Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009462.1 Hibiscus syriacus cultivar Beakdansim tig00113725_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: 20687664
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 91
Found at i:2259567 original size:21 final size:20
Alignment explanation
Indices: 2259525--2259574 Score: 75
Period size: 21 Copynumber: 2.5 Consensus size: 20
2259515 CTTATTCTTG
2259525 GTATCGATACCTCCACATCA
1 GTATCGATACCTCCACATCA
2259545 GTATCGATACTACTCCA-ATCA
1 GTATCGATAC--CTCCACATCA
2259566 GTATCGATA
1 GTATCGATA
2259575 ATATTCATCG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.36
21 13 0.46
22 5 0.18
ACGTcount: A:0.32, C:0.28, G:0.12, T:0.28
Consensus pattern (20 bp):
GTATCGATACCTCCACATCA
Found at i:2262446 original size:23 final size:23
Alignment explanation
Indices: 2262416--2262467 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
2262406 AAAGGGGTAC
2262416 CGATACTACTTACATAGTAGTAT
1 CGATACTACTTACATAGTAGTAT
2262439 CGATACTACTTACATAGTAGTAT
1 CGATACTACTTACATAGTAGTAT
2262462 CGATAC
1 CGATAC
2262468 GTCAGGCCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (23 bp):
CGATACTACTTACATAGTAGTAT
Found at i:2262543 original size:21 final size:21
Alignment explanation
Indices: 2262519--2262558 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2262509 TAACAAAGGT
2262519 AGTACCGATACTCC-CTGTAGG
1 AGTACCGATAC-CCTCTGTAGG
*
2262540 AGTACTGATACCCTCTGTA
1 AGTACCGATACCCTCTGTA
2262559 CTAGGCATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.28
Consensus pattern (21 bp):
AGTACCGATACCCTCTGTAGG
Found at i:2266997 original size:22 final size:24
Alignment explanation
Indices: 2266972--2267023 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 24
2266962 AATATTATGA
*
2266972 AATTATTTTAAAA-TA-TTTATTT
1 AATTATTTTAAAATTAGATTATTT
2266994 AA-T-TTTTAAAATTAGATTATTT
1 AATTATTTTAAAATTAGATTATTT
*
2267016 ATTTATTT
1 AATTATTT
2267024 GAAATAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
20 8 0.33
21 3 0.12
22 9 0.38
23 1 0.04
24 3 0.12
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (24 bp):
AATTATTTTAAAATTAGATTATTT
Found at i:2267226 original size:23 final size:23
Alignment explanation
Indices: 2267187--2267231 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2267177 AAATAATATT
* *
2267187 ATTTCAAATATATAATTTATTTG
1 ATTTCAAAAATATAATTAATTTG
2267210 ATTTCAAAAAT-TAAATTAATTT
1 ATTTCAAAAATAT-AATTAATTT
2267232 TTTATAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 1 0.05
23 18 0.95
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.49
Consensus pattern (23 bp):
ATTTCAAAAATATAATTAATTTG
Found at i:2268171 original size:59 final size:60
Alignment explanation
Indices: 2268104--2268227 Score: 160
Period size: 60 Copynumber: 2.1 Consensus size: 60
2268094 TTTTATTCTC
** * * * *
2268104 AAACTATGACCCTTGTTCTAAATTGATC-TCAAACTTTTGAATATTCTAATTTCATCTTT
1 AAACTATGAAACTTATTCTAAATTGATCACCAAACTTTTAAATATTCCAATTTCATCTTT
* * *
2268163 AAACTATGAAACTTATTTTAAATTGGTCACCAAACTTTTAAATGTTCCAATTTCATCTTT
1 AAACTATGAAACTTATTCTAAATTGATCACCAAACTTTTAAATATTCCAATTTCATCTTT
2268223 AAACT
1 AAACT
2268228 GTGGATGTCT
Statistics
Matches: 55, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
59 23 0.42
60 32 0.58
ACGTcount: A:0.34, C:0.18, G:0.06, T:0.42
Consensus pattern (60 bp):
AAACTATGAAACTTATTCTAAATTGATCACCAAACTTTTAAATATTCCAATTTCATCTTT
Found at i:2280481 original size:183 final size:183
Alignment explanation
Indices: 2280094--2280569 Score: 650
Period size: 183 Copynumber: 2.6 Consensus size: 183
2280084 GATCCAAATT
* * * * * **
2280094 AAAAATGTATCGATCTACAACGATATAACAGGTAAAACTATGACAAAACCAGTATTGAAATGATA
1 AAAAATGTATCGATCAACAACGATATAACAAGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * ** * *
2280159 AAACCGGTAAAGCGGTA-TCAAATATATTTAAAGTGTCGGTACTTTAATATAAGGATCGACAATT
66 AAACCGGTAAAACGATACT-GGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACAATT
* * * * *
2280223 CGTTAATTTAAACGAGGAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTCAA
130 CGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAATGTCGATACTTTAAA
* * *
2280277 AAAAATATATCGATCAACAACGATATAACAAGTAAAAATATGATAAAACTGGTATCAAAATGATG
1 AAAAATGTATCGATCAACAACGATATAACAAGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * * * *
2280342 AAACCGGTAAAACGCTACTGGATATATTGAAAGTGTCGAAACTTT-ATATAAGGATCGACACTTT
66 AAACCGGTAAAACGATACTGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACAATTC
2280406 GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAATGTCGATACTTTAAA
131 GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAATGTCGATACTTTAAA
*
2280459 AAAAATGTATCGATCAAACAACGATATAACATGTAAAAATATGATAAAACCGGTATCAAAATGAT
1 AAAAATGTATCGATC-AACAACGATATAACAAGTAAAAATATGATAAAACCGGTATCAAAATGAT
* * *
2280524 AAAACCGATAAAATGATACCGGATATATTAAAAGTGTCGATACTTT
65 AAAACCGGTAAAACGATACTGGATATATTAAAAGTGTCGATACTTT
2280570 CGTAAGTACG
Statistics
Matches: 257, Mismatches: 34, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
182 79 0.31
183 177 0.69
184 1 0.00
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27
Consensus pattern (183 bp):
AAAAATGTATCGATCAACAACGATATAACAAGTAAAAATATGATAAAACCGGTATCAAAATGATA
AAACCGGTAAAACGATACTGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACAATTC
GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAATGTCGATACTTTAAA
Found at i:2280538 original size:17 final size:20
Alignment explanation
Indices: 2280499--2280541 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
2280489 ATGTAAAAAT
2280499 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGGTATCAAA
2280519 ATGATAAAACC-G-AT-AAA
1 ATGATAAAACCGGTATCAAA
2280536 ATGATA
1 ATGATA
2280542 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 2 0.09
19 1 0.04
20 11 0.48
ACGTcount: A:0.53, C:0.12, G:0.14, T:0.21
Consensus pattern (20 bp):
ATGATAAAACCGGTATCAAA
Found at i:2282361 original size:19 final size:22
Alignment explanation
Indices: 2282313--2282367 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 22
2282303 TTTTTTATGT
2282313 TTTTATATAAAATGATAGTATAA
1 TTTTATATAAAA-GATAGTATAA
2282336 TTATTATATAAAA-ATA-TA-AA
1 TT-TTATATAAAAGATAGTATAA
2282356 TTTTATTATAAA
1 TTTTA-TATAAA
2282368 TGCAGGTTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
19 3 0.10
20 10 0.33
21 2 0.07
22 3 0.10
23 2 0.07
24 10 0.33
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (22 bp):
TTTTATATAAAAGATAGTATAA
Found at i:2282673 original size:15 final size:15
Alignment explanation
Indices: 2282653--2282685 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2282643 TAGTTGTATT
2282653 GGGGGATGACAGTGA
1 GGGGGATGACAGTGA
*
2282668 GGGGGATGACGGTGA
1 GGGGGATGACAGTGA
2282683 GGG
1 GGG
2282686 AAAACAGAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.21, C:0.06, G:0.61, T:0.12
Consensus pattern (15 bp):
GGGGGATGACAGTGA
Found at i:2282795 original size:21 final size:21
Alignment explanation
Indices: 2282769--2282809 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2282759 AAGACAATCA
2282769 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAT
* *
2282790 AGAGTCGAAGATACACTTGA
1 AGAGTCGAAGAGAAACTTGA
2282810 GAGACATAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.12, G:0.27, T:0.20
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAT
Found at i:2282888 original size:33 final size:33
Alignment explanation
Indices: 2282846--2282911 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
2282836 AAATAGATGG
*
2282846 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
*
2282879 AGTGGTGAAAGAAGTTGAGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
2282912 TCTTAAGATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.30, C:0.00, G:0.47, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:2286886 original size:185 final size:185
Alignment explanation
Indices: 2286572--2286921 Score: 621
Period size: 185 Copynumber: 1.9 Consensus size: 185
2286562 ATATCAGCAT
*
2286572 AAAGTGTCGATACATTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTA
1 AAAGTGTCGATACATTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCACAATTATAATGTA
*
2286637 ATAGGTAATTTTGTAATATAACCGGTATATATATACCGGTTTTATGAGAGAATAGGTATACAACC
66 ATAGGTAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTATACAACC
2286702 TATATCGACACTTTTTAATATTGTGTCGC-TACTTTATGTCCAGAATGGATGAAAA
131 TATATCGACACTTTTTAATATTGTGTC-CATACTTTATGTCCAGAATGGATGAAAA
* *
2286757 AAAGTGTCGATACCTTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCACAATTATAATTTA
1 AAAGTGTCGATACATTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCACAATTATAATGTA
* * *
2286822 ATAGGTAATTTTTTAATATAACCGTTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAACC
66 ATAGGTAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTATACAACC
2286887 TATATCGACACTTTTTAATATTGTGTCCATACTTT
131 TATATCGACACTTTTTAATATTGTGTCCATACTTT
2286922 TAAGTAACGC
Statistics
Matches: 157, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
184 1 0.01
185 156 0.99
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (185 bp):
AAAGTGTCGATACATTTTCAAAAAGTGTCGATTGAAAAAACATCGGAACCCACAATTATAATGTA
ATAGGTAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTATACAACC
TATATCGACACTTTTTAATATTGTGTCCATACTTTATGTCCAGAATGGATGAAAA
Found at i:2290276 original size:182 final size:182
Alignment explanation
Indices: 2289620--2291337 Score: 2182
Period size: 182 Copynumber: 9.6 Consensus size: 182
2289610 ATTTACCTTT
* * *
2289620 TTTAAAAGAGAAGAAGTTATATCGTCAATAAAGTGTCGATACTTTATAAAAATGCATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
*
2289685 AACAATATAACATGTAAAAATATGACAAAATCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
66 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
*
2289750 CGGTTATGTTGAAAGTGTCGATAATTTATTATACGTATCGACACTTTTGGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
* *
2289802 TTTAAAAGAGAAG-AGTTATAGCGCCAAAAAAGTATCGATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
* *
2289866 AACAATATAAGATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAACGCTAC
66 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
*
2289931 CGGTTATGTTGAAAGTGTTGATAATTTATTATAAGTATCG--ACTTTTGGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
* *
2289981 --T--AAGAGAAGAAGTTATAGCGCCAATAACGTGTCGATACTTTATAAAAATGTATCGATCTAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
2290042 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
66 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
2290107 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
* *
2290159 TTTAAAAGAGAAGAAGTTATAGCGTCAATAAAGTGTCGATATTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
* * * *
2290224 AACTATATAAAAGGTAAAAATATGACAAAACCGGTCTCGAAATGATAAAACAGGTAAAGCGCTAC
66 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
*
2290289 CGGATATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
*
2290341 TTTAAAAGAGAAGAAGTTATAGCGTCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
* * * *
2290406 AACAATATAACAGGTAAAAATATGACAAAATCGGTCTCAAAATGACAAAACAGGTAAAGCTCTAC
66 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
* *
2290471 CGGTTATGTTGAAAGTGTCGATAATTTATTATACGTATAGACACTTTTGGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
*
2290523 TTTAAAAGAGAAG-AGTTATAGCGCCAATAAAGTGTCAATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
*
2290587 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAAGTAAAGCGCTAC
66 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
*
2290652 CGGTTATGTTGAAAGTGTCGATAATTTATTATACGTATCGACACTTTTGGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
* * * *
2290704 TTTAAAAGAGAAG-AGTTATAGAGCCAAAAAAGTATCGATACTTTATAAAAATGTATTGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
* * *** * * * * **
2290768 AACAATATAAGATGTAAAAATATGACAAAACAGG--T--AAA-G-CGCTACCGGTTATGTTGAAA
66 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAG-CGCTA
** * * * * *** ** * * * *
2290827 GTGTTGATAATTTATTATAAGTATCGACT--TTTGGAATAAG-AGAAGA-AGTTATAG-C
130 CCG--G-TTATGT-TGA-AAGTGTCGA-TAATTTATTATAAGTA-TCGACACTTTTGGAA
* * * ** * * * * * *
2290882 GTCAATAACGTGTCGATACTTTATA-----AA-AATGTATCGAT-C--TATAACAATATAAC-AT
1 TTTAA-AA-GAGAAGA-A-GTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGAT
* *
2290937 --GTAA-AA-AT---ATG----------ACAAAACCGGTCTCGAAATGACAAAACAGGTAAAACG
62 CCATAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCG
*
2290985 CTACCGGTTATATTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
127 CTACCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
** * *
2291041 TTTAAAAGAGAAGAAGTTATAGCTACAATAAAGTGTCGATATTTTATAAAAATGTATCGATTCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
* * * *
2291106 AATAATATAAAAGGTAAAAATATGATAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
66 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
*
2291171 CGGATATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
* *
2291223 -TTAATAAAAGAAGAAGTTATAGTGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCA
1 TTTAA-AAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCA
* * * **
2291287 TAATAATATAACATGTAAAAATATGATAAAACCAGTCTATAAATGACAAAA
65 TAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAA
2291338 GGTGAACGCA
Statistics
Matches: 1333, Mismatches: 144, Indels: 118
0.84 0.09 0.07
Matches are distributed among these distances:
155 6 0.00
156 18 0.01
157 16 0.01
158 13 0.01
159 4 0.00
160 5 0.00
161 13 0.01
162 7 0.01
164 11 0.01
165 2 0.00
166 3 0.00
167 3 0.00
168 2 0.00
169 4 0.00
170 2 0.00
171 3 0.00
172 2 0.00
173 2 0.00
174 10 0.01
175 15 0.01
176 154 0.12
177 14 0.01
178 16 0.01
179 23 0.02
180 15 0.01
181 409 0.31
182 556 0.42
183 5 0.00
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.28
Consensus pattern (182 bp):
TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
Found at i:2291596 original size:87 final size:86
Alignment explanation
Indices: 2291473--2291634 Score: 252
Period size: 87 Copynumber: 1.9 Consensus size: 86
2291463 AAATAGGTCA
* * *
2291473 ATATAAGCGCTACCTATTACATATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTTT
1 ATATAAACGCTACCTATTACATATATAAGCGCTACCTAATATATTATTGTACTTGATAATATTTC
2291538 CGGTTAAATACCTATTTTATT
66 CGGTTAAATACCTATTTTATT
* * *
2291559 ATATAAACGCTATCTATTATATTATATAAGCGTTACCTAATATATTATTGTACTTGATAATATTT
1 ATATAAACGCTACCTATTACA-TATATAAGCGCTACCTAATATATTATTGTACTTGATAATATTT
*
2291624 CCTGTTAAATA
65 CCGGTTAAATA
2291635 ATATAACATA
Statistics
Matches: 68, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
86 18 0.26
87 50 0.74
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.43
Consensus pattern (86 bp):
ATATAAACGCTACCTATTACATATATAAGCGCTACCTAATATATTATTGTACTTGATAATATTTC
CGGTTAAATACCTATTTTATT
Found at i:2291602 original size:23 final size:23
Alignment explanation
Indices: 2291546--2291606 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
2291536 TTCGGTTAAA
*
2291546 TACCTATTTTATTATATAAACGC
1 TACCTATTATATTATATAAACGC
* * *
2291569 TATCTATTATATTATATAAGCGT
1 TACCTATTATATTATATAAACGC
*
2291592 TACCTAATATATTAT
1 TACCTATTATATTAT
2291607 TGTACTTGAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.36, C:0.13, G:0.05, T:0.46
Consensus pattern (23 bp):
TACCTATTATATTATATAAACGC
Found at i:2292724 original size:2 final size:2
Alignment explanation
Indices: 2292713--2292749 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
2292703 AATTAAATTT
2292713 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2292750 TAACATAAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2296083 original size:41 final size:41
Alignment explanation
Indices: 2296026--2296124 Score: 180
Period size: 41 Copynumber: 2.4 Consensus size: 41
2296016 CTAGTTCCTC
* *
2296026 GTCTAATTCAATGCATTTAATCCTATTGTTAAATGTAGCAT
1 GTCTAATTCAATGCATTTAATCCTACTGTTAAATGCAGCAT
2296067 GTCTAATTCAATGCATTTAATCCTACTGTTAAATGCAGCAT
1 GTCTAATTCAATGCATTTAATCCTACTGTTAAATGCAGCAT
2296108 GTCTAATTCAATGCATT
1 GTCTAATTCAATGCATT
2296125 ATCTTGCTGT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 56 1.00
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.39
Consensus pattern (41 bp):
GTCTAATTCAATGCATTTAATCCTACTGTTAAATGCAGCAT
Found at i:2303138 original size:163 final size:163
Alignment explanation
Indices: 2302863--2303164 Score: 487
Period size: 163 Copynumber: 1.9 Consensus size: 163
2302853 CGGCTTTATC
*
2302863 ATATTTTTACATGTTATATTGTTACATATGGATACATATTTATAAAATAGCGATACTTTATAGGC
1 ATATTTTTACATGTTATATTGTTACATATCGATACATATTTATAAAATAGCGATACTTTATAGGC
*** * *
2302928 GCTATTATTGTTTTTCTTTAAAATTCTATAAGTATCGATAATTATTTGAATGGAATCGATACCTT
66 GCTATTAAACTTTTTCTTTAAAATTCCATAAGTATCAATAATTATTTGAATGGAATCGATACCTT
2302993 CAACATATCTGGTAGCGCTTTACCGGTTTTGTT
131 CAACATATCTGGTAGCGCTTTACCGGTTTTGTT
* * * *
2303026 ATATTTTTACATGTTATATTGTTACGTATCGATACATGTTTATAAAGTATCGATACTTTATAGGC
1 ATATTTTTACATGTTATATTGTTACATATCGATACATATTTATAAAATAGCGATACTTTATAGGC
* *
2303091 GCTATTAAACTTTTTTTTTAAAATTCCATAAGTATCAATACTTATTTGAATGGAATCGATACCTT
66 GCTATTAAACTTTTTCTTTAAAATTCCATAAGTATCAATAATTATTTGAATGGAATCGATACCTT
*
2303156 CAATATATC
131 CAACATATC
2303165 CAATATCTTT
Statistics
Matches: 126, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
163 126 1.00
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.43
Consensus pattern (163 bp):
ATATTTTTACATGTTATATTGTTACATATCGATACATATTTATAAAATAGCGATACTTTATAGGC
GCTATTAAACTTTTTCTTTAAAATTCCATAAGTATCAATAATTATTTGAATGGAATCGATACCTT
CAACATATCTGGTAGCGCTTTACCGGTTTTGTT
Found at i:2303337 original size:182 final size:182
Alignment explanation
Indices: 2303020--2303419 Score: 588
Period size: 182 Copynumber: 2.2 Consensus size: 182
2303010 CTTTACCGGT
* *
2303020 TTTGTTATATTTTTACATGTTATATTGTTACGTATCGATACATGTTTATAAAGTATCGATACTTT
1 TTTGTCATATTTTTACCTGTTATATTGTTACGTATCGATACATGTTTATAAAGTATCGATACTTT
* * * *
2303085 ATAGGCGCTATTAAACTTTTTTTTTAAAATTCCATAAGTATCAATACTTATTTGAATGGAATCGA
66 ATAGACGCTATTAAACTTTTTCTTTAAAATTCCATAAGTATCAATACTTATTTGAATAGAATCAA
* * *
2303150 TACCTTCAATATATCCAATATC-TTTTATCGGTTTTGTCATAATGAAACTGAC
131 TACCTTCAATATATCCAATAGCGTTTTATCGATTTTGTCATAATGAAACCG-C
2303202 TTTGTCATATTTTTACCTGTTATATTGTTACGTATCGATACATGTTTATAAAGTATCGATACTTT
1 TTTGTCATATTTTTACCTGTTATATTGTTACGTATCGATACATGTTTATAAAGTATCGATACTTT
* *
2303267 ATAGACGCTATTAATGC-TTTTCTTTAAAATTCCATAAGTATCGATACTTATTTGAATAGAATCA
66 ATAGACGCTATTAA-ACTTTTTCTTTAAAATTCCATAAGTATCAATACTTATTTGAATAGAATCA
*** * * *
2303331 ATACCTTCAATATATCTGCTAGCGTTTTATCGATTTTGTCATATTGAACCCGG
130 ATACCTTCAATATATCCAATAGCGTTTTATCGATTTTGTCATAATGAAACCGC
* *
2303384 TTATGTCATATTTTTACCTGATATATTGTTATGTAT
1 TT-TGTCATATTTTTACCTGTTATATTGTTACGTAT
2303420 TAATACATAT
Statistics
Matches: 196, Mismatches: 19, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
182 140 0.71
183 56 0.29
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.45
Consensus pattern (182 bp):
TTTGTCATATTTTTACCTGTTATATTGTTACGTATCGATACATGTTTATAAAGTATCGATACTTT
ATAGACGCTATTAAACTTTTTCTTTAAAATTCCATAAGTATCAATACTTATTTGAATAGAATCAA
TACCTTCAATATATCCAATAGCGTTTTATCGATTTTGTCATAATGAAACCGC
Found at i:2307806 original size:50 final size:51
Alignment explanation
Indices: 2307744--2307848 Score: 203
Period size: 50 Copynumber: 2.1 Consensus size: 51
2307734 GAATGATTTA
2307744 AAATTTTCGAGTAAATCATGATTTTCAAAGTCTATGAGTACTTTAGTGATT
1 AAATTTTCGAGTAAATCATGATTTTCAAAGTCTATGAGTACTTTAGTGATT
2307795 AAATTTT-GAGTAAATCATGATTTTCAAAGTCTATGAGTACTTTAGTGATT
1 AAATTTTCGAGTAAATCATGATTTTCAAAGTCTATGAGTACTTTAGTGATT
2307845 AAAT
1 AAAT
2307849 GTGGTATTCG
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
50 47 0.87
51 7 0.13
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.41
Consensus pattern (51 bp):
AAATTTTCGAGTAAATCATGATTTTCAAAGTCTATGAGTACTTTAGTGATT
Found at i:2312370 original size:16 final size:16
Alignment explanation
Indices: 2312349--2312389 Score: 64
Period size: 16 Copynumber: 2.5 Consensus size: 16
2312339 TTTATTTATG
2312349 TTATTTTAAAATTAAA
1 TTATTTTAAAATTAAA
*
2312365 TTATTTTAAGATTAAA
1 TTATTTTAAAATTAAA
2312381 TTAATTTTA
1 TT-ATTTTA
2312390 GTTTATTGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 17 0.74
17 6 0.26
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (16 bp):
TTATTTTAAAATTAAA
Found at i:2315229 original size:16 final size:15
Alignment explanation
Indices: 2315206--2315248 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
2315196 AGTTACATTC
2315206 AAATTTTTTTATCTA
1 AAATTTTTTTATCTA
* *
2315221 AATATTTTTTATTTTTA
1 AA-ATTTTTT-TATCTA
2315238 AAATTTTTTTA
1 AAATTTTTTTA
2315249 GTTATAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 3 0.13
16 14 0.61
17 6 0.26
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (15 bp):
AAATTTTTTTATCTA
Found at i:2327016 original size:65 final size:64
Alignment explanation
Indices: 2326927--2327082 Score: 204
Period size: 65 Copynumber: 2.4 Consensus size: 64
2326917 TACACTTGGG
* * * * * *
2326927 GTGCATCGGTACACTAATTACATTCGATGTTTCAAAAGAGCCAGGAGTGCATCGATGCATAGTCT
1 GTGCATCGGTACACAAAATGCATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATCCAT-GGCT
* * **
2326992 GTGCATTGGTACACAAAATGCATTCGATGTTTCAATAGATTCAAGAGTGCATCGATCCATGGCT
1 GTGCATCGGTACACAAAATGCATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATCCATGGCT
*
2327056 ATGCATCGGTACACAAAATGCATTCGA
1 GTGCATCGGTACACAAAATGCATTCGA
2327083 AATAGGGTGT
Statistics
Matches: 79, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
64 28 0.35
65 51 0.65
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.28
Consensus pattern (64 bp):
GTGCATCGGTACACAAAATGCATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATCCATGGCT
Found at i:2327456 original size:13 final size:13
Alignment explanation
Indices: 2327423--2327456 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
2327413 TAAGATTTTC
2327423 TTTGAAAATCATT
1 TTTGAAAATCATT
*
2327436 TTT-TAAATCATT
1 TTTGAAAATCATT
2327448 TTTGAAAAT
1 TTTGAAAAT
2327457 TACTCCTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (13 bp):
TTTGAAAATCATT
Found at i:2329767 original size:44 final size:44
Alignment explanation
Indices: 2329708--2329814 Score: 142
Period size: 44 Copynumber: 2.4 Consensus size: 44
2329698 CGATGCACTG
* * * *
2329708 CATAGTGTATTGATGCACATTCAAGGCATGCGTCGGTGCACCTT
1 CATAGTGTATCGATGCACATTCAAGGCACGCATCGGTACACCTT
* * * *
2329752 CATAGTGTATCGATGCATATTCAAGGGACGCATCTGTACACTTT
1 CATAGTGTATCGATGCACATTCAAGGCACGCATCGGTACACCTT
2329796 CATAGTGTATCGATGCACA
1 CATAGTGTATCGATGCACA
2329815 ATGCAGAAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 54 1.00
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.30
Consensus pattern (44 bp):
CATAGTGTATCGATGCACATTCAAGGCACGCATCGGTACACCTT
Found at i:2333606 original size:23 final size:24
Alignment explanation
Indices: 2333576--2333620 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
2333566 GAGATTATTT
2333576 TCATTTTTCAATTTT-GAAATATA
1 TCATTTTTCAATTTTAGAAATATA
**
2333599 TCATTTTTGTATTTTAGAAATA
1 TCATTTTTCAATTTTAGAAATA
2333621 ATTTCTCATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (24 bp):
TCATTTTTCAATTTTAGAAATATA
Found at i:2335526 original size:65 final size:64
Alignment explanation
Indices: 2335413--2335568 Score: 190
Period size: 65 Copynumber: 2.4 Consensus size: 64
2335403 TACACTTGGG
* * * *
2335413 GTGCATCAGTACACTAATTACATTCGATGTTTCAAAAGAGCTAGGAGTGCATCGATGCATGGTCT
1 GTGCATCAGTACACAAAATGCATTCGATGTTTCAAAAGAGCTAAGAGTGCATCGATGCATGG-CT
* * *
2335478 GTGCATCGGTACACAAAATGCATTCGATGTTTCAATAA-A-TTCAAGAGTGCATCTATGCATGGC
1 GTGCATCAGTACACAAAATGCATTCGATGTTTCAA-AAGAGCT-AAGAGTGCATCGATGCATGGC
2335541 T
64 T
* *
2335542 ATGCATCAATACACAAAATGCATTCGA
1 GTGCATCAGTACACAAAATGCATTCGA
2335569 AATAGGGTGT
Statistics
Matches: 79, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
64 27 0.34
65 50 0.63
66 2 0.03
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (64 bp):
GTGCATCAGTACACAAAATGCATTCGATGTTTCAAAAGAGCTAAGAGTGCATCGATGCATGGCT
Found at i:2336911 original size:20 final size:20
Alignment explanation
Indices: 2336873--2336911 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2336863 GTCCCCAAAA
* **
2336873 ATACTTTTAGTATTGATACC
1 ATACATTTAGTATCAATACC
2336893 ATACATTTAGTATCAATAC
1 ATACATTTAGTATCAATAC
2336912 TCTTTTAAGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.41
Consensus pattern (20 bp):
ATACATTTAGTATCAATACC
Found at i:2337929 original size:22 final size:23
Alignment explanation
Indices: 2337879--2337996 Score: 71
Period size: 23 Copynumber: 5.1 Consensus size: 23
2337869 ACGCCGAAAT
2337879 ACCACATAGAAAT-TGCACCGAAGTG
1 ACCACATAGAAATGT-C-CCGAAG-G
2337904 -CCACATAG-AATGTCCCGAAGG
1 ACCACATAGAAATGTCCCGAAGG
* * * *
2337925 ACCACAAAGTATTGTCCTGAAGG
1 ACCACATAGAAATGTCCCGAAGG
*** **
2337948 ACCGTGTAGAAATGTCCCGAAAT
1 ACCACATAGAAATGTCCCGAAGG
*** *
2337971 ACCGTGTAGAAATGTTCCGAAGG
1 ACCACATAGAAATGTCCCGAAGG
2337994 ACC
1 ACC
2337997 GCGTAGAACC
Statistics
Matches: 75, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
21 1 0.01
22 13 0.17
23 52 0.69
24 9 0.12
ACGTcount: A:0.35, C:0.24, G:0.23, T:0.19
Consensus pattern (23 bp):
ACCACATAGAAATGTCCCGAAGG
Found at i:2337963 original size:23 final size:22
Alignment explanation
Indices: 2337937--2338004 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 22
2337927 CACAAAGTAT
2337937 TGTCCTGAAGGACCGTGTAGAAA
1 TGTCC-GAAGGACCGTGTAGAAA
**
2337960 TGTCCCGAAATACCGTGTAGAAA
1 TGT-CCGAAGGACCGTGTAGAAA
*
2337983 TGTTCCGAAGGACCGCGTAGAA
1 TG-TCCGAAGGACCGTGTAGAA
2338005 CCCTCGACTC
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
23 35 0.92
24 3 0.08
ACGTcount: A:0.31, C:0.21, G:0.28, T:0.21
Consensus pattern (22 bp):
TGTCCGAAGGACCGTGTAGAAA
Found at i:2343710 original size:22 final size:23
Alignment explanation
Indices: 2343685--2343778 Score: 68
Period size: 23 Copynumber: 4.2 Consensus size: 23
2343675 CATCGAAGTG
*
2343685 CCACATAG-AATATACCGAAGGA
1 CCACATAGAAATGTACCGAAGGA
*** *
2343707 CCACATAGTGTTGTCCCGAAGGA
1 CCACATAGAAATGTACCGAAGGA
* * *
2343730 CCGCATAGAAATGTCCCAAAGGA
1 CCACATAGAAATGTACCGAAGGA
* *
2343753 CCACGTAG-AAT-TATTCGAAGGA
1 CCACATAGAAATGTA-CCGAAGGA
2343775 CCAC
1 CCAC
2343779 GTACAACCCT
Statistics
Matches: 56, Mismatches: 14, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
21 1 0.02
22 21 0.38
23 34 0.61
ACGTcount: A:0.36, C:0.26, G:0.21, T:0.17
Consensus pattern (23 bp):
CCACATAGAAATGTACCGAAGGA
Found at i:2343729 original size:23 final size:23
Alignment explanation
Indices: 2343685--2343762 Score: 77
Period size: 23 Copynumber: 3.4 Consensus size: 23
2343675 CATCGAAGTG
* *
2343685 CCACATAG-AATATACCGAAGGA
1 CCACATAGAAATGTCCCGAAGGA
***
2343707 CCACATAGTGTTGTCCCGAAGGA
1 CCACATAGAAATGTCCCGAAGGA
* *
2343730 CCGCATAGAAATGTCCCAAAGGA
1 CCACATAGAAATGTCCCGAAGGA
*
2343753 CCACGTAGAA
1 CCACATAGAA
2343763 TTATTCGAAG
Statistics
Matches: 44, Mismatches: 11, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
22 8 0.18
23 36 0.82
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (23 bp):
CCACATAGAAATGTCCCGAAGGA
Found at i:2344771 original size:19 final size:20
Alignment explanation
Indices: 2344747--2344785 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2344737 AATTTGATTC
2344747 TAAAAA-TGGTACCGATACT
1 TAAAAATTGGTACCGATACT
*
2344766 TAAAAATTGGTATCGATACT
1 TAAAAATTGGTACCGATACT
2344786 ATTTGAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (20 bp):
TAAAAATTGGTACCGATACT
Found at i:2345752 original size:12 final size:12
Alignment explanation
Indices: 2345737--2345769 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
2345727 GCTTAAAAAA
2345737 CACCCTAAAATT
1 CACCCTAAAATT
2345749 CACCCTAAAATT
1 CACCCTAAAATT
2345761 CACCCTAAA
1 CACCCTAAA
2345770 CACTTATGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.42, C:0.36, G:0.00, T:0.21
Consensus pattern (12 bp):
CACCCTAAAATT
Found at i:2349918 original size:12 final size:12
Alignment explanation
Indices: 2349898--2349967 Score: 52
Period size: 12 Copynumber: 5.8 Consensus size: 12
2349888 GATACATTAC
*
2349898 CTGAATTCTGTT
1 CTGATTTCTGTT
**
2349910 CTGATTTCTAAT
1 CTGATTTCTGTT
2349922 CTGGA-TTCTGTT
1 CT-GATTTCTGTT
* *
2349934 CTGATATCTGAT
1 CTGATTTCTGTT
* *
2349946 ATGAATTCTGTT
1 CTGATTTCTGTT
*
2349958 TTGATTTCTG
1 CTGATTTCTG
2349968 ATATCTCCAT
Statistics
Matches: 43, Mismatches: 13, Indels: 4
0.72 0.22 0.07
Matches are distributed among these distances:
11 2 0.05
12 39 0.91
13 2 0.05
ACGTcount: A:0.19, C:0.14, G:0.17, T:0.50
Consensus pattern (12 bp):
CTGATTTCTGTT
Found at i:2349929 original size:24 final size:24
Alignment explanation
Indices: 2349899--2349971 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
2349889 ATACATTACC
*
2349899 TGAATTCTGTTCTGATTTCTAATC
1 TGAATTCTGTTCTGATTTCTAATA
* * *
2349923 TGGATTCTGTTCTGATATCTGATA
1 TGAATTCTGTTCTGATTTCTAATA
* *
2349947 TGAATTCTGTTTTGATTTCTGATA
1 TGAATTCTGTTCTGATTTCTAATA
2349971 T
1 T
2349972 CTCCATTTAC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.21, C:0.12, G:0.16, T:0.51
Consensus pattern (24 bp):
TGAATTCTGTTCTGATTTCTAATA
Found at i:2349932 original size:48 final size:48
Alignment explanation
Indices: 2349861--2349966 Score: 117
Period size: 48 Copynumber: 2.2 Consensus size: 48
2349851 AAATATTTTA
* * *
2349861 TCTGATTTCTGACTTGAATTCTGTTATGATA-CATTACCTGAATTCTGT
1 TCTGATTTCTAACTTGAATTCTGTTATGATATC-TGACATGAATTCTGT
* * *
2349909 TCTGATTTCTAA-TCTGGATTCTGTTCTGATATCTGATATGAATTCTGT
1 TCTGATTTCTAACT-TGAATTCTGTTATGATATCTGACATGAATTCTGT
*
2349957 TTTGATTTCT
1 TCTGATTTCT
2349967 GATATCTCCA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
47 1 0.02
48 47 0.96
49 1 0.02
ACGTcount: A:0.21, C:0.15, G:0.15, T:0.49
Consensus pattern (48 bp):
TCTGATTTCTAACTTGAATTCTGTTATGATATCTGACATGAATTCTGT
Found at i:2352149 original size:18 final size:18
Alignment explanation
Indices: 2352109--2352150 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
2352099 GTCATAACCC
*
2352109 GACCCGACCCGACCCATT
1 GACCCGACCCGAACCATT
* *
2352127 TACCCGACCCGAACCGTT
1 GACCCGACCCGAACCATT
2352145 GACCCG
1 GACCCG
2352151 TTGACCGTTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.48, G:0.19, T:0.12
Consensus pattern (18 bp):
GACCCGACCCGAACCATT
Found at i:2352159 original size:15 final size:15
Alignment explanation
Indices: 2352139--2352191 Score: 88
Period size: 15 Copynumber: 3.5 Consensus size: 15
2352129 CCCGACCCGA
**
2352139 ACCGTTGACCCGTTG
1 ACCGTTGAAACGTTG
2352154 ACCGTTGAAACGTTG
1 ACCGTTGAAACGTTG
2352169 ACCGTTGAAACGTTG
1 ACCGTTGAAACGTTG
2352184 ACCGTTGA
1 ACCGTTGA
2352192 CCGGCGTTGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.23, C:0.25, G:0.26, T:0.26
Consensus pattern (15 bp):
ACCGTTGAAACGTTG
Found at i:2352160 original size:7 final size:7
Alignment explanation
Indices: 2352139--2352194 Score: 67
Period size: 7 Copynumber: 7.6 Consensus size: 7
2352129 CCCGACCCGA
2352139 ACCGTTG
1 ACCGTTG
2352146 ACCCGTTG
1 A-CCGTTG
2352154 ACCGTTG
1 ACCGTTG
*
2352161 AAACGTTG
1 -ACCGTTG
2352169 ACCGTTG
1 ACCGTTG
*
2352176 AAACGTTG
1 -ACCGTTG
2352184 ACCGTTG
1 ACCGTTG
2352191 ACCG
1 ACCG
2352195 GCGTTGACCA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
7 23 0.55
8 19 0.45
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.25
Consensus pattern (7 bp):
ACCGTTG
Found at i:2354696 original size:12 final size:12
Alignment explanation
Indices: 2354676--2354745 Score: 52
Period size: 12 Copynumber: 5.8 Consensus size: 12
2354666 GATACATTAC
*
2354676 CTGAATTCTGTT
1 CTGATTTCTGTT
*
2354688 CTGATTTCTGAT
1 CTGATTTCTGTT
*
2354700 CTGGA-TTATGTT
1 CT-GATTTCTGTT
* *
2354712 CTGATATCTGAT
1 CTGATTTCTGTT
* *
2354724 ATGAATTCTGTT
1 CTGATTTCTGTT
*
2354736 TTGATTTCTG
1 CTGATTTCTG
2354746 ATATCTCCGT
Statistics
Matches: 43, Mismatches: 13, Indels: 4
0.72 0.22 0.07
Matches are distributed among these distances:
11 2 0.05
12 39 0.91
13 2 0.05
ACGTcount: A:0.19, C:0.13, G:0.19, T:0.50
Consensus pattern (12 bp):
CTGATTTCTGTT
Found at i:2354711 original size:24 final size:24
Alignment explanation
Indices: 2354677--2354749 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
2354667 ATACATTACC
* *
2354677 TGAATTCTGTTCTGATTTCTGATC
1 TGAATTATGTTCTGATTTCTGATA
* *
2354701 TGGATTATGTTCTGATATCTGATA
1 TGAATTATGTTCTGATTTCTGATA
* *
2354725 TGAATTCTGTTTTGATTTCTGATA
1 TGAATTATGTTCTGATTTCTGATA
2354749 T
1 T
2354750 CTCCGTTTAC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.21, C:0.11, G:0.18, T:0.51
Consensus pattern (24 bp):
TGAATTATGTTCTGATTTCTGATA
Found at i:2354717 original size:48 final size:49
Alignment explanation
Indices: 2354639--2354747 Score: 125
Period size: 48 Copynumber: 2.3 Consensus size: 49
2354629 AAATATTTTA
* * *
2354639 TCTGATTTCTGA-CTTGAATTCTGTTATGATA-CATTACCTGAATTCTGT
1 TCTGATTTCTGATCTTGAATTATGTTATGATATC-TGACATGAATTCTGT
* * *
2354687 TCTGATTTCTGATC-TGGATTATGTTCTGATATCTGATATGAATTCTGT
1 TCTGATTTCTGATCTTGAATTATGTTATGATATCTGACATGAATTCTGT
*
2354735 TTTGATTTCTGAT
1 TCTGATTTCTGAT
2354748 ATCTCCGTTT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
48 50 0.96
49 2 0.04
ACGTcount: A:0.21, C:0.14, G:0.17, T:0.49
Consensus pattern (49 bp):
TCTGATTTCTGATCTTGAATTATGTTATGATATCTGACATGAATTCTGT
Found at i:2354915 original size:2 final size:2
Alignment explanation
Indices: 2354908--2354958 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
2354898 ACGGATGGGG
2354908 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2354950 TA TA TA TA T
1 TA TA TA TA T
2354959 GTTTTAAAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2356015 original size:19 final size:19
Alignment explanation
Indices: 2355977--2356043 Score: 53
Period size: 19 Copynumber: 3.3 Consensus size: 19
2355967 TTAAAATAGA
* * *
2355977 AATATTAAAAAAGTATATT
1 AATATTAAAATATTAAATT
2355996 AATATTAAAATATTAAATT
1 AATATTAAAATATTAAATT
* *
2356015 ATAGTTTTAAAATTTATAAATAT
1 A-A-TATTAAAATAT-TAAAT-T
2356038 AATATT
1 AATATT
2356044 TTAGAAGTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
19 17 0.45
20 1 0.03
21 12 0.32
22 6 0.16
23 2 0.05
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (19 bp):
AATATTAAAATATTAAATT
Found at i:2356227 original size:21 final size:21
Alignment explanation
Indices: 2356201--2356248 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
2356191 AATGTTAATA
2356201 AACTTAATACTTGCACAAACC
1 AACTTAATACTTGCACAAACC
*
2356222 AACTTAATACTTGCACAAACT
1 AACTTAATACTTGCACAAACC
2356243 AACTTA
1 AACTTA
2356249 CCTCAGTAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.44, C:0.25, G:0.04, T:0.27
Consensus pattern (21 bp):
AACTTAATACTTGCACAAACC
Found at i:2375882 original size:43 final size:43
Alignment explanation
Indices: 2375817--2376106 Score: 390
Period size: 43 Copynumber: 6.8 Consensus size: 43
2375807 TTAATTACCG
* *
2375817 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTTCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
* *
2375860 TTACAGTTTCCCCAGGTTCCTTTGTTGTGCGCAAGGGTAAGCC
1 TTACAGTTTCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
* *
2375903 TTACAG-TT-CCCAGTTTCTTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTTCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
* **
2375944 TTACAGTTCCCCCAGGCCCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTTCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
* *
2375987 TTACCA-TTTCCCCAGGTTCCTTTGTTATGTGCAAGGGTAAGCC
1 TTA-CAGTTTCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
* *
2376030 TTACAGTTT-CCCAGGTTCTTTTGCTGTGTGCAAGGGTAAGCT
1 TTACAGTTTCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
* * * *
2376072 TTACAGTTTCCCCAGGCTCTTTTGCTATGTACAAG
1 TTACAGTTTCCCCAGGTTCCTTTGCTGTGTGCAAG
2376107 TATAAGACCT
Statistics
Matches: 217, Mismatches: 25, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
41 35 0.16
42 43 0.20
43 137 0.63
44 2 0.01
ACGTcount: A:0.17, C:0.26, G:0.24, T:0.33
Consensus pattern (43 bp):
TTACAGTTTCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
Found at i:2375966 original size:84 final size:84
Alignment explanation
Indices: 2375817--2376106 Score: 375
Period size: 84 Copynumber: 3.4 Consensus size: 84
2375807 TTAATTACCG
* * *
2375817 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTT
1 TTACAGTT-CCCCAGGTTCTTTTGCTATGTGCAAGGGTAAGCCTTACAG-TTCCCCAGGTTCCTT
* *
2375882 TGTTGTGCGCAAGGGTAAGCC
64 TGCTGTGTGCAAGGGTAAGCC
* * **
2375903 TTACAGTT-CCCAGTTTCTTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTCCCCCAGGCCCCTTT
1 TTACAGTTCCCCAGGTTCTTTTGCTATGTGCAAGGGTAAGCCTTACAGTT-CCCCAGGTTCCTTT
2375967 GCTGTGTGCAAGGGTAAGCC
65 GCTGTGTGCAAGGGTAAGCC
* * * * *
2375987 TTACCATTTCCCCAGGTTCCTTTGTTATGTGCAAGGGTAAGCCTTACAGTTTCCCAGGTTCTTTT
1 TTA-CAGTTCCCCAGGTTCTTTTGCTATGTGCAAGGGTAAGCCTTACAGTTCCCCAGGTTCCTTT
*
2376052 GCTGTGTGCAAGGGTAAGCT
65 GCTGTGTGCAAGGGTAAGCC
* *
2376072 TTACAGTTTCCCCAGGCTCTTTTGCTATGTACAAG
1 TTACAG-TTCCCCAGGTTCTTTTGCTATGTGCAAG
2376107 TATAAGACCT
Statistics
Matches: 178, Mismatches: 22, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
83 2 0.01
84 71 0.40
85 60 0.34
86 45 0.25
ACGTcount: A:0.17, C:0.26, G:0.24, T:0.33
Consensus pattern (84 bp):
TTACAGTTCCCCAGGTTCTTTTGCTATGTGCAAGGGTAAGCCTTACAGTTCCCCAGGTTCCTTTG
CTGTGTGCAAGGGTAAGCC
Found at i:2378127 original size:18 final size:18
Alignment explanation
Indices: 2378104--2378142 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
2378094 ACCGGTCATA
2378104 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
2378122 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
2378140 ACC
1 ACC
2378143 GGCGTTGACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.18, C:0.51, G:0.21, T:0.10
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:2380978 original size:43 final size:43
Alignment explanation
Indices: 2380917--2381250 Score: 474
Period size: 43 Copynumber: 7.8 Consensus size: 43
2380907 TTAATTACCG
* *
2380917 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAATGGTAAGCC
1 TTACAGTTCCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
*
2380960 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTCCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
**
2381003 TTACAGTTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTCCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
* * * * *
2381046 TTACAGTT-TCCTAGGTTCTTTTGCTATTTGCAAGGGTAAGCC
1 TTACAGTTCCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
*
2381088 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTCCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
* *
2381131 TTACAGTTTCCCCAGGTTCCTTTGTTGTGTGCAAGGGTAAGCC
1 TTACAGTTCCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
* *
2381174 TTACAGTT-TCCCAGGTTCTTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTCCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
* * * * *
2381216 TTACAGTTTCCCCAAGCTCTTTTGCTATGTGCAAG
1 TTACAGTTCCCCCAGGTTCCTTTGCTGTGTGCAAG
2381251 TATAAGACCT
Statistics
Matches: 265, Mismatches: 24, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
42 77 0.29
43 188 0.71
ACGTcount: A:0.17, C:0.25, G:0.24, T:0.34
Consensus pattern (43 bp):
TTACAGTTCCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
Found at i:2381110 original size:85 final size:86
Alignment explanation
Indices: 2380917--2381250 Score: 492
Period size: 85 Copynumber: 3.9 Consensus size: 86
2380907 TTAATTACCG
* * *
2380917 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAATGGTAAGCCTTACAGTTCCCCCAGGTCCCTT
1 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTT
*
2380982 TGCTGTGTGCAAGGGTAAGCC
66 TGCTATGTGCAAGGGTAAGCC
** * * *
2381003 TTACAGTTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTT-CCTAGGTTCTTT
1 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTT
*
2381067 TGCTATTTGCAAGGGTAAGCC
66 TGCTATGTGCAAGGGTAAGCC
2381088 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTT
1 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTT
* *
2381153 TGTTGTGTGCAAGGGTAAGCC
66 TGCTATGTGCAAGGGTAAGCC
* * * * * *
2381174 TTACAGTT-TCCCAGGTTCTTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAAGCTCTTT
1 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTT
2381238 TGCTATGTGCAAG
66 TGCTATGTGCAAG
2381251 TATAAGACCT
Statistics
Matches: 221, Mismatches: 26, Indels: 3
0.88 0.10 0.01
Matches are distributed among these distances:
85 138 0.62
86 83 0.38
ACGTcount: A:0.17, C:0.25, G:0.24, T:0.34
Consensus pattern (86 bp):
TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTT
TGCTATGTGCAAGGGTAAGCC
Found at i:2381250 original size:128 final size:128
Alignment explanation
Indices: 2380917--2381229 Score: 527
Period size: 128 Copynumber: 2.4 Consensus size: 128
2380907 TTAATTACCG
* * * *
2380917 TTACAGTTCCCCCAGGTCCCTTTGCTGTGTGCAATGGTAAGCCTTACAGTTCCCCCAGGTCCCTT
1 TTACAGTT-TCCCAGGTTCTTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTCCCCCAGGTCCCTT
*
2380982 TGCTGTGTGCAAGGGTAAGCCTTACAGTTTTCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
65 TGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
* * *
2381046 TTACAGTTTCCTAGGTTCTTTTGCTATTTGCAAGGGTAAGCCTTACAGTTCCCCCAGGTCCCTTT
1 TTACAGTTTCCCAGGTTCTTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTCCCCCAGGTCCCTTT
*
2381111 GCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGTTGTGTGCAAGGGTAAGCC
66 GCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
*
2381174 TTACAGTTTCCCAGGTTCTTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCA
1 TTACAGTTTCCCAGGTTCTTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTCCCCCA
2381230 AGCTCTTTTG
Statistics
Matches: 171, Mismatches: 13, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
128 163 0.95
129 8 0.05
ACGTcount: A:0.17, C:0.26, G:0.24, T:0.33
Consensus pattern (128 bp):
TTACAGTTTCCCAGGTTCTTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTCCCCCAGGTCCCTTT
GCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCC
Found at i:2389723 original size:2 final size:2
Alignment explanation
Indices: 2389716--2389740 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2389706 TATCATACGA
2389716 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 A
2389741 AACAACAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2395312 original size:30 final size:30
Alignment explanation
Indices: 2395246--2395317 Score: 99
Period size: 30 Copynumber: 2.4 Consensus size: 30
2395236 TAATGAATAT
* * *
2395246 TTAATTCAGAATAATTAAATAAGATTTTAT
1 TTAATTTAAAATAATTAAATAAGATTTTAA
* *
2395276 TTAATTTGAAATAATTAAATTAGATTTTAA
1 TTAATTTAAAATAATTAAATAAGATTTTAA
2395306 TTAATTTAAAAT
1 TTAATTTAAAAT
2395318 TACAAACCCT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.47, C:0.01, G:0.06, T:0.46
Consensus pattern (30 bp):
TTAATTTAAAATAATTAAATAAGATTTTAA
Found at i:2399365 original size:30 final size:31
Alignment explanation
Indices: 2399319--2399391 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 31
2399309 TCTACAAGCC
* * ** *
2399319 TTAGAAAAATTTAGGGACCATTTTA-TAATT
1 TTAGAAAAGTTAAGGGACCAAATTAGAAATT
*
2399349 TTTGAAAAGTTAAGGGACCAAATTAGAAATT
1 TTAGAAAAGTTAAGGGACCAAATTAGAAATT
2399380 TTAGAAAAGTTA
1 TTAGAAAAGTTA
2399392 TGGGTTATTC
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
30 20 0.57
31 15 0.43
ACGTcount: A:0.44, C:0.05, G:0.16, T:0.34
Consensus pattern (31 bp):
TTAGAAAAGTTAAGGGACCAAATTAGAAATT
Found at i:2400872 original size:21 final size:20
Alignment explanation
Indices: 2400834--2400873 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2400824 ATTATTATAT
*
2400834 GTTTTAAATATTATATGTTG
1 GTTTTAAATATTAAATGTTG
*
2400854 GTTTTAAGTGATTAAATGTT
1 GTTTTAAAT-ATTAAATGTT
2400874 TTTATAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (20 bp):
GTTTTAAATATTAAATGTTG
Found at i:2404819 original size:29 final size:29
Alignment explanation
Indices: 2404776--2404845 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
2404766 TTTTAATGAA
2404776 TATTTAACTTAAAATAATTAAA-AAGATTT
1 TATTTAA-TTAAAATAATTAAATAAGATTT
*
2404805 TATTTAATTAGAAATAATTAAATTAGATTT
1 TATTTAATTA-AAATAATTAAATAAGATTT
*
2404835 TAATTAATTAA
1 TATTTAATTAA
2404846 CAATTACAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
28 3 0.08
29 19 0.51
30 15 0.41
ACGTcount: A:0.50, C:0.01, G:0.04, T:0.44
Consensus pattern (29 bp):
TATTTAATTAAAATAATTAAATAAGATTT
Found at i:2407055 original size:23 final size:23
Alignment explanation
Indices: 2407029--2407076 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
2407019 ATAAAGTACA
*
2407029 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
2407052 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
2407075 AT
1 AT
2407077 TGACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:2407587 original size:23 final size:23
Alignment explanation
Indices: 2407552--2407624 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
2407542 ATACTTTACA
*
2407552 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
2407575 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
* *
2407598 ATATAAGTGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
2407621 ATAT
1 ATAT
2407625 TTTTACCTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:2408021 original size:23 final size:23
Alignment explanation
Indices: 2407991--2408063 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
2407981 ATACTTTACA
*
2407991 ATATAAACACTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
2408014 ATATAAACGCTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
* *
2408037 ATATAAGCGCTACCTATTACATC
1 ATATAAACGCTACCTATTACATT
2408060 ATAT
1 ATAT
2408064 TTTTACCTAT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.40, C:0.22, G:0.04, T:0.34
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:2408514 original size:23 final size:23
Alignment explanation
Indices: 2408479--2408551 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
2408469 ACACTTTACA
*
2408479 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
2408502 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
2408525 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
2408548 ATAT
1 ATAT
2408552 TTTTACCTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:2408595 original size:22 final size:22
Alignment explanation
Indices: 2408569--2408613 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2408559 TATTATATTG
*
2408569 AAAATGTCCATACTTTTTATAA
1 AAAATATCCATACTTTTTATAA
* *
2408591 AAAATATCGATACTTTTTTTAA
1 AAAATATCCATACTTTTTATAA
2408613 A
1 A
2408614 GTTATGTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.42, C:0.11, G:0.04, T:0.42
Consensus pattern (22 bp):
AAAATATCCATACTTTTTATAA
Found at i:2408801 original size:488 final size:490
Alignment explanation
Indices: 2407885--2408838 Score: 1788
Period size: 488 Copynumber: 2.0 Consensus size: 490
2407875 TGTTTTTAAT
2407885 TTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAA
1 TTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAA
*
2407950 AAAAGTATGGACACTTTTATAAAAAGGATAGATACTTTACAATATAAACACTACCTATTACATTA
66 AAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATATAAACACTACCTATTACATTA
2408015 TATAAACGCTACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATT
131 TATAAACGCTACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATT
* *
2408080 GAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTATTTTTAAAGTTATGTAATTTATGTTTC
196 GAAAATGTCCATACTTTTTATAAAAAAGATCGATACTATTTTTAAAGTTATGTAATTTATGTTTC
*
2408145 AATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACA
261 AATTTTTTTTAATAGTATTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACA
*
2408210 AAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTATAATTTAAATTTAACAATATTA
326 AAAAATTATTTGATTATTTTGATATTTTATAAAATAATATTTATAATTTAAATTTAACAATATTA
*
2408275 ACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAAT-ATA-ATAT
391 ACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATAC
2408338 CGTAACGTAAAAAATAAATCATTAGACGCCTATAA
456 CGTAACGTAAAAAATAAATCATTAGACGCCTATAA
2408373 TTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAA
1 TTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAA
*
2408438 AAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATATAAGCACTACCTATTACATTA
66 AAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATATAAACACTACCTATTACATTA
2408503 TATAAACGCTACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATT
131 TATAAACGCTACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATT
* *
2408568 GAAAATGTCCATACTTTTTATAAAAAATATCGATACTTTTTTTAAAGTTATGTAATTTATGTTTC
196 GAAAATGTCCATACTTTTTATAAAAAAGATCGATACTATTTTTAAAGTTATGTAATTTATGTTTC
2408633 AATTTTTTTTAATAGTATTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACA
261 AATTTTTTTTAATAGTATTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACA
*
2408698 AAAAATTATTTGATTATTTTGATATTTTATAAAATATTATTTAGT-ATTTAAATTTAACAATATT
326 AAAAATTATTTGATTATTTTGATATTTTATAAAATAATATTTA-TAATTTAAATTTAACAATATT
2408762 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
390 AACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATA
2408827 CCGTAACGTAAA
455 CCGTAACGTAAA
2408839 GACTAGAGTC
Statistics
Matches: 453, Mismatches: 10, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
488 435 0.96
489 4 0.01
490 14 0.03
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.41
Consensus pattern (490 bp):
TTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAA
AAAAGTATGGACACTTTTATAAAAAGGATAGACACTTTACAATATAAACACTACCTATTACATTA
TATAAACGCTACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATT
GAAAATGTCCATACTTTTTATAAAAAAGATCGATACTATTTTTAAAGTTATGTAATTTATGTTTC
AATTTTTTTTAATAGTATTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACA
AAAAATTATTTGATTATTTTGATATTTTATAAAATAATATTTATAATTTAAATTTAACAATATTA
ACCAAAGATAATAATAAATATGTAATATATATGTTTATTGTTTTTAATTTAATAATAATATATAC
CGTAACGTAAAAAATAAATCATTAGACGCCTATAA
Found at i:2411284 original size:183 final size:183
Alignment explanation
Indices: 2410976--2411913 Score: 1698
Period size: 183 Copynumber: 5.1 Consensus size: 183
2410966 TACTTAAAAT
**
2410976 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAATTGGTATA
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
2411041 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
*
2411106 CGACACTTTTTGACAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
131 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
* *
2411159 TACCGACACAATATTAAAAAGTGTCGATATAGATTGTAGACCTATTTGCTCATAAAACCGGTATA
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
2411224 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
* * *
2411289 CAACACTTTTTGATATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
131 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
*
2411342 TACCCACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
*
2411407 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATTT
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
2411472 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
131 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
*
2411525 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCGATTCGCTCATAAAACCGGTATA
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
*
2411590 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTTCGATGTGTAAATGT
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
* *
2411655 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCTAATATGGACATAAAG
131 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
* * *
2411708 TACCCACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTTATAAAATCGGTATA
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
2411773 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
*
2411838 CGACAC-TTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAG
131 CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
*
2411890 TACAGACACAATATTAAAAAGTGT
1 TACCGACACAATATTAAAAAGTGT
2411914 GAAAACTTTG
Statistics
Matches: 724, Mismatches: 31, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
182 65 0.09
183 659 0.91
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (183 bp):
TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
CGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
Found at i:2413131 original size:3 final size:3
Alignment explanation
Indices: 2413123--2413213 Score: 92
Period size: 3 Copynumber: 30.3 Consensus size: 3
2413113 ACTTGTTTGG
* * * * *
2413123 ATC ATC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GTC AGC TTC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * * * *
2413171 ATC GTC ATC ATC ATC GTC ATC TTC ATC GTC ATC TTC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
2413214 GCTTCATCTT
Statistics
Matches: 68, Mismatches: 20, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.24, C:0.33, G:0.07, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:2413140 original size:12 final size:12
Alignment explanation
Indices: 2413123--2413226 Score: 109
Period size: 12 Copynumber: 8.7 Consensus size: 12
2413113 ACTTGTTTGG
*
2413123 ATCATCATCATC
1 ATCATCATCTTC
*
2413135 ATCATCATCATC
1 ATCATCATCTTC
*
2413147 GTCATCATCTTC
1 ATCATCATCTTC
* *
2413159 ATCGTCAGCTTC
1 ATCATCATCTTC
* *
2413171 ATCGTCATCATC
1 ATCATCATCTTC
*
2413183 ATCGTCATCTTC
1 ATCATCATCTTC
*
2413195 ATCGTCATCTTC
1 ATCATCATCTTC
*
2413207 ATCATCAGCTTC
1 ATCATCATCTTC
*
2413219 ATCTTCAT
1 ATCATCAT
2413227 TGACCGCTTG
Statistics
Matches: 80, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 80 1.00
ACGTcount: A:0.23, C:0.33, G:0.07, T:0.38
Consensus pattern (12 bp):
ATCATCATCTTC
Found at i:2415228 original size:200 final size:200
Alignment explanation
Indices: 2414749--2415446 Score: 1216
Period size: 200 Copynumber: 3.5 Consensus size: 200
2414739 TTATATAGCA
*
2414749 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACCTATTACATTATACTT
1 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTT
* * *
2414814 ATGGGTTTTGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATTGTTGCACCC
66 TTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCC
* * *
2414879 TGTTTGCCATTCATTCTGGACCAAAAATATCGACCCAAACTAAAAAGAGTGTCGACATATTATTT
131 TGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAA-AGTGTCGACACATTATTT
2414944 AGACCT
195 AGACCT
*
2414950 ATTATCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTT
1 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTT
*
2415015 TTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTACGGTTGCACCC
66 TTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCC
2415080 TGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGACACATTATTTA
131 TGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGACACATTATTTA
*
2415145 GACAT
196 GACCT
2415150 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTT
1 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTT
* *
2415215 TTGGTTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCAGCC
66 TTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCC
* * *
2415280 TGTTTGCCATTCATTCTGGACCAGAAATATCGACACAAAGTACAAAAGTGTCGATACATTATTTA
131 TGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGACACATTATTTA
2415345 GACCT
196 GACCT
* * *
2415350 ATTCTCTCATAAAACCGGTATACTTGCACCGATTAGATTGAAAAATTACCTATTACATTATACTT
1 ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTT
*
2415415 TTGGGTTTCGATGTTTTTGGGATCGACACTTT
66 TTGGGTTTCGATGTTTATGGGATCGACACTTT
2415447 ATGGTTGCAC
Statistics
Matches: 474, Mismatches: 23, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
200 306 0.65
201 168 0.35
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (200 bp):
ATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTT
TTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCC
TGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACTACAAAAGTGTCGACACATTATTTA
GACCT
Found at i:2415592 original size:18 final size:18
Alignment explanation
Indices: 2415569--2415629 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
2415559 TCTCATTCAT
*
2415569 AATTATATTCACATACAA
1 AATTATAATCACATACAA
**
2415587 AATTATAAATCGTATACAA
1 AATTAT-AATCACATACAA
**
2415606 AATTATAAATCTTATACAA
1 AATTAT-AATCACATACAA
2415625 AATTA
1 AATTA
2415630 ACCCTACATT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
18 6 0.16
19 32 0.84
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.34
Consensus pattern (18 bp):
AATTATAATCACATACAA
Found at i:2415605 original size:19 final size:19
Alignment explanation
Indices: 2415581--2415629 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
2415571 TTATATTCAC
2415581 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
2415600 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
2415619 ATACAAAATTA
1 ATACAAAATTA
2415630 ACCCTACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:2417448 original size:25 final size:25
Alignment explanation
Indices: 2417420--2417477 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
2417410 CATCTTAATA
*
2417420 TCACCCCTTAACACCCCAACTTCTT
1 TCACCACTTAACACCCCAACTTCTT
* * *
2417445 TCACCACTTCACACCTCTACTTCTT
1 TCACCACTTAACACCCCAACTTCTT
2417470 TCACCACT
1 TCACCACT
2417478 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.22, C:0.47, G:0.00, T:0.31
Consensus pattern (25 bp):
TCACCACTTAACACCCCAACTTCTT
Found at i:2417536 original size:21 final size:21
Alignment explanation
Indices: 2417511--2417575 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
2417501 CCCTTTATGC
* *
2417511 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
2417532 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
2417553 CTATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
2417574 CT
1 CT
2417576 TGATTGTCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.17, C:0.31, G:0.11, T:0.42
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:2419814 original size:17 final size:18
Alignment explanation
Indices: 2419792--2419834 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
2419782 ATATATCCGG
2419792 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
2419809 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
2419829 TATCAT
1 TATCAT
2419835 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:2419852 original size:20 final size:19
Alignment explanation
Indices: 2419797--2419843 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
2419787 TCCGGTATCA
2419797 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
2419816 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
2419837 TTTTACC
1 TTTTACC
2419844 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:2420005 original size:20 final size:20
Alignment explanation
Indices: 2419978--2420024 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
2419968 TACGGTAACG
2419978 TTTTACCGGTTTTATCAT-T
1 TTTTACCGGTTTTATCATAT
2419997 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
2420018 TTTTACC
1 TTTTACC
2420025 TAGTATATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:2420068 original size:181 final size:181
Alignment explanation
Indices: 2419764--2420236 Score: 707
Period size: 181 Copynumber: 2.6 Consensus size: 181
2419754 CGTACTTACG
* *
2419764 AAAGTATCGACACTTTCAATATATCCGGTATCATTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
2419829 TATCATATTTTTACCTGTTATATCGTTGTGGATTGATATATATTTTTAAAGTATCGACACATTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATATAT-TTTTTAAAGTATCGACACATTAT
*
2419894 AGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
130 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* * *
2419945 AAAGTATCAACACTTTCAATATATACGGTAACGTTTTACCGGTTTTATCATTTTGTTACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
2420010 TATCATATTTTTACCTAG-TATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTA
66 TATCATATTTTTACCT-GTTATATCGTTTTGGATCGATATATTTTTT-AAAGTATCGACACATTA
** *
2420074 TAGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
129 TAGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* * * * * **
2420127 AAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTTACCGGTTTTATCATTTCAATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
2420192 TGTCATAGTTTTACCTGTTATATCGTTTTGGATCGATATATTTTT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATATATTTTT
2420237 AATTTAGATC
Statistics
Matches: 262, Mismatches: 26, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
180 5 0.02
181 160 0.61
182 97 0.37
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.42
Consensus pattern (181 bp):
AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATATATTTTTTAAAGTATCGACACATTATA
GGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
Found at i:2427836 original size:7 final size:7
Alignment explanation
Indices: 2427821--2427872 Score: 54
Period size: 7 Copynumber: 7.6 Consensus size: 7
2427811 ATGAGCATTC
*
2427821 AAAATAA
1 AAAAGAA
2427828 AAAAG-A
1 AAAAGAA
2427834 AAAAGTAA
1 AAAAG-AA
2427842 AAAA-AA
1 AAAAGAA
*
2427848 AAGAGAA
1 AAAAGAA
*
2427855 AAAAGAG
1 AAAAGAA
2427862 AAAAGAA
1 AAAAGAA
2427869 AAAA
1 AAAA
2427873 ATAGAATCAA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
6 11 0.30
7 21 0.57
8 5 0.14
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.04
Consensus pattern (7 bp):
AAAAGAA
Found at i:2427842 original size:14 final size:13
Alignment explanation
Indices: 2427821--2427872 Score: 61
Period size: 14 Copynumber: 3.8 Consensus size: 13
2427811 ATGAGCATTC
*
2427821 AAAATAAAAAAGA
1 AAAAGAAAAAAGA
2427834 AAAAGTAAAAAA-A
1 AAAAG-AAAAAAGA
2427847 AAAGAGAAAAAAGA
1 AAA-AGAAAAAAGA
2427861 GAAAAGAAAAAA
1 -AAAAGAAAAAA
2427873 ATAGAATCAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
13 14 0.41
14 17 0.50
15 3 0.09
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.04
Consensus pattern (13 bp):
AAAAGAAAAAAGA
Found at i:2427878 original size:15 final size:16
Alignment explanation
Indices: 2427826--2427878 Score: 53
Period size: 14 Copynumber: 3.6 Consensus size: 16
2427816 CATTCAAAAT
*
2427826 AAAAA-AGAAAA-AGT
1 AAAAAGAGAAAAGAGA
2427840 AAAAA-A-AAAAGAGA
1 AAAAAGAGAAAAGAGA
2427854 AAAAAGAGAAAAGA-A
1 AAAAAGAGAAAAGAGA
*
2427869 AAAAATAGAA
1 AAAAAGAGAA
2427879 TCAAAATGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
13 4 0.12
14 13 0.38
15 11 0.32
16 6 0.18
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (16 bp):
AAAAAGAGAAAAGAGA
Found at i:2435826 original size:26 final size:25
Alignment explanation
Indices: 2435783--2435832 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
2435773 TAATTCCATT
**
2435783 ACATTTTCATTTTTATTTTGATTAA
1 ACATTTTCATTTAAATTTTGATTAA
*
2435808 ACATGTTTCATTTAAATTTTTATTA
1 ACAT-TTTCATTTAAATTTTGATTA
2435833 TTATTTTGCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.30, C:0.08, G:0.04, T:0.58
Consensus pattern (25 bp):
ACATTTTCATTTAAATTTTGATTAA
Found at i:2439204 original size:15 final size:15
Alignment explanation
Indices: 2439186--2439238 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
2439176 AATATATTAG
* *
2439186 ATAAAATGAATAAAA
1 ATAAAATAAAGAAAA
*
2439201 ATAAAATAAAGATAA
1 ATAAAATAAAGAAAA
*
2439216 ATAAAAAAAAGAAAGA
1 ATAAAATAAAGAAA-A
2439232 A-AAAATA
1 ATAAAATA
2439239 TTAATATGAT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
15 29 0.94
16 2 0.06
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (15 bp):
ATAAAATAAAGAAAA
Found at i:2439217 original size:10 final size:11
Alignment explanation
Indices: 2439194--2439366 Score: 52
Period size: 12 Copynumber: 14.7 Consensus size: 11
2439184 AGATAAAATG
2439194 AATAAAAATAA
1 AATAAAAATAA
*
2439205 AATAAAGAT-A
1 AATAAAAATAA
2439215 AATAAAAA-AA
1 AATAAAAATAA
2439225 AGA-AAGAAA-AA
1 A-ATAA-AAATAA
* * *
2439236 ATATTAATATGAT
1 A-ATAAAAAT-AA
*
2439249 AATAAAAACAA
1 AATAAAAATAA
2439260 AATTAAAAATATA
1 AA-TAAAAATA-A
* *
2439273 GATAAATAAAGATA
1 AAT-AA-AAATA-A
**
2439287 AAT-AAAATTT
1 AATAAAAATAA
*
2439297 ACTAAAAAATAA
1 AATA-AAAATAA
*
2439309 AAGAGAAAAAATAA
1 AATA-A-AAA-TAA
2439323 AATAAAAAATAA
1 AAT-AAAAATAA
2439335 AATAAATCAAATAA
1 AAT-AA--AAATAA
2439349 AAT-AAAATAA
1 AATAAAAATAA
2439359 AATAAAAA
1 AATAAAAA
2439367 AAGAAATAAT
Statistics
Matches: 120, Mismatches: 24, Indels: 36
0.67 0.13 0.20
Matches are distributed among these distances:
10 23 0.19
11 28 0.23
12 33 0.28
13 12 0.10
14 23 0.19
15 1 0.01
ACGTcount: A:0.74, C:0.02, G:0.05, T:0.20
Consensus pattern (11 bp):
AATAAAAATAA
Found at i:2439310 original size:5 final size:5
Alignment explanation
Indices: 2439302--2439365 Score: 69
Period size: 5 Copynumber: 12.8 Consensus size: 5
2439292 AATTTACTAA
* * *
2439302 AAAAT AAAAG AGAA- AAAAT AAAAT AAAAAAT AAAAT -AAAT CAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT --AAAAT AAAAT AAAAT AAAAT AAAAT
2439352 AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAA
2439366 AAAGAAATAA
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
4 7 0.14
5 39 0.76
7 5 0.10
ACGTcount: A:0.80, C:0.02, G:0.03, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:2439317 original size:12 final size:13
Alignment explanation
Indices: 2439300--2439375 Score: 57
Period size: 14 Copynumber: 5.7 Consensus size: 13
2439290 AAAATTTACT
2439300 AAAAAATAAAAGA
1 AAAAAATAAAAGA
*
2439313 GAAAAAATAAAA-T
1 -AAAAAATAAAAGA
*
2439326 AAAAAATAAAATA
1 AAAAAATAAAAGA
* *
2439339 AATCAAATAAAATAA
1 AA-AAAATAAAA-GA
2439354 AATAAAATAAAA-A
1 AA-AAAATAAAAGA
*
2439367 AAGAAATAA
1 AAAAAATAA
2439376 TCACAAAAGG
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
12 17 0.32
13 5 0.09
14 19 0.36
15 12 0.23
ACGTcount: A:0.80, C:0.01, G:0.04, T:0.14
Consensus pattern (13 bp):
AAAAAATAAAAGA
Found at i:2439328 original size:26 final size:26
Alignment explanation
Indices: 2439276--2439355 Score: 81
Period size: 26 Copynumber: 3.0 Consensus size: 26
2439266 AAATATAGAT
* ** *
2439276 AAATAAAGATAAATAAAATTTACTAAA
1 AAATAAA-AGAAATAAAATAAAATAAA
2439303 AAATAAAAGAGAA-AAAATAAAATAAA
1 AAATAAAAGA-AATAAAATAAAATAAA
* *
2439329 AAATAAAATAAATCAAATAAAATAAA
1 AAATAAAAGAAATAAAATAAAATAAA
2439355 A
1 A
2439356 TAAAATAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
25 2 0.04
26 34 0.76
27 9 0.20
ACGTcount: A:0.75, C:0.03, G:0.04, T:0.19
Consensus pattern (26 bp):
AAATAAAAGAAATAAAATAAAATAAA
Found at i:2439337 original size:31 final size:31
Alignment explanation
Indices: 2439302--2439360 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
2439292 AATTTACTAA
*
2439302 AAAATAAAAGAGAA-AAAATAAAATAAAAAAT
1 AAAATAAAACA-AATAAAATAAAATAAAAAAT
*
2439333 AAAATAAATCAAATAAAATAAAATAAAA
1 AAAATAAAACAAATAAAATAAAATAAAA
2439361 TAAAAAAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 2 0.08
31 23 0.92
ACGTcount: A:0.80, C:0.02, G:0.03, T:0.15
Consensus pattern (31 bp):
AAAATAAAACAAATAAAATAAAATAAAAAAT
Found at i:2439440 original size:13 final size:13
Alignment explanation
Indices: 2439422--2439446 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2439412 AAAAGAGAAA
2439422 AAAAATAAAAAAT
1 AAAAATAAAAAAT
2439435 AAAAATAAAAAA
1 AAAAATAAAAAA
2439447 GTGAAAAGGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:2440645 original size:3 final size:3
Alignment explanation
Indices: 2440634--2440704 Score: 58
Period size: 3 Copynumber: 23.0 Consensus size: 3
2440624 CTAAAAAAAC
*
2440634 ATA ATTA ATA ATA ATA ATA AAA GATA ATA ATA A-A AGTA ATA ATA ATA
1 ATA A-TA ATA ATA ATA ATA ATA -ATA ATA ATA ATA A-TA ATA ATA ATA
*
2440681 ATA TATA TTA A-A A-A ATA TATA ATA
1 ATA -ATA ATA ATA ATA ATA -ATA ATA
2440705 TATATATTTC
Statistics
Matches: 57, Mismatches: 4, Indels: 14
0.76 0.05 0.19
Matches are distributed among these distances:
2 6 0.11
3 38 0.67
4 13 0.23
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2440692 original size:25 final size:24
Alignment explanation
Indices: 2440637--2440712 Score: 77
Period size: 25 Copynumber: 3.1 Consensus size: 24
2440627 AAAAAACATA
*
2440637 ATTAATAATAATAATAA-AAGATAAT
1 ATTAA-AATAATAATAATAATAT-AT
*
2440662 AATAAAAGTAATAATAATAATATAT
1 ATTAAAA-TAATAATAATAATATAT
2440687 ATTAAAA-AATATATAAT-ATATAT
1 ATTAAAATAATA-ATAATAATATAT
2440710 ATT
1 ATT
2440713 TCAAAAAATA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
23 13 0.29
24 7 0.16
25 21 0.47
26 4 0.09
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (24 bp):
ATTAAAATAATAATAATAATATAT
Found at i:2440707 original size:23 final size:26
Alignment explanation
Indices: 2440671--2440723 Score: 78
Period size: 23 Copynumber: 2.2 Consensus size: 26
2440661 TAATAAAAGT
2440671 AATA-ATAATAATATATA-TT-AAAA
1 AATATATAATAATATATATTTCAAAA
2440694 AATATATAAT-ATATATATTTCAAAA
1 AATATATAATAATATATATTTCAAAA
2440719 AATAT
1 AATAT
2440724 TTTTTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
23 11 0.41
24 7 0.26
25 9 0.33
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (26 bp):
AATATATAATAATATATATTTCAAAA
Found at i:2440745 original size:38 final size:37
Alignment explanation
Indices: 2440691--2441014 Score: 194
Period size: 37 Copynumber: 8.7 Consensus size: 37
2440681 ATATATATTA
* *
2440691 AAAAATATATAATATATATATTTCAAAAAATATTTTTT
1 AAAACTATATATTATATAT-TTTCAAAAAATATTTTTT
* * * * *
2440729 TAAATTATATA-T-TATATTTT-AAAAAAAAGTTTTC
1 AAAACTATATATTATATATTTTCAAAAAATATTTTTT
2440763 AAAACTATATATTATATAGTTTTC-AAAAATGA--TTTT
1 AAAACTATATATTATATA-TTTTCAAAAAAT-ATTTTTT
2440799 AAAA--A-ATATTATATAAGTTTTCAAAAAA-ATGTTTTT
1 AAAACTATATATTATAT-A-TTTTCAAAAAATAT-TTTTT
*
2440835 AAAACTATATATTATATAATTTTTCAAAAAAT-GTTTTT
1 AAAACTATATATTATAT-A-TTTTCAAAAAATATTTTTT
** * *
2440873 AAAACTGCATATTATATAATTTTTTTCAAAAAATGTTGTTT
1 AAAACTATATATTATAT-A---TTTTCAAAAAATATTTTTT
** *
2440914 AAAACTATATATTATATAAGTTTTTC--AAAAT-GCTTTA
1 AAAACTATATATTATAT-A--TTTTCAAAAAATATTTTTT
* * **
2440951 AAAACTATATATTATATCAATTTTC--AAAGTGTTTTAA
1 AAAACTATATATTATAT--ATTTTCAAAAAATATTTTTT
* *
2440988 AAAACTATATACTATATAATTTCAAAA
1 AAAACTATATATTATATATTTTCAAAA
2441015 TGATTTCAAA
Statistics
Matches: 237, Mismatches: 28, Indels: 43
0.77 0.09 0.14
Matches are distributed among these distances:
33 10 0.04
34 28 0.12
35 14 0.06
36 33 0.14
37 50 0.21
38 40 0.17
39 22 0.09
40 19 0.08
41 21 0.09
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (37 bp):
AAAACTATATATTATATATTTTCAAAAAATATTTTTT
Found at i:2440753 original size:34 final size:34
Alignment explanation
Indices: 2440702--2440851 Score: 108
Period size: 34 Copynumber: 4.3 Consensus size: 34
2440692 AAAATATATA
* * ** *
2440702 ATATA-TATATTTCAAAAAATATTTTTTTAAATT
1 ATATATTATATTTCAAAAAAAAGTTTTCAAAACT
*
2440735 ATATATTATATTTTAAAAAAAAGTTTTCAAAACT
1 ATATATTATATTTCAAAAAAAAGTTTTCAAAACT
** * *
2440769 ATATATTATATAGTTTTCAAAAATGA-TTTTAAAAAAT
1 ATATA-T-TATA--TTTCAAAAAAAAGTTTTCAAAACT
* * *
2440806 ATTATATAAGT-TTTCAAAAAAATGTTTTTAAAACT
1 A-TATATTA-TATTTCAAAAAAAAGTTTTCAAAACT
2440841 ATATATTATAT
1 ATATATTATAT
2440852 AATTTTTCAA
Statistics
Matches: 90, Mismatches: 18, Indels: 17
0.72 0.14 0.14
Matches are distributed among these distances:
33 6 0.07
34 43 0.48
35 11 0.12
36 5 0.06
37 12 0.13
38 13 0.14
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.45
Consensus pattern (34 bp):
ATATATTATATTTCAAAAAAAAGTTTTCAAAACT
Found at i:2440922 original size:151 final size:152
Alignment explanation
Indices: 2440732--2441009 Score: 356
Period size: 151 Copynumber: 1.8 Consensus size: 152
2440722 ATTTTTTTAA
2440732 ATTATATATTATATTTTAAAAAAAAGTTTTCAAAACTATATATTATAT-AG-TTTTCAAAAATGA
1 ATTATATATTATATTTTAAAAAAAAGTTTTCAAAACTATATATTATATAAGTTTTTC-AAAATGA
* * *
2440795 TTTTAAAA-A-ATATTATAT-AAGTTTTCAAAAAAATGTTTT-TAAAACTATATATTATATAATT
65 TTTAAAAACATATATTATATCAA-TTTTC---AAAATGTTTTAAAAAACTATATACTATATAATT
2440856 TTTCAAAAAATGTTTTTAAAACTGCAT
126 TTTCAAAAAATGTTTTTAAAACTGCAT
* * *
2440883 ATTATATAATT-T-TTTTCAAAAAATGTTGTTTAAAACTATATATTATATAAGTTTTTCAAAATG
1 ATTATAT-ATTATATTTTAAAAAAAAGTT-TTCAAAACTATATATTATATAAGTTTTTCAAAATG
* *
2440946 CTTTAAAAACTATATATTATATCAATTTTCAAAGTGTTTTAAAAAACTATATACTATATAATTT
64 ATTTAAAAAC-ATATATTATATCAATTTTCAAAATGTTTTAAAAAACTATATACTATATAATTT
2441010 CAAAATGATT
Statistics
Matches: 110, Mismatches: 8, Indels: 16
0.82 0.06 0.12
Matches are distributed among these distances:
150 13 0.12
151 27 0.25
152 27 0.25
153 26 0.24
154 1 0.01
155 14 0.13
156 2 0.02
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.45
Consensus pattern (152 bp):
ATTATATATTATATTTTAAAAAAAAGTTTTCAAAACTATATATTATATAAGTTTTTCAAAATGAT
TTAAAAACATATATTATATCAATTTTCAAAATGTTTTAAAAAACTATATACTATATAATTTTTCA
AAAAATGTTTTTAAAACTGCAT
Found at i:2440951 original size:36 final size:36
Alignment explanation
Indices: 2440691--2441038 Score: 272
Period size: 38 Copynumber: 9.6 Consensus size: 36
2440681 ATATATATTA
* * *
2440691 AAAAATATATAATATAT-ATATTTCAAAAAATATTTTTT
1 AAAACTATATATTATATAAT-TTTC-AAAAAT-GTTTTT
* * ** * *
2440729 TAAATTATATATTATAT--TTTAAAAAAAAGTTTTC
1 AAAACTATATATTATATAATTTTCAAAAATGTTTTT
* *
2440763 AAAACTATATATTATATAGTTTTCAAAAATGATTTT
1 AAAACTATATATTATATAATTTTCAAAAATGTTTTT
2440799 AAAA--A-ATATTATATAAGTTTTCAAAAAAATGTTTTT
1 AAAACTATATATTATATAA-TTTTC--AAAAATGTTTTT
2440835 AAAACTATATATTATATAATTTTTCAAAAAATGTTTTT
1 AAAACTATATATTATATAA-TTTTC-AAAAATGTTTTT
**
2440873 AAAACTGCATATTATATAATTTTTTTCAAAAAATGTTGTTT
1 AAAACTATATATTATATAA---TTTTC-AAAAATGTT-TTT
* *
2440914 AAAACTATATATTATATAAGTTTTTC-AAAATGCTTTA
1 AAAACTATATATTATATAA--TTTTCAAAAATGTTTTT
* *
2440951 AAAACTATATATTATATCAATTTTC-AAAGTGTTTTAA
1 AAAACTATATATTATAT-AATTTTCAAAAATGTTTT-T
* *
2440988 AAAACTATATACTATATAA-TTTC-AAAATG-ATTT
1 AAAACTATATATTATATAATTTTCAAAAATGTTTTT
*
2441021 CAAACTATA-A-TATATAAT
1 AAAACTATATATTATATAAT
2441039 ATATATATAT
Statistics
Matches: 264, Mismatches: 32, Indels: 34
0.80 0.10 0.10
Matches are distributed among these distances:
31 7 0.03
32 1 0.00
33 18 0.07
34 27 0.10
35 14 0.05
36 48 0.18
37 37 0.14
38 54 0.20
39 16 0.06
40 22 0.08
41 20 0.08
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (36 bp):
AAAACTATATATTATATAATTTTCAAAAATGTTTTT
Found at i:2441042 original size:2 final size:2
Alignment explanation
Indices: 2441026--2441059 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
2441016 GATTTCAAAC
2441026 TA TA -A TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2441060 AATAAAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2441820 original size:84 final size:80
Alignment explanation
Indices: 2441613--2442753 Score: 915
Period size: 84 Copynumber: 14.0 Consensus size: 80
2441603 TTTTTGTTAA
* * *
2441613 CAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATTTGATATGCCTTTGAGCTGAGTGTAATCA
1 CAGATAACCCTTCTTGCCTTGAGCTATGCTACAAA--TGATGTGCCTTTGAGCTGAGTGTAATCA
*
2441678 AACACAAAGGTCTTTGG
64 AACTCAAAGGTCTTTGG
* * *
2441695 CAGGTAACCCTTCTTGTCTTGAGCTATACTACAAATGATGTGCCTTTGAGCTGAGTGTAATCAAA
1 CAGATAACCCTTCTTGCCTTGAGCTATGCTACAAATGATGTGCCTTTGAGCTGAGTGTAATCAAA
2441760 CTCAAAGGTCTTTTGTTGG
66 CTCAAAGGTC---T-TTGG
* * * * *
2441779 CAGATAACCCTTCTAGCCTTGAGTTATGCTACAAATGATGTGTC-TTGAAGCTGAATGTAATCGA
1 CAGATAACCCTTCTTGCCTTGAGCTATGCTACAAATGATGTGCCTTTG-AGCTGAGTGTAATCAA
*
2441843 ACTCGAAGGTCTTTGG
65 ACTCAAAGGTCTTTGG
** *
2441859 CAGATAACCCTTCTTGCCTTGAGCTATGCCGCAAATGATGTGCCTTTGAGCTGAGTG------AG
1 CAGATAACCCTTCTTGCCTTGAGCTATGCTACAAATGATGTGCCTTTGAGCTGAGTGTAATCAAA
** *
2441918 CT---ATTTTTTTGG
66 CTCAAAGGTCTTTGG
* * *
2441930 CAGATAACCCTT-TTAGCCTTGAGTTATGCTACAAATGATGTGCCTTGGAGCTGAGTGTAATCGA
1 CAGATAACCCTTCTT-GCCTTGAGCTATGCTACAAATGATGTGCCTTTGAGCTGAGTGTAATCAA
*
2441994 ACTCGAAGGTCTTTGG
65 ACTCAAAGGTCTTTGG
* * * * ** * *
2442010 CAGGTAGCCCTTTTTGCCTTAAGCTATGCTGTAAATGATATGCCTTT-AGCTAAGTGTAATCAAA
1 CAGATAACCCTTCTTGCCTTGAGCTATGCTACAAATGATGTGCCTTTGAGCTGAGTGTAATCAAA
*
2442074 CTCGAAGGTCTTTTGATGG
66 CTCAAAGGTC--TT--TGG
* * * ** * * * *
2442093 TATATAACCCTTCTAGCCTTGATTTATGCTGCAAATGATGTGACTTGGAGCTGAGTGTAATCGAA
1 CAGATAACCCTTCTTGCCTTGAGCTATGCTACAAATGATGTGCCTTTGAGCTGAGTGTAATCAAA
* *
2442158 CTCGAAGGTATTTGG
66 CTCAAAGGTCTTTGG
* * *
2442173 CA-AGTAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAGTCAA
1 CAGA-TAACCCTTCTTGCCTTGAGCTATGCTACAAATGATGTGCCTTTGAGCTGAGTGTAATCAA
*
2442237 ACTCGAAGGTCTTTGGTTGG
65 ACTCAAAGGTC--T--TTGG
* * * * * * * * * *
2442257 CAGATAACCCTTATAGCATTGAGTTATGCTGCAAATGATATGCCTTTGAGTTGAGCGTAGTCGAA
1 CAGATAACCCTTCTTGCCTTGAGCTATGCTACAAATGATGTGCCTTTGAGCTGAGTGTAATCAAA
*
2442322 CTCGAAGGTCTTTTGTTGG
66 CTCAAAGGTC---T-TTGG
* * * * * * *
2442341 AAAATAACCCTTCTTGCCTTGAGCTATGTTACAAATGATGTGCCTTGGAGTTGAGCGTAGTCAAA
1 CAGATAACCCTTCTTGCCTTGAGCTATGCTACAAATGATGTGCCTTTGAGCTGAGTGTAATCAAA
*
2442406 CTCGAAGGTCTTTCGTTGG
66 CTCAAAGGTC--T--TTGG
* * * * * * *
2442425 CAGATAACCCTTCTAT-CCTTGAGTTATGTTGCAAATGATATGCCTTTGAGCTGAGCGTAGTCGA
1 CAGATAACCCTTCT-TGCCTTGAGCTATGCTACAAATGATGTGCCTTTGAGCTGAGTGTAATCAA
* *
2442489 ACTCGAAGGTATTTTGTTGG
65 ACTCAAAGG---TCT-TTGG
* * * ** * * * * **
2442509 CAAATAGCCATTCTTGCCTTGAGCTATATTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTTGAA
1 CAGATAACCCTTCTTGCCTTGAGCTATGCTACAAATGATGTGCCTTTGAGCTGAGTGTAATCAAA
**
2442574 CTTGAAGGTCTTTGGTTGG
66 CTCAAAGGTC--T--TTGG
* * * * * * * * *
2442593 CAGATAACCATTCTAGCCTTGAGTTATGCTGCAAATGATCTGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTTGCCTTGAGCTATGCTACAAATGATGTGCCTTTGAGCTGAGTGTAATCAAA
* *
2442658 CTCGAAGGACTTTTGGTGG
66 CTCAAAGG--TCTT--TGG
* * *
2442677 CAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTAAGCTGAGTGTAATCAAA
1 CAGATAACCCTTCTTGCCTTGAGCTATGCTACAAATGATGTGCCTTTGAGCTGAGTGTAATCAAA
*
2442742 CTCGAAGGTCTT
66 CTCAAAGGTCTT
2442754 GGTTGATAGA
Statistics
Matches: 886, Mismatches: 131, Indels: 84
0.80 0.12 0.08
Matches are distributed among these distances:
70 2 0.00
71 57 0.06
74 3 0.00
77 3 0.00
79 26 0.03
80 198 0.22
81 9 0.01
82 37 0.04
83 46 0.05
84 497 0.56
85 6 0.01
86 1 0.00
87 1 0.00
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (80 bp):
CAGATAACCCTTCTTGCCTTGAGCTATGCTACAAATGATGTGCCTTTGAGCTGAGTGTAATCAAA
CTCAAAGGTCTTTGG
Found at i:2441970 original size:71 final size:71
Alignment explanation
Indices: 2441854--2441986 Score: 214
Period size: 71 Copynumber: 1.9 Consensus size: 71
2441844 CTCGAAGGTC
* *
2441854 TTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCCGCAAATGATGTGCCTTTGAGCTGAGTGAGC
1 TTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCCACAAATGATGTGCCTTGGAGCTGAGTGAGC
2441919 TATTTT
66 TATTTT
* *
2441925 TTTGGCAGATAACCCTT-TTAGCCTTGAGTTATGCTACAAATGATGTGCCTTGGAGCTGAGTG
1 TTTGGCAGATAACCCTTCTT-GCCTTGAGCTATGCCACAAATGATGTGCCTTGGAGCTGAGTG
2441987 TAATCGAACT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
70 2 0.04
71 55 0.96
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.35
Consensus pattern (71 bp):
TTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCCACAAATGATGTGCCTTGGAGCTGAGTGAGC
TATTTT
Found at i:2442460 original size:168 final size:168
Alignment explanation
Indices: 2441926--2442787 Score: 1116
Period size: 168 Copynumber: 5.2 Consensus size: 168
2441916 AGCTATTTTT
* * * * *
2441926 TTGGCAGATAACCCTTTTAGCCTTGAGTTATGCTACAAATGATGTGCCTTGGAGCTGAGTGTAAT
1 TTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGT
** * * * *
2441991 CGAACTCGAAGGTC---T-TTGGCAGGTAGCCCTTTTTGCCTTAAGCTATGCTGTAAATGATATG
66 CGAACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTG
* * *
2442052 CCTTT-AGCTAAGTGTAATCAAACTCGAAGGTCTTTTG
131 CCTTTGAGCTGAGTGTAGTCAAACTCGAAGGTCTTTGG
* * * * * * * *
2442089 ATGGTATATAACCCTTCTAGCCTTGATTTATGCTGCAAATGATGTGACTTGGAGCTGAGTGTAAT
1 TTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGT
* *
2442154 CGAACTCGAAGG---TAT-TTGGCAAGTAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTG
66 CGAACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTG
2442215 CCTTTGAGCTGAGTGTAGTCAAACTCGAAGGTCTTTGG
131 CCTTTGAGCTGAGTGTAGTCAAACTCGAAGGTCTTTGG
* * * *
2442253 TTGGCAGATAACCCTTATAGCATTGAGTTATGCTGCAAATGATATGCCTTTGAGTTGAGCGTAGT
1 TTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGT
* * * *
2442318 CGAACTCGAAGGTCTTTTGTTGGAAAATAACCCTTCTTGCCTTGAGCTATGTTACAAATGATGTG
66 CGAACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTG
* * * *
2442383 CCTTGGAGTTGAGCGTAGTCAAACTCGAAGGTCTTTCG
131 CCTTTGAGCTGAGTGTAGTCAAACTCGAAGGTCTTTGG
* * *
2442421 TTGGCAGATAACCCTTCTATCCTTGAGTTATGTTGCAAATGATATGCCTTTGAGCTGAGCGTAGT
1 TTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGT
* * **
2442486 CGAACTCGAAGGTATTTTGTTGGCAAATAGCCATTCTTGCCTTGAGCTATATTGCAAATGATGTG
66 CGAACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTG
* * ** *
2442551 CCTTAGAGCTGAGCGTAGTTGAACTTGAAGGTCTTTGG
131 CCTTTGAGCTGAGTGTAGTCAAACTCGAAGGTCTTTGG
* *
2442589 TTGGCAGATAACCATTCTAGCCTTGAGTTATGCTGCAAATGATCTGCCTTGGAGCTGAGCGTAGT
1 TTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGT
* * *
2442654 CGAACTCGAAGGACTTTTGGTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTG
66 CGAACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTG
* *
2442719 CCTTTAAGCTGAGTGTAATCAAACTCGAAGGTC-TTGG
131 CCTTTGAGCTGAGTGTAGTCAAACTCGAAGGTCTTTGG
** *
2442756 TTGATAGATAACCCTTATCA-CCTTGAGTTATG
1 TTGGCAGATAACCCTTCT-AGCCTTGAGTTATG
2442788 TTACCGATAG
Statistics
Matches: 614, Mismatches: 77, Indels: 12
0.87 0.11 0.02
Matches are distributed among these distances:
163 117 0.19
164 94 0.15
167 32 0.05
168 371 0.60
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (168 bp):
TTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGT
CGAACTCGAAGGTCTTTTGTTGGCAAATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTG
CCTTTGAGCTGAGTGTAGTCAAACTCGAAGGTCTTTGG
Found at i:2442544 original size:252 final size:249
Alignment explanation
Indices: 2441590--2442787 Score: 1151
Period size: 252 Copynumber: 4.9 Consensus size: 249
2441580 CTGAATGGAA
* *
2441590 TCGAACTCGAAAGT-TTTTGTT--AACAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATTTG
1 TCGAACTCGAAGGTCTTTTGTTGGAA-A-ATAACCCTTCTAGCCTTGAGTTATGCTGCAAA--TG
* * * * * * * * * *
2441652 ATATGCCTTTGAGCTGAGTGTAATCAAACACAAAGG-TCT-TTGGCAGGTAACCCTTCTTGTCTT
62 ATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGCTTTGTTGGCAGATAACCCTTCTTGCCTT
* * *
2441715 GAGCTATACTACAAATGATGTGCCTTTGAGCTGAGTGTAATCAAACTCAAAGGTCTTTTGTTGGC
127 GAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGT-TTTTGTTGGC
* * * * * * * ** *
2441780 AGATAACCCTTCTAGCCTTGAGTTATGCTACAAATGATGTGTC-TTGAAGCTGAATGTAA
191 AGATAGCCCTTATTGCCTTGAGCTATGCTGCAAATGATATGCCTTTG-AGCTGAGCGTAG
* * * * *
2441839 TCGAACTCGAAGGTC---T-TTGGCAGATAACCCTTCTTGCCTTGAGCTATGCCGCAAATGATGT
1 TCGAACTCGAAGGTCTTTTGTTGGAAAATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGT
* * * *
2441900 GCCTTTGAGCT----G-AGT-GAGCT---A--TTTTTTTGGCAGATAACCCTT-TTAGCCTTGAG
66 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGCTTTGTTGGCAGATAACCCTTCTT-GCCTTGAG
* * * * * *
2441953 TTATGCTACAAATGATGTGCCTTGGAGCTGAGTGTAATCGAACTCGAAGG--TCT-TTGGCAGGT
130 CTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTTTTTGTTGGCAGAT
* * * * * *
2442015 AGCCCTTTTTGCCTTAAGCTATGCTGTAAATGATATGCCTTT-AGCTAAGTGTAA
195 AGCCCTTATTGCCTTGAGCTATGCTGCAAATGATATGCCTTTGAGCTGAGCGTAG
* * * * *
2442069 TCAAACTCGAAGGTCTTTTGATGGTATATAACCCTTCTAGCCTTGATTTATGCTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTTGTTGGAAAATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGT
* * * * *
2442134 GACTTGGAGCTGAGTGTAATCGAACTCGAAGG-TAT-TTGGCA-AGTAGCCCTTCTTGCCTTGAG
66 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGCTTTGTTGGCAGA-TAACCCTTCTTGCCTTGAG
* *
2442196 CTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAGTCAAACTCGAAGGTCTTTGGTTGGCAGA
130 CTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGT-TTTTGTTGGCAGA
* * * * *
2442261 TAACCCTTATAGCATTGAGTTATGCTGCAAATGATATGCCTTTGAGTTGAGCGTAG
194 TAGCCCTTATTGCCTTGAGCTATGCTGCAAATGATATGCCTTTGAGCTGAGCGTAG
* * * *
2442317 TCGAACTCGAAGGTCTTTTGTTGGAAAATAACCCTTCTTGCCTTGAGCTATGTTACAAATGATGT
1 TCGAACTCGAAGGTCTTTTGTTGGAAAATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGT
* *
2442382 GCCTTGGAGTTGAGCGTAGTCAAACTCGAAGGTCTTTCGTTGGCAGATAACCCTTCTAT-CCTTG
66 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGG-CTTT-GTTGGCAGATAACCCTTCT-TGCCTTG
* * * * * *
2442446 AGTTATGTTGCAAATGATATGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTATTTTGTTGGCA
128 AGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGT-TTTTGTTGGCA
* * * ** * *
2442511 AATAGCCATTCTTGCCTTGAGCTATATTGCAAATGATGTGCCTTAGAGCTGAGCGTAG
192 GATAGCCCTTATTGCCTTGAGCTATGCTGCAAATGATATGCCTTTGAGCTGAGCGTAG
* * * * * * *
2442569 TTGAACTTGAAGGTCTTTGGTTGGCAGATAACCATTCTAGCCTTGAGTTATGCTGCAAATGATCT
1 TCGAACTCGAAGGTCTTTTGTTGGAAAATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGT
* *
2442634 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGACTTTTGGTGGCAGATAGCCCTTCTTGCCTTGA
66 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGG-C-TTTGTTGGCAGATAACCCTTCTTGCCTTGA
* * * **
2442699 GCTATGCTGCAAATGATGTGCCTTTAAGCTGAGTGTAATCAAACTCGAAGGTCTTGGTTGATAGA
129 GCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTTTTTGTTGGCAGA
* ** *
2442764 TAACCCTTATCACCTTGAGTTATG
194 TAGCCCTTATTGCCTTGAGCTATG
2442788 TTACCGATAG
Statistics
Matches: 778, Mismatches: 134, Indels: 72
0.79 0.14 0.07
Matches are distributed among these distances:
230 24 0.03
231 38 0.05
232 4 0.01
233 1 0.00
234 51 0.07
235 68 0.09
238 3 0.00
239 4 0.01
240 5 0.01
242 1 0.00
243 67 0.09
244 20 0.03
246 33 0.04
247 44 0.06
248 92 0.12
249 13 0.02
250 2 0.00
251 26 0.03
252 277 0.36
253 5 0.01
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.33
Consensus pattern (249 bp):
TCGAACTCGAAGGTCTTTTGTTGGAAAATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGT
GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGCTTTGTTGGCAGATAACCCTTCTTGCCTTGAGC
TATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTTTTTGTTGGCAGATA
GCCCTTATTGCCTTGAGCTATGCTGCAAATGATATGCCTTTGAGCTGAGCGTAG
Found at i:2443237 original size:17 final size:16
Alignment explanation
Indices: 2443203--2443237 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
2443193 GAAGCTGCAA
*
2443203 AAAAATTATGCATGTG
1 AAAAATTATGCATATG
2443219 AAAAATTATGCAATATG
1 AAAAATTATGC-ATATG
2443236 AA
1 AA
2443238 TTAGTCTTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.51, C:0.06, G:0.14, T:0.29
Consensus pattern (16 bp):
AAAAATTATGCATATG
Found at i:2444102 original size:95 final size:95
Alignment explanation
Indices: 2443931--2444131 Score: 314
Period size: 95 Copynumber: 2.1 Consensus size: 95
2443921 GGACAGCTCA
* *
2443931 ATATTATAATCACCTTTATCAGGCTAGCTGAATATTATCTATAAATTCGGGGCATTTAACCAATT
1 ATATTATAATCACCTTTATCAGGCTAGCTGAATATTATCCATAAACTCGGGGCATTTAACCAATT
*
2443996 GCTCTAGAGGGACAACTCAAGCTTTATTGT
66 GCTCTACAGGGACAACTCAAGCTTTATTGT
* * *
2444026 ATATTATAATCACCTTTGTCAGGCTAGCTGAATCTTATCCATAAAGCT-GGGGCGTTTAACCAAT
1 ATATTATAATCACCTTTATCAGGCTAGCTGAATATTATCCATAAA-CTCGGGGCATTTAACCAAT
*
2444090 TGCTTTACAGGGACAACTCAAGCTTTATTGT
65 TGCTCTACAGGGACAACTCAAGCTTTATTGT
2444121 ATATATATAAT
1 ATAT-TATAAT
2444132 ACTATAATCT
Statistics
Matches: 97, Mismatches: 7, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
95 90 0.93
96 7 0.07
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (95 bp):
ATATTATAATCACCTTTATCAGGCTAGCTGAATATTATCCATAAACTCGGGGCATTTAACCAATT
GCTCTACAGGGACAACTCAAGCTTTATTGT
Found at i:2447472 original size:11 final size:11
Alignment explanation
Indices: 2447458--2447488 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
2447448 AATAAATAAA
2447458 TAAATAAATGC
1 TAAATAAATGC
2447469 TAAATAAATGC
1 TAAATAAATGC
2447480 TAAATAAAT
1 TAAATAAAT
2447489 CGAAAGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.29
Consensus pattern (11 bp):
TAAATAAATGC
Found at i:2447572 original size:45 final size:44
Alignment explanation
Indices: 2447480--2447566 Score: 108
Period size: 45 Copynumber: 2.0 Consensus size: 44
2447470 AAATAAATGC
**
2447480 TAAATAAATCGAAAGAAAAAATTTTAAAAAAAATATTTAAATAAA
1 TAAATAAATCGAAAGAAAAAA-TTTAAAAAAAATATACAAATAAA
2447525 TAAATAAATC-AAAGGAAAAAA-TTAAATAAAAA-ATACAAATAA
1 TAAATAAATCGAAA-GAAAAAATTTAAA-AAAAATATACAAATAA
2447567 TAATAATAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
43 13 0.34
44 8 0.21
45 17 0.45
ACGTcount: A:0.69, C:0.03, G:0.05, T:0.23
Consensus pattern (44 bp):
TAAATAAATCGAAAGAAAAAATTTAAAAAAAATATACAAATAAA
Found at i:2447695 original size:2 final size:2
Alignment explanation
Indices: 2447651--2447675 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2447641 AGTAAACAAT
2447651 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2447676 GAATCCTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2448826 original size:15 final size:15
Alignment explanation
Indices: 2448792--2448836 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
2448782 AAAAGAAAGA
2448792 AAAAAT-AATAAA-T
1 AAAAATAAATAAATT
2448805 AACAAATAAATAAATT
1 AA-AAATAAATAAATT
2448821 AAAAATTAAA-AAATT
1 AAAAA-TAAATAAATT
2448836 A
1 A
2448837 TTTTTTAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 2 0.07
14 4 0.14
15 15 0.54
16 7 0.25
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (15 bp):
AAAAATAAATAAATT
Found at i:2448978 original size:36 final size:36
Alignment explanation
Indices: 2448923--2449124 Score: 257
Period size: 36 Copynumber: 5.5 Consensus size: 36
2448913 ATTTTAAAGC
*
2448923 TATATATATTTTCCAAAATGTTTTTAAAAAATTATATAT
1 TATATATATTTT-CAAAATG-TTTT-AAAAACTATATAT
* *
2448962 TCTA-A-GTTTTCAAAATGATTTTAAAAACTATATAT
1 TATATATATTTTCAAAATG-TTTTAAAAACTATATAT
2448997 TATATATATTTTCTAAAATGTTTTAAAAACTATATAT
1 TATATATATTTTC-AAAATGTTTTAAAAACTATATAT
* * *
2449034 TATATA-GTTTTCAAAAATATTTTAAAAACAATATAT
1 TATATATATTTTC-AAAATGTTTTAAAAACTATATAT
2449070 TATATATATTTTCAAAATGTTTTAAAAACTATATAT
1 TATATATATTTTCAAAATGTTTTAAAAACTATATAT
2449106 TATATACATATTTTCAAAA
1 TATAT--ATATTTTCAAAA
2449125 ACCATTTGAA
Statistics
Matches: 144, Mismatches: 13, Indels: 13
0.85 0.08 0.08
Matches are distributed among these distances:
35 15 0.10
36 70 0.49
37 37 0.26
38 19 0.13
39 3 0.02
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (36 bp):
TATATATATTTTCAAAATGTTTTAAAAACTATATAT
Found at i:2449094 original size:72 final size:72
Alignment explanation
Indices: 2448923--2449111 Score: 292
Period size: 72 Copynumber: 2.6 Consensus size: 72
2448913 ATTTTAAAGC
* *
2448923 TATATATATTTTCCAAAATGTTTTTAAAAAATTATATATTCTA-AGTTTTCAAAATGATTTTAAA
1 TATATATATTTT-CAAAATG-TTTT-AAAAACTATATATTATATAGTTTTCAAAATGATTTTAAA
*
2448987 AACTATATAT
63 AACAATATAT
2448997 TATATATATTTTCTAAAATGTTTTAAAAACTATATATTATATAGTTTTCAAAAAT-ATTTTAAAA
1 TATATATATTTTC-AAAATGTTTTAAAAACTATATATTATATAGTTTTC-AAAATGATTTTAAAA
2449061 ACAATATAT
64 ACAATATAT
2449070 TATATATATTTTCAAAATGTTTTAAAAACTATATATTATATA
1 TATATATATTTTCAAAATGTTTTAAAAACTATATATTATATA
2449112 CATATTTTCA
Statistics
Matches: 109, Mismatches: 3, Indels: 8
0.91 0.03 0.07
Matches are distributed among these distances:
72 44 0.40
73 42 0.39
74 23 0.21
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (72 bp):
TATATATATTTTCAAAATGTTTTAAAAACTATATATTATATAGTTTTCAAAATGATTTTAAAAAC
AATATAT
Found at i:2450223 original size:18 final size:19
Alignment explanation
Indices: 2450200--2450236 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
2450190 CTGCGCTTAT
2450200 TTTTCAAAATCAAA-ATAG
1 TTTTCAAAATCAAAGATAG
2450218 TTTTCAAAATCAAAGATAG
1 TTTTCAAAATCAAAGATAG
2450237 ACTTTGGTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.49, C:0.11, G:0.08, T:0.32
Consensus pattern (19 bp):
TTTTCAAAATCAAAGATAG
Found at i:2453167 original size:29 final size:29
Alignment explanation
Indices: 2453125--2453182 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
2453115 TCTTTTCTTT
2453125 ATTATTTGTTTCCTCTCTTTTCTAATAAC
1 ATTATTTGTTTCCTCTCTTTTCTAATAAC
2453154 ATTATTTGTTTCCTCTCTTTTCTAATAAC
1 ATTATTTGTTTCCTCTCTTTTCTAATAAC
2453183 TCACAAGAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.21, C:0.21, G:0.03, T:0.55
Consensus pattern (29 bp):
ATTATTTGTTTCCTCTCTTTTCTAATAAC
Found at i:2456390 original size:20 final size:20
Alignment explanation
Indices: 2456343--2456392 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
2456333 ACTAATATAT
2456343 ATATATAAAATTATAAAATA
1 ATATATAAAATTATAAAATA
* * *
2456363 TTAAATAATATT-TAAGAATA
1 ATATATAAAATTATAA-AATA
2456383 ATATATAAAA
1 ATATATAAAA
2456393 ATATTAAGAA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
19 3 0.13
20 20 0.87
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (20 bp):
ATATATAAAATTATAAAATA
Found at i:2456395 original size:23 final size:22
Alignment explanation
Indices: 2456359--2456403 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
2456349 AAAATTATAA
2456359 AATATTAAATAATATTTAAGAAT
1 AATATTAAATAATA-TTAAGAAT
2456382 AATATATAAA-AATATTAAGAAT
1 AATAT-TAAATAATATTAAGAAT
2456404 TTATCTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 8 0.38
23 9 0.43
24 4 0.19
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (22 bp):
AATATTAAATAATATTAAGAAT
Found at i:2461149 original size:20 final size:20
Alignment explanation
Indices: 2461103--2461151 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
2461093 AGGATGGCAG
2461103 TAGTATCGATACCAAGCATC
1 TAGTATCGATACCAAGCATC
* *
2461123 -CGATATCGATACCGAGCATC
1 TAG-TATCGATACCAAGCATC
2461143 TAGTATCGA
1 TAGTATCGA
2461152 CACTACAACC
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 1 0.04
20 22 0.92
21 1 0.04
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (20 bp):
TAGTATCGATACCAAGCATC
Found at i:2461253 original size:20 final size:20
Alignment explanation
Indices: 2461228--2461265 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2461218 TTTCATCCAA
2461228 GTTCATCCAGTATCGATATT
1 GTTCATCCAGTATCGATATT
* *
2461248 GTTCATCTAGTATTGATA
1 GTTCATCCAGTATCGATA
2461266 CTTGAACCCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (20 bp):
GTTCATCCAGTATCGATATT
Found at i:2469152 original size:104 final size:104
Alignment explanation
Indices: 2468973--2469170 Score: 254
Period size: 104 Copynumber: 1.9 Consensus size: 104
2468963 ATTCGACACA
* * * * * * *
2468973 ATTATCAATATAAATTGTGATGATTTTTTTTACATTAAAAATATATTTTGTAACCATCAATATTG
1 ATTATCAAAAGAAATTATGATAATTTATTTGACATTAAAAATATATTTTGTAACCACCAATATTG
2469038 TCACACTAAGT-ATTTTTAGTGACCAAATTTTTGAAACT
66 TCACACTAAGTGATTTTTAGTGACCAAATTTTTGAAACT
* * ** *
2469076 ATTATCAAAAGAAATTATGATAAATTTATTTGACATTGAAAGTATATTTTGTGCCCACCAATGTT
1 ATTATCAAAAGAAATTATGAT-AATTTATTTGACATTAAAAATATATTTTGTAACCACCAATATT
* *
2469141 GTCACAGTAAGTGTTTTTTAGTGACCAAAT
65 GTCACACTAAGTGATTTTTAGTGACCAAAT
2469171 GTTCAATACT
Statistics
Matches: 79, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
103 18 0.23
104 45 0.57
105 16 0.20
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.41
Consensus pattern (104 bp):
ATTATCAAAAGAAATTATGATAATTTATTTGACATTAAAAATATATTTTGTAACCACCAATATTG
TCACACTAAGTGATTTTTAGTGACCAAATTTTTGAAACT
Found at i:2473478 original size:3 final size:3
Alignment explanation
Indices: 2473414--2473464 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
2473404 AAGTCAAGTT
** * * *
2473414 ATG ATG ATG ATG ATG GCG ACG ATG ATG ATG ATG GTG ACG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
2473462 ATG
1 ATG
2473465 GTGGTTGTGA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.29, C:0.06, G:0.37, T:0.27
Consensus pattern (3 bp):
ATG
Found at i:2473478 original size:18 final size:18
Alignment explanation
Indices: 2473416--2473467 Score: 95
Period size: 18 Copynumber: 2.9 Consensus size: 18
2473406 GTCAAGTTAT
*
2473416 GATGATGATGATGGCGAC
1 GATGATGATGATGGTGAC
2473434 GATGATGATGATGGTGAC
1 GATGATGATGATGGTGAC
2473452 GATGATGATGATGGTG
1 GATGATGATGATGGTG
2473468 GTTGTGATGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.27, C:0.06, G:0.40, T:0.27
Consensus pattern (18 bp):
GATGATGATGATGGTGAC
Found at i:2473478 original size:21 final size:21
Alignment explanation
Indices: 2473414--2473469 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
2473404 AAGTCAAGTT
* * *
2473414 ATGATGATGATGATGGCGACG
1 ATGATGATGATGGTGACGATG
2473435 ATGATGATGATGGTGACGATG
1 ATGATGATGATGGTGACGATG
*
2473456 ATGATGATGGTGGT
1 ATGATGATGATGGT
2473470 TGTGATGATC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.27, C:0.05, G:0.39, T:0.29
Consensus pattern (21 bp):
ATGATGATGATGGTGACGATG
Found at i:2475593 original size:35 final size:35
Alignment explanation
Indices: 2475547--2475670 Score: 160
Period size: 36 Copynumber: 3.5 Consensus size: 35
2475537 AAAAGATGAA
2475547 CAATTGAATCGAAAGTG-CGGATGCTTCCTTCCGTT
1 CAATTGAATCGAAAGTGTC-GATGCTTCCTTCCGTT
*
2475582 CAATTGAATCGAAAGTGTCGATGCTTCCTTTCGTT
1 CAATTGAATCGAAAGTGTCGATGCTTCCTTCCGTT
** * *
2475617 CTTCTTGAATCGAAAATGTCGATACTTCCTTCCGTT
1 C-AATTGAATCGAAAGTGTCGATGCTTCCTTCCGTT
*
2475653 CACTTTGAATCGAAAGTG
1 CA-ATTGAATCGAAAGTG
2475671 CTAATGCTTC
Statistics
Matches: 77, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
35 33 0.43
36 44 0.57
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (35 bp):
CAATTGAATCGAAAGTGTCGATGCTTCCTTCCGTT
Found at i:2475637 original size:36 final size:35
Alignment explanation
Indices: 2475550--2475689 Score: 149
Period size: 36 Copynumber: 3.9 Consensus size: 35
2475540 AGATGAACAA
*
2475550 TTGAATCGAAAGTGCGGATGCTTCCTTCCGTTCAA
1 TTGAATCGAAAGTGCGGATGCTTCCTTCCGTTCAC
* *
2475585 TTGAATCGAAAGTGTC-GATGCTTCCTTTCGTTCTTC
1 TTGAATCGAAAGTG-CGGATGCTTCCTTCCGTTC-AC
* *
2475621 TTGAATCGAAAATGTC-GATACTTCCTTCCGTTCAC
1 TTGAATCGAAAGTG-CGGATGCTTCCTTCCGTTCAC
** * *
2475656 TTTGAATCGAAAGTGCTAATGCTTCTTTTCGTTC
1 -TTGAATCGAAAGTGCGGATGCTTCCTTCCGTTC
2475690 TTCTTATTCA
Statistics
Matches: 89, Mismatches: 12, Indels: 7
0.82 0.11 0.06
Matches are distributed among these distances:
35 32 0.36
36 57 0.64
ACGTcount: A:0.21, C:0.22, G:0.19, T:0.38
Consensus pattern (35 bp):
TTGAATCGAAAGTGCGGATGCTTCCTTCCGTTCAC
Found at i:2475686 original size:72 final size:71
Alignment explanation
Indices: 2475550--2475694 Score: 204
Period size: 72 Copynumber: 2.0 Consensus size: 71
2475540 AGATGAACAA
* * *
2475550 TTGAATCGAAAGTGCGGATGCTTCCTTCCGTTCAATTGAATCGAAAGTGTCGATGCTTCCTTTCG
1 TTGAATCGAAAATGCGGATACTTCCTTCCGTTCAATTGAATCGAAAGTGTCAATGCTTCCTTTCG
2475615 TTCTTC
66 TTCTTC
* *
2475621 TTGAATCGAAAATGTC-GATACTTCCTTCCGTTCACTTTGAATCGAAAGTG-CTAATGCTTCTTT
1 TTGAATCGAAAATG-CGGATACTTCCTTCCGTTCA-ATTGAATCGAAAGTGTC-AATGCTTCCTT
2475684 TCGTTCTTC
63 TCGTTCTTC
2475693 TT
1 TT
2475695 ATTCACCTTC
Statistics
Matches: 66, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
71 31 0.47
72 35 0.53
ACGTcount: A:0.21, C:0.22, G:0.18, T:0.39
Consensus pattern (71 bp):
TTGAATCGAAAATGCGGATACTTCCTTCCGTTCAATTGAATCGAAAGTGTCAATGCTTCCTTTCG
TTCTTC
Done.