Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168026.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_28, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 15507587
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 97000 characters in sequence are not A, C, G, or T
File 80 of 91
Found at i:13474209 original size:27 final size:27
Alignment explanation
Indices: 13474156--13474210 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
13474146 TTTATAAATA
* * *
13474156 ATATTATATTAATAAATAAATATTAAT
1 ATATTATATAAATAAATAAAGAATAAT
13474183 ATATTA-ATAAATAATATAAAGAATAAT
1 ATATTATATAAATAA-ATAAAGAATAAT
13474210 A
1 A
13474211 AATAATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 7 0.29
27 17 0.71
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (27 bp):
ATATTATATAAATAAATAAAGAATAAT
Found at i:13474258 original size:19 final size:18
Alignment explanation
Indices: 13474231--13474353 Score: 65
Period size: 19 Copynumber: 6.6 Consensus size: 18
13474221 TTTTAAGTAT
*
13474231 TTTTTATATTAACATAATA
1 TTTTAATATTAA-ATAATA
*
13474250 TTTTAATATTAAATATTA
1 TTTTAATATTAAATAATA
* * *
13474268 TTATTAA-AATATAATTATT
1 TT-TTAATATTA-AATAATA
*
13474287 TTTTAATATT-AATAATT
1 TTTTAATATTAAATAATA
*
13474304 TTAATAATAAATATTTCAAT-ATA
1 TT--T--T-AATA-TTAAATAATA
*
13474327 TTTTAATAATAAATAAT-
1 TTTTAATATTAAATAATA
13474344 TTTTAATATT
1 TTTTAATATT
13474354 TTAATAGTTA
Statistics
Matches: 81, Mismatches: 12, Indels: 24
0.69 0.10 0.21
Matches are distributed among these distances:
17 21 0.26
18 20 0.25
19 25 0.31
21 2 0.02
22 4 0.05
23 6 0.07
24 3 0.04
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTTAATATTAAATAATA
Found at i:13474301 original size:20 final size:19
Alignment explanation
Indices: 13474228--13474303 Score: 59
Period size: 18 Copynumber: 4.1 Consensus size: 19
13474218 TTATTTTAAG
*
13474228 TATTTTTT-ATATTAACAT
1 TATTTTTTAATATTAAAAT
* *
13474246 AATATTTTAATATTAAATAT
1 TATTTTTTAATATTAAA-AT
* * *
13474266 TA-TTATTAA-AATATAAT
1 TATTTTTTAATATTAAAAT
13474283 TATTTTTTAATATTAATAAT
1 TATTTTTTAATATTAA-AAT
13474303 T
1 T
13474304 TTAATAATAA
Statistics
Matches: 42, Mismatches: 11, Indels: 8
0.69 0.18 0.13
Matches are distributed among these distances:
17 4 0.10
18 16 0.38
19 15 0.36
20 7 0.17
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.55
Consensus pattern (19 bp):
TATTTTTTAATATTAAAAT
Found at i:13474331 original size:25 final size:26
Alignment explanation
Indices: 13474297--13474359 Score: 87
Period size: 25 Copynumber: 2.5 Consensus size: 26
13474287 TTTTAATATT
13474297 AATA-ATTTTAATAATAAAT-ATTTC
1 AATATATTTTAATAATAAATAATTTC
*
13474321 AATATATTTTAATAATAAATAATTTT
1 AATATATTTTAATAATAAATAATTTC
*
13474347 TA-ATATTTTAATA
1 AATATATTTTAATA
13474360 GTTATATTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
24 4 0.11
25 26 0.74
26 5 0.14
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (26 bp):
AATATATTTTAATAATAAATAATTTC
Found at i:13480691 original size:17 final size:18
Alignment explanation
Indices: 13480671--13480712 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
13480661 TTTACATATT
13480671 ATTTTTTTCAAAAC-ACA
1 ATTTTTTTCAAAACAACA
* *
13480688 ATTTTGTTCAAAGCAACA
1 ATTTTTTTCAAAACAACA
13480706 ATTTTTT
1 ATTTTTT
13480713 CAGTGTGTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.36, C:0.14, G:0.05, T:0.45
Consensus pattern (18 bp):
ATTTTTTTCAAAACAACA
Found at i:13484343 original size:52 final size:50
Alignment explanation
Indices: 13484253--13484353 Score: 127
Period size: 52 Copynumber: 2.0 Consensus size: 50
13484243 TAGTTTTTTT
13484253 AATTATTATAATCATAATCAAGTATTACATTCATATAATTAACTGAATAATC
1 AATTATTATAATCATAATCAAG-ATTACATTCATATAATTAACT-AATAATC
13484305 AATTATTAT-ATCATAATCAA-ATTACAATT-ACTGAATAATTAACTAATAA
1 AATTATTATAATCATAATCAAGATTAC-ATTCA-T--ATAATTAACTAATAA
13484354 ATTATAATAT
Statistics
Matches: 45, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
49 6 0.13
50 4 0.09
51 16 0.36
52 19 0.42
ACGTcount: A:0.49, C:0.11, G:0.03, T:0.38
Consensus pattern (50 bp):
AATTATTATAATCATAATCAAGATTACATTCATATAATTAACTAATAATC
Found at i:13500294 original size:12 final size:12
Alignment explanation
Indices: 13500277--13500301 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
13500267 TTTTTGTTTT
13500277 AAAGAATATAAA
1 AAAGAATATAAA
13500289 AAAGAATATAAA
1 AAAGAATATAAA
13500301 A
1 A
13500302 GATAAAANNN
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (12 bp):
AAAGAATATAAA
Found at i:13515152 original size:12 final size:13
Alignment explanation
Indices: 13515128--13515166 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 13
13515118 TAAGAATTTA
*
13515128 ATATATATA-TAT
1 ATATCTATACTAT
13515140 ATATCTAT-CTAT
1 ATATCTATACTAT
13515152 ATATCTATACTAT
1 ATATCTATACTAT
13515165 AT
1 AT
13515167 TAAAAAACGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
12 18 0.75
13 6 0.25
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (13 bp):
ATATCTATACTAT
Found at i:13517055 original size:22 final size:22
Alignment explanation
Indices: 13517028--13517074 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
13517018 GTGAACAAAG
13517028 GTTTTAGTTTT-CTGAAAAATAA
1 GTTTTAGTTTTGC-GAAAAATAA
*
13517050 GTTTTAGTTTTGCGGAAAATAA
1 GTTTTAGTTTTGCGAAAAATAA
13517072 GTT
1 GTT
13517075 CTTCTCTGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 22 0.96
23 1 0.04
ACGTcount: A:0.32, C:0.04, G:0.19, T:0.45
Consensus pattern (22 bp):
GTTTTAGTTTTGCGAAAAATAA
Found at i:13518569 original size:12 final size:12
Alignment explanation
Indices: 13518552--13518576 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
13518542 TTTTTGTTTT
13518552 AAAGAATATAAA
1 AAAGAATATAAA
13518564 AAAGAATATAAA
1 AAAGAATATAAA
13518576 A
1 A
13518577 GATAAACACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (12 bp):
AAAGAATATAAA
Found at i:13519700 original size:2 final size:2
Alignment explanation
Indices: 13519693--13519728 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
13519683 ATTAGTTGGA
*
13519693 AT AT AT AT AT AT AT AT AT AT AT AG 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
13519729 TTGTATACTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 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:13520745 original size:23 final size:25
Alignment explanation
Indices: 13520688--13520748 Score: 72
Period size: 23 Copynumber: 2.5 Consensus size: 25
13520678 TATATATTTT
*
13520688 AAAAATTATTTATTTGAATTTAAATG
1 AAAATTTATTT-TTTGAATTTAAATG
* *
13520714 CAAATTTATTTTTTG-TTTTAAA-G
1 AAAATTTATTTTTTGAATTTAAATG
13520737 AAAATTTATTTT
1 AAAATTTATTTT
13520749 GCTTTCAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
23 12 0.39
24 6 0.19
25 4 0.13
26 9 0.29
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.52
Consensus pattern (25 bp):
AAAATTTATTTTTTGAATTTAAATG
Found at i:13529998 original size:28 final size:28
Alignment explanation
Indices: 13529949--13530007 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
13529939 AATAAAATTA
* *
13529949 TAAATTTAAATATTATACTAAAATATTT
1 TAAATTTAAATATTACACTAAAACATTT
13529977 TAAATTTTAAATATTACA-TAAAACATTT
1 TAAA-TTTAAATATTACACTAAAACATTT
13530005 TAA
1 TAA
13530008 TCCTACTCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 16 0.57
29 12 0.43
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (28 bp):
TAAATTTAAATATTACACTAAAACATTT
Found at i:13532787 original size:2 final size:2
Alignment explanation
Indices: 13532780--13532805 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
13532770 AGTTGTATGA
13532780 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
13532806 TCATATCTAT
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:13533314 original size:21 final size:21
Alignment explanation
Indices: 13533287--13533334 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
13533277 CCTTTGTTGT
*
13533287 TTTTTTTTAA-TTATTTTTTA
1 TTTTTTTAAATTTATTTTTTA
13533307 TGTTTTTTAAATTTATTTTTTA
1 T-TTTTTTAAATTTATTTTTTA
13533329 TTTTTT
1 TTTTTT
13533335 ATTTTTGAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 1 0.04
21 13 0.52
22 11 0.44
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (21 bp):
TTTTTTTAAATTTATTTTTTA
Found at i:13545163 original size:19 final size:19
Alignment explanation
Indices: 13545117--13545183 Score: 66
Period size: 19 Copynumber: 3.5 Consensus size: 19
13545107 ATCAATACTT
* *
13545117 TTAATTATATAATATT-TA
1 TTAATAATATATTATTATA
13545135 TTAATAAATATATTATTATA
1 TTAAT-AATATATTATTATA
* *
13545155 TAAATAATAT-TCTAATATA
1 TTAATAATATAT-TATTATA
13545174 TTAATAATAT
1 TTAATAATAT
13545184 TCTAAAAATA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
18 6 0.15
19 29 0.71
20 6 0.15
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (19 bp):
TTAATAATATATTATTATA
Found at i:13545181 original size:11 final size:11
Alignment explanation
Indices: 13545167--13545213 Score: 53
Period size: 11 Copynumber: 4.3 Consensus size: 11
13545157 AATAATATTC
13545167 TAATATATTAA
1 TAATATATTAA
13545178 TAATAT-TCTAA
1 TAATATAT-TAA
*
13545189 AAATAATATT-A
1 TAAT-ATATTAA
13545200 TAATATATTAA
1 TAATATATTAA
13545211 TAA
1 TAA
13545214 ATAATATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
10 6 0.20
11 20 0.67
12 3 0.10
13 1 0.03
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (11 bp):
TAATATATTAA
Found at i:13545184 original size:19 final size:19
Alignment explanation
Indices: 13545133--13545213 Score: 75
Period size: 19 Copynumber: 4.5 Consensus size: 19
13545123 ATATAATATT
*
13545133 TATTAATAAATATAT-TATTA
1 TATTAAT-AATAT-TCTAATA
*
13545153 TATAAATAATATTCTAATA
1 TATTAATAATATTCTAATA
13545172 TATTAATAATATTCT-A-A
1 TATTAATAATATTCTAATA
*
13545189 -A--AATAATATTATAATA
1 TATTAATAATATTCTAATA
13545205 TATTAATAA
1 TATTAATAA
13545214 ATAATATAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
14 10 0.20
15 1 0.02
16 2 0.04
17 2 0.04
18 2 0.04
19 28 0.55
20 6 0.12
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
TATTAATAATATTCTAATA
Found at i:13545193 original size:33 final size:34
Alignment explanation
Indices: 13545151--13545231 Score: 110
Period size: 33 Copynumber: 2.4 Consensus size: 34
13545141 AATATATTAT
* * *
13545151 TATATAAATAATATTCTAATATATTAAT-AATAT
1 TATAAAAATAATATTATAATATATTAATAAATAA
*
13545184 TCTAAAAATAATATTATAATATATTAATAAATAA
1 TATAAAAATAATATTATAATATATTAATAAATAA
13545218 TATAAAGAATAATA
1 TATAAA-AATAATA
13545232 AATAATTTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
33 25 0.61
34 9 0.22
35 7 0.17
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (34 bp):
TATAAAAATAATATTATAATATATTAATAAATAA
Found at i:13545195 original size:25 final size:25
Alignment explanation
Indices: 13545124--13545221 Score: 66
Period size: 23 Copynumber: 4.0 Consensus size: 25
13545114 CTTTTAATTA
13545124 TATAATATTTATTAATAAAT-ATATTAT
1 TATAATA--TATTAATAAATAATA-TAT
* **
13545151 TAT-ATA-AATAATATTCTAATATAT
1 TATAATATATTAATA-AATAATATAT
13545175 TAATAATAT-TCTAA-AAAT-A-ATAT
1 T-ATAATATAT-TAATAAATAATATAT
13545198 TATAATATATTAATAAATAATATA
1 TATAATATATTAATAAATAATATA
13545222 AAGAATAATA
Statistics
Matches: 55, Mismatches: 6, Indels: 22
0.66 0.07 0.27
Matches are distributed among these distances:
22 10 0.18
23 16 0.29
24 7 0.13
25 9 0.16
26 7 0.13
27 6 0.11
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
TATAATATATTAATAAATAATATAT
Found at i:13545311 original size:14 final size:15
Alignment explanation
Indices: 13545297--13545362 Score: 53
Period size: 15 Copynumber: 4.3 Consensus size: 15
13545287 TATTAAAATA
*
13545297 TAATTATTTTTATAT
1 TAATAATTTTTATAT
*
13545312 TAATAATTTTAATAAT
1 TAATAATTTTTAT-AT
*
13545328 AAATAATTTTTAATAT
1 TAATAATTTTT-ATAT
* **
13545344 T-TTAATAGTTATAT
1 TAATAATTTTTATAT
13545358 TAATA
1 TAATA
13545363 TTATTTGAAA
Statistics
Matches: 39, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
14 5 0.13
15 19 0.49
16 13 0.33
17 2 0.05
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (15 bp):
TAATAATTTTTATAT
Found at i:13545312 original size:35 final size:32
Alignment explanation
Indices: 13545232--13545314 Score: 85
Period size: 32 Copynumber: 2.5 Consensus size: 32
13545222 AAGAATAATA
* * * *
13545232 AATAATTTTATTTTAAGTATTTTTATAAACAT
1 AATATTTTTATATTAAATATTATTATAAACAT
* *
13545264 AATATTTTAATATTAAATATTATTATTAAAATAT
1 AATATTTTTATATTAAATATTATTA-T-AAACAT
13545298 AATTATTTTTATATTAA
1 AA-TATTTTTATATTAA
13545315 TAATTTTAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
32 20 0.49
33 1 0.02
34 7 0.17
35 13 0.32
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (32 bp):
AATATTTTTATATTAAATATTATTATAAACAT
Found at i:13545349 original size:34 final size:32
Alignment explanation
Indices: 13545225--13545350 Score: 93
Period size: 31 Copynumber: 3.8 Consensus size: 32
13545215 TAATATAAAG
13545225 AATAATAAATAA-TTTTAT-TTTAAGT-ATTTT
1 AATAATAAATAATTTTTATATTTAA-TAATTTT
* * *
13545255 TATAA-ACATAATATTTTAATATTAAATATTATTATT
1 AATAATAAATAAT-TTTT-ATATTTAATA--ATT-TT
*
13545291 AA-AATATAATTATTTTTATA-TTAATAATTTT
1 AATAATA-AATAATTTTTATATTTAATAATTTT
13545322 AATAATAAATAATTTTTAATATTTTAATA
1 AATAATAAATAATTTTT-ATA-TTTAATA
13545351 GTTATATTAA
Statistics
Matches: 74, Mismatches: 8, Indels: 24
0.70 0.08 0.23
Matches are distributed among these distances:
29 5 0.07
30 4 0.05
31 17 0.23
32 13 0.18
33 4 0.05
34 11 0.15
35 8 0.11
36 8 0.11
37 4 0.05
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.52
Consensus pattern (32 bp):
AATAATAAATAATTTTTATATTTAATAATTTT
Found at i:13545362 original size:34 final size:34
Alignment explanation
Indices: 13545262--13545362 Score: 84
Period size: 34 Copynumber: 2.9 Consensus size: 34
13545252 TTTTATAAAC
*
13545262 ATAATATTTTAATA-TTAAATATTATTATTAA-AAT
1 ATAAT-TTTTAATATTTTAATATTA-TATTAATAAT
* * * *
13545296 ATAATTATTT-TTATATTAATAATTTTAATAATAA-
1 ATAATT-TTTAATATTTTAAT-ATTATATTAATAAT
13545330 ATAATTTTTAATATTTTAATAGTTATATTAATA
1 ATAATTTTTAATATTTTAATA-TTATATTAATA
13545363 TTATTTGAAA
Statistics
Matches: 52, Mismatches: 9, Indels: 12
0.71 0.12 0.16
Matches are distributed among these distances:
33 7 0.13
34 40 0.77
35 5 0.10
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (34 bp):
ATAATTTTTAATATTTTAATATTATATTAATAAT
Found at i:13550141 original size:18 final size:19
Alignment explanation
Indices: 13550115--13550187 Score: 76
Period size: 19 Copynumber: 3.7 Consensus size: 19
13550105 AGTATAATTT
*
13550115 TATTTATAAATAATAT-TA
1 TATTAATAAATAATATATA
13550133 TATTAATAAATAAATATTAATA
1 TATTAATAAAT-AATA-T-ATA
*
13550155 TATTAATAAATAATATAAA
1 TATTAATAAATAATATATA
* *
13550174 GAATAATAAATAAT
1 TATTAATAAATAAT
13550188 TTTATTTTAA
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
18 10 0.21
19 18 0.38
20 2 0.04
21 4 0.09
22 13 0.28
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (19 bp):
TATTAATAAATAATATATA
Found at i:13550145 original size:22 final size:22
Alignment explanation
Indices: 13550120--13550172 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
13550110 AATTTTATTT
*
13550120 ATAAATAATATTATATTAATAA
1 ATAAATAATAATATATTAATAA
*
13550142 ATAAATATTAATATATTAATAA
1 ATAAATAATAATATATTAATAA
13550164 ATAATATAA
1 ATAA-ATAA
13550173 AGAATAATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 24 0.89
23 3 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
ATAAATAATAATATATTAATAA
Found at i:13550180 original size:27 final size:27
Alignment explanation
Indices: 13550127--13550181 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
13550117 TTTATAAATA
* * *
13550127 ATATTATATTAATAAATAAATATTAAT
1 ATATTATATAAATAAATAAAGAATAAT
13550154 ATATTA-ATAAATAATATAAAGAATAAT
1 ATATTATATAAATAA-ATAAAGAATAAT
13550181 A
1 A
13550182 AATAATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 7 0.29
27 17 0.71
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (27 bp):
ATATTATATAAATAAATAAAGAATAAT
Found at i:13550229 original size:19 final size:18
Alignment explanation
Indices: 13550202--13550323 Score: 72
Period size: 19 Copynumber: 6.6 Consensus size: 18
13550192 TTTTAAGTAT
*
13550202 TTTTTATATTAACATAATA
1 TTTTAATATTAA-ATAATA
*
13550221 TTTTAATATTAAATATTA
1 TTTTAATATTAAATAATA
* * *
13550239 TTATTAA-AATATAATTATT
1 TT-TTAATATTA-AATAATA
*
13550258 TTTTAATATT-AATAATT
1 TTTTAATATTAAATAATA
*
13550275 TTATAATAAATATTTCAAT-ATA
1 TT-T--T-AATA-TTAAATAATA
*
13550297 TTTTAATAATAAATAAT-
1 TTTTAATATTAAATAATA
13550314 TTTTAATATT
1 TTTTAATATT
13550324 TTAATAGTTA
Statistics
Matches: 81, Mismatches: 12, Indels: 22
0.70 0.10 0.19
Matches are distributed among these distances:
17 21 0.26
18 21 0.26
19 24 0.30
20 1 0.01
21 5 0.06
22 6 0.07
23 3 0.04
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTTAATATTAAATAATA
Found at i:13550270 original size:17 final size:17
Alignment explanation
Indices: 13550194--13550282 Score: 63
Period size: 17 Copynumber: 5.0 Consensus size: 17
13550184 TAATTTTATT
*
13550194 TTAAGTATTTTTT-ATA
1 TTAATTATTTTTTAATA
* *
13550210 TTAACATAATATTTTAATA
1 TT-A-ATTATTTTTTAATA
* *
13550229 TTAAATATTATTATTAAAA
1 TTAATTATT-TT-TTAATA
13550248 TATAATTATTTTTTAATA
1 T-TAATTATTTTTTAATA
* *
13550266 TTAATAATTTTATAATA
1 TTAATTATTTTTTAATA
13550283 AATATTTCAA
Statistics
Matches: 56, Mismatches: 11, Indels: 11
0.72 0.14 0.14
Matches are distributed among these distances:
16 2 0.04
17 18 0.32
18 16 0.29
19 13 0.23
20 7 0.12
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (17 bp):
TTAATTATTTTTTAATA
Found at i:13550272 original size:20 final size:19
Alignment explanation
Indices: 13550199--13550274 Score: 59
Period size: 18 Copynumber: 4.1 Consensus size: 19
13550189 TTATTTTAAG
*
13550199 TATTTTTT-ATATTAACAT
1 TATTTTTTAATATTAAAAT
* *
13550217 AATATTTTAATATTAAATAT
1 TATTTTTTAATATTAAA-AT
* * *
13550237 TA-TTATTAA-AATATAAT
1 TATTTTTTAATATTAAAAT
13550254 TATTTTTTAATATTAATAAT
1 TATTTTTTAATATTAA-AAT
13550274 T
1 T
13550275 TTATAATAAA
Statistics
Matches: 42, Mismatches: 11, Indels: 8
0.69 0.18 0.13
Matches are distributed among these distances:
17 4 0.10
18 16 0.38
19 15 0.36
20 7 0.17
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.55
Consensus pattern (19 bp):
TATTTTTTAATATTAAAAT
Found at i:13550307 original size:25 final size:26
Alignment explanation
Indices: 13550268--13550329 Score: 78
Period size: 25 Copynumber: 2.5 Consensus size: 26
13550258 TTTTAATATT
13550268 AATA-ATTTT-ATAATAAAT-ATTTC
1 AATATATTTTAATAATAAATAATTTC
*
13550291 AATATATTTTAATAATAAATAATTTT
1 AATATATTTTAATAATAAATAATTTC
*
13550317 TA-ATATTTTAATA
1 AATATATTTTAATA
13550330 GTTATATTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 4 0.12
24 5 0.15
25 20 0.59
26 5 0.15
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (26 bp):
AATATATTTTAATAATAAATAATTTC
Found at i:13550317 original size:17 final size:17
Alignment explanation
Indices: 13550175--13550321 Score: 54
Period size: 19 Copynumber: 8.2 Consensus size: 17
13550165 TAATATAAAG
13550175 AATAATAAATAA-TTTT
1 AATAATAAATAATTTTT
** *
13550191 -ATTTTAAGT-ATTTTT
1 AATAATAAATAATTTTT
* *
13550206 TATATTAACATAATATTTT
1 AATAATAA-ATAAT-TTTT
* *
13550225 AATATTAAATATTATTATT
1 AATAATAAATA--ATTTTT
*
13550244 AA-AATATAATTATTTTTT
1 AATAATA-AA-TAATTTTT
*
13550262 AAT-ATTAATAATTTTAT
1 AATAATAAATAATTTT-T
13550279 AATAAATATTTCAAT-ATATTTT
1 AAT-AATA----AATAAT-TTTT
13550301 AATAATAAATAATTTTT
1 AATAATAAATAATTTTT
13550318 AATA
1 AATA
13550322 TTTTAATAGT
Statistics
Matches: 99, Mismatches: 13, Indels: 37
0.66 0.09 0.25
Matches are distributed among these distances:
14 1 0.01
15 10 0.10
16 12 0.12
17 18 0.18
18 18 0.18
19 20 0.20
20 4 0.04
21 4 0.04
22 6 0.06
23 6 0.06
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (17 bp):
AATAATAAATAATTTTT
Found at i:13550321 original size:39 final size:38
Alignment explanation
Indices: 13550218--13550321 Score: 106
Period size: 39 Copynumber: 2.7 Consensus size: 38
13550208 TATTAACATA
* * *
13550218 ATATTTTAATATTAAAT-ATTATTATTAAAATATAATT
1 ATATTTTAATAATAAATAATTTTTAATAAAATATAATT
* * *
13550255 ATTTTTTAAT-ATTAATAATTTTATAATAAATATTTCAA-T
1 ATATTTTAATAATAAATAATTTT-TAATAAA-ATAT-AATT
13550294 ATATTTTAATAATAAATAATTTTTAATA
1 ATATTTTAATAATAAATAATTTTTAATA
13550322 TTTTAATAGT
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
36 4 0.07
37 13 0.24
38 6 0.11
39 18 0.33
40 13 0.24
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (38 bp):
ATATTTTAATAATAAATAATTTTTAATAAAATATAATT
Found at i:13554844 original size:24 final size:24
Alignment explanation
Indices: 13554813--13554867 Score: 94
Period size: 23 Copynumber: 2.3 Consensus size: 24
13554803 TTCAAAAAAA
*
13554813 TTTATTTCCTTTTAACAA-TTAAG
1 TTTATTTTCTTTTAACAATTTAAG
13554836 TTTATTTTCTTTTAACAATTTAAG
1 TTTATTTTCTTTTAACAATTTAAG
13554860 TTTATTTT
1 TTTATTTT
13554868 TAATGATACA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 17 0.57
24 13 0.43
ACGTcount: A:0.27, C:0.09, G:0.04, T:0.60
Consensus pattern (24 bp):
TTTATTTTCTTTTAACAATTTAAG
Found at i:13567359 original size:25 final size:25
Alignment explanation
Indices: 13567326--13567397 Score: 74
Period size: 25 Copynumber: 2.8 Consensus size: 25
13567316 AATAAACAAT
13567326 AAATTTTAATTAAAATTTAATTTTA
1 AAATTTTAATTAAAATTTAATTTTA
* * *
13567351 AAATATTAATATAAAA-ATATTTTTA
1 AAATTTTAAT-TAAAATTTAATTTTA
* *
13567376 ACATTTTAATAACAAATTTAAT
1 AAATTTTAATTA-AAATTTAAT
13567398 AATAGGTAAA
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
24 1 0.03
25 27 0.75
26 8 0.22
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (25 bp):
AAATTTTAATTAAAATTTAATTTTA
Found at i:13568702 original size:12 final size:12
Alignment explanation
Indices: 13568687--13568752 Score: 73
Period size: 12 Copynumber: 5.3 Consensus size: 12
13568677 ATTTTTAATA
13568687 TAAATATAAAAT
1 TAAATATAAAAT
13568699 TAAATATATATAA-
1 TAAATATA-A-AAT
*
13568712 AAATATATAAAAT
1 TAA-ATATAAAAT
13568725 TAAATATAAAAT
1 TAAATATAAAAT
13568737 TAAATA-AATAAT
1 TAAATATAA-AAT
13568749 TAAA
1 TAAA
13568753 AAATAAATTT
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
11 2 0.04
12 32 0.68
13 6 0.13
14 7 0.15
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
TAAATATAAAAT
Found at i:13568761 original size:12 final size:13
Alignment explanation
Indices: 13568695--13568761 Score: 54
Period size: 12 Copynumber: 5.4 Consensus size: 13
13568685 TATAAATATA
*
13568695 AAATTAAATATAT
1 AAATTAAATAAAT
*
13568708 ATAA--AAATATAT
1 A-AATTAAATAAAT
*
13568720 AAAATTAAATATA-
1 -AAATTAAATAAAT
13568733 AAATTAAATAAAT
1 AAATTAAATAAAT
13568746 -AATTAAA-AAAT
1 AAATTAAATAAAT
13568757 AAATT
1 AAATT
13568762 TTTTATATAT
Statistics
Matches: 47, Mismatches: 1, Indels: 13
0.77 0.02 0.21
Matches are distributed among these distances:
11 4 0.09
12 32 0.68
13 2 0.04
14 9 0.19
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
AAATTAAATAAAT
Found at i:13569840 original size:3 final size:3
Alignment explanation
Indices: 13569827--13569880 Score: 90
Period size: 3 Copynumber: 17.7 Consensus size: 3
13569817 CGAGTCTTTT
13569827 ATA ATTA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
13569873 ATA CTA AT
1 ATA ATA AT
13569881 GCTAATATAT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 45 0.94
4 3 0.06
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:13571299 original size:17 final size:17
Alignment explanation
Indices: 13571277--13571309 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
13571267 AAAAAAAAGT
13571277 ATAAAAAAATAATAATA
1 ATAAAAAAATAATAATA
*
13571294 ATAAAAAATTAATAAT
1 ATAAAAAAATAATAAT
13571310 TTCTTTAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
ATAAAAAAATAATAATA
Found at i:13571467 original size:15 final size:14
Alignment explanation
Indices: 13571447--13571613 Score: 72
Period size: 15 Copynumber: 11.7 Consensus size: 14
13571437 CGTTTTCTTT
*
13571447 AAACCCTAAATTTCA
1 AAACCCTAAAATT-A
13571462 AAACCCTAAAATTA
1 AAACCCTAAAATTA
* *
13571476 AAACCTTAAAA-TC
1 AAACCCTAAAATTA
* * *
13571489 AAACCCCAAACACCTC
1 AAACCCTAAA-A-TTA
**
13571505 AAACCCTAAAA-CG
1 AAACCCTAAAATTA
* *
13571518 AAACTCC-AAACCTTC
1 AAAC-CCTAAA-ATTA
*
13571533 AAACCCTAAAA-TG
1 AAACCCTAAAATTA
* * *
13571546 AAACCCCAAACCTTT
1 AAACCCTAAA-ATTA
*
13571561 AAACCTTAAAATTA
1 AAACCCTAAAATTA
* * *
13571575 AAACTCTAAACCTTC
1 AAACCCTAAA-ATTA
*
13571590 AAACCCTAAAATCA
1 AAACCCTAAAATTA
13571604 AAACCCTAAA
1 AAACCCTAAA
13571614 CCTTATAAAC
Statistics
Matches: 114, Mismatches: 28, Indels: 21
0.70 0.17 0.13
Matches are distributed among these distances:
13 26 0.23
14 37 0.32
15 40 0.35
16 11 0.10
ACGTcount: A:0.50, C:0.31, G:0.01, T:0.19
Consensus pattern (14 bp):
AAACCCTAAAATTA
Found at i:13571508 original size:29 final size:28
Alignment explanation
Indices: 13571476--13571770 Score: 206
Period size: 29 Copynumber: 10.4 Consensus size: 28
13571466 CCTAAAATTA
* *
13571476 AAACCTTAAAATCAAACCCCAAACACCTC
1 AAACCCTAAAATCAAACCCCAAAC-CTTC
*
13571505 AAACCCTAAAA-CGAAACTCCAAACCTTC
1 AAACCCTAAAATC-AAACCCCAAACCTTC
* *
13571533 AAACCCTAAAATGAAACCCCAAACCTTT
1 AAACCCTAAAATCAAACCCCAAACCTTC
* * * *
13571561 AAACCTTAAAATTAAAACTCTAAACCTTC
1 AAACCCTAAAA-TCAAACCCCAAACCTTC
* *
13571590 AAACCCTAAAATCAAAACCCTAAACCTTAT
1 AAACCCTAAAATC-AAACCCCAAACCTT-C
* *
13571620 AAACCCT-TAATCAAAACCCCAAATCTT-
1 AAACCCTAAAATC-AAACCCCAAACCTTC
* * *
13571647 AAACCTTAAAAGTAAAACTCCAAACCTTC
1 AAACCCTAAAA-TCAAACCCCAAACCTTC
* * ***
13571676 AAACACTAAAATTAAACTGTAAATCC-TC
1 AAACCCTAAAATCAAACCCCAAA-CCTTC
* ** *
13571704 TAAACCCTAAAACCAAAACTTCAAATC-TC
1 -AAACCCTAAAATC-AAACCCCAAACCTTC
* *
13571733 AAACCTTAAAATCAAAACCCCAAATC-TC
1 AAACCCTAAAATC-AAACCCCAAACCTTC
13571761 AAACCCTAAA
1 AAACCCTAAA
13571771 CCCCAAAATC
Statistics
Matches: 216, Mismatches: 39, Indels: 23
0.78 0.14 0.08
Matches are distributed among these distances:
27 6 0.03
28 97 0.45
29 98 0.45
30 15 0.07
ACGTcount: A:0.48, C:0.31, G:0.01, T:0.20
Consensus pattern (28 bp):
AAACCCTAAAATCAAACCCCAAACCTTC
Found at i:13571543 original size:57 final size:57
Alignment explanation
Indices: 13571476--13571770 Score: 217
Period size: 57 Copynumber: 5.2 Consensus size: 57
13571466 CCTAAAATTA
* *
13571476 AAACCTTAAAATCAAACCCCAAACACCTCAAACCCTAAAA-CGAAACTCCAAACCTTC
1 AAACCCTAAAATCAAACCCCAAAC-CCTCAAACCCTAAAATCAAAACTCCAAACCTTC
* * * * * *
13571533 AAACCCTAAAATGAAACCCCAAACCTTTAAACCTTAAAATTAAAACTCTAAACCTTC
1 AAACCCTAAAATCAAACCCCAAACCCTCAAACCCTAAAATCAAAACTCCAAACCTTC
* * * * * *
13571590 AAACCCTAAAATCAAAACCCTAAACCTTATAAACCCT-TAATCAAAACCCCAAATCTT-
1 AAACCCTAAAATC-AAACCCCAAACCCT-CAAACCCTAAAATCAAAACTCCAAACCTTC
* * * * * * **
13571647 AAACCTTAAAAGTAAAACTCCAAACCTTCAAACACTAAAAT-TAAACTGTAAATCC-TC
1 AAACCCTAAAA-TCAAACCCCAAACCCTCAAACCCTAAAATCAAAACTCCAAA-CCTTC
* ** * * * *
13571704 TAAACCCTAAAACCAAAACTTCAAA-TCTCAAACCTTAAAATCAAAACCCCAAATC-TC
1 -AAACCCTAAAATC-AAACCCCAAACCCTCAAACCCTAAAATCAAAACTCCAAACCTTC
13571761 AAACCCTAAA
1 AAACCCTAAA
13571771 CCCCAAAATC
Statistics
Matches: 187, Mismatches: 41, Indels: 21
0.75 0.16 0.08
Matches are distributed among these distances:
56 36 0.19
57 89 0.48
58 55 0.29
59 7 0.04
ACGTcount: A:0.48, C:0.31, G:0.01, T:0.20
Consensus pattern (57 bp):
AAACCCTAAAATCAAACCCCAAACCCTCAAACCCTAAAATCAAAACTCCAAACCTTC
Found at i:13571657 original size:86 final size:86
Alignment explanation
Indices: 13571443--13571770 Score: 312
Period size: 86 Copynumber: 3.8 Consensus size: 86
13571433 TTCACGTTTT
* * * * *
13571443 CTTTAAACCCTAAATTTCAAAACCCTAAAAT-TAAAACCTTAAAA-TCAAACCCCAAACACCTCA
1 CTTTAAACCCTAAA-ATCAAAACCC-CAAATCTTAAACCTTAAAATTAAAACCCCAAAC-CTTCA
*
13571506 AACCCTAAAA-CGAAACTCC-AAAC
63 AACCCTAAAATCAAAAC-CCTAAAC
* * * * *
13571529 CTTCAAACCCTAAAAT-GAAACCCCAAACCTTTAAACCTTAAAATTAAAACTCTAAACCTTCAAA
1 CTTTAAACCCTAAAATCAAAACCCCAAATC-TTAAACCTTAAAATTAAAACCCCAAACCTTCAAA
13571593 CCCTAAAATCAAAACCCTAAAC
65 CCCTAAAATCAAAACCCTAAAC
* * *
13571615 CTTATAAACCCT-TAATCAAAACCCCAAATCTTAAACCTTAAAAGTAAAACTCCAAACCTTCAAA
1 CTT-TAAACCCTAAAATCAAAACCCCAAATCTTAAACCTTAAAATTAAAACCCCAAACCTTCAAA
* * **
13571679 CACTAAAAT-TAAACTGTAAATC
65 CCCTAAAATCAAAACCCTAAA-C
* * ** * * *
13571701 CTCTAAACCCTAAAACCAAAACTTCAAATCTCAAACCTTAAAATCAAAACCCCAAATC-TCAAAC
1 CTTTAAACCCTAAAATCAAAACCCCAAATCTTAAACCTTAAAATTAAAACCCCAAACCTTCAAAC
13571765 CCTAAA
66 CCTAAA
13571771 CCCCAAAATC
Statistics
Matches: 201, Mismatches: 32, Indels: 19
0.80 0.13 0.08
Matches are distributed among these distances:
83 3 0.01
84 6 0.03
85 56 0.28
86 118 0.59
87 18 0.09
ACGTcount: A:0.48, C:0.30, G:0.01, T:0.21
Consensus pattern (86 bp):
CTTTAAACCCTAAAATCAAAACCCCAAATCTTAAACCTTAAAATTAAAACCCCAAACCTTCAAAC
CCTAAAATCAAAACCCTAAAC
Found at i:13571812 original size:21 final size:21
Alignment explanation
Indices: 13571780--13571839 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
13571770 ACCCCAAAAT
13571780 CTAAAA-CTCGAAAACCTAACC
1 CTAAAATC-CGAAAACCTAACC
** *
13571801 CTAAAATCCGAAATGTCAAACC
1 CTAAAATCCGAAA-ACCTAACC
*
13571823 CTAAAATCCAAAAACCT
1 CTAAAATCCGAAAACCT
13571840 CAAAATTCAA
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
21 12 0.40
22 18 0.60
ACGTcount: A:0.48, C:0.30, G:0.05, T:0.17
Consensus pattern (21 bp):
CTAAAATCCGAAAACCTAACC
Found at i:13571825 original size:28 final size:27
Alignment explanation
Indices: 13571754--13571826 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 27
13571744 TCAAAACCCC
*
13571754 AAATCTCAAACCCTAAACCCCAAAATCT
1 AAATCTCAAACCCT-AACCCCAAAATCG
* * *
13571782 AAAACTCGAAAACCTAACCCTAAAATCCG
1 AAATCTC-AAACCCTAACCCCAAAAT-CG
*
13571811 AAATGTCAAACCCTAA
1 AAATCTCAAACCCTAA
13571827 AATCCAAAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
28 24 0.67
29 12 0.33
ACGTcount: A:0.48, C:0.32, G:0.04, T:0.16
Consensus pattern (27 bp):
AAATCTCAAACCCTAACCCCAAAATCG
Found at i:13573574 original size:13 final size:16
Alignment explanation
Indices: 13573534--13573580 Score: 85
Period size: 16 Copynumber: 2.9 Consensus size: 16
13573524 AATAATTTGG
13573534 TAAATAATAATACTTA
1 TAAATAATAATACTTA
13573550 TAAATAATAATACTTA
1 TAAATAATAATACTTA
*
13573566 TAAAAAATAATACTT
1 TAAATAATAATACTT
13573581 TAATATCAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.36
Consensus pattern (16 bp):
TAAATAATAATACTTA
Found at i:13576404 original size:28 final size:28
Alignment explanation
Indices: 13576373--13576442 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 28
13576363 GCCTGGTTGC
* * *
13576373 AATTCAATTGGGCTTCAGGCCCGATTTT
1 AATTCAACTGGGCTTCAAGCCCAATTTT
13576401 AATTCAACTGGGCTTCAAGCCCAATTTT
1 AATTCAACTGGGCTTCAAGCCCAATTTT
*
13576429 AATTTTAACTGGGC
1 AA-TTCAACTGGGC
13576443 CAAAAGTGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
28 27 0.73
29 10 0.27
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (28 bp):
AATTCAACTGGGCTTCAAGCCCAATTTT
Found at i:13577925 original size:11 final size:11
Alignment explanation
Indices: 13577908--13577941 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
13577898 TTTCAATACA
13577908 ATAAAAAAATT
1 ATAAAAAAATT
* *
13577919 TTAAAAAAATA
1 ATAAAAAAATT
13577930 ATAAAAAAATT
1 ATAAAAAAATT
13577941 A
1 A
13577942 ATTAATAAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (11 bp):
ATAAAAAAATT
Found at i:13577935 original size:20 final size:20
Alignment explanation
Indices: 13577891--13577936 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
13577881 AGTATTTATT
* *
13577891 AAAAAATTTTCAATACAATA
1 AAAAAATTTTCAAAAAAATA
13577911 AAAAAATTTT-AAAAAAATA
1 AAAAAATTTTCAAAAAAATA
13577930 ATAAAAA
1 A-AAAAA
13577937 AATTAATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (20 bp):
AAAAAATTTTCAAAAAAATA
Found at i:13579085 original size:22 final size:21
Alignment explanation
Indices: 13579060--13579107 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
13579050 ATTAATAACT
*
13579060 TAATAAGTGAATGATAATTTAA
1 TAATAAATGAATGATAA-TTAA
* *
13579082 TAATAAATTAGTGATAATTAA
1 TAATAAATGAATGATAATTAA
13579103 TAATA
1 TAATA
13579108 GTTCAATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (21 bp):
TAATAAATGAATGATAATTAA
Found at i:13579224 original size:22 final size:22
Alignment explanation
Indices: 13579196--13579305 Score: 73
Period size: 22 Copynumber: 5.0 Consensus size: 22
13579186 GTAAATCAAT
* *
13579196 ATAACTTATTAATAAATAATTA
1 ATAACTTAATAATAAATAATGA
* *
13579218 ATAACTTAATAGTAAATTATGA
1 ATAACTTAATAATAAATAATGA
*
13579240 ATAATTTAAT-ATAAATAAGTG-
1 ATAACTTAATAATAAATAA-TGA
* * * * *
13579261 ATAAGTTGATAGTTAATCAT-A
1 ATAACTTAATAATAAATAATGA
*
13579282 GATAATTTAATAATAAATCAATGA
1 -ATAACTTAATAATAAAT-AATGA
13579306 GAATTTTATA
Statistics
Matches: 65, Mismatches: 17, Indels: 10
0.71 0.18 0.11
Matches are distributed among these distances:
21 15 0.23
22 47 0.72
23 2 0.03
24 1 0.02
ACGTcount: A:0.51, C:0.04, G:0.08, T:0.37
Consensus pattern (22 bp):
ATAACTTAATAATAAATAATGA
Found at i:13579254 original size:43 final size:44
Alignment explanation
Indices: 13579180--13579299 Score: 120
Period size: 43 Copynumber: 2.8 Consensus size: 44
13579170 CATTAGAAAT
* * * * *
13579180 TTAAAAGTAAATCA-ATATAACTTATTAATAAATAATTAATAAC
1 TTAATAGTAAATCATAGATAATTTAATAATAAATAAGTAATAAC
* * *
13579223 TTAATAGTAAATTAT-GAATAATTTAAT-ATAAATAAGTGATAAG
1 TTAATAGTAAATCATAG-ATAATTTAATAATAAATAAGTAATAAC
* *
13579266 TTGATAGTTAATCATAGATAATTTAATAATAAAT
1 TTAATAGTAAATCATAGATAATTTAATAATAAAT
13579300 CAATGAGAAT
Statistics
Matches: 62, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
43 47 0.76
44 15 0.24
ACGTcount: A:0.52, C:0.03, G:0.07, T:0.38
Consensus pattern (44 bp):
TTAATAGTAAATCATAGATAATTTAATAATAAATAAGTAATAAC
Found at i:13579310 original size:22 final size:23
Alignment explanation
Indices: 13579223--13579349 Score: 72
Period size: 22 Copynumber: 5.7 Consensus size: 23
13579213 AATTAATAAC
*
13579223 TTAATAGTAAAT-TAT-GAATAAT
1 TTAATAGTAAATCAATCGAA-AAT
* *
13579245 TTAATA-TAAAT-AAGT-GATAAG
1 TTAATAGTAAATCAA-TCGAAAAT
* * * *
13579266 TTGATAGTTAATC-ATAGATAAT
1 TTAATAGTAAATCAATCGAAAAT
* *
13579288 TTAATAATAAATCAAT-GAGAAT
1 TTAATAGTAAATCAATCGAAAAT
*
13579310 TTTATAGTAAAT-AATCGAAAAT
1 TTAATAGTAAATCAATCGAAAAT
*
13579332 TAAATAGTAAAATCAATC
1 TTAATAGT-AAATCAATC
13579350 NNNNNNNNNN
Statistics
Matches: 82, Mismatches: 15, Indels: 14
0.74 0.14 0.13
Matches are distributed among these distances:
21 17 0.21
22 55 0.67
23 6 0.07
24 4 0.05
ACGTcount: A:0.50, C:0.04, G:0.10, T:0.35
Consensus pattern (23 bp):
TTAATAGTAAATCAATCGAAAAT
Found at i:13583718 original size:25 final size:25
Alignment explanation
Indices: 13583685--13583756 Score: 74
Period size: 25 Copynumber: 2.8 Consensus size: 25
13583675 AATAAATAAT
13583685 AAATTTTAATTAAAATTTAATTTTA
1 AAATTTTAATTAAAATTTAATTTTA
* * *
13583710 AAATATTAATATAAAA-ATATTTTTA
1 AAATTTTAAT-TAAAATTTAATTTTA
* *
13583735 ACATTTTAATAACAAATTTAAT
1 AAATTTTAATTA-AAATTTAAT
13583757 AATAGGTAAA
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
24 1 0.03
25 27 0.75
26 8 0.22
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (25 bp):
AAATTTTAATTAAAATTTAATTTTA
Found at i:13584516 original size:13 final size:14
Alignment explanation
Indices: 13584483--13584516 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
13584473 CATGGGATTT
13584483 TTTTAAAAAATATA
1 TTTTAAAAAATATA
*
13584497 TTATAAAAAATA-A
1 TTTTAAAAAATATA
13584510 TTTTAAA
1 TTTTAAA
13584517 TTGAATAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TTTTAAAAAATATA
Found at i:13585106 original size:12 final size:13
Alignment explanation
Indices: 13585053--13585121 Score: 67
Period size: 12 Copynumber: 5.4 Consensus size: 13
13585043 ATATTATTTT
13585053 TAATATAAATATAA
1 TAAT-TAAATATAA
13585067 -AATTAAATATATA
1 TAATTAAATATA-A
13585080 TAA--AAATATATA
1 TAATTAAATATA-A
13585092 TAATTAAATA-AA
1 TAATTAAATATAA
13585104 TAATTCAAA-ATAA
1 TAATT-AAATATAA
13585117 TAATT
1 TAATT
13585122 TTTTTATATA
Statistics
Matches: 49, Mismatches: 0, Indels: 13
0.79 0.00 0.21
Matches are distributed among these distances:
12 27 0.55
13 15 0.31
14 7 0.14
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.36
Consensus pattern (13 bp):
TAATTAAATATAA
Found at i:13586195 original size:3 final size:3
Alignment explanation
Indices: 13586182--13586236 Score: 83
Period size: 3 Copynumber: 18.0 Consensus size: 3
13586172 CGAGTCTTTT
*
13586182 ATA ATTA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA CTA
1 ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
13586228 ATA CTA ATA
1 ATA ATA ATA
13586237 TATATTTTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
3 44 0.94
4 3 0.06
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:13587470 original size:42 final size:41
Alignment explanation
Indices: 13587399--13587480 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 41
13587389 AAAATGAAAA
*
13587399 TAAAATAGGATAATAACTAATAATTAAAAATATTAAAAATGC
1 TAAAATA-GATAATAACTAATAATTAAAAATAATAAAAATGC
13587441 TAAAATA-ATAATAA-TAATAATTTAAAAAAATAATAAAAAT
1 TAAAATAGATAATAACTAATAA-TT--AAAAATAATAAAAAT
13587481 TGAATATTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
39 6 0.17
40 9 0.25
42 21 0.58
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (41 bp):
TAAAATAGATAATAACTAATAATTAAAAATAATAAAAATGC
Found at i:13587813 original size:14 final size:15
Alignment explanation
Indices: 13587780--13587824 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
13587770 CGTTTTCTTT
*
13587780 AAACCCTAAATTTCA
1 AAACCCTAAAATTCA
13587795 AAACCCTAAAATT-A
1 AAACCCTAAAATTCA
*
13587809 AAACCTTAAAA-TCA
1 AAACCCTAAAATTCA
13587823 AA
1 AA
13587825 CCCCAAACAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
13 1 0.04
14 14 0.52
15 12 0.44
ACGTcount: A:0.56, C:0.22, G:0.00, T:0.22
Consensus pattern (15 bp):
AAACCCTAAAATTCA
Found at i:13587838 original size:9 final size:9
Alignment explanation
Indices: 13587824--13587850 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
13587814 TTAAAATCAA
13587824 ACCCCAAAC
1 ACCCCAAAC
13587833 ACCCCAAAC
1 ACCCCAAAC
13587842 ACCCCAAAC
1 ACCCCAAAC
13587851 CCTAAAACGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.56, G:0.00, T:0.00
Consensus pattern (9 bp):
ACCCCAAAC
Found at i:13587921 original size:57 final size:57
Alignment explanation
Indices: 13587846--13588112 Score: 217
Period size: 57 Copynumber: 4.7 Consensus size: 57
13587836 CCAAACACCC
** *
13587846 CAAACCCTAAAA-CGAAACTCTAAACCTTCAAACCCTAAAATGAAACCCCAAACCTT
1 CAAACCCTAAAATTAAAACTCTAAACCTTCAAACCCTAAAATAAAACCCCAAACCTT
* * *
13587902 TAAACCTTAAAATTAAAACTCTAAACCTTCAAACCCTAAAATCAAAACCCTAAACCTT
1 CAAACCCTAAAATTAAAACTCTAAACCTTCAAACCCTAAAAT-AAAACCCCAAACCTT
* * * * * * *
13587960 ACAAACCCT-CAATCAAAACCCCAAATCTT-AAACCTTAAAAGTAAAACTCCAAACCTT
1 -CAAACCCTAAAATTAAAACTCTAAACCTTCAAACCCTAAAA-TAAAACCCCAAACCTT
* ** *
13588017 CAAACCCTAAAATT-AAAC-CGTAAATCC-TCTAAACCCTAAAACCAAAACTTCAAATC-T
1 CAAACCCTAAAATTAAAACTC-TAAA-CCTTC-AAACCCTAAAA-TAAAACCCCAAACCTT
* * * * *
13588074 CAAACCTTAAAATCAAAACCCCAAATC-TCAAACCCTAAA
1 CAAACCCTAAAATTAAAACTCTAAACCTTCAAACCCTAAA
13588113 CCCCAAAATC
Statistics
Matches: 171, Mismatches: 29, Indels: 22
0.77 0.13 0.10
Matches are distributed among these distances:
55 1 0.01
56 36 0.21
57 70 0.41
58 57 0.33
59 7 0.04
ACGTcount: A:0.48, C:0.31, G:0.01, T:0.19
Consensus pattern (57 bp):
CAAACCCTAAAATTAAAACTCTAAACCTTCAAACCCTAAAATAAAACCCCAAACCTT
Found at i:13587926 original size:14 final size:14
Alignment explanation
Indices: 13587875--13588033 Score: 65
Period size: 14 Copynumber: 11.1 Consensus size: 14
13587865 CTAAACCTTC
*
13587875 AAACCCTAAAA-TG
1 AAACCCTAAAATTA
* * *
13587888 AAACCCCAAACCTTT
1 AAACCCTAAA-ATTA
*
13587903 AAACCTTAAAATTA
1 AAACCCTAAAATTA
* * *
13587917 AAACTCTAAACCTTC
1 AAACCCTAAA-ATTA
*
13587932 AAACCCTAAAATCA
1 AAACCCTAAAATTA
*
13587946 AAACCCTAAACCTTA
1 AAACCCTAAA-ATTA
* *
13587961 CAAACCCT-CAATCA
1 -AAACCCTAAAATTA
* *
13587975 AAACCC-CAAATCTT
1 AAACCCTAAAAT-TA
* *
13587989 AAACCTTAAAAGTA
1 AAACCCTAAAATTA
* *
13588003 AAACTCC-AAACCTTC
1 AAAC-CCTAAA-ATTA
13588018 AAACCCTAAAATTA
1 AAACCCTAAAATTA
13588032 AA
1 AA
13588034 CCGTAAATCC
Statistics
Matches: 102, Mismatches: 33, Indels: 21
0.65 0.21 0.13
Matches are distributed among these distances:
13 18 0.18
14 42 0.41
15 35 0.34
16 7 0.07
ACGTcount: A:0.49, C:0.30, G:0.01, T:0.20
Consensus pattern (14 bp):
AAACCCTAAAATTA
Found at i:13587930 original size:29 final size:29
Alignment explanation
Indices: 13587846--13588112 Score: 214
Period size: 28 Copynumber: 9.4 Consensus size: 29
13587836 CCAAACACCC
*
13587846 CAAACCCTAAAA-CGAAACTCTAAACCTT
1 CAAACCCTAAAATCAAAACTCTAAACCTT
* * *
13587874 CAAACCCTAAAAT-GAAACCCCAAACCTT
1 CAAACCCTAAAATCAAAACTCTAAACCTT
* * *
13587902 TAAACCTTAAAATTAAAACTCTAAACCTT
1 CAAACCCTAAAATCAAAACTCTAAACCTT
*
13587931 CAAACCCTAAAATCAAAACCCTAAACCTT
1 CAAACCCTAAAATCAAAACTCTAAACCTT
* * * *
13587960 ACAAACCCT-CAATCAAAACCCCAAATCTT
1 -CAAACCCTAAAATCAAAACTCTAAACCTT
* *
13587989 -AAACCTTAAAAGT-AAAACTCCAAACCTT
1 CAAACCCTAAAA-TCAAAACTCTAAACCTT
*
13588017 CAAACCCTAAAAT-TAAAC-CGTAAATCC-T
1 CAAACCCTAAAATCAAAACTC-TAAA-CCTT
* *
13588045 CTAAACCCTAAAACCAAAACT-TCAAATC-T
1 C-AAACCCTAAAATCAAAACTCT-AAACCTT
* * * *
13588074 CAAACCTTAAAATCAAAACCCCAAATC-T
1 CAAACCCTAAAATCAAAACTCTAAACCTT
13588102 CAAACCCTAAA
1 CAAACCCTAAA
13588113 CCCCAAAATC
Statistics
Matches: 197, Mismatches: 29, Indels: 26
0.78 0.12 0.10
Matches are distributed among these distances:
27 7 0.04
28 93 0.47
29 82 0.42
30 15 0.08
ACGTcount: A:0.48, C:0.31, G:0.01, T:0.19
Consensus pattern (29 bp):
CAAACCCTAAAATCAAAACTCTAAACCTT
Found at i:13587955 original size:86 final size:86
Alignment explanation
Indices: 13587846--13588112 Score: 296
Period size: 86 Copynumber: 3.1 Consensus size: 86
13587836 CCAAACACCC
* * *
13587846 CAAACCCTAAAA-CGAAACTCTAAACCTTCAAACCCTAAAAT-GAAACCCCAAACCTTTAAACCT
1 CAAACCCTAAAATCAAAACCCTAAACCTTCAAACCCTAAAATCAAAACCCCAAACC-TTAAACCT
* *
13587909 TAAAATTAAAACTCTAAACCTT
65 TAAAAGTAAAACTCCAAACCTT
* *
13587931 CAAACCCTAAAATCAAAACCCTAAACCTTACAAACCCT-CAATCAAAACCCCAAATCTTAAACCT
1 CAAACCCTAAAATCAAAACCCTAAACCTT-CAAACCCTAAAATCAAAACCCCAAACCTTAAACCT
13587995 TAAAAGTAAAACTCCAAACCTT
65 TAAAAGTAAAACTCCAAACCTT
* * * ** * *
13588017 CAAACCCTAAAAT-TAAACCGTAAATCC-TCTAAACCCTAAAACCAAAACTTCAAATCTCAAACC
1 CAAACCCTAAAATCAAAACCCTAAA-CCTTC-AAACCCTAAAATCAAAACCCCAAACCTTAAACC
* *
13588080 TTAAAA-TCAAAACCCCAAATC-T
64 TTAAAAGT-AAAACTCCAAACCTT
13588102 CAAACCCTAAA
1 CAAACCCTAAA
13588113 CCCCAAAATC
Statistics
Matches: 159, Mismatches: 16, Indels: 14
0.84 0.08 0.07
Matches are distributed among these distances:
84 1 0.01
85 42 0.26
86 97 0.61
87 19 0.12
ACGTcount: A:0.48, C:0.31, G:0.01, T:0.19
Consensus pattern (86 bp):
CAAACCCTAAAATCAAAACCCTAAACCTTCAAACCCTAAAATCAAAACCCCAAACCTTAAACCTT
AAAAGTAAAACTCCAAACCTT
Found at i:13588154 original size:21 final size:21
Alignment explanation
Indices: 13588122--13588181 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
13588112 ACCCCAAAAT
13588122 CTAAAA-CTCGAAAACCTAACC
1 CTAAAATC-CGAAAACCTAACC
** *
13588143 CTAAAATCCGAAATGTCAAACC
1 CTAAAATCCGAAA-ACCTAACC
*
13588165 CTAAAATCCAAAAACCT
1 CTAAAATCCGAAAACCT
13588182 CAAAATTCAA
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
21 12 0.40
22 18 0.60
ACGTcount: A:0.48, C:0.30, G:0.05, T:0.17
Consensus pattern (21 bp):
CTAAAATCCGAAAACCTAACC
Found at i:13588167 original size:28 final size:27
Alignment explanation
Indices: 13588096--13588168 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 27
13588086 TCAAAACCCC
*
13588096 AAATCTCAAACCCTAAACCCCAAAATCT
1 AAATCTCAAACCCT-AACCCCAAAATCG
* * *
13588124 AAAACTCGAAAACCTAACCCTAAAATCCG
1 AAATCTC-AAACCCTAACCCCAAAAT-CG
*
13588153 AAATGTCAAACCCTAA
1 AAATCTCAAACCCTAA
13588169 AATCCAAAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
28 24 0.67
29 12 0.33
ACGTcount: A:0.48, C:0.32, G:0.04, T:0.16
Consensus pattern (27 bp):
AAATCTCAAACCCTAACCCCAAAATCG
Found at i:13589911 original size:13 final size:16
Alignment explanation
Indices: 13589871--13589917 Score: 85
Period size: 16 Copynumber: 2.9 Consensus size: 16
13589861 GAATAATTTG
13589871 TAAATAATAATACTTA
1 TAAATAATAATACTTA
13589887 TAAATAATAATACTTA
1 TAAATAATAATACTTA
*
13589903 TAAAAAATAATACTT
1 TAAATAATAATACTT
13589918 TAATATCAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.36
Consensus pattern (16 bp):
TAAATAATAATACTTA
Found at i:13591904 original size:2 final size:2
Alignment explanation
Indices: 13591897--13591926 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
13591887 AGTAATGATT
13591897 AG AG AG AG AG AG AG AG AG AG AG AG AG -G AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
13591927 CCTTGACTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:13592725 original size:28 final size:28
Alignment explanation
Indices: 13592694--13592763 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 28
13592684 GCCTGGTTGC
* * *
13592694 AATTTAATTGGGCTTCAGGCCCGATTTT
1 AATTTAACTGGGCTTCAAGCCCAATTTT
* *
13592722 AATTCAACTGGGTTTCAAGCCCAATTTT
1 AATTTAACTGGGCTTCAAGCCCAATTTT
13592750 AATTTTAACTGGGC
1 AA-TTTAACTGGGC
13592764 CAAAAGTGAT
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
28 25 0.74
29 9 0.26
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.37
Consensus pattern (28 bp):
AATTTAACTGGGCTTCAAGCCCAATTTT
Found at i:13594246 original size:19 final size:21
Alignment explanation
Indices: 13594208--13594247 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
13594198 AGTATTTATT
*
13594208 AAAAAATTTTCAATACAATAA
1 AAAAAATTTTCAATAAAATAA
13594229 AAAAAATTTT-AA-AAAATAA
1 AAAAAATTTTCAATAAAATAA
13594248 TAAATTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 2 0.11
21 10 0.56
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.28
Consensus pattern (21 bp):
AAAAAATTTTCAATAAAATAA
Found at i:13595386 original size:22 final size:21
Alignment explanation
Indices: 13595361--13595419 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
13595351 ATTAATAACT
* *
13595361 TAATAAGTGAATGATAATTTAA
1 TAATAAATCAATGATAA-TTAA
*
13595383 TAATAAATCAGTGATAATTAA
1 TAATAAATCAATGATAATTAA
*
13595404 TAATAGATCAAT-ATAA
1 TAATAAATCAATGATAA
13595420 GTTTAACAGT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 4 0.12
21 14 0.44
22 14 0.44
ACGTcount: A:0.53, C:0.03, G:0.10, T:0.34
Consensus pattern (21 bp):
TAATAAATCAATGATAATTAA
Found at i:13595405 original size:21 final size:22
Alignment explanation
Indices: 13595372--13595413 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
13595362 AATAAGTGAA
13595372 TGATAATTTAATAATAAATCAG
1 TGATAATTTAATAATAAATCAG
*
13595394 TGATAA-TTAATAATAGATCA
1 TGATAATTTAATAATAAATCA
13595414 ATATAAGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.50, C:0.05, G:0.10, T:0.36
Consensus pattern (22 bp):
TGATAATTTAATAATAAATCAG
Found at i:13595535 original size:22 final size:22
Alignment explanation
Indices: 13595510--13595573 Score: 58
Period size: 22 Copynumber: 3.0 Consensus size: 22
13595500 ACTTATTAAT
13595510 AAATAATTAATAACTTAATAGC
1 AAATAATTAATAACTTAATAGC
* * * *
13595532 AAATTATGAATAATTTAATA-T
1 AAATAATTAATAACTTAATAGC
* * *
13595553 AAATAAGTGATAACTTGATAG
1 AAATAATTAATAACTTAATAG
13595574 TTAATTATAG
Statistics
Matches: 31, Mismatches: 10, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
21 14 0.45
22 17 0.55
ACGTcount: A:0.52, C:0.05, G:0.09, T:0.34
Consensus pattern (22 bp):
AAATAATTAATAACTTAATAGC
Found at i:13595566 original size:43 final size:44
Alignment explanation
Indices: 13595497--13595600 Score: 122
Period size: 43 Copynumber: 2.4 Consensus size: 44
13595487 GTAAATCAAT
* * *
13595497 ATAACTTATTAATAAATAATTAATAACTTAATAGCAAATTAT-G
1 ATAATTTAATAATAAATAAGTAATAACTTAATAGCAAATTATAG
* * **
13595540 AATAATTTAAT-ATAAATAAGTGATAACTTGATAGTTAATTATAG
1 -ATAATTTAATAATAAATAAGTAATAACTTAATAGCAAATTATAG
13595584 ATAATTTAATAATAAAT
1 ATAATTTAATAATAAAT
13595601 CAATGAGAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
43 36 0.71
44 15 0.29
ACGTcount: A:0.51, C:0.04, G:0.07, T:0.38
Consensus pattern (44 bp):
ATAATTTAATAATAAATAAGTAATAACTTAATAGCAAATTATAG
Found at i:13595621 original size:22 final size:22
Alignment explanation
Indices: 13595586--13595649 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
13595576 AATTATAGAT
* *
13595586 AATTTAATAATAAATCAAT-GAG
1 AATTTAATAGTAAA-CAATCGAA
*
13595608 AATTTTATAGTAAACAATCGAA
1 AATTTAATAGTAAACAATCGAA
*
13595630 AATTAAATAGTAAACCAATC
1 AATTTAATAGTAAA-CAATC
13595650 ATAACATAGT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
21 4 0.11
22 26 0.74
23 5 0.14
ACGTcount: A:0.53, C:0.09, G:0.08, T:0.30
Consensus pattern (22 bp):
AATTTAATAGTAAACAATCGAA
Found at i:13595662 original size:22 final size:22
Alignment explanation
Indices: 13595637--13595687 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
13595627 GAAAATTAAA
*
13595637 TAGTAAAC-CAATCATAACATAG
1 TAGTAAACAC-ATAATAACATAG
* *
13595659 TAGTAAATACATAATAATATAG
1 TAGTAAACACATAATAACATAG
13595681 TAGTAAA
1 TAGTAAA
13595688 TTATTGATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 24 0.96
23 1 0.04
ACGTcount: A:0.53, C:0.10, G:0.10, T:0.27
Consensus pattern (22 bp):
TAGTAAACACATAATAACATAG
Found at i:13595697 original size:22 final size:23
Alignment explanation
Indices: 13595650--13595753 Score: 78
Period size: 22 Copynumber: 4.8 Consensus size: 23
13595640 TAAACCAATC
13595650 ATAACATAGTAGTAAA-TACATA
1 ATAACATAGTAGTAAATTACATA
* * *
13595672 ATAATATAGTAGTAAATTA-TTG
1 ATAACATAGTAGTAAATTACATA
* *
13595694 ATAACATAGCACTAAATTAC-TA
1 ATAACATAGTAGTAAATTACATA
* *
13595716 ATAGCATAGCAGT---TTAC-TA
1 ATAACATAGTAGTAAATTACATA
* *
13595735 ATAACTTAGTTGTAAATTA
1 ATAACATAGTAGTAAATTA
13595754 GTAACAATTT
Statistics
Matches: 64, Mismatches: 13, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
19 15 0.23
22 47 0.73
23 2 0.03
ACGTcount: A:0.46, C:0.10, G:0.11, T:0.34
Consensus pattern (23 bp):
ATAACATAGTAGTAAATTACATA
Found at i:13595856 original size:22 final size:22
Alignment explanation
Indices: 13595831--13595893 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 22
13595821 TAAGTCAATT
*
13595831 ATAACTTCATAATAAATTACCA
1 ATAACTTCATAATAAATCACCA
* **
13595853 ATAACTTTATGGTAAATCACCA
1 ATAACTTCATAATAAATCACCA
* * *
13595875 ATAATTTGATAGTAAATCA
1 ATAACTTCATAATAAATCA
13595894 TTTAGCTTAA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.46, C:0.14, G:0.06, T:0.33
Consensus pattern (22 bp):
ATAACTTCATAATAAATCACCA
Found at i:13596295 original size:22 final size:22
Alignment explanation
Indices: 13596254--13596295 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
13596244 TAAAAATAAG
* *
13596254 TGATAATTTAATAGTTAATCTC
1 TGATAATTTAATAATAAATCTC
*
13596276 TGATAATTTAGTAATAAATC
1 TGATAATTTAATAATAAATC
13596296 AATCACAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (22 bp):
TGATAATTTAATAATAAATCTC
Found at i:13596405 original size:21 final size:22
Alignment explanation
Indices: 13596379--13596746 Score: 111
Period size: 22 Copynumber: 16.8 Consensus size: 22
13596369 AATTTGGTAA
13596379 TAAATC-ATAAATAACTT-ATAG
1 TAAATCAAT-AATAACTTAATAG
*
13596400 TAAATCAATAATAATTTAATAG
1 TAAATCAATAATAACTTAATAG
* * * *
13596422 TTAATCACTAGA-AACTTAAAAA
1 TAAATCAATA-ATAACTTAATAG
* *
13596444 TAAATCAAT-ATAATTTAGTAG
1 TAAATCAATAATAACTTAATAG
* *
13596465 TAAATTATTGAA-AACTTAATAG
1 TAAATCAAT-AATAACTTAATAG
* * * *
13596487 TTAATCAGTGATAATTTAATAG
1 TAAATCAATAATAACTTAATAG
* *
13596509 TAAATC-ATGGACAACTTAATA-
1 TAAATCAAT-AATAACTTAATAG
* * *
13596530 TAAATCAGTGATAACTTGATAG
1 TAAATCAATAATAACTTAATAG
* * *
13596552 TGAATC-ATGAGATAA-TTAGGTAA
1 TAAATCAAT-A-ATAACTTA-ATAG
* * * **
13596575 TAAATCTAGAATAATTTTGTAG
1 TAAATCAATAATAACTTAATAG
*
13596597 TAAAT-AATCAA-AAATTAAGTAG
1 TAAATCAAT-AATAACTTAA-TAG
* *
13596619 TAAATCAATGAT-A-TTATAGTAA
1 TAAATCAATAATAACTTA-A-TAG
* *
13596641 TAAATGC-ATAATAAATATAATAT
1 TAAAT-CAATAATAACT-TAATAG
* *
13596664 TAAATC-ATCGATAATTTAATAG
1 TAAATCAAT-AATAACTTAATAG
* * * *
13596686 TAAATTATTGATAACTTAGTAG
1 TAAATCAATAATAACTTAATAG
* *
13596708 TAAACCATTAATAA-TATAATAG
1 TAAATCAATAATAACT-TAATAG
* * *
13596730 GAAATTACTAATAACTT
1 TAAATCAATAATAACTT
13596747 GTTACAAATC
Statistics
Matches: 257, Mismatches: 62, Indels: 55
0.69 0.17 0.15
Matches are distributed among these distances:
20 1 0.00
21 54 0.21
22 162 0.63
23 35 0.14
24 3 0.01
25 2 0.01
ACGTcount: A:0.49, C:0.07, G:0.10, T:0.35
Consensus pattern (22 bp):
TAAATCAATAATAACTTAATAG
Found at i:13596552 original size:43 final size:44
Alignment explanation
Indices: 13596391--13596560 Score: 150
Period size: 43 Copynumber: 3.9 Consensus size: 44
13596381 AATCATAAAT
* * * * *
13596391 AACTT-ATAGTAAATCAATAATAATTTAATAGTTAATCACTAG-A
1 AACTTAATAGTAAATCAGTGATAACTTAATAGTAAATCA-TGGAA
* * * * * * *
13596434 AACTTAAAAATAAATCAAT-ATAATTTAGTAGTAAATTATTGAA
1 AACTTAATAGTAAATCAGTGATAACTTAATAGTAAATCATGGAA
* * *
13596477 AACTTAATAGTTAATCAGTGATAATTTAATAGTAAATCATGGAC
1 AACTTAATAGTAAATCAGTGATAACTTAATAGTAAATCATGGAA
* *
13596521 AACTTAATA-TAAATCAGTGATAACTTGATAGTGAATCATG
1 AACTTAATAGTAAATCAGTGATAACTTAATAGTAAATCATG
13596561 AGATAATTAG
Statistics
Matches: 106, Mismatches: 18, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
42 2 0.02
43 64 0.60
44 40 0.38
ACGTcount: A:0.47, C:0.08, G:0.11, T:0.34
Consensus pattern (44 bp):
AACTTAATAGTAAATCAGTGATAACTTAATAGTAAATCATGGAA
Found at i:13596848 original size:22 final size:22
Alignment explanation
Indices: 13596823--13597040 Score: 90
Period size: 22 Copynumber: 10.0 Consensus size: 22
13596813 ATAATTTTGA
13596823 AGTAAATCAATGATAAATTAAT
1 AGTAAATCAATGATAAATTAAT
* *
13596845 AGTAAATCAATTATAACTT--T
1 AGTAAATCAATGATAAATTAAT
* * * * *
13596865 AATAAA-CTATCAGTAACTTAGT
1 AGTAAATCAATGA-TAAATTAAT
* ** * *
13596887 AGAAAATCAACAACAATTTAAT
1 AGTAAATCAATGATAAATTAAT
* * * *
13596909 AGGAAA-CTATTAAAAACTTAAT
1 AGTAAATCAATGATAAA-TTAAT
* * * *
13596931 GGTAAATTATTCATAAATTAAT
1 AGTAAATCAATGATAAATTAAT
* *
13596953 AGTAAATTAAT-ACTAATTTAAT
1 AGTAAATCAATGA-TAAATTAAT
* * * *
13596975 AATAAATTATTGATAACTTAAT
1 AGTAAATCAATGATAAATTAAT
13596997 AGTAAAT-AATTGATAACA-TAAT
1 AGTAAATCAA-TGATAA-ATTAAT
* *
13597019 AGTAAATCAATAATAACTTAAT
1 AGTAAATCAATGATAAATTAAT
13597041 TGTTAATTAT
Statistics
Matches: 147, Mismatches: 37, Indels: 24
0.71 0.18 0.12
Matches are distributed among these distances:
19 4 0.03
20 12 0.08
21 7 0.05
22 113 0.77
23 11 0.07
ACGTcount: A:0.51, C:0.08, G:0.07, T:0.34
Consensus pattern (22 bp):
AGTAAATCAATGATAAATTAAT
Found at i:13596958 original size:11 final size:11
Alignment explanation
Indices: 13596926--13597040 Score: 67
Period size: 11 Copynumber: 10.5 Consensus size: 11
13596916 TATTAAAAAC
*
13596926 TTAATGGTAAA
1 TTAATAGTAAA
*
13596937 TTATTCA-TAAA
1 TTAAT-AGTAAA
13596948 TTAATAGTAAA
1 TTAATAGTAAA
* *
13596959 TTAATACTAAT
1 TTAATAGTAAA
*
13596970 TTAATAATAAA
1 TTAATAGTAAA
* *
13596981 TT-ATTGATAAC
1 TTAATAG-TAAA
13596992 TTAATAGTAAA
1 TTAATAGTAAA
*
13597003 -TAATTGATAACA
1 TTAATAG-TAA-A
13597015 -TAATAGTAAA
1 TTAATAGTAAA
* * *
13597025 TCAATAATAAC
1 TTAATAGTAAA
13597036 TTAAT
1 TTAAT
13597041 TGTTAATTAT
Statistics
Matches: 79, Mismatches: 18, Indels: 14
0.71 0.16 0.13
Matches are distributed among these distances:
10 9 0.11
11 61 0.77
12 9 0.11
ACGTcount: A:0.50, C:0.05, G:0.06, T:0.38
Consensus pattern (11 bp):
TTAATAGTAAA
Found at i:13596993 original size:66 final size:66
Alignment explanation
Indices: 13596923--13597056 Score: 171
Period size: 66 Copynumber: 2.0 Consensus size: 66
13596913 AACTATTAAA
* * * * *
13596923 AACTTAATGGTAAATTATTCATAA-ATTAATAGTAAATTAATACTAATTTAATAATAAATTATTG
1 AACTTAATAGTAAATAATTCATAACA-TAATAGTAAATCAATAATAACTTAATAATAAATTATTG
13596987 AT
65 AT
* ** *
13596989 AACTTAATAGTAAATAATTGATAACATAATAGTAAATCAATAATAACTTAATTGTTAATTATTGA
1 AACTTAATAGTAAATAATTCATAACATAATAGTAAATCAATAATAACTTAATAATAAATTATTGA
13597054 T
66 T
13597055 AA
1 AA
13597057 TTTTATTATA
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
66 57 0.98
67 1 0.02
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.39
Consensus pattern (66 bp):
AACTTAATAGTAAATAATTCATAACATAATAGTAAATCAATAATAACTTAATAATAAATTATTGA
T
Found at i:13597056 original size:22 final size:22
Alignment explanation
Indices: 13596904--13597056 Score: 137
Period size: 22 Copynumber: 7.0 Consensus size: 22
13596894 CAACAACAAT
* * * *
13596904 TTAATAGGAAACTATTAAAAAC
1 TTAATAGTAAATTATTGATAAC
* * *
13596926 TTAATGGTAAATTATTCATAAA
1 TTAATAGTAAATTATTGATAAC
* *
13596948 TTAATAGTAAATTAAT-ACTAAT
1 TTAATAGTAAATTATTGA-TAAC
*
13596970 TTAATAATAAATTATTGATAAC
1 TTAATAGTAAATTATTGATAAC
*
13596992 TTAATAGTAAATAATTGATAAC
1 TTAATAGTAAATTATTGATAAC
* * * *
13597014 ATAATAGTAAATCAATAATAAC
1 TTAATAGTAAATTATTGATAAC
* *
13597036 TTAATTGTTAATTATTGATAA
1 TTAATAGTAAATTATTGATAA
13597057 TTTTATTATA
Statistics
Matches: 105, Mismatches: 24, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
21 1 0.01
22 103 0.98
23 1 0.01
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.38
Consensus pattern (22 bp):
TTAATAGTAAATTATTGATAAC
Found at i:13597653 original size:21 final size:22
Alignment explanation
Indices: 13597605--13597659 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
13597595 ATATGAAAGG
* *
13597605 TTATCAAAGTTACATCAAGATG
1 TTATCAAAATTACATCAAGATA
*
13597627 TTATCAAAATTTCATCAA-ATA
1 TTATCAAAATTACATCAAGATA
13597648 TTATCAAAATTA
1 TTATCAAAATTA
13597660 TATTAATGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 13 0.45
22 16 0.55
ACGTcount: A:0.45, C:0.13, G:0.05, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTACATCAAGATA
Found at i:13597732 original size:21 final size:21
Alignment explanation
Indices: 13597674--13597789 Score: 69
Period size: 21 Copynumber: 5.7 Consensus size: 21
13597664 AATGATTAGT
13597674 AAAATTATAT-AATAAGTTACC
1 AAAATTATATCAA-AAGTTACC
* ** *
13597695 -AAACTA-ATCGTAGGTTACC
1 AAAATTATATCAAAAGTTACC
* *
13597714 AAAATTATATCGAAAGTTATC
1 AAAATTATATCAAAAGTTACC
* **
13597735 AAAATTTTATCAAAAGTTTTC
1 AAAATTATATCAAAAGTTACC
* * * *
13597756 AAACTTCTAACAAAGGTTACC
1 AAAATTATATCAAAAGTTACC
*
13597777 AAAA-CATATCAAA
1 AAAATTATATCAAA
13597790 GGTGATCAAA
Statistics
Matches: 71, Mismatches: 21, Indels: 7
0.72 0.21 0.07
Matches are distributed among these distances:
19 9 0.13
20 16 0.23
21 46 0.65
ACGTcount: A:0.47, C:0.15, G:0.08, T:0.30
Consensus pattern (21 bp):
AAAATTATATCAAAAGTTACC
Found at i:13601657 original size:33 final size:30
Alignment explanation
Indices: 13601619--13601689 Score: 72
Period size: 30 Copynumber: 2.3 Consensus size: 30
13601609 TTGATTAAAA
13601619 ATATATTTATTAACTTTAACAATTGATTTATTT-
1 ATATATTTA-T-ACTTTAA-AATT-ATTTATTTG
* * *
13601652 ATATATATATAGTTTTAAATTATTTATTTG
1 ATATATTTATACTTTAAAATTATTTATTTG
13601682 ATATATTT
1 ATATATTT
13601690 CATTTCTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
29 8 0.24
30 11 0.33
31 5 0.15
32 1 0.03
33 8 0.24
ACGTcount: A:0.37, C:0.03, G:0.04, T:0.56
Consensus pattern (30 bp):
ATATATTTATACTTTAAAATTATTTATTTG
Found at i:13602273 original size:22 final size:22
Alignment explanation
Indices: 13602248--13602296 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
13602238 TAATATCATC
*
13602248 TTATCATCACTTGCTCATAATT
1 TTATCATCACTTACTCATAATT
*
13602270 TTATCATCTCTTACTCATAATT
1 TTATCATCACTTACTCATAATT
13602292 TTATC
1 TTATC
13602297 CTGTCATTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.27, C:0.22, G:0.02, T:0.49
Consensus pattern (22 bp):
TTATCATCACTTACTCATAATT
Found at i:13602395 original size:91 final size:91
Alignment explanation
Indices: 13602280--13602461 Score: 319
Period size: 91 Copynumber: 2.0 Consensus size: 91
13602270 TTATCATCTC
* * *
13602280 TTACTCATAATTTTATCCTGTCATTAGCCCCTTTTCTTGTACATTGTTTATAAAATTTGTCTCAG
1 TTACTCAAAATTTTATCCTATCATTAGCCCCTTTTCTTGTACATAGTTTATAAAATTTGTCTCAG
*
13602345 AATCATAAGTTAGAAATACATAAAAA
66 AATCATAAGTCAGAAATACATAAAAA
*
13602371 TTACTCAAAATTTTATCCTATCATTAGCCCTTTTTCTTGTACATAGTTTATAAAATTTGTCTCAG
1 TTACTCAAAATTTTATCCTATCATTAGCCCCTTTTCTTGTACATAGTTTATAAAATTTGTCTCAG
13602436 AATCATAAGTCAGAAATACATAAAAA
66 AATCATAAGTCAGAAATACATAAAAA
13602462 CTGCTAAACT
Statistics
Matches: 86, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
91 86 1.00
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (91 bp):
TTACTCAAAATTTTATCCTATCATTAGCCCCTTTTCTTGTACATAGTTTATAAAATTTGTCTCAG
AATCATAAGTCAGAAATACATAAAAA
Found at i:13607467 original size:130 final size:129
Alignment explanation
Indices: 13607313--13607625 Score: 335
Period size: 129 Copynumber: 2.4 Consensus size: 129
13607303 TATATGTTAT
* * * * *
13607313 TTAACATTTAATAAGTAATTTAATATTGCTATTATAGTGAA-TTTCAAACAAAATTTCACATGTC
1 TTAAAATTTAATATGTAATTTAATAGTGCTATTATAGT-AATTTTCAAACAAAATATCACATATC
** * * *
13607377 AAATTTTTAGGTTTA-CAACGGTAAGGGTATTTTAATAATTTAGTATGT-AGTTAATTTTATATG
65 AAATTTTTA--TAAACCAACGGTAAGGATATTTTAATAATTTAATATATGA-TTAATTTTATATG
13607440 ATG
127 ATG
* * * * *
13607443 TTAAAATTTCATATGTAATCTAATAGTGTTATTATAGTAATTTTTAAATAAAATATCACATATCA
1 TTAAAATTTAATATGTAATTTAATAGTGCTATTATAGTAATTTTCAAACAAAATATCACATATCA
** * *
13607508 AATTTTTATAAACCAATTGTAATGATATTTTAATAATTTAATATATGATTAATTTTATATTATG
66 AATTTTTATAAACCAACGGTAAGGATATTTTAATAATTTAATATATGATTAATTTTATATGATG
* * * * * * *
13607572 TTAAAAATTAATATATAATTTAATAGAGATATTATAATAATTTTAAAATAAAAT
1 TTAAAATTTAATATGTAATTTAATAGTGCTATTATAGTAATTTTCAAACAAAAT
13607626 GCAACATATC
Statistics
Matches: 153, Mismatches: 27, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
128 2 0.01
129 90 0.59
130 61 0.40
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (129 bp):
TTAAAATTTAATATGTAATTTAATAGTGCTATTATAGTAATTTTCAAACAAAATATCACATATCA
AATTTTTATAAACCAACGGTAAGGATATTTTAATAATTTAATATATGATTAATTTTATATGATG
Found at i:13609781 original size:23 final size:23
Alignment explanation
Indices: 13609750--13609794 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
13609740 ATTGCTAATT
*
13609750 TTAATAATAACTTGGAAAAGATA
1 TTAACAATAACTTGGAAAAGATA
*
13609773 TTAACAATAACTTGGAGAAGAT
1 TTAACAATAACTTGGAAAAGAT
13609795 GGAGAATAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.49, C:0.07, G:0.16, T:0.29
Consensus pattern (23 bp):
TTAACAATAACTTGGAAAAGATA
Found at i:13615102 original size:240 final size:240
Alignment explanation
Indices: 13614679--13615398 Score: 1291
Period size: 240 Copynumber: 3.0 Consensus size: 240
13614669 ATTTTATACG
* * * * *
13614679 TTGACATAATTAAAAATTTAGATAAGTGAATGGAAATATATATTCATACTTTGTGTTGATGGTCA
1 TTGACATAATTAAAAACTTAGATGAGTGAATTGAAATATATATTCATACCTTGTGTTGATGGTCG
*
13614744 GAAGCTTTCAATTCTATTGTAGCTTAAATCCAAGTTCATCAAAATTT-TCAAATTATTCAATCCT
66 GAAGCTTTCAATTCTATTGTAGCTTAAATCCAAGTTCATC-AAATTTGTCAGATTATTCAATCCT
* *
13614808 ATTCAATGCCTATGAGTAATTAATAGTACATATAATAGCAAATGATATGCAATATCTTTTCCTGA
130 ATTCAATGCCGATGAGTAATTAATATTACATATAATAGCAAATGATATGCAATATCTTTTCCTGA
*
13614873 AACAACAATTGATTTGAACATAAAAGAAAGATAAAGCAAGTTTATT
195 AACAACAATTGATTTGAACATAAAAGAAAGATAAAGCAAGTTTATC
13614919 TTGACATAATTAAAAACTTAGATGAGTGAATTGAAATATATATTCATACCTTGTGTTGATGGTCG
1 TTGACATAATTAAAAACTTAGATGAGTGAATTGAAATATATATTCATACCTTGTGTTGATGGTCG
13614984 GAAGCTTTCAATTCTATTGTAGCTTAAATCCAAGTTCATCAAATTTGTCAGATTATTCAATCCTA
66 GAAGCTTTCAATTCTATTGTAGCTTAAATCCAAGTTCATCAAATTTGTCAGATTATTCAATCCTA
*
13615049 TTCAATGCCGATGAGTAATTAATATTACATATAATAGCAAATGAAATGCAATATCTTTTCCTGAA
131 TTCAATGCCGATGAGTAATTAATATTACATATAATAGCAAATGATATGCAATATCTTTTCCTGAA
13615114 ACAACAATTGATTTGAACATAAAAGAAAGATAAAGCAAGTTTATC
196 ACAACAATTGATTTGAACATAAAAGAAAGATAAAGCAAGTTTATC
13615159 TTGACATAATTAAAAACTTAGATGAGTGAATTGAAATATATATTCATACCTTGTGTTGATGGTCG
1 TTGACATAATTAAAAACTTAGATGAGTGAATTGAAATATATATTCATACCTTGTGTTGATGGTCG
*
13615224 GAAGCTTTCAATTCTATTGTAGCTTAAATGCAAGTTCATCAAATTTGTCAGATTATTCAATCCTA
66 GAAGCTTTCAATTCTATTGTAGCTTAAATCCAAGTTCATCAAATTTGTCAGATTATTCAATCCTA
* *
13615289 TTCAATGCCGATGAGTAATTAATATTACATATAATAGCAAATGATATGCAATACCTTTTCTTGAA
131 TTCAATGCCGATGAGTAATTAATATTACATATAATAGCAAATGATATGCAATATCTTTTCCTGAA
13615354 ACAACAATTGATTTGAACATAAAAGAAAGATAAAGTC-AGTTTATC
196 ACAACAATTGATTTGAACATAAAAGAAAGATAAAG-CAAGTTTATC
13615399 ATGAAAATGA
Statistics
Matches: 464, Mismatches: 14, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
239 6 0.01
240 457 0.98
241 1 0.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (240 bp):
TTGACATAATTAAAAACTTAGATGAGTGAATTGAAATATATATTCATACCTTGTGTTGATGGTCG
GAAGCTTTCAATTCTATTGTAGCTTAAATCCAAGTTCATCAAATTTGTCAGATTATTCAATCCTA
TTCAATGCCGATGAGTAATTAATATTACATATAATAGCAAATGATATGCAATATCTTTTCCTGAA
ACAACAATTGATTTGAACATAAAAGAAAGATAAAGCAAGTTTATC
Found at i:13619509 original size:26 final size:25
Alignment explanation
Indices: 13619471--13619538 Score: 86
Period size: 26 Copynumber: 2.6 Consensus size: 25
13619461 TTTCTCTTCA
13619471 TTTTATTTT-TA-TTTTTATTTTTAT
1 TTTTATTTTATATTTTTTA-TTTTAT
13619495 TTTGTATTTTATATTTTTTATTTTAT
1 TTT-TATTTTATATTTTTTATTTTAT
13619521 TTTTATTATTATTATTTT
1 TTTTATT-TTA-TATTTT
13619539 ATATATGTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
24 3 0.08
25 10 0.26
26 14 0.36
27 12 0.31
ACGTcount: A:0.19, C:0.00, G:0.01, T:0.79
Consensus pattern (25 bp):
TTTTATTTTATATTTTTTATTTTAT
Found at i:13619518 original size:44 final size:48
Alignment explanation
Indices: 13619470--13619577 Score: 79
Period size: 46 Copynumber: 2.4 Consensus size: 48
13619460 TTTTCTCTTC
* * *
13619470 ATTTTATTTTTATTTTTA-T-TTTTAT-TTTGTATTTTATATTTTTTATT
1 ATTTTATTTTTATTTTTATTATTTTATATATGTA-TATATATATTTT-TT
*
13619517 -TTATT-TT--TATTATTATTATTTTATATATGTATATATATATTTTTT
1 ATT-TTATTTTTATTTTTATTATTTTATATATGTATATATATATTTTTT
* *
13619562 CTTTT-CTTTTATTTTT
1 ATTTTATTTTTATTTTT
13619578 TTCTTAGGTA
Statistics
Matches: 48, Mismatches: 6, Indels: 14
0.71 0.09 0.21
Matches are distributed among these distances:
44 7 0.15
45 6 0.12
46 22 0.46
47 13 0.27
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.75
Consensus pattern (48 bp):
ATTTTATTTTTATTTTTATTATTTTATATATGTATATATATATTTTTT
Found at i:13619536 original size:6 final size:6
Alignment explanation
Indices: 13619471--13619533 Score: 83
Period size: 6 Copynumber: 10.2 Consensus size: 6
13619461 TTTCTCTTCA
13619471 TTTTAT TTTTAT TTTTAT TTTTAT TTTGTAT TTTATAT TTTT-T ATTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTT-TAT TTT-TAT TTTTAT -TTTTAT
*
13619521 TTTTAT TATTAT T
1 TTTTAT TTTTAT T
13619534 ATTTTATATA
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
5 1 0.02
6 38 0.73
7 13 0.25
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (6 bp):
TTTTAT
Found at i:13619539 original size:20 final size:19
Alignment explanation
Indices: 13619477--13619540 Score: 78
Period size: 19 Copynumber: 3.3 Consensus size: 19
13619467 TTCATTTTAT
13619477 TTTTATTTTTATTTTTATT-
1 TTTTATTTTTA-TTTTATTA
*
13619496 TTGTATTTTATATTTT-TTA
1 TTTTATTTT-TATTTTATTA
13619515 TTTTATTTTTATTATTATTA
1 TTTTATTTTTATT-TTATTA
13619535 TTTTAT
1 TTTTAT
13619541 ATATGTATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
18 6 0.15
19 22 0.56
20 11 0.28
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (19 bp):
TTTTATTTTTATTTTATTA
Found at i:13619689 original size:22 final size:21
Alignment explanation
Indices: 13619662--13619725 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
13619652 TATTTATGTA
13619662 TTATCTGTTATTTAATTTTAAT
1 TTATCTGTTATTT-ATTTTAAT
*
13619684 TTATCTGTTAATTT-TTTTTAT
1 TTATCTGTT-ATTTATTTTAAT
*
13619705 TTATC--TTATTTATTTTCAT
1 TTATCTGTTATTTATTTTAAT
13619724 TT
1 TT
13619726 GATTTTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
18 4 0.11
19 10 0.26
21 11 0.29
22 9 0.24
23 4 0.11
ACGTcount: A:0.22, C:0.06, G:0.03, T:0.69
Consensus pattern (21 bp):
TTATCTGTTATTTATTTTAAT
Found at i:13619706 original size:21 final size:21
Alignment explanation
Indices: 13619645--13619710 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 21
13619635 CTTTTTTCTC
* *
13619645 CTGTTAATATTTATGTA-TTAT
1 CTGTTAAT-TTTTTTTATTTAT
*
13619666 CTGTT-ATTTAATTTTAATTTAT
1 CTGTTAATTT--TTTTTATTTAT
13619688 CTGTTAATTTTTTTTATTTAT
1 CTGTTAATTTTTTTTATTTAT
13619709 CT
1 CT
13619711 TATTTATTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
19 2 0.05
20 2 0.05
21 20 0.54
22 9 0.24
23 4 0.11
ACGTcount: A:0.24, C:0.06, G:0.06, T:0.64
Consensus pattern (21 bp):
CTGTTAATTTTTTTTATTTAT
Found at i:13619744 original size:14 final size:15
Alignment explanation
Indices: 13619710--13619748 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
13619700 TTTATTTATC
*
13619710 TTATTTATTTTCATT
1 TTATTTTTTTTCATT
*
13619725 TGATTTTTTTTC-TT
1 TTATTTTTTTTCATT
13619739 TTATTTTTTT
1 TTATTTTTTT
13619749 GATTTATCTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.13, C:0.05, G:0.03, T:0.79
Consensus pattern (15 bp):
TTATTTTTTTTCATT
Found at i:13620227 original size:20 final size:19
Alignment explanation
Indices: 13620185--13620227 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
13620175 TTGACGAACT
* *
13620185 TCCGACGAAAAACCTAGAT
1 TCCGACGAAAAACCCAGAA
13620204 TCCGACGAAAAATCCCAGAA
1 TCCGACGAAAAA-CCCAGAA
13620224 TCCG
1 TCCG
13620228 GTGAATATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.40, C:0.30, G:0.16, T:0.14
Consensus pattern (19 bp):
TCCGACGAAAAACCCAGAA
Found at i:13620571 original size:4 final size:4
Alignment explanation
Indices: 13620564--13620595 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
13620554 TTTTTTTTAA
*
13620564 ATTT ATTT ATTT ATTT GTTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
13620596 TATTAGATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:13620586 original size:16 final size:16
Alignment explanation
Indices: 13620565--13620595 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
13620555 TTTTTTTAAA
13620565 TTTATTTATTTATTTG
1 TTTATTTATTTATTTG
13620581 TTTATTTATTTATTT
1 TTTATTTATTTATTT
13620596 TATTAGATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.77
Consensus pattern (16 bp):
TTTATTTATTTATTTG
Found at i:13620640 original size:5 final size:5
Alignment explanation
Indices: 13620623--13620717 Score: 72
Period size: 5 Copynumber: 18.4 Consensus size: 5
13620613 TTAATATTCT
* *
13620623 TTTTA TCTTTA TTTTA TTTTTA TTTTTG TTTTA CTTTT- CTTTA TTTTA
1 TTTTA T-TTTA TTTTA -TTTTA -TTTTA TTTTA -TTTTA TTTTA TTTTA
*
13620671 TTTTA --TTA TTTTA TTTT- TATTTA TTTTCA CTTTTA TTTTG TTTTA
1 TTTTA TTTTA TTTTA TTTTA T-TTTA TTTT-A -TTTTA TTTTA TTTTA
13620716 TT
1 TT
13620718 ATTCTATTTT
Statistics
Matches: 74, Mismatches: 6, Indels: 20
0.74 0.06 0.20
Matches are distributed among these distances:
3 3 0.04
4 4 0.05
5 41 0.55
6 22 0.30
7 4 0.05
ACGTcount: A:0.16, C:0.05, G:0.02, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:13620643 original size:6 final size:6
Alignment explanation
Indices: 13620622--13620709 Score: 51
Period size: 6 Copynumber: 14.7 Consensus size: 6
13620612 TTTAATATTC
* * *
13620622 TTTTTA TCTTTA -TTTTA TTTTTA TTTTT- GTTTTA CTTTTCTT TATTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA -TTTT-TA T-TTTTA
* *
13620671 -TTTTA TTATTTTA TTTTTA --TTTA TTTTCA CTTTTA TTTT
1 TTTTTA -T-TTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTT
13620710 GTTTTATTAT
Statistics
Matches: 62, Mismatches: 10, Indels: 20
0.67 0.11 0.22
Matches are distributed among these distances:
4 4 0.06
5 13 0.21
6 30 0.48
7 6 0.10
8 9 0.15
ACGTcount: A:0.16, C:0.06, G:0.01, T:0.77
Consensus pattern (6 bp):
TTTTTA
Found at i:13620667 original size:32 final size:30
Alignment explanation
Indices: 13620628--13620715 Score: 99
Period size: 28 Copynumber: 2.9 Consensus size: 30
13620618 ATTCTTTTTA
13620628 TCTTTATTTTATTTTTATTTTTGTTTTACTTT
1 TCTTTATTTTA-TTTTA-TTTTGTTTTACTTT
* *
13620660 TCTTTATTTTATTTTA--TTATTTTATTTT
1 TCTTTATTTTATTTTATTTTGTTTTACTTT
*
13620688 TATTTATTTTCACTTTTATTTTGTTTTA
1 TCTTTATTTT-A-TTTTATTTTGTTTTA
13620716 TTATTCTATT
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
28 19 0.40
29 1 0.02
30 5 0.10
31 5 0.10
32 18 0.38
ACGTcount: A:0.16, C:0.06, G:0.02, T:0.76
Consensus pattern (30 bp):
TCTTTATTTTATTTTATTTTGTTTTACTTT
Found at i:13620715 original size:45 final size:45
Alignment explanation
Indices: 13620631--13620727 Score: 123
Period size: 40 Copynumber: 2.3 Consensus size: 45
13620621 CTTTTTATCT
* *
13620631 TTATTTTATTTTTATTTTTGTTTTACTTTTCTTTATTTTATTTTA
1 TTATTTTATTTTTATTTATGTTTCACTTTTCTTTATTTTATTTTA
*
13620676 TTATTTTATTTTTATTTAT-TTTCAC---T-TTTATTTTGTTTTA
1 TTATTTTATTTTTATTTATGTTTCACTTTTCTTTATTTTATTTTA
*
13620716 TTATTCTATTTT
1 TTATTTTATTTT
13620728 CTTTAAATAA
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
40 24 0.50
41 1 0.02
44 5 0.10
45 18 0.38
ACGTcount: A:0.16, C:0.05, G:0.02, T:0.76
Consensus pattern (45 bp):
TTATTTTATTTTTATTTATGTTTCACTTTTCTTTATTTTATTTTA
Found at i:13620815 original size:58 final size:59
Alignment explanation
Indices: 13620743--13621018 Score: 367
Period size: 58 Copynumber: 4.7 Consensus size: 59
13620733 AATAAAAATA
* *
13620743 AAAAAAATCTTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAATTTTC
1 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAGTTTC
** * *
13620801 AAAAAAAGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTC
1 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAGTTTC
* * * * * *
13620860 CAAAGAATATTTTTAGAGAAAAGTTGAAAGTATCAATTTTTCTTAAAAAT-AAATTTTC
1 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAGTTTC
** * *
13620918 AAAAAAAGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTC
1 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAGTTTC
* * *
13620977 CAAAGAATATTTTTTGGGAAAAGTTGAAAGTATCAATTTTCC
1 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
13621019 CTGCACAAAA
Statistics
Matches: 185, Mismatches: 31, Indels: 3
0.84 0.14 0.01
Matches are distributed among these distances:
58 94 0.51
59 91 0.49
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.35
Consensus pattern (59 bp):
AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAGTTTC
Found at i:13620892 original size:117 final size:117
Alignment explanation
Indices: 13620760--13621018 Score: 491
Period size: 117 Copynumber: 2.2 Consensus size: 117
13620750 TCTTTTTGGG
13620760 GAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAAGGTTTTTGAGGAAAAGT
1 GAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAAGGTTTTTGAGGAAAAGT
13620825 TGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCCAAAGAATATTTTTAGA
66 TGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCCAAAGAATATTTTTAGA
*
13620877 GAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTCAAAAAAAGGTTTTTGAGGAAAAGT
1 GAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAAGGTTTTTGAGGAAAAGT
* *
13620942 TGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCCAAAGAATATTTTTTGG
66 TGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCCAAAGAATATTTTTAGA
13620994 GAAAAGTTGAAAGTATCAATTTTCC
1 GAAAAGTTGAAAGTATCAATTTTCC
13621019 CTGCACAAAA
Statistics
Matches: 138, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
117 138 1.00
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.35
Consensus pattern (117 bp):
GAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAAGGTTTTTGAGGAAAAGT
TGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCCAAAGAATATTTTTAGA
Found at i:13629727 original size:8 final size:8
Alignment explanation
Indices: 13629714--13629771 Score: 75
Period size: 8 Copynumber: 7.5 Consensus size: 8
13629704 GCTTGAAAAA
13629714 AAATGAAT
1 AAATGAAT
13629722 AAATGAAT
1 AAATGAAT
*
13629730 AAATGAAA
1 AAATGAAT
13629738 AAATGAAT
1 AAATGAAT
13629746 AAATGAA-
1 AAATGAAT
* *
13629753 AAGTGAAA
1 AAATGAAT
13629761 AAATGAA-
1 AAATGAAT
13629768 AAAT
1 AAAT
13629772 AAAAAAATAA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
7 10 0.22
8 35 0.78
ACGTcount: A:0.67, C:0.00, G:0.14, T:0.19
Consensus pattern (8 bp):
AAATGAAT
Found at i:13629735 original size:16 final size:15
Alignment explanation
Indices: 13629714--13629784 Score: 81
Period size: 15 Copynumber: 4.7 Consensus size: 15
13629704 GCTTGAAAAA
13629714 AAATGAATAAATGAAT
1 AAATGAA-AAATGAAT
13629730 AAATGAAAAAATGAAT
1 AAATG-AAAAATGAAT
* *
13629746 AAATGAAAAGTGAAA
1 AAATGAAAAATGAAT
* *
13629761 AAATGAAAAATAAAA
1 AAATGAAAAATGAAT
13629776 AAAT-AAAAA
1 AAATGAAAAA
13629785 AAATAAAAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
14 5 0.10
15 25 0.50
16 18 0.36
17 2 0.04
ACGTcount: A:0.72, C:0.00, G:0.11, T:0.17
Consensus pattern (15 bp):
AAATGAAAAATGAAT
Found at i:13629743 original size:24 final size:23
Alignment explanation
Indices: 13629711--13629819 Score: 106
Period size: 23 Copynumber: 4.9 Consensus size: 23
13629701 TATGCTTGAA
13629711 AAAAAATGAATAAATGAATAAATG
1 AAAAAATGAATAAATGAA-AAATG
*
13629735 AAAAAATGAATAAATGAAAAGTG
1 AAAAAATGAATAAATGAAAAATG
*
13629758 AAAAAATGAA-AAATAAAAAAAT-
1 AAAAAATGAATAAAT-GAAAAATG
*
13629780 AAAAAA--AATAAA--AAAAAGG
1 AAAAAATGAATAAATGAAAAATG
*
13629799 AAAAAAAGAA-AAAGTGAAAAA
1 AAAAAATGAATAAA-TGAAAAA
13629820 GGAGGACTTA
Statistics
Matches: 73, Mismatches: 4, Indels: 17
0.78 0.04 0.18
Matches are distributed among these distances:
18 5 0.07
19 6 0.08
20 5 0.07
21 5 0.07
22 10 0.14
23 24 0.33
24 18 0.25
ACGTcount: A:0.75, C:0.00, G:0.12, T:0.13
Consensus pattern (23 bp):
AAAAAATGAATAAATGAAAAATG
Found at i:13629777 original size:8 final size:8
Alignment explanation
Indices: 13629766--13629795 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
13629756 TGAAAAAATG
13629766 AAAAATAA
1 AAAAATAA
13629774 AAAAATAAA
1 AAAAAT-AA
13629783 AAAAATAA
1 AAAAATAA
13629791 AAAAA
1 AAAAA
13629796 AGGAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (8 bp):
AAAAATAA
Found at i:13629787 original size:10 final size:9
Alignment explanation
Indices: 13629766--13629811 Score: 58
Period size: 9 Copynumber: 5.2 Consensus size: 9
13629756 TGAAAAAATG
13629766 AAAAAT-AA
1 AAAAATAAA
13629774 AAAAATAAA
1 AAAAATAAA
13629783 AAAAATAAA
1 AAAAATAAA
**
13629792 AAAAAGGAA
1 AAAAATAAA
*
13629801 AAAAAGAAA
1 AAAAATAAA
13629810 AA
1 AA
13629812 GTGAAAAAGG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
8 6 0.18
9 28 0.82
ACGTcount: A:0.87, C:0.00, G:0.07, T:0.07
Consensus pattern (9 bp):
AAAAATAAA
Found at i:13630879 original size:41 final size:41
Alignment explanation
Indices: 13630828--13631082 Score: 312
Period size: 41 Copynumber: 6.1 Consensus size: 41
13630818 ATGATTGTCA
*
13630828 AGGAGTAATTTACTTTCCAAAGTCGTGGAGCCTCTGTTTAG
1 AGGAGCAATTTACTTTCCAAAGTCGTGGAGCCTCTGTTTAG
*
13630869 AGGAGCAATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAG
1 AGGAGCAATTTACTTTCCAAAGTCGTGGAGCCTCTGTTTAG
* * * *
13630910 AGGAGCAATTTGCTTTTCAAAGTCGTGGTGCCTCTGATTAG
1 AGGAGCAATTTACTTTCCAAAGTCGTGGAGCCTCTGTTTAG
* *
13630951 AGGAGCAATTTACTTTCCAAAAGTCGTGGTGCCTCTGTTTAA
1 AGGAGCAATTTACTTTCC-AAAGTCGTGGAGCCTCTGTTTAG
* * * * * * * *
13630993 ATGAGTAATTTATTTTTCAAAGTTGTTGAGCCTTTGATTAG
1 AGGAGCAATTTACTTTCCAAAGTCGTGGAGCCTCTGTTTAG
* * *
13631034 AGGAGCCATTTATGTTTCTCAAAGTCGTTGAGCCTCTGTTTAG
1 AGGAGCAATTTA-CTTTC-CAAAGTCGTGGAGCCTCTGTTTAG
13631077 AGGAGC
1 AGGAGC
13631083 TTTGATCAAA
Statistics
Matches: 184, Mismatches: 27, Indels: 4
0.86 0.13 0.02
Matches are distributed among these distances:
41 119 0.65
42 38 0.21
43 27 0.15
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (41 bp):
AGGAGCAATTTACTTTCCAAAGTCGTGGAGCCTCTGTTTAG
Found at i:13630991 original size:124 final size:125
Alignment explanation
Indices: 13630828--13631082 Score: 327
Period size: 124 Copynumber: 2.0 Consensus size: 125
13630818 ATGATTGTCA
* *
13630828 AGGAGTAATTTACTTTCCAAAGTCGTGGAGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTC
1 AGGAGCAATTTACTTTCCAAAGTCGTGGAGCCTCTGTTTAAAGGAGCAATTTACTTTCCAAAGTC
* * *
13630893 GTGGTGCCTCTGTTTAGAGGAG-CAATT-TGCTTT-TCAAAGTCGTGGTGCCTCTGATTAG
66 GTGGAGCCTCTGATTAGAGGAGCCAATTATG-TTTCTCAAAGTCGTGGAGCCTCTGATTAG
* * * * *
13630951 AGGAGCAATTTACTTTCCAAAAGTCGTGGTGCCTCTGTTTAAATGAGTAATTTATTTTTCAAAGT
1 AGGAGCAATTTACTTTCC-AAAGTCGTGGAGCCTCTGTTTAAAGGAGCAATTTACTTTCCAAAGT
* * * * * *
13631016 TGTTGAGCCTTTGATTAGAGGAGCCATTTATGTTTCTCAAAGTCGTTGAGCCTCTGTTTAG
65 CGTGGAGCCTCTGATTAGAGGAGCCAATTATGTTTCTCAAAGTCGTGGAGCCTCTGATTAG
13631077 AGGAGC
1 AGGAGC
13631083 TTTGATCAAA
Statistics
Matches: 112, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
123 17 0.15
124 58 0.52
125 7 0.06
126 30 0.27
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (125 bp):
AGGAGCAATTTACTTTCCAAAGTCGTGGAGCCTCTGTTTAAAGGAGCAATTTACTTTCCAAAGTC
GTGGAGCCTCTGATTAGAGGAGCCAATTATGTTTCTCAAAGTCGTGGAGCCTCTGATTAG
Found at i:13631031 original size:83 final size:82
Alignment explanation
Indices: 13630827--13631081 Score: 339
Period size: 83 Copynumber: 3.1 Consensus size: 82
13630817 CATGATTGTC
* *
13630827 AAGGAGTAATTTACTTTCCAAAGTCGTGGAGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGT
1 AAGGAGTAATTTACTTTTCAAAGTCGTGGAGCCTCTGATTAGAGGAGCAATTTACTTTCCAAAGT
13630892 CGTGGTGCCTCTGTTTA
66 CGTGGTGCCTCTGTTTA
* * * *
13630909 GAGGAGCAATTTGCTTTTCAAAGTCGTGGTGCCTCTGATTAGAGGAGCAATTTACTTTCCAAAAG
1 AAGGAGTAATTTACTTTTCAAAGTCGTGGAGCCTCTGATTAGAGGAGCAATTTACTTTCC-AAAG
13630974 TCGTGGTGCCTCTGTTTA
65 TCGTGGTGCCTCTGTTTA
* * * * * * *
13630992 AATGAGTAATTTATTTTTCAAAGTTGTTGAGCCTTTGATTAGAGGAGCCATTTATGTTTCTCAAA
1 AAGGAGTAATTTACTTTTCAAAGTCGTGGAGCCTCTGATTAGAGGAGCAATTTA-CTTTC-CAAA
* *
13631057 GTCGTTGAGCCTCTGTTTA
64 GTCGTGGTGCCTCTGTTTA
*
13631076 GAGGAG
1 AAGGAG
13631082 CTTTGATCAA
Statistics
Matches: 149, Mismatches: 21, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
82 54 0.36
83 66 0.44
84 28 0.19
85 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (82 bp):
AAGGAGTAATTTACTTTTCAAAGTCGTGGAGCCTCTGATTAGAGGAGCAATTTACTTTCCAAAGT
CGTGGTGCCTCTGTTTA
Found at i:13631300 original size:5 final size:5
Alignment explanation
Indices: 13631290--13631349 Score: 59
Period size: 5 Copynumber: 11.4 Consensus size: 5
13631280 TTTTCTCTTC
* *
13631290 ATTTT ATTTT ATTTTT TTTTGT ATTTT ACATTT ATTTT ATTTT -TTTT
1 ATTTT ATTTT A-TTTT ATTT-T ATTTT A-TTTT ATTTT ATTTT ATTTT
13631337 ATTATT ATTTT AT
1 ATT-TT ATTTT AT
13631350 ATATGTATAT
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
4 4 0.09
5 25 0.54
6 17 0.37
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.77
Consensus pattern (5 bp):
ATTTT
Found at i:13631305 original size:11 final size:11
Alignment explanation
Indices: 13631290--13631349 Score: 54
Period size: 11 Copynumber: 5.6 Consensus size: 11
13631280 TTTTCTCTTC
13631290 ATTTTA-TTTT
1 ATTTTATTTTT
*
13631300 ATTTTTTTTTGT
1 ATTTTATTTT-T
**
13631312 ATTTTACATTT
1 ATTTTATTTTT
13631323 ATTTTA-TTTT
1 ATTTTATTTTT
*
13631333 -TTTTATTATT
1 ATTTTATTTTT
13631343 ATTTTAT
1 ATTTTAT
13631350 ATATGTATAT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
9 5 0.12
10 11 0.28
11 16 0.40
12 8 0.20
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.77
Consensus pattern (11 bp):
ATTTTATTTTT
Found at i:13631507 original size:21 final size:21
Alignment explanation
Indices: 13631463--13631521 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
13631453 TATTTATGTA
13631463 TTATCTGTTATTTAATTTTAAT
1 TTATCTGTTATTT-ATTTTAAT
*
13631485 TTATCTGTTAATTT-TTTTTAT
1 TTATCTGTT-ATTTATTTTAAT
13631506 TTATC--TTATTTATTTT
1 TTATCTGTTATTTATTTT
13631522 CGTTTGATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
18 4 0.12
19 6 0.18
21 11 0.32
22 9 0.26
23 4 0.12
ACGTcount: A:0.22, C:0.05, G:0.03, T:0.69
Consensus pattern (21 bp):
TTATCTGTTATTTATTTTAAT
Done.