Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009072.1 Hibiscus syriacus cultivar Beakdansim tig00112503_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: 2600608
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 13
Found at i:2121440 original size:19 final size:19
Alignment explanation
Indices: 2121347--2121482 Score: 94
Period size: 19 Copynumber: 7.6 Consensus size: 19
2121337 TAGTTTACTT
* **
2121347 TCGCAACACGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
***
2121367 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
2121387 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2121406 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
2121420 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2121439 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
2121453 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2121472 TCGCAATGCGA
1 TCGCAACGCGA
2121483 TTTGTGTTTT
Statistics
Matches: 94, Mismatches: 11, Indels: 23
0.73 0.09 0.18
Matches are distributed among these distances:
14 20 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 37 0.39
20 24 0.26
21 1 0.01
ACGTcount: A:0.43, C:0.24, G:0.21, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:2121511 original size:14 final size:13
Alignment explanation
Indices: 2121489--2121519 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
2121479 GCGATTTGTG
2121489 TTTTGCGTTGCGA
1 TTTTGCGTTGCGA
2121502 TTTTGTCGTTGCGA
1 TTTTG-CGTTGCGA
2121516 TTTT
1 TTTT
2121520 CATTTCGCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.06, C:0.13, G:0.26, T:0.55
Consensus pattern (13 bp):
TTTTGCGTTGCGA
Found at i:2121532 original size:19 final size:19
Alignment explanation
Indices: 2121510--2121546 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
2121500 GATTTTGTCG
2121510 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2121529 TTGCGATTTTCATTTCGC
1 TTGCGATTTTCATTTCGC
2121547 GTTGTGATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.14, C:0.22, G:0.16, T:0.49
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:2121561 original size:19 final size:19
Alignment explanation
Indices: 2121520--2121593 Score: 67
Period size: 20 Copynumber: 3.8 Consensus size: 19
2121510 TTGCGATTTT
* ***
2121520 CATTTCGCATTGCGATTTT
1 CATTTCGCGTTGCGATAGC
*
2121539 CATTTCGCGTTGTGATAGC
1 CATTTCGCGTTGCGATAGC
*
2121558 CATTTTCGCGTTGCGATAGT
1 CA-TTTCGCGTTGCGATAGC
*
2121578 CATTTTCGCTTTGCGA
1 CA-TTTCGCGTTGCGA
2121594 AGTAAGTTTC
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
19 16 0.35
20 30 0.65
ACGTcount: A:0.15, C:0.22, G:0.22, T:0.42
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:2121566 original size:20 final size:20
Alignment explanation
Indices: 2121541--2121593 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
2121531 GCGATTTTCA
*
2121541 TTTCGCGTTGTGATAGCCAT
1 TTTCGCGTTGCGATAGCCAT
*
2121561 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGCCAT
*
2121581 TTTCGCTTTGCGA
1 TTTCGCGTTGCGA
2121594 AGTAAGTTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.13, C:0.21, G:0.25, T:0.42
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGCCAT
Found at i:2121618 original size:20 final size:20
Alignment explanation
Indices: 2121561--2121618 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
2121551 TGATAGCCAT
* * * *
2121561 TTTCGCGTTGCGATAGTCAT
1 TTTCGTGTTGCGAAAGTAAG
2121581 TTTCGCT-TTGCG-AAGTAAG
1 TTTCG-TGTTGCGAAAGTAAG
2121600 TTTCGTGTTGCGAAAGTAA
1 TTTCGTGTTGCGAAAGTAA
2121619 ACTATTCTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
18 1 0.03
19 14 0.45
20 16 0.52
ACGTcount: A:0.21, C:0.16, G:0.26, T:0.38
Consensus pattern (20 bp):
TTTCGTGTTGCGAAAGTAAG
Found at i:2123361 original size:14 final size:13
Alignment explanation
Indices: 2123326--2123377 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
2123316 TTGATTGTTT
2123326 AATTGATTTGTAA
1 AATTGATTTGTAA
*
2123339 AAATGATTTGTAA
1 AATTGATTTGTAA
* **
2123352 ATGTTGATTTGTTT
1 A-ATTGATTTGTAA
*
2123366 AATTGATGTGTA
1 AATTGATTTGTA
2123378 CATAATTCTT
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
13 21 0.70
14 9 0.30
ACGTcount: A:0.33, C:0.00, G:0.19, T:0.48
Consensus pattern (13 bp):
AATTGATTTGTAA
Found at i:2124197 original size:15 final size:15
Alignment explanation
Indices: 2124177--2124223 Score: 76
Period size: 15 Copynumber: 3.1 Consensus size: 15
2124167 AGTCAGAATC
2124177 GCGTTGCGAAAGTCA
1 GCGTTGCGAAAGTCA
*
2124192 GCGTTGCGAAAGTCGC
1 GCGTTGCGAAAGTC-A
2124208 GCGTTGCGAAAGTCA
1 GCGTTGCGAAAGTCA
2124223 G
1 G
2124224 TATCGCGTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 15 0.52
16 14 0.48
ACGTcount: A:0.23, C:0.21, G:0.36, T:0.19
Consensus pattern (15 bp):
GCGTTGCGAAAGTCA
Found at i:2124214 original size:31 final size:33
Alignment explanation
Indices: 2124158--2124223 Score: 100
Period size: 31 Copynumber: 2.0 Consensus size: 33
2124148 GTCAGAATCT
2124158 CGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAG
1 CGTTGCGAAAGTCAG-A-CGCGTTGCGAAAGTCAG
2124193 CGTTGCGAAAGTC-G-CGCGTTGCGAAAGTCAG
1 CGTTGCGAAAGTCAGACGCGTTGCGAAAGTCAG
2124224 TATCGCGTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
31 17 0.55
34 1 0.03
35 13 0.42
ACGTcount: A:0.26, C:0.21, G:0.33, T:0.20
Consensus pattern (33 bp):
CGTTGCGAAAGTCAGACGCGTTGCGAAAGTCAG
Found at i:2124232 original size:20 final size:20
Alignment explanation
Indices: 2124133--2124268 Score: 103
Period size: 20 Copynumber: 7.2 Consensus size: 20
2124123 GATTCTGTAT
* *
2124133 TATCTCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* *
2124153 AATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
2124173 AATCGCGTTGCGAAAGTC--
1 TATCGCGTTGCGAAAGTCAG
2124191 -A--GCGTTGCGAAAGTC-G
1 TATCGCGTTGCGAAAGTCAG
2124207 ---CGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
** *
2124224 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
2124245 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
2124265 TATC
1 TATC
2124269 ACATTGCGAT
Statistics
Matches: 99, Mismatches: 8, Indels: 18
0.79 0.06 0.14
Matches are distributed among these distances:
15 14 0.14
16 14 0.14
17 2 0.02
19 3 0.03
20 50 0.51
21 14 0.14
22 2 0.02
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:2124297 original size:41 final size:41
Alignment explanation
Indices: 2124211--2124299 Score: 99
Period size: 41 Copynumber: 2.2 Consensus size: 41
2124201 AAGTCGCGCG
* * * ** * *
2124211 TTGCGAAAGTCAGTATCGCGTTGCGATTTTGTATTATCGCG
1 TTGCGATAGTCAGTATCACATTGCGATTTTCAAATATCGCA
2124252 TTGCGATAGTCAGTATCACATTGCGATTTTCCAAAT-TCGCA
1 TTGCGATAGTCAGTATCACATTGCGATTTT-CAAATATCGCA
2124293 TTGCGAT
1 TTGCGAT
2124300 TTACTTATTC
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
41 38 0.95
42 2 0.05
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.36
Consensus pattern (41 bp):
TTGCGATAGTCAGTATCACATTGCGATTTTCAAATATCGCA
Found at i:2124360 original size:21 final size:22
Alignment explanation
Indices: 2124308--2124360 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
2124298 ATTTACTTAT
*
2124308 TCGCATTGTG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
2124329 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
2124350 TCGCATTGCGA
1 TCGCATTGCGA
2124361 TAGTCATAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.23
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:2124867 original size:22 final size:24
Alignment explanation
Indices: 2124842--2124889 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 24
2124832 TATCTTAAAG
*
2124842 TAAAATATTAGAGA-CAAAAT-AC
1 TAAAATAATAGAGATCAAAATGAC
*
2124864 TAAAATAATATAGATCAAAATGAC
1 TAAAATAATAGAGATCAAAATGAC
2124888 TA
1 TA
2124890 TTTTAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 12 0.55
23 6 0.27
24 4 0.18
ACGTcount: A:0.58, C:0.08, G:0.08, T:0.25
Consensus pattern (24 bp):
TAAAATAATAGAGATCAAAATGAC
Found at i:2125072 original size:30 final size:29
Alignment explanation
Indices: 2125036--2125092 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
2125026 ATTCTGTTGT
* * *
2125036 TAAATCTGAGTGAGCAATTGTTCAAATAAA
1 TAAATCTAAGCGAGC-AGTGTTCAAATAAA
2125066 TAAATCTAAGCGAGCAGTGTTCAAATA
1 TAAATCTAAGCGAGCAGTGTTCAAATA
2125093 CAATCTGCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 11 0.46
30 13 0.54
ACGTcount: A:0.42, C:0.12, G:0.18, T:0.28
Consensus pattern (29 bp):
TAAATCTAAGCGAGCAGTGTTCAAATAAA
Found at i:2129935 original size:2 final size:2
Alignment explanation
Indices: 2129928--2129960 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2129918 AACTAATAAG
2129928 AT AT 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 AT AT A
2129961 CTATTTATGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2130633 original size:108 final size:106
Alignment explanation
Indices: 2130521--2130845 Score: 263
Period size: 98 Copynumber: 3.0 Consensus size: 106
2130511 TCAACATATT
* * *
2130521 AGGTAGCGCCTAAAATGTTACCAAAGTTTAAGATGATGGAGCCTTAGAAATCCGACGAAAACCAA
1 AGGTAGCGCCTAAAATGTTACCAAAGTTTAAGCTGATGGAGTCTTAGAAATCCGACGAAAACAAA
*
2130586 ATAGGTTAATTATTGGAAACATTATCAATCAGAATAACATAAC
66 ATAAGTTAATTATTGGAAACATTAT-AATCA-AATAACATAAC
* ** ** *
2130629 AGGTAGCGCTTATGTAACGTAATAAG-TAGCGTATTTTTAAAGCTGATTGAGTCTTAGAAATCCG
1 AGGTAGCGC----CTAA---AAT--GTTA-CCAAAGTTT-AAGCTGATGGAGTCTTAGAAATCCG
* * * * * **
2130693 ACG-AAACAAAATATGTTAATTATTTG--A-TTTGTTATC-AAT---ATATT
55 ACGAAAACAAAATAAGTTAATTATTGGAAACATTATAATCAAATAACATAAC
* * *
2130737 AGGTAGCACCTAAAATGTTACCAAAGTTTAAGCTGATGGAGTTTTAGAAATCCGACGATAACAAA
1 AGGTAGCGCCTAAAATGTTACCAAAGTTTAAGCTGATGGAGTCTTAGAAATCCGACGAAAACAAA
*
2130802 ATAAGTTAATTATTGGAAACATTATTAACCATAATAACATAAC
66 ATAAGTTAATTATTGGAAACATTA-TAATCA-AATAACATAAC
2130845 A
1 A
2130846 AGTGTCGCTT
Statistics
Matches: 162, Mismatches: 33, Indels: 44
0.68 0.14 0.18
Matches are distributed among these distances:
98 26 0.16
99 26 0.16
100 2 0.01
101 4 0.02
102 2 0.01
103 3 0.02
104 3 0.02
105 3 0.02
108 24 0.15
111 3 0.02
112 3 0.02
113 3 0.02
114 3 0.02
115 4 0.02
116 2 0.01
117 26 0.16
118 25 0.15
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.30
Consensus pattern (106 bp):
AGGTAGCGCCTAAAATGTTACCAAAGTTTAAGCTGATGGAGTCTTAGAAATCCGACGAAAACAAA
ATAAGTTAATTATTGGAAACATTATAATCAAATAACATAAC
Found at i:2130812 original size:216 final size:217
Alignment explanation
Indices: 2130363--2130950 Score: 707
Period size: 216 Copynumber: 2.7 Consensus size: 217
2130353 TTAATATAAC
* * *
2130363 AGTTAATTACTGGAAACATTATTGACCATAATAACATAACAGGTAGCACTTATGTAATGTAATAA
1 AGTTAATTATTGGAAACATTATTAACCATAATAACATAACAGGTAGCGCTTATGTAATGTAATAA
* * * * ** * *
2130428 GTAGCACATTTTTTAAGTTAATAG-GACTTTAGAAATTTGACGATAATAAAATAAATTAATTACT
66 GTAGCGCATTTTTAAAGCTGATAGAGAC-TTAGAAATCCGACGATAACAAAATAAGTTAATTACT
*
2130492 TGATTTGTTATCAATATTATCAACATATTAGGTAGCGCCTAAAATGTTACCAAAGTTTAAGATGA
130 TGATTTGTTATC---A--AT----ATATTAGGTAGCACCTAAAATGTTACCAAAGTTTAAGATGA
*
2130557 TGGAGCCTTAGAAATCCGACGAAAACCAAATA
186 TGGAGCCTTAGAAATCCGACGAAAACAAAATA
* * * * *
2130589 GGTTAATTATTGGAAACATTATCAATCAGAATAACATAACAGGTAGCGCTTATGTAACGTAATAA
1 AGTTAATTATTGGAAACATTATTAACCATAATAACATAACAGGTAGCGCTTATGTAATGTAATAA
* * * * *
2130654 GTAGCGTATTTTTAAAGCTGATTGAGTCTTAGAAATCCGACGA-AACAAAATATGTTAATTATTT
66 GTAGCGCATTTTTAAAGCTGATAGAGACTTAGAAATCCGACGATAACAAAATAAGTTAATTACTT
* **
2130718 GATTTGTTATCAATATATTAGGTAGCACCTAAAATGTTACCAAAGTTTAAGCTGATGGAGTTTTA
131 GATTTGTTATCAATATATTAGGTAGCACCTAAAATGTTACCAAAGTTTAAGATGATGGAGCCTTA
*
2130783 GAAATCCGACGATAACAAAATA
196 GAAATCCGACGAAAACAAAATA
* * *
2130805 AGTTAATTATTGGAAACATTATTAACCATAATAACATAACAAGT-GTCGCTTATTTCATGTAATA
1 AGTTAATTATTGGAAACATTATTAACCATAATAACATAACAGGTAG-CGCTTATGTAATGTAATA
* * * * * *
2130869 AGTAGCGCCTGTTTAAAGGTGATGGAGCCTTAGAAATCCGAC-ATTAACAAAATAGGTTAATTAC
65 AGTAGCGCATTTTTAAAGCTGATAGAGACTTAGAAATCCGACGA-TAACAAAATAAGTTAATTAC
*
2130933 TTGATTTGTTTTCAATAT
129 TTGATTTGTTATCAATAT
2130951 TATCAACATA
Statistics
Matches: 314, Mismatches: 44, Indels: 17
0.84 0.12 0.05
Matches are distributed among these distances:
215 2 0.01
216 157 0.50
217 34 0.11
220 2 0.01
222 1 0.00
225 28 0.09
226 88 0.28
227 2 0.01
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (217 bp):
AGTTAATTATTGGAAACATTATTAACCATAATAACATAACAGGTAGCGCTTATGTAATGTAATAA
GTAGCGCATTTTTAAAGCTGATAGAGACTTAGAAATCCGACGATAACAAAATAAGTTAATTACTT
GATTTGTTATCAATATATTAGGTAGCACCTAAAATGTTACCAAAGTTTAAGATGATGGAGCCTTA
GAAATCCGACGAAAACAAAATA
Found at i:2131206 original size:130 final size:128
Alignment explanation
Indices: 2130961--2131303 Score: 325
Period size: 130 Copynumber: 2.7 Consensus size: 128
2130951 TATCAACATA
*
2130961 TTACCGTGTACATTGTTAATTTACATATTACTTTAAAGTAATAGGTTTCAAAATTATAAGAATCG
1 TTACCGTGTACATTGTTAATTTAC-TATTACTTTAAAGTAATAGGTTTCAAAATTATAAGTATCG
* *** * * * **
2131026 ATA-TATATACGA-CAATATAGATACTTGTACATTTACACATAATTTTATTATATTGGTATAAAC
65 ATACTTTATAC-ATGTGTATCGATACCTGTACATTTACACATAATTTCATTATACCGG--TAAAC
2131089 GT
127 GT
* ** * *
2131091 TTGCCGTGTACATTGTTAATTTATCTATTACTTTAAAGTAATAGGTTTCAAAATTCCATGTATTG
1 TTACCGTGTACATTGTTAATTTA-CTATTACTTTAAAGTAATAGGTTTCAAAATTATAAGTATCG
** * * * *
2131156 ATACTTTATACATGTGTATCGATACCTG-ATGTTTACGCCT-ATTGTCATTATACCGGTAGACTT
65 ATACTTTATACATGTGTATCGATACCTGTACATTTACACATAATT-TCATTATACCGGTAAACGT
* * * * * * * *
2131219 TTACCATTTTCATTGTAAATTAACCTATTACTTTAAAGTAATAGGTTTCGAAATTATAGGTATCA
1 TTACCGTGTACATTGTTAATTTA-CTATTACTTTAAAGTAATAGGTTTCAAAATTATAAGTATCG
*
2131284 ATACTTTATATATGTGTATC
65 ATACTTTATACATGTGTATC
2131304 AGTACATTTT
Statistics
Matches: 174, Mismatches: 35, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
128 76 0.44
129 3 0.02
130 78 0.45
131 17 0.10
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (128 bp):
TTACCGTGTACATTGTTAATTTACTATTACTTTAAAGTAATAGGTTTCAAAATTATAAGTATCGA
TACTTTATACATGTGTATCGATACCTGTACATTTACACATAATTTCATTATACCGGTAAACGT
Found at i:2131487 original size:197 final size:198
Alignment explanation
Indices: 2131189--2131657 Score: 559
Period size: 197 Copynumber: 2.4 Consensus size: 198
2131179 ACCTGATGTT
* * *
2131189 TACGCCTATTGTCATTATACCGGTAGACTTTTACCATTTTCATTGTAAATTAACCTATTACTTTA
1 TACGCCTATTATCATTATACCGGTAGACTTTTACCATTTACATTGTAAATTTACCTATTACTTTA
* *
2131254 AAGTAATAGGTTTCGAAATTATAGGTATCAATACTTTATATATGTGTATC-AGTACATTTTGCG-
66 AAGTAATAGGTTTCAAAATTATAGGTATCAATACTTTATACATGTGTATCGA-TACATTTTGCGT
* * * * *
2131317 GCAAATTGTTTGAAAAACATATTATAATAAAAGTATTGATACCTATATAGACATTATCGATACTT
130 ACAAATTG-TTGAAAAACATATTATAATAAAAGTATCGATACATATATAGAAAATATCGATACTT
2131382 GGT-A
194 GGTAA
* * ** * *
2131386 TATGCCTATTATCAATATACCAATAGATTTTTACCATTTACATTATAAATTTACCTATTACTTTA
1 TACGCCTATTATCATTATACCGGTAGACTTTTACCATTTACATTGTAAATTTACCTATTACTTTA
* * * *
2131451 AAGTAATCGGTTTTAAAATTCT-GAGTATCGATACTTTATACATGTGTATCGATACATTTTGCGT
66 AAGTAATAGGTTTCAAAATTATAG-GTATCAATACTTTATACATGTGTATCGATACATTTTGCGT
* * * * * * *
2131515 ATAAATTGTTGAGAAGCATATTGTACTAAAATTATCGATACATATATATAAAATATCGATACTTG
130 ACAAATTGTTGAAAAACATATTATAATAAAAGTATCGATACATATATAGAAAATATCGATACTTG
2131580 GTAAA
195 GT-AA
* * * * * * *
2131585 TACGCCTATTCTCATTATACTGGTAAAGTTTTACCCTTGACATTGTTAATTTACCTATTACTTTA
1 TACGCCTATTATCATTATACCGGTAGACTTTTACCATTTACATTGTAAATTTACCTATTACTTTA
*
2131650 TAGTAATA
66 AAGTAATA
2131658 AAGTAATTTA
Statistics
Matches: 226, Mismatches: 41, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
196 1 0.00
197 158 0.70
198 7 0.03
199 60 0.27
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.40
Consensus pattern (198 bp):
TACGCCTATTATCATTATACCGGTAGACTTTTACCATTTACATTGTAAATTTACCTATTACTTTA
AAGTAATAGGTTTCAAAATTATAGGTATCAATACTTTATACATGTGTATCGATACATTTTGCGTA
CAAATTGTTGAAAAACATATTATAATAAAAGTATCGATACATATATAGAAAATATCGATACTTGG
TAA
Found at i:2132046 original size:19 final size:21
Alignment explanation
Indices: 2132008--2132048 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
2131998 GAAAGCCCAA
2132008 GTATCGATACTTTTTATATGT
1 GTATCGATACTTTTTATATGT
2132029 GTATCGATA-TTTTT-TATGT
1 GTATCGATACTTTTTATATGT
2132048 G
1 G
2132049 CAAATTGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 6 0.30
20 5 0.25
21 9 0.45
ACGTcount: A:0.22, C:0.07, G:0.17, T:0.54
Consensus pattern (21 bp):
GTATCGATACTTTTTATATGT
Found at i:2132152 original size:533 final size:530
Alignment explanation
Indices: 2131193--2132190 Score: 1125
Period size: 533 Copynumber: 1.9 Consensus size: 530
2131183 GATGTTTACG
* * * * * *
2131193 CCTATTGTCATTATACCGGTAGACTTTTACCATTTTCATTGTAAATTAACCTATTACTTTAAAGT
1 CCTATTATCATTAAACCGGTAGACTTTTACCATTTACATTATAAATTAACATATTAATTTAAAGT
* * * * * * *
2131258 AATAGGTTTCGAAATTATAGGTATCAATACTTTATATATGTGTATCAGTACATTTTGCGGCAAAT
66 AATAAGTTTCGAAAGTACAAGTATCAATACTTTATATATGTGTAGCAGTACATTTTACGACAAAT
* *
2131323 TGTTTGAAAAACATATTATAATAAAAGTATTGATACCTATATAGACATTATCGATACTTGGTATA
131 TGTTTGAAAAACATATTAGAATAAAAGTATCGATACCTATATAGACATTATCGATACTTGGTATA
* * * *
2131388 TGCCTATTATCAATATACCAATAGATTTTTACCATTTACATTATAAATTTACCTATTACTTTAAA
196 CGCCCATTATCAATAAACCAATAGATTTTTACCATGTACATTATAAATTTACCTATTACTTTAAA
** * ** ** * *
2131453 GTAATCGGTTTTAAAATTCTGAGTATCGATACTTTATACATGTGTATCGATACATTTTGCGTATA
261 GTAATAAGTTTCAAAAGCCCAAGTATCGATACTTTATACATGTGTATCGATACATTTTACGTACA
* * * *
2131518 AATTGTTGAGAAGCATATTGTACTAAAATTATCGATACATATATATAAAATATCGATACTTGGTA
326 AATTGTTGAGAAGCATACTGGAATAAAATTATCGATACATATATATAAAATATCGATACTTGATA
* * ** * *
2131583 AATACGCCTATTCTCATTATACTGGTAAAGTTTTACCCTTGACATTGTTAATTTACCTATTACTT
391 AATACGCCTATTATCATTAAACTAATAAAGTTTTACCCTTGACATTATAAATTTACCTATTACTT
*
2131648 TATAGTAATAAAGTAATTTACCTATTATCATTATATCGATGCCTATATAATAAATATAGATAATT
456 TAAAGTAATAAAGTAATTTACCTATTATCATTATATCGATGCCTATATAATAAATATAGATAATT
2131713 TATATTTATT
521 TATATTTATT
* * *
2131723 CCTATTATCATTAAACTGGTAGATTTTTACCATTTACATTATAAATTTACATATTAATTTAAAGT
1 CCTATTATCATTAAACCGGTAGACTTTTACCATTTACATTATAAATTAACATATTAATTTAAAGT
* * *
2131788 AATAAGTTTCGAAAGTCCAAGTATCGATACTTGT-TATATGTGTAGC-GATACTTTTTACGAACA
66 AATAAGTTTCGAAAGTACAAGTATCAATACTT-TATATATGTGTAGCAG-TACATTTTACG-ACA
* ** *
2131851 AATTGTTTGAGATGCATATTGGAATAACAA-TATCGATACCTATATA-A-ATGTATCGATACTTT
128 AATTGTTTGAAAAACATATTAGAATAA-AAGTATCGATACCTATATAGACAT-TATCGATAC--T
* * * * * *
2131913 ATGTTTTACGCCCATTATCATTAAACCATTAGATTTTTACCGTGTACATTGTAAATTTACCTATT
189 -TGGTATACGCCCATTATCAATAAACCAATAGATTTTTACCATGTACATTATAAATTTACCTATT
* * * * * **
2131978 ATTTTAATGTAATAAGTTTCGAAAGCCCAAGTATCGATACTTTTTATATGTGTATCGATATTTTT
253 ACTTTAAAGTAATAAGTTTCAAAAGCCCAAGTATCGATACTTTATACATGTGTATCGATACATTT
* * * * *
2132043 TATGTGCAAATTGTTTGAGATGCATACTGGAATAACAA-TAT-GATACCTATATA-ATAAGTATC
318 TACGTACAAATTG-TTGAGAAGCATACTGGAATAA-AATTATCGATACATATATATA-AAATATC
* *** * * * * *
2132105 -AGTACTTTATGTTTACGCCTATTATCATTAAA-TCAATAGATTTTTACCGTTTATATTATAAAT
380 GA-TACTTGATAAATACGCCTATTATCATTAAACT-AATAAAGTTTTACCCTTGACATTATAAAT
2132168 TTACCTATTACTTTAAAGTAATA
443 TTACCTATTACTTTAAAGTAATA
2132191 GGTTTCGAAA
Statistics
Matches: 379, Mismatches: 76, Indels: 23
0.79 0.16 0.05
Matches are distributed among these distances:
529 3 0.01
530 112 0.30
531 40 0.11
532 6 0.02
533 196 0.52
534 20 0.05
535 2 0.01
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (530 bp):
CCTATTATCATTAAACCGGTAGACTTTTACCATTTACATTATAAATTAACATATTAATTTAAAGT
AATAAGTTTCGAAAGTACAAGTATCAATACTTTATATATGTGTAGCAGTACATTTTACGACAAAT
TGTTTGAAAAACATATTAGAATAAAAGTATCGATACCTATATAGACATTATCGATACTTGGTATA
CGCCCATTATCAATAAACCAATAGATTTTTACCATGTACATTATAAATTTACCTATTACTTTAAA
GTAATAAGTTTCAAAAGCCCAAGTATCGATACTTTATACATGTGTATCGATACATTTTACGTACA
AATTGTTGAGAAGCATACTGGAATAAAATTATCGATACATATATATAAAATATCGATACTTGATA
AATACGCCTATTATCATTAAACTAATAAAGTTTTACCCTTGACATTATAAATTTACCTATTACTT
TAAAGTAATAAAGTAATTTACCTATTATCATTATATCGATGCCTATATAATAAATATAGATAATT
TATATTTATT
Found at i:2132209 original size:199 final size:200
Alignment explanation
Indices: 2131680--2132303 Score: 873
Period size: 200 Copynumber: 3.1 Consensus size: 200
2131670 TATTATCATT
* * * * ** **
2131680 ATATCGATGCCTATATAATAAATAT-AGATAATTTATATTTATTCCTATTATCATTAAACTGGTA
1 ATATCGATACCTATATAATAAGTATCAGATACTTTATGTTTACGCCTATTATCATTAAAC-AATA
* *
2131744 GATTTTTACCATTTACATTATAAATTTACATATTAATTTAAAGTAATAAGTTTCGAAAGTCCAAG
65 GATTTTTACCGTTTACATTATAAATTTACCTATTAATTTAAAGTAATAAGTTTCGAAAGTCCAAG
* ** *
2131809 TATCGATACTTGTTATATGTGTAGCGATACTTTTTACGAACAAATTGTTTGAGATGCATATTGGA
130 TATCGATACTTGTTATATGTGTATCGATACTTTTTACGTGCAAATTGTTTGAGATGCATACTGGA
2131874 ATAACA
195 ATAACA
* * *
2131880 ATATCGATACCTATATAA-ATGTATC-GATACTTTATGTTTTACGCCCATTATCATTAAACCATT
1 ATATCGATACCTATATAATAAGTATCAGATACTTTATG-TTTACGCCTATTATCATTAAA-CAAT
* * * * *
2131943 AGATTTTTACCGTGTACATTGTAAATTTACCTATTATTTTAATGTAATAAGTTTCGAAAGCCCAA
64 AGATTTTTACCGTTTACATTATAAATTTACCTATTAATTTAAAGTAATAAGTTTCGAAAGTCCAA
* * *
2132008 GTATCGATACTTTTTATATGTGTATCGATATTTTTTATGTGCAAATTGTTTGAGATGCATACTGG
129 GTATCGATACTTGTTATATGTGTATCGATACTTTTTACGTGCAAATTGTTTGAGATGCATACTGG
2132073 AATAACA
194 AATAACA
2132080 ATAT-GATACCTATATAATAAGTATCAG-TACTTTATGTTTACGCCTATTATCATTAAATCAATA
1 ATATCGATACCTATATAATAAGTATCAGATACTTTATGTTTACGCCTATTATCATTAAA-CAATA
* * *
2132143 GATTTTTACCGTTTATATTATAAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAAGTCCAAG
65 GATTTTTACCGTTTACATTATAAATTTACCTATTAATTTAAAGTAATAAGTTTCGAAAGTCCAAG
* * *
2132208 TATTGATACTTGTTATATGTGT-TGCGATACTTTTTGCGTGCAAATTGTTTGAGATGCATACCGG
130 TATCGATACTTGTTATATGTGTAT-CGATACTTTTTACGTGCAAATTGTTTGAGATGCATACTGG
2132272 AATAACA
194 AATAACA
*
2132279 ATATTGATACCTATATAATAAGTAT
1 ATATCGATACCTATATAATAAGTAT
2132304 GAAACTTGTA
Statistics
Matches: 376, Mismatches: 41, Indels: 14
0.87 0.10 0.03
Matches are distributed among these distances:
198 1 0.00
199 175 0.47
200 198 0.53
201 2 0.01
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (200 bp):
ATATCGATACCTATATAATAAGTATCAGATACTTTATGTTTACGCCTATTATCATTAAACAATAG
ATTTTTACCGTTTACATTATAAATTTACCTATTAATTTAAAGTAATAAGTTTCGAAAGTCCAAGT
ATCGATACTTGTTATATGTGTATCGATACTTTTTACGTGCAAATTGTTTGAGATGCATACTGGAA
TAACA
Found at i:2133505 original size:14 final size:14
Alignment explanation
Indices: 2133485--2133518 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2133475 CGGTAGTATG
2133485 CATTTTAAATTATT
1 CATTTTAAATTATT
* *
2133499 TATTTTAATTTATT
1 CATTTTAAATTATT
2133513 CATTTT
1 CATTTT
2133519 TTTAGTAATG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (14 bp):
CATTTTAAATTATT
Found at i:2133821 original size:7 final size:7
Alignment explanation
Indices: 2133809--2133840 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
2133799 AAGAAAATAT
2133809 TTTAGGG
1 TTTAGGG
2133816 TTTAGGG
1 TTTAGGG
2133823 TTTAGGG
1 TTTAGGG
2133830 TTTAGGG
1 TTTAGGG
2133837 TTTA
1 TTTA
2133841 AAATTTAGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.16, C:0.00, G:0.38, T:0.47
Consensus pattern (7 bp):
TTTAGGG
Found at i:2133847 original size:21 final size:21
Alignment explanation
Indices: 2133809--2133849 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2133799 AAGAAAATAT
***
2133809 TTTAGGGTTTAGGGTTTAGGG
1 TTTAGGGTTTAAAATTTAGGG
2133830 TTTAGGGTTTAAAATTTAGG
1 TTTAGGGTTTAAAATTTAGG
2133850 TTCAATGTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.22, C:0.00, G:0.34, T:0.44
Consensus pattern (21 bp):
TTTAGGGTTTAAAATTTAGGG
Found at i:2136050 original size:6 final size:6
Alignment explanation
Indices: 2136033--2136063 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
2136023 ATAGTGGAGC
*
2136033 TCAAAT TGAAAT TCAAAT TCAAAT TCAAAT T
1 TCAAAT TCAAAT TCAAAT TCAAAT TCAAAT T
2136064 GAGAACTGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.13, G:0.03, T:0.35
Consensus pattern (6 bp):
TCAAAT
Found at i:2138650 original size:18 final size:18
Alignment explanation
Indices: 2138629--2138668 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2138619 TGATTTGATC
*
2138629 AGAAGCTCTTACTTGAGA
1 AGAAGATCTTACTTGAGA
**
2138647 AGAAGATCTTGGTTGAGA
1 AGAAGATCTTACTTGAGA
2138665 AGAA
1 AGAA
2138669 CTTCATCTCG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.10, G:0.28, T:0.25
Consensus pattern (18 bp):
AGAAGATCTTACTTGAGA
Found at i:2139462 original size:180 final size:178
Alignment explanation
Indices: 2139141--2139478 Score: 453
Period size: 179 Copynumber: 1.9 Consensus size: 178
2139131 TGTTTGTGAC
* * * * * *
2139141 TCATTATACCAGTAGATATTTACCGTTTATATTGTAAATTAACCTTTAGTTTAAAATAATAGGTT
1 TCATTAGACCAATAGATATTTACCGTTTACATTGTAAATTAACATTTACTTTAAAATAAAAGGTT
** * *
2139206 TCAAAATTCCAAGTATCGATACTTTATATATGTGTATCGATATTTTTTAAGTACAAATTGTTTGA
66 TCAAAATTCCAAGTATAAATACTTTATATATATGTATCGATATTTTTTAACTACAAATTGTTTGA
*
2139271 GATGGATACTGTAATAAAAGTATCGATACTTTATGTTTACGCCTATTA
131 GATGCATACTGTAATAAAAGTATCGATACTTTATGTTTACGCCTATTA
* * * *
2139319 TCATTAGACCAATAGATTTTTACCGTTTACATTGTAAATTTACATATTACTTTAAAGTAAAATGT
1 TCATTAGACCAATAGATATTTACCGTTTACATTGTAAATTAACAT-TTACTTTAAAATAAAAGGT
* * * ** *
2139384 TTCTAAATTCTAAGTATAAATTCTTGT-TATATATGTATCGATACTTTTTTTCCTGCAAATTGTT
65 TTCAAAATTCCAAGTATAAATACTT-TATATATATGTATCGATA-TTTTTTAACTACAAATTGTT
2139448 TGAGATGCATACTGTAATAAAAGTATCGATA
128 TGAGATGCATACTGTAATAAAAGTATCGATA
2139479 GCTATATTAA
Statistics
Matches: 136, Mismatches: 21, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
178 39 0.29
179 50 0.37
180 47 0.35
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.42
Consensus pattern (178 bp):
TCATTAGACCAATAGATATTTACCGTTTACATTGTAAATTAACATTTACTTTAAAATAAAAGGTT
TCAAAATTCCAAGTATAAATACTTTATATATATGTATCGATATTTTTTAACTACAAATTGTTTGA
GATGCATACTGTAATAAAAGTATCGATACTTTATGTTTACGCCTATTA
Found at i:2139630 original size:201 final size:197
Alignment explanation
Indices: 2139275--2140720 Score: 1361
Period size: 201 Copynumber: 7.1 Consensus size: 197
2139265 GTTTGAGATG
* * *
2139275 GATACTGTAATAAAAGTATCGATACTTTATGTTTACGCCTATTATCATTAGACCA-ATAGATTTT
1 GATACTAT-ATAAAAGTATCGATACTTTATGTTTACGCCTATTATCATTA-AACATGTAGATTTT
* * * * **
2139339 TACCGTTTACATTGTAAATTTACATATTACTTTAAAGTAAAATGTTTCTAAATTCTAAGTATAAA
64 TACCGTTTACATTGTAAATTTACCTATTACTTTAAAGTAAAAGGTTTCGAAATTCCAAGTATCGA
* * **
2139404 TTCTTGTTATATATGTATCGATACTTT-TTTTCCTGCAAATTGTTTGAGATGCATACTGTAATAA
129 TACTT-TTATATGTGTATCGATACTTTGTTTT-GGGCAAATTGTTTGAGATGCATACTG-AATAA
2139468 AAGTATC
191 AAGTATC
**
2139475 GATAGCTATATTAAAAGTATCGATACTTTATGTTTATTCCTATTATCATTAAACATGTAGATTTT
1 GATA-CTATA-TAAAAGTATCGATACTTTATGTTTACGCCTATTATCATTAAACATGTAGATTTT
* * *
2139540 TACCGTTTACATTGTAAATTTACCTATTACTTTCAAGTAAACGGTTTCGAAATTCTAAGTATCGA
64 TACCGTTTACATTGTAAATTTACCTATTACTTTAAAGTAAAAGGTTTCGAAATTCCAAGTATCGA
** * *
2139605 TACTTGTTATATGTACATCGATAC-TT-TTTTGCGTGCAAATTGCTTGAGATGCATACTAAAATA
129 TACTT-TTATATGTGTATCGATACTTTGTTTTG-G-GCAAATTGTTTGAGATGCATACT-GAATA
*
2139668 AAAATATC
190 AAAGTATC
* * *
2139676 GATGCTTATATAATAAGTATCGATACTTTATGTTTACGCCTATTATTATTAAACTTGTAGATTTT
1 GATAC-TATATAA-AAGTATCGATACTTTATGTTTACGCCTATTATCATTAAACATGTAGATTTT
*
2139741 TACTGTTT-CAATTGTAAATTTACCTATTACTTTAAAG-AAATAGGTTTCGAAATTCCAAGTATC
64 TACCGTTTAC-ATTGTAAATTTACCTATTACTTTAAAGTAAA-AGGTTTCGAAATTCCAAGTATC
* * *
2139804 GATACTTTATATATGTGTATCGATACTTTGTTGTGGGCAAATTGTTTGAGA-ACAAAACTAGAAT
127 GATACTTT-TATATGTGTATCGATACTTTGTTTTGGGCAAATTGTTTGAGATGC-ATACT-GAAT
2139868 AAAAGTATC
189 AAAAGTATC
* *
2139877 GATACAGATATACAAAGTATCGATATTTTATGTTTACGCCTATTATCATTAAACCA-GTAGATTT
1 GATAC-TATATA-AAAGTATCGATACTTTATGTTTACGCCTATTATCATTAAA-CATGTAGATTT
* *
2139941 TTACCGTTT-CTATTGTAAATTTACCTATTACTTTAAAGTAATAGGTTTTGAAATTCCAAGTATC
63 TTACCGTTTAC-ATTGTAAATTTACCTATTACTTTAAAGTAAAAGGTTTCGAAATTCCAAGTATC
* * * * *
2140005 GATACTATATATATGGGTATCGATACTTTGTTATGGACAAATTGTTTGAGATGCATAGTGGAATA
127 GATACT-TTTATATGTGTATCGATACTTTGTTTTGGGCAAATTGTTTGAGATGCATACT-GAATA
* * *
2140070 ACATTATT
190 AAAGTATC
* * *
2140078 GATACCTATATAATAAGTATTTG-TACTTTATGTTTACGCCTATTATCATT-AA-AT-TGGTTAT
1 GATA-CTATATAA-AAGTA-TCGATACTTTATGTTTACGCCTATTATCATTAAACATGTAGAT-T
* * * * * **
2140139 TTTACCATTTCCATTGTAAATTTACCTATGACTTCAAAGTAATAGGTTTTAAAATTCCAAGTATC
62 TTTACCGTTTACATTGTAAATTTACCTATTACTTTAAAGTAAAAGGTTTCGAAATTCCAAGTATC
* * *
2140204 GATAC-TTTATATTTGGTATCGATACTTTGTTGTGGGCAAATTGTTTGAGA-ACTATACTAGAAT
127 GATACTTTTATATGT-GTATCGATACTTTGTTTTGGGCAAATTGTTTGAGATGC-ATACT-GAAT
* *
2140267 AAAAATATT
189 AAAAGTATC
* * * * * *
2140276 GATACGGATATAAAAATATCGATACTTTATATTTACGCCTATTACCATTAAAC-CGATAGAGTTT
1 GATAC-TATATAAAAGTATCGATACTTTATGTTTACGCCTATTATCATTAAACATG-TAGATTTT
* * * ** * *
2140340 TACTGTTTACATTGTAAATTTACATATTACTTTAAAGTAAAAGGTTTTGAAATTATAATTATTGA
64 TACCGTTTACATTGTAAATTTACCTATTACTTTAAAGTAAAAGGTTTCGAAATTCCAAGTATCGA
* * *
2140405 TACTTGTTATATATGTATTGATAC--TCTTTTGCGTGCAAATTGTTTGAGATGCATACTGGAATA
129 TACTT-TTATATGTGTATCGATACTTTGTTTTG-G-GCAAATTGTTTGAGATGCATACT-GAATA
2140468 AAAGTATC
190 AAAGTATC
* * *
2140476 GATATTTATATAATAAATATCAATACTTTATGTTTACGATATTTTATGTTTACGCCTATTATCAT
1 G--------ATACT--ATAT-AA-A----A-GTAT-CGATACTTTATGTTTACGCCTATTATCAT
* * * *
2140541 TAAACCA-GTAGATTTTTACCCG-TTCCATTGTCAATTTACCTATTACTTTAAAATAATAGGTTT
48 TAAA-CATGTAGATTTTTA-CCGTTTACATTGTAAATTTACCTATTACTTTAAAGTAAAAGGTTT
* * ** *
2140604 CAAAATTCCAAGTATCGATA-TTTTATACACAG-GTATCGATACTTTGTTGCGGACAAATTGTTT
111 CGAAATTCCAAGTATCGATACTTTTAT--A-TGTGTATCGATACTTTGTTTTGGGCAAATTGTTT
** *
2140667 GAGAACCATACTAGAATAAGAGTATC
173 GAGATGCATACT-GAATAAAAGTATC
* *
2140693 GATACGGATATAAAAAGTATCGAAACTT
1 GATAC-TATAT-AAAAGTATCGATACTT
2140721 GGACATTTTC
Statistics
Matches: 1037, Mismatches: 144, Indels: 129
0.79 0.11 0.10
Matches are distributed among these distances:
196 2 0.00
197 37 0.04
198 69 0.07
199 125 0.12
200 72 0.07
201 542 0.52
202 15 0.01
203 5 0.00
207 1 0.00
208 9 0.01
209 7 0.01
210 2 0.00
211 1 0.00
215 5 0.00
216 4 0.00
217 132 0.13
218 5 0.00
219 4 0.00
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (197 bp):
GATACTATATAAAAGTATCGATACTTTATGTTTACGCCTATTATCATTAAACATGTAGATTTTTA
CCGTTTACATTGTAAATTTACCTATTACTTTAAAGTAAAAGGTTTCGAAATTCCAAGTATCGATA
CTTTTATATGTGTATCGATACTTTGTTTTGGGCAAATTGTTTGAGATGCATACTGAATAAAAGTA
TC
Found at i:2140032 original size:402 final size:396
Alignment explanation
Indices: 2139275--2140720 Score: 1600
Period size: 402 Copynumber: 3.6 Consensus size: 396
2139265 GTTTGAGATG
* *
2139275 GATACTGTA-ATAA-AAGTATCGATACTTTATGTTTACGCCTATTATCATTAGACCAATAGATTT
1 GATACT-TATATAATAAGTATCGATACTTTATGTTTACGCCTATTATCATTAAACCAGTAGATTT
* * * *
2139338 TTACCGTTT-ACATTGTAAATTTACATATTACTTTAAAGTAAA-ATGTTTCTAAATTCTAAGTAT
65 TTACCGTTTCA-ATTGTAAATTTACCTATTACTTTAAAG-AAATAGGTTTCAAAATTCCAAGTAT
** * * ** *
2139401 AAATTCTTGTTATATAT-GTATCGATACTTT-TTTTCCTGCAAATTGTTTGAGATGCATACT-GT
128 CGATAC-T-TTATATATGGTATCGATACTTTGTTGT-GGGCAAATTGTTTGAGA-ACATACTAG-
* **
2139463 AATAAAAGTATCGATA-GCTATATTAAAAGTATCGATACTTTATGTTTATTCCTATTATCATTAA
188 AATAAAAGTATCGATACG-GATA-TAAAAGTATCGATACTTTATGTTTACGCCTATTATCATTAA
* *
2139527 A-CATGTAGATTTTTACCGTTTACATTGTAAATTTACCTATTACTTTCAAGTAAACGGTTTCGAA
251 ACCA-GTAGATTTTTACCGTTTACATTGTAAATTTACCTATTACTTTAAAGTAAA-GGTTTTGAA
* *
2139591 ATTCTAAGTATCGATACTTGTTATAT-GTACATCGATACTTTTTTGCGTGCAAATTGCTTGAGAT
314 ATTCTAAGTATCGATACTT-ATATATGGT--ATCGATACTTTTTTGCGTGCAAATTGTTTGAGAT
**
2139655 GCATACTAAAATAAAAATATC
376 GCATACTGGAATAAAAATATC
* * **
2139676 GATGCTTATATAATAAGTATCGATACTTTATGTTTACGCCTATTATTATTAAACTTGTAGATTTT
1 GATACTTATATAATAAGTATCGATACTTTATGTTTACGCCTATTATCATTAAACCAGTAGATTTT
* *
2139741 TACTGTTTCAATTGTAAATTTACCTATTACTTTAAAGAAATAGGTTTCGAAATTCCAAGTATCGA
66 TACCGTTTCAATTGTAAATTTACCTATTACTTTAAAGAAATAGGTTTCAAAATTCCAAGTATCGA
*
2139806 TACTTTATATATGTGTATCGATACTTTGTTGTGGGCAAATTGTTTGAGAACAAAACTAGAATAAA
131 TACTTTATATATG-GTATCGATACTTTGTTGTGGGCAAATTGTTTGAGAAC-ATACTAGAATAAA
* *
2139871 AGTATCGATACAGATATACAAAGTATCGATATTTTATGTTTACGCCTATTATCATTAAACCAGTA
194 AGTATCGATACGGATATA-AAAGTATCGATACTTTATGTTTACGCCTATTATCATTAAACCAGTA
*
2139936 GATTTTTACCGTTT-CTATTGTAAATTTACCTATTACTTTAAAGTAATAGGTTTTGAAATTCCAA
258 GATTTTTACCGTTTAC-ATTGTAAATTTACCTATTACTTTAAAGTAA-AGGTTTTGAAATTCTAA
* *
2140000 GTATCGATACTATATATATGGGTATCGATACTTTGTTATG-G-ACAAATTGTTTGAGATGCATAG
321 GTATCGATACT-TATATAT-GGTATCGATACTTT-TT-TGCGTGCAAATTGTTTGAGATGCATAC
* * *
2140063 TGGAATAACATTATT
382 TGGAATAAAAATATC
* * *** *
2140078 GATACCTATATAATAAGTATTTG-TACTTTATGTTTACGCCTATTATCATTAAATTGGT-TA-TT
1 GATACTTATATAATAAGTA-TCGATACTTTATGTTTACGCCTATTATCATTAAACCAGTAGATTT
* * * * * *
2140140 TTACCATTTCCATTGTAAATTTACCTATGACTTCAAAGTAATAGGTTTTAAAATTCCAAGTATCG
65 TTACCGTTTCAATTGTAAATTTACCTATTACTTTAAAGAAATAGGTTTCAAAATTCCAAGTATCG
*
2140205 ATACTTTATATTTGGTATCGATACTTTGTTGTGGGCAAATTGTTTGAGAACTATACTAGAATAAA
130 ATACTTTATATATGGTATCGATACTTTGTTGTGGGCAAATTGTTTGAGAAC-ATACTAGAATAAA
* * * * *
2140270 AATATTGATACGGATATAAAAATATCGATACTTTATATTTACGCCTATTACCATTAAACC-GATA
194 AGTATCGATACGGATATAAAAGTATCGATACTTTATGTTTACGCCTATTATCATTAAACCAG-TA
* * * * *
2140334 GAGTTTTACTGTTTACATTGTAAATTTACATATTACTTTAAAGTAAAAGGTTTTGAAATTATAAT
258 GATTTTTACCGTTTACATTGTAAATTTACCTATTACTTTAAAGT-AAAGGTTTTGAAATTCTAAG
* * *
2140399 TATTGATACTTGTTATATAT-GTATTGATACTCTTTTGCGTGCAAATTGTTTGAGATGCATACTG
322 TATCGATAC---TTATATATGGTATCGATACTTTTTTGCGTGCAAATTGTTTGAGATGCATACTG
*
2140463 GAATAAAAGTATC
384 GAATAAAAATATC
* * *
2140476 GATATTTATATAATAAATATCAATACTTTATGTTTACGATATTTTATGTTTACGCCTATTATCAT
1 G--A--TA-CT--T--ATAT-AATA----A-GTAT-CGATACTTTATGTTTACGCCTATTATCAT
* *
2140541 TAAACCAGTAGATTTTTACCCG-TTCCATTGTCAATTTACCTATTACTTTAAA-ATAATAGGTTT
50 TAAACCAGTAGATTTTTA-CCGTTTCAATTGTAAATTTACCTATTACTTTAAAGA-AATAGGTTT
* * * * *
2140604 CAAAATTCCAAGTATCGATATTTTATACACAGGTATCGATACTTTGTTGCGGACAAATTGTTTGA
113 CAAAATTCCAAGTATCGATACTTTATATA-TGGTATCGATACTTTGTTGTGGGCAAATTGTTTGA
* *
2140669 GAACCATACTAGAATAAGAGTATCGATACGGATATAAAAAGTATCGAAACTT
177 GAA-CATACTAGAATAAAAGTATCGATACGGATAT-AAAAGTATCGATACTT
2140721 GGACATTTTC
Statistics
Matches: 892, Mismatches: 101, Indels: 87
0.83 0.09 0.08
Matches are distributed among these distances:
396 2 0.00
397 4 0.00
398 146 0.16
399 67 0.08
400 90 0.10
401 19 0.02
402 355 0.40
403 14 0.02
404 4 0.00
405 1 0.00
407 4 0.00
408 4 0.00
412 2 0.00
413 3 0.00
414 31 0.03
415 1 0.00
416 66 0.07
417 64 0.07
418 15 0.02
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (396 bp):
GATACTTATATAATAAGTATCGATACTTTATGTTTACGCCTATTATCATTAAACCAGTAGATTTT
TACCGTTTCAATTGTAAATTTACCTATTACTTTAAAGAAATAGGTTTCAAAATTCCAAGTATCGA
TACTTTATATATGGTATCGATACTTTGTTGTGGGCAAATTGTTTGAGAACATACTAGAATAAAAG
TATCGATACGGATATAAAAGTATCGATACTTTATGTTTACGCCTATTATCATTAAACCAGTAGAT
TTTTACCGTTTACATTGTAAATTTACCTATTACTTTAAAGTAAAGGTTTTGAAATTCTAAGTATC
GATACTTATATATGGTATCGATACTTTTTTGCGTGCAAATTGTTTGAGATGCATACTGGAATAAA
AATATC
Found at i:2140695 original size:217 final size:217
Alignment explanation
Indices: 2140295--2140696 Score: 501
Period size: 217 Copynumber: 1.9 Consensus size: 217
2140285 ATAAAAATAT
*
2140295 CGATACTTTATATTTACGCCTATTACCATTAAACCGATAGAGTTTTACTGTTTACATTGTAAATT
1 CGATACTTTATATTTACGCCTATTACCATTAAACCGATAGAGTTTTACCGTTTACATTGTAAATT
* ** * * * * * *
2140360 TACATATTACTTTAAAGTAAAAGGTTTTGAAATTATAATTATTGATACTTGTTATATATGTATTG
66 TACATATTACTTTAAAATAAAAGGTTTCAAAATTACAAGTATCGATACTTGTTATACAGGTATCG
** *
2140425 ATACTCTTTTGCGTGCAAATTGTTTGAGATGCATACTGGAATAAAAGTATCGATATTTATATAAT
131 ATACTCTTTTGCGTGCAAATTGTTTGAGAACCATACTAGAATAAAAGTATCGATATTTATATAAT
2140490 AAATATCAATACTTTATGTTTA
196 AAATATCAATACTTTATGTTTA
* * * * * *
2140512 CGATATTTTATGTTTACGCCTATTATCATTAAACC-AGTAGATTTTTACCCG-TTCCATTGTCAA
1 CGATACTTTATATTTACGCCTATTACCATTAAACCGA-TAGAGTTTTA-CCGTTTACATTGTAAA
* * *
2140575 TTTACCTATTACTTTAAAATAATAGGTTTCAAAATTCCAAGTATCGATA-TT-TTATACACAGGT
64 TTTACATATTACTTTAAAATAAAAGGTTTCAAAATTACAAGTATCGATACTTGTTAT--ACAGGT
*
2140638 ATCGATACT-TTGTTGCG-GACAAATTGTTTGAGAACCATACTAGAATAAGAGTATCGATA
127 ATCGATACTCTT-TTGCGTG-CAAATTGTTTGAGAACCATACTAGAATAAAAGTATCGATA
2140697 CGGATATAAA
Statistics
Matches: 156, Mismatches: 23, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
215 4 0.03
216 6 0.04
217 144 0.92
218 2 0.01
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (217 bp):
CGATACTTTATATTTACGCCTATTACCATTAAACCGATAGAGTTTTACCGTTTACATTGTAAATT
TACATATTACTTTAAAATAAAAGGTTTCAAAATTACAAGTATCGATACTTGTTATACAGGTATCG
ATACTCTTTTGCGTGCAAATTGTTTGAGAACCATACTAGAATAAAAGTATCGATATTTATATAAT
AAATATCAATACTTTATGTTTA
Found at i:2147002 original size:37 final size:37
Alignment explanation
Indices: 2146952--2147022 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
2146942 TTTATTCAAC
2146952 ATACAAGTATCGATAACTAATCCTATAGTAACCGAAT
1 ATACAAGTATCGATAACTAATCCTATAGTAACCGAAT
2146989 ATACAAGTATCGATAACTAATCCTATAGTAACCG
1 ATACAAGTATCGATAACTAATCCTATAGTAACCG
2147023 GGTTTTCTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.42, C:0.20, G:0.11, T:0.27
Consensus pattern (37 bp):
ATACAAGTATCGATAACTAATCCTATAGTAACCGAAT
Found at i:2147018 original size:21 final size:21
Alignment explanation
Indices: 2146957--2147018 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
2146947 TCAACATACA
2146957 AGTATCGATAACTAATCCTAT
1 AGTATCGATAACTAATCCTAT
* *
2146978 AGTAACCG--AA-T-ATAC-A-
1 AGT-ATCGATAACTAATCCTAT
2146994 AGTATCGATAACTAATCCTAT
1 AGTATCGATAACTAATCCTAT
2147015 AGTA
1 AGTA
2147019 ACCGGGTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 14
0.62 0.08 0.29
Matches are distributed among these distances:
15 3 0.10
16 3 0.10
17 3 0.10
18 4 0.13
19 4 0.13
20 3 0.10
21 7 0.23
22 3 0.10
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.29
Consensus pattern (21 bp):
AGTATCGATAACTAATCCTAT
Found at i:2148002 original size:20 final size:21
Alignment explanation
Indices: 2147977--2148086 Score: 79
Period size: 20 Copynumber: 5.4 Consensus size: 21
2147967 ACTTTACCGA
2147977 TTTTGTCAAATTGAAACT-GG
1 TTTTGTCAAATTGAAACTCGG
*
2147997 TTTTGTCAAATT-AAAATCGG
1 TTTTGTCAAATTGAAACTCGG
* **
2148017 TTTTGTCAATTTCCAA-TCGG
1 TTTTGTCAAATTGAAACTCGG
* **
2148037 TTTAGTCAAATTCGTTACAT--G
1 TTTTGTCAAATT-GAAAC-TCGG
*
2148058 TTTTGTCAAATTGAAA-TCGA
1 TTTTGTCAAATTGAAACTCGG
*
2148078 ATTTGTCAA
1 TTTTGTCAA
2148087 TTTCAACCTG
Statistics
Matches: 70, Mismatches: 13, Indels: 14
0.72 0.13 0.14
Matches are distributed among these distances:
18 1 0.01
19 4 0.06
20 49 0.70
21 15 0.21
23 1 0.01
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.42
Consensus pattern (21 bp):
TTTTGTCAAATTGAAACTCGG
Found at i:2157670 original size:40 final size:40
Alignment explanation
Indices: 2157598--2157708 Score: 114
Period size: 40 Copynumber: 2.8 Consensus size: 40
2157588 CTAGACTTCT
* * * * * * *
2157598 TCAACACGAAGGAACAATATCGTCCACCGACCAGATCTTC
1 TCAACGCGAAGGAGCAATGTCATCCTCAGACCAGATCTCC
* * *
2157638 TCAACGTGAATGAGTAATGTCATCCTCAGACCAGATCTCC
1 TCAACGCGAAGGAGCAATGTCATCCTCAGACCAGATCTCC
* *
2157678 TCAACGCGAAGGAGCAGTGTCATCCTTAGAC
1 TCAACGCGAAGGAGCAATGTCATCCTCAGAC
2157709 AATTAGACTT
Statistics
Matches: 56, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
40 56 1.00
ACGTcount: A:0.32, C:0.29, G:0.19, T:0.21
Consensus pattern (40 bp):
TCAACGCGAAGGAGCAATGTCATCCTCAGACCAGATCTCC
Found at i:2158335 original size:178 final size:178
Alignment explanation
Indices: 2158059--2158460 Score: 413
Period size: 178 Copynumber: 2.2 Consensus size: 178
2158049 ACTAGGTCAT
* * *** * **
2158059 AAAAAATTGTCACAACAAATAATGAGATAT-AAATTTGTTGTGACAAATTTTGTTTGTGATTATA
1 AAAAAATTGTCACAACAAATAATGAAAT-TCAAATTT-TTGTGAAAAACAGTGTTCGCCATTATA
* * * *
2158123 TATTTTAATTATAGTGATAAAATGTATAGTCACAAATGATTAT-CTCGA-A-TTTTGTACAAAAA
64 TATTTTAATTATAATGACAAAATATATAGTCACAAA-GATT-TCCTCGATATTTTTGCACAAAAA
* * *
2158185 CAAAATCATATAGTGACATGA-TTTGTAACTATAAACT-ATAATTATTTTTACAA
127 -AAAATCATATAGTGACA-AATTTTGTAACTAT-AACTGATAATAATTATTACAA
2158238 AAAAAATTGTCACAACAAATAATGAAATTCAAATTTTTAGT-AAAAACAGTGTTCGCCATTATAT
1 AAAAAATTGTCACAACAAATAATGAAATTCAAATTTTT-GTGAAAAACAGTGTTCGCCATTATAT
* * * * *
2158302 GTTTTAATTATAATGACAAAATATATTGTCACAAAGATTTCCCTCTATATTTTTTGCGCCAAAAA
65 ATTTTAATTATAATGACAAAATATATAGTCACAAAGATTT-CCTCGATA-TTTTTGCACAAAAAA
** * * *
2158367 ATGTCATATATTGACAAATTTTGTAACTATAAGTGTTAATAATTATTACAA
128 AAATCATATAGTGACAAATTTTGTAACTATAACTGATAATAATTATTACAA
* *
2158418 AAAAAATTGTCACAAACAAATAATGATATTCACATTTTTGTGA
1 AAAAAATTGTCAC-AACAAATAATGAAATTCAAATTTTTGTGA
2158461 CAAATTATAT
Statistics
Matches: 185, Mismatches: 27, Indels: 20
0.80 0.12 0.09
Matches are distributed among these distances:
176 1 0.01
177 4 0.02
178 53 0.29
179 40 0.22
180 53 0.29
181 34 0.18
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.37
Consensus pattern (178 bp):
AAAAAATTGTCACAACAAATAATGAAATTCAAATTTTTGTGAAAAACAGTGTTCGCCATTATATA
TTTTAATTATAATGACAAAATATATAGTCACAAAGATTTCCTCGATATTTTTGCACAAAAAAAAA
TCATATAGTGACAAATTTTGTAACTATAACTGATAATAATTATTACAA
Found at i:2158422 original size:179 final size:179
Alignment explanation
Indices: 2157970--2158460 Score: 455
Period size: 179 Copynumber: 2.7 Consensus size: 179
2157960 GATTTTTTTA
*
2157970 TCACAAATG-TTTCCCTCCAATTTTTTGACGCCAAATTAAAAG-CATATAATGACAAATTTTGCA
1 TCACAAATGATTTCCCTCCAATTTTTTG-CGCCAAA--AAAAGTCATATAATGACAAATTTTGTA
* * * * * *
2158033 ACTAAAAGTTTTAGTAACTAGGT-CATAAAAAATTGTCACAACAAATAATGAGATAT-AAATTTG
63 ACTATAAG-TTTAATAATTA-TTACAAAAAAAATTGTCACAACAAATAATGAAAT-TCAAATTT-
* *** * ** * * *
2158096 TTGTGACAAATTTTGTTTGTGATTATATATTTTAATTATAGTGATAAAATGTATAG
124 TTGTGAAAAACAGTGTTCGCCATTATATATTTTAATTATAATGACAAAATATATAG
* ** * * * *
2158152 TCACAAATGATTAT--CTCGAA--TTTTGTACAAAAACAAAATCATATAGTGACATGA-TTTGTA
1 TCACAAATGATT-TCCCTCCAATTTTTTGCGCCAAAA-AAAGTCATATAATGACA-AATTTTGTA
* * * *
2158212 ACTATAAACTATAATTATTTTTACAAAAAAAATTGTCACAACAAATAATGAAATTCAAATTTTTA
63 ACTAT-AAGTTTAATAATTATTACAAAAAAAATTGTCACAACAAATAATGAAATTCAAATTTTT-
* *
2158277 GT-AAAAACAGTGTTCGCCATTATATGTTTTAATTATAATGACAAAATATATTG
126 GTGAAAAACAGTGTTCGCCATTATATATTTTAATTATAATGACAAAATATATAG
* * *
2158330 TCACAAA-GATTTCCCTCTATATTTTTTGCGCCAAAAAATGTCATATATTGACAAATTTTGTAAC
1 TCACAAATGATTTCCCTCCA-ATTTTTTGCGCCAAAAAAAGTCATATAATGACAAATTTTGTAAC
* *
2158394 TATAAGTGTTAATAATTATTACAAAAAAAATTGTCACAAACAAATAATGATATTCACATTTTTGT
65 TATAAGT-TTAATAATTATTACAAAAAAAATTGTCAC-AACAAATAATGAAATTCAAATTTTTGT
2158459 GA
128 GA
2158461 CAAATTATAT
Statistics
Matches: 247, Mismatches: 44, Indels: 37
0.75 0.13 0.11
Matches are distributed among these distances:
176 1 0.00
177 5 0.02
178 57 0.23
179 72 0.29
180 61 0.25
181 34 0.14
182 14 0.06
183 2 0.01
184 1 0.00
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.36
Consensus pattern (179 bp):
TCACAAATGATTTCCCTCCAATTTTTTGCGCCAAAAAAAGTCATATAATGACAAATTTTGTAACT
ATAAGTTTAATAATTATTACAAAAAAAATTGTCACAACAAATAATGAAATTCAAATTTTTGTGAA
AAACAGTGTTCGCCATTATATATTTTAATTATAATGACAAAATATATAG
Found at i:2158725 original size:60 final size:61
Alignment explanation
Indices: 2158659--2158782 Score: 142
Period size: 62 Copynumber: 2.0 Consensus size: 61
2158649 ATCATTATAA
* * * * *
2158659 AAAATATACTATCAGAATCA-TTTCTCTATATTTTTAGTGTCAAAAATGTTATATAGTAAC
1 AAAATATACTATCAGAAACATTTTCTCTATATTTTTAGCGCCAAAAAAGTCATATAGTAAC
* * * * *
2158719 AAAATATATTGTCATAAAGATTTTTCTCTATATTTTTTGCGCCAAAAAAGTCATATAGTAAC
1 AAAATATACTATCAGAAACA-TTTTCTCTATATTTTTAGCGCCAAAAAAGTCATATAGTAAC
2158781 AA
1 AA
2158783 TTTTGTAACT
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
60 15 0.29
62 37 0.71
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.39
Consensus pattern (61 bp):
AAAATATACTATCAGAAACATTTTCTCTATATTTTTAGCGCCAAAAAAGTCATATAGTAAC
Found at i:2162294 original size:36 final size:36
Alignment explanation
Indices: 2162247--2162318 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
2162237 TGTGAAGAAA
*
2162247 CTGTTTGTGGAGCGAACATGAAACTATGGGATTCCG
1 CTGTTTGTGGAGCGAACAGGAAACTATGGGATTCCG
2162283 CTGTTTGTGGAGCGAACAGGAAACTATGGGATTCCG
1 CTGTTTGTGGAGCGAACAGGAAACTATGGGATTCCG
2162319 GAGCTGGAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.25, C:0.17, G:0.32, T:0.26
Consensus pattern (36 bp):
CTGTTTGTGGAGCGAACAGGAAACTATGGGATTCCG
Found at i:2162675 original size:36 final size:35
Alignment explanation
Indices: 2162628--2162767 Score: 203
Period size: 36 Copynumber: 3.9 Consensus size: 35
2162618 TGAATAAGAA
*
2162628 GAACGAAAGGAAGCATC-AGCATTTTCGATTCAAAGT
1 GAACGAAAGGAAGCATCGA-CACTTTCGATTC-AAGT
* *
2162664 GAACGGAAGGAAGCATCGACACTTTCGATTCAAGAA
1 GAACGAAAGGAAGCATCGACACTTTCGATTCAAG-T
2162700 GAACGAAAGGAAGCATCGACACTTTCGATTCAAGT
1 GAACGAAAGGAAGCATCGACACTTTCGATTCAAGT
2162735 GAACGAAAGGAAGCATC-AGCACTTTCGATTCAA
1 GAACGAAAGGAAGCATCGA-CACTTTCGATTCAA
2162768 TTGTTCATTT
Statistics
Matches: 96, Mismatches: 5, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
34 1 0.01
35 34 0.35
36 60 0.62
37 1 0.01
ACGTcount: A:0.39, C:0.19, G:0.23, T:0.19
Consensus pattern (35 bp):
GAACGAAAGGAAGCATCGACACTTTCGATTCAAGT
Found at i:2162766 original size:71 final size:72
Alignment explanation
Indices: 2162623--2162767 Score: 233
Period size: 71 Copynumber: 2.0 Consensus size: 72
2162613 GAAGGTGAAT
* *
2162623 AAGAAGAACGAAAGGAAGCATCAGCATTTTCGATTCAAAGTGAACGGAAGGAAGCATCGACACTT
1 AAGAAGAACGAAAGGAAGCATCAGCACTTTCGATTCAAAGTGAACGAAAGGAAGCATCGACACTT
2162688 TCGATTC
66 TCGATTC
2162695 AAGAAGAACGAAAGGAAGCATC-GACACTTTCGATTC-AAGTGAACGAAAGGAAGCATC-AGCAC
1 AAGAAGAACGAAAGGAAGCATCAG-CACTTTCGATTCAAAGTGAACGAAAGGAAGCATCGA-CAC
2162757 TTTCGATTC
64 TTTCGATTC
2162766 AA
1 AA
2162768 TTGTTCATTT
Statistics
Matches: 69, Mismatches: 2, Indels: 5
0.91 0.03 0.07
Matches are distributed among these distances:
70 1 0.01
71 35 0.51
72 33 0.48
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.19
Consensus pattern (72 bp):
AAGAAGAACGAAAGGAAGCATCAGCACTTTCGATTCAAAGTGAACGAAAGGAAGCATCGACACTT
TCGATTC
Found at i:2165517 original size:23 final size:23
Alignment explanation
Indices: 2165473--2165517 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2165463 TAATAAAATG
* *
2165473 ATTTAGTCACAATAATACGTTAA
1 ATTTAGTCACAATAAAAAGTTAA
2165496 ATTTAGTCA-AAGTAAAAAGTTA
1 ATTTAGTCACAA-TAAAAAGTTA
2165518 TGTCAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.47, C:0.09, G:0.11, T:0.33
Consensus pattern (23 bp):
ATTTAGTCACAATAAAAAGTTAA
Found at i:2165555 original size:197 final size:198
Alignment explanation
Indices: 2165295--2165680 Score: 562
Period size: 197 Copynumber: 2.0 Consensus size: 198
2165285 AATAACATAG
** * *
2165295 TAAATTTAGTCAAAAATAAAATTTTATGCCAAATTTATTTTGTCACAAAATTTTGTTAAAATAAA
1 TAAATTTAGTCAAAAATAAAAAGTTATGCCAAATTTATTTCGTCACAAAATTTTGTCAAAATAAA
*
2165360 AATTATGACAAATTTATTTAATCTAAAA-AATAATTTATAACAAATATTAATTTCACATCATAAA
66 AATTATGACAAATTTATTTAATC-AAAATAACAATTTATAACAAATATTAATTTCACATCATAAA
* * * * *
2165424 AAATTGTAACAAGTAATATTCTTTCACAATAACAAATTGTAATAAAATGATTTAGTCACAATAAT
130 AAACTATAACAAATAATAATCTTTCACAATAACAAATTGTAACAAAATGATTTAGTCACAATAAT
2165489 ACGT
195 ACGT
* * *
2165493 TAAATTTAGTC-AAAGTAAAAAGTTATGTCAAATTTATTTCGTC-CTAATATTTTGTCAAAATAA
1 TAAATTTAGTCAAAAATAAAAAGTTATGCCAAATTTATTTCGTCAC-AAAATTTTGTCAAAATAA
* * *
2165556 AAATTTTGACAAATTTATTTAATCAAAATAACAATTTATAACAAATATTAATTTCTCATTATAAA
65 AAATTATGACAAATTTATTTAATCAAAATAACAATTTATAACAAATATTAATTTCACATCATAAA
* * *
2165621 AAACTATGACAAATAATAATCTTTCACAATAATAAATTGTAACAAAATTATTTAGTCACA
130 AAACTATAACAAATAATAATCTTTCACAATAACAAATTGTAACAAAATGATTTAGTCACA
2165681 GTAAAAGTTA
Statistics
Matches: 167, Mismatches: 19, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
196 5 0.03
197 151 0.90
198 11 0.07
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.37
Consensus pattern (198 bp):
TAAATTTAGTCAAAAATAAAAAGTTATGCCAAATTTATTTCGTCACAAAATTTTGTCAAAATAAA
AATTATGACAAATTTATTTAATCAAAATAACAATTTATAACAAATATTAATTTCACATCATAAAA
AACTATAACAAATAATAATCTTTCACAATAACAAATTGTAACAAAATGATTTAGTCACAATAATA
CGT
Found at i:2165807 original size:21 final size:19
Alignment explanation
Indices: 2165782--2165824 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
2165772 TTAATATTAT
*
2165782 AATTTAACTTAATTGTGATGA
1 AATTT-ACTT-ATTGTGATAA
*
2165803 AATTTACTTTTTGTGATAA
1 AATTTACTTATTGTGATAA
2165822 AAT
1 AAT
2165825 AATTATTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 11 0.55
20 4 0.20
21 5 0.25
ACGTcount: A:0.37, C:0.05, G:0.12, T:0.47
Consensus pattern (19 bp):
AATTTACTTATTGTGATAA
Found at i:2167389 original size:15 final size:15
Alignment explanation
Indices: 2167365--2167395 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2167355 GTGGTCACTG
2167365 ATCTACTTTGATTTT
1 ATCTACTTTGATTTT
*
2167380 ATCTATTTTGATTTT
1 ATCTACTTTGATTTT
2167395 A
1 A
2167396 GCCCCTTGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.10, G:0.06, T:0.61
Consensus pattern (15 bp):
ATCTACTTTGATTTT
Found at i:2167500 original size:29 final size:29
Alignment explanation
Indices: 2167441--2167505 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
2167431 TTCTGCTATG
* * **
2167441 TTATTTAATTGCATATTAACTGCTAACTT
1 TTATTTTATTGCACATTAACCACTAACTT
2167470 TTATTTTATTGCACATTAACCACTGAA-TT
1 TTATTTTATTGCACATTAACCACT-AACTT
2167499 TTATTTT
1 TTATTTT
2167506 CTTTCATTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 29 0.94
30 2 0.06
ACGTcount: A:0.29, C:0.14, G:0.06, T:0.51
Consensus pattern (29 bp):
TTATTTTATTGCACATTAACCACTAACTT
Found at i:2169334 original size:65 final size:65
Alignment explanation
Indices: 2169254--2169381 Score: 256
Period size: 65 Copynumber: 2.0 Consensus size: 65
2169244 GATTTTTTGG
2169254 TAAAACACAAACCATTTTTTCGTCTTTTAATGATTTTTCTAAACTCATTAAAATGATATTTTAAA
1 TAAAACACAAACCATTTTTTCGTCTTTTAATGATTTTTCTAAACTCATTAAAATGATATTTTAAA
2169319 TAAAACACAAACCATTTTTTCGTCTTTTAATGATTTTTCTAAACTCATTAAAATGATATTTTA
1 TAAAACACAAACCATTTTTTCGTCTTTTAATGATTTTTCTAAACTCATTAAAATGATATTTTA
2169382 GGTATTCAAC
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 63 1.00
ACGTcount: A:0.38, C:0.14, G:0.05, T:0.44
Consensus pattern (65 bp):
TAAAACACAAACCATTTTTTCGTCTTTTAATGATTTTTCTAAACTCATTAAAATGATATTTTAAA
Found at i:2175534 original size:27 final size:27
Alignment explanation
Indices: 2175499--2175554 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
2175489 CCGCCATCAC
*
2175499 CACTTTGAACTTGAAACTCCATAGCAT
1 CACTTTGAACTTGAAACTCCACAGCAT
*
2175526 CACTTTGAACTTGAAAGTCCACAGCAT
1 CACTTTGAACTTGAAACTCCACAGCAT
2175553 CA
1 CA
2175555 AGATCTTCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.34, C:0.27, G:0.12, T:0.27
Consensus pattern (27 bp):
CACTTTGAACTTGAAACTCCACAGCAT
Found at i:2176151 original size:24 final size:23
Alignment explanation
Indices: 2176119--2176174 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 23
2176109 TTAAATAATT
2176119 TTATATTAAAATTTTACATTATAG
1 TTAT-TTAAAATTTTACATTATAG
** *
2176143 TTAATTTAATTTTTTTCATTATAG
1 TT-ATTTAAAATTTTACATTATAG
2176167 TTATTTAA
1 TTATTTAA
2176175 CAATGTTAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 6 0.21
24 20 0.71
25 2 0.07
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.57
Consensus pattern (23 bp):
TTATTTAAAATTTTACATTATAG
Found at i:2176156 original size:23 final size:23
Alignment explanation
Indices: 2176130--2176174 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
2176120 TATATTAAAA
2176130 TTTTACATTATAGTTAATTTAATT
1 TTTTACATTATAGTT-ATTTAATT
*
2176154 TTTTTCATTATAGTTATTTAA
1 TTTTACATTATAGTTATTTAA
2176175 CAATGTTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.60
Consensus pattern (23 bp):
TTTTACATTATAGTTATTTAATT
Found at i:2176541 original size:19 final size:19
Alignment explanation
Indices: 2176485--2176542 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 19
2176475 TGGTTCACGA
* * *
2176485 AATATAAGATTATTTTTAG
1 AATATAAAATTATTATGAG
2176504 AA-ATAAAATTA--ATGA-
1 AATATAAAATTATTATGAG
*
2176519 AATATAACATTATTATGAG
1 AATATAAAATTATTATGAG
2176538 AATAT
1 AATAT
2176543 TGTATTACAT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
15 2 0.06
16 10 0.32
18 12 0.39
19 7 0.23
ACGTcount: A:0.52, C:0.02, G:0.09, T:0.38
Consensus pattern (19 bp):
AATATAAAATTATTATGAG
Found at i:2179853 original size:21 final size:21
Alignment explanation
Indices: 2179829--2179873 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
2179819 ATTTAATTAA
*
2179829 ACTCCAAATTTTATAAATTCG
1 ACTCAAAATTTTATAAATTCG
*
2179850 ACTCAAAATTTTATAAATTTG
1 ACTCAAAATTTTATAAATTCG
2179871 ACT
1 ACT
2179874 AGGCTCGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.16, G:0.04, T:0.40
Consensus pattern (21 bp):
ACTCAAAATTTTATAAATTCG
Found at i:2180030 original size:27 final size:27
Alignment explanation
Indices: 2180012--2180074 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 27
2180002 ATTATGTGAA
2180012 AATATATGAATAATCATATATGTATAT
1 AATATATGAATAATCATATATGTATAT
* *
2180039 CATATATGAATAATTATATATGTATAT
1 AATATATGAATAATCATATATGTATAT
*
2180066 CATATATGA
1 AATATATGA
2180075 TTATTAAAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (27 bp):
AATATATGAATAATCATATATGTATAT
Found at i:2180042 original size:13 final size:14
Alignment explanation
Indices: 2180013--2180074 Score: 83
Period size: 13 Copynumber: 4.6 Consensus size: 14
2180003 TTATGTGAAA
2180013 ATATATGAATAATC
1 ATATATGAATAATC
*
2180027 ATATATGTAT-ATC
1 ATATATGAATAATC
*
2180040 ATATATGAATAATT
1 ATATATGAATAATC
*
2180054 ATATATGTAT-ATC
1 ATATATGAATAATC
2180067 ATATATGA
1 ATATATGA
2180075 TTATTAAAAG
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
13 21 0.51
14 20 0.49
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (14 bp):
ATATATGAATAATC
Found at i:2181238 original size:19 final size:20
Alignment explanation
Indices: 2181200--2181239 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2181190 TTTTATAATA
*
2181200 TTAAATATTTTTATTCATAT
1 TTAAATATTTTAATTCATAT
*
2181220 TTAATTATTTTAATT-ATAT
1 TTAAATATTTTAATTCATAT
2181239 T
1 T
2181240 ATAACATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (20 bp):
TTAAATATTTTAATTCATAT
Found at i:2181331 original size:19 final size:17
Alignment explanation
Indices: 2181300--2181334 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 17
2181290 AAATTTAAAA
2181300 ATATATTTTATAATTTT
1 ATATATTTTATAATTTT
2181317 ATATATTATTGATAATTT
1 ATATATT-TT-ATAATTT
2181335 GAATATGTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 2 0.12
19 7 0.44
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (17 bp):
ATATATTTTATAATTTT
Found at i:2189767 original size:277 final size:273
Alignment explanation
Indices: 2189169--2189720 Score: 951
Period size: 277 Copynumber: 2.0 Consensus size: 273
2189159 TTTTGGTCAT
* * *
2189169 TAACCAAAATTTGGGGTATTAAAACTCTCCTCCCTTAAGAAAAATTTTTCGTCTAATTTTAATAC
1 TAACCAAAATCT--GGTATCAAAACTCTCCTCCATTAAGAAAAATTTTTCGTCTAATTTTAATAC
2189234 GTACATAATGGGAAGAGGTGTGTATATTGTCTTTTTATGTGATATTCTTTTCCTTGGTCGCTTAC
64 GTACATAATGGGAAGAGGTGTGTATATTGTCTTTTTATGTGATATTCTTTTCCTTGGTCGCTTAC
2189299 TCGATTTTATGATTTCTCCAAAGAACTTGACCAAAGGAATCGTCTTTTCCTGAAGTTCTTTGACT
129 TCGATTTTATGATTTCTCCAAAGAACTTGACCAAAGGAATCGTCTTTTCCTGAAGTTCTTTGACT
2189364 TATCAAGCCAAAATCTCAATTGTTTCCTCTTCATAGGTCAATCTGGTCGAATCTCTATATATTCT
194 TATCAAGCCAAAATCTCAATTGTTTCCTCTTCATAGGTCAATCTGGTCGAATCTCTATATATTCT
**
2189429 GATGTGATTTTGGTC
259 GATGTGATAATGGTC
* * *
2189444 ATTAACCAAAATTTGGGGTATTAAAACTCTCCTCCCTTAAGAAAAATTTTTCGTCTAATTTTAAT
1 --TAACCAAAATCT--GGTATCAAAACTCTCCTCCATTAAGAAAAATTTTTCGTCTAATTTTAAT
2189509 ACGTACATAATGGGAAGAGGTGTGTATATTGTCTTTTTATGTGATATTCTTTTTCCTTGGTCGCT
62 ACGTACATAATGGGAAGAGGTGTGTATATTGTCTTTTTATGTGATATTC-TTTTCCTTGGTCGCT
2189574 TACTCGATTTTATGATTTCTCCAAAGAACTTTGACCAAAGGAATCGTCTTTTCCTGAAGTTCTTT
126 TACTCGATTTTATGATTTCTCCAAAGAAC-TTGACCAAAGGAATCGTCTTTTCCTGAAGTTCTTT
2189639 GACTTATCAAGCCAAAATCTCAATTGTTTCCTCTTCATAGGTCAAATCTGGTCGAATCTCTATAT
190 GACTTATCAAGCCAAAATCTCAATTGTTTCCTCTTCATAGGTC-AATCTGGTCGAATCTCTATAT
2189704 ATTCTGATGTGATAATG
254 ATTCTGATGTGATAATG
2189721 TGCGACGGAT
Statistics
Matches: 270, Mismatches: 2, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
277 112 0.41
278 44 0.16
279 78 0.29
280 36 0.13
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (273 bp):
TAACCAAAATCTGGTATCAAAACTCTCCTCCATTAAGAAAAATTTTTCGTCTAATTTTAATACGT
ACATAATGGGAAGAGGTGTGTATATTGTCTTTTTATGTGATATTCTTTTCCTTGGTCGCTTACTC
GATTTTATGATTTCTCCAAAGAACTTGACCAAAGGAATCGTCTTTTCCTGAAGTTCTTTGACTTA
TCAAGCCAAAATCTCAATTGTTTCCTCTTCATAGGTCAATCTGGTCGAATCTCTATATATTCTGA
TGTGATAATGGTC
Found at i:2194603 original size:23 final size:23
Alignment explanation
Indices: 2194577--2194647 Score: 88
Period size: 23 Copynumber: 3.1 Consensus size: 23
2194567 ATTACCACAG
* *
2194577 CACGTATAAATGCACCGAAGTGC
1 CACGTAGAATTGCACCGAAGTGC
* * *
2194600 CACGTAGAATTACACTGAAGTGT
1 CACGTAGAATTGCACCGAAGTGC
*
2194623 CACGTAGAATTGCACCGTAGTGC
1 CACGTAGAATTGCACCGAAGTGC
2194646 CA
1 CA
2194648 TATAAGATTA
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.32, C:0.24, G:0.23, T:0.21
Consensus pattern (23 bp):
CACGTAGAATTGCACCGAAGTGC
Found at i:2195414 original size:63 final size:63
Alignment explanation
Indices: 2195337--2195475 Score: 188
Period size: 63 Copynumber: 2.2 Consensus size: 63
2195327 CTTAAGGAGG
* * * * *
2195337 TGCATCGATGCACTCCTTAAGTATCGATGTACTGAGGGCATTCGATGTTCATTTAATTGAAAA
1 TGCATCGATGCACTCCTTAAGCATCGATGCACTGACGACATTCGATGTTCAATTAATTGAAAA
* * * **
2195400 TGCATTGATGCACTCCTTATGCATCGATGCACTGACGACATTCGATGTTCAATTACTTGAGGA
1 TGCATCGATGCACTCCTTAAGCATCGATGCACTGACGACATTCGATGTTCAATTAATTGAAAA
2195463 TGCATCGATGCAC
1 TGCATCGATGCAC
2195476 ATTCAATGTG
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
63 65 1.00
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.32
Consensus pattern (63 bp):
TGCATCGATGCACTCCTTAAGCATCGATGCACTGACGACATTCGATGTTCAATTAATTGAAAA
Found at i:2201072 original size:22 final size:23
Alignment explanation
Indices: 2201039--2201098 Score: 95
Period size: 22 Copynumber: 2.7 Consensus size: 23
2201029 CTCGTATAAA
2201039 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
2201062 TGCA-CGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
2201084 TGTACCGTAGTGCCA
1 TGCACCGAAGTGCCA
2201099 TATAAGATTG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
22 21 0.62
23 13 0.38
ACGTcount: A:0.28, C:0.25, G:0.27, T:0.20
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:2204359 original size:61 final size:62
Alignment explanation
Indices: 2204263--2204385 Score: 230
Period size: 61 Copynumber: 2.0 Consensus size: 62
2204253 ACTTCAAGAC
*
2204263 CTCTAGAATCAAACCCCAACTTAATTTCATCAAATACATATTTCCCCTAAAGCTAGGGTTTG
1 CTCTAGAATCAAACCCAAACTTAATTTCATCAAATACATATTTCCCCTAAAGCTAGGGTTTG
2204325 CTCTAG-ATCAAACCCAAACTTAATTTCATCAAATACATATTTCCCCTAAAGCTAGGGTTTG
1 CTCTAGAATCAAACCCAAACTTAATTTCATCAAATACATATTTCCCCTAAAGCTAGGGTTTG
2204386 GATGAAACAA
Statistics
Matches: 60, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
61 54 0.90
62 6 0.10
ACGTcount: A:0.34, C:0.25, G:0.10, T:0.31
Consensus pattern (62 bp):
CTCTAGAATCAAACCCAAACTTAATTTCATCAAATACATATTTCCCCTAAAGCTAGGGTTTG
Found at i:2205663 original size:31 final size:26
Alignment explanation
Indices: 2205625--2205693 Score: 86
Period size: 25 Copynumber: 2.5 Consensus size: 26
2205615 TTGGGGCTCC
2205625 AAATCAAGCAAAGAAAATATGACATCCTCAT
1 AAATCAAGCAAAGAAAA-AT---AT-CTCAT
2205656 AAATCAAGC-AAGAAAAATATCTCAT
1 AAATCAAGCAAAGAAAAATATCTCAT
2205681 AAATCAAGCAAAG
1 AAATCAAGCAAAG
2205694 TACATCAGGA
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
25 14 0.38
26 5 0.14
29 2 0.05
30 7 0.19
31 9 0.24
ACGTcount: A:0.55, C:0.17, G:0.10, T:0.17
Consensus pattern (26 bp):
AAATCAAGCAAAGAAAAATATCTCAT
Found at i:2206930 original size:20 final size:20
Alignment explanation
Indices: 2206879--2206936 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 20
2206869 TTATTCATTT
2206879 AGTACTGATATTGTTCTTAGTC
1 AGTACTGATATTGTTCTTA--C
2206901 AGTA-TCGATATTGTTCTT-C
1 AGTACT-GATATTGTTCTTAC
2206920 AAGTACTGATATTGTTC
1 -AGTACTGATATTGTTC
2206937 ACGCAACCTC
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
19 1 0.03
20 14 0.42
21 2 0.06
22 16 0.48
ACGTcount: A:0.24, C:0.14, G:0.17, T:0.45
Consensus pattern (20 bp):
AGTACTGATATTGTTCTTAC
Found at i:2207747 original size:17 final size:17
Alignment explanation
Indices: 2207725--2207758 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2207715 AAGCAGAATG
*
2207725 CTATTTTGGTACCGATA
1 CTATTTTAGTACCGATA
*
2207742 CTATTTTAGTACGGATA
1 CTATTTTAGTACCGATA
2207759 TTACTTTTCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.41
Consensus pattern (17 bp):
CTATTTTAGTACCGATA
Found at i:2211029 original size:99 final size:100
Alignment explanation
Indices: 2210848--2211041 Score: 356
Period size: 100 Copynumber: 1.9 Consensus size: 100
2210838 AGACTTCACA
2210848 TATGCAGCAGCGCTGCAGCATGGGGACAAGACATAGATATGCCGGACATAATGTAAATGCCGAAT
1 TATGCAGCAGCGCTGCAGCATGGGGACAAGACATAGATATGCCGGACATAATGTAAATGCCGAAT
2210913 AGCGTCGGTCAGTTGGATCG-CGGTTATCGAGGTC
66 AGCGTCGGTCAGTTGGATCGCCGGTTATCGAGGTC
*
2210947 TATGCTGCAGCAGCTGCAGCATGGGGACAAGACATAGATATGCCGGACATAATGT-AATGCCGAA
1 TATGCAGCAGC-GCTGCAGCATGGGGACAAGACATAGATATGCCGGACATAATGTAAATGCCGAA
2211011 TAGCGTCGGTCAGTTGGATCGCCGGTTATCG
65 TAGCGTCGGTCAGTTGGATCGCCGGTTATCG
2211042 GTCAATTCTG
Statistics
Matches: 92, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
99 40 0.43
100 52 0.57
ACGTcount: A:0.27, C:0.21, G:0.31, T:0.22
Consensus pattern (100 bp):
TATGCAGCAGCGCTGCAGCATGGGGACAAGACATAGATATGCCGGACATAATGTAAATGCCGAAT
AGCGTCGGTCAGTTGGATCGCCGGTTATCGAGGTC
Found at i:2211177 original size:125 final size:124
Alignment explanation
Indices: 2210955--2211209 Score: 460
Period size: 125 Copynumber: 2.0 Consensus size: 124
2210945 TCTATGCTGC
2210955 AGCAGCTGCAGCATGGGGACAAGACATAGATATGCCGGACATAATGTAATGCCGAATAGCGTCGG
1 AGCAGCTGCAGCATGGGGACAAGACATAGATATGCCGGACATAATGTAA-GCCGAATAGCGTCGG
2211020 TCAGTTGGATCGCCGGTTATCGGTCAATTCTGTGTAGGCACCTAGTATGTTTAGCCCTGG
65 TCAGTTGGATCGCCGGTTATCGGTCAATTCTGTGTAGGCACCTAGTATGTTTAGCCCTGG
2211080 AGCAGCTGCAGCATGGGGACAAGACATAGATATGCCGGACATAATGTTAA-CCGAATAGCGTCGG
1 AGCAGCTGCAGCATGGGGACAAGACATAGATATGCCGGACATAATG-TAAGCCGAATAGCGTCGG
2211144 TCAGTTGGATCGCCGGTTATCGAGGTC-ATTCTGTGTAGGCACCTAGTATGTTTAGCCCTGG
65 TCAGTTGGATCGCCGGTTATC--GGTCAATTCTGTGTAGGCACCTAGTATGTTTAGCCCTGG
2211205 AGCAG
1 AGCAG
2211210 TAACATCGGC
Statistics
Matches: 127, Mismatches: 0, Indels: 6
0.95 0.00 0.05
Matches are distributed among these distances:
124 35 0.28
125 85 0.67
126 7 0.06
ACGTcount: A:0.25, C:0.21, G:0.30, T:0.24
Consensus pattern (124 bp):
AGCAGCTGCAGCATGGGGACAAGACATAGATATGCCGGACATAATGTAAGCCGAATAGCGTCGGT
CAGTTGGATCGCCGGTTATCGGTCAATTCTGTGTAGGCACCTAGTATGTTTAGCCCTGG
Found at i:2211508 original size:307 final size:304
Alignment explanation
Indices: 2210954--2211565 Score: 1124
Period size: 307 Copynumber: 2.0 Consensus size: 304
2210944 GTCTATGCTG
2210954 CAGCAGCTGCAGCATGGGGACAAGACATAGATATGCCGGACATAATGTAATGCCGAATAGCGTCG
1 CAGCAGCTGCAGCATGGGGACAAGACATAGATATGCCGGACATAATGTAATGCCGAATAGCGTCG
2211019 GTCAGTTGGATCGCCGGTTATCGGTCAATTCTGTGTAGGCACCTAGTATGTTTAGCCCTGGAGCA
66 GTCAGTTGGATCGCCGGTTATCGGTCAATTCTGTGTAGGCACCTAGTATGTTTAGCCCTGGAGCA
2211084 GCTGCAGCATGGGGACAAGACATAGATATGCCGGACATAATGTTAACCGAATAGCGTCGGTCAGT
131 GCTGCAGCATGGGGACAAGACATAGATATGCCGGACATAATGTTAACCGAATAGCGTCGGTCAGT
2211149 TGGATCGCCGGTTATCGAGGTCATTCTGTGTAGGCACCTAGTATGTTTAGCCCTGGAGCAGTAAC
196 TGGATCGCCGGTTATCGAGGTCATTC-GTGTAGGCACCTAGTATGTTTAGCCCTGGAGCAGTAAC
2211214 ATC-GGCTGGCCATGGGAACTTGGGAAGTCTTGCGTTAGGAACGA
260 ATCGGGCTGGCCATGGGAACTTGGGAAGTCTTGCGTTAGGAACGA
2211258 CAGCAGCTGCAGCATGGGGACAAGACATAGATATG-CGGACATAATGTTAAATGCCGAATAGCGT
1 CAGCAGCTGCAGCATGGGGACAAGACATAGATATGCCGGACATAATG-T-AATGCCGAATAGCGT
2211322 CGGTCAGTTGGATCGCCGGTTATCGAGGTCAATTCTGTGTAGGCACCTAGTATGTTTAGCCCTGG
64 CGGTCAGTTGGATCGCCGGTTATC--GGTCAATTCTGTGTAGGCACCTAGTATGTTTAGCCCTGG
2211387 AGCAGCTGCAGCATGGGGACAAGACATAGATATGCCGGACATAATGTTAAATGCCGAATAGCGTC
127 AGCAGCTGCAGCATGGGGACAAGACATAGATATGCCGGACATAATGTT-AA--CCGAATAGCGTC
2211452 GGTCAGTTGGATCGCCGGTTATCGAGGTCATTC-TGTAGGCACCTAGTATG-TTAGCCCTGGAGC
189 GGTCAGTTGGATCGCCGGTTATCGAGGTCATTCGTGTAGGCACCTAGTATGTTTAGCCCTGGAGC
2211515 AGTAACATCGGGCTGGCCATGGGAACTTGGGAAGTCTTGCGTTAGGAACGA
254 AGTAACATCGGGCTGGCCATGGGAACTTGGGAAGTCTTGCGTTAGGAACGA
2211566 AAATAAAGGG
Statistics
Matches: 300, Mismatches: 0, Indels: 12
0.96 0.00 0.04
Matches are distributed among these distances:
303 11 0.04
304 36 0.12
305 39 0.13
307 109 0.36
308 60 0.20
310 45 0.15
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.24
Consensus pattern (304 bp):
CAGCAGCTGCAGCATGGGGACAAGACATAGATATGCCGGACATAATGTAATGCCGAATAGCGTCG
GTCAGTTGGATCGCCGGTTATCGGTCAATTCTGTGTAGGCACCTAGTATGTTTAGCCCTGGAGCA
GCTGCAGCATGGGGACAAGACATAGATATGCCGGACATAATGTTAACCGAATAGCGTCGGTCAGT
TGGATCGCCGGTTATCGAGGTCATTCGTGTAGGCACCTAGTATGTTTAGCCCTGGAGCAGTAACA
TCGGGCTGGCCATGGGAACTTGGGAAGTCTTGCGTTAGGAACGA
Found at i:2214460 original size:21 final size:20
Alignment explanation
Indices: 2214434--2214531 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
2214424 ATCAGTTTCC
2214434 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTG
* **
2214455 AAAATCGCAATGCGATAGT-
1 AAAATCGCAACGCGATTTTG
***
2214474 ACAAATTCGCGTTGCGATTTTGG
1 A-AAA-TCGCAACGCGATTTT-G
* *
2214497 AAAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTTTG
2214517 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
2214532 ACACATAAAT
Statistics
Matches: 61, Mismatches: 12, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
19 1 0.02
20 20 0.33
21 36 0.59
22 3 0.05
23 1 0.02
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.21
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTG
Found at i:2214560 original size:20 final size:20
Alignment explanation
Indices: 2214498--2214720 Score: 213
Period size: 20 Copynumber: 11.2 Consensus size: 20
2214488 CGATTTTGGA
* ** *
2214498 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
2214518 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
2214538 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
2214558 AAATCGC-ACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
2214577 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
2214597 -AATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
2214616 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
2214636 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
2214656 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
2214676 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
2214696 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
2214716 AAATC
1 AAATC
2214721 ACACACTGAA
Statistics
Matches: 168, Mismatches: 27, Indels: 16
0.80 0.13 0.08
Matches are distributed among these distances:
19 36 0.21
20 130 0.77
21 2 0.01
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:2215423 original size:24 final size:24
Alignment explanation
Indices: 2215396--2215442 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2215386 CGAATTGGTC
2215396 TTGGTCAATATC-CGGACTTTGATA
1 TTGGTCAATA-CACGGACTTTGATA
*
2215420 TTGGTCAATACACGGATTTTGAT
1 TTGGTCAATACACGGACTTTGAT
2215443 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATACACGGACTTTGATA
Found at i:2217905 original size:33 final size:33
Alignment explanation
Indices: 2217854--2218047 Score: 176
Period size: 33 Copynumber: 5.9 Consensus size: 33
2217844 CGGAAATTAC
* *
2217854 AATCGCAACGA-GAGAATCGCAATGCGAAATAAA
1 AATCGCAAC-ATGAAAATCGCAATGCGAAATGAA
*
2217887 AATCCCAACATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACATGAAAATCGCAATGC-GAAATGAA
2217921 AATCGCAAC--GAGAAATCGCAATGCGAAATG-A
1 AATCGCAACATGA-AAATCGCAATGCGAAATGAA
*
2217952 AATCGCAATGCGAAATG-AAATCGCAA--CGAGA-GAA
1 AATCGCAA--C---ATGAAAATCGCAATGCGAAATGAA
2217986 AAT-GCGAA-ATGAAAATCGCAATGCGAAATGAA
1 AATCGC-AACATGAAAATCGCAATGCGAAATGAA
*
2218018 AATCGCAACGA-GAGAATCGCAATGCGAAAT
1 AATCGCAAC-ATGAAAATCGCAATGCGAAAT
2218048 TATAAATGCA
Statistics
Matches: 135, Mismatches: 7, Indels: 38
0.75 0.04 0.21
Matches are distributed among these distances:
28 3 0.02
29 9 0.07
31 13 0.10
32 17 0.13
33 57 0.42
34 26 0.19
36 9 0.07
38 1 0.01
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (33 bp):
AATCGCAACATGAAAATCGCAATGCGAAATGAA
Found at i:2217937 original size:47 final size:46
Alignment explanation
Indices: 2217886--2218035 Score: 162
Period size: 47 Copynumber: 3.1 Consensus size: 46
2217876 TGCGAAATAA
2217886 AAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAG
1 AAATCCCAACATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAG
*
2217933 AAATCGCAATGCGAAATG-AAATCGCAATGCGAAATG-AAATCGCAACGAGAG
1 AAATCCCAA--C---ATGAAAATCGCAATGCGAAATGAAAATCGCAAC--GAG
* *
2217984 AAAATGCGAA-ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAG
1 -AAATCCCAACATGAAAATCGCAATGCGAAATGAAAATCGCAACGAG
2218030 AGAATC
1 A-AATC
2218036 GCAATGCGAA
Statistics
Matches: 87, Mismatches: 5, Indels: 23
0.76 0.04 0.20
Matches are distributed among these distances:
45 1 0.01
46 9 0.10
47 26 0.30
48 10 0.11
49 11 0.13
50 6 0.07
51 15 0.17
52 9 0.10
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.13
Consensus pattern (46 bp):
AAATCCCAACATGAAAATCGCAATGCGAAATGAAAATCGCAACGAG
Found at i:2218010 original size:19 final size:19
Alignment explanation
Indices: 2217986--2218025 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
2217976 AACGAGAGAA
2217986 AATGCGAAATGAAAATCGC
1 AATGCGAAATGAAAATCGC
2218005 AATGCGAAATGAAAATCGC
1 AATGCGAAATGAAAATCGC
2218024 AA
1 AA
2218026 CGAGAGAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.50, C:0.15, G:0.20, T:0.15
Consensus pattern (19 bp):
AATGCGAAATGAAAATCGC
Found at i:2218111 original size:49 final size:51
Alignment explanation
Indices: 2218058--2218162 Score: 164
Period size: 49 Copynumber: 2.1 Consensus size: 51
2218048 TATAAATGCA
2218058 TGCGATTCTCTCGTT-CGA-TTTCATTCCGCATTGCGA-TTTCATTTCGCAT
1 TGCGATT-TCTCGTTGCGATTTTCATTCCGCATTGCGATTTTCATTTCGCAT
*
2218107 TGCGA-TTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
1 TGCGATTTCTCGTTGCGATTTTCATTCCGCATTGCGATTTTCATTTCGCAT
2218157 TGCGAT
1 TGCGAT
2218163 AGTCATTTTT
Statistics
Matches: 51, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
47 7 0.14
48 4 0.08
49 22 0.43
50 18 0.35
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (51 bp):
TGCGATTTCTCGTTGCGATTTTCATTCCGCATTGCGATTTTCATTTCGCAT
Found at i:2218170 original size:19 final size:18
Alignment explanation
Indices: 2218073--2218162 Score: 111
Period size: 19 Copynumber: 5.2 Consensus size: 18
2218063 TTCTCTCGTT
*
2218073 CGATTTCATTCCGCATTG
1 CGATTTCATTTCGCATTG
2218091 CGATTTCATTTCGCATTG
1 CGATTTCATTTCGCATTG
2218109 CGA-TTC---TCG--TTG
1 CGATTTCATTTCGCATTG
2218121 CGATTTTCATTTCGCATTG
1 CGA-TTTCATTTCGCATTG
2218140 CGATTTTCATTTCGCATTG
1 CGA-TTTCATTTCGCATTG
2218159 CGAT
1 CGAT
2218163 AGTCATTTTT
Statistics
Matches: 64, Mismatches: 1, Indels: 14
0.81 0.01 0.18
Matches are distributed among these distances:
12 6 0.09
14 6 0.09
17 6 0.09
18 21 0.33
19 25 0.39
ACGTcount: A:0.16, C:0.23, G:0.18, T:0.43
Consensus pattern (18 bp):
CGATTTCATTTCGCATTG
Found at i:2218380 original size:12 final size:12
Alignment explanation
Indices: 2218363--2218399 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
2218353 ATCAACTTTT
2218363 ACAATCAATTAA
1 ACAATCAATTAA
*
2218375 ACAATCAA-AAA
1 ACAATCAATTAA
2218386 ACAATCAATTAA
1 ACAATCAATTAA
2218398 AC
1 AC
2218400 TATTGAATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 10 0.45
12 12 0.55
ACGTcount: A:0.62, C:0.19, G:0.00, T:0.19
Consensus pattern (12 bp):
ACAATCAATTAA
Found at i:2220268 original size:14 final size:14
Alignment explanation
Indices: 2220249--2220304 Score: 67
Period size: 14 Copynumber: 3.7 Consensus size: 14
2220239 GCGAAATGAA
*
2220249 AATCGCAACGACAG
1 AATCGCAACGAAAG
2220263 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
2220280 AAATCGCAACGAAAG
1 -AATCGCAACGAAAG
2220295 AATCGCAACG
1 AATCGCAACG
2220305 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 18 0.49
15 1 0.03
16 9 0.24
17 1 0.03
18 8 0.22
ACGTcount: A:0.45, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:2220289 original size:32 final size:33
Alignment explanation
Indices: 2220230--2220321 Score: 159
Period size: 32 Copynumber: 2.8 Consensus size: 33
2220220 GCGAAACCAA
*
2220230 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
2220263 AATCGCAATGCGAAATG-AAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
2220295 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
2220322 TGCGATTTTG
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.47, C:0.22, G:0.21, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:2220319 original size:19 final size:19
Alignment explanation
Indices: 2220193--2220326 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
2220183 TAGTTTACTT
* *
2220193 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
2220213 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
2220232 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2220251 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
2220265 TCGCAATGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
2220283 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
2220297 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
2220316 TCGCAATGCGA
1 TCGCAACGCGA
2220327 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 19
0.78 0.06 0.15
Matches are distributed among these distances:
14 16 0.16
15 1 0.01
16 15 0.15
17 6 0.06
18 8 0.08
19 39 0.40
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:2220338 original size:19 final size:19
Alignment explanation
Indices: 2220322--2220436 Score: 141
Period size: 19 Copynumber: 6.3 Consensus size: 19
2220312 AAAATCGCAA
2220322 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
2220341 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
2220360 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
2220374 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
2220393 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
2220412 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
2220432 TGCGA
1 TGCGA
2220437 AGTAAACTAT
Statistics
Matches: 83, Mismatches: 7, Indels: 11
0.82 0.07 0.11
Matches are distributed among these distances:
14 11 0.13
16 1 0.01
17 1 0.01
18 1 0.01
19 56 0.67
20 13 0.16
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:2220653 original size:92 final size:93
Alignment explanation
Indices: 2220483--2220944 Score: 859
Period size: 92 Copynumber: 5.1 Consensus size: 93
2220473 ATGGATTGCA
2220483 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
2220548 TAGCA-AATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
2220575 TTACTTTCAACCAAAAGACAAAAC-AAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
2220639 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
2220667 TTACTTTCAACCAAAAGACAAAACAAAGAC-AATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
2220731 TAGCAGAATTGGCAG---CCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
2220756 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
2220821 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
2220849 TTACTTTCAA-CAAAAGACAAAAC-AAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
2220912 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
2220940 TTACT
1 TTACT
2220945 AAGCAATCTA
Statistics
Matches: 363, Mismatches: 1, Indels: 13
0.96 0.00 0.03
Matches are distributed among these distances:
89 40 0.11
90 49 0.13
91 117 0.32
92 132 0.36
93 25 0.07
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.23
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:2222663 original size:20 final size:20
Alignment explanation
Indices: 2222631--2222725 Score: 82
Period size: 20 Copynumber: 5.2 Consensus size: 20
2222621 TTTTGGTTGA
2222631 AATG-AAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
2222650 AATGACTGTCGCAACGAGTA-
1 AATGAAAATCGCAACGAG-AG
2222670 AATGAAAATCGCAAC--GAG
1 AATGAAAATCGCAACGAGAG
*
2222688 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
2222703 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
2222723 AAT
1 AAT
2222726 CGCAACGCGA
Statistics
Matches: 59, Mismatches: 7, Indels: 19
0.69 0.08 0.22
Matches are distributed among these distances:
14 9 0.15
16 4 0.07
17 3 0.05
18 1 0.02
19 16 0.27
20 25 0.42
21 1 0.02
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.13
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:2222695 original size:14 final size:14
Alignment explanation
Indices: 2222676--2222732 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2222666 AGTAAATGAA
2222676 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
2222690 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
2222709 AATCGCAACGAGAG
1 AATCGCAACGAGAG
2222723 AATCGCAACG
1 AATCGCAACG
2222733 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:2222709 original size:33 final size:33
Alignment explanation
Indices: 2222658--2222749 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 33
2222648 AGAATGACTG
*
2222658 TCGCAACGAGTAAATGAAAATCGCAACGAGAGAA
1 TCGCAACGCG-AAATGAAAATCGCAACGAGAGAA
2222692 TCGCAACGCGAAATGAAAATCGCAACGAGAGAA
1 TCGCAACGCGAAATGAAAATCGCAACGAGAGAA
2222725 TCGCAACGCGAAATGAAAATCGCAA
1 TCGCAACGCGAAATGAAAATCGCAA
2222750 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
33 48 0.84
34 9 0.16
ACGTcount: A:0.46, C:0.21, G:0.23, T:0.11
Consensus pattern (33 bp):
TCGCAACGCGAAATGAAAATCGCAACGAGAGAA
Found at i:2222714 original size:19 final size:19
Alignment explanation
Indices: 2222629--2222754 Score: 85
Period size: 19 Copynumber: 7.1 Consensus size: 19
2222619 TCTTTTGGTT
*
2222629 GAAATG-AAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*** *
2222647 GAGAATGACTGTCGCAACGA
1 GA-AATGAAAATCGCAACGC
2222667 GTAAATGAAAATCGCAA--C
1 G-AAATGAAAATCGCAACGC
*
2222685 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
2222701 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
2222718 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
2222734 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
2222753 GA
1 GA
2222755 TTTTGGTTTC
Statistics
Matches: 83, Mismatches: 12, Indels: 25
0.69 0.10 0.21
Matches are distributed among these distances:
14 20 0.24
15 2 0.02
16 4 0.05
17 2 0.02
18 5 0.06
19 28 0.34
20 21 0.25
21 1 0.01
ACGTcount: A:0.44, C:0.19, G:0.25, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:2222785 original size:14 final size:14
Alignment explanation
Indices: 2222766--2222822 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2222756 TTTGGTTTCG
2222766 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2222780 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
2222799 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2222813 CGTTGCGATT
1 CGTTGCGATT
2222823 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2222798 original size:33 final size:33
Alignment explanation
Indices: 2222750--2222830 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
2222740 AAAATCGCAA
**
2222750 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
2222783 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
2222816 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
2222831 TCTCGTTGCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:2222833 original size:21 final size:21
Alignment explanation
Indices: 2222807--2222882 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
2222797 CGCGTTGCGA
2222807 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
2222828 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
2222848 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
2222869 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
2222883 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:2222863 original size:41 final size:41
Alignment explanation
Indices: 2222806--2222883 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
2222796 TCGCGTTGCG
*
2222806 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
2222847 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
2222884 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:2223003 original size:29 final size:32
Alignment explanation
Indices: 2222961--2223027 Score: 95
Period size: 29 Copynumber: 2.2 Consensus size: 32
2222951 AATACTAACT
2222961 TGAAAATCGCAACGA-AG-A-GCAACGCGAAA
1 TGAAAATCGCAACGACAGAACGCAACGCGAAA
*
2222990 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAA-CGCAACGCGAAA
2223023 TGAAA
1 TGAAA
2223028 TCTAAGTGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
29 15 0.45
30 2 0.06
31 1 0.03
33 15 0.45
ACGTcount: A:0.48, C:0.19, G:0.22, T:0.10
Consensus pattern (32 bp):
TGAAAATCGCAACGACAGAACGCAACGCGAAA
Found at i:2223255 original size:21 final size:22
Alignment explanation
Indices: 2223204--2223257 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
2223194 TGGTTGTGAG
**
2223204 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
2223226 GGAAATCTTCGGAGAT-GGGAC
1 GGATTTCTTCGGAGATGGGGAC
2223247 GGATTTCTTCG
1 GGATTTCTTCG
2223258 CCGTAGAGTG
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 14 0.54
22 12 0.46
ACGTcount: A:0.20, C:0.17, G:0.39, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:2223426 original size:20 final size:20
Alignment explanation
Indices: 2223401--2223594 Score: 212
Period size: 20 Copynumber: 9.7 Consensus size: 20
2223391 CTTTAAATAT
2223401 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
2223421 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
2223443 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
2223462 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
** **
2223482 CGTATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
2223502 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
2223522 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
2223542 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
2223562 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
2223582 CGCGTTGCGATTT
1 CGCGTTGCGATTT
2223595 TGGTAAATCG
Statistics
Matches: 145, Mismatches: 24, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:2223588 original size:60 final size:60
Alignment explanation
Indices: 2223401--2223594 Score: 244
Period size: 60 Copynumber: 3.2 Consensus size: 60
2223391 CTTTAAATAT
**
2223401 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* ** *** *
2223462 CGCGTTGCGATATACGGATACGTATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
2223522 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
2223582 CGCGTTGCGATTT
1 CGCGTTGCGATTT
2223595 TGGTAAATCG
Statistics
Matches: 110, Mismatches: 23, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
60 83 0.75
61 27 0.25
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:2223611 original size:21 final size:21
Alignment explanation
Indices: 2223587--2223637 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
2223577 ATATTCGCGT
2223587 TGCGATTTTGGTA-AATCGCAA
1 TGCGATTTT-GTACAATCGCAA
* * *
2223608 TGCGAATTTGTACTATCGCAT
1 TGCGATTTTGTACAATCGCAA
2223629 TGCGATTTT
1 TGCGATTTT
2223638 CAAGAATCGC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 3 0.12
21 22 0.88
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.39
Consensus pattern (21 bp):
TGCGATTTTGTACAATCGCAA
Found at i:2224109 original size:22 final size:22
Alignment explanation
Indices: 2224061--2224110 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
2224051 TTTGAGATTT
*
2224061 ATTTTAAATATATAATTATAAG
1 ATTTTAAATATATAATTATAAA
* *
2224083 TTTTTCAAA-ATATAATTTTAAA
1 ATTTT-AAATATATAATTATAAA
2224105 ATTTTA
1 ATTTTA
2224111 TAAACGTAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
21 1 0.04
22 19 0.83
23 3 0.13
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (22 bp):
ATTTTAAATATATAATTATAAA
Found at i:2229894 original size:32 final size:31
Alignment explanation
Indices: 2229858--2229930 Score: 103
Period size: 31 Copynumber: 2.3 Consensus size: 31
2229848 TTTTTTATTT
2229858 AAAATATTTTAAAACAAT-AATATATAATTTTG
1 AAAATATTTT-AAA-AATGAATATATAATTTTG
* *
2229890 AAAATATTTTGAAAATGTATATATAATTTTG
1 AAAATATTTTAAAAATGAATATATAATTTTG
2229921 AAAATATTTT
1 AAAATATTTT
2229931 TGAAAATATT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
30 3 0.08
31 25 0.66
32 10 0.26
ACGTcount: A:0.49, C:0.01, G:0.05, T:0.44
Consensus pattern (31 bp):
AAAATATTTTAAAAATGAATATATAATTTTG
Found at i:2229900 original size:11 final size:11
Alignment explanation
Indices: 2229884--2229941 Score: 50
Period size: 11 Copynumber: 5.4 Consensus size: 11
2229874 ATAATATATA
2229884 ATTTTGAAAAT
1 ATTTTGAAAAT
2229895 ATTTTGAAAAT
1 ATTTTGAAAAT
* * *
2229906 -GTAT--ATAT
1 ATTTTGAAAAT
2229914 AATTTTGAAAAT
1 -ATTTTGAAAAT
2229926 ATTTTTGAAAAT
1 A-TTTTGAAAAT
2229938 ATTT
1 ATTT
2229942 ATTAGTTTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 10
0.69 0.12 0.19
Matches are distributed among these distances:
8 3 0.08
10 4 0.11
11 15 0.42
12 14 0.39
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (11 bp):
ATTTTGAAAAT
Found at i:2229915 original size:31 final size:32
Alignment explanation
Indices: 2229877--2229937 Score: 115
Period size: 31 Copynumber: 1.9 Consensus size: 32
2229867 TAAAACAATA
2229877 ATATATAATTTTGAAAATA-TTTTGAAAATGT
1 ATATATAATTTTGAAAATATTTTTGAAAATGT
2229908 ATATATAATTTTGAAAATATTTTTGAAAAT
1 ATATATAATTTTGAAAATATTTTTGAAAAT
2229938 ATTTATTAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 19 0.66
32 10 0.34
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (32 bp):
ATATATAATTTTGAAAATATTTTTGAAAATGT
Found at i:2229933 original size:12 final size:12
Alignment explanation
Indices: 2229916--2229941 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2229906 GTATATATAA
2229916 TTTTGAAAATAT
1 TTTTGAAAATAT
2229928 TTTTGAAAATAT
1 TTTTGAAAATAT
2229940 TT
1 TT
2229942 ATTAGTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (12 bp):
TTTTGAAAATAT
Found at i:2230002 original size:36 final size:36
Alignment explanation
Indices: 2229947--2230452 Score: 271
Period size: 36 Copynumber: 13.7 Consensus size: 36
2229937 TATTTATTAG
*
2229947 TTTAAAACAATTTTTGAAAAAATATATAATATATAGTC
1 TTTAAAAC-A-TTTTGAAAAAATATATAATATATAGTT
*
2229985 TTTAAAACATTTTGAAAACATATATAATATATAGTT
1 TTTAAAACATTTTGAAAAAATATATAATATATAGTT
* **
2230021 TTTAAAAATATTTTGAAAATTTTATATAATATATAGTT
1 TTT-AAAACATTTTGAAAA-AATATATAATATATAGTT
****
2230059 TTTAATTTTTTTTGAAAAATATATATAATATATAGTT
1 TTTAAAACATTTTGAAAAA-ATATATAATATATAGTT
* ** * * *
2230096 TTTAAAAAAAATT--CAAACT-TATAATATATAGTC
1 TTTAAAACATTTTGAAAAAATATATAATATATAGTT
* *
2230129 TTT-AAA-ATTTT-AAAATATATATATTTTTAAAATTTA-TT
1 TTTAAAACATTTTGAAAA-A-ATATA----TAATATATAGTT
* * *
2230167 AGTTTAAAACATTTTTTGAAAATATATAGTTTTTTAAAATTTA-TT
1 --TTTAAAACA--TTTTGAAAA-A-ATA----TATAATATATAGTT
*
2230212 AGTTTAAAACAATTTTTGAAAAAATATATATAATATATAGTC
1 --TTTAAAAC-A-TTTTG-AAAAA-ATATATAATATATAGTT
* **
2230254 TTTAAAACATTTAGAAAACTTATATAATATATAGTT
1 TTTAAAACATTTTGAAAAAATATATAATATATAGTT
* * * * * * *
2230290 TTTGAAA-A-TTT-ATATAATATATAGTTTTTAATT
1 TTTAAAACATTTTGAAAAAATATATAATATATAGTT
*
2230323 TTT-----TTTTTGAAAATATATATATAATATATAGTT
1 TTTAAAACATTTTGAAAA-A-ATATATAATATATAGTT
2230356 TTTAAAACATTTTG--AAAATATATAATATATAGTT
1 TTTAAAACATTTTGAAAAAATATATAATATATAGTT
2230390 TTTAAAAACATTTTTG--AAAATATATAATATATAGTT
1 TTT-AAAACA-TTTTGAAAAAATATATAATATATAGTT
*
2230426 TTGAAAACATTTT-AAAACAATAATATA
1 TTTAAAACATTTTGAAAA-AAT-ATATA
2230453 TAATTTTTGA
Statistics
Matches: 374, Mismatches: 54, Indels: 81
0.73 0.11 0.16
Matches are distributed among these distances:
30 3 0.01
31 5 0.01
32 6 0.02
33 50 0.13
34 28 0.07
35 21 0.06
36 81 0.22
37 59 0.16
38 37 0.10
39 8 0.02
40 11 0.03
41 11 0.03
42 2 0.01
44 4 0.01
45 42 0.11
46 5 0.01
49 1 0.00
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (36 bp):
TTTAAAACATTTTGAAAAAATATATAATATATAGTT
Found at i:2230034 original size:74 final size:73
Alignment explanation
Indices: 2229947--2230466 Score: 274
Period size: 74 Copynumber: 7.1 Consensus size: 73
2229937 TATTTATTAG
*
2229947 TTTAAAACA-ATTTTTGAAAAAATATATAATATATAGTCTTTAAAACATTTTGAAAACATATATA
1 TTTAAAA-ATATTTTTGAAAAAATATATAATATATAGT-TTTAAAACATTTTGAAAATATATATA
2230011 ATATATAGTT
64 ATATATAGTT
** ****
2230021 TTTAAAAATA-TTTTGAAAATTTTATATAATATATAGTTTTTAATTTTTTTTGAAAAATATATAT
1 TTTAAAAATATTTTTGAAAA-AATATATAATATATAG-TTTTAAAACATTTTG-AAAATATATAT
2230085 AATATATAGTT
63 AATATATAGTT
** * * *
2230096 TTTAAAAA-A-AATT--CAAACT-TATAATATATAGTCTTT-AAA-ATTTTAAAATATATATATT
1 TTTAAAAATATTTTTGAAAAAATATATAATATATAGT-TTTAAAACATTTTGAAA-ATATATA--
* *
2230154 TTTAAAATTTA-TT
62 --TAATATATAGTT
* *
2230167 AGTTTAAAACAT-TTTTTGAAAATATATAGTTTTTTAAAATTTATTAG-TTTAAAACAATTTTTG
1 --TTTAAAA-ATATTTTTGAAAA-A-ATA------TATAATATA-TAGTTTTAAAAC-A-TTTTG
*
2230230 AAAAAATATATATAATATATAGTC
52 --AAAATATATATAATATATAGTT
* * ** *
2230254 TTT-AAAACA-TTTAGAAAACTTATATAATATATAG---T------TTTTGAAAATTTATATAAT
1 TTTAAAAATATTTTTGAAAAAATATATAATATATAGTTTTAAAACATTTTGAAAATATATATAAT
2230308 ATATAGTT
66 ATATAGTT
*** *
2230316 TTTAATTTTTTTTTTGAAAATATATATATAATATATAGTTTTTAAAACATTTTG-AAA-ATATAT
1 TTTAAAAATATTTTTGAAAA-A-ATATATAATATATAG-TTTTAAAACATTTTGAAAATATATAT
2230379 AATATATAGTT
63 AATATATAGTT
* *
2230390 TTTAAAAACATTTTTG--AAAATATATAATATATAGTTTTGAAAACATTTT--AAA-ACA-ATAA
1 TTTAAAAATATTTTTGAAAAAATATATAATATATAGTTTT-AAAACATTTTGAAAATATATATAA
*
2230449 TATATAATT
65 TATATAGTT
*
2230458 TTTGAAAAT
1 TTTAAAAAT
2230467 GTATATAATA
Statistics
Matches: 342, Mismatches: 54, Indels: 106
0.68 0.11 0.21
Matches are distributed among these distances:
62 23 0.07
63 1 0.00
64 13 0.04
66 14 0.04
67 3 0.01
68 30 0.09
69 11 0.03
70 41 0.12
71 4 0.01
72 12 0.04
73 17 0.05
74 66 0.19
75 42 0.12
76 5 0.01
77 2 0.01
78 1 0.00
79 1 0.00
81 2 0.01
83 9 0.03
84 3 0.01
85 6 0.02
86 17 0.05
87 4 0.01
88 1 0.00
89 4 0.01
90 7 0.02
91 3 0.01
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (73 bp):
TTTAAAAATATTTTTGAAAAAATATATAATATATAGTTTTAAAACATTTTGAAAATATATATAAT
ATATAGTT
Found at i:2230072 original size:37 final size:36
Alignment explanation
Indices: 2229958--2230151 Score: 193
Period size: 37 Copynumber: 5.5 Consensus size: 36
2229948 TTAAAACAAT
* * *
2229958 TTTTGAAAAAATATATAATATATAGTCTTTAAAACA
1 TTTTGAAAATATATATAATATATAGTTTTTAAAATA
*
2229994 TTTTGAAAACATATATAATATATAGTTTTTAAAAATA
1 TTTTGAAAATATATATAATATATAGTTTTT-AAAATA
* ** *
2230031 TTTTGAAAATTTTATATAATATATAGTTTTTAATTTT
1 TTTTGAAAA-TATATATAATATATAGTTTTTAAAATA
*
2230068 TTTTGAAAAATATATATAATATATAGTTTTTAAAAAA
1 TTTTG-AAAATATATATAATATATAGTTTTTAAAATA
** * * *
2230105 AATT-CAAA-CT-TATAATATATAGTCTTT-AAA-A
1 TTTTGAAAATATATATAATATATAGTTTTTAAAATA
2230136 TTTT-AAAATATATATA
1 TTTTGAAAATATATATA
2230152 TTTTTAAAAT
Statistics
Matches: 131, Mismatches: 22, Indels: 13
0.79 0.13 0.08
Matches are distributed among these distances:
31 6 0.05
32 4 0.03
33 20 0.15
34 1 0.01
35 3 0.02
36 28 0.21
37 46 0.35
38 23 0.18
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (36 bp):
TTTTGAAAATATATATAATATATAGTTTTTAAAATA
Found at i:2230199 original size:17 final size:18
Alignment explanation
Indices: 2230179--2230216 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
2230169 TTTAAAACAT
2230179 TTTTTGAAAATATA-TAG
1 TTTTTGAAAATATATTAG
* *
2230196 TTTTTTAAAATTTATTAG
1 TTTTTGAAAATATATTAG
2230214 TTT
1 TTT
2230217 AAAACAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (18 bp):
TTTTTGAAAATATATTAG
Found at i:2230201 original size:18 final size:18
Alignment explanation
Indices: 2230178--2230216 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2230168 GTTTAAAACA
2230178 TTTTTTGAAAATATA-TAG
1 TTTTTT-AAAATATATTAG
*
2230196 TTTTTTAAAATTTATTAG
1 TTTTTTAAAATATATTAG
2230214 TTT
1 TTT
2230217 AAAACAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.59
Consensus pattern (18 bp):
TTTTTTAAAATATATTAG
Found at i:2230201 original size:45 final size:45
Alignment explanation
Indices: 2230136--2230242 Score: 173
Period size: 45 Copynumber: 2.4 Consensus size: 45
2230126 GTCTTTAAAA
*
2230136 TTTT-AAAATATATATATTTTTAAAATTTATTAGTTTAAAACATT
1 TTTTGAAAATATATATATTTTTAAAATTTATTAGTTTAAAACAAT
2230180 TTTTGAAAATATATAGT-TTTTTAAAATTTATTAGTTTAAAACAAT
1 TTTTGAAAATATATA-TATTTTTAAAATTTATTAGTTTAAAACAAT
*
2230225 TTTTGAAAAAATATATAT
1 TTTTGAAAATATATATAT
2230243 AATATATAGT
Statistics
Matches: 58, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
44 5 0.09
45 52 0.90
46 1 0.02
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.50
Consensus pattern (45 bp):
TTTTGAAAATATATATATTTTTAAAATTTATTAGTTTAAAACAAT
Found at i:2230302 original size:26 final size:26
Alignment explanation
Indices: 2230267--2230318 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
2230257 AAAACATTTA
2230267 GAAAACTTATATAATATATAGTTTTT
1 GAAAACTTATATAATATATAGTTTTT
*
2230293 GAAAATTTATATAATATATAGTTTTT
1 GAAAACTTATATAATATATAGTTTTT
2230319 AATTTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (26 bp):
GAAAACTTATATAATATATAGTTTTT
Found at i:2230315 original size:100 final size:99
Alignment explanation
Indices: 2230214--2230397 Score: 260
Period size: 102 Copynumber: 1.8 Consensus size: 99
2230204 AATTTATTAG
2230214 TTTAAAACAATTTTTGAAAAAATATATATAATATATAGTCTTTAAAACATTTAGAAAACTTATAT
1 TTTAAAACAATTTTTGAAAAAATATATATAATATATAGTCTTTAAAACATTTAGAAAA--TATAT
*
2230279 AATATATAGTTTTTGAAAATTTATATAATATATAGTT
64 AATATATAGTTTTTAAAAATTTATATAATATATAG-T
***** * * *
2230316 TTTAATTTTTTTTTTGAAAATATATATATAATATATAGTTTTTAAAACATTTTGAAAATATATAA
1 TTTAAAACAATTTTTGAAAAAATATATATAATATATAGTCTTTAAAACATTTAGAAAATATATAA
2230381 TATATAGTTTTTAAAAA
66 TATATAGTTTTTAAAAA
2230398 CATTTTTGAA
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
100 23 0.32
102 50 0.68
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (99 bp):
TTTAAAACAATTTTTGAAAAAATATATATAATATATAGTCTTTAAAACATTTAGAAAATATATAA
TATATAGTTTTTAAAAATTTATATAATATATAGT
Found at i:2230349 original size:158 final size:155
Alignment explanation
Indices: 2230067--2230362 Score: 343
Period size: 158 Copynumber: 1.9 Consensus size: 155
2230057 TTTTTAATTT
* *
2230067 TTTTTGAAAAATATATATAATATATAGTTTTTAAAAAAAATTCAAACTTATAATATATAGTCTTT
1 TTTTTGAAAAATATATATAATATATAGTCTTTAAAAAAAATTAAAACTTATAATATATAGTCTTT
* *
2230132 AAAATTTTAAAATATATATATTTTTAAAATTTATTAGTTTAAAACATTTTTTGAAAATATATAGT
66 AAAATTTTAAAATATATATATTTTT-AAATTTATTAGTTTAAAACATTATATGAAAATATATAG-
2230197 TTTTTAAAATTTATTAGTTTAAAACAA
129 TTTTTAAAATTTATTAGTTTAAAACAA
* *
2230224 TTTTTGAAAAAATATATATAATATATAGTCTTT-AAAACATTTAGAAAACTTATATAATATATAG
1 TTTTTG-AAAAATATATATAATATATAGTCTTTAAAAAAAATT--AAAAC-T-TATAATATATAG
* * * ** * *
2230288 TTTTTGAAAATTTATATAATATATA-GTTTTT-AATTT-TTTTTTTGAAA-ATATATAT-ATAAT
61 TCTTT-AAAATTT-TAAAATATATATATTTTTAAATTTATTAGTTTAAAACAT-TATATGAAAAT
2230348 ATATAGTTTTTAAAA
123 ATATAGTTTTTAAAA
2230363 CATTTTGAAA
Statistics
Matches: 118, Mismatches: 13, Indels: 16
0.80 0.09 0.11
Matches are distributed among these distances:
157 22 0.19
158 37 0.31
159 15 0.13
160 6 0.05
161 16 0.14
162 12 0.10
163 10 0.08
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (155 bp):
TTTTTGAAAAATATATATAATATATAGTCTTTAAAAAAAATTAAAACTTATAATATATAGTCTTT
AAAATTTTAAAATATATATATTTTTAAATTTATTAGTTTAAAACATTATATGAAAATATATAGTT
TTTAAAATTTATTAGTTTAAAACAA
Found at i:2230501 original size:35 final size:35
Alignment explanation
Indices: 2230454--2230592 Score: 105
Period size: 37 Copynumber: 4.0 Consensus size: 35
2230444 AATAATATAT
2230454 AATTTTTGAAAATGTATATAATATA-ATTTTGAAAA-
1 AATTTTTGAAAA-GTATATAATATACATTTT-AAAAC
* *
2230489 TATTTTTGAAAA-TATAT-AT-TA-GTTTTAAAAC
1 AATTTTTGAAAAGTATATAATATACATTTTAAAAC
* * *
2230520 AAATTTTGAAAA-TATATATATTATATAGTTTGAAAAC
1 AATTTTTGAAAAGTATATA-A-TATACA-TTTTAAAAC
2230557 AATTTTT-AAAAGCATATATAATATACAGTTTTAAAA
1 AATTTTTGAAAAG--TATATAATATACA-TTTTAAAA
2230593 TGTTTTTTAT
Statistics
Matches: 85, Mismatches: 9, Indels: 18
0.76 0.08 0.16
Matches are distributed among these distances:
30 4 0.05
31 21 0.25
32 2 0.02
33 6 0.07
34 1 0.01
35 13 0.15
36 4 0.05
37 27 0.32
38 1 0.01
39 6 0.07
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (35 bp):
AATTTTTGAAAAGTATATAATATACATTTTAAAAC
Found at i:2230504 original size:31 final size:31
Alignment explanation
Indices: 2230469--2230540 Score: 76
Period size: 31 Copynumber: 2.3 Consensus size: 31
2230459 TTGAAAATGT
* *
2230469 ATATAATATAATTTTGAAAA-TATTTTTGAAA
1 ATATAATATAATTTT-AAAACAAATTTTGAAA
*
2230500 ATAT-ATATTAGTTTTAAAACAAATTTTGAAA
1 ATATAATA-TAATTTTAAAACAAATTTTGAAA
2230531 ATATATATAT
1 ATATA-ATAT
2230541 TATATAGTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
30 7 0.21
31 23 0.68
32 1 0.03
33 3 0.09
ACGTcount: A:0.49, C:0.01, G:0.06, T:0.44
Consensus pattern (31 bp):
ATATAATATAATTTTAAAACAAATTTTGAAA
Found at i:2230537 original size:33 final size:33
Alignment explanation
Indices: 2230457--2230576 Score: 93
Period size: 33 Copynumber: 3.5 Consensus size: 33
2230447 AATATATAAT
* * *
2230457 TTTTGAAAATGTATATAATATAATTTTGAAAATAT
1 TTTTGAAAATATATAT-AT-TAATTTTGAAAAAAA
*
2230492 TTTTG-AAA-ATATATATTAGTTTT-AAAACAAA
1 TTTTGAAAATATATATATTAATTTTGAAAA-AAA
*
2230523 TTTTGAAAATATATATATTATATAGTTTGAAAACAA
1 TTTTGAAAATATATATATTA-AT--TTTGAAAAAAA
* *
2230559 TTTTTAAAAGCATATATA
1 TTTTGAAAA-TATATATA
2230577 ATATACAGTT
Statistics
Matches: 69, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
30 4 0.06
31 12 0.17
32 5 0.07
33 15 0.22
34 4 0.06
35 5 0.07
36 13 0.19
37 11 0.16
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (33 bp):
TTTTGAAAATATATATATTAATTTTGAAAAAAA
Found at i:2230556 original size:37 final size:36
Alignment explanation
Indices: 2230500--2230592 Score: 109
Period size: 37 Copynumber: 2.6 Consensus size: 36
2230490 ATTTTTGAAA
*
2230500 ATATATAT-TAGTTTTAAAACAAATTTTGAAAA-TAT
1 ATATATATATAGTTTTAAAAC-AATTTTGAAAAGCAT
* *
2230535 ATATATTATATAGTTTGAAAACAATTTTTAAAAGCAT
1 ATATA-TATATAGTTTTAAAACAATTTTGAAAAGCAT
*
2230572 ATATAATATACAGTTTTAAAA
1 ATAT-ATATATAGTTTTAAAA
2230593 TGTTTTTTAT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
35 5 0.10
36 13 0.27
37 30 0.61
38 1 0.02
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.41
Consensus pattern (36 bp):
ATATATATATAGTTTTAAAACAATTTTGAAAAGCAT
Found at i:2230577 original size:297 final size:290
Alignment explanation
Indices: 2229994--2230588 Score: 647
Period size: 297 Copynumber: 2.0 Consensus size: 290
2229984 CTTTAAAACA
*
2229994 TTTTGAAAACATATATAATATATAGTTTTTAAAAATATTTTGAAAATTTTATATAATATATAGTT
1 TTTTGAAAACATATATAATATATAGTTTTTAAAAATATTTTGAAAATTATATATAATATATAGTT
**** *
2230059 TTTAATTTTTTTTGAAAAATATATATAATATATAGTTTTTAAAAAAAATTCAAACTTATAATATA
66 TTTAAAACATTTTG-AAAATATATATAATATATAGTTTTTAAAAAAAATTCAAAATTATAATATA
* *
2230124 TAGTCTTTAAAATTTTAAAATATATATATTTTTAAAATTTATTAGTTTAAAACATTTTTTGAAAA
130 TAGTCTTTAAAATTTTAAAATATATATATTTTTAAAATGTATTA--TTAAAACATATTTTG-AAA
* *
2230189 TATATAGTTTTTTAAAATTTATTAGTTTAAAACAATTTTTGAAAAAATATATATAATATATAGTC
192 TATATAGTTTTTGAAAATTTATTAGTTTAAAACAAATTTTG-AAAAATATATATAATATATAGTC
* * *
2230254 TTTAAAACATTTAGAAAACTTATATAATATATAGT
256 TTGAAAACATTTAGAAAACATATATAATATACAGT
** *** *
2230289 TTTTGAAAATTTATATAATATATAGTTTTTAATTTTTTTTTTGAAAATATATATATAATATATAG
1 TTTTGAAAACATATATAATATATAGTTTTTAA-AAATATTTTGAAAAT-TATATATAATATATAG
** *
2230354 TTTTTAAAACATTTTG-AAA-ATATATAATATATAGTTTTTAAAAACATTTTTGAAAATATATAA
64 TTTTTAAAACATTTTGAAAATATATATAATATATAGTTTTTAAAAA-A-AATTCAAAAT-TATAA
* *
2230417 TATATAGT-TTTGAAAACATTTTAAAACAATAATATATAATTTTTGAAAATGTA-TA-TAATATA
126 TATATAGTCTTT--AAA-ATTTT--AA-AAT-ATATAT-ATTTTT-AAAATGTATTATTAAAACA
2230479 -ATTTTG-AA-A-ATA-TTTTTGAAAATATATATTAGTTTTAAAACAAATTTTG-AAAATATATA
182 TATTTTGAAATATATAGTTTTTGAAAAT-T-TATTAG-TTTAAAACAAATTTTGAAAAATATATA
* **
2230538 TATTATATAGT-TTGAAAACAATTTTTAAAAGCATATATAATATACAGT
244 TAATATATAGTCTTGAAAAC-ATTTAGAAAA-CATATATAATATACAGT
2230586 TTT
1 TTT
2230589 AAAATGTTTT
Statistics
Matches: 254, Mismatches: 27, Indels: 36
0.80 0.09 0.11
Matches are distributed among these distances:
294 25 0.10
295 51 0.20
296 52 0.20
297 65 0.26
298 20 0.08
299 5 0.02
300 5 0.02
301 7 0.03
302 3 0.01
303 6 0.02
304 8 0.03
305 7 0.03
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (290 bp):
TTTTGAAAACATATATAATATATAGTTTTTAAAAATATTTTGAAAATTATATATAATATATAGTT
TTTAAAACATTTTGAAAATATATATAATATATAGTTTTTAAAAAAAATTCAAAATTATAATATAT
AGTCTTTAAAATTTTAAAATATATATATTTTTAAAATGTATTATTAAAACATATTTTGAAATATA
TAGTTTTTGAAAATTTATTAGTTTAAAACAAATTTTGAAAAATATATATAATATATAGTCTTGAA
AACATTTAGAAAACATATATAATATACAGT
Found at i:2230614 original size:7 final size:7
Alignment explanation
Indices: 2230602--2230644 Score: 50
Period size: 7 Copynumber: 5.7 Consensus size: 7
2230592 ATGTTTTTTA
2230602 TTATTAT
1 TTATTAT
2230609 TTATTAT
1 TTATTAT
2230616 TTATTTTAT
1 TTA--TTAT
*
2230625 TTGTTAT
1 TTATTAT
2230632 TTATTTAT
1 TTA-TTAT
2230640 TTATT
1 TTATT
2230645 TATTCCCTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
7 18 0.58
8 7 0.23
9 6 0.19
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (7 bp):
TTATTAT
Found at i:2230619 original size:4 final size:4
Alignment explanation
Indices: 2230605--2230648 Score: 56
Period size: 4 Copynumber: 11.2 Consensus size: 4
2230595 TTTTTTATTA
*
2230605 TTAT TTA- TTAT TTATT TTAT TT-G TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTA-T TTAT TTAT TTAT TTAT TTAT TTAT TTAT T
2230649 CCCTTTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
3 5 0.14
4 26 0.74
5 4 0.11
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (4 bp):
TTAT
Found at i:2230648 original size:16 final size:16
Alignment explanation
Indices: 2230598--2230644 Score: 69
Period size: 16 Copynumber: 2.9 Consensus size: 16
2230588 TAAAATGTTT
2230598 TTTATTATTATTTATTA
1 TTTATT-TTATTTATTA
*
2230615 TTTATTTTATTTGTTA
1 TTTATTTTATTTATTA
2230631 TTTA-TTTATTTATT
1 TTTATTTTATTTATT
2230645 TATTCCCTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 9 0.32
16 13 0.46
17 6 0.21
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (16 bp):
TTTATTTTATTTATTA
Found at i:2231874 original size:17 final size:18
Alignment explanation
Indices: 2231854--2231995 Score: 66
Period size: 17 Copynumber: 7.9 Consensus size: 18
2231844 AAATTTAACC
2231854 TTTT-TTATTATTTTTTA
1 TTTTATTATTATTTTTTA
**
2231871 TTTTATT-TCGTTTTCTTA
1 TTTTATTATTATTTT-TTA
* **
2231889 TTTTTTTATT-TTCATTA
1 TTTTATTATTATTTTTTA
*
2231906 TTTTCTTATTATTTTTCT-
1 TTTTATTATTATTTTT-TA
* *
2231924 TTTT-TTATTA--CTTCA
1 TTTTATTATTATTTTTTA
2231939 TTTTCATTATTATTTATTTA
1 TTTT-ATTATTATTT-TTTA
* *
2231959 TCCCTTTTAATATT-TTTTGTA
1 ----TTTTATTATTATTTTTTA
2231980 TTTTATTATTATTTTT
1 TTTTATTATTATTTTT
2231996 AAAAGTATTT
Statistics
Matches: 92, Mismatches: 17, Indels: 31
0.66 0.12 0.22
Matches are distributed among these distances:
15 6 0.07
17 42 0.46
18 24 0.26
19 2 0.02
20 3 0.03
21 3 0.03
22 3 0.03
23 5 0.05
24 4 0.04
ACGTcount: A:0.18, C:0.08, G:0.01, T:0.73
Consensus pattern (18 bp):
TTTTATTATTATTTTTTA
Found at i:2231884 original size:26 final size:26
Alignment explanation
Indices: 2231854--2231957 Score: 77
Period size: 28 Copynumber: 3.8 Consensus size: 26
2231844 AAATTTAACC
2231854 TTTTTTATTATTTTTTATTTT-ATT-
1 TTTTTTATTATTTTTTATTTTCATTA
* *
2231878 TCGTTTTCTTATTTTTTTATTTTCATTA
1 T-TTTTTATTA-TTTTTTATTTTCATTA
* *
2231906 TTTTCTTATTATTTTTCTTTTTTTATTA
1 TTTT-TTATTATTTTT-TATTTTCATTA
*
2231934 CTTCATTTTCATTATTATTTATTT
1 -TT--TTTT-ATTATTTTTTATTT
2231958 ATCCCTTTTA
Statistics
Matches: 62, Mismatches: 8, Indels: 14
0.74 0.10 0.17
Matches are distributed among these distances:
24 1 0.02
25 7 0.11
26 11 0.18
27 10 0.16
28 15 0.24
29 2 0.03
30 6 0.10
31 10 0.16
ACGTcount: A:0.16, C:0.08, G:0.01, T:0.75
Consensus pattern (26 bp):
TTTTTTATTATTTTTTATTTTCATTA
Found at i:2231909 original size:42 final size:40
Alignment explanation
Indices: 2231855--2231957 Score: 116
Period size: 42 Copynumber: 2.5 Consensus size: 40
2231845 AATTTAACCT
* ** *
2231855 TTTTTATTATTTTTTATTTTATTTCGTTTTCTTATTTTTTTA
1 TTTTCATTATTTTTTATTTT-TTTC-TTTTCTTATTACTTCA
*
2231897 TTTTCATTATTTTCTTATTATTTTTCTTTTTTTATTACTTCA
1 TTTTCATTATTTT-TTATT-TTTTTCTTTTCTTATTACTTCA
*
2231939 TTTTCATTATTATTTATTT
1 TTTTCATTATTTTTTATTT
2231958 ATCCCTTTTA
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
40 1 0.02
41 5 0.09
42 36 0.68
43 9 0.17
44 2 0.04
ACGTcount: A:0.17, C:0.08, G:0.01, T:0.75
Consensus pattern (40 bp):
TTTTCATTATTTTTTATTTTTTTCTTTTCTTATTACTTCA
Found at i:2231919 original size:20 final size:21
Alignment explanation
Indices: 2231894--2231949 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
2231884 TCTTATTTTT
*
2231894 TTATTTTCATTATTTTCTTA-
1 TTATTTTCATTATTTTATTAC
*
2231914 TTATTTTTC-TTTTTTTATTAC
1 TTA-TTTTCATTATTTTATTAC
2231935 TTCATTTTCATTATT
1 TT-ATTTTCATTATT
2231950 ATTTATTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
20 12 0.41
21 12 0.41
22 5 0.17
ACGTcount: A:0.18, C:0.11, G:0.00, T:0.71
Consensus pattern (21 bp):
TTATTTTCATTATTTTATTAC
Done.