Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008959.1 Hibiscus syriacus cultivar Beakdansim tig00112293_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: 4521124
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 21
Found at i:3168727 original size:8 final size:8
Alignment explanation
Indices: 3168714--3168741 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
3168704 TATTATTATT
3168714 TTTTTTTA
1 TTTTTTTA
3168722 TTTTTTTA
1 TTTTTTTA
3168730 TTTTTTTA
1 TTTTTTTA
3168738 TTTT
1 TTTT
3168742 AATATCTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTTTTA
Found at i:3170365 original size:15 final size:15
Alignment explanation
Indices: 3170345--3170374 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3170335 CAGAAAAAGG
3170345 CGCACATCAGGAAGA
1 CGCACATCAGGAAGA
3170360 CGCACATCAGGAAGA
1 CGCACATCAGGAAGA
3170375 ACAAGAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.27, G:0.27, T:0.07
Consensus pattern (15 bp):
CGCACATCAGGAAGA
Found at i:3174556 original size:15 final size:15
Alignment explanation
Indices: 3174526--3174558 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
3174516 TCAAAAAATG
3174526 CAGTGCAAAAAAAAA
1 CAGTGCAAAAAAAAA
*
3174541 CAGTGCAGAAAAAAA
1 CAGTGCAAAAAAAAA
3174556 CAG
1 CAG
3174559 ATTTGGTTCG
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:0.61, C:0.15, G:0.18, T:0.06
Consensus pattern (15 bp):
CAGTGCAAAAAAAAA
Found at i:3174888 original size:3 final size:3
Alignment explanation
Indices: 3174861--3174937 Score: 93
Period size: 3 Copynumber: 26.0 Consensus size: 3
3174851 TTTATTTTTT
* * * * *
3174861 TTA TTT TTA TTT TTA TTA CTA TTA TTA TTA TTT TTA TTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
3174909 TTA TTA TTA TTA ATA TTA TTA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3174938 CAGATATAAC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
2 2 0.03
3 59 0.97
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3176195 original size:20 final size:20
Alignment explanation
Indices: 3176148--3176206 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
3176138 TAATATTTTG
*
3176148 AATTATTATCTTTAGTTTTA-
1 AATT-TTATATTTAGTTTTAT
*
3176168 ATACTTTATATTTAGTTTTAT
1 A-ATTTTATATTTAGTTTTAT
3176189 AATTTTA-ATTTA-TTTTAT
1 AATTTTATATTTAGTTTTAT
3176207 TTTGATCATT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
18 6 0.18
19 5 0.15
20 20 0.59
21 3 0.09
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (20 bp):
AATTTTATATTTAGTTTTAT
Found at i:3177160 original size:19 final size:19
Alignment explanation
Indices: 3177145--3177198 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
3177135 CTTATTATTT
3177145 TTATATTATTTTATTAATA
1 TTATATTATTTTATTAATA
*
3177164 TTATTTTATTTTATTAAGATA
1 TTATATTATTTTATT-A-ATA
3177185 TTA-ATTATTTTATT
1 TTATATTATTTTATT
3177199 TGTCTATTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
19 14 0.45
20 11 0.35
21 6 0.19
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (19 bp):
TTATATTATTTTATTAATA
Found at i:3177164 original size:14 final size:14
Alignment explanation
Indices: 3177147--3177173 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3177137 TATTATTTTT
3177147 ATATTATTTTATTA
1 ATATTATTTTATTA
3177161 ATATTATTTTATT
1 ATATTATTTTATT
3177174 TTATTAAGAT
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
ATATTATTTTATTA
Found at i:3178792 original size:33 final size:34
Alignment explanation
Indices: 3178737--3178801 Score: 105
Period size: 33 Copynumber: 1.9 Consensus size: 34
3178727 GTACTATACA
3178737 ATTTGCATTTTTATTGTTACATTCACATATTTAC
1 ATTTGCATTTTTATTGTTACATTCACATATTTAC
**
3178771 ATTTGCATTTTT-TTGTTACATTTTCATATTT
1 ATTTGCATTTTTATTGTTACATTCACATATTT
3178802 CCATAATTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 17 0.59
34 12 0.41
ACGTcount: A:0.23, C:0.12, G:0.06, T:0.58
Consensus pattern (34 bp):
ATTTGCATTTTTATTGTTACATTCACATATTTAC
Found at i:3181234 original size:90 final size:84
Alignment explanation
Indices: 3181121--3181279 Score: 219
Period size: 84 Copynumber: 1.8 Consensus size: 84
3181111 GATAGCCATG
*
3181121 TTATATTATTATATACAATAAAGCTTGAGTTGTCCCACTAGAGCAAATGGTTAATCACCCCAGCT
1 TTATATTATTATATACAATAAAGC------TGTCCCACTAGAGCAAATGGCTAATCACCCCAGCT
3181186 TTATGGATAATATTCACCCAACCCA
60 TTATGGATAATATTCACCCAACCCA
** * *
3181211 TTATATTATTATATGTAATAAAGCTGTCCCACTAGAGCAAATGGCTAATCGCCCCGGCTTTATGG
1 TTATATTATTATATACAATAAAGCTGTCCCACTAGAGCAAATGGCTAATCACCCCAGCTTTATGG
3181276 ATAA
66 ATAA
3181280 GTTTCAATTA
Statistics
Matches: 64, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
84 42 0.66
90 22 0.34
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.31
Consensus pattern (84 bp):
TTATATTATTATATACAATAAAGCTGTCCCACTAGAGCAAATGGCTAATCACCCCAGCTTTATGG
ATAATATTCACCCAACCCA
Found at i:3183407 original size:114 final size:114
Alignment explanation
Indices: 3183207--3183423 Score: 344
Period size: 114 Copynumber: 1.9 Consensus size: 114
3183197 CATGTTCTCG
* * * * *
3183207 TAGTAGAAATAAGGAGCCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
1 TAGTAGAAATAAGAAGACCCAATAGCATCTTCTAGAAGTATTCTTTGAGTTATCTGATCTGGTTC
* * * *
3183272 GGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATAAATTTGCTCA
66 GGTAGGAACCCCAAAACCAATCAGTGGAATTAAAAGATAAATTTGCTCA
3183321 TAGTAGAAATAAGAAGACCCAATAGCATCTTCTAGAAGTATTCTTTGAGTTATCTGATCTGGTTC
1 TAGTAGAAATAAGAAGACCCAATAGCATCTTCTAGAAGTATTCTTTGAGTTATCTGATCTGGTTC
*
3183386 GGTAGGAACCCCAGAACCAATCAGTGGAATTAAAAGAT
66 GGTAGGAACCCCAAAACCAATCAGTGGAATTAAAAGAT
3183424 GAACTGCATG
Statistics
Matches: 93, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
114 93 1.00
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (114 bp):
TAGTAGAAATAAGAAGACCCAATAGCATCTTCTAGAAGTATTCTTTGAGTTATCTGATCTGGTTC
GGTAGGAACCCCAAAACCAATCAGTGGAATTAAAAGATAAATTTGCTCA
Found at i:3184993 original size:54 final size:54
Alignment explanation
Indices: 3184904--3185059 Score: 233
Period size: 54 Copynumber: 2.9 Consensus size: 54
3184894 AGAAATCTTG
* *
3184904 GCAGAAGCCAC-AGAAAAGGATGAATGTGTTGTCAAATGCTTTACGAACATCTGA
1 GCAGAAACCACAAG-AAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGA
*
3184958 GTAGAAACCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGA
1 GCAGAAACCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGA
* * * *
3185012 GCAGAAGCCACAGGAAAGGATGAATGCGCTGTCAAATGTTTTACGAAC
1 GCAGAAACCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
3185060 CTGCTATTCT
Statistics
Matches: 93, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
54 91 0.98
55 2 0.02
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.22
Consensus pattern (54 bp):
GCAGAAACCACAAGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGA
Found at i:3185457 original size:22 final size:22
Alignment explanation
Indices: 3185426--3185480 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
3185416 ATCTACACTC
*
3185426 TTCAAAGATGATAGATTC-CATT
1 TTCAAAGATGACAGATTCTC-TT
*
3185448 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
3185470 TTCAAAGATGA
1 TTCAAAGATGA
3185481 AAGTTTTATC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 28 0.97
23 1 0.03
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCTCTT
Found at i:3186081 original size:113 final size:111
Alignment explanation
Indices: 3185880--3186208 Score: 480
Period size: 113 Copynumber: 2.9 Consensus size: 111
3185870 TTAGCAAAGT
* * *
3185880 TCAAATTCATCACTCGATGGATCAGCAGTGCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATTCATCACTCGATGGATCAGCATTTCCAG-AAGAGTTCATAATGAGAAGAACTCATCTGA
* *
3185945 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAATTTTTGC
65 AGAA-GAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAATTTTTGC
* * * *
3185993 TCGAATTCATCACTCGATGGATCAACTTTTCCAGAGAGAGTTCATAATGAGAATAACTCATCTGA
1 TCAAATTCATCACTCGATGGATCAGCATTTCCAGA-AGAGTTCATAATGAGAAGAACTCATCTGA
*
3186058 AGAAGAAAGAAGAAATTCATAATGAGAAGAATTTGTTCAATTTTTTGC
65 AGAAG-AAGAAGAAATTCATAATGAGAAGAATTTGTTCAAATTTTTGC
* * *
3186106 TCAAATCCATCACTTGATGGATCAGCATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAA
1 TCAAATTCATCACTCGATGGATCAGCATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAA
*
3186171 GAAGGAGAA-AAAGTTCATAATGAGAAGAATTTGTTCAA
66 GAAGAAGAAGAAA-TTCATAATGAGAAGAATTTGTTCAA
3186209 CCTTGCCTTA
Statistics
Matches: 195, Mismatches: 18, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
110 3 0.02
111 29 0.15
112 33 0.17
113 130 0.67
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (111 bp):
TCAAATTCATCACTCGATGGATCAGCATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAA
GAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAATTTTTGC
Found at i:3186466 original size:79 final size:81
Alignment explanation
Indices: 3186318--3186497 Score: 251
Period size: 79 Copynumber: 2.3 Consensus size: 81
3186308 GAGGAAGAAG
* * ** *
3186318 GAGTTCATAATGAGAAGAACTTGCTTAACCTTTTTCCAGATTACATCACAGAAGGAGATGAATTG
1 GAGTTCATAATGAGAAGAACTTGCTTAACCTTTTTCCAAATTACATCACAAAAGGAGACAAATTA
3186383 TCATCCCCAAT-GAAA
66 TCATCCCCAATGGAAA
* *
3186398 GAGTTCATAATGAGAAGAACTTG-TTAA-CTTTTTGCTAAATTACATTACAAAAGGAGACAAATT
1 GAGTTCATAATGAGAAGAACTTGCTTAACCTTTTT-CCAAATTACATCACAAAAGGAGACAAATT
*
3186461 ATCATCCCCAGTGGAAA
65 ATCATCCCCAATGGAAA
3186478 -AGTTCATAATGAGAAGAACT
1 GAGTTCATAATGAGAAGAACT
3186498 AATCCCAAAG
Statistics
Matches: 90, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
78 6 0.07
79 57 0.63
80 27 0.30
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.28
Consensus pattern (81 bp):
GAGTTCATAATGAGAAGAACTTGCTTAACCTTTTTCCAAATTACATCACAAAAGGAGACAAATTA
TCATCCCCAATGGAAA
Found at i:3186667 original size:3 final size:3
Alignment explanation
Indices: 3186652--3186717 Score: 80
Period size: 3 Copynumber: 22.0 Consensus size: 3
3186642 ATTTGGTTTT
* * * *
3186652 TTA TTA -TA TTTA TTA TTT TTA TTT TTA TTA CTA TTA TTA TTA TTT
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3186697 TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA
3186718 ATTTATTACA
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
2 2 0.04
3 49 0.92
4 2 0.04
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:3186686 original size:21 final size:21
Alignment explanation
Indices: 3186662--3186726 Score: 94
Period size: 21 Copynumber: 3.0 Consensus size: 21
3186652 TTATTATATT
*
3186662 TATTATTTTTATTTTTATTAC
1 TATTATTATTATTTTTATTAC
*
3186683 TATTATTATTATTTTTATTAT
1 TATTATTATTATTTTTATTAC
3186704 TATTATTATTATTAATTTATTAC
1 TATTATTATTATT--TTTATTAC
3186727 AGATACAACC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
21 32 0.82
23 7 0.18
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (21 bp):
TATTATTATTATTTTTATTAC
Found at i:3187988 original size:19 final size:20
Alignment explanation
Indices: 3187936--3187988 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
3187926 TTTTGAATTA
*
3187936 TTATCTTTATTTTTAATACT
1 TTATATTTATTTTTAATACT
3187956 TTATATTTAGTTTTATAAT--T
1 TTATATTTA-TTTT-TAATACT
3187976 TTA-ATTTATTTTT
1 TTATATTTATTTTT
3187989 TGATCATTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
17 1 0.03
18 4 0.13
19 5 0.17
20 12 0.40
21 4 0.13
22 4 0.13
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (20 bp):
TTATATTTATTTTTAATACT
Found at i:3188045 original size:11 final size:11
Alignment explanation
Indices: 3188009--3188039 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
3187999 TTAATTACAA
*
3188009 TATTATTTTGT
1 TATTACTTTGT
3188020 TATTACTTTGT
1 TATTACTTTGT
3188031 TATTACTTT
1 TATTACTTT
3188040 TATATTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.19, C:0.06, G:0.06, T:0.68
Consensus pattern (11 bp):
TATTACTTTGT
Found at i:3190243 original size:76 final size:75
Alignment explanation
Indices: 3190152--3190316 Score: 224
Period size: 76 Copynumber: 2.2 Consensus size: 75
3190142 TTAAACTCAA
*
3190152 ATTTAGGATAATATTTTAAACATTATAT-TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAAT
1 ATTTAGGATATTATTTT-AACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGG-TTTTAAT
3190216 ATTTTAATTAAG
64 ATTTTAATTAAG
* * * * * *
3190228 TTTTAGGATATTATTTTTATATTTTATCTTTATCTTTGTATTTTAGTTTCAATAGGTTTTAGTAT
1 ATTTAGGATATTATTTTAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAATAT
*
3190293 TTTAATTAGG
66 TTTAATTAAG
*
3190303 ATTTAGAATATTAT
1 ATTTAGGATATTAT
3190317 ATTATTTTTT
Statistics
Matches: 78, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
75 36 0.46
76 42 0.54
ACGTcount: A:0.30, C:0.03, G:0.10, T:0.56
Consensus pattern (75 bp):
ATTTAGGATATTATTTTAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAATAT
TTTAATTAAG
Found at i:3190990 original size:22 final size:23
Alignment explanation
Indices: 3190965--3191013 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 23
3190955 CTTTAATTTG
*
3190965 TTTATTTAATTATT-TTTTTTCT
1 TTTATTTAATTATTATTTTTTAT
*
3190987 TTTATTTAATTCTTATTTTTTAT
1 TTTATTTAATTATTATTTTTTAT
3191010 TTTA
1 TTTA
3191014 ACCACAAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 13 0.54
23 11 0.46
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (23 bp):
TTTATTTAATTATTATTTTTTAT
Found at i:3196051 original size:16 final size:16
Alignment explanation
Indices: 3196030--3196062 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3196020 AATAAAATAC
3196030 TAATAATA-GTAATATA
1 TAATAATATGT-ATATA
3196046 TAATAATATGTATATA
1 TAATAATATGTATATA
3196062 T
1 T
3196063 TAAAAACTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.88
17 2 0.12
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (16 bp):
TAATAATATGTATATA
Found at i:3196074 original size:28 final size:28
Alignment explanation
Indices: 3196042--3196096 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
3196032 ATAATAGTAA
3196042 TATATAATA-ATATGTATATATT-AAAAAC
1 TATATAATATATAT-TATAT-TTCAAAAAC
3196070 TATATAATATATATTATATTTCAAAAA
1 TATATAATATATATTATATTTCAAAAA
3196097 AAAATATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 2 0.08
28 19 0.76
29 4 0.16
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.42
Consensus pattern (28 bp):
TATATAATATATATTATATTTCAAAAAC
Found at i:3196097 original size:29 final size:29
Alignment explanation
Indices: 3196040--3196108 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
3196030 TAATAATAGT
3196040 AATATATAATA-ATATGTATATATTAAAA
1 AATATATAATATATATGTATATATTAAAA
*
3196068 ACTATATAATATATAT-TATAT-TTCAAAAA
1 AATATATAATATATATGTATATATT--AAAA
*
3196097 AAAATATAATAT
1 AATATATAATAT
3196109 GTTTTCAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 2 0.06
28 15 0.43
29 18 0.51
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (29 bp):
AATATATAATATATATGTATATATTAAAA
Found at i:3196144 original size:28 final size:28
Alignment explanation
Indices: 3196109--3196163 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
3196099 AATATAATAT
*
3196109 GTTTTCAAAAATTACT-TATATTATATAC
1 GTTTTCAAAAACTA-TATATATTATATAC
3196137 GTTTTCAAAAACTATATATATTATATA
1 GTTTTCAAAAACTATATATATTATATA
3196164 TATTTGAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 1 0.04
28 24 0.96
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.45
Consensus pattern (28 bp):
GTTTTCAAAAACTATATATATTATATAC
Found at i:3196154 original size:2 final size:2
Alignment explanation
Indices: 3196149--3196220 Score: 66
Period size: 2 Copynumber: 38.0 Consensus size: 2
3196139 TTTCAAAAAC
* *
3196149 TA TA TA TA T- TA TA TA TA TT TGA AA T- TA T- TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA
3196189 TA TA TA TA T- TA TCA TA TA TA T- TA TA TA -A TA TA
1 TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA
3196221 AAAAATGTAA
Statistics
Matches: 58, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
1 6 0.10
2 50 0.86
3 2 0.03
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3196161 original size:26 final size:26
Alignment explanation
Indices: 3196100--3196161 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 26
3196090 TCAAAAAAAA
* * *
3196100 ATATAATATGTTTTCAAAAATTACTT
1 ATATTATACGTTTTCAAAAACTACTT
3196126 ATATTATATACGTTTTCAAAAACTA-TAT
1 ATA-T-TATACGTTTTCAAAAACTACT-T
3196154 ATATTATA
1 ATATTATA
3196162 TATATTTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
26 7 0.23
27 3 0.10
28 20 0.67
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (26 bp):
ATATTATACGTTTTCAAAAACTACTT
Found at i:3202540 original size:62 final size:63
Alignment explanation
Indices: 3202474--3202600 Score: 247
Period size: 62 Copynumber: 2.0 Consensus size: 63
3202464 TGAGATTGAA
3202474 GAAAAAAAGTTTTTAAAGGAATTATTGAGATAGAGTTCATAAATAAGTTTTGTAGTG-AATTT
1 GAAAAAAAGTTTTTAAAGGAATTATTGAGATAGAGTTCATAAATAAGTTTTGTAGTGAAATTT
3202536 GAAAAAAAGTTTTTAAAGGAATTATTGAGATAGAGTTCATAAATAAGTTTTGTAGTGAAATTT
1 GAAAAAAAGTTTTTAAAGGAATTATTGAGATAGAGTTCATAAATAAGTTTTGTAGTGAAATTT
3202599 GA
1 GA
3202601 CTTGCCATTA
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
62 57 0.89
63 7 0.11
ACGTcount: A:0.43, C:0.02, G:0.20, T:0.36
Consensus pattern (63 bp):
GAAAAAAAGTTTTTAAAGGAATTATTGAGATAGAGTTCATAAATAAGTTTTGTAGTGAAATTT
Found at i:3204471 original size:29 final size:30
Alignment explanation
Indices: 3204432--3204488 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
3204422 ACATTATCAA
* *
3204432 CTATGTCCTTCGGGATATATGGA-AGGTAC
1 CTATGTCCTTCGGAACATATGGATAGGTAC
*
3204461 CTATGTTCTTCGGAACATATGGATAGGT
1 CTATGTCCTTCGGAACATATGGATAGGT
3204489 CCTTCGGGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 20 0.83
30 4 0.17
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33
Consensus pattern (30 bp):
CTATGTCCTTCGGAACATATGGATAGGTAC
Found at i:3207895 original size:21 final size:20
Alignment explanation
Indices: 3207868--3207943 Score: 82
Period size: 21 Copynumber: 3.6 Consensus size: 20
3207858 GGATGCATGG
3207868 GGTATCGATACCTAT-AAGA
1 GGTATCGATACCTATGAAGA
3207887 GCAGTATCGATACCATATGGAAGA
1 G--GTATCGATACC-TAT-GAAGA
**
3207911 GGTATCGATACCTATGTGGAA
1 GGTATCGATACCTATGAAG-A
3207932 GGTATCGATACC
1 GGTATCGATACC
3207944 CGAGGGAATT
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
19 1 0.02
20 2 0.04
21 27 0.55
22 14 0.29
24 5 0.10
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (20 bp):
GGTATCGATACCTATGAAGA
Found at i:3209991 original size:21 final size:20
Alignment explanation
Indices: 3209964--3210039 Score: 82
Period size: 21 Copynumber: 3.6 Consensus size: 20
3209954 GGATGCATGG
3209964 GGTATCGATACCTAT-AAGA
1 GGTATCGATACCTATGAAGA
3209983 GTAGTATCGATACCATATGGAAGA
1 G--GTATCGATACC-TAT-GAAGA
**
3210007 GGTATCGATACCTATGTGGAA
1 GGTATCGATACCTATGAAG-A
3210028 GGTATCGATACC
1 GGTATCGATACC
3210040 CGAGGGAATT
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
19 1 0.02
20 2 0.04
21 27 0.55
22 14 0.29
24 5 0.10
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (20 bp):
GGTATCGATACCTATGAAGA
Found at i:3210503 original size:18 final size:20
Alignment explanation
Indices: 3210444--3210503 Score: 58
Period size: 18 Copynumber: 3.2 Consensus size: 20
3210434 TGTTATGATT
3210444 TATATGTGTG-CATGA-A-TG
1 TATATGT-TGACATGATATTG
* *
3210462 TATATGTTGACATGCTATTA
1 TATATGTTGACATGATATTG
3210482 TATATGTT-ACATGAT-TTG
1 TATATGTTGACATGATATTG
3210500 TATA
1 TATA
3210504 AGTACATGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
17 2 0.06
18 17 0.49
19 7 0.20
20 9 0.26
ACGTcount: A:0.30, C:0.07, G:0.18, T:0.45
Consensus pattern (20 bp):
TATATGTTGACATGATATTG
Found at i:3211509 original size:32 final size:29
Alignment explanation
Indices: 3211454--3211541 Score: 86
Period size: 32 Copynumber: 2.9 Consensus size: 29
3211444 AGTCGAGGGT
*
3211454 TACCTATGTCTTTCGAGACATATGGACAGTA
1 TACCTATGT-TTTCGGGACATATGGACAG-A
* * *
3211485 TCACCTATGTTATTCGGGATATATGGATAGG
1 T-ACCTATGTT-TTCGGGACATATGGACAGA
*
3211516 TACCTATGTTCTTCGGAACATATGGA
1 TACCTATGTT-TTCGGGACATATGGA
3211542 TAGGTCCTTC
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
30 22 0.46
31 3 0.06
32 23 0.48
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (29 bp):
TACCTATGTTTTCGGGACATATGGACAGA
Found at i:3211523 original size:30 final size:30
Alignment explanation
Indices: 3211487--3211546 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
3211477 GGACAGTATC
* *
3211487 ACCTATGTTATTCGGGATATATGGATAGGT
1 ACCTATGTTATTCGGAACATATGGATAGGT
*
3211517 ACCTATGTTCTTCGGAACATATGGATAGGT
1 ACCTATGTTATTCGGAACATATGGATAGGT
3211547 CCTTCGGGAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.27, C:0.13, G:0.25, T:0.35
Consensus pattern (30 bp):
ACCTATGTTATTCGGAACATATGGATAGGT
Found at i:3212449 original size:20 final size:20
Alignment explanation
Indices: 3212404--3212443 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
3212394 CATCGTTAAG
3212404 GTAAAATATTTGAACAATGA
1 GTAAAATATTTGAACAATGA
3212424 GTAAAATATTTGAACAATGA
1 GTAAAATATTTGAACAATGA
3212444 TCAAAACAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.05, G:0.15, T:0.30
Consensus pattern (20 bp):
GTAAAATATTTGAACAATGA
Found at i:3212485 original size:21 final size:22
Alignment explanation
Indices: 3212461--3212502 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
3212451 AGTTATGAGC
*
3212461 AAAACAT-AATTAATTATTCAT
1 AAAACATAAAATAATTATTCAT
3212482 AAAACATAAAATAATTATTCA
1 AAAACATAAAATAATTATTCA
3212503 GACAAACAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (22 bp):
AAAACATAAAATAATTATTCAT
Found at i:3219707 original size:90 final size:90
Alignment explanation
Indices: 3219551--3219728 Score: 302
Period size: 90 Copynumber: 2.0 Consensus size: 90
3219541 CCTAACACAC
* *
3219551 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATATAT
* *
3219616 ATTTAATTAATTGGAATTTAATAAT
66 ATTTAATTAATTGAAATTAAATAAT
* *
3219641 CCTTTTATATCCAAGTTATCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATATAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATATAT
3219706 ATTTAATTAATTGAAATTAAATA
66 ATTTAATTAATTGAAATTAAATA
3219729 TTCAGAATTA
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
90 82 1.00
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.46
Consensus pattern (90 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATATAT
ATTTAATTAATTGAAATTAAATAAT
Found at i:3224871 original size:28 final size:27
Alignment explanation
Indices: 3224814--3224884 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 27
3224804 TATTAAGCCC
3224814 TTATATAT-TTATATA-TTTTCAAAAA
1 TTATATATATTATATATTTTTCAAAAA
* * *
3224839 CTATATATATTATATATTTTTGAAATTA
1 TTATATATATTATATATTTTTCAAA-AA
3224867 TTATATATATTATCATAT
1 TTATATATATTAT-ATAT
3224885 ATAATATATA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
25 7 0.18
26 7 0.18
27 7 0.18
28 13 0.34
29 4 0.11
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.54
Consensus pattern (27 bp):
TTATATATATTATATATTTTTCAAAAA
Found at i:3224962 original size:10 final size:9
Alignment explanation
Indices: 3224934--3224976 Score: 50
Period size: 10 Copynumber: 4.4 Consensus size: 9
3224924 ATCCAAGATG
3224934 AAAATAAGAT
1 AAAATAA-AT
*
3224944 GAAATAAAT
1 AAAATAAAT
3224953 AAAATAAAAT
1 AAAAT-AAAT
3224963 AAAAGTAAAT
1 AAAA-TAAAT
3224973 AAAA
1 AAAA
3224977 ATAGATAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 6 0.21
10 22 0.76
11 1 0.03
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (9 bp):
AAAATAAAT
Found at i:3225025 original size:16 final size:16
Alignment explanation
Indices: 3224994--3225052 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 16
3224984 AGAAAAGGAA
*
3224994 AATAAAATACTAATAAT
1 AATAATATA-TAATAAT
3225011 AATAATATATAATAAT
1 AATAATATATAATAAT
* *
3225027 -AT-GTATATATTAA-
1 AATAATATATAATAAT
3225040 AA-AATATATAATA
1 AATAATATATAATA
3225053 CATATTATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
14 18 0.51
15 2 0.06
16 7 0.20
17 8 0.23
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (16 bp):
AATAATATATAATAAT
Found at i:3225046 original size:28 final size:27
Alignment explanation
Indices: 3225014--3225081 Score: 86
Period size: 28 Copynumber: 2.4 Consensus size: 27
3225004 TAATAATAAT
3225014 AATATATAATAATATGTATATATT-AAAA
1 AATATATAATAATAT-TATAT-TTCAAAA
3225042 AATATATAATACATATTATATTTCAAAA
1 AATATATAATA-ATATTATATTTCAAAA
3225070 ACA-ATATAATAA
1 A-ATATATAATAA
3225082 ATTTTCAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
27 3 0.08
28 29 0.78
29 5 0.14
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.37
Consensus pattern (27 bp):
AATATATAATAATATTATATTTCAAAA
Found at i:3225184 original size:22 final size:22
Alignment explanation
Indices: 3225130--3225208 Score: 88
Period size: 22 Copynumber: 3.5 Consensus size: 22
3225120 ACCGTTTTAA
*
3225130 AAAAACTATATATTATACATTTT-
1 AAAAACTATATA--ATATATTTTC
* * *
3225153 TAAAATTATATAATATGTTTTC
1 AAAAACTATATAATATATTTTC
*
3225175 AAAAACTATATTATATATTTTC
1 AAAAACTATATAATATATTTTC
3225197 AAAAACTATATA
1 AAAAACTATATA
3225209 TATTATATAA
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
21 7 0.15
22 29 0.63
23 10 0.22
ACGTcount: A:0.48, C:0.08, G:0.01, T:0.43
Consensus pattern (22 bp):
AAAAACTATATAATATATTTTC
Found at i:3225255 original size:12 final size:11
Alignment explanation
Indices: 3225203--3225268 Score: 61
Period size: 10 Copynumber: 6.4 Consensus size: 11
3225193 TTTCAAAAAC
3225203 TATATATATTA
1 TATATATATTA
*
3225214 TATA-ATTTTA
1 TATATATATTA
*
3225224 -AAAT-TATTA
1 TATATATATTA
3225233 TATATATA-TA
1 TATATATATTA
*
3225243 TATAT-TATCA
1 TATATATATTA
3225253 TATATATTATTA
1 TATATA-TATTA
3225265 TATA
1 TATA
3225269 ATGTAAAAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
9 8 0.19
10 21 0.49
11 6 0.14
12 8 0.19
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (11 bp):
TATATATATTA
Found at i:3225257 original size:14 final size:15
Alignment explanation
Indices: 3225226--3225265 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
3225216 TAATTTTAAA
*
3225226 ATTATTATATATATAT
1 ATTATTAT-CATATAT
3225242 ATATATTATCATATAT
1 AT-TATTATCATATAT
3225258 ATTATTAT
1 ATTATTAT
3225266 ATAATGTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 6 0.27
16 10 0.45
17 6 0.27
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTATTATCATATAT
Found at i:3226060 original size:29 final size:29
Alignment explanation
Indices: 3226027--3226088 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
3226017 CTCCTTGCCA
* * *
3226027 TATTCGTGTTGTAACAAGGTAATTTAAAG
1 TATTCATGTTGTAACAAGATAATTGAAAG
3226056 TATTCATGTTGTAACAAGATAATTGAAAG
1 TATTCATGTTGTAACAAGATAATTGAAAG
3226085 TATT
1 TATT
3226089 TATAATAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.37, C:0.06, G:0.18, T:0.39
Consensus pattern (29 bp):
TATTCATGTTGTAACAAGATAATTGAAAG
Found at i:3226662 original size:51 final size:50
Alignment explanation
Indices: 3226597--3226709 Score: 145
Period size: 51 Copynumber: 2.2 Consensus size: 50
3226587 TTAGCAATAA
* ** *
3226597 AGCGCGCCCCCTGCACCGCGCTATACGATGATTTGGCGTCACGTGGGGTAT
1 AGCGCGCCCCCTGCACCACGCTATACGATGAGCTGGCGCCACGT-GGGTAT
* *
3226648 AGCGTGCCCCCTGCACCACGCTATACGGTGAGCTGGCGCCACGTGGGTAT
1 AGCGCGCCCCCTGCACCACGCTATACGATGAGCTGGCGCCACGTGGGTAT
* *
3226698 AGTGCGGCCCCT
1 AGCGCGCCCCCT
3226710 AAAGCGCGCT
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
50 15 0.28
51 38 0.72
ACGTcount: A:0.15, C:0.34, G:0.32, T:0.19
Consensus pattern (50 bp):
AGCGCGCCCCCTGCACCACGCTATACGATGAGCTGGCGCCACGTGGGTAT
Found at i:3226885 original size:12 final size:10
Alignment explanation
Indices: 3226844--3226884 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
3226834 TTTATCACAC
3226844 CAAATTCTCT
1 CAAATTCTCT
3226854 CAAATTCTCT
1 CAAATTCTCT
3226864 -AAATTTCTCT
1 CAAA-TTCTCT
*
3226874 CAAATACTCT
1 CAAATTCTCT
3226884 C
1 C
3226885 TTTTTAAGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 22 0.79
11 3 0.11
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:3227148 original size:110 final size:111
Alignment explanation
Indices: 3227008--3227228 Score: 363
Period size: 110 Copynumber: 2.0 Consensus size: 111
3226998 TGGAAATCAT
* *
3227008 ATATCTCTACACTTTGCTGATATGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* * * * *
3227073 TATTTAGTT-ATTTATTTAATGCATGATTATTATATTAATAATTAA
66 TAATTAGTTGATTCATTTAATACATGATTATTAGATTAAGAATTAA
*
3227118 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTATTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
3227183 TAATTAGTTGATTCATTTAATACATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTCATTTAATACATGATTATTAGATTAAGAATTAA
3227229 TTTTTGTAAT
Statistics
Matches: 102, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
110 70 0.69
111 32 0.31
ACGTcount: A:0.36, C:0.08, G:0.09, T:0.47
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTCATTTAATACATGATTATTAGATTAAGAATTAA
Found at i:3229317 original size:26 final size:24
Alignment explanation
Indices: 3229245--3229317 Score: 62
Period size: 25 Copynumber: 3.0 Consensus size: 24
3229235 TTATATTTGT
3229245 ATTTACTTTATTTTGTTAAATTGTA
1 ATTTACTTTATTTTGTTAAATT-TA
* *
3229270 ATTT-TTTTATTATT-TCT-CATTTA
1 ATTTACTTTATT-TTGT-TAAATTTA
3229293 ATACTTACTTTATTTTGTTAAATTT
1 AT--TTACTTTATTTTGTTAAATTT
3229318 GTTGAACTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 13
0.69 0.07 0.24
Matches are distributed among these distances:
23 4 0.11
24 10 0.27
25 12 0.32
26 11 0.30
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.63
Consensus pattern (24 bp):
ATTTACTTTATTTTGTTAAATTTA
Found at i:3231772 original size:27 final size:27
Alignment explanation
Indices: 3231733--3231788 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
3231723 GCCGGTGACG
3231733 GAGGACTAGAGGGAGGATGAGGAGAAAA
1 GAGGACTAGAGGGAGGATGAGGA-AAAA
3231761 GAGG-CTAGAGGGAGGATGAGGAAAAA
1 GAGGACTAGAGGGAGGATGAGGAAAAA
3231787 GA
1 GA
3231789 AACAGATGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 6 0.21
27 18 0.64
28 4 0.14
ACGTcount: A:0.43, C:0.04, G:0.46, T:0.07
Consensus pattern (27 bp):
GAGGACTAGAGGGAGGATGAGGAAAAA
Found at i:3234837 original size:17 final size:15
Alignment explanation
Indices: 3234774--3234846 Score: 51
Period size: 15 Copynumber: 4.6 Consensus size: 15
3234764 AATGAAATAC
*
3234774 TAAAATTAAAAAAAA
1 TAAAATTAAAAAAAT
* *
3234789 TAAAAGTTAGATATAATT
1 TAAAA-TTA-A-AAAAAT
3234807 TAAAA--AATAAAAATT
1 TAAAATTAA-AAAAA-T
3234822 TAAATATTAAAAAAAT
1 TAAA-ATTAAAAAAAT
3234838 TAAAATTAA
1 TAAAATTAA
3234847 TAATTTATAT
Statistics
Matches: 46, Mismatches: 5, Indels: 14
0.71 0.08 0.22
Matches are distributed among these distances:
14 5 0.11
15 16 0.35
16 9 0.20
17 6 0.13
18 10 0.22
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (15 bp):
TAAAATTAAAAAAAT
Found at i:3237516 original size:7 final size:7
Alignment explanation
Indices: 3237513--3237547 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
3237503 CTAAATAATA
3237513 AATAAA-
1 AATAAAT
3237519 AATAAAT
1 AATAAAT
3237526 AATAAAT
1 AATAAAT
3237533 AATAAAT
1 AATAAAT
3237540 AA-AAAT
1 AATAAAT
3237546 AA
1 AA
3237548 ACAAACAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 12 0.43
7 16 0.57
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (7 bp):
AATAAAT
Found at i:3237518 original size:4 final size:4
Alignment explanation
Indices: 3237504--3237572 Score: 62
Period size: 4 Copynumber: 19.0 Consensus size: 4
3237494 GACTTGGACC
3237504 TAAA T-AA TAAA T-AA -AAA TAAA T-AA TAAA T-AA TAAA T-AA -AAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
* * *
3237545 TAAA CAAA CAAA CAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
3237573 GTATAAAATA
Statistics
Matches: 56, Mismatches: 2, Indels: 14
0.78 0.03 0.19
Matches are distributed among these distances:
3 17 0.30
4 39 0.70
ACGTcount: A:0.75, C:0.04, G:0.00, T:0.20
Consensus pattern (4 bp):
TAAA
Found at i:3237581 original size:16 final size:16
Alignment explanation
Indices: 3237512--3237593 Score: 52
Period size: 16 Copynumber: 5.4 Consensus size: 16
3237502 CCTAAATAAT
3237512 AAATA-AAAATAAAT-
1 AAATATAAAATAAATA
3237526 -AATA-AATAATAAATA
1 AAATATAA-AATAAATA
* *
3237541 AAA-AT-AAACAAACA
1 AAATATAAAATAAATA
*
3237555 AACAAAT-AAATAAATA
1 AA-ATATAAAATAAATA
* *
3237571 AAGTATAAAATATATA
1 AAATATAAAATAAATA
3237587 AAATATA
1 AAATATA
3237594 TTTTGAAAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
13 6 0.11
14 15 0.28
15 5 0.09
16 27 0.51
ACGTcount: A:0.73, C:0.04, G:0.01, T:0.22
Consensus pattern (16 bp):
AAATATAAAATAAATA
Found at i:3237754 original size:41 final size:41
Alignment explanation
Indices: 3237686--3237791 Score: 191
Period size: 41 Copynumber: 2.7 Consensus size: 41
3237676 AAAAAATTTT
3237686 AAAACTATA-TATAT-TATATATAT-TTCAAAATGTTTTCA
1 AAAACTATATTATATATATATATATATTCAAAATGTTTTCA
3237724 AAAACTATATTATATATATATATATATTCAAAATGTTTTCA
1 AAAACTATATTATATATATATATATATTCAAAATGTTTTCA
3237765 AAAACTATATTATATATATATATATAT
1 AAAACTATATTATATATATATATATAT
3237792 ATATATATAT
Statistics
Matches: 65, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
38 9 0.14
39 5 0.08
40 9 0.14
41 42 0.65
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (41 bp):
AAAACTATATTATATATATATATATATTCAAAATGTTTTCA
Found at i:3237782 original size:2 final size:2
Alignment explanation
Indices: 3237770--3237805 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
3237760 TTTCAAAAAC
3237770 TA TA T- 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
3237806 GTATTAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:3238529 original size:200 final size:202
Alignment explanation
Indices: 3238246--3238725 Score: 562
Period size: 200 Copynumber: 2.4 Consensus size: 202
3238236 GCTACTATAC
* * * *
3238246 GGTTGATAAGCCTTCGAGCTGAATCGAAACAAACTTGAAAGTTTTTTGTTGACATATAGCCCTTA
1 GGTTGATAAGCCATCGAGCTGAATGGAATCAAACTTGAAAG-TTTTTGTTGACATATAGCCCTTC
* * * * * *
3238311 TCGACTTGAGCTATGCTGTAAATTCGGCTGAGAGATAGTTCCTTGTTGCTAGATCGCAGCCGACC
65 TCGCCTTGAGCTATGCTGTAAATTCGGCTGAGAGATAGTTCATTGCTGCTAAAGCGCAGCCAACC
* * *
3238376 TAAGTCTTCTTCTAGGCTCAAAGACCTTGGCT-TAAAATTGAACCAGAAAGTAG-TCCTTAC-A-
130 TAAGTCTTCTTCTAGACTCAAAGACCTCGG-TATAAAATTCAACCAGAAAGTAGTTCC-T-CGAT
3238437 GCTACCATG-A
192 GCTACCATGCA
* * * * *
3238447 GGTTGATATGCCATCGAGCTAAAAGGAATCAAACTCGAAAGTTTTCGTTGACATATAGCCCTTCT
1 GGTTGATAAGCCATCGAGCTGAATGGAATCAAACTTGAAAGTTTTTGTTGACATATAGCCCTTCT
* * *
3238512 CGCCTTGAG-TCATGCTGTAAATTTGGCTGGGAGATAGTTCATTGCTGCTAAAGCGCCGCCAACC
66 CGCCTTGAGCT-ATGCTGTAAATTCGGCTGAGAGATAGTTCATTGCTGCTAAAGCGCAGCCAACC
* * * * **
3238576 TAGGTCTTCTTCTTGACTTAAAGACCTCGGTATAAACTTCAACTGGAAAGTAGTTCCTCGATGCT
130 TAAGTCTTCTTCTAGACTCAAAGACCTCGGTATAAAATTCAACCAGAAAGTAGTTCCTCGATGCT
3238641 ACCATGCA
195 ACCATGCA
* * * * *
3238649 -ATTGATACA-CCCTCGAGCTGAATGAAATCGAACTTGAAAGTTTTTGTTGACAGATAGCCCTTC
1 GGTTGATA-AGCCATCGAGCTGAATGGAATCAAACTTGAAAGTTTTTGTTGACATATAGCCCTTC
3238712 TCGCCTTGAGCTAT
65 TCGCCTTGAGCTAT
3238726 TATACGAACA
Statistics
Matches: 234, Mismatches: 37, Indels: 16
0.82 0.13 0.06
Matches are distributed among these distances:
199 3 0.01
200 119 0.51
201 110 0.47
202 2 0.01
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.30
Consensus pattern (202 bp):
GGTTGATAAGCCATCGAGCTGAATGGAATCAAACTTGAAAGTTTTTGTTGACATATAGCCCTTCT
CGCCTTGAGCTATGCTGTAAATTCGGCTGAGAGATAGTTCATTGCTGCTAAAGCGCAGCCAACCT
AAGTCTTCTTCTAGACTCAAAGACCTCGGTATAAAATTCAACCAGAAAGTAGTTCCTCGATGCTA
CCATGCA
Found at i:3240081 original size:39 final size:39
Alignment explanation
Indices: 3240038--3240120 Score: 130
Period size: 39 Copynumber: 2.1 Consensus size: 39
3240028 ATGTACACCG
* *
3240038 GGTAAGGTCTTATCATGTACATAAAGTAGAGGAGCCTGC
1 GGTAAGGTCTTATCATGTACATAAAGCAGAGGAGCCTGA
* *
3240077 GGTAAGGTCTTATCCTGTGCATAAAGCAGAGGAGCCTGA
1 GGTAAGGTCTTATCATGTACATAAAGCAGAGGAGCCTGA
3240116 GGTAA
1 GGTAA
3240121 CGGTAAGGAC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.30, C:0.16, G:0.30, T:0.24
Consensus pattern (39 bp):
GGTAAGGTCTTATCATGTACATAAAGCAGAGGAGCCTGA
Found at i:3240152 original size:44 final size:44
Alignment explanation
Indices: 3240076--3240398 Score: 421
Period size: 44 Copynumber: 7.3 Consensus size: 44
3240066 GAGGAGCCTG
* * * * * *
3240076 CGGTAAGGTCTTATCCTGTGCATAAAGCAGAGGAGCCTGAGGTAA
1 CGGTAAGGACTTACCCT-TGCACATAGTAGAGGAGCCTGCGGTAA
* * * *
3240121 CGGTAAGGACTTACCTTTTCACATAGCAGAGGAGCTTGCGGTAA
1 CGGTAAGGACTTACCCTTGCACATAGTAGAGGAGCCTGCGGTAA
*
3240165 CGGTAAGGACTTACCCTTGCACATAGTAGAGGAGTCTGCGGTAA
1 CGGTAAGGACTTACCCTTGCACATAGTAGAGGAGCCTGCGGTAA
*
3240209 CGGTAAGGACTTACCCTTGCACATAGTAGAGGAGCCTGTGGTAA
1 CGGTAAGGACTTACCCTTGCACATAGTAGAGGAGCCTGCGGTAA
* * *
3240253 AGGTAAAGACTTACCCTTGCACATAGTAGAGGAGCATGCGGTAA
1 CGGTAAGGACTTACCCTTGCACATAGTAGAGGAGCCTGCGGTAA
* * *
3240297 CGGTAAGGACTTACCCTTGCACATAGTAAATGAGCCTACGGTAA
1 CGGTAAGGACTTACCCTTGCACATAGTAGAGGAGCCTGCGGTAA
* * ** *
3240341 AGGTAAAGACTTACCCTTGCACATAACAGATGAGCCTGCGGTAA
1 CGGTAAGGACTTACCCTTGCACATAGTAGAGGAGCCTGCGGTAA
*
3240385 CAGTAAGGACTTAC
1 CGGTAAGGACTTAC
3240399 AAGTCATAGA
Statistics
Matches: 244, Mismatches: 34, Indels: 1
0.87 0.12 0.00
Matches are distributed among these distances:
44 230 0.94
45 14 0.06
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.22
Consensus pattern (44 bp):
CGGTAAGGACTTACCCTTGCACATAGTAGAGGAGCCTGCGGTAA
Found at i:3248440 original size:36 final size:38
Alignment explanation
Indices: 3248390--3248483 Score: 104
Period size: 36 Copynumber: 2.5 Consensus size: 38
3248380 ATTTTTTTAT
* *
3248390 ATTTTAAAGGAAATAAATAAAT-AAATAAATAA-GTTAA
1 ATTTTAAAGAAAATAAA-AAATGAAATAAAAAAGGTTAA
*
3248427 TTTTTAAA-AAAATAAAAAATGAAATAAAAAAGGTTAA
1 ATTTTAAAGAAAATAAAAAATGAAATAAAAAAGGTTAA
* *
3248464 ATTTTGGAAGTAAATAAAAA
1 ATTTT-AAAGAAAATAAAAA
3248484 CAGAATAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
35 4 0.09
36 16 0.34
37 16 0.34
38 2 0.04
39 9 0.19
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.29
Consensus pattern (38 bp):
ATTTTAAAGAAAATAAAAAATGAAATAAAAAAGGTTAA
Found at i:3249773 original size:4 final size:4
Alignment explanation
Indices: 3249746--3249802 Score: 66
Period size: 4 Copynumber: 14.8 Consensus size: 4
3249736 ACTTGGACCG
* *
3249746 AAAT AAAA ATAAT -AAT AAAT -AAT AAAT AAA- CAAT AAAT AAAT AAAT
1 AAAT AAAT A-AAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
3249792 AAAT AAAT AAA
1 AAAT AAAT AAA
3249803 GTATAAAATA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
3 8 0.18
4 35 0.78
5 2 0.04
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:3249792 original size:23 final size:23
Alignment explanation
Indices: 3249746--3249802 Score: 78
Period size: 27 Copynumber: 2.3 Consensus size: 23
3249736 ACTTGGACCG
3249746 AAATAAAAATAATAATAAATAAT
1 AAATAAAAATAATAATAAATAAT
3249769 AAATAAACAATAAATAAATAAATAAAT
1 AAATAAA-AAT-AAT-AATAAAT-AAT
3249796 AAATAAA
1 AAATAAA
3249803 GTATAAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
23 7 0.23
24 3 0.10
25 3 0.10
26 7 0.23
27 10 0.33
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (23 bp):
AAATAAAAATAATAATAAATAAT
Found at i:3249919 original size:65 final size:65
Alignment explanation
Indices: 3249847--3250087 Score: 265
Period size: 65 Copynumber: 3.7 Consensus size: 65
3249837 TATGCATATG
* * * *
3249847 ATATATTTTCAAAAACATTTTAAAATTATATATTATGTATA-ATTTT-TAAATGTTTTC-AAAAC
1 ATATATTAT-AAAAATATTTTAAAATTATATATTATATATATATTTTCAAAATGTTTTCAAAAAC
3249909 T
65 T
* * *
3249910 ATGTATATT-TCAAAATGTTTTAAAAAACTATATTATATATATATATATTTTCAAAATGTTTTCA
1 A--TATATTATAAAAATATTTT--AAAATTATA-TAT-TATATATATATTTTCAAAATGTTTTCA
3249974 AAAACT
60 AAAACT
* * * *
3249980 ATATATTATATATATATTTTTAAATTATATATTATATATATATTTTCAAAATGATTTCAAAAACT
1 ATATATTATAAAAATATTTTAAAATTATATATTATATATATATTTTCAAAATGTTTTCAAAAACT
* * *
3250045 ATATATTATATATATTTTTTAAAATTATATATTATATATATAT
1 ATATATTATAAAAATATTTTAAAATTATATATTATATATATAT
3250088 ATTATATGTA
Statistics
Matches: 153, Mismatches: 15, Indels: 18
0.82 0.08 0.10
Matches are distributed among these distances:
63 9 0.06
64 1 0.01
65 87 0.57
66 6 0.04
67 14 0.09
68 11 0.07
69 18 0.12
70 7 0.05
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (65 bp):
ATATATTATAAAAATATTTTAAAATTATATATTATATATATATTTTCAAAATGTTTTCAAAAACT
Found at i:3249925 original size:28 final size:30
Alignment explanation
Indices: 3249880--3249940 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
3249870 AATTATATAT
** *
3249880 TATGTATAATTTTTAAATGTTTT-CAAAAC
1 TATGTATAATTTCAAAATGTTTTAAAAAAC
3249909 TATGTAT-ATTTCAAAATGTTTTAAAAAAC
1 TATGTATAATTTCAAAATGTTTTAAAAAAC
3249938 TAT
1 TAT
3249941 ATTATATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 13 0.46
29 15 0.54
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.46
Consensus pattern (30 bp):
TATGTATAATTTCAAAATGTTTTAAAAAAC
Found at i:3249964 original size:41 final size:39
Alignment explanation
Indices: 3249913--3249999 Score: 140
Period size: 41 Copynumber: 2.2 Consensus size: 39
3249903 CAAAACTATG
3249913 TATA-TTTCAAAATGTTTTAAAAAACTATATTATATATATA
1 TATATTTTCAAAATGTTTTAAAAAACTATA-TAT-TATATA
*
3249953 TATATTTTCAAAATGTTTTCAAAAACTATATATTATATA
1 TATATTTTCAAAATGTTTTAAAAAACTATATATTATATA
3249992 TATATTTT
1 TATATTTT
3250000 TAAATTATAT
Statistics
Matches: 45, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
39 14 0.31
40 7 0.16
41 24 0.53
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (39 bp):
TATATTTTCAAAATGTTTTAAAAAACTATATATTATATA
Found at i:3249999 original size:28 final size:28
Alignment explanation
Indices: 3249968--3250030 Score: 94
Period size: 26 Copynumber: 2.3 Consensus size: 28
3249958 TTTCAAAATG
3249968 TTTTCAAAAACTATATATTATATATATA
1 TTTTCAAAAACTATATATTATATATATA
* *
3249996 TTTT--TAAATTATATATTATATATATA
1 TTTTCAAAAACTATATATTATATATATA
3250022 TTTTCAAAA
1 TTTTCAAAA
3250031 TGATTTCAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 24 0.80
28 6 0.20
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (28 bp):
TTTTCAAAAACTATATATTATATATATA
Found at i:3250058 original size:9 final size:9
Alignment explanation
Indices: 3250044--3250100 Score: 51
Period size: 9 Copynumber: 6.0 Consensus size: 9
3250034 TTTCAAAAAC
3250044 TATATATTA
1 TATATATTA
*
3250053 TATATATTT
1 TATATATTA
* *
3250062 TTTAAAATTA
1 TAT-ATATTA
3250072 TATATTATATA
1 TATA-TAT-TA
3250083 TATATATTA
1 TATATATTA
*
3250092 TATGTATTA
1 TATATATTA
3250101 AATAGAACCG
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
9 21 0.55
10 11 0.29
11 6 0.16
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (9 bp):
TATATATTA
Found at i:3254118 original size:60 final size:58
Alignment explanation
Indices: 3254025--3254140 Score: 160
Period size: 60 Copynumber: 2.0 Consensus size: 58
3254015 TCTACGATGC
* * * *
3254025 CGACATTTAGGTCGAACAAGCTGGTAGTTGAATGCCTTCCCTTTGAACTTGAAGGCATCT
1 CGACATTGAGGTCGAACAAGCTCGCAGTTGAATGCC--CCCTTGGAACTTGAAGGCATCT
* *
3254085 CGACATTGAGGTCGAAGAAGCTCGCAGTTGAATGCCCCCTTGGAATTTGAAGGCAT
1 CGACATTGAGGTCGAACAAGCTCGCAGTTGAATGCCCCCTTGGAACTTGAAGGCAT
3254141 AGTTTCAAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
58 18 0.36
60 32 0.64
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.27
Consensus pattern (58 bp):
CGACATTGAGGTCGAACAAGCTCGCAGTTGAATGCCCCCTTGGAACTTGAAGGCATCT
Found at i:3254765 original size:7 final size:7
Alignment explanation
Indices: 3254753--3254786 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
3254743 GATACTAGGT
3254753 TCAAGGC
1 TCAAGGC
3254760 TCAAGGC
1 TCAAGGC
3254767 TCAAGGC
1 TCAAGGC
3254774 TCAAGGC
1 TCAAGGC
3254781 TCAAGG
1 TCAAGG
3254787 ATGGATCATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.29, C:0.26, G:0.29, T:0.15
Consensus pattern (7 bp):
TCAAGGC
Found at i:3264655 original size:28 final size:29
Alignment explanation
Indices: 3264622--3264694 Score: 82
Period size: 27 Copynumber: 2.7 Consensus size: 29
3264612 CAGGGCTTGA
*
3264622 GGTATTTTAGGTCATTTCT-CACTTCAGG
1 GGTATTTTAGGTCATTTCTACACTTCAAG
* *
3264650 GGTATTTT-GGTTATTT-TACAGTTCAAG
1 GGTATTTTAGGTCATTTCTACACTTCAAG
*
3264677 GGTGTTTTA-GTCATTTCT
1 GGTATTTTAGGTCATTTCT
3264695 TTCCATCTAG
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
26 1 0.03
27 27 0.73
28 9 0.24
ACGTcount: A:0.18, C:0.12, G:0.22, T:0.48
Consensus pattern (29 bp):
GGTATTTTAGGTCATTTCTACACTTCAAG
Found at i:3273163 original size:19 final size:19
Alignment explanation
Indices: 3273139--3273186 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
3273129 ATGATTCTAG
3273139 TGAGAAGGAAAAGAAAAAA
1 TGAGAAGGAAAAGAAAAAA
3273158 TGAGAAAGG--AAGAAAAAA
1 TGAG-AAGGAAAAGAAAAAA
3273176 T--GAAGGAAAAG
1 TGAGAAGGAAAAG
3273187 GTGAAATGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
15 4 0.15
16 1 0.04
17 3 0.12
18 10 0.38
19 4 0.15
20 4 0.15
ACGTcount: A:0.65, C:0.00, G:0.29, T:0.06
Consensus pattern (19 bp):
TGAGAAGGAAAAGAAAAAA
Found at i:3283943 original size:22 final size:22
Alignment explanation
Indices: 3283917--3283965 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
3283907 TTTATAAAAG
*
3283917 TTATTTTT-TTTATATGTTTTCT
1 TTATTTTTCTTTA-AAGTTTTCT
3283939 TTATTTTTCTTTAAAGTTTTCT
1 TTATTTTTCTTTAAAGTTTTCT
3283961 TTATT
1 TTATT
3283966 ATTAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 21 0.84
23 4 0.16
ACGTcount: A:0.16, C:0.06, G:0.04, T:0.73
Consensus pattern (22 bp):
TTATTTTTCTTTAAAGTTTTCT
Found at i:3284783 original size:13 final size:13
Alignment explanation
Indices: 3284765--3284805 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
3284755 AACGATGTGT
3284765 GTCAATTCTCGTG
1 GTCAATTCTCGTG
3284778 GTCAATTCTCGTG
1 GTCAATTCTCGTG
* *
3284791 CTC-ATGCTCGTG
1 GTCAATTCTCGTG
3284803 GTC
1 GTC
3284806 GTGGACAAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
12 10 0.40
13 15 0.60
ACGTcount: A:0.12, C:0.27, G:0.24, T:0.37
Consensus pattern (13 bp):
GTCAATTCTCGTG
Found at i:3289378 original size:25 final size:25
Alignment explanation
Indices: 3289349--3289428 Score: 74
Period size: 30 Copynumber: 3.1 Consensus size: 25
3289339 TTACGAGAGT
3289349 TTATAATTTTGAAATTTTAATTTAA
1 TTATAATTTTGAAATTTTAATTTAA
*
3289374 TTATAATTTTGAGAATATTTTTTGATTTAA
1 TTATAATTTT--GAA-A--TTTTAATTTAA
* *
3289404 ATATAATTTT-AAA-TTTAATTAAA
1 TTATAATTTTGAAATTTTAATTTAA
3289427 TT
1 TT
3289429 TATTTTAATC
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
23 9 0.20
25 10 0.22
26 1 0.02
27 5 0.11
28 1 0.02
30 19 0.42
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (25 bp):
TTATAATTTTGAAATTTTAATTTAA
Found at i:3294166 original size:39 final size:41
Alignment explanation
Indices: 3294063--3294167 Score: 97
Period size: 41 Copynumber: 2.6 Consensus size: 41
3294053 TAGTGGCATT
** ** *
3294063 TTTAGCGGCGTTTGGAAAGTAAACGCCACAAAAATTAAACA
1 TTTAGCGGCGTTTACAAAACAAACGCCACAAAAATGAAACA
* ** *
3294104 TATAGCGGCGTTTACAATTCAAACGCCAC-AAAATGATAC-
1 TTTAGCGGCGTTTACAAAACAAACGCCACAAAAATGAAACA
**
3294143 TTTAGCGGCGTTTTTAAAACAAACG
1 TTTAGCGGCGTTTACAAAACAAACG
3294168 TCGCTATTGA
Statistics
Matches: 51, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
39 20 0.39
40 8 0.16
41 23 0.45
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.25
Consensus pattern (41 bp):
TTTAGCGGCGTTTACAAAACAAACGCCACAAAAATGAAACA
Found at i:3294331 original size:42 final size:42
Alignment explanation
Indices: 3294284--3294432 Score: 174
Period size: 42 Copynumber: 3.5 Consensus size: 42
3294274 AAAAGCCATG
* *
3294284 AAAGTATAAGTATTTAGCGGCGTTTGTGCTTAAAACGCCACT
1 AAAGCATAAGTATTTAGCGGCGTTTGTGCTTAAAACGCCGCT
* * * * *
3294326 AAAGTA-AGAGTCTTTAGCGGCGTTTGTGCTTAACACACTGCT
1 AAAGCATA-AGTATTTAGCGGCGTTTGTGCTTAAAACGCCGCT
** * *
3294368 AAAGCACGAGTATTTAGCGGCGTTTTTTCTTAAAACGCCGCT
1 AAAGCATAAGTATTTAGCGGCGTTTGTGCTTAAAACGCCGCT
*
3294410 AAAGCATGAGTATTTAGCGGCGT
1 AAAGCATAAGTATTTAGCGGCGT
3294433 GTGATACTAA
Statistics
Matches: 91, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
41 1 0.01
42 90 0.99
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.30
Consensus pattern (42 bp):
AAAGCATAAGTATTTAGCGGCGTTTGTGCTTAAAACGCCGCT
Found at i:3298393 original size:43 final size:42
Alignment explanation
Indices: 3298278--3298628 Score: 425
Period size: 43 Copynumber: 8.2 Consensus size: 42
3298268 GTTTTAATTC
* * *
3298278 GCGGCGTTTGTAT-AAAAAACGCAGCTATAGATCTGACTTTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATCTGACCTTTT
**
3298320 GCGGCGTTTGTTCCAAAAACGTAGCTATAGATCTGACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTT
* * * * *
3298362 ACGGCGTTTGTATCTATAAATGCCGTTATAGATCTGACCTTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATCTGACCTTTT
* *
3298405 ACGGCTTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTT
* * * *
3298447 GTGGCGTTTGTCTCCAAAAATGCCGCTATCGATATGACCTTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATCTGACCTTTT
*
3298490 GCGGCGTTTGTATCCAAAAACGCCACTATAGATCTCGACCTTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATCT-GACCTTTT
* * *
3298534 GCGGCGTTTGTTCCGAAAACGCCGCTATAGATATCGACCTCTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCT-GACCTTTT
* * *
3298577 GCGGCGTTTGTTCCAAAAATGCCGCGATAGATCTTGACCTATT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATC-TGACCTTTT
3298620 GCGGCGTTT
1 GCGGCGTTT
3298629 TTTGTTCACA
Statistics
Matches: 268, Mismatches: 36, Indels: 9
0.86 0.12 0.03
Matches are distributed among these distances:
41 1 0.00
42 82 0.31
43 165 0.62
44 20 0.07
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (42 bp):
GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTT
Found at i:3298558 original size:86 final size:85
Alignment explanation
Indices: 3298278--3298628 Score: 420
Period size: 85 Copynumber: 4.1 Consensus size: 85
3298268 GTTTTAATTC
* * * *
3298278 GCGGCGTTTGTAT-AAAAAACGCAGCTATAGATCTGACTTTTTGCGGCGTTTGTTCCAAAAACG-
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTTGCGGCGTTTGTTCCAAAAACGC
*
3298341 TAGCTATAGATCTGACCTTTT
66 CA-CTATAGATCTGACCTTTT
* * * * * * * *
3298362 ACGGCGTTTGTATCTATAAATGCCGTTATAGATCTGACCTTTTACGGCTTTTGTTCCAAAAACGC
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTTGCGGCGTTTGTTCCAAAAACGC
*
3298427 CGCTATAGATCTGACCTTTT
66 CACTATAGATCTGACCTTTT
* * * *
3298447 GTGGCGTTTGTCTCCAAAAATGCCGCTATCGATATGACCTTTTGCGGCGTTTGTATCCAAAAACG
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTTGCGGCGTTTGT-TCCAAAAACG
3298512 CCACTATAGATCTCGACCTTTT
65 CCACTATAGATCT-GACCTTTT
* * *
3298534 GCGGCGTTTGT-TCCGAAAACGCCGCTATAGATATCGACCTCTTGCGGCGTTTGTTCCAAAAATG
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATAT-GACCTTTTGCGGCGTTTGTTCCAAAAACG
* * *
3298598 CCGCGATAGATCTTGACCTATT
65 CCACTATAGATC-TGACCTTTT
3298620 GCGGCGTTT
1 GCGGCGTTT
3298629 TTTGTTCACA
Statistics
Matches: 230, Mismatches: 31, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
84 12 0.05
85 104 0.45
86 77 0.33
87 37 0.16
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (85 bp):
GCGGCGTTTGTATCCAAAAACGCCGCTATAGATATGACCTTTTGCGGCGTTTGTTCCAAAAACGC
CACTATAGATCTGACCTTTT
Found at i:3311203 original size:245 final size:245
Alignment explanation
Indices: 3310773--3311264 Score: 957
Period size: 245 Copynumber: 2.0 Consensus size: 245
3310763 GAATTTACTA
3310773 AATTTGGTTGAATATATATTCTTAATAAGTTTATAACCCAGAGTTGAGTGGATAGTCCTAATTGA
1 AATTTGGTTGAATATATATTCTTAATAAGTTTATAACCCAGAGTTGAGTGGATAGTCCTAATTGA
3310838 GAAAGACAAGATGAACTTACCGCTAGAAAGGTTGAGTTTTATGAAAACTCTTAATGGATTCAAAT
66 GAAAGACAAGATGAACTTACCGCTAGAAAGGTTGAGTTTTATGAAAACTCTTAATGGATTCAAAT
*
3310903 CCAAGAGTTTGGATGGTTTTACTGAGAATGACTTATTGAATTCACCGATTAATTAGATTGAATAT
131 CCAAGAATTTGGATGGTTTTACTGAGAATGACTTATTGAATTCACCGATTAATTAGATTGAATAT
3310968 TTATTCTTAATGATTTCTTATAATAGAGTATGGGTGGTTCATTTATAATG
196 TTATTCTTAATGATTTCTTATAATAGAGTATGGGTGGTTCATTTATAATG
* *
3311018 AATTTGGTTGAATATATATTCTTAATAAGTTTATAACCCAGAGTTGAGTGGATTGTCGTAATTGA
1 AATTTGGTTGAATATATATTCTTAATAAGTTTATAACCCAGAGTTGAGTGGATAGTCCTAATTGA
3311083 GAAAGACAAGATGAACTTACCGCTAGAAAGGTTGAGTTTTATGAAAACTCTTAATGGATTCAAAT
66 GAAAGACAAGATGAACTTACCGCTAGAAAGGTTGAGTTTTATGAAAACTCTTAATGGATTCAAAT
3311148 CCAAGAATTTGGATGGTTTTACTGAGAATGACTTATTGAATTCACCGATTAATTAGATTGAATAT
131 CCAAGAATTTGGATGGTTTTACTGAGAATGACTTATTGAATTCACCGATTAATTAGATTGAATAT
3311213 TTATTCTTAATGATTTCTTATAATAGAGTATGGGTGGTTCATTTATAATG
196 TTATTCTTAATGATTTCTTATAATAGAGTATGGGTGGTTCATTTATAATG
3311263 AA
1 AA
3311265 CTTGAAGAAA
Statistics
Matches: 244, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
245 244 1.00
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.37
Consensus pattern (245 bp):
AATTTGGTTGAATATATATTCTTAATAAGTTTATAACCCAGAGTTGAGTGGATAGTCCTAATTGA
GAAAGACAAGATGAACTTACCGCTAGAAAGGTTGAGTTTTATGAAAACTCTTAATGGATTCAAAT
CCAAGAATTTGGATGGTTTTACTGAGAATGACTTATTGAATTCACCGATTAATTAGATTGAATAT
TTATTCTTAATGATTTCTTATAATAGAGTATGGGTGGTTCATTTATAATG
Found at i:3313267 original size:3 final size:3
Alignment explanation
Indices: 3313261--3313308 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
3313251 TTGAAAAGAG
* * * *
3313261 AAT AAT AAT AAT AAT AAA AAT AAA AAT AAT GAT AAC AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3313309 GTGTTTGAGG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:3313309 original size:18 final size:18
Alignment explanation
Indices: 3313261--3313309 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
3313251 TTGAAAAGAG
*
3313261 AATAATAATAATAATAAA
1 AATAATAATAATGATAAA
* *
3313279 AATAAAAATAATGATAAC
1 AATAATAATAATGATAAA
3313297 AATAATAATAATG
1 AATAATAATAATG
3313310 TGTTTGAGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (18 bp):
AATAATAATAATGATAAA
Found at i:3313899 original size:10 final size:9
Alignment explanation
Indices: 3313882--3313906 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3313872 TTCTAAAATA
3313882 TATTTTTTT
1 TATTTTTTT
3313891 TATTTTTTT
1 TATTTTTTT
3313900 TATTTTT
1 TATTTTT
3313907 GTTTTCAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
TATTTTTTT
Found at i:3315114 original size:2 final size:2
Alignment explanation
Indices: 3315107--3315133 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3315097 ACTAGACATG
3315107 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3315134 ATTCATTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3316202 original size:36 final size:37
Alignment explanation
Indices: 3316155--3316227 Score: 121
Period size: 36 Copynumber: 2.0 Consensus size: 37
3316145 TTAGCTCCAA
3316155 ACATTTCAAGAATAACCCATCTCCAAGA-GAGAGCAT
1 ACATTTCAAGAATAACCCATCTCCAAGATGAGAGCAT
* *
3316191 ACATTTCAAGAATCACCCATGTCCAAGATGAGAGCAT
1 ACATTTCAAGAATAACCCATCTCCAAGATGAGAGCAT
3316228 GGTAATGAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
36 26 0.76
37 8 0.24
ACGTcount: A:0.40, C:0.25, G:0.15, T:0.21
Consensus pattern (37 bp):
ACATTTCAAGAATAACCCATCTCCAAGATGAGAGCAT
Found at i:3321048 original size:208 final size:212
Alignment explanation
Indices: 3320665--3321076 Score: 679
Period size: 208 Copynumber: 2.0 Consensus size: 212
3320655 ATGCAAATGG
* * *
3320665 GGGGGGATATAGCATAAGAAATGGCCTTGCTGATCCAAAGAATAATTACAAGCTTCAACTATTAT
1 GGGGGGATATAGCA-AAGAAATGACCCTGCTGATCCAAAGAATAATTACAAGCTTCAAATATTAT
* * * *
3320730 AACATGTACTGAGGACGGATTGCAACTTCAATCAAGTAGAGAGTAATCTAAGATTAATAGAAGCA
65 AACAAGTACCGAGGACGGATTGCAACTTCAATCAAGCAGAGAGTAATATAAGATTAATAGAAGCA
3320795 TAACAATGAGCCAAAAACATTAAAGAATGGCTCAATGGATTCACAAGAGTTATGTATGGAGCAAG
130 TAACAATGAGCCAAAAACATTAAAGAATGGCTCAATGGATTCACAAGAGTTATGTATGGAGCAAG
3320860 GGATGGACAGAGGGGGAC
195 GGATGGACAGAGGGGGAC
**
3320878 GGGGGGATATAGC-AAGAGTTGACCCTGCTGATCCAAAGAATAATTACAAGCTTCAAATA-TATA
1 GGGGGGATATAGCAAAGAAATGACCCTGCTGATCCAAAGAATAATTACAAGCTTCAAATATTATA
3320941 ACAAGTACCGAGGACGGATTGCAACTTCAATCAAGCAG-GAGTAATATAAGATTAATAGAAGCAT
66 ACAAGTACCGAGGACGGATTGCAACTTCAATCAAGCAGAGAGTAATATAAGATTAATAGAAGCAT
* * *
3321005 AGCGATGA-CCAAAAACATTAAAGAATGGCTCAATGGGTTCACAAGAGTTATGTATGGAGCAAGG
131 AACAATGAGCCAAAAACATTAAAGAATGGCTCAATGGATTCACAAGAGTTATGTATGGAGCAAGG
3321069 GATGGACA
196 GATGGACA
3321077 AAGTGGGGTG
Statistics
Matches: 187, Mismatches: 12, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
208 63 0.34
209 31 0.17
210 39 0.21
211 41 0.22
213 13 0.07
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.22
Consensus pattern (212 bp):
GGGGGGATATAGCAAAGAAATGACCCTGCTGATCCAAAGAATAATTACAAGCTTCAAATATTATA
ACAAGTACCGAGGACGGATTGCAACTTCAATCAAGCAGAGAGTAATATAAGATTAATAGAAGCAT
AACAATGAGCCAAAAACATTAAAGAATGGCTCAATGGATTCACAAGAGTTATGTATGGAGCAAGG
GATGGACAGAGGGGGAC
Found at i:3324118 original size:32 final size:32
Alignment explanation
Indices: 3324033--3324144 Score: 112
Period size: 32 Copynumber: 3.6 Consensus size: 32
3324023 TTGAATATTT
3324033 ATATTATATAGTTTTAAAGTATTTTGAAATAA
1 ATATTATATAGTTTTAAAGTATTTTGAAATAA
*
3324065 A-A-TATATAGTTTTTACA-TATTTTGAAA-AA
1 ATATTATATAG-TTTTAAAGTATTTTGAAATAA
*
3324094 TATTATTATATAG-TTTAAAGTATTTTGAATGTAA
1 -A-TATTATATAGTTTTAAAGTATTTTGAA-ATAA
3324128 ATA-TACTATA-TTTTAAA
1 ATATTA-TATAGTTTTAAA
3324145 ACTTGTTTTT
Statistics
Matches: 67, Mismatches: 3, Indels: 20
0.74 0.03 0.22
Matches are distributed among these distances:
29 2 0.03
30 18 0.27
31 14 0.21
32 23 0.34
33 8 0.12
34 2 0.03
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.47
Consensus pattern (32 bp):
ATATTATATAGTTTTAAAGTATTTTGAAATAA
Found at i:3324335 original size:34 final size:34
Alignment explanation
Indices: 3324294--3324383 Score: 96
Period size: 33 Copynumber: 2.6 Consensus size: 34
3324284 TTTAAAAACT
3324294 ATATAATTTTGGAAATGTTTTAAAAAACA-ATATA
1 ATATAATTTTGGAAATGTTTTAAAAAA-ATATATA
* * *
3324328 ATATAA-TTT-AAAATATTTTTAAAAAAATATATT
1 ATATAATTTTGGAAAT-GTTTTAAAAAAATATATA
3324361 ATATAGATTTTTGGAAATGTTTT
1 ATATA-A-TTTTGGAAATGTTTT
3324384 TATTTTTTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
32 5 0.11
33 22 0.49
34 7 0.16
36 7 0.16
37 4 0.09
ACGTcount: A:0.47, C:0.01, G:0.08, T:0.44
Consensus pattern (34 bp):
ATATAATTTTGGAAATGTTTTAAAAAAATATATA
Found at i:3324417 original size:32 final size:31
Alignment explanation
Indices: 3324380--3324447 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 31
3324370 TTTGGAAATG
** *
3324380 TTTTTATTTTTTTA-TTTATTTATTTACCTTTT
1 TTTTTATTTTAATATTTTACTTATTTA--TTTT
3324412 TTTTTATTTTAATATTTTACTTATTTATTTT
1 TTTTTATTTTAATATTTTACTTATTTATTTT
3324443 TTTTT
1 TTTTT
3324448 GTTGCAGGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 9 0.28
32 12 0.38
33 11 0.34
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (31 bp):
TTTTTATTTTAATATTTTACTTATTTATTTT
Found at i:3328194 original size:149 final size:149
Alignment explanation
Indices: 3328007--3328304 Score: 564
Period size: 149 Copynumber: 2.0 Consensus size: 149
3327997 CTATATCAGT
3328007 GACCACCTACTATTGCTCGTTTTCATTTTGACCACATTTTTGAAATTTTGTAAGTCACTCAATTG
1 GACCACCTACTATTGCTCGTTTTCATTTTGACCACA-TTTTGAAATTTTGTAAGTCACTCAATTG
3328072 -TTTAAATTCATTCAATTAAGCCATTTATCATTAATATATGAATGTCTTTAAATAGTTGGATCTC
65 TTTTAAATTCATTCAATTAAGCCATTTATCATTAATATATGAATGTCTTTAAATAGTTGGATCTC
3328136 ATTTATGATATCCGATCAAG
130 ATTTATGATATCCGATCAAG
3328156 GACCACCTACTATTGCTCG-TTTCATTTTGACCACCATTTTGAAATTTTGTAAGTCACTCAATTG
1 GACCACCTACTATTGCTCGTTTTCATTTTGACCA-CATTTTGAAATTTTGTAAGTCACTCAATTG
3328220 TTTTAAATTCATTCAATTAAGCCATTTATCATTAATATATGAATGTCTTTAAATAGTTGGATCTC
65 TTTTAAATTCATTCAATTAAGCCATTTATCATTAATATATGAATGTCTTTAAATAGTTGGATCTC
3328285 ATTTATGATATCCGATCAAG
130 ATTTATGATATCCGATCAAG
3328305 TTACAGAAGT
Statistics
Matches: 147, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
148 42 0.29
149 105 0.71
ACGTcount: A:0.30, C:0.17, G:0.11, T:0.41
Consensus pattern (149 bp):
GACCACCTACTATTGCTCGTTTTCATTTTGACCACATTTTGAAATTTTGTAAGTCACTCAATTGT
TTTAAATTCATTCAATTAAGCCATTTATCATTAATATATGAATGTCTTTAAATAGTTGGATCTCA
TTTATGATATCCGATCAAG
Found at i:3330369 original size:81 final size:81
Alignment explanation
Indices: 3329995--3330720 Score: 885
Period size: 81 Copynumber: 9.0 Consensus size: 81
3329985 CTATTTTAAA
* * * * * *
3329995 TAAAATATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCTAGATAGATTAAA-
1 TAAAAGATTAATTGCCTAGTTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
3330059 GTTAAAAACCTTTGAG
66 GTTAAATACCTTTGAG
* * * * *
3330075 TAAAAGATTACTTGTCTAGCTGTGCGTTTGATAGAAATGTGTCAATTATGCCAGTTAGAT-AAAG
1 TAAAAGATTAATTGCCTAGTTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
3330139 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * *
3330155 TAAAAGATTGA-TGCCTAGTTGTGCATTTGATAGAAATGTATCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGTTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
3330219 ATTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * *
3330235 T-AAAGATTAATTGCCTAGTTTTGCATTTGATATAAAGGTATCAATTATGCCAGTTTGATGAAAG
1 TAAAAGATTAATTGCCTAGTTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
3330299 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* *
3330315 TAAAAGATTAATTGCCTAGTTGTGTATTTGATAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGTTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
3330380 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* ** * *
3330396 TAAAATATTAATTGCCTAGTAT-TATATTTGACAGAAAGGTGTCAAATATGCCAGTTAGATGAAA
1 TAAAAGATTAATTGCCTAGT-TGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAA
* *
3330460 GGTTAAATGCCTTTAAG
65 GGTTAAATACCTTTGAG
** * * * * *
3330477 TAAAAGATTAATTGCCTACCTGTGCCTTTGACAAAAAGCTGTCAATTATGCTAGTTAGATGAAA-
1 TAAAAGATTAATTGCCTAGTTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
3330541 --TAAATGCCTTTGAG
66 GTTAAATACCTTTGAG
* ** * *
3330555 TAAAATATTAATTGTGTAGCTGTGCATTTGATAGAAAGGTGTCAATTATGACAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGTTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
* *
3330620 GCTAAATGCCTTTGAG
66 GTTAAATACCTTTGAG
* ** * * * *
3330636 CT-AAAGATTAAATGCCTAGTTGTGCATTTGGCAGAAAGATATCAATCATGCAAGTTAGATGAAA
1 -TAAAAGATTAATTGCCTAGTTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAA
* * *
3330700 GGCTAAATGCCTTTGGG
65 GGTTAAATACCTTTGAG
3330717 TAAA
1 TAAA
3330721 CACTAAATGA
Statistics
Matches: 566, Mismatches: 69, Indels: 21
0.86 0.11 0.03
Matches are distributed among these distances:
78 67 0.12
79 55 0.10
80 163 0.29
81 279 0.49
82 2 0.00
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.33
Consensus pattern (81 bp):
TAAAAGATTAATTGCCTAGTTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
GTTAAATACCTTTGAG
Found at i:3330553 original size:240 final size:240
Alignment explanation
Indices: 3329989--3330713 Score: 949
Period size: 240 Copynumber: 3.0 Consensus size: 240
3329979 TAAGAACTAT
* * * *
3329989 TTTAAATAAAATATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCTAGATAGA
1 TTTAAGTAAAAGATTAATTGCCTAGCTGTGCATTTGACAAAAAGGTGTCAATTATGCTAGTTAGA
* * * *
3330054 TTAAAGTTAAAAACCTTTGAGTAAAAGATTACTTGTCTAGCTGTGCGTTTGATAGAAATGTGTCA
66 TGAAAG-TAAATACCTTTGAGTAAAAGATTAATTGTCTAGCTGTGCATTTGATAGAAATGTGTCA
*
3330119 ATTATGCCAGTTAGAT-AAAGGTTAAATACCTTTGAGTAAAAGATTGATGCCTAGTTGTGCATTT
130 ATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGCCTAGTTGTGCATTT
* * * * *
3330183 GATAGAAATGTATCAATTATGCCAGTTAGATGAAAGATTAAATACC
195 GACAGAAAGGTATCAAATATGCCAGTTAGATGAAAGGTTAAATGCC
* * * * * * * *
3330229 TTTGAGT-AAAGATTAATTGCCTAGTTTTGCATTTGATATAAAGGTATCAATTATGCCAGTTTGA
1 TTTAAGTAAAAGATTAATTGCCTAGCTGTGCATTTGACAAAAAGGTGTCAATTATGCTAGTTAGA
* * *
3330293 TGAAAGGTTAAATACCTTTGAGTAAAAGATTAATTGCCTAGTTGTGTATTTGATAGAAATGTGTC
66 TGAAA-G-TAAATACCTTTGAGTAAAAGATTAATTGTCTAGCTGTGCATTTGATAGAAATGTGTC
* **
3330358 AATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAATATTAATTGCCTAGTAT-TATA
129 AATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAA-TGCCTAGT-TGTGCA
*
3330422 TTTGACAGAAAGGTGTCAAATATGCCAGTTAGATGAAAGGTTAAATGCC
192 TTTGACAGAAAGGTATCAAATATGCCAGTTAGATGAAAGGTTAAATGCC
* * *
3330471 TTTAAGTAAAAGATTAATTGCCTACCTGTGCCTTTGACAAAAAGCTGTCAATTATGCTAGTTAGA
1 TTTAAGTAAAAGATTAATTGCCTAGCTGTGCATTTGACAAAAAGGTGTCAATTATGCTAGTTAGA
* * * *
3330536 TGAAA-TAAATGCCTTTGAGTAAAATATTAATTGTGTAGCTGTGCATTTGATAGAAAGGTGTCAA
66 TGAAAGTAAATACCTTTGAGTAAAAGATTAATTGTCTAGCTGTGCATTTGATAGAAATGTGTCAA
* * *
3330600 TTATGACAGTTAGATGAAAGGCTAAATGCCTTTGAGCT-AAAGATTAAATGCCTAGTTGTGCATT
131 TTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAG-TAAAAGATT-AATGCCTAGTTGTGCATT
* * * *
3330664 TGGCAGAAAGATATC-AATCATGCAAGTTAGATGAAAGGCTAAATGCC
194 TGACAGAAAGGTATCAAAT-ATGCCAGTTAGATGAAAGGTTAAATGCC
3330711 TTT
1 TTT
3330714 GGGTAAACAC
Statistics
Matches: 419, Mismatches: 57, Indels: 18
0.85 0.12 0.04
Matches are distributed among these distances:
239 56 0.13
240 219 0.52
241 32 0.08
242 59 0.14
243 53 0.13
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.34
Consensus pattern (240 bp):
TTTAAGTAAAAGATTAATTGCCTAGCTGTGCATTTGACAAAAAGGTGTCAATTATGCTAGTTAGA
TGAAAGTAAATACCTTTGAGTAAAAGATTAATTGTCTAGCTGTGCATTTGATAGAAATGTGTCAA
TTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAGATTAATGCCTAGTTGTGCATTTG
ACAGAAAGGTATCAAATATGCCAGTTAGATGAAAGGTTAAATGCC
Found at i:3330618 original size:159 final size:159
Alignment explanation
Indices: 3329995--3330720 Score: 834
Period size: 159 Copynumber: 4.5 Consensus size: 159
3329985 CTATTTTAAA
* * * * * *
3329995 TAAAATATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCTAGATAGATTAAAG
1 TAAAAGATTAATTGCCTAGTTGTGCATTTGACA-AAAAGTGTCAATTATGCCAGTTAGATGAAAG
* * * * *
3330060 TTAAAAACCTTTGAGTAAAAGATTACTTGTCTAGCTGTGCGTTTGATAGAAATGTGTCAATTATG
65 -TAAATACCTTTGAGTAAAAGATTAATTGCCTAGCTGTGCATTTGATAGAAAGGTGTCAATTATG
3330125 CCAGTTAGAT-AAAGGTTAAATACCTTTGAG
129 CCAGTTAGATGAAAGGTTAAATACCTTTGAG
* * * *
3330155 TAAAAGATTGA-TGCCTAGTTGTGCATTTGATAGAAATGTATCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGTTGTGCATTTGACA-AAAAGTGTCAATTATGCCAGTTAGATGAAAG
* * * *
3330219 ATTAAATACCTTTGAGT-AAAGATTAATTGCCTAGTTTTGCATTTGATATAAAGGTATCAATTAT
65 --TAAATACCTTTGAGTAAAAGATTAATTGCCTAGCTGTGCATTTGATAGAAAGGTGTCAATTAT
*
3330283 GCCAGTTTGATGAAAGGTTAAATACCTTTGAG
128 GCCAGTTAGATGAAAGGTTAAATACCTTTGAG
* * *
3330315 TAAAAGATTAATTGCCTAGTTGTGTATTTGATAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGTTGTGCATTTGACA-AAAAGTGTCAATTATGCCAGTTAGATGAAA-
* * ** * *
3330380 GTTAAATACCTTTGAGTAAAATATTAATTGCCTAG-TATTATATTTGACAGAAAGGTGTCAAATA
64 G-TAAATACCTTTGAGTAAAAGATTAATTGCCTAGCT-GTGCATTTGATAGAAAGGTGTCAATTA
* *
3330444 TGCCAGTTAGATGAAAGGTTAAATGCCTTTAAG
127 TGCCAGTTAGATGAAAGGTTAAATACCTTTGAG
** * *
3330477 TAAAAGATTAATTGCCTACCTGTGCCTTTGACAAAAAGCTGTCAATTATGCTAGTTAGATGAAA-
1 TAAAAGATTAATTGCCTAGTTGTGCATTTGACAAAAAG-TGTCAATTATGCCAGTTAGATGAAAG
* * ** *
3330541 TAAATGCCTTTGAGTAAAATATTAATTGTGTAGCTGTGCATTTGATAGAAAGGTGTCAATTATGA
65 TAAATACCTTTGAGTAAAAGATTAATTGCCTAGCTGTGCATTTGATAGAAAGGTGTCAATTATGC
* *
3330606 CAGTTAGATGAAAGGCTAAATGCCTTTGAG
130 CAGTTAGATGAAAGGTTAAATACCTTTGAG
* * * * * *
3330636 CT-AAAGATTAAATGCCTAGTTGTGCATTTGGCAGAAAGATATCAATCATGCAAGTTAGATGAAA
1 -TAAAAGATTAATTGCCTAGTTGTGCATTTGACAAAAAG-TGTCAATTATGCCAGTTAGATGAAA
* *
3330700 GGCTAAATGCCTTTGGGTAAA
64 -G-TAAATACCTTTGAGTAAA
3330721 CACTAAATGA
Statistics
Matches: 493, Mismatches: 61, Indels: 22
0.86 0.11 0.04
Matches are distributed among these distances:
159 229 0.46
160 56 0.11
161 71 0.14
162 137 0.28
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.33
Consensus pattern (159 bp):
TAAAAGATTAATTGCCTAGTTGTGCATTTGACAAAAAGTGTCAATTATGCCAGTTAGATGAAAGT
AAATACCTTTGAGTAAAAGATTAATTGCCTAGCTGTGCATTTGATAGAAAGGTGTCAATTATGCC
AGTTAGATGAAAGGTTAAATACCTTTGAG
Found at i:3330749 original size:321 final size:321
Alignment explanation
Indices: 3329995--3330749 Score: 796
Period size: 321 Copynumber: 2.4 Consensus size: 321
3329985 CTATTTTAAA
* * * * * * * * *
3329995 TAAAATATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCTAGATAGATTAAA-
1 TAAAAGATTAAATGCCTAGTTGTGCATTTGACAGAAATGTATCAATCATGCAAGTTAGATGAAAG
* * * * * ** * * * * *
3330059 GTTAAAAACCTTTGAGTAAAAGATTACTTGTCTAGCTGTGC--GTTTGATAGAAATGTGTCAATT
66 GCTAAATACCTTTGAGTAAAATAATAATTAACTAG-T-AGCATATTTGACAGAAAGGTGTCAAAT
* * ** *
3330122 ATGCCAGTTAGATAAAGGTTAAATACCTTTGAGTAAAAGATTGATGCCTAGTTGTGCATTTGATA
129 ATGCCAGTTAGATAAAGGTTAAATACCTTTAAGTAAAAGATTAATGCCTACCTGTGCATTTGACA
*
3330187 GAAATGTATCAATTATGCCAGTTAGATGAAAGATTAAATACCTTTGAGTAAAGATTAATTGCCTA
194 GAAAAGTATCAATTATGCCAGTTAGATGAAAGATTAAATACCTTTGAGTAAAGATTAATTGCCTA
* * * * * *
3330252 GTTTTGCATTTGATATAAAGGTATCAATTATGCCAGTTTGATGAAAGGTTAAATACCTTTGAG
259 GCTGTGCATTTGATAGAAAGGTATCAATTATGACAGTTAGATGAAAGGCTAAATACCTTTGAG
* * * * * *
3330315 TAAAAGATTAATTGCCTAGTTGTGTATTTGATAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAAATGCCTAGTTGTGCATTTGACAGAAATGTATCAATCATGCAAGTTAGATGAAAG
* * ** **
3330380 GTTAAATACCTTTGAGTAAAATATTAATTGCCTAGTATTATATTTGACAGAAAGGTGTCAAATAT
66 GCTAAATACCTTTGAGTAAAATAATAATTAACTAGTAGCATATTTGACAGAAAGGTGTCAAATAT
* *
3330445 GCCAGTTAGATGAAAGGTTAAATGCCTTTAAGTAAAAGATTAATTGCCTACCTGTGCCTTTGACA
131 GCCAGTTAGAT-AAAGGTTAAATACCTTTAAGTAAAAGATTAA-TGCCTACCTGTGCATTTGACA
* * * * **
3330510 -AAAAGCTGTCAATTATGCTAGTTAGATG-AA-A-TAAATGCCTTTGAGTAAAATATTAATTGTG
194 GAAAAG-TATCAATTATGCCAGTTAGATGAAAGATTAAATACCTTTGAGT-AAAGATTAATTGCC
* *
3330571 TAGCTGTGCATTTGATAGAAAGGTGTCAATTATGACAGTTAGATGAAAGGCTAAATGCCTTTGAG
257 TAGCTGTGCATTTGATAGAAAGGTATCAATTATGACAGTTAGATGAAAGGCTAAATACCTTTGAG
*
3330636 CT-AAAGATTAAATGCCTAGTTGTGCATTTGGCAGAAA-GATATCAATCATGCAAGTTAGATGAA
1 -TAAAAGATTAAATGCCTAGTTGTGCATTTGACAGAAATG-TATCAATCATGCAAGTTAGATGAA
* * *
3330699 AGGCTAAATGCCTTTGGGTAAACACTAAATGATTAAC-AGT-GCAT-TTTGACA
64 AGGCTAAATACCTTTGAGTAAA-A-T-AATAATTAACTAGTAGCATATTTGACA
3330750 AACAAGTCAT
Statistics
Matches: 366, Mismatches: 57, Indels: 23
0.82 0.13 0.05
Matches are distributed among these distances:
320 72 0.20
321 209 0.57
322 38 0.10
323 41 0.11
324 6 0.02
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.33
Consensus pattern (321 bp):
TAAAAGATTAAATGCCTAGTTGTGCATTTGACAGAAATGTATCAATCATGCAAGTTAGATGAAAG
GCTAAATACCTTTGAGTAAAATAATAATTAACTAGTAGCATATTTGACAGAAAGGTGTCAAATAT
GCCAGTTAGATAAAGGTTAAATACCTTTAAGTAAAAGATTAATGCCTACCTGTGCATTTGACAGA
AAAGTATCAATTATGCCAGTTAGATGAAAGATTAAATACCTTTGAGTAAAGATTAATTGCCTAGC
TGTGCATTTGATAGAAAGGTATCAATTATGACAGTTAGATGAAAGGCTAAATACCTTTGAG
Found at i:3335631 original size:81 final size:81
Alignment explanation
Indices: 3335526--3336342 Score: 1195
Period size: 81 Copynumber: 10.1 Consensus size: 81
3335516 CTGTTTTAAA
* * ** * *
3335526 TAAAAGATTAATTGCCTAGATGTGCATTTGGCAGAAATATGTCAATTATGCTAGTTAGATGAAAT
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
3335591 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * * *
3335607 TAAAAGATTAATTGTCTTGCTGTGCATTTTACAGAAATGTGTCAATTATGACAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
3335672 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * *
3335688 TAAAAGATTAATTGCCTAGCTATGCATTTCATAGAAAGGTGTCAATTATGCCAATTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
3335753 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * *
3335769 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAATGGTGTCAATTATGCCAGTTAAACGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
3335834 GTTAAATACATTTGAG
66 GTTAAATACCTTTGAG
* * *
3335850 TAAAAGATTAATTGTCTAGCTGTGCATTTGACAGAAAGATGTCAATTATGACAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
3335915 GTTAAATGCCTTTGAG
66 GTTAAATACCTTTGAG
3335931 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
3335996 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * *
3336012 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGTCGGTTAGATGAAAT
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
3336077 GTTAAATGCCTTTGAG
66 GTTAAATACCTTTGAG
3336093 TAAAAGATTAATTGCCTA-CATGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAA
1 TAAAAGATTAATTGCCTAGC-TGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAA
**
3336157 GGTTAAATGTCTTTGAG
65 GGTTAAATACCTTTGAG
* * * * * * *
3336174 TGAAAGATTAATTGTCTAGCTGTTCATTTGATAGAAATGTGTCAATTATACAAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
* *
3336239 GCTAAATGCCTTTGAG
66 GTTAAATACCTTTGAG
* * * * *
3336255 TTAAAGATTAAATGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATCATGCAAGTTAGATGAAAG
1 TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
* * *
3336320 GCTAAATGCCTTTGGG
66 GTTAAATACCTTTGAG
3336336 TAAAAGA
1 TAAAAGA
3336343 CTAAATGATT
Statistics
Matches: 667, Mismatches: 67, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
80 1 0.00
81 665 1.00
82 1 0.00
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.32
Consensus pattern (81 bp):
TAAAAGATTAATTGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
GTTAAATACCTTTGAG
Found at i:3336979 original size:2 final size:2
Alignment explanation
Indices: 3336972--3336999 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3336962 AGTGATTTAA
3336972 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
3337000 GTGTGTGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3340899 original size:27 final size:27
Alignment explanation
Indices: 3340841--3340902 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
3340831 TTGGGTACTA
*
3340841 AAATGACCAAAATACCCTCGAGCTCTT
1 AAATGACCAAAATACCCTCGAGCTATT
* *
3340868 AAATGACCAAGATATCCTCGAG-TATT
1 AAATGACCAAAATACCCTCGAGCTATT
*
3340894 GCAATGACC
1 -AAATGACC
3340903 TAAACATCCT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 3 0.10
27 27 0.90
ACGTcount: A:0.37, C:0.26, G:0.15, T:0.23
Consensus pattern (27 bp):
AAATGACCAAAATACCCTCGAGCTATT
Found at i:3342953 original size:20 final size:20
Alignment explanation
Indices: 3342915--3342953 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3342905 AGTATCGATA
*
3342915 CTATATGAACAATATTGATT
1 CTATATGAACAATACTGATT
*
3342935 CTATATGAACATTACTGAT
1 CTATATGAACAATACTGAT
3342954 AATGTTAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.38
Consensus pattern (20 bp):
CTATATGAACAATACTGATT
Found at i:3344473 original size:19 final size:21
Alignment explanation
Indices: 3344436--3344483 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
3344426 AATTATTTTC
*
3344436 TTTT-AAAAGTAAAATTG-AA
1 TTTTGAAAAGCAAAATTGAAA
3344455 TTTTGAAAAGCAAAA-TGAAA
1 TTTTGAAAAGCAAAATTGAAA
3344475 TTTTGAAAA
1 TTTTGAAAA
3344484 ATGATTTTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 6 0.23
20 20 0.77
ACGTcount: A:0.52, C:0.02, G:0.12, T:0.33
Consensus pattern (21 bp):
TTTTGAAAAGCAAAATTGAAA
Found at i:3351392 original size:21 final size:20
Alignment explanation
Indices: 3351359--3351401 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
3351349 ACCTACTTTC
* *
3351359 AAAGGATCATGATGGTCCTCA
1 AAAGGAACATGATGAT-CTCA
*
3351380 AAAGGAACTTGATGATCTCA
1 AAAGGAACATGATGATCTCA
3351400 AA
1 AA
3351402 GTTTCATTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (20 bp):
AAAGGAACATGATGATCTCA
Found at i:3353544 original size:25 final size:27
Alignment explanation
Indices: 3353503--3353553 Score: 70
Period size: 25 Copynumber: 1.9 Consensus size: 27
3353493 AATGGTTTTA
3353503 CTTTTTATCAAATGGATGT-TAAAAGTG
1 CTTTTTA-CAAATGGATGTATAAAAGTG
*
3353530 CTTTTTA-AAATGGATTTATAAAAG
1 CTTTTTACAAATGGATGTATAAAAG
3353554 AAGTGTGTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 9 0.41
26 6 0.27
27 7 0.32
ACGTcount: A:0.37, C:0.06, G:0.16, T:0.41
Consensus pattern (27 bp):
CTTTTTACAAATGGATGTATAAAAGTG
Found at i:3357904 original size:12 final size:12
Alignment explanation
Indices: 3357887--3357911 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3357877 AATATTCATG
3357887 TGGTACTGATAC
1 TGGTACTGATAC
3357899 TGGTACTGATAC
1 TGGTACTGATAC
3357911 T
1 T
3357912 ATTAGTCTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (12 bp):
TGGTACTGATAC
Found at i:3358883 original size:28 final size:28
Alignment explanation
Indices: 3358843--3358897 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
3358833 AGATCCTTTC
*
3358843 TGATATTAAAAGTCTGACTCTTTTATTA
1 TGATATTAAAAGTATGACTCTTTTATTA
3358871 TGATATTAAAAGTATGACTCTTTTATT
1 TGATATTAAAAGTATGACTCTTTTATT
3358898 TGAAATAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.33, C:0.09, G:0.11, T:0.47
Consensus pattern (28 bp):
TGATATTAAAAGTATGACTCTTTTATTA
Found at i:3358913 original size:26 final size:28
Alignment explanation
Indices: 3358857--3358913 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
3358847 ATTAAAAGTC
* **
3358857 TGACTCTTTTATTATGATATTAAAAGTA
1 TGACTCTTTTATTATGATAATAAAAACA
3358885 TGACTCTTTTATT-TGA-AATAAAAACA
1 TGACTCTTTTATTATGATAATAAAAACA
3358911 TGA
1 TGA
3358914 TTTCCGATCT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 10 0.38
27 3 0.12
28 13 0.50
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.42
Consensus pattern (28 bp):
TGACTCTTTTATTATGATAATAAAAACA
Found at i:3359942 original size:10 final size:10
Alignment explanation
Indices: 3359914--3359964 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
3359904 AATTATATTT
*
3359914 TTAAAAATGA
1 TTAAAAATAA
*
3359924 TT-TAAATAA
1 TTAAAAATAA
*
3359933 TTAGAAATAA
1 TTAAAAATAA
3359943 TTAAATAATAA
1 TTAAA-AATAA
*
3359954 ATAAAAATAA
1 TTAAAAATAA
3359964 T
1 T
3359965 AAATAAATGT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
9 7 0.21
10 17 0.52
11 9 0.27
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (10 bp):
TTAAAAATAA
Found at i:3359956 original size:7 final size:7
Alignment explanation
Indices: 3359937--3359970 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
3359927 AAATAATTAG
3359937 AAATAATT
1 AAATAA-T
3359945 AAATAAT
1 AAATAAT
3359952 AAATAA-
1 AAATAAT
3359958 AAATAAT
1 AAATAAT
3359965 AAATAA
1 AAATAA
3359971 ATGTAAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 6 0.24
7 13 0.52
8 6 0.24
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (7 bp):
AAATAAT
Found at i:3359963 original size:13 final size:13
Alignment explanation
Indices: 3359945--3359971 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3359935 AGAAATAATT
3359945 AAATAATAAATAA
1 AAATAATAAATAA
3359958 AAATAATAAATAA
1 AAATAATAAATAA
3359971 A
1 A
3359972 TGTAAATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (13 bp):
AAATAATAAATAA
Found at i:3361998 original size:15 final size:16
Alignment explanation
Indices: 3361978--3362011 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
3361968 ATCCTCCATT
3361978 GAGTGGGAACACT-AG
1 GAGTGGGAACACTAAG
3361993 GAGTGGGAACACTAAG
1 GAGTGGGAACACTAAG
3362009 GAG
1 GAG
3362012 CAAAGATTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.35, C:0.12, G:0.41, T:0.12
Consensus pattern (16 bp):
GAGTGGGAACACTAAG
Found at i:3362811 original size:23 final size:23
Alignment explanation
Indices: 3362744--3362818 Score: 96
Period size: 23 Copynumber: 3.3 Consensus size: 23
3362734 CAAACTCTTA
* * * *
3362744 ACAGCTGCCTAACAAACTCATAC
1 ACAGCAGCTTAACAGACTCATGC
*
3362767 ACAACAGCTTAACAGACTCATGC
1 ACAGCAGCTTAACAGACTCATGC
3362790 ACAGCAGCTTAACAGACTCATGC
1 ACAGCAGCTTAACAGACTCATGC
*
3362813 ATAGCA
1 ACAGCA
3362819 AGCAATGCAT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.39, C:0.31, G:0.13, T:0.17
Consensus pattern (23 bp):
ACAGCAGCTTAACAGACTCATGC
Found at i:3376578 original size:19 final size:19
Alignment explanation
Indices: 3376554--3376603 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
3376544 ACCCTACAAA
3376554 TCTGTTCATTATATGTTTG
1 TCTGTTCATTATATGTTTG
*
3376573 TCTGTT-ATGTGTATGTTTG
1 TCTGTTCAT-TATATGTTTG
*
3376592 TGTGATTCATTA
1 TCTG-TTCATTA
3376604 AAGATGTCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
18 2 0.08
19 18 0.72
20 3 0.12
21 2 0.08
ACGTcount: A:0.16, C:0.08, G:0.20, T:0.56
Consensus pattern (19 bp):
TCTGTTCATTATATGTTTG
Found at i:3379632 original size:15 final size:15
Alignment explanation
Indices: 3379598--3379656 Score: 55
Period size: 15 Copynumber: 3.8 Consensus size: 15
3379588 AAATTCCTTA
*
3379598 TTTTACTTTTTCTAGGT
1 TTTTCCTTTTT-T-GGT
**
3379615 TTTTGGTTTTTTGGT
1 TTTTCCTTTTTTGGT
*
3379630 TTTTCCTTTTTTGAT
1 TTTTCCTTTTTTGGT
*
3379645 TTTTTCTTTTTT
1 TTTTCCTTTTTT
3379657 TCTTCAAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
15 26 0.72
16 1 0.03
17 9 0.25
ACGTcount: A:0.05, C:0.08, G:0.12, T:0.75
Consensus pattern (15 bp):
TTTTCCTTTTTTGGT
Found at i:3380091 original size:113 final size:111
Alignment explanation
Indices: 3379893--3380118 Score: 384
Period size: 113 Copynumber: 2.0 Consensus size: 111
3379883 TGATTGTAGT
3379893 TAAAGAATAAAGCTTAGGGGTCTAGACTTAATTAAAGGATGAGATGATATATGGATTAGATTGTT
1 TAAAGAATAAAGCTTAGGGGTCTAGACTTAATTAAAGGA-GAGATGATATATGGATTAGATTGTT
3379958 TTCACATATAGGATTTTGAATGGAGAAT-AAGCTGCTATAAGATTAAGA
65 TTCACATATAGGATTTTGAATGGAGAATAAAGCTGCTAT-A-ATTAAGA
*
3380006 TAAAGAATAAAGCTTAGGGGTCTAGACTTAATTAAAGGA-CGATGATATATGGATTAGATTGTTT
1 TAAAGAATAAAGCTTAGGGGTCTAGACTTAATTAAAGGAGAGATGATATATGGATTAGATTG-TT
3380070 TTCACAATATAGGATTTTGAATGGAGAATAAAGCTGCTATAATTAAGA
65 TTCAC-ATATAGGATTTTGAATGGAGAATAAAGCTGCTATAATTAAGA
3380118 T
1 T
3380119 TCATATAATG
Statistics
Matches: 109, Mismatches: 1, Indels: 7
0.93 0.01 0.06
Matches are distributed among these distances:
111 21 0.19
112 15 0.14
113 63 0.58
114 10 0.09
ACGTcount: A:0.39, C:0.07, G:0.22, T:0.32
Consensus pattern (111 bp):
TAAAGAATAAAGCTTAGGGGTCTAGACTTAATTAAAGGAGAGATGATATATGGATTAGATTGTTT
TCACATATAGGATTTTGAATGGAGAATAAAGCTGCTATAATTAAGA
Found at i:3381607 original size:32 final size:32
Alignment explanation
Indices: 3381539--3381618 Score: 99
Period size: 32 Copynumber: 2.5 Consensus size: 32
3381529 TACTACTACA
3381539 CATTATCT-AATTGCAACACTGACACTGCTGTG
1 CATTATCTGAA-TGCAACACTGACACTGCTGTG
* ** * *
3381571 CATTATCTGAATGCAGCACTGACTTTGTTGTT
1 CATTATCTGAATGCAACACTGACACTGCTGTG
3381603 CATTATCTGAATGCAA
1 CATTATCTGAATGCAA
3381619 AATTTATAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
32 39 0.95
33 2 0.05
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (32 bp):
CATTATCTGAATGCAACACTGACACTGCTGTG
Found at i:3391380 original size:56 final size:56
Alignment explanation
Indices: 3391264--3391380 Score: 162
Period size: 56 Copynumber: 2.1 Consensus size: 56
3391254 AGTTACCACG
* ** * *
3391264 ATAAAAAATTTACATGGATAGTTAAATGTGTAACAACCTTACTCCTTTGTAATCAG
1 ATAAGAAATTTACATGGATAACTAAATGTGTAACAACCTTACTCCTTTGTAACCAA
* * *
3391320 ATAAGAAATTTACATGGATAACTAAATGTTTAACAACCTTTCTCCTTTTTAACCAA
1 ATAAGAAATTTACATGGATAACTAAATGTGTAACAACCTTACTCCTTTGTAACCAA
3391376 ATAAG
1 ATAAG
3391381 GTTAATTGTA
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.34
Consensus pattern (56 bp):
ATAAGAAATTTACATGGATAACTAAATGTGTAACAACCTTACTCCTTTGTAACCAA
Found at i:3394309 original size:2 final size:2
Alignment explanation
Indices: 3394302--3394326 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3394292 GGACTTTCAT
3394302 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 T
3394327 TTATTTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3394428 original size:2 final size:2
Alignment explanation
Indices: 3394421--3394457 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
3394411 AACTTCGTAC
3394421 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3394458 CTCTATTTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3394642 original size:16 final size:17
Alignment explanation
Indices: 3394616--3394647 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
3394606 TAGATATTTT
3394616 CTTTAAATTTTCTCTAA
1 CTTTAAATTTTCTCTAA
3394633 CTTT-AATTTTCTCTA
1 CTTTAAATTTTCTCTA
3394648 TTAGGACAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.25, C:0.19, G:0.00, T:0.56
Consensus pattern (17 bp):
CTTTAAATTTTCTCTAA
Found at i:3404079 original size:21 final size:21
Alignment explanation
Indices: 3404053--3404103 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
3404043 TAAATGTTGC
*
3404053 ATCGATACTCAGGTTTGGAGT
1 ATCGATACTCAGGCTTGGAGT
3404074 ATCGATACTCAGGCTTGGAGT
1 ATCGATACTCAGGCTTGGAGT
*
3404095 ATCGGTACT
1 ATCGATACT
3404104 ACATGCATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (21 bp):
ATCGATACTCAGGCTTGGAGT
Found at i:3404382 original size:64 final size:64
Alignment explanation
Indices: 3404262--3404382 Score: 163
Period size: 64 Copynumber: 1.9 Consensus size: 64
3404252 TCGGCACTAC
* * * **
3404262 AGTGCATTTTTATACATTATTATCGATACCAGTATCGGTACCACATGAACGTTATTGACACTGA
1 AGTGCATTTTTACACATTAGTATCGATACCAGTATCGATACCACATGAACAATATTGACACTGA
* *
3404326 AGTGTATTTTTACACATTAGTATTGGA-ACCAGTATCGATACCACATGAACAATATTG
1 AGTGCATTTTTACACATTAGTA-TCGATACCAGTATCGATACCACATGAACAATATTG
3404383 GTACTCTAGG
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
64 46 0.94
65 3 0.06
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (64 bp):
AGTGCATTTTTACACATTAGTATCGATACCAGTATCGATACCACATGAACAATATTGACACTGA
Found at i:3406429 original size:2 final size:2
Alignment explanation
Indices: 3406424--3406451 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3406414 GTGTATAAAG
3406424 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
3406452 GGATATGGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3406525 original size:10 final size:10
Alignment explanation
Indices: 3406510--3406541 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
3406500 TATGTAAGTT
3406510 TGTGTGTATG
1 TGTGTGTATG
3406520 TGTGTGTATG
1 TGTGTGTATG
*
3406530 TGTGTGTGTG
1 TGTGTGTATG
3406540 TG
1 TG
3406542 GAAATATGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.06, C:0.00, G:0.44, T:0.50
Consensus pattern (10 bp):
TGTGTGTATG
Found at i:3406627 original size:2 final size:2
Alignment explanation
Indices: 3406577--3406608 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3406567 AAAAAATGTT
3406577 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
3406609 GTTAAAAATA
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
Done.