Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014306.1 Kokia drynarioides strain JFW-HI SEQ_129342, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 546136
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 40 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:364153 original size:18 final size:19
Alignment explanation
Indices: 364103--364170 Score: 77
Period size: 19 Copynumber: 3.6 Consensus size: 19
364093 ACAAAAATTA
* *
364103 CAAAATAATTTTCAAAAATT
1 CAAAAT-ATTTTTAAAAATC
*
364123 TAAAATAATTTTT-AAAATC
1 CAAAAT-ATTTTTAAAAATC
364142 CAAAATATTTTTAAAAATC
1 CAAAATATTTTTAAAAATC
364161 CAAAAT-TTTT
1 CAAAATATTTT
364171 ATTTTTAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
18 10 0.23
19 22 0.51
20 11 0.26
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (19 bp):
CAAAATATTTTTAAAAATC
Found at i:364629 original size:6 final size:6
Alignment explanation
Indices: 364620--364693 Score: 53
Period size: 6 Copynumber: 12.0 Consensus size: 6
364610 CAATTTTATT
* * *
364620 TTTAAA TTT-AT TTTAAG TTTAAA TTTAAA TTT-AT TTTAAA TTTAAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA
* *
364667 TTTTCTAAA CTTAAT TTTAAA TTTAAA
1 --TT-TAAA TTTAAA TTTAAA TTTAAA
364694 AAGTCTATTT
Statistics
Matches: 53, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
5 8 0.15
6 35 0.66
7 4 0.08
9 5 0.09
10 1 0.02
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:364646 original size:23 final size:23
Alignment explanation
Indices: 364620--364693 Score: 85
Period size: 23 Copynumber: 3.0 Consensus size: 23
364610 CAATTTTATT
*
364620 TTTAAATTTATTTTAAGTTTAAA
1 TTTAAATTTATTTTAAATTTAAA
364643 TTTAAATTTATTTTAAATTTAAAA
1 TTTAAATTTATTTTAAATTT-AAA
*
364667 TTTTCTAAACTTAATTTTAAATTTAAA
1 --TT-TAAA-TTTATTTTAAATTTAAA
364694 AAGTCTATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
23 19 0.43
24 3 0.07
26 2 0.05
27 7 0.16
28 13 0.30
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (23 bp):
TTTAAATTTATTTTAAATTTAAA
Found at i:364664 original size:17 final size:17
Alignment explanation
Indices: 364614--364665 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
364604 TAAACCCAAT
*
364614 TTTATTTTTAAATTT-AT
1 TTTA-TTTTAAATTTAAA
*
364631 TTTAAGTTTAAATTTAAA
1 TTT-ATTTTAAATTTAAA
364649 TTTATTTTAAATTTAAA
1 TTTATTTTAAATTTAAA
364666 ATTTTCTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 25 0.83
18 5 0.17
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
TTTATTTTAAATTTAAA
Found at i:366258 original size:59 final size:59
Alignment explanation
Indices: 366193--366432 Score: 224
Period size: 59 Copynumber: 4.1 Consensus size: 59
366183 AGAAATCATG
* * * * ** *
366193 TTTGACCTCCAAATTTTTTAAAACTTACATTTTTA-CGCTAAACTTTGCAAGGATTATAT
1 TTTGACC-CCAAATTTTTTAAAAATTATATTTTTACCCCTAAACTTTCCAAAAATTACAT
* *
366252 TTTGACCCTCAAA-CTTTCAAGAAATTATA-TTTTACCCCTAAACTTTCCAAAAATTACAT
1 TTTGACCC-CAAATTTTTTAA-AAATTATATTTTTACCCCTAAACTTTCCAAAAATTACAT
* * * **
366311 TTTGACCCCAAATTTCTTAAAAGTTATATTTTGACCTTTAAACTTTCCAAAAATTACAT
1 TTTGACCCCAAATTTTTTAAAAATTATATTTTTACCCCTAAACTTTCCAAAAATTACAT
* * * * * *
366370 TTT-CCCCCAAA-CTTTCAAAAATTAAATTTTTATCCCTAAACTTT-CAAAAATCACAT
1 TTTGACCCCAAATTTTTTAAAAATTATATTTTTACCCCTAAACTTTCCAAAAATTACAT
366426 TTT-ACCC
1 TTTGACCC
366433 TCGTACTTCC
Statistics
Matches: 148, Mismatches: 28, Indels: 13
0.78 0.15 0.07
Matches are distributed among these distances:
56 17 0.11
57 24 0.16
58 29 0.20
59 78 0.53
ACGTcount: A:0.35, C:0.22, G:0.04, T:0.39
Consensus pattern (59 bp):
TTTGACCCCAAATTTTTTAAAAATTATATTTTTACCCCTAAACTTTCCAAAAATTACAT
Found at i:366446 original size:57 final size:54
Alignment explanation
Indices: 366221--366508 Score: 182
Period size: 59 Copynumber: 5.0 Consensus size: 54
366211 TAAAACTTAC
** * * * * *
366221 ATTTTTACGCTAAACTTTGCAAGGATTATATTTTGACCCTCAAACTTTCAAGAAATTAT
1 ATTTTTAC-CTAAACTTT-CAAAAATTACATTTT--CCCCCAAACTTCCAA-AAATCAA
* * * * * *
366280 A-TTTTACCCCTAAACTTTCCAAAAATTACATTTTGACCCCAAATTTCTTAAAAGTTAT
1 ATTTTTA--CCTAAACTTT-CAAAAATTACATTTT-CCCCCAAACTTC-CAAAAATCAA
* * *
366338 ATTTTGACCTTTAAACTTTCCAAAAATTACATTTTCCCCCAAACTTTCAAAAATTAA
1 ATTTTTACC--TAAACTTT-CAAAAATTACATTTTCCCCCAAACTTCCAAAAATCAA
* * ** *
366395 ATTTTTATCCCTAAACTTTCAAAAATCACATTTTACCCTCGTACTTCCAAAAATCAC
1 ATTTTTA--CCTAAACTTTCAAAAATTACATTTT-CCCCCAAACTTCCAAAAATCAA
* *
366452 ATTTTTACCTCGAACTTCTCAAAAATTACATTTTTTCCCCTAAACTTCCAAAAATCA
1 ATTTTTACCT-AAACTT-TCAAAAATTACA--TTTTCCCCCAAACTTCCAAAAATCA
366509 CCACTTTACC
Statistics
Matches: 184, Mismatches: 32, Indels: 27
0.76 0.13 0.11
Matches are distributed among these distances:
55 3 0.02
56 19 0.10
57 57 0.31
58 46 0.25
59 58 0.32
60 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.04, T:0.37
Consensus pattern (54 bp):
ATTTTTACCTAAACTTTCAAAAATTACATTTTCCCCCAAACTTCCAAAAATCAA
Found at i:366474 original size:86 final size:85
Alignment explanation
Indices: 366355--366522 Score: 232
Period size: 86 Copynumber: 2.0 Consensus size: 85
366345 CCTTTAAACT
* * *
366355 TTCCAAAAATTACATTTTCCCCCAAACTTTCAAAAATTAAATTTTTAT-CCCTAAACTTTCAAAA
1 TTCCAAAAATCACATTTTACCCCAAACTTTCAAAAATTAAATTTTT-TCCCCTAAACTTCCAAAA
*
366419 ATCA-CATTTTACCCTCGTAC
65 ATCACCACTTTACCCTCGTAC
* * *
366439 TTCCAAAAATCACATTTTTACCTCGAACTTCTCAAAAATTACATTTTTTCCCCTAAACTTCCAAA
1 TTCCAAAAATCACA-TTTTACCCCAAACTT-TCAAAAATTAAATTTTTTCCCCTAAACTTCCAAA
366504 AATCACCACTTTACCCTCG
64 AATCACCACTTTACCCTCG
366523 AGCATCCTAA
Statistics
Matches: 73, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
84 13 0.18
85 13 0.18
86 35 0.48
87 12 0.16
ACGTcount: A:0.35, C:0.29, G:0.02, T:0.35
Consensus pattern (85 bp):
TTCCAAAAATCACATTTTACCCCAAACTTTCAAAAATTAAATTTTTTCCCCTAAACTTCCAAAAA
TCACCACTTTACCCTCGTAC
Found at i:366486 original size:29 final size:28
Alignment explanation
Indices: 366212--366506 Score: 188
Period size: 29 Copynumber: 10.2 Consensus size: 28
366202 CAAATTTTTT
*
366212 AAAACTTACATTTTTACGCT-AAACTTTGC
1 AAAAATTACATTTTTAC-CTCAAACTTT-C
** * *
366241 AAGGATTATATTTTGACCCTCAAACTTTC
1 AAAAATTACATTTTTA-CCTCAAACTTTC
* *
366270 AAGAAATTATA-TTTTACCCCTAAACTTTCC
1 AA-AAATTACATTTTTACCTC-AAACTTT-C
* *
366300 AAAAATTACATTTTGACCCCAAA-TTTC
1 AAAAATTACATTTTTACCTCAAACTTTC
* * * *
366327 TTAAAAGTTATATTTTGACCTTTAAACTTTCC
1 --AAAAATTACATTTTTACC-TCAAACTTT-C
* *
366359 AAAAATTACA-TTTTCCCCCAAACTTTC
1 AAAAATTACATTTTTACCTCAAACTTTC
*
366386 AAAAATTAAATTTTTATCC-CTAAACTTTC
1 AAAAATTACATTTTTA-CCTC-AAACTTTC
* ** *
366415 AAAAATCACA-TTTTACCCTCGTACTTCC
1 AAAAATTACATTTTTA-CCTCAAACTTTC
* *
366443 AAAAATCACATTTTTACCTCGAACTTCTC
1 AAAAATTACATTTTTACCTCAAACTT-TC
* * *
366472 AAAAATTACATTTTTTCCCCTAAACTTCC
1 AAAAATTACATTTTTACCTC-AAACTTTC
366501 AAAAAT
1 AAAAAT
366507 CACCACTTTA
Statistics
Matches: 212, Mismatches: 36, Indels: 36
0.75 0.13 0.13
Matches are distributed among these distances:
27 11 0.05
28 49 0.23
29 107 0.50
30 41 0.19
31 3 0.01
32 1 0.00
ACGTcount: A:0.36, C:0.23, G:0.04, T:0.37
Consensus pattern (28 bp):
AAAAATTACATTTTTACCTCAAACTTTC
Found at i:366544 original size:86 final size:84
Alignment explanation
Indices: 366360--366547 Score: 213
Period size: 86 Copynumber: 2.2 Consensus size: 84
366350 AAACTTTCCA
* *
366360 AAAATTA-CATTTTCCCCCAAACTTTCAAAAATTAAATTTTTATCCCTAAACTTTCAAAAATCAC
1 AAAATTACCATTTTACCCCAAACTTTCAAAAATTAAATTTTTATCCCTAAACTTCCAAAAATCAC
* *
366424 ATTTTACCCTCGTACTTCC
66 ACTTTACCCTCGTACATCC
* * * *
366443 AAAAAT-CACATTTTTACCTCGAACTTCTCAAAAATTACATTTTT-TCCCCTAAACTTCCAAAAA
1 AAAATTAC-CA-TTTTACCCCAAACTT-TCAAAAATTAAATTTTTAT-CCCTAAACTTCCAAAAA
366506 TCACCACTTTACCCTCG-AGCATCC
62 TCA-CACTTTACCCTCGTA-CATCC
*
366530 TAAATTACCATTTTACCC
1 AAAATTACCATTTTACCC
366548 TTAATTCTCC
Statistics
Matches: 86, Mismatches: 11, Indels: 13
0.78 0.10 0.12
Matches are distributed among these distances:
83 5 0.06
84 2 0.02
85 13 0.15
86 43 0.50
87 22 0.26
88 1 0.01
ACGTcount: A:0.35, C:0.29, G:0.02, T:0.34
Consensus pattern (84 bp):
AAAATTACCATTTTACCCCAAACTTTCAAAAATTAAATTTTTATCCCTAAACTTCCAAAAATCAC
ACTTTACCCTCGTACATCC
Found at i:369012 original size:21 final size:23
Alignment explanation
Indices: 368988--369036 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
368978 ATTAAAATTA
368988 AAAAAAATAA-TT-TAAAAAAAT
1 AAAAAAATAATTTGTAAAAAAAT
* *
369009 AAAAATATAATTTGTTAAAAAAT
1 AAAAAAATAATTTGTAAAAAAAT
369032 AAAAA
1 AAAAA
369037 CATGGAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 9 0.38
22 2 0.08
23 13 0.54
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (23 bp):
AAAAAAATAATTTGTAAAAAAAT
Found at i:374818 original size:17 final size:16
Alignment explanation
Indices: 374798--374835 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 16
374788 CAATTTACAC
374798 ATCAGCATTCCAAGCAA
1 ATCAG-ATTCCAAGCAA
374815 ATCAAGATTCCAAGCAA
1 ATC-AGATTCCAAGCAA
374832 ATCA
1 ATCA
374836 AGAAACATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 1 0.05
17 17 0.85
18 2 0.10
ACGTcount: A:0.45, C:0.26, G:0.11, T:0.18
Consensus pattern (16 bp):
ATCAGATTCCAAGCAA
Found at i:374836 original size:17 final size:17
Alignment explanation
Indices: 374804--374838 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
374794 ACACATCAGC
374804 ATTCCAAGCAAATCAAG
1 ATTCCAAGCAAATCAAG
374821 ATTCCAAGCAAATCAAG
1 ATTCCAAGCAAATCAAG
374838 A
1 A
374839 AACATGTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.23, G:0.11, T:0.17
Consensus pattern (17 bp):
ATTCCAAGCAAATCAAG
Found at i:375075 original size:3 final size:3
Alignment explanation
Indices: 375067--375102 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
375057 AACTAAGTGC
375067 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
375103 ATAAAAAACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:382250 original size:46 final size:50
Alignment explanation
Indices: 382169--382287 Score: 124
Period size: 50 Copynumber: 2.5 Consensus size: 50
382159 TATATAAATT
* * *
382169 ATATGGTGTAATACTAGTTATGCACATTGGC-A-A-TATTT-TAGTTATA
1 ATATGGTGTACTACTAATTATGTACATTGGCAATATTATTTGTAGTTATA
* * * *
382215 ATGTTGTGTACTACTAATTATGTAC-TTGGATAATATTATTTGTAGTTATC
1 ATATGGTGTACTACTAATTATGTACATTGG-CAATATTATTTGTAGTTATA
382265 ATATGGTGTACTACTAATT-TGTA
1 ATATGGTGTACTACTAATTATGTA
382288 ATAATAACTG
Statistics
Matches: 59, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
45 4 0.07
46 20 0.34
47 1 0.02
48 1 0.02
49 9 0.15
50 24 0.41
ACGTcount: A:0.30, C:0.08, G:0.17, T:0.45
Consensus pattern (50 bp):
ATATGGTGTACTACTAATTATGTACATTGGCAATATTATTTGTAGTTATA
Found at i:382662 original size:13 final size:14
Alignment explanation
Indices: 382628--382659 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
382618 AAATATTAAC
*
382628 TTTTTCAGAAATCA
1 TTTTTCAAAAATCA
382642 TTTTTCAAAAATCA
1 TTTTTCAAAAATCA
382656 TTTT
1 TTTT
382660 CAATCAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.34, C:0.12, G:0.03, T:0.50
Consensus pattern (14 bp):
TTTTTCAAAAATCA
Found at i:383092 original size:14 final size:14
Alignment explanation
Indices: 383069--383108 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
383059 GTACTTAATA
*
383069 ATAATGTTTAATTT
1 ATAATTTTTAATTT
*
383083 ATAATTTTTAAATT
1 ATAATTTTTAATTT
383097 ATAA-TTTTAATT
1 ATAATTTTTAATT
383109 GAAAGTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 7 0.30
14 16 0.70
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (14 bp):
ATAATTTTTAATTT
Found at i:384115 original size:20 final size:21
Alignment explanation
Indices: 384090--384130 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
384080 AGATTTAATC
*
384090 TTAAAAGGA-TTTAATAAAAA
1 TTAAAAGGACTTAAATAAAAA
384110 TTAAAAGGACTTAAATAAAAA
1 TTAAAAGGACTTAAATAAAAA
384131 CAAAATAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.61, C:0.02, G:0.10, T:0.27
Consensus pattern (21 bp):
TTAAAAGGACTTAAATAAAAA
Found at i:384135 original size:20 final size:20
Alignment explanation
Indices: 384092--384135 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
384082 ATTTAATCTT
* *
384092 AAAAGGATTTAATAAAAATT
1 AAAAGGATTAAATAAAAATC
384112 AAAAGGACTTAAATAAAAA-C
1 AAAAGGA-TTAAATAAAAATC
384132 AAAA
1 AAAA
384136 TAGAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.66, C:0.05, G:0.09, T:0.20
Consensus pattern (20 bp):
AAAAGGATTAAATAAAAATC
Found at i:385027 original size:7 final size:7
Alignment explanation
Indices: 385015--385048 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
385005 TTTCAAAATG
385015 TAAATAA
1 TAAATAA
385022 TAAATAA
1 TAAATAA
385029 TAAATAA
1 TAAATAA
*
385036 AAAATAA
1 TAAATAA
*
385043 AAAATA
1 TAAATA
385049 TATATGTATG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (7 bp):
TAAATAA
Found at i:385768 original size:18 final size:18
Alignment explanation
Indices: 385745--385782 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
385735 ACTTTAGGAA
385745 GATAGGATTTAGCGTCGT
1 GATAGGATTTAGCGTCGT
*
385763 GATAGGATTTAGCGTTGT
1 GATAGGATTTAGCGTCGT
385781 GA
1 GA
385783 CTTCATCTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.08, G:0.34, T:0.34
Consensus pattern (18 bp):
GATAGGATTTAGCGTCGT
Found at i:385973 original size:43 final size:43
Alignment explanation
Indices: 385925--386149 Score: 150
Period size: 46 Copynumber: 5.0 Consensus size: 43
385915 AGAGTTATGT
385925 GTGGCTTCAATATGCCCCTAC-TGAATTAGGGGTAAAAGATTGG
1 GTGGCTTCAATATG-CCCTACTTGAATTAGGGGTAAAAGATTGG
* *
385968 GTGGCTTCAATCTGCCCTACTTGACTTAGGGGTAAAAGATTGGATG
1 GTGGCTTCAATATGCCCTACTTGAATTAGGGGTAAAAGATT-G--G
* * * * *
386014 GTGGCTTTAATCTACCTCT-CTTGACTTTAGGGGTAAAAGTTTGG
1 GTGGCTTCAATATGCC-CTACTTGA-ATTAGGGGTAAAAGATTGG
* * * * * *
386058 ATGATGACTTCAGTCTG-CCGATCTTGACTTAGGGGTAGAAGATTGG
1 --G-TGGCTTCAATATGCCCTA-CTTGAATTAGGGGTAAAAGATTGG
* * * * *
386104 ATAGTGACTTCAATCTGTCCTTCTTGACTTAGGGGTAAAAGATTGG
1 ---GTGGCTTCAATATGCCCTACTTGAATTAGGGGTAAAAGATTGG
386150 ATGGTGATAT
Statistics
Matches: 149, Mismatches: 20, Indels: 23
0.78 0.10 0.12
Matches are distributed among these distances:
42 6 0.04
43 32 0.21
44 2 0.01
45 1 0.01
46 74 0.50
47 34 0.23
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.32
Consensus pattern (43 bp):
GTGGCTTCAATATGCCCTACTTGAATTAGGGGTAAAAGATTGG
Found at i:386037 original size:46 final size:46
Alignment explanation
Indices: 385950--386156 Score: 253
Period size: 46 Copynumber: 4.5 Consensus size: 46
385940 CCCTACTGAA
*
385950 TTAGGGGTAAAAGATT-G--GGTGGCTTCAATCTGCC-CTACTTGAC
1 TTAGGGGTAAAAGATTGGATGGTGACTTCAATCTGCCTCT-CTTGAC
* * *
385993 TTAGGGGTAAAAGATTGGATGGTGGCTTTAATCTACCTCTCTTGAC
1 TTAGGGGTAAAAGATTGGATGGTGACTTCAATCTGCCTCTCTTGAC
* * * **
386039 TTTAGGGGTAAAAGTTTGGATGATGACTTCAGTCTGCCGATCTTGAC
1 -TTAGGGGTAAAAGATTGGATGGTGACTTCAATCTGCCTCTCTTGAC
* *
386086 TTAGGGGTAGAAGATTGGATAGTGACTTCAATCTGTCCT-TCTTGAC
1 TTAGGGGTAAAAGATTGGATGGTGACTTCAATCTG-CCTCTCTTGAC
386132 TTAGGGGTAAAAGATTGGATGGTGA
1 TTAGGGGTAAAAGATTGGATGGTGA
386157 TATAACTTCA
Statistics
Matches: 140, Mismatches: 18, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
43 16 0.11
44 1 0.01
46 81 0.58
47 42 0.30
ACGTcount: A:0.25, C:0.14, G:0.29, T:0.33
Consensus pattern (46 bp):
TTAGGGGTAAAAGATTGGATGGTGACTTCAATCTGCCTCTCTTGAC
Found at i:386084 original size:93 final size:91
Alignment explanation
Indices: 385950--386152 Score: 261
Period size: 93 Copynumber: 2.2 Consensus size: 91
385940 CCCTACTGAA
* *
385950 TTAGGGGTAAAAGATTGG--GTGGCTTCAATCTGCCCTACTTGACTTAGGGGTAAAAGATTGGAT
1 TTAGGGGTAAAAGATTGGATGTGACTTCAATCTGCCATACTTGACTTAGGGGTAAAAGATTGGAT
* * *
386013 GGTGGCTTTAATCT-ACCTCTCTTGAC
66 AGTGACTTCAATCTGACCT-TCTTGAC
* * *
386039 TTTAGGGGTAAAAGTTTGGATGATGACTTCAGTCTGCCGAT-CTTGACTTAGGGGTAGAAGATTG
1 -TTAGGGGTAAAAGATTGGATG-TGACTTCAATCTGCC-ATACTTGACTTAGGGGTAAAAGATTG
*
386103 GATAGTGACTTCAATCTGTCCTTCTTGAC
63 GATAGTGACTTCAATCTGACCTTCTTGAC
386132 TTAGGGGTAAAAGATTGGATG
1 TTAGGGGTAAAAGATTGGATG
386153 GTGATATAAC
Statistics
Matches: 98, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
90 17 0.17
92 21 0.21
93 56 0.57
94 4 0.04
ACGTcount: A:0.25, C:0.14, G:0.28, T:0.33
Consensus pattern (91 bp):
TTAGGGGTAAAAGATTGGATGTGACTTCAATCTGCCATACTTGACTTAGGGGTAAAAGATTGGAT
AGTGACTTCAATCTGACCTTCTTGAC
Found at i:386464 original size:189 final size:188
Alignment explanation
Indices: 386248--386861 Score: 820
Period size: 189 Copynumber: 3.2 Consensus size: 188
386238 AGATATAAAA
* * * *
386248 TTTGGTGCTTCACTCTACTCCACTATAACCTTAGGGACGTTGAGAGCTGCTACCTGTTTTGACCC
1 TTTGGTGCTTCACTCCACTCTACTATAACCTCAGGGACGTTGAGATCTGCTACCTGTTTTGACCC
* * * *
386313 ACTTCTCTGTACCTCACCAGGAAGATGGGATTTGAAGTCTCACTTCACTCAATTATAACCTCAAG
66 ACTTCTCTGTACCTTACCAGGAAGATGGGATTTGAAGTCTCACTTCACTCCACTGTAACCTCAAG
* * *
386378 GACGTTGAGCTCTGCTTTATTGTTTTAATCTGACCTACTGCAATTCAGGCGTATAGGGT
131 GACGTTGAGCTCTGCTTTATTATTTTAATCTGACCCACTGTAATTCAGG-GTATAGGGT
* * * * * *
386437 TTTGGTGCTTCACTTCACTCTACTATAACATCAGGAACATTGAGATCTGCTACCTATTTTAACCC
1 TTTGGTGCTTCACTCCACTCTACTATAACCTCAGGGACGTTGAGATCTGCTACCTGTTTTGACCC
* * * *
386502 ACTTCTCTATACCTTACCAGGAAGATGGGATTTGAAGTTTCACTTCACCCCACTGTAACCTCAGG
66 ACTTCTCTGTACCTTACCAGGAAGATGGGATTTGAAGTCTCACTTCACTCCACTGTAACCTCAAG
* *
386567 GACGTTGAGCTCTGCTTCATTATTTTAATCTGACCCACTGTAATTCAGGGGTATAAGGT
131 GACGTTGAGCTCTGCTTTATTATTTTAATCTGACCCACTGTAATTCA-GGGTATAGGGT
* * ** *
386626 TTTGGTGCTTCACTCCACT-TCACTATAACTTCAGGGAC-ATGAAGATCTATTACATGTTTTGAC
1 TTTGGTGCTTCACTCCACTCT-ACTATAACCTCAGGGACGTTG-AGATCTGCTACCTGTTTTGAC
* * *
386689 CCACTTCTCTGTACCTTACCAAGAAGATGAGATTTGAAGTCTCACTCCACTCCACTGTAACCTCA
64 CCACTTCTCTGTACCTTACCAGGAAGATGGGATTTGAAGTCTCACTTCACTCCACTGTAACCTCA
* * * *
386754 AGGACGTTGAGCTCTGCTTTATTACTTTAAT-TCAACCCACTATAATTTAAGGGTATAGGGT
129 AGGACGTTGAGCTCTGCTTTATTATTTTAATCT-GACCCACTGTAA-TTCAGGGTATAGGGT
* *
386815 TTTGGTGCTTCTCTCCACTCTACTGTAACCTCAGGGACGTTGAGATC
1 TTTGGTGCTTCACTCCACTCTACTATAACCTCAGGGACGTTGAGATC
386862 CACTTTTGTT
Statistics
Matches: 369, Mismatches: 49, Indels: 14
0.85 0.11 0.03
Matches are distributed among these distances:
188 4 0.01
189 357 0.97
190 8 0.02
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.33
Consensus pattern (188 bp):
TTTGGTGCTTCACTCCACTCTACTATAACCTCAGGGACGTTGAGATCTGCTACCTGTTTTGACCC
ACTTCTCTGTACCTTACCAGGAAGATGGGATTTGAAGTCTCACTTCACTCCACTGTAACCTCAAG
GACGTTGAGCTCTGCTTTATTATTTTAATCTGACCCACTGTAATTCAGGGTATAGGGT
Found at i:386661 original size:94 final size:93
Alignment explanation
Indices: 386352--386663 Score: 254
Period size: 94 Copynumber: 3.3 Consensus size: 93
386342 ATTTGAAGTC
* * * * *
386352 TCACTTCACTCAATTATAACCTCAAGGACGTTGAGCTCTGCTTTATTGTTTTAATCTGACCTACT
1 TCACTTCACTC-ACTATAACCTCAGGGACGTTGAGCTCTGCTTCATTATTTTAATCTGACCCACT
* *
386417 GCAATTCAGGCGTATAGGGTTTTGGTGCT
65 GTAATTCAGGAGTATAGGGTTTTGGTGCT
* * * * * * ** * *
386446 TCACTTCACTCTACTATAACATCAGGAACATTGAGATCTGCTAC-CTATTTTAA-CCCACTTCTC
1 TCACTTCACTC-ACTATAACCTCAGGGACGTTGAGCTCTGCTTCATTATTTTAATCTGAC-CCAC
* * * ** *
386509 TATACCTTACCAGGAAG-AT-GGGATTTGAAGTT
64 TGTA-ATT--CAGG-AGTATAGGGTTTTGGTGCT
* *
386541 TCACTTCACCCCACTGTAACCTCAGGGACGTTGAGCTCTGCTTCATTATTTTAATCTGACCCACT
1 TCACTTCA-CTCACTATAACCTCAGGGACGTTGAGCTCTGCTTCATTATTTTAATCTGACCCACT
* *
386606 GTAATTCAGGGGTATAAGGTTTTGGTGCT
65 GTAATTCAGGAGTATAGGGTTTTGGTGCT
* *
386635 TCACTCCACTTCACTATAACTTCAGGGAC
1 TCACTTCAC-TCACTATAACCTCAGGGAC
386664 ATGAAGATCT
Statistics
Matches: 159, Mismatches: 48, Indels: 22
0.69 0.21 0.10
Matches are distributed among these distances:
92 4 0.03
93 17 0.11
94 68 0.43
95 45 0.28
96 21 0.13
97 4 0.03
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.34
Consensus pattern (93 bp):
TCACTTCACTCACTATAACCTCAGGGACGTTGAGCTCTGCTTCATTATTTTAATCTGACCCACTG
TAATTCAGGAGTATAGGGTTTTGGTGCT
Found at i:387038 original size:42 final size:42
Alignment explanation
Indices: 386992--387073 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
386982 CCTTTACAAC
* *
386992 TTTGAGATTCGTCTTTGCGGCTTCAATCTACTTCTCCTCAGT
1 TTTGAGATTCGCCTTTGCGGCTTCAAGCTACTTCTCCTCAGT
* *
387034 TTTGAGATTTGCCTTTGTGGCTTCAAGCTACTTCTCCTCA
1 TTTGAGATTCGCCTTTGCGGCTTCAAGCTACTTCTCCTCA
387074 TCTTCGAGGT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.15, C:0.26, G:0.17, T:0.43
Consensus pattern (42 bp):
TTTGAGATTCGCCTTTGCGGCTTCAAGCTACTTCTCCTCAGT
Found at i:387125 original size:49 final size:49
Alignment explanation
Indices: 387081--387264 Score: 208
Period size: 49 Copynumber: 3.8 Consensus size: 49
387071 TCATCTTCGA
* * *
387081 GGTATAAGATTCACCGTTGTGGCTTTAATCTTTCCCTTC-ACATCTCTAG
1 GGTATAAGATTCGCCGTTGCGGCTTCAATCTTTCCC-TCAACATCTCTAG
* * * * * *
387130 GGTATAAGGTTCGCCTTTGCAGCTTCAATCTTTCCCTCTATATCTCTAA
1 GGTATAAGATTCGCCGTTGCGGCTTCAATCTTTCCCTCAACATCTCTAG
* * *
387179 GGTATAAGATTTGTCGTTGCGGCTTCAATCTTTCCCTCAACATCTTTAG
1 GGTATAAGATTCGCCGTTGCGGCTTCAATCTTTCCCTCAACATCTCTAG
* * * *
387228 GGTACAATATTCGCCATTGAGGCTTCAATCTTTCCCT
1 GGTATAAGATTCGCCGTTGCGGCTTCAATCTTTCCCT
387265 TCATGTCTTC
Statistics
Matches: 111, Mismatches: 23, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
48 2 0.02
49 109 0.98
ACGTcount: A:0.21, C:0.25, G:0.16, T:0.38
Consensus pattern (49 bp):
GGTATAAGATTCGCCGTTGCGGCTTCAATCTTTCCCTCAACATCTCTAG
Found at i:387197 original size:98 final size:98
Alignment explanation
Indices: 387080--387264 Score: 248
Period size: 98 Copynumber: 1.9 Consensus size: 98
387070 CTCATCTTCG
* * * *
387080 AGGTATAAGATTCACCGTTGTGGCTTTAATCTTTCCCTTC-ACATCTCTAGGGTATAAGGTTCGC
1 AGGTATAAGATTCACCGTTGCGGCTTCAATCTTTCCC-TCAACATCTCTAGGGTACAAGATTCGC
*
387144 CTTTGCA-GCTTCAATCTTTCCCTCTATATCTCTA
65 CATTG-AGGCTTCAATCTTTCCCTCTATATCTCTA
*** * *
387178 AGGTATAAGATTTGTCGTTGCGGCTTCAATCTTTCCCTCAACATCTTTAGGGTACAATATTCGCC
1 AGGTATAAGATTCACCGTTGCGGCTTCAATCTTTCCCTCAACATCTCTAGGGTACAAGATTCGCC
387243 ATTGAGGCTTCAATCTTTCCCT
66 ATTGAGGCTTCAATCTTTCCCT
387265 TCATGTCTTC
Statistics
Matches: 75, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
97 3 0.04
98 72 0.96
ACGTcount: A:0.21, C:0.25, G:0.16, T:0.38
Consensus pattern (98 bp):
AGGTATAAGATTCACCGTTGCGGCTTCAATCTTTCCCTCAACATCTCTAGGGTACAAGATTCGCC
ATTGAGGCTTCAATCTTTCCCTCTATATCTCTA
Found at i:387882 original size:113 final size:112
Alignment explanation
Indices: 387719--387936 Score: 328
Period size: 113 Copynumber: 1.9 Consensus size: 112
387709 TATCGTTAGA
* ** * * *
387719 CCACTAATCGTTATTTCAATGTAAAAATGCTTGAACATGATTGTAAGGTGGATAAAATTAAATTT
1 CCACTAACCGTTATTTCAATCAAAAAATGCTTGAACAAGATTGTAAGGTGGAAAAAACTAAATTT
*
387784 TATTGGAGGCAAAGCTCGCATGAATGAAAAAATTAAAAATAATTGGT
66 TATTGGAGGAAAAGCTCGCATGAATGAAAAAATTAAAAATAATTGGT
* * *
387831 CCACTAACCGTTATTTCGATACAAAAAATGCTTGAACAAGGTTGTAAGGTGGAAAAAACTGAATT
1 CCACTAACCGTTATTTCAAT-CAAAAAATGCTTGAACAAGATTGTAAGGTGGAAAAAACTAAATT
*
387896 TTATTGGAGGAAAAGCTCGCATGAATGAAAAGATTAAAAAT
65 TTATTGGAGGAAAAGCTCGCATGAATGAAAAAATTAAAAAT
387937 GACAAACATT
Statistics
Matches: 94, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
112 18 0.19
113 76 0.81
ACGTcount: A:0.42, C:0.11, G:0.19, T:0.28
Consensus pattern (112 bp):
CCACTAACCGTTATTTCAATCAAAAAATGCTTGAACAAGATTGTAAGGTGGAAAAAACTAAATTT
TATTGGAGGAAAAGCTCGCATGAATGAAAAAATTAAAAATAATTGGT
Found at i:388262 original size:7 final size:7
Alignment explanation
Indices: 388246--388393 Score: 178
Period size: 7 Copynumber: 20.7 Consensus size: 7
388236 CGACCACTCC
388246 TTTTTC-
1 TTTTTCT
388252 TTTTTC-
1 TTTTTCT
388258 TTTTTCTT
1 TTTTTC-T
388266 TTCATTTCT
1 TT--TTTCT
*
388275 TCTTTCT
1 TTTTTCT
*
388282 TCTTTCT
1 TTTTTCT
388289 TTTTTCT
1 TTTTTCT
388296 TTTTTCT
1 TTTTTCT
388303 TTTTTCT
1 TTTTTCT
388310 TTTTTCT
1 TTTTTCT
388317 TTTTTCT
1 TTTTTCT
388324 TTTTTCT
1 TTTTTCT
388331 TTTTTCT
1 TTTTTCT
388338 TTTTTCT
1 TTTTTCT
388345 TTTTTCT
1 TTTTTCT
388352 TTTTT-T
1 TTTTTCT
388358 TTTCCTT-T
1 TTT--TTCT
*
388366 TCTTTCT
1 TTTTTCT
388373 TTTTTCT
1 TTTTTCT
388380 CTTTTTCT
1 -TTTTTCT
388388 CTTTTT
1 -TTTTT
388394 TTGGGTGAAA
Statistics
Matches: 130, Mismatches: 4, Indels: 14
0.88 0.03 0.09
Matches are distributed among these distances:
6 18 0.14
7 86 0.66
8 20 0.15
9 2 0.02
10 4 0.03
ACGTcount: A:0.01, C:0.18, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTTTCT
Found at i:388377 original size:1 final size:1
Alignment explanation
Indices: 388288--388360 Score: 65
Period size: 1 Copynumber: 73.0 Consensus size: 1
388278 TTCTTCTTTC
* * * * * * * * *
388288 TTTTTTCTTTTTTCTTTTTTCTTTTTTCTTTTTTCTTTTTTCTTTTTTCTTTTTTCTTTTTTCTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
388353 TTTTTTTT
1 TTTTTTTT
388361 CCTTTTCTTT
Statistics
Matches: 54, Mismatches: 18, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 54 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (1 bp):
T
Found at i:389216 original size:18 final size:17
Alignment explanation
Indices: 389195--389234 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
389185 GACTTTTTCA
*
389195 TTCTTTTCTCTATTTTTT
1 TTCTTTTCTCT-TTTATT
*
389213 TTCTTTTTTCTTTTATT
1 TTCTTTTCTCTTTTATT
389230 TTCTT
1 TTCTT
389235 AGGTTTCAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80
Consensus pattern (17 bp):
TTCTTTTCTCTTTTATT
Found at i:392788 original size:17 final size:17
Alignment explanation
Indices: 392766--392816 Score: 68
Period size: 16 Copynumber: 2.9 Consensus size: 17
392756 AAAGTCTTCC
392766 TCTTTCTCTTCTTCTTT
1 TCTTTCTCTTCTTCTTT
392783 TCTTTCT-TTCTTCTTT
1 TCTTTCTCTTCTTCTTT
392799 TCTCTTCTGGCTTCTTCT
1 TCT-TTCT--CTTCTTCT
392817 CCTCAATACC
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
16 12 0.40
17 11 0.37
20 7 0.23
ACGTcount: A:0.00, C:0.29, G:0.04, T:0.67
Consensus pattern (17 bp):
TCTTTCTCTTCTTCTTT
Found at i:392790 original size:21 final size:21
Alignment explanation
Indices: 392767--392806 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
392757 AAGTCTTCCT
*
392767 CTTTC-TCTTCTTCTTTTCTTT
1 CTTTCTTCTT-TTCTCTTCTTT
392788 CTTTCTTCTTTTCTCTTCT
1 CTTTCTTCTTTTCTCTTCT
392807 GGCTTCTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (21 bp):
CTTTCTTCTTTTCTCTTCTTT
Found at i:403667 original size:7 final size:7
Alignment explanation
Indices: 403655--403705 Score: 52
Period size: 7 Copynumber: 7.6 Consensus size: 7
403645 TCAGAAAAAG
403655 TCAACGA
1 TCAACGA
*
403662 TCAACGG
1 TCAACGA
*
403669 TCAAAG-
1 TCAACGA
*
403675 TCAACGG
1 TCAACGA
403682 TCAACGA
1 TCAACGA
*
403689 TCAAAG-
1 TCAACGA
403695 TCAACGA
1 TCAACGA
403702 TCAA
1 TCAA
403706 AGTAAACAGT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
6 10 0.28
7 26 0.72
ACGTcount: A:0.41, C:0.25, G:0.18, T:0.16
Consensus pattern (7 bp):
TCAACGA
Found at i:403676 original size:20 final size:20
Alignment explanation
Indices: 403651--403705 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
403641 TTTTTCAGAA
*
403651 AAAGTCAACGATCAACGGTC
1 AAAGTCAACGATCAACGATC
*
403671 AAAGTCAACGGTCAACGATC
1 AAAGTCAACGATCAACGATC
403691 AAAGTCAACGATCAA
1 AAAGTCAACGATCAA
403706 AGTAAACAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.44, C:0.24, G:0.18, T:0.15
Consensus pattern (20 bp):
AAAGTCAACGATCAACGATC
Found at i:403697 original size:13 final size:13
Alignment explanation
Indices: 403651--403708 Score: 64
Period size: 13 Copynumber: 4.4 Consensus size: 13
403641 TTTTTCAGAA
403651 AAAGTCAACGATC
1 AAAGTCAACGATC
* *
403664 AACGGTCAAAG-TC
1 AA-AGTCAACGATC
*
403677 AACGGTCAACGATC
1 AA-AGTCAACGATC
403691 AAAGTCAACGATC
1 AAAGTCAACGATC
403704 AAAGT
1 AAAGT
403709 AAACAGTCAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
13 29 0.74
14 10 0.26
ACGTcount: A:0.43, C:0.22, G:0.19, T:0.16
Consensus pattern (13 bp):
AAAGTCAACGATC
Found at i:403706 original size:33 final size:33
Alignment explanation
Indices: 403662--403725 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
403652 AAGTCAACGA
* * *
403662 TCAACGGTCAAAGTCAACGGTCAACGATCAAAG
1 TCAACGATCAAAGTAAACAGTCAACGATCAAAG
*
403695 TCAACGATCAAAGTAAACAGTCAACGGTCAA
1 TCAACGATCAAAGTAAACAGTCAACGATCAA
403726 TGTTCAAAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.42, C:0.23, G:0.19, T:0.16
Consensus pattern (33 bp):
TCAACGATCAAAGTAAACAGTCAACGATCAAAG
Found at i:403716 original size:20 final size:19
Alignment explanation
Indices: 403651--403735 Score: 80
Period size: 20 Copynumber: 4.3 Consensus size: 19
403641 TTTTTCAGAA
*
403651 AAAGTCAACGATCAACGGTC
1 AAAGTCAACGATCAA-AGTC
* *
403671 AAAGTCAACGGTCAACGATC
1 AAAGTCAACGATCAAAG-TC
*
403691 AAAGTCAACGATCAAAGTA
1 AAAGTCAACGATCAAAGTC
* *
403710 AACAGTCAACGGTCAATGTTC
1 AA-AGTCAACGATCAAAG-TC
403731 AAAGT
1 AAAGT
403736 TAATGGTTAA
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
19 4 0.07
20 47 0.87
21 3 0.06
ACGTcount: A:0.42, C:0.21, G:0.19, T:0.18
Consensus pattern (19 bp):
AAAGTCAACGATCAAAGTC
Found at i:403717 original size:40 final size:40
Alignment explanation
Indices: 403651--403735 Score: 118
Period size: 40 Copynumber: 2.1 Consensus size: 40
403641 TTTTTCAGAA
* *
403651 AAAGTCAACGATCAACGGTCAAAGTCAACGGTCAACGATC
1 AAAGTCAACGATCAACAGTAAAAGTCAACGGTCAACGATC
* *
403691 AAAGTCAACGATCAA-AGTAAACAGTCAACGGTCAATGTTC
1 AAAGTCAACGATCAACAGTAAA-AGTCAACGGTCAACGATC
403731 AAAGT
1 AAAGT
403736 TAATGGTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
39 4 0.10
40 36 0.90
ACGTcount: A:0.42, C:0.21, G:0.19, T:0.18
Consensus pattern (40 bp):
AAAGTCAACGATCAACAGTAAAAGTCAACGGTCAACGATC
Found at i:403724 original size:7 final size:7
Alignment explanation
Indices: 403654--403725 Score: 51
Period size: 7 Copynumber: 10.7 Consensus size: 7
403644 TTCAGAAAAA
403654 GTCAACG
1 GTCAACG
*
403661 ATCAACG
1 GTCAACG
*
403668 GTCAA-A
1 GTCAACG
403674 GTCAACG
1 GTCAACG
403681 GTCAACG
1 GTCAACG
* *
403688 ATCAA-A
1 GTCAACG
403694 GTCAACG
1 GTCAACG
* *
403701 ATCAA-A
1 GTCAACG
* *
403707 GTAAACA
1 GTCAACG
403714 GTCAACG
1 GTCAACG
403721 GTCAA
1 GTCAA
403726 TGTTCAAAGT
Statistics
Matches: 48, Mismatches: 14, Indels: 6
0.71 0.21 0.09
Matches are distributed among these distances:
6 12 0.25
7 36 0.75
ACGTcount: A:0.42, C:0.24, G:0.19, T:0.15
Consensus pattern (7 bp):
GTCAACG
Found at i:405724 original size:37 final size:37
Alignment explanation
Indices: 405683--405756 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
405673 GTTAATAAAA
405683 TGTGATGCTTATGAATGCATGTATGCATAAGAAACGT
1 TGTGATGCTTATGAATGCATGTATGCATAAGAAACGT
405720 TGTGATGCTTATGAATGCATGTATGCATAAGAAACGT
1 TGTGATGCTTATGAATGCATGTATGCATAAGAAACGT
405757 ATTGACTCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.32
Consensus pattern (37 bp):
TGTGATGCTTATGAATGCATGTATGCATAAGAAACGT
Found at i:407606 original size:18 final size:19
Alignment explanation
Indices: 407583--407623 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
407573 ATTTAATCTT
*
407583 AAAAGGA-TTTAATAAAAA
1 AAAAGGACTTAAATAAAAA
407601 AAAAGGACTTAAATAAAAA
1 AAAAGGACTTAAATAAAAA
407620 AAAA
1 AAAA
407624 CGGAATATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.71, C:0.02, G:0.10, T:0.17
Consensus pattern (19 bp):
AAAAGGACTTAAATAAAAA
Found at i:408521 original size:15 final size:15
Alignment explanation
Indices: 408501--408530 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
408491 TTCAAAATGT
*
408501 AAATAATAAATAATA
1 AAATAAAAAATAATA
408516 AAATAAAAAATAATA
1 AAATAAAAAATAATA
408531 TATATATATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
AAATAAAAAATAATA
Found at i:408991 original size:11 final size:12
Alignment explanation
Indices: 408977--409010 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
408967 GGATTTTAAT
408977 TTTATTTTTGG-
1 TTTATTTTTGGA
408988 TTTATTTTTGGA
1 TTTATTTTTGGA
409000 TTTGATTTTTG
1 TTT-ATTTTTG
409011 AGCCCGAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.52
12 3 0.14
13 7 0.33
ACGTcount: A:0.12, C:0.00, G:0.18, T:0.71
Consensus pattern (12 bp):
TTTATTTTTGGA
Found at i:411410 original size:19 final size:19
Alignment explanation
Indices: 411383--411423 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
411373 AATGGTTTGT
411383 AAAACAAAATGAT-AATACA
1 AAAACAAAATGATGAAT-CA
*
411402 AAAATAAAATGATGAATCA
1 AAAACAAAATGATGAATCA
411421 AAA
1 AAA
411424 CACCTTTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 17 0.85
20 3 0.15
ACGTcount: A:0.68, C:0.07, G:0.07, T:0.17
Consensus pattern (19 bp):
AAAACAAAATGATGAATCA
Found at i:413933 original size:17 final size:18
Alignment explanation
Indices: 413896--413935 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
413886 TAATACATTA
* *
413896 AATTAAAAAATAACTCTT
1 AATTAAAAAATAACACAT
413914 AATTAAAAAATAA-ACAT
1 AATTAAAAAATAACACAT
413931 AATTA
1 AATTA
413936 TCTAAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.30
Consensus pattern (18 bp):
AATTAAAAAATAACACAT
Found at i:427035 original size:30 final size:30
Alignment explanation
Indices: 426994--427051 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
426984 AGTTGCAGAA
* *
426994 GAAGAAGAAGATCCAGATGAAGATCCTGAG
1 GAAGAAAAAGATCCAGAGGAAGATCCTGAG
**
427024 GAAGAAAAAGATCTTGAGGAAGATCCTG
1 GAAGAAAAAGATCCAGAGGAAGATCCTG
427052 TGGAGATTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.43, C:0.12, G:0.29, T:0.16
Consensus pattern (30 bp):
GAAGAAAAAGATCCAGAGGAAGATCCTGAG
Found at i:433206 original size:26 final size:26
Alignment explanation
Indices: 433039--433206 Score: 212
Period size: 26 Copynumber: 6.5 Consensus size: 26
433029 TAAGAGCGTT
*
433039 ACTCTGTCTGGACTCGAATGAGCTAA
1 ACTCTGTCTGGGCTCGAATGAGCTAA
* * *
433065 ACTCTGTCTAGGCTTGAAGGAGCTAA
1 ACTCTGTCTGGGCTCGAATGAGCTAA
* *
433091 ACTCTGTCTGGGCTTGAAGGAGCTAA
1 ACTCTGTCTGGGCTCGAATGAGCTAA
*
433117 ACTCTGTCTAGGCTCGAATGAGCTAA
1 ACTCTGTCTGGGCTCGAATGAGCTAA
* * * *
433143 CCTCTATCTTGGCTCGAATGAGATAA
1 ACTCTGTCTGGGCTCGAATGAGCTAA
433169 ACTCTGTCTGGGCTC-ATATGAGCTAA
1 ACTCTGTCTGGGCTCGA-ATGAGCTAA
*
433195 ACTCTGTTTGGG
1 ACTCTGTCTGGG
433207 TTTGAAAGAG
Statistics
Matches: 124, Mismatches: 17, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
25 1 0.01
26 123 0.99
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.29
Consensus pattern (26 bp):
ACTCTGTCTGGGCTCGAATGAGCTAA
Found at i:444075 original size:17 final size:17
Alignment explanation
Indices: 444050--444090 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
444040 AAATGTGAGA
* *
444050 ACAAGTAAAATGTAGTG
1 ACAATTAAAATGTAATG
*
444067 ATAATTAAAATGTAATG
1 ACAATTAAAATGTAATG
444084 ACAATTA
1 ACAATTA
444091 GAGAGAATAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.51, C:0.05, G:0.15, T:0.29
Consensus pattern (17 bp):
ACAATTAAAATGTAATG
Found at i:444507 original size:15 final size:16
Alignment explanation
Indices: 444486--444524 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
444476 CGGGACAACT
*
444486 TCTTCTTCTTCTTTTC
1 TCTTCTTCTTCTATTC
444502 -CTTCTT-TTCTATTC
1 TCTTCTTCTTCTATTC
444516 TCTTCTTCT
1 TCTTCTTCT
444525 GCTTCAATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
14 7 0.35
15 12 0.60
16 1 0.05
ACGTcount: A:0.03, C:0.31, G:0.00, T:0.67
Consensus pattern (16 bp):
TCTTCTTCTTCTATTC
Found at i:471704 original size:9 final size:9
Alignment explanation
Indices: 471690--471714 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
471680 TACTAAATAT
471690 AAAATGCTA
1 AAAATGCTA
471699 AAAATGCTA
1 AAAATGCTA
471708 AAAATGC
1 AAAATGC
471715 ATGCTAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.56, C:0.12, G:0.12, T:0.20
Consensus pattern (9 bp):
AAAATGCTA
Found at i:478808 original size:20 final size:20
Alignment explanation
Indices: 478783--478822 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
478773 GAGCGAAGAA
478783 GCCAACTTAATCTGCTATAG
1 GCCAACTTAATCTGCTATAG
478803 GCCAACTTAATCTGCTATAG
1 GCCAACTTAATCTGCTATAG
478823 AACCCTCCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (20 bp):
GCCAACTTAATCTGCTATAG
Found at i:497864 original size:22 final size:22
Alignment explanation
Indices: 497839--497882 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
497829 TAGTAAATTA
*
497839 TTTTAAAATTATTAAAATTATTT
1 TTTTAAAA-TAATAAAATTATTT
*
497862 TTTTGAAATAATAAAATTATT
1 TTTTAAAATAATAAAATTATT
497883 AAATAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
TTTTAAAATAATAAAATTATTT
Found at i:499247 original size:19 final size:18
Alignment explanation
Indices: 499201--499252 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
499191 TCCCAAAAAA
499201 AATTTAAATGT-TTTTTTT
1 AATTTAAAT-TATTTTTTT
*
499219 AATTTTAATTATTTTTTT
1 AATTTAAATTATTTTTTT
499237 AAGTTTAAATTCATTT
1 AA-TTTAAATT-ATTT
499253 GCTGACGTGG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 1 0.03
18 17 0.59
19 7 0.24
20 4 0.14
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (18 bp):
AATTTAAATTATTTTTTT
Found at i:503218 original size:6 final size:7
Alignment explanation
Indices: 503202--503227 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
503192 AAAAAATAAG
503202 TTTTTAT
1 TTTTTAT
503209 TTTTTAT
1 TTTTTAT
503216 TTTTTAT
1 TTTTTAT
503223 TTTTT
1 TTTTT
503228 TCAACTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTAT
Found at i:505579 original size:20 final size:20
Alignment explanation
Indices: 505556--505612 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 20
505546 ATTTTCATTT
505556 TTGATTTAGGGTTTTTTATA
1 TTGATTTAGGGTTTTTTATA
*** *
505576 TTGATTT-TCATTTTTTATT
1 TTGATTTAGGGTTTTTTATA
*
505595 TTGATTTAGGGTTATTTA
1 TTGATTTAGGGTTTTTTA
505613 AATATTTGTT
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.19, C:0.02, G:0.16, T:0.63
Consensus pattern (20 bp):
TTGATTTAGGGTTTTTTATA
Found at i:505634 original size:40 final size:38
Alignment explanation
Indices: 505554--505634 Score: 92
Period size: 39 Copynumber: 2.1 Consensus size: 38
505544 TGATTTTCAT
* *
505554 TTTTGATTTAGGGTTTTTTATATTGATTTTCATTTTTTA
1 TTTTGATTTAGGGTTTTTAATATTGA-TTTCATTTGTTA
*
505593 TTTTGATTTAGGGTTATTTAAATATTTG-TTTGATTTGTTA
1 TTTTGATTTAGGGTT-TTT-AATA-TTGATTTCATTTGTTA
505633 TT
1 TT
505635 CACATATTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
39 15 0.42
40 15 0.42
41 3 0.08
42 3 0.08
ACGTcount: A:0.20, C:0.01, G:0.15, T:0.64
Consensus pattern (38 bp):
TTTTGATTTAGGGTTTTTAATATTGATTTCATTTGTTA
Found at i:507907 original size:12 final size:12
Alignment explanation
Indices: 507871--507910 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
507861 TTTAATATTA
507871 TTTTGTATGTTG
1 TTTTGTATGTTG
*
507883 TTCTT-TATTTTG
1 TT-TTGTATGTTG
507895 TTTTGTATGTTG
1 TTTTGTATGTTG
507907 TTTT
1 TTTT
507911 TAATACCCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 2 0.08
12 20 0.83
13 2 0.08
ACGTcount: A:0.07, C:0.03, G:0.17, T:0.72
Consensus pattern (12 bp):
TTTTGTATGTTG
Found at i:509660 original size:16 final size:16
Alignment explanation
Indices: 509639--509669 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
509629 AAACTAGCAC
*
509639 CCATGAGAAGTAACAG
1 CCATGAGAAGCAACAG
509655 CCATGAGAAGCAACA
1 CCATGAGAAGCAACA
509670 ACCAACAAAA
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:0.45, C:0.23, G:0.23, T:0.10
Consensus pattern (16 bp):
CCATGAGAAGCAACAG
Found at i:511615 original size:31 final size:31
Alignment explanation
Indices: 511580--511648 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 31
511570 TATTAAAAAA
511580 TGAAAATATATTAAAAATAAAATAAAATATT
1 TGAAAATATATTAAAAATAAAATAAAATATT
* **
511611 TGAAAATATATTAAAAATAAACTATCATATT
1 TGAAAATATATTAAAAATAAAATAAAATATT
511642 T-AAAATA
1 TGAAAATA
511649 AATAAATAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
30 6 0.17
31 29 0.83
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (31 bp):
TGAAAATATATTAAAAATAAAATAAAATATT
Found at i:511616 original size:10 final size:11
Alignment explanation
Indices: 511582--511629 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
511572 TTAAAAAATG
511582 AAAATATATTA
1 AAAATATATTA
* *
511593 AAAATAAAAT-
1 AAAATATATTA
*
511603 AAAATAT-TTG
1 AAAATATATTA
511613 AAAATATATTA
1 AAAATATATTA
511624 AAAATA
1 AAAATA
511630 AACTATCATA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
9 1 0.03
10 13 0.43
11 16 0.53
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (11 bp):
AAAATATATTA
Found at i:511626 original size:20 final size:21
Alignment explanation
Indices: 511576--511618 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
511566 TTGATATTAA
511576 AAAATGAAAATATATTAAAAAT
1 AAAAT-AAAATATATTAAAAAT
*
511598 AAAATAAAATAT-TTGAAAAT
1 AAAATAAAATATATTAAAAAT
511618 A
1 A
511619 TATTAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 8 0.40
21 7 0.35
22 5 0.25
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (21 bp):
AAAATAAAATATATTAAAAAT
Found at i:512288 original size:25 final size:25
Alignment explanation
Indices: 512254--512304 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
512244 GATCTCTTAA
*
512254 TGAGAATGCAGGTTTTTTATTTATT
1 TGAGAATGCAGGCTTTTTATTTATT
512279 TGAGAATGCAGGCTTTTTATTTATT
1 TGAGAATGCAGGCTTTTTATTTATT
512304 T
1 T
512305 TCATCTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.06, G:0.20, T:0.51
Consensus pattern (25 bp):
TGAGAATGCAGGCTTTTTATTTATT
Found at i:515413 original size:21 final size:22
Alignment explanation
Indices: 515387--515430 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 22
515377 ACACACGATA
515387 AAAAAAATCAATA-AAATTTAT
1 AAAAAAATCAATATAAATTTAT
* *
515408 -AAAAAATTATTATAAATTTAT
1 AAAAAAATCAATATAAATTTAT
515429 AA
1 AA
515431 TTTTTTTATG
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
20 10 0.53
21 8 0.42
22 1 0.05
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (22 bp):
AAAAAAATCAATATAAATTTAT
Found at i:515478 original size:22 final size:21
Alignment explanation
Indices: 515450--515498 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
515440 GTTTACTTTT
*
515450 TAATTTTTAATAAA-ATTTTAA
1 TAATTTTTTATAAATA-TTTAA
*
515471 TATTTTTTTATAAATATTTAA
1 TAATTTTTTATAAATATTTAA
515492 TAATTTT
1 TAATTTT
515499 CATTATTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TAATTTTTTATAAATATTTAA
Found at i:516076 original size:16 final size:18
Alignment explanation
Indices: 516037--516070 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
516027 TAAGTTTATA
516037 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
516054 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
516071 AATTTAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:522245 original size:24 final size:24
Alignment explanation
Indices: 522218--522270 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
522208 ATATGAAAAG
** *
522218 AAATAACAAAGATTTTATGCTAAT
1 AAATAACAAAGATACTATACTAAT
* *
522242 AAATATCAAATATACTATACTAAT
1 AAATAACAAAGATACTATACTAAT
522266 AAATA
1 AAATA
522271 CTAAATCTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.55, C:0.09, G:0.04, T:0.32
Consensus pattern (24 bp):
AAATAACAAAGATACTATACTAAT
Found at i:526834 original size:14 final size:14
Alignment explanation
Indices: 526815--526852 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
526805 GTTTACCAAT
526815 AAAAT-ATTTTTCGA
1 AAAATAATTTTT-GA
526829 AAAATAATTTTTGA
1 AAAATAATTTTTGA
*
526843 AAAATGATTT
1 AAAATAATTT
526853 ACTTTTCTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 16 0.73
15 6 0.27
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (14 bp):
AAAATAATTTTTGA
Found at i:527607 original size:48 final size:48
Alignment explanation
Indices: 527555--527652 Score: 169
Period size: 48 Copynumber: 2.0 Consensus size: 48
527545 AAAGGTATAG
*
527555 ATAGTTTGTCCATGGTATCAATTTTTCTGCTCCAACGGTCACTGAAAT
1 ATAGTTTGTCCATGGTATCAATATTTCTGCTCCAACGGTCACTGAAAT
* *
527603 ATAGTTTGTCCATTGTATCGATATTTCTGCTCCAACGGTCACTGAAAT
1 ATAGTTTGTCCATGGTATCAATATTTCTGCTCCAACGGTCACTGAAAT
527651 AT
1 AT
527653 GGATTTATTA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (48 bp):
ATAGTTTGTCCATGGTATCAATATTTCTGCTCCAACGGTCACTGAAAT
Found at i:529927 original size:30 final size:29
Alignment explanation
Indices: 529893--530069 Score: 162
Period size: 30 Copynumber: 6.0 Consensus size: 29
529883 ATTAAAATCA
* *
529893 GGTCAATTTTGAATTTTTGGCAAATTTAAG
1 GGTCAAATTTGAATTTTTGG-AAATTTAGG
* *
529923 GGTCAAATTGGAATTTTTAGAAAATTTAGG
1 GGTCAAATTTGAATTTTT-GGAAATTTAGG
* *
529953 GGTTAAATTTAAATTTTTGGAAATTTAGG
1 GGTCAAATTTGAATTTTTGGAAATTTAGG
* *
529982 GGTCAAATTTGAATTTTAGAAAATTT-GG
1 GGTCAAATTTGAATTTTTGGAAATTTAGG
* *
530010 GGTTTAAA-TTCAATTTTTTGGAAAATTT-GAG
1 GG-TCAAATTTGAA-TTTTTGG-AAATTTAG-G
**
530041 GGTCAAATTCAAATTTTTGGAAAGTTTAG
1 GGTCAAATTTGAATTTTTGGAAA-TTTAG
530070 TGGTGAAAAA
Statistics
Matches: 120, Mismatches: 19, Indels: 15
0.78 0.12 0.10
Matches are distributed among these distances:
28 8 0.07
29 44 0.37
30 60 0.50
31 8 0.07
ACGTcount: A:0.34, C:0.04, G:0.21, T:0.41
Consensus pattern (29 bp):
GGTCAAATTTGAATTTTTGGAAATTTAGG
Found at i:529985 original size:59 final size:61
Alignment explanation
Indices: 529904--530069 Score: 207
Period size: 59 Copynumber: 2.8 Consensus size: 61
529894 GTCAATTTTG
* * * *
529904 AATTTTTGGCAAATTTAAGGGTCAAATTGGAATTTTTAGAAAATTTAGGGG-TTAAATTTA
1 AATTTTTGGAAAATTTAGGGGTCAAATTCGAATTTTTAGAAAATTTAGGGGTTTAAATTCA
*
529964 AATTTTTGG-AAATTTAGGGGTCAAATTTGAA-TTTTAGAAAATTT-GGGGTTTAAATTCA
1 AATTTTTGGAAAATTTAGGGGTCAAATTCGAATTTTTAGAAAATTTAGGGGTTTAAATTCA
* * * *
530022 ATTTTTTGGAAAATTT-GAGGGTCAAATTCAAATTTTTGGAAAGTTTAG
1 AATTTTTGGAAAATTTAG-GGGTCAAATTCGAATTTTTAGAAAATTTAG
530070 TGGTGAAAAA
Statistics
Matches: 93, Mismatches: 8, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
57 4 0.04
58 30 0.32
59 38 0.41
60 20 0.22
61 1 0.01
ACGTcount: A:0.35, C:0.04, G:0.20, T:0.41
Consensus pattern (61 bp):
AATTTTTGGAAAATTTAGGGGTCAAATTCGAATTTTTAGAAAATTTAGGGGTTTAAATTCA
Found at i:531755 original size:100 final size:100
Alignment explanation
Indices: 531538--531755 Score: 226
Period size: 100 Copynumber: 2.2 Consensus size: 100
531528 CAACCTACTA
* * * **
531538 GATATAGGATTTGATGTTGTAGCTTCATCTTGCTCCACTGCAGCTTCAGGGAGATAAAGATTTGC
1 GATATAGGATTTG-TTTTGTAGCTTCATCTTGCTCCACTGCAACTTCAGAGAGATAAAGATTCAC
* *
531603 TTTCATGACTTTAATCCGACCCACTACAACTTCAGG
65 CTTCATGACTTGAATCCGACCCACTACAACTTCAGG
* * * * *
531639 GGTATA-GATTTGGTTTTGTATCTTCATCTTGCTCTACTGCAACTTTAGAGAGATAATGATTCAC
1 GATATAGGATTT-GTTTTGTAGCTTCATCTTGCTCCACTGCAACTTCAGAGAGATAAAGATTCAC
* * * *
531703 CTTCAT-AGCTTCGAA-CTGATCCACTGCAACTTTAGG
65 CTTCATGA-CTT-GAATCCGACCCACTACAACTTCAGG
*
531739 GATATAGGACTTGTTTT
1 GATATAGGATTTGTTTT
531756 CACTCCATTC
Statistics
Matches: 95, Mismatches: 18, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
99 1 0.01
100 82 0.86
101 12 0.13
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (100 bp):
GATATAGGATTTGTTTTGTAGCTTCATCTTGCTCCACTGCAACTTCAGAGAGATAAAGATTCACC
TTCATGACTTGAATCCGACCCACTACAACTTCAGG
Found at i:531951 original size:39 final size:40
Alignment explanation
Indices: 531882--531972 Score: 121
Period size: 39 Copynumber: 2.3 Consensus size: 40
531872 ATAGCTTTAG
* * *
531882 GGGTAAAAGATCGGATGGTCTTCAATCTGCCCTCTGGTTA
1 GGGTAAAAGATTGGATGGTATTCAATCTGCCCTATGGTTA
* * *
531922 GGGTAAAAGATTGGATTG-ATTCAATCTGCCCTATGTTTG
1 GGGTAAAAGATTGGATGGTATTCAATCTGCCCTATGGTTA
531961 GGGTAAAAGATT
1 GGGTAAAAGATT
531973 CGAGGTTATA
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
39 29 0.64
40 16 0.36
ACGTcount: A:0.26, C:0.14, G:0.27, T:0.32
Consensus pattern (40 bp):
GGGTAAAAGATTGGATGGTATTCAATCTGCCCTATGGTTA
Found at i:532169 original size:50 final size:51
Alignment explanation
Indices: 532023--532155 Score: 191
Period size: 50 Copynumber: 2.7 Consensus size: 51
532013 AAATTCGTCC
* *
532023 TTGC-GACTTCAATCTGCCCCTCTACAGCTTTAGGTGAATGAGATTCGCCA
1 TTGCTGACTTCAATCTGCCCCTCTACAGCTTTAGGTGTATGAGATTTGCCA
*
532073 TTGCTG-CTTCAATCTGCCCCTCTATAGCTTTAGGTGTATGAGATTTGCCA
1 TTGCTGACTTCAATCTGCCCCTCTACAGCTTTAGGTGTATGAGATTTGCCA
* **
532123 TTG-TGACTTCAGTCTGTTCCTCTACAGCTTTAG
1 TTGCTGACTTCAATCTGCCCCTCTACAGCTTTAG
532156 AGGTATAGGA
Statistics
Matches: 74, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
49 2 0.03
50 71 0.96
51 1 0.01
ACGTcount: A:0.19, C:0.26, G:0.20, T:0.36
Consensus pattern (51 bp):
TTGCTGACTTCAATCTGCCCCTCTACAGCTTTAGGTGTATGAGATTTGCCA
Found at i:540223 original size:30 final size:29
Alignment explanation
Indices: 540189--540560 Score: 265
Period size: 30 Copynumber: 12.7 Consensus size: 29
540179 CATTAAAATC
540189 GGGTCAAATTTGAATTTTTGAAAACTTTAA
1 GGGTCAAATTTGAATTTTTGAAAA-TTTAA
** **
540219 GGGTCAAATAAGAATTTTTGGAAAATTTTG
1 GGGTCAAATTTGAATTTTT-GAAAATTTAA
*
540249 GGGTCAAATTAGAATTTTTGAAAAATTTTAA
1 GGGTCAAATTTGAATTTTTG-AAAA-TTTAA
** * *
540280 -GGTCAAATTCAAATTTCTAGAAAGTTTAA
1 GGGTCAAATTTGAATTT-TTGAAAATTTAA
* * **
540309 GGGTC--A--T--ATTTTGGAAATTTTGG
1 GGGTCAAATTTGAATTTTTGAAAATTTAA
* * * * *
540332 GGGTTAATTTTGAATTTTTGGTATATTTAG
1 GGGTCAAATTTGAATTTTT-GAAAATTTAA
* ** *
540362 GGGTTAAATTCAAATTTTTTGAAAATTTAG
1 GGGTCAAATTTGAA-TTTTTGAAAATTTAA
* *
540392 GGGTCAAATTAGAATTTTTGGAAAATTTAT
1 GGGTCAAATTTGAATTTTT-GAAAATTTAA
** * *
540422 GGGTCAAATTCAAATTTTTGGAAAGTTTAC
1 GGGTCAAATTTGAATTTTT-GAAAATTTAA
*
540452 GGGTCAAATTTGAATTTTGGAAAATTTAA
1 GGGTCAAATTTGAATTTTTGAAAATTTAA
* *
540481 GGGTTAAATTTGAATTTTTGAAAAATTTAG
1 GGGTCAAATTTGAATTTTTG-AAAATTTAA
* ** *
540511 GGGTTAAATTCAAATTTTTGGAAAATTTGA
1 GGGTCAAATTTGAATTTTT-GAAAATTTAA
540541 GGGTCAAATTT-AGATTTTTG
1 GGGTCAAATTTGA-ATTTTTG
540561 GATAATTAGG
Statistics
Matches: 275, Mismatches: 50, Indels: 35
0.76 0.14 0.10
Matches are distributed among these distances:
23 12 0.04
24 4 0.01
27 1 0.00
28 1 0.00
29 44 0.16
30 197 0.72
31 16 0.06
ACGTcount: A:0.35, C:0.04, G:0.20, T:0.41
Consensus pattern (29 bp):
GGGTCAAATTTGAATTTTTGAAAATTTAA
Found at i:540253 original size:60 final size:60
Alignment explanation
Indices: 540189--540560 Score: 313
Period size: 60 Copynumber: 6.3 Consensus size: 60
540179 CATTAAAATC
* * * *
540189 GGGTCAAATTTGAATTTTTGAAAACTTTAAGGGTCAAATAAGAATTTTTGGAAAATTTTG
1 GGGTCAAATTTGAATTTTTGAAAATTTTAGGGGTCAAATTAGAATTTTTGGAAAATTTAG
* * * * * *
540249 GGGTCAAATTAGAATTTTTGAAAAATTTTA-AGGTCAAATTCA-AATTTCTAGAAAGTTTAA
1 GGGTCAAATTTGAATTTTTG-AAAATTTTAGGGGTCAAATT-AGAATTTTTGGAAAATTTAG
* * * * * * *
540309 GGGTC--A--T--A-TTTTGGAAATTTTGGGGGTTAATTTTGAATTTTTGGTATATTTAG
1 GGGTCAAATTTGAATTTTTGAAAATTTTAGGGGTCAAATTAGAATTTTTGGAAAATTTAG
* ** *
540362 GGGTTAAATTCAAATTTTTTGAAAA-TTTAGGGGTCAAATTAGAATTTTTGGAAAATTTAT
1 GGGTCAAATTTGAA-TTTTTGAAAATTTTAGGGGTCAAATTAGAATTTTTGGAAAATTTAG
** * * * * *
540422 GGGTCAAATTCAAATTTTTGGAAAGTTTACGGGTCAAATTTGAA-TTTTGGAAAATTTAA
1 GGGTCAAATTTGAATTTTTGAAAATTTTAGGGGTCAAATTAGAATTTTTGGAAAATTTAG
* * *
540481 GGGTTAAATTTGAATTTTTGAAAAATTTAGGGGTTAAATTCA-AATTTTTGGAAAATTT-G
1 GGGTCAAATTTGAATTTTTGAAAATTTTAGGGGTCAAATT-AGAATTTTTGGAAAATTTAG
540540 AGGGTCAAATTT-AGATTTTTG
1 -GGGTCAAATTTGA-ATTTTTG
540561 GATAATTAGG
Statistics
Matches: 248, Mismatches: 47, Indels: 34
0.75 0.14 0.10
Matches are distributed among these distances:
52 7 0.03
53 28 0.11
54 1 0.00
55 1 0.00
58 1 0.00
59 60 0.24
60 133 0.54
61 17 0.07
ACGTcount: A:0.35, C:0.04, G:0.20, T:0.41
Consensus pattern (60 bp):
GGGTCAAATTTGAATTTTTGAAAATTTTAGGGGTCAAATTAGAATTTTTGGAAAATTTAG
Found at i:540506 original size:89 final size:90
Alignment explanation
Indices: 540377--540567 Score: 269
Period size: 89 Copynumber: 2.1 Consensus size: 90
540367 AAATTCAAAT
* * * *
540377 TTTTTGAAAATTTAGGGGTCAAATTAGAATTTTTGGAAAATTTATGGGTCAAATTCAAATTTTTG
1 TTTTGGAAAATTTAAGGGTCAAATTAGAATTTTTGAAAAATTTAGGGGTCAAATTCAAATTTTTG
*
540442 GAAAGTTT-ACGGGTCAAATTT-GAA
66 GAAAATTTGA-GGGTCAAATTTAGAA
* * *
540466 TTTTGGAAAATTTAAGGGTTAAATTTGAATTTTTGAAAAATTTAGGGGTTAAATTCAAATTTTTG
1 TTTTGGAAAATTTAAGGGTCAAATTAGAATTTTTGAAAAATTTAGGGGTCAAATTCAAATTTTTG
*
540531 GAAAATTTGAGGGTCAAATTTAGAT
66 GAAAATTTGAGGGTCAAATTTAGAA
*
540556 TTTTGGATAATT
1 TTTTGGAAAATT
540568 AGGTGGTCGA
Statistics
Matches: 90, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
89 76 0.84
90 14 0.16
ACGTcount: A:0.35, C:0.04, G:0.20, T:0.41
Consensus pattern (90 bp):
TTTTGGAAAATTTAAGGGTCAAATTAGAATTTTTGAAAAATTTAGGGGTCAAATTCAAATTTTTG
GAAAATTTGAGGGTCAAATTTAGAA
Found at i:540587 original size:119 final size:118
Alignment explanation
Indices: 540342--540588 Score: 288
Period size: 119 Copynumber: 2.1 Consensus size: 118
540332 GGGTTAATTT
* * *
540342 TGAATTTTTGGTATATTTAGGGGTTAAATTCAAATTTTTTGAAAATTTAGGGGTCAAATTAGAAT
1 TGAA-TTTTGGAAAATTTAAGGGTTAAATTCAAATTTTTTGAAAATTTAGGGGTCAAATTAGAAT
**
540407 TTTTGGAAAATTTATGGGTCAAATTCAAATTTTTGGAAAGTTTACGGGTCAAATT
65 TTTTGGAAAATTTATGGGTCAAATTCAAATTTTTGGAAAG-TTACGGGTCAAAAA
** *
540462 TGAATTTTGGAAAATTTAAGGGTTAAATTTGAA-TTTTTGAAAAATTTAGGGGTTAAATTCA-AA
1 TGAATTTTGGAAAATTTAAGGGTTAAATTCAAATTTTTTG-AAAATTTAGGGGTCAAATT-AGAA
* * *
540525 TTTTTGGAAAATTTGA-GGGTCAAATTTAGATTTTTGGATAA-TTAGGTGGTCGAAAAA
64 TTTTTGGAAAATTT-ATGGGTCAAATTCAAATTTTTGGA-AAGTTACG-GGTC-AAAAA
540582 T-AATTTT
1 TGAATTTT
540589 AAAATAAAGT
Statistics
Matches: 110, Mismatches: 11, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
118 10 0.09
119 88 0.80
120 12 0.11
ACGTcount: A:0.35, C:0.04, G:0.20, T:0.41
Consensus pattern (118 bp):
TGAATTTTGGAAAATTTAAGGGTTAAATTCAAATTTTTTGAAAATTTAGGGGTCAAATTAGAATT
TTTGGAAAATTTATGGGTCAAATTCAAATTTTTGGAAAGTTACGGGTCAAAAA
Found at i:540587 original size:149 final size:148
Alignment explanation
Indices: 540189--540588 Score: 428
Period size: 143 Copynumber: 2.7 Consensus size: 148
540179 CATTAAAATC
* * * * * *
540189 GGGTCAAATTTGAATTTTTGAAAACTTTAAGGGTCAAA-TAAGAATTTTTGGAAAATTTTGGGGT
1 GGGTTAAATTTGAATTTTTGAAAAATTTAGGGGTTAAATTCA-AATTTTTGGAAAATTTAGGGGT
* * * * * *
540253 CAAATTAGAATTTTTGAAAAATTTTA-AGGTCAAATTCAAATTTCTAGAAAGTTTAAGGGTC--A
65 CAAATTAGAATTTTTGGAAAA-TTTAGGGGTCAAAAT-AAATTTTTGGAAAGTTTACGGGTCAAA
* **
540315 --T--ATTTTGGAAATTTTGG
128 TTTGAATTTTGGAAAATTTAA
* ** * *
540332 GGGTTAATTTTGAATTTTTGGTATATTTAGGGGTTAAATTCAAATTTTTTGAAAATTTAGGGGTC
1 GGGTTAAATTTGAATTTTTGAAAAATTTAGGGGTTAAATTCAAATTTTTGGAAAATTTAGGGGTC
* *
540397 AAATTAGAATTTTTGGAAAATTTATGGGTCAAATTCAAATTTTTGGAAAGTTTACGGGTCAAATT
66 AAATTAGAATTTTTGGAAAATTTAGGGGTCAAAAT-AAATTTTTGGAAAGTTTACGGGTCAAATT
540462 TGAATTTTGGAAAATTTAA
130 TGAATTTTGGAAAATTTAA
540481 GGGTTAAATTTGAATTTTTGAAAAATTTAGGGGTTAAATTCAAATTTTTGGAAAATTT-GAGGGT
1 GGGTTAAATTTGAATTTTTGAAAAATTTAGGGGTTAAATTCAAATTTTTGGAAAATTTAG-GGGT
*
540545 CAAATTTAG-ATTTTTGGATAA-TTAGGTGGTCGAAAA-ATAATTTT
65 CAAA-TTAGAATTTTTGGAAAATTTAGG-GGTC-AAAATA-AATTTT
540589 AAAATAAAGT
Statistics
Matches: 217, Mismatches: 27, Indels: 20
0.82 0.10 0.08
Matches are distributed among these distances:
142 4 0.02
143 101 0.47
144 2 0.01
145 1 0.00
147 1 0.00
148 6 0.03
149 95 0.44
150 7 0.03
ACGTcount: A:0.35, C:0.04, G:0.20, T:0.41
Consensus pattern (148 bp):
GGGTTAAATTTGAATTTTTGAAAAATTTAGGGGTTAAATTCAAATTTTTGGAAAATTTAGGGGTC
AAATTAGAATTTTTGGAAAATTTAGGGGTCAAAATAAATTTTTGGAAAGTTTACGGGTCAAATTT
GAATTTTGGAAAATTTAA
Found at i:542900 original size:15 final size:16
Alignment explanation
Indices: 542880--542912 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
542870 AGCTTATTTC
542880 AAATCTTTATG-CTCA
1 AAATCTTTATGCCTCA
542895 AAATCTTTATGCCTCA
1 AAATCTTTATGCCTCA
542911 AA
1 AA
542913 TTGAAAATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.36, C:0.21, G:0.06, T:0.36
Consensus pattern (16 bp):
AAATCTTTATGCCTCA
Found at i:543437 original size:21 final size:21
Alignment explanation
Indices: 543411--543457 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
543401 AAAAAATATT
543411 GATACCCTTTTAGTAGGTATC
1 GATACCCTTTTAGTAGGTATC
543432 GATACCCTTTTAGTAGGTATC
1 GATACCCTTTTAGTAGGTATC
543453 GATAC
1 GATAC
543458 TCATTGCTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (21 bp):
GATACCCTTTTAGTAGGTATC
Found at i:545152 original size:32 final size:32
Alignment explanation
Indices: 545111--545189 Score: 131
Period size: 32 Copynumber: 2.5 Consensus size: 32
545101 TGTCAATCAT
545111 TTCAATATCCAACAAGATTAAAACATAATAAA
1 TTCAATATCCAACAAGATTAAAACATAATAAA
* *
545143 TTCAATATCCAACAAGTTTAAAACATAATAAT
1 TTCAATATCCAACAAGATTAAAACATAATAAA
*
545175 TTCAAAATCCAACAA
1 TTCAATATCCAACAA
545190 ACTAATTCAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.53, C:0.18, G:0.03, T:0.27
Consensus pattern (32 bp):
TTCAATATCCAACAAGATTAAAACATAATAAA
Done.