Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold40
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: 3440810
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 28138 characters in sequence are not A, C, G, or T
File 22 of 24
Found at i:2922232 original size:9 final size:9
Alignment explanation
Indices: 2922210--2922244 Score: 63
Period size: 9 Copynumber: 4.0 Consensus size: 9
2922200 AAATAAAAAC
2922210 ATATATAT-
1 ATATATATA
2922218 ATATATATA
1 ATATATATA
2922227 ATATATATA
1 ATATATATA
2922236 ATATATATA
1 ATATATATA
2922245 TATTGCAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 8 0.31
9 18 0.69
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (9 bp):
ATATATATA
Found at i:2923727 original size:2 final size:2
Alignment explanation
Indices: 2923720--2923755 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2923710 ATCCGAACGC
2923720 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2923756 GAGAATTGGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2927297 original size:19 final size:18
Alignment explanation
Indices: 2927275--2927333 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
2927265 CTAATTATAT
2927275 ATAAATTTAAATATTATTA
1 ATAAA-TTAAATATTATTA
* *
2927294 ATAAATAAAATAATATTA
1 ATAAATTAAATATTATTA
* * *
2927312 TTTAATTAAA-ATTTTTA
1 ATAAATTAAATATTATTA
2927329 ATAAA
1 ATAAA
2927334 ATTATAAATT
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
17 8 0.26
18 18 0.58
19 5 0.16
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATAAATTAAATATTATTA
Found at i:2929974 original size:3 final size:3
Alignment explanation
Indices: 2929966--2930009 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
2929956 TTGAAATATT
*
2929966 ATA ATA ATA ATG ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2930010 GCCAAAGTGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2930825 original size:39 final size:39
Alignment explanation
Indices: 2930755--2930831 Score: 93
Period size: 39 Copynumber: 2.0 Consensus size: 39
2930745 TTTCAAAATA
* * *
2930755 AAAATAAAATTATAATTATTATAATTTTTAAAATTTTTT
1 AAAATAAAATTATAATTATTAAAATTATTAAAAATTTTT
* *
2930794 AAAATAAATTTAT-TTTATATAAAATTATTAAAAATTTT
1 AAAATAAAATTATAATTAT-TAAAATTATTAAAAATTTT
2930832 AATTATTAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
38 4 0.12
39 28 0.88
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (39 bp):
AAAATAAAATTATAATTATTAAAATTATTAAAAATTTTT
Found at i:2931516 original size:19 final size:18
Alignment explanation
Indices: 2931461--2931520 Score: 63
Period size: 19 Copynumber: 3.4 Consensus size: 18
2931451 AAATATTATT
2931461 TTTAAA-TT-AATAATAA
1 TTTAAATTTAAATAATAA
**
2931477 -TTAAATTTAAATAATTT
1 TTTAAATTTAAATAATAA
*
2931494 TTTATTATTTAAATAATAA
1 TTTA-AATTTAAATAATAA
2931513 TTTAAATT
1 TTTAAATT
2931521 GATCTAAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
15 5 0.15
16 2 0.06
17 6 0.18
18 6 0.18
19 15 0.44
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TTTAAATTTAAATAATAA
Found at i:2931533 original size:20 final size:18
Alignment explanation
Indices: 2931508--2931548 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 18
2931498 TTATTTAAAT
2931508 AATAATTTAAATTGATCTAA
1 AATAATTTAAATT-AT-TAA
*
2931528 AATAATTTGAATTATTAA
1 AATAATTTAAATTATTAA
2931546 AAT
1 AAT
2931549 TCTTAGGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 6 0.30
19 2 0.10
20 12 0.60
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.41
Consensus pattern (18 bp):
AATAATTTAAATTATTAA
Found at i:2931857 original size:2 final size:2
Alignment explanation
Indices: 2931852--2931883 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2931842 TAATGAAATC
2931852 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2931884 CATGTTTCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2932259 original size:22 final size:21
Alignment explanation
Indices: 2932229--2932269 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
2932219 ATTTTATAAG
*
2932229 TATTATAAAATTATATATTTTT
1 TATTATAAAAATATA-ATTTTT
*
2932251 TATTTTAAAAATATAATTT
1 TATTATAAAAATATAATTT
2932270 ATCACTATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TATTATAAAAATATAATTTTT
Found at i:2933200 original size:19 final size:19
Alignment explanation
Indices: 2933176--2933219 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
2933166 TTATTGTTAG
* * *
2933176 TTTAAATTTTAATTTTTAA
1 TTTAAATGTTAAATTTAAA
2933195 TTTAAATGTTAAATTTAAA
1 TTTAAATGTTAAATTTAAA
2933214 TTTAAA
1 TTTAAA
2933220 GATAAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (19 bp):
TTTAAATGTTAAATTTAAA
Found at i:2933219 original size:6 final size:6
Alignment explanation
Indices: 2933176--2933219 Score: 52
Period size: 6 Copynumber: 7.0 Consensus size: 6
2933166 TTATTGTTAG
* *
2933176 TTTAAA TTTTAAT TTTTAA TTTAAA TGTTAAA TTTAAA TTTAAA
1 TTTAAA -TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTAAA
2933220 GATAAAAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
6 21 0.66
7 11 0.34
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:2934085 original size:14 final size:15
Alignment explanation
Indices: 2934047--2934088 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
2934037 ATGACATACG
*
2934047 TAAAAATAAATAATAA
1 TAAATATAAA-AATAA
*
2934063 TATATATAAAAAT-A
1 TAAATATAAAAATAA
2934077 TAAATATAAAAA
1 TAAATATAAAAA
2934089 AAATTTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 12 0.52
15 3 0.13
16 8 0.35
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
TAAATATAAAAATAA
Found at i:2939464 original size:14 final size:15
Alignment explanation
Indices: 2939445--2939475 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2939435 AAGGTAAAAG
2939445 AATAAC-TTATTACA
1 AATAACTTTATTACA
2939459 AATAACTTTATTACA
1 AATAACTTTATTACA
2939474 AA
1 AA
2939476 AAAAATGGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (15 bp):
AATAACTTTATTACA
Found at i:2940457 original size:4 final size:4
Alignment explanation
Indices: 2940448--2940475 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
2940438 ATTTTATTAC
2940448 GAAA GAAA GAAA GAAA GAAA GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA
2940476 TAGAAGAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:2940876 original size:20 final size:20
Alignment explanation
Indices: 2940838--2940881 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2940828 TTGATTAAAG
*
2940838 TATTTTTATTAAATGATAA-
1 TATTTTTATTAAATAATAAC
*
2940857 TATTTATTATTATATAATAAC
1 TATTT-TTATTAAATAATAAC
2940878 TATT
1 TATT
2940882 GAAATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.24
20 12 0.57
21 4 0.19
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (20 bp):
TATTTTTATTAAATAATAAC
Found at i:2941303 original size:9 final size:9
Alignment explanation
Indices: 2941285--2941314 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
2941275 TAAAATTACT
*
2941285 TAACAAAAA
1 TAACATAAA
2941294 TAACATAAA
1 TAACATAAA
2941303 TAACATAAA
1 TAACATAAA
2941312 TAA
1 TAA
2941315 TTTAATTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.70, C:0.10, G:0.00, T:0.20
Consensus pattern (9 bp):
TAACATAAA
Found at i:2941551 original size:16 final size:15
Alignment explanation
Indices: 2941532--2941561 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
2941522 TTTTGATCCA
2941532 TTATTTTTTGTTCTTC
1 TTATTTTTT-TTCTTC
2941548 TTATTTTTTTTCTT
1 TTATTTTTTTTCTT
2941562 AAAATGGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.07, C:0.10, G:0.03, T:0.80
Consensus pattern (15 bp):
TTATTTTTTTTCTTC
Found at i:2944613 original size:3 final size:3
Alignment explanation
Indices: 2944605--2944629 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2944595 TTAATCATAG
2944605 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
2944630 AAATAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:2945067 original size:32 final size:37
Alignment explanation
Indices: 2945029--2945115 Score: 103
Period size: 32 Copynumber: 2.4 Consensus size: 37
2945019 TTTTTCTATT
2945029 TATATTTTTT-TAT-TTAA-AA-TATTATATTTT-TA
1 TATATTTTTTATATATTAATAATTATTATATTTTATA
*
2945061 TATATTTTTTATATATTAATAATTTATTTTATTTTATA
1 TATATTTTTTATATATTAATAA-TTATTATATTTTATA
*
2945099 TATATTTTATTTTATAT
1 TATATTTT-TTATATAT
2945116 ATGAAAAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
32 10 0.22
33 3 0.07
34 4 0.09
35 2 0.04
37 10 0.22
38 10 0.22
39 7 0.15
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (37 bp):
TATATTTTTTATATATTAATAATTATTATATTTTATA
Found at i:2945104 original size:16 final size:16
Alignment explanation
Indices: 2945027--2945117 Score: 71
Period size: 16 Copynumber: 5.6 Consensus size: 16
2945017 TGTTTTTCTA
*
2945027 TTTATAT-TTTTTTA-
1 TTTATATATATTTTAT
* *
2945041 TTTA-AAATATTATATT
1 TTTATATATATTTTA-T
*
2945057 TTTATATATTTTTTAT
1 TTTATATATATTTTAT
*
2945073 ATATTAATAATTTATTTTAT
1 -T-TT-AT-ATATATTTTAT
2945093 TTTATATATATTTTAT
1 TTTATATATATTTTAT
2945109 TTTATATAT
1 TTTATATAT
2945118 GAAAAAAAAT
Statistics
Matches: 60, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
13 1 0.02
14 9 0.15
16 24 0.40
17 10 0.17
18 4 0.07
19 3 0.05
20 9 0.15
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTATATATATTTTAT
Found at i:2945152 original size:13 final size:13
Alignment explanation
Indices: 2945134--2945158 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2945124 AAATTAAGTG
2945134 TTTATATTTTTAA
1 TTTATATTTTTAA
2945147 TTTATATTTTTA
1 TTTATATTTTTA
2945159 TTATTTAAAA
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTATATTTTTAA
Found at i:2945208 original size:19 final size:19
Alignment explanation
Indices: 2945134--2945231 Score: 55
Period size: 19 Copynumber: 5.3 Consensus size: 19
2945124 AAATTAAGTG
*
2945134 TTTATATTTTTAATTT-ATA
1 TTTATATATTT-ATTTCATA
* *
2945153 TTT-T-TA-TTATTTAAAA
1 TTTATATATTTATTTCATA
* * *
2945169 TATTATAAATTTATGTAATA
1 T-TTATATATTTATTTCATA
2945189 TTTATAAATATTT-TTT-ATA
1 TTTAT--ATATTTATTTCATA
*
2945208 TTTGTATATTTATTTCATA
1 TTTATATATTTATTTCATA
2945227 TTTAT
1 TTTAT
2945232 TTTTTTATAT
Statistics
Matches: 61, Mismatches: 9, Indels: 18
0.69 0.10 0.20
Matches are distributed among these distances:
15 4 0.07
16 5 0.08
17 9 0.15
18 5 0.08
19 22 0.36
20 11 0.18
21 5 0.08
ACGTcount: A:0.35, C:0.01, G:0.02, T:0.62
Consensus pattern (19 bp):
TTTATATATTTATTTCATA
Found at i:2945240 original size:25 final size:24
Alignment explanation
Indices: 2945203--2945293 Score: 69
Period size: 24 Copynumber: 3.7 Consensus size: 24
2945193 TAAATATTTT
* *
2945203 TTATATTTGTATATTTATTTCATA
1 TTATTTTTTTATATTTATTTCATA
* *
2945227 TTTATTTTTTTATATTGTGTTTGA-A
1 -TTATTTTTTTATATT-TATTTCATA
* * *
2945252 TTAATTTTTAAT-TTTATATTTATA
1 TTATTTTTTTATATTTAT-TTCATA
2945276 TTATTTTTTATATATTTA
1 TTATTTTTT-TATATTTA
2945294 AAATATTAAA
Statistics
Matches: 51, Mismatches: 10, Indels: 9
0.73 0.14 0.13
Matches are distributed among these distances:
22 2 0.04
23 5 0.10
24 19 0.37
25 16 0.31
26 9 0.18
ACGTcount: A:0.27, C:0.01, G:0.04, T:0.67
Consensus pattern (24 bp):
TTATTTTTTTATATTTATTTCATA
Found at i:2945630 original size:32 final size:34
Alignment explanation
Indices: 2945594--2945674 Score: 87
Period size: 34 Copynumber: 2.4 Consensus size: 34
2945584 AAGTTCGTGT
2945594 TATTTTTTATATTAA-AATATTATATT-TTT-ATA
1 TATTTTTTATATTAATAAT-TTATATTATTTCATA
* *
2945626 TATTTTTTACATATTAATAATTTATTTTATTTCATG
1 TATTTTTT--ATATTAATAATTTATATTATTTCATA
2945662 TATATTTTTATAT
1 TAT-TTTTTATAT
2945675 GTTCGTGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
32 8 0.20
34 13 0.32
35 10 0.24
36 5 0.12
37 5 0.12
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.63
Consensus pattern (34 bp):
TATTTTTTATATTAATAATTTATATTATTTCATA
Found at i:2946132 original size:28 final size:30
Alignment explanation
Indices: 2946091--2946151 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 30
2946081 TTTTAATTTT
**
2946091 AAATTTATTTATTA-AATATT-TTTAAATA
1 AAATTTATGAATTATAATATTATTTAAATA
* *
2946119 AAATTTATGAATTATAATTTTATTTAATTA
1 AAATTTATGAATTATAATATTATTTAAATA
2946149 AAA
1 AAA
2946152 ATTTTATAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 12 0.44
29 5 0.19
30 10 0.37
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (30 bp):
AAATTTATGAATTATAATATTATTTAAATA
Found at i:2946157 original size:43 final size:41
Alignment explanation
Indices: 2946078--2946157 Score: 99
Period size: 43 Copynumber: 1.9 Consensus size: 41
2946068 TTATATGATT
* *
2946078 AAATTTTAATTTTAAATTTATTTATTAAATATTTTTAAATA
1 AAATTTTAATTATAAATTTATTTATTAAATAATTTTAAATA
*
2946119 AAATTTATGAATTATAATTTTATTTAATTAAA-AATTTTA
1 AAATTT-T-AATTATAAATTTATTT-ATTAAATAATTTTA
2946158 TAAATATTGG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
41 6 0.18
42 1 0.03
43 20 0.61
44 6 0.18
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (41 bp):
AAATTTTAATTATAAATTTATTTATTAAATAATTTTAAATA
Found at i:2948813 original size:42 final size:42
Alignment explanation
Indices: 2948727--2948813 Score: 149
Period size: 42 Copynumber: 2.1 Consensus size: 42
2948717 TCATTAAGGT
*
2948727 GAGTTCCTTGGGGCTAGGTTAATAATCCGCTTAGTTTTTCTG
1 GAGTTCCTTGGGGCTAGGTTAATAATCCGCTTAGTTTATCTG
2948769 GAGTTCCTTGGGGCTAGGTTAATAATCCGCTTAGTGTTAT-TG
1 GAGTTCCTTGGGGCTAGGTTAATAATCCGCTTAGT-TTATCTG
2948811 GAG
1 GAG
2948814 ATGTTTTCTA
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
42 40 0.93
43 3 0.07
ACGTcount: A:0.18, C:0.15, G:0.29, T:0.38
Consensus pattern (42 bp):
GAGTTCCTTGGGGCTAGGTTAATAATCCGCTTAGTTTATCTG
Found at i:2950392 original size:1 final size:1
Alignment explanation
Indices: 2950386--2950410 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
2950376 AGGATTTCAA
2950386 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
2950411 TTAAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:2950497 original size:2 final size:2
Alignment explanation
Indices: 2950490--2950523 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2950480 AAAAGCCCAG
2950490 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2950524 ATCGTCATCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2950649 original size:22 final size:23
Alignment explanation
Indices: 2950621--2950663 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
2950611 TAATTTATTT
2950621 TTTAAAAATAATA-TTTAATAAA
1 TTTAAAAATAATATTTTAATAAA
* *
2950643 TTTAAAATTTATATTTTAATA
1 TTTAAAAATAATATTTTAATA
2950664 TTTATAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TTTAAAAATAATATTTTAATAAA
Found at i:2950660 original size:14 final size:15
Alignment explanation
Indices: 2950633--2950674 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
2950623 TAAAAATAAT
*
2950633 ATTTAATAAATTTAAA
1 ATTT-ATAATTTTAAA
*
2950649 ATTTAT-ATTTTAAT
1 ATTTATAATTTTAAA
2950663 ATTTATAATTTT
1 ATTTATAATTTT
2950675 TTTGTTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 12 0.52
15 7 0.30
16 4 0.17
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTTATAATTTTAAA
Found at i:2951626 original size:2 final size:2
Alignment explanation
Indices: 2951619--2951647 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2951609 ATGCAAATTA
2951619 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2951648 AACCAATACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2952201 original size:18 final size:19
Alignment explanation
Indices: 2952179--2952239 Score: 63
Period size: 18 Copynumber: 3.1 Consensus size: 19
2952169 AAGTTTAGTA
2952179 ATTTTTATATATATATTAT
1 ATTTTTATATATATATTAT
2952198 -TTTTTATAT-TATAATTAT
1 ATTTTTATATATAT-ATTAT
*
2952216 ATTTATATTATTATATATTTAT
1 ATTTTTA-TA-TATATA-TTAT
2952238 AT
1 AT
2952240 AATTTTTGAT
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
17 3 0.09
18 14 0.40
19 5 0.14
20 2 0.06
21 2 0.06
22 9 0.26
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
ATTTTTATATATATATTAT
Found at i:2952351 original size:26 final size:26
Alignment explanation
Indices: 2952299--2952383 Score: 68
Period size: 27 Copynumber: 3.3 Consensus size: 26
2952289 AAATACTCAA
* *
2952299 ATTATATTTATATAATTTTTTATATT
1 ATTATATTTACATAATATTTTATATT
*
2952325 ATTATATTTTACATTATATTTTA-ATT
1 ATTATA-TTTACATAATATTTTATATT
* * *
2952351 ATT-T-TTCTCCATCATATCTTATATT
1 ATTATATT-TACATAATATTTTATATT
2952376 ATTCATAT
1 ATT-ATAT
2952384 ATTAATTTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
23 2 0.04
24 11 0.23
25 7 0.15
26 12 0.26
27 14 0.30
28 1 0.02
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (26 bp):
ATTATATTTACATAATATTTTATATT
Found at i:2952593 original size:18 final size:17
Alignment explanation
Indices: 2952566--2952613 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
2952556 TTATTCAATA
2952566 TTAT-AATTTAAATTTAT
1 TTATAAATTTAAA-TTAT
2952583 TTATAAATTT-AATTAT
1 TTATAAATTTAAATTAT
2952599 TTATTTAAATTTAAA
1 TTA--TAAATTTAAA
2952614 AATTTACTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 7 0.26
17 6 0.22
18 12 0.44
19 2 0.07
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTATAAATTTAAATTAT
Found at i:2952618 original size:18 final size:19
Alignment explanation
Indices: 2952575--2952635 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
2952565 ATTATAATTT
*
2952575 AAATTTATTTATAAATTTAA
1 AAATTTACTT-TAAATTTAA
**
2952595 TTATTTA-TTTAAATTTAA
1 AAATTTACTTTAAATTTAA
* *
2952613 AAATTTACTTGATATTTAA
1 AAATTTACTTTAAATTTAA
2952632 AAAT
1 AAAT
2952636 ATTTGAATAA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
18 14 0.41
19 15 0.44
20 5 0.15
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (19 bp):
AAATTTACTTTAAATTTAA
Found at i:2956472 original size:2 final size:2
Alignment explanation
Indices: 2956467--2956498 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2956457 TATACCTGTG
2956467 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2956499 AACTTAGCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2956696 original size:34 final size:34
Alignment explanation
Indices: 2956629--2956844 Score: 292
Period size: 34 Copynumber: 6.4 Consensus size: 34
2956619 ATGTTAGCAG
* * *
2956629 TGTTGATTAAAT-GGTGATTTAGTAGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * * *
2956662 TGTTGATTAAATGGGTGATTTGGTGGTTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
*
2956696 TGTTGACTAAAT-GGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
*
2956729 TGTTGATTAAATGGGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* *
2956763 TGTTGATTAAATGGGTGATTTGGTGGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
2956797 TGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
2956831 TGTTGATTAAATGG
1 TGTTGATTAAATGG
2956845 TGGTTTTTAC
Statistics
Matches: 162, Mismatches: 19, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
33 40 0.25
34 122 0.75
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:2956810 original size:68 final size:67
Alignment explanation
Indices: 2956629--2956846 Score: 319
Period size: 67 Copynumber: 3.2 Consensus size: 67
2956619 ATGTTAGCAG
* * * * *
2956629 TGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 TGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
2956694 AT
66 AT
* * * *
2956696 TGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 TGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
2956761 AT
66 AT
* * *
2956763 TGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTTGC
1 TGTTGATTAAAT-GGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGC
2956828 CAT
65 CAT
2956831 TGTTGATTAAATGGTG
1 TGTTGATTAAATGGTG
2956847 GTTTTTACCA
Statistics
Matches: 134, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
67 73 0.54
68 61 0.46
ACGTcount: A:0.24, C:0.08, G:0.28, T:0.40
Consensus pattern (67 bp):
TGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
AT
Found at i:2961327 original size:34 final size:34
Alignment explanation
Indices: 2961258--2961475 Score: 296
Period size: 34 Copynumber: 6.5 Consensus size: 34
2961248 AAGTGGGAGA
* * *
2961258 ATTGTTGATTAAAT-GGTGATTTAGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
2961291 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
2961325 ATTGTTGACTAAAT-GGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
2961358 ATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
2961392 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
2961426 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
2961460 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
2961476 TGGTTTTTAC
Statistics
Matches: 164, Mismatches: 19, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
33 42 0.26
34 122 0.74
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:2961441 original size:68 final size:67
Alignment explanation
Indices: 2961258--2961477 Score: 323
Period size: 67 Copynumber: 3.3 Consensus size: 67
2961248 AAGTGGGAGA
* * * * *
2961258 ATTGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
2961323 CC
66 CC
* * * *
2961325 ATTGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGAAATTTGGTAGCTTA
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
2961390 CC
66 CC
* * *
2961392 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTT
1 ATTGTTGATTAAAT-GGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTT
2961457 GCC
65 GCC
2961460 ATTGTTGATTAAATGGTG
1 ATTGTTGATTAAATGGTG
2961478 GTTTTTACCA
Statistics
Matches: 136, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
67 75 0.55
68 61 0.45
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (67 bp):
ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
CC
Found at i:2961916 original size:3 final size:3
Alignment explanation
Indices: 2961908--2961946 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
2961898 CTATCAGCCT
2961908 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2961947 AATTCATTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2963542 original size:2 final size:2
Alignment explanation
Indices: 2963537--2963570 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2963527 CTTTTTTCTT
*
2963537 TA TA TA TA TA TA TA TA TA TA TA AA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2963571 GTTGCATAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2964164 original size:22 final size:22
Alignment explanation
Indices: 2964115--2964164 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
2964105 AAAATTATAA
* *
2964115 AAATTATTTTATATTAATATTT
1 AAATAATTTTATATTAATAATT
*
2964137 ATATAATTTTATAATTAA-AATT
1 AAATAATTTTAT-ATTAATAATT
2964159 AAATAA
1 AAATAA
2964165 AAATATTTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AAATAATTTTATATTAATAATT
Found at i:2965436 original size:19 final size:20
Alignment explanation
Indices: 2965409--2965461 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
2965399 GTTAAATTAA
*
2965409 TTATAATTATAAATATTT-T
1 TTATTATTATAAATATTTAT
2965428 TTATTATTAATAAA-ATTTAT
1 TTATTATT-ATAAATATTTAT
*
2965448 TTAAT-TTATAAATA
1 TTATTATTATAAATA
2965462 ATAAATATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
18 5 0.17
19 14 0.48
20 10 0.34
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTATTATTATAAATATTTAT
Found at i:2965885 original size:23 final size:21
Alignment explanation
Indices: 2965834--2965887 Score: 56
Period size: 23 Copynumber: 2.5 Consensus size: 21
2965824 AAATAAATAT
*
2965834 AAATAAATAATAATTTTATTT
1 AAATAAATAATAATTTTATTC
*
2965855 AGAA-AAATAATTTAGTTTTATTC
1 A-AATAAATAA--TAATTTTATTC
2965878 AAATAAATAA
1 AAATAAATAA
2965888 ATTGAGGATT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
21 7 0.26
22 4 0.15
23 16 0.59
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.41
Consensus pattern (21 bp):
AAATAAATAATAATTTTATTC
Found at i:2972419 original size:3 final size:3
Alignment explanation
Indices: 2972411--2972447 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
2972401 TCACCAAAAC
2972411 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2972448 AAGACAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2975039 original size:21 final size:21
Alignment explanation
Indices: 2975015--2975059 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
2975005 ATACAAAAAA
2975015 TTATAT-TATTTAT-ATTAATAT
1 TTATATAT-TTTATAATTAA-AT
2975036 TTATATATTTTATAATTAAAT
1 TTATATATTTTATAATTAAAT
2975057 TTA
1 TTA
2975060 AATAAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTATATATTTTATAATTAAAT
Found at i:2975672 original size:3 final size:3
Alignment explanation
Indices: 2975664--2975702 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
2975654 TTAAAAACTC
2975664 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2975703 AGTAATACTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2976482 original size:18 final size:18
Alignment explanation
Indices: 2976459--2976494 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
2976449 TTTTTTTCAT
2976459 TATATA-ATATTATTTATA
1 TATATACATATT-TTTATA
2976477 TATATACATATTTTTATA
1 TATATACATATTTTTATA
2976495 AAAGATAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (18 bp):
TATATACATATTTTTATA
Found at i:2976980 original size:2 final size:2
Alignment explanation
Indices: 2976975--2977012 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2976965 GAGTTATGTG
2976975 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2977013 TTGATAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2977742 original size:7 final size:7
Alignment explanation
Indices: 2977732--2977759 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
2977722 ATTTATAAAT
2977732 TTGAACA
1 TTGAACA
2977739 TTGAACA
1 TTGAACA
2977746 TTGAACA
1 TTGAACA
2977753 TTGAACA
1 TTGAACA
2977760 AAATTTAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (7 bp):
TTGAACA
Found at i:2977897 original size:17 final size:16
Alignment explanation
Indices: 2977867--2977905 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
2977857 TATATTGACT
*
2977867 TTTTTATTTTTATTAA
1 TTTTAATTTTTATTAA
2977883 TTTTAATTTTATATTAA
1 TTTTAATTTT-TATTAA
*
2977900 ATTTAA
1 TTTTAA
2977906 AAATAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTAATTTTTATTAA
Found at i:2977946 original size:179 final size:183
Alignment explanation
Indices: 2977648--2978013 Score: 578
Period size: 179 Copynumber: 2.0 Consensus size: 183
2977638 ATTAAAAAAA
2977648 TAAAAGAGTTGAAAGTTATATTGACTTTTTTATTTTCATTAATTTTAATTTTATATTAAAATTAA
1 TAAAAGAGTTGAAAGTTATATTGACTTTTTTATTTTCATTAATTTTAATTTTATATTAAAATTAA
2977713 AAATAATAAATTTATAAATTTGAACATTGAACATTGAACATTGAACAAAATTTAGATATTAATGC
66 AAATAATAAATTTATAAA-TT----ATT--A-A-T-AACATTGAACAAAATTTAGATATTAATGC
2977778 ATTTGTTAATTTTAATTATTTGTAAAATATATAATTACATATTTTTAAAATAAATAAGGTAGG
121 ATTTGTTAATTTTAATTATTTGTAAAATATATAATTACATATTTTTAAAATAAATAAGGTAGG
* *
2977841 TAAAAGAGTTGAAAGTTATATTGACTTTTTTATTTTTATTAATTTTAATTTTATATTAAATTTAA
1 TAAAAGAGTTGAAAGTTATATTGACTTTTTTATTTTCATTAATTTTAATTTTATATTAAAATTAA
2977906 AAATAATAAATTTATAAA-T-TT-A-AACATTGAACAAAATTTAGATATTAATGCATTTGTTAAT
66 AAATAATAAATTTATAAATTATTAATAACATTGAACAAAATTTAGATATTAATGCATTTGTTAAT
* *
2977967 TTTAGTTATTTGTAAAATTTATAATTACATATTTTTAAAATAAATAA
131 TTTAATTATTTGTAAAATATATAATTACATATTTTTAAAATAAATAA
2978014 AGTGAGTGAA
Statistics
Matches: 169, Mismatches: 4, Indels: 14
0.90 0.02 0.07
Matches are distributed among these distances:
179 84 0.50
182 1 0.01
186 2 0.01
191 1 0.01
193 81 0.48
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (183 bp):
TAAAAGAGTTGAAAGTTATATTGACTTTTTTATTTTCATTAATTTTAATTTTATATTAAAATTAA
AAATAATAAATTTATAAATTATTAATAACATTGAACAAAATTTAGATATTAATGCATTTGTTAAT
TTTAATTATTTGTAAAATATATAATTACATATTTTTAAAATAAATAAGGTAGG
Found at i:2981471 original size:3 final size:3
Alignment explanation
Indices: 2981463--2981499 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
2981453 TCAACAAAAC
*
2981463 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATG ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2981500 AAGACATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2981807 original size:2 final size:2
Alignment explanation
Indices: 2981802--2981833 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2981792 TTTTTATGAG
*
2981802 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2981834 GAAGACTTGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2983920 original size:2 final size:2
Alignment explanation
Indices: 2983913--2983960 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
2983903 CCATTTAATT
2983913 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2983955 TA TA TA
1 TA TA TA
2983961 AAGCAGAATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2985334 original size:2 final size:2
Alignment explanation
Indices: 2985327--2985366 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2985317 AGATCTTGAG
2985327 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2985367 GTATGTATCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2986100 original size:24 final size:27
Alignment explanation
Indices: 2986032--2986097 Score: 98
Period size: 27 Copynumber: 2.4 Consensus size: 27
2986022 AGCCTTCATA
*
2986032 TTTGACAAATACAAAGGA-AACCACCATT
1 TTTGACAAACACAAA--ATAACCACCATT
2986060 TTTGACAAACACAAAATAACCACCATT
1 TTTGACAAACACAAAATAACCACCATT
2986087 TTTGACAAACA
1 TTTGACAAACA
2986098 AATGGGTGGC
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
26 1 0.03
27 21 0.58
28 14 0.39
ACGTcount: A:0.47, C:0.23, G:0.08, T:0.23
Consensus pattern (27 bp):
TTTGACAAACACAAAATAACCACCATT
Found at i:2988019 original size:21 final size:22
Alignment explanation
Indices: 2987981--2988026 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
2987971 ATTTGTTGAA
* **
2987981 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
2988002 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
2988024 ACT
1 ACT
2988027 TGTCTGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGCGGAGTACT
Found at i:2992492 original size:2 final size:2
Alignment explanation
Indices: 2992487--2992522 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
2992477 ATGCCTAGAA
2992487 AT AT AT AT AT AT AT AT AT AT A- AT AT A- AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2992523 AAGTGAAGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 3 0.10
2 28 0.90
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:2992715 original size:4 final size:4
Alignment explanation
Indices: 2992706--2992736 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
2992696 CAAGAAGTTT
2992706 ATCC ATCC ATCC ATCC ATCC ATCC ATCC ATC
1 ATCC ATCC ATCC ATCC ATCC ATCC ATCC ATC
2992737 TATCTATACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.48, G:0.00, T:0.26
Consensus pattern (4 bp):
ATCC
Found at i:2993017 original size:4 final size:4
Alignment explanation
Indices: 2993010--2993036 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2993000 AGAGTTAGTT
2993010 ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATA
2993037 TACATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:2994424 original size:49 final size:49
Alignment explanation
Indices: 2994371--2994508 Score: 195
Period size: 49 Copynumber: 2.8 Consensus size: 49
2994361 AAAGTGTTGT
* * *
2994371 TATTGTTGACTATTCTTCACCAACTTTTGATAATCGAGAAAAGTGACCG
1 TATTGTTGACTATTCTTCATCAACCTTTGACAATCGAGAAAAGTGACCG
* * *
2994420 TATTGTTGATTATTCTTCATCAACCTTTGACAATCGAGAGAGGTGACCG
1 TATTGTTGACTATTCTTCATCAACCTTTGACAATCGAGAAAAGTGACCG
* *
2994469 TAATTGTTGACGATTCTTCATCAACCTTTGACAATTGAGA
1 T-ATTGTTGACTATTCTTCATCAACCTTTGACAATCGAGA
2994509 GAGGTGGCCA
Statistics
Matches: 79, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
49 44 0.56
50 35 0.44
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (49 bp):
TATTGTTGACTATTCTTCATCAACCTTTGACAATCGAGAAAAGTGACCG
Found at i:2994494 original size:50 final size:50
Alignment explanation
Indices: 2994372--2994531 Score: 214
Period size: 50 Copynumber: 3.2 Consensus size: 50
2994362 AAGTGTTGTT
* * * * * *
2994372 ATTGTTGACTATTCTTCACCAACTTTTGATAATCGAGAAAAGTGACCGT-
1 ATTGTTGACGATTCTTCATCAACCTTTGACAATCGAGAGAGGTGACCGTA
**
2994421 ATTGTTGATTATTCTTCATCAACCTTTGACAATCGAGAGAGGTGACCGTA
1 ATTGTTGACGATTCTTCATCAACCTTTGACAATCGAGAGAGGTGACCGTA
* * *
2994471 ATTGTTGACGATTCTTCATCAACCTTTGACAATTGAGAGAGGTGGCCATA
1 ATTGTTGACGATTCTTCATCAACCTTTGACAATCGAGAGAGGTGACCGTA
2994521 ATTGTTGACGA
1 ATTGTTGACGA
2994532 AATTGTTTTG
Statistics
Matches: 99, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
49 43 0.43
50 56 0.57
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (50 bp):
ATTGTTGACGATTCTTCATCAACCTTTGACAATCGAGAGAGGTGACCGTA
Found at i:2996810 original size:50 final size:50
Alignment explanation
Indices: 2996751--2997010 Score: 412
Period size: 50 Copynumber: 5.2 Consensus size: 50
2996741 AGGTATTGCC
*
2996751 ATTGTTGACTATTTTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTA
* *
2996801 ATTGTTGACTATTCTTCACCAACTTTTGACAATCGAGAGAGGTGGCCGTA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTA
*
2996851 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCCGTA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTA
* * * *
2996901 ATTGTTGACGATTCTTTACCAACCTTTAACAATCGAGAGAGGTGACCATA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTA
* * *
2996951 ATTGTTGACTATTCTTCACCAACTTTTGACAATCGAGAGAAGTTACCGTA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTA
*
2997001 ATTATTGACT
1 ATTGTTGACT
2997011 TTAAGCAATT
Statistics
Matches: 193, Mismatches: 17, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 193 1.00
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.32
Consensus pattern (50 bp):
ATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTA
Found at i:2997269 original size:25 final size:25
Alignment explanation
Indices: 2997232--2997282 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
2997222 AATGCACTAA
2997232 TAATAATAACCCTTGTATTTCAATG
1 TAATAATAACCCTTGTATTTCAATG
*
2997257 TAATAATAGCCCTTGTATTTCAATG
1 TAATAATAACCCTTGTATTTCAATG
2997282 T
1 T
2997283 GATACATTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (25 bp):
TAATAATAACCCTTGTATTTCAATG
Found at i:2999124 original size:2 final size:2
Alignment explanation
Indices: 2999117--2999151 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2999107 TAAAGGAGTT
2999117 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2999152 TTATTACCTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:3000166 original size:3 final size:3
Alignment explanation
Indices: 3000158--3000185 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3000148 AATCCCTATC
3000158 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3000186 AAAAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:3001026 original size:2 final size:2
Alignment explanation
Indices: 3001019--3001048 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3001009 ATTTTATTTA
*
3001019 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3001049 TAAGGGATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3001349 original size:19 final size:20
Alignment explanation
Indices: 3001322--3001359 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3001312 TAAAATTAAA
*
3001322 TAAAAAAT-ATTTTAATTAT
1 TAAAAAATAATTCTAATTAT
*
3001341 TAAATAATAATTCTAATTA
1 TAAAAAATAATTCTAATTA
3001360 AGCTAGATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (20 bp):
TAAAAAATAATTCTAATTAT
Found at i:3004127 original size:27 final size:26
Alignment explanation
Indices: 3004092--3004153 Score: 61
Period size: 27 Copynumber: 2.3 Consensus size: 26
3004082 AAAGAGATTA
*
3004092 TTTAATTATCAATAAATGAATAAATTT
1 TTTATTTATCAATAAATGAAT-AATTT
** * *
3004119 TTTATTTATTGATAAATTAATATTTT
1 TTTATTTATCAATAAATGAATAATTT
3004145 TTTACTTTA
1 TTTA-TTTA
3004154 CAAAGAATAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (26 bp):
TTTATTTATCAATAAATGAATAATTT
Found at i:3004815 original size:15 final size:16
Alignment explanation
Indices: 3004797--3004844 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
3004787 ATTAATTGAT
3004797 AATATATAAAT-TATA
1 AATATATAAATATATA
*
3004812 AATAAATCAAATATATA
1 AATATAT-AAATATATA
* *
3004829 TATATATATATATATA
1 AATATATAAATATATA
3004845 TATTTCAAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 6 0.22
16 12 0.44
17 9 0.33
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (16 bp):
AATATATAAATATATA
Found at i:3004829 original size:2 final size:2
Alignment explanation
Indices: 3004822--3004847 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3004812 AATAAATCAA
3004822 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
3004848 TTCAAAGCCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3007167 original size:21 final size:19
Alignment explanation
Indices: 3007134--3007177 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 19
3007124 AAAAAATTAT
3007134 TTTATTATTTAT-ATTAATA
1 TTTATTATTTATAATTAA-A
3007153 TTTATATATTTTATAATTAAA
1 TTTAT-TA-TTTATAATTAAA
3007174 TTTA
1 TTTA
3007178 AATAAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.23
20 2 0.09
21 10 0.45
22 5 0.23
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTATTATTTATAATTAAA
Found at i:3010439 original size:6 final size:6
Alignment explanation
Indices: 3010428--3010458 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
3010418 ATTAAGTTAT
3010428 AAATAA AAATAA AAATAA AAATAA ATAATAA
1 AAATAA AAATAA AAATAA AAATAA A-AATAA
3010459 TTTTATTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.79
7 5 0.21
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
AAATAA
Found at i:3011061 original size:13 final size:13
Alignment explanation
Indices: 3011024--3011066 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
3011014 GTGTTAGGAT
*
3011024 AAATATTATTTTA
1 AAATATAATTTTA
*
3011037 AAA-A-ATTTTTA
1 AAATATAATTTTA
3011048 AAATATAATTTTA
1 AAATATAATTTTA
3011061 AAATAT
1 AAATAT
3011067 TTAATTATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
11 8 0.32
12 2 0.08
13 15 0.60
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
AAATATAATTTTA
Found at i:3012713 original size:16 final size:16
Alignment explanation
Indices: 3012692--3012723 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
3012682 ATCGGAACAT
3012692 ATAGATTATATAATAA
1 ATAGATTATATAATAA
3012708 ATAGATTATATAATAA
1 ATAGATTATATAATAA
3012724 GGCTTTGTTG
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:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (16 bp):
ATAGATTATATAATAA
Found at i:3013566 original size:34 final size:34
Alignment explanation
Indices: 3013502--3013684 Score: 260
Period size: 34 Copynumber: 5.4 Consensus size: 34
3013492 GAGAATTGCA
* *
3013502 TGTTGATTAAAT-GGTGATTTGGTAGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* *
3013535 TGTTGACTAAATGGGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
3013569 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * * *
3013603 TATTGATTAAATGGGTGATTTGGTGGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
3013637 TGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
3013671 TGTTGATTAAATGG
1 TGTTGATTAAATGG
3013685 TGGTTTTTAC
Statistics
Matches: 132, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
33 11 0.08
34 121 0.92
ACGTcount: A:0.26, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:3014045 original size:19 final size:19
Alignment explanation
Indices: 3013989--3014051 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
3013979 TGGTTGTTGA
**
3013989 GGTACTATTCACGTATATA
1 GGTACTATTCACGTATACG
3014008 GGTACTATTCACGTATACG
1 GGTACTATTCACGTATACG
*
3014027 GGTACTATTCAAGTATACG
1 GGTACTATTCACGTATACG
*
3014046 GTTACT
1 GGTACT
3014052 GTACACGTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (19 bp):
GGTACTATTCACGTATACG
Found at i:3018183 original size:34 final size:34
Alignment explanation
Indices: 3018117--3018301 Score: 264
Period size: 34 Copynumber: 5.5 Consensus size: 34
3018107 AAGTGGGAGA
* *
3018117 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
3018150 ATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
3018184 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
3018218 ATTATTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
3018252 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
3018286 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
3018302 TGGTTTTTAC
Statistics
Matches: 134, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
33 13 0.10
34 121 0.90
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:3019415 original size:2 final size:2
Alignment explanation
Indices: 3019402--3019435 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3019392 TCTAACCTTG
*
3019402 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3019436 TTTTACAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3020337 original size:20 final size:22
Alignment explanation
Indices: 3020294--3020337 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 22
3020284 GTTAATTTAT
* *
3020294 ATATTATATATATTTTAGATTA
1 ATATTATATATATATTAGAGTA
3020316 ATATT-TATA-ATATTAGAGTA
1 ATATTATATATATATTAGAGTA
3020336 AT
1 AT
3020338 TAGCACTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 11 0.55
21 4 0.20
22 5 0.25
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (22 bp):
ATATTATATATATATTAGAGTA
Found at i:3021068 original size:2 final size:2
Alignment explanation
Indices: 3021061--3021091 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3021051 AATACTAATT
3021061 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 T
3021092 TTTATAGGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3021541 original size:30 final size:30
Alignment explanation
Indices: 3021501--3021558 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 30
3021491 GGTATTTTTA
*
3021501 GTTTTTTTATTATC-AT-TTTCATTTCCTTCT
1 GTTTTCTTATT-TCAATCTTTCA-TTCCTTCT
3021531 GTTTTCTTATTTCAATCTTTCATTCCTT
1 GTTTTCTTATTTCAATCTTTCATTCCTT
3021559 ATCATTACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 2 0.08
30 18 0.72
31 5 0.20
ACGTcount: A:0.14, C:0.19, G:0.03, T:0.64
Consensus pattern (30 bp):
GTTTTCTTATTTCAATCTTTCATTCCTTCT
Found at i:3025687 original size:20 final size:20
Alignment explanation
Indices: 3025659--3025699 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
3025649 ACAACAAAAA
3025659 TTAAGTGCATAAATTTAAAT
1 TTAAGTGCATAAATTTAAAT
*
3025679 TTAATTGCATAAATTTAAAT
1 TTAAGTGCATAAATTTAAAT
3025699 T
1 T
3025700 ACAAGGAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (20 bp):
TTAAGTGCATAAATTTAAAT
Found at i:3025720 original size:30 final size:30
Alignment explanation
Indices: 3025681--3025840 Score: 158
Period size: 30 Copynumber: 5.1 Consensus size: 30
3025671 ATTTAAATTT
* *
3025681 AATTGCATAAATTTAAATTACAAGGAAGTA
1 AATTGCATAAATTTAAATTACAAGAAAATA
* * *
3025711 AATTACATAAATTTAAATTATAAAAAAATA
1 AATTGCATAAATTTAAATTACAAGAAAATA
* *
3025741 AATTGCATAAATTAAAAATTACAAGAAACTA
1 AATTGCATAAATT-TAAATTACAAGAAAATA
* * *
3025772 AATTGTATAAATTTAAATTGCAAAAAAAAAAATA
1 AATTGCATAAATTTAAATT----ACAAGAAAATA
**
3025806 AATTGCATAAATAAAAAATTACAAGAAAATA
1 AATTGCATAAAT-TTAAATTACAAGAAAATA
3025837 AATT
1 AATT
3025841 AACTACATGA
Statistics
Matches: 104, Mismatches: 20, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
30 42 0.40
31 38 0.37
34 19 0.18
35 5 0.05
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.29
Consensus pattern (30 bp):
AATTGCATAAATTTAAATTACAAGAAAATA
Found at i:3025727 original size:15 final size:15
Alignment explanation
Indices: 3025674--3025790 Score: 62
Period size: 15 Copynumber: 7.8 Consensus size: 15
3025664 TGCATAAATT
*
3025674 TAAATTT-AATTGCA
1 TAAATTTAAATTACA
3025688 TAAATTTAAATTACA
1 TAAATTTAAATTACA
*
3025703 -AGGAA-GTAAATTACA
1 TA--AATTTAAATTACA
*
3025718 TAAATTTAAATTATA
1 TAAATTTAAATTACA
* ** *
3025733 AAAAAATAAATTGCA
1 TAAATTTAAATTACA
*
3025748 TAAATTAAAAATTACA
1 TAAATT-TAAATTACA
** **
3025764 -AGAAACTAAATTGTA
1 TA-AATTTAAATTACA
3025779 TAAATTTAAATT
1 TAAATTTAAATT
3025791 GCAAAAAAAA
Statistics
Matches: 74, Mismatches: 21, Indels: 15
0.67 0.19 0.14
Matches are distributed among these distances:
14 10 0.14
15 51 0.69
16 13 0.18
ACGTcount: A:0.55, C:0.05, G:0.06, T:0.34
Consensus pattern (15 bp):
TAAATTTAAATTACA
Found at i:3025809 original size:19 final size:20
Alignment explanation
Indices: 3025785--3025824 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
3025775 TGTATAAATT
3025785 TAAATTGCA-AAAAAAAAAA
1 TAAATTGCATAAAAAAAAAA
*
3025804 TAAATTGCATAAATAAAAAA
1 TAAATTGCATAAAAAAAAAA
3025824 T
1 T
3025825 TACAAGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.23
Consensus pattern (20 bp):
TAAATTGCATAAAAAAAAAA
Found at i:3025826 original size:65 final size:60
Alignment explanation
Indices: 3025681--3025841 Score: 196
Period size: 65 Copynumber: 2.6 Consensus size: 60
3025671 ATTTAAATTT
** * * *
3025681 AATTGCATAAATTTAAATTACAAGGAAGTAAATTACATAAATTTAAATTATAAAAAAATA
1 AATTGCATAAATAAAAATTACAAGAAAATAAATTACATAAATTTAAATTAAAAAAAAATA
* **
3025741 AATTGCATAAATTAAAAATTACAAGAAACTAAATTGTATAAATTTAAATTGCAAAAAAAAAAATA
1 AATTGCATAAA-TAAAAATTACAAGAAAATAAATTACATAAATTTAAATT----AAAAAAAAATA
3025806 AATTGCATAAATAAAAAATTACAAGAAAATAAATTA
1 AATTGCATAAAT-AAAAATTACAAGAAAATAAATTA
3025842 ACTACATGAC
Statistics
Matches: 86, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
60 11 0.13
61 32 0.37
64 1 0.01
65 42 0.49
ACGTcount: A:0.60, C:0.06, G:0.06, T:0.29
Consensus pattern (60 bp):
AATTGCATAAATAAAAATTACAAGAAAATAAATTACATAAATTTAAATTAAAAAAAAATA
Found at i:3028968 original size:2 final size:2
Alignment explanation
Indices: 3028961--3028997 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3028951 CAGCATACTT
3028961 TA TA 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 T
3028998 GCAACATGTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3030073 original size:2 final size:2
Alignment explanation
Indices: 3030068--3030097 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3030058 GTGTGTGGTG
*
3030068 TA TA TA TA TA TA TA TA TT TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3030098 AAAGAATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:3030286 original size:2 final size:2
Alignment explanation
Indices: 3030279--3030304 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3030269 CATAGCTAGC
3030279 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
3030305 CAAATTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3030661 original size:3 final size:3
Alignment explanation
Indices: 3030653--3030684 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
3030643 CCAATTACAA
3030653 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3030685 ATCGTATCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3031954 original size:28 final size:28
Alignment explanation
Indices: 3031919--3032008 Score: 69
Period size: 29 Copynumber: 3.1 Consensus size: 28
3031909 TAAATTCGTT
3031919 TATA-TTATATATTTTATTTATTTAAAA
1 TATATTTATATATTTTATTTATTTAAAA
* **
3031946 TATATTTAT-TGTTTTAATTTAATTTTTAA
1 TATATTTATATATTTT-ATTT-ATTTAAAA
* *
3031975 TA-ATTTAATATTTTTTATTAAATTTTAAAA
1 TATATTT-ATATATTTTATT-TA-TTTAAAA
3032005 TATA
1 TATA
3032009 AATAATTTAA
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
27 9 0.19
28 12 0.25
29 14 0.29
30 12 0.25
31 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (28 bp):
TATATTTATATATTTTATTTATTTAAAA
Found at i:3032012 original size:28 final size:31
Alignment explanation
Indices: 3031939--3032012 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 31
3031929 ATTTTATTTA
** *
3031939 TTTAAAATATATTTATTGTTTTAATTTAATT
1 TTTAAAATATAAATATTGTTTTAATTTAAAT
*
3031970 TTTAATAAT-TTAATATT-TTTT-A-TTAAAT
1 TTTAA-AATATAAATATTGTTTTAATTTAAAT
3031998 TTTAAAATATAAATA
1 TTTAAAATATAAATA
3032013 ATTTAACATA
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
27 3 0.08
28 15 0.42
29 1 0.03
30 4 0.11
31 10 0.28
32 3 0.08
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (31 bp):
TTTAAAATATAAATATTGTTTTAATTTAAAT
Found at i:3032060 original size:31 final size:33
Alignment explanation
Indices: 3032025--3032085 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 33
3032015 TTAACATATT
*
3032025 TTTTA-TATTTATATTATAAT-ATTATATATAC
1 TTTTATTATTTATATAATAATAATTATATATAC
* *
3032056 TTTTATTCTTTATATAATATTAATTATATA
1 TTTTATTATTTATATAATAATAATTATATA
3032086 ATATAGATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 5 0.20
32 12 0.48
33 8 0.32
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (33 bp):
TTTTATTATTTATATAATAATAATTATATATAC
Found at i:3032109 original size:25 final size:25
Alignment explanation
Indices: 3032067--3032115 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
3032057 TTTATTCTTT
*
3032067 ATATAATATTAATTATATAATATAG
1 ATATAATATTAATCATATAATATAG
*
3032092 ATATAATA-TAATACATATTATATA
1 ATATAATATTAAT-CATATAATATA
3032116 ATTAAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (25 bp):
ATATAATATTAATCATATAATATAG
Found at i:3032558 original size:18 final size:17
Alignment explanation
Indices: 3032514--3032560 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
3032504 CAATAAGACT
3032514 TAAACAAAA-AAATTAAA
1 TAAA-AAAATAAATTAAA
*
3032531 TCAAATAAATAAATTTAAA
1 T-AAAAAAATAAA-TTAAA
3032550 TAAAAAAATAA
1 TAAAAAAATAA
3032561 GACATGTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 4 0.16
18 15 0.60
19 6 0.24
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.23
Consensus pattern (17 bp):
TAAAAAAATAAATTAAA
Found at i:3033103 original size:28 final size:28
Alignment explanation
Indices: 3033044--3033113 Score: 83
Period size: 27 Copynumber: 2.5 Consensus size: 28
3033034 TCACTCATTT
3033044 ATTTGTCAAAAATGGTGGTTATTTTGTG
1 ATTTGTCAAAAATGGTGGTTATTTTGTG
*
3033072 -TTTGTCAAAAATTGTGGTT-TCCTTTG-G
1 ATTTGTCAAAAATGGTGGTTAT--TTTGTG
*
3033099 ATTTGTCAAATATGG
1 ATTTGTCAAAAATGG
3033114 AGGCTTGTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
26 1 0.03
27 19 0.53
28 16 0.44
ACGTcount: A:0.24, C:0.07, G:0.23, T:0.46
Consensus pattern (28 bp):
ATTTGTCAAAAATGGTGGTTATTTTGTG
Found at i:3035716 original size:21 final size:22
Alignment explanation
Indices: 3035687--3035732 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
3035677 TGTTCAGACA
** *
3035687 AGTAGTACTCCGCAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
3035709 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
3035730 AGT
1 AGT
3035733 TTCAACAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:3045532 original size:2 final size:2
Alignment explanation
Indices: 3045521--3045552 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3045511 ATGCATATTA
3045521 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3045553 AACATTATAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3047423 original size:2 final size:2
Alignment explanation
Indices: 3047416--3047481 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
3047406 TAACTACTTT
3047416 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3047458 TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
3047482 GGGAGAGAGA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3050466 original size:28 final size:27
Alignment explanation
Indices: 3050408--3050471 Score: 85
Period size: 27 Copynumber: 2.3 Consensus size: 27
3050398 CACCCATTTG
*
3050408 TTTGTCAAAAATGGTGATTATTTTGTG
1 TTTGTCAAAAATGGTGATTATTTTGTA
*
3050435 TTTGTCAAAAATGGTGGTT-TCCTTTGTA
1 TTTGTCAAAAATGGTGATTAT--TTTGTA
3050463 TTTGTCAAA
1 TTTGTCAAA
3050472 TATAGAGCCT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
26 1 0.03
27 18 0.55
28 14 0.42
ACGTcount: A:0.25, C:0.08, G:0.20, T:0.47
Consensus pattern (27 bp):
TTTGTCAAAAATGGTGATTATTTTGTA
Found at i:3050508 original size:25 final size:24
Alignment explanation
Indices: 3050480--3050530 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
3050470 AATATAGAGC
3050480 CTTGTTTATTTGTCAAAATTGGTGG
1 CTTG-TTATTTGTCAAAATTGGTGG
*
3050505 CTTGTTGTTTGTCAAAATTGGTGG
1 CTTGTTATTTGTCAAAATTGGTGG
3050529 CT
1 CT
3050531 AATTTTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 21 0.84
25 4 0.16
ACGTcount: A:0.18, C:0.10, G:0.25, T:0.47
Consensus pattern (24 bp):
CTTGTTATTTGTCAAAATTGGTGG
Found at i:3055026 original size:25 final size:24
Alignment explanation
Indices: 3054998--3055122 Score: 97
Period size: 27 Copynumber: 4.9 Consensus size: 24
3054988 AAGCCACCCA
3054998 TTTGTTTGTCAAAAATGGTGGTTATT
1 TTTGTTTGTCAAAAATGGTGG-T-TT
3055024 TTGTGTTTGTCAAAAATGGTGGTTT
1 TT-TGTTTGTCAAAAATGGTGGTTT
* ** *
3055049 CCTTTGTATTTGTCAAATATGAAGGCTTG
1 --TTTG--TTTGTCAAAAATGGTGG-TTT
* * *
3055078 TTTATTTGTCAAAATTGGTGGCTT
1 TTTGTTTGTCAAAAATGGTGGTTT
* *
3055102 GTTGTTTGTCAAAATTGGTGG
1 TTTGTTTGTCAAAAATGGTGG
3055123 CTAATTTTTA
Statistics
Matches: 80, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
24 20 0.25
25 15 0.19
26 5 0.06
27 24 0.30
28 14 0.17
29 2 0.03
ACGTcount: A:0.22, C:0.07, G:0.25, T:0.46
Consensus pattern (24 bp):
TTTGTTTGTCAAAAATGGTGGTTT
Found at i:3055055 original size:28 final size:27
Alignment explanation
Indices: 3055000--3055065 Score: 98
Period size: 27 Copynumber: 2.4 Consensus size: 27
3054990 GCCACCCATT
3055000 TGTTTGTCAAAAATGGTGGTTATTTTG
1 TGTTTGTCAAAAATGGTGGTTATTTTG
3055027 TGTTTGTCAAAAATGGTGGTT-TCCTTTG
1 TGTTTGTCAAAAATGGTGGTTAT--TTTG
*
3055055 TATTTGTCAAA
1 TGTTTGTCAAA
3055066 TATGAAGGCT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
26 1 0.03
27 21 0.58
28 14 0.39
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.47
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTATTTTG
Found at i:3055109 original size:24 final size:25
Alignment explanation
Indices: 3055055--3055124 Score: 90
Period size: 24 Copynumber: 2.8 Consensus size: 25
3055045 GTTTCCTTTG
**
3055055 TATTTGTC-AAATATGAAGGCTTGTT
1 TATTTGTCAAAAT-TGGTGGCTTGTT
3055080 TATTTGTCAAAATTGGTGGCTTG-T
1 TATTTGTCAAAATTGGTGGCTTGTT
*
3055104 TGTTTGTCAAAATTGGTGGCT
1 TATTTGTCAAAATTGGTGGCT
3055125 AATTTTTATT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
24 21 0.51
25 16 0.39
26 4 0.10
ACGTcount: A:0.23, C:0.09, G:0.24, T:0.44
Consensus pattern (25 bp):
TATTTGTCAAAATTGGTGGCTTGTT
Found at i:3056562 original size:24 final size:24
Alignment explanation
Indices: 3056534--3056579 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
3056524 AATAAAAATT
3056534 AGCCACCAATTTTGACAAACAACA
1 AGCCACCAATTTTGACAAACAACA
*
3056558 AGCCACCAATTTTTACAAACAA
1 AGCCACCAATTTTGACAAACAA
3056580 AAATAACCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.46, C:0.28, G:0.07, T:0.20
Consensus pattern (24 bp):
AGCCACCAATTTTGACAAACAACA
Found at i:3056617 original size:28 final size:28
Alignment explanation
Indices: 3056584--3056666 Score: 148
Period size: 28 Copynumber: 3.0 Consensus size: 28
3056574 AAACAAAAAT
*
3056584 AACCACCATATTTGACAAATATAAAGGA
1 AACCACCATATTTGACAAATACAAAGGA
3056612 AACCACCATATTTGACAAATACAAAGGA
1 AACCACCATATTTGACAAATACAAAGGA
*
3056640 AACTACCATATTTGACAAATACAAAGG
1 AACCACCATATTTGACAAATACAAAGG
3056667 GTGGCATTTG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 53 1.00
ACGTcount: A:0.49, C:0.19, G:0.11, T:0.20
Consensus pattern (28 bp):
AACCACCATATTTGACAAATACAAAGGA
Found at i:3058608 original size:21 final size:22
Alignment explanation
Indices: 3058570--3058615 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
3058560 ATCTGTTGAA
* **
3058570 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
3058591 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
3058613 ACT
1 ACT
3058616 TGTCTGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGCGGAGTACT
Found at i:3061189 original size:24 final size:24
Alignment explanation
Indices: 3061161--3061206 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
3061151 AATAAAAATT
3061161 AGCCACCAATTTTGACAAACAACA
1 AGCCACCAATTTTGACAAACAACA
*
3061185 AGCCACCAATTTTTACAAACAA
1 AGCCACCAATTTTGACAAACAA
3061207 AAATAACCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.46, C:0.28, G:0.07, T:0.20
Consensus pattern (24 bp):
AGCCACCAATTTTGACAAACAACA
Found at i:3061244 original size:28 final size:28
Alignment explanation
Indices: 3061211--3061293 Score: 148
Period size: 28 Copynumber: 3.0 Consensus size: 28
3061201 AAACAAAAAT
*
3061211 AACCACCATATTTGACAAATATAAAGGA
1 AACCACCATATTTGACAAATACAAAGGA
3061239 AACCACCATATTTGACAAATACAAAGGA
1 AACCACCATATTTGACAAATACAAAGGA
*
3061267 AACTACCATATTTGACAAATACAAAGG
1 AACCACCATATTTGACAAATACAAAGG
3061294 GTGGCATTTG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 53 1.00
ACGTcount: A:0.49, C:0.19, G:0.11, T:0.20
Consensus pattern (28 bp):
AACCACCATATTTGACAAATACAAAGGA
Found at i:3061964 original size:13 final size:12
Alignment explanation
Indices: 3061942--3061971 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
3061932 TTACAATGTA
3061942 TTTTATTTTAAT
1 TTTTATTTTAAT
3061954 TTTTGATTTTAAT
1 TTTT-ATTTTAAT
3061967 TTTTA
1 TTTTA
3061972 ATTAATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.73
Consensus pattern (12 bp):
TTTTATTTTAAT
Found at i:3065887 original size:12 final size:12
Alignment explanation
Indices: 3065870--3065896 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3065860 TTCCCATCCC
3065870 TTTCCCTTTCCT
1 TTTCCCTTTCCT
3065882 TTTCCCTTTCCT
1 TTTCCCTTTCCT
3065894 TTT
1 TTT
3065897 AGCTTTAGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (12 bp):
TTTCCCTTTCCT
Found at i:3066994 original size:26 final size:27
Alignment explanation
Indices: 3066965--3067015 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
3066955 TATACTCTTG
*
3066965 TTCTCTATTTTAATTTTAAT-TTTCTC
1 TTCTCTATTTTAATTTCAATCTTTCTC
* *
3066991 TTCTGTATTTTGATTTCAATCTTTC
1 TTCTCTATTTTAATTTCAATCTTTC
3067016 ATTCATTGTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 17 0.81
27 4 0.19
ACGTcount: A:0.18, C:0.16, G:0.04, T:0.63
Consensus pattern (27 bp):
TTCTCTATTTTAATTTCAATCTTTCTC
Found at i:3069268 original size:34 final size:34
Alignment explanation
Indices: 3069222--3069406 Score: 257
Period size: 34 Copynumber: 5.5 Consensus size: 34
3069212 GTAAAAACCA
*
3069222 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
3069256 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
3069290 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
3069324 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
3069358 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
3069391 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
3069407 TCTCCCACTT
Statistics
Matches: 135, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
33 18 0.13
34 113 0.84
35 4 0.03
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:3073866 original size:34 final size:34
Alignment explanation
Indices: 3073820--3074003 Score: 246
Period size: 34 Copynumber: 5.4 Consensus size: 34
3073810 GTAAAAACCA
*
3073820 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
3073854 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
3073888 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
3073922 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * * *
3073956 CCATTTAGTCAACAATGATAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
3073989 CCATTTAATCAACAA
1 CCATTTAATCAACAA
3074004 AATTCACATA
Statistics
Matches: 133, Mismatches: 15, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
33 17 0.13
34 112 0.84
35 4 0.03
ACGTcount: A:0.41, C:0.27, G:0.07, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:3075567 original size:2 final size:2
Alignment explanation
Indices: 3075555--3075592 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
3075545 TTCCATTGGA
* *
3075555 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3075593 CATAAGGTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3076216 original size:17 final size:17
Alignment explanation
Indices: 3076191--3076224 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3076181 TAACTTTTTA
*
3076191 AGTATAAGCAGCAAATG
1 AGTACAAGCAGCAAATG
*
3076208 AGTACAAGCAGTAAATG
1 AGTACAAGCAGCAAATG
3076225 TGAGTCAATC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.12, G:0.24, T:0.18
Consensus pattern (17 bp):
AGTACAAGCAGCAAATG
Done.