Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr3
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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 115 of 290
Found at i:39121441 original size:21 final size:19
Alignment explanation
Indices: 39121400--39121442 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
39121390 ATTGCAATTG
* *
39121400 AGTTAAACATTTTTAATCA
1 AGTTAAACATTTTAAAACA
39121419 AGTTAAAACTATTTTAAAACA
1 AGTT-AAAC-ATTTTAAAACA
39121440 AGT
1 AGT
39121443 CGGCATTGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 4 0.20
20 4 0.20
21 12 0.60
ACGTcount: A:0.47, C:0.09, G:0.07, T:0.37
Consensus pattern (19 bp):
AGTTAAACATTTTAAAACA
Found at i:39125795 original size:42 final size:43
Alignment explanation
Indices: 39125694--39125810 Score: 134
Period size: 43 Copynumber: 2.7 Consensus size: 43
39125684 CACGCATCGG
*
39125694 TGCCACTGTCCCACACAGGGTCTTACACG-AAGTCGATTAATGA
1 TGCCACTGTCCCACACAGGGTCTTACACGTAAGTCGA-TAATAA
**
39125737 TGCCGA-TGTCCCACACATAGTCTTACACGTAA-TCG-TAATAAA
1 TGCC-ACTGTCCCACACAGGGTCTTACACGTAAGTCGATAAT-AA
* *
39125779 TGCCACTATCCCACACAGGGTCTTACATGTAA
1 TGCCACTGTCCCACACAGGGTCTTACACGTAA
39125811 ATCACATCTC
Statistics
Matches: 63, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
41 5 0.08
42 27 0.43
43 28 0.44
44 3 0.05
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (43 bp):
TGCCACTGTCCCACACAGGGTCTTACACGTAAGTCGATAATAA
Found at i:39137534 original size:26 final size:25
Alignment explanation
Indices: 39137488--39137538 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
39137478 ATTTTTGTTT
*
39137488 TTATGTTTTTAAATATATTTAATTTA
1 TTATATTTTTAAATATATTT-ATTTA
* *
39137514 TTATATTTTTAAATTTTTTTATTTA
1 TTATATTTTTAAATATATTTATTTA
39137539 ATGAAATAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 5 0.23
26 17 0.77
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (25 bp):
TTATATTTTTAAATATATTTATTTA
Found at i:39144664 original size:16 final size:15
Alignment explanation
Indices: 39144622--39144665 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
39144612 ACTTACTTTT
39144622 ATTTATTATTTA-TC
1 ATTTATTATTTATTC
*
39144636 ATTTATCATTTATTAC
1 ATTTATTATTTATT-C
*
39144652 ATTTATTACTTATT
1 ATTTATTATTTATT
39144666 TAATATTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 11 0.44
15 1 0.04
16 13 0.52
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.61
Consensus pattern (15 bp):
ATTTATTATTTATTC
Found at i:39146655 original size:19 final size:19
Alignment explanation
Indices: 39146627--39146678 Score: 79
Period size: 19 Copynumber: 2.8 Consensus size: 19
39146617 AAAGAATTTG
* *
39146627 TAAAATTTTATAAAAATTA
1 TAAAAATTTATAAAAATCA
39146646 TAAAAATTTATAAAAATCA
1 TAAAAATTTATAAAAATCA
39146665 T-AAAATTTATAAAA
1 TAAAAATTTATAAAA
39146679 TATATAGGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 13 0.42
19 18 0.58
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAAAATTTATAAAAATCA
Found at i:39146679 original size:9 final size:9
Alignment explanation
Indices: 39146621--39146684 Score: 65
Period size: 9 Copynumber: 6.9 Consensus size: 9
39146611 ATATATAAAG
*
39146621 AATTTGTAA
1 AATTTATAA
39146630 AATTTTATAA
1 AA-TTTATAA
*
39146640 AAATTATAAA
1 AATTTAT-AA
39146650 AATTTATAA
1 AATTTATAA
* *
39146659 AAATCATAA
1 AATTTATAA
39146668 AATTTATAA
1 AATTTATAA
*
39146677 AATATATA
1 AATTTATA
39146685 GGAATACAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
9 29 0.64
10 16 0.36
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (9 bp):
AATTTATAA
Found at i:39147215 original size:16 final size:16
Alignment explanation
Indices: 39147194--39147225 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
39147184 TTTATAATAC
39147194 TTTTTACAATTTTATA
1 TTTTTACAATTTTATA
39147210 TTTTTACAATTTTATA
1 TTTTTACAATTTTATA
39147226 AAAAATTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTTACAATTTTATA
Found at i:39147331 original size:10 final size:10
Alignment explanation
Indices: 39147300--39147398 Score: 50
Period size: 9 Copynumber: 10.2 Consensus size: 10
39147290 TATTACAAAC
39147300 TTTTATAAATT
1 TTTTAT-AATT
*
39147311 ATTTA-AGATT
1 TTTTATA-ATT
39147321 TTTTATAA-T
1 TTTTATAATT
*
39147330 TTTTGTAA-T
1 TTTTATAATT
* *
39147339 TTTTGTGA-T
1 TTTTATAATT
39147348 TTTTATAATT
1 TTTTATAATT
*
39147358 TTCTAT-ATT
1 TTTTATAATT
* *
39147367 TTTAATAA-A
1 TTTTATAATT
39147376 TTTTA-AATAT
1 TTTTATAAT-T
39147386 TTTATATAATT
1 TTT-TATAATT
39147397 TT
1 TT
39147399 AAATGTTTTT
Statistics
Matches: 68, Mismatches: 12, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
8 2 0.03
9 35 0.51
10 18 0.26
11 10 0.15
12 3 0.04
ACGTcount: A:0.32, C:0.01, G:0.04, T:0.63
Consensus pattern (10 bp):
TTTTATAATT
Found at i:39147338 original size:9 final size:9
Alignment explanation
Indices: 39147320--39147398 Score: 70
Period size: 9 Copynumber: 8.4 Consensus size: 9
39147310 TATTTAAGAT
39147320 TTTTTATAA
1 TTTTTATAA
*
39147329 TTTTTGTAA
1 TTTTTATAA
* *
39147338 TTTTTGTGA
1 TTTTTATAA
39147347 TTTTTATAA
1 TTTTTATAA
39147356 TTTTCTAT-A
1 TTTT-TATAA
39147365 TTTTTAATAA
1 TTTTT-ATAA
* *
39147375 ATTTTAAATA
1 TTTTTATA-A
39147385 TTTTATATAA
1 TTTT-TATAA
39147395 TTTT
1 TTTT
39147399 AAATGTTTTT
Statistics
Matches: 57, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
8 1 0.02
9 36 0.63
10 17 0.30
11 3 0.05
ACGTcount: A:0.30, C:0.01, G:0.04, T:0.65
Consensus pattern (9 bp):
TTTTTATAA
Found at i:39147399 original size:19 final size:18
Alignment explanation
Indices: 39147346--39147408 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 18
39147336 AATTTTTGTG
**
39147346 ATTTTTATAATTTTCTAT
1 ATTTTTATAATTTTAAAT
39147364 ATTTTTAATAAATTTTAAAT
1 ATTTTT-AT-AATTTTAAAT
39147384 ATTTTATATAATTTTAAAT
1 ATTTT-TATAATTTTAAAT
*
39147403 GTTTTT
1 ATTTTT
39147409 CTTATTGATT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
18 7 0.18
19 16 0.41
20 15 0.38
21 1 0.03
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (18 bp):
ATTTTTATAATTTTAAAT
Found at i:39155325 original size:21 final size:22
Alignment explanation
Indices: 39155283--39155324 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
39155273 AGTACCTAGT
39155283 AAAAGGTATCCATACTTTTTTG
1 AAAAGGTATCCATACTTTTTTG
**
39155305 AAAAGGTATTGATACTTTTT
1 AAAAGGTATCCATACTTTTT
39155325 GTAATTGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (22 bp):
AAAAGGTATCCATACTTTTTTG
Found at i:39161210 original size:22 final size:23
Alignment explanation
Indices: 39161185--39161229 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
39161175 TCTGTTCAAC
39161185 TTTAACTT-TTAT-TCGAAAACAT
1 TTTAACTTGTTATATC-AAAACAT
*
39161207 TTTAATTTGTTATATCAAAACAT
1 TTTAACTTGTTATATCAAAACAT
39161230 ATTATCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 11 0.55
24 2 0.10
ACGTcount: A:0.38, C:0.11, G:0.04, T:0.47
Consensus pattern (23 bp):
TTTAACTTGTTATATCAAAACAT
Found at i:39178457 original size:42 final size:42
Alignment explanation
Indices: 39178374--39178458 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 42
39178364 TACAGGGGTT
* * ** *
39178374 TTCACACGACTTGGAACACGCTCGTGTCCCTGGCGCATGTCC
1 TTCACACGACCTGGAACACGCCCGTGTCCCCAGCCCATGTCC
* *
39178416 TTCACACGGCCTGGAACACGCCCGTGTCCCCAGCCCTTGTCC
1 TTCACACGACCTGGAACACGCCCGTGTCCCCAGCCCATGTCC
39178458 T
1 T
39178459 AGCCCGTGTA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.15, C:0.40, G:0.22, T:0.22
Consensus pattern (42 bp):
TTCACACGACCTGGAACACGCCCGTGTCCCCAGCCCATGTCC
Found at i:39179593 original size:93 final size:92
Alignment explanation
Indices: 39179432--39179605 Score: 226
Period size: 93 Copynumber: 1.9 Consensus size: 92
39179422 AGCGTATCTG
* * *
39179432 TGCTGATGCCATGTCCCAGACATGGTCTTACGCTGACATATCTCGTAGCCAATGCATGTCCCAAA
1 TGCTGATGCCATATCCCAGACATGGTCTTACACTGACATATCTCGTAGCCAATACATGTCCCAAA
39179497 CATGTCTCACACTAGCACTCGTCTCAA
66 CATGTCTCACACTAGCACTCGTCTCAA
* * * *
39179524 TGCTGATGCCATATCCCAG-CATGGTCTTACACTGGC-TCTCATAATGTAGCCGATACATGTCCC
1 TGCTGATGCCATATCCCAGACATGGTCTTACACTGACATATC-T--CGTAGCCAATACATGTCCC
* *
39179587 AGACATGTCTTACACTAGC
63 AAACATGTCTCACACTAGC
39179606 TCACACAAAT
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
90 3 0.04
91 16 0.23
92 18 0.26
93 33 0.47
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (92 bp):
TGCTGATGCCATATCCCAGACATGGTCTTACACTGACATATCTCGTAGCCAATACATGTCCCAAA
CATGTCTCACACTAGCACTCGTCTCAA
Found at i:39182088 original size:17 final size:16
Alignment explanation
Indices: 39182056--39182087 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
39182046 TTTCATCCGA
39182056 CCCTCCTAAATTTTTT
1 CCCTCCTAAATTTTTT
39182072 CCCTCCTAAATTTTTT
1 CCCTCCTAAATTTTTT
39182088 TTCTAGCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.31, G:0.00, T:0.50
Consensus pattern (16 bp):
CCCTCCTAAATTTTTT
Found at i:39182723 original size:24 final size:24
Alignment explanation
Indices: 39182696--39182750 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
39182686 TATTTACAAA
39182696 TAAATAAT-TTAATCTATTTATATT
1 TAAATAATATTAATCTATTTAT-TT
*
39182720 TAAATAATATTAATTTATTTATTT
1 TAAATAATATTAATCTATTTATTT
39182744 TAAATAA
1 TAAATAA
39182751 AAATAAATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 17 0.59
25 12 0.41
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (24 bp):
TAAATAATATTAATCTATTTATTT
Found at i:39182759 original size:25 final size:25
Alignment explanation
Indices: 39182710--39182759 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
39182700 TAATTTAATC
* *
39182710 TATTTATATTTAAATAATATTAATT
1 TATTTATATTTAAATAAAATAAATT
39182735 TATTTAT-TTTAAATAAAAATAAATT
1 TATTTATATTTAAAT-AAAATAAATT
39182760 AATAAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
TATTTATATTTAAATAAAATAAATT
Found at i:39184714 original size:11 final size:11
Alignment explanation
Indices: 39184665--39184743 Score: 56
Period size: 11 Copynumber: 7.3 Consensus size: 11
39184655 CCTTTTAAAC
*
39184665 TTTTATT-TTC
1 TTTTATTATTA
*
39184675 TTTCATTATTTA
1 TTTTATTA-TTA
39184687 TTTTATTA-TA
1 TTTTATTATTA
**
39184697 CAATTATTATTA
1 -TTTTATTATTA
* *
39184709 TTTTATT-GTC
1 TTTTATTATTA
*
39184719 TTTTATTATCA
1 TTTTATTATTA
39184730 TTTTATTATTA
1 TTTTATTATTA
39184741 TTT
1 TTT
39184744 ATTCATCCAT
Statistics
Matches: 51, Mismatches: 13, Indels: 9
0.70 0.18 0.12
Matches are distributed among these distances:
10 16 0.31
11 24 0.47
12 11 0.22
ACGTcount: A:0.24, C:0.06, G:0.01, T:0.68
Consensus pattern (11 bp):
TTTTATTATTA
Found at i:39184724 original size:10 final size:11
Alignment explanation
Indices: 39184686--39184743 Score: 57
Period size: 11 Copynumber: 5.4 Consensus size: 11
39184676 TTCATTATTT
39184686 ATTTTATTATAC
1 ATTTTATTAT-C
* *
39184698 A-ATTATTATT
1 ATTTTATTATC
*
39184708 ATTTTATTGTC
1 ATTTTATTATC
39184719 -TTTTATTATC
1 ATTTTATTATC
*
39184729 ATTTTATTATT
1 ATTTTATTATC
39184740 ATTT
1 ATTT
39184744 ATTCATCCAT
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
10 10 0.27
11 26 0.70
12 1 0.03
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.66
Consensus pattern (11 bp):
ATTTTATTATC
Found at i:39184826 original size:3 final size:3
Alignment explanation
Indices: 39184818--39184884 Score: 75
Period size: 3 Copynumber: 21.7 Consensus size: 3
39184808 CTTGTACATA
39184818 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT CTAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT
*
39184863 CATT TATT TAT ATAT T-T TAT TA
1 TA-T TA-T TAT -TAT TAT TAT TA
39184885 CGAATAGTAC
Statistics
Matches: 57, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
2 4 0.07
3 41 0.72
4 12 0.21
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:39194870 original size:25 final size:25
Alignment explanation
Indices: 39194842--39194893 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
39194832 AAGTTAGCCT
39194842 AAATCACAATCAATCATATTTTAGG
1 AAATCACAATCAATCATATTTTAGG
*
39194867 AAATCACAATCAATCCTATTTTAGG
1 AAATCACAATCAATCATATTTTAGG
39194892 AA
1 AA
39194894 CCACAACTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.44, C:0.17, G:0.08, T:0.31
Consensus pattern (25 bp):
AAATCACAATCAATCATATTTTAGG
Found at i:39197160 original size:79 final size:80
Alignment explanation
Indices: 39197027--39197217 Score: 228
Period size: 79 Copynumber: 2.4 Consensus size: 80
39197017 ATGTACATGC
* * *
39197027 GTGCCCCTGTTTATACTTTGATATCCCTAAATGCACATATGTGCCCTTACTTGTACTTCAATATC
1 GTGCCCCTGTTTGTACTTTGGTATCCCTAAATGCACATACGTGCCCTTACTTGTACTTCAATA-C
39197092 C-CTGAAT-AACATAA
65 CACTGAATGAACATAA
* * * **
39197106 GTGCCCCTGTTTGTACTTCGGTA-CCTCTGAATGCACATACGTGCCCTTATTTGTACTTTGATAC
1 GTGCCCCTGTTTGTACTTTGGTATCC-CTAAATGCACATACGTGCCCTTACTTGTACTTCAATAC
* *
39197170 CACTGAATGCACATAC
65 CACTGAATGAACATAA
*
39197186 GTGCCCCTGTTGGTACTTTGGTAAT-CCTAAAT
1 GTGCCCCTGTTTGTACTTTGGT-ATCCCTAAAT
39197218 CAAATAGTAG
Statistics
Matches: 94, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
78 4 0.04
79 58 0.62
80 30 0.32
81 2 0.02
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.35
Consensus pattern (80 bp):
GTGCCCCTGTTTGTACTTTGGTATCCCTAAATGCACATACGTGCCCTTACTTGTACTTCAATACC
ACTGAATGAACATAA
Found at i:39197202 original size:40 final size:40
Alignment explanation
Indices: 39197014--39197205 Score: 192
Period size: 40 Copynumber: 4.8 Consensus size: 40
39197004 AATTATTGTT
* * *
39197014 TGAATGTACATGCGTGCCCCTGTTTATACTTTGATATCCC
1 TGAATGCACATACGTGCCCCTGTTTGTACTTTGATATCCC
* * * ** **
39197054 TAAATGCACATATGTGCCCTTACTTGTACTTCAATATCCC
1 TGAATGCACATACGTGCCCCTGTTTGTACTTTGATATCCC
* * * *
39197094 TGAAT-AACATAAGTGCCCCTGTTTGTACTTCGGTA-CCTC
1 TGAATGCACATACGTGCCCCTGTTTGTACTTTGATATCC-C
* *
39197133 TGAATGCACATACGTGCCCTTATTTGTACTTTGATA-CCAC
1 TGAATGCACATACGTGCCCCTGTTTGTACTTTGATATCC-C
*
39197173 TGAATGCACATACGTGCCCCTGTTGGTACTTTG
1 TGAATGCACATACGTGCCCCTGTTTGTACTTTG
39197206 GTAATCCTAA
Statistics
Matches: 122, Mismatches: 28, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
38 2 0.02
39 29 0.24
40 91 0.75
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.35
Consensus pattern (40 bp):
TGAATGCACATACGTGCCCCTGTTTGTACTTTGATATCCC
Found at i:39209221 original size:19 final size:19
Alignment explanation
Indices: 39209197--39209235 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
39209187 ATTTTGACTA
39209197 TTTTGA-TTCCAGGTTAATT
1 TTTTGAGTTCCA-GTTAATT
*
39209216 TTTTGAGTTCGAGTTAATT
1 TTTTGAGTTCCAGTTAATT
39209235 T
1 T
39209236 GAGTTCAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.21, C:0.08, G:0.18, T:0.54
Consensus pattern (19 bp):
TTTTGAGTTCCAGTTAATT
Found at i:39220266 original size:19 final size:19
Alignment explanation
Indices: 39220238--39220280 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
39220228 CAGTATTAAA
*
39220238 AAAAATTTGTTA-CACTAC
1 AAAAATTTGTCAGCACTAC
*
39220256 AAAAATGTTGTCAGTACTAC
1 AAAAAT-TTGTCAGCACTAC
39220276 AAAAA
1 AAAAA
39220281 ATTGATGTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 6 0.29
19 5 0.24
20 10 0.48
ACGTcount: A:0.49, C:0.14, G:0.09, T:0.28
Consensus pattern (19 bp):
AAAAATTTGTCAGCACTAC
Found at i:39220652 original size:30 final size:30
Alignment explanation
Indices: 39220608--39220670 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
39220598 ACTTAACAAG
39220608 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
* *
39220638 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
39220668 CAA
1 CAA
39220671 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.57, C:0.14, G:0.03, T:0.25
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:39221249 original size:60 final size:60
Alignment explanation
Indices: 39221167--39221315 Score: 142
Period size: 60 Copynumber: 2.5 Consensus size: 60
39221157 ATTAGGTGCT
* * * * * *
39221167 AAATTAGGAAAATGAGTAAAGTTCAGGTATAAAATTGAACCCCAAAAAAAA-TTAAG-TACC
1 AAATTAGAAAAAAGTGTCAAGTTTAGGTATAAAATTGAA--CCAAAAAAAAGTTAAGATACA
* * * * * *
39221227 AACTTA-AGAAAAAGTGTCAAGTTTGGGTATCAAATTGGACCAAAAAAAAGTTTAGATGCA
1 AAATTAGA-AAAAAGTGTCAAGTTTAGGTATAAAATTGAACCAAAAAAAAGTTAAGATACA
39221287 AAATTAGAAAAAAGTGTCAAGTTTAGGTA
1 AAATTAGAAAAAAGTGTCAAGTTTAGGTA
39221316 CCAAATGTTA
Statistics
Matches: 71, Mismatches: 14, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
58 10 0.14
59 4 0.06
60 56 0.79
61 1 0.01
ACGTcount: A:0.48, C:0.09, G:0.18, T:0.24
Consensus pattern (60 bp):
AAATTAGAAAAAAGTGTCAAGTTTAGGTATAAAATTGAACCAAAAAAAAGTTAAGATACA
Found at i:39221839 original size:16 final size:16
Alignment explanation
Indices: 39221813--39221856 Score: 79
Period size: 16 Copynumber: 2.7 Consensus size: 16
39221803 AAACATGTAT
39221813 TTGTATTTATACATTAA
1 TTGT-TTTATACATTAA
39221830 TTGTTTTATACATTAA
1 TTGTTTTATACATTAA
39221846 TTGTTTTATAC
1 TTGTTTTATAC
39221857 TTGTAAACAC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 23 0.85
17 4 0.15
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.57
Consensus pattern (16 bp):
TTGTTTTATACATTAA
Found at i:39223375 original size:16 final size:18
Alignment explanation
Indices: 39223349--39223381 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
39223339 ATTAATTAAC
39223349 TAAATTAA-TTTCTCAAT
1 TAAATTAATTTTCTCAAT
39223366 TAAA-TAATTTTCTCAA
1 TAAATTAATTTTCTCAA
39223382 CCCAATTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.45
Consensus pattern (18 bp):
TAAATTAATTTTCTCAAT
Found at i:39227748 original size:29 final size:29
Alignment explanation
Indices: 39227706--39227764 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
39227696 GGATAAAGCA
39227706 TGCTCAACATTTAAAAAGAGAAATTATGT
1 TGCTCAACATTTAAAAAGAGAAATTATGT
39227735 TGCTCAACATTTAAAAAGAGAAATTATGT
1 TGCTCAACATTTAAAAAGAGAAATTATGT
39227764 T
1 T
39227765 TTCCTTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.44, C:0.10, G:0.14, T:0.32
Consensus pattern (29 bp):
TGCTCAACATTTAAAAAGAGAAATTATGT
Found at i:39230566 original size:16 final size:16
Alignment explanation
Indices: 39230545--39230583 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
39230535 AAATAAGTTG
39230545 TCTCTCTCTTTTAGAA
1 TCTCTCTCTTTTAGAA
* *
39230561 TCTCTCTCTTTTGGAG
1 TCTCTCTCTTTTAGAA
39230577 TCTCTCT
1 TCTCTCT
39230584 TTAGCTATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.10, C:0.28, G:0.10, T:0.51
Consensus pattern (16 bp):
TCTCTCTCTTTTAGAA
Found at i:39232697 original size:14 final size:14
Alignment explanation
Indices: 39232678--39232706 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
39232668 CTTCCTCACA
39232678 ATTAAGTAAAATTG
1 ATTAAGTAAAATTG
39232692 ATTAAGTAAAATTG
1 ATTAAGTAAAATTG
39232706 A
1 A
39232707 ATAATGGACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.14, T:0.34
Consensus pattern (14 bp):
ATTAAGTAAAATTG
Found at i:39233501 original size:8 final size:8
Alignment explanation
Indices: 39233488--39233522 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
39233478 TGCAAGTATG
39233488 AAAGGGCA
1 AAAGGGCA
*
39233496 AAAGGGAA
1 AAAGGGCA
39233504 AAAGGGCA
1 AAAGGGCA
*
39233512 AAAGTGCA
1 AAAGGGCA
39233520 AAA
1 AAA
39233523 TAAGAGATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.57, C:0.09, G:0.31, T:0.03
Consensus pattern (8 bp):
AAAGGGCA
Found at i:39233655 original size:10 final size:10
Alignment explanation
Indices: 39233610--39233669 Score: 52
Period size: 10 Copynumber: 6.0 Consensus size: 10
39233600 TAATTTTAGG
39233610 ATTTAT-TTT
1 ATTTATCTTT
*
39233619 CATTTACCTTT
1 -ATTTATCTTT
* *
39233630 AATTAACTTT
1 ATTTATCTTT
*
39233640 AATTATCTTT
1 ATTTATCTTT
39233650 ATTTAT-TTGT
1 ATTTATCTT-T
39233660 ATTTATCTTT
1 ATTTATCTTT
39233670 TAGAATTTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
9 2 0.05
10 35 0.83
11 5 0.12
ACGTcount: A:0.25, C:0.10, G:0.02, T:0.63
Consensus pattern (10 bp):
ATTTATCTTT
Found at i:39234420 original size:40 final size:39
Alignment explanation
Indices: 39234376--39234464 Score: 103
Period size: 39 Copynumber: 2.2 Consensus size: 39
39234366 ATTTATATTA
39234376 TTTTTAATTTTTAAAATTTT-AG-TCAAAACTTTTAATTCTG
1 TTTTT-ATTTTT--AATTTTCAGATCAAAACTTTTAATTCTG
*
39234416 TTTTTA-TTTTATTTTTCGAGATCAAAACTTTTAATTCTG
1 TTTTTATTTTTAATTTTC-AGATCAAAACTTTTAATTCTG
39234455 TTTTTTATTT
1 -TTTTTATTT
39234465 CTTTTTTAGG
Statistics
Matches: 43, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
36 5 0.12
38 6 0.14
39 19 0.44
40 11 0.26
41 2 0.05
ACGTcount: A:0.27, C:0.08, G:0.06, T:0.60
Consensus pattern (39 bp):
TTTTTATTTTTAATTTTCAGATCAAAACTTTTAATTCTG
Found at i:39237398 original size:3 final size:3
Alignment explanation
Indices: 39237390--39237445 Score: 53
Period size: 3 Copynumber: 18.7 Consensus size: 3
39237380 CAATTTTTAT
* * *
39237390 TTA TTA TTA TTA TTA TTA TTTC TTT TTA TTT TTA TT- TTA TTA TTTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA -TTA
39237436 TTA TT- TTA TT
1 TTA TTA TTA TT
39237446 TTTTGGATGC
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
2 4 0.09
3 35 0.80
4 5 0.11
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (3 bp):
TTA
Found at i:39237446 original size:12 final size:12
Alignment explanation
Indices: 39237384--39237446 Score: 50
Period size: 12 Copynumber: 5.7 Consensus size: 12
39237374 GCAACCCAAT
39237384 TTTTATTTATTA
1 TTTTATTTATTA
39237396 TTATTA-TTATTA
1 TT-TTATTTATTA
*
39237408 -TTTCTTT-TTA
1 TTTTATTTATTA
39237418 --TT-TTTATT-
1 TTTTATTTATTA
39237426 TTATTATTTATTA
1 TT-TTATTTATTA
39237439 TTTTATTT
1 TTTTATTT
39237447 TTTGGATGCT
Statistics
Matches: 42, Mismatches: 1, Indels: 16
0.71 0.02 0.27
Matches are distributed among these distances:
8 3 0.07
9 4 0.10
10 5 0.12
11 5 0.12
12 20 0.48
13 5 0.12
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTATTTATTA
Found at i:39239420 original size:10 final size:10
Alignment explanation
Indices: 39239407--39239449 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
39239397 TATTTTCATT
39239407 TTTAATTATC
1 TTTAATTATC
39239417 TTTAATTATC
1 TTTAATTATC
*
39239427 TTTATTTAT-
1 TTTAATTATC
*
39239436 TTGTATTTATC
1 TT-TAATTATC
39239447 TTT
1 TTT
39239450 TAGAATTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 2 0.07
10 26 0.87
11 2 0.07
ACGTcount: A:0.23, C:0.07, G:0.02, T:0.67
Consensus pattern (10 bp):
TTTAATTATC
Found at i:39254520 original size:20 final size:20
Alignment explanation
Indices: 39254497--39254542 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
39254487 ATTTGACGTT
*
39254497 CTTGTCGGTGGTTTGGCGTG
1 CTTGGCGGTGGTTTGGCGTG
39254517 CTTGGCGGTGGTTTGGCGTG
1 CTTGGCGGTGGTTTGGCGTG
39254537 CTTGGC
1 CTTGGC
39254543 AATGGTATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.00, C:0.17, G:0.46, T:0.37
Consensus pattern (20 bp):
CTTGGCGGTGGTTTGGCGTG
Found at i:39254548 original size:20 final size:20
Alignment explanation
Indices: 39254505--39254548 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
39254495 TTCTTGTCGG
**
39254505 TGGTTTGGCGTGCTTGGCGG
1 TGGTTTGGCGTGCTTGGCAA
39254525 TGGTTTGGCGTGCTTGGCAA
1 TGGTTTGGCGTGCTTGGCAA
39254545 TGGT
1 TGGT
39254549 ATAACAACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.05, C:0.14, G:0.45, T:0.36
Consensus pattern (20 bp):
TGGTTTGGCGTGCTTGGCAA
Found at i:39261977 original size:6 final size:6
Alignment explanation
Indices: 39261966--39261998 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
39261956 TCCCTAAGCA
*
39261966 AAAAAT AAAAAT AAAAAT AAAAAT AAAATT AAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAA
39261999 GCAATTTCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
AAAAAT
Found at i:39275811 original size:15 final size:15
Alignment explanation
Indices: 39275791--39275820 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
39275781 TGGTTTGCTT
39275791 TTAAAAAAAAATAAA
1 TTAAAAAAAAATAAA
*
39275806 TTAAAAATAAATAAA
1 TTAAAAAAAAATAAA
39275821 AAAATTAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
TTAAAAAAAAATAAA
Found at i:39284627 original size:20 final size:21
Alignment explanation
Indices: 39284602--39284640 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
39284592 CCCTTAAAAC
39284602 AGGGC-ACACGCCCATGTGGA
1 AGGGCAACACGCCCATGTGGA
*
39284622 AGGGCAACACGCCCTTGTG
1 AGGGCAACACGCCCATGTG
39284641 ACCAACTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.23, C:0.31, G:0.33, T:0.13
Consensus pattern (21 bp):
AGGGCAACACGCCCATGTGGA
Found at i:39285809 original size:47 final size:44
Alignment explanation
Indices: 39285741--39285998 Score: 207
Period size: 47 Copynumber: 5.5 Consensus size: 44
39285731 GTGCAGATAC
39285741 CATGTCCCAGACATGGTCTTACACTGGCTCATATATCAAGTCGATG
1 CATGTCCCAGACAT-GTCTTACACTGGCT-ATATATCAAGTCGATG
* * **
39285787 CCATGTCCCAGACATGGTCTTACACTGACTAT-CATCTTGTAGCTGATG
1 -CATGTCCCAGACAT-GTCTTACACTGGCTATATATCAAGT--C-GATG
* * * *
39285835 CATGTCCCAGACATGTCTTACACAGGCT-TACGTCTCGAGGCCGATG
1 CATGTCCCAGACATGTCTTACACTGGCTATA--TATC-AAGTCGATG
* * * *
39285881 CATGTCCCAGACATGTCTTACACTAGCTTTCGTCTCAA-TGCTGATG
1 CATGTCCCAGACATGTCTTACACTGGCTAT-ATATCAAGT-C-GATG
***
39285927 CCATGTCCCAGACATGGTCTTACACTGGCTATCATAATGTGGTCGATG
1 -CATGTCCCAGACAT-GTCTTACACTGGCTAT-AT-ATCAAGTCGATG
39285975 CATGTCCCAGACATGTCTTACACT
1 CATGTCCCAGACATGTCTTACACT
39285999 AGCCAACAAT
Statistics
Matches: 173, Mismatches: 23, Indels: 31
0.76 0.10 0.14
Matches are distributed among these distances:
45 8 0.05
46 62 0.36
47 73 0.42
48 26 0.15
49 3 0.02
50 1 0.01
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (44 bp):
CATGTCCCAGACATGTCTTACACTGGCTATATATCAAGTCGATG
Found at i:39285988 original size:94 final size:93
Alignment explanation
Indices: 39285740--39286001 Score: 311
Period size: 94 Copynumber: 2.8 Consensus size: 93
39285730 AGTGCAGATA
* *
39285740 CCATGTCCCAGACATGGTCTTACACTGGC-TCATATATCAAGTCGATGCCATGTCCCAGACATGG
1 CCATGTCCCAGACATGGTCTTACACTGGCTTCATA-ATGAGGTCGATG-CATGTCCCAGACAT-G
**
39285804 TCTTACACT-GACTATCATCTTGTAGCTGATG
63 TCTTACACTAG-CTATCATCTAATAGCTGATG
* * * *
39285835 -CATGTCCCAGACAT-GTCTTACACAGGCTTACGT-CTCGAGGCCGATGCATGTCCCAGACATGT
1 CCATGTCCCAGACATGGTCTTACACTGGCTT-CATAAT-GAGGTCGATGCATGTCCCAGACATGT
* *
39285897 CTTACACTAGCTTTCGTCTCAAT-GCTGATG
64 CTTACACTAGCTATCATCT-AATAGCTGATG
*
39285927 CCATGTCCCAGACATGGTCTTACACTGGCTATCATAATGTGGTCGATGCATGTCCCAGACATGTC
1 CCATGTCCCAGACATGGTCTTACACTGGCT-TCATAATGAGGTCGATGCATGTCCCAGACATGTC
39285992 TTACACTAGC
65 TTACACTAGC
39286002 CAACAATAAC
Statistics
Matches: 143, Mismatches: 15, Indels: 19
0.81 0.08 0.11
Matches are distributed among these distances:
92 24 0.17
93 43 0.30
94 72 0.50
95 4 0.03
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (93 bp):
CCATGTCCCAGACATGGTCTTACACTGGCTTCATAATGAGGTCGATGCATGTCCCAGACATGTCT
TACACTAGCTATCATCTAATAGCTGATG
Found at i:39285993 original size:140 final size:140
Alignment explanation
Indices: 39285741--39285997 Score: 378
Period size: 140 Copynumber: 1.8 Consensus size: 140
39285731 GTGCAGATAC
*
39285741 CATGTCCCAGACATGGTCTTACACTGGCTCATATATCAAGTCGATGCCATGTCCCAGACATGGTC
1 CATGTCCCAGACATGGTCTTACACTAGCTCATATATCAAGTCGATGCCATGTCCCAGACATGGTC
**
39285806 TTACACTGACTATCATCTTGTAGCTGATGCATGTCCCAGACATGTCTTACACAGGCTTACGTCTC
66 TTACACTGACTATCATAATGTAGCTGATGCATGTCCCAGACATGTCTTACACAGGCTTACGTCTC
39285871 GAGGCCGATG
131 GAGGCCGATG
* * *
39285881 CATGTCCCAGACAT-GTCTTACACTAGCT-TTCGTCTCAA-TGCTGATGCCATGTCCCAGACATG
1 CATGTCCCAGACATGGTCTTACACTAGCTCAT-ATATCAAGT-C-GATGCCATGTCCCAGACATG
* *
39285943 GTCTTACACTGGCTATCATAATGT-GGTCGATGCATGTCCCAGACATGTCTTACAC
63 GTCTTACACTGACTATCATAATGTAGCT-GATGCATGTCCCAGACATGTCTTACAC
39285998 TAGCCAACAA
Statistics
Matches: 105, Mismatches: 8, Indels: 8
0.87 0.07 0.07
Matches are distributed among these distances:
138 2 0.02
139 21 0.20
140 82 0.78
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (140 bp):
CATGTCCCAGACATGGTCTTACACTAGCTCATATATCAAGTCGATGCCATGTCCCAGACATGGTC
TTACACTGACTATCATAATGTAGCTGATGCATGTCCCAGACATGTCTTACACAGGCTTACGTCTC
GAGGCCGATG
Found at i:39298461 original size:229 final size:229
Alignment explanation
Indices: 39298057--39298496 Score: 835
Period size: 229 Copynumber: 1.9 Consensus size: 229
39298047 CTTCATGAAA
39298057 AGTCAATTACTATCATATAGTAATTAAGTCATTTATCAAAAAGAAAAACAACTCATGACCACGTT
1 AGTCAATTACTATCATATAGTAATTAAGTCATTTATCAAAAAGAAAAACAACTCATGACCACGTT
39298122 TACTTTTCATCTATCATGTAATGCCAATGAGAAGATATCATTTACGCATGTCTTGGGCTATGAAT
66 TACTTTTCATCTATCATGTAATGCCAATGAGAAGATATCATTTACGCATGTCTTGGGCTATGAAT
39298187 TCCTCTATTGTGAATGATGCTACATAATGTATAAGTCGGATACCCAATGTACCAACTTTTGGTTC
131 TCCTCTATTGTGAATGATGCTACATAATGTATAAGTCGGATACCCAATGTACCAACTTTTGGTTC
39298252 CTTATTTATTTGGATTCGGGCTTTTACTTACATC
196 CTTATTTATTTGGATTCGGGCTTTTACTTACATC
* *
39298286 AGTCAATTACTATCATATAGTAATTAAGTCATTTATCAAAAAGAAAAGCAACTCGTGACCACGTT
1 AGTCAATTACTATCATATAGTAATTAAGTCATTTATCAAAAAGAAAAACAACTCATGACCACGTT
*
39298351 TACTTTTCATCTATCATGTAATGCCAATGAGAAGATATCATTTACTCATGTCTTGGGCTATGAAT
66 TACTTTTCATCTATCATGTAATGCCAATGAGAAGATATCATTTACGCATGTCTTGGGCTATGAAT
* *
39298416 TCCTCTATTTTGAATGATGCTACATAATGTATAAGTCGTATACCCAATGTACCAACTTTTGGTTC
131 TCCTCTATTGTGAATGATGCTACATAATGTATAAGTCGGATACCCAATGTACCAACTTTTGGTTC
39298481 CTTATTTATTTGGATT
196 CTTATTTATTTGGATT
39298497 TAGGCTGCCA
Statistics
Matches: 206, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
229 206 1.00
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (229 bp):
AGTCAATTACTATCATATAGTAATTAAGTCATTTATCAAAAAGAAAAACAACTCATGACCACGTT
TACTTTTCATCTATCATGTAATGCCAATGAGAAGATATCATTTACGCATGTCTTGGGCTATGAAT
TCCTCTATTGTGAATGATGCTACATAATGTATAAGTCGGATACCCAATGTACCAACTTTTGGTTC
CTTATTTATTTGGATTCGGGCTTTTACTTACATC
Found at i:39303028 original size:18 final size:17
Alignment explanation
Indices: 39303005--39303038 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
39302995 TAGATTTGTA
39303005 AAAAATAAACAGAAAAAT
1 AAAAATAAACA-AAAAAT
39303023 AAAAATAAACAAAAAA
1 AAAAATAAACAAAAAA
39303039 CGAAAGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.82, C:0.06, G:0.03, T:0.09
Consensus pattern (17 bp):
AAAAATAAACAAAAAAT
Found at i:39311044 original size:19 final size:20
Alignment explanation
Indices: 39311022--39311066 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
39311012 TTATGAAACT
*
39311022 TAATGCATATG-ATGAAATG
1 TAATGCAGATGAATGAAATG
*
39311041 TAATGTAGATGAATGAAATG
1 TAATGCAGATGAATGAAATG
39311061 -AATGCA
1 TAATGCA
39311067 AAAAGTAGTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.44, C:0.04, G:0.22, T:0.29
Consensus pattern (20 bp):
TAATGCAGATGAATGAAATG
Found at i:39316628 original size:16 final size:16
Alignment explanation
Indices: 39316592--39316622 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39316582 ATCAATTTGT
39316592 AGGTTAAAAACTGACA
1 AGGTTAAAAACTGACA
*
39316608 AGGTTAAAAATTGAC
1 AGGTTAAAAACTGAC
39316623 GTGGTTGATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.10, G:0.19, T:0.23
Consensus pattern (16 bp):
AGGTTAAAAACTGACA
Found at i:39328023 original size:43 final size:43
Alignment explanation
Indices: 39327962--39328152 Score: 185
Period size: 43 Copynumber: 4.4 Consensus size: 43
39327952 GTTATCGAGA
*
39327962 TGTGATTACATGTAAGACCCTGTGTGGGACAGTGGCATTGTAT
1 TGTGATTACGTGTAAGACCCTGTGTGGGACAGTGGCATTGTAT
* *
39328005 TGTGATTACGTGTAAGACCCTGTGTTGGATAGTGGCATTGTAT
1 TGTGATTACGTGTAAGACCCTGTGTGGGACAGTGGCATTGTAT
** * * *
39328048 TACGATTACGTGTAAGACCATGTGTGGGACA-TCG-ATATCGTTAA
1 TGTGATTACGTGTAAGACCCTGTGTGGGACAGTGGCAT-T-G-TAT
* * *
39328092 T-CGACTT-CGTGTAAGACCCTGTGTGGGACAGTGACATCG-AT
1 TGTGA-TTACGTGTAAGACCCTGTGTGGGACAGTGGCATTGTAT
* *
39328133 ATGTGATAACATGTAAGACC
1 -TGTGATTACGTGTAAGACC
39328153 ATATTTAGGA
Statistics
Matches: 121, Mismatches: 18, Indels: 18
0.77 0.11 0.11
Matches are distributed among these distances:
41 3 0.02
42 5 0.04
43 105 0.87
44 6 0.05
45 2 0.02
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.31
Consensus pattern (43 bp):
TGTGATTACGTGTAAGACCCTGTGTGGGACAGTGGCATTGTAT
Found at i:39328285 original size:29 final size:29
Alignment explanation
Indices: 39328243--39328301 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
39328233 TCAAGTCGAG
*
39328243 AAAGAAAGTGTAAATGAATTAAGCAATGC
1 AAAGAAAGTGTAAATAAATTAAGCAATGC
39328272 AAAGAAAGTGTAAATAAATTAAGCAATGC
1 AAAGAAAGTGTAAATAAATTAAGCAATGC
39328301 A
1 A
39328302 GGTACGTACA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.54, C:0.07, G:0.19, T:0.20
Consensus pattern (29 bp):
AAAGAAAGTGTAAATAAATTAAGCAATGC
Found at i:39331087 original size:15 final size:15
Alignment explanation
Indices: 39331067--39331097 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
39331057 ACGGCCTGTT
39331067 CACATGGGCGTGTGA
1 CACATGGGCGTGTGA
39331082 CACATGGGCGTGTGA
1 CACATGGGCGTGTGA
39331097 C
1 C
39331098 TCACTTGTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.23, G:0.39, T:0.19
Consensus pattern (15 bp):
CACATGGGCGTGTGA
Found at i:39333125 original size:22 final size:23
Alignment explanation
Indices: 39333100--39333154 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 23
39333090 TTCGCCAAAA
*
39333100 TGTCCCACGC-TTCTTTAGAAGT
1 TGTCCCACGCAATCTTTAGAAGT
*
39333122 TGTCGCACTCGCAATCTTTAGAAGT
1 TGTC-C-CACGCAATCTTTAGAAGT
39333147 TGTCCCAC
1 TGTCCCAC
39333155 TTTATCTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
22 4 0.15
23 3 0.11
24 5 0.19
25 15 0.56
ACGTcount: A:0.20, C:0.29, G:0.18, T:0.33
Consensus pattern (23 bp):
TGTCCCACGCAATCTTTAGAAGT
Found at i:39338163 original size:39 final size:38
Alignment explanation
Indices: 39338072--39338221 Score: 203
Period size: 39 Copynumber: 3.9 Consensus size: 38
39338062 ATTCCACTCC
* * *
39338072 CCCCATGCTACTTTGTTTTATTATTAATCAAAAAC-ACT
1 CCCCATACTATTTTGTTTTATTATTAAT-TAAAACTACT
* *
39338110 CCCCATGCTATTTTGTTTTATTATTAATTAAAACTATTT
1 CCCCATACTATTTTGTTTTATTATTAATTAAAACTA-CT
*
39338149 CCCCATACTATTTTGTTTTATTGTTAATTAAAACTACCT
1 CCCCATACTATTTTGTTTTATTATTAATTAAAACTA-CT
*
39338188 CCTCATACTATTTTGTTTTATTATTAATTAAAAC
1 CCCCATACTATTTTGTTTTATTATTAATTAAAAC
39338222 CATACTTTCT
Statistics
Matches: 101, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
37 5 0.05
38 28 0.28
39 68 0.67
ACGTcount: A:0.30, C:0.19, G:0.05, T:0.47
Consensus pattern (38 bp):
CCCCATACTATTTTGTTTTATTATTAATTAAAACTACT
Found at i:39348425 original size:32 final size:32
Alignment explanation
Indices: 39348389--39348449 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
39348379 AAAACACTTA
*
39348389 ACATTTTAGTGACTTAAATAAAAAATTTTTGC
1 ACATTTCAGTGACTTAAATAAAAAATTTTTGC
** *
39348421 ACATTTCAGTGGTTTAAATAAAAACTTTT
1 ACATTTCAGTGACTTAAATAAAAAATTTT
39348450 GAATAGTCCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (32 bp):
ACATTTCAGTGACTTAAATAAAAAATTTTTGC
Found at i:39350186 original size:26 final size:24
Alignment explanation
Indices: 39350156--39350203 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
39350146 GCAAGGGAAT
*
39350156 AGGGAAAGGAAATGAGGAAAAATGCA
1 AGGG-AAGGAAAAGA-GAAAAATGCA
*
39350182 AGGGAATGAAAAGAGAAAAATG
1 AGGGAAGGAAAAGAGAAAAATG
39350204 AGAAAGAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 8 0.40
25 8 0.40
26 4 0.20
ACGTcount: A:0.56, C:0.02, G:0.33, T:0.08
Consensus pattern (24 bp):
AGGGAAGGAAAAGAGAAAAATGCA
Found at i:39355375 original size:26 final size:26
Alignment explanation
Indices: 39355344--39355404 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
39355334 ATAAGAGCCA
* * *
39355344 TAATCAGGAAGTTTACAAAGAAATTT
1 TAATCAGGAAGATCACAAAGAAACTT
* **
39355370 TAATCAGAAAGATCACAAAGAGCCTT
1 TAATCAGGAAGATCACAAAGAAACTT
39355396 TAATCAGGA
1 TAATCAGGA
39355405 GCTCTAAATA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.46, C:0.13, G:0.16, T:0.25
Consensus pattern (26 bp):
TAATCAGGAAGATCACAAAGAAACTT
Found at i:39356551 original size:51 final size:51
Alignment explanation
Indices: 39356495--39356818 Score: 227
Period size: 51 Copynumber: 6.4 Consensus size: 51
39356485 GCATGGACTG
* * * *
39356495 TGTGTAGGCCACTATGTGAAAGTGAAAGTGAT-GGTCACGTGTGTAGTACTA
1 TGTGCAGGCTACTATGTGAACG-GAAAGTGATAGGTCACATGTGTAGTACTA
* * * * * *
39356546 TGTGTAGGCTACTACGTGTAC-CAGAA-TGATAGGTCGCATGTATAGTACTA
1 TGTGCAGGCTACTATGTGAACGGA-AAGTGATAGGTCACATGTGTAGTACTA
* * * * * *
39356596 TGTGCAGGCTACTATGCGTACCGGATAGCT--TCGATCACGTGTGTAGTACTA
1 TGTGCAGGCTACTATGTG-AACGGAAAG-TGATAGGTCACATGTGTAGTACTA
* * * **
39356647 TGTGTAGGCTACTATGTGTAC-CAGAA-TGATAGGTCGTATGTGTAGTACTA
1 TGTGCAGGCTACTATGTGAACGGA-AAGTGATAGGTCACATGTGTAGTACTA
* * * * * *
39356697 TGTGCAGGCTACTATGCGTATCGGATAGCT--TCGATCACGTGTGTAGTACTA
1 TGTGCAGGCTACTATGTG-AACGGAAAG-TGATAGGTCACATGTGTAGTACTA
* * *
39356748 TGTGCAGGCTACTACGTGTATCGGATAGTGAT-GGTCACATGTGTAGTACTA
1 TGTGCAGGCTACTATGTG-AACGGAAAGTGATAGGTCACATGTGTAGTACTA
*
39356799 TGTGCATGCTACTATGTGAA
1 TGTGCAGGCTACTATGTGAA
39356819 TCCGCATCAT
Statistics
Matches: 209, Mismatches: 49, Indels: 31
0.72 0.17 0.11
Matches are distributed among these distances:
48 1 0.00
49 6 0.03
50 69 0.33
51 128 0.61
52 3 0.01
53 2 0.01
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (51 bp):
TGTGCAGGCTACTATGTGAACGGAAAGTGATAGGTCACATGTGTAGTACTA
Found at i:39356646 original size:101 final size:101
Alignment explanation
Indices: 39356529--39356814 Score: 466
Period size: 101 Copynumber: 2.8 Consensus size: 101
39356519 AAAGTGATGG
*
39356529 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCAGAATGATAGGTCGCATGTATAGTAC
1 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCAGAATGATAGGTCGCATGTGTAGTAC
39356594 TATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
66 TATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
* *
39356630 TCACGTGTGTAGTACTATGTGTAGGCTACTATGTGTACCAGAATGATAGGTCGTATGTGTAGTAC
1 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCAGAATGATAGGTCGCATGTGTAGTAC
*
39356695 TATGTGCAGGCTACTATGCGTATCGGATAGCTTCGA
66 TATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
* * * *
39356731 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTGAT-GGTCACATGTGTAGT
1 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCAGA-A-TGATAGGTCGCATGTGTAGT
*
39356795 ACTATGTGCATGCTACTATG
64 ACTATGTGCAGGCTACTATG
39356815 TGAATCCGCA
Statistics
Matches: 172, Mismatches: 11, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
101 135 0.78
102 33 0.19
103 4 0.02
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (101 bp):
TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCAGAATGATAGGTCGCATGTGTAGTAC
TATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
Found at i:39356816 original size:26 final size:26
Alignment explanation
Indices: 39356736--39356816 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 26
39356726 TTCGATCACG
*
39356736 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCATGCTACTA
* * *
39356762 CGTGTA-T-CGGATAGTG-ATGGTCAC-A
1 TGTGTAGTAC-TAT-GTGCATGCT-ACTA
39356787 TGTGTAGTACTATGTGCATGCTACTA
1 TGTGTAGTACTATGTGCATGCTACTA
39356813 TGTG
1 TGTG
39356817 AATCCGCATC
Statistics
Matches: 41, Mismatches: 7, Indels: 14
0.66 0.11 0.23
Matches are distributed among these distances:
24 1 0.02
25 17 0.41
26 22 0.54
27 1 0.02
ACGTcount: A:0.22, C:0.15, G:0.28, T:0.35
Consensus pattern (26 bp):
TGTGTAGTACTATGTGCATGCTACTA
Found at i:39356939 original size:41 final size:42
Alignment explanation
Indices: 39356824--39356950 Score: 161
Period size: 43 Copynumber: 3.0 Consensus size: 42
39356814 GTGAATCCGC
* *
39356824 ATCATTGAATATAAAGGTGGTTGCTAAGTGCTGATTCCACCAT
1 ATCATTGATTAT-AAGGTGGTTGCTAAGTGCTGATTCCACCGT
* *
39356867 ATCCTTGACTGTGA-AAGG-GGTTGCTATGTGCTGATTCC-CCGT
1 ATCATTGA-T-T-ATAAGGTGGTTGCTAAGTGCTGATTCCACCGT
39356909 ATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTCCACCGT
1 ATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTCCACCGT
39356951 GTGACGGTTA
Statistics
Matches: 72, Mismatches: 6, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
39 1 0.01
40 5 0.07
41 20 0.28
42 14 0.19
43 26 0.36
44 4 0.06
45 1 0.01
46 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (42 bp):
ATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTCCACCGT
Found at i:39362876 original size:20 final size:21
Alignment explanation
Indices: 39362853--39362892 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
39362843 TCATGACATT
39362853 AAGCCT-AAAGTCACAACACC
1 AAGCCTCAAAGTCACAACACC
*
39362873 AAGCCTCCAAGGTCACAACA
1 AAGCCT-CAAAGTCACAACA
39362893 TCACTAGTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
22 11 0.65
ACGTcount: A:0.42, C:0.35, G:0.12, T:0.10
Consensus pattern (21 bp):
AAGCCTCAAAGTCACAACACC
Found at i:39375833 original size:6 final size:6
Alignment explanation
Indices: 39375822--39375856 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
39375812 CGTTGCTCTG
39375822 CAAAAA CAAAAA C-AAAA CAAAAA CAAAAA CAAAAA
1 CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA
39375857 ACCATAATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.18
6 23 0.82
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (6 bp):
CAAAAA
Found at i:39375840 original size:11 final size:12
Alignment explanation
Indices: 39375822--39375856 Score: 63
Period size: 11 Copynumber: 3.0 Consensus size: 12
39375812 CGTTGCTCTG
39375822 CAAAAACAAAAA
1 CAAAAACAAAAA
39375834 C-AAAACAAAAA
1 CAAAAACAAAAA
39375845 CAAAAACAAAAA
1 CAAAAACAAAAA
39375857 ACCATAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (12 bp):
CAAAAACAAAAA
Found at i:39375844 original size:17 final size:17
Alignment explanation
Indices: 39375822--39375855 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
39375812 CGTTGCTCTG
39375822 CAAAAACAAAAACAAAA
1 CAAAAACAAAAACAAAA
39375839 CAAAAACAAAAACAAAA
1 CAAAAACAAAAACAAAA
39375856 AACCATAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.82, C:0.18, G:0.00, T:0.00
Consensus pattern (17 bp):
CAAAAACAAAAACAAAA
Found at i:39398317 original size:17 final size:17
Alignment explanation
Indices: 39398295--39398334 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
39398285 CATATGCCTA
*
39398295 AATATTTTGTTTCTGTT
1 AATATTTTGTTTCTATT
39398312 AATATTTTGTTTCTATT
1 AATATTTTGTTTCTATT
39398329 AATATT
1 AATATT
39398335 CTTTAATGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.25, C:0.05, G:0.07, T:0.62
Consensus pattern (17 bp):
AATATTTTGTTTCTATT
Found at i:39399348 original size:237 final size:237
Alignment explanation
Indices: 39398933--39399391 Score: 918
Period size: 237 Copynumber: 1.9 Consensus size: 237
39398923 TTTCCAGTAG
39398933 TAAATGTCACAATAGCACTTATATGTGGATACAAAGTAAAAGGAATGATAGTAAAATTATTAATT
1 TAAATGTCACAATAGCACTTATATGTGGATACAAAGTAAAAGGAATGATAGTAAAATTATTAATT
39398998 TGTTACAATCTAGTACAATTGAAACACATGTTAAAGTAAACCAGAAGTTTATTGATACAAATGTA
66 TGTTACAATCTAGTACAATTGAAACACATGTTAAAGTAAACCAGAAGTTTATTGATACAAATGTA
39399063 TTTACTATTTGGCGTGACCAATTAGACCATACTGGATCATATATGATGCGAAAATTAATTAAAAA
131 TTTACTATTTGGCGTGACCAATTAGACCATACTGGATCATATATGATGCGAAAATTAATTAAAAA
39399128 TTCATATGGACATTCATTAAAGAACTATTATAGTAAAATTAT
196 TTCATATGGACATTCATTAAAGAACTATTATAGTAAAATTAT
39399170 TAAATGTCACAATAGCACTTATATGTGGATACAAAGTAAAAGGAATGATAGTAAAATTATTAATT
1 TAAATGTCACAATAGCACTTATATGTGGATACAAAGTAAAAGGAATGATAGTAAAATTATTAATT
39399235 TGTTACAATCTAGTACAATTGAAACACATGTTAAAGTAAACCAGAAGTTTATTGATACAAATGTA
66 TGTTACAATCTAGTACAATTGAAACACATGTTAAAGTAAACCAGAAGTTTATTGATACAAATGTA
39399300 TTTACTATTTGGCGTGACCAATTAGACCATACTGGATCATATATGATGCGAAAATTAATTAAAAA
131 TTTACTATTTGGCGTGACCAATTAGACCATACTGGATCATATATGATGCGAAAATTAATTAAAAA
39399365 TTCATATGGACATTCATTAAAGAACTA
196 TTCATATGGACATTCATTAAAGAACTA
39399392 GAAGATTCTT
Statistics
Matches: 222, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
237 222 1.00
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.32
Consensus pattern (237 bp):
TAAATGTCACAATAGCACTTATATGTGGATACAAAGTAAAAGGAATGATAGTAAAATTATTAATT
TGTTACAATCTAGTACAATTGAAACACATGTTAAAGTAAACCAGAAGTTTATTGATACAAATGTA
TTTACTATTTGGCGTGACCAATTAGACCATACTGGATCATATATGATGCGAAAATTAATTAAAAA
TTCATATGGACATTCATTAAAGAACTATTATAGTAAAATTAT
Found at i:39402564 original size:16 final size:17
Alignment explanation
Indices: 39402543--39402577 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
39402533 AATAAAATAT
*
39402543 AATTTTAT-TATTTTAA
1 AATTTTATAAATTTTAA
39402559 AATTTTATAAATTTTAA
1 AATTTTATAAATTTTAA
39402576 AA
1 AA
39402578 GGTTAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
AATTTTATAAATTTTAA
Found at i:39406218 original size:113 final size:111
Alignment explanation
Indices: 39406088--39406524 Score: 578
Period size: 113 Copynumber: 4.0 Consensus size: 111
39406078 ATTTTTTAAA
* *
39406088 AAATTATTTTAAAGTTATTTTGTTAGTAGTTTATGATTAGGTTATAAATTGTTTGTGTTTAGTTT
1 AAATTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTTGTATTTAGTTT
39406153 AGTGTTTATTGTGATTTTTTATGAATGTAATATTTTTTTTCTTTTTTT
66 AGTGTTTATTGTGATTTTTTATGAATGTAA-ATTTTTTTT-TTTTTTT
*
39406201 AAATTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTATTTGTATTTAGTTT
1 AAATTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTTGTATTTAGTTT
* *
39406266 AGTGTTTATTATGATTTCTTATGAATGTAAATTTTTTTGTTTGTTTTTT
66 AGTGTTTATTGTGATTTTTTATGAATGTAAA-TTTTTT-TTT-TTTTTT
*
39406315 AAAATTATTTTAAAGTTATTTTTGTTAGTAATTTATGATTAGGTTTTAAA-TGTTTGTATTTAGT
1 -AAATTATTTTAAAGTTA-TTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTTGTATTTAGT
* *
39406379 TTAGTGTTTATTGTGATTTTGTATGAATTTAAA--------TTTTTTT
64 TTAGTGTTTATTGTGATTTTTTATGAATGTAAATTTTTTTTTTTTTTT
*
39406419 AATATT-TTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTATTTG--TTTAGTT
1 AA-ATTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTTGTATTTAGTT
* * * **
39406481 TAATGTGTATTGTGATTTGTTAT-AATGT-AATTTTAATTTTTTTT
65 TAGTGTTTATTGTGATTTTTTATGAATGTAAATTTTTTTTTTTTTT
39406525 GATTTATTTG
Statistics
Matches: 291, Mismatches: 18, Indels: 36
0.84 0.05 0.10
Matches are distributed among these distances:
99 2 0.01
100 4 0.01
101 26 0.09
102 30 0.10
103 18 0.06
104 9 0.03
105 1 0.00
107 6 0.02
112 1 0.00
113 97 0.33
114 8 0.03
115 59 0.20
116 30 0.10
ACGTcount: A:0.27, C:0.00, G:0.14, T:0.59
Consensus pattern (111 bp):
AAATTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTTGTATTTAGTTT
AGTGTTTATTGTGATTTTTTATGAATGTAAATTTTTTTTTTTTTTT
Found at i:39406379 original size:228 final size:214
Alignment explanation
Indices: 39406087--39406514 Score: 617
Period size: 228 Copynumber: 1.9 Consensus size: 214
39406077 AATTTTTTAA
* *
39406087 AAAATTATTTTAAAGTTATTTTGTTAGTAGTTTATGATTAGGTTATAAATTGTTTGTGTTTAGTT
1 AAAATTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTTGTATTTAGTT
*
39406152 TAGTGTTTATTGTGATTTTTTATGAATGTAATATTTTTTTTCTTTTTTTAA-ATTATTTTAAAGT
66 TAGTGTTTATTGTGATTTTGTATGAATGTAA-A---------TTTTTTTAATATT-TTTTAAAGT
* *
39406216 TATTTTGTTAGTAATTTATGATTAGGTTATAAATTATTTGTATTTAGTTTAGTGTTTATTATGAT
120 TATTTTGTTAGTAATTTATGATTAGGTTATAAATTATTTG--TTTAGTTTAATGTGTATTATGAT
39406281 TTCTTATGAATGTAAATTTTTTTGTTTGTTTTTT
183 TTCTTAT-AATGT-AATTTTTTTGTTTGTTTTTT
*
39406315 AAAATTATTTTAAAGTTATTTTTGTTAGTAATTTATGATTAGGTTTTAAA-TGTTTGTATTTAGT
1 AAAATTATTTTAAAGTTA-TTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTTGTATTTAGT
*
39406379 TTAGTGTTTATTGTGATTTTGTATGAATTTAAATTTTTTTAATATTTTTTAAAGTTATTTTGTTA
65 TTAGTGTTTATTGTGATTTTGTATGAATGTAAATTTTTTTAATATTTTTTAAAGTTATTTTGTTA
* *
39406444 GTAATTTATGATTAGGTTATAAATTATTTGTTTAGTTTAATGTGTATTGTGATTTGTTATAATGT
130 GTAATTTATGATTAGGTTATAAATTATTTGTTTAGTTTAATGTGTATTATGATTTCTTATAATGT
39406509 AATTTT
195 AATTTT
39406515 AATTTTTTTT
Statistics
Matches: 189, Mismatches: 9, Indels: 18
0.88 0.04 0.08
Matches are distributed among these distances:
214 6 0.03
215 5 0.03
216 26 0.14
218 58 0.31
219 3 0.02
227 1 0.01
228 61 0.32
229 29 0.15
ACGTcount: A:0.27, C:0.00, G:0.14, T:0.58
Consensus pattern (214 bp):
AAAATTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTTGTATTTAGTT
TAGTGTTTATTGTGATTTTGTATGAATGTAAATTTTTTTAATATTTTTTAAAGTTATTTTGTTAG
TAATTTATGATTAGGTTATAAATTATTTGTTTAGTTTAATGTGTATTATGATTTCTTATAATGTA
ATTTTTTTGTTTGTTTTTT
Found at i:39406769 original size:17 final size:18
Alignment explanation
Indices: 39406737--39406781 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
39406727 ATGAGAATTT
*
39406737 ATTATATTTTTTATTGTA
1 ATTATATTTATTATTGTA
39406755 ATTATA-TTATTATTGT-
1 ATTATATTTATTATTGTA
*
39406771 ACTATATTTAT
1 ATTATATTTAT
39406782 CGTATTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 5 0.21
17 13 0.54
18 6 0.25
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.62
Consensus pattern (18 bp):
ATTATATTTATTATTGTA
Found at i:39406808 original size:21 final size:22
Alignment explanation
Indices: 39406757--39406809 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
39406747 TTATTGTAAT
* *
39406757 TATATTATTATTGTACTATATT
1 TATAATATTATTGTACTATATG
**
39406779 TATCGTATTATT-TACTATATG
1 TATAATATTATTGTACTATATG
39406800 TATAATATTA
1 TATAATATTA
39406810 ATGTTTTTGA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 16 0.62
22 10 0.38
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.55
Consensus pattern (22 bp):
TATAATATTATTGTACTATATG
Found at i:39408913 original size:14 final size:14
Alignment explanation
Indices: 39408894--39408920 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
39408884 TTTAATTCTA
39408894 CAAAAATATAAATG
1 CAAAAATATAAATG
39408908 CAAAAATATAAAT
1 CAAAAATATAAAT
39408921 TTTGTAATTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.07, G:0.04, T:0.22
Consensus pattern (14 bp):
CAAAAATATAAATG
Found at i:39409043 original size:48 final size:48
Alignment explanation
Indices: 39408921--39409082 Score: 163
Period size: 48 Copynumber: 3.4 Consensus size: 48
39408911 AAATATAAAT
* * *
39408921 TTTGTAATTCAAATTAGATTAATTGCAAC----AAACTTTAGACAAAA
1 TTTGTAATTTAAATTAGATTAATTGCAACATTAAAACTTGAAACAAAA
*
39408965 TTTGT-ATTTATTTAATTGAGATTTATTGCAACATTAAAACTTGAAACAAAA
1 TTTGTAATTTA---AATT-AGATTAATTGCAACATTAAAACTTGAAACAAAA
** * *
39409016 TTTGTAATTTAAATTAGATTAATTGCAACATTAAAACGAGGAACAAAC
1 TTTGTAATTTAAATTAGATTAATTGCAACATTAAAACTTGAAACAAAA
* *
39409064 TTTATAATATAAATTAGAT
1 TTTGTAATTTAAATTAGAT
39409083 ATATTGGAGT
Statistics
Matches: 98, Mismatches: 11, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
43 4 0.04
44 5 0.05
46 4 0.04
47 13 0.13
48 45 0.46
49 4 0.04
51 18 0.18
52 5 0.05
ACGTcount: A:0.44, C:0.09, G:0.10, T:0.37
Consensus pattern (48 bp):
TTTGTAATTTAAATTAGATTAATTGCAACATTAAAACTTGAAACAAAA
Found at i:39412761 original size:12 final size:12
Alignment explanation
Indices: 39412732--39412764 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
39412722 TAATTAACAA
*
39412732 TTAATAATAAAT
1 TTAAAAATAAAT
39412744 TT-AAAATAAAT
1 TTAAAAATAAAT
39412755 TTAAAAATAA
1 TTAAAAATAA
39412765 TAAAAAGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
TTAAAAATAAAT
Found at i:39413088 original size:14 final size:15
Alignment explanation
Indices: 39413071--39413100 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
39413061 TATCCTTTCA
39413071 TTTTTC-TTCTTTTT
1 TTTTTCTTTCTTTTT
39413085 TTTTTCTTTCTTTTT
1 TTTTTCTTTCTTTTT
39413100 T
1 T
39413101 CTCCTTCTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (15 bp):
TTTTTCTTTCTTTTT
Found at i:39413099 original size:25 final size:25
Alignment explanation
Indices: 39413065--39413141 Score: 75
Period size: 26 Copynumber: 3.0 Consensus size: 25
39413055 ATTCATTATC
*
39413065 CTTTCATTTTTCTTCTTTTTTTTTT
1 CTTTCTTTTTTCTTCTTTTTTTTTT
* *
39413090 CTTTCTTTTTTCTCCTTCTCTTTTTT
1 CTTTCTTTTTTCTTCTT-TTTTTTTT
* *
39413116 C-TTCTCTTCTGCTATCTTTTTTTTTT
1 CTTTCT-TTTTTCT-TCTTTTTTTTTT
39413142 GTTAAACTAT
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
25 19 0.45
26 20 0.48
27 3 0.07
ACGTcount: A:0.03, C:0.22, G:0.01, T:0.74
Consensus pattern (25 bp):
CTTTCTTTTTTCTTCTTTTTTTTTT
Found at i:39413111 original size:15 final size:15
Alignment explanation
Indices: 39413076--39413117 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
39413066 TTTCATTTTT
* *
39413076 CTTCT-TTTTTTTTT
1 CTTCTCTTTTTTCTC
39413090 CTT-TCTTTTTTCTC
1 CTTCTCTTTTTTCTC
39413104 CTTCTCTTTTTTCT
1 CTTCTCTTTTTTCT
39413118 TCTCTTCTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 1 0.04
14 13 0.54
15 10 0.42
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (15 bp):
CTTCTCTTTTTTCTC
Found at i:39417505 original size:28 final size:28
Alignment explanation
Indices: 39417465--39417521 Score: 98
Period size: 28 Copynumber: 2.0 Consensus size: 28
39417455 TAGATATTCT
39417465 AATTAAGAAATATTC-TTTCCTTAAGTTG
1 AATTAAGAAATATTCTTTTCC-TAAGTTG
39417493 AATTAAGAAATATTCTTTTCCTAAGTTG
1 AATTAAGAAATATTCTTTTCCTAAGTTG
39417521 A
1 A
39417522 TTCAATCTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 23 0.82
29 5 0.18
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.42
Consensus pattern (28 bp):
AATTAAGAAATATTCTTTTCCTAAGTTG
Found at i:39419684 original size:19 final size:19
Alignment explanation
Indices: 39419638--39419685 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
39419628 GTATATATTT
39419638 TAAA-TTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
39419656 TAAATCTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
39419675 TAAGTTTTATT
1 TAAATTTTATT
39419686 CATATTATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 4 0.15
19 22 0.85
ACGTcount: A:0.35, C:0.02, G:0.15, T:0.48
Consensus pattern (19 bp):
TAAATTTTATTTAGGTAGA
Found at i:39419766 original size:42 final size:42
Alignment explanation
Indices: 39419702--39419790 Score: 124
Period size: 42 Copynumber: 2.1 Consensus size: 42
39419692 ATAAGAATAT
* * * *
39419702 TTTTATTTTATCTTTTAGTAGTTTATTAGAATAAGGGAGCTA
1 TTTTCTTTTATATTTTAATAGTTTATTAGAATAAGGGAACTA
* *
39419744 TTTTCTTTTATATTTTAATAGTTTATTAGGATAAGTGAACTA
1 TTTTCTTTTATATTTTAATAGTTTATTAGAATAAGGGAACTA
39419786 TTTTC
1 TTTTC
39419791 CTAATTAGGA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.28, C:0.06, G:0.13, T:0.53
Consensus pattern (42 bp):
TTTTCTTTTATATTTTAATAGTTTATTAGAATAAGGGAACTA
Found at i:39422927 original size:19 final size:19
Alignment explanation
Indices: 39422881--39422928 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
39422871 GTATATATTT
39422881 TAAA-TTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
* *
39422899 TAAATCTTATTTAGTTAGA
1 TAAATTTTATTTAGGTAGA
*
39422918 TAAGTTTTATT
1 TAAATTTTATT
39422929 CATATTCTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 4 0.16
19 21 0.84
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.50
Consensus pattern (19 bp):
TAAATTTTATTTAGGTAGA
Found at i:39423004 original size:42 final size:42
Alignment explanation
Indices: 39422945--39423032 Score: 158
Period size: 42 Copynumber: 2.1 Consensus size: 42
39422935 CTAGGAATAT
39422945 TTTTATTTTATCTTTTAGTAGTTTATTAGAATAAGGGAACTA
1 TTTTATTTTATCTTTTAGTAGTTTATTAGAATAAGGGAACTA
* *
39422987 TTTTCTTTTATGTTTTAGTAGTTTATTAGAATAAGGGAACTA
1 TTTTATTTTATCTTTTAGTAGTTTATTAGAATAAGGGAACTA
39423029 TTTT
1 TTTT
39423033 TCTAATTAGG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.28, C:0.05, G:0.15, T:0.52
Consensus pattern (42 bp):
TTTTATTTTATCTTTTAGTAGTTTATTAGAATAAGGGAACTA
Found at i:39427508 original size:22 final size:22
Alignment explanation
Indices: 39427464--39427509 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
39427454 GTATATATTT
* * *
39427464 CACACGCGCGCACACACACACA
1 CACACGCACGCACACAAAAACA
39427486 CACACGCACGCACACAAAAACA
1 CACACGCACGCACACAAAAACA
39427508 CA
1 CA
39427510 AATGTAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.46, G:0.11, T:0.00
Consensus pattern (22 bp):
CACACGCACGCACACAAAAACA
Found at i:39427802 original size:3 final size:3
Alignment explanation
Indices: 39427794--39427833 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
39427784 CCTTTTACCC
*
39427794 CAT CAT CAT CAT CAT CAT TAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
39427834 GAGAACAACG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.35
Consensus pattern (3 bp):
CAT
Found at i:39435631 original size:35 final size:35
Alignment explanation
Indices: 39434597--39435628 Score: 1728
Period size: 35 Copynumber: 29.5 Consensus size: 35
39434587 GGCAAAGTGC
* * *
39434597 GAAATATAGGTATGGTAT-AACCATACCGAGTTGT
1 GAAATGTAGGTATGGTATCATCCATACCGAGTTGA
** * * *
39434631 GAAATGTAGGTATGGCGTCGTCCATACTGAGCT-A
1 GAAATGTAGGTATGGTATCATCCATACCGAGTTGA
* * * * * *
39434665 TGATACGTGGGTATGGTATTAGCCATACCGAGTTGT
1 -GAAATGTAGGTATGGTATCATCCATACCGAGTTGA
* * * * *
39434701 GAAAAGTAGGTATGGTATTAACCATACCGAGATGT
1 GAAATGTAGGTATGGTATCATCCATACCGAGTTGA
* ** *
39434736 GAAACGTAGGTATGGTATCATTTATACCGAGTTGT
1 GAAATGTAGGTATGGTATCATCCATACCGAGTTGA
*
39434771 GAAATGTATGTATGGTATCATCCATACCGAGTTGA
1 GAAATGTAGGTATGGTATCATCCATACCGAGTTGA
39434806 GAAATGTAGGTATGGTATCATCCATACCGAGTTGA
1 GAAATGTAGGTATGGTATCATCCATACCGAGTTGA
39434841 GAAATGTAGGTATGGTATCATCCATACCGAGTTGA
1 GAAATGTAGGTATGGTATCATCCATACCGAGTTGA
39434876 GAAATGTAGGTATGGTATCATCCATACCGAGTTGA
1 GAAATGTAGGTATGGTATCATCCATACCGAGTTGA
39434911 GAAATGTAGGTATGGTATCATCCATACCGAGTTGA
1 GAAATGTAGGTATGGTATCATCCATACCGAGTTGA
39434946 GAAATGTAGGTATGGTATCATCCATACCGAGTTGA
1 GAAATGTAGGTATGGTATCATCCATACCGAGTTGA
39434981 GAAATGTAGGTATGGTATCATCCATACCGAGTTGA
1 GAAATGTAGGTATGGTATCATCCATACCGAGTTGA
39435016 GAAATGTAGGTATGGTATCATCCATACCGAGTTGA
1 GAAATGTAGGTATGGTATCATCCATACCGAGTTGA
39435051 GAAATGTAGGTATGGTATCATCCATACCGAGTTGA
1 GAAATGTAGGTATGGTATCATCCATACCGAGTTGA
39435086 GAAATGTAGGTATGGTATCATCCATACCGAGTTGA
1 GAAATGTAGGTATGGTATCATCCATACCGAGTTGA
39435121 GAAATGTAGGTATGGTATCATCCATACCGAGTTGA
1 GAAATGTAGGTATGGTATCATCCATACCGAGTTGA
39435156 GAAATGTAGGTATGGTATCATCCATACCGAGTTGA
1 GAAATGTAGGTATGGTATCATCCATACCGAGTTGA
39435191 GAAATGTAGGTATGGTATCATCCATACCGAGTTGA
1 GAAATGTAGGTATGGTATCATCCATACCGAGTTGA
39435226 GAAATGTAGGTATGGTATCATCCATACCGAGTTGA
1 GAAATGTAGGTATGGTATCATCCATACCGAGTTGA
39435261 GAAATGTAGGTATGGTATCATCCATACCGAGTTGA
1 GAAATGTAGGTATGGTATCATCCATACCGAGTTGA
39435296 GAAATGTAGGTATGGTATCATCCATACCGAGTTGA
1 GAAATGTAGGTATGGTATCATCCATACCGAGTTGA
39435331 GAAATGTAGGTATGGTATCATCCATACCGAGTTGA
1 GAAATGTAGGTATGGTATCATCCATACCGAGTTGA
39435366 GAAATGTAGGTATGGTATCATCCATACCGAGTTGA
1 GAAATGTAGGTATGGTATCATCCATACCGAGTTGA
39435401 GAAATGTAGGTATGGTATCATCCATACCGAGTTGA
1 GAAATGTAGGTATGGTATCATCCATACCGAGTTGA
39435436 GAAATGTAGGTATGGTATCATCCATACCGAGTTGA
1 GAAATGTAGGTATGGTATCATCCATACCGAGTTGA
39435471 GAAATGTAGGTATGGTATCATCCATACCGAGTTGA
1 GAAATGTAGGTATGGTATCATCCATACCGAGTTGA
39435506 GAAATGTAGGTATGGTATCATCCATACCGAGTTGA
1 GAAATGTAGGTATGGTATCATCCATACCGAGTTGA
** * * *
39435541 GAAACATAGGTATGGTATTATCCATACTGAGTTAA
1 GAAATGTAGGTATGGTATCATCCATACCGAGTTGA
* * * *
39435576 GAAGTGTAGGTATGGCAT-TTCCCATACCGAGTTGT
1 GAAATGTAGGTATGGTATCAT-CCATACCGAGTTGA
39435611 GAAATGTAGGTATGGTAT
1 GAAATGTAGGTATGGTAT
39435629 TTCAATGAGG
Statistics
Matches: 943, Mismatches: 51, Indels: 7
0.94 0.05 0.01
Matches are distributed among these distances:
34 16 0.02
35 927 0.98
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (35 bp):
GAAATGTAGGTATGGTATCATCCATACCGAGTTGA
Found at i:39435783 original size:35 final size:35
Alignment explanation
Indices: 39435744--39435997 Score: 269
Period size: 35 Copynumber: 7.3 Consensus size: 35
39435734 TTGAATTTAT
39435744 ATGTAGGTATGGTATCATCCATACCGAGTTGAGAA
1 ATGTAGGTATGGTATCATCCATACCGAGTTGAGAA
* *
39435779 ATGTAGGTATGGTATCATCCATACTGAGTTGTGAA
1 ATGTAGGTATGGTATCATCCATACCGAGTTGAGAA
*
39435814 ACGTAGGTATGGTATCATCCATACCGAGTTGAGAA
1 ATGTAGGTATGGTATCATCCATACCGAGTTGAGAA
* * * *
39435849 ATATAGGTATGGTATTATCCATACTGAGTTAAGAA
1 ATGTAGGTATGGTATCATCCATACCGAGTTGAGAA
* * * *
39435884 GTGTAGGTATGGCAT-TTCCCATACCGAGTTGTGAA
1 ATGTAGGTATGGTATCAT-CCATACCGAGTTGAGAA
** * * * *
39435919 ATGTAGGTATGGCGTCGTCCATACTGAGCT-ATGAT
1 ATGTAGGTATGGTATCATCCATACCGAGTTGA-GAA
* * * * *
39435954 ACGTGGGTATGGTATTAGCCATACCGAGTTGTGAA
1 ATGTAGGTATGGTATCATCCATACCGAGTTGAGAA
*
39435989 AAGTAGGTA
1 ATGTAGGTA
39435998 AGTAATGACG
Statistics
Matches: 178, Mismatches: 37, Indels: 8
0.80 0.17 0.04
Matches are distributed among these distances:
34 1 0.01
35 176 0.99
36 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.30
Consensus pattern (35 bp):
ATGTAGGTATGGTATCATCCATACCGAGTTGAGAA
Found at i:39435831 original size:70 final size:70
Alignment explanation
Indices: 39435746--39435997 Score: 317
Period size: 70 Copynumber: 3.6 Consensus size: 70
39435736 GAATTTATAT
*
39435746 GTAGGTATGGTATCATCCATACCGAGTTGAGAAATGTAGGTATGGTATCATCCATACTGAGTTGT
1 GTAGGTATGGTATCATCCATACCGAGTTGAGAAATGTAGGTATGGTATCATCCATACTGAGTTAT
39435811 GAAAC
66 GAAAC
* * *
39435816 GTAGGTATGGTATCATCCATACCGAGTTGAGAAATATAGGTATGGTATTATCCATACTGAGTTAA
1 GTAGGTATGGTATCATCCATACCGAGTTGAGAAATGTAGGTATGGTATCATCCATACTGAGTTAT
**
39435881 GAAGT
66 GAAAC
* * * ** * *
39435886 GTAGGTATGGCAT-TTCCCATACCGAGTTGTGAAATGTAGGTATGGCGTCGTCCATACTGAGCTA
1 GTAGGTATGGTATCAT-CCATACCGAGTTGAGAAATGTAGGTATGGTATCATCCATACTGAGTTA
*
39435950 TGATAC
65 TGAAAC
* * * * *
39435956 GTGGGTATGGTATTAGCCATACCGAGTTGTGAAAAGTAGGTA
1 GTAGGTATGGTATCATCCATACCGAGTTGAGAAATGTAGGTA
39435998 AGTAATGACG
Statistics
Matches: 156, Mismatches: 24, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
69 1 0.01
70 155 0.99
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.30
Consensus pattern (70 bp):
GTAGGTATGGTATCATCCATACCGAGTTGAGAAATGTAGGTATGGTATCATCCATACTGAGTTAT
GAAAC
Found at i:39438064 original size:8 final size:8
Alignment explanation
Indices: 39438051--39438088 Score: 76
Period size: 8 Copynumber: 4.8 Consensus size: 8
39438041 TTTTATGTTT
39438051 TAATATAA
1 TAATATAA
39438059 TAATATAA
1 TAATATAA
39438067 TAATATAA
1 TAATATAA
39438075 TAATATAA
1 TAATATAA
39438083 TAATAT
1 TAATAT
39438089 TTAAAATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
TAATATAA
Found at i:39438101 original size:24 final size:24
Alignment explanation
Indices: 39438051--39438107 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
39438041 TTTTATGTTT
*
39438051 TAATATAATAATATAATAATATAA
1 TAATATAATAATATAATAAAATAA
* *
39438075 TAATATAATAATAT-TTAAAATTTA
1 TAATATAATAATATAATAAAA-TAA
39438099 TAATATAAT
1 TAATATAAT
39438108 TTAATTATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 4 0.14
24 25 0.86
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
TAATATAATAATATAATAAAATAA
Found at i:39445278 original size:12 final size:12
Alignment explanation
Indices: 39445245--39445286 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
39445235 TATGCTCCAC
*
39445245 AAAAGAAAA-AA
1 AAAATAAAATAA
39445256 AAAATTAAAAATAA
1 AAAA-T-AAAATAA
39445270 AAAATAAAATAA
1 AAAATAAAATAA
39445282 AAAAT
1 AAAAT
39445287 CCCTCAGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 4 0.15
12 12 0.44
13 5 0.19
14 6 0.22
ACGTcount: A:0.83, C:0.00, G:0.02, T:0.14
Consensus pattern (12 bp):
AAAATAAAATAA
Found at i:39445278 original size:19 final size:18
Alignment explanation
Indices: 39445245--39445286 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
39445235 TATGCTCCAC
* *
39445245 AAAAGAAAAAAAAAATTA
1 AAAATAAAAAAAAAATAA
39445263 AAAATAAAAAATAAAATAA
1 AAAATAAAAAA-AAAATAA
39445282 AAAAT
1 AAAAT
39445287 CCCTCAGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.83, C:0.00, G:0.02, T:0.14
Consensus pattern (18 bp):
AAAATAAAAAAAAAATAA
Found at i:39451017 original size:45 final size:45
Alignment explanation
Indices: 39450953--39451043 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
39450943 GACGTAAATA
39450953 TATTTGGCTAATATATAAATTTTAATATTAATTTAACATGATTAT
1 TATTTGGCTAATATATAAATTTTAATATTAATTTAACATGATTAT
*
39450998 TATTTGGCTAATATATAAATTTTAATATTAATTTAGCATGATTAT
1 TATTTGGCTAATATATAAATTTTAATATTAATTTAACATGATTAT
39451043 T
1 T
39451044 GAACTTTCTT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.49
Consensus pattern (45 bp):
TATTTGGCTAATATATAAATTTTAATATTAATTTAACATGATTAT
Found at i:39451026 original size:25 final size:25
Alignment explanation
Indices: 39450952--39451026 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
39450942 TGACGTAAAT
39450952 ATATTTGGCTAATATATAAATTTTA
1 ATATTTGGCTAATATATAAATTTTA
*
39450977 ATA--T---TAAT-T-TAACATGATTA
1 ATATTTGGCTAATATATAA-AT-TTTA
*
39450997 TTATTTGGCTAATATATAAATTTTA
1 ATATTTGGCTAATATATAAATTTTA
39451022 ATATT
1 ATATT
39451027 AATTTAGCAT
Statistics
Matches: 37, Mismatches: 4, Indels: 18
0.63 0.07 0.31
Matches are distributed among these distances:
18 3 0.08
19 3 0.08
20 9 0.24
22 1 0.03
23 1 0.03
25 14 0.38
26 3 0.08
27 3 0.08
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.49
Consensus pattern (25 bp):
ATATTTGGCTAATATATAAATTTTA
Found at i:39468436 original size:6 final size:6
Alignment explanation
Indices: 39468427--39468490 Score: 51
Period size: 6 Copynumber: 10.7 Consensus size: 6
39468417 TACCTTGAGC
* * * * *
39468427 TCATCT TCATCT TCATCAT T-GTCT TAATCT TCATCT CCA-CAC TCAACT
1 TCATCT TCATCT TCATC-T TCATCT TCATCT TCATCT TCATC-T TCATCT
39468475 TCATCT TCATCT TCAT
1 TCATCT TCATCT TCAT
39468491 TGGCTTCCTC
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
5 3 0.07
6 40 0.87
7 3 0.07
ACGTcount: A:0.22, C:0.33, G:0.02, T:0.44
Consensus pattern (6 bp):
TCATCT
Found at i:39470648 original size:16 final size:18
Alignment explanation
Indices: 39470609--39470652 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 18
39470599 AACTTGAGAA
39470609 AATTGAGAGAATTAAGAG
1 AATTGAGAGAATTAAGAG
* *
39470627 AGTTGAGAG-TTTAA-AG
1 AATTGAGAGAATTAAGAG
39470643 AATTGAGAGA
1 AATTGAGAGA
39470653 GTTGGATTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 10 0.45
17 4 0.18
18 8 0.36
ACGTcount: A:0.45, C:0.00, G:0.30, T:0.25
Consensus pattern (18 bp):
AATTGAGAGAATTAAGAG
Found at i:39474835 original size:17 final size:17
Alignment explanation
Indices: 39474810--39474849 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
39474800 ATATGATGAG
*
39474810 TAATGTTATTAATTTGT
1 TAATATTATTAATTTGT
39474827 TAATATTATTAATTTGT
1 TAATATTATTAATTTGT
39474844 T-ATATT
1 TAATATT
39474850 TTGGTCATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (17 bp):
TAATATTATTAATTTGT
Found at i:39475159 original size:26 final size:26
Alignment explanation
Indices: 39475130--39475180 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 26
39475120 TTTTACCAAA
39475130 TTTTAAAGGGC-AAATTTTTTTTTAGC
1 TTTTAAA-GGCTAAATTTTTTTTTAGC
39475156 TTTTAAAGGCTTAAATTTTTTTTTA
1 TTTTAAAGGC-TAAATTTTTTTTTA
39475181 CAACCTAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 3 0.13
26 7 0.30
27 13 0.57
ACGTcount: A:0.27, C:0.06, G:0.12, T:0.55
Consensus pattern (26 bp):
TTTTAAAGGCTAAATTTTTTTTTAGC
Found at i:39475505 original size:15 final size:14
Alignment explanation
Indices: 39475474--39475507 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
39475464 TTATAAAATG
39475474 AAAAAAATAATTGA
1 AAAAAAATAATTGA
39475488 AAAATAAAT-ATTGA
1 AAAA-AAATAATTGA
39475502 AAAAAA
1 AAAAAA
39475508 GTTATAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 2 0.11
14 13 0.68
15 4 0.21
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.21
Consensus pattern (14 bp):
AAAAAAATAATTGA
Found at i:39482731 original size:32 final size:32
Alignment explanation
Indices: 39482695--39482759 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
39482685 TTTTTTTAAG
*
39482695 AACAAATCAAGTCAATACAATATAGAAATCAT
1 AACAAATCAAGTCAATACAATATAAAAATCAT
39482727 AACAAATCAAGTCAATACAATATAAAAATCAT
1 AACAAATCAAGTCAATACAATATAAAAATCAT
39482759 A
1 A
39482760 CTTCATGATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.58, C:0.15, G:0.05, T:0.22
Consensus pattern (32 bp):
AACAAATCAAGTCAATACAATATAAAAATCAT
Found at i:39483853 original size:6 final size:6
Alignment explanation
Indices: 39483844--39483875 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
39483834 AATAAAATTG
39483844 AAATAA AAATAA AAATAA AAAT-A AAATAA AAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAA
39483876 GATAAGAGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:39483875 original size:11 final size:11
Alignment explanation
Indices: 39483834--39483875 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
39483824 AAAAGAAAAT
* *
39483834 AATAAAATTGA
1 AATAAAAATAA
39483845 AATAAAAATAAA
1 AATAAAAAT-AA
39483857 AATAAAAATAA
1 AATAAAAATAA
39483868 AATAAAAA
1 AATAAAAA
39483876 GATAAGAGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 18 0.64
12 10 0.36
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (11 bp):
AATAAAAATAA
Found at i:39486337 original size:34 final size:34
Alignment explanation
Indices: 39486294--39486362 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
39486284 TTTACTCCTC
39486294 ATTCCTGCTATCTATCTCATCAAAATAAGGTTTT
1 ATTCCTGCTATCTATCTCATCAAAATAAGGTTTT
*
39486328 ATTCCTGCTATCTATCTCATCAAGATAAGGTTTT
1 ATTCCTGCTATCTATCTCATCAAAATAAGGTTTT
39486362 A
1 A
39486363 ATCGGGTGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.29, C:0.20, G:0.10, T:0.41
Consensus pattern (34 bp):
ATTCCTGCTATCTATCTCATCAAAATAAGGTTTT
Found at i:39493358 original size:4 final size:4
Alignment explanation
Indices: 39493349--39493378 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
39493339 ATTTGCACTC
39493349 TATT TATT TATT TATT TATT TATT TATT TA
1 TATT TATT TATT TATT TATT TATT TATT TA
39493379 ATTTCCCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:39493643 original size:30 final size:30
Alignment explanation
Indices: 39493609--39493669 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
39493599 TTAATTAATC
* *
39493609 TTTTACGGATCTTGTAGAATCTATTGTTAA
1 TTTTACGGATCTTGCAGAACCTATTGTTAA
*
39493639 TTTTACGGTTCTTGCAGAACCTATTGTTAA
1 TTTTACGGATCTTGCAGAACCTATTGTTAA
39493669 T
1 T
39493670 CTTGATGAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.25, C:0.13, G:0.16, T:0.46
Consensus pattern (30 bp):
TTTTACGGATCTTGCAGAACCTATTGTTAA
Found at i:39496034 original size:11 final size:11
Alignment explanation
Indices: 39496018--39496046 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
39496008 TATAGACAAC
39496018 TTTATTTCTAG
1 TTTATTTCTAG
39496029 TTTATTTCTAG
1 TTTATTTCTAG
39496040 TTTATTT
1 TTTATTT
39496047 TACACTTAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.17, C:0.07, G:0.07, T:0.69
Consensus pattern (11 bp):
TTTATTTCTAG
Found at i:39508940 original size:23 final size:24
Alignment explanation
Indices: 39508910--39509059 Score: 111
Period size: 23 Copynumber: 6.6 Consensus size: 24
39508900 GGACTCACTA
39508910 CAGCTCGTAT-GAGCTTACCGATT
1 CAGCTCGTATAGAGCTTACCGATT
*
39508933 CAGCTCGTA-AGAGCTTA-CTATTT
1 CAGCTCGTATAGAGCTTACCGA-TT
* * * *
39508956 TAGCTCAT-TAAAGCTTACCAATT
1 CAGCTCGTATAGAGCTTACCGATT
* *
39508979 CATCTCGTA-AGAGCTTACCGTTT
1 CAGCTCGTATAGAGCTTACCGATT
* * * **
39509002 CATCTCAT-TGGAGCTTACTAATT
1 CAGCTCGTATAGAGCTTACCGATT
*
39509025 CAGCTCG-ATAGAGCTTACTG-TT
1 CAGCTCGTATAGAGCTTACCGATT
39509047 CAGCTCG-ATAGAG
1 CAGCTCGTATAGAG
39509060 GTTTCCGTTT
Statistics
Matches: 100, Mismatches: 20, Indels: 15
0.74 0.15 0.11
Matches are distributed among these distances:
22 17 0.17
23 81 0.81
24 2 0.02
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (24 bp):
CAGCTCGTATAGAGCTTACCGATT
Found at i:39508980 original size:46 final size:46
Alignment explanation
Indices: 39508921--39509052 Score: 151
Period size: 46 Copynumber: 2.9 Consensus size: 46
39508911 AGCTCGTATG
* *
39508921 AGCTTACCGATTCAGCTCGTAAGAGCTTACTATTTTAGCTCATTAA
1 AGCTTACCAATTCAGCTCGTAAGAGCTTACTATTTCAGCTCATTAA
* ** * **
39508967 AGCTTACCAATTCATCTCGTAAGAGCTTACCGTTTCATCTCATTGG
1 AGCTTACCAATTCAGCTCGTAAGAGCTTACTATTTCAGCTCATTAA
* *
39509013 AGCTTACTAATTCAGCTCG-ATAGAGCTTACT-GTTCAGCTC
1 AGCTTACCAATTCAGCTCGTA-AGAGCTTACTATTTCAGCTC
39509053 GATAGAGGTT
Statistics
Matches: 72, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
45 8 0.11
46 64 0.89
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (46 bp):
AGCTTACCAATTCAGCTCGTAAGAGCTTACTATTTCAGCTCATTAA
Found at i:39511952 original size:5 final size:5
Alignment explanation
Indices: 39511942--39511990 Score: 89
Period size: 5 Copynumber: 9.8 Consensus size: 5
39511932 GCTAAAATTT
*
39511942 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAGAA TAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAA
39511991 TATCCTAGCC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 42 1.00
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:39518151 original size:27 final size:29
Alignment explanation
Indices: 39518121--39518174 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
39518111 TCTGAAATAC
39518121 TGATAT-CATGG-CCCGAAGCCAAATCAG
1 TGATATGCATGGCCCCGAAGCCAAATCAG
39518148 TGATATGCATGGCCCCGAAGCCAAATC
1 TGATATGCATGGCCCCGAAGCCAAATC
39518175 GGTTTATCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 6 0.24
28 5 0.20
29 14 0.56
ACGTcount: A:0.31, C:0.28, G:0.22, T:0.19
Consensus pattern (29 bp):
TGATATGCATGGCCCCGAAGCCAAATCAG
Found at i:39521279 original size:13 final size:13
Alignment explanation
Indices: 39521261--39521285 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39521251 CACACATGCA
39521261 ACCTAGCTACATT
1 ACCTAGCTACATT
39521274 ACCTAGCTACAT
1 ACCTAGCTACAT
39521286 ATATCCCGTA
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:0.32, C:0.32, G:0.08, T:0.28
Consensus pattern (13 bp):
ACCTAGCTACATT
Found at i:39524622 original size:17 final size:17
Alignment explanation
Indices: 39524600--39524640 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
39524590 ATGAAGGTCA
* *
39524600 GGCCGTGCGTAAGAGAC
1 GGCCGTGCGCAAGACAC
39524617 GGCCGTGCGCAAGACAC
1 GGCCGTGCGCAAGACAC
*
39524634 GGTCGTG
1 GGCCGTG
39524641 TGATGGTCGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.20, C:0.27, G:0.41, T:0.12
Consensus pattern (17 bp):
GGCCGTGCGCAAGACAC
Found at i:39527586 original size:39 final size:39
Alignment explanation
Indices: 39527531--39527632 Score: 159
Period size: 39 Copynumber: 2.6 Consensus size: 39
39527521 TTTAGATATA
*
39527531 TATATATGGCACTTAGTGTGCGATTCGAGATAGCTTCGGC
1 TATATAT-GCACTTAGTGTGCGATTCGAAATAGCTTCGGC
* *
39527571 TATATATGCACTTAGTCTGCAATTCGAAATAGCTTCGGC
1 TATATATGCACTTAGTGTGCGATTCGAAATAGCTTCGGC
39527610 TATATATGACACTTAGTGTGCGA
1 TATATATG-CACTTAGTGTGCGA
39527633 GACCGAGATA
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
39 37 0.66
40 19 0.34
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (39 bp):
TATATATGCACTTAGTGTGCGATTCGAAATAGCTTCGGC
Found at i:39530137 original size:3 final size:3
Alignment explanation
Indices: 39530129--39530154 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
39530119 ACTATACATA
39530129 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
39530155 CATGGAAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:39535751 original size:10 final size:10
Alignment explanation
Indices: 39535714--39535742 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
39535704 CTAGAAACAA
39535714 ATATATATAC
1 ATATATATAC
39535724 ATATATATAC
1 ATATATATAC
39535734 ATATATATA
1 ATATATATA
39535743 TGTATATATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (10 bp):
ATATATATAC
Found at i:39547771 original size:43 final size:43
Alignment explanation
Indices: 39547648--39547785 Score: 174
Period size: 43 Copynumber: 3.3 Consensus size: 43
39547638 GTCCTAAATG
* * *
39547648 TGGTCTTACATGTAATCACATATCGATGCCACTGTTCCAGACA
1 TGGTCTTACACGTAATCACATATCGATGCCAATGTACCAGACA
* * ** *
39547691 GGGTC-TACACG-AATCAAATA-CGATGCCGGTGTCCCAGACA
1 TGGTCTTACACGTAATCACATATCGATGCCAATGTACCAGACA
*
39547731 TGGTCTTACACGTAATCACATATCGATGCCAATGTACCAGACG
1 TGGTCTTACACGTAATCACATATCGATGCCAATGTACCAGACA
39547774 TGGTCTTACACG
1 TGGTCTTACACG
39547786 AGAACACATA
Statistics
Matches: 80, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
40 21 0.26
41 14 0.17
42 13 0.16
43 32 0.40
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.25
Consensus pattern (43 bp):
TGGTCTTACACGTAATCACATATCGATGCCAATGTACCAGACA
Found at i:39550324 original size:27 final size:27
Alignment explanation
Indices: 39550305--39550595 Score: 395
Period size: 27 Copynumber: 10.8 Consensus size: 27
39550295 ATTACCAAAG
*
39550305 TACCCTCGATTTATAGAATTAACATTT
1 TACCCTCGATTTATAGAATTACCATTT
**
39550332 TACCCTCGATTTATAGAATTACTGTTT
1 TACCCTCGATTTATAGAATTACCATTT
* * *
39550359 TACCTTCGATTTACAGAATTAACATTT
1 TACCCTCGATTTATAGAATTACCATTT
*
39550386 TACCCTCGATTTATAGAGTTACCATTT
1 TACCCTCGATTTATAGAATTACCATTT
39550413 TACCCTCGATTTATAGAATTACCATTT
1 TACCCTCGATTTATAGAATTACCATTT
***
39550440 TACCCTCGATTTATAGAA-TATTGTTT
1 TACCCTCGATTTATAGAATTACCATTT
* *
39550466 TACCCTCGATTTATAGAATTTCTATTT
1 TACCCTCGATTTATAGAATTACCATTT
*
39550493 TACCCTTGATTTATAGAATTACCATTT
1 TACCCTCGATTTATAGAATTACCATTT
* **
39550520 TACCCTTGATTTATAGAATTACTGTTT
1 TACCCTCGATTTATAGAATTACCATTT
* *
39550547 TACCCTCGATTTACAGAATTATCATTT
1 TACCCTCGATTTATAGAATTACCATTT
* *
39550574 TACCCTCGATTTACAAAATTAC
1 TACCCTCGATTTATAGAATTAC
39550596 TAAAATACCC
Statistics
Matches: 232, Mismatches: 31, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
26 23 0.10
27 209 0.90
ACGTcount: A:0.29, C:0.20, G:0.09, T:0.43
Consensus pattern (27 bp):
TACCCTCGATTTATAGAATTACCATTT
Found at i:39550604 original size:27 final size:27
Alignment explanation
Indices: 39550547--39550801 Score: 132
Period size: 27 Copynumber: 9.4 Consensus size: 27
39550537 ATTACTGTTT
* * ***
39550547 TACCCTCGATTTACAGAATTATCATTT
1 TACCCTCGATTTACAAAATTACCAAAA
*
39550574 TACCCTCGATTTACAAAATTACTAAAA
1 TACCCTCGATTTACAAAATTACCAAAA
*
39550601 TACCCT-TAGTTTACAAAATTACCAAAA
1 TACCCTCGA-TTTACAAAATTACCAAAA
* *
39550628 TACCCTCGA-TCAGTAAAATTACCAAAA
1 TACCCTCGATTTA-CAAAATTACCAAAA
* ** **
39550655 TACCC-CTGGTTTGTAAAATTATTAAAA
1 TACCCTC-GATTTACAAAATTACCAAAA
* **
39550682 TACCC-CTGGTTTGTAAAATTACCAAAA
1 TACCCTC-GATTTACAAAATTACCAAAA
* *
39550709 TACCCCTAGCTTGT--AAAATTACCAAAA
1 TA-CCCTCGATT-TACAAAATTACCAAAA
* *
39550736 TACCCTTAGCTTGT--AAAATTACCAAAA
1 TACCC-TCGATT-TACAAAATTACCAAAA
*** *
39550763 TACCC-CTGATTTGTGAAATTATCAAAA
1 TACCCTC-GATTTACAAAATTACCAAAA
*
39550790 TACTCTCGATTT
1 TACCCTCGATTT
39550802 GTAGAATTAT
Statistics
Matches: 190, Mismatches: 25, Indels: 26
0.79 0.10 0.11
Matches are distributed among these distances:
25 1 0.01
26 10 0.05
27 169 0.89
28 9 0.05
29 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.08, T:0.32
Consensus pattern (27 bp):
TACCCTCGATTTACAAAATTACCAAAA
Found at i:39550802 original size:27 final size:26
Alignment explanation
Indices: 39550616--39550824 Score: 156
Period size: 27 Copynumber: 7.8 Consensus size: 26
39550606 TTAGTTTACA
* **
39550616 AAATTACCAAAATA-CCCTCGATCAGT
1 AAATTATCAAAATACCCCT-GATTTGT
* *
39550642 AAAATTACCAAAATACCCCTGGTTTGT
1 -AAATTATCAAAATACCCCTGATTTGT
* *
39550669 AAAATTATTAAAATACCCCTGGTTTGT
1 -AAATTATCAAAATACCCCTGATTTGT
* *
39550696 AAAATTACCAAAATACCCCT-AGCTTGT
1 -AAATTATCAAAATACCCCTGA-TTTGT
* * *
39550723 AAAATTACCAAAATA-CCCTTAGCTTGT
1 -AAATTATCAAAATACCCCTGA-TTTGT
*
39550750 AAAATTACCAAAATACCCCTGATTTGT
1 -AAATTATCAAAATACCCCTGATTTGT
*
39550777 GAAATTATCAAAATA-CTCTCGATTTGT
1 -AAATTATCAAAATACCCCT-GATTTGT
*
39550804 AGAATTATCGAAATACCCCTG
1 A-AATTATCAAAATACCCCTG
39550825 TAGGGTAGAA
Statistics
Matches: 159, Mismatches: 16, Indels: 14
0.84 0.08 0.07
Matches are distributed among these distances:
26 8 0.05
27 139 0.87
28 12 0.08
ACGTcount: A:0.39, C:0.22, G:0.10, T:0.30
Consensus pattern (26 bp):
AAATTATCAAAATACCCCTGATTTGT
Done.