Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014131.1 Kokia drynarioides strain JFW-HI SEQ_129164, 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: 295312
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 72 characters in sequence are not A, C, G, or T
Found at i:41 original size:25 final size:23
Alignment explanation
Indices: 1--62 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 23
* * *
1 TTTTAATTTAATTTAATATAATT
1 TTTTTATTTAATTTAATAGAAAT
24 ATTTTTATTTAATATTAATAGAAAT
1 -TTTTTATTTAAT-TTAATAGAAAT
*
49 TTTTTATTTTATTT
1 TTTTTATTTAATTT
63 TTATAACAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
23 2 0.06
24 22 0.67
25 9 0.27
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (23 bp):
TTTTTATTTAATTTAATAGAAAT
Found at i:108 original size:18 final size:16
Alignment explanation
Indices: 81--121 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 16
71 ATTATTTATA
81 AATTTATAATACATTTT
1 AATTTATAATA-ATTTT
*
98 ATATTTTTAATAATTTT
1 A-ATTTATAATAATTTT
115 AATTTAT
1 AATTTAT
122 TTAAGATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 5 0.24
17 7 0.33
18 9 0.43
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (16 bp):
AATTTATAATAATTTT
Found at i:6652 original size:54 final size:55
Alignment explanation
Indices: 6563--6672 Score: 177
Period size: 54 Copynumber: 2.0 Consensus size: 55
6553 TTGGGATATA
**
6563 AAAAGGCGAGAGATCAAACCATTGCAAAAAAACTATGAAGGAAATCTCGTGACAT
1 AAAAGGCGAGAGAAAAAACCATTGCAAAAAAACTATGAAGGAAATCTCGTGACAT
* *
6618 AAAA-GCGAGAGAAAAAACCATTGCTAAAATACTATGAAGGAAATCTCGTGACAT
1 AAAAGGCGAGAGAAAAAACCATTGCAAAAAAACTATGAAGGAAATCTCGTGACAT
6672 A
1 A
6673 TGCTTTAAGT
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
54 47 0.92
55 4 0.08
ACGTcount: A:0.48, C:0.15, G:0.19, T:0.17
Consensus pattern (55 bp):
AAAAGGCGAGAGAAAAAACCATTGCAAAAAAACTATGAAGGAAATCTCGTGACAT
Found at i:8069 original size:21 final size:22
Alignment explanation
Indices: 8043--8180 Score: 118
Period size: 23 Copynumber: 6.0 Consensus size: 22
8033 CAGAACAAAC
* *
8043 AGAGAGTAC-CAAAGTACTAAT
1 AGAGAGCACACAAAGTGCTAAT
*
8064 AGAGAGCACA-TAAGTGCTAGGCAAT
1 AGAGAGCACACAAAGTGCT----AAT
* *
8089 AGAGAGCACACACAGTGCTAAAC
1 AGAGAGCACACAAAGTGCT-AAT
* *
8112 AGAGAGTACACAAAGTACTAAT
1 AGAGAGCACACAAAGTGCTAAT
8134 CAGAGAGCACACAAAGTGCTAAT
1 -AGAGAGCACACAAAGTGCTAAT
* *
8157 CAAAGAGCACACACAGTGCTAAT
1 -AGAGAGCACACAAAGTGCTAAT
8180 A
1 A
8181 ACAGAGAGCA
Statistics
Matches: 95, Mismatches: 15, Indels: 13
0.77 0.12 0.11
Matches are distributed among these distances:
21 14 0.15
22 3 0.03
23 59 0.62
25 13 0.14
26 6 0.06
ACGTcount: A:0.45, C:0.20, G:0.21, T:0.14
Consensus pattern (22 bp):
AGAGAGCACACAAAGTGCTAAT
Found at i:8122 original size:23 final size:23
Alignment explanation
Indices: 8089--8211 Score: 140
Period size: 23 Copynumber: 5.3 Consensus size: 23
8079 GCTAGGCAAT
8089 AGAGAGCACACACAGTGCTAAAC
1 AGAGAGCACACACAGTGCTAAAC
* * * *
8112 AGAGAGTACACAAAGTACTAATC
1 AGAGAGCACACACAGTGCTAAAC
* *
8135 AGAGAGCACACAAAGTGCTAATC
1 AGAGAGCACACACAGTGCTAAAC
*
8158 AAAGAGCACACACAGTGCTAATAAC
1 AGAGAGCACACACAGTGCT-A-AAC
*
8183 AGAGAGCACGAGAC-GTGCTAAAC
1 AGAGAGCAC-ACACAGTGCTAAAC
8206 AGAGAG
1 AGAGAG
8212 TGCGCTAGTG
Statistics
Matches: 86, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
23 66 0.77
24 2 0.02
25 15 0.17
26 3 0.03
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.11
Consensus pattern (23 bp):
AGAGAGCACACACAGTGCTAAAC
Found at i:8164 original size:69 final size:70
Alignment explanation
Indices: 8039--8188 Score: 209
Period size: 69 Copynumber: 2.1 Consensus size: 70
8029 TATACAGAAC
* *
8039 AAACAGAGAGTACCAAAGTACTAATAGAGAGCACATAAGTGCTAGGCAATAGAGAGCACACACAG
1 AAACAGAGAGTACCAAAGTACTAATAGAGAGCACAAAAGTGCTAAGCAATAGAGAGCACACACAG
8104 TGCT-
66 TGCTA
*
8108 AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCTAATC-A-A-AGAGCACACA
1 AAACAGAGAGTAC-CAAAGTACTAAT-AGAGAGCACA-AAAGTGCTAAGCAATAGAGAGCACACA
8170 CAGTGCTA
63 CAGTGCTA
8178 ATAACAGAGAG
1 A-AACAGAGAG
8189 CACGAGACGT
Statistics
Matches: 73, Mismatches: 3, Indels: 8
0.87 0.04 0.10
Matches are distributed among these distances:
69 30 0.41
70 14 0.19
71 20 0.27
72 9 0.12
ACGTcount: A:0.46, C:0.19, G:0.21, T:0.13
Consensus pattern (70 bp):
AAACAGAGAGTACCAAAGTACTAATAGAGAGCACAAAAGTGCTAAGCAATAGAGAGCACACACAG
TGCTA
Found at i:11773 original size:36 final size:36
Alignment explanation
Indices: 11691--11793 Score: 125
Period size: 36 Copynumber: 2.9 Consensus size: 36
11681 TATAATCAGT
* * * * *
11691 CACATGGCATTAAGAACATACCCATATATTTTTTGT
1 CACATGGCATGAAGAACATACCCACATATTCTCTGG
11727 CACATGGCATGAAGAACATACCCACATATTCTCTGG
1 CACATGGCATGAAGAACATACCCACATATTCTCTGG
* * * *
11763 CAGATTGCATGAAGAACACACCTACATATTC
1 CACATGGCATGAAGAACATACCCACATATTC
11794 ACTTTCACAA
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 58 1.00
ACGTcount: A:0.35, C:0.24, G:0.14, T:0.27
Consensus pattern (36 bp):
CACATGGCATGAAGAACATACCCACATATTCTCTGG
Found at i:11907 original size:23 final size:23
Alignment explanation
Indices: 11888--11994 Score: 133
Period size: 23 Copynumber: 4.7 Consensus size: 23
11878 CACAAATAAA
11888 ATTAATATTTAAGCATAAATCAC
1 ATTAATATTTAAGCATAAATCAC
* *
11911 ACTAATATTTAAACATAAATCAC
1 ATTAATATTTAAGCATAAATCAC
* * *
11934 ATTAATATTTGAGCACAAATCAT
1 ATTAATATTTAAGCATAAATCAC
* ** *
11957 ATTAACATTTAATAATAAATCAT
1 ATTAATATTTAAGCATAAATCAC
11980 ATTAATATTTAAGCA
1 ATTAATATTTAAGCA
11995 CAGTTATAAG
Statistics
Matches: 69, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 69 1.00
ACGTcount: A:0.49, C:0.12, G:0.04, T:0.36
Consensus pattern (23 bp):
ATTAATATTTAAGCATAAATCAC
Found at i:11954 original size:46 final size:46
Alignment explanation
Indices: 11888--11996 Score: 148
Period size: 46 Copynumber: 2.4 Consensus size: 46
11878 CACAAATAAA
* *
11888 ATTAATATTTAAGCATAAATCACACTAATATTTAA-ACATAAATCAC
1 ATTAATATTTAAGCACAAATCACACTAACATTTAATA-ATAAATCAC
* * * *
11934 ATTAATATTTGAGCACAAATCATATTAACATTTAATAATAAATCAT
1 ATTAATATTTAAGCACAAATCACACTAACATTTAATAATAAATCAC
11980 ATTAATATTTAAGCACA
1 ATTAATATTTAAGCACA
11997 GTTATAAGAA
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
46 54 0.98
47 1 0.02
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (46 bp):
ATTAATATTTAAGCACAAATCACACTAACATTTAATAATAAATCAC
Found at i:15236 original size:78 final size:78
Alignment explanation
Indices: 15090--15449 Score: 481
Period size: 79 Copynumber: 4.6 Consensus size: 78
15080 AGTTTAACTG
* * * *
15090 ACTAGAGATGGGCTCACAATTGCGATTTATCTGCTAGCCACTAGGTGTCAGGATTTGACGGATAT
1 ACTAGAGCTGGGCTCACAATTGCGGTTTATCCGCTAGGCACT-GGTGTCAGGATTTGACGGATAT
15155 TGTTGGTTAATCCA
65 TGTTGGTTAATCCA
* * * *
15169 ACTAGAGCTAGGCTCACAATTGTGGTTTATCCACTAGGCACTGGTGTCAAGATTTGACGGATATT
1 ACTAGAGCTGGGCTCACAATTGCGGTTTATCCGCTAGGCACTGGTGTCAGGATTTGACGGATATT
15234 GTTGGTTAATCCA
66 GTTGGTTAATCCA
* *
15247 ACTAGAGTTGGGCTCACAATTGCGGTTTATCCGCTAGGCACTGGATGTCAGGATTTGTCGGATAT
1 ACTAGAGCTGGGCTCACAATTGCGGTTTATCCGCTAGGCACTGG-TGTCAGGATTTGACGGATAT
15312 TGTTGGTTAATCCA
65 TGTTGGTTAATCCA
* * * *
15326 ACTAGAGCTGGGCTCACAATTGCGATTTATCCG-TCAGGCATTGGGTGCCAGGATTTGA-TGATT
1 ACTAGAGCTGGGCTCACAATTGCGGTTTATCCGCT-AGGCACT-GGTGTCAGGATTTGACGGA-T
15389 ATTTGTTGGTTAATCCA
63 A-TTGTTGGTTAATCCA
* * ** *
15406 ACTAGAGTTTGGCTCACTTTTGTGGTTTATCCGCTAGGCACTGG
1 ACTAGAGCTGGGCTCACAATTGCGGTTTATCCGCTAGGCACTGG
15450 GTGCTAGGAT
Statistics
Matches: 248, Mismatches: 27, Indels: 12
0.86 0.09 0.04
Matches are distributed among these distances:
78 78 0.31
79 119 0.48
80 50 0.20
81 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (78 bp):
ACTAGAGCTGGGCTCACAATTGCGGTTTATCCGCTAGGCACTGGTGTCAGGATTTGACGGATATT
GTTGGTTAATCCA
Found at i:17571 original size:20 final size:20
Alignment explanation
Indices: 17540--17593 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
17530 TAAAAAATTT
17540 AAAATTTATAAAAAGCATAAA
1 AAAATTT-TAAAAAGCATAAA
**
17561 AAAATTTTAAAAATTATAAA
1 AAAATTTTAAAAAGCATAAA
* *
17581 AAAGTTGTAAAAA
1 AAAATTTTAAAAA
17594 TTATTTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 22 0.76
21 7 0.24
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.28
Consensus pattern (20 bp):
AAAATTTTAAAAAGCATAAA
Found at i:17572 original size:9 final size:9
Alignment explanation
Indices: 17532--17653 Score: 59
Period size: 9 Copynumber: 12.7 Consensus size: 9
17522 TTTTCGAATA
17532 AAAAATT-T
1 AAAAATTAT
*
17540 AAAATTTAT
1 AAAAATTAT
* *
17549 AAAAAGCATAA
1 AAAAA--TTAT
*
17560 AAAAATTTT
1 AAAAATTAT
17569 AAAAATTAT
1 AAAAATTAT
*
17578 AAAAAAGTTGT
1 -AAAAA-TTAT
17589 AAAAATTATTT
1 AAAAATTA--T
*
17600 AAAAAATAT
1 AAAAATTAT
**
17609 ATCAA-TAT
1 AAAAATTAT
17617 AAAAAACTTAT
1 -AAAAA-TTAT
17628 AAGAAACTTAT
1 AA-AAA-TTAT
*
17639 AAAAATTTT
1 AAAAATTAT
17648 AAAAAT
1 AAAAAT
17654 GAATTTTAAA
Statistics
Matches: 87, Mismatches: 16, Indels: 21
0.70 0.13 0.17
Matches are distributed among these distances:
8 9 0.10
9 32 0.37
10 15 0.17
11 31 0.36
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.32
Consensus pattern (9 bp):
AAAAATTAT
Found at i:17594 original size:20 final size:20
Alignment explanation
Indices: 17556--17597 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
17546 TATAAAAAGC
*
17556 ATAAAAAAATTTTAAAAATT
1 ATAAAAAAATTGTAAAAATT
*
17576 ATAAAAAAGTTGTAAAAATT
1 ATAAAAAAATTGTAAAAATT
17596 AT
1 AT
17598 TTAAAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (20 bp):
ATAAAAAAATTGTAAAAATT
Found at i:21093 original size:20 final size:20
Alignment explanation
Indices: 21046--21099 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
21036 ATTTTGAAGT
*
21046 GTTAAAATGATTTTGACTAA
1 GTTAAAATCATTTTGACTAA
* *
21066 GTTCAAATTATTTTGA-TATA
1 GTTAAAATCATTTTGACTA-A
*
21086 TTTAAAATCATTTT
1 GTTAAAATCATTTT
21100 AACTTGATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
19 2 0.07
20 26 0.93
ACGTcount: A:0.37, C:0.06, G:0.09, T:0.48
Consensus pattern (20 bp):
GTTAAAATCATTTTGACTAA
Found at i:24227 original size:31 final size:32
Alignment explanation
Indices: 24192--24254 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 32
24182 TTATAATCTG
* *
24192 GTCATTAAATTATTTGAAA-TTTTTTATTTAA
1 GTCATTAAATTATTCGAAAGTTTCTTATTTAA
*
24223 GTCATTGAATTATTCGAAAGTTTCTTATTTAA
1 GTCATTAAATTATTCGAAAGTTTCTTATTTAA
24255 ATCACTGAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 17 0.61
32 11 0.39
ACGTcount: A:0.33, C:0.06, G:0.10, T:0.51
Consensus pattern (32 bp):
GTCATTAAATTATTCGAAAGTTTCTTATTTAA
Found at i:24979 original size:12 final size:13
Alignment explanation
Indices: 24958--24986 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
24948 TATCAGTTTC
24958 TTTTCTTTTTTTT
1 TTTTCTTTTTTTT
24971 TTTTCTTTTTTTT
1 TTTTCTTTTTTTT
24984 TTT
1 TTT
24987 ATTTCTCGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (13 bp):
TTTTCTTTTTTTT
Found at i:25081 original size:98 final size:96
Alignment explanation
Indices: 24971--25253 Score: 444
Period size: 99 Copynumber: 2.9 Consensus size: 96
24961 TCTTTTTTTT
*
24971 TTTTCTTTTTTTTTTT-ATTTCTCGAGCTTTTACCGTTCAAAAATGATAGACAAAGCTAAAACGA
1 TTTTCTTTTTTTTTTTAATTTCTCGAGCTTTTACAGTTCAAAAATGA-AGACAAAGCTAAAACGA
25035 AAACCCAAT-TTTACTCCATGGGTATCAGTTTC
65 AAACCC-ATCTTTACTCCATGGGTATCAGTTTC
*
25067 TTTTCTTTTCTTTTTTTAATTTCTCGAGCTTTTACAATTCAAAAATGAAGGACAAAGCTAAAATC
1 TTTTCTTTT-TTTTTTTAATTTCTCGAGCTTTTACAGTTCAAAAATGAA-GACAAAGCTAAAA-C
25132 GAAAACCCATCTTTACTCCATGGGTATCAGTTTC
63 GAAAACCCATCTTTACTCCATGGGTATCAGTTTC
**
25166 TTTTCTTTTTTTTTTTAAATTTCTCGAGCTTTTACAGTTCAAAAATGGCGGACAAAGCTAAAACT
1 TTTTCTTTTTTTTTTT-AATTTCTCGAGCTTTTACAGTTCAAAAAT-GAAGACAAAGCTAAAAC-
25231 GAAAACCCATCTTTACTCCATGG
63 GAAAACCCATCTTTACTCCATGG
25254 AAAATACTAG
Statistics
Matches: 174, Mismatches: 5, Indels: 13
0.91 0.03 0.07
Matches are distributed among these distances:
96 9 0.05
97 8 0.05
98 51 0.29
99 105 0.60
100 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.40
Consensus pattern (96 bp):
TTTTCTTTTTTTTTTTAATTTCTCGAGCTTTTACAGTTCAAAAATGAAGACAAAGCTAAAACGAA
AACCCATCTTTACTCCATGGGTATCAGTTTC
Found at i:35572 original size:98 final size:98
Alignment explanation
Indices: 35400--35595 Score: 374
Period size: 98 Copynumber: 2.0 Consensus size: 98
35390 TTGTAAAGAA
*
35400 GAAAATGACATTTCAGCTAACACTTATTACTGTCAAGATTAAGCAGTTGAAAAGATGGATGTTTT
1 GAAAATGACATTTCAGCTAACACTTATTACTGTCAAGATTAAGCAGTTGAAAAGATGGATGTTAT
*
35465 TTACGAAGTTCAAAGGATGTACATGATGGCATT
66 TTACAAAGTTCAAAGGATGTACATGATGGCATT
35498 GAAAATGACATTTCAGCTAACACTTATTACTGTCAAGATTAAGCAGTTGAAAAGATGGATGTTAT
1 GAAAATGACATTTCAGCTAACACTTATTACTGTCAAGATTAAGCAGTTGAAAAGATGGATGTTAT
35563 TTACAAAGTTCAAAGGATGTACATGATGGCATT
66 TTACAAAGTTCAAAGGATGTACATGATGGCATT
35596 AGCTAGACAT
Statistics
Matches: 96, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
98 96 1.00
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (98 bp):
GAAAATGACATTTCAGCTAACACTTATTACTGTCAAGATTAAGCAGTTGAAAAGATGGATGTTAT
TTACAAAGTTCAAAGGATGTACATGATGGCATT
Found at i:40982 original size:30 final size:29
Alignment explanation
Indices: 40933--41158 Score: 164
Period size: 30 Copynumber: 7.8 Consensus size: 29
40923 AATTATTTTA
* *
40933 ACCCTCAAACTATT-AAAAAATTATGTTTTG
1 ACCCTCAAACT-TTCCAAAAATT-TGATTTG
40963 ACCCTCAAACTTTCCAAAAATTTGAATTTG
1 ACCCTCAAACTTTCCAAAAATTTG-ATTTG
* * *
40993 ACCCT-AAATTTTCCAAAAAATCTAATTTG
1 ACCCTCAAACTTTCC-AAAAATTTGATTTG
41022 A-CC-CAAACTTTCCAAAAATTTGAATTTG
1 ACCCTCAAACTTTCCAAAAATTTG-ATTTG
* ** *
41050 ACCC-CAAATTTTCCAAAAATTCAAATTTA
1 ACCCTCAAACTTTCCAAAAATT-TGATTTG
* *
41079 ACCCT-AAAATTATCCAAAAATTCTAATTTG
1 ACCCTCAAACTT-TCCAAAAATT-TGATTTG
* *
41109 -GCC-CAAACTTTCCAAAAATTCTGATTTA
1 ACCCTCAAACTTTCCAAAAATT-TGATTTG
* *
41137 ACCACT-AAAGTTTTCAAAAATT
1 ACC-CTCAAACTTTCCAAAAATT
41159 CAACTTTGAC
Statistics
Matches: 161, Mismatches: 22, Indels: 26
0.77 0.11 0.12
Matches are distributed among these distances:
27 7 0.04
28 32 0.20
29 57 0.35
30 65 0.40
ACGTcount: A:0.41, C:0.21, G:0.05, T:0.33
Consensus pattern (29 bp):
ACCCTCAAACTTTCCAAAAATTTGATTTG
Found at i:41006 original size:29 final size:29
Alignment explanation
Indices: 40959--41158 Score: 196
Period size: 30 Copynumber: 6.9 Consensus size: 29
40949 AAAATTATGT
*
40959 TTTGACCCTCAAACTTTCCAAAAATTTGAA
1 TTTGACCCT-AAATTTTCCAAAAATTTGAA
*
40989 TTTGACCCTAAATTTTCCAAAAAATCT-AA
1 TTTGACCCTAAATTTTCC-AAAAATTTGAA
*
41018 TTTGACCC-AAACTTTCCAAAAATTTGAA
1 TTTGACCCTAAATTTTCCAAAAATTTGAA
* **
41046 TTTGACCCCAAATTTTCCAAAAATTCAAA
1 TTTGACCCTAAATTTTCCAAAAATTTGAA
* *
41075 TTTAACCCTAAAATTATCCAAAAATTCT-AA
1 TTTGACCCT-AAATTTTCCAAAAATT-TGAA
* *
41105 TTTGGCCC-AAACTTTCCAAAAATTCTG-A
1 TTTGACCCTAAATTTTCCAAAAATT-TGAA
*
41133 TTTAACCACTAAAGTTTT-CAAAAATT
1 TTTGACC-CTAAA-TTTTCCAAAAATT
41159 CAACTTTGAC
Statistics
Matches: 143, Mismatches: 18, Indels: 18
0.80 0.10 0.10
Matches are distributed among these distances:
27 7 0.05
28 40 0.28
29 43 0.30
30 50 0.35
31 3 0.02
ACGTcount: A:0.40, C:0.21, G:0.05, T:0.34
Consensus pattern (29 bp):
TTTGACCCTAAATTTTCCAAAAATTTGAA
Found at i:41037 original size:57 final size:58
Alignment explanation
Indices: 40969--41158 Score: 235
Period size: 57 Copynumber: 3.3 Consensus size: 58
40959 TTTGACCCTC
* *
40969 AAACTTTCCAAAAATTTGAATTTGACCCTAAATTTTCCAAAAAATCTAATTTGACC-C-
1 AAACTTTCCAAAAATTTGAATTTGACCC-AAATTTTCCAAAAATTCTAATTTAACCACT
*
41026 AAACTTTCCAAAAATTTGAATTTGACCCCAAATTTTCCAAAAATTCAAATTTAACC-CT
1 AAACTTTCCAAAAATTTGAATTTGA-CCCAAATTTTCCAAAAATTCTAATTTAACCACT
* * * *
41084 AAAATTATCCAAAAATTCT-AATTTGGCCCAAACTTTCCAAAAATTCTGATTTAACCACT
1 AAACTT-TCCAAAAATT-TGAATTTGACCCAAATTTTCCAAAAATTCTAATTTAACCACT
* *
41143 AAAGTTTTCAAAAATT
1 AAACTTTCCAAAAATT
41159 CAACTTTGAC
Statistics
Matches: 118, Mismatches: 10, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
57 50 0.42
58 44 0.37
59 23 0.19
60 1 0.01
ACGTcount: A:0.42, C:0.21, G:0.05, T:0.33
Consensus pattern (58 bp):
AAACTTTCCAAAAATTTGAATTTGACCCAAATTTTCCAAAAATTCTAATTTAACCACT
Found at i:41089 original size:87 final size:86
Alignment explanation
Indices: 40948--41161 Score: 270
Period size: 87 Copynumber: 2.5 Consensus size: 86
40938 CAAACTATTA
* * * ** * *
40948 AAAAATTATGTTTTGACCCTCAAACTTTCCAAAAATTTGAATTTGACCCTAAATTTTCCAAAAAA
1 AAAAATTCTGATTTGACCC-CAAATTTTCCAAAAATTCAAATTTAACCCTAAATTATCCAAAAAA
41013 TCTAATTTGACCCAAACTTTCC
65 TCTAATTTGACCCAAACTTTCC
41035 AAAAATT-TGAATTTGACCCCAAATTTTCCAAAAATTCAAATTTAACCCTAAAATTATCCAAAAA
1 AAAAATTCTG-ATTTGACCCCAAATTTTCCAAAAATTCAAATTTAACCCT-AAATTATCCAAAAA
* *
41099 TTCTAATTTGGCCCAAACTTTCC
64 ATCTAATTTGACCCAAACTTTCC
* *
41122 AAAAATTCTGATTTAACCACTAAAGTTTT-CAAAAATTCAA
1 AAAAATTCTGATTTGACC-CCAAA-TTTTCCAAAAATTCAA
41162 CTTTGACCTG
Statistics
Matches: 112, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
86 28 0.25
87 63 0.56
88 17 0.15
89 4 0.04
ACGTcount: A:0.41, C:0.21, G:0.05, T:0.33
Consensus pattern (86 bp):
AAAAATTCTGATTTGACCCCAAATTTTCCAAAAATTCAAATTTAACCCTAAATTATCCAAAAAAT
CTAATTTGACCCAAACTTTCC
Found at i:41230 original size:27 final size:26
Alignment explanation
Indices: 41200--41300 Score: 96
Period size: 27 Copynumber: 3.7 Consensus size: 26
41190 AAATCCCTTT
*
41200 TTTTATATGCATATGTATATTATTTTA
1 TTTTAT-TGTATATGTATATTATTTTA
* *
41227 TTTTATTGTATTTTGTATATGTATTATTT
1 TTTTATTGTA-TATGTATAT-TATT-TTA
41256 TCTATTATGTGTATATGTATATTATTTTA
1 T-T-TTAT-TGTATATGTATATTATTTTA
*
41285 TTTTATTTTAT-TGTAT
1 TTTTATTGTATATGTAT
41301 TTTGTATATG
Statistics
Matches: 62, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
25 5 0.08
26 7 0.11
27 18 0.29
28 5 0.08
29 6 0.10
30 5 0.08
31 12 0.19
32 4 0.06
ACGTcount: A:0.25, C:0.02, G:0.09, T:0.64
Consensus pattern (26 bp):
TTTTATTGTATATGTATATTATTTTA
Found at i:41255 original size:31 final size:31
Alignment explanation
Indices: 41217--41326 Score: 145
Period size: 31 Copynumber: 3.5 Consensus size: 31
41207 TGCATATGTA
41217 TATTATTTTATTTTATTGTATTTTGTATATG
1 TATTATTTTATTTTATTGTATTTTGTATATG
* * *
41248 TATTATTTTCTATTATGTGTA-TATGTATAT-
1 TATTATTTTATTTTAT-TGTATTTTGTATATG
41278 TATTTTATTTTATTTTATTGTATTTTGTATATG
1 TA--TTATTTTATTTTATTGTATTTTGTATATG
41311 TATTATTTT-TTTTATT
1 TATTATTTTATTTTATT
41327 ACGTATACTT
Statistics
Matches: 68, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
30 9 0.13
31 33 0.49
32 24 0.35
33 2 0.03
ACGTcount: A:0.23, C:0.01, G:0.08, T:0.68
Consensus pattern (31 bp):
TATTATTTTATTTTATTGTATTTTGTATATG
Found at i:44596 original size:19 final size:20
Alignment explanation
Indices: 44574--44618 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
44564 TTATAGTAGG
44574 ATTTAAT-ATTTAAGATAT-T
1 ATTTAATCATTTAA-ATATGT
*
44593 ATTT-ATCATTTAAATTTGT
1 ATTTAATCATTTAAATATGT
44612 ATTTAAT
1 ATTTAAT
44619 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
18 5 0.23
19 15 0.68
20 2 0.09
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (20 bp):
ATTTAATCATTTAAATATGT
Found at i:45451 original size:22 final size:21
Alignment explanation
Indices: 45426--45472 Score: 85
Period size: 22 Copynumber: 2.2 Consensus size: 21
45416 TTTCTATTTC
45426 TTTTAATTATATTCTCTTTTAT
1 TTTTAATTATATT-TCTTTTAT
45448 TTTTAATTATATTTCTTTTAT
1 TTTTAATTATATTTCTTTTAT
45469 TTTT
1 TTTT
45473 CCTTAGATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 12 0.48
22 13 0.52
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTTAATTATATTTCTTTTAT
Found at i:45713 original size:21 final size:21
Alignment explanation
Indices: 45668--45720 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
45658 TTGCACTAGT
**
45668 TCTACCGATACAAGTATGATT
1 TCTACCGATACAAGTATGACA
45689 TCTACCGATACAAGTTAT-ACA
1 TCTACCGATACAAG-TATGACA
*
45710 TCTACCAATAC
1 TCTACCGATAC
45721 CAAAAACTCC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 25 0.89
22 3 0.11
ACGTcount: A:0.36, C:0.25, G:0.09, T:0.30
Consensus pattern (21 bp):
TCTACCGATACAAGTATGACA
Found at i:53770 original size:8 final size:8
Alignment explanation
Indices: 53754--53806 Score: 54
Period size: 8 Copynumber: 6.4 Consensus size: 8
53744 GGAAGAAATT
53754 AAAAA-AA
1 AAAAAGAA
53761 AAAAAGAA
1 AAAAAGAA
53769 AAAAAGAAA
1 AAAAAG-AA
*
53778 AGGAAAAGGA
1 A--AAAAGAA
53788 AAAAAGAA
1 AAAAAGAA
*
53796 TAAAAGAA
1 AAAAAGAA
53804 AAA
1 AAA
53807 TAAAAAGAGG
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
7 5 0.13
8 23 0.61
9 3 0.08
10 2 0.05
11 5 0.13
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (8 bp):
AAAAAGAA
Found at i:53811 original size:27 final size:27
Alignment explanation
Indices: 53760--53811 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
53750 AATTAAAAAA
*
53760 AAAAAAGAAAAAAAGAAAAGGAAAAGG
1 AAAAAAGAAAAAAAGAAAAAGAAAAGG
* *
53787 AAAAAAGAATAAAAGAAAAATAAAA
1 AAAAAAGAAAAAAAGAAAAAGAAAA
53812 AGAGGAGGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (27 bp):
AAAAAAGAAAAAAAGAAAAAGAAAAGG
Found at i:54769 original size:49 final size:48
Alignment explanation
Indices: 54696--54917 Score: 176
Period size: 49 Copynumber: 4.5 Consensus size: 48
54686 TCTATAGGTT
*
54696 TGAAGGGAAAGATTGAAGCTGCAACGGCAAATCTGATACCCTAGAGATA
1 TGAAGGGAAAGATTGAAGCCGCAACGGCAAATCTG-TACCCTAGAGATA
* * * * * **
54745 TGAAGAGAAAGGTTGAAGCCGCAACGACAAACTTTGTACCTTA-AGGACG
1 TGAAGGGAAAGATTGAAGCCGCAACGGCAAA-TCTGTACCCTAGA-GATA
* * ** *
54794 TGATGGGAAAGATTGAAGCCGCGACGGTGAATCTTGTACCCTAGAGTTA
1 TGAAGGGAAAGATTGAAGCCGCAACGGCAAATC-TGTACCCTAGAGATA
* * * ** * * *
54843 TGGAGGGAAAGGTTGAAGCTGCAACAACGAACCTTGTACCCTAGAGATG
1 TGAAGGGAAAGATTGAAGCCGCAACGGCAAATC-TGTACCCTAGAGATA
* * *
54892 TGAAGGGAATGATTGAGGCCACAACG
1 TGAAGGGAAAGATTGAAGCCGCAACG
54918 ATGAATCTTA
Statistics
Matches: 131, Mismatches: 38, Indels: 8
0.74 0.21 0.05
Matches are distributed among these distances:
48 2 0.02
49 125 0.95
50 4 0.03
ACGTcount: A:0.34, C:0.17, G:0.29, T:0.19
Consensus pattern (48 bp):
TGAAGGGAAAGATTGAAGCCGCAACGGCAAATCTGTACCCTAGAGATA
Found at i:54880 original size:98 final size:99
Alignment explanation
Indices: 54696--54926 Score: 270
Period size: 98 Copynumber: 2.4 Consensus size: 99
54686 TCTATAGGTT
* **
54696 TGAAGGGAAAGATTGAAGCTGCAACGGCAAATC-TGATACCCTAGAGATATGAAGAGAAAGGTTG
1 TGAAGGGAAAGATTGAAGCCGCAACGGTGAATCTTGATACCCTAGAGATATGAAGAGAAAGGTTG
* * *
54760 AAGCCGCAACGACAAACTTTGTACCTTA-AGGACG
66 AAGCCGCAACAACAAACCTTGTACCCTAGA-GACG
* * * * *
54794 TGATGGGAAAGATTGAAGCCGCGACGGTGAATCTTG-TACCCTAGAGTTATGGAGGGAAAGGTTG
1 TGAAGGGAAAGATTGAAGCCGCAACGGTGAATCTTGATACCCTAGAGATATGAAGAGAAAGGTTG
* * *
54858 AAGCTGCAACAACGAACCTTGTACCCTAGAGATG
66 AAGCCGCAACAACAAACCTTGTACCCTAGAGACG
* * * *
54892 TGAAGGGAATGATTGAGGCCACAACGATGAATCTT
1 TGAAGGGAAAGATTGAAGCCGCAACGGTGAATCTT
54927 ACACCCTGAA
Statistics
Matches: 111, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
98 108 0.97
99 3 0.03
ACGTcount: A:0.34, C:0.17, G:0.29, T:0.20
Consensus pattern (99 bp):
TGAAGGGAAAGATTGAAGCCGCAACGGTGAATCTTGATACCCTAGAGATATGAAGAGAAAGGTTG
AAGCCGCAACAACAAACCTTGTACCCTAGAGACG
Found at i:55355 original size:80 final size:79
Alignment explanation
Indices: 55206--55457 Score: 287
Period size: 80 Copynumber: 3.2 Consensus size: 79
55196 AAGTTATAAT
55206 CATCTAATCTTTTACCCTAATCAGAGGGTAGATTGAAGACCATTCC-ATCTTTTACCCTAATCAG
1 CATCTAATCTTTTACCCTAATCAGAGGGTAGATTGAAGACCA-TCCAATCTTTTACCCTAATCAG
55270 AGGGCAGATTGAAGAC
65 AGGGCAGATTGAAG-C
* * * * * *
55286 CATCCAATCTTTTACCTTAATTAGAGGATAGATTGAAGACCATCCAATCTTTTA-CCTCGA-CCG
1 CATCTAATCTTTTACCCTAATCAGAGGGTAGATTGAAGACCATCCAATCTTTTACCCT-AATCAG
*
55349 TGGGGCAGATTGAAGC
65 -AGGGCAGATTGAAGC
* * * * *
55365 AATCTAATCTTTTACCCTAACCAGAGGGTAGATTAAAGACCAT-TAGATCTTTTACCCTAACCAG
1 CATCTAATCTTTTACCCTAATCAGAGGGTAGATTGAAGACCATCCA-ATCTTTTACCCTAATCAG
* *
55429 AGGGTAGATTGAAAAC
65 AGGGCAGATTG-AAGC
*
55445 CATCTGATCTTTT
1 CATCTAATCTTTT
55458 TTAAGGCAAT
Statistics
Matches: 143, Mismatches: 22, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
78 1 0.01
79 63 0.44
80 79 0.55
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (79 bp):
CATCTAATCTTTTACCCTAATCAGAGGGTAGATTGAAGACCATCCAATCTTTTACCCTAATCAGA
GGGCAGATTGAAGC
Found at i:55454 original size:40 final size:40
Alignment explanation
Indices: 55206--55457 Score: 246
Period size: 40 Copynumber: 6.3 Consensus size: 40
55196 AAGTTATAAT
* *
55206 CATCTAATCTTTTACCCTAATCAGAGGGTAGATTGAAGAC
1 CATCTAATCTTTTACCCTAACCAGAGGGTAGATTGAAAAC
* * * *
55246 CAT-TCCATCTTTTACCCTAATCAGAGGGCAGATTGAAGAC
1 CATCT-AATCTTTTACCCTAACCAGAGGGTAGATTGAAAAC
* * ** * *
55286 CATCCAATCTTTTACCTTAATTAGAGGATAGATTGAAGAC
1 CATCTAATCTTTTACCCTAACCAGAGGGTAGATTGAAAAC
* * * * *
55326 CATCCAATCTTTTA-CCTCGACC-GTGGGGCAGATTG-AAGC
1 CATCTAATCTTTTACCCT-AACCAG-AGGGTAGATTGAAAAC
*
55365 AATCTAATCTTTTACCCTAACCAGAGGGTAGATT-AAAGAC
1 CATCTAATCTTTTACCCTAACCAGAGGGTAGATTGAAA-AC
55405 CAT-TAGATCTTTTACCCTAACCAGAGGGTAGATTGAAAAC
1 CATCTA-ATCTTTTACCCTAACCAGAGGGTAGATTGAAAAC
*
55445 CATCTGATCTTTT
1 CATCTAATCTTTT
55458 TTAAGGCAAT
Statistics
Matches: 176, Mismatches: 25, Indels: 22
0.79 0.11 0.10
Matches are distributed among these distances:
39 33 0.19
40 139 0.79
41 4 0.02
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (40 bp):
CATCTAATCTTTTACCCTAACCAGAGGGTAGATTGAAAAC
Found at i:55540 original size:100 final size:100
Alignment explanation
Indices: 55363--55542 Score: 265
Period size: 100 Copynumber: 1.8 Consensus size: 100
55353 GCAGATTGAA
* *
55363 GCAATCTAATCTTTTACCCTAACCAGAGGGTAGATTAAAGACCATTAGATCTTTTACCCTAACCA
1 GCAATCTAATCTTTTACCCTAACCAAAGGGCAGATTAAAGACCATTAGATCTTTTACCCTAACCA
* *
55428 GAGGGTAGATTGAAAACCATCTGATCTTTTTTAAG
66 GAGGGCAAATTGAAAACCATCTGATCTTTTTTAAG
* * *
55463 GCAATCTAATCTTTTACCTTAATCAAAGGGCAGATTAAAGACCATTTA-ATCTTTTACCCTGACC
1 GCAATCTAATCTTTTACCCTAACCAAAGGGCAGATTAAAGACCA-TTAGATCTTTTACCCTAACC
55527 ATGA-GGCAAATTGAAA
65 A-GAGGGCAAATTGAAA
55543 CAATCCAATC
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
100 66 0.93
101 5 0.07
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (100 bp):
GCAATCTAATCTTTTACCCTAACCAAAGGGCAGATTAAAGACCATTAGATCTTTTACCCTAACCA
GAGGGCAAATTGAAAACCATCTGATCTTTTTTAAG
Found at i:55579 original size:39 final size:38
Alignment explanation
Indices: 55510--55797 Score: 245
Period size: 39 Copynumber: 7.3 Consensus size: 38
55500 AAGACCATTT
*
55510 AATCTTTTACCCTGACCATGAGGCAAATTGAAACAATCC
1 AATCTTTTACCCTGACCA-GAGGCAGATTGAAACAATCC
* * * *
55549 AATCTTTTACCCTAACTAGAGGACAGATTGAAGACCATCT
1 AATCTTTTACCCTGACCAGAGG-CAGATTGAA-ACAATCC
* * *
55589 AATCTCTTACCTTGACCATAGGGCAGATTGAAACAATCC
1 AATCTTTTACCCTGACCAGA-GGCAGATTGAAACAATCC
* * *
55628 AATCTTTTACCCTAACCAAAAGGCAGATTGAAGACCATCC
1 AATCTTTTACCCTGACC-AGAGGCAGATTGAA-ACAATCC
* * * * * *
55668 GATCTCTTACCCCGACCATGGGGCAGATTGAAGCAACCC
1 AATCTTTTACCCTGACCA-GAGGCAGATTGAAACAATCC
* * * *
55707 AATCTTTTACCCTCACTAAAGGGCAGATTGAAGACCAT-C
1 AATCTTTTACCCTGACCAGA-GGCAGATTGAA-ACAATCC
** * *
55746 AGATCTCCTACCCCGACCATGAGGCAGATTGAAACAATCT
1 A-ATCTTTTACCCTGACCA-GAGGCAGATTGAAACAATCC
55786 AATCTTTTACCC
1 AATCTTTTACCC
55798 ATAAAGCTAT
Statistics
Matches: 192, Mismatches: 46, Indels: 22
0.74 0.18 0.08
Matches are distributed among these distances:
38 4 0.02
39 98 0.51
40 87 0.45
41 3 0.02
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.24
Consensus pattern (38 bp):
AATCTTTTACCCTGACCAGAGGCAGATTGAAACAATCC
Found at i:55599 original size:79 final size:79
Alignment explanation
Indices: 55464--55797 Score: 431
Period size: 79 Copynumber: 4.2 Consensus size: 79
55454 TTTTTTAAGG
* * * * * *
55464 CAATCTAATCTTTTACCTTAA-TCAAAGGGCAGATTAAAGACCATTTAATCTTTTACCCTGACCA
1 CAATCCAATCTTTTACCCTAACT-AAAGGGCAGATTGAAGACCATCTAATCTCTTACCCCGACCA
*
55528 TGAGGCAAATTGAAA
65 TGAGGCAGATTGAAA
* * **
55543 CAATCCAATCTTTTACCCTAACTAGAGGACAGATTGAAGACCATCTAATCTCTTACCTTGACCAT
1 CAATCCAATCTTTTACCCTAACTAAAGGGCAGATTGAAGACCATCTAATCTCTTACCCCGACCAT
55608 -AGGGCAGATTGAAA
66 GA-GGCAGATTGAAA
* * **
55622 CAATCCAATCTTTTACCCTAACCAAAAGGCAGATTGAAGACCATCCGATCTCTTACCCCGACCAT
1 CAATCCAATCTTTTACCCTAACTAAAGGGCAGATTGAAGACCATCTAATCTCTTACCCCGACCAT
* *
55687 GGGGCAGATTGAAG
66 GAGGCAGATTGAAA
* * *
55701 CAACCCAATCTTTTACCCTCACTAAAGGGCAGATTGAAGACCATC-AGATCTCCTACCCCGACCA
1 CAATCCAATCTTTTACCCTAACTAAAGGGCAGATTGAAGACCATCTA-ATCTCTTACCCCGACCA
55765 TGAGGCAGATTGAAA
65 TGAGGCAGATTGAAA
*
55780 CAATCTAATCTTTTACCC
1 CAATCCAATCTTTTACCC
55798 ATAAAGCTAT
Statistics
Matches: 222, Mismatches: 29, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
78 1 0.00
79 220 0.99
80 1 0.00
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.25
Consensus pattern (79 bp):
CAATCCAATCTTTTACCCTAACTAAAGGGCAGATTGAAGACCATCTAATCTCTTACCCCGACCAT
GAGGCAGATTGAAA
Found at i:55616 original size:40 final size:40
Alignment explanation
Indices: 55464--55797 Score: 277
Period size: 40 Copynumber: 8.4 Consensus size: 40
55454 TTTTTTAAGG
* * * * * *
55464 CAATCTAATCTTTTACCTTAATCAAAGGGCAGATTAAAGA
1 CAATCCAATCTTTTACCCTGACCATAGGGCAGATTGAAGA
* ** *
55504 CCATTTAATCTTTTACCCTGACCAT-GAGGCAAATTGAA-A
1 CAATCCAATCTTTTACCCTGACCATAG-GGCAGATTGAAGA
* * * *
55543 CAATCCAATCTTTTACCCTAACTAGAGGACAGATTGAAGA
1 CAATCCAATCTTTTACCCTGACCATAGGGCAGATTGAAGA
* * * *
55583 CCATCTAATCTCTTACCTTGACCATAGGGCAGATTGAA-A
1 CAATCCAATCTTTTACCCTGACCATAGGGCAGATTGAAGA
* * *
55622 CAATCCAATCTTTTACCCTAACCAAAAGGCAGATTGAAGA
1 CAATCCAATCTTTTACCCTGACCATAGGGCAGATTGAAGA
* * * * *
55662 CCATCCGATCTCTTACCCCGACCATGGGGCAGATTGAAG-
1 CAATCCAATCTTTTACCCTGACCATAGGGCAGATTGAAGA
* * * *
55701 CAACCCAATCTTTTACCCTCACTAAAGGGCAGATTGAAGA
1 CAATCCAATCTTTTACCCTGACCATAGGGCAGATTGAAGA
* ** *
55741 CCAT-CAGATCTCCTACCCCGACCAT-GAGGCAGATTGAA-A
1 CAATCCA-ATCTTTTACCCTGACCATAG-GGCAGATTGAAGA
*
55780 CAATCTAATCTTTTACCC
1 CAATCCAATCTTTTACCC
55798 ATAAAGCTAT
Statistics
Matches: 226, Mismatches: 60, Indels: 17
0.75 0.20 0.06
Matches are distributed among these distances:
39 108 0.48
40 118 0.52
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.25
Consensus pattern (40 bp):
CAATCCAATCTTTTACCCTGACCATAGGGCAGATTGAAGA
Found at i:55619 original size:179 final size:179
Alignment explanation
Indices: 55291--55621 Score: 441
Period size: 179 Copynumber: 1.8 Consensus size: 179
55281 AAGACCATCC
* * * * * *
55291 AATCTTTTACCTTAATTAGAGGATAGATTGAAGACCATCCAATCTTTTACCTCGACCGTGGGGCA
1 AATCTTTTACCTTAATCAAAGGACAGATTAAAGACCATCCAATCTTTTACCTCGACCATGAGGCA
* * * ** *
55356 GATTGAAGCAATCTAATCTTTTACCCTAACCAGAGGGTAGATTAAAGACCATTAGATCTTTTACC
66 AATTGAAACAATCCAATCTTTTACCCTAACCAGAGGACAGATTAAAGACCATTAGATCTCTTACC
*
55421 CTAACCAGAGGGTAGATTGAAAACCATCTGATCTTTTTTAAGGCAATCT
131 CTAACCAGAGGGCAGATTGAAAACCATCTGATCTTTTTTAAGGCAATCT
* **
55470 AATCTTTTACCTTAATCAAAGGGCAGATTAAAGACCATTTAATCTTTTACC-CTGACCATGAGGC
1 AATCTTTTACCTTAATCAAAGGACAGATTAAAGACCATCCAATCTTTTACCTC-GACCATGAGGC
* *
55534 AAATTGAAACAATCCAATCTTTTACCCTAACTAGAGGACAGATTGAAGACCATCTA-ATCTCTTA
65 AAATTGAAACAATCCAATCTTTTACCCTAACCAGAGGACAGATTAAAGACCAT-TAGATCTCTTA
* * *
55598 CCTTGACCATAGGGCAGATTGAAA
129 CCCTAACCAGAGGGCAGATTGAAA
55622 CAATCCAATC
Statistics
Matches: 129, Mismatches: 21, Indels: 4
0.84 0.14 0.03
Matches are distributed among these distances:
178 1 0.01
179 126 0.98
180 2 0.02
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.30
Consensus pattern (179 bp):
AATCTTTTACCTTAATCAAAGGACAGATTAAAGACCATCCAATCTTTTACCTCGACCATGAGGCA
AATTGAAACAATCCAATCTTTTACCCTAACCAGAGGACAGATTAAAGACCATTAGATCTCTTACC
CTAACCAGAGGGCAGATTGAAAACCATCTGATCTTTTTTAAGGCAATCT
Found at i:55665 original size:258 final size:259
Alignment explanation
Indices: 55207--55679 Score: 680
Period size: 258 Copynumber: 1.8 Consensus size: 259
55197 AGTTATAATC
* * * * *
55207 ATCTAATCTTTTACCCTAATCAGAGGGTAGATTGAAGACCATTCCATCTTTTACCCTAATCAGAG
1 ATCTAATCTTTTACCCTAATCAAAGGGCAGATTAAAGACCATTCAATCTTTTACCCTAACCAGAG
* * * * * *
55272 GGCAGATTGAAGACCATCCAATCTTTTACCTTAATTAGAGGATAGATTGAAGACCATCCAATCTT
66 GGCAAATTGAAGACAATCCAATCTTTTACCCTAACTAGAGGACAGATTGAAGACCATCCAATCTC
* * * * * * *
55337 TTACCTCGACCGTGGGGCAGATTGAAGCAATCTAATCTTTTACCCTAACCAGAGGGTAGATTAAA
131 TTACCTCGACCATAGGGCAGATTGAAACAATCCAATCTTTTACCCTAACCAAAAGGCAGATTAAA
* *
55402 GACCATTAGATCTTTTACCCTAACCAGAGGGTAGATTGAAAACCATCTGATCTTTTTTAAGGCA
196 GACCATCAGATCTCTTACCCTAACCAGAGGGTAGATTGAAAACCATCTGATCTTTTTTAAGGCA
* * *
55466 ATCTAATCTTTTACCTTAATCAAAGGGCAGATTAAAGACCATTTAATCTTTTACCCTGACCATGA
1 ATCTAATCTTTTACCCTAATCAAAGGGCAGATTAAAGACCATTCAATCTTTTACCCTAACCA-GA
*
55531 -GGCAAATTGAA-ACAATCCAATCTTTTACCCTAACTAGAGGACAGATTGAAGACCATCTAATCT
65 GGGCAAATTGAAGACAATCCAATCTTTTACCCTAACTAGAGGACAGATTGAAGACCATCCAATCT
* *
55594 CTTACCTTGACCATAGGGCAGATTGAAACAATCCAATCTTTTACCCTAACCAAAAGGCAGATTGA
130 CTTACCTCGACCATAGGGCAGATTGAAACAATCCAATCTTTTACCCTAACCAAAAGGCAGATTAA
*
55659 AGACCATCCGATCTCTTACCC
195 AGACCATCAGATCTCTTACCC
55680 CGACCATGGG
Statistics
Matches: 186, Mismatches: 27, Indels: 3
0.86 0.12 0.01
Matches are distributed among these distances:
258 120 0.65
259 64 0.34
260 2 0.01
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (259 bp):
ATCTAATCTTTTACCCTAATCAAAGGGCAGATTAAAGACCATTCAATCTTTTACCCTAACCAGAG
GGCAAATTGAAGACAATCCAATCTTTTACCCTAACTAGAGGACAGATTGAAGACCATCCAATCTC
TTACCTCGACCATAGGGCAGATTGAAACAATCCAATCTTTTACCCTAACCAAAAGGCAGATTAAA
GACCATCAGATCTCTTACCCTAACCAGAGGGTAGATTGAAAACCATCTGATCTTTTTTAAGGCA
Found at i:57198 original size:30 final size:30
Alignment explanation
Indices: 57153--57209 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
57143 TTTGCTTTTC
*
57153 TTTTTCTTATTTTCAATTCGG-CCTTACAA
1 TTTTACTTATTTTCAATTCGGTCCTTACAA
*
57182 TTTTACTTAGTTTTCAATTTGGTCCTTA
1 TTTTACTTA-TTTTCAATTCGGTCCTTA
57210 ACCCAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 8 0.33
30 11 0.46
31 5 0.21
ACGTcount: A:0.19, C:0.18, G:0.09, T:0.54
Consensus pattern (30 bp):
TTTTACTTATTTTCAATTCGGTCCTTACAA
Found at i:57334 original size:28 final size:29
Alignment explanation
Indices: 57285--57348 Score: 94
Period size: 28 Copynumber: 2.2 Consensus size: 29
57275 ATTTTATTTT
*
57285 AAAATTATTTTTTAATCCCCAAACTATCCA
1 AAAATTATTTTTGAA-CCCCAAACTATCCA
*
57315 AAAATTATTTTTGAA-CCCAAACTTTCCA
1 AAAATTATTTTTGAACCCCAAACTATCCA
57343 AAAATT
1 AAAATT
57349 CAAATTTAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 18 0.56
30 14 0.44
ACGTcount: A:0.42, C:0.20, G:0.02, T:0.36
Consensus pattern (29 bp):
AAAATTATTTTTGAACCCCAAACTATCCA
Found at i:57371 original size:30 final size:30
Alignment explanation
Indices: 57330--57480 Score: 171
Period size: 30 Copynumber: 5.0 Consensus size: 30
57320 TATTTTTGAA
* * *
57330 CCCAAACTTTCCAAAAATTCAAATTTAACC
1 CCCAAATTTTCCAAAAATTCGAATTTGACC
* *
57360 CCCAAATTTTCCAAAAATTTGAATTTAACC
1 CCCAAATTTTCCAAAAATTCGAATTTGACC
* *
57390 CCAAAATTTTCCAAAAATTCCAATTTGACC
1 CCCAAATTTTCCAAAAATTCGAATTTGACC
* * *
57420 CCCAAACTTTCTAAAAATTTTG-ATTTGACC
1 CCCAAATTTTCCAAAAA-TTCGAATTTGACC
*
57450 CCTAAAGTTTT-CAAAAATTCGAATTTGACC
1 CCCAAA-TTTTCCAAAAATTCGAATTTGACC
57480 C
1 C
57481 GATTTTAATG
Statistics
Matches: 102, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
29 3 0.03
30 94 0.92
31 5 0.05
ACGTcount: A:0.38, C:0.25, G:0.05, T:0.32
Consensus pattern (30 bp):
CCCAAATTTTCCAAAAATTCGAATTTGACC
Found at i:57421 original size:60 final size:61
Alignment explanation
Indices: 57301--57480 Score: 196
Period size: 60 Copynumber: 3.0 Consensus size: 61
57291 ATTTTTTAAT
* * *
57301 CCCCAAACTATCCAAAAATTATT--TTTGAA-CCC--AAACTTTCCAAAAATTCAAATTTAAC
1 CCCCAAACTTTCCAAAAATT-TTGATTT-AACCCCTAAAATTTTCCAAAAATTCAAATTTGAC
* *
57359 CCCCAAATTTTCCAAAAA-TTTGAATTTAACCCC-AAAATTTTCCAAAAATTCCAATTTGAC
1 CCCCAAACTTTCCAAAAATTTTG-ATTTAACCCCTAAAATTTTCCAAAAATTCAAATTTGAC
* * * *
57419 CCCCAAACTTTCTAAAAATTTTGATTTGACCCCTAAAGTTTT-CAAAAATTCGAATTTGAC
1 CCCCAAACTTTCCAAAAATTTTGATTTAACCCCTAAAATTTTCCAAAAATTCAAATTTGAC
57479 CC
1 CC
57481 GATTTTAATG
Statistics
Matches: 105, Mismatches: 10, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
56 2 0.02
57 1 0.01
58 18 0.17
59 6 0.06
60 67 0.64
61 11 0.10
ACGTcount: A:0.39, C:0.25, G:0.04, T:0.32
Consensus pattern (61 bp):
CCCCAAACTTTCCAAAAATTTTGATTTAACCCCTAAAATTTTCCAAAAATTCAAATTTGAC
Found at i:57538 original size:27 final size:28
Alignment explanation
Indices: 57508--57632 Score: 123
Period size: 27 Copynumber: 4.4 Consensus size: 28
57498 TTTAAATCCC
*
57508 TTTTTTTTTATATGCA-TATGTATAT-TA
1 TTTTTTTTTAT-TGTATTATGTATATGTA
* *
57535 TTTTATTTTATTGTATTTTGTATATGTA
1 TTTTTTTTTATTGTATTATGTATATGTA
57563 TTATTTTCTATTATGTGTA-TATGTATAT-TA
1 TT-TTTT-T-TTAT-TGTATTATGTATATGTA
* *
57593 TTTTATTTTATTGTATTTTGTATATGTA
1 TTTTTTTTTATTGTATTATGTATATGTA
*
57621 TTATTTTTTATT
1 TTTTTTTTTATT
57633 ATGTATACTT
Statistics
Matches: 81, Mismatches: 9, Indels: 15
0.77 0.09 0.14
Matches are distributed among these distances:
26 7 0.09
27 30 0.37
28 17 0.21
29 6 0.07
30 5 0.06
31 12 0.15
32 4 0.05
ACGTcount: A:0.23, C:0.02, G:0.09, T:0.66
Consensus pattern (28 bp):
TTTTTTTTTATTGTATTATGTATATGTA
Found at i:57560 original size:33 final size:33
Alignment explanation
Indices: 57523--57632 Score: 130
Period size: 33 Copynumber: 3.6 Consensus size: 33
57513 TTTTATATGC
57523 ATATGTATATTATTTTATTTTATTGTATTTTGT
1 ATATGTATATTATTTTATTTTATTGTATTTTGT
* *
57556 ATATG--TATTA--TT-TTCTA-T-TA-TGTGT
1 ATATGTATATTATTTTATTTTATTGTATTTTGT
57581 ATATGTATATTATTTTATTTTATTGTATTTTGT
1 ATATGTATATTATTTTATTTTATTGTATTTTGT
57614 ATATGTATTATT-TTTTATT
1 ATATGTA-TATTATTTTATT
57633 ATGTATACTT
Statistics
Matches: 64, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
25 9 0.14
26 2 0.03
27 6 0.09
28 4 0.06
29 4 0.06
30 4 0.06
31 6 0.09
32 2 0.03
33 23 0.36
34 4 0.06
ACGTcount: A:0.25, C:0.01, G:0.09, T:0.65
Consensus pattern (33 bp):
ATATGTATATTATTTTATTTTATTGTATTTTGT
Found at i:57568 original size:31 final size:31
Alignment explanation
Indices: 57530--57627 Score: 125
Period size: 31 Copynumber: 3.3 Consensus size: 31
57520 TGCATATGTA
57530 TATTATTTTATTTTATTGTATTTTGTATATG
1 TATTATTTTATTTTATTGTATTTTGTATATG
* * *
57561 TATTATTTTCTATTATGTGTA-TATG--TA--
1 TATTATTTTATTTTAT-TGTATTTTGTATATG
57588 TATTATTTTATTTTATTGTATTTTGTATATG
1 TATTATTTTATTTTATTGTATTTTGTATATG
57619 TATTATTTT
1 TATTATTTT
57628 TTATTATGTA
Statistics
Matches: 55, Mismatches: 6, Indels: 12
0.75 0.08 0.16
Matches are distributed among these distances:
26 4 0.07
27 17 0.31
29 4 0.07
31 26 0.47
32 4 0.07
ACGTcount: A:0.23, C:0.01, G:0.09, T:0.66
Consensus pattern (31 bp):
TATTATTTTATTTTATTGTATTTTGTATATG
Found at i:57587 original size:58 final size:58
Alignment explanation
Indices: 57523--57636 Score: 219
Period size: 58 Copynumber: 2.0 Consensus size: 58
57513 TTTTATATGC
57523 ATATGTATATTATTTTATTTTATTGTATTTTGTATATGTATTATTTTCTATTATGTGT
1 ATATGTATATTATTTTATTTTATTGTATTTTGTATATGTATTATTTTCTATTATGTGT
*
57581 ATATGTATATTATTTTATTTTATTGTATTTTGTATATGTATTATTTTTTATTATGT
1 ATATGTATATTATTTTATTTTATTGTATTTTGTATATGTATTATTTTCTATTATGT
57637 ATACTTGTAA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 55 1.00
ACGTcount: A:0.25, C:0.01, G:0.10, T:0.65
Consensus pattern (58 bp):
ATATGTATATTATTTTATTTTATTGTATTTTGTATATGTATTATTTTCTATTATGTGT
Found at i:57635 original size:17 final size:16
Alignment explanation
Indices: 57548--57638 Score: 54
Period size: 16 Copynumber: 6.0 Consensus size: 16
57538 TATTTTATTG
57548 TATTTTGTATATGTAT
1 TATTTTGTATATGTAT
* *
57564 TATTTTCTATTATGT-G
1 TATTTTGTA-TATGTAT
*
57580 TA-TATGTATAT-TAT
1 TATTTTGTATATGTAT
*
57594 T-TTATT-T-TAT-T-G
1 TATT-TTGTATATGTAT
57606 TATTTTGTATATGTAT
1 TATTTTGTATATGTAT
*
57622 TATTTTTTATTATGTAT
1 TATTTTGTA-TATGTAT
57639 ACTTGTAAAT
Statistics
Matches: 56, Mismatches: 9, Indels: 19
0.67 0.11 0.23
Matches are distributed among these distances:
12 3 0.05
13 8 0.14
14 9 0.16
15 6 0.11
16 18 0.32
17 12 0.21
ACGTcount: A:0.24, C:0.01, G:0.10, T:0.65
Consensus pattern (16 bp):
TATTTTGTATATGTAT
Found at i:57645 original size:31 final size:30
Alignment explanation
Indices: 57530--57638 Score: 120
Period size: 31 Copynumber: 3.7 Consensus size: 30
57520 TGCATATGTA
57530 TATTATTTTATT-TTATTGTATTTTGTATATG
1 TATTATTTT-TTATTA-TGTATTTTGTATATG
* * *
57561 TATTATTTTCTATTATGTGTATATGTATAT-
1 TATTATTTTTTATTATGTAT-TTTGTATATG
57591 TATT-TTATTTTA-T-TGTATTTTGTATATG
1 TATTATT-TTTTATTATGTATTTTGTATATG
57619 TATTATTTTTTATTATGTAT
1 TATTATTTTTTATTATGTAT
57639 ACTTGTAAAT
Statistics
Matches: 65, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
27 8 0.12
28 13 0.20
29 6 0.09
30 18 0.28
31 20 0.31
ACGTcount: A:0.24, C:0.01, G:0.09, T:0.66
Consensus pattern (30 bp):
TATTATTTTTTATTATGTATTTTGTATATG
Found at i:61030 original size:18 final size:18
Alignment explanation
Indices: 61009--61065 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
60999 AACCCAATTG
* *
61009 GAACCTAACCCGTTGATC
1 GAACCAAACCTGTTGATC
* *
61027 GAACCCAACCTGTTGACC
1 GAACCAAACCTGTTGATC
*
61045 CAACCCAAACCTGTTGATC
1 GAA-CCAAACCTGTTGATC
61064 GA
1 GA
61066 CTCGACCCAT
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
18 17 0.55
19 14 0.45
ACGTcount: A:0.30, C:0.35, G:0.16, T:0.19
Consensus pattern (18 bp):
GAACCAAACCTGTTGATC
Found at i:61124 original size:21 final size:21
Alignment explanation
Indices: 61098--61138 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
61088 CCCGTTAACT
*
61098 GTTGATCGTTGATCATTGACA
1 GTTGATCGTTGACCATTGACA
61119 GTTGATCGTTGACCATTGAC
1 GTTGATCGTTGACCATTGAC
61139 TTTTTTCAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.37
Consensus pattern (21 bp):
GTTGATCGTTGACCATTGACA
Found at i:68491 original size:15 final size:15
Alignment explanation
Indices: 68471--68501 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
68461 AGCGTAATTA
68471 TAGACTTATTTTATT
1 TAGACTTATTTTATT
68486 TAGACTTATTTTATT
1 TAGACTTATTTTATT
68501 T
1 T
68502 TTTCTTATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.06, G:0.06, T:0.61
Consensus pattern (15 bp):
TAGACTTATTTTATT
Found at i:77349 original size:50 final size:51
Alignment explanation
Indices: 77227--77365 Score: 167
Period size: 50 Copynumber: 2.7 Consensus size: 51
77217 TAAAATATTA
* * *
77227 TAAATAAATATTTATGTTTATGTAAAAATAAT-AGATCTAAACAAAATCCAGT
1 TAAATAAATATTTATATTTATAT-AAAAT-ATCAAATCTAAACAAAATCCAGT
* *
77279 TAAATAAATATTTATTTTTATATAAAATATCAAATTTAAAC-AAAT-CATGT
1 TAAATAAATATTTATATTTATATAAAATATCAAATCTAAACAAAATCCA-GT
* *
77329 TAAATAAATATTTATATTTATTTAAAATATCAGATCT
1 TAAATAAATATTTATATTTATATAAAATATCAAATCT
77366 TGAAAACAAA
Statistics
Matches: 77, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
49 2 0.03
50 41 0.53
51 13 0.17
52 21 0.27
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.40
Consensus pattern (51 bp):
TAAATAAATATTTATATTTATATAAAATATCAAATCTAAACAAAATCCAGT
Found at i:79835 original size:19 final size:20
Alignment explanation
Indices: 79806--79844 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
79796 CCTTTCCCAT
79806 ATAAGGTCTATATCAAACAC
1 ATAAGGTCTATATCAAACAC
79826 ATAA-GTCTATATCAAACAC
1 ATAAGGTCTATATCAAACAC
79845 TTCCTTGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.46, C:0.21, G:0.08, T:0.26
Consensus pattern (20 bp):
ATAAGGTCTATATCAAACAC
Found at i:81444 original size:107 final size:108
Alignment explanation
Indices: 81256--81453 Score: 274
Period size: 107 Copynumber: 1.8 Consensus size: 108
81246 AGGAACATAC
* ** *
81256 TCGATTATGCAAATTCTACAAAAAAATCATACCCAACACTTTAGGACACAATTCTTCGAAGTTAT
1 TCGATTATGCAAATTCTAC-AAAAAATCACACCCAACAAGTTAGGACACAATTCTTCGAAGTTAC
*
81321 CACACAAAAGAATATTGCCTCGATTTTTTTTTTTAAAAGGATAA
65 CACACAAAAGAATATTGCCTCAATTTTTTTTTTTAAAAGGATAA
* * * *
81365 TCGATTGTGTAAATTCTAC-AAAAATCACACCGAACAAGTTAGGGCACAATTCTTCGAAGATT-C
1 TCGATTATGCAAATTCTACAAAAAATCACACCCAACAAGTTAGGACACAATTCTTCGAAG-TTAC
*
81428 CACACAAAAGAATATTGTCTCAATTT
65 CACACAAAAGAATATTGCCTCAATTT
81454 AAAATGTATT
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
107 59 0.76
108 2 0.03
109 17 0.22
ACGTcount: A:0.39, C:0.19, G:0.12, T:0.30
Consensus pattern (108 bp):
TCGATTATGCAAATTCTACAAAAAATCACACCCAACAAGTTAGGACACAATTCTTCGAAGTTACC
ACACAAAAGAATATTGCCTCAATTTTTTTTTTTAAAAGGATAA
Found at i:81777 original size:14 final size:14
Alignment explanation
Indices: 81754--81804 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
81744 TTTTAGAAAC
81754 AAAT-AAAGAATAA
1 AAATAAAAGAATAA
81767 AAATAAAAGAATAA
1 AAATAAAAGAATAA
***
81781 TTTTAAAAGAAATAAA
1 AAATAAAAG-AAT-AA
81797 AAATAAAA
1 AAATAAAA
81805 TGGGTAAATT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
13 4 0.14
14 15 0.52
15 3 0.10
16 7 0.24
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.20
Consensus pattern (14 bp):
AAATAAAAGAATAA
Found at i:82273 original size:21 final size:21
Alignment explanation
Indices: 82226--82285 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
82216 AATGTTTGGA
*
82226 TTTTTTTGTTTCTTGAATCTGCC
1 TTTTTTT-TTTCTTAAATCTG-C
* *
82249 TTTTTTATTTCTTAAATC-GT
1 TTTTTTTTTTCTTAAATCTGC
82269 TTTTTTTTTTACTTAAA
1 TTTTTTTTTT-CTTAAA
82286 AACTGTTCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 9 0.28
21 7 0.22
22 10 0.31
23 6 0.19
ACGTcount: A:0.17, C:0.12, G:0.07, T:0.65
Consensus pattern (21 bp):
TTTTTTTTTTCTTAAATCTGC
Found at i:82530 original size:3 final size:3
Alignment explanation
Indices: 82522--82551 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
82512 AGCCTTCTTT
82522 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
82552 ATGCTTAGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:95086 original size:113 final size:113
Alignment explanation
Indices: 94885--95095 Score: 316
Period size: 113 Copynumber: 1.8 Consensus size: 113
94875 TGAAAAATTT
* * *
94885 AAAGGAGCATACTCGATTATGCAAATTCTACAAAAAAAAATATACCCAACACGTTAGGGCACAAT
1 AAAGGAGAATAATCGATTATGCAAATTCTAC---AAAAAATACACCCAACACGTTAGGGCACAAT
94950 TCTTCAAAGTTTTCACACAAAAGAATATTGCCTTGATTTTTTTTTTTAAAA
63 TCTTCAAAGTTTTCACACAAAAGAATATTGCCTTGATTTTTTTTTTTAAAA
* *
95001 AAAGGAGAATAATCGATTGTGCAAATTCTAC-AAAAATCACACCCAACACGTTAGGGCACAATTT
1 AAAGGAGAATAATCGATTATGCAAATTCTACAAAAAAT-ACACCCAACACGTTAGGGCACAATTC
* *
95065 TTCGAAGTTTTCATACAAAAGAATATTGCCT
65 TTCAAAGTTTTCACACAAAAGAATATTGCCT
95096 CAATTTAAAA
Statistics
Matches: 87, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
112 6 0.07
113 53 0.61
116 28 0.32
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.29
Consensus pattern (113 bp):
AAAGGAGAATAATCGATTATGCAAATTCTACAAAAAATACACCCAACACGTTAGGGCACAATTCT
TCAAAGTTTTCACACAAAAGAATATTGCCTTGATTTTTTTTTTTAAAA
Found at i:96201 original size:3 final size:3
Alignment explanation
Indices: 96193--96222 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
96183 CTTAGCCTTC
96193 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
96223 ATGCTTAGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:99973 original size:25 final size:25
Alignment explanation
Indices: 99942--100018 Score: 154
Period size: 25 Copynumber: 3.1 Consensus size: 25
99932 ATTGAATAGT
99942 AATCAAGTCATTCATCACAAAAACA
1 AATCAAGTCATTCATCACAAAAACA
99967 AATCAAGTCATTCATCACAAAAACA
1 AATCAAGTCATTCATCACAAAAACA
99992 AATCAAGTCATTCATCACAAAAACA
1 AATCAAGTCATTCATCACAAAAACA
100017 AA
1 AA
100019 CGACTCGTGC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 52 1.00
ACGTcount: A:0.53, C:0.23, G:0.04, T:0.19
Consensus pattern (25 bp):
AATCAAGTCATTCATCACAAAAACA
Found at i:100797 original size:47 final size:48
Alignment explanation
Indices: 100728--100896 Score: 144
Period size: 48 Copynumber: 3.5 Consensus size: 48
100718 AACAATGTAT
* * *
100728 TGAATCGTGTGAATCATCGTTGTC-GGCCATTCGAGATGGTAATATAG
1 TGAATGGTATGAACCATCGTTGTCGGGCCATTCGAGATGGTAATATAG
* * * *
100775 TGAATGGTATGAACCATCGTTGTCGGGTCATTCGGGATGGTAATTTAT
1 TGAATGGTATGAACCATCGTTGTCGGGCCATTCGAGATGGTAATATAG
* * * * * * * *
100823 TAAATGGTATAAACCATCATAGTAGGGCTA-TCTGGGATGGTAATATAT
1 TGAATGGTATGAACCATCGTTGTCGGGCCATTC-GAGATGGTAATATAG
* * * *
100871 TGAATTGTAAGAATCATCATTGTCGG
1 TGAATGGTATGAACCATCGTTGTCGG
100897 ACCACCCAAG
Statistics
Matches: 98, Mismatches: 22, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
47 23 0.23
48 75 0.77
ACGTcount: A:0.28, C:0.12, G:0.26, T:0.33
Consensus pattern (48 bp):
TGAATGGTATGAACCATCGTTGTCGGGCCATTCGAGATGGTAATATAG
Found at i:102509 original size:18 final size:19
Alignment explanation
Indices: 102466--102509 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
102456 TGACTTGTTG
102466 AATATAATTAAATATATTA
1 AATATAATTAAATATATTA
* *
102485 AAT-TAATTAAA-ATTTTT
1 AATATAATTAAATATATTA
102502 AATATAAT
1 AATATAAT
102510 AATAATAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 7 0.32
18 12 0.55
19 3 0.14
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
AATATAATTAAATATATTA
Found at i:124376 original size:18 final size:18
Alignment explanation
Indices: 124353--124388 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
124343 GAATCACCCG
124353 TTCTGATGCTCAAGATAA
1 TTCTGATGCTCAAGATAA
*
124371 TTCTGATGCTCATGATAA
1 TTCTGATGCTCAAGATAA
124389 AGCATCTTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.36
Consensus pattern (18 bp):
TTCTGATGCTCAAGATAA
Found at i:136226 original size:18 final size:19
Alignment explanation
Indices: 136203--136238 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
136193 TAAAATCGAA
136203 TAATTAACCAAA-TTAATC
1 TAATTAACCAAACTTAATC
136221 TAATTAACCAAACTTAAT
1 TAATTAACCAAACTTAAT
136239 AGTTAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (19 bp):
TAATTAACCAAACTTAATC
Found at i:141419 original size:51 final size:51
Alignment explanation
Indices: 141359--141455 Score: 158
Period size: 51 Copynumber: 1.9 Consensus size: 51
141349 CACTCACGAT
* * * *
141359 TTTCAAAAGAATGGTGATATAAATGCTTAGCAAATACATTCAAATAGTCTC
1 TTTCAAAAGAATGATAATATAAATACTTAACAAATACATTCAAATAGTCTC
141410 TTTCAAAAGAATGATAATATAAATACTTAACAAATACATTCAAATA
1 TTTCAAAAGAATGATAATATAAATACTTAACAAATACATTCAAATA
141456 ATCATTTGAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 42 1.00
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.31
Consensus pattern (51 bp):
TTTCAAAAGAATGATAATATAAATACTTAACAAATACATTCAAATAGTCTC
Found at i:143939 original size:22 final size:23
Alignment explanation
Indices: 143886--143941 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
143876 TATGATATAT
143886 AATAT-AT-TTTTAATTGAATCA
1 AATATAATATTTTAATTGAATCA
*
143907 GATATAATATTTTAA-TGAGATCA
1 AATATAATATTTTAATTGA-ATCA
143930 AAT-TAATATTTT
1 AATATAATATTTT
143942 TTTATAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
21 4 0.13
22 14 0.47
23 12 0.40
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (23 bp):
AATATAATATTTTAATTGAATCA
Found at i:143942 original size:23 final size:24
Alignment explanation
Indices: 143889--143942 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
143879 GATATATAAT
*
143889 ATATTTTTAATTGAATCAGATATA
1 ATATTTTTAATTGAATCAAATATA
143913 ATA-TTTTAA-TGAGATCAAAT-TA
1 ATATTTTTAATTGA-ATCAAATATA
143935 ATATTTTT
1 ATATTTTT
143943 TTATAAAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 8 0.30
23 16 0.59
24 3 0.11
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.48
Consensus pattern (24 bp):
ATATTTTTAATTGAATCAAATATA
Found at i:145023 original size:41 final size:41
Alignment explanation
Indices: 144977--145072 Score: 156
Period size: 41 Copynumber: 2.3 Consensus size: 41
144967 TAATTTTGTT
* *
144977 TTAACAAGAATTCTAGTCACCCAATTTTAACAATTTCCACC
1 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
*
145018 TTAACAAGAATTCTAGTCACCTAATTCTAACAATCTCCACC
1 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
*
145059 TTGACAAGAATTCT
1 TTAACAAGAATTCT
145073 CTACGAACAA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.36, C:0.26, G:0.06, T:0.31
Consensus pattern (41 bp):
TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
Found at i:149452 original size:41 final size:41
Alignment explanation
Indices: 149405--149518 Score: 201
Period size: 41 Copynumber: 2.8 Consensus size: 41
149395 GAATTTTATT
149405 TTAACAAGAATTCTAGTCACCCAATTCTAACAATTTCCACC
1 TTAACAAGAATTCTAGTCACCCAATTCTAACAATTTCCACC
* *
149446 TTAACAAGAATTCTAATCACTCAATTCTAACAATTTCCACC
1 TTAACAAGAATTCTAGTCACCCAATTCTAACAATTTCCACC
*
149487 TTAACAAGAATTCTAGTCACCTAATTCTAACA
1 TTAACAAGAATTCTAGTCACCCAATTCTAACA
149519 TTAACTACAT
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 68 1.00
ACGTcount: A:0.39, C:0.26, G:0.04, T:0.31
Consensus pattern (41 bp):
TTAACAAGAATTCTAGTCACCCAATTCTAACAATTTCCACC
Found at i:159975 original size:14 final size:15
Alignment explanation
Indices: 159951--159979 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
159941 AGTGAAGAGC
159951 ATTTCCTTCTTTTCT
1 ATTTCCTTCTTTTCT
159966 ATTT-CTTCTTTTCT
1 ATTTCCTTCTTTTCT
159980 CCCTTCGCTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.07, C:0.24, G:0.00, T:0.69
Consensus pattern (15 bp):
ATTTCCTTCTTTTCT
Found at i:160502 original size:41 final size:41
Alignment explanation
Indices: 160455--160568 Score: 201
Period size: 41 Copynumber: 2.8 Consensus size: 41
160445 GAATTTTATT
160455 TTAACAAGAATTCTAGTCACCCAATTCTAACAATTTCCACC
1 TTAACAAGAATTCTAGTCACCCAATTCTAACAATTTCCACC
* *
160496 TTAACAAGAATTCTAATCACTCAATTCTAACAATTTCCACC
1 TTAACAAGAATTCTAGTCACCCAATTCTAACAATTTCCACC
*
160537 TTAACAAGAATTCTAGTCACCTAATTCTAACA
1 TTAACAAGAATTCTAGTCACCCAATTCTAACA
160569 TTAACTACAT
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 68 1.00
ACGTcount: A:0.39, C:0.26, G:0.04, T:0.31
Consensus pattern (41 bp):
TTAACAAGAATTCTAGTCACCCAATTCTAACAATTTCCACC
Found at i:171025 original size:14 final size:15
Alignment explanation
Indices: 171001--171029 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
170991 AGTGAAGAGC
171001 ATTTCCTTCTTTTCT
1 ATTTCCTTCTTTTCT
171016 ATTT-CTTCTTTTCT
1 ATTTCCTTCTTTTCT
171030 CCCTTCGCTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.07, C:0.24, G:0.00, T:0.69
Consensus pattern (15 bp):
ATTTCCTTCTTTTCT
Found at i:171698 original size:22 final size:22
Alignment explanation
Indices: 171670--171762 Score: 73
Period size: 22 Copynumber: 4.2 Consensus size: 22
171660 TATATTGTTA
171670 TTTTGGTGTTGTTTTTTTGCTG
1 TTTTGGTGTTGTTTTTTTGCTG
*
171692 TTTT-G-GTTGCAATTTTTTGCTG
1 TTTTGGTGTTG--TTTTTTTGCTG
* * **
171714 TTTTGATGTTGTATTTTTATTG
1 TTTTGGTGTTGTTTTTTTGCTG
* * *
171736 TTTTTGTTGTTGTTTTTGTGCTA
1 -TTTTGGTGTTGTTTTTTTGCTG
171759 TTTT
1 TTTT
171763 TTTACTATTT
Statistics
Matches: 54, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
20 4 0.07
21 1 0.02
22 29 0.54
23 16 0.30
24 4 0.07
ACGTcount: A:0.06, C:0.04, G:0.22, T:0.68
Consensus pattern (22 bp):
TTTTGGTGTTGTTTTTTTGCTG
Found at i:171808 original size:24 final size:24
Alignment explanation
Indices: 171781--171851 Score: 72
Period size: 24 Copynumber: 3.0 Consensus size: 24
171771 TTTGGTGCTG
171781 TTTTTATTGTTATTTTTGTTGTTA
1 TTTTTATTGTTATTTTTGTTGTTA
* * * *
171805 TTTTT-TCTATTATTTTTGCTGCTG
1 TTTTTAT-TGTTATTTTTGTTGTTA
* *
171829 TTTTGATTGTTATTTTGGTTGTT
1 TTTTTATTGTTATTTTTGTTGTT
171852 TGGATATTAT
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
23 1 0.03
24 34 0.94
25 1 0.03
ACGTcount: A:0.10, C:0.04, G:0.15, T:0.70
Consensus pattern (24 bp):
TTTTTATTGTTATTTTTGTTGTTA
Found at i:171828 original size:48 final size:46
Alignment explanation
Indices: 171734--171851 Score: 148
Period size: 48 Copynumber: 2.5 Consensus size: 46
171724 GTATTTTTAT
* * * *
171734 TGTTTTTGTTGTTGTTTTTG-TGCTATTTTTTTACTATTTTGGTGC
1 TGTTTTTATTGTTATTTTTGTTGTTATTTTTTTACTATTTTGCTGC
*
171779 TGTTTTTATTGTTATTTTTGTTGTTATTTTTTCTATTATTTTTGCTGC
1 TGTTTTTATTGTTATTTTTGTTGTTATTTTTT-TACTA-TTTTGCTGC
* *
171827 TGTTTTGATTGTTATTTTGGTTGTT
1 TGTTTTTATTGTTATTTTTGTTGTT
171852 TGGATATTAT
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
45 18 0.29
46 10 0.16
47 4 0.06
48 31 0.49
ACGTcount: A:0.08, C:0.05, G:0.18, T:0.69
Consensus pattern (46 bp):
TGTTTTTATTGTTATTTTTGTTGTTATTTTTTTACTATTTTGCTGC
Found at i:179652 original size:246 final size:249
Alignment explanation
Indices: 179081--179721 Score: 850
Period size: 246 Copynumber: 2.6 Consensus size: 249
179071 TGTATATATG
* * *
179081 AATAATGTATTTGATTGAGTT-GATATCATAAGTTAACTC-AGCACGAACTCAAGATTGATGACA
1 AATAATGTATTTGATTGAGTTGGA-GTCACAAGTTAACTCGA-CACTAACTCAAGATTGATGACA
* * *
179144 ACACCATGATAAACAATTTAATTTAATTTTTTTCATTTTAATA-ATGTATATATTTTATATATTA
64 ACACCATGATAAACAATTTAATTTAATTTTTTTCATTTTAATAGATGTACATATTTCATATGTTA
* * * *
179208 TTATTAAATAGTTTCAAACCATACATTTCATTATTTATTGCATGTGATTTCTAAAATAAATATTT
129 TTATTAATTAGTTTCAAACCACACATTTCATTATTTATTGCATGTGATTTCTAAAACAAACATTT
* * * * *
179273 GTGTTCTAAATTTGTGGTTTCCACACGTATGCGTGTGCGATAGGATTTTTAGTATT
194 ATGTTCTAAATTTGTGGTTTCCACACGCATACGTGTGCGATAAGATTTCTAGTATT
* * * * * * *
179329 AATAATGTATTTGATTGAGTTGGTGTCGCAAATTAACTCGGCA-TCATCTCAAGACTGATGACTA
1 AATAATGTATTTGATTGAGTTGGAGTCACAAGTTAACTCGACACT-AACTCAAGATTGATGACAA
*
179393 CACCATGATAAACAATTTAATTTACTTTTTTTCATTTTAATAGA-GTACATATTTCATATGTTAT
65 CACCATGATAAACAATTTAATTTAATTTTTTTCATTTTAATAGATGTACATATTTCATATGTTAT
* * * * *
179457 TAATAATTAGTTTTAAACCACACGTTTCATTATTTATTGCATGTGATTT-TTAAACAGACATTTA
130 TATTAATTAGTTTCAAACCACACATTTCATTATTTATTGCATGTGATTTCTAAAACAAACATTTA
* * *
179521 TG-T-TAAAGTTTTTGGTTTCCACACGCATATGTGTGTGATAAGATTTCTAGTATT
195 TGTTCTAAA-TTTGTGGTTTCCACACGCATACGTGTGCGATAAGATTTCTAGTATT
* *
179575 AATAATGTATTTAATTGAGTTGGAGTCACAAGTTAACTCGACACTAACTCAAGATTGATGAAAAC
1 AATAATGTATTTGATTGAGTTGGAGTCACAAGTTAACTCGACACTAACTCAAGATTGATGACAAC
* * * *
179640 ACAATGATAAACAATTTAATCTATTTTTTTTCATTTTAAT-GATGTACATATTTCATGTGTTATT
66 ACCATGATAAACAATTTAATTTAATTTTTTTCATTTTAATAGATGTACATATTTCATATGTTATT
179704 ATTAATTAGTTTCAAACC
131 ATTAATTAGTTTCAAACC
179722 TATAGCAATC
Statistics
Matches: 340, Mismatches: 46, Indels: 16
0.85 0.11 0.04
Matches are distributed among these distances:
245 6 0.02
246 167 0.49
247 13 0.04
248 152 0.45
249 2 0.01
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.42
Consensus pattern (249 bp):
AATAATGTATTTGATTGAGTTGGAGTCACAAGTTAACTCGACACTAACTCAAGATTGATGACAAC
ACCATGATAAACAATTTAATTTAATTTTTTTCATTTTAATAGATGTACATATTTCATATGTTATT
ATTAATTAGTTTCAAACCACACATTTCATTATTTATTGCATGTGATTTCTAAAACAAACATTTAT
GTTCTAAATTTGTGGTTTCCACACGCATACGTGTGCGATAAGATTTCTAGTATT
Found at i:179999 original size:3 final size:3
Alignment explanation
Indices: 179991--180024 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
179981 GGACTTGTGG
179991 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
180025 AGAGATTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.35
Consensus pattern (3 bp):
TGA
Found at i:190591 original size:24 final size:24
Alignment explanation
Indices: 190555--190642 Score: 113
Period size: 24 Copynumber: 3.7 Consensus size: 24
190545 CATACCACAT
** *
190555 TTAGCTCACACGAGCCTAGAATGA
1 TTAGCTCTTACGAGCCTAGAATGG
* * *
190579 TTAGCACTTACGAGCCCAAAATGG
1 TTAGCTCTTACGAGCCTAGAATGG
*
190603 TTAGCTCTTACGAACCTAGAATGG
1 TTAGCTCTTACGAGCCTAGAATGG
190627 TTAGCTCTTACGAGCC
1 TTAGCTCTTACGAGCC
190643 CAGACAGAGT
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 53 1.00
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (24 bp):
TTAGCTCTTACGAGCCTAGAATGG
Found at i:193169 original size:14 final size:14
Alignment explanation
Indices: 193147--193186 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
193137 GGGTACTGGT
*
193147 AACAGAAAGATATG
1 AACAGAAAGAGATG
*
193161 AACAAAAAGAGATG
1 AACAGAAAGAGATG
193175 AACAGAAAGAGA
1 AACAGAAAGAGA
193187 AGCTGTAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.62, C:0.07, G:0.23, T:0.07
Consensus pattern (14 bp):
AACAGAAAGAGATG
Found at i:193820 original size:21 final size:21
Alignment explanation
Indices: 193794--193843 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
193784 GGAGTTTTTG
**
193794 GTATCGGTAGATGTATAACTT
1 GTATCGGTAGAAATATAACTT
* *
193815 GTATCGGTAGAAATCTTACTT
1 GTATCGGTAGAAATATAACTT
193836 GTATCGGT
1 GTATCGGT
193844 CGAACAAGTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.38
Consensus pattern (21 bp):
GTATCGGTAGAAATATAACTT
Found at i:198175 original size:28 final size:28
Alignment explanation
Indices: 198131--198185 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
198121 GATATCTGAT
* *
198131 TTACTCCCTGTTAACCCAAATGTCATGC
1 TTACTCCATGTTAACCCAAAGGTCATGC
*
198159 TTACTCCATGTTGACCCAAAGGTCATG
1 TTACTCCATGTTAACCCAAAGGTCATG
198186 ATGCTCATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.25, C:0.29, G:0.15, T:0.31
Consensus pattern (28 bp):
TTACTCCATGTTAACCCAAAGGTCATGC
Found at i:198209 original size:36 final size:36
Alignment explanation
Indices: 198159--198329 Score: 297
Period size: 36 Copynumber: 4.8 Consensus size: 36
198149 AATGTCATGC
*
198159 TTACTCCATGTTGACCCAAAGGTCATGATGCTCATT
1 TTACTCCCTGTTGACCCAAAGGTCATGATGCTCATT
*
198195 TTACTCCCTATTGACCCAAAGGTCATGATGCTCATT
1 TTACTCCCTGTTGACCCAAAGGTCATGATGCTCATT
* *
198231 TTACTCCTTGTTGACCCAAAGGTCATTATGCTCATT
1 TTACTCCCTGTTGACCCAAAGGTCATGATGCTCATT
198267 TTACTCCCTGTTGACCCAAAGGTCATGATGCTCATT
1 TTACTCCCTGTTGACCCAAAGGTCATGATGCTCATT
*
198303 TTACTCCTTGTTGACCCAAAGGTCATG
1 TTACTCCCTGTTGACCCAAAGGTCATG
198330 CCTTTTACCA
Statistics
Matches: 127, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 127 1.00
ACGTcount: A:0.23, C:0.26, G:0.16, T:0.35
Consensus pattern (36 bp):
TTACTCCCTGTTGACCCAAAGGTCATGATGCTCATT
Found at i:204513 original size:13 final size:13
Alignment explanation
Indices: 204495--204519 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
204485 GTCTTTAGCG
204495 TTGATTGCAAAAT
1 TTGATTGCAAAAT
204508 TTGATTGCAAAA
1 TTGATTGCAAAA
204520 GTTTTATCCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (13 bp):
TTGATTGCAAAAT
Found at i:206493 original size:17 final size:17
Alignment explanation
Indices: 206471--206504 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
206461 AGTAAAGATA
206471 ACCACAAATCGTTTGTC
1 ACCACAAATCGTTTGTC
*
206488 ACCACAGATCGTTTGTC
1 ACCACAAATCGTTTGTC
206505 TTTGTGATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.29, G:0.15, T:0.29
Consensus pattern (17 bp):
ACCACAAATCGTTTGTC
Found at i:207834 original size:124 final size:124
Alignment explanation
Indices: 207612--207855 Score: 373
Period size: 124 Copynumber: 2.0 Consensus size: 124
207602 GTTGCTTGTA
* * * * *
207612 GCTAATCAAATATCACCAGGAGGGTGCTAAAGGTTTTTGCTAAGGTAACTCCACAATCACCAACT
1 GCTAATCAAATATCACCAGGAGGATGCTAAAGATTTTTGCCAAAGTAACTCCACAAGCACCAACT
* *
207677 TGTTTAATTGTGCAAGGCAAGAAGAAAAGGCTAAGTCCAGACTTC-GAAACCAACTTGAT
66 TGTCTAATTGTGCAAGGCAAGAAGAAAAAGCTAAGTCCAGACTTCAG-AACCAACTTGAT
* *
207736 GCTAATCAAATATCACCGGGAGGATGCTAAAGATTTTTGCCAAAGTAACTCCACAAGCACCAATT
1 GCTAATCAAATATCACCAGGAGGATGCTAAAGATTTTTGCCAAAGTAACTCCACAAGCACCAACT
* *
207801 TGTCTACTTGTGCAAGGCAAGGAGAAAAAGCTAAGTCCAGACTTCAGAACCAACT
66 TGTCTAATTGTGCAAGGCAAGAAGAAAAAGCTAAGTCCAGACTTCAGAACCAACT
207856 GAAGCAATTA
Statistics
Matches: 108, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
124 107 0.99
125 1 0.01
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (124 bp):
GCTAATCAAATATCACCAGGAGGATGCTAAAGATTTTTGCCAAAGTAACTCCACAAGCACCAACT
TGTCTAATTGTGCAAGGCAAGAAGAAAAAGCTAAGTCCAGACTTCAGAACCAACTTGAT
Found at i:229615 original size:23 final size:23
Alignment explanation
Indices: 229564--229617 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
229554 ACTCTGAGTT
* * *
229564 AAAGTCAACGGTTTGATTCTGTC
1 AAAGTTAAAGGTTTGATTCAGTC
229587 AAAGTTAAAGGTTTGATTCAGTC
1 AAAGTTAAAGGTTTGATTCAGTC
229610 AAAGTTAA
1 AAAGTTAA
229618 CAGTTCAGGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.33
Consensus pattern (23 bp):
AAAGTTAAAGGTTTGATTCAGTC
Found at i:231010 original size:21 final size:22
Alignment explanation
Indices: 230980--231031 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
230970 TTTTTGTTTC
230980 AATTAATTTCAAACT-AATCTTA
1 AATTAATTTCAAACTCAAT-TTA
*
231002 AATT-ATTTCTAACTCAATTTA
1 AATTAATTTCAAACTCAATTTA
*
231023 ATTTAATTT
1 AATTAATTT
231032 TTGAATATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 15 0.58
22 11 0.42
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (22 bp):
AATTAATTTCAAACTCAATTTA
Found at i:233473 original size:37 final size:37
Alignment explanation
Indices: 233405--233478 Score: 85
Period size: 37 Copynumber: 2.0 Consensus size: 37
233395 GCTTACATTG
* * *
233405 TGTCAATGTATGAAAAGTCTATTAAGTGAGTCCGTGT
1 TGTCAATGCATGAAAAGTCTATAAAGCGAGTCCGTGT
* * * *
233442 TGTCAGTGCATGAAGAGTCTGTAAAGCGAGTCTGTGT
1 TGTCAATGCATGAAAAGTCTATAAAGCGAGTCCGTGT
233479 CTATTTTTTG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.27, C:0.12, G:0.28, T:0.32
Consensus pattern (37 bp):
TGTCAATGCATGAAAAGTCTATAAAGCGAGTCCGTGT
Found at i:233555 original size:13 final size:14
Alignment explanation
Indices: 233528--233556 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
233518 TTTAAACACG
233528 AACTTTAAAATGGA
1 AACTTTAAAATGGA
233542 AACTTTAAAA-GGA
1 AACTTTAAAATGGA
233555 AA
1 AA
233557 AGTTCATGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.55, C:0.07, G:0.14, T:0.24
Consensus pattern (14 bp):
AACTTTAAAATGGA
Found at i:233746 original size:27 final size:27
Alignment explanation
Indices: 233707--233759 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
233697 AAGAAAATGC
*
233707 CTTTGTGGCGAACTCTGAAAGAATAGT
1 CTTTATGGCGAACTCTGAAAGAATAGT
* * *
233734 CTTTATGGTGAACTTTGAAGGAATAG
1 CTTTATGGCGAACTCTGAAAGAATAG
233760 CCTCCGTGGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.30, C:0.11, G:0.26, T:0.32
Consensus pattern (27 bp):
CTTTATGGCGAACTCTGAAAGAATAGT
Found at i:236214 original size:18 final size:18
Alignment explanation
Indices: 236176--236214 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
236166 AGTACTTTTT
* **
236176 AAAAATGTTTTTGAGCTA
1 AAAAATATTTTTGAGAAA
236194 AAAAATATTTTTGAGAAA
1 AAAAATATTTTTGAGAAA
236212 AAA
1 AAA
236215 TTAAAATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.51, C:0.03, G:0.13, T:0.33
Consensus pattern (18 bp):
AAAAATATTTTTGAGAAA
Found at i:240180 original size:22 final size:22
Alignment explanation
Indices: 240155--240208 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 22
240145 TTTTTGTCAC
240155 TATATTTTTTTTAATAGGAGCT
1 TATATTTTTTTTAATAGGAGCT
* *
240177 TATA--TTTTTTAATTGTAGCT
1 TATATTTTTTTTAATAGGAGCT
*
240197 AATATTTTTTTT
1 TATATTTTTTTT
240209 TATTTTTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 17 0.63
22 10 0.37
ACGTcount: A:0.26, C:0.04, G:0.09, T:0.61
Consensus pattern (22 bp):
TATATTTTTTTTAATAGGAGCT
Found at i:250488 original size:62 final size:62
Alignment explanation
Indices: 250391--250838 Score: 727
Period size: 62 Copynumber: 7.2 Consensus size: 62
250381 TGGAAAATGA
* *
250391 AAAGGTTCGATGTCTTCGTGATATCGTGAGTATTACATGAGAAATGAATCCTATTACGGATT
1 AAAGGTCCGATGTCTTTGTGATATCGTGAGTATTACATGAGAAATGAATCCTATTACGGATT
*
250453 AAAGGTCTGATGTCTTTGTGATATCGTGAGTATTACATGAGAAATGAATCCTATTACGGATT
1 AAAGGTCCGATGTCTTTGTGATATCGTGAGTATTACATGAGAAATGAATCCTATTACGGATT
*
250515 AAAGGTCCGAT-TCCTTTGTGATATCGTGAGTATTACATGAGAAATGAATCTTATTACGGATT
1 AAAGGTCCGATGT-CTTTGTGATATCGTGAGTATTACATGAGAAATGAATCCTATTACGGATT
*
250577 AAAGGTCCGATGTCTTTGTGATATCGTGAGTATTACATGAGAAATGAATCCTATTACAGATT
1 AAAGGTCCGATGTCTTTGTGATATCGTGAGTATTACATGAGAAATGAATCCTATTACGGATT
* * *
250639 AAAGGTCCGATGTCTTTGTGATATCATGAGTATTACACGAGAAATGAATCCTAATACGGATT
1 AAAGGTCCGATGTCTTTGTGATATCGTGAGTATTACATGAGAAATGAATCCTATTACGGATT
* * *
250701 AAAGGTCCGATGTCTTCGTGATATCGTGAGTATTACATGAGAAATCAATCCTATTACAGATT
1 AAAGGTCCGATGTCTTTGTGATATCGTGAGTATTACATGAGAAATGAATCCTATTACGGATT
* * * * *
250763 AAAGGTCTGATGTCTTCGTGATATCATGAGTATTACATGAGAAATGAATCCTACTATGGATT
1 AAAGGTCCGATGTCTTTGTGATATCGTGAGTATTACATGAGAAATGAATCCTATTACGGATT
*
250825 TAAGGTCCGATGTC
1 AAAGGTCCGATGTC
250839 GGAAATCTTG
Statistics
Matches: 359, Mismatches: 25, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
61 1 0.00
62 357 0.99
63 1 0.00
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.33
Consensus pattern (62 bp):
AAAGGTCCGATGTCTTTGTGATATCGTGAGTATTACATGAGAAATGAATCCTATTACGGATT
Found at i:259494 original size:30 final size:30
Alignment explanation
Indices: 259454--259541 Score: 149
Period size: 30 Copynumber: 2.9 Consensus size: 30
259444 ATAATATACC
*
259454 TGAAAAAAATGAAGAAGAAAATGTGAGAAA
1 TGAAAAAAATGAGGAAGAAAATGTGAGAAA
* *
259484 TGAAGAAAATGAGGAAGAAAATATGAGAAA
1 TGAAAAAAATGAGGAAGAAAATGTGAGAAA
259514 TGAAAAAAATGAGGAAGAAAATGTGAGA
1 TGAAAAAAATGAGGAAGAAAATGTGAGA
259542 GATAATGTTC
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.60, C:0.00, G:0.26, T:0.14
Consensus pattern (30 bp):
TGAAAAAAATGAGGAAGAAAATGTGAGAAA
Found at i:259502 original size:12 final size:12
Alignment explanation
Indices: 259485--259536 Score: 53
Period size: 12 Copynumber: 4.8 Consensus size: 12
259475 TGTGAGAAAT
259485 GAAGAAAATGAG
1 GAAGAAAATGAG
*
259497 GAAGAAAAT-AT
1 GAAGAAAATGAG
259508 G-AG-AAATGA-
1 GAAGAAAATGAG
259517 -AA-AAAATGAG
1 GAAGAAAATGAG
259527 GAAGAAAATG
1 GAAGAAAATG
259537 TGAGAGATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
9 11 0.33
10 3 0.09
11 4 0.12
12 15 0.45
ACGTcount: A:0.62, C:0.00, G:0.27, T:0.12
Consensus pattern (12 bp):
GAAGAAAATGAG
Found at i:259525 original size:16 final size:16
Alignment explanation
Indices: 259477--259526 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
259467 GAAGAAAATG
*
259477 TGAGAAATGAAGAAAA
1 TGAGAAATGAAAAAAA
* *
259493 TGAGGAA-G-AAAATA
1 TGAGAAATGAAAAAAA
259507 TGAGAAATGAAAAAAA
1 TGAGAAATGAAAAAAA
259523 TGAG
1 TGAG
259527 GAAGAAAATG
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
14 10 0.37
15 2 0.07
16 15 0.56
ACGTcount: A:0.60, C:0.00, G:0.26, T:0.14
Consensus pattern (16 bp):
TGAGAAATGAAAAAAA
Found at i:259569 original size:18 final size:18
Alignment explanation
Indices: 259546--259592 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
259536 GTGAGAGATA
*
259546 ATGTTCACATTTTAAATC
1 ATGTTCACATTTCAAATC
*
259564 ATGTTCACATTTCAAATT
1 ATGTTCACATTTCAAATC
*
259582 ATATTCACATT
1 ATGTTCACATT
259593 GATGGAAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.34, C:0.17, G:0.04, T:0.45
Consensus pattern (18 bp):
ATGTTCACATTTCAAATC
Found at i:265872 original size:27 final size:27
Alignment explanation
Indices: 265834--265902 Score: 77
Period size: 27 Copynumber: 2.6 Consensus size: 27
265824 AGATAGATTA
* * * *
265834 AAAAATTCAAAAATTCAAAAGATTT-T
1 AAAAATTTAAAAAATAAAAAAATTTAT
*
265860 AGAAATTATAAAAAATAAAAAAATTTAT
1 AAAAATT-TAAAAAATAAAAAAATTTAT
265888 AAAAATTTAAAAAAT
1 AAAAATTTAAAAAAT
265903 CTTAAAAATA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
26 6 0.17
27 22 0.63
28 7 0.20
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (27 bp):
AAAAATTTAAAAAATAAAAAAATTTAT
Found at i:265887 original size:19 final size:19
Alignment explanation
Indices: 265865--265902 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
265855 ATTTTAGAAA
265865 TTATAAAAAATAAAAAAAT
1 TTATAAAAAATAAAAAAAT
* *
265884 TTATAAAAATTTAAAAAAT
1 TTATAAAAAATAAAAAAAT
265903 CTTAAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
TTATAAAAAATAAAAAAAT
Found at i:265891 original size:10 final size:9
Alignment explanation
Indices: 265831--265919 Score: 74
Period size: 10 Copynumber: 9.7 Consensus size: 9
265821 ACTAGATAGA
265831 TTAAAAAA-
1 TTAAAAAAT
*
265839 TTCAAAAAT
1 TTAAAAAAT
* *
265848 TCAAAAGAT
1 TTAAAAAAT
* *
265857 TTTAGAAAT
1 TTAAAAAAT
265866 TATAAAAAA-
1 T-TAAAAAAT
*
265875 TAAAAAAAT
1 TTAAAAAAT
265884 TTATAAAAAT
1 TTA-AAAAAT
265894 TTAAAAAAT
1 TTAAAAAAT
265903 CTTAAAAATAT
1 -TTAAAAA-AT
265914 TTAAAA
1 TTAAAA
265920 TAAATAAAAT
Statistics
Matches: 63, Mismatches: 12, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
8 13 0.21
9 21 0.33
10 27 0.43
11 2 0.03
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.31
Consensus pattern (9 bp):
TTAAAAAAT
Found at i:267226 original size:60 final size:59
Alignment explanation
Indices: 267145--267273 Score: 141
Period size: 60 Copynumber: 2.2 Consensus size: 59
267135 AATAAAAAGT
* * * * * **
267145 CTAATAGTTGAGTGATCATTTTATAATTTTTTATAGTTGGATGATAAAAAAAGAAATTAA
1 CTAATAATTGAGCGATAATTTTATAACTTTTCATAGTTAAATGATAAAAAAA-AAATTAA
* * * * *
267205 TTAATAATTGAGCGATAATTTTGTAACTTTTCATAGTTAAATGATCAAAAGAAAATTTA
1 CTAATAATTGAGCGATAATTTTATAACTTTTCATAGTTAAATGATAAAAAAAAAATTAA
267264 CTAATAATTG
1 CTAATAATTG
267274 GATGACTACT
Statistics
Matches: 56, Mismatches: 13, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
59 15 0.27
60 41 0.73
ACGTcount: A:0.42, C:0.05, G:0.13, T:0.40
Consensus pattern (59 bp):
CTAATAATTGAGCGATAATTTTATAACTTTTCATAGTTAAATGATAAAAAAAAAATTAA
Found at i:268694 original size:2 final size:2
Alignment explanation
Indices: 268682--268712 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
268672 ATGATACTTG
268682 AT AT GAT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT
268713 TTGAGTCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:270669 original size:27 final size:27
Alignment explanation
Indices: 270617--270669 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
270607 TACTTCATCT
* **
270617 TCCTCTTCATCTTCTTCCTCCTCGTAG
1 TCCTCATCATCTTCGCCCTCCTCGTAG
270644 TCCTCATCATCTTCGCCCATCC-CGTA
1 TCCTCATCATCTTCGCCC-TCCTCGTA
270670 TCCCGTTTCC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 19 0.86
28 3 0.14
ACGTcount: A:0.11, C:0.43, G:0.08, T:0.38
Consensus pattern (27 bp):
TCCTCATCATCTTCGCCCTCCTCGTAG
Found at i:272617 original size:29 final size:29
Alignment explanation
Indices: 272570--272628 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
272560 GAATTTGATC
*
272570 AAATCAAAATGTTCTGTATATAATTACACA
1 AAATCAAAA-GTTCTGTATACAATTACACA
*
272600 AAATCAAAA-TTCATGTATACAATTGCACA
1 AAATCAAAAGTTC-TGTATACAATTACACA
272629 TTAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 3 0.12
29 14 0.54
30 9 0.35
ACGTcount: A:0.47, C:0.15, G:0.07, T:0.31
Consensus pattern (29 bp):
AAATCAAAAGTTCTGTATACAATTACACA
Found at i:277750 original size:62 final size:62
Alignment explanation
Indices: 277674--277824 Score: 212
Period size: 62 Copynumber: 2.4 Consensus size: 62
277664 ACATCTGATA
* * *
277674 ACTCACGATGACACAGAGTCATCGAACCTTAAATCCGTAATAGGATTCATTTATCATTTAAT
1 ACTCACGATGACACAAAGTCATCGAACCTTAAATCCGTAATAGCATCCATTTATCATTTAAT
* * * * *
277736 ACTCATGATTACACAAAGTCATCGGACCTTTAATCCGTAATAGCATCCATTTCTCATTTAAT
1 ACTCACGATGACACAAAGTCATCGAACCTTAAATCCGTAATAGCATCCATTTATCATTTAAT
* *
277798 ACTCACGATGACACATAGTCGTCGAAC
1 ACTCACGATGACACAAAGTCATCGAAC
277825 ATCATAATTC
Statistics
Matches: 76, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
62 76 1.00
ACGTcount: A:0.34, C:0.24, G:0.13, T:0.30
Consensus pattern (62 bp):
ACTCACGATGACACAAAGTCATCGAACCTTAAATCCGTAATAGCATCCATTTATCATTTAAT
Found at i:277882 original size:52 final size:52
Alignment explanation
Indices: 277796--278136 Score: 501
Period size: 52 Copynumber: 6.6 Consensus size: 52
277786 TTCTCATTTA
* * * * *
277796 ATACTCACGATGACACATAGTCGTCGAACATCATAAT-TCGTAAAAGATTCAT
1 ATACTCACGATGACACATAATCATCGGACCTCATAATCT-GTAAAGGATTCAT
**
277848 ATACTCACGATGACACATAATCATCGGACCTCATAATCAATAAAGGATTCAT
1 ATACTCACGATGACACATAATCATCGGACCTCATAATCTGTAAAGGATTCAT
*
277900 ATACTCACGATGACAC--AGTCATCGGACCTCATAATCTGTAAAGGATTCAT
1 ATACTCACGATGACACATAATCATCGGACCTCATAATCTGTAAAGGATTCAT
* * * *
277950 ATACTCATGATAACACATAGTCATCGGACCTCATAATCTGTAAAGGATTTAT
1 ATACTCACGATGACACATAATCATCGGACCTCATAATCTGTAAAGGATTCAT
*
278002 ATACTCACGATGACACATAATCCTCGGACCTCATAATCCT-TAAAGGATTCAT
1 ATACTCACGATGACACATAATCATCGGACCTCATAAT-CTGTAAAGGATTCAT
*
278054 ATACTCACGATGACACATAATCATCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAATCATCGGACCTCATAATCTGTAAAGGATTCAT
*
278106 ATACTCACGATGACACATAATCATCGAACCT
1 ATACTCACGATGACACATAATCATCGGACCT
278137 TTTTCATTTA
Statistics
Matches: 263, Mismatches: 21, Indels: 10
0.89 0.07 0.03
Matches are distributed among these distances:
50 45 0.17
51 1 0.00
52 215 0.82
53 2 0.01
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (52 bp):
ATACTCACGATGACACATAATCATCGGACCTCATAATCTGTAAAGGATTCAT
Found at i:283405 original size:3 final size:3
Alignment explanation
Indices: 283397--283425 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
283387 CATATTCTAC
283397 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
283426 GTATTTCATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:286379 original size:24 final size:24
Alignment explanation
Indices: 286347--286396 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
286337 AGAAATAATC
*
286347 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTATTTATTTG
286371 TTTCAATTAAACTCTATTTATTTG
1 TTTCAATTAAACTCTATTTATTTG
286395 TT
1 TT
286397 AAAGTCAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.26, C:0.12, G:0.06, T:0.56
Consensus pattern (24 bp):
TTTCAATTAAACTCTATTTATTTG
Found at i:286406 original size:24 final size:24
Alignment explanation
Indices: 286355--286409 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
286345 TCTTTCAATT
* * *
286355 AAACTCTGTTTATTTGTTTCAATT
1 AAACTCTATTTATTTGTTTAAATC
286379 AAACTCTATTTATTTG-TTAAAGTC
1 AAACTCTATTTATTTGTTTAAA-TC
286403 AAACTCT
1 AAACTCT
286410 TATTAGTCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 4 0.15
24 23 0.85
ACGTcount: A:0.31, C:0.15, G:0.07, T:0.47
Consensus pattern (24 bp):
AAACTCTATTTATTTGTTTAAATC
Found at i:288926 original size:40 final size:40
Alignment explanation
Indices: 288871--288950 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
288861 TTTGATCGTT
288871 TTCCTAATTGTCAGTTTGTGTATGAGAAGTTAGGTAAGGA
1 TTCCTAATTGTCAGTTTGTGTATGAGAAGTTAGGTAAGGA
288911 TTCCTAATTGTCAGTTTGTGTATGAGAAGTTAGGTAAGGA
1 TTCCTAATTGTCAGTTTGTGTATGAGAAGTTAGGTAAGGA
288951 ATGAATAAGG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.28, C:0.07, G:0.28, T:0.38
Consensus pattern (40 bp):
TTCCTAATTGTCAGTTTGTGTATGAGAAGTTAGGTAAGGA
Done.