Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008229.1 Hibiscus syriacus cultivar Beakdansim tig00110865_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: 3634043
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 17
Found at i:3013495 original size:27 final size:27
Alignment explanation
Indices: 3013457--3013549 Score: 125
Period size: 27 Copynumber: 3.4 Consensus size: 27
3013447 GTATATATAT
*
3013457 ATATATATATTATATGTTTTCAAATTC
1 ATATATATATTATATGTTCTCAAATTC
**
3013484 ATATATATATTATATGTTCTCAAAACC
1 ATATATATATTATATGTTCTCAAATTC
*
3013511 ATATATATATTATTTGTTCTCAAAATT-
1 ATATATATATTATATGTTCTC-AAATTC
3013538 ATATTATATATT
1 ATA-TATATATT
3013550 TTTAAAACCA
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
27 47 0.81
28 11 0.19
ACGTcount: A:0.39, C:0.09, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATATATATTATATGTTCTCAAATTC
Found at i:3013509 original size:114 final size:116
Alignment explanation
Indices: 3013359--3013617 Score: 276
Period size: 114 Copynumber: 2.2 Consensus size: 116
3013349 ACGTTAAATA
* * * *
3013359 TTTTCAAAACCATATATTTATTATATGTTTTTAAAACTATAT-TA-AATA-TT-TTC-AAAACCA
1 TTTTCAAAACCATATATATATTATATGTTCTCAAAACCATATATATAATATTTGTTCTAAAA--A
* * *
3013419 TATATATTATATGGTTTCAAATCCATATGTATATATATATATATATATTATATG
64 T-TATATTATATAGTTTCAAAACCATATATATATATATATATATATATTATATG
** * *
3013473 TTTTCAAATTCATATATATATTATATGTTCTCAAAACCATATATATATTATTTGTTCTCAAAATT
1 TTTTCAAAACCATATATATATTATATGTTCTCAAAACCATATATATAATATTTGTTCTAAAAATT
* *
3013538 ATATTATATATTTTTAAAACCATATATATATATATATATATATATATACATATTATG
66 ATATTATATAGTTTCAAAACC--ATATATATATATATATATATATAT---TA-TATG
3013595 TTTTCAAAACCATATTATATATT
1 TTTTCAAAACCATA-TATATATT
3013618 TTCAAAGTAA
Statistics
Matches: 118, Mismatches: 15, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
114 36 0.31
115 2 0.02
116 21 0.18
117 4 0.03
118 26 0.22
119 3 0.03
121 2 0.02
122 16 0.14
123 8 0.07
ACGTcount: A:0.41, C:0.09, G:0.03, T:0.47
Consensus pattern (116 bp):
TTTTCAAAACCATATATATATTATATGTTCTCAAAACCATATATATAATATTTGTTCTAAAAATT
ATATTATATAGTTTCAAAACCATATATATATATATATATATATATTATATG
Found at i:3013558 original size:48 final size:54
Alignment explanation
Indices: 3013457--3013574 Score: 151
Period size: 54 Copynumber: 2.3 Consensus size: 54
3013447 GTATATATAT
*
3013457 ATATATATATTATATGTTTTCAAATTCATATATATATTATATGTTCTCAAAACC
1 ATATATATATTATATGTTCTCAAATTCATATATATATTATATGTTCTCAAAACC
*
3013511 ATATATATATTATTTGTTCTCAAAATT-ATAT-TATA-TAT-T-TT-T-AAAACC
1 ATATATATATTATATGTTCTC-AAATTCATATATATATTATATGTTCTCAAAACC
3013559 ATATATATATATATAT
1 ATATATATAT-TATAT
3013575 ATATATATAT
Statistics
Matches: 59, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
48 16 0.27
49 5 0.08
50 2 0.03
51 1 0.02
52 3 0.05
53 4 0.07
54 23 0.39
55 5 0.08
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.48
Consensus pattern (54 bp):
ATATATATATTATATGTTCTCAAATTCATATATATATTATATGTTCTCAAAACC
Found at i:3013564 original size:2 final size:2
Alignment explanation
Indices: 3013559--3013590 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3013549 TTTTAAAACC
*
3013559 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3013591 TATGTTTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3013567 original size:27 final size:27
Alignment explanation
Indices: 3013457--3013576 Score: 108
Period size: 27 Copynumber: 4.6 Consensus size: 27
3013447 GTATATATAT
* **
3013457 ATATATATATTATATGTTTTCAAATTC
1 ATATATATATTATATATTTTCAAAACC
* *
3013484 ATATATATATTATATGTTCTCAAAACC
1 ATATATATATTATATATTTTCAAAACC
* **
3013511 ATATATATATTAT-T-TGTTCTCAA--
1 ATATATATATTATATATTTTCAAAACC
*
3013534 A-AT-TATATTATATATTTTTAAAACC
1 ATATATATATTATATATTTTCAAAACC
3013559 ATATATATATATATATAT
1 ATATATATAT-TATATAT
3013577 ATATATATAC
Statistics
Matches: 75, Mismatches: 11, Indels: 13
0.76 0.11 0.13
Matches are distributed among these distances:
21 8 0.11
22 3 0.04
23 6 0.08
25 6 0.08
26 3 0.04
27 42 0.56
28 7 0.09
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.48
Consensus pattern (27 bp):
ATATATATATTATATATTTTCAAAACC
Found at i:3013631 original size:48 final size:47
Alignment explanation
Indices: 3013463--3013631 Score: 120
Period size: 48 Copynumber: 3.5 Consensus size: 47
3013453 ATATATATAT
* * *
3013463 ATATTATATGTTTTCAAATTCATATAT-ATATTATATGTTCTCAAAACC
1 ATATTATATATTTTCAAA-TAATATATAATA-TATATGTTTTCAAAACC
* *
3013511 ATATATATATTATTTGTTCTCAA-AAT-TATATTATATAT-TTTT-AAAACC
1 ATAT-TATA-TA-TT-TTC-AAATAATATATAATATATATGTTTTCAAAACC
* *
3013559 ATA-TATATATATAT-ATATATATATATACATAT-TATGTTTTCAAAACC
1 ATATTATATAT-TTTCAAATA-ATATATA-ATATATATGTTTTCAAAACC
3013606 ATATTATATATTTTCAAAGTAATATA
1 ATATTATATATTTTCAAA-TAATATA
3013632 ATGTGTACTA
Statistics
Matches: 94, Mismatches: 11, Indels: 32
0.69 0.08 0.23
Matches are distributed among these distances:
42 1 0.01
43 1 0.01
44 4 0.04
45 10 0.11
46 11 0.12
47 11 0.12
48 27 0.29
49 9 0.10
50 9 0.10
51 6 0.06
52 3 0.03
53 2 0.02
ACGTcount: A:0.41, C:0.09, G:0.03, T:0.47
Consensus pattern (47 bp):
ATATTATATATTTTCAAATAATATATAATATATATGTTTTCAAAACC
Found at i:3014613 original size:200 final size:200
Alignment explanation
Indices: 3014141--3014669 Score: 555
Period size: 200 Copynumber: 2.7 Consensus size: 200
3014131 AAGACCTCAG
* * * * * * *
3014141 TTTGAATTTTGACCAGAAGGTAGTTTCTCGTTACTACCATGCATTCAAC-TACTTTCAATTTAAA
1 TTTGAATTTTAACTAGAAGGTAGTTTCTCGTTACTACCATGCAGTCAACGTGCTTTCAAGTTGAG
* * * * * *
3014205 TGAAATCAAACTTAAAAGCTTTGGTCGATAGATAACTCTTCTTGATTTAAGTTATGTCGAGATCT
66 TGAAATTAAACTTGAAAGCTTTTGTCGAAAAATAGCTCTTCTTGATTTAAGTTATGTCGAGATCT
* * *
3014270 ACCTAGGAAATGGTTCTTTGTTGCCAAATCGCAACCCACCTGGGTCTTCTTCTTGGTTTAAAAAC
131 ACCTAGGAAATGGTTCATTGTTGCCAAATCACAACCCACCTGGATCTTCTTCTTGGTTTAAAAAC
*
3014335 TTTGA
196 CTTGA
* * * * * * * * *
3014340 TTTGAATTTTAACTAGAAGGTAGTTTATTGTTGCTACCATGCGGTTAATGTGCTCTCGAGCTGAG
1 TTTGAATTTTAACTAGAAGGTAGTTTCTCGTTACTACCATGCAGTCAACGTGCTTTCAAGTTGAG
* * * * *
3014405 TAAAATTAAACTTGAATGCTTTTGTCGAAATATAGCTCTTCTTGATTTAAGCTATGTAGAGATCT
66 TGAAATTAAACTTGAAAGCTTTTGTCGAAAAATAGCTCTTCTTGATTTAAGTTATGTCGAGATCT
*** * * *
3014470 GGGTA-GAAAGTGGTTCATTGTTGCCAAATCACAACCCACTTGGATCTTCTTCTTGGTTTAGAGA
131 ACCTAGGAAA-TGGTTCATTGTTGCCAAATCACAACCCACCTGGATCTTCTTCTTGGTTTAAAAA
*
3014534 CCTTGG
195 CCTTGA
* * * * * * * * *
3014540 TTTGGATTTTGATTGGAAGGTAGTTCCTCATTACTTCCATGCAGTCAACGTGTTTTCCAGTTGAG
1 TTTGAATTTTAACTAGAAGGTAGTTTCTCGTTACTACCATGCAGTCAACGTGCTTTCAAGTTGAG
* *
3014605 TGAAATT-AACTTGAAAG-TTTTGGTC-AACAAATAGTTCTTCTTAATTTAAGTTATGTCGAGAT
66 TGAAATTAAACTTGAAAGCTTTT-GTCGAA-AAATAGCTCTTCTTGATTTAAGTTATGTCGAGAT
3014667 CTA
129 CTA
3014670 GTTGGGAAGT
Statistics
Matches: 264, Mismatches: 62, Indels: 8
0.79 0.19 0.02
Matches are distributed among these distances:
198 6 0.02
199 87 0.33
200 171 0.65
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.38
Consensus pattern (200 bp):
TTTGAATTTTAACTAGAAGGTAGTTTCTCGTTACTACCATGCAGTCAACGTGCTTTCAAGTTGAG
TGAAATTAAACTTGAAAGCTTTTGTCGAAAAATAGCTCTTCTTGATTTAAGTTATGTCGAGATCT
ACCTAGGAAATGGTTCATTGTTGCCAAATCACAACCCACCTGGATCTTCTTCTTGGTTTAAAAAC
CTTGA
Found at i:3015112 original size:379 final size:379
Alignment explanation
Indices: 3014401--3015112 Score: 869
Period size: 379 Copynumber: 1.9 Consensus size: 379
3014391 GCTCTCGAGC
* * * *
3014401 TGAGTAAAATTAAACTTGAATGCTTTTGTCGAAATATAGCTCTTCTTGATTTAAGCTATGTAGAG
1 TGAGTAAAATTAAACTTGAAAGCTTTGGTCGAAAAATAGCTCTTCTTAATTTAAGCTATGTAGAG
* * ** *
3014466 ATCTGGGTAGAAAGTGGTTCATTGTTGCCAAATCACAACCCACTTGGATCTTCTTCTTGGTTTAG
66 ATCTGGCTAGAAAGTGGTTCATTGTTGCCAAATCACAACCCACTTGGATATTCTTCTTGACTTAA
* * * *** * * *
3014531 AGACCTTGGTTTGGATTTTGATTGGAAGGTAGTTCCTCATTACTTCCATGCAGTCAACGTGTTTT
131 AGACCTCGATTTGGATTTTAACCAGAAGATAGTTCCTCACTACTTCCATGCAGTCAACGTGCTTT
* *
3014596 CCAGTTGAGTGAAATTAACTTGAAAGTTTTGGTCAACAAATAGTTCTTCTTAATTTAAGTTATGT
196 CCAGTTGAGTGAAATAAACTTGAAAGTTTTGGTCAACAAATAGTTCTTCTTAATTTAAGATATGT
* * * * * *
3014661 CGAGATCTAGTTGGGAAGTGGTTTGTTATTGCCAAATCGTAGCCCATCTGGCTTTTCTTCTAGGC
261 CAAGATCTAGCTGGGAAGTGGTTTGTTATTGCCAAATCGCAACCCATCTGGCTCTTCTACTAGGC
3014726 TTAAAGACCTCGGTTTGAATGATGATCGGAAGGTAATTCCTCGTGCCTTCAAGT
326 TTAAAGACCTCGGTTTGAATGATGATCGGAAGGTAATTCCTCGTGCCTTCAAGT
* * *
3014780 TGAGTGAAATTGAACTTGAAAGCTTTGGTC-AACAAATAGCTCTTCTTAATTTAAGCTATGTCGT
1 TGAGTAAAATTAAACTTGAAAGCTTTGGTCGAA-AAATAGCTCTTCTTAATTTAAGCTATGTAG-
* * * * * *
3014844 A-ATCTGGCT-GAGAAGTTGTTCCTTGTTGTCAAATCGCATCCGA-TTCGGATATTCTTCTTGAC
64 AGATCTGGCTAGA-AAGTGGTTCATTGTTGCCAAATCACAACCCACTT-GGATATTCTTCTTGAC
* * ** * *
3014906 TTAAAGACCTCGATTTTGATTTTAACCAGAAGATGGTTCCTTGCTGCTTCCATGCAGTCAATGTG
127 TTAAAGACCTCGATTTGGATTTTAACCAGAAGATAGTTCCTCACTACTTCCATGCAGTCAACGTG
* * * * *
3014971 CTTTCGATTTGAGTGAAATCAAACTTGAAAGTTTTGGTCGACATATAGTTCTTCTTAATTTGAGA
192 CTTTCCAGTTGAGTGAAAT-AAACTTGAAAGTTTTGGTCAACAAATAGTTCTTCTTAATTTAAGA
* * * *
3015036 TATGTCAAGATCTAGCTGGGAATTGGTTTTTTGTTGCCAAATCGCAACCCA-CTTGGGTCTTC-A
256 TATGTCAAGATCTAGCTGGGAAGTGGTTTGTTATTGCCAAATCGCAACCCATC-TGGCTCTTCTA
*
3015099 CTTGGCTTAAAGAC
320 CTAGGCTTAAAGAC
3015113 ATCGATTCAC
Statistics
Matches: 276, Mismatches: 51, Indels: 12
0.81 0.15 0.04
Matches are distributed among these distances:
378 6 0.02
379 178 0.64
380 92 0.33
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.37
Consensus pattern (379 bp):
TGAGTAAAATTAAACTTGAAAGCTTTGGTCGAAAAATAGCTCTTCTTAATTTAAGCTATGTAGAG
ATCTGGCTAGAAAGTGGTTCATTGTTGCCAAATCACAACCCACTTGGATATTCTTCTTGACTTAA
AGACCTCGATTTGGATTTTAACCAGAAGATAGTTCCTCACTACTTCCATGCAGTCAACGTGCTTT
CCAGTTGAGTGAAATAAACTTGAAAGTTTTGGTCAACAAATAGTTCTTCTTAATTTAAGATATGT
CAAGATCTAGCTGGGAAGTGGTTTGTTATTGCCAAATCGCAACCCATCTGGCTCTTCTACTAGGC
TTAAAGACCTCGGTTTGAATGATGATCGGAAGGTAATTCCTCGTGCCTTCAAGT
Found at i:3016887 original size:199 final size:195
Alignment explanation
Indices: 3016591--3017302 Score: 568
Period size: 199 Copynumber: 3.7 Consensus size: 195
3016581 GCTCTCGAGC
* * * * *
3016591 TGAGTAAAATTAAACTTGAATGCTTTT-GTCGAA-ATATAGCTCTTCTTGATTTAAGCTATGTAG
1 TGAGTGAAATTAAACTTGAAAG-TTTTGGTC-AACAAATAGCTCTTCTTAATTTAAGCTATGTCG
* * * * * *
3016654 AGATCTGGGTAGAAAGTGGTTCATTGTTGCCAAATCACAACCCACTTGGATCTTCTTCTTGGTTT
64 AGATCTAGCTGGGAAGTGGTTCATTGTTGCCAAATCGCAACCCA-TTGGATCTTCTTCTTGGCTT
* * *
3016719 AGAGACCTTGGTTTGGATTTTGATTGGAAGGTAGTTCCTCATTACTTCCATGCAGTCAACGTGTT
128 AAAGACCTCGGTTTGGATTTTGATCGGAAGGT-GTTCCT-A-TACTTCCATGCAGTCAACGTG-T
*
3016784 TTCCAGT
189 TTCAAGT
* *
3016791 TGAGTGAAATT-AACTTGAAAGTTTTGGTCAACAAATAGTTCTTCTTAATTTAAGTTATGTCGAG
1 TGAGTGAAATTAAACTTGAAAGTTTTGGTCAACAAATAGCTCTTCTTAATTTAAGCTATGTCGAG
** * * * * * *
3016855 ATCTAGCTGGGAAGTGGTTTGTTATTGCCAAATCGTAGCCCATCTGGCTTTTCTTCTAGGCTTAA
66 ATCTAGCTGGGAAGTGGTTCATTGTTGCCAAATCGCAACCCAT-TGGATCTTCTTCTTGGCTTAA
* *
3016920 AGACCTCGGTTTGAATGTTGATCGGAA-G-G----TA-A-TTCC-T-C-GTGC--C----TTCAA
130 AGACCTCGGTTTGGATTTTGATCGGAAGGTGTTCCTATACTTCCATGCAGT-CAACGTGTTTCAA
3016968 GT
194 GT
* * *
3016970 TGAGTGAAATTGAACTTGAAAGCTTTGGTCAACAAATAGCTCTTCTTGATTTAAGCTATGTCGTA
1 TGAGTGAAATTAAACTTGAAAGTTTTGGTCAACAAATAGCTCTTCTTAATTTAAGCTATGTCG-A
* * * * * * * * *
3017035 -ATCTGGCTGAGAAGTTGTTCCTTGTTGTCAAATCGCATCCGATTCGGATATTCTTCTTGACTTA
65 GATCTAGCTGGGAAGTGGTTCATTGTTGCCAAATCGCAACCCATT-GGATCTTCTTCTTGGCTTA
* * * * * * * * *
3017099 AAGACCTCGATTTTGATTTTAACCAGAAGATGGTTCCTTGCTGCTTCCATGCAGTCAATGTGCTT
129 AAGACCTCGGTTTGGATTTTGATCGGAAGGT-GTTCC-T-ATACTTCCATGCAGTCAACGTG-TT
* *
3017164 TCGATT
190 TCAAGT
* * * * * * *
3017170 TGAGTGAAATCAAACTTGAAAGTTTTGGTCGACATATAGTTCTTCTTAATTTGAGATATGTCAAG
1 TGAGTGAAATTAAACTTGAAAGTTTTGGTCAACAAATAGCTCTTCTTAATTTAAGCTATGTCGAG
* ** * *
3017235 ATCTAGCTGGGAATTGGTTTTTTGTTGCCAAATCGCAACCCACTTGGGTCTTC-ACTTGGCTTAA
66 ATCTAGCTGGGAAGTGGTTCATTGTTGCCAAATCGCAACCCA-TTGGATCTTCTTCTTGGCTTAA
3017299 AGAC
130 AGAC
3017303 ATCGATTCAC
Statistics
Matches: 401, Mismatches: 81, Indels: 61
0.74 0.15 0.11
Matches are distributed among these distances:
179 18 0.04
180 116 0.29
181 1 0.00
183 1 0.00
184 1 0.00
185 2 0.00
186 2 0.00
187 1 0.00
188 5 0.01
189 1 0.00
191 5 0.01
192 2 0.00
193 2 0.00
194 2 0.00
196 1 0.00
198 8 0.02
199 124 0.31
200 107 0.27
201 2 0.00
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.37
Consensus pattern (195 bp):
TGAGTGAAATTAAACTTGAAAGTTTTGGTCAACAAATAGCTCTTCTTAATTTAAGCTATGTCGAG
ATCTAGCTGGGAAGTGGTTCATTGTTGCCAAATCGCAACCCATTGGATCTTCTTCTTGGCTTAAA
GACCTCGGTTTGGATTTTGATCGGAAGGTGTTCCTATACTTCCATGCAGTCAACGTGTTTCAAGT
Found at i:3017302 original size:379 final size:379
Alignment explanation
Indices: 3016591--3017302 Score: 887
Period size: 379 Copynumber: 1.9 Consensus size: 379
3016581 GCTCTCGAGC
* * *
3016591 TGAGTAAAATTAAACTTGAATGCTTTTGTCGAAATATAGCTCTTCTTGATTTAAGCTATGTAGAG
1 TGAGTAAAATTAAACTTGAAAGCTTTGGTCGAAAAATAGCTCTTCTTGATTTAAGCTATGTAGAG
* * ** *
3016656 ATCTGGGTAGAAAGTGGTTCATTGTTGCCAAATCACAACCCACTTGGATCTTCTTCTTGGTTTAG
66 ATCTGGCTAGAAAGTGGTTCATTGTTGCCAAATCACAACCCACTTGGATATTCTTCTTGACTTAA
* * * *** * * *
3016721 AGACCTTGGTTTGGATTTTGATTGGAAGGTAGTTCCTCATTACTTCCATGCAGTCAACGTGTTTT
131 AGACCTCGATTTGGATTTTAACCAGAAGATAGTTCCTCACTACTTCCATGCAGTCAACGTGCTTT
* *
3016786 CCAGTTGAGTGAAATTAACTTGAAAGTTTTGGTCAACAAATAGTTCTTCTTAATTTAAGTTATGT
196 CCAGTTGAGTGAAATAAACTTGAAAGTTTTGGTCAACAAATAGTTCTTCTTAATTTAAGATATGT
* * * * *
3016851 CGAGATCTAGCTGGGAAGTGGTTTGTTATTGCCAAATCGTAGCCCATCTGGCTTTTCTTCTAGGC
261 CAAGATCTAGCTGGGAAGTGGTTTGTTATTGCCAAATCGCAACCCATCTGGCTCTTCTACTAGGC
3016916 TTAAAGACCTCGGTTTGAATGTTGATCGGAAGGTAATTCCTCGTGCCTTCAAGT
326 TTAAAGACCTCGGTTTGAATGTTGATCGGAAGGTAATTCCTCGTGCCTTCAAGT
* * *
3016970 TGAGTGAAATTGAACTTGAAAGCTTTGGTC-AACAAATAGCTCTTCTTGATTTAAGCTATGTCGT
1 TGAGTAAAATTAAACTTGAAAGCTTTGGTCGAA-AAATAGCTCTTCTTGATTTAAGCTATGTAG-
* * * * * *
3017034 A-ATCTGGCT-GAGAAGTTGTTCCTTGTTGTCAAATCGCATCCGA-TTCGGATATTCTTCTTGAC
64 AGATCTGGCTAGA-AAGTGGTTCATTGTTGCCAAATCACAACCCACTT-GGATATTCTTCTTGAC
* * ** * *
3017096 TTAAAGACCTCGATTTTGATTTTAACCAGAAGATGGTTCCTTGCTGCTTCCATGCAGTCAATGTG
127 TTAAAGACCTCGATTTGGATTTTAACCAGAAGATAGTTCCTCACTACTTCCATGCAGTCAACGTG
* * * * *
3017161 CTTTCGATTTGAGTGAAATCAAACTTGAAAGTTTTGGTCGACATATAGTTCTTCTTAATTTGAGA
192 CTTTCCAGTTGAGTGAAAT-AAACTTGAAAGTTTTGGTCAACAAATAGTTCTTCTTAATTTAAGA
* * * *
3017226 TATGTCAAGATCTAGCTGGGAATTGGTTTTTTGTTGCCAAATCGCAACCCA-CTTGGGTCTTC-A
256 TATGTCAAGATCTAGCTGGGAAGTGGTTTGTTATTGCCAAATCGCAACCCATC-TGGCTCTTCTA
*
3017289 CTTGGCTTAAAGAC
320 CTAGGCTTAAAGAC
3017303 ATCGATTCAC
Statistics
Matches: 278, Mismatches: 49, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
378 6 0.02
379 179 0.64
380 93 0.33
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.37
Consensus pattern (379 bp):
TGAGTAAAATTAAACTTGAAAGCTTTGGTCGAAAAATAGCTCTTCTTGATTTAAGCTATGTAGAG
ATCTGGCTAGAAAGTGGTTCATTGTTGCCAAATCACAACCCACTTGGATATTCTTCTTGACTTAA
AGACCTCGATTTGGATTTTAACCAGAAGATAGTTCCTCACTACTTCCATGCAGTCAACGTGCTTT
CCAGTTGAGTGAAATAAACTTGAAAGTTTTGGTCAACAAATAGTTCTTCTTAATTTAAGATATGT
CAAGATCTAGCTGGGAAGTGGTTTGTTATTGCCAAATCGCAACCCATCTGGCTCTTCTACTAGGC
TTAAAGACCTCGGTTTGAATGTTGATCGGAAGGTAATTCCTCGTGCCTTCAAGT
Found at i:3022068 original size:20 final size:20
Alignment explanation
Indices: 3022039--3022086 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
3022029 AATCGGTTTA
3022039 ACCGGTTTTCAACCGGTTCTG
1 ACCGG-TTTCAACCGGTTCTG
* *
3022060 ACTGGTTTCGACCGGTTCTG
1 ACCGGTTTCAACCGGTTCTG
3022080 ACCGGTT
1 ACCGGTT
3022087 CGGTCTGAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 20 0.83
21 4 0.17
ACGTcount: A:0.12, C:0.27, G:0.27, T:0.33
Consensus pattern (20 bp):
ACCGGTTTCAACCGGTTCTG
Found at i:3022087 original size:10 final size:10
Alignment explanation
Indices: 3022050--3022087 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
3022040 CCGGTTTTCA
3022050 ACCGGTTCTG
1 ACCGGTTCTG
*
3022060 ACTGGTT-TCG
1 ACCGGTTCT-G
3022070 ACCGGTTCTG
1 ACCGGTTCTG
3022080 ACCGGTTC
1 ACCGGTTC
3022088 GGTCTGAACC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
9 1 0.04
10 22 0.92
11 1 0.04
ACGTcount: A:0.11, C:0.29, G:0.29, T:0.32
Consensus pattern (10 bp):
ACCGGTTCTG
Found at i:3022140 original size:22 final size:22
Alignment explanation
Indices: 3022115--3022157 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
3022105 CTGGTCTGAC
3022115 CCAACCCGACCCGACCGTTGAT
1 CCAACCCGACCCGACCGTTGAT
3022137 CCAACCCGACCCGACCGTTGA
1 CCAACCCGACCCGACCGTTGA
3022158 CCGTTGACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.47, G:0.19, T:0.12
Consensus pattern (22 bp):
CCAACCCGACCCGACCGTTGAT
Found at i:3029129 original size:10 final size:10
Alignment explanation
Indices: 3029103--3029146 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
3029093 GCTGCTGGAA
*
3029103 ACCGGTTTTCA
1 ACCGGTTTT-G
3029114 ACCGGTTTTG
1 ACCGGTTTTG
3029124 ACCGG-TTTG
1 ACCGGTTTTG
*
3029133 ACCGGTTTCG
1 ACCGGTTTTG
3029143 ACCG
1 ACCG
3029147 ATTCAAACCG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
9 9 0.30
10 12 0.40
11 9 0.30
ACGTcount: A:0.14, C:0.27, G:0.27, T:0.32
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:3029134 original size:9 final size:9
Alignment explanation
Indices: 3029114--3029173 Score: 57
Period size: 9 Copynumber: 6.3 Consensus size: 9
3029104 CCGGTTTTCA
3029114 ACCGGTTTTG
1 ACCGG-TTTG
3029124 ACCGGTTTG
1 ACCGGTTTG
3029133 ACCGGTTTCG
1 ACCGGTTT-G
* **
3029143 ACCGATTCAA
1 ACCGGTT-TG
3029153 ACCGGTTTG
1 ACCGGTTTG
*
3029162 ACCGGTCTG
1 ACCGGTTTG
3029171 ACC
1 ACC
3029174 CAACACGACC
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
9 23 0.56
10 18 0.44
ACGTcount: A:0.17, C:0.28, G:0.27, T:0.28
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:3029138 original size:19 final size:19
Alignment explanation
Indices: 3029114--3029173 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 19
3029104 CCGGTTTTCA
3029114 ACCGGTTTTGACCGGTTTG
1 ACCGGTTTTGACCGGTTTG
* * **
3029133 ACCGGTTTCGACCGATTCAA
1 ACCGGTTTTGACCGGTT-TG
*
3029153 ACCGG-TTTGACCGGTCTG
1 ACCGGTTTTGACCGGTTTG
3029171 ACC
1 ACC
3029174 CAACACGACC
Statistics
Matches: 31, Mismatches: 9, Indels: 3
0.72 0.21 0.07
Matches are distributed among these distances:
18 3 0.10
19 23 0.74
20 5 0.16
ACGTcount: A:0.17, C:0.28, G:0.27, T:0.28
Consensus pattern (19 bp):
ACCGGTTTTGACCGGTTTG
Found at i:3029201 original size:17 final size:17
Alignment explanation
Indices: 3029179--3029212 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3029169 TGACCCAACA
3029179 CGACCCGACCGTTGACC
1 CGACCCGACCGTTGACC
3029196 CGACCCGACCGTTGACC
1 CGACCCGACCGTTGACC
3029213 GTTGACCGTT
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:0.18, C:0.47, G:0.24, T:0.12
Consensus pattern (17 bp):
CGACCCGACCGTTGACC
Found at i:3037270 original size:19 final size:19
Alignment explanation
Indices: 3037190--3037261 Score: 135
Period size: 19 Copynumber: 3.8 Consensus size: 19
3037180 GTCTAATGAT
3037190 GGCAGTACTCAGCGAGATG
1 GGCAGTACTCAGCGAGATG
3037209 GGCAGTACTCAGCGAGATG
1 GGCAGTACTCAGCGAGATG
3037228 GGCAGTACTCAGCGAGATG
1 GGCAGTACTCAGCGAGATG
*
3037247 AGCAGTACTCAGCGA
1 GGCAGTACTCAGCGA
3037262 AATCTGCAGC
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 52 1.00
ACGTcount: A:0.28, C:0.22, G:0.35, T:0.15
Consensus pattern (19 bp):
GGCAGTACTCAGCGAGATG
Found at i:3047615 original size:18 final size:18
Alignment explanation
Indices: 3047594--3047631 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
3047584 ATTCTTTGCT
* *
3047594 TTATTTTTATTTTTATTC
1 TTATTCTTATTTTAATTC
3047612 TTATTCTTATTTTAATTC
1 TTATTCTTATTTTAATTC
3047630 TT
1 TT
3047632 GCATAATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.74
Consensus pattern (18 bp):
TTATTCTTATTTTAATTC
Found at i:3052486 original size:13 final size:14
Alignment explanation
Indices: 3052463--3052492 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
3052453 AATCTTGTGC
3052463 ACATGATATTTCAA
1 ACATGATATTTCAA
3052477 ACAT-ATATTTCAA
1 ACATGATATTTCAA
3052490 ACA
1 ACA
3052493 AGTATATGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.47, C:0.17, G:0.03, T:0.33
Consensus pattern (14 bp):
ACATGATATTTCAA
Found at i:3059271 original size:4 final size:4
Alignment explanation
Indices: 3059257--3059287 Score: 53
Period size: 4 Copynumber: 7.5 Consensus size: 4
3059247 TGAGATAAAG
3059257 ATAA GATAA ATAA ATAA ATAA ATAA ATAA AT
1 ATAA -ATAA ATAA ATAA ATAA ATAA ATAA AT
3059288 TGAAAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 22 0.85
5 4 0.15
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:3061230 original size:153 final size:153
Alignment explanation
Indices: 3061071--3061382 Score: 579
Period size: 153 Copynumber: 2.0 Consensus size: 153
3061061 ATACAAAGAC
* *
3061071 TACAAGATTTTATGGAAAAAGAATTTATAAAGAGATGCAATCAAAGGAACAAATTGAATAAAATG
1 TACAAGAGTTGATGGAAAAAGAATTTATAAAGAGATGCAATCAAAGGAACAAATTGAATAAAATG
* *
3061136 TAAAGTTGAGGGACTAAATTTTAAAATGAAGAAATTTGTTGTCAAAAAGAAGAATTGAAGTTACA
66 TAAAGTTGAGGGACTAAATTTTAAAATGAAGAAATTAGTTGTCAAAAAGAAGAATCGAAGTTACA
3061201 TAGATATTCTTGAATAATAGAAG
131 TAGATATTCTTGAATAATAGAAG
3061224 TACAAGAGTTGATGGAAAAAGAATTTATAAAGAGATGCAATCAAAGGAACAAATTGAATAAAATG
1 TACAAGAGTTGATGGAAAAAGAATTTATAAAGAGATGCAATCAAAGGAACAAATTGAATAAAATG
3061289 TAAAGTTGAGGGACTAAATTTTAAAATGAAGAAATTAGTTGTCAAAAAGAAGAATCGAAGTTACA
66 TAAAGTTGAGGGACTAAATTTTAAAATGAAGAAATTAGTTGTCAAAAAGAAGAATCGAAGTTACA
3061354 TAGATATTCTTGAATAATAGAAG
131 TAGATATTCTTGAATAATAGAAG
*
3061377 AACAAG
1 TACAAG
3061383 TGTTTCAAAT
Statistics
Matches: 154, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
153 154 1.00
ACGTcount: A:0.49, C:0.06, G:0.19, T:0.26
Consensus pattern (153 bp):
TACAAGAGTTGATGGAAAAAGAATTTATAAAGAGATGCAATCAAAGGAACAAATTGAATAAAATG
TAAAGTTGAGGGACTAAATTTTAAAATGAAGAAATTAGTTGTCAAAAAGAAGAATCGAAGTTACA
TAGATATTCTTGAATAATAGAAG
Found at i:3074290 original size:18 final size:18
Alignment explanation
Indices: 3074257--3074302 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
3074247 ATGTTTTGTC
* *
3074257 ATTTTAAATAAAAATAATA
1 ATTTT-AATTAAAATAACA
3074276 ATTTTAATTAAAATAACA
1 ATTTTAATTAAAATAACA
*
3074294 AATTTAATT
1 ATTTTAATT
3074303 CCACGTTACC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 19 0.79
19 5 0.21
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (18 bp):
ATTTTAATTAAAATAACA
Found at i:3075186 original size:29 final size:29
Alignment explanation
Indices: 3075127--3075187 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 29
3075117 TGCAAGATCG
3075127 AAATTATGACAATGACCTAAATAAAAAAA
1 AAATTATGACAATGACCTAAATAAAAAAA
* *
3075156 AAATTATGAACTAATGACCAAAATAAGAAAA
1 AAATTATG-AC-AATGACCTAAATAAAAAAA
3075187 A
1 A
3075188 GCAAGAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 8 0.29
30 2 0.07
31 18 0.64
ACGTcount: A:0.62, C:0.10, G:0.08, T:0.20
Consensus pattern (29 bp):
AAATTATGACAATGACCTAAATAAAAAAA
Found at i:3076309 original size:3 final size:3
Alignment explanation
Indices: 3076295--3076324 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
3076285 AAATAAACAA
*
3076295 TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3076325 ATCCCGGACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:3076629 original size:55 final size:53
Alignment explanation
Indices: 3076464--3077579 Score: 775
Period size: 55 Copynumber: 20.3 Consensus size: 53
3076454 GAGATATCAG
*
3076464 ACTCGAGA-AATCTTCTGA-AAACGGGTTCGCTCCCTATTCTTTTCAGGGAGTATAAA
1 ACTCGA-ACAATCTTCT-ACAAAC-GGTTCGCTCCCTATT-TTTTCAGAGAGTAT-AA
* * * * * *
3076520 ACTCGAACAATCTACTGCAAACGGGTTTGCTCCTTATTCTTTTAAGGGAGTATAGA
1 ACTCGAACAATCTTCTACAAAC-GGTTCGCTCCCTATT-TTTTCAGAGAGTATA-A
* *
3076576 ACTCGAACAATCTTCTACAAACGGTTCGCTCCCTATTCTTTTCAGGGAATATAGA
1 ACTCGAACAATCTTCTACAAACGGTTCGCTCCCTATT-TTTTCAGAGAGTATA-A
* * *
3076631 ACTCGAACAATCTTCTGCAAACGGGTTCACTCCCTATTCTTTTCAGGGAGTATAAA
1 ACTCGAACAATCTTCTACAAAC-GGTTCGCTCCCTATT-TTTTCAGAGAGTAT-AA
* * *
3076687 ACTCGAATAATCTTCTGA-AAATGGGTTCGCTCCCTATTCCTTTT-AGGGAGTATAGA
1 ACTCGAACAATCTTCT-ACAAA-CGGTTCGCTCCCTATT--TTTTCAGAGAGTATA-A
* * * * * * *
3076743 ACTCGAATAATTTTCTGCGAACAGGTTCACTCTCTATTCTTTTCAGGGAGTATAGA
1 ACTCGAACAATCTTCTACAAAC-GGTTCGCTCCCTATT-TTTTCAGAGAGTATA-A
* *
3076799 ACTCGAACAA---TCAACAATC-GTGTCTGCTCCCTATTTCTTT-AGAGAGTATAA
1 ACTCGAACAATCTTCTACAAACGGT-TC-GCTCCCTATTT-TTTCAGAGAGTATAA
* * * * *
3076850 GACTCGGACAATCTTCAACAATC-ATGTCTGCTCCCTATTTCTTCAGAGAGTATAA
1 -ACTCGAACAATCTTCTACAAACGGT-TC-GCTCCCTATTTTTTCAGAGAGTATAA
* * * *
3076905 GGCTCGAACAATCTTCAACAATC-GTGTCTGCTCCCTATTTCTTCAGAGAGTATAA
1 -ACTCGAACAATCTTCTACAAACGGT-TC-GCTCCCTATTTTTTCAGAGAGTATAA
* * * *
3076960 GACTCGAACAATCTTCAACAATCGTGTTCGCTCCCTATTCTTCCAGAGAGTATAA
1 -ACTCGAACAATCTTCTACAAACG-GTTCGCTCCCTATTTTTTCAGAGAGTATAA
* * * **
3077015 GACTCGAACAATCTTCAACAATC-GTGTCTTCTCCCTATTGCTTCAGAGAGTATAA
1 -ACTCGAACAATCTTCTACAAACGGT-TC-GCTCCCTATTTTTTCAGAGAGTATAA
* * * *
3077070 GACTTGAACAATCTTCAACAATCGTGTTCGCTCCCTATTCTTTCAGAGAGTATAA
1 -ACTCGAACAATCTTCTACAAACG-GTTCGCTCCCTATTTTTTCAGAGAGTATAA
* * * *
3077125 GACTCGAACAATCTTCAACAATCGTTTCTGCTCCCTATTTCTTCAGAGAGTATAA
1 -ACTCGAACAATCTTCTACAAACGGTTC-GCTCCCTATTTTTTCAGAGAGTATAA
* * * *
3077180 GACTCGAACAATCTTCAACAATCGTGTTTGCTCCCTATTTCTTCAGAGAGTATAA
1 -ACTCGAACAATCTTCTACAAACG-GTTCGCTCCCTATTTTTTCAGAGAGTATAA
* * *
3077235 GACTCGAACAATCTTCAACAATC-GTGTCTGCTCCCTATTTATTCAGAGAGTATAA
1 -ACTCGAACAATCTTCTACAAACGGT-TC-GCTCCCTATTTTTTCAGAGAGTATAA
* * *
3077290 GACTC-AGACGATCTTCTACAAATGGGTTCGCTCCCTCTTTCTTTCAG-GAAGTATAGA
1 -ACTCGA-ACAATCTTCTACAAA-CGGTTCGCTCCCTATTT-TTTCAGAG-AGTATA-A
* ** *
3077347 ACTCGAATAATCTTCTGTAAACGGGTTCGCTCCCTCTTTCTTTCAG-GAAGTATAGA
1 ACTCGAACAATCTTCTACAAAC-GGTTCGCTCCCTATTT-TTTCAGAG-AGTATA-A
* * * * * * * *
3077403 ACTTGAATAATCTTCTTCATACGGGTTCGCTCTCTCTTTCTTCAGGGAGTATAGA
1 ACTCGAACAATCTTCTACAAAC-GGTTCGCTCCCTATTTTTTCAGAGAGTATA-A
* * * *
3077458 ACTC-AAAAATC-T-T-CAAACGGGCTCGATCCCTCTTTCTTTCA-AGAAGTATAGA
1 ACTCGAACAATCTTCTACAAAC-GGTTCGCTCCCTATTT-TTTCAGAG-AGTATA-A
* * * *
3077510 ACTCGAATAATCTTCTGA-AAACAGGTTCGCTCCCTCTTTCTTT-AGGGAGTATGGA
1 ACTCGAACAATCTTCT-ACAAAC-GGTTCGCTCCCTATTT-TTTCAGAGAGTAT-AA
3077565 ACTCGAACAATCTTC
1 ACTCGAACAATCTTC
3077580 ATTTTCCTCA
Statistics
Matches: 922, Mismatches: 90, Indels: 97
0.83 0.08 0.09
Matches are distributed among these distances:
51 22 0.02
52 38 0.04
53 27 0.03
54 16 0.02
55 492 0.53
56 313 0.34
57 14 0.02
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (53 bp):
ACTCGAACAATCTTCTACAAACGGTTCGCTCCCTATTTTTTCAGAGAGTATAA
Found at i:3076941 original size:110 final size:109
Alignment explanation
Indices: 3076492--3077361 Score: 878
Period size: 110 Copynumber: 7.9 Consensus size: 109
3076482 AAACGGGTTC
* * * * ** * * * *
3076492 GCTCCCTATTCTTTTCAGGGAGTATAAAACTCGAACAATCTACTGCAAACGGGTTTGCTCCTTAT
1 GCTCCCTATT-TCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTTCGCTCCCTAT
* * * *
3076557 TCTTTTAAGGGAGTAT-AGAACTCGAACAATCTTCTACAAACG-GT-T
65 TC--TTCAGAGAGTATAAG-ACTCGAACAATCTTCAACAATCGTGTCT
* * * ** * * *
3076602 CGCTCCCTATTCTTTTCAGGGAATAT-AGAACTCGAACAATCTTCTGCAAACGGGTTCACTCCCT
1 -GCTCCCTATT-TCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAACAATCGTGTTCGCTCCCT
* * * *
3076666 ATTCTTTTCAGGGAGTATAAAACTCGAATAATCTTCTGAA-AAT-GGGT-T
63 ATTC--TTCAGAGAGTATAAGACTCGAACAATCTTC--AACAATCGTGTCT
* * * * * ** * *
3076714 CGCTCCCTATTCCTTTTAGGGAGTAT-AGAACTCGAATAATTTTCTGCGAA-CAG-GTTCACTCT
1 -GCTCCCTATTTC-TTCAGAGAGTATAAG-ACTCGAACAATCTTCAAC-AATC-GTGTTCGCTCC
*
3076776 CTATTCTTTTCAGGGAGTAT-AGAACTCGAACAA---TCAACAATCGTGTCT
61 CTATTC--TTCAGAGAGTATAAG-ACTCGAACAATCTTCAACAATCGTGTCT
* * *
3076824 GCTCCCTATTTCTTTAGAGAGTATAAGACTCGGACAATCTTCAACAATCATG-TCTGCTCCCTAT
1 GCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTTC-GCTCCCTA-
*
3076888 TTCTTCAGAGAGTATAAGGCTCGAACAATCTTCAACAATCGTGTCT
64 TTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCT
3076934 GCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTTCGCTCCCTATT
1 GCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTTCGCTCCCTATT
3076999 CTTCCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCT
66 CTT-CAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCT
* * *
3077044 TCTCCCTATTGCTTCAGAGAGTATAAGACTTGAACAATCTTCAACAATCGTGTTCGCTCCCTATT
1 GCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTTCGCTCCCTATT
*
3077109 CTTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTTTCT
66 C-TTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCT
*
3077154 GCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTTTGCTCCCTATT
1 GCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTTCGCTCCCTA-T
3077219 TCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCT
65 TCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCT
* * * *
3077264 GCTCCCTATTTATTCAGAGAGTATAAGACTC-AGACGATCTTCTACAAAT-GGGTTCGCTCCCTC
1 GCTCCCTATTTCTTCAGAGAGTATAAGACTCGA-ACAATCTTCAAC-AATCGTGTTCGCTCCCT-
* *
3077327 TTTCTTTCAG-GAAGTAT-AGAACTCGAATAATCTTC
63 ATTC-TTCAGAG-AGTATAAG-ACTCGAACAATCTTC
3077362 TGTAAACGGG
Statistics
Matches: 675, Mismatches: 53, Indels: 62
0.85 0.07 0.08
Matches are distributed among these distances:
107 26 0.04
108 37 0.05
109 27 0.04
110 375 0.56
111 122 0.18
112 84 0.12
113 4 0.01
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.32
Consensus pattern (109 bp):
GCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTTCGCTCCCTATT
CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCT
Found at i:3077599 original size:107 final size:107
Alignment explanation
Indices: 3077314--3077580 Score: 318
Period size: 107 Copynumber: 2.4 Consensus size: 107
3077304 TCTACAAATG
* * ** * *
3077314 GGTTCGCTCCCTCTTTCTTTCAGGAAGTATAGAACTCGAATAATCTTCTGTAAACGGGTTCGCTC
1 GGTTCGCTCCCTCTTTC-TTCAGGGAGTATAGAACTC-AAAAATCTTC---AAACGGCCTCGATA
* * ** * *
3077379 CCTCTTTCTTTCAGGAAGTATAGAACTTGAATAATCTTCTTCATACG
61 CCTCTTTCTTTCAAGAAGTATAGAACTCGAATAATCTTCTGAAAACA
* * *
3077426 GGTTCGCTCTCTCTTTCTTCAGGGAGTATAGAACTCAAAAATCTTCAAACGGGCTCGATCCCTCT
1 GGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCAAAAATCTTCAAACGGCCTCGATACCTCT
3077491 TTCTTTCAAGAAGTATAGAACTCGAATAATCTTCTGAAAACA
66 TTCTTTCAAGAAGTATAGAACTCGAATAATCTTCTGAAAACA
* * *
3077533 GGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAACAATCTTCA
1 GGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTC-AAAAATCTTCA
3077581 TTTTCCTCAC
Statistics
Matches: 139, Mismatches: 15, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
107 86 0.62
108 10 0.07
110 9 0.06
111 18 0.13
112 16 0.12
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (107 bp):
GGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCAAAAATCTTCAAACGGCCTCGATACCTCT
TTCTTTCAAGAAGTATAGAACTCGAATAATCTTCTGAAAACA
Found at i:3077656 original size:37 final size:37
Alignment explanation
Indices: 3077587--3077662 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
3077577 TTCATTTTCC
*
3077587 TCACTACTTCTTTGTGAAGGCTTCTAGATGATTTGCT
1 TCACTACTTCTTTGTGAAGGCTTCAAGATGATTTGCT
*
3077624 TCACTAC-TCTTTTGTGAAGGCTT-AAGTTTGATTTGCT
1 TCACTACTTC-TTTGTGAAGGCTTCAAG-ATGATTTGCT
3077661 TC
1 TC
3077663 GAAGGTTGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 4 0.11
37 31 0.89
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.45
Consensus pattern (37 bp):
TCACTACTTCTTTGTGAAGGCTTCAAGATGATTTGCT
Found at i:3078248 original size:20 final size:19
Alignment explanation
Indices: 3078209--3078250 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
3078199 TTTTCTCGAT
3078209 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
3078228 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
3078248 ATT
1 ATT
3078251 TATAAAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:3078361 original size:120 final size:120
Alignment explanation
Indices: 3078117--3078354 Score: 295
Period size: 120 Copynumber: 2.0 Consensus size: 120
3078107 AAAAATATAT
* * * *
3078117 ATTAATTTATATATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAATGACTTCTAGG
1 ATTAATATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAATGACATCCAGG
* *
3078182 TGCCTTAAGACAGCTCTTTTTCTCGATATTAAAAAATAAATAAATAATTAAAACA
66 TGCCTTAAGACAGCTCTCTTTCTCAATATTAAAAAATAAATAAATAATTAAAACA
** *
3078237 ATTAATATATA-ATTTATAAAATAGGATATTTATTTATTTAAAAATATTAGAAAATGGACATCCA
1 ATTAATATATATATTTAT-AAATAAAATATTTATTTATTTAAAAATATCAGAAAAT-GACATCCA
* ** * * *
3078301 GTTGTTTTAAGACTG-TC-CTTTCTTAATATTGAAAAATAAATAAAT-ATTAAAACA
64 GGTGCCTTAAGACAGCTCTCTTTCTCAATATTAAAAAATAAATAAATAATTAAAACA
3078355 GGATTAAAAT
Statistics
Matches: 101, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
118 9 0.09
119 30 0.30
120 45 0.45
121 17 0.17
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (120 bp):
ATTAATATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAATGACATCCAGG
TGCCTTAAGACAGCTCTCTTTCTCAATATTAAAAAATAAATAAATAATTAAAACA
Found at i:3079855 original size:3 final size:3
Alignment explanation
Indices: 3079849--3079896 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
3079839 ATTATTTATT
* *
3079849 TAA TAA TAG TAA T-A TAA T-A TAA TAA TAA TAT TAA -AA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3079894 TAA
1 TAA
3079897 ATAAAACAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
2 6 0.16
3 32 0.84
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:3079886 original size:14 final size:14
Alignment explanation
Indices: 3079858--3079897 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
3079848 TTAATAATAG
*
3079858 TAAT-ATAATATAA
1 TAATAATAATAAAA
*
3079871 TAATAATATTAAAA
1 TAATAATAATAAAA
3079885 TAATAATAATAAA
1 TAATAATAATAAA
3079898 TAAAACAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 4 0.17
14 19 0.83
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
TAATAATAATAAAA
Found at i:3080330 original size:123 final size:115
Alignment explanation
Indices: 3080101--3080778 Score: 464
Period size: 113 Copynumber: 5.9 Consensus size: 115
3080091 ATGACAATTC
* * *
3080101 ATCTCCTTCTGTGA-AGTAATCTAGCAAAAAAGTTGAACAGATTCTTCTCATTATGAA--CTTAT
1 ATCTCCTTCTGTGATAG-AATCT-GC-AAAAGGTTGAACAAATTCTTCTCATTATGAATTCTTCT
* * *
3080163 TCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TCCTTCTAGAAATGCTGATGATG
63 TCCTCTTCAGATGAGTTCTTCTCATTATGAACTTAC-TCTGGAAATGCTGAT--TG
*
3080218 ATATGTCTCCTTCTGTGATAGAGTCATGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCT
1 --A--TCTCCTTCTGTGATAGAATC-TGCAAAAGGTTGAACAAATTCTTCTCATTATGAA-TTCT
* *
3080283 TCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAA---TG-TTG
60 TCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTTACTCTGGAAATGCTGATTG
* * * * *
3080335 A--TCCATCAAGTGAT-GAATTTGAACAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTC
1 ATCTCCTTC-TGTGATAGAATCTG--CAAAAGGTTGAACAAATTCTTCTCATTATGAA-TTCTTC
3080397 TTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC-CTGGAAATGC----TG
62 TTCC-TCTTCAGATGAGTTCTTCTCATTATGAACT-TACTCTGGAAATGCTGATTG
* * * *
3080448 A--TCCATC-GAATGAT-GAATTCAAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAA--CTTC
1 ATCTCCTTCTG--TGATAGAA-TC-TGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTCTTC
*
3080507 TTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTAC-CTGGAAA---TG-TTG
62 TTCCTCTTCAGATGAGTTCTTCTCATTATGAAC-TTACTCTGGAAATGCTGATTG
* * * * * * *
3080557 A--TCCATCAAGTGAT-GGATTTGAACAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCCTC
1 ATCTCCTTC-TGTGATAGAATCTG--CAAAAGGTTGAACAAATTCTTCTCATTATGAA-TTCTTC
*
3080619 TTCCTTTTTCAGATGAGTTCTTCTCATTATGAACTCTAC-CTGGAAA---TG-TTG
62 TTCC-TCTTCAGATGAGTTCTTCTCATTATGAACT-TACTCTGGAAATGCTGATTG
* * * * *
3080670 A--TCCATC-GAATGAT-GAATTCAAGCAAAAAGTTGAACAAGTTCTTTTCATTATGAACTTCTT
1 ATCTCCTTCTG--TGATAGAA-TC-TGCAAAAGGTTGAACAAATTCTTCTCATTATGAA-TTCTT
3080731 CTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACT-TGGAAAT
61 CTTCC-TCTTCAGATGAGTTCTTCTCATTATGAACT-TACTCTGGAAAT
3080779 TTTTTAAGAA
Statistics
Matches: 482, Mismatches: 38, Indels: 83
0.80 0.06 0.14
Matches are distributed among these distances:
107 1 0.00
108 1 0.00
109 84 0.17
110 10 0.02
111 11 0.02
112 52 0.11
113 217 0.45
114 4 0.01
115 3 0.01
117 2 0.00
119 2 0.00
120 31 0.06
121 18 0.04
122 3 0.01
123 41 0.09
124 2 0.00
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (115 bp):
ATCTCCTTCTGTGATAGAATCTGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTCTTCTTCC
TCTTCAGATGAGTTCTTCTCATTATGAACTTACTCTGGAAATGCTGATTG
Found at i:3080453 original size:113 final size:113
Alignment explanation
Indices: 3080245--3080778 Score: 800
Period size: 113 Copynumber: 4.8 Consensus size: 113
3080235 ATAGAGTCAT
* * *
3080245 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCC-TCTTCAGATAAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
3080309 ATTATGAACT-TTCTCTGGAAATGTTGATCCATC-AAGTGATGAATTTGAA
66 ATTATGAACTCTAC-CTGGAAATGTTGATCCATCGAA-TGATGAA-TTCAA
*
3080358 -CAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
3080422 ATTATGAACTCTACCTGGAAATGCTGATCCATCGAATGATGAATTCAA
66 ATTATGAACTCTACCTGGAAATGTTGATCCATCGAATGATGAATTCAA
*
3080470 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAA---CTTCTT-CTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
3080531 ATTATGAACTTTACCTGGAAATGTTGATCCATC-AAGTGATGGATTTGAA
66 ATTATGAACTCTACCTGGAAATGTTGATCCATCGAA-TGAT-GAATTCAA
* * *
3080580 -CAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTTTTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
3080644 ATTATGAACTCTACCTGGAAATGTTGATCCATCGAATGATGAATTCAA
66 ATTATGAACTCTACCTGGAAATGTTGATCCATCGAATGATGAATTCAA
* *
3080692 GCAAAAAGTTGAACAAGTTCTTTTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
3080757 ATTATGAACTCTACTTGGAAAT
66 ATTATGAACTCTACCTGGAAAT
3080779 TTTTTAAGAA
Statistics
Matches: 383, Mismatches: 26, Indels: 24
0.88 0.06 0.06
Matches are distributed among these distances:
108 2 0.01
109 87 0.23
110 12 0.03
112 55 0.14
113 221 0.58
114 6 0.02
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTCTACCTGGAAATGTTGATCCATCGAATGATGAATTCAA
Found at i:3080538 original size:222 final size:223
Alignment explanation
Indices: 3080245--3080778 Score: 901
Period size: 222 Copynumber: 2.4 Consensus size: 223
3080235 ATAGAGTCAT
* * * *
3080245 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATAAGTTCTTCTCA
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAA--TCTTCTTCTTCTTCAGATGAGTTCTTCTCA
3080310 TTATGAACTTT-CTCTGGAAATGTTGATCCATCAAGTGATGAATTTGAACAAAAGGTTAAACAAG
64 TTATGAACTTTAC-CTGGAAATGTTGATCCATCAAGTGATGAATTTGAACAAAAGGTTAAACAAG
*
3080374 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTG
128 TTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTG
3080439 GAAATGCTGATCCATCGAATGATGAATTCAA
193 GAAATGCTGATCCATCGAATGATGAATTCAA
3080470 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAA-CTTCTTCTTCTTCAGATGAGTTCTTCTCATT
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAATCTTCTTCTTCTTCAGATGAGTTCTTCTCATT
*
3080534 ATGAACTTTACCTGGAAATGTTGATCCATCAAGTGATGGATTTGAACAAAAGGTTAAACAAGTTC
66 ATGAACTTTACCTGGAAATGTTGATCCATCAAGTGATGAATTTGAACAAAAGGTTAAACAAGTTC
*
3080599 TTCTCATTATGAACTTCCTCTTCCTTTTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGAA
131 TTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGAA
*
3080664 ATGTTGATCCATCGAATGATGAATTCAA
196 ATGCTGATCCATCGAATGATGAATTCAA
*
3080692 GCAAAAAGTTGAACAAGTTCTTTTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAA--TCTTCTT-CTTCTTCAGATGAGTTCTTCTC
* *
3080757 ATTATGAACTCTACTTGGAAAT
63 ATTATGAACTTTACCTGGAAAT
3080779 TTTTTAAGAA
Statistics
Matches: 293, Mismatches: 11, Indels: 9
0.94 0.04 0.03
Matches are distributed among these distances:
222 213 0.73
223 1 0.00
225 37 0.13
226 42 0.14
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (223 bp):
GCAAAAAGTTGAACAAGTTCTTCTCATTATGAATCTTCTTCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTTTACCTGGAAATGTTGATCCATCAAGTGATGAATTTGAACAAAAGGTTAAACAAGTTC
TTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGAA
ATGCTGATCCATCGAATGATGAATTCAA
Found at i:3080932 original size:76 final size:76
Alignment explanation
Indices: 3080805--3080978 Score: 267
Period size: 76 Copynumber: 2.3 Consensus size: 76
3080795 AAAAACATTT
* * * * *
3080805 TGCACTGTAGGGCTTACAGCTGACTCAAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTT
1 TGCACTGTAGGACTTACAGATGACACAAAGGCTTTAAAAACATCAAAAAGCTCCCGAAGGCTTTT
3080870 TGGACACATCA
66 TGGACACATCA
* *
3080881 TGCACTGTAGGACTTATAGATGACACTAAGGCTTTAAAAACATCAAAAAGCTCCCGAAGGCTTTT
1 TGCACTGTAGGACTTACAGATGACACAAAGGCTTTAAAAACATCAAAAAGCTCCCGAAGGCTTTT
3080946 TGGACACATCA
66 TGGACACATCA
* *
3080957 TACACTGTATGACTTACAGATG
1 TGCACTGTAGGACTTACAGATG
3080979 TGGGAAATAG
Statistics
Matches: 88, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
76 88 1.00
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (76 bp):
TGCACTGTAGGACTTACAGATGACACAAAGGCTTTAAAAACATCAAAAAGCTCCCGAAGGCTTTT
TGGACACATCA
Found at i:3081685 original size:22 final size:22
Alignment explanation
Indices: 3081657--3081733 Score: 127
Period size: 22 Copynumber: 3.5 Consensus size: 22
3081647 CATAAGGCTT
3081657 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
* *
3081679 TCATCTTTAAAAAGAGAACCTA
1 TCATCTTTGAAAAGAGAATCTA
*
3081701 TCATCTTTGAAAATAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
3081723 TCATCTTTGAA
1 TCATCTTTGAA
3081734 GAGTGTAGAT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:3084114 original size:14 final size:14
Alignment explanation
Indices: 3084095--3084123 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3084085 ATGTGGTCTG
3084095 AATTCATCAATTGC
1 AATTCATCAATTGC
3084109 AATTCATCAATTGC
1 AATTCATCAATTGC
3084123 A
1 A
3084124 GAATTGACAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.21, G:0.07, T:0.34
Consensus pattern (14 bp):
AATTCATCAATTGC
Found at i:3090416 original size:9 final size:9
Alignment explanation
Indices: 3090395--3090425 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
3090385 TAACATGCAT
3090395 GAAAAAATAA
1 GAAAAAAT-A
3090405 GAAAAAATA
1 GAAAAAATA
3090414 GAAAAAATA
1 GAAAAAATA
3090423 GAA
1 GAA
3090426 TAGTTAGTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 13 0.62
10 8 0.38
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (9 bp):
GAAAAAATA
Found at i:3091781 original size:111 final size:112
Alignment explanation
Indices: 3091571--3091786 Score: 244
Period size: 111 Copynumber: 1.9 Consensus size: 112
3091561 AAAAATATAT
* * *
3091571 ATTAATTTATATATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAAGGACTTCTAAG
1 ATTAATATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACATCTAAG
* *
3091636 TGCCTTAAGACAGCTCTTTTCCTCGATATTAAAAA-AAATTAAAACA
66 TGCCTTAAGACAGCTCCTTTCCTCAATATTAAAAATAAATTAAAACA
** * *
3091682 ATTAATATATA-ATTTATAAAATAGGATATTTATTTATTTAAAAATATTAGAAAATGGACATC-C
1 ATTAATATATATATTTAT-AAATAAAATATTTATTTATTTAAAAATATCAGAAAA-GGACATCTA
** * *
3091745 AGTTGTTTTAAGACCGC-CCTTT-CTTAATATTGAAAAATAAAT
64 AG-TGCCTTAAGACAGCTCCTTTCCTCAATATT-AAAAATAAAT
3091787 AAATATTAAA
Statistics
Matches: 87, Mismatches: 13, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
110 13 0.15
111 53 0.61
112 21 0.24
ACGTcount: A:0.44, C:0.10, G:0.09, T:0.38
Consensus pattern (112 bp):
ATTAATATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACATCTAAG
TGCCTTAAGACAGCTCCTTTCCTCAATATTAAAAATAAATTAAAACA
Found at i:3093307 original size:3 final size:3
Alignment explanation
Indices: 3093301--3093345 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
3093291 ATTATTTATT
* *
3093301 TAA TAA TAG TAA T-A TAA T-A TAA TAA TAA TAT TAA -AA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3093346 AAAATAAAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
2 6 0.17
3 29 0.83
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:3093346 original size:11 final size:11
Alignment explanation
Indices: 3093302--3093352 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
3093292 TTATTTATTT
*
3093302 AATAATAGTAA
1 AATAATAATAA
*
3093313 TATAAT-ATAA
1 AATAATAATAA
*
3093323 TAATAATATTAA
1 -AATAATAATAA
3093335 AATAATAATAA
1 AATAATAATAA
3093346 AA-AATAA
1 AATAATAA
3093353 AACAAATGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
10 8 0.24
11 22 0.67
12 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (11 bp):
AATAATAATAA
Found at i:3093644 original size:37 final size:37
Alignment explanation
Indices: 3093587--3093781 Score: 270
Period size: 37 Copynumber: 5.3 Consensus size: 37
3093577 CTGATGATCT
* * *
3093587 GATGG-TTTGCTCTAAC-ACTCTTCTGAGAAGGCTTAA
1 GATGGATTTGCT-TCACTACTCTTCGGTGAAGGCTTAA
* *
3093623 AATGGATTTGCTTCACTACTCTTCAGTGAAGGCTTAA
1 GATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAA
3093660 GATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAA
1 GATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAA
**
3093697 GATGGA-TCACTTCACTACTCTTCGGTGAAGGCTTAA
1 GATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAA
*
3093733 GATGGATTTGCTTCACTACTCTTCGGTGAATGCTTAA
1 GATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAA
*
3093770 GATTGACTTTGC
1 GATGGA-TTTGC
3093782 CCCAATCTCC
Statistics
Matches: 143, Mismatches: 12, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
36 41 0.29
37 97 0.68
38 5 0.03
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (37 bp):
GATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAA
Found at i:3093726 original size:73 final size:74
Alignment explanation
Indices: 3093587--3093772 Score: 270
Period size: 73 Copynumber: 2.5 Consensus size: 74
3093577 CTGATGATCT
* * * * **
3093587 GATGG-TTTGCTCTAAC-ACTCTTCTGAGAAGGCTTAAAATGGATTTGCTTCACTACTCTTCAGT
1 GATGGATTTGCT-TCACTACTCTTCGGTGAAGGCTTAAGATGGATTCACTTCACTACTCTTCAGT
3093650 GAAGGCTTAA
65 GAAGGCTTAA
*
3093660 GATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATGGA-TCACTTCACTACTCTTCGGTG
1 GATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATGGATTCACTTCACTACTCTTCAGTG
3093724 AAGGCTTAA
66 AAGGCTTAA
*
3093733 GATGGATTTGCTTCACTACTCTTCGGTGAATGCTTAAGAT
1 GATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGAT
3093773 TGACTTTGCC
Statistics
Matches: 103, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
73 74 0.72
74 29 0.28
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.34
Consensus pattern (74 bp):
GATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATGGATTCACTTCACTACTCTTCAGTG
AAGGCTTAA
Found at i:3099180 original size:21 final size:21
Alignment explanation
Indices: 3099156--3099229 Score: 114
Period size: 21 Copynumber: 3.5 Consensus size: 21
3099146 ATGCAAAGTA
3099156 GTCTTCAT-GTCTTTGTGAATG
1 GTCTTC-TCGTCTTTGTGAATG
*
3099177 GTCTTCTCGTCTTTATGAATG
1 GTCTTCTCGTCTTTGTGAATG
*
3099198 GTCTTCTCGTCCTTGTGAATG
1 GTCTTCTCGTCTTTGTGAATG
3099219 GTCTTCTCGTC
1 GTCTTCTCGTC
3099230 CTTGGTATGG
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
20 1 0.02
21 48 0.98
ACGTcount: A:0.11, C:0.22, G:0.22, T:0.46
Consensus pattern (21 bp):
GTCTTCTCGTCTTTGTGAATG
Found at i:3112300 original size:21 final size:22
Alignment explanation
Indices: 3112276--3112320 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
3112266 GTTTTGACTC
*
3112276 GACTC-TTAATTTCATAAATTT
1 GACTCTTTAATTTCATAAACTT
3112297 GACTCTTTAATTTCATAAACTT
1 GACTCTTTAATTTCATAAACTT
3112319 GA
1 GA
3112321 TTTGATTCGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.33, C:0.16, G:0.07, T:0.44
Consensus pattern (22 bp):
GACTCTTTAATTTCATAAACTT
Found at i:3112767 original size:2 final size:2
Alignment explanation
Indices: 3112760--3112793 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3112750 TTAACCAGTT
3112760 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3112794 ATGAATTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3114123 original size:16 final size:16
Alignment explanation
Indices: 3114099--3114140 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
3114089 ACCAAAGATG
3114099 TCAACTTTGCCAACTT
1 TCAACTTTGCCAACTT
*
3114115 TCAATTTTGCCAACTT
1 TCAACTTTGCCAACTT
*
3114131 TTAACTTTGC
1 TCAACTTTGC
3114141 TAATTTTTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.24, C:0.26, G:0.07, T:0.43
Consensus pattern (16 bp):
TCAACTTTGCCAACTT
Found at i:3115683 original size:18 final size:20
Alignment explanation
Indices: 3115660--3115700 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3115650 CCAACTGTTC
3115660 CTTGTA-GAGA-ACATCTTT
1 CTTGTATGAGATACATCTTT
*
3115678 CTTGTATGAGATCCATCTTT
1 CTTGTATGAGATACATCTTT
3115698 CTT
1 CTT
3115701 TGCAAATACC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 6 0.30
19 4 0.20
20 10 0.50
ACGTcount: A:0.22, C:0.20, G:0.15, T:0.44
Consensus pattern (20 bp):
CTTGTATGAGATACATCTTT
Found at i:3118865 original size:9 final size:9
Alignment explanation
Indices: 3118851--3118914 Score: 52
Period size: 9 Copynumber: 7.8 Consensus size: 9
3118841 CTAAAGATGT
3118851 CAACTTTTC
1 CAACTTTTC
3118860 CAAC-TTT-
1 CAACTTTTC
3118867 CAA-TTTTGC
1 CAACTTTT-C
3118876 CAAC-TTT-
1 CAACTTTTC
*
3118883 CAACTTTGC
1 CAACTTTTC
3118892 CAAC-TTT-
1 CAACTTTTC
*
3118899 CAACTTTGC
1 CAACTTTTC
3118908 CAACTTT
1 CAACTTT
3118915 CAATTTTGTC
Statistics
Matches: 44, Mismatches: 3, Indels: 16
0.70 0.05 0.25
Matches are distributed among these distances:
7 14 0.32
8 9 0.20
9 21 0.48
ACGTcount: A:0.25, C:0.30, G:0.05, T:0.41
Consensus pattern (9 bp):
CAACTTTTC
Found at i:3118878 original size:16 final size:16
Alignment explanation
Indices: 3118850--3118939 Score: 144
Period size: 16 Copynumber: 5.6 Consensus size: 16
3118840 ACTAAAGATG
*
3118850 TCAACTTTTCCAACTT
1 TCAACTTTGCCAACTT
*
3118866 TCAATTTTGCCAACTT
1 TCAACTTTGCCAACTT
3118882 TCAACTTTGCCAACTT
1 TCAACTTTGCCAACTT
3118898 TCAACTTTGCCAACTT
1 TCAACTTTGCCAACTT
* *
3118914 TCAATTTTGTCAACTT
1 TCAACTTTGCCAACTT
3118930 TCAACTTTGC
1 TCAACTTTGC
3118940 TAATTTTTCA
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 67 1.00
ACGTcount: A:0.24, C:0.28, G:0.06, T:0.42
Consensus pattern (16 bp):
TCAACTTTGCCAACTT
Found at i:3120533 original size:17 final size:16
Alignment explanation
Indices: 3120506--3120538 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
3120496 TCAAATATCC
3120506 AACAACCAAAGTAAAA
1 AACAACCAAAGTAAAA
3120522 AACAATCCAAAGTAAAA
1 AACAA-CCAAAGTAAAA
3120539 CAATCATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.67, C:0.18, G:0.06, T:0.09
Consensus pattern (16 bp):
AACAACCAAAGTAAAA
Found at i:3120540 original size:15 final size:16
Alignment explanation
Indices: 3120506--3120543 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
3120496 TCAAATATCC
3120506 AACAA-CCAAAGTAAAA
1 AACAATCCAAAGT-AAA
3120522 AACAATCCAAAGT-AA
1 AACAATCCAAAGTAAA
3120537 AACAATC
1 AACAATC
3120544 ATGAACATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 5 0.24
17 7 0.33
ACGTcount: A:0.63, C:0.21, G:0.05, T:0.11
Consensus pattern (16 bp):
AACAATCCAAAGTAAA
Found at i:3122067 original size:23 final size:23
Alignment explanation
Indices: 3122034--3122098 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
3122024 TCAATTTCCT
3122034 AAAGGAGGGAATCGGTTCCCATTC
1 AAAGG-GGGAATCGGTTCCCATTC
* *
3122058 AAAGGGGGAATCAGTTCCCCTTC
1 AAAGGGGGAATCGGTTCCCATTC
* *
3122081 -AAGGGGGTATCGATTCCC
1 AAAGGGGGAATCGGTTCCC
3122099 TCTGCACTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
22 15 0.42
23 16 0.44
24 5 0.14
ACGTcount: A:0.26, C:0.23, G:0.29, T:0.22
Consensus pattern (23 bp):
AAAGGGGGAATCGGTTCCCATTC
Found at i:3125159 original size:117 final size:117
Alignment explanation
Indices: 3124941--3125162 Score: 288
Period size: 117 Copynumber: 1.9 Consensus size: 117
3124931 CTTTCAAATC
* *
3124941 GAAATTTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAAGATTT
1 GAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAACATTT
* *
3125006 TATTTTGATTTTCAAAATCCATTTTCGTTTCTAAAAGAAGTTTGCTTAATTT
66 CATTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGCTTAATTT
* * * *
3125058 GAAAATTTCTTTTTCAA-AGTTTTCAGATTTTATTTTTGAAAGCTCTAACTCCTT-TCTCAACAT
1 GAAAATTTCTTTTTCAATA-CTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCT-TCAACAT
* * **
3125121 TTCATTTTGATTTTCCAAGTCTGTTTTAGCTTTC-AAAAGAAG
64 TTCATTTTGATTTTCAAAATCCATTTTAG-TTTCTAAAAGAAG
3125163 ATCATTTTTA
Statistics
Matches: 90, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
116 2 0.02
117 84 0.93
118 4 0.04
ACGTcount: A:0.28, C:0.15, G:0.09, T:0.47
Consensus pattern (117 bp):
GAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAACATTT
CATTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGCTTAATTT
Found at i:3126771 original size:12 final size:12
Alignment explanation
Indices: 3126754--3126787 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
3126744 GAATATACTC
3126754 GGAAAATCTTTT
1 GGAAAATCTTTT
3126766 GGAAAATCTTTT
1 GGAAAATCTTTT
3126778 GGAAAATCTT
1 GGAAAATCTT
3126788 AAAATTCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (12 bp):
GGAAAATCTTTT
Found at i:3128646 original size:20 final size:21
Alignment explanation
Indices: 3128616--3128655 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
3128606 TAGCCGTTGG
*
3128616 GCCTGATGGTATTGATACTAA
1 GCCTGATGGTATCGATACTAA
3128637 GCCT-ATGGTATCGATACTA
1 GCCTGATGGTATCGATACTA
3128656 CTATGTAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.33
Consensus pattern (21 bp):
GCCTGATGGTATCGATACTAA
Found at i:3132063 original size:11 final size:12
Alignment explanation
Indices: 3132047--3132077 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
3132037 CCTGATAAGC
3132047 TAAATAATATA-
1 TAAATAATATAT
3132058 TAAATAATATAT
1 TAAATAATATAT
3132070 TAAATAAT
1 TAAATAAT
3132078 TGATAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.58
12 8 0.42
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
TAAATAATATAT
Found at i:3134210 original size:21 final size:21
Alignment explanation
Indices: 3134184--3134225 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
3134174 TGGATTGGAA
3134184 ACCTTCTTCTAGTAGATGGTC
1 ACCTTCTTCTAGTAGATGGTC
3134205 ACCTTCTTCTAGTAGATGGTC
1 ACCTTCTTCTAGTAGATGGTC
3134226 CAAGGAGACG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.38
Consensus pattern (21 bp):
ACCTTCTTCTAGTAGATGGTC
Found at i:3136480 original size:96 final size:96
Alignment explanation
Indices: 3136346--3136538 Score: 368
Period size: 96 Copynumber: 2.0 Consensus size: 96
3136336 CTGATTTACT
*
3136346 TGTTCTTAACATGGCCTAATATAACATTTCTTGTTAATATTATTAGTCAACATATGTCTGATCCT
1 TGTTCTTAACATGGCCTAATATAACATTTCATGTTAATATTATTAGTCAACATATGTCTGATCCT
3136411 AGAGAAGATCATCTTGTTGGTGCCCATAGAA
66 AGAGAAGATCATCTTGTTGGTGCCCATAGAA
*
3136442 TGTTCTTAACATGGCCTAATATAACATTTCATGTTAATATTATTAGTCAACATATGTTTGATCCT
1 TGTTCTTAACATGGCCTAATATAACATTTCATGTTAATATTATTAGTCAACATATGTCTGATCCT
3136507 AGAGAAGATCATCTTGTTGGTGCCCATAGAA
66 AGAGAAGATCATCTTGTTGGTGCCCATAGAA
3136538 T
1 T
3136539 ATTATGGTAC
Statistics
Matches: 95, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
96 95 1.00
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.38
Consensus pattern (96 bp):
TGTTCTTAACATGGCCTAATATAACATTTCATGTTAATATTATTAGTCAACATATGTCTGATCCT
AGAGAAGATCATCTTGTTGGTGCCCATAGAA
Found at i:3138519 original size:21 final size:19
Alignment explanation
Indices: 3138493--3138531 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
3138483 AAATTCGAAT
3138493 TTATATTGAAATATGAATAAC
1 TTATATT-AAATAT-AATAAC
3138514 TTATATTAAATATAATAA
1 TTATATTAAATATAATAA
3138532 AATCGATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 6 0.33
21 7 0.39
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (19 bp):
TTATATTAAATATAATAAC
Found at i:3139145 original size:21 final size:21
Alignment explanation
Indices: 3139119--3139171 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
3139109 TAAAAATTTA
*
3139119 TCCCGAAGGACCACGTATATG
1 TCCCGAAGGACCACATATATG
*
3139140 TCCCGAAAGACCACATATATG
1 TCCCGAAGGACCACATATATG
*
3139161 TCCTGAAGGAC
1 TCCCGAAGGAC
3139172 TACTCCTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.32, C:0.28, G:0.21, T:0.19
Consensus pattern (21 bp):
TCCCGAAGGACCACATATATG
Found at i:3143295 original size:21 final size:21
Alignment explanation
Indices: 3143269--3143326 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
3143259 ATATAGAATT
3143269 TGTCCCGAAGAACCACATATA
1 TGTCCCGAAGAACCACATATA
3143290 TGTCCCGAA-ATACCACATATA
1 TGTCCCGAAGA-ACCACATATA
*
3143311 TGTCCCGAAGGACCAC
1 TGTCCCGAAGAACCAC
3143327 TCCTTAAGGA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
20 1 0.03
21 33 0.97
ACGTcount: A:0.34, C:0.31, G:0.16, T:0.19
Consensus pattern (21 bp):
TGTCCCGAAGAACCACATATA
Found at i:3145875 original size:13 final size:13
Alignment explanation
Indices: 3145857--3145884 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3145847 TCGAGTCAGC
3145857 CCGTTGACTTTGA
1 CCGTTGACTTTGA
3145870 CCGTTGACTTTGA
1 CCGTTGACTTTGA
3145883 CC
1 CC
3145885 ATAAAGTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.29, G:0.21, T:0.36
Consensus pattern (13 bp):
CCGTTGACTTTGA
Found at i:3146059 original size:17 final size:18
Alignment explanation
Indices: 3146019--3146051 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3146009 TTTGGTTTTT
3146019 TGAT-TAAATTCTATTTC
1 TGATGTAAATTCTATTTC
3146036 TGATGTAAATT-TATTT
1 TGATGTAAATTCTATTT
3146052 GTTATGTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55
Consensus pattern (18 bp):
TGATGTAAATTCTATTTC
Found at i:3152488 original size:30 final size:30
Alignment explanation
Indices: 3152444--3152512 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
3152434 CAGGAGGCTC
* *
3152444 ATCAGGTGGTGGTGGAGGAACTTGTTCAAT
1 ATCAGGAGGAGGTGGAGGAACTTGTTCAAT
* * * *
3152474 ATTAGGAGGAGGTGGTGGAATTTGTTCAGT
1 ATCAGGAGGAGGTGGAGGAACTTGTTCAAT
3152504 ATCAGGAGG
1 ATCAGGAGG
3152513 TGGAGGAATC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.25, C:0.07, G:0.39, T:0.29
Consensus pattern (30 bp):
ATCAGGAGGAGGTGGAGGAACTTGTTCAAT
Found at i:3156531 original size:21 final size:21
Alignment explanation
Indices: 3156507--3156559 Score: 63
Period size: 23 Copynumber: 2.5 Consensus size: 21
3156497 AAAGTAATAG
3156507 TATTATATTATATTTTAAAAA
1 TATTATATTATATTTTAAAAA
* *
3156528 TATTAATTAGTATATTTTAAATA
1 TATT-A-TATTATATTTTAAAAA
3156551 TATT-TATTA
1 TATTATATTA
3156560 AAATATTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
20 4 0.15
21 4 0.15
22 1 0.04
23 18 0.67
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
TATTATATTATATTTTAAAAA
Found at i:3156543 original size:23 final size:23
Alignment explanation
Indices: 3156515--3156559 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
3156505 AGTATTATAT
3156515 TATATTTTAAAAATATTAATTAG
1 TATATTTTAAAAATATTAATTAG
* *
3156538 TATATTTTAAATATATTTATTA
1 TATATTTTAAAAATATTAATTA
3156560 AAATATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TATATTTTAAAAATATTAATTAG
Found at i:3156565 original size:23 final size:23
Alignment explanation
Indices: 3156516--3156584 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
3156506 GTATTATATT
* * **
3156516 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAATATATTTATTAAA
3156539 ATATTTTAAATATATTTATTAAA
1 ATATTTTAAATATATTTATTAAA
*
3156562 ATATTATTAGAT-TATTATATTAA
1 ATATT-TTAAATATATT-TATTAA
3156585 TATTAAATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
23 28 0.72
24 11 0.28
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (23 bp):
ATATTTTAAATATATTTATTAAA
Found at i:3156588 original size:34 final size:34
Alignment explanation
Indices: 3156507--3156588 Score: 84
Period size: 35 Copynumber: 2.4 Consensus size: 34
3156497 AAAGTAATAG
3156507 TATTATATT-ATATTTTAAAAATATTAATTAGTA
1 TATTATATTAATATTTTAAAAATATTAATTAGTA
*
3156540 TATT-T-TAAATATATTTATTAAAATATT-ATTAG-A
1 TATTATATTAATAT-TTTA--AAAATATTAATTAGTA
3156573 TTATTATATTAATATT
1 -TATTATATTAATATT
3156589 AAATATATAA
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
31 1 0.03
32 5 0.12
33 9 0.22
34 9 0.22
35 10 0.25
36 6 0.15
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (34 bp):
TATTATATTAATATTTTAAAAATATTAATTAGTA
Found at i:3156622 original size:19 final size:20
Alignment explanation
Indices: 3156554--3156622 Score: 63
Period size: 19 Copynumber: 3.5 Consensus size: 20
3156544 TTAAATATAT
* *
3156554 TTATTAA-AATATTATTAGA
1 TTATTAATAATAATATTAAA
*
3156573 TTATT-ATATTAATATTAAA
1 TTATTAATAATAATATTAAA
* *
3156592 TATATAAATAATAATATT-CA
1 T-TATTAATAATAATATTAAA
3156612 TTATTAATAAT
1 TTATTAATAAT
3156623 TTAATAACAT
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
18 1 0.03
19 24 0.60
20 5 0.12
21 10 0.25
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (20 bp):
TTATTAATAATAATATTAAA
Found at i:3156729 original size:23 final size:23
Alignment explanation
Indices: 3156710--3156772 Score: 117
Period size: 23 Copynumber: 2.7 Consensus size: 23
3156700 ATATAATATC
*
3156710 TTATATTATTATAATATAATTGA
1 TTATTTTATTATAATATAATTGA
3156733 TTATTTTATTATAATATAATTGA
1 TTATTTTATTATAATATAATTGA
3156756 TTATTTTATTATAATAT
1 TTATTTTATTATAATAT
3156773 TAAACATATT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (23 bp):
TTATTTTATTATAATATAATTGA
Found at i:3156787 original size:22 final size:22
Alignment explanation
Indices: 3156757--3156805 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
3156747 TATAATTGAT
*
3156757 TATTTTATTATAATATTA-AACA
1 TATTATATTATAATATTAGAA-A
*
3156779 TATTATATTATATTATTAGAAA
1 TATTATATTATAATATTAGAAA
3156801 TATTA
1 TATTA
3156806 ATAAATATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 22 0.92
23 2 0.08
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (22 bp):
TATTATATTATAATATTAGAAA
Found at i:3162265 original size:2 final size:2
Alignment explanation
Indices: 3162258--3162286 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3162248 TGAGGTTAGG
3162258 AT 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 AT A
3162287 ATAAATAGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3168307 original size:20 final size:20
Alignment explanation
Indices: 3168284--3168448 Score: 156
Period size: 20 Copynumber: 8.2 Consensus size: 20
3168274 AAACTTCCGT
* *
3168284 GTCATTTATAAAGCCTTTGG
1 GTCATTTGTAAAGCCTTCGG
*
3168304 GTCATTTGTAAAGCCTTCAG
1 GTCATTTGTAAAGCCTTCGG
* * * *
3168324 GTCGTTGGTAAAGCCTCCGA
1 GTCATTTGTAAAGCCTTCGG
* *
3168344 GTCATTTGTAAAGCCTCCGA
1 GTCATTTGTAAAGCCTTCGG
*
3168364 GTCATTTGTAAAGCC-TCTAG
1 GTCATTTGTAAAGCCTTC-GG
3168384 GTCATTTGTAAAGCCTTCGG
1 GTCATTTGTAAAGCCTTCGG
**
3168404 GTCATTTACAAAGCCTAT-GG
1 GTCATTTGTAAAGCCT-TCGG
* *
3168424 GTAATTTGTAAATTCCTT-GG
1 GTCATTTGTAAA-GCCTTCGG
3168444 GTCAT
1 GTCAT
3168449 CTGTCAGTCT
Statistics
Matches: 120, Mismatches: 21, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
19 1 0.01
20 113 0.94
21 6 0.05
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (20 bp):
GTCATTTGTAAAGCCTTCGG
Found at i:3168356 original size:60 final size:60
Alignment explanation
Indices: 3168279--3168435 Score: 190
Period size: 60 Copynumber: 2.6 Consensus size: 60
3168269 GCTTAAAACT
* * *
3168279 TCCGTGTCATTTATAAAGCCTTTGGGTCATTTGTAAAGCCT-TCAGGTCGTTGGTAAAGCC
1 TCCGAGTCATTTATAAAGCCTATGGGTCATTTGTAAAGCCTCT-AGGTCATTGGTAAAGCC
* ** * *
3168339 TCCGAGTCATTTGTAAAGCCTCCGAGTCATTTGTAAAGCCTCTAGGTCATTTGTAAAGCC
1 TCCGAGTCATTTATAAAGCCTATGGGTCATTTGTAAAGCCTCTAGGTCATTGGTAAAGCC
* * * *
3168399 TTCGGGTCATTTACAAAGCCTATGGGTAATTTGTAAA
1 TCCGAGTCATTTATAAAGCCTATGGGTCATTTGTAAA
3168436 TTCCTTGGGT
Statistics
Matches: 81, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
60 80 0.99
61 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.34
Consensus pattern (60 bp):
TCCGAGTCATTTATAAAGCCTATGGGTCATTTGTAAAGCCTCTAGGTCATTGGTAAAGCC
Found at i:3168410 original size:40 final size:40
Alignment explanation
Indices: 3168284--3168448 Score: 179
Period size: 40 Copynumber: 4.1 Consensus size: 40
3168274 AAACTTCCGT
* *
3168284 GTCATTTATAAAGCCTTTGGGTCATTTGTAAAGCCTTCAG
1 GTCATTTATAAAGCCTCTGGGTCATTTGTAAAGCCTTCGG
* ** * * * *
3168324 GTCGTTGGTAAAGCCTCCGAGTCATTTGTAAAGCCTCCGA
1 GTCATTTATAAAGCCTCTGGGTCATTTGTAAAGCCTTCGG
* *
3168364 GTCATTTGTAAAGCCTCTAGGTCATTTGTAAAGCCTTCGG
1 GTCATTTATAAAGCCTCTGGGTCATTTGTAAAGCCTTCGG
* * * *
3168404 GTCATTTACAAAGCCTATGGGTAATTTGTAAATTCCTT-GG
1 GTCATTTATAAAGCCTCTGGGTCATTTGTAAA-GCCTTCGG
3168444 GTCAT
1 GTCAT
3168449 CTGTCAGTCT
Statistics
Matches: 102, Mismatches: 22, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
40 98 0.96
41 4 0.04
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (40 bp):
GTCATTTATAAAGCCTCTGGGTCATTTGTAAAGCCTTCGG
Found at i:3169184 original size:11 final size:12
Alignment explanation
Indices: 3169159--3169188 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
3169149 ACATGCCCAA
3169159 GTTACAAGCTCG
1 GTTACAAGCTCG
3169171 GTTACAAG-TCG
1 GTTACAAGCTCG
3169182 GTTACAA
1 GTTACAA
3169189 CCCAACTGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (12 bp):
GTTACAAGCTCG
Found at i:3171022 original size:21 final size:22
Alignment explanation
Indices: 3170993--3171033 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
3170983 TACCTCTAAA
3170993 AATTATGGACCAAA-ATTTTTG
1 AATTATGGACCAAATATTTTTG
*
3171014 AATTCTGGACCAAATATTTT
1 AATTATGGACCAAATATTTT
3171034 CAAAACTCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (22 bp):
AATTATGGACCAAATATTTTTG
Found at i:3171591 original size:22 final size:23
Alignment explanation
Indices: 3171574--3171626 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
3171564 CATATTTTTA
3171574 ATTT-AAAAAATAT-TTATTATT
1 ATTTAAAAAAATATCTTATTATT
*
3171595 ATTTGAAAAAAATATCTTA-TAAT
1 ATTT-AAAAAAATATCTTATTATT
3171618 ATTTAAAAA
1 ATTTAAAAA
3171627 TTTTCATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 4 0.14
22 5 0.18
23 16 0.57
24 3 0.11
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (23 bp):
ATTTAAAAAAATATCTTATTATT
Found at i:3172091 original size:23 final size:23
Alignment explanation
Indices: 3172061--3172108 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
3172051 AATAGTGTTA
3172061 TATTATATTTTAAAAATATTAAT
1 TATTATATTTTAAAAATATTAAT
* *
3172084 TATTATATTTTAAATATATTTAT
1 TATTATATTTTAAAAATATTAAT
3172107 TA
1 TA
3172109 AAATATTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TATTATATTTTAAAAATATTAAT
Found at i:3172114 original size:23 final size:23
Alignment explanation
Indices: 3172065--3172133 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
3172055 GTGTTATATT
* * **
3172065 ATATTTTAAAAATATTAATTATT
1 ATATTTTAAATATATTTATTAAA
3172088 ATATTTTAAATATATTTATTAAA
1 ATATTTTAAATATATTTATTAAA
*
3172111 ATATTATTAGAT-TATTATATTAA
1 ATATT-TTAAATATATT-TATTAA
3172134 TATTAAATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
23 28 0.72
24 11 0.28
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (23 bp):
ATATTTTAAATATATTTATTAAA
Found at i:3172278 original size:23 final size:23
Alignment explanation
Indices: 3172248--3172298 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
3172238 TTAAAATAAA
*
3172248 AATATAATATCTTATATTATTAT
1 AATATAATATATTATATTATTAT
* *
3172271 AATATAATTTATTATTTTATTAT
1 AATATAATATATTATATTATTAT
3172294 AATAT
1 AATAT
3172299 TAAAAATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (23 bp):
AATATAATATATTATATTATTAT
Found at i:3172283 original size:18 final size:18
Alignment explanation
Indices: 3172262--3172296 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3172252 TAATATCTTA
3172262 TATTATTATAATATAATT
1 TATTATTATAATATAATT
* *
3172280 TATTATTTTATTATAAT
1 TATTATTATAATATAAT
3172297 ATTAAAAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TATTATTATAATATAATT
Found at i:3172316 original size:22 final size:23
Alignment explanation
Indices: 3172288--3172334 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
3172278 TTTATTATTT
3172288 TATTATAATATTAAAAATA-TAA
1 TATTATAATATTAAAAATATTAA
* *
3172310 TATTATATTATTAGAAATATTAA
1 TATTATAATATTAAAAATATTAA
3172333 TA
1 TA
3172335 AATATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
TATTATAATATTAAAAATATTAA
Found at i:3172321 original size:30 final size:33
Alignment explanation
Indices: 3172261--3172340 Score: 94
Period size: 32 Copynumber: 2.5 Consensus size: 33
3172251 ATAATATCTT
* * *
3172261 ATATTATTATAATATAATTTATTATTTTATTA-TA
1 ATATTAATA-AATATAA-TTATTATATTATTAGAA
3172295 ATATTAA-AAATATAA-TATTATATTATTAGAA
1 ATATTAATAAATATAATTATTATATTATTAGAA
3172326 ATATTAATAAATATA
1 ATATTAATAAATATA
3172341 TTTTAAATGT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
30 12 0.29
31 8 0.20
32 14 0.34
33 1 0.02
34 6 0.15
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (33 bp):
ATATTAATAAATATAATTATTATATTATTAGAA
Found at i:3172339 original size:22 final size:22
Alignment explanation
Indices: 3172296--3172339 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
3172286 TTTATTATAA
*
3172296 TATTAAAAATATAATATTATAT
1 TATTAAAAATATAATATAATAT
*
3172318 TATTAGAAATATTAATA-AATAT
1 TATTAAAAATA-TAATATAATAT
3172340 ATTTTAAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TATTAAAAATATAATATAATAT
Found at i:3175139 original size:31 final size:30
Alignment explanation
Indices: 3175076--3175154 Score: 79
Period size: 31 Copynumber: 2.5 Consensus size: 30
3175066 TTTTTTTAAA
* *
3175076 ATTTTATTAATAAAAATATTATTATTGGTAT
1 ATTTTATTAATAAAAATATTATAAAT-GTAT
3175107 ATTTTATTGAAATAAAAATATTATAAAT-TAT
1 ATTTTATT--AATAAAAATATTATAAATGTAT
*
3175138 ATTAATTATAAATAAAA
1 ATT--TTATTAATAAAA
3175155 GTAATAGTGT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
31 21 0.51
33 20 0.49
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.46
Consensus pattern (30 bp):
ATTTTATTAATAAAAATATTATAAATGTAT
Found at i:3175198 original size:23 final size:23
Alignment explanation
Indices: 3175170--3175214 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
3175160 AGTGTTATAT
3175170 TATATTTTAAAAATATTAATTAG
1 TATATTTTAAAAATATTAATTAG
* *
3175193 TATATTTTAAATATATTTATTA
1 TATATTTTAAAAATATTAATTA
3175215 AAATATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TATATTTTAAAAATATTAATTAG
Found at i:3175220 original size:23 final size:23
Alignment explanation
Indices: 3175171--3175221 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
3175161 GTGTTATATT
**
3175171 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* *
3175194 ATATTTTAAATATATTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
3175217 ATATT
1 ATATT
3175222 ATTAGATTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:3175277 original size:19 final size:19
Alignment explanation
Indices: 3175209--3175277 Score: 63
Period size: 19 Copynumber: 3.6 Consensus size: 19
3175199 TTAAATATAT
3175209 TTATTAA-AATATTATTAGA
1 TTATTAATAATATTATTA-A
3175228 TTATTAGATTAATATTA--AA
1 TTATTA-A-TAATATTATTAA
* *
3175247 TATATAAATAATATTATTCA
1 T-TATTAATAATATTATTAA
3175267 TTATTAATAAT
1 TTATTAATAAT
3175278 TTAATAACAC
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
18 8 0.20
19 18 0.44
20 8 0.20
22 7 0.17
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (19 bp):
TTATTAATAATATTATTAA
Found at i:3175412 original size:22 final size:23
Alignment explanation
Indices: 3175384--3175430 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
3175374 TTGATTATTT
3175384 TATTATAATATTAAAAATA-TAA
1 TATTATAATATTAAAAATATTAA
* *
3175406 TATTATATTATTATAAATATTAA
1 TATTATAATATTAAAAATATTAA
3175429 TA
1 TA
3175431 AATATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TATTATAATATTAAAAATATTAA
Found at i:3175417 original size:30 final size:34
Alignment explanation
Indices: 3175357--3175436 Score: 105
Period size: 32 Copynumber: 2.4 Consensus size: 34
3175347 ATAATATCTT
* *
3175357 ATATTATTATAATATAATTGATTATTTTATTAT-A
1 ATATTAATA-AATATAATTGATTATATTATTATAA
3175391 ATATTAA-AAATATAA-T-ATTATATTATTATAA
1 ATATTAATAAATATAATTGATTATATTATTATAA
3175422 ATATTAATAAATATA
1 ATATTAATAAATATA
3175437 TTTTAAATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
30 12 0.29
31 9 0.21
32 14 0.33
33 1 0.02
34 6 0.14
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (34 bp):
ATATTAATAAATATAATTGATTATATTATTATAA
Found at i:3175435 original size:22 final size:21
Alignment explanation
Indices: 3175391--3175453 Score: 56
Period size: 22 Copynumber: 2.9 Consensus size: 21
3175381 TTTTATTATA
* *
3175391 ATATTAAAAATA-TAATATTAT
1 ATATTATAAATATTAATA-AAT
3175412 ATTATTATAAATATTAATAAAT
1 A-TATTATAAATATTAATAAAT
* *
3175434 ATATTTTAAATTTTTAATAA
1 ATATTATAAA-TATTAATAA
3175454 TTGATATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
21 9 0.26
22 21 0.60
23 5 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
ATATTATAAATATTAATAAAT
Found at i:3175436 original size:24 final size:22
Alignment explanation
Indices: 3175387--3175443 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
3175377 ATTATTTTAT
* *
3175387 TATAATATTAAAAATATAATAT
1 TATATTATTAAAAATATAATAA
*
3175409 TATATTATTATAAATATTAATAAA
1 TATATTATTAAAAATA-TAAT-AA
3175433 TATATT-TTAAA
1 TATATTATTAAA
3175444 TTTTTAATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 14 0.48
23 8 0.28
24 7 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TATATTATTAAAAATATAATAA
Found at i:3175443 original size:21 final size:23
Alignment explanation
Indices: 3175414--3175463 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
3175404 AATATTATAT
*
3175414 TATTATAAA-TATTAATAAAT-A
1 TATTTTAAATTATTAATAAATGA
* *
3175435 TATTTTAAATTTTTAATAATTGA
1 TATTTTAAATTATTAATAAATGA
3175458 TATTTT
1 TATTTT
3175464 GATTAAAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 8 0.33
22 9 0.38
23 7 0.29
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (23 bp):
TATTTTAAATTATTAATAAATGA
Found at i:3177389 original size:16 final size:16
Alignment explanation
Indices: 3177368--3177401 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3177358 AAATCGTACA
*
3177368 TTTAGTCCTTTATATT
1 TTTAGTACTTTATATT
*
3177384 TTTAGTAGTTTATATT
1 TTTAGTACTTTATATT
3177400 TT
1 TT
3177402 AGACTTATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.06, G:0.09, T:0.65
Consensus pattern (16 bp):
TTTAGTACTTTATATT
Found at i:3184726 original size:20 final size:20
Alignment explanation
Indices: 3184698--3184805 Score: 128
Period size: 20 Copynumber: 5.4 Consensus size: 20
3184688 GCATGATGTT
* *
3184698 TAAAACCTTCGTGTCATTTG
1 TAAAGCCTTCGGGTCATTTG
3184718 TAAAGCCTTCGGGTCATTTG
1 TAAAGCCTTCGGGTCATTTG
* *
3184738 TAAAGCCTCCGAGTCATTTG
1 TAAAGCCTTCGGGTCATTTG
* *
3184758 TAAAGCC-TCTAGGTTATTTG
1 TAAAGCCTTC-GGGTCATTTG
* *
3184778 GAAAGCCTTTGGGTCATTTG
1 TAAAGCCTTCGGGTCATTTG
3184798 TAAAGCCT
1 TAAAGCCT
3184806 ATGGTTAATT
Statistics
Matches: 73, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
19 1 0.01
20 71 0.97
21 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.35
Consensus pattern (20 bp):
TAAAGCCTTCGGGTCATTTG
Found at i:3184816 original size:20 final size:20
Alignment explanation
Indices: 3184710--3184821 Score: 127
Period size: 20 Copynumber: 5.6 Consensus size: 20
3184700 AAACCTTCGT
3184710 GTCATTTGTAAAGCCT-TCGG
1 GTCATTTGTAAAGCCTCT-GG
* *
3184730 GTCATTTGTAAAGCCTCCGA
1 GTCATTTGTAAAGCCTCTGG
*
3184750 GTCATTTGTAAAGCCTCTAG
1 GTCATTTGTAAAGCCTCTGG
* * *
3184770 GTTATTTGGAAAGCCTTTGG
1 GTCATTTGTAAAGCCTCTGG
*
3184790 GTCATTTGTAAAGCCTATGG
1 GTCATTTGTAAAGCCTCTGG
* *
3184810 TTAATTTGTAAA
1 GTCATTTGTAAA
3184822 TTTCTTGGGT
Statistics
Matches: 77, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
20 77 1.00
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (20 bp):
GTCATTTGTAAAGCCTCTGG
Found at i:3186558 original size:16 final size:15
Alignment explanation
Indices: 3186539--3186576 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
3186529 TTTTTATAAC
3186539 TTTTAGTT-TTTTCATA
1 TTTTAGTTATTTT--TA
3186555 TTTTAGTTATTTTTA
1 TTTTAGTTATTTTTA
3186570 TTTTAGT
1 TTTTAGT
3186577 CACTATTATG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 8 0.38
17 4 0.19
ACGTcount: A:0.18, C:0.03, G:0.08, T:0.71
Consensus pattern (15 bp):
TTTTAGTTATTTTTA
Found at i:3186573 original size:15 final size:15
Alignment explanation
Indices: 3186529--3186576 Score: 53
Period size: 17 Copynumber: 3.0 Consensus size: 15
3186519 CGAAATCAGG
3186529 TTTTTATAACTTTTAGT
1 TTTTTAT-A-TTTTAGT
3186546 TTTTTCATATTTTAGT
1 TTTTT-ATATTTTAGT
3186562 TATTTT-TATTTTAGT
1 T-TTTTATATTTTAGT
3186577 CACTATTATG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
15 9 0.31
16 8 0.28
17 10 0.34
18 2 0.07
ACGTcount: A:0.21, C:0.04, G:0.06, T:0.69
Consensus pattern (15 bp):
TTTTTATATTTTAGT
Found at i:3188122 original size:22 final size:20
Alignment explanation
Indices: 3188105--3188160 Score: 58
Period size: 24 Copynumber: 2.5 Consensus size: 20
3188095 CATATTTTTA
3188105 ATTTAAAAAATATTTATTATT
1 ATTTAAAAAA-ATTTATTATT
*
3188126 ATTTGAAAAAATTTATCTCATAAT
1 ATTTAAAAAAATTTAT-T-AT--T
3188150 ATTTAAAAAAA
1 ATTTAAAAAAA
3188161 AATTCATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 6 0.21
21 10 0.34
22 2 0.07
24 11 0.38
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.43
Consensus pattern (20 bp):
ATTTAAAAAAATTTATTATT
Found at i:3188581 original size:26 final size:27
Alignment explanation
Indices: 3188530--3188581 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
3188520 TTATTAATAA
* * *
3188530 AAATAAAAATATTGGTATATTTTATTG
1 AAATAAAAATATTGATAAATTATATTG
3188557 AAATAAAAATATT-ATAAATTATATT
1 AAATAAAAATATTGATAAATTATATT
3188582 AATTATAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (27 bp):
AAATAAAAATATTGATAAATTATATTG
Found at i:3188661 original size:23 final size:23
Alignment explanation
Indices: 3188612--3188662 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
3188602 GTGTTGTATT
**
3188612 ATATTTTAAAAATATTAATTATT
1 ATATTTTAAAAATATTAATTAAA
* * *
3188635 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
3188658 ATATT
1 ATATT
3188663 ATTAGATTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:3188825 original size:23 final size:23
Alignment explanation
Indices: 3188795--3188845 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
3188785 TTAAAATAAA
*
3188795 AATATAATATCTTATATTATTAT
1 AATATAATATATTATATTATTAT
* *
3188818 AATATAATTTATTATTTTATTAT
1 AATATAATATATTATATTATTAT
3188841 AATAT
1 AATAT
3188846 TAAAAAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (23 bp):
AATATAATATATTATATTATTAT
Found at i:3188830 original size:18 final size:18
Alignment explanation
Indices: 3188809--3188843 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3188799 TAATATCTTA
3188809 TATTATTATAATATAATT
1 TATTATTATAATATAATT
* *
3188827 TATTATTTTATTATAAT
1 TATTATTATAATATAAT
3188844 ATTAAAAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TATTATTATAATATAATT
Found at i:3193073 original size:16 final size:15
Alignment explanation
Indices: 3193048--3193091 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
3193038 GGTAAAATCG
3193048 TATA-TTTAGTCCTT
1 TATATTTTAGTCCTT
**
3193062 TATATTTTTAGTAGTT
1 TATA-TTTTAGTCCTT
3193078 TATATTTTAGTCCT
1 TATATTTTAGTCCT
3193092 ATTCGTAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
14 4 0.17
15 8 0.33
16 12 0.50
ACGTcount: A:0.23, C:0.09, G:0.09, T:0.59
Consensus pattern (15 bp):
TATATTTTAGTCCTT
Found at i:3194579 original size:19 final size:19
Alignment explanation
Indices: 3194543--3194580 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
3194533 TTAACAAAAT
*
3194543 CAAAGGTTTTCATTATAAA
1 CAAAGGTTTTCATGATAAA
3194562 CAAAGGGTTTT-ATGATAAA
1 CAAA-GGTTTTCATGATAAA
3194581 GTGAATTGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.42, C:0.08, G:0.16, T:0.34
Consensus pattern (19 bp):
CAAAGGTTTTCATGATAAA
Found at i:3200177 original size:20 final size:20
Alignment explanation
Indices: 3200154--3200298 Score: 170
Period size: 20 Copynumber: 7.2 Consensus size: 20
3200144 AAACCTCTGT
3200154 GTCATTTGTAAAGCCTTCGG
1 GTCATTTGTAAAGCCTTCGG
*
3200174 GTCATTTGTAAAGCCTTTGG
1 GTCATTTGTAAAGCCTTCGG
* *
3200194 GTCATTTGTAAAGCCTCCGA
1 GTCATTTGTAAAGCCTTCGG
*
3200214 GTCATTTGTAAAGCC-TCTAG
1 GTCATTTGTAAAGCCTTC-GG
*
3200234 GTCATTTGTAAAGCCTTCAG
1 GTCATTTGTAAAGCCTTCGG
*
3200254 GTCATTTGTTAAGCCTAT-GG
1 GTCATTTGTAAAGCCT-TCGG
* *
3200274 GTAATTTGTAAATTCCTT-GG
1 GTCATTTGTAAA-GCCTTCGG
3200294 GTCAT
1 GTCAT
3200299 CTGTCAGTCT
Statistics
Matches: 108, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
19 1 0.01
20 101 0.94
21 6 0.06
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.37
Consensus pattern (20 bp):
GTCATTTGTAAAGCCTTCGG
Found at i:3200204 original size:40 final size:40
Alignment explanation
Indices: 3200154--3200298 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
3200144 AAACCTCTGT
*
3200154 GTCATTTGTAAAGCCTTCGGGTCATTTGTAAAGCCTTTGG
1 GTCATTTGTAAAGCCTTCGGGTCATTTGTAAAGCCTATGG
* * * *
3200194 GTCATTTGTAAAGCCTCCGAGTCATTTGTAAAGCCTCTAG
1 GTCATTTGTAAAGCCTTCGGGTCATTTGTAAAGCCTATGG
* *
3200234 GTCATTTGTAAAGCCTTCAGGTCATTTGTTAAGCCTATGG
1 GTCATTTGTAAAGCCTTCGGGTCATTTGTAAAGCCTATGG
* *
3200274 GTAATTTGTAAATTCCTT-GGGTCAT
1 GTCATTTGTAAA-GCCTTCGGGTCAT
3200299 CTGTCAGTCT
Statistics
Matches: 91, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
40 87 0.96
41 4 0.04
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.37
Consensus pattern (40 bp):
GTCATTTGTAAAGCCTTCGGGTCATTTGTAAAGCCTATGG
Found at i:3203012 original size:21 final size:22
Alignment explanation
Indices: 3202983--3203023 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
3202973 TACCTCTCAA
3202983 AATTATGGACCAAA-ATTTTTG
1 AATTATGGACCAAATATTTTTG
*
3203004 AATTTTGGACCAAATATTTT
1 AATTATGGACCAAATATTTT
3203024 CAAAACTCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (22 bp):
AATTATGGACCAAATATTTTTG
Found at i:3203788 original size:21 final size:20
Alignment explanation
Indices: 3203755--3203793 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
3203745 TCCGAAAAAT
3203755 ATTTTCTATAAAATGAATTAA
1 ATTTTCTATAAAAT-AATTAA
3203776 ATTTTCTGA-AAAATAATT
1 ATTTTCT-ATAAAATAATT
3203794 TTTGGAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.24
21 12 0.71
22 1 0.06
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (20 bp):
ATTTTCTATAAAATAATTAA
Found at i:3204000 original size:29 final size:31
Alignment explanation
Indices: 3203966--3204036 Score: 92
Period size: 32 Copynumber: 2.3 Consensus size: 31
3203956 TTTGTTATTG
* *
3203966 AAATATTATTTTTCTA-ATTTTATT-AATAA
1 AAATATTATATTGCTATATTTTATTGAATAA
*
3203995 AAATATTAATATTGGTATATTTTATTGAATAA
1 AAATATT-ATATTGCTATATTTTATTGAATAA
3204027 AAATATTATA
1 AAATATTATA
3204037 AATTATATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 7 0.19
30 6 0.17
31 11 0.31
32 12 0.33
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.49
Consensus pattern (31 bp):
AAATATTATATTGCTATATTTTATTGAATAA
Found at i:3204064 original size:16 final size:16
Alignment explanation
Indices: 3204031--3204064 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3204021 GAATAAAAAT
* *
3204031 ATTATAAATTATATTA
1 ATTATAAATTAAAGTA
3204047 ATTATAAATTAAAGTA
1 ATTATAAATTAAAGTA
3204063 AT
1 AT
3204065 AGTGTTATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (16 bp):
ATTATAAATTAAAGTA
Found at i:3215864 original size:20 final size:20
Alignment explanation
Indices: 3215836--3215984 Score: 172
Period size: 20 Copynumber: 7.5 Consensus size: 20
3215826 TTCGAGCATG
* * *
3215836 ATTTTTAAAACCTCCGTGTC
1 ATTTGTAAAGCCTCCGGGTC
* *
3215856 ATTTATAAAGCCTTCGGGTC
1 ATTTGTAAAGCCTCCGGGTC
*
3215876 ATTTGTAAAGCCTCTGGGTC
1 ATTTGTAAAGCCTCCGGGTC
*
3215896 ATTTGTAAAGCCTCCGAGTC
1 ATTTGTAAAGCCTCCGGGTC
**
3215916 ATTTGTAAAGCCTCTAGGTC
1 ATTTGTAAAGCCTCCGGGTC
*
3215936 ATTTGTAAAGCCTTCGGGTC
1 ATTTGTAAAGCCTCCGGGTC
* ** *
3215956 ATTTATAAAGCCTATGGGTA
1 ATTTGTAAAGCCTCCGGGTC
3215976 ATTTGTAAA
1 ATTTGTAAA
3215985 TTCCTTGGGT
Statistics
Matches: 109, Mismatches: 20, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 109 1.00
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (20 bp):
ATTTGTAAAGCCTCCGGGTC
Found at i:3215908 original size:40 final size:40
Alignment explanation
Indices: 3215853--3215997 Score: 202
Period size: 40 Copynumber: 3.6 Consensus size: 40
3215843 AAACCTCCGT
*
3215853 GTCATTTATAAAGCCTTCGGGTCATTTGTAAAGCCTCTGG
1 GTCATTTGTAAAGCCTTCGGGTCATTTGTAAAGCCTCTGG
* * *
3215893 GTCATTTGTAAAGCCTCCGAGTCATTTGTAAAGCCTCTAG
1 GTCATTTGTAAAGCCTTCGGGTCATTTGTAAAGCCTCTGG
* *
3215933 GTCATTTGTAAAGCCTTCGGGTCATTTATAAAGCCTATGG
1 GTCATTTGTAAAGCCTTCGGGTCATTTGTAAAGCCTCTGG
* *
3215973 GTAATTTGTAAATTCCTT-GGGTCAT
1 GTCATTTGTAAA-GCCTTCGGGTCAT
3215998 CTATCAGTCT
Statistics
Matches: 93, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
40 89 0.96
41 4 0.04
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (40 bp):
GTCATTTGTAAAGCCTTCGGGTCATTTGTAAAGCCTCTGG
Found at i:3218012 original size:16 final size:16
Alignment explanation
Indices: 3217979--3218023 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
3217969 TTTAATATTA
3217979 AATATTATA-ATT-AAT
1 AATATT-TACATTAAAT
3217994 AATATTTACATTAAAT
1 AATATTTACATTAAAT
*
3218010 AATATTTACGTTAA
1 AATATTTACATTAA
3218024 TTTTATGCGT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 2 0.07
15 9 0.33
16 16 0.59
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.44
Consensus pattern (16 bp):
AATATTTACATTAAAT
Found at i:3218615 original size:21 final size:22
Alignment explanation
Indices: 3218589--3218629 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
3218579 TACCTCTAAA
3218589 AATTATGGACCAAA-ATTTTTG
1 AATTATGGACCAAATATTTTTG
3218610 AATTATGGACCAAATATTTT
1 AATTATGGACCAAATATTTT
3218630 CAAAACTCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (22 bp):
AATTATGGACCAAATATTTTTG
Found at i:3219036 original size:74 final size:74
Alignment explanation
Indices: 3218957--3219325 Score: 201
Period size: 74 Copynumber: 5.1 Consensus size: 74
3218947 AGTAATATAG
*
3218957 TATAATTTTTGAAAGTATTTTTGAAAAAATATAATATATAGTTTTCAAAAAATATTTTTTTG-AA
1 TATAATTTTTGAAAGTATTTTTGAAAAAATATAATATATAGTTTT-AAAAAACATTTTTTTGAAA
3219021 ATATATATTA
65 ATATATATTA
* *
3219031 TATAATTTTTTGAAACG--TTTTTGAAAACTTATGTACAATATATAAGTTTT-AAAAACA---TT
1 TATAA-TTTTTGAAA-GTATTTTTGAAAA---A-ATATAATATAT-AGTTTTAAAAAACATTTTT
*
3219090 TTGAAAATTATATAGTA
59 TTGAAAA-TATATATTA
*
3219107 TAT-AGTTTTGAAA-TCA-TTTTG--AAAATATAATATATAGTTTTTAAAAAAACATTTTTTTGA
1 TATAATTTTTGAAAGT-ATTTTTGAAAAAATATAATATATAG-TTTT-AAAAAACATTTTTTTGA
* *
3219167 AAATTTATATAA
63 AAATATATATTA
* * ** * ** * * *
3219179 TAT-ATAGTTTAAAAACATTTTGGAAAACTTAT-ATA-ACA-TTTTTAAAATCA--TTTTTGAAA
1 TATAAT-TTTTGAAAGTATTTTTGAAAAAATATAATATATAGTTTTAAAAAACATTTTTTTGAAA
*
3219238 AT-TATATAA
65 ATATATATTA
* *** * *
3219247 TATATAGTTTTGAAAACGTTTTT----AAATAAAATATATAG-TTTAAAAAATATTTTTTTTGAA
1 TATA-ATTTTTGAAAGTATTTTTGAAAAAATATAATATATAGTTTTAAAAAACA-TTTTTTTGAA
3219307 ACATATATTATTA
64 A-ATATA-TATTA
3219320 TATAAT
1 TATAAT
3219326 CTATATTATT
Statistics
Matches: 227, Mismatches: 34, Indels: 70
0.69 0.10 0.21
Matches are distributed among these distances:
65 3 0.01
66 3 0.01
67 12 0.05
68 23 0.10
69 24 0.11
70 17 0.07
71 8 0.04
72 19 0.08
73 24 0.11
74 39 0.17
75 16 0.07
76 17 0.07
77 7 0.03
78 9 0.04
79 6 0.03
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (74 bp):
TATAATTTTTGAAAGTATTTTTGAAAAAATATAATATATAGTTTTAAAAAACATTTTTTTGAAAA
TATATATTA
Done.