAATGTCTTTGTGGC
1 AATTCTCTGAAAAGCCTTTGTGGC
* * *
27718660 GAATTTTCTGAAATGTCTTTGTGGC
1 -AATTCTCTGAAAAGCCTTTGTGGC
* *
27718685 GAATTCTTTGGAAAGCCTT
1 -AATTCTCTGAAAAGCCTT
27718704 CGTTATGAAC
Statistics
Matches: 109, Mismatches: 26, Indels: 17
0.72 0.17 0.11
Matches are distributed among these distances:
23 4 0.04
24 5 0.05
25 87 0.80
26 11 0.10
27 2 0.02
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.38
Consensus pattern (24 bp):
AATTCTCTGAAAAGCCTTTGTGGC
Found at i:27718657 original size:50 final size:50
Alignment explanation
Indices: 27718603--27718697 Score: 127
Period size: 50 Copynumber: 1.9 Consensus size: 50
27718593 TGAAACATAG
*
27718603 TTGTGGTGAATTCTCTGAAAAGCCTTTGTGGAAAATACTTTGGAATGTCT
1 TTGTGGCGAATTCTCTGAAAAGCCTTTGTGGAAAATACTTTGGAATGTCT
* * * ** *
27718653 TTGTGGCGAATTTTCTGAAATGTCTTTGTGGCGAATTCTTTGGAA
1 TTGTGGCGAATTCTCTGAAAAGCCTTTGTGGAAAATACTTTGGAA
27718698 AGCCTTCGTT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 38 1.00
ACGTcount: A:0.23, C:0.12, G:0.25, T:0.40
Consensus pattern (50 bp):
TTGTGGCGAATTCTCTGAAAAGCCTTTGTGGAAAATACTTTGGAATGTCT
Found at i:27718682 original size:75 final size:75
Alignment explanation
Indices: 27718535--27718703 Score: 196
Period size: 75 Copynumber: 2.3 Consensus size: 75
27718525 GGTAAACACG
* * *
27718535 GAATTCTCTGAAAAGCCTTTGTGGCAATTACTCTGGAACACCTTTGTGGCAATTTTTTTGAAACA
1 GAATTCTCTGAAAAGCCTTTGTGGAAAATACTCTGGAACACCTTTGTGGCAATTTTTCTGAAACA
*
27718600 TAGTTGTGGT
66 TAGTTGTGGC
* *** *
27718610 GAATTCTCTGAAAAGCCTTTGTGGAAAATACTTTGGAATGTCTTTGTGGCGAA-TTTTCTGAAAT
1 GAATTCTCTGAAAAGCCTTTGTGGAAAATACTCTGGAACACCTTTGTGGC-AATTTTTCTGAAAC
* **
27718674 GTCTTTGTGGC
65 ATAGTTGTGGC
* *
27718685 GAATTCTTTGGAAAGCCTT
1 GAATTCTCTGAAAAGCCTT
27718704 CGTTATGAAC
Statistics
Matches: 79, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
75 77 0.97
76 2 0.03
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.38
Consensus pattern (75 bp):
GAATTCTCTGAAAAGCCTTTGTGGAAAATACTCTGGAACACCTTTGTGGCAATTTTTCTGAAACA
TAGTTGTGGC
Done.