Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007916.1 Hibiscus syriacus cultivar Beakdansim tig00110319_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: 3725575
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 16
Found at i:3067028 original size:2 final size:2
Alignment explanation
Indices: 3067021--3067046 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3067011 ATTAACATTA
3067021 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
3067047 TGATTTTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3073030 original size:28 final size:29
Alignment explanation
Indices: 3072975--3073036 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 29
3072965 CTATTATGTT
* * *
3072975 TATCGCCAGTAAGGCCAACCTATGAGATG
1 TATCGCCACTAAGGACAACCTATAAGATG
*
3073004 TATCGCCACTAA-GACAACCTGTAAGATG
1 TATCGCCACTAAGGACAACCTATAAGATG
3073032 TATCG
1 TATCG
3073037 TGTAATTTCC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 18 0.62
29 11 0.38
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.23
Consensus pattern (29 bp):
TATCGCCACTAAGGACAACCTATAAGATG
Found at i:3073811 original size:16 final size:16
Alignment explanation
Indices: 3073778--3073811 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3073768 TTACTAGTCA
*
3073778 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
*
3073794 CGTGAATAGTTAAATT
1 CGTGAATAGTGAAATT
3073810 CG
1 CG
3073812 GTCGGCGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.09, G:0.24, T:0.35
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:3074582 original size:15 final size:16
Alignment explanation
Indices: 3074562--3074593 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
3074552 TGGCAGATCC
3074562 AAATCCAG-ACGGGAA
1 AAATCCAGAACGGGAA
3074577 AAATCCAGAACGGGAA
1 AAATCCAGAACGGGAA
3074593 A
1 A
3074594 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.50, C:0.19, G:0.25, T:0.06
Consensus pattern (16 bp):
AAATCCAGAACGGGAA
Found at i:3078776 original size:2 final size:2
Alignment explanation
Indices: 3078769--3078800 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3078759 ATAAACATGC
3078769 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
3078801 GATCCATGAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3086068 original size:42 final size:42
Alignment explanation
Indices: 3086016--3086097 Score: 146
Period size: 42 Copynumber: 2.0 Consensus size: 42
3086006 TGAGAATGAA
* *
3086016 GTTTCACATTTAAATAGTGAGGGTGGTCAGAATGGTGAAGAG
1 GTTTCACATTTAAATAGTGAGGGTGGCCAAAATGGTGAAGAG
3086058 GTTTCACATTTAAATAGTGAGGGTGGCCAAAATGGTGAAG
1 GTTTCACATTTAAATAGTGAGGGTGGCCAAAATGGTGAAG
3086098 CTGACAGTGA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.32, C:0.09, G:0.32, T:0.28
Consensus pattern (42 bp):
GTTTCACATTTAAATAGTGAGGGTGGCCAAAATGGTGAAGAG
Found at i:3091673 original size:63 final size:68
Alignment explanation
Indices: 3091553--3091684 Score: 184
Period size: 63 Copynumber: 2.0 Consensus size: 68
3091543 ATTAACTGAG
* *
3091553 CCTACATTTGCTCTAATAAAATGTAATTTCTACCTGAAAATATTTTCTTGTTCAATATCGTTAGT
1 CCTACATTTGCTCTAATAAAATGTAATTTCTACCTAAAAATATTTTCTTGCTCAATATCGTTAGT
3091618 GAA
66 GAA
* * *
3091621 CCTACATTTGCTCTAATAAAA-GTGA-TT-T-CC-AAAAATATTTTCTTGCTCAATATGGTTGGT
1 CCTACATTTGCTCTAATAAAATGTAATTTCTACCTAAAAATATTTTCTTGCTCAATATCGTTAGT
3091681 GAA
66 GAA
3091684 C
1 C
3091685 TGTCATTGGT
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
63 30 0.51
64 2 0.03
65 1 0.02
66 2 0.03
67 3 0.05
68 21 0.36
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.39
Consensus pattern (68 bp):
CCTACATTTGCTCTAATAAAATGTAATTTCTACCTAAAAATATTTTCTTGCTCAATATCGTTAGT
GAA
Found at i:3094662 original size:21 final size:21
Alignment explanation
Indices: 3094636--3094758 Score: 189
Period size: 21 Copynumber: 6.0 Consensus size: 21
3094626 CATAATTTCC
*
3094636 TCTTCCTCCGGGTACTCTTCT
1 TCTTCCTCCGGGTCCTCTTCT
3094657 TCTTCCTCCGGGTCCTCTTCT
1 TCTTCCTCCGGGTCCTCTTCT
3094678 TCTTCCTCCGGGTCCTCTTCT
1 TCTTCCTCCGGGTCCTCTTCT
*
3094699 TCTTCCTCTGGGT-C-C-TCT
1 TCTTCCTCCGGGTCCTCTTCT
*
3094717 TCTTCCTCCGGGTCTTCTTCT
1 TCTTCCTCCGGGTCCTCTTCT
*
3094738 TCTTCCTCCGGATCCTCTTCT
1 TCTTCCTCCGGGTCCTCTTCT
3094759 CGCTTCTTAT
Statistics
Matches: 93, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
18 15 0.16
19 1 0.01
20 2 0.02
21 75 0.81
ACGTcount: A:0.02, C:0.41, G:0.14, T:0.44
Consensus pattern (21 bp):
TCTTCCTCCGGGTCCTCTTCT
Found at i:3094679 original size:39 final size:38
Alignment explanation
Indices: 3094636--3094758 Score: 174
Period size: 39 Copynumber: 3.1 Consensus size: 38
3094626 CATAATTTCC
3094636 TCTTCCTCCGGGTACTCTTCTTCTTCCTCCGGGTCCTCTTCT
1 TCTTCCTCCGGGT-CTCTTCTTCTTCCTCCGGGT-C-C-TCT
*
3094678 TCTTCCTCCGGGTCCTCTTCTTCTTCCTCTGGGTCCTCT
1 TCTTCCTCCGGGT-CTCTTCTTCTTCCTCCGGGTCCTCT
*
3094717 TCTTCCTCCGGGTCTTCTTCTTCTTCCTCCGGATCCTCT
1 TCTTCCTCCGGGTC-TCTTCTTCTTCCTCCGGGTCCTCT
3094756 TCT
1 TCT
3094759 CGCTTCTTAT
Statistics
Matches: 76, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
38 1 0.01
39 41 0.54
40 1 0.01
41 1 0.01
42 32 0.42
ACGTcount: A:0.02, C:0.41, G:0.14, T:0.44
Consensus pattern (38 bp):
TCTTCCTCCGGGTCTCTTCTTCTTCCTCCGGGTCCTCT
Found at i:3095619 original size:23 final size:24
Alignment explanation
Indices: 3095569--3095620 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
3095559 CCATGATCCT
*
3095569 TTTGTTGAAAAACCATTGCCCCCA
1 TTTGTTGAAAAACAATTGCCCCCA
3095593 -TTGTTGAAAAACAATTG-CCCCA
1 TTTGTTGAAAAACAATTGCCCCCA
3095615 TTTGTT
1 TTTGTT
3095621 TGACTTTTCC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 5 0.19
23 21 0.81
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.35
Consensus pattern (24 bp):
TTTGTTGAAAAACAATTGCCCCCA
Found at i:3099677 original size:10 final size:10
Alignment explanation
Indices: 3099659--3099689 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
3099649 TACTATTCAT
3099659 ATGAATAGTA
1 ATGAATAGTA
*
3099669 ATTAATAGTA
1 ATGAATAGTA
3099679 ATGAATAGTA
1 ATGAATAGTA
3099689 A
1 A
3099690 CCTCACAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (10 bp):
ATGAATAGTA
Found at i:3104746 original size:35 final size:35
Alignment explanation
Indices: 3104707--3104776 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
3104697 TGTTCTAGCT
3104707 TGTCGATCCATCAGTGTTAAGCTTCATCCATTTGA
1 TGTCGATCCATCAGTGTTAAGCTTCATCCATTTGA
* *
3104742 TGTCGATCCATCTGTGTTGAGCTTCATCCATTTGA
1 TGTCGATCCATCAGTGTTAAGCTTCATCCATTTGA
3104777 CTGGCGGTGG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.20, C:0.23, G:0.19, T:0.39
Consensus pattern (35 bp):
TGTCGATCCATCAGTGTTAAGCTTCATCCATTTGA
Found at i:3112253 original size:60 final size:60
Alignment explanation
Indices: 3112151--3112274 Score: 169
Period size: 60 Copynumber: 2.1 Consensus size: 60
3112141 GTATACAAAC
* * * * ** *
3112151 GGTCTCTCGATTATATGGTGTTGTTTTGTTGAGTTCTTCGACTATTAAAAATTACAAAAT
1 GGTCTCTCGATTATATGGTGTTATTTTATTAAGTCCCCCGACTATTAAAAATTAAAAAAT
3112211 GGTCTC-CTGATTATATGGTGTTATTTTATTAAGTCCCCCGACTATTAAAAATTAAAAAAT
1 GGTCTCTC-GATTATATGGTGTTATTTTATTAAGTCCCCCGACTATTAAAAATTAAAAAAT
3112271 GGTC
1 GGTC
3112275 ACCCTACTAT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
59 1 0.02
60 55 0.98
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (60 bp):
GGTCTCTCGATTATATGGTGTTATTTTATTAAGTCCCCCGACTATTAAAAATTAAAAAAT
Found at i:3119475 original size:35 final size:34
Alignment explanation
Indices: 3119390--3119476 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
3119380 ATTTGGTATT
*
3119390 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
3119424 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
3119462 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
3119477 ACTGAAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:3121774 original size:18 final size:17
Alignment explanation
Indices: 3121742--3121787 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
3121732 GAATTATATT
3121742 AGTAAAATATTAAATAA
1 AGTAAAATATTAAATAA
3121759 AGTAAAATACTTAAATAA
1 AGTAAAATA-TTAAATAA
*
3121777 ATTAAATATAT
1 AGTAAA-ATAT
3121788 AATATTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 9 0.35
18 14 0.54
19 3 0.12
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (17 bp):
AGTAAAATATTAAATAA
Found at i:3122994 original size:40 final size:41
Alignment explanation
Indices: 3122950--3123165 Score: 243
Period size: 40 Copynumber: 5.4 Consensus size: 41
3122940 AGTTTCCATT
3122950 TTCGCAACGCGAATTTGTAAA-TCGCAACACAGAAGTCAAA
1 TTCGCAACGCGAATTTGTAAATTCGCAACACAGAAGTCAAA
* * * *
3122990 TTCGCAACGTG-A-TAGTCAAATTCACAACACAAAAGTCAAA
1 TTCGCAACGCGAATTTGT-AAATTCGCAACACAGAAGTCAAA
3123030 TTCGCAACGCGAATTTGTAAA-TCGCAACACAGAAGTCAAA
1 TTCGCAACGCGAATTTGTAAATTCGCAACACAGAAGTCAAA
* *
3123070 TTCGCAACGCG-A-TAGTCAAATTCGCAACACAAAAGTCAAA
1 TTCGCAACGCGAATTTGT-AAATTCGCAACACAGAAGTCAAA
* * *
3123110 TTCGCAACGCGGAATTT-CAAATTCGC-A-ACTGAATTTCAAA
1 TTCGCAACGC-GAATTTGTAAATTCGCAACACAGAA-GTCAAA
*
3123150 TTCGCAACACGAATTT
1 TTCGCAACGCGAATTT
3123166 AGTTTCGCAA
Statistics
Matches: 150, Mismatches: 16, Indels: 21
0.80 0.09 0.11
Matches are distributed among these distances:
38 6 0.04
39 18 0.12
40 108 0.72
41 13 0.09
42 4 0.03
43 1 0.01
ACGTcount: A:0.40, C:0.23, G:0.15, T:0.22
Consensus pattern (41 bp):
TTCGCAACGCGAATTTGTAAATTCGCAACACAGAAGTCAAA
Found at i:3123040 original size:80 final size:80
Alignment explanation
Indices: 3122950--3123126 Score: 327
Period size: 80 Copynumber: 2.2 Consensus size: 80
3122940 AGTTTCCATT
*
3122950 TTCGCAACGCGAATTTGTAAATCGCAACACAGAAGTCAAATTCGCAACGTGATAGTCAAATTCAC
1 TTCGCAACGCGAATTTGTAAATCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAATTCAC
3123015 AACACAAAAGTCAAA
66 AACACAAAAGTCAAA
*
3123030 TTCGCAACGCGAATTTGTAAATCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAATTCGC
1 TTCGCAACGCGAATTTGTAAATCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAATTCAC
3123095 AACACAAAAGTCAAA
66 AACACAAAAGTCAAA
3123110 TTCGCAACGCGGAATTT
1 TTCGCAACGC-GAATTT
3123127 CAAATTCGCA
Statistics
Matches: 94, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
80 88 0.94
81 6 0.06
ACGTcount: A:0.40, C:0.23, G:0.16, T:0.20
Consensus pattern (80 bp):
TTCGCAACGCGAATTTGTAAATCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAATTCAC
AACACAAAAGTCAAA
Found at i:3123165 original size:20 final size:20
Alignment explanation
Indices: 3122950--3123163 Score: 158
Period size: 20 Copynumber: 10.7 Consensus size: 20
3122940 AGTTTCCATT
*
3122950 TTCGCAACGCGAATTTGT-AAA
1 TTCGCAACACGAA--TGTCAAA
3122971 -TCGCAACACAGAA-GTCAAA
1 TTCGCAACAC-GAATGTCAAA
**
3122990 TTCGCAACGTG-ATAGTCAAA
1 TTCGCAACACGAAT-GTCAAA
* * *
3123010 TTCACAACACAAAAGTCAAA
1 TTCGCAACACGAATGTCAAA
*
3123030 TTCGCAACGCGAATTTGT-AAA
1 TTCGCAACACGAA--TGTCAAA
3123051 -TCGCAACACAGAA-GTCAAA
1 TTCGCAACAC-GAATGTCAAA
*
3123070 TTCGCAACGCG-ATAGTCAAA
1 TTCGCAACACGAAT-GTCAAA
* *
3123090 TTCGCAACACAAAAGTCAAA
1 TTCGCAACACGAATGTCAAA
* *
3123110 TTCGCAACGCGGAATTTCAAA
1 TTCGCAACAC-GAATGTCAAA
* *
3123131 TTCGCAAC-TGAATTTCAAA
1 TTCGCAACACGAATGTCAAA
3123150 TTCGCAACACGAAT
1 TTCGCAACACGAAT
3123164 TTAGTTTCGC
Statistics
Matches: 154, Mismatches: 23, Indels: 33
0.73 0.11 0.16
Matches are distributed among these distances:
18 6 0.04
19 26 0.17
20 94 0.61
21 26 0.17
22 2 0.01
ACGTcount: A:0.40, C:0.23, G:0.15, T:0.21
Consensus pattern (20 bp):
TTCGCAACACGAATGTCAAA
Found at i:3123350 original size:16 final size:15
Alignment explanation
Indices: 3123315--3123353 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
3123305 TCCCCATCTC
3123315 TAATTTTTTTATACA
1 TAATTTTTTTATACA
* *
3123330 TAATTTTATTTCTATA
1 TAATTTT-TTTATACA
3123346 TAATTTTT
1 TAATTTTT
3123354 CAATGATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (15 bp):
TAATTTTTTTATACA
Found at i:3123922 original size:12 final size:12
Alignment explanation
Indices: 3123905--3123932 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
3123895 TTTCTAATAC
3123905 CAAACACAATCT
1 CAAACACAATCT
3123917 CAAACACAATCT
1 CAAACACAATCT
3123929 CAAA
1 CAAA
3123933 ACCCACAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.54, C:0.32, G:0.00, T:0.14
Consensus pattern (12 bp):
CAAACACAATCT
Found at i:3124109 original size:24 final size:24
Alignment explanation
Indices: 3124058--3124111 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
3124048 GTATTCGAAA
*
3124058 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
3124082 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
3124106 TTTGAT
1 TTTGAT
3124112 GATGTGATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:3126403 original size:18 final size:18
Alignment explanation
Indices: 3126377--3126412 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3126367 AAGCAAAAGG
*
3126377 AAATCAAAATCGCAATCA
1 AAATAAAAATCGCAATCA
3126395 AAATAAAAATCGCAATCA
1 AAATAAAAATCGCAATCA
3126413 CAACCGACTT
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:0.58, C:0.19, G:0.06, T:0.17
Consensus pattern (18 bp):
AAATAAAAATCGCAATCA
Found at i:3126808 original size:20 final size:20
Alignment explanation
Indices: 3126783--3126838 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
3126773 AAACCGAAAA
3126783 TCGCGTTGTGAATTTGACTT
1 TCGCGTTGTGAATTTGACTT
* *
3126803 TCGCGTTGTGAAATTAACTT
1 TCGCGTTGTGAATTTGACTT
* *
3126823 TCGGGTTGCGAATTTG
1 TCGCGTTGTGAATTTG
3126839 TACCTTCAAC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.18, C:0.14, G:0.27, T:0.41
Consensus pattern (20 bp):
TCGCGTTGTGAATTTGACTT
Found at i:3128430 original size:21 final size:21
Alignment explanation
Indices: 3128406--3128504 Score: 87
Period size: 21 Copynumber: 4.7 Consensus size: 21
3128396 GCGGGTGGGA
3128406 CCTCTTGAACGATGACG-GGGG
1 CCTCTTGAACGATGA-GAGGGG
* *
3128427 CCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAACGATGAGAGGGG
* * *
3128448 CTTATTCG-ATGATGAGAGGGG
1 CCTCTT-GAACGATGAGAGGGG
*
3128469 CCTCTTGAACGAT-AGGAGGTG
1 CCTCTTGAACGATGA-GAGGGG
*
3128490 CCTCTTGAATGATGA
1 CCTCTTGAACGATGA
3128505 TAGGTGCATC
Statistics
Matches: 61, Mismatches: 12, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
20 3 0.05
21 56 0.92
22 2 0.03
ACGTcount: A:0.21, C:0.18, G:0.36, T:0.24
Consensus pattern (21 bp):
CCTCTTGAACGATGAGAGGGG
Found at i:3128502 original size:42 final size:42
Alignment explanation
Indices: 3128406--3128504 Score: 112
Period size: 42 Copynumber: 2.4 Consensus size: 42
3128396 GCGGGTGGGA
* * *
3128406 CCTCTTGAACGATGACGGGGGCCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAATGATGACGGGGGCCTCTTGAACGATAGGAGGGG
* * *
3128448 CTTATTCG-ATGATGA-GAGGGGCCTCTTGAACGATAGGAGGTG
1 CCTCTT-GAATGATGACG-GGGGCCTCTTGAACGATAGGAGGGG
3128490 CCTCTTGAATGATGA
1 CCTCTTGAATGATGA
3128505 TAGGTGCATC
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
41 2 0.04
42 43 0.93
43 1 0.02
ACGTcount: A:0.21, C:0.18, G:0.36, T:0.24
Consensus pattern (42 bp):
CCTCTTGAATGATGACGGGGGCCTCTTGAACGATAGGAGGGG
Found at i:3128509 original size:21 final size:21
Alignment explanation
Indices: 3128456--3128511 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
3128446 GGCTTATTCG
*
3128456 ATGATGAGAGGGGCCTCTTGA
1 ATGATGAGAGGTGCCTCTTGA
*
3128477 ACGAT-AGGAGGTGCCTCTTGA
1 ATGATGA-GAGGTGCCTCTTGA
*
3128498 ATGATGATAGGTGC
1 ATGATGAGAGGTGC
3128512 ATCGGGCTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 1 0.03
21 27 0.93
22 1 0.03
ACGTcount: A:0.25, C:0.14, G:0.36, T:0.25
Consensus pattern (21 bp):
ATGATGAGAGGTGCCTCTTGA
Found at i:3130521 original size:20 final size:20
Alignment explanation
Indices: 3130509--3130631 Score: 194
Period size: 20 Copynumber: 6.2 Consensus size: 20
3130499 AAACTTAAAT
*
3130509 TCGCAATGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
*
3130529 TCACAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
3130549 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
3130569 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
3130589 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
** *
3130609 TTACAACGCGAAACT-AAAA
1 TCGCAACGCGAAAATGAAAA
3130628 TCGC
1 TCGC
3130632 GTTGCGATTT
Statistics
Matches: 95, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
19 6 0.06
20 89 0.94
ACGTcount: A:0.50, C:0.20, G:0.18, T:0.12
Consensus pattern (20 bp):
TCGCAACGCGAAAATGAAAA
Found at i:3131153 original size:20 final size:20
Alignment explanation
Indices: 3131128--3131377 Score: 240
Period size: 20 Copynumber: 12.4 Consensus size: 20
3131118 GCGTAAAAAC
*
3131128 ATTTGACTTTCGCGTTGAGA
1 ATTTGACTTTCGCGTTGCGA
* *
3131148 ATTTGACTTTTGTGTTGC-A
1 ATTTGACTTTCGCGTTGCGA
* *
3131167 ATTT-ACAAATTCGAGTTGCGA
1 ATTTGAC--TTTCGCGTTGCGA
* * *
3131188 ATTTGACTTTTGTGTTACGA
1 ATTTGACTTTCGCGTTGCGA
*
3131208 ATTTGACTATCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
* *
3131228 ATCTGAC-TTCTGTGTTGCG-
1 ATTTGACTTTC-GCGTTGCGA
* * *
3131247 ATTT-ACAAATTCGTGTTGCAA
1 ATTTGAC--TTTCGCGTTGCGA
* *
3131268 ATTTGACTTTTGTGTTGCGAA
1 ATTTGACTTTCGCGTTGCG-A
* *
3131289 ATTTGACTATCGCGTTACGA
1 ATTTGACTTTCGCGTTGCGA
3131309 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
3131329 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
*
3131349 ATTTGACTTTCGCGTTGCAA
1 ATTTGACTTTCGCGTTGCGA
3131369 ATTTGACTT
1 ATTTGACTT
3131378 ATGTGTTGCG
Statistics
Matches: 190, Mismatches: 29, Indels: 22
0.79 0.12 0.09
Matches are distributed among these distances:
18 4 0.02
19 10 0.05
20 144 0.76
21 28 0.15
22 4 0.02
ACGTcount: A:0.21, C:0.16, G:0.22, T:0.42
Consensus pattern (20 bp):
ATTTGACTTTCGCGTTGCGA
Found at i:3131265 original size:80 final size:79
Alignment explanation
Indices: 3131128--3131376 Score: 304
Period size: 80 Copynumber: 3.1 Consensus size: 79
3131118 GCGTAAAAAC
* * *
3131128 ATTTGACTTTCGCGTTGAGAATTTGACTTTTGTGTTGCAATTTACAAATTCGAGTTGCGAATTTG
1 ATTTGACTATCGCGTTGCGAATTTGAC-TTTGTGTTGCGATTTACAAATTCGAGTTGCGAATTTG
*
3131193 ACTTTTGTGTTACGA
65 ACTTTTGTGTTGCGA
* * *
3131208 ATTTGACTATCGCGTTGCGAATCTGACTTCTGTGTTGCGATTTACAAATTCGTGTTGCAAATTTG
1 ATTTGACTATCGCGTTGCGAATTTGACTT-TGTGTTGCGATTTACAAATTCGAGTTGCGAATTTG
3131273 ACTTTTGTGTTGCGAA
65 ACTTTTGTGTTGCG-A
* * * *
3131289 ATTTGACTATCGCGTTACGAATTTGACTTTCGCGTTGCGAATTTGAC--TTTCGCGTTGCGAATT
1 ATTTGACTATCGCGTTGCGAATTTGACTTT-GTGTTGCG-ATTT-ACAAATTCGAGTTGCGAATT
* * *
3131352 TGACTTTCGCGTTGCAA
63 TGACTTTTGTGTTGCGA
3131369 ATTTGACT
1 ATTTGACT
3131377 TATGTGTTGC
Statistics
Matches: 148, Mismatches: 16, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
79 2 0.01
80 79 0.53
81 61 0.41
82 4 0.03
83 2 0.01
ACGTcount: A:0.21, C:0.16, G:0.22, T:0.41
Consensus pattern (79 bp):
ATTTGACTATCGCGTTGCGAATTTGACTTTGTGTTGCGATTTACAAATTCGAGTTGCGAATTTGA
CTTTTGTGTTGCGA
Found at i:3131306 original size:101 final size:101
Alignment explanation
Indices: 3131131--3131388 Score: 285
Period size: 101 Copynumber: 2.6 Consensus size: 101
3131121 TAAAAACATT
* * * * ** *
3131131 TGACTTTCGCGTTGAGAATTTGACTTTTGTGTTGC-AATTT-ACAAATTCGAGTTGCG-AATTTG
1 TGACTTTCGCGTTGCGAATTTGACATTCGCGTTGCAAATTTGACTTA-T-GTGTTGCGAAATTTG
* * *
3131193 ACTTTTGTGTTACGAATTTGACTATCGCGTTGCGAATC
64 ACTATCGCGTTACGAATTTGACTATCGCGTTGCGAATC
* * *
3131231 TGAC-TTCTGTGTTGCG-ATTT-ACAAATTCGTGTTGCAAATTTGACTTTTGTGTTGCGAAATTT
1 TGACTTTC-GCGTTGCGAATTTGAC--ATTCGCGTTGCAAATTTGACTTATGTGTTGCGAAATTT
* *
3131293 GACTATCGCGTTACGAATTTGACTTTCGCGTTGCGAATT
63 GACTATCGCGTTACGAATTTGACTATCGCGTTGCGAATC
*
3131332 TGACTTTCGCGTTGCGAATTTGACTTTCGCGTTGCAAATTTGACTTATGTGTTGCGA
1 TGACTTTCGCGTTGCGAATTTGACATTCGCGTTGCAAATTTGACTTATGTGTTGCGA
3131389 TTTACATAAT
Statistics
Matches: 132, Mismatches: 17, Indels: 17
0.80 0.10 0.10
Matches are distributed among these distances:
98 2 0.02
99 7 0.05
100 26 0.20
101 86 0.65
102 9 0.07
103 2 0.02
ACGTcount: A:0.21, C:0.16, G:0.22, T:0.41
Consensus pattern (101 bp):
TGACTTTCGCGTTGCGAATTTGACATTCGCGTTGCAAATTTGACTTATGTGTTGCGAAATTTGAC
TATCGCGTTACGAATTTGACTATCGCGTTGCGAATC
Found at i:3131385 original size:20 final size:21
Alignment explanation
Indices: 3131128--3131409 Score: 211
Period size: 20 Copynumber: 14.0 Consensus size: 21
3131118 GCGTAAAAAC
*
3131128 ATTTGACTT-TCGCGTTGAGA
1 ATTTGACTTATCGCGTTGCGA
* *
3131148 ATTTGACTT-TTGTGTTGC-A
1 ATTTGACTTATCGCGTTGCGA
** *
3131167 ATTT-ACAAATTCGAGTTGCGA
1 ATTTGACTTA-TCGCGTTGCGA
* * *
3131188 ATTTGACTT-TTGTGTTACGA
1 ATTTGACTTATCGCGTTGCGA
3131208 ATTTGAC-TATCGCGTTGCGA
1 ATTTGACTTATCGCGTTGCGA
* * *
3131228 ATCTGACTTCT-GTGTTGCG-
1 ATTTGACTTATCGCGTTGCGA
** * *
3131247 ATTT-ACAAATTCGTGTTGCAA
1 ATTTGACTTA-TCGCGTTGCGA
* *
3131268 ATTTGACTT-TTGTGTTGCGAA
1 ATTTGACTTATCGCGTTGCG-A
*
3131289 ATTTGAC-TATCGCGTTACGA
1 ATTTGACTTATCGCGTTGCGA
3131309 ATTTGACTT-TCGCGTTGCGA
1 ATTTGACTTATCGCGTTGCGA
3131329 ATTTGACTT-TCGCGTTGCGA
1 ATTTGACTTATCGCGTTGCGA
*
3131349 ATTTGACTT-TCGCGTTGCAA
1 ATTTGACTTATCGCGTTGCGA
*
3131369 ATTTGACTTAT-GTGTTGCG-
1 ATTTGACTTATCGCGTTGCGA
*
3131388 ATTT-ACATAATCGCGTTGCGA
1 ATTTGAC-TTATCGCGTTGCGA
3131409 A
1 A
3131410 ATTAGAAACT
Statistics
Matches: 209, Mismatches: 36, Indels: 33
0.75 0.13 0.12
Matches are distributed among these distances:
18 6 0.03
19 17 0.08
20 153 0.73
21 29 0.14
22 4 0.02
ACGTcount: A:0.21, C:0.16, G:0.22, T:0.41
Consensus pattern (21 bp):
ATTTGACTTATCGCGTTGCGA
Found at i:3131386 original size:60 final size:60
Alignment explanation
Indices: 3131128--3131409 Score: 247
Period size: 60 Copynumber: 4.7 Consensus size: 60
3131118 GCGTAAAAAC
* * * * * *
3131128 ATTTGACTTTCGCGTTGAGAATTTGACTTTTGTGTTGC-AATTT-ACAAATTCGAGTTGCGA
1 ATTTGACTTTCGTGTTGCGAATTTGACTTTCGCGTTGCGAATTTGAC--TTTCGCGTTGCGA
* * * * *
3131188 ATTTGACTTTTGTGTTACGAATTTGACTATCGCGTTGCGAATCTGAC-TTCTGTGTTGCG-
1 ATTTGACTTTCGTGTTGCGAATTTGACTTTCGCGTTGCGAATTTGACTTTC-GCGTTGCGA
* * * * * *
3131247 ATTT-ACAAATTCGTGTTGCAAATTTGACTTTTGTGTTGCGAAATTTGACTATCGCGTTACGA
1 ATTTGAC--TTTCGTGTTGCGAATTTGACTTTCGCGTTGCG-AATTTGACTTTCGCGTTGCGA
* *
3131309 ATTTGACTTTCGCGTTGCGAATTTGACTTTCGCGTTGCGAATTTGACTTTCGCGTTGCAA
1 ATTTGACTTTCGTGTTGCGAATTTGACTTTCGCGTTGCGAATTTGACTTTCGCGTTGCGA
*
3131369 ATTTGACTTAT-GTGTTGCG-ATTT-ACATAATCGCGTTGCGAA
1 ATTTGACTT-TCGTGTTGCGAATTTGAC-T-TTCGCGTTGCGAA
3131410 ATTAGAAACT
Statistics
Matches: 180, Mismatches: 30, Indels: 24
0.77 0.13 0.10
Matches are distributed among these distances:
58 4 0.02
59 12 0.07
60 109 0.61
61 45 0.25
62 8 0.04
63 2 0.01
ACGTcount: A:0.21, C:0.16, G:0.22, T:0.41
Consensus pattern (60 bp):
ATTTGACTTTCGTGTTGCGAATTTGACTTTCGCGTTGCGAATTTGACTTTCGCGTTGCGA
Found at i:3131426 original size:141 final size:140
Alignment explanation
Indices: 3131176--3131453 Score: 362
Period size: 141 Copynumber: 2.0 Consensus size: 140
3131166 AATTTACAAA
* * * *
3131176 TTCGAGTTGCGAATTTGACTTTTGTGTTACGAATTTGACTATCGCGTTGCGAATCTGACTTCTGT
1 TTCGAGTTGCGAATTTGACTTTCGCGTTACGAATTTGACTATCGCGTTGCAAATCTGACTTATGT
* * *** * *
3131241 GTTGCGATTTACAAATTCGTGTTGCAAATTTGACTTTTGTGTTGCGAAATTTGACTATCGCGTTA
66 GTTGCGATTTACAAATTCGCGTTGCAAATTAGACAACTGGGTTGCGAAATTGGACT-TCGCGTTA
3131306 CGAATTTGACT
130 CGAATTTGACT
* * * *
3131317 TTCGCGTTGCGAATTTGACTTTCGCGTTGCGAATTTGACTTTCGCGTTGCAAATTTGACTTATGT
1 TTCGAGTTGCGAATTTGACTTTCGCGTTACGAATTTGACTATCGCGTTGCAAATCTGACTTATGT
*
3131382 GTTGCGATTTACATAA-TCGCGTTGCGAAATTAGA-AACTGGGTTGCGAAATTGGAGTTCGCGTT
66 GTTGCGATTTACA-AATTCGCGTTGC-AAATTAGACAACTGGGTTGCGAAATTGGACTTCGCGTT
*
3131445 GCGAATTTG
129 ACGAATTTG
3131454 TTGGTCATTT
Statistics
Matches: 118, Mismatches: 17, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
140 15 0.13
141 94 0.80
142 9 0.08
ACGTcount: A:0.21, C:0.16, G:0.24, T:0.39
Consensus pattern (140 bp):
TTCGAGTTGCGAATTTGACTTTCGCGTTACGAATTTGACTATCGCGTTGCAAATCTGACTTATGT
GTTGCGATTTACAAATTCGCGTTGCAAATTAGACAACTGGGTTGCGAAATTGGACTTCGCGTTAC
GAATTTGACT
Found at i:3133526 original size:71 final size:72
Alignment explanation
Indices: 3133368--3133549 Score: 251
Period size: 71 Copynumber: 2.5 Consensus size: 72
3133358 ATCATAAGAT
* *
3133368 TTATTTTTAGGGATTACGATTTAGAGTTTATGATTTTTTGGTAATCCCTAAATTCATTCTAAAAT
1 TTATTTTTAGGGATTACGATTTAGAGTTTATGA-ATTTTGGTAATACCTAAATTCATTCTAAAAT
3133433 GAATCTAA
65 GAATCTAA
* * *
3133441 TAATTTTTATGGATTACGATTGAGAGTTTATGAATTTT-GT-ATACCTAAATTCATTCTAAAAAT
1 TTATTTTTAGGGATTACGATTTAGAGTTTATGAATTTTGGTAATACCTAAATTCATTCT-AAAAT
*
3133504 GAATCTTA
65 GAATCTAA
* * *
3133512 TTATTTTTAGGGATTATGATTTAGAGTTTGTGTATTTT
1 TTATTTTTAGGGATTACGATTTAGAGTTTATGAATTTT
3133550 TTTGGATTTT
Statistics
Matches: 96, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
70 16 0.17
71 46 0.48
72 4 0.04
73 30 0.31
ACGTcount: A:0.31, C:0.07, G:0.15, T:0.47
Consensus pattern (72 bp):
TTATTTTTAGGGATTACGATTTAGAGTTTATGAATTTTGGTAATACCTAAATTCATTCTAAAATG
AATCTAA
Found at i:3139009 original size:54 final size:54
Alignment explanation
Indices: 3138946--3139053 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
3138936 TTCTTTTAGT
3138946 TTTGCACAAATTTAAGACTATTGGATAAGTGAAAATAAATAATTGAGATTAACA
1 TTTGCACAAATTTAAGACTATTGGATAAGTGAAAATAAATAATTGAGATTAACA
3139000 TTTGCACAAATTTAAGACTATTGGATAAGTGAAAATAAATAATTGAGATTAACA
1 TTTGCACAAATTTAAGACTATTGGATAAGTGAAAATAAATAATTGAGATTAACA
3139054 ATAAGAATGA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.46, C:0.07, G:0.15, T:0.31
Consensus pattern (54 bp):
TTTGCACAAATTTAAGACTATTGGATAAGTGAAAATAAATAATTGAGATTAACA
Found at i:3140008 original size:20 final size:20
Alignment explanation
Indices: 3139885--3140016 Score: 74
Period size: 20 Copynumber: 6.6 Consensus size: 20
3139875 AAATGACCAA
3139885 CAAATTCGCAACGCGAACTC
1 CAAATTCGCAACGCGAACTC
* * **
3139905 CAATTTCGCAAC-CCAGTTTC
1 CAAATTCGCAACGCGA-ACTC
* * *
3139925 CAATTTCGCAACGCGAATATG
1 CAAATTCGCAACGCGAA-CTC
* ** *
3139946 TAAA-TCGCAACATAGAAGT-
1 CAAATTCGCAAC-GCGAACTC
* *
3139965 CAAATTCGCAACGTGAAAGT-
1 CAAATTCGCAACGCG-AACTC
3139985 CAAATTCGCAACGCGAACTC
1 CAAATTCGCAACGCGAACTC
*
3140005 CAAATTAGCAAC
1 CAAATTCGCAAC
3140017 ATGAATACTA
Statistics
Matches: 86, Mismatches: 19, Indels: 14
0.72 0.16 0.12
Matches are distributed among these distances:
19 9 0.10
20 69 0.80
21 8 0.09
ACGTcount: A:0.37, C:0.27, G:0.15, T:0.20
Consensus pattern (20 bp):
CAAATTCGCAACGCGAACTC
Found at i:3140043 original size:20 final size:20
Alignment explanation
Indices: 3140018--3140071 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
3140008 ATTAGCAACA
*
3140018 TGAATACTAAAATCGTAACG
1 TGAATAGTAAAATCGTAACG
*
3140038 TGAATAGTAAAATTGTAACG
1 TGAATAGTAAAATCGTAACG
3140058 TGAATAGTAAAATC
1 TGAATAGTAAAATC
3140072 ACAACGAATC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.46, C:0.09, G:0.17, T:0.28
Consensus pattern (20 bp):
TGAATAGTAAAATCGTAACG
Found at i:3140077 original size:20 final size:20
Alignment explanation
Indices: 3139930--3140077 Score: 81
Period size: 20 Copynumber: 7.4 Consensus size: 20
3139920 GTTTCCAATT
*
3139930 TCGCAACGCGAATATGT-AAA
1 TCGCAACGTGAATA-GTAAAA
* *
3139950 TCGCAACAT-AGA-AGTCAAAT
1 TCGCAACGTGA-ATAGT-AAAA
*
3139970 TCGCAACGTGAA-AGTCAAAT
1 TCGCAACGTGAATAGT-AAAA
* ** *
3139990 TCGCAACGCGAACT-CCAAAT
1 TCGCAACGTGAA-TAGTAAAA
* * *
3140010 TAGCAACATGAATACTAAAA
1 TCGCAACGTGAATAGTAAAA
*
3140030 TCGTAACGTGAATAGTAAAA
1 TCGCAACGTGAATAGTAAAA
* *
3140050 TTGTAACGTGAATAGTAAAA
1 TCGCAACGTGAATAGTAAAA
*
3140070 TCACAACG
1 TCGCAACG
3140078 AATCTATATG
Statistics
Matches: 101, Mismatches: 20, Indels: 14
0.75 0.15 0.10
Matches are distributed among these distances:
18 2 0.02
19 3 0.03
20 95 0.94
21 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.21
Consensus pattern (20 bp):
TCGCAACGTGAATAGTAAAA
Found at i:3140470 original size:20 final size:20
Alignment explanation
Indices: 3140447--3140518 Score: 92
Period size: 20 Copynumber: 3.5 Consensus size: 20
3140437 CTAAATTTGT
*
3140447 GTTGCGATTTTTCAATTCAC
1 GTTGCGATTTTTCTATTCAC
* *
3140467 GTTGCGATTTTACTATTCAT
1 GTTGCGATTTTTCTATTCAC
3140487 GTTGCGATTTTTACTATTCAC
1 GTTGCGATTTTT-CTATTCAC
3140508 -TCTGCGATTTT
1 GT-TGCGATTTT
3140519 AGAAACTGAG
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.18, C:0.18, G:0.15, T:0.49
Consensus pattern (20 bp):
GTTGCGATTTTTCTATTCAC
Found at i:3140513 original size:21 final size:20
Alignment explanation
Indices: 3140448--3140518 Score: 83
Period size: 21 Copynumber: 3.5 Consensus size: 20
3140438 TAAATTTGTG
*
3140448 TTGCGATTTTT-CAATTCAC
1 TTGCGATTTTTACTATTCAC
*
3140467 GTTGCGA-TTTTACTATTCATG
1 -TTGCGATTTTTACTATTCA-C
3140488 TTGCGATTTTTACTATTCAC
1 TTGCGATTTTTACTATTCAC
3140508 TCTGCGATTTT
1 T-TGCGATTTT
3140519 AGAAACTGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
19 4 0.09
20 19 0.43
21 21 0.48
ACGTcount: A:0.18, C:0.18, G:0.14, T:0.49
Consensus pattern (20 bp):
TTGCGATTTTTACTATTCAC
Found at i:3140726 original size:21 final size:20
Alignment explanation
Indices: 3140687--3140765 Score: 104
Period size: 21 Copynumber: 3.9 Consensus size: 20
3140677 GATTTTTTAA
*
3140687 ATTCGCGTTGCGATTTTACT
1 ATTCACGTTGCGATTTTACT
*
3140707 ATTTACGTTGCGACTTTTACT
1 ATTCACGTTGCGA-TTTTACT
*
3140728 ATTCACGTTACGATTTTTACT
1 ATTCACGTTGCGA-TTTTACT
*
3140749 ATTCACGCTGCGATTTT
1 ATTCACGTTGCGATTTT
3140766 GGAAACTGAG
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.29
21 36 0.71
ACGTcount: A:0.19, C:0.20, G:0.15, T:0.46
Consensus pattern (20 bp):
ATTCACGTTGCGATTTTACT
Found at i:3144193 original size:4 final size:4
Alignment explanation
Indices: 3144184--3144234 Score: 102
Period size: 4 Copynumber: 12.8 Consensus size: 4
3144174 AATATACCTA
3144184 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
3144232 ATA
1 ATA
3144235 TGGACATATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 47 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:3152982 original size:105 final size:105
Alignment explanation
Indices: 3152791--3153013 Score: 232
Period size: 105 Copynumber: 2.1 Consensus size: 105
3152781 GTCGAGGGTC
* * * * *
3152791 TACGCGGTCCTTCGCGGCATATAGGTATCCTATGGAACATCTATGAGGTCCTTTGCGACACGTAT
1 TACGTGGTCCTTCGAGACATATAGGTATCCTATGGAACATCTATGAGGTCCTTTGAGACACGTAC
* * *
3152856 TTGGTCCTTAG-CATATGTATATGATTCTTAAGGAATTTTT
66 TTGATCCTTAGACATATATATATGATTCTTAAGGAA-TTTA
* * * * * * * * *
3152896 TACGTGGTCCTTCGAGACGTATATGTATTCTTTGGAGCATGTATGAGGTCTTTTGAGATACTTAC
1 TACGTGGTCCTTCGAGACATATAGGTATCCTATGGAACATCTATGAGGTCCTTTGAGACACGTAC
* * *
3152961 TTGATCCTTGGTATATATATATATGGTTCTTAAGGAATTTA
66 TTGATCCTTAG-ACATATATATATGATTCTTAAGGAATTTA
*
3153002 TATGTGGTCCTT
1 TACGTGGTCCTT
3153014 ATGGACAATC
Statistics
Matches: 95, Mismatches: 21, Indels: 3
0.80 0.18 0.03
Matches are distributed among these distances:
105 60 0.63
106 14 0.15
107 21 0.22
ACGTcount: A:0.23, C:0.16, G:0.22, T:0.39
Consensus pattern (105 bp):
TACGTGGTCCTTCGAGACATATAGGTATCCTATGGAACATCTATGAGGTCCTTTGAGACACGTAC
TTGATCCTTAGACATATATATATGATTCTTAAGGAATTTA
Found at i:3155331 original size:21 final size:21
Alignment explanation
Indices: 3155307--3155365 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
3155297 TTCTATGTGG
*
3155307 TCCTTCGGGATATATATGTAA
1 TCCTTCGGGACATATATGTAA
* * **
3155328 TCCTTTGGAACATATATGTTG
1 TCCTTCGGGACATATATGTAA
*
3155349 TTCTTCGGGACATATAT
1 TCCTTCGGGACATATAT
3155366 TTGGTCCTTT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.41
Consensus pattern (21 bp):
TCCTTCGGGACATATATGTAA
Found at i:3155364 original size:42 final size:42
Alignment explanation
Indices: 3155300--3155395 Score: 111
Period size: 42 Copynumber: 2.3 Consensus size: 42
3155290 TTGAAGGTTC
* * *
3155300 TATGTGGTCCTTCGGGATATATATGTAATCCTTTGGAACATA
1 TATGTTGTCCTTCGGGACATATATGTAATCCTTTGGAACACA
* * ** *
3155342 TATGTTGTTCTTCGGGACATATATTTGGTCCTTTGGAATACA
1 TATGTTGTCCTTCGGGACATATATGTAATCCTTTGGAACACA
*
3155384 TATGTTATCCTT
1 TATGTTGTCCTT
3155396 AATGAGTGGT
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.23, C:0.15, G:0.20, T:0.43
Consensus pattern (42 bp):
TATGTTGTCCTTCGGGACATATATGTAATCCTTTGGAACACA
Found at i:3158180 original size:16 final size:18
Alignment explanation
Indices: 3158146--3158214 Score: 61
Period size: 16 Copynumber: 3.7 Consensus size: 18
3158136 TAGGAGGTAG
*
3158146 TTATAATATAATATTTAT
1 TTATAATATAATATATAT
3158164 TTATAAT-T-ATATATAT
1 TTATAATATAATATATAT
*
3158180 TTATTAATAATGCATATATATT
1 TTA-TAAT-AT-AATATATA-T
3158202 TTATAAATATAAT
1 TTAT-AATATAAT
3158215 TACTGAATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
16 10 0.24
17 5 0.12
18 7 0.17
19 1 0.02
20 2 0.05
21 10 0.24
22 7 0.17
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (18 bp):
TTATAATATAATATATAT
Found at i:3158196 original size:21 final size:20
Alignment explanation
Indices: 3158148--3158202 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
3158138 GGAGGTAGTT
*
3158148 ATAAT-ATA-ATATTTATTT
1 ATAATCATATATATTTATTA
*
3158166 ATAATTATATATATTTATTA
1 ATAATCATATATATTTATTA
3158186 ATAATGCATATATATTT
1 ATAAT-CATATATATTT
3158203 TATAAATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
18 5 0.16
19 3 0.09
20 14 0.44
21 10 0.31
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (20 bp):
ATAATCATATATATTTATTA
Found at i:3160667 original size:37 final size:37
Alignment explanation
Indices: 3160591--3160667 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 37
3160581 TTTTTATATT
*
3160591 TTTAATTTTGTAAAACAAATTATATAAATATTCTGAA
1 TTTAATTTTGTAAAACAAATTATATAAATATTCTCAA
* *
3160628 TTTAATTTTTTAAAGA-AAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-ACAAATTATATAAATATTCT-CAA
3160665 TTT
1 TTT
3160668 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 13 0.37
37 21 0.60
38 1 0.03
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAACAAATTATATAAATATTCTCAA
Found at i:3160849 original size:20 final size:20
Alignment explanation
Indices: 3160813--3160850 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3160803 ATCATATTCC
**
3160813 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
3160833 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
3160851 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:3163176 original size:6 final size:6
Alignment explanation
Indices: 3163165--3163202 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
3163155 CTGAAACCTC
3163165 AATAGT AATAGT AATAGT AATAGT AATAGT AATAGT AA
1 AATAGT AATAGT AATAGT AATAGT AATAGT AATAGT AA
3163203 AGGAATCCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.16, T:0.32
Consensus pattern (6 bp):
AATAGT
Found at i:3168963 original size:16 final size:15
Alignment explanation
Indices: 3168936--3168972 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
3168926 ATTGTCTTTG
3168936 AAAAATACTTTTAAA
1 AAAAATACTTTTAAA
*
3168951 AAAAATACTTTTTAA
1 AAAAATACTTTTAAA
3168966 AAAAATA
1 AAAAATA
3168973 ATTTCAAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.32
Consensus pattern (15 bp):
AAAAATACTTTTAAA
Found at i:3172837 original size:29 final size:29
Alignment explanation
Indices: 3172805--3172897 Score: 71
Period size: 29 Copynumber: 3.1 Consensus size: 29
3172795 TTTGTGATGA
3172805 AATTGAAATGTTCAAAAAGTTTGAGAACT
1 AATTGAAATGTTCAAAAAGTTTGAGAACT
*** * * **
3172834 AATTGAGAATGAAGATCATAGTTTGAGGAAGA
1 AATTGA-AATGTTCA-AAAAGTTTGA-GAACT
* *
3172866 AAATGAAATGTTC-AAAAGTTTGAGGACT
1 AATTGAAATGTTCAAAAAGTTTGAGAACT
3172894 AATT
1 AATT
3172898 TAGAATGATA
Statistics
Matches: 44, Mismatches: 17, Indels: 7
0.65 0.25 0.10
Matches are distributed among these distances:
28 5 0.11
29 14 0.32
30 5 0.11
31 12 0.27
32 8 0.18
ACGTcount: A:0.44, C:0.05, G:0.22, T:0.29
Consensus pattern (29 bp):
AATTGAAATGTTCAAAAAGTTTGAGAACT
Found at i:3172884 original size:60 final size:61
Alignment explanation
Indices: 3172803--3172982 Score: 201
Period size: 60 Copynumber: 3.0 Consensus size: 61
3172793 AGTTTGTGAT
*
3172803 GAAATTGAAATGTTCAAAAAGTTTGAGAACTAATTGAGAATGAAGATCATAGTTTGAGGAA
1 GAAATTGAAATGTTCAAAAAGTTTGAGAACTAATTTAGAATGAAGATCATAGTTTGAGGAA
* * **
3172864 GAAAATGAAATGTTC-AAAAGTTTGAGGACTAATTTAGAATGATAG-TCATAGTTT-AGGGGT
1 GAAATTGAAATGTTCAAAAAGTTTGAGAACTAATTTAGAATGA-AGATCATAGTTTGA-GGAA
* * * *
3172924 GAAATTAAAAT-ATCGAAAAGTTT-AGAGACTAATTTAGAAT-AAGAGTCATAATTTGAGGA
1 GAAATTGAAATGTTCAAAAAGTTTGAGA-ACTAATTTAGAATGAAGA-TCATAGTTTGAGGA
3172983 TGCGTGATGC
Statistics
Matches: 101, Mismatches: 11, Indels: 15
0.80 0.09 0.12
Matches are distributed among these distances:
58 2 0.02
59 6 0.06
60 76 0.75
61 17 0.17
ACGTcount: A:0.43, C:0.05, G:0.22, T:0.29
Consensus pattern (61 bp):
GAAATTGAAATGTTCAAAAAGTTTGAGAACTAATTTAGAATGAAGATCATAGTTTGAGGAA
Found at i:3176099 original size:18 final size:18
Alignment explanation
Indices: 3176073--3176113 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
3176063 TCCTTCGATT
*
3176073 GTTCCGGAACAGGATTAC
1 GTTCTGGAACAGGATTAC
3176091 GTTCTGGAACAGGATTAC
1 GTTCTGGAACAGGATTAC
3176109 GTTCT
1 GTTCT
3176114 ATATCTACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (18 bp):
GTTCTGGAACAGGATTAC
Found at i:3176247 original size:20 final size:23
Alignment explanation
Indices: 3176222--3176279 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 23
3176212 AATGAAGGTA
3176222 TGTATCGATGCACTC-T-ACA-G
1 TGTATCGATGCACTCTTAACATG
*
3176242 TGTATCGATGCATCCCTTAACATG
1 TGTATCGATGCA-CTCTTAACATG
3176266 TGTATCGATGCACT
1 TGTATCGATGCACT
3176280 ATCTATGCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 12 0.38
21 2 0.06
22 1 0.03
23 4 0.12
24 13 0.41
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (23 bp):
TGTATCGATGCACTCTTAACATG
Found at i:3181830 original size:66 final size:66
Alignment explanation
Indices: 3181753--3181885 Score: 266
Period size: 66 Copynumber: 2.0 Consensus size: 66
3181743 GTATGTCTCC
3181753 AGTATCATGAATGCATTTTCATTCGCGTGTGGCACATCTAAAGATAGGGTTTTTTTTTATAGGGA
1 AGTATCATGAATGCATTTTCATTCGCGTGTGGCACATCTAAAGATAGGGTTTTTTTTTATAGGGA
3181818 G
66 G
3181819 AGTATCATGAATGCATTTTCATTCGCGTGTGGCACATCTAAAGATAGGGTTTTTTTTTATAGGGA
1 AGTATCATGAATGCATTTTCATTCGCGTGTGGCACATCTAAAGATAGGGTTTTTTTTTATAGGGA
3181884 G
66 G
3181885 A
1 A
3181886 TGCGATGAAC
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.38
Consensus pattern (66 bp):
AGTATCATGAATGCATTTTCATTCGCGTGTGGCACATCTAAAGATAGGGTTTTTTTTTATAGGGA
G
Found at i:3183579 original size:7 final size:7
Alignment explanation
Indices: 3183567--3183607 Score: 73
Period size: 7 Copynumber: 5.9 Consensus size: 7
3183557 GACCCGACCC
3183567 GACCGTT
1 GACCGTT
3183574 GACCGTT
1 GACCGTT
3183581 GACCGTT
1 GACCGTT
*
3183588 TACCGTT
1 GACCGTT
3183595 GACCGTT
1 GACCGTT
3183602 GACCGT
1 GACCGT
3183608 CGACTTTCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.15, C:0.29, G:0.27, T:0.29
Consensus pattern (7 bp):
GACCGTT
Found at i:3190579 original size:61 final size:63
Alignment explanation
Indices: 3190463--3190587 Score: 236
Period size: 62 Copynumber: 2.0 Consensus size: 63
3190453 GCACCATCGT
3190463 GTTCCTTGTGCCGTTCCGAGTTCACGGTTGTCAACCTTGTCGCTGTAGACGGCGGCG-GTGAG
1 GTTCCTTGTGCCGTTCCGAGTTCACGGTTGTCAACCTTGTCGCTGTAGACGGCGGCGCGTGAG
3190525 GTTCCTTGTGCCGTTCCGAGTTCACGG-TGTCAACCTTGTCGCTGTAGACGGCGGCGCGTGAG
1 GTTCCTTGTGCCGTTCCGAGTTCACGGTTGTCAACCTTGTCGCTGTAGACGGCGGCGCGTGAG
3190587 G
1 G
3190588 AGGTGGTGCA
Statistics
Matches: 62, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
61 29 0.47
62 33 0.53
ACGTcount: A:0.11, C:0.26, G:0.34, T:0.28
Consensus pattern (63 bp):
GTTCCTTGTGCCGTTCCGAGTTCACGGTTGTCAACCTTGTCGCTGTAGACGGCGGCGCGTGAG
Found at i:3190755 original size:9 final size:9
Alignment explanation
Indices: 3190741--3190806 Score: 60
Period size: 10 Copynumber: 6.8 Consensus size: 9
3190731 GGCTGCTGGA
3190741 AACCGGTTT
1 AACCGGTTT
3190750 AACCGGTTTT
1 AACCGG-TTT
3190760 CAACCGGTTCT
1 -AACCGGTT-T
*
3190771 GACCGGTTT
1 AACCGGTTT
*
3190780 CAACCGGTTCG
1 -AACCGGTT-T
3190791 AACCGGTTT
1 AACCGGTTT
*
3190800 GACCGGT
1 AACCGGT
3190807 CTGACCCGAC
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
9 13 0.28
10 27 0.57
11 7 0.15
ACGTcount: A:0.18, C:0.27, G:0.26, T:0.29
Consensus pattern (9 bp):
AACCGGTTT
Found at i:3190766 original size:20 final size:21
Alignment explanation
Indices: 3190741--3190799 Score: 86
Period size: 20 Copynumber: 2.9 Consensus size: 21
3190731 GGCTGCTGGA
3190741 AACCGGTT-TAACCGGTTTTC
1 AACCGGTTCTAACCGGTTTTC
*
3190761 AACCGGTTCTGACCGG-TTTC
1 AACCGGTTCTAACCGGTTTTC
*
3190781 AACCGGTTCGAACCGGTTT
1 AACCGGTTCTAACCGGTTT
3190800 GACCGGTCTG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 26 0.76
21 8 0.24
ACGTcount: A:0.19, C:0.27, G:0.24, T:0.31
Consensus pattern (21 bp):
AACCGGTTCTAACCGGTTTTC
Found at i:3190778 original size:30 final size:29
Alignment explanation
Indices: 3190742--3190806 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 29
3190732 GCTGCTGGAA
3190742 ACCGGTTT-AACCGGTTTTC-AACCGGTTCTG
1 ACCGGTTTCAACCGG--TTCGAACCGGTT-TG
3190772 ACCGGTTTCAACCGGTTCGAACCGGTTTG
1 ACCGGTTTCAACCGGTTCGAACCGGTTTG
3190801 ACCGGT
1 ACCGGT
3190807 CTGACCCGAC
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
29 11 0.33
30 16 0.48
31 6 0.18
ACGTcount: A:0.17, C:0.28, G:0.26, T:0.29
Consensus pattern (29 bp):
ACCGGTTTCAACCGGTTCGAACCGGTTTG
Found at i:3190831 original size:7 final size:7
Alignment explanation
Indices: 3190819--3190856 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
3190809 GACCCGACCC
3190819 GACCGTT
1 GACCGTT
3190826 GACCGTT
1 GACCGTT
*
3190833 TACCGTT
1 GACCGTT
*
3190840 GACCATT
1 GACCGTT
3190847 GACCGTT
1 GACCGTT
3190854 GAC
1 GAC
3190857 TTTCTTTGAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.18, C:0.29, G:0.24, T:0.29
Consensus pattern (7 bp):
GACCGTT
Found at i:3191881 original size:52 final size:49
Alignment explanation
Indices: 3191806--3191907 Score: 177
Period size: 52 Copynumber: 2.0 Consensus size: 49
3191796 TCAACATATC
3191806 TCTTGAAGTAAAGATTGTAATGTTTTTATCTGACAAGTTGACTTTATTT
1 TCTTGAAGTAAAGATTGTAATGTTTTTATCTGACAAGTTGACTTTATTT
3191855 TCTTGAAGTAAATCAGATTGTAATGTTTTTATCTGACAAGTTGACTTTATTT
1 TCTTGAAGT-AA--AGATTGTAATGTTTTTATCTGACAAGTTGACTTTATTT
3191907 T
1 T
3191908 GGTGACATGG
Statistics
Matches: 50, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
49 9 0.18
50 2 0.04
52 39 0.78
ACGTcount: A:0.28, C:0.09, G:0.16, T:0.47
Consensus pattern (49 bp):
TCTTGAAGTAAAGATTGTAATGTTTTTATCTGACAAGTTGACTTTATTT
Found at i:3192145 original size:75 final size:78
Alignment explanation
Indices: 3192056--3192211 Score: 282
Period size: 75 Copynumber: 2.0 Consensus size: 78
3192046 TGGATTTTGA
3192056 TAGTATAATTTGTTTATAATTTCATGTTATTTATAA-TGATTTTATA-TGATGGAATAACGGTTG
1 TAGTATAATTTGTTTATAATTTCATGTTATTTATAAGTGATTTTATATTGATGGAATAACGGTTG
3192119 CG-AAAATGTCTT
66 CGAAAAATGTCTT
3192131 TAGTATAATTTGTTTATAATTTCATGTTATTTATAATGTGATTTTATATTGATGGAATAACGGTT
1 TAGTATAATTTGTTTATAATTTCATGTTATTTATAA-GTGATTTTATATTGATGGAATAACGGTT
3192196 GCGAAAAATGTCTT
65 GCGAAAAATGTCTT
3192210 TA
1 TA
3192212 ATAATCATAA
Statistics
Matches: 77, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
75 36 0.47
77 10 0.13
78 19 0.25
79 12 0.16
ACGTcount: A:0.32, C:0.05, G:0.16, T:0.47
Consensus pattern (78 bp):
TAGTATAATTTGTTTATAATTTCATGTTATTTATAAGTGATTTTATATTGATGGAATAACGGTTG
CGAAAAATGTCTT
Found at i:3192930 original size:25 final size:25
Alignment explanation
Indices: 3192902--3192949 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
3192892 ATCCTTTCAT
*
3192902 TATT-TTATTTTTGTTTTAATCATTC
1 TATTATTATTTTT-TTTAAATCATTC
3192927 TATTATTATTTTTTTTAAATCAT
1 TATTATTATTTTTTTTAAATCAT
3192950 ATTTAATGGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.67
Consensus pattern (25 bp):
TATTATTATTTTTTTTAAATCATTC
Found at i:3198813 original size:31 final size:31
Alignment explanation
Indices: 3198775--3198834 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
3198765 TCTATGACCC
3198775 CTAACGTTATCAATATGTTAGATTTTAGTCT
1 CTAACGTTATCAATATGTTAGATTTTAGTCT
* *
3198806 CTAACGTTATTAATATGTTCGATTTTAGT
1 CTAACGTTATCAATATGTTAGATTTTAGT
3198835 TCTTCAATAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.28, C:0.12, G:0.13, T:0.47
Consensus pattern (31 bp):
CTAACGTTATCAATATGTTAGATTTTAGTCT
Found at i:3203365 original size:10 final size:10
Alignment explanation
Indices: 3203352--3203411 Score: 52
Period size: 10 Copynumber: 5.8 Consensus size: 10
3203342 ATTTAAATTA
*
3203352 AATTTTAAAT
1 AATTATAAAT
*
3203362 AATTCATACCAT
1 AATT-ATA-AAT
3203374 AATATTATAAAT
1 AAT-T-ATAAAT
3203386 AATTAT-AAT
1 AATTATAAAT
3203395 -ATTATAAAT
1 AATTATAAAT
3203404 AATTATAA
1 AATTATAA
3203412 TTAAATTTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
8 5 0.12
9 6 0.15
10 13 0.32
11 3 0.07
12 10 0.24
13 4 0.10
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (10 bp):
AATTATAAAT
Found at i:3203395 original size:18 final size:18
Alignment explanation
Indices: 3203372--3203412 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
3203362 AATTCATACC
3203372 ATAATATTATAAATAATT
1 ATAATATTATAAATAATT
3203390 ATAATATTATAAATAATT
1 ATAATATTATAAATAATT
3203408 ATAAT
1 ATAAT
3203413 TAAATTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATAATATTATAAATAATT
Found at i:3205202 original size:6 final size:6
Alignment explanation
Indices: 3205193--3205310 Score: 236
Period size: 6 Copynumber: 19.7 Consensus size: 6
3205183 ATATACATAC
3205193 ACATTT ACATTT ACATTT ACATTT ACATTT ACATTT ACATTT ACATTT
1 ACATTT ACATTT ACATTT ACATTT ACATTT ACATTT ACATTT ACATTT
3205241 ACATTT ACATTT ACATTT ACATTT ACATTT ACATTT ACATTT ACATTT
1 ACATTT ACATTT ACATTT ACATTT ACATTT ACATTT ACATTT ACATTT
3205289 ACATTT ACATTT ACATTT ACAT
1 ACATTT ACATTT ACATTT ACAT
3205311 GTAAATGTTC
Statistics
Matches: 112, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 112 1.00
ACGTcount: A:0.34, C:0.17, G:0.00, T:0.49
Consensus pattern (6 bp):
ACATTT
Found at i:3205419 original size:6 final size:6
Alignment explanation
Indices: 3205380--3205410 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
3205370 AGGCAAAAGG
3205380 ATATAC ATATAC ATATAC ATATAC ATATAC A
1 ATATAC ATATAC ATATAC ATATAC ATATAC A
3205411 CATTTACATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (6 bp):
ATATAC
Found at i:3206529 original size:18 final size:18
Alignment explanation
Indices: 3206508--3206543 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3206498 ATAAAAAAAA
* *
3206508 TTAAAAATAGTTAAAATG
1 TTAAAAAAAGATAAAATG
3206526 TTAAAAAAAGATAAAATG
1 TTAAAAAAAGATAAAATG
3206544 ATCATTTATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.11, T:0.28
Consensus pattern (18 bp):
TTAAAAAAAGATAAAATG
Found at i:3208259 original size:4 final size:4
Alignment explanation
Indices: 3208250--3208279 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
3208240 GGCGTGTCAT
3208250 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GA
3208280 TGGAGACAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:3210427 original size:20 final size:22
Alignment explanation
Indices: 3210395--3210447 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 22
3210385 AGATTTAATT
*
3210395 ATAAATGTTTATAAA-A-TTATA
1 ATAAATTTTTATAAATATTTA-A
3210416 AT-AATTTTTATAAATATTTAA
1 ATAAATTTTTATAAATATTTAA
3210437 ATAAATTTTTA
1 ATAAATTTTTA
3210448 GAACCATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 11 0.39
21 6 0.21
22 11 0.39
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
ATAAATTTTTATAAATATTTAA
Found at i:3211906 original size:30 final size:30
Alignment explanation
Indices: 3211858--3211914 Score: 89
Period size: 31 Copynumber: 1.9 Consensus size: 30
3211848 TAAGGGAGAT
*
3211858 AAAATATAATTAACCATAAATAAATAGGGAC
1 AAAATATAACTAACCATAAA-AAATAGGGAC
3211889 AAAATATAACT-ACCATAAAAAATAGG
1 AAAATATAACTAACCATAAAAAATAGG
3211915 AAAATAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 7 0.28
30 8 0.32
31 10 0.40
ACGTcount: A:0.60, C:0.11, G:0.09, T:0.21
Consensus pattern (30 bp):
AAAATATAACTAACCATAAAAAATAGGGAC
Found at i:3215819 original size:15 final size:15
Alignment explanation
Indices: 3215801--3215857 Score: 53
Period size: 19 Copynumber: 3.5 Consensus size: 15
3215791 TTCTTTTATT
3215801 TTTTATATTTATTTA
1 TTTTATATTTATTTA
3215816 TTTTCAAATTATTTATTTA
1 TTTT---A-TATTTATTTA
3215835 TTTTATATTT-TTTGA
1 TTTTATATTTATTT-A
3215850 CTTTTATA
1 -TTTTATA
3215858 ATTTCTTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
14 3 0.08
15 10 0.28
16 8 0.22
18 1 0.03
19 14 0.39
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (15 bp):
TTTTATATTTATTTA
Found at i:3217094 original size:2 final size:2
Alignment explanation
Indices: 3217087--3217129 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3217077 TACCCTAAAT
3217087 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3217129 T
1 T
3217130 GAATTATATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3223383 original size:18 final size:16
Alignment explanation
Indices: 3223360--3223407 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
3223350 TGTTTCTAAG
3223360 GGAATTGAAATCTGTGAA
1 GGAATTGAAATCTGT--A
3223378 GGAATT-AGAATCTGTA
1 GGAATTGA-AATCTGTA
*
3223394 GGAATTGGAATCTG
1 GGAATTGAAATCTG
3223408 AATCTGAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 13 0.48
17 1 0.04
18 13 0.48
ACGTcount: A:0.35, C:0.06, G:0.29, T:0.29
Consensus pattern (16 bp):
GGAATTGAAATCTGTA
Found at i:3230504 original size:131 final size:131
Alignment explanation
Indices: 3230247--3230504 Score: 286
Period size: 131 Copynumber: 2.0 Consensus size: 131
3230237 GGGTGACCAA
** * * *
3230247 AAACCAAAACATAATGTTAAGTATGATTTTGAAATAAAAAATAGTTGGGTGACCAAAATGGAACA
1 AAACCAAAACATAATGTTAAGTATGATTTCAAAACAAAAAATAATTGGATGACCAAAATGGAACA
* * * * * * * * * *
3230312 AAAGTGATGGTCGGGGTACTAAACATGTAGTTTACCCTTAATTTTTAACGGTGAGTGACCAAAAT
66 AAAATAATAGTCGAGGTACTAAACATGTAGTTTACCCTAAATATGTAACGATGAATCACCAAAAT
3230377 G
131 G
* * *
3230378 AAACCAAAACATAATGTTAGGTATGATTTCAAAACAAAAAATAATTTGATGACTAAAATGGAACA
1 AAACCAAAACATAATGTTAAGTATGATTTCAAAACAAAAAATAATTGGATGACCAAAATGGAACA
* * **
3230443 AAAATAATAGTTGATGTACTAAATGTGTAGTTTA-CCTAAATATGTAAC-ATGCAATACACCAA
66 AAAATAATAGTCGAGGTACTAAACATGTAGTTTACCCTAAATATGTAACGATG-AAT-CACCAA
3230505 CGTGTTTATG
Statistics
Matches: 103, Mismatches: 22, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
129 2 0.02
130 13 0.13
131 88 0.85
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.28
Consensus pattern (131 bp):
AAACCAAAACATAATGTTAAGTATGATTTCAAAACAAAAAATAATTGGATGACCAAAATGGAACA
AAAATAATAGTCGAGGTACTAAACATGTAGTTTACCCTAAATATGTAACGATGAATCACCAAAAT
G
Found at i:3233539 original size:60 final size:60
Alignment explanation
Indices: 3233461--3233596 Score: 236
Period size: 60 Copynumber: 2.3 Consensus size: 60
3233451 AGTACACAAA
*
3233461 TGGTCCTCCGACTATATTATACTACTTTGTTGATTCTCCTAACTATTAAAAGTTATAAAT
1 TGGTCCTCCGACTATATTATACTACTTTATTGATTCTCCTAACTATTAAAAGTTATAAAT
* *
3233521 TGGTCCTCCGACTCTATTATACTATTTTATTGATTCTCCTAACTATTAAAAGTTATAAAT
1 TGGTCCTCCGACTATATTATACTACTTTATTGATTCTCCTAACTATTAAAAGTTATAAAT
*
3233581 TGGTCCTACGACTATA
1 TGGTCCTCCGACTATA
3233597 GGGAGTTGCT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 71 1.00
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.41
Consensus pattern (60 bp):
TGGTCCTCCGACTATATTATACTACTTTATTGATTCTCCTAACTATTAAAAGTTATAAAT
Found at i:3233594 original size:29 final size:29
Alignment explanation
Indices: 3233502--3233595 Score: 68
Period size: 29 Copynumber: 3.2 Consensus size: 29
3233492 GATTCTCCTA
*
3233502 ACTATTAAAAGTTATAAATTGGTCCTCCG
1 ACTATTAAAAGTTATAAATTGGTCCTACG
** ** *
3233531 ACTCTATTATACTATTTTATTGATT-CTCCTA--
1 A--CTATTA-A--AAGTTATAAATTGGTCCTACG
3233562 ACTATTAAAAGTTATAAATTGGTCCTACG
1 ACTATTAAAAGTTATAAATTGGTCCTACG
3233591 ACTAT
1 ACTAT
3233596 AGGGAGTTGC
Statistics
Matches: 46, Mismatches: 11, Indels: 16
0.63 0.15 0.22
Matches are distributed among these distances:
26 8 0.17
27 5 0.11
28 1 0.02
29 12 0.26
31 7 0.15
32 1 0.02
33 4 0.09
34 8 0.17
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (29 bp):
ACTATTAAAAGTTATAAATTGGTCCTACG
Found at i:3234083 original size:2 final size:2
Alignment explanation
Indices: 3234076--3234107 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3234066 AGAATATTTA
3234076 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
3234108 TATTTATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3234456 original size:20 final size:21
Alignment explanation
Indices: 3234431--3234475 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
3234421 TTGAAAGCAA
3234431 TAAATA-ATTTAAAAAAATAT-
1 TAAATAGA-TTAAAAAAATATG
*
3234451 TAAATAGATTAATAAAATATG
1 TAAATAGATTAAAAAAATATG
3234472 TAAA
1 TAAA
3234476 AATCATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (21 bp):
TAAATAGATTAAAAAAATATG
Found at i:3235589 original size:15 final size:15
Alignment explanation
Indices: 3235560--3235601 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
3235550 TTGGTTTCTT
*
3235560 TATAATTTTAGAAAAA
1 TATATTTTTA-AAAAA
3235576 -ATAGTTTTTAAAAAA
1 TATA-TTTTTAAAAAA
3235591 TATATTTTTAA
1 TATATTTTTAA
3235602 GTGTTTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
15 15 0.65
16 8 0.35
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (15 bp):
TATATTTTTAAAAAA
Found at i:3237355 original size:3 final size:3
Alignment explanation
Indices: 3237347--3237389 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
3237337 TTCTAAAATC
*
3237347 AGA AGA AGA AGA AGA AGA AGA AAA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
3237390 AACCTTCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:3237645 original size:15 final size:15
Alignment explanation
Indices: 3237625--3237665 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
3237615 TTTTTAGTGG
*
3237625 CTATTCATTGGTTGC
1 CTATTCATCGGTTGC
*
3237640 CTATTCGTCGGTTGC
1 CTATTCATCGGTTGC
*
3237655 CTGTTCATCGG
1 CTATTCATCGG
3237666 CTTGAAGCCC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.10, C:0.24, G:0.24, T:0.41
Consensus pattern (15 bp):
CTATTCATCGGTTGC
Found at i:3242996 original size:32 final size:32
Alignment explanation
Indices: 3242955--3243021 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
3242945 TGGCCACTTT
3242955 ATCTAACCAGATTTCTACGCATGACGAGAGGA
1 ATCTAACCAGATTTCTACGCATGACGAGAGGA
3242987 ATCTAACCAGATTTCTACGCATGACGAGAGGA
1 ATCTAACCAGATTTCTACGCATGACGAGAGGA
3243019 ATC
1 ATC
3243022 GTCAATTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.22
Consensus pattern (32 bp):
ATCTAACCAGATTTCTACGCATGACGAGAGGA
Found at i:3246229 original size:15 final size:15
Alignment explanation
Indices: 3246206--3246238 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
3246196 CCCGTATCCG
*
3246206 CCCCGCATCCGCCCA
1 CCCCACATCCGCCCA
3246221 CCCCACATCCGCCCA
1 CCCCACATCCGCCCA
3246236 CCC
1 CCC
3246239 AGCTAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.70, G:0.09, T:0.06
Consensus pattern (15 bp):
CCCCACATCCGCCCA
Found at i:3251959 original size:25 final size:25
Alignment explanation
Indices: 3251928--3251979 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
3251918 GATCGATTGA
*
3251928 TGGTGTTG-GAGTTCCGGTCGGTTGG
1 TGGTGTTGAG-GTTCCGGTCGGTCGG
*
3251953 TGGTGTTGAGGTTTCGGTCGGTCGG
1 TGGTGTTGAGGTTCCGGTCGGTCGG
3251978 TG
1 TG
3251980 ACATTAAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 23 0.96
26 1 0.04
ACGTcount: A:0.04, C:0.12, G:0.48, T:0.37
Consensus pattern (25 bp):
TGGTGTTGAGGTTCCGGTCGGTCGG
Found at i:3257382 original size:2 final size:2
Alignment explanation
Indices: 3257375--3257406 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3257365 TTAGTATTTA
3257375 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
3257407 GGAATATTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3264267 original size:2 final size:2
Alignment explanation
Indices: 3264262--3264287 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3264252 TGTCCTCTAA
3264262 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
3264288 GAATATTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3264853 original size:19 final size:19
Alignment explanation
Indices: 3264829--3264866 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
3264819 ATGGTTAATA
*
3264829 AAAAAGTTAACAATCAACG
1 AAAAAGTCAACAATCAACG
*
3264848 AAAAAGTCAACGATCAACG
1 AAAAAGTCAACAATCAACG
3264867 TTTAAAGTCA
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:0.55, C:0.18, G:0.13, T:0.13
Consensus pattern (19 bp):
AAAAAGTCAACAATCAACG
Found at i:3268994 original size:30 final size:30
Alignment explanation
Indices: 3268953--3269229 Score: 536
Period size: 30 Copynumber: 9.2 Consensus size: 30
3268943 AAGGAACATA
*
3268953 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
3268983 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
3269013 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
3269043 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
3269073 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
3269103 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
3269133 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
*
3269163 TGGATAGTTACCGAGGATCATTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
3269193 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
3269223 TGGATAG
1 TGGATAG
3269230 GTCATTCGGA
Statistics
Matches: 244, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
30 244 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (30 bp):
TGGATAGTTACCGAGGATCTTTATGACCTC
Found at i:3272603 original size:21 final size:21
Alignment explanation
Indices: 3272561--3272603 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
3272551 TTTCTGGGCT
* *
3272561 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
3272582 AGGGGAATCGATTCCCCCTCA
1 AGGGGAATCGATACCCACTCA
3272603 A
1 A
3272604 ACGAATATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:3273522 original size:4 final size:4
Alignment explanation
Indices: 3273513--3273909 Score: 776
Period size: 4 Copynumber: 99.2 Consensus size: 4
3273503 AAATGATGAC
* *
3273513 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGC ATGC ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3273561 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3273609 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3273657 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3273705 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3273753 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3273801 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3273849 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3273897 ATGT ATGT ATGT A
1 ATGT ATGT ATGT A
3273910 ATGGTTATAT
Statistics
Matches: 391, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
4 391 1.00
ACGTcount: A:0.25, C:0.01, G:0.25, T:0.49
Consensus pattern (4 bp):
ATGT
Found at i:3274121 original size:31 final size:30
Alignment explanation
Indices: 3274083--3274178 Score: 79
Period size: 31 Copynumber: 3.1 Consensus size: 30
3274073 GTCGAAGAAC
3274083 TACCTATGTCTTTCGAGACATATGGACAGT
1 TACCTATGTCTTTCGAGACATATGGACAGT
*** *
3274113 ATACCTATGTTCTAAGGA-ACATATGGATAGTT
1 -TACCTATG-TCTTTCGAGACATATGGACAG-T
* * *
3274145 TACCTAGGT-TCTTCGGGACCTATGGACAGT
1 TACCTATGTCT-TTCGAGACATATGGACAGT
3274175 TACC
1 TACC
3274179 GAGGATCTTT
Statistics
Matches: 50, Mismatches: 11, Indels: 9
0.71 0.16 0.13
Matches are distributed among these distances:
29 1 0.02
30 7 0.14
31 36 0.72
32 6 0.12
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (30 bp):
TACCTATGTCTTTCGAGACATATGGACAGT
Found at i:3274195 original size:30 final size:30
Alignment explanation
Indices: 3274161--3274442 Score: 521
Period size: 30 Copynumber: 9.4 Consensus size: 30
3274151 GGTTCTTCGG
* *
3274161 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
3274191 GACCTCTGGATAGTTACCGAGGATCTATAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
3274221 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
3274251 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
3274281 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
3274311 GACCTCCGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
3274341 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
3274371 GACCTCTGGATAGTT-CCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
3274400 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
3274430 GACCTCTGGATAG
1 GACCTCTGGATAG
3274443 GTCATTCGGA
Statistics
Matches: 245, Mismatches: 6, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
29 29 0.12
30 216 0.88
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.32
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:3277818 original size:21 final size:21
Alignment explanation
Indices: 3277776--3277818 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
3277766 TTTCTGGGCT
* *
3277776 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
3277797 AGGGGAATCGATTCCCCCTCA
1 AGGGGAATCGATACCCACTCA
3277818 A
1 A
3277819 ACGAATATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:3279032 original size:30 final size:30
Alignment explanation
Indices: 3278998--3279310 Score: 608
Period size: 30 Copynumber: 10.4 Consensus size: 30
3278988 GGTTCTTCGG
* *
3278998 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
3279028 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
3279058 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
3279088 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
3279118 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
3279148 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
3279178 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
3279208 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
3279238 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
3279268 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
3279298 GACCTCTGGATAG
1 GACCTCTGGATAG
3279311 GTCATTCGGA
Statistics
Matches: 281, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
30 281 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.33
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:3282588 original size:31 final size:31
Alignment explanation
Indices: 3282545--3282614 Score: 131
Period size: 31 Copynumber: 2.2 Consensus size: 31
3282535 TTTCACATCC
3282545 ATATCGATTTTTTAGTAAGGATAAAGTGGATG
1 ATAT-GATTTTTTAGTAAGGATAAAGTGGATG
3282577 ATATGATTTTTTAGTAAGGATAAAGTGGATG
1 ATATGATTTTTTAGTAAGGATAAAGTGGATG
3282608 ATATGAT
1 ATATGAT
3282615 CTTAACAGTC
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 34 0.89
32 4 0.11
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.39
Consensus pattern (31 bp):
ATATGATTTTTTAGTAAGGATAAAGTGGATG
Found at i:3285342 original size:36 final size:36
Alignment explanation
Indices: 3285300--3285375 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
3285290 TTATAGCTAA
*
3285300 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
3285336 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
3285372 AAAA
1 AAAA
3285376 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:3289800 original size:3 final size:3
Alignment explanation
Indices: 3289781--3289819 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
3289771 GTAATAATTT
*
3289781 ATA ATA GTA ATTA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA AT
3289820 TATTATTGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:3307379 original size:15 final size:15
Alignment explanation
Indices: 3307359--3307391 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
3307349 TGAGACATTA
*
3307359 CCCGCCCCGCATCCG
1 CCCGCCCCACATCCG
3307374 CCCGCCCCACATCCG
1 CCCGCCCCACATCCG
3307389 CCC
1 CCC
3307392 ACCCAACTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.09, C:0.70, G:0.15, T:0.06
Consensus pattern (15 bp):
CCCGCCCCACATCCG
Found at i:3310612 original size:31 final size:31
Alignment explanation
Indices: 3310574--3310648 Score: 114
Period size: 31 Copynumber: 2.4 Consensus size: 31
3310564 TCAAACGATC
*
3310574 GGGGACCATATTGCAAACATACTAAATGTTG
1 GGGGACCATATTGCAAACAGACTAAATGTTG
* *
3310605 GGGGACCATTTTACAAACAGACTAAATGTTG
1 GGGGACCATATTGCAAACAGACTAAATGTTG
*
3310636 GGGGACTATATTG
1 GGGGACCATATTG
3310649 TAAGTTTTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (31 bp):
GGGGACCATATTGCAAACAGACTAAATGTTG
Found at i:3310900 original size:26 final size:26
Alignment explanation
Indices: 3310844--3310894 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
3310834 TAGAAGAAAT
3310844 ATTTTCTACGATGTAAATACAATCAG
1 ATTTTCTACGATGTAAATACAATCAG
*
3310870 ATTTTCTACTATGTAAATACAATCA
1 ATTTTCTACGATGTAAATACAATCA
3310895 TTTTTTAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (26 bp):
ATTTTCTACGATGTAAATACAATCAG
Found at i:3313184 original size:29 final size:29
Alignment explanation
Indices: 3313151--3313303 Score: 76
Period size: 29 Copynumber: 5.1 Consensus size: 29
3313141 TATAATTCCA
*
3313151 ATTCTAAATTGATGCTTAAACTTTTGAAC
1 ATTCTAAATTGATACTTAAACTTTTGAAC
** * * *
3313180 ATTCTAGTTTCATACTCAAAC-TATGACTCAC
1 ATTCTAAATTGATACTTAAACTTTTGA---AC
* * *
3313211 ATTCTAAATTGGTCCATAAACTTTTGAAC
1 ATTCTAAATTGATACTTAAACTTTTGAAC
* ** * * * *
3313240 ATTCCAGTTTCATACTCAAAC-TATGACTCTC
1 ATTCTAAATTGATACTTAAACTTTTGA---AC
* *
3313271 ATTCTAAATTGATCCCTAAACTTTTGAAC
1 ATTCTAAATTGATACTTAAACTTTTGAAC
3313300 ATTC
1 ATTC
3313304 CAATAAAATC
Statistics
Matches: 83, Mismatches: 33, Indels: 16
0.63 0.25 0.12
Matches are distributed among these distances:
28 8 0.10
29 36 0.43
31 31 0.37
32 8 0.10
ACGTcount: A:0.33, C:0.22, G:0.08, T:0.38
Consensus pattern (29 bp):
ATTCTAAATTGATACTTAAACTTTTGAAC
Found at i:3313201 original size:60 final size:60
Alignment explanation
Indices: 3313134--3313305 Score: 249
Period size: 60 Copynumber: 2.9 Consensus size: 60
3313124 ATCATACATC
* * * * *
3313134 CTCAAACTATAATTCCAATTCTAAATTGATGCTTAAACTTTTGAACATTCTAGTTTCATA
1 CTCAAACTATGACTCCAATTCTAAATTGATCCATAAACTTTTGAACATTCCAGTTTCATA
*
3313194 CTCAAACTATGACT-CACATTCTAAATTGGTCCATAAACTTTTGAACATTCCAGTTTCATA
1 CTCAAACTATGACTCCA-ATTCTAAATTGATCCATAAACTTTTGAACATTCCAGTTTCATA
*
3313254 CTCAAACTATGACTCTC-ATTCTAAATTGATCCCTAAACTTTTGAACATTCCA
1 CTCAAACTATGACTC-CAATTCTAAATTGATCCATAAACTTTTGAACATTCCA
3313306 ATAAAATCCC
Statistics
Matches: 101, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
59 2 0.02
60 98 0.97
62 1 0.01
ACGTcount: A:0.34, C:0.23, G:0.07, T:0.37
Consensus pattern (60 bp):
CTCAAACTATGACTCCAATTCTAAATTGATCCATAAACTTTTGAACATTCCAGTTTCATA
Found at i:3313214 original size:31 final size:31
Alignment explanation
Indices: 3313178--3313276 Score: 80
Period size: 31 Copynumber: 3.3 Consensus size: 31
3313168 AAACTTTTGA
3313178 ACATTCTAGTTTCATACTCAAACTATGACTC
1 ACATTCTAGTTTCATACTCAAACTATGACTC
** ** * *
3313209 ACATTCTAAATTGGTCCAT-AAACTTTTGA---
1 ACATTCTAGTTTCATAC-TCAAAC-TATGACTC
*
3313238 ACATTCCAGTTTCATACTCAAACTATGACTC
1 ACATTCTAGTTTCATACTCAAACTATGACTC
*
3313269 TCATTCTA
1 ACATTCTA
3313277 AATTGATCCC
Statistics
Matches: 47, Mismatches: 15, Indels: 12
0.64 0.20 0.16
Matches are distributed among these distances:
28 5 0.11
29 15 0.32
31 22 0.47
32 5 0.11
ACGTcount: A:0.32, C:0.24, G:0.07, T:0.36
Consensus pattern (31 bp):
ACATTCTAGTTTCATACTCAAACTATGACTC
Found at i:3313818 original size:26 final size:25
Alignment explanation
Indices: 3313789--3313847 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
3313779 ATGTAAACTC
*
3313789 ATAAAATCAT-TTATCAGTATTCAGAA
1 ATAAAA-CATATTATCAG-ACTCAGAA
* *
3313815 ATAAAACATATTTTCAGACTCAGAT
1 ATAAAACATATTATCAGACTCAGAA
3313840 ATAAAACA
1 ATAAAACA
3313848 AAATACAATC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
25 17 0.59
26 12 0.41
ACGTcount: A:0.49, C:0.14, G:0.07, T:0.31
Consensus pattern (25 bp):
ATAAAACATATTATCAGACTCAGAA
Found at i:3314342 original size:30 final size:30
Alignment explanation
Indices: 3314308--3314389 Score: 85
Period size: 31 Copynumber: 2.7 Consensus size: 30
3314298 GGGTACCTTG
3314308 GGGCCTGC-GAGCCTACCCAAGAAAATCTCA
1 GGGCC-GCAGAGCCTACCCAAGAAAATCTCA
* * * *
3314338 GGGCCACGGAGGCTTACCCAATAAAATCTCA
1 GGGCCGCAGA-GCCTACCCAAGAAAATCTCA
* *
3314369 AGGCCGCAAAGCCTACCCAAG
1 GGGCCGCAGAGCCTACCCAAG
3314390 GGTCGCCTTA
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
29 1 0.02
30 16 0.39
31 24 0.59
ACGTcount: A:0.32, C:0.33, G:0.23, T:0.12
Consensus pattern (30 bp):
GGGCCGCAGAGCCTACCCAAGAAAATCTCA
Found at i:3317088 original size:27 final size:27
Alignment explanation
Indices: 3317051--3317104 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
3317041 GGTGTAAAGA
3317051 TTGTTGCTGGCCAAATGAAATTTGAAG
1 TTGTTGCTGGCCAAATGAAATTTGAAG
3317078 TTGTTGCTGGCCAAATGAAATTTGAAG
1 TTGTTGCTGGCCAAATGAAATTTGAAG
3317105 CCAAAGCCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.11, G:0.26, T:0.33
Consensus pattern (27 bp):
TTGTTGCTGGCCAAATGAAATTTGAAG
Found at i:3317792 original size:60 final size:60
Alignment explanation
Indices: 3317680--3317793 Score: 160
Period size: 60 Copynumber: 1.9 Consensus size: 60
3317670 AAGGATATTA
** *
3317680 CTTTGTTGAGTTTATTGATTATTAAAAGTTACAAAATGATCTCCTGACTATATGGCGTTG
1 CTTTGTTGAGTTTATTGATTATTAAAAGTTACAAAATGATAACATGACTATATGGCGTTG
*
3317740 CTTTGTTGAGTCTTA-TGATTATTAAAAGTTACAAAAT-AGTAACATGATTATATG
1 CTTTGTTGAGT-TTATTGATTATTAAAAGTTACAAAATGA-TAACATGACTATATG
3317794 TTCTAAACTC
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
59 1 0.02
60 44 0.92
61 3 0.06
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.41
Consensus pattern (60 bp):
CTTTGTTGAGTTTATTGATTATTAAAAGTTACAAAATGATAACATGACTATATGGCGTTG
Found at i:3317928 original size:28 final size:28
Alignment explanation
Indices: 3317896--3317952 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
3317886 ATCTTCGTTT
*
3317896 ACATTATGTTGTCGAGCCAGTGCTTGAA
1 ACATTATGTTGGCGAGCCAGTGCTTGAA
* *
3317924 ACATTATGTTGGCGGGTCAGTGCTTGAA
1 ACATTATGTTGGCGAGCCAGTGCTTGAA
3317952 A
1 A
3317953 GAAACGACGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.32
Consensus pattern (28 bp):
ACATTATGTTGGCGAGCCAGTGCTTGAA
Found at i:3318465 original size:2 final size:2
Alignment explanation
Indices: 3318458--3318489 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3318448 AAGAGTTAAG
3318458 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3318490 AATTTGAGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3326969 original size:5 final size:5
Alignment explanation
Indices: 3326959--3326988 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
3326949 GGGGTGTAAA
3326959 CGAGT CGAGT CGAGT CGAGT CGAGT CGAGT
1 CGAGT CGAGT CGAGT CGAGT CGAGT CGAGT
3326989 TTGAGTATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.20, C:0.20, G:0.40, T:0.20
Consensus pattern (5 bp):
CGAGT
Found at i:3328118 original size:24 final size:23
Alignment explanation
Indices: 3328090--3328149 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 23
3328080 TTAAGGGGTC
*
3328090 AAATATAATTAGTCATAAAAAATA
1 AAATATAATTAATCAT-AAAAATA
*
3328114 AAATATAATTAATTATAAAAATA
1 AAATATAATTAATCATAAAAATA
*
3328137 AAGAGATAATTAA
1 AA-ATATAATTAA
3328150 AATTATAATG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
23 9 0.28
24 23 0.72
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (23 bp):
AAATATAATTAATCATAAAAATA
Found at i:3332334 original size:28 final size:28
Alignment explanation
Indices: 3332302--3332374 Score: 146
Period size: 28 Copynumber: 2.6 Consensus size: 28
3332292 ATGGTAAGCC
3332302 CGGGTTGGAAATGGTGAAGGCACTGGCA
1 CGGGTTGGAAATGGTGAAGGCACTGGCA
3332330 CGGGTTGGAAATGGTGAAGGCACTGGCA
1 CGGGTTGGAAATGGTGAAGGCACTGGCA
3332358 CGGGTTGGAAATGGTGA
1 CGGGTTGGAAATGGTGA
3332375 GCTCACGTGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.25, C:0.12, G:0.44, T:0.19
Consensus pattern (28 bp):
CGGGTTGGAAATGGTGAAGGCACTGGCA
Found at i:3333280 original size:53 final size:53
Alignment explanation
Indices: 3333164--3333603 Score: 378
Period size: 53 Copynumber: 8.2 Consensus size: 53
3333154 AAATGGGTTC
* ** * **
3333164 GCTCCCTATTTCTTCAGAGGGTATAAGACTTGA-ATCATCTTCAACAAACTTGTCT
1 GCTCCCTATTTCTTCAGAGAGTATAAGAC-CCACA--ATCTTCAACAATCGCGTCT
* * *
3333219 GCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGTGTCT
1 GCTCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCAACAATCGCGTCT
* * *
3333272 GCTCCCTATTTCTTCAGAGAGTATAAGACTCACAATCTTCATCAATCGCATCT
1 GCTCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCAACAATCGCGTCT
* * *
3333325 GC-CCTCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCT
1 GCTCC-CTATTTCTTCAGAGAGTATAAGAC-C-CACAATCTTCAACAATCGCGTCT
* * * *
3333380 GCCCCCTATTTCTTCAGAGAGTATAAGACCGAACAATCTTCAACTATTGCGTCT
1 GCTCCCTATTTCTTCAGAGAGTATAAGACC-CACAATCTTCAACAATCGCGTCT
* *
3333434 GCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCAACAAT-GGGT-T
1 GCTCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCAACAATCGCGTCT
* * * * * * * * *
3333485 CGTTCCCT-CTTCTCCAGGGAGTATAAAACTCGA-AATCTTTTGAA-AA-CGTGTAT
1 -GCTCCCTATTTCTTCAGAGAGTATAAGAC-CCACAATC--TTCAACAATCGCGTCT
* * * * *
3333538 GTTCCCTATTCCTTCATAGAGTATAAGACCCACAATTTTCAACAAAT-GGGT-T
1 GCTCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCAAC-AATCGCGTCT
3333590 CGCTCCCTATTTCT
1 -GCTCCCTATTTCT
3333604 CTAGGGAGTA
Statistics
Matches: 326, Mismatches: 42, Indels: 36
0.81 0.10 0.09
Matches are distributed among these distances:
51 26 0.08
52 27 0.08
53 144 0.44
54 55 0.17
55 72 0.22
56 2 0.01
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.32
Consensus pattern (53 bp):
GCTCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCAACAATCGCGTCT
Found at i:3333287 original size:108 final size:107
Alignment explanation
Indices: 3333164--3333603 Score: 409
Period size: 108 Copynumber: 4.1 Consensus size: 107
3333154 AAATGGGTTC
*
3333164 GCTCCCTATTTCTTCAGAGGGTATAAGACTTGAATC-ATCTTCAACAAACTTGTCTGCCCCCTAT
1 GCTCCCTATTTCTTCAGAGAGTATAAGAC-TGAA-CAATCTTCAACAAACTTGTCTGCCCCCTAT
* *
3333228 TTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGTGTCT
64 TTCTTCAGAGAGTATAAGACCCACAATCTTCAACAATCGCGTCT
* * * *** *
3333272 GCTCCCTATTTCTTCAGAGAGTATAAGACT-CACAATCTTCATCAATCGCATCTGCCCTCTATTT
1 GCTCCCTATTTCTTCAGAGAGTATAAGACTGAACAATCTTCAACAAACTTGTCTGCCCCCTATTT
* * *
3333336 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCT
66 CTTCAGAGAGTATAAGAC-C-CACAATCTTCAACAATCGCGTCT
* * *
3333380 GCCCCCTATTTCTTCAGAGAGTATAAGACCGAACAATCTTCAAC-TA-TTGCGTCTGCCCCCTAT
1 GCTCCCTATTTCTTCAGAGAGTATAAGACTGAACAATCTTCAACAAACTT--GTCTGCCCCCTAT
*
3333443 TTCTTCAGAGAGTATAAGACCCACAATCTTCAACAAT-GGGT-T
64 TTCTTCAGAGAGTATAAGACCCACAATCTTCAACAATCGCGTCT
* * * * * ** * * **
3333485 CGTTCCCT-CTTCTCCAGGGAGTATAAAACTCG-A-AATCTTTTGA-AAACGTGTATGTTCCCTA
1 -GCTCCCTATTTCTTCAGAGAGTATAAGACT-GAACAATC-TTCAACAAACTTGTCTGCCCCCTA
* * * *
3333546 TTCCTTCATAGAGTATAAGACCCACAATTTTCAACAAAT-GGGT-T
63 TTTCTTCAGAGAGTATAAGACCCACAATCTTCAAC-AATCGCGTCT
3333590 CGCTCCCTATTTCT
1 -GCTCCCTATTTCT
3333604 CTAGGGAGTA
Statistics
Matches: 274, Mismatches: 45, Indels: 28
0.79 0.13 0.08
Matches are distributed among these distances:
104 45 0.16
105 39 0.14
106 57 0.21
107 16 0.06
108 75 0.27
109 42 0.15
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.32
Consensus pattern (107 bp):
GCTCCCTATTTCTTCAGAGAGTATAAGACTGAACAATCTTCAACAAACTTGTCTGCCCCCTATTT
CTTCAGAGAGTATAAGACCCACAATCTTCAACAATCGCGTCT
Found at i:3333351 original size:161 final size:161
Alignment explanation
Indices: 3333169--3333479 Score: 466
Period size: 161 Copynumber: 1.9 Consensus size: 161
3333159 GGTTCGCTCC
* *
3333169 CTATTTCTTCAGAGGGTATAAGACTTGAATC-ATCTTCAACAAACTT-GTCTGCCCCCTATTTCT
1 CTATTTCTTCAGAGAGTATAAGACTCGAA-CAATCTTCAAC-AA-TTCGTCTGCCCCCTATTTCT
* * * *
3333232 TCAGAGAGTATAAGACC-CACAATCTTCATCAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTAT
63 TCAGAGAGTATAAGACCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTAT
* *
3333296 AAGACTCACAATCTTCATCAATCGCATCTGCCCT
128 AAGACCCACAATCTTCAACAATCGCATCTGCCCT
*
3333330 CTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCCCTATTTCTTC
1 CTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATT-CGTCTGCCCCCTATTTCTTC
* *
3333395 AGAGAGTATAAGACCGAACAATCTTCAACTATTGCGTCTGCCCCCTATTTCTTCAGAGAGTATAA
65 AGAGAGTATAAGACCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAA
3333460 GACCCACAATCTTCAACAAT
130 GACCCACAATCTTCAACAAT
3333480 GGGTTCGTTC
Statistics
Matches: 135, Mismatches: 11, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
159 2 0.01
160 2 0.01
161 70 0.52
162 61 0.45
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.31
Consensus pattern (161 bp):
CTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATTCGTCTGCCCCCTATTTCTTCA
GAGAGTATAAGACCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAG
ACCCACAATCTTCAACAATCGCATCTGCCCT
Found at i:3333522 original size:51 final size:50
Alignment explanation
Indices: 3333467--3334023 Score: 262
Period size: 51 Copynumber: 10.8 Consensus size: 50
3333457 TAAGACCCAC
* * **
3333467 AATCTTCAACAATGGGTTCGTTCCCTCTTCTCCAGGGAGTATAAAACTCGA
1 AATCTTCAA-AACGGGTTCGCTCCCTCTTCTTTAGGGAGTATAAAACTCGA
* * * * * ** * *
3333518 AATCTTTTGAAAACGTGTAT-GTTCCCTATTCCTTCATAGAGTATAAGAC-CCA
1 AATC--TTCAAAACGGGT-TCGCTCCCTCTT-CTTTAGGGAGTATAAAACTCGA
* * * * *
3333570 CAATTTTCAACAAATGGGTTCGCTCCCTATTTCTCTAGGGAGTATGAAACTCAGA
1 -AATCTTC-A-AAACGGGTTCGCTCCCT-CTTCTTTAGGGAGTATAAAACTC-GA
* * * *
3333625 CATATTCTTC--AACGGGTTCGCTCCTTCCCTCTTTAAGGAGTATAGAACTCGA
1 -A-A-TCTTCAAAACGGGTTCGCTCCCT-CTTCTTTAGGGAGTATAAAACTCGA
* * *
3333677 ACATCTTC-AAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGA
1 A-ATCTTCAAAACGGGTTCGCTCCCTC-TTCTTTAGGGAGTATAAAACTCGA
* *
3333728 ACATC-TC-AAATGGGTTCGCTCCCT-TTCTTTAGGGAGTATAGAACTCGA
1 A-ATCTTCAAAACGGGTTCGCTCCCTCTTCTTTAGGGAGTATAAAACTCGA
*** * ***
3333776 ACATC-TCTTCAC-GGTTCGCCTCCCTCTTTCTCTAGGGAGTATGGGACTCGA
1 A-ATCTTCAAAACGGGTTCG-CTCCCTC-TTCTTTAGGGAGTATAAAACTCGA
* * * **
3333827 ACATCTTC--AACTGGGTTCGCTCCTTCCCTCTTTAAGGAGTATGGAACTCGA
1 A-ATCTTCAAAAC-GGGTTCGCTCCCT-CTTCTTTAGGGAGTATAAAACTCGA
* * * *
3333878 ACATCTT-TAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGCA
1 A-ATCTTCAAAACGGGTTCGCTCCCTC-TTCTTTAGGGAGTATAAAACTCG-A
* * * **
3333930 TATCTTC-ACACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCAGA
1 AATCTTCAAAACGGGTTCGCTCCCTC-TTCTTTAGGGAGTATAAAACTC-GA
* * * *
3333981 CATCTCTTC-AAACGGGTTCACTCCTTCTTTCTTTAAGGAGTAT
1 -A-ATCTTCAAAACGGGTTCGCTCCCTC-TTCTTTAGGGAGTAT
3334024 GGAACTCAAA
Statistics
Matches: 411, Mismatches: 64, Indels: 60
0.77 0.12 0.11
Matches are distributed among these distances:
48 36 0.09
49 7 0.02
50 26 0.06
51 186 0.45
52 34 0.08
53 111 0.27
54 3 0.01
55 3 0.01
56 1 0.00
57 4 0.01
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (50 bp):
AATCTTCAAAACGGGTTCGCTCCCTCTTCTTTAGGGAGTATAAAACTCGA
Done.