Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008953.1 Hibiscus syriacus cultivar Beakdansim tig00112281_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: 2822058
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 15
Found at i:590518 original size:3 final size:3
Alignment explanation
Indices: 590512--590566 Score: 67
Period size: 3 Copynumber: 18.0 Consensus size: 3
590502 TTTTTTTAGT
* *
590512 TTA TTA TTA TTA TTA TTA TTA TAA ATA TTA TTA -TA TATA TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA T-TA TTA
590558 TTA TTA TTA
1 TTA TTA TTA
590567 AATAAAACCC
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
2 2 0.04
3 37 0.80
4 7 0.15
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:591916 original size:2 final size:2
Alignment explanation
Indices: 591909--591935 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
591899 TTTTATAAAT
591909 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
591936 TTAATGTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:591969 original size:19 final size:22
Alignment explanation
Indices: 591928--591973 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
591918 ATATATATAT
*
591928 ATATATATTTAATGTTTTATTA
1 ATATTTATTTAATGTTTTATTA
591950 ATATTTATTT-AT-TTTT-TTA
1 ATATTTATTTAATGTTTTATTA
591969 ATATT
1 ATATT
591974 AAGAAAGGGC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 8 0.35
20 4 0.17
21 2 0.09
22 9 0.39
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (22 bp):
ATATTTATTTAATGTTTTATTA
Found at i:591988 original size:143 final size:142
Alignment explanation
Indices: 591811--592187 Score: 435
Period size: 143 Copynumber: 2.6 Consensus size: 142
591801 GATAACAATG
*
591811 TTTATTTA-TTTTTAAATATTAAGAAAGGGCAGTCTTAAGGCAACTGGATGTCCATTTTCTGATA
1 TTTATTTATTTTTTTAATATTAAGAAAGGGCAGTCTTAAGGCAACTGGATGTCCATTTTCTGATA
* *
591875 TTTTTAATTAAATAAACATCTTATTTTTATAAATTATATA-T-ATATATATATATATATATATTT
66 TTTTTAAATAAATAAATATCTTATTTTTA-AAATTATATATTAATATAT-TAT-TAT-TATATTT
* *
591938 -AATGTTTTATTAA-TA
127 AAAAGTGTT-TTAATTA
** * **
591953 TTTATTTATTTTTTTAATATTAAGAAAGGGCAGTCTTAAAACAATTGGATGTTTATTTTCTGATA
1 TTTATTTATTTTTTTAATATTAAGAAAGGGCAGTCTTAAGGCAACTGGATGTCCATTTTCTGATA
* * *
592018 TTTTTAAATAAATAAATATCCTATTTTTAAAATTATATATTAATCTATTATTATTATTTTTAGAA
66 TTTTTAAATAAATAAATATCTTATTTTTAAAATTATATATTAATATATTATTATTATATTT--AA
592083 AAGTGTTTTAATTA
129 AAGTGTTTTAATTA
* * * * * *
592097 TTTATTTATTTTTTT-ATATCAAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGTCC-TTTTCTGA
1 TTTATTTATTTTTTTAATAT-TAAG-AAAGGGCAGTCTTAAGGCAACTGGATGTCCATTTTCTGA
* *
592160 TATTTCTAAATAAATAAATATTTTATTT
64 TATTTTTAAATAAATAAATATCTTATTT
592188 ATATTTTATA
Statistics
Matches: 199, Mismatches: 27, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
141 6 0.03
142 21 0.11
143 88 0.44
144 64 0.32
145 20 0.10
ACGTcount: A:0.36, C:0.07, G:0.09, T:0.48
Consensus pattern (142 bp):
TTTATTTATTTTTTTAATATTAAGAAAGGGCAGTCTTAAGGCAACTGGATGTCCATTTTCTGATA
TTTTTAAATAAATAAATATCTTATTTTTAAAATTATATATTAATATATTATTATTATATTTAAAA
GTGTTTTAATTA
Found at i:597719 original size:14 final size:12
Alignment explanation
Indices: 597699--597764 Score: 64
Period size: 12 Copynumber: 5.3 Consensus size: 12
597689 CTCATCCAGC
597699 AAAAAAAGAAGA
1 AAAAAAAGAAGA
597711 AGGAAAAAAGAA-A
1 A--AAAAAAGAAGA
*
597724 AAAAAGAAAAAGA
1 AAAAA-AAGAAGA
597737 AAAAAAAGAA-A
1 AAAAAAAGAAGA
*
597748 AGAAAAAAAAAGA
1 A-AAAAAAGAAGA
597761 AAAA
1 AAAA
597765 TTGAATCAAG
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
11 6 0.13
12 20 0.44
13 10 0.22
14 9 0.20
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAAGA
Found at i:597733 original size:15 final size:15
Alignment explanation
Indices: 597715--597764 Score: 84
Period size: 15 Copynumber: 3.3 Consensus size: 15
597705 AGAAGAAGGA
597715 AAAAAGAAAAAAAAG
1 AAAAAGAAAAAAAAG
597730 AAAAAGAAAAAAAAG
1 AAAAAGAAAAAAAAG
597745 -AAAAGAAAAAAAAAG
1 AAAAAG-AAAAAAAAG
597760 AAAAA
1 AAAAA
597765 TTGAATCAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
14 5 0.15
15 24 0.73
16 4 0.12
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAAAAAG
Found at i:597741 original size:24 final size:24
Alignment explanation
Indices: 597699--597764 Score: 91
Period size: 24 Copynumber: 2.8 Consensus size: 24
597689 CTCATCCAGC
* *
597699 AAAAAAAGAAGAAG-GAAAAAAGA
1 AAAAAAAGAAAAAGAAAAAAAAGA
597722 AAAAAAAGAAAAAGAAAAAAAAGA
1 AAAAAAAGAAAAAGAAAAAAAAGA
597746 AAAGAAAA-AAAAAGAAAAA
1 AAA-AAAAGAAAAAGAAAAA
597765 TTGAATCAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
23 13 0.33
24 22 0.56
25 4 0.10
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (24 bp):
AAAAAAAGAAAAAGAAAAAAAAGA
Found at i:602612 original size:22 final size:22
Alignment explanation
Indices: 602586--602662 Score: 145
Period size: 22 Copynumber: 3.5 Consensus size: 22
602576 ATCTACACTC
602586 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
602608 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
602630 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
602652 TTCAAAGATGA
1 TTCAAAGATGA
602663 AAGCTTTATT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:603465 original size:76 final size:76
Alignment explanation
Indices: 603339--604143 Score: 1414
Period size: 76 Copynumber: 10.6 Consensus size: 76
603329 CTATTTCCCA
*
603339 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
603404 AGCCTTAGGGT
66 AGCCTTAGGGT
603415 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
603480 AGCCTTAGGGT
66 AGCCTTAGGGT
* * *
603491 CATTTGTAAGTCCTACAGTGCATGATGTTTCCAAAAATCCTTCCGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
603556 AGCCTTAGTGT
66 AGCCTTAGGGT
* * *
603567 CATCTATAAGTCCCACAGTACATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
603632 ATCCTTAGGGT
66 AGCCTTAGGGT
*
603643 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
603708 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
603719 CATCTGTAAGTCCTACAGTGTATGATGTTTCCAAAAATCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
603784 AGCCTTAGGGT
66 AGCCTTAGGGT
*
603795 CATCTGTAAGTCCCACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
603860 AGCCTTAGGGT
66 AGCCTTAGGGT
603871 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
603936 AGCCTTAGGGT
66 AGCCTTAGGGT
*
603947 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATTTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
604012 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
604023 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAACCTTCGGGAGCTTTATGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
604088 AACCTTCGGGT
66 AGCCTTAGGGT
* * *
604099 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAA-CCTTCGGG
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGG
604144 TCATCTGTAA
Statistics
Matches: 695, Mismatches: 34, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
75 8 0.01
76 687 0.99
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:604146 original size:46 final size:46
Alignment explanation
Indices: 604075--604179 Score: 203
Period size: 46 Copynumber: 2.3 Consensus size: 46
604065 CGGGAGCTTT
604075 ATGATGTTTTC-AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGC
1 ATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGC
604120 ATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGC
1 ATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGC
604166 ATGATGTTTTCAAA
1 ATGATGTTTTCAAA
604180 CATTTCCATC
Statistics
Matches: 59, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
45 11 0.19
46 48 0.81
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (46 bp):
ATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGC
Found at i:604314 original size:6 final size:6
Alignment explanation
Indices: 604303--604371 Score: 68
Period size: 6 Copynumber: 11.0 Consensus size: 6
604293 TTTTTTCAGT
* * *
604303 TTATTA TTATTA TTATTA TTATAA ATATTA TTATTA TTAATA TTA-TA
1 TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA
604350 TATATATA TATATATA TTATTA
1 T-TAT-TA T-TAT-TA TTATTA
604372 AACAAAATAT
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
5 3 0.05
6 38 0.69
7 3 0.05
8 11 0.20
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (6 bp):
TTATTA
Found at i:604336 original size:24 final size:24
Alignment explanation
Indices: 604304--604371 Score: 91
Period size: 24 Copynumber: 2.7 Consensus size: 24
604294 TTTTTCAGTT
604304 TATTATTATTATTATTATTATAAA
1 TATTATTATTATTATTATTATAAA
* *
604328 TATTATTATTATTAATATTATATA
1 TATTATTATTATTATTATTATAAA
604352 TATATATATATATATTATTA
1 TAT-TAT-TAT-TATTATTA
604372 AACAAAATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
24 25 0.66
25 3 0.08
26 3 0.08
27 7 0.18
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TATTATTATTATTATTATTATAAA
Found at i:605942 original size:134 final size:136
Alignment explanation
Indices: 605652--605948 Score: 365
Period size: 134 Copynumber: 2.2 Consensus size: 136
605642 TATAATTCAA
* * **
605652 TTAGATAACAATGTTTATTTATTTTTAAATATTAAGAAAGGGCAGTCTTAAGGCAACTGGATGTC
1 TTAGA-AA-AATGTTTATTTATTTTTTAATATTAAGAAAGGGCAATCTTAAAACAACTGGATGTC
* *
605717 CATTTTCTGATATTTTTAATTAAATAAACATCTTATTTTTATAAATTATATATATATATATATAT
64 CATTTTCTGATATTTTTAAATAAATAAACATCCTATTTTTATAAATTATATATATATATATATAT
605782 TAAATGTT
129 TAAATGTT
** *
605790 TT--ATTAATATTTATTTATTTTTTAATATTAAGAAAGGGCAATCTTAAAACAACTGGATGTCCA
1 TTAGAAAAATGTTTATTTATTTTTTAATATTAAGAAAGGGCAATCTTAAAACAACTGGATGTCCA
* * *
605853 TTTTTTGATATTTTTAAATAAATAAATA-CCTATTTTTA-AAATTATATAT-TA-ATCTATTATT
66 TTTTCTGATATTTTTAAATAAATAAACATCCTATTTTTATAAATTATATATATATATATA-TATT
*
605914 ATTAT-TT
130 A-AATGTT
*
605921 TTAGAAAAATGTTTTAATTATTTATTTA
1 TTAGAAAAATG-TTTATTTATTT-TTTA
605949 TTTTTTATAT
Statistics
Matches: 136, Mismatches: 17, Indels: 15
0.81 0.10 0.09
Matches are distributed among these distances:
130 4 0.03
131 11 0.08
132 13 0.10
133 13 0.10
134 88 0.65
135 4 0.03
136 1 0.01
138 2 0.01
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.47
Consensus pattern (136 bp):
TTAGAAAAATGTTTATTTATTTTTTAATATTAAGAAAGGGCAATCTTAAAACAACTGGATGTCCA
TTTTCTGATATTTTTAAATAAATAAACATCCTATTTTTATAAATTATATATATATATATATATTA
AATGTT
Found at i:606067 original size:17 final size:17
Alignment explanation
Indices: 606029--606067 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
606019 AATATTTTAT
606029 TTATATTTTATATATAA
1 TTATATTTTATATATAA
* * *
606046 ATATATTTTTTATATAC
1 TTATATTTTATATATAA
606063 TTATA
1 TTATA
606068 ACTTTGAAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (17 bp):
TTATATTTTATATATAA
Found at i:615369 original size:15 final size:15
Alignment explanation
Indices: 615349--615379 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
615339 CAAAAAATTA
615349 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
615364 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
615379 A
1 A
615380 TTTAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:615576 original size:20 final size:20
Alignment explanation
Indices: 615540--615577 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
615530 ATCCTATTCC
**
615540 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
615560 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
615578 GTGAACCAAA
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:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:616043 original size:140 final size:138
Alignment explanation
Indices: 615789--616125 Score: 460
Period size: 140 Copynumber: 2.4 Consensus size: 138
615779 TTAATACAGT
* * *
615789 TGAATATTCGATTTGGTCCTCGCCTTAATACTCCAGTTTCCATTTTGATTATTTGATTCAAAAAT
1 TGAATATTCGATTTGGT-CTCGCCTTAAT-GTCCAGGTTCCATTTTGATTATTCGATTCAAAAAT
* * *
615854 TGATTAAAATCAATTAGGATTAATAATTAGAGCCTCCACTCTAGGTTAATTTTACTTTTAGTCCT
64 TGATTAAAATCAATTAGGATTAATAATTAGAGCATCCACTCTAGATTAATTTTACTTTTAGACCT
615919 TTAATTTAGG
129 TTAATTTAGG
* * * *
615929 TGAATATTCGATTTGGTACTCACCTTAATGTCCAAGGTTCCGTTTTAATTATTCGATTCAATAAT
1 TGAATATTCGATTTGGT-CTCGCCTTAATGTCC-AGGTTCCATTTTGATTATTCGATTCAAAAAT
** * *
615994 TGATTAAAATCAATTAGGATTAATAATTAGAGCATGTATTTTAGATTAATTTTACTTTTAGACCT
64 TGATTAAAATCAATTAGGATTAATAATTAGAGCATCCACTCTAGATTAATTTTACTTTTAGACCT
616059 TTAATTTAGG
129 TTAATTTAGG
* * *
616069 -GAATATTCGATTTGGTCATCGCCTTAATGCCCGAGGTTCAATTTTGACTATTCGATT
1 TGAATATTCGATTTGGTC-TCGCCTTAATGTCC-AGGTTCCATTTTGATTATTCGATT
616126 ATGTAATTTG
Statistics
Matches: 173, Mismatches: 22, Indels: 5
0.87 0.11 0.03
Matches are distributed among these distances:
138 1 0.01
139 51 0.29
140 121 0.70
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.42
Consensus pattern (138 bp):
TGAATATTCGATTTGGTCTCGCCTTAATGTCCAGGTTCCATTTTGATTATTCGATTCAAAAATTG
ATTAAAATCAATTAGGATTAATAATTAGAGCATCCACTCTAGATTAATTTTACTTTTAGACCTTT
AATTTAGG
Found at i:616174 original size:139 final size:140
Alignment explanation
Indices: 615789--616174 Score: 408
Period size: 140 Copynumber: 2.8 Consensus size: 140
615779 TTAATACAGT
* * * * * * * * *
615789 TGAATATTCGATTTGGTCCTCGCCTTAATACTCC-AGTTTCCATTTTGATTATTTGATTCAAAAA
1 TGAATATTCGATTTGGTACTCACCTTAATGC-CCAAGGTTCAATTTTAACTATTCGATTCAATAA
* * * * * *
615853 TTGATTAAAATCAATTAGGATTAATAATTAGAGCCTCCACTCTAGGTTAATTTTACTTTTAGTCC
65 TTGACTAAAATCAATTAGGATTAATAATTAGAGCCTACATTTTAGATTAATTTTACTTTTAGACC
615918 TTTAATTTAGG
130 TTTAATTTAGG
* ** *
615929 TGAATATTCGATTTGGTACTCACCTTAATGTCCAAGGTTCCGTTTTAATTATTCGATTCAATAAT
1 TGAATATTCGATTTGGTACTCACCTTAATGCCCAAGGTTCAATTTTAACTATTCGATTCAATAAT
* * **
615994 TGATTAAAATCAATTAGGATTAATAATTAGAGCATGTATTTTAGATTAATTTTACTTTTAGACCT
66 TGACTAAAATCAATTAGGATTAATAATTAGAGCCTACATTTTAGATTAATTTTACTTTTAGACCT
616059 TTAATTTAGG
131 TTAATTTAGG
* * * *
616069 -GAATATTCGATTTGGT-CATCGCCTTAATGCCCGAGGTTCAATTTTGACTATTCGATT-ATGTA
1 TGAATATTCGATTTGGTAC-TCACCTTAATGCCCAAGGTTCAATTTTAACTATTCGATTCA-ATA
* *
616131 ATTTG-CTAAAAT-ATGTTTAGGACTAAT-ATTAGAGCCTACATTTT
64 A-TTGACTAAAATCA--ATTAGGATTAATAATTAGAGCCTACATTTT
616175 TAGGTTTAGT
Statistics
Matches: 210, Mismatches: 30, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
138 3 0.01
139 73 0.35
140 134 0.64
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (140 bp):
TGAATATTCGATTTGGTACTCACCTTAATGCCCAAGGTTCAATTTTAACTATTCGATTCAATAAT
TGACTAAAATCAATTAGGATTAATAATTAGAGCCTACATTTTAGATTAATTTTACTTTTAGACCT
TTAATTTAGG
Found at i:620740 original size:13 final size:12
Alignment explanation
Indices: 620720--620779 Score: 66
Period size: 13 Copynumber: 4.8 Consensus size: 12
620710 ACAATACAAA
620720 ACTTTCATATCTC
1 ACTTTCATAT-TC
*
620733 ATTTTCATCATTC
1 ACTTTCAT-ATTC
620746 ACTTTCATATTC
1 ACTTTCATATTC
*
620758 ACTTTCACATTTC
1 ACTTTCATA-TTC
*
620771 ATTTTCATA
1 ACTTTCATA
620780 ATTCGTACTT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
12 12 0.30
13 26 0.65
14 2 0.05
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (12 bp):
ACTTTCATATTC
Found at i:620796 original size:28 final size:25
Alignment explanation
Indices: 620722--620800 Score: 88
Period size: 25 Copynumber: 3.0 Consensus size: 25
620712 AATACAAAAC
* *
620722 TTTCATATCTCATTTTCATCA-TTCAC
1 TTTCATAT-TCACTTTCA-CATTTCAT
620748 TTTCATATTCACTTTCACATTTCAT
1 TTTCATATTCACTTTCACATTTCAT
620773 TTTCATAATTCGTACTTTCACATTTCAT
1 TTTCAT-ATTC--ACTTTCACATTTCAT
620801 AACTCATTCT
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
24 2 0.04
25 18 0.38
26 12 0.26
28 15 0.32
ACGTcount: A:0.24, C:0.24, G:0.01, T:0.51
Consensus pattern (25 bp):
TTTCATATTCACTTTCACATTTCAT
Found at i:620855 original size:18 final size:18
Alignment explanation
Indices: 620832--620885 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
620822 CATGTTTATG
620832 GATTCATAACTTATTTTA
1 GATTCATAACTTATTTTA
*
620850 GATTCATAACTTAATTTCA
1 GATTCATAACTT-ATTTTA
* *
620869 TATTCATAGCTTATTTT
1 GATTCATAACTTATTTT
620886 CAAGTTCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
18 16 0.52
19 15 0.48
ACGTcount: A:0.31, C:0.13, G:0.06, T:0.50
Consensus pattern (18 bp):
GATTCATAACTTATTTTA
Found at i:620873 original size:19 final size:19
Alignment explanation
Indices: 620832--620887 Score: 69
Period size: 19 Copynumber: 3.0 Consensus size: 19
620822 CATGTTTATG
*
620832 GATTCATAACTT-ATTTTA
1 GATTCATAACTTAATTTCA
620850 GATTCATAACTTAATTTCA
1 GATTCATAACTTAATTTCA
* * *
620869 TATTCATAGCTTATTTTCA
1 GATTCATAACTTAATTTCA
620888 AGTTCACAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
18 12 0.36
19 21 0.64
ACGTcount: A:0.32, C:0.14, G:0.05, T:0.48
Consensus pattern (19 bp):
GATTCATAACTTAATTTCA
Found at i:622762 original size:30 final size:31
Alignment explanation
Indices: 622700--622772 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 31
622690 TACACATCAA
**
622700 CCCCATAACTTTTCAAAATTATTGAATAGGT
1 CCCCATAACTTTTCAAAATTATAAAATAGGT
*
622731 CCCC-TAACTTTCTCAAAATTA-AAAATTGGT
1 CCCCATAACTTT-TCAAAATTATAAAATAGGT
**
622761 CCAAATAACTTT
1 CCCCATAACTTT
622773 CTAAAGCTTG
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
30 15 0.43
31 20 0.57
ACGTcount: A:0.37, C:0.22, G:0.07, T:0.34
Consensus pattern (31 bp):
CCCCATAACTTTTCAAAATTATAAAATAGGT
Found at i:625897 original size:20 final size:20
Alignment explanation
Indices: 625874--625912 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
625864 GATTCAACTC
625874 GAACCAAACTGAGTCAACCT
1 GAACCAAACTGAGTCAACCT
***
625894 GAACCGGCCTGAGTCAACC
1 GAACCAAACTGAGTCAACC
625913 CTAACTGGTC
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:0.33, C:0.33, G:0.21, T:0.13
Consensus pattern (20 bp):
GAACCAAACTGAGTCAACCT
Found at i:630554 original size:22 final size:22
Alignment explanation
Indices: 630529--630570 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
630519 ACCAGACCCG
630529 TTGACT-TTGACCTTTGACCAGT
1 TTGACTGTTGA-CTTTGACCAGT
630551 TTGACTGTTGACTTTGACCA
1 TTGACTGTTGACTTTGACCA
630571 AAACGTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.40
Consensus pattern (22 bp):
TTGACTGTTGACTTTGACCAGT
Found at i:632753 original size:41 final size:41
Alignment explanation
Indices: 632610--632755 Score: 130
Period size: 41 Copynumber: 3.5 Consensus size: 41
632600 TCCGAGCCTA
* * *
632610 ATGATTAAATCCTATGGGTCATATGTAAGTCTTTCGAGCAAG
1 ATGA-TAAATCATTTGGGTCATTTGTAAGTCTTTCGAGCAAG
** * ** * * *
632652 ATGATATGTCATTTGGGCCATTAATAAATCTTTCAAGCATG
1 ATGATAAATCATTTGGGTCATTTGTAAGTCTTTCGAGCAAG
* ** * *
632693 ATGATGAAATCCTCCGGGTCATTTGTCAGTCTTTTGAGCAAG
1 ATGAT-AAATCATTTGGGTCATTTGTAAGTCTTTCGAGCAAG
632735 ATGATAAATCATTTGGGTCAT
1 ATGATAAATCATTTGGGTCAT
632756 CTATAAAGCT
Statistics
Matches: 76, Mismatches: 27, Indels: 3
0.72 0.25 0.03
Matches are distributed among these distances:
41 44 0.58
42 32 0.42
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (41 bp):
ATGATAAATCATTTGGGTCATTTGTAAGTCTTTCGAGCAAG
Found at i:633205 original size:20 final size:20
Alignment explanation
Indices: 633176--633223 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
633166 GTTTTAAAAT
**
633176 TAAA-ATATTATTTATAATA
1 TAAATATATTATAAATAATA
633195 TAAATATATTATAAATAATA
1 TAAATATATTATAAATAATA
*
633215 TTAATATAT
1 TAAATATAT
633224 ACATATGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TAAATATATTATAAATAATA
Found at i:633237 original size:28 final size:29
Alignment explanation
Indices: 633174--633229 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
633164 ATGTTTTAAA
* *
633174 ATTA-AAATATTATTTATAATATAAATAT
1 ATTATAAATAATATTAATAATATAAATAT
*
633202 ATTATAAATAATATTAAT-ATATACATAT
1 ATTATAAATAATATTAATAATATAAATAT
633230 GTTTTAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 13 0.54
29 11 0.46
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (29 bp):
ATTATAAATAATATTAATAATATAAATAT
Found at i:633239 original size:29 final size:30
Alignment explanation
Indices: 633175--633239 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 30
633165 TGTTTTAAAA
* *
633175 TTAAAATATTATTTATAATATAAATATATT
1 TTAAAATAATATTAATAATATAAATATATT
* * *
633205 AT-AAATAATATTAAT-ATATACATATGTT
1 TTAAAATAATATTAATAATATAAATATATT
633233 TTAAAAT
1 TTAAAAT
633240 TAAGTTGTAT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
28 12 0.43
29 15 0.54
30 1 0.04
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (30 bp):
TTAAAATAATATTAATAATATAAATATATT
Found at i:633435 original size:34 final size:35
Alignment explanation
Indices: 633385--633456 Score: 94
Period size: 35 Copynumber: 2.1 Consensus size: 35
633375 TTTTTAGTTA
633385 TTTTATTTAAATATTAAA-TAAAAAATAAAAATAT
1 TTTTATTTAAATATTAAATTAAAAAATAAAAATAT
** *
633419 TTTTATATTAAA-ATTAAATTTTAAAATAAAAGTAT
1 TTTTAT-TTAAATATTAAATTAAAAAATAAAAATAT
633454 TTT
1 TTT
633457 AATAATTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
34 12 0.36
35 21 0.64
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (35 bp):
TTTTATTTAAATATTAAATTAAAAAATAAAAATAT
Found at i:633457 original size:34 final size:33
Alignment explanation
Indices: 633383--633457 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 33
633373 TATTTTTAGT
633383 TATTTTATTTAAATATTAAATAAAAAATAAAAA
1 TATTTTATTTAAATATTAAATAAAAAATAAAAA
** *
633416 TATTTTTATATTAAA-ATTAAATTTTAAAATAAAAG
1 TA-TTTTAT-TTAAATATTAAA-TAAAAAATAAAAA
633451 TATTTTA
1 TATTTTA
633458 ATAATTTTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
33 2 0.06
34 17 0.47
35 17 0.47
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.45
Consensus pattern (33 bp):
TATTTTATTTAAATATTAAATAAAAAATAAAAA
Found at i:634492 original size:13 final size:13
Alignment explanation
Indices: 634471--634525 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
634461 AAGTTCGATA
*
634471 AATTTAAATACTT
1 AATTGAAATACTT
634484 AATTGAAATACTT
1 AATTGAAATACTT
* *
634497 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
634511 AATTGAAATACTT
1 AATTGAAATACTT
634524 AA
1 AA
634526 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.11, G:0.04, T:0.36
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:634607 original size:32 final size:33
Alignment explanation
Indices: 634511--634609 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
634501 AACTCAACAT
* * *
634511 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
634544 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
634577 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
634609 A
1 A
634610 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:634628 original size:21 final size:21
Alignment explanation
Indices: 634604--634643 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
634594 ACTTCAAGTT
634604 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
634625 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
634644 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:637658 original size:5 final size:5
Alignment explanation
Indices: 637648--637948 Score: 520
Period size: 5 Copynumber: 59.8 Consensus size: 5
637638 TCGTTTGTTG
637648 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
637698 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
637748 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA -T-TATA
637800 TTATA TTATA -TATA TTATA TTATA TTATA TTATA TTATA -TATA -TATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
637847 TATATA TTATA TTATA TTATA TTATA TTATA TTATA TATATA TATATA
1 T-TATA TTATA TTATA TTATA TTATA TTATA TTATA T-TATA T-TATA
637895 TATATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA -TATA
1 T-TATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
637945 TTAT
1 TTAT
637949 TATTTATTTT
Statistics
Matches: 289, Mismatches: 0, Indels: 14
0.95 0.00 0.05
Matches are distributed among these distances:
4 16 0.06
5 245 0.85
6 24 0.08
7 4 0.01
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TTATA
Found at i:641718 original size:6 final size:6
Alignment explanation
Indices: 641707--641743 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
641697 TAAGTCGAAG
641707 AAGAAA AAGAAA AAG-AA AAGAAA AA-AAA AGAGAAA AA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA A-AGAAA AA
641744 CGTTTAGGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
5 9 0.32
6 15 0.54
7 4 0.14
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:641724 original size:12 final size:12
Alignment explanation
Indices: 641707--641743 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
641697 TAAGTCGAAG
641707 AAGAAAAAGAAA
1 AAGAAAAAGAAA
641719 AAG-AAAAGAAA
1 AAGAAAAAGAAA
641730 AA-AAAAGAGAAA
1 AAGAAAA-AGAAA
641742 AA
1 AA
641744 CGTTTAGGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (12 bp):
AAGAAAAAGAAA
Found at i:641729 original size:17 final size:17
Alignment explanation
Indices: 641707--641742 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
641697 TAAGTCGAAG
641707 AAGAAAAAGAAAA-AGAA
1 AAGAAAAA-AAAAGAGAA
641724 AAGAAAAAAAAAGAGAA
1 AAGAAAAAAAAAGAGAA
641741 AA
1 AA
641743 ACGTTTAGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (17 bp):
AAGAAAAAAAAAGAGAA
Found at i:642687 original size:56 final size:55
Alignment explanation
Indices: 642569--642717 Score: 163
Period size: 56 Copynumber: 2.6 Consensus size: 55
642559 GCTAGAGTAA
**** * *
642569 ATTTCAACTTCACAACGAAGGATATTGGGCTCAAAGCGACACTATTTACTCGAGATTGG
1 ATTTCAACTTCACAACGAAGGATATCCAACTCAAA---AC-CAATTTACTCGAGATTAG
* *
642628 ATTTCAACTTCACAAATGAAGGATATCCAACTCAAAACCAATTTACTCTAGATTAG
1 ATTTCAACTTCAC-AACGAAGGATATCCAACTCAAAACCAATTTACTCGAGATTAG
* *
642684 ATTTCAACTTCACGACGAAGGATATCCAATTCAA
1 ATTTCAACTTCACAACGAAGGATATCCAACTCAA
642718 GGCTCAACTT
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
55 18 0.23
56 28 0.36
57 2 0.03
59 13 0.17
60 17 0.22
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28
Consensus pattern (55 bp):
ATTTCAACTTCACAACGAAGGATATCCAACTCAAAACCAATTTACTCGAGATTAG
Found at i:643095 original size:249 final size:250
Alignment explanation
Indices: 642806--643399 Score: 874
Period size: 251 Copynumber: 2.4 Consensus size: 250
642796 CTTCAAATTG
* * * *
642806 GATTTCAACTTCACGACGAAGGATATCCAATTCGAGGCTCAACTTCATAATGAATGAGCCATCCA
1 GATTTAAACTTCACGACGAAGGATATCCAATTCGAGGCTCAACTTCACAATGAAAGGGCCATCCA
* * * * *
642871 CGATTTCAATTTCACGACGAAGGATATCGTGC-CA-ACTCTAG-ATTGGATTTCGACTTCACGAC
66 CGATTTCAACTTCACGACGAAGGATATCGT-CTCACA-ACAAGCATTGGATTTCAACTTCACAAC
*
642933 GAAGGATATCCAATTCAAAGCTCAACTTCACAGCGAAGGGGCTTCCCAGTTTCATTCAGAGCTAA
129 GAAGGATATCCAATTCAAAGCTCAACTTCACAGCGAAGGGGCTTCCCAGTTTCATTCAGAGCCAA
*
642998 TTTCAACTTCACGGCGAAGGATATTGGTA-TCGAAACAATACAACTTACACAAGATTA
194 TTTCAACTTCACGGCGAAGGATATTGG-ACTCGAAACAACACAACTTACACAAGATTA
* * *
643055 GATTTAAACTTCACGACGAAAGATATCCAATCCAAGGCTCAACTTCACAATGAAAGGGCCATCCA
1 GATTTAAACTTCACGACGAAGGATATCCAATTCGAGGCTCAACTTCACAATGAAAGGGCCATCCA
*
643120 CGATTTCAACTTCACGACGAAGGATATCGTCTTCACAAGAAGCATTGGATTTCAACTTCACAACG
66 CGATTTCAACTTCACGACGAAGGATATCGTC-TCACAACAAGCATTGGATTTCAACTTCACAACG
* * *
643185 AATGATATCCAATTCAAAGCTCAACTTTACAGCGAATGGGCTTCCCAGTTTCATTCAGAGCCAAT
130 AAGGATATCCAATTCAAAGCTCAACTTCACAGCGAAGGGGCTTCCCAGTTTCATTCAGAGCCAAT
* * * *
643250 TTCAACTTCATGGCGAAGGATATTGGACTTGAAACAACGCAACTTACACAAGATTG
195 TTCAACTTCACGGCGAAGGATATTGGACTCGAAACAACACAACTTACACAAGATTA
* * * *
643306 GATTTTAACTTCACGACGAAGGATATCCAATTCGAGGCTCAACTTCACAA-CAAGGGGCCATCTA
1 GATTTAAACTTCACGACGAAGGATATCCAATTCGAGGCTCAACTTCACAATGAAAGGGCCATCCA
*
643370 CGATTTCAACTTCACGATGAAGGATATCGT
66 CGATTTCAACTTCACGACGAAGGATATCGT
643400 ACCCGAAAGA
Statistics
Matches: 310, Mismatches: 30, Indels: 9
0.89 0.09 0.03
Matches are distributed among these distances:
248 1 0.00
249 87 0.28
250 45 0.15
251 177 0.57
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.25
Consensus pattern (250 bp):
GATTTAAACTTCACGACGAAGGATATCCAATTCGAGGCTCAACTTCACAATGAAAGGGCCATCCA
CGATTTCAACTTCACGACGAAGGATATCGTCTCACAACAAGCATTGGATTTCAACTTCACAACGA
AGGATATCCAATTCAAAGCTCAACTTCACAGCGAAGGGGCTTCCCAGTTTCATTCAGAGCCAATT
TCAACTTCACGGCGAAGGATATTGGACTCGAAACAACACAACTTACACAAGATTA
Found at i:644947 original size:18 final size:18
Alignment explanation
Indices: 644920--644959 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
644910 AACTTAATCC
644920 TTTT-ATTTTATTT-TATT
1 TTTTAATTTTATTTCT-TT
644937 TTTTAATTTTATTTCTTT
1 TTTTAATTTTATTTCTTT
644955 TTTTA
1 TTTTA
644960 TATACGATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 4 0.19
18 16 0.76
19 1 0.05
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTAATTTTATTTCTTT
Found at i:645036 original size:17 final size:17
Alignment explanation
Indices: 645016--645051 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
645006 TATTTGCGTA
645016 TTTCTT-TTTTATATATT
1 TTTCTTCTTTT-TATATT
645033 TTTCTTCTTTTTATATT
1 TTTCTTCTTTTTATATT
645050 TT
1 TT
645052 ATATTTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.14, C:0.08, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTCTTCTTTTTATATT
Found at i:645053 original size:7 final size:7
Alignment explanation
Indices: 645041--645070 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
645031 TTTTTCTTCT
645041 TTTTATA
1 TTTTATA
645048 TTTTATA
1 TTTTATA
645055 TTTTATA
1 TTTTATA
645062 TTTTTATA
1 -TTTTATA
645070 T
1 T
645071 ATTTTTTACT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTTATA
Found at i:645060 original size:14 final size:15
Alignment explanation
Indices: 645041--645070 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
645031 TTTTTCTTCT
645041 TTTTATA-TTTTATA
1 TTTTATATTTTTATA
645055 TTTTATATTTTTATA
1 TTTTATATTTTTATA
645070 T
1 T
645071 ATTTTTTACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTTATATTTTTATA
Found at i:645267 original size:21 final size:22
Alignment explanation
Indices: 645226--645269 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
645216 ATATTGATTT
*
645226 TTTATTTTATTTTTGTTTTATA
1 TTTATTTTATTTTTGTATTATA
645248 TTTA-TTTATTTATT-TATTATA
1 TTTATTTTATTT-TTGTATTATA
645269 T
1 T
645270 ATGTTGTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (22 bp):
TTTATTTTATTTTTGTATTATA
Found at i:645360 original size:13 final size:13
Alignment explanation
Indices: 645342--645384 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
645332 TTTTATCTTG
645342 TTTTATTTATTTA
1 TTTTATTTATTTA
* *
645355 TTTTATTTATCTC
1 TTTTATTTATTTA
*
645368 TTTTATGTATTTCA
1 TTTTATTTATTT-A
645382 TTT
1 TTT
645385 CTTGCCCTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
13 21 0.88
14 3 0.12
ACGTcount: A:0.19, C:0.07, G:0.02, T:0.72
Consensus pattern (13 bp):
TTTTATTTATTTA
Found at i:648253 original size:9 final size:10
Alignment explanation
Indices: 648231--648256 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
648221 AATACATTAC
648231 AAAATAATGA
1 AAAATAATGA
648241 AAAATAATGA
1 AAAATAATGA
648251 AAAATA
1 AAAATA
648257 TAAAATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.19
Consensus pattern (10 bp):
AAAATAATGA
Found at i:648259 original size:22 final size:23
Alignment explanation
Indices: 648209--648259 Score: 54
Period size: 22 Copynumber: 2.3 Consensus size: 23
648199 TTTTTATCAT
* *
648209 AAATA-AATAAAAAATACATTAC
1 AAATATAATAAAAAATACATGAA
*
648231 AAA-ATAATGAAAAATA-ATGAA
1 AAATATAATAAAAAATACATGAA
648252 AAATATAA
1 AAATATAA
648260 AATTAAAGCG
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.22
Consensus pattern (23 bp):
AAATATAATAAAAAATACATGAA
Found at i:649970 original size:20 final size:21
Alignment explanation
Indices: 649945--649985 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
649935 GGTTGCATCT
649945 AAAAT-GTTATAAACGGTAAG
1 AAAATAGTTATAAACGGTAAG
*
649965 AAAATGAGTTATGAACGGTAA
1 AAAAT-AGTTATAAACGGTAA
649986 ATGTTATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
22 13 0.72
ACGTcount: A:0.49, C:0.05, G:0.22, T:0.24
Consensus pattern (21 bp):
AAAATAGTTATAAACGGTAAG
Found at i:650392 original size:185 final size:182
Alignment explanation
Indices: 650010--650518 Score: 563
Period size: 185 Copynumber: 2.8 Consensus size: 182
650000 ATTAACATTT
* * *
650010 TAGGTTGCACCTAAAATGTTACTAGAGTTTAAGTTGATGGTGTCTTAGATATTTTCACGATAAAA
1 TAGGTTGCACCTAAAATGTTACTAGAGTTTAAGTTGATGGGGTCTTAGACATTCTCACGATAAAA
* * * * *
650075 ATAATAATTTAATAGCTAAAAATGTTATGAATA--AT---AAGGTTGTG-CCAAAAATTTCACGG
66 A-AATAAGTTAATAGCTAAAAATGTTATGAATATTATAAAAACGTTGTGCCCAAGAATGTCATGG
* *
650134 TTCACTAAGAAA-TATGTTGTGATATGTAATGTTAATATTTTTATTAATAAAA
130 TTCACTAAGAAAGTAGGTTGTCATATGTAATGTTAATATTTTTATTAATAAAA
* * * *
650186 TAGGTTGAACCTAAAATGTTACTAGAGTTTAGGTTGATGGGGTCTTAGACATTCTCACAATAACA
1 TAGGTTGCACCTAAAATGTTACTAGAGTTTAAGTTGATGGGGTCTTAGACATTCTCACGATAAAA
650251 AAATAAGTTAATAGCTAAAAATGTTATGAATATCTATAACAAACGATTGTGCCCAAGAATGTCAT
66 AAATAAGTTAATAGCTAAAAATGTTATGAATAT-TATAA-AAACG-TTGTGCCCAAGAATGTCAT
* *
650316 GGTTCATTAAGAAAGTAGGTTGTCATCTAG-AATGTTAATATTTTTATTAATAAAA
128 GGTTCACTAAGAAAGTAGGTTGTCATAT-GTAATGTTAATATTTTTATTAATAAAA
* * * * * * * * *
650371 T-GGATTGCGCCTAAAATGTTACTAGAATTTAAGCTAATAGGGCCTTAAACATTCCCACGATAAG
1 TAGG-TTGCACCTAAAATGTTACTAGAGTTTAAGTTGATGGGGTCTTAGACATTCTCACGATAAA
* * ** * *
650435 GAAA-AAGTTAAAAGCTGTAAATATTATGAATATTTATAATAAATAACGTTGCGCCCAAGAATGT
65 AAAATAAGTTAATAGCTAAAAATGTTATGAATA--T-T-ATAAA-AACGTTGTGCCCAAGAATGT
650499 CATGGTTCACTAA-AAAGTAG
125 CATGGTTCACTAAGAAAGTAG
650519 ATTGCAATCG
Statistics
Matches: 281, Mismatches: 36, Indels: 23
0.83 0.11 0.07
Matches are distributed among these distances:
175 30 0.11
176 59 0.21
178 2 0.01
182 3 0.01
183 5 0.02
184 49 0.17
185 94 0.33
186 31 0.11
187 8 0.03
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (182 bp):
TAGGTTGCACCTAAAATGTTACTAGAGTTTAAGTTGATGGGGTCTTAGACATTCTCACGATAAAA
AAATAAGTTAATAGCTAAAAATGTTATGAATATTATAAAAACGTTGTGCCCAAGAATGTCATGGT
TCACTAAGAAAGTAGGTTGTCATATGTAATGTTAATATTTTTATTAATAAAA
Found at i:652233 original size:20 final size:19
Alignment explanation
Indices: 652204--652261 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 19
652194 TAATGGGTCA
*
652204 GGTCGATTCGAGTTGACTC
1 GGTCGGTTCGAGTTGACTC
652223 GGGTCGGTTCG-GTTGACTC
1 -GGTCGGTTCGAGTTGACTC
* *
652242 GGACTGGTTCAAGTTGACTC
1 GGTC-GGTTCGAGTTGACTC
652262 TAACCAATTC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 3 0.09
19 13 0.39
20 17 0.52
ACGTcount: A:0.14, C:0.21, G:0.34, T:0.31
Consensus pattern (19 bp):
GGTCGGTTCGAGTTGACTC
Found at i:652239 original size:19 final size:20
Alignment explanation
Indices: 652204--652243 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
652194 TAATGGGTCA
652204 GGTCGATTCGAGTTGACTCG
1 GGTCGATTCGAGTTGACTCG
*
652224 GGTCGGTTCG-GTTGACTCG
1 GGTCGATTCGAGTTGACTCG
652243 G
1 G
652244 ACTGGTTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.10, C:0.20, G:0.40, T:0.30
Consensus pattern (20 bp):
GGTCGATTCGAGTTGACTCG
Found at i:652250 original size:19 final size:19
Alignment explanation
Indices: 652210--652261 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 19
652200 GTCAGGTCGA
*
652210 TTCGAGTTGACTCGGGTCGG
1 TTCG-GTTGACTCGGCTCGG
652230 TTCGGTTGACTCGGACT-GG
1 TTCGGTTGACTCGG-CTCGG
*
652249 TTCAAGTTGACTC
1 TTC-GGTTGACTC
652262 TAACCAATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.13, C:0.21, G:0.33, T:0.33
Consensus pattern (19 bp):
TTCGGTTGACTCGGCTCGG
Found at i:663095 original size:6 final size:6
Alignment explanation
Indices: 663084--663147 Score: 60
Period size: 6 Copynumber: 10.7 Consensus size: 6
663074 AATTATGCTG
* * *
663084 ATTTCA ATTTCA ATTTGC- A-TTCGA ATTTTA ATTTCA ATTTTA ATTTGA
1 ATTTCA ATTTCA ATTT-CA ATTTC-A ATTTCA ATTTCA ATTTCA ATTTCA
*
663132 ATTTGA ATTTCA ATTT
1 ATTTCA ATTTCA ATTT
663148 GAGCTCCACT
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
4 1 0.02
5 2 0.04
6 43 0.88
7 3 0.06
ACGTcount: A:0.31, C:0.09, G:0.06, T:0.53
Consensus pattern (6 bp):
ATTTCA
Found at i:663116 original size:24 final size:24
Alignment explanation
Indices: 663084--663149 Score: 87
Period size: 24 Copynumber: 2.8 Consensus size: 24
663074 AATTATGCTG
*
663084 ATTTCAATTTCAATTTGCATTCGA
1 ATTTCAATTTCAATTTGAATTCGA
* * *
663108 ATTTTAATTTCAATTTTAATTTGA
1 ATTTCAATTTCAATTTGAATTCGA
*
663132 ATTTGAATTTCAATTTGA
1 ATTTCAATTTCAATTTGA
663150 GCTCCACTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.32, C:0.09, G:0.08, T:0.52
Consensus pattern (24 bp):
ATTTCAATTTCAATTTGAATTCGA
Found at i:663122 original size:12 final size:12
Alignment explanation
Indices: 663084--663149 Score: 71
Period size: 12 Copynumber: 5.5 Consensus size: 12
663074 AATTATGCTG
*
663084 ATTTCAATTTCA
1 ATTTGAATTTCA
*
663096 ATTTGCA-TTCGA
1 ATTTGAATTTC-A
*
663108 ATTTTAATTTCA
1 ATTTGAATTTCA
* *
663120 ATTTTAATTTGA
1 ATTTGAATTTCA
663132 ATTTGAATTTCA
1 ATTTGAATTTCA
663144 ATTTGA
1 ATTTGA
663150 GCTCCACTAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
11 3 0.07
12 39 0.87
13 3 0.07
ACGTcount: A:0.32, C:0.09, G:0.08, T:0.52
Consensus pattern (12 bp):
ATTTGAATTTCA
Found at i:663128 original size:18 final size:18
Alignment explanation
Indices: 663084--663147 Score: 67
Period size: 18 Copynumber: 3.6 Consensus size: 18
663074 AATTATGCTG
*
663084 ATTTCAATTTCAATTTGC
1 ATTTCAATTTCAATTTGA
* *
663102 A-TTCGAATTTTAATTTCA
1 ATTTC-AATTTCAATTTGA
* *
663120 ATTTTAATTTGAATTTGA
1 ATTTCAATTTCAATTTGA
663138 ATTTCAATTT
1 ATTTCAATTT
663148 GAGCTCCACT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
17 3 0.08
18 32 0.86
19 2 0.05
ACGTcount: A:0.31, C:0.09, G:0.06, T:0.53
Consensus pattern (18 bp):
ATTTCAATTTCAATTTGA
Found at i:663962 original size:214 final size:214
Alignment explanation
Indices: 663539--664343 Score: 1183
Period size: 214 Copynumber: 3.8 Consensus size: 214
663529 TGTAATGAAA
* *
663539 TATCGATACTTAGTTAAATTAACAATGTAAACGGTAAAAGTCTACCGGTGTAATGAAAATAGGCG
1 TATCGATACTTAGCTAAATTAACAATGTAAACGGTAAAAGTCTACTGGTGTAATGAAAATAGGCG
* * * *
663604 TAAATAAAAAGTATAACTCCTTGTTTTTTACGACAATTTTCATTATACCGG--AA--TTTATCCG
66 TAAATAAAAAGTATCACTACTTGTTATTTACGACAATTTTCATTATACCGGAAAACTTTTATCTG
663665 TTTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTCCAAGTATCGATACTT
131 TTTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTCCAAGTATCGATACTT
*
663730 GTTATTTACATATATAAAG
196 GTTATTTACATGTATAAAG
* * * *
663749 TATCAATACTTAGCTAAATTATCAATGTAAACGGTAAAAGTATACTGGTGTAATGAAAATAGGTG
1 TATCGATACTTAGCTAAATTAACAATGTAAACGGTAAAAGTCTACTGGTGTAATGAAAATAGGCG
* * * *
663814 TAAATGACAATTATCACTACTTGTTATTTATGACAATTTTCATTATACCGGAAAACTTTTATCTG
66 TAAATAAAAAGTATCACTACTTGTTATTTACGACAATTTTCATTATACCGGAAAACTTTTATCTG
* * *
663879 TTTACATTGTTAATTTACCTATTATTTTAAATTAATAGGTTTCAAAATTCCAAGTATCGATACTT
131 TTTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTCCAAGTATCGATACTT
663944 GTTATTTACATGTATAAAG
196 GTTATTTACATGTATAAAG
* *
663963 TATCGATACTTAGCTAAATTAATAACGTAAACGGTAAAAGTCTACCT-GTGTAATGAAAATAGGC
1 TATCGATACTTAGCTAAATTAACAATGTAAACGGTAAAAGTCTA-CTGGTGTAATGAAAATAGGC
* * * ** * * *
664027 GTAAATGACAAA-TATCGCTACTTGTTATTTACGACCATTTTCATTATAATGGAACACATTTATT
65 GTAAAT-AAAAAGTATCACTACTTGTTATTTACGACAATTTTCATTATACCGGAAAACTTTTATC
*
664091 TGTTTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTTGAAATTCCAAGTATCGATAC
129 TGTTTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTCCAAGTATCGATAC
664156 TTGTTATTTACATGTATAAAG
194 TTGTTATTTACATGTATAAAG
* *
664177 TATCGATACTTAGGTAAATTAACAATGTAAACGGTAAAAGTCTACTAGTGTAATGAAAATAGGCG
1 TATCGATACTTAGCTAAATTAACAATGTAAACGGTAAAAGTCTACTGGTGTAATGAAAATAGGCG
** * * ** *
664242 TAAATAAAAAGTATTGCTACTTGTTATTTACGTCTATTTTCATTATACCATAACACTTTTAT-TC
66 TAAATAAAAAGTATCACTACTTGTTATTTACGACAATTTTCATTATACCGGAAAACTTTTATCT-
*
664306 ATTTACATTGTTAATTTACCTATTACTTTAAAGTAATA
130 GTTTACATTGTTAATTTACCTATTACTTTAAAGTAATA
664344 AAACACCTAT
Statistics
Matches: 534, Mismatches: 52, Indels: 14
0.89 0.09 0.02
Matches are distributed among these distances:
210 103 0.19
212 2 0.00
213 7 0.01
214 418 0.78
215 4 0.01
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (214 bp):
TATCGATACTTAGCTAAATTAACAATGTAAACGGTAAAAGTCTACTGGTGTAATGAAAATAGGCG
TAAATAAAAAGTATCACTACTTGTTATTTACGACAATTTTCATTATACCGGAAAACTTTTATCTG
TTTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTCCAAGTATCGATACTT
GTTATTTACATGTATAAAG
Found at i:664653 original size:75 final size:72
Alignment explanation
Indices: 664533--664694 Score: 211
Period size: 76 Copynumber: 2.2 Consensus size: 72
664523 CTGAACCAGT
* * *
664533 TAAAATAAAATAGGCTACCTATTACGTTAATCACCTACCGGTTTGT-TTAAAGGTTACTAATAAT
1 TAAAA-AAAATAGGCTACATATTACGTTAATCACCTACCGGTTTGTATAAAAAGTTACTAATAAT
664597 GTAAACGA
65 GTAAACGA
664605 TAAAAGAAAATAGGCATTACATATTACGTTATAAT-ACCTACCGGTTTGTATAAAAAGTTACTAA
1 TAAAA-AAAATAGGC--TACATATTACG-T-TAATCACCTACCGGTTTGTATAAAAAGTTACTAA
*
664669 TAATGTAAACGG
61 TAATGTAAACGA
*
664681 TAAAATAAATAGGC
1 TAAAAAAAATAGGC
664695 GTAAATATCC
Statistics
Matches: 79, Mismatches: 6, Indels: 7
0.86 0.07 0.08
Matches are distributed among these distances:
72 14 0.18
74 10 0.13
75 23 0.29
76 32 0.41
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.30
Consensus pattern (72 bp):
TAAAAAAAATAGGCTACATATTACGTTAATCACCTACCGGTTTGTATAAAAAGTTACTAATAATG
TAAACGA
Found at i:666899 original size:5 final size:5
Alignment explanation
Indices: 666889--666929 Score: 50
Period size: 5 Copynumber: 8.2 Consensus size: 5
666879 AATAATTATC
666889 TTTTA TTTTA TTTTA --TTA TTTTCA TTTTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTT-A -TTTTA TTTTA TTTTA T
666930 CTTTTATATT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
3 3 0.09
5 23 0.72
6 2 0.06
7 4 0.12
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:671047 original size:18 final size:18
Alignment explanation
Indices: 671006--671065 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 18
670996 CATGTATTTG
671006 CATTTTATTTACATTTC-A
1 CATTTTATTTAC-TTTCTA
671024 -AGTTTTATTTACTTTCTA
1 CA-TTTTATTTACTTTCTA
671042 CATTTTATTTGTACTTT-TA
1 CATTTTA-TT-TACTTTCTA
671061 CATTT
1 CATTT
671066 ATCTGTTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
17 5 0.14
18 16 0.43
19 10 0.27
20 6 0.16
ACGTcount: A:0.23, C:0.13, G:0.03, T:0.60
Consensus pattern (18 bp):
CATTTTATTTACTTTCTA
Found at i:674503 original size:15 final size:15
Alignment explanation
Indices: 674483--674521 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
674473 TTGAATGATC
*
674483 AAGCTGAATAAGGAA
1 AAGCTGAAGAAGGAA
674498 AAGCTGAAGAAGGAA
1 AAGCTGAAGAAGGAA
*
674513 AAGCCGAAG
1 AAGCTGAAG
674522 GCATATATCC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.51, C:0.10, G:0.31, T:0.08
Consensus pattern (15 bp):
AAGCTGAAGAAGGAA
Found at i:678323 original size:7 final size:7
Alignment explanation
Indices: 678302--678378 Score: 58
Period size: 7 Copynumber: 11.4 Consensus size: 7
678292 TTGCCTGAAG
678302 AAAA-AA
1 AAAAGAA
678308 AAAAG-A
1 AAAAGAA
678314 AAAAG-A
1 AAAAGAA
678320 AAAAGAAA
1 AAAAG-AA
678328 AAAATGAA
1 AAAA-GAA
678336 AAAAG--
1 AAAAGAA
678341 AAAAGAA
1 AAAAGAA
678348 TAAAA-AA
1 -AAAAGAA
*
678355 ATAAGAA
1 AAAAGAA
*
678362 ATAAGAA
1 AAAAGAA
*
678369 AAAATAA
1 AAAAGAA
678376 AAA
1 AAA
678379 TAAATAAAAG
Statistics
Matches: 60, Mismatches: 3, Indels: 15
0.77 0.04 0.19
Matches are distributed among these distances:
5 5 0.08
6 19 0.32
7 20 0.33
8 15 0.25
9 1 0.02
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.06
Consensus pattern (7 bp):
AAAAGAA
Found at i:678330 original size:21 final size:21
Alignment explanation
Indices: 678304--678372 Score: 79
Period size: 21 Copynumber: 3.3 Consensus size: 21
678294 GCCTGAAGAA
678304 AAAAAAAAGAAAAAGAAAAAG
1 AAAAAAAAGAAAAAGAAAAAG
*
678325 AAAAAAATGAAAAA-AGAAAAG
1 AAAAAAAAGAAAAAGA-AAAAG
* *
678346 AATAAAAA-AATAAGAAATAAG
1 AAAAAAAAGAAAAAGAAA-AAG
678367 AAAAAA
1 AAAAAA
678373 TAAAAATAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
20 7 0.17
21 33 0.82
ACGTcount: A:0.83, C:0.00, G:0.12, T:0.06
Consensus pattern (21 bp):
AAAAAAAAGAAAAAGAAAAAG
Found at i:678370 original size:33 final size:31
Alignment explanation
Indices: 678299--678377 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 31
678289 ATTTTGCCTG
*
678299 AAGAAAAAAAAAAGAAAAAGAAAAAGAAAAA
1 AAGAAAAAAAAAAGAAAAAAAAAAAGAAAAA
*
678330 AATGAAAAAAGAAAAGAATAAAAAAATAAG-AAAT
1 AA-GAAAAAA-AAAAGAA-AAAAAAA-AAGAAAAA
678364 AAGAAAAAATAAAA
1 AAGAAAAAA-AAAA
678378 ATAAATAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
31 2 0.05
32 7 0.17
33 18 0.44
34 11 0.27
35 3 0.07
ACGTcount: A:0.82, C:0.00, G:0.11, T:0.06
Consensus pattern (31 bp):
AAGAAAAAAAAAAGAAAAAAAAAAAGAAAAA
Found at i:678372 original size:17 final size:16
Alignment explanation
Indices: 678299--678381 Score: 57
Period size: 17 Copynumber: 5.1 Consensus size: 16
678289 ATTTTGCCTG
* *
678299 AAGAAAAAAAAAAGAAA
1 AAGAAAAAATAAA-AAT
678316 AAGAAAAAGA-AAAAA-
1 AAGAAAAA-ATAAAAAT
* *
678331 ATGAAAAAAGAAAAGA-
1 AAGAAAAAATAAAA-AT
678347 ATA-AAAAAATAAGAAAT
1 A-AGAAAAAATAA-AAAT
678364 AAGAAAAAATAAAAAT
1 AAGAAAAAATAAAAAT
678380 AA
1 AA
678382 ATAAAAGGGG
Statistics
Matches: 56, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
14 1 0.02
15 11 0.20
16 20 0.36
17 23 0.41
18 1 0.02
ACGTcount: A:0.82, C:0.00, G:0.11, T:0.07
Consensus pattern (16 bp):
AAGAAAAAATAAAAAT
Found at i:678379 original size:16 final size:15
Alignment explanation
Indices: 678305--678388 Score: 66
Period size: 16 Copynumber: 5.5 Consensus size: 15
678295 CCTGAAGAAA
*
678305 AAAAAAAG-AAAAAG
1 AAAAAAAGAAAAAAT
*
678319 AAAAAGA-AAAAAAT
1 AAAAAAAGAAAAAAT
*
678333 GAAAAAAGAAAAGAAT
1 AAAAAAAGAAAA-AAT
* *
678349 AAAAAAATAAGAAAT
1 AAAAAAAGAAAAAAT
678364 AAGAAAAA-ATAAAAAT
1 AA-AAAAAGA-AAAAAT
678380 AAATAAAAG
1 AAA-AAAAG
678389 GGGGATTAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
14 16 0.29
15 11 0.20
16 28 0.51
ACGTcount: A:0.81, C:0.00, G:0.11, T:0.08
Consensus pattern (15 bp):
AAAAAAAGAAAAAAT
Found at i:691143 original size:16 final size:14
Alignment explanation
Indices: 691106--691148 Score: 52
Period size: 13 Copynumber: 3.0 Consensus size: 14
691096 AGGGTTATAC
691106 TATTGTTTTAAAAA
1 TATTGTTTTAAAAA
*
691120 TA-TGTTTTAAACTAT
1 TATTGTTTTAAA--AA
691135 TATTGTTTTAAAAA
1 TATTGTTTTAAAAA
691149 GATCTGTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
13 9 0.38
14 3 0.12
15 3 0.12
16 9 0.38
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (14 bp):
TATTGTTTTAAAAA
Found at i:693435 original size:23 final size:23
Alignment explanation
Indices: 693408--693465 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
693398 ACCTGACTCG
* *
693408 TTGACCATTGACCGATATGACCC
1 TTGACCCTTGACCGATATGAACC
693431 TTGACCCTTGACCGATATGAACC
1 TTGACCCTTGACCGATATGAACC
693454 TTGACCCTTGAC
1 TTGACCCTTGAC
693466 TTTAACCCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.24, C:0.31, G:0.17, T:0.28
Consensus pattern (23 bp):
TTGACCCTTGACCGATATGAACC
Found at i:697315 original size:2 final size:2
Alignment explanation
Indices: 697256--697296 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
697246 TTAGGATTAC
697256 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
697297 ATTAGCTATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:699259 original size:5 final size:5
Alignment explanation
Indices: 699249--699281 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
699239 AATGATTATC
*
699249 TTTTA TTTTA TTTTA TTAT- TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
699282 TCTTTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
4 3 0.12
5 22 0.88
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:699273 original size:14 final size:13
Alignment explanation
Indices: 699254--699291 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
699244 TTATCTTTTA
699254 TTTTATTTTATTAT
1 TTTTATTTTATT-T
699268 TTTTATTTTATTT
1 TTTTATTTTATTT
699281 TTCTT-TTTTAT
1 TT-TTATTTTAT
699292 ATTAGATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 9 0.39
14 14 0.61
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTATTTTATTT
Found at i:699282 original size:20 final size:20
Alignment explanation
Indices: 699243--699281 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
699233 TACTCGAATG
699243 ATTATCTTTTATTTTATTTT
1 ATTATCTTTTATTTTATTTT
699263 ATTAT-TTTTATTTTATTTT
1 ATTATCTTTTATTTTATTTT
699282 TCTTTTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.77
Consensus pattern (20 bp):
ATTATCTTTTATTTTATTTT
Found at i:700141 original size:200 final size:199
Alignment explanation
Indices: 699791--700412 Score: 792
Period size: 200 Copynumber: 3.1 Consensus size: 199
699781 GTTCCGACAA
* * * * *
699791 CGTAAACATCAAGTAT-TGATACTTTTTTTCTCGGTATCGATACTTTTATTCCAGCATGCTTATC
1 CGTAAACATAAAGTATCT-ATAC-TTTTATATCGGTATCGATACTTTTATTCCAGTATGCTTCTC
* * *
699855 AAACAATTTGAACGCAAAAAGTATCGATACACTTGTATAAAGTATCGATATTTGGAATTTCAAAA
64 AAACAATTTGAACGCAAAAAGTATCGATACACATATATAAAGTATCGATACTTGGAATTTCAAAA
* *
699920 CCTATTACTTTAAATTAATAGGTAAATTTACAATGTAAACTGTAAAAGCCTACTGGTATAATGAT
129 CCTATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACTGTAAAAGTCTACTGGTATAATGAT
699985 AATAGG
194 AATAGG
* *
699991 TGTAAACATAAAGTATCTATACTATTTATATCGGTATCGATACTTTTATTCCAATATGCTTCTC-
1 CGTAAACATAAAGTATCTATACT-TTTATATCGGTATCGATACTTTTATTCCAGTATGCTTCTCA
* * *
700055 AACAATTTGTACGCAACAAAGTATCGATAC-CAATAAATAAAGTATCGATA-TTGGTAATTTCGA
65 AACAATTTGAACGCAA-AAAGTATCGATACAC-ATATATAAAGTATCGATACTTGG-AATTTCAA
*
700118 AACCTATTACTTTAAAGTAATAGGTAAATTTACAATGTAAA-TGGTAAAAATCTA-TCGGTATAA
127 AACCTATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACT-GTAAAAGTCTACT-GGTATAA
700181 TGATAATAGG
190 TGATAATAGG
* * * *
700191 CGTAAA-TTATAAGTATCGATACGTTTTATATTGGTATTGATACTTTTATTCCAGTATGCTTCTC
1 CGTAAACATA-AAGTATCTATAC-TTTTATATCGGTATCGATACTTTTATTCCAGTATGCTTCTC
* * * * * **
700255 AAACAATTTGCATGCAAAATGTATCGATACACATATATAAAATATCGATACATACAATTTCAAAA
64 AAACAATTTGAACGCAAAAAGTATCGATACACATATATAAAGTATCGATACTTGGAATTTCAAAA
* * * * *
700320 CCTATTACTTTAAAGTAATAGGTTAATTTACAATGAAAACAGTAAATGTCTACCGGTATAATGAT
129 CCTATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACTGTAAAAGTCTACTGGTATAATGAT
700385 AATAGG
194 AATAGG
*
700391 CGTAAACATCAAA-TATCAATAC
1 CGTAAACAT-AAAGTATCTATAC
700413 ACATGTATAA
Statistics
Matches: 368, Mismatches: 38, Indels: 32
0.84 0.09 0.07
Matches are distributed among these distances:
199 25 0.07
200 321 0.87
201 21 0.06
202 1 0.00
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (199 bp):
CGTAAACATAAAGTATCTATACTTTTATATCGGTATCGATACTTTTATTCCAGTATGCTTCTCAA
ACAATTTGAACGCAAAAAGTATCGATACACATATATAAAGTATCGATACTTGGAATTTCAAAACC
TATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACTGTAAAAGTCTACTGGTATAATGATAA
TAGG
Found at i:701002 original size:225 final size:225
Alignment explanation
Indices: 700537--701143 Score: 774
Period size: 225 Copynumber: 2.7 Consensus size: 225
700527 ATGTACACGG
* * * *
700537 TAATATATTGATGATATTGAA-AATAAATCAAGTAATTAA-ACTATTTTATTAGCGTTGGATTTC
1 TAATATATTGATAATATT-AATAACAAATCAAGTAATTAACA-TATTTTATTATCGTCGGATTTC
* * * *
700600 TAAGGTCTCGTCAGCTTTAAACAAGCGATACTTATTACATTAAATAAGCGCTACTTGTTATGTTA
64 TAAGG-CCCGTCAGCTTTAAACAAGCGCTACTTATTACATTAAATAAGCACTACCTGTTATGTTA
* *
700665 TTATGGTTGATAATGTTTCCAATAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGCTCCATC
128 TTATAGTTGATAATGTTTCCAATAATTAACCTATTTTGTTATCGTCGGATTTCTAAAGCTCCATC
* *
700730 AGCTTAAACTTTGACAACTTTTTAGAAGATACA
193 AGATTAAACTTTGACAACATTTTAGAAGATACA
* * *
700763 TAATATGTTGATAATATTAATAACAAATTAAGTAATTAACATATTTTCTTATCGTCGGATTTCTA
1 TAATATATTGATAATATTAATAACAAATCAAGTAATTAACATATTTTATTATCGTCGGATTTCTA
** * *
700828 AGGCCCAACAGCTTTAAACATGCGCTA-TCTATTACATTAAATAAACACTACCTGTTATGTTATT
66 AGGCCCGTCAGCTTTAAACAAGCGCTACT-TATTACATTAAATAAGCACTACCTGTTATGTTATT
* * * *
700892 ATAGTTGATAATGTTTCTAGTAATTGACCTATTTTGTTATCTTCGGATTTCTAAAGCTCCATCAG
130 ATAGTTGATAATGTTTCCAATAATTAACCTATTTTGTTATCGTCGGATTTCTAAAGCTCCATCAG
** ** *
700957 ATTAAACTTTGGTAACATTTTAGGCGCTATC-
195 ATTAAACTTTGACAACATTTTAGAAGATA-CA
* * *
700988 TAATATATTGATAATATTGATAACAAATCAAGTAATTAACATATTTTATTATCATCTGATTTCTA
1 TAATATATTGATAATATTAATAACAAATCAAGTAATTAACATATTTTATTATCGTCGGATTTCTA
* * * *
701053 AGGCCCGTCAGCTTTAAA-AAGGCGCTACTTATTACGTTACATAAGCTCTACCGGTTATGTTATT
66 AGGCCCGTCAGCTTTAAACAA-GCGCTACTTATTACATTAAATAAGCACTACCTGTTATGTTATT
** * *
701117 ACGGTTAATAATATTTCCAATAATTAA
130 ATAGTTGATAATGTTTCCAATAATTAA
701144 TCGGTTATGT
Statistics
Matches: 326, Mismatches: 49, Indels: 13
0.84 0.13 0.03
Matches are distributed among these distances:
224 2 0.01
225 265 0.81
226 58 0.18
227 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.39
Consensus pattern (225 bp):
TAATATATTGATAATATTAATAACAAATCAAGTAATTAACATATTTTATTATCGTCGGATTTCTA
AGGCCCGTCAGCTTTAAACAAGCGCTACTTATTACATTAAATAAGCACTACCTGTTATGTTATTA
TAGTTGATAATGTTTCCAATAATTAACCTATTTTGTTATCGTCGGATTTCTAAAGCTCCATCAGA
TTAAACTTTGACAACATTTTAGAAGATACA
Found at i:701990 original size:8 final size:8
Alignment explanation
Indices: 701977--702006 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
701967 AGAAAAAAAT
701977 ATTTTTAA
1 ATTTTTAA
701985 ATTTTTAA
1 ATTTTTAA
701993 ATTTTTAA
1 ATTTTTAA
702001 ATTTTT
1 ATTTTT
702007 GTGATTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (8 bp):
ATTTTTAA
Found at i:702051 original size:2 final size:2
Alignment explanation
Indices: 702039--702076 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
702029 ATGGTTCTAC
702039 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
702077 TTAATTACTA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:705597 original size:25 final size:25
Alignment explanation
Indices: 705565--705616 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
705555 ATCATCTTCA
705565 ATATCTTACACAACACACTCCTTTC
1 ATATCTTACACAACACACTCCTTTC
* *
705590 ATATCTTACATATCACACTCCTTTC
1 ATATCTTACACAACACACTCCTTTC
705615 AT
1 AT
705617 CTTCAATCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.31, C:0.33, G:0.00, T:0.37
Consensus pattern (25 bp):
ATATCTTACACAACACACTCCTTTC
Found at i:709614 original size:21 final size:21
Alignment explanation
Indices: 709577--709715 Score: 107
Period size: 21 Copynumber: 6.5 Consensus size: 21
709567 GGTTTTACGC
* *
709577 GGTCATTCGAGACATATATGT
1 GGTCCTTCGGGACATATATGT
* * * *
709598 GATCCTTCGGGATATATGTTT
1 GGTCCTTCGGGACATATATGT
* *
709619 GGTCCTTTGGAACATATATGT
1 GGTCCTTCGGGACATATATGT
* * *
709640 GGTCCTACGGGACAATTCTATAT
1 GGTCCTTCGGGAC-A-TATATGT
*
709663 GGTCTTTCGGGACATATATGT
1 GGTCCTTCGGGACATATATGT
* * *
709684 GGTTCTTCGGGATATTCTATGT
1 GGTCCTTCGGGACA-TATATGT
*
709706 GGTACTTCGG
1 GGTCCTTCGG
709716 TGCATATTCT
Statistics
Matches: 89, Mismatches: 26, Indels: 5
0.74 0.22 0.04
Matches are distributed among these distances:
21 56 0.63
22 17 0.19
23 16 0.18
ACGTcount: A:0.21, C:0.16, G:0.26, T:0.37
Consensus pattern (21 bp):
GGTCCTTCGGGACATATATGT
Found at i:709704 original size:22 final size:22
Alignment explanation
Indices: 709635--709726 Score: 71
Period size: 22 Copynumber: 4.1 Consensus size: 22
709625 TTGGAACATA
* * *
709635 TATGTGGTCCTACGGGACAATTC
1 TATGTGGTTCTTCGGGA-TATTC
* * *
709658 TATATGG-TCTTTCGGGACA-TA
1 TATGTGGTTC-TTCGGGATATTC
709679 TATGTGGTTCTTCGGGATATTC
1 TATGTGGTTCTTCGGGATATTC
*
709701 TATGTGGTACTTCGGTGCATATTC
1 TATGTGGTTCTTCGG-G-ATATTC
709725 TA
1 TA
709727 CGCGACACTT
Statistics
Matches: 55, Mismatches: 9, Indels: 9
0.75 0.12 0.12
Matches are distributed among these distances:
21 15 0.27
22 19 0.35
23 13 0.24
24 8 0.15
ACGTcount: A:0.20, C:0.16, G:0.25, T:0.39
Consensus pattern (22 bp):
TATGTGGTTCTTCGGGATATTC
Found at i:709982 original size:2 final size:2
Alignment explanation
Indices: 709975--710001 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
709965 TATTATTAGT
709975 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
710002 CTCACTAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:716835 original size:21 final size:21
Alignment explanation
Indices: 716708--716846 Score: 106
Period size: 21 Copynumber: 6.6 Consensus size: 21
716698 GGTTTTACAC
*
716708 GGTCTTTCGGGACATATATGT
1 GGTCATTCGGGACATATATGT
* *
716729 GATCCTT-GGGAACATATATGT
1 GGTCATTCGGG-ACATATATGT
* * * * *
716750 GATCCTTCGGGATATATGTTT
1 GGTCATTCGGGACATATATGT
*
716771 GGTCATT-GTGAACATATATGT
1 GGTCATTCG-GGACATATATGT
* *
716792 GGTCCA--CAGGACAATTCTATGT
1 GGT-CATTCGGGAC-A-TATATGT
716814 GGTCATTCGGGACATATATGT
1 GGTCATTCGGGACATATATGT
716835 GGTCATTCGGGA
1 GGTCATTCGGGA
716847 TATTCTCTAT
Statistics
Matches: 93, Mismatches: 16, Indels: 18
0.73 0.13 0.14
Matches are distributed among these distances:
20 7 0.08
21 66 0.71
22 15 0.16
23 5 0.05
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.35
Consensus pattern (21 bp):
GGTCATTCGGGACATATATGT
Found at i:716852 original size:43 final size:41
Alignment explanation
Indices: 716738--716852 Score: 101
Period size: 43 Copynumber: 2.7 Consensus size: 41
716728 TGATCCTTGG
* * *
716738 GAACATATATGTGATCCTTCGGGATATATGTTTGGTCATTGT
1 GAACATATATGTGGTCATTCGGGATAT-TCTTTGGTCATTGT
* *
716780 GAACATATATGTGGTCCA--CAGGACAATTCTATGTGGTCATTCG-
1 GAACATATATGTGGT-CATTCGGGA-TATTCT-T-TGGTCATT-GT
*
716823 GGACATATATGTGGTCATTCGGGATATTCT
1 GAACATATATGTGGTCATTCGGGATATTCT
716853 CTATGGCACT
Statistics
Matches: 58, Mismatches: 8, Indels: 13
0.73 0.10 0.16
Matches are distributed among these distances:
41 6 0.10
42 19 0.33
43 28 0.48
44 5 0.09
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (41 bp):
GAACATATATGTGGTCATTCGGGATATTCTTTGGTCATTGT
Found at i:717723 original size:122 final size:122
Alignment explanation
Indices: 717506--717749 Score: 488
Period size: 122 Copynumber: 2.0 Consensus size: 122
717496 CTGTATGTAT
717506 GCACATCAATGTTGACCCATACTTATATGTTGATGATTGTTATAGCTTGCACACTATGCACAACA
1 GCACATCAATGTTGACCCATACTTATATGTTGATGATTGTTATAGCTTGCACACTATGCACAACA
717571 TTTACAGTTGTGACTTCAAATACCTCCCAAATGAAGCATATTAGCCTACATTCACAA
66 TTTACAGTTGTGACTTCAAATACCTCCCAAATGAAGCATATTAGCCTACATTCACAA
717628 GCACATCAATGTTGACCCATACTTATATGTTGATGATTGTTATAGCTTGCACACTATGCACAACA
1 GCACATCAATGTTGACCCATACTTATATGTTGATGATTGTTATAGCTTGCACACTATGCACAACA
717693 TTTACAGTTGTGACTTCAAATACCTCCCAAATGAAGCATATTAGCCTACATTCACAA
66 TTTACAGTTGTGACTTCAAATACCTCCCAAATGAAGCATATTAGCCTACATTCACAA
717750 TTTCTGAGGA
Statistics
Matches: 122, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
122 122 1.00
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.31
Consensus pattern (122 bp):
GCACATCAATGTTGACCCATACTTATATGTTGATGATTGTTATAGCTTGCACACTATGCACAACA
TTTACAGTTGTGACTTCAAATACCTCCCAAATGAAGCATATTAGCCTACATTCACAA
Found at i:726600 original size:19 final size:19
Alignment explanation
Indices: 726576--726619 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
726566 GTCGGGTCAG
*
726576 ACCGGTC-AAACCTGTTCGA
1 ACCGGTCGAAACC-GGTCGA
726595 ACCGGTCGAAACCGGTCGA
1 ACCGGTCGAAACCGGTCGA
726614 ACCGGT
1 ACCGGT
726620 TTTCAGCCAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.25, C:0.32, G:0.27, T:0.16
Consensus pattern (19 bp):
ACCGGTCGAAACCGGTCGA
Found at i:726616 original size:9 final size:9
Alignment explanation
Indices: 726576--726619 Score: 52
Period size: 10 Copynumber: 4.7 Consensus size: 9
726566 GTCGGGTCAG
*
726576 ACCGGTCAA
1 ACCGGTCGA
*
726585 ACCTGTTCGA
1 ACC-GGTCGA
726595 ACCGGTCGAA
1 ACCGGTCG-A
726605 ACCGGTCGA
1 ACCGGTCGA
726614 ACCGGT
1 ACCGGT
726620 TTTCAGCCAC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
9 14 0.47
10 16 0.53
ACGTcount: A:0.25, C:0.32, G:0.27, T:0.16
Consensus pattern (9 bp):
ACCGGTCGA
Found at i:730010 original size:24 final size:23
Alignment explanation
Indices: 729983--730029 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
729973 ATTAAAAGAA
*
729983 AAATAATAAAGTAAACGAATTTAT
1 AAATAATAAA-TAAACGAACTTAT
* *
730007 AAATGATCAATAAACGAACTTAT
1 AAATAATAAATAAACGAACTTAT
730030 TTGTGAACAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.55, C:0.09, G:0.09, T:0.28
Consensus pattern (23 bp):
AAATAATAAATAAACGAACTTAT
Found at i:739426 original size:3 final size:3
Alignment explanation
Indices: 739418--739448 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
739408 TAATATATCA
739418 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
739449 TGTATTAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:742742 original size:14 final size:14
Alignment explanation
Indices: 742720--742751 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
742710 GCACCAAACT
742720 TCAAGGTGGGAGTG
1 TCAAGGTGGGAGTG
*
742734 TCAATGTGGGAGTG
1 TCAAGGTGGGAGTG
742748 TCAA
1 TCAA
742752 ATTTCATGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.25, C:0.09, G:0.41, T:0.25
Consensus pattern (14 bp):
TCAAGGTGGGAGTG
Found at i:744560 original size:59 final size:60
Alignment explanation
Indices: 744463--744576 Score: 142
Period size: 59 Copynumber: 1.9 Consensus size: 60
744453 TTTATCTTTC
* ** *
744463 TATTTCAGTTTAAATATATGTTAGTATTTCAATTAGGATTTAGGATATTATTTTAAATAG
1 TATTTCAGTTTAAATATATGTAAGTATTTCAATTAGGATAAAAGATATTATTTTAAATAG
* **
744523 TATTTTAGTTTAAATAGT-T-TAAGTATTTTTATTAGGATAAAAGATATTATTTTA
1 TATTTCAGTTTAAATA-TATGTAAGTATTTCAATTAGGATAAAAGATATTATTTTA
744577 GGAATCATCT
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
59 29 0.63
60 16 0.35
61 1 0.02
ACGTcount: A:0.36, C:0.02, G:0.12, T:0.50
Consensus pattern (60 bp):
TATTTCAGTTTAAATATATGTAAGTATTTCAATTAGGATAAAAGATATTATTTTAAATAG
Found at i:745153 original size:18 final size:18
Alignment explanation
Indices: 745130--745171 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
745120 CCGATAAATT
745130 TGAGGCAAAGCTGAAGTC
1 TGAGGCAAAGCTGAAGTC
745148 TGAGGCAAAGCTGAAGTC
1 TGAGGCAAAGCTGAAGTC
745166 TGAGGC
1 TGAGGC
745172 TACTTTCGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.31, C:0.17, G:0.36, T:0.17
Consensus pattern (18 bp):
TGAGGCAAAGCTGAAGTC
Found at i:745239 original size:18 final size:18
Alignment explanation
Indices: 745216--745258 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
745206 CTTTAGATTA
* *
745216 TTTATTTAATTATTTTCT
1 TTTATTTAATTATTATAT
*
745234 TTTATTTAATTCTTATAT
1 TTTATTTAATTATTATAT
745252 TTTATTT
1 TTTATTT
745259 TAAAAACAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTATTTAATTATTATAT
Found at i:756707 original size:19 final size:19
Alignment explanation
Indices: 756683--756726 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
756673 TTCGACGCGC
756683 ACGCTCTCCACATCGAGCT
1 ACGCTCTCCACATCGAGCT
756702 ACGCTCTCCACATCGAGCT
1 ACGCTCTCCACATCGAGCT
756721 ACGCTC
1 ACGCTC
756727 CTTGTGGCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.20
Consensus pattern (19 bp):
ACGCTCTCCACATCGAGCT
Found at i:758298 original size:40 final size:40
Alignment explanation
Indices: 758243--758323 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
758233 AATCTAATTG
*
758243 TTGAAGGTGATTTGAAATTCTTGTATTAAGCCTTTAACCC
1 TTGAAGGTGATTTGAAATTCTTGTATTAAGCCATTAACCC
*
758283 TTGAAGGTGGTTTGAAATTCTTGTATTAAGCCATTAACCC
1 TTGAAGGTGATTTGAAATTCTTGTATTAAGCCATTAACCC
758323 T
1 T
758324 AGGTCTATGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.40
Consensus pattern (40 bp):
TTGAAGGTGATTTGAAATTCTTGTATTAAGCCATTAACCC
Found at i:760129 original size:55 final size:55
Alignment explanation
Indices: 760063--760324 Score: 366
Period size: 55 Copynumber: 4.8 Consensus size: 55
760053 GTACTACAGA
*
760063 CACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACATG
1 CACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAACCGTACATG
* *
760118 CACTATGTGTGCAAATCCACGAAATTCATCATGAGTTAATGAATTACCGTACATG
1 CACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAACCGTACATG
* * ** * * *
760173 CACTATGTGTGCAAATCCACGGAATTCATAATGAGTAAATAAATAACCGTATAGG
1 CACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAACCGTACATG
* *
760228 CACTATGTGTGCAAATCCATGAAATTCATCATGAGTTGATGAATAACCGTACAAG
1 CACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAACCGTACATG
* * *
760283 CA-TGATATGTGC-AACCCACAAAATTCATCATGAGTTGATGAA
1 CACT-ATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAA
760325 CTACCATATA
Statistics
Matches: 184, Mismatches: 22, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
54 28 0.15
55 156 0.85
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (55 bp):
CACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAACCGTACATG
Found at i:766277 original size:23 final size:22
Alignment explanation
Indices: 766242--766310 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 22
766232 AGTTCAAGGC
**
766242 TTATTTATTTTTTAAATAAATA
1 TTATTTAAATTTTAAATAAATA
*
766264 TTATTTTAAATTTTAAATATAAAA
1 TTA-TTTAAATTTTAAATA-AATA
* *
766288 TTATTTAAATATTAAAAAAATA
1 TTATTTAAATTTTAAATAAATA
766310 T
1 T
766311 AAAAATGGTA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
22 7 0.18
23 26 0.67
24 6 0.15
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TTATTTAAATTTTAAATAAATA
Found at i:773448 original size:20 final size:21
Alignment explanation
Indices: 773423--773468 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
773413 AATATTCAAT
773423 TTTTTAGTA-TTTAATTTTTA
1 TTTTTAGTATTTTAATTTTTA
773443 TTTTTAGTATTTTAATTTTTA
1 TTTTTAGTATTTTAATTTTTA
773464 TTTTT
1 TTTTT
773469 TTATATATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.74
Consensus pattern (21 bp):
TTTTTAGTATTTTAATTTTTA
Found at i:783173 original size:20 final size:19
Alignment explanation
Indices: 783150--783220 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 19
783140 TTGTCCGCTG
783150 GTATCGATACTAACCTGTTA
1 GTATCGATACTAACCT-TTA
* *
783170 GTATCAATACTAACCCTTGA
1 GTATCGATACTAA-CCTTTA
783190 GTATCGATAC-ACACCTCTT-
1 GTATCGATACTA-ACCT-TTA
783209 GCTATCGATACT
1 G-TATCGATACT
783221 CCTAGCTGAT
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
19 5 0.12
20 34 0.81
21 3 0.07
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (19 bp):
GTATCGATACTAACCTTTA
Found at i:788551 original size:20 final size:20
Alignment explanation
Indices: 788497--788567 Score: 90
Period size: 20 Copynumber: 3.6 Consensus size: 20
788487 CAAGAAAAAT
* * *
788497 CAGATTGCCCCCAGAGGGAA
1 CAGATTCCCCCCAGGGGGTA
*
788517 CAGATTGCCCCCAGGGGGTA
1 CAGATTCCCCCCAGGGGGTA
788537 CAGATTCCCCCCA-GGGGTA
1 CAGATTCCCCCCAGGGGGTA
*
788556 CCGATTCCCCCC
1 CAGATTCCCCCC
788568 TGTCTAACGC
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
19 17 0.36
20 30 0.64
ACGTcount: A:0.21, C:0.38, G:0.27, T:0.14
Consensus pattern (20 bp):
CAGATTCCCCCCAGGGGGTA
Found at i:788981 original size:32 final size:33
Alignment explanation
Indices: 788914--788983 Score: 106
Period size: 34 Copynumber: 2.1 Consensus size: 33
788904 TTTTGTAAAG
*
788914 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-GTAAAAACTA
*
788948 GGGAAAGGTTCTAGTTTAGCCC-GTAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGTAAAAACTA
788980 GGGA
1 GGGA
788984 GTTTGTAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 13 0.38
34 21 0.62
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (33 bp):
GGGAAAGGTTCTAGCTTAGCCCGGTAAAAACTA
Found at i:789867 original size:19 final size:20
Alignment explanation
Indices: 789843--789890 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
789833 AACGATTTTC
*
789843 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
789862 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
789882 TTTTGAAAA
1 TTTTGAAAA
789891 AAGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:791373 original size:21 final size:20
Alignment explanation
Indices: 791289--791372 Score: 132
Period size: 20 Copynumber: 4.2 Consensus size: 20
791279 AATCATATTG
791289 CCCAGGGGGTACAGATTTCCC
1 CCCAGGGGGTACAGA-TTCCC
791310 CCCAGGGGGTACAGATTCCC
1 CCCAGGGGGTACAGATTCCC
*
791330 CCCAGGGGGAACAGATTCCC
1 CCCAGGGGGTACAGATTCCC
* *
791350 CCTAGGGGGTACCGATTCCC
1 CCCAGGGGGTACAGATTCCC
791370 CCC
1 CCC
791373 TGTCTAACGG
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
20 43 0.74
21 15 0.26
ACGTcount: A:0.19, C:0.37, G:0.29, T:0.15
Consensus pattern (20 bp):
CCCAGGGGGTACAGATTCCC
Found at i:794726 original size:15 final size:16
Alignment explanation
Indices: 794706--794736 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
794696 CATTGATCAT
794706 TATCACATAA-ATGTA
1 TATCACATAACATGTA
794721 TATCACATAACATGTA
1 TATCACATAACATGTA
794737 ATGCAATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.45, C:0.16, G:0.06, T:0.32
Consensus pattern (16 bp):
TATCACATAACATGTA
Found at i:795317 original size:21 final size:22
Alignment explanation
Indices: 795291--795343 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
795281 AGTTCCCCTC
795291 GTATCGATACCCTA-CACATA-G
1 GTATCGATACCCTATC-CATAGG
**
795312 GTATCGATACGTTATCCATAGG
1 GTATCGATACCCTATCCATAGG
795334 GTATCGATAC
1 GTATCGATAC
795344 TGCTCATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 16 0.57
22 12 0.43
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (22 bp):
GTATCGATACCCTATCCATAGG
Found at i:804058 original size:21 final size:22
Alignment explanation
Indices: 804032--804084 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
804022 AGTTCCCCCT
804032 GTATCGATACCCTC-CACATA-G
1 GTATCGATACCCTCAC-CATAGG
804053 GTATCGATA-CCTCATCCATAGG
1 GTATCGATACCCTCA-CCATAGG
804075 GTATCGATAC
1 GTATCGATAC
804085 TATTCATACA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
20 4 0.14
21 13 0.46
22 11 0.39
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.26
Consensus pattern (22 bp):
GTATCGATACCCTCACCATAGG
Found at i:807815 original size:42 final size:42
Alignment explanation
Indices: 807756--807839 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
807746 AAAGAGATAC
* *
807756 AGCGACACGGAGATGGCCTTTTGAGATCATGAGTGAAACGGT
1 AGCGACACGAAAATGGCCTTTTGAGATCATGAGTGAAACGGT
*
807798 AGCGACACGAAAATGGCCTTTTGAGATCATTAGTGAAACGGT
1 AGCGACACGAAAATGGCCTTTTGAGATCATGAGTGAAACGGT
807840 CAAGAGATGG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.31, C:0.17, G:0.30, T:0.23
Consensus pattern (42 bp):
AGCGACACGAAAATGGCCTTTTGAGATCATGAGTGAAACGGT
Found at i:809776 original size:24 final size:23
Alignment explanation
Indices: 809732--809777 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 23
809722 GAATTTAATA
809732 TTAATAAAATATTTTAATATTATT
1 TTAATAAAATA-TTTAATATTATT
809756 TTAATCAAAATA-TTAATTATTA
1 TTAAT-AAAATATTTAA-TATTA
809778 AAATATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 4 0.20
24 10 0.50
25 6 0.30
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (23 bp):
TTAATAAAATATTTAATATTATT
Found at i:809826 original size:22 final size:23
Alignment explanation
Indices: 809779--809842 Score: 71
Period size: 22 Copynumber: 2.9 Consensus size: 23
809769 TAATTATTAA
* *
809779 AATATTTAAAAT-ATAT-TTATT
1 AATATTTATAATAATATAATATT
809800 AATATTTATAATAATATAATATT
1 AATATTTATAATAATATAATATT
* *
809823 -ATATTTTTAATATTATAATA
1 AATATTTATAATAATATAATA
809843 AAATAATCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
21 11 0.30
22 22 0.59
23 4 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AATATTTATAATAATATAATATT
Found at i:809941 original size:28 final size:29
Alignment explanation
Indices: 809775--809983 Score: 120
Period size: 29 Copynumber: 7.2 Consensus size: 29
809765 ATATTAATTA
*
809775 TTAA-AATATTTAA-AATATATTTATTAATAT
1 TTAATAATATATAATAAT-TATTTA-T-ATAT
*
809805 TT-ATAATA-AT-ATAA-TA-TTATATTT
1 TTAATAATATATAATAATTATTTATATAT
* * *
809829 TTAATATTATAATAAAATAATCAATTATAT-T
1 TTAATA--AT-ATATAATAATTATTTATATAT
* * *
809860 ATAATAATATA-AGATATTATATTTTTAT-T
1 TTAATAATATATA-ATAAT-TATTTATATAT
809889 TTAATAATATATAATAAATTATTTATATAT
1 TTAATAATATATAAT-AATTATTTATATAT
809919 TTAATAATGA-ATAAT-ATTATTTATATAT
1 TTAATAAT-ATATAATAATTATTTATATAT
* * *
809947 TTAATATTAATATAATAATATAATAATAT-T
1 TTAATAAT-ATATAATAAT-TATTTATATAT
809977 TTAATAA
1 TTAATAA
809984 AGATATTTAA
Statistics
Matches: 143, Mismatches: 17, Indels: 38
0.72 0.09 0.19
Matches are distributed among these distances:
24 5 0.03
25 4 0.03
26 3 0.02
27 5 0.03
28 30 0.21
29 39 0.27
30 36 0.25
31 15 0.10
32 6 0.04
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (29 bp):
TTAATAATATATAATAATTATTTATATAT
Found at i:809970 original size:37 final size:36
Alignment explanation
Indices: 809908--809977 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
809898 TATAATAAAT
* * *
809908 TATTTATATATTTAATAATGAATAATATTATTTATA
1 TATTTATATATTAAATAATAAATAATAATATTTATA
809944 TATTTA-ATATTAATATAATAATATAATAATATTT
1 TATTTATATATTAA-ATAATAA-ATAATAATATTT
809978 TAATAAAGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
35 6 0.21
36 12 0.41
37 11 0.38
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (36 bp):
TATTTATATATTAAATAATAAATAATAATATTTATA
Found at i:810004 original size:23 final size:23
Alignment explanation
Indices: 809978--810022 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
809968 AATAATATTT
809978 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
810001 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
810023 ATATAAAACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:810376 original size:14 final size:14
Alignment explanation
Indices: 810357--810409 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
810347 TCAGAAATAT
*
810357 AATTCATTTTCCAG
1 AATTCAATTTCCAG
*
810371 AATTCAAATTCCAG
1 AATTCAATTTCCAG
*
810385 TAATTC-ATTTTCAG
1 -AATTCAATTTCCAG
810399 AATTCAATTTC
1 AATTCAATTTC
810410 TAAAAAACCA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
13 5 0.16
14 22 0.69
15 5 0.16
ACGTcount: A:0.34, C:0.19, G:0.06, T:0.42
Consensus pattern (14 bp):
AATTCAATTTCCAG
Found at i:817219 original size:5 final size:5
Alignment explanation
Indices: 817209--817242 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
817199 AATTAATGTT
*
817209 AAATA AAATA AAATA AAATAA AAACA AAATA AAA
1 AAATA AAATA AAATA AAAT-A AAATA AAATA AAA
817243 AAGGTATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 22 0.85
6 4 0.15
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (5 bp):
AAATA
Found at i:818653 original size:14 final size:15
Alignment explanation
Indices: 818634--818664 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
818624 TATATTATAT
818634 GTTTTCAAAAA-TAC
1 GTTTTCAAAAACTAC
818648 GTTTTCAAAAACTAC
1 GTTTTCAAAAACTAC
818663 GT
1 GT
818665 ATGTTTTCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.35
Consensus pattern (15 bp):
GTTTTCAAAAACTAC
Found at i:818725 original size:34 final size:35
Alignment explanation
Indices: 818684--818759 Score: 91
Period size: 36 Copynumber: 2.2 Consensus size: 35
818674 AAAAACATTT
* * * * *
818684 TTTTAAAATC-ATATATTATATGTTTTTAAAACCA
1 TTTTAAAAACTATAAATTATACGTTTTCAAAACAA
818718 TTTTAAAAAACTATAAATTATACGTTTTCAAAACAA
1 TTTT-AAAAACTATAAATTATACGTTTTCAAAACAA
818754 TTTTAA
1 TTTTAA
818760 TATATTATCT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
34 4 0.11
35 7 0.20
36 24 0.69
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (35 bp):
TTTTAAAAACTATAAATTATACGTTTTCAAAACAA
Found at i:818788 original size:14 final size:14
Alignment explanation
Indices: 818769--818846 Score: 85
Period size: 14 Copynumber: 5.9 Consensus size: 14
818759 ATATATTATC
818769 TGTTTTCAAAAATA
1 TGTTTTCAAAAATA
818783 TGTTTTCAAAAACTA
1 TGTTTTCAAAAA-TA
* *
818798 --TATT---ATATA
1 TGTTTTCAAAAATA
818807 TGTTTTCAAAAATA
1 TGTTTTCAAAAATA
818821 TGTTTTCAAAAATA
1 TGTTTTCAAAAATA
*
818835 CGTTTTCAAAAA
1 TGTTTTCAAAAA
818847 CTATATATTA
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
9 2 0.04
10 2 0.04
11 3 0.06
13 3 0.06
14 41 0.77
15 2 0.04
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.42
Consensus pattern (14 bp):
TGTTTTCAAAAATA
Found at i:818810 original size:24 final size:24
Alignment explanation
Indices: 818780--818899 Score: 104
Period size: 24 Copynumber: 4.9 Consensus size: 24
818770 GTTTTCAAAA
818780 ATATGTTTTCAAAAACTATATTAT
1 ATATGTTTTCAAAAACTATATTAT
* *
818804 ATATGTTTTCAAAAA-TATGTTTTCAAAA
1 ATATGTTTTCAAAAACTA--TATT---AT
*
818832 ATACGTTTTCAAAAACTATA-TATT
1 ATATGTTTTCAAAAACTATATTA-T
* *
818856 ATATGTTTTCAAAACCTATACTAT
1 ATATGTTTTCAAAAACTATATTAT
*
818880 ATA--TTTTCAATAACTATATT
1 ATATGTTTTCAAAAACTATATT
818900 TGAAATTATT
Statistics
Matches: 78, Mismatches: 10, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
22 14 0.18
23 3 0.04
24 37 0.47
25 5 0.06
26 1 0.01
27 1 0.01
28 15 0.19
29 2 0.03
ACGTcount: A:0.41, C:0.11, G:0.04, T:0.44
Consensus pattern (24 bp):
ATATGTTTTCAAAAACTATATTAT
Found at i:818826 original size:52 final size:52
Alignment explanation
Indices: 818769--818869 Score: 177
Period size: 52 Copynumber: 1.9 Consensus size: 52
818759 ATATATTATC
*
818769 TGTTTTCAAAAATATGTTTTCAAAAACTATAT-TATATATGTTTTCAAAAATA
1 TGTTTTCAAAAATACGTTTTCAAAAACTATATAT-TATATGTTTTCAAAAATA
818821 TGTTTTCAAAAATACGTTTTCAAAAACTATATATTATATGTTTTCAAAA
1 TGTTTTCAAAAATACGTTTTCAAAAACTATATATTATATGTTTTCAAAA
818870 CCTATACTAT
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
52 46 0.98
53 1 0.02
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.44
Consensus pattern (52 bp):
TGTTTTCAAAAATACGTTTTCAAAAACTATATATTATATGTTTTCAAAAATA
Found at i:818880 original size:22 final size:22
Alignment explanation
Indices: 818836--818897 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 22
818826 TCAAAAATAC
* *
818836 GTTTTCAAAAACTATATATTATAT
1 GTTTTC-AAAAC-CTATACTATAT
818860 GTTTTCAAAACCTATACTATAT
1 GTTTTCAAAACCTATACTATAT
*
818882 ATTTTCAATAA-CTATA
1 GTTTTCAA-AACCTATA
818898 TTTGAAATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
22 21 0.62
23 7 0.21
24 6 0.18
ACGTcount: A:0.40, C:0.13, G:0.03, T:0.44
Consensus pattern (22 bp):
GTTTTCAAAACCTATACTATAT
Found at i:832366 original size:36 final size:36
Alignment explanation
Indices: 832321--832613 Score: 186
Period size: 36 Copynumber: 7.8 Consensus size: 36
832311 GTTTTCAAAG
*
832321 AAACTATATATTATATGTTTTCAAAAACATTTTTAA
1 AAACCATATATTATATGTTTTCAAAAACATTTTTAA
* *
832357 AAACCATATATTATATGTTTTCAAAAATACGTTTTCAA
1 AAACCATATATTATATGTTTTC-AAAA-ACATTTTTAA
832395 AAA-C---TA-TATATGTTTTCCAAAAAACCATTTTTTAATA
1 AAACCATATATTATATGTTTT-C-AAAAA-CA-TTTTT-A-A
* * *
832432 AAACCATATATTATAAGTTTTCAAAACCATTTTAAA
1 AAACCATATATTATATGTTTTCAAAAACATTTTTAA
* * *
832468 AAACTATATATTATATGTTTTCAAAAATATGTTTTCA
1 AAACCATATATTATATGTTTTCAAAAACAT-TTTTAA
* * * *
832505 AAATC-TATATTATATATATTTTCAAAAATTCGTTTTCAA
1 AAACCATATA-T-TATATGTTTTCAAAAA--CATTTTTAA
* * * * *
832544 AAACTATATTATATATATATATATTCAAAAATACGTTTTCA
1 AAACCATA-TAT-TATATGT-T-TTCAAAAACA-TTTTTAA
*
832585 AAACC-TATACTATATATATTTTCAAAAAC
1 AAACCATATA-T-TATATGTTTTCAAAAAC
832614 TATATTTGAA
Statistics
Matches: 204, Mismatches: 30, Indels: 44
0.73 0.11 0.16
Matches are distributed among these distances:
33 11 0.05
34 9 0.04
35 4 0.02
36 53 0.26
37 18 0.09
38 39 0.19
39 12 0.06
40 27 0.13
41 14 0.07
42 17 0.08
ACGTcount: A:0.44, C:0.12, G:0.03, T:0.41
Consensus pattern (36 bp):
AAACCATATATTATATGTTTTCAAAAACATTTTTAA
Done.