Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009133.1 Hibiscus syriacus cultivar Beakdansim tig00112632_pilon, 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: 771734
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 1 of 2
Found at i:2343 original size:13 final size:13
Alignment explanation
Indices: 2325--2351 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2315 AGATTAAGAG
2325 CCTTGCATTCTAC
1 CCTTGCATTCTAC
2338 CCTTGCATTCTAC
1 CCTTGCATTCTAC
2351 C
1 C
2352 AACTGAACTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.41, G:0.07, T:0.37
Consensus pattern (13 bp):
CCTTGCATTCTAC
Found at i:2625 original size:21 final size:21
Alignment explanation
Indices: 2599--2643 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2589 AAAATGCGCA
2599 TTTAATACATAAA-TTATTAAT
1 TTTAATACATAAACTT-TTAAT
**
2620 TTTAATATTTAAACTTTTAAT
1 TTTAATACATAAACTTTTAAT
2641 TTT
1 TTT
2644 TTAAAATCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTAATACATAAACTTTTAAT
Found at i:5230 original size:35 final size:35
Alignment explanation
Indices: 5184--5294 Score: 145
Period size: 35 Copynumber: 3.2 Consensus size: 35
5174 AAAACAATCC
*
5184 TCAATTTCATTCTAAACCAC-AAATTCCAAAGTAAT
1 TCAATTTCATTCTAAACC-CTAAATTCCAAAATAAT
5219 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
* * * *
5254 TCAATTACATTCTAAAACCC-AAACTCTAAAATACT
1 TCAATTTCATTCT-AAACCCTAAATTCCAAAATAAT
5289 TCAATT
1 TCAATT
5295 CCCGTCTTTT
Statistics
Matches: 69, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
34 1 0.01
35 62 0.90
36 6 0.09
ACGTcount: A:0.43, C:0.23, G:0.01, T:0.32
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
Found at i:6397 original size:35 final size:35
Alignment explanation
Indices: 6349--6426 Score: 122
Period size: 35 Copynumber: 2.2 Consensus size: 35
6339 ATTCCTCCTT
6349 AAATTGAAATATTTTAGAATTT-GGGTTTTAGAATG
1 AAATTGAAATATTTTAGAATTTAGGG-TTTAGAATG
* *
6384 TAATTGAATTATTTTAGAATTTAGGGTTTAGAATG
1 AAATTGAAATATTTTAGAATTTAGGGTTTAGAATG
6419 AAATTGAA
1 AAATTGAA
6427 GAATGTTTTG
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
35 36 0.92
36 3 0.08
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.42
Consensus pattern (35 bp):
AAATTGAAATATTTTAGAATTTAGGGTTTAGAATG
Found at i:9849 original size:2 final size:2
Alignment explanation
Indices: 9842--9882 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
9832 AGCCCAATAC
9842 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
9883 AGAGTCTGTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:10070 original size:20 final size:20
Alignment explanation
Indices: 10045--10085 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
10035 AAATTTATAT
10045 ATTATA-TATAATTTAATTTA
1 ATTATATTATAA-TTAATTTA
*
10065 ATTATATTTTAATTAATTTA
1 ATTATATTATAATTAATTTA
10085 A
1 A
10086 AAAAATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
ATTATATTATAATTAATTTA
Found at i:10105 original size:17 final size:17
Alignment explanation
Indices: 10079--10131 Score: 97
Period size: 17 Copynumber: 3.1 Consensus size: 17
10069 TATTTTAATT
10079 AATTTAAAAAAATATTTA
1 AATTT-AAAAAATATTTA
10097 AATTTAAAAAATATTTA
1 AATTTAAAAAATATTTA
10114 AATTTAAAAAATATTTA
1 AATTTAAAAAATATTTA
10131 A
1 A
10132 TTAAGTAGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 30 0.86
18 5 0.14
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AATTTAAAAAATATTTA
Found at i:12348 original size:60 final size:60
Alignment explanation
Indices: 12257--12372 Score: 133
Period size: 60 Copynumber: 1.9 Consensus size: 60
12247 GATTATAGAG
* * * * * *
12257 TATTATTTTATTAAGTTATTCGAATATTAAAAATTAGAAAATAATCATTTGACTATAAAA
1 TATTATTTTATTAAGTCACTCGAATAGTAAAAATTACAAAATAATCACTTAACTATAAAA
* * * * *
12317 TATTGTTTTATTAAGTCCCTCGACTAGTAAAAGTTACAAAATGATCACTTAACTAT
1 TATTATTTTATTAAGTCACTCGAATAGTAAAAATTACAAAATAATCACTTAACTAT
12373 TTATTATGTT
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
60 45 1.00
ACGTcount: A:0.41, C:0.10, G:0.09, T:0.40
Consensus pattern (60 bp):
TATTATTTTATTAAGTCACTCGAATAGTAAAAATTACAAAATAATCACTTAACTATAAAA
Found at i:13461 original size:21 final size:21
Alignment explanation
Indices: 13436--13475 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
13426 CCATATCATT
13436 TTTTTAAAATTATT-ATTTATA
1 TTTTT-AAATTATTAATTTATA
*
13457 TTTTTATATTATTAATTTA
1 TTTTTAAATTATTAATTTA
13476 AATCAATCAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTTTAAATTATTAATTTATA
Found at i:16640 original size:35 final size:35
Alignment explanation
Indices: 16565--16670 Score: 137
Period size: 35 Copynumber: 3.0 Consensus size: 35
16555 AACATCTACC
16565 AAAC-TTTACCAAACTTTGAAAAAATATTTTTCAAAG
1 AAACATTTACCAAACTTTG--AAAATATTTTTCAAAG
* *
16601 AAACATTTACCAAACTTTGAAAGTCA-TTTTCAAAT
1 AAACATTTACCAAACTTTGAAAAT-ATTTTTCAAAG
16636 AAACATTTACCAAACTTTGAAAACTA-TTTTCAAAG
1 AAACATTTACCAAACTTTGAAAA-TATTTTTCAAAG
16671 TTGGTTGCCA
Statistics
Matches: 63, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
35 43 0.68
36 6 0.10
37 14 0.22
ACGTcount: A:0.45, C:0.16, G:0.06, T:0.33
Consensus pattern (35 bp):
AAACATTTACCAAACTTTGAAAATATTTTTCAAAG
Found at i:21151 original size:35 final size:36
Alignment explanation
Indices: 21079--21166 Score: 135
Period size: 35 Copynumber: 2.5 Consensus size: 36
21069 AACATCTACC
* *
21079 AAAC-TTTACCCAACTTTGAAAAATATTTTTCAAAG
1 AAACATTTACCAAACTTTGAAAAACATTTTTCAAAG
*
21114 AAACATTTACCAAACTTTGAAAACCA-TTTTCAAAG
1 AAACATTTACCAAACTTTGAAAAACATTTTTCAAAG
21149 AAACATTTACCAAACTTT
1 AAACATTTACCAAACTTT
21167 TTCAAAGTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
35 31 0.63
36 18 0.37
ACGTcount: A:0.44, C:0.19, G:0.05, T:0.32
Consensus pattern (36 bp):
AAACATTTACCAAACTTTGAAAAACATTTTTCAAAG
Found at i:26146 original size:42 final size:41
Alignment explanation
Indices: 26083--26162 Score: 142
Period size: 42 Copynumber: 1.9 Consensus size: 41
26073 ACTAAAAGTG
*
26083 GCCATTTTAGTCCAAAATTTGGGATGAAGGTGAAATTGATA
1 GCCATTTTAGTCCAAAATTTGGGACGAAGGTGAAATTGATA
26124 GCCACTTTTAGTCCAAAATTTGGGACGAAGGTGAAATTG
1 GCCA-TTTTAGTCCAAAATTTGGGACGAAGGTGAAATTG
26163 CTAGATTTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
41 4 0.11
42 33 0.89
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (41 bp):
GCCATTTTAGTCCAAAATTTGGGACGAAGGTGAAATTGATA
Found at i:39373 original size:21 final size:21
Alignment explanation
Indices: 39347--39392 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
39337 GACTACCATG
* *
39347 TCAATACATTAAACTGTCACA
1 TCAATACACTAAACTGCCACA
*
39368 TCAATACACTGAACTGCCACA
1 TCAATACACTAAACTGCCACA
39389 TCAA
1 TCAA
39393 CCTCGTAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.28, G:0.07, T:0.24
Consensus pattern (21 bp):
TCAATACACTAAACTGCCACA
Found at i:48827 original size:28 final size:28
Alignment explanation
Indices: 48769--48832 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 28
48759 TGATGTTATA
* * * **
48769 TGTCATTGGTATCACGTGTCGTGTCGTG
1 TGTCACTGGTATCACATGTCGTGCCACG
*
48797 TGTCACTGGTATCCCATGTCGTGCCACG
1 TGTCACTGGTATCACATGTCGTGCCACG
48825 TGTCACTG
1 TGTCACTG
48833 TTTTGTTGGA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.12, C:0.25, G:0.28, T:0.34
Consensus pattern (28 bp):
TGTCACTGGTATCACATGTCGTGCCACG
Found at i:50035 original size:14 final size:14
Alignment explanation
Indices: 50016--50063 Score: 78
Period size: 14 Copynumber: 3.4 Consensus size: 14
50006 AGGGGCTTGG
50016 GCACTCTGATCCAA
1 GCACTCTGATCCAA
50030 GCACTCTGATCCAA
1 GCACTCTGATCCAA
* *
50044 ACACTCCGATCCAA
1 GCACTCTGATCCAA
50058 GCACTC
1 GCACTC
50064 CAAACCATCA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.29, C:0.40, G:0.12, T:0.19
Consensus pattern (14 bp):
GCACTCTGATCCAA
Found at i:51511 original size:2 final size:2
Alignment explanation
Indices: 51504--51532 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
51494 TAAAATTGTT
51504 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
51533 TATCAAACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:53115 original size:13 final size:13
Alignment explanation
Indices: 53097--53123 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
53087 TCATTGTTTT
53097 ATTAATAAAATTC
1 ATTAATAAAATTC
53110 ATTAATAAAATTC
1 ATTAATAAAATTC
53123 A
1 A
53124 GTTACCATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (13 bp):
ATTAATAAAATTC
Found at i:57019 original size:60 final size:59
Alignment explanation
Indices: 56919--57030 Score: 154
Period size: 60 Copynumber: 1.9 Consensus size: 59
56909 CTATTAAGTC
* *
56919 CCTACTATAGAATGTTTCTTTATTAAATCTTTCAATTATTAAAAATTATCAAATAATCCA
1 CCTACTATAGAATGTTTCTTTATTAAATCTATCAACTATTAAAAATTA-CAAATAATCCA
* * *
56979 CCTACTATAGAATGTTTCTTTATTAAGT-TCATCGACTATTAAAAGTTACAAA
1 CCTACTATAGAATGTTTCTTTATTAAATCT-ATCAACTATTAAAAATTACAAA
57031 ATGATCACCT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
59 5 0.11
60 41 0.89
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.40
Consensus pattern (59 bp):
CCTACTATAGAATGTTTCTTTATTAAATCTATCAACTATTAAAAATTACAAATAATCCA
Found at i:71156 original size:14 final size:14
Alignment explanation
Indices: 71137--71166 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
71127 TCTGTAGGTT
71137 GTGTATTGCTAATA
1 GTGTATTGCTAATA
71151 GTGTATTGCTAATA
1 GTGTATTGCTAATA
71165 GT
1 GT
71167 TAAGAAAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.07, G:0.23, T:0.43
Consensus pattern (14 bp):
GTGTATTGCTAATA
Found at i:73797 original size:31 final size:31
Alignment explanation
Indices: 73759--73833 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
73749 TTAAAACTTA
*
73759 CAATATGGTCCCTAAACATTTAGTATGTTTG
1 CAATATGGTCCCTAAACATTTAGTACGTTTG
* * *
73790 CAATATGGTCCCTCAACATTTATTCCGTTTG
1 CAATATGGTCCCTAAACATTTAGTACGTTTG
*
73821 CAATATGATCCCT
1 CAATATGGTCCCT
73834 GATGTAACTG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.37
Consensus pattern (31 bp):
CAATATGGTCCCTAAACATTTAGTACGTTTG
Found at i:74181 original size:30 final size:30
Alignment explanation
Indices: 74147--74222 Score: 125
Period size: 30 Copynumber: 2.5 Consensus size: 30
74137 CTTTTAAAAC
* *
74147 TTGCAATACGGTCCCCAACATTTAGTTCGT
1 TTGCAATAAGGTCCCCAACATTTAGTCCGT
74177 TTGCAATAAGGTCCCCAACATTTAGTCCGT
1 TTGCAATAAGGTCCCCAACATTTAGTCCGT
*
74207 TTGCAATATGGTCCCC
1 TTGCAATAAGGTCCCC
74223 GACGTAACTG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.24, C:0.28, G:0.17, T:0.32
Consensus pattern (30 bp):
TTGCAATAAGGTCCCCAACATTTAGTCCGT
Found at i:86582 original size:29 final size:30
Alignment explanation
Indices: 86505--86586 Score: 78
Period size: 30 Copynumber: 2.8 Consensus size: 30
86495 GTAAATTATA
* * *
86505 AATTTGATGACTGAATTTTAATATTTTTTT
1 AATTTCATCACTGAATTTTAATATTATTTT
* * *
86535 TATTTCACTCACCGTATTTTAA-ATTATTTT
1 AATTTCA-TCACTGAATTTTAATATTATTTT
*
86565 AATTTTATCACTGAA-TTTAATA
1 AATTTCATCACTGAATTTTAATA
86587 CGTTGAATTT
Statistics
Matches: 40, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
28 5 0.12
29 7 0.17
30 17 0.43
31 11 0.28
ACGTcount: A:0.32, C:0.10, G:0.06, T:0.52
Consensus pattern (30 bp):
AATTTCATCACTGAATTTTAATATTATTTT
Found at i:103945 original size:58 final size:59
Alignment explanation
Indices: 103872--104009 Score: 233
Period size: 58 Copynumber: 2.4 Consensus size: 59
103862 TGCTTTATTA
* *
103872 AGTCCCTTAACTATTAAAATTACAAAATTATCCTCTAACTATAGGGAGTTA-TTTGTTG
1 AGTCACTTAAATATTAAAATTACAAAATTATCCTCTAACTATAGGGAGTTACTTTGTTG
* *
103930 AGTCTCTTAAATATTAAAATTATAAAATTATCCTCTAACTATAGGGAGTTACTTTGTTG
1 AGTCACTTAAATATTAAAATTACAAAATTATCCTCTAACTATAGGGAGTTACTTTGTTG
103989 AGTCACTTAAATATTAAAATT
1 AGTCACTTAAATATTAAAATT
104010 TATAAATTGG
Statistics
Matches: 75, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
58 48 0.64
59 27 0.36
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (59 bp):
AGTCACTTAAATATTAAAATTACAAAATTATCCTCTAACTATAGGGAGTTACTTTGTTG
Found at i:105942 original size:18 final size:18
Alignment explanation
Indices: 105906--105939 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
105896 TTGATTAAGT
105906 ATTACTTTTATTAATTTA
1 ATTACTTTTATTAATTTA
*
105924 ATTATTTTTA-TAATTT
1 ATTACTTTTATTAATTT
105940 TAAGAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (18 bp):
ATTACTTTTATTAATTTA
Found at i:106973 original size:32 final size:33
Alignment explanation
Indices: 106932--107012 Score: 87
Period size: 32 Copynumber: 2.5 Consensus size: 33
106922 TATTTTTTTA
* *
106932 AATAGTTATTTTTTTA-TATTAAT-ATATTTATGT
1 AATA-TTATTTTTTTATTA-AAATAATATTTATAT
106965 AATATTA-TTTTTTATTAAAATAATATTTATAT
1 AATATTATTTTTTTATTAAAATAATATTTATAT
*
106997 AATTATTATTTATTTA
1 AA-TATTATTTTTTTA
107013 GAATTATTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
31 10 0.24
32 16 0.39
33 9 0.22
34 6 0.15
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.59
Consensus pattern (33 bp):
AATATTATTTTTTTATTAAAATAATATTTATAT
Found at i:108737 original size:20 final size:20
Alignment explanation
Indices: 108708--108753 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
108698 GCAGGGGTAC
* *
108708 ATGCCCAGCCCTCACTTCAT
1 ATGCCAAGCCCACACTTCAT
* *
108728 ATGCCAAGCCCACAGTTTAT
1 ATGCCAAGCCCACACTTCAT
108748 ATGCCA
1 ATGCCA
108754 TCTCCGCAGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.26, C:0.37, G:0.13, T:0.24
Consensus pattern (20 bp):
ATGCCAAGCCCACACTTCAT
Found at i:108848 original size:21 final size:21
Alignment explanation
Indices: 108757--108848 Score: 111
Period size: 21 Copynumber: 4.5 Consensus size: 21
108747 TATGCCATCT
* *
108757 CCGCAGGGTTACATTCCGAG-
1 CCGCAGGGTTACATGCCTAGC
*
108777 CCGCAGGGTTAC-TTCCTAGC
1 CCGCAGGGTTACATGCCTAGC
108797 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
108818 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
108839 CCGCAGGGTT
1 CCGCAGGGTT
108849 TTATACCATA
Statistics
Matches: 66, Mismatches: 2, Indels: 7
0.88 0.03 0.09
Matches are distributed among these distances:
19 6 0.09
20 23 0.35
21 37 0.56
ACGTcount: A:0.17, C:0.35, G:0.27, T:0.21
Consensus pattern (21 bp):
CCGCAGGGTTACATGCCTAGC
Found at i:109411 original size:34 final size:34
Alignment explanation
Indices: 109361--109456 Score: 124
Period size: 32 Copynumber: 2.9 Consensus size: 34
109351 AAATGTTTTT
*
109361 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* *
109395 AAAATAAAAATAATATTATTC-AAATTT-AAATT
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* * *
109427 TAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCGAAATTTAA
109457 CATTAAATTT
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
32 21 0.40
33 12 0.23
34 20 0.38
ACGTcount: A:0.55, C:0.04, G:0.03, T:0.38
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCGAAATTTAAAATA
Found at i:110169 original size:127 final size:128
Alignment explanation
Indices: 109851--110342 Score: 805
Period size: 126 Copynumber: 3.9 Consensus size: 128
109841 TGATTTACAT
* *
109851 ATATATCTAGTGTCCCCGAGGGATATGAGTGACATAATAGGGCAATGATAACATATTCTCTGATG
1 ATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACG
* *
109916 AAATAATGGAAGGCGCCCCCCCGGGAATGCGCCTTCATGTGAATAGTGAAATAATAGGTACTG
66 AAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTG
*
109979 --ATATCTAGTGTCCCCGAGGGACATGAGTGACATACTAGGGCAATGATAACATATTCTCTGACG
1 ATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACG
* *** * *
110042 AAATAATGGAAGGCGCGCCCCCGGGAACGCGCATTCATGTCCCCT-GAGAAATAATAGGTAATG
66 AAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGGTACTG
* *
110105 ATATATCTAGTGT-CCCGAGGGACATGAGTGACCTAATAGGGCAATTATAACATATTCTCTGACG
1 ATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACG
110169 AAATAATGGAAGG-GCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTG
66 AAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTG
110231 ATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACG
1 ATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACG
* *
110296 AAATAATGAAAGGCGCGCCCCCGGGAACGCGCCTCCATGTGAATAGT
66 AAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
110343 ACTCCGATAT
Statistics
Matches: 334, Mismatches: 24, Indels: 12
0.90 0.06 0.03
Matches are distributed among these distances:
125 1 0.00
126 167 0.50
127 123 0.37
128 43 0.13
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (128 bp):
ATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACG
AAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTG
Found at i:110300 original size:254 final size:254
Alignment explanation
Indices: 109851--110327 Score: 850
Period size: 254 Copynumber: 1.9 Consensus size: 254
109841 TGATTTACAT
* *
109851 ATATATCTAGTGTCCCCGAGGGATATGAGTGACATAATAGGGCAATGATAACATATTCTCTGATG
1 ATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACG
*
109916 AAATAATGGAAGGCGCCCCCCCGGGAATGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGAT
66 AAATAATGGAAGGCGCCCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGAT
*
109981 ATCTAGTGTCCCCGAGGGACATGAGTGACATACTAGGGCAATGATAACATATTCTCTGACGAAAT
131 ATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAAT
*
110046 AATGGAAGGCGCGCCCCCGGGAACGCGCATTCATGTCCCCTGAGAAATAATAGGTAATG
196 AATGAAAGGCGCGCCCCCGGGAACGCGCATTCATGTCCCCTGAGAAATAATAGGTAATG
* *
110105 ATATATCTAGTGT-CCCGAGGGACATGAGTGACCTAATAGGGCAATTATAACATATTCTCTGACG
1 ATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACG
*
110169 AAATAATGGAAGG-GCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGAT
66 AAATAATGGAAGGCGCCCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTG--
110233 ATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAA
129 ATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAA
110298 ATAATGAAAGGCGCGCCCCCGGGAACGCGC
194 ATAATGAAAGGCGCGCCCCCGGGAACGCGC
110328 CTCCATGTGA
Statistics
Matches: 213, Mismatches: 8, Indels: 4
0.95 0.04 0.02
Matches are distributed among these distances:
252 47 0.22
253 60 0.28
254 106 0.50
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (254 bp):
ATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACG
AAATAATGGAAGGCGCCCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGAT
ATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAAT
AATGAAAGGCGCGCCCCCGGGAACGCGCATTCATGTCCCCTGAGAAATAATAGGTAATG
Found at i:110842 original size:49 final size:48
Alignment explanation
Indices: 110777--110873 Score: 185
Period size: 49 Copynumber: 2.0 Consensus size: 48
110767 GAAGACATTC
110777 ATCTGCAATGCTTATGATCTCAACCCACGTGGCTTCACCAATAATCCA
1 ATCTGCAATGCTTATGATCTCAACCCACGTGGCTTCACCAATAATCCA
110825 ATCTGCAACTGCTTATGATCTCAACCCACGTGGCTTCACCAATAATCCA
1 ATCTGCAA-TGCTTATGATCTCAACCCACGTGGCTTCACCAATAATCCA
110874 TATGGCAACA
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
48 8 0.17
49 40 0.83
ACGTcount: A:0.29, C:0.32, G:0.12, T:0.27
Consensus pattern (48 bp):
ATCTGCAATGCTTATGATCTCAACCCACGTGGCTTCACCAATAATCCA
Found at i:113043 original size:13 final size:13
Alignment explanation
Indices: 113025--113085 Score: 51
Period size: 13 Copynumber: 5.0 Consensus size: 13
113015 TTGTTTCTAA
113025 TTATTTAATATAT
1 TTATTTAATATAT
113038 TTATTTAATATA-
1 TTATTTAATATAT
* *
113050 ATAATTAATAT-T
1 TTATTTAATATAT
*
113062 ATTAGTT-ATATAT
1 -TTATTTAATATAT
113075 TT-TTTAA-ATAT
1 TTATTTAATATAT
113086 AATAATAATT
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
11 6 0.15
12 16 0.41
13 17 0.44
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (13 bp):
TTATTTAATATAT
Found at i:123650 original size:21 final size:21
Alignment explanation
Indices: 123626--123666 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
123616 AAGTTCTATG
123626 TTTTATTTTTAAATTATATAC
1 TTTTATTTTTAAATTATATAC
*
123647 TTTTATTTTTAAATTTTATA
1 TTTTATTTTTAAATTATATA
123667 AAAAAAATTA
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:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTTATTTTTAAATTATATAC
Found at i:133247 original size:59 final size:59
Alignment explanation
Indices: 133169--133306 Score: 240
Period size: 59 Copynumber: 2.3 Consensus size: 59
133159 TGCTTCATTA
* * *
133169 AGTCCCTTAACTATTAAAATTACAAAATTATCCTCTAACTATAGGGAGTTACTTTGTTG
1 AGTCTCTTAAATATTAAAATTACAAAATTATCCTCTAACCATAGGGAGTTACTTTGTTG
*
133228 AGTCTCTTAAATATTAAAATTATAAAATTATCCTCTAACCATAGGGAGTTACTTTGTTG
1 AGTCTCTTAAATATTAAAATTACAAAATTATCCTCTAACCATAGGGAGTTACTTTGTTG
133287 AGTCTCTTAAATATTAAAAT
1 AGTCTCTTAAATATTAAAAT
133307 ATATAAATTG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 75 1.00
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.38
Consensus pattern (59 bp):
AGTCTCTTAAATATTAAAATTACAAAATTATCCTCTAACCATAGGGAGTTACTTTGTTG
Found at i:135295 original size:18 final size:18
Alignment explanation
Indices: 135259--135292 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
135249 TTGATTAAGT
135259 ATTACTTTTATTAATTTA
1 ATTACTTTTATTAATTTA
*
135277 ATTATTTTTA-TAATTT
1 ATTACTTTTATTAATTT
135293 TAAGAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (18 bp):
ATTACTTTTATTAATTTA
Found at i:150986 original size:66 final size:66
Alignment explanation
Indices: 150874--151016 Score: 207
Period size: 66 Copynumber: 2.2 Consensus size: 66
150864 TGGTAGGGTA
* * * * **
150874 GGCAATGTCGGCATGCTTGGAAGTGGAGGTAGAGCTCCAGGCTTGGGTAATGATGGCTGTGTTGT
1 GGCAATGTCGGCATGCTAGGAAGTGGAGGAAGAGCTCCAGGATTGGGTAACGATGGCTGCATTGT
150939 C
66 C
150940 GGCAATGTCGGCATGCTAGGAAGTGGAGGAAGAGCTCTC-GGATTGGGTAACGATGGCTGCATTG
1 GGCAATGTCGGCATGCTAGGAAGTGGAGGAAGAGCTC-CAGGATTGGGTAACGATGGCTGCATTG
151004 TC
65 TC
*
151006 GGAAATGTCGG
1 GGCAATGTCGG
151017 TTGTGGGAGG
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
66 68 0.99
67 1 0.01
ACGTcount: A:0.21, C:0.15, G:0.39, T:0.24
Consensus pattern (66 bp):
GGCAATGTCGGCATGCTAGGAAGTGGAGGAAGAGCTCCAGGATTGGGTAACGATGGCTGCATTGT
C
Found at i:166081 original size:165 final size:164
Alignment explanation
Indices: 165705--166484 Score: 903
Period size: 165 Copynumber: 4.7 Consensus size: 164
165695 CAGCTTCGAG
* * * * * * *
165705 GGCACATCATTTACAGTATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTT
1 GGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATC--TGACC-AAAGACCTTCGAGTT
* * *
165770 CGATTACACTCAGCTT-CGAGGCACATCATTTACAGTATACTCAAGGCTAGAAGGGTTATCTG-T
63 CGATTACACTCAGCTTCCAAGGCACATCATTTACAG-ACACTCAAGGCTAGAAGGGTTATCTGCC
* * * * * *
165833 GACCAAAGACCTTCGAGTTCGATTACACTCAGCTCTGAG
127 AACAAAAGACCTTCGAGTTCGACTACGCTCAGCTC-CAA
* *
165872 GGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTT
1 GGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG---ACCAAAGACCTTCGAGTT
* * * * * *
165937 CGACTACACTCAGC-TCCAAGGCATATCATTTGCAG-CACTTAAGTCTAGAAGGGTTGTCTGCCA
63 CGATTACACTCAGCTTCCAAGGCACATCATTTACAGACACTCAAGGCTAGAAGGGTTATCTGCCA
166000 ACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA
128 ACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA
**
166037 GGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-CCAAAGACCCCCGAGTTCGA
1 GGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGACCAAAGACCTTCGAGTTCGA
* * * ** *
166101 TTACACTCAGCTTCGAGGGCACATCATTTACAGTATAACTCAAGGCTAGAAGGGTTATCTGTGAC
66 TTACACTCAGCTTCCAAGGCACATCATTTACAG-A-CACTCAAGGCTAGAAGGGTTATCTGCCAA
166166 CAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA
129 CAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA
**
166202 GGCACATCATTTGCAGCATAGCTTAAGTATAGAAGGGCTATCTG-CCAAAGACCTTCGAGTTCGA
1 GGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGACCAAAGACCTTCGAGTTCGA
* * * * * * *
166266 TTACACTCAGCTTCGAGGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAA
66 TTACACTCAGCTTCCAAGGCACATCATTTACAG-AC-ACTCAAGGCTAGAAGGGTTATCTGCCAA
* *
166331 CCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAA
129 CAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA
* **
166367 GGCGCATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-CCAAAGACCCCCGAGTTCGA
1 GGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGACCAAAGACCTTCGAGTTCGA
* * * *
166431 TTACACTCAACTT-CGAGGTCATATCATTTACA-ACATAGCTCAAGGCAAGAAGGG
66 TTACACTCAGCTTCCAAGG-CACATCATTTACAGAC--A-CTCAAGGCTAGAAGGG
166485 CTATTTGTCA
Statistics
Matches: 534, Mismatches: 66, Indels: 28
0.85 0.11 0.04
Matches are distributed among these distances:
161 28 0.05
162 17 0.03
163 2 0.00
164 3 0.01
165 368 0.69
166 32 0.06
167 81 0.15
168 3 0.01
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.24
Consensus pattern (164 bp):
GGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGACCAAAGACCTTCGAGTTCGA
TTACACTCAGCTTCCAAGGCACATCATTTACAGACACTCAAGGCTAGAAGGGTTATCTGCCAACA
AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA
Found at i:166174 original size:246 final size:245
Alignment explanation
Indices: 165668--166414 Score: 788
Period size: 246 Copynumber: 3.0 Consensus size: 245
165658 GGGCTATCTG
** * * * * * * * * *
165668 CCAAAGACCCCCGAGTTTGATTACACTCAGCTTCGAGGGCACATCATTTACAGTATAACTCAAGG
1 CCAAAGACCTTCGAGTTCGACTACACTCAGC-TCCAAGGCACATCATTTGCAGCA-AGCTTAAGT
* * *
165733 CTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGATTACACTCAGCTTCGAGGCACATCA
64 CTAGAAGGGTTATCTG-CA-CAAAAGACCTTCGAGTTCGATTACACTCAGCTCCAAGGCACATCA
* * * * **
165798 TTTACAGTATACTCAAGGCTAGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGATTACACTC
127 TTTGCAGCATACTTAAGTCTAGAAGGGTTATC--TG-CCAAAGACCCCCGAGTTCGATTACACTC
* * *
165863 AGCTCTGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAA
189 AGCTCTGAGGGCACATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGCCAA
*
165920 CCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCATATCATTTGCAGC-A-CTTAAGTCT
1 CCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCAAGCTTAAGTCT
* * *
165983 AGAAGGGTTGTCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
66 AGAAGGGTTATCTG-C-ACAAAAGACCTTCGAGTTCGATTACACTCAGCTCCAAGGCACATCATT
* *
166048 TGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCT
129 TGCAGCATA-CTTAAGTCTAGAAGGGTTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCT
* * **
166113 -TCGAGGGCACATCATTTACAGTATAACTCAAGGCTAGAAGGGTTATCTG-TGA
193 CT-GAGGGCACATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGCCAA
*
166165 CCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGT
1 CC-AAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCA-AGCTTAAGT
* * * * *
166230 ATAGAAGGGCTATCTGC-C-AAAGACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCATATCAT
64 CTAGAAGGGTTATCTGCACAAAAGACCTTCGAGTTCGATTACACTCAGC-TCCAAGGCACATCAT
* * *** * *
166293 TTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACCAAAGACCTTTGAGTTCGACTACGCT
128 TTGCAGCA-TACTTAAGTCTAGAAGGGTTATCTG----CCAAAGACCCCCGAGTTCGATTACACT
* * * * * * * *
166358 CAGCTC-CAAGGCGCATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAA
188 CAGCTCTGAGGGCACATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGCCAA
166415 AGACCCCCGA
Statistics
Matches: 416, Mismatches: 64, Indels: 32
0.81 0.12 0.06
Matches are distributed among these distances:
245 31 0.07
246 162 0.39
247 3 0.01
248 72 0.17
249 76 0.18
250 28 0.07
251 17 0.04
252 27 0.06
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.24
Consensus pattern (245 bp):
CCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCAAGCTTAAGTCT
AGAAGGGTTATCTGCACAAAAGACCTTCGAGTTCGATTACACTCAGCTCCAAGGCACATCATTTG
CAGCATACTTAAGTCTAGAAGGGTTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTCTG
AGGGCACATCATTTACAGCATAACTCAAGGCGAGAAGGGTTATCTGCCAA
Found at i:166238 original size:330 final size:329
Alignment explanation
Indices: 165705--166484 Score: 1158
Period size: 330 Copynumber: 2.4 Consensus size: 329
165695 CAGCTTCGAG
* * * * * * * **
165705 GGCACATCATTTACAGTATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTT
1 GGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATC--TG-CC-AAAGACCCCCGAGTT
165770 CGATTACACTCAGCTTCGA-GGCACATCATTTACAGTAT-ACTCAAGGCTAGAAGGGTTATCTGT
62 CGATTACACTCAGCTTCGAGGGCACATCATTTACAGTATAACTCAAGGCTAGAAGGGTTATCTGT
* * *
165833 GACCAAAGACCTTCGAGTTCGATTACACTCAGCTCTGAGGGCACATCATTTGCAGCATAACTTAA
127 GACCAAAGACCTTCGAGTTCGACTACACTCAGCTCTCAAGGCACATCATTTGCAGCATAACTTAA
* *
165898 GTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACACTCAGC-TCCAAGGCATA
192 GTAGAGAAGGGCTATCTG----CCAAAGACCTTCGAGTTCGACTACACTCAGCTTCCAAGGCATA
165962 TCATTTGCAG-C-ACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTCGAGTTCGACTAC
253 TCATTTGCAGACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTCGAGTTCGACTAC
166025 GCTCAGCTCCAA
318 GCTCAGCTCCAA
166037 GGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGAT
1 GGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGAT
166102 TACACTCAGCTTCGAGGGCACATCATTTACAGTATAACTCAAGGCTAGAAGGGTTATCTGTGACC
66 TACACTCAGCTTCGAGGGCACATCATTTACAGTATAACTCAAGGCTAGAAGGGTTATCTGTGACC
* *
166167 AAAAGACCTTCGAGTTCGACTACGCTCAGCTC-CAAGGCACATCATTTGCAGCATAGCTTAAGTA
131 -AAAGACCTTCGAGTTCGACTACACTCAGCTCTCAAGGCACATCATTTGCAGCATAACTTAAGTA
* * * *
166231 TAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTG
195 GAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGACTACACTCAGCTTCCAAGGCATATCATTTG
* *
166296 CAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAG
260 CAG-ACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAG
166361 CTCCAA
324 CTCCAA
*
166367 GGCGCATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGAT
1 GGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGAT
* * * ** * *
166432 TACACTCAACTTCGAGGTCATATCATTTACAACATAGCTCAAGGCAAGAAGGG
66 TACACTCAGCTTCGAGGGCACATCATTTACAGTATAACTCAAGGCTAGAAGGG
166485 CTATTTGTCA
Statistics
Matches: 411, Mismatches: 30, Indels: 16
0.90 0.07 0.04
Matches are distributed among these distances:
326 30 0.07
327 19 0.05
328 32 0.08
329 22 0.05
330 244 0.59
331 29 0.07
332 35 0.09
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.24
Consensus pattern (329 bp):
GGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGAT
TACACTCAGCTTCGAGGGCACATCATTTACAGTATAACTCAAGGCTAGAAGGGTTATCTGTGACC
AAAGACCTTCGAGTTCGACTACACTCAGCTCTCAAGGCACATCATTTGCAGCATAACTTAAGTAG
AGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGACTACACTCAGCTTCCAAGGCATATCATTTGC
AGACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCT
CCAA
Found at i:166488 original size:81 final size:81
Alignment explanation
Indices: 165632--166484 Score: 878
Period size: 81 Copynumber: 10.4 Consensus size: 81
165622 TAAACAAACT
* * ** *
165632 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-CCAAAGACCCCCGAGTTTGATTACACTC
1 ATTTGCAGCATAGCTTAAGTCTAGAAGGGTTATCTGACCAAAGACCTTCGAGTTCGATTACACTC
165696 AGCTTCGAGGGCACATC
66 AGCTTCGA-GGCACATC
* * * * *
165713 ATTTACAGTATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGATTACA
1 ATTTGCAGCATAGCTTAAGTCTAGAAGGGTTATC--TGACC-AAAGACCTTCGAGTTCGATTACA
165778 CTCAGCTTCGAGGCACATC
63 CTCAGCTTCGAGGCACATC
* * * *
165797 ATTTACAGTATA-CTCAAGGCTAGAAGGGTTATCTGTGACCAAAGACCTTCGAGTTCGATTACAC
1 ATTTGCAGCATAGCTTAAGTCTAGAAGGGTTATC--TGACCAAAGACCTTCGAGTTCGATTACAC
165861 TCAGC-TCTGAGGGCACATC
64 TCAGCTTC-GA-GGCACATC
* * *
165880 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACA
1 ATTTGCAGCATAGCTTAAGTCTAGAAGGGTTATCTG---ACCAAAGACCTTCGAGTTCGATTACA
* * *
165945 CTCAGCTCCAAGGCATATC
63 CTCAGCTTCGAGGCACATC
* * * *
165964 ATTTGCAGC--A-CTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAGCTTAAGTCTAGAAGGGTTATCTG---ACCAAAGACCTTCGAGTTCGATTACA
* *
166026 CTCAGCTCCAAGGCACATC
63 CTCAGCTTCGAGGCACATC
* * **
166045 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-CCAAAGACCCCCGAGTTCGATTACACTC
1 ATTTGCAGCATAGCTTAAGTCTAGAAGGGTTATCTGACCAAAGACCTTCGAGTTCGATTACACTC
166109 AGCTTCGAGGGCACATC
66 AGCTTCGA-GGCACATC
* * * * * * *
166126 ATTTACAGTATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAGCTTAAGTCTAGAAGGGTTATC--TGACC-AAAGACCTTCGAGTTCGATTACA
* *
166191 CTCAGCTCCAAGGCACATC
63 CTCAGCTTCGAGGCACATC
* *
166210 ATTTGCAGCATAGCTTAAGTATAGAAGGGCTATCTG-CCAAAGACCTTCGAGTTCGATTACACTC
1 ATTTGCAGCATAGCTTAAGTCTAGAAGGGTTATCTGACCAAAGACCTTCGAGTTCGATTACACTC
*
166274 AGCTTCGAGGGCATATC
66 AGCTTCGA-GGCACATC
* * * * * *
166291 ATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACCAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGCATAGCTTAAGTCTAGAAGGGTTATCTG---ACCAAAGACCTTCGAGTTCGATTACA
* * *
166356 CTCAGCTCCAAGGCGCATC
63 CTCAGCTTCGAGGCACATC
* * **
166375 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-CCAAAGACCCCCGAGTTCGATTACACTC
1 ATTTGCAGCATAGCTTAAGTCTAGAAGGGTTATCTGACCAAAGACCTTCGAGTTCGATTACACTC
* *
166439 AACTTCGAGGTCATATC
66 AGCTTCGAGG-CACATC
* * * * *
166456 ATTTACAACATAGCTCAAGGCAAGAAGGG
1 ATTTGCAGCATAGCTTAAGTCTAGAAGGG
166485 CTATTTGTCA
Statistics
Matches: 656, Mismatches: 91, Indels: 50
0.82 0.11 0.06
Matches are distributed among these distances:
80 89 0.14
81 207 0.32
82 36 0.05
83 51 0.08
84 150 0.23
85 122 0.19
86 1 0.00
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.24
Consensus pattern (81 bp):
ATTTGCAGCATAGCTTAAGTCTAGAAGGGTTATCTGACCAAAGACCTTCGAGTTCGATTACACTC
AGCTTCGAGGCACATC
Found at i:169408 original size:85 final size:84
Alignment explanation
Indices: 169251--169417 Score: 244
Period size: 85 Copynumber: 2.0 Consensus size: 84
169241 GAAAGTGACT
* **
169251 CTAATTTAGTGTTTCGTTAGGGTAAACTACAATTTGGTAACTAGACTATCAGTTCTGGTTTGTTT
1 CTAATTTAGTGTTTCGTTAGGGCAAACTACAATTTGGTAACTAGACTATCAGTTCTGGTCCGTTT
*
169316 TAATACATAAATTTTTATC
66 TAATACATAAACTTTTATC
* * * *
169335 CTAATTTAGTGTTTCGTTAGGGCAAACTATACATTTGTTAATTAGACTATCAGTTTTGGTCCGTT
1 CTAATTTAGTGTTTCGTTAGGGCAAACTACA-ATTTGGTAACTAGACTATCAGTTCTGGTCCGTT
*
169400 TTAGTACATAAACTTTTA
65 TTAATACATAAACTTTTA
169418 AATTTTTTTC
Statistics
Matches: 73, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
84 29 0.40
85 44 0.60
ACGTcount: A:0.28, C:0.13, G:0.16, T:0.44
Consensus pattern (84 bp):
CTAATTTAGTGTTTCGTTAGGGCAAACTACAATTTGGTAACTAGACTATCAGTTCTGGTCCGTTT
TAATACATAAACTTTTATC
Found at i:175419 original size:82 final size:83
Alignment explanation
Indices: 175302--175470 Score: 268
Period size: 83 Copynumber: 2.0 Consensus size: 83
175292 TATAGATCTT
* *
175302 TAGAAGAAATTACTTGAGCAAAGAAAGATAACTAGAAGCA-TTATCAAGAAAAGCATCTTACGAG
1 TAGAAGAAATTACATAAGCAAAGAAAGATAACTAGAAGCACTTATCAAGAAAAGCATCTTACGAG
175366 AAATGATCTTACCAGAGC
66 AAATGATCTTACCAGAGC
* ** *
175384 TAGAAGAAATTAGATAAGCAAAGAAAGATAACTAGACTCACTTATCAAGAAAAGCATCTTACGAT
1 TAGAAGAAATTACATAAGCAAAGAAAGATAACTAGAAGCACTTATCAAGAAAAGCATCTTACGAG
*
175449 AAATGATCTTTCCAGAGC
66 AAATGATCTTACCAGAGC
175467 TAGA
1 TAGA
175471 GGACAAGGCA
Statistics
Matches: 79, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
82 35 0.44
83 44 0.56
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (83 bp):
TAGAAGAAATTACATAAGCAAAGAAAGATAACTAGAAGCACTTATCAAGAAAAGCATCTTACGAG
AAATGATCTTACCAGAGC
Found at i:176820 original size:125 final size:125
Alignment explanation
Indices: 176685--176930 Score: 368
Period size: 125 Copynumber: 2.0 Consensus size: 125
176675 AACTCTATGC
**
176685 ACCTACAATACAAAATTTTTGTACTTGAATGGTCATAAA-AAAATTTAAGGATAGACACAATTAA
1 ACCTACAATACAAAATTTTTGTACTTGAATGAACATAAATAAAATTTAAGGATAGACACAATTAA
* * * * *
176749 CAAAATGAATAACTAATAGAAAAAAAAATCGAATTTTAAAGAGAGAAATTTATATTTCTGT
66 CAAAATGAACAACTAACA-AAAAAAAAATCAAATTTTAAAGAAAGAAATTTAGATTTCTGT
* *
176810 ACCTACAATACAAATTTTTTGTACTTGAGTGAACATAAATAAAATTTAAGGATAGACACAATTAA
1 ACCTACAATACAAAATTTTTGTACTTGAATGAACATAAATAAAATTTAAGGATAGACACAATTAA
* * *
176875 CAGAATGAACAACTAACATAAAAAAATTCAAATTTTAAAGAAAGAAATTTAGATTT
66 CAAAATGAACAACTAACAAAAAAAAAATCAAATTTTAAAGAAAGAAATTTAGATTT
176931 GAAGGTGAGC
Statistics
Matches: 108, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
125 68 0.63
126 40 0.37
ACGTcount: A:0.50, C:0.10, G:0.11, T:0.29
Consensus pattern (125 bp):
ACCTACAATACAAAATTTTTGTACTTGAATGAACATAAATAAAATTTAAGGATAGACACAATTAA
CAAAATGAACAACTAACAAAAAAAAAATCAAATTTTAAAGAAAGAAATTTAGATTTCTGT
Found at i:177362 original size:21 final size:22
Alignment explanation
Indices: 177321--177369 Score: 84
Period size: 21 Copynumber: 2.3 Consensus size: 22
177311 CCCCACTGCA
177321 TGCA-GGCGACCTCTTTCGACG
1 TGCATGGCGACCTCTTTCGACG
177342 TGCATGGCGACCTCTTT-GACG
1 TGCATGGCGACCTCTTTCGACG
177363 TGCATGG
1 TGCATGG
177370 GCATGCAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 15 0.56
22 12 0.44
ACGTcount: A:0.14, C:0.29, G:0.31, T:0.27
Consensus pattern (22 bp):
TGCATGGCGACCTCTTTCGACG
Found at i:177409 original size:31 final size:31
Alignment explanation
Indices: 177374--177466 Score: 168
Period size: 31 Copynumber: 3.0 Consensus size: 31
177364 GCATGGGCAT
* *
177374 GCAAAGCTTCATCCTCTCACCATAGCTCGTA
1 GCAAAGCTTCATCCTCTCGCCACAGCTCGTA
177405 GCAAAGCTTCATCCTCTCGCCACAGCTCGTA
1 GCAAAGCTTCATCCTCTCGCCACAGCTCGTA
177436 GCAAAGCTTCATCCTCTCGCCACAGCTCGTA
1 GCAAAGCTTCATCCTCTCGCCACAGCTCGTA
177467 TAGAACACTT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 60 1.00
ACGTcount: A:0.24, C:0.38, G:0.15, T:0.24
Consensus pattern (31 bp):
GCAAAGCTTCATCCTCTCGCCACAGCTCGTA
Found at i:183399 original size:258 final size:258
Alignment explanation
Indices: 182898--183413 Score: 968
Period size: 259 Copynumber: 2.0 Consensus size: 258
182888 TAGCAGTCTA
182898 TCATCAGTTATGACCCTTCTCTGCCAATCTTCGTTTTATTTGCTCACGTGCACCAACAAAAGTTA
1 TCATCAGTTATGACCCTTCTCTGCCAATCTTCGTTTTATTTGCTCACGTGCACCAACAAAAGTTA
182963 CACCATACACTGAGGTCATTACTGTTTGCTTTACTAATTTTCGATCCACCTTGAAGTTTCAACAT
66 CACCATACACTGAGGTCATTACTGTTTGCTTTACTAATTTTCGATCCACCTTGAAGTTTCAACAT
183028 TTTAATCCGTTAGTTTAAAGGGGGAGAAGTCCGAATTCAAAATCAATTGTAAATAGTTTAGATGT
131 TTTAATCCGTTAGTTTAAAGGGGGAGAAGTCCGAATTCAAAATCAATTGTAAATAGTTTAGATGT
183093 TAACTTCTAGGAAATCTAGTAATTTTAGTTTCAATAAAATCCAGTCCAACC-GATCAATTAAG
196 TAACTTCTAGGAAATCTAGTAATTTTAGTTTCAATAAAATCCAGTCCAACCTGATCAATTAAG
183155 TCATCAGTTATATGACCCTTCTCTGCCAATCTTCGTTTTATTTGCTCACGTGCACCAACAAAAGT
1 TCATCAG-T-TATGACCCTTCTCTGCCAATCTTCGTTTTATTTGCTCACGTGCACCAACAAAAGT
183220 TACACCATACACTGAGGTCATTACTGTTTGCTTTACTAA-TTTCGATCCACCTTGAAGTTTCAAC
64 TACACCATACACTGAGGTCATTACTGTTTGCTTTACTAATTTTCGATCCACCTTGAAGTTTCAAC
183284 ATTTTAATCCGTTAGTTTAAA-GGGG-GAAGTCCGAATTCAAAATCAATTGTAAATAGTTTAGAT
129 ATTTTAATCCGTTAGTTTAAAGGGGGAGAAGTCCGAATTCAAAATCAATTGTAAATAGTTTAGAT
183347 GTTAACTGTTCTAGGAAATCTAGTAATTTTAGTTTCAATAAAATCCAGTCCAACCTGATCAATTA
194 GTTAAC--TTCTAGGAAATCTAGTAATTTTAGTTTCAATAAAATCCAGTCCAACCTGATCAATTA
183412 AG
257 AG
183414 AGCTTAGCCA
Statistics
Matches: 254, Mismatches: 0, Indels: 8
0.97 0.00 0.03
Matches are distributed among these distances:
256 44 0.17
257 11 0.04
258 94 0.37
259 105 0.41
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (258 bp):
TCATCAGTTATGACCCTTCTCTGCCAATCTTCGTTTTATTTGCTCACGTGCACCAACAAAAGTTA
CACCATACACTGAGGTCATTACTGTTTGCTTTACTAATTTTCGATCCACCTTGAAGTTTCAACAT
TTTAATCCGTTAGTTTAAAGGGGGAGAAGTCCGAATTCAAAATCAATTGTAAATAGTTTAGATGT
TAACTTCTAGGAAATCTAGTAATTTTAGTTTCAATAAAATCCAGTCCAACCTGATCAATTAAG
Found at i:199560 original size:60 final size:58
Alignment explanation
Indices: 199496--199654 Score: 153
Period size: 60 Copynumber: 2.7 Consensus size: 58
199486 GATGAAATTG
* *
199496 GGGATGAAATTGAAATATTAAAAAGTTTGAGGACCAATTTAGTTATAAG-GTAATAGTTT
1 GGGATGAAATTAAAATATTAAAAAGTTTAAGGACCAATTTAG--ATAAGAGTAATAGTTT
* * * * *
199555 AGGGATGAGATTAAAACT-TTAAAATGTTTAAGGACTAATCTTAGCTAAGAGTTATAGTTT
1 -GGGATGAAATTAAAA-TATTAAAAAGTTTAAGGACCAAT-TTAGATAAGAGTAATAGTTT
* *
199615 GAGGATAAAATTAAAATATTCACAAA-TTTAAGGACCAATT
1 G-GGATGAAATTAAAATATT-AAAAAGTTTAAGGACCAATT
199655 GAAATGAATG
Statistics
Matches: 81, Mismatches: 12, Indels: 13
0.76 0.11 0.12
Matches are distributed among these distances:
59 7 0.09
60 66 0.81
61 8 0.10
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.33
Consensus pattern (58 bp):
GGGATGAAATTAAAATATTAAAAAGTTTAAGGACCAATTTAGATAAGAGTAATAGTTT
Found at i:208970 original size:24 final size:23
Alignment explanation
Indices: 208936--209000 Score: 80
Period size: 22 Copynumber: 2.9 Consensus size: 23
208926 TGTTACAGGT
*
208936 ATGAACTGTACCGTATGAACATTA
1 ATGAACAGTACCG-ATGAACATTA
*
208960 ATGAACAGTACCG-TGAACATTT
1 ATGAACAGTACCGATGAACATTA
*
208982 ATGAACAATACC-ATGAACA
1 ATGAACAGTACCGATGAACA
209001 GTATCCTACT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
22 25 0.68
24 12 0.32
ACGTcount: A:0.42, C:0.18, G:0.15, T:0.25
Consensus pattern (23 bp):
ATGAACAGTACCGATGAACATTA
Found at i:209892 original size:32 final size:32
Alignment explanation
Indices: 209789--209912 Score: 112
Period size: 31 Copynumber: 3.9 Consensus size: 32
209779 ACCTCGACAA
* *
209789 CTGTCCATAGGTCCCGAAGAACCTAGGT-ATAT
1 CTGTCCATATGTCCCGAAGAACATAGGTAAT-T
* ** * * *
209821 -TGTCCATATGTTCCTTATAACATATGT-ATA
1 CTGTCCATATGTCCCGAAGAACATAGGTAATT
209851 CTGTCCATATGTCCCGAA-AGACATAGGTAATT
1 CTGTCCATATGTCCCGAAGA-ACATAGGTAATT
* *
209883 CTGTCCATATGTTCCGTAGAACATAGGTAA
1 CTGTCCATATGTCCCGAAGAACATAGGTAA
209913 ACCCTTGACT
Statistics
Matches: 73, Mismatches: 15, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
30 1 0.01
31 43 0.59
32 28 0.38
33 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (32 bp):
CTGTCCATATGTCCCGAAGAACATAGGTAATT
Found at i:212863 original size:47 final size:48
Alignment explanation
Indices: 212804--212895 Score: 143
Period size: 47 Copynumber: 1.9 Consensus size: 48
212794 CGTGGAACTG
* *
212804 CACATTTTTCGTCCAA-TTGTTCATGATTGCAGCCTTGTAAGTGTATTC
1 CACATTTTTCGTCCAACAT-TTAATGATTGCAGCCTTGTAAGTGTATTC
212852 CACA-TTTTCGTCCAACATTTAATGATTGCAGCCTTGTAAGTGTA
1 CACATTTTTCGTCCAACATTTAATGATTGCAGCCTTGTAAGTGTA
212896 ACAAAATATC
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
47 36 0.88
48 5 0.12
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (48 bp):
CACATTTTTCGTCCAACATTTAATGATTGCAGCCTTGTAAGTGTATTC
Found at i:229654 original size:15 final size:15
Alignment explanation
Indices: 229612--229655 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
229602 TTTCGCACCT
* *
229612 CTGAATGATTCAATG
1 CTGACTGATTCAGTG
*
229627 CTGACCGATTCAGTG
1 CTGACTGATTCAGTG
229642 CTGACTGATTCAGT
1 CTGACTGATTCAGT
229656 AAAAAAGTGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (15 bp):
CTGACTGATTCAGTG
Found at i:236900 original size:13 final size:13
Alignment explanation
Indices: 236882--236910 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
236872 ACCATCTACT
236882 GTGGTCGAAGATG
1 GTGGTCGAAGATG
236895 GTGGTCGAAGATG
1 GTGGTCGAAGATG
236908 GTG
1 GTG
236911 TCCGACCACC
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:0.21, C:0.07, G:0.48, T:0.24
Consensus pattern (13 bp):
GTGGTCGAAGATG
Found at i:241820 original size:36 final size:36
Alignment explanation
Indices: 241773--241902 Score: 215
Period size: 36 Copynumber: 3.6 Consensus size: 36
241763 TCTATGAGAG
241773 GATCTTACAGGACTTCTGCTGATGCTACACCTCGAA
1 GATCTTACAGGACTTCTGCTGATGCTACACCTCGAA
* *
241809 GATCTTACAGGACTTCTGCTGATGCTCCGCCTCGAA
1 GATCTTACAGGACTTCTGCTGATGCTACACCTCGAA
* **
241845 GATCTTACAGGACTTCTGCTGATGCTTCTTCTCGAA
1 GATCTTACAGGACTTCTGCTGATGCTACACCTCGAA
241881 GATCTTACAGGACTTCTGCTGA
1 GATCTTACAGGACTTCTGCTGA
241903 CGTTTCTCTG
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 89 1.00
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.31
Consensus pattern (36 bp):
GATCTTACAGGACTTCTGCTGATGCTACACCTCGAA
Found at i:249767 original size:23 final size:23
Alignment explanation
Indices: 249741--249795 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
249731 CAGAGAAAAA
* *
249741 TATCACAAAAATAGAGATAAATG
1 TATCACAAAAACAGAGATAAACG
249764 TATCACAAAAACAGAGATAAACG
1 TATCACAAAAACAGAGATAAACG
249787 TATCACAAA
1 TATCACAAA
249796 GACGAAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.56, C:0.15, G:0.11, T:0.18
Consensus pattern (23 bp):
TATCACAAAAACAGAGATAAACG
Found at i:254942 original size:43 final size:45
Alignment explanation
Indices: 254851--254977 Score: 195
Period size: 43 Copynumber: 2.9 Consensus size: 45
254841 GAAAGTTCAA
* *
254851 TTCGATCTTCTCCAACGTTCAGTTTATTTTATCCATGGACGAACT
1 TTCGATCTTCTCCAACGTTCAGATTATTTCATCCATGGACGAACT
*
254896 TTCGATCTTCTCCAAGGTTCAG-TT-TTTCATCCATGGACGAACT
1 TTCGATCTTCTCCAACGTTCAGATTATTTCATCCATGGACGAACT
* *
254939 TTCGATCCTCTCCAACGTTCTGATTATTTCATCCATGGA
1 TTCGATCTTCTCCAACGTTCAGATTATTTCATCCATGGA
254978 TTTTGTCCAA
Statistics
Matches: 75, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
43 37 0.49
44 4 0.05
45 34 0.45
ACGTcount: A:0.21, C:0.26, G:0.14, T:0.39
Consensus pattern (45 bp):
TTCGATCTTCTCCAACGTTCAGATTATTTCATCCATGGACGAACT
Found at i:256881 original size:26 final size:28
Alignment explanation
Indices: 256821--256882 Score: 74
Period size: 31 Copynumber: 2.2 Consensus size: 28
256811 AAGTATTGCT
*
256821 GAGCTCGACTCGACTCGAAAACTCTGAAATG
1 GAGCTCGACTCGACTCGAAAACTCTG--A-C
256852 GAGCTCGACTCGACTCGAAAACTC-G-C
1 GAGCTCGACTCGACTCGAAAACTCTGAC
256878 GAGCT
1 GAGCT
256883 TAAAATTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 5 0.17
30 1 0.03
31 24 0.80
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.18
Consensus pattern (28 bp):
GAGCTCGACTCGACTCGAAAACTCTGAC
Found at i:265650 original size:2 final size:2
Alignment explanation
Indices: 265645--265713 Score: 78
Period size: 2 Copynumber: 37.0 Consensus size: 2
265635 TTTAATTTAA
*
265645 AT AT AT AT AT AT AT AT -T A- AT -T AT -T CT -T AT AT GA- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT
265682 AT AT AT AT 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 AT
265714 CTAATAATTA
Statistics
Matches: 60, Mismatches: 0, Indels: 14
0.81 0.00 0.19
Matches are distributed among these distances:
1 6 0.10
2 53 0.88
3 1 0.02
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (2 bp):
AT
Found at i:271660 original size:42 final size:42
Alignment explanation
Indices: 271597--271716 Score: 213
Period size: 42 Copynumber: 2.9 Consensus size: 42
271587 TTTCCCTGAA
*
271597 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
* *
271639 TTCTCGTGTTTGTTTCACGTAATTTGTTTTCCGGAAAACGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
271681 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
271717 TGTAATTCAT
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 73 1.00
ACGTcount: A:0.16, C:0.19, G:0.19, T:0.46
Consensus pattern (42 bp):
TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
Found at i:271952 original size:22 final size:23
Alignment explanation
Indices: 271905--271996 Score: 73
Period size: 22 Copynumber: 3.8 Consensus size: 23
271895 TAATTATTAA
* *
271905 AATATTTAAAAT-ATAT-TTATT
1 AATATTTATAATAATATAATATT
271926 AATATTTATAATAATATAATATT
1 AATATTTATAATAATATAATATT
*
271949 -ATATTTTTAATATTATATAAAATAATT
1 AATATTTATAATA--ATAT--AAT-ATT
271976 AATTATATTATAATAATATAA
1 AA-TAT-TTATAATAATATAA
271997 GATATTATAT
Statistics
Matches: 57, Mismatches: 4, Indels: 15
0.75 0.05 0.20
Matches are distributed among these distances:
21 11 0.19
22 15 0.26
23 4 0.07
24 4 0.07
26 5 0.09
27 3 0.05
28 5 0.09
29 3 0.05
30 7 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
AATATTTATAATAATATAATATT
Found at i:271992 original size:18 final size:19
Alignment explanation
Indices: 271960--272005 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
271950 TATTTTTAAT
*
271960 ATTATA-TAAAATAAT-TA
1 ATTATATTATAATAATATA
271977 ATTATATTATAATAATATA
1 ATTATATTATAATAATATA
*
271996 A-GATATTATA
1 ATTATATTATA
272006 TTTTTATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 6 0.24
18 16 0.64
19 3 0.12
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
ATTATATTATAATAATATA
Found at i:272028 original size:54 final size:52
Alignment explanation
Indices: 271909--272040 Score: 148
Period size: 54 Copynumber: 2.5 Consensus size: 52
271899 TATTAAAATA
*
271909 TTTAA-AATATATTTATTAA-TATTTATAATAATATAATATTATATTTTTAAT
1 TTTAATAATATA-TAATTAATTATTTATAATAATATAATATTATATTTTTAAT
*
271960 ATTATATAA-A-ATAATTAATTATATTATAATAATATAAGATATTATATTTTT-AT
1 TTTA-ATAATATATAATTAATTAT-TTATAATAATAT-A-ATATTATATTTTTAAT
* *
272013 TTTAATAATATATAATAAATTTTTTATA
1 TTTAATAATATATAATTAATTATTTATA
272041 TATTTAATAA
Statistics
Matches: 68, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
50 6 0.09
51 7 0.10
52 18 0.26
53 14 0.21
54 23 0.34
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (52 bp):
TTTAATAATATATAATTAATTATTTATAATAATATAATATTATATTTTTAAT
Found at i:272485 original size:20 final size:20
Alignment explanation
Indices: 272407--272476 Score: 140
Period size: 20 Copynumber: 3.5 Consensus size: 20
272397 TTTTCAGATG
272407 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
272427 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
272447 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
272467 TTTTCCAGAA
1 TTTTCCAGAA
272477 TTCAAATTCC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:272485 original size:40 final size:40
Alignment explanation
Indices: 272407--272485 Score: 131
Period size: 40 Copynumber: 2.0 Consensus size: 40
272397 TTTTCAGATG
**
272407 TTTTCCAGAAATGTAATTCATTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
*
272447 TTTTCCAGAAATGTAATTCATTTTCCAGAATTCAAATTC
1 TTTTCCAGAAATGTAATTCATTTTCCAGAAATCAAATTC
272486 CAGTAATTCA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (40 bp):
TTTTCCAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
Found at i:272511 original size:30 final size:29
Alignment explanation
Indices: 272459--272540 Score: 119
Period size: 30 Copynumber: 2.8 Consensus size: 29
272449 TTCCAGAAAT
272459 GTAATTCATTTTCCAGAATTCAAATTCCA
1 GTAATTCATTTTCCAGAATTCAAATTCCA
272488 GTAATTCATTTTCCAGAAATTCAAATTCCA
1 GTAATTCATTTTCCAG-AATTCAAATTCCA
* **
272518 ATAATTCAAATTCCAGTAATTCA
1 GTAATTCATTTTCCAG-AATTCA
272541 TTTTCCGGAA
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
29 16 0.33
30 32 0.67
ACGTcount: A:0.38, C:0.20, G:0.06, T:0.37
Consensus pattern (29 bp):
GTAATTCATTTTCCAGAATTCAAATTCCA
Found at i:272546 original size:15 final size:15
Alignment explanation
Indices: 272459--272540 Score: 103
Period size: 15 Copynumber: 5.5 Consensus size: 15
272449 TTCCAGAAAT
**
272459 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
272474 G-AATTCAAATTCCA
1 GTAATTCAAATTCCA
**
272488 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
*
272503 GAAATTCAAATTCCA
1 GTAATTCAAATTCCA
*
272518 ATAATTCAAATTCCA
1 GTAATTCAAATTCCA
272533 GTAATTCA
1 GTAATTCA
272541 TTTTCCGGAA
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
14 12 0.21
15 44 0.79
ACGTcount: A:0.38, C:0.20, G:0.06, T:0.37
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:273791 original size:21 final size:22
Alignment explanation
Indices: 273767--273814 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
273757 TGGGTGACCA
*
273767 TTTATGTAT-TTTACAATAAAT
1 TTTATGTATATCTACAATAAAT
* *
273788 TTTATTTATATCTACAATACAT
1 TTTATGTATATCTACAATAAAT
273810 TTTAT
1 TTTAT
273815 TAGAATTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.35, C:0.08, G:0.02, T:0.54
Consensus pattern (22 bp):
TTTATGTATATCTACAATAAAT
Found at i:274215 original size:12 final size:13
Alignment explanation
Indices: 274198--274227 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
274188 ATTCAGCCCC
274198 AATGAACATTCT-
1 AATGAACATTCTG
274210 AATGAACATTCTG
1 AATGAACATTCTG
274223 AATGA
1 AATGA
274228 TTCAGAATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (13 bp):
AATGAACATTCTG
Found at i:274305 original size:16 final size:16
Alignment explanation
Indices: 274284--274355 Score: 110
Period size: 16 Copynumber: 4.6 Consensus size: 16
274274 ACAAAACTTC
274284 TGAATCATTCAACATT
1 TGAATCATTCAACATT
*
274300 TGAATCGTTCAACATT
1 TGAATCATTCAACATT
*
274316 TGAATCACTCAACATT
1 TGAATCATTCAACATT
*
274332 TGAATCATTCAACACT
1 TGAATCATTCAACATT
274348 T-AATCATT
1 TGAATCATT
274356 TTAAAATAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
15 7 0.14
16 44 0.86
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (16 bp):
TGAATCATTCAACATT
Found at i:276863 original size:18 final size:18
Alignment explanation
Indices: 276840--276876 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
276830 TATGGGAATT
*
276840 TTAAAATTTTATATAAAA
1 TTAAAATTATATATAAAA
*
276858 TTAAAATTATATTTAAAA
1 TTAAAATTATATATAAAA
276876 T
1 T
276877 AACATAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TTAAAATTATATATAAAA
Found at i:285840 original size:2 final size:2
Alignment explanation
Indices: 285833--285862 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
285823 TAATACTCCC
285833 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
285863 TTCATCTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:289243 original size:70 final size:70
Alignment explanation
Indices: 289162--289300 Score: 269
Period size: 70 Copynumber: 2.0 Consensus size: 70
289152 AATTGAGTTT
*
289162 CGAATTTGACAAATTCGTATTGCGAAATGTAAAATCTCGCTTCTTAAAGAAACAATCGTTTTGAT
1 CGAATTTGACAAATTCGTATTGCGAAATGTAAAATCTCGCTTCTTAAAGAAACAATCGTTTTGAC
289227 GGTTA
66 GGTTA
289232 CGAATTTGACAAATTCGTATTGCGAAATGTAAAATCTCGCTTCTTAAAGAAACAATCGTTTTGAC
1 CGAATTTGACAAATTCGTATTGCGAAATGTAAAATCTCGCTTCTTAAAGAAACAATCGTTTTGAC
289297 GGTT
66 GGTT
289301 CATTTGTTTG
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 68 1.00
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (70 bp):
CGAATTTGACAAATTCGTATTGCGAAATGTAAAATCTCGCTTCTTAAAGAAACAATCGTTTTGAC
GGTTA
Found at i:289588 original size:22 final size:22
Alignment explanation
Indices: 289563--289616 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
289553 TCGGTAATTG
289563 AGTTGCGAAATTGGCGAATTCA
1 AGTTGCGAAATTGGCGAATTCA
* *
289585 AGTTTCGAAATTGGCGAATTCG
1 AGTTGCGAAATTGGCGAATTCA
*
289607 AGCTGCGAAA
1 AGTTGCGAAA
289617 ACGAAATCCG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.26
Consensus pattern (22 bp):
AGTTGCGAAATTGGCGAATTCA
Found at i:290748 original size:30 final size:30
Alignment explanation
Indices: 290712--290769 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
290702 TTTTCAATAG
290712 TAAAATTTTATAAGTTCAAATTTACTCTCT
1 TAAAATTTTATAAGTTCAAATTTACTCTCT
* *
290742 TAAAATTTTATATGTTTAAATTTACTCT
1 TAAAATTTTATAAGTTCAAATTTACTCT
290770 TAATATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.36, C:0.10, G:0.03, T:0.50
Consensus pattern (30 bp):
TAAAATTTTATAAGTTCAAATTTACTCTCT
Found at i:301596 original size:2 final size:2
Alignment explanation
Indices: 301589--301615 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
301579 TTCACCCTAA
301589 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
301616 AAACTCAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:302798 original size:25 final size:27
Alignment explanation
Indices: 302770--302824 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
302760 ACCGAATCAA
*
302770 AAAAATGAAACC-TTT-AAACCGAACC
1 AAAAATGAAACCGTTTAAAACCAAACC
*
302795 AAAAATTAAACCGTTTAAAACCAAACC
1 AAAAATGAAACCGTTTAAAACCAAACC
302822 AAA
1 AAA
302825 TCAAACCGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 11 0.42
26 3 0.12
27 12 0.46
ACGTcount: A:0.56, C:0.22, G:0.05, T:0.16
Consensus pattern (27 bp):
AAAAATGAAACCGTTTAAAACCAAACC
Found at i:302798 original size:26 final size:28
Alignment explanation
Indices: 302759--302824 Score: 75
Period size: 27 Copynumber: 2.4 Consensus size: 28
302749 ACTTGAATCG
*
302759 AACCGAATCAAAAAAATGAAACC-TTT-A
1 AACCGAA-CCAAAAAATGAAACCGTTTAA
*
302786 AACCGAACC-AAAAATTAAACCGTTTAA
1 AACCGAACCAAAAAATGAAACCGTTTAA
*
302813 AACCAAACCAAA
1 AACCGAACCAAA
302825 TCAAACCGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
25 11 0.33
26 4 0.12
27 16 0.48
28 2 0.06
ACGTcount: A:0.56, C:0.23, G:0.06, T:0.15
Consensus pattern (28 bp):
AACCGAACCAAAAAATGAAACCGTTTAA
Found at i:302825 original size:25 final size:25
Alignment explanation
Indices: 302771--302832 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
302761 CCGAATCAAA
* *
302771 AAAATGAAACC-TTTAAACCGAACC
1 AAAATCAAACCGTTTAAACCAAACC
*
302795 AAAAATTAAACCGTTTAAAACCAAACC
1 -AAAATCAAACCGTTT-AAACCAAACC
302822 -AAATCAAACCG
1 AAAATCAAACCG
302833 AACCATTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 20 0.62
26 3 0.09
27 9 0.28
ACGTcount: A:0.53, C:0.24, G:0.06, T:0.16
Consensus pattern (25 bp):
AAAATCAAACCGTTTAAACCAAACC
Found at i:305902 original size:12 final size:14
Alignment explanation
Indices: 305885--305921 Score: 51
Period size: 12 Copynumber: 2.7 Consensus size: 14
305875 AGAGATGGAT
305885 GCTGCTGCAAA-A-
1 GCTGCTGCAAAGAG
305897 GCTGCTGCACAAGAG
1 GCTGCTGCA-AAGAG
305912 GCTGCTGCAA
1 GCTGCTGCAA
305922 GGAGTGCAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 9 0.41
13 2 0.09
14 2 0.09
15 9 0.41
ACGTcount: A:0.27, C:0.27, G:0.30, T:0.16
Consensus pattern (14 bp):
GCTGCTGCAAAGAG
Found at i:308340 original size:63 final size:64
Alignment explanation
Indices: 308239--308372 Score: 166
Period size: 63 Copynumber: 2.1 Consensus size: 64
308229 TTTACCATTA
* *
308239 ACGGTTTAATTATCAAAACAGCAACTAAATATCAAAAAAAA-AAAAA-GACCAGACAACAATTCG
1 ACGGTTTAATTATCAAAACAGCAACTAAATACCAAAAAAAACAAAAAGGA-CAAACAACAATTCG
* * * * *
308302 ACGGTTTAATTATCCAAACAGCAA-TCAATAACCCAAAAAAACAAAAAGGACAAACAGCAATTTG
1 ACGGTTTAATTATCAAAACAGCAACTAAAT-ACCAAAAAAAACAAAAAGGACAAACAACAATTCG
308366 ACGGTTT
1 ACGGTTT
308373 GATTGCCGTT
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
62 4 0.07
63 32 0.52
64 23 0.38
65 2 0.03
ACGTcount: A:0.51, C:0.19, G:0.11, T:0.19
Consensus pattern (64 bp):
ACGGTTTAATTATCAAAACAGCAACTAAATACCAAAAAAAACAAAAAGGACAAACAACAATTCG
Found at i:308372 original size:64 final size:63
Alignment explanation
Indices: 308239--308372 Score: 164
Period size: 64 Copynumber: 2.1 Consensus size: 63
308229 TTTACCATTA
* *
308239 ACGGTTTAATTATCAAAACAGCAACTAAATATCAAAAAAAAAAAAAGACCAGACAACAATTCG
1 ACGGTTTAATTATCAAAACAGCAACTAAATACCAAAAAAAAAAAAAGACCAAACAACAATTCG
* * * * *
308302 ACGGTTTAATTATCCAAACAGCAA-TCAATAACCCAAAAAAACAAAAAGGA-CAAACAGCAATTT
1 ACGGTTTAATTATCAAAACAGCAACTAAAT-A-CCAAAAAAA-AAAAAAGACCAAACAACAATTC
308365 G
63 G
308366 ACGGTTT
1 ACGGTTT
308373 GATTGCCGTT
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
62 4 0.07
63 24 0.39
64 26 0.43
65 7 0.11
ACGTcount: A:0.51, C:0.19, G:0.11, T:0.19
Consensus pattern (63 bp):
ACGGTTTAATTATCAAAACAGCAACTAAATACCAAAAAAAAAAAAAGACCAAACAACAATTCG
Found at i:314987 original size:51 final size:51
Alignment explanation
Indices: 314849--315251 Score: 482
Period size: 51 Copynumber: 8.0 Consensus size: 51
314839 ACATTAAGAT
* *
314849 CTGTTGTGGTAGCTGAGTATATGTTTGGGAACCAATTTTTCCACC-T--TG
1 CTGTTGTGGTAGCTGAGTATATGTTTGGGATCCAATGTTTCCACCTTGCTG
** * *
314897 CTGTTGTGGTAGCAAAGTAAATGTCTGGGAAT-CAATGTTTCCACCTTGCTG
1 CTGTTGTGGTAGCTGAGTATATGTTTGGG-ATCCAATGTTTCCACCTTGCTG
* * * *
314948 CTGTTGTGGTAACTGAGCATATGTTTGGGTTCCATTGTTTCCACCTTGCTG
1 CTGTTGTGGTAGCTGAGTATATGTTTGGGATCCAATGTTTCCACCTTGCTG
* * *
314999 CTGATGTGCTAGCAGAGTATATGTTTGGGAAT-CAATGTTTCCACCTTGCTG
1 CTGTTGTGGTAGCTGAGTATATGTTTGGG-ATCCAATGTTTCCACCTTGCTG
**
315050 CTGTTGTGGTAGCACAG--TATGTTTGGGAAT-CAATGTTTCCACCTTGCTG
1 CTGTTGTGGTAGCTGAGTATATGTTTGGG-ATCCAATGTTTCCACCTTGCTG
* * *
315099 CTGTTCTGGTAGATGAGTATATGTTTGGGATCCAATGTTTCCACCTTGCCG
1 CTGTTGTGGTAGCTGAGTATATGTTTGGGATCCAATGTTTCCACCTTGCTG
* * *
315150 CTGATGCGGTAGCTGAGTATATGTTTGGGATCCAAAGTTTCCACCTTGCTG
1 CTGTTGTGGTAGCTGAGTATATGTTTGGGATCCAATGTTTCCACCTTGCTG
* * **
315201 CTGTTGAGGTAGTTGAGTATATGTTTGGGA-CTCTGTGTTTCCACCTTGCTG
1 CTGTTGTGGTAGCTGAGTATATGTTTGGGATC-CAATGTTTCCACCTTGCTG
315252 AGTCTGCGCC
Statistics
Matches: 304, Mismatches: 41, Indels: 17
0.84 0.11 0.05
Matches are distributed among these distances:
48 37 0.12
49 47 0.15
50 4 0.01
51 215 0.71
52 1 0.00
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.37
Consensus pattern (51 bp):
CTGTTGTGGTAGCTGAGTATATGTTTGGGATCCAATGTTTCCACCTTGCTG
Found at i:315109 original size:151 final size:151
Alignment explanation
Indices: 314853--315251 Score: 529
Period size: 151 Copynumber: 2.6 Consensus size: 151
314843 TAAGATCTGT
* *
314853 TGTGGTAGCTGAGTATATGTTTGGGAACCAATTTTTCCACC-T--TGCTGTTGTGGTAGCAAAGT
1 TGTGGTAGCTGAGTATATGTTTGGGAATCAATGTTTCCACCTTGCTGCTGTTGTGGTAGCAAAGT
* * *
314915 AAATGTCTGGGAATCAATGTTTCCACCTTGCTGCTGTTGTGGTA-ACTGAGCATATGTTTGGGTT
66 --ATGTTTGGGAATCAATGTTTCCACCTTGCTGCTGTTCTGGTAGA-TGAGCATATGTTTGGGAT
* *
314979 CCATTGTTTCCACCTTGCTGCTGA
128 CCAATGTTTCCACCTTGCCGCTGA
* * *
315003 TGTGCTAGCAGAGTATATGTTTGGGAATCAATGTTTCCACCTTGCTGCTGTTGTGGTAGCACAGT
1 TGTGGTAGCTGAGTATATGTTTGGGAATCAATGTTTCCACCTTGCTGCTGTTGTGGTAGCAAAGT
*
315068 ATGTTTGGGAATCAATGTTTCCACCTTGCTGCTGTTCTGGTAGATGAGTATATGTTTGGGATCCA
66 ATGTTTGGGAATCAATGTTTCCACCTTGCTGCTGTTCTGGTAGATGAGCATATGTTTGGGATCCA
315133 ATGTTTCCACCTTGCCGCTGA
131 ATGTTTCCACCTTGCCGCTGA
* * * ***
315154 TGCGGTAGCTGAGTATATGTTTGGG-ATCCAAAGTTTCCACCTTGCTGCTGTTGAGGTAGTTGAG
1 TGTGGTAGCTGAGTATATGTTTGGGAAT-CAATGTTTCCACCTTGCTGCTGTTGTGGTAGCAAAG
* **
315218 TATATGTTTGGGACTCTGTGTTTCCACCTTGCTG
65 --TATGTTTGGGAATCAATGTTTCCACCTTGCTG
315252 AGTCTGCGCC
Statistics
Matches: 220, Mismatches: 22, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
150 39 0.18
151 132 0.60
152 1 0.00
153 48 0.22
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.37
Consensus pattern (151 bp):
TGTGGTAGCTGAGTATATGTTTGGGAATCAATGTTTCCACCTTGCTGCTGTTGTGGTAGCAAAGT
ATGTTTGGGAATCAATGTTTCCACCTTGCTGCTGTTCTGGTAGATGAGCATATGTTTGGGATCCA
ATGTTTCCACCTTGCCGCTGA
Found at i:315919 original size:3 final size:3
Alignment explanation
Indices: 315911--315946 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
315901 GATTCAACGA
315911 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
315947 TCCAAGGATA
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):
AAT
Found at i:324723 original size:22 final size:21
Alignment explanation
Indices: 324673--324723 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
324663 ACCAAACAAC
* * *
324673 AAAAAAACTTGTTAAAAAATA
1 AAAAAAACATATTAAAAAACA
324694 AAAGAAAACATATTATAAAAACA
1 AAA-AAAACATATTA-AAAAACA
324717 AAAAAAA
1 AAAAAAA
324724 GAGTGTATCA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 3 0.12
22 13 0.52
23 9 0.36
ACGTcount: A:0.73, C:0.06, G:0.04, T:0.18
Consensus pattern (21 bp):
AAAAAAACATATTAAAAAACA
Found at i:325474 original size:21 final size:20
Alignment explanation
Indices: 325447--325544 Score: 79
Period size: 21 Copynumber: 4.8 Consensus size: 20
325437 AATCAGTTTC
325447 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
325468 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
325489 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
325509 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
325530 GAAAATCGCAACGCG
1 CAAAATCGCAACGCG
325545 TATCCGTAAA
Statistics
Matches: 60, Mismatches: 15, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
20 15 0.25
21 45 0.75
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:325555 original size:20 final size:20
Alignment explanation
Indices: 325512--325721 Score: 235
Period size: 20 Copynumber: 10.5 Consensus size: 20
325502 CGATTTTCCA
* ** *
325512 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
325532 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
325552 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
325572 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
325592 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
325612 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
325632 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
325652 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
325672 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
325692 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
325712 AAATCACAAC
1 AAATCGCAAC
325722 ACTGAAATTT
Statistics
Matches: 163, Mismatches: 23, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
19 1 0.01
20 162 0.99
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.21
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:326442 original size:24 final size:24
Alignment explanation
Indices: 326403--326449 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
326393 AAATTTGGTC
326403 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
326427 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
326450 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:328952 original size:52 final size:52
Alignment explanation
Indices: 328890--329006 Score: 166
Period size: 52 Copynumber: 2.2 Consensus size: 52
328880 GCAACGAGAG
328890 AATCGCAATGCGAAATG-AAATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCCCAACGA-GAAAATCGCAATGC-GAAATGAA
* * *
328942 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAAAATCCCAACGAGAAAATCGCAATGCGAAATGAA
*
328994 AATCGCATTGCGA
1 AATCGCAATGCGA
329007 TTCTCCCGTT
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
52 36 0.61
53 22 0.37
54 1 0.02
ACGTcount: A:0.44, C:0.19, G:0.21, T:0.16
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCCCAACGAGAAAATCGCAATGCGAAATGAA
Found at i:328958 original size:19 final size:19
Alignment explanation
Indices: 328890--329006 Score: 112
Period size: 19 Copynumber: 6.7 Consensus size: 19
328880 GCAACGAGAG
328890 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
*
328908 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
328922 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
328942 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
328961 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
328975 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
328994 AATCGCATTGCGA
1 AATCGCAATGCGA
329007 TTCTCCCGTT
Statistics
Matches: 81, Mismatches: 6, Indels: 23
0.74 0.05 0.21
Matches are distributed among these distances:
13 3 0.04
14 18 0.22
15 1 0.01
16 4 0.05
17 2 0.02
18 8 0.10
19 29 0.36
20 16 0.20
ACGTcount: A:0.44, C:0.19, G:0.21, T:0.16
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:329055 original size:19 final size:19
Alignment explanation
Indices: 329015--329112 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
329005 GATTCTCCCG
329015 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
329035 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
329054 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
329068 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
329087 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
329106 TTGCGAT
1 TTGCGAT
329113 AGTCAATTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:329109 original size:52 final size:53
Alignment explanation
Indices: 328996--329112 Score: 218
Period size: 53 Copynumber: 2.2 Consensus size: 53
328986 GAAATTAAAA
328996 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
*
329049 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
329101 TCGCATTGCGAT
1 TCGCATTGCGAT
329113 AGTCAATTTT
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 30 0.48
53 33 0.52
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:329238 original size:14 final size:14
Alignment explanation
Indices: 329219--329255 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
329209 CATCAATTAC
329219 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
329233 ACAAATCATCTTTT
1 ACAAATCAACTTTT
329247 ACAAATCAA
1 ACAAATCAA
329256 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:330311 original size:14 final size:14
Alignment explanation
Indices: 330292--330348 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
330282 TTTGGTTTCG
330292 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
330306 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
330325 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
330339 CGTTGCGATT
1 CGTTGCGATT
330349 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:330324 original size:33 final size:33
Alignment explanation
Indices: 330287--330356 Score: 140
Period size: 33 Copynumber: 2.1 Consensus size: 33
330277 TTTATTTTGG
330287 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
330320 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
330353 TTTC
1 TTTC
330357 TCTCGTTGCG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.09, C:0.24, G:0.20, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
Found at i:330359 original size:21 final size:21
Alignment explanation
Indices: 330333--330408 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
330323 CGCGTTGCGA
330333 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
****
330354 TTCTCTCGTTGCGACAGACA-
1 TTCTCTCGTTGCGATTTTCAT
330374 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
330395 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
330409 CTCTTCTGCA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.13, C:0.25, G:0.17, T:0.45
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:330389 original size:41 final size:41
Alignment explanation
Indices: 330332--330409 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
330322 TCGCGTTGCG
*
330332 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGAC
330373 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
330410 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.14, C:0.26, G:0.17, T:0.44
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGAC
Found at i:330530 original size:33 final size:33
Alignment explanation
Indices: 330488--330558 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
330478 AATACTAACT
*
330488 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
330521 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
330554 TGAAA
1 TGAAA
330559 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:330788 original size:22 final size:22
Alignment explanation
Indices: 330736--330790 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
330726 TGGTTGTGAG
*
330736 GGATTTCGTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
330758 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
330780 GGATTTCTTCG
1 GGATTTCTTCG
330791 CCGTAGAGAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.20, C:0.15, G:0.40, T:0.25
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:330961 original size:20 final size:20
Alignment explanation
Indices: 330936--331089 Score: 168
Period size: 20 Copynumber: 7.7 Consensus size: 20
330926 CTTTAAATAT
330936 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
330956 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
330978 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
330997 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
331017 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
331037 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
331057 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
331077 CGCGTTGCGATTT
1 CGCGTTGCGATTT
331090 TGGAAAATCG
Statistics
Matches: 113, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.02
20 94 0.83
21 15 0.13
22 2 0.02
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:331063 original size:40 final size:40
Alignment explanation
Indices: 330935--331089 Score: 186
Period size: 40 Copynumber: 3.9 Consensus size: 40
330925 GCTTTAAATA
*
330935 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTGT
** * *
330976 TATCGTTGCGATTTACGGATACGCGTTGCGATATACG-GAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTG-T
* *
331016 ACACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
* ** *
331056 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTT
331090 TGGAAAATCG
Statistics
Matches: 96, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
40 66 0.69
41 30 0.31
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.37
Consensus pattern (40 bp):
TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
Found at i:331106 original size:21 final size:21
Alignment explanation
Indices: 331076--331158 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
331066 ATTTTCATAT
*
331076 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
331097 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
331118 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
331139 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
331159 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:331149 original size:42 final size:43
Alignment explanation
Indices: 331056--331154 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
331046 ATTTATGTGT
* *
331056 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
331097 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
331139 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
331155 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:332447 original size:36 final size:37
Alignment explanation
Indices: 332401--332494 Score: 106
Period size: 36 Copynumber: 2.6 Consensus size: 37
332391 TATTAAAAAT
*
332401 AATTATTATATATATAATATTAATAAATT-TA-ATTTA
1 AATTAATATATATATAATATTAAT-AATTATATATTTA
*
332437 AATTAATATATATAT-ATATATAATATTTATATATTTA
1 AATTAATATATATATAATAT-TAATAATTATATATTTA
*
332474 ATTTAA-ATATATATATATATT
1 AATTAATATATATATA-ATATT
332495 CGGCCCGGTA
Statistics
Matches: 50, Mismatches: 3, Indels: 9
0.81 0.05 0.15
Matches are distributed among these distances:
35 7 0.14
36 28 0.56
37 11 0.22
38 4 0.08
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (37 bp):
AATTAATATATATATAATATTAATAATTATATATTTA
Found at i:332449 original size:2 final size:2
Alignment explanation
Indices: 332442--332493 Score: 54
Period size: 2 Copynumber: 27.0 Consensus size: 2
332432 ATTTAAATTA
* * * *
332442 AT AT AT AT AT AT AT AT A- AT AT TT AT AT AT TT A- AT TT AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
332482 AT AT AT AT AT AT
1 AT AT AT AT AT AT
332494 TCGGCCCGGT
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:332458 original size:42 final size:41
Alignment explanation
Indices: 332397--332493 Score: 146
Period size: 42 Copynumber: 2.4 Consensus size: 41
332387 TAAATATTAA
332397 AAATAAT-TAT-TATATATATAATATTAATAAATTTAATTT
1 AAATAATATATATATATATATAATATTAATAAATTTAATTT
* *
332436 AAATTAATATATATATATATATAATATTTATATATTTAATTT
1 AAA-TAATATATATATATATATAATATTAATAAATTTAATTT
332478 AAAT-ATATATATATAT
1 AAATAATATATATATAT
332494 TCGGCCCGGT
Statistics
Matches: 53, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
39 3 0.06
40 16 0.30
41 4 0.08
42 30 0.57
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (41 bp):
AAATAATATATATATATATATAATATTAATAAATTTAATTT
Found at i:332462 original size:17 final size:17
Alignment explanation
Indices: 332440--332490 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
332430 TAATTTAAAT
332440 TAATATATATATATATA
1 TAATATATATATATATA
*
332457 TAATAT-T-TATATATT
1 TAATATATATATATATA
* *
332472 TAATTTAAATATATATA
1 TAATATATATATATATA
332489 TA
1 TA
332491 TATTCGGCCC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 12 0.43
16 1 0.04
17 15 0.54
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TAATATATATATATATA
Found at i:336352 original size:14 final size:14
Alignment explanation
Indices: 336318--336350 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
336308 TAAACTCAAC
*
336318 TTAGGGTTTATAAT
1 TTAGGGTTTATAAA
336332 TTAGGGTTT-TAAA
1 TTAGGGTTTATAAA
336345 TTAGGG
1 TTAGGG
336351 GTAAGGTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.45
Consensus pattern (14 bp):
TTAGGGTTTATAAA
Found at i:349726 original size:33 final size:33
Alignment explanation
Indices: 349688--349770 Score: 105
Period size: 33 Copynumber: 2.5 Consensus size: 33
349678 TTTCATTTAA
* *
349688 GTTTGTTTACGTTCGTTTATGTACATTTATTGT
1 GTTTGTTTATGTTCGTTTACGTACATTTATTGT
* * *
349721 GTTTGTTTGTGTAT-GTTTACGTTCGTTTATTGT
1 GTTTGTTTATGT-TCGTTTACGTACATTTATTGT
349754 GTTTGTTTATGTTCGTT
1 GTTTGTTTATGTTCGTT
349771 CATTTGTGTT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
32 1 0.02
33 40 0.95
34 1 0.02
ACGTcount: A:0.11, C:0.07, G:0.22, T:0.60
Consensus pattern (33 bp):
GTTTGTTTATGTTCGTTTACGTACATTTATTGT
Found at i:349753 original size:23 final size:24
Alignment explanation
Indices: 349726--349779 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 24
349716 ATTGTGTTTG
*
349726 TTTGTGTATGTTTACGTTCGTTTA
1 TTTGTGTATGTTTACGTTCGTTCA
* *
349750 -TTGTGTTTGTTTATGTTCGTTCA
1 TTTGTGTATGTTTACGTTCGTTCA
349773 TTTGTGT
1 TTTGTGT
349780 TCTTTTATCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.09, C:0.07, G:0.22, T:0.61
Consensus pattern (24 bp):
TTTGTGTATGTTTACGTTCGTTCA
Found at i:356006 original size:8 final size:8
Alignment explanation
Indices: 355993--356025 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
355983 CTGTCTCTCA
355993 CTTCTCTT
1 CTTCTCTT
356001 CTTCTCTT
1 CTTCTCTT
356009 CTTCTCTT
1 CTTCTCTT
*
356017 CTTCACTT
1 CTTCTCTT
356025 C
1 C
356026 GTTCAAAGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.03, C:0.39, G:0.00, T:0.58
Consensus pattern (8 bp):
CTTCTCTT
Found at i:366477 original size:6 final size:6
Alignment explanation
Indices: 366466--366497 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
366456 TTTACCCTAA
*
366466 CCGGAC CCGGAC CCGGAC CCGGAC CCAGAC CC
1 CCGGAC CCGGAC CCGGAC CCGGAC CCGGAC CC
366498 AGATCCAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.19, C:0.53, G:0.28, T:0.00
Consensus pattern (6 bp):
CCGGAC
Found at i:367844 original size:219 final size:219
Alignment explanation
Indices: 367171--368104 Score: 1822
Period size: 219 Copynumber: 4.3 Consensus size: 219
367161 ACCTTTTGTT
367171 TTCTCTTTTAATTGAGTTCATTACGTTTTAGTAGCTTTTTGATGACTGAAACTTGTACTTTCCTG
1 TTCTCTTTTAATTGAGTTCATTACGTTTTAGTAGCTTTTTGATGACTGAAACTTGTACTTTCCTG
367236 AAAATGCTGTTTTTTTTAATAATAAGTTTAGCCTAAGCTTTGTTATAATAAATAATATGATCTTC
66 AAAATGCTGTTTTTTTTAATAATAAGTTTAGCCTAAGCTTTGTTATAATAAATAATATGATCTTC
367301 TTGCTACTAGAAAATGGTATGCCGTTTATTGTATTGTTGTCTGCAATTGAACATTACCATCTTCT
131 TTGCTACTAGAAAATGGTATGCCGTTTATTGTATTGTTGTCTGCAATTGAACATTACCATCTTCT
367366 TTAACATCCAGTGATGGCTACAGA
196 TTAACATCCAGTGATGGCTACAGA
367390 TTCTCTTTTAATTGAGTTCATTACGTTTTAGTAGCTTTTTGATGACTGAAACTTGTACTTTCCTG
1 TTCTCTTTTAATTGAGTTCATTACGTTTTAGTAGCTTTTTGATGACTGAAACTTGTACTTTCCTG
367455 AAAATGCTGTTTTTTTTTAATAATAAGTTTAGCCTAAGCTTTGTTATAATAAATAATATGATCTT
66 AAAATGCTG-TTTTTTTTAATAATAAGTTTAGCCTAAGCTTTGTTATAATAAATAATATGATCTT
367520 CTTGCTACTAGAAAATGGTATGCCGTTTATTGTATTGTTGTCTGCAATTGAACATTACCATCTTC
130 CTTGCTACTAGAAAATGGTATGCCGTTTATTGTATTGTTGTCTGCAATTGAACATTACCATCTTC
367585 TTTAACATCCAGTGATGGCTACAGA
195 TTTAACATCCAGTGATGGCTACAGA
367610 TTCTCTTTTAATTGAGTTCATTACGTTTTAGTAGCTTTTTGATGACTGAAACTTGTACTTTCCTG
1 TTCTCTTTTAATTGAGTTCATTACGTTTTAGTAGCTTTTTGATGACTGAAACTTGTACTTTCCTG
367675 AAAATGCTGTTTTTTTTAATAATAAGTTTAGCCTAAGCTTTGTTATAATAAATAATATGATCTTC
66 AAAATGCTGTTTTTTTTAATAATAAGTTTAGCCTAAGCTTTGTTATAATAAATAATATGATCTTC
367740 TTGCTACTAGAAAATGGTATGCCGTTTATTGTATTGTTGTCTGCAATTGAACATTACCATCTTCT
131 TTGCTACTAGAAAATGGTATGCCGTTTATTGTATTGTTGTCTGCAATTGAACATTACCATCTTCT
367805 TTAACATCCAGTGATGGCTACAGA
196 TTAACATCCAGTGATGGCTACAGA
367829 TTCTCTTTTAATTGAGTTCATTACGTTTTAGTAGCTTTTTGATGACTGAAACTTGTACTTTCCTG
1 TTCTCTTTTAATTGAGTTCATTACGTTTTAGTAGCTTTTTGATGACTGAAACTTGTACTTTCCTG
367894 -AAATGCTG-TTTTTTTAATAATAAGTTTAGCCTAAGCTTTGTTATAATAAATAATATGATCTTC
66 AAAATGCTGTTTTTTTTAATAATAAGTTTAGCCTAAGCTTTGTTATAATAAATAATATGATCTTC
*
367957 TTGCTACTAGAAAATGGCATGCCGTTTATTGTATTGTTGTCTGCAATTGAACATTACCATCTTCT
131 TTGCTACTAGAAAATGGTATGCCGTTTATTGTATTGTTGTCTGCAATTGAACATTACCATCTTCT
368022 TTAACATCCAGTGATGGCTACAGA
196 TTAACATCCAGTGATGGCTACAGA
368046 TTCTCTTTTAATTGAGTTCA-TACGTTTTAGTAGCTTTTTGATGACTGAAAC-TGTACTTT
1 TTCTCTTTTAATTGAGTTCATTACGTTTTAGTAGCTTTTTGATGACTGAAACTTGTACTTT
368105 ACCAATTATC
Statistics
Matches: 713, Mismatches: 1, Indels: 6
0.99 0.00 0.01
Matches are distributed among these distances:
215 8 0.01
216 31 0.04
217 163 0.23
218 8 0.01
219 284 0.40
220 219 0.31
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.43
Consensus pattern (219 bp):
TTCTCTTTTAATTGAGTTCATTACGTTTTAGTAGCTTTTTGATGACTGAAACTTGTACTTTCCTG
AAAATGCTGTTTTTTTTAATAATAAGTTTAGCCTAAGCTTTGTTATAATAAATAATATGATCTTC
TTGCTACTAGAAAATGGTATGCCGTTTATTGTATTGTTGTCTGCAATTGAACATTACCATCTTCT
TTAACATCCAGTGATGGCTACAGA
Found at i:370292 original size:15 final size:15
Alignment explanation
Indices: 370274--370316 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
370264 TGACGACGCT
*
370274 GAGGATGAAGTAGAG
1 GAGGATGAAGAAGAG
* *
370289 GAGGAAGAAGAAGAT
1 GAGGATGAAGAAGAG
*
370304 GAGGATGATGAAG
1 GAGGATGAAGAAG
370317 TTCCTCAGCC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.44, C:0.00, G:0.44, T:0.12
Consensus pattern (15 bp):
GAGGATGAAGAAGAG
Found at i:383907 original size:11 final size:11
Alignment explanation
Indices: 383891--383921 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
383881 TAATACATTT
383891 TTATTTTTTAA
1 TTATTTTTTAA
383902 TTATTTTTTAA
1 TTATTTTTTAA
*
383913 TAATTTTTT
1 TTATTTTTT
383922 GTTTTAAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TTATTTTTTAA
Found at i:393459 original size:2 final size:2
Alignment explanation
Indices: 393452--393478 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
393442 TGCAGGATTA
393452 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
393479 GCTCAGCTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:408676 original size:22 final size:22
Alignment explanation
Indices: 408648--408701 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
408638 ACCTCTCTAT
*
408648 ATATTATTTTCT-TTCAATTAAA
1 ATATTATTTT-TATTCAATAAAA
*
408670 ATATTATTTTTATTGAATAAAA
1 ATATTATTTTTATTCAATAAAA
*
408692 ATAATATTTT
1 ATATTATTTT
408702 AAATAAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 1 0.04
22 27 0.96
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.54
Consensus pattern (22 bp):
ATATTATTTTTATTCAATAAAA
Found at i:408710 original size:22 final size:22
Alignment explanation
Indices: 408667--408710 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
408657 TCTTTCAATT
* * * *
408667 AAAATATTATTTTTATTGAATA
1 AAAATAATATTTTAAATAAATA
408689 AAAATAATATTTTAAATAAATA
1 AAAATAATATTTTAAATAAATA
408711 TATTATTTAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
AAAATAATATTTTAAATAAATA
Found at i:408721 original size:17 final size:18
Alignment explanation
Indices: 408685--408723 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
408675 ATTTTTATTG
408685 AATAAAAATAATATTTTA
1 AATAAAAATAATATTTTA
* * *
408703 AATAAATATATTATTTAA
1 AATAAAAATAATATTTTA
408721 AAT
1 AAT
408724 CGAGTCGAAT
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:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AATAAAAATAATATTTTA
Found at i:409069 original size:22 final size:24
Alignment explanation
Indices: 409044--409091 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 24
409034 TTTATCTTAT
409044 TTACCAAATAAA-AATTCCA-GAA
1 TTACCAAATAAATAATTCCATGAA
**
409066 TTACCACGTAAATAATTCCATGAA
1 TTACCAAATAAATAATTCCATGAA
409090 TT
1 TT
409092 TATTGCTGCC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 10 0.45
23 7 0.32
24 5 0.23
ACGTcount: A:0.46, C:0.19, G:0.06, T:0.29
Consensus pattern (24 bp):
TTACCAAATAAATAATTCCATGAA
Found at i:409309 original size:30 final size:30
Alignment explanation
Indices: 409270--409326 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
409260 ATATTTTTTT
*
409270 ATCATATAAAATAAAAAATTATACAATTTA
1 ATCACATAAAATAAAAAATTATACAATTTA
409300 ATCACATAAAATAAAAAATTATACAAT
1 ATCACATAAAATAAAAAATTATACAAT
409327 CAAGATAGGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (30 bp):
ATCACATAAAATAAAAAATTATACAATTTA
Done.