Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 32 of 226
Found at i:14118078 original size:26 final size:26
Alignment explanation
Indices: 14118042--14118094 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
14118032 AAGTTGTCAA
14118042 AATCATAGTAGAATGATGGCCAGTGT
1 AATCATAGTAGAATGATGGCCAGTGT
14118068 AATCATAGTAGAATGATGGCCAGTGT
1 AATCATAGTAGAATGATGGCCAGTGT
14118094 A
1 A
14118095 TCTCTAAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.36, C:0.11, G:0.26, T:0.26
Consensus pattern (26 bp):
AATCATAGTAGAATGATGGCCAGTGT
Found at i:14131317 original size:18 final size:20
Alignment explanation
Indices: 14131285--14131322 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
14131275 GTTAATTTTA
*
14131285 ATTTTTCAATATTATTTAAT
1 ATTTTTCAATATTATGTAAT
14131305 ATTTTTC-AT-TTATGTAAT
1 ATTTTTCAATATTATGTAAT
14131323 TTTAATTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.47
19 2 0.12
20 7 0.41
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.61
Consensus pattern (20 bp):
ATTTTTCAATATTATGTAAT
Found at i:14133193 original size:26 final size:25
Alignment explanation
Indices: 14133158--14133344 Score: 82
Period size: 24 Copynumber: 7.6 Consensus size: 25
14133148 GCAGCTCTTA
*
14133158 TGAGCATCCCGTTATATGGCTCTTCG
1 TGAGCTTCCCGTTA-ATGGCTCTTCG
* * *
14133184 TGAGCTTCCCGATTAAAGACTCTTTG
1 TGAGCTTCCCG-TTAATGGCTCTTCG
* * * *
14133210 TAAGCTTCCCGTTAGT-GCT-TGCT
1 TGAGCTTCCCGTTAATGGCTCTTCG
* * * *
14133233 TGAACTTCCTGTTATATGGCTATCCG
1 TGAGCTTCCCGTTA-ATGGCTCTTCG
* * **
14133259 -GTGCTTCCCATTAATTACTCTTCG
1 TGAGCTTCCCGTTAATGGCTCTTCG
* * * *
14133283 -GAGCTACTCGTTAATTGCTCTTTG
1 TGAGCTTCCCGTTAATGGCTCTTCG
*
14133307 -GAG-TTACCCGTT-ATAGGCTCTTTG
1 TGAGCTT-CCCGTTAAT-GGCTCTTCG
*
14133331 TGAGCTTCCTGTTA
1 TGAGCTTCCCGTTA
14133345 TATTACCGGG
Statistics
Matches: 117, Mismatches: 35, Indels: 18
0.69 0.21 0.11
Matches are distributed among these distances:
23 15 0.13
24 44 0.38
25 23 0.20
26 32 0.27
27 3 0.03
ACGTcount: A:0.17, C:0.24, G:0.20, T:0.39
Consensus pattern (25 bp):
TGAGCTTCCCGTTAATGGCTCTTCG
Found at i:14133826 original size:11 final size:11
Alignment explanation
Indices: 14133810--14133835 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
14133800 ATTTTTTAAA
14133810 TTTTAAAATAT
1 TTTTAAAATAT
14133821 TTTTAAAATAT
1 TTTTAAAATAT
14133832 TTTT
1 TTTT
14133836 TTTATTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:14133856 original size:31 final size:32
Alignment explanation
Indices: 14133819--14133893 Score: 98
Period size: 31 Copynumber: 2.4 Consensus size: 32
14133809 ATTTTAAAAT
*** **
14133819 ATTTTTAAAATATTTTTTTTATTTTTTTTTTA
1 ATTTTTAAAATATTTTTAAAATACTTTTTTTA
14133851 A-TTTTAAAATATTTTTAAAATACTTTTTTTA
1 ATTTTTAAAATATTTTTAAAATACTTTTTTTA
14133882 ATTTTTAAAATA
1 ATTTTTAAAATA
14133894 AATTTTTGGT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 26 0.70
32 11 0.30
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (32 bp):
ATTTTTAAAATATTTTTAAAATACTTTTTTTA
Found at i:14133856 original size:42 final size:42
Alignment explanation
Indices: 14133795--14133887 Score: 150
Period size: 42 Copynumber: 2.2 Consensus size: 42
14133785 ATAATAAATA
*
14133795 TATTTATTTTTTAAATTTTAAAATATTTTTAAAATATTTTTTT
1 TATTT-TTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTT
*
14133838 TATTTTTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTT
1 TATTTTTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTT
*
14133880 TAATTTTT
1 TATTTTTT
14133888 AAAATAAATT
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
42 42 0.89
43 5 0.11
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (42 bp):
TATTTTTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTT
Found at i:14133899 original size:21 final size:21
Alignment explanation
Indices: 14133861--14133900 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
14133851 ATTTTAAAAT
**
14133861 ATTTTTAAAATACTTTTTTTA
1 ATTTTTAAAATAAATTTTTTA
14133882 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
14133901 GGTATTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTTAAAATAAATTTTTTA
Found at i:14133907 original size:22 final size:21
Alignment explanation
Indices: 14133860--14133918 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
14133850 AATTTTAAAA
* *
14133860 TATTTTTAAAAT-ACTTTTTT
1 TATTTTTAAAATAAATTTTTG
14133880 TAATTTTTAAAATAAATTTTTGG
1 T-ATTTTTAAAATAAATTTTT-G
14133903 TATTTATTAAAA-AAAT
1 TATTT-TTAAAATAAAT
14133919 GGGCCGGGCC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 1 0.03
21 11 0.33
22 14 0.42
23 7 0.21
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (21 bp):
TATTTTTAAAATAAATTTTTG
Found at i:14135771 original size:126 final size:126
Alignment explanation
Indices: 14135545--14135816 Score: 350
Period size: 126 Copynumber: 2.2 Consensus size: 126
14135535 TAAGACCAAA
* * * *
14135545 CAGGAACTATTGTAGAAAAAGAGCGTCCACGTGGGAGGTTTTTTCATCAAATTTATTGACAGTGC
1 CAGGAACTACTGTAGAAAAAGAGAGTCCACGTGAGAGGTTTTTTCATCAAATTTACTGACAGTGC
*
14135610 ATCCTGATTGAAGCGTTTTTAACACCATTTGTTCAGAATTGTCTTCTCAAAATTATTTTTT
66 ATCCTGATTGAAGCGTTTTTAACACCATTTGTTCAGAATCGTCTTCTCAAAATTATTTTTT
* * ** * * *
14135671 TAGGAACTACTATAGAAAAAGAGAGTTTACGTGAGAGTTTTTTTCAGT-AATTTTGCTGACAGTG
1 CAGGAACTACTGTAGAAAAAGAGAGTCCACGTGAGAGGTTTTTTCA-TCAAATTTACTGACAGTG
* * * **
14135735 CATCTTGTTTGAAGCGTTTTTTACATTATCTT-TTCAGAATCGTCTTCTCAAAATTATTTTTT
65 CATCCTGATTGAAGCGTTTTTAACACCAT-TTGTTCAGAATCGTCTTCTCAAAATTATTTTTT
*
14135797 CAGAAACTACTGTAGAAAAA
1 CAGGAACTACTGTAGAAAAA
14135817 AACAAAAGTT
Statistics
Matches: 124, Mismatches: 20, Indels: 4
0.84 0.14 0.03
Matches are distributed among these distances:
126 121 0.98
127 3 0.02
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.38
Consensus pattern (126 bp):
CAGGAACTACTGTAGAAAAAGAGAGTCCACGTGAGAGGTTTTTTCATCAAATTTACTGACAGTGC
ATCCTGATTGAAGCGTTTTTAACACCATTTGTTCAGAATCGTCTTCTCAAAATTATTTTTT
Found at i:14135927 original size:34 final size:34
Alignment explanation
Indices: 14135875--14135940 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
14135865 CAAATTTATT
14135875 TTAAAAAAACTAAACCATAATTTAATTAATTTTC
1 TTAAAAAAACTAAACCATAATTTAATTAATTTTC
** * *
14135909 TTAAAAACCCTAATCCATAATTTAATTTATTT
1 TTAAAAAAACTAAACCATAATTTAATTAATTT
14135941 ATTTTAAACC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (34 bp):
TTAAAAAAACTAAACCATAATTTAATTAATTTTC
Found at i:14156031 original size:18 final size:18
Alignment explanation
Indices: 14156010--14156047 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
14156000 TGTTTTAAAG
14156010 ATGTTCTTTTATTAAGTT
1 ATGTTCTTTTATTAAGTT
14156028 ATGTTCTTTTATTAAGTT
1 ATGTTCTTTTATTAAGTT
14156046 AT
1 AT
14156048 TCTTCTTGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.24, C:0.05, G:0.11, T:0.61
Consensus pattern (18 bp):
ATGTTCTTTTATTAAGTT
Found at i:14161056 original size:16 final size:16
Alignment explanation
Indices: 14161018--14161056 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
14161008 TTTAATTTCG
14161018 TGATTTTATTTTATCA
1 TGATTTTATTTTATCA
* *
14161034 TGGTTTTATTTTATCT
1 TGATTTTATTTTATCA
14161050 TGATTTT
1 TGATTTT
14161057 TGTTTTGTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.18, C:0.05, G:0.10, T:0.67
Consensus pattern (16 bp):
TGATTTTATTTTATCA
Found at i:14161358 original size:3 final size:3
Alignment explanation
Indices: 14161350--14161380 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
14161340 GCATTTAATC
14161350 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
14161381 ACATAAAGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:14166695 original size:18 final size:19
Alignment explanation
Indices: 14166655--14166699 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
14166645 ACTTAACTTC
* *
14166655 TTTTTTAAATAGATCTTAT
1 TTTTTTAAATAAATCTTAA
*
14166674 TTTTTTAATTAAAT-TTAA
1 TTTTTTAAATAAATCTTAA
14166692 TTTTTTAA
1 TTTTTTAA
14166700 GCTTATATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (19 bp):
TTTTTTAAATAAATCTTAA
Found at i:14174352 original size:20 final size:18
Alignment explanation
Indices: 14174312--14174364 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 18
14174302 TTTATATTTT
*
14174312 TAAAAAATTATAAAATTTA
1 TAAAAAA-TATAAAATATA
14174331 TAAAAAATATAACGAATATA
1 TAAAAAATATAA--AATATA
*
14174351 TAAAGAAATTTAAA
1 TAAA-AAATATAAA
14174365 TTTTTTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
18 5 0.17
19 8 0.28
20 9 0.31
21 7 0.24
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (18 bp):
TAAAAAATATAAAATATA
Found at i:14178565 original size:74 final size:74
Alignment explanation
Indices: 14178427--14178603 Score: 203
Period size: 74 Copynumber: 2.4 Consensus size: 74
14178417 GTTGACTTTG
* * * * * * * *
14178427 GTTGGAAAATAGAT-AATTAGAAAAATATGAATAATTATGGTACATTTGAAAAGCTAGTGGAACT
1 GTTGGAAAATAAATAAATGAG-AAAACATGAATAATTATGGGACATTTAAAAAACAAGTGCAACT
14178491 AAACTATTTA
65 AAACTATTTA
* * *
14178501 GTTGGAAAATACATAAATGAGAGAACATGAATAATTATGGGGCATTTAAAAAACAAGTGCAACTA
1 GTTGGAAAATAAATAAATGAGAAAACATGAATAATTATGGGACATTTAAAAAACAAGTGCAACTA
*
14178566 AATTATTTA
66 AACTATTTA
* * *
14178575 GTTGAAAAATAAACAAATGGGAAAACATG
1 GTTGGAAAATAAATAAATGAGAAAACATG
14178604 GGTAATTAAA
Statistics
Matches: 86, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
74 81 0.94
75 5 0.06
ACGTcount: A:0.48, C:0.07, G:0.18, T:0.27
Consensus pattern (74 bp):
GTTGGAAAATAAATAAATGAGAAAACATGAATAATTATGGGACATTTAAAAAACAAGTGCAACTA
AACTATTTA
Found at i:14180914 original size:114 final size:114
Alignment explanation
Indices: 14180726--14181625 Score: 1217
Period size: 114 Copynumber: 7.9 Consensus size: 114
14180716 AAAAATAAGC
* * * * * * *
14180726 TTTAGCGGCATTTTTCACAAAGCGCCGCGAAA-AACCTAAGCCCAACGACGCCATATT-CTGAGC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAATAAACTAAACCCAACGACGCCGT-TTCCTGAGC
* *
14180789 TTTCGCAGATTTAGTGGCG-ATTTTAGTAAGCGCCGCTAATGCTCAGTGCT
65 TTTCGCGGATTTAGTGGCGTTTTTTAGTAAGCGCCGCTAATGCTCAG-GCT
*
14180839 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAATAAACTAAACCCAACGACGACGTTTCCTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAATAAACTAAACCCAACGACGCCGTTTCCTGAGCT
* * *
14180904 TTCACGGATTTAGTGACGTTTTTTAGTAAGCGCCGCTAATGCTCAGACT
66 TTCGCGGATTTAGTGGCGTTTTTTAGTAAGCGCCGCTAATGCTCAGGCT
*
14180953 TTTAGCGGCGTTTTTGATAAAGCGCCGCAAAATAAACTAAACCCAACGACGCCGTTTCCTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAATAAACTAAACCCAACGACGCCGTTTCCTGAGCT
14181018 TTCGCGGATTTAGTGGCGTTTTTTAGTAAGCGCCGCTAATGCTCAGGCT
66 TTCGCGGATTTAGTGGCGTTTTTTAGTAAGCGCCGCTAATGCTCAGGCT
14181067 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAATAAACTAAACCCAACGACGCCGTTTCCTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAATAAACTAAACCCAACGACGCCGTTTCCTGAGCT
14181132 TTCGCGGATTTAGTGGCGTTTTTTAGTAAGCGCCGCTAATGCTCAGGCT
66 TTCGCGGATTTAGTGGCGTTTTTTAGTAAGCGCCGCTAATGCTCAGGCT
*
14181181 TTTAGCGGCGTTTTTGATAAAGCGCCGCAAAATAAACTAAACCCAACGACGCCGTTTCCTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAATAAACTAAACCCAACGACGCCGTTTCCTGAGCT
* * *
14181246 TTCGCGGATTTAGTGGCATTTTTTAGCAAGCGCCGCTAATGCTCAGGGCA
66 TTCGCGGATTTAGTGGCGTTTTTTAGTAAGCGCCGCTAATGCTCA-GGCT
* * * * **
14181296 GTT-GCGGCATTTTTTATG-AAGCGCCGCAAAATAAACTAAGCCCAACGACGCCGTTTTTTGAGC
1 TTTAGCGGCGTTTTTGA-GAAAGCGCCGCAAAATAAACTAAACCCAACGACGCCGTTTCCTGAGC
* * * * *
14181359 TTTCGCGGATTTAGCGGCGTTTCTTAATAAAGCGCCGCTAATGATGAGGGC-
65 TTTCGCGGATTTAGTGGCGTTTTTTAGT-AAGCGCCGCTAATGCTCA-GGCT
* * * * *
14181410 TTTAGCAGCGTTTTTGAGGAAGCGCCGCAAAATAAACTAAGCCCAACGACACCGTTTTCTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAATAAACTAAACCCAACGACGCCGTTTCCTGAGCT
* * * *
14181475 TTTGCGGCTTTAGTGGCG-TTTTTAGGGAAGCACCGCTAATGCTCAGGGCT
66 TTCGCGGATTTAGTGGCGTTTTTTA-GTAAGCGCCGCTAATGCTCA-GGCT
* * * * * *
14181525 TTTAGCGGCGTTTGTGAGAAAGTGCCGCAAAA-AGACATAAGCCCAACGATGCCGTTT-TTGAGC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAATAAAC-TAAACCCAACGACGCCGTTTCCTGAGC
* *
14181588 TTTCAGGGGATTTAGCGGCGTTTTTTA-TGAAGCGCCGC
65 TTTC-GCGGATTTAGTGGCGTTTTTTAGT-AAGCGCCGC
14181626 AAAAAAAAAA
Statistics
Matches: 707, Mismatches: 66, Indels: 26
0.88 0.08 0.03
Matches are distributed among these distances:
113 30 0.04
114 485 0.69
115 186 0.26
116 6 0.01
ACGTcount: A:0.25, C:0.23, G:0.24, T:0.28
Consensus pattern (114 bp):
TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAATAAACTAAACCCAACGACGCCGTTTCCTGAGCT
TTCGCGGATTTAGTGGCGTTTTTTAGTAAGCGCCGCTAATGCTCAGGCT
Found at i:14181743 original size:14 final size:14
Alignment explanation
Indices: 14181724--14181750 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
14181714 GAGTATGGGT
14181724 TTAGGGATTATGGA
1 TTAGGGATTATGGA
14181738 TTAGGGATTATGG
1 TTAGGGATTATGG
14181751 TTTAAGGTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.00, G:0.37, T:0.37
Consensus pattern (14 bp):
TTAGGGATTATGGA
Found at i:14181828 original size:36 final size:36
Alignment explanation
Indices: 14181776--14181864 Score: 160
Period size: 36 Copynumber: 2.5 Consensus size: 36
14181766 TTAGAGGGTT
*
14181776 AGGGGTTTAGGGGTTAGACGTTTGGGGTTAAGAGTC
1 AGGGATTTAGGGGTTAGACGTTTGGGGTTAAGAGTC
14181812 AGGGATTTAGGGGTTAGACGTTTGGGGTTAAGAGTC
1 AGGGATTTAGGGGTTAGACGTTTGGGGTTAAGAGTC
*
14181848 AGGGATTTAGGGTTTAG
1 AGGGATTTAGGGGTTAG
14181865 GGATTCAGGG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 51 1.00
ACGTcount: A:0.21, C:0.04, G:0.43, T:0.31
Consensus pattern (36 bp):
AGGGATTTAGGGGTTAGACGTTTGGGGTTAAGAGTC
Found at i:14182057 original size:15 final size:15
Alignment explanation
Indices: 14182037--14182067 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
14182027 CATATTTTAA
14182037 GGTTTAGGGAGTATG
1 GGTTTAGGGAGTATG
*
14182052 GGTTTAGGGATTATG
1 GGTTTAGGGAGTATG
14182067 G
1 G
14182068 ATTAGAGACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.45, T:0.35
Consensus pattern (15 bp):
GGTTTAGGGAGTATG
Found at i:14182111 original size:21 final size:22
Alignment explanation
Indices: 14182081--14182121 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
14182071 AGAGACTATG
14182081 GTTTAAGGGTT-GGGATTTAAA
1 GTTTAAGGGTTAGGGATTTAAA
* *
14182102 GTTTAGGGGTTAGGGGTTTA
1 GTTTAAGGGTTAGGGATTTA
14182122 GGGGTTAGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.22, C:0.00, G:0.39, T:0.39
Consensus pattern (22 bp):
GTTTAAGGGTTAGGGATTTAAA
Found at i:14182547 original size:26 final size:26
Alignment explanation
Indices: 14182510--14182562 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
14182500 GTTTTATATA
14182510 AAAACGCCGCAAAAAATAAATAAATT
1 AAAACGCCGCAAAAAATAAATAAATT
*
14182536 AAAACGCTGCAAAAAATAAATAAATT
1 AAAACGCCGCAAAAAATAAATAAATT
14182562 A
1 A
14182563 TAAAAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.62, C:0.13, G:0.08, T:0.17
Consensus pattern (26 bp):
AAAACGCCGCAAAAAATAAATAAATT
Found at i:14182721 original size:70 final size:70
Alignment explanation
Indices: 14182640--14182783 Score: 270
Period size: 70 Copynumber: 2.1 Consensus size: 70
14182630 TAAAACGCCA
*
14182640 CAAAAAGTAAATCAATTTATAAAAAACAAAATAAAAAATTTTGTGCATAGCAAAACGGCGTCATT
1 CAAAAAATAAATCAATTTATAAAAAACAAAATAAAAAATTTTGTGCATAGCAAAACGGCGTCATT
*
14182705 TTGTT
66 TCGTT
14182710 CAAAAAATAAATCAATTTATAAAAAACAAAATAAAAAATTTTGTGCATAGCAAAACGGCGTCATT
1 CAAAAAATAAATCAATTTATAAAAAACAAAATAAAAAATTTTGTGCATAGCAAAACGGCGTCATT
14182775 TCGTT
66 TCGTT
14182780 CAAA
1 CAAA
14182784 TTGAAATTGC
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 72 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.27
Consensus pattern (70 bp):
CAAAAAATAAATCAATTTATAAAAAACAAAATAAAAAATTTTGTGCATAGCAAAACGGCGTCATT
TCGTT
Found at i:14182859 original size:175 final size:178
Alignment explanation
Indices: 14182562--14182889 Score: 504
Period size: 175 Copynumber: 1.9 Consensus size: 178
14182552 TAAATAAATT
** *
14182562 ATAAAAAATTATTTACATAGCAAAACGGCGCCATTTTTTTATGAAAATGAAATAGCGGCGTTTTT
1 ATAAAAAATTATTTACATAGCAAAACGGCGCCATTTTCGTATCAAAATGAAATAGCGGCGTTTTT
* *
14182627 CATTAAAACGCCACAAAAAGTAAATCAATTTATAAAAAACAAAATAAAAAATTTTGTGCATAGCA
66 CACTAAAACGCCACAAAAAATAAATCAATTTATAAAAAACAAAATAAAAAATTTTGTGCATAGCA
14182692 AAACGGCGTCATTTTGTTCAAAAAATAAATCAATTTATAAAAAACAAA
131 AAACGGCGTCATTTTGTTCAAAAAATAAATCAATTTATAAAAAACAAA
* * * *
14182740 ATAAAAAATT-TTGTGCATAGCAAAACGGCGTCA-TTTCGT-TCAAATTGAAATTGCGGCGTTTT
1 ATAAAAAATTATT-TACATAGCAAAACGGCGCCATTTTCGTATCAAAATGAAATAGCGGCGTTTT
**
14182802 TC-CTACAAACGCTGCAAAAAATAAATCAATTTA-AAAAAACAAAATAAAAAATTTTGTGCATAG
65 TCACTA-AAACGCCACAAAAAATAAATCAATTTATAAAAAACAAAATAAAAAATTTTGTGCATAG
14182865 CAAAACGGCGTCATTTTGTTCAAAA
129 CAAAACGGCGTCATTTTGTTCAAAA
14182890 TGAAATAATA
Statistics
Matches: 137, Mismatches: 11, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
175 57 0.42
176 46 0.34
177 6 0.04
178 28 0.20
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.28
Consensus pattern (178 bp):
ATAAAAAATTATTTACATAGCAAAACGGCGCCATTTTCGTATCAAAATGAAATAGCGGCGTTTTT
CACTAAAACGCCACAAAAAATAAATCAATTTATAAAAAACAAAATAAAAAATTTTGTGCATAGCA
AAACGGCGTCATTTTGTTCAAAAAATAAATCAATTTATAAAAAACAAA
Found at i:14185751 original size:20 final size:20
Alignment explanation
Indices: 14185719--14185769 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
14185709 TACATTTTTA
* *
14185719 ATATATA-TATTAAAAATTT
1 ATATATACTTTTAAAAACTT
*
14185738 ATATATACTTTTAATAACTT
1 ATATATACTTTTAAAAACTT
14185758 ATATATAACTTT
1 ATATAT-ACTTT
14185770 CATAACTTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 7 0.26
20 15 0.56
21 5 0.19
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATATACTTTTAAAAACTT
Found at i:14185774 original size:20 final size:20
Alignment explanation
Indices: 14185736--14185778 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
14185726 TATTAAAAAT
14185736 TTATATATACTTTTAATAAC
1 TTATATATACTTTTAATAAC
*
14185756 TTATATATAAC-TTTCATAAC
1 TTATATAT-ACTTTTAATAAC
14185776 TTA
1 TTA
14185779 CATAATACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 19 0.90
21 2 0.10
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.49
Consensus pattern (20 bp):
TTATATATACTTTTAATAAC
Found at i:14185776 original size:9 final size:9
Alignment explanation
Indices: 14185762--14186495 Score: 80
Period size: 9 Copynumber: 84.9 Consensus size: 9
14185752 TAACTTATAT
*
14185762 ATAACTTTC
1 ATAACTTAC
14185771 ATAACTTAC
1 ATAACTTAC
14185780 ATAA--TAC
1 ATAACTTAC
*
14185787 ATAGCTTAC
1 ATAACTTAC
* *
14185796 ATGACTTGC
1 ATAACTTAC
14185805 ATAA--TAC
1 ATAACTTAC
*
14185812 ACAACTTAC
1 ATAACTTAC
14185821 ATAAC-T--
1 ATAACTTAC
*
14185827 -TAA-TTAA
1 ATAACTTAC
*
14185834 ATAAATTAC
1 ATAACTTAC
14185843 ATAA--TAC
1 ATAACTTAC
*
14185850 ATAACTTTC
1 ATAACTTAC
14185859 ATAACTTAC
1 ATAACTTAC
*
14185868 ATAATAACTTAA
1 ---ATAACTTAC
*
14185880 ATAAATTAC
1 ATAACTTAC
14185889 ATAA--TAC
1 ATAACTTAC
**
14185896 AT-TTTTA-
1 ATAACTTAC
* *
14185903 ATCACTTGTAT
1 ATAAC-T-TAC
* *
14185914 AAAACTTTC
1 ATAACTTAC
14185923 ATAACTTAC
1 ATAACTTAC
14185932 ATAA--TAC
1 ATAACTTAC
* * *
14185939 ATAGCCTGC
1 ATAACTTAC
** *
14185948 ACGACTTGC
1 ATAACTTAC
*
14185957 ATGA--TAC
1 ATAACTTAC
* *
14185964 ACAACTTGC
1 ATAACTTAC
*
14185973 ATAAATTAC
1 ATAACTTAC
14185982 ATAA--TAC
1 ATAACTTAC
**
14185989 AT-TTTTA-
1 ATAACTTAC
*
14185996 ATAACTTATAT
1 ATAAC-T-TAC
*
14186007 ATAACTTTC
1 ATAACTTAC
14186016 ATAACTTAC
1 ATAACTTAC
*
14186025 ATAA-TAAC
1 ATAACTTAC
14186033 ATAATAACTTAC
1 ---ATAACTTAC
14186045 ATAA--TAC
1 ATAACTTAC
* * *
14186052 ATAGCCTAT
1 ATAACTTAC
* *
14186061 ATGACTTGC
1 ATAACTTAC
14186070 ATAA--TAC
1 ATAACTTAC
*
14186077 ACAACTTAC
1 ATAACTTAC
*
14186086 ATAAATTAC
1 ATAACTTAC
14186095 ATAA--TAC
1 ATAACTTAC
*
14186102 ATAACTTTC
1 ATAACTTAC
*
14186111 ATAACTTAT
1 ATAACTTAC
*
14186120 A-AATCATATC
1 ATAA-CTTA-C
14186130 ATAACTTAC
1 ATAACTTAC
14186139 ATAAC-T-C
1 ATAACTTAC
*
14186146 A-AATTTATC
1 ATAACTTA-C
* *
14186155 A-ATCATATC
1 ATAACTTA-C
*
14186164 ATAACTTAT
1 ATAACTTAC
*
14186173 A-AATCATATC
1 ATAA-CTTA-C
14186183 ATAACTTAC
1 ATAACTTAC
14186192 ATAAC-T-C
1 ATAACTTAC
*
14186199 A-AATTTATC
1 ATAACTTA-C
* *
14186208 A-ATCATATC
1 ATAACTTA-C
*
14186217 ATAACTTATAT
1 ATAAC-T-TAC
14186228 ATACACTTAC
1 ATA-ACTTAC
14186238 ATAA--TAC
1 ATAACTTAC
* *
14186245 CTAACTTAAATA
1 ATAACTT--A-C
*
14186257 ATAACCTAC
1 ATAACTTAC
14186266 ATAACTTAC
1 ATAACTTAC
*
14186275 ATAGAAACTTAT
1 AT---AACTTAC
*
14186287 ATAGAAACTTGC
1 AT---AACTTAC
*
14186299 ATAGCTTACC
1 ATAACTTA-C
*
14186309 A-CACTTA-
1 ATAACTTAC
* *
14186316 AAAACTTAG
1 ATAACTTAC
14186325 ATAA--TAC
1 ATAACTTAC
* *
14186332 ATAGCCTAC
1 ATAACTTAC
*
14186341 ATAACTTAT
1 ATAACTTAC
14186350 ATAACTTAC
1 ATAACTTAC
14186359 ATAA--TAC
1 ATAACTTAC
**
14186366 ACCACTTAC
1 ATAACTTAC
14186375 AT-A---A-
1 ATAACTTAC
*
14186379 ATAACTTGC
1 ATAACTTAC
14186388 ATAA--TAC
1 ATAACTTAC
* *
14186395 ATAGCCTAC
1 ATAACTTAC
14186404 ATAACTTAC
1 ATAACTTAC
* *
14186413 TTAACTTGC
1 ATAACTTAC
14186422 ATAA--TAC
1 ATAACTTAC
**
14186429 ACCACTTAC
1 ATAACTTAC
*
14186438 ATAACTTAA
1 ATAACTTAC
14186447 ATAACTTAC
1 ATAACTTAC
14186456 ATAA--TAC
1 ATAACTTAC
*
14186463 TTAACTTTA-
1 ATAAC-TTAC
14186472 ATAA--TAC
1 ATAACTTAC
*
14186479 ACAACTTAC
1 ATAACTTAC
14186488 ATAACTTA
1 ATAACTTA
14186496 ATTACATTAT
Statistics
Matches: 513, Mismatches: 125, Indels: 174
0.63 0.15 0.21
Matches are distributed among these distances:
4 2 0.00
5 6 0.01
6 6 0.01
7 101 0.20
8 23 0.04
9 286 0.56
10 30 0.06
11 21 0.04
12 38 0.07
ACGTcount: A:0.44, C:0.19, G:0.03, T:0.33
Consensus pattern (9 bp):
ATAACTTAC
Found at i:14185808 original size:25 final size:25
Alignment explanation
Indices: 14185764--14185828 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
14185754 ACTTATATAT
* *
14185764 AACTTTCATAACTTACATAATACAT
1 AACTTACATAACTTACATAATACAC
* * *
14185789 AGCTTACATGACTTGCATAATACAC
1 AACTTACATAACTTACATAATACAC
14185814 AACTTACATAACTTA
1 AACTTACATAACTTA
14185829 ATTAAATAAA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.42, C:0.22, G:0.05, T:0.32
Consensus pattern (25 bp):
AACTTACATAACTTACATAATACAC
Found at i:14185876 original size:21 final size:21
Alignment explanation
Indices: 14185850--14185937 Score: 79
Period size: 21 Copynumber: 4.1 Consensus size: 21
14185840 TACATAATAC
*
14185850 ATAACTTTCATAACTTACATA
1 ATAACTTTAATAACTTACATA
* *
14185871 ATAACTTAAATAAATTACATA
1 ATAACTTTAATAACTTACATA
* * **
14185892 ATACATTTTTAATCACTTGTATA
1 ATA-A-CTTTAATAACTTACATA
*
14185915 A-AACTTTCATAACTTACATA
1 ATAACTTTAATAACTTACATA
14185935 ATA
1 ATA
14185938 CATAGCCTGC
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
20 13 0.26
21 23 0.46
22 2 0.04
23 12 0.24
ACGTcount: A:0.45, C:0.15, G:0.01, T:0.39
Consensus pattern (21 bp):
ATAACTTTAATAACTTACATA
Found at i:14185925 original size:152 final size:154
Alignment explanation
Indices: 14185746--14186053 Score: 408
Period size: 152 Copynumber: 2.0 Consensus size: 154
14185736 TTATATATAC
* * *
14185746 TTTTAATAACTTATATATAACTTTCATAACTTACATAATACATAGCTTACATGACTTGCATAATA
1 TTTTAATAACTTATATAAAACTTTCATAACTTACATAATACATAGCCTACACGACTTGCATAATA
* *
14185811 CACAACTTACATAACTTA-AT-TA-A-ATAAATTACATAATACATAACTTTCATAACTTACATAA
66 CACAACTTACATAAATTACATATACATATAAATAAC-TAATACATAACTTTCATAACTTACATAA
*
14185872 TAACTTAAATAAATTACATAATACAT
130 TAACAT-AATAAATTACATAATACAT
* * * *
14185898 TTTTAATCACTTGTATAAAACTTTCATAACTTACATAATACATAGCCTGCACGACTTGCATGATA
1 TTTTAATAACTTATATAAAACTTTCATAACTTACATAATACATAGCCTACACGACTTGCATAATA
* * * * *
14185963 CACAACTTGCATAAATTACATAATACATTTTTAATAACTTATATATAACTTTCATAACTTACATA
66 CACAACTTACATAAATTACAT-ATACA-TATAAATAACTAATACATAACTTTCATAACTTACATA
*
14186028 ATAACATAATAACTTACATAATACAT
129 ATAACATAATAAATTACATAATACAT
14186054 AGCCTATATG
Statistics
Matches: 134, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
152 74 0.55
153 2 0.01
155 2 0.01
156 19 0.14
157 31 0.23
158 6 0.04
ACGTcount: A:0.44, C:0.17, G:0.03, T:0.36
Consensus pattern (154 bp):
TTTTAATAACTTATATAAAACTTTCATAACTTACATAATACATAGCCTACACGACTTGCATAATA
CACAACTTACATAAATTACATATACATATAAATAACTAATACATAACTTTCATAACTTACATAAT
AACATAATAAATTACATAATACAT
Found at i:14185934 original size:43 final size:43
Alignment explanation
Indices: 14185834--14186030 Score: 135
Period size: 43 Copynumber: 4.3 Consensus size: 43
14185824 ACTTAATTAA
* * * ** **
14185834 ATAAATTACATAATACATAACTTTCATAACTTACATAATAACTTAA
1 ATAAATTACATAATACAT--TTTTAATCACTTGTATAA-AACTTTC
14185880 ATAAATTACATAATACATTTTTAATCACTTGTATAAAACTTTC
1 ATAAATTACATAATACATTTTTAATCACTTGTATAAAACTTTC
* ** ** *
14185923 ATAACTTACATAATACATAGCCTGCA-CGACTTGCATGATACACAACTTGC
1 ATAAATTACATAATACAT--TTTTAATC-ACTTG--T-ATA-A-AACTTTC
* * *
14185973 ATAAATTACATAATACATTTTTAATAACTTATATATAACTTTC
1 ATAAATTACATAATACATTTTTAATCACTTGTATAAAACTTTC
*
14186016 ATAACTTACATAATA
1 ATAAATTACATAATA
14186031 ACATAATAAC
Statistics
Matches: 119, Mismatches: 23, Indels: 21
0.73 0.14 0.13
Matches are distributed among these distances:
43 42 0.35
44 14 0.12
45 10 0.08
46 19 0.16
47 1 0.01
48 9 0.08
49 1 0.01
50 23 0.19
ACGTcount: A:0.44, C:0.17, G:0.04, T:0.36
Consensus pattern (43 bp):
ATAAATTACATAATACATTTTTAATCACTTGTATAAAACTTTC
Found at i:14186039 original size:20 final size:20
Alignment explanation
Indices: 14185994--14186054 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
14185984 AATACATTTT
* *
14185994 TAATAACTTATAT-ATAACTT
1 TAATAACTTACATAATAAC-A
*
14186014 TCATAACTTACATAATAACA
1 TAATAACTTACATAATAACA
14186034 TAATAACTTACATAAT-ACA
1 TAATAACTTACATAATAACA
14186053 TA
1 TA
14186055 GCCTATATGA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
19 5 0.14
20 26 0.72
21 5 0.14
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.36
Consensus pattern (20 bp):
TAATAACTTACATAATAACA
Found at i:14186067 original size:113 final size:113
Alignment explanation
Indices: 14185923--14186142 Score: 325
Period size: 113 Copynumber: 1.9 Consensus size: 113
14185913 TAAAACTTTC
* * *
14185923 ATAACTTACATAATACATAGCCTGCACGACTTGCATGATACACAACTTGCATAAATTACATAATA
1 ATAACTTACATAATACATAGCCTACACGACTTGCATAATACACAACTTACATAAATTACATAATA
* * *
14185988 CAT-TTTTAATAACTTATATATAACTTTCATAACTTACATAATAACATA
66 CATACTTTAATAACTTATAAATAA-TATCATAACTTACATAATAACATA
* *
14186036 ATAACTTACATAATACATAGCCTATATGACTTGCATAATACACAACTTACATAAATTACATAATA
1 ATAACTTACATAATACATAGCCTACACGACTTGCATAATACACAACTTACATAAATTACATAATA
* *
14186101 CATAACTTTCATAACTTATAAATCATATCATAACTTACATAA
66 CAT-ACTTTAATAACTTATAAATAATATCATAACTTACATAA
14186143 CTCAAATTTA
Statistics
Matches: 95, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
113 63 0.66
114 16 0.17
115 16 0.17
ACGTcount: A:0.44, C:0.19, G:0.04, T:0.33
Consensus pattern (113 bp):
ATAACTTACATAATACATAGCCTACACGACTTGCATAATACACAACTTACATAAATTACATAATA
CATACTTTAATAACTTATAAATAATATCATAACTTACATAATAACATA
Found at i:14186133 original size:19 final size:19
Alignment explanation
Indices: 14186109--14186226 Score: 94
Period size: 19 Copynumber: 6.6 Consensus size: 19
14186099 TACATAACTT
14186109 TCATAACTTATAAATCATA
1 TCATAACTTATAAATCATA
*
14186128 TCATAAC-T-TACAT-A-A
1 TCATAACTTATAAATCATA
* *
14186143 CTCA-AATTTATCAATCATA
1 -TCATAACTTATAAATCATA
14186162 TCATAACTTATAAATCATA
1 TCATAACTTATAAATCATA
*
14186181 TCATAAC-T-TACAT-A-A
1 TCATAACTTATAAATCATA
* *
14186196 CTCA-AATTTATCAATCATA
1 -TCATAACTTATAAATCATA
14186215 TCATAACTTATA
1 TCATAACTTATA
14186227 TATACACTTA
Statistics
Matches: 75, Mismatches: 12, Indels: 24
0.68 0.11 0.22
Matches are distributed among these distances:
15 6 0.08
16 10 0.13
17 14 0.19
18 10 0.13
19 35 0.47
ACGTcount: A:0.45, C:0.19, G:0.00, T:0.36
Consensus pattern (19 bp):
TCATAACTTATAAATCATA
Found at i:14186139 original size:53 final size:54
Alignment explanation
Indices: 14186079--14186226 Score: 189
Period size: 53 Copynumber: 2.8 Consensus size: 54
14186069 CATAATACAC
* *
14186079 AACTTACATAAATTACATAATACAT-AA-C-TTTCATAACTTATAAATCATATCAT
1 AACTTACATAAACT-CA-AATACATCAATCATATCATAACTTATAAATCATATCAT
**
14186132 AACTTACAT-AACTCAAATTTATCAATCATATCATAACTTATAAATCATATCAT
1 AACTTACATAAACTCAAATACATCAATCATATCATAACTTATAAATCATATCAT
**
14186185 AACTTACAT-AACTCAAATTTATCAATCATATCATAACTTATA
1 AACTTACATAAACTCAAATACATCAATCATATCATAACTTATA
14186227 TATACACTTA
Statistics
Matches: 88, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
50 5 0.06
51 4 0.05
52 4 0.05
53 75 0.85
ACGTcount: A:0.46, C:0.18, G:0.00, T:0.36
Consensus pattern (54 bp):
AACTTACATAAACTCAAATACATCAATCATATCATAACTTATAAATCATATCAT
Found at i:14186250 original size:53 final size:52
Alignment explanation
Indices: 14186109--14186226 Score: 218
Period size: 53 Copynumber: 2.2 Consensus size: 52
14186099 TACATAACTT
14186109 TCATAACTTATAAATCATATCATAACTTACATAACTCAAATTTATCAATCATA
1 TCATAACTTATAAATCATATCATAAC-TACATAACTCAAATTTATCAATCATA
14186162 TCATAACTTATAAATCATATCATAACTTACATAACTCAAATTTATCAATCATA
1 TCATAACTTATAAATCATATCATAAC-TACATAACTCAAATTTATCAATCATA
14186215 TCATAACTTATA
1 TCATAACTTATA
14186227 TATACACTTA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 65 1.00
ACGTcount: A:0.45, C:0.19, G:0.00, T:0.36
Consensus pattern (52 bp):
TCATAACTTATAAATCATATCATAACTACATAACTCAAATTTATCAATCATA
Found at i:14186257 original size:16 final size:17
Alignment explanation
Indices: 14186232--14186264 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
14186222 TTATATATAC
*
14186232 ACTTACATAAT-ACCTA
1 ACTTAAATAATAACCTA
14186248 ACTTAAATAATAACCTA
1 ACTTAAATAATAACCTA
14186265 CATAACTTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.30
Consensus pattern (17 bp):
ACTTAAATAATAACCTA
Found at i:14186283 original size:12 final size:12
Alignment explanation
Indices: 14186268--14186302 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
14186258 TAACCTACAT
14186268 AACTTACATAGA
1 AACTTACATAGA
*
14186280 AACTTATATAGA
1 AACTTACATAGA
*
14186292 AACTTGCATAG
1 AACTTACATAG
14186303 CTTACCACAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.29
Consensus pattern (12 bp):
AACTTACATAGA
Found at i:14186363 original size:34 final size:33
Alignment explanation
Indices: 14186311--14186462 Score: 152
Period size: 34 Copynumber: 4.7 Consensus size: 33
14186301 AGCTTACCAC
*
14186311 ACTTAAA-AACTTAGATAATACATAGCCTACATA
1 ACTTAAATAACTTACATAATACATA-CCTACATA
* *
14186344 ACTTATATAACTTACATAATAC--ACC-AC-TT
1 ACTTAAATAACTTACATAATACATACCTACATA
* *
14186373 ACATAAATAACTTGCATAATACATAGCCTACATA
1 ACTTAAATAACTTACATAATACATA-CCTACATA
** * * *
14186407 ACTTACTTAACTTGCATAATACACCACTTACATA
1 ACTTAAATAACTTACATAATACA-TACCTACATA
14186441 ACTTAAATAACTTACATAATAC
1 ACTTAAATAACTTACATAATAC
14186463 TTAACTTTAA
Statistics
Matches: 97, Mismatches: 15, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
29 20 0.21
30 2 0.02
31 3 0.03
32 3 0.03
33 8 0.08
34 60 0.62
35 1 0.01
ACGTcount: A:0.45, C:0.22, G:0.03, T:0.30
Consensus pattern (33 bp):
ACTTAAATAACTTACATAATACATACCTACATA
Found at i:14186374 original size:16 final size:16
Alignment explanation
Indices: 14186352--14186491 Score: 81
Period size: 16 Copynumber: 8.7 Consensus size: 16
14186342 TAACTTATAT
14186352 AACTTACATAATACAC
1 AACTTACATAATACAC
* *
14186368 CACTTACAT-A-A-AT
1 AACTTACATAATACAC
* *
14186381 AACTTGCATAATACAT
1 AACTTACATAATACAC
* * **
14186397 AGCCTACATAACTTACTT
1 AACTTACATAA--TACAC
*
14186415 AACTTGCATAATACAC
1 AACTTACATAATACAC
* * *
14186431 CACTTACATAACTTAAAT
1 AACTTACATAA--TACAC
**
14186449 AACTTACATAATACTT
1 AACTTACATAATACAC
14186465 AACTTTA-ATAATACAC
1 AAC-TTACATAATACAC
14186481 AACTTACATAA
1 AACTTACATAA
14186492 CTTAATTACA
Statistics
Matches: 93, Mismatches: 22, Indels: 18
0.70 0.17 0.14
Matches are distributed among these distances:
13 8 0.09
14 2 0.02
15 5 0.05
16 50 0.54
17 3 0.03
18 25 0.27
ACGTcount: A:0.45, C:0.22, G:0.02, T:0.31
Consensus pattern (16 bp):
AACTTACATAATACAC
Found at i:14186429 original size:25 final size:25
Alignment explanation
Indices: 14186401--14186496 Score: 88
Period size: 25 Copynumber: 3.8 Consensus size: 25
14186391 ATACATAGCC
* * **
14186401 TACATAACTTACTTAACTTGCATAA
1 TACACAACTTACATAACTTAAATAA
*
14186426 TACACCACTTACATAACTTAAATAA
1 TACACAACTTACATAACTTAAATAA
* * *
14186451 CTTACATAA--TACTTAACTTTAATAA
1 --TACACAACTTACATAACTTAAATAA
14186476 TACACAACTTACATAACTTAA
1 TACACAACTTACATAACTTAA
14186497 TTACATTATA
Statistics
Matches: 55, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
23 6 0.11
25 44 0.80
27 5 0.09
ACGTcount: A:0.45, C:0.21, G:0.01, T:0.33
Consensus pattern (25 bp):
TACACAACTTACATAACTTAAATAA
Found at i:14188262 original size:21 final size:21
Alignment explanation
Indices: 14188236--14188285 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
14188226 CTGCAGCTTA
* *
14188236 AAGCAGATGCGGTAGCGAGAG
1 AAGCAGAGGCGGCAGCGAGAG
* *
14188257 AAGCAGAGGCTGCAGCGAGGG
1 AAGCAGAGGCGGCAGCGAGAG
14188278 AAGCAGAG
1 AAGCAGAG
14188286 CAGCGTAGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.34, C:0.16, G:0.44, T:0.06
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGCGAGAG
Found at i:14188768 original size:42 final size:42
Alignment explanation
Indices: 14188621--14188873 Score: 215
Period size: 43 Copynumber: 5.9 Consensus size: 42
14188611 GCATTTTTAA
** * * * *
14188621 AAAAAGCGCCGCTAAAGGTCCTGGTCTTTAGCGACGATTCCA-
1 AAAAAGCGCCGCTAAAGAACATGATCTTTAGCGGCG-TTTCAG
*
14188663 AAAGAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTGCAA
1 AAA-AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTT-CAG
* * * *
14188707 AAAAAGCGCTGCTAAAGAACATGATCTGTAGCGGTGTTTTAG
1 AAAAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTCAG
* * *
14188749 ACAAAGCGCCGCTAAAGAACATAATCTTTAGCGGCGTTTGAGG
1 AAAAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTCA-G
* * * *
14188792 GATAAGCACCGCTAAAGTACATGA-CTTTTAGCGGCGCTTGT-AG
1 AAAAAGCGCCGCTAAAGAACATGATC-TTTAGCGGCG-TT-TCAG
* * * * *
14188835 GAAATGCGCCGCTAAAGACCCTGACCTTTAGCGGCGTTT
1 AAAAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTT
14188874 TTTTTGTAGC
Statistics
Matches: 174, Mismatches: 29, Indels: 17
0.79 0.13 0.08
Matches are distributed among these distances:
41 1 0.01
42 44 0.25
43 121 0.70
44 7 0.04
45 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.23
Consensus pattern (42 bp):
AAAAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTCAG
Found at i:14188806 original size:85 final size:86
Alignment explanation
Indices: 14188667--14188873 Score: 233
Period size: 85 Copynumber: 2.4 Consensus size: 86
14188657 ATTCCAAAAG
* *
14188667 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTGCAAAAAAAGCGCTGCTAAAGAACATGA-
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTGCAAAAAAAGCACCGCTAAAGAACATGAC
* *
14188731 TCTGTAGCGGTG-TTTTA-GACA
66 T-TGTAGCGGCGCTTGTAGGA-A
* ** * *
14188752 AAGCGCCGCTAAAGAACATAATCTTTAGCGGCGTTTG-AGGGATAAGCACCGCTAAAGTACATGA
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTGCA-AAAAAAGCACCGCTAAAGAACATGA
*
14188816 CTTTTAGCGGCGCTTGTAGGAA
65 CTTGTAGCGGCGCTTGTAGGAA
* * * *
14188838 ATGCGCCGCTAAAGACCCTGACCTTTAGCGGCGTTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTT
14188874 TTTTTGTAGC
Statistics
Matches: 103, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
84 1 0.01
85 63 0.61
86 37 0.36
87 2 0.02
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (86 bp):
AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTGCAAAAAAAGCACCGCTAAAGAACATGAC
TTGTAGCGGCGCTTGTAGGAA
Found at i:14192094 original size:14 final size:14
Alignment explanation
Indices: 14192069--14192102 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
14192059 TTTTAATTAA
14192069 TAAATTTTTTATTT
1 TAAATTTTTTATTT
14192083 TAAATTTTTTATTT
1 TAAATTTTTTATTT
*
14192097 TTAATT
1 TAAATT
14192103 CATCTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TAAATTTTTTATTT
Found at i:14194595 original size:31 final size:30
Alignment explanation
Indices: 14194545--14194652 Score: 90
Period size: 31 Copynumber: 3.5 Consensus size: 30
14194535 TAATCAATCT
** *
14194545 TTTCTAAAAACTTCAAAGAAAAAAATGAAAA
1 TTTCTAAAAA-TTTGAAGAAAAAAATCAAAA
*** *
14194576 TTTCTAAAAATATTGAAGAAGCCTAATTAAAA
1 TTTCTAAAAAT-TTGAAGAA-AAAAATCAAAA
* *
14194608 TTTCATAAAAATTTGAAGAGAAAAATCAAGA
1 TTTC-TAAAAATTTGAAGAAAAAAATCAAAA
*
14194639 TTTCTTAAAATTTG
1 TTTCTAAAAATTTG
14194653 GAGGGACCAA
Statistics
Matches: 61, Mismatches: 13, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
30 10 0.16
31 26 0.43
32 18 0.30
33 7 0.11
ACGTcount: A:0.52, C:0.08, G:0.09, T:0.31
Consensus pattern (30 bp):
TTTCTAAAAATTTGAAGAAAAAAATCAAAA
Found at i:14200012 original size:15 final size:15
Alignment explanation
Indices: 14199994--14200028 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
14199984 AGAAAACAAG
14199994 GAAGAAGAGAAGAAA
1 GAAGAAGAGAAGAAA
*
14200009 GAAGCAGAGAAGAAA
1 GAAGAAGAGAAGAAA
*
14200024 CAAGA
1 GAAGA
14200029 TGCAGGAGAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.63, C:0.06, G:0.31, T:0.00
Consensus pattern (15 bp):
GAAGAAGAGAAGAAA
Found at i:14200046 original size:18 final size:17
Alignment explanation
Indices: 14199999--14200048 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
14199989 ACAAGGAAGA
14199999 AGAGAAGAAAGAAGCAG
1 AGAGAAGAAAGAAGCAG
*
14200016 AGAAGAA-ACAAGATGCAGG
1 AG-AGAAGA-AAGAAGCA-G
14200035 AGAGAAGAAAGAAG
1 AGAGAAGAAAGAAG
14200049 AAGATCAAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
17 3 0.11
18 20 0.74
19 4 0.15
ACGTcount: A:0.58, C:0.06, G:0.34, T:0.02
Consensus pattern (17 bp):
AGAGAAGAAAGAAGCAG
Found at i:14200393 original size:17 final size:17
Alignment explanation
Indices: 14200371--14200405 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
14200361 CAGATACTCT
14200371 ATATAGCAAACCAAAAA
1 ATATAGCAAACCAAAAA
14200388 ATATAGCAAACCAAAAA
1 ATATAGCAAACCAAAAA
14200405 A
1 A
14200406 ATGCCTGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.66, C:0.17, G:0.06, T:0.11
Consensus pattern (17 bp):
ATATAGCAAACCAAAAA
Found at i:14201079 original size:18 final size:18
Alignment explanation
Indices: 14201056--14201092 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
14201046 ATGCTGGAAA
14201056 AATGAGGCTAATTAAGAC
1 AATGAGGCTAATTAAGAC
*
14201074 AATGAGGCTAGTTAAGAC
1 AATGAGGCTAATTAAGAC
14201092 A
1 A
14201093 TGATCGATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.43, C:0.11, G:0.24, T:0.22
Consensus pattern (18 bp):
AATGAGGCTAATTAAGAC
Found at i:14203889 original size:16 final size:18
Alignment explanation
Indices: 14203859--14203892 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
14203849 TGCATATTTG
14203859 TTTTATATTTAAATAATT
1 TTTTATATTTAAATAATT
14203877 TTTTA-ATTT-AATAATT
1 TTTTATATTTAAATAATT
14203893 CTAAATGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTTATATTTAAATAATT
Found at i:14209612 original size:45 final size:46
Alignment explanation
Indices: 14209563--14209660 Score: 171
Period size: 46 Copynumber: 2.2 Consensus size: 46
14209553 AGATAGAAAC
*
14209563 CAAAATATTATCTCTTAAAC-TTAGCATCTAATCTCCTAATTAAAA
1 CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
14209608 CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
1 CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
*
14209654 GAAAATA
1 CAAAATA
14209661 GATATACACA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
45 19 0.38
46 31 0.62
ACGTcount: A:0.44, C:0.19, G:0.03, T:0.34
Consensus pattern (46 bp):
CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
Found at i:14213714 original size:50 final size:50
Alignment explanation
Indices: 14213599--14213791 Score: 296
Period size: 50 Copynumber: 3.8 Consensus size: 50
14213589 GATAATAACA
* ** *
14213599 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* **
14213650 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
14213700 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
14213750 TGCCAATGCCATGTCCCAGACATGGTCTTACACGGGACCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
14213792 TTACCCAAAT
Statistics
Matches: 129, Mismatches: 13, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
50 96 0.74
51 33 0.26
ACGTcount: A:0.20, C:0.32, G:0.23, T:0.25
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:14213907 original size:13 final size:13
Alignment explanation
Indices: 14213886--14213916 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
14213876 GCTTAGATCA
*
14213886 TCATCAAATAAAT
1 TCATAAAATAAAT
14213899 TCATAAAATAAAT
1 TCATAAAATAAAT
14213912 TCATA
1 TCATA
14213917 GTTGCTGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:14216781 original size:45 final size:46
Alignment explanation
Indices: 14216732--14216829 Score: 171
Period size: 46 Copynumber: 2.2 Consensus size: 46
14216722 AGATAGAAAC
*
14216732 CAAAATATTATCTCTTAAAC-TTAGCATCTAATCTCCTAATTAAAA
1 CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
14216777 CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
1 CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
*
14216823 GAAAATA
1 CAAAATA
14216830 GATATACACA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
45 19 0.38
46 31 0.62
ACGTcount: A:0.44, C:0.19, G:0.03, T:0.34
Consensus pattern (46 bp):
CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
Found at i:14224401 original size:22 final size:22
Alignment explanation
Indices: 14224373--14224417 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
14224363 AATTTCCAGT
14224373 AATGATTATGTCATCGACATAG
1 AATGATTATGTCATCGACATAG
14224395 AATGATTATGTCATCGACATAG
1 AATGATTATGTCATCGACATAG
14224417 A
1 A
14224418 CTAAGGCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (22 bp):
AATGATTATGTCATCGACATAG
Found at i:14227987 original size:19 final size:19
Alignment explanation
Indices: 14227965--14228002 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
14227955 ACAGAATACT
*
14227965 AACTAACTACCTCAACTGC
1 AACTAACTACCACAACTGC
*
14227984 AACTAACTATCACAACTGC
1 AACTAACTACCACAACTGC
14228003 TTGCATTCCT
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:0.39, C:0.34, G:0.05, T:0.21
Consensus pattern (19 bp):
AACTAACTACCACAACTGC
Found at i:14240480 original size:5 final size:5
Alignment explanation
Indices: 14240470--14240531 Score: 115
Period size: 5 Copynumber: 12.4 Consensus size: 5
14240460 GACCTTTCAC
*
14240470 TAGTA TAGTA TAGTA TGGTA TAGTA TAGTA TAGTA TAGTA TAGTA TAGTA
1 TAGTA TAGTA TAGTA TAGTA TAGTA TAGTA TAGTA TAGTA TAGTA TAGTA
14240520 TAGTA TAGTA TA
1 TAGTA TAGTA TA
14240532 TGACAACTGA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 55 1.00
ACGTcount: A:0.39, C:0.00, G:0.21, T:0.40
Consensus pattern (5 bp):
TAGTA
Found at i:14242709 original size:2 final size:2
Alignment explanation
Indices: 14242702--14242742 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
14242692 TCTGTTACTA
14242702 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
14242743 TATAACTTCA
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:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:14244229 original size:40 final size:39
Alignment explanation
Indices: 14244174--14244308 Score: 121
Period size: 40 Copynumber: 3.4 Consensus size: 39
14244164 ACCAGTTTGG
* *
14244174 CACCTAGTGCCTCATCGGATAATTTGAAGTAATAAATTGA
1 CACCCAGTGCCTCATCGGATAATTCGAAGT-ATAAATTGA
* * * * *
14244214 CACCTAGTGTCTCATCGGCTAAATCGAAG--TAAATTGG
1 CACCCAGTGCCTCATCGGATAATTCGAAGTATAAATTGA
* * * *
14244251 CACCCAGTACCTCATCGAATTAATCCAAAGTAGTAAATTGA
1 CACCCAGTGCCTCATCGGA-TAATTCGAAGTA-TAAATTGA
*
14244292 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
14244309 ACTCGAAGTC
Statistics
Matches: 75, Mismatches: 16, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
37 21 0.28
38 7 0.09
40 25 0.33
41 22 0.29
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.27
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGGATAATTCGAAGTATAAATTGA
Found at i:14244610 original size:17 final size:17
Alignment explanation
Indices: 14244588--14244621 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
14244578 AATAAAAATT
14244588 ACAACAATTAATAACTA
1 ACAACAATTAATAACTA
14244605 ACAACAATTAATAACTA
1 ACAACAATTAATAACTA
14244622 GCTTCGGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.18, G:0.00, T:0.24
Consensus pattern (17 bp):
ACAACAATTAATAACTA
Found at i:14247624 original size:18 final size:19
Alignment explanation
Indices: 14247584--14247625 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
14247574 TTTTCTTCTT
* *
14247584 TTTTTTTTTTTTACCCATGA
1 TTTTTATTTCTTACCCA-GA
14247604 TTTTTATTTCTTACCCA-A
1 TTTTTATTTCTTACCCAGA
14247622 TTTT
1 TTTT
14247626 CTTTTAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 5 0.25
20 15 0.75
ACGTcount: A:0.17, C:0.17, G:0.02, T:0.64
Consensus pattern (19 bp):
TTTTTATTTCTTACCCAGA
Found at i:14250220 original size:91 final size:92
Alignment explanation
Indices: 14250058--14250224 Score: 210
Period size: 91 Copynumber: 1.8 Consensus size: 92
14250048 ATTTAAGTCC
* * * * * *
14250058 CTTTTTTTTTGTGCATTCAATTGAGCACTTTAACTTTCAAAATGCATCAAAAAGGCCCTCAAACT
1 CTTTTTTTTTGTCCACTCAATTGAGCACTTGAACTTTCAAAATGCATAAAAAAGACCCTCAAAAT
14250123 ACTTCAAAAAAAGCTTAAGGGCCCTTG
66 ACTTCAAAAAAAGCTTAAGGGCCCTTG
* * * * *
14250150 CTTTTTTTTT-TCCACTCAATTGGGCACTTGAACTTTTAACATGTATAAAAAAGACCCTTAAAAT
1 CTTTTTTTTTGTCCACTCAATTGAGCACTTGAACTTTCAAAATGCATAAAAAAGACCCTCAAAAT
**
14250214 TTTTCAAAAAA
66 ACTTCAAAAAA
14250225 GTAATTAAAC
Statistics
Matches: 62, Mismatches: 13, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
91 52 0.84
92 10 0.16
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.35
Consensus pattern (92 bp):
CTTTTTTTTTGTCCACTCAATTGAGCACTTGAACTTTCAAAATGCATAAAAAAGACCCTCAAAAT
ACTTCAAAAAAAGCTTAAGGGCCCTTG
Found at i:14250663 original size:29 final size:29
Alignment explanation
Indices: 14250631--14250686 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
14250621 ATTTCTATGT
*
14250631 ATTTAATAATTTTTTACGATTTTTATAAA
1 ATTTAACAATTTTTTACGATTTTTATAAA
* *
14250660 ATTTTACATTTTTTTACGATTTTTATA
1 ATTTAACAATTTTTTACGATTTTTATA
14250687 TTTTTTTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.32, C:0.05, G:0.04, T:0.59
Consensus pattern (29 bp):
ATTTAACAATTTTTTACGATTTTTATAAA
Found at i:14250706 original size:11 final size:11
Alignment explanation
Indices: 14250688--14250712 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
14250678 ATTTTTATAT
14250688 TTTTTTTCTAA
1 TTTTTTTCTAA
14250699 TTTTTTTCTAA
1 TTTTTTTCTAA
14250710 TTT
1 TTT
14250713 ATAATAATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTTTTCTAA
Found at i:14250978 original size:90 final size:88
Alignment explanation
Indices: 14250807--14250980 Score: 224
Period size: 90 Copynumber: 2.0 Consensus size: 88
14250797 GAATAAAAGC
** *
14250807 AGGGGATTAATTACTTTTTTTGAAAAAGTTTGAGGGTTTTTTGATACATTTTGAAAGTTCAAGTA
1 AGGGGATTAATTACTTTTTTTGAAAAAGTTTGAGACTTTTTTGATACATTTTGAAAATTCAAGTA
*
14250872 CCCAATTGATTACAAAAAAGAGT
66 CCCAATTGAGTACAAAAAAGAGT
* ** * *
14250895 AGGGGATTAATTGCTTTTTTTTGAAATGGTTTGAAGACTTTTTTTATGCATTTTGAAAATTCAAG
1 AGGGGATTAATTAC-TTTTTTTGAAAAAGTTTG-AGACTTTTTTGATACATTTTGAAAATTCAAG
*
14250960 TACCCAAATT-AGTGCAAAAAA
64 TACCC-AATTGAGTACAAAAAA
14250981 AGCATGGCCT
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
88 13 0.18
89 16 0.22
90 40 0.55
91 4 0.05
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.39
Consensus pattern (88 bp):
AGGGGATTAATTACTTTTTTTGAAAAAGTTTGAGACTTTTTTGATACATTTTGAAAATTCAAGTA
CCCAATTGAGTACAAAAAAGAGT
Found at i:14251003 original size:90 final size:89
Alignment explanation
Indices: 14250804--14251005 Score: 212
Period size: 90 Copynumber: 2.3 Consensus size: 89
14250794 TTTGAATAAA
* * ** *
14250804 AGCAGGGGATTAATTAC-TTTTTTTGAAAAAGTTTGAGGGTTTTTTGATACATTTTGAAAGTTCA
1 AGCAGGGCATTAATTGCTTTTTTTTGAAAAAGTTTGAGACTTTTTTGATACATTTTGAAAATTCA
*
14250868 AGTACCCAATTGATTACAAAAAAG
66 AGTACCCAATTGAGTACAAAAAAG
* * ** * *
14250892 AGTAGGGGATTAATTGCTTTTTTTTGAAATGGTTTGAAGACTTTTTTTATGCATTTTGAAAATTC
1 AGCAGGGCATTAATTGCTTTTTTTTGAAAAAGTTTG-AGACTTTTTTGATACATTTTGAAAATTC
*
14250957 AAGTACCCAAATT-AGTGCAAAAAA-
65 AAGTACCC-AATTGAGTACAAAAAAG
* * **
14250981 AGCATGGCCTTAATTTTTTTTTTTT
1 AGCAGGGCATTAATTGCTTTTTTTT
14251006 AAGTTTGAGG
Statistics
Matches: 94, Mismatches: 17, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
88 15 0.16
89 35 0.37
90 40 0.43
91 4 0.04
ACGTcount: A:0.32, C:0.09, G:0.18, T:0.41
Consensus pattern (89 bp):
AGCAGGGCATTAATTGCTTTTTTTTGAAAAAGTTTGAGACTTTTTTGATACATTTTGAAAATTCA
AGTACCCAATTGAGTACAAAAAAG
Found at i:14254122 original size:42 final size:42
Alignment explanation
Indices: 14254069--14254162 Score: 143
Period size: 42 Copynumber: 2.2 Consensus size: 42
14254059 CCGTGTGGCT
* *
14254069 AGGCAGTGTGGCTCACACGGTCAAGAGACACACCCGTGTCTC
1 AGGCCGTGTGGCTCACACGGTCAAGAGACACACCCATGTCTC
**
14254111 AGGCCGTGTGGCTCACACGGTCAAGAGACATGCCCATGTCTC
1 AGGCCGTGTGGCTCACACGGTCAAGAGACACACCCATGTCTC
*
14254153 AGGTCGTGTG
1 AGGCCGTGTG
14254163 AGTATTCGAA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.21, C:0.29, G:0.31, T:0.19
Consensus pattern (42 bp):
AGGCCGTGTGGCTCACACGGTCAAGAGACACACCCATGTCTC
Found at i:14254774 original size:2 final size:2
Alignment explanation
Indices: 14254724--14254758 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
14254714 TTTCCAAACC
14254724 TA TA TA 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 TA TA TA T
14254759 TTAAGTTGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:14255311 original size:42 final size:42
Alignment explanation
Indices: 14255263--14255459 Score: 313
Period size: 42 Copynumber: 4.7 Consensus size: 42
14255253 TCGAAAGCTT
* * *
14255263 AACAGAAGCTCATAAGAGCTTAACAGAAACTCTTAAGAGTTG
1 AACAGAAGCTCGTAAGAGCTGAACAGAAACTCATAAGAGTTG
14255305 AACAGAAGCTCGTAAGAGCTGAACAGAAACTCATAAGAGTTG
1 AACAGAAGCTCGTAAGAGCTGAACAGAAACTCATAAGAGTTG
*
14255347 AACAGAAGCTCGTAAGAGCTGAACAGAAACTCATAAAAGTTG
1 AACAGAAGCTCGTAAGAGCTGAACAGAAACTCATAAGAGTTG
* *
14255389 AACAGAAGCTCGTAAGAGCTGAACAGAAACTCATATGAGTTA
1 AACAGAAGCTCGTAAGAGCTGAACAGAAACTCATAAGAGTTG
* * *
14255431 AATAGAAGCTCGTAAGAGCTAAATAGAAA
1 AACAGAAGCTCGTAAGAGCTGAACAGAAA
14255460 GTAAAACATG
Statistics
Matches: 145, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 145 1.00
ACGTcount: A:0.45, C:0.16, G:0.21, T:0.18
Consensus pattern (42 bp):
AACAGAAGCTCGTAAGAGCTGAACAGAAACTCATAAGAGTTG
Found at i:14255458 original size:21 final size:21
Alignment explanation
Indices: 14255244--14255450 Score: 229
Period size: 21 Copynumber: 10.0 Consensus size: 21
14255234 CTGATACGCC
*
14255244 AACAGAAGCTCG-AA-AGCTT
1 AACAGAAGCTCGTAAGAGCTG
* *
14255263 AACAGAAGCTCATAAGAGCTT
1 AACAGAAGCTCGTAAGAGCTG
* * *
14255284 AACAGAAACTCTTAAGAGTTG
1 AACAGAAGCTCGTAAGAGCTG
14255305 AACAGAAGCTCGTAAGAGCTG
1 AACAGAAGCTCGTAAGAGCTG
* * *
14255326 AACAGAAACTCATAAGAGTTG
1 AACAGAAGCTCGTAAGAGCTG
14255347 AACAGAAGCTCGTAAGAGCTG
1 AACAGAAGCTCGTAAGAGCTG
* * * *
14255368 AACAGAAACTCATAAAAGTTG
1 AACAGAAGCTCGTAAGAGCTG
14255389 AACAGAAGCTCGTAAGAGCTG
1 AACAGAAGCTCGTAAGAGCTG
* * * * *
14255410 AACAGAAACTCATATGAGTTA
1 AACAGAAGCTCGTAAGAGCTG
*
14255431 AATAGAAGCTCGTAAGAGCT
1 AACAGAAGCTCGTAAGAGCT
14255451 AAATAGAAAG
Statistics
Matches: 154, Mismatches: 32, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
19 11 0.07
20 2 0.01
21 141 0.92
ACGTcount: A:0.43, C:0.17, G:0.22, T:0.18
Consensus pattern (21 bp):
AACAGAAGCTCGTAAGAGCTG
Found at i:14276834 original size:18 final size:17
Alignment explanation
Indices: 14276798--14276836 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
14276788 TTTAAAAATT
14276798 TTTAATTTCTTTATATC
1 TTTAATTTCTTTATATC
* *
14276815 TTTAATATTTTTTGTATC
1 TTTAAT-TTCTTTATATC
14276833 TTTA
1 TTTA
14276837 TTCTTGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.23, C:0.08, G:0.03, T:0.67
Consensus pattern (17 bp):
TTTAATTTCTTTATATC
Found at i:14280246 original size:30 final size:31
Alignment explanation
Indices: 14280180--14280249 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 31
14280170 TCCACCCTTA
* * * *
14280180 AAATATTTACACTATTGATCCTTCAACTTTT
1 AAATATTTACACTATTAACCCCTCAAATTTT
*
14280211 -CATATTTACACT-TTAACCCCTCAAATTTT
1 AAATATTTACACTATTAACCCCTCAAATTTT
14280240 AAATATTTAC
1 AAATATTTAC
14280250 TCTTGGGCAA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
29 13 0.41
30 19 0.59
ACGTcount: A:0.34, C:0.21, G:0.01, T:0.43
Consensus pattern (31 bp):
AAATATTTACACTATTAACCCCTCAAATTTT
Found at i:14280758 original size:12 final size:13
Alignment explanation
Indices: 14280728--14280760 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
14280718 TTTTTATCTA
14280728 TAAAAAACAATAT
1 TAAAAAACAATAT
*
14280741 TAAAAAACAATTT
1 TAAAAAACAATAT
14280754 TAAAAAA
1 TAAAAAA
14280761 TGTATCTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.24
Consensus pattern (13 bp):
TAAAAAACAATAT
Found at i:14293178 original size:24 final size:26
Alignment explanation
Indices: 14293109--14293178 Score: 63
Period size: 28 Copynumber: 2.6 Consensus size: 26
14293099 AAAAGAGAAT
14293109 TTATACAAATTAAATTCAAATTAATTAAC
1 TTATA-AAA-TAAA-TCAAATTAATTAAC
* *
14293138 TTCTGAAAAAAATATCAAATTAATT-AC
1 TTAT-AAAATAA-ATCAAATTAATTAAC
14293165 TTAT-AAATAAATCA
1 TTATAAAATAAATCA
14293179 GATAAAAAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
24 4 0.11
25 5 0.14
27 5 0.14
28 13 0.37
29 7 0.20
30 1 0.03
ACGTcount: A:0.53, C:0.10, G:0.01, T:0.36
Consensus pattern (26 bp):
TTATAAAATAAATCAAATTAATTAAC
Found at i:14301801 original size:11 final size:11
Alignment explanation
Indices: 14301785--14301829 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
14301775 TTATACTAAT
14301785 TAAAATAATAA
1 TAAAATAATAA
* *
14301796 TAAAATATCTCAT
1 TAAAATA-AT-AA
14301809 TAAAATAATAA
1 TAAAATAATAA
14301820 TAAAATAATA
1 TAAAATAATA
14301830 TTTATCTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
11 18 0.64
12 2 0.07
13 8 0.29
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.31
Consensus pattern (11 bp):
TAAAATAATAA
Found at i:14301856 original size:27 final size:27
Alignment explanation
Indices: 14301774--14301857 Score: 66
Period size: 27 Copynumber: 3.0 Consensus size: 27
14301764 TCATCTTTTT
*
14301774 TTTATACTAATTAAAATAATAATAAAATA
1 TTTAT-CTAATT-AAATAATTATAAAATA
* * *
14301803 TCTCAT-TAA-AATAATAA-TAAAATAATA
1 T-TTATCTAATTA-AATAATTATAA-AATA
14301830 TTTATCTAATTAAATAATTATAAAATA
1 TTTATCTAATTAAATAATTATAAAATA
14301857 T
1 T
14301858 CATAAAAATA
Statistics
Matches: 42, Mismatches: 7, Indels: 14
0.67 0.11 0.22
Matches are distributed among these distances:
26 7 0.17
27 23 0.55
28 8 0.19
29 1 0.02
30 3 0.07
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (27 bp):
TTTATCTAATTAAATAATTATAAAATA
Found at i:14302326 original size:16 final size:17
Alignment explanation
Indices: 14302299--14302330 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
14302289 AACTATTTAT
14302299 TTAAAGATAATATTTTG
1 TTAAAGATAATATTTTG
14302316 TTAAA-ATAATATTTT
1 TTAAAGATAATATTTT
14302331 CCCTCTATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (17 bp):
TTAAAGATAATATTTTG
Found at i:14309785 original size:51 final size:51
Alignment explanation
Indices: 14309703--14309917 Score: 333
Period size: 51 Copynumber: 4.2 Consensus size: 51
14309693 CGGATCACAT
*
14309703 TTATCACTTGTCATTTATCACTGATCAGATAAGTGCAACTAAAGCTACCAC
1 TTATCACTTGTCACTTATCACTGATCAGATAAGTGCAACTAAAGCTACCAC
* *
14309754 TTGTCACTTGTCACTTATCACTGATCTGATAAGTGCAACTAAAGCTACCAC
1 TTATCACTTGTCACTTATCACTGATCAGATAAGTGCAACTAAAGCTACCAC
* * * *
14309805 TTATTACTTGTCGCTTATCACTGATCAGATAAGTGTAGCTAAA-CTACCAC
1 TTATCACTTGTCACTTATCACTGATCAGATAAGTGCAACTAAAGCTACCAC
* * *
14309855 TTATCACTTGTCACTTATCACTAATCAGATAAGTGTAGCTAAAGCTACCAC
1 TTATCACTTGTCACTTATCACTGATCAGATAAGTGCAACTAAAGCTACCAC
14309906 TTATCACTTGTC
1 TTATCACTTGTC
14309918 GCTGATCAGA
Statistics
Matches: 151, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
50 47 0.31
51 104 0.69
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.33
Consensus pattern (51 bp):
TTATCACTTGTCACTTATCACTGATCAGATAAGTGCAACTAAAGCTACCAC
Found at i:14309886 original size:101 final size:102
Alignment explanation
Indices: 14309703--14309925 Score: 340
Period size: 101 Copynumber: 2.2 Consensus size: 102
14309693 CGGATCACAT
** *
14309703 TTATCACTTGTCATTTATCACTGATCAGATAAGTGCAACTAAAGCTACCACTTGTCACTTGTCAC
1 TTATCACTTGTCGCTTATCACTGATCAGATAAGTGCAACTAAAGCTACCACTTATCACTTGTCAC
* *
14309768 TTATCACTGATCTGATAAGTGCAACTAAAGCTACCAC
66 TTATCACTAATCAGATAAGTGCAACTAAAGCTACCAC
* * *
14309805 TTATTACTTGTCGCTTATCACTGATCAGATAAGTGTAGCTAAA-CTACCACTTATCACTTGTCAC
1 TTATCACTTGTCGCTTATCACTGATCAGATAAGTGCAACTAAAGCTACCACTTATCACTTGTCAC
* *
14309869 TTATCACTAATCAGATAAGTGTAGCTAAAGCTACCAC
66 TTATCACTAATCAGATAAGTGCAACTAAAGCTACCAC
*
14309906 TTATCACTTGTCGCTGATCA
1 TTATCACTTGTCGCTTATCA
14309926 GAAGTACTCA
Statistics
Matches: 109, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
101 71 0.65
102 38 0.35
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.33
Consensus pattern (102 bp):
TTATCACTTGTCGCTTATCACTGATCAGATAAGTGCAACTAAAGCTACCACTTATCACTTGTCAC
TTATCACTAATCAGATAAGTGCAACTAAAGCTACCAC
Found at i:14310021 original size:17 final size:17
Alignment explanation
Indices: 14309999--14310031 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
14309989 TATTATCAAT
14309999 TCATCA-ACAAATATATC
1 TCATCATAC-AATATATC
14310016 TCATCATACAATATAT
1 TCATCATACAATATAT
14310032 AATTCATGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
TCATCATACAATATATC
Found at i:14325987 original size:16 final size:16
Alignment explanation
Indices: 14325946--14325995 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
14325936 TTCACTTATG
14325946 TTTTA-AAAAATGAATAA
1 TTTTATAAAAAT-AAT-A
14325963 TTTT-T-AAAATAATA
1 TTTTATAAAAATAATA
14325977 TTTTATAAAAATAATA
1 TTTTATAAAAATAATA
14325993 TTT
1 TTT
14325996 CATCCAGATA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
14 5 0.17
15 4 0.13
16 17 0.57
17 4 0.13
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (16 bp):
TTTTATAAAAATAATA
Found at i:14328291 original size:2 final size:2
Alignment explanation
Indices: 14328284--14328313 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
14328274 AGGATGTATA
*
14328284 TG TG TG TG TG TG TG TG TG TG TG TG TC TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
14328314 AGTGAGAGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.03, G:0.47, T:0.50
Consensus pattern (2 bp):
TG
Found at i:14337383 original size:31 final size:31
Alignment explanation
Indices: 14337343--14337405 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
14337333 TTATCAGTCT
* *
14337343 AGTGGCTTAAATAAAAAATTTCAAATAGTTC
1 AGTGACTTAAATAAAAAATTTCAAATAATTC
* * *
14337374 AGTGACTTAAATGAAAACTTTCGAATAATTC
1 AGTGACTTAAATAAAAAATTTCAAATAATTC
14337405 A
1 A
14337406 ATGATCATTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.32
Consensus pattern (31 bp):
AGTGACTTAAATAAAAAATTTCAAATAATTC
Found at i:14343439 original size:21 final size:21
Alignment explanation
Indices: 14343415--14343454 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
14343405 AAACAATCAG
14343415 ATAACAACAACAACAATAATA
1 ATAACAACAACAACAATAATA
* *
14343436 ATAATAACAACAACGATAA
1 ATAACAACAACAACAATAA
14343455 AGAAAAAGCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.65, C:0.17, G:0.03, T:0.15
Consensus pattern (21 bp):
ATAACAACAACAACAATAATA
Found at i:14350168 original size:19 final size:19
Alignment explanation
Indices: 14350142--14350187 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
14350132 AAGAACAAAT
14350142 GAGAAAAA-AAAGAGTCTGAC
1 GAGAAAAATAAA-AGT-TGAC
14350162 GAGAAAAATAAAAGTTGAC
1 GAGAAAAATAAAAGTTGAC
*
14350181 TAGAAAA
1 GAGAAAA
14350188 CAATTTTCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 10 0.42
20 11 0.46
21 3 0.12
ACGTcount: A:0.59, C:0.07, G:0.22, T:0.13
Consensus pattern (19 bp):
GAGAAAAATAAAAGTTGAC
Found at i:14353320 original size:21 final size:22
Alignment explanation
Indices: 14353295--14353338 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
14353285 ATCATCTAAC
*
14353295 TATTAAGATTTTCAA-TTTAAT
1 TATTAAAATTTTCAATTTTAAT
*
14353316 TATTAAAATTTTTAATTTTAAT
1 TATTAAAATTTTCAATTTTAAT
14353338 T
1 T
14353339 TTTTTAATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (22 bp):
TATTAAAATTTTCAATTTTAAT
Found at i:14353342 original size:15 final size:16
Alignment explanation
Indices: 14353310--14353347 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
14353300 AGATTTTCAA
14353310 TTTAATTATTAAAATT
1 TTTAATTATTAAAATT
**
14353326 TTTAATT-TTAATTTT
1 TTTAATTATTAAAATT
14353341 TTTAATT
1 TTTAATT
14353348 GCTCTAGTGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTAATTATTAAAATT
Found at i:14358452 original size:3 final size:3
Alignment explanation
Indices: 14358444--14358478 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
14358434 TTAGTCAAGT
14358444 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
14358479 GCATTTTACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:14368872 original size:5 final size:5
Alignment explanation
Indices: 14368862--14368886 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
14368852 ATTGGGGGTT
14368862 GGGAG GGGAG GGGAG GGGAG GGGAG
1 GGGAG GGGAG GGGAG GGGAG GGGAG
14368887 TAAAAGTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.80, T:0.00
Consensus pattern (5 bp):
GGGAG
Found at i:14369382 original size:6 final size:6
Alignment explanation
Indices: 14369371--14369399 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
14369361 ACTTTTAGAC
14369371 TTTAGT TTTAGT TTTAGT TTTAGT TTTAG
1 TTTAGT TTTAGT TTTAGT TTTAGT TTTAG
14369400 AATTTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.66
Consensus pattern (6 bp):
TTTAGT
Found at i:14369423 original size:20 final size:20
Alignment explanation
Indices: 14369355--14369412 Score: 66
Period size: 18 Copynumber: 3.0 Consensus size: 20
14369345 ATTAAATTAT
* *
14369355 TTTTAGACTTTTAGACTTTAG
1 TTTTAGAATTTTAG-TTTTAG
14369376 TTTTAG--TTTTAGTTTTAG
1 TTTTAGAATTTTAGTTTTAG
*
14369394 TTTTAGAATTTTATTTTTA
1 TTTTAGAATTTTAGTTTTA
14369413 TTTATTAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
18 11 0.33
19 6 0.18
20 10 0.30
21 6 0.18
ACGTcount: A:0.22, C:0.03, G:0.12, T:0.62
Consensus pattern (20 bp):
TTTTAGAATTTTAGTTTTAG
Found at i:14369468 original size:18 final size:18
Alignment explanation
Indices: 14369445--14369489 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
14369435 TTATGATTGG
14369445 GTTGGGTTGGGTAATTAA
1 GTTGGGTTGGGTAATTAA
*
14369463 GTTGGGTTGGGTAATTAG
1 GTTGGGTTGGGTAATTAA
14369481 GTTGGGTTG
1 GTTGGGTTG
14369490 AATGCTTGGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.16, C:0.00, G:0.44, T:0.40
Consensus pattern (18 bp):
GTTGGGTTGGGTAATTAA
Found at i:14376272 original size:37 final size:35
Alignment explanation
Indices: 14376231--14376400 Score: 100
Period size: 37 Copynumber: 4.7 Consensus size: 35
14376221 TAGTATTATA
*
14376231 TATTATGATTTTAGTAAATTCATATAAGAATATTGAT
1 TATTATGATTTTAGTAAATT-ATATAA-AATATTAAT
* * *
14376268 TATTAAGAATTTTATTAAATTATAT---ATTTTAAT
1 TATTATG-ATTTTAGTAAATTATATAAAATATTAAT
* * * *
14376301 TATAAT-ATATTTAATAATAATTATGTTAAATTATCT-A-
1 TATTATGAT-TTTAGT-A-AATTAT-ATAAAATAT-TAAT
*
14376338 TATTATGATTTGAGTAAATTCATATAAGAATATTAAT
1 TATTATGATTTTAGTAAATT-ATATAA-AATATTAAT
* *
14376375 TATTAAGAATTTTATTAAATTATATA
1 TATTATG-ATTTTAGTAAATTATATA
14376401 TTTTAATTAT
Statistics
Matches: 100, Mismatches: 18, Indels: 30
0.68 0.12 0.20
Matches are distributed among these distances:
31 2 0.02
32 5 0.05
33 11 0.11
34 6 0.06
35 9 0.09
36 8 0.08
37 30 0.30
38 28 0.28
39 1 0.01
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (35 bp):
TATTATGATTTTAGTAAATTATATAAAATATTAAT
Found at i:14376310 original size:16 final size:16
Alignment explanation
Indices: 14376289--14376334 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
14376279 TTATTAAATT
14376289 ATATATTTTAATTATA
1 ATATATTTTAATTATA
*
14376305 ATATA-TTTAATAATA
1 ATATATTTTAATTATA
*
14376320 AT-TATGTTAAATTAT
1 ATATAT-TTTAATTAT
14376335 CTATATTATG
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
14 2 0.08
15 11 0.44
16 12 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATTATA
Found at i:14376344 original size:107 final size:108
Alignment explanation
Indices: 14376229--14376439 Score: 397
Period size: 107 Copynumber: 2.0 Consensus size: 108
14376219 TATAGTATTA
* *
14376229 TATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTATATA
1 TATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATA
14376294 TTTTAATTATAATATATTTAATAATAATTATG-TTAAATTATC
66 TTTTAATTATAATATATTTAATAATAATTATGTTTAAATTATC
14376336 TATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATA
1 TATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATA
14376401 TTTTAATTATAATATATTTAATAATAATTATGTTTAAAT
66 TTTTAATTATAATATATTTAATAATAATTATGTTTAAAT
14376440 ATGATTAAAT
Statistics
Matches: 101, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
107 95 0.94
108 6 0.06
ACGTcount: A:0.44, C:0.01, G:0.06, T:0.49
Consensus pattern (108 bp):
TATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATA
TTTTAATTATAATATATTTAATAATAATTATGTTTAAATTATC
Found at i:14376417 original size:16 final size:16
Alignment explanation
Indices: 14376396--14376437 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
14376386 TTATTAAATT
*
14376396 ATATATTTTAATTATA
1 ATATATTTTAATAATA
14376412 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
14376427 AT-TATGTTTAA
1 ATATAT-TTTAA
14376438 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:14376422 original size:15 final size:15
Alignment explanation
Indices: 14376387--14376428 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
14376377 TTAAGAATTT
*
14376387 TATTAAATTAT-ATA
1 TATTTAATTATAATA
14376401 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
14376415 TATTTAATAATAAT
1 TATTTAATTATAAT
14376429 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:14376671 original size:16 final size:16
Alignment explanation
Indices: 14376650--14376695 Score: 74
Period size: 16 Copynumber: 2.9 Consensus size: 16
14376640 AGTTGATTTG
*
14376650 CTATTACATCTCTATT
1 CTATTACACCTCTATT
14376666 CTATTACACCTCTATT
1 CTATTACACCTCTATT
*
14376682 CCATTACACCTCTA
1 CTATTACACCTCTA
14376696 ATCCAATACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.26, C:0.33, G:0.00, T:0.41
Consensus pattern (16 bp):
CTATTACACCTCTATT
Found at i:14376700 original size:16 final size:16
Alignment explanation
Indices: 14376652--14376705 Score: 72
Period size: 16 Copynumber: 3.4 Consensus size: 16
14376642 TTGATTTGCT
* *
14376652 ATTACATCTCTATTCT
1 ATTACACCTCTATTCC
14376668 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
*
14376684 ATTACACCTCTAATCC
1 ATTACACCTCTATTCC
*
14376700 AATACA
1 ATTACA
14376706 GCGGACCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.37
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:14376948 original size:3 final size:3
Alignment explanation
Indices: 14376940--14376964 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
14376930 CGGAGACAAG
14376940 GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA G
14376965 GGAAGGCCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:14381230 original size:22 final size:22
Alignment explanation
Indices: 14381203--14381246 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
14381193 TATATATACT
*
14381203 TGTGCATATATAATTATCTTTA
1 TGTGCATATAAAATTATCTTTA
*
14381225 TGTGCATATAAAATTGTCTTTA
1 TGTGCATATAAAATTATCTTTA
14381247 AAATTGTGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.32, C:0.09, G:0.11, T:0.48
Consensus pattern (22 bp):
TGTGCATATAAAATTATCTTTA
Found at i:14402847 original size:30 final size:30
Alignment explanation
Indices: 14402813--14402875 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
14402803 ACTTAACAAG
14402813 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
* *
14402843 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
14402873 CAA
1 CAA
14402876 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.57, C:0.14, G:0.03, T:0.25
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:14410624 original size:16 final size:16
Alignment explanation
Indices: 14410588--14410620 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
14410578 ATGGAAAATG
*
14410588 TTAATTTTATTATAAT
1 TTAAATTTATTATAAT
14410604 TTAAATTTATT-TAAT
1 TTAAATTTATTATAAT
14410619 TT
1 TT
14410621 TAAAAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTAAATTTATTATAAT
Found at i:14421924 original size:27 final size:28
Alignment explanation
Indices: 14421894--14421962 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 28
14421884 GTTAATTATC
14421894 CGAA-TTTGAACCAAATTAACCAATAAT
1 CGAACTTTGAACCAAATTAACCAATAAT
* *
14421921 CGAACTTTGAA--AAA--AATCATTAAT
1 CGAACTTTGAACCAAATTAACCAATAAT
*
14421945 CGAATTTTG-ACCAAATTA
1 CGAACTTTGAACCAAATTA
14421963 GATCTGTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
23 1 0.03
24 16 0.47
25 3 0.09
26 3 0.09
27 5 0.15
28 6 0.18
ACGTcount: A:0.46, C:0.16, G:0.09, T:0.29
Consensus pattern (28 bp):
CGAACTTTGAACCAAATTAACCAATAAT
Found at i:14426066 original size:22 final size:22
Alignment explanation
Indices: 14426039--14426085 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
14426029 TTAATAGCTT
14426039 TTTAGTTTCAGTGCATTTATAG
1 TTTAGTTTCAGTGCATTTATAG
14426061 TTTAGTTTCAGTGCATTTATAG
1 TTTAGTTTCAGTGCATTTATAG
14426083 TTT
1 TTT
14426086 TTCTTACTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.21, C:0.09, G:0.17, T:0.53
Consensus pattern (22 bp):
TTTAGTTTCAGTGCATTTATAG
Found at i:14426571 original size:3 final size:3
Alignment explanation
Indices: 14426563--14426622 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
14426553 ATTGATTACT
14426563 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
14426611 TAA TAA TAA TAA
1 TAA TAA TAA TAA
14426623 GCACTTCTGT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:14428394 original size:26 final size:26
Alignment explanation
Indices: 14428332--14428403 Score: 87
Period size: 26 Copynumber: 2.8 Consensus size: 26
14428322 AAGTTCAAGC
14428332 GAGCCA-ATATCGGGAAGCTC-CGAA
1 GAGCCATATATCGGGAAGCTCACGAA
*
14428356 GAGCTAT-TAATCGGGAAGCTCACGAA
1 GAGCCATAT-ATCGGGAAGCTCACGAA
* *
14428382 GAGCCATATATCGAGACGCTCA
1 GAGCCATATATCGGGAAGCTCA
14428404 TAAGAGCTAC
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
24 6 0.15
25 12 0.30
26 21 0.52
27 1 0.03
ACGTcount: A:0.33, C:0.24, G:0.26, T:0.17
Consensus pattern (26 bp):
GAGCCATATATCGGGAAGCTCACGAA
Found at i:14428540 original size:24 final size:24
Alignment explanation
Indices: 14428495--14428542 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
14428485 CAAGAACCAT
*
14428495 ATAACGGGAAGCTCATGAGAGCTA
1 ATAACGGGAAGCTCATCAGAGCTA
* * *
14428519 ATAACGGGATGCTCTTCCGAGCTA
1 ATAACGGGAAGCTCATCAGAGCTA
14428543 TGGTGTGTCC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.31, C:0.21, G:0.27, T:0.21
Consensus pattern (24 bp):
ATAACGGGAAGCTCATCAGAGCTA
Found at i:14430203 original size:21 final size:20
Alignment explanation
Indices: 14430177--14430232 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 20
14430167 CATGTTTACT
14430177 TTTTGTTTAGCTCTCACGAGC
1 TTTTGTTTAGCTCT-ACGAGC
* * *
14430198 TTTTGTTTAACTCATATGAGT
1 TTTTGTTTAGCTC-TACGAGC
*
14430219 TTTTGTTCAGCTCT
1 TTTTGTTTAGCTCT
14430233 TTTGAGCTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 1 0.03
21 27 0.93
22 1 0.03
ACGTcount: A:0.16, C:0.18, G:0.16, T:0.50
Consensus pattern (20 bp):
TTTTGTTTAGCTCTACGAGC
Found at i:14430249 original size:42 final size:42
Alignment explanation
Indices: 14430203--14430282 Score: 97
Period size: 42 Copynumber: 1.9 Consensus size: 42
14430193 CGAGCTTTTG
* ** * *
14430203 TTTAACTCATATGAGTTTTTGTTCAGCTCTTTTGAGCTACTA
1 TTTAACCCATATGAGTTTCCGTTCAACTCTTATGAGCTACTA
* *
14430245 TTTAACCCTTATGGGTTTCCGTTCAACTCTTATGAGCT
1 TTTAACCCATATGAGTTTCCGTTCAACTCTTATGAGCT
14430283 TCCGTTCAAC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 31 1.00
ACGTcount: A:0.20, C:0.20, G:0.15, T:0.45
Consensus pattern (42 bp):
TTTAACCCATATGAGTTTCCGTTCAACTCTTATGAGCTACTA
Found at i:14430278 original size:21 final size:21
Alignment explanation
Indices: 14430248--14430305 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
14430238 GCTACTATTT
14430248 AACCCTTATGGGTTTCCGTTC
1 AACCCTTATGGGTTTCCGTTC
* * *
14430269 AACTCTTATGAGCTTCCGTTC
1 AACCCTTATGGGTTTCCGTTC
14430290 AACCCTTATGGGTTTC
1 AACCCTTATGGGTTTC
14430306 TGTTTAGCAC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.17, C:0.28, G:0.17, T:0.38
Consensus pattern (21 bp):
AACCCTTATGGGTTTCCGTTC
Found at i:14431774 original size:14 final size:14
Alignment explanation
Indices: 14431755--14431795 Score: 82
Period size: 14 Copynumber: 2.9 Consensus size: 14
14431745 TAGGTGATAT
14431755 GTGTGAAAAATTTC
1 GTGTGAAAAATTTC
14431769 GTGTGAAAAATTTC
1 GTGTGAAAAATTTC
14431783 GTGTGAAAAATTT
1 GTGTGAAAAATTT
14431796 ATTGTTTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.37, C:0.05, G:0.22, T:0.37
Consensus pattern (14 bp):
GTGTGAAAAATTTC
Found at i:14433782 original size:2 final size:2
Alignment explanation
Indices: 14433770--14433806 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
14433760 AATTGTATGG
*
14433770 TA TA GA TA 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 TA TA TA TA T
14433807 GTAACATGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:14440631 original size:16 final size:16
Alignment explanation
Indices: 14440610--14440644 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
14440600 AAAAATATCA
14440610 TCTTTTCTA-TTTTCTT
1 TCTTTT-TATTTTTCTT
14440626 TCTTTTTATTTTTCTT
1 TCTTTTTATTTTTCTT
14440642 TCT
1 TCT
14440645 AACCAATCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 2 0.11
16 16 0.89
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (16 bp):
TCTTTTTATTTTTCTT
Found at i:14445326 original size:3 final size:3
Alignment explanation
Indices: 14445318--14445343 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
14445308 TATACGAACA
14445318 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
14445344 ACGAGGCGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:14447511 original size:32 final size:31
Alignment explanation
Indices: 14447449--14447508 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
14447439 ATCAGAACAA
14447449 GCAAGGCCTGGGAAGGGCGAAGTCAAAAATT
1 GCAAGGCCTGGGAAGGGCGAAGTCAAAAATT
*
14447480 GCAAGGCCTGGGGAAGGGTGAAG-CAAAAA
1 GCAAGGCCT-GGGAAGGGCGAAGTCAAAAA
14447509 ATTTATTGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 15 0.56
32 12 0.44
ACGTcount: A:0.37, C:0.15, G:0.38, T:0.10
Consensus pattern (31 bp):
GCAAGGCCTGGGAAGGGCGAAGTCAAAAATT
Found at i:14458856 original size:52 final size:52
Alignment explanation
Indices: 14458799--14458903 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
14458789 TTTAACCATG
14458799 TAAAACAAAATAATAATGTTAAGTTGTAGTTTTCATATTTTTAATTTAATTT
1 TAAAACAAAATAATAATGTTAAGTTGTAGTTTTCATATTTTTAATTTAATTT
14458851 TAAAACAAAATAATAATGTTAAGTTGTAGTTTTCATATTTTTAATTTAATTT
1 TAAAACAAAATAATAATGTTAAGTTGTAGTTTTCATATTTTTAATTTAATTT
14458903 T
1 T
14458904 GTTAAGTGTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.49
Consensus pattern (52 bp):
TAAAACAAAATAATAATGTTAAGTTGTAGTTTTCATATTTTTAATTTAATTT
Found at i:14460810 original size:18 final size:17
Alignment explanation
Indices: 14460772--14460813 Score: 52
Period size: 15 Copynumber: 2.5 Consensus size: 17
14460762 ATATTTAATA
14460772 TATTATTTTAATTTAAC
1 TATTATTTTAATTTAAC
*
14460789 --TTATTTTAATTATTAC
1 TATTATTTTAATT-TAAC
14460805 TATTATTTT
1 TATTATTTT
14460814 TATCATATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
15 11 0.52
16 3 0.14
18 7 0.33
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (17 bp):
TATTATTTTAATTTAAC
Found at i:14462067 original size:17 final size:17
Alignment explanation
Indices: 14462034--14462067 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
14462024 TTTATAATAC
*
14462034 TTTATATTATGTTATTT
1 TTTATATTATGTAATTT
*
14462051 TTTATATTTTGTAATTT
1 TTTATATTATGTAATTT
14462068 AAAACACATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (17 bp):
TTTATATTATGTAATTT
Done.